standand imaging workflows with commander

pom.xml

@@ -8,7 +8,7 @@
 		<version>5.0</version> <relativePath /> </parent> -->
 	<groupId>embl.almf</groupId>
 	<artifactId>AutoMicTools_</artifactId>
-	<version>1.1.32-SNAPSHOT</version>
+	<version>1.1.33-SNAPSHOT</version>
 
 	<name>plugins/AutoMicTools_.jar</name>
 	<description>Collection of tools for automated (feedback) microscopy data acquisition and analysis</description>

src/main/java/automic/online/jobdistributors/JobDistributor_AFocus_Offset.java

@@ -4,14 +4,11 @@ package automic.online.jobdistributors;
 import ij.IJ;
 import ij.ImageJ;
 import ij.gui.GenericDialog;
-import ij.gui.WaitForUserDialog;
+
 import ij.plugin.PlugIn;
 
-import automic.online.jobdistributors.JobDistributor_Abstract;
-import automic.online.jobs.common.Job_AutofocusInitOffset;
+import automic.online.jobs.common.Job_AutofocusInit_Commander;
 import automic.online.jobs.common.Job_RecordFinish;
-import automic.parameters.ParameterCollection;
-import automic.parameters.gui.ParameterGuiManager;
 import automic.table.TableModel;
 import automic.table.TableProcessor;
 
@@ -23,23 +20,9 @@ public class JobDistributor_AFocus_Offset extends JobDistributor_Abstract implem
 	@Override
 	protected void fillJobList(){
 		
-		Job_AutofocusInitOffset job1=new Job_AutofocusInitOffset();
-		ParameterCollection job1Parameters=job1.createJobParameters();
-		job1Parameters.setUndefinedValuesFromDefaults();
-		ParameterGuiManager pgManager1=new ParameterGuiManager(job1Parameters);
-		try{
-			pgManager1.refineParametersViaDialog("Coverslip focusing");
-		}catch(Exception _ex){
-			new WaitForUserDialog("error in parameter values");
-		}
-		
-		job1.parseInputParameterValues(pgManager1.getParameterCollection());
-		
-		
-		super.addImageJob(job1,	"DE_1_",  "AFocus",	true);
-		
+		super.addImageJob(Job_AutofocusInit_Commander.class,	"DE_1_",  "AF",	true);
 		super.addImageJob(Job_RecordFinish.class,	"DE_2_", "Result.Image",	true);
-				
+
 	}
 	
 	@Override
@@ -48,7 +31,7 @@ public class JobDistributor_AFocus_Offset extends JobDistributor_Abstract implem
 
 		outTbl.addColumn("Date.Time");
 		
-		outTbl.addFileColumns("AFocus", "IMG");
+		outTbl.addFileColumns("AF", "IMG");
 		outTbl.addFileColumns("Result.Image", "IMG");
 		
 		outTbl.addValueColumn("Success", "BOOL");

src/main/java/automic/online/jobdistributors/commander/imaging/JobDistributor_MicroscopeCommander_AF_LowZoom.java

+package automic.online.jobdistributors.commander.imaging;
+
+
+import ij.IJ;
+import ij.ImageJ;
+import ij.gui.GenericDialog;
+import ij.plugin.PlugIn;
+import automic.online.jobdistributors.JobDistributor_Abstract;
+import automic.online.jobs.common.Job_AutofocusInit_Commander;
+import automic.online.jobs.common.Job_RecordFinish;
+import automic.table.TableModel;
+import automic.table.TableProcessor;
+
+
+public class JobDistributor_MicroscopeCommander_AF_LowZoom extends JobDistributor_Abstract  implements PlugIn{
+	
+	@Override
+	protected void fillJobList(){
+		
+		super.addImageJob(Job_AutofocusInit_Commander.class,				"AF--",  "AF",	true);
+		super.addImageJob(Job_RecordFinish.class,							"LowZoom--", "LowZoom",	true);
+
+	}
+	
+	@Override
+	protected TableModel constructTabModel(String _rpth){
+		TableModel outTbl=new TableModel(_rpth);
+
+		outTbl.addColumn("Date.Time");
+		
+		outTbl.addFileColumns("AF", "IMG");
+		outTbl.addFileColumns("LowZoom", "IMG");
+		
+		outTbl.addValueColumn("Success", "BOOL");
+		
+		outTbl.addRow(new Object[outTbl.getColumnCount()]);
+		return outTbl;
+	}
+	
+	@Override
+	protected TableProcessor configureTableProcessor(TableModel _tModel)throws Exception{
+		TableProcessor tProcessor=new TableProcessor(_tModel);
+		return tProcessor;
+	}
+
+	
+	
+	@Override
+	protected void putProtocolPreferencesToDialog(GenericDialog _dialog){
+	}
+
+	@Override
+	protected void getProtocolPreferencesFromDialog(GenericDialog _dialog){
+	}
+	
+	@Override
+	protected boolean showDialogInDebugRun(){
+		return false;
+	}
+
+
+	
+	@Override
+	protected void setDebugConfiguration(){
+		final String searchPath="D:\\tempDat\\AutoMic-test";
+		this.setGeneralOptions(searchPath, true, false);
+	}
+	
+	/**
+	 * main method for debugging.
+	 * Sets debug configuration via the method defined for each JobDistributor implementation
+	 * Then executes JobDistributor
+	 * 
+	 */
+	public static void main(String[] args) {
+		// set the plugins.dir property to make the plugin appear in the Plugins menu
+		Class<?> clazz = JobDistributor_MicroscopeCommander_AF_LowZoom.class;
+		//String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
+		//String pluginsDir = url.substring(5, url.length() - clazz.getName().length() - 6);
+		//System.setProperty("plugins.dir", pluginsDir);
+
+		// start ImageJ
+		new ImageJ();
+		//DEBUG=true;
+		//Debug.run(plugin, parameters);
+		//new WaitForUserDialog("test Maven project").show();
+		
+		// run the plugin
+		
+		//exrerimentFolderPath="D:/tempDat/AutoFRAP_test";
+		//showDemo=true;
+		//pnum=1;
+		//setDebugConfiguration();
+		
+
+		//IJ.runPlugIn(clazz.getName(),"Debug run");
+		IJ.runPlugIn(clazz.getName(),"");
+
+	}
+}

src/main/java/automic/online/jobdistributors/commander/imaging/JobDistributor_MicroscopeCommander_AF_LowZoom_HighZoom_Manual.java

+package automic.online.jobdistributors.commander.imaging;
+
+
+import ij.IJ;
+import ij.ImageJ;
+import ij.gui.GenericDialog;
+import ij.plugin.PlugIn;
+import automic.online.jobdistributors.JobDistributor_Abstract;
+import automic.online.jobs.common.Job_AutofocusInit_Commander;
+import automic.online.jobs.common.Job_GetMultipleImagingPositions_Manual_Commander;
+import automic.online.jobs.common.Job_RecordFinish;
+import automic.table.TableModel;
+import automic.table.TableProcessor;
+
+
+public class JobDistributor_MicroscopeCommander_AF_LowZoom_HighZoom_Manual extends JobDistributor_Abstract  implements PlugIn{
+	
+
+	
+	@Override
+	protected void fillJobList(){
+		
+		super.addImageJob(Job_AutofocusInit_Commander.class,						"AF--",  "AF",	true);
+		super.addImageJob(Job_GetMultipleImagingPositions_Manual_Commander.class,	"LowZoom--", "LowZoom",	true);
+		super.addImageJob(Job_RecordFinish.class,									"HighZoom--", "HighZoom",true);
+
+	}
+	
+	@Override
+	protected TableModel constructTabModel(String _rpth){
+		TableModel outTbl=new TableModel(_rpth);
+
+		outTbl.addColumn("Date.Time");
+		
+		outTbl.addFileColumns("AF", "IMG");
+		outTbl.addFileColumns("LowZoom", "IMG");
+		outTbl.addFileColumns("HighZoom", "IMG");
+
+		
+		outTbl.addValueColumn("Success", "BOOL");
+		
+		outTbl.addRow(new Object[outTbl.getColumnCount()]);
+		return outTbl;
+	}
+	
+	@Override
+	protected TableProcessor configureTableProcessor(TableModel _tModel)throws Exception{
+		TableProcessor tProcessor=new TableProcessor(_tModel);
+		return tProcessor;
+	}
+
+	
+	
+	@Override
+	protected void putProtocolPreferencesToDialog(GenericDialog _dialog){
+	}
+
+	@Override
+	protected void getProtocolPreferencesFromDialog(GenericDialog _dialog){
+	}
+	
+	@Override
+	protected boolean showDialogInDebugRun(){
+		return false;
+	}
+
+
+	
+	@Override
+	protected void setDebugConfiguration(){
+		final String searchPath="D:\\tempDat\\AutoMic-test";
+		this.setGeneralOptions(searchPath, true, false);
+	}
+	
+	/**
+	 * main method for debugging.
+	 * Sets debug configuration via the method defined for each JobDistributor implementation
+	 * Then executes JobDistributor
+	 * 
+	 */
+	public static void main(String[] args) {
+		// set the plugins.dir property to make the plugin appear in the Plugins menu
+		Class<?> clazz = JobDistributor_MicroscopeCommander_AF_LowZoom_HighZoom_Manual.class;
+		//String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
+		//String pluginsDir = url.substring(5, url.length() - clazz.getName().length() - 6);
+		//System.setProperty("plugins.dir", pluginsDir);
+
+		// start ImageJ
+		new ImageJ();
+		//DEBUG=true;
+		//Debug.run(plugin, parameters);
+		//new WaitForUserDialog("test Maven project").show();
+		
+		// run the plugin
+		
+		//exrerimentFolderPath="D:/tempDat/AutoFRAP_test";
+		//showDemo=true;
+		//pnum=1;
+		//setDebugConfiguration();
+		
+
+		//IJ.runPlugIn(clazz.getName(),"Debug run");
+		IJ.runPlugIn(clazz.getName(),"");
+
+	}
+	
+}

src/main/java/automic/online/jobdistributors/commander/imaging/JobDistributor_MicroscopeCommander_AF_LowZoom_HighZoom_Script.java

+package automic.online.jobdistributors.commander.imaging;
+
+
+import ij.IJ;
+import ij.ImageJ;
+import ij.gui.GenericDialog;
+import ij.plugin.PlugIn;
+import automic.online.jobdistributors.JobDistributor_Abstract;
+import automic.online.jobs.common.Job_AutofocusInit_Commander;
+import automic.online.jobs.common.Job_GetMultipleImagingPositions_Script_Commander;
+import automic.online.jobs.common.Job_RecordFinish;
+import automic.table.TableModel;
+import automic.table.TableProcessor;
+
+
+public class JobDistributor_MicroscopeCommander_AF_LowZoom_HighZoom_Script extends JobDistributor_Abstract  implements PlugIn{
+	
+
+	
+	@Override
+	protected void fillJobList(){
+		
+		super.addImageJob(Job_AutofocusInit_Commander.class,						"AF--",  "AF",	true);
+		super.addImageJob(Job_GetMultipleImagingPositions_Script_Commander.class,	"LowZoom--", "LowZoom",	true);
+		super.addImageJob(Job_RecordFinish.class,									"HighZoom--", "HighZoom",true);
+
+	}
+	
+	@Override
+	protected TableModel constructTabModel(String _rpth){
+		TableModel outTbl=new TableModel(_rpth);
+
+		outTbl.addColumn("Date.Time");
+		
+		outTbl.addFileColumns("AF", "IMG");
+		outTbl.addFileColumns("LowZoom", "IMG");
+		outTbl.addFileColumns("HighZoom", "IMG");
+
+		
+		outTbl.addValueColumn("Success", "BOOL");
+		
+		outTbl.addRow(new Object[outTbl.getColumnCount()]);
+		return outTbl;
+	}
+	
+	@Override
+	protected TableProcessor configureTableProcessor(TableModel _tModel)throws Exception{
+		TableProcessor tProcessor=new TableProcessor(_tModel);
+		return tProcessor;
+	}
+
+	
+	
+	@Override
+	protected void putProtocolPreferencesToDialog(GenericDialog _dialog){
+	}
+
+	@Override
+	protected void getProtocolPreferencesFromDialog(GenericDialog _dialog){
+	}
+	
+	@Override
+	protected boolean showDialogInDebugRun(){
+		return false;
+	}
+
+
+	
+	@Override
+	protected void setDebugConfiguration(){
+		final String searchPath="D:\\tempDat\\AutoMic-test";
+		this.setGeneralOptions(searchPath, true, false);
+	}
+	
+	/**
+	 * main method for debugging.
+	 * Sets debug configuration via the method defined for each JobDistributor implementation
+	 * Then executes JobDistributor
+	 * 
+	 */
+	public static void main(String[] args) {
+		// set the plugins.dir property to make the plugin appear in the Plugins menu
+		Class<?> clazz = JobDistributor_MicroscopeCommander_AF_LowZoom_HighZoom_Script.class;
+		//String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
+		//String pluginsDir = url.substring(5, url.length() - clazz.getName().length() - 6);
+		//System.setProperty("plugins.dir", pluginsDir);
+
+		// start ImageJ
+		new ImageJ();
+		//DEBUG=true;
+		//Debug.run(plugin, parameters);
+		//new WaitForUserDialog("test Maven project").show();
+		
+		// run the plugin
+		
+		//exrerimentFolderPath="D:/tempDat/AutoFRAP_test";
+		//showDemo=true;
+		//pnum=1;
+		//setDebugConfiguration();
+		
+
+		//IJ.runPlugIn(clazz.getName(),"Debug run");
+		IJ.runPlugIn(clazz.getName(),"");
+
+	}
+	
+}

