gmane.comp.lib.itk.user

Re: Problem grafting a C++ array as an ImageToImageFilter output

Matt McCormick — 2013-05-26T01:33:17

Hi Ramon,

The approach of using SetImportPointer on the Output is not guaranteed
to work.  The assumption is that the ImageToImageFilter is creating
its Output.  It is more reliable to copy the produced Output to the
buffer.

HTH,
Matt

On Fri, May 24, 2013 at 7:16 PM, Ramón Casero Cañas <rcasero-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:
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Badoo — 2013-05-25T15:38:11

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AtlasSegmentation

2013-05-25T06:01:04

 Hello!
 I am trying to run the AtlasSegmentation code from InsightApplication-1.80/IBSRValidation, but the programe cannot execute rightly. When the programe execute to "Label image using atlas", it just stop there and cannot execute any longer. I feel puzzled. Please tell me the reason.
 Thank you!
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Problem grafting a C++ array as anImageToImageFilter output

Ramón Casero Cañas — 2013-05-24T23:16:07

Hi all,

I think there may be some problem with some of the itk::ImageToImageFilter
when one tries to graft a C++ array to be used as the filter's output, or
at least with the way I do it.

This was kindly reported by Peter Thalmann in [1], and I'm trying to help
him. This is a problem that I had also noticed with a couple of other
filters.

I have attached a minimal example of a C++ MEX file that creates a function
that can be run from Matlab, with the CMake files to compile it. (I have
tried this with ITK 4.3.1).

Save everything to directory test, and then build the example from the shell

cd test
mkdir bin
cd bin
cmake ..
make install

To run the example from Matlab,

cd test
% create a test binary square with a little hole
im = zeros(15, 15, 'uint8');
im(3:13, 3:13) = 1;
im(7:8, 7) = 0;
im2 = itk_test(im);

This runs filter itk::VotingBinaryIterativeHoleFillingImageFilter on the
image. The program outputs to the Matlab shell both the content of
filter->GetOutput(), and the content of the Matlab output array. As we can
see, the output is not being saved to the array

Filter result, reading from the filter
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Filter result, reading from the Matlab output array
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0


But this approach works for other filters. If we choose the Median filter
instead: in ItkTestSimpleImFilter.cpp, ucomment

  // typedef itk::MedianImageFilter<ImageType, ImageType>
  //   FilterType;

and comment out

  typedef itk::VotingBinaryIterativeHoleFillingImageFilter<ImageType>
    FilterType;

[...]

  // filter parameters only for the
VotingBinaryIterativeHoleFillingImageFilter
  filter->SetMaximumNumberOfIterations(4);
  filter->SetBackgroundValue(0);
  filter->SetForegroundValue(1);
  filter->SetMajorityThreshold(2);

then we can see that the array is actually being used as the filter's output

Filter result, reading from the filter
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 1 1 1 1 1 1 1 1 0 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 0 1 1 1 1 1 1 1 1 1 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Filter result, reading from the Matlab output array
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 1 1 1 1 1 1 1 1 0 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 1 1 0 0
0 0 0 1 1 1 1 1 1 1 1 1 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

I have been looking at itkVotingBinaryIterativeHoleFillingImageFilter.hxx,
and I was wondering whether the problem is in
VotingBinaryIterativeHoleFillingImageFilter< TInputImage >
::GenerateData().

The filter works iteratively, doing

  while ( m_CurrentNumberOfIterations < m_MaximumNumberOfIterations )
    {
    filter->SetInput(input);
    filter->Update();

    m_CurrentNumberOfIterations++;
    progress.CompletedPixel();   // not really a pixel but an iteration
    this->InvokeEvent( IterationEvent() );

    const unsigned int numberOfPixelsChangedInThisIteration =
      filter->GetNumberOfPixelsChanged();
    m_NumberOfPixelsChanged += numberOfPixelsChangedInThisIteration;

    output = filter->GetOutput();
    output->DisconnectPipeline();
    input = output;
    if ( numberOfPixelsChangedInThisIteration == 0 )
      {
      break;
      }
    }
  this->GraftOutput(output);


Here, output gets a DisconnectPipeline(). I have tried commenting that like
out, rebuilding and reinstalling ITK, but it doesn't seem to make a
difference.

