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stardist / stardist-imagej

StarDist plugin for ImageJ
BSD 3-Clause "New" or "Revised" License
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Error with large image #14

Open niederle opened 3 years ago

niederle commented 3 years ago

Hi, I tried to run the StarDist 2D plugin on a 5108x4308 16-bit tiff. Configuration has been like this

Screen Shot 2021-07-27 at 11 36 52

And this is the error message I got

[INFO] Reading available sites from https://imagej.net/
[INFO] Successfully retrieved OPTIONS.
[INFO] Successfully called PropFind, directory exists: .
[INFO] Successfully locked db.xml.gz.lock.
[INFO] Successfully uploaded to db.xml.gz.lock
[INFO] Successfully called PropFind, directory exists: plugins/Scripts/Plugins/Fiji-Tools-for-HCS/Automated_Microscope_Tools/.
[INFO] Successfully uploaded to plugins/Scripts/Plugins/Fiji-Tools-for-HCS/Automated_Microscope_Tools/Macro_CV7000_Make_Field_Montages.ijm-20210726111407
[INFO] Successfully moved  db.xml.gz.lock to db.xml.gz.
[INFO] No TF library found in /Applications/_MyApplications/Fiji.app/lib/.
[INFO] Using default TensorFlow version from JAR: TF 1.12.0 CPU
[INFO] Loading TensorFlow model GenericNetwork_aea3be563cb56b8824f53a8c2382aaa5 from source file file:/var/folders/r9/8yfyqn9n3dn2pzct7lz5p0rc0000gr/T/stardist_model_7482731542518190708.zip
[INFO] Caching TensorFlow models to /Applications/_MyApplications/Fiji.app/models
[INFO] Shape of input tensor: [-1, -1, -1, 1]
[INFO] Shape of output tensor: [-1, -1, -1, 33]
[INFO] Normalize .. 
[INFO] Dataset type: 32-bit signed float, converting to FloatType.
[INFO] Dataset dimensions: [5108, 4308]
[INFO] INPUT NODE: 
[INFO] Mapping of tensor input: 
[INFO]    datasetAxes:[X, Y]
[INFO]    nodeAxes:[(Time, -1), (Y, -1), (X, -1), (Channel, 1)]
[INFO]    mapping:[2, 1, 0, 3]
[INFO] OUTPUT NODE: 
[INFO] Mapping of tensor output: 
[INFO]    datasetAxes:[X, Y]
[INFO]    nodeAxes:[(Time, -1), (Y, -1), (X, -1), (Channel, 33)]
[INFO]    mapping:[2, 1, 0, 3]
[INFO] Complete input axes: [X, Y, Time, Channel]
[INFO] Tiling actions: [TILE_WITH_PADDING, TILE_WITH_PADDING, TILE_WITHOUT_PADDING, NO_TILING]
[INFO] Dividing image into 1 tile(s)..
[INFO] Size of single image tile: [5120, 4320, 1, 1]
[INFO] Final image tiling: [1, 1, 1, 1]
[INFO] Network input size: [5120, 4320, 1, 1]
[INFO] Processing tile 1..
java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Negative capacity: -1375338496
    at java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006)
    at de.csbdresden.csbdeep.network.DefaultModelExecutor.run(DefaultModelExecutor.java:110)
    at de.csbdresden.csbdeep.network.DefaultModelExecutor.run(DefaultModelExecutor.java:71)
    at de.csbdresden.csbdeep.commands.GenericCoreNetwork.tileAndRunNetwork(GenericCoreNetwork.java:594)
    at de.csbdresden.csbdeep.commands.GenericCoreNetwork.tryToTileAndRunNetwork(GenericCoreNetwork.java:567)
    at de.csbdresden.csbdeep.commands.GenericCoreNetwork.mainThread(GenericCoreNetwork.java:469)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Negative capacity: -1375338496
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:593)
    at java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1005)
    ... 10 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Negative capacity: -1375338496
    at java.util.concurrent.ForkJoinTask$AdaptedCallable.exec(ForkJoinTask.java:1431)
    at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
    at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
    at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
    at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
Caused by: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Negative capacity: -1375338496
    at java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.util.concurrent.FutureTask.get(FutureTask.java:192)
    at de.csbdresden.csbdeep.network.model.DefaultNetwork.call(DefaultNetwork.java:110)
    at de.csbdresden.csbdeep.network.model.DefaultNetwork.call(DefaultNetwork.java:51)
    at java.util.concurrent.ForkJoinTask$AdaptedCallable.exec(ForkJoinTask.java:1424)
    ... 4 more
Caused by: java.lang.IllegalArgumentException: Negative capacity: -1375338496
    at java.nio.Buffer.<init>(Buffer.java:199)
    at java.nio.ByteBuffer.<init>(ByteBuffer.java:281)
    at java.nio.ByteBuffer.<init>(ByteBuffer.java:289)
    at java.nio.MappedByteBuffer.<init>(MappedByteBuffer.java:89)
    at java.nio.DirectByteBuffer.<init>(DirectByteBuffer.java:162)
    at org.tensorflow.Tensor.buffer(Native Method)
    at org.tensorflow.Tensor.buffer(Tensor.java:573)
    at org.tensorflow.Tensor.writeTo(Tensor.java:487)
    at net.imagej.tensorflow.Tensors.imgFloat(Tensors.java:171)
    at net.imagej.tensorflow.Tensors.imgFloat(Tensors.java:262)
    at de.csbdresden.csbdeep.network.model.tensorflow.DatasetTensorFlowConverter.tensorToDataset(DatasetTensorFlowConverter.java:70)
    at de.csbdresden.csbdeep.network.model.tensorflow.TensorFlowNetwork.execute(TensorFlowNetwork.java:359)
    at de.csbdresden.csbdeep.network.model.DefaultNetwork.lambda$call$0(DefaultNetwork.java:102)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Negative capacity: -1375338496
    at java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006)
    at de.csbdresden.csbdeep.network.DefaultModelExecutor.run(DefaultModelExecutor.java:110)
    at de.csbdresden.csbdeep.network.DefaultModelExecutor.run(DefaultModelExecutor.java:71)
    at de.csbdresden.csbdeep.commands.GenericCoreNetwork.tileAndRunNetwork(GenericCoreNetwork.java:594)
    at de.csbdresden.csbdeep.commands.GenericCoreNetwork.tryToTileAndRunNetwork(GenericCoreNetwork.java:567)
    at de.csbdresden.csbdeep.commands.GenericCoreNetwork.mainThread(GenericCoreNetwork.java:469)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Negative capacity: -1375338496
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:593)
    at java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1005)
    ... 10 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Negative capacity: -1375338496
    at java.util.concurrent.ForkJoinTask$AdaptedCallable.exec(ForkJoinTask.java:1431)
    at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
    at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
    at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
    at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
Caused by: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Negative capacity: -1375338496
    at java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.util.concurrent.FutureTask.get(FutureTask.java:192)
    at de.csbdresden.csbdeep.network.model.DefaultNetwork.call(DefaultNetwork.java:110)
    at de.csbdresden.csbdeep.network.model.DefaultNetwork.call(DefaultNetwork.java:51)
    at java.util.concurrent.ForkJoinTask$AdaptedCallable.exec(ForkJoinTask.java:1424)
    ... 4 more
Caused by: java.lang.IllegalArgumentException: Negative capacity: -1375338496
    at java.nio.Buffer.<init>(Buffer.java:199)
    at java.nio.ByteBuffer.<init>(ByteBuffer.java:281)
    at java.nio.ByteBuffer.<init>(ByteBuffer.java:289)
    at java.nio.MappedByteBuffer.<init>(MappedByteBuffer.java:89)
    at java.nio.DirectByteBuffer.<init>(DirectByteBuffer.java:162)
    at org.tensorflow.Tensor.buffer(Native Method)
    at org.tensorflow.Tensor.buffer(Tensor.java:573)
    at org.tensorflow.Tensor.writeTo(Tensor.java:487)
    at net.imagej.tensorflow.Tensors.imgFloat(Tensors.java:171)
    at net.imagej.tensorflow.Tensors.imgFloat(Tensors.java:262)
    at de.csbdresden.csbdeep.network.model.tensorflow.DatasetTensorFlowConverter.tensorToDataset(DatasetTensorFlowConverter.java:70)
    at de.csbdresden.csbdeep.network.model.tensorflow.TensorFlowNetwork.execute(TensorFlowNetwork.java:359)
    at de.csbdresden.csbdeep.network.model.DefaultNetwork.lambda$call$0(DefaultNetwork.java:102)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
[INFO] CSBDeep plugin exit (took 272559 milliseconds)
[ERROR] Module threw exception
java.lang.NullPointerException
    at de.csbdresden.stardist.StarDist2D.splitPrediction(StarDist2D.java:338)
    at de.csbdresden.stardist.StarDist2D.run(StarDist2D.java:307)
    at org.scijava.command.CommandModule.run(CommandModule.java:196)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
uschmidt83 commented 3 years ago

I'm not sure what the problem is, maybe it is related to https://github.com/CSBDeep/CSBDeep_website/issues/6? I'd recommend to ask this at the image.sc forum, since there are more knowledgable Java/ImageJ/Fiji folks.

Sorry for the late reply.

Best, Uwe