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Improve output #2

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merged 4 commits into from
Jul 19, 2023
Merged

Improve output #2

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d735d7e
Added Moments (EigenValues)
SafarbatiSami Apr 12, 2023
b64d1bc
Added Date to Output File name.
SafarbatiSami Apr 12, 2023
ae2e6e6
Fix filenames
ppouchin Jul 19, 2023
106aa4d
Remove space
ppouchin Jul 19, 2023
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3 changes: 3 additions & 0 deletions src/main/java/gred/nucleus/core/ComputeNucleiParameters.java
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Original file line number Diff line number Diff line change
Expand Up @@ -117,6 +117,9 @@ public void addConfigParameters(String pathToConfig) {
private String getColNameResult() {
return "NucleusFileName\t" +
"Volume\t" +
"Moment 1\t" +
"Moment 2\t" +
"Moment 3 \t" +
"Flatness\t" +
"Elongation\t" +
"Esr\t" +
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3 changes: 3 additions & 0 deletions src/main/java/gred/nucleus/core/Measure3D.java
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Original file line number Diff line number Diff line change
Expand Up @@ -826,6 +826,9 @@ public String nucleusParameter3D() {
results = this.rawImage.getTitle() + "\t"
// + computeVolumeObject2(255) + "\t"
+ computeVolumeObjectML() + "\t"
+ computeEigenValue3D(255)[0] + "\t"
+ computeEigenValue3D(255)[1] + "\t"
+ computeEigenValue3D(255)[2] + "\t"
+ computeFlatnessAndElongation(255)[0] + "\t"
+ computeFlatnessAndElongation(255)[1] + "\t"
+ equivalentSphericalRadius(volume) + "\t"
Expand Down
18 changes: 12 additions & 6 deletions src/main/java/gred/nucleus/core/NucleusChromocentersAnalysis.java
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Expand Up @@ -56,21 +56,24 @@ public static void computeParameters(String rhfChoice,
String text = imagePlusSegmented.getTitle() + " " + volume + " "
+ measure3D.equivalentSphericalRadius(volume) + " "
+ surfaceArea + " "
+ measure3D.computeEigenValue3D(255)[0] + "\t"
+ measure3D.computeEigenValue3D(255)[1] + "\t"
+ measure3D.computeEigenValue3D(255)[2] + "\t"
+ measure3D.computeFlatnessAndElongation(255)[0] + " "
+ measure3D.computeFlatnessAndElongation(255)[1] + " "
+ measure3D.computeSphericity(volume, surfaceArea);
if (rhfChoice.equals("Volume and intensity")) {
LOGGER.info(
"ImageTitle Volume ESR SurfaceArea Flatness Elongation Sphericity IntensityRHF VolumeRHF NbCc VCcMean VCcTotal DistanceBorderToBorderMean DistanceBarycenterToBorderMean VoxelVolume");
"ImageTitle Volume ESR SurfaceArea Moment 1 Moment 2 Moment 3 Flatness Elongation Sphericity IntensityRHF VolumeRHF NbCc VCcMean VCcTotal DistanceBorderToBorderMean DistanceBarycenterToBorderMean VoxelVolume");
text += " " + measure3D.computeIntensityRHF(imagePlusInput, imagePlusSegmented, imagePlusChromocenter) + " "
+ measure3D.computeVolumeRHF(imagePlusSegmented, imagePlusChromocenter) + " ";
} else if (rhfChoice.equals("Volume")) {
LOGGER.info(
"ImageTitle Volume ESR SurfaceArea Flatness Elongation Sphericity VolumeRHF NbCc VCcMean VCcTotal DistanceBorderToBorderMean DistanceBarycenterToBorderMean VoxelVolume");
"ImageTitle Volume ESR SurfaceArea Moment 1 Moment 2 Moment 3 Flatness Elongation Sphericity VolumeRHF NbCc VCcMean VCcTotal DistanceBorderToBorderMean DistanceBarycenterToBorderMean VoxelVolume");
text += " " + measure3D.computeVolumeRHF(imagePlusSegmented, imagePlusChromocenter) + " ";
} else {
LOGGER.info(
"ImageTitle Volume ESR SurfaceArea Flatness Elongation Sphericity IntensityRHF NbCc VCcMean VCcTotal DistanceBorderToBorderMean DistanceBarycenterToBorderMean VoxelVolume");
"ImageTitle Volume ESR SurfaceArea Moment 1 Moment 2 Moment 3 Flatness Elongation Sphericity IntensityRHF NbCc VCcMean VCcTotal DistanceBorderToBorderMean DistanceBarycenterToBorderMean VoxelVolume");
text += " " +
measure3D.computeIntensityRHF(imagePlusInput, imagePlusSegmented, imagePlusChromocenter) +
" ";
Expand Down Expand Up @@ -132,19 +135,22 @@ public static void computeParameters(String pathResultsFile,
if (!exist) {
if (rhfChoice.equals("Volume and intensity")) {
text =
"ImageTitle\tVolume\tESR\tSurfaceArea\tFlatness\tElongation\tSphericity\tIntensityRHF\tVolumeRHF\tNbCc\tVCcMean\tVCcTotal\tDistanceBorderToBorderMean\tDistanceBarycenterToBorderMean\tVoxelVolume\n";
"ImageTitle\tVolume\tESR\tSurfaceArea\tMoment 1\tMoment 2 \tMoment 3 \tFlatness\tElongation\tSphericity\tIntensityRHF\tVolumeRHF\tNbCc\tVCcMean\tVCcTotal\tDistanceBorderToBorderMean\tDistanceBarycenterToBorderMean\tVoxelVolume\n";
} else if (rhfChoice.equals("Volume")) {
text =
"ImageTitle\tVolume\tESR\tSurfaceArea\tFlatness\tElongation\tSphericity\tVolumeRHF\tNbCc\tVCcMean\tVCcTotal\tDistanceBorderToBorderMean\tDistanceBarycenterToBorderMean\tVoxelVolume\n";
"ImageTitle\tVolume\tESR\tSurfaceArea\tMoment 1\tMoment 2 \tMoment 3 \tFlatness\tElongation\tSphericity\tVolumeRHF\tNbCc\tVCcMean\tVCcTotal\tDistanceBorderToBorderMean\tDistanceBarycenterToBorderMean\tVoxelVolume\n";
} else {
text =
"ImageTitle\tVolume\tESR\tSurfaceArea\tFlatness\tElongation\tSphericity\tIntensityRHF\tNbCc\tVCcMean\tVCcTotal\tDistanceBorderToBorderMean\tDistanceBarycenterToBorderMean\tVoxelVolume\n";
"ImageTitle\tVolume\tESR\tSurfaceArea\tMoment 1 \tMoment 2 \tMoment 3 \tFlatness\tElongation\tSphericity\tIntensityRHF\tNbCc\tVCcMean\tVCcTotal\tDistanceBorderToBorderMean\tDistanceBarycenterToBorderMean\tVoxelVolume\n";
}
}
text += imagePlusSegmented.getTitle() + "\t"
+ volume + "\t"
+ measure3D.equivalentSphericalRadius(volume) + "\t"
+ surfaceArea + "\t"
+ measure3D.computeEigenValue3D(255)[0] + "\t"
+ measure3D.computeEigenValue3D(255)[1] + "\t"
+ measure3D.computeEigenValue3D(255)[2] + "\t"
+ measure3D.computeFlatnessAndElongation(255)[0] + "\t"
+ measure3D.computeFlatnessAndElongation(255)[1] + "\t"
+ measure3D.computeSphericity(volume, surfaceArea) + "\t";
Expand Down
3 changes: 3 additions & 0 deletions src/main/java/gred/nucleus/machinelearning/ComputeNucleiParametersML.java
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Original file line number Diff line number Diff line change
Expand Up @@ -124,6 +124,9 @@ public void run() throws IOException, FormatException {
public String getResultsColumnNames() {
return "NucleusFileName\t" +
"Volume\t" +
"Moment 1\t" +
"Moment 2\t" +
"Moment 3 \t" +
"Flatness\t" +
"Elongation\t" +
"Sphericity\t" +
Expand Down
3 changes: 3 additions & 0 deletions src/main/java/gred/nucleus/mains/ComputeSegmentationParameters.java
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Expand Up @@ -96,6 +96,9 @@ public static void main(String[] args) throws Exception {
public static String getResultsColumnNames() {
return "NucleusFileName\t" +
"Volume\t" +
"Moment 1\t" +
"Moment 2\t" +
"Moment 3 \t" +
"Flatness\t" +
"Elongation\t" +
"Esr\t" +
Expand Down
3 changes: 3 additions & 0 deletions src/main/java/gred/nucleus/mains/ComputeSegmentationParametersDL.java
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Expand Up @@ -140,6 +140,9 @@ public static ImagePlus generateSegmentedImage(ImagePlus imagePlusInput,
public static String getResultsColumnNames() {
return "NucleusFileName\t" +
"Volume\t" +
"Moment 1\t" +
"Moment 2\t" +
"Moment 3 \t" +
"Flatness\t" +
"Elongation\t" +
"Esr\t" +
Expand Down
26 changes: 18 additions & 8 deletions src/main/java/gred/nucleus/segmentation/SegmentationCalling.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,14 @@
import fr.igred.omero.Client;
import fr.igred.omero.exception.AccessException;
import fr.igred.omero.exception.ServiceException;
import fr.igred.omero.repository.DatasetWrapper;
import fr.igred.omero.repository.ImageWrapper;
import fr.igred.omero.roi.ROIWrapper;
import fr.igred.omero.repository.DatasetWrapper;
import gred.nucleus.core.ConvexHullSegmentation;
import gred.nucleus.core.NucleusSegmentation;
import gred.nucleus.files.Directory;
import gred.nucleus.files.FilesNames;
import gred.nucleus.files.OutputTextFile;
import gred.nucleus.core.ConvexHullSegmentation;
import gred.nucleus.core.NucleusSegmentation;
import gred.nucleus.nucleuscaracterisations.NucleusAnalysis;
import ij.ImagePlus;
import ij.io.FileSaver;
Expand All @@ -29,6 +29,7 @@
import java.nio.file.Files;
import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.Date;
import java.util.List;
import java.util.concurrent.ExecutionException;

