Merge remote-tracking branch 'remotes/origin/app_morphological' into develop

Modules/Applications/AppMorphology/app/CMakeLists.txt

@@ -2,6 +2,7 @@ set(OTBAppMorphology_LINK_LIBS
   ${OTBImageBase_LIBRARIES}
   ${OTBApplicationEngine_LIBRARIES}
   ${OTBObjectList_LIBRARIES}
+  ${OTBMorphologicalProfiles_LIBRARIES}
 )
 
 otb_create_application(
@@ -13,3 +14,19 @@ otb_create_application(
   NAME           GrayScaleMorphologicalOperation
   SOURCES        otbGrayScaleMorphologicalOperation.cxx
   LINK_LIBRARIES ${${otb-module}_LIBRARIES})
+
+
+otb_create_application(
+  NAME           MorphologicalClassification
+  SOURCES otbMorphologicalClassification.cxx
+  LINK_LIBRARIES ${${otb-module}_LIBRARIES})
+
+otb_create_application(
+  NAME           MorphologicalProfilesAnalysis
+  SOURCES        otbMorphologicalProfilesAnalysis.cxx
+  LINK_LIBRARIES ${${otb-module}_LIBRARIES})
+
+otb_create_application(
+  NAME           MorphologicalMultiScaleDecomposition
+  SOURCES        otbMorphologicalMultiScaleDecomposition.cxx
+  LINK_LIBRARIES ${${otb-module}_LIBRARIES})

