Commit 105efc80 authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi
Browse files

default parameter values in local variables

parent f79f143e
......@@ -15,9 +15,9 @@
-->
<groupId>embl.almf</groupId>
<version>0.1.0-SNAPSHOT</version>
<version>0.1.1</version>
<name>Fly_Embrio_Feedback</name>
<name>Fly_Embryo_Feedback</name>
<inceptionYear>2017</inceptionYear>
<organization>
<name>EMBL</name>
......@@ -143,6 +143,6 @@
</plugins>
</build>
<artifactId>Fly_Embrio_Feedback</artifactId>
<artifactId>Fly_Embryo_Feedback</artifactId>
<description>Implementation of online feedback procedures for fly embrio screen</description>
</project>
......@@ -20,7 +20,7 @@ public class Job_AutofocusInitOffset extends Job_Default{
public static final String KEY_FOCUS_SLICE_OFFSET="Slice offset";
int sliceOffset;
int sliceOffset=2000;
//private static final Roi nullRoi=null;
......@@ -100,7 +100,7 @@ public class Job_AutofocusInitOffset extends Job_Default{
public ParameterCollection createJobParameters(){
ParameterCollection jobCollection=new ParameterCollection();
jobCollection.addParameter(KEY_FOCUS_SLICE_OFFSET, null, 2000, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_FOCUS_SLICE_OFFSET, null, sliceOffset, ParameterType.INT_PARAMETER);
return jobCollection;
}
......
......@@ -36,7 +36,7 @@ public class Job_FocusEmbryoAuto extends Job_Default{
private Integer selectedZPosition;
private Integer zSubmit;
private int targetChannel;
private int targetChannel=1;
@Override
protected void cleanIterOutput(){
......@@ -86,8 +86,8 @@ public class Job_FocusEmbryoAuto extends Job_Default{
ImporterOptions options = new ImporterOptions();
options.setAutoscale(true);
options.setId(_imageFile.getAbsolutePath());
options.setCBegin(0, targetChannel);
options.setCEnd(0, targetChannel);
options.setCBegin(0, targetChannel-1);
options.setCEnd(0, targetChannel-1);
//options.setTBegin(0, 0);
//options.setTEnd(0, 0);
......@@ -192,14 +192,14 @@ public class Job_FocusEmbryoAuto extends Job_Default{
public ParameterCollection createJobParameters(){
ParameterCollection jobCollection=new ParameterCollection();
jobCollection.addParameter(KEY_FOCUS_CHANNEL_INDEX, null, 1, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_FOCUS_CHANNEL_INDEX, null, targetChannel, ParameterType.INT_PARAMETER);
return jobCollection;
}
@Override
public void parseInputParameterValues(ParameterCollection _jobParameterCollection){
this.targetChannel=(Integer)_jobParameterCollection.getParameterValue(KEY_FOCUS_CHANNEL_INDEX)-1;
this.targetChannel=(Integer)_jobParameterCollection.getParameterValue(KEY_FOCUS_CHANNEL_INDEX);
}
/**
......
......@@ -60,18 +60,18 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
//private boolean selectionMade=false;
//private boolean invert_Z;
private int wellBrightFieldChannel;
private int wellBrightFieldThreshold;
private int embryoFluorChannel;
private double embryoFluorFilterRadius;
private int embryoFluorThreshold;
private double watershedTolerance;
private int embryoMinSize;
private int embryoMaxSize;
private double embryoMinIntensity;
private double embryoMaxIntensity;
private double embryoMinAR;
private double embryoMaxAR;
private int wellBrightFieldChannel=2;
private int wellBrightFieldThreshold=10;
private int embryoFluorChannel=1;
private double embryoFluorFilterRadius=5.0;
private int embryoFluorThreshold=70;
private double watershedTolerance=100.0;
private int embryoMinSize=500;
private int embryoMaxSize=10000;
private double embryoMinIntensity=50.0;
private double embryoMaxIntensity=256.0;
private double embryoMinAR=1.8;
private double embryoMaxAR=10.0;
private int embryoMaxCount;
......@@ -276,19 +276,19 @@ public class Job_SelectMultipleEmbryosAuto extends Job_Default{
public ParameterCollection createJobParameters(){
ParameterCollection jobCollection=new ParameterCollection();
jobCollection.addParameter(KEY_WELL_CHANNEL_INDEX, null, 2, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WELL_CHANNEL_THRESHOLD, null, 10, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_INDEX, null, 1, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_FILTER_RADIUS, null, 5.0, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_THRESHOLD, null, 70, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WATERSHED_TOLERANCE, null, 100.0, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_WELL_CHANNEL_INDEX, null, wellBrightFieldChannel, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WELL_CHANNEL_THRESHOLD, null, wellBrightFieldThreshold, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_INDEX, null, embryoFluorChannel, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_FILTER_RADIUS, null, embryoFluorFilterRadius, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_THRESHOLD, null, embryoFluorThreshold, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WATERSHED_TOLERANCE, null, watershedTolerance, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_SIZE, null, 500, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_SIZE, null, 10000, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_INTENSITY, null, 50.0, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_INTENSITY, null, 256.0, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_AR, null, 1.8, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_AR, null, 10.0, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_SIZE, null, embryoMinSize, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_SIZE, null, embryoMaxSize, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_INTENSITY, null, embryoMinIntensity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_INTENSITY, null, embryoMaxIntensity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_AR, null, embryoMinAR, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_AR, null, embryoMaxAR, ParameterType.DOUBLE_PARAMETER);
......
