carlocastoldi
commented
1 year ago I investigated a little further. I think this has due to QuPath v0.4+ having thoroughly revised the PathClass.
The incriminating lines are the following, to my understanding:https://github.com/BIOP/qupath-extension-abba/blob/d9384ba7e198a454cb8e9da4661988eac7ee285c/src/main/java/qupath/ext/biop/abba/AtlasTools.java#L248 https://github.com/BIOP/qupath-extension-abba/blob/d9384ba7e198a454cb8e9da4661988eac7ee285c/src/main/java/qupath/ext/biop/abba/AtlasTools.java#L260
apparently the objects returned from:
PathClass parent = QP.getPathClass("Right")QP.getDerivedPathClass(parent, annotation.getPathClass().getName()).getParentClass()
have two different hashes (.hashCode()).
I could not reproduce the issue with the following code:
import qupath.ext.biop.abba.*
import qupath.ext.biop.abba.struct.*
import qupath.lib.scripting.*
import qupath.lib.objects.classes.PathClass
import qupath.lib.roi.interfaces.*
import qupath.lib.roi.*
import java.nio.file.Paths;
import java.util.stream.Collectors;
ROI roi = new RectangleROI()
PathObject object = PathObjects.createAnnotationObject(roi)
object.setName("OBJECT NAME");
PathClass parent = QP.getPathClass("Right");
println("parent: "+parent.toString()+" --- hash: "+parent.hashCode())
PathClass pc = QP.getDerivedPathClass(parent, "PATH CLASS"); // "Right\n"+
println("RightPC: '"+pc.toString()+"' --- RightPC hash: "+pc.hashCode()+" --- Parent PC (getClassPath()): '"+parent.toString()+"' --- Parent (getClassPath()) hash: "+parent.hashCode()+" --- parent.isDerivedClass: "+parent.isDerivedClass()+" --- Parent PC (getParentClass()): '"+pc.getParentClass().toString()+"' --- Parent (getParentClass()) hash: "+pc.getParentClass().hashCode()+" --- pc.getParentClass().isDerivedClass: "+pc.getParentClass().isDerivedClass());
object.setPathClass(pc);
object.setLocked(true);
for (var pc_str : PathClass.existingClasses.keySet()) {
pc = PathClass.existingClasses.get(pc_str)
if (pc.getParentClass() != null)
println "${pc.hashCode()} --- key: ${pc_str}, parent: ${pc.getParentClass().hashCode()}, color: ${pc.getColor()}"
else
println "${pc.hashCode()} --- key: ${pc_str}, parent: null, color: ${pc.getColor()}"
}
println PathClass.existingClasses.get("Right").hashCode()
println "'Right' PathClass: ${QP.getPathClass("Right").hashCode()}"
println "'${object}' PathClass: ${object.getPathClass().hashCode()}"
println "'${object}' BaseClass (${object.getPathClass().getBaseClass().getName()}): ${object.getPathClass().getBaseClass().hashCode()}"
println object.getPathClass().toString()output:
INFO: parent: Right --- hash: 9462928
INFO: RightPC: 'Right: PATH CLASS' --- RightPC hash: 1804365739 --- Parent PC (getClassPath()): 'Right' --- Parent (getClassPath()) hash: 9462928 --- parent.isDerivedClass: false --- Parent PC (getParentClass()): 'Right' --- Parent (getParentClass()) hash: 9462928 --- pc.getParentClass().isDerivedClass: false
...
INFO: 9462928 --- key: Right, parent: null, color: -14417340
INFO: 1804365739 --- key: Right\nPATH CLASS, parent: 9462928, color: -12163337
...
INFO: 9462928
INFO: 'Right' PathClass: 9462928
INFO: 'OBJECT NAME (Right: PATH CLASS)' PathClass: 1804365739
INFO: 'OBJECT NAME (Right: PATH CLASS)' BaseClass (Right): 9462928
INFO: Right: PATH CLASSOn the other hand, running AtlasTools.getFlattenedWarpedAtlasRegions() with similar prints gets the following output:
INFO: parent: Right --- hash: 322880273
INFO: GETTING ANNOTATIONS...
INFO: Loading 69 Atlas Regions for 87S_1.czi - Scene #05
INFO: leftROI: Geometry (5691, -2951, 12069, 14278) --- finalTransform: null
INFO: rightROI: Geometry (-4898, -2966, 20880, 16052) --- finalTransform: null
...
INFO: RightPC: 'Right: MOp1' --- RightPC hash: 1107190967 --- Parent PC (getClassPath()): 'Right' --- Parent (getClassPath()) hash: 322880273 --- parent.isDerivedClass: false --- Parent PC (getParentClass()): 'Right' --- Parent (getParentClass()) hash: 463216582 --- pc.getParentClass().isDerivedClass: false
...
INFO: DONE!
INFO: 1107190967 --- key: Right\nMOp1, parent: 463216582, color: -13237402
INFO: 322880273 --- key: Right, parent: null, color: -14417340
INFO: 'Right' PathClass: 322880273
INFO: 'Right' singleton PathClass: 322880273
INFO: 'MOp1 (Right: MOp1)' PathClass: 1107190967
INFO: 'MOp1 (Right: MOp1)' BaseClass (Right): 463216582
INFO: Right: MOp1as you can see, the two hashes of the two PathClass retrieved in two different ways (from a "child" PathClass and from a String name) are different.
Looping over PathClass.existingClasses (the dictionary used to track the existing classes without duplicates) shows that a PathClass child (i.e., a region), references as a parent a PathClass object (i.e., a "Left"/"Right" hemisphere) that is not in the PathClass.existingClasses HashMap!
I don't understand how this is possible. I even tried to briefly look & log QuPath 0.4+, but I was unsuccessful.
I also tried to use PathClass.getSingleton() whenever QP.getPathClass() is called, but it didn't solve the problem.
NicoKiaru
petebankhead
imagesc-bot
GuillaumeLeGoc
Importing regions without splitting left and right works, but the splitting fails with this error: