[Insight-developers] select an item from a binary image
Bradley Lowekamp
blowekamp at mail.nih.gov
Wed Nov 13 08:54:49 EST 2013
Hi,
That is what the BoundingBoxImageLabelMapFilter is suppose to do. It crops an axis aligned bounding box around a label in the label map infrastructure.
What are you trying to do?
And why did you try this approach?
There is the MaskImageFilter[1] that may suit your needs.
Brad
[1] http://www.itk.org/Doxygen/html/classitk_1_1MaskImageFilter.html
On Nov 13, 2013, at 8:25 AM, elhadj meljane <elhadj.meljane at gmail.com> wrote:
> Hi Bradley,
> Thanks, it worked when I added a label image. But it crops the item in a smaller image. Is there a way to keep the initial image size: just mask the other items in the initial image ...
>
> Thanks.
> Best,
> EM
>
>
> On Tue, Nov 12, 2013 at 9:50 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello,
>
> Around ITK programs you need exception handling to determine the errors thrown.
>
> I added the following around your code:
>
> try
> {
> ...
> }
> catch (std::exception &e)
> {
> std::cerr << "Exception: " << e.what() << std::endl;
> return 1;
> }
> catch (...)
> {
> std::cerr << "Unknown Exception!" << std::endl;
> throw;
> }
>
> Note that the itk::ExceptionObject class is derived from std::exception so this will catch that too.
>
> The gave me the following output:
>
> Exception: /Users/blowekamp/src/ITK/Modules/Core/Common/src/itkProcessObject.cxx:1380:
> itk::ERROR: BoundingBoxImageLabelMapFilter(0x7f92bb8bce90): Input FeatureImage is required but not set.
>
> Which says you are missing an input to this filter.
>
> You can provide the input label image as the feature image like so:
>
> toBBILabelMap->SetFeatureImage(reader->GetOutput());
>
> The examples in that modules should be usable. You just need to get your labels correct for the binary/label image. Not too hard to run a ConnectedComponets filter if needed.
>
> Brad
>
> On Nov 12, 2013, at 2:43 PM, elhadj meljane <elhadj.meljane at gmail.com> wrote:
>
>> I don't have a label image to use the example: https://github.com/blowekamp/itkOBBLabelMap/blob/master/test/itkOBBExample.cxx
>>
>> However, I used to write the main method ... where only a binary image is used as input.
>>
>> Thanks!
>> EM
>>
>>
>> On Tue, Nov 12, 2013 at 2:26 PM, elhadj meljane <elhadj.meljane at gmail.com> wrote:
>> Hello!
>> I am using your github extension (I included the files manually in my project)... and wrote the main method below. The code compile but at the run time I got the error:
>>
>> "program.exe has stopped working. A problem caused the program to stop working correctly. Windows will close the program and notify you if a solution is available. "
>> When I click to debug with MS Visual Studio, I got the warning:
>> Unhandled exception at 0x01... in program.exe: 0xC00000005: Acces violation reading location 0x18...
>>
>> Here's the code:
>>
>> #include "itkImageFileReader.h"
>>
>> #include "itkImageFileWriter.h"
>>
>> #include "itkBoundingBoxImageLabelMapFilter.h"
>>
>> #include "itkAttributeImageLabelObject.h"
>>
>> #include "itkBinaryImageToShapeLabelMapFilter.h"
>>
>>
>> const unsigned int Dimension = 2;
>>
>> typedef unsigned char LabelPixelType;
>>
>> typedef itk::Image< LabelPixelType, Dimension > LabelImageType;
>>
>> typedef unsigned char OutputPixelType;
>>
>> typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>>
>> typedef itk::ImageFileReader< OutputImageType > ReaderType;
>>
>> typedef itk::ImageFileWriter< OutputImageType > WriterType;
>>
>> typedef itk::AttributeImageLabelObject< LabelPixelType, Dimension, OutputImageType > LabelObjectAttributeType;
>>
>> typedef itk::LabelMap<LabelObjectAttributeType> LabelMapAttributeType;
>>
>> typedef itk::BinaryImageToShapeLabelMapFilter
>>
>> <OutputImageType, LabelMapAttributeType> LabelMapperAttributeType;
>>
>> typedef itk::LabelMapToLabelImageFilter<LabelMapAttributeType, OutputImageType> LabelMapToLabelImageFilterType;
>>
>> typedef itk::BoundingBoxImageLabelMapFilter<LabelMapAttributeType> BBILabelMapFilter;
>>
>>
>>
>> int main( int argc, char *argv[] )
>>
>> {
>>
>>
>> ReaderType::Pointer reader = ReaderType::New();
>>
>> typedef itk::ImageFileWriter< OutputImageType > WriterType;
>>
>>
>> //input
>>
>> reader->SetFileName( argv[1] );
>>
>>
>> //label image
>>
>> LabelMapperAttributeType::Pointer labelerAttribute = LabelMapperAttributeType::New();
>>
>> labelerAttribute->SetInput( reader->GetOutput() );
>>
>> labelerAttribute->SetComputePerimeter( false );
>>
>> labelerAttribute->SetOutputBackgroundValue(0);
>>
>> labelerAttribute->Update();
>>
>> LabelMapAttributeType::Pointer labelMapAttribute = labelerAttribute->GetOutput();
>>
>>
>> //extract the component with the label 1
>>
>> BBILabelMapFilter::Pointer toBBILabelMap = BBILabelMapFilter::New();
>>
>> toBBILabelMap->SetInput(labelMapAttribute);
>>
>> toBBILabelMap->Update();
>>
>> const LabelObjectAttributeType* labelObjectAttribute = toBBILabelMap->GetOutput()->GetLabelObject(1);
>>
>>
>> //write
>>
>> WriterType::Pointer writer = WriterType::New();
>>
>> writer->SetFileName( "copy_input.jpg" );
>>
>> writer->SetInput( reader->GetOutput());
>>
>> writer->Update();
>>
>>
>> return 0;
>>
>> }
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Tue, Nov 12, 2013 at 1:53 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> Hello,
>>
>> It appears that you are trying to use some code from my github extension:
>>
>> https://github.com/blowekamp/itkOBBLabelMap
>>
>> I am not sure where to begin helping you. You didn't include the run-time error message, and your code fragment is missing key parts. Can you post a minimal compilable example which illustrates the problem? Sometime just narrowing down you code to this part help you figure out your issue.
>>
>> Do the tests for the extension pass for you?
>>
>> Are you able to run the example?
>>
>> https://github.com/blowekamp/itkOBBLabelMap/blob/master/test/itkOBBExample.cxx
>>
>> Brad
>>
>>
>> On Nov 12, 2013, at 1:43 PM, elhadj meljane <elhadj.meljane at gmail.com> wrote:
>>
>>> Hi all,
>>> I am trying to use itk to select a component from a binary image. The binary image contains several items and I want to separate them in different images.
>>>
>>> I used the code below but it doesn't work. I got an error message at the run time. It looks from the debugger that the line
>>>
>>> labelerAttribute->Update()
>>>
>>> causes the error. I gave a valid file as input and checked that ITK reads correctly this file. I would appreciate your help to fix this!
>>>
>>> #include "itkAttributeImageLabelObject.h"
>>>
>>> const unsigned int Dimension = 2;
>>> typedef unsigned char LabelPixelType;
>>> typedef itk::Image< LabelPixelType, Dimension > LabelImageType;
>>> typedef unsigned char OutputPixelType;
>>> typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>>> typedef itk::ImageFileReader< OutputImageType > ReaderType;
>>> typedef itk::ImageFileWriter< OutputImageType > WriterType;
>>> typedef itk::AttributeImageLabelObject< LabelPixelType, Dimension, OutputImageType > LabelObjectAttributeType;
>>> typedef itk::LabelMap<LabelObjectAttributeType> LabelMapAttributeType;
>>> typedef itk::BinaryImageToShapeLabelMapFilter
>>> <OutputImageType, LabelMapAttributeType> LabelMapperAttributeType;
>>> typedef itk::LabelMapToLabelImageFilter<LabelMapAttributeType, OutputImageType> LabelMapToLabelImageFilterType;
>>> typedef itk::BoundingBoxImageLabelMapFilter<LabelMapAttributeType> BBILabelMapFilter;
>>> typedef itk::ImageFileWriter< OutputImageType > WriterType;
>>>
>>> ReaderType::Pointer reader = ReaderType::New();
>>>
>>> reader->SetFileName( argv[1] );
>>>
>>> LabelMapperAttributeType::Pointer labelerAttribute = LabelMapperAttributeType::New();
>>>
>>>
>>> labelerAttribute->SetInput( reader->GetOutput() );
>>> labelerAttribute->SetComputePerimeter( false );
>>> labelerAttribute->SetOutputBackgroundValue(0);
>>> labelerAttribute->Update();
>>>
>>>
>>> //select the item with the label 1
>>> const LabelObjectAttributeType* labelObjectAttribute = toBBILabelMap->GetOutput()->GetLabelObject(1);
>>>
>>> BBILabelMapFilter::Pointer toBBILabelMap = BBILabelMapFilter::New();
>>> toBBILabelMap->SetInput(labelMapAttribute);
>>> toBBILabelMap->Update();
>>>
>>>
>>> Thanks.
>>> Best
>>> EM
>>>
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>>
>>
>>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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