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tries to fix issue in race condition and object detection
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@lacan
lacan committed Sep 6, 2024
1 parent e7d00e7 commit 9d75c28
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Showing 2 changed files with 71 additions and 27 deletions.
2 changes: 1 addition & 1 deletion build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ ext.qupathVersion = gradle.ext.qupathVersion

description = 'QuPath extension to use Cellpose'

version = "0.9.5"
version = "0.9.6-SNAPSHOT"

dependencies {
implementation "io.github.qupath:qupath-gui-fx:${qupathVersion}"
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96 changes: 70 additions & 26 deletions src/main/java/qupath/ext/biop/cellpose/Cellpose2D.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,12 @@

import ij.IJ;
import ij.ImagePlus;
import ij.gui.PolygonRoi;
import ij.gui.Roi;
import ij.gui.Wand;
import ij.measure.ResultsTable;
import ij.process.ColorProcessor;
import ij.process.ImageProcessor;
import javafx.embed.swing.SwingFXUtils;
import javafx.scene.chart.LineChart;
import javafx.scene.chart.NumberAxis;
Expand All @@ -39,6 +44,7 @@
import qupath.ext.biop.cmd.VirtualEnvironmentRunner;
import qupath.fx.dialogs.Dialogs;
import qupath.fx.utils.FXUtils;
import qupath.imagej.tools.IJTools;
import qupath.lib.analysis.features.ObjectMeasurements;
import qupath.lib.analysis.images.ContourTracing;
import qupath.lib.analysis.images.SimpleImage;
Expand Down Expand Up @@ -82,6 +88,7 @@
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import java.util.stream.IntStream;

/**
* Dense object detection based on the cellpose and omnipose publications
Expand Down Expand Up @@ -397,7 +404,7 @@ public void detectObjectsImpl(ImageData<BufferedImage> imageData, Collection<? e
try {
return saveTileImage(opWithPreprocessing, imageData, t, parent);
} catch (IOException e) {
e.printStackTrace();
logger.warn("Could not save tile image", e);
}
return null;
})
Expand Down Expand Up @@ -435,7 +442,7 @@ public void detectObjectsImpl(ImageData<BufferedImage> imageData, Collection<? e

// Convert to detections, dilating to approximate cells if necessary
// Drop cells if they fail (rather than catastrophically give up)
List<PathObject> finalObjects = filteredDetections.parallelStream()
List<PathObject> finalObjects = filteredDetections.stream()
.map(n -> {
try {
return convertToObject(n, parent.getROI().getImagePlane(), expansion, constrainToParent ? mask : null);
Expand Down Expand Up @@ -482,7 +489,7 @@ public void detectObjectsImpl(ImageData<BufferedImage> imageData, Collection<? e
try {
ObjectMeasurements.addIntensityMeasurements(server2, cell, finalDownsample1, measurements, compartments);
} catch (IOException ie) {
logger.info(ie.getLocalizedMessage(), ie);
logger.info("Error adding intensity measurement: "+ie.getLocalizedMessage(), ie);
}
});

Expand Down Expand Up @@ -798,13 +805,7 @@ private void processCellposeFiles(VirtualEnvironmentRunner veRunner, LinkedHashM
allTiles.entrySet().forEach(entry -> {
executor.execute(() -> {
// Read the objects from the file
Collection<CandidateObject> candidates;
try {
candidates = readObjectsFromFile(entry.getValue());
} catch (IOException e) {
throw new RuntimeException(e);
}
entry.getValue().setCandidates(candidates);
entry.getValue().setCandidates(readObjectsFromFile2(entry.getValue()));
});

});
Expand Down Expand Up @@ -849,13 +850,7 @@ private void processCellposeFiles(VirtualEnvironmentRunner veRunner, LinkedHashM
TileFile tile = allTiles.get(set.getKey());
executor.execute(() -> {
// Read the objects from the file
Collection<CandidateObject> candidates;
try {
candidates = readObjectsFromFile(tile);
} catch (IOException e) {
throw new RuntimeException(e);
}
tile.setCandidates(candidates);
tile.setCandidates(readObjectsFromFile(tile));
});
});

Expand Down Expand Up @@ -884,13 +879,7 @@ private void processCellposeFiles(VirtualEnvironmentRunner veRunner, LinkedHashM
TileFile tile = allTiles.get(set.getKey());
executor.execute(() -> {
// Read the objects from the file
Collection<CandidateObject> candidates;
try {
candidates = readObjectsFromFile(tile);
} catch (IOException e) {
throw new RuntimeException(e);
}
tile.setCandidates(candidates);
tile.setCandidates(readObjectsFromFile(tile));
});
});
// Remove them from the list of remaining files
Expand Down Expand Up @@ -936,7 +925,7 @@ public File train() {
return modelFile;

} catch (IOException | InterruptedException e) {
logger.error(e.getMessage(), e);
logger.error("Error while running cellpose training: "+e.getMessage(), e);
}
return null;
}
Expand Down Expand Up @@ -1394,13 +1383,67 @@ private File moveRenameAndReturnModelFile() throws IOException {
return null;
}

private Collection<CandidateObject> readObjectsFromFile2(TileFile tileFile){
RegionRequest request = tileFile.getTile();

logger.info("Reading {}", tileFile.getLabelFile().getName());
// Open the image
ImagePlus label_imp = IJ.openImage(tileFile.getLabelFile().getAbsolutePath());
ImageProcessor ip = label_imp.getProcessor();

Wand wand = new Wand( ip );

// create range list
int width = ip.getWidth();
int height = ip.getHeight();

int[] pixel_width = new int[ width ];
int[] pixel_height = new int[ height ];

IntStream.range(0,width-1).forEach(val -> pixel_width[val] = val);
IntStream.range(0,height-1).forEach(val -> pixel_height[val] = val);

/*
* Will iterate through pixels, when getPixel > 0 ,
* then use the magic wand to create a roi
* finally set value to 0 and add to the roiManager
*/

// will "erase" found ROI by setting them to 0
ip.setColor(0);
List<CandidateObject> rois = new ArrayList<>();

for ( int y_coord : pixel_height) {
for (int x_coord : pixel_width) {
float val = ip.getf(x_coord, y_coord);
if (val > 0.0) {
// use the magic wand at this coordinate
wand.autoOutline(x_coord, y_coord, val, val);
// if there is a region , then it has npoints
if (wand.npoints > 0) {
// get the Polygon, fill with 0 and add to the manager
Roi roi = new PolygonRoi(wand.xpoints, wand.ypoints, wand.npoints, Roi.FREEROI);
// Name the Roi with the position in the stack followed by the label ID
// ip.fill should use roi, otherwise make a rectangle that erases surrounding pixels

CandidateObject o = new CandidateObject(IJTools.convertToROI(roi, -1*request.getX(), -1*request.getY() , request.getDownsample(), request.getImagePlane()).getGeometry(), tileFile.getParent());

rois.add(o);
ip.fill(roi);
}
}
}
}
label_imp.close();
return rois;
}
/**
* convert a label image to a collection of Geometry objects
* @param tileFile the current tileFile we are processing
* @return a collection of CandidateObject that will be added to the total objects
* @throws IOException in case there was a problem reading the label file
*/
private Collection<CandidateObject> readObjectsFromFile(TileFile tileFile) throws IOException {
private Collection<CandidateObject> readObjectsFromFile(TileFile tileFile) {

logger.info("Reading objects from file {}", tileFile.getLabelFile().getName());
try {
Expand Down Expand Up @@ -1429,6 +1472,7 @@ private Collection<CandidateObject> readObjectsFromFile(TileFile tileFile) throw
// Ignore the IDs, because they will be the same across different images, and we don't really need them
if (candidates.isEmpty()) return Collections.emptyList();
return candidates.values();

} catch (IOException e) {
logger.warn("Image {} could not be read for some reason: \n{}", tileFile.getLabelFile(), e.getLocalizedMessage());
}
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