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   // Station 8
  56   SetDistanceMaxToAnteriorPartOfTheSpine(10);
  57   MaskImagePointType p;
  58   p[0] = 15; p[1] = 2; p[2] = 1;
  59   SetEsophagusDiltationForAnt(p);
  60   p[0] = 5; p[1] = 10; p[2] = 1;
  61   SetEsophagusDiltationForRight(p);
  62   SetFuzzyThresholdForS8(0.5);
  63
  64   // Station 7
  65   SetFuzzyThreshold(0.5);
  66   SetStation7Filename("station7.mhd");
  67 }
  68 //--------------------------------------------------------------------
  69
  70
  71 //--------------------------------------------------------------------
  72 template <class TImageType>
  73 void
  74 clitk::ExtractLymphStationsFilter<TImageType>::
  75 GenerateOutputInformation() {
  76   // Get inputs
  77   LoadAFDB();
  78   m_Input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
  79   m_Mediastinum = GetAFDB()->template GetImage <MaskImageType>("Mediastinum");
  80
  81   // Extract Station8
  82   StartNewStep("Station 8");
  83   StartSubStep();
  84   ExtractStation_8();
  85   StopSubStep();
  86
  87   // Compute some interesting points in trachea
  88   // ( ALTERNATIVE -> SKELETON ANALYSIS ?
  89   //    Pb : not sufficient for mostXX points ... )
  90
  91   /* ==> todo (but why ???)
  92      ComputeTracheaCentroidsAboveCarina();
  93      ComputeBronchusExtremaPointsBelowCarina();
  94   */
  95
  96   if (0) { // temporary suppress
  97     // Extract Station7
  98     StartNewStep("Station 7");
  99     StartSubStep();
 100     ExtractStation_7();
 101     StopSubStep();
 102
 103     // Extract Station4RL
 104     StartNewStep("Station 4RL");
 105     StartSubStep();
 106     //ExtractStation_4RL();
 107     StopSubStep();
 108   }
 109
 110
 111   //
 112   //  typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BFilter;
 113   //BFilter::Pointer merge = BFilter::New();
 114   // writeImage<MaskImageType>(m_Output, "ouput.mhd");
 115   //writeImage<MaskImageType>(m_Working_Support, "ws.mhd");
 116   /*merge->SetInput1(m_Station7);
 117     merge->SetInput2(m_Station4RL); // support
 118     merge->SetOperationType(BFilter::AndNot); CHANGE OPERATOR
 119     merge->SetForegroundValue(4);
 120     merge->Update();
 121     m_Output = merge->GetOutput();
 122   */
 123 }
 124 //--------------------------------------------------------------------
 125
 126
 127 //--------------------------------------------------------------------
 128 template <class TImageType>
 129 void
 130 clitk::ExtractLymphStationsFilter<TImageType>::
 131 GenerateInputRequestedRegion() {
 132   DD("GenerateInputRequestedRegion (nothing?)");
 133 }
 134 //--------------------------------------------------------------------
 135
 136
 137 //--------------------------------------------------------------------
 138 template <class TImageType>
 139 void
 140 clitk::ExtractLymphStationsFilter<TImageType>::
 141 GenerateData() {
 142   DD("GenerateData, graft output");
 143
 144   // Final Step -> graft output (if SetNthOutput => redo)
 145   this->GraftOutput(m_ListOfStations["8"]);
 146 }
 147 //--------------------------------------------------------------------
 148
 149
 150 //--------------------------------------------------------------------
 151 template <class TImageType>
 152 void
 153 clitk::ExtractLymphStationsFilter<TImageType>::
 154 ExtractStation_8() {
 155
 156   // Check if m_ListOfStations["8"] exist. If yes -> use it as initial
 157   // support instead of m_Mediastinum
 158   if (m_ListOfStations["8"]) {
 159     DD("Station 8 support already exist -> use it");
 160     m_Working_Support = m_ListOfStations["8"];
 161   }
 162   else m_Working_Support = m_Mediastinum;
 163
 164   ExtractStation_8_SI_Limits();
 165   ExtractStation_8_Post_Limits();
 166   ExtractStation_8_Ant_Limits();
 167   ExtractStation_8_LR_Limits();
 168   // ExtractStation_8_LR_Limits();
 169 }
 170 //--------------------------------------------------------------------
 171
 172
 173 //--------------------------------------------------------------------
 174 template <class TImageType>
 175 void
 176 clitk::ExtractLymphStationsFilter<TImageType>::
 177 ExtractStation_7() {
 178   if (m_ListOfStations["7"]) {
 179     DD("Station 7 support already exist -> use it");
 180     m_Working_Support = m_ListOfStations["7"];
 181   }
 182   else m_Working_Support = m_Mediastinum;
 183   ExtractStation_7_SI_Limits();
 184   ExtractStation_7_RL_Limits();
 185   ExtractStation_7_Posterior_Limits();
 186 }
 187 //--------------------------------------------------------------------
 188
 189
 190 //--------------------------------------------------------------------
 191 template <class TImageType>
 192 void
 193 clitk::ExtractLymphStationsFilter<TImageType>::
 194 ExtractStation_4RL() {
 195   /*
 196     WARNING ONLY 4R FIRST !!! (not same inf limits)
 197   */
 198   ExtractStation_4RL_SI_Limits();
 199   ExtractStation_4RL_LR_Limits();
 200   ExtractStation_4RL_AP_Limits();
 201 }
 202 //--------------------------------------------------------------------
 203
 204
 205 //--------------------------------------------------------------------
 206 template <class TImageType>
 207 void
 208 clitk::ExtractLymphStationsFilter<TImageType>::
 209 FindExtremaPointsInBronchus(MaskImagePointer input,
 210                             int direction,
 211                             double distance_max_from_center_point,
 212                             ListOfPointsType & LR,
 213                             ListOfPointsType & Ant,
 214                             ListOfPointsType & Post)
 215 {
 216
 217   // Other solution ==> with auto bounding box ! (but pb to prevent to
 218   // be too distant from the center point
 219
 220   // Extract slices
 221   std::vector<typename MaskSliceType::Pointer> slices;
 222   clitk::ExtractSlices<MaskImageType>(input, 2, slices);
 223
 224   // Loop on slices
 225   bool found;
 226   for(uint i=0; i<slices.size(); i++) {
 227     /*
 228     // Keep main CCL
 229     slices[i] = Labelize<MaskSliceType>(slices[i], 0, true, 10);
 230     slices[i] = KeepLabels<MaskSliceType>(slices[i],
 231                                           GetBackgroundValue(),
 232                                           GetForegroundValue(), 1, 1, true);
 233     */
 234
 235     // ------- Find rightmost or leftmost point  -------
 236     MaskSliceType::PointType LRMost;
 237     found =
 238       clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i],
 239                                                               GetBackgroundValue(),
 240                                                               0, // axis XY
 241                                                               (direction==0?false:true),  // right or left according to direction
 242                                                               LRMost);
 243     // ------- Find postmost point  -------
 244     MaskSliceType::PointType postMost;
 245     found =
 246       clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i],
 247                                                               GetBackgroundValue(),
 248                                                               1, false, LRMost,
 249                                                               distance_max_from_center_point,
 250                                                               postMost);
 251     // ------- Find antmost point  -------
 252     MaskSliceType::PointType antMost;
 253     found =
 254       clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i],
 255                                                               GetBackgroundValue(),
 256                                                               1, true, LRMost,
 257                                                               distance_max_from_center_point,
 258                                                               antMost);
 259     // Only add point if found
 260     if (found)  {
 261       // ------- Convert 2D to 3D points --------
 262       MaskImageType::PointType p;
 263       clitk::PointsUtils<MaskImageType>::Convert2DTo3D(LRMost, input, i, p);
 264       LR.push_back(p);
 265       clitk::PointsUtils<MaskImageType>::Convert2DTo3D(antMost, input, i, p);
 266       Ant.push_back(p);
 267       clitk::PointsUtils<MaskImageType>::Convert2DTo3D(postMost, input, i, p);
 268       Post.push_back(p);
 269     }
 270   }
 271 }
 272 //--------------------------------------------------------------------
 273
 274 #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX