[Insight-users] Can a metric be negative in ITK?

Fri Mar 2 12:04:01 EST 2012

"High" negative  is what you want from this metric, as I understand it.

Rick
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Sent: Friday, March 02, 2012 12:00 PM
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Today's Topics:

   1. Connecting itk image to vtk with Module_ITKVtkGlue
      (Mathieu Stumpf)
   2. Re: Problem with TransformPoint (brian avants)
   3. Can a metric be negative in ITK? (Christopher Kappe)

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

Message: 1
Date: Fri, 02 Mar 2012 14:49:56 +0100
From: Mathieu Stumpf <mathieu.stumpf at etu.unistra.fr>
Subject: [Insight-users] Connecting itk image to vtk with
	Module_ITKVtkGlue
To: insight-users at itk.org
Message-ID: <1330696196.15121.289.camel at mivstg2011a.u-strasbg.fr>
Content-Type: text/plain; charset="utf-8"

Hello,

I want to make communicate itk with itk in python.

I recompiled itk (from git) with the Module_ITKVtkGlue.

The installation seems ok[1], but I can't launch any working example. I
tried the CannyEdgeDetectionImageFilterConnectVTKITK.py found in
Examples/Visualization but got this error :

        python CannyEdgeDetectionImageFilterConnectVTKITK.py 
        Traceback (most recent call last):
          File "CannyEdgeDetectionImageFilterConnectVTKITK.py", line 33,
        in <module>
            import InsightToolkit as itk
          File "/usr/local/lib/ITK-4.1/Python/InsightToolkit.py", line
        75, in <module>
            from ITKMetricsv4Python import *
        ImportError: No module named ITKMetricsv4Python

Note that the code say "For this to work, you have to build
InsightApplications/ConnectVTKITK". To install it (git version) I had to
change the CMakelists.txt because the conditions around
OPTIONAL_APP(ConnectVTKITK) seems no to be fulfilled.

Putting OPTIONAL_APP(ConnectVTKITK) as is and setting my env as bellow
compiled without error (but with a warning about CMAKE_MODULE_PATH while
configuring with ccmake) :
        export
CableSwig_DIR=/usr/local/WrapITK/lib/CableSwig/:${CableSwig_DIR}
        export CMAKE_MODULE_PATH=${CableSwig_DIR}:${CMAKE_MODULE_PATH}

But I have still the same error when I try to launch
CannyEdgeDetectionImageFilterConnectVTKITK.py

It seems that after all this installations the ITKMetrics wrapper wasn't
generated[2]. Is there any optional module that I missed ?

I also tried to write a little script (see attached file) to open an
image with itk and display it with vtk, but I got the following errors :

        Traceback (most recent call last):
          File
"/home/miv/stumpf/src/farsight-tuto/quick-start/basic_reader.py", line
24, in <module>
            export.SetInput(itk_image) # !!! bug !!!
        TypeError: in method 'itkVTKImageExportIUC2_SetInput', argument
2 of type 'itkImageUC2 const *'
        swig/python detected a memory leak of type
'itkDataObject_Pointer *', no destructor found.

Let me now if you are aware of a simple python module which just open a
nifti picture with itk and display it through vtk.

Kind regards,
Mathieu

[1]
        $ find /usr/local/ -iname *itkVTK*|grep 4.1
        /usr/local/include/ITK-4.1/itkVTKImageExportBase.h
        /usr/local/include/ITK-4.1/itkVTKPolyDataMeshIO.h
        /usr/local/include/ITK-4.1/itkVTKImageExport.h
        /usr/local/include/ITK-4.1/itkVTKImageImport.hxx
        /usr/local/include/ITK-4.1/itkVTKPolyDataMeshIOFactory.h
        /usr/local/include/ITK-4.1/itkVTKPolyDataReader.h
        /usr/local/include/ITK-4.1/itkVTKImageIO.h
        /usr/local/include/ITK-4.1/itkVTKImageToImageFilter.h
        /usr/local/include/ITK-4.1/itkVTKPolyDataWriter.h
        /usr/local/include/ITK-4.1/itkVTKImageImport.h
        /usr/local/include/ITK-4.1/itkVTKImageIOFactory.h
        /usr/local/include/ITK-4.1/itkVTKPolyDataWriter.hxx
        /usr/local/include/ITK-4.1/itkVTKImageToImageFilter.hxx
        /usr/local/include/ITK-4.1/itkVTKPolyDataReader.hxx
        /usr/local/include/ITK-4.1/itkVTKImageExport.hxx
        /usr/local/lib/libITKVtkGlue-4.1.so
        /usr/local/lib/libITKVTK-4.1.so
        /usr/local/lib/libITKVTK-4.1.so.1
        /usr/local/lib/cmake/ITK-4.1/Modules/ITKVtkGlue.cmake
        /usr/local/lib/cmake/ITK-4.1/Modules/ITKVTK.cmake

