From manuel.grizonnet at cnes.fr  Wed Feb  1 02:35:17 2017
From: manuel.grizonnet at cnes.fr (Manuel Grizonnet)
Date: Wed, 1 Feb 2017 08:35:17 +0100
Subject: [ITK] [ITK-dev] Fwd: [Orfeo Toolbox (OTB) 0001354]: Fails to build
	with	GCC 7
In-Reply-To: <b171bd2751d9787a49fde77dab542d8b@bugs.orfeo-toolbox.org>
References: <b171bd2751d9787a49fde77dab542d8b@bugs.orfeo-toolbox.org>
Message-ID: <6470a85c-c0b1-a9a8-135d-cbe3d28259ed@cnes.fr>

Hi all,

FYI ORFEO ToolBox debian packagers report compilation issue for OTB with 
gcc 7.

The error seems to be with ITK (see mantis report below).

I havent investigated it yet but I wanted to transfer it to you as soon 
as possible as it seems that you'we started the RC process for 4.11.

Note that we don't have any platforms on otb dashboard to test gcc 7 
support.

Regards,

Manuel

-------- Message transf?r? --------
Sujet : 	[Orfeo Toolbox (OTB) 0001354]: Fails to build with GCC 7
Date : 	Tue, 31 Jan 2017 19:23:08 +0100
De : 	Mantis Bug Tracker <bugs at orfeo-toolbox.org>
Pour : 	manuel.grizonnet at cnes.fr



A NOTE has been added to this issue.
======================================================================
https://bugs.orfeo-toolbox.org/view.php?id=1354
======================================================================
Reported By:                sebastic
Assigned To:
======================================================================
Project:                    Orfeo Toolbox (OTB)
Issue ID:                   1354
Category:                   General
Reproducibility:            have not tried
Severity:                   minor
Priority:                   normal
Status:                     new
======================================================================
Date Submitted:             2017-01-31 18:48 CET
Last Modified:              2017-01-31 19:23 CET
======================================================================
Summary:                    Fails to build with GCC 7
Description:
As reported by Matthias Klose in Debian Bug
https://bugs.orfeo-toolbox.org/view.php?id=853602
(https://bugs.debian.org/853602):


The package fails to build in a test rebuild on at least amd64 with
gcc-7/g++-7, but succeeds to build with gcc-6/g++-6. The
severity of this report may be raised before the buster release.
There is no need to fix this issue in time for the stretch release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc7-20170126/otb_5.8.0+dfsg-3_unstable_gcc7.log
The last lines of the build log are at the end of this report.

To build with GCC 7, either set CC=gcc-7 CXX=g++-7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

   apt-get -t experimental install g++

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-7/porting_to.html

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../../../../lib/libotbossimplugins-5.8.so
make[3]: Leaving directory '/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu'
[ 17%] Built target otbossimplugins
make[2]: Leaving directory '/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu'
Makefile:130: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu'
dh_auto_build: make -j64 returned exit code 2
debian/rules:81: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
======================================================================

----------------------------------------------------------------------
  (0003986) sebastic (reporter) - 2017-01-31 19:23
  https://bugs.orfeo-toolbox.org/view.php?id=1354#c3986
----------------------------------------------------------------------
Problem seems to be with ITK:

cd
/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/Adapters/OpenThreadsAdapters/src
&& /usr/bin/cmake -E cmake_link_script
CMakeFiles/OTBOpenThreadsAdapters.dir/link.txt --verbose=1
In file included from /usr/include/ITK-4.10/vcl_limits.h:5:0,
                  from /usr/include/ITK-4.10/itkNumericTraits.h:51,
                  from /usr/include/ITK-4.10/itkConceptChecking.h:32,
                  from /usr/include/ITK-4.10/itkAtomicInt.h:38,
                  from /usr/include/ITK-4.10/itkLightObject.h:25,
                  from /usr/include/ITK-4.10/itkObject.h:31,
                  from /usr/include/ITK-4.10/itkCommand.h:21,
                  from
/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/Core/Common/include/otbFilterWatcherBase.h:24,
                  from
/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/Core/Common/src/otbFilterWatcherBase.cxx:21:
/usr/include/ITK-4.10/vcl_compiler.h:79:4: error: #error "Dunno about this gcc"
  #  error "Dunno about this gcc"
     ^~~~~

Issue History
Date Modified    Username       Field                    Change
======================================================================
2017-01-31 18:48 sebastic       New Issue
2017-01-31 19:22 sebastic       File Added: otb_5.8.0+dfsg-3_unstable_gcc7.log
                  
2017-01-31 19:23 sebastic       Note Added: 0003986
======================================================================

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From cr at neuro.ma.uni-heidelberg.de  Wed Feb  1 07:03:23 2017
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Wed, 1 Feb 2017 13:03:23 +0100
Subject: [ITK] [ITK-users] Bug in example ImageFilter
Message-ID: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>

Hi,

I've just downloaded 
https://github.com/lorensen/ITKWikiExamplesTarballs/raw/master/ImageFilter.tar 
which doesn't compile out of the box because ImageFilter.h tries to 
include ImageFilter.txx which does not exist - should be ImageFilter.hxx 
(or ImageFilter.hxx must be renamed to ImageFilter.txx).

Regards,

Christina Ro?manith

_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From blowekamp at mail.nih.gov  Wed Feb  1 09:38:38 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 1 Feb 2017 14:38:38 +0000
Subject: [ITK] [ITK-dev] [Orfeo Toolbox (OTB) 0001354]: Fails to
	build	with	GCC 7
In-Reply-To: <6470a85c-c0b1-a9a8-135d-cbe3d28259ed@cnes.fr>
References: <b171bd2751d9787a49fde77dab542d8b@bugs.orfeo-toolbox.org>
 <6470a85c-c0b1-a9a8-135d-cbe3d28259ed@cnes.fr>
Message-ID: <306707A0-8E5E-4EA6-B120-8C2C65A8679B@mail.nih.gov>

Hello,

Here is the error message from the bottom of the report:

/usr/include/ITK-4.10/vcl_compiler.h:79:4: error: #error "Dunno about this gcc"
 #  error "Dunno about this gcc"

Please note that GCC 7 does not appear to be released yet. https://gcc.gnu.org

What version of CMake is used?

Thanks,
Brad

On Feb 1, 2017, at 2:35 AM, Manuel Grizonnet <manuel.grizonnet at cnes.fr<mailto:manuel.grizonnet at cnes.fr>> wrote:


Hi all,

FYI ORFEO ToolBox debian packagers report compilation issue for OTB with gcc 7.

The error seems to be with ITK (see mantis report below).

I havent investigated it yet but I wanted to transfer it to you as soon as possible as it seems that you'we started the RC process for 4.11.

Note that we don't have any platforms on otb dashboard to test gcc 7 support.

Regards,

Manuel

-------- Message transf?r? --------
Sujet :         [Orfeo Toolbox (OTB) 0001354]: Fails to build with GCC 7
Date :  Tue, 31 Jan 2017 19:23:08 +0100
De :    Mantis Bug Tracker <bugs at orfeo-toolbox.org><mailto:bugs at orfeo-toolbox.org>
Pour :  manuel.grizonnet at cnes.fr<mailto:manuel.grizonnet at cnes.fr>



A NOTE has been added to this issue.
======================================================================
https://bugs.orfeo-toolbox.org/view.php?id=1354
======================================================================
Reported By:                sebastic
Assigned To:
======================================================================
Project:                    Orfeo Toolbox (OTB)
Issue ID:                   1354
Category:                   General
Reproducibility:            have not tried
Severity:                   minor
Priority:                   normal
Status:                     new
======================================================================
Date Submitted:             2017-01-31 18:48 CET
Last Modified:              2017-01-31 19:23 CET
======================================================================
Summary:                    Fails to build with GCC 7
Description:
As reported by Matthias Klose in Debian Bug
https://bugs.orfeo-toolbox.org/view.php?id=853602
(https://bugs.debian.org/853602):


The package fails to build in a test rebuild on at least amd64 with
gcc-7/g++-7, but succeeds to build with gcc-6/g++-6. The
severity of this report may be raised before the buster release.
There is no need to fix this issue in time for the stretch release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc7-20170126/otb_5.8.0+dfsg-3_unstable_gcc7.log
The last lines of the build log are at the end of this report.

To build with GCC 7, either set CC=gcc-7 CXX=g++-7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t experimental install g++

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-7/porting_to.html

[...]
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cd
/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/ThirdParty/OssimPlugins/src
&& /usr/bin/c++   -Dotbossimplugins_EXPORTS
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/Boost/src
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/Core/Common
-I/usr/include/gdal -I/usr/include/geotiff
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src
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-I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/ThirdParty/OssimPlugins/src/ossim
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-Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch
-Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings
-funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof
-Woverloaded-virtual -Wstrict-null-sentinel -g -O2
-fdebug-prefix-map=/<<BUILDDIR>>/otb-5.8.0+dfsg=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -w -O3
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&& /usr/bin/c++   -Dotbossimplugins_EXPORTS
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/Boost/src
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/Core/Common
-I/usr/include/gdal -I/usr/include/geotiff
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src/ossim
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/ThirdParty/OssimPlugins/src/ossim
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src/gdal  -Wall
-Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch
-Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings
-funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof
-Woverloaded-virtual -Wstrict-null-sentinel -g -O2
-fdebug-prefix-map=/<<BUILDDIR>>/otb-5.8.0+dfsg=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -w -O3
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&& /usr/bin/c++   -Dotbossimplugins_EXPORTS
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/Boost/src
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/Core/Common
-I/usr/include/gdal -I/usr/include/geotiff
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src/ossim
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/ThirdParty/OssimPlugins/src/ossim
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src/gdal  -Wall
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-Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings
-funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof
-Woverloaded-virtual -Wstrict-null-sentinel -g -O2
-fdebug-prefix-map=/<<BUILDDIR>>/otb-5.8.0+dfsg=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -w -O3
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&& /usr/bin/c++   -Dotbossimplugins_EXPORTS
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-I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/Core/Common
-I/usr/include/gdal -I/usr/include/geotiff
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src
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-I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/ThirdParty/OssimPlugins/src/ossim
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src/gdal  -Wall
-Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch
-Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings
-funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof
-Woverloaded-virtual -Wstrict-null-sentinel -g -O2
-fdebug-prefix-map=/<<BUILDDIR>>/otb-5.8.0+dfsg=. -fstack-protector-strong
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-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/Boost/src
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/Core/Common
-I/usr/include/gdal -I/usr/include/geotiff
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src/ossim
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/ThirdParty/OssimPlugins/src/ossim
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src/gdal  -Wall
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-Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings
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-I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/Boost/src
-I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/Core/Common
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-Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings
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-Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings
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CMakeFiles/otbossimplugins.dir/ossim/ossimGeometricSarSensorModel.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimPleiadesDimapSupportData.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimPleiadesModel.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimPluginCommon.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimPluginInit.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimPluginProjectionFactory.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimPluginReaderFactory.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimRadarSat2Model.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimRadarSat2ProductDoc.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimRadarSat2RPCModel.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimRadarSat2TiffReader.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimRadarSatModel.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimSarSensorModel.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimSarSensorModelPathsAndKeys.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimSentinel1Model.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimSentinel1SarSensorModel.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimSpot6DimapSupportData.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimSpot6Model.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimStringUtilities.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimTerraSarModel.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimTerraSarProductDoc.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimTerraSarTiffReader.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimTerraSarXSarSensorModel.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimTileMapModel.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimTimeUtilities.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/ossimXmlTools.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/CivilDateTime.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/Coordinate.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/Ephemeris.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/Equation.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/GMSTDateTime.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/GalileanEphemeris.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/GeodesicCoordinate.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/GeographicEphemeris.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/HermiteInterpolator.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/ImageNoise.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/IncidenceAngles.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/InfoIncidenceAngle.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/InfoSceneCoord.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/JSDDateTime.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/JulianDate.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/MJDDateTime.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/Noise.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/PlatformPosition.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/RadarSat2NoiseLevel.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/RectangularCoordinate.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/RefPoint.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/SarSensor.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/SceneCoord.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/Sensor.cpp.o
CMakeFiles/otbossimplugins.dir/ossim/otb/SensorParams.cpp.o -lgdal -lossim
-lOpenThreads -lgeotiff
cd
/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/ThirdParty/OssimPlugins/src
&& /usr/bin/cmake -E cmake_symlink_library
../../../../lib/libotbossimplugins-5.8.so.1
../../../../lib/libotbossimplugins-5.8.so.1
../../../../lib/libotbossimplugins-5.8.so
make[3]: Leaving directory '/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu'
[ 17%] Built target otbossimplugins
make[2]: Leaving directory '/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu'
Makefile:130: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu'
dh_auto_build: make -j64 returned exit code 2
debian/rules:81: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
======================================================================

----------------------------------------------------------------------
 (0003986) sebastic (reporter) - 2017-01-31 19:23
 https://bugs.orfeo-toolbox.org/view.php?id=1354#c3986
----------------------------------------------------------------------
Problem seems to be with ITK:

cd
/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/Adapters/OpenThreadsAdapters/src
&& /usr/bin/cmake -E cmake_link_script
CMakeFiles/OTBOpenThreadsAdapters.dir/link.txt --verbose=1
In file included from /usr/include/ITK-4.10/vcl_limits.h:5:0,
                 from /usr/include/ITK-4.10/itkNumericTraits.h:51,
                 from /usr/include/ITK-4.10/itkConceptChecking.h:32,
                 from /usr/include/ITK-4.10/itkAtomicInt.h:38,
                 from /usr/include/ITK-4.10/itkLightObject.h:25,
                 from /usr/include/ITK-4.10/itkObject.h:31,
                 from /usr/include/ITK-4.10/itkCommand.h:21,
                 from
/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/Core/Common/include/otbFilterWatcherBase.h:24,
                 from
/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/Core/Common/src/otbFilterWatcherBase.cxx:21:
/usr/include/ITK-4.10/vcl_compiler.h:79:4: error: #error "Dunno about this gcc"
 #  error "Dunno about this gcc"
    ^~~~~

Issue History
Date Modified    Username       Field                    Change
======================================================================
2017-01-31 18:48 sebastic       New Issue
2017-01-31 19:22 sebastic       File Added: otb_5.8.0+dfsg-3_unstable_gcc7.log

2017-01-31 19:23 sebastic       Note Added: 0003986
======================================================================



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From francois.budin at kitware.com  Wed Feb  1 11:00:18 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 1 Feb 2017 11:00:18 -0500
Subject: [ITK] ITK headers included using angle brackets
In-Reply-To: <CAHE0P1WTyckPwJ8WnC8SMfmjBPFXkfiA8VC6MHaboWkyW6szvQ@mail.gmail.com>
References: <CAHE0P1WTyckPwJ8WnC8SMfmjBPFXkfiA8VC6MHaboWkyW6szvQ@mail.gmail.com>
Message-ID: <CAHwLD2UBO8YGbKNVQ=7YtjyKn4-gQZDj4-Z_AWRg5K3GE+QovA@mail.gmail.com>

Hello Fijoy,

Including file using double quotes or angle brackets should not create an
issue (although the behavior is implementation-defined). Can you give more
information about the "different compiler" you are using?

Francois

On Tue, Jan 31, 2017 at 12:41 PM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
wrote:

> Hello,
>
> I built ITK 4.10.0 using CMake & Visual Studio Express 2013 on Windows,
> and am running into an issue with header files. In the header files that
> are generated, some of the ITK-specific header files are included using
> angle brackets. For example vcl_compiler.h contains "#include
> <vcl_config_manual.h>". This is causing an issue when I'm trying to link to
> the ITK libraries using a different compiler, which looks for these
> ITK-specific header files in the system path because of the angle brackets.
>
> Is there an option in CMake to make the #includes use quotes instead of
> angle brackets for ITK-specific header files?
>
> Thank you,
> --Fijoy
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From francois.budin at kitware.com  Wed Feb  1 11:13:54 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 1 Feb 2017 11:13:54 -0500
Subject: [ITK] [ITK-users] Bug in example ImageFilter
In-Reply-To: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>
References: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>
Message-ID: <CAHwLD2UBoiokVfEGA93HaTQU+Ce1Vbb-2Ernbi29+YmkaRozAQ@mail.gmail.com>

Hello Christina,

Thank you for the bug report. Could you create an issue and a pull-request
to solve the problem in this repository:
https://github.com/InsightSoftwareConsortium/ITKWikiExamples

Thank you!
Francois

On Wed, Feb 1, 2017 at 7:03 AM, Chr. Rossmanith <
cr at neuro.ma.uni-heidelberg.de> wrote:

> Hi,
>
> I've just downloaded https://github.com/lorensen/IT
> KWikiExamplesTarballs/raw/master/ImageFilter.tar which doesn't compile
> out of the box because ImageFilter.h tries to include ImageFilter.txx which
> does not exist - should be ImageFilter.hxx (or ImageFilter.hxx must be
> renamed to ImageFilter.txx).
>
> Regards,
>
> Christina Ro?manith
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
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From blowekamp at mail.nih.gov  Wed Feb  1 15:48:45 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 1 Feb 2017 20:48:45 +0000
Subject: [ITK] [ITK-users] ITK_COMPILED_CXX_VERSION always set to 1997
 on macOS
In-Reply-To: <EC5A18B6-D728-4EB8-8A07-8B7FC7141433@inria.fr>
References: <A96A5ED1-D452-47C7-A220-E4A40C4F1CE1@inria.fr>
 <B676B4C6-C8B9-4B1D-915E-6629FD513A67@inria.fr>
 <E8C99D9F-8C47-4F4A-9EC5-02A438CA9AE3@mail.nih.gov>
 <EC5A18B6-D728-4EB8-8A07-8B7FC7141433@inria.fr>
Message-ID: <D73BA3E0-50F5-422C-9558-81A62AA44DEA@mail.nih.gov>

Hi,

I am running Xcode 8.2.1 OS 10.11, and cmake 3.4.3. I was not able to reproduce your problem.
For a clean build directory I ran:
  cmake -DCMAKE_CXX_STANDARD=11 ~/src/ITK && grep  ITK_COMPILED_CXX Modules/Core/Common/itkConfigure.h

I got the following:
  #define ITK_COMPILED_CXX_STANDARD_VERSION 201103L
  #if ITK_COMPILED_CXX_STANDARD_VERSION > __cplusplus

There did appear to be a problem with the preprocessor variable used in the version check which I addressed here:
 http://review.source.kitware.com/#/c/22021/

Perhaps you did not start with a clean build directory?

Brad

> On Jan 31, 2017, at 5:02 AM, Olivier Commowick <Olivier.Commowick at inria.fr> wrote:
> 
> Hello
> 
> Thanks for your answer. I am running into this with Xcode 8.2.1, on a macOS 10.12, cmake version 3.6.2, and it happens already when compiling ITK itself.
> 
> I did not put the flag you mentioned. I could try but it seems to me that the VXL part of ITK has the same kind of test and it works. I mean by this that there is a VXL_COMPILED_CXX_STANDARD_VERSION set up in the file Modules/ThirdParty/VNL/src/vxl/config/cmake/config/VXLIntrospectionConfig.cmake . And this one is automatically set to 201103L without needing the flags you mentioned. May be there is something in this cmake file that should be ported back to the ITK equivalent (that?s just a thought of course).
> 
> Thanks
> Olivier
> 
>> On 23 Jan 2017, at 15:25, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov> wrote:
>> 
>> Hello,
>> 
>> What Xcode version are you using? Can you produce a simple CMake command line configuration to reproduce the problem?
>> 
>> If you set "CMAKE_CXX_FLAGS=-std=c++11?, does the same problem occur?
>> 
>> Thanks!
>> Brad
>> 
>>> On Jan 23, 2017, at 9:11 AM, Olivier Commowick <Olivier.Commowick at inria.fr> wrote:
>>> 
>>> Hello,
>>> 
>>> While debugging something else, I realised that the ITK_COMPILED_CXX_VERSION variable in CMake is always set to 199711L on my macOS 10.12. It sounds weird to me since I am always compiling ITK by enforcing to use CMAKE_CXX_STANDARD to 11.
>>> 
>>> It appears to me that Modules/Core/Common/CMakeLists.txt does this test and probably does not account for the fact that cmake uses the 2011 standard or something else. Would someone have any idea of how to correct this or if this is important or not ?
>>> 
>>> Best
>>> Olivier
>>> 
>>> ---
>>> 
>>> Olivier Commowick, Ph.D.
>>> Research Scientist
>>> INRIA Rennes - Bretagne Atlantique, VISAGES Team
>>> Campus de Beaulieu
>>> 35042 Rennes
>>> FRANCE
>>> 
>>> Phone: +33 2 99 84 25 92
>>> Email: Olivier.Commowick at inria.fr
>>> Web: http://olivier.commowick.org/
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _____________________________________
>>> Powered by www.kitware.com
>>> 
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>> 
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>> 
>>> 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://public.kitware.com/mailman/listinfo/insight-users
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>> 
> 
> 
> ---
> 
> Olivier Commowick, Ph.D.
> Research Scientist
> INRIA Rennes - Bretagne Atlantique, VISAGES Team
> Campus de Beaulieu
> 35042 Rennes
> FRANCE
> 
> Phone: +33 2 99 84 25 92
> Email: Olivier.Commowick at inria.fr
> Web: http://olivier.commowick.org/
> 
> 
> 
> 
> 

_____________________________________
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Please keep messages on-topic and check the ITK FAQ at:
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From dzenanz at gmail.com  Wed Feb  1 17:02:25 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 1 Feb 2017 17:02:25 -0500
Subject: [ITK] [ITK-users] Bug in example ImageFilter
In-Reply-To: <CAHwLD2UBoiokVfEGA93HaTQU+Ce1Vbb-2Ernbi29+YmkaRozAQ@mail.gmail.com>
References: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>
 <CAHwLD2UBoiokVfEGA93HaTQU+Ce1Vbb-2Ernbi29+YmkaRozAQ@mail.gmail.com>
Message-ID: <CAPf2UMT8nLYmv6=7nQHYD=vXcCr2crmu_gvepmam39QjOBcNQg@mail.gmail.com>

Hi Christina,

you should not create a pull request for that repository, but rather modify
the example directly on the wiki <https://itk.org/Wiki/ITK/Examples>. The
repository is updated manually by an automated script which scrapes the
wiki. I think that Bill usually invokes it.

Regards,
D?enan

On Wed, Feb 1, 2017 at 11:13 AM, Francois Budin <francois.budin at kitware.com>
wrote:

> Hello Christina,
>
> Thank you for the bug report. Could you create an issue and a pull-request
> to solve the problem in this repository:
> https://github.com/InsightSoftwareConsortium/ITKWikiExamples
>
> Thank you!
> Francois
>
> On Wed, Feb 1, 2017 at 7:03 AM, Chr. Rossmanith <
> cr at neuro.ma.uni-heidelberg.de> wrote:
>
>> Hi,
>>
>> I've just downloaded https://github.com/lorensen/IT
>> KWikiExamplesTarballs/raw/master/ImageFilter.tar which doesn't compile
>> out of the box because ImageFilter.h tries to include ImageFilter.txx which
>> does not exist - should be ImageFilter.hxx (or ImageFilter.hxx must be
>> renamed to ImageFilter.txx).
>>
>> Regards,
>>
>> Christina Ro?manith
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> 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://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
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>
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From bill.lorensen at gmail.com  Wed Feb  1 17:28:55 2017
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Wed, 1 Feb 2017 17:28:55 -0500
Subject: [ITK] [ITK-users] Bug in example ImageFilter
In-Reply-To: <CADZJ4hNACmkbqk_4rN+14U-9NQKt+e-BrrEkUMRTgA3FSoyxJg@mail.gmail.com>
References: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>
 <CAHwLD2UBoiokVfEGA93HaTQU+Ce1Vbb-2Ernbi29+YmkaRozAQ@mail.gmail.com>
 <CAPf2UMT8nLYmv6=7nQHYD=vXcCr2crmu_gvepmam39QjOBcNQg@mail.gmail.com>
 <CADZJ4hNACmkbqk_4rN+14U-9NQKt+e-BrrEkUMRTgA3FSoyxJg@mail.gmail.com>
Message-ID: <CADZJ4hOx7Ci3Vum_HDCZAWTdXgr7V_SmWDSaz+XW9RYG4-Fcfg@mail.gmail.com>

That is correct. Update the wiki version.

On Feb 1, 2017 5:02 PM, "D?enan Zuki?" <dzenanz at gmail.com> wrote:

Hi Christina,

you should not create a pull request for that repository, but rather modify
the example directly on the wiki <https://itk.org/Wiki/ITK/Examples>. The
repository is updated manually by an automated script which scrapes the
wiki. I think that Bill usually invokes it.

Regards,
D?enan

On Wed, Feb 1, 2017 at 11:13 AM, Francois Budin <francois.budin at kitware.com>
wrote:

> Hello Christina,
>
> Thank you for the bug report. Could you create an issue and a pull-request
> to solve the problem in this repository:
> https://github.com/InsightSoftwareConsortium/ITKWikiExamples
>
> Thank you!
> Francois
>
> On Wed, Feb 1, 2017 at 7:03 AM, Chr. Rossmanith <
> cr at neuro.ma.uni-heidelberg.de> wrote:
>
>> Hi,
>>
>> I've just downloaded https://github.com/lorensen/IT
>> KWikiExamplesTarballs/raw/master/ImageFilter.tar which doesn't compile
>> out of the box because ImageFilter.h tries to include ImageFilter.txx which
>> does not exist - should be ImageFilter.hxx (or ImageFilter.hxx must be
>> renamed to ImageFilter.txx).
>>
>> Regards,
>>
>> Christina Ro?manith
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> 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://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
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From dzenanz at gmail.com  Wed Feb  1 18:02:17 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 1 Feb 2017 18:02:17 -0500
Subject: [ITK] [ITK-users] Problem with ITK eigensystem
In-Reply-To: <96DC429F-7F78-49D7-A026-930012074F27@inria.fr>
References: <2444669A-4CBE-4C72-BB82-B3538C4513B1@inria.fr>
 <242A16CD-79C1-4427-94DB-3AFCD1A33851@inria.fr>
 <96DC429F-7F78-49D7-A026-930012074F27@inria.fr>
Message-ID: <CAPf2UMSXgyUd9C6Qr=hx479neq1kwF+-L+eOjDnURUoKfsLPmA@mail.gmail.com>

Hi Olivier,

I tried running you example. One thing struck me right away: ITK version is
much slower (after a few minutes running in release mod I killed it) than
VNL version (about a second in debug mode) for your input.

I can't comment the patch content or the numeric stability. Perhaps Brad
and Hans can pitch in?

Regards,
D?enan

On Tue, Jan 31, 2017 at 11:24 AM, Olivier Commowick <
Olivier.Commowick at inria.fr> wrote:

> Hello,
>
> I think I have found a bug in the behaviour of ITK?s symmetric
> eigensystem. In the attached link (http://olivier.commowick.org/
> tmp/Test.zip) you will find an example code and matrix that fails with it
> and not with VNL?s symmetric eigensystem (run on macOS 10.12, Xcode 8.2.1).
>
> It seems to me that there are subtle differences in between ITK and VNL
> versions, VNL being more robust (and the same as what Matlab gives, I
> didn?t test python). Here is what I have found so far :
>
> - the hypothenuse function (hypot for ITK and pythag for VNL) do not get
> always the exact same result up to a very far away decimal
> - some loop indices were wrong I think in the ITK eigensystem. Some do
> vary in the VNL version, not in ITK?s equivalent
>
> In the patch file attached, I have made a set of corrections that make
> things in ITK eigensystem closer to VNL but still the ITK version fails. I
> have to say I am getting completely lost here so I am calling upon the
> community for help. If anyone knows this enough, could you try the test
> attached and see if you have any ideas of what is going on. That would help
> us a lot.
>
> The test attached can be compiled with cmake and run with the text file
> included : ./test_eigensystem data.txt
>
> Thanks in advance
> Olivier
>
>
>
> ---
>
> Olivier Commowick, Ph.D.
> Research Scientist
> INRIA Rennes - Bretagne Atlantique, VISAGES Team
> Campus de Beaulieu
> 35042 Rennes
> FRANCE
>
> Phone: +33 2 99 84 25 92 <+33%202%2099%2084%2025%2092>
> Email: Olivier.Commowick at inria.fr
> Web: http://olivier.commowick.org/
>
>
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
>
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From Olivier.Commowick at inria.fr  Thu Feb  2 03:27:31 2017
From: Olivier.Commowick at inria.fr (Olivier Commowick)
Date: Thu, 2 Feb 2017 09:27:31 +0100
Subject: [ITK] [ITK-users] Problem with ITK eigensystem
In-Reply-To: <CAPf2UMSXgyUd9C6Qr=hx479neq1kwF+-L+eOjDnURUoKfsLPmA@mail.gmail.com>
References: <2444669A-4CBE-4C72-BB82-B3538C4513B1@inria.fr>
 <242A16CD-79C1-4427-94DB-3AFCD1A33851@inria.fr>
 <96DC429F-7F78-49D7-A026-930012074F27@inria.fr>
 <CAPf2UMSXgyUd9C6Qr=hx479neq1kwF+-L+eOjDnURUoKfsLPmA@mail.gmail.com>
Message-ID: <7FE2FD85-C0C9-47BD-AE85-9B6FE5E1ADE6@inria.fr>

Hi,

Thanks for your test. There might be a bug in my test or the way you ran it since for me it doesn?t take a few minutes but rather less than a second. That being said since it produces nans it might be that on some OS it goes into an infinite loop...

Olivier

> On 2 Feb 2017, at 00:02, D?enan Zuki? <dzenanz at gmail.com> wrote:
> 
> Hi Olivier,
> 
> I tried running you example. One thing struck me right away: ITK version is much slower (after a few minutes running in release mod I killed it) than VNL version (about a second in debug mode) for your input.
> 
> I can't comment the patch content or the numeric stability. Perhaps Brad and Hans can pitch in?
> 
> Regards,
> D?enan
> 
> On Tue, Jan 31, 2017 at 11:24 AM, Olivier Commowick <Olivier.Commowick at inria.fr <mailto:Olivier.Commowick at inria.fr>> wrote:
> Hello,
> 
> I think I have found a bug in the behaviour of ITK?s symmetric eigensystem. In the attached link (http://olivier.commowick.org/tmp/Test.zip <http://olivier.commowick.org/tmp/Test.zip>) you will find an example code and matrix that fails with it and not with VNL?s symmetric eigensystem (run on macOS 10.12, Xcode 8.2.1).
> 
> It seems to me that there are subtle differences in between ITK and VNL versions, VNL being more robust (and the same as what Matlab gives, I didn?t test python). Here is what I have found so far :
> 
> - the hypothenuse function (hypot for ITK and pythag for VNL) do not get always the exact same result up to a very far away decimal
> - some loop indices were wrong I think in the ITK eigensystem. Some do vary in the VNL version, not in ITK?s equivalent
> 
> In the patch file attached, I have made a set of corrections that make things in ITK eigensystem closer to VNL but still the ITK version fails. I have to say I am getting completely lost here so I am calling upon the community for help. If anyone knows this enough, could you try the test attached and see if you have any ideas of what is going on. That would help us a lot.
> 
> The test attached can be compiled with cmake and run with the text file included : ./test_eigensystem data.txt 
> 
> Thanks in advance
> Olivier
> 
> 
> 
> ---
> 
> Olivier Commowick, Ph.D.
> Research Scientist
> INRIA Rennes - Bretagne Atlantique, VISAGES Team
> Campus de Beaulieu
> 35042 Rennes
> FRANCE
> 
> Phone: +33 2 99 84 25 92 <tel:+33%202%2099%2084%2025%2092>
> Email: Olivier.Commowick at inria.fr <mailto:Olivier.Commowick at inria.fr>
> Web: http://olivier.commowick.org/ <http://olivier.commowick.org/>
> 
> 
> 
> 
> 
> 
> _____________________________________
> Powered by www.kitware.com <http://www.kitware.com/>
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html <http://www.kitware.com/opensource/opensource.html>
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php <http://www.kitware.com/products/protraining.php>
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ <http://www.itk.org/Wiki/ITK_FAQ>
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users <http://public.kitware.com/mailman/listinfo/insight-users>
> 
> 


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Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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From Olivier.Commowick at inria.fr  Thu Feb  2 04:06:22 2017
From: Olivier.Commowick at inria.fr (Olivier Commowick)
Date: Thu, 2 Feb 2017 10:06:22 +0100
Subject: [ITK] [ITK-users] Problem with ITK eigensystem
In-Reply-To: <7FE2FD85-C0C9-47BD-AE85-9B6FE5E1ADE6@inria.fr>
References: <2444669A-4CBE-4C72-BB82-B3538C4513B1@inria.fr>
 <242A16CD-79C1-4427-94DB-3AFCD1A33851@inria.fr>
 <96DC429F-7F78-49D7-A026-930012074F27@inria.fr>
 <CAPf2UMSXgyUd9C6Qr=hx479neq1kwF+-L+eOjDnURUoKfsLPmA@mail.gmail.com>
 <7FE2FD85-C0C9-47BD-AE85-9B6FE5E1ADE6@inria.fr>
Message-ID: <779D7A51-94AE-4101-A70B-DEC837408DFC@inria.fr>

Oh, and I remember only now : in fact it might just be that applying the patch I sent in the email solves this problem of infinite loop while still producing nan values

> On 2 Feb 2017, at 09:27, Olivier Commowick <Olivier.Commowick at inria.fr> wrote:
> 
> Hi,
> 
> Thanks for your test. There might be a bug in my test or the way you ran it since for me it doesn?t take a few minutes but rather less than a second. That being said since it produces nans it might be that on some OS it goes into an infinite loop...
> 
> Olivier
> 
>> On 2 Feb 2017, at 00:02, D?enan Zuki? <dzenanz at gmail.com <mailto:dzenanz at gmail.com>> wrote:
>> 
>> Hi Olivier,
>> 
>> I tried running you example. One thing struck me right away: ITK version is much slower (after a few minutes running in release mod I killed it) than VNL version (about a second in debug mode) for your input.
>> 
>> I can't comment the patch content or the numeric stability. Perhaps Brad and Hans can pitch in?
>> 
>> Regards,
>> D?enan
>> 
>> On Tue, Jan 31, 2017 at 11:24 AM, Olivier Commowick <Olivier.Commowick at inria.fr <mailto:Olivier.Commowick at inria.fr>> wrote:
>> Hello,
>> 
>> I think I have found a bug in the behaviour of ITK?s symmetric eigensystem. In the attached link (http://olivier.commowick.org/tmp/Test.zip <http://olivier.commowick.org/tmp/Test.zip>) you will find an example code and matrix that fails with it and not with VNL?s symmetric eigensystem (run on macOS 10.12, Xcode 8.2.1).
>> 
>> It seems to me that there are subtle differences in between ITK and VNL versions, VNL being more robust (and the same as what Matlab gives, I didn?t test python). Here is what I have found so far :
>> 
>> - the hypothenuse function (hypot for ITK and pythag for VNL) do not get always the exact same result up to a very far away decimal
>> - some loop indices were wrong I think in the ITK eigensystem. Some do vary in the VNL version, not in ITK?s equivalent
>> 
>> In the patch file attached, I have made a set of corrections that make things in ITK eigensystem closer to VNL but still the ITK version fails. I have to say I am getting completely lost here so I am calling upon the community for help. If anyone knows this enough, could you try the test attached and see if you have any ideas of what is going on. That would help us a lot.
>> 
>> The test attached can be compiled with cmake and run with the text file included : ./test_eigensystem data.txt 
>> 
>> Thanks in advance
>> Olivier
>> 
>> 
>> 
>> ---
>> 
>> Olivier Commowick, Ph.D.
>> Research Scientist
>> INRIA Rennes - Bretagne Atlantique, VISAGES Team
>> Campus de Beaulieu
>> 35042 Rennes
>> FRANCE
>> 
>> Phone: +33 2 99 84 25 92 <tel:+33%202%2099%2084%2025%2092>
>> Email: Olivier.Commowick at inria.fr <mailto:Olivier.Commowick at inria.fr>
>> Web: http://olivier.commowick.org/ <http://olivier.commowick.org/>
>> 
>> 
>> 
>> 
>> 
>> 
>> _____________________________________
>> Powered by www.kitware.com <http://www.kitware.com/>
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html <http://www.kitware.com/opensource/opensource.html>
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php <http://www.kitware.com/products/protraining.php>
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ <http://www.itk.org/Wiki/ITK_FAQ>
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users <http://public.kitware.com/mailman/listinfo/insight-users>
>> 
>> 
> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> 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://public.kitware.com/mailman/listinfo/insight-users


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Kitware offers ITK Training Courses, for more information visit:
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From Olivier.Commowick at inria.fr  Thu Feb  2 04:09:20 2017
From: Olivier.Commowick at inria.fr (Olivier Commowick)
Date: Thu, 2 Feb 2017 10:09:20 +0100
Subject: [ITK] [ITK-users] ITK_COMPILED_CXX_VERSION always set to 1997
 on macOS
In-Reply-To: <D73BA3E0-50F5-422C-9558-81A62AA44DEA@mail.nih.gov>
References: <A96A5ED1-D452-47C7-A220-E4A40C4F1CE1@inria.fr>
 <B676B4C6-C8B9-4B1D-915E-6629FD513A67@inria.fr>
 <E8C99D9F-8C47-4F4A-9EC5-02A438CA9AE3@mail.nih.gov>
 <EC5A18B6-D728-4EB8-8A07-8B7FC7141433@inria.fr>
 <D73BA3E0-50F5-422C-9558-81A62AA44DEA@mail.nih.gov>
Message-ID: <A968F503-6AE3-466D-9890-E8801D4D424A@inria.fr>

Hi,

Ok now I get it. I was on the release branch and your modification seems to be only in the master branch yet. With it included, I have the same behaviour as yours.

Thanks
Olivier

> On 1 Feb 2017, at 21:48, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov> wrote:
> 
> Hi,
> 
> I am running Xcode 8.2.1 OS 10.11, and cmake 3.4.3. I was not able to reproduce your problem.
> For a clean build directory I ran:
>  cmake -DCMAKE_CXX_STANDARD=11 ~/src/ITK && grep  ITK_COMPILED_CXX Modules/Core/Common/itkConfigure.h
> 
> I got the following:
>  #define ITK_COMPILED_CXX_STANDARD_VERSION 201103L
>  #if ITK_COMPILED_CXX_STANDARD_VERSION > __cplusplus
> 
> There did appear to be a problem with the preprocessor variable used in the version check which I addressed here:
> http://review.source.kitware.com/#/c/22021/
> 
> Perhaps you did not start with a clean build directory?
> 
> Brad
> 
>> On Jan 31, 2017, at 5:02 AM, Olivier Commowick <Olivier.Commowick at inria.fr> wrote:
>> 
>> Hello
>> 
>> Thanks for your answer. I am running into this with Xcode 8.2.1, on a macOS 10.12, cmake version 3.6.2, and it happens already when compiling ITK itself.
>> 
>> I did not put the flag you mentioned. I could try but it seems to me that the VXL part of ITK has the same kind of test and it works. I mean by this that there is a VXL_COMPILED_CXX_STANDARD_VERSION set up in the file Modules/ThirdParty/VNL/src/vxl/config/cmake/config/VXLIntrospectionConfig.cmake . And this one is automatically set to 201103L without needing the flags you mentioned. May be there is something in this cmake file that should be ported back to the ITK equivalent (that?s just a thought of course).
>> 
>> Thanks
>> Olivier
>> 
>>> On 23 Jan 2017, at 15:25, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov> wrote:
>>> 
>>> Hello,
>>> 
>>> What Xcode version are you using? Can you produce a simple CMake command line configuration to reproduce the problem?
>>> 
>>> If you set "CMAKE_CXX_FLAGS=-std=c++11?, does the same problem occur?
>>> 
>>> Thanks!
>>> Brad
>>> 
>>>> On Jan 23, 2017, at 9:11 AM, Olivier Commowick <Olivier.Commowick at inria.fr> wrote:
>>>> 
>>>> Hello,
>>>> 
>>>> While debugging something else, I realised that the ITK_COMPILED_CXX_VERSION variable in CMake is always set to 199711L on my macOS 10.12. It sounds weird to me since I am always compiling ITK by enforcing to use CMAKE_CXX_STANDARD to 11.
>>>> 
>>>> It appears to me that Modules/Core/Common/CMakeLists.txt does this test and probably does not account for the fact that cmake uses the 2011 standard or something else. Would someone have any idea of how to correct this or if this is important or not ?
>>>> 
>>>> Best
>>>> Olivier
>>>> 
>>>> ---
>>>> 
>>>> Olivier Commowick, Ph.D.
>>>> Research Scientist
>>>> INRIA Rennes - Bretagne Atlantique, VISAGES Team
>>>> Campus de Beaulieu
>>>> 35042 Rennes
>>>> FRANCE
>>>> 
>>>> Phone: +33 2 99 84 25 92
>>>> Email: Olivier.Commowick at inria.fr
>>>> Web: http://olivier.commowick.org/
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>> 
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>> 
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>> 
>>>> 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://public.kitware.com/mailman/listinfo/insight-users
>>>> _______________________________________________
>>>> Community mailing list
>>>> Community at itk.org
>>>> http://public.kitware.com/mailman/listinfo/community
>>> 
>> 
>> 
>> ---
>> 
>> Olivier Commowick, Ph.D.
>> Research Scientist
>> INRIA Rennes - Bretagne Atlantique, VISAGES Team
>> Campus de Beaulieu
>> 35042 Rennes
>> FRANCE
>> 
>> Phone: +33 2 99 84 25 92
>> Email: Olivier.Commowick at inria.fr
>> Web: http://olivier.commowick.org/
>> 
>> 
>> 
>> 
>> 
> 


_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From Olivier.Commowick at inria.fr  Thu Feb  2 05:24:55 2017
From: Olivier.Commowick at inria.fr (Olivier Commowick)
Date: Thu, 2 Feb 2017 11:24:55 +0100
Subject: [ITK] [ITK-users] Problem with ITK eigensystem
In-Reply-To: <779D7A51-94AE-4101-A70B-DEC837408DFC@inria.fr>
References: <2444669A-4CBE-4C72-BB82-B3538C4513B1@inria.fr>
 <242A16CD-79C1-4427-94DB-3AFCD1A33851@inria.fr>
 <96DC429F-7F78-49D7-A026-930012074F27@inria.fr>
 <CAPf2UMSXgyUd9C6Qr=hx479neq1kwF+-L+eOjDnURUoKfsLPmA@mail.gmail.com>
 <7FE2FD85-C0C9-47BD-AE85-9B6FE5E1ADE6@inria.fr>
 <779D7A51-94AE-4101-A70B-DEC837408DFC@inria.fr>
Message-ID: <918B17E3-0FE0-4A24-B2F1-99F3DEE974CF@inria.fr>

Hello all,

I have found the bugs, which are tricky. Now my patched version is working on my example. I will submit it to review on gerrit

Best
Olivier



> On 2 Feb 2017, at 10:06, Olivier Commowick <Olivier.Commowick at inria.fr> wrote:
> 
> Oh, and I remember only now : in fact it might just be that applying the patch I sent in the email solves this problem of infinite loop while still producing nan values
> 
>> On 2 Feb 2017, at 09:27, Olivier Commowick <Olivier.Commowick at inria.fr <mailto:Olivier.Commowick at inria.fr>> wrote:
>> 
>> Hi,
>> 
>> Thanks for your test. There might be a bug in my test or the way you ran it since for me it doesn?t take a few minutes but rather less than a second. That being said since it produces nans it might be that on some OS it goes into an infinite loop...
>> 
>> Olivier
>> 
>>> On 2 Feb 2017, at 00:02, D?enan Zuki? <dzenanz at gmail.com <mailto:dzenanz at gmail.com>> wrote:
>>> 
>>> Hi Olivier,
>>> 
>>> I tried running you example. One thing struck me right away: ITK version is much slower (after a few minutes running in release mod I killed it) than VNL version (about a second in debug mode) for your input.
>>> 
>>> I can't comment the patch content or the numeric stability. Perhaps Brad and Hans can pitch in?
>>> 
>>> Regards,
>>> D?enan
>>> 
>>> On Tue, Jan 31, 2017 at 11:24 AM, Olivier Commowick <Olivier.Commowick at inria.fr <mailto:Olivier.Commowick at inria.fr>> wrote:
>>> Hello,
>>> 
>>> I think I have found a bug in the behaviour of ITK?s symmetric eigensystem. In the attached link (http://olivier.commowick.org/tmp/Test.zip <http://olivier.commowick.org/tmp/Test.zip>) you will find an example code and matrix that fails with it and not with VNL?s symmetric eigensystem (run on macOS 10.12, Xcode 8.2.1).
>>> 
>>> It seems to me that there are subtle differences in between ITK and VNL versions, VNL being more robust (and the same as what Matlab gives, I didn?t test python). Here is what I have found so far :
>>> 
>>> - the hypothenuse function (hypot for ITK and pythag for VNL) do not get always the exact same result up to a very far away decimal
>>> - some loop indices were wrong I think in the ITK eigensystem. Some do vary in the VNL version, not in ITK?s equivalent
>>> 
>>> In the patch file attached, I have made a set of corrections that make things in ITK eigensystem closer to VNL but still the ITK version fails. I have to say I am getting completely lost here so I am calling upon the community for help. If anyone knows this enough, could you try the test attached and see if you have any ideas of what is going on. That would help us a lot.
>>> 
>>> The test attached can be compiled with cmake and run with the text file included : ./test_eigensystem data.txt 
>>> 
>>> Thanks in advance
>>> Olivier
>>> 
>>> 
>>> 
>>> ---
>>> 
>>> Olivier Commowick, Ph.D.
>>> Research Scientist
>>> INRIA Rennes - Bretagne Atlantique, VISAGES Team
>>> Campus de Beaulieu
>>> 35042 Rennes
>>> FRANCE
>>> 
>>> Phone: +33 2 99 84 25 92 <tel:+33%202%2099%2084%2025%2092>
>>> Email: Olivier.Commowick at inria.fr <mailto:Olivier.Commowick at inria.fr>
>>> Web: http://olivier.commowick.org/ <http://olivier.commowick.org/>
>>> 
>>> 
>>> 

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_____________________________________
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Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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://public.kitware.com/mailman/listinfo/insight-users

From tofijoy at gmail.com  Thu Feb  2 10:53:44 2017
From: tofijoy at gmail.com (Fijoy Vadakkumpadan)
Date: Thu, 2 Feb 2017 10:53:44 -0500
Subject: [ITK] ITK headers included using angle brackets
In-Reply-To: <CAHwLD2UBO8YGbKNVQ=7YtjyKn4-gQZDj4-Z_AWRg5K3GE+QovA@mail.gmail.com>
References: <CAHE0P1WTyckPwJ8WnC8SMfmjBPFXkfiA8VC6MHaboWkyW6szvQ@mail.gmail.com>
 <CAHwLD2UBO8YGbKNVQ=7YtjyKn4-gQZDj4-Z_AWRg5K3GE+QovA@mail.gmail.com>
Message-ID: <CAHE0P1VZaG2HxdPjijm5gfd=XALh6AHzGAHr3B-QHBbPzW8rbQ@mail.gmail.com>

Hi Francios,

I was able to resolve this problem as I found out about an option to that
different compiler (Lattice C compiler), which made it search for the
include files in the local directory also.

Thanks for your reply.

--Fijoy

On Wed, Feb 1, 2017 at 11:00 AM, Francois Budin <francois.budin at kitware.com>
wrote:

> Hello Fijoy,
>
> Including file using double quotes or angle brackets should not create an
> issue (although the behavior is implementation-defined). Can you give more
> information about the "different compiler" you are using?
>
> Francois
>
> On Tue, Jan 31, 2017 at 12:41 PM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
> wrote:
>
>> Hello,
>>
>> I built ITK 4.10.0 using CMake & Visual Studio Express 2013 on Windows,
>> and am running into an issue with header files. In the header files that
>> are generated, some of the ITK-specific header files are included using
>> angle brackets. For example vcl_compiler.h contains "#include
>> <vcl_config_manual.h>". This is causing an issue when I'm trying to link to
>> the ITK libraries using a different compiler, which looks for these
>> ITK-specific header files in the system path because of the angle brackets.
>>
>> Is there an option in CMake to make the #includes use quotes instead of
>> angle brackets for ITK-specific header files?
>>
>> Thank you,
>> --Fijoy
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>>
>
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From francois.budin at kitware.com  Thu Feb  2 11:00:04 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Thu, 2 Feb 2017 11:00:04 -0500
Subject: [ITK] ITK headers included using angle brackets
In-Reply-To: <CAHE0P1VZaG2HxdPjijm5gfd=XALh6AHzGAHr3B-QHBbPzW8rbQ@mail.gmail.com>
References: <CAHE0P1WTyckPwJ8WnC8SMfmjBPFXkfiA8VC6MHaboWkyW6szvQ@mail.gmail.com>
 <CAHwLD2UBO8YGbKNVQ=7YtjyKn4-gQZDj4-Z_AWRg5K3GE+QovA@mail.gmail.com>
 <CAHE0P1VZaG2HxdPjijm5gfd=XALh6AHzGAHr3B-QHBbPzW8rbQ@mail.gmail.com>
Message-ID: <CAHwLD2Ua3y2DGmNtXeJD0UWdm4h+MuoYNJwZ+oy8aDG9vhcU-Q@mail.gmail.com>

Thanks for sharing the solution. That might help other people having the
same issue.

