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Merge pull request #23 from BIOP/qp-0.6
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tries a more lenient approach to errors
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@lacan
lacan authored Nov 5, 2024
2 parents c0107b2 + 8e84bbd commit 6f45118
Showing 1 changed file with 71 additions and 79 deletions.
150 changes: 71 additions & 79 deletions src/main/java/qupath/ext/warpy/Warpy.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,30 +12,24 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import qupath.lib.analysis.features.ObjectMeasurements;
import qupath.lib.common.GeneralTools;
import qupath.lib.common.Version;
import qupath.lib.gui.QuPathApp;
import qupath.lib.images.ImageData;
import qupath.lib.images.servers.ImageServer;
import qupath.lib.images.servers.TransformedServerBuilder;
import qupath.lib.objects.*;
import qupath.lib.objects.hierarchy.TMAGrid;
import qupath.lib.projects.Project;
import qupath.lib.projects.ProjectImageEntry;
import qupath.lib.roi.GeometryTools;
import qupath.lib.roi.ROIs;
import qupath.lib.roi.interfaces.ROI;
import qupath.lib.scripting.QP;

import java.awt.image.BufferedImage;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.*;
import java.util.function.Predicate;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
Expand All @@ -47,8 +41,8 @@
* Utility class which bridges real transformation of the ImgLib2 world and
* makes it easily usable into JTS world, mainly used by QuPath
* <p>
* See initial forum thread : https://forum.image.sc/t/qupath-arbitrarily-transform-detections-and-annotations/49674
* For documentation regarding this tool, see https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/wsi_registration_fjii_qupath/
* See initial forum thread : <a href="https://forum.image.sc/t/qupath-arbitrarily-transform-detections-and-annotations/49674">...</a>
* For documentation regarding this tool, see <a href="https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/wsi_registration_fjii_qupath/">...</a>
* <p>
* Extra dependencies required for QuPath:
* <p>
Expand All @@ -69,47 +63,47 @@ public class Warpy {
final private static Logger logger = LoggerFactory.getLogger(Warpy.class);

// Pattern to match the transform file
private static Pattern transformFilePattern = Pattern.compile("transform\\_(?<target>\\d+)\\_(?<source>\\d+)\\.json");
private static final Pattern transformFilePattern = Pattern.compile("transform_(?<target>\\d+)_(?<source>\\d+)\\.json");

/**
* Recovers a list of candidate entries in this project that have a RealTransform file that matches the pattern in
* 'transformFilePattern'
* @param targetEntry the entry which should *receive* transformed objects. Typically the active entry.
* @return a collection of project entries that have a useable and valid RealTransform (forward or valid inverse)
*/
public static Collection<ProjectImageEntry> getCandidateSourceEntries(ProjectImageEntry targetEntry) {
public static Collection<ProjectImageEntry<?>> getCandidateSourceEntries(ProjectImageEntry<?> targetEntry) {

Project project = getProject();
Project<?> project = getProject();
// Find in the targetfolder, the source entries that have a Serialized RealTransform file
List<ProjectImageEntry<BufferedImage>> entries = project.getImageList();
List<? extends ProjectImageEntry<?>> entries = project.getImageList();

String targetID = targetEntry.getID();

// Find if there is a forward transform file and return the entry source
Path targetEntryPath = targetEntry.getEntryPath();
Collection<ProjectImageEntry> candidateTransformableEntries = new ArrayList<>();
for (File currentFile : targetEntryPath.toFile().listFiles()) {
Collection<ProjectImageEntry<?>> candidateTransformableEntries = new ArrayList<>();
for (File currentFile : Objects.requireNonNull(targetEntryPath.toFile().listFiles())) {
Matcher matcher = transformFilePattern.matcher(currentFile.getName());
if (matcher.matches()) {
if (matcher.group("target").equals(targetID)) {
// Check the source ID and return if
String sourceID = matcher.group("source");
ProjectImageEntry sourceEntry = getEntryFromID(sourceID);
ProjectImageEntry<?> sourceEntry = getEntryFromID(sourceID);
if (sourceEntry != null) candidateTransformableEntries.add(sourceEntry);
}
}
}

