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 // ITK ENST
  34 #include "RelativePositionPropImageFilter.h"
  35
  36 //--------------------------------------------------------------------
  37 int main(int argc, char * argv[]) {
  38
  39   // Init command line
  40   GGO(clitkTestFilter, args_info);
  41
  42   // Image types
  43   //typedef unsigned char PixelType;
  44   typedef short PixelType;
  45   static const int Dim=3;
  46   typedef itk::Image<PixelType, Dim> InputImageType;
  47
  48   // Read inputs
  49   InputImageType::Pointer input1;
  50   InputImageType::Pointer input2;
  51   InputImageType::Pointer input3;
  52   input1 = clitk::readImage<InputImageType>(args_info.input1_arg, true);
  53   if (args_info.input2_given) input2 = clitk::readImage<InputImageType>(args_info.input2_arg, true);
  54   if (args_info.input3_given) input3 = clitk::readImage<InputImageType>(args_info.input3_arg, true);
  55
  56   // Declare output
  57   InputImageType::Pointer output;
  58
  59   //--------------------------------------------------------------------
  60   // Filter test BooleanOperatorLabelImageFilter
  61   if (0) {
  62     typedef clitk::BooleanOperatorLabelImageFilter<InputImageType> FilterType;
  63     FilterType::Pointer filter = FilterType::New();
  64     filter->SetInput1(input1);
  65     filter->SetInput2(input2);
  66     output = clitk::NewImageLike<InputImageType>(input1);
  67     filter->GraftOutput(output);  /// TO VERIFY !!!
  68     filter->Update();
  69     filter->SetInput2(input3);
  70     filter->Update();
  71     output = filter->GetOutput();
  72     clitk::writeImage<InputImageType>(output, args_info.output_arg);
  73   }
  74
  75   //--------------------------------------------------------------------
  76   // Filter test AutoCropLabelImageFilter
  77   if (1) {
  78     typedef clitk::AutoCropFilter<InputImageType> FilterType;
  79     FilterType::Pointer filter = FilterType::New();
  80     filter->SetInput(input1);
  81     filter->Update();
  82     output = filter->GetOutput();
  83     clitk::writeImage<InputImageType>(output, args_info.output_arg);
  84   }
  85
  86   //--------------------------------------------------------------------
  87   // Filter test RelativePositionPropImageFilter
  88   if (0) {
  89     typedef itk::Image<float, Dim> OutputImageType;
  90     OutputImageType::Pointer outputf;
  91     typedef itk::RelativePositionPropImageFilter<InputImageType, OutputImageType> FilterType;
  92     FilterType::Pointer filter = FilterType::New();
  93     filter->SetInput(input1);
  94
  95     filter->SetAlpha1(clitk::deg2rad(args_info.angle1_arg)); // xy plane
  96     filter->SetAlpha2(clitk::deg2rad(args_info.angle2_arg));
  97     filter->SetK1(M_PI/2.0); // Opening parameter, default = pi/2
  98     filter->SetFast(true);
  99     filter->SetRadius(2);
 100     filter->SetVerboseProgress(true);
 101
 102     /*         A1   A2
 103                Left      0    0
 104                Right   180    0
 105                Ant      90    0
 106                Post    -90    0
 107                Inf       0   90
 108                Sup       0  -90
 109     */
 110
 111     filter->Update();
 112     clitk::writeImage<OutputImageType>(filter->GetOutput(), args_info.output_arg);
 113   }
 114
 115   //--------------------------------------------------------------------
 116   // Filter test
 117   if (0) {
 118     typedef itk::Image<short, Dim> OutputImageType;
 119     typedef clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType> FilterType;
 120     FilterType::Pointer filter = FilterType::New();
 121     filter->SetInput(input1);
 122     filter->SetOutputIsoSpacing(1);
 123     //filter->SetNumberOfThreads(4); // auto
