--- /dev/null
+/*=========================================================================
+
+Program: clitk
+Module: $RCSfile: clitkDicom2Image.cxx,v $
+Language: C++
+Date: $Date: 2010/11/05 00:05:00 $
+Version: $Revision: 1.1 $
+
+Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+l'Image). All rights reserved. See Doc/License.txt or
+http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+This software is distributed WITHOUT ANY WARRANTY; without even
+the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
+/**
+ =================================================
+ * @file clitkDicom2Image.cxx
+ * @author David Sarrut <David.Sarrut@creatis.insa-lyon.fr>
+ * @date 26 Oct 2006
+ *
+ * @brief
+ *
+ =================================================*/
+
+// clitk includes
+#include "clitkDicom2Image_ggo.h"
+#include <clitkCommon.h>
+#include "clitkImageCommon.h"
+
+// itk include
+#include "itkImageRegionIterator.h"
+#include "itkImageRegionConstIterator.h"
+
+// Why this is needed ???
+//const double itk::NumericTraits<double>::Zero = 0.0;
+
+//====================================================================
+int main(int argc, char * argv[]) {
+
+ // init command line
+ GGO(clitkDicom2Image, args_info);
+ std::vector<std::string> input_files;
+ ///if std_input is given, read the input files from stdin
+ if (args_info.std_input_given)
+ {
+ while (true)
+ {
+ std::string tmp;
+ std::cin >> tmp;
+ if(std::cin.good())
+ input_files.push_back(tmp);
+ else break;
+ }
+ args_info.inputs_num=input_files.size();
+ }
+ else for (unsigned int i=0;i<args_info.inputs_num;i++)
+ input_files.push_back(args_info.inputs[i]);
+
+
+ //===========================================
+ /// Get slices locations ...
+ std::vector<double> sliceLocations;
+ for(unsigned int i=0; i<args_info.inputs_num; i++) {
+ //std::cout << "Reading <" << input_files[i] << std::endl;
+ gdcm::File * header = clitk::readDicomHeader(input_files[i]);
+ sliceLocations.push_back(header->GetZOrigin());
+ // check
+ /*if (!header->IsSignedPixelData()) {
+ std::cerr << "Pixel type not signed ! " << std::endl;
+ std::cerr << "In file " << input_files[i] << std::endl;
+ exit(0);
+ }*/
+ if (header->GetPixelSize() != 2) {
+ std::cerr << "Pixel type 2 bytes ! " << std::endl;
+ std::cerr << "In file " << input_files[i] << std::endl;
+ exit(0);
+ }
+ }
+
+ //===========================================
+ // Sort slices locations ...
+ std::vector<int> sliceIndex;
+ clitk::GetSortedIndex(sliceLocations, sliceIndex);
+ if (args_info.verboseSliceLocation_flag) {
+ std::cout << sliceLocations[sliceIndex[0]] << " -> "
+ << sliceIndex[0] << " / " << 0 << " => "
+ << "0 mm "
+ << input_files[sliceIndex[0]]
+ << std::endl;
+ for(unsigned int i=1; i<sliceIndex.size(); i++) {
+ std::cout << sliceLocations[sliceIndex[i]] << " -> "
+ << sliceIndex[i] << " / " << i << " => "
+ << sliceLocations[sliceIndex[i]] - sliceLocations[sliceIndex[i-1]]
+ << "mm "
+ << input_files[sliceIndex[i]]
+ << std::endl;
+ }
+ }
+
+ //===========================================
+ // Analyze slices locations ...
+ double currentDist;
+ double dist=0;
+ double tolerance = args_info.tolerance_arg;
+ double previous = sliceLocations[sliceIndex[0]];
+ for(unsigned int i=1; i<sliceIndex.size(); i++) {
+ currentDist = sliceLocations[sliceIndex[i]]-previous;
+ if (i!=1) {
+ if (fabs(dist-currentDist) > tolerance) {
+ std::cout << "ERROR : " << std::endl
+ << "Current slice pos is = " << sliceLocations[sliceIndex[i]] << std::endl
+ << "Previous slice pos is = " << previous << std::endl
+ << "Current file is = " << input_files[sliceIndex[i]] << std::endl
+ << "Current index is = " << i << std::endl
+ << "Current sortindex is = " << sliceIndex[i] << std::endl
+ << "Current slice diff = " << dist << std::endl
+ << "Current error = " << fabs(dist-currentDist) << std::endl;
+ exit(1);
+ }
+ }
+ else dist = currentDist;
+ previous = sliceLocations[sliceIndex[i]];
+ }
+
+ //===========================================
+ // Create image
+ gdcm::File * header = clitk::readDicomHeader(input_files[sliceIndex.front()]);
+ typedef itk::Image<float, 3> ImageType;
+ typedef itk::Image<signed short, 3> ImageTypeOutput;
+ ImageType::SpacingType spacing;
+ ImageType::SizeType size;
+ ImageType::PointType origin;
+ spacing[0] = header->GetXSpacing();
+ spacing[1] = header->GetYSpacing();
+ spacing[2] = dist;
+ size[0] = header->GetXSize();
+ size[1] = header->GetYSize();
+ size[2] = sliceIndex.size();
+ ///Optional use of special origin scheme used at CLB
+ if (args_info.focal_origin_flag)
+ {
+ origin[0] = -spacing[0]*size[0]/2;
+ origin[1] = -spacing[1]*size[1]/2;
+ }
+ else
+ {
+ origin[0] = header->GetXOrigin();
+ origin[1] = header->GetYOrigin();
+ }
+ origin[2] = header->GetZOrigin();
+ ImageTypeOutput::Pointer output = ImageTypeOutput::New();
+ itk::ImageRegion<3> region;
+ region.SetSize(size);
+ output->SetRegions(region);
+ output->SetOrigin(origin);
+ output->SetSpacing(spacing);
+ output->Allocate();
+
+ //===========================================
+ // Fill image
+ ImageType::Pointer slice;
+ typedef itk::ImageRegionIterator<ImageTypeOutput> IteratorType;
+ typedef itk::ImageRegionConstIterator<ImageType> ConstIteratorType;
+ IteratorType po(output, output->GetLargestPossibleRegion());
+ po.Begin();
+ for(unsigned int i=0; i<sliceIndex.size(); i++) {
+ slice = clitk::readImage<ImageType>(input_files[sliceIndex[i]]);
+ ConstIteratorType pi(slice, slice->GetLargestPossibleRegion());
+ while ( !pi.IsAtEnd() ) {
+ po.Set((signed short)pi.Get());
+ ++po;
+ ++pi;
+ }
+ }
+
+ //===========================================
+ // Write image
+ clitk::writeImage<ImageTypeOutput>(output,
+ args_info.output_arg,
+ args_info.verbose_flag);
+
+ // this is the end my friend
+ return 0;
+}
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