segmentation/clitkExtractLymphStationsFilter.txx

   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
  19 #ifndef CLITKEXTRACTLYMPHSTATIONSFILTER_TXX
  20 #define CLITKEXTRACTLYMPHSTATIONSFILTER_TXX
  21
  22 // clitk
  23 #include "clitkCommon.h"
  24 #include "clitkExtractLymphStationsFilter.h"
  25 #include "clitkAddRelativePositionConstraintToLabelImageFilter.h"
  26 #include "clitkSegmentationUtils.h"
  27 #include "clitkAutoCropFilter.h"
  28 #include "clitkSegmentationUtils.h"
  29 #include "clitkSliceBySliceRelativePositionFilter.h"
  30
  31 // itk
  32 #include <itkStatisticsLabelMapFilter.h>
  33 #include <itkLabelImageToStatisticsLabelMapFilter.h>
  34 #include <itkRegionOfInterestImageFilter.h>
  35 #include <itkBinaryThresholdImageFilter.h>
  36 #include <itkImageSliceConstIteratorWithIndex.h>
  37 #include <itkImageSliceIteratorWithIndex.h>
  38 #include <itkBinaryThinningImageFilter.h>
  39
  40 // itk ENST
  41 #include "RelativePositionPropImageFilter.h"
  42
  43 //--------------------------------------------------------------------
  44 template <class TImageType>
  45 clitk::ExtractLymphStationsFilter<TImageType>::
  46 ExtractLymphStationsFilter():
  47   clitk::FilterBase(),
  48   clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
  49   itk::ImageToImageFilter<TImageType, MaskImageType>()
  50 {
  51   this->SetNumberOfRequiredInputs(1);
  52   SetBackgroundValue(0);
  53   SetForegroundValue(1);
  54
  55   // Default values
  56   ExtractStation_8_SetDefaultValues();
  57   ExtractStation_3P_SetDefaultValues();
  58
  59   // Station 7
  60   SetFuzzyThreshold(0.5);
  61   SetStation7Filename("station7.mhd");
  62 }
  63 //--------------------------------------------------------------------
  64
  65
  66 //--------------------------------------------------------------------
  67 template <class TImageType>
  68 void
  69 clitk::ExtractLymphStationsFilter<TImageType>::
  70 GenerateOutputInformation() {
  71   // Get inputs
  72   LoadAFDB();
  73   m_Input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
  74   m_Mediastinum = GetAFDB()->template GetImage <MaskImageType>("Mediastinum");
  75
  76   // Extract Station8
  77   StartNewStep("Station 8");
  78   StartSubStep();
  79   ExtractStation_8();
  80   StopSubStep();
  81
  82   DD(GetCurrentStepNumber());
  83
  84   // Extract Station3P
  85   StartNewStep("Station 3P");
  86   StartSubStep();
  87   ExtractStation_3P();
  88   StopSubStep();
  89
  90   if (0) { // temporary suppress
  91     // Extract Station7
  92     StartNewStep("Station 7");
  93     StartSubStep();
  94     ExtractStation_7();
  95     StopSubStep();
  96
  97     // Extract Station4RL
  98     StartNewStep("Station 4RL");
  99     StartSubStep();
 100     //ExtractStation_4RL();
 101     StopSubStep();
 102   }
 103
 104
 105   //
 106   //  typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BFilter;
 107   //BFilter::Pointer merge = BFilter::New();
 108   // writeImage<MaskImageType>(m_Output, "ouput.mhd");
 109   //writeImage<MaskImageType>(m_Working_Support, "ws.mhd");
 110   /*merge->SetInput1(m_Station7);
 111     merge->SetInput2(m_Station4RL); // support
 112     merge->SetOperationType(BFilter::AndNot); CHANGE OPERATOR
 113     merge->SetForegroundValue(4);
 114     merge->Update();
 115     m_Output = merge->GetOutput();
 116   */
 117 }
 118 //--------------------------------------------------------------------
 119
 120
 121 //--------------------------------------------------------------------
 122 template <class TImageType>
 123 void
 124 clitk::ExtractLymphStationsFilter<TImageType>::
 125 GenerateInputRequestedRegion() {
 126   DD("GenerateInputRequestedRegion (nothing?)");
 127 }
 128 //--------------------------------------------------------------------
 129
 130
 131 //--------------------------------------------------------------------
 132 template <class TImageType>
 133 void
 134 clitk::ExtractLymphStationsFilter<TImageType>::
 135 GenerateData() {
 136   DD("GenerateData, graft output");
