From f7ae6e7ddd70ac6de5b31c7fab4d517d30eb02a6 Mon Sep 17 00:00:00 2001
From: Julien Malik <julien.malik@c-s.fr>
Date: Thu, 3 Nov 2011 19:22:37 +0100
Subject: [PATCH] ENH: split Hyperspectral application in two application : VCA
and Unmixing
---
Applications/Hyperspectral/CMakeLists.txt | 1 +
.../otbHyperspectralUnmixing.cxx | 255 ++----------------
.../otbVertexComponentAnalysis.cxx | 123 +++++++++
.../Applications/Hyperspectral/CMakeLists.txt | 35 +--
4 files changed, 158 insertions(+), 256 deletions(-)
create mode 100644 Applications/Hyperspectral/otbVertexComponentAnalysis.cxx
diff --git a/Applications/Hyperspectral/CMakeLists.txt b/Applications/Hyperspectral/CMakeLists.txt
index 5d19ce017b..dae81dfbd1 100644
--- a/Applications/Hyperspectral/CMakeLists.txt
+++ b/Applications/Hyperspectral/CMakeLists.txt
@@ -1,2 +1,3 @@
OTB_CREATE_APPLICATION(NAME HyperspectralUnmixing SOURCES otbHyperspectralUnmixing.cxx LINK_LIBRARIES OTBIO;OTBCommon;OTBBasicFilters)
+OTB_CREATE_APPLICATION(NAME VertexComponentAnalysis SOURCES otbVertexComponentAnalysis.cxx LINK_LIBRARIES OTBIO;OTBCommon;OTBBasicFilters)
diff --git a/Applications/Hyperspectral/otbHyperspectralUnmixing.cxx b/Applications/Hyperspectral/otbHyperspectralUnmixing.cxx
index 0042ffe3d8..096281e00a 100644
--- a/Applications/Hyperspectral/otbHyperspectralUnmixing.cxx
+++ b/Applications/Hyperspectral/otbHyperspectralUnmixing.cxx
@@ -42,10 +42,10 @@ typedef otb::StreamingStatisticsVectorImageFilter<DoubleVectorImageType> Streami
typedef otb::EigenvalueLikelihoodMaximisation<double> ELMType;
typedef otb::VCAImageFilter<DoubleVectorImageType> VCAFilterType;
-typedef otb::UnConstrainedLeastSquareImageFilter<DoubleVectorImageType, DoubleVectorImageType, double> UCLSUnmixingFilterType;
-typedef otb::ISRAUnmixingImageFilter<DoubleVectorImageType, DoubleVectorImageType, double> ISRAUnmixingFilterType;
-typedef otb::NCLSUnmixingImageFilter<DoubleVectorImageType, DoubleVectorImageType, double> NCLSUnmixingFilterType;
-typedef otb::FCLSUnmixingImageFilter<DoubleVectorImageType, DoubleVectorImageType, double> FCLSUnmixingFilterType;
+typedef otb::UnConstrainedLeastSquareImageFilter<DoubleVectorImageType,DoubleVectorImageType,double> UCLSUnmixingFilterType;
+typedef otb::ISRAUnmixingImageFilter<DoubleVectorImageType,DoubleVectorImageType,double> ISRAUnmixingFilterType;
+typedef otb::NCLSUnmixingImageFilter<DoubleVectorImageType,DoubleVectorImageType,double> NCLSUnmixingFilterType;
+typedef otb::FCLSUnmixingImageFilter<DoubleVectorImageType,DoubleVectorImageType,double> FCLSUnmixingFilterType;
typedef otb::VectorImageToMatrixImageFilter<DoubleVectorImageType> VectorImageToMatrixImageFilterType;
@@ -72,14 +72,13 @@ enum EndmembersEstimationMethod
enum UnMixingMethod
{
- UnMixingMethod_NONE,
UnMixingMethod_UCLS,
UnMixingMethod_ISRA,
UnMixingMethod_NCLS,
UnMixingMethod_FCLS,
};
-const char* UnMixingMethodNames [] = { "NONE", "UCLS", "ISRA", "NCLS", "FCLS", };
+const char* UnMixingMethodNames [] = { "UCLS", "ISRA", "NCLS", "FCLS", };
class HyperspectralUnmixing : public Application
@@ -104,13 +103,12 @@ private:
SetDescription("Unmix an hyperspectral image");
// Documentation
- SetDocName("Hyper spectral unmixing application");
- SetDocLongDescription("This application \"unmix\" an hyperspectral image.");
+ SetDocName("Hyperspectral data unmixing");
+ SetDocLongDescription("Applies an unmixing algorithm to an hyperspectral data cube");
SetDocLimitations("None");
SetDocAuthors("OTB-Team");
SetDocSeeAlso(" ");
