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