config/config.properties

@@ -1,9 +1,9 @@
-#Wed Jan 24 12:02:38 CET 2018
+#Mon Mar 26 14:15:56 CEST 2018
 autoSaveScanData=true
-createSessionFiles=false
-dataLayout=table
+createSessionFiles=true
+dataLayout=default
 dataPath={data}/{year}_{month}/{date}/{date}_{time}_{name}
-dataProvider=txt
+dataProvider=h5
 dataScanFlushRecords=false
 dataScanPreserveTypes=false
 dataScanReleaseRecords=false
@@ -11,7 +11,7 @@ dataServerPort=5573
 depthDimension=0
 hostName=
 instanceName=Dev
-logDaysToLive=8
+logDaysToLive=50
 logLevel=Fine
 logLevelConsole=Off
 logPath={logs}/{date}_{time}

config/devices.properties

@@ -1,24 +1,24 @@
 dispatcher=ch.psi.pshell.bs.Provider|tcp://localhost:9999|||
-stream=ch.psi.pshell.bs.Stream|<dispatcher> #false:boolean|||
-scalar=ch.psi.pshell.bs.Scalar|stream Int8Scalar|||
-cam=ch.psi.pshell.bs.StreamCamera|"tcp://gfa-lc6-64:10100" 1|||true
-cam_server=ch.psi.pshell.bs.PipelineServer|gfa-lc6-64:8889|||
+cam_server=ch.psi.pshell.bs.PipelineServer|localhost:8889|||true
+#stream=ch.psi.pshell.bs.Stream|<dispatcher> #false:boolean|||
+#scalar=ch.psi.pshell.bs.Scalar|stream Int8Scalar|||
+#cam=ch.psi.pshell.bs.StreamCamera|"tcp://gfa-lc6-64:10100" 1|||true
 #prosilica=ch.psi.pshell.prosilica.Prosilica|119734 "PacketSize=1504;ExposureValue=300000"|||true
-rr=RotationReadback|TESTIOC:TESTCALCOUT:Output|||true
-rp=ch.psi.pshell.epics.Positioner|TESTIOC:TESTCALCOUT:Input null rr|||
+#rr=RotationReadback|TESTIOC:TESTCALCOUT:Output|||true
+#rp=ch.psi.pshell.epics.Positioner|TESTIOC:TESTCALCOUT:Input null rr|||
 #webcam=ch.psi.pshell.webcam.Webcam|:2|||true
-det=ch.psi.pshell.epics.AreaDetector|13SIM1|||false
-PiezoRoll1=ch.psi.pshell.epics.ControlledVariable|"TESTIOC:TESTCALCOUT:Input" TESTIOC:TESTCALCOUT:Output|||true
+#det=ch.psi.pshell.epics.AreaDetector|13SIM1|||false
+PiezoRoll1=ch.psi.pshell.epics.ControlledVariable|"TESTIOC:TESTCALCOUT:Input" TESTIOC:TESTCALCOUT:Output false|||true
 $ser=ch.psi.pshell.serial.TcpDevice||||
 $beam_ok=ch.psi.pshell.epics.ChannelString|CHANNEL|||
-sc1=ch.psi.pshell.epics.Scaler|MTEST-HW3:JS|||true
+#sc1=ch.psi.pshell.epics.Scaler|MTEST-HW3:JS|||true
 #bragg=ch.psi.pshell.crlogic.CrlogicPositioner|MTEST-HW3:MOT1|||
 #wago=ch.psi.pshell.modbus.ModbusTCP|SF-TEST-WAGO1:502|||
 testd=ch.psi.pshell.device.DummyPositioner||||
 #ralays=ch.psi.pshell.modbus.DigitalOutputArray|wago 0 16||1000|
 #relay1=ch.psi.pshell.modbus.DigitalOutput|wago 0||1000|
 #relay2=ch.psi.pshell.modbus.DigitalOutput|wago 1||1000|
-streamcam=ch.psi.pshell.bs.StreamCamera|tcp://gfa-lc6-64:9999||-1000|
+#streamcam=ch.psi.pshell.bs.StreamCamera|tcp://gfa-lc6-64:9999||-1000|
 #camtool_provider=ch.psi.pshell.bs.Provider|tcp://gfa-lc6-64:9999|||
 #camtool_stream=ch.psi.pshell.bs.Stream|camtool_provider|||true
 #camtool_min=ch.psi.pshell.bs.Scalar|camtool_stream min_value|||
@@ -53,7 +53,7 @@ sin=ch.psi.pshell.epics.ChannelDouble|TESTIOC:TESTSINUS:SinCalc 3 true|||true
 #sinx=ch.psi.pshell.epics.ProcessVariable|TESTIOC:TESTSINUS:SinCalc|||true
 #average=ch.psi.pshell.device.Averager|sin||2000|
 isin=ch.psi.pshell.epics.ChannelInteger|TESTIOC:TESTSINUS:SinCalc|||true
-arr=ch.psi.pshell.epics.ChannelDoubleArray|TESTIOC:TESTWF2:MyWF 6 -1 true|||true
+arr=ch.psi.pshell.epics.ChannelDoubleArray|TESTIOC:TESTWF2:MyWF 6 -1 false|||true
 pv=ch.psi.pshell.epics.ProcessVariable|TESTIOC:TESTCALCOUT:Input|||true
 shutter=ch.psi.pshell.epics.BinaryPositioner|TESTIOC:TESTBO:MyBO TESTIOC:TESTBO:MyBO|||true
 $motor=ch.psi.pshell.epics.Motor|MTEST-GOBBO:MOT1|||true
@@ -69,30 +69,41 @@ slit=ch.psi.pshell.device.Slit|motor motor2|||
 #$ps=PowerSupply|T-MMDV5|||
 pe=ch.psi.pshell.epics.Positioner|"TESTIOC:TESTCALCOUT:Input" TESTIOC:TESTCALCOUT:Output|||true
 cv=ch.psi.pshell.epics.ControlledVariable|TESTIOC:TESTCALCOUT:Input TESTIOC:TESTCALCOUT:Output|||true
-detector=ch.psi.pshell.detector.DetectorBase|http://127.0.0.1:8090/|||
+#detector=ch.psi.pshell.detector.DetectorBase|http://127.0.0.1:8090/|||
 #serial=ch.psi.pshell.serial.SerialPortDevice||||
-tcp=ch.psi.pshell.serial.TcpDevice|127.0.0.1:5554|||
-beeper=Beeper||||
-img=ch.psi.pshell.imaging.CameraSource|det||-500|
-imgbis=ch.psi.pshell.imaging.CameraSource|det||-500|
-sc=ch.psi.pshell.imaging.CameraSource|scienta||-500|
-tst=ch.psi.pshell.imaging.FileSource|C:\\Users\\gobbo_a\\Pictures\\beam.jpg|||
-tst2=ch.psi.pshell.imaging.FileSource|C:\\Users\\gobbo_a\\Pictures\\tst.png||-500|
-tst3=ch.psi.pshell.imaging.FileSource|C:\\Users\\gobbo_a\\Pictures\\tst.png||-500|
-rec=ch.psi.pshell.detector.Receiver|tcp://127.0.0.1:5444|||true
+#tcp=ch.psi.pshell.serial.TcpDevice|127.0.0.1:5554|||
+#beeper=Beeper||||
+#img=ch.psi.pshell.imaging.CameraSource|det||-500|
+#imgbis=ch.psi.pshell.imaging.CameraSource|det||-500|
+#sc=ch.psi.pshell.imaging.CameraSource|scienta||-500|
+tst=ch.psi.pshell.imaging.FileSource|/Users/gobbo_a/dev/pshell/config/mxsc/images/snapshot.png|||
+#tst2=ch.psi.pshell.imaging.FileSource|C:\\Users\\gobbo_a\\Pictures\\tst.png||-500|
+#tst3=ch.psi.pshell.imaging.FileSource|C:\\Users\\gobbo_a\\Pictures\\tst.png||-500|
+#rec=ch.psi.pshell.detector.Receiver|tcp://127.0.0.1:5444|||true
 #rec2=ch.psi.pshell.detector.Receiver|tcp://127.0.0.1:5555||-500|false
-pvt=ch.psi.pshell.epics.ProcessVariable|TESTIOC:TESTCALCOUT:Input|Read||
-$master=ch.psi.pshell.modbus.ModbusTCP|127.0.0.1|||
-ai=ch.psi.pshell.modbus.AnalogOutput|master 0|||
-cache=ch.psi.pshell.device.RegisterCache|sin|||
-$scaler=ch.psi.pshell.epics.Scaler|SCALER|||
-testpos=ch.psi.pshell.device.DummyPositioner||||true
-$test=ch.psi.pshell.epics.Motor|X|||true
-arrsrc=ch.psi.pshell.epics.ArraySource|13SIM1:image1:ArrayData 125000||-500|true
+#pvt=ch.psi.pshell.epics.ProcessVariable|TESTIOC:TESTCALCOUT:Input|Read||
+#$master=ch.psi.pshell.modbus.ModbusTCP|127.0.0.1|||
+#ai=ch.psi.pshell.modbus.AnalogOutput|master 0|||
+#cache=ch.psi.pshell.device.RegisterCache|sin|||
+#$scaler=ch.psi.pshell.epics.Scaler|SCALER|||
+#testpos=ch.psi.pshell.device.DummyPositioner||||true
+#$test=ch.psi.pshell.epics.Motor|X|||true
+#arrsrc=ch.psi.pshell.epics.ArraySource|13SIM1:image1:ArrayData 125000||-500|true
 #barrsrc=ch.psi.pshell.epics.ByteArraySource|13SIM1:image1:ArrayData 125000||-500|
 #matrix=ch.psi.pshell.epics.GenericMatrix|13SIM1:image1:ArrayData 1024 640 Int8|||
 #matrix_src=ch.psi.pshell.imaging.RegisterMatrixSource|matrix||-200|
-ga=ch.psi.pshell.epics.GenericArray|13SIM1:image1:ArrayData 125000|||
+#ga=ch.psi.pshell.epics.GenericArray|13SIM1:image1:ArrayData 125000|||
 #img2=ch.psi.pshell.imaging.FileSource|C:\\Users\\gobbo_a\\Pictures\\Chrysanthemum.jpg|||
 #mxd=ch.psi.pshell.epics.AreaDetector|MX-SAMCAM|||
 #mx=ch.psi.pshell.imaging.CameraSource|mxd||-1000|
+$mymot=ch.psi.pshell.epics.Motor|TEST|||true
+$mypos=ch.psi.pshell.epics.Positioner|SETPOINT READBACK|||true
+$mycv=ch.psi.pshell.epics.ProcessVariable|SETPOINT|||true
+mu=ch.psi.pshell.device.DummyMotor||||true
+delta=ch.psi.pshell.device.DummyMotor||||true
+gam=ch.psi.pshell.device.DummyMotor||||true
+eta=ch.psi.pshell.device.DummyMotor||||true
+chi=ch.psi.pshell.device.DummyMotor||||true
+phi=ch.psi.pshell.device.DummyMotor||||true
+sixc=ch.psi.pshell.device.MotorGroupBase|mu delta gam eta chi phi|||
+en=ch.psi.pshell.device.DummyPositioner||||true

config/plugins.properties

@@ -1,43 +1,48 @@
-Nilson.java=disabled
-CameraCalibrationDialog.java=enabled
-ScalarPanel.java=enabled
-CameraConfigDialog.java=disabled
-Inventory.java=disabled
-LayoutParallelScan.py=disabled
-PhaseScan.java=disabled
-PythonInteractive.java=disabled
-RotationReadback.java=enabled
-SfCamera.java=enabled
-ScreenPanel.java=disabled
-Didier.java=disabled
-PersonalizedTheme.java=disabled
-MXSC-1.5.0.jar=disabled
-TestLdap.java=disabled
-TestScan.java=disabled
-MXSC-1.4.0.jar=disabled
-TestPlot.java=disabled
-MatlabTokenMaker.java=enabled
-BandpassFilter.java=disabled
-DataFile.java=disabled
-Commands.java=disabled
-CustomStopAll.java=disabled
-importer.java=disabled
-Beeper.java=enabled
-DarkTheme.java=disabled
-DefaultPlugin.java=disabled
-EnergyScan.java=disabled
-GroovyPlugin.groovy=disabled
-HoloScan.java=disabled
-Image.java=disabled
-ManipulatorScan.java=disabled
-Microscope.java=disabled
-PanelPlugin.java=disabled
-NetbeansPlugin.java=disabled
-panel.py=disabled
-Pearl.java=disabled
-PhotonEnergy.java=disabled
-plugin-1.0-SNAPSHOT.jar=disabled
-PowerSupply.java=disabled
-sb1.groovy=disabled
-test.py=disabled
-XPSSpectrum.java=disabled
+ScreenPanel2.java=disabled
+Correlation2.java=disabled
+Correlation.java=disabled
+Sender.java=disabled
+MXSC-1.9.0.jar=disabled
+Nilson.java=disabled
+CameraCalibrationDialog.java=enabled
+ScalarPanel.java=disabled
+CameraConfigDialog.java=disabled
+Inventory.java=disabled
+LayoutParallelScan.py=disabled
+PhaseScan.java=disabled
+PythonInteractive.java=disabled
+RotationReadback.java=disabled
+SfCamera.java=enabled
+ScreenPanel.java=disabled
+Didier.java=disabled
+PersonalizedTheme.java=disabled
+MXSC-1.5.0.jar=disabled
+TestLdap.java=disabled
+TestScan.java=disabled
+MXSC-1.4.0.jar=disabled
+TestPlot.java=disabled
+MatlabTokenMaker.java=disabled
+BandpassFilter.java=disabled
+DataFile.java=disabled
+Commands.java=disabled
+CustomStopAll.java=disabled
+importer.java=disabled
+Beeper.java=disabled
+DarkTheme.java=disabled
+DefaultPlugin.java=disabled
+EnergyScan.java=disabled
+GroovyPlugin.groovy=disabled
+HoloScan.java=disabled
+Image.java=disabled
+ManipulatorScan.java=disabled
+Microscope.java=disabled
+PanelPlugin.java=disabled
+NetbeansPlugin.java=disabled
+panel.py=disabled
+Pearl.java=disabled
+PhotonEnergy.java=disabled
+plugin-1.0-SNAPSHOT.jar=disabled
+PowerSupply.java=disabled
+sb1.groovy=disabled
+test.py=disabled
+XPSSpectrum.java=disabled

config/tasks.properties

@@ -1,4 +1,5 @@
-#spectrum=1
-#back=1
-#task1=3
-#task2=-1
+#outupdate=0
+#spectrum=1
+#back=1
+#task1=3
+#task2=-1

devices/Add.png.properties

@@ -0,0 +1,20 @@
+#Wed Feb 21 09:01:07 CET 2018
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=NaN
+spatialCalOffsetY=NaN
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+spatialCalUnits=mm
+transpose=false

devices/CurrentCamera provider.properties

@@ -0,0 +1,4 @@
+#Thu Apr 05 14:57:15 CEST 2018
+keepListeningOnStop=false
+parallelHandlerProcessing=true
+socketType=SUB

devices/CurrentCamera.properties

@@ -1,4 +1,4 @@
-#Thu Jan 18 08:50:50 CET 2018
+#Wed Mar 21 12:02:58 CET 2018
 colormap=Flame
 colormapAutomatic=true
 colormapMax=25300.0

devices/DSC_0530.JPG.properties

@@ -0,0 +1,20 @@
+#Tue Feb 20 15:00:20 CET 2018
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=NaN
+spatialCalOffsetY=NaN
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+spatialCalUnits=mm
+transpose=false

devices/IMG_0077.JPG.properties

@@ -0,0 +1,20 @@
+#Tue Feb 20 13:25:23 CET 2018
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=NaN
+spatialCalOffsetY=NaN
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+spatialCalUnits=mm
+transpose=false

devices/IMG_0105.JPG.properties

@@ -0,0 +1,20 @@
+#Tue Feb 20 14:59:27 CET 2018
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=NaN
+spatialCalOffsetY=NaN
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+spatialCalUnits=mm
+transpose=false

devices/Image Averager.properties

@@ -0,0 +1,24 @@
+#Tue Mar 06 11:10:32 CET 2018
+colormap=Flame
+colormapAutomatic=true
+colormapMax=50660.0
+colormapMin=0.0
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=0.0
+spatialCalOffsetY=0.0
+spatialCalScaleX=1.0
+spatialCalScaleY=1.0
+spatialCalUnits=mm
+transpose=false

devices/Open.png.properties

@@ -0,0 +1,20 @@
+#Wed Feb 21 09:56:58 CET 2018
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=NaN
+spatialCalOffsetY=NaN
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+spatialCalUnits=mm
+transpose=false

devices/StepInto.png.properties

@@ -0,0 +1,20 @@
+#Wed Feb 21 09:58:16 CET 2018
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=NaN
+spatialCalOffsetY=NaN
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+spatialCalUnits=mm
+transpose=false

devices/TUSH102f1.png.properties

@@ -0,0 +1,20 @@
+#Tue Feb 20 15:35:03 CET 2018
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=NaN
+spatialCalOffsetY=NaN
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+spatialCalUnits=mm
+transpose=false

devices/TUSH102f2.png.properties

@@ -0,0 +1,20 @@
+#Tue Feb 20 15:08:30 CET 2018
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=NaN
+spatialCalOffsetY=NaN
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+spatialCalUnits=mm
+transpose=false

devices/TUSH102f3.png.properties

@@ -0,0 +1,20 @@
+#Tue Feb 20 18:13:00 CET 2018
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=NaN
+spatialCalOffsetY=NaN
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+spatialCalUnits=mm
+transpose=false

devices/TUSH102f4.png.properties

@@ -0,0 +1,20 @@
+#Tue Feb 20 15:01:57 CET 2018
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=NaN
+spatialCalOffsetY=NaN
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+spatialCalUnits=mm
+transpose=false

devices/arr.png.properties

@@ -0,0 +1,20 @@
+#Tue Feb 20 13:26:51 CET 2018
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=NaN
+spatialCalOffsetY=NaN
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+spatialCalUnits=mm
+transpose=false

devices/cam_server provider.properties

@@ -0,0 +1,5 @@
+#Wed Apr 04 16:34:27 CEST 2018
+disableCompression=false
+keepListeningOnStop=false
+parallelHandlerProcessing=true
+socketType=SUB

devices/cam_server.properties

@@ -1,24 +1,24 @@
-#Tue Nov 14 16:09:47 CET 2017
-colormap=Flame
-colormapAutomatic=true
-colormapMax=NaN
-colormapMin=NaN
-flipHorizontally=false
-flipVertically=false
-grayscale=false
-invert=false
-rescaleFactor=1.0
-rescaleOffset=0.0
-roiHeight=-1
-roiWidth=-1
-roiX=0
-roiY=0
-rotation=0.0
-rotationCrop=false
-scale=1.0
-spatialCalOffsetX=-661.516812111553
-spatialCalOffsetY=-490.5109552096732
-spatialCalScaleX=-25.06265652487295
-spatialCalScaleY=-32.822757470346716
-spatialCalUnits=mm
-transpose=false
+#Thu Mar 22 10:22:45 CET 2018
+colormap=Flame
+colormapAutomatic=true
+colormapMax=NaN
+colormapMin=NaN
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=0.0
+spatialCalOffsetY=0.0
+spatialCalScaleX=1.0
+spatialCalScaleY=1.0
+spatialCalUnits=mm
+transpose=false

devices/chi.properties

@@ -0,0 +1,14 @@
+#Thu Apr 12 11:03:01 CEST 2018
+defaultSpeed=10.0
+estbilizationDelay=0
+maxSpeed=10.0
+maxValue=360.0
+minSpeed=0.1
+minValue=-360.0
+offset=0.0
+precision=2
+resolution=NaN
+rotation=false
+scale=1.0
+startRetries=1
+unit=mm

devices/delta.properties

@@ -0,0 +1,14 @@
+#Mon Apr 16 17:23:26 CEST 2018
+defaultSpeed=50.0
+estbilizationDelay=0
+maxSpeed=50.0
+maxValue=360.0
+minSpeed=0.1
+minValue=-360.0
+offset=0.0
+precision=2
+resolution=NaN
+rotation=false
+scale=1.0
+startRetries=1
+unit=mm

devices/dispatcher.properties

@@ -1,8 +1,14 @@
-#Tue Jul 04 16:16:39 CEST 2017
-alignmentRetries=20
-disableCompression=true
-dropIncomplete=true
-keepListeningOnStop=false
-parallelHandlerProcessing=true
-sendIncompleteMessages=true
-socketType=PULL
+#Wed Apr 04 15:57:04 CEST 2018
+alignmentRetries=20
+disableCompression=true
+dropIncomplete=true
+keepListeningOnStop=false
+mappingIncomplete=fill_null
+parallelHandlerProcessing=true
+sendAwaitFirstMessage=false
+sendBuildChannelConfig=at_startup
+sendIncompleteMessages=true
+sendStrategy=complete_all
+sendSyncTimeout=-1
+socketType=PULL
+validationInconsistency=keep_as_is

devices/en.properties

@@ -0,0 +1,9 @@
+#Mon Apr 16 16:57:32 CEST 2018
+maxValue=100.0
+minValue=0.0
+offset=0.0
+precision=4
+resolution=NaN
+rotation=false
+scale=1.0
+unit=kEv

devices/eta.properties

@@ -0,0 +1,14 @@
+#Thu Apr 12 11:02:49 CEST 2018
+defaultSpeed=10.0
+estbilizationDelay=0
+maxSpeed=10.0
+maxValue=360.0
+minSpeed=0.1
+minValue=-360.0
+offset=0.0
+precision=2
+resolution=NaN
+rotation=false
+scale=1.0
+startRetries=1
+unit=mm

devices/gam.properties

@@ -0,0 +1,14 @@
+#Thu Apr 12 11:02:41 CEST 2018
+defaultSpeed=10.0
+estbilizationDelay=0
+maxSpeed=10.0
+maxValue=360.0
+minSpeed=0.1
+minValue=-360.0
+offset=0.0
+precision=2
+resolution=NaN
+rotation=false
+scale=1.0
+startRetries=1
+unit=mm

devices/h.properties

@@ -0,0 +1,9 @@
+#Thu Apr 12 11:38:15 CEST 2018
+maxValue=10.0
+minValue=-10.0
+offset=0.0
+precision=4
+resolution=0.01
+rotation=false
+scale=1.0
+unit=deg

devices/hkl.properties

@@ -0,0 +1,2 @@
+#Wed Apr 11 11:43:36 CEST 2018
+precision=6

devices/hkl_group.properties

@@ -0,0 +1,2 @@
+#Mon Apr 16 15:45:44 CEST 2018
+precision=-1

devices/hkl_reg.properties

@@ -0,0 +1,2 @@
+#Mon Apr 16 18:25:05 CEST 2018
+precision=-1

devices/k.properties

@@ -0,0 +1,9 @@
+#Thu Apr 12 11:38:04 CEST 2018
+maxValue=10.0
+minValue=-10.0
+offset=0.0
+precision=4
+resolution=0.01
+rotation=false
+scale=1.0
+unit=deg

devices/l.properties

@@ -0,0 +1,9 @@
+#Thu Apr 12 11:37:53 CEST 2018
+maxValue=10.0
+minValue=-10.0
+offset=0.0
+precision=4
+resolution=0.01
+rotation=false
+scale=1.0
+unit=deg

devices/motor.properties

@@ -1,20 +1,20 @@
-#Fri Sep 22 09:54:50 CEST 2017
-accessType=ReadWrite
-channel=MTEST-GOBBO\:MOT1
-defaultSpeed=1.0
-estbilizationDelay=0
-hasEnable=true
-homingDirection=Backward
-homingType=Backward
-maxSpeed=20.0
-maxValue=75.0
-minSpeed=0.1
-minValue=-5.0
-offset=0.0
-precision=4
-resolution=0.00125
-rotation=false
-scale=1.0
-simulation=false
-startRetries=1
-unit=mm
+#Wed Mar 28 11:52:13 CEST 2018
+accessType=ReadWrite
+channel=MTEST-GOBBO\:MOT1
+defaultSpeed=1.0
+estbilizationDelay=0
+hasEnable=true
+homingDirection=Backward
+homingType=Backward
+maxSpeed=20.0
+maxValue=75.0
+minSpeed=0.001
+minValue=-5.0
+offset=0.0
+precision=4
+resolution=0.00125
+rotation=false
+scale=1.0
+simulation=false
+startRetries=2
+unit=mm

devices/mu.properties

@@ -0,0 +1,14 @@
+#Thu Apr 12 11:02:07 CEST 2018
+defaultSpeed=10.0
+estbilizationDelay=0
+maxSpeed=10.0
+maxValue=360.0
+minSpeed=0.1
+minValue=-360.0
+offset=0.0
+precision=2
+resolution=NaN
+rotation=false
+scale=1.0
+startRetries=1
+unit=mm

devices/mycv.properties

@@ -0,0 +1,8 @@
+#Thu Feb 15 17:19:47 CET 2018
+maxValue=100.0
+minValue=-100.0
+offset=0.0
+precision=2
+resolution=0.1
+scale=1.0
+unit=mm

devices/mymot.properties

@@ -0,0 +1,16 @@
+#Thu Feb 15 17:16:13 CET 2018
+defaultSpeed=1.0
+estbilizationDelay=0
+hasEnable=false
+homingType=None
+maxSpeed=10.0
+maxValue=100.0
+minSpeed=0.01
+minValue=-100.0
+offset=0.0
+precision=2
+resolution=0.1
+rotation=false
+scale=1.0
+startRetries=1
+unit=mm

devices/mypos.properties

@@ -0,0 +1,9 @@
+#Thu Feb 15 17:17:18 CET 2018
+maxValue=100.0
+minValue=100.0
+offset=0.0
+precision=2
+resolution=0.1
+rotation=false
+scale=1.0
+unit=mm

devices/phi.properties

@@ -0,0 +1,14 @@
+#Thu Apr 12 11:03:09 CEST 2018
+defaultSpeed=10.0
+estbilizationDelay=0
+maxSpeed=10.0
+maxValue=360.0
+minSpeed=0.1
+minValue=-360.0
+offset=0.0
+precision=2
+resolution=NaN
+rotation=false
+scale=1.0
+startRetries=1
+unit=mm

devices/pipeline_server.properties

@@ -0,0 +1,24 @@
+#Thu Mar 29 13:44:16 CEST 2018
+colormap=Flame
+colormapAutomatic=true
+colormapMax=NaN
+colormapMin=NaN
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=0.0
+spatialCalOffsetY=0.0
+spatialCalScaleX=1.0
+spatialCalScaleY=1.0
+spatialCalUnits=mm
+transpose=false

devices/pos_chi.properties

@@ -0,0 +1,9 @@
+#Fri Apr 06 16:39:10 CEST 2018
+maxValue=NaN
+minValue=NaN
+offset=0.0
+precision=-1
+resolution=NaN
+rotation=false
+scale=1.0
+unit=null

devices/pos_delta.properties

@@ -0,0 +1,9 @@
+#Fri Apr 06 16:39:10 CEST 2018
+maxValue=NaN
+minValue=NaN
+offset=0.0
+precision=-1
+resolution=NaN
+rotation=false
+scale=1.0
+unit=null

devices/pos_en.properties

@@ -0,0 +1,9 @@
+#Fri Apr 06 16:39:10 CEST 2018
+maxValue=NaN
+minValue=NaN
+offset=0.0
+precision=-1
+resolution=NaN
+rotation=false
+scale=1.0
+unit=null

devices/pos_eta.properties

@@ -0,0 +1,9 @@
+#Fri Apr 06 16:39:10 CEST 2018
+maxValue=NaN
+minValue=NaN
+offset=0.0
+precision=-1
+resolution=NaN
+rotation=false
+scale=1.0
+unit=null

devices/pos_gam.properties

@@ -0,0 +1,9 @@
+#Fri Apr 06 16:39:10 CEST 2018
+maxValue=NaN
+minValue=NaN
+offset=0.0
+precision=-1
+resolution=NaN
+rotation=false
+scale=1.0
+unit=null

devices/pos_mu.properties

@@ -0,0 +1,9 @@
+#Fri Apr 06 16:39:10 CEST 2018
+maxValue=NaN
+minValue=NaN
+offset=0.0
+precision=-1
+resolution=NaN
+rotation=false
+scale=1.0
+unit=null

devices/pos_phi.properties

@@ -0,0 +1,9 @@
+#Fri Apr 06 16:39:10 CEST 2018
+maxValue=NaN
+minValue=NaN
+offset=0.0
+precision=-1
+resolution=NaN
+rotation=false
+scale=1.0
+unit=null

devices/positioner.properties

@@ -1,8 +1,9 @@
-#Wed Nov 08 12:33:55 CET 2017
-maxValue=1000.0
-minValue=-1000.0
-offset=0.0
-precision=5
-resolution=Infinity
-scale=1.0
-unit=mm
+#Tue Feb 06 09:47:44 CET 2018
+maxValue=1000.0
+minValue=-1000.0
+offset=0.0
+precision=5
+resolution=Infinity
+rotation=false
+scale=1.0
+unit=mm

devices/scanner.properties

@@ -0,0 +1,9 @@
+#Tue Feb 06 14:46:43 CET 2018
+maxValue=NaN
+minValue=NaN
+offset=0.0
+precision=-1
+resolution=NaN
+rotation=false
+scale=1.0
+unit=null

devices/sim.properties

@@ -1,24 +1,24 @@
-#Thu Sep 21 17:13:36 CEST 2017
-colormap=Flame
-colormapAutomatic=true
-colormapMax=NaN
-colormapMin=NaN
-flipHorizontally=false
-flipVertically=false
-grayscale=false
-invert=false
-rescaleFactor=1.0
-rescaleOffset=0.0
-roiHeight=-1
-roiWidth=-1
-roiX=0
-roiY=0
-rotation=0.0
-rotationCrop=false
-scale=1.0
-spatialCalOffsetX=NaN
-spatialCalOffsetY=NaN
-spatialCalScaleX=NaN
-spatialCalScaleY=NaN
-spatialCalUnits=mm
-transpose=false
+#Fri Mar 02 09:23:50 CET 2018
+colormap=Flame
+colormapAutomatic=true
+colormapMax=200.0
+colormapMin=2.0
+flipHorizontally=false
+flipVertically=false
+grayscale=false
+invert=false
+rescaleFactor=1.0
+rescaleOffset=0.0
+roiHeight=-1
+roiWidth=-1
+roiX=0
+roiY=0
+rotation=0.0
+rotationCrop=false
+scale=1.0
+spatialCalOffsetX=-0.0
+spatialCalOffsetY=0.0
+spatialCalScaleX=-1.0
+spatialCalScaleY=1.0
+spatialCalUnits=mm
+transpose=false

plugins/Correlation.form

@@ -0,0 +1,243 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<Form version="1.5" maxVersion="1.9" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
+  <AuxValues>
+    <AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
+    <AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="1"/>
+    <AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
+  </AuxValues>
+
+  <Layout>
+    <DimensionLayout dim="0">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Group type="102" alignment="1" attributes="0">
+              <EmptySpace max="-2" attributes="0"/>
+              <Component id="jPanel1" min="-2" max="-2" attributes="0"/>
+              <EmptySpace max="-2" attributes="0"/>
+              <Component id="plot" pref="371" max="32767" attributes="0"/>
+          </Group>
+      </Group>
+    </DimensionLayout>
+    <DimensionLayout dim="1">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Group type="102" alignment="0" attributes="0">
+              <EmptySpace max="-2" attributes="0"/>
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Component id="jPanel1" max="32767" attributes="0"/>
+                  <Group type="102" attributes="0">
+                      <Component id="plot" max="32767" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+          </Group>
+      </Group>
+    </DimensionLayout>
+  </Layout>
+  <SubComponents>
+    <Component class="ch.psi.pshell.plot.LinePlotJFree" name="plot">
+      <Properties>
+        <Property name="title" type="java.lang.String" value=""/>
+      </Properties>
+    </Component>
+    <Container class="javax.swing.JPanel" name="jPanel1">
+
+      <Layout>
+        <DimensionLayout dim="0">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" attributes="0">
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="0" attributes="0">
+                      <Component id="jLabel7" linkSize="3" alignment="1" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel6" linkSize="3" alignment="1" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel5" linkSize="3" alignment="1" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel3" linkSize="1" alignment="1" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel2" linkSize="1" alignment="1" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel1" linkSize="1" alignment="1" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel4" linkSize="1" alignment="1" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="0" attributes="0">
+                      <Component id="textDevX" linkSize="4" alignment="0" pref="250" max="32767" attributes="0"/>
+                      <Component id="textDevY" linkSize="4" alignment="0" pref="250" max="32767" attributes="0"/>
+                      <Component id="textCorrelation" linkSize="4" alignment="0" pref="250" max="32767" attributes="0"/>
+                      <Component id="spinnerInterval" linkSize="2" alignment="0" min="-2" max="-2" attributes="0"/>
+                      <Component id="spinnerWindow" linkSize="2" alignment="0" min="-2" max="-2" attributes="0"/>
+                      <Component id="checkBS" alignment="0" min="-2" max="-2" attributes="0"/>
+                      <Component id="textLinear" linkSize="4" alignment="0" pref="250" max="32767" attributes="0"/>
+                      <Component id="textQuadratic" linkSize="4" alignment="0" pref="250" max="32767" attributes="0"/>
+                      <Component id="checkLinear" alignment="0" min="-2" max="-2" attributes="0"/>
+                      <Component id="checkQuadratic" alignment="0" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
+              </Group>
+              <Group type="102" alignment="0" attributes="0">
+                  <EmptySpace max="32767" attributes="0"/>
+                  <Component id="buttonStart" min="-2" pref="189" max="-2" attributes="0"/>
+                  <EmptySpace max="32767" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
+        <DimensionLayout dim="1">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" attributes="0">
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="3" attributes="0">
+                      <Component id="jLabel1" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="textDevX" alignment="3" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="3" attributes="0">
+                      <Component id="jLabel2" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="textDevY" alignment="3" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Component id="checkBS" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace type="separate" max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="3" attributes="0">
+                      <Component id="jLabel3" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="spinnerInterval" alignment="3" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="3" attributes="0">
+                      <Component id="jLabel4" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="spinnerWindow" alignment="3" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace type="separate" max="-2" attributes="0"/>
+                  <Component id="checkLinear" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Component id="checkQuadratic" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace pref="42" max="32767" attributes="0"/>
+                  <Group type="103" groupAlignment="2" attributes="0">
+                      <Component id="textCorrelation" alignment="2" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel5" alignment="2" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace type="unrelated" max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="2" attributes="0">
+                      <Component id="jLabel6" alignment="2" min="-2" max="-2" attributes="0"/>
+                      <Component id="textLinear" alignment="2" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace type="unrelated" max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="2" attributes="0">
+                      <Component id="jLabel7" alignment="2" min="-2" max="-2" attributes="0"/>
+                      <Component id="textQuadratic" alignment="2" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace pref="42" max="32767" attributes="0"/>
+                  <Component id="buttonStart" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace min="-2" pref="45" max="-2" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
+      </Layout>
+      <SubComponents>
+        <Component class="javax.swing.JLabel" name="jLabel1">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="11"/>
+            <Property name="text" type="java.lang.String" value="X device:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JTextField" name="textDevX">
+        </Component>
+        <Component class="javax.swing.JTextField" name="textDevY">
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel2">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="11"/>
+            <Property name="text" type="java.lang.String" value="Y device:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel3">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="11"/>
+            <Property name="text" type="java.lang.String" value="Interval (s):"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JSpinner" name="spinnerInterval">
+          <Properties>
+            <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+              <SpinnerModel initial="0.1" minimum="0.001" numberType="java.lang.Double" stepSize="1.0" type="number"/>
+            </Property>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel4">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="11"/>
+            <Property name="text" type="java.lang.String" value="Window size:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JSpinner" name="spinnerWindow">
+          <Properties>
+            <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+              <SpinnerModel initial="50" minimum="3" numberType="java.lang.Integer" stepSize="1" type="number"/>
+            </Property>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JButton" name="buttonStart">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="Start"/>
+          </Properties>
+          <Events>
+            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonStartActionPerformed"/>
+          </Events>
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel5">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="4"/>
+            <Property name="text" type="java.lang.String" value="Correlation:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JTextField" name="textCorrelation">
+          <Properties>
+            <Property name="editable" type="boolean" value="false"/>
+            <Property name="horizontalAlignment" type="int" value="0"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JCheckBox" name="checkBS">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="Beam synchronous"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel6">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="4"/>
+            <Property name="text" type="java.lang.String" value="Liner fit:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JTextField" name="textLinear">
+          <Properties>
+            <Property name="editable" type="boolean" value="false"/>
+            <Property name="horizontalAlignment" type="int" value="0"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel7">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="4"/>
+            <Property name="text" type="java.lang.String" value="Quadratric fit:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JTextField" name="textQuadratic">
+          <Properties>
+            <Property name="editable" type="boolean" value="false"/>
+            <Property name="horizontalAlignment" type="int" value="0"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JCheckBox" name="checkLinear">
+          <Properties>
+            <Property name="selected" type="boolean" value="true"/>
+            <Property name="text" type="java.lang.String" value="Linear fit"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JCheckBox" name="checkQuadratic">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="Quadratic fit"/>
+          </Properties>
+        </Component>
+      </SubComponents>
+    </Container>
+  </SubComponents>
+</Form>

plugins/Correlation.java

@@ -0,0 +1,375 @@
+/*
+ * Copyright (c) 2014 Paul Scherrer Institute. All rights reserved.
+ */
+
+import ch.psi.pshell.plot.Plot;
+import ch.psi.pshell.ui.App;
+import ch.psi.pshell.ui.Panel;
+import ch.psi.utils.State;
+import java.awt.Component;
+import java.util.HashMap;
+import java.util.List;
+
+/**
+ *
+ */
+public class Correlation extends Panel {
+
+    public Correlation() {
+        initComponents();
+        this.setPersistedComponents(new Component[]{textDevX, textDevY, spinnerInterval, spinnerWindow, checkBS});
+        plot.getAxis(Plot.AxisId.X).setLabel(null);
+        plot.getAxis(Plot.AxisId.Y).setLabel(null);
+    }
+
+     //Overridable callbacks
+    @Override
+    public void onInitialize(int runCount) {
+        super.onInitialize(runCount);
+        this.startTimer(100, 10);
+        if (App.hasArgument("dx")) {
+                textDevX.setText(App.getArgumentValue("dx"));
+        }
+        if (App.hasArgument("dy")) {
+                textDevY.setText(App.getArgumentValue("dy"));
+        }        
+        try{
+            if (App.hasArgument("bs")) {
+                checkBS.setSelected(Boolean.valueOf(App.getArgumentValue("bs")));
+            }        
+        } catch (Exception ex){            
+           System.err.println(ex.getMessage());
+        }
+        try{
+            if (App.hasArgument("interval")) {
+                spinnerInterval.setValue(Double.valueOf(App.getArgumentValue("interval")));
+            }        
+        } catch (Exception ex){            
+            System.err.println(ex.getMessage());
+        }
+        try{
+            if (App.hasArgument("window")) {
+                spinnerWindow.setValue(Integer.valueOf(App.getArgumentValue("window")));
+            }        
+        } catch (Exception ex){            
+            System.err.println(ex.getMessage());
+        }                    
+    }
+    
+    @Override
+    protected void onTimer(){
+        if (isRunning()){
+            updateResults();
+        }
+    }
+    
+    //DecimalFormat formatter = new DecimalFormat("0.##E0");
+    void updateResults(){
+        try{
+            textCorrelation.setText(String.format("%1.4f", Double.valueOf((Double)getContext().getInterpreterVariable("corr"))));            
+        } catch (Exception ex){
+            textCorrelation.setText("");
+        }
+        
+        if (checkLinear.isSelected()){
+            try{
+                List pars = (List)getContext().getInterpreterVariable("pars_lin");            
+                //textLinear.setText(String.format("%1.3fx%+1.3f", (Double)(pars.get(1)),  (Double)(pars.get(0))));            
+                textLinear.setText(String.format("%1.6gx%+1.6g",pars.get(1),  pars.get(0)));            
+            } catch (Exception ex){
+                textLinear.setText("");
+            }        
+        }
+        
+        if (checkQuadratic.isSelected()){
+            try{
+                List pars = (List)getContext().getInterpreterVariable("pars_quad");            
+                //textQuadratic.setText(String.format("%1.2fx\u00B2 %+1.2fx%+1.2f", (Double)(pars.get(0)), (Double)(pars.get(1)),  (Double)(pars.get(0))));            
+                textQuadratic.setText(String.format("%1.3gx\u00B2%+1.3gx%+1.3g", pars.get(0), pars.get(1), pars.get(0)));            
+                //textQuadratic.setText(formatter.format(pars.get(2))+ formatter.format(pars.get(1)) + formatter.format(pars.get(0)));            
+
+            } catch (Exception ex){
+                textQuadratic.setText("");
+            }        
+        }        
+    }
+
+    @Override
+    public void onStateChange(State state, State former) {
+        buttonStart.setEnabled((state==State.Ready) || (state==State.Busy));
+        if (isRunning()){
+            if (state==State.Ready){
+                buttonStart.setText("Start");
+            }
+        } else {
+            if (state==State.Busy){
+                buttonStart.setText("Stop");
+            }
+        }
+        textDevX.setEnabled(state==State.Ready);
+        textDevY.setEnabled(state==State.Ready);
+        spinnerInterval.setEnabled(state==State.Ready);
+        spinnerWindow.setEnabled(state==State.Ready);        
+        checkBS.setEnabled(state==State.Ready);        
+        checkLinear.setEnabled(state==State.Ready);        
+        checkQuadratic.setEnabled(state==State.Ready);        
+        
+        if ((former==State.Initializing) && (state == State.Ready)){
+            if (App.hasArgument("start")) {
+                buttonStartActionPerformed(null);
+            }        
+        }
+        
+    }
+    
+    boolean isRunning(){
+        return buttonStart.getText().equals("Stop");
+    }
+
+    @Override
+    public void onExecutedFile(String fileName, Object result) {
+    }
+
+    
+    //Callback to perform update - in event thread
+    @Override
+    protected void doUpdate() {
+    }
+
+    @SuppressWarnings("unchecked")
+    // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
+    private void initComponents() {
+
+        plot = new ch.psi.pshell.plot.LinePlotJFree();
+        jPanel1 = new javax.swing.JPanel();
+        jLabel1 = new javax.swing.JLabel();
+        textDevX = new javax.swing.JTextField();
+        textDevY = new javax.swing.JTextField();
+        jLabel2 = new javax.swing.JLabel();
+        jLabel3 = new javax.swing.JLabel();
+        spinnerInterval = new javax.swing.JSpinner();
+        jLabel4 = new javax.swing.JLabel();
+        spinnerWindow = new javax.swing.JSpinner();
+        buttonStart = new javax.swing.JButton();
+        jLabel5 = new javax.swing.JLabel();
+        textCorrelation = new javax.swing.JTextField();
+        checkBS = new javax.swing.JCheckBox();
+        jLabel6 = new javax.swing.JLabel();
+        textLinear = new javax.swing.JTextField();
+        jLabel7 = new javax.swing.JLabel();
+        textQuadratic = new javax.swing.JTextField();
+        checkLinear = new javax.swing.JCheckBox();
+        checkQuadratic = new javax.swing.JCheckBox();
+
+        plot.setTitle("");
+
+        jLabel1.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel1.setText("X device:");
+
+        jLabel2.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel2.setText("Y device:");
+
+        jLabel3.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel3.setText("Interval (s):");
+
+        spinnerInterval.setModel(new javax.swing.SpinnerNumberModel(Double.valueOf(0.1d), Double.valueOf(0.001d), null, Double.valueOf(1.0d)));
+
+        jLabel4.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel4.setText("Window size:");
+
+        spinnerWindow.setModel(new javax.swing.SpinnerNumberModel(Integer.valueOf(50), Integer.valueOf(3), null, Integer.valueOf(1)));
+
+        buttonStart.setText("Start");
+        buttonStart.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                buttonStartActionPerformed(evt);
+            }
+        });
+
+        jLabel5.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
+        jLabel5.setText("Correlation:");
+
+        textCorrelation.setEditable(false);
+        textCorrelation.setHorizontalAlignment(javax.swing.JTextField.CENTER);
+
+        checkBS.setText("Beam synchronous");
+
+        jLabel6.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
+        jLabel6.setText("Liner fit:");
+
+        textLinear.setEditable(false);
+        textLinear.setHorizontalAlignment(javax.swing.JTextField.CENTER);
+
+        jLabel7.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
+        jLabel7.setText("Quadratric fit:");
+
+        textQuadratic.setEditable(false);
+        textQuadratic.setHorizontalAlignment(javax.swing.JTextField.CENTER);
+
+        checkLinear.setSelected(true);
+        checkLinear.setText("Linear fit");
+
+        checkQuadratic.setText("Quadratic fit");
+
+        javax.swing.GroupLayout jPanel1Layout = new javax.swing.GroupLayout(jPanel1);
+        jPanel1.setLayout(jPanel1Layout);
+        jPanel1Layout.setHorizontalGroup(
+            jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(jPanel1Layout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(jLabel7, javax.swing.GroupLayout.Alignment.TRAILING)
+                    .addComponent(jLabel6, javax.swing.GroupLayout.Alignment.TRAILING)
+                    .addComponent(jLabel5, javax.swing.GroupLayout.Alignment.TRAILING)
+                    .addComponent(jLabel3, javax.swing.GroupLayout.Alignment.TRAILING)
+                    .addComponent(jLabel2, javax.swing.GroupLayout.Alignment.TRAILING)
+                    .addComponent(jLabel1, javax.swing.GroupLayout.Alignment.TRAILING)
+                    .addComponent(jLabel4, javax.swing.GroupLayout.Alignment.TRAILING))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(textDevX, javax.swing.GroupLayout.DEFAULT_SIZE, 250, Short.MAX_VALUE)
+                    .addComponent(textDevY, javax.swing.GroupLayout.DEFAULT_SIZE, 250, Short.MAX_VALUE)
+                    .addComponent(textCorrelation, javax.swing.GroupLayout.DEFAULT_SIZE, 250, Short.MAX_VALUE)
+                    .addComponent(spinnerInterval, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                    .addComponent(spinnerWindow, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                    .addComponent(checkBS)
+                    .addComponent(textLinear, javax.swing.GroupLayout.DEFAULT_SIZE, 250, Short.MAX_VALUE)
+                    .addComponent(textQuadratic, javax.swing.GroupLayout.DEFAULT_SIZE, 250, Short.MAX_VALUE)
+                    .addComponent(checkLinear)
+                    .addComponent(checkQuadratic))
+                .addGap(0, 0, Short.MAX_VALUE))
+            .addGroup(jPanel1Layout.createSequentialGroup()
+                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addComponent(buttonStart, javax.swing.GroupLayout.PREFERRED_SIZE, 189, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+        );
+
+        jPanel1Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {jLabel1, jLabel2, jLabel3, jLabel4});
+
+        jPanel1Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {spinnerInterval, spinnerWindow});
+
+        jPanel1Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {jLabel5, jLabel6, jLabel7});
+
+        jPanel1Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {textCorrelation, textDevX, textDevY, textLinear, textQuadratic});
+
+        jPanel1Layout.setVerticalGroup(
+            jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(jPanel1Layout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel1)
+                    .addComponent(textDevX, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel2)
+                    .addComponent(textDevY, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addComponent(checkBS)
+                .addGap(18, 18, 18)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel3)
+                    .addComponent(spinnerInterval, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel4)
+                    .addComponent(spinnerWindow, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addGap(18, 18, 18)
+                .addComponent(checkLinear)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addComponent(checkQuadratic)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 42, Short.MAX_VALUE)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
+                    .addComponent(textCorrelation, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                    .addComponent(jLabel5))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
+                    .addComponent(jLabel6)
+                    .addComponent(textLinear, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
+                    .addComponent(jLabel7)
+                    .addComponent(textQuadratic, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 42, Short.MAX_VALUE)
+                .addComponent(buttonStart)
+                .addGap(45, 45, 45))
+        );
+
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
+        this.setLayout(layout);
+        layout.setHorizontalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
+                .addContainerGap()
+                .addComponent(jPanel1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addComponent(plot, javax.swing.GroupLayout.DEFAULT_SIZE, 371, Short.MAX_VALUE))
+        );
+        layout.setVerticalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(layout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(jPanel1, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                    .addGroup(layout.createSequentialGroup()
+                        .addComponent(plot, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                        .addContainerGap())))
+        );
+    }// </editor-fold>//GEN-END:initComponents
+
+    private void buttonStartActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonStartActionPerformed
+        try {
+            if (isRunning()){
+                abort();
+                updateResults();
+                //buttonStart.setText("Start");
+            } else {
+                textCorrelation.setText("");
+                textLinear.setText("");
+                textQuadratic.setText("");
+                HashMap args = new HashMap();
+                args.put("dx", textDevX.getText());
+                args.put("dy", textDevY.getText());
+                args.put("interval", spinnerInterval.getValue());
+                args.put("window", spinnerWindow.getValue());
+                args.put("bs", checkBS.isSelected());
+                args.put("linear_fit", checkLinear.isSelected());
+                args.put("quadratic_fit", checkQuadratic.isSelected());
+
+                args.put("p", plot);
+                runAsync("Correlation/Correlation", args).handle((ok, ex) -> {
+                    if (ex != null) {
+                        ex.printStackTrace();
+                    }            
+                    return ok;
+                }); 
+                ///buttonStart.setText("Stop");
+            }
+
+        } catch (Exception ex) {
+            showException(ex);
+        }        
+    }//GEN-LAST:event_buttonStartActionPerformed
+
+    // Variables declaration - do not modify//GEN-BEGIN:variables
+    private javax.swing.JButton buttonStart;
+    private javax.swing.JCheckBox checkBS;
+    private javax.swing.JCheckBox checkLinear;
+    private javax.swing.JCheckBox checkQuadratic;
+    private javax.swing.JLabel jLabel1;
+    private javax.swing.JLabel jLabel2;
+    private javax.swing.JLabel jLabel3;
+    private javax.swing.JLabel jLabel4;
+    private javax.swing.JLabel jLabel5;
+    private javax.swing.JLabel jLabel6;
+    private javax.swing.JLabel jLabel7;
+    private javax.swing.JPanel jPanel1;
+    private ch.psi.pshell.plot.LinePlotJFree plot;
+    private javax.swing.JSpinner spinnerInterval;
+    private javax.swing.JSpinner spinnerWindow;
+    private javax.swing.JTextField textCorrelation;
+    private javax.swing.JTextField textDevX;
+    private javax.swing.JTextField textDevY;
+    private javax.swing.JTextField textLinear;
+    private javax.swing.JTextField textQuadratic;
+    // End of variables declaration//GEN-END:variables
+}

plugins/Correlation2.form

@@ -0,0 +1,267 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<Form version="1.5" maxVersion="1.9" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
+  <AuxValues>
+    <AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
+    <AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="1"/>
+    <AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
+    <AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
+    <AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
+  </AuxValues>
+
+  <Layout>
+    <DimensionLayout dim="0">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Group type="102" alignment="1" attributes="0">
+              <EmptySpace max="-2" attributes="0"/>
+              <Component id="jPanel1" min="-2" max="-2" attributes="0"/>
+              <EmptySpace max="-2" attributes="0"/>
+              <Component id="plot" pref="345" max="32767" attributes="0"/>
+          </Group>
+      </Group>
+    </DimensionLayout>
+    <DimensionLayout dim="1">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Group type="102" alignment="0" attributes="0">
+              <EmptySpace max="-2" attributes="0"/>
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Component id="jPanel1" max="32767" attributes="0"/>
+                  <Group type="102" attributes="0">
+                      <Component id="plot" max="32767" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+          </Group>
+      </Group>
+    </DimensionLayout>
+  </Layout>
+  <SubComponents>
+    <Component class="ch.psi.pshell.plot.LinePlotJFree" name="plot">
+      <Properties>
+        <Property name="title" type="java.lang.String" value=""/>
+      </Properties>
+    </Component>
+    <Container class="javax.swing.JPanel" name="jPanel1">
+
+      <Layout>
+        <DimensionLayout dim="0">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" alignment="0" attributes="0">
+                  <EmptySpace max="32767" attributes="0"/>
+                  <Component id="buttonStart" min="-2" pref="189" max="-2" attributes="0"/>
+                  <EmptySpace max="32767" attributes="0"/>
+              </Group>
+              <Group type="102" alignment="0" attributes="0">
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="0" attributes="0">
+                      <Component id="jLabel7" linkSize="3" alignment="1" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel6" linkSize="3" alignment="1" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel5" linkSize="3" alignment="1" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel3" linkSize="1" alignment="1" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel2" linkSize="1" alignment="1" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel1" linkSize="1" alignment="1" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel4" linkSize="1" alignment="1" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="0" attributes="0">
+                      <Group type="102" attributes="0">
+                          <Group type="103" groupAlignment="0" attributes="0">
+                              <Component id="comboTypeY" min="-2" max="-2" attributes="0"/>
+                              <Component id="comboTypeX" min="-2" max="-2" attributes="0"/>
+                              <Component id="textCorrelation" linkSize="4" alignment="0" pref="250" max="32767" attributes="0"/>
+                              <Component id="spinnerInterval" linkSize="2" alignment="0" min="-2" max="-2" attributes="0"/>
+                              <Component id="spinnerWindow" linkSize="2" alignment="0" min="-2" max="-2" attributes="0"/>
+                              <Component id="textLinear" linkSize="4" alignment="0" pref="250" max="32767" attributes="0"/>
+                              <Component id="textQuadratic" linkSize="4" alignment="0" pref="250" max="32767" attributes="0"/>
+                              <Component id="checkLinear" alignment="0" min="-2" max="-2" attributes="0"/>
+                              <Component id="checkQuadratic" alignment="0" min="-2" max="-2" attributes="0"/>
+                          </Group>
+                          <EmptySpace min="26" max="32767" attributes="0"/>
+                      </Group>
+                      <Component id="textDevX" max="32767" attributes="0"/>
+                      <Component id="textDevY" alignment="0" max="32767" attributes="0"/>
+                  </Group>
+              </Group>
+          </Group>
+        </DimensionLayout>
+        <DimensionLayout dim="1">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" attributes="0">
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="3" attributes="0">
+                      <Component id="jLabel1" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="textDevX" alignment="3" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Component id="comboTypeX" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace type="unrelated" max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="3" attributes="0">
+                      <Component id="jLabel2" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="textDevY" alignment="3" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace min="-2" pref="3" max="-2" attributes="0"/>
+                  <Component id="comboTypeY" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace type="separate" max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="3" attributes="0">
+                      <Component id="jLabel3" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="spinnerInterval" alignment="3" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="3" attributes="0">
+                      <Component id="jLabel4" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Component id="spinnerWindow" alignment="3" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace type="separate" max="-2" attributes="0"/>
+                  <Component id="checkLinear" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace max="-2" attributes="0"/>
+                  <Component id="checkQuadratic" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace pref="22" max="32767" attributes="0"/>
+                  <Group type="103" groupAlignment="2" attributes="0">
+                      <Component id="textCorrelation" alignment="2" min="-2" max="-2" attributes="0"/>
+                      <Component id="jLabel5" alignment="2" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace type="unrelated" max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="2" attributes="0">
+                      <Component id="jLabel6" alignment="2" min="-2" max="-2" attributes="0"/>
+                      <Component id="textLinear" alignment="2" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace type="unrelated" max="-2" attributes="0"/>
+                  <Group type="103" groupAlignment="2" attributes="0">
+                      <Component id="jLabel7" alignment="2" min="-2" max="-2" attributes="0"/>
+                      <Component id="textQuadratic" alignment="2" min="-2" max="-2" attributes="0"/>
+                  </Group>
+                  <EmptySpace pref="24" max="32767" attributes="0"/>
+                  <Component id="buttonStart" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace min="-2" pref="45" max="-2" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
+      </Layout>
+      <SubComponents>
+        <Component class="javax.swing.JLabel" name="jLabel1">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="11"/>
+            <Property name="text" type="java.lang.String" value="X device:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JTextField" name="textDevX">
+        </Component>
+        <Component class="javax.swing.JTextField" name="textDevY">
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel2">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="11"/>
+            <Property name="text" type="java.lang.String" value="Y device:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel3">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="11"/>
+            <Property name="text" type="java.lang.String" value="Interval (s):"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JSpinner" name="spinnerInterval">
+          <Properties>
+            <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+              <SpinnerModel initial="0.1" minimum="0.001" numberType="java.lang.Double" stepSize="1.0" type="number"/>
+            </Property>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel4">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="11"/>
+            <Property name="text" type="java.lang.String" value="Window size:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JSpinner" name="spinnerWindow">
+          <Properties>
+            <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+              <SpinnerModel initial="50" minimum="3" numberType="java.lang.Integer" stepSize="1" type="number"/>
+            </Property>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JButton" name="buttonStart">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="Start"/>
+          </Properties>
+          <Events>
+            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonStartActionPerformed"/>
+          </Events>
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel5">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="4"/>
+            <Property name="text" type="java.lang.String" value="Correlation:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JTextField" name="textCorrelation">
+          <Properties>
+            <Property name="editable" type="boolean" value="false"/>
+            <Property name="horizontalAlignment" type="int" value="0"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel6">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="4"/>
+            <Property name="text" type="java.lang.String" value="Liner fit:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JTextField" name="textLinear">
+          <Properties>
+            <Property name="editable" type="boolean" value="false"/>
+            <Property name="horizontalAlignment" type="int" value="0"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JLabel" name="jLabel7">
+          <Properties>
+            <Property name="horizontalAlignment" type="int" value="4"/>
+            <Property name="text" type="java.lang.String" value="Quadratric fit:"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JTextField" name="textQuadratic">
+          <Properties>
+            <Property name="editable" type="boolean" value="false"/>
+            <Property name="horizontalAlignment" type="int" value="0"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JCheckBox" name="checkLinear">
+          <Properties>
+            <Property name="selected" type="boolean" value="true"/>
+            <Property name="text" type="java.lang.String" value="Linear fit"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JCheckBox" name="checkQuadratic">
+          <Properties>
+            <Property name="text" type="java.lang.String" value="Quadratic fit"/>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JComboBox" name="comboTypeX">
+          <Properties>
+            <Property name="model" type="javax.swing.ComboBoxModel" editor="org.netbeans.modules.form.editors2.ComboBoxModelEditor">
+              <StringArray count="3">
+                <StringItem index="0" value="Channel"/>
+                <StringItem index="1" value="Stream"/>
+                <StringItem index="2" value="Camera"/>
+              </StringArray>
+            </Property>
+          </Properties>
+        </Component>
+        <Component class="javax.swing.JComboBox" name="comboTypeY">
+          <Properties>
+            <Property name="model" type="javax.swing.ComboBoxModel" editor="org.netbeans.modules.form.editors2.ComboBoxModelEditor">
+              <StringArray count="3">
+                <StringItem index="0" value="Channel"/>
+                <StringItem index="1" value="Stream"/>
+                <StringItem index="2" value="Camera"/>
+              </StringArray>
+            </Property>
+          </Properties>
+        </Component>
+      </SubComponents>
+    </Container>
+  </SubComponents>
+</Form>