src/main/java/automic/online/jobs/common/Job_AutofocusInit_Commander.java

@@ -5,6 +5,8 @@ import java.util.concurrent.TimeUnit;
 
 import automic.geom.Point3D;
 import automic.online.jobs.Job_Default;
+import automic.parameters.ParameterCollection;
+import automic.parameters.ParameterType;
 import automic.utils.imagefiles.ImageOpenerWithBioformats;
 import automic.utils.roi.ROIManipulator2D;
 import ij.ImageJ;
@@ -16,12 +18,18 @@ import ij.gui.ProfilePlot;
 import ij.gui.Roi;
 
 public class Job_AutofocusInit_Commander  extends Job_Default{
+	public static final String KEY_FOCUS_SLICE_OFFSET="Slice offset";
+
+	
 	//private static final Roi nullRoi=null;
 	private ImagePlus img=null;
 	int maxind=-1;
 	int zSubmit=-1;
 	Boolean isLineScan=null;
 	
+	int sliceOffset=0;
+
+	
 	@Override
 	protected void cleanIterOutput(){
 		img=null;
@@ -135,6 +143,21 @@ public class Job_AutofocusInit_Commander  extends Job_Default{
 	}
 	
 	
+	@Override
+	public ParameterCollection createJobParameters(){
+		ParameterCollection jobCollection=new ParameterCollection();
+		
+		jobCollection.addParameter(KEY_FOCUS_SLICE_OFFSET, null, sliceOffset, ParameterType.INT_PARAMETER);
+		
+		return jobCollection;
+	}
+
+	@Override
+	public void parseInputParameterValues(ParameterCollection _jobParameterCollection){
+		this.sliceOffset=(Integer)_jobParameterCollection.getParameterValue(KEY_FOCUS_SLICE_OFFSET);
+	}
+
+	
 	@Override
 	public void  postProcessSuccess()throws Exception{
 		this.microscopeCommander.submitJobPixels(newImgFile, "", new Point3D(null,null,(double)zSubmit));

src/main/java/automic/online/jobs/common/Job_GetMultipleImagingPositions_Manual_Commander.java

