Initial commit

.gitignore

+# Compiled python source #
+*.pyc

CMakeLists.txt

+project(OTBTensorflow)
+
+# Use Tensorflow, or not
+option(OTB_USE_TENSORFLOW "Enable Tensorflow dependent applications" OFF)
+
+if(OTB_USE_TENSORFLOW)
+  message("Tensorflow support enabled")
+
+  # find Tensorflow INCLUDE DIR
+  set(tensorflow_include_dir "" CACHE PATH "The include directory of tensorflow")
+  include_directories(${tensorflow_include_dir})
+
+  # find Tensorflow LIBRARIES
+  find_library(TENSORFLOW_CC_LIB NAMES libtensorflow_cc)
+  find_library(TENSORFLOW_FRAMEWORK_LIB NAMES libtensorflow_framework)
+
+  set(OTBTensorflow_SYSTEM_INCLUDE_DIRS ${tensorflow_include_dir})
+  set(OTBTensorflow_LIBRARIES ${TENSORFLOW_CC_LIB} ${TENSORFLOW_FRAMEWORK_LIB})
+
+else()
+  message("Tensorflow support disabled")
+endif()
+
+otb_module_impl()

LICENSE

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app/CMakeLists.txt

+if(OTB_USE_TENSORFLOW)
+  # Tensorflow-dependent APPS
+  OTB_CREATE_APPLICATION(NAME TensorflowModelServe
+	SOURCES otbTensorflowModelServe.cxx ${${otb-module}_SYSTEM_INCLUDE_DIRS}
+	LINK_LIBRARIES ${${otb-module}_LIBRARIES}
+  )
+
+  OTB_CREATE_APPLICATION(NAME TensorflowModelTrain
+	SOURCES otbTensorflowModelTrain.cxx ${${otb-module}_SYSTEM_INCLUDE_DIRS}
+	LINK_LIBRARIES ${${otb-module}_LIBRARIES}
+  )
+
+  OTB_CREATE_APPLICATION(NAME TrainClassifierFromDeepFeatures
+	SOURCES otbTrainClassifierFromDeepFeatures.cxx ${${otb-module}_SYSTEM_INCLUDE_DIRS}
+	LINK_LIBRARIES ${${otb-module}_LIBRARIES}
+  )
+  
+  OTB_CREATE_APPLICATION(NAME ImageClassifierFromDeepFeatures
+	SOURCES otbImageClassifierFromDeepFeatures.cxx ${${otb-module}_SYSTEM_INCLUDE_DIRS}
+	LINK_LIBRARIES ${${otb-module}_LIBRARIES}
+  )
+endif()
+
+# Tensorflow-independent APPS
+OTB_CREATE_APPLICATION(NAME PatchesExtraction
+	SOURCES otbPatchesExtraction.cxx
+	LINK_LIBRARIES ${OTBCOMMON_LIBRARIES}
+)
+OTB_CREATE_APPLICATION(NAME LabelImageSampleSelection
+	SOURCES otbLabelImageSampleSelection.cxx
+	LINK_LIBRARIES ${OTBCOMMON_LIBRARIES}
+)

