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 vvLandmarks::vvLandmarks(int size)
  33 {
  34     mLandmarks.resize(0);
  35     mFilename = "";
  36
  37     for (int i = 0; i < size; i++)
  38     {
  39         vtkPoints *points = vtkPoints::New();
  40         mPoints.push_back(points);
  41     }
  42     mPolyData = vtkPolyData::New();
  43     mIds = vtkFloatArray::New();
  44 }
  45
  46 vvLandmarks::~vvLandmarks()
  47 {
  48     for (unsigned int i = 0; i < mPoints.size(); i++) {
  49         mPoints[i]->Delete();
  50     }
  51     /*for(unsigned int i = 0; i < mText.size(); i++) {
  52       mText[i]->Delete();
  53       }*/
  54     if (mIds)
  55         mIds->Delete();
  56     if (mPolyData)
  57         mPolyData->Delete();
  58 }
  59
  60 void vvLandmarks::AddLandmark(float x,float y,float z,float t,double value)
  61 {
  62     vvLandmark point;
  63     point.coordinates[0] = x;
  64     point.coordinates[1] = y;
  65     point.coordinates[2] = z;
  66     point.coordinates[3] = t;
  67     point.pixel_value=value;
  68     mLandmarks.push_back(point);
  69     mPoints[int(t)]->InsertNextPoint(x,y,z);
  70
  71     /*std::stringstream numberVal;
  72     numberVal << (mLandmarks.size()-1);
  73     vvLandmarksGlyph *number = vvLandmarksGlyph::New();
  74     number->SetText(numberVal.str().c_str());
  75     number->BackingOff();
  76     mText.push_back(number);*/
  77     mIds->InsertNextTuple1(0.55);
  78     //mIds->InsertTuple1(mLandmarks.size(),mLandmarks.size());
  79     SetTime(int(t));
  80 }
  81
  82 void vvLandmarks::RemoveLastLandmark()
  83 {
  84     mPoints[mLandmarks.back().coordinates[3]]->SetNumberOfPoints(
  85         mPoints[mLandmarks.back().coordinates[3]]->GetNumberOfPoints()-1);
  86     mPolyData->Modified();
  87     //mText.pop_back();
  88     mLandmarks.pop_back();
  89     mIds->RemoveLastTuple();
  90 }
  91
  92 void vvLandmarks::ChangeComments(int index, std::string comments)
  93 {
  94     mLandmarks[index].comments = comments;
  95 }
  96
  97 double vvLandmarks::GetPixelValue(int index)
  98 {
  99     return mLandmarks[index].pixel_value;
 100 }
 101
 102 float* vvLandmarks::GetCoordinates(int index)
 103 {
 104     return mLandmarks[index].coordinates;
 105 }
 106
 107 std::string vvLandmarks::GetComments(int index)
 108 {
 109     return mLandmarks[index].comments;
 110 }
 111
 112 void vvLandmarks::LoadFile(std::string filename)
 113 {
 114     std::ifstream fp(filename.c_str(), std::ios::in|std::ios::binary);
 115     if (!fp.is_open())
 116     {
 117         std::cerr <<"Unable to open file " << filename << std::endl;
 118         return;
 119     }
 120     mFilename = filename;
 121     mLandmarks.clear();
 122     char line[255];
 123     for (unsigned int i = 0; i < mPoints.size();i++)
 124         mPoints[i]->SetNumberOfPoints(0);
 125     bool first_line=true;
 126     while (fp.getline(line,255))
 127     {
 128         std::string stringline = line;
 129         if (first_line)
 130         {
 131             first_line=false;
 132             ///New landmark format: first line is "LANDMARKSXX", where XX is the version number
 133             if (stringline.size() >= 10 && stringline.compare(0,9,"LANDMARKS")==0)
 134             {
 135                 std::istringstream ss(stringline.c_str()+9);
 136                 ss >> mFormatVersion;
 137                 continue; //skip first line
 138             }
 139             else
 140                 mFormatVersion=0;
 141         }
 142         DD(mFormatVersion);
 143         if (stringline.size() > 1)
 144         {
 145             vvLandmark point;
 146             int previousSpace = 0;
 147             int space=0;
 148             if (mFormatVersion>0)
 149             {
 150                 space = stringline.find(" ", previousSpace+1);
 151                 if (space < -1 || space > (int)stringline.size())
 152                 {
 153                     ErrorMsg(mLandmarks.size(),"index");
 154                     continue;
 155                 }
 156                 //int index = atoi(stringline.substr(previousSpace,space - previousSpace).c_str());
 157                 previousSpace = space;
 158             }
 159             space = stringline.find(" ", previousSpace+1);
 160             if (space < -1 || space > (int)stringline.size())
 161             {
 162                 ErrorMsg(mLandmarks.size(),"x position");
 163                 continue;
 164             }
 165             point.coordinates[0] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 166             previousSpace = space;
 167             space = stringline.find(" ", previousSpace+1);
 168             if (space < -1 || space > (int)stringline.size())
 169             {
 170                 ErrorMsg(mLandmarks.size(),"y position");
 171                 continue;
 172             }
 173             point.coordinates[1] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 174             previousSpace = space;
 175             space = stringline.find(" ", previousSpace+1);
 176             if (space < -1 || space > (int)stringline.size())
 177             {
 178                 ErrorMsg(mLandmarks.size(),"z position");
 179                 continue;
 180             }
 181             point.coordinates[2] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 182             previousSpace = space;
 183             if (mFormatVersion>0)
 184             {
 185                 space = stringline.find(" ", previousSpace+1);
 186                 if (space < -1 || space > (int)stringline.size())
 187                 {
 188                     ErrorMsg(mLandmarks.size(),"t position");
 189                     continue;
 190                 }
 191                 point.coordinates[3] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 192                 previousSpace = space;
 193                 space = stringline.find(" ", previousSpace+1);
 194                 if (space < -1 || space > (int)stringline.size())
 195                 {
 196                     ErrorMsg(mLandmarks.size(),"pixel value");
 197                     continue;
 198                 }
 199                 point.pixel_value = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 200             }
 201             else
 202             {
 203                 point.pixel_value=0.; //Not in file
 204                 point.coordinates[3]=0.;
 205             }
 206             previousSpace = space;
 207             //this is the maximum size of comments
 208             space = (stringline.find("\n", previousSpace+1) < 254 ? stringline.find("\n", previousSpace+1) : 254);
 209             point.comments = stringline.substr(previousSpace,space - (previousSpace)).c_str();
 210             mLandmarks.push_back(point);
 211             mIds->InsertNextTuple1(0.55);
 212             mPoints[int(point.coordinates[3])]->InsertNextPoint(
 213                 point.coordinates[0],point.coordinates[1],point.coordinates[2]);
 214         }
 215     }
 216     SetTime(0);
 217 }
 218
 219 bool vvLandmarks::ErrorMsg(int num,const char * text)
 220 {
 221     std::cerr << "error when loading point " << num << " at " << text << std::endl;
 222     return false;
 223 }
 224
 225 void vvLandmarks::SaveFile(std::string filename)
 226 {
 227     std::string fileContent = "LANDMARKS1\n"; //File format version identification
 228     for (unsigned int i = 0; i < mLandmarks.size(); i++) {
 229         std::stringstream out;
 230         out.imbue(std::locale("C")); //This is to specify that the dot is to be used as the decimal separator
 231         out << i << " "
 232             << mLandmarks[i].coordinates[0] << " "
 233             << mLandmarks[i].coordinates[1] << " "
 234             << mLandmarks[i].coordinates[2] << " "
 235             << mLandmarks[i].coordinates[3] << " "
 236             << mLandmarks[i].pixel_value << " ";
 237         fileContent += out.str();
 238         if (mLandmarks[i].comments.size() == 0)
 239             fileContent += " ";
 240         else
 241             fileContent += mLandmarks[i].comments;
 242         fileContent += "\n";
 243     }
 244     std::ofstream fp(filename.c_str(), std::ios::trunc);
 245     if ( !fp )
 246     {
 247         std::cerr << "Unable to open file" << std::endl;
 248         return;
 249     }
 250     fp << fileContent.c_str()<< std::endl;
 251     fp.close();
 252 }
 253
 254 void vvLandmarks::SetTime(int time)
 255 {
 256     if (time >= 0 && time <= ((int)mPoints.size() -1))
 257     {
 258         mPolyData->SetPoints(mPoints[time]);
 259         mPolyData->GetPointData()->SetScalars(mIds);
 260         mPolyData->Modified();
 261         mPolyData->Update();
 262     }
 263 }
 264
 265 std::string vvLandmarks::replace_dots(std::string input)
 266 {
 267     ///Replaces the dots used in the file with the decimal separator in use on the platform
 268     lconv * conv=localeconv();
 269     unsigned int position = input.find( "." );
 270     while ( position < input.size() )
 271     {
 272         input.replace(position, 1, conv->decimal_point);
 273         position = input.find( ".", position + 1 );
 274     }
 275     return input;
 276 }