plugins/Correlation2.java

@@ -0,0 +1,393 @@
+/*
+ * Copyright (c) 2014 Paul Scherrer Institute. All rights reserved.
+ */
+
+import ch.psi.pshell.plot.Plot;
+import ch.psi.pshell.ui.App;
+import ch.psi.pshell.ui.Panel;
+import ch.psi.utils.State;
+import java.awt.Component;
+import java.util.HashMap;
+import java.util.List;
+
+/**
+ *
+ */
+public class Correlation2 extends Panel {
+
+    public Correlation2() {
+        initComponents();
+        this.setPersistedComponents(new Component[]{textDevX, textDevY, spinnerInterval, spinnerWindow, comboTypeX, comboTypeY});
+        plot.getAxis(Plot.AxisId.X).setLabel(null);
+        plot.getAxis(Plot.AxisId.Y).setLabel(null);
+    }
+
+     //Overridable callbacks
+    @Override
+    public void onInitialize(int runCount) {
+        super.onInitialize(runCount);
+        this.startTimer(100, 10);
+        if (App.hasArgument("dx")) {
+                textDevX.setText(App.getArgumentValue("dx"));
+        }
+        if (App.hasArgument("dy")) {
+                textDevY.setText(App.getArgumentValue("dy"));
+        }        
+        try{
+            if (App.hasArgument("dxtype")) {
+                comboTypeX.setSelectedIndex(Integer.valueOf(App.getArgumentValue("dxtype")));
+            }        
+        } catch (Exception ex){            
+           System.err.println(ex.getMessage());
+        }
+        try{
+            if (App.hasArgument("dytype")) {
+                comboTypeY.setSelectedIndex(Integer.valueOf(App.getArgumentValue("dytype")));
+            }        
+        } catch (Exception ex){            
+           System.err.println(ex.getMessage());
+        }
+        try{
+            if (App.hasArgument("interval")) {
+                spinnerInterval.setValue(Double.valueOf(App.getArgumentValue("interval")));
+            }        
+        } catch (Exception ex){            
+            System.err.println(ex.getMessage());
+        }
+        try{
+            if (App.hasArgument("window")) {
+                spinnerWindow.setValue(Integer.valueOf(App.getArgumentValue("window")));
+            }        
+        } catch (Exception ex){            
+            System.err.println(ex.getMessage());
+        }                    
+    }
+    
+    @Override
+    protected void onTimer(){
+        if (isRunning()){
+            updateResults();
+        }
+    }
+    
+    //DecimalFormat formatter = new DecimalFormat("0.##E0");
+    void updateResults(){
+        try{
+            textCorrelation.setText(String.format("%1.4f", Double.valueOf((Double)getContext().getInterpreterVariable("corr"))));            
+        } catch (Exception ex){
+            textCorrelation.setText("");
+        }
+        
+        if (checkLinear.isSelected()){
+            try{
+                List pars = (List)getContext().getInterpreterVariable("pars_lin");            
+                //textLinear.setText(String.format("%1.3fx%+1.3f", (Double)(pars.get(1)),  (Double)(pars.get(0))));            
+                textLinear.setText(String.format("%1.6gx%+1.6g",pars.get(1),  pars.get(0)));            
+            } catch (Exception ex){
+                textLinear.setText("");
+            }        
+        }
+        
+        if (checkQuadratic.isSelected()){
+            try{
+                List pars = (List)getContext().getInterpreterVariable("pars_quad");            
+                //textQuadratic.setText(String.format("%1.2fx\u00B2 %+1.2fx%+1.2f", (Double)(pars.get(0)), (Double)(pars.get(1)),  (Double)(pars.get(0))));            
+                textQuadratic.setText(String.format("%1.3gx\u00B2%+1.3gx%+1.3g", pars.get(0), pars.get(1), pars.get(0)));            
+                //textQuadratic.setText(formatter.format(pars.get(2))+ formatter.format(pars.get(1)) + formatter.format(pars.get(0)));            
+
+            } catch (Exception ex){
+                textQuadratic.setText("");
+            }        
+        }        
+    }
+
+    @Override
+    public void onStateChange(State state, State former) {
+        buttonStart.setEnabled((state==State.Ready) || (state==State.Busy));
+        if (isRunning()){
+            if (state==State.Ready){
+                buttonStart.setText("Start");
+            }
+        } else {
+            if (state==State.Busy){
+                buttonStart.setText("Stop");
+            }
+        }
+        textDevX.setEnabled(state==State.Ready);
+        textDevY.setEnabled(state==State.Ready);
+        spinnerInterval.setEnabled(state==State.Ready);
+        spinnerWindow.setEnabled(state==State.Ready);        
+        comboTypeX.setEnabled(state==State.Ready);        
+        comboTypeY.setEnabled(state==State.Ready);        
+        checkLinear.setEnabled(state==State.Ready);        
+        checkQuadratic.setEnabled(state==State.Ready);        
+        
+        if ((former==State.Initializing) && (state == State.Ready)){
+            if (App.hasArgument("start")) {
+                buttonStartActionPerformed(null);
+            }        
+        }
+        
+    }
+    
+    boolean isRunning(){
+        return buttonStart.getText().equals("Stop");
+    }
+
+    @Override
+    public void onExecutedFile(String fileName, Object result) {
+    }
+
+    
+    //Callback to perform update - in event thread
+    @Override
+    protected void doUpdate() {
+    }
+
+    @SuppressWarnings("unchecked")
+    // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
+    private void initComponents() {
+
+        plot = new ch.psi.pshell.plot.LinePlotJFree();
+        jPanel1 = new javax.swing.JPanel();
+        jLabel1 = new javax.swing.JLabel();
+        textDevX = new javax.swing.JTextField();
+        textDevY = new javax.swing.JTextField();
+        jLabel2 = new javax.swing.JLabel();
+        jLabel3 = new javax.swing.JLabel();
+        spinnerInterval = new javax.swing.JSpinner();
+        jLabel4 = new javax.swing.JLabel();
+        spinnerWindow = new javax.swing.JSpinner();
+        buttonStart = new javax.swing.JButton();
+        jLabel5 = new javax.swing.JLabel();
+        textCorrelation = new javax.swing.JTextField();
+        jLabel6 = new javax.swing.JLabel();
+        textLinear = new javax.swing.JTextField();
+        jLabel7 = new javax.swing.JLabel();
+        textQuadratic = new javax.swing.JTextField();
+        checkLinear = new javax.swing.JCheckBox();
+        checkQuadratic = new javax.swing.JCheckBox();
+        comboTypeX = new javax.swing.JComboBox();
+        comboTypeY = new javax.swing.JComboBox();
+
+        plot.setTitle("");
+
+        jLabel1.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel1.setText("X device:");
+
+        jLabel2.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel2.setText("Y device:");
+
+        jLabel3.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel3.setText("Interval (s):");
+
+        spinnerInterval.setModel(new javax.swing.SpinnerNumberModel(Double.valueOf(0.1d), Double.valueOf(0.001d), null, Double.valueOf(1.0d)));
+
+        jLabel4.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel4.setText("Window size:");
+
+        spinnerWindow.setModel(new javax.swing.SpinnerNumberModel(Integer.valueOf(50), Integer.valueOf(3), null, Integer.valueOf(1)));
+
+        buttonStart.setText("Start");
+        buttonStart.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                buttonStartActionPerformed(evt);
+            }
+        });
+
+        jLabel5.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
+        jLabel5.setText("Correlation:");
+
+        textCorrelation.setEditable(false);
+        textCorrelation.setHorizontalAlignment(javax.swing.JTextField.CENTER);
+
+        jLabel6.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
+        jLabel6.setText("Liner fit:");
+
+        textLinear.setEditable(false);
+        textLinear.setHorizontalAlignment(javax.swing.JTextField.CENTER);
+
+        jLabel7.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
+        jLabel7.setText("Quadratric fit:");
+
+        textQuadratic.setEditable(false);
+        textQuadratic.setHorizontalAlignment(javax.swing.JTextField.CENTER);
+
+        checkLinear.setSelected(true);
+        checkLinear.setText("Linear fit");
+
+        checkQuadratic.setText("Quadratic fit");
+
+        comboTypeX.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Channel", "Stream", "Camera" }));
+
+        comboTypeY.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Channel", "Stream", "Camera" }));
+
+        javax.swing.GroupLayout jPanel1Layout = new javax.swing.GroupLayout(jPanel1);
+        jPanel1.setLayout(jPanel1Layout);
+        jPanel1Layout.setHorizontalGroup(
+            jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(jPanel1Layout.createSequentialGroup()
+                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addComponent(buttonStart, javax.swing.GroupLayout.PREFERRED_SIZE, 189, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+            .addGroup(jPanel1Layout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(jLabel7, javax.swing.GroupLayout.Alignment.TRAILING)
+                    .addComponent(jLabel6, javax.swing.GroupLayout.Alignment.TRAILING)
+                    .addComponent(jLabel5, javax.swing.GroupLayout.Alignment.TRAILING)
+                    .addComponent(jLabel3, javax.swing.GroupLayout.Alignment.TRAILING)
+                    .addComponent(jLabel2, javax.swing.GroupLayout.Alignment.TRAILING)
+                    .addComponent(jLabel1, javax.swing.GroupLayout.Alignment.TRAILING)
+                    .addComponent(jLabel4, javax.swing.GroupLayout.Alignment.TRAILING))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addGroup(jPanel1Layout.createSequentialGroup()
+                        .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                            .addComponent(comboTypeY, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                            .addComponent(comboTypeX, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                            .addComponent(textCorrelation, javax.swing.GroupLayout.DEFAULT_SIZE, 250, Short.MAX_VALUE)
+                            .addComponent(spinnerInterval, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                            .addComponent(spinnerWindow, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                            .addComponent(textLinear, javax.swing.GroupLayout.DEFAULT_SIZE, 250, Short.MAX_VALUE)
+                            .addComponent(textQuadratic, javax.swing.GroupLayout.DEFAULT_SIZE, 250, Short.MAX_VALUE)
+                            .addComponent(checkLinear)
+                            .addComponent(checkQuadratic))
+                        .addContainerGap())
+                    .addComponent(textDevX)
+                    .addComponent(textDevY)))
+        );
+
+        jPanel1Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {jLabel1, jLabel2, jLabel3, jLabel4});
+
+        jPanel1Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {spinnerInterval, spinnerWindow});
+
+        jPanel1Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {jLabel5, jLabel6, jLabel7});
+
+        jPanel1Layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {textCorrelation, textLinear, textQuadratic});
+
+        jPanel1Layout.setVerticalGroup(
+            jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(jPanel1Layout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel1)
+                    .addComponent(textDevX, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addComponent(comboTypeX, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel2)
+                    .addComponent(textDevY, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addGap(3, 3, 3)
+                .addComponent(comboTypeY, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addGap(18, 18, 18)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel3)
+                    .addComponent(spinnerInterval, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel4)
+                    .addComponent(spinnerWindow, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addGap(18, 18, 18)
+                .addComponent(checkLinear)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addComponent(checkQuadratic)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 22, Short.MAX_VALUE)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
+                    .addComponent(textCorrelation, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                    .addComponent(jLabel5))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
+                    .addComponent(jLabel6)
+                    .addComponent(textLinear, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
+                    .addComponent(jLabel7)
+                    .addComponent(textQuadratic, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 24, Short.MAX_VALUE)
+                .addComponent(buttonStart)
+                .addGap(45, 45, 45))
+        );
+
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
+        this.setLayout(layout);
+        layout.setHorizontalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
+                .addContainerGap()
+                .addComponent(jPanel1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addComponent(plot, javax.swing.GroupLayout.DEFAULT_SIZE, 345, Short.MAX_VALUE))
+        );
+        layout.setVerticalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(layout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(jPanel1, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                    .addGroup(layout.createSequentialGroup()
+                        .addComponent(plot, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                        .addContainerGap())))
+        );
+    }// </editor-fold>//GEN-END:initComponents
+
+    private void buttonStartActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonStartActionPerformed
+        try {
+            if (isRunning()){
+                abort();
+                updateResults();
+                //buttonStart.setText("Start");
+            } else {
+                textCorrelation.setText("");
+                textLinear.setText("");
+                textQuadratic.setText("");
+                HashMap args = new HashMap();
+                args.put("dx", textDevX.getText());
+                args.put("dy", textDevY.getText());
+                args.put("interval", spinnerInterval.getValue());
+                args.put("window", spinnerWindow.getValue());
+                args.put("dxtype", comboTypeX.getSelectedIndex());
+                args.put("dytype", comboTypeY.getSelectedIndex());
+                args.put("linear_fit", checkLinear.isSelected());
+                args.put("quadratic_fit", checkQuadratic.isSelected());
+
+                args.put("p", plot);
+                runAsync("Correlation/Correlation2", args).handle((ok, ex) -> {
+                    if (ex != null) {
+                        ex.printStackTrace();
+                    }            
+                    return ok;
+                }); 
+                ///buttonStart.setText("Stop");
+            }
+
+        } catch (Exception ex) {
+            showException(ex);
+        }        
+    }//GEN-LAST:event_buttonStartActionPerformed
+
+    // Variables declaration - do not modify//GEN-BEGIN:variables
+    private javax.swing.JButton buttonStart;
+    private javax.swing.JCheckBox checkLinear;
+    private javax.swing.JCheckBox checkQuadratic;
+    private javax.swing.JComboBox comboTypeX;
+    private javax.swing.JComboBox comboTypeY;
+    private javax.swing.JLabel jLabel1;
+    private javax.swing.JLabel jLabel2;
+    private javax.swing.JLabel jLabel3;
+    private javax.swing.JLabel jLabel4;
+    private javax.swing.JLabel jLabel5;
+    private javax.swing.JLabel jLabel6;
+    private javax.swing.JLabel jLabel7;
+    private javax.swing.JPanel jPanel1;
+    private ch.psi.pshell.plot.LinePlotJFree plot;
+    private javax.swing.JSpinner spinnerInterval;
+    private javax.swing.JSpinner spinnerWindow;
+    private javax.swing.JTextField textCorrelation;
+    private javax.swing.JTextField textDevX;
+    private javax.swing.JTextField textDevY;
+    private javax.swing.JTextField textLinear;
+    private javax.swing.JTextField textQuadratic;
+    // End of variables declaration//GEN-END:variables
+}

plugins/ScreenPanel2.form.txt

@@ -38,7 +38,7 @@
                   <Group type="102" alignment="0" attributes="0">
                       <Component id="sidePanel" min="-2" max="-2" attributes="0"/>
                       <EmptySpace min="-2" max="-2" attributes="0"/>
-                      <Component id="renderer" pref="578" max="32767" attributes="0"/>
+                      <Component id="renderer" max="32767" attributes="0"/>
                   </Group>
                   <Group type="102" alignment="0" attributes="0">
                       <EmptySpace min="-2" max="-2" attributes="0"/>
@@ -68,7 +68,7 @@
       <Layout>
         <DimensionLayout dim="0">
           <Group type="103" groupAlignment="0" attributes="0">
-              <Group type="102" alignment="0" attributes="0">
+              <Group type="102" attributes="0">
                   <EmptySpace max="-2" attributes="0"/>
                   <Group type="103" groupAlignment="1" max="-2" attributes="0">
                       <Component id="jPanel5" max="32767" attributes="0"/>
@@ -78,7 +78,7 @@
                       <Component id="panelScreen" max="32767" attributes="0"/>
                       <Component id="panelFilter" max="32767" attributes="0"/>
                   </Group>
-                  <EmptySpace max="-2" attributes="0"/>
+                  <EmptySpace max="32767" attributes="0"/>
               </Group>
           </Group>
         </DimensionLayout>
@@ -97,6 +97,7 @@
                   <Component id="panelScreen" min="-2" max="-2" attributes="0"/>
                   <EmptySpace max="-2" attributes="0"/>
                   <Component id="panelFilter" min="-2" max="-2" attributes="0"/>
+                  <EmptySpace max="32767" attributes="0"/>
               </Group>
           </Group>
         </DimensionLayout>
@@ -433,16 +434,27 @@
                       <Component id="textState" min="-2" pref="80" max="-2" attributes="0"/>
                       <EmptySpace max="-2" attributes="0"/>
                   </Group>
+                  <Group type="102" alignment="1" attributes="0">
+                      <EmptySpace max="32767" attributes="0"/>
+                      <Component id="filler1" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace min="-2" pref="56" max="-2" attributes="0"/>
+                  </Group>
               </Group>
             </DimensionLayout>
             <DimensionLayout dim="1">
               <Group type="103" groupAlignment="0" attributes="0">
                   <Group type="102" alignment="0" attributes="0">
                       <EmptySpace min="-2" pref="4" max="-2" attributes="0"/>
-                      <Group type="103" groupAlignment="3" attributes="0">
-                          <Component id="buttonServer" alignment="3" min="-2" max="-2" attributes="0"/>
-                          <Component id="buttonDirect" alignment="3" min="-2" max="-2" attributes="0"/>
-                          <Component id="textState" linkSize="2" alignment="3" min="-2" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Group type="102" alignment="0" attributes="0">
+                              <Component id="textState" linkSize="2" min="-2" max="-2" attributes="0"/>
+                              <EmptySpace max="32767" attributes="0"/>
+                              <Component id="filler1" min="-2" max="-2" attributes="0"/>
+                          </Group>
+                          <Group type="103" groupAlignment="3" attributes="0">
+                              <Component id="buttonServer" alignment="3" min="-2" max="-2" attributes="0"/>
+                              <Component id="buttonDirect" alignment="3" min="-2" max="-2" attributes="0"/>
+                          </Group>
                       </Group>
                       <EmptySpace max="-2" attributes="0"/>
                   </Group>
@@ -483,6 +495,16 @@
                 <Property name="enabled" type="boolean" value="false"/>
               </Properties>
             </Component>
+            <Component class="javax.swing.Box$Filler" name="filler1">
+              <Properties>
+                <Property name="maximumSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+                  <Dimension value="[0, 32767]"/>
+                </Property>
+              </Properties>
+              <AuxValues>
+                <AuxValue name="classDetails" type="java.lang.String" value="Box.Filler.VerticalGlue"/>
+              </AuxValues>
+            </Component>
           </SubComponents>
         </Container>
         <Container class="javax.swing.JPanel" name="panelScreen">
@@ -865,19 +887,13 @@
       <Layout>
         <DimensionLayout dim="0">
           <Group type="103" groupAlignment="0" attributes="0">
-              <Group type="102" attributes="0">
+              <Group type="102" alignment="1" attributes="0">
                   <Component id="toolBar" min="-2" max="-2" attributes="0"/>
                   <EmptySpace type="separate" max="-2" attributes="0"/>
-                  <Component id="jLabel1" min="-2" max="-2" attributes="0"/>
-                  <EmptySpace min="-2" max="-2" attributes="0"/>
-                  <Component id="comboCameras" max="32767" attributes="0"/>
-                  <EmptySpace min="-2" max="-2" attributes="0"/>
-                  <Component id="jLabel5" min="-2" max="-2" attributes="0"/>
-                  <EmptySpace min="-2" max="-2" attributes="0"/>
-                  <Component id="comboType" min="-2" max="-2" attributes="0"/>
-                  <EmptySpace type="separate" max="-2" attributes="0"/>
-                  <Component id="pauseSelection" min="-2" max="-2" attributes="0"/>
-                  <EmptySpace min="-2" pref="0" max="-2" attributes="0"/>
+                  <Component id="panelCameraSelection" max="32767" attributes="0"/>
+                  <EmptySpace min="-2" pref="18" max="-2" attributes="0"/>
+                  <Component id="pauseSelection" min="-2" pref="334" max="-2" attributes="0"/>
+                  <EmptySpace max="-2" attributes="0"/>
               </Group>
           </Group>
         </DimensionLayout>
@@ -885,61 +901,16 @@
           <Group type="103" groupAlignment="1" attributes="0">
               <Group type="102" attributes="0">
                   <EmptySpace min="-2" pref="1" max="-2" attributes="0"/>
-                  <Group type="103" groupAlignment="0" attributes="0">
-                      <Component id="toolBar" min="-2" pref="25" max="-2" attributes="0"/>
-                      <Group type="103" groupAlignment="3" attributes="0">
-                          <Component id="jLabel1" alignment="3" min="-2" max="-2" attributes="0"/>
-                          <Component id="comboCameras" alignment="3" min="-2" max="-2" attributes="0"/>
-                          <Component id="jLabel5" alignment="3" min="-2" max="-2" attributes="0"/>
-                          <Component id="comboType" alignment="3" min="-2" max="-2" attributes="0"/>
-                      </Group>
+                  <Group type="103" groupAlignment="2" attributes="0">
+                      <Component id="pauseSelection" alignment="2" min="-2" pref="29" max="-2" attributes="0"/>
+                      <Component id="toolBar" alignment="2" min="-2" max="-2" attributes="0"/>
+                      <Component id="panelCameraSelection" alignment="2" min="-2" max="-2" attributes="0"/>
                   </Group>
               </Group>
-              <Component id="pauseSelection" alignment="0" min="-2" pref="29" max="-2" attributes="0"/>
           </Group>
         </DimensionLayout>
       </Layout>
       <SubComponents>
-        <Component class="javax.swing.JComboBox" name="comboCameras">
-          <Properties>
-            <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
-              <Font name="Dialog" size="14" style="1"/>
-            </Property>
-            <Property name="maximumRowCount" type="int" value="30"/>
-          </Properties>
-          <Events>
-            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="comboCamerasActionPerformed"/>
-          </Events>
-        </Component>
-        <Component class="javax.swing.JLabel" name="jLabel1">
-          <Properties>
-            <Property name="text" type="java.lang.String" value="Camera:"/>
-          </Properties>
-        </Component>
-        <Component class="javax.swing.JLabel" name="jLabel5">
-          <Properties>
-            <Property name="text" type="java.lang.String" value="Type:"/>
-          </Properties>
-        </Component>
-        <Component class="javax.swing.JComboBox" name="comboType">
-          <Properties>
-            <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
-              <Font name="Dialog" size="14" style="1"/>
-            </Property>
-            <Property name="maximumRowCount" type="int" value="30"/>
-            <Property name="model" type="javax.swing.ComboBoxModel" editor="org.netbeans.modules.form.editors2.ComboBoxModelEditor">
-              <StringArray count="4">
-                <StringItem index="0" value="All"/>
-                <StringItem index="1" value="Laser"/>
-                <StringItem index="2" value="Electrons"/>
-                <StringItem index="3" value="Photonics"/>
-              </StringArray>
-            </Property>
-          </Properties>
-          <Events>
-            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="comboTypeActionPerformed"/>
-          </Events>
-        </Component>
         <Container class="javax.swing.JToolBar" name="toolBar">
           <Properties>
             <Property name="floatable" type="boolean" value="false"/>
@@ -977,30 +948,6 @@
                 <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonStreamDataActionPerformed"/>
               </Events>
             </Component>
-            <Component class="javax.swing.JButton" name="buttonArgs">
-              <Properties>
-                <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
-                  <Connection code="getIcon(&quot;Data&quot;)" type="code"/>
-                </Property>
-                <Property name="text" type="java.lang.String" value=" "/>
-                <Property name="toolTipText" type="java.lang.String" value="Camera Setup"/>
-                <Property name="horizontalTextPosition" type="int" value="0"/>
-              </Properties>
-              <Events>
-                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonArgsActionPerformed"/>
-              </Events>
-            </Component>
-            <Component class="javax.swing.JToolBar$Separator" name="jSeparator5">
-              <Properties>
-                <Property name="maximumSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
-                  <Dimension value="[20, 32767]"/>
-                </Property>
-                <Property name="preferredSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
-                  <Dimension value="[20, 0]"/>
-                </Property>
-                <Property name="requestFocusEnabled" type="boolean" value="false"/>
-              </Properties>
-            </Component>
             <Component class="javax.swing.JToggleButton" name="buttonSave">
               <Properties>
                 <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
@@ -1106,6 +1053,19 @@
                 <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonReticleActionPerformed"/>
               </Events>
             </Component>
+            <Component class="javax.swing.JToggleButton" name="buttonTitle">
+              <Properties>
+                <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+                  <Connection code="getIcon(&quot;Title&quot;)" type="code"/>
+                </Property>
+                <Property name="text" type="java.lang.String" value=" "/>
+                <Property name="toolTipText" type="java.lang.String" value="Show Camera Name"/>
+                <Property name="horizontalTextPosition" type="int" value="0"/>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonTitleActionPerformed"/>
+              </Events>
+            </Component>
           </SubComponents>
         </Container>
         <Component class="ch.psi.pshell.swing.ValueSelection" name="pauseSelection">
@@ -1113,6 +1073,88 @@
             <Property name="decimals" type="int" value="0"/>
           </Properties>
         </Component>
+        <Container class="javax.swing.JPanel" name="panelCameraSelection">
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="jLabel1" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                      <Component id="comboCameras" min="-2" pref="222" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="jLabel5" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace max="-2" attributes="0"/>
+                      <Component id="comboType" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+            <DimensionLayout dim="1">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="0">
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="2" attributes="0">
+                          <Component id="comboType" alignment="2" min="-2" max="-2" attributes="0"/>
+                          <Component id="jLabel5" alignment="2" min="-2" max="-2" attributes="0"/>
+                          <Component id="jLabel1" alignment="2" min="-2" max="-2" attributes="0"/>
+                          <Component id="comboCameras" alignment="2" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+          </Layout>
+          <SubComponents>
+            <Component class="javax.swing.JLabel" name="jLabel1">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Camera:"/>
+              </Properties>
+            </Component>
+            <Component class="javax.swing.JComboBox" name="comboCameras">
+              <Properties>
+                <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
+                  <Font name="Dialog" size="14" style="1"/>
+                </Property>
+                <Property name="maximumRowCount" type="int" value="30"/>
+                <Property name="model" type="javax.swing.ComboBoxModel" editor="org.netbeans.modules.form.editors2.ComboBoxModelEditor">
+                  <StringArray count="0"/>
+                </Property>
+                <Property name="minimumSize" type="java.awt.Dimension" editor="org.netbeans.beaninfo.editors.DimensionEditor">
+                  <Dimension value="[127, 27]"/>
+                </Property>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="comboCamerasActionPerformed"/>
+              </Events>
+            </Component>
+            <Component class="javax.swing.JLabel" name="jLabel5">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Type:"/>
+              </Properties>
+            </Component>
+            <Component class="javax.swing.JComboBox" name="comboType">
+              <Properties>
+                <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
+                  <Font name="Dialog" size="14" style="1"/>
+                </Property>
+                <Property name="maximumRowCount" type="int" value="30"/>
+                <Property name="model" type="javax.swing.ComboBoxModel" editor="org.netbeans.modules.form.editors2.ComboBoxModelEditor">
+                  <StringArray count="4">
+                    <StringItem index="0" value="All"/>
+                    <StringItem index="1" value="Laser"/>
+                    <StringItem index="2" value="Electrons"/>
+                    <StringItem index="3" value="Photonics"/>
+                  </StringArray>
+                </Property>
+              </Properties>
+              <Events>
+                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="comboTypeActionPerformed"/>
+              </Events>
+            </Component>
+          </SubComponents>
+        </Container>
       </SubComponents>
     </Container>
     <Component class="ch.psi.pshell.imaging.Renderer" name="renderer">

plugins/ScreenPanel2.java

@@ -183,13 +183,15 @@ public class ScreenPanel2 extends Panel {
                 x_center_of_mass = getServerDouble("x_center_of_mass", cache);
                 y_center_of_mass = getServerDouble("y_center_of_mass", cache);
                 x_rms = getServerDouble("x_rms", cache);
-                y_rms = getServerDouble("y_rms", cache);
+                y_rms = getServerDouble("y_rms", cache);           
                 if (goodRegion) {
                     double[] gX2 = new double[x_profile.length];
                     Arrays.fill(gX2, Double.NaN);
                     try {
                         double x = getServerDoubleArray("gr_x_axis", cache)[0];
-                        System.arraycopy(x_fit_gauss_function, 0, gX2, (int) ((renderer.getCalibration() != null) ? renderer.getCalibration().convertToImageX(x) : x), x_fit_gauss_function.length);
+                        gr_size_x = x_fit_gauss_function.length;
+                        gr_pos_x = (int) ((renderer.getCalibration() != null) ? renderer.getCalibration().convertToImageX(x) : x);
+                        System.arraycopy(x_fit_gauss_function, 0, gX2, gr_pos_x , gr_size_x);
                     } catch (Exception ex) {
                     }
                     x_fit_gauss_function = gX2;
@@ -197,7 +199,9 @@ public class ScreenPanel2 extends Panel {
                     Arrays.fill(gY2, Double.NaN);
                     try {
                         double y = getServerDoubleArray("gr_y_axis", cache)[0];
-                        System.arraycopy(y_fit_gauss_function, 0, gY2, (int) ((renderer.getCalibration() != null) ? renderer.getCalibration().convertToImageY(y) : y), y_fit_gauss_function.length);
+                        gr_size_y = y_fit_gauss_function.length;
+                        gr_pos_y = (int) ((renderer.getCalibration() != null) ? renderer.getCalibration().convertToImageY(y) : y);                       
+                        System.arraycopy(y_fit_gauss_function, 0, gY2, gr_pos_y, y_fit_gauss_function.length);
                     } catch (Exception ex) {
                     }
                     y_fit_gauss_function = gY2;
@@ -228,6 +232,10 @@ public class ScreenPanel2 extends Panel {
         public double[] x_fit_gauss_function;
         public double[] y_profile;
         public double[] y_fit_gauss_function;
+        public int gr_size_x;
+        public int gr_pos_x;
+        public int gr_size_y;
+        public int gr_pos_y;
         public PointDouble[] sliceCenters;
         public StreamValue cache;
     }
@@ -664,7 +672,7 @@ public class ScreenPanel2 extends Panel {
             try {
                 fo = getFitOverlays(data);
             } catch (Exception ex) {
-                System.err.println(ex);
+                ex.printStackTrace();
             }
         }
         synchronized (lockOverlays) {
@@ -1300,60 +1308,75 @@ public class ScreenPanel2 extends Panel {
 
                     profileSize /= 4;
                     if (pX != null) {
-                        int[] x = Arr.indexesInt(pX.length);
-                        int[] y = new int[pX.length];
-                        int[] p = new int[pX.length];
+                        int[] xp = Arr.indexesInt(pX.length);
+                        int[] xg = xp;
+                        int[] yp = new int[pX.length];
+                        int[] yg = new int[pX.length];
+
                         List<Double> l = Arrays.asList((Double[]) Convert.toWrapperArray(pX));
-                        Double min = Collections.min(l);
-                        Double max = Collections.max(l);
-                        double minPlot = min;
-                        double rangePlot = max - min;
-
-                        for (int i = 0; i < x.length; i++) {
+                        double minProfile = Collections.min(l);
+                        double maxProfile = Collections.max(l);
+                        double rangeProfile = maxProfile - minProfile;
+                        double minGauss = minProfile;
+                        double rangeGauss  = rangeProfile;                             
+                        //If not good region, range of profile and fit  are similar so save this calcultion
+                        if (goodRegion && id.gr_size_x>0){
+                            l = Arrays.asList( (Double[]) Convert.toWrapperArray(Arrays.copyOfRange(gX, id.gr_pos_x, id.gr_pos_x + id.gr_size_x)));
+                            minGauss = Collections.min(l);  
+                            rangeGauss = Collections.max(l) - minGauss;
+                        }
+                        
+                        for (int i = 0; i < xp.length; i++) {
                             if (gX != null) {
-                                y[i] = (int) (height - 1 - (((gX[i] - minPlot) / rangePlot) * profileSize));
+                                yg[i] = (int) (height - 1 - (((gX[i] - minGauss) / rangeGauss) * profileSize));
                             }
-                            p[i] = (int) (height - 1 - (((pX[i] - minPlot) / rangePlot) * profileSize));
+                            yp[i] = (int) (height - 1 - (((pX[i] - minProfile) / rangeProfile) * profileSize));
                         }
-
-                        if (goodRegion) {
-                            for (int i = 0; i < x.length; i++) {
-                                y[i] = (Double.isNaN(gX[i])) ? 100000 : y[i];
-                            }
+                        
+                        if (goodRegion && id.gr_size_x>0){
+                            xg = Arrays.copyOfRange(xg, id.gr_pos_x, id.gr_pos_x + id.gr_size_x);
+                            yg = Arrays.copyOfRange(yg, id.gr_pos_x, id.gr_pos_x + id.gr_size_x);
                         }
-
-                        vgaussian = new Overlays.Polyline(penFit, x, y);
-                        vprofile = new Overlays.Polyline(renderer.getPenProfile(), x, p);
+                        
+                        vgaussian = new Overlays.Polyline(penFit, xg, yg);
+                        vprofile = new Overlays.Polyline(renderer.getPenProfile(), xp, yp);
                     }
 
                     if (pY != null) {
-                        int[] y = Arr.indexesInt(pY.length);
-                        int[] x = new int[pY.length];
-                        int[] p = new int[pY.length];
+                        int[] xp = new int[pY.length];
+                        int[] xg =  new int[pY.length];
+                        int[] yp = Arr.indexesInt(pY.length);
+                        int[] yg = yp;
 
                         List<Double> l = Arrays.asList((Double[]) Convert.toWrapperArray(pY));
-                        Double min = Collections.min(l);
-                        Double max = Collections.max(l);
-                        double minPlot = min;
-                        double rangePlot = max - min;
+                        double minProfile = Collections.min(l);
+                        double maxProfile = Collections.max(l);
+                        double rangeProfile = maxProfile - minProfile;
+                        double minGauss = minProfile;
+                        double rangeGauss  = rangeProfile;                             
+                        //If not good region, range of profile and fit  are similar so save this calcultion
+                        if (goodRegion && id.gr_size_y>0){             
+                            l = Arrays.asList( (Double[]) Convert.toWrapperArray(Arrays.copyOfRange(gY, id.gr_pos_y, id.gr_pos_y + id.gr_size_y)));
+                            minGauss = Collections.min(l);
+                            rangeGauss = Collections.max(l) - minGauss;                         
+                        }
 
-                        for (int i = 0; i < x.length; i++) {
+                        for (int i = 0; i < xp.length; i++) {
                             if (gY != null) {
-                                x[i] = (int) (((gY[i] - minPlot) / rangePlot) * profileSize);
+                                xg[i] = (int) (((gY[i] - minGauss) / rangeGauss) * profileSize);
                             }
-                            p[i] = (int) (((pY[i] - minPlot) / rangePlot) * profileSize);
+                            xp[i] = (int) (((pY[i] - minProfile) / rangeProfile) * profileSize);
                         }
 
-                        if (goodRegion) {
-                            for (int i = 0; i < x.length; i++) {
-                                x[i] = (Double.isNaN(gY[i])) ? -1 : x[i];
-                            }
+                        if (goodRegion && id.gr_size_x>0){
+                            xg = Arrays.copyOfRange(xg, id.gr_pos_y, id.gr_pos_y + id.gr_size_y);
+                            yg = Arrays.copyOfRange(yg, id.gr_pos_y, id.gr_pos_y + id.gr_size_y);
                         }
-                        hgaussian = new Overlays.Polyline(penFit, x, y);
-                        hprofile = new Overlays.Polyline(renderer.getPenProfile(), p, y);
+                        hgaussian = new Overlays.Polyline(penFit, xg, yg);
+                        hprofile = new Overlays.Polyline(renderer.getPenProfile(), xp, yp);
                     }
                 } catch (Exception ex) {
-                    System.err.println(ex.getMessage());
+                    ex.printStackTrace();
                     return null;
                 }
             } else {
@@ -2190,6 +2213,11 @@ public class ScreenPanel2 extends Panel {
                 } catch (Exception ex) {
                     dataTableModel.addRow(new Object[]{"Stream", ex.getMessage()});
                 }
+                try {
+                    dataTableModel.addRow(new Object[]{"PID", value.getPulseId()});
+                } catch (Exception ex) {
+                    dataTableModel.addRow(new Object[]{"PID", ex.getMessage()});
+                }                
                 Collections.sort(ids);
                 for (String id : ids) {
                     dataTableModel.addRow(new Object[]{id, ""});
@@ -2197,7 +2225,7 @@ public class ScreenPanel2 extends Panel {
             }
             Frame frame = getCurrentFrame();
             if ((frame != null) && (frame.cache!=null)){
-                for (int i = 2; i < dataTableModel.getRowCount(); i++) {
+                for (int i = 3; i < dataTableModel.getRowCount(); i++) {
                     String id = String.valueOf(dataTableModel.getValueAt(i, 0));
                     //Object obj = server.getValue(id);
                     Object obj = frame.cache.getValue(id);

script/*.scan

@@ -0,0 +1 @@
+[ "Time series", [ ], [ [ "CamServer", "http://localhost:8889/simulation_sp1?channel=x_fit_mean", 3, 0.1, null ] ], false, [ ], "", 20, 0.0, 0.1, true, true, true, true, "", "", "Default", "h5", 0, null, null, "Positioner" ]

script/20150418_1152_DyE_minus2.xml

@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<configuration xmlns="http://www.psi.ch/~ebner/models/scan/1.0" numberOfExecution="1" failOnSensorError="true">
+    <data format="txt" fileName="DyE_minus"/>
+    <scan id="">
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="ACOAU-ACCU:OP-MODE" value="Light Available" operation="wait"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="X07MA-ID:MODE" value="CIRC -" delay="1.0"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="X07MA-ID:DONE" value="DONE" operation="wait"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="X07MA-ID:ENERGY-OFFS" value="-4.0"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="X07MA-ID:DONE" value="DONE" operation="wait"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="E1" value="1265"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="E2" value="1355"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="TIME" value="3"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="FOLDER" value="2015_04/20150418"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="X07MA-PHS-E:GO.A" value="1265" operation="putq"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="X07MA-PHS:alldone" value="1" operation="wait" delay="0.5"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="FILE" value="DyE_minus" delay="0.1"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="X07MA-OP-VG13:WT_SET" value="Try open" delay="10.0"/>
+        <preAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="START" value="1"/>
+        <postAction xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="ChannelAction" channel="START" value="STOP" operation="wait" delay="2.0"/>
+    </scan>
+</configuration>

script/Correlation/Correlation.py

@@ -0,0 +1,172 @@
+import math
+import sys, traceback          
+from mathutils import fit_polynomial, PolynomialFunction
+from plotutils import plot_line, plot_function
+from ch.psi.pshell.swing.Shell import STDOUT_COLOR
+import org.apache.commons.math3.stat.correlation.PearsonsCorrelation as PearsonsCorrelation
+
+start_task("outupdate", 0.0, 0.0)
+
+if get_exec_pars().source == CommandSource.ui:
+    #dx = "SINEG01-RLLE-REF10:SIG-PHASE-AVG"
+    #dy = "SINEG01-RLLE-REF20:SIG-PHASE-AVG"     
+    #dx = "SINEG01-RGUN-PUP10:SIG-AMPLT-AVG 4"
+    #dy = "SINEG01-RGUN-PUP20:SIG-AMPLT-AVG 4"
+
+    #dx = "SINDI01-RKLY-DCP10:REF-AMPLT"
+    #dy = "SINDI01-RKLY-DCP10:REF-PHASE"
+            
+    #dx = "SINDI01-RLLE-REF10:SIG-PHASE-AVG"
+    #dy = "SINDI01-RLLE-REF20:SIG-PHASE-AVG"
+
+    dx = "TESTIOC:TESTCALCOUT:Input"
+    dx = "TESTIOC:TESTCALCOUT:Output"
+
+    dy = "TESTIOC:TESTSINUS:SinCalc"
+ 
+    #dx = "SINEG01-DICT215:B1_CHARGE"
+    #dy = "SINEG01-DBPM314:Q1"     
+    
+    
+    #dx=gsx.getReadback()
+    #dy=gsy.getReadback()
+    interval = 0.1
+    window = 40
+    p = plot(None)[0]    
+    bs = False
+    linear_fit = True
+    quadratic_fit = True
+#print dx
+#print dy
+corr = None
+pars_lin = None 
+pars_quad = None
+
+
+for s in p.getAllSeries():
+    p.removeSeries(s)    
+
+_stream = None
+
+instances = []
+
+def _get_device(d):
+    global _stream
+    egu = None
+    if isinstance(d, basestring):    
+        name = d.strip()
+        d = None
+        try:
+            d = get_device(name) 
+            if d is None: 
+                d = eval(name)
+            #print name
+            if d is not None:
+                if not isinstance(r, Device): 
+                    d = None
+                else:
+                    try:
+                        egu = d.unit
+                    except:
+                        pass                            
+        except:
+            pass
+        if d is None:
+            offset = 0
+            if " " in name:
+                tokens = name.split(" ")
+                name = tokens[0]
+                offset = int(tokens[1])
+            if bs == True:
+                if _stream == None:
+                    _stream = Stream("corr_stream", dispatcher)
+                    instances.append(_stream)
+                d = _stream.addScalar(name, name, int(interval*100), offset)
+            else:
+                d =  Channel(name)    
+                instances.append(d)
+            try:
+                egu = caget(name+".EGU",'s')
+            except:
+                pass            
+    else:
+        try:
+            egu = d.unit
+        except:
+            pass            
+        
+    return d, egu
+
+dx, egux = _get_device(dx)
+dy, eguy = _get_device(dy)
+
+p.getAxis(p.AxisId.X).setLabel(egux)
+p.getAxis(p.AxisId.Y).setLabel(eguy)
+
+
+try:
+    if _stream != None:
+        _stream.initialize()
+        _stream.start(True)
+    p.addSeries(LinePlotSeries("Data")) 
+    sd=p.getSeries(0)
+    sd.setLinesVisible(False)    
+    
+    sd.setPointSize(4)
+
+    if get_exec_pars().source == CommandSource.ui:
+        if globals().has_key("marker"):
+            p.removeMarker(marker)    
+        marker=None
+            
+    
+    while(True):
+        #Sample and plot data
+        if bs == True:
+            _stream.waitValueNot(_stream.take(), 10000)
+            (x,y) = _stream.take().values
+        else:
+            x=dx.read()  
+            y=dy.read()
+        sd.appendData(x, y)
+        if len(sd.x) > window:
+            #Remove First Element
+            sd.token.remove(0)    
+        ax = sd.x
+        ay = sd.y
+        if len(ax)>2:
+            x1, x2 = min(ax), max(ax)  
+            res = (x2-x1)/100     
+            if x1!=x2:
+                #Display correlation
+                corr= PearsonsCorrelation().correlation(to_array(ax,'d'), to_array(ay,'d'))        
+                s = "Correlation=" + str(round(corr,4))
+                #print s
+                if get_exec_pars().source == CommandSource.ui:
+                    if marker is not None: 
+                        p.removeMarker(marker)
+                    marker = p.addMarker(x2+res, p.AxisId.X, s,  p.getBackground())
+                    marker.setLabelPaint(STDOUT_COLOR)
+                if linear_fit:
+                    #Calculate, print and plot linear fit
+                    pars_lin = (a0,a1) = fit_polynomial(ay, ax, 1)
+                    #print "Fit lin  a1:" , a1, " a0:",a0        
+                    y1 = poly(x1, pars_lin)
+                    y2 = poly(x2, pars_lin)
+                    plot_line(p, x1, y1, x2, y2, width = 2, color = Color.BLUE, name = "Fit Linear")
+                if quadratic_fit:
+                    #Calculate, print and plot quadratic fit
+                    pars_quad = (a0,a1,a2) = fit_polynomial(ay, ax, 2)
+                    #print "Fit quad a2:" , a2, "a1:" , a1, " a0:",a0        
+                    fitted_quad_function = PolynomialFunction(pars_quad)
+                    ax = frange(x1, x2, res, True)
+                    plot_function(p, fitted_quad_function, "Fit Quadratic", ax, color=Color.GREEN)
+        if bs != True:
+            time.sleep(interval)         
+finally:
+    for dev in instances:
+        dev.close()
+        stop_task("outupdate")
+
+
+        

script/Correlation/Correlation2.py

@@ -0,0 +1,197 @@
+import math
+import sys, traceback          
+from mathutils import fit_polynomial, PolynomialFunction
+from plotutils import plot_line, plot_function
+from ch.psi.pshell.swing.Shell import STDOUT_COLOR
+import org.apache.commons.math3.stat.correlation.PearsonsCorrelation as PearsonsCorrelation
+import ch.psi.pshell.bs.PipelineServer as PipelineServer
+
+start_task("outupdate", 0.0, 0.0)
+TYPE_CHANNEL = 0
+TYPE_STREAM = 1
+TYPE_CAMERA= 2
+
+if get_exec_pars().source == CommandSource.ui:
+    #dx = "SINDI01-RLLE-STA:SLAVE1-CPUTIMER"
+    dx = "Int16Scalar" 
+    ##dx = "SLG-LCAM-C042 x_rms"
+    dxtype = TYPE_STREAM
+    #dxtype = TYPE_CHANNEL
+    #dxtype = TYPE_CAMERA
+    #dy = "SINDI01-RLLE-STA:SLAVE1-DLTIMER"
+    #dy = "SLG-LCAM-C042 y_rms"
+    dy = "Int8Scalar"
+    dytype = TYPE_STREAM
+    #dytype = TYPE_CHANNEL
+    #dytype = TYPE_CAMERA
+    interval = 0.10
+    window = 40
+    p = plot(None)[0]    
+    linear_fit = True
+    quadratic_fit = True
+print dx, dxtype
+print dy, dytype
+
+corr = None
+pars_lin = None 
+pars_quad = None
+
+
+
+bs = TYPE_STREAM in [dxtype, dytype]
+
+
+for s in p.getAllSeries():
+    p.removeSeries(s)    
+
+_stream = None
+_camname = None
+
+instances = []
+
+def _get_device(d, type):
+    global _stream, _camname
+    egu = None
+    if isinstance(d, basestring):    
+        name = d.strip()
+        d = None
+        try:
+            d = get_device(name) 
+            if d is None: 
+                d = eval(name)
+            #print name
+            if d is not None:
+                if not isinstance(r, Device): 
+                    d = None
+                else:
+                    try:
+                        egu = d.unit
+                    except:
+                        pass                            
+        except:
+            pass
+        if d is None:            
+            offset = 0
+            
+            if type==TYPE_STREAM:
+                if " " in name:
+                    tokens = name.split(" ")
+                    name = tokens[0]
+                    offset = int(tokens[1])
+                if _stream == None:
+                    _stream = Stream("corr_stream", dispatcher)
+                    instances.append(_stream)
+                d = _stream.addScalar(name, name, int(interval*100), offset)
+            elif type==TYPE_CHANNEL:
+                d =  Channel(name)    
+                d.set_monitored(True)
+            elif  type==TYPE_CAMERA:
+                tokens = name.split(" ")
+                _camname = tokens[0]
+                field = tokens[1]
+                return field, ""
+            else:
+                raise Exception("Invalid type: " + str(type))
+            if not isinstance(d, basestring):    
+                instances.append(d)
+            try:
+                egu = caget(name+".EGU",'s')
+            except:
+                pass            
+    else:
+        try:
+            egu = d.unit
+        except:
+            pass                    
+    return d, egu
+
+dx, egux = _get_device(dx, dxtype)
+dy, eguy = _get_device(dy, dytype)
+
+p.getAxis(p.AxisId.X).setLabel(egux)
+p.getAxis(p.AxisId.Y).setLabel(eguy)
+
+
+try:
+    if _stream != None:
+        _stream.initialize()
+        _stream.start(True)
+    if _camname != None:
+        cam_server.start(_camname )
+        cam_server.stream.waitCacheChange(10000);
+        if  dxtype==TYPE_CAMERA:
+            dx=cam_server.stream.getChild(dx)
+        if  dytype==TYPE_CAMERA:
+            dy=cam_server.stream.getChild(dy)
+        
+    p.addSeries(LinePlotSeries("Data")) 
+    sd=p.getSeries(0)
+    sd.setLinesVisible(False)    
+    
+    sd.setPointSize(4)
+    
+    if get_exec_pars().source == CommandSource.ui:
+        if globals().has_key("marker"):
+            p.removeMarker(marker)    
+        marker=None
+            
+    
+    while(True):
+        #Sample and plot data
+        if bs == True:
+            _stream.waitValueNot(_stream.take(), 10000)
+            bsdata = list(_stream.take().values)
+        
+        if dxtype==TYPE_CHANNEL:
+            x=dx.read() 
+        elif dxtype==TYPE_STREAM:
+            x=bsdata.pop(0)
+        elif dxtype==TYPE_CAMERA:
+            x=dx.read()
+                        
+        if dytype==TYPE_CHANNEL:
+            y=dy.read()
+        elif dytype==TYPE_STREAM:
+            y=bsdata.pop(0)
+        elif dytype==TYPE_CAMERA:
+            y=dy.read()
+        
+        sd.appendData(x, y)
+        if len(sd.x) > window:
+            #Remove First Element
+            sd.token.remove(0)    
+        ax = sd.x
+        ay = sd.y
+        if len(ax)>2:
+            x1, x2 = min(ax), max(ax)  
+            res = (x2-x1)/100     
+            if x1!=x2:
+                #Display correlation
+                corr= PearsonsCorrelation().correlation(to_array(ax,'d'), to_array(ay,'d'))        
+                s = "Correlation=" + str(round(corr,4))
+                #print s
+                if get_exec_pars().source == CommandSource.ui:
+                    if marker is not None: 
+                        p.removeMarker(marker)
+                    marker = p.addMarker(x2+res, p.AxisId.X, s,  p.getBackground())
+                    marker.setLabelPaint(STDOUT_COLOR)
+                if linear_fit:
+                    #Calculate, print and plot linear fit
+                    pars_lin = (a0,a1) = fit_polynomial(ay, ax, 1)
+                    #print "Fit lin  a1:" , a1, " a0:",a0        
+                    y1 = poly(x1, pars_lin)
+                    y2 = poly(x2, pars_lin)
+                    plot_line(p, x1, y1, x2, y2, width = 2, color = Color.BLUE, name = "Fit Linear")
+                if quadratic_fit:
+                    #Calculate, print and plot quadratic fit
+                    pars_quad = (a0,a1,a2) = fit_polynomial(ay, ax, 2)
+                    #print "Fit quad a2:" , a2, "a1:" , a1, " a0:",a0        
+                    fitted_quad_function = PolynomialFunction(pars_quad)
+                    ax = frange(x1, x2, res, True)
+                    plot_function(p, fitted_quad_function, "Fit Quadratic", ax, color=Color.GREEN)
+        if bs != True:
+            time.sleep(interval)         
+finally:
+    for dev in instances:
+        dev.close()
+    stop_task("outupdate")

script/Devices/Elements.py

@@ -0,0 +1,300 @@
+DBPM = 1
+DWSC = 2
+DBLM = 3
+DLAC = 4 
+
+elements = (
+    (DBPM,	"SINEG01-DBPM340", 3.0149),
+    (DBPM, "SINSB01-DBPM150", 7.9459), 
+    (DBPM, "SINSB02-DBPM150", 12.9489),
+    (DBPM, "SINLH01-DBPM060", 14.5560),
+    (DBPM, "SINLH02-DBPM210", 16.4806),
+    (DBLM, "SINLH02-DBLM230", 16.8546),
+    (DBPM, "SINLH02-DBPM240", 17.4826),
+    (DBLM, "SINLH02-DBLM235", 17.4049),
+    (DBPM, "SINLH03-DBPM010", 19.2172),
+    (DBPM, "SINLH03-DBPM050", 20.4632),
+    (DBPM, "SINLH03-DBPM090", 21.6002),
+    (DBPM, "SINSB03-DBPM120", 26.9202),
+    (DBPM, "SINSB03-DBPM220", 32.4202),
+    (DBPM, "SINSB04-DBPM120", 37.9202),
+    (DBPM, "SINSB04-DBPM220", 43.4202),
+    (DBPM, "SINSB05-DBPM120", 48.9202),
+    (DBPM, "SINSB05-DBPM220", 54.4202),
+    (DBPM, "SINXB01-DBPM120", 56.2420),
+    (DBPM, "SINBC01-DBPM010", 60.2912),
+    (DBPM, "SINBC01-DBPM030", 61.0912),
+    (DBPM, "SINBC01-DBPM080", 64.4172),
+    (DBPM, "SINBC01-DBPM100", 65.9432),
+    (DBPM, "SINBC02-DBPM140", 69.3739),
+    (DBPM, "SINBC02-DBPM320", 77.5610),
+    (DBPM, "SINDI01-DBPM010", 82.0967),
+    (DBPM, "SINDI01-DBPM060", 83.5117),
+    (DWSC, "SINDI01-DWSC090", 84.2537),    
+    (DBPM, "SINDI02-DBPM010", 86.0767),
+    (DBLM, "SINDI02-DBLM025", 86.862),    
+    (DBPM, "SINDI02-DBPM040", 88.3857),
+    (DLAC, "SINDI02-DLAC0550", 89.05), 
+    (DBPM, "SINDI02-DBPM080", 90.6297),
+    (DBLM, "SINDI02-DBLM085", 90.7796),    
+    (DBPM, "S10CB01-DBPM220", 95.3947),
+    (DBPM, "S10CB01-DBPM420", 100.2947),
+    (DBPM, "S10CB02-DBPM220", 105.1947),
+    (DBPM, "S10CB02-DBPM420", 110.0947),
+    (DWSC, "S10DI01-DWSC010", 110.8237),
+    (DBLM, "S10DI01-DBLM045", 111.67),    
+    (DBLM, "S10DI01-DBLM015", 113.632),    
+    (DBPM, "S10BD01-DBPM020", 114.6628),
+    (DBPM, "S10DI01-DBPM110", 114.9947),
+    (DBPM, "S10CB03-DBPM220", 119.8947),
+    (DBPM, "S10CB03-DBPM420", 124.7947),
+    (DWSC, "S10CB03-DWSC440", 125.2127),
+    (DBPM, "S10CB04-DBPM220", 129.6947),
+    (DBLM, "S10CB04-DBLM240", 130.1525),    
+    (DBPM, "S10CB04-DBPM420", 134.5947),
+    (DBPM, "S10CB05-DBPM220", 139.4947),
+    (DBPM, "S10CB05-DBPM420", 144.3947),
+    (DWSC, "S10CB05-DWSC440", 144.8127),
+    (DBPM, "S10CB06-DBPM220", 149.2947),
+    (DBLM, "S10CB06-DBLM240", 149.7525),    
+    (DBPM, "S10CB06-DBPM420", 154.1947),
+    (DBPM, "S10CB07-DBPM220", 159.0947),
+    (DBPM, "S10CB07-DBPM420", 163.9947),
+    (DWSC, "S10CB07-DWSC440", 164.4127),
+    (DBPM, "S10CB08-DBPM220", 168.8947),
+    (DBLM, "S10CB08-DBLM240", 169.3525),    
+    (DBPM, "S10CB08-DBPM420", 173.7947),
+    (DBPM, "S10CB09-DBPM220", 178.6947),
+    (DBPM, "S10BC01-DBPM010", 183.5947),
+    (DWSC, "S10BC01-DWSC030", 184.0127),
+    (DBPM, "S10BC01-DBPM050", 187.8307),
+    (DBLM, "S10BC01-DBLM065", 188.684),    
+    (DBPM, "S10BC01-DBPM090", 192.2847),
+    (DBPM, "S10BC02-DBPM140", 196.7798),
+    (DBPM, "S10BC02-DBPM320", 206.5399),
+    (DBPM, "S10MA01-DBPM010", 211.2940),
+    (DBPM, "S10MA01-DBPM060", 215.6600),
+    (DBPM, "S10MA01-DBPM120", 220.1200),
+    (DBPM, "S20CB01-DBPM420", 229.0850),
+    (DWSC, "S20CB01-DWSC440", 229.5030),
+    (DBPM, "S20CB02-DBPM420", 238.1850),
+    (DBLM, "S20CB02-DBLM435", 238.6325),    
+    (DBPM, "S20CB03-DBPM420", 247.2850),
+    (DBPM, "S20SY01-DBPM010", 256.3850),
+    (DBPM, "S20SY01-DBPM040", 262.5020),
+    (DBPM, "S20SY01-DBPM060", 263.6280),
+    (DWSC, "S20SY01-DWSC070", 263.8280),
+    (DBLM, "S20SY02-DBLM075", 268.617),    
+    (DBPM, "S20SY02-DBPM080", 269.1300),
+    (DBPM, "S20SY02-DBPM120", 271.0800),
+    (DBPM, "S20SY02-DBPM150", 272.7600),
+    (DWSC, "S20SY02-DWSC160", 273.1350),
+    (DBPM, "SATSY01-DBPM010", 279.1202),
+    (DBPM, "S20SY03-DBPM010", 280.6200),
+    (DBLM, "S20SY03-DBLM025", 281.156),    
+    (DBPM, "SATSY01-DBPM060", 284.6202),
+    (DBPM, "S20SY03-DBPM040", 286.9200),
+    (DBPM, "SATSY01-DBPM100", 288.9352),
+    (DBPM, "S20SY03-DBPM080", 294.3800),
+    (DWSC, "S20SY03-DWSC090", 294.5800),    
+    (DBLM, "S20SY03-DBLM110", 295.258),
+    (DBPM, "SATSY01-DBPM240", 296.1202),
+    (DBPM, "SATSY01-DBPM290", 302.8202),
+    (DBPM, "S30CB01-DBPM420", 303.8150),
+    (DWSC, "S30CB01-DWSC440", 304.2330),
+    (DBPM, "SATSY02-DBPM020", 306.8663),
+    (DBPM, "SATSY02-DBPM210", 312.6833),
+    (DBPM, "S30CB02-DBPM420", 312.9150),
+    (DBLM, "S30CB02-DBLM445", 313.3625),
+    (DBPM, "SATSY03-DBPM030", 317.2003),
+    (DBPM, "SATSY03-DBPM060", 320.0003),
+    (DBPM, "S30CB03-DBPM420", 322.0150),
+    (DBPM, "SATSY03-DBPM090", 322.8003),
+    (DWSC, "SATSY03-DWSC110", 325.1663),
+    (DBPM, "SATSY03-DBPM120", 325.6003),
+    (DBPM, "S30CB04-DBPM420", 331.1150),
+    (DBLM, "SATCL01-DBLM135", 331.1179),    
+    (DBPM, "SATCL01-DBPM140", 331.9185),
+    (DBPM, "S30CB05-DBPM420", 340.2150),
+    (DWSC, "S30CB05-DWSC440", 340.6330),
+    (DBPM, "SATDI01-DBPM030", 340.8637),
+    (DBPM, "SATDI01-DBPM060", 342.7637),
+    (DWSC, "SATDI01-DWSC065", 342.9837),
+    (DBPM, "SATDI01-DBPM210", 349.2197),
+    (DBPM, "S30CB06-DBPM420", 349.3150),
+    (DBLM, "S30CB06-DBLM445", 349.7625),
+    (DBLM, "SATDI01-DBLM225", 349.5613),    
+    (DBPM, "SATDI01-DBPM240", 352.1997),
+    (DBPM, "SATDI01-DBPM270", 355.1797),
+    (DWSC, "SATDI01-DWSC290", 356.4797),
+    (DBPM, "SATDI01-DBPM320", 357.0907),
+    (DBPM, "S30CB07-DBPM420", 358.4150),
+    (DBPM, "SATCB01-DBPM220", 361.5357),
+    (DBLM, "SATCB01-DBLM245", 361.8578),    
+    (DBPM, "SATCB01-DBPM420", 366.4357),
+    (DBPM, "S30CB08-DBPM420", 367.5150),
+    (DBPM, "S30CB09-DBPM420", 376.6150),
+    (DWSC, "S30CB09-DWSC440", 377.0330),
+    (DBPM, "SATMA01-DBPM010", 377.2657),
+    (DBPM, "SATMA01-DBPM020", 379.3147),
+    (DBPM, "SATMA01-DBPM040", 381.3637),
+    (DBLM, "SATMA01-DBLM065", 381.6948),    
+    (DBPM, "S30CB10-DBPM420", 385.7150),
+    (DBLM, "S30CB10-DBLM445", 386.271),    
+    (DBPM, "S30CB11-DBPM420", 394.8150),
+    (DBPM, "S30CB12-DBPM420", 403.9150),
+    (DBPM, "S30CB13-DBPM420", 413.0150),
+    (DWSC, "S30CB13-DWSC440", 413.4330),
+    (DBPM, "S30CB14-DBPM420", 422.1150),
+    (DBLM, "S30CB14-DBLM445", 422.691),    
+    (DBPM, "S30CB15-DBPM420", 431.2150),
+    (DBPM, "SARCL01-DBPM010", 440.3150),
+    (DBPM, "SARCL01-DBPM060", 444.6750),
+    (DBPM, "SARCL01-DBPM120", 450.7750),
+    (DBPM, "SARCL01-DBPM150", 452.1510),
+    (DWSC, "SARCL01-DWSC160", 452.3510),
+    (DBPM, "SARCL02-DBPM110", 456.9100),
+    (DBLM, "SARCL02-DBLM135", 457.9854),    
+    (DBPM, "SARCL02-DBPM220", 460.9609),
+    (DBPM, "SARCL02-DBPM260", 462.7569),
+    (DWSC, "SARCL02-DWSC270", 462.9769),
+    (DBPM, "SARCL02-DBPM330", 466.6909),
+    (DBLM, "SARCL02-DBLM355", 467.686),    
+    (DBPM, "SARCL02-DBPM470", 471.1067),
+    (DBPM, "SARMA01-DBPM040", 476.4267),
+    (DBPM, "SARMA01-DBPM100", 483.2767),
+    (DBPM, "SARMA02-DBPM010", 487.9617),
+    (DBPM, "SARMA02-DBPM020", 490.0107),
+    (DBPM, "SARMA02-DBPM040", 492.0597),
+    (DWSC, "SARMA02-DWSC060", 492.3767),
+    (DBPM, "SARMA02-DBPM110", 496.8097),
+    (DBLM, "SARUN01-DBLM065", 497.8392),    
+    (DBPM, "SARUN01-DBPM070", 501.5597),
+    (DBPM, "SARUN02-DBPM070", 506.3097),
+    (DBLM, "SARUN03-DBLM030", 506.671),    
+    (DBPM, "SARUN03-DBPM070", 511.0597),
+    (DBLM, "SARUN04-DBLM030", 511.421),    
+    (DBPM, "SARUN04-DBPM070", 515.8097),
+    (DBLM, "SARUN05-DBLM030", 516.171),    
+    (DBPM, "SARUN05-DBPM070", 520.5597),
+    (DBLM, "SARUN06-DBLM030", 520.921),    
+    (DBPM, "SARUN06-DBPM070", 525.3097),
+    (DBLM, "SARUN07-DBLM030", 525.671),
+    (DBPM, "SARUN07-DBPM070", 530.0597),
+    (DBLM, "SARUN08-DBLM030", 530.421),
+    (DBPM, "SARUN08-DBPM070", 534.8097),
+    (DBLM, "SARUN09-DBLM030", 535.171),
+    (DBPM, "SARUN09-DBPM070", 539.5597),
+    (DBLM, "SARUN10-DBLM030", 539.921),
+    (DBPM, "SARUN10-DBPM070", 544.3097),
+    (DBLM, "SARUN11-DBLM030", 544.671),
+    (DBPM, "SARUN11-DBPM070", 549.0597),
+    (DBLM, "SARUN12-DBLM030", 549.421),
+    (DBPM, "SARUN12-DBPM070", 553.8097),
+    (DBLM, "SARUN13-DBLM030", 554.171),
+    (DBPM, "SARUN13-DBPM070", 558.5597),
+    (DBLM, "SARUN14-DBLM030", 558.921),
+    (DBPM, "SARUN14-DBPM070", 563.3097),
+    (DBLM, "SARUN15-DBLM030", 563.671),
+    (DBLM, "SARUN15-DBLM035", 567.970985),
+    (DBPM, "SARUN15-DBPM070", 568.0597),
+    (DBPM, "SARUN16-DBPM070", 572.8097),
+    (DBPM, "SARUN17-DBPM070", 577.5597),
+    (DBPM, "SARUN18-DBPM070", 582.3097),
+    (DBPM, "SARUN19-DBPM070", 587.0597),
+    (DWSC, "SARUN20-DWSC010", 587.3767),
+    (DBLM, "SARUN20-DBLM035", 590.41),
+    (DBPM, "SARUN20-DBPM070", 591.8097),
+    (DBPM, "SARBD01-DBPM040", 593.9132),
+    (DBPM, "SARBD02-DBPM010", 596.9584),
+    (DBPM, "SARBD02-DBPM040", 598.3943),
+)
+
+def get_section(element):
+    return element[1:3]
+
+def get_section_type(element):
+    section = get_section(element)
+    if section == "AR": return "ARAMIS"
+    if section == "AT": return "ATH0S"
+    if section == "IN": return "INJECTOR"
+    if section in["10", "20", "30"] : return "LINAC"
+    return None
+
+def get_beamline(element):
+    section = get_section(element)
+    if section == "AR": return "ARAMIS"
+    if section == "AT": return "ATH0S"
+    return None
+    
+def get_blms():
+    ret = []
+    for element in elements:
+        if element[0]==DBLM:
+            ret.append(element[1]) 
+    return ret
+
+
+def get_bpms():
+    ret = []
+    for element in elements:
+        if element[0]==DBPM:
+            ret.append(element[1]) 
+    return ret
+
+def get_wire_scanners():
+    ret = []
+    for element in elements:
+        if element[0]==DWSC:
+            ret.append(element[1]) 
+    return ret
+
+def get_dlacs():
+    ret = []
+    for element in elements:
+        if element[0]==DLAC:
+            ret.append(element[1]) 
+    return ret
+
+def get_wire_scanners_bpms(wire_scan):
+    last = None 
+    ret = []
+    for element in elements:
+        if element[0]==DWSC and element[1] == wire_scan:
+            ret = [last,]
+        elif element[0]==DBPM:
+            if get_beamline(element[1]) == get_beamline(wire_scan):
+                if len(ret) > 0:
+                    return [ret[0],element[1]]              
+                last = element[1]
+    return None
+
+
+def get_wire_scanners_blms(wire_scan):
+    last = None 
+    ret = None
+    for element in elements:                    
+        if element[0]==DWSC and element[1] == wire_scan:
+            ret = []
+        elif element[0]==DBLM and (ret is not None):
+            bl = get_beamline(element[1])
+            if bl == get_beamline(wire_scan):
+                ret.append(element[1])
+                if len(ret) == 2:
+                    return ret
+    if ret is not None and len(ret)==1:
+        ret.append(None)
+    return ret
+
+def get_camera_type(camera_name):
+    if "LCAM" in camera_name: return "LASER"
+    if "DSCR" in camera_name or \
+       "DSRM" in camera_name or \
+       "DLAC" in camera_name: return "ELECTRONS"
+    if "PROF" in camera_name or \
+       "PPRM" in camera_name or \
+       "PSSS" in camera_name or \
+       "PSCR" in camera_name or \
+       "PSRD" in camera_name: return "PHOTONICS"
+    return "UNKNOWN"
+

script/Diagnostics/sig_process_wrapper.py

@@ -0,0 +1,29 @@
+from jeputils import *
+
+MODULE = "Diagnostics/sig_process"
+
+def noise_evaluation(noise):
+    return call_jep(MODULE, "noise_evaluation", [to_npa(noise),])
+
+def blm_remove_spikes(x):
+    ret = call_jep(MODULE, "blm_remove_spikes", [to_npa(x),])
+    return ret if ret is None or is_list(ret) else ret.data
+
+def blm_normalize(x, q):
+    ret = call_jep(MODULE, "blm_normalize", [to_npa(x), q])
+    return ret if ret is None or is_list(ret) else ret.data
+
+def motor_to_wire_cs(pos, ctype = 'u', center_pos = 0.0):
+    return call_jep(MODULE, "motor_to_wire_cs", [pos, ctype, center_pos ])
+
+def remove_beam_jitter(pos, bpm1, bpm2, d_b1_w=1, d_w_b2=1):
+    ret = call_jep(MODULE, "remove_beam_jitter", [to_npa(pos),to_npa(bpm1), to_npa(bpm2), d_b1_w, d_w_b2 ])
+    return ret if ret is None or is_list(ret) else ret.data
+
+def profile_gauss_stats(x, y, off=None, amp=None, com=None, sigma=None):
+    ret = call_jep(MODULE, "profile_gauss_stats", [to_npa(x), to_npa(y), off, amp, com, sigma])
+    return ret if ret is None or is_list(ret) else ret.data
+
+def profile_rms_stats(x, y, noise_std=0, n_sigma=3.5):
+    return call_jep(MODULE, "profile_rms_stats", [to_npa(x), to_npa(y), noise_std, n_sigma])
+

script/HklScan.py

@@ -0,0 +1,23 @@
+
+vector = [[1.0,1.0,1.0], [1.0,1.0,1.1], [1.0,1.0,1.2], [1.0,1.0,1.4]]
+
+
+
+def hklscan(vector, readables,latency = 0.0,  **pars):
+    readables=to_list(string_to_obj(readables))
+    #names = [readable.name for readable in readables]
+    scan = ManualScan([h, k, l], readables ,vector[0], vector[-1], [len(vector)-1] * 3, dimensions = 1)
+    if not "domain_axis" in pars.keys(): 
+        pars["domain_axis"] = "Index"
+    processScanPars(scan, pars)
+    scan.start()
+    try:
+        for pos in vector:
+            hkl.write(pos)
+            time.sleep(1.0)
+            scan.append ([h.take(), k.take(), l.take()], [h.getPosition(), k.getPosition(), l.getPosition()], [readable.read() for readable in readables ])
+    finally:
+        scan.end()    
+
+
+hklscan(vector, [sin, arr], 0.9) #,  = "Index" )#, line_plots = [sin])

script/TestPlot.py

@@ -1,6 +0,0 @@
-start = 0
-end = 10.0
-steps = 10
-
-
-r = lscan (out, sin, start, end, steps, 0.2)

script/TestProsilica.py

@@ -1,39 +0,0 @@
-
-prosilica.writeParameter("FrameStartTriggerMode","Freerun")
-prosilica.writeParameter("PixelFormat","Bayer8" )
-prosilica.writeParameter("GainValue",0)
-prosilica.writeParameter("ExposureValue",15000)
-prosilica.writeParameter("FrameRate",5.000)
-
-
-
-
-print prosilica.readParameter("AcquisitionMode")
-print prosilica.readParameter("AcquisitionFrameCount")
-print prosilica.readParameter("FrameRate")
-
-
-print prosilica.readParameterRange("AcquisitionMode")
-print prosilica.readParameterRange("AcquisitionFrameCount")
-print prosilica.readParameterRange("FrameRate")
-
-
-print prosilica.writeParameter("AcquisitionMode", "SingleFrame")
-print prosilica.writeParameter("AcquisitionFrameCount", 2)
-print prosilica.writeParameter("FrameRate", 6.0)
-
-
-print prosilica.readParameter("AcquisitionMode")
-print prosilica.readParameter("AcquisitionFrameCount")
-print prosilica.readParameter("FrameRate")
-
-
-
-print prosilica.writeParameter("AcquisitionMode", "Continuous")
-print prosilica.writeParameter("AcquisitionFrameCount", 1)
-print prosilica.writeParameter("FrameRate", 5.0)
-
-
-print prosilica.readParameter("AcquisitionMode")
-print prosilica.readParameter("AcquisitionFrameCount")
-print prosilica.readParameter("FrameRate")

script/TestScan.py

@@ -1,16 +0,0 @@
-print args
-if get_exec_pars().source == CommandSource.ui:
-    msg = None
-    start = 0
-    end = 10.0
-    steps = 10    
-else:
-    msg = args[0]
-    start = float(args[1])
-    end  = float(args[2])
-    steps  = int(args[3])    
-
-
-print msg
-r = lscan (out, sin, start, end, steps, 0.2)
-

script/_Lib/epics/CaChannel.py

@@ -0,0 +1,988 @@
+"""
+CaChannel class having identical API as of caPython/CaChannel class,
+based on PythonCA ( > 1.20.1beta2)
+
+Author:     Xiaoqiang Wang
+Created:    Sep. 22, 2008
+Changes:
+"""
+# python 2 -> 3 compatible layer
+import sys
+if sys.hexversion >= 0x03000000:
+    long = int
+
+import ca
+
+ca.cs_never_search = 4
+
+# retrieve numeric waveforms as numpy arrays, default No
+USE_NUMPY = False
+
+class CaChannelException(Exception):
+    def __init__(self, status):
+        self.status = str(status)
+    def __str__(self):
+        return self.status
+
+class CaChannel:
+    """CaChannel: A Python class with identical API as of caPython/CaChannel.
+
+    This class implements the methods to operate on channel access so that you can find
+    their  C library counterparts ,
+    http://www.aps.anl.gov/epics/base/R3-14/12-docs/CAref.html#Function.
+    Therefore an understanding of C API helps much.
+
+    To get started easily, convenient methods are created for often used operations,
+
+    ==========    ======
+    Operation     Method
+    ==========    ======
+    connect       :meth:`searchw`
+    read          :meth:`getw`
+    write         :meth:`putw`
+    ==========    ======
+
+    They have shorter names and default arguments. It is recommended to start with these methods.
+    Study the other C alike methods when necessary.
+
+    >>> import CaChannel
+    >>> chan = CaChannel.CaChannel('catest')
+    >>> chan.searchw()
+    >>> chan.putw(12.3)
+    >>> chan.getw()
+    12.3
+    """
+
+    ca_timeout = 3.0
+
+    dbr_d = {}
+    dbr_d[ca.DBR_SHORT] = int
+    dbr_d[ca.DBR_INT]   = int
+    dbr_d[ca.DBR_LONG]  = int
+    dbr_d[ca.DBR_FLOAT] = float
+    dbr_d[ca.DBR_DOUBLE]= float
+    dbr_d[ca.DBR_CHAR]  = int
+    dbr_d[ca.DBR_STRING]= str
+    dbr_d[ca.DBR_ENUM]  = int
+
+    def __init__(self, pvName=None):
+        self.pvname = pvName
+        self.__chid = None
+        self.__evid = None
+        self.__timeout = None
+        self._field_type = None
+        self._element_count = None
+        self._puser = None
+        self._conn_state = None
+        self._host_name = None
+        self._raccess = None
+        self._waccess = None
+
+        self._callbacks={}
+
+    def __del__(self):
+        try:
+            self.clear_event()
+            self.clear_channel()
+            self.flush_io()
+        except:
+            pass
+
+    def version(self):
+        return "CaChannel, version v28-03-12"
+#
+# Class helper methods
+#
+    def setTimeout(self, timeout):
+        """Set the timeout for this channel object. It overrides the class timeout.
+
+        :param float timeout:  timeout in seconds
+
+        """
+        if (timeout>=0 or timeout is None):
+            self.__timeout = timeout
+        else:
+            raise ValueError
+    def getTimeout(self):
+        """Retrieve the timeout set for this channel object.
+
+        :return: timeout in seconds for this channel instance
+
+        """
+        if self.__timeout is None:
+            timeout = CaChannel.ca_timeout
+        else:
+            timeout = self.__timeout
+
+        return timeout
+
+
+#
+# *************** Channel access medthod ***************
+#
+
+#
+# Connection methods
+#   search_and_connect
+#   search
+#   clear_channel
+
+    def search_and_connect(self, pvName, callback, *user_args):
+        """Attempt to establish a connection to a process variable.
+
+        :param str pvName:          process variable name
+        :param callable callback:   function called when connection completes and connection status changes later on.
+        :param user_args:           user provided arguments that are passed to callback when it is invoked.
+        :raises CaChannelException: if error happens
+
+        The user arguments are returned to the user in a tuple in the callback function.
+        The order of the arguments is preserved.
+
+        Each Python callback function is required to have two arguments.
+        The first argument is a tuple containing the results of the action.
+        The second argument is a tuple containing any user arguments specified by ``user_args``.
+        If no arguments were specified then the tuple is empty.
+
+
+        .. note:: All remote operation requests such as the above are accumulated (buffered)
+           and not forwarded to the IOC until one of execution methods (:meth:`pend_io`, :meth:`poll`, :meth:`pend_event`, :meth:`flush_io`)
+           is called. This allows several requests to be efficiently sent over the network in one message.
+
+        >>> chan = CaChannel('catest')
+        >>> def connCB(epicsArgs, userArgs):
+        ...     chid = epicsArgs[0]
+        ...     connection_state = epicsArgs[1]
+        ...     if connection_state == ca.CA_OP_CONN_UP:
+        ...         print('%s is connected' % ca.name(chid))
+        >>> chan.search_and_connect(None, connCB, chan)
+        >>> status = chan.pend_event(2)
+        catest is connected
+        """
+        if pvName is None:
+            pvName = self.pvname
+        else:
+            self.pvname = pvName
+        self._callbacks['connCB']=(callback, user_args)
+        try:
+            self.__chid = ca.search(pvName, self._conn_callback)
+        except ca.error:
+            msg = sys.exc_info()[1]
+            raise CaChannelException(msg)
+
+    def search(self, pvName=None):
+        """Attempt to establish a connection to a process variable.
+
+        :param str pvName: process variable name
+        :raises CaChannelException: if error happens
+
+        .. note:: All remote operation requests such as the above are accumulated (buffered)
+           and not forwarded to the IOC until one of execution methods (:meth:`pend_io`, :meth:`poll`, :meth:`pend_event`, :meth:`flush_io`)
+           is called. This allows several requests to be efficiently sent over the network in one message.
+
+        >>> chan = CaChannel()
+        >>> chan.search('catest')
+        >>> status = chan.pend_io(1)
+        >>> chan.state()
+        2
+        """
+        if pvName is None:
+            pvName = self.pvname
+        else:
+            self.pvname = pvName
+        try:
+            self.__chid = ca.search(pvName, None)
+        except ca.error:
+            msg = sys.exc_info()[1]
+            raise CaChannelException(msg)
+
+    def clear_channel(self):
+        """Close a channel created by one of the search functions.
+
+        Clearing a channel does not cause its connection handler to be called.
+        Clearing a channel does remove any monitors registered for that channel.
+        If the channel is currently connected then resources are freed only some
+        time after this request is flushed out to the server.
+
+        .. note:: All remote operation requests such as the above are accumulated (buffered)
+           and not forwarded to the IOC until one of execution methods (:meth:`pend_io`, :meth:`poll`, :meth:`pend_event`, :meth:`flush_io`)
+           is called. This allows several requests to be efficiently sent over the network in one message.
+
+        """
+        if(self.__chid is not None):
+            try:
+                ca.clear(self.__chid)
+            except ca.error:
+                msg = sys.exc_info()[1]
+                raise CaChannelException(msg)
+
+#
+# Write methods
+#   array_put
+#   array_put_callback
+#
+
+    def _setup_put(self,value, req_type, count = None):
+        if count is None:
+            count = self.element_count()
+        else:
+            count = max(1, min(self.element_count(), count) )
+
+        if req_type == -1:
+            req_type = self.field_type()
+
+        # single numeric value
+        if (isinstance(value, int) or
+                isinstance(value, long) or
+                isinstance(value, float) or
+                isinstance(value, bool)):
+            pval = (CaChannel.dbr_d[req_type](value),)
+        # single string value
+        #   if DBR_CHAR, split into chars
+        #   otherwise convert to field type
+        elif isinstance(value, str):
+            if req_type == ca.DBR_CHAR:
+                if len(value) < count:
+                    count = len(value)
+                pval = [ord(x) for x in value[:count]]
+            else:
+                pval = (CaChannel.dbr_d[req_type](value),)
+        # assumes other sequence type
+        else:
+            if len(value) < count:
+                count = len(value)
+            pval = [CaChannel.dbr_d[req_type](x) for x in value[:count]]
+
+        return pval
+
+    def array_put(self, value, req_type=None, count=None):
+        """Write a value or array of values to a channel
+
+        :param value:           data to be written. For multiple values use a list or tuple
+        :param req_type:        database request type (``ca.DBR_XXXX``). Defaults to be the native data type.
+        :param int count:       number of data values to write. Defaults to be the native count.
+
+        >>> chan = CaChannel('catest')
+        >>> chan.searchw()
+        >>> chan.array_put(123)
+        >>> chan.flush_io()
+        >>> chan.getw()
+        123.0
+        >>> chan = CaChannel('cabo')
+        >>> chan.searchw()
+        >>> chan.array_put('Busy', ca.DBR_STRING)
+        >>> chan.flush_io()
+        >>> chan.getw()
+        1
+        >>> chan = CaChannel('cawave')
+        >>> chan.searchw()
+        >>> chan.array_put([1,2,3])
+        >>> chan.flush_io()
+        >>> chan.getw()
+        [1.0, 2.0, 3.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+        >>> chan.getw(count=3, use_numpy=True)
+        array([ 1.,  2.,  3.])
+        >>> chan = CaChannel('cawavec')
+        >>> chan.searchw()
+        >>> chan.array_put('1234',count=3)
+        >>> chan.flush_io()
+        >>> chan.getw(count=4)
+        [49, 50, 51, 0]
+        """
+        if req_type is None: req_type = -1
+        val = self._setup_put(value, req_type, count)
+        try:
+            ca.put(self.__chid, val, None, None, req_type)
+        except ca.error:
+            msg = sys.exc_info()[1]
+            raise CaChannelException(msg)
+
+    def array_put_callback(self, value, req_type, count, callback, *user_args):
+        """Write a value or array of values to a channel and execute the user
+        supplied callback after the put has completed.
+
+        :param value:           data to be written. For multiple values use a list or tuple.
+        :param req_type:        database request type (``ca.DBR_XXXX``). Defaults to be the native data type.
+        :param int count:       number of data values to write, Defaults to be the native count.
+        :param callable callback: function called when the write is completed.
+        :param user_args:       user provided arguments that are passed to callback when it is invoked.
+        :raises CaChannelException: if error happens
+
+        Each Python callback function is required to have two arguments.
+        The first argument is a dictionary containing the results of the action.
+
+        =======  =====  =======
+        field    type   comment
+        =======  =====  =======
+        chid     int    channels id structure
+        type     int    database request type (ca.DBR_XXXX)
+        count    int    number of values to transfered
+        status   int    CA status return code (ca.ECA_XXXX)
+        =======  =====  =======
+
+        The second argument is a tuple containing any user arguments specified by ``user_args``.
+        If no arguments were specified then the tuple is empty.
+
+
+        >>> def putCB(epicsArgs, userArgs):
+        ...     print('%s put completed' % ca.name(epicsArgs['chid']))
+        >>> chan = CaChannel('catest')
+        >>> chan.searchw()
+        >>> chan.array_put_callback(145, None, None, putCB)
+        >>> status = chan.pend_event(1)
+        catest put completed
+        >>> chan = CaChannel('cabo')
+        >>> chan.searchw()
+        >>> chan.array_put_callback('Busy', ca.DBR_STRING, None, putCB)
+        >>> status = chan.pend_event(1)
+        cabo put completed
+        >>> chan = CaChannel('cawave')
+        >>> chan.searchw()
+        >>> chan.array_put_callback([1,2,3], None, None, putCB)
+        >>> status = chan.pend_event(1)
+        cawave put completed
+        >>> chan = CaChannel('cawavec')
+        >>> chan.searchw()
+        >>> chan.array_put_callback('123', None, None, putCB)
+        >>> status = chan.pend_event(1)
+        cawavec put completed
+        """
+        if req_type is None: req_type = 0
+        val = self._setup_put(value, req_type, count)
+        self._callbacks['putCB']=(callback, user_args)
+        try:
+            ca.put(self.__chid, val, None, self._put_callback, req_type)
+        except ca.error:
+            msg = sys.exc_info()[1]
+            raise CaChannelException(msg)
+#
+# Read methods
+#   getValue
+#   array_get
+#   array_get_callback
+#
+
+    # Obtain read value after ECA_NORMAL is returned on an array_get().
+    def getValue(self):
+        """Return the value(s) after array_get has completed"""
+        return self.val
+
+    # Simulate with a synchronous getw function call
+    def array_get(self, req_type=None, count=None, **keywords):
+        """Read a value or array of values from a channel. The new value is
+        retrieved by a call to getValue method.
+
+        :param req_type:    database request type (``ca.DBR_XXXX``). Defaults to be the native data type.
+        :param int count:   number of data values to read, Defaults to be the native count.
+        :param keywords:    optional arguments assigned by keywords
+
+                            ===========   =====
+                            keyword       value
+                            ===========   =====
+                            use_numpy     True if waveform should be returned as numpy array. Default :data:`CaChannel.USE_NUMPY`.
+                            ===========   =====
+
+        :raises CaChannelException: if error happens
+
+        .. note:: All remote operation requests such as the above are accumulated (buffered)
+           and not forwarded to the IOC until one of execution methods (``pend_io``, ``poll``, ``pend_event``, ``flush_io``)
+           is called. This allows several requests to be efficiently sent over the network in one message.
+
+
+        >>> chan = CaChannel('catest')
+        >>> chan.searchw()
+        >>> chan.putw(123)
+        >>> chan.array_get()
+        >>> chan.getValue()
+        123.0
+        """
+        self.val = self.getw(req_type, count, **keywords)
+
+    def array_get_callback(self, req_type, count, callback, *user_args, **keywords):
+        """Read a value or array of values from a channel and execute the user
+        supplied callback after the get has completed.
+
+        :param req_type:        database request type (``ca.DBR_XXXX``). Defaults to be the native data type.
+        :param int count:       number of data values to read, Defaults to be the native count.
+        :param callable callback:  function called when the get is completed.
+        :param user_args:       user provided arguments that are passed to callback when it is invoked.
+        :param keywords:        optional arguments assigned by keywords
+
+                                ===========   =====
+                                keyword       value
+                                ===========   =====
+                                use_numpy     True if waveform should be returned as numpy array. Default :data:`CaChannel.USE_NUMPY`.
+                                ===========   =====
+
+        :raises CaChannelException: if error happens
+
+        Each Python callback function is required to have two arguments.
+        The first argument is a dictionary containing the results of the action.
+
+        +-----------------+---------------+------------------------------------+-------------------------+---------------+-------------+---------------+
+        | field           |  type         |  comment                           |       request type                                                    |
+        |                 |               |                                    +----------+--------------+---------------+-------------+---------------+
+        |                 |               |                                    | DBR_XXXX | DBR_STS_XXXX | DBR_TIME_XXXX | DBR_GR_XXXX | DBR_CTRL_XXXX |
+        +=================+===============+====================================+==========+==============+===============+=============+===============+
+        | chid            |   int         |   channels id number               |    X     |       X      |     X         |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | type            |   int         |   database request type            |    X     |       X      |     X         |   X         | X             |
+        |                 |               |   (ca.DBR_XXXX)                    |          |              |               |             |               |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | count           |   int         |   number of values to transfered   |    X     |       X      |     X         |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | status          |   int         |   CA status return code            |    X     |       X      |     X         |   X         | X             |
+        |                 |               |   (ca.ECA_XXXX)                    |          |              |               |             |               |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_value        |               |   PV value                         |    X     |       X      |     X         |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_status       |   int         |   PV alarm status                  |          |       X      |     X         |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_severity     |   int         |   PV alarm severity                |          |       X      |     X         |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_seconds      |   float       |   timestamp                        |          |              |     X         |             |               |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_nostrings    |   int         |   ENUM PV's number of states       |          |              |               |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_statestrings |   string list |   ENUM PV's states string          |          |              |               |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_units        |   string      |   units                            |          |              |               |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_precision    |   int         |   precision                        |          |              |               |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_updislim     |   float       |   upper display limit              |          |              |               |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_lodislim     |   float       |   lower display limit              |          |              |               |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_upalarmlim   |   float       |   upper alarm limit                |          |              |               |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_upwarnlim    |   float       |   upper warning limit              |          |              |               |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_loalarmlim   |   float       |   lower alarm limit                |          |              |               |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_lowarnlim    |   float       |   lower warning limit              |          |              |               |   X         | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_upctrllim    |   float       |   upper control limit              |          |              |               |             | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+        | pv_loctrllim    |   float       |   lower control limit              |          |              |               |             | X             |
+        +-----------------+---------------+------------------------------------+----------+--------------+---------------+-------------+---------------+
+
+        The second argument is a tuple containing any user arguments specified by ``user_args``.
+        If no arguments were specified then the tuple is empty.
+
+        .. note:: All remote operation requests such as the above are accumulated (buffered)
+           and not forwarded to the IOC until one of execution methods (``pend_io``, ``poll``, ``pend_event``, ``flush_io``)
+           is called. This allows several requests to be efficiently sent over the network in one message.
+
+        >>> def getCB(epicsArgs, userArgs):
+        ...     for item in sorted(epicsArgs.keys()):
+        ...         if item.startswith('pv_'):
+        ...             print('%s %s' % (item,epicsArgs[item]))
+        >>> chan = CaChannel('catest')
+        >>> chan.searchw()
+        >>> chan.putw(145)
+        >>> chan.array_get_callback(ca.DBR_CTRL_DOUBLE, 1, getCB)
+        >>> status = chan.pend_event(1)
+        pv_loalarmlim -20.0
+        pv_loctrllim 0.0
+        pv_lodislim 0.0
+        pv_lowarnlim -10.0
+        pv_precision 3
+        pv_severity 2
+        pv_status 3
+        pv_units mm
+        pv_upalarmlim 20.0
+        pv_upctrllim 0.0
+        pv_updislim 0.0
+        pv_upwarnlim 10.0
+        pv_value 145.0
+        >>> chan = CaChannel('cabo')
+        >>> chan.searchw()
+        >>> chan.putw(0)
+        >>> chan.array_get_callback(ca.DBR_CTRL_ENUM, 1, getCB)
+        >>> status = chan.pend_event(1)
+        pv_nostrings 2
+        pv_severity 0
+        pv_statestrings ('Done', 'Busy')
+        pv_status 0
+        pv_value 0
+        """
+        if req_type is None: req_type = ca.dbf_type_to_DBR(self.field_type())
+        if count is None: count = self.element_count()
+        self._callbacks['getCB']=(callback, user_args)
+        try:
+            ca.get(self.__chid, self._get_callback, req_type, count, keywords.get('use_numpy', USE_NUMPY))
+        except ca.error:
+            msg = sys.exc_info()[1]
+            raise CaChannelException(msg)
+
+#
+# Monitor methods
+#   add_masked_array_event
+#   clear_event
+#
+
+    # Creates a new event id and stores it on self.__evid.  Only one event registered
+    # per CaChannel object.  If an event is already registered the event is cleared
+    # before registering a new event.
+    def add_masked_array_event(self, req_type, count, mask, callback, *user_args, **keywords):
+        """Specify a callback function to be executed whenever changes occur to a PV.
+
+        :param req_type:        database request type (``ca.DBR_XXXX``). Defaults to be the native data type.
+        :param int  count:      number of data values to read, Defaults to be the native count.
+        :param mask:            logical or of ``ca.DBE_VALUE``, ``ca.DBE_LOG``, ``ca.DBE_ALARM``.
+                                Defaults to be ``ca.DBE_VALUE|ca.DBE_ALARM``.
+        :param callable callback:        function called when the get is completed.
+        :param user_args:       user provided arguments that are passed to callback when
+                                it is invoked.
+        :param keywords:        optional arguments assigned by keywords
+
+                                ===========   =====
+                                keyword       value
+                                ===========   =====
+                                use_numpy     True if waveform should be returned as numpy array. Default :data:`CaChannel.USE_NUMPY`.
+                                ===========   =====
+
+        :raises CaChannelException: if error happens
+
+        .. note:: All remote operation requests such as the above are accumulated (buffered)
+           and not forwarded to the IOC until one of execution methods (:meth:`pend_io`, :meth:`poll`, :meth:`pend_event`, :meth:`flush_io`)
+           is called. This allows several requests to be efficiently sent over the network in one message.
+
+        >>> def eventCB(epicsArgs, userArgs):
+        ...     print('pv_value %s' % epicsArgs['pv_value'])
+        ...     print('pv_status %d %s' % (epicsArgs['pv_status'], ca.alarmStatusString(epicsArgs['pv_status'])))
+        ...     print('pv_severity %d %s' % (epicsArgs['pv_severity'], ca.alarmSeverityString(epicsArgs['pv_severity'])))
+        >>> chan = CaChannel('cabo')
+        >>> chan.searchw()
+        >>> chan.putw(1)
+        >>> chan.add_masked_array_event(ca.DBR_STS_ENUM, None, None, eventCB)
+        >>> status = chan.pend_event(1)
+        pv_value 1
+        pv_status 7 STATE
+        pv_severity 1 MINOR
+        >>> chan.clear_event()
+        >>> chan.add_masked_array_event(ca.DBR_STS_STRING, None, None, eventCB)
+        >>> status = chan.pend_event(1)
+        pv_value Busy
+        pv_status 7 STATE
+        pv_severity 1 MINOR
+        >>> chan.clear_event()
+        """
+        if req_type is None: req_type = ca.dbf_type_to_DBR(self.field_type())
+        if count is None: count = self.element_count()
+        if mask is None: mask = ca.DBE_VALUE|ca.DBE_ALARM
+        if self.__evid is not None:
+            self.clear_event()
+            self.flush_io()
+        self._callbacks['eventCB']=(callback, user_args)
+        try:
+            self.__evid = ca.monitor(self.__chid, self._event_callback, count, mask, req_type, keywords.get('use_numpy', USE_NUMPY))
+        except ca.error:
+            msg = sys.exc_info()[1]
+            raise CaChannelException(msg)
+
+    def clear_event(self):
+        """Remove previously installed callback function.
+
+        .. note:: All remote operation requests such as the above are accumulated (buffered)
+           and not forwarded to the IOC until one of execution methods (:meth:`pend_io`, :meth:`poll`, :meth:`pend_event`, :meth:`flush_io`)
+           is called. This allows several requests to be efficiently sent over the network in one message.
+        """
+        if self.__evid is not None:
+            try:
+                ca.clear_monitor(self.__evid)
+                self.__evid = None
+            except ca.error:
+                msg = sys.exc_info()[1]
+                raise CaChannelException(msg)
+
+#
+# Execute methods
+#   pend_io
+#   pend_event
+#   poll
+#   flush_io
+#
+
+    def pend_io(self,timeout=None):
+        """Flush the send buffer and wait until outstanding queries (``search``, ``array_get``) complete
+        or the specified timeout expires.
+
+        :param float timeout:         seconds to wait
+        :raises CaChannelException: if timeout or other error happens
+
+        """
+        if timeout is None:
+            timeout = self.getTimeout()
+        status = ca.pend_io(float(timeout))
+        if status != 0:
+            raise CaChannelException(ca.caError._caErrorMsg[status])
+
+    def pend_event(self,timeout=None):
+        """Flush the send buffer and process background activity (connect/get/put/monitor callbacks) for ``timeout`` seconds.
+
+        It will not return before the specified timeout expires and all unfinished channel access labor has been processed.
+
+        :param float timeout:  seconds to wait
+
+        """
+        if timeout is None:
+            timeout = 0.1
+        status = ca.pend_event(timeout)
+        # status is always ECA_TIMEOUT
+        return status
+
+    def poll(self):
+        """Flush the send buffer and execute any outstanding background activity.
+
+        .. note:: It is an alias to ``pend_event(1e-12)``.
+        """
+        status = ca.poll()
+        # status is always ECA_TIMEOUT
+        return status
+
+    def flush_io(self):
+        """Flush the send buffer and does not execute outstanding background activity."""
+        status = ca.flush()
+        if status != 0:
+            raise CaChannelException(ca.caError._caErrorMsg[status])
+
+#
+# Channel Access Macros
+#   field_type
+#   element_count
+#   name
+#   state
+#   host_name
+#   read_access
+#   write_access
+#
+    def get_info(self):
+        try:
+            info=(self._field_type, self._element_count, self._puser,
+                  self._conn_state, self._host_name, self._raccess,
+                  self._waccess) = ca.ch_info(self.__chid)
+        except ca.error:
+            msg = sys.exc_info()[1]
+            raise CaChannelException(msg)
+        return info
+
+
+    def field_type(self):
+        """Native type of the PV in the server (``ca.DBF_XXXX``).
+
+        >>> chan = CaChannel('catest')
+        >>> chan.searchw()
+        >>> ftype = chan.field_type()
+        >>> ftype
+        6
+        >>> ca.dbf_text(ftype)
+        'DBF_DOUBLE'
+        >>> ca.DBF_DOUBLE == ftype
+        True
+        """
+        self.get_info()
+        return self._field_type
+
+    def element_count(self):
+        """Maximum array element count of the PV in the server.
+
+        >>> chan = CaChannel('catest')
+        >>> chan.searchw()
+        >>> chan.element_count()
+        1
+        """
+        self.get_info()
+        return self._element_count
+
+    def name(self):
+        """Channel name specified when the channel was created.
+
+        >>> chan = CaChannel('catest')
+        >>> chan.searchw()
+        >>> chan.name()
+        'catest'
+        """
+        return ca.name(self.__chid)
+
+    def state(self):
+        """Current state of the CA connection.
+
+            ==================    =============
+            States                Meaning
+            ==================    =============
+            ca.cs_never_conn      PV not found
+            ca.cs_prev_conn       PV was found but unavailable
+            ca.cs_conn            PV was found and available
+            ca.cs_closed          PV not closed
+            ca.cs_never_search    PV not searched yet
+            ==================    =============
+
+        >>> chan = CaChannel('catest')
+        >>> chan.searchw()
+        >>> chan.state()
+        2
+        """
+        if self.__chid is None:
+            return ca.cs_never_search
+        else:
+            self.get_info()
+            return self._conn_state
+
+    def host_name(self):
+        """Host name that hosts the process variable."""
+        self.get_info()
+        return self._host_name
+
+    def read_access(self):
+        """Access right to read the channel.
+
+         :return: True if the channel can be read, False otherwise.
+
+         """
+        self.get_info()
+        return self._raccess
+
+    def write_access(self):
+        """Access right to write the channel.
+
+        :return: True if the channel can be written, False otherwise.
+
+        """
+        self.get_info()
+        return self._waccess
+#
+# Wait functions
+#
+# These functions wait for completion of the requested action.
+    def searchw(self, pvName=None):
+        """Attempt to establish a connection to a process variable.
+
+        :param str pvName:          process variable name
+        :raises CaChannelException: if timeout or error happens
+
+        .. note:: This method waits for connection to be established or fail with exception.
+
+        >>> chan = CaChannel('non-exist-channel')
+        >>> chan.searchw()
+        Traceback (most recent call last):
+            ...
+        CaChannelException: User specified timeout on IO operation expired
+        """
+        if pvName is None:
+            pvName = self.pvname
+        else:
+            self.pvname = pvName
+        self.__chid = ca.search(pvName, None)
+        timeout = self.getTimeout()
+        status = ca.pend_io(timeout)
+        if status != 0:
+            raise CaChannelException(ca.caError._caErrorMsg[status])
+
+    def putw(self, value, req_type=None):
+        """Write a value or array of values to a channel
+
+        If the request type is omitted the data is written as the Python type corresponding to the native format.
+        Multi-element data is specified as a tuple or a list.
+        Internally the sequence is converted to a list before inserting the values into a C array.
+        Access using non-numerical types is restricted to the first element in the data field.
+        Mixing character types with numerical types writes bogus results but is not prohibited at this time.
+        DBF_ENUM fields can be written using DBR_ENUM and DBR_STRING types.
+        DBR_STRING writes of a field of type DBF_ENUM must be accompanied by a valid string out of the possible enumerated values.
+
+        :param value:           data to be written. For multiple values use a list or tuple
+        :param req_type:        database request type (``ca.DBR_XXXX``). Defaults to be the native data type.
+        :raises CaChannelException: if timeout or error happens
+
+        .. note:: This method does flush the request to the channel access server.
+
+        >>> chan = CaChannel('catest')
+        >>> chan.searchw()
+        >>> chan.putw(145)
+        >>> chan.getw()
+        145.0
+        >>> chan = CaChannel('cabo')
+        >>> chan.searchw()
+        >>> chan.putw('Busy', ca.DBR_STRING)
+        >>> chan.getw()
+        1
+        >>> chan.getw(ca.DBR_STRING)
+        'Busy'
+        >>> chan = CaChannel('cawave')
+        >>> chan.searchw()
+        >>> chan.putw([1,2,3])
+        >>> chan.getw(req_type=ca.DBR_LONG,count=4)
+        [1, 2, 3, 0]
+        >>> chan = CaChannel('cawavec')
+        >>> chan.searchw()
+        >>> chan.putw('123')
+        >>> chan.getw(count=4)
+        [49, 50, 51, 0]
+        >>> chan = CaChannel('cawaves')
+        >>> chan.searchw()
+        >>> chan.putw(['string 1','string 2'])
+        >>> chan.getw()
+        ['string 1', 'string 2', '']
+        """
+        if req_type is None: req_type = -1
+        val = self._setup_put(value, req_type)
+        try:
+            ca.put(self.__chid, val, None, None, req_type)
+        except ca.error:
+            msg = sys.exc_info()[1]
+            raise CaChannelException(msg)
+        self.flush_io()
+
+    def getw(self, req_type=None, count=None, **keywords):
+        """Read the value from a channel.
+
+        :param req_type:        database request type. Defaults to be the native data type.
+        :param int count:       number of data values to read, Defaults to be the native count.
+        :param keywords:        optional arguments assigned by keywords
+
+                                ===========   =====
+                                keyword       value
+                                ===========   =====
+                                use_numpy     True if waveform should be returned as numpy array. Default :data:`CaChannel.USE_NUMPY`.
+                                ===========   =====
+        :return:                If req_type is plain request type, only the value is returned. Otherwise a dict returns
+                                with information depending on the request type, same as the first argument passed to user's callback.
+                                See :meth:`array_get_callback`.
+
+        :raises CaChannelException: if timeout error happens
+
+        If the request type is omitted the data is returned to the user as the Python type corresponding to the native format.
+        Multi-element data has all the elements returned as items in a list and must be accessed using a numerical type.
+        Access using non-numerical types is restricted to the first element in the data field.
+        DBF_ENUM fields can be read using DBR_ENUM and DBR_STRING types.
+        DBR_STRING reads of a field of type DBF_ENUM returns the string corresponding to the current enumerated value.
+
+        """
+        updated = [False]
+        value = [0]
+        def update_value(args):
+            if args is None:
+                return
+            try:
+                value[0] = self._format_cb_args(args)
+            finally:
+                updated[0] = True
+        if req_type is None: req_type = ca.dbf_type_to_DBR(self.field_type())
+        if count is None: count = self.element_count()
+        try:
+            ca.get(self.__chid, update_value, req_type, count, keywords.get('use_numpy', USE_NUMPY))
+        except ca.error:
+            msg = sys.exc_info()[1]
+            raise CaChannelException(msg)
+        timeout = self.getTimeout()
+        self.flush_io()
+        n = timeout / 0.001
+        while n > 0 and not updated[0]:
+            ca.pend_event(0.001)
+            n-=1
+        if not updated[0]:
+            raise CaChannelException(ca.caError._caErrorMsg[10]) # ECA_TIMEOUT
+        if ca.dbr_type_is_plain(req_type):
+            return value[0]['pv_value']
+        else:
+            return value[0]
+
+#
+# Callback functions
+#
+# These functions hook user supplied callback functions to CA extension
+
+    def _conn_callback(self):
+        callback = self._callbacks.get('connCB')
+        if callback is None:
+            return
+        callbackFunc, userArgs = callback
+        if self.state() == 2: OP = 6
+        else: OP = 7
+        epicsArgs = (self.__chid, OP)
+        try:
+            callbackFunc(epicsArgs, userArgs)
+        except:
+            pass
+
+    def _put_callback(self, args):
+        callback = self._callbacks.get('putCB')
+        if callback is None:
+            return
+        callbackFunc, userArgs = callback
+        epicsArgs={}
+        epicsArgs['chid']=self.__chid
+        epicsArgs['type']=self.field_type()
+        epicsArgs['count']=self.element_count()
+        epicsArgs['status']=args[1]
+        try:
+            callbackFunc(epicsArgs, userArgs)
+        except:
+            pass
+
+    def _get_callback(self, args):
+        callback = self._callbacks.get('getCB')
+        if callback is None:
+            return
+        callbackFunc, userArgs = callback
+        epicsArgs = self._format_cb_args(args)
+        try:
+            callbackFunc(epicsArgs, userArgs)
+        except:
+            pass
+
+    def _event_callback(self, args):
+        callback = self._callbacks.get('eventCB')
+        if callback is None:
+            return
+        callbackFunc, userArgs = callback
+        epicsArgs = self._format_cb_args(args)
+        try:
+            callbackFunc(epicsArgs, userArgs)
+        except:
+            pass
+
+    def _format_cb_args(self, args):
+        epicsArgs={}
+        epicsArgs['chid']   = self.__chid
+        # dbr_type is not returned
+        # use dbf_type instead
+        epicsArgs['type']   = self.field_type()
+        epicsArgs['count']  = self.element_count()
+        # status flag is not returned,
+        # args[1] is alarm status
+        # assume ECA_NORMAL
+        epicsArgs['status'] = 1
+        if len(args)==2:          # Error
+            epicsArgs['pv_value']   = args[0] # always None
+            epicsArgs['status']     = args[1]
+        if len(args)>=3:          # DBR_Plain
+            epicsArgs['pv_value']   = args[0]
+            epicsArgs['pv_severity']= args[1]
+            epicsArgs['pv_status']  = args[2]
+        if len(args)==4:          # DBR_TIME, 0.0 for others
+            epicsArgs['pv_seconds'] = args[3]
+        if len(args)==5:
+            if len(args[4])==2:   # DBR_CTRL_ENUM
+                epicsArgs['pv_nostrings']   = args[4][0]
+                epicsArgs['pv_statestrings']= args[4][1]
+            if len(args[4])>=7:   # DBR_GR
+                epicsArgs['pv_units']       = args[4][0]
+                epicsArgs['pv_updislim']    = args[4][1]
+                epicsArgs['pv_lodislim']    = args[4][2]
+                epicsArgs['pv_upalarmlim']  = args[4][3]
+                epicsArgs['pv_upwarnlim']   = args[4][4]
+                epicsArgs['pv_loalarmlim']  = args[4][5]
+                epicsArgs['pv_lowarnlim']   = args[4][6]
+            if len(args[4])==8:   # DBR_GR_FLOAT or DBR_GR_DOUBLE
+                epicsArgs['pv_precision']   = args[4][7]
+            if len(args[4])>=9:   # DBR_CTRL
+                epicsArgs['pv_upctrllim']   = args[4][7]
+                epicsArgs['pv_loctrllim']   = args[4][8]
+            if len(args[4])==10:  # DBR_CTRL_FLOAT or DBR_CTRL_DOUBLE
+                epicsArgs['pv_precision']   = args[4][9]
+        return epicsArgs
+
+if __name__ == "__main__":
+    import doctest
+    doctest.testmod()

script/_Lib/epics/_ca.py

@@ -0,0 +1,212 @@
+import sys
+import traceback
+import java.lang.System
+import java.lang.Thread
+import java.lang.InterruptedException
+import gov.aps.jca.CAStatus
+import gov.aps.jca.JCALibrary
+import gov.aps.jca.configuration.DefaultConfiguration
+import gov.aps.jca.dbr.DBRType
+import gov.aps.jca.dbr.Severity
+import gov.aps.jca.event.PutListener
+import gov.aps.jca.event.GetListener
+import gov.aps.jca.event.MonitorListener
+import ch.psi.jcae.impl.JcaeProperties
+
+version = "PShell wrapper"
+release = "1.0.0"
+revision = "1.0.0"
+error = Exception
+
+def dbf_type_is_valid(type):
+    return (type >= 0) and (type <= LAST_TYPE)
+def dbr_type_is_valid(type):
+    return (type >= 0) and (type <= LAST_BUFFER_TYPE)
+def dbr_type_is_plain(type):
+    return (type >= DBR_STRING) and (type <= DBR_DOUBLE)
+def dbr_type_is_STS(type):
+    return (type >= DBR_STS_STRING) and (type <= DBR_STS_DOUBLE)
+def dbr_type_is_TIME(type):
+    return (type >= DBR_TIME_STRING) and (type <= DBR_TIME_DOUBLE)
+def dbr_type_is_GR(type):
+    return (type >= DBR_GR_STRING) and (type <= DBR_GR_DOUBLE)
+def dbr_type_is_CTRL(type):
+    return (type >= DBR_CTRL_STRING) and (type <= DBR_CTRL_DOUBLE)
+def dbr_type_is_STRING(type):
+    return (type >= 0) and (type <= LAST_BUFFER_TYPE) and (type%(LAST_TYPE+1) == DBR_STRING)
+def dbr_type_is_SHORT(type):
+    return (type >= 0) and (type <= LAST_BUFFER_TYPE) and (type%(LAST_TYPE+1) == DBR_SHORT)
+def dbr_type_is_FLOAT(type):
+    return (type >= 0) and (type <= LAST_BUFFER_TYPE) and (type%(LAST_TYPE+1) == DBR_FLOAT)
+def dbr_type_is_ENUM(type):
+    return (type >= 0) and (type <= LAST_BUFFER_TYPE) and (type%(LAST_TYPE+1) == DBR_ENUM)
+def dbr_type_is_CHAR(type):
+    return (type >= 0) and (type <= LAST_BUFFER_TYPE) and (type%(LAST_TYPE+1) == DBR_CHAR)
+def dbr_type_is_LONG(type):
+    return (type >= 0) and (type <= LAST_BUFFER_TYPE) and (type%(LAST_TYPE+1) == DBR_LONG)
+def dbr_type_is_DOUBLE(type):
+    return (type >= 0) and (type <= LAST_BUFFER_TYPE) and (type%(LAST_TYPE+1) == DBR_DOUBLE)
+
+#I am assuming have JCAE, but it is possible to implement over JCA only, prividing the configuration
+properties  = ch.psi.jcae.impl.JcaeProperties.getInstance()
+jca= gov.aps.jca.JCALibrary.getInstance()
+context = None
+configuration = gov.aps.jca.configuration.DefaultConfiguration("jython ca context")
+configuration.setAttribute("class", gov.aps.jca.JCALibrary.CHANNEL_ACCESS_JAVA)
+configuration.setAttribute("addr_list", properties.getAddressList())
+configuration.setAttribute("auto_addr_list", str(properties.isAutoAddressList()));
+if properties.getMaxArrayBytes() is not None:
+    configuration.setAttribute("max_array_bytes", properties.getMaxArrayBytes())
+if properties.getServerPort() is not None:
+    configuration.setAttribute("server_port", properties.getServerPort())
+
+def initialize():    
+    global jca
+    global context
+    global configuration
+
+    if context is not None:
+        context.destroy()
+
+    context= jca.createContext(configuration)
+
+initialize()
+
+
+class PutListener(gov.aps.jca.event.PutListener):
+    def __init__(self, callback):
+        self.callback = callback
+    def putCompleted(self, put_ev):
+        if  put_ev is None:
+            self.callback(None , None , None)
+        else:
+            count = put_ev.getCount() 
+            status = put_ev.getStatus() 
+            dbr_type = put_ev.getType()        
+            self.callback([count, status, dbr_type]) #TODO: Check these: status must be second par
+
+def formatCbArgs(status, dbr):
+    dbrType = dbr.getType()
+    if status <> gov.aps.jca.CAStatus.NORMAL:
+        cb_args=[None, status.getValue()]
+    else:
+        try:
+            val = dbr.getValue()
+            if val is not None:
+                val = val.tolist()
+                if len(val) == 1:
+                    val = val[0]
+            if dbr.isSTS():
+                cb_args = [val, dbr.getSeverity().getValue(), status.getValue()]
+            else:
+                cb_args = [val, gov.aps.jca.dbr.Severity.NO_ALARM, status.getValue()]
+            if dbr.isTIME():
+                timestamp = dbr.getTimeStamp()
+                cb_args.append( timestamp.nsec() if (timestamp is not None) else 0.0)
+            else:
+                cb_args.append(0.0)        
+            if dbr.isENUM():
+                cb_args.append([None, None]) #TODO
+            elif dbr.isGR():
+                gr=[dbr.getUnits(), dbr.getUpperDispLimit(), dbr.getLowerDispLimit(), 
+                    dbr.getUpperAlarmLimit(), dbr.getUpperWarningLimit(), 
+                    dbr.getLowerAlarmLimit(), dbr.getLowerWarningLimit()]
+                if (dbr.isCTRL()):
+                    gr.append(dbr.getUpperCtrlLimit())
+                    gr.append(dbr.getLowerCtrlLimit())
+                if (dbr.isPRECSION()):
+                    gr.append(dbr.getPrecision())
+                cb_args.append(gr)        
+        except:
+            traceback.print_exc(file=sys.stderr)
+            cb_args=[None, None]            
+    return cb_args
+
+
+class GetListener(gov.aps.jca.event.GetListener):
+    def __init__(self, callback):
+        self.callback = callback
+    def getCompleted(self, get_ev):
+        status = get_ev.getStatus() 
+        dbr = get_ev.getDBR()   
+        self.callback(formatCbArgs(status, dbr))
+
+class MonitorListener(gov.aps.jca.event.MonitorListener):
+    def __init__(self, callback):
+        self.callback = callback
+    def monitorChanged(self, monitor_ev):        
+        status = monitor_ev.getStatus() 
+        dbr = monitor_ev.getDBR()   
+        self.callback(formatCbArgs(status, dbr))
+        #print dbr.getValue()
+
+def search(name, callback): #returns channel
+    ch= context.createChannel(name)
+    context.pendIO(1.0)
+    return ch    
+
+def name(channel):
+    return channel.getName() 
+
+def clear(channel):
+    channel.destroy() 
+    flush()
+
+def put(channel, val, not_used, put_callback, req_type):
+    type = gov.aps.jca.dbr.DBRType.forValue(req_type) 
+    if put_callback is not None:
+        listener = PutListener(put_callback)
+        channel.put(val, listener)
+    else:
+        channel.put(val)
+    flush()  
+
+def get(channel, get_callback, req_type, count, *args):
+    listener = GetListener(get_callback)
+    type = gov.aps.jca.dbr.DBRType.forValue(req_type) 
+    channel.get(type, count, listener)
+    flush() 
+
+
+def monitor(channel, event_callback, count, mask, req_type, *args):
+    listener = MonitorListener(event_callback)
+    type = gov.aps.jca.dbr.DBRType.forValue(req_type)
+    monitor = channel.addMonitor(type, count, mask, listener) 
+    flush()
+    return monitor
+
+def clear_monitor(event_id):
+    event_id.removeMonitorListener(event_id.getMonitorListener())
+    flush()
+
+def ch_info(channel):
+    return (channel.getFieldType().getValue(), channel.getElementCount() ,
+         None, channel.getConnectionState().getValue(), channel.getHostName(), 
+         channel.getReadAccess() , channel.getWriteAccess())
+
+
+def pend_io(timeout):
+    context.pendIO(timeout)
+    _checkInterrupted()
+    return 0 #for OK
+
+
+def pend_event(timeout):
+    context.pendEvent(timeout) 
+    _checkInterrupted()
+    return 80 #C library always returns  ECA_TIMEOUT
+    
+def poll():
+    return pend_event(1e-12)
+
+def flush():
+    context.flushIO()
+    _checkInterrupted()
+    return 0
+
+
+def _checkInterrupted():    
+    java.lang.Thread.currentThread().sleep(0)
+    if java.lang.Thread.currentThread().isInterrupted():
+        raise java.lang.InterruptedException()
+

script/_Lib/epics/_ca_fnal.py

@@ -0,0 +1,88 @@
+
+from _ca import *
+from cadefs import *
+import caError
+
+def alarmSeverityString(sevr):
+    try:
+        return AlarmSeverity.Strings[sevr]
+    except:
+        return "Unkown Severity"
+
+def alarmStatusString(status):
+    try:
+        return AlarmStatus.Strings[status]
+    except:
+        return "Unknown Alarm"
+
+def message(status):
+    try:
+        return caError._caErrorMsg[caError.CA_EXTRACT_MSG_NO(status)]
+    except:
+        return str(status)
+
+def dbf_type_is_valid(dbftype):
+    return dbftype >= 0 and dbftype <= LAST_TYPE
+def dbr_type_is_valid(dbrtype):
+    return dbrtype >= 0 and dbrtype <= LAST_BUFFER_TYPE
+
+def dbr_type_is_plain(dbrtype):
+    return (dbrtype >= DBR_STRING and dbrtype <= DBR_DOUBLE)
+def dbr_type_is_STS(dbrtype):
+    return (dbrtype >= DBR_STS_STRING and dbrtype <= DBR_STS_DOUBLE)
+def dbr_type_is_TIME(dbrtype):
+    return (dbrtype >= DBR_TIME_STRING and dbrtype <= DBR_TIME_DOUBLE)
+def dbr_type_is_GR(dbrtype):
+    return (dbrtype >= DBR_GR_STRING and dbrtype <= DBR_GR_DOUBLE)
+def dbr_type_is_CTRL(dbrtype):
+    return (dbrtype >= DBR_CTRL_STRING and dbrtype <= DBR_CTRL_DOUBLE)
+
+def dbr_type_is_STRING(dbrtype):
+    return (dbrtype >= 0 and dbrtype <= LAST_BUFFER_TYPE and
+         dbrtype%(LAST_TYPE+1) == DBR_STRING)
+def dbr_type_is_SHORT(dbrtype):
+    return (dbrtype >= 0 and dbrtype <= LAST_BUFFER_TYPE and
+         dbrtype%(LAST_TYPE+1) == DBR_SHORT)
+def dbr_type_is_FLOAT(dbrtype):
+    return (dbrtype >= 0 and dbrtype <= LAST_BUFFER_TYPE and
+         dbrtype%(LAST_TYPE+1) == DBR_FLOAT)
+def dbr_type_is_ENUM(dbrtype):
+    return (dbrtype >= 0 and dbrtype <= LAST_BUFFER_TYPE and
+         dbrtype%(LAST_TYPE+1) == DBR_ENUM)
+def dbr_type_is_CHAR(dbrtype):
+    return (dbrtype >= 0 and dbrtype <= LAST_BUFFER_TYPE and
+         dbrtype%(LAST_TYPE+1) == DBR_CHAR)
+def dbr_type_is_LONG(dbrtype):
+    return (dbrtype >= 0 and dbrtype <= LAST_BUFFER_TYPE and
+         dbrtype%(LAST_TYPE+1) == DBR_LONG)
+def dbr_type_is_DOUBLE(dbrtype):
+    return (dbrtype >= 0 and dbrtype <= LAST_BUFFER_TYPE and
+         dbrtype%(LAST_TYPE+1) == DBR_DOUBLE)
+
+def dbf_type_to_DBR(dbftype):
+    if dbftype>=0 and dbftype <= LAST_TYPE:
+        return dbftype
+    else:
+        return -1
+
+def dbf_type_to_DBR_STS(dbftype):
+    if dbftype>=0 and dbftype <= LAST_TYPE:
+        return dbftype + LAST_TYPE+1
+    else:
+        return -1
+
+def dbf_type_to_DBR_TIME(dbftype):
+    if dbftype>=0 and dbftype <= LAST_TYPE:
+        return dbftype + (LAST_TYPE+1)*2
+    else:
+        return -1
+def dbf_type_to_DBR_GR(dbftype):
+    if dbftype>=0 and dbftype <= LAST_TYPE:
+        return dbftype + (LAST_TYPE+1)*3
+    else:
+        return -1
+def dbf_type_to_DBR_CTRL(dbftype):
+    if dbftype>=0 and dbftype <= LAST_TYPE:
+        return dbftype + (LAST_TYPE+1)*4
+    else:
+        return -1