package feedback.fly.embryo.jobs;
import java.awt.Color;
import java.awt.geom.Point2D;
import java.io.File;
import java.util.concurrent.TimeUnit;
import automic.online.jobdistributors.ZeissKeys;
import automic.online.jobs.Job_Default;
import automic.parameters.ParameterCollection;
import automic.parameters.ParameterType;
import automic.utils.ArrIndUtils;
import automic.utils.DebugVisualiserSettings;
import automic.utils.roi.ParticleFilterer;
import automic.utils.roi.ROIManipulator2D;
import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.gui.Overlay;
import ij.gui.Roi;
import ij.plugin.Duplicator;
import ij.plugin.filter.ParticleAnalyzer;
import ij.plugin.filter.RankFilters;
import ij.plugin.frame.RoiManager;
import loci.plugins.BF;
import loci.plugins.in.ImporterOptions;
public class Job_SelectMultipleEmbryosAutoInit extends Job_SelectMultipleEmbryosAuto{
......
......@@ -62,24 +62,21 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
//private boolean selectionMade=false;
//private boolean invert_Z;
private int wellBrightFieldChannel;
private int wellBrightFieldThreshold;
private int embryoFluorChannel;
private double embryoFluorFilterRadius;
private int embryoFluorThreshold;
private double watershedTolerance;
private int embryoMinSize;
private int embryoMaxSize;
private double embryoMinIntensity;
private double embryoMaxIntensity;
private double embryoMinAR;
private double embryoMaxAR;
private int wellBrightFieldChannel=2;
private int wellBrightFieldThreshold=10;
private int embryoFluorChannel=1;
private double embryoFluorFilterRadius=5.0;
private int embryoFluorThreshold=70;
private double watershedTolerance=100.0;
private int embryoMinSize=500;
private int embryoMaxSize=10000;
private double embryoMinIntensity=50.0;
private double embryoMaxIntensity=256.0;
private double embryoMinAR=1.8;
private double embryoMaxAR=10.0;
private int embryoMaxCount;
private int embryoMaxCount=5;
//private int initialLocationY;
@Override
protected void cleanIterOutput(){
......@@ -286,23 +283,21 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
public ParameterCollection createJobParameters(){
ParameterCollection jobCollection=new ParameterCollection();
jobCollection.addParameter(KEY_WELL_CHANNEL_INDEX, null, 2, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WELL_CHANNEL_THRESHOLD, null, 10, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_INDEX, null, 1, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_FILTER_RADIUS, null, 5.0, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_THRESHOLD, null, 70, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WATERSHED_TOLERANCE, null, 100.0, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_WELL_CHANNEL_INDEX, null, wellBrightFieldChannel, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WELL_CHANNEL_THRESHOLD, null, wellBrightFieldThreshold, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_INDEX, null, embryoFluorChannel, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_FILTER_RADIUS, null, embryoFluorFilterRadius, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_THRESHOLD, null, embryoFluorThreshold, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WATERSHED_TOLERANCE, null, watershedTolerance, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_SIZE, null, 500, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_SIZE, null, 10000, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_INTENSITY, null, 50.0, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_INTENSITY, null, 256.0, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_AR, null, 1.8, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_AR, null, 10.0, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_SIZE, null, embryoMinSize, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_SIZE, null, embryoMaxSize, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_INTENSITY, null, embryoMinIntensity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_INTENSITY, null, embryoMaxIntensity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_AR, null, embryoMinAR, 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, embryoMaxCount, ParameterType.INT_PARAMETER);
return jobCollection;
......@@ -317,7 +312,6 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
this.embryoFluorThreshold=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_CHANNEL_THRESHOLD);
this.watershedTolerance=(Double)_jobParameterCollection.getParameterValue(KEY_WATERSHED_TOLERANCE);
this.embryoMinSize=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MIN_SIZE);
this.embryoMaxSize=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_SIZE);
this.embryoMinIntensity=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MIN_INTENSITY);
......@@ -325,9 +319,6 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
this.embryoMinAR=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MIN_AR);
this.embryoMaxAR=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_AR);
this.embryoMaxCount=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_COUNT);
}
......
......@@ -2,21 +2,10 @@ package feedback.fly.embryo.jobtests;
import ij.IJ;
import ij.ImageJ;
import ij.io.OpenDialog;
import ij.plugin.PlugIn;
import loci.formats.ImageReader;
import loci.formats.MetadataTools;
import loci.formats.meta.IMetadata;
import java.io.File;
import automic.online.jobs.TestJobGui;
//import javax.swing.table.AbstractTableModel;
import automic.table.ManualControlFrame;
import automic.table.TableModel;
import automic.utils.FileUtils;
import automic.utils.Utils;
import feedback.fly.embryo.jobs.Job_SelectMultipleEmbryosAuto;
......
......@@ -11,7 +11,7 @@ public class RunAutoDistributor {
// start ImageJ
new ImageJ();
IJ.runPlugIn(clazz.getName(),"Debug run");
//IJ.runPlugIn(clazz.getName(),"");
//IJ.runPlugIn(clazz.getName(),"Debug run");
IJ.runPlugIn(clazz.getName(),"");
}
}
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