diff --git "a/SimpleExtractionTools/app/otbZonalStatistics_r\303\251mi.cxx" "b/SimpleExtractionTools/app/otbZonalStatistics_r\303\251mi.cxx"
deleted file mode 100644
index 0dfb49cfcb480002e3d045ecc264f78567baf8a6..0000000000000000000000000000000000000000
--- "a/SimpleExtractionTools/app/otbZonalStatistics_r\303\251mi.cxx"
+++ /dev/null
@@ -1,279 +0,0 @@
-/*=========================================================================
-
- Copyright (c) Remi Cresson (IRSTEA). All rights reserved.
-
-
- 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 "itkFixedArray.h"
-#include "itkObjectFactory.h"
-
-// Elevation handler
-#include "otbWrapperElevationParametersHandler.h"
-#include "otbWrapperApplicationFactory.h"
-
-// Application engine
-#include "otbStandardFilterWatcher.h"
-#include "itkFixedArray.h"
-
-// Filter
-#include "otbVectorDataToLabelImageFilter.h"
-#include "otbVectorDataIntoImageProjectionFilter.h"
-
-// Vnl vector
-#include "vnl/vnl_vector.h"
-
-// itk iterator
-#include "itkImageRegionConstIterator.h"
-
-#include <map>
-
-using namespace std;
-
-namespace otb {
-
-namespace Wrapper {
-
-class ZonalStatistics : public Application {
-
- public:
- /** Standard class typedefs. */
- typedef ZonalStatistics Self;
- typedef Application Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
-
- /* vector data filters */
- typedef size_t LabelValueType;
- typedef otb::Image<LabelValueType, 2> LabelImageType;
- typedef otb::VectorData<double, 2> VectorDataType;
-
- typedef otb::VectorDataIntoImageProjectionFilter<VectorDataType,
- FloatVectorImageType> VectorDataReprojFilterType;
-
- typedef otb::VectorDataToLabelImageFilter<VectorDataType,
- LabelImageType> RasterizeFilterType;
-
- typedef VectorDataType::DataTreeType DataTreeType;
- typedef itk::PreOrderTreeIterator<DataTreeType> TreeIteratorType;
- typedef VectorDataType::DataNodeType DataNodeType;
- typedef DataNodeType::PolygonListPointerType PolygonListPointerType;
-
- /** Statistics */
- typedef vnl_matrix<double> RealMatrix;
- typedef vnl_vector<LabelValueType> SizeVector;
-
- /** Image iterator */
- typedef itk::ImageRegionConstIterator<LabelImageType> LabelIteratorType;
- typedef itk::ImageRegionConstIterator<FloatVectorImageType> ImageIteratorType;
-
- /** Standard macro */
- itkNewMacro(Self);
- itkTypeMacro(ZonalStatistics, Application);
-
- VectorDataType::Pointer shp;
- VectorDataType::Pointer vdWithFid;
- VectorDataType::Pointer vdWithStats;
- VectorDataReprojFilterType::Pointer m_VectorDataReprojectionFilter;
- RasterizeFilterType::Pointer m_RasterizeFilter;
-
- void DoInit() {
-
- SetName("ZonalStatistics");
- SetDescription("Computes zonal statistics");
-
- // Documentation
- SetDocName("ZonalStatistics");
- SetDocLongDescription("This application zonal statistics");
- SetDocLimitations("None");
- SetDocAuthors("Remi Cresson");
-
- AddDocTag(Tags::Manip);
-
- // Inputs
- AddParameter(ParameterType_InputImage, "in", "Input Image");
- AddParameter(ParameterType_InputVectorData, "vec", "Input vector data");