Francois

On Thu, Feb 2, 2017 at 10:53 AM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
wrote:

> Hi Francios,
>
> I was able to resolve this problem as I found out about an option to that
> different compiler (Lattice C compiler), which made it search for the
> include files in the local directory also.
>
> Thanks for your reply.
>
> --Fijoy
>
> On Wed, Feb 1, 2017 at 11:00 AM, Francois Budin <
> francois.budin at kitware.com> wrote:
>
>> Hello Fijoy,
>>
>> Including file using double quotes or angle brackets should not create an
>> issue (although the behavior is implementation-defined). Can you give more
>> information about the "different compiler" you are using?
>>
>> Francois
>>
>> On Tue, Jan 31, 2017 at 12:41 PM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
>> wrote:
>>
>>> Hello,
>>>
>>> I built ITK 4.10.0 using CMake & Visual Studio Express 2013 on Windows,
>>> and am running into an issue with header files. In the header files that
>>> are generated, some of the ITK-specific header files are included using
>>> angle brackets. For example vcl_compiler.h contains "#include
>>> <vcl_config_manual.h>". This is causing an issue when I'm trying to link to
>>> the ITK libraries using a different compiler, which looks for these
>>> ITK-specific header files in the system path because of the angle brackets.
>>>
>>> Is there an option in CMake to make the #includes use quotes instead of
>>> angle brackets for ITK-specific header files?
>>>
>>> Thank you,
>>> --Fijoy
>>>
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>>>
>>>
>>
>
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From tofijoy at gmail.com  Thu Feb  2 15:05:29 2017
From: tofijoy at gmail.com (Fijoy Vadakkumpadan)
Date: Thu, 2 Feb 2017 15:05:29 -0500
Subject: [ITK] Unresolved __imp_UuidCreate
Message-ID: <CAHE0P1VTHmT-E_su0spLTEc97FMQ-+fA99CJhzT80F7d1_SRmA@mail.gmail.com>

Hello,

I'm trying to link to ITK static libraries in Windows from an application,
and getting the following error. Does anyone know how to resolve this?

libitkgdcmMSFF-4.10-debug.lib(gdcmUIDGenerator.obj) : error LNK2019:
unresolved external symbol __imp_UuidCreate referenced in function "public:
char const * __cdecl gdcm::UIDGenerator::Generate(void)"

The ITK libraries were generated using CMake and Microsoft Visual Studio
Express 2013 (in Release mode). I used the default configuration options in
CMake, except that I turned BUILD_TESTING and BUILD_EXAMPLES to OFF, and I
changed CMAKE_INSTALL_PREFIX to a desired directory. I know that one of the
libraries, libitkgdcmuuid-4.10, was not generated during the build. Is this
the issue? If so, is there a CMake option that will generate the library?

Thanks,
--Fijoy
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From cr at neuro.ma.uni-heidelberg.de  Fri Feb  3 02:38:24 2017
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Fri, 3 Feb 2017 08:38:24 +0100
Subject: [ITK] [ITK-users] Bug in example ImageFilter
In-Reply-To: <CADZJ4hOx7Ci3Vum_HDCZAWTdXgr7V_SmWDSaz+XW9RYG4-Fcfg@mail.gmail.com>
References: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>
 <CAHwLD2UBoiokVfEGA93HaTQU+Ce1Vbb-2Ernbi29+YmkaRozAQ@mail.gmail.com>
 <CAPf2UMT8nLYmv6=7nQHYD=vXcCr2crmu_gvepmam39QjOBcNQg@mail.gmail.com>
 <CADZJ4hNACmkbqk_4rN+14U-9NQKt+e-BrrEkUMRTgA3FSoyxJg@mail.gmail.com>
 <CADZJ4hOx7Ci3Vum_HDCZAWTdXgr7V_SmWDSaz+XW9RYG4-Fcfg@mail.gmail.com>
Message-ID: <f5e09bc1-5941-aae6-044c-9a4fc60d507a@neuro.ma.uni-heidelberg.de>

I have to modify the source code in the tar archive, which I can 
download from the wiki, not the wiki itself. But I think, I have no 
access to that tar file.

Regards,
Christina

On 01.02.2017 23:28, Bill Lorensen wrote:
> That is correct. Update the wiki version.
>
> On Feb 1, 2017 5:02 PM, "D?enan Zuki?" <dzenanz at gmail.com 
> <mailto:dzenanz at gmail.com>> wrote:
>
>     Hi Christina,
>
>     you should not create a pull request for that repository, but
>     rather modify the example directly on the wiki
>     <https://itk.org/Wiki/ITK/Examples>. The repository is updated
>     manually by an automated script which scrapes the wiki. I think
>     that Bill usually invokes it.
>
>     Regards,
>     D?enan
>
>     On Wed, Feb 1, 2017 at 11:13 AM, Francois Budin
>     <francois.budin at kitware.com <mailto:francois.budin at kitware.com>>
>     wrote:
>
>         Hello Christina,
>
>         Thank you for the bug report. Could you create an issue and a
>         pull-request to solve the problem in this repository:
>         https://github.com/InsightSoftwareConsortium/ITKWikiExamples
>         <https://github.com/InsightSoftwareConsortium/ITKWikiExamples>
>
>         Thank you!
>         Francois
>
>         On Wed, Feb 1, 2017 at 7:03 AM, Chr. Rossmanith
>         <cr at neuro.ma.uni-heidelberg.de
>         <mailto:cr at neuro.ma.uni-heidelberg.de>> wrote:
>
>             Hi,
>
>             I've just downloaded
>             https://github.com/lorensen/ITKWikiExamplesTarballs/raw/master/ImageFilter.tar
>             <https://github.com/lorensen/ITKWikiExamplesTarballs/raw/master/ImageFilter.tar>
>             which doesn't compile out of the box because ImageFilter.h
>             tries to include ImageFilter.txx which does not exist -
>             should be ImageFilter.hxx (or ImageFilter.hxx must be
>             renamed to ImageFilter.txx).
>
>             Regards,
>
>             Christina Ro?manith
>
>             _____________________________________
>
>
>
>         _____________________________________
>         Powered by www.kitware.com <http://www.kitware.com>
>
>         Visit other Kitware open-source projects at
>         http://www.kitware.com/opensource/opensource.html
>         <http://www.kitware.com/opensource/opensource.html>
>
>         Kitware offers ITK Training Courses, for more information visit:
>         http://www.kitware.com/products/protraining.php
>         <http://www.kitware.com/products/protraining.php>
>
>         Please keep messages on-topic and check the ITK FAQ at:
>         http://www.itk.org/Wiki/ITK_FAQ <http://www.itk.org/Wiki/ITK_FAQ>
>
>         Follow this link to subscribe/unsubscribe:
>         http://public.kitware.com/mailman/listinfo/insight-users
>         <http://public.kitware.com/mailman/listinfo/insight-users>
>
>
>

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_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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://public.kitware.com/mailman/listinfo/insight-users

From bill.lorensen at gmail.com  Fri Feb  3 07:32:04 2017
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 3 Feb 2017 07:32:04 -0500
Subject: [ITK] [ITK-users] Bug in example ImageFilter
In-Reply-To: <f5e09bc1-5941-aae6-044c-9a4fc60d507a@neuro.ma.uni-heidelberg.de>
References: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>
 <CAHwLD2UBoiokVfEGA93HaTQU+Ce1Vbb-2Ernbi29+YmkaRozAQ@mail.gmail.com>
 <CAPf2UMT8nLYmv6=7nQHYD=vXcCr2crmu_gvepmam39QjOBcNQg@mail.gmail.com>
 <CADZJ4hNACmkbqk_4rN+14U-9NQKt+e-BrrEkUMRTgA3FSoyxJg@mail.gmail.com>
 <CADZJ4hOx7Ci3Vum_HDCZAWTdXgr7V_SmWDSaz+XW9RYG4-Fcfg@mail.gmail.com>
 <f5e09bc1-5941-aae6-044c-9a4fc60d507a@neuro.ma.uni-heidelberg.de>
Message-ID: <CADZJ4hMk4ev_CLkWZBjCdfVf7hCe17mBHs=-dTToEVkyJA6c8w@mail.gmail.com>

Change the wiki file. The archive will be updated overnight..


On Fri, Feb 3, 2017 at 2:38 AM, Chr. Rossmanith
<cr at neuro.ma.uni-heidelberg.de> wrote:
> I have to modify the source code in the tar archive, which I can download
> from the wiki, not the wiki itself. But I think, I have no access to that
> tar file.
>
> Regards,
> Christina
>
>
> On 01.02.2017 23:28, Bill Lorensen wrote:
>
> That is correct. Update the wiki version.
>
> On Feb 1, 2017 5:02 PM, "D?enan Zuki?" <dzenanz at gmail.com> wrote:
>
> Hi Christina,
>
> you should not create a pull request for that repository, but rather modify
> the example directly on the wiki. The repository is updated manually by an
> automated script which scrapes the wiki. I think that Bill usually invokes
> it.
>
> Regards,
> D?enan
>
> On Wed, Feb 1, 2017 at 11:13 AM, Francois Budin <francois.budin at kitware.com>
> wrote:
>>
>> Hello Christina,
>>
>> Thank you for the bug report. Could you create an issue and a pull-request
>> to solve the problem in this repository:
>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples
>>
>> Thank you!
>> Francois
>>
>> On Wed, Feb 1, 2017 at 7:03 AM, Chr. Rossmanith
>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>
>>> Hi,
>>>
>>> I've just downloaded
>>> https://github.com/lorensen/ITKWikiExamplesTarballs/raw/master/ImageFilter.tar
>>> which doesn't compile out of the box because ImageFilter.h tries to include
>>> ImageFilter.txx which does not exist - should be ImageFilter.hxx (or
>>> ImageFilter.hxx must be renamed to ImageFilter.txx).
>>>
>>> Regards,
>>>
>>> Christina Ro?manith
>>>
>>> _____________________________________
>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> 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://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
>



-- 
Unpaid intern in BillsBasement at noware dot com
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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://public.kitware.com/mailman/listinfo/insight-users

From dzenanz at gmail.com  Fri Feb  3 08:42:15 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 3 Feb 2017 08:42:15 -0500
Subject: [ITK] [ITK-users] Bug in example ImageFilter
In-Reply-To: <CADZJ4hMk4ev_CLkWZBjCdfVf7hCe17mBHs=-dTToEVkyJA6c8w@mail.gmail.com>
References: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>
 <CAHwLD2UBoiokVfEGA93HaTQU+Ce1Vbb-2Ernbi29+YmkaRozAQ@mail.gmail.com>
 <CAPf2UMT8nLYmv6=7nQHYD=vXcCr2crmu_gvepmam39QjOBcNQg@mail.gmail.com>
 <CADZJ4hNACmkbqk_4rN+14U-9NQKt+e-BrrEkUMRTgA3FSoyxJg@mail.gmail.com>
 <CADZJ4hOx7Ci3Vum_HDCZAWTdXgr7V_SmWDSaz+XW9RYG4-Fcfg@mail.gmail.com>
 <f5e09bc1-5941-aae6-044c-9a4fc60d507a@neuro.ma.uni-heidelberg.de>
 <CADZJ4hMk4ev_CLkWZBjCdfVf7hCe17mBHs=-dTToEVkyJA6c8w@mail.gmail.com>
Message-ID: <CAPf2UMR4R=H09kXbOJdC4_+Y2eepghnroQpDwLfbXRQ0RV4S_g@mail.gmail.com>

Which example are you trying to modify Christina?

On Fri, Feb 3, 2017 at 7:32 AM, Bill Lorensen <bill.lorensen at gmail.com>
wrote:

> Change the wiki file. The archive will be updated overnight..
>
>
> On Fri, Feb 3, 2017 at 2:38 AM, Chr. Rossmanith
> <cr at neuro.ma.uni-heidelberg.de> wrote:
> > I have to modify the source code in the tar archive, which I can download
> > from the wiki, not the wiki itself. But I think, I have no access to that
> > tar file.
> >
> > Regards,
> > Christina
> >
> >
> > On 01.02.2017 23:28, Bill Lorensen wrote:
> >
> > That is correct. Update the wiki version.
> >
> > On Feb 1, 2017 5:02 PM, "D?enan Zuki?" <dzenanz at gmail.com> wrote:
> >
> > Hi Christina,
> >
> > you should not create a pull request for that repository, but rather
> modify
> > the example directly on the wiki. The repository is updated manually by
> an
> > automated script which scrapes the wiki. I think that Bill usually
> invokes
> > it.
> >
> > Regards,
> > D?enan
> >
> > On Wed, Feb 1, 2017 at 11:13 AM, Francois Budin <
> francois.budin at kitware.com>
> > wrote:
> >>
> >> Hello Christina,
> >>
> >> Thank you for the bug report. Could you create an issue and a
> pull-request
> >> to solve the problem in this repository:
> >> https://github.com/InsightSoftwareConsortium/ITKWikiExamples
> >>
> >> Thank you!
> >> Francois
> >>
> >> On Wed, Feb 1, 2017 at 7:03 AM, Chr. Rossmanith
> >> <cr at neuro.ma.uni-heidelberg.de> wrote:
> >>>
> >>> Hi,
> >>>
> >>> I've just downloaded
> >>> https://github.com/lorensen/ITKWikiExamplesTarballs/raw/
> master/ImageFilter.tar
> >>> which doesn't compile out of the box because ImageFilter.h tries to
> include
> >>> ImageFilter.txx which does not exist - should be ImageFilter.hxx (or
> >>> ImageFilter.hxx must be renamed to ImageFilter.txx).
> >>>
> >>> Regards,
> >>>
> >>> Christina Ro?manith
> >>>
> >>> _____________________________________
> >>
> >>
> >>
> >> _____________________________________
> >> Powered by www.kitware.com
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
> >> Kitware offers ITK Training Courses, for more information visit:
> >> http://www.kitware.com/products/protraining.php
> >>
> >> 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://public.kitware.com/mailman/listinfo/insight-users
> >>
> >
> >
> >
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
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_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From blowekamp at mail.nih.gov  Fri Feb  3 08:48:00 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 3 Feb 2017 13:48:00 +0000
Subject: [ITK] Unresolved __imp_UuidCreate
In-Reply-To: <CAHE0P1VTHmT-E_su0spLTEc97FMQ-+fA99CJhzT80F7d1_SRmA@mail.gmail.com>
References: <CAHE0P1VTHmT-E_su0spLTEc97FMQ-+fA99CJhzT80F7d1_SRmA@mail.gmail.com>
Message-ID: <D2A95390-F4C3-4247-9D54-9E31E9717B92@mail.nih.gov>

Hello,

I noticed that you say you have compiled ITK in ?Release? mode, but the error line you included includes ?debug?.

Do you have multiple builds and installed of ITK? Perhaps the configuration has gotten the versions and or locations confused?

HTH,
Brad

On Feb 2, 2017, at 3:05 PM, Fijoy Vadakkumpadan <tofijoy at gmail.com<mailto:tofijoy at gmail.com>> wrote:

Hello,

I'm trying to link to ITK static libraries in Windows from an application, and getting the following error. Does anyone know how to resolve this?

libitkgdcmMSFF-4.10-debug.lib(gdcmUIDGenerator.obj) : error LNK2019: unresolved external symbol __imp_UuidCreate referenced in function "public: char const * __cdecl gdcm::UIDGenerator::Generate(void)"

The ITK libraries were generated using CMake and Microsoft Visual Studio Express 2013 (in Release mode). I used the default configuration options in CMake, except that I turned BUILD_TESTING and BUILD_EXAMPLES to OFF, and I changed CMAKE_INSTALL_PREFIX to a desired directory. I know that one of the libraries, libitkgdcmuuid-4.10, was not generated during the build. Is this the issue? If so, is there a CMake option that will generate the library?

Thanks,
--Fijoy


_______________________________________________
Community mailing list
Community at itk.org<mailto:Community at itk.org>
http://public.kitware.com/mailman/listinfo/community

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From cr at neuro.ma.uni-heidelberg.de  Fri Feb  3 09:40:34 2017
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Fri, 3 Feb 2017 15:40:34 +0100
Subject: [ITK] [ITK-users] Bug in example ImageFilter
In-Reply-To: <CADZJ4hMk4ev_CLkWZBjCdfVf7hCe17mBHs=-dTToEVkyJA6c8w@mail.gmail.com>
References: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>
 <CAHwLD2UBoiokVfEGA93HaTQU+Ce1Vbb-2Ernbi29+YmkaRozAQ@mail.gmail.com>
 <CAPf2UMT8nLYmv6=7nQHYD=vXcCr2crmu_gvepmam39QjOBcNQg@mail.gmail.com>
 <CADZJ4hNACmkbqk_4rN+14U-9NQKt+e-BrrEkUMRTgA3FSoyxJg@mail.gmail.com>
 <CADZJ4hOx7Ci3Vum_HDCZAWTdXgr7V_SmWDSaz+XW9RYG4-Fcfg@mail.gmail.com>
 <f5e09bc1-5941-aae6-044c-9a4fc60d507a@neuro.ma.uni-heidelberg.de>
 <CADZJ4hMk4ev_CLkWZBjCdfVf7hCe17mBHs=-dTToEVkyJA6c8w@mail.gmail.com>
Message-ID: <3c7f0f13-6bd9-6f7c-f32e-aeb52a6e23f4@neuro.ma.uni-heidelberg.de>

Currently ImageFilter.h in the wiki 
<https://itk.org/Wiki/ITK/Examples/Developer/ImageFilter#ImageFilter.h> 
includes ImageFilter.hxx but ImageFilter.h from the tar archive includes 
ImageFilter.txx - that makes it difficult for me to believe that the tar 
archive is created from the wiki content.

Regards
Christina

On 03.02.2017 13:32, Bill Lorensen wrote:
> Change the wiki file. The archive will be updated overnight..
>
>
> On Fri, Feb 3, 2017 at 2:38 AM, Chr. Rossmanith
> <cr at neuro.ma.uni-heidelberg.de> wrote:
>> I have to modify the source code in the tar archive, which I can download
>> from the wiki, not the wiki itself. But I think, I have no access to that
>> tar file.
>>
>> Regards,
>> Christina
>>
>>
>> On 01.02.2017 23:28, Bill Lorensen wrote:
>>
>> That is correct. Update the wiki version.
>>
>> On Feb 1, 2017 5:02 PM, "D?enan Zuki?" <dzenanz at gmail.com> wrote:
>>
>> Hi Christina,
>>
>> you should not create a pull request for that repository, but rather modify
>> the example directly on the wiki. The repository is updated manually by an
>> automated script which scrapes the wiki. I think that Bill usually invokes
>> it.
>>
>> Regards,
>> D?enan
>>
>> On Wed, Feb 1, 2017 at 11:13 AM, Francois Budin <francois.budin at kitware.com>
>> wrote:
>>> Hello Christina,
>>>
>>> Thank you for the bug report. Could you create an issue and a pull-request
>>> to solve the problem in this repository:
>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples
>>>
>>> Thank you!
>>> Francois
>>>
>>> On Wed, Feb 1, 2017 at 7:03 AM, Chr. Rossmanith
>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>> Hi,
>>>>
>>>> I've just downloaded
>>>> https://github.com/lorensen/ITKWikiExamplesTarballs/raw/master/ImageFilter.tar
>>>> which doesn't compile out of the box because ImageFilter.h tries to include
>>>> ImageFilter.txx which does not exist - should be ImageFilter.hxx (or
>>>> ImageFilter.hxx must be renamed to ImageFilter.txx).
>>>>
>>>> Regards,
>>>>
>>>> Christina Ro?manith
>>>>
>>>> _____________________________________
>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> 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://public.kitware.com/mailman/listinfo/insight-users
>>>
>>
>>
>
>

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Kitware offers ITK Training Courses, for more information visit:
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From dzenanz at gmail.com  Fri Feb  3 09:45:45 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 3 Feb 2017 09:45:45 -0500
Subject: [ITK] [ITK-users] Bug in example ImageFilter
In-Reply-To: <3c7f0f13-6bd9-6f7c-f32e-aeb52a6e23f4@neuro.ma.uni-heidelberg.de>
References: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>
 <CAHwLD2UBoiokVfEGA93HaTQU+Ce1Vbb-2Ernbi29+YmkaRozAQ@mail.gmail.com>
 <CAPf2UMT8nLYmv6=7nQHYD=vXcCr2crmu_gvepmam39QjOBcNQg@mail.gmail.com>
 <CADZJ4hNACmkbqk_4rN+14U-9NQKt+e-BrrEkUMRTgA3FSoyxJg@mail.gmail.com>
 <CADZJ4hOx7Ci3Vum_HDCZAWTdXgr7V_SmWDSaz+XW9RYG4-Fcfg@mail.gmail.com>
 <f5e09bc1-5941-aae6-044c-9a4fc60d507a@neuro.ma.uni-heidelberg.de>
 <CADZJ4hMk4ev_CLkWZBjCdfVf7hCe17mBHs=-dTToEVkyJA6c8w@mail.gmail.com>
 <3c7f0f13-6bd9-6f7c-f32e-aeb52a6e23f4@neuro.ma.uni-heidelberg.de>
Message-ID: <CAPf2UMQYeDodJcdSvFgynTu1JZzUMU3DFTJ7i-7AApXQM8N4vg@mail.gmail.com>

Hi Bill,

was the file structure in the git repo created manually? Or a better
question: is the file structure in git repo updated automatically when file
names on the wiki are changed? File content does seem to be updated.

Regards,
D?enan

On Fri, Feb 3, 2017 at 9:40 AM, Chr. Rossmanith <
cr at neuro.ma.uni-heidelberg.de> wrote:

> Currently ImageFilter.h in the wiki
> <https://itk.org/Wiki/ITK/Examples/Developer/ImageFilter#ImageFilter.h>
> includes ImageFilter.hxx but ImageFilter.h from the tar archive includes
> ImageFilter.txx - that makes it difficult for me to believe that the tar
> archive is created from the wiki content.
>
> Regards
> Christina
>
>
> On 03.02.2017 13:32, Bill Lorensen wrote:
>
> Change the wiki file. The archive will be updated overnight..
>
>
> On Fri, Feb 3, 2017 at 2:38 AM, Chr. Rossmanith<cr at neuro.ma.uni-heidelberg.de> <cr at neuro.ma.uni-heidelberg.de> wrote:
>
> I have to modify the source code in the tar archive, which I can download
> from the wiki, not the wiki itself. But I think, I have no access to that
> tar file.
>
> Regards,
> Christina
>
>
> On 01.02.2017 23:28, Bill Lorensen wrote:
>
> That is correct. Update the wiki version.
>
> On Feb 1, 2017 5:02 PM, "D?enan Zuki?" <dzenanz at gmail.com> <dzenanz at gmail.com> wrote:
>
> Hi Christina,
>
> you should not create a pull request for that repository, but rather modify
> the example directly on the wiki. The repository is updated manually by an
> automated script which scrapes the wiki. I think that Bill usually invokes
> it.
>
> Regards,
> D?enan
>
> On Wed, Feb 1, 2017 at 11:13 AM, Francois Budin <francois.budin at kitware.com> <francois.budin at kitware.com>
> wrote:
>
> Hello Christina,
>
> Thank you for the bug report. Could you create an issue and a pull-request
> to solve the problem in this repository:https://github.com/InsightSoftwareConsortium/ITKWikiExamples
>
> Thank you!
> Francois
>
> On Wed, Feb 1, 2017 at 7:03 AM, Chr. Rossmanith<cr at neuro.ma.uni-heidelberg.de> <cr at neuro.ma.uni-heidelberg.de> wrote:
>
> Hi,
>
> I've just downloadedhttps://github.com/lorensen/ITKWikiExamplesTarballs/raw/master/ImageFilter.tar
> which doesn't compile out of the box because ImageFilter.h tries to include
> ImageFilter.txx which does not exist - should be ImageFilter.hxx (or
> ImageFilter.hxx must be renamed to ImageFilter.txx).
>
> Regards,
>
> Christina Ro?manith
>
> _____________________________________
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects athttp://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
>
>
>
>
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_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From bill.lorensen at gmail.com  Fri Feb  3 10:01:38 2017
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 3 Feb 2017 10:01:38 -0500
Subject: [ITK] [ITK-users] Bug in example ImageFilter
In-Reply-To: <CAPf2UMQYeDodJcdSvFgynTu1JZzUMU3DFTJ7i-7AApXQM8N4vg@mail.gmail.com>
References: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>
 <CAHwLD2UBoiokVfEGA93HaTQU+Ce1Vbb-2Ernbi29+YmkaRozAQ@mail.gmail.com>
 <CAPf2UMT8nLYmv6=7nQHYD=vXcCr2crmu_gvepmam39QjOBcNQg@mail.gmail.com>
 <CADZJ4hNACmkbqk_4rN+14U-9NQKt+e-BrrEkUMRTgA3FSoyxJg@mail.gmail.com>
 <CADZJ4hOx7Ci3Vum_HDCZAWTdXgr7V_SmWDSaz+XW9RYG4-Fcfg@mail.gmail.com>
 <f5e09bc1-5941-aae6-044c-9a4fc60d507a@neuro.ma.uni-heidelberg.de>
 <CADZJ4hMk4ev_CLkWZBjCdfVf7hCe17mBHs=-dTToEVkyJA6c8w@mail.gmail.com>
 <3c7f0f13-6bd9-6f7c-f32e-aeb52a6e23f4@neuro.ma.uni-heidelberg.de>
 <CAPf2UMQYeDodJcdSvFgynTu1JZzUMU3DFTJ7i-7AApXQM8N4vg@mail.gmail.com>
Message-ID: <CADZJ4hNd7YJURSZ8FBVG1-y+-RksOfZKFkNL7JdAQnnJ9cnztQ@mail.gmail.com>

It should change when the wiki is changed. I'll look into this.


On Fri, Feb 3, 2017 at 9:45 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> Hi Bill,
>
> was the file structure in the git repo created manually? Or a better
> question: is the file structure in git repo updated automatically when file
> names on the wiki are changed? File content does seem to be updated.
>
> Regards,
> D?enan
>
> On Fri, Feb 3, 2017 at 9:40 AM, Chr. Rossmanith
> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>
>> Currently ImageFilter.h in the wiki includes ImageFilter.hxx but
>> ImageFilter.h from the tar archive includes ImageFilter.txx - that makes it
>> difficult for me to believe that the tar archive is created from the wiki
>> content.
>>
>> Regards
>> Christina
>>
>>
>> On 03.02.2017 13:32, Bill Lorensen wrote:
>>
>> Change the wiki file. The archive will be updated overnight..
>>
>>
>> On Fri, Feb 3, 2017 at 2:38 AM, Chr. Rossmanith
>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>
>> I have to modify the source code in the tar archive, which I can download
>> from the wiki, not the wiki itself. But I think, I have no access to that
>> tar file.
>>
>> Regards,
>> Christina
>>
>>
>> On 01.02.2017 23:28, Bill Lorensen wrote:
>>
>> That is correct. Update the wiki version.
>>
>> On Feb 1, 2017 5:02 PM, "D?enan Zuki?" <dzenanz at gmail.com> wrote:
>>
>> Hi Christina,
>>
>> you should not create a pull request for that repository, but rather
>> modify
>> the example directly on the wiki. The repository is updated manually by an
>> automated script which scrapes the wiki. I think that Bill usually invokes
>> it.
>>
>> Regards,
>> D?enan
>>
>> On Wed, Feb 1, 2017 at 11:13 AM, Francois Budin
>> <francois.budin at kitware.com>
>> wrote:
>>
>> Hello Christina,
>>
>> Thank you for the bug report. Could you create an issue and a pull-request
>> to solve the problem in this repository:
>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples
>>
>> Thank you!
>> Francois
>>
>> On Wed, Feb 1, 2017 at 7:03 AM, Chr. Rossmanith
>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>
>> Hi,
>>
>> I've just downloaded
>>
>> https://github.com/lorensen/ITKWikiExamplesTarballs/raw/master/ImageFilter.tar
>> which doesn't compile out of the box because ImageFilter.h tries to
>> include
>> ImageFilter.txx which does not exist - should be ImageFilter.hxx (or
>> ImageFilter.hxx must be renamed to ImageFilter.txx).
>>
>> Regards,
>>
>> Christina Ro?manith
>>
>> _____________________________________
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> 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://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>>
>>
>



-- 
Unpaid intern in BillsBasement at noware dot com
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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://public.kitware.com/mailman/listinfo/insight-users

From bill.lorensen at gmail.com  Fri Feb  3 10:25:04 2017
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 3 Feb 2017 10:25:04 -0500
Subject: [ITK] [ITK-users] Bug in example ImageFilter
In-Reply-To: <CADZJ4hNd7YJURSZ8FBVG1-y+-RksOfZKFkNL7JdAQnnJ9cnztQ@mail.gmail.com>
References: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>
 <CAHwLD2UBoiokVfEGA93HaTQU+Ce1Vbb-2Ernbi29+YmkaRozAQ@mail.gmail.com>
 <CAPf2UMT8nLYmv6=7nQHYD=vXcCr2crmu_gvepmam39QjOBcNQg@mail.gmail.com>
 <CADZJ4hNACmkbqk_4rN+14U-9NQKt+e-BrrEkUMRTgA3FSoyxJg@mail.gmail.com>
 <CADZJ4hOx7Ci3Vum_HDCZAWTdXgr7V_SmWDSaz+XW9RYG4-Fcfg@mail.gmail.com>
 <f5e09bc1-5941-aae6-044c-9a4fc60d507a@neuro.ma.uni-heidelberg.de>
 <CADZJ4hMk4ev_CLkWZBjCdfVf7hCe17mBHs=-dTToEVkyJA6c8w@mail.gmail.com>
 <3c7f0f13-6bd9-6f7c-f32e-aeb52a6e23f4@neuro.ma.uni-heidelberg.de>
 <CAPf2UMQYeDodJcdSvFgynTu1JZzUMU3DFTJ7i-7AApXQM8N4vg@mail.gmail.com>
 <CADZJ4hNd7YJURSZ8FBVG1-y+-RksOfZKFkNL7JdAQnnJ9cnztQ@mail.gmail.com>
Message-ID: <CADZJ4hN1VwoFmQvdWF6Y57xCaWYCiwjDghEUxCc+RHNQ7O=F0w@mail.gmail.com>

For some reason the tar file is not being updated by the nightly sync
script.. I'll check onto it.


On Fri, Feb 3, 2017 at 10:01 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> It should change when the wiki is changed. I'll look into this.
>
>
> On Fri, Feb 3, 2017 at 9:45 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>> Hi Bill,
>>
>> was the file structure in the git repo created manually? Or a better
>> question: is the file structure in git repo updated automatically when file
>> names on the wiki are changed? File content does seem to be updated.
>>
>> Regards,
>> D?enan
>>
>> On Fri, Feb 3, 2017 at 9:40 AM, Chr. Rossmanith
>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>
>>> Currently ImageFilter.h in the wiki includes ImageFilter.hxx but
>>> ImageFilter.h from the tar archive includes ImageFilter.txx - that makes it
>>> difficult for me to believe that the tar archive is created from the wiki
>>> content.
>>>
>>> Regards
>>> Christina
>>>
>>>
>>> On 03.02.2017 13:32, Bill Lorensen wrote:
>>>
>>> Change the wiki file. The archive will be updated overnight..
>>>
>>>
>>> On Fri, Feb 3, 2017 at 2:38 AM, Chr. Rossmanith
>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>
>>> I have to modify the source code in the tar archive, which I can download
>>> from the wiki, not the wiki itself. But I think, I have no access to that
>>> tar file.
>>>
>>> Regards,
>>> Christina
>>>
>>>
>>> On 01.02.2017 23:28, Bill Lorensen wrote:
>>>
>>> That is correct. Update the wiki version.
>>>
>>> On Feb 1, 2017 5:02 PM, "D?enan Zuki?" <dzenanz at gmail.com> wrote:
>>>
>>> Hi Christina,
>>>
>>> you should not create a pull request for that repository, but rather
>>> modify
>>> the example directly on the wiki. The repository is updated manually by an
>>> automated script which scrapes the wiki. I think that Bill usually invokes
>>> it.
>>>
>>> Regards,
>>> D?enan
>>>
>>> On Wed, Feb 1, 2017 at 11:13 AM, Francois Budin
>>> <francois.budin at kitware.com>
>>> wrote:
>>>
>>> Hello Christina,
>>>
>>> Thank you for the bug report. Could you create an issue and a pull-request
>>> to solve the problem in this repository:
>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples
>>>
>>> Thank you!
>>> Francois
>>>
>>> On Wed, Feb 1, 2017 at 7:03 AM, Chr. Rossmanith
>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>
>>> Hi,
>>>
>>> I've just downloaded
>>>
>>> https://github.com/lorensen/ITKWikiExamplesTarballs/raw/master/ImageFilter.tar
>>> which doesn't compile out of the box because ImageFilter.h tries to
>>> include
>>> ImageFilter.txx which does not exist - should be ImageFilter.hxx (or
>>> ImageFilter.hxx must be renamed to ImageFilter.txx).
>>>
>>> Regards,
>>>
>>> Christina Ro?manith
>>>
>>> _____________________________________
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> 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://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>>
>>>
>>
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com



-- 
Unpaid intern in BillsBasement at noware dot com
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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://public.kitware.com/mailman/listinfo/insight-users

From tofijoy at gmail.com  Fri Feb  3 10:47:21 2017
From: tofijoy at gmail.com (Fijoy Vadakkumpadan)
Date: Fri, 3 Feb 2017 10:47:21 -0500
Subject: [ITK] Unresolved __imp_UuidCreate
In-Reply-To: <D2A95390-F4C3-4247-9D54-9E31E9717B92@mail.nih.gov>
References: <CAHE0P1VTHmT-E_su0spLTEc97FMQ-+fA99CJhzT80F7d1_SRmA@mail.gmail.com>
 <D2A95390-F4C3-4247-9D54-9E31E9717B92@mail.nih.gov>
Message-ID: <CAHE0P1X0aTkURi_p1YNy6Ux5F+u7VRPoUs8umQikrSiH4+Y1kQ@mail.gmail.com>

Hi Brad,

I resolved the issue by including the (system) library rpcrt4.l in building
the application. Initial tests indicate that the application works, but I
need to do additional testing.

It appears that the Windows build of ITK does not build the library
libitkgdcmuuid.lib, which contains __imp_UuidCreate. The Unix build did
generate libitkgdcmuuid.a, so this was not an issue there. Do you or anyone
know if this is a bug?

--Fijoy

On Fri, Feb 3, 2017 at 8:48 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Hello,
>
> I noticed that you say you have compiled ITK in ?Release? mode, but the
> error line you included includes ?debug?.
>
> Do you have multiple builds and installed of ITK? Perhaps the
> configuration has gotten the versions and or locations confused?
>
> HTH,
> Brad
>
> On Feb 2, 2017, at 3:05 PM, Fijoy Vadakkumpadan <tofijoy at gmail.com> wrote:
>
> Hello,
>
> I'm trying to link to ITK static libraries in Windows from an application,
> and getting the following error. Does anyone know how to resolve this?
>
> libitkgdcmMSFF-4.10-debug.lib(gdcmUIDGenerator.obj) : error LNK2019:
> unresolved external symbol __imp_UuidCreate referenced in function "public:
> char const * __cdecl gdcm::UIDGenerator::Generate(void)"
>
> The ITK libraries were generated using CMake and Microsoft Visual Studio
> Express 2013 (in Release mode). I used the default configuration options
> in CMake, except that I turned BUILD_TESTING and BUILD_EXAMPLES to OFF,
> and I changed CMAKE_INSTALL_PREFIX to a desired directory. I know that one
> of the libraries, libitkgdcmuuid-4.10, was not generated during the
> build. Is this the issue? If so, is there a CMake option that will generate
> the library?
>
> Thanks,
> --Fijoy
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
>
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From bill.lorensen at gmail.com  Fri Feb  3 12:11:33 2017
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 3 Feb 2017 12:11:33 -0500
Subject: [ITK] [ITK-users] Bug in example ImageFilter
In-Reply-To: <CADZJ4hN1VwoFmQvdWF6Y57xCaWYCiwjDghEUxCc+RHNQ7O=F0w@mail.gmail.com>
References: <089fe6fa-d9c7-616b-8723-c64184a66049@neuro.ma.uni-heidelberg.de>
 <CAHwLD2UBoiokVfEGA93HaTQU+Ce1Vbb-2Ernbi29+YmkaRozAQ@mail.gmail.com>
 <CAPf2UMT8nLYmv6=7nQHYD=vXcCr2crmu_gvepmam39QjOBcNQg@mail.gmail.com>
 <CADZJ4hNACmkbqk_4rN+14U-9NQKt+e-BrrEkUMRTgA3FSoyxJg@mail.gmail.com>
 <CADZJ4hOx7Ci3Vum_HDCZAWTdXgr7V_SmWDSaz+XW9RYG4-Fcfg@mail.gmail.com>
 <f5e09bc1-5941-aae6-044c-9a4fc60d507a@neuro.ma.uni-heidelberg.de>
 <CADZJ4hMk4ev_CLkWZBjCdfVf7hCe17mBHs=-dTToEVkyJA6c8w@mail.gmail.com>
 <3c7f0f13-6bd9-6f7c-f32e-aeb52a6e23f4@neuro.ma.uni-heidelberg.de>
 <CAPf2UMQYeDodJcdSvFgynTu1JZzUMU3DFTJ7i-7AApXQM8N4vg@mail.gmail.com>
 <CADZJ4hNd7YJURSZ8FBVG1-y+-RksOfZKFkNL7JdAQnnJ9cnztQ@mail.gmail.com>
 <CADZJ4hN1VwoFmQvdWF6Y57xCaWYCiwjDghEUxCc+RHNQ7O=F0w@mail.gmail.com>
Message-ID: <CADZJ4hMJrDetAkvYMBXafGaa-qD5viSx7idAnhuGbZm3txOdGQ@mail.gmail.com>

i found the problem. twi examples in the sane directory had a
ImageFilter.h file. I have fixed the offending example and all should
be OK now.

Thanks for reporting the problem.

Bill

On Fri, Feb 3, 2017 at 10:25 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> For some reason the tar file is not being updated by the nightly sync
> script.. I'll check onto it.
>
>
> On Fri, Feb 3, 2017 at 10:01 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>> It should change when the wiki is changed. I'll look into this.
>>
>>
>> On Fri, Feb 3, 2017 at 9:45 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>> Hi Bill,
>>>
>>> was the file structure in the git repo created manually? Or a better
>>> question: is the file structure in git repo updated automatically when file
>>> names on the wiki are changed? File content does seem to be updated.
>>>
>>> Regards,
>>> D?enan
>>>
>>> On Fri, Feb 3, 2017 at 9:40 AM, Chr. Rossmanith
>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>>
>>>> Currently ImageFilter.h in the wiki includes ImageFilter.hxx but
>>>> ImageFilter.h from the tar archive includes ImageFilter.txx - that makes it
>>>> difficult for me to believe that the tar archive is created from the wiki
>>>> content.
>>>>
>>>> Regards
>>>> Christina
>>>>
>>>>
>>>> On 03.02.2017 13:32, Bill Lorensen wrote:
>>>>
>>>> Change the wiki file. The archive will be updated overnight..
>>>>
>>>>
>>>> On Fri, Feb 3, 2017 at 2:38 AM, Chr. Rossmanith
>>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>>
>>>> I have to modify the source code in the tar archive, which I can download
>>>> from the wiki, not the wiki itself. But I think, I have no access to that
>>>> tar file.
>>>>
>>>> Regards,
>>>> Christina
>>>>
>>>>
>>>> On 01.02.2017 23:28, Bill Lorensen wrote:
>>>>
>>>> That is correct. Update the wiki version.
>>>>
>>>> On Feb 1, 2017 5:02 PM, "D?enan Zuki?" <dzenanz at gmail.com> wrote:
>>>>
>>>> Hi Christina,
>>>>
>>>> you should not create a pull request for that repository, but rather
>>>> modify
>>>> the example directly on the wiki. The repository is updated manually by an
>>>> automated script which scrapes the wiki. I think that Bill usually invokes
>>>> it.
>>>>
>>>> Regards,
>>>> D?enan
>>>>
>>>> On Wed, Feb 1, 2017 at 11:13 AM, Francois Budin
>>>> <francois.budin at kitware.com>
>>>> wrote:
>>>>
>>>> Hello Christina,
>>>>
>>>> Thank you for the bug report. Could you create an issue and a pull-request
>>>> to solve the problem in this repository:
>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples
>>>>
>>>> Thank you!
>>>> Francois
>>>>
>>>> On Wed, Feb 1, 2017 at 7:03 AM, Chr. Rossmanith
>>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>>
>>>> Hi,
>>>>
>>>> I've just downloaded
>>>>
>>>> https://github.com/lorensen/ITKWikiExamplesTarballs/raw/master/ImageFilter.tar
>>>> which doesn't compile out of the box because ImageFilter.h tries to
>>>> include
>>>> ImageFilter.txx which does not exist - should be ImageFilter.hxx (or
>>>> ImageFilter.hxx must be renamed to ImageFilter.txx).
>>>>
>>>> Regards,
>>>>
>>>> Christina Ro?manith
>>>>
>>>> _____________________________________
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> 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://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com



-- 
Unpaid intern in BillsBasement at noware dot com
_____________________________________
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From matt.mccormick at kitware.com  Fri Feb  3 15:53:50 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 3 Feb 2017 15:53:50 -0500
Subject: [ITK] [ITK-dev] [Orfeo Toolbox (OTB) 0001354]: Fails to build
	with	GCC 7
In-Reply-To: <6470a85c-c0b1-a9a8-135d-cbe3d28259ed@cnes.fr>
References: <b171bd2751d9787a49fde77dab542d8b@bugs.orfeo-toolbox.org>
 <6470a85c-c0b1-a9a8-135d-cbe3d28259ed@cnes.fr>
Message-ID: <CALzTN-S1LPxD51ARytGQfLnRRo-3NVgi3E_wtyu=NoiRNhD78w@mail.gmail.com>

Hi Manuel,

Thanks for the note. The Debian Med folks have done an outstanding job
packaging ITK, and they have even started a package for the recently
released v4.11.0 [1].

Unfortunately, 4.11.0 still has a few issues with GCC 7. This topic branch
addresses most [2]. There is still one failing test, but we could give that
a look again after GCC 7 has been released.

Thanks,
Matt

[1] https://lists.debian.org/debian-med/2017/01/msg00124.html

[2]
http://review.source.kitware.com/#/q/status:open+project:ITK+branch:master+topic:GCC7-for-release

On Wed, Feb 1, 2017 at 2:35 AM, Manuel Grizonnet <manuel.grizonnet at cnes.fr>
wrote:

> Hi all,
>
> FYI ORFEO ToolBox debian packagers report compilation issue for OTB with
> gcc 7.
>
> The error seems to be with ITK (see mantis report below).
> I havent investigated it yet but I wanted to transfer it to you as soon as
> possible as it seems that you'we started the RC process for 4.11.
>
> Note that we don't have any platforms on otb dashboard to test gcc 7
> support.
>
> Regards,
>
> Manuel
>
> -------- Message transf?r? --------
> Sujet : [Orfeo Toolbox (OTB) 0001354]: Fails to build with GCC 7
> Date : Tue, 31 Jan 2017 19:23:08 +0100
> De : Mantis Bug Tracker <bugs at orfeo-toolbox.org> <bugs at orfeo-toolbox.org>
> Pour : manuel.grizonnet at cnes.fr
>
> A NOTE has been added to this issue.
> ====================================================================== https://bugs.orfeo-toolbox.org/view.php?id=1354
> ======================================================================
> Reported By:                sebastic
> Assigned To:
> ======================================================================
> Project:                    Orfeo Toolbox (OTB)
> Issue ID:                   1354
> Category:                   General
> Reproducibility:            have not tried
> Severity:                   minor
> Priority:                   normal
> Status:                     new
> ======================================================================
> Date Submitted:             2017-01-31 18:48 CET
> Last Modified:              2017-01-31 19:23 CET
> ======================================================================
> Summary:                    Fails to build with GCC 7
> Description:
> As reported by Matthias Klose in Debian Bughttps://bugs.orfeo-toolbox.org/view.php?id=853602
> (https://bugs.debian.org/853602):
>
>
> The package fails to build in a test rebuild on at least amd64 with
> gcc-7/g++-7, but succeeds to build with gcc-6/g++-6. The
> severity of this report may be raised before the buster release.
> There is no need to fix this issue in time for the stretch release.
>
> The full build log can be found at:http://people.debian.org/~doko/logs/gcc7-20170126/otb_5.8.0+dfsg-3_unstable_gcc7.log
> The last lines of the build log are at the end of this report.
>
> To build with GCC 7, either set CC=gcc-7 CXX=g++-7 explicitly,
> or install the gcc, g++, gfortran, ... packages from experimental.
>
>   apt-get -t experimental install g++
>
> Common build failures are new warnings resulting in build failures with
> -Werror turned on, or new/dropped symbols in Debian symbols files.
> For other C/C++ related build failures see the porting guide athttp://gcc.gnu.org/gcc-7/porting_to.html
>
> [...]
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> -I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/ThirdParty/OssimPlugins/src/ossim
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> -I/usr/include/gdal -I/usr/include/geotiff
> -I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src
> -I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src/ossim
> -I/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/ThirdParty/OssimPlugins/src/ossim
> -I/<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/ThirdParty/OssimPlugins/src/gdal  -Wall
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> cd
> /<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/ThirdParty/SiftFast/src
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> CMakeFiles/otbossimplugins.dir/ossim/RadarSat/Leader/Leader.cpp.o
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> CMakeFiles/otbossimplugins.dir/ossim/RadarSat/RadarSatRecord.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/RadarSat/RadarSatRecordFactory.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/RadarSat/RadarSatRecordHeader.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/RadarSat/Trailer/Trailer.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/RadarSat/Trailer/TrailerFactory.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/RadarSat/VolumeDir/FilePointerRecord.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/RadarSat/VolumeDir/TextRecord.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/RadarSat/VolumeDir/VolumeDescriptorRecord.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/RadarSat/VolumeDir/VolumeDir.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/RadarSat/VolumeDir/VolumeDirFactory.cpp.o
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> CMakeFiles/otbossimplugins.dir/ossim/erssar/ErsSarFacilityData.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/erssar/ErsSarFileDescriptor.cpp.o
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> CMakeFiles/otbossimplugins.dir/ossim/ossimGeometricSarSensorModel.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/ossimPleiadesDimapSupportData.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/ossimPleiadesModel.cpp.o
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> CMakeFiles/otbossimplugins.dir/ossim/ossimPluginInit.cpp.o
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> CMakeFiles/otbossimplugins.dir/ossim/ossimSentinel1Model.cpp.o
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> CMakeFiles/otbossimplugins.dir/ossim/otb/SceneCoord.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/otb/Sensor.cpp.o
> CMakeFiles/otbossimplugins.dir/ossim/otb/SensorParams.cpp.o -lgdal -lossim
> -lOpenThreads -lgeotiff
> cd
> /<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/ThirdParty/OssimPlugins/src
> && /usr/bin/cmake -E cmake_symlink_library
> ../../../../lib/libotbossimplugins-5.8.so.1
> ../../../../lib/libotbossimplugins-5.8.so.1
> ../../../../lib/libotbossimplugins-5.8.so
> make[3]: Leaving directory '/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu'
> [ 17%] Built target otbossimplugins
> make[2]: Leaving directory '/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu'
> Makefile:130: recipe for target 'all' failed
> make[1]: *** [all] Error 2
> make[1]: Leaving directory '/<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu'
> dh_auto_build: make -j64 returned exit code 2
> debian/rules:81: recipe for target 'build' failed
> make: *** [build] Error 2
> dpkg-buildpackage: error: debian/rules build gave error exit status 2
> ======================================================================
>
> ----------------------------------------------------------------------
>  (0003986) sebastic (reporter) - 2017-01-31 19:23
>  https://bugs.orfeo-toolbox.org/view.php?id=1354#c3986
> ----------------------------------------------------------------------
> Problem seems to be with ITK:
>
> cd
> /<<BUILDDIR>>/otb-5.8.0+dfsg/obj-x86_64-linux-gnu/Modules/Adapters/OpenThreadsAdapters/src
> && /usr/bin/cmake -E cmake_link_script
> CMakeFiles/OTBOpenThreadsAdapters.dir/link.txt --verbose=1
> In file included from /usr/include/ITK-4.10/vcl_limits.h:5:0,
>                  from /usr/include/ITK-4.10/itkNumericTraits.h:51,
>                  from /usr/include/ITK-4.10/itkConceptChecking.h:32,
>                  from /usr/include/ITK-4.10/itkAtomicInt.h:38,
>                  from /usr/include/ITK-4.10/itkLightObject.h:25,
>                  from /usr/include/ITK-4.10/itkObject.h:31,
>                  from /usr/include/ITK-4.10/itkCommand.h:21,
>                  from
> /<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/Core/Common/include/otbFilterWatcherBase.h:24,
>                  from
> /<<BUILDDIR>>/otb-5.8.0+dfsg/Modules/Core/Common/src/otbFilterWatcherBase.cxx:21:
> /usr/include/ITK-4.10/vcl_compiler.h:79:4: error: #error "Dunno about this gcc"
>  #  error "Dunno about this gcc"
>     ^~~~~
>
> Issue History
> Date Modified    Username       Field                    Change
> ======================================================================
> 2017-01-31 18:48 sebastic       New Issue
> 2017-01-31 19:22 sebastic       File Added: otb_5.8.0+dfsg-3_unstable_gcc7.log
>
> 2017-01-31 19:23 sebastic       Note Added: 0003986
> ======================================================================
>
>
>
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From 10811130d at gmail.com  Fri Feb  3 23:50:21 2017
From: 10811130d at gmail.com (jiancong wang)
Date: Fri, 3 Feb 2017 23:50:21 -0500
Subject: [ITK] [ITK-users] Questions on
	the	itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx
Message-ID: <CALjoVPNT941OGqx4Wa0YhEoYLNExVcVHSPxzOipaiGsyMNMj_A@mail.gmail.com>

Hi guys,
I am working on replicating this image registration metric on gpu and has
some questions that I want to ask.

