vv/vvLandmarks.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 #include "vvLandmarks.h"
  19
  20 #include <ios>
  21 #include <fstream>
  22 #include <sstream>
  23 #include <string>
  24 #include <locale.h>
  25
  26 #include "vtkPolyData.h"
  27 #include "vtkPoints.h"
  28 #include "vtkFloatArray.h"
  29 #include "vtkPointData.h"
  30 #include "clitkCommon.h"
  31 #include <itksys/SystemTools.hxx>
  32
  33 //--------------------------------------------------------------------
  34 vvLandmarks::vvLandmarks(int size)
  35 {
  36   mLandmarks.resize(0);
  37   mFilename = "";
  38
  39   for (int i = 0; i < size; i++) {
  40     vtkPoints *points = vtkPoints::New();
  41     mPoints.push_back(points);
  42   }
  43   mPolyData = vtkPolyData::New();
  44   mIds = vtkFloatArray::New();
  45   mLabels = vtkStringArray::New();
  46   mLabels->SetName("labels");
  47 }
  48 //--------------------------------------------------------------------
  49
  50
  51 //--------------------------------------------------------------------
  52 vvLandmarks::~vvLandmarks()
  53 {
  54   for (unsigned int i = 0; i < mPoints.size(); i++) {
  55     mPoints[i]->Delete();
  56   }
  57   /*for(unsigned int i = 0; i < mText.size(); i++) {
  58     mText[i]->Delete();
  59     }*/
  60   if (mIds)
  61     mIds->Delete();
  62   if (mPolyData)
  63     mPolyData->Delete();
  64   if (mLabels)
  65     mLabels->Delete();
  66 }
  67 //--------------------------------------------------------------------
  68
  69
  70 //--------------------------------------------------------------------
  71 void vvLandmarks::AddLandmark(float x,float y,float z,float t,double value)
  72 {
  73   vvLandmark point;
  74   vtkIdType idPoint;
  75   point.coordinates[0] = x;
  76   point.coordinates[1] = y;
  77   point.coordinates[2] = z;
  78   point.coordinates[3] = t;
  79   point.pixel_value=value;
  80   mLandmarks.push_back(point);
  81
  82   idPoint = mPoints[int(t)]->InsertNextPoint(x,y,z);
  83   std::string str_vtkIdType;        // string which will contain the result
  84   std::ostringstream convert;       // stream used for the conversion
  85   convert << idPoint;                   // insert the textual representation of 'idPoint' in the characters in the stream
  86   str_vtkIdType = convert.str();    // set 'str_vtkIdType' to the contents of the stream
  87   mLabels->InsertNextValue(str_vtkIdType.c_str());
  88
  89   std::stringstream numberVal;
  90   numberVal << (mLandmarks.size()-1);
  91   /*
  92   vvLandmarksGlyph *number = vvLandmarksGlyph::New();
  93   number->SetText(numberVal.str().c_str());
  94   number->BackingOff();
  95   DD(numberVal.str().c_str());
  96   mText.push_back(number);
  97   */
  98
  99   mIds->InsertNextTuple1(0.55);
 100   //mIds->InsertTuple1(mLandmarks.size(),mLandmarks.size());
 101   SetTime(int(t));
 102 }
 103 //--------------------------------------------------------------------
 104
 105
 106 //--------------------------------------------------------------------
 107 void vvLandmarks::RemoveLastLandmark()
 108 {
 109   mPoints[mLandmarks.back().coordinates[3]]->SetNumberOfPoints(
 110                                                                mPoints[mLandmarks.back().coordinates[3]]->GetNumberOfPoints()-1);
 111   //  mText.pop_back();
 112   mLandmarks.pop_back();
 113   mIds->RemoveLastTuple();
 114   mLabels->SetNumberOfValues(mLabels->GetNumberOfValues()-1);
 115   mLabels->Modified();
 116   mPolyData->Modified();
 117 }
 118 //--------------------------------------------------------------------
 119
 120
 121 //--------------------------------------------------------------------
 122 void vvLandmarks::RemoveLandmark(int index)
 123 {
 124   // erase a vtkPoint by shifiting the array .
 125   // not a problem here because there are no
 126   // pologyons linking the points
 127   int npoints = mPoints[mLandmarks[index].coordinates[3]]->GetNumberOfPoints();
 128   int t = mLandmarks[index].coordinates[3];
 129   for (int i = index; i < npoints - 1; i++) {
 130     mPoints[t]->InsertPoint(i, mPoints[t]->GetPoint(i+1));
 131         std::string str_i;                   // string which will contain the result
 132         std::ostringstream convert;      // stream used for the conversion
 133         convert << i;                        // insert the textual representation of 'i' in the characters in the stream
 134         str_i = convert.str();           // set 'str_i' to the contents of the stream
 135         mLabels->SetValue(i,str_i.c_str());
 136     }
 137   mPoints[t]->SetNumberOfPoints(npoints-1);
 138   mLabels->SetNumberOfValues(npoints-1);
 139   mLabels->Modified();
 140   mPolyData->Modified();
 141
 142   mLandmarks.erase(mLandmarks.begin() + index);
 143   mIds->RemoveLastTuple();
 144 }
 145 //--------------------------------------------------------------------
 146
 147
 148 //--------------------------------------------------------------------
 149 void vvLandmarks::ChangeComments(int index, std::string comments)
 150 {
 151   mLandmarks[index].comments = comments;
 152 }
 153 //--------------------------------------------------------------------
 154
 155
 156 //--------------------------------------------------------------------
 157 double vvLandmarks::GetPixelValue(int index)
 158 {
 159   return mLandmarks[index].pixel_value;
 160 }
 161 //--------------------------------------------------------------------
 162
 163
 164 //--------------------------------------------------------------------
 165 float* vvLandmarks::GetCoordinates(int index)
 166 {
 167   return mLandmarks[index].coordinates;
 168 }
 169 //--------------------------------------------------------------------
 170
 171
 172 //--------------------------------------------------------------------
 173 std::string vvLandmarks::GetComments(int index)
 174 {
 175   return mLandmarks[index].comments;
 176 }
 177 //--------------------------------------------------------------------
 178
 179
 180 //--------------------------------------------------------------------
 181 bool vvLandmarks::LoadFile(std::string filename)
 182 {
 183   std::string extension = itksys::SystemTools::GetFilenameExtension(filename);
 184   if (extension == ".txt")
 185     return LoadTxtFile(filename);
 186   else if (extension == ".pts")
 187     return LoadPtsFile(filename);
 188
 189   return false;
 190 }
 191
 192 //--------------------------------------------------------------------
 193 bool vvLandmarks::LoadTxtFile(std::string filename)
 194 {
 195   std::ifstream fp(filename.c_str(), std::ios::in|std::ios::binary);
 196   if (!fp.is_open()) {
 197     std::cerr <<"Unable to open file " << filename << std::endl;
 198     return false;
 199   }
 200   mFilename = filename;
 201   mLandmarks.clear();
 202   vtkIdType idPoint;
 203   char line[255];
 204   for (unsigned int i = 0; i < mPoints.size(); i++)
 205     mPoints[i]->SetNumberOfPoints(0);
 206   bool first_line=true;
 207   while (fp.getline(line,255)) {
 208     //    DD(line);
 209     std::string stringline = line;
 210     if (first_line) {
 211       first_line=false;
 212       ///New landmark format: first line is "LANDMARKSXX", where XX is the version number
 213       if (stringline.size() >= 10 && stringline.compare(0,9,"LANDMARKS")==0) {
 214         std::istringstream ss(stringline.c_str()+9);
 215         ss >> mFormatVersion;
 216         continue; //skip first line
 217       } else
 218         mFormatVersion=0;
 219     }
 220     if (stringline.size() > 1) {
 221       vvLandmark point;
 222       int previousSpace = 0;
 223       int space=0;
 224       if (mFormatVersion>0) {
 225         space = stringline.find(" ", previousSpace+1);
 226         if (space < -1 || space > (int)stringline.size()) {
 227           ErrorMsg(mLandmarks.size(),"index");
 228           continue;
 229         }
 230         //int index = atoi(stringline.substr(previousSpace,space - previousSpace).c_str());
 231         previousSpace = space;
 232       }
 233       space = stringline.find(" ", previousSpace+1);
 234       if (space < -1 || space > (int)stringline.size()) {
 235         ErrorMsg(mLandmarks.size(),"x position");
 236         continue;
 237       }
 238       point.coordinates[0] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 239       //      DD(point.coordinates[0]);
 240       previousSpace = space;
 241       space = stringline.find(" ", previousSpace+1);
 242       if (space < -1 || space > (int)stringline.size()) {
 243         ErrorMsg(mLandmarks.size(),"y position");
 244         continue;
 245       }
 246       point.coordinates[1] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 247       //      DD(point.coordinates[1]);
 248       previousSpace = space;
 249       space = stringline.find(" ", previousSpace+1);
 250       if (space < -1 || space > (int)stringline.size()) {
 251         ErrorMsg(mLandmarks.size(),"z position");
 252         continue;
 253       }
 254       point.coordinates[2] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 255       previousSpace = space;
 256       if (mFormatVersion>0) {
 257         space = stringline.find(" ", previousSpace+1);
 258         if (space < -1 || space > (int)stringline.size()) {
 259           ErrorMsg(mLandmarks.size(),"t position");
 260           continue;
 261         }
 262         point.coordinates[3] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 263         previousSpace = space;
 264         space = stringline.find(" ", previousSpace+1);
 265         if (space < -1 || space > (int)stringline.size()) {
 266           ErrorMsg(mLandmarks.size(),"pixel value");
 267           continue;
 268         }
 269         point.pixel_value = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 270         //        DD(point.pixel_value);
 271       } else {
 272         point.pixel_value=0.; //Not in file
 273         point.coordinates[3]=0.;
 274       }
 275       previousSpace = space;
 276       //this is the maximum size of comments
 277       space = (stringline.find("\n", previousSpace+1) < 254 ? stringline.find("\n", previousSpace+1) : 254);
 278       if (previousSpace != -1) {
 279         point.comments = stringline.substr(previousSpace,space - (previousSpace)).c_str();
 280       }
 281       //      DD(point.comments);
 282       mLandmarks.push_back(point);
 283       mIds->InsertNextTuple1(0.55);
 284      idPoint = mPoints[int(point.coordinates[3])]->InsertNextPoint(
 285                                                           point.coordinates[0],point.coordinates[1],point.coordinates[2]);
 286      std::string str_vtkIdType;     // string which will contain the result
 287      std::ostringstream convert;        // stream used for the conversion
 288      convert << idPoint;                    // insert the textual representation of 'idPoint' in the characters in the stream
 289      str_vtkIdType = convert.str(); // set 'str_vtkIdType' to the contents of the stream
 290      mLabels->InsertNextValue(str_vtkIdType.c_str());
 291     }
 292   }
 293   SetTime(0);
 294
 295   return true;
 296 }
 297 //--------------------------------------------------------------------
 298
 299 //--------------------------------------------------------------------
 300 bool vvLandmarks::LoadPtsFile(std::string filename)
 301 {
 302   std::ifstream fp(filename.c_str(), std::ios::in|std::ios::binary);
 303   if (!fp.is_open()) {
 304     std::cerr <<"Unable to open file " << filename << std::endl;
 305     return false;
 306   }
 307   mFilename = filename;
 308   mLandmarks.clear();
 309   vtkIdType idPoint;
 310   char line[255];
 311   for (unsigned int i = 0; i < mPoints.size(); i++)
 312     mPoints[i]->SetNumberOfPoints(0);
 313   bool first_line=true;
 314   while (fp.getline(line,255)) {
 315     //    DD(line);
 316     std::string stringline = line;
 317     if (stringline.size() > 1) {
 318       vvLandmark point;
 319       int previousSpace = 0;
 320       int space=0;
 321
 322       if (stringline[0] == '#') // comments
 323         continue;
 324
 325       space = stringline.find("\t", previousSpace+1);
 326       if (space < -1 || space > (int)stringline.size()) {
 327         ErrorMsg(mLandmarks.size(),"x position");
 328         continue;
 329       }
 330       point.coordinates[0] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 331       //      DD(point.coordinates[0]);
 332       previousSpace = space;
 333       space = stringline.find("\t", previousSpace+1);
 334       if (space < -1 || space > (int)stringline.size()) {
 335         ErrorMsg(mLandmarks.size(),"y position");
 336         continue;
 337       }
 338       point.coordinates[1] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 339       //      DD(point.coordinates[1]);
 340       previousSpace = space;
 341       space = stringline.find("\t", previousSpace+1);
 342       if (space < -1 || space > (int)stringline.size()) {
 343         ErrorMsg(mLandmarks.size(),"z position");
 344         continue;
 345       }
 346       point.coordinates[2] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 347       previousSpace = space;
 348       if (mFormatVersion>0) {
 349         space = stringline.find("\t", previousSpace+1);
 350         if (space < -1 || space > (int)stringline.size()) {
 351           ErrorMsg(mLandmarks.size(),"t position");
 352           continue;
 353         }
 354         point.coordinates[3] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 355         previousSpace = space;
 356         space = stringline.find("\t", previousSpace+1);
 357         if (space < -1 || space > (int)stringline.size()) {
 358           ErrorMsg(mLandmarks.size(),"pixel value");
 359           continue;
 360         }
 361         point.pixel_value = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 362         //        DD(point.pixel_value);
 363       } else {
 364         point.pixel_value=0.; //Not in file
 365         point.coordinates[3]=0.;
 366       }
 367       previousSpace = space;
 368       //this is the maximum size of comments
 369       space = (stringline.find("\n", previousSpace+1) < 254 ? stringline.find("\n", previousSpace+1) : 254);
 370       if (previousSpace != -1) {
 371         point.comments = stringline.substr(previousSpace,space - (previousSpace)).c_str();
 372       }
 373       //      DD(point.comments);
 374       mLandmarks.push_back(point);
 375       mIds->InsertNextTuple1(0.55);
 376      idPoint = mPoints[int(point.coordinates[3])]->InsertNextPoint(
 377                                                           point.coordinates[0],point.coordinates[1],point.coordinates[2]);
 378      std::string str_vtkIdType;     // string which will contain the result
 379      std::ostringstream convert;  // stream used for the conversion
 380      convert << idPoint;        // insert the textual representation of 'idPoint' in the characters in the stream
 381      str_vtkIdType = convert.str(); // set 'str_vtkIdType' to the contents of the stream
 382      mLabels->InsertNextValue(str_vtkIdType.c_str());
 383     }
 384   }
 385   SetTime(0);
 386
 387   return true;
 388 }
 389 //--------------------------------------------------------------------
 390
 391 //--------------------------------------------------------------------
 392 bool vvLandmarks::ErrorMsg(int num,const char * text)
 393 {
 394   std::cerr << "error when loading point " << num << " at " << text << std::endl;
 395   return false;
 396 }
 397 //--------------------------------------------------------------------
 398
 399
 400 //--------------------------------------------------------------------
 401 void vvLandmarks::SaveFile(std::string filename)
 402 {
 403   std::string fileContent = "LANDMARKS1\n"; //File format version identification
 404   for (unsigned int i = 0; i < mLandmarks.size(); i++) {
 405     std::stringstream out;
 406     out.imbue(std::locale("C")); //This is to specify that the dot is to be used as the decimal separator
 407     out << i << " "
 408         << mLandmarks[i].coordinates[0] << " "
 409         << mLandmarks[i].coordinates[1] << " "
 410         << mLandmarks[i].coordinates[2] << " "
 411         << mLandmarks[i].coordinates[3] << " "
 412         << mLandmarks[i].pixel_value << " ";
 413     fileContent += out.str();
 414     if (mLandmarks[i].comments.size() == 0)
 415       fileContent += " ";
 416     else
 417       fileContent += mLandmarks[i].comments;
 418     fileContent += "\n";
 419   }
 420   std::ofstream fp(filename.c_str(), std::ios::trunc);
 421   if ( !fp ) {
 422     std::cerr << "Unable to open file" << std::endl;
 423     return;
 424   }
 425   fp << fileContent.c_str()<< std::endl;
 426   fp.close();
 427 }
 428 //--------------------------------------------------------------------
 429
 430
 431 //--------------------------------------------------------------------
 432 void vvLandmarks::SetTime(int time)
 433 {
 434   if (time >= 0 && time <= ((int)mPoints.size() -1)) {
 435     mPolyData->SetPoints(mPoints[time]);
 436     mPolyData->GetPointData()->SetScalars(mIds);
 437     mPolyData->GetPointData()->AddArray(mLabels);
 438     mPolyData->Modified();
 439     mPolyData->Update();
 440   }
 441 }
 442 //--------------------------------------------------------------------
 443
 444
 445 //--------------------------------------------------------------------
 446 std::string vvLandmarks::replace_dots(std::string input)
 447 {
 448   ///Replaces the dots used in the file with the decimal separator in use on the platform
 449   lconv * conv=localeconv();
 450   unsigned int position = input.find( "." );
 451   while ( position < input.size() ) {
 452     input.replace(position, 1, conv->decimal_point);
 453     position = input.find( ".", position + 1 );
 454   }
 455   return input;
 456 }
 457 //--------------------------------------------------------------------