tools/clitkDicom2Image.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 // clitk includes
  20 #include "clitkIO.h"
  21 #include "clitkDicom2Image_ggo.h"
  22 #include "clitkCommon.h"
  23 #include "clitkImageCommon.h"
  24 #include "vvImageReader.h"
  25 #include "vvImageWriter.h"
  26 #include <gdcmFile.h>
  27 #include <vtkVersion.h>
  28 #include <vtkImageChangeInformation.h>
  29 #if GDCM_MAJOR_VERSION >= 2
  30   #include <gdcmImageHelper.h>
  31   #include <gdcmAttribute.h>
  32   #include <gdcmReader.h>
  33 #endif
  34
  35 #include <set>
  36
  37 //====================================================================
  38 int main(int argc, char * argv[])
  39 {
  40   // init command line
  41   GGO(clitkDicom2Image, args_info);
  42   CLITK_INIT;
  43
  44   std::vector<std::string> input_files;
  45   ///if std_input is given, read the input files from stdin
  46   if (args_info.std_input_given) {
  47     while (true) {
  48       std::string tmp;
  49       std::cin >> tmp;
  50       if(std::cin.good())
  51         input_files.push_back(tmp);
  52       else break;
  53     }
  54     args_info.inputs_num=input_files.size();
  55   } else for (unsigned int i=0; i<args_info.inputs_num; i++)
  56       input_files.push_back(args_info.inputs[i]);
  57
  58
  59   //===========================================
  60   /// Get slices locations ...
  61   int series_number = -1;
  62   std::set<int> series_numbers;
  63   std::map< int, std::vector<double> > theorigin;
  64   std::map< int, std::vector<double> > theorientation;
  65   std::map< int, std::vector<double> > sliceLocations;
  66   std::map< int, std::vector<std::string> > seriesFiles;
  67 #if GDCM_MAJOR_VERSION >= 2
  68   if (args_info.verbose_flag)
  69     std::cout << "Using GDCM-2.x" << std::endl;
  70 #else
  71   if (args_info.verbose_flag) {
  72     std::cout << "Not using GDCM-2.x" << std::endl;
  73     std::cout<< "The image orientation is not supported with this version of GDCM" <<std::endl;
  74   }
  75 #endif
  76   for(unsigned int i=0; i<args_info.inputs_num; i++) {
  77     if (args_info.verbose_flag)
  78         std::cout << "Reading <" << input_files[i] << std::endl;
  79 #if GDCM_MAJOR_VERSION >= 2
  80     gdcm::Reader hreader;
  81     hreader.SetFileName(input_files[i].c_str());
  82     hreader.Read();
  83     gdcm::DataSet& ds = hreader.GetFile().GetDataSet();
  84
  85     if (args_info.extract_series_flag) {
  86       gdcm::Attribute<0x20,0x11> series_number_att;
  87       series_number_att.SetFromDataSet(ds);
  88       series_number = series_number_att.GetValue();
  89     }
  90
  91     series_numbers.insert(series_number);
  92     theorigin[series_number] = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
  93     theorientation[series_number] = gdcm::ImageHelper::GetDirectionCosinesValue(hreader.GetFile());
  94     if (args_info.patientSystem_flag) {
  95       double n1 = theorientation[series_number][1]*theorientation[series_number][5]-
  96                   theorientation[series_number][2]*theorientation[series_number][4];
  97       double n2 = theorientation[series_number][3]*theorientation[series_number][2]-
  98                   theorientation[series_number][5]*theorientation[series_number][0];
  99       double n3 = theorientation[series_number][0]*theorientation[series_number][4]-
 100                   theorientation[series_number][1]*theorientation[series_number][3];
 101       double sloc = theorigin[series_number][0]*n1+
 102                     theorigin[series_number][1]*n2+
 103                     theorigin[series_number][2]*n3;
 104       sliceLocations[series_number].push_back(sloc);
 105     } else
 106       sliceLocations[series_number].push_back(theorigin[series_number][2]);
 107     seriesFiles[series_number].push_back(input_files[i]);
 108
 109     gdcm::Attribute<0x28, 0x100> pixel_size;
 110     pixel_size.SetFromDataSet(ds);
 111     /* if (pixel_size.GetValue() != 16)
 112        {
 113        std::cerr << "Pixel type not 2 bytes ! " << std::endl;
 114        std::cerr << "In file " << input_files[i] << std::endl;
 115        exit(0);
 116        }
 117     */
 118 #else
 119   gdcm::File *header = new gdcm::File();
 120   header->SetFileName(input_files[i]);
 121   header->SetMaxSizeLoadEntry(16384); // required ?
 122   header->Load();
 123
 124   if (args_info.extract_series_flag) {
 125     series_number = atoi(header->GetEntryValue(0x20,0x11).c_str());
 126   }
 127
 128   series_numbers.insert(series_number);
 129   theorigin[series_number].resize(3);
 130   theorigin[series_number][0] = header->GetXOrigin();
 131   theorigin[series_number][1] = header->GetYOrigin();
 132   theorigin[series_number][2] = header->GetZOrigin();
 133   sliceLocations[series_number].push_back(theorigin[series_number][2]);
 134   seriesFiles[series_number].push_back(input_files[i]);
 135   /*if (header->GetPixelSize() != 2) {
 136     std::cerr << "Pixel type 2 bytes ! " << std::endl;
 137     std::cerr << "In file " << input_files[i] << std::endl;
 138     exit(0);
 139   }
 140   */
 141 #endif
 142   }
 143
 144   //===========================================
 145   // Sort slices locations ...
 146   std::set<int>::iterator sn = series_numbers.begin();
 147   while ( sn != series_numbers.end() ) {
 148     std::vector<double> locs = sliceLocations[*sn];
 149     std::vector<double> origin = theorigin[*sn];
 150     std::vector<std::string> files = seriesFiles[*sn];
 151     std::vector<int> sliceIndex;
 152     clitk::GetSortedIndex(locs, sliceIndex);
 153     if (args_info.verbose_flag) {
 154       std::cout << locs[sliceIndex[0]] << " -> "
 155                 << sliceIndex[0] << " / " << 0 << " => "
 156                 << "0 mm "
 157                 << files[sliceIndex[0]]
 158                 << std::endl;
 159       for(unsigned int i=1; i<sliceIndex.size(); i++) {
 160         std::cout << locs[sliceIndex[i]] << " -> "
 161                   << sliceIndex[i] << " / " << i << " => "
 162                   << locs[sliceIndex[i]] - locs[sliceIndex[i-1]]
 163                   << "mm "
 164                   << files[sliceIndex[i]]
 165                   << std::endl;
 166       }
 167     }
 168
 169     //===========================================
 170     // Analyze slices locations ...
 171     double currentDist;
 172     double dist=0;
 173     double tolerance = args_info.tolerance_arg;
 174     double previous = locs[sliceIndex[0]];
 175     for(unsigned int i=1; i<sliceIndex.size(); i++) {
 176       currentDist = locs[sliceIndex[i]]-previous;
 177       if (i!=1) {
 178         if (fabs(dist-currentDist) > tolerance) {
 179           std::cout << "ERROR : " << std::endl
 180                     << "Current slice pos is  = " << locs[sliceIndex[i]] << std::endl
 181                     << "Previous slice pos is = " << previous << std::endl
 182                     << "Current file is       = " << files[sliceIndex[i]] << std::endl
 183                     << "Current index is      = " << i << std::endl
 184                     << "Current sortindex is  = " << sliceIndex[i] << std::endl
 185                     << "Current slice diff    = " << dist << std::endl
 186                     << "Current error         = " << fabs(dist-currentDist) << std::endl;
 187           exit(1);
 188         }
 189       } else dist = currentDist;
 190       previous = locs[sliceIndex[i]];
 191     }
 192
 193     //===========================================
 194     // Create ordered vector of filenames
 195     std::vector<std::string> sorted_files;
 196     sorted_files.resize(sliceIndex.size());
 197     for(unsigned int i=0; i<sliceIndex.size(); i++)
 198       sorted_files[i] = files[ sliceIndex[i] ];
 199
 200     //===========================================
 201     // Read write serie
 202     vvImageReader::Pointer reader = vvImageReader::New();
 203     reader->SetInputFilenames(sorted_files);
 204     reader->Update(vvImageReader::DICOM);
 205     if (reader->GetLastError().size() != 0) {
 206       std::cerr << reader->GetLastError() << std::endl;
 207       return 1;
 208     }
 209
 210     vvImage::Pointer image = reader->GetOutput();
 211     vtkImageData* vtk_image = image->GetFirstVTKImageData();
 212     vtkImageChangeInformation* modifier = vtkImageChangeInformation::New();
 213     if  (args_info.focal_origin_given) {
 214       std::vector<double> spacing = image->GetSpacing();
 215       std::vector<int> size = image->GetSize();
 216       origin[0] = -spacing[0]*size[0]/2.0;
 217       origin[1] = -spacing[1]*size[1]/2.0;
 218 #if VTK_MAJOR_VERSION <= 5
 219       modifier->SetInput(vtk_image);
 220 #else
 221       modifier->SetInputData(vtk_image);
 222 #endif
 223       modifier->SetOutputOrigin(origin[0], origin[1], locs[sliceIndex[0]]);
 224       modifier->Update();
 225       vvImage::Pointer focal_image = vvImage::New();
 226       focal_image->AddVtkImage(modifier->GetOutput());
 227       image = focal_image;
 228     }
 229
 230     std::string outfile;
 231     if (series_numbers.size() == 1)
 232       outfile = args_info.output_arg;
 233     else {
 234       std::ostringstream name;
 235       std::vector<std::string> directory = clitk::SplitFilename(args_info.output_arg);
 236       if (directory.size() == 2)
 237         name << directory[0] << "/" << *sn << "_" << directory[1];
 238       else
 239         name << *sn << "_" << args_info.output_arg;
 240       outfile = name.str();
 241     }
 242     vvImageWriter::Pointer writer = vvImageWriter::New();
 243     writer->SetInput(image);
 244     if (args_info.patientSystem_flag && !image->GetTransform().empty())
 245       writer->SetSaveTransform(true);
 246     writer->SetOutputFileName(outfile);
 247     writer->Update();
 248
 249     modifier->Delete();
 250
 251     sn++;
 252   }
 253
 254   return 0;
 255 }