Expand Down Expand Up @@ -280,20 +281,24 @@ public String runOneImage(String filePath) throws IOException, FormatException {
LOGGER.info("End: {}", timeStampStart);
return log;
}


public void saveCropGeneralInfo() {
Date date = new Date() ;
SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd HH.mm.ss") ;
LOGGER.info("Saving crop general info.");
OutputTextFile resultFileOutputOTSU = new OutputTextFile(this.segmentationParameters.getOutputFolder()
+ "OTSU"
+ File.separator
+ "result_Segmentation_Analyse_OTSU.csv");
+ dateFormat.format(date)
+ "-result_Segmentation_Analyse_OTSU.csv");
resultFileOutputOTSU.saveTextFile(this.outputCropGeneralInfoOTSU, true);
if (this.segmentationParameters.getConvexHullDetection()) {
OutputTextFile resultFileOutputConvexHull = new OutputTextFile(this.segmentationParameters.getOutputFolder()
+ NucleusSegmentation.CONVEX_HULL_ALGORITHM
+ File.separator
+ "result_Segmentation_Analyse_" +
+ dateFormat.format(date)
+ "-result_Segmentation_Analyse_" +
NucleusSegmentation.CONVEX_HULL_ALGORITHM +
".csv");
resultFileOutputConvexHull.saveTextFile(this.outputCropGeneralInfoConvexHull, true);
Expand Down Expand Up @@ -342,10 +347,12 @@ public String runSeveralImagesOMERO(List<ImageWrapper> images, Long output, Clie

public void saveCropGeneralInfoOmero(Client client, Long output)
throws ServiceException, AccessException, ExecutionException, InterruptedException {
Date date = new Date() ;
SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd HH.mm.ss") ;
LOGGER.info("Saving OTSU results.");
DatasetWrapper dataset = client.getProject(output).getDatasets("OTSU").get(0);

String path = "." + File.separator + "result_Segmentation_Analyse.csv";
String path = "." + File.separator + dateFormat.format(date) + "-result_Segmentation_Analyse.csv";
try {
path = new File(path).getCanonicalPath();
} catch (IOException e) {
Expand Down Expand Up @@ -504,6 +511,9 @@ private void preProcessImage(ImagePlus img) {
public String getResultsColumnNames() {
return "NucleusFileName\t" +
"Volume\t" +
"Moment 1 \t" +
"Moment 2 \t" +
"Moment 3 \t" +
"Flatness\t" +
"Elongation\t" +
"Esr\t" +
Expand Down