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
  32 //--------------------------------------------------------------------
  33 vvLandmarks::vvLandmarks(int size)
  34 {
  35   mLandmarks.resize(0);
  36   mFilename = "";
  37
  38   for (int i = 0; i < size; i++) {
  39     vtkPoints *points = vtkPoints::New();
  40     mPoints.push_back(points);
  41   }
  42   mPolyData = vtkPolyData::New();
  43   mIds = vtkFloatArray::New();
  44 }
  45 //--------------------------------------------------------------------
  46
  47
  48 //--------------------------------------------------------------------
  49 vvLandmarks::~vvLandmarks()
  50 {
  51   for (unsigned int i = 0; i < mPoints.size(); i++) {
  52     mPoints[i]->Delete();
  53   }
  54   /*for(unsigned int i = 0; i < mText.size(); i++) {
  55     mText[i]->Delete();
  56     }*/
  57   if (mIds)
  58     mIds->Delete();
  59   if (mPolyData)
  60     mPolyData->Delete();
  61 }
  62 //--------------------------------------------------------------------
  63
  64
  65 //--------------------------------------------------------------------
  66 void vvLandmarks::AddLandmark(float x,float y,float z,float t,double value)
  67 {
  68   vvLandmark point;
  69   point.coordinates[0] = x;
  70   point.coordinates[1] = y;
  71   point.coordinates[2] = z;
  72   point.coordinates[3] = t;
  73   point.pixel_value=value;
  74   mLandmarks.push_back(point);
  75   mPoints[int(t)]->InsertNextPoint(x,y,z);
  76
  77   std::stringstream numberVal;
  78   numberVal << (mLandmarks.size()-1);
  79   /*
  80   vvLandmarksGlyph *number = vvLandmarksGlyph::New();
  81   number->SetText(numberVal.str().c_str());
  82   number->BackingOff();
  83   DD(numberVal.str().c_str());
  84   mText.push_back(number);
  85   */
  86
  87   mIds->InsertNextTuple1(0.55);
  88   //mIds->InsertTuple1(mLandmarks.size(),mLandmarks.size());
  89   SetTime(int(t));
  90 }
  91 //--------------------------------------------------------------------
  92
  93
  94 //--------------------------------------------------------------------
  95 void vvLandmarks::RemoveLastLandmark()
  96 {
  97   mPoints[mLandmarks.back().coordinates[3]]->SetNumberOfPoints(
  98                                                                mPoints[mLandmarks.back().coordinates[3]]->GetNumberOfPoints()-1);
  99   mPolyData->Modified();
 100   //  mText.pop_back();
 101   mLandmarks.pop_back();
 102   mIds->RemoveLastTuple();
 103 }
 104 //--------------------------------------------------------------------
 105
 106
 107 //--------------------------------------------------------------------
 108 void vvLandmarks::RemoveLandmark(int index)
 109 {
 110   // erase a vtkPoint by shifiting the array .
 111   // not a problem here because there are no
 112   // pologyons linking the points
 113   int npoints = mPoints[mLandmarks[index].coordinates[3]]->GetNumberOfPoints();
 114   int t = mLandmarks[index].coordinates[3];
 115   for (int i = index; i < npoints - 1; i++)
 116     mPoints[t]->InsertPoint(i, mPoints[t]->GetPoint(i+1));
 117   mPoints[t]->SetNumberOfPoints(npoints-1);
 118   mPolyData->Modified();
 119
 120   mLandmarks.erase(mLandmarks.begin() + index);
 121   mIds->RemoveLastTuple();
 122 }
 123 //--------------------------------------------------------------------
 124
 125
 126 //--------------------------------------------------------------------
 127 void vvLandmarks::ChangeComments(int index, std::string comments)
 128 {
 129   mLandmarks[index].comments = comments;
 130 }
 131 //--------------------------------------------------------------------
 132
 133
 134 //--------------------------------------------------------------------
 135 double vvLandmarks::GetPixelValue(int index)
 136 {
 137   return mLandmarks[index].pixel_value;
 138 }
 139 //--------------------------------------------------------------------
 140
 141
 142 //--------------------------------------------------------------------
 143 float* vvLandmarks::GetCoordinates(int index)
 144 {
 145   return mLandmarks[index].coordinates;
 146 }
 147 //--------------------------------------------------------------------
 148
 149
 150 //--------------------------------------------------------------------
 151 std::string vvLandmarks::GetComments(int index)
 152 {
 153   return mLandmarks[index].comments;
 154 }
 155 //--------------------------------------------------------------------
 156
 157
 158 //--------------------------------------------------------------------
 159 void vvLandmarks::LoadFile(std::string filename)
 160 {
 161   std::ifstream fp(filename.c_str(), std::ios::in|std::ios::binary);
 162   if (!fp.is_open()) {
 163     std::cerr <<"Unable to open file " << filename << std::endl;
 164     return;
 165   }
 166   mFilename = filename;
 167   mLandmarks.clear();
 168   char line[255];
 169   for (unsigned int i = 0; i < mPoints.size(); i++)
 170     mPoints[i]->SetNumberOfPoints(0);
 171   bool first_line=true;
 172   while (fp.getline(line,255)) {
 173     //    DD(line);
 174     std::string stringline = line;
 175     if (first_line) {
 176       first_line=false;
 177       ///New landmark format: first line is "LANDMARKSXX", where XX is the version number
 178       if (stringline.size() >= 10 && stringline.compare(0,9,"LANDMARKS")==0) {
 179         std::istringstream ss(stringline.c_str()+9);
 180         ss >> mFormatVersion;
 181         continue; //skip first line
 182       } else
 183         mFormatVersion=0;
 184     }
 185     if (stringline.size() > 1) {
 186       vvLandmark point;
 187       int previousSpace = 0;
 188       int space=0;
 189       if (mFormatVersion>0) {