[1]
https://groups.google.com/forum/?fromgroups#!topic/gerardus-users/pLH0iR0H74o

Best regards,

Ramon.

Re: HOW DO I BUILD ITK-SNAP

Cary lorey — 2013-05-24T22:50:37

Hi,

Unfortunately not :( , have you any idea how to compile it?

I found a link where I download the application ITK-SNAP.exe :
http://sourceforge.net/projects/itk-snap/files/itk-snap/2.4.0/
http://sourceforge.net/p/itk-snap/src/ci/master/tree/

thank you


2013/5/24 Zarko <zarko-D75R7NkCqfQ< at >public.gmane.org>

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Re: ITK Apps - How to create 3D image ???

Xiaoxiao Liu — 2013-05-24T15:20:30

Are you trying to create a 3D volume from a bunch of 2D images?
You might find the following very useful:
https://sites.google.com/site/pierrefillard/coding-blog/createa3dvolumefromseveral2dimages



On Fri, May 24, 2013 at 10:57 AM, Zarko <zarko-D75R7NkCqfQ< at >public.gmane.org> wrote:

Re: HOW DO I BUILD ITK-SNAP

Zarko — 2013-05-24T15:03:52

Hi Cary.

Have you succeeded in running the ITK SNAP ?

Z



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ITK Apps - How to create 3D image ???

Zarko — 2013-05-24T14:57:25

Few of ITK Apps such as Fast Marching Segmentation Level Set requires as
input 3 D image with at least 10 pixel in all dimensions. Is there in ITK
examples, ITK tests or in ITKApps some solution which can be used to convert
set of images, dicoms, into one 3D image that i can further use in ITKApps
???

Regards

Z



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Re: RGBImageType to FloatImageType witCastImageFilter

Bradley Lowekamp — 2013-05-24T13:05:44

Hello,

You may need some of the operations available in here:

http://www.insight-journal.org/browse/publication/780

I have not done this in ITK my self. But you would need to convert to a color space such as Luv, then process just he L channel, then convert back to RGB.

Alternatively, you can just process the channel as 3 independent components, by running the filter on each component. SimpleITK does this automatically for VectorImages

https://github.com/SimpleITK/SimpleITK/blob/master/TemplateComponents/ExecuteInternalVectorImages.cxx.in#L34

I know I have seen a Wiki example which does a very simular thing too:

http://www.itk.org/Wiki/ITK/Examples

Brad

On May 24, 2013, at 8:50 AM, chasank <chasank-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:


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Re: Peel an image

Bradley Lowekamp — 2013-05-24T12:54:42

Gib,

What was the morphological operation you were doing?

ITK's grayscale morph operations are great. However, you need to keep in mind the cost of the different shapes of structuring elements. Unfortunately the binary methods use are single threaded algorithm with a complexity dependent on the number of boundary pixel. I am guessing this the algorithm you were using. If you have a binary image you should actually be able to use the grayscale morp ops to get the same results!

I am a little hesitant to share this because I haven't used it for a bit, so I'm not certain of it's current state. I spent a little time writing a new binary morph algorithm. It's only works for crosses and box/flat structuring elements. But one thread to one thread compared to the current algorithm is was more than 10X faster, and it didn't take much longer O(Radius/32) for larger structuring elements. It's also multi-threadeded so you could easily get 100X speedup compared to the current version. I've had similar sized data set that I could run binary morphological operations in like a minute.

Also keep in mind you can resample to a lower resolution for some of these larger structures, when a course segmentation is needed.

