[Insight-users] LabelShapeOpeningImageFilter Attribute input

Wed Mar 30 10:44:42 EDT 2011

Hi,

Le 30 mars 11 à 14:51, Ella Maria Kadas a écrit :

> Hi,
>
>  Yes i already tried that and in the by default the Attribute value  
> is "Size", which as far as i understood is the Perimeter of the shape

This is the number of pixels in the object. It has been renamed in ITK  
v4 in NumberOfPixels.

> that has a specific label (length-coding)-don't know how that  
> applies to 3D images,

that's still the number of pixels independently of the image  
dimension :-)

> but trying to apply the itkBinaryShapeOpeningImageFilter i get the  
> following error (my input image is a float one).

Your image should have an integer pixel type. There is no point in  
using that class with a real pixel type.
I'm not sure this is your problem, though. Can you provide a minimum  
example so we can try to reproduce the problem?

Regards,

Gaëtan

> Start BinaryShapeOpeningImageFilter "filter"  
> BinaryShapeOpeningImageFilter (0x402d160)
>   RTTI typeinfo:    
> itk::BinaryShapeOpeningImageFilter<itk::Image<float, 3u> >
>   Reference Count: 3
>   Modified Time: 1082
>   Debug: Off
>   Observers:
>     StartEvent(SimpleMemberCommand)
>     EndEvent(SimpleMemberCommand)
>     ProgressEvent(SimpleMemberCommand)
>     IterationEvent(SimpleMemberCommand)
>     AbortEvent(SimpleMemberCommand)
>   Number Of Required Inputs: 1
>   Number Of Required Outputs: 1
>   Number Of Threads: 8
>   ReleaseDataFlag: Off
>   ReleaseDataBeforeUpdateFlag: Off
>   Input 0: (0x402cde0)
>   Output 0: (0x402d380)
>   AbortGenerateData: Off
>   Progress: 0
>   Multithreader:
>     RTTI typeinfo:   itk::MultiThreader
>     Reference Count: 1
>     Modified Time: 1069
>     Debug: Off
>     Observers:
>       none
>     Thread Count: 8
>     Global Maximum Number Of Threads: 128
>     Global Default Number Of Threads: 8
>   FullyConnected: 0
>   BackgroundValue: 0
>   ForegroundValue: 255
>   Lambda: 500
>   ReverseOrdering: 0
>   Attribute: Size (0)
> Progress  | 0 | 0.00292969 | 0.00585938 | 0.00878906 | 0.0117188 |  
> 0.0146484 | 0.0175781 | 0.0205078 | 0.0234375 | 0.0263672
>  | 0.0292969 | 0.0322266 | 0.0351562 | 0.0380859 | 0.0410156 |  
> 0.0439453 | 0.046875 | 0.0498047 | 0.0527344 | 0.0556641
>  | 0.0585938 | 0.0615234 | 0.0644531 | 0.0673828 | 0.0703125 |  
> 0.0732422 | 0.0761719 | 0.0791016 | 0.0820312 | 0.0849609
>  | 0.0878906 | 0.0908203 | 0.09375 | 0.0966797 | 0.0996094 |  
> 0.102539 | 0.105469 | 0.108398 | 0.111328 | 0.114258
>  | 0.117188 | 0.120117 | 0.123047 | 0.125977 | 0.128906 | 0.131836 |  
> 0.134766 | 0.137695 | 0.140625 | 0.143555
>  | 0.146484 | 0.149414 | 0.152344 | 0.155273 | 0.158203 | 0.161133 |  
> 0.164062 | 0.166992 | 0.169922 | 0.172852
>  | 0.175781 | 0.178711 | 0.181641 | 0.18457 | 0.1875 | 0.19043 |  
> 0.193359 | 0.196289 | 0.199219 | 0.202148
>  | 0.205078 | 0.208008 | 0.210938 | 0.213867 | 0.216797 | 0.219727 |  
> 0.222656 | 0.225586 | 0.228516 | 0.231445
>  | 0.234375 | 0.237305 | 0.240234 | 0.243164 | 0.246094 | 0.249023 |  
> 0.251953 | 0.254883 | 0.257812 | 0.260742
>  | 0.263672 | 0.266602 | 0.269531 | 0.272461 | 0.275391 | 0.27832 |  
> 0.28125 | 0.28418 | 0.287109 | 0.290039
>  | 0.292969 | 0.295898 | 0.298828Brain(6480,0xa0047540) malloc: ***  
> mmap(size=4263636992) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
>  | 0.3
>
> --- Richard Beare <richard.beare at gmail.com> schrieb am Mi, 30.3.2011:
>
> Von: Richard Beare <richard.beare at gmail.com>
> Betreff: Re: [Insight-users] LabelShapeOpeningImageFilter Attribute  
> input
> An: "Ella Maria Kadas" <ella_kadas at yahoo.com>
> CC: "insight-users at itk.org" <insight-users at itk.org>
> Datum: Mittwoch, 30. März, 2011 15:03 Uhr
>
> There is a convenience class in the Review directory that is derived  
> from this contribution called itk::BinaryShapeOpeningImageFilter.  
> This includes all of the labelling and conversion to and from label  