In both of the UpdateQueue functions I saw a line like this:
......
for ( SizeValueType indct = i; indct < hoodlen; indct += ( diameter +
NumericTraits<SizeValueType>::OneValue() ) )
......

Why the index is incremented by the diameter of the NCC window instead of
by 1? Isn't this suppose accumulate local pixel values for reuse purpose?
Also why there is only one for loop here? How do they handle 3D data in
this case?

I read the original paper and they are trying to cache the local sum value
(for example for a 7 by 7 window they are supposed to accumulate 7by1
column window, that each time it proceeds it only has to recompute the next
7by1 column instead of the full 7by7 window).

Any help is greatly appreciated! Thanks!
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From bakkari.abdelkhalek at hotmail.fr  Sat Feb  4 13:28:11 2017
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Sat, 4 Feb 2017 18:28:11 +0000
Subject: [ITK] [ITK-users] Binary Fill hole Image Filter for 3D Image
In-Reply-To: <AM2PR09MB056246C3B8E78649D362CF1F834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
References: <AM2PR09MB0562E9A01ADA7267BFDAC1B4834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>,
 <AM2PR09MB056246C3B8E78649D362CF1F834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
Message-ID: <AM2PR09MB0562C47CECCEC157E909B522834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>





Dear ITK-users,

I tried to adopt the BinaryFillholeImageFilter for 3D image (contour.mha). Unfortunately,  the result which I obtained is not what I expect.

The fragment of  code which I used is :

                                                // Lecture of the contour.mha
                                                typedef itk::Image< unsigned char, 3 > UCharImageType;
                                               typedef itk::ImageFileReader<UCharImageType> ImageReaderType;
                                       ImageReaderType::Pointer reader = ImageReaderType::New();
                                        reader->SetFileName("contour.mha");
                                        reader->Update();

                                               // Binary Fill Hole Image Filter
                                                typedef itk::BinaryFillholeImageFilter< UCharImageType > FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput( reader->GetOutput() );
filter->SetForegroundValue( itk::NumericTraits< unsigned char >::min() );
filter->Update();
                                                // Save the BinaryFillHoleImage
{
typedef itk::ImageFileWriter<UCharImageType> ImageWriterType;
ImageWriterType::Pointer writer = ImageWriterType::New();
writer->SetFileName("BinaryFillHoleImage.mha");
writer->SetInput(filter->GetOutput());
try{
writer->Update();
}catch(itk::ExceptionObject &e){
std::cerr << e << std::endl;
}
}



Thank you in advance.

Kind regards,



Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland


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From dzenanz at gmail.com  Sat Feb  4 13:37:14 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 4 Feb 2017 13:37:14 -0500
Subject: [ITK] [ITK-users] Questions on
	the	itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.hxx
In-Reply-To: <CALjoVPNT941OGqx4Wa0YhEoYLNExVcVHSPxzOipaiGsyMNMj_A@mail.gmail.com>
References: <CALjoVPNT941OGqx4Wa0YhEoYLNExVcVHSPxzOipaiGsyMNMj_A@mail.gmail.com>
Message-ID: <CAPf2UMRC2ztZtjqbkqa8XoYcU8ysmMZ4vBPOkNpXjOd-ruiwmQ@mail.gmail.com>

Hi Jiancong,

I have not seen this class before, so I can't answer your questions.
However I can recommend you to run
itkANTSNeighborhoodCorrelationImageToImageMetricv4Test.cxx under debugger
and inspect the loop of interest. Then change ImageDimension to 3 and run
it again. It looks like the test was written with such experimentation in
mind, so it should run. You might also play with imageSize (currently 6) to
have a smaller or large image.

Hopefully this will help you to understand how that code works.

Regards

On Fri, Feb 3, 2017 at 11:50 PM, jiancong wang <10811130d at gmail.com> wrote:

> Hi guys,
> I am working on replicating this image registration metric on gpu and has
> some questions that I want to ask.
>
> In both of the UpdateQueue functions I saw a line like this:
> ......
> for ( SizeValueType indct = i; indct < hoodlen; indct += ( diameter +
> NumericTraits<SizeValueType>::OneValue() ) )
> ......
>
> Why the index is incremented by the diameter of the NCC window instead of
> by 1? Isn't this suppose accumulate local pixel values for reuse purpose?
> Also why there is only one for loop here? How do they handle 3D data in
> this case?
>
> I read the original paper and they are trying to cache the local sum value
> (for example for a 7 by 7 window they are supposed to accumulate 7by1
> column window, that each time it proceeds it only has to recompute the next
> 7by1 column instead of the full 7by7 window).
>
> Any help is greatly appreciated! Thanks!
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
>
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From dzenanz at gmail.com  Sat Feb  4 14:03:09 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 4 Feb 2017 14:03:09 -0500
Subject: [ITK] [ITK-users] Binary Fill hole Image Filter for 3D Image
In-Reply-To: <AM2PR09MB0562C47CECCEC157E909B522834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
References: <AM2PR09MB0562E9A01ADA7267BFDAC1B4834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
 <AM2PR09MB056246C3B8E78649D362CF1F834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
 <AM2PR09MB0562C47CECCEC157E909B522834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
Message-ID: <CAPf2UMRLKa-x617Zih8YXdPE9NJJ7Qg-Z-qR-BnetgBucwA8=Q@mail.gmail.com>

Hi Abdelkhalek,

your image does not have any holes! The input and output images are binary
identical (examined using file compare tool). If I modify your input image
to also contain a real hole (not connected to image edge or the
background), it gets filled properly. See attached.

Regards,
D?enan

On Sat, Feb 4, 2017 at 1:28 PM, Abdelkhalek Bakkari <
bakkari.abdelkhalek at hotmail.fr> wrote:

>
>
>
>
> Dear ITK-users,
>
> I tried to adopt the BinaryFillholeImageFilter for 3D image (contour.mha).
> Unfortunately,  the result which I obtained is not what I expect.
>
> The fragment of  code which I used is :
>
>                                                 // Lecture of the
> contour.mha
>                                                 typedef itk::Image<
> unsigned char, 3 > UCharImageType;
>                                                typedef
> itk::ImageFileReader<UCharImageType> ImageReaderType;
>                                        ImageReaderType::Pointer reader =
> ImageReaderType::New();
>                                         reader->SetFileName("contour.
> mha");
>                                         reader->Update();
>
>                                                // Binary Fill Hole Image
> Filter
>                                                 typedef itk::BinaryFillholeImageFilter<
> UCharImageType > FilterType;
> FilterType::Pointer filter = FilterType::New();
> filter->SetInput( reader->GetOutput() );
> filter->SetForegroundValue( itk::NumericTraits< unsigned char >::min() );
> filter->Update();
>                                                 // Save the
> BinaryFillHoleImage
> {
> typedef itk::ImageFileWriter<UCharImageType> ImageWriterType;
> ImageWriterType::Pointer writer = ImageWriterType::New();
> writer->SetFileName("BinaryFillHoleImage.mha");
> writer->SetInput(filter->GetOutput());
> try{
> writer->Update();
> }catch(itk::ExceptionObject &e){
> std::cerr << e << std::endl;
> }
> }
>
>
>
> Thank you in advance.
>
> Kind regards,
>
>
> Abdelkhalek Bakkari
> Ph.D candidate in Computer Science
> Institute of Applied Computer Science
> Lodz University of Technology, Poland
>
>
>
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From dzenanz at gmail.com  Sat Feb  4 14:46:25 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 4 Feb 2017 14:46:25 -0500
Subject: [ITK] [ITK-users] Binary Fill hole Image Filter for 3D Image
In-Reply-To: <AM2PR09MB05627C84EB9057870247163D834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
References: <AM2PR09MB0562E9A01ADA7267BFDAC1B4834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
 <AM2PR09MB056246C3B8E78649D362CF1F834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
 <AM2PR09MB0562C47CECCEC157E909B522834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
 <CAPf2UMRLKa-x617Zih8YXdPE9NJJ7Qg-Z-qR-BnetgBucwA8=Q@mail.gmail.com>
 <AM2PR09MB05627C84EB9057870247163D834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
Message-ID: <CAPf2UMSw4jwytMH7jByQ13_CrNuGL2P07OEEwjLaLigdiwDdHg@mail.gmail.com>

Hi Abdelkhalek,

try using binary opening/closing
<https://itk.org/Doxygen/html/classitk_1_1BinaryMorphologicalClosingImageFilter.html>,
which are implemented as binary dilation and erosion.

https://itk.org/Doxygen/html/group__MathematicalMorphologyImageFilters.html
Regards,
D?enan

On Sat, Feb 4, 2017 at 2:43 PM, Abdelkhalek Bakkari <
bakkari.abdelkhalek at hotmail.fr> wrote:

> Hi Dzenan,
>
>
> My goal is to obtain the big contour of the 3D image. For this reason, I
> tried to use Binary Fill hole Image Filter  and after the
> BinaryContourImageFilter.
>
> Could you provide me another way using ITK, please?
>
>
> Best regards,
>
>
>
>
> ------------------------------
> *From:* D?enan Zuki? <dzenanz at gmail.com>
> *Sent:* 04 February 2017 20:03
> *To:* Abdelkhalek Bakkari
> *Cc:* insight-users
> *Subject:* Re: Binary Fill hole Image Filter for 3D Image
>
> Hi Abdelkhalek,
>
> your image does not have any holes! The input and output images are binary
> identical (examined using file compare tool). If I modify your input image
> to also contain a real hole (not connected to image edge or the
> background), it gets filled properly. See attached.
>
> Regards,
> D?enan
>
> On Sat, Feb 4, 2017 at 1:28 PM, Abdelkhalek Bakkari <
> bakkari.abdelkhalek at hotmail.fr> wrote:
>
>>
>>
>>
>>
>> Dear ITK-users,
>>
>> I tried to adopt the BinaryFillholeImageFilter for 3D image (contour.mha).
>> Unfortunately,  the result which I obtained is not what I expect.
>>
>> The fragment of  code which I used is :
>>
>>                                                 // Lecture of the
>> contour.mha
>>                                                 typedef itk::Image<
>> unsigned char, 3 > UCharImageType;
>>                                                typedef
>> itk::ImageFileReader<UCharImageType> ImageReaderType;
>>                                        ImageReaderType::Pointer reader =
>> ImageReaderType::New();
>>                                         reader->SetFileName("contour.m
>> ha");
>>                                         reader->Update();
>>
>>                                                // Binary Fill Hole Image
>> Filter
>>                                                 typedef
>> itk::BinaryFillholeImageFilter< UCharImageType > FilterType;
>> FilterType::Pointer filter = FilterType::New();
>> filter->SetInput( reader->GetOutput() );
>> filter->SetForegroundValue( itk::NumericTraits< unsigned char >::min() );
>> filter->Update();
>>                                                 // Save the
>> BinaryFillHoleImage
>> {
>> typedef itk::ImageFileWriter<UCharImageType> ImageWriterType;
>> ImageWriterType::Pointer writer = ImageWriterType::New();
>> writer->SetFileName("BinaryFillHoleImage.mha");
>> writer->SetInput(filter->GetOutput());
>> try{
>> writer->Update();
>> }catch(itk::ExceptionObject &e){
>> std::cerr << e << std::endl;
>> }
>> }
>>
>>
>>
>> Thank you in advance.
>>
>> Kind regards,
>>
>>
>> Abdelkhalek Bakkari
>> Ph.D candidate in Computer Science
>> Institute of Applied Computer Science
>> Lodz University of Technology, Poland
>>
>>
>>
>
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From bakkari.abdelkhalek at hotmail.fr  Sat Feb  4 14:43:07 2017
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Sat, 4 Feb 2017 19:43:07 +0000
Subject: [ITK] [ITK-users] Binary Fill hole Image Filter for 3D Image
In-Reply-To: <CAPf2UMRLKa-x617Zih8YXdPE9NJJ7Qg-Z-qR-BnetgBucwA8=Q@mail.gmail.com>
References: <AM2PR09MB0562E9A01ADA7267BFDAC1B4834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
 <AM2PR09MB056246C3B8E78649D362CF1F834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>
 <AM2PR09MB0562C47CECCEC157E909B522834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>,
 <CAPf2UMRLKa-x617Zih8YXdPE9NJJ7Qg-Z-qR-BnetgBucwA8=Q@mail.gmail.com>
Message-ID: <AM2PR09MB05627C84EB9057870247163D834E0@AM2PR09MB0562.eurprd09.prod.outlook.com>

Hi Dzenan,


My goal is to obtain the big contour of the 3D image. For this reason, I tried to use Binary Fill hole Image Filter  and after the BinaryContourImageFilter.

Could you provide me another way using ITK, please?


Best regards,




________________________________
From: D?enan Zuki? <dzenanz at gmail.com>
Sent: 04 February 2017 20:03
To: Abdelkhalek Bakkari
Cc: insight-users
Subject: Re: Binary Fill hole Image Filter for 3D Image

Hi Abdelkhalek,

your image does not have any holes! The input and output images are binary identical (examined using file compare tool). If I modify your input image to also contain a real hole (not connected to image edge or the background), it gets filled properly. See attached.

Regards,
D?enan

On Sat, Feb 4, 2017 at 1:28 PM, Abdelkhalek Bakkari <bakkari.abdelkhalek at hotmail.fr<mailto:bakkari.abdelkhalek at hotmail.fr>> wrote:




Dear ITK-users,

I tried to adopt the BinaryFillholeImageFilter for 3D image (contour.mha). Unfortunately,  the result which I obtained is not what I expect.

The fragment of  code which I used is :

                                                // Lecture of the contour.mha
                                                typedef itk::Image< unsigned char, 3 > UCharImageType;
                                               typedef itk::ImageFileReader<UCharImageType> ImageReaderType;
                                       ImageReaderType::Pointer reader = ImageReaderType::New();
                                        reader->SetFileName("contour.mha");
                                        reader->Update();

                                               // Binary Fill Hole Image Filter
                                                typedef itk::BinaryFillholeImageFilter< UCharImageType > FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput( reader->GetOutput() );
filter->SetForegroundValue( itk::NumericTraits< unsigned char >::min() );
filter->Update();
                                                // Save the BinaryFillHoleImage
{
typedef itk::ImageFileWriter<UCharImageType> ImageWriterType;
ImageWriterType::Pointer writer = ImageWriterType::New();
writer->SetFileName("BinaryFillHoleImage.mha");
writer->SetInput(filter->GetOutput());
try{
writer->Update();
}catch(itk::ExceptionObject &e){
std::cerr << e << std::endl;
}
}



Thank you in advance.

Kind regards,



Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland



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From woodsb02 at gmail.com  Sun Feb  5 08:24:08 2017
From: woodsb02 at gmail.com (Ben Woods)
Date: Sun, 5 Feb 2017 21:24:08 +0800
Subject: [ITK] Captcha image not working when trying to create Jira account
Message-ID: <CAOc73CCREmiTm9m3z0FvX9QnofKrj7+p6uy0Lg+ZOzSiHyNtDA@mail.gmail.com>

Hi everyone,

When trying to sign up for an account on the Jira ITK issue tracker just
now, the Captcha image is not loading. I tried on multiple different
browsers, and on Windows and FreeBSD. None worked.

Could someone else please test if it is working for them?

Regards,
Ben

--
From: Benjamin Woods
woodsb02 at gmail.com
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From woodsb02 at gmail.com  Sun Feb  5 08:24:33 2017
From: woodsb02 at gmail.com (Ben Woods)
Date: Sun, 5 Feb 2017 21:24:33 +0800
Subject: [ITK] ITK fails to build with clang 4.0
Message-ID: <CAOc73CAXbtkvr=ydUUK_zUaxa8NwseB0--ULNZexmKGtLTT-tg@mail.gmail.com>

Hi everyone,

ITK fails to build with the new clang compiler version 4.0.

The specific build error is:

Modules/ThirdParty/VNL/src/vxl/v3p/netlib/linalg/lsqrBase.cxx:565:14:
error: ordered comparison between pointer and zero ('std::ostream *'
(aka 'basic_ostream<char> *') and 'int')
    if (nout > 0)
        ~~~~ ^ ~

build log: http://package18.nyi.freebsd.org/data/headamd64PR216008-default/2017-01-29_16h09m05s/logs/errors/InsightToolkit-4.10.1.log
regressed by: https://github.com/llvm-mirror/clang/commit/4b6ad14285f3


This was originally raised on the FreeBSD issue tracker here:
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=216617

Could somebody please look into this, and perhaps raise it on the Jira ITK
issue tracker? (I am having trouble creating an account).

Regards,
Ben

--
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woodsb02 at gmail.com
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From dzenanz at gmail.com  Sun Feb  5 10:39:53 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sun, 5 Feb 2017 10:39:53 -0500
Subject: [ITK] Captcha image not working when trying to create Jira
	account
In-Reply-To: <CAOc73CCREmiTm9m3z0FvX9QnofKrj7+p6uy0Lg+ZOzSiHyNtDA@mail.gmail.com>
References: <CAOc73CCREmiTm9m3z0FvX9QnofKrj7+p6uy0Lg+ZOzSiHyNtDA@mail.gmail.com>
Message-ID: <CAPf2UMSPEbqZGvkfxbGkbhRD6o-xS+h2y+=+f2pN5ZptJTLfhQ@mail.gmail.com>

Hi Ben,

captcha on signup page
<https://issues.itk.org/jira/secure/Signup!default.jspa> does not work for
me either. Trying to open the missing captcha image in a new tab revealed
the problem:

*Cause: *
java.lang.RuntimeException: java.io.IOException: No space left on device

Regards,
D?enan

On Sun, Feb 5, 2017 at 8:24 AM, Ben Woods <woodsb02 at gmail.com> wrote:

> Hi everyone,
>
> When trying to sign up for an account on the Jira ITK issue tracker just
> now, the Captcha image is not loading. I tried on multiple different
> browsers, and on Windows and FreeBSD. None worked.
>
> Could someone else please test if it is working for them?
>
> Regards,
> Ben
>
> --
> From: Benjamin Woods
> woodsb02 at gmail.com
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From taylor at braun-jones.org  Mon Feb  6 10:54:45 2017
From: taylor at braun-jones.org (Taylor Braun-Jones)
Date: Mon, 6 Feb 2017 10:54:45 -0500
Subject: [ITK] [ITK-dev] JIRA down
Message-ID: <CAKfKJYsGxpx+d8kPCi7Dn=6PXCPp5xhBZ0LzJOunBBYP88hYTA@mail.gmail.com>

Hello,

Looks like JIRA is down. I was able to login, but most JIRA pages give
me  "An internal server error occurred when requesting resource" error
messages. On one page the error dump look like it was related to a full
disk.

Taylor
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From matt.mccormick at kitware.com  Mon Feb  6 11:37:37 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 6 Feb 2017 11:37:37 -0500
Subject: [ITK] Curve2DExtraction parametemer
In-Reply-To: <104762312.4242714.1481701998477@mail.yahoo.com>
References: <104762312.4242714.1481701998477.ref@mail.yahoo.com>
 <104762312.4242714.1481701998477@mail.yahoo.com>
Message-ID: <CALzTN-TTfO8c7Hts93vTEXOm+wqWUoT2=mFG1cx077AZFzRYyw@mail.gmail.com>

Hi Belen,

The MinimalPathExtraction module offers a good curve extraction
framework that could be configured to be robust to parameter tuning:

  https://github.com/InsightSoftwareConsortium/ITKMinimalPathExtraction

Hope this helps,
Matt

On Wed, Dec 14, 2016 at 2:53 AM, Belen Martin via Community
<community at itk.org> wrote:
> Dear ITK list,
>
> Is there anyway in Curve2DExtraction (or with further implementation) to
> automate the result as much as possible, meaning tuning all parameters,
> sigma, and Spatial Function parameters?
>
> If not can you recommend me a different module in ITK? I am using
> Curve2DExtraction application to extract center lines in X-ray or DSA images
> previous to the calculation stenosis. I do not want the physician have to
> know about pyramid or spatial function to tune results.
>
>
> Thanks in advance
>
>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From francois.budin at kitware.com  Mon Feb  6 11:43:47 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Mon, 6 Feb 2017 11:43:47 -0500
Subject: [ITK] [ITK-dev] JIRA down
In-Reply-To: <CAKfKJYsGxpx+d8kPCi7Dn=6PXCPp5xhBZ0LzJOunBBYP88hYTA@mail.gmail.com>
References: <CAKfKJYsGxpx+d8kPCi7Dn=6PXCPp5xhBZ0LzJOunBBYP88hYTA@mail.gmail.com>
Message-ID: <CAHwLD2XMdL6k5i4ZdtM6=cyMbHL6j2gM8Ldx=_r3NYq_Bu+0PQ@mail.gmail.com>

It works right now for me. Maybe the issue has been solved or maybe it is a
network issue for you?

Francois

On Mon, Feb 6, 2017 at 10:54 AM, Taylor Braun-Jones <taylor at braun-jones.org>
wrote:

> Hello,
>
> Looks like JIRA is down. I was able to login, but most JIRA pages give
> me  "An internal server error occurred when requesting resource" error
> messages. On one page the error dump look like it was related to a full
> disk.
>
> Taylor
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-developers
>
>
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From taylor at braun-jones.org  Mon Feb  6 12:10:40 2017
From: taylor at braun-jones.org (Taylor Braun-Jones)
Date: Mon, 6 Feb 2017 12:10:40 -0500
Subject: [ITK] [ITK-dev] JIRA down
In-Reply-To: <CAHwLD2XMdL6k5i4ZdtM6=cyMbHL6j2gM8Ldx=_r3NYq_Bu+0PQ@mail.gmail.com>
References: <CAKfKJYsGxpx+d8kPCi7Dn=6PXCPp5xhBZ0LzJOunBBYP88hYTA@mail.gmail.com>
 <CAHwLD2XMdL6k5i4ZdtM6=cyMbHL6j2gM8Ldx=_r3NYq_Bu+0PQ@mail.gmail.com>
Message-ID: <CAKfKJYsnLBqPvXak0Q3jovjee9nPk4RNfFOZhHHqp3evv_eS=w@mail.gmail.com>

It's back up for me and my co-workers as well. If it was something that
just fixed itself it might be worth checking the JIRA logs to see what the
root issue might have been.

On Mon, Feb 6, 2017 at 11:43 AM, Francois Budin <francois.budin at kitware.com>
wrote:

> It works right now for me. Maybe the issue has been solved or maybe it is
> a network issue for you?
>
> Francois
>
> On Mon, Feb 6, 2017 at 10:54 AM, Taylor Braun-Jones <
> taylor at braun-jones.org> wrote:
>
>> Hello,
>>
>> Looks like JIRA is down. I was able to login, but most JIRA pages give
>> me  "An internal server error occurred when requesting resource" error
>> messages. On one page the error dump look like it was related to a full
>> disk.
>>
>> Taylor
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://kitware.com/products/protraining.php
>>
>> 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://public.kitware.com/mailman/listinfo/insight-developers
>>
>>
>
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From dzenanz at gmail.com  Mon Feb  6 12:14:41 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 6 Feb 2017 12:14:41 -0500
Subject: [ITK] [ITK-dev] JIRA down
In-Reply-To: <CAKfKJYsnLBqPvXak0Q3jovjee9nPk4RNfFOZhHHqp3evv_eS=w@mail.gmail.com>
References: <CAKfKJYsGxpx+d8kPCi7Dn=6PXCPp5xhBZ0LzJOunBBYP88hYTA@mail.gmail.com>
 <CAHwLD2XMdL6k5i4ZdtM6=cyMbHL6j2gM8Ldx=_r3NYq_Bu+0PQ@mail.gmail.com>
 <CAKfKJYsnLBqPvXak0Q3jovjee9nPk4RNfFOZhHHqp3evv_eS=w@mail.gmail.com>
Message-ID: <CAPf2UMSsLnNgPw7nyr55_jEuSdVKw0giHi0Vxgu2j8ocCOE=FQ@mail.gmail.com>

The "disk is full" was probably the root cause. Over the weekend somebody
also reported CAPTCHA problem which was due to full disk too.

On Mon, Feb 6, 2017 at 12:10 PM, Taylor Braun-Jones <taylor at braun-jones.org>
wrote:

> It's back up for me and my co-workers as well. If it was something that
> just fixed itself it might be worth checking the JIRA logs to see what the
> root issue might have been.
>
> On Mon, Feb 6, 2017 at 11:43 AM, Francois Budin <
> francois.budin at kitware.com> wrote:
>
>> It works right now for me. Maybe the issue has been solved or maybe it is
>> a network issue for you?
>>
>> Francois
>>
>> On Mon, Feb 6, 2017 at 10:54 AM, Taylor Braun-Jones <
>> taylor at braun-jones.org> wrote:
>>
>>> Hello,
>>>
>>> Looks like JIRA is down. I was able to login, but most JIRA pages give
>>> me  "An internal server error occurred when requesting resource" error
>>> messages. On one page the error dump look like it was related to a full
>>> disk.
>>>
>>> Taylor
>>>
>>> _______________________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://kitware.com/products/protraining.php
>>>
>>> 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://public.kitware.com/mailman/listinfo/insight-developers
>>>
>>>
>>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-developers
>
>
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From hans-johnson at uiowa.edu  Mon Feb  6 12:31:11 2017
From: hans-johnson at uiowa.edu (Johnson, Hans J)
Date: Mon, 6 Feb 2017 17:31:11 +0000
Subject: [ITK] [ITK-dev] JIRA down
In-Reply-To: <CAPf2UMSsLnNgPw7nyr55_jEuSdVKw0giHi0Vxgu2j8ocCOE=FQ@mail.gmail.com>
References: <CAKfKJYsGxpx+d8kPCi7Dn=6PXCPp5xhBZ0LzJOunBBYP88hYTA@mail.gmail.com>
 <CAHwLD2XMdL6k5i4ZdtM6=cyMbHL6j2gM8Ldx=_r3NYq_Bu+0PQ@mail.gmail.com>
 <CAKfKJYsnLBqPvXak0Q3jovjee9nPk4RNfFOZhHHqp3evv_eS=w@mail.gmail.com>
 <CAPf2UMSsLnNgPw7nyr55_jEuSdVKw0giHi0Vxgu2j8ocCOE=FQ@mail.gmail.com>
Message-ID: <97A6DC52-2047-47BB-B361-73217EE3EEFD@uiowa.edu>

We are reviewing and attempting to fix now.  Thank you for the information.


Hans

--


From: Insight-developers <insight-developers-bounces at itk.org> on behalf of D?enan Zuki? <dzenanz at gmail.com>
Date: Monday, February 6, 2017 at 11:14 AM
To: Taylor Braun-Jones <taylor at braun-jones.org>
Cc: ITK Developers <insight-developers at itk.org>
Subject: Re: [ITK-dev] JIRA down

The "disk is full" was probably the root cause. Over the weekend somebody also reported CAPTCHA problem which was due to full disk too.

On Mon, Feb 6, 2017 at 12:10 PM, Taylor Braun-Jones <taylor at braun-jones.org<mailto:taylor at braun-jones.org>> wrote:
It's back up for me and my co-workers as well. If it was something that just fixed itself it might be worth checking the JIRA logs to see what the root issue might have been.

On Mon, Feb 6, 2017 at 11:43 AM, Francois Budin <francois.budin at kitware.com<mailto:francois.budin at kitware.com>> wrote:
It works right now for me. Maybe the issue has been solved or maybe it is a network issue for you?
Francois

On Mon, Feb 6, 2017 at 10:54 AM, Taylor Braun-Jones <taylor at braun-jones.org<mailto:taylor at braun-jones.org>> wrote:
Hello,

Looks like JIRA is down. I was able to login, but most JIRA pages give me  "An internal server error occurred when requesting resource" error messages. On one page the error dump look like it was related to a full disk.

Taylor

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From bakkari.abdelkhalek at hotmail.fr  Tue Feb  7 06:29:48 2017
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Tue, 7 Feb 2017 11:29:48 +0000
Subject: [ITK] [ITK-users] Binary Contour Detection for 3D Image using ITK
	-	Thickness -
Message-ID: <AM2PR09MB05626AE920412B9B7080D01383430@AM2PR09MB0562.eurprd09.prod.outlook.com>

Dear ITK users,


After using the BinaryFillHoleFilter for a 3D Dicom image (see attached), I adopted the BinaryContourImageFilter in order to obtain the contour of the image.  However, the thikness of the contour is very big. My goal is to obtain 1 pixel of thickness.


The fragment of my code is :


------------------------------------------------------

#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkCannyEdgeDetectionImageFilter.h"
#include <itkBinaryContourImageFilter.h>
#include <vtkImageData.h>
#include <vtkExtractVOI.h>
#include <itkLabelToRGBImageFilter.h>
#include <itkImageToVTKImageFilter.h>
#include <itkVTKImageToImageFilter.h>
#include <vtkSmartPointer.h>

int main(int argc, char **argv)
{


       const unsigned int     Dimension = 3;
typedef unsigned char InputPixelType;
typedef unsigned char  OutputPixelType;

typedef itk::Image<InputPixelType, Dimension>  InputImageType;
typedef itk::Image<OutputPixelType, Dimension> OutputImageType;

typedef itk::ImageFileReader< InputImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName("BinaryFillHoleImage.mha");
reader->Update();

//Slice by Slice Binary Contour
// Binary Contour Filter
typedef itk::BinaryContourImageFilter <InputImageType, InputImageType > binaryContourImageFilterType;

binaryContourImageFilterType::Pointer binaryContourFilter = binaryContourImageFilterType::New ();
binaryContourFilter->SetInput(reader->GetOutput());
binaryContourFilter->SetFullyConnected(1); // true makes thicker contours
binaryContourFilter->SetBackgroundValue(0);
binaryContourFilter->SetForegroundValue(255); // the value of your binary mask
binaryContourFilter->Update();

typedef itk::RescaleIntensityImageFilter< InputImageType, InputImageType > RescaleType;
RescaleType::Pointer rescaler = RescaleType::New();
rescaler->SetInput( binaryContourFilter->GetOutput() );
rescaler->SetOutputMinimum( 0 );
rescaler->SetOutputMaximum( 255 );

typedef itk::CastImageFilter< InputImageType, OutputImageType > FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput( rescaler->GetOutput() );

// Save the contour
{
typedef itk::ImageFileWriter<OutputImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName("Cannybinarycontour.mha");
writer->SetInput(filter->GetOutput());

try{
writer->Update();
}
catch(itk::ExceptionObject &e)
{
std::cerr << e << std::endl;
}
}

    return EXIT_SUCCESS;
}


------------------------------------------------------


Thank you in advance.


Best regards,


Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland


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From dzenanz at gmail.com  Tue Feb  7 07:46:49 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 7 Feb 2017 07:46:49 -0500
Subject: [ITK] [ITK-users] Binary Contour Detection for 3D Image using
	ITK -	Thickness -
In-Reply-To: <AM2PR09MB05626AE920412B9B7080D01383430@AM2PR09MB0562.eurprd09.prod.outlook.com>
References: <AM2PR09MB05626AE920412B9B7080D01383430@AM2PR09MB0562.eurprd09.prod.outlook.com>
Message-ID: <CAPf2UMQGcFAq6qgaAKYc=Xe+1T_nNozUwdJKfh1JjNzveR8UuQ@mail.gmail.com>

Try SetUsePixelSpacingOff.

On Feb 7, 2017 06:30, "Abdelkhalek Bakkari" <bakkari.abdelkhalek at hotmail.fr>
wrote:

> Dear ITK users,
>
>
> After using the BinaryFillHoleFilter for a 3D Dicom image (see attached),
> I adopted the BinaryContourImageFilter in order to obtain the contour of
> the image.  However, the thikness of the contour is very big. My goal is to
> obtain 1 pixel of thickness.
>
>
> The fragment of my code is :
>
>
> ------------------------------------------------------
>
> #include "itkImage.h"
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
> #include "itkRescaleIntensityImageFilter.h"
> #include "itkCastImageFilter.h"
> #include "itkCannyEdgeDetectionImageFilter.h"
> #include <itkBinaryContourImageFilter.h>
> #include <vtkImageData.h>
> #include <vtkExtractVOI.h>
> #include <itkLabelToRGBImageFilter.h>
> #include <itkImageToVTKImageFilter.h>
> #include <itkVTKImageToImageFilter.h>
> #include <vtkSmartPointer.h>
>
> int main(int argc, char **argv)
> {
>
>        const unsigned int     Dimension = 3;
> typedef unsigned char InputPixelType;
> typedef unsigned char  OutputPixelType;
>
> typedef itk::Image<InputPixelType, Dimension>  InputImageType;
> typedef itk::Image<OutputPixelType, Dimension> OutputImageType;
>
> typedef itk::ImageFileReader< InputImageType > ReaderType;
> ReaderType::Pointer reader = ReaderType::New();
> reader->SetFileName("BinaryFillHoleImage.mha");
> reader->Update();
>
> //Slice by Slice Binary Contour
> // Binary Contour Filter
> typedef itk::BinaryContourImageFilter <InputImageType, InputImageType >
> binaryContourImageFilterType;
>
> binaryContourImageFilterType::Pointer binaryContourFilter =
> binaryContourImageFilterType::New ();
> binaryContourFilter->SetInput(reader->GetOutput());
> binaryContourFilter->SetFullyConnected(1); // true makes thicker contours
> binaryContourFilter->SetBackgroundValue(0);
> binaryContourFilter->SetForegroundValue(255); // the value of your binary
> mask
> binaryContourFilter->Update();
>
> typedef itk::RescaleIntensityImageFilter< InputImageType, InputImageType
> > RescaleType;
> RescaleType::Pointer rescaler = RescaleType::New();
> rescaler->SetInput( binaryContourFilter->GetOutput() );
> rescaler->SetOutputMinimum( 0 );
> rescaler->SetOutputMaximum( 255 );
>
> typedef itk::CastImageFilter< InputImageType, OutputImageType > FilterType;
> FilterType::Pointer filter = FilterType::New();
> filter->SetInput( rescaler->GetOutput() );
>
> // Save the contour
> {
> typedef itk::ImageFileWriter<OutputImageType> WriterType;
> WriterType::Pointer writer = WriterType::New();
> writer->SetFileName("Cannybinarycontour.mha");
> writer->SetInput(filter->GetOutput());
>
> try{
> writer->Update();
> }
> catch(itk::ExceptionObject &e)
> {
> std::cerr << e << std::endl;
> }
> }
>
>     return EXIT_SUCCESS;
> }
>
> ------------------------------------------------------
>
> Thank you in advance.
>
>
> Best regards,
>
>
> Abdelkhalek Bakkari
> Ph.D candidate in Computer Science
> Institute of Applied Computer Science
> Lodz University of Technology, Poland
>
>
>
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From bakkari.abdelkhalek at hotmail.fr  Tue Feb  7 08:33:41 2017
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Tue, 7 Feb 2017 13:33:41 +0000
Subject: [ITK] [ITK-users] Binary Contour Detection for 3D Image using
	ITK -	Thickness -
In-Reply-To: <CAPf2UMQGcFAq6qgaAKYc=Xe+1T_nNozUwdJKfh1JjNzveR8UuQ@mail.gmail.com>
References: <AM2PR09MB05626AE920412B9B7080D01383430@AM2PR09MB0562.eurprd09.prod.outlook.com>,
 <CAPf2UMQGcFAq6qgaAKYc=Xe+1T_nNozUwdJKfh1JjNzveR8UuQ@mail.gmail.com>
Message-ID: <AM2PR09MB0562A9B9B10FB88CCBDB230083430@AM2PR09MB0562.eurprd09.prod.outlook.com>

I am sorry but i did not find the SetUsePixelSpacingOff. Could you explain to me the way of using it. Also, what actually does it mean to turn off the spacing between slices and slice pixel and how is it related to contour generation .
Kind regards,

Sent from my iPhone

On 7 Feb 2017, at 13:46, D?enan Zuki? <dzenanz at gmail.com<mailto:dzenanz at gmail.com>> wrote:

Try SetUsePixelSpacingOff.

On Feb 7, 2017 06:30, "Abdelkhalek Bakkari" <bakkari.abdelkhalek at hotmail.fr<mailto:bakkari.abdelkhalek at hotmail.fr>> wrote:

Dear ITK users,


After using the BinaryFillHoleFilter for a 3D Dicom image (see attached), I adopted the BinaryContourImageFilter in order to obtain the contour of the image.  However, the thikness of the contour is very big. My goal is to obtain 1 pixel of thickness.


The fragment of my code is :


------------------------------------------------------

#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkCannyEdgeDetectionImageFilter.h"
#include <itkBinaryContourImageFilter.h>
#include <vtkImageData.h>
#include <vtkExtractVOI.h>
#include <itkLabelToRGBImageFilter.h>
#include <itkImageToVTKImageFilter.h>
#include <itkVTKImageToImageFilter.h>
#include <vtkSmartPointer.h>

int main(int argc, char **argv)
{


       const unsigned int     Dimension = 3;
typedef unsigned char InputPixelType;
typedef unsigned char  OutputPixelType;

typedef itk::Image<InputPixelType, Dimension>  InputImageType;
typedef itk::Image<OutputPixelType, Dimension> OutputImageType;

typedef itk::ImageFileReader< InputImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName("BinaryFillHoleImage.mha");
reader->Update();

//Slice by Slice Binary Contour
// Binary Contour Filter
typedef itk::BinaryContourImageFilter <InputImageType, InputImageType > binaryContourImageFilterType;

binaryContourImageFilterType::Pointer binaryContourFilter = binaryContourImageFilterType::New ();
binaryContourFilter->SetInput(reader->GetOutput());
binaryContourFilter->SetFullyConnected(1); // true makes thicker contours
binaryContourFilter->SetBackgroundValue(0);
binaryContourFilter->SetForegroundValue(255); // the value of your binary mask
binaryContourFilter->Update();

typedef itk::RescaleIntensityImageFilter< InputImageType, InputImageType > RescaleType;
RescaleType::Pointer rescaler = RescaleType::New();
rescaler->SetInput( binaryContourFilter->GetOutput() );
rescaler->SetOutputMinimum( 0 );
rescaler->SetOutputMaximum( 255 );

typedef itk::CastImageFilter< InputImageType, OutputImageType > FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput( rescaler->GetOutput() );

// Save the contour
{
typedef itk::ImageFileWriter<OutputImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName("Cannybinarycontour.mha");
writer->SetInput(filter->GetOutput());

try{
writer->Update();
}
catch(itk::ExceptionObject &e)
{
std::cerr << e << std::endl;
}
}

    return EXIT_SUCCESS;
}


------------------------------------------------------


Thank you in advance.


Best regards,


Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland


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From blowekamp at mail.nih.gov  Tue Feb  7 08:52:41 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 7 Feb 2017 13:52:41 +0000
Subject: [ITK] [ITK-users] Binary Contour Detection for 3D
	Image	using	ITK -	Thickness -
In-Reply-To: <AM2PR09MB0562A9B9B10FB88CCBDB230083430@AM2PR09MB0562.eurprd09.prod.outlook.com>
References: <AM2PR09MB05626AE920412B9B7080D01383430@AM2PR09MB0562.eurprd09.prod.outlook.com>
 <CAPf2UMQGcFAq6qgaAKYc=Xe+1T_nNozUwdJKfh1JjNzveR8UuQ@mail.gmail.com>
 <AM2PR09MB0562A9B9B10FB88CCBDB230083430@AM2PR09MB0562.eurprd09.prod.outlook.com>
Message-ID: <9E696551-65FF-4702-9A12-F685C8174AA6@mail.nih.gov>

Hello,

I believe that the BinaryCountourImageFilter operates in voxel space so the pixel spacing would not have an effect.

I think you are using the wrong metric to determine if the contour is ?1 pixel thick?. You need to remember that you are dealing with a 3D space where the contour is a 2-manifold in the 3-d space. That is to say your ?contour" has 2 dimensions of thickness and 1 dimension that only 1 pixel thick. If you have planar edges this can result in large areas that are solid contours. Please look at the results of ?unexpected? contours in the xy-plane xz-plane _and_ yz_ plane to understand the geometry.

Alternatively, if the requirement is to have each slice look like a 1-d contour you can run contour filter in the SliceBySliceImageFitler[1]. However, this will omit the edges that are between slices.

HTH,
Brad

[1] https://itk.org/Doxygen/html/classitk_1_1SliceBySliceImageFilter.html



On Feb 7, 2017, at 8:33 AM, Abdelkhalek Bakkari <bakkari.abdelkhalek at hotmail.fr<mailto:bakkari.abdelkhalek at hotmail.fr>> wrote:

I am sorry but i did not find the SetUsePixelSpacingOff. Could you explain to me the way of using it. Also, what actually does it mean to turn off the spacing between slices and slice pixel and how is it related to contour generation .
Kind regards,

Sent from my iPhone

On 7 Feb 2017, at 13:46, D?enan Zuki? <dzenanz at gmail.com<mailto:dzenanz at gmail.com>> wrote:

Try SetUsePixelSpacingOff.

On Feb 7, 2017 06:30, "Abdelkhalek Bakkari" <bakkari.abdelkhalek at hotmail.fr<mailto:bakkari.abdelkhalek at hotmail.fr>> wrote:

Dear ITK users,


After using the BinaryFillHoleFilter for a 3D Dicom image (see attached), I adopted the BinaryContourImageFilter in order to obtain the contour of the image.  However, the thikness of the contour is very big. My goal is to obtain 1 pixel of thickness.


The fragment of my code is :


------------------------------------------------------

#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkCannyEdgeDetectionImageFilter.h"
#include <itkBinaryContourImageFilter.h>
#include <vtkImageData.h>
#include <vtkExtractVOI.h>
#include <itkLabelToRGBImageFilter.h>
#include <itkImageToVTKImageFilter.h>
#include <itkVTKImageToImageFilter.h>
#include <vtkSmartPointer.h>

int main(int argc, char **argv)
{



       const unsigned int     Dimension = 3;
typedef unsigned char InputPixelType;
typedef unsigned char  OutputPixelType;

typedef itk::Image<InputPixelType, Dimension>  InputImageType;
typedef itk::Image<OutputPixelType, Dimension> OutputImageType;

typedef itk::ImageFileReader< InputImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName("BinaryFillHoleImage.mha");
reader->Update();

//Slice by Slice Binary Contour
// Binary Contour Filter
typedef itk::BinaryContourImageFilter <InputImageType, InputImageType > binaryContourImageFilterType;

binaryContourImageFilterType::Pointer binaryContourFilter = binaryContourImageFilterType::New ();
binaryContourFilter->SetInput(reader->GetOutput());
binaryContourFilter->SetFullyConnected(1); // true makes thicker contours
binaryContourFilter->SetBackgroundValue(0);
binaryContourFilter->SetForegroundValue(255); // the value of your binary mask
binaryContourFilter->Update();

typedef itk::RescaleIntensityImageFilter< InputImageType, InputImageType > RescaleType;
RescaleType::Pointer rescaler = RescaleType::New();
rescaler->SetInput( binaryContourFilter->GetOutput() );
rescaler->SetOutputMinimum( 0 );
rescaler->SetOutputMaximum( 255 );

typedef itk::CastImageFilter< InputImageType, OutputImageType > FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput( rescaler->GetOutput() );

// Save the contour
{
typedef itk::ImageFileWriter<OutputImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName("Cannybinarycontour.mha");
writer->SetInput(filter->GetOutput());

try{
writer->Update();
}
catch(itk::ExceptionObject &e)
{
std::cerr << e << std::endl;
}
}

    return EXIT_SUCCESS;
}




------------------------------------------------------


Thank you in advance.



Best regards,


Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland


_____________________________________
Powered by www.kitware.com<http://www.kitware.com>

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http://www.itk.org/Wiki/ITK_FAQ

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From francois.budin at kitware.com  Tue Feb  7 13:57:48 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Tue, 7 Feb 2017 13:57:48 -0500
Subject: [ITK] ITK fails to build with clang 4.0
In-Reply-To: <CAOc73CAXbtkvr=ydUUK_zUaxa8NwseB0--ULNZexmKGtLTT-tg@mail.gmail.com>
References: <CAOc73CAXbtkvr=ydUUK_zUaxa8NwseB0--ULNZexmKGtLTT-tg@mail.gmail.com>
Message-ID: <CAHwLD2VGeoxyaPv6Nz7qS=9gmH=VCWFZ6hzYv4jxPuLEjxd_7w@mail.gmail.com>

Hi Ben,

Thanks for the report! The issue has been addressed in ITK [1] and a patch
has been submitted upstream in VXL [2] to solve the issue in that library.
To test the new version, you can download the ITK git repository.

Hope this helps,
Francois

[1] http://review.source.kitware.com/#/c/22043/
[2] https://github.com/vxl/vxl/pull/374

On Sun, Feb 5, 2017 at 8:24 AM, Ben Woods <woodsb02 at gmail.com> wrote:

> Hi everyone,
>
> ITK fails to build with the new clang compiler version 4.0.
>
> The specific build error is:
>
> Modules/ThirdParty/VNL/src/vxl/v3p/netlib/linalg/lsqrBase.cxx:565:14: error: ordered comparison between pointer and zero ('std::ostream *' (aka 'basic_ostream<char> *') and 'int')
>     if (nout > 0)
>         ~~~~ ^ ~
>
> build log: http://package18.nyi.freebsd.org/data/headamd64PR216008-default/2017-01-29_16h09m05s/logs/errors/InsightToolkit-4.10.1.log
> regressed by: https://github.com/llvm-mirror/clang/commit/4b6ad14285f3
>
>
> This was originally raised on the FreeBSD issue tracker here:
> https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=216617
>
> Could somebody please look into this, and perhaps raise it on the Jira ITK
> issue tracker? (I am having trouble creating an account).
>
> Regards,
> Ben
>
> --
> From: Benjamin Woods
> woodsb02 at gmail.com
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From insight-users at itk.org  Tue Feb  7 15:16:28 2017
From: insight-users at itk.org (Vova via Insight-users)
Date: Tue, 7 Feb 2017 20:16:28 +0000 (UTC)
Subject: [ITK] [ITK-users] ITK TubeTK Module
References: <872656895.3037131.1486498588647.ref@mail.yahoo.com>
Message-ID: <872656895.3037131.1486498588647@mail.yahoo.com>

Hi
New version of ITK 4.11 has TubeTK module included there.
When I am trying to Generate the project in CMake (windows 10) following successful configuration step I am getting the ?error:
CMake Error in Modules/Remote/TubeTKITK/Base/Registration/CMakeLists.txt:
Target "TubeTKRegistration" INTERFACE_INCLUDE_DIRECTORIES property contains
path:

"D:/ITK/InsightToolkit-4.11.0/Modules/Remote/TubeTKITK/Base/Registration"

which is prefixed in the source directory.

CMake Error in Modules/Remote/TubeTKITK/Base/Segmentation/CMakeLists.txt:
Target "TubeTKSegmentation" INTERFACE_INCLUDE_DIRECTORIES property contains
path:

"D:/ITK/InsightToolkit-4.11.0/Modules/Remote/TubeTKITK/Base/Segmentation"

which is prefixed in the source directory.
Is there any way around this problem for CMake to generate the project ?
Regards,
Vlad.
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From matt.mccormick at kitware.com  Tue Feb  7 15:21:41 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 7 Feb 2017 15:21:41 -0500
Subject: [ITK] [ITK-users] ITK TubeTK Module
In-Reply-To: <872656895.3037131.1486498588647@mail.yahoo.com>
References: <872656895.3037131.1486498588647.ref@mail.yahoo.com>
 <872656895.3037131.1486498588647@mail.yahoo.com>
Message-ID: <CALzTN-Tiyyx9u-u4jS4LmO7LBkQJhREVyvRbv8Wo9_xswAkyeg@mail.gmail.com>

Hi Vlad,

This module was merged pre-maturely and is still a work in progress.