Brad

On May 23, 2013, at 5:58 PM, Gib Bogle <g.bogle-1/NbpDiVQt6SYBAHRPvY1A< at >public.gmane.org> wrote:

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Re: RGBImageType to FloatImageType witCastImageFilter

chasank — 2013-05-24T12:50:57

Thanks for quick answers. Yes I've used the RGBToLuminanceImageFilter before
processing the blur filter. However I'm dealing with an another problem,
After converting original RGB image to grayscale image. How can I obtain its
original color map for converting grayscale to RGB ?

typedef itk::Image< itk::RGBPixel <unsigned char>,  2 >  RGBImageType;
typedef itk::Image< unsigned char, 2>                    ScalarImageType;

int main(int argc, char **argv)
{
    try
    {
        itk::ImageFileReader < RGBImageType >::Pointer reader =
                itk::ImageFileReader < RGBImageType >::New();
        itk::JPEGImageIO::Pointer jpegIO = itk::JPEGImageIO::New();
        reader->SetFileName("./sample.jpg");
        reader->SetImageIO(jpegIO);
        reader->Update();
        
        RGBImageType::Pointer image;

        itk::RGBToLuminanceImageFilter<RGBImageType,
ScalarImageType>::Pointer luminanceFilter =
                itk::RGBToLuminanceImageFilter<RGBImageType,
ScalarImageType>::New();
        luminanceFilter->SetInput(reader->GetOutput());
        luminanceFilter->Update();

        FilterCallBack::Pointer callBack = FilterCallBack::New();

        itk::BinomialBlurImageFilter< ScalarImageType, ScalarImageType
                itk::BinomialBlurImageFilter < ScalarImageType,
ScalarImageType> ::New();
        blurFilter->SetInput(luminanceFilter->GetOutput());
        blurFilter->AddObserver(itk::ProgressEvent(), callBack);
        blurFilter->SetRepetitions(3);
        blurFilter->Update();

        itk::ScalarToRGBColormapImageFilter< ScalarImageType, RGBImageType
                itk::ScalarToRGBColormapImageFilter< ScalarImageType,
RGBImageType>::New();
        colorMapFilter->SetInput(blurFilter->GetOutput());
       
colorMapFilter->SetColormap(itk::ScalarToRGBColormapImageFilter<ScalarImageType,
RGBImageType>::Jet); // Something like reader->GetOutput()->GetColorMap()
???
        colorMapFilter->Update();

        QuickView view;

        view.AddRGBImage(reader->GetOutput(), true, "Original");
        view.AddRGBImage(colorMapFilter->GetOutput(), true, "Blur
Filtered");
        view.Visualize();

    }
    catch ( itk::ExceptionObject &exception)
    {
        std::cerr << exception << std::endl;
    }

    return 0;
}



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Re: RGBImageType to FloatImageType witCastImageFilter

Bill Lorensen — 2013-05-24T11:43:56

Try RGBToLuminanceImageFilter

http://itk.org/Wiki/ITK/Examples/ImageProcessing/RGBToLuminanceImageFilter

Bill



On Fri, May 24, 2013 at 5:02 AM, chasank <chasank-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

RGBImageType to FloatImageType wit CastImageFilter

chasank — 2013-05-24T09:02:33

Hi,

I'm reading a JPEG Image and trying to process a blur filter
(BinomialBlurImageFilter) on it. Because BinomialBlurImageFilter does not
accept RGBImageType, first I'm trying to convert the RGBImageType to
FloatImageType however I'm getting compiling errors; The sample code is
below; What conversion should I do for processing a RGB Image ?

typedef itk::Image< itk::RGBPixel <unsigned char>,  2 >  RGBImageType;
typedef itk::Image< float, 2 >                                      
FloatImageType;

        itk::VTKImageToImageFilter< RGBImageType >::Pointer converter =
                itk::VTKImageToImageFilter<RGBImageType> :: New();
        converter->SetInput(this->image);
        converter->Update();

        itk::CastImageFilter<RGBImageType, FloatImageType>::Pointer caster =
                itk::CastImageFilter<RGBImageType, FloatImageType>::New();
        caster->SetInput(converter->GetOutput());
        caster->Update();

        itk::BinomialBlurImageFilter< FloatImageType, FloatImageType >
::Pointer blurFilter =
                itk::BinomialBlurImageFilter < FloatImageType,
FloatImageType> ::New();
        blurFilter->SetInput( caster->GetOutput() );
        blurFilter->SetRepetitions(2);
        blurFilter->Update();

        itk::CastImageFilter<FloatImageType, RGBImageType>::Pointer caster2
=
                itk::CastImageFilter<FloatImageType, RGBImageType>::New();
        caster2->SetInput(blurFilter->GetOutput());
        caster2->Update();

