ENH: add RadiometricVegetationIndices appli + test

Applications/CMakeLists.txt

@@ -12,5 +12,6 @@ add_subdirectory(Projections)
 add_subdirectory(Segmentation)
 add_subdirectory(Util)
 add_subdirectory(Radiometry)
+add_subdirectory(RadiometricIndices)
 
 add_subdirectory(Test)

Applications/RadiometricIndices/CMakeLists.txt

+
+OTB_CREATE_APPLICATION(NAME           RadiometricVegetationIndices
+                       SOURCES        otbRadiometricVegetationIndices.cxx
+                       LINK_LIBRARIES OTBIO;OTBRadiometry)
+

Applications/RadiometricIndices/otbRadiometricVegetationIndices.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 "otbWrapperApplication.h"
+#include "otbWrapperApplicationFactory.h"
+
+#include "otbMultiChannelRAndNIRIndexImageFilter.h"
+#include "otbVegetationIndicesFunctor.h"
+
+#include "otbImageList.h"
+#include "otbImageListToVectorImageFilter.h"
+
+#include "otbWrapperNumericalParameter.h"
+
+namespace otb
+{
+namespace Wrapper
+{
+
+class RadiometricVegetationIndices: public Application
+{
+public:
+  /** Standard class typedefs. */
+  typedef RadiometricVegetationIndices  Self;
+  typedef Application                   Superclass;
+  typedef itk::SmartPointer<Self>       Pointer;
+  typedef itk::SmartPointer<const Self> ConstPointer;
+
+  /** Standard macro */
+  itkNewMacro(Self);
+
+  itkTypeMacro(RadiometricVegetationIndices, otb::Wrapper::Application);
+
+  /** Output  containers typedef */
+  typedef ObjectList<itk::ProcessObject>  FilterListType;
+  typedef ImageList<FloatImageType> ImageListType;
+  typedef ImageListToVectorImageFilter<ImageListType, FloatVectorImageType> ImageListToVectorImageFilter;
+
+  /** Radiometric indices functors typedef */
+  typedef Functor::NDVI<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType, FloatImageType::PixelType> NDVIFunctor;
+  typedef Functor::TNDVI<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType, FloatImageType::PixelType> TNDVIFunctor;
+  typedef Functor::RVI<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType, FloatImageType::PixelType> RVIFunctor;
+  typedef Functor::SAVI<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType, FloatImageType::PixelType> SAVIFunctor;
+  typedef Functor::TSAVI<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType, FloatImageType::PixelType> TSAVIFunctor;
+  typedef Functor::MSAVI<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType, FloatImageType::PixelType> MSAVIFunctor;
+  typedef Functor::MSAVI2<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType, FloatImageType::PixelType> MSAVI2Functor;
+  typedef Functor::GEMI<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType, FloatImageType::PixelType> GEMIFunctor;
+  typedef Functor::IPVI<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType, FloatImageType::PixelType> IPVIFunctor;
+  typedef Functor::LAIFromNDVILogarithmic<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType, FloatImageType::PixelType> LAIFromNDVILogFunctor;
+  typedef Functor::LAIFromReflectancesLinear<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType, FloatImageType::PixelType> LAIFromReflLinearFunctor;
+  typedef Functor::LAIFromNDVIFormosat2Functor<FloatVectorImageType::InternalPixelType, FloatVectorImageType::InternalPixelType, FloatImageType::PixelType> LAIFromNDVIFormoFunctor;
+
+  /** Radiometric indices filters typedef */
+  typedef MultiChannelRAndNIRIndexImageFilter<FloatVectorImageType, FloatImageType, NDVIFunctor> NDVIFilter;
+  typedef MultiChannelRAndNIRIndexImageFilter<FloatVectorImageType, FloatImageType, TNDVIFunctor> TNDVIFilter;
+  typedef MultiChannelRAndNIRIndexImageFilter<FloatVectorImageType, FloatImageType, RVIFunctor> RVIFilter;
+  typedef MultiChannelRAndNIRIndexImageFilter<FloatVectorImageType, FloatImageType, SAVIFunctor> SAVIFilter;
+  typedef MultiChannelRAndNIRIndexImageFilter<FloatVectorImageType, FloatImageType, TSAVIFunctor> TSAVIFilter;
+  typedef MultiChannelRAndNIRIndexImageFilter<FloatVectorImageType, FloatImageType, MSAVIFunctor> MSAVIFilter;