- SetDocCLExample(" ");
- AddDocTag("Image manipulation");
+ SetDocCLExample("otbApplicationLauncherCommandLine VertexComponentAnalysis ${OTB-BIN}/bin --in ${INPUTDATA}/Hyperspectral/synthetic/hsi_cube.tif --ie ${INPUTDATA}/Hyperspectral/synthetic/endmembers.tif --out ${TEMP}/apTvHyHyperspectralUnmixing_UCLS.tif double --ua ucls");
AddDocTag("Hyperspectral");
}
@@ -121,45 +119,31 @@ private:
void DoCreateParameters()
{
AddParameter(ParameterType_InputImage, "in", "Input Image");
- AddParameter(ParameterType_OutputImage, "out", "Output Image");
- MandatoryOff("out");
-
- AddParameter(ParameterType_Choice, "dr", "Dimension reduction");
- AddChoice("dr.pca", "PCA");
- AddChoice("dr.mnf", "MNF");
- AddChoice("dr.napca", "NAPCA");
- MandatoryOff("dr");
-
- AddParameter(ParameterType_Int, "ne", "Number of endmembers");
- SetDefaultParameterInt("ne", 1);
- MandatoryOff("ne");
-
- AddParameter(ParameterType_Choice, "de", "Dimensionnality estimation");
- MandatoryOff("de");
- AddChoice("de.elm", "ELM (Eigen Value Likelihood Estimation)");
+ SetParameterDescription("in","The hyperspectral data cube to unmix");
- AddParameter(ParameterType_Choice, "ee", "Endmembers estimation method");
- MandatoryOff("ee");
- AddChoice("ee.vca", "VCA (Vertex Component Analysis)");
+ AddParameter(ParameterType_OutputImage, "out", "Output Image");
+ SetParameterDescription("out","The output abundance map");
- AddParameter(ParameterType_InputImage, "ie", "Input endmembers image");
- MandatoryOff("ie");
+ AddParameter(ParameterType_InputImage, "ie", "Input endmembers");
+ SetParameterDescription("ie","The endmembers to use for unmixing. Must be stored as a multispectral image, where each pixel is interpreted as an endmember");
AddParameter(ParameterType_Choice, "ua", "Unmixing algorithm");
+ SetParameterDescription("ua", "The algorithm to use for unmixing");
MandatoryOff("ua");
- AddChoice("ua.none", "None");
AddChoice("ua.ucls", "UCLS");
+ SetParameterDescription("ua.ucls", "Unconstrained Least Square");
+
AddChoice("ua.isra", "ISRA");
+ SetParameterDescription("ua.isra", "Image Space Reconstruction Algorithm");
+
AddChoice("ua.ncls", "NCLS");
+ SetParameterDescription("ua.ncls", "Non-negative constrained Least Square");
+
AddChoice("ua.fcls", "FCLS");
- //SetParameterString("ua", "none");
+ SetParameterDescription("ua.fcls", "Fully constrained Least Square");
- AddParameter(ParameterType_OutputImage, "oe", "Output Endmembers");
- MandatoryOff("oe");
+ SetParameterString("ua", "ucls");
- AddParameter(ParameterType_RAM, "ram", "Available RAM");
- SetDefaultParameterInt("ram", 256);
- MandatoryOff("ram");
}
void DoUpdateParameters()
@@ -171,177 +155,8 @@ private:
{
m_ProcessObjects.clear();
- /*
- *
- * EXTRACT PARAMETERS
- *
- */
- // Dimension Reduction
- DimReductionMethod dimReduction = DimReductionMethod_NONE;
- if ( IsParameterEnabled("dr") && HasValue("dr") )
- {
- std::string dimReductionStr = GetParameterString("dr");
- if ( boost::to_upper_copy(dimReductionStr) == "PCA" )
- {
- dimReduction = DimReductionMethod_PCA;
- }
- else if ( boost::to_upper_copy(dimReductionStr) == "MNF" )
- {
- dimReduction = DimReductionMethod_MNF;
- }
- }
- otbAppLogDEBUG(<< "Using "
- << (dimReduction == DimReductionMethod_NONE ? "NONE" : (dimReduction == DimReductionMethod_PCA ? "PCA" : "MNF") )
- << " dimensionality reduction method")
-
- // Number of endmembers
- unsigned int nbEndmembers = 0;
- if ( IsParameterEnabled("ne") && HasValue("ne") )
- {
- nbEndmembers = GetParameterInt("ne");
