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Update for 0.6 and lint
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@alanocallaghan
alanocallaghan committed Dec 10, 2024
1 parent 3eeadef commit e7b8e01
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Showing 3 changed files with 51 additions and 107 deletions.
7 changes: 6 additions & 1 deletion build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,10 @@ base {
group = "io.github.qupath"
}
ext.qupathVersion = gradle.ext.qupathVersion
ext.qupathJavaVersion = 17
ext.qupathJavaVersion = libs.versions.jdk.get() as Integer

dependencies {
implementation libs.qupath.fxtras
shadow "io.github.qupath:qupath-gui-fx:${qupathVersion}"
shadow "org.slf4j:slf4j-api:1.7.30"
}
Expand All @@ -54,3 +55,7 @@ java {
withSourcesJar()
withJavadocJar()
}

javafx {
modules = ["javafx.base", "javafx.swing", "javafx.controls", "javafx.graphics"]
}
2 changes: 1 addition & 1 deletion settings.gradle
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
rootProject.name = 'qupath-extension-align'

gradle.ext.qupathVersion = "0.5.0"
gradle.ext.qupathVersion = "0.6.0-SNAPSHOT"

dependencyResolutionManagement {

Expand Down
149 changes: 44 additions & 105 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 @@ -82,7 +82,6 @@
import javafx.scene.control.Label;
import javafx.scene.control.ListCell;
import javafx.scene.control.ListView;
import javafx.scene.control.SelectionMode;
import javafx.scene.control.Slider;
import javafx.scene.control.SplitPane;
import javafx.scene.control.TextArea;
Expand All @@ -102,9 +101,9 @@
import javafx.scene.transform.NonInvertibleTransformException;
import javafx.scene.transform.TransformChangedEvent;
import javafx.stage.Stage;
import qupath.fx.dialogs.Dialogs;
import qupath.lib.geom.Point2;
import qupath.lib.gui.QuPathGUI;
import qupath.lib.gui.dialogs.Dialogs;
import qupath.lib.gui.images.stores.ImageRenderer;
import qupath.lib.gui.tools.GuiTools;
import qupath.lib.gui.tools.PaneTools;
Expand Down Expand Up @@ -135,17 +134,17 @@
*/
public class ImageAlignmentPane {

private static Logger logger = LoggerFactory.getLogger(ImageAlignmentPane.class);
private static final Logger logger = LoggerFactory.getLogger(ImageAlignmentPane.class);

private QuPathGUI qupath;
private QuPathViewer viewer;
private final QuPathGUI qupath;
private final QuPathViewer viewer;

private ObservableList<ImageData<BufferedImage>> images = FXCollections.observableArrayList();
private ObjectProperty<ImageData<BufferedImage>> selectedImageData = new SimpleObjectProperty<>();
private DoubleProperty rotationIncrement = new SimpleDoubleProperty(1.0);
private final ObservableList<ImageData<BufferedImage>> images = FXCollections.observableArrayList();
private final ObjectProperty<ImageData<BufferedImage>> selectedImageData = new SimpleObjectProperty<>();
private final DoubleProperty rotationIncrement = new SimpleDoubleProperty(1.0);

private StringProperty affineStringProperty;
private StringProperty filterText = new SimpleStringProperty();
private final StringProperty affineStringProperty;
private final StringProperty filterText = new SimpleStringProperty();

private static enum RegistrationType {
AFFINE, RIGID;
Expand All @@ -162,7 +161,7 @@ public String toString() {
}
}

private ObjectProperty<RegistrationType> registrationType = new SimpleObjectProperty<>(RegistrationType.AFFINE);
private final ObjectProperty<RegistrationType> registrationType = new SimpleObjectProperty<>(RegistrationType.AFFINE);

private static enum AlignmentMethod {
INTENSITY, AREA_ANNOTATIONS, POINT_ANNOTATIONS;
Expand All @@ -181,22 +180,15 @@ public String toString() {
}
}

private ObjectProperty<AlignmentMethod> alignmentMethod = new SimpleObjectProperty<>(AlignmentMethod.INTENSITY);
private final ObjectProperty<AlignmentMethod> alignmentMethod = new SimpleObjectProperty<>(AlignmentMethod.INTENSITY);