Thanks,
Matt

On Tue, Feb 7, 2017 at 3:16 PM, Vova via Insight-users
<insight-users at itk.org> wrote:
> Hi
>
> New version of ITK 4.11 has TubeTK module included there.
>
> When I am trying to Generate the project in CMake (windows 10) following
> successful configuration step I am getting the  error:
>
> CMake Error in Modules/Remote/TubeTKITK/Base/Registration/CMakeLists.txt:
> Target "TubeTKRegistration" INTERFACE_INCLUDE_DIRECTORIES property contains
> path:
>
> "D:/ITK/InsightToolkit-4.11.0/Modules/Remote/TubeTKITK/Base/Registration"
>
> which is prefixed in the source directory.
>
> CMake Error in Modules/Remote/TubeTKITK/Base/Segmentation/CMakeLists.txt:
> Target "TubeTKSegmentation" INTERFACE_INCLUDE_DIRECTORIES property contains
> path:
>
> "D:/ITK/InsightToolkit-4.11.0/Modules/Remote/TubeTKITK/Base/Segmentation"
>
> which is prefixed in the source directory.
>
> Is there any way around this problem for CMake to generate the project ?
>
> Regards,
>
> Vlad.
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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From blowekamp at mail.nih.gov  Wed Feb  8 08:34:28 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 8 Feb 2017 13:34:28 +0000
Subject: [ITK] [ITK-dev] InDoxygenGroup Test  with Python 3.6 failures
Message-ID: <DCED0E2A-9C4B-4AE9-8CB2-91ED96F29644@mail.nih.gov>

Hello,

We had Python 3.6 installed on several build servers yesterday. This is resulting in failure of the InDoxygenGroup tests:
https://open.cdash.org/viewTest.php?onlyfailed&buildid=4758514

It looks like the mcdoc.py script need to be updated.

Test output

Traceback (most recent call last):
  File "C:/d/itk-vs9-64rs/ITK/CMake/../Utilities/Doxygen/mcdoc.py", line 175, in <module>
    ret = main()
  File "C:/d/itk-vs9-64rs/ITK/CMake/../Utilities/Doxygen/mcdoc.py", line 139, in main
    ret = max( ret, checkGroup(fname2, module) )
  File "C:/d/itk-vs9-64rs/ITK/CMake/../Utilities/Doxygen/mcdoc.py", line 84, in checkGroup
    if not re.search(r"\ingroup .*"+group+"(\s|$)", dcontent, re.MULTILINE):
  File "C:\Python36\lib\re.py", line 182, in search
    return _compile(pattern, flags).search(string)
  File "C:\Python36\lib\re.py", line 301, in _compile
    p = sre_compile.compile(pattern, flags)
  File "C:\Python36\lib\sre_compile.py", line 562, in compile
    p = sre_parse.parse(p, flags)
  File "C:\Python36\lib\sre_parse.py", line 856, in parse
    p = _parse_sub(source, pattern, flags & SRE_FLAG_VERBOSE, False)
  File "C:\Python36\lib\sre_parse.py", line 415, in _parse_sub
    itemsappend(_parse(source, state, verbose))
  File "C:\Python36\lib\sre_parse.py", line 501, in _parse
    code = _escape(source, this, state)
  File "C:\Python36\lib\sre_parse.py", line 401, in _escape
    raise source.error("bad escape %s" % escape, len(escape))
sre_constants.error: bad escape \i at position 0

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From deman.pierre at gmail.com  Wed Feb  8 12:10:06 2017
From: deman.pierre at gmail.com (pdeman)
Date: Wed, 8 Feb 2017 10:10:06 -0700 (MST)
Subject: [ITK] [ITK-users] problem installation from git
Message-ID: <1486573806190-7589605.post@n2.nabble.com>

Hi,

I have made a git clone, did the "configuration" using ccmake.
I am working on ubuntu 14.04
and now, when I try to do the make, I have an error message saying "Protocol
https not supported or disabled in libcurl" but they are enabled...
I have the last version of curl and done the configuration --with-ssl.
I have SSL support: enabled (OpenSSL)
and Protocols: ... HTTP HTTPS etc ...

I don't get the error ...

regards



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/problem-installation-from-git-tp7589605.html
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_____________________________________
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From francois.budin at kitware.com  Wed Feb  8 14:31:30 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 8 Feb 2017 14:31:30 -0500
Subject: [ITK] [ITK-users] problem installation from git
In-Reply-To: <1486573806190-7589605.post@n2.nabble.com>
References: <1486573806190-7589605.post@n2.nabble.com>
Message-ID: <CAHwLD2Xx22xwGJVEvVcstSy+eGFROR366WwsK5H=W5L6gC2MOA@mail.gmail.com>

Hello Pierre,

Did you compile CMake yourself or are you using the one packaged with
Ubuntu 14.04?
Could you run the following commands on your computer and let us know what
results you got?
1) cmake --version
2) which cmake
3) strings `which cmake` |grep OPENSSL

Thanks,
Francois


On Wed, Feb 8, 2017 at 12:10 PM, pdeman <deman.pierre at gmail.com> wrote:

> Hi,
>
> I have made a git clone, did the "configuration" using ccmake.
> I am working on ubuntu 14.04
> and now, when I try to do the make, I have an error message saying
> "Protocol
> https not supported or disabled in libcurl" but they are enabled...
> I have the last version of curl and done the configuration --with-ssl.
> I have SSL support: enabled (OpenSSL)
> and Protocols: ... HTTP HTTPS etc ...
>
> I don't get the error ...
>
> regards
>
>
>
> --
> View this message in context: http://itk-insight-users.
> 2283740.n2.nabble.com/problem-installation-from-git-tp7589605.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
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From francois.budin at kitware.com  Wed Feb  8 15:25:51 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 8 Feb 2017 15:25:51 -0500
Subject: [ITK] [ITK-dev] InDoxygenGroup Test with Python 3.6 failures
In-Reply-To: <DCED0E2A-9C4B-4AE9-8CB2-91ED96F29644@mail.nih.gov>
References: <DCED0E2A-9C4B-4AE9-8CB2-91ED96F29644@mail.nih.gov>
Message-ID: <CAHwLD2WxOi-xi9ijnsK_R7=qdYK7AdF0YWwgpyo1-P4PDiPmRQ@mail.gmail.com>

Thanks for the report. I have submitted a patch to address this error.

Please review http://review.source.kitware.com/#/c/22051/

Francois

On Wed, Feb 8, 2017 at 8:34 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Hello,
>
> We had Python 3.6 installed on several build servers yesterday. This is
> resulting in failure of the InDoxygenGroup tests:
> https://open.cdash.org/viewTest.php?onlyfailed&buildid=4758514
>
> It looks like the mcdoc.py script need to be updated.
>
> *Test output*
>
> Traceback (most recent call last):
>   File "C:/d/itk-vs9-64rs/ITK/CMake/../Utilities/Doxygen/mcdoc.py", line 175, in <module>
>     ret = main()
>   File "C:/d/itk-vs9-64rs/ITK/CMake/../Utilities/Doxygen/mcdoc.py", line 139, in main
>     ret = max( ret, checkGroup(fname2, module) )
>   File "C:/d/itk-vs9-64rs/ITK/CMake/../Utilities/Doxygen/mcdoc.py", line 84, in checkGroup
>     if not re.search(r"\ingroup .*"+group+"(\s|$)", dcontent, re.MULTILINE):
>   File "C:\Python36\lib\re.py", line 182, in search
>     return _compile(pattern, flags).search(string)
>   File "C:\Python36\lib\re.py", line 301, in _compile
>     p = sre_compile.compile(pattern, flags)
>   File "C:\Python36\lib\sre_compile.py", line 562, in compile
>     p = sre_parse.parse(p, flags)
>   File "C:\Python36\lib\sre_parse.py", line 856, in parse
>     p = _parse_sub(source, pattern, flags & SRE_FLAG_VERBOSE, False)
>   File "C:\Python36\lib\sre_parse.py", line 415, in _parse_sub
>     itemsappend(_parse(source, state, verbose))
>   File "C:\Python36\lib\sre_parse.py", line 501, in _parse
>     code = _escape(source, this, state)
>   File "C:\Python36\lib\sre_parse.py", line 401, in _escape
>     raise source.error("bad escape %s" % escape, len(escape))
> sre_constants.error: bad escape \i at position 0
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
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From deman.pierre at gmail.com  Thu Feb  9 06:13:15 2017
From: deman.pierre at gmail.com (pdeman)
Date: Thu, 9 Feb 2017 04:13:15 -0700 (MST)
Subject: [ITK] [ITK-users] problem installation from git
In-Reply-To: <CAHwLD2Xx22xwGJVEvVcstSy+eGFROR366WwsK5H=W5L6gC2MOA@mail.gmail.com>
References: <1486573806190-7589605.post@n2.nabble.com>
 <CAHwLD2Xx22xwGJVEvVcstSy+eGFROR366WwsK5H=W5L6gC2MOA@mail.gmail.com>
Message-ID: <CAKqjrL2h6BuhJfo2efy+FdvKhFYhWHXXKKWuZtVaiAattrsU1g@mail.gmail.com>

Hi,

I add to download a version of cmake.
so I have the version 3.5.2 now.
which cmake give me /usr/local/bin/cmake

I haven't get what I have to type for 3.
if I copy directly without changing anything
i have "no return", no error but nothing is replied.

Thanks

On Wed, Feb 8, 2017 at 8:32 PM, Francois Budin-3 [via ITK Insight Users] <
ml-node+s2283740n7589606h40 at n2.nabble.com> wrote:

> Hello Pierre,
>
> Did you compile CMake yourself or are you using the one packaged with
> Ubuntu 14.04?
> Could you run the following commands on your computer and let us know what
> results you got?
> 1) cmake --version
> 2) which cmake
> 3) strings `which cmake` |grep OPENSSL
>
> Thanks,
> Francois
>
>
> On Wed, Feb 8, 2017 at 12:10 PM, pdeman <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=7589606&i=0>> wrote:
>
>> Hi,
>>
>> I have made a git clone, did the "configuration" using ccmake.
>> I am working on ubuntu 14.04
>> and now, when I try to do the make, I have an error message saying
>> "Protocol
>> https not supported or disabled in libcurl" but they are enabled...
>> I have the last version of curl and done the configuration --with-ssl.
>> I have SSL support: enabled (OpenSSL)
>> and Protocols: ... HTTP HTTPS etc ...
>>
>> I don't get the error ...
>>
>> regards
>>
>>
>>
>> --
>> View this message in context: http://itk-insight-users.22837
>> 40.n2.nabble.com/problem-installation-from-git-tp7589605.html
>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> 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://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
>
> ------------------------------
> If you reply to this email, your message will be added to the discussion
> below:
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Mobile : +33 7 82 57 80 94




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From dzenanz at gmail.com  Thu Feb  9 10:02:32 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 9 Feb 2017 10:02:32 -0500
Subject: [ITK] [ITK-users] problem installation from git
In-Reply-To: <CAKqjrL2h6BuhJfo2efy+FdvKhFYhWHXXKKWuZtVaiAattrsU1g@mail.gmail.com>
References: <1486573806190-7589605.post@n2.nabble.com>
 <CAHwLD2Xx22xwGJVEvVcstSy+eGFROR366WwsK5H=W5L6gC2MOA@mail.gmail.com>
 <CAKqjrL2h6BuhJfo2efy+FdvKhFYhWHXXKKWuZtVaiAattrsU1g@mail.gmail.com>
Message-ID: <CAPf2UMTOMMB8uLa=gRU8N+mU5OfQkuYPZ9aB5iP+obH=sF3WbQ@mail.gmail.com>

Hi Pierre,

your original problem was that CMake was not built with SSL support. If you
built it yourself, enable SSL support by e.g. linking to system curl.
Probably the easiest solution is to download <https://cmake.org/download/>
a pre-compiled binary for your OS and use that.

Regards,
D?enan

On Thu, Feb 9, 2017 at 6:13 AM, pdeman <deman.pierre at gmail.com> wrote:

> Hi,
>
> I add to download a version of cmake.
> so I have the version 3.5.2 now.
> which cmake give me /usr/local/bin/cmake
>
> I haven't get what I have to type for 3.
> if I copy directly without changing anything
> i have "no return", no error but nothing is replied.
>
> Thanks
>
> On Wed, Feb 8, 2017 at 8:32 PM, Francois Budin-3 [via ITK Insight Users] <
> ml-node+s2283740n7589606h40 at n2.nabble.com> wrote:
>
> > Hello Pierre,
> >
> > Did you compile CMake yourself or are you using the one packaged with
> > Ubuntu 14.04?
> > Could you run the following commands on your computer and let us know
> what
> > results you got?
> > 1) cmake --version
> > 2) which cmake
> > 3) strings `which cmake` |grep OPENSSL
> >
> > Thanks,
> > Francois
> >
> >
> > On Wed, Feb 8, 2017 at 12:10 PM, pdeman <[hidden email]
> > <http:///user/SendEmail.jtp?type=node&node=7589606&i=0>> wrote:
> >
> >> Hi,
> >>
> >> I have made a git clone, did the "configuration" using ccmake.
> >> I am working on ubuntu 14.04
> >> and now, when I try to do the make, I have an error message saying
> >> "Protocol
> >> https not supported or disabled in libcurl" but they are enabled...
> >> I have the last version of curl and done the configuration --with-ssl.
> >> I have SSL support: enabled (OpenSSL)
> >> and Protocols: ... HTTP HTTPS etc ...
> >>
> >> I don't get the error ...
> >>
> >> regards
> >>
> >>
> >>
> >> --
> >> View this message in context: http://itk-insight-users.22837
> >> 40.n2.nabble.com/problem-installation-from-git-tp7589605.html
> >> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> >> _____________________________________
> >> Powered by www.kitware.com
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
> >> Kitware offers ITK Training Courses, for more information visit:
> >> http://www.kitware.com/products/protraining.php
> >>
> >> 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://public.kitware.com/mailman/listinfo/insight-users
> >>
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > 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://public.kitware.com/mailman/listinfo/insight-users
> >
> >
> > ------------------------------
> > If you reply to this email, your message will be added to the discussion
> > below:
> > http://itk-insight-users.2283740.n2.nabble.com/problem-
> > installation-from-git-tp7589605p7589606.html
> > To unsubscribe from problem installation from git, click here
> > <http://itk-insight-users.2283740.n2.nabble.com/
> template/NamlServlet.jtp?macro=unsubscribe_by_code&node=7589605&code=
> ZGVtYW4ucGllcnJlQGdtYWlsLmNvbXw3NTg5NjA1fDIxMDcyMjE0Mzc=>
> > .
> > NAML
> > <http://itk-insight-users.2283740.n2.nabble.com/
> template/NamlServlet.jtp?macro=macro_viewer&id=instant_
> html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.
> BasicNamespace-nabble.view.web.template.NabbleNamespace-
> nabble.view.web.template.NodeNamespace&breadcrumbs=
> notify_subscribers%21nabble%3Aemail.naml-instant_emails%
> 21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
> >
>
>
>
> --
> DEMAN Pierre
> Mobile : +33 7 82 57 80 94
>
>
>
>
> --
> View this message in context: http://itk-insight-users.
> 2283740.n2.nabble.com/problem-installation-from-git-tp7589605p7589609.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From tofijoy at gmail.com  Thu Feb  9 17:54:14 2017
From: tofijoy at gmail.com (Fijoy Vadakkumpadan)
Date: Thu, 9 Feb 2017 17:54:14 -0500
Subject: [ITK] Size of pixel component type
Message-ID: <CAHE0P1XRreNhGhBmOZdBbW14sYLQnw_hUM5CfmsF9yqAj=oQ+A@mail.gmail.com>

Hello,

If I read an image file (of unknown pixel type) into an itk::Image object
using ITK, will the component type of a pixel of that image object be the
same, regardless of the environment (C++ compiler, hardware, etc.)?

If yes, can I assume that the sizes for each component type are as follows?

UCHAR & CHAR        - 1 byte
USHORT & SHORT    - 2 bytes
UINT, INT, & FLOAT    - 4 bytes
ULONG, LONG, & DOUBLE         - 8 bytes

The method I'm using to read an image of unknown type is similar to the one
at this link:
https://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html

Thank you,
--Fijoy
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From matt.mccormick at kitware.com  Thu Feb  9 18:11:14 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 9 Feb 2017 18:11:14 -0500
Subject: [ITK] Size of pixel component type
In-Reply-To: <CAHE0P1XRreNhGhBmOZdBbW14sYLQnw_hUM5CfmsF9yqAj=oQ+A@mail.gmail.com>
References: <CAHE0P1XRreNhGhBmOZdBbW14sYLQnw_hUM5CfmsF9yqAj=oQ+A@mail.gmail.com>
Message-ID: <CALzTN-TLA0Ot56Ezk4j4QCraq9Rb4m0cwzX0U2T9FMHo494T_g@mail.gmail.com>

Hi Fijoy,

They are generally pretty consistent, but unfortunately unsigned long
and long are usually 4 bytes on Windows but are 8 bytes on Unix-like
systems.

HTH,
Matt

On Thu, Feb 9, 2017 at 5:54 PM, Fijoy Vadakkumpadan <tofijoy at gmail.com> wrote:
> Hello,
>
> If I read an image file (of unknown pixel type) into an itk::Image object
> using ITK, will the component type of a pixel of that image object be the
> same, regardless of the environment (C++ compiler, hardware, etc.)?
>
> If yes, can I assume that the sizes for each component type are as follows?
>
> UCHAR & CHAR        - 1 byte
> USHORT & SHORT    - 2 bytes
> UINT, INT, & FLOAT    - 4 bytes
> ULONG, LONG, & DOUBLE         - 8 bytes
>
> The method I'm using to read an image of unknown type is similar to the one
> at this link:
> https://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html
>
> Thank you,
> --Fijoy
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From deman.pierre at gmail.com  Fri Feb 10 02:48:24 2017
From: deman.pierre at gmail.com (pdeman)
Date: Fri, 10 Feb 2017 00:48:24 -0700 (MST)
Subject: [ITK] [ITK-users] problem installation from git
In-Reply-To: <CAPf2UMTOMMB8uLa=gRU8N+mU5OfQkuYPZ9aB5iP+obH=sF3WbQ@mail.gmail.com>
References: <1486573806190-7589605.post@n2.nabble.com>
 <CAHwLD2Xx22xwGJVEvVcstSy+eGFROR366WwsK5H=W5L6gC2MOA@mail.gmail.com>
 <CAKqjrL2h6BuhJfo2efy+FdvKhFYhWHXXKKWuZtVaiAattrsU1g@mail.gmail.com>
 <CAPf2UMTOMMB8uLa=gRU8N+mU5OfQkuYPZ9aB5iP+obH=sF3WbQ@mail.gmail.com>
Message-ID: <CAKqjrL3Zk4MJAKKijzhs6KjEh4aXCT4ZjtPRQzdiKPODnGaHvQ@mail.gmail.com>

Hi,
I have download the binary for cmake 3.8.
but in a terminal if I do cmake --version it's still the 3.5.

How do I make the 3.8 the by default one ?

Pierre

On Thu, Feb 9, 2017 at 4:03 PM, dzenanz [via ITK Insight Users] <
ml-node+s2283740n7589610h64 at n2.nabble.com> wrote:

> Hi Pierre,
>
> your original problem was that CMake was not built with SSL support. If
> you built it yourself, enable SSL support by e.g. linking to system curl.
> Probably the easiest solution is to download <https://cmake.org/download/>
> a pre-compiled binary for your OS and use that.
>
> Regards,
> D?enan
>
> On Thu, Feb 9, 2017 at 6:13 AM, pdeman <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=7589610&i=0>> wrote:
>
>> Hi,
>>
>> I add to download a version of cmake.
>> so I have the version 3.5.2 now.
>> which cmake give me /usr/local/bin/cmake
>>
>> I haven't get what I have to type for 3.
>> if I copy directly without changing anything
>> i have "no return", no error but nothing is replied.
>>
>> Thanks
>>
>> On Wed, Feb 8, 2017 at 8:32 PM, Francois Budin-3 [via ITK Insight Users] <
>> [hidden email] <http:///user/SendEmail.jtp?type=node&node=7589610&i=1>>
>> wrote:
>>
>> > Hello Pierre,
>> >
>> > Did you compile CMake yourself or are you using the one packaged with
>> > Ubuntu 14.04?
>> > Could you run the following commands on your computer and let us know
>> what
>> > results you got?
>> > 1) cmake --version
>> > 2) which cmake
>> > 3) strings `which cmake` |grep OPENSSL
>> >
>> > Thanks,
>> > Francois
>> >
>> >
>> > On Wed, Feb 8, 2017 at 12:10 PM, pdeman <[hidden email]
>> > <http:///user/SendEmail.jtp?type=node&node=7589606&i=0>> wrote:
>> >
>> >> Hi,
>> >>
>> >> I have made a git clone, did the "configuration" using ccmake.
>> >> I am working on ubuntu 14.04
>> >> and now, when I try to do the make, I have an error message saying
>> >> "Protocol
>> >> https not supported or disabled in libcurl" but they are enabled...
>> >> I have the last version of curl and done the configuration --with-ssl.
>> >> I have SSL support: enabled (OpenSSL)
>> >> and Protocols: ... HTTP HTTPS etc ...
>> >>
>> >> I don't get the error ...
>> >>
>> >> regards
>> >>
>> >>
>> >>
>> >> --
>> >> View this message in context: http://itk-insight-users.22837
>> >> 40.n2.nabble.com/problem-installation-from-git-tp7589605.html
>> >> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> >> _____________________________________
>> >> Powered by www.kitware.com
>> >>
>> >> Visit other Kitware open-source projects at
>> >> http://www.kitware.com/opensource/opensource.html
>> >>
>> >> Kitware offers ITK Training Courses, for more information visit:
>> >> http://www.kitware.com/products/protraining.php
>> >>
>> >> 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://public.kitware.com/mailman/listinfo/insight-users
>> >>
>> >
>> >
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > 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://public.kitware.com/mailman/listinfo/insight-users
>> >
>> >
>> > ------------------------------
>> > If you reply to this email, your message will be added to the discussion
>> > below:
>> > http://itk-insight-users.2283740.n2.nabble.com/problem-
>> > installation-from-git-tp7589605p7589606.html
>> > To unsubscribe from problem installation from git, click here
>> > <http://itk-insight-users.2283740.n2.nabble.com/template/
>> NamlServlet.jtp?macro=unsubscribe_by_code&node=
>> 7589605&code=ZGVtYW4ucGllcnJlQGdtYWlsLmNvbXw3NTg5NjA1fDIxMDcyMjE0Mzc=>
>> > .
>> > NAML
>> > <http://itk-insight-users.2283740.n2.nabble.com/template/
>> NamlServlet.jtp?macro=macro_viewer&id=instant_html%
>> 21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNa
>> mespace-nabble.view.web.template.NabbleNamespace-nabbl
>> e.view.web.template.NodeNamespace&breadcrumbs=notify_
>> subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%
>> 3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>> >
>>
>>
>>
>> --
>> DEMAN Pierre
>> Mobile : <a href="tel:%2B33%207%2082%2057%2080%2094" value="+33782578094
>> <+33%207%2082%2057%2080%2094>">+33 7 82 57 80 94
>> <+33%207%2082%2057%2080%2094>
>>
>>
>>
>>
>> --
>> View this message in context: http://itk-insight-users.22837
>> 40.n2.nabble.com/problem-installation-from-git-tp7589605p7589609.html
>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> 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://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
>
> ------------------------------
> If you reply to this email, your message will be added to the discussion
> below:
> http://itk-insight-users.2283740.n2.nabble.com/problem-
> installation-from-git-tp7589605p7589610.html
> To unsubscribe from problem installation from git, click here
> <http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=7589605&code=ZGVtYW4ucGllcnJlQGdtYWlsLmNvbXw3NTg5NjA1fDIxMDcyMjE0Mzc=>
> .
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> <http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>



-- 
DEMAN Pierre
Mobile : +33 7 82 57 80 94




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/problem-installation-from-git-tp7589605p7589611.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
_____________________________________
Powered by www.kitware.com

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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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From cr at neuro.ma.uni-heidelberg.de  Fri Feb 10 08:02:16 2017
From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith)
Date: Fri, 10 Feb 2017 14:02:16 +0100
Subject: [ITK] [ITK-users] Fwd: Re:  problem installation from git
In-Reply-To: <e6e3cb80-a777-18e5-ae0b-ad21a1cbaa39@neuro.ma.uni-heidelberg.de>
References: <e6e3cb80-a777-18e5-ae0b-ad21a1cbaa39@neuro.ma.uni-heidelberg.de>
Message-ID: <e47da5b5-d458-c558-b589-6236d4b3b673@neuro.ma.uni-heidelberg.de>

forgot to send a copy to the list...



-------- Forwarded Message --------
Subject: 	Re: [ITK-users] problem installation from git
Date: 	Fri, 10 Feb 2017 11:01:58 +0100
From: 	Chr. Rossmanith <cr at neuro.ma.uni-heidelberg.de>
To: 	pdeman <deman.pierre at gmail.com>



Hi,

sounds like your PATH variable is set to a value, that cmake 3.5 is
found first. Where did you install cmake 3.8? Make sure that this path
is listed before the cmake 3.5 path in your PATH variable.

1) echo $PATH   shows you the list of paths searched for executables
2) locate -b '\cmake'|grep bin     shows you where cmake executables are
living on your machine

Regards,
Christina

On 10.02.2017 08:48, pdeman wrote:
> Hi,I have download the binary for cmake 3.8.but in a terminal if I do cmake --version it's still the 3.5.
> How do I make the 3.8 the by default one ?
> Pierre
> On Thu, Feb 9, 2017 at 4:03 PM, dzenanz [via ITK Insight Users] <ml-node+s2283740n7589610h64 at n2.nabble.com> wrote:
>> Hi Pierre,>> your original problem was that CMake was not built with SSL support. If> you built it yourself, enable SSL support by e.g. linkingto system curl.> Probably the easiest solution is to download <https://cmake.org/download/>> a pre-compiled binary for your OS and use that.>> Regards,> D?enan>> On Thu, Feb 9, 2017 at 6:13 AM, pdeman <[hidden email]> <http:///user/SendEmail.jtp?type=node&node=7589610&i=0>> wrote:>>> Hi,>>>> I add to download a version of cmake.>> so I have the version 3.5.2 now.>> which cmake give me /usr/local/bin/cmake>>>> I haven't getwhat I have to type for 3.>> if I copy directly without changing anything>> i have "no return", no error but nothing is replied.>>>> Thanks>>>> On Wed, Feb 8, 2017 at 8:32 PM, Francois Budin-3 [via ITK Insight Users] <>> [hidden email] <http:///user/SendEmail.jtp?type=node&node=7589610&i=1>>>> wrote:>>>> > Hello Pierre,>> >>> > Did you compile CMake yourself or are you using the one packaged with>> > Ubuntu 14.04?>> > Could yourun the following commands on your computer and let us know>> what>> > results you got?>> > 1) cmake --version>> > 2) which cmake>> > 3) strings `which cmake` |grep OPENSSL>> >>> > Thanks,>> > Francois>> >>> >>> > On Wed, Feb 8, 2017 at 12:10 PM, pdeman <[hidden email]>> > <http:///user/SendEmail.jtp?type=node&node=7589606&i=0>> wrote:>> >>> >> Hi,>> >>>> >> I have made a git clone, did the "configuration" using ccmake.>> >> I am working on ubuntu 14.04>> >> and now, when I try to do the make, I have an error message saying>> >> "Protocol>> >> https not supported or disabled in libcurl" but they are enabled...>> >> I have the last version of curl and done the configuration --with-ssl.>> >> I have SSL support: enabled (OpenSSL)>> >> and Protocols: ... HTTP HTTPS etc ...>> >>>> >> I don't get the error ...>> >>>> >> regards>> >>>> >>>> >>>> >> -->> >> View this message in context: http://itk-insight-users.22837>> >> 40.n2.nabble.com/problem-installation-from-git-tp7589605.html>> >> Sent from the ITK Insight Users mailing list archive at Nabble.com.>> >> _____________________________________>> >> Powered by www.kitware.com>> >>>> >> Visit other Kitware open-source projects at>> >> http://www.kitware.com/opensource/opensource.html>> >>>> >> Kitware offers ITK Training Courses, for more information visit:>> >> http://www.kitware.com/products/protraining.php>> >>>> >> 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://public.kitware.com/mailman/listinfo/insight-users>> >>>>>>> >>> > _____________________________________>> > Powered by www.kitware.com>> >>> > Visit other Kitware open-source projects at>> > http://www.kitware.com/opensource/opensource.html>> >>> > Kitware offers ITK Training Courses, for more information visit:>> > http://www.kitware.com/products/protraining.php>> >>> > 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://public.kitware.com/mailman/listinfo/insight-users>> >>> >>> > ------------------------------>> > If you replyto this email, your message will be added to the discussion>> > below:>>> http://itk-insight-users.2283740.n2.nabble.com/problem->> > installation-from-git-tp7589605p7589606.html>> > To unsubscribe from problem installation from git, click here>> > <http://itk-insight-users.2283740.n2.nabble.com/template/>> NamlServlet.jtp?macro=unsubscribe_by_code&node=>> 7589605&code=ZGVtYW4ucGllcnJlQGdtYWlsLmNvbXw3NTg5NjA1fDIxMDcyMjE0Mzc=>>> > .>> > NAML>> > <http://itk-insight-users.2283740.n2.nabble.com/template/>> NamlServlet.jtp?macro=macro_viewer&id=instant_html%>> 21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNa>> mespace-nabble.view.web.template.NabbleNamespace-nabbl>> e.view.web.template.NodeNamespace&breadcrumbs=notify_>> subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%>> 3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>>> >>>>>>>>> -->> DEMAN Pierre>> Mobile : <a href="tel:%2B33%207%2082%2057%2080%2094" value="+33782578094>> <+33%207%2082%2057%2080%2094>">+33 7 82 57 80 94>> <+33%207%2082%2057%2080%2094>>>>>>>>>>> -->> View this message in context: http://itk-insight-users.22837>> 40.n2.nabble.com/problem-installation-from-git-tp7589605p7589609.html>> Sent from the ITK Insight Users mailing list archive at Nabble.com.>> _____________________________________>> Powered by www.kitware.com>>>> Visit other Kitware open-source projects at>> http://www.kitware.com/opensource/opensource.html>>>> Kitwareoffers ITK Training Courses, for more information visit:>> http://www.kitware.com/products/protraining.php>>>> 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://public.kitware.com/mailman/listinfo/insight-users>>>>> _____________________________________> Powered by www.kitware.com>> Visit other Kitware open-source projects at> http://www.kitware.com/opensource/opensource.html>> Kitware offers ITK Training Courses, for more information visit:> http://www.kitware.com/products/protraining.php>> 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://public.kitware.com/mailman/listinfo/insight-users>>> ------------------------------> If you reply to this email, your message will be added to the discussion> below:> http://itk-insight-users.2283740.n2.nabble.com/problem-> installation-from-git-tp7589605p7589610.html> To unsubscribe from problem installation from git, click here> <http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=7589605&code=ZGVtYW4ucGllcnJlQGdtYWlsLmNvbXw3NTg5NjA1fDIxMDcyMjE0Mzc=>> .> NAML> <http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>>
>
> -- DEMAN PierreMobile : +33 7 82 57 80 94
>
>
>
> --View this message in context: http://itk-insight-users.2283740.n2.nabble.com/problem-installation-from-git-tp7589605p7589611.htmlSent from theITK Insight Users mailing list archive at Nabble.com._____________________________________Powered by www.kitware.com
> Visit other Kitware open-source projects athttp://www.kitware.com/opensource/opensource.html
> Kitware offers ITK Training Courses, for more information visit:http://www.kitware.com/products/protraining.php
> 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://public.kitware.com/mailman/listinfo/insight-users



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Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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From blowekamp at mail.nih.gov  Fri Feb 10 09:57:46 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 10 Feb 2017 14:57:46 +0000
Subject: [ITK] [ITK-dev] Topic for the release branch
Message-ID: <36D0128D-C927-4C6C-91E3-8ADE60F52CC0@mail.nih.gov>

Hello,

This patch fixes a valgrind defect detected by SimpleITK:
http://review.source.kitware.com/#/c/22049/

Can this please be merged into the release branch ASAP?

Thanks,
Brad
_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

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From francois.budin at kitware.com  Fri Feb 10 10:18:51 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Fri, 10 Feb 2017 10:18:51 -0500
Subject: [ITK] [ITK-dev] Topic for the release branch
In-Reply-To: <36D0128D-C927-4C6C-91E3-8ADE60F52CC0@mail.nih.gov>
References: <36D0128D-C927-4C6C-91E3-8ADE60F52CC0@mail.nih.gov>
Message-ID: <CAHwLD2WEFNj6==oZ+u_if8AvmvjpKne1n08eVdZG7fz1-Bq2iA@mail.gmail.com>

Done [1].

[1] https://itk.org/gitweb?p=ITK.git;a=shortlog;h=refs/heads/release

On Fri, Feb 10, 2017 at 9:57 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Hello,
>
> This patch fixes a valgrind defect detected by SimpleITK:
> http://review.source.kitware.com/#/c/22049/
>
> Can this please be merged into the release branch ASAP?
>
> Thanks,
> Brad
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-developers
>
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_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From matt.mccormick at kitware.com  Fri Feb 10 10:30:42 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 10 Feb 2017 10:30:42 -0500
Subject: [ITK] Insight Toolkit on ResearchGate
Message-ID: <CALzTN-QMFbzsebr8WLZ4xoCPrnuBDrWOW_RrAZR3fKdsNNLR1g@mail.gmail.com>

Hi folks,

To improve project exposure, I created an "Insight Toolkit (ITK)"
project on ResearchGate:

https://www.researchgate.net/project/Insight-Toolkit-ITK

Researchers can "Follow" updates related to the project.

If you have a ResearchGate account and would like to be added as a
Collaborator on the project, please let me know. Sharing updates on
your ITK-related work is welcome and encouraged.

Thanks,
Matt

From matt.mccormick at kitware.com  Fri Feb 10 10:32:02 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 10 Feb 2017 10:32:02 -0500
Subject: [ITK] ITK on GitHub
Message-ID: <CALzTN-RA4OKdSngEMEjT4n+5Y7QnPXGFFoseTurinU9EHi5o2g@mail.gmail.com>

Hi folks,

To help improve project exposure, please "star" the ITK GitHub repository:

  https://github.com/InsightSoftwareConsortium/ITK

Thanks,
Matt

From blowekamp at mail.nih.gov  Fri Feb 10 10:41:05 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 10 Feb 2017 15:41:05 +0000
Subject: [ITK] Insight Toolkit on ResearchGate
In-Reply-To: <CALzTN-QMFbzsebr8WLZ4xoCPrnuBDrWOW_RrAZR3fKdsNNLR1g@mail.gmail.com>
References: <CALzTN-QMFbzsebr8WLZ4xoCPrnuBDrWOW_RrAZR3fKdsNNLR1g@mail.gmail.com>
Message-ID: <9AA8F45B-23E4-43AE-9148-503B7F0047A5@mail.nih.gov>

Matt,

This sounds like a great idea to promote ITK and related projects.

I would appreciate being added to the project.

Thanks,
Brad

> On Feb 10, 2017, at 10:30 AM, Matt McCormick <matt.mccormick at kitware.com> wrote:
> 
> Hi folks,
> 
> To improve project exposure, I created an "Insight Toolkit (ITK)"
> project on ResearchGate:
> 
> https://www.researchgate.net/project/Insight-Toolkit-ITK
> 
> Researchers can "Follow" updates related to the project.
> 
> If you have a ResearchGate account and would like to be added as a
> Collaborator on the project, please let me know. Sharing updates on
> your ITK-related work is welcome and encouraged.
> 
> Thanks,
> Matt
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From matt.mccormick at kitware.com  Fri Feb 10 11:01:09 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 10 Feb 2017 11:01:09 -0500
Subject: [ITK] Insight Toolkit on ResearchGate
In-Reply-To: <9AA8F45B-23E4-43AE-9148-503B7F0047A5@mail.nih.gov>
References: <CALzTN-QMFbzsebr8WLZ4xoCPrnuBDrWOW_RrAZR3fKdsNNLR1g@mail.gmail.com>
 <9AA8F45B-23E4-43AE-9148-503B7F0047A5@mail.nih.gov>
Message-ID: <CALzTN-QnKD_9HYcG7YWoL_1W-5DZf1=TEHRtcbqsx6RMCs2mMQ@mail.gmail.com>

Will do.

I am finding a limitation in their system: your account must either
co-author an indexed article with my account or follow my account:

  https://www.researchgate.net/profile/Matthew_Mccormick2

to be listed on the project correctly.

Thanks,
Matt

On Fri, Feb 10, 2017 at 10:41 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
<blowekamp at mail.nih.gov> wrote:
> Matt,
>
> This sounds like a great idea to promote ITK and related projects.
>
> I would appreciate being added to the project.
>
> Thanks,
> Brad
>
>> On Feb 10, 2017, at 10:30 AM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>>
>> Hi folks,
>>
>> To improve project exposure, I created an "Insight Toolkit (ITK)"
>> project on ResearchGate:
>>
>> https://www.researchgate.net/project/Insight-Toolkit-ITK
>>
>> Researchers can "Follow" updates related to the project.
>>
>> If you have a ResearchGate account and would like to be added as a
>> Collaborator on the project, please let me know. Sharing updates on
>> your ITK-related work is welcome and encouraged.
>>
>> Thanks,
>> Matt
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>

From bakkari.abdelkhalek at hotmail.fr  Fri Feb 10 15:45:37 2017
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Fri, 10 Feb 2017 20:45:37 +0000
Subject: [ITK] [ITK-users] Watershed for 3D Image Segmentation - One Seed
	Point -
Message-ID: <HE1PR09MB0572B52D3B64C1DF9DAF974683440@HE1PR09MB0572.eurprd09.prod.outlook.com>

Dear ITK users,


I Would like to know if there is an algorithm in ITK that is proposed for a semi-automatic segmentation of three-dimensional images.

One seed location should be chosen like in Region Growing.

Thank you in advance.

Best regards,


Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland


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Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From richard.beare at gmail.com  Fri Feb 10 16:00:12 2017
From: richard.beare at gmail.com (Richard Beare)
Date: Sat, 11 Feb 2017 08:00:12 +1100
Subject: [ITK] [ITK-users] Watershed for 3D Image Segmentation - One
	Seed	Point -
In-Reply-To: <HE1PR09MB0572B52D3B64C1DF9DAF974683440@HE1PR09MB0572.eurprd09.prod.outlook.com>
References: <HE1PR09MB0572B52D3B64C1DF9DAF974683440@HE1PR09MB0572.eurprd09.prod.outlook.com>
Message-ID: <CA+V7QS-PzGSwoLXNA6aoh9mdJ3_=Ba=jm5yDHUZRPYXXQWxXZg@mail.gmail.com>

The greedy approaches, like MorphologicalWatershedFromMarkers, require 2
seeds. One is the background seed. Sometimes that can be something very
simple like the image boundary. The advantage of greedy approaches is that
you don't need to specify stopping conditions. The cost is obviously the
extra seed. Another advantage is that most  of the methods naturally
support lots of independent seeds, if you want them.

On Sat, Feb 11, 2017 at 7:45 AM, Abdelkhalek Bakkari <
bakkari.abdelkhalek at hotmail.fr> wrote:

> Dear ITK users,
>
>
> I Would like to know if there is an algorithm in ITK that is proposed for a semi-automatic segmentation of three-dimensional images.
>
> One seed location should be chosen like in Region Growing.
>
> Thank you in advance.
>
> Best regards,
>
>
> Abdelkhalek Bakkari
> Ph.D candidate in Computer Science
> Institute of Applied Computer Science
> Lodz University of Technology, Poland
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
>
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From tobias.wood at kcl.ac.uk  Fri Feb 10 17:02:49 2017
From: tobias.wood at kcl.ac.uk (Wood, Tobias)
Date: Fri, 10 Feb 2017 22:02:49 +0000
Subject: [ITK] Bruker Format
In-Reply-To: <41096FAF-701D-44C8-84F0-2850E31E15E5@kcl.ac.uk>
References: <ABBCA68C-6975-408C-BD46-B092320B04CB@kcl.ac.uk>
 <CAPf2UMQ8TyPWVqu_uRd2=ryyS_YVeT5W-6RmzOEs3TfvH+V26A@mail.gmail.com>
 <CALzTN-Ss32S2NPMXt7pWDsqpPZTW2bwvB093L2qG=peuDv9mzQ@mail.gmail.com>
 <41096FAF-701D-44C8-84F0-2850E31E15E5@kcl.ac.uk>
Message-ID: <AD7C8283-8314-46DE-86F3-EAD0D73C49E9@kcl.ac.uk>

Hello,

I?ve made some progress on rewriting the Bruker code. I?m stuck on when the ImageIO classes should apply scalings/offsets.

Bruker?s default data type is INT16. They store a scaling and offset that must be applied to the data. For whatever reason, the scaling tends to very small - about 1e-5. Hence a lot of values should be scaled down to < 1. Obviously, if this is done at INT16 precision then most of the data is rounded to zero and lost.

I tried to copy the NifiIO class which also applies scaling (See lines 707 onwarsds in itkNiftiImageIO.cxx). However - if I read this correctly, it is applying the scaling at the precision/datatype of the image file, not the PixelType requested by the itkImage template parameter to itkImageFileReader.

At what point is the buffer read by the ImageIO classes converted to the PixelType of the requested itkImage? How do I supply the scaling and offset to this conversion?

As always, I hope I?m missing something obvious.
Thanks,
Toby

On 16/01/2017, 09:27, "Wood, Tobias" <tobias.wood at kcl.ac.uk> wrote:

    >    In addition to ?D?enan's suggestion, the code could be cleaned up, moved out of the ITKReview module, and placed in its own module in the IO group. This will enable it to be automatically registered like the other ImageIOs. 
        
    Thanks Matt and D?enan, that?s what I was wondering. I will experiment with the code and submit a patch if I find time.
    
    Best wishes,
    Toby
    
    


From dzenanz at gmail.com  Fri Feb 10 18:43:13 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 10 Feb 2017 18:43:13 -0500
Subject: [ITK] Bruker Format
In-Reply-To: <AD7C8283-8314-46DE-86F3-EAD0D73C49E9@kcl.ac.uk>
References: <ABBCA68C-6975-408C-BD46-B092320B04CB@kcl.ac.uk>
 <CAPf2UMQ8TyPWVqu_uRd2=ryyS_YVeT5W-6RmzOEs3TfvH+V26A@mail.gmail.com>
 <CALzTN-Ss32S2NPMXt7pWDsqpPZTW2bwvB093L2qG=peuDv9mzQ@mail.gmail.com>
 <41096FAF-701D-44C8-84F0-2850E31E15E5@kcl.ac.uk>
 <AD7C8283-8314-46DE-86F3-EAD0D73C49E9@kcl.ac.uk>
Message-ID: <CAPf2UMSaOwW+CHjv75hmKXMH+5REjicBPDgpK8pqZjfaRU_kew@mail.gmail.com>

Hi Tobias,

reading is done in function void NiftiImageIO::Read(void *buffer) in
file C:\Dev\ITK-git\Modules\IO\NIFTI\src\itkNiftiImageIO.cxx

This function is supposed to read image data from disk into the given
buffer pointer. The data type of this buffer is of this->m_ComponentType.
In case that NIFTI reader detects it needs to do rescale/slope
transformation (in function ReadImageInformation), it says that
this->m_ComponentType=FLOAT, no matter what is the real component type on
disk. Then Read reads the image data, converts it to float, does
rescale/slope transformation in place (float to float).

Later ImageFileReader (which calls ImageIO::Read()) does C++ cast from
this->m_ComponentType into the type with which ImageFileReader was
instantiated.

Regards,
D?enan

On Fri, Feb 10, 2017 at 5:02 PM, Wood, Tobias <tobias.wood at kcl.ac.uk> wrote:

> Hello,
>
> I?ve made some progress on rewriting the Bruker code. I?m stuck on when
> the ImageIO classes should apply scalings/offsets.
>
> Bruker?s default data type is INT16. They store a scaling and offset that
> must be applied to the data. For whatever reason, the scaling tends to very
> small - about 1e-5. Hence a lot of values should be scaled down to < 1.
> Obviously, if this is done at INT16 precision then most of the data is
> rounded to zero and lost.
>
> I tried to copy the NifiIO class which also applies scaling (See lines 707
> onwarsds in itkNiftiImageIO.cxx). However - if I read this correctly, it is
> applying the scaling at the precision/datatype of the image file, not the
> PixelType requested by the itkImage template parameter to
> itkImageFileReader.
>
> At what point is the buffer read by the ImageIO classes converted to the
> PixelType of the requested itkImage? How do I supply the scaling and offset
> to this conversion?
>
> As always, I hope I?m missing something obvious.
> Thanks,
> Toby
>
> On 16/01/2017, 09:27, "Wood, Tobias" <tobias.wood at kcl.ac.uk> wrote:
>
>     >    In addition to ?D?enan's suggestion, the code could be cleaned
> up, moved out of the ITKReview module, and placed in its own module in the
> IO group. This will enable it to be automatically registered like the other
> ImageIOs.
>
>     Thanks Matt and D?enan, that?s what I was wondering. I will experiment
> with the code and submit a patch if I find time.
>
>     Best wishes,
>     Toby
>
>
>
>
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From dzenanz at gmail.com  Fri Feb 10 18:44:55 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 10 Feb 2017 18:44:55 -0500
Subject: [ITK] Bruker Format
In-Reply-To: <CAPf2UMSaOwW+CHjv75hmKXMH+5REjicBPDgpK8pqZjfaRU_kew@mail.gmail.com>
References: <ABBCA68C-6975-408C-BD46-B092320B04CB@kcl.ac.uk>
 <CAPf2UMQ8TyPWVqu_uRd2=ryyS_YVeT5W-6RmzOEs3TfvH+V26A@mail.gmail.com>
 <CALzTN-Ss32S2NPMXt7pWDsqpPZTW2bwvB093L2qG=peuDv9mzQ@mail.gmail.com>
 <41096FAF-701D-44C8-84F0-2850E31E15E5@kcl.ac.uk>
 <AD7C8283-8314-46DE-86F3-EAD0D73C49E9@kcl.ac.uk>
 <CAPf2UMSaOwW+CHjv75hmKXMH+5REjicBPDgpK8pqZjfaRU_kew@mail.gmail.com>
Message-ID: <CAPf2UMSkpN7qnQUCPbVHcNKeCn3fuvDXiFtcKVYsoYS5tnCx1Q@mail.gmail.com>

This alternation of behavior is accomplished by this check:
  if ( this->MustRescale() )
    {
    if ( this->m_ComponentType == CHAR
         || this->m_ComponentType == UCHAR
         || this->m_ComponentType == SHORT
         || this->m_ComponentType == USHORT
         || this->m_ComponentType == INT
         || this->m_ComponentType == UINT
         || this->m_ComponentType == LONG
         || this->m_ComponentType == ULONG )
      {
      this->m_ComponentType = FLOAT;
      }
    }

Regards

On Fri, Feb 10, 2017 at 6:43 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Tobias,
>
> reading is done in function void NiftiImageIO::Read(void *buffer) in
> file C:\Dev\ITK-git\Modules\IO\NIFTI\src\itkNiftiImageIO.cxx
>
> This function is supposed to read image data from disk into the given
> buffer pointer. The data type of this buffer is of this->m_ComponentType.
> In case that NIFTI reader detects it needs to do rescale/slope
> transformation (in function ReadImageInformation), it says that
> this->m_ComponentType=FLOAT, no matter what is the real component type on
> disk. Then Read reads the image data, converts it to float, does
> rescale/slope transformation in place (float to float).
>
> Later ImageFileReader (which calls ImageIO::Read()) does C++ cast from
> this->m_ComponentType into the type with which ImageFileReader was
> instantiated.
>
> Regards,
> D?enan
>
> On Fri, Feb 10, 2017 at 5:02 PM, Wood, Tobias <tobias.wood at kcl.ac.uk>
> wrote:
>
>> Hello,
>>
>> I?ve made some progress on rewriting the Bruker code. I?m stuck on when
>> the ImageIO classes should apply scalings/offsets.
>>
>> Bruker?s default data type is INT16. They store a scaling and offset that
>> must be applied to the data. For whatever reason, the scaling tends to very
>> small - about 1e-5. Hence a lot of values should be scaled down to < 1.
>> Obviously, if this is done at INT16 precision then most of the data is
>> rounded to zero and lost.
>>
>> I tried to copy the NifiIO class which also applies scaling (See lines
>> 707 onwarsds in itkNiftiImageIO.cxx). However - if I read this correctly,
>> it is applying the scaling at the precision/datatype of the image file, not
>> the PixelType requested by the itkImage template parameter to
>> itkImageFileReader.
>>
>> At what point is the buffer read by the ImageIO classes converted to the
>> PixelType of the requested itkImage? How do I supply the scaling and offset
>> to this conversion?
>>
>> As always, I hope I?m missing something obvious.
>> Thanks,
>> Toby
>>
>> On 16/01/2017, 09:27, "Wood, Tobias" <tobias.wood at kcl.ac.uk> wrote:
>>
>>     >    In addition to ?D?enan's suggestion, the code could be cleaned
>> up, moved out of the ITKReview module, and placed in its own module in the
>> IO group. This will enable it to be automatically registered like the other
>> ImageIOs.
>>
>>     Thanks Matt and D?enan, that?s what I was wondering. I will
>> experiment with the code and submit a patch if I find time.
>>
>>     Best wishes,
>>     Toby
>>
>>
>>
>>
>
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From bakkari.abdelkhalek at hotmail.fr  Sat Feb 11 10:58:16 2017
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Sat, 11 Feb 2017 15:58:16 +0000
Subject: [ITK] [ITK-users] Watershed for 3D Image Segmentation - One
 Seed Point -
In-Reply-To: <CA+V7QS-PzGSwoLXNA6aoh9mdJ3_=Ba=jm5yDHUZRPYXXQWxXZg@mail.gmail.com>
References: <HE1PR09MB0572B52D3B64C1DF9DAF974683440@HE1PR09MB0572.eurprd09.prod.outlook.com>,
 <CA+V7QS-PzGSwoLXNA6aoh9mdJ3_=Ba=jm5yDHUZRPYXXQWxXZg@mail.gmail.com>
Message-ID: <AM2PR09MB0562F97ED9E4D3A4A55D179683470@AM2PR09MB0562.eurprd09.prod.outlook.com>

Dear Dr Richard Beare,


I am trying your code source which is published in the insight journal about the " The watershed transform in ITK - discussion and new developments".


