Commit d105b68f authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi
Browse files

delay time for opening is an additional parameter

parent 4ac01a78
...@@ -95,6 +95,7 @@ public class JobDistributor_AutoSelectionMultiple_AFocus_Rotation extends JobDis ...@@ -95,6 +95,7 @@ public class JobDistributor_AutoSelectionMultiple_AFocus_Rotation extends JobDis
outTbl.addValueColumn("Zoom.X", "NUM"); outTbl.addValueColumn("Zoom.X", "NUM");
outTbl.addValueColumn("Zoom.Y", "NUM"); outTbl.addValueColumn("Zoom.Y", "NUM");
outTbl.addValueColumn("Rotation", "NUM");
outTbl.addValueColumn("Focus.Z", "NUM"); outTbl.addValueColumn("Focus.Z", "NUM");
...@@ -155,9 +156,9 @@ public class JobDistributor_AutoSelectionMultiple_AFocus_Rotation extends JobDis ...@@ -155,9 +156,9 @@ public class JobDistributor_AutoSelectionMultiple_AFocus_Rotation extends JobDis
@Override @Override
protected void setDebugConfiguration(){ protected void setDebugConfiguration(){
final String searchPath="C:/tempDat/AutoFRAP_test"; final String searchPath="C:/tempDat/AutoMic_test";
this.setGeneralOptions(searchPath, true, false); this.setGeneralOptions(searchPath, true, false);
this.fileExtension="czi"; this.fileExtension="lsm";
//manualTrackParameterCollectionSelect=new Job_SelectMultipleEmbryosAutoInit().createJobParameters(); //manualTrackParameterCollectionSelect=new Job_SelectMultipleEmbryosAutoInit().createJobParameters();
//manualTrackParameterCollectionSelect.setUndefinedValuesFromDefaults(); //manualTrackParameterCollectionSelect.setUndefinedValuesFromDefaults();
......
...@@ -44,6 +44,7 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{ ...@@ -44,6 +44,7 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
public static final String KEY_EMBRYO_MAX_COUNT="Maximal number of embryos from well"; public static final String KEY_EMBRYO_MAX_COUNT="Maximal number of embryos from well";
public static final String KEY_WAIT_IMAGE_OPENING="Wait for image opening (milliseconds)";
//private static final Roi nullRoi=null; //private static final Roi nullRoi=null;
...@@ -74,7 +75,8 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{ ...@@ -74,7 +75,8 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
private double embryoMaxAR=10.0; private double embryoMaxAR=10.0;
private int embryoMaxCount; private int embryoMaxCount=5;
private int imageOpeningTimeDelay=3000;
//private int initialLocationY; //private int initialLocationY;
...@@ -96,7 +98,7 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{ ...@@ -96,7 +98,7 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
Exper_nm=Exper_nm.substring(0, Exper_nm.indexOf(fileTag)); Exper_nm=Exper_nm.substring(0, Exper_nm.indexOf(fileTag));
this.setSharedValue("Experiment Name", Exper_nm); this.setSharedValue("Experiment Name", Exper_nm);
TimeUnit.MILLISECONDS.sleep(2000); TimeUnit.MILLISECONDS.sleep(imageOpeningTimeDelay);
//img=ImageOpenerWithBioformats.openImage(newImgFile); //img=ImageOpenerWithBioformats.openImage(newImgFile);
img=openSelectedSlices(newImgFile); img=openSelectedSlices(newImgFile);
} }
...@@ -291,9 +293,8 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{ ...@@ -291,9 +293,8 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
jobCollection.addParameter(KEY_EMBRYO_MAX_AR, null, embryoMaxAR, ParameterType.DOUBLE_PARAMETER); jobCollection.addParameter(KEY_EMBRYO_MAX_AR, null, embryoMaxAR, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_COUNT,null, 5, ParameterType.INT_PARAMETER); jobCollection.addParameter(KEY_EMBRYO_MAX_COUNT,null, 5, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WAIT_IMAGE_OPENING,null, imageOpeningTimeDelay, ParameterType.INT_PARAMETER);
return jobCollection; return jobCollection;
} }
...@@ -316,9 +317,8 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{ ...@@ -316,9 +317,8 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
this.embryoMaxAR=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_AR); this.embryoMaxAR=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_AR);
this.embryoMaxCount=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_COUNT); this.embryoMaxCount=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_COUNT);
this.imageOpeningTimeDelay=(Integer)_jobParameterCollection.getParameterValue(KEY_WAIT_IMAGE_OPENING);
} }
@Override @Override
......
package feedback.fly.embryo.jobs; package feedback.fly.embryo.jobs;
import java.util.concurrent.TimeUnit;
import ij.ImageJ; import ij.ImageJ;
public class Job_SelectMultipleEmbryosAutoInit extends Job_SelectMultipleEmbryosAuto{ public class Job_SelectMultipleEmbryosAutoInit extends Job_SelectMultipleEmbryosAuto{
...@@ -11,15 +9,7 @@ public class Job_SelectMultipleEmbryosAutoInit extends Job_SelectMultipleEmbryo ...@@ -11,15 +9,7 @@ public class Job_SelectMultipleEmbryosAutoInit extends Job_SelectMultipleEmbryo
protected void preProcessOnline()throws Exception{ protected void preProcessOnline()throws Exception{
super.clearSharedData(); super.clearSharedData();
currentTable.cleanRecord(curDInd); currentTable.cleanRecord(curDInd);
currentTable.setFileAbsolutePath(newImgFile, curDInd, imgColumnNm, "IMG"); super.preProcessOnline();
String Exper_nm=newImgFile.getName();
Exper_nm=Exper_nm.substring(0, Exper_nm.indexOf(fileTag));
this.setSharedValue("Experiment Name", Exper_nm);
TimeUnit.MILLISECONDS.sleep(2000);
//img=ImageOpenerWithBioformats.openImage(newImgFile);
img=openSelectedSlices(newImgFile);
} }
/** /**
......
...@@ -45,6 +45,7 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{ ...@@ -45,6 +45,7 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
public static final String KEY_EMBRYO_MAX_COUNT="Maximal number of embryos from well"; public static final String KEY_EMBRYO_MAX_COUNT="Maximal number of embryos from well";
public static final String KEY_WAIT_IMAGE_OPENING="Wait for image opening (milliseconds)";
//private static final Roi nullRoi=null; //private static final Roi nullRoi=null;
...@@ -76,6 +77,7 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{ ...@@ -76,6 +77,7 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
private double embryoMaxAR=10.0; private double embryoMaxAR=10.0;
private int embryoMaxCount=5; private int embryoMaxCount=5;
private int imageOpeningTimeDelay=3000;
@Override @Override
...@@ -96,7 +98,7 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{ ...@@ -96,7 +98,7 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
Exper_nm=Exper_nm.substring(0, Exper_nm.indexOf(fileTag)); Exper_nm=Exper_nm.substring(0, Exper_nm.indexOf(fileTag));
this.setSharedValue("Experiment Name", Exper_nm); this.setSharedValue("Experiment Name", Exper_nm);
TimeUnit.MILLISECONDS.sleep(2000); TimeUnit.MILLISECONDS.sleep(imageOpeningTimeDelay);
//img=ImageOpenerWithBioformats.openImage(newImgFile); //img=ImageOpenerWithBioformats.openImage(newImgFile);
img=openSelectedSlices(newImgFile); img=openSelectedSlices(newImgFile);
} }
...@@ -298,6 +300,7 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{ ...@@ -298,6 +300,7 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
jobCollection.addParameter(KEY_EMBRYO_MAX_AR, null, embryoMaxAR, ParameterType.DOUBLE_PARAMETER); jobCollection.addParameter(KEY_EMBRYO_MAX_AR, null, embryoMaxAR, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_COUNT,null, embryoMaxCount, ParameterType.INT_PARAMETER); jobCollection.addParameter(KEY_EMBRYO_MAX_COUNT,null, embryoMaxCount, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WAIT_IMAGE_OPENING,null, imageOpeningTimeDelay, ParameterType.INT_PARAMETER);
return jobCollection; return jobCollection;
...@@ -320,6 +323,7 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{ ...@@ -320,6 +323,7 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
this.embryoMaxAR=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_AR); this.embryoMaxAR=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_AR);
this.embryoMaxCount=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_COUNT); this.embryoMaxCount=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_COUNT);
this.imageOpeningTimeDelay=(Integer)_jobParameterCollection.getParameterValue(KEY_WAIT_IMAGE_OPENING);
} }
@Override @Override
......
package jobdistributors.run.debug;
import feedback.fly.embryo.jobdistributors.JobDistributor_AutoSelectionMultiple_AFocus_Rotation;
import ij.IJ;
import ij.ImageJ;
public class RunAutoDistributorRotation {
public static void main(String[] args) {
Class<?> clazz = JobDistributor_AutoSelectionMultiple_AFocus_Rotation.class;
// start ImageJ
new ImageJ();
IJ.runPlugIn(clazz.getName(),"Debug run");
//IJ.runPlugIn(clazz.getName(),"");
}
}
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