 137
 138   // Final Step -> graft output (if SetNthOutput => redo)
 139   this->GraftOutput(m_ListOfStations["8"]);
 140 }
 141 //--------------------------------------------------------------------
 142
 143
 144 //--------------------------------------------------------------------
 145 template <class TImageType>
 146 bool
 147 clitk::ExtractLymphStationsFilter<TImageType>::
 148 CheckForStation(std::string station)
 149 {
 150   // Compute Station name
 151   std::string s = "Station"+station;
 152
 153
 154   // Check if station already exist in DB
 155   bool found = false;
 156   if (GetAFDB()->TagExist(s)) {
 157     m_ListOfStations[station] = GetAFDB()->template GetImage<MaskImageType>(s);
 158     found = true;
 159   }
 160
 161   // Define the starting support
 162   if (found && GetComputeStation("8")) {
 163     std::cout << "Station " << station << " already exists, but re-computation forced." << std::endl;
 164   }
 165   if (!found || GetComputeStation("8")) {
 166     m_Working_Support = m_Mediastinum = GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
 167     return true;
 168   }
 169   else {
 170     std::cout << "Station " << station << " found. I used it" << std::endl;
 171     return false;
 172   }
 173 }
 174 //--------------------------------------------------------------------
 175
 176
 177 //--------------------------------------------------------------------
 178 template <class TImageType>
 179 bool
 180 clitk::ExtractLymphStationsFilter<TImageType>::
 181 GetComputeStation(std::string station)
 182 {
 183   return (m_ComputeStationMap.find(station) != m_ComputeStationMap.end());
 184 }
 185 //--------------------------------------------------------------------
 186
 187
 188 //--------------------------------------------------------------------
 189 template <class TImageType>
 190 void
 191 clitk::ExtractLymphStationsFilter<TImageType>::
 192 AddComputeStation(std::string station)
 193 {
 194   m_ComputeStationMap[station] = true;
 195 }
 196 //--------------------------------------------------------------------
 197
 198
 199 //--------------------------------------------------------------------
 200 template <class TImageType>
 201 void
 202 clitk::ExtractLymphStationsFilter<TImageType>::
 203 ExtractStation_8()
 204 {
 205   if (CheckForStation("8")) {
 206     ExtractStation_8_SI_Limits();
 207     ExtractStation_8_Post_Limits();
 208     ExtractStation_8_Ant_Limits();
 209     ExtractStation_8_LR_Limits();
 210     // Store image filenames into AFDB
 211     writeImage<MaskImageType>(m_ListOfStations["8"], "seg/Station8.mhd");
 212     GetAFDB()->SetImageFilename("Station8", "seg/Station8.mhd");
 213     WriteAFDB();
 214   }
 215 }
 216 //--------------------------------------------------------------------
 217
 218
 219 //--------------------------------------------------------------------
 220 template <class TImageType>
 221 void
 222 clitk::ExtractLymphStationsFilter<TImageType>::
 223 ExtractStation_3P()
 224 {
 225   if (CheckForStation("3P")) {
 226     ExtractStation_3P_SI_Limits();
 227     // Store image filenames into AFDB
 228     writeImage<MaskImageType>(m_ListOfStations["3P"], "seg/Station3P.mhd");
 229     GetAFDB()->SetImageFilename("Station3P", "seg/Station3P.mhd");
 230   }
 231 }
 232 //--------------------------------------------------------------------
 233
 234
 235 //--------------------------------------------------------------------
 236 template <class TImageType>
 237 void
 238 clitk::ExtractLymphStationsFilter<TImageType>::
 239 ExtractStation_7() {
 240   if (m_ListOfStations["7"]) {
 241     DD("Station 7 support already exist -> use it");
 242     m_Working_Support = m_ListOfStations["7"];
 243   }
 244   else m_Working_Support = m_Mediastinum;
 245   ExtractStation_7_SI_Limits();
 246   ExtractStation_7_RL_Limits();
 247   ExtractStation_7_Posterior_Limits();
 248 }
 249 //--------------------------------------------------------------------
 250
 251
 252 //--------------------------------------------------------------------
 253 template <class TImageType>
 254 void
 255 clitk::ExtractLymphStationsFilter<TImageType>::
 256 ExtractStation_4RL() {
 257   /*
 258     WARNING ONLY 4R FIRST !!! (not same inf limits)
 259   */
 260   ExtractStation_4RL_SI_Limits();
 261   ExtractStation_4RL_LR_Limits();
 262   ExtractStation_4RL_AP_Limits();
 263 }
 264 //--------------------------------------------------------------------
 265
 266
 267 //--------------------------------------------------------------------
 268
 269
 270 //--------------------------------------------------------------------
 271 template <class TImageType>
 272 void
 273 clitk::ExtractLymphStationsFilter<TImageType>::
 274 FindExtremaPointsInBronchus(MaskImagePointer input,
 275                             int direction,
 276                             double distance_max_from_center_point,
 277                             ListOfPointsType & LR,
 278                             ListOfPointsType & Ant,
 279                             ListOfPointsType & Post)
 280 {
 281
 282   // Other solution ==> with auto bounding box ! (but pb to prevent to
 283   // be too distant from the center point
 284
 285   // Extract slices
 286   std::vector<typename MaskSliceType::Pointer> slices;
 287   clitk::ExtractSlices<MaskImageType>(input, 2, slices);
 288
 289   // Loop on slices
 290   bool found;
 291   for(uint i=0; i<slices.size(); i++) {
 292     /*
 293     // Keep main CCL
 294     slices[i] = Labelize<MaskSliceType>(slices[i], 0, true, 10);
 295     slices[i] = KeepLabels<MaskSliceType>(slices[i],
 296                                           GetBackgroundValue(),
 297                                           GetForegroundValue(), 1, 1, true);
 298     */
 299
 300     // ------- Find rightmost or leftmost point  -------
 301     MaskSliceType::PointType LRMost;
 302     found =
 303       clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i],
 304                                                               GetBackgroundValue(),
 305                                                               0, // axis XY
 306                                                               (direction==0?false:true),  // right or left according to direction
 307                                                               LRMost);
 308     // ------- Find postmost point  -------
 309     MaskSliceType::PointType postMost;
 310     found =
 311       clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i],
 312                                                               GetBackgroundValue(),
 313                                                               1, false, LRMost,
 314                                                               distance_max_from_center_point,
 315                                                               postMost);
 316     // ------- Find antmost point  -------
 317     MaskSliceType::PointType antMost;
 318     found =
 319       clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i],
 320                                                               GetBackgroundValue(),
 321                                                               1, true, LRMost,
 322                                                               distance_max_from_center_point,
 323                                                               antMost);
 324     // Only add point if found
 325     if (found)  {
 326       // ------- Convert 2D to 3D points --------
 327       MaskImageType::PointType p;
 328       clitk::PointsUtils<MaskImageType>::Convert2DTo3D(LRMost, input, i, p);
 329       LR.push_back(p);
 330       clitk::PointsUtils<MaskImageType>::Convert2DTo3D(antMost, input, i, p);
 331       Ant.push_back(p);
 332       clitk::PointsUtils<MaskImageType>::Convert2DTo3D(postMost, input, i, p);
 333       Post.push_back(p);
 334     }
 335   }
 336 }
 337 //--------------------------------------------------------------------
 338
 339 #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX