[Insight-users] help:Java Integration with ITK,VTK
srinivasan jeyavel
jsrinivasan2k at gmail.com
Thu Apr 23 12:36:25 EDT 2009
Hi everybody,
I would like to know where i can find information about
*how to integrate java with itk , vtk?*
regards
srinivasan
On Thu, Apr 23, 2009 at 9:30 PM, <insight-users-request at itk.org> wrote:
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> Today's Topics:
>
> 1. 2D rigid registration problems (Auron Ford Huton)
> 2. Re: Problem building ITK 3.12 with GDCM 2.x (Mathieu Malaterre)
> 3. Re: Incremental Region Growing (Carlos S?nchez Mendoza)
> 4. Re: Incremental Region Growing (Bill Lorensen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 23 Apr 2009 16:17:57 +0200
> From: Auron Ford Huton <auron at hotmail.es>
> Subject: [Insight-users] 2D rigid registration problems
> To: <insight-users at itk.org>
> Message-ID: <BLU123-W25B1C5B3CC5F2B65BAC88FDF750 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi everybody!!
>
> I?m an ITK newbie who is triyng to do a 2D rigid registration, so my
> apologizes if I say some stupids things below :P.
>
> I have compiled and executed all the examples from ImageRegistration1.cxx
> to ImageRegistration9.cxx of ITK with the brain images that can be found in
> the Data directory of ITK and all works perfect. But, when I try to use that
> examples with my images (2D .png images taken from a citology), the results
> are far away from the expected ones.
>
> I also did a program that uses an AffinTransform with a
> MattesMutualInformationImageToImageMetric and I executed it with all the
> possible variations in the parameters that define de metric or the
> optimizer, with no results too.
>
> Any ideas of which could be my mistakes???
>
> I don?t know if it is enough information for you to help me. If not, let me
> know and I will reply with all the information you need.
>
> Thanks in advance to everyone.
>
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> ------------------------------
>
> Message: 2
> Date: Thu, 23 Apr 2009 17:23:11 +0200
> From: Mathieu Malaterre <mathieu.malaterre at gmail.com>
> Subject: Re: [Insight-users] Problem building ITK 3.12 with GDCM 2.x
> To: Johan MOREAU <johan.moreau at ircad.fr>
> Cc: insight-users at itk.org
> Message-ID:
> <bf0c3b3f0904230823y154cc60ag7c5036ad32052736 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Mon, Apr 20, 2009 at 9:41 AM, Johan MOREAU <johan.moreau at ircad.fr>
> wrote:
> > Hello Mathieu,
> >
> > sorry but with the trunk (1.330 +), the same problem appears.
> >
> > My CMake opt :
> > -DBUILD_EXAMPLES:BOOL=OFF
> > -DBUILD_SHARED_LIBS:BOOL=ON
> > -DBUILD_TESTING:BOOL=OFF
> > -DBUILD_DOXYGEN:BOOL=OFF
> > -DITK_USE_SYSTEM_JPEG:BOOL=ON
> > -DITK_USE_SYSTEM_PNG:BOOL=ON
> > -DITK_USE_SYSTEM_TIFF:BOOL=ON
> > -DITK_USE_SYSTEM_VXL:BOOL=ON
> > -DITK_USE_SYSTEM_ZLIB:BOOL=ON
> > --with-insight=$COMEXT/lib/
> > -DITK_USE_SYSTEM_GDCM:BOOL=ON
> > -DITK_USE_REVIEW:BOOL=$IS_ITK_REVIEW
> > -DITK_USE_SYSTEM_LIBXML2:BOOL=ON
> > -DGDCM_DIR:PATH=$COMEXT_BUILD/gdcm/"$os"_$BUILD_MODE
> > -DLIBXML2_INCLUDE_DIR:PATH=$COMEXT_INC/libxml2
> > -DLIBXML2_LIBRARIES:PATH=$COMEXT_LIB/libxml2$SO
> > -DLIBXML2_XMLLINT_EXECUTABLE:PATH=$COMEXT_BIN/xmllint
> > -DPNG_LIBRARY:PATH=$COMEXT_LIB/libpng$SO
> -DPNG_INCLUDE_DIR:PATH=$COMEXT_INC
> > -DTIFF_INCLUDE_DIR=$COMEXT_INC
> > -DTIFF_LIBRARY:PATH=$COMEXT_LIB/libtiff$SO
> > -DVXL_DIR:PATH=$COMEXT/share/vxl/cmake
> > -DZLIB_INCLUDE_DIR:PATH=$COMEXT_INC
> -DZLIB_LIBRARY:PATH=$COMEXT_LIB/libz$SO
> >
> > ($os, $SO, $COMEXT_LIB, $COMEXT_INC, $COMEXT_BUILD, $COMEXT_BIN,
> > $BUILD_MODE are defined)
> >
> > If ITK_USE_SYSTEM_TIFF is setting to OFF, no change...
