config/preferences.json

@@ -76,7 +76,7 @@
   "plotsDetached" : false,
   "plotLayout" : "Vertical",
   "quality" : "High",
-  "defaultPlotColormap" : "Grayscale",
+  "defaultPlotColormap" : "Viridis",
   "markerSize" : 2,
   "plotBackground" : null,
   "gridColor" : null,

config/sessions.properties

@@ -1,2 +1,2 @@
-#Fri Oct 07 10:08:47 CEST 2022
-SessionCounter=78
+#Sun Nov 20 14:52:28 CET 2022
+SessionCounter=79

config/settings.properties

@@ -1,26 +1,33 @@
-#Wed Nov 09 08:38:27 CET 2022
+#Tue Nov 22 15:07:09 CET 2022
+HARMONIC_ID_1=1
 RSYNC_USER=
-CFF=2.25
+CFF=2
 OUTLIERS_THRESHOLD=1000000000
 NORM_FILE=/sls/X11MA/data/e18927/Data1/2022_10/20221017/20221017_Take_Image/i221017_042/i221017_042\#001.tif
 AUTO_SWITCH_VALVE=false
 DRY_RUN=true
-POL_ID_2=Lin_Hor
-ID=ID2
+POL_ID_2=Lin
+OFFSET_ID_1=0.0
+ID=PGM_ID2
+OFFSET_ID_2=0.0
 proposal=proposal
-ENERGY=800
+ENERGY=715.0
 proposer=proposer
 GRATING=G3_600
 image_shift_angle=1.0963912950426833
+POL_ID_1=Circ_Plus
 RSYNC_HOST=
 sample=sample
 RSYNC_PATH=
 pgroup=pgroup
 AUTO_SWITCH_BEAMLINE=false
 AUTO_SWITCH_SHUTTER=true
+ALPHA_ID_2=90.0
+ALPHA_ID_1=0.0
 RSYNC_DEL=true
 DIFF_ORD=1
 image_shift_scale=3.296579966879864
 AVERAGING_DETECTOR=true
 FdaBrowser=false
 authors=author1|author2
+HARMONIC_ID_2=1

config/variables.properties

@@ -1,4 +1,4 @@
-#Wed Nov 09 14:48:58 CET 2022
-LastRunDate=221109
-FileSequentialNumber=17887
-DaySequentialNumber=13
+#Tue Nov 22 16:33:39 CET 2022
+LastRunDate=221122
+FileSequentialNumber=18002
+DaySequentialNumber=88

devices/ci221110_001.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 09:31:17 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/ci221110_003.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 09:32:48 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/ci221115_002#002.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 15 15:16:57 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/ci221122_012#001.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:17:31 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/ci221122_012#002.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:17:31 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/ci221122_017#001.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:37:12 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/ci221122_017#002.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:37:13 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/ci221122_026#001.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:51:51 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17906_001.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 11:09:28 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17907_001.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 11:10:24 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17907_002.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 11:10:26 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17907_003.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 11:10:26 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17909_001.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 11:29:57 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17909_002.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 11:30:00 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17909_003.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 11:30:03 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17966_001.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:02:41 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17971_001.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:10:51 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17971_002.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:10:52 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17971_003.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:10:53 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17971_005.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:10:58 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/cs17971_006.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:11:45 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221110_003#001.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 10:19:21 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221110_003#003.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 10:24:18 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221110_003.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 09:32:47 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221110_005#001.tif.properties

@@ -0,0 +1,20 @@
+#Thu Nov 10 10:19:17 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221111_005.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 15 14:06:16 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221111_006#001.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 15 13:34:23 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221111_006.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 15 14:06:25 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221115_005.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 15 15:25:56 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221115_006.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 15 15:37:08 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221116_006#001.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:20:17 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221116_006#002.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:20:19 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221116_006#003.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:20:21 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221116_006#004.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:20:23 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221116_006#005.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:20:23 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221116_006#006.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:20:24 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221122_002#001.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:20:50 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221122_002#002.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:20:48 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221122_012#001.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:17:36 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221122_012#002.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:17:37 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221122_017#001.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:37:10 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/i221122_017#002.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:37:11 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/image.properties

