From jianming.tom at gmail.com  Mon Feb  2 02:08:26 2015
From: jianming.tom at gmail.com (Jianming)
Date: Mon, 2 Feb 2015 15:08:26 +0800
Subject: [ITK-users] [ITK-dev] Probelm building project with VTK 6.1 + ITK
	4.7
Message-ID: <CABPMCkeK15d3kq-hA4AjLQZ1azzc0U95EaozLQSGt1Ka21U2dw@mail.gmail.com>

Hi,

I have the previous working fine code when I used VTK 5.6.1+ITK 3.20.1, but
I got lots of problem when I wanted to reuse the code while upgrading to
the new VTK/ITK version.

My environment, Ubuntu 12.04, CMake 2.8.12.2, VTK 6.1, ITK 4.7. ItkVtkGlue
is turned ON.

The CMakeLists.txt is as the following, I checked the example,

cmake_minimum_required(VERSION 2.8)

PROJECT(BackProjection)

FIND_PACKAGE(ITK REQUIRED)
INCLUDE(${ITK_USE_FILE})

if (ITKVtkGlue_LOADED)
  find_package(VTK REQUIRED)
  include(${VTK_USE_FILE})
else()
  find_package(ItkVtkGlue REQUIRED)
  include(${ItkVtkGlue_USE_FILE})
  set(Glue ItkVtkGlue)
endif()
add_executable(ReadPLY MACOSX_BUNDLE ReadPLY.cxx)
target_link_libraries(ReadPLY ${Glue} ${VTK_LIBRARIES} ${ITK_LIBRARIES})

###

When I build with make, the error is,

[100%] Building CXX object CMakeFiles/ReadPLY.dir/ReadPLY.cxx.o
Linking CXX executable ReadPLY
CMakeFiles/ReadPLY.dir/ReadPLY.cxx.o: In function
`vtkSmartPointer<vtkPLYReader>::New()':
ReadPLY.cxx:(.text._ZN15vtkSmartPointerI12vtkPLYReaderE3NewEv[_ZN15vtkSmartPointerI12vtkPLYReaderE3NewEv]+0xd):
undefined reference to `vtkPLYReader::New()'
collect2: error: ld returned 1 exit status
make[2]: *** [ReadPLY] Error 1
make[1]: *** [CMakeFiles/ReadPLY.dir/all] Error 2
make: *** [all] Error 2

Interestingly, when I fully remove anything about ITK in my CMakeLists.txt,
it doesn't show any error. So I suspect it is the ITK's build macro which
is breaking my VTK code compiling.
The working CMakeLists.txt is like,

cmake_minimum_required(VERSION 2.8)

PROJECT(ReadPLY)

find_package(VTK REQUIRED)
include(${VTK_USE_FILE})

add_executable(ReadPLY MACOSX_BUNDLE ReadPLY.cxx)

if(VTK_LIBRARIES)
  target_link_libraries(ReadPLY ${VTK_LIBRARIES})
else()
  target_link_libraries(ReadPLY vtkHybrid vtkWidgets)
endif()


####

And the ReadPLY.cxx source code is, it is actually a VTK example, doesn't
contain any ITK code. But I have the other source code file has ITK code,
presenting this example just to show the problem.

#include <vtkPolyData.h>
#include <vtkPLYReader.h>
#include <vtkSmartPointer.h>
#include <vtkPolyDataMapper.h>
#include <vtkActor.h>
#include <vtkRenderWindow.h>
#include <vtkRenderer.h>
#include <vtkRenderWindowInteractor.h>

int main ( int argc, char *argv[] )
{
  if(argc != 2)
    {
    std::cout << "Usage: " << argv[0] << "  Filename(.ply)" << std::endl;
    return EXIT_FAILURE;
    }

  std::string inputFilename = argv[1];

  vtkSmartPointer<vtkPLYReader> reader =
    vtkSmartPointer<vtkPLYReader>::New();
  reader->SetFileName ( inputFilename.c_str() );

  // Visualize
  vtkSmartPointer<vtkPolyDataMapper> mapper =
    vtkSmartPointer<vtkPolyDataMapper>::New();
  mapper->SetInputConnection(reader->GetOutputPort());

  vtkSmartPointer<vtkActor> actor =
    vtkSmartPointer<vtkActor>::New();
  actor->SetMapper(mapper);

  vtkSmartPointer<vtkRenderer> renderer =
    vtkSmartPointer<vtkRenderer>::New();
  vtkSmartPointer<vtkRenderWindow> renderWindow =
    vtkSmartPointer<vtkRenderWindow>::New();
  renderWindow->AddRenderer(renderer);
  vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
    vtkSmartPointer<vtkRenderWindowInteractor>::New();
  renderWindowInteractor->SetRenderWindow(renderWindow);

  renderer->AddActor(actor);
  renderer->SetBackground(0.1804,0.5451,0.3412); // Sea green

  renderWindow->Render();
  renderWindowInteractor->Start();

  return EXIT_SUCCESS;
}

####
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From grothausmann.roman at mh-hannover.de  Mon Feb  2 05:41:41 2015
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Mon, 02 Feb 2015 11:41:41 +0100
Subject: [ITK-users] [Paraview] compile itk (VTKGlue ON) with vtk from
 paraview
In-Reply-To: <CALzTN-SEHwLwzO99QcL0JGVn4TZD2c=Tzpy+cB6KCXiEOBR60w@mail.gmail.com>
References: <54C0CF2E.3060106@mh-hannover.de>	<54C2125D.7090801@mh-hannover.de>	<CALzTN-SJcZYJT+twE_fXXWi7tyTe6u9JhFSGy1W03-C9PU-=LA@mail.gmail.com>	<54C6029C.4040600@mh-hannover.de>	<CALzTN-S8KLZcp30bLkdNEpTK8zR3L3xT6D--XhmF5JVjKngz6A@mail.gmail.com>	<54C8CFC2.4000305@mh-hannover.de>
 <CALzTN-SEHwLwzO99QcL0JGVn4TZD2c=Tzpy+cB6KCXiEOBR60w@mail.gmail.com>
Message-ID: <54CF5465.9050009@mh-hannover.de>

Hi Matt,

On 31/01/15 17:25, Matt McCormick wrote:
>>> I would recommend creating build instructions to build against a
>>> ParaView build tree.  I have just verified that ITK builds with the
>>> ITKVtkGlue module ON when pointing VTK_DIR to the <ParaView-build>/VTK
>>> directory.
>>
>> Did You use BUILD_SHARED_LIBS ON for both ITK and ParaView? ITK also
>> compiles fine without any errors for me if I use BUILD_SHARED_LIBS OFF,
>> however the problems then arise when compiling the plugin.
>
> I was using BUILD_SHARED_LIBS for both.  What issue were you seeing?

If I configure ITK with:

BUILD_SHARED_LIBS                ON
Module_ITKVtkGlue                ON
VTK_DIR                          /opt/compilation/paraview-git_build/VTK/


cmake is happy but I get linker errors at the end of the compilation of ITK when 
the VTKGlue is due. After switching off all PV plugin builds leaves:

Linking CXX shared library ../../../../lib/libITKVtkGlue-4.6.so
/usr/bin/ld: cannot find -lvtkPVPythonCatalyst
/usr/bin/ld: cannot find -lvtkUtilitiesPythonInitializer

Both libraries seem to be missing entries in 
/opt/compilation/paraview-git_build/VTK/VTKTargets.cmake

I guess that's why the linker cannot find these libraries which are there but 
with the ending *-pv4.3.so. So a

cd /opt/compilation/paraview-git_build/lib/
for i in *-pv*.so; do ln -s $i ${i%-pv*}.so; done

did the trick but I guess that's not the way it ought to be done.
My guess is that either some lines need to be added to VTKTargets.cmake or that 
the ITK-build needs to be told that there is no need to link against these 
libraries for the ITKVtkGlue (if that is true).

> Again, I think the best approach is to build VTK separately, then
> build both ParaView and ITK against that version.

OK, I tried that with vtk-git of today but then paraview cmake complains:

cmake -DUSE_EXTERNAL_VTK:BOOL=ON ../paraview-git/
-- Determined Source Version : 4.3.1-18-g04df19f
-- Using External VTK from "/opt/vtk-git_150202/lib/cmake/vtk-6.2"
CMake Error at CMake/ParaViewModuleTop.cmake:61 (include):
   include could not find load file:

     vtkGroups
Call Stack (most recent call first):
   CMakeLists.txt:605 (include)


CMake Error at CMake/ParaViewModuleTop.cmake:184 (include):
   include could not find load file:

     TopologicalSort
Call Stack (most recent call first):
   CMakeLists.txt:605 (include)


CMake Error at CMake/ParaViewModuleTop.cmake:185 (topological_sort):
   Unknown CMake command "topological_sort".
Call Stack (most recent call first):
   CMakeLists.txt:605 (include)


-- Configuring incomplete, errors occurred!

I also tried a VTK-6.1 but that just yielded other errors.
How do I figure out what VTK-version ParaView needs? Otherwise I think this is 
not a suitable instruction to give in the publication as the VTK-Version needed 
is likely to change in future ParaView releases.
Therefore I prefer instructions that use the VTK bundled with ParaView.
What could be the reason that You did not have the linker problems when 
ITKVtkGlue was compiled?

Again, many thanks for looking into this.
Roman

>> On 26/01/15 17:54, Matt McCormick wrote:
>>>
>>> Hi Roman,
>>>
>>> Thanks for the update. Great to hear about the Midas Journal article!
>>>
>>> I do not think the Midas Journal will be able to build your plugin.
>>>
>>> I would recommend creating build instructions to build against a
>>> ParaView build tree.  I have just verified that ITK builds with the
>>> ITKVtkGlue module ON when pointing VTK_DIR to the <ParaView-build>/VTK
>>> directory.
>>>
>>> I don't see the install tree VTKTargets.cmake file in my ParaView
>>> build, either. In the long term, the ParaView CMake configuration
>>> should be corrected.
>>>
>>> HTH,
>>> Matt
>>>
>>> On Mon, Jan 26, 2015 at 4:02 AM, Dr. Roman Grothausmann
>>> <grothausmann.roman at mh-hannover.de> wrote:
>>>>
>>>> Hi Matt,
>>>>
>>>>
>>>> Thank You very much for Your reply.
>>>> I can only find one VTKTargets.cmake in
>>>> /opt/compilation/paraview-git_build/VTK/
>>>> It seems though that it is lacking the relevant entries for the libraries
>>>> that troubled me, e.g. vtkPVPythonCatalyst and
>>>> vtkUtilitiesPythonInitializer.
>>>>
>>>> I'm about to publish the ITK-VTK PV plugin in the Midas Journal, what
>>>> installation instructions should I give there?
>>>> Will the testing environment be able to compile this plugin and its tests
>>>> or
>>>> should I disable automatic testing for this contribution?
>>>>
>>>> Many thanks for looking into this.
>>>> Roman
>>>>
>>>>
>>>> On 23/01/15 18:15, Matt McCormick wrote:
>>>>>
>>>>>
>>>>> Hi Roman,
>>>>>
>>>>> Thanks for looking into the issue and reporting it to the mailing list.
>>>>>
>>>>> Paraview should be installing VTKTargets.cmake, which tells the build
>>>>> system where to find the libraries.  Note that there might be two
>>>>> VTKTargets.cmake files that are generated -- one for the build tree
>>>>> and one for the install tree.
>>>>>
>>>>> HTH,
>>>>> Matt
>>>>>
>>>>> On Fri, Jan 23, 2015 at 4:20 AM, Dr. Roman Grothausmann
>>>>> <grothausmann.roman at mh-hannover.de> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 22/01/15 11:21, Dr. Roman Grothausmann wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Adding the abs. file locations to the build command does not help nor
>>>>>>> does
>>>>>>> -L/opt/paraview-4.3.1_git/lib/paraview-4.3/
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> I figured that the vtk dynamic libraries of PV have the ending
>>>>>> *-pv4.3.so
>>>>>> which seems to be the reason why the linker does not find them. If I
>>>>>> create
>>>>>> symbolic links to these files without the extension:
>>>>>>
>>>>>> cd /opt/compilation/paraview-git_build/lib/
>>>>>> for i in *-pv*.so; do ln -s $i ${i%-pv*}.so; done
>>>>>>
>>>>>> and adding -L/opt/compilation/paraview-git_build/lib/ to
>>>>>> CMAKE_CXX_FLAGS
>>>>>> the compilation of ITK succeeds.
>>>>>>
>>>>>> I wonder, is that the way it's meant to be done?
>>>>>>
>>>>>>
>>>>>>
>>>>>>> What am I missing in my configuration of PV and ITK?
>>>>>>>
>>>>>>> When and where should I specify:
>>>>>>> CMAKE_CXX_FLAGS                  -fPIC
>>>>>>> BUILD_SHARED_LIBS                ON/OFF
>>>>>>>
>>>>>>> Is this the right VTK_DIR specification for ITK:
>>>>>>> /opt/compilation/ParaView-v4.3.1/build/VTK
>>>>>>> or
>>>>>>> /opt/paraview-4.3.1_git/lib/cmake/paraview-4.3
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Many thanks for any help or hints.
>>>>>>> Roman
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Dr. Roman Grothausmann
>>>>>>
>>>>>> Tomographie und Digitale Bildverarbeitung
>>>>>> Tomography and Digital Image Analysis
>>>>>>
>>>>>> Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
>>>>>> Medizinische Hochschule Hannover
>>>>>> Carl-Neuberg-Str. 1
>>>>>> D-30625 Hannover
>>>>>>
>>>>>> Tel. +49 511 532-9574
>>>>>> _____________________________________
>>>>>> 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
>>>>
>>>>
>>>>
>>>> --
>>>> Dr. Roman Grothausmann
>>>>
>>>> Tomographie und Digitale Bildverarbeitung
>>>> Tomography and Digital Image Analysis
>>>>
>>>> Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
>>>> Medizinische Hochschule Hannover
>>>> Carl-Neuberg-Str. 1
>>>> D-30625 Hannover
>>>>
>>>> Tel. +49 511 532-9574
>>
>>
>> --
>> Dr. Roman Grothausmann
>>
>> Tomographie und Digitale Bildverarbeitung
>> Tomography and Digital Image Analysis
>>
>> Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
>> Medizinische Hochschule Hannover
>> Carl-Neuberg-Str. 1
>> D-30625 Hannover
>>
>> Tel. +49 511 532-9574

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574

From bill.lorensen at gmail.com  Mon Feb  2 08:34:50 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Mon, 2 Feb 2015 08:34:50 -0500
Subject: [ITK-users] [ITK-dev] Probelm building project with VTK 6.1 +
	ITK 4.7
In-Reply-To: <CABPMCkeK15d3kq-hA4AjLQZ1azzc0U95EaozLQSGt1Ka21U2dw@mail.gmail.com>
References: <CABPMCkeK15d3kq-hA4AjLQZ1azzc0U95EaozLQSGt1Ka21U2dw@mail.gmail.com>
Message-ID: <CADZJ4hMGSioaFKOu86jZGpSB9181X9+DcHB8dx9eradhCEpphw@mail.gmail.com>

What you have should work. I just built this example:
http://itk.org/Wiki/ITK/Examples/Smoothing/MedianImageFilter

no problems. Can you try the same example?

On Mon, Feb 2, 2015 at 2:08 AM, Jianming <jianming.tom at gmail.com> wrote:
>
>
>
>
> Hi,
>
> I have the previous working fine code when I used VTK 5.6.1+ITK 3.20.1, but
> I got lots of problem when I wanted to reuse the code while upgrading to the
> new VTK/ITK version.
>
> My environment, Ubuntu 12.04, CMake 2.8.12.2, VTK 6.1, ITK 4.7. ItkVtkGlue
> is turned ON.
>
> The CMakeLists.txt is as the following, I checked the example,
>
> cmake_minimum_required(VERSION 2.8)
>
> PROJECT(BackProjection)
>
> FIND_PACKAGE(ITK REQUIRED)
> INCLUDE(${ITK_USE_FILE})
>
> if (ITKVtkGlue_LOADED)
>   find_package(VTK REQUIRED)
>   include(${VTK_USE_FILE})
> else()
>   find_package(ItkVtkGlue REQUIRED)
>   include(${ItkVtkGlue_USE_FILE})
>   set(Glue ItkVtkGlue)
> endif()
> add_executable(ReadPLY MACOSX_BUNDLE ReadPLY.cxx)
> target_link_libraries(ReadPLY ${Glue} ${VTK_LIBRARIES} ${ITK_LIBRARIES})
>
> ###
>
> When I build with make, the error is,
>
> [100%] Building CXX object CMakeFiles/ReadPLY.dir/ReadPLY.cxx.o
> Linking CXX executable ReadPLY
> CMakeFiles/ReadPLY.dir/ReadPLY.cxx.o: In function
> `vtkSmartPointer<vtkPLYReader>::New()':
> ReadPLY.cxx:(.text._ZN15vtkSmartPointerI12vtkPLYReaderE3NewEv[_ZN15vtkSmartPointerI12vtkPLYReaderE3NewEv]+0xd):
> undefined reference to `vtkPLYReader::New()'
> collect2: error: ld returned 1 exit status
> make[2]: *** [ReadPLY] Error 1
> make[1]: *** [CMakeFiles/ReadPLY.dir/all] Error 2
> make: *** [all] Error 2
>
> Interestingly, when I fully remove anything about ITK in my CMakeLists.txt,
> it doesn't show any error. So I suspect it is the ITK's build macro which is
> breaking my VTK code compiling.
> The working CMakeLists.txt is like,
>
> cmake_minimum_required(VERSION 2.8)
>
> PROJECT(ReadPLY)
>
> find_package(VTK REQUIRED)
> include(${VTK_USE_FILE})
>
> add_executable(ReadPLY MACOSX_BUNDLE ReadPLY.cxx)
>
> if(VTK_LIBRARIES)
>   target_link_libraries(ReadPLY ${VTK_LIBRARIES})
> else()
>   target_link_libraries(ReadPLY vtkHybrid vtkWidgets)
> endif()
>
>
> ####
>
> And the ReadPLY.cxx source code is, it is actually a VTK example, doesn't
> contain any ITK code. But I have the other source code file has ITK code,
> presenting this example just to show the problem.
>
> #include <vtkPolyData.h>
> #include <vtkPLYReader.h>
> #include <vtkSmartPointer.h>
> #include <vtkPolyDataMapper.h>
> #include <vtkActor.h>
> #include <vtkRenderWindow.h>
> #include <vtkRenderer.h>
> #include <vtkRenderWindowInteractor.h>
>
> int main ( int argc, char *argv[] )
> {
>   if(argc != 2)
>     {
>     std::cout << "Usage: " << argv[0] << "  Filename(.ply)" << std::endl;
>     return EXIT_FAILURE;
>     }
>
>   std::string inputFilename = argv[1];
>
>   vtkSmartPointer<vtkPLYReader> reader =
>     vtkSmartPointer<vtkPLYReader>::New();
>   reader->SetFileName ( inputFilename.c_str() );
>
>   // Visualize
>   vtkSmartPointer<vtkPolyDataMapper> mapper =
>     vtkSmartPointer<vtkPolyDataMapper>::New();
>   mapper->SetInputConnection(reader->GetOutputPort());
>
>   vtkSmartPointer<vtkActor> actor =
>     vtkSmartPointer<vtkActor>::New();
>   actor->SetMapper(mapper);
>
>   vtkSmartPointer<vtkRenderer> renderer =
>     vtkSmartPointer<vtkRenderer>::New();
>   vtkSmartPointer<vtkRenderWindow> renderWindow =
>     vtkSmartPointer<vtkRenderWindow>::New();
>   renderWindow->AddRenderer(renderer);
>   vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
>     vtkSmartPointer<vtkRenderWindowInteractor>::New();
>   renderWindowInteractor->SetRenderWindow(renderWindow);
>
>   renderer->AddActor(actor);
>   renderer->SetBackground(0.1804,0.5451,0.3412); // Sea green
>
>   renderWindow->Render();
>   renderWindowInteractor->Start();
>
>   return EXIT_SUCCESS;
> }
>
> ####
>
>
> _____________________________________
> 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

From matt.mccormick at kitware.com  Mon Feb  2 08:48:03 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 2 Feb 2015 08:48:03 -0500
Subject: [ITK-users] [ITK-dev] Probelm building project with VTK 6.1 +
	ITK 4.7
In-Reply-To: <CADZJ4hMGSioaFKOu86jZGpSB9181X9+DcHB8dx9eradhCEpphw@mail.gmail.com>
References: <CABPMCkeK15d3kq-hA4AjLQZ1azzc0U95EaozLQSGt1Ka21U2dw@mail.gmail.com>
 <CADZJ4hMGSioaFKOu86jZGpSB9181X9+DcHB8dx9eradhCEpphw@mail.gmail.com>
Message-ID: <CALzTN-Qr+L+KNZR2MWFNhGQi4h=dgJS7X0VHCyFifs2=0MONug@mail.gmail.com>

Hi Jianming,

Could you please also try VTK Git master and report your results?

Thanks,
Matt

On Mon, Feb 2, 2015 at 8:34 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> What you have should work. I just built this example:
> http://itk.org/Wiki/ITK/Examples/Smoothing/MedianImageFilter
>
> no problems. Can you try the same example?
>
> On Mon, Feb 2, 2015 at 2:08 AM, Jianming <jianming.tom at gmail.com> wrote:
>>
>>
>>
>>
>> Hi,
>>
>> I have the previous working fine code when I used VTK 5.6.1+ITK 3.20.1, but
>> I got lots of problem when I wanted to reuse the code while upgrading to the
>> new VTK/ITK version.
>>
>> My environment, Ubuntu 12.04, CMake 2.8.12.2, VTK 6.1, ITK 4.7. ItkVtkGlue
>> is turned ON.
>>
>> The CMakeLists.txt is as the following, I checked the example,
>>
>> cmake_minimum_required(VERSION 2.8)
>>
>> PROJECT(BackProjection)
>>
>> FIND_PACKAGE(ITK REQUIRED)
>> INCLUDE(${ITK_USE_FILE})
>>
>> if (ITKVtkGlue_LOADED)
>>   find_package(VTK REQUIRED)
>>   include(${VTK_USE_FILE})
>> else()
>>   find_package(ItkVtkGlue REQUIRED)
>>   include(${ItkVtkGlue_USE_FILE})
>>   set(Glue ItkVtkGlue)
>> endif()
>> add_executable(ReadPLY MACOSX_BUNDLE ReadPLY.cxx)
>> target_link_libraries(ReadPLY ${Glue} ${VTK_LIBRARIES} ${ITK_LIBRARIES})
>>
>> ###
>>
>> When I build with make, the error is,
>>
>> [100%] Building CXX object CMakeFiles/ReadPLY.dir/ReadPLY.cxx.o
>> Linking CXX executable ReadPLY
>> CMakeFiles/ReadPLY.dir/ReadPLY.cxx.o: In function
>> `vtkSmartPointer<vtkPLYReader>::New()':
>> ReadPLY.cxx:(.text._ZN15vtkSmartPointerI12vtkPLYReaderE3NewEv[_ZN15vtkSmartPointerI12vtkPLYReaderE3NewEv]+0xd):
>> undefined reference to `vtkPLYReader::New()'
>> collect2: error: ld returned 1 exit status
>> make[2]: *** [ReadPLY] Error 1
>> make[1]: *** [CMakeFiles/ReadPLY.dir/all] Error 2
>> make: *** [all] Error 2
>>
>> Interestingly, when I fully remove anything about ITK in my CMakeLists.txt,
>> it doesn't show any error. So I suspect it is the ITK's build macro which is
>> breaking my VTK code compiling.
>> The working CMakeLists.txt is like,
>>
>> cmake_minimum_required(VERSION 2.8)
>>
>> PROJECT(ReadPLY)
>>
>> find_package(VTK REQUIRED)
>> include(${VTK_USE_FILE})
>>
>> add_executable(ReadPLY MACOSX_BUNDLE ReadPLY.cxx)
>>
>> if(VTK_LIBRARIES)
>>   target_link_libraries(ReadPLY ${VTK_LIBRARIES})
>> else()
>>   target_link_libraries(ReadPLY vtkHybrid vtkWidgets)
>> endif()
>>
>>
>> ####
>>
>> And the ReadPLY.cxx source code is, it is actually a VTK example, doesn't
>> contain any ITK code. But I have the other source code file has ITK code,
>> presenting this example just to show the problem.
>>
>> #include <vtkPolyData.h>
>> #include <vtkPLYReader.h>
>> #include <vtkSmartPointer.h>
>> #include <vtkPolyDataMapper.h>
>> #include <vtkActor.h>
>> #include <vtkRenderWindow.h>
>> #include <vtkRenderer.h>
>> #include <vtkRenderWindowInteractor.h>
>>
>> int main ( int argc, char *argv[] )
>> {
>>   if(argc != 2)
>>     {
>>     std::cout << "Usage: " << argv[0] << "  Filename(.ply)" << std::endl;
>>     return EXIT_FAILURE;
>>     }
>>
>>   std::string inputFilename = argv[1];
>>
>>   vtkSmartPointer<vtkPLYReader> reader =
>>     vtkSmartPointer<vtkPLYReader>::New();
>>   reader->SetFileName ( inputFilename.c_str() );
>>
>>   // Visualize
>>   vtkSmartPointer<vtkPolyDataMapper> mapper =
>>     vtkSmartPointer<vtkPolyDataMapper>::New();
>>   mapper->SetInputConnection(reader->GetOutputPort());
>>
>>   vtkSmartPointer<vtkActor> actor =
>>     vtkSmartPointer<vtkActor>::New();
>>   actor->SetMapper(mapper);
>>
>>   vtkSmartPointer<vtkRenderer> renderer =
>>     vtkSmartPointer<vtkRenderer>::New();
>>   vtkSmartPointer<vtkRenderWindow> renderWindow =
>>     vtkSmartPointer<vtkRenderWindow>::New();
>>   renderWindow->AddRenderer(renderer);
>>   vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
>>     vtkSmartPointer<vtkRenderWindowInteractor>::New();
>>   renderWindowInteractor->SetRenderWindow(renderWindow);
>>
>>   renderer->AddActor(actor);
>>   renderer->SetBackground(0.1804,0.5451,0.3412); // Sea green
>>
>>   renderWindow->Render();
>>   renderWindowInteractor->Start();
>>
>>   return EXIT_SUCCESS;
>> }
>>
>> ####
>>
>>
>> _____________________________________
>> 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 emily-hammond at uiowa.edu  Mon Feb  2 15:53:54 2015
From: emily-hammond at uiowa.edu (Hammond, Emily M)
Date: Mon, 2 Feb 2015 20:53:54 +0000
Subject: [ITK-users] applying transform to point
Message-ID: <2609C492EC89AB4CAAD3647B8D1A43CC2F186914@ITSNT437.iowa.uiowa.edu>

Hello all,

Here is the flow of my program.

1. read in fiducial points noted with Slicer (to my understanding to get from Slicer to ITK, invert the first two coordinates)
2. read in transform from files with TransformFileReaderTemplate class. This reads in the transforms as a list and I can add multiple transforms to the list.
3. apply the transforms in the list (in order) to the fiducials using the TransformPoint method for each transform. Here is the code I am using to apply the transforms.

// create iterator to parse through the transform list
TransformListType::const_iterator itTrans = this->m_TransformList.begin();
for(; itTrans != this->m_TransformList.end(); itTrans++ )
{
// determine what type of transform it is
if( !strcmp( (*itTrans)->GetNameOfClass(), "AffineTransform" ) )
{
// extract transform
AffineTransformType::Pointer affineTrans = static_cast< AffineTransformType * >( (*itTrans).GetPointer() );

// apply to landmarks
LandmarksType::const_iterator itLM = this->m_TransformedMovingLandmarks.begin();
for(; itLM != this->m_TransformedMovingLandmarks.end(); itLM++ )
{
this->m_TransformedMovingLandmarks[ itLM->first ] = affineTrans->TransformPoint( itLM->second );
}
}
else if( !strcmp( (*itTrans)->GetNameOfClass(), "BSplineTransform" ) )
{
// extract transforms
BSplineTransformType::Pointer bsplineTrans = static_cast< BSplineTransformType * >( (*itTrans).GetPointer() );

// apply to landmarks
LandmarksType::const_iterator itLM = this->m_TransformedMovingLandmarks.begin();
for(; itLM != this->m_TransformedMovingLandmarks.end(); itLM++ )
{
this->m_TransformedMovingLandmarks[ itLM->first ] = bsplineTrans->TransformPoint( itLM->second );
}
}
else
{
std::cerr << "TransformType is not recognized." << std::endl;
}
}

NOTE: m_TransformedMovingList is initialized to the original read in fiducial list

4. read out the transform fiducials (invert first two coordinates for observation in Slicer purposes)
5. Compare the results using Slicer

Problem: This method works just fine with scaling and translation transforms (given the last coordinate is inverted instead of the first two -> first question), however, once rotation (and shearing) is applied the result is wrong. Can anyone give some insight? I'm assuming there is some coordinate system conversion that needs to take place on the transform.

Thanks!
Emily Hammond
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From lasso at queensu.ca  Mon Feb  2 17:22:21 2015
From: lasso at queensu.ca (Andras Lasso)
Date: Mon, 2 Feb 2015 22:22:21 +0000
Subject: [ITK-users] [ITK]  applying transform to point
In-Reply-To: <2609C492EC89AB4CAAD3647B8D1A43CC2F186914@ITSNT437.iowa.uiowa.edu>
References: <2609C492EC89AB4CAAD3647B8D1A43CC2F186914@ITSNT437.iowa.uiowa.edu>
Message-ID: <B6FC5543F5C41E479B8B89158B0C58FF31E93BD9@QU-MBX02-PRD.AD.QUEENSU.CA>

RAS/LPS conversion is more complex than just inverting the sign of the first two coordinates of a point. There may be also modeling/resampling transform mismatch.

See detailed explanation and sample conversion code in the Transform files section of this page:
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms

Andras
________________________________
From: Hammond, Emily M<mailto:emily-hammond at uiowa.edu>
Sent: ?2015-?02-?02 15:59
To: insight users<mailto:insight-users at itk.org>
Subject: [ITK] [ITK-users] applying transform to point

Hello all,

Here is the flow of my program.

1. read in fiducial points noted with Slicer (to my understanding to get from Slicer to ITK, invert the first two coordinates)
2. read in transform from files with TransformFileReaderTemplate class. This reads in the transforms as a list and I can add multiple transforms to the list.
3. apply the transforms in the list (in order) to the fiducials using the TransformPoint method for each transform. Here is the code I am using to apply the transforms.

// create iterator to parse through the transform list
TransformListType::const_iterator itTrans = this->m_TransformList.begin();
for(; itTrans != this->m_TransformList.end(); itTrans++ )
{
// determine what type of transform it is
if( !strcmp( (*itTrans)->GetNameOfClass(), "AffineTransform" ) )
{
// extract transform
AffineTransformType::Pointer affineTrans = static_cast< AffineTransformType * >( (*itTrans).GetPointer() );

// apply to landmarks
LandmarksType::const_iterator itLM = this->m_TransformedMovingLandmarks.begin();
for(; itLM != this->m_TransformedMovingLandmarks.end(); itLM++ )
{
this->m_TransformedMovingLandmarks[ itLM->first ] = affineTrans->TransformPoint( itLM->second );
}
}
else if( !strcmp( (*itTrans)->GetNameOfClass(), "BSplineTransform" ) )
{
// extract transforms
BSplineTransformType::Pointer bsplineTrans = static_cast< BSplineTransformType * >( (*itTrans).GetPointer() );

// apply to landmarks
LandmarksType::const_iterator itLM = this->m_TransformedMovingLandmarks.begin();
for(; itLM != this->m_TransformedMovingLandmarks.end(); itLM++ )
{
this->m_TransformedMovingLandmarks[ itLM->first ] = bsplineTrans->TransformPoint( itLM->second );
}
}
else
{
std::cerr << "TransformType is not recognized." << std::endl;
}
}

NOTE: m_TransformedMovingList is initialized to the original read in fiducial list

4. read out the transform fiducials (invert first two coordinates for observation in Slicer purposes)
5. Compare the results using Slicer

Problem: This method works just fine with scaling and translation transforms (given the last coordinate is inverted instead of the first two -> first question), however, once rotation (and shearing) is applied the result is wrong. Can anyone give some insight? I'm assuming there is some coordinate system conversion that needs to take place on the transform.

Thanks!
Emily Hammond
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From jianming.tom at gmail.com  Mon Feb  2 21:15:40 2015
From: jianming.tom at gmail.com (Jianming)
Date: Tue, 3 Feb 2015 10:15:40 +0800
Subject: [ITK-users] [ITK-dev] Probelm building project with VTK 6.1 +
	ITK 4.7
In-Reply-To: <CALzTN-Qr+L+KNZR2MWFNhGQi4h=dgJS7X0VHCyFifs2=0MONug@mail.gmail.com>
References: <CABPMCkeK15d3kq-hA4AjLQZ1azzc0U95EaozLQSGt1Ka21U2dw@mail.gmail.com>
 <CADZJ4hMGSioaFKOu86jZGpSB9181X9+DcHB8dx9eradhCEpphw@mail.gmail.com>
 <CALzTN-Qr+L+KNZR2MWFNhGQi4h=dgJS7X0VHCyFifs2=0MONug@mail.gmail.com>
Message-ID: <CABPMCkfTQOzTYz=RqC5tBPbi+1TiOhbm+7oW-66=C979MN8qzg@mail.gmail.com>

@Bill, the compiling of the the normal ITK examples are fine for me here.
It just when it links the ITK and VTK together problem happens.

@Matt, I will test it once I have the time.

I kind of did a workaround, since I just need the VXL in ITK code, so I
gave up linking ITK, but used the following CMakeLists.txt

cmake_minimum_required(VERSION 2.8)

PROJECT(BackProjection)

find_package(VTK REQUIRED)
include(${VTK_USE_FILE})

FIND_PACKAGE( OpenCV REQUIRED )
INCLUDE_DIRECTORIES(${OPENCV_INCLUDE_DIR})

FIND_PACKAGE(VXL REQUIRED)
INCLUDE(${VXL_CMAKE_DIR}/UseVXL.cmake)

SET(CMAKE_CXX_FLAGS "-g -O2 -fopenmp")

add_executable(BackProjection MACOSX_BUNDLE BackProjection)
add_executable(deviation MACOSX_BUNDLE deviation)
add_executable(imageviewer MACOSX_BUNDLE imageviewer)
add_executable(deviation_autopipeline MACOSX_BUNDLE deviation_autopipeline)
add_executable(ReadPLY MACOSX_BUNDLE ReadPLY.cxx)

target_link_libraries(ReadPLY ${VTK_LIBRARIES} )
target_link_libraries(BackProjection vnl vnl_algo ${VTK_LIBRARIES}
${OpenCV_LIBS})
target_link_libraries(deviation ${OpenCV_LIBS})
target_link_libraries(imageviewer ${OpenCV_LIBS})
target_link_libraries(deviation_autopipeline ${OpenCV_LIBS})

On 2 February 2015 at 21:48, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Jianming,
>
> Could you please also try VTK Git master and report your results?
>
> Thanks,
> Matt
>
> On Mon, Feb 2, 2015 at 8:34 AM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
> > What you have should work. I just built this example:
> > http://itk.org/Wiki/ITK/Examples/Smoothing/MedianImageFilter
> >
> > no problems. Can you try the same example?
> >
> > On Mon, Feb 2, 2015 at 2:08 AM, Jianming <jianming.tom at gmail.com> wrote:
> >>
> >>
> >>
> >>
> >> Hi,
> >>
> >> I have the previous working fine code when I used VTK 5.6.1+ITK 3.20.1,
> but
> >> I got lots of problem when I wanted to reuse the code while upgrading
> to the
> >> new VTK/ITK version.
> >>
> >> My environment, Ubuntu 12.04, CMake 2.8.12.2, VTK 6.1, ITK 4.7.
> ItkVtkGlue
> >> is turned ON.
> >>
> >> The CMakeLists.txt is as the following, I checked the example,
> >>
> >> cmake_minimum_required(VERSION 2.8)
> >>
> >> PROJECT(BackProjection)
> >>
> >> FIND_PACKAGE(ITK REQUIRED)
> >> INCLUDE(${ITK_USE_FILE})
> >>
> >> if (ITKVtkGlue_LOADED)
> >>   find_package(VTK REQUIRED)
> >>   include(${VTK_USE_FILE})
> >> else()
> >>   find_package(ItkVtkGlue REQUIRED)
> >>   include(${ItkVtkGlue_USE_FILE})
> >>   set(Glue ItkVtkGlue)
> >> endif()
> >> add_executable(ReadPLY MACOSX_BUNDLE ReadPLY.cxx)
> >> target_link_libraries(ReadPLY ${Glue} ${VTK_LIBRARIES} ${ITK_LIBRARIES})
> >>
> >> ###
> >>
> >> When I build with make, the error is,
> >>
> >> [100%] Building CXX object CMakeFiles/ReadPLY.dir/ReadPLY.cxx.o
> >> Linking CXX executable ReadPLY
> >> CMakeFiles/ReadPLY.dir/ReadPLY.cxx.o: In function
> >> `vtkSmartPointer<vtkPLYReader>::New()':
> >>
> ReadPLY.cxx:(.text._ZN15vtkSmartPointerI12vtkPLYReaderE3NewEv[_ZN15vtkSmartPointerI12vtkPLYReaderE3NewEv]+0xd):
> >> undefined reference to `vtkPLYReader::New()'
> >> collect2: error: ld returned 1 exit status
> >> make[2]: *** [ReadPLY] Error 1
> >> make[1]: *** [CMakeFiles/ReadPLY.dir/all] Error 2
> >> make: *** [all] Error 2
> >>
> >> Interestingly, when I fully remove anything about ITK in my
> CMakeLists.txt,
> >> it doesn't show any error. So I suspect it is the ITK's build macro
> which is
> >> breaking my VTK code compiling.
> >> The working CMakeLists.txt is like,
> >>
> >> cmake_minimum_required(VERSION 2.8)
> >>
> >> PROJECT(ReadPLY)
> >>
> >> find_package(VTK REQUIRED)
> >> include(${VTK_USE_FILE})
> >>
> >> add_executable(ReadPLY MACOSX_BUNDLE ReadPLY.cxx)
> >>
> >> if(VTK_LIBRARIES)
> >>   target_link_libraries(ReadPLY ${VTK_LIBRARIES})
> >> else()
> >>   target_link_libraries(ReadPLY vtkHybrid vtkWidgets)
> >> endif()
> >>
> >>
> >> ####
> >>
> >> And the ReadPLY.cxx source code is, it is actually a VTK example,
> doesn't
> >> contain any ITK code. But I have the other source code file has ITK
> code,
> >> presenting this example just to show the problem.
> >>
> >> #include <vtkPolyData.h>
> >> #include <vtkPLYReader.h>
> >> #include <vtkSmartPointer.h>
> >> #include <vtkPolyDataMapper.h>
> >> #include <vtkActor.h>
> >> #include <vtkRenderWindow.h>
> >> #include <vtkRenderer.h>
> >> #include <vtkRenderWindowInteractor.h>
> >>
> >> int main ( int argc, char *argv[] )
> >> {
> >>   if(argc != 2)
> >>     {
> >>     std::cout << "Usage: " << argv[0] << "  Filename(.ply)" <<
> std::endl;
> >>     return EXIT_FAILURE;
> >>     }
> >>
> >>   std::string inputFilename = argv[1];
> >>
> >>   vtkSmartPointer<vtkPLYReader> reader =
> >>     vtkSmartPointer<vtkPLYReader>::New();
> >>   reader->SetFileName ( inputFilename.c_str() );
> >>
> >>   // Visualize
> >>   vtkSmartPointer<vtkPolyDataMapper> mapper =
> >>     vtkSmartPointer<vtkPolyDataMapper>::New();
> >>   mapper->SetInputConnection(reader->GetOutputPort());
> >>
> >>   vtkSmartPointer<vtkActor> actor =
> >>     vtkSmartPointer<vtkActor>::New();
> >>   actor->SetMapper(mapper);
> >>
> >>   vtkSmartPointer<vtkRenderer> renderer =
> >>     vtkSmartPointer<vtkRenderer>::New();
> >>   vtkSmartPointer<vtkRenderWindow> renderWindow =
> >>     vtkSmartPointer<vtkRenderWindow>::New();
> >>   renderWindow->AddRenderer(renderer);
> >>   vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
> >>     vtkSmartPointer<vtkRenderWindowInteractor>::New();
> >>   renderWindowInteractor->SetRenderWindow(renderWindow);
> >>
> >>   renderer->AddActor(actor);
> >>   renderer->SetBackground(0.1804,0.5451,0.3412); // Sea green
> >>
> >>   renderWindow->Render();
> >>   renderWindowInteractor->Start();
> >>
> >>   return EXIT_SUCCESS;
> >> }
> >>
> >> ####
> >>
> >>
> >> _____________________________________
> >> 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
>
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From matt.mccormick at kitware.com  Mon Feb  2 21:47:12 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 2 Feb 2015 21:47:12 -0500
Subject: [ITK-users] [ITK-dev] Probelm building project with VTK 6.1 +
	ITK 4.7
In-Reply-To: <CABPMCkfTQOzTYz=RqC5tBPbi+1TiOhbm+7oW-66=C979MN8qzg@mail.gmail.com>
References: <CABPMCkeK15d3kq-hA4AjLQZ1azzc0U95EaozLQSGt1Ka21U2dw@mail.gmail.com>
 <CADZJ4hMGSioaFKOu86jZGpSB9181X9+DcHB8dx9eradhCEpphw@mail.gmail.com>
 <CALzTN-Qr+L+KNZR2MWFNhGQi4h=dgJS7X0VHCyFifs2=0MONug@mail.gmail.com>
 <CABPMCkfTQOzTYz=RqC5tBPbi+1TiOhbm+7oW-66=C979MN8qzg@mail.gmail.com>
Message-ID: <CALzTN-S-ba0LCevrrwuS7eNAdUY1y_OwhZL6PPrTSwxz2FQ2dg@mail.gmail.com>

Hi,

I thought this patch [1] had been merged, but after re-checking it is
not yet in VTK master.  If you test against this branch, you may be
able to verify that it fixes your issue.