> >
> > These options work without trouble on win32, darwin, linux32, but crash
> > on linux64 (x86_64)
> >
> > And just to see, I disable ITK_USE_SYSTEM_GDCM. Same problem occurs :
> > ../../bin/libitkgdcm.so.3.13.0: undefined reference to
> > `itk_jpeg16_jpeg_read_header'
> > ../../bin/libitkgdcm.so.3.13.0: undefined reference to
> > `itk_jpeg16_jpeg_CreateCompress'
> > ../../bin/libitkgdcm.so.3.13.0: undefined reference to
> > `itk_jpeg12_jpeg_start_decompress'
> > ../../bin/libitkgdcm.so.3.13.0: undefined reference to
> > `itk_jpeg12_jpeg_simple_lossless'
> > ../../bin/libITKIO.so.3.13.0: undefined reference to
> > `itk_jpeg8_jpeg_finish_compress'
> > ../../bin/libitkgdcm.so.3.13.0: undefined reference to
> > `itk_jpeg16_jpeg_read_scanlines'
> > ../../bin/libitkgdcm.so.3.13.0: undefined reference to
> > `itk_jpeg12_jpeg_read_header'
> > ../../bin/libitkgdcm.so.3.13.0: undefined reference to
> > `itk_jpeg16_jpeg_finish_compress'
> > ../../bin/libitkgdcm.so.3.13.0: undefined reference to
> > `itk_jpeg12_jpeg_write_scanlines'
> > ../../bin/libITKIO.so.3.13.0: undefined reference to
> > `itk_jpeg8_jpeg_set_quality'
>
> Add a safety check.
>
> $ cvs di Code/IO/itkJPEGImageIO* Utilities/itkjpeg
> Index: Code/IO/itkJPEGImageIO.cxx
> ===================================================================
> RCS file: /cvsroot/Insight/Insight/Code/IO/itkJPEGImageIO.cxx,v
> retrieving revision 1.26
> diff -u -r1.26 itkJPEGImageIO.cxx
> --- Code/IO/itkJPEGImageIO.cxx 24 Oct 2008 16:21:55 -0000 1.26
> +++ Code/IO/itkJPEGImageIO.cxx 23 Apr 2009 15:20:44 -0000
> @@ -33,6 +33,10 @@
> #include <setjmp.h>
> }
>
> +#ifndef itk_secret_symbol_mangled_jpeg8
> +#error Sorry something went wrong with your configuration, you are
> using a system jpeglib.h instead of the special mangled one
> +#endif
> +
>
> // create an error handler for jpeg that
> // can longjmp out of the jpeg library
> Index: Utilities/itkjpeg/mangle_jpeg8bits.h
> ===================================================================
> RCS file: /cvsroot/Insight/Insight/Utilities/itkjpeg/mangle_jpeg8bits.h,v
> retrieving revision 1.1
> diff -u -r1.1 mangle_jpeg8bits.h
> --- Utilities/itkjpeg/mangle_jpeg8bits.h 29 Oct 2004 14:36:45
> -0000 1.1
> +++ Utilities/itkjpeg/mangle_jpeg8bits.h 23 Apr 2009 15:20:44 -0000
> @@ -12,6 +12,7 @@
>
> nm libitkitk_jpeg8.a | grep " [R|T] " | colrm 1 11 | sort
> */
> +#define itk_secret_symbol_mangled_jpeg8
>
>
> #define jcopy_block_row itk_jpeg8_jcopy_block_row
>
>
> $ cvs ci -m"BUG: Some user were passing include flag using the
> CMAKE_CXX_FLAGS, which would conflict with the behavior of
> include_directories(before bla)" Code/IO/itkJPEGImageIO*
> Utilities/itkjpeg
> Running style check
> Running style check
> Processing itkJPEGImageIO.cxx
>
>
>
> /cvsroot/Insight/Insight/Code/IO/itkJPEGImageIO.cxx,v <--
> Code/IO/itkJPEGImageIO.cxx
> new revision: 1.27; previous revision: 1.26
> /cvsroot/Insight/Insight/Utilities/itkjpeg/mangle_jpeg8bits.h,v <--
> Utilities/itkjpeg/mangle_jpeg8bits.h
> new revision: 1.2; previous revision: 1.1
>
>
>
> --
> Mathieu
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 23 Apr 2009 17:37:05 +0200
> From: Carlos S?nchez Mendoza <carlos.sanchez.mendoza at gmail.com>
> Subject: Re: [Insight-users] Incremental Region Growing
> To: Bill Lorensen <bill.lorensen at gmail.com>
> Cc: insight-users at itk.org
> Message-ID:
> <d367da130904230837r5ba3944cp6cb9e139e56925e2 at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> That worked perfect. Thank you so much!!!
