[Insight-users] Watershed Segmentation - problem running itkWSRawToPNG.cxx
neha k
itkneha1 at yahoo.com
Mon, 1 Mar 2004 14:56:31 -0800 (PST)
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Hi Luis,
Initially, While trying program "itkWatershedSegmentationExample.cxx" I used very small PGM file (24*7) just to see the working of above program, and it gave me 5 output files of RAW format(With Level = 0.50) for Level values 0.10, 0.20...0.50
But yet I do not know how the original file looks lilke. I tried to use second program "itkWSRawToPNG.cxx" to see the output in PNG format but it crashes on reader->update().
I am currently reading "Breast.raw" (256*256 - unsigned short-little endian) using MetaImage Reader, then apply AnisotropicDiffusionFilter and then GradientFilter on it.
Here, I checked by writing the output of those to a file and it gives me correct output with AnisotropicDiffusionFilter->GradientFilter->writer.
But when I apply watershed as -
AnisotropicDiffusionFilter->GradientFilter->watershed->writer
I get the output file of 0 bytes
I have added the lines suggested by you as follows: (Pls. scroll down for complete code)
watershed->SetThreshold(threshold);
watershed->SetLevel(floodLevel);
watershed->SetInput(gradientFilter->GetOutput());
watershed->Update();
watershed->GetInput()->Print( std::cout );
watershed->GetOutput()->Print( std::cout );
writer->SetInput(watershed->GetOutput());
writer->update();
I have attached a word file containing the output of above.
My Questions
---------------------
1. To see the segmented output, should I convert output of watershed(after getting file size of original input file), to PNG format?
2. What is missing in the my program ?
Please let me know what is going wrong. Thank you very much,
Neha
Luis Ibanez <luis.ibanez at kitware.com> wrote:
Hi Neha,
If your image size really
24 pixels by 7 pixels ?
The chances of getting any significant
segmentation from such a small image are
very slim.
You said that the output of the GradientMagnitude
filter is working ok, did you verified this by
saving the image to a file ?
Could you please add the lines:
watershed->Update();
watershed->GetInput()->Print( std::cout );
watershed->GetOutput()->Print( std::cout );
Put this lines just before you invoke the writer's
Update() method, execute the program and post the
results to the list.
Thanks
Luis
-----------------
neha k wrote:
> Hi Luis,
>
> Due to problem in example program itkWSRawToPNG.cxx, I have written
> following simple code for experiment to work on RAW grayscale file. I
> am using this pipeline of filters->
> reader--->AnisotropicDiffusionFilter--->GradientMagnitudeFilter--->WaterShed
>
> Problem is : Output file is of "0" Bytes. But From
> GradientMagnitudeFilter, I get desired output. But watershed does not
> give output file of original input size, instead it is Zero.
> I tried with 3 different values for conductance_term, threshold and
> Level. But still the output file has 0 bytes.
>
> Please let me know if I am missing anything while using watershed.
>
> Following the simple code i am using ->
> ***********************************************************************************
>
> void segment()
>
> {
>
> _// declarations_
>
> int threshold = 0.30, floodLevel = 0.50;
>
> int noOfIterations = 3, retVal = 1, checkExtn =0;
>
> char answer='y', inputFile[255]="breast.mhd", //256*256-little endian
> outputFile[255]="breast_op.mhd";
>
> float timeStep = 0.25,
>
> conductance = 5.0;
>
> typedef itk::Image< InputPixelType, 2 > InputImageType; // float type
>
> typedef itk::Image< OutputPixelType, 2 > OutputImageType; // float type
>
> typedef itk::Image LabeledImageType;
>
> typedef itk::Image ScalarImageType;
>
> typedef itk::Image WriteImageType;
>
> typedef itk::GradientAnisotropicDiffusionImageFilter [input] > OutputImageType > FilterType;
>
> FilterType::Pointer filter = FilterType::New();
>
> // Instantiate Gradient Magnitude Filter typedef
> itk::GradientMagnitudeImageFilter [input]
>
> GradientFilterType;
>
> GradientFilterType::Pointer gradientFilter = GradientFilterType::New();
>
> typedef itk::WatershedImageFilter WatershedFilterType;
>
> WatershedFilterType::Pointer watershed = WatershedFilterType::New();
>
> typedef itk::ImageFileWriter< WriteImageType > WriterType; // write
> output image as short - use rescaler
>
> WriterType::Pointer writer = WriterType::New();
>
> typedef itk::ImageFileReader< InputImageType > ReaderType; // read input
> image as float
>
> ReaderType::Pointer reader = ReaderType::New();
>
> reader->SetFileName(inputFile);
>
> writer->SetFileName( outputFile );
>
> _// Read Input Image of RAW Type (uses MetaImage Header)_
>
> try { reader->Update(); }
>
> catch( itk::ExceptionObject & e ) {
>
> std::cerr << "Exception caught during Raw file reading " << std::endl;
>
> std::cerr << e << std::endl;
>
> std::cout<< "\n\nMake Sure if the file name you specified already
> exists...\n";
>
> return -1;
>
> }
>
> _// First apply Edge Preserving smoothing filter "Anisotropic Diffusion
> Filter"_
>
> filter->SetInput( reader->GetOutput() );
>
> filter->SetIterations(noOfIterations); // default value -> 3
>
> filter->SetConductanceParameter(conductance); // default value -> 5.0
>
> filter->SetTimeStep(timeStep); // default value -> 0.25 for 2-D image
>
> _// Pass the output of Anisotropic Diffusion Filter to
> GradientMagnitudeFilter_
>
> gradientFilter->SetInput( filter->GetOutput() );
>
> _// Apply Watershed Segmentation_
>
> watershed->SetInput(gradientFilter->GetOutput());
>
> watershed->SetThreshold(threshold); // 0.30
>
> watershed->SetLevel(floodLevel); // 0.50
>
> writer->SetInput(watershed->GetOutput());
>
> _// Execute the pipeline_
>
> try { writer->Update(); }
>
> catch( itk::ExceptionObject & excep ){
>
> std::cerr << "Exception caught !" << std::endl;
>
> std::cerr << excep << std::endl;
>
> retVal = -1;
>
> }
>
> }
>
>
> ***********************************************************************************
>
> */Joshua Cates /* wrote:
>
> Hi,
>
> Thanks for the feedback on the watershed example. This code is old and
> probably in need of updating for more recent developments in the ITK IO
> classes. I will take a look.
>
> Josh.
>
> On Mon, 23 Feb 2004, neha k wrote:
>
> >
> > Hi All,
> >
> > I am trying to run exampleI programs in Watershed segmetnation. I
> tried
> > the example program with Input file as PGM file (in.pgm) which is of
> > size (24*7). When I run itkWatershedSegmentationExample.cxx, I get 5
> > output files of raw format (with level = 0.50). When I set any of
> those
> > 5 output files as an input file to second program
> itkWSRawToPNG.cxx so
> > that I can convert it to png file to view, program crashes( on
> statement
> > reader_update()). What should be the input file given to this second
> > program? Also, if i want to segment the raw br est images, what
> reader
> > should I use and how should i generate the output files? What
> filters,
> > mappers should I use to apply watershed segmentation on grayscale
> breast
> > images of Raw format to find out if there is any lesion inside
> the brest
> > image? (Currently, I am using MetaImageReader to apply other ITK
> filters
> > on breast images.)
> >
> > Any suggestions are appreiated.
> >
> > My input PGM file is as follows
> >
> >
> ***************************************************************************************
> >
> > P2
> >
> > 24 7
> >
> > 15
> >
> > 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> >
> > 0 3 3 3 3 0 0 7 7 7 7 0 0 11 11 11 11 0 0 15 15 15 15 0
> >
> > 0 3 0 0 0 0 0 7 0 0 0 0 0 11 0 0 0 0 0 15 0 0 15 0
> >
> > 0 3 3 3 0 0 0 7 7 7 0 0 0 11 11 11 0 0 0 15 15 15 15 0
> >
> > 0 3 0 0 0 0 0 7 0 0 0 0 0 11 0 0 0 0 0 15 0 0 0 0
> > *> 0 3 0 0 0 0 0 7 7 7 7 0 0 11 11 11 11 0 0 15 0 0 0 0
> >
> > 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> >
> >
> >
> >
> ***************************************************************************************
>
> >
> > Thanks,
> >
> > Neha
> >
> >
> > ---------------------------------
> > Do you Yahoo!?
> > Yahoo! Mail SpamGuard - Read only the mail you want.
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users*
>
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Content-Type: text/html; charset=us-ascii
<DIV>
<DIV>Hi Luis,</DIV>
<DIV> </DIV>
<DIV>Initially, While trying program "itkWatershedSegmentationExample.cxx" I used very small PGM file (24*7) just to see the working of above program, and it gave me 5 output files of RAW format(With Level = 0.50) for Level values 0.10, 0.20...0.50</DIV>
<DIV> </DIV>
<DIV>But yet I do not know how the original file looks lilke. I tried to use second program "itkWSRawToPNG.cxx" to see the output in PNG format but it crashes on reader->update().</DIV>
<DIV> </DIV>
<DIV>I am currently reading "Breast.raw" (256*256 - unsigned short-little endian) using MetaImage Reader, then apply AnisotropicDiffusionFilter and then GradientFilter on it.</DIV>
<DIV>Here, I checked by writing the output of those to a file and it gives me correct output with AnisotropicDiffusionFilter->GradientFilter->writer.</DIV>
<DIV> </DIV>
<DIV>But when I apply watershed as -</DIV>
<DIV>AnisotropicDiffusionFilter->GradientFilter->watershed->writer</DIV>
<DIV> </DIV>
<DIV>I get the output file of 0 bytes</DIV>
<DIV> </DIV>
<DIV>I have added the lines suggested by you as follows: (Pls. scroll down for complete code)</DIV>
<DIV> </DIV>
<DIV> watershed->SetThreshold(threshold);<BR> watershed->SetLevel(floodLevel); <BR> watershed->SetInput(gradientFilter->GetOutput());</DIV>
<DIV> watershed->Update();</DIV>
<DIV> watershed->GetInput()->Print( std::cout );<BR> watershed->GetOutput()->Print( std::cout ); <BR> writer->SetInput(watershed->GetOutput()); </DIV>
<DIV> writer->update();</DIV>
<DIV> </DIV>
<DIV>I have attached a word file containing the output of above.</DIV>
<DIV> </DIV>
<DIV>
<DIV>My Questions</DIV>
<DIV>---------------------</DIV>
<DIV>1. To see the segmented output, should I convert output of watershed(after getting file size of original input file), to PNG format?</DIV>
<DIV>2. What is missing in the my program ?</DIV></DIV>
<DIV> </DIV>
<DIV>Please let me know what is going wrong. Thank you very much,</DIV>
<DIV> </DIV>
<DIV>Neha</DIV>
<DIV> </DIV>
<DIV><BR><B><I>Luis Ibanez <luis.ibanez at kitware.com></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"><BR>Hi Neha,<BR><BR><BR>If your image size really<BR><BR>24 pixels by 7 pixels ?<BR><BR><BR>The chances of getting any significant<BR>segmentation from such a small image are<BR>very slim.<BR><BR><BR>You said that the output of the GradientMagnitude<BR>filter is working ok, did you verified this by<BR>saving the image to a file ?<BR><BR><BR><BR>Could you please add the lines:<BR><BR>watershed->Update();<BR>watershed->GetInput()->Print( std::cout );<BR>watershed->GetOutput()->Print( std::cout );<BR><BR>Put this lines just before you invoke the writer's<BR>Update() method, execute the program and post the<BR>results to the list.<BR><BR><BR><BR>Thanks<BR><BR><BR>Luis<BR><BR><BR><BR>-----------------<BR>neha k wrote:<BR><BR>> Hi Luis,<BR>> <BR>> Due to problem in example program itkWSRawToPNG.cxx, I have written <BR>> following simple code for experiment to work
on RAW grayscale file. I <BR>> am using this pipeline of filters-><BR>> reader--->AnisotropicDiffusionFilter--->GradientMagnitudeFilter--->WaterShed<BR>> <BR>> Problem is : Output file is of "0" Bytes. But From <BR>> GradientMagnitudeFilter, I get desired output. But watershed does not <BR>> give output file of original input size, instead it is Zero.<BR>> I tried with 3 different values for conductance_term, threshold and <BR>> Level. But still the output file has 0 bytes.<BR>> <BR>> Please let me know if I am missing anything while using watershed.<BR>> <BR>> Following the simple code i am using -><BR>> ***********************************************************************************<BR>> <BR>> void segment()<BR>> <BR>> {<BR>> <BR>> _// declarations_<BR>> <BR>> int threshold = 0.30, floodLevel = 0.50;<BR>> <BR>> int noOfIterations = 3, retVal = 1, checkExtn =0;<BR>> <BR>> char answer='y',
inputFile[255]="breast.mhd", //256*256-little endian<BR>> outputFile[255]="breast_op.mhd";<BR>> <BR>> float timeStep = 0.25,<BR>> <BR>> conductance = 5.0;<BR>> <BR>> typedef itk::Image< InputPixelType, 2 > InputImageType; // float type<BR>> <BR>> typedef itk::Image< OutputPixelType, 2 > OutputImageType; // float type<BR>> <BR>> typedef itk::Image<UNSIGNED 2 long,> LabeledImageType;<BR>> <BR>> typedef itk::Image<FLOAT, 2> ScalarImageType;<BR>> <BR>> typedef itk::Image<UNSIGNED 2 long,> WriteImageType;<BR>> <BR>> typedef itk::GradientAnisotropicDiffusionImageFilter<INPUTIMAGETYPE, <br>> OutputImageType > FilterType;<BR>> <BR>> FilterType::Pointer filter = FilterType::New();<BR>> <BR>> // Instantiate Gradient Magnitude Filter typedef <BR>> itk::GradientMagnitudeImageFilter<INPUTIMAGETYPE, OutputImageType><BR>> <BR>> GradientFilterType;<BR>> <BR>> GradientFilterType::Pointer gradientFilter =
GradientFilterType::New();<BR>> <BR>> typedef itk::WatershedImageFilter<SCALARIMAGETYPE> WatershedFilterType;<BR>> <BR>> WatershedFilterType::Pointer watershed = WatershedFilterType::New();<BR>> <BR>> typedef itk::ImageFileWriter< WriteImageType > WriterType; // write <BR>> output image as short - use rescaler<BR>> <BR>> WriterType::Pointer writer = WriterType::New();<BR>> <BR>> typedef itk::ImageFileReader< InputImageType > ReaderType; // read input <BR>> image as float<BR>> <BR>> ReaderType::Pointer reader = ReaderType::New();<BR>> <BR>> reader->SetFileName(inputFile);<BR>> <BR>> writer->SetFileName( outputFile );<BR>> <BR>> _// Read Input Image of RAW Type (uses MetaImage Header)_<BR>> <BR>> try { reader->Update(); }<BR>> <BR>> catch( itk::ExceptionObject & e ) {<BR>> <BR>> std::cerr << "Exception caught during Raw file reading " << std::endl;<BR>> <BR>>
std::cerr << e << std::endl;<BR>> <BR>> std::cout<< "\n\nMake Sure if the file name you specified already <BR>> exists...\n";<BR>> <BR>> return -1;<BR>> <BR>> }<BR>> <BR>> _// First apply Edge Preserving smoothing filter "Anisotropic Diffusion <BR>> Filter"_<BR>> <BR>> filter->SetInput( reader->GetOutput() );<BR>> <BR>> filter->SetIterations(noOfIterations); // default value -> 3<BR>> <BR>> filter->SetConductanceParameter(conductance); // default value -> 5.0<BR>> <BR>> filter->SetTimeStep(timeStep); // default value -> 0.25 for 2-D image<BR>> <BR>> _// Pass the output of Anisotropic Diffusion Filter to <BR>> GradientMagnitudeFilter_<BR>> <BR>> gradientFilter->SetInput( filter->GetOutput() );<BR>> <BR>> _// Apply Watershed Segmentation_<BR>> <BR>> watershed->SetInput(gradientFilter->GetOutput());<BR>> <BR>>