private Map<ImageData<BufferedImage>, ImageServerOverlay> mapOverlays = new WeakHashMap<>();
private EventHandler<TransformChangedEvent> transformEventHandler = new EventHandler<TransformChangedEvent>() {
@Override
public void handle(TransformChangedEvent event) {
affineTransformUpdated();
}
};
private final Map<ImageData<BufferedImage>, ImageServerOverlay> mapOverlays = new WeakHashMap<>();
private final EventHandler<TransformChangedEvent> transformEventHandler = event -> affineTransformUpdated();

private RefineTransformMouseHandler mouseEventHandler = new RefineTransformMouseHandler();
private final RefineTransformMouseHandler mouseEventHandler = new RefineTransformMouseHandler();

private ObjectBinding<ImageServerOverlay> selectedOverlay = Bindings.createObjectBinding(
() -> {
return mapOverlays.get(selectedImageData.get());
},
private final ObjectBinding<ImageServerOverlay> selectedOverlay = Bindings.createObjectBinding(
() -> mapOverlays.get(selectedImageData.get()),
selectedImageData);

private BooleanBinding noOverlay = selectedOverlay.isNull();
Expand Down Expand Up @@ -260,7 +252,7 @@ public ImageAlignmentPane(final QuPathGUI qupath) {
if (!n.isEmpty()) {
try {
rotationIncrement.set(Double.parseDouble(n));
} catch (Exception e) {}
} catch (Exception ignored) {}
}
});
Label labelRotationIncrement = new Label("Rotation increment: ");
Expand Down Expand Up @@ -520,35 +512,28 @@ void promptToAddImages() {

// Find the entries currently selected
Set<ProjectImageEntry<BufferedImage>> alreadySelected =
images.stream().map(i -> project.getEntry(i)).collect(Collectors.toSet());
images.stream()
.map(project::getEntry)
.collect(Collectors.toSet());
if (currentEntry != null)
alreadySelected.remove(currentEntry);

entries.removeAll(alreadySelected);

// Create a list to display, with the appropriate selections
ListSelectionView<ProjectImageEntry<BufferedImage>> list = new ListSelectionView<>();
list.getSourceItems().setAll(entries);

//list.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
/*
for (int i = 0; i < entries.size(); i++) {
if (alreadySelected.contains(entries.get(i)))
list.getSelectionModel().select(i);
}
*/
list.setCellFactory(c -> new ProjectEntryListCell());

// Add a filter text field
TextField tfFilter = new TextField();
tfFilter.textProperty().bindBidirectional(filterText);
filterText.addListener((v, o, n) -> updateImageList(list, entries, alreadySelected, n));

if (tfFilter.getText() != "")
if (!tfFilter.getText().isEmpty())
updateImageList(list, entries, alreadySelected, tfFilter.getText());

//tfFilter.textProperty().addListener((v, o, n) -> updateImageList(list, entries, alreadySelected, n));

Dialog<ButtonType> dialog = new Dialog<>();
dialog.getDialogPane().getButtonTypes().addAll(ButtonType.OK, ButtonType.CANCEL);
dialog.setHeaderText("Select images to include");
Expand All @@ -558,7 +543,7 @@ void promptToAddImages() {
list.setSourceFooter(tfFilter);

// Set now, so that the label will be triggered if needed
if (alreadySelected != null && !alreadySelected.isEmpty()) {
if (!alreadySelected.isEmpty()) {
list.getSourceItems().removeAll(alreadySelected);
list.getTargetItems().addAll(alreadySelected);
}
Expand All @@ -569,53 +554,23 @@ void promptToAddImages() {
return;

// We now need to add some & remove some (potentially)
Set<ProjectImageEntry<BufferedImage>> toSelect = new LinkedHashSet<>(getTargetItems(list));
Set<ProjectImageEntry<BufferedImage>> toSelect = new LinkedHashSet<>(list.getTargetItems());
Set<ProjectImageEntry<BufferedImage>> toRemove = new HashSet<>(alreadySelected);

/*
logger.info("Before clean-up...");
for (ProjectImageEntry<BufferedImage> entry : toRemove) {
logger.info("alreadySelected: "+entry.toString());
}
for (ProjectImageEntry<BufferedImage> entry : toSelect) {
logger.info("toSelect: "+entry.toString());
}
for (ProjectImageEntry<BufferedImage> entry : getSourceItems((list))) {
logger.info("toRemove: "+entry.toString());
}
*/

toRemove.remove(currentEntry);
toRemove.removeAll(toSelect);
toSelect.removeAll(alreadySelected);