Thanks,
Matt

[1] http://review.source.kitware.com/#/t/5170/

On Mon, Feb 2, 2015 at 9:15 PM, Jianming <jianming.tom at gmail.com> wrote:
> @Bill, the compiling of the the normal ITK examples are fine for me here. It
> just when it links the ITK and VTK together problem happens.
>
> @Matt, I will test it once I have the time.
>
> I kind of did a workaround, since I just need the VXL in ITK code, so I gave
> up linking ITK, but used the following CMakeLists.txt
>
> cmake_minimum_required(VERSION 2.8)
>
> PROJECT(BackProjection)
>
> find_package(VTK REQUIRED)
> include(${VTK_USE_FILE})
>
> FIND_PACKAGE( OpenCV REQUIRED )
> INCLUDE_DIRECTORIES(${OPENCV_INCLUDE_DIR})
>
> FIND_PACKAGE(VXL REQUIRED)
> INCLUDE(${VXL_CMAKE_DIR}/UseVXL.cmake)
>
> SET(CMAKE_CXX_FLAGS "-g -O2 -fopenmp")
>
> add_executable(BackProjection MACOSX_BUNDLE BackProjection)
> add_executable(deviation MACOSX_BUNDLE deviation)
> add_executable(imageviewer MACOSX_BUNDLE imageviewer)
> add_executable(deviation_autopipeline MACOSX_BUNDLE deviation_autopipeline)
> add_executable(ReadPLY MACOSX_BUNDLE ReadPLY.cxx)
>
> target_link_libraries(ReadPLY ${VTK_LIBRARIES} )
> target_link_libraries(BackProjection vnl vnl_algo ${VTK_LIBRARIES}
> ${OpenCV_LIBS})
> target_link_libraries(deviation ${OpenCV_LIBS})
> target_link_libraries(imageviewer ${OpenCV_LIBS})
> target_link_libraries(deviation_autopipeline ${OpenCV_LIBS})
>
> On 2 February 2015 at 21:48, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>>
>> Hi Jianming,
>>
>> Could you please also try VTK Git master and report your results?
>>
>> Thanks,
>> Matt
>>
>> On Mon, Feb 2, 2015 at 8:34 AM, Bill Lorensen <bill.lorensen at gmail.com>
>> wrote:
>> > What you have should work. I just built this example:
>> > http://itk.org/Wiki/ITK/Examples/Smoothing/MedianImageFilter
>> >
>> > no problems. Can you try the same example?
>> >
>> > On Mon, Feb 2, 2015 at 2:08 AM, Jianming <jianming.tom at gmail.com> wrote:
>> >>
>> >>
>> >>
>> >>
>> >> Hi,
>> >>
>> >> I have the previous working fine code when I used VTK 5.6.1+ITK 3.20.1,
>> >> but
>> >> I got lots of problem when I wanted to reuse the code while upgrading
>> >> to the
>> >> new VTK/ITK version.
>> >>
>> >> My environment, Ubuntu 12.04, CMake 2.8.12.2, VTK 6.1, ITK 4.7.
>> >> ItkVtkGlue
>> >> is turned ON.
>> >>
>> >> The CMakeLists.txt is as the following, I checked the example,
>> >>
>> >> cmake_minimum_required(VERSION 2.8)
>> >>
>> >> PROJECT(BackProjection)
>> >>
>> >> FIND_PACKAGE(ITK REQUIRED)
>> >> INCLUDE(${ITK_USE_FILE})
>> >>
>> >> if (ITKVtkGlue_LOADED)
>> >>   find_package(VTK REQUIRED)
>> >>   include(${VTK_USE_FILE})
>> >> else()
>> >>   find_package(ItkVtkGlue REQUIRED)
>> >>   include(${ItkVtkGlue_USE_FILE})
>> >>   set(Glue ItkVtkGlue)
>> >> endif()
>> >> add_executable(ReadPLY MACOSX_BUNDLE ReadPLY.cxx)
>> >> target_link_libraries(ReadPLY ${Glue} ${VTK_LIBRARIES}
>> >> ${ITK_LIBRARIES})
>> >>
>> >> ###
>> >>
>> >> When I build with make, the error is,
>> >>
>> >> [100%] Building CXX object CMakeFiles/ReadPLY.dir/ReadPLY.cxx.o
>> >> Linking CXX executable ReadPLY
>> >> CMakeFiles/ReadPLY.dir/ReadPLY.cxx.o: In function
>> >> `vtkSmartPointer<vtkPLYReader>::New()':
>> >>
>> >> ReadPLY.cxx:(.text._ZN15vtkSmartPointerI12vtkPLYReaderE3NewEv[_ZN15vtkSmartPointerI12vtkPLYReaderE3NewEv]+0xd):
>> >> undefined reference to `vtkPLYReader::New()'
>> >> collect2: error: ld returned 1 exit status
>> >> make[2]: *** [ReadPLY] Error 1
>> >> make[1]: *** [CMakeFiles/ReadPLY.dir/all] Error 2
>> >> make: *** [all] Error 2
>> >>
>> >> Interestingly, when I fully remove anything about ITK in my
>> >> CMakeLists.txt,
>> >> it doesn't show any error. So I suspect it is the ITK's build macro
>> >> which is
>> >> breaking my VTK code compiling.
>> >> The working CMakeLists.txt is like,
>> >>
>> >> cmake_minimum_required(VERSION 2.8)
>> >>
>> >> PROJECT(ReadPLY)
>> >>
>> >> find_package(VTK REQUIRED)
>> >> include(${VTK_USE_FILE})
>> >>
>> >> add_executable(ReadPLY MACOSX_BUNDLE ReadPLY.cxx)
>> >>
>> >> if(VTK_LIBRARIES)
>> >>   target_link_libraries(ReadPLY ${VTK_LIBRARIES})
>> >> else()
>> >>   target_link_libraries(ReadPLY vtkHybrid vtkWidgets)
>> >> endif()
>> >>
>> >>
>> >> ####
>> >>
>> >> And the ReadPLY.cxx source code is, it is actually a VTK example,
>> >> doesn't
>> >> contain any ITK code. But I have the other source code file has ITK
>> >> code,
>> >> presenting this example just to show the problem.
>> >>
>> >> #include <vtkPolyData.h>
>> >> #include <vtkPLYReader.h>
>> >> #include <vtkSmartPointer.h>
>> >> #include <vtkPolyDataMapper.h>
>> >> #include <vtkActor.h>
>> >> #include <vtkRenderWindow.h>
>> >> #include <vtkRenderer.h>
>> >> #include <vtkRenderWindowInteractor.h>
>> >>
>> >> int main ( int argc, char *argv[] )
>> >> {
>> >>   if(argc != 2)
>> >>     {
>> >>     std::cout << "Usage: " << argv[0] << "  Filename(.ply)" <<
>> >> std::endl;
>> >>     return EXIT_FAILURE;
>> >>     }
>> >>
>> >>   std::string inputFilename = argv[1];
>> >>
>> >>   vtkSmartPointer<vtkPLYReader> reader =
>> >>     vtkSmartPointer<vtkPLYReader>::New();
>> >>   reader->SetFileName ( inputFilename.c_str() );
>> >>
>> >>   // Visualize
>> >>   vtkSmartPointer<vtkPolyDataMapper> mapper =
>> >>     vtkSmartPointer<vtkPolyDataMapper>::New();
>> >>   mapper->SetInputConnection(reader->GetOutputPort());
>> >>
>> >>   vtkSmartPointer<vtkActor> actor =
>> >>     vtkSmartPointer<vtkActor>::New();
>> >>   actor->SetMapper(mapper);
>> >>
>> >>   vtkSmartPointer<vtkRenderer> renderer =
>> >>     vtkSmartPointer<vtkRenderer>::New();
>> >>   vtkSmartPointer<vtkRenderWindow> renderWindow =
>> >>     vtkSmartPointer<vtkRenderWindow>::New();
>> >>   renderWindow->AddRenderer(renderer);
>> >>   vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
>> >>     vtkSmartPointer<vtkRenderWindowInteractor>::New();
>> >>   renderWindowInteractor->SetRenderWindow(renderWindow);
>> >>
>> >>   renderer->AddActor(actor);
>> >>   renderer->SetBackground(0.1804,0.5451,0.3412); // Sea green
>> >>
>> >>   renderWindow->Render();
>> >>   renderWindowInteractor->Start();
>> >>
>> >>   return EXIT_SUCCESS;
>> >> }
>> >>
>> >> ####
>> >>
>> >>
>> >> _____________________________________
>> >> 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 gunjan.gemini29 at gmail.com  Tue Feb  3 02:16:38 2015
From: gunjan.gemini29 at gmail.com (Gunjan Gautam)
Date: Tue, 3 Feb 2015 12:46:38 +0530
Subject: [ITK-users] Query regarding LAPACK and ITK
Message-ID: <CAHvOzZExx5WSfBrg2tfu_Tkk59qFQ++rVAY1ZQW5HrpFtx7wvg@mail.gmail.com>

Hi All,

I need CMake, ITK 3.14 or higher  and LAPACK 3.2.1 for my work. I got
installed CMake and ITK 4.7.0  in my system. Does ITK 3.2.1 come with
LAPACK routines or I should get it seperately.

Please guide me in this regard as I've less knowledge about this.


Thanks in advance.
Gunjan
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From franciscolopezdelafranca at gmail.com  Wed Feb  4 08:40:47 2015
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Wed, 4 Feb 2015 14:40:47 +0100
Subject: [ITK-users] Calculation of 3D Convex Hull
Message-ID: <CAJqi3E+ME+XrStzbA7wHCQ+EwzGTX2KGiDqUyHAxMifvVyX2oQ@mail.gmail.com>

Hi everybody.

I've got an image in NIFTI format containing a 3D object and I need to
retrieve its 3D convex hull.

I've seen that VTK provides several ways to do it, but I'd like to know if
it is possible in ITK.

Thanks a lot.
Best regards.
/Francisco
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From blowekamp at mail.nih.gov  Wed Feb  4 09:42:54 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 4 Feb 2015 09:42:54 -0500
Subject: [ITK-users] [ITK-dev] [ANNOUNCE] SimpleITK 0.8.1 Release
In-Reply-To: <96262E2C-0CF1-4C15-B17C-5D063F830B45@mail.nih.gov>
References: <96262E2C-0CF1-4C15-B17C-5D063F830B45@mail.nih.gov>
Message-ID: <41D67579-08C8-4365-8CF8-0BE762D41221@mail.nih.gov>

Hello,

I just wanted to follow up that we now have Window binaries on Binstar for the Anaconda Python distribution. Specifically for 32-bit and 64-bit OS as well as Python version 2.7 and 3.4.

More information can be found on the wiki:
http://www.itk.org/Wiki/SimpleITK/GettingStarted#Anaconda_Distribution

Brad

On Dec 23, 2014, at 11:34 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:

> We are pleased to announce the SimpleITK 0.8.1 Release.
> 
> SimpleITK is a simplified layer built on top of ITK, intended to facilitate its use in rapid prototyping, education and interpreted languages. SimpleITK provides binaries for several wrapped languages to enable users to rapidly get started using ITK.
> 
> Information on how to get started and download the binaries: http://www.itk.org/Wiki/SimpleITK/GettingStarted#Binaries
> 
> 
> This patch release updates the ITK version to the newly released 4.7.0. Additionally, this patch contains improved support for CMake 3.0, fixes for compilation issues, the addition of the LabelOverlapMeasures filter, and a fix for the ClampCast filter.
> 
> 
> Also, we are now compiling for Python 3.4, and have stopped compiling for Python 3.2.  Lastly, we are providing some binaries for the Anaconda Python distribution on Binstar.
> 
> 
> Binary distributions for many platforms and languages are available for downloading: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.8.1/
> 
> Release Doxygen Documentation: http://www.itk.org/SimpleITKDoxygen08/html/index.html
> 
> Additional Release Notes: http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.8.1_Release
> 
> Enjoy,
> 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


From samah.bouzidi at gmail.com  Wed Feb  4 13:59:46 2015
From: samah.bouzidi at gmail.com (samah bouzidi)
Date: Wed, 4 Feb 2015 19:59:46 +0100
Subject: [ITK-users] problem with 3d region growing
Message-ID: <CAN8_LjFBYg4YHRgV3zyWAKZ-187ShcGCY3DmW9ioaVC9M11-HA@mail.gmail.com>

hello itk users,

I am a beginner ITK users. I am trying to segment a volume using region
growing algorithm. I am able to do it in a 2D image (dicom) but not for a
volume.
1) I saw that for 3D region growing the seed point have 3 coordinates (x, y,
z). In my case, z is the slice number (i am using .img format). Can I use an
(x,y) seed point?
2) I have another idea,  reading an image series  and applied the filter for
each image and then writing them in volume. Are there any examples (
applied a filter in image series) that one could help me?

regards
Samah.

My source code is as follows
================================
#include "itkConnectedThresholdImageFilter.h"
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

int main( int argc, char *argv[])
{
  typedef   signed short         InternalPixelType;
  typedef   unsigned char        OutputPixelType;
  const     unsigned int           Dimension = 3;
  typedef itk::Image< InternalPixelType, Dimension > InternalImageType;

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

  typedef  itk::ImageFileReader< InternalImageType > ReaderType;
  typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;

  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();

    reader->SetFileName( "/home/doctorant/T?l?chargements/Images/in.img" );
    writer->SetFileName( "/home/doctorant/T?l?chargements/Images/out.img");


  typedef itk::ConnectedThresholdImageFilter< InternalImageType,
OutputImageType > ConnectedFilterType;

  ConnectedFilterType::Pointer connectedThreshold =
ConnectedFilterType::New();

  connectedThreshold->SetInput( reader->GetOutput() );
  writer->SetInput( connectedThreshold->GetOutput() );


  const InternalPixelType lowerThreshold =  -1050  ;
  const InternalPixelType upperThreshold = -600;

  connectedThreshold->SetLower(  lowerThreshold  );
  connectedThreshold->SetUpper(  upperThreshold  );

  connectedThreshold->SetReplaceValue( 255 );




  InternalImageType::IndexType  index;
  index[0] = 250;
  index[1] = 239;

  connectedThreshold->SetSeed( index );


  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & excep )
    {
    std::cerr << "Exception caught !" << std::endl;
    std::cerr << excep << std::endl;
    }

  return 0;
}
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From taylor at braun-jones.org  Wed Feb  4 14:22:21 2015
From: taylor at braun-jones.org (Taylor Braun-Jones)
Date: Wed, 4 Feb 2015 14:22:21 -0500
Subject: [ITK-users] bug in EuclideanDistancePointMetric
Message-ID: <CAKfKJYsavegEDdkUJgvTnqtRu7BKZiWWv_2RZu71hDwmB0mZOg@mail.gmail.com>

Marcel Schenderlein <marcel.schenderlein at ...> writes:
>
> it seems to me as if there is a bug in itk::EuclideanDistancePointMetric
> or at least a misconception. Correct me if I am wrong. I do not have the
> full Insight into ITK yet
>
> I came across this when I wanted to use this metric together with an
> itk::Rigid3DPerspectiveTransform and the
> itk::PointSetToPointSetRegistrationMethod to do 3D-2D point
> registration. The bug will not be noticed when two point sets of the
> same dimensionality would be used.
>
> BUG:
> -------
> In the itk::EuclideanDistancePointMetric class there is a single
> iterator type used for both FixedPointSet and MovingPointSet (typedef
> typename Superclass::PointIterator PointIterator) in the method
> GetValue(...) at lines 76,77
>
>  > PointIterator pointItr = movingPointSet->GetPoints()->Begin();
>  > PointIterator pointEnd = movingPointSet->GetPoints()->End();
>
> and lines 118,119
>
>  > PointIterator pointItr2 = fixedPointSet->GetPoints()->Begin();
>  > PointIterator pointEnd2 = fixedPointSet->GetPoints()->End();
>
> in itkEuclideanDistancePointMetric.txx. The problem that arises is that
> if I use this metric with an itk::PointSet< double, 2 > as
> FixedPointSetType and and itk::PointSet< double, 3 > as the
> MovingPointSetType (as I would do for 3D-2D registration) then the
> compiler complains about the lines 76,77 because PointIterator is
> actually a FixedPointSetType::PointsContainer::ConstIterator (from
> itk::PointSetToPointSetMetric). Note that the lines 118,119 work
> perfectly but the naming of the iterator does not point to the type used.
> I did the following to fix this:
>
> FIX:
> --------------------------------
> I introduced two new iterators (itkEuclideanDistancePointMetric.h):
>
>  > typedef typename FixedPointSetType::PointsContainer::ConstIterator
> FixedPointIterator;
>  > typedef typename MovingPointSetType::PointsContainer::ConstIterator
> MovingPointIterator;
>
> The iterator PointIterator is obsolete then.
>
> I also had to change the distance map part of the template
> declaration(?) (itkEuclideanDistancePointMetric.h). The dimension of the
> distance map has to be of type TFixedPointSet instead of
> TMovingPointSet, since the moving points are transformed (into the
> FixedPointType) and then compared to the fixed points. So it is now:
>
>  > template < class TFixedPointSet, class TMovingPointSet,
>  >  class TDistanceMap = ::itk::Image<unsigned short,
>  >  ::itk::GetPointSetDimension<TFixedPointSet>::PointDimension> >
>  > class ITK_EXPORT EuclideanDistancePointMetric :
>
> In the definition of GetValue(...) (itkEuclideanDistancePointMetric.txx)
> I changed the lines 76,77 to
>
>  > MovingPointIterator pointItr = movingPointSet->GetPoints()->Begin();
>  > MovingPointIterator pointEnd = movingPointSet->GetPoints()->End();
>
> and lines 118,119 to
>
>  > FixedPointIterator pointItr2 = fixedPointSet->GetPoints()->Begin();
>  > FixedPointIterator pointEnd2 = fixedPointSet->GetPoints()->End();
>
> After that it compiles well and the registration seems to work. I have
> not testet the fix with point sets of the same dimensionality but
> looking at the code I see no reason why it should not still work this way.


I'm looking at a current ITK master and see the same problem. Marcel's
patch
seems to work for me. Is it agreed that this is a bug and that Marcel's
solution is the correct one?

Thanks,
Taylor
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From matt.mccormick at kitware.com  Wed Feb  4 14:32:41 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 4 Feb 2015 14:32:41 -0500
Subject: [ITK-users] bug in EuclideanDistancePointMetric
In-Reply-To: <CAKfKJYsavegEDdkUJgvTnqtRu7BKZiWWv_2RZu71hDwmB0mZOg@mail.gmail.com>
References: <CAKfKJYsavegEDdkUJgvTnqtRu7BKZiWWv_2RZu71hDwmB0mZOg@mail.gmail.com>
Message-ID: <CALzTN-RpN9CpUYOJQ6KY6Pub05AN-h8TAJpFTT0MYMv8XcETtg@mail.gmail.com>

Hi Taylor, Marcel,

Yes this sounds like a bug, and the proposed solution looks good.

Please consider submitting a patch [1] that includes a new test that
does 3D-2D point set registration.

Thanks,
Matt

[1] https://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/SubmitAPatchToGerrit/index.html

On Wed, Feb 4, 2015 at 2:22 PM, Taylor Braun-Jones
<taylor at braun-jones.org> wrote:
> Marcel Schenderlein <marcel.schenderlein at ...> writes:
>>
>> it seems to me as if there is a bug in itk::EuclideanDistancePointMetric
>> or at least a misconception. Correct me if I am wrong. I do not have the
>> full Insight into ITK yet
>>
>> I came across this when I wanted to use this metric together with an
>> itk::Rigid3DPerspectiveTransform and the
>> itk::PointSetToPointSetRegistrationMethod to do 3D-2D point
>> registration. The bug will not be noticed when two point sets of the
>> same dimensionality would be used.
>>
>> BUG:
>> -------
>> In the itk::EuclideanDistancePointMetric class there is a single
>> iterator type used for both FixedPointSet and MovingPointSet (typedef
>> typename Superclass::PointIterator PointIterator) in the method
>> GetValue(...) at lines 76,77
>>
>>  > PointIterator pointItr = movingPointSet->GetPoints()->Begin();
>>  > PointIterator pointEnd = movingPointSet->GetPoints()->End();
>>
>> and lines 118,119
>>
>>  > PointIterator pointItr2 = fixedPointSet->GetPoints()->Begin();
>>  > PointIterator pointEnd2 = fixedPointSet->GetPoints()->End();
>>
>> in itkEuclideanDistancePointMetric.txx. The problem that arises is that
>> if I use this metric with an itk::PointSet< double, 2 > as
>> FixedPointSetType and and itk::PointSet< double, 3 > as the
>> MovingPointSetType (as I would do for 3D-2D registration) then the
>> compiler complains about the lines 76,77 because PointIterator is
>> actually a FixedPointSetType::PointsContainer::ConstIterator (from
>> itk::PointSetToPointSetMetric). Note that the lines 118,119 work
>> perfectly but the naming of the iterator does not point to the type used.
>> I did the following to fix this:
>>
>> FIX:
>> --------------------------------
>> I introduced two new iterators (itkEuclideanDistancePointMetric.h):
>>
>>  > typedef typename FixedPointSetType::PointsContainer::ConstIterator
>> FixedPointIterator;
>>  > typedef typename MovingPointSetType::PointsContainer::ConstIterator
>> MovingPointIterator;
>>
>> The iterator PointIterator is obsolete then.
>>
>> I also had to change the distance map part of the template
>> declaration(?) (itkEuclideanDistancePointMetric.h). The dimension of the
>> distance map has to be of type TFixedPointSet instead of
>> TMovingPointSet, since the moving points are transformed (into the
>> FixedPointType) and then compared to the fixed points. So it is now:
>>
>>  > template < class TFixedPointSet, class TMovingPointSet,
>>  >  class TDistanceMap = ::itk::Image<unsigned short,
>>  >  ::itk::GetPointSetDimension<TFixedPointSet>::PointDimension> >
>>  > class ITK_EXPORT EuclideanDistancePointMetric :
>>
>> In the definition of GetValue(...) (itkEuclideanDistancePointMetric.txx)
>> I changed the lines 76,77 to
>>
>>  > MovingPointIterator pointItr = movingPointSet->GetPoints()->Begin();
>>  > MovingPointIterator pointEnd = movingPointSet->GetPoints()->End();
>>
>> and lines 118,119 to
>>
>>  > FixedPointIterator pointItr2 = fixedPointSet->GetPoints()->Begin();
>>  > FixedPointIterator pointEnd2 = fixedPointSet->GetPoints()->End();
>>
>> After that it compiles well and the registration seems to work. I have
>> not testet the fix with point sets of the same dimensionality but
>> looking at the code I see no reason why it should not still work this way.
>
>
> I'm looking at a current ITK master and see the same problem. Marcel's patch
> seems to work for me. Is it agreed that this is a bug and that Marcel's
> solution is the correct one?
>
> Thanks,
> 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://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 matt.mccormick at kitware.com  Wed Feb  4 14:36:32 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 4 Feb 2015 14:36:32 -0500
Subject: [ITK-users] problem with 3d region growing
In-Reply-To: <CAN8_LjFBYg4YHRgV3zyWAKZ-187ShcGCY3DmW9ioaVC9M11-HA@mail.gmail.com>
References: <CAN8_LjFBYg4YHRgV3zyWAKZ-187ShcGCY3DmW9ioaVC9M11-HA@mail.gmail.com>
Message-ID: <CALzTN-QujxHeP5zNTRaBA9RPdr1frErTwJ_Q1WKH=eB9VgjpkQ@mail.gmail.com>

Hi Samah,

Welcome to ITK!

For a 3D image, the third index of the seed does need to be defined.

To apply a filter on each slice independently, use the
SliceBySliceImageFilter [1].

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1SliceBySliceImageFilter.html

On Wed, Feb 4, 2015 at 1:59 PM, samah bouzidi <samah.bouzidi at gmail.com> wrote:
> hello itk users,
>
> I am a beginner ITK users. I am trying to segment a volume using region
> growing algorithm. I am able to do it in a 2D image (dicom) but not for a
> volume.
> 1) I saw that for 3D region growing the seed point have 3 coordinates (x, y,
> z). In my case, z is the slice number (i am using .img format). Can I use an
> (x,y) seed point?
> 2) I have another idea,  reading an image series  and applied the filter for
> each image and then writing them in volume. Are there any examples ( applied
> a filter in image series) that one could help me?
>
> regards
> Samah.
>
> My source code is as follows
> ================================
> #include "itkConnectedThresholdImageFilter.h"
> #include "itkImage.h"
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
>
> int main( int argc, char *argv[])
> {
>   typedef   signed short         InternalPixelType;
>   typedef   unsigned char        OutputPixelType;
>   const     unsigned int           Dimension = 3;
>   typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
>
>   typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>
>   typedef  itk::ImageFileReader< InternalImageType > ReaderType;
>   typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
>
>   ReaderType::Pointer reader = ReaderType::New();
>   WriterType::Pointer writer = WriterType::New();
>
>     reader->SetFileName( "/home/doctorant/T?l?chargements/Images/in.img" );
>     writer->SetFileName( "/home/doctorant/T?l?chargements/Images/out.img");
>
>
>   typedef itk::ConnectedThresholdImageFilter< InternalImageType,
> OutputImageType > ConnectedFilterType;
>
>   ConnectedFilterType::Pointer connectedThreshold =
> ConnectedFilterType::New();
>
>   connectedThreshold->SetInput( reader->GetOutput() );
>   writer->SetInput( connectedThreshold->GetOutput() );
>
>
>   const InternalPixelType lowerThreshold =  -1050  ;
>   const InternalPixelType upperThreshold = -600;
>
>   connectedThreshold->SetLower(  lowerThreshold  );
>   connectedThreshold->SetUpper(  upperThreshold  );
>
>   connectedThreshold->SetReplaceValue( 255 );
>
>
>
>
>   InternalImageType::IndexType  index;
>   index[0] = 250;
>   index[1] = 239;
>
>   connectedThreshold->SetSeed( index );
>
>
>   try
>     {
>     writer->Update();
>     }
>   catch( itk::ExceptionObject & excep )
>     {
>     std::cerr << "Exception caught !" << std::endl;
>     std::cerr << excep << std::endl;
>     }
>
>   return 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://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 samah.bouzidi at gmail.com  Wed Feb  4 15:14:38 2015
From: samah.bouzidi at gmail.com (samah bouzidi)
Date: Wed, 4 Feb 2015 21:14:38 +0100
Subject: [ITK-users] problem with 3d region growing
In-Reply-To: <CALzTN-QujxHeP5zNTRaBA9RPdr1frErTwJ_Q1WKH=eB9VgjpkQ@mail.gmail.com>
References: <CAN8_LjFBYg4YHRgV3zyWAKZ-187ShcGCY3DmW9ioaVC9M11-HA@mail.gmail.com>
 <CALzTN-QujxHeP5zNTRaBA9RPdr1frErTwJ_Q1WKH=eB9VgjpkQ@mail.gmail.com>
Message-ID: <CAN8_LjGAPnDgiOQ-NkYAEoco3mQKo8d2MaHO=17hgUiAW_0xZQ@mail.gmail.com>

hi Matt,

thank you for replying.

I can't find the error in my code (a black volume result)

can you please look at my code.



Regards
Samah



2015-02-04 20:36 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi Samah,
>
> Welcome to ITK!
>
> For a 3D image, the third index of the seed does need to be defined.
>
> To apply a filter on each slice independently, use the
> SliceBySliceImageFilter [1].
>
> HTH,
> Matt
>
> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1SliceBySliceImageFilter.html
>
> On Wed, Feb 4, 2015 at 1:59 PM, samah bouzidi <samah.bouzidi at gmail.com>
> wrote:
> > hello itk users,
> >
> > I am a beginner ITK users. I am trying to segment a volume using region
> > growing algorithm. I am able to do it in a 2D image (dicom) but not for a
> > volume.
> > 1) I saw that for 3D region growing the seed point have 3 coordinates
> (x, y,
> > z). In my case, z is the slice number (i am using .img format). Can I
> use an
> > (x,y) seed point?
> > 2) I have another idea,  reading an image series  and applied the filter
> for
> > each image and then writing them in volume. Are there any examples (
> applied
> > a filter in image series) that one could help me?
> >
> > regards
> > Samah.
> >
> > My source code is as follows
> > ================================
> > #include "itkConnectedThresholdImageFilter.h"
> > #include "itkImage.h"
> > #include "itkImageFileReader.h"
> > #include "itkImageFileWriter.h"
> >
> > int main( int argc, char *argv[])
> > {
> >   typedef   signed short         InternalPixelType;
> >   typedef   unsigned char        OutputPixelType;
> >   const     unsigned int           Dimension = 3;
> >   typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
> >
> >   typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
> >
> >   typedef  itk::ImageFileReader< InternalImageType > ReaderType;
> >   typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
> >
> >   ReaderType::Pointer reader = ReaderType::New();
> >   WriterType::Pointer writer = WriterType::New();
> >
> >     reader->SetFileName( "/home/doctorant/T?l?chargements/Images/in.img"
> );
> >     writer->SetFileName(
> "/home/doctorant/T?l?chargements/Images/out.img");
> >
> >
> >   typedef itk::ConnectedThresholdImageFilter< InternalImageType,
> > OutputImageType > ConnectedFilterType;
> >
> >   ConnectedFilterType::Pointer connectedThreshold =
> > ConnectedFilterType::New();
> >
> >   connectedThreshold->SetInput( reader->GetOutput() );
> >   writer->SetInput( connectedThreshold->GetOutput() );
> >
> >
> >   const InternalPixelType lowerThreshold =  -1050  ;
> >   const InternalPixelType upperThreshold = -600;
> >
> >   connectedThreshold->SetLower(  lowerThreshold  );
> >   connectedThreshold->SetUpper(  upperThreshold  );
> >
> >   connectedThreshold->SetReplaceValue( 255 );
> >
> >
> >
> >
> >   InternalImageType::IndexType  index;
> >   index[0] = 250;
> >   index[1] = 239;
> >
> >   connectedThreshold->SetSeed( index );
> >
> >
> >   try
> >     {
> >     writer->Update();
> >     }
> >   catch( itk::ExceptionObject & excep )
> >     {
> >     std::cerr << "Exception caught !" << std::endl;
> >     std::cerr << excep << std::endl;
> >     }
> >
> >   return 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://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 christopher.mullins at kitware.com  Wed Feb  4 15:24:07 2015
From: christopher.mullins at kitware.com (Christopher Mullins)
Date: Wed, 4 Feb 2015 15:24:07 -0500
Subject: [ITK-users] problem with 3d region growing
In-Reply-To: <CAN8_LjGAPnDgiOQ-NkYAEoco3mQKo8d2MaHO=17hgUiAW_0xZQ@mail.gmail.com>
References: <CAN8_LjFBYg4YHRgV3zyWAKZ-187ShcGCY3DmW9ioaVC9M11-HA@mail.gmail.com>
 <CALzTN-QujxHeP5zNTRaBA9RPdr1frErTwJ_Q1WKH=eB9VgjpkQ@mail.gmail.com>
 <CAN8_LjGAPnDgiOQ-NkYAEoco3mQKo8d2MaHO=17hgUiAW_0xZQ@mail.gmail.com>
Message-ID: <CABVTP-KCh=K-8woe=qndXdD5Z44exu=652ustkNTVi0HX=qbNw@mail.gmail.com>

The ConnectedThresholdImageFilter example [1] might be of use.