@@ -1,4 +1,4 @@
-#Mon Oct 25 14:11:15 CEST 2021
+#Thu Nov 10 20:50:06 CET 2022
 spatialCalOffsetY=NaN
 spatialCalOffsetX=NaN
 colormapLogarithmic=false
@@ -6,10 +6,10 @@ scale=1.0
 grayscale=false
 spatialCalScaleX=NaN
 spatialCalScaleY=NaN
-colormapMax=2000.0
+colormapMax=140.171
 rescaleOffset=0.0
 roiWidth=-1
-colormap=Grayscale
+colormap=Flame
 invert=false
 colormapMin=0.0
 rotationCrop=false
@@ -19,7 +19,7 @@ spatialCalUnits=null
 flipVertically=false
 roiHeight=-1
 flipHorizontally=false
-colormapAutomatic=true
+colormapAutomatic=false
 roiY=0
 roiX=0
 transpose=false

devices/raw.properties

@@ -1,4 +1,4 @@
-#Wed Nov 09 14:28:01 CET 2022
+#Wed Nov 16 10:21:29 CET 2022
 spatialCalOffsetY=NaN
 spatialCalOffsetX=NaN
 colormapLogarithmic=false
@@ -19,7 +19,7 @@ spatialCalUnits=mm
 flipVertically=false
 roiHeight=-1
 flipHorizontally=false
-colormapAutomatic=false
+colormapAutomatic=true
 roiY=0
 roiX=0
 transpose=false

devices/s17971_001.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:11:04 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/s17971_002.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:11:04 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/s17971_003.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:11:05 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/s17971_004.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:11:06 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/s17971_005.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:11:07 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/s17971_006.tif.properties

@@ -0,0 +1,20 @@
+#Tue Nov 22 14:11:36 CET 2022
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

plugins/DataAcquisition.form

@@ -901,12 +901,12 @@
                   <Group type="102" alignment="0" attributes="0">
                       <EmptySpace max="-2" attributes="0"/>
                       <Component id="panelSpectrum" min="-2" max="-2" attributes="0"/>
-                      <EmptySpace min="-2" pref="57" max="-2" attributes="0"/>
+                      <EmptySpace type="separate" max="-2" attributes="0"/>
                       <Group type="103" groupAlignment="1" attributes="0">
                           <Component id="jPanel6" min="-2" max="-2" attributes="0"/>
                           <Component id="panelParameters1" min="-2" max="-2" attributes="0"/>
                       </Group>
-                      <EmptySpace min="0" pref="40" max="32767" attributes="0"/>
+                      <EmptySpace min="0" pref="55" max="32767" attributes="0"/>
                   </Group>
               </Group>
             </DimensionLayout>
@@ -958,6 +958,7 @@
                               <Component id="checkSpecSaveSpectrum" alignment="0" min="-2" max="-2" attributes="0"/>
                               <Component id="checkSpecSaveImages" alignment="0" min="-2" max="-2" attributes="0"/>
                               <Component id="checkSpecWithI0" alignment="0" min="-2" max="-2" attributes="0"/>
+                              <Component id="checkDriftCorrectionSpec" alignment="0" min="-2" max="-2" attributes="0"/>
                           </Group>
                           <EmptySpace max="32767" attributes="0"/>
                       </Group>
@@ -977,6 +978,8 @@
                                   <EmptySpace max="-2" attributes="0"/>
                                   <Component id="checkSpecSaveImages" min="-2" max="-2" attributes="0"/>
                                   <EmptySpace max="-2" attributes="0"/>
+                                  <Component id="checkDriftCorrectionSpec" min="-2" max="-2" attributes="0"/>
+                                  <EmptySpace max="-2" attributes="0"/>
                                   <Component id="checkSpecWithI0" min="-2" max="-2" attributes="0"/>
                                   <EmptySpace type="unrelated" max="-2" attributes="0"/>
                                   <Group type="103" groupAlignment="3" attributes="0">
@@ -1202,6 +1205,11 @@
                     <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonSpecAbortActionPerformed"/>
                   </Events>
                 </Component>
+                <Component class="javax.swing.JCheckBox" name="checkDriftCorrectionSpec">
+                  <Properties>
+                    <Property name="text" type="java.lang.String" value="Drift correction"/>
+                  </Properties>
+                </Component>
               </SubComponents>
             </Container>
             <Container class="javax.swing.JPanel" name="jPanel6">

