/*=========================================================================
-
-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
- *
- =================================================*/
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
// clitk includes
+#include "clitkIO.h"
#include "clitkDicom2Image_ggo.h"
-#include <clitkCommon.h>
+#include "clitkCommon.h"
#include "clitkImageCommon.h"
+#include "vvImageReader.h"
+#include "vvImageWriter.h"
+#include <gdcmFile.h>
+#include <vtkVersion.h>
+#include <vtkImageChangeInformation.h>
+#if GDCM_MAJOR_VERSION >= 2
+ #include <gdcmImageHelper.h>
+ #include <gdcmAttribute.h>
+ #include <gdcmReader.h>
+#endif
-// itk include
-#include "itkImageRegionIterator.h"
-#include "itkImageRegionConstIterator.h"
-
-// Why this is needed ???
-//const double itk::NumericTraits<double>::Zero = 0.0;
+#include <set>
//====================================================================
-int main(int argc, char * argv[]) {
-
+int main(int argc, char * argv[])
+{
// init command line
GGO(clitkDicom2Image, args_info);
+ CLITK_INIT;
+
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++)
+ 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);
- }
+ int series_number = -1;
+ std::set<int> series_numbers;
+ std::map< int, std::vector<double> > theorigin;
+ std::map< int, std::vector<double> > theorientation;
+ std::map< int, std::vector<double> > sliceLocations;
+ std::map< int, std::vector<std::string> > seriesFiles;
+#if GDCM_MAJOR_VERSION >= 2
+ if (args_info.verbose_flag)
+ std::cout << "Using GDCM-2.x" << std::endl;
+#else
+ if (args_info.verbose_flag) {
+ std::cout << "Not using GDCM-2.x" << std::endl;
+ std::cout<< "The image orientation is not supported with this version of GDCM" <<std::endl;
+ }
+#endif
+ for(unsigned int i=0; i<args_info.inputs_num; i++) {
+ if (args_info.verbose_flag)
+ std::cout << "Reading <" << input_files[i] << std::endl;
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::Reader hreader;
+ hreader.SetFileName(input_files[i].c_str());
+ hreader.Read();
+ gdcm::DataSet& ds = hreader.GetFile().GetDataSet();
+
+ if (args_info.extract_series_flag) {
+ gdcm::Attribute<0x20,0x11> series_number_att;
+ series_number_att.SetFromDataSet(ds);
+ series_number = series_number_att.GetValue();
}
- //===========================================
- // Sort slices locations ...
+ series_numbers.insert(series_number);
+ theorigin[series_number] = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
+ theorientation[series_number] = gdcm::ImageHelper::GetDirectionCosinesValue(hreader.GetFile());
+ if (args_info.patientSystem_flag) {
+ double n1 = theorientation[series_number][1]*theorientation[series_number][5]-
+ theorientation[series_number][2]*theorientation[series_number][4];
+ double n2 = theorientation[series_number][3]*theorientation[series_number][2]-
+ theorientation[series_number][5]*theorientation[series_number][0];
+ double n3 = theorientation[series_number][0]*theorientation[series_number][4]-
+ theorientation[series_number][1]*theorientation[series_number][3];
+ double sloc = theorigin[series_number][0]*n1+
+ theorigin[series_number][1]*n2+
+ theorigin[series_number][2]*n3;
+ sliceLocations[series_number].push_back(sloc);
+ } else
+ sliceLocations[series_number].push_back(theorigin[series_number][2]);
+ seriesFiles[series_number].push_back(input_files[i]);
+
+ gdcm::Attribute<0x28, 0x100> pixel_size;
+ pixel_size.SetFromDataSet(ds);
+ /* if (pixel_size.GetValue() != 16)
+ {
+ std::cerr << "Pixel type not 2 bytes ! " << std::endl;
+ std::cerr << "In file " << input_files[i] << std::endl;
+ exit(0);
+ }
+ */
+#else
+ gdcm::File *header = new gdcm::File();
+ header->SetFileName(input_files[i]);
+ header->SetMaxSizeLoadEntry(16384); // required ?
+ header->Load();
+
+ if (args_info.extract_series_flag) {
+ series_number = atoi(header->GetEntryValue(0x20,0x11).c_str());
+ }
+
+ series_numbers.insert(series_number);
+ theorigin[series_number].resize(3);
+ theorigin[series_number][0] = header->GetXOrigin();
+ theorigin[series_number][1] = header->GetYOrigin();
+ theorigin[series_number][2] = header->GetZOrigin();
+ sliceLocations[series_number].push_back(theorigin[series_number][2]);
+ seriesFiles[series_number].push_back(input_files[i]);
+ /*if (header->GetPixelSize() != 2) {
+ std::cerr << "Pixel type 2 bytes ! " << std::endl;
+ std::cerr << "In file " << input_files[i] << std::endl;
+ exit(0);
+ }
+ */
+#endif
+ }
+
+ //===========================================
+ // Sort slices locations ...
+ std::set<int>::iterator sn = series_numbers.begin();
+ while ( sn != series_numbers.end() ) {
+ std::vector<double> locs = sliceLocations[*sn];
+ std::vector<double> origin = theorigin[*sn];
+ std::vector<std::string> files = seriesFiles[*sn];
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;
+ clitk::GetSortedIndex(locs, sliceIndex);
+ if (args_info.verbose_flag) {
+ std::cout << locs[sliceIndex[0]] << " -> "
+ << sliceIndex[0] << " / " << 0 << " => "
+ << "0 mm "
+ << 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;
+ std::cout << locs[sliceIndex[i]] << " -> "
+ << sliceIndex[i] << " / " << i << " => "
+ << locs[sliceIndex[i]] - locs[sliceIndex[i-1]]
+ << "mm "
+ << files[sliceIndex[i]]
+ << std::endl;
}
}
double currentDist;
double dist=0;
double tolerance = args_info.tolerance_arg;
- double previous = sliceLocations[sliceIndex[0]];
+ double previous = locs[sliceIndex[0]];
for(unsigned int i=1; i<sliceIndex.size(); i++) {
- currentDist = sliceLocations[sliceIndex[i]]-previous;
+ currentDist = locs[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]];
+ if (fabs(dist-currentDist) > tolerance) {
+ std::cout << "ERROR : " << std::endl
+ << "Current slice pos is = " << locs[sliceIndex[i]] << std::endl
+ << "Previous slice pos is = " << previous << std::endl
+ << "Current file is = " << 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 = locs[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;
+ // Create ordered vector of filenames
+ std::vector<std::string> sorted_files;
+ sorted_files.resize(sliceIndex.size());
+ for(unsigned int i=0; i<sliceIndex.size(); i++)
+ sorted_files[i] = files[ sliceIndex[i] ];
+
+ //===========================================
+ // Read write serie
+ vvImageReader::Pointer reader = vvImageReader::New();
+ reader->SetInputFilenames(sorted_files);
+ reader->Update(vvImageReader::DICOM);
+ if (reader->GetLastError().size() != 0) {
+ std::cerr << reader->GetLastError() << std::endl;
+ return 1;
}
- else
- {
- origin[0] = header->GetXOrigin();
- origin[1] = header->GetYOrigin();
+
+ vvImage::Pointer image = reader->GetOutput();
+ vtkImageData* vtk_image = image->GetFirstVTKImageData();
+ vtkImageChangeInformation* modifier = vtkImageChangeInformation::New();
+ if (args_info.focal_origin_given) {
+ std::vector<double> spacing = image->GetSpacing();
+ std::vector<int> size = image->GetSize();
+ origin[0] = -spacing[0]*size[0]/2.0;
+ origin[1] = -spacing[1]*size[1]/2.0;
+#if VTK_MAJOR_VERSION <= 5
+ modifier->SetInput(vtk_image);
+#else
+ modifier->SetInputData(vtk_image);
+#endif
+ modifier->SetOutputOrigin(origin[0], origin[1], locs[sliceIndex[0]]);
+ modifier->Update();
+ vvImage::Pointer focal_image = vvImage::New();
+ focal_image->AddVtkImage(modifier->GetOutput());
+ image = focal_image;
}
- 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;
- }
+
+ std::string outfile;
+ if (series_numbers.size() == 1)
+ outfile = args_info.output_arg;
+ else {
+ std::ostringstream name;
+ std::vector<std::string> directory = clitk::SplitFilename(args_info.output_arg);
+ if (directory.size() == 2)
+ name << directory[0] << "/" << *sn << "_" << directory[1];
+ else
+ name << *sn << "_" << args_info.output_arg;
+ outfile = name.str();
}
+ vvImageWriter::Pointer writer = vvImageWriter::New();
+ writer->SetInput(image);
+ if (args_info.patientSystem_flag && !image->GetTransform().empty())
+ writer->SetSaveTransform(true);
+ writer->SetOutputFileName(outfile);
+ writer->Update();
- //===========================================
- // Write image
- clitk::writeImage<ImageTypeOutput>(output,
- args_info.output_arg,
- args_info.verbose_flag);
-
- // this is the end my friend
- return 0;
+ modifier->Delete();
+
+ sn++;
+ }
+
+ return 0;
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff