[ome-users] SCIFIO hangs reading on Windows

[Mark Hiner]

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
>
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