plugins/DataAcquisition.java

@@ -391,6 +391,7 @@ public class DataAcquisition extends Panel {
         HashMap args = new HashMap();
         args.put("SAVE_SPECTRUM", checkSpecSaveSpectrum.isSelected());
         args.put("SAVE_IMAGES", checkSpecSaveImages.isSelected());
+        args.put("DRIFT_CORRECTION", checkDriftCorrectionSpec.isSelected());
         args.put("WITH_I0", checkSpecWithI0.isSelected());
         args.put("SWITCH_POL", checkSpecSwitchPol.isSelected());
         args.put("EXPOSURE", spinnerSpecExp.getValue());
@@ -563,6 +564,7 @@ public class DataAcquisition extends Panel {
         buttonClear = new javax.swing.JButton();
         buttonSpecStart = new javax.swing.JButton();
         buttonSpecAbort = new javax.swing.JButton();
+        checkDriftCorrectionSpec = new javax.swing.JCheckBox();
         jPanel6 = new javax.swing.JPanel();
         panelParameters1 = new javax.swing.JPanel();
         jLabel6 = new javax.swing.JLabel();
@@ -1256,6 +1258,8 @@ public class DataAcquisition extends Panel {
             }
         });
 
+        checkDriftCorrectionSpec.setText("Drift correction");
+
         javax.swing.GroupLayout panelSpectrumLayout = new javax.swing.GroupLayout(panelSpectrum);
         panelSpectrum.setLayout(panelSpectrumLayout);
         panelSpectrumLayout.setHorizontalGroup(
@@ -1287,7 +1291,8 @@ public class DataAcquisition extends Panel {
                 .addGroup(panelSpectrumLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                     .addComponent(checkSpecSaveSpectrum)
                     .addComponent(checkSpecSaveImages)
-                    .addComponent(checkSpecWithI0))
+                    .addComponent(checkSpecWithI0)
+                    .addComponent(checkDriftCorrectionSpec))
                 .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
         );
 
@@ -1308,6 +1313,8 @@ public class DataAcquisition extends Panel {
                         .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                         .addComponent(checkSpecSaveImages)
                         .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(checkDriftCorrectionSpec)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                         .addComponent(checkSpecWithI0)
                         .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                         .addGroup(panelSpectrumLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
@@ -1473,11 +1480,11 @@ public class DataAcquisition extends Panel {
             .addGroup(jPanel3Layout.createSequentialGroup()
                 .addContainerGap()
                 .addComponent(panelSpectrum, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                .addGap(57, 57, 57)
+                .addGap(18, 18, 18)
                 .addGroup(jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
                     .addComponent(jPanel6, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                     .addComponent(panelParameters1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
-                .addGap(0, 40, Short.MAX_VALUE))
+                .addGap(0, 55, Short.MAX_VALUE))
         );
 
         jTabbedPane1.addTab("Absorption Spectrum", jPanel3);
@@ -1789,6 +1796,7 @@ public class DataAcquisition extends Panel {
     private javax.swing.JButton buttonSpecAbort;
     private javax.swing.JButton buttonSpecStart;
     private javax.swing.JCheckBox checkDriftCorrection;
+    private javax.swing.JCheckBox checkDriftCorrectionSpec;
     private javax.swing.JCheckBox checkImgAutosave;
     private javax.swing.JCheckBox checkImgOTFSaveImages;
     private javax.swing.JCheckBox checkSpecSaveImages;

