Pixel Classifier - Data on OMERO public

[romainGuiet]

IMPORTANT!

Before we begin...

Before submitting your bug report, please check the following:

• I've definitely found a bug (it you're not sure, please use image.sc instead)
• I've checked https://qupath.github.io for a new release that might already have fixed the issue
• I've checked the Changelog to see if the bug has already been fixed in the next release
• I've checked for existing GitHub issues describing the same problem

Bug report

Describe the bug

it looks like the pixel classifier can't access all the pixels of the image, therefore during "training" it doesn't display the overlay class on the entire image , but still one can save a pixel classifier.
BUT when loading the pixel classifier, it will return this error

java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.io.IOException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Could not decode image from response
java.io.IOException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.io.IOException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Could not decode image from response
	at qupath.lib.analysis.images.ContourTracing.traceGeometriesImpl(ContourTracing.java:1074)
	at qupath.lib.analysis.images.ContourTracing.traceGeometries(ContourTracing.java:1022)
	at qupath.opencv.ml.pixel.PixelClassifierTools.createObjectsFromPixelClassifier(PixelClassifierTools.java:426)
	at qupath.opencv.ml.pixel.PixelClassifierTools.createObjectsFromPredictions(PixelClassifierTools.java:227)
	at qupath.opencv.ml.pixel.PixelClassifierTools.createDetectionsFromPixelClassifier(PixelClassifierTools.java:140)
	at qupath.opencv.ml.pixel.PixelClassifierTools.createDetectionsFromPixelClassifier(PixelClassifierTools.java:162)
	at qupath.process.gui.commands.ml.PixelClassifierUI.promptToCreateObjects(PixelClassifierUI.java:398)
	at qupath.process.gui.commands.ml.PixelClassifierUI.lambda$createPixelClassifierButtons$3(PixelClassifierUI.java:155)
	at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
	at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
	at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
	at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
	at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
	at javafx.event.Event.fireEvent(Event.java:199)
	at javafx.scene.Node.fireEvent(Node.java:8963)
	at javafx.scene.control.Button.fire(Button.java:203)
	at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:207)
	at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274)
	at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247)
	at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
	at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
	at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
	at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
	at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
	at javafx.event.Event.fireEvent(Event.java:199)
	at javafx.scene.Scene$MouseHandler.process(Scene.java:3987)
	at javafx.scene.Scene.processMouseEvent(Scene.java:1893)
	at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2711)
	at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:411)
	at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:301)
	at java.base/java.security.AccessController.doPrivileged(Unknown Source)
	at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450)
	at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:430)
	at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449)
	at com.sun.glass.ui.View.handleMouseEvent(View.java:560)
	at com.sun.glass.ui.View.notifyMouse(View.java:946)
	at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
	at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184)
	at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.io.IOException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Could not decode image from response
	at java.base/java.util.concurrent.FutureTask.report(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.get(Unknown Source)
	at qupath.lib.analysis.images.ContourTracing.invokeAll(ContourTracing.java:1033)
	at qupath.lib.analysis.images.ContourTracing.traceGeometriesImpl(ContourTracing.java:1049)
	... 60 more
Caused by: java.lang.RuntimeException: java.io.IOException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Could not decode image from response
	at qupath.lib.analysis.images.ContourTracing.traceGeometries(ContourTracing.java:1121)
	at qupath.lib.analysis.images.ContourTracing.lambda$traceGeometriesImpl$11(ContourTracing.java:1049)
	at qupath.lib.analysis.images.ContourTracing.lambda$invokeAll$10(ContourTracing.java:1029)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	... 1 more
Caused by: java.io.IOException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Could not decode image from response
	at qupath.ext.omero.core.pixelapis.web.WebReader.readTile(WebReader.java:67)
	at qupath.ext.omero.core.imageserver.OmeroImageServer.readTile(OmeroImageServer.java:95)
	at qupath.lib.images.servers.AbstractTileableImageServer.lambda$prerequestTiles$2(AbstractTileableImageServer.java:519)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at qupath.lib.images.servers.AbstractTileableImageServer.prerequestTiles(AbstractTileableImageServer.java:521)
	at qupath.lib.images.servers.AbstractTileableImageServer.readRegion(AbstractTileableImageServer.java:298)
	at qupath.lib.images.servers.AbstractTileableImageServer.readRegion(AbstractTileableImageServer.java:60)
	at qupath.lib.images.servers.ServerTools.getPaddedRequest(ServerTools.java:256)
	at qupath.opencv.ops.ImageOps$ChannelImageDataOp.apply(ImageOps.java:407)
	at qupath.opencv.ml.pixel.OpenCVPixelClassifier.applyClassification(OpenCVPixelClassifier.java:104)
	at qupath.lib.classifiers.pixel.PixelClassificationImageServer.readTile(PixelClassificationImageServer.java:308)
	at qupath.lib.images.servers.AbstractTileableImageServer.lambda$getTile$0(AbstractTileableImageServer.java:213)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at qupath.lib.images.servers.AbstractTileableImageServer.getTile(AbstractTileableImageServer.java:217)
	at qupath.lib.images.servers.AbstractTileableImageServer.readRegion(AbstractTileableImageServer.java:290)
	at qupath.lib.images.servers.AbstractTileableImageServer.readRegion(AbstractTileableImageServer.java:60)
	at qupath.lib.gui.viewer.overlays.PixelClassificationOverlay.lambda$requestTile$5(PixelClassificationOverlay.java:575)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	... 4 more
Caused by: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Could not decode image from response
	at java.base/java.util.concurrent.CompletableFuture.reportGet(Unknown Source)
	at java.base/java.util.concurrent.CompletableFuture.get(Unknown Source)
	at qupath.ext.omero.core.pixelapis.web.WebReader.readTile(WebReader.java:61)
	... 21 more
Caused by: java.lang.IllegalArgumentException: Could not decode image from response
	at qupath.ext.omero.core.RequestSender.lambda$getImage$5(RequestSender.java:218)
	at java.base/java.util.concurrent.CompletableFuture$UniApply.tryFire(Unknown Source)
	at java.base/java.util.concurrent.CompletableFuture$Completion.exec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool.scan(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinWorkerThread.run(Unknown Source)

