segmentation/clitkTestFilter.cxx

   1
   2 /*=========================================================================
   3   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   4
   5   Authors belong to:
   6   - University of LYON              http://www.universite-lyon.fr/
   7   - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
   8   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   9
  10   This software is distributed WITHOUT ANY WARRANTY; without even
  11   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  12   PURPOSE.  See the copyright notices for more information.
  13
  14   It is distributed under dual licence
  15
  16   - BSD        See included LICENSE.txt file
  17   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  18   ======================================================================-====*/
  19
  20 // clitk
  21 #include "clitkTestFilter_ggo.h"
  22 #include "clitkImageCommon.h"
  23 #include "clitkBooleanOperatorLabelImageFilter.h"
  24 #include "clitkAutoCropFilter.h"
  25 //#include "clitkRelativePositionConstraintLabelImageFilter.h"
  26 #include "clitkResampleImageWithOptionsFilter.h"
  27 #include "clitkAddRelativePositionConstraintToLabelImageFilter.h"
  28
  29 #include "clitkExtractLungFilter.h"
  30 #include "clitkExtractPatientFilter.h"
  31 #include "clitkExtractMediastinumFilter.h"
  32
  33 #include "clitkTestStation7.h"
  34
  35 // ITK ENST
  36 #include "RelativePositionPropImageFilter.h"
  37
  38 //--------------------------------------------------------------------
  39 int main(int argc, char * argv[]) {
  40
  41   // Init command line
  42   GGO(clitkTestFilter, args_info);
  43
  44   // Image types
  45   //typedef unsigned char PixelType;
  46   typedef short PixelType;
  47   static const int Dim=3;
  48   typedef itk::Image<PixelType, Dim> InputImageType;
  49
  50   // Read inputs
  51   InputImageType::Pointer input1;
  52   InputImageType::Pointer input2;
  53   InputImageType::Pointer input3;
  54   if (args_info.input1_given) input1 = clitk::readImage<InputImageType>(args_info.input1_arg, true);
  55   if (args_info.input2_given) input2 = clitk::readImage<InputImageType>(args_info.input2_arg, true);
  56   if (args_info.input3_given) input3 = clitk::readImage<InputImageType>(args_info.input3_arg, true);
  57
  58   // Declare output
  59   InputImageType::Pointer output;
  60
  61   //--------------------------------------------------------------------
  62   // Filter test BooleanOperatorLabelImageFilter
  63   if (0) {
  64     typedef clitk::BooleanOperatorLabelImageFilter<InputImageType> FilterType;
  65     FilterType::Pointer filter = FilterType::New();
  66     filter->SetInput1(input1);
  67     filter->SetInput2(input2);
  68     output = clitk::NewImageLike<InputImageType>(input1);
  69     filter->GraftOutput(output);  /// TO VERIFY !!!
  70     filter->Update();
  71     filter->SetInput2(input3);
  72     filter->Update();
  73     output = filter->GetOutput();
  74     clitk::writeImage<InputImageType>(output, args_info.output_arg);
  75   }
  76
  77   //--------------------------------------------------------------------
  78   // Filter test AutoCropLabelImageFilter
  79   if (0) {
  80     typedef clitk::AutoCropFilter<InputImageType> FilterType;
  81     FilterType::Pointer filter = FilterType::New();
  82     filter->SetInput(input1);
  83     filter->Update();
  84     output = filter->GetOutput();
  85     clitk::writeImage<InputImageType>(output, args_info.output_arg);
  86   }
  87
  88   //--------------------------------------------------------------------
  89   // Filter test RelativePositionPropImageFilter
  90   if (0) {
  91     typedef itk::Image<float, Dim> OutputImageType;
  92     OutputImageType::Pointer outputf;
  93     typedef itk::RelativePositionPropImageFilter<InputImageType, OutputImageType> FilterType;
  94     FilterType::Pointer filter = FilterType::New();
  95     filter->SetInput(input1);
  96
  97     filter->SetAlpha1(clitk::deg2rad(args_info.angle1_arg)); // xy plane
  98     filter->SetAlpha2(clitk::deg2rad(args_info.angle2_arg));
  99     filter->SetK1(M_PI/2.0); // Opening parameter, default = pi/2
 100     filter->SetFast(true);
 101     filter->SetRadius(2);
 102     filter->SetVerboseProgress(true);
 103
 104     /*         A1   A2
 105                Left      0    0
 106                Right   180    0
 107                Ant      90    0
 108                Post    -90    0
 109                Inf       0   90
 110                Sup       0  -90
 111     */
 112
 113     filter->Update();
 114     clitk::writeImage<OutputImageType>(filter->GetOutput(), args_info.output_arg);
 115   }
 116
 117   //--------------------------------------------------------------------
 118   // Filter test
 119   if (0) {
 120     typedef itk::Image<short, Dim> OutputImageType;
 121     typedef clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType> FilterType;
 122     FilterType::Pointer filter = FilterType::New();
 123     filter->SetInput(input1);
 124     filter->SetOutputIsoSpacing(1);
 125     //filter->SetNumberOfThreads(4); // auto
 126     filter->SetGaussianFilteringEnabled(false);
 127     filter->Update();
 128     clitk::writeImage<OutputImageType>(filter->GetOutput(), args_info.output_arg);
 129   }
 130
 131   //--------------------------------------------------------------------
 132   // Filter AddRelativePositionConstraintToLabelImageFilter test
 133   if (0) {
 134     /*
 135     typedef clitk::AddRelativePositionConstraintToLabelImageFilter<InputImageType> FilterType;
 136     FilterType::Pointer filter = FilterType::New();
 137     filter->SetInput(input1);
 138     filter->SetInputObject(input2);
 139     filter->SetOrientationType(FilterType::LeftTo);
 140     filter->SetIntermediateSpacing(5);
 141     filter->SetFuzzyThreshold(0.5);
 142     filter->VerboseStepOn();
 143     filter->WriteStepOff();
 144     filter->Update();
 145
 146     filter->SetInput(filter->GetOutput());
 147     filter->SetInputObject(input2);
 148     filter->SetOrientationType(FilterType::RightTo);
 149     filter->SetIntermediateSpacing(5);
 150     filter->SetFuzzyThreshold(0.5);
 151     filter->Update();
 152
 153     clitk::writeImage<InputImageType>(filter->GetOutput(), args_info.output_arg);
 154     */
 155   }
 156
 157   //--------------------------------------------------------------------
 158   // Filter test ExtractPatientFilter
 159   if (0) {
 160     /*
 161     typedef itk::Image<char, Dim> OutputImageType;
 162     typedef clitk::ExtractPatientFilter<InputImageType, OutputImageType> FilterType;
 163     FilterType::Pointer filter = FilterType::New();
 164     filter->SetInput(input1);
 165     filter->VerboseStepOn();
 166     filter->WriteStepOn();
 167     // options (default)
 168     filter->SetUpperThreshold(-300);
 169     filter->FinalOpenCloseOff(); // default=on (not rezally needed ?)
 170     filter->Update();
 171     OutputImageType::Pointer output = filter->GetOutput();
 172     clitk::writeImage<OutputImageType>(output, args_info.output_arg);
 173     */
 174   }
 175
 176   //--------------------------------------------------------------------
 177   // Filter test ExtractLungsFilter
 178   if (0) {
 179     /*
 180     typedef itk::Image<PixelType, Dim> OutputImageType; // to change into char
 181     typedef clitk::ExtractLungFilter<InputImageType, OutputImageType> FilterType;
 182     FilterType::Pointer filter = FilterType::New();
 183     // DD(filter->GetNumberOfSteps());
 184     filter->SetInput(input1); // CT
 185     filter->SetInputPatientMask(input2, 0); // Patient mask and BG value
 186     filter->VerboseStepOn();
 187     filter->WriteStepOn();
 188     // options (default)
 189     //filter->SetBackgroundValue(0);
 190     filter->SetUpperThreshold(-300);
 191     // filter->SetMinimumComponentSize(100);
 192
 193     filter->Update();
 194     OutputImageType::Pointer output = filter->GetOutput();
 195     clitk::writeImage<OutputImageType>(output, args_info.output_arg);
 196     */
 197   }
 198
 199   //--------------------------------------------------------------------
 200   // Filter test ExtractMediastinumFilter
 201   if (0) {
 202     /*
 203     typedef clitk::ExtractMediastinumFilter<InputImageType> FilterType;
 204     FilterType::Pointer filter = FilterType::New();
 205     filter->SetInputPatientLabelImage(input1);
 206     filter->SetInputLungLabelImage(input2, 0, 1, 2); // BG, FG Left Lung, FG Right Lung
 207     filter->SetInputBonesLabelImage(input3);
 208     filter->VerboseStepOn();
 209     filter->WriteStepOn();
 210     filter->Update();
 211     output = filter->GetOutput();
 212     clitk::writeImage<InputImageType>(output, args_info.output_arg);
 213     */
 214   }
 215
 216   //--------------------------------------------------------------------
 217   // Test for auto register sub-task in a segmentation process
 218   if (1) {
 219     ExtractLymphStation_7 * s7 = new ExtractLymphStation_7;
 220     //    s7->SetArgsInfo<args_info_clitkTestFilter>(args_info);
 221     // GetParent->SetArgsInfo<>
 222     s7->StartSegmentation();
 223   }
 224
 225   // This is the end my friend
 226   return EXIT_SUCCESS;
 227 }// end main
 228 //--------------------------------------------------------------------