>
> El 22 de abril de 2009 16:07, Bill Lorensen <bill.lorensen at gmail.com
> >escribi?:
>
> > When you say that it didn't work, what do you mean?
> >
> > If it failed to change the output, try applying a Modified() to the
> > filter before each Update(). A recent bug was reported that the filter
> > was not behaving properly when the seeds were cleared:
> > BUG: 7480: ClearSeeds() was not calling Modified() in region growing
> > filters.
> >
> > Bill
> >
> >
> > 2009/4/22 Carlos S?nchez Mendoza <carlos.sanchez.mendoza at gmail.com>:
> > > Hi all,
> > >
> > > I would like to perform several confidence connected region growing
> > stages
> > > for increasing multiplier. For the sake of efficiency I would like to
> be
> > > able to provide previous growth output as input for current growth. I
> > tried
> > > providing the whole region pixel per pixel as individual seeds but it
> > didn't
> > > work.
> > >
> > > Any ideas?
> > >
> > > Thanks in advance.
> > > Carlos S. Mendoza.
> > > _____________________________________
> > > Powered by www.kitware.com
> > >
> > > Visit other Kitware open-source projects at
> > > http://www.kitware.com/opensource/opensource.html
> > >
> > > Please keep messages on-topic and check the ITK FAQ at:
> > > http://www.itk.org/Wiki/ITK_FAQ
> > >
> > > Follow this link to subscribe/unsubscribe:
> > > http://www.itk.org/mailman/listinfo/insight-users
> > >
> > >
> >
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> ------------------------------
>
> Message: 4
> Date: Thu, 23 Apr 2009 11:47:44 -0400
> From: Bill Lorensen <bill.lorensen at gmail.com>
> Subject: Re: [Insight-users] Incremental Region Growing
> To: Carlos S?nchez Mendoza <carlos.sanchez.mendoza at gmail.com>
> Cc: insight-users at itk.org
> Message-ID:
> <4db4735c0904230847y4992e8ban1dd53b282116ffd4 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> This is repaired and the fix will be in the next release. But, for
> now, we are happy to hear that the Modified() calls fixed your
> problem.
>
>
> 2009/4/23 Carlos S?nchez Mendoza <carlos.sanchez.mendoza at gmail.com>:
> > That worked perfect. Thank you so much!!!
> >
> > El 22 de abril de 2009 16:07, Bill Lorensen <bill.lorensen at gmail.com>
> > escribi?:
> >>
> >> When you say that it didn't work, what do you mean?
> >>
> >> If it failed to change the output, try applying a Modified() to the
> >> filter before each Update(). A recent bug was reported that the filter
> >> was not behaving properly when the seeds were cleared:
> >> BUG: 7480: ClearSeeds() was not calling Modified() in region growing
> >> filters.
> >>
> >> Bill
> >>
> >>
> >> 2009/4/22 Carlos S?nchez Mendoza <carlos.sanchez.mendoza at gmail.com>:
> >> > Hi all,
> >> >
> >> > I would like to perform several confidence connected region growing
> >> > stages
> >> > for increasing multiplier. For the sake of efficiency I would like to
> be
> >> > able to provide previous growth output as input for current growth. I
> >> > tried
> >> > providing the whole region pixel per pixel as individual seeds but it
> >> > didn't
> >> > work.
> >> >
> >> > Any ideas?
> >> >
> >> > Thanks in advance.
> >> > Carlos S. Mendoza.
> >> > _____________________________________
> >> > Powered by www.kitware.com
> >> >
> >> > Visit other Kitware open-source projects at
> >> > http://www.kitware.com/opensource/opensource.html
> >> >
> >> > Please keep messages on-topic and check the ITK FAQ at:
> >> > http://www.itk.org/Wiki/ITK_FAQ
> >> >
> >> > Follow this link to subscribe/unsubscribe:
> >> > http://www.itk.org/mailman/listinfo/insight-users
> >> >
> >> >
> >
> >
>
>
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>
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>
> End of Insight-users Digest, Vol 60, Issue 80
> *********************************************
>
--
Regards
Srinivasan
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