I debugged the perf3D and mperf3D. However, in the mperf3D, it needs two input images. Could you please explain for me the way of adopting it for a .mha file ?


Thank you in advance.


Best regards,


Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland




________________________________
From: Richard Beare <richard.beare at gmail.com>
Sent: 10 February 2017 22:00
To: Abdelkhalek Bakkari
Cc: insight-users
Subject: Re: [ITK-users] Watershed for 3D Image Segmentation - One Seed Point -

The greedy approaches, like MorphologicalWatershedFromMarkers, require 2 seeds. One is the background seed. Sometimes that can be something very simple like the image boundary. The advantage of greedy approaches is that you don't need to specify stopping conditions. The cost is obviously the extra seed. Another advantage is that most  of the methods naturally support lots of independent seeds, if you want them.

On Sat, Feb 11, 2017 at 7:45 AM, Abdelkhalek Bakkari <bakkari.abdelkhalek at hotmail.fr<mailto:bakkari.abdelkhalek at hotmail.fr>> wrote:

Dear ITK users,


I Would like to know if there is an algorithm in ITK that is proposed for a semi-automatic segmentation of three-dimensional images.

One seed location should be chosen like in Region Growing.

Thank you in advance.

Best regards,


Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland



_____________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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://public.kitware.com/mailman/listinfo/insight-users


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_____________________________________
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Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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From richard.beare at gmail.com  Sat Feb 11 16:41:54 2017
From: richard.beare at gmail.com (Richard Beare)
Date: Sun, 12 Feb 2017 08:41:54 +1100
Subject: [ITK] [ITK-users] Watershed for 3D Image Segmentation - One
	Seed	Point -
In-Reply-To: <AM2PR09MB0562F97ED9E4D3A4A55D179683470@AM2PR09MB0562.eurprd09.prod.outlook.com>
References: <HE1PR09MB0572B52D3B64C1DF9DAF974683440@HE1PR09MB0572.eurprd09.prod.outlook.com>
 <CA+V7QS-PzGSwoLXNA6aoh9mdJ3_=Ba=jm5yDHUZRPYXXQWxXZg@mail.gmail.com>
 <AM2PR09MB0562F97ED9E4D3A4A55D179683470@AM2PR09MB0562.eurprd09.prod.outlook.com>
Message-ID: <CA+V7QS_ds6EAZJvAWfB0TH5R9xX9hPG7pXTELkb4x4K_i4LcTA@mail.gmail.com>

The usual thing I do when testing watersheds in a new application is to
manually create marker images using an image segmentation tool, such as
itksnap or fslview. The format of the image doesn't matter, as long as ITK
can read it. The key thing is to make sure you save a label image - i.e one
with each marker having a different voxel value. This gives you an idea of
how sensitive the problem is to marker placement and what sort of control
image you might need.

On Sun, Feb 12, 2017 at 2:58 AM, Abdelkhalek Bakkari <
bakkari.abdelkhalek at hotmail.fr> wrote:

> Dear Dr Richard Beare,
>
>
> I am trying your code source which is published in the insight journal
> about the " The watershed transform in ITK - discussion and new
> developments".
>
>
> I debugged the perf3D and mperf3D. However, in the mperf3D, it needs two
> input images. Could you please explain for me the way of adopting it for a
> .mha file ?
>
>
> Thank you in advance.
>
>
> Best regards,
>
>
> Abdelkhalek Bakkari
> Ph.D candidate in Computer Science
> Institute of Applied Computer Science
> Lodz University of Technology, Poland
>
>
>
>
> ------------------------------
> *From:* Richard Beare <richard.beare at gmail.com>
> *Sent:* 10 February 2017 22:00
> *To:* Abdelkhalek Bakkari
> *Cc:* insight-users
> *Subject:* Re: [ITK-users] Watershed for 3D Image Segmentation - One Seed
> Point -
>
> The greedy approaches, like MorphologicalWatershedFromMarkers, require 2
> seeds. One is the background seed. Sometimes that can be something very
> simple like the image boundary. The advantage of greedy approaches is that
> you don't need to specify stopping conditions. The cost is obviously the
> extra seed. Another advantage is that most  of the methods naturally
> support lots of independent seeds, if you want them.
>
> On Sat, Feb 11, 2017 at 7:45 AM, Abdelkhalek Bakkari <
> bakkari.abdelkhalek at hotmail.fr> wrote:
>
>> Dear ITK users,
>>
>>
>> I Would like to know if there is an algorithm in ITK that is proposed for a semi-automatic segmentation of three-dimensional images.
>>
>> One seed location should be chosen like in Region Growing.
>>
>> Thank you in advance.
>>
>> Best regards,
>>
>>
>> Abdelkhalek Bakkari
>> Ph.D candidate in Computer Science
>> Institute of Applied Computer Science
>> Lodz University of Technology, Poland
>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> 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://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
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_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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://public.kitware.com/mailman/listinfo/insight-users

From tobias.wood at kcl.ac.uk  Sat Feb 11 17:21:33 2017
From: tobias.wood at kcl.ac.uk (Wood, Tobias)
Date: Sat, 11 Feb 2017 22:21:33 +0000
Subject: [ITK] Bruker Format
In-Reply-To: <CAAKhGh-Psk=-M_+7dWhcq7vtt8SXkxrNWAmf5ODecqXmbvF74w@mail.gmail.com>
References: <ABBCA68C-6975-408C-BD46-B092320B04CB@kcl.ac.uk>
 <CAPf2UMQ8TyPWVqu_uRd2=ryyS_YVeT5W-6RmzOEs3TfvH+V26A@mail.gmail.com>
 <CALzTN-Ss32S2NPMXt7pWDsqpPZTW2bwvB093L2qG=peuDv9mzQ@mail.gmail.com>
 <41096FAF-701D-44C8-84F0-2850E31E15E5@kcl.ac.uk>
 <AD7C8283-8314-46DE-86F3-EAD0D73C49E9@kcl.ac.uk>
 <CAPf2UMSaOwW+CHjv75hmKXMH+5REjicBPDgpK8pqZjfaRU_kew@mail.gmail.com>
 <CAPf2UMSkpN7qnQUCPbVHcNKeCn3fuvDXiFtcKVYsoYS5tnCx1Q@mail.gmail.com>
 <CAAKhGh-Psk=-M_+7dWhcq7vtt8SXkxrNWAmf5ODecqXmbvF74w@mail.gmail.com>
Message-ID: <28971E3C-41E7-41D4-9ED8-373D69A90A30@kcl.ac.uk>

Hi Dzenan,

> In case that NIFTI reader detects it needs to do rescale/slope transformation (in function ReadImageInformation), it says that this->m_ComponentType=FLOAT, no matter what is the real component type on disk. Then Read reads the image data, converts it to float, does rescale/slope transformation in place (float to float).

Thanks so much - I had missed this part. I have copied the NIFTI code, and the rescaling is working now. There are two functions (CastCopy and RescaleFunction) that I have copied & pasted - these could go into a common file somewhere, but I have no idea where is appropriate in the ITK heirarchy.

> On 11/02/2017, 16:18, "Jon Haitz Legarreta" <jhlegarreta at vicomtech.org> wrote:
> Hi Tobias,
> if you are to move the classes out of review/external module, please provide a test (if it does not already exist).
> I can help you if required. You can add me as a reviewer to the gerrit topic.
> Kind regards,
> JON HAITZ

Hi Jon,

There does not appear to be a meaningful test at the moment - only a skeleton file that doesn?t actually test anything. I would like to implement a test but I?m not planning on extending the class to be able to write as well as read Bruker.  I have no use case for this, and I doubt anyone else would either. Hence without checking an actual file into the repo I?m not sure what test would be useful?

I will work on this code more before submitting it to gerrit - there are a lot of corner cases I haven?t implemented yet.

Best wishes,
Toby


From dzenanz at gmail.com  Sat Feb 11 19:45:21 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 11 Feb 2017 19:45:21 -0500
Subject: [ITK] Bruker Format
In-Reply-To: <28971E3C-41E7-41D4-9ED8-373D69A90A30@kcl.ac.uk>
References: <ABBCA68C-6975-408C-BD46-B092320B04CB@kcl.ac.uk>
 <CAPf2UMQ8TyPWVqu_uRd2=ryyS_YVeT5W-6RmzOEs3TfvH+V26A@mail.gmail.com>
 <CALzTN-Ss32S2NPMXt7pWDsqpPZTW2bwvB093L2qG=peuDv9mzQ@mail.gmail.com>
 <41096FAF-701D-44C8-84F0-2850E31E15E5@kcl.ac.uk>
 <AD7C8283-8314-46DE-86F3-EAD0D73C49E9@kcl.ac.uk>
 <CAPf2UMSaOwW+CHjv75hmKXMH+5REjicBPDgpK8pqZjfaRU_kew@mail.gmail.com>
 <CAPf2UMSkpN7qnQUCPbVHcNKeCn3fuvDXiFtcKVYsoYS5tnCx1Q@mail.gmail.com>
 <CAAKhGh-Psk=-M_+7dWhcq7vtt8SXkxrNWAmf5ODecqXmbvF74w@mail.gmail.com>
 <28971E3C-41E7-41D4-9ED8-373D69A90A30@kcl.ac.uk>
Message-ID: <CAPf2UMQVqn8nQSh7AnGWVCQ72T+8AW6LGMYxKJEU_Mxu8uQhSA@mail.gmail.com>

Hi Tobias,

you can see the inheritance
<https://itk.org/Doxygen/html/classitk_1_1ImageIOBase.html> diagram of
ImageIOs (you have to click to expand). If you want to have some things
common with NIFTIImageIO, you could create a new class (you could call it
RescalableImageBase or something like that), and have both Bruker and Nifti
inherit from it (similar to how a few IOs inherit from IPLCommonImageIO).
Of course, put common methods inside that class. But CastCopy and
RescaleFunction are so small that I don't think it is nearly worth the
effort.

Regards,
D?enan

On Sat, Feb 11, 2017 at 5:21 PM, Wood, Tobias <tobias.wood at kcl.ac.uk> wrote:

> Hi Dzenan,
>
> > In case that NIFTI reader detects it needs to do rescale/slope
> transformation (in function ReadImageInformation), it says that
> this->m_ComponentType=FLOAT, no matter what is the real component type on
> disk. Then Read reads the image data, converts it to float, does
> rescale/slope transformation in place (float to float).
>
> Thanks so much - I had missed this part. I have copied the NIFTI code, and
> the rescaling is working now. There are two functions (CastCopy and
> RescaleFunction) that I have copied & pasted - these could go into a common
> file somewhere, but I have no idea where is appropriate in the ITK
> heirarchy.
>
> > On 11/02/2017, 16:18, "Jon Haitz Legarreta" <jhlegarreta at vicomtech.org>
> wrote:
> > Hi Tobias,
> > if you are to move the classes out of review/external module, please
> provide a test (if it does not already exist).
> > I can help you if required. You can add me as a reviewer to the gerrit
> topic.
> > Kind regards,
> > JON HAITZ
>
> Hi Jon,
>
> There does not appear to be a meaningful test at the moment - only a
> skeleton file that doesn?t actually test anything. I would like to
> implement a test but I?m not planning on extending the class to be able to
> write as well as read Bruker.  I have no use case for this, and I doubt
> anyone else would either. Hence without checking an actual file into the
> repo I?m not sure what test would be useful?
>
> I will work on this code more before submitting it to gerrit - there are a
> lot of corner cases I haven?t implemented yet.
>
> Best wishes,
> Toby
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
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From jhlegarreta at vicomtech.org  Sun Feb 12 04:33:28 2017
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Sun, 12 Feb 2017 10:33:28 +0100
Subject: [ITK] Bruker Format
In-Reply-To: <CAPf2UMQVqn8nQSh7AnGWVCQ72T+8AW6LGMYxKJEU_Mxu8uQhSA@mail.gmail.com>
References: <ABBCA68C-6975-408C-BD46-B092320B04CB@kcl.ac.uk>
 <CAPf2UMQ8TyPWVqu_uRd2=ryyS_YVeT5W-6RmzOEs3TfvH+V26A@mail.gmail.com>
 <CALzTN-Ss32S2NPMXt7pWDsqpPZTW2bwvB093L2qG=peuDv9mzQ@mail.gmail.com>
 <41096FAF-701D-44C8-84F0-2850E31E15E5@kcl.ac.uk>
 <AD7C8283-8314-46DE-86F3-EAD0D73C49E9@kcl.ac.uk>
 <CAPf2UMSaOwW+CHjv75hmKXMH+5REjicBPDgpK8pqZjfaRU_kew@mail.gmail.com>
 <CAPf2UMSkpN7qnQUCPbVHcNKeCn3fuvDXiFtcKVYsoYS5tnCx1Q@mail.gmail.com>
 <CAAKhGh-Psk=-M_+7dWhcq7vtt8SXkxrNWAmf5ODecqXmbvF74w@mail.gmail.com>
 <28971E3C-41E7-41D4-9ED8-373D69A90A30@kcl.ac.uk>
 <CAPf2UMQVqn8nQSh7AnGWVCQ72T+8AW6LGMYxKJEU_Mxu8uQhSA@mail.gmail.com>
Message-ID: <CAAKhGh8c6f+MOSNyYCHdkGugihSg73DGxP3ufsL8Dsr9go-fyA@mail.gmail.com>

Hi Tobias,
as for the testing, ITK will require an input file and checking that your
contribution is working as expected, and that all new/refactored code is
being covered by the test case.

I haven't had a look myself into the existing Bruker-related classes, and
even if writing is not within your plans, if progress is made concerning
the reading part, I think it is already worthwhile.

So sounds like a good plan; once you think you have something to share,
submitting to gerrit will allow us to make further progress concerning the
testing.

Kind regards,
JON HAITZ


--


On 12 February 2017 at 01:45, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Tobias,
>
> you can see the inheritance
> <https://itk.org/Doxygen/html/classitk_1_1ImageIOBase.html> diagram of
> ImageIOs (you have to click to expand). If you want to have some things
> common with NIFTIImageIO, you could create a new class (you could call it
> RescalableImageBase or something like that), and have both Bruker and Nifti
> inherit from it (similar to how a few IOs inherit from IPLCommonImageIO).
> Of course, put common methods inside that class. But CastCopy and
> RescaleFunction are so small that I don't think it is nearly worth the
> effort.
>
> Regards,
> D?enan
>
> On Sat, Feb 11, 2017 at 5:21 PM, Wood, Tobias <tobias.wood at kcl.ac.uk>
> wrote:
>
>> Hi Dzenan,
>>
>> > In case that NIFTI reader detects it needs to do rescale/slope
>> transformation (in function ReadImageInformation), it says that
>> this->m_ComponentType=FLOAT, no matter what is the real component type on
>> disk. Then Read reads the image data, converts it to float, does
>> rescale/slope transformation in place (float to float).
>>
>> Thanks so much - I had missed this part. I have copied the NIFTI code,
>> and the rescaling is working now. There are two functions (CastCopy and
>> RescaleFunction) that I have copied & pasted - these could go into a common
>> file somewhere, but I have no idea where is appropriate in the ITK
>> heirarchy.
>>
>> > On 11/02/2017, 16:18, "Jon Haitz Legarreta" <jhlegarreta at vicomtech.org>
>> wrote:
>> > Hi Tobias,
>> > if you are to move the classes out of review/external module, please
>> provide a test (if it does not already exist).
>> > I can help you if required. You can add me as a reviewer to the gerrit
>> topic.
>> > Kind regards,
>> > JON HAITZ
>>
>> Hi Jon,
>>
>> There does not appear to be a meaningful test at the moment - only a
>> skeleton file that doesn?t actually test anything. I would like to
>> implement a test but I?m not planning on extending the class to be able to
>> write as well as read Bruker.  I have no use case for this, and I doubt
>> anyone else would either. Hence without checking an actual file into the
>> repo I?m not sure what test would be useful?
>>
>> I will work on this code more before submitting it to gerrit - there are
>> a lot of corner cases I haven?t implemented yet.
>>
>> Best wishes,
>> Toby
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>
>
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From swetha.bsharma at gmail.com  Mon Feb 13 07:00:06 2017
From: swetha.bsharma at gmail.com (Swetha Sharma)
Date: Mon, 13 Feb 2017 17:30:06 +0530
Subject: [ITK] [ITK-users] set center for affinetransform
Message-ID: <CACDHZETvqxu5YRHV5x0-cDbOZ+0R4_b-64iOwcc6pQTzexZvGw@mail.gmail.com>

Hi All,

  I want the set the center of rotation for the affinetransform .I used the
function setCenter function ,the signature is defined as
setCenter(itk::MatrixOffsetTransformBase<double,3U,3U>::InputType&center).I
tried to set the center in the following way,

itk::MatrixOffsetTransformBase<double,3U,3U> centerType;

"itk::MatrixOffsetTransformBase<TParametersValueType, NInputDimensions,
NOutputDimensions>::MatrixOffsetTransformBase() [with
TParametersValueType=double, NInputDimensions=3U, NOutputDimensions=3U]"
(declared at line 482 of
"D:\itk\InsightToolkit-4.9.1\src\Modules\Core\Transform\include\itkMatrixOffsetTransformBase.h")
is inaccessible


Is it possible to define the center of rotation point for the transform?
How do I do it?
-swetha
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_____________________________________
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From dzenanz at gmail.com  Mon Feb 13 09:43:20 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 13 Feb 2017 09:43:20 -0500
Subject: [ITK] [ITK-users] set center for affinetransform
In-Reply-To: <CACDHZETvqxu5YRHV5x0-cDbOZ+0R4_b-64iOwcc6pQTzexZvGw@mail.gmail.com>
References: <CACDHZETvqxu5YRHV5x0-cDbOZ+0R4_b-64iOwcc6pQTzexZvGw@mail.gmail.com>
Message-ID: <CAPf2UMRSReZmk-_w6bG0s+pn3W5iijav0AMCUfcYsP-jWOjhwA@mail.gmail.com>

Hi Swetha,

of course it is possible. CenterType is just a typedef for point. So you
have two ways. First uses transform type to get center type:
typedef itk::AffineTransform<double, 3> TransformType;
TransformType::CenterType center;
transform->SetCenter(center);

Second typedefs point directly:
typedef itk::Point<double, 3> CenterType;
CenterType center;
transform->SetCenter(center);

Regards,
D?enan

On Mon, Feb 13, 2017 at 7:00 AM, Swetha Sharma <swetha.bsharma at gmail.com>
wrote:

> Hi All,
>
>   I want the set the center of rotation for the affinetransform .I used
> the function setCenter function ,the signature is defined as setCenter(itk::
> MatrixOffsetTransformBase<double,3U,3U>::InputType&center).I tried to set
> the center in the following way,
>
> itk::MatrixOffsetTransformBase<double,3U,3U> centerType;
>
> "itk::MatrixOffsetTransformBase<TParametersValueType, NInputDimensions,
> NOutputDimensions>::MatrixOffsetTransformBase() [with
> TParametersValueType=double, NInputDimensions=3U, NOutputDimensions=3U]"
> (declared at line 482 of "D:\itk\InsightToolkit-4.9.1\
> src\Modules\Core\Transform\include\itkMatrixOffsetTransformBase.h") is
> inaccessible
>
>
> Is it possible to define the center of rotation point for the transform?
> How do I do it?
> -swetha
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
>
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Powered by www.kitware.com

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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From swetha.bsharma at gmail.com  Mon Feb 13 12:17:18 2017
From: swetha.bsharma at gmail.com (Swetha Sharma)
Date: Mon, 13 Feb 2017 17:17:18 +0000
Subject: [ITK] [ITK-users] set center for affinetransform
In-Reply-To: <CAPf2UMRSReZmk-_w6bG0s+pn3W5iijav0AMCUfcYsP-jWOjhwA@mail.gmail.com>
References: <CACDHZETvqxu5YRHV5x0-cDbOZ+0R4_b-64iOwcc6pQTzexZvGw@mail.gmail.com>
 <CAPf2UMRSReZmk-_w6bG0s+pn3W5iijav0AMCUfcYsP-jWOjhwA@mail.gmail.com>
Message-ID: <CACDHZES6jjSMyR1TKx=-q77G-s1wE+hoHE3TOH=X+D8-F3+_Vw@mail.gmail.com>

Thanks.

On Mon, 13 Feb 2017, 20:13 D?enan Zuki?, <dzenanz at gmail.com> wrote:

> Hi Swetha,
>
> of course it is possible. CenterType is just a typedef for point. So you
> have two ways. First uses transform type to get center type:
> typedef itk::AffineTransform<double, 3> TransformType;
> TransformType::CenterType center;
> transform->SetCenter(center);
>
> Second typedefs point directly:
> typedef itk::Point<double, 3> CenterType;
> CenterType center;
> transform->SetCenter(center);
>
> Regards,
> D?enan
>
> On Mon, Feb 13, 2017 at 7:00 AM, Swetha Sharma <swetha.bsharma at gmail.com>
> wrote:
>
> Hi All,
>
>   I want the set the center of rotation for the affinetransform .I used
> the function setCenter function ,the signature is defined as
> setCenter(itk::MatrixOffsetTransformBase<double,3U,3U>::InputType&center).I
> tried to set the center in the following way,
>
> itk::MatrixOffsetTransformBase<double,3U,3U> centerType;
>
> "itk::MatrixOffsetTransformBase<TParametersValueType, NInputDimensions,
> NOutputDimensions>::MatrixOffsetTransformBase() [with
> TParametersValueType=double, NInputDimensions=3U, NOutputDimensions=3U]"
> (declared at line 482 of
> "D:\itk\InsightToolkit-4.9.1\src\Modules\Core\Transform\include\itkMatrixOffsetTransformBase.h")
> is inaccessible
>
>
> Is it possible to define the center of rotation point for the transform?
> How do I do it?
> -swetha
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
>
>
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_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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://public.kitware.com/mailman/listinfo/insight-users

From giuseppe.amatulli at gmail.com  Mon Feb 13 15:56:13 2017
From: giuseppe.amatulli at gmail.com (Giuseppe Amatulli)
Date: Mon, 13 Feb 2017 15:56:13 -0500
Subject: [ITK] image segmentation
Message-ID: <CAKoiDHJkxZPz8734sriv+jxb2jh60=Yd6vw9khPb3mscFRETQg@mail.gmail.com>

Hi,
I'm new in ITK <https://itk.org/> and would like to have some
directions/suggestions.

I'm trying to segment the image in Figure 1 and be able to identify
"valleys" between each one of the blue point.  In other words I would like
to obtain a red-line on the valleys like the one show in Figure 2.

Is this possible with ITK and if yes which are the commands/libraries that
should use?
Is there any python-itk example that I can use to obtain something similar.

Thanks
Best Giuseppe


FIGURE 1
[image: Inline images 2]

FIGURE 2

[image: Inline images 1]



-- 
Giuseppe Amatulli, Ph.D.

Research scientist at
Yale School of Forestry & Environmental Studies
Yale Center for Research Computing
Center for Science and Social Science Information
New Haven, 06511
Teaching: http://spatial-ecology.org
Work:  https://environment.yale.edu/profile/giuseppe-amatulli/
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From matt.mccormick at kitware.com  Mon Feb 13 16:14:28 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 13 Feb 2017 16:14:28 -0500
Subject: [ITK] image segmentation
In-Reply-To: <CAKoiDHJkxZPz8734sriv+jxb2jh60=Yd6vw9khPb3mscFRETQg@mail.gmail.com>
References: <CAKoiDHJkxZPz8734sriv+jxb2jh60=Yd6vw9khPb3mscFRETQg@mail.gmail.com>
Message-ID: <CALzTN-QoXQOnLx4zcLBY8dO5AtwX-uQTL2ZPd0ZkiV7n6dRt0w@mail.gmail.com>

Hi Giuseppe,

Welcome to ITK!

Yes, the itk.MorphologicalWatershedImageFilter can generate the desired
segmentation. For more information, see this article:

  http://www.insight-journal.org/browse/publication/92

Hope this helps,
Matt

On Mon, Feb 13, 2017 at 3:56 PM, Giuseppe Amatulli <
giuseppe.amatulli at gmail.com> wrote:

>
> Hi,
> I'm new in ITK <https://itk.org/> and would like to have some
> directions/suggestions.
>
> I'm trying to segment the image in Figure 1 and be able to identify
> "valleys" between each one of the blue point.  In other words I
> would like to obtain a red-line on the valleys like the one show in Figure
> 2.
>
> Is this possible with ITK and if yes which are the commands/libraries that
> should use?
> Is there any python-itk example that I can use to obtain something
> similar.
>
> Thanks
> Best Giuseppe
>
>
> FIGURE 1
> [image: Inline images 2]
>
> FIGURE 2
>
> [image: Inline images 1]
>
>
>
> --
> Giuseppe Amatulli, Ph.D.
>
> Research scientist at
> Yale School of Forestry & Environmental Studies
> Yale Center for Research Computing
> Center for Science and Social Science Information
> New Haven, 06511
> Teaching: http://spatial-ecology.org
> Work:  https://environment.yale.edu/profile/giuseppe-amatulli/
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From francois.budin at kitware.com  Mon Feb 13 16:15:48 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Mon, 13 Feb 2017 16:15:48 -0500
Subject: [ITK] image segmentation
In-Reply-To: <CAKoiDHJkxZPz8734sriv+jxb2jh60=Yd6vw9khPb3mscFRETQg@mail.gmail.com>
References: <CAKoiDHJkxZPz8734sriv+jxb2jh60=Yd6vw9khPb3mscFRETQg@mail.gmail.com>
Message-ID: <CAHwLD2UJwwxqbD8W+D3F7yMC5SNAbe8BAFQ8A=jjnGaKdSWnRw@mail.gmail.com>

Hello Giuseppe,

Yes it is possible to create this type of segmentation with ITK.
The first step would be to convert your RGB(A) image into a grayscale image
using RGBToLuminanceImageFilter [1]. The second step would be to run a
watershed filter such as MorphologicalWatershedImageFilter [2]. If you want
to keep the lines, use "MarkWatershedLineOn()".

Hope this helps,
Francois

[1] https://itk.org/Doxygen/html/classitk_1_1RGBToLuminanceImageFilter.html
[2]
https://itk.org/Doxygen/html/classitk_1_1MorphologicalWatershedImageFilter.html

On Mon, Feb 13, 2017 at 3:56 PM, Giuseppe Amatulli <
giuseppe.amatulli at gmail.com> wrote:

>
> Hi,
> I'm new in ITK <https://itk.org/> and would like to have some
> directions/suggestions.
>
> I'm trying to segment the image in Figure 1 and be able to identify
> "valleys" between each one of the blue point.  In other words I
> would like to obtain a red-line on the valleys like the one show in Figure
> 2.
>
> Is this possible with ITK and if yes which are the commands/libraries that
> should use?
> Is there any python-itk example that I can use to obtain something
> similar.
>
> Thanks
> Best Giuseppe
>
>
> FIGURE 1
> [image: Inline images 2]
>
> FIGURE 2
>
> [image: Inline images 1]
>
>
>
> --
> Giuseppe Amatulli, Ph.D.
>
> Research scientist at
> Yale School of Forestry & Environmental Studies
> Yale Center for Research Computing
> Center for Science and Social Science Information
> New Haven, 06511
> Teaching: http://spatial-ecology.org
> Work:  https://environment.yale.edu/profile/giuseppe-amatulli/
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From lqshen10 at gmail.com  Tue Feb 14 09:11:49 2017
From: lqshen10 at gmail.com (Longzhu Shen)
Date: Tue, 14 Feb 2017 09:11:49 -0500
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
Message-ID: <86wpcs50be.fsf@gmail.com>


Hello,

I'm trying to compile simpleitk on my freebsd system.
The issue I encountered is ldl is not found.
After some searching, I found libdl is not needed on freebsd. It is
included in libc. Wondering how I can turn it off in the make file.
I did not find  ldl in the Makefile under Simpleitk-build.

I followed the instrutions from the link below.

https://chsasank.github.io/sitk-docs/building/unix.html#obtaining-source-code

Thanks.

Longzhu 


-- 
Longzhu Shen, Ph.D.
Postdoc Research Associate
School of Forestry and Environmental Studies
Yale University
195 Prospect Street
New Haven, CT 06511

From blowekamp at mail.nih.gov  Tue Feb 14 10:36:25 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 14 Feb 2017 15:36:25 +0000
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
In-Reply-To: <86wpcs50be.fsf@gmail.com>
References: <86wpcs50be.fsf@gmail.com>
Message-ID: <DA2915A530468E47B3C4845298E6EB038361F537@msgb06.nih.gov>

Hello Longzu,

You are using freebsd, that is new and exciting. I have not used that OS for developing.

There are two things in the ITK/SimpleITK build that are related to this.

First, there is an option in ITK ( which I have not used ) call ITK_DYNAMIC_LOADING. If you pass -DITK_DYNAMIC_LOADING:BOOL=0 to cmake for the Superbuild, it should propagate to the ITK project and this feature will be remove. This may solve your problem.

The second is CMake variable CMAKE_DL_LIBS. I believe it is the dl library that is causing the problem [1]. Setting it to an empty string may also remove it from the linking lines. Getting that to propagate to the ITK project will not happen automatically and would need to be done manually in the ITK build.

HTH,
Brad

[1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/src/CMakeLists.txt#L142

________________________________________
From: Longzhu Shen [lqshen10 at gmail.com]
Sent: Tuesday, February 14, 2017 9:11 AM
To: community at itk.org
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?

Hello,

I'm trying to compile simpleitk on my freebsd system.
The issue I encountered is ldl is not found.
After some searching, I found libdl is not needed on freebsd. It is
included in libc. Wondering how I can turn it off in the make file.
I did not find  ldl in the Makefile under Simpleitk-build.

I followed the instrutions from the link below.

https://chsasank.github.io/sitk-docs/building/unix.html#obtaining-source-code

Thanks.

Longzhu


--
Longzhu Shen, Ph.D.
Postdoc Research Associate
School of Forestry and Environmental Studies
Yale University
195 Prospect Street
New Haven, CT 06511
_______________________________________________
Community mailing list
Community at itk.org
http://public.kitware.com/mailman/listinfo/community

From lqshen10 at gmail.com  Tue Feb 14 15:53:19 2017
From: lqshen10 at gmail.com (Longzhu Shen)
Date: Tue, 14 Feb 2017 15:53:19 -0500
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
In-Reply-To: <DA2915A530468E47B3C4845298E6EB038361F537@msgb06.nih.gov>
References: <86wpcs50be.fsf@gmail.com>
 <DA2915A530468E47B3C4845298E6EB038361F537@msgb06.nih.gov>
Message-ID: <86shngmr40.fsf@gmail.com>

Hi Brad,

Many thanks for the advice.
I made an attempt to follow the first approach but it did not seem
work. Here is what I did and the errors I got. 

-----------------------------------------------------
$ cmake ../SuperBuild -DITK_DYNAMIC_LOADING:BOOL=0


[ 80%] Building CXX object
Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/sitkPyCommand.cxx.o
[ 80%] Building CXX object
Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/SimpleITKPYTHON_wrap.cxx.o
[ 80%] Linking CXX executable bin/SimpleITKTclsh
/usr/bin/ld: cannot find -ldl
c++: error: linker command failed with exit code 1 (use -v to see
invocation)
--- Wrapping/Tcl/bin/SimpleITKTclsh ---
*** [Wrapping/Tcl/bin/SimpleITKTclsh] Error code 1
-----------------------------------------------------

I planned to try the 2nd approach. However, I could not find the
CMAKE_DL_LIBS easily. I checked the subfolder of Superbuild, 
and SimpleITK-build/ITK-build. I did not find it in
 Code/Common/src/CMakeLists.txt as well.

The only place I found "CMAKE_DL_LIBS" is in the file
CMake/sitkTargetLinkLibrariesWithDynamicLookup.cmake

279:        target_link_libraries(main \"${CMAKE_DL_LIBS}\")

I was wondering I may get further directions to modify CMAKE_DL_LIBS
variable. Many thanks.

sincerely,

Longzhu 


Lowekamp @ 2017-02-14 15:36 UTC:

> Hello Longzu,
>
> You are using freebsd, that is new and exciting. I have not used that OS for developing.
>
> There are two things in the ITK/SimpleITK build that are related to this.
>
> First, there is an option in ITK ( which I have not used ) call ITK_DYNAMIC_LOADING. If you pass -DITK_DYNAMIC_LOADING:BOOL=0 to cmake for the Superbuild, it should propagate to the ITK project and this feature will be remove. This may solve your problem.
>
> The second is CMake variable CMAKE_DL_LIBS. I believe it is the dl library that is causing the problem [1]. Setting it to an empty string may also remove it from the linking lines. Getting that to propagate to the ITK project will not happen automatically and would need to be done manually in the ITK build.
>
> HTH,
> Brad
>
> [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/src/CMakeLists.txt#L142
>
> ________________________________________
> From: Longzhu Shen [lqshen10 at gmail.com]
> Sent: Tuesday, February 14, 2017 9:11 AM
> To: community at itk.org
> Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
>
> Hello,
>
> I'm trying to compile simpleitk on my freebsd system.
> The issue I encountered is ldl is not found.
> After some searching, I found libdl is not needed on freebsd. It is
> included in libc. Wondering how I can turn it off in the make file.
> I did not find  ldl in the Makefile under Simpleitk-build.
>
> I followed the instrutions from the link below.
>
> https://chsasank.github.io/sitk-docs/building/unix.html#obtaining-source-code
>
> Thanks.
>
> Longzhu


-- 
Longzhu Shen, Ph.D.
Postdoc Research Associate
School of Forestry and Environmental Studies
Yale University
195 Prospect Street
New Haven, CT 06511

From giuseppe.amatulli at gmail.com  Tue Feb 14 16:11:17 2017
From: giuseppe.amatulli at gmail.com (Giuseppe Amatulli)
Date: Tue, 14 Feb 2017 16:11:17 -0500
Subject: [ITK] image segmentation
In-Reply-To: <CAHwLD2UJwwxqbD8W+D3F7yMC5SNAbe8BAFQ8A=jjnGaKdSWnRw@mail.gmail.com>
References: <CAKoiDHJkxZPz8734sriv+jxb2jh60=Yd6vw9khPb3mscFRETQg@mail.gmail.com>
 <CAHwLD2UJwwxqbD8W+D3F7yMC5SNAbe8BAFQ8A=jjnGaKdSWnRw@mail.gmail.com>
Message-ID: <CAKoiDHKcqsTy4ha=nj2P-ve6Wq+z4xVbQQmnwW_-wOXH-gQk0w@mail.gmail.com>

Hi,
thanks for the input.
I try to follow your suggestion to build up a watershed segmentation image
starting from external markers, but i get something strange.

These are the files that i used

wget  https://dl.dropboxusercontent.com/u/29337496/small_core.tif
wget  https://dl.dropboxusercontent.com/u/29337496/cost_Int32.tif

python

import SimpleITK as sitk

img  = sitk.ReadImage("cost_Int32.tif")
core = sitk.ReadImage("small_core.tif")

feature_img = sitk.GradientMagnitude(img)
marker_img = sitk.ConnectedComponent(core, fullyConnected=False)

ws = sitk.MorphologicalWatershedFromMarkers(feature_img, marker_img,
markWatershedLine=True, fullyConnected=False)

sitk.WriteImage(ws,  'watershed.jpg' )


Moreover, I also try to save the final image as tiff, but i get the
following error.

sitk.WriteImage(ws,  'watershed.tif' )
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/dist-packages/SimpleITK/SimpleITK.py",
line 7942, in WriteImage
    return _SimpleITK.WriteImage(*args)
RuntimeError: Exception thrown in SimpleITK WriteImage:
/tmp/SimpleITK-build/ITK/Modules/IO/TIFF/src/itkTIFFImageIO.cxx:544:
itk::ERROR: TIFFImageIO(0x2e6d880): TIFF supports unsigned/signed char,
unsigned/signed short, and float

seams to me the tiff is not supported or i miss some modules of ITK

May anyone help me

Thank you
Best
Giuseppe





On 13 February 2017 at 16:15, Francois Budin <francois.budin at kitware.com>
wrote:

> Hello Giuseppe,
>
> Yes it is possible to create this type of segmentation with ITK.
> The first step would be to convert your RGB(A) image into a grayscale
> image using RGBToLuminanceImageFilter [1]. The second step would be to run
> a watershed filter such as MorphologicalWatershedImageFilter [2]. If you
> want to keep the lines, use "MarkWatershedLineOn()".
>
> Hope this helps,
> Francois
>
> [1] https://itk.org/Doxygen/html/classitk_1_1RGBToLuminanceImageFilter.
> html
> [2] https://itk.org/Doxygen/html/classitk_1_1MorphologicalWatershedImageFi
> lter.html
>
> On Mon, Feb 13, 2017 at 3:56 PM, Giuseppe Amatulli <
> giuseppe.amatulli at gmail.com> wrote:
>
>>
>> Hi,
>> I'm new in ITK <https://itk.org/> and would like to have some
>> directions/suggestions.
>>
>> I'm trying to segment the image in Figure 1 and be able to identify
>> "valleys" between each one of the blue point.  In other words I
>> would like to obtain a red-line on the valleys like the one show in Figure
>> 2.
>>
>> Is this possible with ITK and if yes which are the commands/libraries
>> that should use?
>> Is there any python-itk example that I can use to obtain something
>> similar.
>>
>> Thanks
>> Best Giuseppe
>>
>>
>> FIGURE 1
>> [image: Inline images 2]
>>
>> FIGURE 2
>>
>> [image: Inline images 1]
>>
>>
>>
>> --
>> Giuseppe Amatulli, Ph.D.
>>
>> Research scientist at
>> Yale School of Forestry & Environmental Studies
>> Yale Center for Research Computing
>> Center for Science and Social Science Information
>> New Haven, 06511
>> Teaching: http://spatial-ecology.org
>> Work:  https://environment.yale.edu/profile/giuseppe-amatulli/
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>>
>


-- 
Giuseppe Amatulli, Ph.D.

Research scientist at
Yale School of Forestry & Environmental Studies
Yale Center for Research Computing
Center for Science and Social Science Information
New Haven, 06511
Teaching: http://spatial-ecology.org
Work:  https://environment.yale.edu/profile/giuseppe-amatulli/
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From blowekamp at mail.nih.gov  Tue Feb 14 16:32:42 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 14 Feb 2017 21:32:42 +0000
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
In-Reply-To: <86shngmr40.fsf@gmail.com>
References: <86wpcs50be.fsf@gmail.com>
 <DA2915A530468E47B3C4845298E6EB038361F537@msgb06.nih.gov>
 <86shngmr40.fsf@gmail.com>
Message-ID: <8907FC5F-A787-4FDC-BDF8-B101444D3544@mail.nih.gov>

Hi,

Are we sure the first case was not close to mostly working? Did other wrapped language link OK? did SimpleITK tests link OK? If ITK tests are enable with ITK_DYNAMIC_LOADING:BOOL=0 do they compile and work? We need to know if ITK is OK before moving to SimpleITK.

@Matt
I am not very familiar with CMAKE_DL_LIBS either [1]. I know Matt added the ITK_DYNAMIC_LOADING CMake variable to ITK, so he may have insight into this problem too. My guess is that CMAKE_DL_LIBS variable is not entered into the cache but CMake provides a default value for platform. I expect you can overrride it with command line values.

I hacked a patch to enable CMAKE_DL_LIBS to propgate down from the Superbuild [2]. If you checkout that path you should be able to do a supberbuild of -DCMAKE_DL_LIBS=??. That may work, but I don?t know for sure.

HTH,
Brad

[1] https://cmake.org/cmake/help/v3.0/variable/CMAKE_DL_LIBS.html
[2] https://github.com/SimpleITK/SimpleITK/pull/104


On Feb 14, 2017, at 3:53 PM, Longzhu Shen <lqshen10 at gmail.com<mailto:lqshen10 at gmail.com>> wrote:

Hi Brad,

Many thanks for the advice.
I made an attempt to follow the first approach but it did not seem
work. Here is what I did and the errors I got.

-----------------------------------------------------
$ cmake ../SuperBuild -DITK_DYNAMIC_LOADING:BOOL=0


[ 80%] Building CXX object
Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/sitkPyCommand.cxx.o
[ 80%] Building CXX object
Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/SimpleITKPYTHON_wrap.cxx.o
[ 80%] Linking CXX executable bin/SimpleITKTclsh
/usr/bin/ld: cannot find -ldl
c++: error: linker command failed with exit code 1 (use -v to see
invocation)
--- Wrapping/Tcl/bin/SimpleITKTclsh ---
*** [Wrapping/Tcl/bin/SimpleITKTclsh] Error code 1
-----------------------------------------------------

I planned to try the 2nd approach. However, I could not find the
CMAKE_DL_LIBS easily. I checked the subfolder of Superbuild,
and SimpleITK-build/ITK-build. I did not find it in
Code/Common/src/CMakeLists.txt as well.

The only place I found "CMAKE_DL_LIBS" is in the file
CMake/sitkTargetLinkLibrariesWithDynamicLookup.cmake

279:        target_link_libraries(main \"${CMAKE_DL_LIBS}\")

I was wondering I may get further directions to modify CMAKE_DL_LIBS
variable. Many thanks.

sincerely,

Longzhu


Lowekamp @ 2017-02-14 15:36 UTC:

Hello Longzu,

You are using freebsd, that is new and exciting. I have not used that OS for developing.

There are two things in the ITK/SimpleITK build that are related to this.

First, there is an option in ITK ( which I have not used ) call ITK_DYNAMIC_LOADING. If you pass -DITK_DYNAMIC_LOADING:BOOL=0 to cmake for the Superbuild, it should propagate to the ITK project and this feature will be remove. This may solve your problem.

The second is CMake variable CMAKE_DL_LIBS. I believe it is the dl library that is causing the problem [1]. Setting it to an empty string may also remove it from the linking lines. Getting that to propagate to the ITK project will not happen automatically and would need to be done manually in the ITK build.

HTH,
Brad

[1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/src/CMakeLists.txt#L142

________________________________________
From: Longzhu Shen [lqshen10 at gmail.com<mailto:lqshen10 at gmail.com>]
Sent: Tuesday, February 14, 2017 9:11 AM
To: community at itk.org<mailto:community at itk.org>
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?

Hello,

I'm trying to compile simpleitk on my freebsd system.
The issue I encountered is ldl is not found.
After some searching, I found libdl is not needed on freebsd. It is
included in libc. Wondering how I can turn it off in the make file.
I did not find  ldl in the Makefile under Simpleitk-build.

I followed the instrutions from the link below.

https://chsasank.github.io/sitk-docs/building/unix.html#obtaining-source-code

Thanks.

Longzhu


--
Longzhu Shen, Ph.D.
Postdoc Research Associate
School of Forestry and Environmental Studies
Yale University
195 Prospect Street
New Haven, CT 06511

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From matt.mccormick at kitware.com  Tue Feb 14 16:48:05 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 14 Feb 2017 16:48:05 -0500
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
In-Reply-To: <8907FC5F-A787-4FDC-BDF8-B101444D3544@mail.nih.gov>
References: <86wpcs50be.fsf@gmail.com>
 <DA2915A530468E47B3C4845298E6EB038361F537@msgb06.nih.gov>
 <86shngmr40.fsf@gmail.com> <8907FC5F-A787-4FDC-BDF8-B101444D3544@mail.nih.gov>
Message-ID: <CALzTN-RHEpJJATQE0aShTiCx9NZ7jEq+L4QwFtxjYwEMFBo3Fw@mail.gmail.com>

Hi,

It is not likely that the errors are related to ITK_DYNAMIC_LOADING.

FreeBSD has a package for ITK, which gives its configuration:

https://www.freshports.org/science/InsightToolkit/
https://reviews.freebsd.org/diffusion/P/browse/head/science/InsightToolkit/Makefile

HTH,
Matt

On Tue, Feb 14, 2017 at 4:32 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
<blowekamp at mail.nih.gov> wrote:
> Hi,
>
> Are we sure the first case was not close to mostly working? Did other
> wrapped language link OK? did SimpleITK tests link OK? If ITK tests are
> enable with ITK_DYNAMIC_LOADING:BOOL=0 do they compile and work? We need to
> know if ITK is OK before moving to SimpleITK.
>
> @Matt
> I am not very familiar with CMAKE_DL_LIBS either [1]. I know Matt added the
> ITK_DYNAMIC_LOADING CMake variable to ITK, so he may have insight into this
> problem too. My guess is that CMAKE_DL_LIBS variable is not entered into the
> cache but CMake provides a default value for platform. I expect you can
> overrride it with command line values.
>
> I hacked a patch to enable CMAKE_DL_LIBS to propgate down from the
> Superbuild [2]. If you checkout that path you should be able to do a
> supberbuild of -DCMAKE_DL_LIBS=??. That may work, but I don?t know for sure.
>
> HTH,
> Brad
>
> [1] https://cmake.org/cmake/help/v3.0/variable/CMAKE_DL_LIBS.html
> [2] https://github.com/SimpleITK/SimpleITK/pull/104
>
>
> On Feb 14, 2017, at 3:53 PM, Longzhu Shen <lqshen10 at gmail.com> wrote:
>
> Hi Brad,
>
> Many thanks for the advice.
> I made an attempt to follow the first approach but it did not seem
> work. Here is what I did and the errors I got.
>
> -----------------------------------------------------
> $ cmake ../SuperBuild -DITK_DYNAMIC_LOADING:BOOL=0
>
>
> [ 80%] Building CXX object
> Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/sitkPyCommand.cxx.o
> [ 80%] Building CXX object
> Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/SimpleITKPYTHON_wrap.cxx.o
> [ 80%] Linking CXX executable bin/SimpleITKTclsh
> /usr/bin/ld: cannot find -ldl
> c++: error: linker command failed with exit code 1 (use -v to see
> invocation)
> --- Wrapping/Tcl/bin/SimpleITKTclsh ---
> *** [Wrapping/Tcl/bin/SimpleITKTclsh] Error code 1
> -----------------------------------------------------
>
> I planned to try the 2nd approach. However, I could not find the
> CMAKE_DL_LIBS easily. I checked the subfolder of Superbuild,
> and SimpleITK-build/ITK-build. I did not find it in
> Code/Common/src/CMakeLists.txt as well.
>
> The only place I found "CMAKE_DL_LIBS" is in the file
> CMake/sitkTargetLinkLibrariesWithDynamicLookup.cmake
>
> 279:        target_link_libraries(main \"${CMAKE_DL_LIBS}\")
>
> I was wondering I may get further directions to modify CMAKE_DL_LIBS
> variable. Many thanks.
>
> sincerely,
>
> Longzhu
>
>
> Lowekamp @ 2017-02-14 15:36 UTC:
>
> Hello Longzu,
>
> You are using freebsd, that is new and exciting. I have not used that OS for
> developing.
>
> There are two things in the ITK/SimpleITK build that are related to this.
>
> First, there is an option in ITK ( which I have not used ) call
> ITK_DYNAMIC_LOADING. If you pass -DITK_DYNAMIC_LOADING:BOOL=0 to cmake for
> the Superbuild, it should propagate to the ITK project and this feature will
> be remove. This may solve your problem.
>
> The second is CMake variable CMAKE_DL_LIBS. I believe it is the dl library
> that is causing the problem [1]. Setting it to an empty string may also
> remove it from the linking lines. Getting that to propagate to the ITK
> project will not happen automatically and would need to be done manually in
> the ITK build.
>
> HTH,
> Brad
>
> [1]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/src/CMakeLists.txt#L142
>
> ________________________________________
> From: Longzhu Shen [lqshen10 at gmail.com]
> Sent: Tuesday, February 14, 2017 9:11 AM
> To: community at itk.org
> Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
>
> Hello,
>
> I'm trying to compile simpleitk on my freebsd system.
> The issue I encountered is ldl is not found.
> After some searching, I found libdl is not needed on freebsd. It is
> included in libc. Wondering how I can turn it off in the make file.
> I did not find  ldl in the Makefile under Simpleitk-build.
>
> I followed the instrutions from the link below.
>
> https://chsasank.github.io/sitk-docs/building/unix.html#obtaining-source-code
>
> Thanks.
>
> Longzhu
>
>
>
> --
> Longzhu Shen, Ph.D.
> Postdoc Research Associate
> School of Forestry and Environmental Studies
> Yale University
> 195 Prospect Street
> New Haven, CT 06511
>
>

From matt.mccormick at kitware.com  Tue Feb 14 17:14:24 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 14 Feb 2017 17:14:24 -0500
Subject: [ITK] image segmentation
In-Reply-To: <CAKoiDHKcqsTy4ha=nj2P-ve6Wq+z4xVbQQmnwW_-wOXH-gQk0w@mail.gmail.com>
References: <CAKoiDHJkxZPz8734sriv+jxb2jh60=Yd6vw9khPb3mscFRETQg@mail.gmail.com>
 <CAHwLD2UJwwxqbD8W+D3F7yMC5SNAbe8BAFQ8A=jjnGaKdSWnRw@mail.gmail.com>
 <CAKoiDHKcqsTy4ha=nj2P-ve6Wq+z4xVbQQmnwW_-wOXH-gQk0w@mail.gmail.com>
Message-ID: <CALzTN-Qo1Ne=FXjTZrRrQK+8gUsV=eCnEvqjAK0R4MvLiEHCzA@mail.gmail.com>

Hi Giuseppe,

Not all file formats support all pixel types. One approach is to cast the
image to a different type.  See `help(sitk.Cast)`.

