[ITK] [ITK-users] uncompress failed

[Matt McCormick]

Hi Matias,

.Z is not a supported file extension as I can tell.  If it is a "raw"
image, the RawImageIO will need to be used explicitly with the correct
metadata added.  See [1].

HTH,
Matt

[1] http://itk.org/Insight/Doxygen/html/classitk_1_1RawImageIO.html

On Sat, Jan 31, 2015 at 8:17 AM, Matias Montroull <matimontg at gmail.com> wrote:
> Hi,
>
> I'm running the ImageSeriesWriter example:
>
> /*=========================================================================
> *
> * Copyright Insight Software Consortium
> *
> * Licensed under the Apache License, Version 2.0 (the "License");
> * you may not use this file except in compliance with the License.
> * You may obtain a copy of the License at
> *
> * http://www.apache.org/licenses/LICENSE-2.0.txt
> *
> * Unless required by applicable law or agreed to in writing, software
> * distributed under the License is distributed on an "AS IS" BASIS,
> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
> * See the License for the specific language governing permissions and
> * limitations under the License.
> *
> *=========================================================================*/
> #include "itkGDCMImageIO.h"
> #include "itkNumericSeriesFileNames.h"
> #include "itkImageFileReader.h"
> #include "itkImageSeriesWriter.h"
> #include "itkMetaDataObject.h"
> #include <vector>
> #include "itksys/SystemTools.hxx"
> // Software Guide : BeginLatex
> //
> // This example illustrates how to read a 3D image from a non DICOM file and
> write it as a series of DICOM slices.
> // with some changed header information. Header
> //
> // Please note that modifying the content of a DICOM header is a very risky
> // operation. The Header contains fundamental information about the patient
> // and therefore its consistency must be protected from any data corruption.
> // Before attempting to modify the DICOM headers of your files, you must
> make
> // sure that you have a very good reason for doing so, and that you can
> ensure
> // that this information change will not result in a lower quality of health
> // care to be delivered to the patient.
> //
> // \index{DICOM!Writing Series}
> //
> // Software Guide : EndLatex
> int main( int argc, char* argv[] )
> {
> if( argc < 3 )
> {
> std::cerr << "Usage: " << argv[0];
> std::cerr << " InputImage OutputDicomDirectory" << std::endl;
> return EXIT_FAILURE;
> }
> typedef signed short PixelType;
> const unsigned int Dimension = 3;
> typedef itk::Image< PixelType, Dimension > ImageType;
> typedef itk::ImageFileReader< ImageType > ReaderType;
> ReaderType::Pointer reader = ReaderType::New();
> reader->SetFileName( argv[1] );
> try
> {
> reader->Update();
> }
> catch (itk::ExceptionObject &excp)
> {
> std::cerr << "Exception thrown while writing the image" << std::endl;
> std::cerr << excp << std::endl;
> return EXIT_FAILURE;
> }
> typedef itk::GDCMImageIO ImageIOType;
> typedef itk::NumericSeriesFileNames NamesGeneratorType;
> ImageIOType::Pointer gdcmIO = ImageIOType::New();
> const char * outputDirectory = argv[2];
> itksys::SystemTools::MakeDirectory( outputDirectory );
> typedef signed short OutputPixelType;
> const unsigned int OutputDimension = 2;
> typedef itk::Image< OutputPixelType, OutputDimension > Image2DType;
> typedef itk::ImageSeriesWriter<
> ImageType, Image2DType > SeriesWriterType;
> NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
> itk::MetaDataDictionary & dict = gdcmIO->GetMetaDataDictionary();
> std::string tagkey, value;
> tagkey = "0008|0060"; // Modality
> value = "MR";
> itk::EncapsulateMetaData<std::string>(dict, tagkey, value );
> tagkey = "0008|0008"; // Image Type
> value = "DERIVED\\SECONDARY";
> itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
> tagkey = "0008|0064"; // Conversion Type
> value = "DV";
> itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
> SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
> seriesWriter->SetInput( reader->GetOutput() );
> seriesWriter->SetImageIO( gdcmIO );
> ImageType::RegionType region =
> reader->GetOutput()->GetLargestPossibleRegion();
> ImageType::IndexType start = region.GetIndex();
> ImageType::SizeType size = region.GetSize();
> std::string format = outputDirectory;
> format += "/image%03d.dcm";
> namesGenerator->SetSeriesFormat( format.c_str() );
> namesGenerator->SetStartIndex( start[2] );
> namesGenerator->SetEndIndex( start[2] + size[2] - 1 );
> namesGenerator->SetIncrementIndex( 1 );
> seriesWriter->SetFileNames( namesGenerator->GetFileNames() );
> seriesWriter->UseCompressionOn();
> try
> {
> seriesWriter->Update();
> }
> catch( itk::ExceptionObject & excp )
> {
> std::cerr << "Exception thrown while writing the series " << std::endl;
> std::cerr << excp << std::endl;
> return EXIT_FAILURE;
> }
> return EXIT_SUCCESS;
> }
>
>
> And when reading images in .Z format (I believe it is Zraw), it returns an
> error indicating: "Uncompress Failed".
>
> Any hint why this may be happening?
>
> Thank you,
>
> Matias.
>
>
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