Initial commit

bin/psss_panel

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+
+/opt/gfa/pshell/pshell \
+	-version=v1_17 \
+	-py3 \
+	-m=/opt/gfa/pshell/apps/psss_panel \
+	-z \
+	-nbcf=true \
+	-laf=dark \
+	-d \
+	-pini=true \
+        -clog=WARNING \
+        -sbar \
+        $@ 

bin/psss_panel_editor

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+
+/opt/gfa/pshell/pshell \
+	-py3 \
+        -version=v1_17 \
+	-z \
+	-nbcf=true \
+	-laf=dark \
+	-pini=true \
+        -setp=/opt/gfa/pshell/apps/psss_panel/config/setup.properties \
+        -p=PSSS.java \
+        $@ 

config/devices.properties

@@ -0,0 +1,16 @@
+psss_fwhm_avg=ch.psi.pshell.epics.ChannelDouble|SARFE10-PSSS059:REL-E-SPREAD|||true
+dispatcher=ch.psi.pshell.bs.Dispatcher|https://dispatcher-api.psi.ch/sf|||
+cam_server=ch.psi.pshell.bs.PipelineServer|sf-daqsync-01:8889|||
+energy_machine=ch.psi.pshell.epics.ChannelDouble|SARFE10-PBPG050:ENERGY|||true
+psss_energy=ch.psi.pshell.epics.ChannelDouble|SARFE10-PSSS059:ENERGY|||true
+psss_spectrum_x=ch.psi.pshell.epics.ChannelDoubleArray|SARFE10-PSSS059:SPECTRUM_X -1 -3|||true
+psss_spectrum_y=ch.psi.pshell.epics.ChannelDoubleArray|SARFE10-PSSS059:SPECTRUM_Y -1 -3|||true
+psss_center=ch.psi.pshell.epics.ChannelDouble|SARFE10-PSSS059:SPECTRUM_CENTER|||true
+psss_fwhm=ch.psi.pshell.epics.ChannelDouble|SARFE10-PSSS059:SPECTRUM_FWHM|||true
+psss_roi_min=ch.psi.pshell.epics.ChannelInteger|SARFE10-PSSS059:SPC_ROI_YMIN|||true
+psss_roi_max=ch.psi.pshell.epics.ChannelInteger|SARFE10-PSSS059:SPC_ROI_YMAX|||true
+histo_center=ch.psi.pshell.device.HistogramGenerator|psss_center|||true
+histo_fwhm=ch.psi.pshell.device.HistogramGenerator|psss_fwhm|||true
+psss_spectrum_y_average=ch.psi.pshell.device.ArrayAverager|psss_spectrum_y|||true
+psss_center_average=ch.psi.pshell.device.Averager|psss_center|||true
+psss_fwhm_average=ch.psi.pshell.device.Averager|psss_fwhm|||true

config/jcae.properties

@@ -0,0 +1,12 @@
+#Mon Feb 22 20:35:07 CET 2021
+ch.psi.jcae.ContextFactory.addressList=
+ch.psi.jcae.ContextFactory.serverPort=
+ch.psi.jcae.ContextFactory.maxArrayBytes=50000000
+ch.psi.jcae.ChannelFactory.retries=1
+ch.psi.jcae.ChannelFactory.timeout=1250
+ch.psi.jcae.impl.DefaultChannelService.retries=4
+ch.psi.jcae.impl.DefaultChannelService.timeout=1000
+ch.psi.jcae.ContextFactory.autoAddressList=true
+ch.psi.jcae.ContextFactory.useShellVariables=true
+ch.psi.jcae.ContextFactory.addLocalBroadcastInterfaces=false
+ch.psi.jcae.ContextFactory.maxSendArrayBytes=1000000

config/setup.properties

@@ -0,0 +1,23 @@
+#Tue Jul 06 13:13:12 CEST 2021
+scriptPath=/opt/gfa/pshell/apps/psss_panel/script
+sessionsPath={outp}/sessions
+pluginsPath=/opt/gfa/pshell/apps/psss_panel/plugins
+configFileDevices=/opt/gfa/pshell/apps/psss_panel/config/devices.properties
+consoleSessionsPath={sessions}/console
+libraryPath={script}; {script}/Lib
+contextPath={outp}/context
+configFilePlugins={config}/plugins.properties
+extensionsPath={home}/extensions
+configPath={home}/config
+configFileSessions={config}/sessions.properties
+userSessionsPath={sessions}/user
+dataPath={outp}/data
+devicesPath=/opt/gfa/pshell/apps/psss_panel/devices
+configFileVariables={config}/variables.properties
+configFileSettings={config}/settings.properties
+wwwPath={home}/www
+logPath={outp}/log
+imagesPath={outp}/images
+configFile={config}/config.properties
+scriptType=py
+configFileTasks={config}/tasks.properties

devices/cam_server.properties

@@ -0,0 +1,25 @@
+#Mon Jan 17 16:00:40 CET 2022
+spatialCalOffsetY=-50.02549719530852
+spatialCalOffsetX=-50.01953888237593
+colormapLogarithmic=false
+scale=1.0
+grayscale=false
+spatialCalScaleX=-1.0
+spatialCalScaleY=-1.0
+colormapMax=255.0
+rescaleOffset=0.0
+roiWidth=-1
+colormap=Temperature
+invert=false
+colormapMin=0.0
+rotationCrop=false
+rotation=0.0
+rescaleFactor=1.0
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+flipHorizontally=false
+colormapAutomatic=true
+roiY=0
+roiX=0
+transpose=false

devices/dispatcher.properties

@@ -0,0 +1,13 @@
+#Wed Jun 03 18:45:57 CEST 2020
+sendStrategy=complete_all
+dropIncomplete=false
+keepListeningOnStop=false
+disableCompression=false
+parallelHandlerProcessing=true
+sendBuildChannelConfig=at_startup
+sendAwaitFirstMessage=false
+socketType=DEFAULT
+validationInconsistency=keep_as_is
+byteBufferAllocator=false
+mappingIncomplete=fill_null
+sendSyncTimeout=0

devices/histo_center.properties

@@ -0,0 +1,6 @@
+#Tue Jun 15 11:03:15 CEST 2021
+bins=1000
+min=11400.0
+max=11200.0
+precision=-1
+numberOfSamples=10000

devices/histo_fwhm.properties

@@ -0,0 +1,6 @@
+#Fri Apr 30 07:45:13 CEST 2021
+bins=1000
+min=0.0
+max=40.0
+precision=-1
+numberOfSamples=10000

devices/psss_center_average.properties

@@ -0,0 +1,4 @@
+#Mon May 03 09:21:35 CEST 2021
+measures=10
+precision=-1
+interval=-1

devices/psss_fwhm_average.properties

@@ -0,0 +1,4 @@
+#Mon May 03 09:21:52 CEST 2021
+measures=10
+precision=-1
+interval=-1

devices/psss_spectrum_y_average.properties

@@ -0,0 +1,5 @@
+#Mon May 03 09:15:04 CEST 2021
+measures=10
+precision=-1
+interval=-1
+integrate=false

nb/PSSS/build.xml

@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- You may freely edit this file. See commented blocks below for -->
+<!-- some examples of how to customize the build. -->
+<!-- (If you delete it and reopen the project it will be recreated.) -->
+<!-- By default, only the Clean and Build commands use this build script. -->
+<!-- Commands such as Run, Debug, and Test only use this build script if -->
+<!-- the Compile on Save feature is turned off for the project. -->
+<!-- You can turn off the Compile on Save (or Deploy on Save) setting -->
+<!-- in the project's Project Properties dialog box.-->
+<project name="PSSS" default="default" basedir=".">
+    <description>Builds, tests, and runs the project PSSS.</description>
+    <import file="nbproject/build-impl.xml"/>
+    <!--
+
+    There exist several targets which are by default empty and which can be 
+    used for execution of your tasks. These targets are usually executed 
+    before and after some main targets. They are: 
+
+      -pre-init:                 called before initialization of project properties
+      -post-init:                called after initialization of project properties
+      -pre-compile:              called before javac compilation
+      -post-compile:             called after javac compilation
+      -pre-compile-single:       called before javac compilation of single file
+      -post-compile-single:      called after javac compilation of single file
+      -pre-compile-test:         called before javac compilation of JUnit tests
+      -post-compile-test:        called after javac compilation of JUnit tests
+      -pre-compile-test-single:  called before javac compilation of single JUnit test
+      -post-compile-test-single: called after javac compilation of single JUunit test
+      -pre-jar:                  called before JAR building
+      -post-jar:                 called after JAR building
+      -post-clean:               called after cleaning build products
+
+    (Targets beginning with '-' are not intended to be called on their own.)
+
+    Example of inserting an obfuscator after compilation could look like this:
+
+        <target name="-post-compile">
+            <obfuscate>
+                <fileset dir="${build.classes.dir}"/>
+            </obfuscate>
+        </target>
+
+    For list of available properties check the imported 
+    nbproject/build-impl.xml file. 
+
+
+    Another way to customize the build is by overriding existing main targets.
+    The targets of interest are: 
+
+      -init-macrodef-javac:     defines macro for javac compilation
+      -init-macrodef-junit:     defines macro for junit execution
+      -init-macrodef-debug:     defines macro for class debugging
+      -init-macrodef-java:      defines macro for class execution
+      -do-jar:                  JAR building
+      run:                      execution of project 
+      -javadoc-build:           Javadoc generation
+      test-report:              JUnit report generation
+
+    An example of overriding the target for project execution could look like this:
+
+        <target name="run" depends="PSSS-impl.jar">
+            <exec dir="bin" executable="launcher.exe">
+                <arg file="${dist.jar}"/>
+            </exec>
+        </target>
+
+    Notice that the overridden target depends on the jar target and not only on 
+    the compile target as the regular run target does. Again, for a list of available 
+    properties which you can use, check the target you are overriding in the
+    nbproject/build-impl.xml file. 
+
+    -->
+</project>

nb/PSSS/nbproject/genfiles.properties

@@ -0,0 +1,8 @@
+build.xml.data.CRC32=cb48e78e
+build.xml.script.CRC32=f58963e5
+build.xml.stylesheet.CRC32=f85dc8f2@1.97.0.48
+# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
+# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
+nbproject/build-impl.xml.data.CRC32=cb48e78e
+nbproject/build-impl.xml.script.CRC32=1f638965
+nbproject/build-impl.xml.stylesheet.CRC32=d549e5cc@1.97.0.48

nb/PSSS/nbproject/private/private.properties

@@ -0,0 +1,8 @@
+compile.on.save=true
+do.depend=false
+do.jar=true
+do.jlink=false
+javac.debug=true
+javadoc.preview=true
+jlink.strip=false
+user.properties.file=/afs/psi.ch/user/g/gobbo_a/.netbeans/12.2/build.properties

nb/PSSS/nbproject/private/private.xml

@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project-private xmlns="http://www.netbeans.org/ns/project-private/1">
+    <editor-bookmarks xmlns="http://www.netbeans.org/ns/editor-bookmarks/2" lastBookmarkId="0"/>
+</project-private>

nb/PSSS/nbproject/project.properties

@@ -0,0 +1,99 @@
+annotation.processing.enabled=true
+annotation.processing.enabled.in.editor=false
+annotation.processing.processors.list=
+annotation.processing.run.all.processors=true
+annotation.processing.source.output=${build.generated.sources.dir}/ap-source-output
+application.title=PSSS
+application.vendor=gobbo_a
+build.classes.dir=${build.dir}/classes
+build.classes.excludes=**/*.java,**/*.form
+# This directory is removed when the project is cleaned:
+build.dir=build
+build.generated.dir=${build.dir}/generated
+build.generated.sources.dir=${build.dir}/generated-sources
+# Only compile against the classpath explicitly listed here:
+build.sysclasspath=ignore
+build.test.classes.dir=${build.dir}/test/classes
+build.test.results.dir=${build.dir}/test/results
+# Uncomment to specify the preferred debugger connection transport:
+#debug.transport=dt_socket
+debug.classpath=\
+    ${run.classpath}
+debug.modulepath=\
+    ${run.modulepath}
+debug.test.classpath=\
+    ${run.test.classpath}
+debug.test.modulepath=\
+    ${run.test.modulepath}
+# Files in build.classes.dir which should be excluded from distribution jar
+dist.archive.excludes=
+# This directory is removed when the project is cleaned:
+dist.dir=dist
+dist.jar=${dist.dir}/PSSS.jar
+dist.javadoc.dir=${dist.dir}/javadoc
+dist.jlink.dir=${dist.dir}/jlink
+dist.jlink.output=${dist.jlink.dir}/PSSS
+endorsed.classpath=
+excludes=
+file.reference.pshell-latest.jar=../../../../head/pshell-latest.jar
+file.reference.psss_panel-plugins=../../plugins
+file.reference.psss_panel-script=../../script
+includes=**/*.java
+jar.compress=false
+javac.classpath=\
+    ${file.reference.pshell-latest.jar}
+# Space-separated list of extra javac options
+javac.compilerargs=
+javac.deprecation=false
+javac.external.vm=true
+javac.modulepath=
+javac.processormodulepath=
+javac.processorpath=\
+    ${javac.classpath}
+javac.source=11
+javac.target=11
+javac.test.classpath=\
+    ${javac.classpath}:\
+    ${build.classes.dir}
+javac.test.modulepath=\
+    ${javac.modulepath}
+javac.test.processorpath=\
+    ${javac.test.classpath}
+javadoc.additionalparam=
+javadoc.author=false
+javadoc.encoding=${source.encoding}
+javadoc.html5=false
+javadoc.noindex=false
+javadoc.nonavbar=false
+javadoc.notree=false
+javadoc.private=false
+javadoc.splitindex=true
+javadoc.use=true
+javadoc.version=false
+javadoc.windowtitle=
+# The jlink additional root modules to resolve
+jlink.additionalmodules=
+# The jlink additional command line parameters
+jlink.additionalparam=
+jlink.launcher=true
+jlink.launcher.name=PSSS
+meta.inf.dir=${src.dir}/META-INF
+mkdist.disabled=true
+platform.active=default_platform
+run.classpath=\
+    ${javac.classpath}:\
+    ${build.classes.dir}
+# Space-separated list of JVM arguments used when running the project.
+# You may also define separate properties like run-sys-prop.name=value instead of -Dname=value.
+# To set system properties for unit tests define test-sys-prop.name=value:
+run.jvmargs=
+run.modulepath=\
+    ${javac.modulepath}
+run.test.classpath=\
+    ${javac.test.classpath}:\
+    ${build.test.classes.dir}
+run.test.modulepath=\
+    ${javac.test.modulepath}
+source.encoding=UTF-8
+src.plugins.dir=${file.reference.psss_panel-plugins}
+src.script.dir=${file.reference.psss_panel-script}

nb/PSSS/nbproject/project.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://www.netbeans.org/ns/project/1">
+    <type>org.netbeans.modules.java.j2seproject</type>
+    <configuration>
+        <data xmlns="http://www.netbeans.org/ns/j2se-project/3">
+            <name>PSSS</name>
+            <source-roots>
+                <root id="src.plugins.dir" name="Plugins"/>
+                <root id="src.script.dir" name="Scripts"/>
+            </source-roots>
+            <test-roots/>
+        </data>
+    </configuration>
+</project>