app/otbDensePolygonClassStatistics.cxx

+/*=========================================================================
+
+  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 "otbWrapperApplication.h"
+#include "otbWrapperApplicationFactory.h"
+
+#include "otbStatisticsXMLFileWriter.h"
+#include "otbWrapperElevationParametersHandler.h"
+
+#include "otbVectorDataToLabelImageFilter.h"
+#include "otbImageToNoDataMaskFilter.h"
+#include "otbStreamingStatisticsMapFromLabelImageFilter.h"
+#include "otbVectorDataIntoImageProjectionFilter.h"
+#include "otbImageToVectorImageCastFilter.h"
+
+#include "otbOGR.h"
+
+namespace otb
+{
+namespace Wrapper
+{
+/** Utility function to negate std::isalnum */
+bool IsNotAlphaNum(char c)
+  {
+  return !std::isalnum(c);
+  }
+
+class DensePolygonClassStatistics : public Application
+{
+public:
+  /** Standard class typedefs. */
+  typedef DensePolygonClassStatistics        Self;
+  typedef Application                   Superclass;
+  typedef itk::SmartPointer<Self>       Pointer;
+  typedef itk::SmartPointer<const Self> ConstPointer;
+
+  /** Standard macro */
+  itkNewMacro(Self);
+
+  itkTypeMacro(DensePolygonClassStatistics, otb::Application);
+
+  /** DataObjects typedef */
+  typedef UInt32ImageType                           LabelImageType;
+  typedef UInt8ImageType                            MaskImageType;
+  typedef VectorData<>                              VectorDataType;
+
+  /** ProcessObjects typedef */
+  typedef otb::VectorDataIntoImageProjectionFilter<VectorDataType,
+      FloatVectorImageType>                                                       VectorDataReprojFilterType;
+
+  typedef otb::VectorDataToLabelImageFilter<VectorDataType, LabelImageType>       RasterizeFilterType;
+
+  typedef otb::VectorImage<MaskImageType::PixelType>                              InternalMaskImageType;
+  typedef otb::ImageToNoDataMaskFilter<FloatVectorImageType, MaskImageType>       NoDataMaskFilterType;
+  typedef otb::ImageToVectorImageCastFilter<MaskImageType, InternalMaskImageType> CastFilterType;
+
+  typedef otb::StreamingStatisticsMapFromLabelImageFilter<InternalMaskImageType,
+      LabelImageType>                                                             StatsFilterType;
+
+  typedef otb::StatisticsXMLFileWriter<FloatVectorImageType::PixelType>           StatWriterType;
+
+
+private:
+  DensePolygonClassStatistics()
+    {
+   
+    }
+
+  void DoInit() override
+  {
+    SetName("DensePolygonClassStatistics");
+    SetDescription("Computes statistics on a training polygon set.");
+
+    // Documentation
+    SetDocName("Fast Polygon Class Statistics");
+    SetDocLongDescription("The application processes a dense set of polygons "
+      "intended for training (they should have a field giving the associated "
+      "class). The geometries are analyzed against a support image to compute "
+      "statistics : \n"
+      "  - number of samples per class\n"
+      "  - number of samples per geometry\n");
+    SetDocLimitations("None");
+    SetDocAuthors("Remi Cresson");
+    SetDocSeeAlso(" ");
+
+    AddDocTag(Tags::Learning);
+
+    AddParameter(ParameterType_InputImage,  "in",   "Input image");
+    SetParameterDescription("in", "Support image that will be classified");
+    
+    AddParameter(ParameterType_InputVectorData, "vec", "Input vectors");
+    SetParameterDescription("vec","Input geometries to analyze");
+    
+    AddParameter(ParameterType_OutputFilename, "out", "Output XML statistics file");
+    SetParameterDescription("out","Output file to store statistics (XML format)");
+
+    AddParameter(ParameterType_ListView, "field", "Field Name");
+    SetParameterDescription("field","Name of the field carrying the class number in the input vectors.");
+    SetListViewSingleSelectionMode("field",true);
+
+    ElevationParametersHandler::AddElevationParameters(this, "elev");
+
+    AddRAMParameter();
+
+    // Doc example parameter settings
+    SetDocExampleParameterValue("in", "support_image.tif");
+    SetDocExampleParameterValue("vec", "variousVectors.shp");
+    SetDocExampleParameterValue("field", "label");
+    SetDocExampleParameterValue("out","polygonStat.xml");
+
+    SetOfficialDocLink();
+  }
+
+  void DoUpdateParameters() override
+  {
+     if ( HasValue("vec") )
+      {
+      std::string vectorFile = GetParameterString("vec");
+      ogr::DataSource::Pointer ogrDS =
+        ogr::DataSource::New(vectorFile, ogr::DataSource::Modes::Read);
+      ogr::Layer layer = ogrDS->GetLayer(0);
+      ogr::Feature feature = layer.ogr().GetNextFeature();
+
+      ClearChoices("field");
+      
+      for(int iField=0; iField<feature.ogr().GetFieldCount(); iField++)
+        {
+        std::string key, item = feature.ogr().GetFieldDefnRef(iField)->GetNameRef();
+        key = item;
+        std::string::iterator end = std::remove_if(key.begin(),key.end(),IsNotAlphaNum);
+        std::transform(key.begin(), end, key.begin(), tolower);
+        
+        OGRFieldType fieldType = feature.ogr().GetFieldDefnRef(iField)->GetType();
+        
+        if(fieldType == OFTString || fieldType == OFTInteger || ogr::version_proxy::IsOFTInteger64(fieldType))
+          {
+          std::string tmpKey="field."+key.substr(0, end - key.begin());
+          AddChoice(tmpKey,item);
+          }
