[Insight-developers] select an item from a binary image

[Bradley Lowekamp]

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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> 
> 
> 

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