watershed->SetThreshold(threshold); // 0.30<BR>> <BR>> watershed->SetLevel(floodLevel); // 0.50<BR>> <BR>> writer->SetInput(watershed->GetOutput());<BR>> <BR>> _// Execute the pipeline_<BR>> <BR>> try { writer->Update(); }<BR>> <BR>> catch( itk::ExceptionObject & excep ){<BR>> <BR>> std::cerr << "Exception caught !" << std::endl;<BR>> <BR>> std::cerr << excep << std::endl;<BR>> <BR>> retVal = -1;<BR>> <BR>> }<BR>> <BR>> }<BR>> <BR>> <BR>> ***********************************************************************************<BR>> <BR>> */Joshua Cates <CATES at SCI.UTAH.EDU>/* wrote:<BR>> <BR>> Hi,<BR>> <BR>> Thanks for the feedback on the watershed example. This code is old and<BR>> probably in need of updating for more recent developments in the ITK IO<BR>> classes. I will take a look.<BR>> <BR>> Josh.<BR>> <BR>> On Mon, 23 Feb 2004, neha k
wrote:<BR>> <BR>> ><BR>> > Hi All,<BR>> ><BR>> > I am trying to run exampleI programs in Watershed segmetnation. I<BR>> tried<BR>> > the example program with Input file as PGM file (in.pgm) which is of<BR>> > size (24*7). When I run itkWatershedSegmentationExample.cxx, I get 5<BR>> > output files of raw format (with level = 0.50). When I set any of<BR>> those<BR>> > 5 output files as an input file to second program<BR>> itkWSRawToPNG.cxx so<BR>> > that I can convert it to png file to view, program crashes( on<BR>> statement<BR>> > reader_update()). What should be the input file given to this second<BR>> > program? Also, if i want to segment the raw br est images, what<BR>> reader<BR>> > should I use and how should i generate the output files? What<BR>> filters,<BR>> > mappers should I use to apply watershed segmentation on grayscale<BR>> breast<BR>> > images of Raw format to
find out if there is any lesion inside<BR>> the brest<BR>> > image? (Currently, I am using MetaImageReader to apply other ITK<BR>> filters<BR>> > on breast images.)<BR>> ><BR>> > Any suggestions are appreiated.<BR>> ><BR>> > My input PGM file is as follows<BR>> ><BR>> ><BR>> ***************************************************************************************<BR>> ><BR>> > P2<BR>> ><BR>> > 24 7<BR>> ><BR>> > 15<BR>> ><BR>> > 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0<BR>> ><BR>> > 0 3 3 3 3 0 0 7 7 7 7 0 0 11 11 11 11 0 0 15 15 15 15 0<BR>> ><BR>> > 0 3 0 0 0 0 0 7 0 0 0 0 0 11 0 0 0 0 0 15 0 0 15 0<BR>> ><BR>> > 0 3 3 3 0 0 0 7 7 7 0 0 0 11 11 11 0 0 0 15 15 15 15 0<BR>> ><BR>> > 0 3 0 0 0 0 0 7 0 0 0 0 0 11 0 0 0 0 0 15 0 0 0 0<BR>> > *> 0 3 0 0 0 0 0 7 7 7 7 0 0 11 11 11 11 0 0 15 0 0 0 0<BR>> ><BR>> >
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0<BR>> ><BR>> ><BR>> ><BR>> ><BR>> ***************************************************************************************<BR>> <BR>> ><BR>> > Thanks,<BR>> ><BR>> > Neha<BR>> ><BR>> ><BR>> > ---------------------------------<BR>> > Do you Yahoo!?<BR>> > Yahoo! Mail SpamGuard - Read only the mail you want.<BR>> <BR>> _______________________________________________<BR>> Insight-users mailing list<BR>> Insight-users at itk.org<BR>> http://www.itk.org/mailman/listinfo/insight-users*<BR>> <BR>> ------------------------------------------------------------------------<BR>> *Do you Yahoo!?<BR>> Get better spam protection with Yahoo! Mail <BR>> <HTTP: tools antispam.yahoo.com *http: mailtag_us us.rd.yahoo.com>*<BR><BR><BR><BR>_______________________________________________<BR>Insight-users mailing
list<BR>Insight-users at itk.org<BR>http://www.itk.org/mailman/listinfo/insight-users</BLOCKQUOTE></DIV><p><hr SIZE=1>
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