[ome-users] BioFormats as an ITK plugin segmentation fault on Mac, working on Windows

[Joe Ping-Lin Hsiao]

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