 190         space = stringline.find(" ", previousSpace+1);
 191         if (space < -1 || space > (int)stringline.size()) {
 192           ErrorMsg(mLandmarks.size(),"index");
 193           continue;
 194         }
 195         //int index = atoi(stringline.substr(previousSpace,space - previousSpace).c_str());
 196         previousSpace = space;
 197       }
 198       space = stringline.find(" ", previousSpace+1);
 199       if (space < -1 || space > (int)stringline.size()) {
 200         ErrorMsg(mLandmarks.size(),"x position");
 201         continue;
 202       }
 203       point.coordinates[0] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 204       //      DD(point.coordinates[0]);
 205       previousSpace = space;
 206       space = stringline.find(" ", previousSpace+1);
 207       if (space < -1 || space > (int)stringline.size()) {
 208         ErrorMsg(mLandmarks.size(),"y position");
 209         continue;
 210       }
 211       point.coordinates[1] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 212       //      DD(point.coordinates[1]);
 213       previousSpace = space;
 214       space = stringline.find(" ", previousSpace+1);
 215       if (space < -1 || space > (int)stringline.size()) {
 216         ErrorMsg(mLandmarks.size(),"z position");
 217         continue;
 218       }
 219       point.coordinates[2] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 220       previousSpace = space;
 221       if (mFormatVersion>0) {
 222         space = stringline.find(" ", previousSpace+1);
 223         if (space < -1 || space > (int)stringline.size()) {
 224           ErrorMsg(mLandmarks.size(),"t position");
 225           continue;
 226         }
 227         point.coordinates[3] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 228         previousSpace = space;
 229         space = stringline.find(" ", previousSpace+1);
 230         if (space < -1 || space > (int)stringline.size()) {
 231           ErrorMsg(mLandmarks.size(),"pixel value");
 232           continue;
 233         }
 234         point.pixel_value = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 235         //        DD(point.pixel_value);
 236       } else {
 237         point.pixel_value=0.; //Not in file
 238         point.coordinates[3]=0.;
 239       }
 240       previousSpace = space;
 241       //this is the maximum size of comments
 242       space = (stringline.find("\n", previousSpace+1) < 254 ? stringline.find("\n", previousSpace+1) : 254);
 243       if (previousSpace != -1) {
 244         point.comments = stringline.substr(previousSpace,space - (previousSpace)).c_str();
 245       }
 246       //      DD(point.comments);
 247       mLandmarks.push_back(point);
 248       mIds->InsertNextTuple1(0.55);
 249       mPoints[int(point.coordinates[3])]->InsertNextPoint(
 250                                                           point.coordinates[0],point.coordinates[1],point.coordinates[2]);
 251     }
 252   }
 253   SetTime(0);
 254 }
 255 //--------------------------------------------------------------------
 256
 257
 258 //--------------------------------------------------------------------
 259 bool vvLandmarks::ErrorMsg(int num,const char * text)
 260 {
 261   std::cerr << "error when loading point " << num << " at " << text << std::endl;
 262   return false;
 263 }
 264 //--------------------------------------------------------------------
 265
 266
 267 //--------------------------------------------------------------------
 268 void vvLandmarks::SaveFile(std::string filename)
 269 {
 270   std::string fileContent = "LANDMARKS1\n"; //File format version identification
 271   for (unsigned int i = 0; i < mLandmarks.size(); i++) {
 272     std::stringstream out;
 273     out.imbue(std::locale("C")); //This is to specify that the dot is to be used as the decimal separator
 274     out << i << " "
 275         << mLandmarks[i].coordinates[0] << " "
 276         << mLandmarks[i].coordinates[1] << " "
 277         << mLandmarks[i].coordinates[2] << " "
 278         << mLandmarks[i].coordinates[3] << " "
 279         << mLandmarks[i].pixel_value << " ";
 280     fileContent += out.str();
 281     if (mLandmarks[i].comments.size() == 0)
 282       fileContent += " ";
 283     else
 284       fileContent += mLandmarks[i].comments;
 285     fileContent += "\n";
 286   }
 287   std::ofstream fp(filename.c_str(), std::ios::trunc);
 288   if ( !fp ) {
 289     std::cerr << "Unable to open file" << std::endl;
 290     return;
 291   }
 292   fp << fileContent.c_str()<< std::endl;
 293   fp.close();
 294 }
 295 //--------------------------------------------------------------------
 296
 297
 298 //--------------------------------------------------------------------
 299 void vvLandmarks::SetTime(int time)
 300 {
 301   if (time >= 0 && time <= ((int)mPoints.size() -1)) {
 302     mPolyData->SetPoints(mPoints[time]);
 303     mPolyData->GetPointData()->SetScalars(mIds);
 304     mPolyData->Modified();
 305     mPolyData->Update();
 306   }
 307 }
 308 //--------------------------------------------------------------------
 309
 310
 311 //--------------------------------------------------------------------
 312 std::string vvLandmarks::replace_dots(std::string input)
 313 {
 314   ///Replaces the dots used in the file with the decimal separator in use on the platform
 315   lconv * conv=localeconv();
 316   unsigned int position = input.find( "." );
 317   while ( position < input.size() ) {
 318     input.replace(position, 1, conv->decimal_point);
 319     position = input.find( ".", position + 1 );
 320   }
 321   return input;
 322 }
 323 //--------------------------------------------------------------------