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://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 #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::ChangeComments(int index, std::string comments)
 109 {
 110   mLandmarks[index].comments = comments;
 111 }
 112 //--------------------------------------------------------------------
 113
 114
 115 //--------------------------------------------------------------------
 116 double vvLandmarks::GetPixelValue(int index)
 117 {
 118   return mLandmarks[index].pixel_value;
 119 }
 120 //--------------------------------------------------------------------
 121
 122
 123 //--------------------------------------------------------------------
 124 float* vvLandmarks::GetCoordinates(int index)
 125 {
 126   return mLandmarks[index].coordinates;
 127 }
 128 //--------------------------------------------------------------------
 129
 130
 131 //--------------------------------------------------------------------
 132 std::string vvLandmarks::GetComments(int index)
 133 {
 134   return mLandmarks[index].comments;
 135 }
 136 //--------------------------------------------------------------------
 137
 138
 139 //--------------------------------------------------------------------
 140 void vvLandmarks::LoadFile(std::string filename)
 141 {
 142   std::ifstream fp(filename.c_str(), std::ios::in|std::ios::binary);
 143   if (!fp.is_open()) {
 144     std::cerr <<"Unable to open file " << filename << std::endl;
 145     return;
 146   }
 147   mFilename = filename;
 148   mLandmarks.clear();
 149   char line[255];
 150   for (unsigned int i = 0; i < mPoints.size(); i++)
 151     mPoints[i]->SetNumberOfPoints(0);
 152   bool first_line=true;
 153   while (fp.getline(line,255)) {
 154     //    DD(line);
 155     std::string stringline = line;
 156     if (first_line) {
 157       first_line=false;
 158       ///New landmark format: first line is "LANDMARKSXX", where XX is the version number
 159       if (stringline.size() >= 10 && stringline.compare(0,9,"LANDMARKS")==0) {
 160         std::istringstream ss(stringline.c_str()+9);
 161         ss >> mFormatVersion;
 162         continue; //skip first line
 163       } else
 164         mFormatVersion=0;
 165     }
 166     if (stringline.size() > 1) {
 167       vvLandmark point;
 168       int previousSpace = 0;
 169       int space=0;
 170       if (mFormatVersion>0) {
 171         space = stringline.find(" ", previousSpace+1);
 172         if (space < -1 || space > (int)stringline.size()) {
 173           ErrorMsg(mLandmarks.size(),"index");
 174           continue;
 175         }
 176         //int index = atoi(stringline.substr(previousSpace,space - previousSpace).c_str());
 177         previousSpace = space;
 178       }
 179       space = stringline.find(" ", previousSpace+1);
 180       if (space < -1 || space > (int)stringline.size()) {
 181         ErrorMsg(mLandmarks.size(),"x position");
 182         continue;
 183       }
 184       point.coordinates[0] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 185       //      DD(point.coordinates[0]);
 186       previousSpace = space;
 187       space = stringline.find(" ", previousSpace+1);
 188       if (space < -1 || space > (int)stringline.size()) {
 189         ErrorMsg(mLandmarks.size(),"y position");
 190         continue;
 191       }
 192       point.coordinates[1] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 193       //      DD(point.coordinates[1]);
 194       previousSpace = space;
 195       space = stringline.find(" ", previousSpace+1);
 196       if (space < -1 || space > (int)stringline.size()) {
 197         ErrorMsg(mLandmarks.size(),"z position");
 198         continue;
 199       }
 200       point.coordinates[2] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 201       previousSpace = space;
 202       if (mFormatVersion>0) {
 203         space = stringline.find(" ", previousSpace+1);
 204         if (space < -1 || space > (int)stringline.size()) {
 205           ErrorMsg(mLandmarks.size(),"t position");
 206           continue;
 207         }
 208         point.coordinates[3] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 209         previousSpace = space;
 210         space = stringline.find(" ", previousSpace+1);
 211         if (space < -1 || space > (int)stringline.size()) {
 212           ErrorMsg(mLandmarks.size(),"pixel value");
 213           continue;
 214         }
 215         point.pixel_value = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 216         //        DD(point.pixel_value);
 217       } else {
 218         point.pixel_value=0.; //Not in file
 219         point.coordinates[3]=0.;
 220       }
 221       previousSpace = space;
 222       //this is the maximum size of comments
 223       space = (stringline.find("\n", previousSpace+1) < 254 ? stringline.find("\n", previousSpace+1) : 254);
 224       if (previousSpace != -1) {
 225         point.comments = stringline.substr(previousSpace,space - (previousSpace)).c_str();
 226       }
 227       //      DD(point.comments);
 228       mLandmarks.push_back(point);
 229       mIds->InsertNextTuple1(0.55);
 230       mPoints[int(point.coordinates[3])]->InsertNextPoint(
 231                                                           point.coordinates[0],point.coordinates[1],point.coordinates[2]);
 232     }
 233   }
 234   SetTime(0);
 235 }
 236 //--------------------------------------------------------------------
 237
 238
 239 //--------------------------------------------------------------------
 240 bool vvLandmarks::ErrorMsg(int num,const char * text)
 241 {
 242   std::cerr << "error when loading point " << num << " at " << text << std::endl;
 243   return false;
 244 }
 245 //--------------------------------------------------------------------
 246
 247
 248 //--------------------------------------------------------------------
 249 void vvLandmarks::SaveFile(std::string filename)
 250 {
 251   std::string fileContent = "LANDMARKS1\n"; //File format version identification
 252   for (unsigned int i = 0; i < mLandmarks.size(); i++) {
 253     std::stringstream out;
 254     out.imbue(std::locale("C")); //This is to specify that the dot is to be used as the decimal separator
 255     out << i << " "
 256         << mLandmarks[i].coordinates[0] << " "
 257         << mLandmarks[i].coordinates[1] << " "
 258         << mLandmarks[i].coordinates[2] << " "
 259         << mLandmarks[i].coordinates[3] << " "
 260         << mLandmarks[i].pixel_value << " ";
 261     fileContent += out.str();
 262     if (mLandmarks[i].comments.size() == 0)
 263       fileContent += " ";
 264     else
 265       fileContent += mLandmarks[i].comments;
 266     fileContent += "\n";
 267   }
 268   std::ofstream fp(filename.c_str(), std::ios::trunc);
 269   if ( !fp ) {
 270     std::cerr << "Unable to open file" << std::endl;
 271     return;
 272   }
 273   fp << fileContent.c_str()<< std::endl;
 274   fp.close();
 275 }
 276 //--------------------------------------------------------------------
 277
 278
 279 //--------------------------------------------------------------------
 280 void vvLandmarks::SetTime(int time)
 281 {
 282   if (time >= 0 && time <= ((int)mPoints.size() -1)) {
 283     mPolyData->SetPoints(mPoints[time]);
 284     mPolyData->GetPointData()->SetScalars(mIds);
 285     mPolyData->Modified();
 286     mPolyData->Update();
 287   }
 288 }
 289 //--------------------------------------------------------------------
 290
 291
 292 //--------------------------------------------------------------------
 293 std::string vvLandmarks::replace_dots(std::string input)
 294 {
 295   ///Replaces the dots used in the file with the decimal separator in use on the platform
 296   lconv * conv=localeconv();
 297   unsigned int position = input.find( "." );
 298   while ( position < input.size() ) {
 299     input.replace(position, 1, conv->decimal_point);
 300     position = input.find( ".", position + 1 );
 301   }
 302   return input;
 303 }
 304 //--------------------------------------------------------------------