/*
logger.info("After clean-up...");
for (ProjectImageEntry<BufferedImage> entry : toSelect) {
logger.info("toSelect: "+entry.toString());
}
for (ProjectImageEntry<BufferedImage> entry : toRemove) {
logger.info("toRemove (without source items): "+entry.toString());
}
*/

// Rather convoluted... but remove anything that needs to go, from the list, map & overlay
if (!toRemove.isEmpty()) {
List<ImageData<BufferedImage>> imagesToRemove = new ArrayList<>();
ImageData<BufferedImage> imageData = null;
for (ProjectImageEntry<BufferedImage> entry : toRemove) {
try {
imageData = entry.readImageData();
for (ImageData<BufferedImage> temp : images) {
if (temp.getServerPath().equals(imageData.getServerPath())) {
imagesToRemove.add(temp);
}
for (ImageData<BufferedImage> temp : images) {
if (entry == currentEntry) {
imagesToRemove.add(temp);
}
} catch (IOException e) {
logger.error("Unable to read ImageData for " + entry.getImageName(), e);
continue;
}
}
}
images.removeAll(imagesToRemove);
for (ImageData<BufferedImage> temp : imagesToRemove) {
ImageServerOverlay overlay = mapOverlays.remove(temp);
Expand All @@ -635,7 +590,6 @@ void promptToAddImages() {
// Read annotations from any data file
try {
// Try to get data from an open viewer first, if possible

for (var viewer : qupath.getAllViewers()) {
var tempData = viewer.getImageData();
if (tempData != null && temp.equals(project.getEntry(viewer.getImageData()))) {
Expand Down Expand Up @@ -663,16 +617,13 @@ void promptToAddImages() {
continue;
}
ImageServerOverlay overlay = new ImageServerOverlay(viewer, imageData.getServer());
//@phaub Support of viewer display settings
overlay.setRenderer(renderer);

overlay.getAffine().addEventHandler(TransformChangedEvent.ANY, transformEventHandler);
mapOverlays.put(imageData, overlay);
// viewer.getCustomOverlayLayers().add(overlay);
imagesToAdd.add(imageData);
}
images.addAll(0, imagesToAdd);

}


Expand All @@ -698,15 +649,12 @@ private void affineTransformUpdated() {
Affine affine = overlay.getAffine();
affineStringProperty.set(
String.format(
"%.4f, \t %.4f,\t %.4f,\n" +
"%.4f,\t %.4f,\t %.4f",
// String.format("Transform: [\n" +
// " %.3f, %.3f, %.3f,\n" +
// " %.3f, %.3f, %.3f\n" +
// "]",
affine.getMxx(), affine.getMxy(), affine.getTx(),
affine.getMyx(), affine.getMyy(), affine.getTy())
);
"%.4f, \t %.4f,\t %.4f,\n" +
"%.4f,\t %.4f,\t %.4f",
affine.getMxx(), affine.getMxy(), affine.getTx(),
affine.getMyx(), affine.getMyy(), affine.getTy()
)
);
}


Expand Down Expand Up @@ -737,14 +685,14 @@ static BufferedImage ensureGrayScale(BufferedImage img) {
/**
* Auto-align the selected image overlay with the base image in the viewer.
*
* @param requestedPixelSizeMicrons
* @param requestedPixelSizeMicrons The requested pixel size in microns.
* @throws IOException
*/
void autoAlign(double requestedPixelSizeMicrons) throws IOException {
ImageData<BufferedImage> imageDataBase = viewer.getImageData();
ImageData<BufferedImage> imageDataSelected = selectedImageData.get();
if (imageDataBase == null) {
Dialogs.showNoImageError("Auto-alignment");
Dialogs.showErrorMessage("Auto-alignment", "No image is available!");
return;
}
if (imageDataSelected == null) {
Expand Down Expand Up @@ -789,12 +737,10 @@ void autoAlign(double requestedPixelSizeMicrons) throws IOException {
}
Mat matBase = pointsToMat(pointsBase);
Mat matSelected = pointsToMat(pointsSelected);