script/Users/PEEM/Armin/heating.py

@@ -0,0 +1,6 @@
+i = 1
+while i < 12:
+    fil.write(i*200)
+    time.sleep(300.0)
+    i += 1
+fil.write(0)

script/devices/eiger.py

@@ -201,13 +201,38 @@ def _save_as_tiff(data, filename, check=False, show = False, metadata={}):
         read = get_ip_array(ip)   
         #print (" ------> Error reading array: " + str(filename))
         #TODO: Original checkcode was deleted!
-    
+
+
+calculated_shifts={}    
 def save_as_tiff(data, filename, check=False, show = False, parallel=True, metadata={}):
     if parallel:
         return fork((_save_as_tiff,(data, filename, check, show, metadata)),)
     else:
         _save_as_tiff(data, filename, check, show, metadata)
 
+def _shift_and_save_as_tiff(data, filename, reference=None, roi=None, image_drift =None, check=False, show = False, metadata={}):
+    global calculated_shifts
+    try:
+        if image_drift is None:
+            xoff, yoff, error, diffphase, image_drift = calculate_shift(reference,data, roi)
+            print xoff, yoff, error, diffphase, image_drift
+            if (abs(xoff) > MAX_SHIFT) or (abs(yoff) > MAX_SHIFT):
+                raise Exception("Shift too big:" + str(xoff, yoff))
+            print "-> Calculated shift: ", xoff, yoff, error, diffphase
+        shifted_frame = apply_shift(data, image_drift)  
+        calculated_shifts[filename]=image_drift    
+    except:
+        print "-> Error shifting image: " + str(sys.exc_info()[1])
+        return
+    save_as_tiff(shifted_frame, filename, check, show, parallel=False, metadata=metadata)        
+
+def shift_and_save_as_tiff(data, filename, reference=None, roi=None, shift=None, check=False, show = False, parallel=True, metadata={}):
+    if parallel:
+        return fork((_shift_and_save_as_tiff,(data, filename, reference, roi, shift, check, show, metadata)),)
+    else:
+        _shift_and_save_as_tiff(data, filename, reference, roi, shift, check, show, metadata)
+
+
 def trigger_eiger(wait=True):
     eiger.waitReady(5000)
     eiger.start()
@@ -395,7 +420,7 @@ def get_outliers_mask(data_type='f'):
 
 class ProcImage(Filter):
     def __init__(self):
-        Filter.__init__(self, "image")
+        Filter.__init__(self, "image_filter")
         self.roi=None
         self.outliers_threshold=None
         self.outliers_mask =None
@@ -419,12 +444,12 @@ class ProcImage(Filter):
         return None #Does not generate BufferedImage here
         
 #image.removeAllListeners()
-proc_image=ProcImage()
-raw.addListener(proc_image)
-
+proc_image_filter=ProcImage()
+raw.addListener(proc_image_filter)
 
+proc_image=ColormapAdapter("image", proc_image_filter)
 add_device(proc_image, True)
-image.refresh() 
+raw.refresh() 
 
 eiger.setDataType(DataType.Float32)
 eiger.getDataArray().monitored=True

script/imaging/shifts.py

@@ -620,8 +620,9 @@ def to_ip(obj):
             obj = load_image(obj)
     else:
         if type(obj) == Data:
-            obj = obj.toBufferedImage(False)
-        if type(obj) == BufferedImage:
+            #obj = obj.toBufferedImage(False)
+            obj = load_array(obj.matrix)
+        elif type(obj) == BufferedImage:
             obj = load_image(obj)
     return obj
 
