[Insight-developers] select an item from a binary image
elhadj meljane
elhadj.meljane at gmail.com
Wed Nov 13 09:07:11 EST 2013
Hi,
I used
LabelMapMaskImageFilter
it looks more appropriate for my current need ( the output looks
promising) ... However, your BoundingBoxImageLabelMapFilter may be useful
latter in my application.
Thanks!
Best,
EM
On Wed, Nov 13, 2013 at 8:54 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>wrote:
> 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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>>>>
>>>>
>>>
>>
>>
>> _______________________________________________
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>>
>> Visit other Kitware open-source projects at
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>>
>> 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:
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>>
>
>
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