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imglib / imglib2

A generic next-generation Java library for image processing
http://imglib2.net/
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ops.image().watershed failed on large image #274

Open bpavie opened 4 years ago

bpavie commented 4 years ago

I ran the following macro

// @OpService ops
// @Dataset inputData

import net.imagej.ops.Ops
import net.imglib2.img.display.imagej.ImageJFunctions
import net.imglib2.type.numeric.integer.UnsignedByteType 

//Thresold the Output mask from fiji (where 0 is false and 255 is true)
maskBitType = ops.threshold().apply(inputData, new UnsignedByteType(128));
//Fill the holes
maskFilled = ops.morphology().fillHoles(maskBitType);

//Perform the watershed
useEightConnectivity=true
drawWatersheds=false
double sigma=2.0
watershedImgLabeling=ops.image().watershed(null,maskFilled,useEightConnectivity,drawWatersheds,sigma,maskFilled)

//Display the result
watershedImg=watershedImgLabeling.getIndexImg()
watershedImgLabelingImp=ImageJFunctions.wrap(watershedImg, "wrapped")
watershedImgLabelingImp.show()

which work on small dataset image_test_small.zip but not if the image is large (image_test.zip.

The output error for the large image is the following:

Started watershed.groovy at Wed Nov 27 14:00:32 CET 2019
java.lang.IllegalArgumentException: No matching 'net.imagej.ops.Ops$Image$DistanceTransform' op

Request:
-   net.imagej.ops.Ops$Image$DistanceTransform(
        DefaultDataset)

Candidates:
1.  (RandomAccessibleInterval out?) =
    net.imagej.ops.image.distancetransform.DistanceTransform2D(
        RandomAccessibleInterval out?,
        RandomAccessibleInterval in)
    Inputs do not conform to op rules
        out = null
        in = test_image.tif
2.  (RandomAccessibleInterval out?) =
    net.imagej.ops.image.distancetransform.DistanceTransform2DCalibration(
        RandomAccessibleInterval out?,
        RandomAccessibleInterval in,
        double[] calibration)
    Not enough arguments: 1 < 2
3.  (RandomAccessibleInterval out?) =
    net.imagej.ops.image.distancetransform.DistanceTransform3D(
        RandomAccessibleInterval out?,
        RandomAccessibleInterval in)
    Inputs do not conform to op rules
        out = null
        in = test_image.tif
4.  (RandomAccessibleInterval out?) =
    net.imagej.ops.image.distancetransform.DistanceTransform3DCalibration(
        RandomAccessibleInterval out?,
        RandomAccessibleInterval in,
        double[] calibration)
    Not enough arguments: 1 < 2
5.  (RandomAccessibleInterval out?) =
    net.imagej.ops.image.distancetransform.DefaultDistanceTransform(
        RandomAccessibleInterval out?,
        RandomAccessibleInterval in)
    Inputs do not conform to op rules
        out = null
        in = test_image.tif
6.  (RandomAccessibleInterval out?) =
    net.imagej.ops.image.distancetransform.DefaultDistanceTransformCalibration(
        RandomAccessibleInterval out?,
        RandomAccessibleInterval in,
        double[] calibration)
    Not enough arguments: 1 < 2

