vv/vvLandmarks.cxx

   1 /*=========================================================================
   2
   3  Program:   vv
   4  Language:  C++
   5  Author :   Pierre Seroul (pierre.seroul@gmail.com)
   6
   7 Copyright (C) 2008
   8 Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
   9 CREATIS-LRMN http://www.creatis.insa-lyon.fr
  10
  11 This program is free software: you can redistribute it and/or modify
  12 it under the terms of the GNU General Public License as published by
  13 the Free Software Foundation, version 3 of the License.
  14
  15 This program is distributed in the hope that it will be useful,
  16 but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  18 GNU General Public License for more details.
  19
  20 You should have received a copy of the GNU General Public License
  21 along with this program.  If not, see <http://www.gnu.org/licenses/>.
  22
  23 =========================================================================*/
  24 #include "vvLandmarks.h"
  25
  26 #include <ios>
  27 #include <fstream>
  28 #include <sstream>
  29 #include <string>
  30 #include <locale.h>
  31
  32 #include "vtkPolyData.h"
  33 #include "vtkPoints.h"
  34 #include "vtkFloatArray.h"
  35 #include "vtkPointData.h"
  36 #include "clitkCommon.h"
  37
  38 vvLandmarks::vvLandmarks(int size)
  39 {
  40     mLandmarks.resize(0);
  41     mFilename = "";
  42
  43     for (int i = 0; i < size; i++)
  44     {
  45         vtkPoints *points = vtkPoints::New();
  46         mPoints.push_back(points);
  47     }
  48     mPolyData = vtkPolyData::New();
  49     mIds = vtkFloatArray::New();
  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 }
  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 void vvLandmarks::RemoveLastLandmark()
  89 {
  90     mPoints[mLandmarks.back().coordinates[3]]->SetNumberOfPoints(
  91         mPoints[mLandmarks.back().coordinates[3]]->GetNumberOfPoints()-1);
  92     mPolyData->Modified();
  93     //mText.pop_back();
  94     mLandmarks.pop_back();
  95     mIds->RemoveLastTuple();
  96 }
  97
  98 void vvLandmarks::ChangeComments(int index, std::string comments)
  99 {
 100     mLandmarks[index].comments = comments;
 101 }
 102
 103 double vvLandmarks::GetPixelValue(int index)
 104 {
 105     return mLandmarks[index].pixel_value;
 106 }
 107
 108 float* vvLandmarks::GetCoordinates(int index)
 109 {
 110     return mLandmarks[index].coordinates;
 111 }
 112
 113 std::string vvLandmarks::GetComments(int index)
 114 {
 115     return mLandmarks[index].comments;
 116 }
 117
 118 void vvLandmarks::LoadFile(std::string filename)
 119 {
 120     std::ifstream fp(filename.c_str(), std::ios::in|std::ios::binary);
 121     if (!fp.is_open())
 122     {
 123         std::cerr <<"Unable to open file " << filename << std::endl;
 124         return;
 125     }
 126     mFilename = filename;
 127     mLandmarks.clear();
 128     char line[255];
 129     for (unsigned int i = 0; i < mPoints.size();i++)
 130         mPoints[i]->SetNumberOfPoints(0);
 131     bool first_line=true;
 132     while (fp.getline(line,255))
 133     {
 134         std::string stringline = line;
 135         if (first_line)
 136         {
 137             first_line=false;
 138             ///New landmark format: first line is "LANDMARKSXX", where XX is the version number
 139             if (stringline.size() >= 10 && stringline.compare(0,9,"LANDMARKS")==0)
 140             {
 141                 std::istringstream ss(stringline.c_str()+9);
 142                 ss >> mFormatVersion;
 143                 continue; //skip first line
 144             }
 145             else
 146                 mFormatVersion=0;
 147         }
 148         DD(mFormatVersion);
 149         if (stringline.size() > 1)
 150         {
 151             vvLandmark point;
 152             int previousSpace = 0;
 153             int space=0;
 154             if (mFormatVersion>0)
 155             {
 156                 space = stringline.find(" ", previousSpace+1);
 157                 if (space < -1 || space > (int)stringline.size())
 158                 {
 159                     ErrorMsg(mLandmarks.size(),"index");
 160                     continue;
 161                 }
 162                 //int index = atoi(stringline.substr(previousSpace,space - previousSpace).c_str());
 163                 previousSpace = space;
 164             }
 165             space = stringline.find(" ", previousSpace+1);
 166             if (space < -1 || space > (int)stringline.size())
 167             {
 168                 ErrorMsg(mLandmarks.size(),"x position");
 169                 continue;
 170             }