-
- AddParameter(ParameterType_Int, "band", "Image band");
- // AddParameter(ParameterType_Int, "ram", "ram");
- AddParameter(ParameterType_StringList, "stats", "Computed statistics");
-
- // Output
- AddParameter(ParameterType_StringList, "out", "Output vector data");
-
- AddRAMParameter();
- }
-
- void DoUpdateParameters(){
- // Nothing to do here : all parameters are independent
- }
-
- void DoExecute(){
-
- // Get inputs
- FloatVectorImageType::Pointer img = GetParameterImage("in");
- VectorDataType* shp = GetParameterVectorData("vec");
-
- // Add a FID field
- LabelValueType internalFID = 1;
- const string internalFIDField = "__fid___";
- vdWithFid = VectorDataType::New();
- DataNodeType::Pointer root1 = vdWithFid->GetDataTree()->GetRoot()->Get();
- DataNodeType::Pointer document1 = DataNodeType::New();
- document1->SetNodeType(otb::DOCUMENT);
- vdWithFid->GetDataTree()->Add(document1, root1);
- DataNodeType::Pointer folder1 = DataNodeType::New();
- folder1->SetNodeType(otb::FOLDER);
- vdWithFid->GetDataTree()->Add(folder1, document1);
- vdWithFid->SetProjectionRef(shp->GetProjectionRef());
- TreeIteratorType itVector1(shp->GetDataTree());
- itVector1.GoToBegin();
-
- while (!itVector1.IsAtEnd()){
- if (!itVector1.Get()->IsRoot() && !itVector1.Get()->IsDocument() && !itVector1.Get()->IsFolder()){
- DataNodeType::Pointer currentGeometry = itVector1.Get();
- currentGeometry->SetFieldAsInt(internalFIDField, internalFID );
- vdWithFid->GetDataTree()->Add(currentGeometry, folder1);
- internalFID++;
- }
- ++itVector1;
- } // next feature
-
- // Rasterize vector data
- m_RasterizeFilter = RasterizeFilterType::New();
-
- m_RasterizeFilter->AddVectorData(vdWithFid);
- m_RasterizeFilter->SetOutputOrigin(img->GetOrigin());
- m_RasterizeFilter->SetOutputSpacing(img->GetSignedSpacing());
- m_RasterizeFilter->SetOutputSize(img->GetLargestPossibleRegion().GetSize());
- m_RasterizeFilter->SetOutputProjectionRef(img->GetProjectionRef());
- m_RasterizeFilter->SetBurnAttribute(internalFIDField);
- m_RasterizeFilter->UpdateOutputInformation();
-
- // Computing stats
- otbAppLogINFO("Computing stats");
-
- // Explicit streaming over the input target image, based on the RAM parameter
- typedef otb::RAMDrivenStrippedStreamingManager<FloatVectorImageType> StreamingManagerType;
- StreamingManagerType::Pointer m_StreamingManager = StreamingManagerType::New();
-
- m_StreamingManager->SetAvailableRAMInMB(GetParameterInt("ram"));
- m_StreamingManager->PrepareStreaming(img, img->GetLargestPossibleRegion() );
-
- // Init. stats containers
- const LabelValueType N = internalFID;
- const unsigned int nBands = 1;
-
- RealMatrix sum (nBands, N, 0);
- RealMatrix means (nBands, N, 0);
-
- SizeVector counts(N,0);
-
- if (m_RasterizeFilter->GetOutput()->GetLargestPossibleRegion().GetNumberOfPixels()
- != img->GetLargestPossibleRegion().GetNumberOfPixels() ){
- otbAppLogFATAL("Rasterized image and input image don't have the same number of pixels");
- }
-