/usr/local/include/ITK-4.3/itkConceptChecking.h: In member function 'void
itk::Concept::Convertible<T1, T2>::Constraints::constraints() [with T1 =
itk::RGBPixel<unsigned char>, T2 = float]':
/usr/local/include/ITK-4.3/itkConceptChecking.h:192:   instantiated from
'itk::Concept::Convertible<itk::RGBPixel&lt;unsigned char>, float>'
/usr/local/include/ITK-4.3/itkCastImageFilter.h:116:   instantiated from
'itk::CastImageFilter<itk::Image&lt;itk::RGBPixel&lt;unsigned char>, 2u>,
itk::Image<float, 2u> >'
../Program/program.cpp:67:   instantiated from here
/usr/local/include/ITK-4.3/itkConceptChecking.h:185: error: invalid
static_cast from type 'itk::RGBPixel<unsigned char>' to type 'float'
/usr/local/include/ITK-4.3/itkCastImageFilter.h: In member function 'TOutput
itk::Functor::Cast<TInput, TOutput>::operator()(const TInput&) const [with
TInput = itk::RGBPixel<unsigned char>, TOutput = float]':
/usr/local/include/ITK-4.3/itkUnaryFunctorImageFilter.hxx:175:  
instantiated from 'void itk::UnaryFunctorImageFilter<TInputImage,
TOutputImage, TFunction>::ThreadedGenerateData(const typename
TOutputImage::RegionType&, itk::ThreadIdType) [with TInputImage =
itk::Image<itk::RGBPixel&lt;unsigned char>, 2u>, TOutputImage =
itk::Image<float, 2u>, TFunction =
itk::Functor::Cast<itk::RGBPixel&lt;unsigned char>, float>]'
../Program/program.cpp:151:   instantiated from here
/usr/local/include/ITK-4.3/itkCastImageFilter.h:83: error: invalid
static_cast from type 'const itk::RGBPixel<unsigned char>' to type 'float'



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Re: Peel an image

Gib Bogle — 2013-05-23T21:58:32

Richard, in our images dx=dy=dz, so in principle the closing should work fine in 
3D.  In fact I think the size of our images is going to make it impractical.  I 
ran a test last night on a partial image, which is 1300x1100x200, about 1/5 of a 
full image (still being generated by the microscopy rig).  It was still running 
after 9 hours this morning, when I stopped it, at 100% of the 8 cores on my PC.  
This is not really practical.

I did implement the grayscale closing, but not exactly as in your code.  I've 
been using ITK for a while, but in a very naive way, and writing a lot of my own 
code.  I am not a C++ expert by any means, and in particular I do not know 
anything about templates. It is not important (since I have something that 
works) but if you felt motivated to send me a simple example of a main program 
that calls doClosing() I'm sure I would find it very instructional.

It is not clear to me yet what radius to use for the structuring element.  I've 
tried 30, 40 and 50.  To generate the mask I guess I need to set the threshold 
level to something like 1 or 2 - some experimentation is needed.

To process the whole 3D image I'm thinking about using a slice-by-slice method, 
on the XY slices, then the YZ, then the XZ.  The idea is to process each 2D 
slice as if to peel it, but leaving the image unchanged and just recording all 
the voxels that are to be removed.  The final step will be to zero out all these 
voxels.  I think it is necessary to do it like this to avoid multiple peeling.

It will be interesting to compare the active contour approach with the grayscale 
closing method to generate the mask.