plugins/PSSS.form

@@ -0,0 +1,715 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<Form version="1.5" maxVersion="1.9" type="org.netbeans.modules.form.forminfo.JPanelFormInfo">
+  <NonVisualComponents>
+    <Component class="javax.swing.ButtonGroup" name="buttonGroup1">
+    </Component>
+  </NonVisualComponents>
+  <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">
+          <Component id="tab" alignment="0" max="32767" attributes="0"/>
+      </Group>
+    </DimensionLayout>
+    <DimensionLayout dim="1">
+      <Group type="103" groupAlignment="0" attributes="0">
+          <Component id="tab" alignment="1" max="32767" attributes="0"/>
+      </Group>
+    </DimensionLayout>
+  </Layout>
+  <SubComponents>
+    <Container class="javax.swing.JTabbedPane" name="tab">
+      <Events>
+        <EventHandler event="stateChanged" listener="javax.swing.event.ChangeListener" parameters="javax.swing.event.ChangeEvent" handler="tabStateChanged"/>
+      </Events>
+
+      <Layout class="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout"/>
+      <SubComponents>
+        <Container class="javax.swing.JPanel" name="jPanel1">
+          <Constraints>
+            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
+              <JTabbedPaneConstraints tabName="Spectrum">
+                <Property name="tabTitle" type="java.lang.String" value="Spectrum"/>
+              </JTabbedPaneConstraints>
+            </Constraint>
+          </Constraints>
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" attributes="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 max="-2" attributes="0"/>
+                              <Component id="spinnerAverage" min="-2" max="-2" attributes="0"/>
+                          </Group>
+                          <Component id="history" alignment="0" pref="453" max="32767" attributes="0"/>
+                          <Component id="plot" alignment="0" max="32767" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="-2" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Group type="102" attributes="0">
+                              <EmptySpace min="12" pref="12" max="-2" attributes="0"/>
+                              <Component id="histogramGeneratorFwhm" min="-2" pref="372" max="-2" attributes="0"/>
+                          </Group>
+                          <Component id="histogramGeneratorPanelCenter" alignment="0" min="-2" pref="372" max="-2" attributes="0"/>
+                      </Group>
+                      <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" alignment="0" 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="spinnerAverage" alignment="3" min="-2" max="-2" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="-2" pref="6" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="histogramGeneratorPanelCenter" alignment="0" pref="194" max="32767" attributes="0"/>
+                          <Component id="plot" alignment="0" pref="0" max="32767" attributes="0"/>
+                      </Group>
+                      <EmptySpace min="-2" max="-2" attributes="0"/>
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <Component id="history" pref="194" max="32767" attributes="0"/>
+                          <Component id="histogramGeneratorFwhm" pref="0" max="32767" attributes="0"/>
+                      </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>
+            <Component class="ch.psi.pshell.plot.TimePlotJFree" name="history">
+            </Component>
+            <Component class="javax.swing.JLabel" name="jLabel1">
+              <Properties>
+                <Property name="text" type="java.lang.String" value="Average:"/>
+              </Properties>
+            </Component>
+            <Component class="javax.swing.JSpinner" name="spinnerAverage">
+              <Properties>
+                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                  <SpinnerModel initial="1" maximum="100" minimum="1" numberType="java.lang.Integer" stepSize="1" type="number"/>
+                </Property>
+              </Properties>
+              <Events>
+                <EventHandler event="stateChanged" listener="javax.swing.event.ChangeListener" parameters="javax.swing.event.ChangeEvent" handler="spinnerAverageStateChanged"/>
+              </Events>
+            </Component>
+            <Component class="ch.psi.pshell.swing.HistogramGeneratorPanel" name="histogramGeneratorPanelCenter">
+              <Properties>
+                <Property name="deviceName" type="java.lang.String" value="histo_center"/>
+              </Properties>
+            </Component>
+            <Component class="ch.psi.pshell.swing.HistogramGeneratorPanel" name="histogramGeneratorFwhm">
+              <Properties>
+                <Property name="deviceName" type="java.lang.String" value="histo_fwhm"/>
+              </Properties>
+            </Component>
+          </SubComponents>
+        </Container>
+        <Container class="javax.swing.JPanel" name="jPanel4">
+          <Constraints>
+            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
+              <JTabbedPaneConstraints tabName="Camera">
+                <Property name="tabTitle" type="java.lang.String" value="Camera"/>
+              </JTabbedPaneConstraints>
+            </Constraint>
+          </Constraints>
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <EmptySpace min="0" pref="843" max="32767" attributes="0"/>
+                  <Group type="103" rootIndex="1" groupAlignment="0" attributes="0">
+                      <Component id="renderer" alignment="0" pref="843" max="32767" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+            <DimensionLayout dim="1">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <EmptySpace min="0" pref="432" max="32767" attributes="0"/>
+                  <Group type="103" rootIndex="1" groupAlignment="0" attributes="0">
+                      <Component id="renderer" alignment="0" pref="432" max="32767" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+          </Layout>
+          <SubComponents>
+            <Component class="ch.psi.pshell.imaging.Renderer" name="renderer">
+            </Component>
+          </SubComponents>
+        </Container>
+        <Container class="javax.swing.JPanel" name="jPanel3">
+          <Constraints>
+            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
+              <JTabbedPaneConstraints tabName="Alignment">
+                <Property name="tabTitle" type="java.lang.String" value="Alignment"/>
+              </JTabbedPaneConstraints>
+            </Constraint>
+          </Constraints>
+
+          <Layout>
+            <DimensionLayout dim="0">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="0" attributes="0">
+                      <Component id="jPanel2" min="-2" max="-2" attributes="0"/>
+                      <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                      <Component id="plotScan" pref="614" max="32767" attributes="0"/>
+                  </Group>
+              </Group>
+            </DimensionLayout>
+            <DimensionLayout dim="1">
+              <Group type="103" groupAlignment="0" attributes="0">
+                  <Component id="jPanel2" max="32767" attributes="0"/>
+                  <Component id="plotScan" pref="432" max="32767" attributes="0"/>
+              </Group>
+            </DimensionLayout>
+          </Layout>
+          <SubComponents>
+            <Container class="javax.swing.JPanel" name="jPanel2">
+
+              <Layout>
+                <DimensionLayout dim="0">
+                  <Group type="103" groupAlignment="0" attributes="0">
+                      <Group type="102" attributes="0">
+                          <EmptySpace min="-2" pref="12" max="-2" attributes="0"/>
+                          <Group type="103" groupAlignment="0" max="-2" attributes="0">
+                              <Component id="jPanel5" alignment="0" max="32767" attributes="0"/>
+                              <Component id="radioCrystalScan" alignment="0" min="-2" max="-2" attributes="0"/>
+                              <Component id="radioCameraScan" alignment="0" min="-2" max="-2" attributes="0"/>
+                              <Component id="radioEnergyScan" alignment="0" min="-2" max="-2" attributes="0"/>
+                              <Component id="btAbort" alignment="0" pref="213" max="32767" attributes="0"/>
+                          </Group>
+                          <EmptySpace max="-2" attributes="0"/>
+                      </Group>
+                  </Group>
+                </DimensionLayout>
+                <DimensionLayout dim="1">
+                  <Group type="103" groupAlignment="0" attributes="0">
+                      <Group type="102" alignment="1" attributes="0">
+                          <EmptySpace min="-2" pref="20" max="-2" attributes="0"/>
+                          <Component id="radioEnergyScan" min="-2" max="-2" attributes="0"/>
+                          <EmptySpace type="unrelated" min="-2" max="-2" attributes="0"/>
+                          <Component id="radioCameraScan" min="-2" max="-2" attributes="0"/>
+                          <EmptySpace type="unrelated" min="-2" max="-2" attributes="0"/>
+                          <Component id="radioCrystalScan" min="-2" max="-2" attributes="0"/>
+                          <EmptySpace min="-2" max="-2" attributes="0"/>
+                          <Component id="jPanel5" max="32767" attributes="0"/>
+                          <EmptySpace type="unrelated" min="-2" max="-2" attributes="0"/>
+                          <Component id="btAbort" min="-2" max="-2" attributes="0"/>
+                          <EmptySpace min="-2" max="-2" attributes="0"/>
+                      </Group>
+                  </Group>
+                </DimensionLayout>
+              </Layout>
+              <SubComponents>
+                <Component class="javax.swing.JButton" name="btAbort">
+                  <Properties>
+                    <Property name="text" type="java.lang.String" value="Abort"/>
+                  </Properties>
+                  <Events>
+                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="btAbortActionPerformed"/>
+                  </Events>
+                </Component>
+                <Component class="javax.swing.JRadioButton" name="radioEnergyScan">
+                  <Properties>
+                    <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                      <ComponentRef name="buttonGroup1"/>
+                    </Property>
+                    <Property name="selected" type="boolean" value="true"/>
+                    <Property name="text" type="java.lang.String" value="Energy Scan"/>
+                  </Properties>
+                  <Events>
+                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="radioEnergyScanActionPerformed"/>
+                  </Events>
+                </Component>
+                <Component class="javax.swing.JRadioButton" name="radioCameraScan">
+                  <Properties>
+                    <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                      <ComponentRef name="buttonGroup1"/>
+                    </Property>
+                    <Property name="text" type="java.lang.String" value="Camera Scan"/>
+                  </Properties>
+                  <Events>
+                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="radioCameraScanActionPerformed"/>
+                  </Events>
+                </Component>
+                <Component class="javax.swing.JRadioButton" name="radioCrystalScan">
+                  <Properties>
+                    <Property name="buttonGroup" type="javax.swing.ButtonGroup" editor="org.netbeans.modules.form.RADComponent$ButtonGroupPropertyEditor">
+                      <ComponentRef name="buttonGroup1"/>
+                    </Property>
+                    <Property name="text" type="java.lang.String" value="Crystal Height Scan"/>
+                  </Properties>
+                  <Events>
+                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="radioCrystalScanActionPerformed"/>
+                  </Events>
+                </Component>
+                <Container class="javax.swing.JPanel" name="jPanel5">
+
+                  <Layout>
+                    <DimensionLayout dim="0">
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
+                          <Group type="103" rootIndex="1" groupAlignment="0" attributes="0">
+                              <Group type="102" alignment="0" attributes="0">
+                                  <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
+                                  <Component id="panelScan" min="-2" max="-2" attributes="0"/>
+                                  <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                              </Group>
+                          </Group>
+                      </Group>
+                    </DimensionLayout>
+                    <DimensionLayout dim="1">
+                      <Group type="103" groupAlignment="0" attributes="0">
+                          <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
+                          <Group type="103" rootIndex="1" groupAlignment="0" attributes="0">
+                              <Group type="102" attributes="0">
+                                  <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
+                                  <Component id="panelScan" max="32767" attributes="0"/>
+                                  <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
+                              </Group>
+                          </Group>
+                      </Group>
+                    </DimensionLayout>
+                  </Layout>
+                  <SubComponents>
+                    <Container class="javax.swing.JPanel" name="panelScan">
+
+                      <Layout class="org.netbeans.modules.form.compat2.layouts.DesignCardLayout"/>
+                      <SubComponents>
+                        <Container class="javax.swing.JPanel" name="panelEnergyScan">
+                          <Constraints>
+                            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignCardLayout" value="org.netbeans.modules.form.compat2.layouts.DesignCardLayout$CardConstraintsDescription">
+                              <CardConstraints cardName="energy"/>
+                            </Constraint>
+                          </Constraints>
+
+                          <Layout>
+                            <DimensionLayout dim="0">
+                              <Group type="103" groupAlignment="0" attributes="0">
+                                  <Group type="102" attributes="0">
+                                      <EmptySpace max="32767" attributes="0"/>
+                                      <Group type="103" groupAlignment="0" attributes="0">
+                                          <Group type="102" alignment="0" attributes="0">
+                                              <Component id="jLabel7" linkSize="7" min="-2" max="-2" attributes="0"/>
+                                              <EmptySpace max="-2" attributes="0"/>
+                                              <Component id="spToEn" linkSize="8" min="-2" pref="80" max="-2" attributes="0"/>
+                                          </Group>
+                                          <Group type="102" alignment="0" attributes="0">
+                                              <Component id="jLabel6" linkSize="7" min="-2" max="-2" attributes="0"/>
+                                              <EmptySpace max="-2" attributes="0"/>
+                                              <Component id="spFromEn" linkSize="8" min="-2" pref="80" max="-2" attributes="0"/>
+                                          </Group>
+                                          <Group type="102" alignment="0" attributes="0">
+                                              <Component id="jLabel8" linkSize="7" min="-2" max="-2" attributes="0"/>
+                                              <EmptySpace max="-2" attributes="0"/>
+                                              <Component id="spStepsEn" linkSize="8" min="-2" max="-2" attributes="0"/>
+                                          </Group>
+                                          <Group type="102" alignment="0" attributes="0">
+                                              <Component id="jLabel9" linkSize="7" min="-2" max="-2" attributes="0"/>
+                                              <EmptySpace max="-2" attributes="0"/>
+                                              <Component id="spShotsEn" linkSize="8" min="-2" max="-2" attributes="0"/>
+                                          </Group>
+                                      </Group>
+                                      <EmptySpace max="-2" attributes="0"/>
+                                  </Group>
+                                  <Component id="btStartEn" alignment="1" max="32767" attributes="0"/>
+                              </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="3" attributes="0">
+                                          <Component id="jLabel6" alignment="3" min="-2" max="-2" attributes="0"/>
+                                          <Component id="spFromEn" alignment="3" min="-2" max="-2" attributes="0"/>
+                                      </Group>
+                                      <EmptySpace max="-2" attributes="0"/>
+                                      <Group type="103" groupAlignment="3" attributes="0">
+                                          <Component id="jLabel7" alignment="3" min="-2" max="-2" attributes="0"/>
+                                          <Component id="spToEn" alignment="3" min="-2" max="-2" attributes="0"/>
+                                      </Group>
+                                      <EmptySpace max="-2" attributes="0"/>
+                                      <Group type="103" groupAlignment="3" attributes="0">
+                                          <Component id="jLabel8" alignment="3" min="-2" max="-2" attributes="0"/>
+                                          <Component id="spStepsEn" alignment="3" min="-2" max="-2" attributes="0"/>
+                                      </Group>
+                                      <EmptySpace max="-2" attributes="0"/>
+                                      <Group type="103" groupAlignment="3" attributes="0">
+                                          <Component id="jLabel9" alignment="3" min="-2" max="-2" attributes="0"/>
+                                          <Component id="spShotsEn" alignment="3" min="-2" max="-2" attributes="0"/>
+                                      </Group>
+                                      <EmptySpace max="32767" attributes="0"/>
+                                      <Component id="btStartEn" min="-2" max="-2" attributes="0"/>
+                                      <EmptySpace max="-2" attributes="0"/>
+                                  </Group>
+                              </Group>
+                            </DimensionLayout>
+                          </Layout>
+                          <SubComponents>
+                            <Component class="javax.swing.JSpinner" name="spFromEn">
+                              <Properties>
+                                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                                  <SpinnerModel initial="7200.0" maximum="20000.0" minimum="1.0" numberType="java.lang.Double" stepSize="10.0" type="number"/>
+                                </Property>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JLabel" name="jLabel6">
+                              <Properties>
+                                <Property name="horizontalAlignment" type="int" value="11"/>
+                                <Property name="text" type="java.lang.String" value="Range From:"/>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JLabel" name="jLabel7">
+                              <Properties>
+                                <Property name="horizontalAlignment" type="int" value="11"/>
+                                <Property name="text" type="java.lang.String" value="Range To:"/>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JSpinner" name="spToEn">
+                              <Properties>
+                                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                                  <SpinnerModel initial="7340.0" maximum="20000.0" minimum="1.0" numberType="java.lang.Double" stepSize="10.0" type="number"/>
+                                </Property>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JSpinner" name="spStepsEn">
+                              <Properties>
+                                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                                  <SpinnerModel initial="20" maximum="1000" minimum="1" numberType="java.lang.Integer" stepSize="1" type="number"/>
+                                </Property>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JLabel" name="jLabel8">
+                              <Properties>
+                                <Property name="horizontalAlignment" type="int" value="11"/>
+                                <Property name="text" type="java.lang.String" value="Steps:"/>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JLabel" name="jLabel9">
+                              <Properties>
+                                <Property name="horizontalAlignment" type="int" value="11"/>
+                                <Property name="text" type="java.lang.String" value="Num Shots:"/>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JSpinner" name="spShotsEn">
+                              <Properties>
+                                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                                  <SpinnerModel initial="100" maximum="1000" minimum="1" numberType="java.lang.Integer" stepSize="1" type="number"/>
+                                </Property>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JButton" name="btStartEn">
+                              <Properties>
+                                <Property name="text" type="java.lang.String" value="Start Energy Scan"/>
+                              </Properties>
+                              <Events>
+                                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="btStartEnActionPerformed"/>
+                              </Events>
+                            </Component>
+                          </SubComponents>
+                        </Container>
+                        <Container class="javax.swing.JPanel" name="panelCameraScan">
+                          <Constraints>
+                            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignCardLayout" value="org.netbeans.modules.form.compat2.layouts.DesignCardLayout$CardConstraintsDescription">
+                              <CardConstraints cardName="camera"/>
+                            </Constraint>
+                          </Constraints>
+
+                          <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">
+                                          <Group type="102" alignment="0" attributes="0">
+                                              <Component id="jLabel11" linkSize="10" min="-2" max="-2" attributes="0"/>
+                                              <EmptySpace max="-2" attributes="0"/>
+                                              <Component id="spToCam" linkSize="11" min="-2" pref="80" max="-2" attributes="0"/>
+                                          </Group>
+                                          <Group type="102" alignment="0" attributes="0">
+                                              <Component id="jLabel10" linkSize="10" min="-2" max="-2" attributes="0"/>
+                                              <EmptySpace max="-2" attributes="0"/>
+                                              <Component id="spFromCam" linkSize="11" min="-2" pref="80" max="-2" attributes="0"/>
+                                          </Group>
+                                          <Group type="102" alignment="0" attributes="0">
+                                              <Component id="jLabel12" linkSize="10" min="-2" max="-2" attributes="0"/>
+                                              <EmptySpace max="-2" attributes="0"/>
+                                              <Component id="spStepsCam" linkSize="11" min="-2" max="-2" attributes="0"/>
+                                          </Group>
+                                          <Group type="102" alignment="0" attributes="0">
+                                              <Component id="jLabel13" linkSize="10" min="-2" max="-2" attributes="0"/>
+                                              <EmptySpace max="-2" attributes="0"/>
+                                              <Component id="spShotsCam" linkSize="11" min="-2" max="-2" attributes="0"/>
+                                          </Group>
+                                      </Group>
+                                      <EmptySpace max="32767" attributes="0"/>
+                                  </Group>
+                                  <Component id="btStartCam" alignment="0" max="32767" attributes="0"/>
+                              </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="3" attributes="0">
+                                          <Component id="jLabel10" alignment="3" min="-2" max="-2" attributes="0"/>
+                                          <Component id="spFromCam" alignment="3" min="-2" max="-2" attributes="0"/>
+                                      </Group>
+                                      <EmptySpace max="-2" attributes="0"/>
+                                      <Group type="103" groupAlignment="3" attributes="0">
+                                          <Component id="jLabel11" alignment="3" min="-2" max="-2" attributes="0"/>
+                                          <Component id="spToCam" alignment="3" min="-2" max="-2" attributes="0"/>
+                                      </Group>
+                                      <EmptySpace max="-2" attributes="0"/>
+                                      <Group type="103" groupAlignment="3" attributes="0">
+                                          <Component id="jLabel12" alignment="3" min="-2" max="-2" attributes="0"/>
+                                          <Component id="spStepsCam" alignment="3" min="-2" max="-2" attributes="0"/>
+                                      </Group>
+                                      <EmptySpace max="-2" attributes="0"/>
+                                      <Group type="103" groupAlignment="3" attributes="0">
+                                          <Component id="jLabel13" alignment="3" min="-2" max="-2" attributes="0"/>
+                                          <Component id="spShotsCam" alignment="3" min="-2" max="-2" attributes="0"/>
+                                      </Group>
+                                      <EmptySpace max="32767" attributes="0"/>
+                                      <Component id="btStartCam" min="-2" max="-2" attributes="0"/>
+                                      <EmptySpace max="-2" attributes="0"/>
+                                  </Group>
+                              </Group>
+                            </DimensionLayout>
+                          </Layout>
+                          <SubComponents>
+                            <Component class="javax.swing.JLabel" name="jLabel10">
+                              <Properties>
+                                <Property name="horizontalAlignment" type="int" value="11"/>
+                                <Property name="text" type="java.lang.String" value="Range From:"/>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JSpinner" name="spFromCam">
+                              <Properties>
+                                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                                  <SpinnerModel initial="-17.0" maximum="30.0" minimum="-30.0" numberType="java.lang.Double" stepSize="1.0" type="number"/>
+                                </Property>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JLabel" name="jLabel11">
+                              <Properties>
+                                <Property name="horizontalAlignment" type="int" value="11"/>
+                                <Property name="text" type="java.lang.String" value="Range To:"/>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JSpinner" name="spToCam">
+                              <Properties>
+                                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                                  <SpinnerModel initial="-11.0" maximum="30.0" minimum="-30.0" numberType="java.lang.Double" stepSize="1.0" type="number"/>
+                                </Property>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JLabel" name="jLabel12">
+                              <Properties>
+                                <Property name="horizontalAlignment" type="int" value="11"/>
+                                <Property name="text" type="java.lang.String" value="Steps:"/>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JSpinner" name="spStepsCam">
+                              <Properties>
+                                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                                  <SpinnerModel initial="20" maximum="1000" minimum="1" numberType="java.lang.Integer" stepSize="1" type="number"/>
+                                </Property>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JLabel" name="jLabel13">
+                              <Properties>
+                                <Property name="horizontalAlignment" type="int" value="11"/>
+                                <Property name="text" type="java.lang.String" value="Num Shots:"/>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JSpinner" name="spShotsCam">
+                              <Properties>
+                                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                                  <SpinnerModel initial="100" maximum="1000" minimum="1" numberType="java.lang.Integer" stepSize="1" type="number"/>
+                                </Property>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JButton" name="btStartCam">
+                              <Properties>
+                                <Property name="text" type="java.lang.String" value="Start Camera Scan"/>
+                              </Properties>
+                              <Events>
+                                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="btStartCamActionPerformed"/>
+                              </Events>
+                            </Component>
+                          </SubComponents>
+                        </Container>
+                        <Container class="javax.swing.JPanel" name="panelCrystalScan">
+                          <Constraints>
+                            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignCardLayout" value="org.netbeans.modules.form.compat2.layouts.DesignCardLayout$CardConstraintsDescription">
+                              <CardConstraints cardName="crystal"/>
+                            </Constraint>
+                          </Constraints>
+
+                          <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">
+                                          <Group type="102" attributes="0">
+                                              <Component id="jLabel3" linkSize="6" min="-2" max="-2" attributes="0"/>
+                                              <EmptySpace max="-2" attributes="0"/>
+                                              <Component id="spToCr" linkSize="9" min="-2" pref="80" max="-2" attributes="0"/>
+                                          </Group>
+                                          <Group type="102" alignment="0" attributes="0">
+                                              <Component id="jLabel2" linkSize="6" min="-2" max="-2" attributes="0"/>
+                                              <EmptySpace max="-2" attributes="0"/>
+                                              <Component id="spFromCr" linkSize="9" min="-2" pref="80" max="-2" attributes="0"/>
+                                          </Group>
+                                          <Group type="102" attributes="0">
+                                              <Component id="jLabel4" linkSize="6" min="-2" max="-2" attributes="0"/>
+                                              <EmptySpace max="-2" attributes="0"/>
+                                              <Component id="spStepsCr" linkSize="9" min="-2" max="-2" attributes="0"/>
+                                          </Group>
+                                          <Group type="102" attributes="0">
+                                              <Component id="jLabel5" linkSize="6" min="-2" max="-2" attributes="0"/>
+                                              <EmptySpace max="-2" attributes="0"/>
+                                              <Component id="spShotsCr" linkSize="9" min="-2" max="-2" attributes="0"/>
+                                          </Group>
+                                      </Group>
+                                      <EmptySpace max="32767" attributes="0"/>
+                                  </Group>
+                                  <Component id="btStartCr" alignment="0" max="32767" attributes="0"/>
+                              </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="3" attributes="0">
+                                          <Component id="jLabel2" alignment="3" min="-2" max="-2" attributes="0"/>
+                                          <Component id="spFromCr" alignment="3" min="-2" max="-2" attributes="0"/>
+                                      </Group>
+                                      <EmptySpace max="-2" attributes="0"/>
+                                      <Group type="103" groupAlignment="3" attributes="0">
+                                          <Component id="jLabel3" alignment="3" min="-2" max="-2" attributes="0"/>
+                                          <Component id="spToCr" 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="spStepsCr" alignment="3" min="-2" max="-2" attributes="0"/>
+                                      </Group>
+                                      <EmptySpace max="-2" attributes="0"/>
+                                      <Group type="103" groupAlignment="3" attributes="0">
+                                          <Component id="jLabel5" alignment="3" min="-2" max="-2" attributes="0"/>
+                                          <Component id="spShotsCr" alignment="3" min="-2" max="-2" attributes="0"/>
+                                      </Group>
+                                      <EmptySpace max="32767" attributes="0"/>
+                                      <Component id="btStartCr" min="-2" max="-2" attributes="0"/>
+                                      <EmptySpace max="-2" attributes="0"/>
+                                  </Group>
+                              </Group>
+                            </DimensionLayout>
+                          </Layout>
+                          <SubComponents>
+                            <Component class="javax.swing.JLabel" name="jLabel2">
+                              <Properties>
+                                <Property name="horizontalAlignment" type="int" value="11"/>
+                                <Property name="text" type="java.lang.String" value="Range From:"/>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JSpinner" name="spFromCr">
+                              <Properties>
+                                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                                  <SpinnerModel initial="-0.8" maximum="10.0" minimum="-10.0" numberType="java.lang.Double" stepSize="0.1" type="number"/>
+                                </Property>
+                              </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="Range To:"/>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JSpinner" name="spToCr">
+                              <Properties>
+                                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                                  <SpinnerModel initial="-1.7" maximum="10.0" minimum="-10.0" numberType="java.lang.Double" stepSize="0.1" 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="Steps:"/>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JSpinner" name="spStepsCr">
+                              <Properties>
+                                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                                  <SpinnerModel initial="20" maximum="1000" minimum="1" numberType="java.lang.Integer" stepSize="1" type="number"/>
+                                </Property>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JLabel" name="jLabel5">
+                              <Properties>
+                                <Property name="horizontalAlignment" type="int" value="11"/>
+                                <Property name="text" type="java.lang.String" value="Num Shots:"/>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JSpinner" name="spShotsCr">
+                              <Properties>
+                                <Property name="model" type="javax.swing.SpinnerModel" editor="org.netbeans.modules.form.editors2.SpinnerModelEditor">
+                                  <SpinnerModel initial="100" maximum="1000" minimum="1" numberType="java.lang.Integer" stepSize="1" type="number"/>
+                                </Property>
+                              </Properties>
+                            </Component>
+                            <Component class="javax.swing.JButton" name="btStartCr">
+                              <Properties>
+                                <Property name="text" type="java.lang.String" value="Start Crystal Height Scan"/>
+                              </Properties>
+                              <Events>
+                                <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="btStartCrActionPerformed"/>
+                              </Events>
+                            </Component>
+                          </SubComponents>
+                        </Container>
+                      </SubComponents>
+                    </Container>
+                  </SubComponents>
+                </Container>
+              </SubComponents>
+            </Container>
+            <Component class="ch.psi.pshell.plot.LinePlotJFree" name="plotScan">
+              <Properties>
+                <Property name="title" type="java.lang.String" value=""/>
+              </Properties>
+            </Component>
+          </SubComponents>
+        </Container>
+      </SubComponents>
+    </Container>
+  </SubComponents>
+</Form>

plugins/PSSS.java

@@ -0,0 +1,760 @@
+import ch.psi.pshell.bs.PipelineServer;
+import ch.psi.pshell.core.Context;
+import ch.psi.pshell.epics.ChannelDouble;
+import ch.psi.pshell.imaging.RendererMode;
+import ch.psi.pshell.plot.Plot;
+import ch.psi.pshell.plot.LinePlotJFree;
+import ch.psi.pshell.ui.Panel;
+import ch.psi.utils.Convert;
+import ch.psi.utils.State;
+import ch.psi.utils.Str;
+import java.awt.CardLayout;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+
+
+/**
+ *
+ */
+public class PSSS extends Panel {
+
+    final String CAMERA_NAME = "SARFE10-PSSS059";
+    PipelineServer pipelineServer;
+    volatile boolean updatingPlot;
+    volatile boolean updatingImage;    
+            
+    public PSSS() {
+        initComponents();
+        plot.getAxis(Plot.AxisId.X).setLabel(null);
+        plot.getAxis(Plot.AxisId.Y).setLabel(null);
+        renderer.setMode(RendererMode.Stretch);
+    }
+
+    //Overridable callbacks
+    @Override
+    public void onInitialize(int runCount) {
+        startTimer(1000);
+        
+        try {
+            setGlobalVar("PSSS_PLOT", plot);
+            setGlobalVar("HISTORY_PLOT", history);
+            setGlobalVar("PSSS_RENDERER", renderer);                        
+            
+            pipelineServer = (PipelineServer) getDevice("cam_server");
+            ((LinePlotJFree)histogramGeneratorPanelCenter.getPlot()).setLegendVisible(true);
+            ((LinePlotJFree)histogramGeneratorFwhm.getPlot()).setLegendVisible(true);
+            histogramGeneratorPanelCenter.getPlot().getAxis(Plot.AxisId.Y).setRange(0, 100);
+            histogramGeneratorFwhm.getPlot().getAxis(Plot.AxisId.Y).setRange(0, 100);
+            //setImageEnabled(true);
+            tabStateChanged(null);
+                                                
+            spinnerAverage.setValue(( (Number) eval("get_psss_averaging()", true)).intValue());
+            
+            try{
+                Double energy = (((ChannelDouble)getDevice("energy_machine")).take(-1));
+                energy=Convert.roundDouble(energy, 0);
+                spFromEn.setValue(energy-150);
+                spToEn.setValue(energy+150);
+            } catch (Exception ex) {
+                getLogger().log(Level.WARNING, null, ex);
+            } 
+            
+            
+        } catch (Exception ex) {
+            getLogger().log(Level.WARNING, null, ex);
+        }        
+    }
+
+    @Override
+    public void onStateChange(State state, State former) {
+        this.btStartCr.setEnabled(state ==  State.Ready);
+        this.btStartEn.setEnabled(state ==  State.Ready);
+        this.btStartCam.setEnabled(state ==  State.Ready);
+        radioEnergyScan.setEnabled(state ==  State.Ready);
+        radioCrystalScan.setEnabled(state ==  State.Ready);
+        radioCameraScan.setEnabled(state ==  State.Ready);
+        this.btAbort.setEnabled(state.isRunning());
+    }
+
+    @Override
+    public void onExecutedFile(String fileName, Object result) {
+    }
+    
+    @Override
+    public void onTimer() {
+        try {
+            if (!updatingPlot){
+                updatingPlot = true;
+                //evalAsync("plot_psss(PSSS_PLOT, HISTORY_PLOT, " + spinnerAverage.getValue() + ")", true).handle((ret,ex)->{                
+                evalAsync("plot_psss(PSSS_PLOT, HISTORY_PLOT)", true).handle((ret,ex)->{                
+                    updatingPlot = false;
+                    return ret;
+                });
+            }
+            if (isImageEnabled()){
+                if (!updatingImage){
+                    updatingImage = true;
+                    evalAsync("update_psss_image(PSSS_RENDERER)", true).handle((ret,ex)->{                
+                        updatingImage = false;
+                        return ret;
+                    });
+                }
+            }
+        } catch (Exception ex) {
+            getLogger().log(Level.WARNING, null, ex);
+        }
+    }
+    
+    //Callback to perform update - in event thread
+    @Override
+    protected void doUpdate() {
+    }    
+    
+    void setImageEnabled(boolean enabled){
+        try{    
+            imageEnabled = enabled;
+            evalAsync("enable_psss_image(" + Str.capitalizeFirst(String.valueOf(enabled)) + ", PSSS_RENDERER)", true);
+        } catch (Exception ex) {
+            getLogger().log(Level.WARNING, null, ex);
+        }          
+    }
+    volatile boolean imageEnabled;
+    
+    boolean isImageEnabled(){
+        return imageEnabled;
+    }
+    
+    
+    void runScan(String name, Map args){
+        try {
+            args.put("PLOT", plotScan);    
+            this.runAsync(name, args).handle((ret,ex)->{
+                if (ex!=null){
+                    if (!getContext().isAborted()){
+                        showException((Exception)ex);
+                    }
+                }
+                return ret;
+            });
+        } catch (Context.ContextStateException ex) {
+            showException(ex);
+        }    
+    }
+
+    @SuppressWarnings("unchecked")
+    // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
+    private void initComponents() {
+
+        buttonGroup1 = new javax.swing.ButtonGroup();
+        tab = new javax.swing.JTabbedPane();
+        jPanel1 = new javax.swing.JPanel();
+        plot = new ch.psi.pshell.plot.LinePlotJFree();
+        history = new ch.psi.pshell.plot.TimePlotJFree();
+        jLabel1 = new javax.swing.JLabel();
+        spinnerAverage = new javax.swing.JSpinner();
+        histogramGeneratorPanelCenter = new ch.psi.pshell.swing.HistogramGeneratorPanel();
+        histogramGeneratorFwhm = new ch.psi.pshell.swing.HistogramGeneratorPanel();
+        jPanel4 = new javax.swing.JPanel();
+        renderer = new ch.psi.pshell.imaging.Renderer();
+        jPanel3 = new javax.swing.JPanel();
+        jPanel2 = new javax.swing.JPanel();
+        btAbort = new javax.swing.JButton();
+        radioEnergyScan = new javax.swing.JRadioButton();
+        radioCameraScan = new javax.swing.JRadioButton();
+        radioCrystalScan = new javax.swing.JRadioButton();
+        jPanel5 = new javax.swing.JPanel();
+        panelScan = new javax.swing.JPanel();
+        panelEnergyScan = new javax.swing.JPanel();
+        spFromEn = new javax.swing.JSpinner();
+        jLabel6 = new javax.swing.JLabel();
+        jLabel7 = new javax.swing.JLabel();
+        spToEn = new javax.swing.JSpinner();
+        spStepsEn = new javax.swing.JSpinner();
+        jLabel8 = new javax.swing.JLabel();
+        jLabel9 = new javax.swing.JLabel();
+        spShotsEn = new javax.swing.JSpinner();
+        btStartEn = new javax.swing.JButton();
+        panelCameraScan = new javax.swing.JPanel();
+        jLabel10 = new javax.swing.JLabel();
+        spFromCam = new javax.swing.JSpinner();
+        jLabel11 = new javax.swing.JLabel();
+        spToCam = new javax.swing.JSpinner();
+        jLabel12 = new javax.swing.JLabel();
+        spStepsCam = new javax.swing.JSpinner();
+        jLabel13 = new javax.swing.JLabel();
+        spShotsCam = new javax.swing.JSpinner();
+        btStartCam = new javax.swing.JButton();
+        panelCrystalScan = new javax.swing.JPanel();
+        jLabel2 = new javax.swing.JLabel();
+        spFromCr = new javax.swing.JSpinner();
+        jLabel3 = new javax.swing.JLabel();
+        spToCr = new javax.swing.JSpinner();
+        jLabel4 = new javax.swing.JLabel();
+        spStepsCr = new javax.swing.JSpinner();
+        jLabel5 = new javax.swing.JLabel();
+        spShotsCr = new javax.swing.JSpinner();
+        btStartCr = new javax.swing.JButton();
+        plotScan = new ch.psi.pshell.plot.LinePlotJFree();
+
+        tab.addChangeListener(new javax.swing.event.ChangeListener() {
+            public void stateChanged(javax.swing.event.ChangeEvent evt) {
+                tabStateChanged(evt);
+            }
+        });
+
+        plot.setTitle("");
+
+        jLabel1.setText("Average:");
+
+        spinnerAverage.setModel(new javax.swing.SpinnerNumberModel(1, 1, 100, 1));
+        spinnerAverage.addChangeListener(new javax.swing.event.ChangeListener() {
+            public void stateChanged(javax.swing.event.ChangeEvent evt) {
+                spinnerAverageStateChanged(evt);
+            }
+        });
+
+        histogramGeneratorPanelCenter.setDeviceName("histo_center");
+
+        histogramGeneratorFwhm.setDeviceName("histo_fwhm");
+
+        javax.swing.GroupLayout jPanel1Layout = new javax.swing.GroupLayout(jPanel1);
+        jPanel1.setLayout(jPanel1Layout);
+        jPanel1Layout.setHorizontalGroup(
+            jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(jPanel1Layout.createSequentialGroup()
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addGroup(jPanel1Layout.createSequentialGroup()
+                        .addContainerGap()
+                        .addComponent(jLabel1)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spinnerAverage, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                    .addComponent(history, javax.swing.GroupLayout.DEFAULT_SIZE, 453, Short.MAX_VALUE)
+                    .addComponent(plot, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addGroup(jPanel1Layout.createSequentialGroup()
+                        .addGap(12, 12, 12)
+                        .addComponent(histogramGeneratorFwhm, javax.swing.GroupLayout.PREFERRED_SIZE, 372, javax.swing.GroupLayout.PREFERRED_SIZE))
+                    .addComponent(histogramGeneratorPanelCenter, javax.swing.GroupLayout.PREFERRED_SIZE, 372, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addGap(0, 0, 0))
+        );
+        jPanel1Layout.setVerticalGroup(
+            jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(jPanel1Layout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel1)
+                    .addComponent(spinnerAverage, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addGap(6, 6, 6)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(histogramGeneratorPanelCenter, javax.swing.GroupLayout.DEFAULT_SIZE, 194, Short.MAX_VALUE)
+                    .addComponent(plot, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addComponent(history, javax.swing.GroupLayout.DEFAULT_SIZE, 194, Short.MAX_VALUE)
+                    .addComponent(histogramGeneratorFwhm, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE)))
+        );
+
+        tab.addTab("Spectrum", jPanel1);
+
+        javax.swing.GroupLayout jPanel4Layout = new javax.swing.GroupLayout(jPanel4);
+        jPanel4.setLayout(jPanel4Layout);
+        jPanel4Layout.setHorizontalGroup(
+            jPanel4Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGap(0, 843, Short.MAX_VALUE)
+            .addGroup(jPanel4Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                .addComponent(renderer, javax.swing.GroupLayout.DEFAULT_SIZE, 843, Short.MAX_VALUE))
+        );
+        jPanel4Layout.setVerticalGroup(
+            jPanel4Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGap(0, 432, Short.MAX_VALUE)
+            .addGroup(jPanel4Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                .addComponent(renderer, javax.swing.GroupLayout.DEFAULT_SIZE, 432, Short.MAX_VALUE))
+        );
+
+        tab.addTab("Camera", jPanel4);
+
+        btAbort.setText("Abort");
+        btAbort.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                btAbortActionPerformed(evt);
+            }
+        });
+
+        buttonGroup1.add(radioEnergyScan);
+        radioEnergyScan.setSelected(true);
+        radioEnergyScan.setText("Energy Scan");
+        radioEnergyScan.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                radioEnergyScanActionPerformed(evt);
+            }
+        });
+
+        buttonGroup1.add(radioCameraScan);
+        radioCameraScan.setText("Camera Scan");
+        radioCameraScan.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                radioCameraScanActionPerformed(evt);
+            }
+        });
+
+        buttonGroup1.add(radioCrystalScan);
+        radioCrystalScan.setText("Crystal Height Scan");
+        radioCrystalScan.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                radioCrystalScanActionPerformed(evt);
+            }
+        });
+
+        panelScan.setLayout(new java.awt.CardLayout());
+
+        spFromEn.setModel(new javax.swing.SpinnerNumberModel(7200.0d, 1.0d, 20000.0d, 10.0d));
+
+        jLabel6.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel6.setText("Range From:");
+
+        jLabel7.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel7.setText("Range To:");
+
+        spToEn.setModel(new javax.swing.SpinnerNumberModel(7340.0d, 1.0d, 20000.0d, 10.0d));
+
+        spStepsEn.setModel(new javax.swing.SpinnerNumberModel(20, 1, 1000, 1));
+
+        jLabel8.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel8.setText("Steps:");
+
+        jLabel9.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel9.setText("Num Shots:");
+
+        spShotsEn.setModel(new javax.swing.SpinnerNumberModel(100, 1, 1000, 1));
+
+        btStartEn.setText("Start Energy Scan");
+        btStartEn.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                btStartEnActionPerformed(evt);
+            }
+        });
+
+        javax.swing.GroupLayout panelEnergyScanLayout = new javax.swing.GroupLayout(panelEnergyScan);
+        panelEnergyScan.setLayout(panelEnergyScanLayout);
+        panelEnergyScanLayout.setHorizontalGroup(
+            panelEnergyScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(panelEnergyScanLayout.createSequentialGroup()
+                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addGroup(panelEnergyScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addGroup(panelEnergyScanLayout.createSequentialGroup()
+                        .addComponent(jLabel7)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spToEn, javax.swing.GroupLayout.PREFERRED_SIZE, 80, javax.swing.GroupLayout.PREFERRED_SIZE))
+                    .addGroup(panelEnergyScanLayout.createSequentialGroup()
+                        .addComponent(jLabel6)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spFromEn, javax.swing.GroupLayout.PREFERRED_SIZE, 80, javax.swing.GroupLayout.PREFERRED_SIZE))
+                    .addGroup(panelEnergyScanLayout.createSequentialGroup()
+                        .addComponent(jLabel8)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spStepsEn, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                    .addGroup(panelEnergyScanLayout.createSequentialGroup()
+                        .addComponent(jLabel9)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spShotsEn, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
+                .addContainerGap())
+            .addComponent(btStartEn, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+        );
+
+        panelEnergyScanLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {jLabel6, jLabel7, jLabel8, jLabel9});
+
+        panelEnergyScanLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {spFromEn, spShotsEn, spStepsEn, spToEn});
+
+        panelEnergyScanLayout.setVerticalGroup(
+            panelEnergyScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(panelEnergyScanLayout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(panelEnergyScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel6)
+                    .addComponent(spFromEn, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(panelEnergyScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel7)
+                    .addComponent(spToEn, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(panelEnergyScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel8)
+                    .addComponent(spStepsEn, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(panelEnergyScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel9)
+                    .addComponent(spShotsEn, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addComponent(btStartEn)
+                .addContainerGap())
+        );
+
+        panelScan.add(panelEnergyScan, "energy");
+
+        jLabel10.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel10.setText("Range From:");
+
+        spFromCam.setModel(new javax.swing.SpinnerNumberModel(-17.0d, -30.0d, 30.0d, 1.0d));
+
+        jLabel11.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel11.setText("Range To:");
+
+        spToCam.setModel(new javax.swing.SpinnerNumberModel(-11.0d, -30.0d, 30.0d, 1.0d));
+
+        jLabel12.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel12.setText("Steps:");
+
+        spStepsCam.setModel(new javax.swing.SpinnerNumberModel(20, 1, 1000, 1));
+
+        jLabel13.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel13.setText("Num Shots:");
+
+        spShotsCam.setModel(new javax.swing.SpinnerNumberModel(100, 1, 1000, 1));
+
+        btStartCam.setText("Start Camera Scan");
+        btStartCam.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                btStartCamActionPerformed(evt);
+            }
+        });
+
+        javax.swing.GroupLayout panelCameraScanLayout = new javax.swing.GroupLayout(panelCameraScan);
+        panelCameraScan.setLayout(panelCameraScanLayout);
+        panelCameraScanLayout.setHorizontalGroup(
+            panelCameraScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(panelCameraScanLayout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(panelCameraScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addGroup(panelCameraScanLayout.createSequentialGroup()
+                        .addComponent(jLabel11)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spToCam, javax.swing.GroupLayout.PREFERRED_SIZE, 80, javax.swing.GroupLayout.PREFERRED_SIZE))
+                    .addGroup(panelCameraScanLayout.createSequentialGroup()
+                        .addComponent(jLabel10)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spFromCam, javax.swing.GroupLayout.PREFERRED_SIZE, 80, javax.swing.GroupLayout.PREFERRED_SIZE))
+                    .addGroup(panelCameraScanLayout.createSequentialGroup()
+                        .addComponent(jLabel12)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spStepsCam, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                    .addGroup(panelCameraScanLayout.createSequentialGroup()
+                        .addComponent(jLabel13)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spShotsCam, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
+                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+            .addComponent(btStartCam, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+        );
+
+        panelCameraScanLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {jLabel10, jLabel11, jLabel12, jLabel13});
+
+        panelCameraScanLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {spFromCam, spShotsCam, spStepsCam, spToCam});
+
+        panelCameraScanLayout.setVerticalGroup(
+            panelCameraScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(panelCameraScanLayout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(panelCameraScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel10)
+                    .addComponent(spFromCam, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(panelCameraScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel11)
+                    .addComponent(spToCam, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(panelCameraScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel12)
+                    .addComponent(spStepsCam, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(panelCameraScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel13)
+                    .addComponent(spShotsCam, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addComponent(btStartCam)
+                .addContainerGap())
+        );
+
+        panelScan.add(panelCameraScan, "camera");
+
+        jLabel2.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel2.setText("Range From:");
+
+        spFromCr.setModel(new javax.swing.SpinnerNumberModel(-0.8d, -10.0d, 10.0d, 0.1d));
+
+        jLabel3.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel3.setText("Range To:");
+
+        spToCr.setModel(new javax.swing.SpinnerNumberModel(-1.7d, -10.0d, 10.0d, 0.1d));
+
+        jLabel4.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel4.setText("Steps:");
+
+        spStepsCr.setModel(new javax.swing.SpinnerNumberModel(20, 1, 1000, 1));
+
+        jLabel5.setHorizontalAlignment(javax.swing.SwingConstants.TRAILING);
+        jLabel5.setText("Num Shots:");
+
+        spShotsCr.setModel(new javax.swing.SpinnerNumberModel(100, 1, 1000, 1));
+
+        btStartCr.setText("Start Crystal Height Scan");
+        btStartCr.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                btStartCrActionPerformed(evt);
+            }
+        });
+
+        javax.swing.GroupLayout panelCrystalScanLayout = new javax.swing.GroupLayout(panelCrystalScan);
+        panelCrystalScan.setLayout(panelCrystalScanLayout);
+        panelCrystalScanLayout.setHorizontalGroup(
+            panelCrystalScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(panelCrystalScanLayout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(panelCrystalScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                    .addGroup(panelCrystalScanLayout.createSequentialGroup()
+                        .addComponent(jLabel3)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spToCr, javax.swing.GroupLayout.PREFERRED_SIZE, 80, javax.swing.GroupLayout.PREFERRED_SIZE))
+                    .addGroup(panelCrystalScanLayout.createSequentialGroup()
+                        .addComponent(jLabel2)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spFromCr, javax.swing.GroupLayout.PREFERRED_SIZE, 80, javax.swing.GroupLayout.PREFERRED_SIZE))
+                    .addGroup(panelCrystalScanLayout.createSequentialGroup()
+                        .addComponent(jLabel4)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spStepsCr, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                    .addGroup(panelCrystalScanLayout.createSequentialGroup()
+                        .addComponent(jLabel5)
+                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                        .addComponent(spShotsCr, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
+                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+            .addComponent(btStartCr, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+        );
+
+        panelCrystalScanLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {jLabel2, jLabel3, jLabel4, jLabel5});
+
+        panelCrystalScanLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {spFromCr, spShotsCr, spStepsCr, spToCr});
+
+        panelCrystalScanLayout.setVerticalGroup(
+            panelCrystalScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(panelCrystalScanLayout.createSequentialGroup()
+                .addContainerGap()
+                .addGroup(panelCrystalScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel2)
+                    .addComponent(spFromCr, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(panelCrystalScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel3)
+                    .addComponent(spToCr, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(panelCrystalScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel4)
+                    .addComponent(spStepsCr, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addGroup(panelCrystalScanLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+                    .addComponent(jLabel5)
+                    .addComponent(spShotsCr, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addComponent(btStartCr)
+                .addContainerGap())
+        );
+
+        panelScan.add(panelCrystalScan, "crystal");
+
+        javax.swing.GroupLayout jPanel5Layout = new javax.swing.GroupLayout(jPanel5);
+        jPanel5.setLayout(jPanel5Layout);
+        jPanel5Layout.setHorizontalGroup(
+            jPanel5Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGap(0, 0, Short.MAX_VALUE)
+            .addGroup(jPanel5Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                .addGroup(jPanel5Layout.createSequentialGroup()
+                    .addGap(0, 0, Short.MAX_VALUE)
+                    .addComponent(panelScan, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                    .addGap(0, 0, 0)))
+        );
+        jPanel5Layout.setVerticalGroup(
+            jPanel5Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGap(0, 0, Short.MAX_VALUE)
+            .addGroup(jPanel5Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                .addGroup(jPanel5Layout.createSequentialGroup()
+                    .addGap(0, 0, Short.MAX_VALUE)
+                    .addComponent(panelScan, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                    .addGap(0, 0, 0)))
+        );
+
+        javax.swing.GroupLayout jPanel2Layout = new javax.swing.GroupLayout(jPanel2);
+        jPanel2.setLayout(jPanel2Layout);
+        jPanel2Layout.setHorizontalGroup(
+            jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(jPanel2Layout.createSequentialGroup()
+                .addGap(12, 12, 12)
+                .addGroup(jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
+                    .addComponent(jPanel5, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                    .addComponent(radioCrystalScan)
+                    .addComponent(radioCameraScan)
+                    .addComponent(radioEnergyScan)
+                    .addComponent(btAbort, javax.swing.GroupLayout.DEFAULT_SIZE, 213, Short.MAX_VALUE))
+                .addContainerGap())
+        );
+        jPanel2Layout.setVerticalGroup(
+            jPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, jPanel2Layout.createSequentialGroup()
+                .addGap(20, 20, 20)
+                .addComponent(radioEnergyScan)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                .addComponent(radioCameraScan)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                .addComponent(radioCrystalScan)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                .addComponent(jPanel5, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+                .addComponent(btAbort)
+                .addContainerGap())
+        );
+
+        plotScan.setTitle("");
+
+        javax.swing.GroupLayout jPanel3Layout = new javax.swing.GroupLayout(jPanel3);
+        jPanel3.setLayout(jPanel3Layout);
+        jPanel3Layout.setHorizontalGroup(
+            jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(jPanel3Layout.createSequentialGroup()
+                .addComponent(jPanel2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addGap(0, 0, 0)
+                .addComponent(plotScan, javax.swing.GroupLayout.DEFAULT_SIZE, 614, Short.MAX_VALUE))
+        );
+        jPanel3Layout.setVerticalGroup(
+            jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addComponent(jPanel2, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+            .addComponent(plotScan, javax.swing.GroupLayout.DEFAULT_SIZE, 432, Short.MAX_VALUE)
+        );
+
+        tab.addTab("Alignment", jPanel3);
+
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
+        this.setLayout(layout);
+        layout.setHorizontalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addComponent(tab)
+        );
+        layout.setVerticalGroup(
+            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addComponent(tab, javax.swing.GroupLayout.Alignment.TRAILING)
+        );
+    }// </editor-fold>//GEN-END:initComponents
+
+    private void tabStateChanged(javax.swing.event.ChangeEvent evt) {//GEN-FIRST:event_tabStateChanged
+        setImageEnabled(tab.getSelectedIndex()==1);
+    }//GEN-LAST:event_tabStateChanged
+
+    private void btAbortActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_btAbortActionPerformed
+        try {
+            abort();
+        } catch (Exception ex) {
+            showException(ex);
+        }
+    }//GEN-LAST:event_btAbortActionPerformed
+
+    private void btStartCrActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_btStartCrActionPerformed
+        Map args = new HashMap();
+        args.put("RANGE_FROM", spFromCr.getValue());
+        args.put("RANGE_TO", spToCr.getValue());
+        args.put("STEPS", spStepsCr.getValue());
+        args.put("NUM_SHOTS", spShotsCr.getValue());        
+        runScan("psss/CrystalHeightScan",args);
+    }//GEN-LAST:event_btStartCrActionPerformed
+
+    private void btStartCamActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_btStartCamActionPerformed
+        Map args = new HashMap();
+        args.put("RANGE_FROM", spFromCam.getValue());
+        args.put("RANGE_TO", spToCam.getValue());
+        args.put("STEPS", spStepsCam.getValue());
+        args.put("NUM_SHOTS", spShotsCam.getValue());  
+        runScan("psss/CameraScan",args);
+    }//GEN-LAST:event_btStartCamActionPerformed
+
+    private void btStartEnActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_btStartEnActionPerformed
+        Map args = new HashMap();
+        args.put("RANGE_OFF", null);
+        args.put("RANGE_FROM", spFromEn.getValue());
+        args.put("RANGE_TO", spToEn.getValue());
+        args.put("STEPS", spStepsEn.getValue());
+        args.put("NUM_SHOTS", spShotsEn.getValue());
+        runScan("psss/EnergyScan",args);
+    }//GEN-LAST:event_btStartEnActionPerformed
+
+    private void radioEnergyScanActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_radioEnergyScanActionPerformed
+        ((CardLayout)panelScan.getLayout()).show(panelScan, "energy");
+    }//GEN-LAST:event_radioEnergyScanActionPerformed
+
+    private void radioCameraScanActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_radioCameraScanActionPerformed
+        ((CardLayout)panelScan.getLayout()).show(panelScan, "camera");
+    }//GEN-LAST:event_radioCameraScanActionPerformed
+
+    private void radioCrystalScanActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_radioCrystalScanActionPerformed
+        ((CardLayout)panelScan.getLayout()).show(panelScan, "crystal");
+    }//GEN-LAST:event_radioCrystalScanActionPerformed
+
+    private void spinnerAverageStateChanged(javax.swing.event.ChangeEvent evt) {//GEN-FIRST:event_spinnerAverageStateChanged
+        try {
+            eval("set_psss_averaging(" + spinnerAverage.getValue() + ")", true); 
+        } catch (Exception ex) {
+            showException(ex);
+        }
+    }//GEN-LAST:event_spinnerAverageStateChanged
+
+    // Variables declaration - do not modify//GEN-BEGIN:variables
+    private javax.swing.JButton btAbort;
+    private javax.swing.JButton btStartCam;
+    private javax.swing.JButton btStartCr;
+    private javax.swing.JButton btStartEn;
+    private javax.swing.ButtonGroup buttonGroup1;
+    private ch.psi.pshell.swing.HistogramGeneratorPanel histogramGeneratorFwhm;
+    private ch.psi.pshell.swing.HistogramGeneratorPanel histogramGeneratorPanelCenter;
+    private ch.psi.pshell.plot.TimePlotJFree history;
+    private javax.swing.JLabel jLabel1;
+    private javax.swing.JLabel jLabel10;
+    private javax.swing.JLabel jLabel11;
+    private javax.swing.JLabel jLabel12;
+    private javax.swing.JLabel jLabel13;
+    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.JLabel jLabel8;
+    private javax.swing.JLabel jLabel9;
+    private javax.swing.JPanel jPanel1;
+    private javax.swing.JPanel jPanel2;
+    private javax.swing.JPanel jPanel3;
+    private javax.swing.JPanel jPanel4;
+    private javax.swing.JPanel jPanel5;
+    private javax.swing.JPanel panelCameraScan;
+    private javax.swing.JPanel panelCrystalScan;
+    private javax.swing.JPanel panelEnergyScan;
+    private javax.swing.JPanel panelScan;
+    private ch.psi.pshell.plot.LinePlotJFree plot;
+    private ch.psi.pshell.plot.LinePlotJFree plotScan;
+    private javax.swing.JRadioButton radioCameraScan;
+    private javax.swing.JRadioButton radioCrystalScan;
+    private javax.swing.JRadioButton radioEnergyScan;
+    private ch.psi.pshell.imaging.Renderer renderer;
+    private javax.swing.JSpinner spFromCam;
+    private javax.swing.JSpinner spFromCr;
+    private javax.swing.JSpinner spFromEn;
+    private javax.swing.JSpinner spShotsCam;
+    private javax.swing.JSpinner spShotsCr;
+    private javax.swing.JSpinner spShotsEn;
+    private javax.swing.JSpinner spStepsCam;
+    private javax.swing.JSpinner spStepsCr;
+    private javax.swing.JSpinner spStepsEn;
+    private javax.swing.JSpinner spToCam;
+    private javax.swing.JSpinner spToCr;
+    private javax.swing.JSpinner spToEn;
+    private javax.swing.JSpinner spinnerAverage;
+    private javax.swing.JTabbedPane tab;
+    // End of variables declaration//GEN-END:variables
+}

script/Lib/builtin_classes.py

@@ -0,0 +1,587 @@
+from builtin_utils import *
+
+import ch.psi.utils.Threading as Threading
+import ch.psi.utils.State as State
+import ch.psi.utils.Convert as Convert
+import ch.psi.utils.Str as Str
+import ch.psi.utils.Sys as Sys
+import ch.psi.utils.Arr as Arr
+import ch.psi.utils.IO as IO
+import ch.psi.utils.Chrono as Chrono
+import ch.psi.utils.Folder as Folder
+import ch.psi.utils.Histogram as Histogram
+import ch.psi.utils.History as History
+import ch.psi.utils.Condition as Condition
+import ch.psi.utils.ArrayProperties as ArrayProperties
+import ch.psi.utils.Audio as Audio
+import ch.psi.utils.BitMask as BitMask
+import ch.psi.utils.Config as Config
+import ch.psi.utils.Inventory as Inventory
+import ch.psi.utils.DataAPI as DataAPI
+import ch.psi.utils.DispatcherAPI as DispatcherAPI
+import ch.psi.utils.EpicsBootInfoAPI as EpicsBootInfoAPI
+import ch.psi.utils.Mail as Mail
+import ch.psi.utils.Posix as Posix
+import ch.psi.utils.ProcessFactory as ProcessFactory
+import ch.psi.utils.Range as Range
+import ch.psi.utils.Reflection as Reflection
+import ch.psi.utils.Serializer as Serializer
+import ch.psi.utils.Windows as Windows
+import ch.psi.utils.NumberComparator as NumberComparator
+
+
+import ch.psi.pshell.core.CommandSource as CommandSource
+import ch.psi.pshell.core.ContextAdapter as ContextListener
+import ch.psi.pshell.core.Context
+import ch.psi.pshell.core.InlineDevice as InlineDevice
+
+import ch.psi.pshell.data.DataSlice as DataSlice
+import ch.psi.pshell.data.PlotDescriptor as PlotDescriptor
+import ch.psi.pshell.data.Table as Table
+import ch.psi.pshell.data.Provider as  Provider
+import ch.psi.pshell.data.ProviderHDF5 as  ProviderHDF5
+import ch.psi.pshell.data.ProviderText as  ProviderText
+import ch.psi.pshell.data.ProviderCSV as  ProviderCSV
+import ch.psi.pshell.data.ProviderFDA as  ProviderFDA
+import ch.psi.pshell.data.Converter as  DataConverter
+import ch.psi.pshell.data.Layout as  Layout
+import  ch.psi.pshell.data.LayoutBase as LayoutBase
+import  ch.psi.pshell.data.LayoutDefault as LayoutDefault
+import  ch.psi.pshell.data.LayoutTable as LayoutTable
+import  ch.psi.pshell.data.LayoutFDA as LayoutFDA
+import  ch.psi.pshell.data.LayoutSF as LayoutSF
+
+import ch.psi.pshell.device.Device as Device
+import ch.psi.pshell.device.DeviceBase as DeviceBase
+import ch.psi.pshell.device.GenericDevice as GenericDevice 
+import ch.psi.pshell.device.DeviceConfig as DeviceConfig
+import ch.psi.pshell.device.PositionerConfig as PositionerConfig
+import ch.psi.pshell.device.RegisterConfig as RegisterConfig
+import ch.psi.pshell.device.ReadonlyProcessVariableConfig as ReadonlyProcessVariableConfig
+import ch.psi.pshell.device.ProcessVariableConfig as ProcessVariableConfig
+import ch.psi.pshell.device.MotorConfig as MotorConfig
+import ch.psi.pshell.device.Register as Register
+import ch.psi.pshell.device.RegisterBase as RegisterBase
+import ch.psi.pshell.device.ProcessVariableBase as ProcessVariableBase
+import ch.psi.pshell.device.ControlledVariableBase as ControlledVariableBase
+import ch.psi.pshell.device.PositionerBase as PositionerBase
+import ch.psi.pshell.device.MasterPositioner as MasterPositioner
+import ch.psi.pshell.device.MotorBase as MotorBase
+import ch.psi.pshell.device.DiscretePositionerBase as DiscretePositionerBase
+import ch.psi.pshell.device.MotorGroupBase as MotorGroupBase
+import ch.psi.pshell.device.MotorGroupDiscretePositioner as MotorGroupDiscretePositioner
+import ch.psi.pshell.device.ReadonlyRegisterBase as ReadonlyRegisterBase
+import ch.psi.pshell.device.ReadonlyAsyncRegisterBase as ReadonlyAsyncRegisterBase
+import ch.psi.pshell.device.Register as Register
+import ch.psi.pshell.device.Register.RegisterArray as RegisterArray
+import ch.psi.pshell.device.Register.RegisterNumber as RegisterNumber
+import ch.psi.pshell.device.Register.RegisterBoolean as RegisterBoolean
+import ch.psi.pshell.device.RegisterCache as RegisterCache
+import ch.psi.pshell.device.ReadonlyRegister.ReadonlyRegisterArray as ReadonlyRegisterArray
+import ch.psi.pshell.device.ReadonlyRegister.ReadonlyRegisterMatrix as ReadonlyRegisterMatrix
+import ch.psi.pshell.device.DummyPositioner as DummyPositioner
+import ch.psi.pshell.device.DummyMotor as DummyMotor
+import ch.psi.pshell.device.DummyRegister as DummyRegister
+import ch.psi.pshell.device.Timestamp as Timestamp
+import ch.psi.pshell.device.Interlock as Interlock
+import ch.psi.pshell.device.Readable as Readable
+import ch.psi.pshell.device.Readable.ReadableArray as ReadableArray
+import ch.psi.pshell.device.Readable.ReadableMatrix as ReadableMatrix
+import ch.psi.pshell.device.Readable.ReadableCalibratedArray as ReadableCalibratedArray
+import ch.psi.pshell.device.Readable.ReadableCalibratedMatrix as ReadableCalibratedMatrix
+import ch.psi.pshell.device.ArrayCalibration as ArrayCalibration
+import ch.psi.pshell.device.MatrixCalibration as MatrixCalibration
+import ch.psi.pshell.device.Writable as Writable
+import ch.psi.pshell.device.Writable.WritableArray as WritableArray
+import ch.psi.pshell.device.Stoppable as Stoppable
+import ch.psi.pshell.device.Averager as Averager
+import ch.psi.pshell.device.ArrayAverager as ArrayAverager
+import ch.psi.pshell.device.Delta as Delta
+import ch.psi.pshell.device.DeviceAdapter as DeviceListener
+import ch.psi.pshell.device.ReadbackDeviceAdapter as ReadbackDeviceListener
+import ch.psi.pshell.device.MotorAdapter as MotorListener
+import ch.psi.pshell.device.MoveMode as MoveMode
+import ch.psi.pshell.device.SettlingCondition as SettlingCondition
+import ch.psi.pshell.device.HistogramGenerator as HistogramGenerator
+
+import ch.psi.pshell.epics.Epics as Epics
+import ch.psi.pshell.epics.EpicsScan as EpicsScan
+import ch.psi.pshell.epics.ChannelSettlingCondition as ChannelSettlingCondition
+import ch.psi.pshell.epics.AreaDetector as AreaDetector
+import ch.psi.pshell.epics.BinaryPositioner as BinaryPositioner
+import ch.psi.pshell.epics.ChannelByte as ChannelByte
+import ch.psi.pshell.epics.ChannelByteArray as ChannelByteArray
+import ch.psi.pshell.epics.ChannelByteMatrix as ChannelByteMatrix
+import ch.psi.pshell.epics.ChannelDouble as ChannelDouble
+import ch.psi.pshell.epics.ChannelDoubleArray as ChannelDoubleArray
+import ch.psi.pshell.epics.ChannelDoubleMatrix as ChannelDoubleMatrix
+import ch.psi.pshell.epics.ChannelFloat as ChannelFloat
+import ch.psi.pshell.epics.ChannelFloatArray as ChannelFloatArray
+import ch.psi.pshell.epics.ChannelFloatMatrix as ChannelFloatMatrix
+import ch.psi.pshell.epics.ChannelInteger as ChannelInteger
+import ch.psi.pshell.epics.ChannelIntegerArray as ChannelIntegerArray
+import ch.psi.pshell.epics.ChannelIntegerMatrix as ChannelIntegerMatrix
+import ch.psi.pshell.epics.ChannelShort as ChannelShort
+import ch.psi.pshell.epics.ChannelShortArray as ChannelShortArray
+import ch.psi.pshell.epics.ChannelShortMatrix as ChannelShortMatrix
+import ch.psi.pshell.epics.ChannelString as ChannelString
+import ch.psi.pshell.epics.ControlledVariable as ControlledVariable
+import ch.psi.pshell.epics.DiscretePositioner as DiscretePositioner
+import ch.psi.pshell.epics.GenericChannel as GenericChannel
+import ch.psi.pshell.epics.GenericArray as GenericArray
+import ch.psi.pshell.epics.GenericMatrix as GenericMatrix
+import ch.psi.pshell.epics.Manipulator as Manipulator
+import ch.psi.pshell.epics.Motor as EpicsMotor
+import ch.psi.pshell.epics.Positioner as Positioner
+import ch.psi.pshell.epics.ProcessVariable as ProcessVariable
+import ch.psi.pshell.epics.ReadonlyProcessVariable as ReadonlyProcessVariable
+import ch.psi.pshell.epics.Scaler as Scaler
+import ch.psi.pshell.epics.Scienta as Scienta
+import ch.psi.pshell.epics.Slit as Slit
+import ch.psi.pshell.epics.AreaDetectorSource as AreaDetectorSource
+import ch.psi.pshell.epics.ArraySource as ArraySource
+import ch.psi.pshell.epics.ByteArraySource as ByteArraySource
+import ch.psi.pshell.epics.PsiCamera as PsiCamera
+import ch.psi.pshell.epics.CAS as CAS
+
+import ch.psi.pshell.serial.SerialPortDevice as SerialPortDevice
+import ch.psi.pshell.serial.TcpDevice as TcpDevice
+import ch.psi.pshell.serial.UdpDevice as UdpDevice
+import ch.psi.pshell.serial.SerialPortDeviceConfig as SerialPortDeviceConfig
+import ch.psi.pshell.serial.SocketDeviceConfig as SocketDeviceConfig
+
+import ch.psi.pshell.modbus.ModbusTCP as ModbusTCP
+import ch.psi.pshell.modbus.ModbusUDP as ModbusUDP
+import ch.psi.pshell.modbus.ModbusSerial as ModbusSerial
+import ch.psi.pshell.modbus.AnalogInput as ModbusAI
+import ch.psi.pshell.modbus.AnalogInputArray as ModbusMAI
+import ch.psi.pshell.modbus.AnalogOutput as ModbusAO
+import ch.psi.pshell.modbus.AnalogOutputArray as ModbusMAO
+import ch.psi.pshell.modbus.DigitalInput as ModbusDO
+import ch.psi.pshell.modbus.DigitalInputArray as ModbusMDI
+import ch.psi.pshell.modbus.DigitalOutput as ModbusDO
+import ch.psi.pshell.modbus.DigitalOutputArray as ModbusMDO
+import ch.psi.pshell.modbus.Register  as ModbusReg
+import ch.psi.pshell.modbus.ReadonlyProcessVariable  as ModbusROPV
+import ch.psi.pshell.modbus.ProcessVariable as ModbusPV
+import ch.psi.pshell.modbus.ControlledVariable  as ModbusCB
+import ch.psi.pshell.modbus.ModbusDeviceConfig as ModbusDeviceConfig
+
+import ch.psi.pshell.imaging.Source as Source
+import ch.psi.pshell.imaging.SourceBase as SourceBase
+import ch.psi.pshell.imaging.DirectSource as DirectSource
+import ch.psi.pshell.imaging.RegisterArraySource as RegisterArraySource
+import ch.psi.pshell.imaging.RegisterMatrixSource as RegisterMatrixSource
+import ch.psi.pshell.imaging.ImageListener as ImageListener
+import ch.psi.pshell.imaging.ImageMeasurement as ImageMeasurement
+import ch.psi.pshell.imaging.CameraSource as CameraSource
+import ch.psi.pshell.imaging.ColormapAdapter as ColormapAdapter
+import ch.psi.pshell.imaging.FileSource as FileSource
+import ch.psi.pshell.imaging.MjpegSource as MjpegSource
+import ch.psi.pshell.imaging.Webcam as Webcam
+import ch.psi.pshell.imaging.Filter as Filter
+import ch.psi.pshell.imaging.Utils as ImagingUtils
+import ch.psi.pshell.imaging.Overlay as Overlay
+import ch.psi.pshell.imaging.Overlays as Overlays
+import ch.psi.pshell.imaging.Pen as Pen
+import ch.psi.pshell.imaging.Data as Data
+import ch.psi.pshell.imaging.Colormap as Colormap
+import ch.psi.pshell.imaging.Renderer as Renderer
+
+
+import ch.psi.pshell.plot.Plot as Plot
+import ch.psi.pshell.plot.Plot.AxisId as AxisId
+import ch.psi.pshell.plot.LinePlot.Style as LinePlotStyle
+import ch.psi.pshell.plot.RangeSelectionPlot as RangeSelectionPlot
+import ch.psi.pshell.plot.RangeSelectionPlot.RangeSelectionPlotListener as RangeSelectionPlotListener
+import ch.psi.pshell.plot.LinePlot as LinePlot
+import ch.psi.pshell.plot.MatrixPlot as MatrixPlot
+import ch.psi.pshell.plot.TimePlot as TimePlot
+import ch.psi.pshell.plot.SlicePlot as SlicePlot
+
+import ch.psi.pshell.plot.LinePlotJFree as LinePlotJFree
+import ch.psi.pshell.plot.MatrixPlotJFree as MatrixPlotJFree
+import ch.psi.pshell.plot.TimePlotJFree as TimePlotJFree
+import ch.psi.pshell.plot.SlicePlotDefault as SlicePlotDefault
+
+import ch.psi.pshell.plot.LinePlotSeries as LinePlotSeries
+import ch.psi.pshell.plot.LinePlotErrorSeries as LinePlotErrorSeries
+import ch.psi.pshell.plot.MatrixPlotSeries as MatrixPlotSeries
+import ch.psi.pshell.plot.TimePlotSeries as TimePlotSeries
+import ch.psi.pshell.plot.SlicePlotSeries as SlicePlotSeries
+
+import ch.psi.pshell.scan.ScanBase as ScanBase
+import ch.psi.pshell.scan.LineScan
+import ch.psi.pshell.scan.ContinuousScan
+import ch.psi.pshell.scan.AreaScan
+import ch.psi.pshell.scan.VectorScan
+import ch.psi.pshell.scan.ManualScan
+import ch.psi.pshell.scan.HardwareScan
+import ch.psi.pshell.scan.RegionScan
+import ch.psi.pshell.scan.TimeScan
+import ch.psi.pshell.scan.MonitorScan
+import ch.psi.pshell.scan.BinarySearch
+import ch.psi.pshell.scan.HillClimbingSearch
+import ch.psi.pshell.scan.ScanResult
+import ch.psi.pshell.scan.Otf as Otf
+import ch.psi.pshell.scan.ScanCallbacks as ScanCallbacks
+
+import ch.psi.pshell.crlogic.CrlogicPositioner as CrlogicPositioner
+import ch.psi.pshell.crlogic.CrlogicSensor as CrlogicSensor
+
+import ch.psi.pshell.scan.ScanAbortedException as ScanAbortedException
+
+import ch.psi.pshell.bs.BsScan
+import ch.psi.pshell.bs.Stream as Stream
+import ch.psi.pshell.bs.Provider as Provider
+import ch.psi.pshell.bs.Dispatcher as Dispatcher
+import ch.psi.pshell.bs.Scalar as Scalar
+import ch.psi.pshell.bs.Waveform as Waveform
+import ch.psi.pshell.bs.Matrix as Matrix
+import ch.psi.pshell.bs.StreamCamera as StreamCamera
+import ch.psi.pshell.bs.CameraServer as CameraServer
+import ch.psi.pshell.bs.PipelineServer as PipelineServer
+import ch.psi.pshell.bs.ProviderConfig as ProviderConfig
+import ch.psi.pshell.bs.StreamConfig as StreamConfig
+import ch.psi.pshell.bs.ScalarConfig as ScalarConfig
+import ch.psi.pshell.bs.WaveformConfig as WaveformConfig
+import ch.psi.pshell.bs.MatrixConfig as MatrixConfig
+
+import ch.psi.pshell.detector.DetectorConfig as DetectorConfig
+
+import ch.psi.pshell.ui.App as App
+
+import ch.psi.pshell.scripting.ViewPreference as Preference
+import ch.psi.pshell.scripting.ScriptUtils as ScriptUtils
+import ch.psi.pshell.scripting.ScriptType as ScriptType
+
+from ch.psi.pshell.device.Record import *
+from javax.swing.SwingUtilities import invokeLater, invokeAndWait
+
+import org.jfree.ui.RectangleAnchor as RectangleAnchor
+import org.jfree.ui.TextAnchor as TextAnchor
+
+
+def string_to_obj(o):
+    if is_string(o):
+        o=str(o)
+        if "://" in o:
+            return InlineDevice(o)
+        ret =  get_context().getInterpreterVariable(o)
+        if ret is None:
+            try:
+                return get_context().scriptManager.evalBackground(o).result
+            except:                        
+                return None
+        return ret
+    elif is_list(o):
+        ret = []
+        for i in o:
+            ret.append(string_to_obj(i))
+        return ret
+    return o
+
+def json_to_obj(o):
+    if is_string(o):
+        import json
+        return json.loads(o)
+    elif is_list(o):
+        ret = []
+        for i in o:
+            ret.append(json_to_obj(i))
+        return ret
+    return o
+
+###################################################################################################
+#Scan classes
+###################################################################################################
+
+def __no_args(f):
+    ret = f.func_code.co_argcount
+    return (ret-1) if type(f)==PyMethod else ret
+
+def __before_readout(scan, pos):
+    try:
+        if scan.before_read != None:
+            args = __no_args(scan.before_read)
+            if   args==0: scan.before_read()
+            elif args==1: scan.before_read(pos.tolist())
+            elif args==2: scan.before_read(pos.tolist(), scan)
+    except AttributeError:
+        pass
+
+def __after_readout(scan, record):
+    try:
+        if scan.after_read != None:
+            args = __no_args(scan.after_read)
+            if   args==0: scan.after_read()
+            elif args==1: scan.after_read(record)
+            elif args==2: scan.after_read(record, scan)
+    except AttributeError:
+        pass
+
+def __before_pass(scan, num_pass):
+    try:
+        if scan.before_pass != None:
+            args = __no_args(scan.before_pass)
+            if   args==0:scan.before_pass()
+            elif args==1:scan.before_pass(num_pass)
+            elif args==2:scan.before_pass(num_pass, scan)
+    except AttributeError:
+        pass
+
+def __after_pass(scan, num_pass):
+    try:
+        if scan.after_pass != None:
+            args = __no_args(scan.after_pass)
+            if   args==0:scan.after_pass()
+            elif args==1:scan.after_pass(num_pass)
+            elif args==2:scan.after_pass(num_pass, scan)
+    except AttributeError:
+        pass
+
+def __before_region(scan, num_region):
+    try:
+        if scan.before_region != None:
+            args = __no_args(scan.before_region)
+            if   args==0:scan.before_region()
+            elif args==1:scan.before_region(num_region)
+            elif args==2:scan.before_region(num_region, scan)
+    except AttributeError:
+        pass
+
+class LineScan(ch.psi.pshell.scan.LineScan):
+    def onBeforeReadout(self, pos): __before_readout(self, pos)
+    def onAfterReadout(self, rec): __after_readout(self, rec)
+    def onBeforePass(self, num): __before_pass(self, num)
+    def onAfterPass(self, num): __after_pass(self, num)
+
+class AreaScan(ch.psi.pshell.scan.AreaScan):
+    def onBeforeReadout(self, pos): __before_readout(self, pos)
+    def onAfterReadout(self, rec): __after_readout(self, rec)
+    def onBeforePass(self, num): __before_pass(self, num)
+    def onAfterPass(self, num): __after_pass(self, num)
+
+class RegionScan(ch.psi.pshell.scan.RegionScan):
+    def onBeforeReadout(self, pos): __before_readout(self, pos)
+    def onAfterReadout(self, rec): __after_readout(self, rec)
+    def onBeforePass(self, num): __before_pass(self, num)
+    def onAfterPass(self, num): __after_pass(self, num)
+    def onBeforeRegion(self, num): __before_region(self,num)
+
+class VectorScan(ch.psi.pshell.scan.VectorScan):
+    def onBeforeReadout(self, pos): __before_readout(self, pos)
+    def onAfterReadout(self, rec): __after_readout(self, rec)
+    def onBeforePass(self, num): __before_pass(self, num)
+    def onAfterPass(self, num): __after_pass(self, num)
+
+class ContinuousScan(ch.psi.pshell.scan.ContinuousScan):
+    def onBeforeReadout(self, pos): __before_readout(self, pos)
+    def onAfterReadout(self, rec): __after_readout(self, rec)
+    def onBeforePass(self, num): __before_pass(self, num)
+    def onAfterPass(self, num): __after_pass(self, num)
+
+class TimeScan(ch.psi.pshell.scan.TimeScan):
+    def onBeforeReadout(self, pos): __before_readout(self, pos)
+    def onAfterReadout(self, rec): __after_readout(self, rec)
+    def onBeforePass(self, num): __before_pass(self, num)
+    def onAfterPass(self, num): __after_pass(self, num)
+
+class MonitorScan(ch.psi.pshell.scan.MonitorScan):
+    def onBeforeReadout(self, pos): __before_readout(self, pos)
+    def onAfterReadout(self, rec): __after_readout(self, rec)
+    def onBeforePass(self, num): __before_pass(self, num)
+    def onAfterPass(self, num): __after_pass(self, num)
+
+class BsScan(ch.psi.pshell.bs.BsScan):
+    def onBeforeReadout(self, pos): __before_readout(self, pos)
+    def onAfterReadout(self, rec): __after_readout(self, rec)
+    def onBeforePass(self, num): __before_pass(self, num)
+    def onAfterPass(self, num): __after_pass(self, num)
+
+class ManualScan (ch.psi.pshell.scan.ManualScan):
+    def __init__(self, writables, readables, start = None, end = None, steps = None, relative = False, dimensions = None, **pars):
+        ch.psi.pshell.scan.ManualScan.__init__(self, writables, readables, start, end, steps, relative)
+        self._dimensions = dimensions
+        processScanPars(self, pars)
+
+    def append(self,setpoints, positions, values, timestamps=None):
+        ch.psi.pshell.scan.ManualScan.append(self, to_array(setpoints), to_array(positions), to_array(values), None if (timestamps is None) else to_array(timestamps))
+
+    def getDimensions(self):
+        if self._dimensions == None:
+            return ch.psi.pshell.scan.ManualScan.getDimensions(self)
+        else:
+            return self._dimensions
+
+class BinarySearch(ch.psi.pshell.scan.BinarySearch):
+    def onBeforeReadout(self, pos): __before_readout(self, pos)
+    def onAfterReadout(self, rec): __after_readout(self, rec)
+
+class HillClimbingSearch(ch.psi.pshell.scan.HillClimbingSearch):
+    def onBeforeReadout(self, pos): __before_readout(self, pos)
+    def onAfterReadout(self, rec): __after_readout(self, rec)
+
+def processScanPars(scan, pars):
+    scan.before_read = pars.pop("before_read",None)
+    scan.after_read = pars.pop("after_read",None)
+    scan.before_pass = pars.pop("before_pass",None)
+    scan.after_pass =  pars.pop("after_pass",None)
+    scan.before_region= pars.pop("before_region",None)
+    scan.setPlotTitle(pars.pop("title",None))
+    scan.setHidden(pars.pop("hidden",False))
+    scan.setSettleTimeout (pars.pop("settle_timeout",ScanBase.getScansSettleTimeout()))
+    scan.setUseWritableReadback (pars.pop("use_readback",ScanBase.getScansUseWritableReadback()))
+    scan.setInitialMove(pars.pop("initial_move",ScanBase.getScansTriggerInitialMove()))
+    scan.setParallelPositioning(pars.pop("parallel_positioning",ScanBase.getScansParallelPositioning()))
+    scan.setAbortOnReadableError(pars.pop("abort_on_error",ScanBase.getAbortScansOnReadableError()))
+    scan.setRestorePosition (pars.pop("restore_position",ScanBase.getRestorePositionOnRelativeScans()))
+    scan.setCheckPositions(pars.pop("check_positions",ScanBase.getScansCheckPositions()))
+    scan.setMonitors(to_list(string_to_obj(pars.pop("monitors",None))))
+    scan.setSnaps(to_list(string_to_obj(pars.pop("snaps",None))))
+    scan.setDiags(to_list(string_to_obj(pars.pop("diags",None))))
+    scan.setMeta(pars.pop("meta",None))
+    get_context().setCommandPars(scan, pars)
+
+
+
+###################################################################################################
+#Simple EPICS Channel abstraction
+###################################################################################################
+
+def create_channel(name, type=None, size=None):
+    return Epics.newChannel(name, Epics.getChannelType(type), size)
+
+#Not using finalizer: closing channels in garbage collection generate errors
+class Channel(java.beans.PropertyChangeListener, Writable, Readable, DeviceBase):
+    def __init__(self, channel_name, type = None, size = None, callback=None, alias = None, monitored=None, name = None):
+        """ Create an object that encapsulates an Epics PV connection.
+        Args:
+            channel_name(str):name of the channel
+            type(str, optional): type of PV. By default gets the PV standard field type.
+                Scalar values: 'b', 'i', 'l', 'd', 's'.
+                Array values: '[b', '[i,', '[l', '[d', '[s'.
+            size(int, optional): the size of the channel
+            callback(function, optional): The monitor callback.
+            alias(str): name to be used on scans.
+        """
+        super(DeviceBase, self).__init__(name if (name is not None) else channel_name.replace(":","_").replace(".","_"))
+        self.channel = create_channel(channel_name, type, size)
+        self.callback = callback
+        self._alias = alias
+        if monitored is not None:self.setMonitored(monitored)
+        self.initialize()
+
+    def get_channel_name(self):
+        """Return the name of the channel.
+        """
+        return self.channel.name
+
+    def get_size(self):
+        """Return the size of the channel.
+        """
+        return self.channel.size
+
+    def set_size(self, size):
+        """Set the size of the channel.
+        """
+        self.channel.size = size
+
+    def is_connected(self):
+        """Return True if channel is connected.
+        """
+        return self.channel.connected
+
+    def doSetMonitored(self, value):
+        self.channel.monitored = value
+        if (value):
+            self.channel.addPropertyChangeListener(self)
+        else:
+            self.channel.removePropertyChangeListener(self)    
+        
+        
+    def is_monitored(self):
+        """Return True if channel is monitored
+        """
+        return self.channel.monitored
+
+    def set_monitored(self, value):
+        """Set a channel monitor to trigger the callback function defined in the constructor.
+        """
+        self.setMonitored(value)
+
+    def propertyChange(self, pce):
+        if pce.getPropertyName() == "value":
+            value=pce.getNewValue()
+            self.setCache(value, None)        
+            if self.callback is not None:
+                self.callback(value)
+
+    def put(self, value, timeout=None):
+        """Write to channel and wait value change. In the case of a timeout throws a TimeoutException.
+        Args:
+            value(obj): value to be written
+            timeout(float, optional): timeout in seconds. If none waits forever.
+        """
+        if (timeout==None):
+            self.channel.setValue(value)
+        else:
+            self.channel.setValueAsync(value).get(int(timeout*1000), java.util.concurrent.TimeUnit.MILLISECONDS)
+        self.setCache(value, None)
+
+    def putq(self, value):
+        """Write to channel and don't wait.
+        """
+        self.channel.setValueNoWait(value)
+
+    def get(self, force = False):
+        """Get channel value.
+        """
+        ret = self.channel.getValue(force)
+        self.setCache(ret, None)
+        return ret
+
+    def wait_for_value(self, value, timeout=None, comparator=None):
+        """Wait channel to reach a value, using a given comparator. In the case of a timeout throws a TimeoutException.
+        Args:
+            value(obj): value to be verified.
+            timeout(float, optional): timeout in seconds. If None waits forever.
+            comparator (java.util.Comparator, optional). If None, uses Object.equals.
+        """
+        if comparator is None:
+            if timeout is None:
+                self.channel.waitForValue(value)
+            else:
+                self.channel.waitForValue(value, int(timeout*1000))
+            self.setCache(value, None)
+        else:
+            if timeout is None:
+                self.channel.waitForValue(value, comparator)
+            else:
+                self.channel.waitForValue(value, comparator, int(timeout*1000))
+
+    def doUpdate(self):
+        self.get()
+        
+    def close(self):
+        """Close the channel.
+        """
+        Epics.closeChannel(self.channel)
+
+    def setAlias(self, alias):
+        self._alias = alias
+
+    def getAlias(self):
+        return self._alias if self._alias else self.getName()
+
+    def write(self, value):
+        self.put(value)
+
+    def read(self):
+        return self.get()
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, *args):
+        self.close()

script/Lib/builtin_utils.py

@@ -0,0 +1,174 @@
+import sys
+import time
+import math
+import os.path
+from operator import add, mul, sub, truediv
+from time import sleep
+from array import array
+import jarray
+
+import java.lang.Class as Class
+import java.lang.Object as Object
+import java.lang.System as System
+import java.beans.PropertyChangeListener
+import java.util.concurrent.Callable
+import java.util.List
+import java.util.ArrayList
+import java.lang.reflect.Array
+import java.lang.Thread
+import java.awt.image.BufferedImage as BufferedImage
+import java.awt.Color as Color
+import java.awt.Point as Point
+import java.awt.Dimension as Dimension
+import java.awt.Rectangle as Rectangle
+import java.awt.Font as Font
+import org.python.core.PyArray as PyArray
+import org.python.core.PyFunction as PyFunction
+import org.python.core.PyMethod as PyMethod
+import org.python.core.PyGenerator as PyGenerator
+
+import java.lang.Boolean
+import java.lang.Integer
+import java.lang.Float
+import java.lang.Double
+import java.lang.Short
+import java.lang.Byte
+import java.lang.Long
+import java.lang.String
+
+import ch.psi.pshell.core.Context
+import ch.psi.pshell.scripting.ScriptUtils as ScriptUtils
+import ch.psi.utils.Convert as Convert
+import ch.psi.utils.Arr as Arr
+
+
+###################################################################################################
+#Type conversion and checking
+###################################################################################################
+
+def to_array(obj, type = None, primitive = True):
+    """Convert Python list to Java array.
+
+    Args:
+        obj(list): Original data.
+        type(str): array type 'b' = byte, 'h' = short, 'i' = int, 'l' = long,  'f' = float, 'd' = double,
+                              'c' = char, 'z' = boolean, 's' = String,  'o' = Object
+    Returns:
+        Java array.
+    """
+    if obj is None:
+        return None
+    if type is None:
+        type = 'o'
+        enforceArrayType=False
+    else:
+        enforceArrayType=True
+    if type[0] == '[':
+        type = type[1:]        
+    element_type = ScriptUtils.getPrimitiveType(type) if primitive else ScriptUtils.getType(type)
+
+    def convert_1d_array(obj):
+        try:
+            if primitive:
+                #If primitive, first try converting with jarray.array
+                return jarray.array(obj,type)
+        except:
+            pass    
+       
+        if type == 'c':
+            ret = java.lang.reflect.Array.newInstance(element_type,len(obj))
+            for i in range(len(obj)): ret[i] = chr(obj[i])
+            return ret
+        if type == 'z':
+            ret = java.lang.reflect.Array.newInstance(element_type,len(obj))
+            for i in range(len(obj)):
+                ret[i]= True if obj[i] else False
+            return ret
+        if type == 'o':
+            ret = java.lang.reflect.Array.newInstance(element_type,len(obj))
+            for i in range(len(obj)):
+                ret[i]= obj[i] 
+            return ret
+        if type == "s":
+            return Convert.toStringArray(obj)   
+        if primitive:   
+            ret = Convert.toPrimitiveArray(obj, element_type)  
+        else:
+            ret = java.lang.reflect.Array.newInstance(element_type,len(obj))
+            for i in range(len(obj)): ret[i] = Convert.toType(obj[i],element_type)
+        return ret
+                
+    if isinstance(obj,PyArray):
+        if enforceArrayType:
+            if Arr.getComponentType(obj) != element_type:
+                rank = Arr.getRank(obj)
+                if (rank== 1):
+                    obj=convert_1d_array(obj)
+                elif (rank>1):  
+                    pars, aux = [element_type], obj
+                    for i  in range(rank):
+                        pars.append(len(aux))
+                        aux = aux[0]
+                    ret = java.lang.reflect.Array.newInstance(*pars)    
+                    for i in range(len(obj)):
+                        ret[i]=to_array(obj[i], type)                        
+                    obj = ret
+    elif is_list(obj):        
+        if type=='o':
+            ret = java.lang.reflect.Array.newInstance(element_type, len(obj))
+            for i in range (len(obj)):
+                if is_list(obj[i]) or isinstance(obj[i],PyArray):
+                    ret[i] = to_array(obj[i],type)
+                else:
+                    ret[i] = obj[i]
+            obj=ret
+        elif len(obj)>0 and (is_list(obj[0]) or isinstance(obj[0],PyArray)):
+            pars, aux = [element_type], obj
+            while len(aux)>0 and (is_list(aux[0]) or isinstance(aux[0],PyArray)):
+                pars.append(len(aux))
+                aux = aux[0]
+            pars.append(0)
+            ret = java.lang.reflect.Array.newInstance(*pars)
+            for i in range(len(obj)):
+                ret[i]=to_array(obj[i], type)
+            obj=ret
+        else:
+         obj= convert_1d_array(obj)
+    return obj
+
+def to_list(obj):
+    """Convert an object into a Python List.
+
+    Args:
+        obj(tuple or array or List): Original data.
+    
+    Returns:
+        List.
+    """
+    if obj is None:
+        return None
+    if isinstance(obj,tuple) or isinstance(obj,java.util.List) :
+        return list(obj)
+    #if isinstance(obj,PyArray):
+    #    return obj.tolist()
+    if not isinstance(obj,list):
+        return [obj,]
+    return obj
+
+def is_list(obj):
+    return isinstance(obj,tuple) or isinstance(obj,list) or isinstance (obj, java.util.List)
+
+def is_string(obj):
+    return (type(obj) is str) or (type(obj) is unicode)
+
+def is_interpreter_thread():
+    return java.lang.Thread.currentThread().name == "MainThread"
+
+###################################################################################################
+#Access to context singleton
+###################################################################################################
+def get_context():
+    return ch.psi.pshell.core.Context.getInstance()
+
+
+

