registration/clitkLists.txx

   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 #ifndef clitkLists_txx
  19 #define clitkLists_txx
  20 #include "clitkLists.h"
  21
  22 using namespace std;
  23
  24 namespace clitk
  25 {
  26
  27   //---------------------------------------------------------------------
  28   // Read
  29   //---------------------------------------------------------------------
  30   template<class ListItemType>
  31   void Lists< ListItemType>::Read(const std::vector<string>& filenames, bool verbose)
  32   {
  33
  34     // Make the lists
  35     this->resize(filenames.size());
  36
  37     // Read the lists
  38     for (unsigned int i=0; i<filenames.size();i++)
  39       this->at(i).Read(filenames[i],verbose);
  40
  41   }
  42
  43   //---------------------------------------------------------------------
  44   // Norm
  45   //---------------------------------------------------------------------
  46   template<class ListItemType>
  47   Lists<itk::FixedArray<double,1> > Lists<ListItemType>::Norm(void)
  48   {
  49     Lists<itk::FixedArray<double,1> > norm;
  50
  51     // Normalize the lists
  52     for (unsigned int i=0; i<this->size();i++)
  53       norm.push_back(this->at(i).Norm());
  54
  55     return norm;
  56   }
  57
  58   //---------------------------------------------------------------------
  59   // ReadPointPairs (specific for DARS- IX point list format)
  60   //---------------------------------------------------------------------
  61   template<class ListItemType>
  62   void
  63   Lists<ListItemType>::ReadAndConvertPointPairs(const std::vector<std::string>& fileNames, ListType& refList, const typename ImageType::Pointer referenceImage, bool verbose)
  64   {
  65
  66     // Init
  67     this->resize(fileNames.size());
  68     refList.resize(0);
  69     bool pointWasFound=true;
  70     unsigned int pointNumber=0;
  71     itk::ContinuousIndex<ValueType, Dimension> item1;
  72     std::vector<itk::ContinuousIndex<ValueType, Dimension> > item2(fileNames.size());
  73     itk::Point<ValueType, Dimension> point1, point2;
  74     unsigned int totalNumberOfPoints=0;
  75     std::vector<unsigned int> addedNumberOfPoints,ommittedNumberOfPoints;
  76     std::vector<bool> pointIsUnsure(fileNames.size());
  77     std::vector<std::vector<bool> > ommittedNumberOfPointsUnsure;
  78
  79     // Loop over the points
  80     while (pointWasFound)
  81       {
  82
  83         if (verbose) std::cout<<std::endl<<"Processing point number: "<<pointNumber<<"..."<<std::endl;
  84         if (verbose) std::cout<<"Point number: "<<pointNumber<<" was found in list number: ";
  85
  86         // Loop over lists
  87         bool veryUnsure=false;
  88         for (unsigned int i =0; i< fileNames.size(); i++)
  89           {
  90             // Get the point
  91             pointWasFound=this->at(i).ReadPointPair(fileNames[i],pointNumber,item1,item2[i],veryUnsure);
  92             if (verbose && pointWasFound) std::cout<<" "<<i;
  93
  94             // Set unsure
  95             pointIsUnsure[i]= veryUnsure;
  96
  97             // point not found
  98             if(!pointWasFound) break;
  99           }
 100         if (verbose) std::cout<<std::endl;
 101
 102         // The point was found
 103         if (pointWasFound)
 104           {
 105             totalNumberOfPoints++;
 106
 107             // Point unsure?
 108             bool unsure=false;
 109             for (unsigned int i =0; i< fileNames.size(); i++)
 110               if (pointIsUnsure[i])
 111                 {
 112                   unsure=true;
 113                   break;
 114                 }
 115
 116             // At least one of the lists had it tagged as veryUnsure
 117             if (unsure)
 118               {
 119                 ommittedNumberOfPoints.push_back(pointNumber);
 120                 ommittedNumberOfPointsUnsure.push_back(pointIsUnsure);
 121                 if (verbose) std::cout<<"Omitting item "<<pointNumber<<" (very unsure): "<<item1<<" ; "<<item2[0]<<std::endl;
 122               }
 123             else
 124               {
 125                 addedNumberOfPoints.push_back(pointNumber);
 126                 // Add the point to all the lists
 127                 for (unsigned int i =0; i< fileNames.size(); i++)
 128                   {
 129                     if (verbose) std::cout<<"Adding item "<<pointNumber<<": "<<item1<<" ; "<<item2[i]<<std::endl;
 130                     if (i==0)
 131                       {
 132                         referenceImage->TransformContinuousIndexToPhysicalPoint(item1, point1);
 133                         refList.push_back(point1);
 134                       }
 135                     referenceImage->TransformContinuousIndexToPhysicalPoint(item2[i], point2);
 136                     if (verbose) std::cout<<"Converted items "<<pointNumber<<" to points: "<<point1<<" ; "<<point2<<std::endl;
 137                     this->at(i).push_back(point2);
 138                   }
 139               }
 140           }
 141
 142         // Next point
 143         pointNumber++;
 144
 145       }
 146
 147     if (verbose)
 148       {
 149         std::cout<<std::endl<<totalNumberOfPoints<<" points processed, "<< ommittedNumberOfPoints.size() <<" points omitted, "<< addedNumberOfPoints.size()<<" points added."<<std::endl;
 150         std::cout<<"Added point numbers: "<< std::endl;
 151         for (unsigned int i=0; i< addedNumberOfPoints.size();i++)
 152           std::cout<<addedNumberOfPoints[i] <<std::endl;
 153         std::cout<<"Omitted point numbers: "<< std::endl;
 154             for (unsigned int i=0; i< ommittedNumberOfPoints.size();i++)
 155               {
 156                 std::cout<<ommittedNumberOfPoints[i] <<"\t";
 157                 for (unsigned int j=0; j< fileNames.size();j++)
 158                   std::cout<<ommittedNumberOfPointsUnsure[i][j]<<" ";
 159                 std::cout<<std::endl;
 160               }
 161       }
 162   }
 163
 164
 165
 166
 167   //---------------------------------------------------------------------
 168   // Write
 169   //---------------------------------------------------------------------
 170   template<class ListItemType>
 171   void Lists<ListItemType>::Write(const std::vector<std::string> fileNames, const bool verbose)
 172   {
 173     for (unsigned int i =0; i< fileNames.size(); i++)
 174       this->at(i).Write(fileNames[i], verbose);
 175   }
 176
 177
 178 } // namespace
 179
 180 #endif