Best regards
Gib

On 23/05/2013 10:04 p.m., Richard Beare wrote:
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Re: Peel an image

Gib Bogle — 2013-05-23T21:29:34

Thanks Dan.  The active contour method sounds very interesting, I'll give it a try.

Gib

On 23/05/2013 7:36 p.m., Dan Mueller wrote:
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Re: [ome-users] bioformats and ITK

Joe Ping-Lin Hsiao — 2013-05-23T14:29:55

I got it working.
My local repository doesn't have the new variable SCIFIO_SEP, and it still
uses ":" for separator. I change it to ";" and it works. The program also
works without SCIFIO_PATH being set. So the separator fix should resolve
this issue.

Thanks for you help!
Joe


On Thu, May 23, 2013 at 9:52 AM, Joe Ping-Lin Hsiao <phsiao-+5Oa3zvhR2o3uPMLIKxrzw< at >public.gmane.org>wrote:

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Re: [ome-users] bioformats and ITK

Joe Ping-Lin Hsiao — 2013-05-23T13:52:39

Mark,

Adding the SCIFIO_PATH environment variable doesn't work for me. I
experimented with 'build/lib/jars' and 'build/lib/jars/', but I still have
the same error.
I can wait for the bug fix in ITK to get approved and try again.

Thanks,
Joe


On Wed, May 22, 2013 at 3:00 PM, Mark Hiner <hiner-63mtpxcE9Cs< at >public.gmane.org> wrote:

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Re: Bad crop with mouse click

David Doria — 2013-05-23T11:59:29

On Wed, May 22, 2013 at 7:28 PM, Cary lorey
<developement.unity-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

It sounds like this is really a VTK question (if your comment that the
right values are not produced by the GetComputedWorldValue function is
correct). Have you seen these examples?

http://www.vtk.org/Wiki/VTK/Examples/Cxx/Images/PickingAPixel
http://www.vtk.org/Wiki/VTK/Examples/Cxx/Images/PickingAPixel2

David
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Re: Peel an image

Richard Beare — 2013-05-23T10:04:39

The steps I've given should also work in 3D if the slice thickness is low
enough to provide the connectivity between slices. Personally, I haven't
had much luck with the vesselness family. My rule of thumb is that if they
happen to work, then a simple morphological approach will probably work
too, more reliably and with fewer parameters to fiddle :-).


On Thu, May 23, 2013 at 5:36 PM, Dan Mueller <dan.muel-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

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Re: Peel an image

Dan Mueller — 2013-05-23T07:36:19

Hi Gib,

Some more food for thought:

(1) If you have a 3D image (as opposed to 2D slices) you may consider
using Hessian-based vesselness enhancement:
http://www.itk.org/Doxygen/html/classitk_1_1Hessian3DToVesselnessMeasureImageFilter.html
http://www.itk.org/Doxygen/html/classitk_1_1MultiScaleHessianBasedMeasureImageFilter.html
http://www.insight-journal.org/browse/publication/314
http://www.insight-journal.org/browse/publication/175
http://www.insight-journal.org/browse/publication/163

This class of filters can enhance tube-like structures (e.g. vessels),
while suppressing sheet like structures i.e. the outer border of your
object.

(2) You could consider using an active contour method to segment the
outer structure (replacing step 1 in Richard's proposal above). You
could achieve this by initializing the contour as the edge of your
image, then shrink the contour until it attaches to the boundary of
the tissue. Then continue to follow Richard's second step and remove
the outer structure by erosion + masking.

Good luck.

Cheers, Dan

On 23 May 2013 11:16, Gib Bogle <g.bogle< at >auckland.ac.nz> wrote:
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Re: Peel an image

Gib Bogle — 2013-05-23T01:46:49

Hi Richard,

I don't have other staining.

Thanks for your suggestion of a procedure.  I will have to study it and 
understand it, before I can comment on it.

Gib

On 23/05/2013 12:25 p.m., Richard Beare wrote: