[Insight-users] Watershed Behavior
Richard Beare
richard.beare at gmail.com
Thu Feb 8 21:28:59 EST 2007
Yes,
I just discovered the 2 slices. My code is still crashing when reading
the input. Not sure what is going on there yet....
On 2/9/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> Hi Richard,
>
> Thanks for the note on the file reader and writer. They sure will help me
> clean up my code sometimes. =)
>
> The image is actually 3D with 2 slices of the identical 2D checkerboard
> image. I am using ITK 3.0.1 and the morphological watershed downloaded from
> Gaetan's link.
>
> The rmin and hmin outputs seem reasonable. I am now trying to look at the
> itkMorphologicalWatershedFromMarkersImageFilter.
>
> Albert
>
> ----- Original Message -----
> From: "Richard Beare" <richard.beare at gmail.com>
> To: "Albert Huang" <alberth+itk at ece.ubc.ca>
> Cc: "Gaetan Lehmann" <gaetan.lehmann at jouy.inra.fr>; <insight-users at itk.org>
> Sent: Thursday, February 08, 2007 5:49 PM
> Subject: Re: [Insight-users] Watershed Behavior
>
> Hi,
>
> I've built your code but get a segmentation fault under linux. I'm not
> sure which version of the morphological watershed code you're using.
> Gaetan mentioned that it is in the latest version of ITK - I'm using
> 3.0.1 and it doesn't seem to be there. So I'm using the version from
> Gaetan's repository.
>
> A couple of things stand out that you might want to check:
>
> The images are 2D - you've defined them as 3D in the default.h
>
> You're explicitly calling the reader and writers for specific file
> types. This isn't necessary. Setting the extensions on the command
> line will do the job for you. My reader and writer helper functions
> look like this:
>
> #include <itkImageFileWriter.h>
> #include <itkImageFileReader.h>
> template <class TImage>
> void writeIm(typename TImage::Pointer Im, std::string filename)
> {
> typedef typename itk::ImageFileWriter<TImage> WriterType;
> typename WriterType::Pointer writer = WriterType::New();
> writer->SetInput(Im);
> writer->SetFileName(filename.c_str());
> writer->Update();
> }
> template <class TImage>
> typename TImage::Pointer readIm(std::string filename)
> {
> typedef typename itk::ImageFileReader<TImage> ReaderType;
> typename ReaderType::Pointer reader = ReaderType::New();
> reader->SetFileName(filename.c_str());
> typename TImage::Pointer result = reader->GetOutput();
> try
> {
> result->Update();
> }
> catch(itk::ExceptionObject &ex)
> {
> std::cout << ex << std::endl;
> std::cout << filename << std::endl;
> return 0;
> }
> result->DisconnectPipeline();
> return(result);
> }
>
>
> I've packaged them in functions, which you may not want to do, but the
> critical thing to note is that pretty much everything can be done by
> calling the ImageFileReader and ImageFileWriter directly.
>
> On 2/9/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> > Hi Richard
> >
> > You can find my input file and code setup here here:
> > http://www.ece.ubc.ca/~alberth/checker_debug.zip
> > It outputs both the gradient magnitude and the watershed labels.
> >
> > The only problem I have with this code is that the (unsigned int)
> > filewriter
> > writes header as 32-bit real. Walkaround is to manually change the output
> > header from 32-bit real to 32-bit int in MRIcro.
> >
> > Look forward to the bug fixes.
> > Thanks!
> > Albert
> >
> > ----- Original Message -----
> > From: "Richard Beare" <richard.beare at gmail.com>
> > To: "Albert Huang" <alberth+itk at ece.ubc.ca>
> > Cc: "Gaetan Lehmann" <gaetan.lehmann at jouy.inra.fr>;
> > <insight-users at itk.org>
> > Sent: Thursday, February 08, 2007 4:58 PM
> > Subject: Re: [Insight-users] Watershed Behavior
> >
> > I see what you mean. That is a mystery.
> >
> > Can you package the code and input image too. This certainly suggests
> > a bug that we should sort out.
> >
> > On 2/9/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> > > Sorry. I can't seem to be able to save anything correctly. So I've
> > > attached
> > > my ANALYZE output volume in 32 bit int format which can be opened with
> > > MRIcro.
> > >
> > > http://www.ece.ubc.ca/~alberth/watershed_checker_label.img.gz
> > > http://www.ece.ubc.ca/~alberth/watershed_checker_label.hdr
> > >
> > > Thanks
> > > Albert
> > >
> > > ----- Original Message -----
> > > From: "Richard Beare" <richard.beare at gmail.com>
> > > To: "Albert Huang" <alberth+itk at ece.ubc.ca>
> > > Cc: "Gaetan Lehmann" <gaetan.lehmann at jouy.inra.fr>;
> > > <insight-users at itk.org>
> > > Sent: Thursday, February 08, 2007 4:33 PM
> > > Subject: Re: [Insight-users] Watershed Behavior
> > >
> > > The png I get from the website is 8 bit - I can't see the problem.
> > >
> > > Can you try unsigned short tif or your current pixel type as nii.
> > >
> > > Thanks
> > >
> > > On 2/9/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> > > > Thanks for the fast reply Richard.
> > > >
> > > > I quickly remove the relabel filter and save the output of watershed
> > > > as
> > > > unsigned int. As you can see with the grayscale image here:
> > > > http://www.ece.ubc.ca/~alberth/watershed_morph2.png
> > > > The outputs are labeled as:
> > > > 001 002 003 004 005 006 007 ... 018 <---------- topmost
> > > > 325 326 327 328 329 330 331 ... 342
> > > > ..........
> > > > 019 020 021 022 023 024 025 ... 036
> > > > 001 002 003 004 005 006 007 ... 018 <---------- bottommost
> > > > Where the topmost and bottommost rows are labeled as the same numbers
> > > > or
> > > > wrap around as I called it.
> > > >
> > > > Albert
> > > >
> > > > ----- Original Message -----
> > > > From: "Richard Beare" <richard.beare at gmail.com>
> > > > To: "Albert Huang" <alberth+itk at ece.ubc.ca>
> > > > Cc: "Gaetan Lehmann" <gaetan.lehmann at jouy.inra.fr>;
> > > > <insight-users at itk.org>
> > > > Sent: Thursday, February 08, 2007 2:58 PM
> > > > Subject: Re: [Insight-users] Watershed Behavior
> > > >
> > > > Hi,
> > > > I'm having difficulty determining what you mean by wrap around - from
> > > > the example it looks as though it could be wrap around of the
> > > > colormap, rather than the watershed.
> > > >
> > > > Try saving the output of the watershed filter, rather than the
> > > > relabeller/coloring step and probe the values. For example, save as
> > > > unsigned short tif and use the ImageView or some other tool to check
> > > > the values. There shouldn't be any wrap around, but you never know.
> > > >
> > > > On 2/9/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> > > > > Thanks Richard and Gaetan
> > > > >
> > > > > The new filter works very well on the edges for my application.
> > > > > However,
> > > > > when I relabel my image after the morphological watershed, I get a
> > > > > wrap
> > > > > around on the very top and bottom grids (even though they are
> > > > > alternating
> > > > > intensity blocks). Is that a known behavior?
> > > > >
> > > > > http://www.ece.ubc.ca/~alberth/watershed_morph.png
> > > > >
> > > > > The left and right image edge labels are ok with no wrap around.
> > > > > Checking
> > > > > the gradient magnitude image, all image edges have 0 gradient (top,
> > > > > bottom,
> > > > > left, right).
> > > > >
> > > > > My morphological watershed filter has
> > > > > input (double)
> > > > > output (unsigned long)
> > > > > SetMarkWatershedLine=false.
> > > > > My relabel component image filter has
> > > > > input (unsigned long)
> > > > > output (unsigned int)
> > > > > The relabeler outputs for my example are [1...342] which seems to be
> > > > > still
> > > > > well within the range of my output type.
> > > > >
> > > > > Albert
> > > > >
> > > > > ----- Original Message -----
> > > > > From: "Gaetan Lehmann" <gaetan.lehmann at jouy.inra.fr>
> > > > > To: "Albert Huang" <alberth+itk at ece.ubc.ca>
> > > > > Cc: <Richard.Beare at ieee.org>; <insight-users at itk.org>
> > > > > Sent: Thursday, February 08, 2007 1:48 AM
> > > > > Subject: Re: [Insight-users] Watershed Behavior
> > > > >
> > > > >
> > > > > Hi,
> > > > >
> > > > > You may also want to test the morphological watershed Richard and I
> > > > > have
> > > > > contributed, and see if it gives better results.
> > > > >
> > > > > http://hdl.handle.net/1926/202
> > > > >
> > > > > You can also found this new filter in ITK cvs now.
> > > > >
> > > > > Regards,
> > > > >
> > > > > Gaetan
> > > > >
> > > > >
> > > > > On Thu, 08 Feb 2007 04:34:39 +0100, Richard Beare
> > > > > <richard.beare at gmail.com> wrote:
> > > > >
> > > > > > Have a look at the gradient image and dheck whether there are
> > > > > > plateaus
> > > > > > in the zig-zag area. The behaviour of the standard itk watershed
> > > > > > is
> > > > > > somewhat arbitary in the presence of plateaus.
> > > > > >
> > > > > >
> > > > > > On 2/8/07, Albert Huang <alberth+itk at ece.ubc.ca> wrote:
> > > > > >>
> > > > > >>
> > > > > >> Dear experts
> > > > > >>
> > > > > >> I was just playing with the watershed pipeline a few days ago
> > > > > >> using
> > > > > >> a
> > > > > >> checkerboard pattern (with uint8 grids of black=64, gray=153,
> > > > > >> white=192),
> > > > > >> and observed a zig-zaggy pattern on some edges (see
> > > > > >> http://www.ece.ubc.ca/~alberth/watershed.png). Adding a
> > > > > >> smooth field on the checkboard results in more zig-zaggy
> > > > > >> behaviors
> > > > > >> on
> > > > > >> edges
> > > > > >> that seem fairly strong in the input image. I am wondering if
> > > > > >> this
> > > > > >> is
> > > > > >> normal
> > > > > >> behavior for the itkWatershedImageFilter?
> > > > > >>
> > > > > >> My pipeline (ITK 3.0.1) setup is as below:
> > > > > >> file reader ->
> > > > > >> vector gradient magnitude image filter (pca off) ->
> > > > > >> watershed (level=0.2, threshold=0.0) ->
> > > > > >> relabel component
> > > > > >>
> > > > > >> p.s. The black regions in the outputs are colormap problems and
> > > > > >> not
> > > > > >> a
> > > > > >> watershed issue. =)
> > > > > >>
> > > > > >> Thanks
> > > > > >> Albert
> > > > > >>
> > > > > >> _______________________________________________
> > > > > >> Insight-users mailing list
> > > > > >> Insight-users at itk.org
> > > > > >> http://www.itk.org/mailman/listinfo/insight-users
> > > > > >>
> > > > > >>
> > > > > > _______________________________________________
> > > > > > Insight-users mailing list
> > > > > > Insight-users at itk.org
> > > > > > http://www.itk.org/mailman/listinfo/insight-users
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > 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
> > > > >
> > > > >
> > > >
> > >
> >
>
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