+package automic.online.jobs.common;
+
+import java.awt.Color;
+import java.awt.Polygon;
+import java.awt.Rectangle;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.io.File;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.concurrent.TimeUnit;
+
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+import javax.swing.Timer;
+
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import automic.online.jobs.Job_Default;
+import automic.parameters.ParameterCollection;
+import automic.parameters.ParameterType;
+import automic.utils.imagefiles.ImageOpenerWithBioformats;
+import ij.IJ;
+import ij.ImageJ;
+import ij.ImagePlus;
+import ij.gui.ImageCanvas;
+import ij.gui.ImageWindow;
+import ij.gui.OvalRoi;
+import ij.gui.Overlay;
+import ij.gui.Roi;
+import ij.gui.Toolbar;
+import loci.plugins.in.ImporterOptions;
+import mcib3d.geom.Point3D;
+
+public class Job_GetMultipleImagingPositions_Manual_Commander extends Job_Default{
+	public static final String INPUT_IMG_TAG="Selection";
+	//public static String FRAP_IMG_TAG="PA";
+	
+	private boolean selectionMade=false;
+	
+	public static final String KEY_LOCATION_X="Selection window location X";
+	public static final String KEY_LOCATION_Y="Selection window location Y";
+	
+	public static final String KEY_RESPONCE_TIME="Time to wait for responce";
+	public static final String KEY_USE_ROIS_TIME_END="Proceed with selected ROIs if time expires";
+	public static final String KEY_CAN_MOVE_ROI="Can move Roi after drawing";
+	public static final String KEY_REGION_TYPE="Region type (circle, rectangle, polygon)";
+	//TODO: for now only "circle" is implemented in ZenBlue interface. Implement other shapes in future
+	public static final String KEY_BLEACH_RADIUS="Bleach radius for circle";
+	
+	
+	//region keys
+	public static final String CIRCLE_REGION="circle";
+	public static final String RECTANGLE_REGION="rectangle";
+	public static final String POLYGON_REGION="polygon";
+	
+	
+	
+	private ImagePlus inImg;
+	
+	Point3D selPoint;
+	
+	private int initialLocationX=1000;
+	private int initialLocationY=120;
+	private int responceTime=30;
+	private boolean useRoisTimeEnd=true;
+	private boolean canMoveRoi=false;
+	
+	private String regionType=CIRCLE_REGION;
+	private int bleachRadius=40;
+	
+	//String xRoisString;
+	//String yRoisString;
+	
+
+	SelectionManadgement selectedRoiManager;
+	/*
+	class RoiCommand{
+		private String xRoiString;
+		private String yRoiString;
+		
+		public RoiCommand(Roi _selectedRoi) {
+			
+			if(_selectedRoi.getType()!=getExpectedSelectionType())
+				throw new RuntimeException ("Region does not match specified type");
+
+			
+			switch(regionType) {
+				case CIRCLE_REGION: 
+					
+					Polygon pointPolygon=_selectedRoi.getPolygon();
+					int selectedXPosition=pointPolygon.xpoints[0];
+					int selectedYPosition=pointPolygon.ypoints[0];
+						
+					xRoiString=""+selectedXPosition+", "+(selectedXPosition+bleachRadius);
+					yRoiString=""+selectedYPosition+", "+(selectedYPosition);
+					
+					break;
+				
+				case RECTANGLE_REGION: 
+					
+					Rectangle bounds=_selectedRoi.getBounds();
+					xRoiString=""+bounds.x+", "+(bounds.x+bounds.width);
+					yRoiString=""+bounds.y+", "+(bounds.y+bounds.height);
+					break;
+				
+				case POLYGON_REGION: 
+					
+					Polygon pointPolygon2=_selectedRoi.getPolygon();
+					int nPoints=pointPolygon2.npoints;
+					xRoiString="";
+					yRoiString="";
+					for (int iPoint=0;iPoint<nPoints;iPoint++) {
+						if(iPoint!=0) {
+							xRoiString+=", ";
+							yRoiString+=", ";
+						}
+						xRoiString+=pointPolygon2.xpoints[iPoint];
+						yRoiString+=pointPolygon2.ypoints[iPoint];
+					}
+					
+					break;
+				
+				default: throw new RuntimeException ("Region type specified wrongly");
+			}
+		}
+		
+		
+		public String getXRoiString() {
+			return xRoiString;
+		}
+		
+		public String getYRoiString() {
+			return yRoiString;
+		}
+		
+		
+	}