[Insight-users] [slicer-devel] itkLabelMapMaskImageFilter issue

Wed Jan 29 16:52:53 EST 2014

Thank you Bradley for your answer.
(I think the link to the example is missing. At least I cannot see it.
Would it be possible for you to send it again ? Thank you).

What I have for now is the output of RelabelComponentImageFilter, which is
a "labelmap" with a label and the size for each object.

Now, I loop over all labels found, and I check the size. If the size is in
a range (defined by me), I want to use the label corresponding to mask
(remove) these voxels from the original image.

The problem for now is I cannot even compile the code. Everything compile
and work until I try to create the itk::LabelMapMaskImageFilter, then I got
compilation error about LabelMapFilter.h not having LabelObjectType, and
Iterator (I checked on LabelMapFilter.h and LabelMapMaskFilter.h and they
both have a typedef for LabelObjectType).

I created an image type, unsigned short with 3 dimensions, and I passed
this as input and output type for LabelMapMaskImageFilter (that I typedef
MaskFilter). Is it what's required for this filter ?

But when I try to do:
  typename MaskFilter::Pointer mFilter = MaskFilter::New();

I got the error at compilation about LabelObjectType.

This is how I built all other ITK filters so far. I don't understand why
this one is not compiling.

Thank you very much.
-Laurent

On Wed, Jan 29, 2014 at 4:38 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>wrote:

Laurent,
>
> I am moving this question to the ITK users list as JC suggested.
>
> Your task is well suited to transforming from pixel based work to ITK's
> LabelMap base selection. It should be faster and reduce memory usage using
> this approach.
>
> I encourage you to read the Insight Journal article on the LabelMaps there
> is a lot there are many different ways to put the pieces together.
>
> The hard part is getting the segmentation done, you seem to indicate that
> you have done that already thought :)
>
>
> The basic flow is to select "objects" based on a attribute criteria, with
> an input of a binary image and a output of the same:
>
>
> BinaryImageToShapeLabelMapFilter[1]->AttributeOpeningImageFilter[2]->LabelMapToBinaryImageFilter[3]
>
>
> This pipeline is composed into the BinaryShapeOpeningImageFilter[4], but I
> think you will need to have a couple of AttributeOpening filters in your
> pipeline, so building the pipeline your self is the flexibility you need
> for your case.
>
> If all you need is a masked feature image output and not the opened binary
> image, you what you initially tried, the LabelMapMaskImageFilter[5]
>
> This is a useful example[6].
>
> Hope this helps,
> Brad
>
> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1BinaryImageToShapeLabelMapFilter.html
> [2]
> http://www.itk.org/Doxygen/html/classitk_1_1AttributeOpeningLabelMapFilter.html
> [3]
> http://www.itk.org/Doxygen/html/classitk_1_1LabelMapToBinaryImageFilter.html
> [4]
> http://www.itk.org/Doxygen/html/classitk_1_1BinaryShapeOpeningImageFilter.html
> [5]
> http://www.itk.org/Doxygen/html/classitk_1_1LabelMapMaskImageFilter.html
> [6]
>
> On Jan 29, 2014, at 3:56 PM, Laurent Chauvin <lchauvin at bwh.harvard.edu>
> wrote:
>
>
>  Hello Bradley,
>>
>> I understand.
>> However my goal is too detect object with a certain number of pixels, and
>> use the other "objects" (bigger or smaller than my range) to mask my
>> original image to remove them, so I would only keep the object with the
>> number of pixel in my range in my image.
>>
>> I applied a ConnectedComponentImageFilter, and then a
>> RelabelComponentImageFilter to label object by size of pixels.
>> Now from these filter, for each object, I would like to look if the
>> number of pixel is in my range, and if not use the label created by
>> RelabelComponentImageFilter to mask my original image (to remove the object
>> from the original image).
>>
>> I don't think I can specify a label in MaskImageFilter, can I ?
>>
>> Thank you very much.
>> -Laurent
>>
>>
>> On Wed, Jan 29, 2014 at 3:34 PM, Bradley Lowekamp <blowekamp at mail.nih.gov
>> > wrote:
>>
>>
>> Hello Laurent,
>>
>> The ITK "LabelMap" class is different that the Slicer concept of a label
>> map. The ITK LabelMap is a run-length encode image designed to map label ID
>> to associated data to facilitate label based attribute filtering. This was
>> contributed in an Insight Journal article[1]. There are a great many things
>> that can be efficiently computed in the framework.
>>
>> You are using it wrong as it's not suppose to work with the ITK Image but
>> the ITK LabelMap class. You are likely looking for just the regular
>> MaskImageFilter[2] in ITK.
>>
>> [1] http://www.insight-journal.org/browse/publication/176
>> [2] http://www.itk.org/Doxygen/html/classitk_1_1MaskImageFilter.html
>>
>> On Jan 29, 2014, at 3:22 PM, Laurent Chauvin <lchauvin at bwh.harvard.edu>
>> wrote:
>>
>>
>>  Hello slicer developers,
>>>
>>> I'm trying to create a CLI that use some itk filters, and it's working,
>>> but now I want to include a itkLabelMapMaskImageFilter but I got some
>>> errors.
>>>
>>> This is the code:
>>>
>>>   const    unsigned int      Dimension  = 3;
>>>   typedef unsigned short  IntegralPixelType;
>>>   typedef itk::Image<IntegralPixelType, Dimension>  IntegralImageType;
>>>   typedef itk::LabelMapMaskImageFilter<IntegralImageType,
>>> IntegralImageType> MaskFilter;
>>>
>>>
>>>   // This line create an issue
>>>   typename MaskFilter::Pointer mFilter = MaskFilter::New();
>>>
>>>
>>> Here is the error:
>>>
>>>  In file included from
>>> /home/snr/Slicer4/Slicer-Debug/ITKv4/Modules/Filtering/LabelMap/include/itkLabelMapMaskImageFilter.h:21:0,
>>>
>>>                  from
>>> /home/snr/Slicer4/ExternalModules/PointillismRegistration/PointillismRegistration/PointillismRegistration.cxx:7:
>>>
>>> /home/snr/Slicer4/Slicer-Debug/ITKv4/Modules/Filtering/LabelMap/include/itkLabelMapFilter.h:
>>> In instantiation of 'class itk::LabelMapFilter<itk::Image<short unsigned
>>> int, 3u>, itk::Image<short unsigned int, 3u> >':
>>>
>>> /home/snr/Slicer4/Slicer-Debug/ITKv4/Modules/Filtering/LabelMap/include/itkLabelMapMaskImageFilter.h:47:7:
>>>   required from 'class itk::LabelMapMaskImageFilter<itk::Image<short
>>> unsigned int, 3u>, itk::Image<short unsigned int, 3u> >'
>>>
>>> /home/snr/Slicer4/ExternalModules/PointillismRegistration/PointillismRegistration/PointillismRegistration.cxx:74:22:
>>>   required from here
>>>
>>> /home/snr/Slicer4/Slicer-Debug/ITKv4/Modules/Filtering/LabelMap/include/itkLabelMapFilter.h:80:55:
>>> error: no type named 'LabelObjectType' in
>>> 'itk::LabelMapFilter<itk::Image<short unsigned int, 3u>, itk::Image<short
>>> unsigned int, 3u> >::InputImageType {aka class itk::Image<short unsigned
>>> int, 3u>}'
>>> /home/snr/Slicer4/Slicer-Debug/ITKv4/Modules/Filtering/LabelMap/include/itkLabelMapFilter.h:127:37:
>>> error: no type named 'Iterator' in 'itk::LabelMapFilter<itk::Image<short
>>> unsigned int, 3u>, itk::Image<short unsigned int, 3u> >::InputImageType
>>> {aka class itk::Image<short unsigned int, 3u>}'
>>>
>>>
>>> I'm not sure why LabelObjectType cannot be found in LabelMapFilter (and
>>> why it's looking LabelMapFilter for it and not in LabelMapMaskFilter).
>>>
>>> I tried to find examples of code with itkLabelMapMaskImageFilter but I
>>> couldn't find any.
>>>
>>> Is there something wrong in the class or is it in my code ?
>>>
>>> Thank you.
>>> -Laurent
>>>
>>> --
>>> Laurent Chauvin, MS
>>> Surgical Navigation and Robotics Laboratory, Radiology Department
>>> Brigham And Women's Hospital, Harvard Medical School
>>> http://wiki.ncigt.org/index.php/User:Lchauvin
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>>
>> --
>> Laurent Chauvin, MS
>> Surgical Navigation and Robotics Laboratory, Radiology Department
>> Brigham And Women's Hospital, Harvard Medical School
>> http://wiki.ncigt.org/index.php/User:Lchauvin
>>
>
-- 
Laurent Chauvin, MS
Surgical Navigation and Robotics Laboratory, Radiology Department
Brigham And Women's Hospital, Harvard Medical School
http://wiki.ncigt.org/index.php/User:Lchauvin

-- 
Laurent Chauvin, MS
Surgical Navigation and Robotics Laboratory, Radiology Department
Brigham And Women's Hospital, Harvard Medical School
http://wiki.ncigt.org/index.php/User:Lchauvin
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