// Find is there are inverse transforms available by going through all entries
for (ProjectImageEntry entry : entries) {
for (ProjectImageEntry<?> entry : entries) {
if (!entry.equals(targetEntry)) {
for (File currentFile : entry.getEntryPath().toFile().listFiles()) {
for (File currentFile : Objects.requireNonNull(entry.getEntryPath().toFile().listFiles())) {
Matcher matcher = transformFilePattern.matcher(currentFile.getName());
if (matcher.matches()) {
if (matcher.group("source").equals(targetID)) {
// Check the source ID and return it
String inverseSourceID = matcher.group("target");
ProjectImageEntry inverseSourceEntry = getEntryFromID(inverseSourceID);
ProjectImageEntry<?> inverseSourceEntry = getEntryFromID(inverseSourceID);
if (inverseSourceEntry != null) {
// Try to get the transform and see if it works
RealTransform rt = getRealTransform(currentFile);
Expand Down Expand Up @@ -138,7 +132,7 @@ public static Collection<ProjectImageEntry> getCandidateSourceEntries(ProjectIma
* @param sourceEntry the entry from which we want to extract the objects
* @return a collection of PathObjects, in hierarchical form
*/
public static Collection<PathObject> getPathObjectsFromEntry(ProjectImageEntry sourceEntry) {
public static Collection<PathObject> getPathObjectsFromEntry(ProjectImageEntry<?> sourceEntry) {
try {
// Do not return the TMA cores
return sourceEntry.readHierarchy().getRootObject().getChildObjects().stream().filter(Predicate.not(PathObject::isTMACore)).collect(Collectors.toList());
Expand All @@ -148,7 +142,7 @@ public static Collection<PathObject> getPathObjectsFromEntry(ProjectImageEntry s
return null;
}

public static TMAGrid getTMAGridFromEntry(ProjectImageEntry sourceEntry) {
public static TMAGrid getTMAGridFromEntry(ProjectImageEntry<?> sourceEntry) {
try {
return sourceEntry.readHierarchy().getTMAGrid();
} catch (IOException e) {
Expand Down Expand Up @@ -214,16 +208,9 @@ public static Collection<PathObject> transformPathObjects(Collection<PathObject>
CoordinateSequenceFilter transformer = getJTSFilter(transform);

// Transforms all objects and add them to a new list
List<PathObject> transformedObjects = new ArrayList<>();

for (PathObject o : objects) {
try {
transformedObjects.add(transformPathObjectAndChildren(o, transformer, true, true));
} catch (Exception e) {
logger.info("Could not transform object " + o, e);
}
}
return transformedObjects;
return objects.stream().map(o-> transformPathObjectAndChildren(o, transformer, true, true) )
.filter(Objects::nonNull)
.collect(Collectors.toList());
}

/**
Expand All @@ -232,8 +219,8 @@ public static Collection<PathObject> transformPathObjects(Collection<PathObject>
* @param id the ID to get the ImageEntry from
* @return the corresponding ProjectImageEntry or null if none is found
*/
private static ProjectImageEntry getEntryFromID(String id) {
for (ProjectImageEntry entry : QP.getProject().getImageList()) {
private static ProjectImageEntry<?> getEntryFromID(String id) {
for (ProjectImageEntry<?> entry : getProject().getImageList()) {
if (entry.getID().equals(id)) return entry;
}
return null;
Expand All @@ -247,13 +234,13 @@ private static ProjectImageEntry getEntryFromID(String id) {
* Warpy can work out if the serialized transform is a forward one or an inverse transform.
* @return the RealTransform to use for warping pathObjects
*/
public static RealTransform getRealTransform(ProjectImageEntry sourceEntry, ProjectImageEntry targetEntry) {
public static RealTransform getRealTransform(ProjectImageEntry<?> sourceEntry, ProjectImageEntry<?> targetEntry) {

// Search Forward
String targetID = targetEntry.getID();
String sourceID = sourceEntry.getID();
Path targetEntryPath = targetEntry.getEntryPath();
for (File currentFile : targetEntryPath.toFile().listFiles()) {
for (File currentFile : Objects.requireNonNull(targetEntryPath.toFile().listFiles())) {
Matcher matcher = transformFilePattern.matcher(currentFile.getName());
if (matcher.matches()) {
if (matcher.group("target").equals(targetID)) {
Expand All @@ -268,7 +255,7 @@ public static RealTransform getRealTransform(ProjectImageEntry sourceEntry, Proj

// Search Backwards
Path sourceEntryPath = sourceEntry.getEntryPath();
for (File currentFile : sourceEntryPath.toFile().listFiles()) {
for (File currentFile : Objects.requireNonNull(sourceEntryPath.toFile().listFiles())) {
Matcher matcher = transformFilePattern.matcher(currentFile.getName());
if (matcher.matches()) {
if (matcher.group("source").equals(targetID)) {
Expand All @@ -279,7 +266,7 @@ public static RealTransform getRealTransform(ProjectImageEntry sourceEntry, Proj
if (rt instanceof InvertibleRealTransform) {
return ((InvertibleRealTransform) rt).inverse();
} else {
logger.error("Could not invert transform from file {}. This error should not exist.");
logger.error("Could not invert transform from file {}. This error should not exist.", currentFile.getAbsolutePath());
return null;
}
}
Expand All @@ -299,17 +286,16 @@ public static RealTransform getRealTransform(ProjectImageEntry sourceEntry, Proj
* @throws Exception an error in case that the objects could not be measured
*/
public static void addIntensityMeasurements(Collection<PathObject> objects, double downsample) throws Exception {
ImageServer server = getCurrentServer();


ImageServer<BufferedImage> server = (ImageServer<BufferedImage>) getCurrentServer();
//If the image is RGB, this line can be added to import the correct measurements (DAB, etc.):
//cf https://forum.image.sc/t/transferring-segmentation-predictions-from-custom-masks-to-qupath/43408/15
ImageData.ImageType type = getProjectEntry().readImageData().getImageType();

if (type.equals(ImageData.ImageType.BRIGHTFIELD_H_DAB) ||
type.equals(ImageData.ImageType.BRIGHTFIELD_H_DAB) ||
type.equals(ImageData.ImageType.BRIGHTFIELD_H_E) ||
type.equals(ImageData.ImageType.BRIGHTFIELD_OTHER)) {
server = new qupath.lib.images.servers.TransformedServerBuilder(server)
server = new TransformedServerBuilder(server)
.deconvolveStains(getCurrentImageData().getColorDeconvolutionStains(), 1, 2)
.build();
}
Expand Down Expand Up @@ -344,20 +330,25 @@ public static void addIntensityMeasurements(Collection<PathObject> objects, Imag
*
* @param object qupath annotation or detection object
* @param transform jts free form transformation
* @param copyMeasurements whether or not to transfer all the source PathObject Measurements to the resulting PathObject
* @param copyMeasurements whether to transfer all the source PathObject Measurements to the resulting PathObject
*/
private static PathObject transformPathObjectAndChildren(PathObject object, CoordinateSequenceFilter transform, boolean checkGeometryValidity, boolean copyMeasurements) throws Exception {
private static PathObject transformPathObjectAndChildren(PathObject object, CoordinateSequenceFilter transform, boolean checkGeometryValidity, boolean copyMeasurements) {

PathObject transformedObject = transformPathObject(object, transform, checkGeometryValidity, copyMeasurements);

if (object.hasChildObjects()) {
for (PathObject child : object.getChildObjects()) {
transformedObject.addChildObject(transformPathObjectAndChildren(child, transform, checkGeometryValidity, copyMeasurements));
}
PathObject transformedObject = null;
try {
transformedObject = transformPathObject(object, transform, checkGeometryValidity, copyMeasurements);
} catch (Exception e) {
logger.error("Could not transform object {}, error is {}", object, e.getLocalizedMessage());
}

// Re-add name if it exists
transformedObject.setName(object.getName());
if (object.hasChildObjects() && transformedObject != null ) {
logger.info("Transforming {}", object);
List<PathObject> children = object.getChildObjects().stream()
.map(child -> transformPathObjectAndChildren(child, transform, checkGeometryValidity, copyMeasurements))
.filter(Objects::nonNull)
.collect(Collectors.toList());
transformedObject.addChildObjects(children);
}

return transformedObject;
}
Expand Down Expand Up @@ -391,33 +382,36 @@ private static PathObject transformPathObject(PathObject object, CoordinateSeque
ROI transformed_roi = GeometryTools.geometryToROI(geometry, original_roi.getImagePlane());

PathObject transformedObject;
if (object instanceof PathAnnotationObject) {
transformedObject = PathObjects.createAnnotationObject(transformed_roi, object.getPathClass(), copyMeasurements ? object.getMeasurementList() : null);
} 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();

GeometryTools.attemptOperation(nuc_geometry, (g) -> {
g.apply(transform);
return g;
});
transformed_nuc_roi = GeometryTools.geometryToROI(nuc_geometry, original_roi.getImagePlane());
switch (object) {
case PathAnnotationObject pathAnnotationObject ->
transformedObject = PathObjects.createAnnotationObject(transformed_roi, pathAnnotationObject.getPathClass(), copyMeasurements ? object.getMeasurementList() : null);
case PathCellObject pathCellObject -> {
// Need to transform the nucleus as well
ROI original_nuc = pathCellObject.getNucleusROI();
ROI transformed_nuc_roi = null;
if (original_nuc != null) {

Geometry nuc_geometry = original_nuc.getGeometry();

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);
}
transformedObject = PathObjects.createCellObject(transformed_roi, transformed_nuc_roi, object.getPathClass(), copyMeasurements ? object.getMeasurementList() : null);

} else if (object instanceof PathDetectionObject) {
transformedObject = PathObjects.createDetectionObject(transformed_roi, object.getPathClass(), copyMeasurements ? object.getMeasurementList() : null);
} else {
throw new Exception("Unknown PathObject class for class " + object.getClass().getSimpleName());
case PathDetectionObject pathDetectionObject ->
transformedObject = PathObjects.createDetectionObject(transformed_roi, pathDetectionObject.getPathClass(), copyMeasurements ? object.getMeasurementList() : null);
default -> throw new Exception("Unknown PathObject class for class " + object.getClass().getSimpleName());
}

// Return the same ID as the original object
transformedObject.setID(object.getID());
// Add the name and ID here
transformedObject.setName(object.getName());
transformedObject.setID(object.getID());
transformedObject.setLocked(object.isLocked());

return transformedObject;
}

Expand All @@ -434,8 +428,7 @@ public static RealTransform getRealTransform(File f) {
JsonObject element = new Gson().fromJson(fileReader, JsonObject.class);
fileReader.close();
element = (JsonObject) RealTransformSerializer.fixAffineTransform(element); // Fix missing type element in old versions
RealTransform rt = RealTransformSerializer.getRealTransformAdapter().fromJson(element, RealTransform.class);
return rt;
return RealTransformSerializer.getRealTransformAdapter().fromJson(element, RealTransform.class);
} catch (FileNotFoundException e) {
logger.error("Transform file " + f.getName() + " not found", e);
} catch (IOException e) {
Expand Down Expand Up @@ -482,10 +475,9 @@ public boolean isGeometryChanged() {
/**
* Main class for debugging
*
* @param args
* @throws Exception
* @param args some inputs we do not need
*/
public static void main(String... args) throws Exception {
public static void main(String... args) {
//String projectPath = "\\\\svfas6.epfl.ch\\biop\\public\\luisa.spisak_UPHUELSKEN\\Overlay\\qp\\project.qpproj";
QuPathApp.launch(QuPathApp.class);//, projectPath);
}
Expand Down

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