[ITK Community] [Insight-developers] select an item from a binary image
Bradley Lowekamp
blowekamp at mail.nih.gov
Tue Nov 12 21:50:44 EST 2013
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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