+        }
+      }
+
+     // Check that the extension of the output parameter is XML (mandatory for
+     // StatisticsXMLFileWriter)
+     // Check it here to trigger the error before polygons analysis
+     
+     if ( HasValue("out") )
+       {
+       // Store filename extension
+       // Check that the right extension is given : expected .xml
+       const std::string extension = itksys::SystemTools::GetFilenameLastExtension(this->GetParameterString("out"));
+
+       if (itksys::SystemTools::LowerCase(extension) != ".xml")
+         {
+         otbAppLogFATAL( << extension << " is a wrong extension for parameter \"out\": Expected .xml" );
+         }
+       }
+  }
+
+  void DoExecute() override
+  {
+
+  // Filters
+  VectorDataReprojFilterType::Pointer m_VectorDataReprojectionFilter;
+  RasterizeFilterType::Pointer m_RasterizeFIDFilter;
+  RasterizeFilterType::Pointer m_RasterizeClassFilter;
+  NoDataMaskFilterType::Pointer m_NoDataFilter;
+  CastFilterType::Pointer m_NoDataCastFilter;
+  StatsFilterType::Pointer m_FIDStatsFilter;
+  StatsFilterType::Pointer m_ClassStatsFilter;
+
+  // Retrieve the field name
+  std::vector<int> selectedCFieldIdx = GetSelectedItems("field");
+
+  if(selectedCFieldIdx.empty())
+    {
+    otbAppLogFATAL(<<"No field has been selected for data labelling!");
+    }
+
+  std::vector<std::string> cFieldNames = GetChoiceNames("field");  
+  std::string fieldName = cFieldNames[selectedCFieldIdx.front()];
+
+  otb::Wrapper::ElevationParametersHandler::SetupDEMHandlerFromElevationParameters(this,"elev");
+
+  // Get inputs
+  FloatVectorImageType::Pointer xs = GetParameterImage("in");
+  VectorDataType* shp = GetParameterVectorData("vec");
+
+  // Reproject vector data
+  m_VectorDataReprojectionFilter = VectorDataReprojFilterType::New();
+  m_VectorDataReprojectionFilter->SetInputVectorData(shp);
+  m_VectorDataReprojectionFilter->SetInputImage(xs);
+  m_VectorDataReprojectionFilter->Update();
+
+  // Internal no-data value
+  const LabelImageType::ValueType intNoData =
+      itk::NumericTraits<LabelImageType::ValueType>::max();
+
+  // Rasterize vector data (geometry ID)
+  m_RasterizeFIDFilter = RasterizeFilterType::New();
+  m_RasterizeFIDFilter->AddVectorData(m_VectorDataReprojectionFilter->GetOutput());
+  m_RasterizeFIDFilter->SetOutputOrigin(xs->GetOrigin());
+  m_RasterizeFIDFilter->SetOutputSpacing(xs->GetSignedSpacing());
+  m_RasterizeFIDFilter->SetOutputSize(xs->GetLargestPossibleRegion().GetSize());
+  m_RasterizeFIDFilter->SetBurnAttribute("________"); // Trick to get the polygon ID
+  m_RasterizeFIDFilter->SetGlobalWarningDisplay(false);
+  m_RasterizeFIDFilter->SetOutputProjectionRef(xs->GetProjectionRef());
+  m_RasterizeFIDFilter->SetBackgroundValue(intNoData);
+  m_RasterizeFIDFilter->SetDefaultBurnValue(0);
+
+  // Rasterize vector data (geometry class)
+  m_RasterizeClassFilter = RasterizeFilterType::New();
+  m_RasterizeClassFilter->AddVectorData(m_VectorDataReprojectionFilter->GetOutput());
+  m_RasterizeClassFilter->SetOutputOrigin(xs->GetOrigin());
+  m_RasterizeClassFilter->SetOutputSpacing(xs->GetSignedSpacing());
+  m_RasterizeClassFilter->SetOutputSize(xs->GetLargestPossibleRegion().GetSize());
+  m_RasterizeClassFilter->SetBurnAttribute(fieldName);
+  m_RasterizeClassFilter->SetOutputProjectionRef(xs->GetProjectionRef());
+  m_RasterizeClassFilter->SetBackgroundValue(intNoData);
+  m_RasterizeClassFilter->SetDefaultBurnValue(0);
+
+  // No data mask
+  m_NoDataFilter = NoDataMaskFilterType::New();
+  m_NoDataFilter->SetInput(xs);
+  m_NoDataCastFilter = CastFilterType::New();
+  m_NoDataCastFilter->SetInput(m_NoDataFilter->GetOutput());
+
+  // Stats (geometry ID)
+  m_FIDStatsFilter = StatsFilterType::New();
+  m_FIDStatsFilter->SetInput(m_NoDataCastFilter->GetOutput());
+  m_FIDStatsFilter->SetInputLabelImage(m_RasterizeFIDFilter->GetOutput());
+  m_FIDStatsFilter->GetStreamer()->SetAutomaticAdaptativeStreaming(GetParameterInt("ram"));
+  AddProcess(m_FIDStatsFilter->GetStreamer(), "Computing number of samples per vector");
+  m_FIDStatsFilter->Update();
+
+  // Stats (geometry class)
+  m_ClassStatsFilter = StatsFilterType::New();
+  m_ClassStatsFilter->SetInput(m_NoDataCastFilter->GetOutput());
+  m_ClassStatsFilter->SetInputLabelImage(m_RasterizeClassFilter->GetOutput());
+  m_ClassStatsFilter->GetStreamer()->SetAutomaticAdaptativeStreaming(GetParameterInt("ram"));
+  AddProcess(m_ClassStatsFilter->GetStreamer(), "Computing number of samples per class");
+  m_ClassStatsFilter->Update();
+
+  // Remove the no-data entries
+  StatsFilterType::LabelPopulationMapType fidMap = m_FIDStatsFilter->GetLabelPopulationMap();
+  StatsFilterType::LabelPopulationMapType classMap = m_ClassStatsFilter->GetLabelPopulationMap();
+  fidMap.erase(intNoData);
+  classMap.erase(intNoData);
+
+  StatWriterType::Pointer statWriter = StatWriterType::New();
+  statWriter->SetFileName(this->GetParameterString("out"));
+  statWriter->AddInputMap<StatsFilterType::LabelPopulationMapType>("samplesPerClass",classMap);
+  statWriter->AddInputMap<StatsFilterType::LabelPopulationMapType>("samplesPerVector",fidMap);
+  statWriter->Update();
+
+  }
+  
+
+};
+
+} // end of namespace Wrapper
+} // end of namespace otb
+
+OTB_APPLICATION_EXPORT(otb::Wrapper::DensePolygonClassStatistics)

app/otbImageClassifierFromDeepFeatures.cxx

+/*=========================================================================
+
+  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"
+#include "otbWrapperCompositeApplication.h"
+
+// Application engine
+#include "otbStandardFilterWatcher.h"
+#include "itkFixedArray.h"
+
+// TF (used to get the environment variable for the number of inputs)
+#include "otbTensorflowCommon.h"
+
+namespace otb
+{
+
+namespace Wrapper
+{
+
+class ImageClassifierFromDeepFeatures : public CompositeApplication
+{
+public:
+  /** Standard class typedefs. */
+  typedef ImageClassifierFromDeepFeatures              Self;
+  typedef Application                         Superclass;
+  typedef itk::SmartPointer<Self>             Pointer;
+  typedef itk::SmartPointer<const Self>       ConstPointer;
+
+  /** Standard macro */
+  itkNewMacro(Self);
+  itkTypeMacro(ImageClassifierFromDeepFeatures, otb::Wrapper::CompositeApplication);
+
+private:
+
+  //
+  // Add an input source, which includes:
+  // -an input image list
+  // -an input patchsize (dimensions of samples)
+  //
+  void AddAnInputImage(int inputNumber = 0)
+  {
+    inputNumber++;
+
+    // Create keys and descriptions
+    std::stringstream ss_key_group, ss_desc_group;
+    ss_key_group << "source" << inputNumber;
+    ss_desc_group << "Parameters for source " << inputNumber;
+
+    // Populate group
+    ShareParameter(ss_key_group.str(), "tfmodel." + ss_key_group.str(), ss_desc_group.str());
+
+  }
+
+
+  void DoInit()
+  {
+
+    SetName("ImageClassifierFromDeepFeatures");
+    SetDescription("Classify image using features from a deep net and an OTB machine learning classification model");
+
+    // Documentation
+    SetDocName("ImageClassifierFromDeepFeatures");
+    SetDocLongDescription("See ImageClassifier application");
+    SetDocLimitations("None");
+    SetDocAuthors("Remi Cresson");
+    SetDocSeeAlso(" ");
+
+    ClearApplications();
+
+    // Add applications
+    AddApplication("ImageClassifier",      "classif", "Images classifier"  );
+    AddApplication("TensorflowModelServe", "tfmodel", "Serve the TF model" );
+
+    // Model shared parameters