script/_Lib/epics/_ca_kek.py

@@ -0,0 +1,545 @@
+#!/usr/bin/env python
+## @package ca: EPICS-CA interface module for Python.
+"""CA modlue : EPICS-CA interface module for Python.
+This module provide a  version of EPICS-CA and Python interface.
+It users C module _ca. _ca module basically maps C-API in EPICS ca library into python. Interface between ca.py and _ca module is  subject for change. You should not depend on it. API in ca.py will be preserved in future releases as much as possible.
+Author: Noboru Yamamoto, KEK, JAPAN. -2007.
+$Revision: 1.1 $
+"""
+from __future__ import print_function
+__version__ = "$Revision: 1.1 $"
+# $Source: /cvs/G/EPICS/extensions/src/PythonCA/src/_ca_kek.py,v $
+#
+try:
+    import signal
+except:
+    print("signal module is not avaialble")
+    
+import time,thread,gc,sys,atexit
+from exceptions import ValueError
+
+# autGIL is not compatible with Tkinter and wx. So code was removed
+
+# force thread module to call PyEval_InitThread in it.
+__foo_lock=thread.allocate_lock()
+def __foo():
+    """
+    test function foo
+
+    This function is used to ensure thread module is initialized before
+    loading _ca module.
+    """
+    global __foo_lock
+    __foo_lock.release()
+    thread.exit_thread()
+# See Python/Include/ceval.h
+__foo_lock.acquire()
+thread.start_new_thread(__foo,()) # __foo release lock
+__foo_lock.acquire() # make sure threading is activated
+
+import _ca
+# version from _ca314.cpp
+version=_ca.version
+revision=_ca.release
+
+# some constants for EPICS channel Access library
+from cadefs import *
+from caError import *
+
+#export pend_xxx routines for global operation
+pendio =_ca.pendio
+pend_io=_ca.pendio
+pend_event=_ca.pend_event
+poll=_ca.poll
+poll_event=_ca.poll
+flush_io=_ca.flush
+flush=_ca.flush
+test_io=_ca.test_io # test_io retunrs 42 for IODONE , 43 for IOINPROGRESS
+add_fd_registration=_ca.add_fd_registration
+
+#Error Object
+error=_ca.error
+shutdown=_ca.__ca_task_exit
+
+#private dictionary for Get/Put functions
+
+__ca_dict={}
+__ca_dict_lock=thread.allocate_lock()
+_channel__debug=False
+
+class channel:
+    """
+    a channel object for EPICS Channel Access.
+
+    It does not have direct connection
+    to channel object in C-library for EPICS Channel Access. 
+    for creation just supply channel name to connect
+    """
+    dbr_types=(
+        DBR_NATIVE, # default type
+        DBR_STRING, DBR_CHAR, DBR_FLOAT,
+        DBR_SHORT, #/* same as DBR_INT */
+        DBR_ENUM, DBR_LONG, DBR_DOUBLE,
+        DBR_TIME_STRING, DBR_TIME_CHAR, DBR_TIME_FLOAT,
+        DBR_TIME_SHORT, #:/* same as DBR_TIME_INT */
+        DBR_TIME_ENUM, DBR_TIME_LONG, DBR_TIME_DOUBLE,
+        DBR_CTRL_CHAR, DBR_CTRL_LONG,
+        DBR_CTRL_ENUM, DBR_CTRL_DOUBLE
+        )
+
+    def __init__(self, name, cb=None,noflush=None):
+        if (not cb) : cb=self.update_info
+        if name == "":
+            raise ValueError(name)
+        self.name=name
+        self.field_type = None
+        self.element_count = None
+        self.puser = None
+        self.conn_state = -1
+        self.hostname = None
+        self.raccess = None
+        self.waccess = None
+        self.sevr=None
+        self.ts=None
+        self.status=None
+        self.evid=[]
+        self.autoEvid=None
+        self.__callbacks={}
+        self.cbstate=None
+        self.updated=False
+        self.val=None
+        self.chid=_ca.search(name,cb)
+        if not noflush:
+            self.flush()
+        
+    def clear(self):
+        if self.chid:
+            self.clear_monitor()
+            self.flush()
+            _ca.clear(self.chid)
+            self.flush()
+        self.chid=None
+ 
+    def __del__(self):
+        self.clear()
+
+    def wait_conn(self, wait=20, dt=0.05):
+        n=0
+        self.pend_event(dt)
+        self.update_info()
+        self.poll()
+        while (not self.isConnected()):
+            self.update_info()
+            self.pend_event(dt)
+            n=n+1
+            if (n > wait ) :
+                raise  ECA_BADCHID("%s %d"%(self.name,n))
+                return -1
+        
+    def get(self,cb=None,Type=DBR_NATIVE, count=0, type=DBR_NATIVE, type_=DBR_NATIVE):
+        try:
+            if not self.isConnected():
+                raise ECA_BADCHID(self.name)
+        except:
+            raise ECA_BADCHID(self.name)
+        if (Type == DBR_NATIVE):
+            if not(type == DBR_NATIVE):
+                Type=type
+            elif not(type_ == DBR_NATIVE):
+                Type=type_
+        rType=max(Type,type,type_)
+        if rType not in self.dbr_types:
+            raise TypeError(rType)
+        if not cb: cb=self.update_val
+
+        self.cbstate=None
+        self.updated=False
+        try:
+            _ca.get(self.chid, cb, Type, count)
+        finally:
+            pass
+        
+    def put(self,*val,**kw):
+        """
+        channel.put(valu) will put scalar value to channel. You may need to call channel.flush()
+        
+        """
+        if( val == ()):
+            print("No value(s) to put")
+        else:
+            if kw.has_key('cb'):
+                cb=kw['cb']
+            else:
+                cb=None
+            #self.__lock.acquire()
+            try:
+                _ca.put(self.chid, val, self.val, cb, DBR_NATIVE)
+            finally:
+                #self.__lock.release()
+                pass
+
+    def put_and_notify(self,*val,**kw):
+        if kw.has_key('cb'):
+            cb=kw['cb']
+        else:
+            cb=None # ca_put_array_callback does not return value.
+        if( val == ()):
+            print("No value(s) to put")
+        else:
+            #self.__lock.acquire()
+            try:
+                _ca.put(self.chid,val,self.val,cb, DBR_NATIVE)
+            finally:
+                #self.__lock.release()
+                pass
+            
+    def monitor(self,callback=None,count=0,evmask=(DBE_VALUE|DBE_ALARM)):
+        if(not callback):
+            raise PyCa_NoCallback
+        if (self.conn_state != 2):
+            #print self.name,self.get_info()
+            raise ECA_BADCHID(self.name)
+
+        self.update_info()
+        if (self.field_type == DBR_NATIVE):
+            #print self.name,self.get_info()
+            raise ECA_BADTYPE(self.name)
+        self.evid.append(_ca.monitor(self.chid,callback,count,evmask))
+        self.__callbacks[self.evid[-1]]=callback
+        return self.evid[-1]
+    
+    def __clear_event(self,evid):
+        if(_channel__debug): print("clearing evid:",evid)
+        _ca.clear_monitor(evid)
+        del self.__callbacks[evid]
+         
+    def clear_monitor(self,evid=None):
+        if(evid):
+            if ( evid in self.evid):
+                self.__clear_event(evid)
+                i=self.evid.index(evid)
+                del self.evid[i]
+                i=self.evid.index(evid)
+                del self.evid[i]
+        else:
+            for evid in self.evid:
+                self.__clear_event(evid) 
+            self.evid=[]
+
+    def autoUpdate(self):
+        if self.autoEvid == None:
+            self.monitor(self.update_val)
+            self.autoEvid=self.evid[-1]
+        self.flush()
+        
+    def clearAutoUpdate(self):
+        if self.autoEvid is not None:
+            self.clear_monitor(self.autoEvid)
+            self.autoEvid=None
+        self.flush()
+        
+    def pendio(self,tmo=0.001):
+        v=_ca.pendio(float(tmo))
+        return v
+
+    def pend_io(self,tmo=0.001):
+        v=_ca.pendio(float(tmo))
+        return v
+
+    def pend_event(self,tmo=0.001):
+        v=_ca.pend_event(float(tmo))
+        return v
+
+    def poll(self):
+        _ca.poll()
+            
+    def flush(self,wait=0.001):
+        v=_ca.flush(wait)
+        return v
+
+    def update_val(self,valstat=None):
+        if valstat ==None:
+            raise caError("No value")
+        #self.__lock.acquire()
+        try:
+            self.val=valstat[0]
+            self.sevr=valstat[1]
+            self.status=valstat[2]
+            self.cbstate=1
+            try:
+                self.ts=valstat[3]
+            except:
+                pass
+            try:
+                self.ctrl=valstat[4]
+            except:
+                pass
+        finally:
+            #self.__lock.release()
+            self.updated=True
+            pass
+
+    def clear_cbstate(self):
+        #self.__lock.acquire()
+        self.cbstate=None
+        #self.__lock.release()
+        
+    def state(self):
+        self.get_info()
+        return (self.conn_state - ch_state.cs_conn)
+
+    def isNeverConnected(self):
+        self.get_info()
+        return (self.conn_state == ch_state.cs_never_conn)
+
+    def isConnected(self):
+        self.get_info()
+        return (self.conn_state == ch_state.cs_conn)
+
+    def isPreviouslyConnected(self):
+        self.get_info()
+        return (self.conn_state == ch_state.cs_prev_conn)
+
+    def isDisonnected(self):
+        self.get_info()
+        return (self.conn_state == ch_state.cs_prev_conn)
+    
+    def isClosed(self):
+        self.get_info()
+        return (self.conn_state == ch_state.cs_closed)
+    
+    def get_info(self):
+        """
+        update channel status information. return channel staus as a tuple.
+        """
+        #self.__lock.acquire()
+        try:
+            info=(self.field_type, self.element_count, self.puser,
+                  self.conn_state, self.hostname, self.raccess,
+                  self.waccess) = _ca.ch_info(self.chid)
+        finally:
+            #self.__lock.release()
+            pass
+        return info
+
+    def update_info(self):
+        """
+        Just update channel status information. No return value. 
+        """
+        self.get_info()
+
+    def fileno(self):
+        """returns socket number used to connect.Scoket id is shared by
+        channels which are connected to the same IOC.
+        It became obsolete in EPICS 3.14 version of Python-CA.
+        You need to use fd_register function. But you may not need it anyway in multi-thread environment.
+        """
+        return _ca.fileno(self.chid)
+
+# convenient functions
+# you need to call Clear() function before stopping Python, otherwise it cause coredump. 2009/2/11 NY
+def __Ch(name,tmo=0.01):
+    if (type(name) == type("")):
+        if (__ca_dict.has_key(name)):
+            ch=__ca_dict[name]
+        else:
+            try:
+                ch=channel(name)
+                ch.wait_conn()
+            except:
+                raise ECA_BADCHID(name)
+            tmo=20*tmo
+            __ca_dict_lock.acquire()
+            try:
+                __ca_dict[name]=ch
+            finally:
+                __ca_dict_lock.release()
+        if( ch.state() != 0):
+            ch.wait_conn(10)
+        return ch
+    else:
+        raise ECA_BADTYPE(name)
+
+def Info(name = "",tmo=0.01):
+    """
+    returns a tuple as channel information.
+    tuple format=(field_type, element_count, puser argument,
+                  connection_status, hostname:port,
+                  read access mode, write access mode)
+    """
+    ch=__Ch(name,tmo=tmo)
+    return ch.get_info()
+
+def ClearAll():
+    for name in __ca_dict.keys():
+        Clear(name)
+
+# __ca_dict should be cleared before Stopping Python
+atexit.register(ClearAll)
+
+def Clear(name= ""):
+    if (type(name) == type("")):
+        __ca_dict_lock.acquire()
+        try:
+            if (__ca_dict.has_key(name)):
+                ch=__ca_dict[name]
+                del __ca_dict[name]
+                ch.clear()
+                del ch
+            else:
+                __ca_dict_lock.release()
+                raise ECA_BADTYPE(name)
+        finally:
+            __ca_dict_lock.release()
+    else:
+        raise ECA_BADTYPE(name)
+
+def Get(name="",count=0,Type=DBR_NATIVE,tmo=0.01,maxtmo=3):
+    """
+    Get value from a channel "name".
+    """
+    ch=__Ch(name,tmo)
+    def CB(vals,ch=ch):
+        ch.update_val(vals)
+    ch.get(cb=CB,Type=Type,count=count)
+    ch.flush()
+    while not ch.updated:
+        time.sleep(tmo)
+        maxtmo -=tmo
+        if maxtmo <=0:
+            raise caError("No get response")
+    return ch.val
+
+def Put_and_Notify(name,val=None,cb=None):
+    """
+    Convenient function:Put_and_Notify 
+
+    calls put_and_notify with callback. 
+    If callback is None, then just put data to a channel.
+    """
+    ch=__Ch(name,tmo=0.1)
+    ch.put_and_notify(val,cb=cb)
+    ch.flush()
+    return ch.val
+
+# define synonym
+Put=Put_and_Notify
+
+def Put_and_Notify_Array(name,val,cb=None):
+    """
+    put array test version : not tested with string arrays yet
+    2007.8.30 T. Matsumoto
+    """
+    ch=__Ch(name,tmo=0.1)
+    apply(ch.put_and_notify,val,dict(cb=cb))
+    ch.flush()
+    return ch.val
+
+# define synonym
+Put_Array=Put_and_Notify_Array
+                
+def Monitor(name,cb=None,evmask=(DBE_VALUE|DBE_ALARM)):
+    ch=__Ch(name,tmo=0.1)
+    if not cb:
+        def myCB(val,ch=ch):
+            print(ch.name,":",val[0],val[1],val[2],TS2Ascii(val[3]))
+    else:
+        def myCB(val, ch=ch, cb=cb):
+            cb(ch,val)
+    ch.clear_monitor()
+    evid=ch.monitor(myCB,evmask=evmask)
+    ch.flush()
+    return evid
+
+def ClearMonitor(name,evid=None):
+    ch=__Ch(name,tmo=0.1)
+    try:
+        ch.clear_monitor(evid)
+        return
+    except:
+        raise ECA_BADCHID(name)
+#
+def isIODone():
+    if _ca.test_io()== 42:
+        return 1
+    else:
+        return 0
+#
+# syncronus group class
+# Author: N.Yamamoto 
+# Date: May 27.1999 (first version)
+#
+
+class SyncGroup:
+    def __init__(self):
+        self.gid=_ca.sg_create()
+        self.chs={}
+
+    def add(self, chs):
+        try:
+            for ch in chs:
+                if(not self.chs.has_key(ch)):
+                    self.chs[ch]=0
+        except:
+            if(not self.chs.has_key(chs)):
+                self.chs[chs]=0
+
+    def test(self):
+        return _ca.sg_test(self.gid)
+
+    def reset(self):
+        return _ca.sg_reset(self.gid)
+
+    def wait(self,tmo=1.0):
+        return _ca.sg_block(self.gid,float(tmo))
+
+    def put(self,ch,*value,**kw):
+        if kw.has_key("Type"):
+            Type=kw["Type"]
+        else:
+            Type=DBR_NATIVE
+        if self.chs.has_key(ch):
+            self.chs[ch]=_ca.sg_put(self.gid, ch.chid,
+                        self.chs[ch], value , Type)
+
+    def get(self,ch):
+        if self.chs.has_key(ch):
+            self.chs[ch]=_ca.sg_get(self.gid,
+                   ch.chid, self.chs[ch])
+        else:
+            pass
+
+    def convert(self,ch):
+        if self.chs.has_key(ch):
+            val=_ca.ca_convert(ch.chid, self.chs[ch])
+            ch.update_val(val[0])
+            
+    def GetAll(self,tmo=1.0):
+        for ch in self.chs.keys():
+            self.chs[ch]=_ca.sg_get(self.gid,
+                   ch.chid, self.chs[ch])
+        st=_ca.sg_block(self.gid,tmo)
+        if st == 0:
+            for ch in self.chs.keys():
+                val=_ca.ca_convert(ch.chid,self.chs[ch])
+                ch.update_val(val[0])
+        else:
+            raise Exception("CA_SG time out")
+
+# TimeStamp utilities
+# time.gmtime(631152000.0)=(1990, 1, 1, 0, 0, 0, 0, 1, 0)
+#
+__EPICS_TS_EPOCH=631152000.0
+
+def TS2Ascii(ts):
+    import math
+    tstr=time.ctime(ts+__EPICS_TS_EPOCH)
+    nsstr=".%03d"%(math.modf(ts + __EPICS_TS_EPOCH)[0]*1000)
+    return tstr[:-5]+nsstr+tstr[-5:]
+
+def TS2time(ts):
+    return time.localtime(ts+__EPICS_TS_EPOCH)
+
+def TS2UTC(ts):
+    return (ts+__EPICS_TS_EPOCH)
+

script/_Lib/epics/ca.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+## @package ca: EPICS-CA interface module for Python.
+"""CA modlue : EPICS-CA interface module for Python.
+This module provide a  version of EPICS-CA and Python interface.
+It users C module _ca. _ca module basically maps C-API in EPICS ca library into python. Interface between ca.py and _ca module is  subject for change. You should not depend on it. API in ca.py will be preserved in future releases as much as possible.
+Author: Noboru Yamamoto, KEK, JAPAN. -2007.
+$Revision: 1.4 $
+"""
+
+__version__ = "$Revision: 1.4 $"
+# $Source: /cvs/G/EPICS/extensions/src/PythonCA/src/ca.py,v $
+
+import time,gc,sys,atexit
+if sys.hexversion >= 0x03000000:
+  import _thread as thread
+else:
+  import thread
+
+# autGIL is not compatible with Tkinter and wx. So code was removed
+
+# force thread module to call PyEval_InitThread in it.
+__foo_lock=thread.allocate_lock()
+def __foo():
+    """
+    test function foo
+
+    This function is used to ensure thread module is initialized before
+    loading _ca module.
+    """
+    global __foo_lock
+    __foo_lock.release()
+    thread.exit_thread()
+
+# See Python/Include/ceval.h
+__foo_lock.acquire()
+thread.start_new_thread(__foo,()) # __foo release lock
+__foo_lock.acquire() # make sure threading is activated
+
+import _ca
+# version from _ca314.cpp
+version=_ca.version
+revision=_ca.release
+
+# some constants for EPICS channel Access library
+from cadefs import *
+from caError import *
+
+# for FNAL version you need to provide _ca_fnal.py and import every thin from them
+from _ca_fnal import *

script/_Lib/epics/caError.py

@@ -0,0 +1,461 @@
+import sys
+if sys.hexversion >= 0x03000000:
+    intern = sys.intern
+
+from ca import _ca
+class caError(_ca.error):
+  """ EPICS ca.py Errors"""
+  pass
+
+__caErrorMsg=(
+"Normal successful completion",
+"Maximum simultaneous IOC connections exceeded",
+"Unknown internet host",
+"Unknown internet service",
+"Unable to allocate a new socket",
+"Unable to connect to internet host or service",
+"Unable to allocate additional dynamic memory",
+"Unknown IO channel",
+"Record field specified inappropriate for channel specified",
+"The requested data transfer is greater than available memory or EPICS_CA_MAX_ARRAY_BYTES",
+"User specified timeout on IO operation expired",
+"Sorry, that feature is planned but not supported at this time",
+"The supplied string is unusually large",
+"The request was ignored because the specified channel is disconnected",
+"The data type specifed is invalid",
+"Remote Channel not found",
+"Unable to locate all user specified channels",
+"Channel Access Internal Failure",
+"The requested local DB operation failed",
+"Channel read request failed",
+"Channel write request failed",
+"Channel subscription request failed",
+"Invalid element count requested",
+"Invalid string",
+"Virtual circuit disconnect",
+"Identical process variable names on multiple servers",
+"Request inappropriate within subscription (monitor) update callback",
+"Database value get for that channel failed during channel search",
+"Unable to initialize without the vxWorks VX_FP_TASK task option set",
+"Event queue overflow has prevented first pass event after event add",
+"Bad event subscription (monitor) identifier",
+"Remote channel has new network address",
+"New or resumed network connection",
+"Specified task isnt a member of a CA context",
+"Attempt to use defunct CA feature failed",
+"The supplied string is empty",
+"Unable to spawn the CA repeater thread- auto reconnect will fail",
+"No channel id match for search reply- search reply ignored",
+"Reseting dead connection- will try to reconnect",
+"Server (IOC) has fallen behind or is not responding- still waiting",
+"No internet interface with broadcast available",
+"Invalid event selection mask",
+"IO operations have completed",
+"IO operations are in progress",
+"Invalid synchronous group identifier",
+"Put callback timed out",
+"Read access denied",
+"Write access denied",
+"Requested feature is no longer supported",
+"Empty PV search address list",
+"No reasonable data conversion between client and server types",
+"Invalid channel identifier",
+"Invalid function pointer",
+"Thread is already attached to a client context",
+"Not supported by attached service",
+"User destroyed channel",
+"Invalid channel priority",
+"Preemptive callback not enabled - additional threads may not join context",
+"Client's protocol revision does not support transfers exceeding 16k bytes",
+"Virtual circuit connection sequence aborted",
+"Virtual circuit unresponsive",
+)
+_caErrorMsg=map(intern,__caErrorMsg)
+if sys.hexversion >= 0x03000000:
+    _caErrorMsg = list(_caErrorMsg)
+
+ErrCode2Class={}
+class PyCa_NoCallback(caError):
+    __doc__="Null callback routine"
+CA_M_MSG_NO    = 0x0000FFF8
+CA_M_SEVERITY  = 0x00000007
+CA_M_LEVEL     = 0x00000003
+CA_M_SUCCESS   = 0x00000001
+CA_M_ERROR     = 0x00000002
+CA_M_SEVERE    = 0x00000004
+CA_S_MSG_NO= 0x0D
+CA_S_SEVERITY=0x03
+CA_V_MSG_NO=     0x03
+CA_V_SEVERITY=   0x00
+CA_V_SUCCESS=    0x00
+
+def CA_EXTRACT_MSG_NO(code): return ( ( (code) & CA_M_MSG_NO )  >> CA_V_MSG_NO )
+def CA_EXTRACT_SEVERITY(code): return ( ( (code) & CA_M_SEVERITY )    >> CA_V_SEVERITY) 
+def CA_EXTRACT_SUCCESS(code): ( ( (code) & CA_M_SUCCESS )     >> CA_V_SUCCESS )
+
+class ECA_NORMAL(caError):
+    __doc__=_caErrorMsg[0]
+    __errcode__=1
+
+ErrCode2Class[1]=ECA_NORMAL
+
+class ECA_MAXIOC(caError):
+    __doc__=_caErrorMsg[1]
+    __errcode__=10
+
+ErrCode2Class[10]=ECA_MAXIOC
+
+class ECA_UKNHOST(caError):
+    __doc__=_caErrorMsg[2]
+    __errcode__=18
+
+ErrCode2Class[18]=ECA_UKNHOST
+
+class ECA_UKNSERV(caError):
+    __doc__=_caErrorMsg[3]
+    __errcode__=26
+
+ErrCode2Class[26]=ECA_UKNSERV
+
+class ECA_SOCK(caError):
+    __doc__=_caErrorMsg[4]
+    __errcode__=34
+
+ErrCode2Class[34]=ECA_SOCK
+
+class ECA_CONN(caError):
+    __doc__=_caErrorMsg[5]
+    __errcode__=40
+
+ErrCode2Class[40]=ECA_CONN
+
+class ECA_ALLOCMEM(caError):
+    __doc__=_caErrorMsg[6]
+    __errcode__=48
+
+ErrCode2Class[48]=ECA_ALLOCMEM
+
+class ECA_UKNCHAN(caError):
+    __doc__=_caErrorMsg[7]
+    __errcode__=56
+
+ErrCode2Class[56]=ECA_UKNCHAN
+
+class ECA_UKNFIELD(caError):
+    __doc__=_caErrorMsg[8]
+    __errcode__=64
+
+ErrCode2Class[64]=ECA_UKNFIELD
+
+class ECA_TOLARGE(caError):
+    __doc__=_caErrorMsg[9]
+    __errcode__=72
+
+ErrCode2Class[72]=ECA_TOLARGE
+
+class ECA_TIMEOUT(caError):
+    __doc__=_caErrorMsg[10]
+    __errcode__=80
+
+ErrCode2Class[80]=ECA_TIMEOUT
+
+class ECA_NOSUPPORT(caError):
+    __doc__=_caErrorMsg[11]
+    __errcode__=88
+
+ErrCode2Class[88]=ECA_NOSUPPORT
+
+class ECA_STRTOBIG(caError):
+    __doc__=_caErrorMsg[12]
+    __errcode__=96
+
+ErrCode2Class[96]=ECA_STRTOBIG
+
+class ECA_DISCONNCHID(caError):
+    __doc__=_caErrorMsg[13]
+    __errcode__=106
+
+ErrCode2Class[106]=ECA_DISCONNCHID
+
+class ECA_BADTYPE(caError):
+    __doc__=_caErrorMsg[14]
+    __errcode__=114
+
+ErrCode2Class[114]=ECA_BADTYPE
+
+class ECA_CHIDNOTFND(caError):
+    __doc__=_caErrorMsg[15]
+    __errcode__=123
+
+ErrCode2Class[123]=ECA_CHIDNOTFND
+
+class ECA_CHIDRETRY(caError):
+    __doc__=_caErrorMsg[16]
+    __errcode__=131
+
+ErrCode2Class[131]=ECA_CHIDRETRY
+
+class ECA_INTERNAL(caError):
+    __doc__=_caErrorMsg[17]
+    __errcode__=142
+
+ErrCode2Class[142]=ECA_INTERNAL
+
+class ECA_DBLCLFAIL(caError):
+    __doc__=_caErrorMsg[18]
+    __errcode__=144
+
+ErrCode2Class[144]=ECA_DBLCLFAIL
+
+class ECA_GETFAIL(caError):
+    __doc__=_caErrorMsg[19]
+    __errcode__=152
+
+ErrCode2Class[152]=ECA_GETFAIL
+
+class ECA_PUTFAIL(caError):
+    __doc__=_caErrorMsg[20]
+    __errcode__=160
+
+ErrCode2Class[160]=ECA_PUTFAIL
+
+class ECA_ADDFAIL(caError):
+    __doc__=_caErrorMsg[21]
+    __errcode__=168
+
+ErrCode2Class[168]=ECA_ADDFAIL
+
+class ECA_BADCOUNT(caError):
+    __doc__=_caErrorMsg[22]
+    __errcode__=176
+
+ErrCode2Class[176]=ECA_BADCOUNT
+
+class ECA_BADSTR(caError):
+    __doc__=_caErrorMsg[23]
+    __errcode__=186
+
+ErrCode2Class[186]=ECA_BADSTR
+
+class ECA_DISCONN(caError):
+    __doc__=_caErrorMsg[24]
+    __errcode__=192
+
+ErrCode2Class[192]=ECA_DISCONN
+
+class ECA_DBLCHNL(caError):
+    __doc__=_caErrorMsg[25]
+    __errcode__=200
+
+ErrCode2Class[200]=ECA_DBLCHNL
+
+class ECA_EVDISALLOW(caError):
+    __doc__=_caErrorMsg[26]
+    __errcode__=210
+
+ErrCode2Class[210]=ECA_EVDISALLOW
+
+class ECA_BUILDGET(caError):
+    __doc__=_caErrorMsg[27]
+    __errcode__=216
+
+ErrCode2Class[216]=ECA_BUILDGET
+
+class ECA_NEEDSFP(caError):
+    __doc__=_caErrorMsg[28]
+    __errcode__=224
+
+ErrCode2Class[224]=ECA_NEEDSFP
+
+class ECA_OVEVFAIL(caError):
+    __doc__=_caErrorMsg[29]
+    __errcode__=232
+
+ErrCode2Class[232]=ECA_OVEVFAIL
+
+class ECA_BADMONID(caError):
+    __doc__=_caErrorMsg[30]
+    __errcode__=242
+
+ErrCode2Class[242]=ECA_BADMONID
+
+class ECA_NEWADDR(caError):
+    __doc__=_caErrorMsg[31]
+    __errcode__=248
+
+ErrCode2Class[248]=ECA_NEWADDR
+
+class ECA_NEWCONN(caError):
+    __doc__=_caErrorMsg[32]
+    __errcode__=259
+
+ErrCode2Class[259]=ECA_NEWCONN
+
+class ECA_NOCACTX(caError):
+    __doc__=_caErrorMsg[33]
+    __errcode__=264
+
+ErrCode2Class[264]=ECA_NOCACTX
+
+class ECA_DEFUNCT(caError):
+    __doc__=_caErrorMsg[34]
+    __errcode__=278
+
+ErrCode2Class[278]=ECA_DEFUNCT
+
+class ECA_EMPTYSTR(caError):
+    __doc__=_caErrorMsg[35]
+    __errcode__=280
+
+ErrCode2Class[280]=ECA_EMPTYSTR
+
+class ECA_NOREPEATER(caError):
+    __doc__=_caErrorMsg[36]
+    __errcode__=288
+
+ErrCode2Class[288]=ECA_NOREPEATER
+
+class ECA_NOCHANMSG(caError):
+    __doc__=_caErrorMsg[37]
+    __errcode__=296
+
+ErrCode2Class[296]=ECA_NOCHANMSG
+
+class ECA_DLCKREST(caError):
+    __doc__=_caErrorMsg[38]
+    __errcode__=304
+
+ErrCode2Class[304]=ECA_DLCKREST
+
+class ECA_SERVBEHIND(caError):
+    __doc__=_caErrorMsg[39]
+    __errcode__=312
+
+ErrCode2Class[312]=ECA_SERVBEHIND
+
+class ECA_NOCAST(caError):
+    __doc__=_caErrorMsg[40]
+    __errcode__=320
+
+ErrCode2Class[320]=ECA_NOCAST
+
+class ECA_BADMASK(caError):
+    __doc__=_caErrorMsg[41]
+    __errcode__=330
+
+ErrCode2Class[330]=ECA_BADMASK
+
+class ECA_IODONE(caError):
+    __doc__=_caErrorMsg[42]
+    __errcode__=339
+
+ErrCode2Class[339]=ECA_IODONE
+
+class ECA_IOINPROGRESS(caError):
+    __doc__=_caErrorMsg[43]
+    __errcode__=347
+
+ErrCode2Class[347]=ECA_IOINPROGRESS
+
+class ECA_BADSYNCGRP(caError):
+    __doc__=_caErrorMsg[44]
+    __errcode__=354
+
+ErrCode2Class[354]=ECA_BADSYNCGRP
+
+class ECA_PUTCBINPROG(caError):
+    __doc__=_caErrorMsg[45]
+    __errcode__=362
+
+ErrCode2Class[362]=ECA_PUTCBINPROG
+
+class ECA_NORDACCESS(caError):
+    __doc__=_caErrorMsg[46]
+    __errcode__=368
+
+ErrCode2Class[368]=ECA_NORDACCESS
+
+class ECA_NOWTACCESS(caError):
+    __doc__=_caErrorMsg[47]
+    __errcode__=376
+
+ErrCode2Class[376]=ECA_NOWTACCESS
+
+class ECA_ANACHRONISM(caError):
+    __doc__=_caErrorMsg[48]
+    __errcode__=386
+
+ErrCode2Class[386]=ECA_ANACHRONISM
+
+class ECA_NOSEARCHADDR(caError):
+    __doc__=_caErrorMsg[49]
+    __errcode__=392
+
+ErrCode2Class[392]=ECA_NOSEARCHADDR
+
+class ECA_NOCONVERT(caError):
+    __doc__=_caErrorMsg[50]
+    __errcode__=400
+
+ErrCode2Class[400]=ECA_NOCONVERT
+
+class ECA_BADCHID(caError):
+    __doc__=_caErrorMsg[51]
+    __errcode__=410
+
+ErrCode2Class[410]=ECA_BADCHID
+
+class ECA_BADFUNCPTR(caError):
+    __doc__=_caErrorMsg[52]
+    __errcode__=418
+
+ErrCode2Class[418]=ECA_BADFUNCPTR
+
+class ECA_ISATTACHED(caError):
+    __doc__=_caErrorMsg[53]
+    __errcode__=424
+
+ErrCode2Class[424]=ECA_ISATTACHED
+
+class ECA_UNAVAILINSERV(caError):
+    __doc__=_caErrorMsg[54]
+    __errcode__=432
+
+ErrCode2Class[432]=ECA_UNAVAILINSERV
+
+class ECA_CHANDESTROY(caError):
+    __doc__=_caErrorMsg[55]
+    __errcode__=440
+
+ErrCode2Class[440]=ECA_CHANDESTROY
+
+class ECA_BADPRIORITY(caError):
+    __doc__=_caErrorMsg[56]
+    __errcode__=450
+
+ErrCode2Class[450]=ECA_BADPRIORITY
+
+class ECA_NOTTHREADED(caError):
+    __doc__=_caErrorMsg[57]
+    __errcode__=458
+
+ErrCode2Class[458]=ECA_NOTTHREADED
+
+class ECA_16KARRAYCLIENT(caError):
+    __doc__=_caErrorMsg[58]
+    __errcode__=464
+
+ErrCode2Class[464]=ECA_16KARRAYCLIENT
+
+class ECA_CONNSEQTMO(caError):
+    __doc__=_caErrorMsg[59]
+    __errcode__=472
+
+ErrCode2Class[472]=ECA_CONNSEQTMO
+
+class ECA_UNRESPTMO(caError):
+    __doc__=_caErrorMsg[60]
+    __errcode__=480
+
+ErrCode2Class[480]=ECA_UNRESPTMO
+

script/_Lib/epics/ca_util.py

@@ -0,0 +1,647 @@
+# ca_util.py - a thin wrapper around CaChannel
+# Tim Mooney 12/05/2008
+#
+# Modified by Xiaoqiang Wang to be Python 3 compatible.
+
+"""ca_util.py is a wrapper around CaChannel that allows the caller to write,
+e.g.,
+    caget("xxx:m1")
+instead of having to write
+    m1 = CaChannel()
+    m1.searchw("xxx:m1")
+    m1.getw()
+Also, ca_util defends against null PV names and some effects of short-term
+CA disconnections, and it can verify that caput*() operations succeeded.
+"""
+
+version = "2.0"
+
+import ca
+import CaChannel
+import time
+import sys
+
+# DBR types
+# ca.DBR_STRING = 0
+# ca.DBR_SHORT = 1 
+# ca.DBR_INT = 1 
+# ca.DBR_FLOAT = 2
+# ca.DBR_ENUM = 3
+# ca.DBR_CHAR = 4
+# ca.DBR_LONG = 5
+# ca.DBR_DOUBLE = 6
+
+# If caller imported CaChannel using "from CaChannel import *", then the
+# class CaChannel will have the same name as the module CaChannel, and
+# we won't be able to see the module attribute, 'CaChannel.__file__'.
+def getCaChannelFileName():
+	""" For internal ca_util use"""
+	return CaChannel.__file__
+
+#######################################################################
+# Human readable exception description
+#	try:
+#		x = x + 1
+#	except:
+#		print formatExceptionInfo()
+import sys
+import traceback
+def formatExceptionInfo(maxTBlevel=5):
+	cla, exc, trbk = sys.exc_info()
+	excName = cla.__name__
+	try:
+		excArgs = exc.__dict__["args"]
+	except KeyError:
+		excArgs = "<no args>"
+	excTb = traceback.format_tb(trbk, maxTBlevel)
+	return (excName, excArgs, excTb)
+
+#######################################################################
+# channel-access connection states
+ca_states = {}
+# ...from cadef.h:
+ca_states[ca.cs_never_conn] = "never connected"
+ca_states[ca.cs_prev_conn] = "previously connected"
+ca_states[ca.cs_conn] = "connected"
+ca_states[ca.cs_closed] = "closed"
+ca_states[ca.cs_never_search] = "never searched"
+
+
+
+#######################################################################
+# default settings for ca_util
+defaultTimeout = None		# 'None' means use CaChannel's timeout
+defaultRetries = 3
+readCheckTolerance = None	# 'None" means don't check
+
+def set_ca_util_defaults(timeout=None, retries=None, read_check_tolerance=None):
+	"""
+	usage: old = set_ca_util_defaults(timeout=None, retries=None,
+	             read_check_tolerance=None)
+	alternate: set_ca_util_defaults(defaultsList), where defaultsList is like
+	the list returned by get_ca_util_defaults()
+	Setting an argument to the string "NONE" disables it.
+	Returns the list of previous default values:
+	    [defaultTimeout, defaultRetries, readCheckTolerance]
+	"""
+	global defaultTimeout, defaultRetries, readCheckTolerance
+	old = [defaultTimeout, defaultRetries, readCheckTolerance]
+	if type(timeout) == type([]):
+		argList = timeout
+		timeout = argList[0]
+		retries = argList[1]
+		read_check_tolerance = argList[2]
+	if (timeout!=None) : defaultTimeout = timeout
+	if (retries!=None) : defaultRetries = retries
+	if (read_check_tolerance!=None) : readCheckTolerance = read_check_tolerance
+	return old
+
+def get_ca_util_defaults():
+	"""
+	usage: myList = get_ca_util_defaults()
+	myList is set to [defaultTimeout, defaultRetries, readCheckTolerance]
+	"""
+	global defaultTimeout, defaultRetries, readCheckTolerance
+	return [defaultTimeout, defaultRetries, readCheckTolerance]
+
+def set_ca_util_default_timeout(timeout=None):
+	"""
+	usage: old = set_ca_util_default_timeout(timeout=None)
+	If timeout == "NONE", then ca_util doesn't specify any timeout in
+	calls to underlying software.
+	Returns previous default timeout.
+	"""
+	global defaultTimeout
+	old = defaultTimeout
+	defaultTimeout = timeout
+	return old
+
+def get_ca_util_default_timeout():
+	global defaultTimeout
+	return defaultTimeout
+
+def set_ca_util_default_retries(retries=None):
+	"""
+	usage: old = set_ca_util_default_retries(retries=None)
+	If retries == "NONE", then ca_util doesn't do any retries.
+	Returns previous default retries.
+	"""
+	global defaultRetries
+	old = defaultRetries
+	defaultRetries = retries
+	return old
+
+def get_ca_util_default_retries():
+	global defaultRetries
+	return defaultRetries
+
+def set_ca_util_default_read_check_tolerance(read_check_tolerance=None):
+	"""
+	usage: old = set_ca_util_default_read_check_tolerance(read_check_tolerance=None)
+	If read_check_tolerance == "NONE", then ca_util doesn't compare the value
+	it reads to the value it wrote.
+	Returns previous default tolerance.
+	"""
+	global readCheckTolerance
+	old = readCheckTolerance
+	readCheckTolerance = read_check_tolerance
+	return old
+
+def get_ca_util_default_read_check_tolerance():
+	global readCheckTolerance
+	return readCheckTolerance
+
+
+#######################################################################
+# The dictionary, cadict, will be used to associate PV names with the
+# machinery required to talk to EPICS PV's.  If no entry is found (the
+# name hasn't been used yet in a ca call), then we create a new instance
+# of CaChannel, connect it to the PV, and put it in the dictionary.  We also
+# include a flag some of the ca_util routines can use to check if a callback
+# has occurred for this PV.
+
+class cadictEntry:
+	def __init__(self, channel):
+		self.channel = channel
+		self.callbackReceived = 0	# reserved for use by caputw()
+		self.field_type = channel.field_type()
+		self.element_count = channel.element_count()
+		#self.host_name = channel.host_name()
+
+cadict = {}
+
+#######################################################################
+ca_utilExceptionStrings = ["No name was provided.", "Readback disagrees with put value.",
+                           "PV is not connected."]
+EXCEPTION_NULL_NAME          = 0
+EXCEPTION_READBACK_DISAGREES = 1
+EXCEPTION_NOT_CONNECTED      = 2
+
+class ca_utilException(Exception):
+	def __init__(self, *args):
+		Exception.__init__(self, *args)
+		self.errorNumber = args[0]
+
+	def __int__(self):
+		return int(self.errorNumber)
+
+	def __str__(self):
+		return ca_utilExceptionStrings[self.errorNumber]
+
+
+#######################################################################
+def convertToType(type, value):
+	if type == ca.DBR_STRING:
+		return str(value)
+	elif type == ca.DBR_SHORT or type == ca.DBR_INT or type == ca.DBR_LONG:
+		try:
+			n = int(value)
+		except:
+			n = 0
+		return n
+	elif type == ca.DBR_FLOAT or type == ca.DBR_DOUBLE:
+		try:
+			n = float(value)
+		except:
+			n = 0.0
+		return n
+	elif type == ca.DBR_ENUM:
+		return value
+	elif type == ca.DBR_CHAR:
+		return value
+	else:
+		return value
+
+#######################################################################
+def checkName(name, timeout=None, retries=None):
+	"""
+	usage: checkName("xxx:m1.VAL", timeout=None, retries=None)
+	Intended for internal use by ca_util functions.
+	"""
+
+	global cadict, defaultTimeout, defaultRetries
+	if not name:
+		raise ca_utilException(EXCEPTION_NULL_NAME)
+
+	if ((timeout == None) and (defaultTimeout != None)): timeout = defaultTimeout
+	if (timeout == "NONE"): timeout = None
+
+	if ((retries == None) and (defaultRetries != None)): retries = defaultRetries
+	if ((retries == None) or (retries == "NONE")): retries = 0
+
+	tries = 0
+	while (name not in cadict) and (tries <= retries):
+		# Make a new entry in the PV-name dictionary
+		try:
+			channel = CaChannel.CaChannel()
+			if (timeout != None): channel.setTimeout(timeout)
+			channel.searchw(name)
+			cadict[name] = cadictEntry(channel)
+		except CaChannel.CaChannelException:
+			status = sys.exc_info()[1]
+			del channel
+			tries += 1
+
+	if (name not in cadict):
+		print("ca_util.checkName: Can't connect to '%s'" % name)
+		raise CaChannel.CaChannelException(status)
+
+#######################################################################
+def castate(name=None, timeout=None, retries=None):
+	"""usage: val = castate("xxx:m1.VAL", timeout=None, retries=None)
+	   Try to read a PV, to find out whether it's really connected, and
+	   whether caller is permitted to read and write it, without allowing
+	   any exceptions to be thrown at the caller.
+	"""
+
+	global cadict, defaultTimeout, defaultRetries
+
+	if not name: return "Null name has no state"
+
+	# The only reliable way to check the *current* state of a PV is to attempt to use it.
+	try:
+		val = caget(name, timeout=timeout, retries=retries)
+	except CaChannel.CaChannelException:
+		pass
+
+	try:
+		checkName(name, timeout=timeout)
+	except CaChannel.CaChannelException:
+		return "not connected"
+	except:
+		return "error"
+
+	try:
+		state = cadict[name].channel.state()
+	except CaChannel.CaChannelException:
+		return "not connected"
+	except:
+		return "error"
+	else:
+		try:
+			read_access = cadict[name].channel.read_access()
+			write_access = cadict[name].channel.write_access()
+			if state in ca_states:
+				s = ca_states[state]
+			else:
+				s = "unknown state"
+			if not read_access: s += ", noread"
+			if not write_access: s += ", nowrite"
+			return s
+		except:
+			return "error"
+
+#######################################################################
+def caget(name, timeout=None, retries=None, req_type=None, req_count=None):
+	"""usage: val = caget("xxx:m1.VAL", timeout=None, retries=None,
+	                req_type=None, req_count=None)"""
+
+	global cadict, defaultTimeout, defaultRetries
+
+	if not name:
+		print("caget: no PV name supplied")
+		raise ca_utilException(EXCEPTION_NULL_NAME)
+	if ((timeout==None) and (defaultTimeout != None)): timeout = defaultTimeout
+	if (timeout == "NONE"): timeout = None
+	if ((retries==None) and (defaultRetries != None)): retries = defaultRetries
+	if ((retries == None) or (retries == "NONE")): retries = 0
+	retries = max(retries,0)
+	retry = retries + 1
+	success = 0
+
+	# CaChannel sometimes chokes when it tries to process a channel that has been disconnected.
+	# The simplest fix is to clear the channel and reconnect to the PV, which we can do cleanly
+	# by deleting our dict entry for the channel, and calling checkName() to make a new entry.
+
+	while ((not success) and (retry > 0)):
+		checked = 0
+		while ((not checked) and (retry > 0)):
+			retry -= 1
+			try:
+				checkName(name, timeout=timeout)
+			except CaChannel.CaChannelException:
+				if retry <= 0:
+					raise
+			else:
+				checked = 1
+
+		entry = cadict[name]
+		if (timeout != None): entry.channel.setTimeout(timeout)
+		if req_type == None:
+			req_type=entry.field_type
+		# kludge for broken DBR_CHAR
+		if req_type == ca.DBR_CHAR:
+			req_type = ca.DBR_INT
+		if req_count == None:
+			req_count = entry.element_count
+		req_count = max(0, min(req_count, entry.element_count))
+		try:
+			val = entry.channel.getw(req_type=req_type, count=req_count)
+		except CaChannel.CaChannelException:
+			status = sys.exc_info()[1]
+			#print "getw threw an exception (%s)" % status
+			if ((int(status) == ca.ECA_BADTYPE) or (int(status) == ca.ECA_DISCONN)):
+				# Delete dictionary entry.  This clears the CA connection.
+				print("caget: Repairing CA connection to ", name)
+				del cadict[name]
+				retry += 1
+			if retry <= 0:
+				raise
+		else:
+			success = 1
+	return val
+
+def isNumber(s):
+	try:
+		n = int(s)
+	except:
+		return False
+	return True
+
+#######################################################################
+def same(value, readback, native_readback, field_type, read_check_tolerance):
+	"""For internal use by ca_util"""
+	#print "ca_util.same(): field_type=%s" % field_type
+	#print "ca_util.same(): value='%s'; readback='%s', native_readback='%s'" % (str(value), str(readback), str(native_readback))
+	#print "ca_util.same(): type(value)=%s; type(readback)=%s, type(native_readback)=%s" % (type(value),
+	#	type(readback), type(native_readback))
+
+	if field_type in [ca.DBR_FLOAT, ca.DBR_DOUBLE]:
+		return (abs(float(readback)-float(value)) < read_check_tolerance)
+	elif field_type in [ca.DBR_INT, ca.DBR_SHORT, ca.DBR_LONG]:
+		return (abs(int(readback)-int(value)) == 0)
+	elif field_type == ca.DBR_ENUM:
+		if str(value) == str(readback):
+			return True
+		if str(value) == str(native_readback):
+			return True
+		return False
+	else:
+		return (str(value) == str(readback))
+
+#######################################################################
+def caput(name, value, timeout=None, req_type=None, retries=None, read_check_tolerance=None):
+	"""
+	usage: caput("xxx:m1.VAL", new_value, timeout=None, req_type=None,
+	       retries=None, read_check_tolerance=None)
+	Put a value, and optionally check that the value arrived safely.
+	If read_check_tolerance == None (or is not supplied) then the default
+	read-check tolerance is used.  If read_check_tolerance == "NONE", then no
+	read check is done.
+	If read_check_tolerance != "NONE", then floating point numbers must be
+	closer than the tolerance, and other types must agree exactly.
+	Note that defaults for timeout, retries, and read_check_tolerance can be
+	set for all ca_util functions, using the command set_ca_util_defaults().
+	"""
+
+	_caput("caput", name, value, 0, timeout, req_type, retries, read_check_tolerance)
+
+
+#######################################################################
+def __ca_util_waitCB(epics_args, user_args):
+	"""Function for internal use by caputw()."""
+	#print "__ca_util_waitCB: %s done\n" % user_args[0]
+	cadict[user_args[0]].callbackReceived = 1
+
+#######################################################################
+def caputw(name, value, wait_timeout=None, timeout=None, req_type=None, retries=None,
+ read_check_tolerance=None):
+	"""
+	usage: caputw("xxx:m1.VAL", new_value, wait_timeout=None, timeout=None,
+	       req_type=None, retries=None, read_check_tolerance=None)
+	Put a value, optionally check that the value arrived safely, and wait (no
+	longer than wait_timeout) for processing to complete. If
+	read_check_tolerance == None (or is not supplied) then the default
+	read-check tolerance is used.  If read_check_tolerance == "NONE", then no
+	read check is done. If read_check_tolerance != "NONE", then floating point
+	numbers must be closer than the tolerance, and other types must agree
+	exactly. Note that defaults for timeout, retries, and read_check_tolerance
+	can be set for all ca_util functions, using the command
+	set_ca_util_defaults().
+	"""
+
+	_caput("caputw", name, value, wait_timeout, timeout, req_type, retries, read_check_tolerance)
+
+
+#######################################################################
+def _caput(function, name, value, wait_timeout=None, timeout=None, req_type=None, retries=None, read_check_tolerance=None):
+
+	global cadict, defaultTimeout, defaultRetries, readCheckTolerance
+
+	#print function
+	if not name:
+		print("%s: no PV name supplied" % function)
+		raise ca_utilException(EXCEPTION_NULL_NAME)
+	if ((timeout == None) and (defaultTimeout != None)): timeout = defaultTimeout
+	if ((retries == None) and (defaultRetries != None)): retries = defaultRetries
+	if ((retries == None) or (retries == "NONE")): retries = 0
+	if ((read_check_tolerance == None) and (readCheckTolerance != None)):
+		read_check_tolerance = readCheckTolerance
+
+	retries = max(retries,0)
+	retry = retries + 1
+	success = 0
+
+	checkName(name, timeout=timeout, retries=retries)
+
+	while ((not success) and (retry > 0)):
+
+		retry -= 1
+		entry = cadict[name]
+
+		state = castate(name, timeout)
+		#print "%s: state='%s'" % (function, state)
+		if (state != 'connected'):
+			print("%s: Repairing CA connection to '%s'" % (function, name))
+			del cadict[name]
+			retry += 1
+		else:
+			if req_type == None:
+				req_type=entry.field_type
+			if ((timeout != None) and (timeout != "NONE")): entry.channel.setTimeout(timeout)
+			entry.callbackReceived = 0 # in case we're doing caputw()
+			#value = convertToType(value, req_type)
+			try:
+				if function == "caput":
+					entry.channel.putw(value, req_type=req_type)
+				else: #caputw
+					retval = entry.channel.array_put_callback(value,req_type,entry.element_count,__ca_util_waitCB,name)
+			except CaChannel.CaChannelException:
+				status = sys.exc_info()[1]
+				print("put() threw an exception (%s)" % status)
+				if ((int(status) == ca.ECA_BADTYPE) or (int(status) == ca.ECA_DISCONN)):
+					# Delete dictionary entry.  This clears the CA connection.
+					print("%s: Repairing CA connection to '%s'" % (function, name))
+					del cadict[name]
+					retry += 1
+				if retry <= 0:
+					raise
+					entry.callbackReceived = 1
+					return
+			else:
+				if ((read_check_tolerance == None) or (read_check_tolerance == "NONE")):
+					success = True
+				else:
+					if timeout:
+						ca.pend_io(timeout)
+					else:
+						ca.pend_io(1.0)
+					readback_success = False
+					count = 0
+					while ((not readback_success) and (count < retries+1)):
+						try:
+							readback = caget(name, req_type=req_type)
+							native_readback = caget(name)
+							readback_success = True
+							if same(value, readback, native_readback, entry.field_type, read_check_tolerance):
+								success = True
+								#print "%s: Success\n" % (function)
+							else:
+								print("%s: readback '%s' disagrees with the value '%s' we wrote." % (function, readback, value))
+								raise ca_utilException(EXCEPTION_READBACK_DISAGREES)
+								entry.callbackReceived = 1
+						except CaChannel.CaChannelException:
+							print("%s: exception during readback." % (function))
+							count += 1
+
+	if success and (function == "caputw"):
+		start_time = time.time()
+		timed_out = 0
+		while (not entry.callbackReceived) and (not timed_out):
+			#print "waiting for ", name
+			time.sleep(0.1)
+			#ca.pend_io(0.1)
+			ca.poll()
+			if (not wait_timeout):
+				timed_out = 0
+			else:
+				timed_out = ((time.time()-start_time) > wait_timeout)
+
+		if not entry.callbackReceived:
+			print("Execution not completed by wait_timeout (%d seconds)" % wait_timeout)
+
+#######################################################################
+def camonitor(name, function, user_args=None, timeout=None, retries=None):
+	"""
+	usage: camonitor("xxx:m1.VAL", python_function, user_args, timeout=None,
+	       retries=None)
+	Don't forget to call ca.pend_event(<pend_time_in_seconds>) periodically.
+	"""
+
+	global defaultTimeout, defaultRetries
+
+	if not name:
+		print("camonitor: no PV name supplied")
+		raise ca_utilException(EXCEPTION_NULL_NAME)
+	if not function:
+		print("camonitor: no callback function supplied")
+		raise ca_utilException(EXCEPTION_NULL_NAME)
+	if not user_args: user_args = name
+	if ((timeout==None) and (defaultTimeout != None)): timeout = defaultTimeout
+	if ((retries==None) and (defaultRetries != None)): retries = defaultRetries
+	if ((retries == None) or (retries == "NONE")): retries = 0
+
+	retries = max(retries,0)
+	retry = retries + 1
+	success = 0
+
+	while ((not success) and (retry > 0)):
+		checked = 0
+		while ((not checked) and (retry > 0)):
+			retry -= 1
+			try:
+				checkName(name, timeout=timeout)
+			except CaChannel.CaChannelException:
+				if retry <= 0:
+					raise
+			else:
+				checked = 1
+
+		entry = cadict[name]
+		if ((timeout != None) and (timeout != "NONE")): entry.channel.setTimeout(timeout)
+		try:
+			entry.channel.add_masked_array_event(entry.field_type,entry.element_count,ca.DBE_VALUE, function, user_args)
+		except CaChannel.CaChannelException:
+			status = sys.exc_info()[1]
+			#print "add_masked_array_event threw an exception (%s)" % status
+			if ((int(status) == ca.ECA_BADTYPE) or (int(status) == ca.ECA_DISCONN)):
+				# Delete dictionary entry.  This clears the CA connection.
+				print("camonitor: Repairing CA connection to %s" % name)
+				del cadict[name]
+				retry += 1
+			if retry <= 0:
+				raise
+		else:
+			success = 1
+
+#######################################################################
+def caunmonitor(name, timeout=None):
+	"""usage: caunmonitor("xxx:m1.VAL", timeout=None)"""
+
+	global defaultTimeout
+
+	if not name:
+		print("caunmonitor: no PV name supplied")
+		raise ca_utilException(EXCEPTION_NULL_NAME)
+	if ((timeout==None) and (defaultTimeout != None)): timeout = defaultTimeout
+
+	if name not in cadict:
+		print("ca_util has no connection to '%s'" % name)
+		raise ca_utilException(EXCEPTION_NOT_CONNECTED)
+
+	channel = cadict[name].channel
+	if ((timeout != None) and (timeout != "NONE")): channel.setTimeout(timeout)
+	try:
+		channel.clear_event()
+	except CaChannel.CaChannelException:
+		status = sys.exc_info()[1]
+		print("caunmonitor: CaChannel exception, status=%d (%s)" % (status, ca.message(status)))
+		return
+
+#######################################################################
+def test_monitor_function(epics_args, user_args):
+	"""Example callback routine for use with camonitor()."""
+	print('test_monitor_function:')
+	print("...epics_args: %s" % repr(epics_args))
+	print("...user_args: %s" % repr(user_args))
+
+
+
+
+
+#-------------------------------------------------------------------------------------------
+# miscellaneous functions that might be useful, but haven't been integrated into the package
+
+#######################################################################
+def endianUs():
+	"""
+	usage: endianUs()
+	Returns one of "Little Endian", "Big Endian", "Unknown Endian".
+	"""
+
+	from struct import pack
+	if pack('<h', 1) == pack('=h',1):
+		return "Little Endian"
+	elif pack('>h', 1) == pack('=h',1):
+		return "Big Endian"
+	else:
+		return "Unknown Endian"
+
+#######################################################################
+def printExceptionInfo(maxTBlevel=15):
+	"""Intended for internal use by ca_util functions."""
+
+	import sys, traceback
+	cla, exc, trbk = sys.exc_info()
+	excName = cla.__name__
+	try:
+		excArgs = exc.__dict__["args"]
+	except KeyError:
+		excArgs = "<no args>"
+	excTb = traceback.format_tb(trbk, maxTBlevel)
+	print("Unanticipated exception: %s %s\n" % (excName, excArgs))
+	if (len(excTb) > 0):
+		print("Traceback:")
+		for trace in excTb:
+			print(trace)
+	return

script/_Lib/epics/cadefs.py

@@ -0,0 +1,189 @@
+""" @package cadefs
+contstants and enumerated conststant
+
+This defines constants  and classes useful to inteprete code returned from CA library.
+"""
+#
+CA_OP_GET = 0
+CA_OP_PUT = 1
+CA_OP_CREATE_CHANNEL = 2
+CA_OP_ADD_EVENT = 3
+CA_OP_CLEAR_EVENT = 4
+CA_OP_OTHER = 5
+# used with connection callbacks
+CA_OP_CONN_UP = 6
+CA_OP_CONN_DOWN = 7
+# imported from caeventmask.h
+DBE_VALUE =(1<<0)
+DBE_LOG   =(1<<1)
+DBE_ALARM =(1<<2)
+DBE_PROPERTY=(1<<3)
+# also chekc ECA_IODONE/ECA_IOINPROGRESS in caError.py
+IODONE = 42
+IOINPROGRESS = 43
+#
+DBF_NATIVE=-1
+DBF_STRING=0
+DBF_INT = 1
+DBF_SHORT =1
+DBF_FLOAT =2
+DBF_ENUM  =3
+DBF_CHAR  =4
+DBF_LONG  = 5
+DBF_DOUBLE = 6
+DBF_NO_ACCES = 	7
+LAST_TYPE = DBF_DOUBLE
+
+def VALID_DB_FIELD(x):
+    return ((x >= 0) and (x <= LAST_TYPE))
+def INVALID_DB_FIELD(x):
+    return ((x < 0) or (x > LAST_TYPE))
+
+#/* data request buffer types */
+DBR_NATIVE= DBF_NATIVE
+DBR_STRING = 	DBF_STRING
+DBR_INT	 =	DBF_INT
+DBR_SHORT = DBF_INT
+DBR_FLOAT = DBF_FLOAT
+DBR_ENUM = DBF_ENUM
+DBR_CHAR = DBF_CHAR
+DBR_LONG = DBF_LONG
+DBR_DOUBLE = DBF_DOUBLE
+DBR_STS_STRING = 7
+DBR_STS_SHORT = 8
+DBR_STS_INT = DBR_STS_SHORT
+DBR_STS_FLOAT = 9
+DBR_STS_ENUM = 10
+DBR_STS_CHAR = 11
+DBR_STS_LONG = 12
+DBR_STS_DOUBLE = 13
+DBR_TIME_STRING = 14
+DBR_TIME_INT = 15
+DBR_TIME_SHORT = 15
+DBR_TIME_FLOAT = 16
+DBR_TIME_ENUM = 17
+DBR_TIME_CHAR = 18
+DBR_TIME_LONG = 19
+DBR_TIME_DOUBLE = 20
+DBR_GR_STRING = 21
+DBR_GR_SHORT = 22
+DBR_GR_INT = DBR_GR_SHORT
+DBR_GR_FLOAT = 23
+DBR_GR_ENUM = 24
+DBR_GR_CHAR = 25
+DBR_GR_LONG = 26
+DBR_GR_DOUBLE = 27
+DBR_CTRL_STRING = 28
+DBR_CTRL_SHORT = 	29
+DBR_CTRL_INT = 	DBR_CTRL_SHORT
+DBR_CTRL_FLOAT = 30
+DBR_CTRL_ENUM = 31
+DBR_CTRL_CHAR = 32
+DBR_CTRL_LONG = 33
+DBR_CTRL_DOUBLE	 = 34
+DBR_PUT_ACKT = 	DBR_CTRL_DOUBLE + 1
+DBR_PUT_ACKS = DBR_PUT_ACKT + 1
+DBR_STSACK_STRING = DBR_PUT_ACKS + 1
+LAST_BUFFER_TYPE = DBR_STSACK_STRING
+
+def VALID_DB_REQ(x):
+    return ((x >= 0) and (x <= LAST_BUFFER_TYPE))
+def INVALID_DB_REQ(x):
+    return ((x < 0) or (x > LAST_BUFFER_TYPE))
+
+class AlarmSeverity:
+    """Alarm Severity class
+
+    AlarmSeverity class is provided to keep constants representing EPICS channel severity status.
+    It also keeps strings and colors for each severity states.
+    """
+    NO_ALARM  =0x0
+    MINOR_ALARM=0x1
+    MAJOR_ALARM=0x2
+    INVALID_ALARM=0x3
+    ALARM_NSEV=INVALID_ALARM+1
+    Strings=(
+	"NO_ALARM",
+	"MINOR",
+	"MAJOR",
+	"INVALID",
+        )
+    Colors=("green","yellow","red","grey")
+
+class AlarmStatus:
+    """!
+    AlarmStatus class provides constants returned by EPICS Channe Access library as channel status code.
+    It also gives you strings for corresponding channel status.
+    """
+    NO_ALARM = 0
+    READ_ALARM = 1
+    WRITE_ALARM = 2
+    #/* ANALOG ALARMS */
+    HIHI_ALARM = 3
+    HIGH_ALARM = 4
+    LOLO_ALARM = 5
+    LOW_ALARM = 6
+    #/* BINARY ALARMS */
+    STATE_ALARM = 7
+    COS_ALARM = 8
+    #/* other alarms */
+    COMM_ALARM = 9
+    TIMEOUT_ALARM = 10
+    HW_LIMIT_ALARM = 11
+    CALC_ALARM = 12
+    SCAN_ALARM = 13
+    LINK_ALARM = 14
+    SOFT_ALARM = 15
+    BAD_SUB_ALARM = 16
+    UDF_ALARM = 17
+    DISABLE_ALARM = 18
+    SIMM_ALARM = 19
+    READ_ACCESS_ALARM = 20
+    WRITE_ACCESS_ALARM = 21
+    Strings=(
+        "NO_ALARM",
+        "READ",
+        "WRITE",
+        "HIHI",
+        "HIGH",
+        "LOLO",
+        "LOW",
+        "STATE",
+        "COS",
+        "COMM",
+        "TIMEOUT",
+        "HWLIMIT",
+        "CALC",
+        "SCAN",
+        "LINK",
+        "SOFT",
+        "BAD_SUB",
+        "UDF",
+        "DISABLE",
+        "SIMM",
+        "READ_ACCESS",
+        "WRITE_ACCESS",
+        )
+
+
+# ch_state={cs_never_conn=0, cs_prev_conn, cs_conn, cs_closed}
+
+cs_never_conn= 0
+cs_prev_conn = 1
+cs_conn      = 2
+cs_closed    = 3
+
+class ch_state:
+    """
+    ch_state class provides constants representing channel connection status.
+    """
+    cs_never_conn= 0
+    cs_prev_conn = 1
+    cs_conn      = 2
+    cs_closed    = 3
+    Strings=(
+        "channel never connected",
+        "channel previously connected",
+        "channel connected",
+        "channel already closed",
+        )