 171             point.coordinates[0] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 172             previousSpace = space;
 173             space = stringline.find(" ", previousSpace+1);
 174             if (space < -1 || space > (int)stringline.size())
 175             {
 176                 ErrorMsg(mLandmarks.size(),"y position");
 177                 continue;
 178             }
 179             point.coordinates[1] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 180             previousSpace = space;
 181             space = stringline.find(" ", previousSpace+1);
 182             if (space < -1 || space > (int)stringline.size())
 183             {
 184                 ErrorMsg(mLandmarks.size(),"z position");
 185                 continue;
 186             }
 187             point.coordinates[2] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 188             previousSpace = space;
 189             if (mFormatVersion>0)
 190             {
 191                 space = stringline.find(" ", previousSpace+1);
 192                 if (space < -1 || space > (int)stringline.size())
 193                 {
 194                     ErrorMsg(mLandmarks.size(),"t position");
 195                     continue;
 196                 }
 197                 point.coordinates[3] = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 198                 previousSpace = space;
 199                 space = stringline.find(" ", previousSpace+1);
 200                 if (space < -1 || space > (int)stringline.size())
 201                 {
 202                     ErrorMsg(mLandmarks.size(),"pixel value");
 203                     continue;
 204                 }
 205                 point.pixel_value = atof(replace_dots(stringline.substr(previousSpace,space - previousSpace)).c_str());
 206             }
 207             else
 208             {
 209                 point.pixel_value=0.; //Not in file
 210                 point.coordinates[3]=0.;
 211             }
 212             previousSpace = space;
 213             //this is the maximum size of comments
 214             space = (stringline.find("\n", previousSpace+1) < 254 ? stringline.find("\n", previousSpace+1) : 254);
 215             point.comments = stringline.substr(previousSpace,space - (previousSpace)).c_str();
 216             mLandmarks.push_back(point);
 217             mIds->InsertNextTuple1(0.55);
 218             mPoints[int(point.coordinates[3])]->InsertNextPoint(
 219                 point.coordinates[0],point.coordinates[1],point.coordinates[2]);
 220         }
 221     }
 222     SetTime(0);
 223 }
 224
 225 bool vvLandmarks::ErrorMsg(int num,const char * text)
 226 {
 227     std::cerr << "error when loading point " << num << " at " << text << std::endl;
 228     return false;
 229 }
 230
 231 void vvLandmarks::SaveFile(std::string filename)
 232 {
 233     std::string fileContent = "LANDMARKS1\n"; //File format version identification
 234     for (unsigned int i = 0; i < mLandmarks.size(); i++) {
 235         std::stringstream out;
 236         out.imbue(std::locale("C")); //This is to specify that the dot is to be used as the decimal separator
 237         out << i << " "
 238             << mLandmarks[i].coordinates[0] << " "
 239             << mLandmarks[i].coordinates[1] << " "
 240             << mLandmarks[i].coordinates[2] << " "
 241             << mLandmarks[i].coordinates[3] << " "
 242             << mLandmarks[i].pixel_value << " ";
 243         fileContent += out.str();
 244         if (mLandmarks[i].comments.size() == 0)
 245             fileContent += " ";
 246         else
 247             fileContent += mLandmarks[i].comments;
 248         fileContent += "\n";
 249     }
 250     std::ofstream fp(filename.c_str(), std::ios::trunc);
 251     if ( !fp )
 252     {
 253         std::cerr << "Unable to open file" << std::endl;
 254         return;
 255     }
 256     fp << fileContent.c_str()<< std::endl;
 257     fp.close();
 258 }
 259
 260 void vvLandmarks::SetTime(int time)
 261 {
 262     if (time >= 0 && time <= ((int)mPoints.size() -1))
 263     {
 264         mPolyData->SetPoints(mPoints[time]);
 265         mPolyData->GetPointData()->SetScalars(mIds);
 266         mPolyData->Modified();
 267         mPolyData->Update();
 268     }
 269 }
 270
 271 std::string vvLandmarks::replace_dots(std::string input)
 272 {
 273     ///Replaces the dots used in the file with the decimal separator in use on the platform
 274     lconv * conv=localeconv();
 275     unsigned int position = input.find( "." );
 276     while ( position < input.size() )
 277     {
 278         input.replace(position, 1, conv->decimal_point);
 279         position = input.find( ".", position + 1 );
 280     }
 281     return input;
 282 }