Commit d5dfcd79 authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi
Browse files

selecting embryos based on circularity and solidity

parent 84f0f410
......@@ -45,6 +45,12 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
public static final String KEY_EMBRYO_MIN_AR="Embryo minimal aspect ratio";
public static final String KEY_EMBRYO_MAX_AR="Embryo maximal aspect ratio";
public static final String KEY_EMBRYO_MIN_CIRCULARITY="Embryo minimal circularity";
public static final String KEY_EMBRYO_MAX_CIRCULARITY="Embryo maximal circularity";
public static final String KEY_EMBRYO_MIN_SOLIDITY="Embryo minimal solidity";
public static final String KEY_EMBRYO_MAX_SOLIDITY="Embryo maximal solidity";
public static final String KEY_EMBRYO_MAX_COUNT="Maximal number of embryos from well";
......@@ -82,7 +88,13 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
private double embryoMinAR=1.8;
private double embryoMaxAR=10.0;
private double embryoMinCircularity=0.0;
private double embryoMaxCircularity=1.0;
private double embryoMinSolidity=0.0;
private double embryoMaxSolidity=1.0;
private int embryoMaxCount=5;
private int imageOpeningTimeDelay=3000;
......@@ -220,6 +232,10 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
embryoFilter.filterThr(ParticleFilterer.MEAN, embryoMinMeanIntensity, embryoMaxMeanIntensity);
embryoFilter.filterThr(ParticleFilterer.MEDIAN, embryoMinMedianIntensity, embryoMaxMedianIntensity);
embryoFilter.filterThr(ParticleFilterer.ASPECT_RATIO, embryoMinAR, embryoMaxAR);
embryoFilter.filterThr(ParticleFilterer.CIRCULARITY, embryoMinCircularity, embryoMaxCircularity);
embryoFilter.filterThr(ParticleFilterer.SOLIDITY, embryoMinSolidity, embryoMaxSolidity);
embryoRois=embryoFilter.getPassedRois();
if (embryoRois==null)
......@@ -306,9 +322,16 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
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);
jobCollection.addParameter(KEY_EMBRYO_MIN_CIRCULARITY, null, embryoMinCircularity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_CIRCULARITY, null, embryoMaxCircularity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_SOLIDITY, null, embryoMinSolidity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_SOLIDITY, null, embryoMaxSolidity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_COUNT,null, embryoMaxCount, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WAIT_IMAGE_OPENING,null, imageOpeningTimeDelay, ParameterType.INT_PARAMETER);
......@@ -333,6 +356,13 @@ public class Job_SelectMultipleEmbryosAutoRotation extends Job_Default{
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);
this.embryoMinCircularity=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MIN_CIRCULARITY);
this.embryoMaxCircularity=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_CIRCULARITY);
this.embryoMinSolidity=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MIN_SOLIDITY);
this.embryoMaxSolidity=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_SOLIDITY);
this.embryoMaxCount=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_COUNT);
this.imageOpeningTimeDelay=(Integer)_jobParameterCollection.getParameterValue(KEY_WAIT_IMAGE_OPENING);
......
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