[1]
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/Segmentation/ConnectedThresholdImageFilter.cxx

On Wed, Feb 4, 2015 at 3:14 PM, samah bouzidi <samah.bouzidi at gmail.com>
wrote:

> hi Matt,
>
> thank you for replying.
>
> I can't find the error in my code (a black volume result)
>
> can you please look at my code.
>
>
>
> Regards
> Samah
>
>
>
> 2015-02-04 20:36 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>
>> Hi Samah,
>>
>> Welcome to ITK!
>>
>> For a 3D image, the third index of the seed does need to be defined.
>>
>> To apply a filter on each slice independently, use the
>> SliceBySliceImageFilter [1].
>>
>> HTH,
>> Matt
>>
>> [1]
>> http://www.itk.org/Doxygen/html/classitk_1_1SliceBySliceImageFilter.html
>>
>> On Wed, Feb 4, 2015 at 1:59 PM, samah bouzidi <samah.bouzidi at gmail.com>
>> wrote:
>> > hello itk users,
>> >
>> > I am a beginner ITK users. I am trying to segment a volume using region
>> > growing algorithm. I am able to do it in a 2D image (dicom) but not for
>> a
>> > volume.
>> > 1) I saw that for 3D region growing the seed point have 3 coordinates
>> (x, y,
>> > z). In my case, z is the slice number (i am using .img format). Can I
>> use an
>> > (x,y) seed point?
>> > 2) I have another idea,  reading an image series  and applied the
>> filter for
>> > each image and then writing them in volume. Are there any examples (
>> applied
>> > a filter in image series) that one could help me?
>> >
>> > regards
>> > Samah.
>> >
>> > My source code is as follows
>> > ================================
>> > #include "itkConnectedThresholdImageFilter.h"
>> > #include "itkImage.h"
>> > #include "itkImageFileReader.h"
>> > #include "itkImageFileWriter.h"
>> >
>> > int main( int argc, char *argv[])
>> > {
>> >   typedef   signed short         InternalPixelType;
>> >   typedef   unsigned char        OutputPixelType;
>> >   const     unsigned int           Dimension = 3;
>> >   typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
>> >
>> >   typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>> >
>> >   typedef  itk::ImageFileReader< InternalImageType > ReaderType;
>> >   typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
>> >
>> >   ReaderType::Pointer reader = ReaderType::New();
>> >   WriterType::Pointer writer = WriterType::New();
>> >
>> >     reader->SetFileName(
>> "/home/doctorant/T?l?chargements/Images/in.img" );
>> >     writer->SetFileName(
>> "/home/doctorant/T?l?chargements/Images/out.img");
>> >
>> >
>> >   typedef itk::ConnectedThresholdImageFilter< InternalImageType,
>> > OutputImageType > ConnectedFilterType;
>> >
>> >   ConnectedFilterType::Pointer connectedThreshold =
>> > ConnectedFilterType::New();
>> >
>> >   connectedThreshold->SetInput( reader->GetOutput() );
>> >   writer->SetInput( connectedThreshold->GetOutput() );
>> >
>> >
>> >   const InternalPixelType lowerThreshold =  -1050  ;
>> >   const InternalPixelType upperThreshold = -600;
>> >
>> >   connectedThreshold->SetLower(  lowerThreshold  );
>> >   connectedThreshold->SetUpper(  upperThreshold  );
>> >
>> >   connectedThreshold->SetReplaceValue( 255 );
>> >
>> >
>> >
>> >
>> >   InternalImageType::IndexType  index;
>> >   index[0] = 250;
>> >   index[1] = 239;
>> >
>> >   connectedThreshold->SetSeed( index );
>> >
>> >
>> >   try
>> >     {
>> >     writer->Update();
>> >     }
>> >   catch( itk::ExceptionObject & excep )
>> >     {
>> >     std::cerr << "Exception caught !" << std::endl;
>> >     std::cerr << excep << std::endl;
>> >     }
>> >
>> >   return 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://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
>
>


-- 
Christopher Mullins
R&D Engineer
Kitware Inc.,
919.869.8871
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From franciscolopezdelafranca at gmail.com  Thu Feb  5 11:51:32 2015
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Thu, 5 Feb 2015 17:51:32 +0100
Subject: [ITK-users] Connectivity in BinaryToShapeLabelMapFilter?
Message-ID: <CAJqi3ELXyY4xNSHGK=YHJ_VpZBR4ka_WUkuHNBSvrNN0w4_rDw@mail.gmail.com>

Hi.
Does anyone know which type of connecticity this filter uses?
I mean, in 2D 4 or 8 connectivity, in 3D 26-connectivity.
For instance, in Matlab you must specify the connectivity in the bwlabel
function in order to separate the different blobs in the image.
Thank you very much.
Kind regards.
/Francisco
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From blowekamp at mail.nih.gov  Thu Feb  5 12:00:01 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 5 Feb 2015 12:00:01 -0500
Subject: [ITK-users] [ITK] Connectivity in BinaryToShapeLabelMapFilter?
In-Reply-To: <CAJqi3ELXyY4xNSHGK=YHJ_VpZBR4ka_WUkuHNBSvrNN0w4_rDw@mail.gmail.com>
References: <CAJqi3ELXyY4xNSHGK=YHJ_VpZBR4ka_WUkuHNBSvrNN0w4_rDw@mail.gmail.com>
Message-ID: <388D5D49-F6CA-4E38-B4DF-CD8E4B617F4E@mail.nih.gov>

Hello,

There is a boolean member variable called "FullyConnected" which controls this behavior:
http://itk.org/Insight/Doxygen/html/classitk_1_1BinaryImageToShapeLabelMapFilter.html#a7448c70c44ba3ef5d10984e06722ef47

Brad


On Feb 5, 2015, at 11:51 AM, Francisco Lopez de la Franca <franciscolopezdelafranca at gmail.com> wrote:

> Hi.
> Does anyone know which type of connecticity this filter uses?
> I mean, in 2D 4 or 8 connectivity, in 3D 26-connectivity.
> For instance, in Matlab you must specify the connectivity in the bwlabel function in order to separate the different blobs in the image.
> Thank you very much.
> Kind regards.
> /Francisco
> 
> _____________________________________
> 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

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From matimontg at gmail.com  Fri Feb  6 09:47:23 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Fri, 6 Feb 2015 11:47:23 -0300
Subject: [ITK-users] What is StepLenght?
Message-ID: <CAKKNfu+PiwqQsEaJ_XY6NkVk17fsnA5xohM3b_8k2hFykhTsew@mail.gmail.com>

Hi,

I'm new to registration and I'm trying to understand what StepLenght is. I
can play with the values but I'm not really sure what it is.

Can someone explain?

Thank you,

Matias.
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From Bharath.Shivapuram at LntTechservices.com  Fri Feb  6 05:22:55 2015
From: Bharath.Shivapuram at LntTechservices.com (Bharath Shivapuram)
Date: Fri, 6 Feb 2015 10:22:55 +0000
Subject: [ITK-users] Error in Fast Marching Filter : Discriminat of
 quadratic equation is negative
Message-ID: <EE486B6BBB430B449FB492F8581AB2B51E7F73E2@POCITMSEXMB03.LntUniverse.com>

Hi ITK users,

I am facing this peculiar issue in fast marching filter. Tried searching about it, but dint have much of help.


Fast Marching filter throws an "Discriminant of quadratic equation is negative"



I tried to dig into the code and found that the exception is defined in the line 492 of itkFastMarchingImageFilter.cxx.



Any info about what why this exception would be thrown or what should be changed would be of great help.

Thanks a lot in advance.



Thanks and Regards
Bharath.S.D
Software Engineer

L&T Technology Services limited
KIADB Industrial Area | Hebbal | Hootagalli
Mysore - 570 018 | INDIA


L&T Technology Services Ltd

www.LntTechservices.com<http://www.lnttechservices.com/>

This Email may contain confidential or privileged information for the intended recipient (s). If you are not the intended recipient, please do not use or disseminate the information, notify the sender and delete it from your system.
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From yagodiezdonoso at gmail.com  Fri Feb  6 14:32:47 2015
From: yagodiezdonoso at gmail.com (Yago Diez)
Date: Fri, 6 Feb 2015 20:32:47 +0100
Subject: [ITK-users] cannot acces virtual void itk::Rigid3DTransform<
 TScalar >::SetMatrix (const MatrixType & matrix,
 double tolerance ) from the Rigid3D transform class.
Message-ID: <CALiCtPgvrEz-EiVMyctEeVZnHn-LoE9WMAKPdbzO6-9HjFYAUQ@mail.gmail.com>

Hi all,

I want to store a 3D rotation matrix that I have computed in some format
that itk can understand (and use to transform points and images, not to as
the starting point of any optimization process). The problem is that the
matrix is not "as orthogonal as it should be" due to numerical problems:


So far I am using the Rigid3DTransform which looks the best way to go (but
am willing to change if this is wrong). The numerical problems express like
this:

1) if I use the "MatrixIsOrthogonal(,)" function I get a "yes" for a 1e-5
tolerance but not for the default "1e-10" tolerance.
2) Consequently, if I use the SetMatrix() function I get an exception.

I am pretty confident that I can get away with what I need to do if I
convince the class to just swallow the "not very orthogonal" matrix (by
using a less restrictive tolerance). I have seen that there exists a
function to do just that but I am having problems using it.

Specifically, I cannot seem to access the

itk::Rigid3DTransform< TScalar >::SetMatrix     (const MatrixType &
matrix, double      tolerance      )      function

>From the Rigid3D transform class.

Consequently, the following code returns a compilation error :

error: no matching function for call to
> ?itk::Rigid3DTransform<double>::SetMatrix(smallMatrixType&, double)?
> XXXXXXXXXXXX: note: candidate is:
> PATH/Code/Common/itkRigid3DTransform.txx:93:1: note: void
> itk::Rigid3DTransform<TScalarType>::SetMatrix(const MatrixType&) [with
> TScalarType = double, itk::Rigid3DTransform<TScalarType>::MatrixType =
> itk::Matrix<double, 3u, 3u>]
> PATH/Code/Common/itkRigid3DTransform.txx:93:1: note:   candidate expects 1
> argument, 2 provided
>

I have checked that the itkRigid3DTransform.txx file has indeed only the
definition of the setmatrix method with one parameter.

I assume I am looking for the setmatrix function with two parameters "in
the wrong place", but have not yet managed to find the right one, any ideas?


Here is the detailed code


typedef itk::Matrix<double, 3, 3> smallMatrixType;
> smallMatrixType auxMatrix;
>
> // matrix initialization, matrix M1 is orthogonal but I have numerical
problems

auxMatrix[0][0]=M1[0][0];
auxMatrix[0][1]=M1[0][1];
auxMatrix[0][2]=M1[0][2];
auxMatrix[1][0]=M1[1][0];
auxMatrix[1][1]=M1[1][1];
auxMatrix[1][2]=M1[1][2];
auxMatrix[2][0]=M1[2][0];
auxMatrix[2][1]=M1[2][1];
auxMatrix[2][2]=M1[2][2];


typedef itk::Rigid3DTransform<double>  TransformType;
TransformType::Pointer  rotation = TransformType::New();

// rotation->MatrixIsOrthogonal(auxMatrix,1e-10) outputs 0, but
rotation->MatrixIsOrthogonal(auxMatrix,1e-5) outputs 1

rotation->SetMatrix(auxMatrix,1e-5); // this produces a compilation error


//rotation->SetMatrix(auxMatrix); // THIS RESULTS IN AN EXCEPTION:
itk::ERROR: Rigid3DTransform(0x1dec800): Attempting to set a non-orthogonal
rotation matrix


Thanks you very much for any help that you can provide.



Yago Diez Donoso (PhD)
Computer Vision and Robotics Group http://vicorob.udg.es/
E-mail: yago at eia.udg.es; yagodiezdonoso at gmail.com
Phone: (int. code) 34 972418013
University of Girona
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From samah.bouzidi at gmail.com  Fri Feb  6 15:59:18 2015
From: samah.bouzidi at gmail.com (samah bouzidi)
Date: Fri, 6 Feb 2015 21:59:18 +0100
Subject: [ITK-users] problem with 3d region growing
In-Reply-To: <CABVTP-KCh=K-8woe=qndXdD5Z44exu=652ustkNTVi0HX=qbNw@mail.gmail.com>
References: <CAN8_LjFBYg4YHRgV3zyWAKZ-187ShcGCY3DmW9ioaVC9M11-HA@mail.gmail.com>
 <CALzTN-QujxHeP5zNTRaBA9RPdr1frErTwJ_Q1WKH=eB9VgjpkQ@mail.gmail.com>
 <CAN8_LjGAPnDgiOQ-NkYAEoco3mQKo8d2MaHO=17hgUiAW_0xZQ@mail.gmail.com>
 <CABVTP-KCh=K-8woe=qndXdD5Z44exu=652ustkNTVi0HX=qbNw@mail.gmail.com>
Message-ID: <CAN8_LjFvu4EXorOAaby4kKBtyngHwOqKyTEzRf6WziSftAjhOA@mail.gmail.com>

hi,

sincerely, I fail to understand the response of this filter, the
algorithm succeeds
to segment the region .however, in 3D, the first  slice is the same  used to
check the segmentation in 2D, I am not getting at least for the first slice the
region obtained in 2D.
ps: the modified code takes into account the third dimension :


InternalImageType::IndexType  index;
  index[0] = 250;
  index[1] = 239;
  index[2]= 1;

  connectedThreshold->SetSeed( index );


any help will be appreciated.
thanks in advance.



2015-02-04 21:24 GMT+01:00 Christopher Mullins <
christopher.mullins at kitware.com>:

> The ConnectedThresholdImageFilter example [1] might be of use.
>
> [1]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/Segmentation/ConnectedThresholdImageFilter.cxx
>
> On Wed, Feb 4, 2015 at 3:14 PM, samah bouzidi <samah.bouzidi at gmail.com>
> wrote:
>
>> hi Matt,
>>
>> thank you for replying.
>>
>> I can't find the error in my code (a black volume result)
>>
>> can you please look at my code.
>>
>>
>>
>> Regards
>> Samah
>>
>>
>>
>> 2015-02-04 20:36 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>>
>>> Hi Samah,
>>>
>>> Welcome to ITK!
>>>
>>> For a 3D image, the third index of the seed does need to be defined.
>>>
>>> To apply a filter on each slice independently, use the
>>> SliceBySliceImageFilter [1].
>>>
>>> HTH,
>>> Matt
>>>
>>> [1]
>>> http://www.itk.org/Doxygen/html/classitk_1_1SliceBySliceImageFilter.html
>>>
>>> On Wed, Feb 4, 2015 at 1:59 PM, samah bouzidi <samah.bouzidi at gmail.com>
>>> wrote:
>>> > hello itk users,
>>> >
>>> > I am a beginner ITK users. I am trying to segment a volume using region
>>> > growing algorithm. I am able to do it in a 2D image (dicom) but not
>>> for a
>>> > volume.
>>> > 1) I saw that for 3D region growing the seed point have 3 coordinates
>>> (x, y,
>>> > z). In my case, z is the slice number (i am using .img format). Can I
>>> use an
>>> > (x,y) seed point?
>>> > 2) I have another idea,  reading an image series  and applied the
>>> filter for
>>> > each image and then writing them in volume. Are there any examples (
>>> applied
>>> > a filter in image series) that one could help me?
>>> >
>>> > regards
>>> > Samah.
>>> >
>>> > My source code is as follows
>>> > ================================
>>> > #include "itkConnectedThresholdImageFilter.h"
>>> > #include "itkImage.h"
>>> > #include "itkImageFileReader.h"
>>> > #include "itkImageFileWriter.h"
>>> >
>>> > int main( int argc, char *argv[])
>>> > {
>>> >   typedef   signed short         InternalPixelType;
>>> >   typedef   unsigned char        OutputPixelType;
>>> >   const     unsigned int           Dimension = 3;
>>> >   typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
>>> >
>>> >   typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>>> >
>>> >   typedef  itk::ImageFileReader< InternalImageType > ReaderType;
>>> >   typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
>>> >
>>> >   ReaderType::Pointer reader = ReaderType::New();
>>> >   WriterType::Pointer writer = WriterType::New();
>>> >
>>> >     reader->SetFileName(
>>> "/home/doctorant/T?l?chargements/Images/in.img" );
>>> >     writer->SetFileName(
>>> "/home/doctorant/T?l?chargements/Images/out.img");
>>> >
>>> >
>>> >   typedef itk::ConnectedThresholdImageFilter< InternalImageType,
>>> > OutputImageType > ConnectedFilterType;
>>> >
>>> >   ConnectedFilterType::Pointer connectedThreshold =
>>> > ConnectedFilterType::New();
>>> >
>>> >   connectedThreshold->SetInput( reader->GetOutput() );
>>> >   writer->SetInput( connectedThreshold->GetOutput() );
>>> >
>>> >
>>> >   const InternalPixelType lowerThreshold =  -1050  ;
>>> >   const InternalPixelType upperThreshold = -600;
>>> >
>>> >   connectedThreshold->SetLower(  lowerThreshold  );
>>> >   connectedThreshold->SetUpper(  upperThreshold  );
>>> >
>>> >   connectedThreshold->SetReplaceValue( 255 );
>>> >
>>> >
>>> >
>>> >
>>> >   InternalImageType::IndexType  index;
>>> >   index[0] = 250;
>>> >   index[1] = 239;
>>> >
>>> >   connectedThreshold->SetSeed( index );
>>> >
>>> >
>>> >   try
>>> >     {
>>> >     writer->Update();
>>> >     }
>>> >   catch( itk::ExceptionObject & excep )
>>> >     {
>>> >     std::cerr << "Exception caught !" << std::endl;
>>> >     std::cerr << excep << std::endl;
>>> >     }
>>> >
>>> >   return 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://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
>>
>>
>
>
> --
> Christopher Mullins
> R&D Engineer
> Kitware Inc.,
> 919.869.8871
>
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From samah.bouzidi at gmail.com  Sun Feb  8 07:07:44 2015
From: samah.bouzidi at gmail.com (samah bouzidi)
Date: Sun, 8 Feb 2015 13:07:44 +0100
Subject: [ITK-users] problem with 3d region growing
In-Reply-To: <CAN8_LjFvu4EXorOAaby4kKBtyngHwOqKyTEzRf6WziSftAjhOA@mail.gmail.com>
References: <CAN8_LjFBYg4YHRgV3zyWAKZ-187ShcGCY3DmW9ioaVC9M11-HA@mail.gmail.com>
 <CALzTN-QujxHeP5zNTRaBA9RPdr1frErTwJ_Q1WKH=eB9VgjpkQ@mail.gmail.com>
 <CAN8_LjGAPnDgiOQ-NkYAEoco3mQKo8d2MaHO=17hgUiAW_0xZQ@mail.gmail.com>
 <CABVTP-KCh=K-8woe=qndXdD5Z44exu=652ustkNTVi0HX=qbNw@mail.gmail.com>
 <CAN8_LjFvu4EXorOAaby4kKBtyngHwOqKyTEzRf6WziSftAjhOA@mail.gmail.com>
Message-ID: <CAN8_LjFHC0Ejisf9YjxVU2siSdQGLO-ZKHNmQ3Aof2hnUNBJmA@mail.gmail.com>

hi,

I finished the slice by slice region growing version of code. unfortunately I
have these errors:

1) no matching function for call to 'itk :: ConnectedThresholdImageFilter <
itk :: Image <short int, 2u>, itk :: Image <unsigned char, 2u>> :: SetSeed (
itk :: Image <short int, 3u> :: INDEXTYPE &) '
connectedThreshold-> SetSeed (index)

2)
/home/doctorant/src/InsightToolkit-4.7.0/Modules/Segmentation/RegionGrowing/include/itkConnectedThresholdImageFilter.hxx:53:1:
note:   no known conversion for argument 1 from ?itk::Image<short int,
3u>::IndexType {aka itk::Index<3u>}? to ?const IndexType& {aka const
itk::Index<2u>&}?


here is my code :

#include "itkConnectedThresholdImageFilter.h"
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkSliceBySliceImageFilter.h"
#include "iostream"

int main( int argc, char *argv[])
{
  typedef   signed short         InternalPixelType;
  typedef   unsigned char        OutputPixelType;
  const     unsigned int         Dimension = 3;
  const     int                  sliceDim =2;
  typedef itk::Image< InternalPixelType, Dimension > InternalImageType; //
input
  typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
//output

  typedef  itk::ImageFileReader< InternalImageType > ReaderType;
  typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;

  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();

  reader->SetFileName( "/home/doctorant/T?l?chargements/Images/in.img" );
  writer->SetFileName( "/home/doctorant/T?l?chargements/Images/out.img");


  typedef itk::SliceBySliceImageFilter< InternalImageType,OutputImageType>
SliceBySliceFilterType;

  SliceBySliceFilterType::Pointer sliceBySliceFilter =
SliceBySliceFilterType::New();

  typedef itk::ConnectedThresholdImageFilter<
SliceBySliceFilterType::InternalInputImageType,
          SliceBySliceFilterType::InternalOutputImageType >
ConnectedFilterType;
  ConnectedFilterType::Pointer connectedThreshold
=ConnectedFilterType::New();

  const InternalPixelType lowerThreshold =  -3700 ;
  const InternalPixelType upperThreshold = -600;

 connectedThreshold->SetLower(  lowerThreshold   );  // error here
 connectedThreshold->SetUpper(  upperThreshold  );  //error here
    connectedThreshold->SetReplaceValue( 255 );  // error here

    InternalImageType::IndexType  index;
    index[0] = 257;
    index[1] = 449;
    connectedThreshold->SetSeed(index);  // error here

  sliceBySliceFilter -> SetInput(reader->GetOutput());
  sliceBySliceFilter->SetFilter(connectedThreshold);
  writer->SetInput( sliceBySliceFilter->GetOutput());
  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & excep )
    {
    std::cerr << "Exception caught !" << std::endl;
    std::cerr << excep << std::endl;
    }

  return 0;
}

2015-02-06 21:59 GMT+01:00 samah bouzidi <samah.bouzidi at gmail.com>:

> hi,
>
> sincerely, I fail to understand the response of this filter, the
> algorithm succeeds to segment the region .however, in 3D, the first  slice is
> the same  used to check the segmentation in 2D, I am not getting at least for
> the first slice the region obtained in 2D.
> ps: the modified code takes into account the third dimension :
>
>
> InternalImageType::IndexType  index;
>   index[0] = 250;
>   index[1] = 239;
>   index[2]= 1;
>
>   connectedThreshold->SetSeed( index );
>
>
> any help will be appreciated.
> thanks in advance.
>
>
>
> 2015-02-04 21:24 GMT+01:00 Christopher Mullins <
> christopher.mullins at kitware.com>:
>
>> The ConnectedThresholdImageFilter example [1] might be of use.
>>
>> [1]
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/Segmentation/ConnectedThresholdImageFilter.cxx
>>
>> On Wed, Feb 4, 2015 at 3:14 PM, samah bouzidi <samah.bouzidi at gmail.com>
>> wrote:
>>
>>> hi Matt,
>>>
>>> thank you for replying.
>>>
>>> I can't find the error in my code (a black volume result)
>>>
>>> can you please look at my code.
>>>
>>>
>>>
>>> Regards
>>> Samah
>>>
>>>
>>>
>>> 2015-02-04 20:36 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>>>
>>>> Hi Samah,
>>>>
>>>> Welcome to ITK!
>>>>
>>>> For a 3D image, the third index of the seed does need to be defined.
>>>>
>>>> To apply a filter on each slice independently, use the
>>>> SliceBySliceImageFilter [1].
>>>>
>>>> HTH,
>>>> Matt
>>>>
>>>> [1]
>>>> http://www.itk.org/Doxygen/html/classitk_1_1SliceBySliceImageFilter.html
>>>>
>>>> On Wed, Feb 4, 2015 at 1:59 PM, samah bouzidi <samah.bouzidi at gmail.com>
>>>> wrote:
>>>> > hello itk users,
>>>> >
>>>> > I am a beginner ITK users. I am trying to segment a volume using
>>>> region
>>>> > growing algorithm. I am able to do it in a 2D image (dicom) but not
>>>> for a
>>>> > volume.
>>>> > 1) I saw that for 3D region growing the seed point have 3 coordinates
>>>> (x, y,
>>>> > z). In my case, z is the slice number (i am using .img format). Can I
>>>> use an
>>>> > (x,y) seed point?
>>>> > 2) I have another idea,  reading an image series  and applied the
>>>> filter for
>>>> > each image and then writing them in volume. Are there any examples (
>>>> applied
>>>> > a filter in image series) that one could help me?
>>>> >
>>>> > regards
>>>> > Samah.
>>>> >
>>>> > My source code is as follows
>>>> > ================================
>>>> > #include "itkConnectedThresholdImageFilter.h"
>>>> > #include "itkImage.h"
>>>> > #include "itkImageFileReader.h"
>>>> > #include "itkImageFileWriter.h"
>>>> >
>>>> > int main( int argc, char *argv[])
>>>> > {
>>>> >   typedef   signed short         InternalPixelType;
>>>> >   typedef   unsigned char        OutputPixelType;
>>>> >   const     unsigned int           Dimension = 3;
>>>> >   typedef itk::Image< InternalPixelType, Dimension >
>>>> InternalImageType;
>>>> >
>>>> >   typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>>>> >
>>>> >   typedef  itk::ImageFileReader< InternalImageType > ReaderType;
>>>> >   typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
>>>> >
>>>> >   ReaderType::Pointer reader = ReaderType::New();
>>>> >   WriterType::Pointer writer = WriterType::New();
>>>> >
>>>> >     reader->SetFileName(
>>>> "/home/doctorant/T?l?chargements/Images/in.img" );
>>>> >     writer->SetFileName(
>>>> "/home/doctorant/T?l?chargements/Images/out.img");
>>>> >
>>>> >
>>>> >   typedef itk::ConnectedThresholdImageFilter< InternalImageType,
>>>> > OutputImageType > ConnectedFilterType;
>>>> >
>>>> >   ConnectedFilterType::Pointer connectedThreshold =
>>>> > ConnectedFilterType::New();
>>>> >
>>>> >   connectedThreshold->SetInput( reader->GetOutput() );
>>>> >   writer->SetInput( connectedThreshold->GetOutput() );
>>>> >
>>>> >
>>>> >   const InternalPixelType lowerThreshold =  -1050  ;
>>>> >   const InternalPixelType upperThreshold = -600;
>>>> >
>>>> >   connectedThreshold->SetLower(  lowerThreshold  );
>>>> >   connectedThreshold->SetUpper(  upperThreshold  );
>>>> >
>>>> >   connectedThreshold->SetReplaceValue( 255 );
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >   InternalImageType::IndexType  index;
>>>> >   index[0] = 250;
>>>> >   index[1] = 239;
>>>> >
>>>> >   connectedThreshold->SetSeed( index );
>>>> >
>>>> >
>>>> >   try
>>>> >     {
>>>> >     writer->Update();
>>>> >     }
>>>> >   catch( itk::ExceptionObject & excep )
>>>> >     {
>>>> >     std::cerr << "Exception caught !" << std::endl;
>>>> >     std::cerr << excep << std::endl;
>>>> >     }
>>>> >
>>>> >   return 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://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
>>>
>>>
>>
>>
>> --
>> Christopher Mullins
>> R&D Engineer
>> Kitware Inc.,
>> 919.869.8871
>>
>
>
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From matt.mccormick at kitware.com  Sun Feb  8 15:27:17 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 8 Feb 2015 15:27:17 -0500
Subject: [ITK-users] cannot acces virtual void itk::Rigid3DTransform<
 TScalar >::SetMatrix (const MatrixType & matrix,
 double tolerance ) from the Rigid3D transform class.
In-Reply-To: <CALiCtPgvrEz-EiVMyctEeVZnHn-LoE9WMAKPdbzO6-9HjFYAUQ@mail.gmail.com>
References: <CALiCtPgvrEz-EiVMyctEeVZnHn-LoE9WMAKPdbzO6-9HjFYAUQ@mail.gmail.com>
Message-ID: <CALzTN-Rtfn0HprHA+A=ZYXyvRHcx=3DUVZyZYcS6vo1KgCZ4nQ@mail.gmail.com>

Hi Yago,

The tolerance parameter was added in a very recent version of ITK.
Make sure you are using the latest version of ITK.

HTH,
Matt

On Fri, Feb 6, 2015 at 2:32 PM, Yago Diez <yagodiezdonoso at gmail.com> wrote:
>
>
> Hi all,
>
> I want to store a 3D rotation matrix that I have computed in some format
> that itk can understand (and use to transform points and images, not to as
> the starting point of any optimization process). The problem is that the
> matrix is not "as orthogonal as it should be" due to numerical problems:
>
>
> So far I am using the Rigid3DTransform which looks the best way to go (but
> am willing to change if this is wrong). The numerical problems express like
> this:
>
> 1) if I use the "MatrixIsOrthogonal(,)" function I get a "yes" for a 1e-5
> tolerance but not for the default "1e-10" tolerance.
> 2) Consequently, if I use the SetMatrix() function I get an exception.
>
> I am pretty confident that I can get away with what I need to do if I
> convince the class to just swallow the "not very orthogonal" matrix (by
> using a less restrictive tolerance). I have seen that there exists a
> function to do just that but I am having problems using it.
>
> Specifically, I cannot seem to access the
>
> itk::Rigid3DTransform< TScalar >::SetMatrix     (const MatrixType &
> matrix, double      tolerance      )      function
>
> From the Rigid3D transform class.
>
> Consequently, the following code returns a compilation error :
>
>> error: no matching function for call to
>> ?itk::Rigid3DTransform<double>::SetMatrix(smallMatrixType&, double)?
>> XXXXXXXXXXXX: note: candidate is:
>> PATH/Code/Common/itkRigid3DTransform.txx:93:1: note: void
>> itk::Rigid3DTransform<TScalarType>::SetMatrix(const MatrixType&) [with
>> TScalarType = double, itk::Rigid3DTransform<TScalarType>::MatrixType =
>> itk::Matrix<double, 3u, 3u>]
>> PATH/Code/Common/itkRigid3DTransform.txx:93:1: note:   candidate expects 1
>> argument, 2 provided
>
>
> I have checked that the itkRigid3DTransform.txx file has indeed only the
> definition of the setmatrix method with one parameter.
>
> I assume I am looking for the setmatrix function with two parameters "in the
> wrong place", but have not yet managed to find the right one, any ideas?
>
>
> Here is the detailed code
>
>
>> typedef itk::Matrix<double, 3, 3> smallMatrixType;
>> smallMatrixType auxMatrix;
>>
> // matrix initialization, matrix M1 is orthogonal but I have numerical
> problems
>
> auxMatrix[0][0]=M1[0][0];
> auxMatrix[0][1]=M1[0][1];
> auxMatrix[0][2]=M1[0][2];
> auxMatrix[1][0]=M1[1][0];
> auxMatrix[1][1]=M1[1][1];
> auxMatrix[1][2]=M1[1][2];
> auxMatrix[2][0]=M1[2][0];
> auxMatrix[2][1]=M1[2][1];
> auxMatrix[2][2]=M1[2][2];
>
>
> typedef itk::Rigid3DTransform<double>  TransformType;
> TransformType::Pointer  rotation = TransformType::New();
>
> // rotation->MatrixIsOrthogonal(auxMatrix,1e-10) outputs 0, but
> rotation->MatrixIsOrthogonal(auxMatrix,1e-5) outputs 1
>
> rotation->SetMatrix(auxMatrix,1e-5); // this produces a compilation error
>
>
> //rotation->SetMatrix(auxMatrix); // THIS RESULTS IN AN EXCEPTION:
> itk::ERROR: Rigid3DTransform(0x1dec800): Attempting to set a non-orthogonal
> rotation matrix
>
>
> Thanks you very much for any help that you can provide.
>
>
>
> Yago Diez Donoso (PhD)
> Computer Vision and Robotics Group http://vicorob.udg.es/
> E-mail: yago at eia.udg.es; yagodiezdonoso at gmail.com
> Phone: (int. code) 34 972418013
> University of Girona
>
> _____________________________________
> 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 matt.mccormick at kitware.com  Sun Feb  8 15:52:56 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 8 Feb 2015 15:52:56 -0500
Subject: [ITK-users] What is StepLenght?
In-Reply-To: <CAKKNfu+PiwqQsEaJ_XY6NkVk17fsnA5xohM3b_8k2hFykhTsew@mail.gmail.com>
References: <CAKKNfu+PiwqQsEaJ_XY6NkVk17fsnA5xohM3b_8k2hFykhTsew@mail.gmail.com>
Message-ID: <CALzTN-TTAAqZ--y-GYDEUWp_HYHniRB84Q_a2ZV7Bo9cfmsbXw@mail.gmail.com>

Hi Matias,

The follow examples from the ITK Software Guide may be helpful:

  http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ImageRegistration1_8cxx-example.html

  http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ImageRegistration4_8cxx-example.html

  http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ImageRegistration5_8cxx-example.html

  http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ImageRegistration9_8cxx-example.html

HTH,
Matt



On Fri, Feb 6, 2015 at 9:47 AM, Matias Montroull <matimontg at gmail.com> wrote:
> Hi,
>
> I'm new to registration and I'm trying to understand what StepLenght is. I
> can play with the values but I'm not really sure what it is.
>
> Can someone explain?
>
> Thank you,
>
> Matias.
>
> _____________________________________
> 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 matt.mccormick at kitware.com  Sun Feb  8 15:58:10 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 8 Feb 2015 15:58:10 -0500
Subject: [ITK-users] problem with 3d region growing
In-Reply-To: <CAN8_LjFHC0Ejisf9YjxVU2siSdQGLO-ZKHNmQ3Aof2hnUNBJmA@mail.gmail.com>
References: <CAN8_LjFBYg4YHRgV3zyWAKZ-187ShcGCY3DmW9ioaVC9M11-HA@mail.gmail.com>
 <CALzTN-QujxHeP5zNTRaBA9RPdr1frErTwJ_Q1WKH=eB9VgjpkQ@mail.gmail.com>
 <CAN8_LjGAPnDgiOQ-NkYAEoco3mQKo8d2MaHO=17hgUiAW_0xZQ@mail.gmail.com>
 <CABVTP-KCh=K-8woe=qndXdD5Z44exu=652ustkNTVi0HX=qbNw@mail.gmail.com>
 <CAN8_LjFvu4EXorOAaby4kKBtyngHwOqKyTEzRf6WziSftAjhOA@mail.gmail.com>
 <CAN8_LjFHC0Ejisf9YjxVU2siSdQGLO-ZKHNmQ3Aof2hnUNBJmA@mail.gmail.com>
Message-ID: <CALzTN-R9vzWFgNwX76q0W0m-i1-xOQtmHT0A7LV7kouzNXhZTA@mail.gmail.com>

Hi,

These errors suggest that a 2D IndexType must be passed.

HTH,
Matt

On Sun, Feb 8, 2015 at 7:07 AM, samah bouzidi <samah.bouzidi at gmail.com> wrote:
> hi,
>
> I finished the slice by slice region growing version of code. unfortunately
> I have these errors:
>
> 1) no matching function for call to 'itk :: ConnectedThresholdImageFilter
> <itk :: Image <short int, 2u>, itk :: Image <unsigned char, 2u>> :: SetSeed
> (itk :: Image <short int, 3u> :: INDEXTYPE &) '
> connectedThreshold-> SetSeed (index)
>
> 2)
> /home/doctorant/src/InsightToolkit-4.7.0/Modules/Segmentation/RegionGrowing/include/itkConnectedThresholdImageFilter.hxx:53:1:
> note:   no known conversion for argument 1 from ?itk::Image<short int,
> 3u>::IndexType {aka itk::Index<3u>}? to ?const IndexType& {aka const
> itk::Index<2u>&}?
>
>
> here is my code :
>
> #include "itkConnectedThresholdImageFilter.h"
> #include "itkImage.h"
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
> #include "itkSliceBySliceImageFilter.h"
> #include "iostream"
>
> int main( int argc, char *argv[])
> {
>   typedef   signed short         InternalPixelType;
>   typedef   unsigned char        OutputPixelType;
>   const     unsigned int         Dimension = 3;
>   const     int                  sliceDim =2;
>   typedef itk::Image< InternalPixelType, Dimension > InternalImageType; //
> input
>   typedef itk::Image< OutputPixelType, Dimension > OutputImageType; //output
>
>   typedef  itk::ImageFileReader< InternalImageType > ReaderType;
>   typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
>
>   ReaderType::Pointer reader = ReaderType::New();
>   WriterType::Pointer writer = WriterType::New();
>
>   reader->SetFileName( "/home/doctorant/T?l?chargements/Images/in.img" );
>   writer->SetFileName( "/home/doctorant/T?l?chargements/Images/out.img");
>
>
>   typedef itk::SliceBySliceImageFilter< InternalImageType,OutputImageType>
> SliceBySliceFilterType;
>
>   SliceBySliceFilterType::Pointer sliceBySliceFilter =
> SliceBySliceFilterType::New();
>
>   typedef itk::ConnectedThresholdImageFilter<
> SliceBySliceFilterType::InternalInputImageType,
>           SliceBySliceFilterType::InternalOutputImageType >
> ConnectedFilterType;
>   ConnectedFilterType::Pointer connectedThreshold
> =ConnectedFilterType::New();
>
>   const InternalPixelType lowerThreshold =  -3700 ;
>   const InternalPixelType upperThreshold = -600;
>
>  connectedThreshold->SetLower(  lowerThreshold   );  // error here
>  connectedThreshold->SetUpper(  upperThreshold  );  //error here
>     connectedThreshold->SetReplaceValue( 255 );  // error here
>
>     InternalImageType::IndexType  index;
>     index[0] = 257;
>     index[1] = 449;
>     connectedThreshold->SetSeed(index);  // error here
>
>   sliceBySliceFilter -> SetInput(reader->GetOutput());
>   sliceBySliceFilter->SetFilter(connectedThreshold);
>   writer->SetInput( sliceBySliceFilter->GetOutput());
>   try
>     {
>     writer->Update();
>     }
>   catch( itk::ExceptionObject & excep )
>     {
>     std::cerr << "Exception caught !" << std::endl;
>     std::cerr << excep << std::endl;
>     }
>
>   return 0;
> }
>
> 2015-02-06 21:59 GMT+01:00 samah bouzidi <samah.bouzidi at gmail.com>:
>>
>> hi,
>>
>> sincerely, I fail to understand the response of this filter, the algorithm
>> succeeds to segment the region .however, in 3D, the first  slice is the same
>> used to check the segmentation in 2D, I am not getting at least for the
>> first slice the region obtained in 2D.
>> ps: the modified code takes into account the third dimension :
>>
>>
>> InternalImageType::IndexType  index;
>>   index[0] = 250;
>>   index[1] = 239;
>>   index[2]= 1;
>>
>>   connectedThreshold->SetSeed( index );
>>
>>
>> any help will be appreciated.
>> thanks in advance.
>>
>>
>>
>> 2015-02-04 21:24 GMT+01:00 Christopher Mullins
>> <christopher.mullins at kitware.com>:
>>>
>>> The ConnectedThresholdImageFilter example [1] might be of use.
>>>
>>> [1]
>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/Segmentation/ConnectedThresholdImageFilter.cxx
>>>
>>> On Wed, Feb 4, 2015 at 3:14 PM, samah bouzidi <samah.bouzidi at gmail.com>
>>> wrote:
>>>>
>>>> hi Matt,
>>>>
>>>> thank you for replying.
>>>>
>>>> I can't find the error in my code (a black volume result)
>>>>
>>>> can you please look at my code.
>>>>
>>>>
>>>>
>>>> Regards
>>>> Samah
>>>>
>>>>
>>>>
>>>> 2015-02-04 20:36 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>>>>>
>>>>> Hi Samah,
>>>>>
>>>>> Welcome to ITK!
>>>>>
>>>>> For a 3D image, the third index of the seed does need to be defined.
>>>>>
>>>>> To apply a filter on each slice independently, use the
>>>>> SliceBySliceImageFilter [1].
>>>>>
>>>>> HTH,
>>>>> Matt
>>>>>
>>>>> [1]
>>>>> http://www.itk.org/Doxygen/html/classitk_1_1SliceBySliceImageFilter.html
>>>>>
>>>>> On Wed, Feb 4, 2015 at 1:59 PM, samah bouzidi <samah.bouzidi at gmail.com>
>>>>> wrote:
>>>>> > hello itk users,
>>>>> >
>>>>> > I am a beginner ITK users. I am trying to segment a volume using
>>>>> > region
>>>>> > growing algorithm. I am able to do it in a 2D image (dicom) but not
>>>>> > for a
>>>>> > volume.
>>>>> > 1) I saw that for 3D region growing the seed point have 3 coordinates
>>>>> > (x, y,
>>>>> > z). In my case, z is the slice number (i am using .img format). Can I
>>>>> > use an
>>>>> > (x,y) seed point?
>>>>> > 2) I have another idea,  reading an image series  and applied the
>>>>> > filter for
>>>>> > each image and then writing them in volume. Are there any examples (
>>>>> > applied
>>>>> > a filter in image series) that one could help me?
>>>>> >
>>>>> > regards
>>>>> > Samah.
>>>>> >
>>>>> > My source code is as follows
>>>>> > ================================
>>>>> > #include "itkConnectedThresholdImageFilter.h"
>>>>> > #include "itkImage.h"
>>>>> > #include "itkImageFileReader.h"
>>>>> > #include "itkImageFileWriter.h"
>>>>> >
>>>>> > int main( int argc, char *argv[])
>>>>> > {
>>>>> >   typedef   signed short         InternalPixelType;
>>>>> >   typedef   unsigned char        OutputPixelType;
>>>>> >   const     unsigned int           Dimension = 3;
>>>>> >   typedef itk::Image< InternalPixelType, Dimension >
>>>>> > InternalImageType;
>>>>> >
>>>>> >   typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>>>>> >
>>>>> >   typedef  itk::ImageFileReader< InternalImageType > ReaderType;
>>>>> >   typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
>>>>> >
>>>>> >   ReaderType::Pointer reader = ReaderType::New();
>>>>> >   WriterType::Pointer writer = WriterType::New();
>>>>> >
>>>>> >     reader->SetFileName(
>>>>> > "/home/doctorant/T?l?chargements/Images/in.img" );
>>>>> >     writer->SetFileName(
>>>>> > "/home/doctorant/T?l?chargements/Images/out.img");
>>>>> >
>>>>> >
>>>>> >   typedef itk::ConnectedThresholdImageFilter< InternalImageType,
>>>>> > OutputImageType > ConnectedFilterType;
>>>>> >
>>>>> >   ConnectedFilterType::Pointer connectedThreshold =
>>>>> > ConnectedFilterType::New();
>>>>> >
>>>>> >   connectedThreshold->SetInput( reader->GetOutput() );
>>>>> >   writer->SetInput( connectedThreshold->GetOutput() );
>>>>> >
>>>>> >
>>>>> >   const InternalPixelType lowerThreshold =  -1050  ;
>>>>> >   const InternalPixelType upperThreshold = -600;
>>>>> >
>>>>> >   connectedThreshold->SetLower(  lowerThreshold  );
>>>>> >   connectedThreshold->SetUpper(  upperThreshold  );
>>>>> >
>>>>> >   connectedThreshold->SetReplaceValue( 255 );
>>>>> >
>>>>> >
>>>>> >
>>>>> >
>>>>> >   InternalImageType::IndexType  index;
>>>>> >   index[0] = 250;
>>>>> >   index[1] = 239;
>>>>> >
>>>>> >   connectedThreshold->SetSeed( index );
>>>>> >
>>>>> >
>>>>> >   try
>>>>> >     {
>>>>> >     writer->Update();
>>>>> >     }
>>>>> >   catch( itk::ExceptionObject & excep )
>>>>> >     {
>>>>> >     std::cerr << "Exception caught !" << std::endl;
>>>>> >     std::cerr << excep << std::endl;
>>>>> >     }
>>>>> >
>>>>> >   return 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://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
>>>>
>>>
>>>
>>>
>>> --
>>> Christopher Mullins
>>> R&D Engineer
>>> Kitware Inc.,
>>> 919.869.8871
>>
>>
>
>
> _____________________________________
> 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 samah.bouzidi at gmail.com  Sun Feb  8 16:59:45 2015
From: samah.bouzidi at gmail.com (samah bouzidi)
Date: Sun, 8 Feb 2015 22:59:45 +0100
Subject: [ITK-users] problem with 3d region growing
In-Reply-To: <CALzTN-R9vzWFgNwX76q0W0m-i1-xOQtmHT0A7LV7kouzNXhZTA@mail.gmail.com>
References: <CAN8_LjFBYg4YHRgV3zyWAKZ-187ShcGCY3DmW9ioaVC9M11-HA@mail.gmail.com>
 <CALzTN-QujxHeP5zNTRaBA9RPdr1frErTwJ_Q1WKH=eB9VgjpkQ@mail.gmail.com>
 <CAN8_LjGAPnDgiOQ-NkYAEoco3mQKo8d2MaHO=17hgUiAW_0xZQ@mail.gmail.com>
 <CABVTP-KCh=K-8woe=qndXdD5Z44exu=652ustkNTVi0HX=qbNw@mail.gmail.com>
 <CAN8_LjFvu4EXorOAaby4kKBtyngHwOqKyTEzRf6WziSftAjhOA@mail.gmail.com>
 <CAN8_LjFHC0Ejisf9YjxVU2siSdQGLO-ZKHNmQ3Aof2hnUNBJmA@mail.gmail.com>
 <CALzTN-R9vzWFgNwX76q0W0m-i1-xOQtmHT0A7LV7kouzNXhZTA@mail.gmail.com>
Message-ID: <CAN8_LjGgvmEDRXQdu_S8_M2WFggUtrLP8iknG-qZr8P9WOt6XA@mail.gmail.com>

hi,

thank you Matt McCormick for your reply.
I* finally fixed "The Problem"*.

// the code

#include "itkConnectedThresholdImageFilter.h"
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkSliceBySliceImageFilter.h"

int main( int argc, char *argv[])
{
  typedef   signed short         InternalPixelType;
  typedef   unsigned char        OutputPixelType;
  const     unsigned int         Dimension = 3;
  const     unsigned int         sliceDim =2;
  typedef itk::Image< InternalPixelType, Dimension > InternalImageType; //
input
  typedef itk::Image< InternalPixelType, sliceDim > sliceType; // input
  typedef itk::Image< OutputPixelType, Dimension > OutputImageType; //output

  typedef  itk::ImageFileReader< InternalImageType > ReaderType;
  typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;

  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();

 reader->SetFileName( "/home/doctorant/T?l?chargements/Images/in.img" );
 writer->SetFileName( "/home/doctorant/T?l?chargements/Images/out.img");


  typedef itk::SliceBySliceImageFilter< InternalImageType,OutputImageType>
SliceBySliceFilterType;

  SliceBySliceFilterType::Pointer sliceBySliceFilter =
SliceBySliceFilterType::New();

  typedef itk::ConnectedThresholdImageFilter<
SliceBySliceFilterType::InternalInputImageType,
          SliceBySliceFilterType::InternalOutputImageType >
ConnectedFilterType;
  ConnectedFilterType::Pointer connectedThreshold
=ConnectedFilterType::New();

  SliceBySliceFilterType::InternalInputImageType::InternalPixelType
lowerThreshold =  -1100;
  SliceBySliceFilterType::InternalInputImageType::InternalPixelType
upperThreshold = -600;
  SliceBySliceFilterType::InternalOutputImageType::InternalPixelType x =
255;
  connectedThreshold->SetLower(lowerThreshold);
  connectedThreshold->SetUpper(  upperThreshold  );
  connectedThreshold->SetReplaceValue( x );
  // 250, 239
  SliceBySliceFilterType::InternalInputImageType::IndexType  index;
    index[0] = 252;
    index[1] = 275;
  connectedThreshold->SetSeed(index);

  sliceBySliceFilter -> SetInput(reader->GetOutput());
  sliceBySliceFilter->SetFilter(connectedThreshold);
  writer->SetInput( sliceBySliceFilter->GetOutput());
  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & excep )
    {
    std::cerr << "Exception caught !" << std::endl;
    std::cerr << excep << std::endl;
    }

  return 0;
}





2015-02-08 21:58 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:

> Hi,
>
> These errors suggest that a 2D IndexType must be passed.
>
> HTH,
> Matt
>
> On Sun, Feb 8, 2015 at 7:07 AM, samah bouzidi <samah.bouzidi at gmail.com>
> wrote:
> > hi,
> >
> > I finished the slice by slice region growing version of code.
> unfortunately
> > I have these errors:
> >
> > 1) no matching function for call to 'itk :: ConnectedThresholdImageFilter
> > <itk :: Image <short int, 2u>, itk :: Image <unsigned char, 2u>> ::
> SetSeed
> > (itk :: Image <short int, 3u> :: INDEXTYPE &) '
> > connectedThreshold-> SetSeed (index)
> >
> > 2)
> >
> /home/doctorant/src/InsightToolkit-4.7.0/Modules/Segmentation/RegionGrowing/include/itkConnectedThresholdImageFilter.hxx:53:1:
> > note:   no known conversion for argument 1 from ?itk::Image<short int,
> > 3u>::IndexType {aka itk::Index<3u>}? to ?const IndexType& {aka const
> > itk::Index<2u>&}?
> >
> >
> > here is my code :
> >
> > #include "itkConnectedThresholdImageFilter.h"
> > #include "itkImage.h"
> > #include "itkImageFileReader.h"
> > #include "itkImageFileWriter.h"
> > #include "itkSliceBySliceImageFilter.h"
> > #include "iostream"
> >
> > int main( int argc, char *argv[])
> > {
> >   typedef   signed short         InternalPixelType;
> >   typedef   unsigned char        OutputPixelType;
> >   const     unsigned int         Dimension = 3;
> >   const     int                  sliceDim =2;
> >   typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
> //
> > input
> >   typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
> //output
> >
> >   typedef  itk::ImageFileReader< InternalImageType > ReaderType;
> >   typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
> >
> >   ReaderType::Pointer reader = ReaderType::New();
> >   WriterType::Pointer writer = WriterType::New();
> >
> >   reader->SetFileName( "/home/doctorant/T?l?chargements/Images/in.img" );
> >   writer->SetFileName( "/home/doctorant/T?l?chargements/Images/out.img");
> >
> >
> >   typedef itk::SliceBySliceImageFilter<
> InternalImageType,OutputImageType>
> > SliceBySliceFilterType;
> >
> >   SliceBySliceFilterType::Pointer sliceBySliceFilter =
> > SliceBySliceFilterType::New();
> >
> >   typedef itk::ConnectedThresholdImageFilter<
> > SliceBySliceFilterType::InternalInputImageType,
> >           SliceBySliceFilterType::InternalOutputImageType >
> > ConnectedFilterType;
> >   ConnectedFilterType::Pointer connectedThreshold
> > =ConnectedFilterType::New();
> >
> >   const InternalPixelType lowerThreshold =  -3700 ;
> >   const InternalPixelType upperThreshold = -600;
> >
> >  connectedThreshold->SetLower(  lowerThreshold   );  // error here
> >  connectedThreshold->SetUpper(  upperThreshold  );  //error here
> >     connectedThreshold->SetReplaceValue( 255 );  // error here
> >
> >     InternalImageType::IndexType  index;
> >     index[0] = 257;
> >     index[1] = 449;
> >     connectedThreshold->SetSeed(index);  // error here
> >
> >   sliceBySliceFilter -> SetInput(reader->GetOutput());
> >   sliceBySliceFilter->SetFilter(connectedThreshold);
> >   writer->SetInput( sliceBySliceFilter->GetOutput());
> >   try
> >     {
> >     writer->Update();
> >     }
> >   catch( itk::ExceptionObject & excep )
> >     {
> >     std::cerr << "Exception caught !" << std::endl;
> >     std::cerr << excep << std::endl;
> >     }
> >
> >   return 0;
> > }
> >
> > 2015-02-06 21:59 GMT+01:00 samah bouzidi <samah.bouzidi at gmail.com>:
> >>
> >> hi,
> >>
> >> sincerely, I fail to understand the response of this filter, the
> algorithm
> >> succeeds to segment the region .however, in 3D, the first  slice is the
> same
> >> used to check the segmentation in 2D, I am not getting at least for the
> >> first slice the region obtained in 2D.
> >> ps: the modified code takes into account the third dimension :
> >>
> >>
> >> InternalImageType::IndexType  index;
> >>   index[0] = 250;
> >>   index[1] = 239;
> >>   index[2]= 1;
> >>
> >>   connectedThreshold->SetSeed( index );
> >>
> >>
> >> any help will be appreciated.
> >> thanks in advance.
> >>
> >>
> >>
> >> 2015-02-04 21:24 GMT+01:00 Christopher Mullins
> >> <christopher.mullins at kitware.com>:
> >>>
> >>> The ConnectedThresholdImageFilter example [1] might be of use.
> >>>
> >>> [1]
> >>>
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/Segmentation/ConnectedThresholdImageFilter.cxx
> >>>
> >>> On Wed, Feb 4, 2015 at 3:14 PM, samah bouzidi <samah.bouzidi at gmail.com
> >
> >>> wrote:
> >>>>
> >>>> hi Matt,
> >>>>
> >>>> thank you for replying.
> >>>>
> >>>> I can't find the error in my code (a black volume result)
> >>>>
> >>>> can you please look at my code.
> >>>>
> >>>>
> >>>>
> >>>> Regards
> >>>> Samah
> >>>>
> >>>>
> >>>>
> >>>> 2015-02-04 20:36 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com
> >:
> >>>>>
> >>>>> Hi Samah,
> >>>>>
> >>>>> Welcome to ITK!
> >>>>>
> >>>>> For a 3D image, the third index of the seed does need to be defined.
> >>>>>
> >>>>> To apply a filter on each slice independently, use the
> >>>>> SliceBySliceImageFilter [1].
> >>>>>
> >>>>> HTH,
> >>>>> Matt
> >>>>>
> >>>>> [1]
> >>>>>
> http://www.itk.org/Doxygen/html/classitk_1_1SliceBySliceImageFilter.html
> >>>>>
> >>>>> On Wed, Feb 4, 2015 at 1:59 PM, samah bouzidi <
> samah.bouzidi at gmail.com>
> >>>>> wrote:
> >>>>> > hello itk users,
> >>>>> >
> >>>>> > I am a beginner ITK users. I am trying to segment a volume using
> >>>>> > region
> >>>>> > growing algorithm. I am able to do it in a 2D image (dicom) but not
> >>>>> > for a
> >>>>> > volume.
> >>>>> > 1) I saw that for 3D region growing the seed point have 3
> coordinates
> >>>>> > (x, y,
> >>>>> > z). In my case, z is the slice number (i am using .img format).
> Can I
> >>>>> > use an
> >>>>> > (x,y) seed point?
> >>>>> > 2) I have another idea,  reading an image series  and applied the
> >>>>> > filter for
> >>>>> > each image and then writing them in volume. Are there any examples
> (
> >>>>> > applied
> >>>>> > a filter in image series) that one could help me?
> >>>>> >
> >>>>> > regards
> >>>>> > Samah.
> >>>>> >
> >>>>> > My source code is as follows
> >>>>> > ================================
> >>>>> > #include "itkConnectedThresholdImageFilter.h"
> >>>>> > #include "itkImage.h"
> >>>>> > #include "itkImageFileReader.h"
> >>>>> > #include "itkImageFileWriter.h"
> >>>>> >
> >>>>> > int main( int argc, char *argv[])
> >>>>> > {
> >>>>> >   typedef   signed short         InternalPixelType;
> >>>>> >   typedef   unsigned char        OutputPixelType;
> >>>>> >   const     unsigned int           Dimension = 3;
> >>>>> >   typedef itk::Image< InternalPixelType, Dimension >
> >>>>> > InternalImageType;
> >>>>> >
> >>>>> >   typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
> >>>>> >
> >>>>> >   typedef  itk::ImageFileReader< InternalImageType > ReaderType;
> >>>>> >   typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
> >>>>> >
> >>>>> >   ReaderType::Pointer reader = ReaderType::New();
> >>>>> >   WriterType::Pointer writer = WriterType::New();
> >>>>> >
> >>>>> >     reader->SetFileName(
> >>>>> > "/home/doctorant/T?l?chargements/Images/in.img" );
> >>>>> >     writer->SetFileName(
> >>>>> > "/home/doctorant/T?l?chargements/Images/out.img");
> >>>>> >
> >>>>> >
> >>>>> >   typedef itk::ConnectedThresholdImageFilter< InternalImageType,
> >>>>> > OutputImageType > ConnectedFilterType;
> >>>>> >
> >>>>> >   ConnectedFilterType::Pointer connectedThreshold =
> >>>>> > ConnectedFilterType::New();
> >>>>> >
> >>>>> >   connectedThreshold->SetInput( reader->GetOutput() );
> >>>>> >   writer->SetInput( connectedThreshold->GetOutput() );
> >>>>> >
> >>>>> >
> >>>>> >   const InternalPixelType lowerThreshold =  -1050  ;
> >>>>> >   const InternalPixelType upperThreshold = -600;
> >>>>> >
> >>>>> >   connectedThreshold->SetLower(  lowerThreshold  );
> >>>>> >   connectedThreshold->SetUpper(  upperThreshold  );
> >>>>> >
> >>>>> >   connectedThreshold->SetReplaceValue( 255 );
> >>>>> >
> >>>>> >
> >>>>> >
> >>>>> >
> >>>>> >   InternalImageType::IndexType  index;
> >>>>> >   index[0] = 250;
> >>>>> >   index[1] = 239;
> >>>>> >
> >>>>> >   connectedThreshold->SetSeed( index );
> >>>>> >
> >>>>> >
> >>>>> >   try
> >>>>> >     {
> >>>>> >     writer->Update();
> >>>>> >     }
> >>>>> >   catch( itk::ExceptionObject & excep )
> >>>>> >     {
> >>>>> >     std::cerr << "Exception caught !" << std::endl;
> >>>>> >     std::cerr << excep << std::endl;
> >>>>> >     }
> >>>>> >
> >>>>> >   return 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://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
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Christopher Mullins
> >>> R&D Engineer
> >>> Kitware Inc.,
> >>> 919.869.8871
> >>
> >>
> >
> >
> > _____________________________________
> > 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 yagodiezdonoso at gmail.com  Mon Feb  9 06:13:51 2015
From: yagodiezdonoso at gmail.com (yagoDiez)
Date: Mon, 9 Feb 2015 04:13:51 -0700 (MST)
Subject: [ITK-users] Rigid3DTransform make error
In-Reply-To: <CB2DC38A.2C037%hans-johnson@uiowa.edu>
References: <A4B94B55-A833-49BC-BD90-04C5BF26C8AF@u.washington.edu>
 <CABDpjTncU3Os7MDj62vW-5CWrffFbj69eV8NKa5gA9+=PihFLA@mail.gmail.com>
 <799E43A7-6B72-4C7E-90A2-0E0604C15CDB@u.washington.edu>
 <CABDpjTkoMHmkgzNXvTowxt-+f4NdMsJ=wBdMn8hjnJzcDQEwYg@mail.gmail.com>
 <917C757C-D5BC-45C0-A0F6-ED12E79A1877@gmail.com>
 <CB2DC38A.2C037%hans-johnson@uiowa.edu>
Message-ID: <1423480431340-7586887.post@n2.nabble.com>

Some more information on this:

The details mentioned by  Nicholas Tustison are here:

http://mitk.org/wiki/ITK_v4_Migration_Guide

I encountered a similar problem to the one originating the thread (just
migrated to itk 4.7). I solved it by using the itkv3 rigid transformation
class.

http://www.itk.org/Doxygen43/html/classitkv3_1_1Rigid3DTransform.html

So, all you would need to do is change the typedef to 

typedef itkv3::Rigid3DTransform<double>  TransformType;

and 

include the following file.

#include <itkv3Rigid3DTransform.h>

Probably just using the itk 3 compatibility flag would also work.

In my case, I used this solution because I needed to use the setmatrix (with
orthogonality tolerance) function with a previously computed rotation
matrix. I don't feel too happy about it but I did not see a direct way to
use the versor3D class (which I do use for my "normal" rigid registrations
and encourage others to use). Will post again if I get a better solution.





--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Rigid3DTransform-make-error-tp7160305p7586887.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From yagodiezdonoso at gmail.com  Mon Feb  9 06:44:26 2015
From: yagodiezdonoso at gmail.com (yagoDiez)
Date: Mon, 9 Feb 2015 04:44:26 -0700 (MST)
Subject: [ITK-users] cannot acces virtual void itk::Rigid3DTransform<
 TScalar >::SetMatrix (const MatrixType & matrix,
 double tolerance ) from the Rigid3D transform class.
In-Reply-To: <CALzTN-Rtfn0HprHA+A=ZYXyvRHcx=3DUVZyZYcS6vo1KgCZ4nQ@mail.gmail.com>
References: <CALiCtPgvrEz-EiVMyctEeVZnHn-LoE9WMAKPdbzO6-9HjFYAUQ@mail.gmail.com>
 <CALzTN-Rtfn0HprHA+A=ZYXyvRHcx=3DUVZyZYcS6vo1KgCZ4nQ@mail.gmail.com>
Message-ID: <1423482266729-7586888.post@n2.nabble.com>

Hi Matt,

Thanks for pointing this out, I migrated to the latest (4.7) version and it
works now.

While migrating I encountered a new problem (rigid3D translation is sort of
deprecated now). More information here:

http://itk-insight-users.2283740.n2.nabble.com/Rigid3DTransform-make-error-td7160305.html#a7586887

I had to resort to using an "intermediate itkv3 rigid transformation class".
It does work but I am not sure it is a "lasting" solution.

Does anybody know which class is better for my original problem:

- I have a previously computed rotation matrix which I want to store in a
format that itk can use. 
- Consequently, I am pretty sure that I want to use the setMatrix method
(ideally with the possibility to specify a tolerance). 

Thanks!
Yago





--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-cannot-acces-virtual-void-itk-Rigid3DTransform-TScalar-SetMatrix-const-MatrixType-matrix-d-tp7586880p7586888.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From matimontg at gmail.com  Mon Feb  9 10:20:05 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Mon, 9 Feb 2015 12:20:05 -0300
Subject: [ITK-users] What is StepLenght?
In-Reply-To: <CALzTN-TTAAqZ--y-GYDEUWp_HYHniRB84Q_a2ZV7Bo9cfmsbXw@mail.gmail.com>
References: <CAKKNfu+PiwqQsEaJ_XY6NkVk17fsnA5xohM3b_8k2hFykhTsew@mail.gmail.com>
 <CALzTN-TTAAqZ--y-GYDEUWp_HYHniRB84Q_a2ZV7Bo9cfmsbXw@mail.gmail.com>
Message-ID: <CAKKNfuLY7E3ygFnSGueqUtm672KmGYCYqKZ84NZCp1SD_O4ouA@mail.gmail.com>

Thanks, I'll take a look.
Also, what learning rate is?

On Sun, Feb 8, 2015 at 5:52 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Matias,
>
> The follow examples from the ITK Software Guide may be helpful:
>
>
> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ImageRegistration1_8cxx-example.html
>
>
> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ImageRegistration4_8cxx-example.html
>
>
> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ImageRegistration5_8cxx-example.html
>
>
> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ImageRegistration9_8cxx-example.html
>
> HTH,
> Matt
>
>
>
> On Fri, Feb 6, 2015 at 9:47 AM, Matias Montroull <matimontg at gmail.com>
> wrote:
> > Hi,
> >
> > I'm new to registration and I'm trying to understand what StepLenght is.
> I
> > can play with the values but I'm not really sure what it is.
> >
> > Can someone explain?
> >
> > Thank you,
> >
> > Matias.
> >
> > _____________________________________
> > 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 Param.Rajpura at LntTechservices.com  Tue Feb 10 07:27:21 2015
From: Param.Rajpura at LntTechservices.com (Param Rajpura)
Date: Tue, 10 Feb 2015 12:27:21 +0000
Subject: [ITK-users] Chan and Vese Segmentation for 3D data
Message-ID: <8BF3D5D84855AD42BA4EE916729347C2763127@POCITMSEXMB05.LntUniverse.com>


Hi all,

I am using ITK for segmentation from 3D MR Images data.


Initially applying ChanandVeseFilter on 2D images I could segment successfully but 3D data generates a problem.
I am using the same code provided in the example: "Single Phase Chan and Vese" the only difference is I am loading fast marching output instead of generating here.

I am unable to catch any exceptions here, but while debugging my code, first chance exception is thrown at:


1.       Inside levelSetFilter->Update();

2.       In ImportImageContainer.hxx

3.       Line 181, data = new TElement[size];

Below is my code.



                typedef itk::ImageFileReader< MainType > ReaderType;
                ReaderType::Pointer reader = ReaderType::New();
                reader->SetFileName("E:\\Intermediate Results\\Sample001_MRI.mhd");
                try
                {
                                reader->Update();
                }
                catch (itk::ExceptionObject & excep)
                {
                                std::cerr << "Exception caught in read !" << std::endl;
                                std::cerr << excep << std::endl;
                                return -1;
                }
                typedef itk::CastImageFilter<MainType, InternalImageType> FloatConversionFilter;
                FloatConversionFilter::Pointer ImgTypeConverter = FloatConversionFilter::New();
                ImgTypeConverter->SetInput(reader->GetOutput());
                ImgTypeConverter->Update();

                typedef itk::ImageFileWriter< InternalImageType > WriterType;
                WriterType::Pointer writer = WriterType::New();
                writer->SetFileName("E:\\Intermediate Results\\Out.mhd");


                typedef itk::ImageFileReader< InternalImageType > ReaderType1;
                ReaderType1::Pointer reader1 = ReaderType1::New();
                reader1->SetFileName("E:\\Intermediate Results\\FastMarching.mhd");
                reader1->Update();
                InternalImageType::Pointer Image = InternalImageType::New();
                Image = ImgTypeConverter->GetOutput();
                Image->Print(std::cout);

                typedef itk::ChangeInformationImageFilter<InternalImageType> ChangeFilter;
                ChangeFilter::Pointer change = ChangeFilter::New();
                change->ChangeAll();
                change->UseReferenceImageOn();
                change->SetReferenceImage(Image);
                change->SetInput(reader1->GetOutput());
                try
                {
                                change->Update();
                }
                catch (itk::ExceptionObject & excep)
                {
                                std::cerr << "Exception caught in change !" << std::endl;
                                std::cerr << excep << std::endl;
                                return -1;
                }

                Image = change->GetOutput();
                Image->Print(std::cout);






                unsigned int nb_iteration = 1;
                double rms = 0.;
                double epsilon = 2.;
                double curvature_weight = 0.;
                double area_weight = 0.;
                double reinitialization_weight = 0.;
                double volume_weight = 0.5;
                double volume = 0.5;
                double l1 = 1.;
                double l2 = 1.;
                double overlap_weight = 100.0;
                //
                //  We now define the image type using a particular pixel type and
                //  dimension. In this case the \code{float} type is used for the pixels
                //  due to the requirements of the smoothing filter.
                //
                const unsigned int Dimension = 3;
                typedef float ScalarPixelType;
                typedef itk::Image< ScalarPixelType, Dimension > InternalImageType;
                typedef itk::Image< unsigned short, Dimension > MainType;





                typedef itk::ScalarChanAndVeseLevelSetFunctionData< InternalImageType,
                                InternalImageType > DataHelperType;

                typedef itk::ConstrainedRegionBasedLevelSetFunctionSharedData<
                                InternalImageType, InternalImageType, DataHelperType > SharedDataHelperType;

                typedef itk::ScalarChanAndVeseLevelSetFunction< InternalImageType,
                                InternalImageType, SharedDataHelperType > LevelSetFunctionType;


                //  We declare now the type of the numerically discretized Step and Delta functions that
                //  will be used in the level-set computations for foreground and background regions
                //
                typedef itk::AtanRegularizedHeavisideStepFunction< ScalarPixelType,
                                ScalarPixelType >  DomainFunctionType;

                DomainFunctionType::Pointer domainFunction = DomainFunctionType::New();
                domainFunction->SetEpsilon(epsilon);



                typedef itk::ScalarChanAndVeseSparseLevelSetImageFilter< InternalImageType,
                                InternalImageType, InternalImageType, LevelSetFunctionType,
                                SharedDataHelperType > MultiLevelSetType;

                MultiLevelSetType::Pointer levelSetFilter = MultiLevelSetType::New();

                //  We set the function count to 1 since a single level-set is being evolved.
                //
                levelSetFilter->SetFunctionCount(1);

                //  Set the feature image and initial level-set image as output of the
                //  fast marching image filter.
                //
                levelSetFilter->SetFeatureImage(ImgTypeConverter->GetOutput());
                levelSetFilter->SetLevelSet(0, change->GetOutput());
                //levelSetFilter->SetLevelSet(1, fastMarching1->GetOutput());
                //  Once activiated the level set evolution will stop if the convergence
                //  criteria or if the maximum number of iterations is reached.  The
                //  convergence criteria is defined in terms of the root mean squared (RMS)
                //  change in the level set function. The evolution is said to have
                //  converged if the RMS change is below a user specified threshold.  In a
                //  real application is desirable to couple the evolution of the zero set
                //  to a visualization module allowing the user to follow the evolution of
                //  the zero set. With this feedback, the user may decide when to stop the
                //  algorithm before the zero set leaks through the regions of low gradient
                //  in the contour of the anatomical structure to be segmented.
                //
                levelSetFilter->SetNumberOfIterations(nb_iteration);
                levelSetFilter->SetMaximumRMSError(rms);
                //  Often, in real applications, images have different pixel resolutions. In such
                //  cases, it is best to use the native spacings to compute derivatives etc rather
                //  than sampling the images.
                //
                //levelSetFilter->SetUseImageSpacing(1);

                //  For large images, we may want to compute the level-set over the initial supplied
                //  level-set image. This saves a lot of memory.
                //
                levelSetFilter->SetInPlace(false);
                //  For the level set with phase 0, set different parameters and weights. This may
                //  to be set in a loop for the case of multiple level-sets evolving simultaneously.
                //



                for (unsigned int i = 0; i < 1; i++)
                {
                                levelSetFilter->GetDifferenceFunction(i)->SetDomainFunction(domainFunction);
                                levelSetFilter->GetDifferenceFunction(i)->SetCurvatureWeight(curvature_weight);
                                levelSetFilter->GetDifferenceFunction(i)->SetAreaWeight(area_weight);
                                //levelSetFilter->GetDifferenceFunction(i)->SetOverlapPenaltyWeight(overlap_weight);
                                levelSetFilter->GetDifferenceFunction(i)->SetVolumeMatchingWeight(volume_weight);
                                levelSetFilter->GetDifferenceFunction(i)->SetVolume(volume);
                                levelSetFilter->GetDifferenceFunction(i)->SetLambda1(l1);
                                levelSetFilter->GetDifferenceFunction(i)->SetLambda2(l2);
                }

                try
                {
                                levelSetFilter->Update();
                }
                catch (itk::ExceptionObject & excep)
                {
                                std::cerr << "Exception caught !" << std::endl;
                                std::cerr << excep << std::endl;
                                return -1;
                }
                catch (...)
                {
                                std::cerr << "Exception Caught!!!!!" << std::endl;
                                return -1;
                }
                Image = levelSetFilter->GetOutput();
                Image->Print(std::cout);
                writer->SetInput(levelSetFilter->GetOutput());
                writer->Update();
                return EXIT_SUCCESS;
}
Also I would like to know what difference it makes when I use 3D data for fast marching. By looking at the distance map it doesn't look like a shere centered at the given seed point in 3D.
And what data should ideally be passed to ChanVese from FastMarching for 3D dataset.


Pls help!

Param


L&T Technology Services Ltd

www.LntTechservices.com<http://www.lnttechservices.com/>

This Email may contain confidential or privileged information for the intended recipient (s). If you are not the intended recipient, please do not use or disseminate the information, notify the sender and delete it from your system.
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From gunjan.gemini29 at gmail.com  Tue Feb 10 08:21:09 2015
From: gunjan.gemini29 at gmail.com (Gunjan Gautam)
Date: Tue, 10 Feb 2015 18:51:09 +0530
Subject: [ITK-users] Problem in installing ITK
Message-ID: <CAHvOzZF2pNRBe=KRvV8SdFDicw7XCHNP+V=QQeSnkz5CvDtyCw@mail.gmail.com>

Hi All,

While installing ITK-4.7.0 as per the instructions from
*http://www.itk.org/Wiki/ITK_Configuring_and_Building_for_Ubuntu_Linux
<http://www.itk.org/Wiki/ITK_Configuring_and_Building_for_Ubuntu_Linux>* I
am stuck at the below command

$ sudo ccmake -DITK_USE_REVIEW=ON ..

Terminal must show the below option:

BUILD_DOXYGEN                   *OFF
BUILD_EXAMPLES                  *ON
BUILD_SHARED_LIBS               *ON
BUILD_TESTING                   *ON
CMAKE_BACKWARDS_COMPATIBILITY   *2.4
CMAKE_BUILD_TYPE                *Release
CMAKE_INSTALL_PREFIX            */usr/local
ITK_USE_KWSTYLE                 *OFF


But my terminal is showing the options as mentioned below and I don't know
how to set the values including path and all.

 BUILD_EXAMPLES
*ON
 BUILD_SHARED_LIBS
*OFF
 BUILD_TESTING
*ON
 CMAKE_BUILD_TYPE
*Release
 ITKV3_COMPATIBILITY
*OFF
 ITK_BUILD_DEFAULT_MODULES    *ON
 ITK_WRAP_PYTHON
*OFF


Please help !!


-- 
Best Regards,
Gunjan
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From jhlegarreta at vicomtech.org  Tue Feb 10 09:02:46 2015
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Tue, 10 Feb 2015 15:02:46 +0100
Subject: [ITK-users] Problem in installing ITK
In-Reply-To: <CAHvOzZF2pNRBe=KRvV8SdFDicw7XCHNP+V=QQeSnkz5CvDtyCw@mail.gmail.com>
References: <CAHvOzZF2pNRBe=KRvV8SdFDicw7XCHNP+V=QQeSnkz5CvDtyCw@mail.gmail.com>
Message-ID: <CAAKhGh8xKM-921xm0dFYkzHPiZkpfzhPWwDkn5Q=uyX-P0Dp=Q@mail.gmail.com>

Hi Gunjan,
the order of the flags is not an important issue; it is their value which
matters.

As for some of the ones you are posting,
BUILD_SHARED_LIBS: you may want to use static libraries (OFF) instead of
dynamic libraries.
BUILD_TESTING: turning the testing OFF will create a lighter project and
may have great impact in saving compilation time, you may want to turn
BUILD_EXAMPLES: turning the examples ON may be useful if you are a newbie.
But turning them off does not hurt.
ITKV3_COMPATIBILITY: depending on your purposes, you may need to turn it on.
ITK_USE_REVIEW: this is an interesting option if you want to use filters
that are still under review process/published in the IJ [1], and not yet
integrated into the Modules.
BUILD_DOXYGEN: it is just about generating doxygen documentation files. ITK
is well documented in the Web [2], so it's not necessary.

Although, I'm not an expert in building ITK in a Unix OS, in theory, once
you set your binary directory (there where your makefiles will be
generated), you shouldn't need to set any other path.

You may not be seeing all flags if you don't turn the Advanced flag to ON
(CMake GUI at least).

HTH,
JON HAITZ



[1] http://www.insight-journal.org/
[2] http://www.itk.org/Doxygen/html/classes.html


On 10 February 2015 at 14:21, Gunjan Gautam <gunjan.gemini29 at gmail.com>
wrote:

> Hi All,
>
> While installing ITK-4.7.0 as per the instructions from *http://www.itk.org/Wiki/ITK_Configuring_and_Building_for_Ubuntu_Linux
> <http://www.itk.org/Wiki/ITK_Configuring_and_Building_for_Ubuntu_Linux>*
> I am stuck at the below command
>
> $ sudo ccmake -DITK_USE_REVIEW=ON ..
>
> Terminal must show the below option:
>
> BUILD_DOXYGEN                   *OFF
> BUILD_EXAMPLES                  *ON
> BUILD_SHARED_LIBS               *ON
> BUILD_TESTING                   *ON
> CMAKE_BACKWARDS_COMPATIBILITY   *2.4
> CMAKE_BUILD_TYPE                *Release
> CMAKE_INSTALL_PREFIX            */usr/local
> ITK_USE_KWSTYLE                 *OFF
>
>
> But my terminal is showing the options as mentioned below and I don't know
> how to set the values including path and all.
>
>  BUILD_EXAMPLES
> *ON
>  BUILD_SHARED_LIBS
> *OFF
>  BUILD_TESTING
> *ON
>  CMAKE_BUILD_TYPE
> *Release
>  ITKV3_COMPATIBILITY
> *OFF
>  ITK_BUILD_DEFAULT_MODULES
> *ON
>  ITK_WRAP_PYTHON
> *OFF
>
>
> Please help !!
>
>
> --
> Best Regards,
> Gunjan
>
> _____________________________________
> 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 matimontg at gmail.com  Wed Feb 11 08:50:47 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 11 Feb 2015 10:50:47 -0300
Subject: [ITK-users] MultiResImageRegistration3 | Joint PDF summed to Zero
Message-ID: <CAKKNfuLWYtn-XM_Ymt40q70k5KW61fy618mELguTTnxJbRp3ww@mail.gmail.com>

Hi,

I'm trying to do 3D Registration using TranslationTransform as
transformtype. I've downloaded MultiResImageRegistration3.cxx and when I
run it I get this error:

*Description: itk::ERROR:
MattesMutualInformationImageToImageMetric(04067A40): Joint PDF summed to
zero*

Is this due to the initial parameters?

Thanks,

Matias.
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From blowekamp at mail.nih.gov  Wed Feb 11 09:01:19 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 11 Feb 2015 09:01:19 -0500
Subject: [ITK-users] MultiResImageRegistration3 | Joint PDF summed to
	Zero
In-Reply-To: <CAKKNfuLWYtn-XM_Ymt40q70k5KW61fy618mELguTTnxJbRp3ww@mail.gmail.com>
References: <CAKKNfuLWYtn-XM_Ymt40q70k5KW61fy618mELguTTnxJbRp3ww@mail.gmail.com>
Message-ID: <6095C926-2A02-4D63-B295-34ADA2B53F01@mail.nih.gov>

Hello,

This message occurs when the images don't overlap.

If this error message occurs at the first iteration, its due to the initial parameters. If not then the optimizer is not setup correctly and is miss behaving due to scale, minimizing/maximizing, gradient noise etc..

Typically the CenterTransformInitializer[1] can be used to get reasonable initial parameters for many cases.

Also you are using the older ITKv3 registration framework. I would recommend using the v4 version of the example[2], I believe it give a clearer error message for this case.

Brad


[1] http://www.itk.org/Doxygen/html/classitk_1_1CenteredTransformInitializer.html
[2] http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2MultiResImageRegistration1_8cxx-example.html
On Feb 11, 2015, at 8:50 AM, Matias Montroull <matimontg at gmail.com> wrote:

> Hi,
> 
> I'm trying to do 3D Registration using TranslationTransform as transformtype. I've downloaded MultiResImageRegistration3.cxx and when I run it I get this error:
> 
> Description: itk::ERROR: MattesMutualInformationImageToImageMetric(04067A40): Joint PDF summed to zero
> 
> Is this due to the initial parameters?
> 
> Thanks,
> 
> Matias.
> _____________________________________
> 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 matimontg at gmail.com  Wed Feb 11 09:18:42 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 11 Feb 2015 11:18:42 -0300
Subject: [ITK-users] MultiResImageRegistration3 | Joint PDF summed to
	Zero
In-Reply-To: <6095C926-2A02-4D63-B295-34ADA2B53F01@mail.nih.gov>
References: <CAKKNfuLWYtn-XM_Ymt40q70k5KW61fy618mELguTTnxJbRp3ww@mail.gmail.com>
 <6095C926-2A02-4D63-B295-34ADA2B53F01@mail.nih.gov>
Message-ID: <CAKKNfu+e4zJHYqXMeXSwx2j6xqA=DYBxGhuvVOu4L1piWC+1ww@mail.gmail.com>

Thanks Btradley,

I'm using ITV4 with compatibility set to V3, not sure if that would be an
issue.

I tried adding the Centeredtransforminitializer to my example but it seems
I need to change the transformtype to CenterRigidTransform rather than
TranslationTransform, is that true? (I'm getting compilation erros)..

The example you point is 2D, I don't think there has been a 3D version of
the MultiResImageRegistration1 with V4.. I'll try though to see if I can
convert to 3D, it was pretty simple with the V3 version example.

Thanks again.

Matias.

On Wed, Feb 11, 2015 at 11:01 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> This message occurs when the images don't overlap.
>
> If this error message occurs at the first iteration, its due to the
> initial parameters. If not then the optimizer is not setup correctly and is
> miss behaving due to scale, minimizing/maximizing, gradient noise etc..
>
> Typically the CenterTransformInitializer[1] can be used to get reasonable
> initial parameters for many cases.
>
> Also you are using the older ITKv3 registration framework. I would
> recommend using the v4 version of the example[2], I believe it give a
> clearer error message for this case.
>
> Brad
>
>
> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1CenteredTransformInitializer.html
> [2]
> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2MultiResImageRegistration1_8cxx-example.html
> On Feb 11, 2015, at 8:50 AM, Matias Montroull <matimontg at gmail.com> wrote:
>
> Hi,
>
> I'm trying to do 3D Registration using TranslationTransform as
> transformtype. I've downloaded MultiResImageRegistration3.cxx and when I
> run it I get this error:
>
> *Description: itk::ERROR:
> MattesMutualInformationImageToImageMetric(04067A40): Joint PDF summed to
> zero*
>
> Is this due to the initial parameters?
>
> Thanks,
>
> Matias.
> _____________________________________
> 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 matimontg at gmail.com  Wed Feb 11 09:28:48 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 11 Feb 2015 11:28:48 -0300
Subject: [ITK-users] 'GetCurrentStepLength' : is not a member of
	'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
Message-ID: <CAKKNfuLPf93BL9iQ+WPV4UUt2vAq7a6Zc01NQ++uhuY=cJChGg@mail.gmail.com>

Hi,

I'm trying to run this example:
http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2MultiResImageRegistration1_8cxx-example.html

and I get the following compilation error:

'GetCurrentStepLength' : is not a member of
'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'

Any clues what I have missed? I compiled ITK with the V3 compatibility set
to ON.

Thank you,

Matias.
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From blowekamp at mail.nih.gov  Wed Feb 11 09:34:38 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 11 Feb 2015 09:34:38 -0500
Subject: [ITK-users] MultiResImageRegistration3 | Joint PDF summed to
	Zero
In-Reply-To: <CAKKNfu+e4zJHYqXMeXSwx2j6xqA=DYBxGhuvVOu4L1piWC+1ww@mail.gmail.com>
References: <CAKKNfuLWYtn-XM_Ymt40q70k5KW61fy618mELguTTnxJbRp3ww@mail.gmail.com>
 <6095C926-2A02-4D63-B295-34ADA2B53F01@mail.nih.gov>
 <CAKKNfu+e4zJHYqXMeXSwx2j6xqA=DYBxGhuvVOu4L1piWC+1ww@mail.gmail.com>
Message-ID: <7DC4D83B-241C-43E4-890C-27612B2B82E5@mail.nih.gov>

Hello,

If this is the example you are using[1], while its in the RegistrationITKv4 directory it is using the ITKv3 version of the framework.

If you compare it to the MultiResImageRegistration1.cxx example, its significantly more complicated. With the ITKv4 framework its an intrinsic part of the registration method. I would encourage you to base your registration program on example 1 and modify it for 3D.

You are right about the TranslationTransform not working with that Initializer. But it does work with any transform derived from the MatrixOffsetBase. 

Brad

[1] http://itk.org/Insight/Doxygen/html/Examples_2RegistrationITKv4_2MultiResImageRegistration3_8cxx-example.html

On Feb 11, 2015, at 9:18 AM, Matias Montroull <matimontg at gmail.com> wrote:

> Thanks Btradley,
> 
> I'm using ITV4 with compatibility set to V3, not sure if that would be an issue.
> 
> I tried adding the Centeredtransforminitializer to my example but it seems I need to change the transformtype to CenterRigidTransform rather than TranslationTransform, is that true? (I'm getting compilation erros)..
> 
> The example you point is 2D, I don't think there has been a 3D version of the MultiResImageRegistration1 with V4.. I'll try though to see if I can convert to 3D, it was pretty simple with the V3 version example.
> 
> Thanks again.
> 
> Matias.
> 
> On Wed, Feb 11, 2015 at 11:01 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello,
> 
> This message occurs when the images don't overlap.
> 
> If this error message occurs at the first iteration, its due to the initial parameters. If not then the optimizer is not setup correctly and is miss behaving due to scale, minimizing/maximizing, gradient noise etc..
> 
> Typically the CenterTransformInitializer[1] can be used to get reasonable initial parameters for many cases.
> 
> Also you are using the older ITKv3 registration framework. I would recommend using the v4 version of the example[2], I believe it give a clearer error message for this case.
> 
> Brad
> 
> 
> [1] http://www.itk.org/Doxygen/html/classitk_1_1CenteredTransformInitializer.html
> [2] http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2MultiResImageRegistration1_8cxx-example.html
> On Feb 11, 2015, at 8:50 AM, Matias Montroull <matimontg at gmail.com> wrote:
> 
>> Hi,
>> 
>> I'm trying to do 3D Registration using TranslationTransform as transformtype. I've downloaded MultiResImageRegistration3.cxx and when I run it I get this error:
>> 
>> Description: itk::ERROR: MattesMutualInformationImageToImageMetric(04067A40): Joint PDF summed to zero
>> 
>> Is this due to the initial parameters?
>> 
>> Thanks,
>> 
>> Matias.
>> _____________________________________
>> 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 jhlegarreta at vicomtech.org  Wed Feb 11 09:48:13 2015
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Wed, 11 Feb 2015 15:48:13 +0100
Subject: [ITK-users] 'GetCurrentStepLength' : is not a member of
	'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
In-Reply-To: <CAKKNfuLPf93BL9iQ+WPV4UUt2vAq7a6Zc01NQ++uhuY=cJChGg@mail.gmail.com>
References: <CAKKNfuLPf93BL9iQ+WPV4UUt2vAq7a6Zc01NQ++uhuY=cJChGg@mail.gmail.com>
Message-ID: <CAAKhGh8Z5B4qs5hYbkp4mPaZGOUX38znbxKgX1+mPYSB27OYTA@mail.gmail.com>

Hi Matias,
are you sure this filter needs the VTK COMPATIBILITY flag to ON?

On the other hand, according to the nightly doxygen (ITK 4.8.0), the filter
does have that member, so you may want to check the ITK version you are
actually using.

HTH,
JON HAITZ


On 11 February 2015 at 15:28, Matias Montroull <matimontg at gmail.com> wrote:

> Hi,
>
> I'm trying to run this example:
>
> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2MultiResImageRegistration1_8cxx-example.html
>
> and I get the following compilation error:
>
> 'GetCurrentStepLength' : is not a member of
> 'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
>
> Any clues what I have missed? I compiled ITK with the V3 compatibility set
> to ON.
>
> Thank you,
>
> Matias.
>
> _____________________________________
> 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 matimontg at gmail.com  Wed Feb 11 10:08:50 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 11 Feb 2015 12:08:50 -0300
Subject: [ITK-users] 'GetCurrentStepLength' : is not a member of
	'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
In-Reply-To: <CAAKhGh8Z5B4qs5hYbkp4mPaZGOUX38znbxKgX1+mPYSB27OYTA@mail.gmail.com>
References: <CAKKNfuLPf93BL9iQ+WPV4UUt2vAq7a6Zc01NQ++uhuY=cJChGg@mail.gmail.com>
 <CAAKhGh8Z5B4qs5hYbkp4mPaZGOUX38znbxKgX1+mPYSB27OYTA@mail.gmail.com>
Message-ID: <CAKKNfuLMfnRZf-NBoCA=-etYu+mxb+c2GgnYP1L40Wy2hF2Yag@mail.gmail.com>

Thanks for the answer Jon,

I actually set the flag to ON to run some ITK Apps I downloaded but I can
go back and set it to OFF if that's causing an issue.

Is there an easy way to check which version of ITK I'm using?

Thanks,

Matias.

On Wed, Feb 11, 2015 at 11:48 AM, Jon Haitz Legarreta <
jhlegarreta at vicomtech.org> wrote:

> Hi Matias,
> are you sure this filter needs the VTK COMPATIBILITY flag to ON?
>
> On the other hand, according to the nightly doxygen (ITK 4.8.0), the
> filter does have that member, so you may want to check the ITK version you
> are actually using.
>
> HTH,
> JON HAITZ
>
>
> On 11 February 2015 at 15:28, Matias Montroull <matimontg at gmail.com>
> wrote:
>
>> Hi,
>>
>> I'm trying to run this example:
>>
>> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2MultiResImageRegistration1_8cxx-example.html
>>
>> and I get the following compilation error:
>>
>> 'GetCurrentStepLength' : is not a member of
>> 'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
>>
>> Any clues what I have missed? I compiled ITK with the V3 compatibility
>> set to ON.
>>
>> Thank you,
>>
>> Matias.
>>
>> _____________________________________
>> 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 jhlegarreta at vicomtech.org  Wed Feb 11 10:16:08 2015
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Wed, 11 Feb 2015 16:16:08 +0100
Subject: [ITK-users] 'GetCurrentStepLength' : is not a member of
	'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
In-Reply-To: <CAKKNfuLMfnRZf-NBoCA=-etYu+mxb+c2GgnYP1L40Wy2hF2Yag@mail.gmail.com>
References: <CAKKNfuLPf93BL9iQ+WPV4UUt2vAq7a6Zc01NQ++uhuY=cJChGg@mail.gmail.com>
 <CAAKhGh8Z5B4qs5hYbkp4mPaZGOUX38znbxKgX1+mPYSB27OYTA@mail.gmail.com>
 <CAKKNfuLMfnRZf-NBoCA=-etYu+mxb+c2GgnYP1L40Wy2hF2Yag@mail.gmail.com>
Message-ID: <CAAKhGh_EFtKD0rWo5Re846E3xKDUCnvhaE_CUe7T6i2cPEF1Kw@mail.gmail.com>

Hi Mat?as,
I don't think it's causing the issue.

You've at least one possibility: to check in your ITKConfig.cmake file
(built in your binary folder) which is the value of the ITK_VERSION_MAJOR,
ITK_VERSION_MINOR, and ITK_VERSION_PATCH variables (look for those strings).

JON HAITZ



On 11 February 2015 at 16:08, Matias Montroull <matimontg at gmail.com> wrote:

> Thanks for the answer Jon,
>
> I actually set the flag to ON to run some ITK Apps I downloaded but I can
> go back and set it to OFF if that's causing an issue.
>
> Is there an easy way to check which version of ITK I'm using?
>
> Thanks,
>
> Matias.
>
> On Wed, Feb 11, 2015 at 11:48 AM, Jon Haitz Legarreta <
> jhlegarreta at vicomtech.org> wrote:
>
>> Hi Matias,
>> are you sure this filter needs the VTK COMPATIBILITY flag to ON?
>>
>> On the other hand, according to the nightly doxygen (ITK 4.8.0), the
>> filter does have that member, so you may want to check the ITK version you
>> are actually using.
>>
>> HTH,
>> JON HAITZ
>>
>>
>> On 11 February 2015 at 15:28, Matias Montroull <matimontg at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> I'm trying to run this example:
>>>
>>> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2MultiResImageRegistration1_8cxx-example.html
>>>
>>> and I get the following compilation error:
>>>
>>> 'GetCurrentStepLength' : is not a member of
>>> 'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
>>>
>>> Any clues what I have missed? I compiled ITK with the V3 compatibility
>>> set to ON.
>>>
>>> Thank you,
>>>
>>> Matias.
>>>
>>> _____________________________________
>>> 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 matimontg at gmail.com  Wed Feb 11 10:40:01 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 11 Feb 2015 12:40:01 -0300
Subject: [ITK-users] 'GetCurrentStepLength' : is not a member of
	'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
In-Reply-To: <CAAKhGh_EFtKD0rWo5Re846E3xKDUCnvhaE_CUe7T6i2cPEF1Kw@mail.gmail.com>
References: <CAKKNfuLPf93BL9iQ+WPV4UUt2vAq7a6Zc01NQ++uhuY=cJChGg@mail.gmail.com>
 <CAAKhGh8Z5B4qs5hYbkp4mPaZGOUX38znbxKgX1+mPYSB27OYTA@mail.gmail.com>
 <CAKKNfuLMfnRZf-NBoCA=-etYu+mxb+c2GgnYP1L40Wy2hF2Yag@mail.gmail.com>
 <CAAKhGh_EFtKD0rWo5Re846E3xKDUCnvhaE_CUe7T6i2cPEF1Kw@mail.gmail.com>
Message-ID: <CAKKNfu++oCg+SMfhSTqA6hVCy6yTUr6Ui9SGehkG+bqo2uu2cg@mail.gmail.com>

Thanks, this is what I see in the ITKConfig.cmake:

set(ITK_VERSION_MAJOR "4")
set(ITK_VERSION_MINOR "6")
set(ITK_VERSION_PATCH "1")

On Wed, Feb 11, 2015 at 12:16 PM, Jon Haitz Legarreta <
jhlegarreta at vicomtech.org> wrote:

> Hi Mat?as,
> I don't think it's causing the issue.
>
> You've at least one possibility: to check in your ITKConfig.cmake file
> (built in your binary folder) which is the value of the ITK_VERSION_MAJOR,
> ITK_VERSION_MINOR, and ITK_VERSION_PATCH variables (look for those strings).
>
> JON HAITZ
>
>
>
>
> On 11 February 2015 at 16:08, Matias Montroull <matimontg at gmail.com>
> wrote:
>
>> Thanks for the answer Jon,
>>
>> I actually set the flag to ON to run some ITK Apps I downloaded but I can
>> go back and set it to OFF if that's causing an issue.
>>
>> Is there an easy way to check which version of ITK I'm using?
>>
>> Thanks,
>>
>> Matias.
>>
>> On Wed, Feb 11, 2015 at 11:48 AM, Jon Haitz Legarreta <
>> jhlegarreta at vicomtech.org> wrote:
>>
>>> Hi Matias,
>>> are you sure this filter needs the VTK COMPATIBILITY flag to ON?
>>>
>>> On the other hand, according to the nightly doxygen (ITK 4.8.0), the
>>> filter does have that member, so you may want to check the ITK version you
>>> are actually using.
>>>
>>> HTH,
>>> JON HAITZ
>>>
>>>
>>> On 11 February 2015 at 15:28, Matias Montroull <matimontg at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm trying to run this example:
>>>>
>>>> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2MultiResImageRegistration1_8cxx-example.html
>>>>
>>>> and I get the following compilation error:
>>>>
>>>> 'GetCurrentStepLength' : is not a member of
>>>> 'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
>>>>
>>>> Any clues what I have missed? I compiled ITK with the V3 compatibility
>>>> set to ON.
>>>>
>>>> Thank you,
>>>>
>>>> Matias.
>>>>
>>>> _____________________________________
>>>> 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 jhlegarreta at vicomtech.org  Wed Feb 11 11:08:20 2015
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Wed, 11 Feb 2015 17:08:20 +0100
Subject: [ITK-users] 'GetCurrentStepLength' : is not a member of
	'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
In-Reply-To: <CAKKNfu++oCg+SMfhSTqA6hVCy6yTUr6Ui9SGehkG+bqo2uu2cg@mail.gmail.com>
References: <CAKKNfuLPf93BL9iQ+WPV4UUt2vAq7a6Zc01NQ++uhuY=cJChGg@mail.gmail.com>
 <CAAKhGh8Z5B4qs5hYbkp4mPaZGOUX38znbxKgX1+mPYSB27OYTA@mail.gmail.com>
 <CAKKNfuLMfnRZf-NBoCA=-etYu+mxb+c2GgnYP1L40Wy2hF2Yag@mail.gmail.com>
 <CAAKhGh_EFtKD0rWo5Re846E3xKDUCnvhaE_CUe7T6i2cPEF1Kw@mail.gmail.com>
 <CAKKNfu++oCg+SMfhSTqA6hVCy6yTUr6Ui9SGehkG+bqo2uu2cg@mail.gmail.com>
Message-ID: <CAAKhGh-rDpnRSxWxPMtCE_4E5f9f_N9zr2DLvzrUCKgvDRdTtA@mail.gmail.com>

Well, then it's ITK 4.6.1. Find whether that version of ITK has that member
for that filter, and if yes, then the problem lies somewhere else.

Try to debug and reach that file otherwise.

JON HAITZ


On 11 February 2015 at 16:40, Matias Montroull <matimontg at gmail.com> wrote:

> Thanks, this is what I see in the ITKConfig.cmake:
>
> set(ITK_VERSION_MAJOR "4")
> set(ITK_VERSION_MINOR "6")
> set(ITK_VERSION_PATCH "1")
>
> On Wed, Feb 11, 2015 at 12:16 PM, Jon Haitz Legarreta <
> jhlegarreta at vicomtech.org> wrote:
>
>> Hi Mat?as,
>> I don't think it's causing the issue.
>>
>> You've at least one possibility: to check in your ITKConfig.cmake file
>> (built in your binary folder) which is the value of the ITK_VERSION_MAJOR,
>> ITK_VERSION_MINOR, and ITK_VERSION_PATCH variables (look for those strings).
>>
>> JON HAITZ
>>
>>
>>
>>
>> On 11 February 2015 at 16:08, Matias Montroull <matimontg at gmail.com>
>> wrote:
>>
>>> Thanks for the answer Jon,
>>>
>>> I actually set the flag to ON to run some ITK Apps I downloaded but I
>>> can go back and set it to OFF if that's causing an issue.
>>>
>>> Is there an easy way to check which version of ITK I'm using?
>>>
>>> Thanks,
>>>
>>> Matias.
>>>
>>> On Wed, Feb 11, 2015 at 11:48 AM, Jon Haitz Legarreta <
>>> jhlegarreta at vicomtech.org> wrote:
>>>
>>>> Hi Matias,
>>>> are you sure this filter needs the VTK COMPATIBILITY flag to ON?
>>>>
>>>> On the other hand, according to the nightly doxygen (ITK 4.8.0), the
>>>> filter does have that member, so you may want to check the ITK version you
>>>> are actually using.
>>>>
>>>> HTH,
>>>> JON HAITZ
>>>>
>>>>
>>>> On 11 February 2015 at 15:28, Matias Montroull <matimontg at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm trying to run this example:
>>>>>
>>>>> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2MultiResImageRegistration1_8cxx-example.html
>>>>>
>>>>> and I get the following compilation error:
>>>>>
>>>>> 'GetCurrentStepLength' : is not a member of
>>>>> 'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
>>>>>
>>>>> Any clues what I have missed? I compiled ITK with the V3 compatibility
>>>>> set to ON.
>>>>>
>>>>> Thank you,
>>>>>
>>>>> Matias.
>>>>>
>>>>> _____________________________________
>>>>> 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 matimontg at gmail.com  Wed Feb 11 14:34:58 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 11 Feb 2015 16:34:58 -0300
Subject: [ITK-users] 'GetCurrentStepLength' : is not a member of
	'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
In-Reply-To: <CAAKhGh-rDpnRSxWxPMtCE_4E5f9f_N9zr2DLvzrUCKgvDRdTtA@mail.gmail.com>
References: <CAKKNfuLPf93BL9iQ+WPV4UUt2vAq7a6Zc01NQ++uhuY=cJChGg@mail.gmail.com>
 <CAAKhGh8Z5B4qs5hYbkp4mPaZGOUX38znbxKgX1+mPYSB27OYTA@mail.gmail.com>
 <CAKKNfuLMfnRZf-NBoCA=-etYu+mxb+c2GgnYP1L40Wy2hF2Yag@mail.gmail.com>
 <CAAKhGh_EFtKD0rWo5Re846E3xKDUCnvhaE_CUe7T6i2cPEF1Kw@mail.gmail.com>
 <CAKKNfu++oCg+SMfhSTqA6hVCy6yTUr6Ui9SGehkG+bqo2uu2cg@mail.gmail.com>
 <CAAKhGh-rDpnRSxWxPMtCE_4E5f9f_N9zr2DLvzrUCKgvDRdTtA@mail.gmail.com>
Message-ID: <CAKKNfu+6nsUGqetSwLX5oKkt5aHbqQfky_UihGUq+qFWQ6hVfQ@mail.gmail.com>

Thanks Jon, I solved it by replacing the line of code which had the error
with this:
   optimizer->SetMaximumStepLength( optimizer->GetMaximumStepLength() / 4.0
);

On Wed, Feb 11, 2015 at 1:08 PM, Jon Haitz Legarreta <
jhlegarreta at vicomtech.org> wrote:

> Well, then it's ITK 4.6.1. Find whether that version of ITK has that
> member for that filter, and if yes, then the problem lies somewhere else.
>
> Try to debug and reach that file otherwise.
>
> JON HAITZ
>
>
>
> On 11 February 2015 at 16:40, Matias Montroull <matimontg at gmail.com>
> wrote:
>
>> Thanks, this is what I see in the ITKConfig.cmake:
>>
>> set(ITK_VERSION_MAJOR "4")
>> set(ITK_VERSION_MINOR "6")
>> set(ITK_VERSION_PATCH "1")
>>
>> On Wed, Feb 11, 2015 at 12:16 PM, Jon Haitz Legarreta <
>> jhlegarreta at vicomtech.org> wrote:
>>
>>> Hi Mat?as,
>>> I don't think it's causing the issue.
>>>
>>> You've at least one possibility: to check in your ITKConfig.cmake file
>>> (built in your binary folder) which is the value of the ITK_VERSION_MAJOR,
>>> ITK_VERSION_MINOR, and ITK_VERSION_PATCH variables (look for those strings).
>>>
>>> JON HAITZ
>>>
>>>
>>>
>>>
>>> On 11 February 2015 at 16:08, Matias Montroull <matimontg at gmail.com>
>>> wrote:
>>>
>>>> Thanks for the answer Jon,
>>>>
>>>> I actually set the flag to ON to run some ITK Apps I downloaded but I
>>>> can go back and set it to OFF if that's causing an issue.
>>>>
>>>> Is there an easy way to check which version of ITK I'm using?
>>>>
>>>> Thanks,
>>>>
>>>> Matias.
>>>>
>>>> On Wed, Feb 11, 2015 at 11:48 AM, Jon Haitz Legarreta <
>>>> jhlegarreta at vicomtech.org> wrote:
>>>>
>>>>> Hi Matias,
>>>>> are you sure this filter needs the VTK COMPATIBILITY flag to ON?
>>>>>
>>>>> On the other hand, according to the nightly doxygen (ITK 4.8.0), the
>>>>> filter does have that member, so you may want to check the ITK version you
>>>>> are actually using.
>>>>>
>>>>> HTH,
>>>>> JON HAITZ
>>>>>
>>>>>
>>>>> On 11 February 2015 at 15:28, Matias Montroull <matimontg at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm trying to run this example:
>>>>>>
>>>>>> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2MultiResImageRegistration1_8cxx-example.html
>>>>>>
>>>>>> and I get the following compilation error:
>>>>>>
>>>>>> 'GetCurrentStepLength' : is not a member of
>>>>>> 'itk::RegularStepGradientDescentOptimizerv4<TInternalComputationValueType>'
>>>>>>
>>>>>> Any clues what I have missed? I compiled ITK with the V3
>>>>>> compatibility set to ON.
>>>>>>
>>>>>> Thank you,
>>>>>>
>>>>>> Matias.
>>>>>>
>>>>>> _____________________________________
>>>>>> 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 matt.mccormick at kitware.com  Thu Feb 12 00:14:46 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 12 Feb 2015 00:14:46 -0500
Subject: [ITK-users] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-TTZ4e0vCz5DfHiXegw-GiuDD1sfxJbXPekSRv-t3g1uA@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss, design, and
learn with your fellow ITK community members.


On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/events/chnqhe892r77l7q7qdf53os2ldg


On Friday, 11:00 AM Eastern USA time, an ITK development conference,

  https://plus.google.com/events/ckcqudctda6cpclqclbchonlft8


For those that cannot join via Hangout, telephone call-in is also possible.
Dial:

  585-632-6296

Enter pin:

  31423



To get regular invites to these events, join the ITK Bar Camp G+ Community:

  https://plus.google.com/u/0/communities/111375098792764998322



All are welcome.  Hope to talk to you then!

From matt.mccormick at kitware.com  Thu Feb 12 11:52:43 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 12 Feb 2015 11:52:43 -0500
Subject: [ITK-users] What is StepLenght?
In-Reply-To: <CAKKNfuLY7E3ygFnSGueqUtm672KmGYCYqKZ84NZCp1SD_O4ouA@mail.gmail.com>
References: <CAKKNfu+PiwqQsEaJ_XY6NkVk17fsnA5xohM3b_8k2hFykhTsew@mail.gmail.com>
 <CALzTN-TTAAqZ--y-GYDEUWp_HYHniRB84Q_a2ZV7Bo9cfmsbXw@mail.gmail.com>
 <CAKKNfuLY7E3ygFnSGueqUtm672KmGYCYqKZ84NZCp1SD_O4ouA@mail.gmail.com>
Message-ID: <CALzTN-TXV-2Eoutuv_XLM-ZpN8OSa48R8xsACL1V79evwgNGuw@mail.gmail.com>

Hi Matias,

The class descriptions found here [1] and here [2] explain the learning rate.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1RegularStepGradientDescentOptimizerv4.html

[2] http://www.itk.org/Doxygen/html/classitk_1_1GradientDescentOptimizerv4Template.html

On Mon, Feb 9, 2015 at 10:20 AM, Matias Montroull <matimontg at gmail.com> wrote:
> Thanks, I'll take a look.
> Also, what learning rate is?
>
> On Sun, Feb 8, 2015 at 5:52 PM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>>
>> Hi Matias,
>>
>> The follow examples from the ITK Software Guide may be helpful:
>>
>>
>> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ImageRegistration1_8cxx-example.html
>>
>>
>> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ImageRegistration4_8cxx-example.html
>>
>>
>> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ImageRegistration5_8cxx-example.html
>>
>>
>> http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ImageRegistration9_8cxx-example.html
>>
>> HTH,
>> Matt
>>
>>
>>
>> On Fri, Feb 6, 2015 at 9:47 AM, Matias Montroull <matimontg at gmail.com>
>> wrote:
>> > Hi,
>> >
>> > I'm new to registration and I'm trying to understand what StepLenght is.
>> > I
>> > can play with the values but I'm not really sure what it is.
>> >
>> > Can someone explain?
>> >
>> > Thank you,
>> >
>> > Matias.
>> >
>> > _____________________________________
>> > 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 matt.mccormick at kitware.com  Thu Feb 12 11:55:41 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 12 Feb 2015 11:55:41 -0500
Subject: [ITK-users] cannot acces virtual void itk::Rigid3DTransform<
 TScalar >::SetMatrix (const MatrixType & matrix,
 double tolerance ) from the Rigid3D transform class.
In-Reply-To: <1423482266729-7586888.post@n2.nabble.com>
References: <CALiCtPgvrEz-EiVMyctEeVZnHn-LoE9WMAKPdbzO6-9HjFYAUQ@mail.gmail.com>
 <CALzTN-Rtfn0HprHA+A=ZYXyvRHcx=3DUVZyZYcS6vo1KgCZ4nQ@mail.gmail.com>
 <1423482266729-7586888.post@n2.nabble.com>
Message-ID: <CALzTN-QtTHDxHsqyTcZsy41GzTP9aJZjWqmrzrYpOBsqbpUZqA@mail.gmail.com>

Hi Yago,

The VersorRigid3DTransform [1] may work.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1VersorRigid3DTransform.html

On Mon, Feb 9, 2015 at 6:44 AM, yagoDiez <yagodiezdonoso at gmail.com> wrote:
> Hi Matt,
>
> Thanks for pointing this out, I migrated to the latest (4.7) version and it
> works now.
>
> While migrating I encountered a new problem (rigid3D translation is sort of
> deprecated now). More information here:
>
> http://itk-insight-users.2283740.n2.nabble.com/Rigid3DTransform-make-error-td7160305.html#a7586887
>
> I had to resort to using an "intermediate itkv3 rigid transformation class".
> It does work but I am not sure it is a "lasting" solution.
>
> Does anybody know which class is better for my original problem:
>
> - I have a previously computed rotation matrix which I want to store in a
> format that itk can use.
> - Consequently, I am pretty sure that I want to use the setMatrix method
> (ideally with the possibility to specify a tolerance).
>
> Thanks!
> Yago
>
>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-cannot-acces-virtual-void-itk-Rigid3DTransform-TScalar-SetMatrix-const-MatrixType-matrix-d-tp7586880p7586888.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

From davis.vigneault at gmail.com  Fri Feb 13 07:14:17 2015
From: davis.vigneault at gmail.com (DVigneault)
Date: Fri, 13 Feb 2015 05:14:17 -0700 (MST)
Subject: [ITK-users] How to compile a new module inside the ITK build tree?
Message-ID: <1423829657975-35242.post@n7.nabble.com>

All--

Two related questions concerning development of an external module.

1.  How can I compile a single (external) module, rather than all of ITK? 
The module template for insight submission [1] states "[n]ow you could
compile the new module inside your ITK build tree," which suggests to me
that this is possible, but I'm not sure how to go about it.
2.  It is possible to build tests for one module only?  The closest thread I
was able to find [2] is useful for running individual tests after they are
built, and the wiki page on Modularization [3] didn't specifically discuss
testing.

Thanks in advance,

--Davis

[1]
https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/tree/ModularTemplate/Source
[2] http://itk-users.7.n7.nabble.com/run-test-manually-td32868.html
[3]
http://www.itk.org/Wiki/ITK/Release_4/Modularization/Configure_and_build_ITK



--
View this message in context: http://itk-users.7.n7.nabble.com/How-to-compile-a-new-module-inside-the-ITK-build-tree-tp35242.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From matimontg at gmail.com  Fri Feb 13 07:33:53 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Fri, 13 Feb 2015 09:33:53 -0300
Subject: [ITK-users] Evaluate results of registration
Message-ID: <CAKKNfuKq5_wESFhyRXHLbVRaPzwsTp3XJ5O0s_1G4K_wBoyWgg@mail.gmail.com>

Hi,

I'm using a check-board output (CheckerBoardImageFilter) to evaluate the
results of a CT/RM registration, now I would like to write something where
I could change the WL WC of the 2 images independently to really make sure
the registration is right; I guess is not possible with ITK itself and I
need to write some code for visualizing the CT and the RM and then change
window levels independently, am I right?

Thank you,

Matias.
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From blowekamp at mail.nih.gov  Fri Feb 13 07:34:16 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 13 Feb 2015 07:34:16 -0500
Subject: [ITK-users] How to compile a new module inside the ITK build
	tree?
In-Reply-To: <1423829657975-35242.post@n7.nabble.com>
References: <1423829657975-35242.post@n7.nabble.com>
Message-ID: <078030B2-B445-47C5-BABC-FE9E8B7D2675@mail.nih.gov>

Hello Davis,

1. Currently you must build a module inside of ITK, it can't be build separately. This is a feature on my wish list too. However, most of the ITK modules I have written don't actually have a compiled library. So use the module in other projects I have added the ITK module as a git submodule and just included the include directory. While this doesn't build testing it does work OK for using the classes from the ITK module in another project.
2.  I assume you are using make. Type running "make help"; this will list all the target in the make file. There should be one call "YourModule-all" this will build the module and tests.

Brad

On Feb 13, 2015, at 7:14 AM, DVigneault <davis.vigneault at gmail.com> wrote:

> All--
> 
> Two related questions concerning development of an external module.
> 
> 1.  How can I compile a single (external) module, rather than all of ITK? 
> The module template for insight submission [1] states "[n]ow you could
> compile the new module inside your ITK build tree," which suggests to me
> that this is possible, but I'm not sure how to go about it.
> 2.  It is possible to build tests for one module only?  The closest thread I
> was able to find [2] is useful for running individual tests after they are
> built, and the wiki page on Modularization [3] didn't specifically discuss
> testing.
> 
> Thanks in advance,
> 
> --Davis
> 
> [1]
> https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/tree/ModularTemplate/Source
> [2] http://itk-users.7.n7.nabble.com/run-test-manually-td32868.html
> [3]
> http://www.itk.org/Wiki/ITK/Release_4/Modularization/Configure_and_build_ITK
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/How-to-compile-a-new-module-inside-the-ITK-build-tree-tp35242.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


From matt.mccormick at kitware.com  Fri Feb 13 15:26:11 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 13 Feb 2015 15:26:11 -0500
Subject: [ITK-users] Gerrit to GitHub/OAuth email update instructions
Message-ID: <CALzTN-RySCpYj4_AdUJcYGXT9KhgfHKS+cfs5nHrGxAcGNTXuQ@mail.gmail.com>

Hi,

We will be soon be updating our Gerrit instance [1] to support GitHub
/ OAuth authentication instead of the OpenID based authentication,
which is no longer supported.

Account migration will occur by matching your currently registered
Gerrit email with an email registered on your GitHub account.
However, if you have multiple Gerrit accounts that match GitHub
emails, ambiguity occurs. Only one of the Gerrit  accounts can use
GitHub / OAuth authentication.

Please log into Gerrit [1] and ensure that the email address
associated with your GitHub account is registered, and is only
registered, with your desired Gerrit account.

Login -> Settings -> Identities


Select any email addresses that need to be deleted with the checkbox,
and hit the ?Delete? button.  Once deleted, the checkbox will no
longer be available.


Thanks,
Matt

[1] http://review.source.kitware.com

From matt.mccormick at kitware.com  Fri Feb 13 15:31:22 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 13 Feb 2015 15:31:22 -0500
Subject: [ITK-users] Evaluate results of registration
In-Reply-To: <CAKKNfuKq5_wESFhyRXHLbVRaPzwsTp3XJ5O0s_1G4K_wBoyWgg@mail.gmail.com>
References: <CAKKNfuKq5_wESFhyRXHLbVRaPzwsTp3XJ5O0s_1G4K_wBoyWgg@mail.gmail.com>
Message-ID: <CALzTN-S09-Qgm76PShexJEN7TZDC7Zo8xHTsQz+8gD-HfyPBgQ@mail.gmail.com>

Hi Matias,

Yes, it is possible to get the intensities on similar scales with the
RescaleIntensityImageFilter [1] or the IntensityWindowingImageFilter
[2] before passing into the CheckerBoardImageFilter.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1RescaleIntensityImageFilter.html

[2] http://www.itk.org/Doxygen316/html/classitk_1_1RescaleIntensityImageFilter.htmlhttp://www.itk.org/Doxygen316/html/classitk_1_1RescaleIntensityImageFilter.html

On Fri, Feb 13, 2015 at 7:33 AM, Matias Montroull <matimontg at gmail.com> wrote:
> Hi,
>
> I'm using a check-board output (CheckerBoardImageFilter) to evaluate the
> results of a CT/RM registration, now I would like to write something where I
> could change the WL WC of the 2 images independently to really make sure the
> registration is right; I guess is not possible with ITK itself and I need to
> write some code for visualizing the CT and the RM and then change window
> levels independently, am I right?
>
> Thank you,
>
> Matias.
>
> _____________________________________
> 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 matt.mccormick at kitware.com  Fri Feb 13 15:37:48 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 13 Feb 2015 15:37:48 -0500
Subject: [ITK-users] How to compile a new module inside the ITK build
	tree?
In-Reply-To: <078030B2-B445-47C5-BABC-FE9E8B7D2675@mail.nih.gov>
References: <1423829657975-35242.post@n7.nabble.com>
 <078030B2-B445-47C5-BABC-FE9E8B7D2675@mail.nih.gov>
Message-ID: <CALzTN-SpUcA7xsfQQmBLu86mUa3iLvMfgpQ9Dhg4E6M_eb0Z7Q@mail.gmail.com>

Hi,

While it is true that a module can't be built out of ITK (there are
some features from VTK modularization that could be ported here), it
is possible to build just a module and its dependencies.

Clone or symlink the module repository in the

  Modules/External directory.

Enable the module in your CMake configuration -- it should be a
boolean variable name Module_<mymodulename>.  This will build the
given module and all its dependencies.  To not build all the other
modules, turn BUILD_DEFAULT_MODULES to OFF.

There are some more tips on module enablement in the ITK Software Guide.

HTH,
Matt


On Fri, Feb 13, 2015 at 7:34 AM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> Hello Davis,
>
> 1. Currently you must build a module inside of ITK, it can't be build separately. This is a feature on my wish list too. However, most of the ITK modules I have written don't actually have a compiled library. So use the module in other projects I have added the ITK module as a git submodule and just included the include directory. While this doesn't build testing it does work OK for using the classes from the ITK module in another project.
> 2.  I assume you are using make. Type running "make help"; this will list all the target in the make file. There should be one call "YourModule-all" this will build the module and tests.
>
> Brad
>
> On Feb 13, 2015, at 7:14 AM, DVigneault <davis.vigneault at gmail.com> wrote:
>
>> All--
>>
>> Two related questions concerning development of an external module.
>>
>> 1.  How can I compile a single (external) module, rather than all of ITK?
>> The module template for insight submission [1] states "[n]ow you could
>> compile the new module inside your ITK build tree," which suggests to me
>> that this is possible, but I'm not sure how to go about it.
>> 2.  It is possible to build tests for one module only?  The closest thread I
>> was able to find [2] is useful for running individual tests after they are
>> built, and the wiki page on Modularization [3] didn't specifically discuss
>> testing.
>>
>> Thanks in advance,
>>
>> --Davis
>>
>> [1]
>> https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/tree/ModularTemplate/Source
>> [2] http://itk-users.7.n7.nabble.com/run-test-manually-td32868.html
>> [3]
>> http://www.itk.org/Wiki/ITK/Release_4/Modularization/Configure_and_build_ITK
>>
>>
>>
>> --
>> View this message in context: http://itk-users.7.n7.nabble.com/How-to-compile-a-new-module-inside-the-ITK-build-tree-tp35242.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
>
> _____________________________________
> 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 lasso at queensu.ca  Fri Feb 13 16:41:08 2015
From: lasso at queensu.ca (Andras Lasso)
Date: Fri, 13 Feb 2015 21:41:08 +0000
Subject: [ITK-users] [ITK]  Evaluate results of registration
In-Reply-To: <CALzTN-S09-Qgm76PShexJEN7TZDC7Zo8xHTsQz+8gD-HfyPBgQ@mail.gmail.com>
References: <CAKKNfuKq5_wESFhyRXHLbVRaPzwsTp3XJ5O0s_1G4K_wBoyWgg@mail.gmail.com>
 <CALzTN-S09-Qgm76PShexJEN7TZDC7Zo8xHTsQz+8gD-HfyPBgQ@mail.gmail.com>
Message-ID: <B6FC5543F5C41E479B8B89158B0C58FF31EBE7E4@QU-MBX02-PRD.AD.QUEENSU.CA>

Hi Matias,

Checkerboard pattern image is easy to generate but conveys very limited information while taking up a lot of space. The main issue is that you can only see displacement (residual registration error) along gridlines, but only at those points where a linear image feature (for example, an organ contour) crosses a gridline. So, in an entire image you can estimate the displacement only at a couple of relevant points. Using a more dense grid does not help much, because it makes image features harder to recognize.

I would suggest the following representation instead:

1. Show only the fixed image with the following information overlaid (in one or more images)
- contours segmented on the moving image with/without registration: this allows evaluation of displacement along the entire segmented contour, not just at a few points; the segmentation can be also used for quantitative evaluation (e.g., Hausdorff distance)
- vector field of the registration transform (shown as arrows, distorted grid, etc.): this is important because very often registration at the contours look perfect but in areas where the image gradients are smaller the registration transform may become very irregular

2. Visualize the vector field of the transformation (with arrows or distorted grid) in 3D: this allows the evaluation of how realistic the computed displacements are

These visual representations have not been very easy to generate in the past but since we added full support of real-time visualization of non-linear transforms to 3D Slicer, this should not be a problem anymore. Slicer can read ITK transforms (even composite transforms), concatenate them, invert them, and apply them to any 3D volume, surface mesh, point cloud, etc. and visualize them in 2D and 3D. See some example visualizations here: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms. 

Andras

-----Original Message-----
From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt McCormick
Sent: Friday, February 13, 2015 3:31 PM
To: Matias Montroull
Cc: insight-users at itk.org Users
Subject: Re: [ITK] [ITK-users] Evaluate results of registration

Hi Matias,

Yes, it is possible to get the intensities on similar scales with the RescaleIntensityImageFilter [1] or the IntensityWindowingImageFilter [2] before passing into the CheckerBoardImageFilter.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1RescaleIntensityImageFilter.html

[2] http://www.itk.org/Doxygen316/html/classitk_1_1RescaleIntensityImageFilter.htmlhttp://www.itk.org/Doxygen316/html/classitk_1_1RescaleIntensityImageFilter.html

On Fri, Feb 13, 2015 at 7:33 AM, Matias Montroull <matimontg at gmail.com> wrote:
> Hi,
>
> I'm using a check-board output (CheckerBoardImageFilter) to evaluate 
> the results of a CT/RM registration, now I would like to write 
> something where I could change the WL WC of the 2 images independently 
> to really make sure the registration is right; I guess is not possible 
> with ITK itself and I need to write some code for visualizing the CT 
> and the RM and then change window levels independently, am I right?
>
> Thank you,
>
> Matias.
>
> _____________________________________
> 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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http://public.kitware.com/mailman/listinfo/community

From matimontg at gmail.com  Sat Feb 14 08:27:00 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Sat, 14 Feb 2015 10:27:00 -0300
Subject: [ITK-users] [ITK]  Evaluate results of registration
In-Reply-To: <B6FC5543F5C41E479B8B89158B0C58FF31EBE7E4@QU-MBX02-PRD.AD.QUEENSU.CA>
References: <CAKKNfuKq5_wESFhyRXHLbVRaPzwsTp3XJ5O0s_1G4K_wBoyWgg@mail.gmail.com>
 <CALzTN-S09-Qgm76PShexJEN7TZDC7Zo8xHTsQz+8gD-HfyPBgQ@mail.gmail.com>
 <B6FC5543F5C41E479B8B89158B0C58FF31EBE7E4@QU-MBX02-PRD.AD.QUEENSU.CA>
Message-ID: <CAKKNfuL1vL9Rthh5F=ApHzHPUkxZj4X44_gs6j7h1My0w6tdSg@mail.gmail.com>

Thanks all for your answers, much appreciated, I will follow your
suggestions and learn in the process, thanks again.

Matias.

On Fri, Feb 13, 2015 at 6:41 PM, Andras Lasso <lasso at queensu.ca> wrote:

> Hi Matias,
>
> Checkerboard pattern image is easy to generate but conveys very limited
> information while taking up a lot of space. The main issue is that you can
> only see displacement (residual registration error) along gridlines, but
> only at those points where a linear image feature (for example, an organ
> contour) crosses a gridline. So, in an entire image you can estimate the
> displacement only at a couple of relevant points. Using a more dense grid
> does not help much, because it makes image features harder to recognize.
>
> I would suggest the following representation instead:
>
> 1. Show only the fixed image with the following information overlaid (in
> one or more images)
> - contours segmented on the moving image with/without registration: this
> allows evaluation of displacement along the entire segmented contour, not
> just at a few points; the segmentation can be also used for quantitative
> evaluation (e.g., Hausdorff distance)
> - vector field of the registration transform (shown as arrows, distorted
> grid, etc.): this is important because very often registration at the
> contours look perfect but in areas where the image gradients are smaller
> the registration transform may become very irregular
>
> 2. Visualize the vector field of the transformation (with arrows or
> distorted grid) in 3D: this allows the evaluation of how realistic the
> computed displacements are
>
> These visual representations have not been very easy to generate in the
> past but since we added full support of real-time visualization of
> non-linear transforms to 3D Slicer, this should not be a problem anymore.
> Slicer can read ITK transforms (even composite transforms), concatenate
> them, invert them, and apply them to any 3D volume, surface mesh, point
> cloud, etc. and visualize them in 2D and 3D. See some example
> visualizations here:
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms
> .
>
> Andras
>
> -----Original Message-----
> From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt
> McCormick
> Sent: Friday, February 13, 2015 3:31 PM
> To: Matias Montroull
> Cc: insight-users at itk.org Users
> Subject: Re: [ITK] [ITK-users] Evaluate results of registration
>
> Hi Matias,
>
> Yes, it is possible to get the intensities on similar scales with the
> RescaleIntensityImageFilter [1] or the IntensityWindowingImageFilter [2]
> before passing into the CheckerBoardImageFilter.
>
> HTH,
> Matt
>
> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1RescaleIntensityImageFilter.html
>
> [2]
> http://www.itk.org/Doxygen316/html/classitk_1_1RescaleIntensityImageFilter.htmlhttp://www.itk.org/Doxygen316/html/classitk_1_1RescaleIntensityImageFilter.html
>
> On Fri, Feb 13, 2015 at 7:33 AM, Matias Montroull <matimontg at gmail.com>
> wrote:
> > Hi,
> >
> > I'm using a check-board output (CheckerBoardImageFilter) to evaluate
> > the results of a CT/RM registration, now I would like to write
> > something where I could change the WL WC of the 2 images independently
> > to really make sure the registration is right; I guess is not possible
> > with ITK itself and I need to write some code for visualizing the CT
> > and the RM and then change window levels independently, am I right?
> >
> > Thank you,
> >
> > Matias.
> >
> > _____________________________________
> > 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
>
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From grothausmann.roman at mh-hannover.de  Mon Feb 16 04:28:14 2015
From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann)
Date: Mon, 16 Feb 2015 10:28:14 +0100
Subject: [ITK-users] [ITK] How to make ITK-binaries NOT ignore kernel
 out of memory messages?
In-Reply-To: <53C678BD.2040908@mh-hannover.de>
References: <53917A66.2060402@mh-hannover.de>	<CABAUzPrPjJj3h3vtnJs2PBd52PfUxYJXUojyt6V0UUfzUFYhNA@mail.gmail.com>	<53A80327.9050701@mh-hannover.de>
 <CALzTN-QZzjUdYmREq__vdV1diBZbY3gvZ+zEqZwdT7t7KKTk5Q@mail.gmail.com>
 <53C678BD.2040908@mh-hannover.de>
Message-ID: <54E1B82E.7030908@mh-hannover.de>

Dear mailing list members,


After much trial and error I now found a solution or workaround for the afore 
mentioned problem.

On our imaging server with a Debian7, 12*2 cores (two Intel Xeon CPU E5-2630L), 
256GB RAM, no SWAP loaded and the default Debian7-kernel, it seems that the 
oom-killer heuristics select the wrong processes for the oom-killer to end. 
Concluded, because setting:

echo 0 > /proc/sys/vm/oom_kill_allocating_task #choose process by heuristics, 
the default

makes test programs such as:

loop-calloc #from 
http://www.linuxdevcenter.com/pub/a/linux/2006/11/30/linux-out-of-memory.html

to crash our server, likely due to thrashing. Setting:

echo 1 > /proc/sys/vm/oom_kill_allocating_task #kill process causing oom

yields the expected behaviour that the kernel kills (running) process seemingly 
at random, BUT at least finally kills the "rogue memory-hogging task" which was 
not the case (even after days) when the heuristic was used on our server.
As the heuristic works fine on e.g. a simple desktop PC (same Debian7, AMD 
FX-4100 Quad-Core, 8GB RAM, no SWAP loaded and the default Debian7-kernel) I 
suspect that either the many CPUs or the much RAM cause the problem, possibly 
the heuristic picks the kswapd (even turning up in top although no swap was 
loaded and echo 0 > /proc/sys/vm/swappiness) to be killed causing a new kswapd 
to be started by the kernel an so on.
I did not test what is the critical # of CPUs or # of RAM (or perhaps 
hyper-threading) that causes the problem. Possibly, this would involve removing 
CPUs or RAM boards (or disabling hyperthreading in EFI) from our server, or 
would there be an easier way using e.g. kernel parameters?

Disabling overcommiting
echo 2 > /proc/sys/vm/overcommit_memory
prevented thrashing too, but is not needed with vm.oom_kill_allocating_task= 1

Our server now configured with:
echo "vm.oom_kill_allocating_task = 1" >> /etc/sysctl.conf
Has not crashed since then, not even when running any of the test programs that 
used to crash it.

By the way, Luis' test program posted before did not crash the server even 
before the reconfiguration and always work as expected on both the server and 
the desktop PC. Possibly it was allocating bigger chunks of memory such that 
kswapd was not running as hard as with smaller chunks and therefore was not 
picked by the oom-killer heuristics.

Any comments or other explanations welcome.

Regards,
Roman


On 16/07/14 15:06, Dr. Roman Grothausmann wrote:
> Hi Matt,
>
>
> Many thanks for Your reply. I'll check if ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
> prevents the problems. Although I'd be astonished if it does because
> BinaryMask3DMeshSource seems to use only one core anyway.
>
> Thanks again for Your help
> Roman
>
> On 15/07/14 02:55, Matt McCormick wrote:
>> Hi Roman,
>>
>> The CMake configuration variable:
>>
>>    ITK_COMPUTER_MEMORY_SIZE
>>
>> is only used to choose which unit tests to run, and has no effect on
>> your program.
>>
>>
>> It may be worth a try to run
>>
>>    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
>>
>> before starting your program on the server to see the effect.  It is
>> possible that too many threads or being spawned or that the amount of
>> memory consumed is scaling (poorly) with the number of threads used.
>>
>> Hope this helps,
>> Matt
>>
>> On Mon, Jun 23, 2014 at 6:36 AM, Dr. Roman Grothausmann
>> <grothausmann.roman at mh-hannover.de> wrote:
>>> Dear Luis,
>>>
>>>
>>> Many thanks for Your reply. It took me some time to reproduce the problem,
>>> because Your test program works as expected on our server:
>>>
>>> ~$ ~/itk/simple/build_itk-4.5.1/memtest_01 1000
>>> ITK Hello World !
>>>
>>> ~$ ~/itk/simple/build_itk-4.5.1/memtest_01 10000
>>> /opt/itk-4.5.1/include/ITK-4.5/itkImportImageContainer.hxx:192:
>>>
>>> Failed to allocate memory for image.
>>>
>>> One program of mine for which the problem exists is below. The problem
>>> occurs when BinaryMask3DMeshSource acquires more memory after running for
>>> some minutes. The very strange thing to me is, that the program is killed by
>>> the kernel as expected on my desktop PC:
>>>
>>> ~/itk/simple/build_itk4_pc3G48243/euler-characteristic_01 13-511_EAA_ot.mha
>>> 255
>>> component type is: unsigned_char
>>> numDimensions: 3
>>> component size: 1
>>> pixel type (string): scalar
>>> pixel type: 1
>>> _________________________
>>>
>>> Executing ImageFileReader  done. Took 2.78 seconds.
>>> Executing BinaryMask3DMeshSource Killed
>>>
>>>
>>> The header of 13-511_EAA_ot.mha:
>>>
>>> ObjectType = Image
>>> NDims = 3
>>> BinaryData = True
>>> BinaryDataByteOrderMSB = False
>>> CompressedData = True
>>> CompressedDataSize = 20474538
>>> TransformMatrix = 1 0 0 0 1 0 0 0 1
>>> Offset = 0 0 0
>>> CenterOfRotation = 0 0 0
>>> AnatomicalOrientation = RAI
>>> ElementSpacing = 1 1 1
>>> DimSize = 998 998 1034
>>> ElementType = MET_UCHAR
>>> ElementDataFile = LOCAL
>>>
>>>
>>> However on the server it is not terminated when the RAM runs out, instead
>>> many processes go nuts that had been mostly sleeping and finally the system
>>> does not respond any more at all and a cold start is necessary. The
>>> itk-4.5.1 is configured on the server with (see attached
>>> CMakeCache_itk-4.5.1.txt):
>>>
>>> ITK_COMPUTER_MEMORY_SIZE  190
>>>
>>> The server has 256GB of RAM an no Swap enabled:
>>>
>>> free
>>>               total       used       free     shared    buffers     cached
>>> Mem:     264498496    1341020  263157476          0     285760     289120
>>> -/+ buffers/cache:     766140  263732356
>>> Swap:            0          0          0
>>>
>>>
>>> Has 12x2 Intel(R) Xeon(R) CPUs:
>>>
>>> cat /proc/cpuinfo
>>> processor       : 0
>>> vendor_id       : GenuineIntel
>>> cpu family      : 6
>>> model           : 45
>>> model name      : Intel(R) Xeon(R) CPU E5-2630L 0 @ 2.00GHz
>>> stepping        : 7
>>> microcode       : 0x710
>>> cpu MHz         : 1200.000
>>> cache size      : 15360 KB
>>> physical id     : 0
>>> siblings        : 12
>>> core id         : 0
>>> cpu cores       : 6
>>> apicid          : 0
>>> initial apicid  : 0
>>> fpu             : yes
>>> fpu_exception   : yes
>>> cpuid level     : 13
>>> wp              : yes
>>> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
>>> cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx
>>> pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology
>>> nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2
>>> ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer
>>> aes xsave avx lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi
>>> flexpriority ept vpid
>>> bogomips        : 4000.56
>>> clflush size    : 64
>>> cache_alignment : 64
>>> address sizes   : 46 bits physical, 48 bits virtual
>>> power management:
>>> .
>>> .
>>> .
>>>
>>>
>>> The server runs a Debian Wheezy (7.2):
>>> uname -a
>>> Linux img1-serv 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3+deb7u2 x86_64 GNU/Linux
>>>
>>> My desktop PC has the same Debian (also same update state):
>>> uname -a
>>> Linux pc3G48243 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3+deb7u2 x86_64 GNU/Linux
>>>
>>> free
>>>               total       used       free     shared    buffers     cached
>>> Mem:       8180356    1185364    6994992          0      23348     216084
>>> -/+ buffers/cache:     945932    7234424
>>> Swap:            0          0          0
>>>
>>>
>>> and 4 AMD FX(tm)-4100 Quad-Core Processors:
>>>
>>> cat /proc/cpuinfo
>>> processor       : 0
>>> vendor_id       : AuthenticAMD
>>> cpu family      : 21
>>> model           : 1
>>> model name      : AMD FX(tm)-4100 Quad-Core Processor
>>> stepping        : 2
>>> microcode       : 0x6000626
>>> cpu MHz         : 1400.000
>>> cache size      : 2048 KB
>>> physical id     : 0
>>> siblings        : 4
>>> core id         : 0
>>> cpu cores       : 2
>>> apicid          : 16
>>> initial apicid  : 0
>>> fpu             : yes
>>> fpu_exception   : yes
>>> cpuid level     : 13
>>> wp              : yes
>>> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
>>> cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt
>>> pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc extd_apicid
>>> aperfmperf pni pclmulqdq monitor ssse3 cx16 sse4_1 sse4_2 popcnt aes xsave
>>> avx lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse
>>> 3dnowprefetch osvw ibs xop skinit wdt lwp fma4 nodeid_msr topoext
>>> perfctr_core arat cpb hw_pstate npt lbrv svm_lock nrip_save tsc_scale
>>> vmcb_clean flushbyasid decodeassists pausefilter pfthreshold
>>> bogomips        : 7233.41
>>> TLB size        : 1536 4K pages
>>> clflush size    : 64
>>> cache_alignment : 64
>>> address sizes   : 48 bits physical, 48 bits virtual
>>> power management: ts ttp tm 100mhzsteps hwpstate [9]
>>>
>>>
>>> Knowing now, that itk checks for available RAM, the only sources for this
>>> problem I can think of would be an odd configuration of ITK itself or its
>>> use in programs compiled on the server, or some configuration differences in
>>> the (Debian) system, or some hardware problem.
>>>
>>> Do You have any idea what it could be?
>>> Or do You have any suggestions how I should go on searching for the cause?
>>>
>>>
>>> Any help or hints are very much appriciated.
>>> Many thanks for Your help again!
>>>
>>> Roman
>>>
>>>
>>> _____________________________________________
>>>
>>>
>>>
>>> ////program to calculate the Euler characteristic of a binary image
>>> converted to itkQuadEdgeMesh
>>> ////THEREFORE does NOT take filled regions into account only covering
>>> surfaces!
>>> ////if fillings should be accounted use instead a vtk program taking 3D
>>> cells into account
>>>
>>>
>>>
>>> #include <itkImageFileReader.h>
>>> //#include <itkImage.h>
>>> #include <itkBinaryMask3DMeshSource.h> //itk marching cubes (mc) very slow
>>> and resource hungry :-(
>>> #include <itkQuadEdgeMeshTopologyChecker.h>
>>> #include <itkQuadEdgeMeshBoundaryEdgesMeshFunction.h>
>>>
>>>
>>>
>>> #include "itkFilterWatcher2.h"
>>>
>>>
>>>
>>>
>>> void dispatch_cT(itk::ImageIOBase::IOPixelType,
>>> itk::ImageIOBase::IOComponentType, size_t, int, char **);
>>>
>>> template<typename InputComponentType>
>>> void dispatch_pT(itk::ImageIOBase::IOPixelType pixelType, size_t, int, char
>>> **);
>>>
>>> template<typename InputComponentType, typename InputPixelType>
>>> void dispatch_D(size_t, int, char **);
>>>
>>> template<typename InputComponentType, typename InputPixelType, size_t
>>> Dimension>
>>> int DoIt(int, char *argv[]);
>>>
>>>
>>>
>>>
>>>
>>> template<typename InputComponentType, typename InputPixelType, size_t
>>> Dimension>
>>> int DoIt(int argc, char *argv[]){
>>>
>>>    typedef InputPixelType  OutputPixelType;
>>>
>>>    typedef itk::Image<InputPixelType, Dimension>  InputImageType;
>>>    typedef itk::Image<OutputPixelType, Dimension>  OutputImageType;
>>>
>>>
>>>    typedef itk::ImageFileReader<InputImageType> ReaderType;
>>>    typename ReaderType::Pointer reader = ReaderType::New();
>>>
>>>    reader->SetFileName(argv[1]);
>>>    FilterWatcher watcherI(reader, "reading");
>>>    watcherI.QuietOn();
>>>    watcherI.ReportTimeOn();
>>>    try
>>>      {
>>>        reader->Update();
>>>      }
>>>    catch (itk::ExceptionObject &ex)
>>>      {
>>>        if (!strcmp(ex.GetDescription(), "Filter does not have progress.")){
>>>        std::cerr << ex.GetDescription() << std::endl;
>>>        return EXIT_FAILURE;
>>>        }
>>>      }
>>>
>>>
>>>    typedef double        CoordType;
>>>
>>>    //typedef itk::Mesh<CoordType> MeshType;
>>>    typedef itk::QuadEdgeMesh<CoordType, Dimension> InputMeshType;
>>>
>>>    const InputPixelType isoValue= static_cast<InputPixelType>(atof(argv[2]));
>>>
>>>    typedef itk::BinaryMask3DMeshSource<InputImageType, InputMeshType>
>>> MeshSourceType;
>>>    typename MeshSourceType::Pointer meshSource = MeshSourceType::New();
>>>
>>>    meshSource->SetInput(reader->GetOutput());
>>>    meshSource->SetObjectValue(isoValue);
>>>
>>>    FilterWatcher watcher(meshSource, "BinaryMask3DMeshSource");
>>>    watcher.QuietOn();
>>>    watcher.ReportTimeOn();
>>>    try
>>>      {
>>>        meshSource->Update();
>>>      }
>>>    catch (itk::ExceptionObject &ex)
>>>      {
>>>        if (!strcmp(ex.GetDescription(), "Filter does not have progress.")){
>>>          std::cerr << ex.GetDescription() << std::endl;
>>>          return EXIT_FAILURE;
>>>        }
>>>      }
>>>
>>>
>>>    std::cout << "Nodes = " << meshSource->GetNumberOfNodes() << std::endl;
>>>    std::cout << "Cells = " << meshSource->GetNumberOfCells() << std::endl;
>>>
>>>    typename InputMeshType::Pointer mesh= meshSource->GetOutput();
>>>
>>>    //// check if meshSource can be represented as an itkQuadEdgeMesh
>>>    //// if BinaryMask3DMeshSource caps boundary surfaces this check is not
>>> necessary!
>>>
>>>    typedef itk::QuadEdgeMeshTopologyChecker<InputMeshType> TQEchecker;
>>>    typename TQEchecker::Pointer QEchecker = TQEchecker::New();
>>>    QEchecker->SetMesh(mesh);
>>>    std::cerr << "Executing
>>> QuadEdgeMeshTopologyChecker->ValidateEulerCharacteristic()";
>>>    if(!QEchecker->ValidateEulerCharacteristic()){
>>>      std::cerr << "Not a valid QuadEdgeMesh! Aborting." << std::endl;
>>>      return EXIT_FAILURE;
>>>    }
>>>    std::cerr << " done." << std::endl;
>>>
>>>    //// calc Euler characteristics \xi
>>>    //// For closed smooth manifolds, the Euler characteristic coincides with
>>> the Euler number:
>>> http://en.wikipedia.org/wiki/Euler_characteristic#Relations_to_other_invariants
>>>    //// general formula see:
>>> http://en.wikipedia.org/wiki/Genus_%28mathematics%29#Orientable_surface
>>>    ////
>>>    ////
>>>    ////
>>>    //// good QuadEdge explanation:
>>> http://www.cs.cmu.edu/afs/andrew/scs/cs/15-463/2001/pub/src/a2/quadedge.html
>>>    /// from itkQuadEdgeMeshTopologyChecker.hxx
>>>
>>>    typedef itk::QuadEdgeMeshBoundaryEdgesMeshFunction<InputMeshType>
>>> BoundaryEdges;
>>>
>>>    typename BoundaryEdges::Pointer boundaryEdges = BoundaryEdges::New();
>>>
>>>    // Number of USED points
>>>    typedef typename InputMeshType::PointIdentifier
>>> PointIdentifier;
>>>    std::cerr << "ComputeNumberOfPoints";
>>>    PointIdentifier numPoints = mesh->ComputeNumberOfPoints();
>>>    std::cerr << " done." << std::endl;
>>>    // Number of USED edges
>>>    typedef typename InputMeshType::CellIdentifier
>>> CellIdentifier;
>>>    std::cerr << "ComputeNumberOfEdges";
>>>    CellIdentifier numEdges  = mesh->ComputeNumberOfEdges();
>>>    std::cerr << " done." << std::endl;
>>>    // Number of USED faces
>>>    std::cerr << "ComputeNumberOfFaces";
>>>    CellIdentifier numFaces  = mesh->ComputeNumberOfFaces();
>>>    std::cerr << " done." << std::endl;
>>>    // Number of Boundaries
>>>    std::cerr << "ComputeNumberOfBoundaryEdges";
>>>    typename BoundaryEdges::OutputType
>>>      listOfBoundaries = boundaryEdges->Evaluate((*mesh));
>>>    std::cerr << " done." << std::endl;
>>>    CellIdentifier numBounds = listOfBoundaries->size();
>>>    delete listOfBoundaries;
>>>
>>>    /**
>>>     * Number of points
>>>     *
>>>     * There are two methods to get the number of points.
>>>     * 1. itk::QuadEdgeMesh::ComputeNumberOfPoints()
>>>     * 2. itk::Mesh::GetNumberOfPoints()
>>>     *
>>>     * As an itk::QuadEdgeMesh is an itk::Mesh by inheritance, the user
>>>     * can use both. 1. will returned the number of points actually
>>>     * used by at least one edge, while 2. will give you the number
>>>     * of points in the container. Number of unused points can be found
>>>     * by making the difference between the two values.
>>>     */
>>>    if(mesh->GetNumberOfPoints() != numPoints){
>>>      std::cerr << "There are isolated vertices! Aborting." << std::endl;
>>>      return EXIT_FAILURE;
>>>    }
>>>
>>>    // The euler formula states:
>>>    // numFaces - numEdges + numPoints == 2 - 2 * genus - numBounds == \xi
>>>    // hence 2 * genus= 2 - numBounds - numFaces + numEdges - numPoints must
>>> be an oddeven number.
>>>
>>>    typedef ::itk::OffsetValueType    OffsetValueType;
>>>
>>>    OffsetValueType xi=
>>>      + OffsetValueType(numFaces)
>>>      - OffsetValueType(numEdges)
>>>      + OffsetValueType(numPoints);
>>>
>>>    std::cout << "The Euler characteristic Xi is: " << xi << std::endl;
>>>
>>>    OffsetValueType twiceGenus=
>>>      + OffsetValueType(2) - OffsetValueType(numBounds)
>>>      - xi;
>>>
>>>    std::cout << "The genus is: " << twiceGenus/OffsetValueType(2) <<
>>> std::endl;
>>>
>>>    return EXIT_SUCCESS;
>>>
>>> }
>>>
>>>
>>> void dispatch_cT(itk::ImageIOBase::IOComponentType componentType,
>>> itk::ImageIOBase::IOPixelType pixelType, size_t dimensionType, int argc,
>>> char *argv[]){
>>>
>>>
>>> //http://www.itk.org/Doxygen45/html/classitk_1_1ImageIOBase.html#a8dc783055a0af6f0a5a26cb080feb178
>>>
>>>    //http://www.itk.org/Doxygen45/html/itkImageIOBase_8h_source.html#l00107
>>>    //IOComponentType: UNKNOWNCOMPONENTTYPE, UCHAR, CHAR, USHORT, SHORT, UINT,
>>> INT, ULONG, LONG, FLOAT, DOUBLE
>>>
>>>    switch (componentType){
>>>    case itk::ImageIOBase::UCHAR:{
>>>      typedef unsigned char InputComponentType;
>>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>>    }
>>>      break;
>>>    case itk::ImageIOBase::CHAR:{
>>>      typedef char InputComponentType;
>>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>>    }
>>>      break;
>>>    case itk::ImageIOBase::USHORT:{
>>>      typedef unsigned short InputComponentType;
>>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>>    }
>>>      break;
>>>    case itk::ImageIOBase::SHORT:{
>>>      typedef short InputComponentType;
>>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>>    }
>>>      break;
>>>    case itk::ImageIOBase::UINT:{
>>>      typedef unsigned int InputComponentType;
>>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>>    }
>>>      break;
>>>    case itk::ImageIOBase::INT:{
>>>      typedef int InputComponentType;
>>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>>    }
>>>      break;
>>>    // case itk::ImageIOBase::ULONG:{
>>>    //   typedef unsigned long InputComponentType;
>>>    //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
>>> argv);
>>>    // }
>>>    //   break;
>>>    // case itk::ImageIOBase::LONG:{
>>>    //   typedef long InputComponentType;
>>>    //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
>>> argv);
>>>    // }
>>>    //   break;
>>>    // case itk::ImageIOBase::FLOAT:{
>>>    //   typedef float InputComponentType;
>>>    //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
>>> argv);
>>>    // }
>>>    //   break;
>>>    // case itk::ImageIOBase::DOUBLE:{
>>>    //   typedef double InputComponentType;
>>>    //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
>>> argv);
>>>    // }
>>>    // break;
>>>    case itk::ImageIOBase::UNKNOWNCOMPONENTTYPE:
>>>    default:
>>>      std::cout << "unknown component type" << std::endl;
>>>      break;
>>>    }//switch
>>> }
>>>
>>> template<typename InputComponentType>
>>> void dispatch_pT(itk::ImageIOBase::IOPixelType pixelType, size_t
>>> dimensionType, int argc, char *argv[]){
>>>
>>>
>>> //http://www.itk.org/Doxygen45/html/classitk_1_1ImageIOBase.html#abd189f096c2a1b3ea559bc3e4849f658
>>>
>>>      //http://www.itk.org/Doxygen45/html/itkImageIOBase_8h_source.html#l00099
>>>      //IOPixelType:: UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR,
>>> POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D,
>>> COMPLEX, FIXEDARRAY, MATRIX
>>>
>>>    switch (pixelType){
>>>    case itk::ImageIOBase::SCALAR:{
>>>      typedef InputComponentType InputPixelType;
>>>      //typedef itk::SCALARPixel<InputComponentType> InputPixelType;
>>>      dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
>>> argv);
>>>    }
>>>      break;
>>>    // case itk::ImageIOBase::RGB:{
>>>    //   typedef itk::RGBPixel<InputComponentType> InputPixelType;
>>>    //   dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
>>> argv);
>>>    // }
>>>    //   break;
>>>    // case itk::ImageIOBase::RGBA:{
>>>    //   typedef itk::RGBAPixel<InputComponentType> InputPixelType;
>>>    //   dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
>>> argv);
>>>    // }
>>>    //   break;
>>>    // case itk::ImageIOBase::VECTOR:{
>>>    //   //typedef itk::VECTORPixel<InputComponentType> InputPixelType; //does
>>> not work!
>>>    //   typedef itk::VariableLengthVector<InputComponentType> InputPixelType;
>>>    //   dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
>>> argv);
>>>    // }
>>>    //   break;
>>>    case itk::ImageIOBase::UNKNOWNPIXELTYPE:
>>>    default:
>>>      std::cout << "unknown pixel type" << std::endl;
>>>      break;
>>>    }//switch
>>> }
>>>
>>>
>>> template<typename InputComponentType, typename InputPixelType>
>>> void dispatch_D(size_t dimensionType, int argc, char *argv[]){
>>>    switch (dimensionType){
>>>    // case 1:
>>>    //   DoIt<InputComponentType, InputPixelType, 1>(argc, argv);
>>>    //   break;
>>>    // case 2:
>>>    //   DoIt<InputComponentType, InputPixelType, 2>(argc, argv);
>>>    //   break;
>>>    case 3:
>>>      DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
>>>      break;
>>>    case 4:
>>>      DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
>>>      break;
>>>    case 5:
>>>      DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
>>>      break;
>>>    default:
>>>      std::cout << "Images of dimension " << dimensionType << " are not
>>> supported!" << std::endl;
>>>      break;
>>>    }
>>> }
>>>
>>>
>>>
>>> ////from
>>> http://itk-users.7.n7.nabble.com/Pad-image-with-0-but-keep-its-type-what-ever-it-is-td27442.html
>>>
>>> //namespace itk{
>>>    // Description:
>>>    // Get the PixelType and ComponentType from fileName
>>>
>>> void GetImageType (std::string fileName,
>>>      itk::ImageIOBase::IOPixelType &pixelType,
>>>      itk::ImageIOBase::IOComponentType &componentType,
>>>      size_t &dimensionType
>>>      //ImageIOBase::IODimensionType &dimensionType
>>>      ){
>>>      typedef itk::Image<unsigned char, 3> ImageType;
>>>      itk::ImageFileReader<ImageType>::Pointer imageReader=
>>> itk::ImageFileReader<ImageType>::New();
>>>      imageReader->SetFileName(fileName.c_str());
>>>      imageReader->UpdateOutputInformation();
>>>
>>>      pixelType = imageReader->GetImageIO()->GetPixelType();
>>>      componentType = imageReader->GetImageIO()->GetComponentType();
>>>      dimensionType= imageReader->GetImageIO()->GetNumberOfDimensions();
>>>
>>>      //std::cerr << "Pixel Type is " <<
>>> imageReader->GetImageIO()->GetComponentTypeAsString(pixelType) << std::endl;
>>>      std::cerr << "component type is: " <<
>>> imageReader->GetImageIO()->GetComponentTypeAsString(componentType) <<
>>> std::endl;
>>>      std::cerr << "numDimensions: " << dimensionType << std::endl;
>>>      std::cerr << "component size: " <<
>>> imageReader->GetImageIO()->GetComponentSize() << std::endl;
>>>      std::cerr << "pixel type (string): " <<
>>> imageReader->GetImageIO()->GetPixelTypeAsString(imageReader->GetImageIO()->GetPixelType())
>>>
>>> << std::endl;
>>>      std::cerr << "pixel type: " << pixelType << std::endl <<
>>> "_________________________"  << std::endl << std::endl;
>>>
>>>
>>>      }
>>>
>>>
>>>
>>> int main(int argc, char *argv[]){
>>>      if ( argc != 3 )
>>>          {
>>>          std::cerr << "Missing Parameters: "
>>>                    << argv[0]
>>>                    << " Input_Image"
>>>                    << " isoValue"
>>>                    << std::endl;
>>>
>>>          return EXIT_FAILURE;
>>>          }
>>>
>>>      std::string ifn = argv[1];
>>>      // std::string ofn = argv[2];
>>>      // int compress= atoi(argv[3]);
>>>
>>>      itk::ImageIOBase::IOPixelType pixelType;
>>>      typename itk::ImageIOBase::IOComponentType componentType;
>>>      //itk::ImageIOBase::IOComponentType componentType1;
>>>      //itk::ImageIOBase::IODimensionType dimensionType1;
>>>      size_t dimensionType;
>>>
>>>
>>>      try
>>>          {
>>>          GetImageType(argv[1], pixelType, componentType, dimensionType);
>>>
>>>          dispatch_cT(componentType, pixelType, dimensionType, argc, argv);
>>>          }//try
>>>      catch( itk::ExceptionObject &excep)
>>>          {
>>>          std::cerr << argv[0] << ": exception caught !" << std::endl;
>>>          std::cerr << excep << std::endl;
>>>          return EXIT_FAILURE;
>>>          }
>>>
>>>      return EXIT_SUCCESS;
>>>
>>>      }
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 08/06/14 15:51, Luis Ibanez wrote:
>>>>
>>>>
>>>> Roman,
>>>>
>>>>
>>>> Could you please share with the list an example
>>>> of a program where you are observing this behavior ?
>>>>
>>>> In particular, we would like to see if this is occurring with
>>>> Image filters, or rather with other types of ITK objects.
>>>>
>>>>
>>>>
>>>> The itk::Image does listen to the (potential) memory allocation messages
>>>> (that is, the bad_alloc exception).
>>>>
>>>>
>>>>
>>>> The itk::Image class uses a helper class to store the pixel data.
>>>>
>>>>
>>>>
>>>> This helper is the:
>>>>
>>>> itk::ImportImageContainer
>>>>
>>>>
>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkImportImageContainer.h
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> and its memory allocation is typically done in the AllocateElements()
>>>> function
>>>> in line:
>>>>
>>>>
>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkImportImageContainer.hxx#L173
>>>>
>>>>
>>>> the code looks like
>>>>
>>>>     TElement *data;
>>>>
>>>>     try
>>>>       {
>>>>       if ( UseDefaultConstructor )
>>>>         {
>>>>         data = new TElement[size](); //POD types initialized to 0, others
>>>> use
>>>> default constructor.
>>>>         }
>>>>       else
>>>>         {
>>>>         data = new TElement[size]; //Faster but uninitialized
>>>>         }
>>>>       }
>>>>     catch ( ... )
>>>>       {
>>>>       data = ITK_NULLPTR;
>>>>       }
>>>>     if ( !data )
>>>>       {
>>>>       // We cannot construct an error string here because we may be out
>>>>       // of memory.  Do not use the exception macro.
>>>>       throw MemoryAllocationError(__FILE__, __LINE__,
>>>>                                   "Failed to allocate memory for image.",
>>>>                                   ITK_LOCATION);
>>>>       }
>>>>     return data;
>>>>
>>>>
>>>>
>>>> As you can see, the case of exceptions is managed in that function.
>>>>
>>>>
>>>> Here is an example of a test program demonstrating that ITK image
>>>> will throw exceptions when allocating memory beyond limits.
>>>>
>>>>
>>>> #include "itkImage.h"
>>>> #include <iostream>
>>>>
>>>> int main(int argc, char * argv[] )
>>>> {
>>>>     if( argc < 2 )
>>>>       {
>>>>       std::cerr << "Missing arguments" << std::endl;
>>>>       return 1;
>>>>       }
>>>>
>>>>     typedef itk::Image< unsigned short, 3 > ImageType;
>>>>
>>>>     ImageType::Pointer image = ImageType::New();
>>>>
>>>>     ImageType::RegionType region;
>>>>     ImageType::SizeType size;
>>>>
>>>>     size_t side = atoi( argv[1] );
>>>>
>>>>     size[0] = side;
>>>>     size[1] = side;
>>>>     size[2] = side;
>>>>
>>>>     region.SetSize( size );
>>>>
>>>>     image->SetRegions( region );
>>>>
>>>>     try
>>>>       {
>>>>       image->Allocate();
>>>>       }
>>>>     catch( std::exception & excp )
>>>>       {
>>>>       std::cerr << excp.what() << std::endl;
>>>>       return 1;
>>>>       }
>>>>
>>>>     std::cout << "ITK Hello World !" << std::endl;
>>>>
>>>>     return 0;
>>>> }
>>>>
>>>>
>>>> and what happens when executing in an Ubuntu Linux machine with 32GB or
>>>> RAM
>>>>
>>>>
>>>> $ ./HelloWorld  1000
>>>> ITK Hello World !
>>>>
>>>>
>>>> $ ./HelloWorld  1000000
>>>>
>>>> /home/ibanez/src/ITK/Modules/Core/Common/include/itkImportImageContainer.hxx:199:
>>>>
>>>> Failed to allocate memory for image.
>>>>
>>>>
>>>>
>>>>
>>>> Please share with the list a minimal example of the problem you are
>>>> observing,
>>>> and in this way we will be able to help track the issue.
>>>>
>>>>
>>>>      Thanks
>>>>
>>>>
>>>>          Luis
>>>>
>>>>
>>>
>>> --
>>> Dr. Roman Grothausmann
>>>
>>> Tomographie und Digitale Bildverarbeitung
>>> Tomography and Digital Image Analysis
>>>
>>> Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
>>> Medizinische Hochschule Hannover
>>> Carl-Neuberg-Str. 1
>>> D-30625 Hannover
>>>
>>> Tel. +49 511 532-9574
>>>
>>> _____________________________________
>>> 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
>>>
>

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574

From l.onofri at outlook.com  Tue Feb 17 06:38:19 2015
From: l.onofri at outlook.com (Leonardo Onofri)
Date: Tue, 17 Feb 2015 12:38:19 +0100
Subject: [ITK-users] ICB BSpline
Message-ID: <DUB122-W42B63B4C37C51BDC617A918D2F0@phx.gbl>

Dear users, I would like to use ICP registration with BSpline transform. The problem is that I cannot use the LBFGS optimizer since I get this error: 'void itk::PointSetToPointSetRegistrationMethod<PointSetType,PointSetType>::SetOptimizer(itk::PointSetToPointSetRegistrationMethod<PointSetType,PointSetType>::OptimizerType *)' : cannot convert argument 1 from 'itk::LBFGSOptimizer::Pointer' to 'itk::PointSetToPointSetRegistrationMethod<PointSetType,PointSetType>::OptimizerType *' Regards, 		 	   		  
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From matt.mccormick at kitware.com  Tue Feb 17 11:16:46 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 17 Feb 2015 11:16:46 -0500
Subject: [ITK-users] ICB BSpline
In-Reply-To: <DUB122-W42B63B4C37C51BDC617A918D2F0@phx.gbl>
References: <DUB122-W42B63B4C37C51BDC617A918D2F0@phx.gbl>
Message-ID: <CALzTN-T3XnR7VLO-KzB3AtTYK-UmQ_Nq_topp-erd-aCg5LkHw@mail.gmail.com>

Hi Leonardo,

When investigating the PointSetToPointSetRegistrationMethod [1],
doxygen or the source code shows that OptimizerType
MultipleValuedNonLinearOptimizer [2], and LBFGS does not inherit from
MultipleValuedNonLinearOptimizer [3] (click the Inheritance diagram
tab).

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1PointSetToPointSetRegistrationMethod.html

[2] http://www.itk.org/Doxygen/html/classitk_1_1MultipleValuedNonLinearOptimizer.html

[3] http://www.itk.org/Doxygen/html/classitk_1_1LBFGSOptimizer.html

On Tue, Feb 17, 2015 at 6:38 AM, Leonardo Onofri <l.onofri at outlook.com> wrote:
> Dear users,
>
>
>
> I would like to use ICP registration with BSpline transform.
>
>
>
> The problem is that I cannot use the LBFGS optimizer since I get this error:
>
>
>
> 'void
> itk::PointSetToPointSetRegistrationMethod<PointSetType,PointSetType>::SetOptimizer(itk::PointSetToPointSetRegistrationMethod<PointSetType,PointSetType>::OptimizerType
> *)' : cannot convert argument 1 from 'itk::LBFGSOptimizer::Pointer' to
> 'itk::PointSetToPointSetRegistrationMethod<PointSetType,PointSetType>::OptimizerType
> *'
>
>
>
> Regards,
>
>
> _____________________________________
> 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 franciscolopezdelafranca at gmail.com  Wed Feb 18 06:17:28 2015
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Wed, 18 Feb 2015 12:17:28 +0100
Subject: [ITK-users] Integration ITK with Qt Creator
Message-ID: <CAJqi3E+p0eRdMdJ+qDj=xMgKw6gG+QWgpQuaK6HYqNgnShvAwQ@mail.gmail.com>

Hi.
I've been using recently ITK but with no IDE, and I've been recommended to
use Qt platform.
I've downloaded Qt Creator but I don?t find the documentation and the way
to integrate ITK with it.

That's why I post this message, in order to know if anyone has any
reference or guide explaining how to do it.

Thank you very much in advance.

Kind regards,
/Francisco
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From jhlegarreta at vicomtech.org  Wed Feb 18 06:40:04 2015
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Wed, 18 Feb 2015 12:40:04 +0100
Subject: [ITK-users] Integration ITK with Qt Creator
In-Reply-To: <CAJqi3E+p0eRdMdJ+qDj=xMgKw6gG+QWgpQuaK6HYqNgnShvAwQ@mail.gmail.com>
References: <CAJqi3E+p0eRdMdJ+qDj=xMgKw6gG+QWgpQuaK6HYqNgnShvAwQ@mail.gmail.com>
Message-ID: <CAAKhGh9NvbE8UTFL4AyrrwOrRg8zYbTfbM=sF92_kxT87q4V3g@mail.gmail.com>

Dear Francisco,
I assume you mean "with no GUI" when you say "with no IDE".

Note that Qt Creator is just a tool of Qt to facilitate the task of
creating GUIs, but in order to actually have a GUI for your application,
you will need to download Qt itself [1]. You can download the binaries, and
thus you can avoid any complication derived from building the sources.

Assuming you are using CMake to generate your project, in order to build
your application with Qt as the GUI library, you should include Qt among
the libraries to look for and link with in your CMakeLists [2].

HTH,
JON HAITZ


[1] https://qt-project.org/
[2] http://www.cmake.org/Wiki/CMake/Tutorials/Qt



On 18 February 2015 at 12:17, Francisco Lopez de la Franca <
franciscolopezdelafranca at gmail.com> wrote:

> Hi.
> I've been using recently ITK but with no IDE, and I've been recommended to
> use Qt platform.
> I've downloaded Qt Creator but I don?t find the documentation and the way
> to integrate ITK with it.
>
> That's why I post this message, in order to know if anyone has any
> reference or guide explaining how to do it.
>
> Thank you very much in advance.
>
> Kind regards,
> /Francisco
>
> _____________________________________
> 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 matt.mccormick at kitware.com  Wed Feb 18 10:38:20 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 18 Feb 2015 10:38:20 -0500
Subject: [ITK-users] ICB BSpline
In-Reply-To: <DUB122-W40A68E6BF7D05D930D2DE08D2C0@phx.gbl>
References: <DUB122-W42B63B4C37C51BDC617A918D2F0@phx.gbl>
 <CALzTN-T3XnR7VLO-KzB3AtTYK-UmQ_Nq_topp-erd-aCg5LkHw@mail.gmail.com>
 <DUB122-W40A68E6BF7D05D930D2DE08D2C0@phx.gbl>
Message-ID: <CALzTN-SxnH7U_i=Pd=bqcGioZs+b3b1qMaHwBNsy9wcF-vJRvw@mail.gmail.com>

Hi Leonardo,

Yes, this means you cannot use the LBFGS optimizer.

Examing the doxygen inheritance diagram from the
MultipleValuedNonLinearOptimizer class, it shows that the
LevenbergMarquardtOptimizer or the CumulativeGaussianOptimizer.

HTH,
Matt

On Wed, Feb 18, 2015 at 5:20 AM, Leonardo Onofri <l.onofri at outlook.com> wrote:
> Hi Matt,
>
> Thank you for your answer.
>
> This means that I cannot use the LBFGS optimizer, right?
>
> If so, which are good alternatives?
>
> Regards,
> Leonardo
>
>> Date: Tue, 17 Feb 2015 11:16:46 -0500
>> Subject: Re: [ITK-users] ICB BSpline
>> From: matt.mccormick at kitware.com
>> To: l.onofri at outlook.com
>> CC: insight-users at itk.org
>
>>
>> Hi Leonardo,
>>
>> When investigating the PointSetToPointSetRegistrationMethod [1],
>> doxygen or the source code shows that OptimizerType
>> MultipleValuedNonLinearOptimizer [2], and LBFGS does not inherit from
>> MultipleValuedNonLinearOptimizer [3] (click the Inheritance diagram
>> tab).
>>
>> HTH,
>> Matt
>>
>> [1]
>> http://www.itk.org/Doxygen/html/classitk_1_1PointSetToPointSetRegistrationMethod.html
>>
>> [2]
>> http://www.itk.org/Doxygen/html/classitk_1_1MultipleValuedNonLinearOptimizer.html
>>
>> [3] http://www.itk.org/Doxygen/html/classitk_1_1LBFGSOptimizer.html
>>
>> On Tue, Feb 17, 2015 at 6:38 AM, Leonardo Onofri <l.onofri at outlook.com>
>> wrote:
>> > Dear users,
>> >
>> >
>> >
>> > I would like to use ICP registration with BSpline transform.
>> >
>> >
>> >
>> > The problem is that I cannot use the LBFGS optimizer since I get this
>> > error:
>> >
>> >
>> >
>> > 'void
>> >
>> > itk::PointSetToPointSetRegistrationMethod<PointSetType,PointSetType>::SetOptimizer(itk::PointSetToPointSetRegistrationMethod<PointSetType,PointSetType>::OptimizerType
>> > *)' : cannot convert argument 1 from 'itk::LBFGSOptimizer::Pointer' to
>> >
>> > 'itk::PointSetToPointSetRegistrationMethod<PointSetType,PointSetType>::OptimizerType
>> > *'
>> >
>> >
>> >
>> > Regards,
>> >
>> >
>> > _____________________________________
>> > 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 franciscolopezdelafranca at gmail.com  Wed Feb 18 12:03:05 2015
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Wed, 18 Feb 2015 18:03:05 +0100
Subject: [ITK-users] Integration ITK with Qt Creator
In-Reply-To: <CAAKhGh9NvbE8UTFL4AyrrwOrRg8zYbTfbM=sF92_kxT87q4V3g@mail.gmail.com>
References: <CAJqi3E+p0eRdMdJ+qDj=xMgKw6gG+QWgpQuaK6HYqNgnShvAwQ@mail.gmail.com>
 <CAAKhGh9NvbE8UTFL4AyrrwOrRg8zYbTfbM=sF92_kxT87q4V3g@mail.gmail.com>
Message-ID: <CAJqi3EKd1QAnYxB8RyFO1X7PZ=tnQ1MexpXxnkf7Rya-UE6C3w@mail.gmail.com>

Hi.
I went to the Qt project web page. Then to the Download link and downloaded
the Qt Community release that includes Qt Creator and, I think, Qt
libraries as well because Qt Creator detects automatically the Qt 5.4.0
MinGw 32-bit KIT.
In fact, if I run "qmake -version ", then I get:

C:\Qt\5.4\mingw491_32\bin>qmake -version

QMake version 3.0
Using Qt version 5.4.0 in C:/Qt/5.4/mingw491_32/lib


By an IDE I meant an environment with an Editor, Compiler, Debugger, etc.
And so far, I've been working with a simple text editor, compiling from a
DOS prompt and not debugging but tracing with "cout" commands. That's why I
needed to find a real IDE like Eclipse or something like that, and try to
work with ITK in the best comfortable way, like I do when programming in
Java.

So, is it possible to program with ITK within an  IDE and not to worry
about CMake configuration and shells/DOS prompts to compile and, besides,
to have a debugger?

Thanks a lot.
Best regards,
/Francisco

2015-02-18 12:40 GMT+01:00 Jon Haitz Legarreta <jhlegarreta at vicomtech.org>:

> Dear Francisco,
> I assume you mean "with no GUI" when you say "with no IDE".
>
> Note that Qt Creator is just a tool of Qt to facilitate the task of
> creating GUIs, but in order to actually have a GUI for your application,
> you will need to download Qt itself [1]. You can download the binaries, and
> thus you can avoid any complication derived from building the sources.
>
> Assuming you are using CMake to generate your project, in order to build
> your application with Qt as the GUI library, you should include Qt among
> the libraries to look for and link with in your CMakeLists [2].
>
> HTH,
> JON HAITZ
>
>
> [1] https://qt-project.org/
> [2] http://www.cmake.org/Wiki/CMake/Tutorials/Qt
>
>
>
> On 18 February 2015 at 12:17, Francisco Lopez de la Franca <
> franciscolopezdelafranca at gmail.com> wrote:
>
>> Hi.
>> I've been using recently ITK but with no IDE, and I've been recommended
>> to use Qt platform.
>> I've downloaded Qt Creator but I don?t find the documentation and the way
>> to integrate ITK with it.
>>
>> That's why I post this message, in order to know if anyone has any
>> reference or guide explaining how to do it.
>>
>> Thank you very much in advance.
>>
>> Kind regards,
>> /Francisco
>>
>> _____________________________________
>> 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 matt.mccormick at kitware.com  Wed Feb 18 12:07:18 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 18 Feb 2015 12:07:18 -0500
Subject: [ITK-users] Integration ITK with Qt Creator
In-Reply-To: <CAJqi3EKd1QAnYxB8RyFO1X7PZ=tnQ1MexpXxnkf7Rya-UE6C3w@mail.gmail.com>
References: <CAJqi3E+p0eRdMdJ+qDj=xMgKw6gG+QWgpQuaK6HYqNgnShvAwQ@mail.gmail.com>
 <CAAKhGh9NvbE8UTFL4AyrrwOrRg8zYbTfbM=sF92_kxT87q4V3g@mail.gmail.com>
 <CAJqi3EKd1QAnYxB8RyFO1X7PZ=tnQ1MexpXxnkf7Rya-UE6C3w@mail.gmail.com>
Message-ID: <CALzTN-Q2+b2oXfjs0iYWYGo_ss-67UVNjRvdEZf3EmiZEjZs0A@mail.gmail.com>

Hi Francisco,

You will want to use QtCreator with CMake.  QtCreator has support for
CMake.  See, for example:

  http://doc.qt.digia.com/qtcreator-2.2/creator-project-cmake.html

HTH,
Matt

On Wed, Feb 18, 2015 at 12:03 PM, Francisco Lopez de la Franca <
franciscolopezdelafranca at gmail.com> wrote:

> Hi.
> I went to the Qt project web page. Then to the Download link and
> downloaded the Qt Community release that includes Qt Creator and, I think,
> Qt libraries as well because Qt Creator detects automatically the Qt 5.4.0
> MinGw 32-bit KIT.
> In fact, if I run "qmake -version ", then I get:
>
> C:\Qt\5.4\mingw491_32\bin>qmake -version
>
> QMake version 3.0
> Using Qt version 5.4.0 in C:/Qt/5.4/mingw491_32/lib
>
>
> By an IDE I meant an environment with an Editor, Compiler, Debugger, etc.
> And so far, I've been working with a simple text editor, compiling from a
> DOS prompt and not debugging but tracing with "cout" commands. That's why I
> needed to find a real IDE like Eclipse or something like that, and try to
> work with ITK in the best comfortable way, like I do when programming in
> Java.
>
> So, is it possible to program with ITK within an  IDE and not to worry
> about CMake configuration and shells/DOS prompts to compile and, besides,
> to have a debugger?
>
> Thanks a lot.
> Best regards,
> /Francisco
>
> 2015-02-18 12:40 GMT+01:00 Jon Haitz Legarreta <jhlegarreta at vicomtech.org>
> :
>
>> Dear Francisco,
>> I assume you mean "with no GUI" when you say "with no IDE".
>>
>> Note that Qt Creator is just a tool of Qt to facilitate the task of
>> creating GUIs, but in order to actually have a GUI for your application,
>> you will need to download Qt itself [1]. You can download the binaries, and
>> thus you can avoid any complication derived from building the sources.
>>
>> Assuming you are using CMake to generate your project, in order to build
>> your application with Qt as the GUI library, you should include Qt among
>> the libraries to look for and link with in your CMakeLists [2].
>>
>> HTH,
>> JON HAITZ
>>
>>
>> [1] https://qt-project.org/
>> [2] http://www.cmake.org/Wiki/CMake/Tutorials/Qt
>>
>>
>>
>> On 18 February 2015 at 12:17, Francisco Lopez de la Franca <
>> franciscolopezdelafranca at gmail.com> wrote:
>>
>>> Hi.
>>> I've been using recently ITK but with no IDE, and I've been recommended
>>> to use Qt platform.
>>> I've downloaded Qt Creator but I don?t find the documentation and the
>>> way to integrate ITK with it.
>>>
>>> That's why I post this message, in order to know if anyone has any
>>> reference or guide explaining how to do it.
>>>
>>> Thank you very much in advance.
>>>
>>> Kind regards,
>>> /Francisco
>>>
>>> _____________________________________
>>> 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 jhlegarreta at vicomtech.org  Wed Feb 18 12:24:37 2015
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Wed, 18 Feb 2015 18:24:37 +0100
Subject: [ITK-users] Integration ITK with Qt Creator
In-Reply-To: <CALzTN-Q2+b2oXfjs0iYWYGo_ss-67UVNjRvdEZf3EmiZEjZs0A@mail.gmail.com>
References: <CAJqi3E+p0eRdMdJ+qDj=xMgKw6gG+QWgpQuaK6HYqNgnShvAwQ@mail.gmail.com>
 <CAAKhGh9NvbE8UTFL4AyrrwOrRg8zYbTfbM=sF92_kxT87q4V3g@mail.gmail.com>
 <CAJqi3EKd1QAnYxB8RyFO1X7PZ=tnQ1MexpXxnkf7Rya-UE6C3w@mail.gmail.com>
 <CALzTN-Q2+b2oXfjs0iYWYGo_ss-67UVNjRvdEZf3EmiZEjZs0A@mail.gmail.com>
Message-ID: <CAAKhGh_mu74BF3J38RzCD4vBx_JfUk3ygDv0Nuot2fzKQy0+GQ@mail.gmail.com>

Dear Francisco,
additionally to what Matt has posted, ITK does not rely on any particular
IDE; you can use virtually any IDE of your choice.

QtCreator may be one of them.

If you work in Windows, as apparently you do, a popular choice would be
Microsoft's Visual Studio [1]. You can download the Express edition.

If you work in OS X, Xcode [2] is a good option.

I'm not an expert in IDEs for Linux systems, but a quick search gives the
following options (don't whether they would all be valid for a particular
distribution): NetBeans [3] Code::Blocks [4], CodeLite [5] or KDevelop [6].

BTW, using CMake will save you a lot of time and headaches.

HTH,
JON HAITZ

[1]
http://www.visualstudio.com/en-us/downloads/download-visual-studio-vs.aspx
[2] https://developer.apple.com/xcode/
[3] https://netbeans.org/features/cpp/
[4] http://www.codeblocks.org/
[5] http://codelite.org/
[6] https://www.kdevelop.org/



On 18 February 2015 at 18:07, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Francisco,
>
> You will want to use QtCreator with CMake.  QtCreator has support for
> CMake.  See, for example:
>
>   http://doc.qt.digia.com/qtcreator-2.2/creator-project-cmake.html
>
> HTH,
> Matt
>
> On Wed, Feb 18, 2015 at 12:03 PM, Francisco Lopez de la Franca <
> franciscolopezdelafranca at gmail.com> wrote:
>
>> Hi.
>> I went to the Qt project web page. Then to the Download link and
>> downloaded the Qt Community release that includes Qt Creator and, I think,
>> Qt libraries as well because Qt Creator detects automatically the Qt 5.4.0
>> MinGw 32-bit KIT.
>> In fact, if I run "qmake -version ", then I get:
>>
>> C:\Qt\5.4\mingw491_32\bin>qmake -version
>>
>> QMake version 3.0
>> Using Qt version 5.4.0 in C:/Qt/5.4/mingw491_32/lib
>>
>>
>> By an IDE I meant an environment with an Editor, Compiler, Debugger, etc.
>> And so far, I've been working with a simple text editor, compiling from a
>> DOS prompt and not debugging but tracing with "cout" commands. That's why I
>> needed to find a real IDE like Eclipse or something like that, and try to
>> work with ITK in the best comfortable way, like I do when programming in
>> Java.
>>
>> So, is it possible to program with ITK within an  IDE and not to worry
>> about CMake configuration and shells/DOS prompts to compile and, besides,
>> to have a debugger?
>>
>> Thanks a lot.
>> Best regards,
>> /Francisco
>>
>> 2015-02-18 12:40 GMT+01:00 Jon Haitz Legarreta <jhlegarreta at vicomtech.org
>> >:
>>
>>> Dear Francisco,
>>> I assume you mean "with no GUI" when you say "with no IDE".
>>>
>>> Note that Qt Creator is just a tool of Qt to facilitate the task of
>>> creating GUIs, but in order to actually have a GUI for your application,
>>> you will need to download Qt itself [1]. You can download the binaries, and
>>> thus you can avoid any complication derived from building the sources.
>>>
>>> Assuming you are using CMake to generate your project, in order to build
>>> your application with Qt as the GUI library, you should include Qt among
>>> the libraries to look for and link with in your CMakeLists [2].
>>>
>>> HTH,
>>> JON HAITZ
>>>
>>>
>>> [1] https://qt-project.org/
>>> [2] http://www.cmake.org/Wiki/CMake/Tutorials/Qt
>>>
>>>
>>>
>>> On 18 February 2015 at 12:17, Francisco Lopez de la Franca <
>>> franciscolopezdelafranca at gmail.com> wrote:
>>>
>>>> Hi.
>>>> I've been using recently ITK but with no IDE, and I've been recommended
>>>> to use Qt platform.
>>>> I've downloaded Qt Creator but I don?t find the documentation and the
>>>> way to integrate ITK with it.
>>>>
>>>> That's why I post this message, in order to know if anyone has any
>>>> reference or guide explaining how to do it.
>>>>
>>>> Thank you very much in advance.
>>>>
>>>> Kind regards,
>>>> /Francisco
>>>>
>>>> _____________________________________
>>>> 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 dr.tim.allman at gmail.com  Wed Feb 18 12:51:04 2015
From: dr.tim.allman at gmail.com (Tim Allman)
Date: Wed, 18 Feb 2015 12:51:04 -0500
Subject: [ITK-users] Integration ITK with Qt Creator
In-Reply-To: <CAAKhGh_mu74BF3J38RzCD4vBx_JfUk3ygDv0Nuot2fzKQy0+GQ@mail.gmail.com>
References: <CAJqi3E+p0eRdMdJ+qDj=xMgKw6gG+QWgpQuaK6HYqNgnShvAwQ@mail.gmail.com>
 <CAAKhGh9NvbE8UTFL4AyrrwOrRg8zYbTfbM=sF92_kxT87q4V3g@mail.gmail.com>
 <CAJqi3EKd1QAnYxB8RyFO1X7PZ=tnQ1MexpXxnkf7Rya-UE6C3w@mail.gmail.com>
 <CALzTN-Q2+b2oXfjs0iYWYGo_ss-67UVNjRvdEZf3EmiZEjZs0A@mail.gmail.com>
 <CAAKhGh_mu74BF3J38RzCD4vBx_JfUk3ygDv0Nuot2fzKQy0+GQ@mail.gmail.com>
Message-ID: <4B895794-61FC-4617-A214-EF699F99D217@gmail.com>

I have done a fair amount of development with Eclipse and NetBeans in a Linux environment. My impression of Eclipse is that it is happiest when coding in Java and less so with C/C++. I don?t know about integrating QtCreator and CMake but I expect both are possible.

NetBeans does support CMake and Qt and much work has been done to integrate C++.

Both of these are available on Windows.

And, I have found that there is a bit of a steep and long learning curve in using these products but it?s worth the effort.

--------------------------
Tim Allman Ph.D.
35 Margaret St.,
Guelph Ont.,
N1E 5R6
Canada

519-837-0276




On Feb 18, 2015, at 12:24 PM, Jon Haitz Legarreta <jhlegarreta at vicomtech.org> wrote:

> Dear Francisco,
> additionally to what Matt has posted, ITK does not rely on any particular IDE; you can use virtually any IDE of your choice.
> 
> QtCreator may be one of them. 
> 
> If you work in Windows, as apparently you do, a popular choice would be Microsoft's Visual Studio [1]. You can download the Express edition.
> 
> If you work in OS X, Xcode [2] is a good option.
> 
> I'm not an expert in IDEs for Linux systems, but a quick search gives the following options (don't whether they would all be valid for a particular distribution): NetBeans [3] Code::Blocks [4], CodeLite [5] or KDevelop [6].
> 
> BTW, using CMake will save you a lot of time and headaches.
> 
> HTH,
> JON HAITZ
> 
> [1] http://www.visualstudio.com/en-us/downloads/download-visual-studio-vs.aspx
> [2] https://developer.apple.com/xcode/
> [3] https://netbeans.org/features/cpp/
> [4] http://www.codeblocks.org/
> [5] http://codelite.org/
> [6] https://www.kdevelop.org/
> 
> 
> 
> On 18 February 2015 at 18:07, Matt McCormick <matt.mccormick at kitware.com> wrote:
> Hi Francisco,
> 
> You will want to use QtCreator with CMake.  QtCreator has support for CMake.  See, for example:
> 
>   http://doc.qt.digia.com/qtcreator-2.2/creator-project-cmake.html
> 
> HTH,
> Matt
> 
> On Wed, Feb 18, 2015 at 12:03 PM, Francisco Lopez de la Franca <franciscolopezdelafranca at gmail.com> wrote:
> Hi.
> I went to the Qt project web page. Then to the Download link and downloaded the Qt Community release that includes Qt Creator and, I think, Qt libraries as well because Qt Creator detects automatically the Qt 5.4.0 MinGw 32-bit KIT.
> In fact, if I run "qmake -version ", then I get: 
> 
> C:\Qt\5.4\mingw491_32\bin>qmake -version
> 
> QMake version 3.0
> Using Qt version 5.4.0 in C:/Qt/5.4/mingw491_32/lib
> 
> 
> By an IDE I meant an environment with an Editor, Compiler, Debugger, etc. And so far, I've been working with a simple text editor, compiling from a DOS prompt and not debugging but tracing with "cout" commands. That's why I needed to find a real IDE like Eclipse or something like that, and try to work with ITK in the best comfortable way, like I do when programming in Java.
> 
> So, is it possible to program with ITK within an  IDE and not to worry about CMake configuration and shells/DOS prompts to compile and, besides, to have a debugger?
> 
> Thanks a lot.
> Best regards,
> /Francisco
> 
> 2015-02-18 12:40 GMT+01:00 Jon Haitz Legarreta <jhlegarreta at vicomtech.org>:
> Dear Francisco,
> I assume you mean "with no GUI" when you say "with no IDE". 
> 
> Note that Qt Creator is just a tool of Qt to facilitate the task of creating GUIs, but in order to actually have a GUI for your application, you will need to download Qt itself [1]. You can download the binaries, and thus you can avoid any complication derived from building the sources.
> 
> Assuming you are using CMake to generate your project, in order to build your application with Qt as the GUI library, you should include Qt among the libraries to look for and link with in your CMakeLists [2].
> 
> HTH,
> JON HAITZ
> 
> 
> [1] https://qt-project.org/
> [2] http://www.cmake.org/Wiki/CMake/Tutorials/Qt
> 
> 
> 
> On 18 February 2015 at 12:17, Francisco Lopez de la Franca <franciscolopezdelafranca at gmail.com> wrote:
> Hi.
> I've been using recently ITK but with no IDE, and I've been recommended to use Qt platform.
> I've downloaded Qt Creator but I don?t find the documentation and the way to integrate ITK with it.
> 
> That's why I post this message, in order to know if anyone has any reference or guide explaining how to do it.
> 
> Thank you very much in advance.
> 
> Kind regards,
> /Francisco
> 
> _____________________________________
> 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 matt.mccormick at kitware.com  Wed Feb 18 15:17:42 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 18 Feb 2015 15:17:42 -0500
Subject: [ITK-users] [ANNOUNCE] ITK 4.7.1 has been released!
Message-ID: <CALzTN-SV70M5q=rZPFcCWCBudm9siRoEGCvvdFd1Kd0t_OrdGg@mail.gmail.com>

On behalf of the Insight Toolkit Community, we are happy to announce the
release of ITK 4.7.1!

This is a patch release that addresses critical issues, regressions,
important documentation, and compiler support. The 4.7.1 release fixes
improves Visual Studio support, addresses Python wrapping runtime warnings,
includes fixes for the ITK Software Guide, and addresses a few
miscellaneous bugs.

Changes were added to improve support for Visual Studio 2013, the
ITKVtkGlue module with Visual Studio, and for the upcoming Visual Studio
2015 release. Visual Studio 2013 (Professional and Community Editions)
generated faulty code when compiled for Intel Win64 with SSE2 instructions
in Release mode and/or when ITK_USE_64BITS_IDS was ON (Microsoft Visual
Studio Bug ID 1060166
<http://connect.microsoft.com/VisualStudio/feedbackdetail/view/1060166>and
1093610
<http://connect.microsoft.com/VisualStudio/feedbackdetail/view/1093610>).
Workarounds were made to ITK?s code and the issues were reported to
upstream Visual Studio, who have addressed the bugs in Visual Studio 2015.

Common WrapITK Python runtime warnings have all been addressed.

Fixes and style changes were made for the hardcopy of the The ITK Software
Guide, which is now available at:

 http://www.itk.org/ITK/help/book.html


Congratulations and thanks to everyone who contributed to this release.
Questions and comments are welcome on the ITK mailing lists.

Release files can be downloaded from:

 http://itk.org/ITK/resources/software.html

The next feature release of 4.8.0 is scheduled for June.


Enjoy ITK!


Changes from v4.7.0 to v4.7.1:

Brad King (1):
     COMP: Fix variable reference in ITKVtkGlue module files

Bradley Lowekamp (8):
     BUG: Enable setting all zeroes for fixed parameters for displacement
     COMP: Fix unsafe usage of sprintf
     BUG: Fix incorrectly ordering of template parameters
     COMP: check for search.h in libtiff
     BUG: restore the center point fixed parameters for scale transforms
     COMP: Use _timezone for Visual Studio
     BUG: Restore IO support for BSplineDeformableTransform
     BUG: Enable VectorImage to work with the ImageSeriesWriter

Christopher Mullins (2):
     BUG: Return a correct voronoi partition in Danielsson filter example.
     STYLE: Fix Latex blocks in documentation to include newlines.

D?enan Zuki? (2):
     COMP: VS 2012+ compile fixes and CMake warnings
     COMP: fixing quote matching in vtkGlue-related .cmake file

Julien Jomier (1):
     BUG: Output pointer origin is not set causing a memory access error.

Marius Staring, Niels Dekker, Floris Berendsen (2):
     BUG: workaround for 64bit VS2013 Release segfaults (Visual Studio Bug
ID 1060166
<http://connect.microsoft.com/VisualStudio/feedbackdetail/view/1060166>)
     COMP: workaround for 64bit VS2013 Release ICE (Visual Studio Bug ID
1093610
<http://connect.microsoft.com/VisualStudio/feedbackdetail/view/1093610>)

Matthew McCormick (9):
     ENH: Add wrapping for ITKImageNoise module.
     ENH: Bump release branch version to 4.7.1.
     BUG: Clear TransformIO's list of transforms in TransformFileReader.
     COMP: Fix wrapping runtime warning on unknown itk::Matrix.
     COMP: Add missing types for MeshTraits wrapping.
     COMP: Do not wrap the Container types for CellInterface * types.
     COMP: Add wrapping for CellTraitsInfo.
     COMP: Wrap missing Mesh templates.
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From blowekamp at mail.nih.gov  Thu Feb 19 11:08:22 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 19 Feb 2015 11:08:22 -0500
Subject: [ITK-users] [ANNOUNCE] SimpleITK 0.9  REGISTRATION beta 1 release
Message-ID: <FFB3B5F4-27F6-46B2-943D-412891FE655A@mail.nih.gov>

We are pleased to announce the SimpleITK 0.9 beta 1!

NOW WITH REGISTRATION

We encourage the community to use and test this registration interface and to provide feedback on the design and features.

This beta features the ImageRegistrationMethod which brings a SimpleITK style interface to the modular ITKv4 registration framework. This adds support for a variety of transforms including affine, b-spline, and deformation fields. The metrics supported include correlation, means squares, ANTS neighborhood correlation, and mutual information. A variety of optimizers are available along with scales estimators for the optimized transformation parameters and built in multi-scale registration support. http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html

Additionally, a number of registration filters have been added: DemonsRegistrationFilter, DiffeomorphicDemonsRegistrationFilter, FastSymmetricForcesDemonsRegistrationFilter, LevelSetMotionRegistrationFilter and SymmetricForcesDemonsRegistrationFilter.
Several examples can be found in the examples directory to help you get started. These examples include Affine registration, BSpline, Demons and Displacement fields. http://www.itk.org/SimpleITKDoxygen/html/examples.html

We have also added the following filters: AdditiveGaussianNoiseImageFilter, AggregateLabelMapFilter, BinaryImageToLabelMapFilter, ChangeLabelLabelMapFilter, CollidingFrontsImageFilter, DisplacementFieldJacobianDeterminantFilter, FastMarchingBaseImageFilter, FastMarchingUpwindGradientImageFilter, InverseDisplacementFieldImageFilter, InvertDisplacementFieldImageFilter, LabelImageToLabelMapFilter, LabelShapeStatisticsImageFilter, LabelStatisticsImageFilter, LabelUniqueLabelMapFilter, MergeLabelMapFilter, RelabelLabelMapFilter, SaltAndPepperNoiseImageFilter, ShotNoiseImageFilter, SpeckleNoiseImageFilter and TransformToDisplacementFieldFilter

Note: We have run into a limitation with Visual Studio that prevents successful building and packaging for Windows 64. This will be addressed before the final release. Please try the 32-bit Windows version for smaller images.

Before the final release we will work on improving testing, adding more examples and documentation, and fixing bugs. We believe the beta is feature complete for doing registration work, but are open to critical features reported from the community.


You will need to manually download the beta binaries, then explicitly install the downloaded beta file.

Information on how to get started and download the binaries: http://www.itk.org/Wiki/SimpleITK/GettingStarted#Binaries

Binary distributions for many platforms and languages are available for downloading: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9b01/

Nightly Doxygen Documentation: http://www.itk.org/SimpleITKDoxygen/html/index.html

Additional Release Notes: http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#Beta_1_Announcement


Enjoy!

From alfonso.castro at udc.es  Thu Feb 19 12:44:36 2015
From: alfonso.castro at udc.es (Alfonso Castro)
Date: Thu, 19 Feb 2015 18:44:36 +0100
Subject: [ITK-users] Problem compiling HelloWorld.cxx with ITK 4.7.1
Message-ID: <74975975.Iyg6Sylb1S@hinata>

Hi.

I downladed and install ITK 4.7.1 version on OpenSuSE 13.2 x86-64. I activated the different 
modules and the use of CUDA with shared libs off.

The compile was without problem and I installed in directory: /opt/mia/itk. I fixed 
ITK_DIR=/opt/mia/itk/lib/cmake/ITK-4.7.

