[ImageJ-bugs] [Bug 1200] New: large file pairwais stitching problem
bugzilla at fiji.sc
bugzilla at fiji.sc
Wed Dec 2 07:58:07 CST 2015
http://fiji.sc/bugzilla/show_bug.cgi?id=1200
Bug ID: 1200
Summary: large file pairwais stitching problem
Product: Fiji
Version: unspecified
Hardware: PC
OS: Windows
Status: NEW
Severity: normal
Priority: P4
Component: Plugins
Assignee: imagej-bugs at imagej.net
Reporter: alexandros.sountoulidis at su.se
CC: alexandros.sountoulidis at su.se
Hello,
I know that would be nice to send the images but the files are too big. File1
4.7 GB (3072x4608 z=120 steps 8 bit, 3 channels) File2 3.7GB ( 2560x4608 z=112
steps 8 bit, 3 channels). I tried to used pairwise stitching because the
overlap at the z-axis and I took the following error
Exception in thread "Thread-51" java.lang.NegativeArraySizeException
at
mpicbg.imglib.container.basictypecontainer.array.FloatArray.<init>(FloatArray.java:54)
at
mpicbg.imglib.container.array.ArrayContainerFactory.createFloatInstance(ArrayContainerFactory.java:147)
at
mpicbg.imglib.type.numeric.complex.ComplexFloatType.createSuitableDirectAccessContainer(ComplexFloatType.java:83)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:69)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:55)
at mpicbg.imglib.image.Image.<init>(Image.java:113)
at mpicbg.imglib.image.Image.<init>(Image.java:136)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:69)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:72)
at
mpicbg.imglib.algorithm.fft.FFTFunctions.computeFFT(FFTFunctions.java:389)
at
mpicbg.imglib.algorithm.fft.FourierTransform.process(FourierTransform.java:268)
at
mpicbg.imglib.algorithm.fft.PhaseCorrelation$3.run(PhaseCorrelation.java:706)
at java.lang.Thread.run(Thread.java:662)
Exception in thread "Thread-52" java.lang.NegativeArraySizeException
at
mpicbg.imglib.container.basictypecontainer.array.FloatArray.<init>(FloatArray.java:54)
at
mpicbg.imglib.container.array.ArrayContainerFactory.createFloatInstance(ArrayContainerFactory.java:147)
at
mpicbg.imglib.type.numeric.complex.ComplexFloatType.createSuitableDirectAccessContainer(ComplexFloatType.java:83)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:69)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:55)
at mpicbg.imglib.image.Image.<init>(Image.java:113)
at mpicbg.imglib.image.Image.<init>(Image.java:136)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:69)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:72)
at
mpicbg.imglib.algorithm.fft.FFTFunctions.computeFFT(FFTFunctions.java:389)
at
mpicbg.imglib.algorithm.fft.FourierTransform.process(FourierTransform.java:268)
at
mpicbg.imglib.algorithm.fft.PhaseCorrelation$3.run(PhaseCorrelation.java:711)
at java.lang.Thread.run(Thread.java:662)
version = 1.5
C:\Users\Samakovlis\.ImageJ_3D_Viewer.props (The system cannot find the file
specified)
nFrames = 1
version = 1.5
nFrames = 1
Exception in thread "Thread-2707" java.lang.NegativeArraySizeException
at
mpicbg.imglib.container.basictypecontainer.array.FloatArray.<init>(FloatArray.java:54)
at
mpicbg.imglib.container.array.ArrayContainerFactory.createFloatInstance(ArrayContainerFactory.java:147)
at
mpicbg.imglib.type.numeric.complex.ComplexFloatType.createSuitableDirectAccessContainer(ComplexFloatType.java:83)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:69)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:55)
at mpicbg.imglib.image.Image.<init>(Image.java:113)
at mpicbg.imglib.image.Image.<init>(Image.java:136)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:69)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:72)
at
mpicbg.imglib.algorithm.fft.FFTFunctions.computeFFT(FFTFunctions.java:389)
at
mpicbg.imglib.algorithm.fft.FourierTransform.process(FourierTransform.java:268)
at
mpicbg.imglib.algorithm.fft.PhaseCorrelation$3.run(PhaseCorrelation.java:706)
at java.lang.Thread.run(Thread.java:662)
Exception in thread "Thread-2708" java.lang.NegativeArraySizeException
at
mpicbg.imglib.container.basictypecontainer.array.FloatArray.<init>(FloatArray.java:54)
at
mpicbg.imglib.container.array.ArrayContainerFactory.createFloatInstance(ArrayContainerFactory.java:147)
at
mpicbg.imglib.type.numeric.complex.ComplexFloatType.createSuitableDirectAccessContainer(ComplexFloatType.java:83)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:69)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:55)
at mpicbg.imglib.image.Image.<init>(Image.java:113)
at mpicbg.imglib.image.Image.<init>(Image.java:136)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:69)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:72)
at
mpicbg.imglib.algorithm.fft.FFTFunctions.computeFFT(FFTFunctions.java:389)
at
mpicbg.imglib.algorithm.fft.FourierTransform.process(FourierTransform.java:268)
at
mpicbg.imglib.algorithm.fft.PhaseCorrelation$3.run(PhaseCorrelation.java:711)
at java.lang.Thread.run(Thread.java:662)
Exception in thread "Thread-4059" java.lang.NegativeArraySizeException
at
mpicbg.imglib.container.basictypecontainer.array.FloatArray.<init>(FloatArray.java:54)
at
mpicbg.imglib.container.array.ArrayContainerFactory.createFloatInstance(ArrayContainerFactory.java:147)
at
mpicbg.imglib.type.numeric.complex.ComplexFloatType.createSuitableDirectAccessContainer(ComplexFloatType.java:83)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:69)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:55)
at mpicbg.imglib.image.Image.<init>(Image.java:113)
at mpicbg.imglib.image.Image.<init>(Image.java:136)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:69)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:72)
at
mpicbg.imglib.algorithm.fft.FFTFunctions.computeFFT(FFTFunctions.java:389)
at
mpicbg.imglib.algorithm.fft.FourierTransform.process(FourierTransform.java:268)
at
mpicbg.imglib.algorithm.fft.PhaseCorrelation$3.run(PhaseCorrelation.java:706)
at java.lang.Thread.run(Thread.java:662)
Exception in thread "Thread-4058" java.lang.NegativeArraySizeException
at
mpicbg.imglib.container.basictypecontainer.array.FloatArray.<init>(FloatArray.java:54)
at
mpicbg.imglib.container.array.ArrayContainerFactory.createFloatInstance(ArrayContainerFactory.java:147)
at
mpicbg.imglib.type.numeric.complex.ComplexFloatType.createSuitableDirectAccessContainer(ComplexFloatType.java:83)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:69)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:55)
at mpicbg.imglib.image.Image.<init>(Image.java:113)
at mpicbg.imglib.image.Image.<init>(Image.java:136)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:69)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:72)
at
mpicbg.imglib.algorithm.fft.FFTFunctions.computeFFT(FFTFunctions.java:389)
at
mpicbg.imglib.algorithm.fft.FourierTransform.process(FourierTransform.java:268)
at
mpicbg.imglib.algorithm.fft.PhaseCorrelation$3.run(PhaseCorrelation.java:711)
at java.lang.Thread.run(Thread.java:662)
Exception in thread "Thread-5409" java.lang.NegativeArraySizeException
at
mpicbg.imglib.container.basictypecontainer.array.FloatArray.<init>(FloatArray.java:54)
at
mpicbg.imglib.container.array.ArrayContainerFactory.createFloatInstance(ArrayContainerFactory.java:147)
at
mpicbg.imglib.type.numeric.complex.ComplexFloatType.createSuitableDirectAccessContainer(ComplexFloatType.java:83)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:69)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:55)
at mpicbg.imglib.image.Image.<init>(Image.java:113)
at mpicbg.imglib.image.Image.<init>(Image.java:136)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:69)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:72)
at
mpicbg.imglib.algorithm.fft.FFTFunctions.computeFFT(FFTFunctions.java:389)
at
mpicbg.imglib.algorithm.fft.FourierTransform.process(FourierTransform.java:268)
at
mpicbg.imglib.algorithm.fft.PhaseCorrelation$3.run(PhaseCorrelation.java:706)
at java.lang.Thread.run(Thread.java:662)
Exception in thread "Thread-5410" java.lang.NegativeArraySizeException
at
mpicbg.imglib.container.basictypecontainer.array.FloatArray.<init>(FloatArray.java:54)
at
mpicbg.imglib.container.array.ArrayContainerFactory.createFloatInstance(ArrayContainerFactory.java:147)
at
mpicbg.imglib.type.numeric.complex.ComplexFloatType.createSuitableDirectAccessContainer(ComplexFloatType.java:83)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:69)
at
mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:55)
at mpicbg.imglib.image.Image.<init>(Image.java:113)
at mpicbg.imglib.image.Image.<init>(Image.java:136)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:69)
at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:72)
at
mpicbg.imglib.algorithm.fft.FFTFunctions.computeFFT(FFTFunctions.java:389)
at
mpicbg.imglib.algorithm.fft.FourierTransform.process(FourierTransform.java:268)
at
mpicbg.imglib.algorithm.fft.PhaseCorrelation$3.run(PhaseCorrelation.java:711)
at java.lang.Thread.run(Thread.java:662)
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Done: Checksummer
There is no problem if I reduce the dimensions of the images 50%. Since the
sytem has 12 physical cores (and 12 logical) and 64GB RAM, I think that it has
to do with the settings of the plugin.
Can you help me please?
Thank you very much for your great work and the help, of coarse.
Kind regards,
Alex
Information about your version of Java:
os.arch => amd64
os.name => Windows NT (unknown)
os.version => 6.2
java.version => 1.6.0_24
java.vendor => Sun Microsystems Inc.
java.runtime.name => Java(TM) SE Runtime Environment
java.runtime.version => 1.6.0_24-b07
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
java.vm.version => 19.1-b02
java.vm.vendor => Sun Microsystems Inc.
java.vm.info => mixed mode
java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
java.specification.name => Java Platform API Specification
java.specification.version => 1.6
sun.cpu.endian => little
sun.desktop => windows
file.separator => \
The up-to-date check says: REMIND_LATER
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to: C:\Fiji.app/java/win64/jdk1.6.0_24//jre
imagej.dir => C:\Fiji.app
Information about the version of each plugin:
Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20151122025629)
Fiji: http://update.fiji.sc/ (last check:20151126153359)
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