Modules/Applications/AppMorphology/app/otbMorphologicalClassification.cxx

+/*=========================================================================
+
+  Program:   ORFEO Toolbox
+  Language:  C++
+  Date:      $Date$
+  Version:   $Revision$
+
+
+  Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
+  See OTBCopyright.txt for details.
+
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+
+#include "otbGeodesicMorphologyDecompositionImageFilter.h"
+#include "otbWrapperApplication.h"
+#include "otbWrapperApplicationFactory.h"
+
+#include "itkBinaryBallStructuringElement.h"
+#include "itkBinaryCrossStructuringElement.h"
+
+#include "itkBinaryDilateImageFilter.h"
+#include "itkBinaryErodeImageFilter.h"
+#include "itkBinaryMorphologicalOpeningImageFilter.h"
+#include "itkBinaryMorphologicalClosingImageFilter.h"
+
+#include "otbMultiToMonoChannelExtractROI.h"
+#include "otbImageList.h"
+#include "otbImageListToVectorImageFilter.h"
+
+#include "itkTimeProbe.h"
+#include "otbConvexOrConcaveClassificationFilter.h"
+#include "otbMorphologicalProfilesSegmentationFilter.h"
+
+namespace otb {
+namespace Wrapper {
+
+class MorphologicalClassification : public Application {
+public:
+/** Standard class typedefs. */
+  typedef MorphologicalClassification Self;
+  typedef Application Superclass;
+  typedef itk::SmartPointer<Self> Pointer;
+  typedef itk::SmartPointer<const Self> ConstPointer;
+
+  typedef FloatVectorImageType::InternalPixelType InputPixelType;
+  typedef otb::Image<InputPixelType, 2> FloatImageType;
+
+  typedef unsigned short LabeledPixelType;
+  typedef otb::Image<LabeledPixelType, 2> LabeledImageType;
+
+  typedef otb::MultiToMonoChannelExtractROI<FloatVectorImageType::InternalPixelType, InputPixelType>
+          ExtractorFilterType;
+
+  typedef otb::ConvexOrConcaveClassificationFilter<FloatImageType, LabeledImageType> ClassificationFilterType;
+
+  typedef itk::BinaryBallStructuringElement<InputPixelType, 2> BallStructuringElementType;
+  typedef itk::BinaryCrossStructuringElement<InputPixelType, 2> CrossStructuringElementType;
+
+/** Standard macro */
+  itkNewMacro( Self );
+
+  itkTypeMacro( MorphologicalClassification, otb::Application );
+
+private:
+
+  void DoInit() ITK_OVERRIDE
+  {
+    SetName( "MorphologicalClassification" );
+    SetDescription( "Performs morphological convex, concave and flat classification on an input image channel" );
+
+    // Documentation
+    SetDocName( "Morphological Classification" );
+    SetDocLongDescription( "This algorithm is based on the following publication:\n"
+                                   "\n"
+                                   "Martino Pesaresi and Jon Alti Benediktsson, Member, IEEE: A new approach\n"
+                                   "for the morphological segmentation of high resolution satellite imagery.\n"
+                                   "IEEE Transactions on geoscience and remote sensing, vol. 39, NO. 2,\n"
+                                   "February 2001, p. 309-320.\n"
+                                   "\n"
+                                   "This application perform the following decision rule to classify a pixel\n"
+                                   "between the three classes Convex, Concave and Flat. Let :math:`f` denote\n"
+                                   "the input image and :math:`\\psi_{N}(f)` the geodesic leveling of\n"
+                                   ":math:`f` with a structuring element of size :math:`N`. One can derive\n"
+                                   "the following decision rule to classify :math:`f` into Convex (label\n"
+                                   ":math:`\\stackrel{\\smile}{k}`), Concave (label\n"
+                                   ":math:`\\stackrel{rown}{k}`) and Flat (label :math:`\\bar{k}`): \n"
+                                   "\n"
+                                   ":math:`f(n) = \\begin{cases} \\stackrel{\\smile}{k} &:& f-\\psi_{N}(f)>\\sigma \\\\ \\stackrel{\\frown}{k} &:& \\psi_{N}(f)-f>\\sigma\\\\ \\bar{k}&:&\\mid f - \\psi_{N}(f) \\mid \\leq \\sigma \\end{cases}`"
+                                   "\n\n"
+                                   "This output is a labeled image (0 : Flat, 1 : Convex, 2 : Concave)" );
+    SetDocLimitations( "Generation of the morphological classification is not streamable, pay attention to this fact when setting the radius size of the structuring element." );
+    SetDocAuthors( "OTB-Team" );
+    SetDocSeeAlso( "otbConvexOrConcaveClassificationFilter class" );
+
+    AddDocTag( "MorphologicalClassification" );
+
+    AddParameter( ParameterType_InputImage, "in", "Input Image" );
