[ome-users] SCIFIO hangs reading on Windows

[Joe Ping-Lin Hsiao]

Mark,

The patch works well. Thank for the fast response.

Joe


On Wed, May 29, 2013 at 2:43 PM, Mark Hiner <hiner at wisc.edu> wrote:

> Joe,
>
>  Is this resolved with the changes you and Cory made?
>
>  I updated the latest gerrit changeset<http://review.source.kitware.com/#/c/11375/>to include your updated scifio-imageio.
>
> Thank you for the help on this issue!
>
> - Mark
>
>
> On Tue, May 28, 2013 at 2:40 PM, Joe Ping-Lin Hsiao <phsiao at cs.unc.edu>wrote:
>
>> I have a test program modified from an example I found online. It reads a
>> 4-d image and extract the z-stack from each time step and save it as a
>> .ome.tiff.
>>
>> The program works fine on Mac, but on Windows it hangs at itksysProcess_WaitForData()
>> in itkSCIFIOImageIO.cxx.
>>
>> I use the SCIFIO from ITK by enabling fetch_SCIFIO.
>>
>> Here is the the code:
>>
>> #if defined(_MSC_VER) #pragma warning ( disable : 4786 ) #endif #include
>> <iostream> #include <fstream> #include "itkSCIFIOImageIO.h" #include
>> "itkImageFileReader.h" #include "itkImageFileWriter.h" #include
>> "itkImage.h" #include "itkRGBPixel.h" #include "itkMetaDataObject.h"
>> #include "itkExtractImageFilter.h" #include <itkImageIORegion.h> #if
>> defined(ITK_USE_MODULAR_BUILD) #define SPECIFIC_IMAGEIO_MODULE_TEST #endif
>> int main( int argc, char * argv [] ) { if( argc < 2) { std::cerr << "Usage:
>> " << argv[0] << " input"; return EXIT_FAILURE; } typedef unsigned short
>> PixelType; const unsigned int Dimension = 4; typedef itk::Image< PixelType,
>> Dimension > ImageType; typedef itk::ImageFileReader<ImageType> ReaderType;
>> typedef itk::ImageIORegion ImageIORegionType; typedef
>> itk::ImageFileWriter<ImageType> WriterType; typedef
>> itk::ExtractImageFilter<ImageType, ImageType> ExtractImageFilter; // This
>> ImageIO won't actually be used, it's just a reference to remember how many
>> // T-slices there are, as the extracted ImageIO will be truncated.
>> itk::SCIFIOImageIO::Pointer io = itk::SCIFIOImageIO::New(); io->DebugOn();
>> std::string inputFilename = argv[1]; std::cout << argv[1] << std::endl;
>> std::cout << "before setfilename" << std::endl; io->SetFileName(argv[1]);
>> std::cout << "after setfilename" << std::endl; io->ReadImageInformation();
>> std::cout << "after readImageInformation" << std::endl; unsigned int
>> numberOfDim = io->GetNumberOfDimensions(); // Similarly this region will be
>> reused to ensure when we know how big the image is when // we try to
>> extract a single T-slice ImageIORegionType region(4); for( unsigned long i
>> = 0; i < numberOfDim; i++ ) { std::cout << "Setting index: " << i << " to:
>> " << io->GetDimensions(i) << std::endl; region.SetIndex( i, 0 );
>> region.SetSize( i, io->GetDimensions(i) ); } ReaderType::Pointer reader =
>> ReaderType::New(); reader->SetFileName(argv[1]); reader->UseStreamingOn();
>> WriterType::Pointer writer = WriterType::New(); for( unsigned int i = 0; i
>> < region.GetSize( numberOfDim-1 ); i++ ) { std::cout << i << std::endl; //
>> When I was persisting these objects between iterations I ran into // I ran
>> into errors based on remembering the wrong region sizes
>> itk::SCIFIOImageIO::Pointer imageIO = itk::SCIFIOImageIO::New();
>> ExtractImageFilter::Pointer extractor = ExtractImageFilter::New();
>> imageIO->DebugOn(); imageIO->SetFileName(argv[1]);
>> imageIO->SetUseStreamedReading(true); imageIO->SetUseStreamedWriting(true);
>> // reset to the largest possible region, so that the extraction region is
>> contained imageIO->SetIORegion( region ); imageIO->ReadImageInformation();
>> reader->SetImageIO(imageIO); std::cout << "ImageIO Region: " << imageIO <<
>> std::endl; ImageType::IndexType start; ImageType::SizeType size; for(
>> unsigned int j = 0; j < numberOfDim; j++ ) { start[j] = 0; size[j] =
>> io->GetDimensions(j); } start[ numberOfDim-1 ] = i; //size[ numberOfDim-2 ]
>> = 1; size[ numberOfDim-1 ] = 1; ImageType::RegionType desiredRegion;
>> desiredRegion.SetSize(size); desiredRegion.SetIndex(start);
>> extractor->SetExtractionRegion(desiredRegion); std::cout << "Region of
>> extraction: " << extractor->GetExtractionRegion() << std::endl; std::cout
>> << "Largest possible reader region, pre-update: " <<
>> reader->GetImageIO()->GetIORegion() << std::endl;
>> extractor->SetInput(reader->GetOutput()); extractor->Update(); std::cout <<
>> "Largest possible reader region, post-update: " <<
>> reader->GetImageIO()->GetIORegion() << std::endl; std::ostringstream
>> istream; istream << i << ".ome.tiff"; std::string fname = istream.str();
>> writer->SetFileName( fname.c_str() ); writer->SetImageIO(imageIO);
>> writer->SetInput(extractor->GetOutput()); try { writer->Update(); } catch
>> (itk::ExceptionObject &e) { std::cerr << e << std::endl; return
>> EXIT_FAILURE; } } return EXIT_SUCCESS; }
>>
>> Best,
>> Joe
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
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>>
>>
>
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