// @deprecated Use cv::estimateAffine2D, cv::estimateAffinePartial2D instead. If you are using this function
// with images, extract points using cv::calcOpticalFlowPyrLK and then use the estimation functions.
transform = opencv_video.estimateRigidTransform(matBase, matSelected, registrationType.get() == RegistrationType.AFFINE);
// if (registrationType.get() == RegistrationType.AFFINE)
// transform = opencv_calib3d.estimateAffine2D(matBase, matSelected);
// else
// transform = opencv_calib3d.estimateAffinePartial2D(matBase, matSelected);
matToAffine(transform, affine, 1.0);
return;
}
Expand All @@ -803,7 +749,7 @@ void autoAlign(double requestedPixelSizeMicrons) throws IOException {
logger.debug("Image alignment using area annotations");
Map<PathClass, Integer> labels = new LinkedHashMap<>();
int label = 1;
labels.put(PathClassFactory.getPathClassUnclassified(), label++);
labels.put(PathClass.NULL_CLASS, label++);
for (var annotation : imageDataBase.getHierarchy().getAnnotationObjects()) {
var pathClass = annotation.getPathClass();
if (pathClass != null && !labels.containsKey(pathClass))
Expand Down Expand Up @@ -866,17 +812,14 @@ static void autoAlign(ImageServer<BufferedImage> serverBase, ImageServer<Buffere
downsample = requestedPixelSizeMicrons / calBase.getAveragedPixelSizeMicrons();
}

BufferedImage imgBase = serverBase.readBufferedImage(RegionRequest.createInstance(serverBase.getPath(), downsample, 0, 0, serverBase.getWidth(), serverBase.getHeight()));
BufferedImage imgOverlay = serverOverlay.readBufferedImage(RegionRequest.createInstance(serverOverlay.getPath(), downsample, 0, 0, serverOverlay.getWidth(), serverOverlay.getHeight()));
BufferedImage imgBase = serverBase.readRegion(RegionRequest.createInstance(serverBase.getPath(), downsample, 0, 0, serverBase.getWidth(), serverBase.getHeight()));
BufferedImage imgOverlay = serverOverlay.readRegion(RegionRequest.createInstance(serverOverlay.getPath(), downsample, 0, 0, serverOverlay.getWidth(), serverOverlay.getHeight()));

imgBase = ensureGrayScale(imgBase);
imgOverlay = ensureGrayScale(imgOverlay);

Mat matBase = OpenCVTools.imageToMat(imgBase);
Mat matOverlay = OpenCVTools.imageToMat(imgOverlay);

// opencv_imgproc.threshold(matBase, matBase, opencv_imgproc.THRESH_OTSU, 255, opencv_imgproc.THRESH_BINARY_INV + opencv_imgproc.THRESH_OTSU);
// opencv_imgproc.threshold(matOverlay, matOverlay, opencv_imgproc.THRESH_OTSU, 255, opencv_imgproc.THRESH_BINARY_INV + opencv_imgproc.THRESH_OTSU);

Mat matTransform = Mat.eye(2, 3, opencv_core.CV_32F).asMat();
// Initialize using existing transform
Expand Down Expand Up @@ -1012,8 +955,7 @@ public void handle(MouseEvent event) {

if (event.getEventType() == MouseEvent.MOUSE_PRESSED) {
pDragging = viewer.componentPointToImagePoint(event.getX(), event.getY(), pDragging, true);
return;
} else if (event.getEventType() == MouseEvent.MOUSE_DRAGGED) {
} else if (event.getEventType() == MouseEvent.MOUSE_DRAGGED) {
Point2D p = viewer.componentPointToImagePoint(event.getX(), event.getY(), null, true);
if (event.isShiftDown() && pDragging != null) {
double dx = p.getX() - pDragging.getX();
Expand Down Expand Up @@ -1186,9 +1128,6 @@ private static void updateImageList(final ListSelectionView<ProjectImageEntry<Bu
// Get an update source items list
List<ProjectImageEntry<BufferedImage>> sourceItems = new ArrayList<>(availableImages);

//var targetItems = listImages.getItems();
//sourceItems.removeAll(targetItems);

// Apply filter text
if (text.length() > 0 && !sourceItems.isEmpty()) {
Iterator<ProjectImageEntry<BufferedImage>> iter = sourceItems.iterator();
Expand All @@ -1202,4 +1141,4 @@ private static void updateImageList(final ListSelectionView<ProjectImageEntry<Bu
return;
getSourceItems(listSelectionView).setAll(sourceItems);
}
}
}

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