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Commit 84f0f410 authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi
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add median selection on low zoom images

parent 0fd78966
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pom.xml
View file @ 84f0f410
......@@ -15,7 +15,7 @@
-->
<groupId>embl.almf</groupId>
<version>0.1.1</version>
<version>0.1.2-SNAPSHOT</version>
<name>Fly_Embryo_Feedback</name>
<inceptionYear>2017</inceptionYear>
......@@ -87,7 +87,7 @@
<dependency>
<groupId>embl.almf</groupId>
<artifactId>AutoMicTools_</artifactId>
<version>1.1.2-SNAPSHOT</version>
<version>1.1.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>net.imagej</groupId>
......
src/main/java/feedback/fly/embryo/jobs/Job_AutofocusInitOffset.java
View file @ 84f0f410
......@@ -2,7 +2,7 @@ package feedback.fly.embryo.jobs;
import java.awt.Color;
import automic.online.jobdistributors.ZeissKeys;
import automic.online.microscope.ZeissKeys;
import automic.online.jobs.Job_Default;
import automic.parameters.ParameterCollection;
import automic.parameters.ParameterType;
......
src/main/java/feedback/fly/embryo/jobs/Job_FocusEmbryoAuto.java
View file @ 84f0f410
......@@ -6,7 +6,7 @@ import java.awt.geom.Point2D;
import java.io.File;
import java.util.concurrent.TimeUnit;
import automic.online.jobdistributors.ZeissKeys;
import automic.online.microscope.ZeissKeys;
import automic.online.jobs.Job_Default;
//import automic.utils.imagefiles.ImageOpenerWithBioformats;
import automic.parameters.ParameterCollection;
......
src/main/java/feedback/fly/embryo/jobs/Job_FocusEmbryoManual.java
View file @ 84f0f410
......@@ -9,7 +9,7 @@ import java.awt.geom.Point2D;
import java.io.File;
import java.util.concurrent.TimeUnit;
import automic.online.jobdistributors.ZeissKeys;
import automic.online.microscope.ZeissKeys;
import automic.online.jobs.Job_Default;
//import automic.utils.imagefiles.ImageOpenerWithBioformats;
import automic.parameters.ParameterCollection;
......
src/main/java/feedback/fly/embryo/jobs/Job_SelectEmbryoManual.java
View file @ 84f0f410
......@@ -10,7 +10,7 @@ import java.io.File;
import java.util.concurrent.TimeUnit;
import automic.online.jobdistributors.ZeissKeys;
import automic.online.microscope.ZeissKeys;
import automic.online.jobs.Job_Default;
//import automic.utils.imagefiles.ImageOpenerWithBioformats;
import automic.parameters.ParameterCollection;
......
src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosAuto.java
View file @ 84f0f410
......@@ -5,7 +5,7 @@ import java.awt.geom.Point2D;
import java.io.File;
import java.util.concurrent.TimeUnit;
import automic.online.jobdistributors.ZeissKeys;
import automic.online.microscope.ZeissKeys;
import automic.online.jobs.Job_Default;
import automic.parameters.ParameterCollection;
import automic.parameters.ParameterType;
......
src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosAutoRotation.java
View file @ 84f0f410
......@@ -5,7 +5,7 @@ import java.awt.geom.Point2D;
import java.io.File;
import java.util.concurrent.TimeUnit;
import automic.online.jobdistributors.ZeissKeys;
import automic.online.microscope.ZeissKeys;
import automic.online.jobs.Job_Default;
import automic.parameters.ParameterCollection;
import automic.parameters.ParameterType;
......@@ -38,8 +38,11 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
public static final String KEY_WATERSHED_TOLERANCE="Watershed tolerance";
public static final String KEY_EMBRYO_MIN_SIZE="Embryo minimal size (pixels)";
public static final String KEY_EMBRYO_MAX_SIZE="Embryo maximal size (pixels)";
public static final String KEY_EMBRYO_MIN_INTENSITY="Embryo minimal intensity";
public static final String KEY_EMBRYO_MAX_INTENSITY="Embryo maximal intensity";
public static final String KEY_EMBRYO_MIN_MEAN_INTENSITY="Embryo minimal mean intensity";
public static final String KEY_EMBRYO_MAX_MEAN_INTENSITY="Embryo maximal mean intensity";
public static final String KEY_EMBRYO_MIN_MEDIAN_INTENSITY="Embryo minimal median intensity";
public static final String KEY_EMBRYO_MAX_MEDIAN_INTENSITY="Embryo maximal median intensity";
public static final String KEY_EMBRYO_MIN_AR="Embryo minimal aspect ratio";
public static final String KEY_EMBRYO_MAX_AR="Embryo maximal aspect ratio";
......@@ -71,8 +74,12 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
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 embryoMinMeanIntensity=50.0;
private double embryoMaxMeanIntensity=256.0;
private double embryoMinMedianIntensity=50.0;
private double embryoMaxMedianIntensity=256.0;
private double embryoMinAR=1.8;
private double embryoMaxAR=10.0;
......@@ -210,7 +217,8 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
ParticleFilterer embryoFilter=new ParticleFilterer(_embryoImage.getProcessor(), identifiedRois);
embryoFilter.filterInRoi(wellRoi);
embryoFilter.filterThr(ParticleFilterer.MEAN, embryoMinIntensity, embryoMaxIntensity);
embryoFilter.filterThr(ParticleFilterer.MEAN, embryoMinMeanIntensity, embryoMaxMeanIntensity);
embryoFilter.filterThr(ParticleFilterer.MEDIAN, embryoMinMedianIntensity, embryoMaxMedianIntensity);
embryoFilter.filterThr(ParticleFilterer.ASPECT_RATIO, embryoMinAR, embryoMaxAR);
embryoRois=embryoFilter.getPassedRois();
......@@ -294,8 +302,10 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
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_MEAN_INTENSITY, null, embryoMinMeanIntensity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_MEAN_INTENSITY, null, embryoMaxMeanIntensity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_MEDIAN_INTENSITY, null, embryoMinMedianIntensity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_MEDIAN_INTENSITY, null, embryoMaxMedianIntensity, 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);
......@@ -317,8 +327,10 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
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);
this.embryoMaxIntensity=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_INTENSITY);
this.embryoMinMeanIntensity=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MIN_MEAN_INTENSITY);
this.embryoMaxMeanIntensity=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_MEAN_INTENSITY);
this.embryoMinMedianIntensity=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MIN_MEDIAN_INTENSITY);
this.embryoMaxMedianIntensity=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_MEDIAN_INTENSITY);
this.embryoMinAR=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MIN_AR);
this.embryoMaxAR=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_AR);
......
src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosManual.java
View file @ 84f0f410
......@@ -6,7 +6,7 @@ import java.awt.geom.Point2D;
import java.io.File;
import java.util.concurrent.TimeUnit;
import automic.online.jobdistributors.ZeissKeys;
import automic.online.microscope.ZeissKeys;
import automic.online.jobs.Job_Default;
import automic.parameters.ParameterCollection;
import ij.IJ;
......
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