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/itkVTKImageI
mportSwigInterface.h.in

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/ITKVtkGlue.m
dx

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/ITKVTK.mdx

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/itkVTKImageI
O.i

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/itkVTKImageI
mport.idx

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/itkVTKImageE
xport.idx

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/itkVTKImageI
mport.i

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/itkVTKImageT
oImageFilter.idx

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/itkVTKImageE
xportSwigInterface.h.in

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/itkVTKImageT
oImageFilterSwigInterface.h.in

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/ITKVtkGlue.i

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/itkVTKImageE
xport.i

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/itkVTKImageI
O.idx

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/ITKVTK.i

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/itkVTKImageI
OSwigInterface.h.in

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/itkVTKImageT
oImageFilter.i

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/python/itkVT
KImageIO_ext.i

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/python/ITKVT
K_ext.i

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/python/itkVT
KImageImport_ext.i

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/python/itkVT
KImageToImageFilter_ext.i

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/python/itkVT
KImageExport_ext.i

/usr/local/lib/cmake/ITK-4.1/WrapITK/Configuration/Typedefs/python/ITKVt
kGlue_ext.i
        /usr/local/lib/ITK-4.1/Python/itkVTKImageToImageFilterPython.py
        /usr/local/lib/ITK-4.1/Python/itkVTKImageIOPython.py
        /usr/local/lib/ITK-4.1/Python/ITKVtkGlue.py
        /usr/local/lib/ITK-4.1/Python/itkVTKImageExportPython.py
        /usr/local/lib/ITK-4.1/Python/_ITKVTKPython.so
        /usr/local/lib/ITK-4.1/Python/ITKVTK.py
        /usr/local/lib/ITK-4.1/Python/_ITKVtkGluePython.so
        /usr/local/lib/ITK-4.1/Python/ITKVTKPython.py
        /usr/local/lib/ITK-4.1/Python/itkVTKImageImportPython.py
        /usr/local/lib/ITK-4.1/Python/ITKVtkGluePython.py
        /usr/local/lib/ITK-4.1/Python/Configuration/ITKVtkGlueConfig.py
        /usr/local/lib/ITK-4.1/Python/Configuration/ITKVTKConfig.py
        /usr/local/lib/libITKVTK-4.1.a
        /usr/local/lib/libITKVtkGlue-4.1.so.1

        [2] 
        $ locate ITKMetricsv4

/home/miv/stumpf/src/itk-git/build/Modules/Registration/Metricsv4/CMakeF
iles/ITKMetricsv4-all.dir

/home/miv/stumpf/src/itk-git/build/Modules/Registration/Metricsv4/CMakeF
iles/ITKMetricsv4.cmake

/home/miv/stumpf/src/itk-git/build/Modules/Registration/Metricsv4/CMakeF
iles/ITKMetricsv4-all.dir/DependInfo.cmake

/home/miv/stumpf/src/itk-git/build/Modules/Registration/Metricsv4/CMakeF
iles/ITKMetricsv4-all.dir/build.make

/home/miv/stumpf/src/itk-git/build/Modules/Registration/Metricsv4/CMakeF
iles/ITKMetricsv4-all.dir/cmake_clean.cmake

/home/miv/stumpf/src/itk-git/build/Modules/Registration/Metricsv4/CMakeF
iles/ITKMetricsv4-all.dir/depend.internal

/home/miv/stumpf/src/itk-git/build/Modules/Registration/Metricsv4/CMakeF
iles/ITKMetricsv4-all.dir/depend.make

/home/miv/stumpf/src/itk-git/build/Modules/Registration/Metricsv4/CMakeF
iles/ITKMetricsv4-all.dir/progress.make

/home/miv/stumpf/src/itk-git/build/Modules/Registration/Metricsv4/test/I
TKMetricsv4TestDriver.cxx

/home/miv/stumpf/src/itk-git/build/Utilities/Doxygen/Modules/ITKMetricsv
4.dox

/home/miv/stumpf/src/itk-git/build/Utilities/Doxygen/html/ITKMetricsv4_8
dox.html

/home/miv/stumpf/src/itk-git/build/Utilities/Doxygen/html/group__ITKMetr
icsv4.html
        /home/miv/stumpf/src/itk-git/build/Wrapping/Modules/ITKMetricsv4

/home/miv/stumpf/src/itk-git/build/Wrapping/Modules/ITKMetricsv4/CMakeFi
les

/home/miv/stumpf/src/itk-git/build/Wrapping/Modules/ITKMetricsv4/CTestTe
stfile.cmake

/home/miv/stumpf/src/itk-git/build/Wrapping/Modules/ITKMetricsv4/Makefil
e

/home/miv/stumpf/src/itk-git/build/Wrapping/Modules/ITKMetricsv4/cmake_i
nstall.cmake

/home/miv/stumpf/src/itk-git/build/Wrapping/Modules/ITKMetricsv4/CMakeFi
les/CMakeDirectoryInformation.cmake

/home/miv/stumpf/src/itk-git/build/Wrapping/Modules/ITKMetricsv4/CMakeFi
les/progress.marks

/home/miv/stumpf/src/itk-git/build/lib/cmake/ITK-4.1/Modules/ITKMetricsv
4.cmake

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4-all.dir

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4.cmake

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTest1.dir

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTestClean.dir

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4-all.dir/DependInfo.cmake

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4-all.dir/build.make

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4-all.dir/cmake_clean.cmake

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4-all.dir/depend.internal

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4-all.dir/depend.make

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4-all.dir/progress.make

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTest1.dir/DependInfo.cmake

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTest1.dir/build.make

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTest1.dir/cmake_clean.cmake

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTest1.dir/depend.make

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTest1.dir/flags.make

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTest1.dir/link.txt

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTest1.dir/progress.make

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTest1.dir/test

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTestClean.dir/DependInfo.cmake

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTestClean.dir/build.make

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTestClean.dir/cmake_clean.cmake

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/CMa
keFiles/ITKMetricsv4HeaderTestClean.dir/progress.make

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/tes
t/ITKMetricsv4TestDriver.cxx

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/tes
t/CMakeFiles/ITKMetricsv4TestDriver.dir

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/tes
t/CMakeFiles/ITKMetricsv4TestDriver.dir/DependInfo.cmake

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/tes
t/CMakeFiles/ITKMetricsv4TestDriver.dir/Labels.txt

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/tes
t/CMakeFiles/ITKMetricsv4TestDriver.dir/build.make

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/tes
t/CMakeFiles/ITKMetricsv4TestDriver.dir/cmake_clean.cmake

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/tes
t/CMakeFiles/ITKMetricsv4TestDriver.dir/depend.make

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/tes
t/CMakeFiles/ITKMetricsv4TestDriver.dir/flags.make

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/tes
t/CMakeFiles/ITKMetricsv4TestDriver.dir/link.txt

/home/miv/stumpf/src/itk-stable/build/Modules/Registration/Metricsv4/tes
t/CMakeFiles/ITKMetricsv4TestDriver.dir/progress.make

/home/miv/stumpf/src/itk-stable/build/Utilities/Doxygen/Modules/ITKMetri
csv4.dox

/home/miv/stumpf/src/itk-stable/build/Wrapping/Modules/ITKMetricsv4

/home/miv/stumpf/src/itk-stable/build/Wrapping/Modules/ITKMetricsv4/CMak
eFiles

/home/miv/stumpf/src/itk-stable/build/Wrapping/Modules/ITKMetricsv4/CTes
tTestfile.cmake

/home/miv/stumpf/src/itk-stable/build/Wrapping/Modules/ITKMetricsv4/Make
file

/home/miv/stumpf/src/itk-stable/build/Wrapping/Modules/ITKMetricsv4/cmak
e_install.cmake

/home/miv/stumpf/src/itk-stable/build/Wrapping/Modules/ITKMetricsv4/CMak
eFiles/CMakeDirectoryInformation.cmake

/home/miv/stumpf/src/itk-stable/build/Wrapping/Modules/ITKMetricsv4/CMak
eFiles/progress.marks

/home/miv/stumpf/src/itk-stable/build/lib/cmake/ITK-4.0/Modules/ITKMetri
csv4.cmake
        /usr/local/lib/cmake/ITK-4.0/Modules/ITKMetricsv4.cmake
        /usr/local/lib/cmake/ITK-4.1/Modules/ITKMetricsv4.cmake

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

Message: 2
Date: Fri, 2 Mar 2012 09:03:25 -0500
From: brian avants <stnava at gmail.com>
Subject: Re: [Insight-users] Problem with TransformPoint
To: "Clemens M. Hentschke" <cmh at isg.cs.uni-magdeburg.de>
Cc: insight-users at itk.org
Message-ID:

<CABWzF4XSUxqw-506Edz0sxxSJuUL=G7OJOCAK_Y2rpKW_50mXQ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

hi clemens

the transform, when applied to resample a moving image to a fixed image,
calls transformpoint on each fixed point to get the corresponding moving
point.

you might want to try using the inverse of your transform when mapping
from the moving space to the fixed space.  i.e. your code should be
almost the same except that you use the inverse transform.