Then I created a HelloWord project to check all work correctly using the CMakelist.txt included 
in Software Guide.


However, when I run make, the system shows the next error:

/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: no se puede 
encontrar -lSmoothingRecursiveYvvGaussianFilter
collect2: error: ld returned 1 exit status
CMakeFiles/hola.dir/build.make:337: recipe for target 'hola' failed
make[2]: *** [hola] Error 1
CMakeFiles/Makefile2:60: recipe for target 'CMakeFiles/hola.dir/all' failed
make[1]: *** [CMakeFiles/hola.dir/all] Error 2
Makefile:76: recipe for target 'all' failed
make: *** [all] Error 2

I tried to find the reason of the error but I am not able.

What is the reason of the error? How I can resolve it?

Thanks in advance.
Alfonso Castro Mart?nez
Facullty of Computer Science
University of A Coruna
Spain

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From franciscolopezdelafranca at gmail.com  Thu Feb 19 14:35:45 2015
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Thu, 19 Feb 2015 20:35:45 +0100
Subject: [ITK-users] Integration ITK with Qt Creator
In-Reply-To: <4B895794-61FC-4617-A214-EF699F99D217@gmail.com>
References: <CAJqi3E+p0eRdMdJ+qDj=xMgKw6gG+QWgpQuaK6HYqNgnShvAwQ@mail.gmail.com>
 <CAAKhGh9NvbE8UTFL4AyrrwOrRg8zYbTfbM=sF92_kxT87q4V3g@mail.gmail.com>
 <CAJqi3EKd1QAnYxB8RyFO1X7PZ=tnQ1MexpXxnkf7Rya-UE6C3w@mail.gmail.com>
 <CALzTN-Q2+b2oXfjs0iYWYGo_ss-67UVNjRvdEZf3EmiZEjZs0A@mail.gmail.com>
 <CAAKhGh_mu74BF3J38RzCD4vBx_JfUk3ygDv0Nuot2fzKQy0+GQ@mail.gmail.com>
 <4B895794-61FC-4617-A214-EF699F99D217@gmail.com>
Message-ID: <CAJqi3E+TK9FMoF0GbD1BRRBQGRnMCgpzWji5Lbxqjd1kncygOA@mail.gmail.com>

Hi again.
After re-installing Qt 5.4.0 several times, it always throws the following
error just when launched for the CMakeProjectManager:

Cannot load plugin because dependency failed to load: Designer(3.3.0)

Reason: Could not resolve dependency 'ResourceEditor(3.3.0)'

I know this is not the right forum because it is a Qt issue, but I ask the
question in case someone has found with the same error and know how to
solve it.

Sincerely, thank you very much.
Best regards.
/Francisco


2015-02-18 18:51 GMT+01:00 Tim Allman <dr.tim.allman at gmail.com>:

> I have done a fair amount of development with Eclipse and NetBeans in a
> Linux environment. My impression of Eclipse is that it is happiest when
> coding in Java and less so with C/C++. I don?t know about integrating
> QtCreator and CMake but I expect both are possible.
>
> NetBeans does support CMake and Qt and much work has been done to
> integrate C++.
>
> Both of these are available on Windows.
>
> And, I have found that there is a bit of a steep and long learning curve
> in using these products but it?s worth the effort.
>
> --------------------------
> Tim Allman Ph.D.
> 35 Margaret St.,
> Guelph Ont.,
> N1E 5R6
> Canada
>
> 519-837-0276
>
>
>
>
> On Feb 18, 2015, at 12:24 PM, Jon Haitz Legarreta <
> jhlegarreta at vicomtech.org> wrote:
>
> Dear Francisco,
> additionally to what Matt has posted, ITK does not rely on any particular
> IDE; you can use virtually any IDE of your choice.
>
> QtCreator may be one of them.
>
> If you work in Windows, as apparently you do, a popular choice would be
> Microsoft's Visual Studio [1]. You can download the Express edition.
>
> If you work in OS X, Xcode [2] is a good option.
>
> I'm not an expert in IDEs for Linux systems, but a quick search gives the
> following options (don't whether they would all be valid for a particular
> distribution): NetBeans [3] Code::Blocks [4], CodeLite [5] or KDevelop [6].
>
> BTW, using CMake will save you a lot of time and headaches.
>
> HTH,
> JON HAITZ
>
> [1]
> http://www.visualstudio.com/en-us/downloads/download-visual-studio-vs.aspx
> [2] https://developer.apple.com/xcode/
> [3] https://netbeans.org/features/cpp/
> [4] http://www.codeblocks.org/
> [5] http://codelite.org/
> [6] https://www.kdevelop.org/
>
>
>
> On 18 February 2015 at 18:07, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>
>> Hi Francisco,
>>
>> You will want to use QtCreator with CMake.  QtCreator has support for
>> CMake.  See, for example:
>>
>>   http://doc.qt.digia.com/qtcreator-2.2/creator-project-cmake.html
>>
>> HTH,
>> Matt
>>
>> On Wed, Feb 18, 2015 at 12:03 PM, Francisco Lopez de la Franca <
>> franciscolopezdelafranca at gmail.com> wrote:
>>
>>> Hi.
>>> I went to the Qt project web page. Then to the Download link and
>>> downloaded the Qt Community release that includes Qt Creator and, I think,
>>> Qt libraries as well because Qt Creator detects automatically the Qt 5.4.0
>>> MinGw 32-bit KIT.
>>> In fact, if I run "qmake -version ", then I get:
>>>
>>> C:\Qt\5.4\mingw491_32\bin>qmake -version
>>>
>>> QMake version 3.0
>>> Using Qt version 5.4.0 in C:/Qt/5.4/mingw491_32/lib
>>>
>>>
>>> By an IDE I meant an environment with an Editor, Compiler, Debugger,
>>> etc. And so far, I've been working with a simple text editor, compiling
>>> from a DOS prompt and not debugging but tracing with "cout" commands.
>>> That's why I needed to find a real IDE like Eclipse or something like that,
>>> and try to work with ITK in the best comfortable way, like I do when
>>> programming in Java.
>>>
>>> So, is it possible to program with ITK within an  IDE and not to worry
>>> about CMake configuration and shells/DOS prompts to compile and, besides,
>>> to have a debugger?
>>>
>>> Thanks a lot.
>>> Best regards,
>>> /Francisco
>>>
>>> 2015-02-18 12:40 GMT+01:00 Jon Haitz Legarreta <
>>> jhlegarreta at vicomtech.org>:
>>>
>>>> Dear Francisco,
>>>> I assume you mean "with no GUI" when you say "with no IDE".
>>>>
>>>> Note that Qt Creator is just a tool of Qt to facilitate the task of
>>>> creating GUIs, but in order to actually have a GUI for your application,
>>>> you will need to download Qt itself [1]. You can download the binaries, and
>>>> thus you can avoid any complication derived from building the sources.
>>>>
>>>> Assuming you are using CMake to generate your project, in order to
>>>> build your application with Qt as the GUI library, you should include Qt
>>>> among the libraries to look for and link with in your CMakeLists [2].
>>>>
>>>> HTH,
>>>> JON HAITZ
>>>>
>>>>
>>>> [1] https://qt-project.org/
>>>> [2] http://www.cmake.org/Wiki/CMake/Tutorials/Qt
>>>>
>>>>
>>>>
>>>> On 18 February 2015 at 12:17, Francisco Lopez de la Franca <
>>>> franciscolopezdelafranca at gmail.com> wrote:
>>>>
>>>>> Hi.
>>>>> I've been using recently ITK but with no IDE, and I've been
>>>>> recommended to use Qt platform.
>>>>> I've downloaded Qt Creator but I don?t find the documentation and the
>>>>> way to integrate ITK with it.
>>>>>
>>>>> That's why I post this message, in order to know if anyone has any
>>>>> reference or guide explaining how to do it.
>>>>>
>>>>> Thank you very much in advance.
>>>>>
>>>>> Kind regards,
>>>>> /Francisco
>>>>>
>>>>> _____________________________________
>>>>> 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
>
>
>
> _____________________________________
> 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 ds_prakash at rediffmail.com  Thu Feb 19 23:11:36 2015
From: ds_prakash at rediffmail.com (Surya Prakash)
Date: 20 Feb 2015 04:11:36 -0000
Subject: [ITK-users] =?utf-8?q?output_of_connected_threshold?=
Message-ID: <20150220041136.8277.qmail@f4mail-235-214.rediffmail.com>

Hello,
I am making an interactive region growing application using connectedThreshold. Seed point etc I want to collect interactively. After collecting the inputs, I will execute something like this.

smoothing->SetInput( reader->GetOutput() );
connectedThreshold->SetInput( smoothing->GetOutput() );

I want to access the output by calling connectedThreshold->GetOutput()

How I can access the output (In memory), so that I can render it on the original image. I am making MFC application.

Thanks & regards
Prakash
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From matt.mccormick at kitware.com  Fri Feb 20 02:03:26 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 20 Feb 2015 02:03:26 -0500
Subject: [ITK-users] Problem compiling HelloWorld.cxx with ITK 4.7.1
In-Reply-To: <74975975.Iyg6Sylb1S@hinata>
References: <74975975.Iyg6Sylb1S@hinata>
Message-ID: <CALzTN-TqgrT6EuqQL5q_38gMtNvkuYM5gWuMLkQZSO-1iZUJjA@mail.gmail.com>

Hi Alfonso,

Welcome to ITK!

You have uncovered a bug in the SmoothingRecursiveYvvGaussianFilter
module.  I have created a patch [1], but until the patch is
integrated, please try using ITK without that module.

Thanks,
Matt

[1] https://github.com/thewtex/SmoothingRecursiveYvvGaussianFilter/commit/785139ccedac9ee513be84b79a674775fc38f442

On Thu, Feb 19, 2015 at 12:44 PM, Alfonso Castro <alfonso.castro at udc.es> wrote:
> Hi.
>
>
>
> I downladed and install ITK 4.7.1 version on OpenSuSE 13.2 x86-64. I
> activated the different modules and the use of CUDA with shared libs off.
>
>
>
> The compile was without problem and I installed in directory: /opt/mia/itk.
> I fixed ITK_DIR=/opt/mia/itk/lib/cmake/ITK-4.7.
>
>
>
> Then I created a HelloWord project to check all work correctly using the
> CMakelist.txt included in Software Guide.
>
> However, when I run make, the system shows the next error:
>
>
>
> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld:
> no se puede encontrar -lSmoothingRecursiveYvvGaussianFilter
>
> collect2: error: ld returned 1 exit status
>
> CMakeFiles/hola.dir/build.make:337: recipe for target 'hola' failed
>
> make[2]: *** [hola] Error 1
>
> CMakeFiles/Makefile2:60: recipe for target 'CMakeFiles/hola.dir/all' failed
>
> make[1]: *** [CMakeFiles/hola.dir/all] Error 2
>
> Makefile:76: recipe for target 'all' failed
>
> make: *** [all] Error 2
>
>
>
> I tried to find the reason of the error but I am not able.
>
>
>
> What is the reason of the error? How I can resolve it?
>
>
>
> Thanks in advance.
>
> Alfonso Castro Mart?nez
>
> Facullty of Computer Science
>
> University of A Coruna
>
> Spain
>
>
>
>
> _____________________________________
> 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 matt.mccormick at kitware.com  Fri Feb 20 02:08:12 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 20 Feb 2015 02:08:12 -0500
Subject: [ITK-users] output of connected threshold
In-Reply-To: <20150220041136.8277.qmail@f4mail-235-214.rediffmail.com>
References: <20150220041136.8277.qmail@f4mail-235-214.rediffmail.com>
Message-ID: <CALzTN-TRd9VaMJRrb+cJeWTqYfJX9P05SjovZ6ap6NSs=i_vLg@mail.gmail.com>

Hi Prakash,

The GetBufferPointer() [1] on an itk::Image's ImportImageContainer has a
pointer to the pixel data.

HTH,
Matt


http://www.itk.org/Doxygen/html/classitk_1_1ImportImageContainer.html#afc6357f6772ca6c3c4410e7a6c4a3285


On Thu, Feb 19, 2015 at 11:11 PM, Surya Prakash <ds_prakash at rediffmail.com>
wrote:

> Hello,
> I am making an interactive region growing application using
> connectedThreshold. Seed point etc I want to collect interactively. After
> collecting the inputs, I will execute something like this.
>
> smoothing->SetInput( reader->GetOutput() );
> connectedThreshold->SetInput( smoothing->GetOutput() );
>
> I want to access the output by calling connectedThreshold->GetOutput()
>
> How I can access the output (In memory), so that I can render it on the
> original image. I am making MFC application.
>
> Thanks & regards
> Prakash
>
>
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm at Middle?>
> Get your own *FREE* website, *FREE* domain & *FREE* mobile app with
> Company email.
> *Know More >*
> <http://track.rediff.com/click?url=___http://businessemail.rediff.com?sc_cid=sign-1-10-13___&cmp=host&lnk=sign-1-10-13&nsrv1=host>
> _____________________________________
> 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 alfonso.castro at udc.es  Fri Feb 20 03:58:39 2015
From: alfonso.castro at udc.es (Alfonso Castro =?utf-8?Q?Mart=C3=ADnez?=)
Date: Fri, 20 Feb 2015 09:58:39 +0100 (CET)
Subject: [ITK-users] Problem compiling HelloWorld.cxx with ITK 4.7.1
In-Reply-To: <CALzTN-TqgrT6EuqQL5q_38gMtNvkuYM5gWuMLkQZSO-1iZUJjA@mail.gmail.com>
References: <74975975.Iyg6Sylb1S@hinata>
 <CALzTN-TqgrT6EuqQL5q_38gMtNvkuYM5gWuMLkQZSO-1iZUJjA@mail.gmail.com>
Message-ID: <1653838465.32219028.1424422719339.JavaMail.zimbra@udc.es>

Many thanks.

Alfonso Castro Mart?nez
Facullty of Computer Science
University of A Coruna
Spain

----- Mensaje original -----
De: "Matt McCormick" <matt.mccormick at kitware.com>
Para: "Alfonso Castro" <alfonso.castro at udc.es>
CC: insight-users at itk.org
Enviados: Viernes, 20 de Febrero 2015 8:03:26
Asunto: Re: [ITK-users] Problem compiling HelloWorld.cxx with ITK 4.7.1

Hi Alfonso,

Welcome to ITK!

You have uncovered a bug in the SmoothingRecursiveYvvGaussianFilter
module.  I have created a patch [1], but until the patch is
integrated, please try using ITK without that module.

Thanks,
Matt

[1] https://github.com/thewtex/SmoothingRecursiveYvvGaussianFilter/commit/785139ccedac9ee513be84b79a674775fc38f442

On Thu, Feb 19, 2015 at 12:44 PM, Alfonso Castro <alfonso.castro at udc.es> wrote:
> Hi.
>
>
>
> I downladed and install ITK 4.7.1 version on OpenSuSE 13.2 x86-64. I
> activated the different modules and the use of CUDA with shared libs off.
>
>
>
> The compile was without problem and I installed in directory: /opt/mia/itk.
> I fixed ITK_DIR=/opt/mia/itk/lib/cmake/ITK-4.7.
>
>
>
> Then I created a HelloWord project to check all work correctly using the
> CMakelist.txt included in Software Guide.
>
> However, when I run make, the system shows the next error:
>
>
>
> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld:
> no se puede encontrar -lSmoothingRecursiveYvvGaussianFilter
>
> collect2: error: ld returned 1 exit status
>
> CMakeFiles/hola.dir/build.make:337: recipe for target 'hola' failed
>
> make[2]: *** [hola] Error 1
>
> CMakeFiles/Makefile2:60: recipe for target 'CMakeFiles/hola.dir/all' failed
>
> make[1]: *** [CMakeFiles/hola.dir/all] Error 2
>
> Makefile:76: recipe for target 'all' failed
>
> make: *** [all] Error 2
>
>
>
> I tried to find the reason of the error but I am not able.
>
>
>
> What is the reason of the error? How I can resolve it?
>
>
>
> Thanks in advance.
>
> Alfonso Castro Mart?nez
>
> Facullty of Computer Science
>
> University of A Coruna
>
> Spain
>
>
>
>
> _____________________________________
> 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 stephen.aylward at kitware.com  Sat Feb 21 11:56:57 2015
From: stephen.aylward at kitware.com (Stephen Aylward)
Date: Sat, 21 Feb 2015 11:56:57 -0500
Subject: [ITK-users] Let the NLM know that ITK is important to you and your
	research
Message-ID: <CALcsBJKMJovYin3Z_WjaA5CxyW6N215AYp5qb=T2j+SLA9+s-A@mail.gmail.com>

The NLM is requesting input on the value and future needs of its programs,
including the Insight Toolkit (ITK).   Please use the link below to share
your thoughts and experiences with ITK.  Let the NLM know that impact that
ITK is having!

Some thoughts on ITK:  ITK was originated at the NLM in 1999, and now ITK
is used in thousands of academic and commercial applications.  It has
become the foundation for the exchange of algorithms and ideas in medical
image analysis.  It has accelerated the pace of research by reducing
duplication and enabling new research to build upon and to be compared with
the state of the art.  It has propelled academic research into commercial
reality and patient care through its open-source licensing and high
software standards.  It has served as an educational tool for thousands of
students in engineering and science. The continued support and expansion of
ITK should be given top priority at the NLM.

For more information on the NLM's request-for-information regarding the
impact and future of its projects and programs, go to
http://grants.nih.gov/grants/guide/notice-files/NOT-OD-15-067.html

To submit a response using the NLM's online form, go to
http://grants.nih.gov/grants/rfi/rfi.cfm?ID=41

Deadline for comments is March 13, 2015.

-- 
====================================================
Stephen R. Aylward, Ph.D.
Senior Director of Operations, North Carolina, Kitware, Inc.
http://www.kitware.com and http://www.aylward.org
(919) 969-6990 x300
====================================================
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From tobias.noebauer at imp.ac.at  Mon Feb 23 13:00:27 2015
From: tobias.noebauer at imp.ac.at (=?iso-8859-1?Q?N=F6bauer=2CTobias?=)
Date: Mon, 23 Feb 2015 18:00:27 +0000
Subject: [ITK-users] Registration: Fix transform parameter?
Message-ID: <DF64C042-FBB3-4D3A-9E38-134E76BA5131@imp.ac.at>

Hi all,

is there a simple/generic way to exclude a transform parameter from getting optimized during a registration process, i.e. just hold it at its initial value? I would for example like to allow for rotations around x, but not y, in a VersorRigid3DTransform, because I know the latter can't happen. Would it make sense to set the corresponding optimizer scale value to an extremely high value? -- This would not really disable this DOF, but just make larg values unlikely, correct?

I'm using the current alpha version of SimpleITK 0.9 (Python wrapped), so it would be even greater if a solution existed within SimpleITK...

Thanks a lot (also, for the great software),
Tobias

From matt.mccormick at kitware.com  Mon Feb 23 13:24:39 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 23 Feb 2015 13:24:39 -0500
Subject: [ITK-users] Registration: Fix transform parameter?
In-Reply-To: <DF64C042-FBB3-4D3A-9E38-134E76BA5131@imp.ac.at>
References: <DF64C042-FBB3-4D3A-9E38-134E76BA5131@imp.ac.at>
Message-ID: <CALzTN-SiDGzOmbsHQdoKvFgcCM7B38kPhEvcyUnO3C93CJ502g@mail.gmail.com>

Hi Tobias,

Welcome to ITK!

Yes, SetWeights can be used to fix a parameter.  See the class
documentation here [1].

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1ObjectToObjectOptimizerBaseTemplate.html

On Mon, Feb 23, 2015 at 1:00 PM, N?bauer,Tobias
<tobias.noebauer at imp.ac.at> wrote:
> Hi all,
>
> is there a simple/generic way to exclude a transform parameter from getting optimized during a registration process, i.e. just hold it at its initial value? I would for example like to allow for rotations around x, but not y, in a VersorRigid3DTransform, because I know the latter can't happen. Would it make sense to set the corresponding optimizer scale value to an extremely high value? -- This would not really disable this DOF, but just make larg values unlikely, correct?
>
> I'm using the current alpha version of SimpleITK 0.9 (Python wrapped), so it would be even greater if a solution existed within SimpleITK...
>
> Thanks a lot (also, for the great software),
> Tobias
> _____________________________________
> 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 blowekamp at mail.nih.gov  Mon Feb 23 13:17:32 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 23 Feb 2015 13:17:32 -0500
Subject: [ITK-users] Registration: Fix transform parameter?
In-Reply-To: <DF64C042-FBB3-4D3A-9E38-134E76BA5131@imp.ac.at>
References: <DF64C042-FBB3-4D3A-9E38-134E76BA5131@imp.ac.at>
Message-ID: <699396B2-4831-40AF-A77E-F8688C218791@mail.nih.gov>

Hello Tobias,

You are correct that it is generally recommended to explicitly set the optimizer scale to an extremely high value to disable the optimization in that space.

However, please keep in mind that the VersorRigid3DTransform parameters are not X,Y,Z rotations they are the components of a versor. You can look into the Euler3DTransform which is paramerterized with the angles.

The alternative to this would be to write your own transform class.

Brad

On Feb 23, 2015, at 1:00 PM, N?bauer,Tobias <tobias.noebauer at imp.ac.at> wrote:

> Hi all,
> 
> is there a simple/generic way to exclude a transform parameter from getting optimized during a registration process, i.e. just hold it at its initial value? I would for example like to allow for rotations around x, but not y, in a VersorRigid3DTransform, because I know the latter can't happen. Would it make sense to set the corresponding optimizer scale value to an extremely high value? -- This would not really disable this DOF, but just make larg values unlikely, correct?
> 
> I'm using the current alpha version of SimpleITK 0.9 (Python wrapped), so it would be even greater if a solution existed within SimpleITK...
> 
> Thanks a lot (also, for the great software),
> Tobias
> _____________________________________
> 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 samah.bouzidi at gmail.com  Tue Feb 24 16:56:21 2015
From: samah.bouzidi at gmail.com (Sunshine)
Date: Tue, 24 Feb 2015 14:56:21 -0700 (MST)
Subject: [ITK-users] region growing with adaptative Threshold
Message-ID: <1424814981495-35272.post@n7.nabble.com>

HI,

I'm trying to segment the airways from 3D Ct image using this algorithm 
 1- determine the seed point and the intial threshold
 2- calculte the average intensity of voxels already classified to the
region (A)
 3- if the intensity  of the voxel  and  all closest (connected) neighbours
= (+/-) 0,05 A(step 2). voxel is classified to the region.

As explained, the threshold depends on the processed data, is their any
example in which the threshold is not defined as a constante like in the
region growing examples?

Best regards
SAmah

 



--
View this message in context: http://itk-users.7.n7.nabble.com/region-growing-with-adaptative-Threshold-tp35272.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From matimontg at gmail.com  Wed Feb 25 06:29:08 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 25 Feb 2015 08:29:08 -0300
Subject: [ITK-users] [vtkusers] vtkDICOMImageReader does not support to
 read all Dicom image format
In-Reply-To: <C824B527DF093F47B87947D7CDF1D7B101797148@POCITMSEXMB04.LntUniverse.com>
References: <C824B527DF093F47B87947D7CDF1D7B101796C21@POCITMSEXMB04.LntUniverse.com>
 <CAKKNfu+g=vndeq9p5vR4Xr-ecgF8k+WNdrW7tB0ZA9j9kr9GdQ@mail.gmail.com>
 <C824B527DF093F47B87947D7CDF1D7B101797148@POCITMSEXMB04.LntUniverse.com>
Message-ID: <CAKKNfu+ROXSo_TF_X+XupKSuc5QAyhL6RD8rGUUY_Zm+-xoy3w@mail.gmail.com>

Oh you are right.
I uncompress the images before passing to VTK.
It would be nice to add this feature in future releases of VTK.
Matias.
On Feb 25, 2015 1:44 AM, "Ravi HM" <Ravi.HM at lnttechservices.com> wrote:

>  Hi Matias,
>
>
>
> vtkDicomImageReader supports to read only uncompressed Dicom image.
>
>
>
> When any Dicom image is compressed (Compressed in any format)
> vtkDicomImageReader doesn?t support.
>
>
>
> Regards,
>
> Ravi
>
>
>
> *From:* Matias Montroull [mailto:matimontg at gmail.com]
> *Sent:* Tuesday, February 24, 2015 7:54 PM
> *To:* Ravi HM
> *Cc:* vtkusers at vtk.org
> *Subject:* Re: [vtkusers] vtkDICOMImageReader does not support to read
> all Dicom image format
>
>
>
> Hi Ravi, which DICOM formats / Pixel Type does not support?
>
>
>
> On Tue, Feb 24, 2015 at 2:29 AM, Ravi HM <Ravi.HM at lnttechservices.com>
> wrote:
>
>  Hi All,
>
>
>
> Why vtkDICOMImageReader does not support to read all Dicom image format.
>
>
>
> Regards,
>
> Ravi
>
>
>
> *L&T Technology Services Ltd*
>
> www.LntTechservices.com <http://www.lnttechservices.com/>
>
> This Email may contain confidential or privileged information for the
> intended recipient (s). If you are not the intended recipient, please do
> not use or disseminate the information, notify the sender and delete it
> from your system.
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
> Search the list archives at: http://markmail.org/search/?q=vtkusers
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/vtkusers
>
>
>
> *L&T Technology Services Ltd*
>
> www.LntTechservices.com <http://www.lnttechservices.com/>
>
> This Email may contain confidential or privileged information for the
> intended recipient (s). If you are not the intended recipient, please do
> not use or disseminate the information, notify the sender and delete it
> from your system.
>
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From bill.lorensen at gmail.com  Wed Feb 25 08:46:56 2015
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Wed, 25 Feb 2015 08:46:56 -0500
Subject: [ITK-users] region growing with adaptative Threshold
In-Reply-To: <1424814981495-35272.post@n7.nabble.com>
References: <1424814981495-35272.post@n7.nabble.com>
Message-ID: <CADZJ4hPt9TtUi6Wu0p62mwUPF3sLE-VYCT5Ev7gWmt_AHsU3Dg@mail.gmail.com>

Take a look at the ConfidenceConnectedImageFilter

http://itk.org/Wiki/ITK/Examples/ImageSegmentation/ConfidenceConnectedImageFilter

On Tue, Feb 24, 2015 at 4:56 PM, Sunshine <samah.bouzidi at gmail.com> wrote:
> HI,
>
> I'm trying to segment the airways from 3D Ct image using this algorithm
>  1- determine the seed point and the intial threshold
>  2- calculte the average intensity of voxels already classified to the
> region (A)
>  3- if the intensity  of the voxel  and  all closest (connected) neighbours
> = (+/-) 0,05 A(step 2). voxel is classified to the region.
>
> As explained, the threshold depends on the processed data, is their any
> example in which the threshold is not defined as a constante like in the
> region growing examples?
>
> Best regards
> SAmah
>
>
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.com/region-growing-with-adaptative-Threshold-tp35272.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



-- 
Unpaid intern in BillsBasement at noware dot com

From matimontg at gmail.com  Thu Feb 26 06:08:47 2015
From: matimontg at gmail.com (Matias Montroull)
Date: Thu, 26 Feb 2015 08:08:47 -0300
Subject: [ITK-users] [vtkusers] vtkDICOMImageReader does not support to
 read all Dicom image format
In-Reply-To: <C824B527DF093F47B87947D7CDF1D7B101797994@POCITMSEXMB04.LntUniverse.com>
References: <C824B527DF093F47B87947D7CDF1D7B101796C21@POCITMSEXMB04.LntUniverse.com>
 <CAKKNfu+g=vndeq9p5vR4Xr-ecgF8k+WNdrW7tB0ZA9j9kr9GdQ@mail.gmail.com>
 <C824B527DF093F47B87947D7CDF1D7B101797148@POCITMSEXMB04.LntUniverse.com>
 <CAKKNfu+ROXSo_TF_X+XupKSuc5QAyhL6RD8rGUUY_Zm+-xoy3w@mail.gmail.com>
 <C824B527DF093F47B87947D7CDF1D7B10179735D@POCITMSEXMB04.LntUniverse.com>
 <CAKKNfuKE30Ta=1war7VNo7mdnbxei3228mCyux3Of0_Vy847dA@mail.gmail.com>
 <C824B527DF093F47B87947D7CDF1D7B1017973A7@POCITMSEXMB04.LntUniverse.com>
 <CAKKNfu+yHtu9whBFPicokG1GwJ4PFLu1LGWtwD7bqpcMvMjrzA@mail.gmail.com>
 <C824B527DF093F47B87947D7CDF1D7B101797994@POCITMSEXMB04.LntUniverse.com>
Message-ID: <CAKKNfuL4ZnUJD8jBO4ZJTvHpL=X4=+6YUVd0hNeX8jCFRFP29Q@mail.gmail.com>

Hi Ravi, yes itbis called SimpleITK..
On Feb 26, 2015 3:04 AM, "Ravi HM" <Ravi.HM at lnttechservices.com> wrote:

>
>
> Hi Matias,
>
>
>
> Do I get *ITK* package like *VTK (Kitware.Activiz.NET
> <http://Kitware.Activiz.NET>)* package for visual studio C# application
>
>
>
> Regards,
>
> Ravi
>
>
>
> *From:* Matias Montroull [mailto:matimontg at gmail.com]
> *Sent:* Wednesday, February 25, 2015 6:01 PM
> *To:* Ravi HM; vtkusers at vtk.org
> *Subject:* Re: [vtkusers] vtkDICOMImageReader does not support to read
> all Dicom image format
>
>
>
> You can use command line tool to dump this type of information, eg
> gdcminfo:
>
> $ gdcminfo 012345.002.050.dcm
>
> MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
>
> TransferSyntax is 1.2.840.10008.1.2.4.70 [JPEG Lossless, Non-Hierarchical, First-Order Prediction (Process 14 [Selection Value 1]): Default Transfer Syntax for Lossless JPEG Image Compression]
>
> ...
>
>  Pay attention that for the case of JPEG 2000 and JPEG-LS the transfer
> syntax itself is not sufficient to indicate whether or not the Pixel Data
> stream has been lossy or lossless compressed. This could be important for
> your organisation as lossy compression could impact professional
> interpretation.
>
> Ref: http://gdcm.sourceforge.net/html/gdcminfo.html
>
>
>
> On Wed, Feb 25, 2015 at 8:59 AM, Ravi HM <Ravi.HM at lnttechservices.com>
> wrote:
>
>  Hi Matias,
>
>
>
> Thank you for your kind support.
>
>
>
> Regards,
>
> Ravi
>
>
>
> *From:* Matias Montroull [mailto:matimontg at gmail.com]
> *Sent:* Wednesday, February 25, 2015 5:21 PM
> *To:* Ravi HM
> *Cc:* vtkusers at vtk.org
>
> *Subject:* RE: [vtkusers] vtkDICOMImageReader does not support to read
> all Dicom image format
>
>
>
> There is a way to identify compressed images yes I will have to look. I
> use Fo-Dicom not gdcm but I know there are methods to determine when an
> image is compressed.
>
> On Feb 25, 2015 8:46 AM, "Ravi HM" <Ravi.HM at lnttechservices.com> wrote:
>
>  Hi Matias,
>
>
>
> Yep, it would be nice if this feature is added.
>
>
>
> Is there any Dicom TAG to identify uncompressed Dicom image using GDCM or
> RZDCX
>
>
>
> Regards,
>
> Ravi
>
>
>
> *From:* Matias Montroull [mailto:matimontg at gmail.com]
> *Sent:* Wednesday, February 25, 2015 4:59 PM
> *To:* Ravi HM
> *Cc:* insight-users at itk.org Users
> *Subject:* RE: [vtkusers] vtkDICOMImageReader does not support to read
> all Dicom image format
>
>
>
> Oh you are right.
> I uncompress the images before passing to VTK.
> It would be nice to add this feature in future releases of VTK.
> Matias.
>
> On Feb 25, 2015 1:44 AM, "Ravi HM" <Ravi.HM at lnttechservices.com> wrote:
>
>  Hi Matias,
>
>
>
> vtkDicomImageReader supports to read only uncompressed Dicom image.
>
>
>
> When any Dicom image is compressed (Compressed in any format)
> vtkDicomImageReader doesn?t support.
>
>
>
> Regards,
>
> Ravi
>
>
>
> *From:* Matias Montroull [mailto:matimontg at gmail.com]
> *Sent:* Tuesday, February 24, 2015 7:54 PM
> *To:* Ravi HM
> *Cc:* vtkusers at vtk.org
> *Subject:* Re: [vtkusers] vtkDICOMImageReader does not support to read
> all Dicom image format
>
>
>
> Hi Ravi, which DICOM formats / Pixel Type does not support?
>
>
>
> On Tue, Feb 24, 2015 at 2:29 AM, Ravi HM <Ravi.HM at lnttechservices.com>
> wrote:
>
>  Hi All,
>
>
>
> Why vtkDICOMImageReader does not support to read all Dicom image format.
>
>
>
> Regards,
>
> Ravi
>
>
>
> *L&T Technology Services Ltd*
>
> www.LntTechservices.com <http://www.lnttechservices.com/>
>
> This Email may contain confidential or privileged information for the
> intended recipient (s). If you are not the intended recipient, please do
> not use or disseminate the information, notify the sender and delete it
> from your system.
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
> Search the list archives at: http://markmail.org/search/?q=vtkusers
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/vtkusers
>
>
>
> *L&T Technology Services Ltd*
>
> www.LntTechservices.com <http://www.lnttechservices.com/>
>
> This Email may contain confidential or privileged information for the
> intended recipient (s). If you are not the intended recipient, please do
> not use or disseminate the information, notify the sender and delete it
> from your system.
>
>  *L&T Technology Services Ltd*
>
> www.LntTechservices.com <http://www.lnttechservices.com/>
>
> This Email may contain confidential or privileged information for the
> intended recipient (s). If you are not the intended recipient, please do
> not use or disseminate the information, notify the sender and delete it
> from your system.
>
>    *L&T Technology Services Ltd*
>
> www.LntTechservices.com <http://www.lnttechservices.com/>
>
> This Email may contain confidential or privileged information for the
> intended recipient (s). If you are not the intended recipient, please do
> not use or disseminate the information, notify the sender and delete it
> from your system.
>
>
>
> *L&T Technology Services Ltd*
>
> www.LntTechservices.com <http://www.lnttechservices.com/>
>
> This Email may contain confidential or privileged information for the
> intended recipient (s). If you are not the intended recipient, please do
> not use or disseminate the information, notify the sender and delete it
> from your system.
>
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From peter.bloomfield at camhpet.ca  Thu Feb 26 09:59:54 2015
From: peter.bloomfield at camhpet.ca (PmB)
Date: Thu, 26 Feb 2015 09:59:54 -0500
Subject: [ITK-users] Itk, python and pyinstaller
Message-ID: <54EF34EA.5070305@camhpet.ca>

Hi,

I have tried this to the pyinstaller list, and it was suggested I tried 
here.

I am working on a linux box using ITK V4.7.1 within a python script, 
which executes without error.
However, when I build an executable with pyinstaller, on execution I get 
the following error

     Information
         Filename : junk.img
     Traceback (most recent call last):
       File "Segment_Image.py", line 97, in <module>
         image_type = itk.Image[itk.F, 3]
     NameError: name 'itk' is not defined

I tried
     python pyinstaller.py --hidden-import=itk Segment_Image.py
but during the build I get the message
     52820 INFO: Hidden import 'itk' has been found otherwise

Can anyone point me in the direction to resolve this.

Thanks

Peter
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From ds_prakash at rediffmail.com  Thu Feb 19 04:47:54 2015
From: ds_prakash at rediffmail.com (Surya Prakash)
Date: 19 Feb 2015 09:47:54 -0000
Subject: [ITK-users] =?utf-8?q?output_of_connected_threshold?=
Message-ID: <20150219094754.15737.qmail@f4mail-235-189.rediffmail.com>

Hello,
I am making an interactive region growing application using connectedThreshold. Seed point etc I want to collect interactively. After collecting the inputs, I will execute something like this.

	 smoothing->SetInput( reader->GetOutput() );
	connectedThreshold->SetInput( smoothing->GetOutput() );

I want to access the output by calling connectedThreshold->GetOutput()

How I can access the output (In memory), so that I can render it on the original image. I am making MFC application.

Thanks & regards
Prakash

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From michkapopoff at gmail.com  Thu Feb 26 16:26:39 2015
From: michkapopoff at gmail.com (michkapopoff at gmail.com)
Date: Thu, 26 Feb 2015 22:26:39 +0100
Subject: [ITK-users] Itk, python and pyinstaller
In-Reply-To: <54EF34EA.5070305@camhpet.ca>
References: <54EF34EA.5070305@camhpet.ca>
Message-ID: <F6D91F85-AF48-4C2B-96D8-07AB1253B1BD@gmail.com>

Hi 

I tried to use pyinstaller 1 or 2 years ago to install ITK with one of my apps, but it never worked.
Pyinstaller has a hook system to add dependencies, so you can update the itk hook to make it work.
Still, I did not find enough documentation or examples to make it work and did not invest more time
to read pyinstaller?s source code. It?s maybe complicated because it implies moving libs and stuff around ?

But it would be very nice if it worked. Maybe somebody here could give a try.

Michka

> On 26 Feb 2015, at 15:59, PmB <peter.bloomfield at camhpet.ca> wrote:
> 
> Hi,
> 
> I have tried this to the pyinstaller list, and it was suggested I tried here.
> 
> I am working on a linux box using ITK V4.7.1 within a python script, which executes without error.
> However, when I build an executable with pyinstaller, on execution I get the following error
> 
>     Information
>         Filename : junk.img
>     Traceback (most recent call last):
>       File "Segment_Image.py", line 97, in <module>
>         image_type = itk.Image[itk.F, 3]
>     NameError: name 'itk' is not defined
> 
> I tried
>     python pyinstaller.py --hidden-import=itk Segment_Image.py
> but during the build I get the message
>     52820 INFO: Hidden import 'itk' has been found otherwise
> 
> Can anyone point me in the direction to resolve this. 
> 
> Thanks
> 
> Peter
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