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fiji / register_virtual_stack_slices

Fiji package for registering and transforming arbitrarily large sequences of images
https://imagej.net/Register_Virtual_Stack_Slices
GNU General Public License v3.0
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Error "Wrong dimensions of stack" when using TIF 16 bits as source images #9

Open racagalro opened 4 years ago

racagalro commented 4 years ago

I'm trying to register 4 TIF uncompressed 16 bits images. The reference image is loaded ok but when loading slice 2 the following exception appears on console: java.lang.IllegalArgumentException: Wrong dimensions for this stack at ij.ImagePlus.setProcessor(ImagePlus.java:617) at register_virtual_stack.Register_Virtual_Stack_MT.register(Register_Virtual_Stack_MT.java:1863) at If I try the same with same four images but register_virtual_stack.Register_Virtual_Stack_MT.exec(Register_Virtual_Stack_MT.java:1238) at register_virtual_stack.Register_Virtual_Stack_MT.exec(Register_Virtual_Stack_MT.java:421) at register_virtual_stack.Register_Virtual_Stack_MT.exec(Register_Virtual_Stack_MT.java:333) at register_virtual_stack.Register_Virtual_Stack_MT.run(Register_Virtual_Stack_MT.java:288) at ij.IJ.runUserPlugIn(IJ.java:230) at ij.IJ.runPlugIn(IJ.java:193) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at java.lang.Thread.run(Thread.java:748)

In debug mode, the following messages are write in log: windowActivated: Registered tif_1920 setKeyUp: -1 runPlugIn: register_virtual_stack.Register_Virtual_Stack_MT actionPerformed: time=1592322219649, java.awt.event.ActionEvent[ACTION_PERFORMED,cmd=Register Virtual Stack Slices,when=1592322219647,modifiers=] on menuitem0 runUserPlugIn: register_virtual_stack.Register_Virtual_Stack_MT, arg= GenericDialog font: false java.awt.Font[family=Dialog,name=Dialog,style=plain,size=12] windowActivated: Registered tif_1920 focusGained: img["Registered tif_1920" (-85), 24-bit, 4913x3215x1x4x1] openImage: "tif", /home/rafa/fotos/prueba_fiji/TIF_16bits/DSC_0859.tif windowActivated: Registered tif_1920 focusGained: img["Registered tif_1920" (-85), 24-bit, 4913x3215x1x4x1]

DSC_0859.tif: opening 256, "ImageWidth", value=4310 257, "ImageLength", value=2868 258, "BitsPerSample", value=218, count=3 259, "Compression", value=1 262, "PhotoInterp", value=2 266, "???", value=1 273, "StripOffsets", value=224, count=2868 277, "SamplesPerPixel", value=3 278, "RowsPerStrip", value=1 279, "StripByteCount", value=11696, count=2868 282, "XResolution", value=23168 283, "YResolution", value=23176 284, "PlanarConfiguration", value=1 296, "ResolutionUnit", value=2 339, "SampleFormat", value=23184, count=3 700, "???", value=23190, count=2558 34675, "???", value=25748, count=9044 nextIFD=0 number of IFDs: 1 offset to first image: 34792 gap between images: 0 little-endian byte order: true

FileInfo: name=DSC_0859.tif, dir=/home/rafa/fotos/prueba_fiji/TIF_16bits/, width=4310, height=2868, nImages=1, offset=34792, gap=0, type=RGB48, byteOrder=little, format=2, url=, whiteIsZero=f, lutSize=0, comp=1, ranges=null, samples=3 stack.viewers: 1 CompositeImage: img["DSC_0859.tif" (-89), 16-bit, 4310x2868x3x1x1] 1 3 stack.viewers: 2 openImage: "tif", /home/rafa/fotos/prueba_fiji/TIF_16bits/DSC_0860.tif

DSC_0860.tif: opening 256, "ImageWidth", value=4310 257, "ImageLength", value=2868 258, "BitsPerSample", value=218, count=3 259, "Compression", value=1 262, "PhotoInterp", value=2 266, "???", value=1 273, "StripOffsets", value=224, count=2868 277, "SamplesPerPixel", value=3 278, "RowsPerStrip", value=1 279, "StripByteCount", value=11696, count=2868 282, "XResolution", value=23168 283, "YResolution", value=23176 284, "PlanarConfiguration", value=1 296, "ResolutionUnit", value=2 339, "SampleFormat", value=23184, count=3 700, "???", value=23190, count=2558 34675, "???", value=25748, count=9044 nextIFD=0 number of IFDs: 1 offset to first image: 34792 gap between images: 0 little-endian byte order: true

FileInfo: name=DSC_0860.tif, dir=/home/rafa/fotos/prueba_fiji/TIF_16bits/, width=4310, height=2868, nImages=1, offset=34792, gap=0, type=RGB48, byteOrder=little, format=2, url=, whiteIsZero=f, lutSize=0, comp=1, ranges=null, samples=3 stack.viewers: 1 CompositeImage: img["DSC_0860.tif" (-94), 16-bit, 4310x2868x3x1x1] 1 3 stack.viewers: 2 err >java.lang.IllegalArgumentException: Wrong dimensions for this stack err > at ij.ImagePlus.setProcessor(ImagePlus.java:617) err > at register_virtual_stack.Register_Virtual_Stack_MT.register(Register_Virtual_Stack_MT.java:1863) err > at register_virtual_stack.Register_Virtual_Stack_MT.exec(Register_Virtual_Stack_MT.java:1238) err > at register_virtual_stack.Register_Virtual_Stack_MT.exec(Register_Virtual_Stack_MT.java:421) err > at register_virtual_stack.Register_Virtual_Stack_MT.exec(Register_Virtual_Stack_MT.java:333) err > at register_virtual_stack.Register_Virtual_Stack_MT.run(Register_Virtual_Stack_MT.java:288) err > at ij.IJ.runUserPlugIn(IJ.java:230) err > at ij.IJ.runPlugIn(IJ.java:193) err > at ij.Executer.runCommand(Executer.java:137) err > at ij.Executer.run(Executer.java:66) err > at java.lang.Thread.run(Thread.java:748) setKeyUp: -1 setKeyUp: 18 setKeyDown: 18 keyPressed: code=18 (Alt), char="￿" (65535), flags=Alt setKeyUp: 18 setKeyDown: 18 keyPressed: code=18 (Alt), char="￿" (65535), flags=Alt setKeyUp: 18 actionPerformed: time=1592322435423, java.awt.event.ActionEvent[ACTION_PERFORMED,cmd=Register Virtual Stack Slices,when=1592322435422,modifiers=] on menuitem0 runPlugIn: register_virtual_stack.Register_Virtual_Stack_MT runUserPlugIn: register_virtual_stack.Register_Virtual_Stack_MT, arg= GenericDialog font: false java.awt.Font[family=Dialog,name=Dialog,style=plain,size=12] windowActivated: Registered tif_1920 focusGained: img["Registered tif_1920" (-85), 24-bit, 4913x3215x1x4x1] openImage: "tif", /home/rafa/fotos/prueba_fiji/TIF_32bits/DSC_0859.tif windowActivated: Registered tif_1920 focusGained: img["Registered tif_1920" (-85), 24-bit, 4913x3215x1x4x1] err >java.lang.NullPointerException err > at register_virtual_stack.Register_Virtual_Stack_MT.exec(Register_Virtual_Stack_MT.java:1204) err > at register_virtual_stack.Register_Virtual_Stack_MT.exec(Register_Virtual_Stack_MTIf I try the same with same four images but .java:421) err > at register_virtual_stack.Register_Virtual_Stack_MT.exec(Register_Virtual_Stack_MT.java:333) err > at register_virtual_stack.Register_Virtual_Stack_MT.run(Register_Virtual_Stack_MT.java:288) err > at ij.IJ.runUserPlugIn(IJ.java:230) err > at ij.IJ.runPlugIn(IJ.java:193) err > at ij.Executer.runCommand(Executer.java:137) err > at ij.Executer.run(Executer.java:66) err > at java.lang.Thread.run(Thread.java:748)

If I use TIF 8bits uncompressed images as input, I have no problem. My version of ImageJ is 1.52p. I don't know the version of Registration plugin but it must be the last one because I had updated all plugins before testing.

iarganda commented 3 years ago

Sorry for the late answer, @racagalro I tried reproducing the error but it works fine on my machine. Did you figure out if it was a problem with your images?