- int m_NumberOfDivisions = m_StreamingManager->GetNumberOfSplits();
-
- std::map<int,std::map<int,int>> dico;
-
- const unsigned int band = GetParameterInt("band");
- for (int m_CurrentDivision = 0; m_CurrentDivision < m_NumberOfDivisions; m_CurrentDivision++){
-
- FloatVectorImageType::RegionType streamRegion = m_StreamingManager->GetSplit(m_CurrentDivision);
-
- img->SetRequestedRegion(streamRegion);
- img->PropagateRequestedRegion();
- img->UpdateOutputData();
-
- m_RasterizeFilter->GetOutput()->SetRequestedRegion(streamRegion);
- m_RasterizeFilter->GetOutput()->PropagateRequestedRegion();
- m_RasterizeFilter->GetOutput()->UpdateOutputData();
-
- LabelIteratorType it(m_RasterizeFilter->GetOutput(), streamRegion);
- ImageIteratorType it_in(img, streamRegion);
-
- for (it.GoToBegin(), it_in.GoToBegin(); !it.IsAtEnd(); ++it, ++it_in){
- const LabelValueType fid = it.Get();
- const FloatVectorImageType::PixelType pix = it_in.Get();
- const FloatVectorImageType::InternalPixelType val = pix[band];
-
- if ( dico[fid].find(val) == dico[fid].end() ) {
- dico[fid][val] = 1;
- } else {
- dico[fid][val]++;
- }
-
- sum[0][fid]+=val;
- counts[fid]++;
- } // next pixel
- }
-
- // Summarize stats
- otbAppLogINFO("Summarizing stats");
- for (LabelValueType fid = 0 ; fid < N ; fid++){
-
- const LabelValueType count = counts[fid];
-
- if (count>0){
- means[0][fid] = sum[0][fid] / static_cast<FloatVectorImageType::InternalPixelType>(count);
- }
- }
-
- std::vector<std::string> statistiques = GetParameterStringList("stats");
-
- std::vector<std::string> resultats;
- std::ostringstream ss;
-
- bool compute_mean = false;
-
- for (unsigned int i = 0; i < statistiques.size(); i++){
- if (statistiques.at(i) == ("mean")){
- compute_mean = true;
- }
- }
-
- resultats.reserve(N-1);
-
- if(compute_mean){
- for (LabelValueType fid = 1 ; fid < N ; fid++){
- ss << means[0][fid];
- resultats.push_back(ss.str());
- ss.str("");
- ss.clear();
- }
- }else{
-
- for (LabelValueType fid = 1 ; fid < N ; fid++){
-
- float Maj_count = 0.0;
- float Maj_count_perc = 0.0;
-
- for(auto t : dico[fid]){
- if((float(t.second)/float(counts[fid]))*100.0 > Maj_count_perc ){
- Maj_count = t.first;
- Maj_count_perc = (float(t.second)/float(counts[fid]))*100.0;
- }
- }
-
- ss << counts[fid] << " " << Maj_count << " " << Maj_count_perc;
- resultats.push_back(ss.str());
- ss.str("");
- ss.clear();
- }
- }
-
- SetParameterStringList("out", resultats);
-
- }
-
-};
-}
-}
-
-OTB_APPLICATION_EXPORT(otb::Wrapper::ZonalStatistics)
\ No newline at end of file
diff --git "a/SimpleExtractionTools/app/otbZonalStatistics_t\303\251moin.cxx" "b/SimpleExtractionTools/app/otbZonalStatistics_t\303\251moin.cxx"
deleted file mode 100644
index b72e48c331f35efd943eb1850e50920f6ad5ec01..0000000000000000000000000000000000000000
--- "a/SimpleExtractionTools/app/otbZonalStatistics_t\303\251moin.cxx"
+++ /dev/null
@@ -1,358 +0,0 @@
-/*=========================================================================
-
- Copyright (c) Remi Cresson (IRSTEA). All rights reserved.