> maps. You just need to call the SetAttribute and SetForegroundValue  
> appropriately. It should work fine for 3D. If you look inside that  
> class you should also find the standard combination of steps you  
> need to go through to use the LabelMap filters.
>
> On Wed, Mar 30, 2011 at 9:09 PM, Ella Maria Kadas <ella_kadas at yahoo.com 
> > wrote:
> Hi all,
>
>     I am trying to remove some objects from a 3D image that have a  
> volume lower then a specific value.
>    I tried to use the Label object representation and manipulation  
> with ITK that Gae ̈tan Lehmann
> implemented but i still don't know what that attribute parameter  
> should look like. (in the python example it looks a s it would be a  
> char
> size =  
> itk 
> .ShapeOpeningLabelMapFilter 
> [LabelMapType].New(stats,Attribute=’Size’, Lambda=100)
>  I want to use the ShapeLabelObject, and it's attributes to do a  
> LabelShapeOpeningFilter.
>  As i was getting no result i tried to do it in 2D first.
>  This is my code:
> First i use the ConnectedComponentImageFilter, then  
> RelabelComponentImageFilter and create a ShapeLabelMap from the  
> relabel's output.
>
> typedef unsigned long LabelType;
>   typedef itk::ShapeLabelObject< LabelType, dim > LabelObjectType;
>   typedef itk::LabelMap< LabelObjectType > LabelMapType;
>
>
>   typedef itk::LabelImageToShapeLabelMapFilter< LabelImageType,  
> LabelMapType > ConverterType;
>   ConverterType::Pointer converter = ConverterType::New();
>   converter->SetInput( relabel->GetOutput() );
>   converter->Update();
> !!!! Why does it not work if i use this part of code from the journal
> /*
>
> and valuate the attributes with the dedicated filter:  
> ShapeLabelMapFilter
> typedef itk::ShapeLabelMapFilter< LabelMapType > ShapeFilterType;  
> ShapeFilterType::Pointer shape = ShapeFilterType::New(); shape- 
> >SetInput( converter->GetOutput() );
> update the shape filter, so its output will be up to date
> shape->Update();
>
> */
>
>
>   LabelMapType::Pointer labelMap = converter->GetOutput();
> std::cout<<"nr of label objects"<<labelMap- 
> >GetNumberOfLabelObjects()<<std::endl;
>
>   for( unsigned int label=1; label<=labelMap- 
> >GetNumberOfLabelObjects(); label++ )
>     {
>
>     const LabelObjectType * labelObject = labelMap- 
> >GetLabelObject( label );
>     std::cout << label << "\t" << labelObject->GetPhysicalSize() <<  
> "\t" << labelObject->GetCentroid() << std::endl;
>     }
>
> typedef itk::LabelShapeOpeningImageFilter< LabelImageType >  
> LabelOpeningType;
> LabelOpeningType::Pointer opening = LabelOpeningType::New();
> opening->SetInput( relabel->GetOutput());
> opening->SetBackgroundValue(0);
> opening->SetLambda( 100 );
> opening->SetReverseOrdering( false );
> //NO IDEA About the Attribute
> //I thought it should be the labelMap->Size()) should be as attribute
> opening->SetAttribute("PERIMETER");
> itk::SimpleFilterWatcher watcher(opening, "filter");
>
> Then i would like to get back the binary image and see it but i  
> can't get the proper image types as input to  
> LabelMapToLabelIamgeFilter....So the commented part is not working
>
> /*typedef itk::LabelMapToLabelImageFilter< LabelImageType,  
> LabelImageType > L2IType;
> L2IType::Pointer l2i = L2IType::New();
> l2i->SetInput( opening->GetOutput() );
>
> typedef itk::ImageFileWriter< LabelImageType > WriterType;
> WriterType::Pointer writer = WriterType::New();
> writer->SetInput( l2i->GetOutput() );
> writer->SetFileName( "/Users/ellaK/Documents/Morphology/ 
> Opening.gipl");
> writer->Update();*/
> std::getchar();
>
>
>
> Maybe i am doing this the wrong way, and i can't use it for 3D images.
> If anybody already already worked with this filters please give me a  
> hint to what i am doing wrong.
> Thanks,
>    Ella
>
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-- 
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
http://voxel.jouy.inra.fr  http://www.itk.org
http://www.mandriva.org  http://www.bepo.fr

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