registration/clitkList.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://oncora1.lyon.fnclcc.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 CLITKLIST_TXX
  19 #define CLITKLIST_TXX
  20 #include "clitkList.h"
  21
  22 using namespace std;
  23
  24 namespace clitk
  25 {
  26
  27
  28   //---------------------------------------------------------------------
  29   // Read
  30   //---------------------------------------------------------------------
  31   template<class ListItemType>
  32   void List< ListItemType>::Read(const string& filename, bool verbose)
  33   {
  34     std::ifstream is;
  35     openFileForReading(is, filename);
  36
  37     this->resize(0);
  38     ListItemType item;
  39     ValueType x;
  40
  41     if(verbose)std::cout<<"Reading "<<filename<<"..."<<std::endl;
  42     for (unsigned int dim=0; dim<Dimension; dim++)
  43       {
  44         skipComment(is);
  45         is >> x;
  46         item[dim]=x;
  47       }
  48
  49     while (!is.eof())
  50       {
  51         this->push_back(item);
  52         for (unsigned int dim=0; dim<Dimension; dim++)
  53           {
  54             skipComment(is);
  55             is >> x;
  56             item[dim]=x;
  57           }
  58       }
  59   }
  60
  61
  62   //---------------------------------------------------------------------
  63   // ReadPointPairs (specific for DARS- IX point list format)
  64   //---------------------------------------------------------------------
  65   template<class ListItemType>
  66   void
  67   List<ListItemType>::ReadAndConvertPointPairs(const std::string& fileName, List& correspList, const typename ImageType::Pointer referenceImage, bool verbose)
  68   {
  69     // Init
  70     this->resize(0);
  71     correspList.resize(0);
  72
  73     // Tags
  74     IndexType item1, item2;
  75     itk::Point<ValueType, Dimension> point1,point2;
  76     unsigned int pointNumber=0;
  77     bool veryUnsure=false;
  78
  79     // Read first point
  80     bool pointWasFound=ReadPointPair(fileName, pointNumber, item1, item2, veryUnsure);
  81
  82     // Loop over all points
  83     while (pointWasFound)
  84       {
  85         // Store the values
  86         if(veryUnsure)
  87           {
  88             if (verbose) std::cout<<"Omitting item "<<pointNumber<<" (very unsure): "<<item1<<" ; "<<item2<<std::endl;
  89           }
  90         else
  91           {
  92             if (verbose) std::cout<<"Adding item "<<pointNumber<<": "<<item1<<" ; "<<item2<<std::endl;
  93             referenceImage->TransformContinuousIndexToPhysicalPoint(item1, point1);
  94             referenceImage->TransformContinuousIndexToPhysicalPoint(item2, point2);
  95             if (verbose) std::cout<<"Converted items "<<pointNumber<<" to points: "<<point1<<" ; "<<point2<<std::endl;
  96             this->push_back(point1);
  97             correspList.push_back(point2);
  98           }
  99
 100         // Next point
 101         pointNumber++;
 102         pointWasFound=ReadPointPair(fileName, pointNumber, item1, item2, veryUnsure);
 103       }
 104   }
 105
 106   //---------------------------------------------------------------------
 107   // Read one point
 108   //---------------------------------------------------------------------
 109   template<class ListItemType>
 110   bool
 111   List< ListItemType>::ReadPointPair(const std::string& fileName, const unsigned int& pointNumber, IndexType& item1, IndexType& item2, bool& veryUnsure)
 112   {
 113     // bool
 114     bool pointWasFound=false;
 115     veryUnsure=false;
 116     item1.Fill(0.0);
 117     item2.Fill(0.0);
 118
 119     // Open the file
 120     ifstream listStream(fileName.c_str());
 121     string line;
 122     if(!listStream.is_open()){
 123       std::cerr << "ERROR: Couldn't open file " << fileName << " in List::Read" << std::endl;
 124       return false;
 125     }
 126
 127     // Skip the configuration lines
 128     while ( !listStream.eof())
 129       {
 130         // Get the line
 131         skipComment(listStream);
 132         getline(listStream, line);
 133
 134         // Get the line type
 135         unsigned int endIndexItemType= line.find_first_of ("_",0)-1;