@@ -630,7 +631,7 @@ def calculate_shift(ref,img, roi, g_sigma=3.0, upscale_factor=100, max_error=2.0
     ref = to_ip(ref)
     img = to_ip(img)      
     stack = create_stack([ref,img])
-    ipr, ipi = complex_edge_filtering(stack, g_sigma=g_sigma, show=False) 
+    ipr, ipi = complex_edge_filtering(stack, g_sigma=g_sigma, show=False, java_code=True) 
     shifts = calculate_shifts(ipr, ipi, roi, upscale_factor=upscale_factor, java_code=True)
     xoff, yoff =  shifts[1][3], shifts[1][2]
     error, diffphase =  shifts[1][4], shifts[1][5]

script/local.py

@@ -8,10 +8,12 @@ from mathutils import estimate_peak_indexes, fit_gaussians, create_fit_point_lis
 from mathutils import fit_polynomial,fit_gaussian, fit_harmonic, calculate_peaks
 from mathutils import PolynomialFunction, Gaussian, HarmonicOscillator
 from collections import OrderedDict
-run ("imaging/shifts")
 
 ProviderCSV.setDefaultItemSeparator(", ")
 get_context().dataManager.createLogs=False
+
+IMAGING_ROI = None
+
 """
 OTF_START = "X11MA-OTF:GO"
 OTF_E1 = "X11MA-OTF:E1"
@@ -749,7 +751,7 @@ def apply_beamline_setup(id,en=None,pol1=None,alp1=None,har1=None,off1=None,pol2
         if off2 is not None:
             put_id_offset(2, float(off2)) #offset on ID2
 
-# Monochromator part
+    # Monochromator part
     if grat is not None:
         if grat=='G1_300':
             Grating.write("0")
@@ -925,8 +927,11 @@ def fit(ydata, xdata = None, limit_to_range=False):
 ###################################################################################################
 #Additional initialization
 ###################################################################################################
-
+DEFAULT_ROI =  Rectangle(128,128,256,256)
+#DEFAULT_ROI =  Rectangle(0,0,512,512)
+
 run("templates/FocusScan")  
+run ("imaging/shifts")
 
 def auto_focus(scan_type="all", range_obj=4.0, step_obj=0.2, range_stig=20.0, step_stig=2.0, average=1, runs=2, renderer = None, roi=None, exposure=None):
     """

script/templates/Eiger2Img.py

@@ -18,11 +18,7 @@ print "Starting 2Img: ", METHOD, SWITCHING, SEQUENCE , MEASUREMENTS, AUTO_SAVE,
     
 #SEQUENCE = "B": C+,C-,C+,C-,C+,-;C+,C-. 
     
-SHOW_IMAGES = True
-SAVE_DIAGS = True
-DEFAULT_ROI =  Rectangle(128,128,256,256) 
-
-#DEFAULT_ROI =  Rectangle(0,0,512,512)    
+SHOW_IMAGES = True
 SAVE_DIAGS = True          
 
 ID = get_setting("ID")    
@@ -37,7 +33,7 @@ if METHOD == "Two_Energies":
 
 start = time.time()
 threads = []
-image_drift=None
+image_drift=None
 calculated_shifts={}
 #path = "{data}/{year}_{month}/{date}" + "/" + "{seq}%03d_" +  METHOD 
 #set_exec_pars(path= path, format="txt", layout="table", open=True)
@@ -58,17 +54,15 @@ def get_image_file_name(cycle=-1, frame_index=0, short_name=False, shifted=False
     abs_index=run_index + frame_index    
     max_index= max(max_index, frame_index)
     #prefix = get_context().setup.expandPath("i{date}%02d_{seq}%03d")
-    prefix = get_context().setup.expandPath("i{date}%02d_" + ("%03d" % (abs_index,)))
-
-    if (shifted):
     prefix = get_context().setup.expandPath("i{date}%02d_" + ("%03d" % (abs_index,)))
         
+    if cycle < 0:
+        if (shifted):
             prefix = "c" + prefix
         ret = root + prefix + ".tif"    
-    else:
-        ret= root + prefix + "/i{date}%02d"+ ("_%03d#%03d"  % (abs_index,cycle)) + ".tif"
-    return get_context().setup.expandPath(ret)
-    
+    else:
+        prefix = prefix + ("_corr/c" if shifted else "/")
+        ret= root + prefix + "i{date}%02d"+ ("_%03d#%03d"  % (abs_index,cycle)) + ".tif"
     return get_context().setup.expandPath(ret)    
 
