Hi Joe,<br><br> Thanks for using the BF-ITK plug-in. I'm sorry it took so long to get a response to you.<br><br> I think this is just a build configuration error of ITK, and was completely our fault for incomplete build instructions.<br>
<br> 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 <a href="http://www.itk.org/pipermail/insight-users/2010-March/035917.html">this thread</a>).<br>
<br> <a href="http://loci.wisc.edu/bio-formats/itk">The instructions</a> 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!<br>
<br>Thanks again,<br>Mark<br><br><div class="gmail_quote">On Thu, Nov 1, 2012 at 3:53 PM, Joe Ping-Lin Hsiao <span dir="ltr"><<a href="mailto:phsiao@cs.unc.edu" target="_blank">phsiao@cs.unc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
   I followed this link <a href="http://loci.wisc.edu/bio-formats/itk" target="_blank">http://loci.wisc.edu/bio-formats/itk</a> to build<br>
a bioformats ITK plugin. When I try to read a .ics file with<br>
ImageHistogram1, which is a program from ITK's bin folder, I got the<br>
following output:<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,<br>
line 130<br>
BioFormatsImageIO (0x109beabe0): BioFormatsImageIO constructor<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,<br>
line 162<br>
BioFormatsImageIO (0x109beabe0): BioFormatsImageIO base command:<br>
/usr/bin/java -Xmx256m -Djava.awt.headless=true -cp<br>
/Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[0]<br>
= /usr/bin/java<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[1] = -Xmx256m<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[2]<br>
= -Djava.awt.headless=true<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[3] = -cp<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[4]<br>
= /Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[5]<br>
= loci.formats.itk.ITKBridgePipes<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::toCArray::args[6]<br>
= waitForInput<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,<br>
line 130<br>
BioFormatsImageIO (0x109beadb0): BioFormatsImageIO constructor<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,<br>
line 162<br>
BioFormatsImageIO (0x109beadb0): BioFormatsImageIO base command:<br>
/usr/bin/java -Xmx256m -Djava.awt.headless=true -cp<br>
/Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[0]<br>
= /usr/bin/java<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[1] = -Xmx256m<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[2]<br>
= -Djava.awt.headless=true<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[3] = -cp<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[4]<br>
= /Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[5]<br>
= loci.formats.itk.ITKBridgePipes<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::toCArray::args[6]<br>
= waitForInput<br>
<br>
Error ImageIO factory did not return an ImageIOBase: BioFormatsImageIO<br>
Error ImageIO factory did not return an ImageIOBase: BioFormatsImageIO<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,<br>
line 269<br>
BioFormatsImageIO (0x109beabe0): BioFormatsImageIO::~BioFormatsImageIO<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,<br>
line 269<br>
BioFormatsImageIO (0x109beadb0): BioFormatsImageIO::~BioFormatsImageIO<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,<br>
line 130<br>
BioFormatsImageIO (0x109be94f0): BioFormatsImageIO constructor<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,<br>
line 162<br>
BioFormatsImageIO (0x109be94f0): BioFormatsImageIO base command:<br>
/usr/bin/java -Xmx256m -Djava.awt.headless=true -cp<br>
/Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[0]<br>
= /usr/bin/java<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[1] = -Xmx256m<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[2]<br>
= -Djava.awt.headless=true<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[3] = -cp<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[4]<br>
= /Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[5]<br>
= loci.formats.itk.ITKBridgePipes<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be94f0): BioFormatsImageIO::toCArray::args[6]<br>
= waitForInput<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,<br>
line 130<br>
BioFormatsImageIO (0x109be99c0): BioFormatsImageIO constructor<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.cxx,<br>
line 162<br>
BioFormatsImageIO (0x109be99c0): BioFormatsImageIO base command:<br>
/usr/bin/java -Xmx256m -Djava.awt.headless=true -cp<br>
/Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[0]<br>
= /usr/bin/java<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[1] = -Xmx256m<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[2]<br>
= -Djava.awt.headless=true<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[3] = -cp<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[4]<br>
= /Users/phsiao/dev/bioformats-itk/dist/bf-itk/loci_tools.jar:/Users/phsiao/dev/bioformats-itk/dist/bf-itk/<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[5]<br>
= loci.formats.itk.ITKBridgePipes<br>
<br>
Debug: In /Users/phsiao/dev/src/bioformats/components/native/bf-itk-pipe/itkBioFormatsImageIO.h,<br>
line 117<br>
BioFormatsImageIO (0x109be99c0): BioFormatsImageIO::toCArray::args[6]<br>
= waitForInput<br>
<br>
Segmentation fault<br>
----------------------------<br>
However, the program works fine on Windows (Windows 7).<br>
<br>
Here is some information about my environment:<br>
<br>
Mac OSX 10.6.8<br>
The latest bioformats code from git, as of 11/1/2012<br>
The latest ITK from git, as of 11/1/2012, with ITK_USE_REVIEW on<br>
'java -version' output:<br>
java version "1.6.0_37"<br>
Java(TM) SE Runtime Environment (build 1.6.0_37-b06-434-10M3909)<br>
Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01-434, mixed mode)<br>
<br>
Here is the output from running gdb:<br>
<br>
Program received signal EXC_BAD_ACCESS, Could not access memory.<br>
Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000<br>
0x00000001000649b7 in itk::ImageFileReader<itk::Image<unsigned char,<br>
2u>, itk::DefaultConvertPixelTraits<unsigned char><br>
>::GenerateOutputInformation ()<br>
(gdb) where<br>
#0  0x00000001000649b7 in itk::ImageFileReader<itk::Image<unsigned<br>
char, 2u>, itk::DefaultConvertPixelTraits<unsigned char><br>
>::GenerateOutputInformation ()<br>
#1  0x00000001000cea85 in itk::ProcessObject::UpdateOutputInformation ()<br>
#2  0x0000000100051481 in itk::ImageBase<2u>::UpdateOutputInformation ()<br>
#3  0x00000001000e3095 in itk::DataObject::Update ()<br>
#4  0x000000010004edc9 in main ()<br>
<br>
<br>
Thanks,<br>
Joe<br>
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</blockquote></div><br>