HTH,
Matt

On Tue, Feb 14, 2017 at 4:11 PM, Giuseppe Amatulli <
giuseppe.amatulli at gmail.com> wrote:

> Hi,
> thanks for the input.
> I try to follow your suggestion to build up a watershed segmentation image
> starting from external markers, but i get something strange.
>
> These are the files that i used
>
> wget  https://dl.dropboxusercontent.com/u/29337496/small_core.tif
> wget  https://dl.dropboxusercontent.com/u/29337496/cost_Int32.tif
>
> python
>
> import SimpleITK as sitk
>
> img  = sitk.ReadImage("cost_Int32.tif")
> core = sitk.ReadImage("small_core.tif")
>
> feature_img = sitk.GradientMagnitude(img)
> marker_img = sitk.ConnectedComponent(core, fullyConnected=False)
>
> ws = sitk.MorphologicalWatershedFromMarkers(feature_img, marker_img,
> markWatershedLine=True, fullyConnected=False)
>
> sitk.WriteImage(ws,  'watershed.jpg' )
>
>
> Moreover, I also try to save the final image as tiff, but i get the
> following error.
>
> sitk.WriteImage(ws,  'watershed.tif' )
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/local/lib/python2.7/dist-packages/SimpleITK/SimpleITK.py",
> line 7942, in WriteImage
>     return _SimpleITK.WriteImage(*args)
> RuntimeError: Exception thrown in SimpleITK WriteImage:
> /tmp/SimpleITK-build/ITK/Modules/IO/TIFF/src/itkTIFFImageIO.cxx:544:
> itk::ERROR: TIFFImageIO(0x2e6d880): TIFF supports unsigned/signed char,
> unsigned/signed short, and float
>
> seams to me the tiff is not supported or i miss some modules of ITK
>
> May anyone help me
>
> Thank you
> Best
> Giuseppe
>
>
>
>
>
> On 13 February 2017 at 16:15, Francois Budin <francois.budin at kitware.com>
> wrote:
>
>> Hello Giuseppe,
>>
>> Yes it is possible to create this type of segmentation with ITK.
>> The first step would be to convert your RGB(A) image into a grayscale
>> image using RGBToLuminanceImageFilter [1]. The second step would be to run
>> a watershed filter such as MorphologicalWatershedImageFilter [2]. If you
>> want to keep the lines, use "MarkWatershedLineOn()".
>>
>> Hope this helps,
>> Francois
>>
>> [1] https://itk.org/Doxygen/html/classitk_1_1RGBToLuminanceImage
>> Filter.html
>> [2] https://itk.org/Doxygen/html/classitk_1_1MorphologicalWaters
>> hedImageFilter.html
>>
>> On Mon, Feb 13, 2017 at 3:56 PM, Giuseppe Amatulli <
>> giuseppe.amatulli at gmail.com> wrote:
>>
>>>
>>> Hi,
>>> I'm new in ITK <https://itk.org/> and would like to have some
>>> directions/suggestions.
>>>
>>> I'm trying to segment the image in Figure 1 and be able to identify
>>> "valleys" between each one of the blue point.  In other words I
>>> would like to obtain a red-line on the valleys like the one show in Figure
>>> 2.
>>>
>>> Is this possible with ITK and if yes which are the commands/libraries
>>> that should use?
>>> Is there any python-itk example that I can use to obtain something
>>> similar.
>>>
>>> Thanks
>>> Best Giuseppe
>>>
>>>
>>> FIGURE 1
>>> [image: Inline images 2]
>>>
>>> FIGURE 2
>>>
>>> [image: Inline images 1]
>>>
>>>
>>>
>>> --
>>> Giuseppe Amatulli, Ph.D.
>>>
>>> Research scientist at
>>> Yale School of Forestry & Environmental Studies
>>> Yale Center for Research Computing
>>> Center for Science and Social Science Information
>>> New Haven, 06511
>>> Teaching: http://spatial-ecology.org
>>> Work:  https://environment.yale.edu/profile/giuseppe-amatulli/
>>>
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>>>
>>>
>>
>
>
> --
> Giuseppe Amatulli, Ph.D.
>
> Research scientist at
> Yale School of Forestry & Environmental Studies
> Yale Center for Research Computing
> Center for Science and Social Science Information
> New Haven, 06511
> Teaching: http://spatial-ecology.org
> Work:  https://environment.yale.edu/profile/giuseppe-amatulli/
>
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From lqshen10 at gmail.com  Tue Feb 14 21:24:59 2017
From: lqshen10 at gmail.com (Longzhu Shen)
Date: Tue, 14 Feb 2017 21:24:59 -0500
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
In-Reply-To: <CALzTN-RHEpJJATQE0aShTiCx9NZ7jEq+L4QwFtxjYwEMFBo3Fw@mail.gmail.com>
References: <86wpcs50be.fsf@gmail.com>
 <DA2915A530468E47B3C4845298E6EB038361F537@msgb06.nih.gov>
 <86shngmr40.fsf@gmail.com>
 <8907FC5F-A787-4FDC-BDF8-B101444D3544@mail.nih.gov>
 <CALzTN-RHEpJJATQE0aShTiCx9NZ7jEq+L4QwFtxjYwEMFBo3Fw@mail.gmail.com>
Message-ID: <86r330ur5w.fsf@gmail.com>


Hi Brad and Matt,

Many thanks for the kind advice. I'm very new to ITK. Some of my
questions may be naive. I hope you could bear with me. I really hope to
get it working if I could. Thank you very much. 

I checked out the freebsd port but I could not install it. (errors below)

Then I went back to the ITK src (I mistakenly thought simpleITK contains
ITK before) and tried to follow the manual to install it.

The cmake was fine for the most part but some errors did appear (
attached). Assuming those errors were not fatal, I
proceeded with make. The program stopped at the line below. 

make[2]: don't know how to make ExternalData/Testing/Data/Input/MetaIO/Small\. Stop

It is the same error when I tried to compile from the ports. 

Wondering whether I can seek some insight here or it is hopeless with
freebsd by this point. Thanks for advice.

sincerely,

Longzhu

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Matt McCormick @ 2017-02-14 21:48 UTC:

> Hi,
>
> It is not likely that the errors are related to ITK_DYNAMIC_LOADING.
>
> FreeBSD has a package for ITK, which gives its configuration:
>
> https://www.freshports.org/science/InsightToolkit/
> https://reviews.freebsd.org/diffusion/P/browse/head/science/InsightToolkit/Makefile
>
> HTH,
> Matt
>
> On Tue, Feb 14, 2017 at 4:32 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
> <blowekamp at mail.nih.gov> wrote:
>> Hi,
>>
>> Are we sure the first case was not close to mostly working? Did other
>> wrapped language link OK? did SimpleITK tests link OK? If ITK tests are
>> enable with ITK_DYNAMIC_LOADING:BOOL=0 do they compile and work? We need to
>> know if ITK is OK before moving to SimpleITK.
>>
>> @Matt
>> I am not very familiar with CMAKE_DL_LIBS either [1]. I know Matt added the
>> ITK_DYNAMIC_LOADING CMake variable to ITK, so he may have insight into this
>> problem too. My guess is that CMAKE_DL_LIBS variable is not entered into the
>> cache but CMake provides a default value for platform. I expect you can
>> overrride it with command line values.
>>
>> I hacked a patch to enable CMAKE_DL_LIBS to propgate down from the
>> Superbuild [2]. If you checkout that path you should be able to do a
>> supberbuild of -DCMAKE_DL_LIBS=??. That may work, but I don?t know for sure.
>>
>> HTH,
>> Brad
>>
>> [1] https://cmake.org/cmake/help/v3.0/variable/CMAKE_DL_LIBS.html
>> [2] https://github.com/SimpleITK/SimpleITK/pull/104
>>
>>
>> On Feb 14, 2017, at 3:53 PM, Longzhu Shen <lqshen10 at gmail.com> wrote:
>>
>> Hi Brad,
>>
>> Many thanks for the advice.
>> I made an attempt to follow the first approach but it did not seem
>> work. Here is what I did and the errors I got.
>>
>> -----------------------------------------------------
>> $ cmake ../SuperBuild -DITK_DYNAMIC_LOADING:BOOL=0
>>
>>
>> [ 80%] Building CXX object
>> Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/sitkPyCommand.cxx.o
>> [ 80%] Building CXX object
>> Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/SimpleITKPYTHON_wrap.cxx.o
>> [ 80%] Linking CXX executable bin/SimpleITKTclsh
>> /usr/bin/ld: cannot find -ldl
>> c++: error: linker command failed with exit code 1 (use -v to see
>> invocation)
>> --- Wrapping/Tcl/bin/SimpleITKTclsh ---
>> *** [Wrapping/Tcl/bin/SimpleITKTclsh] Error code 1
>> -----------------------------------------------------
>>
>> I planned to try the 2nd approach. However, I could not find the
>> CMAKE_DL_LIBS easily. I checked the subfolder of Superbuild,
>> and SimpleITK-build/ITK-build. I did not find it in
>> Code/Common/src/CMakeLists.txt as well.
>>
>> The only place I found "CMAKE_DL_LIBS" is in the file
>> CMake/sitkTargetLinkLibrariesWithDynamicLookup.cmake
>>
>> 279:        target_link_libraries(main \"${CMAKE_DL_LIBS}\")
>>
>> I was wondering I may get further directions to modify CMAKE_DL_LIBS
>> variable. Many thanks.
>>
>> sincerely,
>>
>> Longzhu
>>
>>
>> Lowekamp @ 2017-02-14 15:36 UTC:
>>
>> Hello Longzu,
>>
>> You are using freebsd, that is new and exciting. I have not used that OS for
>> developing.
>>
>> There are two things in the ITK/SimpleITK build that are related to this.
>>
>> First, there is an option in ITK ( which I have not used ) call
>> ITK_DYNAMIC_LOADING. If you pass -DITK_DYNAMIC_LOADING:BOOL=0 to cmake for
>> the Superbuild, it should propagate to the ITK project and this feature will
>> be remove. This may solve your problem.
>>
>> The second is CMake variable CMAKE_DL_LIBS. I believe it is the dl library
>> that is causing the problem [1]. Setting it to an empty string may also
>> remove it from the linking lines. Getting that to propagate to the ITK
>> project will not happen automatically and would need to be done manually in
>> the ITK build.
>>
>> HTH,
>> Brad
>>
>> [1]
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/src/CMakeLists.txt#L142
>>
>> ________________________________________
>> From: Longzhu Shen [lqshen10 at gmail.com]
>> Sent: Tuesday, February 14, 2017 9:11 AM
>> To: community at itk.org
>> Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
>>
>> Hello,
>>
>> I'm trying to compile simpleitk on my freebsd system.
>> The issue I encountered is ldl is not found.
>> After some searching, I found libdl is not needed on freebsd. It is
>> included in libc. Wondering how I can turn it off in the make file.
>> I did not find  ldl in the Makefile under Simpleitk-build.
>>
>> I followed the instrutions from the link below.
>>
>> https://chsasank.github.io/sitk-docs/building/unix.html#obtaining-source-code
>>
>> Thanks.
>>
>> Longzhu
>>
>>
>>
>> --
>> Longzhu Shen, Ph.D.
>> Postdoc Research Associate
>> School of Forestry and Environmental Studies
>> Yale University
>> 195 Prospect Street
>> New Haven, CT 06511
>>
>>


-- 
Longzhu Shen, Ph.D.
Postdoc Research Associate
School of Forestry and Environmental Studies
Yale University
195 Prospect Street
New Haven, CT 06511

From blowekamp at mail.nih.gov  Tue Feb 14 21:26:13 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 15 Feb 2017 02:26:13 +0000
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
In-Reply-To: <CALzTN-RHEpJJATQE0aShTiCx9NZ7jEq+L4QwFtxjYwEMFBo3Fw@mail.gmail.com>
References: <86wpcs50be.fsf@gmail.com>
 <DA2915A530468E47B3C4845298E6EB038361F537@msgb06.nih.gov>
 <86shngmr40.fsf@gmail.com>
 <8907FC5F-A787-4FDC-BDF8-B101444D3544@mail.nih.gov>
 <CALzTN-RHEpJJATQE0aShTiCx9NZ7jEq+L4QwFtxjYwEMFBo3Fw@mail.gmail.com>
Message-ID: <4F2EE629-9A47-4A92-BAA8-6842B385D85B@mail.nih.gov>

Thanks for the info and links Matt!

Now that we know that ITK work on FreeBSD, the next thing to check does SimpleITK build, run and test OK if wrapping is disabled?

Brad

> On Feb 14, 2017, at 4:48 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
> 
> Hi,
> 
> It is not likely that the errors are related to ITK_DYNAMIC_LOADING.
> 
> FreeBSD has a package for ITK, which gives its configuration:
> 
> https://www.freshports.org/science/InsightToolkit/
> https://reviews.freebsd.org/diffusion/P/browse/head/science/InsightToolkit/Makefile
> 
> HTH,
> Matt
> 
> On Tue, Feb 14, 2017 at 4:32 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
> <blowekamp at mail.nih.gov> wrote:
>> Hi,
>> 
>> Are we sure the first case was not close to mostly working? Did other
>> wrapped language link OK? did SimpleITK tests link OK? If ITK tests are
>> enable with ITK_DYNAMIC_LOADING:BOOL=0 do they compile and work? We need to
>> know if ITK is OK before moving to SimpleITK.
>> 
>> @Matt
>> I am not very familiar with CMAKE_DL_LIBS either [1]. I know Matt added the
>> ITK_DYNAMIC_LOADING CMake variable to ITK, so he may have insight into this
>> problem too. My guess is that CMAKE_DL_LIBS variable is not entered into the
>> cache but CMake provides a default value for platform. I expect you can
>> overrride it with command line values.
>> 
>> I hacked a patch to enable CMAKE_DL_LIBS to propgate down from the
>> Superbuild [2]. If you checkout that path you should be able to do a
>> supberbuild of -DCMAKE_DL_LIBS=??. That may work, but I don?t know for sure.
>> 
>> HTH,
>> Brad
>> 
>> [1] https://cmake.org/cmake/help/v3.0/variable/CMAKE_DL_LIBS.html
>> [2] https://github.com/SimpleITK/SimpleITK/pull/104
>> 
>> 
>> On Feb 14, 2017, at 3:53 PM, Longzhu Shen <lqshen10 at gmail.com> wrote:
>> 
>> Hi Brad,
>> 
>> Many thanks for the advice.
>> I made an attempt to follow the first approach but it did not seem
>> work. Here is what I did and the errors I got.
>> 
>> -----------------------------------------------------
>> $ cmake ../SuperBuild -DITK_DYNAMIC_LOADING:BOOL=0
>> 
>> 
>> [ 80%] Building CXX object
>> Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/sitkPyCommand.cxx.o
>> [ 80%] Building CXX object
>> Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/SimpleITKPYTHON_wrap.cxx.o
>> [ 80%] Linking CXX executable bin/SimpleITKTclsh
>> /usr/bin/ld: cannot find -ldl
>> c++: error: linker command failed with exit code 1 (use -v to see
>> invocation)
>> --- Wrapping/Tcl/bin/SimpleITKTclsh ---
>> *** [Wrapping/Tcl/bin/SimpleITKTclsh] Error code 1
>> -----------------------------------------------------
>> 
>> I planned to try the 2nd approach. However, I could not find the
>> CMAKE_DL_LIBS easily. I checked the subfolder of Superbuild,
>> and SimpleITK-build/ITK-build. I did not find it in
>> Code/Common/src/CMakeLists.txt as well.
>> 
>> The only place I found "CMAKE_DL_LIBS" is in the file
>> CMake/sitkTargetLinkLibrariesWithDynamicLookup.cmake
>> 
>> 279:        target_link_libraries(main \"${CMAKE_DL_LIBS}\")
>> 
>> I was wondering I may get further directions to modify CMAKE_DL_LIBS
>> variable. Many thanks.
>> 
>> sincerely,
>> 
>> Longzhu
>> 
>> 
>> Lowekamp @ 2017-02-14 15:36 UTC:
>> 
>> Hello Longzu,
>> 
>> You are using freebsd, that is new and exciting. I have not used that OS for
>> developing.
>> 
>> There are two things in the ITK/SimpleITK build that are related to this.
>> 
>> First, there is an option in ITK ( which I have not used ) call
>> ITK_DYNAMIC_LOADING. If you pass -DITK_DYNAMIC_LOADING:BOOL=0 to cmake for
>> the Superbuild, it should propagate to the ITK project and this feature will
>> be remove. This may solve your problem.
>> 
>> The second is CMake variable CMAKE_DL_LIBS. I believe it is the dl library
>> that is causing the problem [1]. Setting it to an empty string may also
>> remove it from the linking lines. Getting that to propagate to the ITK
>> project will not happen automatically and would need to be done manually in
>> the ITK build.
>> 
>> HTH,
>> Brad
>> 
>> [1]
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/src/CMakeLists.txt#L142
>> 
>> ________________________________________
>> From: Longzhu Shen [lqshen10 at gmail.com]
>> Sent: Tuesday, February 14, 2017 9:11 AM
>> To: community at itk.org
>> Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
>> 
>> Hello,
>> 
>> I'm trying to compile simpleitk on my freebsd system.
>> The issue I encountered is ldl is not found.
>> After some searching, I found libdl is not needed on freebsd. It is
>> included in libc. Wondering how I can turn it off in the make file.
>> I did not find  ldl in the Makefile under Simpleitk-build.
>> 
>> I followed the instrutions from the link below.
>> 
>> https://chsasank.github.io/sitk-docs/building/unix.html#obtaining-source-code
>> 
>> Thanks.
>> 
>> Longzhu
>> 
>> 
>> 
>> --
>> Longzhu Shen, Ph.D.
>> Postdoc Research Associate
>> School of Forestry and Environmental Studies
>> Yale University
>> 195 Prospect Street
>> New Haven, CT 06511
>> 
>> 


From blowekamp at mail.nih.gov  Wed Feb 15 06:52:20 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 15 Feb 2017 11:52:20 +0000
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
In-Reply-To: <86r330ur5w.fsf@gmail.com>
References: <86wpcs50be.fsf@gmail.com>
 <DA2915A530468E47B3C4845298E6EB038361F537@msgb06.nih.gov>
 <86shngmr40.fsf@gmail.com>
 <8907FC5F-A787-4FDC-BDF8-B101444D3544@mail.nih.gov>
 <CALzTN-RHEpJJATQE0aShTiCx9NZ7jEq+L4QwFtxjYwEMFBo3Fw@mail.gmail.com>
 <86r330ur5w.fsf@gmail.com>
Message-ID: <E46D6743-14D2-4CCB-BBFC-FACF0CE84198@mail.nih.gov>

It looks like our e-mails crossed last night.

I think you were really close to building building SimpleITK. If your goal is to use the SimpleITK language binding I would recommend continuing to use the SimpleITK superbuild. From your previous message the Superbuild compiled all of ITK, and the SimpleITK libraries, and maybe even the SimpleITK testing too. It just appears to have failed on linking for the Tcl wrapping.

When you do the Superbuild of SimpleITK it automatically downloads the correct version of ITK, and compiles it with the correct options to build with SimpleITK.

My recommendation to to verify that the core SimpleITK libraries are being built correctly and that the SimpleITK testing drivers get linked OK. If this is the case it tells us there is something not right with the way the linking is done for the wrapping and we need to closely look at that command line and the options CMake has.

HTH,
Brad

> On Feb 14, 2017, at 9:24 PM, Longzhu Shen <lqshen10 at gmail.com> wrote:
> 
> 
> Hi Brad and Matt,
> 
> Many thanks for the kind advice. I'm very new to ITK. Some of my
> questions may be naive. I hope you could bear with me. I really hope to
> get it working if I could. Thank you very much. 
> 
> I checked out the freebsd port but I could not install it. (errors below)
> 
> Then I went back to the ITK src (I mistakenly thought simpleITK contains
> ITK before) and tried to follow the manual to install it.
> 
> The cmake was fine for the most part but some errors did appear (
> attached). Assuming those errors were not fatal, I
> proceeded with make. The program stopped at the line below. 
> 
> make[2]: don't know how to make ExternalData/Testing/Data/Input/MetaIO/Small\. Stop
> 
> It is the same error when I tried to compile from the ports. 
> 
> Wondering whether I can seek some insight here or it is hopeless with
> freebsd by this point. Thanks for advice.
> 
> sincerely,
> 
> Longzhu
> 
> <cmake_err.log>
> 
> 
> Matt McCormick @ 2017-02-14 21:48 UTC:
> 
>> Hi,
>> 
>> It is not likely that the errors are related to ITK_DYNAMIC_LOADING.
>> 
>> FreeBSD has a package for ITK, which gives its configuration:
>> 
>> https://www.freshports.org/science/InsightToolkit/
>> https://reviews.freebsd.org/diffusion/P/browse/head/science/InsightToolkit/Makefile
>> 
>> HTH,
>> Matt
>> 
>> On Tue, Feb 14, 2017 at 4:32 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
>> <blowekamp at mail.nih.gov> wrote:
>>> Hi,
>>> 
>>> Are we sure the first case was not close to mostly working? Did other
>>> wrapped language link OK? did SimpleITK tests link OK? If ITK tests are
>>> enable with ITK_DYNAMIC_LOADING:BOOL=0 do they compile and work? We need to
>>> know if ITK is OK before moving to SimpleITK.
>>> 
>>> @Matt
>>> I am not very familiar with CMAKE_DL_LIBS either [1]. I know Matt added the
>>> ITK_DYNAMIC_LOADING CMake variable to ITK, so he may have insight into this
>>> problem too. My guess is that CMAKE_DL_LIBS variable is not entered into the
>>> cache but CMake provides a default value for platform. I expect you can
>>> overrride it with command line values.
>>> 
>>> I hacked a patch to enable CMAKE_DL_LIBS to propgate down from the
>>> Superbuild [2]. If you checkout that path you should be able to do a
>>> supberbuild of -DCMAKE_DL_LIBS=??. That may work, but I don?t know for sure.
>>> 
>>> HTH,
>>> Brad
>>> 
>>> [1] https://cmake.org/cmake/help/v3.0/variable/CMAKE_DL_LIBS.html
>>> [2] https://github.com/SimpleITK/SimpleITK/pull/104
>>> 
>>> 
>>> On Feb 14, 2017, at 3:53 PM, Longzhu Shen <lqshen10 at gmail.com> wrote:
>>> 
>>> Hi Brad,
>>> 
>>> Many thanks for the advice.
>>> I made an attempt to follow the first approach but it did not seem
>>> work. Here is what I did and the errors I got.
>>> 
>>> -----------------------------------------------------
>>> $ cmake ../SuperBuild -DITK_DYNAMIC_LOADING:BOOL=0
>>> 
>>> 
>>> [ 80%] Building CXX object
>>> Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/sitkPyCommand.cxx.o
>>> [ 80%] Building CXX object
>>> Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/SimpleITKPYTHON_wrap.cxx.o
>>> [ 80%] Linking CXX executable bin/SimpleITKTclsh
>>> /usr/bin/ld: cannot find -ldl
>>> c++: error: linker command failed with exit code 1 (use -v to see
>>> invocation)
>>> --- Wrapping/Tcl/bin/SimpleITKTclsh ---
>>> *** [Wrapping/Tcl/bin/SimpleITKTclsh] Error code 1
>>> -----------------------------------------------------
>>> 
>>> I planned to try the 2nd approach. However, I could not find the
>>> CMAKE_DL_LIBS easily. I checked the subfolder of Superbuild,
>>> and SimpleITK-build/ITK-build. I did not find it in
>>> Code/Common/src/CMakeLists.txt as well.
>>> 
>>> The only place I found "CMAKE_DL_LIBS" is in the file
>>> CMake/sitkTargetLinkLibrariesWithDynamicLookup.cmake
>>> 
>>> 279:        target_link_libraries(main \"${CMAKE_DL_LIBS}\")
>>> 
>>> I was wondering I may get further directions to modify CMAKE_DL_LIBS
>>> variable. Many thanks.
>>> 
>>> sincerely,
>>> 
>>> Longzhu
>>> 
>>> 
>>> Lowekamp @ 2017-02-14 15:36 UTC:
>>> 
>>> Hello Longzu,
>>> 
>>> You are using freebsd, that is new and exciting. I have not used that OS for
>>> developing.
>>> 
>>> There are two things in the ITK/SimpleITK build that are related to this.
>>> 
>>> First, there is an option in ITK ( which I have not used ) call
>>> ITK_DYNAMIC_LOADING. If you pass -DITK_DYNAMIC_LOADING:BOOL=0 to cmake for
>>> the Superbuild, it should propagate to the ITK project and this feature will
>>> be remove. This may solve your problem.
>>> 
>>> The second is CMake variable CMAKE_DL_LIBS. I believe it is the dl library
>>> that is causing the problem [1]. Setting it to an empty string may also
>>> remove it from the linking lines. Getting that to propagate to the ITK
>>> project will not happen automatically and would need to be done manually in
>>> the ITK build.
>>> 
>>> HTH,
>>> Brad
>>> 
>>> [1]
>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/src/CMakeLists.txt#L142
>>> 
>>> ________________________________________
>>> From: Longzhu Shen [lqshen10 at gmail.com]
>>> Sent: Tuesday, February 14, 2017 9:11 AM
>>> To: community at itk.org
>>> Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
>>> 
>>> Hello,
>>> 
>>> I'm trying to compile simpleitk on my freebsd system.
>>> The issue I encountered is ldl is not found.
>>> After some searching, I found libdl is not needed on freebsd. It is
>>> included in libc. Wondering how I can turn it off in the make file.
>>> I did not find  ldl in the Makefile under Simpleitk-build.
>>> 
>>> I followed the instrutions from the link below.
>>> 
>>> https://chsasank.github.io/sitk-docs/building/unix.html#obtaining-source-code
>>> 
>>> Thanks.
>>> 
>>> Longzhu
>>> 
>>> 
>>> 
>>> --
>>> Longzhu Shen, Ph.D.
>>> Postdoc Research Associate
>>> School of Forestry and Environmental Studies
>>> Yale University
>>> 195 Prospect Street
>>> New Haven, CT 06511
>>> 
>>> 
> 
> 
> -- 
> Longzhu Shen, Ph.D.
> Postdoc Research Associate
> School of Forestry and Environmental Studies
> Yale University
> 195 Prospect Street
> New Haven, CT 06511


From aharr8 at uwo.ca  Wed Feb 15 09:39:03 2017
From: aharr8 at uwo.ca (Andrew Harris)
Date: Wed, 15 Feb 2017 09:39:03 -0500
Subject: [ITK] [ITK-users]  Combining two images after registration
Message-ID: <CAJ0LxQJhsgdJDsYPYvuF64RfR91DqKCg71O2BBxG4TmdUz1pwA@mail.gmail.com>

Hello,
Hopefully someone can point me in the right direction.  I have a successful
image registration between two images of the same size I have confirmed by
outputting two .mha files and blending them in Slicer.  What I would like
to be able to do is to combine them within C++ and output a single .mha
file. As a further complication, part of the moving image gets left off
because the image rotates outside the bounds of the original image size,
and it would be preferable if I could figure out how to pad the moving
image automatically in the dimensions necessary to prevent this from
happening.

Any thoughts are welcome.

--

AH


-----------------------------------------------------------------------------------------------

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
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Kitware offers ITK Training Courses, for more information visit:
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From aharr8 at uwo.ca  Wed Feb 15 10:01:22 2017
From: aharr8 at uwo.ca (Andrew Harris)
Date: Wed, 15 Feb 2017 10:01:22 -0500
Subject: [ITK] [ITK-users]  Combining two images after registration
In-Reply-To: <1794402278.6753322.1487169757019@mail.yahoo.com>
References: <CAJ0LxQJhsgdJDsYPYvuF64RfR91DqKCg71O2BBxG4TmdUz1pwA@mail.gmail.com>
 <1794402278.6753322.1487169757019@mail.yahoo.com>
Message-ID: <CAJ0LxQ+xKUVKVh1W=hPBDkVoLk5CqRd24BaxE0PFrtEFyz2hbw@mail.gmail.com>

Thanks for getting back to me,
I looked at that filter and it has a warning that said ?No numeric overflow
checking is performed in this filter?, so I assumed that meant that if I
put an image through it there would be a simple addition pixelwise across
the image.  That would make the overlap region brighter than the
non-overlap region which I was trying to avoid.

--

AH


-----------------------------------------------------------------------------------------------

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
thereto.*

On Wed, Feb 15, 2017 at 9:42 AM, ibraheem aldhamari <ibr_ex at yahoo.com>
wrote:

> Hey,
> In Slicer you can use Add Scalar Volume plugin.
> In itk use this :
>     https://itk.org/Doxygen/html/classitk_1_1AddImageFilter.html
>     https://itk.org/Wiki/ITK/Examples/ImageProcessing/AddImageFilter
>
> Best regards and have a nice day!
> Ibraheem
>
>
> ------------------------------
> *From:* Andrew Harris <aharr8 at uwo.ca>
> *To:* Insight-users <insight-users at itk.org>
> *Sent:* Wednesday, February 15, 2017 3:39 PM
> *Subject:* [ITK-users] [ITK] Combining two images after registration
>
> Hello,
> Hopefully someone can point me in the right direction.  I have a
> successful image registration between two images of the same size I have
> confirmed by outputting two .mha files and blending them in Slicer.  What I
> would like to be able to do is to combine them within C++ and output a
> single .mha file. As a further complication, part of the moving image gets
> left off because the image rotates outside the bounds of the original image
> size, and it would be preferable if I could figure out how to pad the
> moving image automatically in the dimensions necessary to prevent this from
> happening.
>
> Any thoughts are welcome.
> --
> AH
>
> ------------------------------------------------------------
> -----------------------------------
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
>
>
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_____________________________________
Powered by www.kitware.com

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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From aharr8 at uwo.ca  Wed Feb 15 12:40:26 2017
From: aharr8 at uwo.ca (Andrew Harris)
Date: Wed, 15 Feb 2017 12:40:26 -0500
Subject: [ITK] [ITK-users]  Combining two images after registration
In-Reply-To: <828723854.6878428.1487171256467@mail.yahoo.com>
References: <CAJ0LxQJhsgdJDsYPYvuF64RfR91DqKCg71O2BBxG4TmdUz1pwA@mail.gmail.com>
 <1794402278.6753322.1487169757019@mail.yahoo.com>
 <CAJ0LxQ+xKUVKVh1W=hPBDkVoLk5CqRd24BaxE0PFrtEFyz2hbw@mail.gmail.com>
 <828723854.6878428.1487171256467@mail.yahoo.com>
Message-ID: <CAJ0LxQ+_CFsYnGYwqkipt_BN5qWu7zDpJjEv1qhLezzRHmKZrQ@mail.gmail.com>

That will work for the region inside the overlap region, but the region
outside the overlap region would then have their value reduced by half.  Is
there a filter pre-written that checks for information in the overlap
region before doing the scaling?  I have something partially written that
does that but it doesn't fix the portion of the image that is cut off
because it rotates outside the original image bounds.

Thanks for your help.

--

AH


-----------------------------------------------------------------------------------------------

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
thereto.*

On Wed, Feb 15, 2017 at 10:07 AM, ibraheem aldhamari <ibr_ex at yahoo.com>
wrote:

> save the images in the same datatype then multiply each image by 0.5
> before adding
> https://itk.org/ITKExamples/src/Filtering/ImageIntensity/
> MultiplyImageByScalar/Documentation.html
>
>
> Best regards and have a nice day!
> Ibraheem
>
>
> ------------------------------
> *From:* Andrew Harris <aharr8 at uwo.ca>
> *To:* ibraheem aldhamari <ibr_ex at yahoo.com>
> *Cc:* Insight-users <insight-users at itk.org>
> *Sent:* Wednesday, February 15, 2017 4:01 PM
> *Subject:* Re: [ITK-users] [ITK] Combining two images after registration
>
> Thanks for getting back to me,
> I looked at that filter and it has a warning that said ?No numeric
> overflow checking is performed in this filter?, so I assumed that meant
> that if I put an image through it there would be a simple addition
> pixelwise across the image.  That would make the overlap region brighter
> than the non-overlap region which I was trying to avoid.
>
> --
> AH
>
> ------------------------------------------------------------
> -----------------------------------
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> On Wed, Feb 15, 2017 at 9:42 AM, ibraheem aldhamari <ibr_ex at yahoo.com>
> wrote:
>
> Hey,
> In Slicer you can use Add Scalar Volume plugin.
> In itk use this :
>     https://itk.org/Doxygen/ html/classitk_1_ 1AddImageFilter.html
> <https://itk.org/Doxygen/html/classitk_1_1AddImageFilter.html>
>     https://itk.org/Wiki/ITK/ Examples/ImageProcessing/ AddImageFilter
> <https://itk.org/Wiki/ITK/Examples/ImageProcessing/AddImageFilter>
>
> Best regards and have a nice day!
> Ibraheem
>
>
> ------------------------------
> *From:* Andrew Harris <aharr8 at uwo.ca>
> *To:* Insight-users <insight-users at itk.org>
> *Sent:* Wednesday, February 15, 2017 3:39 PM
> *Subject:* [ITK-users] [ITK] Combining two images after registration
>
> Hello,
> Hopefully someone can point me in the right direction.  I have a
> successful image registration between two images of the same size I have
> confirmed by outputting two .mha files and blending them in Slicer.  What I
> would like to be able to do is to combine them within C++ and output a
> single .mha file. As a further complication, part of the moving image gets
> left off because the image rotates outside the bounds of the original image
> size, and it would be preferable if I could figure out how to pad the
> moving image automatically in the dimensions necessary to prevent this from
> happening.
>
> Any thoughts are welcome.
> --
> AH
>
> ------------------------------ ------------------------------
> ------------------------------ -----
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> ______________________________ _______
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/ opensource/opensource.html
> <http://www.kitware.com/opensource/opensource.html>
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/ products/protraining.php
> <http://www.kitware.com/products/protraining.php>
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_ FAQ <http://www.itk.org/Wiki/ITK_FAQ>
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/ mailman/listinfo/insight-users
> <http://public.kitware.com/mailman/listinfo/insight-users>
>
>
>
>
>
>
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From blowekamp at mail.nih.gov  Thu Feb 16 09:58:06 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 16 Feb 2017 14:58:06 +0000
Subject: [ITK] [ANN] SimpleITK 1.0 Release Candidate 1
Message-ID: <DA2915A530468E47B3C4845298E6EB038362398C@msgb06.nih.gov>


On behalf of the SimpleITK developers and the Insight Software Consortium community, we please to announce the release of the SimpleITK 1.0 Release Candidate 1!

For the first release candidate we are only providing source code distributions. The source-balls can be found on GitHub(https://github.com/SimpleITK/SimpleITK/releases/tag/v1.0rc1) and SourceForge (https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0rc1/Source/).


We encourage users to try to build SimpleITK v1.0rc1 from the source (https://itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself).

There are a number of new and updated language specific "front-ends" to use:
 - Python - https://github.com/SimpleITK/SimpleITKPythonPackage
 - R - https://github.com/SimpleITK/SimpleITKRInstaller
 - Lua - https://github.com/SimpleITK/SimpleITKLuaRock
 - Anaconda - https://github.com/SimpleITK/SimpleITKCondaRecipe

Release Notes:

* Key Improvements:
   - Improved Python data bridge
     - New Python method `GetArrayViewFromImage` provides copy free read-only access
     - Updated Python data structures to use `memory view` objects
   - Building SimpleITK wrappers:
     - R devtools based installer (https://github.com/SimpleITK/SimpleITKRInstaller).
     - Python: scripts for building wheels (https://github.com/SimpleITK/SimpleITKPythonPackage) and a Conda recipe (https://github.com/SimpleITK/SimpleITKCondaRecipe).
  - Support use of virtual image domain in the `ImageRegistrationMethod`.
  - OnePlusOneOptimizer added to registration framework.
  - Improved support for R: propogating C++ exceptions into R, additional R tests.
  - Additional tests for Java.
  - Python and R notebooks repository illustrating the basics and more advanced functionality of SimpleITK (https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks).
  - Added continous integration via CircleCI.
  - Updated version and improved integration of Google Test.
  - Updated ITK version to 4.11
  - Updated minimal required CMake version to 3.0, and numerous CMake changes to support various build configurations.
  - Updated to usage of SWIG 3.0.11 ( using the latest SIWG is strongly recommended for R )
  - Reorganized examples directory into example based sub-directories with multiple languages
  - Improvements to documentation transmogrification scripts
  - Many bug fixes and improvement to the build system!

* API changes:
  - R methods which previously unnecessarily returned self return void.
  - New method `Image::GetNumberOfPixels`
  - New method `LabelMapContourOverlayImageFilter::SetColormap`
  - New method `LabelMapToRGBImageFilter::SetColormap`
  - New method `ImageRegistrationMethod::SetVirtualDomain` 
  - New method `ImageRegistrationMethod::SetVirtualDomainFromImage`
  - New seed parameter to `ImageRegistrationMethod::AddMetricSamplingSeed` method
  - `CastImageFilter::SetOutputPixelType` method no longer accepts the pixel ID by value, uses only enumerated type.


Please try out SimpleITK 1.0rc1, and report any issues!

Enjoy!

Bradley Lowekamp

From tamanupadhaya at gmail.com  Thu Feb 16 11:42:00 2017
From: tamanupadhaya at gmail.com (Tmn)
Date: Thu, 16 Feb 2017 09:42:00 -0700 (MST)
Subject: [ITK] [ITK-users] Grey Level Run Length Matrix
Message-ID: <1487263320349-7589629.post@n2.nabble.com>

Hi all,

I am using itk library to extract Run Length Matrix texture feature using
itk::Statistics::ScalarImageToRunLengthMatrixFilter<>; however, the total
frequency of the matrix is more than the total number of pixel.   

For all the 13 different matrices the total frequency is sometime less than
and some time higher than total number of pixel.
These are the parameter I have provided, do I need to provide more parameter
than this ?

RunLenFilter->SetOffset(offset);
RunLenFilter->SetDistanceValueMinMax( 0, pointMin.EuclideanDistanceTo(
pointMax ) );  
RunLenFilter->SetPixelValueMinMax(minValue,maxValue); 
RunLenFilter->SetNumberOfBinsPerAxis(Bins);

Can someone please provide me with some inside of Run Length Matrix
function/method? 

Thank you for your time!



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Grey-Level-Run-Length-Matrix-tp7589629.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
_____________________________________
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From francois.budin at kitware.com  Thu Feb 16 16:45:34 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Thu, 16 Feb 2017 16:45:34 -0500
Subject: [ITK] [ITK-users]  Combining two images after registration
In-Reply-To: <CAJ0LxQ+_CFsYnGYwqkipt_BN5qWu7zDpJjEv1qhLezzRHmKZrQ@mail.gmail.com>
References: <CAJ0LxQJhsgdJDsYPYvuF64RfR91DqKCg71O2BBxG4TmdUz1pwA@mail.gmail.com>
 <1794402278.6753322.1487169757019@mail.yahoo.com>
 <CAJ0LxQ+xKUVKVh1W=hPBDkVoLk5CqRd24BaxE0PFrtEFyz2hbw@mail.gmail.com>
 <828723854.6878428.1487171256467@mail.yahoo.com>
 <CAJ0LxQ+_CFsYnGYwqkipt_BN5qWu7zDpJjEv1qhLezzRHmKZrQ@mail.gmail.com>
Message-ID: <CAHwLD2XTnFsgtoO0eSLEgxM0UAExOyyMmWoSNa6w3VFVUvb5HA@mail.gmail.com>

Hello Andrew,

There is currently no complete implementation of what you are doing in ITK.
However, there are a few pieces that are available and that you can use.
1) To combine multiple images that partially overlap, you can refer to this
insight Journal article [1].
2) To compute the size of the output image that you need, you can look at
[2] (computing transformed image bounding box).
3) If you create a more complete implementation that solves this problem,
feel free to contribute to ITK. The easiest way to contribute to ITK is to
write an Insight Journal article and implement an external ITK module. You
can refer to the ITK software guide for more information about the process
[3].

Hope this helps,
Francois

[1] http://www.insight-journal.org/browse/publication/914
[2] https://github.com/fbudin69500/ITKTransformTools
[3] https://itk.org/ITK/help/documentation.html


On Wed, Feb 15, 2017 at 12:40 PM, Andrew Harris <aharr8 at uwo.ca> wrote:

> That will work for the region inside the overlap region, but the region
> outside the overlap region would then have their value reduced by half.  Is
> there a filter pre-written that checks for information in the overlap
> region before doing the scaling?  I have something partially written that
> does that but it doesn't fix the portion of the image that is cut off
> because it rotates outside the original image bounds.
>
> Thanks for your help.
>
> --
>
> AH
>
>
> ------------------------------------------------------------
> -----------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> On Wed, Feb 15, 2017 at 10:07 AM, ibraheem aldhamari <ibr_ex at yahoo.com>
> wrote:
>
>> save the images in the same datatype then multiply each image by 0.5
>> before adding
>> https://itk.org/ITKExamples/src/Filtering/ImageIntensity/Mul
>> tiplyImageByScalar/Documentation.html
>>
>>
>> Best regards and have a nice day!
>> Ibraheem
>>
>>
>> ------------------------------
>> *From:* Andrew Harris <aharr8 at uwo.ca>
>> *To:* ibraheem aldhamari <ibr_ex at yahoo.com>
>> *Cc:* Insight-users <insight-users at itk.org>
>> *Sent:* Wednesday, February 15, 2017 4:01 PM
>> *Subject:* Re: [ITK-users] [ITK] Combining two images after registration
>>
>> Thanks for getting back to me,
>> I looked at that filter and it has a warning that said ?No numeric
>> overflow checking is performed in this filter?, so I assumed that meant
>> that if I put an image through it there would be a simple addition
>> pixelwise across the image.  That would make the overlap region brighter
>> than the non-overlap region which I was trying to avoid.
>>
>> --
>> AH
>>
>> ------------------------------------------------------------
>> -----------------------------------
>> *This email and any attachments thereto may contain private,
>> confidential, and privileged materials for the sole use of the intended
>> recipient. Any reviewing, copying, or distribution of this email (or any
>> attachments thereto) by other than the intended recipient is strictly
>> prohibited. If you are not the intended recipient, please contact the
>> sender immediately and permanently destroy this email and any attachments
>> thereto.*
>>
>> On Wed, Feb 15, 2017 at 9:42 AM, ibraheem aldhamari <ibr_ex at yahoo.com>
>> wrote:
>>
>> Hey,
>> In Slicer you can use Add Scalar Volume plugin.
>> In itk use this :
>>     https://itk.org/Doxygen/ html/classitk_1_ 1AddImageFilter.html
>> <https://itk.org/Doxygen/html/classitk_1_1AddImageFilter.html>
>>     https://itk.org/Wiki/ITK/ Examples/ImageProcessing/ AddImageFilter
>> <https://itk.org/Wiki/ITK/Examples/ImageProcessing/AddImageFilter>
>>
>> Best regards and have a nice day!
>> Ibraheem
>>
>>
>> ------------------------------
>> *From:* Andrew Harris <aharr8 at uwo.ca>
>> *To:* Insight-users <insight-users at itk.org>
>> *Sent:* Wednesday, February 15, 2017 3:39 PM
>> *Subject:* [ITK-users] [ITK] Combining two images after registration
>>
>> Hello,
>> Hopefully someone can point me in the right direction.  I have a
>> successful image registration between two images of the same size I have
>> confirmed by outputting two .mha files and blending them in Slicer.  What I
>> would like to be able to do is to combine them within C++ and output a
>> single .mha file. As a further complication, part of the moving image gets
>> left off because the image rotates outside the bounds of the original image
>> size, and it would be preferable if I could figure out how to pad the
>> moving image automatically in the dimensions necessary to prevent this from
>> happening.
>>
>> Any thoughts are welcome.
>> --
>> AH
>>
>> ------------------------------ ------------------------------
>> ------------------------------ -----
>> *This email and any attachments thereto may contain private,
>> confidential, and privileged materials for the sole use of the intended
>> recipient. Any reviewing, copying, or distribution of this email (or any
>> attachments thereto) by other than the intended recipient is strictly
>> prohibited. If you are not the intended recipient, please contact the
>> sender immediately and permanently destroy this email and any attachments
>> thereto.*
>>
>> ______________________________ _______
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/ opensource/opensource.html
>> <http://www.kitware.com/opensource/opensource.html>
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/ products/protraining.php
>> <http://www.kitware.com/products/protraining.php>
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_ FAQ <http://www.itk.org/Wiki/ITK_FAQ>
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/ mailman/listinfo/insight-users
>> <http://public.kitware.com/mailman/listinfo/insight-users>
>>
>>
>>
>>
>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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>
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Kitware offers ITK Training Courses, for more information visit:
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From bill.lorensen at gmail.com  Fri Feb 17 08:08:47 2017
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 17 Feb 2017 08:08:47 -0500
Subject: [ITK] [ITK-dev] Mac Sierra 10.12.3 linker errors
Message-ID: <CADZJ4hNDOHYkV3_knyKy4iGtF9J76VdyeTnKWbWFmPHLs_UcwQ@mail.gmail.com>

On my new Sierra MacOS,
Apple LLVM version 8.0.0 (clang-800.0.42.1)
fails to link.

This change id:
http://review.source.kitware.com/#/c/21946/

causes the problem.