 
@@ -93,8 +87,8 @@ if METHOD == "Two_Pol" or (SWITCH_POL and (METHOD == "Take_Image")):
     
 def imageinfo(info):
     pass
-
-
+
+ref_images = {}
 def save_image_file(frame, cycle=-1, frame_index=0, processed_shift=False):
     if frame is None:
         raise Exception("Cannot save frame - None: cycle: "  + str(cycle) + " index: " + str(frame_index))
@@ -110,23 +104,39 @@ def save_image_file(frame, cycle=-1, frame_index=0):
             log(msg)
         else:
             p=plots[0]
-            p.getAxis(p.AxisId.Y).setInverted(True)
+            p.getAxis(p.AxisId.Y).setInverted(True)
     if AUTO_SAVE and (frame is not None):            
+        filename = get_image_file_name(cycle, frame_index)
+        if processed_shift:
             filename = get_image_file_name(cycle, frame_index, shifted=True)
-        metadata = get_diags() if SAVE_DIAGS else {}
+        metadata = get_diags() if SAVE_DIAGS else {}
+                
         threads.append(save_as_tiff(frame, filename,  metadata=metadata))
         
         log(filename)
         print filename
-
+
         if DRIFT_CORRECTION and (not processed_shift):
-            filename = get_image_file_name(cycle, frame_index, shifted=True)
-            if image_drift is not None:
-                print "->", filename
-                shifted_frame = apply_shift(frame, image_drift)
-                threads.append(save_as_tiff(shifted_frame, filename, check=False, parallel=True,  metadata=metadata))
-            elif frame_index==0:
-                print "->", filename
+            filename = get_image_file_name(cycle, frame_index, shifted=True)
+            #print " *** ", cycle, frame_index
+            if cycle>0:
+                if cycle==1:
+                    ref_images[frame_index] = frame
+                    threads.append(save_as_tiff(frame, filename,  metadata=metadata))
+                else:                
+                    """
+                    if image_drift is not None:
+                        print "-> Shifting ", filename
+                        #shifted_frame = apply_shift(frame, image_drift)
+                        #threads.append(save_as_tiff(shifted_frame, filename,  metadata=metadata))
+                        threads.append(shift_and_save_as_tiff(frame,  shift=image_drift,  metadata=metadata))
+                    """                                                            
+                    if frame_index==2:
+                        #shift = calculated_shifts[get_image_file_name(cycle, 0, shifted=True)]
+                        #threads.append(shift_and_save_as_tiff(frame, filename, shift=shift,  metadata=metadata))
+                        pass
+                    else:
+                        threads.append(shift_and_save_as_tiff(frame, filename, ref_images[0], calc_roi, metadata=metadata))
                     
                 
         # log("SV:"+Format(startvoltage,"0.000")+" OB:"+Format(objective,"0.00")+" ST:"+Format(LEEMtemp,"0.0"))		
@@ -137,7 +147,7 @@ print " ---- Run index : %d" %(run_index,)
 print " ---- Run index : %d" %(run_index,)
 max_index=0
 
-if DRIFT_CORRECTION:
+if DRIFT_CORRECTION:
     roi = IMAGING_ROI
     if roi is None:
         roi = DEFAULT_ROI
@@ -164,7 +174,7 @@ try:
             av = average_eiger_frames(AVERAGE, roi=None, wait_next=True)
             #print "--- Time: " + str(time.time() - s)
             #time.sleep(1)  #added by Armin
-            frames.append(av)
+            frames.append(av)
             """
             if (i==0) and DRIFT_CORRECTION and (calc_roi is not None):
                     if ref_image is None:
@@ -181,7 +191,7 @@ try:
                                 image_drift = None
                         except:
                             print "-> Error calculating shift: " + str(sys.exc_info()[1])
-                            image_drift = None
+                            image_drift = None
             """            
             imageinfo("I")             
             save_image_file(frames[i], cycle, i)                       
@@ -211,7 +221,24 @@ try:
 
     print "Waiting file writing threads to finish..."
     for t in threads:
+        join(t)
     
+    if (MEASUREMENTS > 1) and (AUTO_SAVE == 1):
+        if DRIFT_CORRECTION and len(frames)==3:     
+            print "Dividing drifted images..."
+            for cycle in range(1, MEASUREMENTS + 1):             
+                if (METHOD == "Two_Energies") or (SEQUENCE == "B") or ((cycle%2)==1):
+                    file1 = get_image_file_name(cycle, 0, shifted=True)
+                    file2 = get_image_file_name(cycle, 1, shifted=True)
+                else:
+                    file1 = get_image_file_name(cycle, 1, shifted=True)
+                    file2 = get_image_file_name(cycle, 0, shifted=True)
+                print file1
+                print file2
+                ip1 = open_image(file1)
+                ip2 = open_image(file2)
+                op_image(ip1, ip2, "divide", float_result=True, in_place=True)
+                save_image_file(ip1,cycle, 2, processed_shift=True)   
     
         print "--- Averaging..."
         for i in range(len(frames)):
@@ -236,6 +263,24 @@ try:
                     integration =integrate_ips ([integration, ip], as_float=True)
             av=op_const(integration, "divide", float(MEASUREMENTS), in_place=True)                                        
             save_image_file(av, -1, i)     
+
+            if DRIFT_CORRECTION:                               
+                integration = None
+                measurements = 0
+                for cycle in range(1, MEASUREMENTS + 1):                
+                    filename = get_image_file_name(cycle, i, shifted=True)
+                    print "Open " , filename
+                    try:
+                        ip = open_image(filename)
+                        if integration is None:
+                            integration = ip
+                        else:
+                            integration =integrate_ips ([integration, ip], as_float=True)
+                        measurements=measurements+1
+                    except:
+                        print "Error integrating frame: ", filename
+                if measurements>0:
+                    av=op_const(integration, "divide", float(measurements), in_place=True)                                        
                     save_image_file(av, -1, i, processed_shift=True)     
     
     if SWITCH_POL and (METHOD == "Take_Image"):

script/templates/EigerAbsSpec.py

@@ -9,10 +9,12 @@ if (get_exec_pars().source == CommandSource.ui) and (get_exec_pars().script == "
     AVERAGE = 2
     NUMBER_SCANS =1       
     RANGES = [[500.0, 1000.0, 100.0]]
+    DRIFT_CORRECTION = True
 
 print "Starting AbsSpec: ",SAVE_SPECTRUM, SAVE_IMAGES, WITH_I0, SWITCH_POL, EXPOSURE, AVERAGE, NUMBER_SCANS, RANGES
 
 SAVE_DIAGS = True
+calculated_shifts={}
 
 if SWITCH_POL:
     init_pol_switch("Normal")
@@ -69,7 +71,18 @@ def grab_image(position, scan):
        filename = get_exec_pars().path + "/" + str(scan.currentPass) + "/s" + "{seq}%03d" + "_" + ("%03d.tif" % scan.recordIndex)       
        filename = get_context().setup.expandPath(filename)
        print filename       
-       save_as_tiff(av, filename, metadata=(get_diags() if SAVE_DIAGS else {}))
+       metadata = get_diags() if SAVE_DIAGS else {}
+       save_as_tiff(av, filename, metadata=metadata)
+       if DRIFT_CORRECTION and (calc_roi is not None):
+            global ref_image
+            filename = get_exec_pars().path + "/" + str(scan.currentPass) + "_corr/cs" + "{seq}%03d" + "_" + ("%03d.tif" % scan.recordIndex)       
+            filename = get_context().setup.expandPath(filename)
+            if ref_image is None:
+                ref_image = av
+                save_as_tiff(av, filename, metadata=metadata)
+            else:
+                shift_and_save_as_tiff(av, filename, ref_image, calc_roi, metadata=metadata)
+                   
            
 class Average(ReadableMatrix):
     def read(self):
@@ -111,6 +124,12 @@ wait_channel("X11PHS:alldone", 1)
 """
 