+  typedef MultiChannelRAndNIRIndexImageFilter<FloatVectorImageType, FloatImageType, MSAVI2Functor> MSAVI2Filter;
+  typedef MultiChannelRAndNIRIndexImageFilter<FloatVectorImageType, FloatImageType, GEMIFunctor> GEMIFilter;
+  typedef MultiChannelRAndNIRIndexImageFilter<FloatVectorImageType, FloatImageType, IPVIFunctor> IPVIFilter;
+  typedef MultiChannelRAndNIRIndexImageFilter<FloatVectorImageType, FloatImageType, LAIFromNDVILogFunctor> LAIFromNDVILogFilter;
+  typedef MultiChannelRAndNIRIndexImageFilter<FloatVectorImageType, FloatImageType, LAIFromReflLinearFunctor> LAIFromReflLinearFilter;
+  typedef MultiChannelRAndNIRIndexImageFilter<FloatVectorImageType, FloatImageType, LAIFromNDVIFormoFunctor> LAIFromNDVIFormoFilter;
+
+private:
+  RadiometricVegetationIndices()
+  {
+    SetName("RadiometricVegetationIndices");
+    SetDescription("Compute radimetric indices based Red and NIT channels.");
+
+    // Documentation
+    SetDocName("Images Concatenation Application");
+    SetDocLongDescription("This application computes radiometric indices that uses red and NIR channels of the input image. The output image is a multi channel one which each channel is one of the selected index. The channel order is the one of the selected indices.");
+    SetDocLimitations("None");
+    SetDocAuthors("OTB-Team");
+    SetDocSeeAlso("otbVecgetationIndices class");
+    SetDocCLExample("otbApplicationLauncherCommandLine RadiometricVegetationIndices ${OTB-BIN}/bin --in ${OTB-DATA}/Inputqb_RoadExtract.img --index.ndvi 1 --index.rvi 1 --index.ipvi 1 --out otbRadiometricVegetationIndicesImages.tif");
+    AddDocTag("Radiometric Indices");
+    AddDocTag("Vegetation Indices");
+    AddDocTag("Feature");
+  }
+
+  virtual ~RadiometricVegetationIndices()
+  {
+  }
+
+  void DoCreateParameters()
+  {
+    AddParameter(ParameterType_InputImage, "in", "Input Image");
+    SetParameterDescription("in", "Input image, with at least red and NIR channels");
+
+    AddParameter(ParameterType_OutputImage, "out", "output Image");
+    SetParameterDescription("out", "Radiometric indices output image");
+
+    AddParameter(ParameterType_Group, "channels", "Channels selection");
+    AddParameter(ParameterType_Int,  "channels.red",  "Red Channel");
+    SetParameterInt("channels.red", 3);
+    AddParameter(ParameterType_Int,  "channels.nir",  "NIR Channel");
+    SetParameterInt("channels.nir", 4);
+    
+    AddParameter(ParameterType_Group, "index", "Indices selection");
+    AddParameter(ParameterType_Empty, "index.ndvi", "NDVI");
+    MandatoryOff("index.ndvi");
+    SetParameterDescription("index.ndvi", "Normalized Difference Vegetation Index");
+    
+    AddParameter(ParameterType_Empty, "index.tndvi", "TNDVI");
+    MandatoryOff("index.tndvi");
+    SetParameterDescription("index.tndvi", " Transformed Normalized Difference Vegetation Index");
+    
+    AddParameter(ParameterType_Empty, "index.rvi", "RVI");
+    MandatoryOff("index.rvi");
+    SetParameterDescription("index.rvi", "Ratio Vegetation Index");
+
+    AddParameter(ParameterType_Empty, "index.savi", "SAVI");
+    MandatoryOff("index.savi");
+    SetParameterDescription("index.savi", "Soil Adjusted Vegetation Inde");
+
+    AddParameter(ParameterType_Empty, "index.tsavi", "TSAVI");
+    MandatoryOff("index.tsavi");
+    SetParameterDescription("index.tsavi", "Transformed Soil Adjusted Vegetation Index");
+
+    AddParameter(ParameterType_Empty, "index.msavi", "MSAVI");
+    MandatoryOff("index.msavi");
+    SetParameterDescription("index.msavi", "Modified Soil Adjusted Vegetation Index");
+
+    AddParameter(ParameterType_Empty, "index.msavi2", "MSAVI2");
+    MandatoryOff("index.msavi2");
+    SetParameterDescription("index.msavi2", "Modified Soil Adjusted Vegetation Index 2");
+
+    AddParameter(ParameterType_Empty, "index.gemi", "GEMI");
+    MandatoryOff("index.gemi");
+    SetParameterDescription("index.gemi", "Global Environment Monitoring Index");
+
+    AddParameter(ParameterType_Empty, "index.ipvi", "IPVI");
+    MandatoryOff("index.ipvi");