- otbAppLogDEBUG(<< "nbEndmembers: " << nbEndmembers)
- }
-
- // Dimensionnality estimation
- if ( IsParameterEnabled("de") && HasValue("de") )
- {
- std::string dimEstMethodStr = GetParameterString("de");
- if (boost::to_upper_copy(dimEstMethodStr) != "ELM")
- {
- std::cerr << "Only ELM is supported for parameter DimensionalityEstimationMethod" << std::endl;
- }
- otbAppLogDEBUG(<< "dimEstMethodStr: " << dimEstMethodStr)
-
- }
-
- if ( IsParameterEnabled("ee") && HasValue("ee") )
- {
- std::string eeEstMethodStr = GetParameterString("ee");
- if (boost::to_upper_copy(eeEstMethodStr) != "VCA")
- {
- std::cerr << "Only VCA is supported for parameter EndmembersEstimationMethod" << std::endl;
- }
- otbAppLogDEBUG(<< "eeEstMethodStr: " << eeEstMethodStr)
- }
-
- std::string inputEndmembers;
- if ( IsParameterEnabled("ie") && HasValue("ie") )
- {
- inputEndmembers = GetParameterString("ie");
- otbAppLogDEBUG("inputEndmembers: " << inputEndmembers)
- }
-
- UnMixingMethod unmixingAlgo = UnMixingMethod_NONE;
- if ( IsParameterEnabled("ua") && HasValue("ua") )
- {
- std::string unmixingAlgoStr = GetParameterString("ua");
-
- if ( boost::to_upper_copy(unmixingAlgoStr) == "UCLS" )
- {
- unmixingAlgo = UnMixingMethod_UCLS;
- }
- else if ( boost::to_upper_copy(unmixingAlgoStr) == "NCLS" )
- {
- unmixingAlgo = UnMixingMethod_NCLS;
- }
- else if ( boost::to_upper_copy(unmixingAlgoStr) == "FCLS" )
- {
- unmixingAlgo = UnMixingMethod_FCLS;
- }
- else if ( boost::to_upper_copy(unmixingAlgoStr) == "ISRA" )
- {
- unmixingAlgo = UnMixingMethod_ISRA;
- }
- }
- otbAppLogDEBUG( << "Using "
- << UnMixingMethodNames[unmixingAlgo]
- << " unmixing algorithm")
-
- std::string outputEndmembers;
- if ( IsParameterEnabled("oe") && HasValue("oe") && inputEndmembers.empty() )
- {
- outputEndmembers = GetParameterString("oe");
- }
- otbAppLogDEBUG( << "IsParameterEnabled(oe) " << IsParameterEnabled("oe") )
- otbAppLogDEBUG( << "HasValue(oe) " << HasValue("oe") )
- otbAppLogDEBUG( << "inputEndmembers.empty() " << inputEndmembers.empty() )
- otbAppLogDEBUG( << "outputEndmembers: " << outputEndmembers )
-
-
- /*
- *
- * PROCESSING
- *
- */
-
DoubleVectorImageType::Pointer inputImage = GetParameterImage<DoubleVectorImageType>("in");
-
- DoubleVectorImageType::Pointer endmembersImage;
- if ( inputEndmembers.empty() )
- {
- if( nbEndmembers == 0 )
- {
- /*
- * Compute stats of input image
- */
-
- std::cout << "Computing stats" << std::endl;
-
- StreamingStatisticsVectorImageFilterType::Pointer stats = StreamingStatisticsVectorImageFilterType::New();
-
- stats->SetInput(inputImage);
- otb::StandardWriterWatcher watcher(stats->GetStreamer(), stats->GetFilter(), "Computing image stats");
- stats->Update();
-
- VectorType mean (stats->GetMean().GetDataPointer(), stats->GetMean().GetSize());
- MatrixType covariance = stats->GetCovariance().GetVnlMatrix();
- MatrixType correlation = stats->GetCorrelation().GetVnlMatrix();
-
- /*
- * Estimate Endmembers Numbers
- */
- std::cout << "Estimate Endmembers Numbers by ELM" << std::endl;
-
- ELMType::Pointer elm = ELMType::New();
- elm->SetCovariance(covariance);
- elm->SetCorrelation(correlation);
- elm->SetNumberOfPixels(inputImage->GetLargestPossibleRegion().GetNumberOfPixels());
- elm->Compute();
-
- nbEndmembers = elm->GetNumberOfEndmembers();
-
- std::cout << "ELM : " << nbEndmembers << " estimated endmembers" << std::endl;
-
- std::cout << "ELM likelihood values: " << elm->GetLikelihood() << std::endl;
-
- }
- else
- {
- std::cout << "Using " << nbEndmembers << " endmembers" << std::endl;
- }
-
- /*
- * Estimate Endmembers
- */
- std::cout << "Estimate Endmembers by VCA" << std::endl;
-
- VCAFilterType::Pointer vca = VCAFilterType::New();
- vca->SetNumberOfEndmembers(nbEndmembers);
- vca->SetInput(inputImage);
-
- endmembersImage = vca->GetOutput();
- m_ProcessObjects.push_back(vca.GetPointer());
- }
- else
- {
- /*
- * Read input endmembers
- */
- std::cout << "Read Endmembers " << inputEndmembers << std::endl;
- endmembersImage = GetParameterImage<DoubleVectorImageType>("ie");
-
- }
- // endmembersRef->Update();
+ DoubleVectorImageType::Pointer endmembersImage = GetParameterImage<DoubleVectorImageType>("ie");
/*
* Transform Endmembers image to matrix representation
@@ -359,10 +174,9 @@ private:
* Unmix
*/
DoubleVectorImageType::Pointer abundanceMap;
- switch (unmixingAlgo)
+
+ switch ( static_cast<UnMixingMethod>(GetParameterInt("ua")) )
{
- case UnMixingMethod_NONE:
- break;
case UnMixingMethod_UCLS:
{
std::cout << "UCLS Unmixing" << std::endl;
@@ -425,25 +239,8 @@ private:
break;
}
- if ( !outputEndmembers.empty() )
- {
- /*
- * Write endmembers
- */
- std::cout << "Write endmembers " << outputEndmembers << std::endl;
-
- SetParameterOutputImage<DoubleVectorImageType>("oe", endmembersImage);
- }
+ SetParameterOutputImage<DoubleVectorImageType>("out", abundanceMap);
- if ( unmixingAlgo != UnMixingMethod_NONE )
- {
- /*
- * Write abundance map
- */
- //std::cout << "Write abundance map" << outputImageName << std::endl;
-
- SetParameterOutputImage<DoubleVectorImageType>("out", abundanceMap);
- }
}
std::vector<itk::ProcessObject::Pointer> m_ProcessObjects;
diff --git a/Applications/Hyperspectral/otbVertexComponentAnalysis.cxx b/Applications/Hyperspectral/otbVertexComponentAnalysis.cxx
new file mode 100644
index 0000000000..a8e24171b6
--- /dev/null
+++ b/Applications/Hyperspectral/otbVertexComponentAnalysis.cxx
@@ -0,0 +1,123 @@
+/*=========================================================================
+
+ 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 <boost/algorithm/string.hpp>
+
+#include "otbStreamingStatisticsVectorImageFilter.h"
+#include "otbEigenvalueLikelihoodMaximisation.h"
+#include "otbVcaImageFilter.h"
+#include "otbUnConstrainedLeastSquareImageFilter.h"
+#include "otbISRAUnmixingImageFilter.h"
+#include "otbNCLSUnmixingImageFilter.h"
+#include "otbFCLSUnmixingImageFilter.h"
+
+#include "otbVectorImageToMatrixImageFilter.h"
+
+
+namespace otb
+{
+namespace Wrapper
+{
+
+const unsigned int Dimension = 2;
+
+typedef otb::VCAImageFilter<DoubleVectorImageType> VCAFilterType;
+typedef otb::VectorImageToMatrixImageFilter<DoubleVectorImageType> VectorImageToMatrixImageFilterType;
+
+
+class VertexComponentAnalysis : public Application
+{
+public:
+ /** Standard class typedefs. */
+ typedef VertexComponentAnalysis Self;
+ typedef Application Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Standard macro */
+ itkNewMacro(Self);
+
+ itkTypeMacro(VertexComponentAnalysis, otb::Application);
+
+private:
+
+ VertexComponentAnalysis()
+ {
+ SetName("VertexComponentAnalysis");
+ SetDescription("Find endmembers in hyperspectral images with Vertex Component Analysis");
+
+ // Documentation
+ SetDocName("Vertex Component Analysis");
+ SetDocLongDescription("Applies the Vertex Component Analysis to an hyperspectral image to extract endmembers");
+ SetDocLimitations("None");
+ SetDocAuthors("OTB-Team");
+ SetDocSeeAlso(" ");
+ SetDocCLExample("otbApplicationLauncherCommandLine VertexComponentAnalysis ${OTB-BIN}/bin --in ${OTB_DATA_ROOT}/Input/Hyperspectral/synthetic/hsi_cube.tif --ne 5 --outendm ${TEMP}/apTvHyHyperspectralUnmixing_VCA.tif double");
+ AddDocTag("Hyperspectral");
+
+ }
+
+ virtual ~VertexComponentAnalysis()
+ {
+ }
+
+ void DoCreateParameters()
+ {
+ AddParameter(ParameterType_InputImage, "in", "Input Image");
+ SetParameterDescription("out","Input hyperspectral data cube");
+
+ AddParameter(ParameterType_Int, "ne", "Number of endmembers");
+ SetParameterDescription("ne","The number of endmembers to extract from the data cube");
+ SetParameterInt("ne", 1);
+ MandatoryOn("ne");
+
+ AddParameter(ParameterType_OutputImage, "outendm", "Output Endmembers");
+ SetParameterDescription("outendm","The endmebers, stored in a one-line multi-spectral image, each pixel representing an endmember");
+ MandatoryOn("outendm");
+ }
+
+ void DoUpdateParameters()
+ {
+ // Nothing to do here : all parameters are independent
+ }
+
+ void DoExecute()
+ {
+ DoubleVectorImageType::Pointer inputImage = GetParameterImage<DoubleVectorImageType>("in");
+ DoubleVectorImageType::Pointer endmembersImage;
+
+ const unsigned int nbEndmembers = GetParameterInt("ne");
+ VCAFilterType::Pointer vca = VCAFilterType::New();
+ vca->SetNumberOfEndmembers(nbEndmembers);
+ vca->SetInput(inputImage);
+
+ endmembersImage = vca->GetOutput();
+ m_Ref = vca.GetPointer();
+
+ SetParameterOutputImage<DoubleVectorImageType>("outendm", endmembersImage);
+ }
+
+ itk::LightObject::Pointer m_Ref;
+};
+
+}
+}
+
+OTB_APPLICATION_EXPORT(otb::Wrapper::VertexComponentAnalysis)
diff --git a/Testing/Applications/Hyperspectral/CMakeLists.txt b/Testing/Applications/Hyperspectral/CMakeLists.txt
index cdb0d3c0a2..5893421db1 100644
--- a/Testing/Applications/Hyperspectral/CMakeLists.txt
+++ b/Testing/Applications/Hyperspectral/CMakeLists.txt
@@ -52,37 +52,18 @@ add_test(NAME apTvHyHyperspectralUnmixing_FCLS
--ie ${INPUTDATA}/Hyperspectral/synthetic/endmembers.tif
--out ${TEMP}/apTvHyHyperspectralUnmixing_FCLS.tif double
--ua fcls )
-
-add_test(NAME apTvHyHyperspectralUnmixing_VCA
- COMMAND otbTestDriver
- --compare-image ${EPSILON_9}
- ${BASELINE}/apTvHyHyperspectralUnmixing_VCA.tif
- ${TEMP}/apTvHyHyperspectralUnmixing_VCA.tif
- Execute $<TARGET_FILE:otbApplicationLauncherCommandLine>
- HyperspectralUnmixing
- $<TARGET_FILE_DIR:otbapp_HyperspectralUnmixing>
- --in ${INPUTDATA}/Hyperspectral/synthetic/hsi_cube.tif
- --ne 5
- --oe ${TEMP}/apTvHyHyperspectralUnmixing_VCA.tif double )
-add_test(NAME apTvHyHyperspectralUnmixing_VCA_UCLS
- COMMAND otbTestDriver
- Execute $<TARGET_FILE:otbApplicationLauncherCommandLine>
- HyperspectralUnmixing
- $<TARGET_FILE_DIR:otbapp_HyperspectralUnmixing>
- --in ${OTB_DATA_ROOT}/Input/Hyperspectral/synthetic/hsi_cube.tif
- --out ${TEMP}/apTvHyHyperspectralUnmixing_ucls.tif double
- --ne 5
- --ua ucls )
+#--- VertexComponentAnalysis ---#
-add_test(NAME apTvHyHyperspectralUnmixing_VCA_FCLS
+add_test(NAME apTvHyVertexComponentAnalysis
COMMAND otbTestDriver
Execute $<TARGET_FILE:otbApplicationLauncherCommandLine>
- HyperspectralUnmixing
- $<TARGET_FILE_DIR:otbapp_HyperspectralUnmixing>
+ VertexComponentAnalysis
+ $<TARGET_FILE_DIR:otbapp_VertexComponentAnalysis>
--in ${OTB_DATA_ROOT}/Input/Hyperspectral/synthetic/hsi_cube.tif
- --out ${TEMP}/apTvHyHyperspectralUnmixing_fcls.tif double
--ne 5
- --ua fcls )
+ --outendm ${TEMP}/apTvHyHyperspectralUnmixing_VCA.tif double )
+
+
-
\ No newline at end of file
+
--
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