To Reproduce

Steps to reproduce the behavior:

1. Use this qupath project qp_bone.zip (data are on a public OMERO)
2. open the second image ( analysis_whole) run load pixel classifier "bone_classifier"

3. Click "Create objects" , on "Full image" => get the error
4. Alternatively, with annotations, it works with annotation "A" but fails with same error for "B" and "C"

Expected behavior

Pixel classifier dislay results

Desktop (please complete the following information):

• OS: Win11
• QuPath Version: 0.6.0
• OMERO extension: 0.1.2

Additional context

• Connection to omero-public (using the WEB API from the omero extension) + image import + pixel classifier => error reproduced

• Download image locally + image import + pixel classifier ==> no error

• Connection to omero NON-public (using the ICE API from the omero extension) + image import + pixel classifier => no error

• Connection to omero NON-public (using the WEB API from the omero extension) + image import + pixel classifier => error reproduced

So, it seems that the error comes from the omero extension .

Thank you in advance for your help,

Cheers

ping : @Rdornier ,@NicoKiaru

[petebankhead]

So, it seems that the error comes from the omero extension .

I think so too, so I've transferred it to the OMERO extension repo.

I can replicate exceptions in the log without using the pixel classifier at all. It seems that some of the requests are returning 404 errors, e.g. https://omero-public.epfl.ch/webgateway/render_image_region/568578/0/0/?tile=3,5,10,512,512

[Rdornier]

Seems to be related to #42 (comment)

[Rylern]

Yes, it definitely seems related to #42. Just to be sure, is it possible to share the image?

The issue was fixed before, but only when the ICE API is used to read the image. I tried to find a way of implementing the same fix with the WEB API, but this API doesn't give enough information on the image (namely the width/height of each resolution level), so it doesn't seem to be possible.

There's an image.sc issue about this (https://forum.image.sc/t/qupath-omero-weird-pyramid-levels/65484/8) in which it is mentionned that a fix in BioFormats would be implemented, but I don't know if this was done.

Therefore, the only workaround I see is to use the ICE API.

[Rdornier]

Just to be sure, is it possible to share the image?

Yes, the image is freely accessibly from the qupath project qp_bone.zip (data are on a public OMERO server without any credentials to access it)

There's an image.sc issue about this (https://forum.image.sc/t/qupath-omero-weird-pyramid-levels/65484/8) in which it is mentionned that a fix in BioFormats would be implemented, but I don't know if this was done.

Ok ! Maybe re-opening that thread would be a good idea, to ask for a fix from their side.

[Rylern]

Yes, the image is freely accessibly from the qupath project qp_bone.zip (data are on a public OMERO server without any credentials to access it)

I would like to open the image with the OMERO ICE API, so I need it to be accessible on a non-public OMERO server I have access to. So I think the best way is to have the original file, so that I can upload it to my OMERO server and try from there.

It's not an issue if you can't share the image, all of this is just to confirm that this issue is the same as #42.

Ok ! Maybe re-opening that thread would be a good idea, to ask for a fix from their side.

Actually I looked more at the topic and it seems that the proposal fix is just a new option, not something activated by default, so it's unlikely to solve our issue.

[romainGuiet]

Hi @Rylern ,

you can find the image here : https://zenodo.org/records/17453126

Cheers

R

[Rylern]

Thanks, so I can confirm this is the same issue as #42. I'll leave the issue open in case a workaround comes up later, but until then the solution is to use the ICE API when dealing with such images.