 136         string typeString= line.substr(0 , endIndexItemType+1);
 137
 138         // Check
 139         if  (typeString=="Point")
 140           break;
 141       }
 142
 143     // Get the point number
 144     unsigned int beginIndexItemNumber= line.find_first_of ("_",0)+1;
 145     unsigned int endIndexItemNumber= line.find_first_of ("->",0)-1;
 146     stringstream numberString( line.substr(beginIndexItemNumber , endIndexItemNumber-beginIndexItemNumber+1) );
 147     unsigned int itemNumber;
 148     numberString>> itemNumber;
 149
 150     // FF to the pointNumber
 151     while ( (itemNumber != pointNumber) && (!listStream.eof()) )
 152       {
 153         // Skipcomment
 154         skipComment(listStream);
 155
 156         // Get Line
 157         getline(listStream, line);
 158
 159         // Get the point number
 160         beginIndexItemNumber= line.find_first_of ("_",0)+1;
 161         endIndexItemNumber= line.find_first_of ("->",0)-1;
 162         stringstream numberString( line.substr(beginIndexItemNumber , endIndexItemNumber-beginIndexItemNumber+1) );
 163         numberString>> itemNumber;
 164       }
 165
 166     // Go over all fields of the pointNumber
 167     while (itemNumber == pointNumber && (!listStream.eof()) )
 168       {
 169         // point found
 170         pointWasFound=true;
 171
 172         // Get the tag
 173         unsigned int beginIndexItemTag= line.find_first_of ("->",0)+2;
 174         unsigned int endIndexItemTag= line.find_first_of ("=",0)-1;
 175         string itemTag= line.substr(beginIndexItemTag , endIndexItemTag-beginIndexItemTag+1);
 176
 177         // Get the point Value
 178         unsigned int beginIndexItemValue= line.find_first_of ("=",0)+1;
 179         stringstream valueString( line.substr(beginIndexItemValue) );
 180         double itemValue;
 181         valueString>> itemValue;
 182
 183         // Fill the items
 184         if (itemTag=="X")
 185           item1[0]=itemValue;
 186         if (itemTag=="Y")
 187           item1[1]=itemValue;
 188         if (itemTag=="Z")
 189           item1[2]=itemValue;
 190         if (itemTag=="X_Corresp")
 191           item2[0]=itemValue;
 192         if (itemTag=="Y_Corresp")
 193           item2[1]=itemValue;
 194         if (itemTag=="Z_Corresp")
 195           item2[2]=itemValue;
 196         if (itemTag=="VeryUnsure")
 197           veryUnsure=itemValue;
 198
 199         // Get the next line
 200         skipComment(listStream);
 201         getline(listStream, line);
 202
 203         // Get the point number
 204         unsigned int beginIndexItemNumber= line.find_first_of ("_",0)+1;
 205         unsigned int endIndexItemNumber= line.find_first_of ("->",0)-1;
 206         stringstream numberString( line.substr(beginIndexItemNumber , endIndexItemNumber-beginIndexItemNumber+1) );
 207         numberString >> itemNumber;
 208       }
 209
 210     return pointWasFound;
 211   }
 212
 213
 214  //---------------------------------------------------------------------
 215   // Print
 216   //---------------------------------------------------------------------
 217   template<class ListItemType>
 218   void List< ListItemType>::Print()
 219   {
 220     for (unsigned int i=0; i< this->size(); i++)
 221       std::cout<<this->at(i)<<std::endl;
 222   }
 223
 224
 225   //---------------------------------------------------------------------
 226   // Write
 227   //---------------------------------------------------------------------
 228   template<class ListItemType>
 229   void List<ListItemType>::Write(const string fileName, const bool verbose)
 230   {
 231     ofstream listStream(fileName.c_str());
 232     if(!listStream.is_open()){
 233       cerr << "ERROR: Couldn't open file " << fileName << " in List::Write" << endl;
 234       return;
 235     }
 236
 237     typename ListType::iterator it=this->begin();
 238     while(it!=this->end()) {
 239       listStream << (*it)[0];
 240       for (unsigned int i=1; i< this->at(0).Size(); i++)
 241         listStream <<" "<< (*it)[i];
 242       listStream<< endl;
 243       it++;
 244     }
 245     listStream.close();
 246   }
 247
 248   //---------------------------------------------------------------------
 249   // Norm
 250   //---------------------------------------------------------------------