    at net.imagej.ops.DefaultOpMatchingService.singleMatch(DefaultOpMatchingService.java:432)
    at net.imagej.ops.DefaultOpMatchingService.findMatch(DefaultOpMatchingService.java:97)
    at net.imagej.ops.DefaultOpMatchingService.findMatch(DefaultOpMatchingService.java:83)
    at net.imagej.ops.OpEnvironment.module(OpEnvironment.java:269)
    at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:157)
    at net.imagej.ops.image.ImageNamespace.distancetransform(ImageNamespace.java:134)
    at net.imagej.ops.image.watershed.WatershedBinarySingleSigma.compute(WatershedBinarySingleSigma.java:103)
    at net.imagej.ops.image.watershed.WatershedBinarySingleSigma.compute(WatershedBinarySingleSigma.java:80)
    at net.imagej.ops.special.hybrid.UnaryHybridCF.calculate(UnaryHybridCF.java:61)
    at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:71)
    at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:97)
    at org.scijava.command.CommandModule.run(CommandModule.java:199)
    at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:950)
    at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:157)
    at net.imagej.ops.image.ImageNamespace.watershed(ImageNamespace.java:602)
    at net.imagej.ops.image.ImageNamespace$watershed.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at Script9.run(Script9.groovy:21)
    at org.scijava.plugins.scripting.groovy.GroovyScriptEngine.eval(GroovyScriptEngine.java:303)
    at org.scijava.plugins.scripting.groovy.GroovyScriptEngine.eval(GroovyScriptEngine.java:122)
    at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
    at org.scijava.script.ScriptModule.run(ScriptModule.java:160)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Started watershed.groovy at Wed Nov 27 14:18:12 CET 2019
java.lang.ClassCastException: net.imglib2.type.numeric.integer.UnsignedByteType cannot be cast to net.imglib2.type.numeric.integer.UnsignedShortType
    at net.imglib2.type.numeric.integer.UnsignedShortType.compareTo(UnsignedShortType.java:50)
    at net.imagej.ops.threshold.apply.ApplyThresholdComparable.compute(ApplyThresholdComparable.java:56)
    at net.imagej.ops.threshold.apply.ApplyThresholdComparable.compute(ApplyThresholdComparable.java:46)
    at net.imagej.ops.special.computer.BinaryComputerOp.compute(BinaryComputerOp.java:93)
    at net.imagej.ops.map.MapIterableToIterable.compute(MapIterableToIterable.java:58)
    at net.imagej.ops.map.MapIterableToIterable.compute(MapIterableToIterable.java:47)
    at net.imagej.ops.threshold.apply.ApplyConstantThreshold.compute(ApplyConstantThreshold.java:73)
    at net.imagej.ops.threshold.apply.ApplyConstantThreshold.compute(ApplyConstantThreshold.java:50)
    at net.imagej.ops.threshold.AbstractApplyThresholdIterable.compute(AbstractApplyThresholdIterable.java:52)
    at net.imagej.ops.threshold.AbstractApplyThresholdIterable.compute(AbstractApplyThresholdIterable.java:43)
    at net.imagej.ops.special.hybrid.UnaryHybridCF.calculate(UnaryHybridCF.java:61)
    at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:71)
    at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:97)
    at org.scijava.command.CommandModule.run(CommandModule.java:199)
    at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:950)
    at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:157)
    at net.imagej.ops.threshold.ThresholdNamespace.apply(ThresholdNamespace.java:82)
    at net.imagej.ops.threshold.ThresholdNamespace$apply.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
    at Script10.run(Script10.groovy:13)
    at org.scijava.plugins.scripting.groovy.GroovyScriptEngine.eval(GroovyScriptEngine.java:303)
    at org.scijava.plugins.scripting.groovy.GroovyScriptEngine.eval(GroovyScriptEngine.java:122)
    at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
    at org.scijava.script.ScriptModule.run(ScriptModule.java:160)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Started watershed.groovy at Wed Nov 27 14:18:34 CET 2019
Started watershed.groovy at Wed Nov 27 14:19:17 CET 2019
java.lang.ClassCastException
Started watershed.groovy at Wed Nov 27 14:19:50 CET 2019
Started watershed.groovy at Wed Nov 27 14:20:15 CET 2019
Started watershed.groovy at Wed Nov 27 14:21:50 CET 2019
java.lang.IllegalArgumentException: No matching 'net.imagej.ops.Ops$Image$DistanceTransform' op

Request:
-   net.imagej.ops.Ops$Image$DistanceTransform(
        DefaultDataset)

Candidates:
1.  (RandomAccessibleInterval out?) =
    net.imagej.ops.image.distancetransform.DistanceTransform2D(
        RandomAccessibleInterval out?,
        RandomAccessibleInterval in)
    Inputs do not conform to op rules
        out = null
        in = test_image.tif
2.  (RandomAccessibleInterval out?) =
    net.imagej.ops.image.distancetransform.DistanceTransform2DCalibration(
        RandomAccessibleInterval out?,
        RandomAccessibleInterval in,
        double[] calibration)
    Not enough arguments: 1 < 2
3.  (RandomAccessibleInterval out?) =
    net.imagej.ops.image.distancetransform.DistanceTransform3D(
        RandomAccessibleInterval out?,
        RandomAccessibleInterval in)
    Inputs do not conform to op rules
        out = null
        in = test_image.tif
4.  (RandomAccessibleInterval out?) =
    net.imagej.ops.image.distancetransform.DistanceTransform3DCalibration(
        RandomAccessibleInterval out?,
        RandomAccessibleInterval in,
        double[] calibration)
    Not enough arguments: 1 < 2
5.  (RandomAccessibleInterval out?) =
    net.imagej.ops.image.distancetransform.DefaultDistanceTransform(
        RandomAccessibleInterval out?,
        RandomAccessibleInterval in)
    Inputs do not conform to op rules
        out = null
        in = test_image.tif
6.  (RandomAccessibleInterval out?) =
    net.imagej.ops.image.distancetransform.DefaultDistanceTransformCalibration(
        RandomAccessibleInterval out?,
        RandomAccessibleInterval in,
        double[] calibration)
    Not enough arguments: 1 < 2

    at net.imagej.ops.DefaultOpMatchingService.singleMatch(DefaultOpMatchingService.java:432)
    at net.imagej.ops.DefaultOpMatchingService.findMatch(DefaultOpMatchingService.java:97)
    at net.imagej.ops.DefaultOpMatchingService.findMatch(DefaultOpMatchingService.java:83)
    at net.imagej.ops.OpEnvironment.module(OpEnvironment.java:269)
    at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:157)
    at net.imagej.ops.image.ImageNamespace.distancetransform(ImageNamespace.java:134)
    at net.imagej.ops.image.watershed.WatershedBinarySingleSigma.compute(WatershedBinarySingleSigma.java:103)
    at net.imagej.ops.image.watershed.WatershedBinarySingleSigma.compute(WatershedBinarySingleSigma.java:80)
    at net.imagej.ops.special.hybrid.UnaryHybridCF.calculate(UnaryHybridCF.java:61)
    at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:71)
    at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:97)
    at org.scijava.command.CommandModule.run(CommandModule.java:199)
    at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:950)
    at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:157)
    at net.imagej.ops.image.ImageNamespace.watershed(ImageNamespace.java:602)
    at net.imagej.ops.image.ImageNamespace$watershed.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at Script15.run(Script15.groovy:21)
    at org.scijava.plugins.scripting.groovy.GroovyScriptEngine.eval(GroovyScriptEngine.java:303)
    at org.scijava.plugins.scripting.groovy.GroovyScriptEngine.eval(GroovyScriptEngine.java:122)
    at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
    at org.scijava.script.ScriptModule.run(ScriptModule.java:160)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
imagejan commented 4 years ago

That's an imagej-ops issue, I believe.

The distanceTransform ops (which are used by the watershed op) have a rather restrictive conforms() check:

https://github.com/imagej/imagej-ops/blob/7870ad17a3cd36e5c9915580a25d53da5893f5c3/src/main/java/net/imagej/ops/image/distancetransform/DefaultDistanceTransform.java#L75-L81

Your sample image is 35206 * 42619 pixels, and the ops will only match if:

(x*x) + (y*y) < Integer.MAX_VALUE

There is currently no ops implementation that matches for the given request.

bpavie commented 4 years ago

Thanks a lot for your quick answer!

So it means we cannot perform this ops on image with more than Integer.MAX_VALUE/2 pixels (so no more than 1,073,741,823, or roughly 32,000*32,000).

Is there any reason for this limit, because it should be more linked to the memory size available. It looks like somewhere in the code, an int array is used in this ops with a length equal of the number of the pixel in the image, which probably explain this limitation since java array length are limited to Integer.MAX_VALUE , could it be modified to store them into a List to avoid this limitation? It looks to me like an old imagej1 limitation...

Benjamin