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Autoscale the affine transform when viewer and overlay images have different pixel sizes. #10

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Merged
Rylern merged 7 commits into from
May 30, 2025
Merged

Autoscale the affine transform when viewer and overlay images have different pixel sizes. #10

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ed80f03
added calculateAffine()
zindy Aug 19, 2024
836aa17
rewrote the scaling helper function
zindy Aug 20, 2024
6bd2ddb
reset to a scaled identity
zindy Aug 20, 2024
a662e99
Test if overlay is null before attempting to reset affine transform
zindy Apr 12, 2025
7179bb6
changed viewer and overlay calibration variable names
zindy Apr 12, 2025
d6e1400
added a check to ensure scaling can be calculated, otherwise defaults…
zindy Apr 12, 2025
9791473
restored a lost comment and updated one of mine
zindy Apr 12, 2025
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5 changes: 1 addition & 4 deletions src/main/java/qupath/ext/align/gui/ImageAlignmentPane.java
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Original file line number Diff line number Diff line change
Expand Up @@ -370,10 +370,7 @@ public ImageAlignmentPane(final QuPathGUI qupath) {
Button btnReset = new Button("Reset");
btnReset.setOnAction(e -> {
var overlay = getSelectedOverlay();
var affine = overlay == null ? null : overlay.getAffine();
if (affine == null)
return;
affine.setToIdentity();
overlay.resetAffine();
});
Button btnInvert = new Button("Invert");
btnInvert.setOnAction(e -> {
Expand Down
31 changes: 28 additions & 3 deletions src/main/java/qupath/ext/align/gui/ImageServerOverlay.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@
import qupath.lib.gui.viewer.overlays.PathOverlay;
import qupath.lib.images.ImageData;
import qupath.lib.images.servers.ImageServer;
import qupath.lib.images.servers.PixelCalibration;
import qupath.lib.regions.ImageRegion;

/**
Expand All @@ -60,6 +61,9 @@ public class ImageServerOverlay extends AbstractOverlay {

private AffineTransform transform;
private AffineTransform transformInverse;

private PixelCalibration viewerCalibration;
private PixelCalibration serverCalibration;

/**
* Constructor.
Expand All @@ -82,8 +86,15 @@ public ImageServerOverlay(final QuPathViewer viewer, final ImageServer<BufferedI
this.server = server;
this.transform = new AffineTransform();
this.transformInverse = null;//transform.createInverse();
// Request repaint any time the transform changes

this.affine = affine;
// Access the PixelCalibration from the viewer and server and
// reset the affine transform to a scaled identity
this.viewerCalibration = viewer.getImageData().getServer().getPixelCalibration();
this.serverCalibration = server.getPixelCalibration();
resetAffine();

// Request repaint any time the transform changes
this.affine.addEventHandler(TransformChangedEvent.ANY, e -> {
updateTransform();
viewer.repaintEntireImage();
Expand Down Expand Up @@ -115,7 +126,21 @@ public void setRenderer(ImageRenderer renderer) {
public Affine getAffine() {
return affine;
}


/**
* Reset the affine transform to its pixel-correct scaled identity
*/
public void resetAffine() {
if (this.affine == null)
return;

// Calculate the a and y scaling factor
double mxx = this.viewerCalibration.getPixelWidthMicrons() / serverCalibration.getPixelWidthMicrons();
double myy = this.viewerCalibration.getPixelHeightMicrons() / serverCalibration.getPixelHeightMicrons();

this.affine.setToTransform(mxx, 0, 0, 0, myy, 0);
}

private void updateTransform() {
transform.setTransform(
affine.getMxx(),
Expand Down Expand Up @@ -159,4 +184,4 @@ public void paintOverlay(Graphics2D g2d, ImageRegion imageRegion, double downsam

}

}
}