script/Lib/ijutils.py

@@ -0,0 +1,782 @@
+####################################################################################################
+#  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 ImagingUtils
+from startup import get_context, expand_path, is_string
+import java.awt.image.BufferedImage as BufferedImage
+import jarray
+import os
+
+import ij.IJ as IJ
+import ij.ImageJ as ImageJ
+import ij.WindowManager as WindowManager
+import ij.ImagePlus as ImagePlus
+import ij.ImageStack as ImageStack
+import ij.Prefs as Prefs
+import ij.io.FileSaver as FileSaver
+import ij.io.Opener as Opener
+from ij.gui import Roi
+
+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 = None):    
+    """
+    image: file name or BufferedImage
+    """    
+    if is_string(image):
+        try:
+            file = expand_path(image)
+        except:
+            pass
+        try:
+            image = ImagingUtils.newImage(file)
+        except:
+            #try loading from assembly
+            image = get_context().setup.getAssemblyImage(image)
+        if title is None:
+            title = os.path.basename(file)
+    return ImagePlus("img" if title is None else 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, metadata={}):
+    """
+    Saves image or stack
+    If parameters omitted, saves image again in same location, with same format.
+    """
+    fs = FileSaver(ip)
+
+    info = ""
+    for key,val in metadata.items():
+        info = info + ("\n" if len(info)>0 else "") + str(key) + ": " + str(val)        
+    ip.setProperty("Info", info)
+
+    if path == None: fs.save()
+    else:
+        try:
+            path = 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 open_image(path, index=1):
+    """
+    Open file using ij.io,Opener
+    """
+    try:
+        path = expand_path(path)
+    except:
+        pass  
+    opener = Opener()
+    return opener.openImage(path, index)
+
+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 get_ip_array(ip):
+    """
+    Returns data array of ImagePlus
+    """
+    if type(ip.getProcessor()) == FloatProcessor:
+        return ip.getProcessor().getFloatArray()
+    else:
+        return ip.getProcessor().getIntArray()
+
+
+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 measurements
+###################################################################################################
+
+def get_measurement(ip, measurement):
+    """
+    Return image measurement:
+    "Area", "Mean", "StdDev", "Mode", "Min", "Max", "X", "Y", "XM", "YM", "Perim.", "BX", "BY",
+    "Width", "Height", "Major", "Minor", "Angle", "Circ.", "Feret", "IntDen", "Median", "Skew",
+    "Kurt", "%Area", "RawIntDen", "Ch", "Slice", "Frame", "FeretX", "FeretY", "FeretAngle",
+    "MinFeret", "AR", "Round", "Solidity", "MinThr" or "MaxThr"
+    """
+    return IJ.getValue(ip,measurement)
+
+###################################################################################################
+#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(count, iterations, 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, duplicate=True, title = None):
+    stack = Concatenator().concatenate(ip_list, duplicate)
+    if title is not None:
+        stack.setTitle(title)
+    return stack
+
+def open_stack(path_list, title=None):
+    """
+    Open list of files as a stack using ij.io,Opener
+    """
+    ip_list = []
+    for path in path_list:
+        ip_list.append(open_image(path))
+    return  create_stack(ip_list, duplicate=False, title = "stack" if title is None else title)
+
+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
+    
+    
+ 
+###############################################################################
+# ImagePlus list operations
+###############################################################################
+
+def integrate_ips(ips, as_float=True):    
+    """
+    Integrate list if ImagePlus with the same size.
+    """ 
+    aux = None
+    for i in range(len(ips)):
+        if i==0:        
+            img_type = "float" if as_float else "short"
+            aux = new_image(ips[i].width, ips[i].height, image_type=img_type, title = "sum", fill_color = None)
+        op_image(aux, ips[i], "add", float_result=as_float, in_place=True)    
+    return aux
+
+def average_ips (ips, roi=None, as_float=True):   
+    """
+    Average list if ImagePlus with the same size.
+    """ 
+    aux = integrate_ips(ips, as_float)     
+    op_const(aux, "divide", float(len(ips)), in_place=True)    
+    return aux

script/Lib/jeputils.py

@@ -0,0 +1,239 @@
+###################################################################################################
+# 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') 
+
+
+#In principle just add JEP jar and library to the extensions folder.
+#
+#Alternatively on Linux:
+#   Python 2:
+#       - Add <python home>/lib/python3.X/site-packages/jep to LD_LIBRARY_PATH
+#       - Add <python home>/lib/python3.X/site-packages/jep/jep-X.X.X.jar to the class path
+#
+#Python3:
+#       - Add JEP library folder to LD_LIBRARY_PATH
+#       - If using OpenJDK, add also python <python home>/lib folder to LD_LIBRARY_PATH			
+#	- Set LD_PRELOAD=<python home>/lib/libpython3.5m.so
+
+
+import sys
+import os
+import jep.Jep
+import jep.SharedInterpreter
+import jep.NDArray
+import java.lang.Thread
+import org.python.core.PyArray as PyArray
+import java.lang.String as String
+import java.util.List
+import java.util.Map 
+import java.util.HashMap 
+import ch.psi.pshell.scripting.ScriptUtils as ScriptUtils
+
+
+from startup import to_array, get_context, _get_caller, Convert, Arr
+
+__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.SharedInterpreter()
+    #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()")
+
+    #Import reload on Python 3
+    j.eval("try:\n" + 
+           "    reload  # Python 2.7\n" +
+           "except NameError:\n" + 
+           "    try:\n" +
+           "        from importlib import reload  # Python 3.4+\n" +
+           "    except ImportError:\n" +
+           "        from imp import reload  # Python 3.0 - 3.3\n")
+
+def __print_stdout():
+    j=__get_jep()
+    output = None
+    err = None
+    try:
+        output = j.getValue("sys.stdout.str")
+        err = j.getValue("sys.stderr.str")
+        j.eval("sys.stdout.clear()")
+        j.eval("sys.stderr.clear()")
+    except:
+        pass
+    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 = [], kwargs = {}, reload=False):
+    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:
+        if reload:
+            eval_jep("import " + module)
+            eval_jep("_=reload(" + module+")")
+        eval_jep("from " + module + " import " + function + " as " + f)    
+        if (kwargs is not None) and (len(kwargs)>0):
+            #invoke with kwargs only available in JEP>3.8
+            hm=java.util.HashMap()
+            hm.update(kwargs)            
+            #The only way to get the overloaded method...
+            m = j.getClass().getMethod("invoke", [String, ScriptUtils.getType("[o"), java.util.Map])
+            ret = m.invoke(j, [f, to_array(args,'o'), hm])
+        else:
+            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):   
+    if (not isinstance(data, PyArray)) or (type is not None):
+        data = to_array(data,'d' if type is None else type)
+    return jep.NDArray(data, dimensions)    
+
+#recursivelly converts all NumPy arrays to Java arrys
+def rec_from_npa(obj):
+    if isinstance(obj, jep.NDArray):
+        ret = obj.data
+        if len(obj.dimensions)>1:
+            ret=Convert.reshape(ret, obj.dimensions)
+        return ret
+    if isinstance(obj, java.util.List) or isinstance(obj,tuple) or isinstance(obj,list):
+        ret=[]
+        for i in range(len(obj)):            
+            ret.append(rec_from_npa(obj[i]))
+        if isinstance(obj,tuple):
+            return type(ret)
+        return ret
+    if isinstance(obj, java.util.Map) or isinstance(obj,dict):
+        ret = {} if isinstance(obj,dict) else java.util.HashMap()
+        for k in obj.keys():            
+            ret[k] = rec_from_npa(obj[k])    
+        return ret    
+    return obj
+
+#recursivelly converts all Java arrays to NumPy arrys
+def rec_to_npa(obj):
+    if isinstance(obj, PyArray):
+        dimensions = Arr.getShape(obj)
+        if len(dimensions)>1:
+            obj = Convert.flatten(obj)
+        return to_npa(obj, dimensions = dimensions)
+    if isinstance(obj, java.util.List) or isinstance(obj,tuple) or isinstance(obj,list):
+        ret=[]
+        for i in range(len(obj)):            
+            ret.append(rec_to_npa(obj[i]))
+        if isinstance(obj,tuple):
+            return tuple(ret)
+        return ret
+    if isinstance(obj, java.util.Map) or isinstance(obj,dict):        
+        ret = {} if isinstance(obj,dict) else java.util.HashMap()
+        for k in obj.keys():            
+            ret[k] = rec_to_npa(obj[k])    
+        return ret    
+    return obj  
+
+def call_py(module, function, reload_function, *args, **kwargs):      
+    """
+    Calls a CPython function recursively crecursively converting Java arrays in arguments to NumPy,
+    and  NumPy arrays in return values to Java arrays.
+    """
+    ret =  call_jep(module, function, rec_to_npa(args), rec_to_npa(kwargs), reload=reload_function)
+    return rec_from_npa(ret)
+    
+def import_py(module, function):  
+    """
+    Adds a CPython function  to globals, creating a wrapper call to JEP, with 
+    recurvive convertion of Java arrays in arguments to NumPy arrays,
+    and  NumPy arrays in return values to Java arrays.
+    """
+    def jep_wrapper(*args, **kwargs):
+        reload_function =  jep_wrapper.reload
+        jep_wrapper.reload = False
+        return call_py(module, function, reload_function, *args, **kwargs)
+    jep_wrapper.reload=True
+    _get_caller().f_globals[function] = jep_wrapper   
+    

script/Lib/mathutils.py

@@ -0,0 +1,681 @@
+###################################################################################################
+#  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: (a, b, 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
+
+def fit_gaussian_exp_bkg(y, x, start_point = None, weights = None):
+    """Fits data into a gaussian with exponential background.
+       f(x) = a * math.exp(-(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: (a,b , 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[len(x)/2]
+        #com = 11.9
+        amp = max(y) - off
+        sigma = trapz([v-off for v in y], x) / (amp*math.sqrt(2*math.pi))                 
+        start_point = [1, 1, 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))))
+                bkg=math.exp(-(x[i]/b))
+                model = a*bkg + c * v 
+                value.setEntry(i, model)                                    
+                jacobian.setEntry(i, 0, bkg)               # derivative with respect to p0 = a                        
+                jacobian.setEntry(i, 1, a*x[i]*bkg/math.pow(b, 2))    # 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
+
+###################################################################################################
+#Functions
+###################################################################################################
+
+class GaussianOffset(UnivariateFunction):
+    def __init__(self, offset, normalization, mean_value, sigma):
+        self.gaussian = Gaussian(normalization, mean_value, sigma)
+        self.offset = offset
+    def value(self,x):
+        return self.gaussian.value(x) + self.offset
+
+class GaussianLinear(UnivariateFunction):
+    def __init__(self, a,b, normalization, mean_value, sigma):
+        self.gaussian = Gaussian(normalization, mean_value, sigma)
+        self.a = a
+        self.b = b
+    def value(self,x):
+        return self.gaussian.value(x) + self.a * x + self.b
+        
+class GaussianExpBkg(UnivariateFunction):
+    def __init__(self, a, b, normalization, mean_value, sigma):
+        self.gaussian = Gaussian(normalization, mean_value, sigma)
+        self.a = a
+        self.b = b
+    def value(self,x):
+        return self.gaussian.value(x) + self.a * math.exp(-(x/self.b))
+
+###################################################################################################
+#Least squares
+###################################################################################################
+
+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.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/rsync.py

@@ -0,0 +1,149 @@
+####################################################################################################
+#  Utilities for synchronizing folders with rsync
+#  On RH7  (not SL6)
+#  Change permission of the account, otherwise SSH keys are not accepted:
+#       ~/.ssh    from drwxr-S--- to drwx----
+#       ~ :       from drwxrws--- to drwxr-s---
+####################################################################################################
+
+import sys
+import os
+import os.path
+import shutil
+import ch.psi.utils.Sys
+
+from startup import exec_cmd, log
+
+RSYNC_GENERATE_USER_KEY = True
+XTERM = "/opt/X11/bin/xterm" if ch.psi.utils.Sys.getOSFamily().name()=="Mac" else "xterm"
+
+def rsync(src, dest, key):
+    #cmd = 'rsync -e "ssh -i ' + key + ' -o LogLevel=quiet" --chmod=ug=rwx --verbose --modify-window=1 --times --recursive ' + src + ' ' + dest
+    #ret = exec_cmd(cmd)
+    cmd = 'rsync -e "ssh -i ' + key + '" --chmod=ug=rwx --verbose --modify-window=1 --times --recursive ' + src + ' ' + dest
+    ret = exec_cmd(cmd, False)
+    lines = ret.split("\n")
+    lines =  filter(lambda x: x != "", lines)
+    if len(lines)<3:
+        print "Invalid return from rsync:\n", ret
+        raise Exception ("Invalid format")
+    #files = lines[1:-2]
+    files = []
+    head,tail=os.path.split(src)
+    for l in lines:
+        f = os.path.join(head,l)
+        if os.path.exists(f):
+            files.append(f)
+    try:
+        stats = lines[-2].replace(",", "").replace(".", "")
+        stats = [int(s) for s in stats.split() if s.isdigit()]
+        bytes_sent, bytes_received = stats[0], stats[1]
+    except:
+        print "Invalid statistics from rsync:\n", ret
+        bytes_sent, bytes_received = None, None
+
+    return files, bytes_sent, bytes_received
+
+def sync_user_data(user, src, dest, host= "localhost", remove_local_folder=False, remove_local_files=False, do_log=True, do_print=True):
+    try:
+        if do_log:
+            log("Start synchronizing %s to %s:%s" % (src, user, dest), False )
+        key = os.path.expanduser("~/.ssh/" + ("ke" if RSYNC_GENERATE_USER_KEY else "id_rsa"))
+        if not os.path.isfile(key):
+            raise Exception ("Invalid key file")
+        dest = "'" + dest.replace(" ", "\ ") + "'"
+        dest = user + "@" + host + ":" + dest
+        files, bytes_sent, bytes_received = rsync(src,dest,key)
+        msg = "Transferred " + str(bytes_sent) + " bytes to " + user + ": "
+        for f in files:
+            msg = msg + "\n" + f
+        if do_log:
+            log(msg, False)
+        if do_print:
+            print msg
+        if remove_local_folder:
+            if do_log:
+                log("Removing folder: " + src)
+            shutil.rmtree(src)
+        elif remove_local_files:
+            for f in files:
+                if not os.path.samefile(f, src):
+                    if os.path.isfile(f):
+                        if do_log:
+                            log("Removing file: " + f)
+                        os.remove(f)
+                    elif os.path.isdir(f):
+                        if do_log:
+                            log("Removing folder: " + f)
+                        shutil.rmtree(f)
+
+    except:
+        msg = "Error transferring user data to " + user + ": " + str(sys.exc_info()[1])
+        if do_log:
+            log(msg, False)
+        if do_print:
+            print >> sys.stderr, msg
+    return msg
+
+def remove_user_key(do_print=True):
+    cmd = "rm ~/.ssh/ke;"
+    cmd = cmd + "rm ~/.ssh/ke.pub"
+    ret = exec_cmd(cmd, False)     
+    if do_print:
+        if not ret.strip():
+            ret = "Success removing ssh keys"
+        print ret    
+
+def reset_user_key(do_print=True):
+    remove_user_key(do_print)
+    cmd = "ssh-keygen -N '' -f ~/.ssh/ke -t rsa;"
+    ret = exec_cmd(cmd)
+    if do_print:
+        print ret
+
+def authorize_user(user, aux_file = os.path.expanduser("~/.rsync.tmp"), fix_permissions=True, do_print=True):
+    if (os.path.isfile(aux_file)):
+        os.remove(aux_file)
+    with open(aux_file, "w") as fh:
+        fh.write("Cannot access file: " + aux_file)
+    os.chmod(aux_file, 0o777)
+
+    success_msg = 'Success transfering authorization key for: ' + user
+    cmd =  'echo Authorizing: ' + user + ";"
+    cmd = cmd + 'echo Invalid user or password > ' + aux_file + ";"
+    cmd = cmd + "export PK_SUCCESS=FAILURE;"
+    if RSYNC_GENERATE_USER_KEY:
+        reset_user_key(do_print)
+        cmd = cmd + "export PK=`cat ~/.ssh/ke.pub`;"
+    else:
+        cmd = cmd + "export PK=`cat ~/.ssh/id_rsa.pub`;"
+    cmd = cmd + 'su - ' + user + ' bash -c "'
+    cmd = cmd + 'echo $PK >> .ssh/authorized_keys;'
+    #cmd = cmd + 'sort .ssh/authorized_keys | uniq > .ssh/authorized_keys.uniq;'
+    #cmd = cmd + 'mv .ssh/authorized_keys.uniq .ssh/authorized_keys;'
+    if fix_permissions:
+        cmd = cmd + 'chmod g-w ~' + ";"
+    cmd = cmd + 'echo ' + success_msg + ";"
+    cmd = cmd + 'echo ' + success_msg + " > " + aux_file + ";"
+    cmd = cmd + '"'
+    #xterm_options = '-hold -T "Authentication" -into 44040199' #Get Winfow ID with 'wmctrl -lp'
+    xterm_options = '-T "Authentication" -fa monaco -fs 14 -bg black -fg green -geometry 80x15+400+100'
+    try:
+        ret = exec_cmd(XTERM + " " + xterm_options + " -e '" + cmd + "'")
+        with open (aux_file, "r") as myfile:
+            ret=myfile.read()
+        #;if [ "$depth" -eq "1" ]; then echo ' + success_msg + '; fi')
+        if not success_msg in ret:
+            raise Exception (ret)
+    except:
+        if RSYNC_GENERATE_USER_KEY:
+            remove_user_key(do_print)
+        raise  Exception ("Error authenticating user: " + str(sys.exc_info()[1]))
+    finally:
+        if (os.path.isfile(aux_file)):
+            os.remove(aux_file)
+    return ret
+
+def is_authorized():
+    key = os.path.expanduser("~/.ssh/" + ("ke" if RSYNC_GENERATE_USER_KEY else "id_rsa"))
+    return os.path.isfile(key)

script/Lib/sessions.py

@@ -0,0 +1,348 @@
+from startup import get_context, set_exec_pars
+import ch.psi.utils.SciCat as SciCat
+import java.lang.Boolean
+
+def _sm():
+    return get_context().sessionManager
+
+
+def session_start(name, metadata=None):
+    """ Starts new session. If a session os open, completes it first.
+
+    Args:
+         name(str): Session name.
+         metadata(dict): Map of initial metadata parameters
+                         If None(Default) use the default metadata definition. 
+
+    Returns:
+        session id (int)     
+    """
+    set_exec_pars(open=False)
+    return _sm().start(name, metadata)
+
+def session_complete():
+    """ Completes current session, if started.         
+    """
+    set_exec_pars(open=False)
+    return _sm().stop()
+
+def session_pause():
+    """ Pauses current session, if started.         
+    """
+    return _sm().pause()    
+
+def session_resume():
+    """ Resumes current session, if paused.         
+    """
+    return _sm().resume()    
+
+def session_cancel():
+    """ Cancels current session, if started and empty (no generated data).      
+    """
+    return _sm().cancel()        
+
+def session_restart(id):
+    """ Reopens a completed if not yet archived and if belongs to the same user.
+
+    Args:
+         id(int): Session id.
+    """
+    return _sm().restart(id)  
+
+def session_move(origin, files, dest):
+    """ Moves a list of run files (relative to root) to another session.
+        Sessions must not be archived and belong to the same user.
+
+    Args:
+        origin(int): Origin session id.
+        files(list): file names
+        dest(int): Destination session id.
+    """
+    return _sm().move(origin, files, dest)  
+
+def session_detach(name, id, files):
+    """ Detaches a list of run files (relative to root) to a new session.
+        Session must not be archived and  belong to the same user.
+
+    Args:
+        name(str): Name of new session.
+        id(int): Session id.
+        files(list): file names        
+
+    Returns:
+        New session id (int)  
+    """
+    return _sm().detach(name, id, files)  
+
+
+def session_create(name, files, metadata=None, root=None):
+    """ Create a session from existing data files.
+
+    Args:
+        name(str): Name of new session.
+        files(list): file names relative to root       
+        metadata(dict): Map of initial metadata parameters
+                         If None(Default) use the default metadata definition. 
+        root(str): data root path. If None(Default) uses default data path.
+
+    Returns:
+        New session id (int)  
+    """
+    return _sm().create(name, files, metadata, root)  
+
+def session_id():
+    """ Returns current session id (0 if no session is started).
+
+    Returns:
+        session id (int)       
+    """
+    return _sm().getCurrentSession()
+
+
+def session_name():
+    """ Returns current session name ("unknown" if no session is started) 
+
+    Returns:
+        session name(str)       
+    """
+    return _sm().getCurrentName()
+
+def session_started():
+    """ Returns true if a session is started.
+
+    Returns:
+        bool       
+    """
+    return _sm().isStarted()
+            
+def session_paused():
+    """ Returns true if current session is paused.
+
+    Returns:
+        bool    
+    """
+    return _sm().isPaused()
+
+        
+def session_add_file(path):
+    """ Adds additional file to session, if started. 
+
+    Args:
+         path(str): Relative to data path or absolute.
+    """
+    return _sm().addAdditionalFile(path)
+
+
+def session_ids():
+    """ Returns list of completed sessions.
+
+    Returns:
+        list of int        
+    """
+    return _sm().getIDs()
+
+def session_get_name(id=None):
+    """ Return the name of a session.
+
+    Args:
+         id(int): Session id. Default (None) is the current session.
+
+    Returns:
+        session name (str)         
+    """
+    return _sm().getName() if id is None else _sm().getName(id)
+
+
+def session_get_state(id=None):
+    """ Returns the session state 
+
+    Args:
+         id(int): Session id. Default (None) is the current session.
+
+    Returns:
+        session state (str)    
+    """
+    return _sm().getState() if id is None else _sm().getState(id)  
+
+def session_get_start(id=None):
+    """ Returns the start timestamp of a session.
+
+    Args:
+         id(int): Session id. Default (None) is the current session.
+
+    Returns:
+        long  
+    """
+    return _sm().getStart() if id is None else _sm().getStart(id)
+
+def session_get_stop(id):
+    """ Returns the stop timestamp of a completed session.
+
+    Args:
+         id(int): Session id. 
+    Returns:
+        Timestamp (long)         
+    """
+    return _sm().getStop(id)    
+
+def session_get_root(id=None):
+    """ Returns the root data path of a session.
+
+    Args:
+         id(int): Session id. Default (None) is the current session.
+
+    Returns:
+        str
+    """
+    return _sm().getRoot() if id is None else _sm().getRoot(id)    
+
+
+def session_get_info(id=None):
+    """ Returns the session information.
+
+    Args:
+         id(int): Session id. Default (None) is the current session.
+
+    Returns:
+        session info (dict)    
+    """
+    return _sm().getInfo() if id is None else _sm().getInfo(id)  
+
+
+def session_get_metadata(id=None):
+    """ Returns a session info metadata.
+
+    Args:
+         id(int): Session id. Default (None) is the current session.
+
+    Returns:
+        session metadata (dict)    
+    """
+    return _sm().getMetadata() if id is None else _sm().getMetadata(id)  
+
+
+def session_set_metadata(key, value,id=None):
+    """ Set session  metadata entry.
+
+    Args:
+         key(str): Metadata key
+         value(obj): Metadata value
+         id(int): Session id. Default (None) is the current session.
+    """
+    return _sm().setMetadata(key, value) if id is None else _sm().setMetadata(id,key, value)  
+
+    
+def session_get_metadata_keys():
+    """ Return the default metadata definition for samples.
+    
+    Returns:
+        list of map entries       
+    """
+    return [str(e.key) for e in _sm().getMetadataDefinition()]
+
+
+def session_get_metadata_type(key):
+    """ Return the metadata type for a given key:
+        String, Integer, Double, Boolean, List or Map.
+    Args:
+         key(str): Metadata key.
+
+    Returns:
+        str         
+    """
+    return str(_sm().getMetadataType(key))
+       
+def session_get_metadata_default(key):
+    """ Return the metadata default value for a given key.
+        
+    Args:
+         key(str): Metadata key.
+
+    Returns:
+         Object    
+    """
+    return _sm().getMetadataDefault(key)
+
+def session_get_runs(id=None, relative=True):
+    """ Return the runs of a session.
+
+    Args:
+         id(int): Session id. Default (None) is the current session.
+         relative(bool): if True use relative file names (for files under the data root path)
+
+    Returns:
+        List of dicts     
+    """
+    return _sm().getRuns(java.lang.Boolean(relative)) if id is None else _sm().getRuns(id, relative)
+
+
+def session_set_run_enabled(enabled, id=None, index=-1):
+    """ Enable or disable a run.
+        
+    Args:
+        enabled(bool): true for enabling, false for disabling
+        id(int): Session id. Default (None) is the current session.
+        index: Index of the run. Default (-1) for the last run.
+
+    Returns:
+         Object    
+    """
+    return _sm().setRunEnabled(index, enabled) if id is None else  _sm().setRunEnabled(id, index, enabled)
+
+def session_get_additional_files(id=None, relative=True):
+    """ Return additional files of a session.
+
+    Args:
+         id(int): Session id. Default (None) is the current session.
+         relative(bool): if True use relative file names (for files under the data root path)
+
+    Returns:
+        List of str     
+    """
+    return _sm().getAdditionalFiles(java.lang.Boolean(relative)) if id is None else _sm().getAdditionalFiles(id, relative)
+
+def session_get_file_list(id=None, relative=True):
+    """ Return complete list of data files of a session.
+
+    Args:
+         id(int): Session id. Default (None) is the current session.
+         relative(bool): if True use relative file names (for files under the data root path)
+
+    Returns:
+        List of str     
+    """
+    return _sm().getFileList(java.lang.Boolean(relative)) if id is None else _sm().getFileList(id, relative)
+
+def session_create_zip(file_name, id=None, preserve_folder_structure=True):
+    """ Create ZIP file with session contents
+
+    Args:
+        file_name(str): name of the zip file
+        id(int): Session id. Default (None) is the current session.
+        preserve_folder_structure: if False all data files are added to the root of the file.
+                                   if True the folder structure under data root is preserved.
+    """
+    return _sm().createZipFile(file_name, preserve_folder_structure) if id is None else _sm().createZipFile(id, file_name, preserve_folder_structure)
+
+
+def session_ingest_scicat(id, matadata={}):
+    """ Ingest a completed session to SciCat
+    
+    Args:
+        id(int): Session id. 
+        matadata(dict): session metadata 
+        
+    Returns:
+        Tuple (Dataset Name, Dataset ID) in case of success. Otherwise throws an exception.               
+    """
+    sciCat= SciCat()
+    result  = sciCat.ingest(id, matadata)
+    print result.output
+    if not result.success:
+        raise  Exception ("Error ingesting session " + str(id))
+    return result.datasetName, result.datasetId
+    
+
+
+
+

script/Lib/startup.py

@@ -0,0 +1,207 @@
+###################################################################################################
+#  Global definitions and built-in functions
+###################################################################################################
+
+from builtin_utils import *
+from builtin_classes import *
+from builtin_functions import *
+
+
+###################################################################################################
+#Default empty callbacks
+###################################################################################################
+def on_command_started(info): pass
+def on_command_finished(info): pass
+def on_session_started(id): pass
+def on_session_finished(id): pass
+def on_change_data_path(path): pass
+
+
+###################################################################################################
+#Help and access to function documentation
+###################################################################################################
+def _getBuiltinFunctions(filter = None):
+    ret = []
+    for name in globals().keys():
+        val = globals()[name]
+        if type(val) is PyFunction:
+            if filter is None or filter in name:
+                #Only "public" documented functions
+                if not name.startswith('_') and (val.__doc__ is not None):
+                    ret.append(val)
+    return to_array(ret)
+
+
+def _getBuiltinFunctionNames(filter = None):
+    ret = []
+    for function in _getBuiltinFunctions(filter):
+        ret.append(function.func_name)
+    return to_array(ret)
+
+def _getFunctionDoc(function):
+    if is_string(function):
+        if function not in globals():
+            return
+        function = globals()[function]
+    if type(function) is PyFunction and '__doc__' in dir(function):
+        ac = function.func_code.co_argcount
+        var = function.func_code.co_varnames
+        args = list(var)[:ac]
+        defs = function.func_defaults
+        if defs is not None:
+            for i in range (len(defs)):
+                index = len(args) - len(defs) + i
+                args[index] = args[index] + " = " + str(defs[i])
+        flags = function.func_code.co_flags
+        if flags & 4 > 0:
+            args.append('*' + var[ac])
+            ac=ac+1
+        if flags & 8 > 0:
+            args.append('**' + var[ac])
+        d = function.func_doc
+        return function.func_name+ "(" + ", ".join(args) + ")" + "\n\n" + (d if (d is not None) else "")
+
+def help(object = None):
+    """
+    Print help message for function or object (if available).
+
+    Args:
+        object (any, optional): function or object to get help.
+                    If null prints a list of the builtin functions.
+
+    Returns:
+        None
+    """
+    if object is None:
+        print "Built-in functions:"
+        for f in _getBuiltinFunctionNames():
+            print "\t" + f
+    else:
+        if type(object) is PyFunction:
+            print _getFunctionDoc(object)
+        elif '__doc__' in dir(object):
+            #The default doc is now shown
+            import org.python.core.BuiltinDocs.object_doc
+            if object.__doc__ != org.python.core.BuiltinDocs.object_doc:
+                print object.__doc__
+
+###################################################################################################
+#Variable injection
+###################################################################################################
+
+def _get_caller():
+    #Not doing inspect.currentframe().f_back because inspect is slow to load
+    return sys._getframe(1).f_back if hasattr(sys, "_getframe") else None
+
+def inject():
+    """Restore initial globals: re-inject devices and startup variables to the interpreter.
+
+    Args:
+        None
+
+    Returns:
+        None
+    """
+    if __name__ == "__main__":
+        get_context().injectVars()
+    else:
+        _get_caller().f_globals.update(get_context().scriptManager.injections)
+
+
+###################################################################################################
+#Script evaluation and return values
+###################################################################################################
+
+def run(script_name, args = None, locals = None):
+    """Run script: can be absolute path, relative, or short name to be search in the path.
+    Args:
+        args(Dict ot List): Sets sys.argv (if list) or gobal variables(if dict) to the script.
+        locals(Dict): If not none sets the locals()for the runing script.
+                      If locals is used then script definitions will not go to global namespace.
+
+    Returns:
+        The script return value (if set with set_return)
+    """
+    script = get_context().scriptManager.library.resolveFile(script_name)
+    if script is not None and os.path.isfile(script):
+        info = get_context().startScriptExecution(script_name, args)
+        try:
+            set_return(None)
+            if args is not None:
+                if isinstance(args,list) or isinstance(args,tuple):
+                    sys.argv =  list(args)
+                    globals()["args"] = sys.argv
+                else:
+                    for arg in args.keys():
+                        globals()[arg] = args[arg]
+            if (locals is None):
+                execfile(script, globals())
+            else:
+                execfile(script, globals(), locals)
+            ret = get_return()
+            get_context().finishScriptExecution(info, ret)
+            return ret
+        except Exception, ex:
+            get_context().finishScriptExecution(info, ex)
+            raise ex
+    raise IOError("Invalid script: " + str(script_name))
+
+def abort():
+    """Abort the execution of ongoing task. It can be called from the script to quit.
+
+    Args:
+        None
+
+    Returns:
+        None
+    """
+    fork(get_context().abort) #Cannot be on script execution thread
+    while True: sleep(10.0)
+
+def set_return(value):
+    """Sets the script return value. This value is returned by the "run" function.
+
+    Args:
+        value(Object): script return value.
+
+    Returns:
+        None
+    """
+    #In Jython, the output of last statement is not returned  when running a file
+    if __name__ == "__main__":
+        global __THREAD_EXEC_RESULT__
+        if is_interpreter_thread():
+            global _
+            _=value
+        __THREAD_EXEC_RESULT__[java.lang.Thread.currentThread()]=value         #Used when running file
+    else:
+        #if startup is imported, cannot set global
+        caller = _get_caller()
+        if is_interpreter_thread():
+            caller.f_globals["_"]=value
+        if not "__THREAD_EXEC_RESULT__" in caller.f_globals.keys():
+            caller.f_globals["__THREAD_EXEC_RESULT__"] = {}
+        caller.f_globals["__THREAD_EXEC_RESULT__"][java.lang.Thread.currentThread()]=value
+    return value    #Used when parsing file
+
+def get_return():
+    if __name__ == "__main__":
+        global __THREAD_EXEC_RESULT__
+        return __THREAD_EXEC_RESULT__[java.lang.Thread.currentThread()]
+    else:
+        return _get_caller().f_globals["__THREAD_EXEC_RESULT__"][java.lang.Thread.currentThread()]
+
+
+###################################################################################################
+#Executed on startup
+###################################################################################################
+
+if __name__ == "__main__":
+    ca_channel_path=os.path.join(get_context().setup.getStandardLibraryPath(), "epics")
+    sys.path.append(ca_channel_path)
+    #This is to destroy previous context of _ca (it is not shared with PShell)
+    if run_count > 0:
+        if sys.modules.has_key("_ca"):
+            print
+            import _ca
+            _ca.initialize()

script/Lib/statsutils.py

@@ -0,0 +1,191 @@
+###################################################################################################
+# Utilities for generating reports from command statistics files
+###################################################################################################
+
+#CsvJdbc JAR file must be downloaded to extensions folder:
+#http://central.maven.org/maven2/net/sourceforge/csvjdbc/csvjdbc/1.0.34/csvjdbc-1.0.34.jar
+
+
+import java.sql.DriverManager as DriverManager
+import java.sql.ResultSet as ResultSet
+import java.util.Properties as Properties
+import java.lang.Class as Class
+import os
+from startup import get_context, expand_path
+import ch.psi.pshell.core.CommandManager.CommandStatisticsFileRange as CommandStatisticsFileRange
+
+stmt = None 
+STAT_COLUMN_NAMES = ["Command","Args","Source","Start","End","Background","Result","Return"]
+def get_stats_connection():
+    global stmt
+    Class.forName("org.relique.jdbc.csv.CsvDriver");   
+    db = os.path.abspath(expand_path("{home}/statistics"))
+    props = Properties()
+    props.put("fileExtension", ".csv")
+    props.put("separator", ";")     
+    props.put("timestampFormat", "dd/MM/yy HH:mm:ss.SSS")      
+    props.put("indexedFiles", "true");
+    props.put("columnTypes", "String,String,String,Timestamp,Timestamp,Boolean,String,String");
+    
+    fileRange = get_context().commandManager.commandStatisticsConfig.fileRange    
+    if fileRange==CommandStatisticsFileRange.Daily:
+        props.put("fileTailPattern", "(\\d+)_(\\d+)_(\\d+)"); 
+        props.put("fileTailParts", "Year,Month,Day");
+    elif fileRange==CommandStatisticsFileRange.Monthly:
+        props.put("fileTailPattern", "(\\d+)_(\\d+)"); #props.put("fileTailPattern", "-(\\d+)_(\\d+)");
+        props.put("fileTailParts", "Year,Month");
+    elif fileRange==CommandStatisticsFileRange.Yearly:
+        props.put("fileTailPattern", "(\\d+)"); 
+        props.put("fileTailParts", "Year");    
+ 
+    conn = DriverManager.getConnection("jdbc:relique:csv:" + db, props);
+    stmt = conn.createStatement(ResultSet.TYPE_SCROLL_SENSITIVE,ResultSet.CONCUR_READ_ONLY);
+    return conn
+
+def _get_count(sql):
+    ret = 0
+    results = stmt.executeQuery("SELECT COUNT(*) AS count FROM . WHERE " + sql) 
+    if results.first():
+        ret = results.getInt("count")    
+    return ret
+
+def _add_sql_time(sql, start, end):
+    if start:
+        if len(start)==8:
+            start = start + " 00:00:00.000"          
+        sql = sql + " AND Start>='" + start + "'"
+    if end:
+        if len(end)==8:
+            end = end + " 00:00:00.000"          
+        sql = sql +  " AND (\"End\"<'" + end + "')"    
+    return sql   
+        
+def get_count(command= "%%", start = None, end = None, result= "%%"):
+    sql = "Command LIKE '"+ command +"' AND Result LIKE '"+ result +"'"
+    sql = _add_sql_time(sql, start, end)
+    return _get_count(sql)
+
+def get_return_count(command= "%%", start = None, end = None, ret= "%%"):
+    sql = "Command LIKE '"+ command +"' AND Return = '"+ ret +"'"
+    sql = _add_sql_time(sql, start, end)
+    return _get_count(sql)    
+
+def get_cmd_stats(command = "%", start = None, end = None):
+    s = get_count(command, start, end, "success")
+    a = get_count(command, start, end, "abort")
+    e = get_count(command, start, end, "error")
+    return (s,a,e)
+
+def get_errors(command = "%", start = None, end = None):
+    sql = "SELECT Return, Count(Return) as count FROM . WHERE Command LIKE '"+ command +"' AND Result='error'"
+    sql = _add_sql_time(sql, start, end)
+    sql = sql + " GROUP BY Return ORDER BY count DESC"
+    results = stmt.executeQuery(sql) 
+    ret = []
+    while results.next():  
+        ret.append((results.getInt("count"), results.getString("Return")))           
+    return ret
+
+
+def get_cmd_records(command = "%", start = None, end = None, result= "%%"):
+    sql = "SELECT * FROM . WHERE Command LIKE '"+ command +"' AND Result LIKE '"+ result +"'"
+    sql = _add_sql_time(sql, start, end)
+    results = stmt.executeQuery(sql) 
+    ret = []
+    while results.next():  
+        rec={}
+        for col in STAT_COLUMN_NAMES:
+            rec[col]= results.getString(col)
+        ret.append(rec)           
+    return ret    
+
+def get_commands(commands =None, start = None, end = None):
+    ret = []
+    if (commands is None) or (len(commands)==0):
+        sql = "SELECT * FROM . WHERE Command != ''"
+        sql = _add_sql_time(sql, start, end)
+        sql = sql + " GROUP BY Command"
+        results = stmt.executeQuery(sql) 
+        while results.next():  
+            cmd = results.getString("Command")
+            if cmd and not " " in cmd:  
+                ret.append(cmd)           
+    else:
+        for cmd in commands:
+            if get_count(cmd, start, end) >0 :
+                ret.append(cmd)  
+    return ret
+
+def print_cmd_stats(command = "%", start = None, end = None):
+    print "-----------------------------------------------------------"
+    print "Statistics from ",  start  , " to ",  end 
+    (s,a,e) = get_cmd_stats(command, start, end)
+    t=s+a+e #get_count(command, start, end, "%")
+    print "Command: " , command , " Records: ", t    
+    if t>0: 
+        print "%-10s %7.2f%% - %d" % ("Success", (float(s)/t) * 100, s)
+        print "%-10s %7.2f%% - %d" % ("Abort",   (float(a)/t) * 100, a)
+        print "%-10s %7.2f%% - %d" % ("Error",   (float(e)/t) * 100, e)
+        
+        print "\nErrors:"
+        print "%5s   %s" % ("Count", "Error")
+        errors =  get_errors(command, start, end)    
+        for error in errors:
+            print "%5d   %s" % (error[0], error[1])
+    print "-----------------------------------------------------------"     
+
+def print_cmd_records(command = "%", start = None, end = None, result= "%%"):
+    print "-----------------------------------------------------------"
+    print "Records from ",  start  , " to ",  end 
+    info = get_cmd_records(command, start, end, result)
+    print "Command: " , command , " Result: ", result,  " Records: ", len(info)  
+        
+    for col in STAT_COLUMN_NAMES:
+        print col+ "; " ,
+    print
+    
+    for cmd in info:
+        s = "" 
+        for col in STAT_COLUMN_NAMES:
+            s = s + cmd[col]+ "; "
+        print s
+    print "-----------------------------------------------------------"  
+       
+def print_stats(commands = None, start = None, end = None):
+    print "-----------------------------------------------------------"
+    print "Statistics from ",  start  , " to ",  end 
+    print "%-20s %-5s %8s %8s %8s" % ("Command", "Total", "Success", "Abort", "Error")
+    cmds = get_commands(commands)   
+    for cmd in cmds:
+        (s,a,e) = get_cmd_stats(cmd, start, end)
+        t=s+a+e 
+        if t>0:
+            print "%-20s %-5d %7.2f%% %7.2f%% %7.2f%%" % (cmd, t, (float(s)/t) * 100, (float(a)/t) * 100, (float(e)/t) * 100)
+        else:
+            print "%-20s %-5d" % (cmd, t)
+    print "-----------------------------------------------------------"  
+        
+
+
+
+if __name__=='__main__': 
+    conn = get_stats_connection()
+    
+    #Print stats of all commands, with no time range
+    print_stats()
+
+    cmds = ["%scan1%", "%scan2%"]
+    start= "01/03/19" 
+    end=   "01/04/19"  
+       
+    #Print stats all commands containing 'scan1' and 'scan2' in the month 03.2019
+    print_stats(cmds, start, end)
+    
+    #Print individual statistics, including error count, for commands containing 'scan1' and 'scan2'
+    for cmd in cmds:
+        print_cmd_stats (cmd, start, end)
+    
+    #Print all records for commands containing 'scan1'
+    print_cmd_records("%scan1%%", start, end, "error")        
+    conn.close()   
+

script/local.py

@@ -0,0 +1,7 @@
+###################################################################################################
+#  Deployment specific global definitions - executed after startup.py
+###################################################################################################
+
+run("psss/psss")
+
+

script/psss/CameraScan.py

@@ -0,0 +1,73 @@
+#Scan the PSSS camera position
+#Purpose:
+#To set or confirm the camera is positioned with the measured spectrum in the centre of the spectral integration window
+
+#If running from editor
+if get_exec_pars().source == CommandSource.ui:  
+#User inputs - define travel range of camera
+    RANGE_FROM = -17
+    RANGE_TO = -11
+    STEPS = 20
+    NUM_SHOTS= 10 #100
+    PLOT=None
+p = plot(None, title="Data")[0] if (PLOT is None) else PLOT
+p.clear()
+p.removeMarker(None)
+p.setLegendVisible(True)
+p.addSeries(LinePlotSeries("PSSS Spectrum Average")) 
+
+
+run("cpython/wrapper")
+
+if not is_dry_run():
+    cam_x=Channel("SARFE10-PSSS059:MOTOR_X5.VAL", name="cam_x")
+else:
+    cam_x=DummyRegister("cam_x")
+
+av = create_averager(psss_spectrum_y, NUM_SHOTS, interval=-1, name="spectrum_average")
+av_samples = av.samples
+av_samples.alias = "spectrum_samples"
+
+
+#Scan and take data
+def after_read(record, scan):
+    p.getSeries(0).setData(psss_spectrum_x.take(), record[av])
+    p.setTitle("Cam X = %1.3f" %(record[cam_x]))
+
+r = lscan(cam_x, (av, av_samples), RANGE_FROM, RANGE_TO, STEPS, latency=0.0, after_read = after_read, save=False)
+average, samples, cam_range = r.getReadable(0), r.getReadable(1), r.getPositions(0) 
+
+signal_centre, projection = get_signal_centre(samples, cam_range)
+
+#Set max position
+cam_x.write(signal_centre)
+cam_x.close()
+
+
+
+"""
+plt.figure(figsize=[10,5])
+plt.subplot(121)
+plt.title('PSSS scan of camera position')
+plt.pcolormesh(np.arange(0,Scan_spec.shape[2]), Cam_range, Scan_spec.mean(axis=1),cmap='CMRmap')
+plt.xlim([0,Scan_spec.shape[2]])
+plt.xlabel('Camera pixel dispersive direction')
+plt.ylabel('Set PSSS cam_x _pos [mm] \n'+PSSS_cam_x_PV_name[0:-4])
+plt.subplot(122)
+plt.plot(projection,Cam_range,linewidth = 2, color = 'orange',label ='projected signal')
+plt.title('Spectrum centred at %.1f [mm] (from signal max) \n trace should have hard edges'%signal_centre)
+plt.xticks([])
+plt.legend()
+plt.grid(True)
+"""
+#PLOT.clear()
+#plot_data(PLOT, projection, "Data", xdata=cam_range,  show_points = True, color=Color.BLUE)
+#p,pars = plot_gauss_fit(cam_range, projection, gauss_pars=None, p=PLOT, title = "Data")
+
+p.clear()
+p.setTitle("")
+plot_data(p, projection, "Projection", xdata=cam_range,  show_points = True, color=Color.BLUE)
+p.addMarker(signal_centre, None, "Signal Centre=" + str(round(signal_centre,2)), Color.LIGHT_GRAY)
+
+
+set_return(signal_centre)

script/psss/CrystalHeightScan.py

@@ -0,0 +1,81 @@
+###############################################################################
+#Scan the PSSS crystal height
+#Purpose:
+#The PSSS signal level is very sensitive to the crystal height. This script will scan the height and set the position to the maximum signal
+
+if get_exec_pars().source == CommandSource.ui:  
+#User inputs - define travel range of camera
+    RANGE_FROM = -0.8
+    RANGE_TO = -1.7
+    STEPS = 10 #20
+    NUM_SHOTS= 10 # 100
+    PLOT=None
+
+p = plot(None, title="Data")[0] if (PLOT is None) else PLOT
+p.clear()
+p.removeMarker(None)
+p.setLegendVisible(True)
+p.addSeries(LinePlotSeries("PSSS Spectrum Average")) 
+
+run("cpython/wrapper")
+
+
+#Setup and functions setup¶
+if not is_dry_run():
+    xstal_height=Channel("SARFE10-PSSS059:MOTOR_Y3.VAL", name="xstal_height")
+else:
+    xstal_height=DummyRegister("xstal_height")
+
+av = create_averager(psss_spectrum_y, NUM_SHOTS, interval=-1, name="spectrum_average")
+av_samples = av.samples
+av_samples.alias = "spectrum_samples"
+       
+#Scan and take data
+def after_read(record, scan):
+    p.getSeries(0).setData(psss_spectrum_x.take(), record[av])
+    p.setTitle("Xtal Height = %1.3f" %(record[xstal_height]))
+    
+r = lscan(xstal_height, (av, av_samples), RANGE_FROM, RANGE_TO, STEPS, latency=2.0, after_read = after_read, save=False)
+
+#User inputs - define travel range of crystal
+#It is unlikely these values need to be changed
+average, samples, xstal_range =  r.getReadable(0), r.getReadable(1), r.getPositions(0)  
+
+#return maxium position
+[amp, mean_val, sigma, offset], projection = fit_crystal_height(RANGE_FROM, RANGE_TO, STEPS+1, samples)
+print(mean_val)
+
+if not (RANGE_FROM < mean_val < RANGE_TO or RANGE_TO < mean_val < RANGE_FROM):
+    raise Exception ("Invalid fit mean: " + str(mean_val))  
+
+
+#Set max position
+#Cell below will push the maximum position to the xstal height
+xstal_height.write(mean_val)
+xstal_height.close()
+
+#Plots
+"""    
+plt.figure(figsize=[10,5])
+plt.subplot(121)
+plt.title('PSSS scan of crystal height')
+plt.pcolormesh(energy_axis, xstal_range, Scan_spec.mean(axis=1),cmap='CMRmap')
+plt.xlim([energy_axis[0],energy_axis[-1]])
+plt.ylim([xstal_range[0], xstal_range[-1]])
+plt.xlabel('PSSS energy axis')
+plt.ylabel('Set crystal position [mm] \n'+PSSS_xstal_height_name[0:-4])
+plt.subplot(122)
+plt.plot(projection,xstal_range,linewidth = 2, color = 'orange',label ='projected signal')
+plt.plot(gaus(xstal_range_fit,*popt),xstal_range_fit,'r:',label='fit')
+plt.ylim([xstal_range[0], xstal_range[-1]])
+plt.title('Signal max at %.3f [mm] (from fit)'%popt[1])
+plt.xticks([])
+plt.legend()
+plt.grid(True)
+"""
+p.clear()
+p.setTitle("")
+plot_gauss_fit(xstal_range, projection, gauss_pars=(offset, amp, mean_val, sigma), p=p, title = "Data")
+
+
+set_return(mean_val)

script/psss/EnergyScan.py

@@ -0,0 +1,101 @@
+###############################################################################
+#Scan the PSSS photon energy
+#Purpose: To find and centre the PSSS photon energy so the measured spectrum is centred on the camera chip
+
+#PARAMETERS
+#User inputs - define energy range to scan below by running the appropiate cell
+#Below is for a large scan range assuming offset from machine upto $\pm$ 300 eV
+
+#If running from editor
+if get_exec_pars().source == CommandSource.ui:   
+    RANGE_OFF = None
+    RANGE_FROM = 11100
+    RANGE_TO = 11300
+    STEPS = 5 #60
+    NUM_SHOTS= 10 #100
+    PLOT=None
+p = plot(None, title="Data")[0] if (PLOT is None) else PLOT
+p.clear()
+p.removeMarker(None)
+p.setLegendVisible(True)
+p.addSeries(LinePlotSeries("PSSS Spectrum Average")) 
+
+if RANGE_OFF is not None:    
+    RANGE_FROM = energy_machine.read()-RANGE_OFF
+    RANGE_TO = energy_machine.read()+RANGE_OFF
+
+run("cpython/wrapper")
+
+
+
+
+#Scan and take data
+class PSSS_energy(Writable):
+    def write(self, value):
+        if not is_dry_run():
+            psss_energy.write(value)
+            exec_cpython("/ioc/modules/qt/PSSS_motion.py", args = ["-m1", "SARFE10-PSSS059"])
+            # python / ioc / modules / qt / PSSS_motion.py - m1 SARFE10 - PSSS059
+        time.sleep(1)
+        print(value)
+
+en = PSSS_energy()
+en.alias = "energy"
+
+av = create_averager(psss_spectrum_y, NUM_SHOTS, interval=-1, name="spectrum_average")
+av_samples = av.samples
+av_samples.alias = "spectrum_samples"
+
+
+def after_read(record, scan):
+    p.getSeries(0).setData(psss_spectrum_x.take(), record[av])
+    p.setTitle("Energy = %1.3f" %(record[en]))
+      
+r = lscan(en, (av, av_samples), RANGE_FROM, RANGE_TO, STEPS, latency=0.0, after_read = after_read, save=False )
+average, samples, energy_range =  r.getReadable(0), r.getReadable(1), r.getPositions(0)    
+
+[amp, mean_val, sigma, offset],centre_line_out  = fit_energy(RANGE_FROM, RANGE_TO, STEPS+1, NUM_SHOTS, samples)
+
+if not (RANGE_FROM < mean_val < RANGE_TO or RANGE_TO < mean_val < RANGE_FROM):
+    raise Exception ("Invalid fit mean: " + str(mean_val))  
+
+    
+measured_offset = energy_machine.read() - mean_val
+#Set fitted energy
+print "measured offset", measured_offset
+
+en.write(mean_val)
+
+
+#Plot
+"""
+plt.figure(figsize=[10,5])
+plt.subplot(121)
+plt.title('PSSS scan of set photon energy')
+plt.pcolormesh(np.arange(0,Scan_spec.shape[2]), Energy_range, Scan_spec.mean(axis=1),cmap='CMRmap')
+plt.vlines(int(Scan_spec.shape[2]/2), Energy_range[0], Energy_range[-1],linestyles='--', colors='orange')
+plt.xlim([0,Scan_spec.shape[2]])
+plt.xlabel('Camera pixel')
+plt.ylabel('Set PSSS energy [eV] \n SARFE10-PSSS059:ENERGY')
+
+plt.subplot(122)
+plt.title('At camera centre pixel %1i \nCalibrated energy = %.1f [eV]\n Offset from machine = %.1f [eV]'%(int(Scan_spec.shape[2]/2),popt[1],measured_offset))
+plt.plot(centre_line_out,Energy_range,linewidth = 2, color = 'orange',label ='measured')
+plt.plot(gaus(Energy_range_fit,*popt),Energy_range_fit,'r:',label='fit')
+plt.xticks([])
+plt.legend()
+plt.grid(True)
+"""
+
+p.clear()
+p.setTitle("")
+plot_gauss_fit(energy_range, centre_line_out, gauss_pars=(offset, amp, mean_val, sigma), p=PLOT, title = "Data")
+
+
+set_return(mean_val)
+
+
+
+
+
+

script/psss/psss.py

@@ -0,0 +1,188 @@
+import org.jfree.ui.RectangleAnchor as RectangleAnchor
+import org.jfree.ui.TextAnchor as TextAnchor
+import ch.psi.pshell.imaging.Overlay as Overlay
+import ch.psi.pshell.plot.RangeSelectionPlot as RangeSelectionPlot
+from collections import deque
+
+PSSS_CAMERA_NAME = "SARFE10-PSSS059";
+
+def integrate_arrays(arrays):
+    if arrays is None or (len(arrays)==0):
+        return None
+    ret = arrays[0]
+    for a in arrays[1:]:
+        ret=arradd(ret, a)
+    return ret
+
+def average_arrays(arrays):
+    ret = integrate_arrays(arrays)
+    if ret is not None:
+        s=len(arrays)        
+        ret = [x/s for x in ret]      
+    return ret 
+
+
+def get_psss_data(average=1):
+    ax,ay,ac,af=[],[],[],[]
+    x = psss_spectrum_x.take()
+    for i in range(average):
+        y =  psss_spectrum_y.take()
+        center,fwhm = psss_center.take(), psss_fwhm.take()  
+        if average==1: 
+            return x,y,center,fwhm 
+        #ax.append(x)  
+        ay.append(y)
+        ac.append(center)
+        af.append(fwhm)        
+        if i < (average-1):                        
+            psss_spectrum_y.waitCacheChange(2000)
+            #psss_center.waitCacheChange(1)
+            #psss_fwhm.waitCacheChange(1)                    
+#x=average_arrays(ax)
+    y=average_arrays(ay)
+    center=mean(ac)
+    fwhm=mean(af)
+    return x,y,center,fwhm 
+
+def plot_psss(p, h=None, average = None):
+    """
+    if len(p.getMarkers())==0:
+        m1=p.addMarker(0,None,"",Color.WHITE)
+        m2=p.addMarker(0,None,"",Color.WHITE)
+        m2.setLabelAnchor(RectangleAnchor.TOP) 
+    else:
+        m1,m2 = p.getMarkers()
+    """
+
+    #Manipulate axis (use PSSS_PLOT for the global object):
+    #p.getAxis(LinePlot.AxisId.X).
+
+     # Setup queues
+    if p.getNumberOfSeries()==0: 
+        center_queue = deque(maxlen=100)
+        fwhm_queue = deque(maxlen=100)
+    
+    # Setup figures
+    
+    if p.getNumberOfSeries()==0:
+        p.addSeries(LinePlotSeries("spectrum"))
+        p.addSeries(LinePlotSeries("average"))
+        p.setLegendVisible(True)
+        p.getAxis(LinePlot.AxisId.X)
+        p.getAxis(LinePlot.AxisId.X).setLabel("Energy [eV]")
+        p.getAxis(LinePlot.AxisId.Y).setLabel("Sum counts")
+    if len(p.getMarkers())==0:
+        paint = RangeSelectionPlot().getSelectionColor() #p.chart.getBackgroundPaint()
+        m=p.addIntervalMarker(0,0, None,"", paint)    
+        m.setLabelAnchor(RectangleAnchor.BOTTOM) 
+        m.alpha=0.2
+        m.setLabelPaint(Color.WHITE)
+    else:
+        m = p.getMarkers()[0]
+   
+
+    x,y, = psss_spectrum_x.take(), psss_spectrum_y.take()
+    # update spectral plot
+    if (x is None) or (y is None):
+        p.getSeries(0).clear()
+    else:
+        p.getSeries(0).setData(x,y) 
+    if (x is None) or (y is None):
+        p.getSeries(0).clear()
+    else:
+        p.getSeries(0).setData(x,y)           
+
+    if average is not None:
+        print "Average: ", average
+        x,y, center,fwhm  = get_psss_data(average)
+    else:
+        y = psss_spectrum_y_average.take()
+        center = psss_center_average.take()            
+        fwhm  = psss_fwhm_average.take()
+    
+    if (x is None) or (y is None):
+        p.getSeries(1).clear()
+    else:
+        p.getSeries(1).setData(x,y)  
+        
+           
+    if (center!= None) and (fwhm!=None):
+        center=center.doubleValue()
+        fwhm=fwhm.doubleValue()
+        m.startValue, m.endValue =  center - fwhm/2, center + fwhm/2
+        m.label = str(center)     
+        
+        if h:
+            if h.getNumberOfSeries()==0:
+                    h.addSeries(TimePlotSeries("centre"))
+                    h.addSeries(TimePlotSeries("Energy spread SS",2))
+                    h.addSeries(TimePlotSeries("Energy spread cum avg",2))
+                    h.setLegendVisible(True)
+                    h.setTimeAxisLabel("")
+                    h.getAxis(Timeplot.AxisId.Y1).setLabel("Central energy [eV]")              
+            per_mil = (fwhm/center)*1e3
+            per_mil_avg = psss_fwhm_avg.take()
+            h.getSeries(0).appendData(center)
+            h.getSeries(1).appendData(per_mil)
+            h.getSeries(2).appendData(per_mil_avg)
+    return center,fwhm
+
+ovmin, ovmax, ovavg = None, None, None
+
+def update_psss_image(renderer):
+    global ovmin, ovmax
+    #if ovmin: ovmin.update(Point(0,psss_roi_min.take()))
+    #if ovmax: ovmax.update(Point(0,psss_roi_max.take()))
+    
+    
+    width=psss_spectrum_x.size
+    if ovmin: ovmin.update(Point(0,psss_roi_min.take()), Point(width, psss_roi_min.take()))
+    if ovmax: ovmax.update(Point(0,psss_roi_max.take()), Point(width, psss_roi_max.take()))
+    try:
+        data = renderer.data
+        av = "%1.2f" %(data.integrate(False)/data.width/data.height)
+    except:
+        av = ""
+    if ovavg: ovavg.update(av)
+
+def enable_psss_image(enabled, renderer):
+    global ovmin, ovmax, ovavg    
+    try:
+        if (enabled):
+            #Start or connect to ScreenPanel pipeline
+            renderer.setDevice(cam_server)       
+            renderer.setProfile(renderer.Profile.Both)
+            renderer.setShowProfileLimits(False)
+
+            #Changing colormap
+            #print Colormap.values() #Check values
+            cam_server.config.colormap=Colormap.Temperature
+            
+            
+            cam_server.start(PSSS_CAMERA_NAME + "_sp", PSSS_CAMERA_NAME + "_sp1")       
+            #ovmin, ovmax= Overlays.Crosshairs(renderer.getPenMarker(), Dimension(-1,1)), \
+            #              Overlays.Crosshairs(renderer.getPenMarker(), Dimension(-1,1))
+            ovmin, ovmax= Overlays.Line(renderer.getPenMarker()), Overlays.Line(renderer.getPenMarker())           
+             
+            ovavg = Overlays.Text(Pen(java.awt.Color.GREEN.darker()), "", \
+                    java.awt.Font("Verdana", java.awt.Font.PLAIN, 12), java.awt.Point(-50,20))
+            ovavg.fixed=True
+            ovavg.anchor=Overlay.ANCHOR_IMAGE_TOP_RIGHT
+            renderer.addOverlays([ovmin, ovmax, ovavg])
+            update_psss_image(renderer)
+        else:
+            ovmin, ovmax, ovavg = None, None, None
+            renderer.setDevice(None)
+            renderer.clearOverlays()
+            cam_server.stop()
+    except:
+        log(sys.exc_info()[1])
+
+
+def get_psss_averaging():
+    return psss_spectrum_y_average.config.measures    
+
+def set_psss_averaging(measures):
+    psss_spectrum_y_average.config.measures=measures        
+    psss_center_average.config.measures=measures        
+    psss_fwhm_average.config.measures=measures