 251   template<class ListItemType>
 252   List<itk::FixedArray<double, 1> > List< ListItemType>::Norm()
 253   {
 254     List<itk::FixedArray<double, 1> > norm;
 255     itk::FixedArray<double, 1> n;
 256     unsigned int d;
 257     for (unsigned int i=0; i< this->size(); i++)
 258       {
 259         n[0]=0;
 260         for (d=0; d< Dimension; d++)
 261           n[0]+=this->at(i)[d] * this->at(i)[d];
 262         n[0]=sqrt(n[0]);
 263         norm.push_back(n);
 264       }
 265     return norm;
 266   }
 267
 268
 269
 270
 271 }
 272
 273 #endif //#define CLITKLIST
 274
 275
 276     //    // Open the file
 277     //     ifstream listStream(fileName.c_str());
 278     //     ListItemType item;
 279     //     string line;
 280     //     if(!listStream.is_open()){
 281     //       std::cerr << "ERROR: Couldn't open file " << fileName << " in List::Read" << std::endl;
 282     //       return;
 283     //     }
 284     //     skipComment(listStream);
 285
 286     //     // Skip the configuration lines
 287     //     while (true)
 288     //       {
 289     //  // Get the line
 290     //  skipComment(listStream);
 291     //  getline(listStream, line);
 292
 293     //  // Get the line type
 294     //  unsigned int endIndexItemType= line.find_first_of ("_",0)-1;
 295     //  string typeString= line.substr(0 , endIndexItemType+1);
 296
 297     //  // Check
 298     //  if  (typeString=="Point")
 299     //    break;
 300     //       }
 301
 302     //     // Get the point number
 303     //     unsigned int beginIndexItemNumber= line.find_first_of ("_",0)+1;
 304     //     unsigned int endIndexItemNumber= line.find_first_of ("->",0)-1;
 305     //     stringstream numberString( line.substr(beginIndexItemNumber , endIndexItemNumber-beginIndexItemNumber+1) );
 306     //     unsigned int itemNumber;
 307     //     numberString>> itemNumber;
 308
 309     //     // Go over all the lines
 310     //     while(!listStream.eof())
 311     //       {
 312     //  // Stored data
 313     //  itk::Point<ValueType, Dimension> point1, point2;
 314     //  point1.Fill(0.);
 315     //  point2.Fill(0.);
 316     //  bool veryUnsure=false;
 317
 318     //  // Retrieved data
 319     //  itk::ContinuousIndex<ValueType, Dimension> item1, item2;
 320     //  item1.Fill(0.);
 321     //  item2.Fill(0.);
 322
 323     //  // Go over all lines corresponding to this point
 324     //  unsigned int currentNumber=itemNumber;
 325     //  while (itemNumber == currentNumber && (!listStream.eof()) )
 326     //    {
 327     //      // Get the tag
 328     //      unsigned int beginIndexItemTag= line.find_first_of ("->",0)+2;
 329     //      unsigned int endIndexItemTag= line.find_first_of ("=",0)-1;
 330     //      string itemTag= line.substr(beginIndexItemTag , endIndexItemTag-beginIndexItemTag+1);
 331
 332     //      // Get the point Value
 333     //      unsigned int beginIndexItemValue= line.find_first_of ("=",0)+1;
 334     //      stringstream valueString( line.substr(beginIndexItemValue) );
 335     //      double itemValue;
 336     //      valueString>> itemValue;
 337
 338     //      // Fill the items
 339     //      if (itemTag=="X")
 340     //        item1[0]=itemValue;
 341     //      if (itemTag=="Y")
 342     //        item1[1]=itemValue;
 343     //      if (itemTag=="Z")
 344     //        item1[2]=itemValue;
 345     //      if (itemTag=="X_Corresp")
 346     //        item2[0]=itemValue;
 347     //      if (itemTag=="Y_Corresp")
 348     //        item2[1]=itemValue;
 349     //      if (itemTag=="Z_Corresp")
 350     //         item2[2]=itemValue;
 351     //      if (itemTag=="VeryUnsure")
 352     //        veryUnsure=itemValue;
 353
 354     //      // Get the next line
 355     //      skipComment(listStream);
 356     //      getline(listStream, line);
 357
 358     //      // Get the point number
 359     //      unsigned int beginIndexItemNumber= line.find_first_of ("_",0)+1;
 360     //      unsigned int endIndexItemNumber= line.find_first_of ("->",0)-1;
 361     //      stringstream numberString( line.substr(beginIndexItemNumber , endIndexItemNumber-beginIndexItemNumber+1) );
 362     //      numberString>> itemNumber;
 363     //    }