+    SetParameterDescription( "in", "The input image to be classified." );
+
+    AddParameter( ParameterType_OutputImage, "out", "Output Image" );
+    SetParameterDescription( "out",
+                             "The output classified image with 3 different values (0 : Flat, 1 : Convex, 2 : Concave)" );
+
+    AddParameter( ParameterType_Int, "channel", "Selected Channel" );
+    SetParameterDescription( "channel", "The selected channel index for input image" );
+    SetDefaultParameterInt( "channel", 1 );
+    SetMinimumParameterIntValue( "channel", 1 );
+
+    AddRAMParameter();
+
+    // Structuring Element (Ball | Cross)
+    AddParameter( ParameterType_Choice, "structype", "Structuring Element Type" );
+    SetParameterDescription( "structype", "Choice of the structuring element type" );
+    AddChoice( "structype.ball", "Ball" );
+    AddChoice( "structype.cross", "Cross" );
+
+    AddParameter( ParameterType_Int, "radius", "Radius" );
+    SetParameterDescription( "radius", "Radius of the structuring element (in pixels)" );
+    SetDefaultParameterInt( "radius", 5 );
+    SetMinimumParameterIntValue( "radius", 1 );
+
+    AddParameter( ParameterType_Float, "sigma", "Sigma value for leveling tolerance" );
+    SetParameterDescription( "sigma", "Sigma value for leveling tolerance" );
+    SetDefaultParameterFloat( "sigma", 0.5 );
+    SetMinimumParameterFloatValue( "sigma", 0 );
+
+    SetDocExampleParameterValue( "in", "ROI_IKO_PAN_LesHalles.tif" );
+    SetDocExampleParameterValue( "channel", "1" );
+    SetDocExampleParameterValue( "structype", "ball" );
+    SetDocExampleParameterValue( "radius", "5" );
+    SetDocExampleParameterValue( "sigma", "0.5" );
+    SetDocExampleParameterValue( "out", "output.tif" );
+
+  }
+
+  void DoUpdateParameters() ITK_OVERRIDE
+  {
+    // Nothing to do here : all parameters are independent
+  }
+
+  void DoExecute() ITK_OVERRIDE
+  {
+    FloatVectorImageType::Pointer inImage = GetParameterImage( "in" );
+
+    int nBComp = inImage->GetNumberOfComponentsPerPixel();
+    int selectedChannel = GetParameterInt( "channel" );
+
+    if ( selectedChannel > nBComp )
+      {
+      itkExceptionMacro( << "The specified channel index for input image is invalid." );
+      }
+
+    m_ExtractorFilter = ExtractorFilterType::New();
+    m_ExtractorFilter->SetInput( inImage );
+    m_ExtractorFilter->SetStartX( static_cast<unsigned int>(inImage->GetLargestPossibleRegion().GetIndex( 0 )) );
+    m_ExtractorFilter->SetStartY( static_cast<unsigned int>(inImage->GetLargestPossibleRegion().GetIndex( 1 )) );
+    m_ExtractorFilter->SetSizeX( inImage->GetLargestPossibleRegion().GetSize( 0 ) );
+    m_ExtractorFilter->SetSizeY( inImage->GetLargestPossibleRegion().GetSize( 1 ) );
+    m_ExtractorFilter->SetChannel( static_cast<unsigned int>(selectedChannel) );
+
+    unsigned int sigma = static_cast<unsigned int>(GetParameterInt( "sigma" ));
+    unsigned int radius = static_cast<unsigned int>(GetParameterInt( "radius" ));
+
+    m_ClassificationFilter = ClassificationFilterType::New();
+    m_ClassificationFilter->SetInput( m_ExtractorFilter->GetOutput() );
+    m_ClassificationFilter->SetSigma( sigma );
+    m_ClassificationFilter->SetFlatLabel( 0 );
+    m_ClassificationFilter->SetConvexLabel( 1 );
+    m_ClassificationFilter->SetConcaveLabel( 2 );
+
+    if ( GetParameterString( "structype" ) == "ball" )
+      {
+      performClassification<BallStructuringElementType>( radius );
+      } else // Cross
+      {
+      performClassification<CrossStructuringElementType>( radius );
+      }
+
+    SetParameterOutputImage( "out", m_ClassificationFilter->GetOutput() );
+
+  }
+
+  template<typename TStructuringElement>
+  void performClassification(unsigned int radius_size) {
+
+    typedef otb::GeodesicMorphologyDecompositionImageFilter<FloatImageType, FloatImageType, TStructuringElement> TDecompositionImageFilter;
+
+    typename TDecompositionImageFilter::Pointer decompositionImageFilter;
+    decompositionImageFilter = TDecompositionImageFilter::New();
+    decompositionImageFilter->SetInput( m_ExtractorFilter->GetOutput() );
+
+    typename TStructuringElement::RadiusType radius;
+    radius.Fill( radius_size );
+    decompositionImageFilter->SetRadius( radius );
+    AddProcess(decompositionImageFilter, "Image Decomposition");
+    decompositionImageFilter->Update();
+
+    m_ClassificationFilter->SetInputLeveling( decompositionImageFilter->GetOutput() );
+  }
+
+  ExtractorFilterType::Pointer m_ExtractorFilter;
+  ClassificationFilterType::Pointer m_ClassificationFilter;
+
+};
+}
+}
+
+OTB_APPLICATION_EXPORT( otb::Wrapper::MorphologicalClassification )
+

Modules/Applications/AppMorphology/otb-module.cmake

@@ -6,6 +6,7 @@ otb_module(OTBAppMorphology
     OTBObjectList
     OTBITK
     OTBApplicationEngine
+    OTBMorphologicalProfiles
 
   TEST_DEPENDS
     OTBTestKernel

Modules/Applications/AppMorphology/test/CMakeLists.txt

@@ -28,3 +28,101 @@ otb_test_application(NAME  apTvFEGrayScaleMorphologicalOperation
                    			 ${BASELINE}/apTvFEGrayScaleMorphologicalOperation.tif
                  		     ${TEMP}/apTvFEGrayScaleMorphologicalOperation.tif)
 
+
+#----------- MorphologicalMultiScaleDecomposition TESTS ----------------
+otb_test_application(NAME  apTvFEMorphologicalMultiScaleDecomposition
+					 APP  MorphologicalMultiScaleDecomposition
+					 OPTIONS -in ${INPUTDATA}/ROI_IKO_PAN_LesHalles.tif
+							 -channel 1
+							 -radius 4
+		 					 -structype ball
+							 -outleveling ${TEMP}/apTvFEMorphologicalMultiScaleDecomposition_levelingIteration_1.tif
+							 -outconcave ${TEMP}/apTvFEMorphologicalMultiScaleDecomposition_concaveIteration_1.tif
+							 -outconvex ${TEMP}/apTvFEMorphologicalMultiScaleDecomposition_convexIteration_1.tif
+					 VALID   --compare-n-images ${NOTOL} 3
+							 ${BASELINE}/apTvFEMorphologicalMultiScaleDecomposition_levelingIteration_1.tif
+							 ${TEMP}/apTvFEMorphologicalMultiScaleDecomposition_levelingIteration_1.tif
+							 ${BASELINE}/apTvFEMorphologicalMultiScaleDecomposition_concaveIteration_1.tif
+							 ${TEMP}/apTvFEMorphologicalMultiScaleDecomposition_concaveIteration_1.tif
+							 ${BASELINE}/apTvFEMorphologicalMultiScaleDecomposition_convexIteration_1.tif
+							 ${TEMP}/apTvFEMorphologicalMultiScaleDecomposition_convexIteration_1.tif)
+
+
+#----------- Iterative MorphologicalMultiScaleDecomposition TESTS ----------------
+otb_test_application(NAME  apTvFEMorphologicalMultiScaleDecompositionIteratif
+					 APP  MorphologicalMultiScaleDecomposition
+					 OPTIONS -in ${INPUTDATA}/ROI_IKO_PAN_LesHalles.tif
+							 -channel 1
+							 -levels 2
+		                     -structype ball
+							 -step 3
+							 -radius 2
+							 -outleveling ${TEMP}/apTvFEMorphologicalMultiScaleDecomposition_levelingIteration_2.tif
+							 -outconcave ${TEMP}/apTvFEMorphologicalMultiScaleDecomposition_concaveIteration_2.tif
+							 -outconvex ${TEMP}/apTvFEMorphologicalMultiScaleDecomposition_convexIteration_2.tif
+					 VALID   --compare-n-images ${NOTOL} 3
+							 ${BASELINE}/apTvFEMorphologicalMultiScaleDecomposition_levelingIteration_2.tif
+							 ${TEMP}/apTvFEMorphologicalMultiScaleDecomposition_levelingIteration_2.tif
+							 ${BASELINE}/apTvFEMorphologicalMultiScaleDecomposition_concaveIteration_2.tif
+							 ${TEMP}/apTvFEMorphologicalMultiScaleDecomposition_concaveIteration_2.tif
+							 ${BASELINE}/apTvFEMorphologicalMultiScaleDecomposition_convexIteration_2.tif
+							 ${TEMP}/apTvFEMorphologicalMultiScaleDecomposition_convexIteration_2.tif)
+
+
+#----------- MorphologicalClassification TESTS ----------------
+otb_test_application(NAME  apTvFEMorphologicalClassification
+		             APP  MorphologicalClassification
+		             OPTIONS -in ${INPUTDATA}/ROI_IKO_PAN_LesHalles.tif
+			                 -channel 1
+		                     -structype ball
+		                     -radius 5
+							 -sigma 0.5
+		                     -out ${TEMP}/apTvFEMorphologicalProfilesClassification.tif
+		             VALID   --compare-image ${NOTOL}
+							 ${BASELINE}/apTvFEMorphologicalProfilesClassification.tif
+					         ${TEMP}/apTvFEMorphologicalProfilesClassification.tif)
+
+
+
+#----------- Opening MorphologicalProfilesAnalysis TESTS ----------------
+otb_test_application(NAME  apTvFEMorphologicalProfilesAnalysisOpening
+					 APP  MorphologicalProfilesAnalysis
+					 OPTIONS -in ${INPUTDATA}/ROI_IKO_PAN_LesHalles.tif
+		                     -channel 1
+		                     -structype ball
+		                     -profile closing
+		                     -size 4
+		                     -radius 1
+		                     -step 1
+							 -out ${TEMP}/apTvFEMorphologicalProfilesOpeningAnalysis.tif)
+
+#----------- Closing MorphologicalProfilesAnalysis TESTS ----------------
+otb_test_application(NAME  apTvFEMorphologicalProfilesAnalysisClosing
+					 APP  MorphologicalProfilesAnalysis
+					 OPTIONS -in ${INPUTDATA}/ROI_IKO_PAN_LesHalles.tif
+					         -channel 1
+					         -structype ball
+					         -profile closing
+					         -size 4
+					         -radius 1
+					         -step 1
+					         -out ${TEMP}/apTvFEMorphologicalProfilesClosingAnalysis.tif
+					 VALID   --compare-image ${NOTOL}
+					         ${BASELINE}/apTvFEMorphologicalProfilesClosingAnalysis.tif
+					         ${TEMP}/apTvFEMorphologicalProfilesClosingAnalysis.tif)
+
+#----------- Classfication MorphologicalProfilesAnalysis TESTS ----------------
+otb_test_application(NAME  apTvFEMorphologicalProfilesAnalysisClassification
+					 APP  MorphologicalProfilesAnalysis
+					 OPTIONS -in ${INPUTDATA}/ROI_IKO_PAN_LesHalles.tif
+						     -channel 1
+						     -structype ball
+						     -profile classification
+						     -size 5
+						     -radius 1
+						     -step 1
+							 -profile.classification.sigma 1
+						     -out ${TEMP}/apTvFEMorphologicalProfilesClosingAnalysis.tif
+					 VALID   --compare-image ${NOTOL}
+							 ${BASELINE}/msMultiScaleConvexOrConcaveClassificationFilterOutput.tif
+					 		 ${TEMP}/apTvFEMorphologicalProfilesClosingAnalysis.tif)

Modules/Segmentation/MorphologicalProfiles/include/otbGeodesicMorphologyDecompositionImageFilter.h

@@ -174,6 +174,8 @@ private:
   bool m_PreserveIntensities;
   /** Use fully connected morphological operators */
   bool m_FullyConnected;
+  /** Progress accumulator to report internal filter progress */
+  itk::ProgressAccumulator::Pointer m_Progress;
 
 };
 } // End namespace otb

Modules/Segmentation/MorphologicalProfiles/include/otbGeodesicMorphologyDecompositionImageFilter.txx

@@ -36,12 +36,24 @@ GeodesicMorphologyDecompositionImageFilter<TInputImage, TOutputImage, TStructuri
 
   m_Radius.Fill(1);
 
+  // Create a process accumulator for tracking the progress of minipipeline
+  m_Progress = itk::ProgressAccumulator::New();
+  m_Progress->SetMiniPipelineFilter(this);
+
   m_OpeningFilter  = OpeningFilterType::New();
   m_ClosingFilter  = ClosingFilterType::New();
   m_LevelingFilter = LevelingFilterType::New();
   m_ConvexFilter   = ConvexFilterType::New();
   m_ConcaveFilter  = ConcaveFilterType::New();
 
+  // Register Internal Filter for progress
+  m_Progress->RegisterInternalFilter(m_OpeningFilter, 0.2);
+  m_Progress->RegisterInternalFilter(m_ClosingFilter, 0.2);
+  m_Progress->RegisterInternalFilter(m_LevelingFilter, 0.2);
+  m_Progress->RegisterInternalFilter(m_ConvexFilter, 0.2);
+  m_Progress->RegisterInternalFilter(m_ConcaveFilter, 0.2);
+
+
   m_FullyConnected = true;
   m_PreserveIntensities = true;
 }

Modules/Segmentation/MorphologicalProfiles/include/otbGeodesicMorphologyIterativeDecompositionImageFilter.h

@@ -146,6 +146,8 @@ private:
   unsigned int m_InitialValue;
   /** The number of iterations */
   unsigned int m_NumberOfIterations;
+  /** Progress accumulator to report internal filter progress */
+  itk::ProgressAccumulator::Pointer m_Progress;
 
 };
 } // End namespace otb

Modules/Segmentation/MorphologicalProfiles/include/otbGeodesicMorphologyIterativeDecompositionImageFilter.txx

@@ -32,6 +32,10 @@ template <class TImage, class TStructuringElement>
 GeodesicMorphologyIterativeDecompositionImageFilter<TImage, TStructuringElement>
 ::GeodesicMorphologyIterativeDecompositionImageFilter()
 {
+  // Create a process accumulator for tracking the progress of minipipeline
+  m_Progress = itk::ProgressAccumulator::New();
+  m_Progress->SetMiniPipelineFilter(this);
+
   this->SetNumberOfRequiredInputs(1);
   this->SetNumberOfRequiredOutputs(3);
   m_NumberOfIterations  = 2;
@@ -185,6 +189,10 @@ GeodesicMorphologyIterativeDecompositionImageFilter<TImage, TStructuringElement>
   while (i < m_NumberOfIterations)
     {
     filter = DecompositionFilterType::New();
+
+    // Register Internal Filter for progress
+    m_Progress->RegisterInternalFilter(filter, 1./m_NumberOfIterations);
+
     typename StructuringElementType::RadiusType radius;
     radius.Fill(m_InitialValue + i * m_Step);
     filter->SetRadius(radius);
@@ -195,8 +203,8 @@ GeodesicMorphologyIterativeDecompositionImageFilter<TImage, TStructuringElement>
     filter->GetOutput()->UpdateOutputData();
 
     outputPtr->SetNthElement(i, filter->GetOutput());
-    concOutputPtr->SetNthElement(i, filter->GetConvexMap());
-    convOutputPtr->SetNthElement(i, filter->GetConcaveMap());
+    concOutputPtr->SetNthElement(i, filter->GetConcaveMap());
+    convOutputPtr->SetNthElement(i, filter->GetConvexMap());
 
     current = filter->GetOutput();