The error is:
100%] Linking CXX executable
../../../ThirdParty/VNL/src/vxl/bin/ITKVtkGlueTestDriver
Undefined symbols for architecture x86_64:
  "itk::Detail::AtomicOps<4ul>::Load(itk::Detail::AtomicOps<4ul>::AtomicType
const*)", referenced from:
      itk::LightObject::GetReferenceCount() const in ITKVtkGlueTestDriver.cxx.o
      itk::LightObject::GetReferenceCount() const in
itkVtkConnectedComponentImageFilterTest.cxx.o
      itk::LightObject::GetReferenceCount() const in
itkVtkMedianFilterTest.cxx.o
      itk::LightObject::GetReferenceCount() const in
itkImageToVTKImageFilterTest.cxx.o
      itk::LightObject::GetReferenceCount() const in
itkImageToVTKImageFilterRGBTest.cxx.o
      itk::LightObject::GetReferenceCount() const in
itkVTKImageToImageFilterTest.cxx.o
      itk::LightObject::GetReferenceCount() const in QuickViewTest.cxx.o
      ...
ld: symbol(s) not found for architecture x86_64


-- 
Unpaid intern in BillsBasement at noware dot com
_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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From blowekamp at mail.nih.gov  Fri Feb 17 08:38:36 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 17 Feb 2017 13:38:36 +0000
Subject: [ITK] [ITK-dev]   Mac Sierra 10.12.3 linker errors
In-Reply-To: <CADZJ4hNDOHYkV3_knyKy4iGtF9J76VdyeTnKWbWFmPHLs_UcwQ@mail.gmail.com>
References: <CADZJ4hNDOHYkV3_knyKy4iGtF9J76VdyeTnKWbWFmPHLs_UcwQ@mail.gmail.com>
Message-ID: <D461FCFC-F8B1-473B-AC64-ABB179F13881@mail.nih.gov>

Hello Bill,

Francois is work on a patch for this issue:
http://review.source.kitware.com/#/c/22081/

Good to hear from you,
Brad
> On Feb 17, 2017, at 8:08 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> 
> On my new Sierra MacOS,
> Apple LLVM version 8.0.0 (clang-800.0.42.1)
> fails to link.
> 
> This change id:
> http://review.source.kitware.com/#/c/21946/
> 
> causes the problem.
> 
> The error is:
> 100%] Linking CXX executable
> ../../../ThirdParty/VNL/src/vxl/bin/ITKVtkGlueTestDriver
> Undefined symbols for architecture x86_64:
>  "itk::Detail::AtomicOps<4ul>::Load(itk::Detail::AtomicOps<4ul>::AtomicType
> const*)", referenced from:
>      itk::LightObject::GetReferenceCount() const in ITKVtkGlueTestDriver.cxx.o
>      itk::LightObject::GetReferenceCount() const in
> itkVtkConnectedComponentImageFilterTest.cxx.o
>      itk::LightObject::GetReferenceCount() const in
> itkVtkMedianFilterTest.cxx.o
>      itk::LightObject::GetReferenceCount() const in
> itkImageToVTKImageFilterTest.cxx.o
>      itk::LightObject::GetReferenceCount() const in
> itkImageToVTKImageFilterRGBTest.cxx.o
>      itk::LightObject::GetReferenceCount() const in
> itkVTKImageToImageFilterTest.cxx.o
>      itk::LightObject::GetReferenceCount() const in QuickViewTest.cxx.o
>      ...
> ld: symbol(s) not found for architecture x86_64
> 
> 
> -- 
> Unpaid intern in BillsBasement at noware dot com
> _______________________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
> 
> 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://public.kitware.com/mailman/listinfo/insight-developers
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

_______________________________________________
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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From bill.lorensen at gmail.com  Fri Feb 17 09:01:30 2017
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 17 Feb 2017 09:01:30 -0500
Subject: [ITK] [ITK-dev]   Mac Sierra 10.12.3 linker errors
In-Reply-To: <D461FCFC-F8B1-473B-AC64-ABB179F13881@mail.nih.gov>
References: <CADZJ4hNDOHYkV3_knyKy4iGtF9J76VdyeTnKWbWFmPHLs_UcwQ@mail.gmail.com>
 <D461FCFC-F8B1-473B-AC64-ABB179F13881@mail.nih.gov>
Message-ID: <CADZJ4hMD+qT8GajFRBPCK3pjsbqCTEROTa8-Svavv5K2KV2Z6A@mail.gmail.com>

Brad,  I'm celebrating a new hip.

Bill

On Feb 17, 2017 8:38 AM, "Lowekamp, Bradley (NIH/NLM/LHC) [C]" <
blowekamp at mail.nih.gov> wrote:

> Hello Bill,
>
> Francois is work on a patch for this issue:
> http://review.source.kitware.com/#/c/22081/
>
> Good to hear from you,
> Brad
> > On Feb 17, 2017, at 8:08 AM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
> >
> > On my new Sierra MacOS,
> > Apple LLVM version 8.0.0 (clang-800.0.42.1)
> > fails to link.
> >
> > This change id:
> > http://review.source.kitware.com/#/c/21946/
> >
> > causes the problem.
> >
> > The error is:
> > 100%] Linking CXX executable
> > ../../../ThirdParty/VNL/src/vxl/bin/ITKVtkGlueTestDriver
> > Undefined symbols for architecture x86_64:
> >  "itk::Detail::AtomicOps<4ul>::Load(itk::Detail::AtomicOps<
> 4ul>::AtomicType
> > const*)", referenced from:
> >      itk::LightObject::GetReferenceCount() const in
> ITKVtkGlueTestDriver.cxx.o
> >      itk::LightObject::GetReferenceCount() const in
> > itkVtkConnectedComponentImageFilterTest.cxx.o
> >      itk::LightObject::GetReferenceCount() const in
> > itkVtkMedianFilterTest.cxx.o
> >      itk::LightObject::GetReferenceCount() const in
> > itkImageToVTKImageFilterTest.cxx.o
> >      itk::LightObject::GetReferenceCount() const in
> > itkImageToVTKImageFilterRGBTest.cxx.o
> >      itk::LightObject::GetReferenceCount() const in
> > itkVTKImageToImageFilterTest.cxx.o
> >      itk::LightObject::GetReferenceCount() const in QuickViewTest.cxx.o
> >      ...
> > ld: symbol(s) not found for architecture x86_64
> >
> >
> > --
> > Unpaid intern in BillsBasement at noware dot com
> > _______________________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://kitware.com/products/protraining.php
> >
> > 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://public.kitware.com/mailman/listinfo/insight-developers
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> > Community mailing list
> > Community at itk.org
> > http://public.kitware.com/mailman/listinfo/community
>
>
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From nour_sn at hotmail.fr  Fri Feb 17 07:30:15 2017
From: nour_sn at hotmail.fr (jaki19)
Date: Fri, 17 Feb 2017 05:30:15 -0700 (MST)
Subject: [ITK] [ITK-users] How to add new points inside a 3D structure and
 connect them with neighboring points
Message-ID: <1487334615917-37925.post@n7.nabble.com>

Hallo,

I have a DICOM images of a vertebra, that I converted to stl file and using
vtkreadstlfile I converted it into vtkpolydata. I would like to know if
there are some functions that can help me to add some new points (with
random coordinates) inside my structure and connect those new points to
neighboring points that exist in a specific distance??

Thanks  



--
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Sent from the ITK - Users mailing list archive at Nabble.com.
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From mdccnunes at hotmail.com  Tue Feb 21 06:29:45 2017
From: mdccnunes at hotmail.com (Miguel Nunes)
Date: Tue, 21 Feb 2017 11:29:45 +0000
Subject: [ITK] Build issue with ITK 4.11
Message-ID: <CY1PR14MB0582950B70E8DA831F031D64A5510@CY1PR14MB0582.namprd14.prod.outlook.com>

Hello,

I have just downloaded the new ITK 4.11 and I am having a couple of issues compiling in Windows 10, 64bit release, Visual Studio (version 12 - update 5).
I also have the new AMD APP SDK 3.0 (for openCL libs and includes).

The error is as follows:

mylibraries\itk\insighttoolkit-4.11.0\modules\core\gpucommon\include\itkGPUImage.h(179): error C3668: 'itk::GPUImage<unsigned char,1>::Graft' : method with override specifier 'override' did not override any base class methods

I also went to git hub and downloaded the master. I tried compiling it but got different errors.

Any help is appreciated!

Best regards
Miguel
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From mdccnunes at hotmail.com  Tue Feb 21 07:29:14 2017
From: mdccnunes at hotmail.com (sharkpt)
Date: Tue, 21 Feb 2017 05:29:14 -0700 (MST)
Subject: [ITK] [ITK-users] ITK 4.11 build issue
Message-ID: <1487680154437-37926.post@n7.nabble.com>

Hello,

I have just downloaded the new ITK 4.11 and I am having a couple of issues
compiling in Windows 10, 64bit release, Visual Studio (version 12 - update
5). 
I also have the new AMD APP SDK 3.0 (for openCL libs and includes). 

The error is as follows: 

mylibraries\itk\insighttoolkit-4.11.0\modules\core\gpucommon\include\itkGPUImage.h(179):
error C3668: 'itk::GPUImage<unsigned char,1>::Graft' : method with override
specifier 'override' did not override any base class methods

I also went to git hub and downloaded the master. I tried compiling it but
got different errors. 

Any help is appreciated! 

Best regards
Miguel



--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-4-11-build-issue-tp37926.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From zack.galbreath at kitware.com  Tue Feb 21 09:57:31 2017
From: zack.galbreath at kitware.com (Zack Galbreath)
Date: Tue, 21 Feb 2017 09:57:31 -0500
Subject: [ITK] [ITK-dev] open.cdash.org updated
Message-ID: <CANgkMA6Jqv6SPP-ZbtdNzoiSmskYmcBR4R8hNWF0XiSkrwXh_A@mail.gmail.com>

Hi folks,

I just upgraded open.cdash.org.  The most visible change you'll notice is
that the Update column now shows the commit that was built rather than the
number of files that changed.

Going forward, I've set a reminder for myself to upgrade open.cdash.org
once a month around this time (the 21st).
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From blowekamp at mail.nih.gov  Tue Feb 21 11:10:46 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 21 Feb 2017 16:10:46 +0000
Subject: [ITK] [ITK-dev] open.cdash.org updated
In-Reply-To: <CANgkMA6Jqv6SPP-ZbtdNzoiSmskYmcBR4R8hNWF0XiSkrwXh_A@mail.gmail.com>
References: <CANgkMA6Jqv6SPP-ZbtdNzoiSmskYmcBR4R8hNWF0XiSkrwXh_A@mail.gmail.com>
Message-ID: <DB259B32-2201-46DC-80E2-61FD1B330DFC@mail.nih.gov>

Zack,

I do like the seeing the revision hash there. That is nice to know what is built.


- 2 cents:

However, is there a way to still get the list of files changed? Or the update commit range? I have found this very important when tracking down failures. You find on the dashboard where things start failing, then you can look at the changed files between builds. I guess the best git like way to do this would be something like showing: "old_hash?new_hash? this should play nicely with git log tools.

Thanks of for keeping thing updated!
Brad

On Feb 21, 2017, at 9:57 AM, Zack Galbreath <zack.galbreath at kitware.com<mailto:zack.galbreath at kitware.com>> wrote:

Hi folks,

I just upgraded open.cdash.org<http://open.cdash.org/>.  The most visible change you'll notice is that the Update column now shows the commit that was built rather than the number of files that changed.

Going forward, I've set a reminder for myself to upgrade open.cdash.org<http://open.cdash.org/> once a month around this time (the 21st).
_______________________________________________
Powered by www.kitware.com<http://www.kitware.com>

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From bill.lorensen at gmail.com  Tue Feb 21 11:25:30 2017
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Tue, 21 Feb 2017 11:25:30 -0500
Subject: [ITK] [ITK-dev] open.cdash.org updated
In-Reply-To: <DB259B32-2201-46DC-80E2-61FD1B330DFC@mail.nih.gov>
References: <CANgkMA6Jqv6SPP-ZbtdNzoiSmskYmcBR4R8hNWF0XiSkrwXh_A@mail.gmail.com>
 <DB259B32-2201-46DC-80E2-61FD1B330DFC@mail.nih.gov>
Message-ID: <CADZJ4hOQx_hbJgMnVtBSyDJPKT8xRxzntNQnsLs5X03TLS4=Xg@mail.gmail.com>

I agree with Brad. We really need to see what files have been updated.


On Tue, Feb 21, 2017 at 11:10 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
<blowekamp at mail.nih.gov> wrote:
> Zack,
>
> I do like the seeing the revision hash there. That is nice to know what is
> built.
>
>
> - 2 cents:
>
> However, is there a way to still get the list of files changed? Or the
> update commit range? I have found this very important when tracking down
> failures. You find on the dashboard where things start failing, then you can
> look at the changed files between builds. I guess the best git like way to
> do this would be something like showing: "old_hash?new_hash? this should
> play nicely with git log tools.
>
> Thanks of for keeping thing updated!
> Brad
>
> On Feb 21, 2017, at 9:57 AM, Zack Galbreath <zack.galbreath at kitware.com>
> wrote:
>
> Hi folks,
>
> I just upgraded open.cdash.org.  The most visible change you'll notice is
> that the Update column now shows the commit that was built rather than the
> number of files that changed.
>
> Going forward, I've set a reminder for myself to upgrade open.cdash.org once
> a month around this time (the 21st).
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-developers
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-developers
>



-- 
Unpaid intern in BillsBasement at noware dot com
_______________________________________________
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From zack.galbreath at kitware.com  Tue Feb 21 11:58:36 2017
From: zack.galbreath at kitware.com (Zack Galbreath)
Date: Tue, 21 Feb 2017 11:58:36 -0500
Subject: [ITK] [ITK-dev] open.cdash.org updated
In-Reply-To: <DB259B32-2201-46DC-80E2-61FD1B330DFC@mail.nih.gov>
References: <CANgkMA6Jqv6SPP-ZbtdNzoiSmskYmcBR4R8hNWF0XiSkrwXh_A@mail.gmail.com>
 <DB259B32-2201-46DC-80E2-61FD1B330DFC@mail.nih.gov>
Message-ID: <CANgkMA7kzSrmLmm-ZiOcdAdfaFrktZL_Poev38O_muzWOzsh=A@mail.gmail.com>

On Tue, Feb 21, 2017 at 11:10 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Zack,
>
> I do like the seeing the revision hash there. That is nice to know what is
> built.
>
>
> - 2 cents:
>
> However, is there a way to still get the list of files changed? Or the
> update commit range? I have found this very important when tracking down
> failures. You find on the dashboard where things start failing, then you
> can look at the changed files between builds. I guess the best git like way
> to do this would be something like showing: "old_hash?new_hash? this should
> play nicely with git log tools.
>

AFAIK this hasn't changed.  For example, if I click on the update column
for the Nightly Expected CMake build from dash1win7.kitware, it brings me
here:

https://open.cdash.org/viewUpdate.php?buildid=4777108

This shows the previous commit, the current commit, and the files that
changed in between.
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From zack.galbreath at kitware.com  Tue Feb 21 12:06:17 2017
From: zack.galbreath at kitware.com (Zack Galbreath)
Date: Tue, 21 Feb 2017 12:06:17 -0500
Subject: [ITK] [ITK-dev] [CDash] open.cdash.org updated
In-Reply-To: <81aaa674-c3ca-b004-2ca1-203b6bb6d7dc@gmail.com>
References: <CANgkMA6Jqv6SPP-ZbtdNzoiSmskYmcBR4R8hNWF0XiSkrwXh_A@mail.gmail.com>
 <81aaa674-c3ca-b004-2ca1-203b6bb6d7dc@gmail.com>
Message-ID: <CANgkMA4zPnpJoBqdt+iMwu=sVy8eGSTUrPfHBvzkUipNWZU7iw@mail.gmail.com>

On Tue, Feb 21, 2017 at 10:03 AM, Nils Gladitz <nilsgladitz at gmail.com>
wrote:

> Could the prebuilt branch be updated along with it?
>

Good idea!  I just updated the prebuilt branch too.
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From bill.lorensen at gmail.com  Tue Feb 21 12:07:03 2017
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Tue, 21 Feb 2017 12:07:03 -0500
Subject: [ITK] [ITK-dev] open.cdash.org updated
In-Reply-To: <CANgkMA7kzSrmLmm-ZiOcdAdfaFrktZL_Poev38O_muzWOzsh=A@mail.gmail.com>
References: <CANgkMA6Jqv6SPP-ZbtdNzoiSmskYmcBR4R8hNWF0XiSkrwXh_A@mail.gmail.com>
 <DB259B32-2201-46DC-80E2-61FD1B330DFC@mail.nih.gov>
 <CANgkMA7kzSrmLmm-ZiOcdAdfaFrktZL_Poev38O_muzWOzsh=A@mail.gmail.com>
Message-ID: <CADZJ4hPzqiv1Kt5-R_taz2FQqa53L7C7CXbrVPVYY1B_9MvqmA@mail.gmail.com>

Zach,

I don't see that behavior on the VTK dashboard.
https://open.cdash.org/viewUpdate.php?buildid=4778001

Bill

On Tue, Feb 21, 2017 at 11:58 AM, Zack Galbreath
<zack.galbreath at kitware.com> wrote:
> On Tue, Feb 21, 2017 at 11:10 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
> <blowekamp at mail.nih.gov> wrote:
>>
>> Zack,
>>
>> I do like the seeing the revision hash there. That is nice to know what is
>> built.
>>
>>
>> - 2 cents:
>>
>> However, is there a way to still get the list of files changed? Or the
>> update commit range? I have found this very important when tracking down
>> failures. You find on the dashboard where things start failing, then you can
>> look at the changed files between builds. I guess the best git like way to
>> do this would be something like showing: "old_hash?new_hash? this should
>> play nicely with git log tools.
>
>
> AFAIK this hasn't changed.  For example, if I click on the update column for
> the Nightly Expected CMake build from dash1win7.kitware, it brings me here:
>
> https://open.cdash.org/viewUpdate.php?buildid=4777108
>
> This shows the previous commit, the current commit, and the files that
> changed in between.
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-developers
>



-- 
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_______________________________________________
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From francois.budin at kitware.com  Tue Feb 21 12:11:02 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Tue, 21 Feb 2017 12:11:02 -0500
Subject: [ITK] [ITK-users] ITK 4.11 build issue
In-Reply-To: <1487680154437-37926.post@n7.nabble.com>
References: <1487680154437-37926.post@n7.nabble.com>
Message-ID: <CAHwLD2VJdcsa-25ZGw02R-QUVRyvqn+6yCg5MQGX7xxKBJsOxw@mail.gmail.com>

Hello Miguel,

Thanks for reporting this issue. I have submitted a patch that should solve
the problem. The patch is in review. You can download it and test it [1].

Regards,
Francois

[1] http://review.source.kitware.com/#/c/22089/

On Tue, Feb 21, 2017 at 7:29 AM, sharkpt <mdccnunes at hotmail.com> wrote:

> Hello,
>
> I have just downloaded the new ITK 4.11 and I am having a couple of issues
> compiling in Windows 10, 64bit release, Visual Studio (version 12 - update
> 5).
> I also have the new AMD APP SDK 3.0 (for openCL libs and includes).
>
> The error is as follows:
>
> mylibraries\itk\insighttoolkit-4.11.0\modules\core\gpucommon\include\
> itkGPUImage.h(179):
> error C3668: 'itk::GPUImage<unsigned char,1>::Graft' : method with override
> specifier 'override' did not override any base class methods
>
> I also went to git hub and downloaded the master. I tried compiling it but
> got different errors.
>
> Any help is appreciated!
>
> Best regards
> Miguel
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-4-11-build-issue-tp37926.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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From zack.galbreath at kitware.com  Tue Feb 21 13:24:20 2017
From: zack.galbreath at kitware.com (Zack Galbreath)
Date: Tue, 21 Feb 2017 13:24:20 -0500
Subject: [ITK] [ITK-dev] open.cdash.org updated
In-Reply-To: <CADZJ4hPzqiv1Kt5-R_taz2FQqa53L7C7CXbrVPVYY1B_9MvqmA@mail.gmail.com>
References: <CANgkMA6Jqv6SPP-ZbtdNzoiSmskYmcBR4R8hNWF0XiSkrwXh_A@mail.gmail.com>
 <DB259B32-2201-46DC-80E2-61FD1B330DFC@mail.nih.gov>
 <CANgkMA7kzSrmLmm-ZiOcdAdfaFrktZL_Poev38O_muzWOzsh=A@mail.gmail.com>
 <CADZJ4hPzqiv1Kt5-R_taz2FQqa53L7C7CXbrVPVYY1B_9MvqmA@mail.gmail.com>
Message-ID: <CANgkMA797QTgWDeREyDzL_Bdx2FobrSHJXzFjBNE5UcdarusvA@mail.gmail.com>

On Tue, Feb 21, 2017 at 12:07 PM, Bill Lorensen <bill.lorensen at gmail.com>
wrote:

> Zach,
>
> I don't see that behavior on the VTK dashboard.
> https://open.cdash.org/viewUpdate.php?buildid=4778001


For comparison, I rolled back testing.cdash.org to a previous commit so we
can compare and contrast.

https://open.cdash.org/index.php?project=VTK&date=2017-02-21
http://testing.cdash.org/index.php?project=VTK&date=2017-02-21

This data was also missing before the latest upgrade, but it was easier to
identify builds with meaningful update data because they didn't have "0" in
this column.

I'll work with the VTK team to get good update info for all our recurring
builds.
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From bill.lorensen at gmail.com  Tue Feb 21 13:30:49 2017
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Tue, 21 Feb 2017 13:30:49 -0500
Subject: [ITK] [ITK-dev] open.cdash.org updated
In-Reply-To: <CANgkMA797QTgWDeREyDzL_Bdx2FobrSHJXzFjBNE5UcdarusvA@mail.gmail.com>
References: <CANgkMA6Jqv6SPP-ZbtdNzoiSmskYmcBR4R8hNWF0XiSkrwXh_A@mail.gmail.com>
 <DB259B32-2201-46DC-80E2-61FD1B330DFC@mail.nih.gov>
 <CANgkMA7kzSrmLmm-ZiOcdAdfaFrktZL_Poev38O_muzWOzsh=A@mail.gmail.com>
 <CADZJ4hPzqiv1Kt5-R_taz2FQqa53L7C7CXbrVPVYY1B_9MvqmA@mail.gmail.com>
 <CANgkMA797QTgWDeREyDzL_Bdx2FobrSHJXzFjBNE5UcdarusvA@mail.gmail.com>
Message-ID: <CADZJ4hOC7C7kUVCVudum5pzuMdrUiN3+eWUoO1_CQCk4djsXTA@mail.gmail.com>

Thanks!

On Tue, Feb 21, 2017 at 1:24 PM, Zack Galbreath
<zack.galbreath at kitware.com> wrote:
> On Tue, Feb 21, 2017 at 12:07 PM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
>>
>> Zach,
>>
>> I don't see that behavior on the VTK dashboard.
>> https://open.cdash.org/viewUpdate.php?buildid=4778001
>
>
> For comparison, I rolled back testing.cdash.org to a previous commit so we
> can compare and contrast.
>
> https://open.cdash.org/index.php?project=VTK&date=2017-02-21
> http://testing.cdash.org/index.php?project=VTK&date=2017-02-21
>
> This data was also missing before the latest upgrade, but it was easier to
> identify builds with meaningful update data because they didn't have "0" in
> this column.
>
> I'll work with the VTK team to get good update info for all our recurring
> builds.



-- 
Unpaid intern in BillsBasement at noware dot com
_______________________________________________
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From francois.budin at kitware.com  Tue Feb 21 17:54:41 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Tue, 21 Feb 2017 17:54:41 -0500
Subject: [ITK] [ITK-dev] New and build controls for C++11 and C++14
Message-ID: <CAHwLD2Ubkn6+tL49Kh3N=jaixh8n7LWRHTCj9MLgCrNFnEEAYA@mail.gmail.com>

Hello everybody,

Some new builds controls have been added to the ones already available to
initiate builds on Gerrit.
The new commands are:
request build: cpp11 request build: cpp14
These are pretty self-explanatory and will trigger a build compiling ITK
respectively with C++11 or C++14. These commands are passed using the
comment section on Gerrit.
An exhausitve list of the available commands is available here [1].

[1] https://itk.org/Wiki/ITK/Git/Develop

Best,
Francois
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From hans-johnson at uiowa.edu  Tue Feb 21 18:17:44 2017
From: hans-johnson at uiowa.edu (Johnson, Hans J)
Date: Tue, 21 Feb 2017 23:17:44 +0000
Subject: [ITK] [ITK-dev] New and build controls for C++11 and C++14
In-Reply-To: <CAHwLD2Ubkn6+tL49Kh3N=jaixh8n7LWRHTCj9MLgCrNFnEEAYA@mail.gmail.com>
References: <CAHwLD2Ubkn6+tL49Kh3N=jaixh8n7LWRHTCj9MLgCrNFnEEAYA@mail.gmail.com>
Message-ID: <2AA674C2-9691-47A5-B613-EE98F3E45ED4@uiowa.edu>

NICE!


--


From: Insight-developers <insight-developers-bounces at itk.org> on behalf of Francois Budin <francois.budin at kitware.com>
Date: Tuesday, February 21, 2017 at 4:54 PM
To: ITK Developers <insight-developers at itk.org>
Subject: [ITK-dev] New and build controls for C++11 and C++14

Hello everybody,
Some new builds controls have been added to the ones already available to initiate builds on Gerrit.
The new commands are:
request build: cpp11
request build: cpp14
These are pretty self-explanatory and will trigger a build compiling ITK respectively with C++11 or C++14. These commands are passed using the comment section on Gerrit.
An exhausitve list of the available commands is available here [1].

[1] https://itk.org/Wiki/ITK/Git/Develop
Best,
Francois
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From mdccnunes at hotmail.com  Wed Feb 22 04:04:50 2017
From: mdccnunes at hotmail.com (sharkpt)
Date: Wed, 22 Feb 2017 02:04:50 -0700 (MST)
Subject: [ITK] [ITK-users] ITK 4.11 build issue
In-Reply-To: <CAHwLD2VJdcsa-25ZGw02R-QUVRyvqn+6yCg5MQGX7xxKBJsOxw@mail.gmail.com>
References: <1487680154437-37926.post@n7.nabble.com>
 <CAHwLD2VJdcsa-25ZGw02R-QUVRyvqn+6yCg5MQGX7xxKBJsOxw@mail.gmail.com>
Message-ID: <1487754290631-37928.post@n7.nabble.com>

Francois Budin-3,
Thank you for the reply. 

It worked but 2 other errors appeared related to the override thing:
itkGPUImageToImageFilter.h Lines 76 and 77. I manually removed the
IT_OVERRIDE and everything compiled. 

Thanks! 




--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-4-11-build-issue-tp37926p37928.html
Sent from the ITK - Users mailing list archive at Nabble.com.
_____________________________________
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From cyril.mory at creatis.insa-lyon.fr  Wed Feb 22 04:38:14 2017
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 22 Feb 2017 10:38:14 +0100
Subject: [ITK] [ITK-users] Filter working on both itk::Image and
	itk::VectorImage
In-Reply-To: <41eb944a-306a-db60-de1f-7ad8414c3173@creatis.insa-lyon.fr>
References: <41eb944a-306a-db60-de1f-7ad8414c3173@creatis.insa-lyon.fr>
Message-ID: <6d96de7a-acc0-b62c-8fe5-6f3cc9e39455@creatis.insa-lyon.fr>

Hi ITK users,

I am writing an itk::ImageToImageFilter<T>, and I want the filter to 
work with T=itk::Image as well as with T=itk::VectorImage.

To set/get the vectorLength of an image (which is 1 for an itk::Image, 
and varies for an itk::VectorImage), I have successfully used the 
functions Set/GetNumberOfComponentsPerPixel from the itk::ImageBase 
class, which work for both itk::Image and itk::VectorImage.

But I cannot find a way to initialize one of the pixels to a given 
value, that would work for both cases, i.e. whether that pixel is a 
scalar or a variableLengthVector. For now, the best I could do is define 
a function FillPixel in my filter, like this:

OutputImagePixelType FillPixel(OutputImageInternalPixelType value) 
{return value;}

and write a template specialization when my filter is instantiated with 
itk::VectorImage<float, 3>, like this:

template <>
itk::VariableLengthVector<float>
rtk::ConstantImageSource<itk::VectorImage<float, 3> >
::FillPixel(float value)
{
   itk::VariableLengthVector<float> vect;
   vect.SetSize(this->GetVectorLength());
   vect.Fill(value);
   return (vect);
}

Did I miss something ? Is there a better way of doing this in ITK ?

Looking forward to reading you,
Cyril

_____________________________________
Powered by www.kitware.com

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http://www.kitware.com/opensource/opensource.html

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From cyril.mory at creatis.insa-lyon.fr  Wed Feb 22 05:52:22 2017
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 22 Feb 2017 11:52:22 +0100
Subject: [ITK] [ITK-users] Filter working on both itk::Image and
 itk::VectorImage
In-Reply-To: <6d96de7a-acc0-b62c-8fe5-6f3cc9e39455@creatis.insa-lyon.fr>
References: <41eb944a-306a-db60-de1f-7ad8414c3173@creatis.insa-lyon.fr>
 <6d96de7a-acc0-b62c-8fe5-6f3cc9e39455@creatis.insa-lyon.fr>
Message-ID: <49fe2e35-b655-44bd-54f0-5949e5b1e926@creatis.insa-lyon.fr>

Answering my own question:

I found a way to do what I needed using itk::NumericTraits<T> :

   OutputImagePixelType pix;
   itk::NumericTraits<OutputImagePixelType>::SetLength(pix, 
this->GetVectorLength());
   pix = itk::NumericTraits<OutputImagePixelType>::OneValue(pix) * value;

It works for both cases with the same code. However, if there is a 
better way (cleaner, safer, more compact, ... whatever the wayin which 
it is better), I'd be happy to learn about it.

Best regards,
Cyril

On 22/02/2017 10:38, Cyril Mory wrote:
> Hi ITK users,
>
> I am writing an itk::ImageToImageFilter<T>, and I want the filter to 
> work with T=itk::Image as well as with T=itk::VectorImage.
>
> To set/get the vectorLength of an image (which is 1 for an itk::Image, 
> and varies for an itk::VectorImage), I have successfully used the 
> functions Set/GetNumberOfComponentsPerPixel from the itk::ImageBase 
> class, which work for both itk::Image and itk::VectorImage.
>
> But I cannot find a way to initialize one of the pixels to a given 
> value, that would work for both cases, i.e. whether that pixel is a 
> scalar or a variableLengthVector. For now, the best I could do is 
> define a function FillPixel in my filter, like this:
>
> OutputImagePixelType FillPixel(OutputImageInternalPixelType value) 
> {return value;}
>
> and write a template specialization when my filter is instantiated 
> with itk::VectorImage<float, 3>, like this:
>
> template <>
> itk::VariableLengthVector<float>
> rtk::ConstantImageSource<itk::VectorImage<float, 3> >
> ::FillPixel(float value)
> {
>   itk::VariableLengthVector<float> vect;
>   vect.SetSize(this->GetVectorLength());
>   vect.Fill(value);
>   return (vect);
> }
>
> Did I miss something ? Is there a better way of doing this in ITK ?
>
> Looking forward to reading you,
> Cyril
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users

_____________________________________
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From blowekamp at mail.nih.gov  Wed Feb 22 09:41:22 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 22 Feb 2017 14:41:22 +0000
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
In-Reply-To: <E46D6743-14D2-4CCB-BBFC-FACF0CE84198@mail.nih.gov>
References: <86wpcs50be.fsf@gmail.com>
 <DA2915A530468E47B3C4845298E6EB038361F537@msgb06.nih.gov>
 <86shngmr40.fsf@gmail.com>
 <8907FC5F-A787-4FDC-BDF8-B101444D3544@mail.nih.gov>
 <CALzTN-RHEpJJATQE0aShTiCx9NZ7jEq+L4QwFtxjYwEMFBo3Fw@mail.gmail.com>
 <86r330ur5w.fsf@gmail.com>
 <E46D6743-14D2-4CCB-BBFC-FACF0CE84198@mail.nih.gov>
Message-ID: <9EA174E0-46EC-4C1E-BCD0-8169845783FB@mail.nih.gov>

Hello Longzhu,

We have address the issue in ITK:
http://review.source.kitware.com/#/c/22080/

And updated the SimpleITK master branch to use this patched version of ITK. You may need to do a "git checkout master && git pull"

If you checkout the current SimpleITK master, I expect that is should just compile and build with the default options. However, to ensure it works I?d recommend the following initial configuration line:

$ cmake -DITK_DYNAMIC_LOADING:BOOL=0 -DCMAKE_DL_LIBS=?? ../SimpleITK/SuperBuild

That should work for you now. Please give it a try and report back.

Thanks for trying out SimpleITK!
Brad

 cmake ../SuperBuild -DITK_DYNAMIC_LOADING:BOOL=0

On Feb 15, 2017, at 6:52 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:

It looks like our e-mails crossed last night.

I think you were really close to building building SimpleITK. If your goal is to use the SimpleITK language binding I would recommend continuing to use the SimpleITK superbuild. From your previous message the Superbuild compiled all of ITK, and the SimpleITK libraries, and maybe even the SimpleITK testing too. It just appears to have failed on linking for the Tcl wrapping.

When you do the Superbuild of SimpleITK it automatically downloads the correct version of ITK, and compiles it with the correct options to build with SimpleITK.

My recommendation to to verify that the core SimpleITK libraries are being built correctly and that the SimpleITK testing drivers get linked OK. If this is the case it tells us there is something not right with the way the linking is done for the wrapping and we need to closely look at that command line and the options CMake has.

HTH,
Brad

On Feb 14, 2017, at 9:24 PM, Longzhu Shen <lqshen10 at gmail.com<mailto:lqshen10 at gmail.com>> wrote:


Hi Brad and Matt,

Many thanks for the kind advice. I'm very new to ITK. Some of my
questions may be naive. I hope you could bear with me. I really hope to
get it working if I could. Thank you very much.

I checked out the freebsd port but I could not install it. (errors below)

Then I went back to the ITK src (I mistakenly thought simpleITK contains
ITK before) and tried to follow the manual to install it.

The cmake was fine for the most part but some errors did appear (
attached). Assuming those errors were not fatal, I
proceeded with make. The program stopped at the line below.

make[2]: don't know how to make ExternalData/Testing/Data/Input/MetaIO/Small\. Stop

It is the same error when I tried to compile from the ports.

Wondering whether I can seek some insight here or it is hopeless with
freebsd by this point. Thanks for advice.

sincerely,

Longzhu

<cmake_err.log>


Matt McCormick @ 2017-02-14 21:48 UTC:

Hi,

It is not likely that the errors are related to ITK_DYNAMIC_LOADING.

FreeBSD has a package for ITK, which gives its configuration:

https://www.freshports.org/science/InsightToolkit/
https://reviews.freebsd.org/diffusion/P/browse/head/science/InsightToolkit/Makefile

HTH,
Matt

On Tue, Feb 14, 2017 at 4:32 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
<blowekamp at mail.nih.gov> wrote:
Hi,

Are we sure the first case was not close to mostly working? Did other
wrapped language link OK? did SimpleITK tests link OK? If ITK tests are
enable with ITK_DYNAMIC_LOADING:BOOL=0 do they compile and work? We need to
know if ITK is OK before moving to SimpleITK.

@Matt
I am not very familiar with CMAKE_DL_LIBS either [1]. I know Matt added the
ITK_DYNAMIC_LOADING CMake variable to ITK, so he may have insight into this
problem too. My guess is that CMAKE_DL_LIBS variable is not entered into the
cache but CMake provides a default value for platform. I expect you can
overrride it with command line values.

I hacked a patch to enable CMAKE_DL_LIBS to propgate down from the
Superbuild [2]. If you checkout that path you should be able to do a
supberbuild of -DCMAKE_DL_LIBS=??. That may work, but I don?t know for sure.

HTH,
Brad

[1] https://cmake.org/cmake/help/v3.0/variable/CMAKE_DL_LIBS.html
[2] https://github.com/SimpleITK/SimpleITK/pull/104


On Feb 14, 2017, at 3:53 PM, Longzhu Shen <lqshen10 at gmail.com> wrote:

Hi Brad,

Many thanks for the advice.
I made an attempt to follow the first approach but it did not seem
work. Here is what I did and the errors I got.

-----------------------------------------------------
$ cmake ../SuperBuild -DITK_DYNAMIC_LOADING:BOOL=0


[ 80%] Building CXX object
Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/sitkPyCommand.cxx.o
[ 80%] Building CXX object
Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/SimpleITKPYTHON_wrap.cxx.o
[ 80%] Linking CXX executable bin/SimpleITKTclsh
/usr/bin/ld: cannot find -ldl
c++: error: linker command failed with exit code 1 (use -v to see
invocation)
--- Wrapping/Tcl/bin/SimpleITKTclsh ---
*** [Wrapping/Tcl/bin/SimpleITKTclsh] Error code 1
-----------------------------------------------------

I planned to try the 2nd approach. However, I could not find the
CMAKE_DL_LIBS easily. I checked the subfolder of Superbuild,
and SimpleITK-build/ITK-build. I did not find it in
Code/Common/src/CMakeLists.txt as well.

The only place I found "CMAKE_DL_LIBS" is in the file
CMake/sitkTargetLinkLibrariesWithDynamicLookup.cmake

279:        target_link_libraries(main \"${CMAKE_DL_LIBS}\")

I was wondering I may get further directions to modify CMAKE_DL_LIBS
variable. Many thanks.

sincerely,

Longzhu


Lowekamp @ 2017-02-14 15:36 UTC:

Hello Longzu,

You are using freebsd, that is new and exciting. I have not used that OS for
developing.

There are two things in the ITK/SimpleITK build that are related to this.

First, there is an option in ITK ( which I have not used ) call
ITK_DYNAMIC_LOADING. If you pass -DITK_DYNAMIC_LOADING:BOOL=0 to cmake for
the Superbuild, it should propagate to the ITK project and this feature will
be remove. This may solve your problem.

The second is CMake variable CMAKE_DL_LIBS. I believe it is the dl library
that is causing the problem [1]. Setting it to an empty string may also
remove it from the linking lines. Getting that to propagate to the ITK
project will not happen automatically and would need to be done manually in
the ITK build.

HTH,
Brad

[1]
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/src/CMakeLists.txt#L142

________________________________________
From: Longzhu Shen [lqshen10 at gmail.com]
Sent: Tuesday, February 14, 2017 9:11 AM
To: community at itk.org
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?

Hello,

I'm trying to compile simpleitk on my freebsd system.
The issue I encountered is ldl is not found.
After some searching, I found libdl is not needed on freebsd. It is
included in libc. Wondering how I can turn it off in the make file.
I did not find  ldl in the Makefile under Simpleitk-build.

I followed the instrutions from the link below.

https://chsasank.github.io/sitk-docs/building/unix.html#obtaining-source-code

Thanks.

Longzhu



--
Longzhu Shen, Ph.D.
Postdoc Research Associate
School of Forestry and Environmental Studies
Yale University
195 Prospect Street
New Haven, CT 06511




--
Longzhu Shen, Ph.D.
Postdoc Research Associate
School of Forestry and Environmental Studies
Yale University
195 Prospect Street
New Haven, CT 06511

_______________________________________________
Community mailing list
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From francois.budin at kitware.com  Wed Feb 22 10:43:00 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 22 Feb 2017 10:43:00 -0500
Subject: [ITK] [ITK-users] ITK 4.11 build issue
In-Reply-To: <1487754290631-37928.post@n7.nabble.com>
References: <1487680154437-37926.post@n7.nabble.com>
 <CAHwLD2VJdcsa-25ZGw02R-QUVRyvqn+6yCg5MQGX7xxKBJsOxw@mail.gmail.com>
 <1487754290631-37928.post@n7.nabble.com>
Message-ID: <CAHwLD2VpqVTQ9MEu1MyeudWwhNTBMjtaPuUxi2B85iLoGX_P6A@mail.gmail.com>

Thank you for reporting this issue. I just submitted a new patch [1] and
this should be integrated in ITK soon.
If you create a reviewer profile on Gerrit, I can add you as a reviewer.
You can find more information about how to do it here [2]

Regards,
Francois

[1] http://review.source.kitware.com/#/c/22092/1
[2] https://itk.org/Wiki/ITK/Git/Develop

On Wed, Feb 22, 2017 at 4:04 AM, sharkpt <mdccnunes at hotmail.com> wrote:

> Francois Budin-3,
> Thank you for the reply.
>
> It worked but 2 other errors appeared related to the override thing:
> itkGPUImageToImageFilter.h Lines 76 and 77. I manually removed the
> IT_OVERRIDE and everything compiled.
>
> Thanks!
>
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/ITK-4-11-build-issue-tp37926p37928.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
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_____________________________________
Powered by www.kitware.com

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Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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From davood.karimi at gmail.com  Wed Feb 22 10:43:41 2017
From: davood.karimi at gmail.com (engineeringmath)
Date: Wed, 22 Feb 2017 08:43:41 -0700 (MST)
Subject: [ITK] [ITK-users] Missing filters in ITK installation
Message-ID: <1487778221335-7589640.post@n2.nabble.com>

Hello,

I have been using SimpleITK for a while. But I recently needed filters that
were not available in SimpleITK, so I installed ITK. However, after
importing ITK into my python IDE, I see that those filters are not
available. Also, searching my computer I cannot find those filters. The
filters I am looking for are AverageOutwardFluxImageFilter and
MedialCurveImageFilter (please see the links below).

Am I making a mistake during the installation?  

Your help is greatly appreciated.

http://www.insight-journal.org/browse/publication/165
http://www.dtic.upf.edu/~afrangi/articles/tij2007.pdf




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Missing-filters-in-ITK-installation-tp7589640.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From francois.budin at kitware.com  Wed Feb 22 11:01:10 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 22 Feb 2017 11:01:10 -0500
Subject: [ITK] [ITK-users] Missing filters in ITK installation
In-Reply-To: <1487778221335-7589640.post@n2.nabble.com>
References: <1487778221335-7589640.post@n2.nabble.com>
Message-ID: <CAHwLD2UuD0iqN+dQpU+d3jjJ-2_3F0L2S7iSTX5EvBBZ4WXXXA@mail.gmail.com>

Hello,

These filters have been published as part of the Insight Journal article
you referenced. However, no ITK remote module has been created to directly
make them available in ITK. This means that currently one has to download
the source code of these filters outside of the ITK source code.
Additionally, these filters are not wrapped in Python.
The source code would need to be updated (probably just reorganize the
files to respect the expected folder structure) to allow these filters to
be part of an ITK remote module and completed to create the Python wrapping.
You could contact the authors of the paper to see if they are willing to do
it, or you are also more than welcome to do it. It would be great to add
this filter directly in ITK and I would gladly help you to get started.
The ITK Software Guide (chapter 9) provides a lot of information on how to
proceed to create an ITK module [1]. You can also look at filters that have
an existing ITK remote module, such as [2].

Thank you for your help,
Francois

[1] https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1.html
[2] https://github.com/InsightSoftwareConsortium/ITKCuberille


On Wed, Feb 22, 2017 at 10:43 AM, engineeringmath <davood.karimi at gmail.com>
wrote:

> Hello,
>
> I have been using SimpleITK for a while. But I recently needed filters that
> were not available in SimpleITK, so I installed ITK. However, after
> importing ITK into my python IDE, I see that those filters are not
> available. Also, searching my computer I cannot find those filters. The
> filters I am looking for are AverageOutwardFluxImageFilter and
> MedialCurveImageFilter (please see the links below).
>
> Am I making a mistake during the installation?
>
> Your help is greatly appreciated.
>
> http://www.insight-journal.org/browse/publication/165
> http://www.dtic.upf.edu/~afrangi/articles/tij2007.pdf
>
>
>
>
> --
> View this message in context: http://itk-insight-users.
> 2283740.n2.nabble.com/Missing-filters-in-ITK-installation-tp7589640.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
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_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

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From matt.mccormick at kitware.com  Wed Feb 22 11:39:15 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 22 Feb 2017 11:39:15 -0500
Subject: [ITK] [ITK-users] Filter working on both itk::Image
	and	itk::VectorImage
In-Reply-To: <49fe2e35-b655-44bd-54f0-5949e5b1e926@creatis.insa-lyon.fr>
References: <41eb944a-306a-db60-de1f-7ad8414c3173@creatis.insa-lyon.fr>
 <6d96de7a-acc0-b62c-8fe5-6f3cc9e39455@creatis.insa-lyon.fr>
 <49fe2e35-b655-44bd-54f0-5949e5b1e926@creatis.insa-lyon.fr>
Message-ID: <CALzTN-QZ0Q6yeG-TLpsdow9pHR10vJqzKuwx-1aebb7=i7m_ng@mail.gmail.com>

Hi Cyril,

Yes, this is a good approach.  Thanks for sharing your investigation.

Matt

On Wed, Feb 22, 2017 at 5:52 AM, Cyril Mory
<cyril.mory at creatis.insa-lyon.fr> wrote:
> Answering my own question:
>
> I found a way to do what I needed using itk::NumericTraits<T> :
>
>   OutputImagePixelType pix;
>   itk::NumericTraits<OutputImagePixelType>::SetLength(pix,
> this->GetVectorLength());
>   pix = itk::NumericTraits<OutputImagePixelType>::OneValue(pix) * value;
>
> It works for both cases with the same code. However, if there is a better
> way (cleaner, safer, more compact, ... whatever the wayin which it is
> better), I'd be happy to learn about it.
>
> Best regards,
> Cyril
>
>
> On 22/02/2017 10:38, Cyril Mory wrote:
>>
>> Hi ITK users,
>>
>> I am writing an itk::ImageToImageFilter<T>, and I want the filter to work
>> with T=itk::Image as well as with T=itk::VectorImage.
>>
>> To set/get the vectorLength of an image (which is 1 for an itk::Image, and
>> varies for an itk::VectorImage), I have successfully used the functions
>> Set/GetNumberOfComponentsPerPixel from the itk::ImageBase class, which work
>> for both itk::Image and itk::VectorImage.
>>
>> But I cannot find a way to initialize one of the pixels to a given value,
>> that would work for both cases, i.e. whether that pixel is a scalar or a
>> variableLengthVector. For now, the best I could do is define a function
>> FillPixel in my filter, like this:
>>
>> OutputImagePixelType FillPixel(OutputImageInternalPixelType value) {return
>> value;}
>>
>> and write a template specialization when my filter is instantiated with
>> itk::VectorImage<float, 3>, like this:
>>
>> template <>
>> itk::VariableLengthVector<float>
>> rtk::ConstantImageSource<itk::VectorImage<float, 3> >
>> ::FillPixel(float value)
>> {
>>   itk::VariableLengthVector<float> vect;
>>   vect.SetSize(this->GetVectorLength());
>>   vect.Fill(value);
>>   return (vect);
>> }
>>
>> Did I miss something ? Is there a better way of doing this in ITK ?
>>
>> Looking forward to reading you,
>> Cyril
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> 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://public.kitware.com/mailman/listinfo/insight-users
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From lqshen10 at gmail.com  Wed Feb 22 22:53:45 2017
From: lqshen10 at gmail.com (Longzhu Shen)
Date: Wed, 22 Feb 2017 22:53:45 -0500
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
In-Reply-To: <9EA174E0-46EC-4C1E-BCD0-8169845783FB@mail.nih.gov>
References: <86wpcs50be.fsf@gmail.com>
 <DA2915A530468E47B3C4845298E6EB038361F537@msgb06.nih.gov>
 <86shngmr40.fsf@gmail.com>
 <8907FC5F-A787-4FDC-BDF8-B101444D3544@mail.nih.gov>
 <CALzTN-RHEpJJATQE0aShTiCx9NZ7jEq+L4QwFtxjYwEMFBo3Fw@mail.gmail.com>
 <86r330ur5w.fsf@gmail.com>
 <E46D6743-14D2-4CCB-BBFC-FACF0CE84198@mail.nih.gov>
 <9EA174E0-46EC-4C1E-BCD0-8169845783FB@mail.nih.gov>
Message-ID: <86k28h36ly.fsf@gmail.com>


Hi Bradley,

Many thanks for addressing this issue.

I checked out the latest git and just finished the compiling.

It appears to be successful to me. 

------------------------------------------------
[ 98%] No install step for 'SimpleITKExamples'
[100%] Completed 'SimpleITKExamples'
[100%] Built target SimpleITKExamples
------------------------------------------------

The bin folder has only one file sitkCompareDriver-1.0-1.

I'll look into the manual to test it.

Thanks again for addressing the issue.

sincerely,

Longzhu 




Lowekamp @ 2017-02-22 14:41 UTC:

> Hello Longzhu,
>
> We have address the issue in ITK:
> http://review.source.kitware.com/#/c/22080/
>
> And updated the SimpleITK master branch to use this patched version of ITK. You may need to do a "git checkout master && git pull"
>
> If you checkout the current SimpleITK master, I expect that is should just compile and build with the default options. However, to ensure it works I?d recommend the following initial configuration line:
>
> $ cmake -DITK_DYNAMIC_LOADING:BOOL=0 -DCMAKE_DL_LIBS=?? ../SimpleITK/SuperBuild
>
> That should work for you now. Please give it a try and report back.
>
> Thanks for trying out SimpleITK!
> Brad
>
>  cmake ../SuperBuild -DITK_DYNAMIC_LOADING:BOOL=0
>
> On Feb 15, 2017, at 6:52 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:
>
> It looks like our e-mails crossed last night.
>
> I think you were really close to building building SimpleITK. If your goal is to use the SimpleITK language binding I would recommend continuing to use the SimpleITK superbuild. From your previous message the Superbuild compiled all of ITK, and the SimpleITK libraries, and maybe even the SimpleITK testing too. It just appears to have failed on linking for the Tcl wrapping.
>
> When you do the Superbuild of SimpleITK it automatically downloads the correct version of ITK, and compiles it with the correct options to build with SimpleITK.
>
> My recommendation to to verify that the core SimpleITK libraries are being built correctly and that the SimpleITK testing drivers get linked OK. If this is the case it tells us there is something not right with the way the linking is done for the wrapping and we need to closely look at that command line and the options CMake has.
>
> HTH,
> Brad
>
> On Feb 14, 2017, at 9:24 PM, Longzhu Shen <lqshen10 at gmail.com<mailto:lqshen10 at gmail.com>> wrote:
>
>
> Hi Brad and Matt,
>
> Many thanks for the kind advice. I'm very new to ITK. Some of my
> questions may be naive. I hope you could bear with me. I really hope to
> get it working if I could. Thank you very much.
>
> I checked out the freebsd port but I could not install it. (errors below)
>
> Then I went back to the ITK src (I mistakenly thought simpleITK contains
> ITK before) and tried to follow the manual to install it.
>
> The cmake was fine for the most part but some errors did appear (
> attached). Assuming those errors were not fatal, I
> proceeded with make. The program stopped at the line below.
>
> make[2]: don't know how to make ExternalData/Testing/Data/Input/MetaIO/Small\. Stop
>
> It is the same error when I tried to compile from the ports.
>
> Wondering whether I can seek some insight here or it is hopeless with
> freebsd by this point. Thanks for advice.
>
> sincerely,
>
> Longzhu
>
> <cmake_err.log>
>
>
> Matt McCormick @ 2017-02-14 21:48 UTC:
>
> Hi,
>
> It is not likely that the errors are related to ITK_DYNAMIC_LOADING.
>
> FreeBSD has a package for ITK, which gives its configuration:
>
> https://www.freshports.org/science/InsightToolkit/
> https://reviews.freebsd.org/diffusion/P/browse/head/science/InsightToolkit/Makefile
>
> HTH,
> Matt
>
> On Tue, Feb 14, 2017 at 4:32 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
> <blowekamp at mail.nih.gov> wrote:
> Hi,
>
> Are we sure the first case was not close to mostly working? Did other
> wrapped language link OK? did SimpleITK tests link OK? If ITK tests are
> enable with ITK_DYNAMIC_LOADING:BOOL=0 do they compile and work? We need to
> know if ITK is OK before moving to SimpleITK.
>
> @Matt
> I am not very familiar with CMAKE_DL_LIBS either [1]. I know Matt added the
> ITK_DYNAMIC_LOADING CMake variable to ITK, so he may have insight into this
> problem too. My guess is that CMAKE_DL_LIBS variable is not entered into the
> cache but CMake provides a default value for platform. I expect you can
> overrride it with command line values.
>
> I hacked a patch to enable CMAKE_DL_LIBS to propgate down from the
> Superbuild [2]. If you checkout that path you should be able to do a
> supberbuild of -DCMAKE_DL_LIBS=??. That may work, but I don?t know for sure.
>
> HTH,
> Brad
>
> [1] https://cmake.org/cmake/help/v3.0/variable/CMAKE_DL_LIBS.html
> [2] https://github.com/SimpleITK/SimpleITK/pull/104
>
>
> On Feb 14, 2017, at 3:53 PM, Longzhu Shen <lqshen10 at gmail.com> wrote:
>
> Hi Brad,
>
> Many thanks for the advice.
> I made an attempt to follow the first approach but it did not seem
> work. Here is what I did and the errors I got.
>
> -----------------------------------------------------
> $ cmake ../SuperBuild -DITK_DYNAMIC_LOADING:BOOL=0
>
>
> [ 80%] Building CXX object
> Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/sitkPyCommand.cxx.o
> [ 80%] Building CXX object
> Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/SimpleITKPYTHON_wrap.cxx.o
> [ 80%] Linking CXX executable bin/SimpleITKTclsh
> /usr/bin/ld: cannot find -ldl
> c++: error: linker command failed with exit code 1 (use -v to see
> invocation)
> --- Wrapping/Tcl/bin/SimpleITKTclsh ---
> *** [Wrapping/Tcl/bin/SimpleITKTclsh] Error code 1
> -----------------------------------------------------
>
> I planned to try the 2nd approach. However, I could not find the
> CMAKE_DL_LIBS easily. I checked the subfolder of Superbuild,
> and SimpleITK-build/ITK-build. I did not find it in
> Code/Common/src/CMakeLists.txt as well.
>
> The only place I found "CMAKE_DL_LIBS" is in the file
> CMake/sitkTargetLinkLibrariesWithDynamicLookup.cmake
>
> 279:        target_link_libraries(main \"${CMAKE_DL_LIBS}\")
>
> I was wondering I may get further directions to modify CMAKE_DL_LIBS
> variable. Many thanks.
>
> sincerely,
>
> Longzhu
>
>
> Lowekamp @ 2017-02-14 15:36 UTC:
>
> Hello Longzu,
>
> You are using freebsd, that is new and exciting. I have not used that OS for
> developing.
>
> There are two things in the ITK/SimpleITK build that are related to this.
>
> First, there is an option in ITK ( which I have not used ) call
> ITK_DYNAMIC_LOADING. If you pass -DITK_DYNAMIC_LOADING:BOOL=0 to cmake for
> the Superbuild, it should propagate to the ITK project and this feature will
> be remove. This may solve your problem.
>
> The second is CMake variable CMAKE_DL_LIBS. I believe it is the dl library
> that is causing the problem [1]. Setting it to an empty string may also
> remove it from the linking lines. Getting that to propagate to the ITK
> project will not happen automatically and would need to be done manually in
> the ITK build.
>
> HTH,
> Brad
>
> [1]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/src/CMakeLists.txt#L142
>
> ________________________________________
> From: Longzhu Shen [lqshen10 at gmail.com]
> Sent: Tuesday, February 14, 2017 9:11 AM
> To: community at itk.org
> Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
>
> Hello,
>
> I'm trying to compile simpleitk on my freebsd system.
> The issue I encountered is ldl is not found.
> After some searching, I found libdl is not needed on freebsd. It is
> included in libc. Wondering how I can turn it off in the make file.
> I did not find  ldl in the Makefile under Simpleitk-build.
>
> I followed the instrutions from the link below.
>
> https://chsasank.github.io/sitk-docs/building/unix.html#obtaining-source-code
>
> Thanks.
>
> Longzhu
>
>
>
> --
> Longzhu Shen, Ph.D.
> Postdoc Research Associate
> School of Forestry and Environmental Studies
> Yale University
> 195 Prospect Street
> New Haven, CT 06511


-- 
Longzhu Shen, Ph.D.
Postdoc Research Associate
School of Forestry and Environmental Studies
Yale University
195 Prospect Street
New Haven, CT 06511

From blowekamp at mail.nih.gov  Thu Feb 23 09:29:00 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 23 Feb 2017 14:29:00 +0000
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?
In-Reply-To: <86k28h36ly.fsf@gmail.com>
References: <86wpcs50be.fsf@gmail.com>
 <DA2915A530468E47B3C4845298E6EB038361F537@msgb06.nih.gov>
 <86shngmr40.fsf@gmail.com>
 <8907FC5F-A787-4FDC-BDF8-B101444D3544@mail.nih.gov>
 <CALzTN-RHEpJJATQE0aShTiCx9NZ7jEq+L4QwFtxjYwEMFBo3Fw@mail.gmail.com>
 <86r330ur5w.fsf@gmail.com>
 <E46D6743-14D2-4CCB-BBFC-FACF0CE84198@mail.nih.gov>
 <9EA174E0-46EC-4C1E-BCD0-8169845783FB@mail.nih.gov>
 <86k28h36ly.fsf@gmail.com>
Message-ID: <5EA18C54-C384-4285-97B1-8BE33E954C65@mail.nih.gov>

Hello,

That is great to hear you compiled it successfully with the changes. Thanks for getting back to us.

The top-level superbuild does not have SimpleITK's testing, that would be in the SimpleITK-build sub-directory. In the sub-directory you should be able to run ?ctest ? to run the test suite.

In the top-level superbuild ?bin? directory it is expected only to have the sitkCompareDriver executable. In the lib directory there should be a bunch of SimpleITK libraries.

In the SimpleITK-build sub-directory, there should be wrapping for the languages you enabled. In this subdirectory, if you make the ?dist? target, it will create some binary packages for certain languages. Like for python is will create a binary ?whl? suitable of installation or the setup.py can be used [1].

If there is a particular languages you are trying to use, I can point you to more specific instructions.

Enjoy,
Brad

[1] https://itk.org/Wiki/SimpleITK/GettingStarted#Python_installation

On Feb 22, 2017, at 10:53 PM, Longzhu Shen <lqshen10 at gmail.com<mailto:lqshen10 at gmail.com>> wrote:


Hi Bradley,

Many thanks for addressing this issue.

I checked out the latest git and just finished the compiling.

It appears to be successful to me.

------------------------------------------------
[ 98%] No install step for 'SimpleITKExamples'
[100%] Completed 'SimpleITKExamples'
[100%] Built target SimpleITKExamples
------------------------------------------------

The bin folder has only one file sitkCompareDriver-1.0-1.

I'll look into the manual to test it.

Thanks again for addressing the issue.

sincerely,

Longzhu




Lowekamp @ 2017-02-22 14:41 UTC:

Hello Longzhu,

We have address the issue in ITK:
http://review.source.kitware.com/#/c/22080/

And updated the SimpleITK master branch to use this patched version of ITK. You may need to do a "git checkout master && git pull"

If you checkout the current SimpleITK master, I expect that is should just compile and build with the default options. However, to ensure it works I?d recommend the following initial configuration line:

$ cmake -DITK_DYNAMIC_LOADING:BOOL=0 -DCMAKE_DL_LIBS=?? ../SimpleITK/SuperBuild

That should work for you now. Please give it a try and report back.

Thanks for trying out SimpleITK!
Brad

cmake ../SuperBuild -DITK_DYNAMIC_LOADING:BOOL=0

On Feb 15, 2017, at 6:52 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:

It looks like our e-mails crossed last night.

I think you were really close to building building SimpleITK. If your goal is to use the SimpleITK language binding I would recommend continuing to use the SimpleITK superbuild. From your previous message the Superbuild compiled all of ITK, and the SimpleITK libraries, and maybe even the SimpleITK testing too. It just appears to have failed on linking for the Tcl wrapping.

When you do the Superbuild of SimpleITK it automatically downloads the correct version of ITK, and compiles it with the correct options to build with SimpleITK.

My recommendation to to verify that the core SimpleITK libraries are being built correctly and that the SimpleITK testing drivers get linked OK. If this is the case it tells us there is something not right with the way the linking is done for the wrapping and we need to closely look at that command line and the options CMake has.

HTH,
Brad

On Feb 14, 2017, at 9:24 PM, Longzhu Shen <lqshen10 at gmail.com<mailto:lqshen10 at gmail.com>> wrote:


Hi Brad and Matt,

Many thanks for the kind advice. I'm very new to ITK. Some of my
questions may be naive. I hope you could bear with me. I really hope to
get it working if I could. Thank you very much.

I checked out the freebsd port but I could not install it. (errors below)

Then I went back to the ITK src (I mistakenly thought simpleITK contains
ITK before) and tried to follow the manual to install it.

The cmake was fine for the most part but some errors did appear (
attached). Assuming those errors were not fatal, I
proceeded with make. The program stopped at the line below.

make[2]: don't know how to make ExternalData/Testing/Data/Input/MetaIO/Small\. Stop

It is the same error when I tried to compile from the ports.

Wondering whether I can seek some insight here or it is hopeless with
freebsd by this point. Thanks for advice.

sincerely,

Longzhu

<cmake_err.log>


Matt McCormick @ 2017-02-14 21:48 UTC:

Hi,

It is not likely that the errors are related to ITK_DYNAMIC_LOADING.

FreeBSD has a package for ITK, which gives its configuration:

https://www.freshports.org/science/InsightToolkit/
https://reviews.freebsd.org/diffusion/P/browse/head/science/InsightToolkit/Makefile

HTH,
Matt

On Tue, Feb 14, 2017 at 4:32 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C]
<blowekamp at mail.nih.gov> wrote:
Hi,

Are we sure the first case was not close to mostly working? Did other
wrapped language link OK? did SimpleITK tests link OK? If ITK tests are
enable with ITK_DYNAMIC_LOADING:BOOL=0 do they compile and work? We need to
know if ITK is OK before moving to SimpleITK.

@Matt
I am not very familiar with CMAKE_DL_LIBS either [1]. I know Matt added the
ITK_DYNAMIC_LOADING CMake variable to ITK, so he may have insight into this
problem too. My guess is that CMAKE_DL_LIBS variable is not entered into the
cache but CMake provides a default value for platform. I expect you can
overrride it with command line values.

I hacked a patch to enable CMAKE_DL_LIBS to propgate down from the
Superbuild [2]. If you checkout that path you should be able to do a
supberbuild of -DCMAKE_DL_LIBS=??. That may work, but I don?t know for sure.

HTH,
Brad

[1] https://cmake.org/cmake/help/v3.0/variable/CMAKE_DL_LIBS.html
[2] https://github.com/SimpleITK/SimpleITK/pull/104


On Feb 14, 2017, at 3:53 PM, Longzhu Shen <lqshen10 at gmail.com> wrote:

Hi Brad,

Many thanks for the advice.
I made an attempt to follow the first approach but it did not seem
work. Here is what I did and the errors I got.

-----------------------------------------------------
$ cmake ../SuperBuild -DITK_DYNAMIC_LOADING:BOOL=0


[ 80%] Building CXX object
Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/sitkPyCommand.cxx.o
[ 80%] Building CXX object
Wrapping/Python/CMakeFiles/SimpleITK_PYTHON.dir/SimpleITKPYTHON_wrap.cxx.o
[ 80%] Linking CXX executable bin/SimpleITKTclsh
/usr/bin/ld: cannot find -ldl
c++: error: linker command failed with exit code 1 (use -v to see
invocation)
--- Wrapping/Tcl/bin/SimpleITKTclsh ---
*** [Wrapping/Tcl/bin/SimpleITKTclsh] Error code 1
-----------------------------------------------------

I planned to try the 2nd approach. However, I could not find the
CMAKE_DL_LIBS easily. I checked the subfolder of Superbuild,
and SimpleITK-build/ITK-build. I did not find it in
Code/Common/src/CMakeLists.txt as well.

The only place I found "CMAKE_DL_LIBS" is in the file
CMake/sitkTargetLinkLibrariesWithDynamicLookup.cmake

279:        target_link_libraries(main \"${CMAKE_DL_LIBS}\")

I was wondering I may get further directions to modify CMAKE_DL_LIBS
variable. Many thanks.

sincerely,

Longzhu


Lowekamp @ 2017-02-14 15:36 UTC:

Hello Longzu,

You are using freebsd, that is new and exciting. I have not used that OS for
developing.

There are two things in the ITK/SimpleITK build that are related to this.

First, there is an option in ITK ( which I have not used ) call
ITK_DYNAMIC_LOADING. If you pass -DITK_DYNAMIC_LOADING:BOOL=0 to cmake for
the Superbuild, it should propagate to the ITK project and this feature will
be remove. This may solve your problem.

The second is CMake variable CMAKE_DL_LIBS. I believe it is the dl library
that is causing the problem [1]. Setting it to an empty string may also
remove it from the linking lines. Getting that to propagate to the ITK
project will not happen automatically and would need to be done manually in
the ITK build.

HTH,
Brad

[1]
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/src/CMakeLists.txt#L142

________________________________________
From: Longzhu Shen [lqshen10 at gmail.com]
Sent: Tuesday, February 14, 2017 9:11 AM
To: community at itk.org
Subject: [ITK] compiling itk on freebsd, how to flag out ldl?

Hello,

I'm trying to compile simpleitk on my freebsd system.
The issue I encountered is ldl is not found.
After some searching, I found libdl is not needed on freebsd. It is
included in libc. Wondering how I can turn it off in the make file.
I did not find  ldl in the Makefile under Simpleitk-build.

I followed the instrutions from the link below.

https://chsasank.github.io/sitk-docs/building/unix.html#obtaining-source-code

Thanks.

Longzhu



--
Longzhu Shen, Ph.D.
Postdoc Research Associate
School of Forestry and Environmental Studies
Yale University
195 Prospect Street
New Haven, CT 06511


--
Longzhu Shen, Ph.D.
Postdoc Research Associate
School of Forestry and Environmental Studies
Yale University
195 Prospect Street
New Haven, CT 06511

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From matt.mccormick at kitware.com  Thu Feb 23 14:43:32 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 23 Feb 2017 14:43:32 -0500
Subject: [ITK] [ITK-dev] open.cdash.org updated
In-Reply-To: <CANgkMA6Jqv6SPP-ZbtdNzoiSmskYmcBR4R8hNWF0XiSkrwXh_A@mail.gmail.com>
References: <CANgkMA6Jqv6SPP-ZbtdNzoiSmskYmcBR4R8hNWF0XiSkrwXh_A@mail.gmail.com>
Message-ID: <CALzTN-QUZArFSiwN+SWyJtO8Vg5QhuyohJm7Ozwsz9E7EWEOBQ@mail.gmail.com>

Hi Zack,

Thanks for the updates!

Another bug I noticed, that I think we present before the recent
upgrade, too, is that when clicking one "expected" checkbox, it
enables all other "expected" checkboxes.

Thanks,
Matt

On Tue, Feb 21, 2017 at 9:57 AM, Zack Galbreath
<zack.galbreath at kitware.com> wrote:
> Hi folks,
>
> I just upgraded open.cdash.org.  The most visible change you'll notice is
> that the Update column now shows the commit that was built rather than the
> number of files that changed.
>
> Going forward, I've set a reminder for myself to upgrade open.cdash.org once
> a month around this time (the 21st).
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-developers
>
_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php

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://public.kitware.com/mailman/listinfo/insight-developers

From cyril.mory at creatis.insa-lyon.fr  Mon Feb 27 06:09:00 2017
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Mon, 27 Feb 2017 12:09:00 +0100
Subject: [ITK] [ITK-users] Filter working on both itk::Image and
 itk::VectorImage
In-Reply-To: <CALzTN-QZ0Q6yeG-TLpsdow9pHR10vJqzKuwx-1aebb7=i7m_ng@mail.gmail.com>
References: <41eb944a-306a-db60-de1f-7ad8414c3173@creatis.insa-lyon.fr>
 <6d96de7a-acc0-b62c-8fe5-6f3cc9e39455@creatis.insa-lyon.fr>
 <49fe2e35-b655-44bd-54f0-5949e5b1e926@creatis.insa-lyon.fr>
 <CALzTN-QZ0Q6yeG-TLpsdow9pHR10vJqzKuwx-1aebb7=i7m_ng@mail.gmail.com>
Message-ID: <07d017c1-cb58-28f7-0bd0-1e2250c3cf2e@creatis.insa-lyon.fr>

Hi,

Still the same topic, but a different issue:

I have a filter that is templated over its image input type, usually 
itk::Image<T, dim>. I want to modify it so that it also works when that 
type is itk::VectorImage<T, dim>.

This filter internally defines SliceType = 
itk::Image<InputImageType::InternalPixelType, dim - 1>. But when 
processing an itk::VectorImage, I would like this SliceType to be 
itk::VectorImage<InputImageType::InternalPixelType, dim - 1>.

I don't think there is a way in C++ to recover the itk::Image<> or the 
itk::VectorImage<> "un-templated", and define a type with whole new 
template arguments. But is there an ITK mechanism that would solve my 
problem ?

Best regards,

Cyril

On 22/02/2017 17:39, Matt McCormick wrote:
> Hi Cyril,
>
> Yes, this is a good approach.  Thanks for sharing your investigation.
>
> Matt
>
> On Wed, Feb 22, 2017 at 5:52 AM, Cyril Mory
> <cyril.mory at creatis.insa-lyon.fr> wrote:
>> Answering my own question:
>>
>> I found a way to do what I needed using itk::NumericTraits<T> :
>>
>>    OutputImagePixelType pix;
>>    itk::NumericTraits<OutputImagePixelType>::SetLength(pix,
>> this->GetVectorLength());
>>    pix = itk::NumericTraits<OutputImagePixelType>::OneValue(pix) * value;
>>
>> It works for both cases with the same code. However, if there is a better
>> way (cleaner, safer, more compact, ... whatever the wayin which it is
>> better), I'd be happy to learn about it.
>>
>> Best regards,
>> Cyril
>>
>>
>> On 22/02/2017 10:38, Cyril Mory wrote:
>>> Hi ITK users,
>>>
>>> I am writing an itk::ImageToImageFilter<T>, and I want the filter to work
>>> with T=itk::Image as well as with T=itk::VectorImage.
>>>
>>> To set/get the vectorLength of an image (which is 1 for an itk::Image, and
>>> varies for an itk::VectorImage), I have successfully used the functions
>>> Set/GetNumberOfComponentsPerPixel from the itk::ImageBase class, which work
>>> for both itk::Image and itk::VectorImage.
>>>
>>> But I cannot find a way to initialize one of the pixels to a given value,
>>> that would work for both cases, i.e. whether that pixel is a scalar or a
>>> variableLengthVector. For now, the best I could do is define a function
>>> FillPixel in my filter, like this:
>>>
>>> OutputImagePixelType FillPixel(OutputImageInternalPixelType value) {return
>>> value;}
>>>
>>> and write a template specialization when my filter is instantiated with
>>> itk::VectorImage<float, 3>, like this:
>>>
>>> template <>
>>> itk::VariableLengthVector<float>
>>> rtk::ConstantImageSource<itk::VectorImage<float, 3> >
>>> ::FillPixel(float value)
>>> {
>>>    itk::VariableLengthVector<float> vect;
>>>    vect.SetSize(this->GetVectorLength());
>>>    vect.Fill(value);
>>>    return (vect);
>>> }
>>>
>>> Did I miss something ? Is there a better way of doing this in ITK ?
>>>
>>> Looking forward to reading you,
>>> Cyril
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> 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://public.kitware.com/mailman/listinfo/insight-users
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> 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://public.kitware.com/mailman/listinfo/insight-users

_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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://public.kitware.com/mailman/listinfo/insight-users

From cyril.mory at creatis.insa-lyon.fr  Mon Feb 27 10:24:21 2017
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Mon, 27 Feb 2017 16:24:21 +0100
Subject: [ITK] [ITK-users] Filter working on both itk::Image and
 itk::VectorImage
In-Reply-To: <07d017c1-cb58-28f7-0bd0-1e2250c3cf2e@creatis.insa-lyon.fr>
References: <41eb944a-306a-db60-de1f-7ad8414c3173@creatis.insa-lyon.fr>
 <6d96de7a-acc0-b62c-8fe5-6f3cc9e39455@creatis.insa-lyon.fr>
 <49fe2e35-b655-44bd-54f0-5949e5b1e926@creatis.insa-lyon.fr>
 <CALzTN-QZ0Q6yeG-TLpsdow9pHR10vJqzKuwx-1aebb7=i7m_ng@mail.gmail.com>
 <07d017c1-cb58-28f7-0bd0-1e2250c3cf2e@creatis.insa-lyon.fr>
Message-ID: <57c3c8a0-65cf-87b3-7544-53768437bb28@creatis.insa-lyon.fr>

I found some help outside this mailing list, so again, I'm answering my 
own question (I'll try not to make it a habit). There is a solution 
using C++11, and features derived from "Substitution failure is not an 
error". The following code does it. I've added quite a lot of comments, 
so it should be understandable.



#include <itkImage.h>
#include <itkVectorImage.h>
#include <itkImageToImageFilter.h>
#include <itkImageFileReader.h>
#include <itkImageRegionConstIterator.h>
#include <itkImageRegionIterator.h>

#include <type_traits>
#include <typeinfo>

namespace itk
{

template <class TInputImage >
class ITK_EXPORT SFINAETestFilter :
     public itk::ImageToImageFilter< TInputImage, TInputImage >
{
public:
   /** Standard class typedefs. */
   typedef SFINAETestFilter Self;
   typedef itk::ImageToImageFilter<TInputImage, TInputImage> Superclass;
   typedef itk::SmartPointer<Self> Pointer;
   typedef itk::SmartPointer<const Self> ConstPointer;

   // Define the types that a slice can take, depending on whether 
TInputImage is an itk::Image or and itk::VectorImage
   typedef itk::Image<typename TInputImage::InternalPixelType, 
TInputImage::ImageDimension - 1>          ImageSliceType;
   typedef itk::VectorImage<typename TInputImage::InternalPixelType, 
TInputImage::ImageDimension - 1>    VectorImageSliceType;

   // Define SliceType
   // std::is_same<T1, T2>::value is true is T1 and T2 are the same 
type, and false otherwise
   // std::conditional<B, T3, T4>::type is T3 if B is true, T4 otherwise
   // The code checks if TInputImage::PixelType is an 
itk::VariableLengthVector. If so, it uses VectorImageSliceType as SliceType
   // Otherwise, it uses ImageSliceType as SliceType
   typedef typename std::conditional<std::is_same<typename 
TInputImage::PixelType,
itk::VariableLengthVector<typename TInputImage::InternalPixelType> 
 >::value,
                                     VectorImageSliceType,
                                     ImageSliceType>::type SliceType;

   /** Method for creation through the object factory */
   itkNewMacro(Self);

   /** Run-time type information (and related methods). */
   itkTypeMacro(SFINAETestFilter, ImageToImageFilter);

   /** Superclass typedefs. */
   typedef typename Superclass::OutputImageRegionType 
OutputImageRegionType;
   typedef typename Superclass::OutputImagePointer OutputImagePointer;

   /** ImageDimension constants */
   itkStaticConstMacro(InputImageDimension, unsigned int,
                       TInputImage::ImageDimension);

   typename SliceType::Pointer GetSlice()
   {
   // Create the slice
   typename SliceType::Pointer firstSlice = SliceType::New();

   // Determine its size
   typename TInputImage::RegionType largest = 
this->GetInput()->GetLargestPossibleRegion();
   typename SliceType::RegionType region;
   typename SliceType::SizeType size;
   typename SliceType::IndexType index;
   for (unsigned int dim = 0; dim < SliceType::ImageDimension; dim++)
     {
     size[dim] = largest.GetSize()[dim];
     index[dim] = largest.GetIndex()[dim];
     }
   region.SetSize(size);
   region.SetIndex(index);

   // Allocate
   firstSlice->SetRegions(region);
firstSlice->SetNumberOfComponentsPerPixel(this->GetInput()->GetNumberOfComponentsPerPixel()); 

   firstSlice->Allocate();

   // Fill
   itk::ImageRegionIterator<SliceType> sliceIt(firstSlice, region);
   itk::ImageRegionConstIterator<TInputImage> inputIt(this->GetInput(), 
largest);
   while(!sliceIt.IsAtEnd())
     {
     sliceIt.Set(inputIt.Get());
     ++sliceIt;
     ++inputIt;
     }

   // Return
   return firstSlice;
   }

};

} /* end namespace itk */


int main(){

typedef itk::Image<float, 3> ImageType;
typedef itk::VectorImage<float, 3> VectorImageType;

// With the itk::Image template
typedef itk::SFINAETestFilter<ImageType> SFINAEWithImageType;
typename SFINAEWithImageType::Pointer withImageType = 
SFINAEWithImageType::New();
typedef itk::ImageFileReader<ImageType> ImageReaderType;
ImageReaderType::Pointer imageReader = ImageReaderType::New();
imageReader->SetFileName("image.mha");
imageReader->Update();
withImageType->SetInput(imageReader->GetOutput());
withImageType->GetSlice()->Print(std::cout);

itk::Image<float, 2>::IndexType firstPixelIndex;
firstPixelIndex.Fill(0);
std::cout << withImageType->GetSlice()->GetPixel(firstPixelIndex) << 
std::endl;

// With the itk::VectorImage template
typedef itk::SFINAETestFilter<VectorImageType> SFINAEWithVectorImageType;
typename SFINAEWithVectorImageType::Pointer withVectorImageType = 
SFINAEWithVectorImageType::New();
typedef itk::ImageFileReader<VectorImageType> VectorImageReaderType;
VectorImageReaderType::Pointer vectorImageReader = 
VectorImageReaderType::New();
vectorImageReader->SetFileName("vectorImage.mha");
vectorImageReader->Update();
withVectorImageType->SetInput(vectorImageReader->GetOutput());
withVectorImageType->GetSlice()->Print(std::cout);

std::cout << withVectorImageType->GetSlice()->GetPixel(firstPixelIndex) 
<< std::endl;

return EXIT_SUCCESS;
}



On 27/02/2017 12:09, Cyril Mory wrote:
> Hi,
>
> Still the same topic, but a different issue:
>
> I have a filter that is templated over its image input type, usually 
> itk::Image<T, dim>. I want to modify it so that it also works when 
> that type is itk::VectorImage<T, dim>.
>
> This filter internally defines SliceType = 
> itk::Image<InputImageType::InternalPixelType, dim - 1>. But when 
> processing an itk::VectorImage, I would like this SliceType to be 
> itk::VectorImage<InputImageType::InternalPixelType, dim - 1>.
>
> I don't think there is a way in C++ to recover the itk::Image<> or the 
> itk::VectorImage<> "un-templated", and define a type with whole new 
> template arguments. But is there an ITK mechanism that would solve my 
> problem ?
>
> Best regards,
>
> Cyril
>
> On 22/02/2017 17:39, Matt McCormick wrote:
>> Hi Cyril,
>>
>> Yes, this is a good approach.  Thanks for sharing your investigation.
>>
>> Matt
>>
>> On Wed, Feb 22, 2017 at 5:52 AM, Cyril Mory
>> <cyril.mory at creatis.insa-lyon.fr> wrote:
>>> Answering my own question:
>>>
>>> I found a way to do what I needed using itk::NumericTraits<T> :
>>>
>>>    OutputImagePixelType pix;
>>> itk::NumericTraits<OutputImagePixelType>::SetLength(pix,
>>> this->GetVectorLength());
>>>    pix = itk::NumericTraits<OutputImagePixelType>::OneValue(pix) * 
>>> value;
>>>
>>> It works for both cases with the same code. However, if there is a 
>>> better
>>> way (cleaner, safer, more compact, ... whatever the wayin which it is
>>> better), I'd be happy to learn about it.
>>>
>>> Best regards,
>>> Cyril
>>>
>>>
>>> On 22/02/2017 10:38, Cyril Mory wrote:
>>>> Hi ITK users,
>>>>
>>>> I am writing an itk::ImageToImageFilter<T>, and I want the filter 
>>>> to work
>>>> with T=itk::Image as well as with T=itk::VectorImage.
>>>>
>>>> To set/get the vectorLength of an image (which is 1 for an 
>>>> itk::Image, and
>>>> varies for an itk::VectorImage), I have successfully used the 
>>>> functions
>>>> Set/GetNumberOfComponentsPerPixel from the itk::ImageBase class, 
>>>> which work
>>>> for both itk::Image and itk::VectorImage.
>>>>
>>>> But I cannot find a way to initialize one of the pixels to a given 
>>>> value,
>>>> that would work for both cases, i.e. whether that pixel is a scalar 
>>>> or a
>>>> variableLengthVector. For now, the best I could do is define a 
>>>> function
>>>> FillPixel in my filter, like this:
>>>>
>>>> OutputImagePixelType FillPixel(OutputImageInternalPixelType value) 
>>>> {return
>>>> value;}
>>>>
>>>> and write a template specialization when my filter is instantiated 
>>>> with
>>>> itk::VectorImage<float, 3>, like this:
>>>>
>>>> template <>
>>>> itk::VariableLengthVector<float>
>>>> rtk::ConstantImageSource<itk::VectorImage<float, 3> >
>>>> ::FillPixel(float value)
>>>> {
>>>>    itk::VariableLengthVector<float> vect;
>>>>    vect.SetSize(this->GetVectorLength());
>>>>    vect.Fill(value);
>>>>    return (vect);
>>>> }
>>>>
>>>> Did I miss something ? Is there a better way of doing this in ITK ?
>>>>
>>>> Looking forward to reading you,
>>>> Cyril
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> 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://public.kitware.com/mailman/listinfo/insight-users
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> 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://public.kitware.com/mailman/listinfo/insight-users
>

_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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://public.kitware.com/mailman/listinfo/insight-users

From francois.budin at kitware.com  Mon Feb 27 13:21:41 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Mon, 27 Feb 2017 13:21:41 -0500
Subject: [ITK] [ITK-users] Filter working on both itk::Image
	and	itk::VectorImage
In-Reply-To: <57c3c8a0-65cf-87b3-7544-53768437bb28@creatis.insa-lyon.fr>
References: <41eb944a-306a-db60-de1f-7ad8414c3173@creatis.insa-lyon.fr>
 <6d96de7a-acc0-b62c-8fe5-6f3cc9e39455@creatis.insa-lyon.fr>
 <49fe2e35-b655-44bd-54f0-5949e5b1e926@creatis.insa-lyon.fr>
 <CALzTN-QZ0Q6yeG-TLpsdow9pHR10vJqzKuwx-1aebb7=i7m_ng@mail.gmail.com>
 <07d017c1-cb58-28f7-0bd0-1e2250c3cf2e@creatis.insa-lyon.fr>
 <57c3c8a0-65cf-87b3-7544-53768437bb28@creatis.insa-lyon.fr>
Message-ID: <CAHwLD2VpHs0YbqGOOgmUV+MTuASd2NdZ7eXrHkp8N_72Zd2=xQ@mail.gmail.com>

Hey Cyril,

This is a good idea. If you want to keep it compatible without requiring
C++11, you might be able to do so using the "EnableIf" functions that are
implemented in ITK, following the same paradigm (SFINAE) than you found.

hth,
Francois

On Mon, Feb 27, 2017 at 10:24 AM, Cyril Mory <
cyril.mory at creatis.insa-lyon.fr> wrote:

> I found some help outside this mailing list, so again, I'm answering my
> own question (I'll try not to make it a habit). There is a solution using
> C++11, and features derived from "Substitution failure is not an error".
> The following code does it. I've added quite a lot of comments, so it
> should be understandable.
>
>
>
> #include <itkImage.h>
> #include <itkVectorImage.h>
> #include <itkImageToImageFilter.h>
> #include <itkImageFileReader.h>
> #include <itkImageRegionConstIterator.h>
> #include <itkImageRegionIterator.h>
>
> #include <type_traits>
> #include <typeinfo>
>
> namespace itk
> {
>
> template <class TInputImage >
> class ITK_EXPORT SFINAETestFilter :
>     public itk::ImageToImageFilter< TInputImage, TInputImage >
> {
> public:
>   /** Standard class typedefs. */
>   typedef SFINAETestFilter Self;
>   typedef itk::ImageToImageFilter<TInputImage, TInputImage> Superclass;
>   typedef itk::SmartPointer<Self> Pointer;
>   typedef itk::SmartPointer<const Self> ConstPointer;
>
>   // Define the types that a slice can take, depending on whether
> TInputImage is an itk::Image or and itk::VectorImage
>   typedef itk::Image<typename TInputImage::InternalPixelType,
> TInputImage::ImageDimension - 1>          ImageSliceType;
>   typedef itk::VectorImage<typename TInputImage::InternalPixelType,
> TInputImage::ImageDimension - 1>    VectorImageSliceType;
>
>   // Define SliceType
>   // std::is_same<T1, T2>::value is true is T1 and T2 are the same type,
> and false otherwise
>   // std::conditional<B, T3, T4>::type is T3 if B is true, T4 otherwise
>   // The code checks if TInputImage::PixelType is an
> itk::VariableLengthVector. If so, it uses VectorImageSliceType as SliceType
>   // Otherwise, it uses ImageSliceType as SliceType
>   typedef typename std::conditional<std::is_same<typename
> TInputImage::PixelType,
> itk::VariableLengthVector<typename TInputImage::InternalPixelType>
> >::value,
>                                     VectorImageSliceType,
>                                     ImageSliceType>::type SliceType;
>
>   /** Method for creation through the object factory */
>   itkNewMacro(Self);
>
>   /** Run-time type information (and related methods). */
>   itkTypeMacro(SFINAETestFilter, ImageToImageFilter);
>
>   /** Superclass typedefs. */
>   typedef typename Superclass::OutputImageRegionType
> OutputImageRegionType;
>   typedef typename Superclass::OutputImagePointer OutputImagePointer;
>
>   /** ImageDimension constants */
>   itkStaticConstMacro(InputImageDimension, unsigned int,
>                       TInputImage::ImageDimension);
>
>   typename SliceType::Pointer GetSlice()
>   {
>   // Create the slice
>   typename SliceType::Pointer firstSlice = SliceType::New();
>
>   // Determine its size
>   typename TInputImage::RegionType largest = this->GetInput()->GetLargestPo
> ssibleRegion();
>   typename SliceType::RegionType region;
>   typename SliceType::SizeType size;
>   typename SliceType::IndexType index;
>   for (unsigned int dim = 0; dim < SliceType::ImageDimension; dim++)
>     {
>     size[dim] = largest.GetSize()[dim];
>     index[dim] = largest.GetIndex()[dim];
>     }
>   region.SetSize(size);
>   region.SetIndex(index);
>
>   // Allocate
>   firstSlice->SetRegions(region);
> firstSlice->SetNumberOfComponentsPerPixel(this->GetInput()->
> GetNumberOfComponentsPerPixel());
>   firstSlice->Allocate();
>
>   // Fill
>   itk::ImageRegionIterator<SliceType> sliceIt(firstSlice, region);
>   itk::ImageRegionConstIterator<TInputImage> inputIt(this->GetInput(),
> largest);
>   while(!sliceIt.IsAtEnd())
>     {
>     sliceIt.Set(inputIt.Get());
>     ++sliceIt;
>     ++inputIt;
>     }
>
>   // Return
>   return firstSlice;
>   }
>
> };
>
> } /* end namespace itk */
>
>
> int main(){
>
> typedef itk::Image<float, 3> ImageType;
> typedef itk::VectorImage<float, 3> VectorImageType;
>
> // With the itk::Image template
> typedef itk::SFINAETestFilter<ImageType> SFINAEWithImageType;
> typename SFINAEWithImageType::Pointer withImageType =
> SFINAEWithImageType::New();
> typedef itk::ImageFileReader<ImageType> ImageReaderType;
> ImageReaderType::Pointer imageReader = ImageReaderType::New();
> imageReader->SetFileName("image.mha");
> imageReader->Update();
> withImageType->SetInput(imageReader->GetOutput());
> withImageType->GetSlice()->Print(std::cout);
>
> itk::Image<float, 2>::IndexType firstPixelIndex;
> firstPixelIndex.Fill(0);
> std::cout << withImageType->GetSlice()->GetPixel(firstPixelIndex) <<
> std::endl;
>
> // With the itk::VectorImage template
> typedef itk::SFINAETestFilter<VectorImageType> SFINAEWithVectorImageType;
> typename SFINAEWithVectorImageType::Pointer withVectorImageType =
> SFINAEWithVectorImageType::New();
> typedef itk::ImageFileReader<VectorImageType> VectorImageReaderType;
> VectorImageReaderType::Pointer vectorImageReader =
> VectorImageReaderType::New();
> vectorImageReader->SetFileName("vectorImage.mha");
> vectorImageReader->Update();
> withVectorImageType->SetInput(vectorImageReader->GetOutput());
> withVectorImageType->GetSlice()->Print(std::cout);
>
> std::cout << withVectorImageType->GetSlice()->GetPixel(firstPixelIndex)
> << std::endl;
>
> return EXIT_SUCCESS;
>
> }
>
>
>
> On 27/02/2017 12:09, Cyril Mory wrote:
>
>> Hi,
>>
>> Still the same topic, but a different issue:
>>
>> I have a filter that is templated over its image input type, usually
>> itk::Image<T, dim>. I want to modify it so that it also works when that
>> type is itk::VectorImage<T, dim>.
>>
>> This filter internally defines SliceType = itk::Image<InputImageType::InternalPixelType,
>> dim - 1>. But when processing an itk::VectorImage, I would like this
>> SliceType to be itk::VectorImage<InputImageType::InternalPixelType, dim
>> - 1>.
>>
>> I don't think there is a way in C++ to recover the itk::Image<> or the
>> itk::VectorImage<> "un-templated", and define a type with whole new
>> template arguments. But is there an ITK mechanism that would solve my
>> problem ?
>>
>> Best regards,
>>
>> Cyril
>>
>> On 22/02/2017 17:39, Matt McCormick wrote:
>>
>>> Hi Cyril,
>>>
>>> Yes, this is a good approach.  Thanks for sharing your investigation.
>>>
>>> Matt
>>>
>>> On Wed, Feb 22, 2017 at 5:52 AM, Cyril Mory
>>> <cyril.mory at creatis.insa-lyon.fr> wrote:
>>>
>>>> Answering my own question:
>>>>
>>>> I found a way to do what I needed using itk::NumericTraits<T> :
>>>>
>>>>    OutputImagePixelType pix;
>>>> itk::NumericTraits<OutputImagePixelType>::SetLength(pix,
>>>> this->GetVectorLength());
>>>>    pix = itk::NumericTraits<OutputImagePixelType>::OneValue(pix) *
>>>> value;
>>>>
>>>> It works for both cases with the same code. However, if there is a
>>>> better
>>>> way (cleaner, safer, more compact, ... whatever the wayin which it is
>>>> better), I'd be happy to learn about it.
>>>>
>>>> Best regards,
>>>> Cyril
>>>>
>>>>
>>>> On 22/02/2017 10:38, Cyril Mory wrote:
>>>>
>>>>> Hi ITK users,
>>>>>
>>>>> I am writing an itk::ImageToImageFilter<T>, and I want the filter to
>>>>> work
>>>>> with T=itk::Image as well as with T=itk::VectorImage.
>>>>>
>>>>> To set/get the vectorLength of an image (which is 1 for an itk::Image,
>>>>> and
>>>>> varies for an itk::VectorImage), I have successfully used the functions
>>>>> Set/GetNumberOfComponentsPerPixel from the itk::ImageBase class,
>>>>> which work
>>>>> for both itk::Image and itk::VectorImage.
>>>>>
>>>>> But I cannot find a way to initialize one of the pixels to a given
>>>>> value,
>>>>> that would work for both cases, i.e. whether that pixel is a scalar or
>>>>> a
>>>>> variableLengthVector. For now, the best I could do is define a function
>>>>> FillPixel in my filter, like this:
>>>>>
>>>>> OutputImagePixelType FillPixel(OutputImageInternalPixelType value)
>>>>> {return
>>>>> value;}
>>>>>
>>>>> and write a template specialization when my filter is instantiated with
>>>>> itk::VectorImage<float, 3>, like this:
>>>>>
>>>>> template <>
>>>>> itk::VariableLengthVector<float>
>>>>> rtk::ConstantImageSource<itk::VectorImage<float, 3> >
>>>>> ::FillPixel(float value)
>>>>> {
>>>>>    itk::VariableLengthVector<float> vect;
>>>>>    vect.SetSize(this->GetVectorLength());
>>>>>    vect.Fill(value);
>>>>>    return (vect);
>>>>> }
>>>>>
>>>>> Did I miss something ? Is there a better way of doing this in ITK ?
>>>>>
>>>>> Looking forward to reading you,
>>>>> Cyril
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.php
>>>>>
>>>>> 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://public.kitware.com/mailman/listinfo/insight-users
>>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> 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://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>
>>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
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From blowekamp at mail.nih.gov  Mon Feb 27 13:46:52 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Mon, 27 Feb 2017 18:46:52 +0000
Subject: [ITK] [ITK-users] Filter working on both itk::Image and
 itk::VectorImage
In-Reply-To: <07d017c1-cb58-28f7-0bd0-1e2250c3cf2e@creatis.insa-lyon.fr>
References: <41eb944a-306a-db60-de1f-7ad8414c3173@creatis.insa-lyon.fr>
 <6d96de7a-acc0-b62c-8fe5-6f3cc9e39455@creatis.insa-lyon.fr>
 <49fe2e35-b655-44bd-54f0-5949e5b1e926@creatis.insa-lyon.fr>
 <CALzTN-QZ0Q6yeG-TLpsdow9pHR10vJqzKuwx-1aebb7=i7m_ng@mail.gmail.com>
 <07d017c1-cb58-28f7-0bd0-1e2250c3cf2e@creatis.insa-lyon.fr>
Message-ID: <91FCAC15-89FB-4F88-9AFC-A15FFF2D33E8@mail.nih.gov>

Hello,

Sorry I didn?t see this sooner.

You want to look at the itk::Image::Rebind class. I created it for this exact purpose. [1] 

You can look at itkSmoothingRecursiveGaussianImageFilter.h for an example usage.

HTH,
Brad

[1] https://itk.org/Doxygen/html/structitk_1_1Image_1_1Rebind.html

> On Feb 27, 2017, at 6:09 AM, Cyril Mory <cyril.mory at creatis.insa-lyon.fr> wrote:
> 
> Hi,
> 
> Still the same topic, but a different issue:
> 
> I have a filter that is templated over its image input type, usually itk::Image<T, dim>. I want to modify it so that it also works when that type is itk::VectorImage<T, dim>.
> 
> This filter internally defines SliceType = itk::Image<InputImageType::InternalPixelType, dim - 1>. But when processing an itk::VectorImage, I would like this SliceType to be itk::VectorImage<InputImageType::InternalPixelType, dim - 1>.
> 
> I don't think there is a way in C++ to recover the itk::Image<> or the itk::VectorImage<> "un-templated", and define a type with whole new template arguments. But is there an ITK mechanism that would solve my problem ?
> 
> Best regards,
> 
> Cyril
> 
> On 22/02/2017 17:39, Matt McCormick wrote:
>> Hi Cyril,
>> 
>> Yes, this is a good approach.  Thanks for sharing your investigation.
>> 
>> Matt
>> 
>> On Wed, Feb 22, 2017 at 5:52 AM, Cyril Mory
>> <cyril.mory at creatis.insa-lyon.fr> wrote:
>>> Answering my own question:
>>> 
>>> I found a way to do what I needed using itk::NumericTraits<T> :
>>> 
>>>   OutputImagePixelType pix;
>>>   itk::NumericTraits<OutputImagePixelType>::SetLength(pix,
>>> this->GetVectorLength());
>>>   pix = itk::NumericTraits<OutputImagePixelType>::OneValue(pix) * value;
>>> 
>>> It works for both cases with the same code. However, if there is a better
>>> way (cleaner, safer, more compact, ... whatever the wayin which it is
>>> better), I'd be happy to learn about it.
>>> 
>>> Best regards,
>>> Cyril
>>> 
>>> 
>>> On 22/02/2017 10:38, Cyril Mory wrote:
>>>> Hi ITK users,
>>>> 
>>>> I am writing an itk::ImageToImageFilter<T>, and I want the filter to work
>>>> with T=itk::Image as well as with T=itk::VectorImage.
>>>> 
>>>> To set/get the vectorLength of an image (which is 1 for an itk::Image, and
>>>> varies for an itk::VectorImage), I have successfully used the functions
>>>> Set/GetNumberOfComponentsPerPixel from the itk::ImageBase class, which work
>>>> for both itk::Image and itk::VectorImage.
>>>> 
>>>> But I cannot find a way to initialize one of the pixels to a given value,
>>>> that would work for both cases, i.e. whether that pixel is a scalar or a
>>>> variableLengthVector. For now, the best I could do is define a function
>>>> FillPixel in my filter, like this:
>>>> 
>>>> OutputImagePixelType FillPixel(OutputImageInternalPixelType value) {return
>>>> value;}
>>>> 
>>>> and write a template specialization when my filter is instantiated with
>>>> itk::VectorImage<float, 3>, like this:
>>>> 
>>>> template <>
>>>> itk::VariableLengthVector<float>
>>>> rtk::ConstantImageSource<itk::VectorImage<float, 3> >
>>>> ::FillPixel(float value)
>>>> {
>>>>   itk::VariableLengthVector<float> vect;
>>>>   vect.SetSize(this->GetVectorLength());
>>>>   vect.Fill(value);
>>>>   return (vect);
>>>> }
>>>> 
>>>> Did I miss something ? Is there a better way of doing this in ITK ?
>>>> 
>>>> Looking forward to reading you,
>>>> Cyril
>>>> 
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>> 
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>> 
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>> 
>>>> 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://public.kitware.com/mailman/listinfo/insight-users
>>> 
>>> _____________________________________
>>> Powered by www.kitware.com
>>> 
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>> 
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>> 
>>> 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://public.kitware.com/mailman/listinfo/insight-users
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> 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://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

_____________________________________
Powered by www.kitware.com

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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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From zack.galbreath at kitware.com  Mon Feb 27 16:35:59 2017
From: zack.galbreath at kitware.com (Zack Galbreath)
Date: Mon, 27 Feb 2017 16:35:59 -0500
Subject: [ITK] [ITK-dev] open.cdash.org updated
In-Reply-To: <CALzTN-QUZArFSiwN+SWyJtO8Vg5QhuyohJm7Ozwsz9E7EWEOBQ@mail.gmail.com>
References: <CANgkMA6Jqv6SPP-ZbtdNzoiSmskYmcBR4R8hNWF0XiSkrwXh_A@mail.gmail.com>
 <CALzTN-QUZArFSiwN+SWyJtO8Vg5QhuyohJm7Ozwsz9E7EWEOBQ@mail.gmail.com>
Message-ID: <CANgkMA5zkTXS-fk5LURycu7+nqZpA6rRnwAj8Gsob5pLe0W-+g@mail.gmail.com>

On Thu, Feb 23, 2017 at 2:43 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Zack,
>
> Thanks for the updates!
>
> Another bug I noticed, that I think we present before the recent
> upgrade, too, is that when clicking one "expected" checkbox, it
> enables all other "expected" checkboxes.
>

I see what you mean.  These boxes are checked if your local representation
of this build has its expected value set to 1.  So if you check it for one
group they all get turned on.  So technically I think it's doing the right
thing here, but I agree that it looks funny.

This indicates to me that our UI for this form could stand to be improved.
I'll whip something up and request feedback.
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