 124     filter->SetGaussianFilteringEnabled(false);
 125     filter->Update();
 126     clitk::writeImage<OutputImageType>(filter->GetOutput(), args_info.output_arg);
 127   }
 128
 129   //--------------------------------------------------------------------
 130   // Filter AddRelativePositionConstraintToLabelImageFilter test
 131   if (0) {
 132     /*
 133     typedef clitk::AddRelativePositionConstraintToLabelImageFilter<InputImageType> FilterType;
 134     FilterType::Pointer filter = FilterType::New();
 135     filter->SetInput(input1);
 136     filter->SetInputObject(input2);
 137     filter->SetOrientationType(FilterType::LeftTo);
 138     filter->SetIntermediateSpacing(5);
 139     filter->SetFuzzyThreshold(0.5);
 140     filter->VerboseStepOn();
 141     filter->WriteStepOff();
 142     filter->Update();
 143
 144     filter->SetInput(filter->GetOutput());
 145     filter->SetInputObject(input2);
 146     filter->SetOrientationType(FilterType::RightTo);
 147     filter->SetIntermediateSpacing(5);
 148     filter->SetFuzzyThreshold(0.5);
 149     filter->Update();
 150
 151     clitk::writeImage<InputImageType>(filter->GetOutput(), args_info.output_arg);
 152     */
 153   }
 154
 155   //--------------------------------------------------------------------
 156   // Filter test ExtractPatientFilter
 157   if (0) {
 158     typedef itk::Image<char, Dim> OutputImageType;
 159     typedef clitk::ExtractPatientFilter<InputImageType, OutputImageType> FilterType;
 160     FilterType::Pointer filter = FilterType::New();
 161     filter->SetInput(input1);
 162     filter->VerboseStepOn();
 163     filter->WriteStepOn();
 164     // options (default)
 165     filter->SetUpperThreshold(-300);
 166     filter->FinalOpenCloseOff(); // default=on (not rezally needed ?)
 167     filter->Update();
 168     OutputImageType::Pointer output = filter->GetOutput();
 169     clitk::writeImage<OutputImageType>(output, args_info.output_arg);
 170   }
 171
 172   //--------------------------------------------------------------------
 173   // Filter test ExtractLungsFilter
 174   if (0) {
 175     typedef itk::Image<PixelType, Dim> OutputImageType; // to change into char
 176     typedef clitk::ExtractLungFilter<InputImageType, OutputImageType> FilterType;
 177     FilterType::Pointer filter = FilterType::New();
 178     // DD(filter->GetNumberOfSteps());
 179     filter->SetInput(input1); // CT
 180     filter->SetInputPatientMask(input2, 0); // Patient mask and BG value
 181     filter->VerboseStepOn();
 182     filter->WriteStepOn();
 183     // options (default)
 184     //filter->SetBackgroundValue(0);
 185     filter->SetUpperThreshold(-300);
 186     // filter->SetMinimumComponentSize(100);
 187
 188     filter->Update();
 189     OutputImageType::Pointer output = filter->GetOutput();
 190     clitk::writeImage<OutputImageType>(output, args_info.output_arg);
 191   }
 192
 193   //--------------------------------------------------------------------
 194   // Filter test ExtractMediastinumFilter
 195   if (0) {
 196     typedef clitk::ExtractMediastinumFilter<InputImageType> FilterType;
 197     FilterType::Pointer filter = FilterType::New();
 198     filter->SetInputPatientLabelImage(input1);
 199     filter->SetInputLungLabelImage(input2, 0, 1, 2); // BG, FG Left Lung, FG Right Lung
 200     filter->SetInputBonesLabelImage(input3);
 201     filter->VerboseStepOn();
 202     filter->WriteStepOn();
 203     filter->Update();
 204     output = filter->GetOutput();
 205     clitk::writeImage<InputImageType>(output, args_info.output_arg);
 206   }
 207
 208   // This is the end my friend
 209   return EXIT_SUCCESS;
 210 }// end main
 211 //--------------------------------------------------------------------