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     vvLandmarksGlyph *number = vvLandmarksGlyph::New();
  80     number->SetText(numberVal.str().c_str());
  81     number->BackingOff();
  82     mText.push_back(number);*/
  83   mIds->InsertNextTuple1(0.55);
  84   //mIds->InsertTuple1(mLandmarks.size(),mLandmarks.size());
  85   SetTime(int(t));
  86 }
  87 //--------------------------------------------------------------------
  88
  89
  90 //--------------------------------------------------------------------
  91 void vvLandmarks::RemoveLastLandmark()
  92 {
  93   mPoints[mLandmarks.back().coordinates[3]]->SetNumberOfPoints(
  94                                                                mPoints[mLandmarks.back().coordinates[3]]->GetNumberOfPoints()-1);
  95   mPolyData->Modified();
  96   //mText.pop_back();
  97   mLandmarks.pop_back();
  98   mIds->RemoveLastTuple();
  99 }
 100 //--------------------------------------------------------------------
 101
 102
 103 //--------------------------------------------------------------------
 104 void vvLandmarks::ChangeComments(int index, std::string comments)
 105 {
 106   mLandmarks[index].comments = comments;
 107 }
 108 //--------------------------------------------------------------------
 109
 110
 111 //--------------------------------------------------------------------
 112 double vvLandmarks::GetPixelValue(int index)
 113 {
 114   return mLandmarks[index].pixel_value;
 115 }
 116 //--------------------------------------------------------------------
 117
 118
 119 //--------------------------------------------------------------------
 120 float* vvLandmarks::GetCoordinates(int index)
 121 {
 122   return mLandmarks[index].coordinates;
 123 }
 124 //--------------------------------------------------------------------
 125
 126
 127 //--------------------------------------------------------------------
 128 std::string vvLandmarks::GetComments(int index)
 129 {
 130   return mLandmarks[index].comments;
 131 }
 132 //--------------------------------------------------------------------
 133
 134
 135 //--------------------------------------------------------------------
 136 void vvLandmarks::LoadFile(std::string filename)
 137 {
 138   std::ifstream fp(filename.c_str(), std::ios::in|std::ios::binary);
 139   if (!fp.is_open()) {
 140     std::cerr <<"Unable to open file " << filename << std::endl;
 141     return;
 142   }
 143   mFilename = filename;
 144   mLandmarks.clear();
 145   char line[255];
 146   for (unsigned int i = 0; i < mPoints.size(); i++)
 147     mPoints[i]->SetNumberOfPoints(0);
 148   bool first_line=true;
 149   while (fp.getline(line,255)) {
 150     //    DD(line);
 151     std::string stringline = line;
 152     if (first_line) {
 153       first_line=false;
 154       ///New landmark format: first line is "LANDMARKSXX", where XX is the version number
 155       if (stringline.size() >= 10 && stringline.compare(0,9,"LANDMARKS")==0) {
 156         std::istringstream ss(stringline.c_str()+9);
 157         ss >> mFormatVersion;
 158         continue; //skip first line
 159       } else
 160         mFormatVersion=0;
 161     }
 162     if (stringline.size() > 1) {
 163       vvLandmark point;
 164       int previousSpace = 0;
 165       int space=0;
 166       if (mFormatVersion>0) {
 167         space = stringline.find(" ", previousSpace+1);
 168         if (space < -1 || space > (int)stringline.size()) {
 169           ErrorMsg(mLandmarks.size(),"index");
 170           continue;
 171         }
 172         //int index = atoi(stringline.substr(previousSpace,space - previousSpace).c_str());
 173         previousSpace = space;
 174       }
 175       space = stringline.find(" ", previousSpace+1);
 176       if (space < -1 || space > (int)stringline.size()) {
 177         ErrorMsg(mLandmarks.size(),"x position");
 178         continue;
 179       }
 180       point.coordinates[0] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 181       //      DD(point.coordinates[0]);
 182       previousSpace = space;
 183       space = stringline.find(" ", previousSpace+1);
 184       if (space < -1 || space > (int)stringline.size()) {
 185         ErrorMsg(mLandmarks.size(),"y position");
 186         continue;
 187       }
 188       point.coordinates[1] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 189       //      DD(point.coordinates[1]);
 190       previousSpace = space;
 191       space = stringline.find(" ", previousSpace+1);
 192       if (space < -1 || space > (int)stringline.size()) {
 193         ErrorMsg(mLandmarks.size(),"z position");
 194         continue;
 195       }
 196       point.coordinates[2] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 197       previousSpace = space;
 198       if (mFormatVersion>0) {
 199         space = stringline.find(" ", previousSpace+1);
 200         if (space < -1 || space > (int)stringline.size()) {
 201           ErrorMsg(mLandmarks.size(),"t position");
 202           continue;
 203         }
 204         point.coordinates[3] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 205         previousSpace = space;
 206         space = stringline.find(" ", previousSpace+1);
 207         if (space < -1 || space > (int)stringline.size()) {
 208           ErrorMsg(mLandmarks.size(),"pixel value");
 209           continue;
 210         }
 211         point.pixel_value = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 212         //        DD(point.pixel_value);
 213       } else {
 214         point.pixel_value=0.; //Not in file
 215         point.coordinates[3]=0.;
 216       }
 217       previousSpace = space;
 218       //this is the maximum size of comments
 219       space = (stringline.find("\n", previousSpace+1) < 254 ? stringline.find("\n", previousSpace+1) : 254);
 220       if (previousSpace != -1) {
 221         point.comments = stringline.substr(previousSpace,space - (previousSpace)).c_str();
 222       }
 223       //      DD(point.comments);
 224       mLandmarks.push_back(point);
 225       mIds->InsertNextTuple1(0.55);
 226       mPoints[int(point.coordinates[3])]->InsertNextPoint(
 227                                                           point.coordinates[0],point.coordinates[1],point.coordinates[2]);
 228     }
 229   }
 230   SetTime(0);
 231 }
 232 //--------------------------------------------------------------------
 233
 234
 235 //--------------------------------------------------------------------
 236 bool vvLandmarks::ErrorMsg(int num,const char * text)
 237 {
 238   std::cerr << "error when loading point " << num << " at " << text << std::endl;
 239   return false;
 240 }
 241 //--------------------------------------------------------------------
 242
 243
 244 //--------------------------------------------------------------------
 245 void vvLandmarks::SaveFile(std::string filename)
 246 {
 247   std::string fileContent = "LANDMARKS1\n"; //File format version identification
 248   for (unsigned int i = 0; i < mLandmarks.size(); i++) {
 249     std::stringstream out;
 250     out.imbue(std::locale("C")); //This is to specify that the dot is to be used as the decimal separator
 251     out << i << " "
 252         << mLandmarks[i].coordinates[0] << " "
 253         << mLandmarks[i].coordinates[1] << " "
 254         << mLandmarks[i].coordinates[2] << " "
 255         << mLandmarks[i].coordinates[3] << " "
 256         << mLandmarks[i].pixel_value << " ";
 257     fileContent += out.str();
 258     if (mLandmarks[i].comments.size() == 0)
 259       fileContent += " ";
 260     else
 261       fileContent += mLandmarks[i].comments;
 262     fileContent += "\n";
 263   }
 264   std::ofstream fp(filename.c_str(), std::ios::trunc);
 265   if ( !fp ) {
 266     std::cerr << "Unable to open file" << std::endl;
 267     return;
 268   }
 269   fp << fileContent.c_str()<< std::endl;
 270   fp.close();
 271 }
 272 //--------------------------------------------------------------------
 273
 274
 275 //--------------------------------------------------------------------
 276 void vvLandmarks::SetTime(int time)
 277 {
 278   if (time >= 0 && time <= ((int)mPoints.size() -1)) {
 279     mPolyData->SetPoints(mPoints[time]);
 280     mPolyData->GetPointData()->SetScalars(mIds);
 281     mPolyData->Modified();
 282     mPolyData->Update();
 283   }
 284 }
 285 //--------------------------------------------------------------------
 286
 287
 288 //--------------------------------------------------------------------
 289 std::string vvLandmarks::replace_dots(std::string input)
 290 {
 291   ///Replaces the dots used in the file with the decimal separator in use on the platform
 292   lconv * conv=localeconv();
 293   unsigned int position = input.find( "." );
 294   while ( position < input.size() ) {
 295     input.replace(position, 1, conv->decimal_point);
 296     position = input.find( ".", position + 1 );
 297   }
 298   return input;
 299 }
 300 //--------------------------------------------------------------------