script/_Lib/epics/epicsMotor.py

@@ -0,0 +1,357 @@
+"""
+This module provides support for the EPICS motor record.
+
+Author:         Mark Rivers
+Created:        Sept. 16, 2002
+Modifications:
+"""
+import time
+
+import epicsPV
+
+class epicsMotor:
+   """
+   This module provides a class library for the EPICS motor record.
+   It uses the epicsPV class, which is in turn a subclass of CaChannel.
+
+   Virtual attributes:
+      These attributes do not appear in the dictionary for this class, but
+      are implemented with the __getattr__ and __setattr__ methods.  They
+      simply do getw() or putw(value) to the appropriate motor record fields.
+      All attributes can be both read and written unless otherwise noted.
+
+      Attribute        Description                  Field
+      ---------        -----------------------      -----
+      slew_speed       Slew speed or velocity       .VELO
+      base_speed       Base or starting speed       .VBAS
+      acceleration     Acceleration time (sec)      .ACCL
+      description      Description of motor         .DESC
+      resolution       Resolution (units/step)      .MRES
+      high_limit       High soft limit (user)       .HLM
+      low_limit        Low soft limit (user)        .LLM
+      dial_high_limit  High soft limit (dial)       .DHLM
+      dial_low_limit   Low soft limit (dial)        .DLLM
+      backlash         Backlash distance            .BDST
+      offset           Offset from dial to user     .OFF
+      done_moving      1=Done, 0=Moving, read-only  .DMOV
+ 
+   Exceptions:
+      The check_limits() method raises an "epicsMotorException" if a soft limit
+      or hard limit is detected.  The move() and wait() methods call 
+      check_limits() before they return, unless they are called with the 
+      ignore_limits=1 keyword set.
+
+   Example use:
+      from epicsMotor import *
+      m=epicsMotor('13BMD:m38')
+      m.move(10)               # Move to position 10 in user coordinates
+      m.move(100, dial=1)      # Move to position 100 in dial coordinates
+      m.move(1, step=1, relative=1) # Move 1 step relative to current position
+      m.wait()                 # Wait for motor to stop moving
+      m.wait(start=1)          # Wait for motor to start moving
+      m.wait(start=1, stop=1)  # Wait for motor to start, then to stop
+      m.stop()                 # Stop moving immediately
+      high = m.high_limit      # Get the high soft limit in user coordinates
+      m.dial_high_limit = 100  # Set the high limit to 100 in dial coodinates
+      speed = m.slew_speed     # Get the slew speed
+      m.acceleration = 0.1     # Set the acceleration to 0.1 seconds
+      p=m.get_position()       # Get the desired motor position in user coordinates
+      p=m.get_position(dial=1) # Get the desired motor position in dial coordinates
+      p=m.get_position(readback=1) # Get the actual position in user coordinates
+      p=m.get_position(readback=1, step=1) Get the actual motor position in steps
+      p=m.set_position(100)   # Set the current position to 100 in user coordinates
+         # Puts motor in Set mode, writes value, puts back in Use mode.
+      p=m.set_position(10000, step=1) # Set the current position to 10000 steps
+"""
+
+   def __init__(self, name):
+      """
+      Creates a new epicsMotor instance.
+
+      Inputs:
+         name:
+            The name of the EPICS motor record without any trailing period or field
+            name.
+
+      Example:
+         m=epicsMotor('13BMD:m38')
+      """
+      self.pvs = {'val' : epicsPV.epicsPV(name+'.VAL',  wait=0), 
+                  'dval': epicsPV.epicsPV(name+'.DVAL', wait=0),
+                  'rval': epicsPV.epicsPV(name+'.RVAL', wait=0),
+                  'rlv' : epicsPV.epicsPV(name+'.RLV',  wait=0),
+                  'rbv' : epicsPV.epicsPV(name+'.RBV',  wait=0),
+                  'drbv': epicsPV.epicsPV(name+'.DRBV', wait=0),
+                  'rrbv': epicsPV.epicsPV(name+'.RRBV', wait=0),
+                  'dmov': epicsPV.epicsPV(name+'.DMOV', wait=0),
+                  'stop': epicsPV.epicsPV(name+'.STOP', wait=0),
+                  'velo': epicsPV.epicsPV(name+'.VELO', wait=0),
+                  'vbas': epicsPV.epicsPV(name+'.VBAS', wait=0),
+                  'accl': epicsPV.epicsPV(name+'.ACCL', wait=0),
+                  'desc': epicsPV.epicsPV(name+'.DESC', wait=0),
+                  'mres': epicsPV.epicsPV(name+'.MRES', wait=0),
+                  'hlm':  epicsPV.epicsPV(name+'.HLM',  wait=0),
+                  'llm':  epicsPV.epicsPV(name+'.LLM',  wait=0),
+                  'dhlm': epicsPV.epicsPV(name+'.DHLM', wait=0),
+                  'dllm': epicsPV.epicsPV(name+'.DLLM', wait=0),
+                  'bdst': epicsPV.epicsPV(name+'.BDST', wait=0),
+                  'set':  epicsPV.epicsPV(name+'.SET',  wait=0),
+                  'lvio': epicsPV.epicsPV(name+'.LVIO', wait=0),
+                  'lls':  epicsPV.epicsPV(name+'.LLS',  wait=0),
+                  'hls':  epicsPV.epicsPV(name+'.HLS',  wait=0),
+                  'off':  epicsPV.epicsPV(name+'.OFF',  wait=0)
+                  }
+      # Wait for all PVs to connect
+      self.pvs['val'].pend_io() 
+
+   def move(self, value, relative=0, dial=0, step=0, ignore_limits=0):
+      """
+      Moves a motor to an absolute position or relative to the current position
+      in user, dial or step coordinates.
+         
+      Inputs:
+         value:
+            The absolute position or relative amount of the move
+            
+      Keywords:
+         relative:
+            Set relative=1 to move relative to current position.
+            The default is an absolute move.
+            
+         dial:
+            Set dial=1 if "value" is in dial coordinates.
+            The default is user coordinates.
+            
+         step:
+            Set step=1 if "value" is in steps.
+            The default is user coordinates.
+            
+         ignore_limits:
+            Set ignore_limits=1 to suppress raising exceptions
+            if the move results in a soft or hard limit violation.
+            
+      Notes:
+         The "step" and "dial" keywords are mutually exclusive.
+         The "relative" keyword can be used in user, dial or step 
+         coordinates.
+         
+      Examples:
+         m=epicsMotor('13BMD:m38')
+         m.move(10)          # Move to position 10 in user coordinates
+         m.move(100, dial=1) # Move to position 100 in dial coordinates
+         m.move(2, step=1, relative=1) # Move 2 steps 
+      """
+      if (dial != 0):
+         # Position in dial coordinates
+         if (relative != 0):
+            current = self.get_position(dial=1)
+            self.pvs['dval'].putw(current+value)
+         else:
+            self.pvs['dval'].putw(value)
+    
+      elif (step != 0):
+         # Position in steps
+         if (relative != 0):
+            current = self.get_position(step=1)
+            self.pvs['rval'].putw(current + value)
+         else:
+            self.pvs['rval'].putw(value)
+      else:
+         # Position in user coordinates
+         if (relative != 0):
+            self.pvs['rlv'].putw(value)
+         else:
+            self.pvs['val'].putw(value)
+
+      # Check for limit violations
+      if (ignore_limits == 0): self.check_limits()
+
+   def check_limits(self):
+      limit = self.pvs['lvio'].getw()
+      if (limit!=0): 
+         raise epicsMotorException('Soft limit violation')
+      limit = self.pvs['lls'].getw()
+      if (limit!=0): 
+         raise epicsMotorException('Low hard limit violation')
+      limit = self.pvs['hls'].getw()
+      if (limit!=0): 
+         raise epicsMotorException('High hard limit violation')
+
+   
+   def stop(self):
+      """
+      Immediately stops a motor from moving by writing 1 to the .STOP field.
+         
+      Examples:
+         m=epicsMotor('13BMD:m38')
+         m.move(10)          # Move to position 10 in user coordinates
+         m.stop()            # Stop motor
+      """
+      self.pvs['stop'].putw(1)
+
+   def get_position(self, dial=0, readback=0, step=0):
+      """
+      Returns the target or readback motor position in user, dial or step
+      coordinates.
+      
+      Keywords:
+         readback:
+            Set readback=1 to return the readback position in the
+            desired coordinate system.  The default is to return the
+            target position of the motor.
+            
+         dial:
+            Set dial=1 to return the position in dial coordinates.
+            The default is user coordinates.
+            
+         step:
+            Set step=1 to return the position in steps.
+            The default is user coordinates.
+
+         Notes:
+            The "step" and "dial" keywords are mutually exclusive.
+            The "readback" keyword can be used in user, dial or step 
+            coordinates.
+            
+      Examples:
+         m=epicsMotor('13BMD:m38')
+         m.move(10)          # Move to position 10 in user coordinates
+         p=m.get_position(dial=1) # Read the target position in 
+                                  # dial coordinates
+         p=m.get_position(readback=1, step=1) # Read the actual position in 
+                                              # steps
+      """
+      if (dial != 0):
+         if (readback != 0):
+            return self.pvs['drbv'].getw()
+         else:
+            return self.pvs['dval'].getw()
+      elif (step != 0):
+         if (readback != 0):
+            return self.pvs['rrbv'].getw()
+         else:
+            return self.pvs['rval'].getw()
+      else:
+         if (readback != 0):
+            return self.pvs['rbv'].getw()
+         else:
+            return self.pvs['val'].getw()
+   
+   def set_position(self, position, dial=0, step=0):
+      """
+      Sets the motor position in user, dial or step coordinates.
+      
+      Inputs:
+         position:
+            The new motor position
+            
+      Keywords:
+         dial:
+            Set dial=1 to set the position in dial coordinates.
+            The default is user coordinates.
+            
+         step:
+            Set step=1 to set the position in steps.
+            The default is user coordinates.
+            
+      Notes:
+         The "step" and "dial" keywords are mutually exclusive.
+         
+      Examples:
+         m=epicsMotor('13BMD:m38')
+         m.set_position(10, dial=1)   # Set the motor position to 10 in 
+                                      # dial coordinates
+         m.set_position(1000, step=1) # Set the motor position to 1000 steps
+      """
+      # Put the motor in "SET" mode
+      self.pvs['set'].putw(1)
+      if (dial != 0):
+         self.pvs['dval'].putw(position)
+      elif (step != 0):
+         self.pvs['rval'].putw(position)
+      else:
+         self.pvs['val'].putw(position)
+      # Put the motor back in "Use" mode
+      self.pvs['set'].putw(0)
+
+
+   def wait(self, start=0, stop=0, poll=0.01, ignore_limits=0):
+      """
+      Waits for the motor to start moving and/or stop moving.
+      
+      Keywords:
+         start:
+            Set start=1 to wait for the motor to start moving.
+            
+         stop:
+            Set stop=1 to wait for the motor to stop moving.
+            
+         poll:
+            Set this keyword to the time to wait between reading the
+            .DMOV field of the record to see if the motor is moving.
+            The default is 0.01 seconds.
+            
+         ignore_limits:
+            Set ignore_limits=1 to suppress raising an exception if a soft or
+            hard limit is detected
+            
+      Notes:
+         If neither the "start" nor "stop" keywords are set then "stop"
+         is set to 1, so the routine waits for the motor to stop moving.
+         If only "start" is set to 1 then the routine only waits for the
+         motor to start moving.
+         If both "start" and "stop" are set to 1 then the routine first
+         waits for the motor to start moving, and then to stop moving.
+         
+      Examples:
+         m=epicsMotor('13BMD:m38')
+         m.move(100)               # Move to position 100
+         m.wait(start=1, stop=1)   # Wait for the motor to start moving
+                                   # and then to stop moving
+      """
+      if (start == 0) and (stop == 0): stop=1
+      if (start != 0):
+         while(1):
+            done = self.pvs['dmov'].getw()
+            if (done != 1): break
+            time.sleep(poll)
+      if (stop != 0):
+         while(1):
+            done = self.pvs['dmov'].getw()
+            if (done != 0): break
+            time.sleep(poll)
+      if (ignore_limits == 0): self.check_limits()
+
+   def __getattr__(self, attrname):
+      if   (attrname == 'slew_speed'):      return self.pvs['velo'].getw()
+      elif (attrname == 'base_speed'):      return self.pvs['vbas'].getw()
+      elif (attrname == 'acceleration'):    return self.pvs['accl'].getw()
+      elif (attrname == 'description'):     return self.pvs['desc'].getw()
+      elif (attrname == 'resolution'):      return self.pvs['mres'].getw()
+      elif (attrname == 'high_limit'):      return self.pvs['hlm'].getw()
+      elif (attrname == 'low_limit'):       return self.pvs['llm'].getw()
+      elif (attrname == 'dial_high_limit'): return self.pvs['dhlm'].getw()
+      elif (attrname == 'dial_low_limit'):  return self.pvs['dllm'].getw()
+      elif (attrname == 'backlash'):        return self.pvs['bdst'].getw()
+      elif (attrname == 'offset'):          return self.pvs['off'].getw()
+      elif (attrname == 'done_moving'):     return self.pvs['dmov'].getw()
+      else: raise AttributeError(attrname)
+
+   def __setattr__(self, attrname, value):
+      if   (attrname == 'pvs'): self.__dict__[attrname]=value
+      elif (attrname == 'slew_speed'):      self.pvs['velo'].putw(value)
+      elif (attrname == 'base_speed'):      self.pvs['vbas'].putw(value)
+      elif (attrname == 'acceleration'):    self.pvs['accl'].putw(value)
+      elif (attrname == 'description'):     self.pvs['desc'].putw(value)
+      elif (attrname == 'resolution'):      self.pvs['mres'].putw(value)
+      elif (attrname == 'high_limit'):      self.pvs['hlm'].putw(value)
+      elif (attrname == 'low_limit'):       self.pvs['llm'].putw(value)
+      elif (attrname == 'dial_high_limit'): self.pvs['dhlm'].putw(value)
+      elif (attrname == 'dial_low_limit'):  self.pvs['dllm'].putw(value)
+      elif (attrname == 'backlash'):        self.pvs['bdst'].putw(value)
+      elif (attrname == 'offset'):          self.pvs['off'].putw(value)
+      else: raise AttributeError(attrname)
+
+class epicsMotorException(Exception):
+   def __init__(self, args=None):
+      self.args=args

script/_Lib/epics/epicsPV.py

@@ -0,0 +1,273 @@
+"""
+This module defines the epicsPV class, which adds additional features to
+Geoff Savage's CaChannel class.
+
+Author:         Mark Rivers
+Created:        Sept. 16, 2002.
+Modifications:
+"""
+import CaChannel
+
+class epicsPV(CaChannel.CaChannel):
+   """
+   This class subclasses Geoff Savage's CaChannel class to add the following
+   features:
+   
+      - If a PV name is given then the class constructor will do a searchw()
+        by default.
+        
+      - setMonitor() sets a generic callback routine for value change events.
+        Subsequent getw(), getValue() or array_get() calls will return the
+        value from the most recent callback, and hence do not result in any
+        network activity or latency.  This can greatly improve performance.
+        
+      - checkMonitor() returns a flag to indicate if a callback has occured
+        since the last call to checkMonitor(), getw(), getValue() or
+        array_get().  It can be used to increase efficiency in polling
+        applications.
+        
+      - getControl() reads the "control" and other information from an
+        EPICS PV without having to use callbacks.
+        In addition to the PV value, this will return the graphic, control and
+        alarm limits, etc.
+
+      - putWait() calls array_put_callback() and waits for the callback to
+        occur before it returns.  This allows programs to use array_put_callback()
+        synchronously and without user-written callbacks.
+        
+   Created:  Mark Rivers, Sept. 16, 2002.
+   Modifications:
+   """
+
+   def __init__(self, pvName=None, wait=1):
+      """
+      Keywords:
+         pvName:
+            An optional name of an EPICS Process Variable.
+         
+         wait:
+            If wait==1 and pvName != None then this constructor will do a
+            CaChannel.searchw() on the PV.  If wait==0 and pvName != None then
+            this constructor will do a CaChannel.search() on the PV, and the user
+            must subsequently do a pend_io() on this or another epicsPV or CaChannel
+            object.
+            
+      Procedure:
+         Invokes CaChannel.__init__() and then searchw() or search() as explained
+         above
+      """
+      # Invoke the base class initialization
+      self.callBack = callBack()
+      CaChannel.CaChannel.__init__(self)
+      if (pvName != None):
+         if (wait):
+            self.searchw(pvName)
+         else:
+            self.search(pvName)
+
+   def setMonitor(self):
+      """
+      Sets a generic callback routine for value change events.
+      Subsequent getw(), getValue() or array_get() calls will return the
+      value from the most recent callback, do not result in any network
+      latency.  This can greatly improve efficiency.
+      """
+      self.add_masked_array_event(None, None, CaChannel.ca.DBE_VALUE, 
+                                  getCallback, self.callBack)
+      self.callBack.monitorState = 1
+
+   def clearMonitor(self):
+      """
+      Cancels the effect of a previous call to setMonitor().
+      Calls CaChannel.clear_event().
+      Subsequent getw(), getValue() or array_get() calls will no longer
+      return the value from the most recent callback, but will actually result
+      in channel access calls. 
+      """
+      self.clear_event()
+      self.callBack.monitorState = 0
+
+   def checkMonitor(self):
+      """
+      Returns 1 to indicate if a value callback has occured
+      since the last call to checkMonitor(), getw(), getValue() or
+      array_get(), indicating that a new value is available.  Returns 0 if
+      no such callback has occurred.
+      It can be used to increase efficiency in polling applications.
+      """
+      # This should be self.poll(), but that is generating errors
+      self.pend_event(.0001)
+      m = self.callBack.newMonitor
+      self.callBack.newMonitor = 0
+      return m
+
+   def getControl(self, req_type=None, count=None, wait=1, poll=.01):
+      """
+      Provides a method to read the "control" and other information from an
+      EPICS PV without having to use callbacks.
+      It calls CaChannel.array_get_callback() with a database request type of
+      CaChannel.ca.dbf_type_to_DBR_CTRL(req_type).
+      In addition to the PV value, this will return the graphic, control and
+      alarm limits, etc.
+      
+      Example:
+      >>> pv = epicsPV('13IDC:m1')
+      >>> pv.getControl()
+      >>> for field in dir(pv.callBack):
+      >>>    print field, ':', getattr(pv.callBack, field)
+          chid : _bfffec34_chid_p
+          count : 1
+          monitorState : 0
+          newMonitor : 1
+          putComplete : 0
+          pv_loalarmlim : 0.0
+          pv_loctrllim : -22.0
+          pv_lodislim : -22.0
+          pv_lowarnlim : 0.0
+          pv_precision : 4
+          pv_riscpad0 : 256
+          pv_severity : 0
+          pv_status : 0
+          pv_units : mm
+          pv_upalarmlim : 0.0
+          pv_upctrllim : 28.0
+          pv_updislim : 28.0
+          pv_upwarnlim : 0.0
+          pv_value : -15.0
+          status : 1
+          type : 34
+
+      Note the fields such as pv_plocrtllim, the lower control limit, and
+      pv_precision, the display precision.
+
+      Keywords:
+         wait:
+            If this keyword is 1 (the default) then this routine waits for
+            the callback before returning.  If this keyword is 0 then it is
+            the user's responsibility to wait or check for the callback
+            by calling checkMonitor().
+            
+         poll:
+            The timeout for pend_event() calls, waiting for the callback
+            to occur.  Shorter times reduce the latency at the price of CPU
+            cycles.
+      """
+      if (req_type == None): req_type = self.field_type()
+      if (wait != 0): self.callBack.newMonitor = 0
+      self.array_get_callback(CaChannel.ca.dbf_type_to_DBR_CTRL(req_type),
+                              count, getCallback, self.callBack)
+      if (wait != 0):
+         while(self.callBack.newMonitor == 0):
+            self.pend_event(poll)            
+
+   def array_get(self, req_type=None, count=None):
+      """
+      If setMonitor() has not been called then this function simply calls
+      CaChannel.array_get().  If setMonitor has been called then it calls
+      CaChannel.pend_event() with a very short timeout, and then returns the
+      PV value from the last callback.
+      """
+      if (self.callBack.monitorState != 0):
+         # This should be self.poll(), but that is generating errors
+         self.pend_event(.0001)
+      if (self.callBack.monitorState == 2):
+         self.callBack.newMonitor = 0
+         return self.callBack.pv_value
+      else:
+         return CaChannel.CaChannel.array_get(self, req_type, count)
+
+   def getw(self, req_type=None, count=None):
+      """
+      If setMonitor() has not been called then this function simply calls
+      CaChannel.getw().  If setMonitor has been called then it calls
+      CaChannel.pend_event() with a very short timeout, and then returns the
+      PV value from the last callback.
+      """
+      if (self.callBack.monitorState != 0):
+         # This should be self.poll(), but that is generating errors
+         self.pend_event(.0001)
+      if (self.callBack.monitorState == 2):
+         self.callBack.newMonitor = 0
+         if (count == None):
+            return self.callBack.pv_value
+         else:
+            return self.callBack.pv_value[0:count]
+      else:
+         return CaChannel.CaChannel.getw(self, req_type, count)
+
+   def getValue(self):
+      """
+      If setMonitor() has not been called then this function simply calls
+      CaChannel.getValue().  If setMonitor has been called then it calls
+      CaChannel.pend_event() with a very short timeout, and then returns the
+      PV value from the last callback.
+      """
+      if (self.callBack.monitorState != 0):
+         # This should be self.poll(), but that is generating errors
+         self.pend_event(.0001)
+      if (self.callBack.monitorState == 2):
+         self.callBack.newMonitor = 0
+         return self.callBack.pv_value
+      else:         
+         return CaChannel.CaChannel.getValue(self)
+
+   def putWait(self, value, req_type=None, count=None, poll=.01):
+      """
+      Calls CaChannel.array_put_callback() and waits for the callback to
+      occur before it returns.  This allows programs to use array_put_callback()
+      without having to handle asynchronous callbacks.
+      
+      Keywords:
+         req_type:
+            See CaChannel.array_put_callback()
+            
+         count:
+            See CaChannel.array_put_callback()
+            
+         poll:
+            The timeout for pend_event() calls, waiting for the callback
+            to occur.  Shorter times reduce the latency at the price of CPU
+            cycles.
+      """
+      self.callBack.putComplete=0
+      self.array_put_callback(value, req_type, count, putCallBack, self.callBack)
+      while(self.callBack.putComplete == 0):
+         self.pend_event(poll)         
+
+class callBack:
+   """
+   This class is used by the epicsPV class to handle callbacks.  It is required
+   to avoid circular references to the epicsPV object itself when dealing with
+   callbacks, in order to allow the CaChannel destructor to be called.
+   Users will only be interested in the fields that are copied to this class in
+   the callback resulting from a call to epicsPV.getControl().
+   """
+   def __init__(self):
+      self.newMonitor = 0
+      self.putComplete = 0
+      self.monitorState = 0
+      # monitorState:  
+      #   0=not monitored 
+      #   1=monitor requested, but no callback yet
+      #   2=monitor requested, callback has arrived
+
+
+def putCallBack(epicsArgs, userArgs):
+   """
+   This is the generic callback function used by the epicsPV.putWait() method.
+   It simply sets the callBack.putComplete flag to 1.
+   """
+   userArgs[0].putComplete=1
+
+def getCallback(epicsArgs, userArgs):
+   """
+   This is the generic callback function enabled by the epicsPV.setMonitor() method.
+   It sets the callBack.monitorState flag to 2, indicating that a monitor has
+   been received.  It copies all of the attributes in the epicsArgs dictionary
+   to the callBack attribute of the epicsPV object.
+   """
+   for key in epicsArgs.keys():
+      setattr(userArgs[0], key, epicsArgs[key])
+   if (userArgs[0].monitorState == 1): userArgs[0].monitorState = 2
+   userArgs[0].newMonitor = 1
+

script/_Lib/ijutils.js

@@ -0,0 +1,896 @@
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//  Facade to ImageJ functionality
+///////////////////////////////////////////////////////////////////////////////////////////////////
+
+//More information on:
+//   Image:   https://imagej.nih.gov/ij/docs/guide/146-28.htmltoc-Section-28
+//   Process: https://imagej.nih.gov/ij/docs/guide/146-29.html#toc-Section-29
+//   Analyze: https://imagej.nih.gov/ij/docs/guide/146-30.html#toc-Section-30
+
+Utils = Java.type('ch.psi.pshell.imaging.Utils')
+Pair = Java.type('org.apache.commons.math3.util.Pair')
+
+
+IJ = Java.type('ij.IJ')
+ImageJ = Java.type('ij.ImageJ')
+WindowManager = Java.type('ij.WindowManager')
+ImagePlus = Java.type('ij.ImagePlus')
+Prefs = Java.type('ij.Prefs')
+FileSaver = Java.type('ij.io.FileSaver')
+
+ImageProcessor = Java.type('ij.process.ImageProcessor')
+ByteProcessor = Java.type('ij.process.ByteProcessor')
+ShortProcessor = Java.type('ij.process.ShortProcessor')
+ColorProcessor = Java.type('ij.process.ColorProcessor')
+FloatProcessor = Java.type('ij.process.FloatProcessor')
+ImageConverter = Java.type('ij.process.ImageConverter')
+AutoThresholder = Java.type('ij.process.AutoThresholder')
+LUT = Java.type('ij.process.LUT')
+Measurements = Java.type('ij.measure.Measurements')
+
+ResultsTable = Java.type('ij.measure.ResultsTable')
+Analyzer = Java.type('ij.plugin.filter.Analyzer')
+GaussianBlur = Java.type('ij.plugin.filter.GaussianBlur')
+Filters = Java.type('ij.plugin.filter.Filters')
+FFTFilter = Java.type('ij.plugin.filter.FFTFilter')
+BackgroundSubtracter = Java.type('ij.plugin.filter.BackgroundSubtracter')
+EDM = Java.type('ij.plugin.filter.EDM')
+Shadows = Java.type('ij.plugin.filter.Shadows')
+UnsharpMask = Java.type('ij.plugin.filter.UnsharpMask')
+MaximumFinder = Java.type('ij.plugin.filter.MaximumFinder') 
+EDM = Java.type('ij.plugin.filter.EDM')
+Shadows = Java.type('ij.plugin.filter.Shadows')
+UnsharpMask = Java.type('ij.plugin.filter.UnsharpMask')
+RankFilters = Java.type('ij.plugin.filter.RankFilters')
+Convolver = Java.type('ij.plugin.filter.Convolver')
+ParticleAnalyzer = Java.type('ij.plugin.filter.ParticleAnalyzer')
+
+ContrastEnhancer = Java.type('ij.plugin.ContrastEnhancer')
+Thresholder = Java.type('ij.plugin.Thresholder')
+ImageCalculator = Java.type('ij.plugin.ImageCalculator')
+FFT = Java.type('ij.plugin.FFT')
+Concatenator = Java.type('ij.plugin.Concatenator')
+
+//ImageJ customizations
+FFTMath = Java.type('ch.psi.pshell.imaging.ij.FFTMath')
+FFTFilter = Java.type('ch.psi.pshell.imaging.ij.FFTFilter')
+Binary = Java.type('ch.psi.pshell.imaging.ij.Binary')
+Slicer = Java.type('ch.psi.pshell.imaging.ij.Slicer')
+
+
+//This eliminates the error messages due to the bug on ij.gui.ImageWindow row 555 (ij is null)
+try{
+    _image_j
+} catch(ex) {   	
+    _image_j = new ImageJ(null, ImageJ.NO_SHOW)
+}    
+    
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//Image creation, copying & saving
+///////////////////////////////////////////////////////////////////////////////////////////////////
+        
+function  load_image(image, title){
+    /*
+    image: file name or BufferedImage
+    */    
+    if (!is_defined(title))    title ="img"
+    
+    if (typeof image == 'string') 
+        try{
+            file = get_context().setup.expandPath(image)
+        } catch(ex) {
+        }
+        try{
+            image = Utils.newImage(file)
+        } catch(ex) {
+            //try loading from assembly
+            image = get_context().setup.getAssemblyImage(image)
+        }
+    return new ImagePlus(title, image)
+}
+        
+function load_array(array, width, height, title){
+    /*
+    array: 1d array if width and height defined , or else 2d array to be flattened.
+    */  
+    if (!is_defined(width))    width = null
+    if (!is_defined(height))    height = null
+    if (!is_defined(title))    title ="img"  
+    //2D
+    if ((width==null) && (height==null)){
+        if (array.typecode == '[B') proc = new ByteProcessor(array[0].length, array.length, Convert.flatten(array))
+        else if (array.typecode == '[S') proc = new ShortProcessor(array[0].length, array.length, Convert.flatten(array), null)
+        else if (array.typecode == '[I') proc = new FloatProcessor(array[0].length, array.length, Convert.flatten(array))        
+        else if (array.typecode == '[F') proc = new FloatProcessor(array[0].length, array.length, Convert.flatten(array))        
+        else if (array.typecode == '[D') proc = new FloatProcessor(array[0].length, array.length, Convert.flatten(array))        
+        else throw "Invalid array type"
+    //1D
+    }else{
+        if (array.length > width*height)
+            array = array.slice[0, width*height]
+        if (array.typecode == 'b') proc = new yteProcessor(width, height, array)
+        else if (array.typecode == 'h') proc = new ShortProcessor(width, height, array, null)
+        else if (array.typecode == 'i') proc = new FloatProcessor(width, height, array)
+        else if (array.typecode == 'f') proc = new FloatProcessor(width, height, array)
+        else if (array.typecode == 'd') proc = new FloatProcessor(width, height, array)
+        else throw "Invalid array type"
+    }
+    return new ImagePlus(title, proc)
+}
+        
+function save_image(ip, path, format){
+    /*
+    Saves image or stack
+    If parameters omitted, saves image again in same location, with same format.
+    */
+    if (!is_defined(path))    path = null
+    if (!is_defined(format))    format = null
+    var fs = new FileSaver(ip)
+    if (path == null)fs.save()
+    else{
+        try{
+            path = get_context().setup.expandPath(path)
+        } catch(ex) {
+        }      
+        if (format == "bmp") fs.saveAsBmp(path) 
+        else if (format == "fits") fs.saveAsFits(path) 
+        else if (format == "gif") fs.saveAsGif(path) 
+        else if (format == "jpeg") fs.saveAsJpeg(path) 
+        else if (format == "lut") fs.saveAsLut(path) 
+        else if (format == "pgm") fs.saveAsPgm(path) 
+        else if (format == "png") fs.saveAsPng(path) 
+        else if (format == "raw" && (ip.getImageStackSize()>1)) fs.saveAsRawStack(path) 
+        else if (format == "raw") fs.saveAsRaw(path) 
+        else if (format == "txt") fs.saveAsText(path)
+        else if (format == "tiff" && (ip.getImageStackSize()>1)) fs.saveAsTiffStack(path)
+        else if (format == "tiff") fs.saveAsTiff(path)
+        else if (format == "zip") fs.saveAsZip(path)   
+    }
+}
+        
+function new_image(width, height, image_type, title, fill_color){
+    /*
+    type = "byte", "short", "color" or "float"
+    */
+    if (!is_defined(image_type))    image_type = "byte"
+    if (!is_defined(title))    title = "img"
+    if (!is_defined(fill_color))    fill_color = null
+    if (image_type == "byte")  p= new ByteProcessor(width, height)
+    else if (image_type == "short") p= new ShortProcessor(width, height)
+    else if (image_type == "color") p= new ColorProcessor(width, height)
+    else if (image_type == "float") p= new FloatProcessor(width, height)
+    else  throw ("Invalid image type " + str(image_type))
+    ret = new ImagePlus(title, p)    
+    if (fill_color != null){
+        p.setColor(fill_color)
+        p.resetRoi()
+        p.fill()
+    }
+    return ret    
+}
+        
+function sub_image(ip, x, y, width, height){
+    /*
+    Returns new ImagePlus
+    */
+    ip.setRoi(x, y, width, height)
+    p=ip.getProcessor().crop()
+    return new ImagePlus(ip.getTitle() + " subimage", p)    
+}
+        
+function copy_image(ip){
+    return ip.duplicate()
+}
+        
+function copy_image_to(ip_source, ip_dest, x, y){
+    ip_source.deleteRoi()    
+    ip_source.copy()
+    ip_dest.setRoi(x, y, ip_source.getWidth(), ip_source.getHeight())
+    ip_dest.paste()
+    ip_dest.changes = false
+    ip_dest.deleteRoi()
+}
+        
+function pad_image(ip, left, right, top, bottom, fill_color){
+	if (!is_defined(left))    left = 0
+	if (!is_defined(right))    right = 0
+	if (!is_defined(top))    top = 0
+	if (!is_defined(bottom))    bottom = 0
+	if (!is_defined(fill_color))    fill_color = null
+    p=ip.getProcessor()
+    width = p.getWidth() + left + right
+    height =  p.getHeight() + top + bottom        
+    image_type = get_image_type(ip)
+    ret = new_image(width, height, image_type, ip.getTitle() + " padded", fill_color)
+    ip.deleteRoi()
+    ip.copy()
+    ret.setRoi(left, top, p.getWidth(), p.getHeight())
+    ret.paste()
+    ret.changes = false
+    ret.deleteRoi()
+    return ret    
+}
+        
+function get_image_type(ip){
+    /*
+    Returns: "byte", "short", "color" or "float"
+    */
+    p=ip.getProcessor()
+    if (p instanceof ShortProcessor) return "short"
+    else if (p instanceof ColorProcessor) return "color"
+    else if (p instanceof FloatProcessor) return "float"
+    return "byte"
+}
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//Image type conversion
+///////////////////////////////////////////////////////////////////////////////////////////////////
+        
+function grayscale(ip, in_place){
+	if (!is_defined(in_place))    in_place = true
+    ip = (in_place==true) ? ip : ip.duplicate()
+    ic = new ImageConverter(ip)
+    ic.convertToGray8()
+    return ip
+}
+        
+function  get_channel(ip, channel){
+    /*
+    Return a channel from a color image as a new  ImagePlus.
+    channel: "red", "green","blue", "alpha", "brightness", 
+    */
+    proc = ip.getProcessor()    
+    if (channel ==   "red") ret = proc.getChannel(1, null)
+    else if (channel == "green") ret = proc.getChannel(2, null)
+    else if (channel == "blue") ret = proc.getChannel(3, null)
+    else if (channel == "alpha") ret = proc.getChannel(4, null)
+    else if (channel == "brightness") ret =	proc.getBrightness()
+    else throw ("Invalid channel " + channel)
+    return new ImagePlus(ip.getTitle() + " channel: " + channel, ret)
+}
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//Thresholder
+///////////////////////////////////////////////////////////////////////////////////////////////////
+        
+function threshold(ip, min_threshold, max_threshold, in_place){
+	if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    ip.getProcessor().setThreshold(min_threshold, max_threshold, ImageProcessor.NO_LUT_UPDATE)    
+    WindowManager.setTempCurrentImage(ip)
+    new Thresholder().run("mask")
+    return ip
+}
+        
+function auto_threshold(ip, dark_background, method, in_place){
+	if (!is_defined(dark_background))    dark_background = false
+	if (!is_defined(method))    method = AutoThresholder.getMethods()[0]
+	if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    ip.getProcessor().setAutoThreshold(method, dark_background , ImageProcessor.NO_LUT_UPDATE)
+    WindowManager.setTempCurrentImage(ip)
+    thresholder=new Thresholder().run("mask")
+    return ip
+}
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//Binary functions    
+///////////////////////////////////////////////////////////////////////////////////////////////////
+        
+function binary_op(ip, op, dark_background, iterations, count, in_place){
+    /*
+    op = "erode","dilate", "open","close", "outline", "fill holes", "skeletonize"
+    */
+    if (!is_defined(dark_background))    dark_background = false
+    if (!is_defined(iterations))    iterations = 1
+    if (!is_defined(count))    count = 1
+    if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    binary = new Binary()    
+    Binary.count = count
+    Binary.iterations = iterations
+    Prefs.blackBackground=dark_background      
+    binary.setup(op, ip)
+    binary.run(ip.getProcessor())
+    return ip
+}
+        
+function binary_erode(ip, dark_background, iterations, count, in_place){
+    return binary_op(ip, "erode", dark_background, iterations, count, in_place)
+}
+        
+function binary_dilate(ip, dark_background, iterations, count, in_place){
+    return binary_op(ip, "dilate", dark_background, iterations, count, in_place)
+}
+        
+function binary_open(ip, dark_background, iterations, count, in_place){
+    return binary_op(ip, "open", dark_background, iterations, count, in_place)
+}
+        
+function binary_close(ip, dark_background, iterations, count, in_place){
+    return binary_op(ip, "close", dark_background, iterations, count, in_place)
+}
+        
+function binary_outline(ip, dark_background, in_place){
+    return binary_op(ip, "outline", dark_background, 1, 1, in_place)
+}
+        
+function binary_fill_holes(ip, dark_background, in_place){
+    return binary_op(ip, "fill holes", dark_background, 1, 1, in_place)
+}
+        
+function  binary_skeletonize(ip, dark_background, in_place){
+    return binary_op(ip, "skeletonize", dark_background, 1, 1, in_place)
+}    
+        
+function analyse_particles(ip, min_size, max_size, fill_holes, exclude_edges, extra_measurements,print_table, output_image, minCirc, maxCirc){
+    /*
+    Returns: tuple (ResultsTable results_table, ImagePlus output_image)
+    output_image = "outlines", "overlay_outlines", "masks", "overlay_masks", "roi_masks" or null
+    extra_measurements = mask with Measurements.CENTROID, PERIMETER, RECT, MIN_MAX, ELLIPSE, CIRCULARITY, AREA_FRACTION, INTEGRATED_DENSITY, INVERT_Y, FERET, KURTOSIS, MEDIAN, MODE, SKEWNESS, STD_DEV 
+    Measurements is a mask of flags: https://imagej.nih.gov/ij/developer/api/ij/measure/Measurements.html.
+    Returned ResultsTable hold public fields: https://imagej.nih.gov/ij/developer/api/ij/measure/ResultsTable.html
+    
+    */
+    if (!is_defined(fill_holes))    fill_holes = true
+    if (!is_defined(exclude_edges))    exclude_edges = true
+    if (!is_defined(extra_measurements))    extra_measurements = 0
+    if (!is_defined(print_table))    print_table = false
+    if (!is_defined(output_image))    output_image = "outlines"
+    if (!is_defined(minCirc))    minCirc = 0.0
+    if (!is_defined(maxCirc))    maxCirc = 1.0
+    rt = new ResultsTable()
+    show_summary = false 
+    var options = ParticleAnalyzer.SHOW_RESULTS | ParticleAnalyzer.CLEAR_WORKSHEET 
+    /*
+        ParticleAnalyzer.SHOW_ROI_MASKS | \
+        //ParticleAnalyzer.RECORD_STARTS | \
+        //ParticleAnalyzer.ADD_TO_MANAGER | \
+        //ParticleAnalyzer.FOUR_CONNECTED | \
+        //ParticleAnalyzer.IN_SITU_SHOW | \
+        //ParticleAnalyzer.SHOW_NONE | \
+    */
+    if (show_summary)             options = options | ParticleAnalyzer.DISPLAY_SUMMARY 
+    if (output_image == "outlines") options = options | ParticleAnalyzer.SHOW_OUTLINES 
+    else if (output_image == "overlay_outlines") options = options | ParticleAnalyzer.SHOW_OVERLAY_OUTLINES
+    else if (output_image == "masks")     options = options | ParticleAnalyzer.SHOW_MASKS
+    else if (output_image == "overlay_masks")     options = options | ParticleAnalyzer.SHOW_OVERLAY_MASKS
+    else if (output_image == "roi_masks")     options = options | ParticleAnalyzer.SHOW_ROI_MASKS
+    //ParticleAnalyzer.SHOW_ROI_MASKS
+    if (exclude_edges)            options = options | ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES
+    if (fill_holes)               options = options | ParticleAnalyzer.INCLUDE_HOLES
+    measurements = Measurements.AREA  | Measurements.MEAN  |  Measurements.CENTER_OF_MASS | Measurements.RECT
+    pa = new ParticleAnalyzer(options, measurements, rt, min_size, max_size, minCirc, maxCirc)
+    pa.setHideOutputImage(true)
+    ParticleAnalyzer.setResultsTable(rt)
+    if (pa.analyze(ip)){
+        if (print_table){
+            print (rt.getColumnHeadings())
+            for (var row= 0; row<rt.counter; row++){
+                print (rt.getRowAsString(row))
+            }
+        }
+        return [rt, pa.getOutputImage()]
+    }
+}        
+
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//Image operators
+///////////////////////////////////////////////////////////////////////////////////////////////////
+        
+function op_image(ip1, ip2, op, float_result, in_place){
+    /*
+    op = "add","subtract",  "multiply","divide", "and", "or", "xor", "min", "max", "average", "difference" or "copy"
+    */
+    if (!is_defined(float_result))    float_result = false
+    if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    ic = new ImageCalculator()
+    pars = op
+    if (float_result) op = op + " float" 
+    ic.run(pars, ip1, ip2)
+    return ip1
+}
+        
+function  op_const(ip, op, val, in_place){
+    /*
+    op = "add","subtract",  "multiply","divide", "and", "or", "xor", "min", "max", "gamma", "set" or "log", "exp", "sqr", "sqrt","abs"
+    */
+    if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    pr = ip.getProcessor()
+    if (op == 'add') pr.add(val)
+    else if (op == 'sub') pr.subtract(val)
+    else if (op == 'multiply') pr.multiply(val)
+    else if (op == 'divide' && val!=0) pr.multiply(1.0/val)
+    else if (op == 'and') pr.and(val)
+    else if (op == 'or') pr.or(val)
+    else if (op == 'xor') pr.xor(val)
+    else if (op == 'min') {pr.min(val);pr.resetMinAndMax()}
+    else if (op == 'max') {pr.max(val);pr.resetMinAndMax()}
+    else if (op == 'gamma' && (0.05 < val) && (val < 5.0)) pr.gamma(val)
+    else if (op == 'set') pr.set(val)
+    else if (op == 'log') pr.log()
+    else if (op == 'exp') pr.exp()        
+    else if (op == 'sqr') pr.sqr()        
+    else if (op == 'sqrt') pr.sqrt()        
+    else if (op == 'abs') {pr.abs();pr.resetMinAndMax()}
+    else throw "Invalid operation " + op
+    return ip
+}
+        
+function op_fft(ip1, ip2, op, do_inverse){
+    /*
+    Images must have same sizes, and multiple of  2  height and width.
+    op = "correlate" (complex conjugate multiply), "convolve" (Fourier domain multiply), "deconvolve" (Fourier domain divide)
+    */
+    if (!is_defined(do_inverse))    do_inverse = true
+    var op_index
+    if   (op == "correlate") op_index = 0
+    else if (op == "convolve") op_index = 1
+    else if (op == "deconvolve")  op_index = 2
+    else throw "Invalid operation " + op  
+    return new FFTMath().doMath(ip1, ip2, op_index, do_inverse)
+}
+        
+function op_rank(ip, op, kernel_radius ,  dark_outliers ,threshold, in_place){
+    /*
+    op = "mean", "min", "max", "variance", "median", "close_maxima", "open_maxima", "remove_outliers", "remove_nan", "despeckle"
+    */
+    if (!is_defined(kernel_radius))    kernel_radius = 1
+    if (!is_defined(dark_outliers))    dark_outliers = false
+    if (!is_defined(threshold))    threshold = 50
+    if (!is_defined(in_place))    in_place = true
+    var filter_type 
+    if   (op == "mean") filter_type = RankFilters.MEAN
+    else if (op == "min") filter_type = RankFilters.MIN
+    else if (op == "max") filter_type = RankFilters.MAX
+    else if (op == "variance") filter_type = RankFilters.VARIANCE
+    else if (op == "median") filter_type = RankFilters.MEDIAN
+    else if (op == "close_maxima") filter_type = RankFilters.CLOSE
+    else if (op == "open_maxima") filter_type = RankFilters.OPEN
+    else if (op == "remove_outliers") filter_type = RankFilters.OUTLIERS
+    else if (op == "remove_nan") filter_type = RankFilters.REMOVE_NAN
+    else if (op == "despeckle") {filter_type = RankFilters.MEDIAN, kernel_radius = 1}
+    else throw "Invalid operation " + op
+    ip = in_place ? ip : ip.duplicate()
+    new RankFilters().rank(ip.getProcessor(), kernel_radius, filter_type, dark_outliers ? RankFilters.DARK_OUTLIERS : RankFilters.BRIGHT_OUTLIERS ,threshold)
+    return ip    
+}
+        
+function op_edm(ip, op, dark_background, in_place){
+    /*
+    Euclidian distance map & derived  operations
+    op ="edm", "watershed","points", "voronoi"
+    */    
+    if (!is_defined(op))    op = "edm"
+    if (!is_defined(dark_background))    dark_background = false
+    if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    pr = ip.getProcessor()
+    var edm=new EDM()
+    Prefs.blackBackground=dark_background      
+    if  (op=="edm"){      
+        //pr.setPixels(0, edm.makeFloatEDM(pr, 0, false));
+        //pr.resetMinAndMax();                
+        if (dark_background)  pr.invert()
+        edm.toEDM(pr)
+    }else{
+        edm.setup(op, ip)
+        edm.run(pr)
+    }
+    return ip
+}
+        
+function watershed(ip, dark_background, in_place){
+	if (!is_defined(dark_background))    dark_background = false
+	if (!is_defined(in_place))    in_place = true
+    return op_edm(ip, "watershed", dark_background, in_place)
+}
+        
+function ultimate_points(ip, dark_background, in_place){
+	if (!is_defined(dark_background))    dark_background = false
+	if (!is_defined(in_place))    in_place = true
+    return op_edm(ip, "points", dark_background, in_place)
+}
+        
+function veronoi(ip, dark_background, in_place){
+	if (!is_defined(dark_background))    dark_background = false
+	if (!is_defined(in_place))    in_place = true
+    return op_edm(ip, "voronoi", dark_background, in_place)
+}
+        
+function edm(ip, dark_background, in_place){
+	if (!is_defined(dark_background))    dark_background = false
+	if (!is_defined(in_place))    in_place = true
+    return op_edm(ip, "edm", dark_background, in_place)
+}
+        
+function op_filter(ip, op, in_place){
+
+    /*
+    This is redundant as just calls processor methods.
+    op ="invert", "smooth", "sharpen", "edge", "add"
+    */    
+    if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    f = new Filters()
+    f.setup(op, ip )
+    f.run(ip.getProcessor())
+    return ip
+}
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//Other operations
+///////////////////////////////////////////////////////////////////////////////////////////////////
+        
+function gaussian_blur(ip, sigma_x, sigma_y, accuracy, in_place){
+	if (!is_defined(sigma_x))    sigma_x = 3.0
+	if (!is_defined(sigma_y))    sigma_y = 3.0
+	if (!is_defined(accuracy))    accuracy = 0.01
+	if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    new GaussianBlur().blurGaussian(ip.getProcessor(),  sigma_x, sigma_y, accuracy)
+    return ip
+}
+        
+function find_maxima(ip, tolerance, threshold, output_type, exclude_on_edges, is_edm ){
+    /*
+    Returns new ImagePlus
+    tolerance:  maxima are accepted only if protruding more than this value  from the ridge to a higher maximum
+    threshhold: minimum height of a maximum (uncalibrated);
+    output_type = SINGLE_POINTS, IN_TOLERANCE or SEGMENTED.  No output image is created for output types POINT_SELECTION, LIST and COUNT.   
+    */
+    if (!is_defined(tolerance))    tolerance = 25
+    if (!is_defined(threshold))    threshold =  ImageProcessor.NO_THRESHOLD
+    if (!is_defined(output_type))    output_type = MaximumFinder.IN_TOLERANCE
+    if (!is_defined(exclude_on_edges))    exclude_on_edges = false
+    if (!is_defined(is_edm))    is_edm = false
+    byte_processor =  new MaximumFinder().findMaxima(ip.getProcessor(), tolerance, threshold, output_type, exclude_on_edges, is_edm)     
+    return new ImagePlus(ip.getTitle() + " maxima", byte_processor)
+}
+        
+function get_maxima_points(ip, tolerance, exclude_on_edges){
+    if (!is_defined(tolerance))    tolerance = 25
+    if (!is_defined(exclude_on_edges))    exclude_on_edges = false
+    polygon =  new MaximumFinder().getMaxima(ip.getProcessor(), tolerance, exclude_on_edges)
+    return (polygon.xpoints, polygon.ypoints)
+}
+        
+function enhance_contrast(ip, equalize_histo, saturated_pixels, normalize, stack_histo, in_place){
+	if (!is_defined(equalize_histo))    equalize_histo = true
+	if (!is_defined(saturated_pixels))    saturated_pixels =  0.5
+	if (!is_defined(normalize))    normalize = false
+	if (!is_defined(stack_histo))    stack_histo = false
+	if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    ce = new ContrastEnhancer()
+    if (equalize_histo){
+        ce.equalize(ip.getProcessor());
+    } else{
+        ce.stretchHistogram(ip.getProcessor(), saturated_pixels)
+        if (normalize){
+            ip.getProcessor().setMinAndMax(0,(ip.getProcessor().getBitDepth()==32) ? 1.0 : ip.getProcessor().maxValue())
+        }
+    }
+    return ip   
+}
+        
+function shadows(ip, op, in_place){
+    /*
+    op ="north","northeast", "east", "southeast","south", "southwest", "west","northwest"
+    */
+    if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    shadows= new Shadows()
+    shadows.setup(op, ip)
+    shadows.run(ip.getProcessor())
+    return ip
+}
+        
+function unsharp_mask(ip, sigma, weight, in_place){
+    /*
+    Float processor
+    */    
+    if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    ip.getProcessor().snapshot()
+    unsharp=new UnsharpMask()
+    USmask.setup("  ", ip)
+    USmask.sharpenFloat( ip.getProcessor(),sigma, weight)
+    return ip
+}
+        
+function subtract_background(ip, radius, create_background, dark_background, use_paraboloid, do_presmooth, correctCorners, rgb_brightness, in_place){
+	if (!is_defined(radius))    radius = 50
+	if (!is_defined(create_background))    create_background = false
+	if (!is_defined(dark_background))    dark_background = false
+	if (!is_defined(use_paraboloid))    use_paraboloid = true
+	if (!is_defined(do_presmooth))    do_presmooth = true
+	if (!is_defined(correctCorners))    correctCorners = true
+    if (!is_defined(rgb_brightness))    rgb_brightness = false
+    if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    if (rgb_brightness)
+        new BackgroundSubtracter().rollingBallBrightnessBackground(ip.getProcessor(), radius, create_background,! dark_background, use_paraboloid, do_presmooth, correctCorners)
+    else
+        new BackgroundSubtracter().rollingBallBackground(ip.getProcessor(), radius, create_background, !dark_background, use_paraboloid, do_presmooth, correctCorners)        
+    return ip
+}
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//FFT
+///////////////////////////////////////////////////////////////////////////////////////////////////
+        
+function image_fft(ip, show){
+	if (!is_defined(show))    show = true
+    WindowManager.setTempCurrentImage(ip)
+    fft = new FFT()
+    fft.run("fft")    
+    //TODO: how to avoid it to be created?
+    //ret =  ImagePlus("FHT of " + ip.getTitle(), WindowManager.getCurrentImage().getProcessor())
+    ret = WindowManager.getCurrentImage()
+    if (show == false)
+        WindowManager.getCurrentImage().hide()
+    return ret
+}
+        
+function image_ffti(ip, show){
+	if (!is_defined(show))    show = true
+    WindowManager.setTempCurrentImage(ip)
+    fft = new FFT()
+    fft.run("inverse")
+    //WindowManager.getCurrentImage().hide()
+    //TODO: how to avoid it to be created?
+    //ret = WindowManager.getCurrentImage()
+    //WindowManager.getCurrentImage().hide()
+    //ret =  ImagePlus(ip.getTitle() + " ffti", WindowManager.getCurrentImage().getProcessor())
+    ret = WindowManager.getCurrentImage()
+    if (show == false)
+        WindowManager.getCurrentImage().hide()
+    
+    return ret
+}
+        
+function bandpass_filter(ip, small_dia_px, large_dia_px, suppress_stripes, stripes_tolerance_direction, autoscale_after_filtering, saturate_if_autoscale, display_filter, in_place){
+    /*
+    suppress_stripes = 0 for none, 1 for horizontal, 2 for vertical
+    */
+    if (!is_defined(suppress_stripes))    suppress_stripes = 0
+    if (!is_defined(stripes_tolerance_direction))    stripes_tolerance_direction = 5.0
+    if (!is_defined(autoscale_after_filtering))    autoscale_after_filtering = false
+    if (!is_defined(saturate_if_autoscale))    saturate_if_autoscale = false
+    if (!is_defined(display_filter))    display_filter = false
+    if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    filter=  new FFTFilter();
+    FFTFilter.filterLargeDia = large_dia_px
+    FFTFilter.filterSmallDia = small_dia_px
+    FFTFilter.choiceIndex = suppress_stripes
+    FFTFilter.toleranceDia = stripes_tolerance_direction
+    FFTFilter.doScalingDia = autoscale_after_filtering
+    FFTFilter.saturateDia = saturate_if_autoscale
+    FFTFilter.displayFilter =display_filter
+    filter.setup(null, ip);
+    filter.run(ip.getProcessor())
+    return ip
+}
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//Convolution
+///////////////////////////////////////////////////////////////////////////////////////////////////
+
+KERNEL_BLUR = [[0.1111, 0.1111, 0.1111], [0.1111, 0.1111, 0.1111], [0.1111, 0.1111, 0.1111]]
+KERNEL_SHARPEN = [[0.0, -0.75, 0.0], [-0.75, 4.0, -0.75], [0.0, -0.75, 0.0]]
+KERNEL_SHARPEN_2 = [[-1.0, -1.0, -1.0], [-1.0, 9.0, -1.0], [-1.0, -1.0, -1.0]]
+KERNEL_LIGHT = [[0.1, 0.1, 0.1], [0.1, 1.0, 0.1],[0.1, 0.1, 0.1]]
+KERNEL_DARK = [[0.01, 0.01, 0.01],[0.01, 0.5, 0.01],[0.01, 0.01, 0.01]]
+KERNEL_EDGE_DETECT = [[0.0, -0.75, 0.0], [-0.75, 3.0, -0.75], [0.0, -0.75, 0.0]]
+KERNEL_EDGE_DETECT_2 = [[-0.5, -0.5, -0.5], [-0.5, 4.0, -0.5], [-0.5, -0.5, -0.5]]
+KERNEL_DIFFERENTIAL_EDGE_DETECT = [[-1.0, 0.0, 1.0], [0.0, 0.0, 0.0], [1.0, 0.0, -1.0]]
+KERNEL_PREWITT = [[-2.0, -1.0, 0.0], [-1.0,  0.0,  1.0 ], [0.0, 1.0, 2.0]]
+KERNEL_SOBEL = [[2.0, 2.0, 0.0], [2.0,  0.0,  -2.0 ],  [0.0, -2.0, -2.0]]
+        
+function  convolve(ip, kernel, in_place){
+    /*
+    kernel: list of lists
+    */
+    if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    kernel_width = kernel.length
+    kernel_height= kernel[0].length
+    kernel =flatten(kernel)
+    
+    //Convolver().convolve(ip.getProcessor(), kernel, kernel_width, kernel_height) 
+    //ip.getProcessor().convolve(to_array(kernel, '[f'), kernel_width, kernel_height)
+    ip.getProcessor().convolve(kernel, kernel_width, kernel_height)
+    return ip
+}
+        
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//Shortcut  to ImageProcessor methods
+///////////////////////////////////////////////////////////////////////////////////////////////////
+        
+function invert(ip, in_place){
+	if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    ip.getProcessor().invert()
+    return ip
+}
+        
+function smooth(ip, in_place){
+	if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    ip.getProcessor().smooth()
+    return ip
+}
+        
+function sharpen(ip, in_place){
+	if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    ip.getProcessor().sharpen()
+    return ip
+}
+        
+function edges(ip, in_place){ //Sobel
+	if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    ip.getProcessor().findEdges()
+    return ip
+}
+        
+function noise(ip, sigma, in_place){
+	if (!is_defined(sigma))    sigma =  25.0
+	if (!is_defined(in_place))    in_place = true
+    ip = in_place ? ip : ip.duplicate()
+    ip.getProcessor().noise(sigma)
+    return ip
+}
+        
+function remap(ip, min, max, in_place){
+	if (!is_defined(min))    min = null
+	if (!is_defined(max))    max = null
+	if (!is_defined(in_place))    in_place = true	
+    ip = in_place ? ip : ip.duplicate()
+    if ((min ==null) || (max == null)){
+        stats = get_statistics(ip, Measurements.MIN_MAX)
+        if (min== null) min = stats.min
+        if (max == null) max = stats.max
+    }
+    ip.getProcessor().setMinAndMax(min, max)
+    return ip
+}
+        
+function set_lut(ip, r, g, b){
+    /*
+    r,g and b are lists of 256 integers
+    */
+    r =  r.map(function(x) {return (x<128) ? x : (x-256 )})
+    g =  g.map(function(x) {return (x<128) ? x : (x-256 )})
+    b =  b.map(function(x) {return (x<128) ? x : (x-256 )})    
+    ip.setLut(new LUT(to_array(r,'b'),to_array(g,'b'),to_array(b,'b')))
+}
+        
+function resize(ip, width, height){
+    /*
+    Returns new ImagePlus
+    */
+    p = ip.getProcessor().resize(width, height)
+    return new ImagePlus(ip.getTitle() + " resized", p)
+}
+        
+function binning(ip, factor){
+    p=ip.getProcessor().bin(factor)
+    return new ImagePlus(ip.getTitle() + " resized", p)
+}
+        
+function get_histogram(ip, hist_min, hist_max, hist_bins, roi){
+    /*
+    hist_min, hist_max, hist_bins used only for float images (otherwise fixed to 0,255,256)
+    roi is list  [x,y,w,h]
+    */
+    if (!is_defined(hist_min))    hist_min = 0
+    if (!is_defined(hist_max))    hist_max = 0
+    if (!is_defined(hist_bins))    hist_bins = 256
+    if (!is_defined(roi))    roi = null
+    if (roi == null) {
+    	ip.deleteRoi()    
+    } else {
+    	ip.setRoi(roi[0],roi[1],roi[2],roi[3])
+    }
+    image_statistics = ip.getStatistics(0, hist_bins, hist_min, hist_max)    
+    return to_array(image_statistics.getHistogram())
+}
+        
+function get_array(ip){
+    return ip.getProcessor().getIntArray()
+}
+        
+function get_line(ip, x1, y1, x2, y2){
+    return ip.getProcessor().getLine(x1, y1, x2, y2)
+}
+        
+function get_pixel_range(ip){
+    return (ip.getProcessor().getMin(), ip.getProcessor().getMax())
+}
+        
+function get_num_channels(ip){
+    return ip.getProcessor().getNChannels()
+}
+        
+function is_binary(ip){
+    return ip.getProcessor().isBinary()    
+}
+        
+function get_pixel(ip, x, y){
+    return ip.getProcessor().getPixel(x,y)
+}
+        
+function get_pixel_array(ip, x, y){
+    a = [0]*get_num_channels(ip)
+    return ip.getProcessor().getPixel(x,y,a)
+}
+        
+function get_pixels(ip){
+    return ip.getProcessor().getPixels()
+}
+        
+function get_width(ip){
+    return ip.getProcessor().getWidth()
+}
+        
+function get_height(ip){
+    return ip.getProcessor().getHeight()
+}
+        
+function get_row(ip, y){
+    a = [0]*get_width(ip)
+    array = jarray.array(a,'i')
+    ip.getProcessor().getRow(0, y, array, get_width(ip))
+    return array
+}
+        
+function get_col(ip, x){
+    a = [0]*get_height(ip)
+    array = jarray.array(a,'i')
+    ip.getProcessor().getColumn(x, 0, array, get_height(ip))
+    return array     
+}
+        
+function get_statistics(ip, measurements){
+    /*
+    Measurements is a mask of flags: https://imagej.nih.gov/ij/developer/api/ij/measure/Measurements.html.
+    Statistics object hold public fields: https://imagej.nih.gov/ij/developer/api/ij/process/ImageStatistics.html
+    */
+    if (!is_defined(measurements))    measurements = null
+    if (measurements == null){
+        return ip.getStatistics()
+    } else {
+        return ip.getStatistics(measurements)
+    }
+}
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//Image stack functions
+///////////////////////////////////////////////////////////////////////////////////////////////////
+        
+function create_stack(ip_list, keep, title){
+    if (!is_defined(keep))    keep = true
+    if (!is_defined(title))    title = null
+    stack = new Concatenator().concatenate(ip_list, keep)
+    if (title != null)
+        stack.setTitle(title)
+    return stack
+}
+        
+function reslice(stack, start_at, vertically, flip, output_pixel_spacing, avoid_interpolation, title){
+	if (!is_defined(start_at))    start_at = "Top"
+	if (!is_defined(vertically))    vertically = true
+	if (!is_defined(flip))    flip = true
+	if (!is_defined(output_pixel_spacing))    output_pixel_spacing = 1.0
+	if (!is_defined(avoid_interpolation))    avoid_interpolation = true
+	if (!is_defined(title))    title = null
+    ss = new Slicer()
+    ss.rotate = vertically
+    ss.startAt = start_at 
+    ss.flip = flip
+    ss.nointerpolate =  avoid_interpolation
+    ss.outputZSpacing = output_pixel_spacing
+    stack =  ss.reslice(stack)
+    if (title != null)
+        stack.setTitle(title)
+    return stack
+}

script/_Lib/ijutils.py

@@ -0,0 +1,707 @@
+####################################################################################################
+#  Facade to ImageJ functionality
+####################################################################################################
+
+#More information on:
+#   Image:   https://imagej.nih.gov/ij/docs/guide/146-28.html#toc-Section-28
+#   Process: https://imagej.nih.gov/ij/docs/guide/146-29.html#toc-Section-29
+#   Analyze: https://imagej.nih.gov/ij/docs/guide/146-30.html#toc-Section-30
+
+import ch.psi.utils.Convert as Convert
+import ch.psi.pshell.imaging.Utils as Utils
+from startup import get_context
+import java.awt.image.BufferedImage as BufferedImage
+import jarray
+
+import ij.IJ as IJ
+import ij.ImageJ as ImageJ
+import ij.WindowManager as WindowManager
+import ij.ImagePlus as ImagePlus
+import ij.Prefs as Prefs
+import ij.io.FileSaver as FileSaver
+
+import ij.process.ImageProcessor as ImageProcessor
+import ij.process.ByteProcessor as ByteProcessor
+import ij.process.ShortProcessor as ShortProcessor
+import ij.process.ColorProcessor as ColorProcessor
+import ij.process.FloatProcessor as FloatProcessor
+import ij.process.ImageConverter as ImageConverter
+import ij.process.AutoThresholder as AutoThresholder
+import ij.process.LUT as LUT
+import ij.measure.Measurements as Measurements
+import ij.measure.ResultsTable as ResultsTable
+import ij.plugin.filter.Analyzer as Analyzer
+import ij.plugin.filter.GaussianBlur as GaussianBlur
+import ij.plugin.filter.Filters as Filters
+import ij.plugin.filter.FFTFilter as FFTFilter
+import ij.plugin.filter.BackgroundSubtracter as BackgroundSubtracter
+import ij.plugin.filter.EDM as EDM
+import ij.plugin.filter.Shadows as Shadows
+import ij.plugin.filter.UnsharpMask as UnsharpMask
+import ij.plugin.filter.MaximumFinder as MaximumFinder 
+import ij.plugin.filter.EDM as EDM
+import ij.plugin.filter.Shadows as Shadows
+import ij.plugin.filter.UnsharpMask as UnsharpMask
+import ij.plugin.filter.RankFilters as RankFilters
+import ij.plugin.filter.Convolver as Convolver
+import ij.plugin.filter.ParticleAnalyzer as ParticleAnalyzer
+
+import ij.plugin.ContrastEnhancer as ContrastEnhancer
+import ij.plugin.Thresholder as Thresholder
+import ij.plugin.ImageCalculator as ImageCalculator
+import ij.plugin.FFT as FFT
+import ij.plugin.Concatenator as Concatenator
+
+#ImageJ customizations
+import ch.psi.pshell.imaging.ij.FFTMath as FFTMath
+import ch.psi.pshell.imaging.ij.FFTFilter as FFTFilter
+import ch.psi.pshell.imaging.ij.Binary as Binary
+import ch.psi.pshell.imaging.ij.Slicer as Slicer
+
+
+#This eliminates the error messages due to the bug on ij.gui.ImageWindow row 555 (ij is null)
+if not "_image_j" in globals().keys():
+    _image_j = ImageJ(None, ImageJ.NO_SHOW)
+    
+###################################################################################################
+#Image creation, copying & saving
+###################################################################################################
+def load_image(image, title = "img"):    
+    """
+    image: file name or BufferedImage
+    """    
+    if isinstance(image, str):
+        try:
+            file = get_context().setup.expandPath(image)
+        except:
+            pass
+        try:
+            image = Utils.newImage(file)
+        except:
+            #try loading from assembly
+            image = get_context().setup.getAssemblyImage(image)
+    return ImagePlus(title, image)
+
+
+
+def load_array(array, width=None, height=None, title = "img"):    
+    """
+    array: 1d array if width and height defined , or else 2d array to be flattened.
+    """    
+    #2D
+    if (width==None) and (height==None):
+        if array.typecode == '[B': proc = ByteProcessor(len(array[0]), len(array), Convert.flatten(array))
+        elif array.typecode == '[S': proc = ShortProcessor(len(array[0]), len(array), Convert.flatten(array), None)
+        elif array.typecode in ['[I','[F', '[D']: proc = FloatProcessor(len(array[0]), len(array), Convert.flatten(array))        
+        else: raise Exception("Invalid array type")   
+    #1D
+    else:
+        if (len(array) > width*height):
+            array = array[:(width*height)]
+        if array.typecode == 'b': proc = ByteProcessor(width, height, array)
+        elif array.typecode == 'h': proc = ShortProcessor(width, height, array, None)
+        elif array.typecode in ['i','f','d']: proc = FloatProcessor(width, height, array)
+        else: raise Exception("Invalid array type")   
+    return ImagePlus(title, proc)
+
+def save_image(ip, path=None, format = None):
+    """
+    Saves image or stack
+    If parameters omitted, saves image again in same location, with same format.
+    """
+    fs = FileSaver(ip)
+    if path == None: fs.save()
+    else:
+        try:
+            path = get_context().setup.expandPath(path)
+        except:
+            pass           
+        if format == "bmp": fs.saveAsBmp(path) 
+        elif format == "fits": fs.saveAsFits(path) 
+        elif format == "gif": fs.saveAsGif(path) 
+        elif format == "jpeg": fs.saveAsJpeg(path) 
+        elif format == "lut": fs.saveAsLut(path) 
+        elif format == "pgm": fs.saveAsPgm(path) 
+        elif format == "png": fs.saveAsPng(path) 
+        elif format == "raw" and ip.getImageStackSize()>1: fs.saveAsRawStack(path) 
+        elif format == "raw": fs.saveAsRaw(path) 
+        elif format == "txt": fs.saveAsText(path)
+        elif format == "tiff" and ip.getImageStackSize()>1: fs.saveAsTiffStack(path)
+        elif format == "tiff": fs.saveAsTiff(path)
+        elif format == "zip": fs.saveAsZip(path)   
+
+def new_image(width, height, image_type="byte", title = "img", fill_color = None):
+    """
+    type = "byte", "short", "color" or "float"
+    """
+    if image_type == "byte": p=ByteProcessor(width, height)
+    elif image_type == "short": p=ShortProcessor(width, height)
+    elif image_type == "color": p=ColorProcessor(width, height)
+    elif image_type == "float": p=FloatProcessor(width, height)
+    else: raise Exception("Invalid image type " + str(image_type))
+    ret = ImagePlus(title, p)    
+    if fill_color is not None:
+        p.setColor(fill_color)
+        p.resetRoi()
+        p.fill()
+    return ret    
+
+def sub_image(ip, x, y, width, height):
+    """
+    Returns new ImagePlus
+    """
+    ip.setRoi(x, y, width, height)
+    p=ip.getProcessor().crop()
+    return ImagePlus(ip.getTitle() + " subimage", p)    
+
+def copy_image(ip):
+    return ip.duplicate()
+
+def copy_image_to(ip_source, ip_dest, x, y):
+    ip_source.deleteRoi()    
+    ip_source.copy()
+    ip_dest.setRoi(x, y, ip_source.getWidth(), ip_source.getHeight())
+    ip_dest.paste()
+    ip_dest.changes = False
+    ip_dest.deleteRoi()
+        
+def pad_image(ip, left=0, right=0, top=0, bottom=0, fill_color = None):
+    p=ip.getProcessor()
+    width = p.getWidth() + left + right
+    height =  p.getHeight() + top + bottom        
+    image_type = get_image_type(ip)
+    ret = new_image(width, height, image_type, ip.getTitle() + " padded", fill_color)
+    ip.deleteRoi()
+    ip.copy()
+    ret.setRoi(left, top, p.getWidth(), p.getHeight())
+    ret.paste()
+    ret.changes = False
+    ret.deleteRoi()
+    return ret    
+
+def get_image_type(ip):
+    """
+    Returns: "byte", "short", "color" or "float"
+    """
+    p=ip.getProcessor()
+    if type(p) == ShortProcessor: return "short"
+    elif type(p) == ColorProcessor: return "color"
+    elif type(p) == FloatProcessor: return "float"
+    return "byte"
+
+###################################################################################################
+#Image type conversion
+###################################################################################################
+def grayscale(ip, do_scaling=None, in_place=True):
+    ip = ip if in_place else ip.duplicate()
+    ic = ImageConverter(ip)
+    if do_scaling is not None:
+        ic.setDoScaling(do_scaling)
+    ic.convertToGray8()
+    return ip
+
+def get_channel(ip, channel):
+    """
+    Return a channel from a color image as a new  ImagePlus.
+    channel: "red", "green","blue", "alpha", "brightness", 
+    """
+    proc = ip.getProcessor()    
+    if channel ==   "red": ret = proc.getChannel(1, None)
+    elif channel == "green": ret = proc.getChannel(2, None)
+    elif channel == "blue": ret = proc.getChannel(3, None)
+    elif channel == "alpha": ret = proc.getChannel(4, None)
+    elif channel == "brightness": ret =	proc.getBrightness()
+    else: raise Exception("Invalid channel " + str(channel))
+    return ImagePlus(ip.getTitle() + " channel: " + channel, ret)
+
+###################################################################################################
+#Thresholder
+###################################################################################################
+def threshold(ip, min_threshold, max_threshold, in_place=True):
+    ip = ip if in_place else ip.duplicate()
+    ip.getProcessor().setThreshold(min_threshold, max_threshold, ImageProcessor.NO_LUT_UPDATE)    
+    WindowManager.setTempCurrentImage(ip)
+    Thresholder().run("mask")
+    return ip
+
+def auto_threshold(ip, dark_background = False, method = AutoThresholder.getMethods()[0], in_place=True):
+    ip = ip if in_place else ip.duplicate()
+    ip.getProcessor().setAutoThreshold(method, dark_background , ImageProcessor.NO_LUT_UPDATE)
+    WindowManager.setTempCurrentImage(ip)
+    thresholder=Thresholder().run("mask")
+    return ip
+
+###################################################################################################
+#Binary functions    
+###################################################################################################
+def binary_op(ip, op, dark_background=False, iterations=1, count=1, in_place=True):
+    """
+    op = "erode","dilate", "open","close", "outline", "fill holes", "skeletonize"
+    """
+    ip = ip if in_place else ip.duplicate()
+    binary = Binary()    
+    Binary.count = count
+    Binary.iterations = iterations
+    Prefs.blackBackground=dark_background      
+    binary.setup(op, ip)
+    binary.run(ip.getProcessor())
+    return ip
+
+def binary_erode(ip, dark_background=False, iterations=1, count=1, in_place=True):
+    return binary_op(ip, "erode", dark_background, iterations, count, in_place)
+
+def binary_dilate(ip, dark_background=False, iterations=1, count=1, in_place=True):
+    return binary_op(ip, "dilate", dark_background, iterations, count, in_place)
+
+def binary_open(ip, dark_background=False, iterations=1, count=1, in_place=True):
+    return binary_op(ip, "open", dark_background, iterations, count, in_place)
+
+def binary_close(ip, dark_background=False, iterations=1, count=1, in_place=True):
+    return binary_op(ip, "close", dark_background, iterations, count)
+
+def binary_outline(ip, dark_background=False, in_place=True):
+    return binary_op(ip, "outline", dark_background, in_place=in_place)
+    
+def binary_fill_holes(ip, dark_background=False, in_place=True):
+    return binary_op(ip, "fill holes", dark_background, in_place=in_place)
+
+def binary_skeletonize(ip, dark_background=False, in_place=True):
+    return binary_op(ip, "skeletonize", dark_background, in_place=in_place)
+
+def  analyse_particles(ip, min_size, max_size, fill_holes = True, exclude_edges = True, extra_measurements = 0, \
+                       print_table = False, output_image = "outlines", minCirc = 0.0, maxCirc = 1.0):
+    """
+    Returns: tuple (ResultsTable results_table, ImagePlus output_image)
+    output_image = "outlines", "overlay_outlines", "masks", "overlay_masks", "roi_masks" or None
+    extra_measurements = mask with Measurements.CENTROID, PERIMETER, RECT, MIN_MAX, ELLIPSE, CIRCULARITY, AREA_FRACTION, INTEGRATED_DENSITY, INVERT_Y, FERET, KURTOSIS, MEDIAN, MODE, SKEWNESS, STD_DEV 
+    Measurements is a mask of flags: https://imagej.nih.gov/ij/developer/api/ij/measure/Measurements.html.
+    Returned ResultsTable hold public fields: https://imagej.nih.gov/ij/developer/api/ij/measure/ResultsTable.html
+    
+    """
+    rt = ResultsTable()
+    show_summary = False 
+    options = ParticleAnalyzer.SHOW_RESULTS | ParticleAnalyzer.CLEAR_WORKSHEET 
+    """
+        ParticleAnalyzer.SHOW_ROI_MASKS | \
+        #ParticleAnalyzer.RECORD_STARTS | \
+        #ParticleAnalyzer.ADD_TO_MANAGER | \
+        #ParticleAnalyzer.FOUR_CONNECTED | \
+        #ParticleAnalyzer.IN_SITU_SHOW | \
+        #ParticleAnalyzer.SHOW_NONE | \
+    """
+    if show_summary:             options = options | ParticleAnalyzer.DISPLAY_SUMMARY 
+    if output_image == "outlines": options = options | ParticleAnalyzer.SHOW_OUTLINES 
+    elif output_image == "overlay_outlines": options = options | ParticleAnalyzer.SHOW_OVERLAY_OUTLINES
+    elif output_image == "masks":     options = options | ParticleAnalyzer.SHOW_MASKS
+    elif output_image == "overlay_masks":     options = options | ParticleAnalyzer.SHOW_OVERLAY_MASKS
+    elif output_image == "roi_masks":     options = options | ParticleAnalyzer.SHOW_ROI_MASKS
+    #ParticleAnalyzer.SHOW_ROI_MASKS
+    if exclude_edges:            options = options | ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES
+    if fill_holes:               options = options | ParticleAnalyzer.INCLUDE_HOLES
+    measurements = Measurements.AREA  | Measurements.MEAN  |  Measurements.CENTER_OF_MASS | Measurements.RECT
+    pa = ParticleAnalyzer(options, measurements, rt, min_size, max_size, minCirc, maxCirc)
+    pa.setHideOutputImage(True)
+    pa.setResultsTable(rt)
+    if pa.analyze(ip):
+        if print_table:
+            print rt.getColumnHeadings()
+            for row in range (rt.counter):
+                print rt.getRowAsString(row)    
+        return (rt, pa.getOutputImage())
+
+###################################################################################################
+#Image operators
+###################################################################################################
+def op_image(ip1, ip2, op, float_result=False, in_place=True):
+    """
+    op = "add","subtract",  "multiply","divide", "and", "or", "xor", "min", "max", "average", "difference" or "copy"
+    """
+    ip1 = ip1 if in_place else ip1.duplicate()
+    ic = ImageCalculator()
+    pars = op
+    if float_result:
+        op = op + " float" 
+    ic.run(pars, ip1, ip2)
+    return ip1
+
+def op_const(ip, op, val, in_place=True):
+    """
+    op = "add","subtract",  "multiply","divide", "and", "or", "xor", "min", "max", "gamma", "set" or "log", "exp", "sqr", "sqrt","abs"
+    """
+    ip = ip if in_place else ip.duplicate()
+    pr = ip.getProcessor()
+    if op == 'add': pr.add(val)
+    elif op == 'sub': pr.subtract(val)
+    elif op == 'multiply': pr.multiply(val)
+    elif op == 'divide' and val!=0: pr.multiply(1.0/val)
+    elif op == 'and': pr.and(val)
+    elif op == 'or': pr.or(val)
+    elif op == 'xor': pr.xor(val)
+    elif op == 'min': pr.min(val);pr.resetMinAndMax()
+    elif op == 'max': pr.max(val);pr.resetMinAndMax()
+    elif op == 'gamma' and 0.05 < val < 5.0: pr.gamma(val)
+    elif op == 'set': pr.set(val)
+    elif op == 'log': pr.log()
+    elif op == 'exp': pr.exp()        
+    elif op == 'sqr': pr.sqr()        
+    elif op == 'sqrt': pr.sqrt()        
+    elif op == 'abs': pr.abs();pr.resetMinAndMax()
+    else: raise Exception("Invalid operation " + str(op))    
+    return ip
+
+def op_fft(ip1, ip2, op, do_inverse = True) :
+    """
+    Images must have same sizes, and multiple of  2  height and width.
+    op = "correlate" (complex conjugate multiply), "convolve" (Fourier domain multiply), "deconvolve" (Fourier domain divide)
+    """
+    if   op == "correlate": op_index = 0
+    elif op == "convolve":  op_index = 1
+    elif op == "deconvolve":  op_index = 2
+    else: raise Exception("Invalid operation " + str(op))    
+    return FFTMath().doMath(ip1, ip2, op_index, do_inverse)
+
+def op_rank(ip, op, kernel_radius =1 ,  dark_outliers = False ,threshold = 50, in_place=True):
+    """
+    op = "mean", "min", "max", "variance", "median", "close_maxima", "open_maxima", "remove_outliers", "remove_nan", "despeckle"
+    """
+    if   op == "mean": filter_type = RankFilters.MEAN
+    elif op == "min": filter_type = RankFilters.MIN
+    elif op == "max": filter_type = RankFilters.MAX
+    elif op == "variance": filter_type = RankFilters.VARIANCE
+    elif op == "median": filter_type = RankFilters.MEDIAN
+    elif op == "close_maxima": filter_type = RankFilters.CLOSE
+    elif op == "open_maxima": filter_type = RankFilters.OPEN
+    elif op == "remove_outliers": filter_type = RankFilters.OUTLIERS
+    elif op == "remove_nan": filter_type = RankFilters.REMOVE_NAN
+    elif op == "despeckle": filter_type, kernel_radius = RankFilters.MEDIAN, 1
+    else: raise Exception("Invalid operation " + str(op))
+    ip = ip if in_place else ip.duplicate()            
+    RankFilters().rank(ip.getProcessor(), kernel_radius, filter_type, RankFilters.DARK_OUTLIERS if dark_outliers else RankFilters.BRIGHT_OUTLIERS ,threshold)
+    return ip    
+
+def op_edm(ip, op="edm", dark_background=False, in_place=True):
+    """
+    Euclidian distance map & derived  operations
+    op ="edm", "watershed","points", "voronoi"
+    """    
+    ip = ip if in_place else ip.duplicate()        
+    pr = ip.getProcessor()
+    edm=EDM()
+    Prefs.blackBackground=dark_background      
+    if  op=="edm":        
+        #pr.setPixels(0, edm.makeFloatEDM(pr, 0, False));
+        #pr.resetMinAndMax();                
+        if dark_background:
+            pr.invert()
+        edm.toEDM(pr)
+    else:
+        edm.setup(op, ip)
+        edm.run(pr)
+    return ip
+
+def watershed(ip, dark_background=False, in_place=True):
+    return op_edm(ip, "watershed", dark_background, in_place)
+
+def ultimate_points(ip, dark_background=False, in_place=True):
+    return op_edm(ip, "points", dark_background, in_place)
+
+def veronoi(ip, dark_background=False, in_place=True):
+    return op_edm(ip, "voronoi", dark_background, in_place)
+
+def edm(ip, dark_background=False, in_place=True):
+    return op_edm(ip, "edm", dark_background, in_place)
+
+def op_filter(ip, op, in_place=True):    
+    """
+    This is redundant as just calls processor methods.
+    op ="invert", "smooth", "sharpen", "edge", "add"
+    """    
+    ip = ip if in_place else ip.duplicate()
+    f = Filters()
+    f.setup(op, ip )
+    f.run(ip.getProcessor())
+    return ip
+
+###################################################################################################
+#Other operations
+###################################################################################################
+def gaussian_blur(ip, sigma_x=3.0, sigma_y=3.0, accuracy = 0.01, in_place=True):
+    ip = ip if in_place else ip.duplicate()
+    GaussianBlur().blurGaussian(ip.getProcessor(),  sigma_x, sigma_y, accuracy)
+    return ip
+
+def find_maxima(ip, tolerance=25, threshold = ImageProcessor.NO_THRESHOLD, output_type=MaximumFinder.IN_TOLERANCE, exclude_on_edges = False, is_edm = False):
+    """
+    Returns new ImagePlus
+    tolerance:  maxima are accepted only if protruding more than this value  from the ridge to a higher maximum
+    threshhold: minimum height of a maximum (uncalibrated);
+    output_type = SINGLE_POINTS, IN_TOLERANCE or SEGMENTED.  No output image is created for output types POINT_SELECTION, LIST and COUNT.   
+    """
+    byte_processor =  MaximumFinder().findMaxima(ip.getProcessor(), tolerance, threshold, output_type, exclude_on_edges, is_edm)     
+    return ImagePlus(ip.getTitle() + " maxima", byte_processor)
+
+
+def get_maxima_points(ip, tolerance=25, exclude_on_edges = False):
+    polygon =  MaximumFinder().getMaxima(ip.getProcessor(), tolerance, exclude_on_edges)
+    return (polygon.xpoints, polygon.ypoints)
+    
+def enhance_contrast(ip, equalize_histo = True, saturated_pixels = 0.5, normalize = False, stack_histo = False, in_place=True):
+    ip = ip if in_place else ip.duplicate()
+    ce = ContrastEnhancer()
+    if equalize_histo:
+        ce.equalize(ip.getProcessor());
+    else:
+        ce.stretchHistogram(ip.getProcessor(), saturated_pixels)
+        if normalize:
+            ip.getProcessor().setMinAndMax(0,1.0 if (ip.getProcessor().getBitDepth()==32) else ip.getProcessor().maxValue())
+    return ip   
+
+def shadows(ip, op, in_place=True):
+    """
+    op ="north","northeast", "east", "southeast","south", "southwest", "west","northwest"
+    """
+    ip = ip if in_place else ip.duplicate()
+    shadows= Shadows()
+    shadows.setup(op, ip)
+    shadows.run(ip.getProcessor())
+    return ip
+
+def unsharp_mask(ip, sigma, weight, in_place=True):
+    """
+    Float processor
+    """    
+    ip = ip if in_place else ip.duplicate()
+    ip.getProcessor().snapshot()
+    unsharp=UnsharpMask()
+    USmask.setup("  ", ip)
+    USmask.sharpenFloat( ip.getProcessor(),sigma, weight)
+    return ip
+
+def subtract_background(ip, radius = 50, create_background=False, dark_background=False, use_paraboloid =True, do_presmooth = True, correctCorners = True, rgb_brightness=False, in_place=True):
+    ip = ip if in_place else ip.duplicate()
+    if rgb_brightness:        
+        BackgroundSubtracter().rollingBallBrightnessBackground(ip.getProcessor(), radius, create_background,not dark_background, use_paraboloid, do_presmooth, correctCorners)
+    else:
+        BackgroundSubtracter().rollingBallBackground(ip.getProcessor(), radius, create_background, not dark_background, use_paraboloid, do_presmooth, correctCorners)        
+    return ip
+
+###################################################################################################
+#FFT
+###################################################################################################
+def image_fft(ip, show = True):   
+    WindowManager.setTempCurrentImage(ip)
+    fft = FFT()
+    fft.run("fft")    
+    #TODO: how to avoid it to be created?
+    #ret =  ImagePlus("FHT of " + ip.getTitle(), WindowManager.getCurrentImage().getProcessor())
+    ret = WindowManager.getCurrentImage()
+    if not show:
+        WindowManager.getCurrentImage().hide()
+    return ret
+    
+
+def image_ffti(ip, show = True):   
+    WindowManager.setTempCurrentImage(ip)
+    fft = FFT()
+    fft.run("inverse")
+    #WindowManager.getCurrentImage().hide()
+    #TODO: how to avoid it to be created?
+    #ret = WindowManager.getCurrentImage()
+    #WindowManager.getCurrentImage().hide()
+    #ret =  ImagePlus(ip.getTitle() + " ffti", WindowManager.getCurrentImage().getProcessor())
+    ret = WindowManager.getCurrentImage()
+    if not show:
+        WindowManager.getCurrentImage().hide()
+    
+    return ret
+
+def bandpass_filter(ip, small_dia_px, large_dia_px, suppress_stripes = 0, stripes_tolerance_direction = 5.0, autoscale_after_filtering = False, saturate_if_autoscale = False, display_filter = False, in_place=True):
+    """
+    suppress_stripes = 0 for none, 1 for horizontal, 2 for vertical
+    """
+    ip = ip if in_place else ip.duplicate()
+    filter=  FFTFilter();
+    FFTFilter.filterLargeDia = large_dia_px
+    FFTFilter.filterSmallDia = small_dia_px
+    FFTFilter.choiceIndex = suppress_stripes
+    FFTFilter.toleranceDia = stripes_tolerance_direction
+    FFTFilter.doScalingDia = autoscale_after_filtering
+    FFTFilter.saturateDia = saturate_if_autoscale
+    FFTFilter.displayFilter =display_filter
+    filter.setup(None, ip);
+    filter.run(ip.getProcessor())
+    return ip
+
+###################################################################################################
+#Convolution
+###################################################################################################
+
+KERNEL_BLUR = [[0.1111, 0.1111, 0.1111], [0.1111, 0.1111, 0.1111], [0.1111, 0.1111, 0.1111]]
+KERNEL_SHARPEN = [[0.0, -0.75, 0.0], [-0.75, 4.0, -0.75], [0.0, -0.75, 0.0]]
+KERNEL_SHARPEN_2 = [[-1.0, -1.0, -1.0], [-1.0, 9.0, -1.0], [-1.0, -1.0, -1.0]]
+KERNEL_LIGHT = [[0.1, 0.1, 0.1], [0.1, 1.0, 0.1],[0.1, 0.1, 0.1]]
+KERNEL_DARK = [[0.01, 0.01, 0.01],[0.01, 0.5, 0.01],[0.01, 0.01, 0.01]]
+KERNEL_EDGE_DETECT = [[0.0, -0.75, 0.0], [-0.75, 3.0, -0.75], [0.0, -0.75, 0.0]]
+KERNEL_EDGE_DETECT_2 = [[-0.5, -0.5, -0.5], [-0.5, 4.0, -0.5], [-0.5, -0.5, -0.5]]
+KERNEL_DIFFERENTIAL_EDGE_DETECT = [[-1.0, 0.0, 1.0], [0.0, 0.0, 0.0], [1.0, 0.0, -1.0]]
+KERNEL_PREWITT = [[-2.0, -1.0, 0.0], [-1.0,  0.0,  1.0 ], [0.0, 1.0, 2.0]]
+KERNEL_SOBEL = [[2.0, 2.0, 0.0], [2.0,  0.0,  -2.0 ],  [0.0, -2.0, -2.0]]
+
+
+def convolve(ip, kernel, in_place=True):
+    """
+    kernel: list of lists
+    """
+    ip = ip if in_place else ip.duplicate()
+    kernel_width = len(kernel)
+    kernel_height= len(kernel[0])
+    kernel = [item for row in kernel for item in row]
+    #Convolver().convolve(ip.getProcessor(), kernel, kernel_width, kernel_height) 
+    ip.getProcessor().convolve(kernel, kernel_width, kernel_height)
+    return ip
+
+        
+###################################################################################################
+#Shortcut  to ImageProcessor methods
+###################################################################################################
+def invert(ip, in_place=True):
+    ip = ip if in_place else ip.duplicate()
+    ip.getProcessor().invert()
+    return ip
+
+def smooth(ip, in_place=True):
+    ip = ip if in_place else ip.duplicate()
+    ip.getProcessor().smooth()
+    return ip
+            
+def sharpen(ip, in_place=True):
+    ip = ip if in_place else ip.duplicate()
+    ip.getProcessor().sharpen()
+    return ip
+
+def edges(ip, in_place=True): #Sobel
+    ip = ip if in_place else ip.duplicate()
+    ip.getProcessor().findEdges()
+    return ip
+
+def noise(ip, sigma = 25.0, in_place=True):
+    ip = ip if in_place else ip.duplicate()
+    ip.getProcessor().noise(sigma)
+    return ip
+
+def remap(ip, min=None, max=None, in_place=True):
+    ip = ip if in_place else ip.duplicate()
+    if min is None or max is None:
+        stats = get_statistics(ip, Measurements.MIN_MAX)
+        if min is None: min = stats.min
+        if max is None: max = stats.max
+    ip.getProcessor().setMinAndMax(min, max)
+    return ip
+
+def set_lut(ip, r, g, b):
+    """
+    r,g and b are lists of 256 integers
+    """
+    r = [x if x<128 else x-256 for x in r]
+    g = [x if x<128 else x-256 for x in g]
+    b = [x if x<128 else x-256 for x in b]    
+    ip.setLut(LUT(jarray.array(r,'b'),jarray.array(g,'b'),jarray.array(b,'b')))
+
+def resize(ip, width, height):
+    """
+    Returns new ImagePlus
+    """
+    p = ip.getProcessor().resize(width, height)
+    return ImagePlus(ip.getTitle() + " resized", p)
+
+def binning(ip, factor):
+    p=ip.getProcessor().bin(factor)
+    return ImagePlus(ip.getTitle() + " resized", p)
+
+def get_histogram(ip, hist_min = 0, hist_max = 0, hist_bins = 256, roi=None):
+    """
+    hist_min, hist_max, hist_bins used only for float images (otherwise fixed to 0,255,256)
+    roi is list  [x,y,w,h]
+    """
+    if roi == None: ip.deleteRoi()    
+    else: ip.setRoi(roi[0],roi[1],roi[2],roi[3])
+    image_statistics = ip.getStatistics(0, hist_bins, hist_min, hist_max)    
+    return image_statistics.getHistogram()
+
+
+def get_array(ip):
+    return ip.getProcessor().getIntArray()
+
+def get_line(ip, x1, y1, x2, y2):
+    return ip.getProcessor().getLine(x1, y1, x2, y2)
+
+def get_pixel_range(ip):
+    return (ip.getProcessor().getMin(), ip.getProcessor().getMax())
+
+def get_num_channels(ip):
+    return ip.getProcessor().getNChannels()
+
+def is_binary(ip):
+    return ip.getProcessor().isBinary()    
+
+def get_pixel(ip, x, y):
+    return ip.getProcessor().getPixel(x,y)
+
+def get_pixel_array(ip, x, y):
+    a = [0]*get_num_channels(ip)
+    return ip.getProcessor().getPixel(x,y,a)
+
+def get_pixels(ip):
+    return ip.getProcessor().getPixels()
+
+def get_width(ip):
+    return ip.getProcessor().getWidth()
+
+def get_height(ip):
+    return ip.getProcessor().getHeight()
+
+def get_row(ip, y):
+    a = [0]*get_width(ip)
+    array = jarray.array(a,'i')
+    ip.getProcessor().getRow(0, y, array, get_width(ip))
+    return array
+
+def get_col(ip, x):
+    a = [0]*get_height(ip)
+    array = jarray.array(a,'i')
+    ip.getProcessor().getColumn(x, 0, array, get_height(ip))
+    return array     
+
+def get_statistics(ip, measurements = None):
+    """
+    Measurements is a mask of flags: https://imagej.nih.gov/ij/developer/api/ij/measure/Measurements.html.
+    Statistics object hold public fields: https://imagej.nih.gov/ij/developer/api/ij/process/ImageStatistics.html
+    """
+    if measurements is None:
+        return ip.getStatistics()
+    else:
+        return ip.getStatistics(measurements)
+
+###################################################################################################
+#Image stack functions
+###################################################################################################
+def create_stack(ip_list, keep=True, title = None):
+    stack = Concatenator().concatenate(ip_list, keep)
+    if title is not None:
+        stack.setTitle(title)
+    return stack
+
+def reslice(stack, start_at = "Top", vertically = True, flip = True, output_pixel_spacing=1.0, avoid_interpolation = True, title = None):
+    ss = Slicer()
+    ss.rotate = vertically
+    ss.startAt = start_at 
+    ss.flip = flip
+    ss.nointerpolate =  avoid_interpolation
+    ss.outputZSpacing = output_pixel_spacing
+    stack =  ss.reslice(stack)
+    if title is not None:
+        stack.setTitle(title)
+    return stack
+    
+    
+ 

script/_Lib/jeputils.js

@@ -0,0 +1,148 @@
+/////////////////////////////////////////////////////////////////////////////////////////////////// 
+//  Facade to JEP: Embedded Python
+/////////////////////////////////////////////////////////////////////////////////////////////////// 
+
+//Matplotlib won't work out of the box because it's default backend (Qt) uses signals, which only works in
+//the main thread. Ideally should find a fix, in order to mark the running thread as the main.
+//As  a workaround, one can use the Tk backend:
+//
+//import matplotlib
+//matplotlib.use('TkAgg') 
+
+
+importClass(java.io.File)
+importClass(java.lang.Thread)
+
+Jep = Java.type('jep.Jep')
+NDArray = Java.type('jep.NDArray')
+
+
+__jep = {}
+
+function __get_jep(){
+    t = java.lang.Thread.currentThread()
+    if (!(t in __jep)){
+        init_jep()
+    }
+    return __jep[t]
+}
+
+function __close_jep(){
+    t = java.lang.Thread.currentThread()
+    if (t in __jep){
+        __jep[t].close()
+    }
+}        
+
+function init_jep(){ 
+    //TODO: Should do it but generates errors
+    //__close_jep()
+    j = new Jep(false)
+    //Faster, but statements must be complete
+    j.setInteractive(false) 
+    __jep[java.lang.Thread.currentThread()] = j
+    j.eval("import sys")
+    //sys.argv is not present in JEP and may be needed for certain modules (as Tkinter)
+    j.eval("sys.argv = ['PShell']");
+    //Add standard script path to python path
+    j.eval("sys.path.append('" + get_context().setup.getScriptPath() + "')")
+    
+    //Redirect stdout
+    j.eval("class JepStdout:\n" + 
+           "    def write(self, str):\n" +
+           "        self.str += str\n" + 
+           "    def clear(self):\n" +
+           "        self.str = ''\n" +
+           "    def flush(self):\n" +
+           "        pass\n")
+    j.eval("sys.stdout=JepStdout()") 
+    j.eval("sys.stderr=JepStdout()")    
+    j.eval("sys.stdout.clear()")
+    j.eval("sys.stderr.clear()")
+}    
+
+function __print_stdout(){
+    j=__get_jep()
+    output = j.getValue("sys.stdout.str")
+    err = j.getValue("sys.stderr.str")
+    j.eval("sys.stdout.clear()")
+    j.eval("sys.stderr.clear()")
+    if ((output != null) && (output.length>0)){
+        print (output)
+    }
+    if ((err != null) && (err.length>0)){
+        java.lang.System.err.println(err)
+    }
+}        
+        
+function run_jep(script_name, vars){ 
+	if (!script_name.toLowerCase().endsWith(".py")){
+		script_name += ".py"
+	}
+	if (!is_defined(vars)) {
+		vars = {};
+	}	
+    script = get_context().scriptManager.library.resolveFile(script_name)
+    if (script == null){    	
+        script= new File(script_name).getAbsolutePath()
+    }
+    j=__get_jep()
+            
+    for (var v in vars){
+        j.set(v, vars[v])
+    }
+    try{
+        j.runScript(script)
+    } finally {
+        __print_stdout()
+    }
+}        
+
+function eval_jep(line){ 
+    j=__get_jep()
+    try{
+        j.eval(line)
+    } finally {
+        __print_stdout()
+    }
+}        
+
+function set_jep(v, value){ 
+    j=__get_jep()
+    j.set(v, value)
+}    
+
+function get_jep(v){
+    j=__get_jep()  
+    return j.getValue(v)
+}    
+
+function call_jep(module, func, args){
+	if (!is_defined(args)) {
+		args = [];
+	}	
+	
+    j=__get_jep()
+    f = module+"_" + func +"_"+ j.hashCode()
+    try{
+        eval_jep("from " + module + " import " + func + " as " + f)    
+        ret = j.invoke(f, to_array(args,'o'))
+    } finally {
+        __print_stdout()
+    }
+    return ret
+}    
+
+function to_npa(data, dimensions, type){
+	if (!is_defined(dimensions)) {
+		dimensions = null;
+	}
+    if (!is_defined(type)) {
+    	type='d'
+    }	
+    data = to_array(data, type)
+    return new NDArray(data, dimensions)    
+}
+
+
+    

script/_Lib/jeputils.py

@@ -0,0 +1,128 @@
+###################################################################################################
+# Facade to JEP: Embedded Python
+###################################################################################################
+
+#Matplotlib won't work out of the box because it's default backend (Qt) uses signals, which only works in
+#the main thread. Ideally should find a fix, in order to mark the running thread as the main.
+#As  a workaround, one can use the Tk backend:
+#
+#import matplotlib
+#matplotlib.use('TkAgg') 
+
+
+import sys
+import os
+import jep.Jep
+import jep.NDArray
+import java.lang.Thread
+from startup import to_array, get_context
+
+__jep = {}
+
+def __get_jep(): 
+    t = java.lang.Thread.currentThread()
+    if not t in __jep:
+        init_jep()
+    return __jep[t]
+
+def __close_jep(): 
+    t = java.lang.Thread.currentThread()
+    if t in __jep:    
+        __jep[t].close()
+
+def init_jep():    
+    #TODO: Should do it but generates errors
+    #__close_jep()
+    j = jep.Jep(False)
+    #Faster, but statements must be complete
+    j.setInteractive(False) 
+    __jep[java.lang.Thread.currentThread()] = j
+    j.eval("import sys")
+    #sys.argv is not present in JEP and may be needed for certain modules (as Tkinter)
+    j.eval("sys.argv = ['PShell']");
+    #Add standard script path to python path
+    j.eval("sys.path.append('" + get_context().setup.getScriptPath() + "')")
+    
+    #Redirect stdout
+    j.eval("class JepStdout:\n" + 
+           "    def write(self, str):\n" +
+           "        self.str += str\n" + 
+           "    def clear(self):\n" +
+           "        self.str = ''\n" +
+           "    def flush(self):\n" +
+           "        pass\n")
+    j.eval("sys.stdout=JepStdout()");    
+    j.eval("sys.stderr=JepStdout()");    
+    j.eval("sys.stdout.clear()")
+    j.eval("sys.stderr.clear()")
+
+def __print_stdout():
+    j=__get_jep()
+    output = j.getValue("sys.stdout.str")
+    err = j.getValue("sys.stderr.str")
+    j.eval("sys.stdout.clear()")
+    j.eval("sys.stderr.clear()")
+    if (output is not None) and len(output)>0:
+        print output
+    if (err is not None) and len(err)>0:
+        print >> sys.stderr, err
+        
+def run_jep(script_name, vars = {}):    
+    global __jep
+    script = get_context().scriptManager.library.resolveFile(script_name)
+    if script is None : 
+        script= os.path.abspath(script_name)
+    j=__get_jep()
+            
+    for v in vars:
+        j.set(v, vars[v])
+    try:
+        j.runScript(script)
+    finally:
+        __print_stdout()
+
+def eval_jep(line):    
+    j=__get_jep()
+    try:
+        j.eval(line)
+    finally:
+        __print_stdout()    
+
+def set_jep(var, value):    
+    j=__get_jep()
+    j.set(var, value)
+
+def get_jep(var):  
+    j=__get_jep()  
+    return j.getValue(var)
+
+def call_jep(module, function, args = []):
+    j=__get_jep()
+    if "/" in module: 
+        script = get_context().scriptManager.library.resolveFile(module)       
+        if "\\" in script: 
+            #Windows paths
+            module_path = script[0:script.rfind("\\")]
+            module = script[script.rfind("\\")+1:]
+        else:
+            #Linux paths
+            module_path = script[0:script.rfind("/")]
+            module = script[script.rfind("/")+1:]
+        eval_jep("import sys")    
+        eval_jep("sys.path.append('" + module_path + "')")        
+    if module.endswith(".py"): 
+        module = module[0:-3]
+    
+    f = module+"_" + function+"_"+str(j.hashCode())
+    try:
+        eval_jep("from " + module + " import " + function + " as " + f)    
+        ret = j.invoke(f, args)
+    finally:
+        __print_stdout()    
+    return ret
+
+#Converts pythonlist or Java array to numpy array
+def to_npa(data, dimensions = None, type = None):
+   
+    data = to_array(data,'d' if type is None else type)
+    return jep.NDArray(data, dimensions)    

script/_Lib/jsonrpclib/SimpleJSONRPCServer.py

@@ -0,0 +1,234 @@
+import jsonrpclib
+from jsonrpclib import Fault
+from jsonrpclib.jsonrpc import USE_UNIX_SOCKETS
+import SimpleXMLRPCServer
+import SocketServer
+import socket
+import logging
+import os
+import types
+import traceback
+import sys
+try:
+    import fcntl
+except ImportError:
+    # For Windows
+    fcntl = None
+
+
+def get_version(request):
+    # must be a dict
+    if 'jsonrpc' in request.keys():
+        return 2.0
+    if 'id' in request.keys():
+        return 1.0
+    return None
+
+
+def validate_request(request):
+    if not isinstance(request, dict):
+        fault = Fault(
+            -32600, 'Request must be {}, not %s.' % type(request)
+        )
+        return fault
+    rpcid = request.get('id', None)
+    version = get_version(request)
+    if not version:
+        fault = Fault(-32600, 'Request %s invalid.' % request, rpcid=rpcid)
+        return fault
+    request.setdefault('params', [])
+    method = request.get('method', None)
+    params = request.get('params')
+    param_types = (types.ListType, types.DictType, types.TupleType)
+    if not method or type(method) not in types.StringTypes or \
+            type(params) not in param_types:
+        fault = Fault(
+            -32600, 'Invalid request parameters or method.', rpcid=rpcid
+        )
+        return fault
+    return True
+
+
+class SimpleJSONRPCDispatcher(SimpleXMLRPCServer.SimpleXMLRPCDispatcher):
+
+    def __init__(self, encoding=None):
+        SimpleXMLRPCServer.SimpleXMLRPCDispatcher.__init__(
+            self, allow_none=True, encoding=encoding)
+
+    def _marshaled_dispatch(self, data, dispatch_method=None):
+        response = None
+        try:
+            request = jsonrpclib.loads(data)
+        except Exception, e:
+            fault = Fault(-32700, 'Request %s invalid. (%s)' % (data, e))
+            response = fault.response()
+            return response
+        if not request:
+            fault = Fault(-32600, 'Request invalid -- no request data.')
+            return fault.response()
+        if isinstance(request, list):
+            # This SHOULD be a batch, by spec
+            responses = []
+            for req_entry in request:
+                result = validate_request(req_entry)
+                if type(result) is Fault:
+                    responses.append(result.response())
+                    continue
+                resp_entry = self._marshaled_single_dispatch(req_entry)
+                if resp_entry is not None:
+                    responses.append(resp_entry)
+            if len(responses) > 0:
+                response = '[%s]' % ','.join(responses)
+            else:
+                response = ''
+        else:
+            result = validate_request(request)
+            if type(result) is Fault:
+                return result.response()
+            response = self._marshaled_single_dispatch(request)
+        return response
+
+    def _marshaled_single_dispatch(self, request):
+        # TODO - Use the multiprocessing and skip the response if
+        # it is a notification
+        # Put in support for custom dispatcher here
+        # (See SimpleXMLRPCServer._marshaled_dispatch)
+        method = request.get('method')
+        params = request.get('params')
+        try:
+            response = self._dispatch(method, params)
+        except:
+            exc_type, exc_value, exc_tb = sys.exc_info()
+            fault = Fault(-32603, '%s:%s' % (exc_type, exc_value))
+            return fault.response()
+        if 'id' not in request.keys() or request['id'] is None:
+            # It's a notification
+            return None
+        try:
+            response = jsonrpclib.dumps(response,
+                                        methodresponse=True,
+                                        rpcid=request['id']
+                                        )
+            return response
+        except:
+            exc_type, exc_value, exc_tb = sys.exc_info()
+            fault = Fault(-32603, '%s:%s' % (exc_type, exc_value))
+            return fault.response()
+
+    def _dispatch(self, method, params):
+        func = None
+        try:
+            func = self.funcs[method]
+        except KeyError:
+            if self.instance is not None:
+                if hasattr(self.instance, '_dispatch'):
+                    return self.instance._dispatch(method, params)
+                else:
+                    try:
+                        func = SimpleXMLRPCServer.resolve_dotted_attribute(
+                            self.instance,
+                            method,
+                            True
+                            )
+                    except AttributeError:
+                        pass
+        if func is not None:
+            try:
+                if isinstance(params, types.ListType):
+                    response = func(*params)
+                else:
+                    response = func(**params)
+                return response
+            # except TypeError:
+            #     return Fault(-32602, 'Invalid parameters.')
+            except:
+                err_lines = traceback.format_exc().splitlines()
+                trace_string = '%s | %s' % (err_lines[-3], err_lines[-1])
+                fault = jsonrpclib.Fault(-32603, 'Server error: %s' %
+                                         trace_string)
+                return fault
+        else:
+            return Fault(-32601, 'Method %s not supported.' % method)
+
+
+class SimpleJSONRPCRequestHandler(
+        SimpleXMLRPCServer.SimpleXMLRPCRequestHandler):
+
+    def do_POST(self):
+        if not self.is_rpc_path_valid():
+            self.report_404()
+            return
+        try:
+            max_chunk_size = 10*1024*1024
+            size_remaining = int(self.headers["content-length"])
+            L = []
+            while size_remaining:
+                chunk_size = min(size_remaining, max_chunk_size)
+                L.append(self.rfile.read(chunk_size))
+                size_remaining -= len(L[-1])
+            data = ''.join(L)
+            response = self.server._marshaled_dispatch(data)
+            self.send_response(200)
+        except Exception:
+            self.send_response(500)
+            err_lines = traceback.format_exc().splitlines()
+            trace_string = '%s | %s' % (err_lines[-3], err_lines[-1])
+            fault = jsonrpclib.Fault(-32603, 'Server error: %s' % trace_string)
+            response = fault.response()
+        if response is None:
+            response = ''
+        self.send_header("Content-type", "application/json-rpc")
+        self.send_header("Content-length", str(len(response)))
+        self.end_headers()
+        self.wfile.write(response)
+        self.wfile.flush()
+        self.connection.shutdown(1)
+
+
+class SimpleJSONRPCServer(SocketServer.TCPServer, SimpleJSONRPCDispatcher):
+
+    allow_reuse_address = True
+
+    def __init__(self, addr, requestHandler=SimpleJSONRPCRequestHandler,
+                 logRequests=True, encoding=None, bind_and_activate=True,
+                 address_family=socket.AF_INET):
+        self.logRequests = logRequests
+        SimpleJSONRPCDispatcher.__init__(self, encoding)
+        # TCPServer.__init__ has an extra parameter on 2.6+, so
+        # check Python version and decide on how to call it
+        vi = sys.version_info
+        self.address_family = address_family
+        if USE_UNIX_SOCKETS and address_family == socket.AF_UNIX:
+            # Unix sockets can't be bound if they already exist in the
+            # filesystem. The convention of e.g. X11 is to unlink
+            # before binding again.
+            if os.path.exists(addr):
+                try:
+                    os.unlink(addr)
+                except OSError:
+                    logging.warning("Could not unlink socket %s", addr)
+        # if python 2.5 and lower
+        if vi[0] < 3 and vi[1] < 6:
+            SocketServer.TCPServer.__init__(self, addr, requestHandler)
+        else:
+            SocketServer.TCPServer.__init__(
+                self, addr, requestHandler, bind_and_activate)
+        if fcntl is not None and hasattr(fcntl, 'FD_CLOEXEC'):
+            flags = fcntl.fcntl(self.fileno(), fcntl.F_GETFD)
+            flags |= fcntl.FD_CLOEXEC
+            fcntl.fcntl(self.fileno(), fcntl.F_SETFD, flags)
+
+
+class CGIJSONRPCRequestHandler(SimpleJSONRPCDispatcher):
+
+    def __init__(self, encoding=None):
+        SimpleJSONRPCDispatcher.__init__(self, encoding)
+
+    def handle_jsonrpc(self, request_text):
+        response = self._marshaled_dispatch(request_text)
+        print 'Content-Type: application/json-rpc'
+        print 'Content-Length: %d' % len(response)
+        print
+        sys.stdout.write(response)
+
+    handle_xmlrpc = handle_jsonrpc

script/_Lib/jsonrpclib/__init__.py

@@ -0,0 +1,6 @@
+from jsonrpclib.config import Config
+config = Config.instance()
+from jsonrpclib.history import History
+history = History.instance()
+from jsonrpclib.jsonrpc import Server, MultiCall, Fault
+from jsonrpclib.jsonrpc import ProtocolError, loads, dumps

script/_Lib/jsonrpclib/config.py

@@ -0,0 +1,40 @@
+import sys
+
+
+class LocalClasses(dict):
+    def add(self, cls):
+        self[cls.__name__] = cls
+
+
+class Config(object):
+    """
+    This is pretty much used exclusively for the 'jsonclass'
+    functionality... set use_jsonclass to False to turn it off.
+    You can change serialize_method and ignore_attribute, or use
+    the local_classes.add(class) to include "local" classes.
+    """
+    use_jsonclass = True
+    # Change to False to keep __jsonclass__ entries raw.
+    serialize_method = '_serialize'
+    # The serialize_method should be a string that references the
+    # method on a custom class object which is responsible for
+    # returning a tuple of the constructor arguments and a dict of
+    # attributes.
+    ignore_attribute = '_ignore'
+    # The ignore attribute should be a string that references the
+    # attribute on a custom class object which holds strings and / or
+    # references of the attributes the class translator should ignore.
+    classes = LocalClasses()
+    # The list of classes to use for jsonclass translation.
+    version = 2.0
+    # Version of the JSON-RPC spec to support
+    user_agent = 'jsonrpclib/0.1 (Python %s)' % \
+        '.'.join([str(ver) for ver in sys.version_info[0:3]])
+    # User agent to use for calls.
+    _instance = None
+
+    @classmethod
+    def instance(cls):
+        if not cls._instance:
+            cls._instance = cls()
+        return cls._instance

script/_Lib/jsonrpclib/history.py

@@ -0,0 +1,40 @@
+class History(object):
+    """
+    This holds all the response and request objects for a
+    session. A server using this should call "clear" after
+    each request cycle in order to keep it from clogging
+    memory.
+    """
+    requests = []
+    responses = []
+    _instance = None
+
+    @classmethod
+    def instance(cls):
+        if not cls._instance:
+            cls._instance = cls()
+        return cls._instance
+
+    def add_response(self, response_obj):
+        self.responses.append(response_obj)
+
+    def add_request(self, request_obj):
+        self.requests.append(request_obj)
+
+    @property
+    def request(self):
+        if len(self.requests) == 0:
+            return None
+        else:
+            return self.requests[-1]
+
+    @property
+    def response(self):
+        if len(self.responses) == 0:
+            return None
+        else:
+            return self.responses[-1]
+
+    def clear(self):
+        del self.requests[:]
+        del self.responses[:]

script/_Lib/jsonrpclib/jsonclass.py

@@ -0,0 +1,155 @@
+import types
+import inspect
+import re
+
+from jsonrpclib import config
+
+iter_types = [
+    types.DictType,
+    types.ListType,
+    types.TupleType
+]
+
+string_types = [
+    types.StringType,
+    types.UnicodeType
+]
+
+numeric_types = [
+    types.IntType,
+    types.LongType,
+    types.FloatType
+]
+
+value_types = [
+    types.BooleanType,
+    types.NoneType
+]
+
+supported_types = iter_types+string_types+numeric_types+value_types
+invalid_module_chars = r'[^a-zA-Z0-9\_\.]'
+
+
+class TranslationError(Exception):
+    pass
+
+
+def dump(obj, serialize_method=None, ignore_attribute=None, ignore=[]):
+    if not serialize_method:
+        serialize_method = config.serialize_method
+    if not ignore_attribute:
+        ignore_attribute = config.ignore_attribute
+    obj_type = type(obj)
+    # Parse / return default "types"...
+    if obj_type in numeric_types+string_types+value_types:
+        return obj
+    if obj_type in iter_types:
+        if obj_type in (types.ListType, types.TupleType):
+            new_obj = []
+            for item in obj:
+                new_obj.append(
+                    dump(item, serialize_method, ignore_attribute, ignore))
+            if isinstance(obj_type, types.TupleType):
+                new_obj = tuple(new_obj)
+            return new_obj
+        # It's a dict...
+        else:
+            new_obj = {}
+            for key, value in obj.iteritems():
+                new_obj[key] = dump(
+                    value, serialize_method, ignore_attribute, ignore)
+            return new_obj
+    # It's not a standard type, so it needs __jsonclass__
+    module_name = inspect.getmodule(obj).__name__
+    class_name = obj.__class__.__name__
+    json_class = class_name
+    if module_name not in ['', '__main__']:
+        json_class = '%s.%s' % (module_name, json_class)
+    return_obj = {"__jsonclass__": [json_class]}
+    # If a serialization method is defined..
+    if serialize_method in dir(obj):
+        # Params can be a dict (keyword) or list (positional)
+        # Attrs MUST be a dict.
+        serialize = getattr(obj, serialize_method)
+        params, attrs = serialize()
+        return_obj['__jsonclass__'].append(params)
+        return_obj.update(attrs)
+        return return_obj
+    # Otherwise, try to figure it out
+    # Obviously, we can't assume to know anything about the
+    # parameters passed to __init__
+    return_obj['__jsonclass__'].append([])
+    attrs = {}
+    ignore_list = getattr(obj, ignore_attribute, [])+ignore
+    for attr_name, attr_value in obj.__dict__.iteritems():
+        if type(attr_value) in supported_types and \
+                attr_name not in ignore_list and \
+                attr_value not in ignore_list:
+            attrs[attr_name] = dump(
+                attr_value, serialize_method, ignore_attribute, ignore)
+    return_obj.update(attrs)
+    return return_obj
+
+
+def load(obj):
+    if type(obj) in string_types + numeric_types + value_types:
+        return obj
+
+    if isinstance(obj, list):
+        return_list = []
+        for entry in obj:
+            return_list.append(load(entry))
+        return return_list
+    # Othewise, it's a dict type
+    if '__jsonclass__' not in obj:
+        return_dict = {}
+        for key, value in obj.iteritems():
+            new_value = load(value)
+            return_dict[key] = new_value
+        return return_dict
+    # It's a dict, and it's a __jsonclass__
+    orig_module_name = obj['__jsonclass__'][0]
+    params = obj['__jsonclass__'][1]
+    if orig_module_name == '':
+        raise TranslationError('Module name empty.')
+    json_module_clean = re.sub(invalid_module_chars, '', orig_module_name)
+    if json_module_clean != orig_module_name:
+        raise TranslationError('Module name %s has invalid characters.' %
+                               orig_module_name)
+    json_module_parts = json_module_clean.split('.')
+    json_class = None
+    if len(json_module_parts) == 1:
+        # Local class name -- probably means it won't work
+        if json_module_parts[0] not in config.classes.keys():
+            raise TranslationError('Unknown class or module %s.' %
+                                   json_module_parts[0])
+        json_class = config.classes[json_module_parts[0]]
+    else:
+        json_class_name = json_module_parts.pop()
+        json_module_tree = '.'.join(json_module_parts)
+        try:
+            temp_module = __import__(json_module_tree)
+        except ImportError:
+            raise TranslationError('Could not import %s from module %s.' %
+                                   (json_class_name, json_module_tree))
+
+        # The returned class is the top-level module, not the one we really
+        # want.  (E.g., if we import a.b.c, we now have a.)  Walk through other
+        # path components to get to b and c.
+        for i in json_module_parts[1:]:
+            temp_module = getattr(temp_module, i)
+
+        json_class = getattr(temp_module, json_class_name)
+    # Creating the object...
+    new_obj = None
+    if isinstance(params, list):
+        new_obj = json_class(*params)
+    elif isinstance(params, dict):
+        new_obj = json_class(**params)
+    else:
+        raise TranslationError('Constructor args must be a dict or list.')
+    for key, value in obj.iteritems():
+        if key == '__jsonclass__':
+            continue
+        setattr(new_obj, key, value)
+    return new_obj

script/_Lib/jsonrpclib/jsonrpc.py

@@ -0,0 +1,596 @@
+"""
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+   http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+============================
+JSONRPC Library (jsonrpclib)
+============================
+
+This library is a JSON-RPC v.2 (proposed) implementation which
+follows the xmlrpclib API for portability between clients. It
+uses the same Server / ServerProxy, loads, dumps, etc. syntax,
+while providing features not present in XML-RPC like:
+
+* Keyword arguments
+* Notifications
+* Versioning
+* Batches and batch notifications
+
+Eventually, I'll add a SimpleXMLRPCServer compatible library,
+and other things to tie the thing off nicely. :)
+
+For a quick-start, just open a console and type the following,
+replacing the server address, method, and parameters
+appropriately.
+>>> import jsonrpclib
+>>> server = jsonrpclib.Server('http://localhost:8181')
+>>> server.add(5, 6)
+11
+>>> server._notify.add(5, 6)
+>>> batch = jsonrpclib.MultiCall(server)
+>>> batch.add(3, 50)
+>>> batch.add(2, 3)
+>>> batch._notify.add(3, 5)
+>>> batch()
+[53, 5]
+
+See http://code.google.com/p/jsonrpclib/ for more info.
+"""
+
+import types
+from xmlrpclib import Transport as XMLTransport
+from xmlrpclib import SafeTransport as XMLSafeTransport
+from xmlrpclib import ServerProxy as XMLServerProxy
+from xmlrpclib import _Method as XML_Method
+import string
+import random
+
+# Library includes
+from jsonrpclib import config
+from jsonrpclib import history
+
+# JSON library importing
+cjson = None
+json = None
+try:
+    import cjson
+except ImportError:
+    try:
+        import json
+    except ImportError:
+        try:
+            import simplejson as json
+        except ImportError:
+            raise ImportError(
+                'You must have the cjson, json, or simplejson ' +
+                'module(s) available.'
+            )
+
+IDCHARS = string.ascii_lowercase+string.digits
+
+
+class UnixSocketMissing(Exception):
+    """
+    Just a properly named Exception if Unix Sockets usage is
+    attempted on a platform that doesn't support them (Windows)
+    """
+    pass
+
+
+# JSON Abstractions
+
+
+def jdumps(obj, encoding='utf-8'):
+    # Do 'serialize' test at some point for other classes
+    global cjson
+    if cjson:
+        return cjson.encode(obj)
+    else:
+        return json.dumps(obj, encoding=encoding)
+
+
+def jloads(json_string):
+    global cjson
+    if cjson:
+        return cjson.decode(json_string)
+    else:
+        return json.loads(json_string)
+
+
+# XMLRPClib re-implementations
+
+
+class ProtocolError(Exception):
+    pass
+
+
+class TransportMixIn(object):
+    """ Just extends the XMLRPC transport where necessary. """
+    user_agent = config.user_agent
+    # for Python 2.7 support
+    _connection = (None, None)
+    _extra_headers = []
+
+    def send_content(self, connection, request_body):
+        connection.putheader("Content-Type", "application/json-rpc")
+        connection.putheader("Content-Length", str(len(request_body)))
+        connection.endheaders()
+        if request_body:
+            connection.send(request_body)
+
+    def getparser(self):
+        target = JSONTarget()
+        return JSONParser(target), target
+
+
+class JSONParser(object):
+    def __init__(self, target):
+        self.target = target
+
+    def feed(self, data):
+        self.target.feed(data)
+
+    def close(self):
+        pass
+
+
+class JSONTarget(object):
+    def __init__(self):
+        self.data = []
+
+    def feed(self, data):
+        self.data.append(data)
+
+    def close(self):
+        return ''.join(self.data)
+
+
+class Transport(TransportMixIn, XMLTransport):
+    def __init__(self):
+        TransportMixIn.__init__(self)
+        XMLTransport.__init__(self)
+
+
+class SafeTransport(TransportMixIn, XMLSafeTransport):
+    def __init__(self):
+        TransportMixIn.__init__(self)
+        XMLSafeTransport.__init__(self)
+
+from httplib import HTTP, HTTPConnection
+from socket import socket
+
+USE_UNIX_SOCKETS = False
+
+try:
+    from socket import AF_UNIX, SOCK_STREAM
+    USE_UNIX_SOCKETS = True
+except ImportError:
+    pass
+
+if (USE_UNIX_SOCKETS):
+
+    class UnixHTTPConnection(HTTPConnection):
+        def connect(self):
+            self.sock = socket(AF_UNIX, SOCK_STREAM)
+            self.sock.connect(self.host)
+
+    class UnixHTTP(HTTP):
+        _connection_class = UnixHTTPConnection
+
+    class UnixTransport(TransportMixIn, XMLTransport):
+
+        def make_connection(self, host):
+            host, extra_headers, x509 = self.get_host_info(host)
+            return UnixHTTP(host)
+
+
+class ServerProxy(XMLServerProxy):
+    """
+    Unfortunately, much more of this class has to be copied since
+    so much of it does the serialization.
+    """
+
+    def __init__(self, uri, transport=None, encoding=None,
+                 verbose=0, version=None):
+        import urllib
+        if not version:
+            version = config.version
+        self.__version = version
+        schema, uri = urllib.splittype(uri)
+        if schema not in ('http', 'https', 'unix'):
+            raise IOError('Unsupported JSON-RPC protocol.')
+        if schema == 'unix':
+            if not USE_UNIX_SOCKETS:
+                # Don't like the "generic" Exception...
+                raise UnixSocketMissing("Unix sockets not available.")
+            self.__host = uri
+            self.__handler = '/'
+        else:
+            self.__host, self.__handler = urllib.splithost(uri)
+            if not self.__handler:
+                # Not sure if this is in the JSON spec?
+                # self.__handler = '/'
+                self.__handler == '/'
+        if transport is None:
+            if schema == 'unix':
+                transport = UnixTransport()
+            elif schema == 'https':
+                transport = SafeTransport()
+            else:
+                transport = Transport()
+        self.__transport = transport
+        self.__encoding = encoding
+        self.__verbose = verbose
+
+    def _request(self, methodname, params, rpcid=None):
+        request = dumps(params, methodname, encoding=self.__encoding,
+                        rpcid=rpcid, version=self.__version)
+        response = self._run_request(request)
+        check_for_errors(response)
+        return response['result']
+
+    def _request_notify(self, methodname, params, rpcid=None):
+        request = dumps(params, methodname, encoding=self.__encoding,
+                        rpcid=rpcid, version=self.__version, notify=True)
+        response = self._run_request(request, notify=True)
+        check_for_errors(response)
+        return
+
+    def _run_request(self, request, notify=None):
+        history.add_request(request)
+
+        response = self.__transport.request(
+            self.__host,
+            self.__handler,
+            request,
+            verbose=self.__verbose
+        )
+
+        # Here, the XMLRPC library translates a single list
+        # response to the single value -- should we do the
+        # same, and require a tuple / list to be passed to
+        # the response object, or expect the Server to be
+        # outputting the response appropriately?
+
+        history.add_response(response)
+        if not response:
+            return None
+        return_obj = loads(response)
+        return return_obj
+
+    def __getattr__(self, name):
+        # Same as original, just with new _Method reference
+        return _Method(self._request, name)
+
+    @property
+    def _notify(self):
+        # Just like __getattr__, but with notify namespace.
+        return _Notify(self._request_notify)
+
+
+class _Method(XML_Method):
+
+    def __call__(self, *args, **kwargs):
+        if len(args) > 0 and len(kwargs) > 0:
+            raise ProtocolError(
+                'Cannot use both positional and keyword arguments '
+                '(according to JSON-RPC spec.)')
+        if len(args) > 0:
+            return self.__send(self.__name, args)
+        else:
+            return self.__send(self.__name, kwargs)
+
+    def __getattr__(self, name):
+        return _Method(self.__send, "%s.%s" % (self.__name, name))
+
+    def __repr__(self):
+        return '<{} "{}">'.format(self.__class__.__name__, self.__name)
+
+    def __str__(self):
+        return self.__repr__()
+
+    def __dir__(self):
+        return self.__dict__.keys()
+
+
+class _Notify(object):
+    def __init__(self, request):
+        self._request = request
+
+    def __getattr__(self, name):
+        return _Method(self._request, name)
+
+
+# Batch implementation
+
+
+class MultiCallMethod(object):
+
+    def __init__(self, method, notify=False):
+        self.method = method
+        self.params = []
+        self.notify = notify
+
+    def __call__(self, *args, **kwargs):
+        if len(kwargs) > 0 and len(args) > 0:
+            raise ProtocolError('JSON-RPC does not support both ' +
+                                'positional and keyword arguments.')
+        if len(kwargs) > 0:
+            self.params = kwargs
+        else:
+            self.params = args
+
+    def request(self, encoding=None, rpcid=None):
+        return dumps(self.params, self.method, version=2.0,
+                     encoding=encoding, rpcid=rpcid, notify=self.notify)
+
+    def __repr__(self):
+        return '%s' % self.request()
+
+    def __getattr__(self, method):
+        new_method = '%s.%s' % (self.method, method)
+        self.method = new_method
+        return self
+
+
+class MultiCallNotify(object):
+
+    def __init__(self, multicall):
+        self.multicall = multicall
+
+    def __getattr__(self, name):
+        new_job = MultiCallMethod(name, notify=True)
+        self.multicall._job_list.append(new_job)
+        return new_job
+
+
+class MultiCallIterator(object):
+
+    def __init__(self, results):
+        self.results = results
+
+    def __iter__(self):
+        for i in range(0, len(self.results)):
+            yield self[i]
+        raise StopIteration
+
+    def __getitem__(self, i):
+        item = self.results[i]
+        check_for_errors(item)
+        return item['result']
+
+    def __len__(self):
+        return len(self.results)
+
+
+class MultiCall(object):
+
+    def __init__(self, server):
+        self._server = server
+        self._job_list = []
+
+    def _request(self):
+        if len(self._job_list) < 1:
+            # Should we alert? This /is/ pretty obvious.
+            return
+        request_body = '[ {0} ]'.format(
+            ','.join([job.request() for job in self._job_list]))
+        responses = self._server._run_request(request_body)
+        del self._job_list[:]
+        if not responses:
+            responses = []
+        return MultiCallIterator(responses)
+
+    @property
+    def _notify(self):
+        return MultiCallNotify(self)
+
+    def __getattr__(self, name):
+        new_job = MultiCallMethod(name)
+        self._job_list.append(new_job)
+        return new_job
+
+    __call__ = _request
+
+# These lines conform to xmlrpclib's "compatibility" line.
+# Not really sure if we should include these, but oh well.
+Server = ServerProxy
+
+
+class Fault(object):
+    # JSON-RPC error class
+
+    def __init__(self, code=-32000, message='Server error', rpcid=None):
+        self.faultCode = code
+        self.faultString = message
+        self.rpcid = rpcid
+
+    def error(self):
+        return {'code': self.faultCode, 'message': self.faultString}
+
+    def response(self, rpcid=None, version=None):
+        if not version:
+            version = config.version
+        if rpcid:
+            self.rpcid = rpcid
+        return dumps(
+            self, methodresponse=True, rpcid=self.rpcid, version=version
+        )
+
+    def __repr__(self):
+        return '<Fault %s: %s>' % (self.faultCode, self.faultString)
+
+
+def random_id(length=8):
+    return_id = ''
+    for i in range(length):
+        return_id += random.choice(IDCHARS)
+    return return_id
+
+
+class Payload(dict):
+    def __init__(self, rpcid=None, version=None):
+        if not version:
+            version = config.version
+        self.id = rpcid
+        self.version = float(version)
+
+    def request(self, method, params=[]):
+        if type(method) not in types.StringTypes:
+            raise ValueError('Method name must be a string.')
+        if not self.id:
+            self.id = random_id()
+        request = {'id': self.id, 'method': method}
+        if params:
+            request['params'] = params
+        if self.version >= 2:
+            request['jsonrpc'] = str(self.version)
+        return request
+
+    def notify(self, method, params=[]):
+        request = self.request(method, params)
+        if self.version >= 2:
+            del request['id']
+        else:
+            request['id'] = None
+        return request
+
+    def response(self, result=None):
+        response = {'result': result, 'id': self.id}
+        if self.version >= 2:
+            response['jsonrpc'] = str(self.version)
+        else:
+            response['error'] = None
+        return response
+
+    def error(self, code=-32000, message='Server error.'):
+        error = self.response()
+        if self.version >= 2:
+            del error['result']
+        else:
+            error['result'] = None
+        error['error'] = {'code': code, 'message': message}
+        return error
+
+
+def dumps(
+        params=[], methodname=None, methodresponse=None,
+        encoding=None, rpcid=None, version=None, notify=None):
+    """
+    This differs from the Python implementation in that it implements
+    the rpcid argument since the 2.0 spec requires it for responses.
+    """
+    if not version:
+        version = config.version
+    valid_params = (types.TupleType, types.ListType, types.DictType)
+    if methodname in types.StringTypes and \
+            type(params) not in valid_params and \
+            not isinstance(params, Fault):
+        """
+        If a method, and params are not in a listish or a Fault,
+        error out.
+        """
+        raise TypeError('Params must be a dict, list, tuple or Fault ' +
+                        'instance.')
+    # Begin parsing object
+    payload = Payload(rpcid=rpcid, version=version)
+    if not encoding:
+        encoding = 'utf-8'
+    if type(params) is Fault:
+        response = payload.error(params.faultCode, params.faultString)
+        return jdumps(response, encoding=encoding)
+
+    if type(methodname) not in types.StringTypes and \
+            methodresponse is not True:
+        raise ValueError(
+            'Method name must be a string, or methodresponse must '
+            'be set to True.')
+
+    if config.use_jsonclass is True:
+        from jsonrpclib import jsonclass
+        params = jsonclass.dump(params)
+    if methodresponse is True:
+        if rpcid is None:
+            raise ValueError('A method response must have an rpcid.')
+        response = payload.response(params)
+        return jdumps(response, encoding=encoding)
+    request = None
+    if notify is True:
+        request = payload.notify(methodname, params)
+    else:
+        request = payload.request(methodname, params)
+    return jdumps(request, encoding=encoding)
+
+
+def loads(data):
+    """
+    This differs from the Python implementation, in that it returns
+    the request structure in Dict format instead of the method, params.
+    It will return a list in the case of a batch request / response.
+    """
+    if data == '':
+        # notification
+        return None
+    result = jloads(data)
+    # if the above raises an error, the implementing server code
+    # should return something like the following:
+    # { 'jsonrpc':'2.0', 'error': fault.error(), id: None }
+    if config.use_jsonclass is True:
+        from jsonrpclib import jsonclass
+        result = jsonclass.load(result)
+    return result
+
+
+def check_for_errors(result):
+    if not result:
+        # Notification
+        return result
+
+    if not isinstance(result, dict):
+        raise TypeError('Response is not a dict.')
+    if 'jsonrpc' in result.keys() and float(result['jsonrpc']) > 2.0:
+        raise NotImplementedError('JSON-RPC version not yet supported.')
+    if 'result' not in result.keys() and 'error' not in result.keys():
+        raise ValueError('Response does not have a result or error key.')
+    if 'error' in result.keys() and result['error'] is not None:
+        code = result['error']['code']
+        message = result['error']['message']
+        raise ProtocolError((code, message))
+    return result
+
+
+def isbatch(result):
+    if type(result) not in (types.ListType, types.TupleType):
+        return False
+    if len(result) < 1:
+        return False
+    if not isinstance(result[0], dict):
+        return False
+    if 'jsonrpc' not in result[0].keys():
+        return False
+    try:
+        version = float(result[0]['jsonrpc'])
+    except ValueError:
+        raise ProtocolError('"jsonrpc" key must be a float(able) value.')
+    if version < 2:
+        return False
+    return True
+
+
+def isnotification(request):
+    if 'id' not in request.keys():
+        # 2.0 notification
+        return True
+    if request['id'] is None:
+        # 1.0 notification
+        return True
+    return False

script/_Lib/mathutils.js

@@ -0,0 +1,599 @@
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//  Facade to Apache Commons Math
+///////////////////////////////////////////////////////////////////////////////////////////////////
+
+importClass(java.util.List)
+importClass(java.lang.Class)
+
+FastMath = Java.type('org.apache.commons.math3.util.FastMath')
+Pair = Java.type('org.apache.commons.math3.util.Pair')
+Complex = Java.type('org.apache.commons.math3.complex.Complex')
+
+DifferentiableUnivariateFunction = Java.type('org.apache.commons.math3.analysis.DifferentiableUnivariateFunction')
+Gaussian = Java.type('org.apache.commons.math3.analysis.function.Gaussian')
+HarmonicOscillator = Java.type('org.apache.commons.math3.analysis.function.HarmonicOscillator')
+DerivativeStructure = Java.type('org.apache.commons.math3.analysis.differentiation.DerivativeStructure')
+FiniteDifferencesDifferentiator = Java.type('org.apache.commons.math3.analysis.differentiation.FiniteDifferencesDifferentiator')
+SimpsonIntegrator = Java.type('org.apache.commons.math3.analysis.integration.SimpsonIntegrator')
+TrapezoidIntegrator = Java.type('org.apache.commons.math3.analysis.integration.TrapezoidIntegrator')
+RombergIntegrator = Java.type('org.apache.commons.math3.analysis.integration.RombergIntegrator')
+MidPointIntegrator = Java.type('org.apache.commons.math3.analysis.integration.MidPointIntegrator')
+PolynomialFunction = Java.type('org.apache.commons.math3.analysis.polynomials.PolynomialFunction')
+PolynomialFunctionLagrangeForm = Java.type('org.apache.commons.math3.analysis.polynomials.PolynomialFunctionLagrangeForm')
+LaguerreSolver = Java.type('org.apache.commons.math3.analysis.solvers.LaguerreSolver')
+UnivariateFunction = Java.type('org.apache.commons.math3.analysis.UnivariateFunction')
+SplineInterpolator = Java.type('org.apache.commons.math3.analysis.interpolation.SplineInterpolator')
+LinearInterpolator = Java.type('org.apache.commons.math3.analysis.interpolation.LinearInterpolator')
+NevilleInterpolator = Java.type('org.apache.commons.math3.analysis.interpolation.NevilleInterpolator')
+LoessInterpolator = Java.type('org.apache.commons.math3.analysis.interpolation.LoessInterpolator')
+DividedDifferenceInterpolator = Java.type('org.apache.commons.math3.analysis.interpolation.DividedDifferenceInterpolator')
+AkimaSplineInterpolator = Java.type('org.apache.commons.math3.analysis.interpolation.AkimaSplineInterpolator')
+
+GaussianCurveFitter = Java.type('org.apache.commons.math3.fitting.GaussianCurveFitter')
+PolynomialCurveFitter = Java.type('org.apache.commons.math3.fitting.PolynomialCurveFitter')
+HarmonicCurveFitter = Java.type('org.apache.commons.math3.fitting.HarmonicCurveFitter')
+WeightedObservedPoint = Java.type('org.apache.commons.math3.fitting.WeightedObservedPoint')
+MultivariateJacobianFunction = Java.type('org.apache.commons.math3.fitting.leastsquares.MultivariateJacobianFunction')
+LeastSquaresBuilder = Java.type('org.apache.commons.math3.fitting.leastsquares.LeastSquaresBuilder')
+LevenbergMarquardtOptimizer = Java.type('org.apache.commons.math3.fitting.leastsquares.LevenbergMarquardtOptimizer')
+GaussNewtonOptimizer = Java.type('org.apache.commons.math3.fitting.leastsquares.GaussNewtonOptimizer')
+
+SimpleRegression = Java.type('org.apache.commons.math3.stat.regression.SimpleRegression')
+
+FastFourierTransformer = Java.type('org.apache.commons.math3.transform.FastFourierTransformer')
+DftNormalization = Java.type('org.apache.commons.math3.transform.DftNormalization')
+TransformType = Java.type('org.apache.commons.math3.transform.TransformType')
+
+ArrayRealVector = Java.type('org.apache.commons.math3.linear.ArrayRealVector')
+Array2DRowRealMatrix = Java.type('org.apache.commons.math3.linear.Array2DRowRealMatrix')
+MatrixUtils = Java.type('org.apache.commons.math3.linear.MatrixUtils')
+ 
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//Derivative and interpolation
+///////////////////////////////////////////////////////////////////////////////////////////////////
+
+function get_values(f, xdata){
+    /*
+    Return list of values of a function
+
+    Args:
+        f(UnivariateFunction): function
+        xdata(float array or list): Domain values
+    Returns:
+        List of doubles
+
+    */ 
+    v = []
+    for (var x in xdata){
+        v.push(f.value(xdata[x]))
+    }
+    return v
+}    
+
+function interpolate(data, xdata, interpolation_type){
+    /*
+    Interpolate data array or list to a UnivariateFunction
+
+    Args:
+        data(float array or list): The values to interpolate
+        xdata(float array or list, optional): Domain values
+        interpolation_type(str , optional): "linear", "cubic", "akima", "neville", "loess", "newton"
+    Returns:
+        UnivariateDifferentiableFunction object
+
+    */ 
+    if (!is_defined(xdata))    xdata =null
+    if (!is_defined(interpolation_type))    interpolation_type ="linear"
+    if (xdata == null){
+        xdata = range(0, data.length, 1.0)      
+    }
+    if ((data.length != xdata.length) || (data.length<2)){
+        throw "Dimension mismatch"
+    }
+    if (interpolation_type == "cubic"){
+        i = new SplineInterpolator()
+    } else if (interpolation_type == "linear"){
+        i = new LinearInterpolator()
+    } else if (interpolation_type == "akima"){
+        i = new AkimaSplineInterpolator()
+    } else if (interpolation_type == "neville"){
+        i = new NevilleInterpolator()
+    } else if (interpolation_type == "loess"){
+        i = new LoessInterpolator()
+    } else if (interpolation_type == "newton"){
+        i = new DividedDifferenceInterpolator()
+    }else{
+        throw "Invalid interpolation type"
+    }
+    return i.interpolate(to_array(xdata,'d'), to_array(data,'d'))
+}
+       
+function deriv(f, xdata, interpolation_type){
+    /*
+    Calculate derivative of UnivariateFunction, array or list.
+
+    Args:
+        f(UnivariateFunction or array): The function object. If array it is interpolated.
+        xdata(float array or list, optional): Domain values to process.
+        interpolation_type(str , optional): "linear", "cubic", "akima", "neville", "loess", "newton"
+    Returns:
+        List with the derivative values for xdata
+
+    */ 
+    if (!is_defined(xdata))    xdata =null
+    if (!is_defined(interpolation_type))    interpolation_type ="linear"
+
+    if (! (f instanceof UnivariateFunction)){
+        if (xdata == null){
+            xdata = range(0, f.length, 1.0)              
+        }
+        f = interpolate(f, xdata, interpolation_type)
+    }
+    if (xdata == null){
+        if (f instanceof DifferentiableUnivariateFunction){
+            return f.derivative() 
+        }
+        throw "Domain range not defined"
+    }
+    d = []    
+    for (var x in xdata){
+        var xds = new DerivativeStructure(1, 2, 0, x)
+        var yds = f.value(xds)
+        d.push( yds.getPartialDerivative(1))
+    }
+    return d
+}
+        
+function integrate(f, range, xdata , interpolation_type , integrator_type){
+    /*
+    Integrate UnivariateFunction, array or list in an interval.
+
+    Args:
+        f(UnivariateFunction or array): The function object. If array it is interpolated.
+        range(list, optional): integration range ([min, max]).
+        xdata(float array or list, optional): disregarded if f is UnivariateFunction.
+        interpolation_type(str , optional): "linear", "cubic", "akima", "neville", "loess", "newton"
+        integrator_type(str , optional): "simpson", "trapezoid", "romberg" or "midpoint"
+    Returns:
+        Integrated value (Float)
+
+    */     
+    if (!is_defined(range))    range =null
+    if (!is_defined(xdata))    xdata =null
+    if (!is_defined(interpolation_type))    interpolation_type ="linear"
+    if (!is_defined(integrator_type))    integrator_type ="simpson"
+    
+    if (! (f instanceof UnivariateFunction)){
+        if (xdata == null){
+            xdata = range(0, f.length, 1.0) 
+        }
+        if (range == null){ 
+            range = xdata
+        }
+        f = interpolate(f, xdata, interpolation_type)
+    }
+    if (range == null){
+        throw "Domain range not defined"
+    }
+    d = []    
+    if (integrator_type == "simpson"){
+        integrator = new SimpsonIntegrator()
+    } else if (integrator_type == "trapezoid"){
+        integrator = new TrapezoidIntegrator()
+    } else if (integrator_type == "romberg"){
+        integrator = new RombergIntegrator()
+    } else if (integrator_type == "midpoint"){
+        integrator = new MidPointIntegrator()
+        throw "Invalid integrator type"
+    }
+    max_eval = 1000000
+    lower = Math.min.apply(null, range)
+    upper = Math.max.apply(null, range)
+    return integrator.integrate(max_eval,  f, lower, upper)     
+}
+
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//Fitting and peak search
+///////////////////////////////////////////////////////////////////////////////////////////////////
+
+MAX_FLOAT = 1.7976931348623157e+308 
+
+MAX_ITERATIONS = 1000
+MAX_EVALUATIONS = 1000
+
+function calculate_peaks(func, start_value, end_value, positive){
+    /*
+    Calculate peaks of a DifferentiableUnivariateFunction in a given range by finding the roots of the derivative
+
+    Args:
+        function(DifferentiableUnivariateFunction): The function object.
+        start_value(float): start of range
+        end_value(float, optional): end of range
+        positive (boolean, optional): True for searching positive peaks, False for negative.
+    Returns:
+        List of peaks in the interval
+
+    */ 
+    if (!is_defined(end_value))    end_value =MAX_FLOAT
+    if (!is_defined(positive))    positive =true
+    derivative = func.derivative() 
+    derivative2 = derivative.derivative() 
+    var peaks = []
+    solver = new LaguerreSolver()
+    var ret = solver.solveAllComplex(derivative.coefficients, start_value)
+    for (var complex in ret){
+        var r = ret[complex].getReal()
+        if ((start_value < r) && (r < end_value)){
+            if ((positive && (derivative2.value(r) < 0)) || ( (!positive) && (derivative2.value(r) > 0)))
+                peaks.push(r)
+        }
+    }
+    return peaks
+}
+
+function estimate_peak_indexes(data, xdata, threshold, min_peak_distance, positive){
+    /*
+    Estimation of peaks in an array by ordering local maxima according to given criteria.
+
+    Args:
+        data(float array or list)
+        xdata(float array or list, optional): if not null must have the same length as data.
+        threshold(float, optional): if specified filter peaks below this value
+        min_peak_distance(float, optional): if specified defines minimum distance between two peaks.
+                              if xdata == null, it represents index counts, otherwise in xdata units.
+        positive (boolean, optional): True for searching positive peaks, False for negative.
+    Returns:
+        List of peaks indexes.
+    */ 
+    if (!is_defined(xdata))    xdata =null
+    if (!is_defined(threshold))    threshold =null
+    if (!is_defined(min_peak_distance))    min_peak_distance =null
+    if (!is_defined(positive))    positive =true
+    peaks = []
+    indexes = sort_indexes(data, positive)
+    for (var index in indexes){
+        first = (indexes[index] == 0)
+        last = (indexes[index] == (data.length-1))
+        val=data[indexes[index]]
+        prev = first ? Number.NaN : data[indexes[index]-1]
+        next = last ? Number.NaN : data[indexes[index]+1]
+
+        if (threshold != null){
+            if ((positive && (val<threshold)) || ((!positive) && (val>threshold)))
+                break
+        }
+        if  ( ( (positive) && (first || val>prev ) && (last || val>=next ) )  || (  
+               (!positive) && (first || val<prev ) && (last || val<=next ) ) ) { 
+                var append = true
+                if (min_peak_distance != null){
+                    for (var peak in peaks){
+                        if  (   ((xdata == null) && (Math.abs(peaks[peak]-indexes[index]) < min_peak_distance)) || 
+                                ((xdata != null) && (Math.abs(xdata[peaks[peak]]-xdata[indexes[index]]) < min_peak_distance)) ){
+                            append = false    
+                            break
+                        }
+                    }
+                }
+                if (append)   peaks.push(indexes[index])
+        }
+    }
+    return peaks
+}
+        
+function _assert_valid_for_fit(fy,fx){
+    if ((fy.length<2) || ((fx != null) && (fx.length>fy.length)))
+        throw "Invalid data for fit"
+}
+        
+function fit_gaussians(fy, fx, peak_indexes){
+    /*
+    Fits data on multiple gaussians on the given peak indexes.
+
+    Args:
+        x(float array or list)
+        y(float array or list)
+        peak_indexes(list of int)
+    Returns:
+        List of tuples of gaussian parameters: (normalization, mean, sigma)
+    */ 
+    fx = to_array(fx)
+    fy = to_array(fy)
+    _assert_valid_for_fit(fy,fx)
+    ret = []    
+
+    minimum = Math.min.apply(null, fy)
+    for (var peak in peak_indexes){
+        //Copy data
+        data = fy.slice(0)
+        //Remover data from other peaks
+        for (var p in peak_indexes){
+            limit = Math.floor(Math.round((peak_indexes[p]+peak_indexes[peak])/2))
+            if (peak_indexes[p] > peak_indexes[peak]){
+            	for (var x = limit; x< fy.length; x++){
+            		data[x] = minimum
+            	}
+            } else if (peak_indexes[p] < peak_indexes[peak]){
+            	for (var x = 0; x< limit; x++){
+            		data[x] = minimum
+            	}
+            }
+        }        
+        //Build fit point list
+        values = create_fit_point_list(data, fx)                        
+        maximum = Math.max.apply(null, data)        
+        gaussian_fitter = GaussianCurveFitter.create().withStartPoint([(maximum-minimum)/2,fx[peak_indexes[peak]],1.0]).withMaxIterations(MAX_ITERATIONS)
+        //Fit return parameters: (normalization, mean, sigma) 
+        try{
+            ret.push(to_array(gaussian_fitter.fit(values)))         
+        } catch(ex) {
+            ret.push(null) //Fitting error
+        }
+    }
+    return ret
+}
+        
+function create_fit_point_list(fy, fx, weights){
+	if (!is_defined(weights))    weights =null
+    values = []
+    for (var i = 0; i< fx.length; i++)
+        if (weights == null){
+            values.push(new WeightedObservedPoint(1.0, fx[i], fy[i]))
+        } else {
+            values.push(new WeightedObservedPoint(weights[i], fx[i], fy[i]))
+        }
+    return values
+}
+        
+function fit_polynomial(fy, fx, order, start_point, weights){
+    /*
+    Fits data into a polynomial.
+
+    Args:
+        x(float array or list): observed points x 
+        y(float array or list): observed points y 
+        order(int): if start_point is provided order parameter is disregarded - set to  len(start_point)-1.
+        start_point(optional tuple of float): initial parameters (a0, a1, a2, ...)
+        weights(optional float array or list): weight for each observed point
+    Returns:
+        Tuples of polynomial parameters: (a0, a1, a2, ...)
+    */ 
+    if (!is_defined(start_point))    start_point =null
+    if (!is_defined(weights))    weights =null
+    _assert_valid_for_fit(fy,fx)
+    fit_point_list = create_fit_point_list(fy, fx, weights)
+    if (start_point == null){
+        polynomial_fitter = PolynomialCurveFitter.create(order).withMaxIterations(MAX_ITERATIONS)
+    } else {
+        polynomial_fitter =  PolynomialCurveFitter.create(0).withStartPoint(start_point).withMaxIterations(MAX_ITERATIONS)
+    }
+    try{
+        return to_array(polynomial_fitter.fit(fit_point_list))
+    } catch(ex) {
+        throw "Fitting failure"
+    }
+}
+        
+function fit_gaussian(fy, fx, start_point, weights){
+    /*
+    Fits data into a gaussian.
+
+    Args:
+        x(float array or list): observed points x 
+        y(float array or list): observed points y 
+        start_point(optional tuple of float): initial parameters (normalization, mean, sigma)
+        weights(optional float array or list): weight for each observed point
+    Returns:
+        Tuples of gaussian parameters: (normalization, mean, sigma)
+    */ 
+    if (!is_defined(start_point))    start_point =null
+    if (!is_defined(weights))    weights =null
+    _assert_valid_for_fit(fy,fx)
+    fit_point_list = create_fit_point_list(fy, fx, weights)
+
+    //If start point not provided, start on peak
+    if (start_point == null){
+        peaks = estimate_peak_indexes(fy, fx)
+        minimum = Math.min.apply(null, fy)
+        maximum = Math.max.apply(null, fy)        
+        start_point = [(maximum-minimum)/2,fx[peaks[0]],1.0]
+    }
+    gaussian_fitter = GaussianCurveFitter.create().withStartPoint(start_point).withMaxIterations(MAX_ITERATIONS)
+    try{
+        return to_array(gaussian_fitter.fit(fit_point_list))  //     (normalization, mean, sigma)
+    } catch(ex) {
+        throw "Fitting failure"
+    }
+}
+        
+function fit_harmonic(fy, fx, start_point, weights){
+    /*
+    Fits data into an harmonic.
+
+    Args:
+        x(float array or list): observed points x 
+        y(float array or list): observed points y 
+        start_point(optional tuple of float): initial parameters (amplitude, angular_frequency, phase)
+        weights(optional float array or list): weight for each observed point
+    Returns:
+        Tuples of harmonic parameters: (amplitude, angular_frequency, phase)
+    */
+    if (!is_defined(start_point))    start_point =null
+    if (!is_defined(weights))    weights =null
+    _assert_valid_for_fit(fy,fx)
+    fit_point_list = create_fit_point_list(fy, fx, weights)
+    if (start_point == null){
+        harmonic_fitter = HarmonicCurveFitter.create().withMaxIterations(MAX_ITERATIONS)
+    } else { 
+        harmonic_fitter = HarmonicCurveFitter.create().withStartPoint(start_point).withMaxIterations(MAX_ITERATIONS)
+    }
+    try{
+        return to_array(harmonic_fitter.fit(fit_point_list))  // (amplitude, angular_frequency, phase)
+    } catch(ex) {
+        throw "Fitting failure"
+    }
+}
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//Least squares problem
+///////////////////////////////////////////////////////////////////////////////////////////////////
+        
+function  optimize_least_squares(model, target, initial, weights){
+    if (is_array(weights)){
+        weights = MatrixUtils.createRealDiagonalMatrix(weights)
+    }
+    problem = new LeastSquaresBuilder().start(initial).model(model).target(target).lazyEvaluation(false).maxEvaluations(MAX_EVALUATIONS).maxIterations(MAX_ITERATIONS).weight(weights).build()
+    optimizer = new LevenbergMarquardtOptimizer()
+    optimum = optimizer.optimize(problem)    
+
+    parameters=to_array(optimum.getPoint().toArray())
+    residuals = to_array(optimum.getResiduals().toArray())
+    rms = optimum.getRMS()
+    evals = optimum.getEvaluations()
+    iters = optimum.getIterations()
+    return [parameters, residuals, rms, evals, iters]
+}
+
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//FFT
+///////////////////////////////////////////////////////////////////////////////////////////////////
+
+function is_power_of_2(n){
+    return n && (n & (n - 1)) === 0;
+}
+
+function bit_length(num) {
+    return num.toString(2).length
+}
+
+
+function is_complex(v) {
+    return v instanceof Complex
+}
+
+  
+function pad_to_power_of_two(data){
+    if (is_power_of_2(data.length)){
+        return data
+    }
+    pad =(1 << bit_length(data.length)) -  data.length
+    elem = is_complex(data[0])  ? new Complex(0,0) : [0.0,]
+    for (var i=0; i<pad; i++){
+    	data.push(elem)
+    }
+    return data
+}
+
+        
+function get_real(values){
+    /*
+    Returns real part of a complex numbers vector.
+    Args:
+        values: List of complex.
+    Returns:
+        List of float
+    */
+    var ret = []
+    for (var c in values){
+        ret.push(values[c].getReal())
+    }
+    return ret
+}
+        
+function get_imag(values){
+    /*
+    Returns imaginary part of a complex numbers vector.
+    Args:
+        values: List of complex.
+    Returns:
+        List of float
+    */
+    var ret = []
+    for (var c in values){
+        ret.push(values[c].getImaginary())
+    }
+    return ret
+}
+        
+function get_modulus(values){
+    /*
+    Returns the modulus of a complex numbers vector.
+    Args:
+        values: List of complex.
+    Returns:
+        List of float
+    */
+    var ret = []
+    for (var c in values){
+        ret.push(hypot(values[c].getImaginary(),values[c].getReal()))
+    }
+    return ret
+}
+        
+function get_phase(values){
+    /*
+    Returns the phase of a complex numbers vector.
+    Args:
+        values: List of complex.
+    Returns:
+        List of float
+    */
+    var ret = []
+    for (var c in values){
+        ret.push(Math.atan(values[c].getImaginary()/values[c].getReal()))
+    }
+    return ret
+}
+
+function fft(f){
+    /*
+    Calculates the Fast Fourrier Transform of a vector, padding to the next power of 2 elements.
+    Args:
+        values(): List of float or complex 
+    Returns:
+        List of complex
+    */        
+    f = pad_to_power_of_two(f)    
+    if (is_complex(f[0])){
+        aux = []
+        for (var c in f){
+            aux.append(Complex(f[c].getReal(), f[c].getImaginary()))
+        }
+        f = aux               
+    } else {
+        f = to_array(f,'d')  
+    }
+    fftt = new FastFourierTransformer(DftNormalization.STANDARD)
+    var ret = []
+    transform = fftt.transform(f,TransformType.FORWARD)
+    for (var c in transform){
+        ret.push(new Complex(transform[c].getReal(),transform[c].getImaginary()))
+    }
+    return ret
+}
+
+        
+function  ffti(f){
+    /*
+    Calculates the Inverse Fast Fourrier Transform of a vector, padding to the next power of 2 elements.
+    Args:
+        values(): List of float or complex 
+    Returns:
+        List of complex
+    */
+    f = pad_to_power_of_two(f)
+    if (is_complex(f[0])){
+        aux = []
+        for (var c in f){
+            aux.append(Complex(f[c].getReal(), f[c].getImaginary()))
+        }
+        f = aux               
+    }  else {
+        f = to_array(f,'d')  
+    }       
+    fftt = new FastFourierTransformer(DftNormalization.STANDARD)
+    var ret = []
+    transform = fftt.transform(f,TransformType.INVERSE )
+    for (var c in transform){
+        ret.push(new Complex(transform[c].getReal(),transform[c].getImaginary()))
+    }
+    return ret
+}    

script/_Lib/mathutils.py

@@ -0,0 +1,609 @@
+###################################################################################################
+#  Facade to Apache Commons Math
+###################################################################################################
+
+import sys
+import math
+import operator
+
+import java.util.List
+import java.lang.reflect.Array
+import java.lang.Class as Class
+import jarray
+import org.python.core.PyArray as PyArray
+import ch.psi.utils.Convert as Convert
+
+import org.apache.commons.math3.util.FastMath as FastMath
+import org.apache.commons.math3.util.Pair as Pair
+import org.apache.commons.math3.complex.Complex as Complex
+
+import org.apache.commons.math3.analysis.DifferentiableUnivariateFunction as DifferentiableUnivariateFunction
+import org.apache.commons.math3.analysis.function.Gaussian as Gaussian
+import org.apache.commons.math3.analysis.function.HarmonicOscillator as HarmonicOscillator 
+import org.apache.commons.math3.analysis.differentiation.DerivativeStructure as DerivativeStructure
+import org.apache.commons.math3.analysis.differentiation.FiniteDifferencesDifferentiator as FiniteDifferencesDifferentiator
+import org.apache.commons.math3.analysis.integration.SimpsonIntegrator as SimpsonIntegrator
+import org.apache.commons.math3.analysis.integration.TrapezoidIntegrator as TrapezoidIntegrator
+import org.apache.commons.math3.analysis.integration.RombergIntegrator as RombergIntegrator
+import org.apache.commons.math3.analysis.integration.MidPointIntegrator as MidPointIntegrator
+import org.apache.commons.math3.analysis.polynomials.PolynomialFunction as PolynomialFunction
+import org.apache.commons.math3.analysis.polynomials.PolynomialFunctionLagrangeForm as PolynomialFunctionLagrangeForm
+import org.apache.commons.math3.analysis.solvers.LaguerreSolver as LaguerreSolver
+import org.apache.commons.math3.analysis.UnivariateFunction as UnivariateFunction
+import org.apache.commons.math3.analysis.interpolation.SplineInterpolator as SplineInterpolator
+import org.apache.commons.math3.analysis.interpolation.LinearInterpolator as LinearInterpolator
+import org.apache.commons.math3.analysis.interpolation.NevilleInterpolator as NevilleInterpolator
+import org.apache.commons.math3.analysis.interpolation.LoessInterpolator as LoessInterpolator
+import org.apache.commons.math3.analysis.interpolation.DividedDifferenceInterpolator as DividedDifferenceInterpolator
+import org.apache.commons.math3.analysis.interpolation.AkimaSplineInterpolator as AkimaSplineInterpolator
+
+import org.apache.commons.math3.fitting.GaussianCurveFitter as GaussianCurveFitter
+import org.apache.commons.math3.fitting.PolynomialCurveFitter as PolynomialCurveFitter
+import org.apache.commons.math3.fitting.HarmonicCurveFitter as HarmonicCurveFitter
+import org.apache.commons.math3.fitting.WeightedObservedPoint as WeightedObservedPoint
+import org.apache.commons.math3.fitting.leastsquares.MultivariateJacobianFunction as MultivariateJacobianFunction
+import org.apache.commons.math3.fitting.leastsquares.LeastSquaresBuilder as LeastSquaresBuilder
+import org.apache.commons.math3.fitting.leastsquares.LevenbergMarquardtOptimizer as LevenbergMarquardtOptimizer
+import org.apache.commons.math3.fitting.leastsquares.GaussNewtonOptimizer as GaussNewtonOptimizer
+
+import org.apache.commons.math3.stat.regression.SimpleRegression as SimpleRegression
+
+import org.apache.commons.math3.transform.FastFourierTransformer as FastFourierTransformer
+import org.apache.commons.math3.transform.DftNormalization as DftNormalization
+import org.apache.commons.math3.transform.TransformType as TransformType
+
+import org.apache.commons.math3.linear.ArrayRealVector as ArrayRealVector
+import org.apache.commons.math3.linear.Array2DRowRealMatrix as Array2DRowRealMatrix
+import org.apache.commons.math3.linear.MatrixUtils as MatrixUtils
+
+
+ 
+###################################################################################################
+#Derivative and interpolation
+###################################################################################################
+
+def get_values(f, xdata):
+    """Return list of values of a function
+
+    Args:
+        f(UnivariateFunction): function
+        xdata(float array or list): Domain values
+    Returns:
+        List of doubles
+
+    """ 
+    v = []
+    for x in xdata:
+        v.append(f.value(x))
+    return v
+
+def interpolate(data, xdata = None, interpolation_type = "linear"): 
+    """Interpolate data array or list to a UnivariateFunction
+
+    Args:
+        data(float array or list): The values to interpolate
+        xdata(float array or list, optional): Domain values
+        interpolation_type(str , optional): "linear", "cubic", "akima", "neville", "loess", "newton"
+    Returns:
+        UnivariateDifferentiableFunction object
+
+    """ 
+    if xdata is None:
+        from startup import frange
+        xdata = frange(0, len(data), 1.0)      
+    else:
+        #X must be ordered
+        xy = sorted(zip(xdata,data), key=operator.itemgetter(0))
+        xdata, data = zip(*xy)        
+    if len(data) != len(xdata) or len(data)<2:
+        raise Exception("Dimension mismatch")   
+    
+    if interpolation_type == "cubic":
+        i = SplineInterpolator()
+    elif interpolation_type == "linear":
+        i = LinearInterpolator()
+    elif interpolation_type == "akima":
+        i = AkimaSplineInterpolator()
+    elif interpolation_type == "neville":
+        i = NevilleInterpolator()
+    elif interpolation_type == "loess":
+        i = LoessInterpolator()
+    elif interpolation_type == "newton":
+        i = DividedDifferenceInterpolator()
+    else:
+        raise Exception("Invalid interpolation type")
+    from startup import to_array
+    return i.interpolate(to_array(xdata,'d'), to_array(data,'d'))
+        
+def deriv(f, xdata = None, interpolation_type = "linear"):
+    """Calculate derivative of UnivariateFunction, array or list.
+
+    Args:
+        f(UnivariateFunction or array): The function object. If array it is interpolated.
+        xdata(float array or list, optional): Domain values to process.
+        interpolation_type(str , optional): "linear", "cubic", "akima", "neville", "loess", "newton"
+    Returns:
+        List with the derivative values for xdata
+
+    """ 
+    if not isinstance(f,UnivariateFunction):
+        if xdata is None:
+            from startup import frange
+            xdata = frange(0, len(f), 1.0)              
+        f = interpolate(f, xdata, interpolation_type)
+    if xdata is None:
+        if isinstance(f,DifferentiableUnivariateFunction):
+            return f.derivative() 
+        raise Exception("Domain range not defined")  
+    d = []    
+    for x in xdata:
+        xds = DerivativeStructure(1, 2, 0, x)
+        yds = f.value(xds)
+        d.append( yds.getPartialDerivative(1))
+    return d
+
+def integrate(f, range = None, xdata = None, interpolation_type = "linear", integrator_type = "simpson"):
+    """Integrate UnivariateFunction, array or list in an interval.
+
+    Args:
+        f(UnivariateFunction or array): The function object. If array it is interpolated.
+        range(list, optional): integration range ([min, max]).
+        xdata(float array or list, optional): disregarded if f is UnivariateFunction.
+        interpolation_type(str , optional): "linear", "cubic", "akima", "neville", "loess", "newton"
+        integrator_type(str , optional): "simpson", "trapezoid", "romberg" or "midpoint"
+    Returns:
+        Integrated value (Float)
+
+    """     
+    if not isinstance(f, UnivariateFunction):
+        from startup import frange
+        if xdata is None:            
+            xdata = frange(0, len(f), 1.0) 
+        if range is None: 
+            range = xdata
+        f = interpolate(f, xdata, interpolation_type)
+    if range is None:
+        raise Exception("Domain range not defined")  
+    d = []    
+    if integrator_type == "simpson":
+        integrator = SimpsonIntegrator()
+    elif integrator_type == "trapezoid":
+        integrator = TrapezoidIntegrator()
+    elif integrator_type == "romberg":
+        integrator = RombergIntegrator()
+    elif integrator_type == "midpoint":
+        integrator = MidPointIntegrator()
+        raise Exception("Invalid integrator type")        
+    lower = min(range)
+    upper = max(range)
+    return integrator.integrate(MAX_EVALUATIONS,  f, lower, upper)     
+
+def trapz(y, xdata=None):
+    """Integrate an array or list using the composite trapezoidal rule.
+
+    Args:
+        y(array or list)
+        xdata(float array or list, optional)
+    """
+    return integrate(y, range = None, xdata = xdata, interpolation_type = "linear", integrator_type = "trapezoid")
+
+###################################################################################################
+#Fitting and peak search
+###################################################################################################
+
+try:
+    MAX_FLOAT = sys.float_info.max 
+except: # Python 2.5
+    MAX_FLOAT = 1.7976931348623157e+308 
+
+MAX_ITERATIONS = 1000
+MAX_EVALUATIONS = 1000000
+
+def calculate_peaks(function, start_value, end_value = MAX_FLOAT, positive=True):
+    """Calculate peaks of a DifferentiableUnivariateFunction in a given range by finding the roots of the derivative
+
+    Args:
+        function(DifferentiableUnivariateFunction): The function object.
+        start_value(float): start of range
+        end_value(float, optional): end of range
+        positive (boolean, optional): True for searching positive peaks, False for negative.
+    Returns:
+        List of peaks in the interval
+
+    """ 
+    derivative = function.derivative() 
+    derivative2 = derivative.derivative() 
+    ret = []
+    solver = LaguerreSolver()
+    for complex in solver.solveAllComplex(derivative.coefficients, start_value):
+        r = complex.real
+        if start_value < r < end_value:
+            if (positive and (derivative2.value(r) < 0)) or ( (not positive) and (derivative2.value(r) > 0)):         
+                ret.append(r)
+    return ret
+
+
+def estimate_peak_indexes(data, xdata = None, threshold = None, min_peak_distance = None, positive = True):
+    """Estimation of peaks in an array by ordering local maxima according to given criteria.
+
+    Args:
+        data(float array or list)
+        xdata(float array or list, optional): if not None must have the same length as data.
+        threshold(float, optional): if specified filter peaks below this value
+        min_peak_distance(float, optional): if specified defines minimum distance between two peaks.
+                              if xdata == None, it represents index counts, otherwise in xdata units.
+        positive (boolean, optional): True for searching positive peaks, False for negative.
+    Returns:
+        List of peaks indexes.
+    """ 
+    peaks = []
+    indexes = sorted(range(len(data)),key=lambda x:data[x])
+    if positive:
+        indexes = reversed(indexes)
+    for index in indexes:
+        first = (index == 0)
+        last = (index == (len(data)-1))
+        val=data[index]
+        prev = float('NaN') if first else data[index-1]
+        next = float('NaN') if last else data[index+1]
+
+        if threshold is not None:
+            if (positive and (val<threshold)) or ((not positive) and (val>threshold)):
+                break
+        if  (  positive       and (first or val>prev ) and (last or val>=next ) )  or (  
+               (not positive) and (first or val<prev ) and (last or val<=next ) ):            
+                append = True
+                if min_peak_distance is not None:
+                    for peak in peaks:
+                        if  ((xdata is None) and (abs(peak-index) < min_peak_distance)) or (
+                                (xdata is not None) and (abs(xdata[peak]-xdata[index]) < min_peak_distance)):
+                            append = False    
+                            break
+                if append:
+                    peaks.append(index)
+    return peaks
+
+def _assert_valid_for_fit(y,x):
+    if len(y)<2 or ((x is not None) and (len(x)>len(y))):
+        raise Exception("Invalid data for fit")
+
+def fit_gaussians(y, x, peak_indexes):
+    """Fits data on multiple gaussians on the given peak indexes.
+
+    Args:
+        x(float array or list)
+        y(float array or list)
+        peak_indexes(list of int)
+    Returns:
+        List of tuples of gaussian parameters: (normalization, mean, sigma)
+    """ 
+    _assert_valid_for_fit(y,x)
+    ret = []    
+
+    minimum = min(y)
+    for peak in peak_indexes:
+        #Copy data
+        data = y[:]
+        #Remover data from other peaks
+        for p in peak_indexes:
+            limit = int(round((p+peak)/2))
+            if (p > peak):
+                data[limit : len(y)] =[minimum] * (len(y)-limit)
+            elif (p < peak):
+                data[0:limit] = [minimum] *limit
+        #Build fit point list
+        values = create_fit_point_list(data, x)
+        maximum = max(data)
+        gaussian_fitter = GaussianCurveFitter.create().withStartPoint([(maximum-minimum)/2,x[peak],1.0]).withMaxIterations(MAX_ITERATIONS)
+        #Fit return parameters: (normalization, mean, sigma) 
+        try:
+            ret.append(gaussian_fitter.fit(values).tolist())         
+        except:
+            ret.append(None) #Fitting error
+    return ret
+
+
+def create_fit_point_list(y, x, weights = None):
+    values = []
+    for i in sorted(range(len(x)),key=lambda v:x[v]):  #Creating list ordered by x, needed for gauss fit
+        if weights is None:
+            values.append(WeightedObservedPoint(1.0, x[i], y[i]))
+        else:
+            values.append(WeightedObservedPoint(weights[i], x[i], y[i]))
+    return values
+
+def fit_polynomial(y, x, order, start_point = None, weights = None):
+    """Fits data into a polynomial.
+
+    Args:
+        x(float array or list): observed points x 
+        y(float array or list): observed points y 
+        order(int): if start_point is provided order parameter is disregarded - set to  len(start_point)-1.
+        start_point(optional tuple of float): initial parameters (a0, a1, a2, ...)
+        weights(optional float array or list): weight for each observed point
+    Returns:
+        Tuples of polynomial parameters: (a0, a1, a2, ...)
+    """ 
+    _assert_valid_for_fit(y,x)
+    fit_point_list = create_fit_point_list(y, x, weights)
+    if start_point is None:
+        polynomial_fitter = PolynomialCurveFitter.create(order).withMaxIterations(MAX_ITERATIONS)
+    else:
+        polynomial_fitter =  PolynomialCurveFitter.create(0).withStartPoint(start_point).withMaxIterations(MAX_ITERATIONS)
+    try:
+        return polynomial_fitter.fit(fit_point_list).tolist()
+    except: 
+        raise Exception("Fitting failure")
+
+def fit_gaussian(y, x, start_point = None, weights = None):
+    """Fits data into a gaussian.
+
+    Args:
+        x(float array or list): observed points x 
+        y(float array or list): observed points y 
+        start_point(optional tuple of float): initial parameters (normalization, mean, sigma)
+                If None, use a custom initial estimation.
+                Set to "default" to force  Commons.Math the default (GaussianCurveFitter.ParameterGuesser).     
+        weights(optional float array or list): weight for each observed point
+    Returns:
+        Tuples of gaussian parameters: (normalization, mean, sigma)
+    """ 
+    _assert_valid_for_fit(y,x)
+    fit_point_list = create_fit_point_list(y, x, weights)
+
+    #If start point not provided, start on peak
+    if start_point is None:
+        maximum, minimum = max(y), min(y)
+        norm = maximum - minimum
+        mean = x[y.index(maximum)]         
+        sigma =  trapz([v-minimum for v in y], x)  / (norm*math.sqrt(2*math.pi))
+        start_point = (norm, mean, sigma)
+    elif start_point == "simple":   
+        start_point = [(max(y)-min(y))/2, x[y.index(max(y))], 1.0]
+    elif start_point == "default":
+        start_point = GaussianCurveFitter.ParameterGuesser(fit_point_list).guess().tolist()
+    gaussian_fitter = GaussianCurveFitter.create().withStartPoint(start_point).withMaxIterations(MAX_ITERATIONS)
+    try:
+        return gaussian_fitter.fit(fit_point_list).tolist()  #     (normalization, mean, sigma)
+    except: 
+        raise Exception("Fitting failure")
+
+def fit_harmonic(y, x, start_point = None, weights = None):
+    """Fits data into an harmonic.
+
+    Args:
+        x(float array or list): observed points x 
+        y(float array or list): observed points y 
+        start_point(optional tuple of float): initial parameters (amplitude, angular_frequency, phase)
+        weights(optional float array or list): weight for each observed point
+    Returns:
+        Tuples of harmonic parameters: (amplitude, angular_frequency, phase)
+    """
+    _assert_valid_for_fit(y,x)
+    fit_point_list = create_fit_point_list(y, x, weights)
+    if start_point is None:
+        harmonic_fitter = HarmonicCurveFitter.create().withMaxIterations(MAX_ITERATIONS)
+    else:
+        harmonic_fitter =  HarmonicCurveFitter.create().withStartPoint(start_point).withMaxIterations(MAX_ITERATIONS)
+    try:
+        return harmonic_fitter.fit(fit_point_list).tolist()  # (amplitude, angular_frequency, phase)
+    except: 
+        raise Exception("Fitting failure")
+
+
+def fit_gaussian_offset(y, x, start_point = None, weights = None):
+    """Fits data into a gaussian with offset (constant background).
+       f(x) = a + b * exp(-(pow((x - c), 2) / (2 * pow(d, 2))))
+
+    Args:
+        x(float array or list): observed points x 
+        y(float array or list): observed points y 
+        start_point(optional tuple of float): initial parameters (normalization, mean, sigma)
+        weights(optional float array or list): weight for each observed point
+    Returns:
+        Tuples of gaussian parameters: (offset, normalization, mean, sigma)
+    """     
+
+    # For normalised gauss curve sigma=1/(amp*sqrt(2*pi))
+    if start_point is None:
+        off = min(y)  # good enough starting point for offset
+        com = x[y.index(max(y))]
+        amp = max(y) - off
+        sigma = trapz([v-off for v in y], x) / (amp*math.sqrt(2*math.pi))                 
+        start_point = [off, amp, com , sigma]                                       
+        
+    class Model(MultivariateJacobianFunction):
+        def value(self, variables):
+            value = ArrayRealVector(len(x))
+            jacobian = Array2DRowRealMatrix(len(x), 4)        
+            for i in range(len(x)):
+                (a,b,c,d) = (variables.getEntry(0), variables.getEntry(1), variables.getEntry(2), variables.getEntry(3))   
+                v = math.exp(-(math.pow((x[i] - c), 2) / (2 * math.pow(d, 2))))
+                model = a + b * v
+                value.setEntry(i, model)                                    
+                jacobian.setEntry(i, 0, 1)                  # derivative with respect to p0 = a                        
+                jacobian.setEntry(i, 1, v)                  # derivative with respect to p1 = b            
+                v2 = b*v*((x[i] - c)/math.pow(d, 2))
+                jacobian.setEntry(i, 2, v2)                 # derivative with respect to p2 = c        
+                jacobian.setEntry(i, 3, v2*(x[i] - c)/d )   # derivative with respect to p3 = d       
+            return Pair(value, jacobian)
+    
+    model = Model()
+    target = [v for v in y]      #the target is to have all points at the positios    
+    (parameters, residuals, rms, evals, iters) = optimize_least_squares(model, target, start_point, weights)        
+    return parameters
+
+
+def fit_gaussian_linear(y, x, start_point = None, weights = None):
+    """Fits data into a gaussian with linear background.
+       f(x) = a * x +  b  + c * exp(-(pow((x - d), 2) / (2 * pow(e, 2)))) 
+
+    Args:
+        x(float array or list): observed points x 
+        y(float array or list): observed points y 
+        start_point(optional tuple of float): initial parameters (normalization, mean, sigma)
+        weights(optional float array or list): weight for each observed point
+    Returns:
+        Tuples of gaussian parameters: (offset, normalization, mean, sigma)
+    """     
+
+    # For normalised gauss curve sigma=1/(amp*sqrt(2*pi))
+    if start_point is None:
+        off = min(y)  # good enough starting point for offset
+        com = x[y.index(max(y))]
+        amp = max(y) - off
+        sigma = trapz([v-off for v in y], x) / (amp*math.sqrt(2*math.pi))                 
+        start_point = [0, off, amp, com, sigma]                                       
+        
+    class Model(MultivariateJacobianFunction):
+        def value(self, variables):
+            value = ArrayRealVector(len(x))
+            jacobian = Array2DRowRealMatrix(len(x), 5)        
+            for i in range(len(x)):
+                (a,b,c,d,e) = (variables.getEntry(0), variables.getEntry(1), variables.getEntry(2), variables.getEntry(3), variables.getEntry(4))   
+                v = math.exp(-(math.pow((x[i] - d), 2) / (2 * math.pow(e, 2))))
+                model = a*x[i] + b + c * v 
+                value.setEntry(i, model)                                    
+                jacobian.setEntry(i, 0, x[i])               # derivative with respect to p0 = a                        
+                jacobian.setEntry(i, 1, 1)                  # derivative with respect to p1 = b
+                jacobian.setEntry(i, 2, v)                  # derivative with respect to p2 = c            
+                v2 = c*v*((x[i] - d)/math.pow(e, 2))
+                jacobian.setEntry(i, 3, v2)                 # derivative with respect to p3 = d        
+                jacobian.setEntry(i, 4, v2*(x[i] - d)/e )   # derivative with respect to p4 = e       
+            return Pair(value, jacobian)
+    
+    model = Model()
+    target = [v for v in y]      #the target is to have all points at the positios    
+    (parameters, residuals, rms, evals, iters) = optimize_least_squares(model, target, start_point, weights)        
+    return parameters
+
+###################################################################################################
+#Least squares problem
+###################################################################################################
+
+def optimize_least_squares(model, target, initial, weights):   
+    """Fits a parametric model to a set of observed values by minimizing a cost function.
+
+    Args:
+        model(MultivariateJacobianFunction): observed points x 
+        target(float array or list): observed data
+        initial(optional tuple of float): initial guess
+        weights(optional float array or list): weight for each observed point
+    Returns:
+        Tuples of harmonic parameters: (amplitude, angular_frequency, phase)
+    """
+    if isinstance(weights,tuple) or isinstance(weights,list):
+        weights = MatrixUtils.createRealDiagonalMatrix(weights)
+    problem = LeastSquaresBuilder().start(initial).model(model).target(target).lazyEvaluation(False).maxEvaluations(MAX_EVALUATIONS).maxIterations(MAX_ITERATIONS).weight(weights).build()
+    optimizer = LevenbergMarquardtOptimizer()
+    optimum = optimizer.optimize(problem)    
+
+    parameters=optimum.getPoint().toArray().tolist()
+    residuals = optimum.getResiduals().toArray().tolist()
+    rms = optimum.getRMS()
+    evals = optimum.getEvaluations()
+    iters = optimum.getIterations()
+    return (parameters, residuals, rms, evals, iters)
+
+
+###################################################################################################
+#FFT
+###################################################################################################
+
+def is_power(num, base):
+    if base<=1: return num == 1
+    power = int (math.log (num, base) + 0.5)
+    return base ** power == num
+  
+def pad_to_power_of_two(data):
+    if is_power(len(data),2):
+        return data
+    pad =(1 << len(data).bit_length()) -  len(data)
+    elem = complex(0,0) if type(data[0]) is complex else [0.0,]
+    return data + elem * pad  
+
+def get_real(values):
+    """Returns real part of a complex numbers vector.
+    Args:
+        values: List of complex.
+    Returns:
+        List of float
+    """
+    ret = []
+    for c in values:
+        ret.append(c.real)
+    return ret
+
+def get_imag(values):
+    """Returns imaginary part of a complex numbers vector.
+    Args:
+        values: List of complex.
+    Returns:
+        List of float
+    """
+    ret = []
+    for c in values:
+        ret.append(c.imag)
+    return ret
+
+def get_modulus(values):
+    """Returns the modulus of a complex numbers vector.
+    Args:
+        values: List of complex.
+    Returns:
+        List of float
+    """
+    ret = []
+    for c in values:
+        ret.append(math.hypot(c.imag,c.real))
+    return ret
+
+def get_phase(values):
+    """Returns the phase of a complex numbers vector.
+    Args:
+        values: List of complex.
+    Returns:
+        List of float
+    """
+    ret = []
+    for c in values:
+        ret.append(math.atan(c.imag/c.real))
+    return ret
+
+def fft(f):
+    """Calculates the Fast Fourrier Transform of a vector, padding to the next power of 2 elements.
+    Args:
+        values(): List of float or complex 
+    Returns:
+        List of complex
+    """
+    f = pad_to_power_of_two(f)
+    if type(f[0]) is complex:
+        aux = []
+        for c in f:
+            aux.append(Complex(c.real, c.imag))
+        f = aux                        
+    fftt = FastFourierTransformer(DftNormalization.STANDARD)
+    ret = []
+    for c in fftt.transform(f,TransformType.FORWARD ):
+        ret.append(complex(c.getReal(),c.getImaginary()))
+    return ret
+
+def ffti(f):
+    """Calculates the Inverse Fast Fourrier Transform of a vector, padding to the next power of 2 elements.
+    Args:
+        values(): List of float or complex 
+    Returns:
+        List of complex
+    """
+    f = pad_to_power_of_two(f)
+    if type(f[0]) is complex:
+        aux = []
+        for c in f:
+            aux.append(Complex(c.real, c.imag))
+        f = aux
+    fftt = FastFourierTransformer(DftNormalization.STANDARD)
+    ret = []
+    for c in fftt.transform(f,TransformType.INVERSE ):
+        ret.append(complex(c.getReal(),c.getImaginary()))
+    return ret

script/_Lib/plotutils.js

@@ -0,0 +1,116 @@
+///////////////////////////////////////////////////////////////////////////////////////////////////
+//  Plot utilities
+///////////////////////////////////////////////////////////////////////////////////////////////////
+
+
+function plot_function(plot, func, name, range, show_points, show_lines, color){
+    /*
+     Plots a function to a plot.
+
+    Args:
+        plot(LinePlot)
+        func(UnivariateFunction): Gaussian, PolynomialFunction, HarmonicOscillator...
+        name(str): name of the series
+        range(list or array of floats): x values to plot
+    Returns:
+        Tuples of harmonic parameters: (amplitude, angular_frequency, phase)
+    */    
+    if (!is_defined(show_points))    show_points =true
+    if (!is_defined(show_lines))    show_lines = true
+    if (!is_defined(color))    color = null
+    
+    if (plot.getStyle().isError()){
+        s = new LinePlotErrorSeries(name, color)
+    }
+    else{
+        s = new LinePlotSeries(name, color)    
+    }
+    plot.addSeries(s)
+    s.setPointsVisible(show_points)
+    s.setLinesVisible(show_lines)
+    for (var x in range){
+        s.appendData(range[x], func.value(range[x]))   
+    }
+    return s
+}        
+
+function plot_point(plot, x, y, size, color, name){
+    if (!is_defined(size))    size =3
+    if (!is_defined(name))    name = "Point"
+    if (!is_defined(color))    color = null
+    s = new LinePlotSeries(name, color)
+    plot.addSeries(s)
+    s.setPointSize(size)
+    s.appendData(x, y)
+    return s
+}    
+
+function plot_line(plot, x1, y1, x2, y2, width, color, name){
+    if (!is_defined(width))    width = 1
+    if (!is_defined(name))    name = "Line"
+    if (!is_defined(color))    color = null
+    s = new LinePlotSeries(name, color)    
+    plot.addSeries(s)
+    s.setLineWidth(width)
+    s.setPointsVisible(false)
+    s.appendData(x1, y1)        
+    s.appendData(x2, y2)        
+    return s
+}    
+
+function plot_cross(plot, x, y, size, width, color, name){
+    if (!is_defined(size))    size =1
+    if (!is_defined(width))    width = 1
+    if (!is_defined(color))    color = null
+    if (!is_defined(name))    name = "Cross"
+    s = new LinePlotSeries(name, color)    
+    plot.addSeries(s)   
+    s.setLineWidth(width)
+    s.setPointsVisible(false)
+    s.appendData(NaN, NaN)        
+    s.appendData(x-size/2, y)        
+    s.appendData(x+size/2, y)        
+    s.appendData(NaN, NaN)        
+    s.appendData(x, y-size/2)     
+    s.appendData(x, y+size/2)     
+    return s    
+ }
+
+function plot_rectangle(plot, x1, y1, x2, y2, width, color, name){
+    if (!is_defined(width))    width = 1
+    if (!is_defined(name))    name = "Rectangle"
+    if (!is_defined(color))    color = null
+    s = new LinePlotSeries(name, color)    
+    plot.addSeries(s)
+    s.setLineWidth(width)
+    s.setPointsVisible(false)
+    s.appendData(x1, y1)        
+    s.appendData(x1, y2)        
+    s.appendData(x2, y2)        
+    s.appendData(x2, y1)        
+    s.appendData(x1, y1)  
+    return s
+}    
+
+function plot_circle(plot, cx, cy, radius, width, color, name){
+    if (!is_defined(width))    width = 1
+    if (!is_defined(name))    name = "Circle"
+    if (!is_defined(color))    color = null	
+    s = new LinePlotSeries(name, color)    
+    plot.addSeries(s)
+    s.setLineWidth(width)
+    s.setPointsVisible(false) 
+    res=radius / 100.0
+    epson = 1e-12
+    for (var xp = cx+radius-epson ; xp >= ( cx-radius+epson) ; xp-=res){
+        yp = Math.sqrt(Math.pow(radius, 2) - Math.pow(xp - cx, 2)) + cy
+        s.appendData(xp, yp)        
+    }
+    for (var xp = cx-radius+epson ; xp <= ( cx+radius-epson) ; xp+=res){
+        yp = -Math.sqrt(Math.pow(radius, 2) - Math.pow(xp - cx, 2)) + cy
+        s.appendData(xp, yp)  
+    }     
+    if (s.getCount()>0)
+        s.appendData(s.getX()[0], s.getY()[0])  
+    return s
+}        

script/_Lib/plotutils.py

@@ -0,0 +1,119 @@
+###################################################################################################
+#  Plot utilities
+###################################################################################################
+
+import ch.psi.pshell.plot.LinePlotSeries as LinePlotSeries
+import ch.psi.pshell.plot.LinePlotErrorSeries as LinePlotErrorSeries
+import math
+from startup import frange, to_array
+
+def plot_function(plot, function, name, range, show_points = True, show_lines = True, color = None):
+    """Plots a function to a plot.
+
+    Args:
+        plot(LinePlot)
+        function(UnivariateFunction): Gaussian, PolynomialFunction, HarmonicOscillator...
+        name(str): name of the series
+        range(list or array of floats): x values to plot
+    Returns:
+        Tuples of harmonic parameters: (amplitude, angular_frequency, phase)
+    """
+    if plot.style.isError():
+        s = LinePlotErrorSeries(name, color)
+    else:
+        s = LinePlotSeries(name, color)    
+    plot.addSeries(s)
+    s.setPointsVisible(show_points)
+    s.setLinesVisible(show_lines)
+    for x in range:
+        s.appendData(x, function.value(x))   
+    return s
+
+def plot_data(plot, data, name, xdata = None,  error = None, show_points = True, show_lines = True, color = None):
+    """Plots a subscriptable object to a plot.
+
+    Args:
+        plot(LinePlot)
+        data(subscriptable): Y data
+        name(str): name of the series
+        xdata(subscriptable): X data
+        error(subscriptable): Error data (only for error plots)
+    Returns:
+        Tuples of harmonic parameters: (amplitude, angular_frequency, phase)
+    """
+    if plot.style.isError():
+        s = LinePlotErrorSeries(name, color)
+    else:
+        s = LinePlotSeries(name, color)    
+    plot.addSeries(s)
+    s.setPointsVisible(show_points)
+    s.setLinesVisible(show_lines)
+    if xdata is None: 
+        xdata = range(len(data))
+    xdata = to_array(xdata, 'd')
+    data = to_array(data, 'd')
+    if plot.style.isError():
+        error = to_array(error, 'd')
+        s.setData(xdata, data, error)
+    else:
+        s.setData(xdata, data)
+    return s
+
+def plot_point(plot, x, y, size = 3, color = None, name = "Point"):
+    s = LinePlotSeries(name, color)
+    plot.addSeries(s)
+    s.setPointSize(size)
+    s.appendData(x, y)
+    return s
+
+def plot_line(plot, x1, y1, x2, y2, width = 1, color = None, name = "Line"):
+    s = LinePlotSeries(name, color)    
+    plot.addSeries(s)
+    s.setLineWidth(width)
+    s.setPointsVisible(False)
+    s.appendData(x1, y1)        
+    s.appendData(x2, y2)     
+    return s
+
+def plot_cross(plot, x, y, size = 1.0, width = 1, color = None, name = "Cross"):
+    size = float(size)
+    s = LinePlotSeries(name, color)     
+    plot.addSeries(s)
+    s.setLineWidth(width)
+    s.setPointsVisible(False)
+    s.appendData(float('nan'), float('nan'))        
+    s.appendData(x-size/2, y)        
+    s.appendData(x+size/2, y)        
+    s.appendData(float('nan'), float('nan'))        
+    s.appendData(x, y-size/2)     
+    s.appendData(x, y+size/2)     
+    return s    
+
+def plot_rectangle(plot, x1, y1, x2, y2, width = 1, color = None, name = "Rectangle"):
+    s = LinePlotSeries(name, color)    
+    plot.addSeries(s)
+    s.setLineWidth(width)
+    s.setPointsVisible(False)
+    s.appendData(x1, y1)        
+    s.appendData(x1, y2)        
+    s.appendData(x2, y2)        
+    s.appendData(x2, y1)        
+    s.appendData(x1, y1)      
+    return s
+
+def plot_circle(plot, cx, cy, radius, width = 1, color = None, name = "Circle"):
+    s = LinePlotSeries(name, color)    
+    plot.addSeries(s)
+    s.setLineWidth(width)
+    s.setPointsVisible(False) 
+    res=float(radius) / 100.0
+    epson = 1e-12
+    for xp in frange (cx+radius-epson , cx-radius+epson , -res):
+        yp = math.sqrt(math.pow(radius, 2) - math.pow(xp - cx, 2)) + cy
+        s.appendData(xp, yp)        
+    for xp in frange (cx-radius+epson , cx+radius-epson, res):
+        yp = -math.sqrt(math.pow(radius, 2) - math.pow(xp - cx, 2)) + cy
+        s.appendData(xp, yp)       
+    if s.getCount()>0:
+        s.appendData(s.getX()[0], s.getY()[0])  
+    return s

script/_Lib/requests-2.4.3-py2.7.egg-info

@@ -0,0 +1,963 @@
+Metadata-Version: 1.1
+Name: requests
+Version: 2.4.3
+Summary: Python HTTP for Humans.
+Home-page: http://python-requests.org
+Author: Kenneth Reitz
+Author-email: me@kennethreitz.com
+License: Apache 2.0
+Description: Requests: HTTP for Humans
+        =========================
+        
+        .. image:: https://badge.fury.io/py/requests.png
+            :target: http://badge.fury.io/py/requests
+        
+        .. image:: https://pypip.in/d/requests/badge.png
+                :target: https://crate.io/packages/requests/
+        
+        
+        Requests is an Apache2 Licensed HTTP library, written in Python, for human
+        beings.
+        
+        Most existing Python modules for sending HTTP requests are extremely
+        verbose and cumbersome. Python's builtin urllib2 module provides most of
+        the HTTP capabilities you should need, but the api is thoroughly broken.
+        It requires an enormous amount of work (even method overrides) to
+        perform the simplest of tasks.
+        
+        Things shouldn't be this way. Not in Python.
+        
+        .. code-block:: pycon
+        
+            >>> r = requests.get('https://api.github.com', auth=('user', 'pass'))
+            >>> r.status_code
+            204
+            >>> r.headers['content-type']
+            'application/json'
+            >>> r.text
+            ...
+        
+        See `the same code, without Requests <https://gist.github.com/973705>`_.
+        
+        Requests allow you to send HTTP/1.1 requests. You can add headers, form data,
+        multipart files, and parameters with simple Python dictionaries, and access the
+        response data in the same way. It's powered by httplib and `urllib3
+        <https://github.com/shazow/urllib3>`_, but it does all the hard work and crazy
+        hacks for you.
+        
+        
+        Features
+        --------
+        
+        - International Domains and URLs
+        - Keep-Alive & Connection Pooling
+        - Sessions with Cookie Persistence
+        - Browser-style SSL Verification
+        - Basic/Digest Authentication
+        - Elegant Key/Value Cookies
+        - Automatic Decompression
+        - Unicode Response Bodies
+        - Multipart File Uploads
+        - Connection Timeouts
+        - Thread-safety
+        - HTTP(S) proxy support
+        
+        
+        Installation
+        ------------
+        
+        To install Requests, simply:
+        
+        .. code-block:: bash
+        
+            $ pip install requests
+        
+        
+        Documentation
+        -------------
+        
+        Documentation is available at http://docs.python-requests.org/.
+        
+        
+        Contribute
+        ----------
+        
+        #. Check for open issues or open a fresh issue to start a discussion around a feature idea or a bug. There is a `Contributor Friendly`_ tag for issues that should be ideal for people who are not very familiar with the codebase yet.
+        #. If you feel uncomfortable or uncertain about an issue or your changes, feel free to email @sigmavirus24 and he will happily help you via email, Skype, remote pairing or whatever you are comfortable with.
+        #. Fork `the repository`_ on GitHub to start making your changes to the **master** branch (or branch off of it).
+        #. Write a test which shows that the bug was fixed or that the feature works as expected.
+        #. Send a pull request and bug the maintainer until it gets merged and published. :) Make sure to add yourself to AUTHORS_.
+        
+        .. _`the repository`: http://github.com/kennethreitz/requests
+        .. _AUTHORS: https://github.com/kennethreitz/requests/blob/master/AUTHORS.rst
+        .. _Contributor Friendly: https://github.com/kennethreitz/requests/issues?direction=desc&labels=Contributor+Friendly&page=1&sort=updated&state=open
+        
+        
+        .. :changelog:
+        
+        Release History
+        ---------------
+        
+        2.4.3 (2014-10-06)
+        ++++++++++++++++++
+        
+        **Bugfixes**
+        
+        - Unicode URL improvements for Python 2.
+        - Re-order JSON param for backwards compat.
+        - Automatically defrag authentication schemes from host/pass URIs. (`#2249 <https://github.com/kennethreitz/requests/issues/2249>`_)
+        
+        
+        2.4.2 (2014-10-05)
+        ++++++++++++++++++
+        
+        **Improvements**
+        
+        - FINALLY! Add json parameter for uploads! (`#2258 <https://github.com/kennethreitz/requests/pull/2258>`_)
+        - Support for bytestring URLs on Python 3.x (`#2238 <https://github.com/kennethreitz/requests/pull/2238>`_)
+        
+        **Bugfixes**
+        
+        - Avoid getting stuck in a loop (`#2244 <https://github.com/kennethreitz/requests/pull/2244>`_)
+        - Multiple calls to iter* fail with unhelpful error. (`#2240 <https://github.com/kennethreitz/requests/issues/2240>`_, `#2241 <https://github.com/kennethreitz/requests/issues/2241>`_)
+        
+        **Documentation**
+        
+        - Correct redirection introduction (`#2245 <https://github.com/kennethreitz/requests/pull/2245/>`_)
+        - Added example of how to send multiple files in one request. (`#2227 <https://github.com/kennethreitz/requests/pull/2227/>`_)
+        - Clarify how to pass a custom set of CAs (`#2248 <https://github.com/kennethreitz/requests/pull/2248/>`_)
+        
+        
+        
+        2.4.1 (2014-09-09)
+        ++++++++++++++++++
+        
+        - Now has a "security" package extras set, ``$ pip install requests[security]``
+        - Requests will now use Certifi if it is available.
+        - Capture and re-raise urllib3 ProtocolError
+        - Bugfix for responses that attempt to redirect to themselves forever (wtf?).
+        
+        
+        2.4.0 (2014-08-29)
+        ++++++++++++++++++
+        
+        **Behavioral Changes**
+        
+        - ``Connection: keep-alive`` header is now sent automatically.
+        
+        **Improvements**
+        
+        - Support for connect timeouts! Timeout now accepts a tuple (connect, read) which is used to set individual connect and read timeouts.
+        - Allow copying of PreparedRequests without headers/cookies.
+        - Updated bundled urllib3 version.
+        - Refactored settings loading from environment — new `Session.merge_environment_settings`.
+        - Handle socket errors in iter_content.
+        
+        
+        2.3.0 (2014-05-16)
+        ++++++++++++++++++
+        
+        **API Changes**
+        
+        - New ``Response`` property ``is_redirect``, which is true when the
+          library could have processed this response as a redirection (whether
+          or not it actually did).
+        - The ``timeout`` parameter now affects requests with both ``stream=True`` and
+          ``stream=False`` equally.
+        - The change in v2.0.0 to mandate explicit proxy schemes has been reverted.
+          Proxy schemes now default to ``http://``.
+        - The ``CaseInsensitiveDict`` used for HTTP headers now behaves like a normal
+          dictionary when references as string or viewed in the interpreter.
+        
+        **Bugfixes**
+        
+        - No longer expose Authorization or Proxy-Authorization headers on redirect.
+          Fix CVE-2014-1829 and CVE-2014-1830 respectively.
+        - Authorization is re-evaluated each redirect.
+        - On redirect, pass url as native strings.
+        - Fall-back to autodetected encoding for JSON when Unicode detection fails.
+        - Headers set to ``None`` on the ``Session`` are now correctly not sent.
+        - Correctly honor ``decode_unicode`` even if it wasn't used earlier in the same
+          response.
+        - Stop advertising ``compress`` as a supported Content-Encoding.
+        - The ``Response.history`` parameter is now always a list.
+        - Many, many ``urllib3`` bugfixes.
+        
+        2.2.1 (2014-01-23)
+        ++++++++++++++++++
+        
+        **Bugfixes**
+        
+        - Fixes incorrect parsing of proxy credentials that contain a literal or encoded '#' character.
+        - Assorted urllib3 fixes.
+        
+        2.2.0 (2014-01-09)
+        ++++++++++++++++++
+        
+        **API Changes**
+        
+        - New exception: ``ContentDecodingError``. Raised instead of ``urllib3``
+          ``DecodeError`` exceptions.
+        
+        **Bugfixes**
+        
+        - Avoid many many exceptions from the buggy implementation of ``proxy_bypass`` on OS X in Python 2.6.
+        - Avoid crashing when attempting to get authentication credentials from ~/.netrc when running as a user without a home directory.
+        - Use the correct pool size for pools of connections to proxies.
+        - Fix iteration of ``CookieJar`` objects.
+        - Ensure that cookies are persisted over redirect.
+        - Switch back to using chardet, since it has merged with charade.
+        
+        2.1.0 (2013-12-05)
+        ++++++++++++++++++
+        
+        - Updated CA Bundle, of course.
+        - Cookies set on individual Requests through a ``Session`` (e.g. via ``Session.get()``) are no longer persisted to the ``Session``.
+        - Clean up connections when we hit problems during chunked upload, rather than leaking them.
+        - Return connections to the pool when a chunked upload is successful, rather than leaking it.
+        - Match the HTTPbis recommendation for HTTP 301 redirects.
+        - Prevent hanging when using streaming uploads and Digest Auth when a 401 is received.
+        - Values of headers set by Requests are now always the native string type.
+        - Fix previously broken SNI support.
+        - Fix accessing HTTP proxies using proxy authentication.
+        - Unencode HTTP Basic usernames and passwords extracted from URLs.
+        - Support for IP address ranges for no_proxy environment variable
+        - Parse headers correctly when users override the default ``Host:`` header.
+        - Avoid munging the URL in case of case-sensitive servers.
+        - Looser URL handling for non-HTTP/HTTPS urls.
+        - Accept unicode methods in Python 2.6 and 2.7.
+        - More resilient cookie handling.
+        - Make ``Response`` objects pickleable.
+        - Actually added MD5-sess to Digest Auth instead of pretending to like last time.
+        - Updated internal urllib3.
+        - Fixed @Lukasa's lack of taste.
+        
+        2.0.1 (2013-10-24)
+        ++++++++++++++++++
+        
+        - Updated included CA Bundle with new mistrusts and automated process for the future
+        - Added MD5-sess to Digest Auth
+        - Accept per-file headers in multipart file POST messages.
+        - Fixed: Don't send the full URL on CONNECT messages.
+        - Fixed: Correctly lowercase a redirect scheme.
+        - Fixed: Cookies not persisted when set via functional API.
+        - Fixed: Translate urllib3 ProxyError into a requests ProxyError derived from ConnectionError.
+        - Updated internal urllib3 and chardet.
+        
+        2.0.0 (2013-09-24)
+        ++++++++++++++++++
+        
+        **API Changes:**
+        
+        - Keys in the Headers dictionary are now native strings on all Python versions,
+          i.e. bytestrings on Python 2, unicode on Python 3.
+        - Proxy URLs now *must* have an explicit scheme. A ``MissingSchema`` exception
+          will be raised if they don't.
+        - Timeouts now apply to read time if ``Stream=False``.
+        - ``RequestException`` is now a subclass of ``IOError``, not ``RuntimeError``.
+        - Added new method to ``PreparedRequest`` objects: ``PreparedRequest.copy()``.
+        - Added new method to ``Session`` objects: ``Session.update_request()``. This
+          method updates a ``Request`` object with the data (e.g. cookies) stored on
+          the ``Session``.
+        - Added new method to ``Session`` objects: ``Session.prepare_request()``. This
+          method updates and prepares a ``Request`` object, and returns the
+          corresponding ``PreparedRequest`` object.
+        - Added new method to ``HTTPAdapter`` objects: ``HTTPAdapter.proxy_headers()``.
+          This should not be called directly, but improves the subclass interface.
+        - ``httplib.IncompleteRead`` exceptions caused by incorrect chunked encoding
+          will now raise a Requests ``ChunkedEncodingError`` instead.
+        - Invalid percent-escape sequences now cause a Requests ``InvalidURL``
+          exception to be raised.
+        - HTTP 208 no longer uses reason phrase ``"im_used"``. Correctly uses
+          ``"already_reported"``.
+        - HTTP 226 reason added (``"im_used"``).
+        
+        **Bugfixes:**
+        
+        - Vastly improved proxy support, including the CONNECT verb. Special thanks to
+          the many contributors who worked towards this improvement.
+        - Cookies are now properly managed when 401 authentication responses are
+          received.
+        - Chunked encoding fixes.
+        - Support for mixed case schemes.
+        - Better handling of streaming downloads.
+        - Retrieve environment proxies from more locations.
+        - Minor cookies fixes.
+        - Improved redirect behaviour.
+        - Improved streaming behaviour, particularly for compressed data.
+        - Miscellaneous small Python 3 text encoding bugs.
+        - ``.netrc`` no longer overrides explicit auth.
+        - Cookies set by hooks are now correctly persisted on Sessions.
+        - Fix problem with cookies that specify port numbers in their host field.
+        - ``BytesIO`` can be used to perform streaming uploads.
+        - More generous parsing of the ``no_proxy`` environment variable.
+        - Non-string objects can be passed in data values alongside files.
+        
+        1.2.3 (2013-05-25)
+        ++++++++++++++++++
+        
+        - Simple packaging fix
+        
+        
+        1.2.2 (2013-05-23)
+        ++++++++++++++++++
+        
+        - Simple packaging fix
+        
+        
+        1.2.1 (2013-05-20)
+        ++++++++++++++++++
+        
+        - 301 and 302 redirects now change the verb to GET for all verbs, not just
+          POST, improving browser compatibility.
+        - Python 3.3.2 compatibility
+        - Always percent-encode location headers
+        - Fix connection adapter matching to be most-specific first
+        - new argument to the default connection adapter for passing a block argument
+        - prevent a KeyError when there's no link headers
+        
+        1.2.0 (2013-03-31)
+        ++++++++++++++++++
+        
+        - Fixed cookies on sessions and on requests
+        - Significantly change how hooks are dispatched - hooks now receive all the
+          arguments specified by the user when making a request so hooks can make a
+          secondary request with the same parameters. This is especially necessary for
+          authentication handler authors
+        - certifi support was removed
+        - Fixed bug where using OAuth 1 with body ``signature_type`` sent no data
+        - Major proxy work thanks to @Lukasa including parsing of proxy authentication
+          from the proxy url
+        - Fix DigestAuth handling too many 401s
+        - Update vendored urllib3 to include SSL bug fixes
+        - Allow keyword arguments to be passed to ``json.loads()`` via the
+          ``Response.json()`` method
+        - Don't send ``Content-Length`` header by default on ``GET`` or ``HEAD``
+          requests
+        - Add ``elapsed`` attribute to ``Response`` objects to time how long a request
+          took.
+        - Fix ``RequestsCookieJar``
+        - Sessions and Adapters are now picklable, i.e., can be used with the
+          multiprocessing library
+        - Update charade to version 1.0.3
+        
+        The change in how hooks are dispatched will likely cause a great deal of
+        issues.
+        
+        1.1.0 (2013-01-10)
+        ++++++++++++++++++
+        
+        - CHUNKED REQUESTS
+        - Support for iterable response bodies
+        - Assume servers persist redirect params
+        - Allow explicit content types to be specified for file data
+        - Make merge_kwargs case-insensitive when looking up keys
+        
+        1.0.3 (2012-12-18)
+        ++++++++++++++++++
+        
+        - Fix file upload encoding bug
+        - Fix cookie behavior
+        
+        1.0.2 (2012-12-17)
+        ++++++++++++++++++
+        
+        - Proxy fix for HTTPAdapter.
+        
+        1.0.1 (2012-12-17)
+        ++++++++++++++++++
+        
+        - Cert verification exception bug.
+        - Proxy fix for HTTPAdapter.
+        
+        1.0.0 (2012-12-17)
+        ++++++++++++++++++
+        
+        - Massive Refactor and Simplification
+        - Switch to Apache 2.0 license
+        - Swappable Connection Adapters
+        - Mountable Connection Adapters
+        - Mutable ProcessedRequest chain
+        - /s/prefetch/stream
+        - Removal of all configuration
+        - Standard library logging
+        - Make Response.json() callable, not property.
+        - Usage of new charade project, which provides python 2 and 3 simultaneous chardet.
+        - Removal of all hooks except 'response'
+        - Removal of all authentication helpers (OAuth, Kerberos)
+        
+        This is not a backwards compatible change.
+        
+        0.14.2 (2012-10-27)
+        +++++++++++++++++++
+        
+        - Improved mime-compatible JSON handling
+        - Proxy fixes
+        - Path hack fixes
+        - Case-Insensistive Content-Encoding headers
+        - Support for CJK parameters in form posts
+        
+        
+        0.14.1 (2012-10-01)
+        +++++++++++++++++++
+        
+        - Python 3.3 Compatibility
+        - Simply default accept-encoding
+        - Bugfixes
+        
+        
+        0.14.0 (2012-09-02)
+        ++++++++++++++++++++
+        
+        - No more iter_content errors if already downloaded.
+        
+        0.13.9 (2012-08-25)
+        +++++++++++++++++++
+        
+        - Fix for OAuth + POSTs
+        - Remove exception eating from dispatch_hook
+        - General bugfixes
+        
+        0.13.8 (2012-08-21)
+        +++++++++++++++++++
+        
+        - Incredible Link header support :)
+        
+        0.13.7 (2012-08-19)
+        +++++++++++++++++++
+        
+        - Support for (key, value) lists everywhere.
+        - Digest Authentication improvements.
+        - Ensure proxy exclusions work properly.
+        - Clearer UnicodeError exceptions.
+        - Automatic casting of URLs to tsrings (fURL and such)
+        - Bugfixes.
+        
+        0.13.6 (2012-08-06)
+        +++++++++++++++++++
+        
+        - Long awaited fix for hanging connections!
+        
+        0.13.5 (2012-07-27)
+        +++++++++++++++++++
+        
+        - Packaging fix
+        
+        0.13.4 (2012-07-27)
+        +++++++++++++++++++
+        
+        - GSSAPI/Kerberos authentication!
+        - App Engine 2.7 Fixes!
+        - Fix leaking connections (from urllib3 update)
+        - OAuthlib path hack fix
+        - OAuthlib URL parameters fix.
+        
+        0.13.3 (2012-07-12)
+        +++++++++++++++++++
+        
+        - Use simplejson if available.
+        - Do not hide SSLErrors behind Timeouts.
+        - Fixed param handling with urls containing fragments.
+        - Significantly improved information in User Agent.
+        - client certificates are ignored when verify=False
+        
+        0.13.2 (2012-06-28)
+        +++++++++++++++++++
+        
+        - Zero dependencies (once again)!
+        - New: Response.reason
+        - Sign querystring parameters in OAuth 1.0
+        - Client certificates no longer ignored when verify=False
+        - Add openSUSE certificate support
+        
+        0.13.1 (2012-06-07)
+        +++++++++++++++++++
+        
+        - Allow passing a file or file-like object as data.
+        - Allow hooks to return responses that indicate errors.
+        - Fix Response.text and Response.json for body-less responses.
+        
+        0.13.0 (2012-05-29)
+        +++++++++++++++++++
+        
+        - Removal of Requests.async in favor of `grequests <https://github.com/kennethreitz/grequests>`_
+        - Allow disabling of cookie persistiance.
+        - New implimentation of safe_mode
+        - cookies.get now supports default argument
+        - Session cookies not saved when Session.request is called with return_response=False
+        - Env: no_proxy support.
+        - RequestsCookieJar improvements.
+        - Various bug fixes.
+        
+        0.12.1 (2012-05-08)
+        +++++++++++++++++++
+        
+        - New ``Response.json`` property.
+        - Ability to add string file uploads.
+        - Fix out-of-range issue with iter_lines.
+        - Fix iter_content default size.
+        - Fix POST redirects containing files.
+        
+        0.12.0 (2012-05-02)
+        +++++++++++++++++++
+        
+        - EXPERIMENTAL OAUTH SUPPORT!
+        - Proper CookieJar-backed cookies interface with awesome dict-like interface.
+        - Speed fix for non-iterated content chunks.
+        - Move ``pre_request`` to a more usable place.
+        - New ``pre_send`` hook.
+        - Lazily encode data, params, files.
+        - Load system Certificate Bundle if ``certify`` isn't available.
+        - Cleanups, fixes.
+        
+        0.11.2 (2012-04-22)
+        +++++++++++++++++++
+        
+        - Attempt to use the OS's certificate bundle if ``certifi`` isn't available.
+        - Infinite digest auth redirect fix.
+        - Multi-part file upload improvements.
+        - Fix decoding of invalid %encodings in URLs.
+        - If there is no content in a response don't throw an error the second time that content is attempted to be read.
+        - Upload data on redirects.
+        
+        0.11.1 (2012-03-30)
+        +++++++++++++++++++
+        
+        * POST redirects now break RFC to do what browsers do: Follow up with a GET.
+        * New ``strict_mode`` configuration to disable new redirect behavior.
+        
+        
+        0.11.0 (2012-03-14)
+        +++++++++++++++++++
+        
+        * Private SSL Certificate support
+        * Remove select.poll from Gevent monkeypatching
+        * Remove redundant generator for chunked transfer encoding
+        * Fix: Response.ok raises Timeout Exception in safe_mode
+        
+        0.10.8 (2012-03-09)
+        +++++++++++++++++++
+        
+        * Generate chunked ValueError fix
+        * Proxy configuration by environment variables
+        * Simplification of iter_lines.
+        * New `trust_env` configuration for disabling system/environment hints.
+        * Suppress cookie errors.
+        
+        0.10.7 (2012-03-07)
+        +++++++++++++++++++
+        
+        * `encode_uri` = False
+        
+        0.10.6 (2012-02-25)
+        +++++++++++++++++++
+        
+        * Allow '=' in cookies.
+        
+        0.10.5 (2012-02-25)
+        +++++++++++++++++++
+        
+        * Response body with 0 content-length fix.
+        * New async.imap.
+        * Don't fail on netrc.
+        
+        
+        0.10.4 (2012-02-20)
+        +++++++++++++++++++
+        
+        * Honor netrc.
+        
+        0.10.3 (2012-02-20)
+        +++++++++++++++++++
+        
+        * HEAD requests don't follow redirects anymore.
+        * raise_for_status() doesn't raise for 3xx anymore.
+        * Make Session objects picklable.
+        * ValueError for invalid schema URLs.
+        
+        0.10.2 (2012-01-15)
+        +++++++++++++++++++
+        
+        * Vastly improved URL quoting.
+        * Additional allowed cookie key values.
+        * Attempted fix for "Too many open files" Error
+        * Replace unicode errors on first pass, no need for second pass.
+        * Append '/' to bare-domain urls before query insertion.
+        * Exceptions now inherit from RuntimeError.
+        * Binary uploads + auth fix.
+        * Bugfixes.
+        
+        
+        0.10.1 (2012-01-23)
+        +++++++++++++++++++
+        
+        * PYTHON 3 SUPPORT!
+        * Dropped 2.5 Support. (*Backwards Incompatible*)
+        
+        0.10.0 (2012-01-21)
+        +++++++++++++++++++
+        
+        * ``Response.content`` is now bytes-only. (*Backwards Incompatible*)
+        * New ``Response.text`` is unicode-only.
+        * If no ``Response.encoding`` is specified and ``chardet`` is available, ``Respoonse.text`` will guess an encoding.
+        * Default to ISO-8859-1 (Western) encoding for "text" subtypes.
+        * Removal of `decode_unicode`. (*Backwards Incompatible*)
+        * New multiple-hooks system.
+        * New ``Response.register_hook`` for registering hooks within the pipeline.
+        * ``Response.url`` is now Unicode.
+        
+        0.9.3 (2012-01-18)
+        ++++++++++++++++++
+        
+        * SSL verify=False bugfix (apparent on windows machines).
+        
+        0.9.2 (2012-01-18)
+        ++++++++++++++++++
+        
+        * Asynchronous async.send method.
+        * Support for proper chunk streams with boundaries.
+        * session argument for Session classes.
+        * Print entire hook tracebacks, not just exception instance.
+        * Fix response.iter_lines from pending next line.
+        * Fix but in HTTP-digest auth w/ URI having query strings.
+        * Fix in Event Hooks section.
+        * Urllib3 update.
+        
+        
+        0.9.1 (2012-01-06)
+        ++++++++++++++++++
+        
+        * danger_mode for automatic Response.raise_for_status()
+        * Response.iter_lines refactor
+        
+        0.9.0 (2011-12-28)
+        ++++++++++++++++++
+        
+        * verify ssl is default.
+        
+        
+        0.8.9 (2011-12-28)
+        ++++++++++++++++++
+        
+        * Packaging fix.
+        
+        
+        0.8.8 (2011-12-28)
+        ++++++++++++++++++
+        
+        * SSL CERT VERIFICATION!
+        * Release of Cerifi: Mozilla's cert list.
+        * New 'verify' argument for SSL requests.
+        * Urllib3 update.
+        
+        0.8.7 (2011-12-24)
+        ++++++++++++++++++
+        
+        * iter_lines last-line truncation fix
+        * Force safe_mode for async requests
+        * Handle safe_mode exceptions more consistently
+        * Fix iteration on null responses in safe_mode
+        
+        0.8.6 (2011-12-18)
+        ++++++++++++++++++
+        
+        * Socket timeout fixes.
+        * Proxy Authorization support.
+        
+        0.8.5 (2011-12-14)
+        ++++++++++++++++++
+        
+        * Response.iter_lines!
+        
+        0.8.4 (2011-12-11)
+        ++++++++++++++++++
+        
+        * Prefetch bugfix.
+        * Added license to installed version.
+        
+        0.8.3 (2011-11-27)
+        ++++++++++++++++++
+        
+        * Converted auth system to use simpler callable objects.
+        * New session parameter to API methods.
+        * Display full URL while logging.
+        
+        0.8.2 (2011-11-19)
+        ++++++++++++++++++
+        
+        * New Unicode decoding system, based on over-ridable `Response.encoding`.
+        * Proper URL slash-quote handling.
+        * Cookies with ``[``, ``]``, and ``_`` allowed.
+        
+        0.8.1 (2011-11-15)
+        ++++++++++++++++++
+        
+        * URL Request path fix
+        * Proxy fix.
+        * Timeouts fix.
+        
+        0.8.0 (2011-11-13)
+        ++++++++++++++++++
+        
+        * Keep-alive support!
+        * Complete removal of Urllib2
+        * Complete removal of Poster
+        * Complete removal of CookieJars
+        * New ConnectionError raising
+        * Safe_mode for error catching
+        * prefetch parameter for request methods
+        * OPTION method
+        * Async pool size throttling
+        * File uploads send real names
+        * Vendored in urllib3
+        
+        0.7.6 (2011-11-07)
+        ++++++++++++++++++
+        
+        * Digest authentication bugfix (attach query data to path)
+        
+        0.7.5 (2011-11-04)
+        ++++++++++++++++++
+        
+        * Response.content = None if there was an invalid repsonse.
+        * Redirection auth handling.
+        
+        0.7.4 (2011-10-26)
+        ++++++++++++++++++
+        
+        * Session Hooks fix.
+        
+        0.7.3 (2011-10-23)
+        ++++++++++++++++++
+        
+        * Digest Auth fix.
+        
+        
+        0.7.2 (2011-10-23)
+        ++++++++++++++++++
+        
+        * PATCH Fix.
+        
+        
+        0.7.1 (2011-10-23)
+        ++++++++++++++++++
+        
+        * Move away from urllib2 authentication handling.
+        * Fully Remove AuthManager, AuthObject, &c.
+        * New tuple-based auth system with handler callbacks.
+        
+        
+        0.7.0 (2011-10-22)
+        ++++++++++++++++++
+        
+        * Sessions are now the primary interface.
+        * Deprecated InvalidMethodException.
+        * PATCH fix.
+        * New config system (no more global settings).
+        
+        
+        0.6.6 (2011-10-19)
+        ++++++++++++++++++
+        
+        * Session parameter bugfix (params merging).
+        
+        
+        0.6.5 (2011-10-18)
+        ++++++++++++++++++
+        
+        * Offline (fast) test suite.
+        * Session dictionary argument merging.
+        
+        
+        0.6.4 (2011-10-13)
+        ++++++++++++++++++
+        
+        * Automatic decoding of unicode, based on HTTP Headers.
+        * New ``decode_unicode`` setting.
+        * Removal of ``r.read/close`` methods.
+        * New ``r.faw`` interface for advanced response usage.*
+        * Automatic expansion of parameterized headers.
+        
+        
+        0.6.3 (2011-10-13)
+        ++++++++++++++++++
+        
+        * Beautiful ``requests.async`` module, for making async requests w/ gevent.
+        
+        
+        0.6.2 (2011-10-09)
+        ++++++++++++++++++
+        
+        * GET/HEAD obeys allow_redirects=False.
+        
+        
+        0.6.1 (2011-08-20)
+        ++++++++++++++++++
+        
+        * Enhanced status codes experience ``\o/``
+        * Set a maximum number of redirects (``settings.max_redirects``)
+        * Full Unicode URL support
+        * Support for protocol-less redirects.
+        * Allow for arbitrary request types.
+        * Bugfixes
+        
+        
+        0.6.0 (2011-08-17)
+        ++++++++++++++++++
+        
+        * New callback hook system
+        * New persistient sessions object and context manager
+        * Transparent Dict-cookie handling
+        * Status code reference object
+        * Removed Response.cached
+        * Added Response.request
+        * All args are kwargs
+        * Relative redirect support
+        * HTTPError handling improvements
+        * Improved https testing
+        * Bugfixes
+        
+        
+        0.5.1 (2011-07-23)
+        ++++++++++++++++++
+        
+        * International Domain Name Support!
+        * Access headers without fetching entire body (``read()``)
+        * Use lists as dicts for parameters
+        * Add Forced Basic Authentication
+        * Forced Basic is default authentication type
+        * ``python-requests.org`` default User-Agent header
+        * CaseInsensitiveDict lower-case caching
+        * Response.history bugfix
+        
+        
+        0.5.0 (2011-06-21)
+        ++++++++++++++++++
+        
+        * PATCH Support
+        * Support for Proxies
+        * HTTPBin Test Suite
+        * Redirect Fixes
+        * settings.verbose stream writing
+        * Querystrings for all methods
+        * URLErrors (Connection Refused, Timeout, Invalid URLs) are treated as explicity raised
+          ``r.requests.get('hwe://blah'); r.raise_for_status()``
+        
+        
+        0.4.1 (2011-05-22)
+        ++++++++++++++++++
+        
+        * Improved Redirection Handling
+        * New 'allow_redirects' param for following non-GET/HEAD Redirects
+        * Settings module refactoring
+        
+        
+        0.4.0 (2011-05-15)
+        ++++++++++++++++++
+        
+        * Response.history: list of redirected responses
+        * Case-Insensitive Header Dictionaries!
+        * Unicode URLs
+        
+        
+        0.3.4 (2011-05-14)
+        ++++++++++++++++++
+        
+        * Urllib2 HTTPAuthentication Recursion fix (Basic/Digest)
+        * Internal Refactor
+        * Bytes data upload Bugfix
+        
+        
+        
+        0.3.3 (2011-05-12)
+        ++++++++++++++++++
+        
+        * Request timeouts
+        * Unicode url-encoded data
+        * Settings context manager and module
+        
+        
+        0.3.2 (2011-04-15)
+        ++++++++++++++++++
+        
+        * Automatic Decompression of GZip Encoded Content
+        * AutoAuth Support for Tupled HTTP Auth
+        
+        
+        0.3.1 (2011-04-01)
+        ++++++++++++++++++
+        
+        * Cookie Changes
+        * Response.read()
+        * Poster fix
+        
+        
+        0.3.0 (2011-02-25)
+        ++++++++++++++++++
+        
+        * Automatic Authentication API Change
+        * Smarter Query URL Parameterization
+        * Allow file uploads and POST data together
+        * New Authentication Manager System
+            - Simpler Basic HTTP System
+            - Supports all build-in urllib2 Auths
+            - Allows for custom Auth Handlers
+        
+        
+        0.2.4 (2011-02-19)
+        ++++++++++++++++++
+        
+        * Python 2.5 Support
+        * PyPy-c v1.4 Support
+        * Auto-Authentication tests
+        * Improved Request object constructor
+        
+        0.2.3 (2011-02-15)
+        ++++++++++++++++++
+        
+        * New HTTPHandling Methods
+            - Response.__nonzero__ (false if bad HTTP Status)
+            - Response.ok (True if expected HTTP Status)
+            - Response.error (Logged HTTPError if bad HTTP Status)
+            - Response.raise_for_status() (Raises stored HTTPError)
+        
+        
+        0.2.2 (2011-02-14)
+        ++++++++++++++++++
+        
+        * Still handles request in the event of an HTTPError. (Issue #2)
+        * Eventlet and Gevent Monkeypatch support.
+        * Cookie Support (Issue #1)
+        
+        
+        0.2.1 (2011-02-14)
+        ++++++++++++++++++
+        
+        * Added file attribute to POST and PUT requests for multipart-encode file uploads.
+        * Added Request.url attribute for context and redirects
+        
+        
+        0.2.0 (2011-02-14)
+        ++++++++++++++++++
+        
+        * Birth!
+        
+        
+        0.0.1 (2011-02-13)
+        ++++++++++++++++++
+        
+        * Frustration
+        * Conception
+        
+        
+Platform: UNKNOWN
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Natural Language :: English
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 2.6
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.3
+Classifier: Programming Language :: Python :: 3.4

script/_Lib/requests/__init__.py

@@ -0,0 +1,77 @@
+# -*- coding: utf-8 -*-
+
+#   __
+#  /__)  _  _     _   _ _/   _
+# / (   (- (/ (/ (- _)  /  _)
+#          /
+
+"""
+requests HTTP library
+~~~~~~~~~~~~~~~~~~~~~
+
+Requests is an HTTP library, written in Python, for human beings. Basic GET
+usage:
+
+   >>> import requests
+   >>> r = requests.get('https://www.python.org')
+   >>> r.status_code
+   200
+   >>> 'Python is a programming language' in r.content
+   True
+
+... or POST:
+
+   >>> payload = dict(key1='value1', key2='value2')
+   >>> r = requests.post('http://httpbin.org/post', data=payload)
+   >>> print(r.text)
+   {
+     ...
+     "form": {
+       "key2": "value2",
+       "key1": "value1"
+     },
+     ...
+   }
+
+The other HTTP methods are supported - see `requests.api`. Full documentation
+is at <http://python-requests.org>.
+
+:copyright: (c) 2014 by Kenneth Reitz.
+:license: Apache 2.0, see LICENSE for more details.
+
+"""
+
+__title__ = 'requests'
+__version__ = '2.4.3'
+__build__ = 0x020403
+__author__ = 'Kenneth Reitz'
+__license__ = 'Apache 2.0'
+__copyright__ = 'Copyright 2014 Kenneth Reitz'
+
+# Attempt to enable urllib3's SNI support, if possible
+try:
+    from .packages.urllib3.contrib import pyopenssl
+    pyopenssl.inject_into_urllib3()
+except ImportError:
+    pass
+
+from . import utils
+from .models import Request, Response, PreparedRequest
+from .api import request, get, head, post, patch, put, delete, options
+from .sessions import session, Session
+from .status_codes import codes
+from .exceptions import (
+    RequestException, Timeout, URLRequired,
+    TooManyRedirects, HTTPError, ConnectionError
+)
+
+# Set default logging handler to avoid "No handler found" warnings.
+import logging
+try:  # Python 2.7+
+    from logging import NullHandler
+except ImportError:
+    class NullHandler(logging.Handler):
+        def emit(self, record):
+            pass
+
+logging.getLogger(__name__).addHandler(NullHandler())

script/_Lib/requests/adapters.py

@@ -0,0 +1,426 @@
+# -*- coding: utf-8 -*-
+
+"""
+requests.adapters
+~~~~~~~~~~~~~~~~~
+
+This module contains the transport adapters that Requests uses to define
+and maintain connections.
+"""
+
+import socket
+
+from .models import Response
+from .packages.urllib3 import Retry
+from .packages.urllib3.poolmanager import PoolManager, proxy_from_url
+from .packages.urllib3.response import HTTPResponse
+from .packages.urllib3.util import Timeout as TimeoutSauce
+from .compat import urlparse, basestring
+from .utils import (DEFAULT_CA_BUNDLE_PATH, get_encoding_from_headers,
+                    prepend_scheme_if_needed, get_auth_from_url, urldefragauth)
+from .structures import CaseInsensitiveDict
+from .packages.urllib3.exceptions import ConnectTimeoutError
+from .packages.urllib3.exceptions import HTTPError as _HTTPError
+from .packages.urllib3.exceptions import MaxRetryError
+from .packages.urllib3.exceptions import ProxyError as _ProxyError
+from .packages.urllib3.exceptions import ProtocolError
+from .packages.urllib3.exceptions import ReadTimeoutError
+from .packages.urllib3.exceptions import SSLError as _SSLError
+from .cookies import extract_cookies_to_jar
+from .exceptions import (ConnectionError, ConnectTimeout, ReadTimeout, SSLError,
+                         ProxyError)
+from .auth import _basic_auth_str
+
+DEFAULT_POOLBLOCK = False
+DEFAULT_POOLSIZE = 10
+DEFAULT_RETRIES = 0
+
+
+class BaseAdapter(object):
+    """The Base Transport Adapter"""
+
+    def __init__(self):
+        super(BaseAdapter, self).__init__()
+
+    def send(self):
+        raise NotImplementedError
+
+    def close(self):
+        raise NotImplementedError
+
+
+class HTTPAdapter(BaseAdapter):
+    """The built-in HTTP Adapter for urllib3.
+
+    Provides a general-case interface for Requests sessions to contact HTTP and
+    HTTPS urls by implementing the Transport Adapter interface. This class will
+    usually be created by the :class:`Session <Session>` class under the
+    covers.
+
+    :param pool_connections: The number of urllib3 connection pools to cache.
+    :param pool_maxsize: The maximum number of connections to save in the pool.
+    :param int max_retries: The maximum number of retries each connection
+        should attempt. Note, this applies only to failed connections and
+        timeouts, never to requests where the server returns a response.
+    :param pool_block: Whether the connection pool should block for connections.
+
+    Usage::
+
+      >>> import requests
+      >>> s = requests.Session()
+      >>> a = requests.adapters.HTTPAdapter(max_retries=3)
+      >>> s.mount('http://', a)
+    """
+    __attrs__ = ['max_retries', 'config', '_pool_connections', '_pool_maxsize',
+                 '_pool_block']
+
+    def __init__(self, pool_connections=DEFAULT_POOLSIZE,
+                 pool_maxsize=DEFAULT_POOLSIZE, max_retries=DEFAULT_RETRIES,
+                 pool_block=DEFAULT_POOLBLOCK):
+        self.max_retries = max_retries
+        self.config = {}
+        self.proxy_manager = {}
+
+        super(HTTPAdapter, self).__init__()
+
+        self._pool_connections = pool_connections
+        self._pool_maxsize = pool_maxsize
+        self._pool_block = pool_block
+
+        self.init_poolmanager(pool_connections, pool_maxsize, block=pool_block)
+
+    def __getstate__(self):
+        return dict((attr, getattr(self, attr, None)) for attr in
+                    self.__attrs__)
+
+    def __setstate__(self, state):
+        # Can't handle by adding 'proxy_manager' to self.__attrs__ because
+        # because self.poolmanager uses a lambda function, which isn't pickleable.
+        self.proxy_manager = {}
+        self.config = {}
+
+        for attr, value in state.items():
+            setattr(self, attr, value)
+
+        self.init_poolmanager(self._pool_connections, self._pool_maxsize,
+                              block=self._pool_block)
+
+    def init_poolmanager(self, connections, maxsize, block=DEFAULT_POOLBLOCK, **pool_kwargs):
+        """Initializes a urllib3 PoolManager.
+
+        This method should not be called from user code, and is only
+        exposed for use when subclassing the
+        :class:`HTTPAdapter <requests.adapters.HTTPAdapter>`.
+
+        :param connections: The number of urllib3 connection pools to cache.
+        :param maxsize: The maximum number of connections to save in the pool.
+        :param block: Block when no free connections are available.
+        :param pool_kwargs: Extra keyword arguments used to initialize the Pool Manager.
+        """
+        # save these values for pickling
+        self._pool_connections = connections
+        self._pool_maxsize = maxsize
+        self._pool_block = block
+
+        self.poolmanager = PoolManager(num_pools=connections, maxsize=maxsize,
+                                       block=block, **pool_kwargs)
+
+    def proxy_manager_for(self, proxy, **proxy_kwargs):
+        """Return urllib3 ProxyManager for the given proxy.
+
+        This method should not be called from user code, and is only
+        exposed for use when subclassing the
+        :class:`HTTPAdapter <requests.adapters.HTTPAdapter>`.
+
+        :param proxy: The proxy to return a urllib3 ProxyManager for.
+        :param proxy_kwargs: Extra keyword arguments used to configure the Proxy Manager.
+        :returns: ProxyManager
+        """
+        if not proxy in self.proxy_manager:
+            proxy_headers = self.proxy_headers(proxy)
+            self.proxy_manager[proxy] = proxy_from_url(
+                proxy,
+                proxy_headers=proxy_headers,
+                num_pools=self._pool_connections,
+                maxsize=self._pool_maxsize,
+                block=self._pool_block,
+                **proxy_kwargs)
+
+        return self.proxy_manager[proxy]
+
+    def cert_verify(self, conn, url, verify, cert):
+        """Verify a SSL certificate. This method should not be called from user
+        code, and is only exposed for use when subclassing the
+        :class:`HTTPAdapter <requests.adapters.HTTPAdapter>`.
+
+        :param conn: The urllib3 connection object associated with the cert.
+        :param url: The requested URL.
+        :param verify: Whether we should actually verify the certificate.
+        :param cert: The SSL certificate to verify.
+        """
+        if url.lower().startswith('https') and verify:
+
+            cert_loc = None
+
+            # Allow self-specified cert location.
+            if verify is not True:
+                cert_loc = verify
+
+            if not cert_loc:
+                cert_loc = DEFAULT_CA_BUNDLE_PATH
+
+            if not cert_loc:
+                raise Exception("Could not find a suitable SSL CA certificate bundle.")
+
+            conn.cert_reqs = 'CERT_REQUIRED'
+            conn.ca_certs = cert_loc
+        else:
+            conn.cert_reqs = 'CERT_NONE'
+            conn.ca_certs = None
+
+        if cert:
+            if not isinstance(cert, basestring):
+                conn.cert_file = cert[0]
+                conn.key_file = cert[1]
+            else:
+                conn.cert_file = cert
+
+    def build_response(self, req, resp):
+        """Builds a :class:`Response <requests.Response>` object from a urllib3
+        response. This should not be called from user code, and is only exposed
+        for use when subclassing the
+        :class:`HTTPAdapter <requests.adapters.HTTPAdapter>`
+
+        :param req: The :class:`PreparedRequest <PreparedRequest>` used to generate the response.
+        :param resp: The urllib3 response object.
+        """
+        response = Response()
+
+        # Fallback to None if there's no status_code, for whatever reason.
+        response.status_code = getattr(resp, 'status', None)
+
+        # Make headers case-insensitive.
+        response.headers = CaseInsensitiveDict(getattr(resp, 'headers', {}))
+
+        # Set encoding.
+        response.encoding = get_encoding_from_headers(response.headers)
+        response.raw = resp
+        response.reason = response.raw.reason
+
+        if isinstance(req.url, bytes):
+            response.url = req.url.decode('utf-8')
+        else:
+            response.url = req.url
+
+        # Add new cookies from the server.
+        extract_cookies_to_jar(response.cookies, req, resp)
+
+        # Give the Response some context.
+        response.request = req
+        response.connection = self
+
+        return response
+
+    def get_connection(self, url, proxies=None):
+        """Returns a urllib3 connection for the given URL. This should not be
+        called from user code, and is only exposed for use when subclassing the
+        :class:`HTTPAdapter <requests.adapters.HTTPAdapter>`.
+
+        :param url: The URL to connect to.
+        :param proxies: (optional) A Requests-style dictionary of proxies used on this request.
+        """
+        proxies = proxies or {}
+        proxy = proxies.get(urlparse(url.lower()).scheme)
+
+        if proxy:
+            proxy = prepend_scheme_if_needed(proxy, 'http')
+            proxy_manager = self.proxy_manager_for(proxy)
+            conn = proxy_manager.connection_from_url(url)
+        else:
+            # Only scheme should be lower case
+            parsed = urlparse(url)
+            url = parsed.geturl()
+            conn = self.poolmanager.connection_from_url(url)
+
+        return conn
+
+    def close(self):
+        """Disposes of any internal state.
+
+        Currently, this just closes the PoolManager, which closes pooled
+        connections.
+        """
+        self.poolmanager.clear()
+
+    def request_url(self, request, proxies):
+        """Obtain the url to use when making the final request.
+
+        If the message is being sent through a HTTP proxy, the full URL has to
+        be used. Otherwise, we should only use the path portion of the URL.
+
+        This should not be called from user code, and is only exposed for use
+        when subclassing the
+        :class:`HTTPAdapter <requests.adapters.HTTPAdapter>`.
+
+        :param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
+        :param proxies: A dictionary of schemes to proxy URLs.
+        """
+        proxies = proxies or {}
+        scheme = urlparse(request.url).scheme
+        proxy = proxies.get(scheme)
+
+        if proxy and scheme != 'https':
+            url = urldefragauth(request.url)
+        else:
+            url = request.path_url
+
+        return url
+
+    def add_headers(self, request, **kwargs):
+        """Add any headers needed by the connection. As of v2.0 this does
+        nothing by default, but is left for overriding by users that subclass
+        the :class:`HTTPAdapter <requests.adapters.HTTPAdapter>`.
+
+        This should not be called from user code, and is only exposed for use
+        when subclassing the
+        :class:`HTTPAdapter <requests.adapters.HTTPAdapter>`.
+
+        :param request: The :class:`PreparedRequest <PreparedRequest>` to add headers to.
+        :param kwargs: The keyword arguments from the call to send().
+        """
+        pass
+
+    def proxy_headers(self, proxy):
+        """Returns a dictionary of the headers to add to any request sent
+        through a proxy. This works with urllib3 magic to ensure that they are
+        correctly sent to the proxy, rather than in a tunnelled request if
+        CONNECT is being used.
+
+        This should not be called from user code, and is only exposed for use
+        when subclassing the
+        :class:`HTTPAdapter <requests.adapters.HTTPAdapter>`.
+
+        :param proxies: The url of the proxy being used for this request.
+        :param kwargs: Optional additional keyword arguments.
+        """
+        headers = {}
+        username, password = get_auth_from_url(proxy)
+
+        if username and password:
+            headers['Proxy-Authorization'] = _basic_auth_str(username,
+                                                             password)
+
+        return headers
+
+    def send(self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None):
+        """Sends PreparedRequest object. Returns Response object.
+
+        :param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
+        :param stream: (optional) Whether to stream the request content.
+        :param timeout: (optional) How long to wait for the server to send
+            data before giving up, as a float, or a (`connect timeout, read
+            timeout <user/advanced.html#timeouts>`_) tuple.
+        :type timeout: float or tuple
+        :param verify: (optional) Whether to verify SSL certificates.
+        :param cert: (optional) Any user-provided SSL certificate to be trusted.
+        :param proxies: (optional) The proxies dictionary to apply to the request.
+        """
+
+        conn = self.get_connection(request.url, proxies)
+
+        self.cert_verify(conn, request.url, verify, cert)
+        url = self.request_url(request, proxies)
+        self.add_headers(request)
+
+        chunked = not (request.body is None or 'Content-Length' in request.headers)
+
+        if isinstance(timeout, tuple):
+            try:
+                connect, read = timeout
+                timeout = TimeoutSauce(connect=connect, read=read)
+            except ValueError as e:
+                # this may raise a string formatting error.
+                err = ("Invalid timeout {0}. Pass a (connect, read) "
+                       "timeout tuple, or a single float to set "
+                       "both timeouts to the same value".format(timeout))
+                raise ValueError(err)
+        else:
+            timeout = TimeoutSauce(connect=timeout, read=timeout)
+
+        try:
+            if not chunked:
+                resp = conn.urlopen(
+                    method=request.method,
+                    url=url,
+                    body=request.body,
+                    headers=request.headers,
+                    redirect=False,
+                    assert_same_host=False,
+                    preload_content=False,
+                    decode_content=False,
+                    retries=Retry(self.max_retries, read=False),
+                    timeout=timeout
+                )
+
+            # Send the request.
+            else:
+                if hasattr(conn, 'proxy_pool'):
+                    conn = conn.proxy_pool
+
+                low_conn = conn._get_conn(timeout=timeout)
+
+                try:
+                    low_conn.putrequest(request.method,
+                                        url,
+                                        skip_accept_encoding=True)
+
+                    for header, value in request.headers.items():
+                        low_conn.putheader(header, value)
+
+                    low_conn.endheaders()
+
+                    for i in request.body:
+                        low_conn.send(hex(len(i))[2:].encode('utf-8'))
+                        low_conn.send(b'\r\n')
+                        low_conn.send(i)
+                        low_conn.send(b'\r\n')
+                    low_conn.send(b'0\r\n\r\n')
+
+                    r = low_conn.getresponse()
+                    resp = HTTPResponse.from_httplib(
+                        r,
+                        pool=conn,
+                        connection=low_conn,
+                        preload_content=False,
+                        decode_content=False
+                    )
+                except:
+                    # If we hit any problems here, clean up the connection.
+                    # Then, reraise so that we can handle the actual exception.
+                    low_conn.close()
+                    raise
+                else:
+                    # All is well, return the connection to the pool.
+                    conn._put_conn(low_conn)
+
+        except (ProtocolError, socket.error) as err:
+            raise ConnectionError(err, request=request)
+
+        except MaxRetryError as e:
+            if isinstance(e.reason, ConnectTimeoutError):
+                raise ConnectTimeout(e, request=request)
+
+            raise ConnectionError(e, request=request)
+
+        except _ProxyError as e:
+            raise ProxyError(e)
+
+        except (_SSLError, _HTTPError) as e:
+            if isinstance(e, _SSLError):
+                raise SSLError(e, request=request)
+            elif isinstance(e, ReadTimeoutError):
+                raise ReadTimeout(e, request=request)
+            else:
+                raise
+
+        return self.build_response(request, resp)

script/_Lib/requests/api.py

@@ -0,0 +1,126 @@
+# -*- coding: utf-8 -*-
+
+"""
+requests.api
+~~~~~~~~~~~~
+
+This module implements the Requests API.
+
+:copyright: (c) 2012 by Kenneth Reitz.
+:license: Apache2, see LICENSE for more details.
+
+"""
+
+from . import sessions
+
+
+def request(method, url, **kwargs):
+    """Constructs and sends a :class:`Request <Request>`.
+    Returns :class:`Response <Response>` object.
+
+    :param method: method for the new :class:`Request` object.
+    :param url: URL for the new :class:`Request` object.
+    :param params: (optional) Dictionary or bytes to be sent in the query string for the :class:`Request`.
+    :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`.
+    :param json: (optional) json data to send in the body of the :class:`Request`.
+    :param headers: (optional) Dictionary of HTTP Headers to send with the :class:`Request`.
+    :param cookies: (optional) Dict or CookieJar object to send with the :class:`Request`.
+    :param files: (optional) Dictionary of ``'name': file-like-objects`` (or ``{'name': ('filename', fileobj)}``) for multipart encoding upload.
+    :param auth: (optional) Auth tuple to enable Basic/Digest/Custom HTTP Auth.
+    :param timeout: (optional) How long to wait for the server to send data
+        before giving up, as a float, or a (`connect timeout, read timeout
+        <user/advanced.html#timeouts>`_) tuple.
+    :type timeout: float or tuple
+    :param allow_redirects: (optional) Boolean. Set to True if POST/PUT/DELETE redirect following is allowed.
+    :type allow_redirects: bool
+    :param proxies: (optional) Dictionary mapping protocol to the URL of the proxy.
+    :param verify: (optional) if ``True``, the SSL cert will be verified. A CA_BUNDLE path can also be provided.
+    :param stream: (optional) if ``False``, the response content will be immediately downloaded.
+    :param cert: (optional) if String, path to ssl client cert file (.pem). If Tuple, ('cert', 'key') pair.
+
+    Usage::
+
+      >>> import requests
+      >>> req = requests.request('GET', 'http://httpbin.org/get')
+      <Response [200]>
+    """
+
+    session = sessions.Session()
+    return session.request(method=method, url=url, **kwargs)
+
+
+def get(url, **kwargs):
+    """Sends a GET request. Returns :class:`Response` object.
+
+    :param url: URL for the new :class:`Request` object.
+    :param \*\*kwargs: Optional arguments that ``request`` takes.
+    """
+
+    kwargs.setdefault('allow_redirects', True)
+    return request('get', url, **kwargs)
+
+
+def options(url, **kwargs):
+    """Sends a OPTIONS request. Returns :class:`Response` object.
+
+    :param url: URL for the new :class:`Request` object.
+    :param \*\*kwargs: Optional arguments that ``request`` takes.
+    """
+
+    kwargs.setdefault('allow_redirects', True)
+    return request('options', url, **kwargs)
+
+
+def head(url, **kwargs):
+    """Sends a HEAD request. Returns :class:`Response` object.
+
+    :param url: URL for the new :class:`Request` object.
+    :param \*\*kwargs: Optional arguments that ``request`` takes.
+    """
+
+    kwargs.setdefault('allow_redirects', False)
+    return request('head', url, **kwargs)
+
+
+def post(url, data=None, json=None, **kwargs):
+    """Sends a POST request. Returns :class:`Response` object.
+
+    :param url: URL for the new :class:`Request` object.
+    :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`.
+    :param json: (optional) json data to send in the body of the :class:`Request`.
+    :param \*\*kwargs: Optional arguments that ``request`` takes.
+    """
+
+    return request('post', url, data=data, json=json, **kwargs)
+
+
+def put(url, data=None, **kwargs):
+    """Sends a PUT request. Returns :class:`Response` object.
+
+    :param url: URL for the new :class:`Request` object.
+    :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`.
+    :param \*\*kwargs: Optional arguments that ``request`` takes.
+    """
+
+    return request('put', url, data=data, **kwargs)
+
+
+def patch(url, data=None, **kwargs):
+    """Sends a PATCH request. Returns :class:`Response` object.
+
+    :param url: URL for the new :class:`Request` object.
+    :param data: (optional) Dictionary, bytes, or file-like object to send in the body of the :class:`Request`.
+    :param \*\*kwargs: Optional arguments that ``request`` takes.
+    """
+
+    return request('patch', url,  data=data, **kwargs)
+
+
+def delete(url, **kwargs):
+    """Sends a DELETE request. Returns :class:`Response` object.
+
+    :param url: URL for the new :class:`Request` object.
+    :param \*\*kwargs: Optional arguments that ``request`` takes.
+    """
+
+    return request('delete', url, **kwargs)

script/_Lib/requests/auth.py

@@ -0,0 +1,197 @@
+# -*- coding: utf-8 -*-
+
+"""
+requests.auth
+~~~~~~~~~~~~~
+
+This module contains the authentication handlers for Requests.
+"""
+
+import os
+import re
+import time
+import hashlib
+
+from base64 import b64encode
+
+from .compat import urlparse, str
+from .cookies import extract_cookies_to_jar
+from .utils import parse_dict_header, to_native_string
+
+CONTENT_TYPE_FORM_URLENCODED = 'application/x-www-form-urlencoded'
+CONTENT_TYPE_MULTI_PART = 'multipart/form-data'
+
+
+def _basic_auth_str(username, password):
+    """Returns a Basic Auth string."""
+
+    authstr = 'Basic ' + to_native_string(
+        b64encode(('%s:%s' % (username, password)).encode('latin1')).strip()
+    )
+
+    return authstr
+
+
+class AuthBase(object):
+    """Base class that all auth implementations derive from"""
+
+    def __call__(self, r):
+        raise NotImplementedError('Auth hooks must be callable.')
+
+
+class HTTPBasicAuth(AuthBase):
+    """Attaches HTTP Basic Authentication to the given Request object."""
+    def __init__(self, username, password):
+        self.username = username
+        self.password = password
+
+    def __call__(self, r):
+        r.headers['Authorization'] = _basic_auth_str(self.username, self.password)
+        return r
+
+
+class HTTPProxyAuth(HTTPBasicAuth):
+    """Attaches HTTP Proxy Authentication to a given Request object."""
+    def __call__(self, r):
+        r.headers['Proxy-Authorization'] = _basic_auth_str(self.username, self.password)
+        return r
+
+
+class HTTPDigestAuth(AuthBase):
+    """Attaches HTTP Digest Authentication to the given Request object."""
+    def __init__(self, username, password):
+        self.username = username
+        self.password = password
+        self.last_nonce = ''
+        self.nonce_count = 0
+        self.chal = {}
+        self.pos = None
+
+    def build_digest_header(self, method, url):
+
+        realm = self.chal['realm']
+        nonce = self.chal['nonce']
+        qop = self.chal.get('qop')
+        algorithm = self.chal.get('algorithm')
+        opaque = self.chal.get('opaque')
+
+        if algorithm is None:
+            _algorithm = 'MD5'
+        else:
+            _algorithm = algorithm.upper()
+        # lambdas assume digest modules are imported at the top level
+        if _algorithm == 'MD5' or _algorithm == 'MD5-SESS':
+            def md5_utf8(x):
+                if isinstance(x, str):
+                    x = x.encode('utf-8')
+                return hashlib.md5(x).hexdigest()
+            hash_utf8 = md5_utf8
+        elif _algorithm == 'SHA':
+            def sha_utf8(x):
+                if isinstance(x, str):
+                    x = x.encode('utf-8')
+                return hashlib.sha1(x).hexdigest()
+            hash_utf8 = sha_utf8
+
+        KD = lambda s, d: hash_utf8("%s:%s" % (s, d))
+
+        if hash_utf8 is None:
+            return None
+
+        # XXX not implemented yet
+        entdig = None
+        p_parsed = urlparse(url)
+        path = p_parsed.path
+        if p_parsed.query:
+            path += '?' + p_parsed.query
+
+        A1 = '%s:%s:%s' % (self.username, realm, self.password)
+        A2 = '%s:%s' % (method, path)
+
+        HA1 = hash_utf8(A1)
+        HA2 = hash_utf8(A2)
+
+        if nonce == self.last_nonce:
+            self.nonce_count += 1
+        else:
+            self.nonce_count = 1
+        ncvalue = '%08x' % self.nonce_count
+        s = str(self.nonce_count).encode('utf-8')
+        s += nonce.encode('utf-8')
+        s += time.ctime().encode('utf-8')
+        s += os.urandom(8)
+
+        cnonce = (hashlib.sha1(s).hexdigest()[:16])
+        noncebit = "%s:%s:%s:%s:%s" % (nonce, ncvalue, cnonce, qop, HA2)
+        if _algorithm == 'MD5-SESS':
+            HA1 = hash_utf8('%s:%s:%s' % (HA1, nonce, cnonce))
+
+        if qop is None:
+            respdig = KD(HA1, "%s:%s" % (nonce, HA2))
+        elif qop == 'auth' or 'auth' in qop.split(','):
+            respdig = KD(HA1, noncebit)
+        else:
+            # XXX handle auth-int.
+            return None
+
+        self.last_nonce = nonce
+
+        # XXX should the partial digests be encoded too?
+        base = 'username="%s", realm="%s", nonce="%s", uri="%s", ' \
+               'response="%s"' % (self.username, realm, nonce, path, respdig)
+        if opaque:
+            base += ', opaque="%s"' % opaque
+        if algorithm:
+            base += ', algorithm="%s"' % algorithm
+        if entdig:
+            base += ', digest="%s"' % entdig
+        if qop:
+            base += ', qop="auth", nc=%s, cnonce="%s"' % (ncvalue, cnonce)
+
+        return 'Digest %s' % (base)
+
+    def handle_401(self, r, **kwargs):
+        """Takes the given response and tries digest-auth, if needed."""
+
+        if self.pos is not None:
+            # Rewind the file position indicator of the body to where
+            # it was to resend the request.
+            r.request.body.seek(self.pos)
+        num_401_calls = getattr(self, 'num_401_calls', 1)
+        s_auth = r.headers.get('www-authenticate', '')
+
+        if 'digest' in s_auth.lower() and num_401_calls < 2:
+
+            setattr(self, 'num_401_calls', num_401_calls + 1)
+            pat = re.compile(r'digest ', flags=re.IGNORECASE)
+            self.chal = parse_dict_header(pat.sub('', s_auth, count=1))
+
+            # Consume content and release the original connection
+            # to allow our new request to reuse the same one.
+            r.content
+            r.raw.release_conn()
+            prep = r.request.copy()
+            extract_cookies_to_jar(prep._cookies, r.request, r.raw)
+            prep.prepare_cookies(prep._cookies)
+
+            prep.headers['Authorization'] = self.build_digest_header(
+                prep.method, prep.url)
+            _r = r.connection.send(prep, **kwargs)
+            _r.history.append(r)
+            _r.request = prep
+
+            return _r
+
+        setattr(self, 'num_401_calls', 1)
+        return r
+
+    def __call__(self, r):
+        # If we have a saved nonce, skip the 401
+        if self.last_nonce:
+            r.headers['Authorization'] = self.build_digest_header(r.method, r.url)
+        try:
+            self.pos = r.body.tell()
+        except AttributeError:
+            pass
+        r.register_hook('response', self.handle_401)
+        return r

script/_Lib/requests/certs.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+certs.py
+~~~~~~~~
+
+This module returns the preferred default CA certificate bundle.
+
+If you are packaging Requests, e.g., for a Linux distribution or a managed
+environment, you can change the definition of where() to return a separately
+packaged CA bundle.
+"""
+import os.path
+
+try:
+    from certifi import where
+except ImportError:
+    def where():
+        """Return the preferred certificate bundle."""
+        # vendored bundle inside Requests
+        return os.path.join(os.path.dirname(__file__), 'cacert.pem')
+
+if __name__ == '__main__':
+    print(where())