[ome-users] BioFormats as an ITK plugin segmentation fault on Mac, working on Windows
Mark Hiner
hiner at wisc.edu
Tue Nov 6 19:25:15 GMT 2012
Hi Joe,
Thanks for using the BF-ITK plug-in. I'm sorry it took so long to get a
response to you.
I think this is just a build configuration error of ITK, and was
completely our fault for incomplete build instructions.
ITK should also be configured with BUILD_SHARED_LIBS = ON. I tried a build
from the latest ITK.git configured once with shared libs ON, once OFF, and
verified that there are linker errors when it's set to OFF. These errors
cause the BF-ITK imageIO creation to fail (as suggested in this
thread<http://www.itk.org/pipermail/insight-users/2010-March/035917.html>
).
The instructions <http://loci.wisc.edu/bio-formats/itk> have been updated.
Try going through the steps again, building ITK with both BUILD_SHARED_LIBS
= ON and ITK_USE_REVIEW = ON. That should work, but if it doesn't just let
me know and I'll try again!
Thanks again,
Mark
On Thu, Nov 1, 2012 at 3:53 PM, Joe Ping-Lin Hsiao <phsiao at cs.unc.edu>wrote:
> Hi,
>
> I followed this link http://loci.wisc.edu/bio-formats/itk to build
> a bioformats ITK plugin. When I try to read a .ics file with
> ImageHistogram1, which is a program from ITK's bin folder, I got the
> following output:
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,
> line 130
> BioFormatsImageIO (0x109beabe0): BioFormatsImageIO constructor
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,
> line 162
> BioFormatsImageIO (0x109beabe0): BioFormatsImageIO base command:
> /usr/bin/java -Xmx256m -Djava.awt.headless=true -cp
>
> /Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[0]
> = /usr/bin/java
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[1] =
> -Xmx256m
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[2]
> = -Djava.awt.headless=true
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[3] = -cp
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[4]
> =
> /Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[5]
> = loci.formats.itk.ITKBridgePipes
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[6]
> = waitForInput
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,
> line 130
> BioFormatsImageIO (0x109beadb0): BioFormatsImageIO constructor
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,
> line 162
> BioFormatsImageIO (0x109beadb0): BioFormatsImageIO base command:
> /usr/bin/java -Xmx256m -Djava.awt.headless=true -cp
>
> /Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[0]
> = /usr/bin/java
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[1] =
> -Xmx256m
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[2]
> = -Djava.awt.headless=true
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[3] = -cp
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[4]
> =
> /Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[5]
> = loci.formats.itk.ITKBridgePipes
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[6]
> = waitForInput
>
> Error ImageIO factory did not return an ImageIOBase: BioFormatsImageIO
> Error ImageIO factory did not return an ImageIOBase: BioFormatsImageIO
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,
> line 269
> BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::~BioFormatsImageIO
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,
> line 269
> BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::~BioFormatsImageIO
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,
> line 130
> BioFormatsImageIO (0x109be94f0): BioFormatsImageIO constructor
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,
> line 162
> BioFormatsImageIO (0x109be94f0): BioFormatsImageIO base command:
> /usr/bin/java -Xmx256m -Djava.awt.headless=true -cp
>
> /Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[0]
> = /usr/bin/java
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[1] =
> -Xmx256m
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[2]
> = -Djava.awt.headless=true
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[3] = -cp
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[4]
> =
> /Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[5]
> = loci.formats.itk.ITKBridgePipes
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[6]
> = waitForInput
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,
> line 130
> BioFormatsImageIO (0x109be99c0): BioFormatsImageIO constructor
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,
> line 162
> BioFormatsImageIO (0x109be99c0): BioFormatsImageIO base command:
> /usr/bin/java -Xmx256m -Djava.awt.headless=true -cp
>
> /Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[0]
> = /usr/bin/java
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[1] =
> -Xmx256m
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[2]
> = -Djava.awt.headless=true
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[3] = -cp
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[4]
> =
> /Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[5]
> = loci.formats.itk.ITKBridgePipes
>
> Debug: In
> /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,
> line 117
> BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[6]
> = waitForInput
>
> Segmentation fault
> ----------------------------
> However, the program works fine on Windows (Windows 7).
>
> Here is some information about my environment:
>
> Mac OSX 10.6.8
> The latest bioformats code from git, as of 11/1/2012
> The latest ITK from git, as of 11/1/2012, with ITK_USE_REVIEW on
> 'java -version' output:
> java version "1.6.0_37"
> Java(TM) SE Runtime Environment (build 1.6.0_37-b06-434-10M3909)
> Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01-434, mixed mode)
>
> Here is the output from running gdb:
>
> Program received signal EXC_BAD_ACCESS, Could not access memory.
> Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000
> 0x00000001000649b7 in itk::ImageFileReader<itk::Image<unsigned char,
> 2u>, itk::DefaultConvertPixelTraits<unsigned char>
> >::GenerateOutputInformation ()
> (gdb) where
> #0 0x00000001000649b7 in itk::ImageFileReader<itk::Image<unsigned
> char, 2u>, itk::DefaultConvertPixelTraits<unsigned char>
> >::GenerateOutputInformation ()
> #1 0x00000001000cea85 in itk::ProcessObject::UpdateOutputInformation ()
> #2 0x0000000100051481 in itk::ImageBase<2u>::UpdateOutputInformation ()
> #3 0x00000001000e3095 in itk::DataObject::Update ()
> #4 0x000000010004edc9 in main ()
>
>
> Thanks,
> Joe
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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