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Qp 0.6 #22

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merged 6 commits into from
Nov 5, 2024
Merged

Qp 0.6 #22

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f3ef0a8
changes methods to match new signature of AbstractServers
lacan Oct 31, 2024
b592958
fixes possibility that cells have no nucleus
lacan Oct 31, 2024
f4080f0
bumps version
lacan Oct 31, 2024
93ec570
addresses #7 by copying the ObjectID and name
lacan Nov 5, 2024
982eb4b
make SNAPSHOT version for now
lacan Nov 5, 2024
2c59d54
fixes 'getMetadata' issue
lacan Nov 5, 2024
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4 changes: 2 additions & 2 deletions build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ ext.qupathVersion = gradle.ext.qupathVersion

ext.moduleName = "qupath.ext.warpy"
description = "QuPath extension to use Warpy"
version = "0.3.2-SNAPSHOT"
version = "0.4.0-SNAPSHOT"

dependencies {
implementation "io.github.qupath:qupath-gui-fx:${qupathVersion}"
Expand Down Expand Up @@ -56,7 +56,7 @@ tasks.register("copyDependencies", Copy) {
*/
java {
toolchain {
languageVersion = JavaLanguageVersion.of(17)
languageVersion = JavaLanguageVersion.of(21)
}
if (project.properties['sources'])
withSourcesJar()
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10 changes: 5 additions & 5 deletions ...ava/qupath/ext/imagecombinerwarpy/gui/AffineTransformInterpolationImageServerBuilder.java
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Expand Up @@ -18,6 +18,7 @@
import java.net.URI;
import java.util.Collection;
import java.util.Map;
import java.util.Optional;

import qupath.lib.images.servers.ImageServer;
import qupath.lib.images.servers.ImageServerMetadata;
Expand All @@ -43,10 +44,6 @@ protected ImageServer<BufferedImage> buildOriginal() throws Exception {
return new AffineTransformInterpolationImageServer(builder.build(), transforminterpolation);
}

protected ImageServerMetadata getMetadata() {
return metadata;
}

@Override
public ImageServer<BufferedImage> build() throws Exception {
var server = buildOriginal();
Expand All @@ -67,8 +64,11 @@ public ServerBuilder<BufferedImage> updateURIs(Map<URI, URI> updateMap) {
ServerBuilder<BufferedImage> newBuilder = builder.updateURIs(updateMap);
if (newBuilder == builder)
return this;
return new AffineTransformInterpolationImageServerBuilder(getMetadata(), newBuilder, transforminterpolation);
return new AffineTransformInterpolationImageServerBuilder(getMetadata().get(), newBuilder, transforminterpolation);
}

public Optional<ImageServerMetadata> getMetadata() {
return Optional.of(metadata);
}

}
10 changes: 6 additions & 4 deletions src/main/java/qupath/ext/imagecombinerwarpy/gui/RealTransformImageServerBuilder.java
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Expand Up @@ -18,6 +18,7 @@
import java.net.URI;
import java.util.Collection;
import java.util.Map;
import java.util.Optional;

import qupath.lib.images.servers.ImageServer;
import qupath.lib.images.servers.ImageServerMetadata;
Expand Down Expand Up @@ -45,9 +46,6 @@ protected ImageServer<BufferedImage> buildOriginal() throws Exception {
return new RealTransformImageServer(builder.build(), realtransforminterpolation, interpolation);
}

protected ImageServerMetadata getMetadata() {
return metadata;
}

@Override
public ImageServer<BufferedImage> build() throws Exception {
Expand All @@ -69,7 +67,11 @@ public ServerBuilder<BufferedImage> updateURIs(Map<URI, URI> updateMap) {
ServerBuilder<BufferedImage> newBuilder = builder.updateURIs(updateMap);
if (newBuilder == builder)
return this;
return new RealTransformImageServerBuilder(getMetadata(), newBuilder, realtransforminterpolation);
return new RealTransformImageServerBuilder(getMetadata().get(), newBuilder, realtransforminterpolation);
}

public Optional<ImageServerMetadata> getMetadata() {
return Optional.of(metadata);
}

}
18 changes: 12 additions & 6 deletions src/main/java/qupath/ext/warpy/Warpy.java
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Expand Up @@ -396,14 +396,17 @@ private static PathObject transformPathObject(PathObject object, CoordinateSeque
} else if (object instanceof PathCellObject) {
// Need to transform the nucleus as well
ROI original_nuc = ((PathCellObject) object).getNucleusROI();
ROI transformed_nuc_roi = null;
if (original_nuc != null) {

Geometry nuc_geometry = original_nuc.getGeometry();
Geometry nuc_geometry = original_nuc.getGeometry();

GeometryTools.attemptOperation(nuc_geometry, (g) -> {
g.apply(transform);
return g;
});
ROI transformed_nuc_roi = GeometryTools.geometryToROI(nuc_geometry, original_roi.getImagePlane());
GeometryTools.attemptOperation(nuc_geometry, (g) -> {
g.apply(transform);
return g;
});
transformed_nuc_roi = GeometryTools.geometryToROI(nuc_geometry, original_roi.getImagePlane());
}
transformedObject = PathObjects.createCellObject(transformed_roi, transformed_nuc_roi, object.getPathClass(), copyMeasurements ? object.getMeasurementList() : null);

} else if (object instanceof PathDetectionObject) {
Expand All @@ -412,6 +415,9 @@ private static PathObject transformPathObject(PathObject object, CoordinateSeque
throw new Exception("Unknown PathObject class for class " + object.getClass().getSimpleName());
}

// Return the same ID as the original object
transformedObject.setID(object.getID());
transformedObject.setName(object.getName());
return transformedObject;
}

Expand Down
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