brian

On Thu, Mar 1, 2012 at 8:39 AM, Clemens M. Hentschke
<cmh at isg.cs.uni-magdeburg.de> wrote:
> Hi,
>
> I want to transform points with the TransformPoint() method from one 
> coordinate system (moving image) to another coordinate system (fixed
image).
> So far, I checked the transformation works fine by applying it to the 
> image, the result image was as I expected correct.
> As I am only interested in single pixels (and their respective 
> transformed coordinates), I only used the TransformPoint() method of 
> Similarity3DTransform insted of transforming the whole image.
> I converted from pixel to physical coordinates on the moving image, 
> transformed this coordinates and converted the physical coordinates to

> pixel coordinates on the fixed image.
> However, the pixels from the moving image do not correspond to the 
> fixed image.
> I use ITK 3.20 with Windows 7 and the MinGW compiler.
> Has anyone an idea what the problem may could be?
> Thanks in advance.
>
> I attached a code snippet:
>
> typedef TransformType::InputPointType CenterType;
>
> ? ?typedef itk::Similarity3DTransform<double> TransformType; ? 
> ?TransformType::Pointer transform =TransformType::New();
>
> ? ? ?CenterType center;
> ? ? ?center[0] = 3.3874403492;
> ? ? ?center[1] = -17.7840881162;
> ? ? ?center[2] = 50.2830146457;
> ? ? ?transform->SetCenter(center); // setting the center coordinates 
> manually
>
> ? ? ?readerMoving->Update();
> ? ? ?readerFixed->Update();
> ? ? ?ImageType::Pointer mImage = readerMoving->GetOutput(); //the 
> moving image ? ? ?ImageType::Pointer fImage = 
> readerFixed->GetOutput(); //the fixed image
>
> ? ? ?TransformType::ParametersType
> paramsInput(transform->GetNumberOfParameters());
> ? ? ?paramsInput[0] = 0.244805;
> ? ? ?paramsInput[1] = 0.009105;
> ? ? ?paramsInput[2] = -0.056415;
> ? ? ?paramsInput[3] = -7.963562;
> ? ? ?paramsInput[4] = -29.462040;
> ? ? ?paramsInput[5] = 61.358929;
> ? ? ?paramsInput[6] = 0.981010;
>
> ? ? ?transform->SetParameters(paramsInput); //setting the parameters 
> manually
>
> ? ? ?ImageType::IndexType indexIn;
> ? ? ?indexIn[0] = 162; ?//some sample pixel from the moving image ? ? 
> ?indexIn[1] = 218; ? ? ?indexIn[2] = 81;
>
> ? ? ?TransformType::InputPointType pt;
>
> ? ? ?mImage->TransformIndexToPhysicalPoint(indexIn, pt);
>
> ? ? ?TransformType::OutputPointType output = 
> ?transform->TransformPoint(pt);
>
> ? ? ?ImageType::IndexType indexOut;
> ? ? ?fImage->TransformPhysicalPointToIndex(output, indexOut);
>
> ? ? ?for (int i=0; i<3; i++)
> ? ? ? ? ?cout << indexOut[i] << endl; //the output coordinates are 
> obviously wrong, they do NOT match to the input (moving image) 
> coordinates _____________________________________
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------------------------------

Message: 3
Date: Fri, 02 Mar 2012 15:47:15 +0100
From: Christopher Kappe <cpkappe at gmx.de>
Subject: [Insight-users] Can a metric be negative in ITK?
To: insight-users at itk.org
Message-ID: <110895240.NtNZXj0R7c at chrisbook.site>
Content-Type: text/plain; charset="us-ascii"

Hello everybody, 

I'm new to this list. 
I'm trying to do registration with two 3D images. I basically used the
ImageRegistration8.cxx example (using itk 4.0 btw) but with
MattesMutualInformationMetric instead of MeanSquaresMetric. 
And, well, I got output like this from the observer: 

0   -0.00130253  
1   -0.000181399 
2   -0.00019049   
3   -5.82618e-06
4   -6.76423e-06 
5   -1.81517e-05  
6   -1.78196e-05   
7   -7.79246e-06  
8   -4.0121e-06
9   -3.87818e-06 
10   -1.20782e-05   
11   -2.655e-06   
12   -1.13154e-05  
13   -7.53967e-06  
14   -8.0584e-06  
15   -3.52788e-06 
16   -2.35729e-06
17   -5.10754e-06
18   -6.61478e-05
19   -0.000101335
...
49   -0.000806308 
Optimizer stop condition: VersorRigid3DTransformOptimizer: Maximum
number of iterations (50) exceeded.
          Probe Tag    Starts    Stops             Time (s)
        Registration           1            1           4509.42

The thing is, it's not even converging (at least not towards 0).
And is it okay to get a negative metric as result in the first place?

Best
Paul Muetze

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

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