-
-
- 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 "itkFixedArray.h"
-#include "itkObjectFactory.h"
-
-// Elevation handler
-#include "otbWrapperElevationParametersHandler.h"
-#include "otbWrapperApplicationFactory.h"
-
-// Application engine
-#include "otbStandardFilterWatcher.h"
-#include "itkFixedArray.h"
-
-// Filter
-#include "otbVectorDataToLabelImageFilter.h"
-#include "otbVectorDataIntoImageProjectionFilter.h"
-
-// Vnl vector
-#include "vnl/vnl_vector.h"
-
-// itk iterator
-#include "itkImageRegionConstIterator.h"
-
-#include <map>
-
-using namespace std;
-
-namespace otb {
-
-namespace Wrapper {
-
-class ZonalStatistics : public Application {
-
- public:
- /** Standard class typedefs. */
- typedef ZonalStatistics Self;
- typedef Application Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
-
- /* vector data filters */
- typedef size_t LabelValueType;
- typedef otb::Image<LabelValueType, 2> LabelImageType;
- typedef otb::VectorData<double, 2> VectorDataType;
-
- typedef otb::VectorDataToLabelImageFilter<VectorDataType,
- LabelImageType> RasterizeFilterType;
-
- typedef VectorDataType::DataTreeType DataTreeType;
- typedef itk::PreOrderTreeIterator<DataTreeType> TreeIteratorType;
- typedef VectorDataType::DataNodeType DataNodeType;
- typedef DataNodeType::PolygonListPointerType PolygonListPointerType;
-
- /** Statistics */
- typedef vnl_matrix<double> RealMatrix;
- typedef vnl_vector<LabelValueType> SizeVector;
-
- /** Image iterator */
- typedef itk::ImageRegionConstIterator<LabelImageType> LabelIteratorType;
- typedef itk::ImageRegionConstIterator<FloatVectorImageType> ImageIteratorType;
-
- /** Standard macro */
- itkNewMacro(Self);
- itkTypeMacro(ZonalStatistics, Application);
-
- VectorDataType::Pointer shp;
- VectorDataType::Pointer vdWithFid;
- VectorDataType::Pointer vdWithStats;
- RasterizeFilterType::Pointer m_RasterizeFilter;
-
- void DoInit() {
-
- SetName("ZonalStatistics");
- SetDescription("Computes zonal statistics");
-
- // Documentation
- SetDocName("ZonalStatistics");
- SetDocLongDescription("This application zonal statistics");
- SetDocLimitations("None");
- SetDocAuthors("Remi Cresson");
-
- AddDocTag(Tags::Manip);
-
- // Inputs
- AddParameter(ParameterType_InputImageList, "il", "Input List Images");
- AddParameter(ParameterType_InputVectorDataList, "vec", "Input List vector data");
- AddParameter(ParameterType_StringList, "stats", "Computed statistics");
-
- // Output
- AddParameter(ParameterType_StringList, "out", "Output vector data");
-
- AddRAMParameter();
- }
-
- void DoUpdateParameters(){
- // Nothing to do here : all parameters are independent
- }
-
- void ComputeMean(FloatVectorImageListType::Pointer listes_image, VectorDataListType::Pointer listes_vecteur){
-
- }
-
- void DoExecute(){
-
- // Get inputs
- FloatVectorImageListType::Pointer listes_image = GetParameterImageList("il");
- VectorDataListType::Pointer listes_vecteur = GetParameterVectorDataList("vec");
-
- ComputeMean(listes_image, listes_vecteur);
-
- std::map<int, int> liste_poly;
-
- /*
- Vecteur : vec_i
- Image : img_i
- Bande : band_b
- poly_p
- */
-
- std::map<int,std::map<int,RealMatrix>> dico_sum;
- std::map<int,std::map<int,RealMatrix>> dico_count;
-
- std::map<int, LabelValueType> liste_taille;
-
- for (unsigned int vec = 0; vec < listes_vecteur->Size(); vec++){
- VectorDataType::Pointer shp = listes_vecteur->GetNthElement(vec);
-
- // Add a FID field
- LabelValueType internalFID = 1;
-
- const string internalFIDField = "__fid___";
- vdWithFid = VectorDataType::New();
- DataNodeType::Pointer root1 = vdWithFid->GetDataTree()->GetRoot()->Get();
- DataNodeType::Pointer document1 = DataNodeType::New();
- document1->SetNodeType(otb::DOCUMENT);
- vdWithFid->GetDataTree()->Add(document1, root1);
- DataNodeType::Pointer folder1 = DataNodeType::New();
- folder1->SetNodeType(otb::FOLDER);
- vdWithFid->GetDataTree()->Add(folder1, document1);
- vdWithFid->SetProjectionRef(shp->GetProjectionRef());
- TreeIteratorType itVector1(shp->GetDataTree());
- itVector1.GoToBegin();
-
- while (!itVector1.IsAtEnd()){
- if (!itVector1.Get()->IsRoot() && !itVector1.Get()->IsDocument() && !itVector1.Get()->IsFolder()){
- DataNodeType::Pointer currentGeometry = itVector1.Get();
- currentGeometry->SetFieldAsInt(internalFIDField, internalFID );
- vdWithFid->GetDataTree()->Add(currentGeometry, folder1);
- internalFID++;
- }
- ++itVector1;
- } // next feature
-
- liste_poly[vec] = (internalFID - 1);
- liste_taille[vec] = internalFID;
-
- for (unsigned int img = 0; img < listes_image->Size(); img++){
- FloatVectorImageType::Pointer image = listes_image->GetNthElement(img);
-
- // Rasterize vector data
- m_RasterizeFilter = RasterizeFilterType::New();
-
- m_RasterizeFilter->AddVectorData(vdWithFid);
- m_RasterizeFilter->SetOutputOrigin(image->GetOrigin());
- m_RasterizeFilter->SetOutputSpacing(image->GetSignedSpacing());
- m_RasterizeFilter->SetOutputSize(image->GetLargestPossibleRegion().GetSize());
- m_RasterizeFilter->SetOutputProjectionRef(image->GetProjectionRef());
- m_RasterizeFilter->SetBurnAttribute(internalFIDField);
-
- m_RasterizeFilter->UpdateOutputInformation();
-
- // Computing stats
- otbAppLogINFO("Computing stats");
-
- // Explicit streaming over the input target image, based on the RAM parameter
- typedef otb::RAMDrivenStrippedStreamingManager<FloatVectorImageType> StreamingManagerType;
- StreamingManagerType::Pointer m_StreamingManager = StreamingManagerType::New();
-
- m_StreamingManager->SetAvailableRAMInMB(GetParameterInt("ram"));
- m_StreamingManager->PrepareStreaming(image, image->GetLargestPossibleRegion());
-
- // Init. stats containers
- const LabelValueType N = internalFID;
- const unsigned int nBands = image->GetNumberOfComponentsPerPixel();
-
- RealMatrix sum (nBands, N, 0);
- RealMatrix counts (nBands, N, 0);
-
- if (m_RasterizeFilter->GetOutput()->GetLargestPossibleRegion().GetNumberOfPixels()
- != image->GetLargestPossibleRegion().GetNumberOfPixels() ){
- otbAppLogFATAL("Rasterized image and input image don't have the same number of pixels");
- }
-
- int m_NumberOfDivisions = m_StreamingManager->GetNumberOfSplits();
-
- for (int m_CurrentDivision = 0; m_CurrentDivision < m_NumberOfDivisions; m_CurrentDivision++){
- FloatVectorImageType::RegionType streamRegion = m_StreamingManager->GetSplit(m_CurrentDivision);
-
- image->SetRequestedRegion(streamRegion);
- image->PropagateRequestedRegion();
- image->UpdateOutputData();
-
- m_RasterizeFilter->GetOutput()->SetRequestedRegion(streamRegion);
- m_RasterizeFilter->GetOutput()->PropagateRequestedRegion();
- m_RasterizeFilter->GetOutput()->UpdateOutputData();
-
- LabelIteratorType it(m_RasterizeFilter->GetOutput(), streamRegion);
- ImageIteratorType it_in(image, streamRegion);
-
- for (it.GoToBegin(), it_in.GoToBegin(); !it.IsAtEnd(); ++it, ++it_in){
- const LabelValueType fid = it.Get();
- const FloatVectorImageType::PixelType pix = it_in.Get();
-
- for (unsigned int band = 0 ; band < nBands ; band++){
-
- const FloatVectorImageType::InternalPixelType val = pix[band];
-
- // if ( dico[fid].find(val) == dico[fid].end() ) {
- // dico[fid][val] = 1;
- // } else {
- // dico[fid][val]++;
- // }
-
- sum[band][fid] += val;
- counts[band][fid]++;
- }
- } // next pixel
- }
-
- dico_sum[vec][img] = sum;
- dico_count[vec][img] = counts;
- }
- }
-
- // Summarize stats
- otbAppLogINFO("Summarizing stats");
-
- std::map<int,std::map<int,RealMatrix>> dico_mean;
-
- for (unsigned int vec = 0; vec < listes_vecteur->Size(); vec++){
-
- LabelValueType N = liste_taille[vec];
- for (unsigned int img = 0; img < listes_image->Size(); img++){
- RealMatrix means (listes_image->GetNthElement(img)->GetNumberOfComponentsPerPixel(), N, 0);
-
- for (unsigned int band = 0 ; band < listes_image->GetNthElement(img)->GetNumberOfComponentsPerPixel() ; band++){
-
- for (LabelValueType fid = 1 ; fid < N ; fid++){
- const LabelValueType count = dico_count[vec][img][band][fid];
- if (count>0){
- means[band][fid] = dico_sum[vec][img][band][fid] / static_cast<FloatVectorImageType::InternalPixelType>(count);
- }
- }
- }
- dico_mean[vec][img] = means;
- }
- }
-
- std::vector<std::string> statistiques = GetParameterStringList("stats");
-
- std::vector<std::string> resultats;
- std::ostringstream ss;
-
- bool compute_mean = false;
-
- for (unsigned int i = 0; i < statistiques.size(); i++){
- if (statistiques.at(i) == ("mean")){
- compute_mean = true;
- }
- }
-
- unsigned int taille = 0;
-
- for (unsigned int t = 0; t < listes_image->Size(); t++){
- taille += listes_image->GetNthElement(t)->GetNumberOfComponentsPerPixel();
- }
-
- int nombre_poly = 0;
-
- for (unsigned int p = 0; p < liste_poly.size(); p++){
- nombre_poly += liste_poly[p];
- }
-
- // std::cout << nombre_poly << std::endl;
- // std::cout << taille << std::endl;
- // std::cout << nombre_poly*taille << std::endl;
-
- resultats.reserve(taille);
-
- std::string separator = ";" ;
-
- if(compute_mean){
- std::cout << "Compute mean" << std::endl;
-
- for (unsigned int vec = 0; vec < dico_mean.size(); vec++){
-
- LabelValueType N = liste_taille[vec];
- for (unsigned int img = 0; img < dico_mean[vec].size(); img++){
- for (unsigned int band = 0; band < listes_image->GetNthElement(img)->GetNumberOfComponentsPerPixel(); band++){
- for (unsigned int poly = 1; poly < N ; poly++){
- // std::cout << dico_mean[img][vec][band][poly] << " ";
- ss << dico_mean[vec][img][band][poly] << " ";
- }
- ss << separator ;
- }
- // std::cout << ";" << std::endl;
- resultats.push_back(ss.str());
- ss.str("");
- ss.clear();
- }
- }
- // for (LabelValueType fid = 1 ; fid < N ; fid++){
- // ss << means[0][fid];
- // resultats.push_back(ss.str());
- // ss.str("");
- // ss.clear();
- // }
- } //else{
-
- // for (LabelValueType fid = 1 ; fid < N ; fid++){
-
- // float percent = 0.0;
- // float Maj_count = 0.0;
- // float Maj_count_perc = 0.0;
-
- // for(auto t : dico[fid]){
- // if((float(t.second)/float(counts[fid]))*100.0 > percent ){
- // Maj_count = t.first;
- // Maj_count_perc = (float(t.second)/float(counts[fid]))*100.0;
- // percent = Maj_count_perc;
- // }
- // }
-
- // ss << counts[fid] << " " << Maj_count << " " << Maj_count_perc;
- // resultats.push_back(ss.str());
- // ss.str("");
- // ss.clear();
- // }
- // }
-
- SetParameterStringList("out", resultats);
-
- }
-
-};
-}
-}
-
-OTB_APPLICATION_EXPORT(otb::Wrapper::ZonalStatistics)
\ No newline at end of file