[Insight-users] Bio-Formats in ITK (was: Re: ITK for fluorescence microscopy - BioImageXD)

Wed May 20 02:43:12 EDT 2009

Le 13 mai 09 à 00:14, Curtis Rueden a écrit :

>
> On Tue, May 12, 2009 at 6:38 AM, alex gouaillard <Alexandre_Gouaillard at hms.harvard.edu 
> > wrote:
> curtis any news on the wrapping (in C++) and using the IO mechanism  
> in ITK? More specifically, anything we could do to help you?
>
> Yes!
>
> The C++ bindings are completely functional on Windows (with Visual C+ 
> +), and Mac OS X and Linux (with gcc).
>
> The ITK plugin is functional on Mac OS X and Linux, but I hit a  
> roadblock on Windows.
>
> For the past month or so I have been swamped with other projects and  
> have not had time to investigate further. If anyone on this list  
> wants to try the C++ bindings and the ITK plugin themselves, I would  
> be extremely appreciative.
>   * If you are a scientist who needs to access life sciences data  
> within ITK, the plugin is likely to be useful as-is.
>   * If you are a C++ software developer, I come from a primarily  
> Java background and have no prior experience with CMake, so I would  
> highly value any improvements or "best practices" fixes to my build  
> system.
>
> You can check out the code from our SVN repository:
>   https://skyking.microscopy.wisc.edu/svn/java/trunk/
>
> The Bio-Formats C++ bindings are located in the components/native/bf- 
> cpp subtree.
>
> The Bio-Formats ITK plugin is located in the components/native/itk- 
> plugin subtree.
>
> You can find my directions for building these components in the  
> respective readme files, available online at:
>   https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/native/bf-cpp/readme.txt
>   https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/native/bf-cpp/readme-windows.txt
>   https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/native/bf-cpp/readme-macosx.txt
>   https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/native/bf-cpp/readme-linux.txt
>   https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/native/itk-plugin/readme.txt
>
> Please do not hesitate to contact me with any questions or problems.  
> I need your help to finish up this project!

Hi Curtis,

I'm trying to fix the problems we had yesterday on my macbook with itk- 
plugin. One of the required jar file seems to not be used - I've added  
it in the list.

[glehmann at gbook itk-plugin]$ svn diff
Index: itkBioFormatsImageIO.cxx
===================================================================

--- itkBioFormatsImageIO.cxx	(revision 5115)
+++ itkBioFormatsImageIO.cxx	(working copy)
@@ -68,7 +68,7 @@
      StaticVmLoader loader(JNI_VERSION_1_4);
      OptionList list;
      list.push_back(jace::ClassPath(
-      "jace-runtime.jar:bio-formats.jar:loci_tools.jar"
+      "jace.jar:jace-runtime.jar:bio-formats.jar:loci_tools.jar"
      ));
      list.push_back(jace::CustomOption("-Xcheck:jni"));
      list.push_back(jace::CustomOption("-Xmx256m"));


The program is running a bit longer now, but I still get an error:

[glehmann at gbook build]$ python -c 'import itk; reader =  
itk.ImageFileReader.IUC3.New(FileName="/Users/glehmann/Desktop/ 
nonSauvegarde/3.lsm"); reader()'
BioFormatsImageIO constuctor
Creating JVM...
JVM created.
Creating Bio-Formats objects...
Created reader and writer.
BioFormatsImageIO::CanReadFile: FileNameToRead=/Users/glehmann/Desktop/ 
nonSauvegarde/3.lsm
BioFormatsImageIO::CanReadFile: isType=1
BioFormatsImageIO::ReadImageInformation: m_FileName=/Users/glehmann/ 
Desktop/nonSauvegarde/3.lsm
Initializing...
Initialized.
	SeriesCount = 1
	Bytes per pixel = 2
	SizeX = 512
	SizeY = 512
	SizeZ = 19
	SizeC = 3
	SizeT = 1
	Image Count = 57
BioFormatsImageIO::Read
	Region dimension = 3
	X index = 0
	X count = 512
	Y index = 0
	Y count = 512
	Plane index = 0
	Plane count = 57
	Bytes per plane = 524288
Reading image plane 0 (1/57 of 57 available planes)
2009-05-20 08:33:40.005 Python[4538:613] Apple AWT Java VM was loaded  
on first thread -- can't start AWT.
Traceback (most recent call last):
   File "<string>", line 1, in <module>
   File "/usr/local/lib/InsightToolkit/WrapITK/lib/ 
ITKCommonBasePython.py", line 2395, in __call__
     self.UpdateLargestPossibleRegion()
RuntimeError: java.lang.InternalError: Can't start the AWT because  
Java was started on the first thread.  Make sure StartOnFirstThread is  
not specified in your application's Info.plist or on the command line

Any idea about what is wrong with the threads?
Also, do you now why it tries to start AWT? A GUI shouldn't be useful  
in that case!

Regards,

Gaëtan


-- 
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
http://voxel.jouy.inra.fr  http://www.mandriva.org
http://www.itk.org  http://www.clavier-dvorak.org

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