[Insight-users] extract filter problem

[Luis Ibanez]

Hi Michael,

Thanks for running the tests and sending
the results.  After experimenting with
your code we were able to reproduce the
problem that you reported.

This seems to be a bug on the use of
regions in the DiscreteGradientImageFilter.

A bug report has been created in the
phpBugtracker database. You will find it
under Bug #1136

http://www.itk.org/Bug/bug.php?op=show&bugid=1136&pos=0

You can register your email in the CC field in
order to get updates on the status of this bug.


Regards,


   Luis


--------------------
Michael Kuhn wrote:

> Hi,
> 
> A) here the output of "preFilter->GetOutput()->Print(std::cout)" after
> modifying the program.
> 
> 
> Image (0136A100)
>   RTTI typeinfo:   class itk::Image<double,3>
>   Reference Count: 2
>   Modified Time: 199
>   Debug: Off
>   Observers:
>     none
>   Source: (0136A220)
>   Source output index: 0
>   Release Data: Off
>   Data Released: False
>   Global Release Data: Off
>   PipelineMTime: 126
>   UpdateMTime: 200
>   LargestPossibleRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [65, 65, 127]
>   BufferedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [65, 65, 127]
>   RequestedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [65, 65, 127]
>   Spacing: [0.127664, 0.127664, 0.127664]
>   Origin: [0, 0, 0]
>   PixelContainer:
>     ImportImageContainer (0136A090)
>       RTTI typeinfo:   class itk::ImportImageContainer<unsigned long,double>
>       Reference Count: 1
>       Modified Time: 134
>       Debug: Off
>       Observers:
>         none
>       Pointer: 0136A0C0
>       Container manages memory: true
>       Size: 536575
>       Capacity: 536575
> 
> 
> B) The behaviour using the RegionOfInterestImageFilter is identical.
> 
> When going through the program with a debugger, it crashes in
> DiscreteGaussianImageFilter after line 201.
> 
> Thanks,
> 
> Michael
> 
> P.S.: When should I use the RegionOfInterestImageFilter and when the
> ExtractImageFilter (only if I want to change the dimensionality?)?
> 
> 
> 
> 
> 
> 
>>Hi Michael
>>
>>
>>
>>Please do the following:
>>
>>
>>
>>A) Check on image size
>>
>>1) In the try/catch block
>>
>> > 	try {
>> > 		extractFilter->Update();
>> > 	} catch (itk::ExceptionObject &e) {
>>
>>replace "extractFilter" with the gradientFilter
>>"preFilter". Then just after Update() add
>>
>>   preFilter->GetOutput()->Print( std::cout );
>>
>>2) Rerun your program
>>
>>3) Let us know the region sized that are printed.
>>
>>
>>
>>
>>B) Check for a bug in the ExtractImageFilter
>>
>>   1) Replace the ExtractImageFilter with the
>>      "RegionOfInterestImageFilter"
>>
>>   This filter is described in the SoftwareGuide
>>
>>        http://www.itk.org/ItkSoftwareGuide.pdf
>>
>>   Section 7.4, pdf-page 225.
>>
>>
>>If your program works with this filter, then there
>>is probably a buggy condition in the ExtractImageFilter.
>>
>>
>>
>>   Please let us know what you find.
>>
>>
>>          Thanks
>>
>>
>>             Luis
>>
>>
>>
>>---------------------------
>>michakuhn at gmx.ch wrote:
>>
>>
>>>Hi,
>>>
>>>I've written the following program, which is supposed to create the
>>
>>gradient
>>
>>>image for a particular region of the input image.
>>>
>>>----
>>>
>>>#include <iostream>
>>>
>>>#include "itkImage.h"
>>>#include "itkImageFileReader.h"
>>>#include "itkImageFileWriter.h"
>>>#include "itkGradientImageFilter.h"
>>>#include "itkGradientRecursiveGaussianImageFilter.h"
>>>#include "itkNumericTraits.h"
>>>#include "itkImageRegionConstIterator.h"
>>>#include "itkDiscreteGaussianImageFilter.h"
>>>#include "itkCastImageFilter.h"
>>>#include "itkExtractImageFilter.h"
>>>
>>>int main(int argc, char** argv)
>>>{
>>>	const unsigned int Dimension = 3;
>>>	typedef short PixelType;
>>>	typedef itk::Image<PixelType, Dimension> ImageType;
>>>
>>>	typedef double RealType;
>>>
>>>	typedef itk::Image<RealType, Dimension> IntermediateImageType;
>>>
>>>	typedef itk::CovariantVector<RealType, Dimension> GradientPixelType;
>>>	typedef itk::Image<GradientPixelType, Dimension> GradientImageType;
>>>	
>>>	
>>>	typedef itk::ImageFileReader<ImageType> ReaderType;
>>>
>>>	ReaderType::Pointer reader = ReaderType::New();
>>>
>>>	if (argc < 2) {
>>>		std::cout << "image in required" << std::endl;
>>>		return -1;
>>>	}
>>>	reader->SetFileName(argv[1]);
>>>
>>>	try {
>>>		reader->Update();
>>>	} catch (itk::ExceptionObject &e) {
>>>		std::cout << e << std::endl;
>>>		return -1;
>>>	}
>>>
>>>	typedef itk::CastImageFilter<ImageType, IntermediateImageType>
>>>		CastFilterType;
>>>
>>>	CastFilterType::Pointer castFilter = CastFilterType::New();
>>>
>>>	castFilter->SetInput(reader->GetOutput());
>>>
>>>
>>>	typedef itk::DiscreteGaussianImageFilter<IntermediateImageType,
>>>		IntermediateImageType>	PreFilterType;
>>>
>>>	PreFilterType::Pointer preFilter = PreFilterType::New();
>>>	preFilter->SetInput(castFilter->GetOutput());
>>>	preFilter->SetUseImageSpacing(false);
>>>	preFilter->SetMaximumKernelWidth(8);
>>>	std::cout << "default variance: " << preFilter->GetVariance() <<
>>
>>std::endl;
>>
>>>	preFilter->SetVariance(1);
>>>
>>>	typedef itk::GradientImageFilter<IntermediateImageType, RealType, 
>>>		RealType> Filter1Type;
>>>
>>>	Filter1Type::Pointer filter1 = Filter1Type::New();
>>>	filter1->SetInput(preFilter->GetOutput());
>>>
>>>	typedef itk::ExtractImageFilter<GradientImageType, GradientImageType>
>>>		ExtractFilterType;
>>>	ExtractFilterType::Pointer extractFilter = ExtractFilterType::New();
>>>
>>>	extractFilter->SetInput(filter1->GetOutput());
>>>
>>>	typedef GradientImageType::RegionType RegionType;
>>>	RegionType region;
>>>	RegionType::SizeType size;
>>>	RegionType::IndexType index;
>>>
>>>	size[0] = 1;
>>>	size[1] = 32;
>>>	size[2] = 32;
>>>
>>>	index[0] = 64;
>>>	index[1] = 0;
>>>	index[2] = 0;
>>>
>>>	region.SetSize(size);
>>>	region.SetIndex(index);
>>>
>>>	extractFilter->SetExtractionRegion(region);
>>>
>>>	try {
>>>		extractFilter->Update();
>>>	} catch (itk::ExceptionObject &e) {
>>>		std::cout << e << std::endl;
>>>		return -1;
>>>	}
>>>
>>>	GradientImageType::Pointer image1 = extractFilter->GetOutput();
>>>
>>>	std::cout << "image1: " << image1 << std::endl;
>>>
>>>	return 0;
>>>}
>>>
>>>----
>>>
>>>This program crashes, if my input image has a size of 65x65x127 pixels.
>>
>>It
>>
>>>works fine, however, as soon as I change (in the source code) "index[0]
>>
>>=
>>
>>>64" to "index[0] = 63". It still works when increasing size[0] to 2
>>
>>after
>>
>>>changing the index. Can somebody explain me, why I am not allowed to
>>
>>extract
>>
>>>this particular region I've set in the code? Or is there something else
>>>wrong?
>>>
>>>Thanks,
>>>
>>>Michael
>>>
>>>P.S.: Below the input image file (in.mhd):
>>>
>>>----
>>>
>>>ObjectType = Image
>>>NDims = 3
>>>BinaryData = True
>>>BinaryDataByteOrderMSB = False
>>>ElementSpacing = 0.127664 0.127664 0.127664
>>>DimSize = 65 65 127
>>>ElementType = MET_SHORT
>>>ElementDataFile = in.raw
>>>
>>>----
>>>
>>
>>
>>
>>
>>_______________________________________________
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>>Insight-users at itk.org
>>http://www.itk.org/mailman/listinfo/insight-users
>>
> 
>