+    SetParameterDescription("index.ipvi", "Infrared Percentage Vegetation Index");
+
+    AddParameter(ParameterType_Empty, "index.laindvilog", "LAIFromNDVILog");
+    MandatoryOff("index.laindvilog");
+    SetParameterDescription("index.laindvilog", "Leaf Area Index from NDVI using a logarithmic relationship");
+
+    AddParameter(ParameterType_Empty, "index.lairefl", "LAIFromReflLinear");
+    MandatoryOff("index.lairefl"); 
+    SetParameterDescription("index.lairefl", "Leaf Area Index from reflectances using a linear relationship");
+
+    AddParameter(ParameterType_Empty, "index.laindviformo", "LAIFromNDVIFormo");
+    MandatoryOff("index.laindviformo"); 
+    SetParameterDescription("index.laindviformo", "Leaf Area Index from reflectances using using formula a*(exp(nir-red)/((red+nir)*b)-exp(c*b)), with a = 0.1519 b = 3.9443 c = 0.13. This formula is only valid for Formosat 2 reflectance TOCa linear relationship");
+  }
+
+  void DoUpdateParameters()
+  {
+    if ( HasValue("in") )
+      {
+       // Put the limit of the channel indices
+      dynamic_cast< NumericalParameter<int> * >(GetParameterByKey("channels.red"))->SetMinimumValue(1); 
+      dynamic_cast< NumericalParameter<int> * >(GetParameterByKey("channels.red"))->SetMaximumValue(GetParameterImage("in")->GetNumberOfComponentsPerPixel());
+      dynamic_cast< NumericalParameter<int> * >(GetParameterByKey("channels.nir"))->SetMinimumValue(1); 
+      dynamic_cast< NumericalParameter<int> * >(GetParameterByKey("channels.nir"))->SetMaximumValue(GetParameterImage("in")->GetNumberOfComponentsPerPixel());
+      }
+  }
+
+#define otbRadiometricVegetationIndicesMacro( key, type )             \
+  if( this->IsParameterEnabled(key) )                                 \
+    {                                                                 \
+    type##Filter::Pointer l_##type##Filter = type##Filter::New();     \
+    l_##type##Filter->SetRedIndex(redChannel);                        \
+    l_##type##Filter->SetNIRIndex(nirChannel);                        \
+    l_##type##Filter->SetInput(inImage);                              \
+    m_FilterList->PushBack( l_##type##Filter );                       \
+    m_ImageList->PushBack( l_##type##Filter->GetOutput() );           \
+    otbAppLogINFO(key << " indice added.");                            \
+    }
+
+  void DoExecute()
+  {
+    m_FilterList = FilterListType::New();
+    m_ImageList = ImageListType::New();
+    m_Concatener = ImageListToVectorImageFilter::New();
+
+    unsigned int redChannel = this->GetParameterInt("channels.red");
+    unsigned int nirChannel = this->GetParameterInt("channels.nir");
+    FloatVectorImageType* inImage = GetParameterImage("in");
+
+    otbRadiometricVegetationIndicesMacro("index.ndvi", NDVI);
+    otbRadiometricVegetationIndicesMacro("index.tndvi", TNDVI);
+    otbRadiometricVegetationIndicesMacro("index.rvi", RVI);
+    otbRadiometricVegetationIndicesMacro("index.savi", SAVI);
+    otbRadiometricVegetationIndicesMacro("index.tsavi", TSAVI);
+    otbRadiometricVegetationIndicesMacro("index.msavi", MSAVI);
+    otbRadiometricVegetationIndicesMacro("index.msavi2", MSAVI2);
+    otbRadiometricVegetationIndicesMacro("index.gemi", GEMI);
+    otbRadiometricVegetationIndicesMacro("index.ipvi", IPVI);
+    otbRadiometricVegetationIndicesMacro("index.laindvilog", LAIFromNDVILog);
+    otbRadiometricVegetationIndicesMacro("index.lairefl", LAIFromReflLinear);
+    otbRadiometricVegetationIndicesMacro("index.laindviformo", LAIFromNDVIFormo);
+    
+      if( m_ImageList->Size() == 0 )
+        {
+        otbAppLogCRITICAL("No indices selected...");
+        return;
+        }
+
+      m_Concatener->SetInput( m_ImageList );
+      m_Concatener->UpdateOutputInformation();
+      SetParameterOutputImage("out", m_Concatener->GetOutput());
+  }
+  
+  FilterListType::Pointer  m_FilterList;
+  ImageListType::Pointer m_ImageList;
+  ImageListToVectorImageFilter::Pointer m_Concatener;
+
+};
+
+}
+}
+
+OTB_APPLICATION_EXPORT(otb::Wrapper::RadiometricVegetationIndices)

Applications/Util/otbConcatenateImages.cxx

@@ -64,7 +64,7 @@ private:
     SetDocLimitations("None");
     SetDocAuthors("OTB-Team");
     SetDocSeeAlso("Rescale application, Convert application");
-    SetDocCLExample("otbApplicationLauncherCommandLine ConcatenateImages ${OTB-BIN}/bin --in ${OTB-DATA}/poupees_sub_c1.png ${OTB-DATA}/poupees_sub_c2.png ${OTB-DATA}/poupees_sub_c3.png --out otbConcatenateImages.png uchar");
+    SetDocCLExample("otbApplicationLauncherCommandLine ConcatenateImages ${OTB-BIN}/bin --in ${OTB-DATA/Input}/poupees_sub_c1.png ${OTB-DATA}/poupees_sub_c2.png ${OTB-DATA}/poupees_sub_c3.png --out otbConcatenateImages.png uchar");
     AddDocTag("Concatenation");
     AddDocTag("Multi channel");
 

Testing/Applications/CMakeLists.txt

@@ -53,6 +53,7 @@ add_subdirectory(FeatureExtraction)
 add_subdirectory(Hyperspectral)
 add_subdirectory(Projections)
 add_subdirectory(Radiometry)
+add_subdirectory(RadiometricIndices)
 add_subdirectory(Segmentation)
 add_subdirectory(Util)
 

Testing/Applications/RadiometricIndices/CMakeLists.txt

+set(TEST_DRIVER otbTestDriver
+    --add-before-env ITK_AUTOLOAD_PATH $<TARGET_FILE_DIR:otbapp_ReadImageInfo> )
+
+add_test(NAME apTvRIRadiometricVegetationIndices
+         COMMAND otbTestDriver --compare-image ${NOTOL}
+                    ${BASELINE}/apTvRIRadiometricVegetationIndices.tif
+                    ${TEMP}/apTvRIRadiometricVegetationIndices.tif
+         
+                 Execute $<TARGET_FILE:otbApplicationLauncherCommandLine>
+                    RadiometricVegetationIndices
+                    $<TARGET_FILE_DIR:otbapp_RadiometricVegetationIndices>
+                    --in ${INPUTDATA}/qb_RoadExtract.img
+                    --index.ndvi 1 
+                    --index.rvi 1 
+                    --index.ipvi 1
+                    --out ${TEMP}/apTvRIRadiometricVegetationIndices.tif
+                    )
+