 
+if DRIFT_CORRECTION:
+    roi = IMAGING_ROI
+    if roi is None:
+        roi = DEFAULT_ROI
+    calc_roi = Roi(roi.x,roi.y,roi.width, roi.height)
+    ref_image = None # grab_frame(image, None, True)
 
 def after_pass(pass_number, scan):
     if SWITCH_POL:

script/test/TestShiftData.py

@@ -0,0 +1,56 @@
+f1=open_image("/sls/X11MA/data/X11MA/Data1/public/PEEM/2022_11/20221111/20221111_Two_Pol/i221111_006/i221111_006#002.tif")
+f2=open_image("/sls/X11MA/data/X11MA/Data1/public/PEEM/2022_11/20221111/20221111_Two_Pol/i221111_006_corr/ci221111_006#002.tif")
+"""
+f1=load_image("/sls/X11MA/data/X11MA/Data1/public/PEEM/2022_11/20221109/20221109_Take_Image/i221109_019/i221109_019#002.tif")
+f2=load_image("/sls/X11MA/data/X11MA/Data1/public/PEEM/2022_11/20221109/20221109_Take_Image/i221109_019_shifted/i221109_019#002.tif")
+
+f1 = load_image("/sls/X11MA/data/X11MA/Data1/public/PEEM/2022_11/20221109/20221109_Two_Energies/i221109_034/i221109_034#002.tif")
+f2 = load_image("/sls/X11MA/data/X11MA/Data1/public/PEEM/2022_11/20221109/20221109_Two_Energies/i221109_034_shifted/i221109_034#002.tif")
+
+f1 = load_image("/sls/X11MA/data/X11MA/Data1/public/PEEM/2022_11/20221110/20221110_17909_AbsortionSpectrum/1/s17909_001.tif")
+f2 = load_image("/sls/X11MA/data/X11MA/Data1/public/PEEM/2022_11/20221110/20221110_17909_AbsortionSpectrum/1_corr/cs17909_001.tif")
+"""
+
+
+"""
+s1=[]
+s2=[]
+j=4
+for i in range(1, 10, 1):
+    f1=open_image("/sls/X11MA/data/X11MA/Data1/public/PEEM/2022_11/20221111/20221111_Two_Pol/i221111_00" + str(j) + "/i221111_00" + str(j) + "#00" + str(i) + ".tif")
+    f2=open_image("/sls/X11MA/data/X11MA/Data1/public/PEEM/2022_11/20221111/20221111_Two_Pol/i221111_00" + str(j) + "_corr/ci221111_00" + str(j) + "#00" + str(i) + ".tif")
+    a1 = get_ip_array(f1)
+    a2 = get_ip_array(f2)
+    s1.append(a1)
+    s2.append(a2)
+plot([s1,  s2], name=["a1", "a2"])
+"""
+
+#plot([a1[150],  a2[150]], name=["a1", "a2"])
+#p1 = [sum(x) for x in a1]
+#p2 = [sum(x) for x in a2]
+#plot([p1,  p2], name=["P1", "P2"])
+
+
+s1=[]
+s2=[]
+month = "2022_11"
+date = "20221115"
+index="024"
+method = "Two_Pol"
+method = "Take_Image"
+method = "Two_Energies"
+try:
+    for i in range(1, 10, 1):
+        f1=open_image("/sls/X11MA/data/X11MA/Data1/public/PEEM/" + month + "/"  + date + "/"  + date + "_" +  method + "/i221115_" + index + "/i221115_" + index + "#00" + str(i) + ".tif")
+        f2=open_image("/sls/X11MA/data/X11MA/Data1/public/PEEM/" + month + "/"  + date + "/"  + date + "_" +  method + "/i221115_" + index + "_corr/ci221115_" + index + "#00" + str(i) + ".tif")
+        a1 = get_ip_array(f1)
+        a2 = get_ip_array(f2)
+        s1.append(a1)
+        s2.append(a2)
+except:
+    pass
+plot([s1,  s2], name=["a1", "a2"])
+
+
+