Merge branch 'develop' of gitlab-ssh.irstea.fr:remi.cresson/otbtf

app/CMakeLists.txt

@@ -22,6 +22,10 @@ if(OTB_USE_TENSORFLOW)
 endif()
 
 # Tensorflow-independent APPS
+OTB_CREATE_APPLICATION(NAME PatchesSelection
+	SOURCES otbPatchesSelection.cxx
+	LINK_LIBRARIES ${${otb-module}_LIBRARIES}
+)
 OTB_CREATE_APPLICATION(NAME PatchesExtraction
 	SOURCES otbPatchesExtraction.cxx
 	LINK_LIBRARIES ${${otb-module}_LIBRARIES}

app/otbPatchesExtraction.cxx

@@ -163,6 +163,12 @@ public:
     // Input vector data
     AddParameter(ParameterType_InputVectorData, "vec", "Positions of the samples (must be in the same projection as input image)");
 
+    // No data parameters
+    AddParameter(ParameterType_Bool, "usenodata", "Reject samples that have no-data value");
+    MandatoryOff                    ("usenodata");
+    AddParameter(ParameterType_Float, "nodataval", "No data value (used only if \"usenodata\" is on)");
+    SetDefaultParameterFloat(         "nodataval", 0.0);
+
     // Output label
     AddParameter(ParameterType_OutputImage, "outlabels", "output labels");
     SetDefaultOutputPixelType              ("outlabels", ImagePixelType_uint8);
@@ -191,6 +197,8 @@ public:
     SamplerType::Pointer sampler = SamplerType::New();
     sampler->SetInputVectorData(GetParameterVectorData("vec"));
     sampler->SetField(GetParameterAsString("field"));
+    sampler->SetRejectPatchesWithNodata(GetParameterInt("usenodata")==1);
+    sampler->SetNodataValue(GetParameterFloat("nodataval"));
     for (auto& bundle: m_Bundles)
     {
       sampler->PushBackInputWithPatchSize(bundle.m_ImageSource.Get(), bundle.m_PatchSize);

include/otbTensorflowSampler.h

@@ -24,6 +24,9 @@
 // Tree iterator
 #include "itkPreOrderTreeIterator.h"
 
+// Image iterator
+#include "itkImageRegionConstIterator.h"
+
 namespace otb
 {
 
@@ -80,6 +83,8 @@ public:
                                                   ExtractROIMultiFilterPointerType;
   typedef typename std::vector<ImagePointerType>  ImagePointerListType;
   typedef typename std::vector<SizeType>          SizeListType;
+  typedef typename itk::ImageRegionConstIterator<ImageType>
+                                                  IteratorType;
 
   /** Vector data typedefs */
   typedef TVectorData                             VectorDataType;
@@ -104,6 +109,12 @@ public:
   virtual void PushBackInputWithPatchSize(const ImageType *input, SizeType & patchSize);
   const ImageType* GetInput(unsigned int index);
 
+  /** Set / get no-data related parameters */
+  itkSetMacro(NodataValue, InternalPixelType);
+  itkGetMacro(NodataValue, InternalPixelType);
+  itkSetMacro(RejectPatchesWithNodata, bool);
+  itkGetMacro(RejectPatchesWithNodata, bool);
+
   /** Do the real work */
   virtual void Update();
 
@@ -134,6 +145,10 @@ private:
   unsigned long        m_NumberOfAcceptedSamples;
   unsigned long        m_NumberOfRejectedSamples;
 
+  // No data stuff
+  InternalPixelType    m_NodataValue;
+  bool                 m_RejectPatchesWithNodata;
+
 }; // end class
 
 } // end namespace otb

include/otbTensorflowSampler.hxx

@@ -181,6 +181,29 @@ TensorflowSampler<TInputImage, TVectorData>
           // If not, reject this sample
           hasBeenSampled = false;
         }
+        // Check if it contains no-data values
+        if (m_RejectPatchesWithNodata && hasBeenSampled)
+          {
+          IndexType outIndex;
+          outIndex[0] = 0;
+          outIndex[1] = count * m_PatchSizes[i][1];
+          RegionType region(outIndex, m_PatchSizes[i]);
+
+          IteratorType it(m_OutputPatchImages[i], region);
+          for (it.GoToBegin(); !it.IsAtEnd(); ++it)
+            {
+            PixelType pix = it.Get();
+            for (int i; i<pix.Size(); i++)
+              if (pix[i] == m_NodataValue)
+              {
+                hasBeenSampled = false;
+                break;
+              }
+            if (hasBeenSampled)
+              break;
+            }
+
+          }
       } // Next input
       if (hasBeenSampled)
       {

include/otbTensorflowSamplingUtils.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 "otbTensorflowSamplingUtils.h"
+
+namespace otb
+{
+namespace tf
+{
+
+//
+// Update the distribution of the patch located at the specified location
+//
+template<class TImage, class TDistribution>
+bool UpdateDistributionFromPatch(const typename TImage::Pointer inPtr,
+    typename TImage::PointType point, typename TImage::SizeType patchSize,
+    TDistribution & dist)
+{
+  typename TImage::IndexType index;
+  bool canTransform = inPtr->TransformPhysicalPointToIndex(point, index);
+  if (canTransform)
+  {
+    index[0] -= patchSize[0] / 2;
+    index[1] -= patchSize[1] / 2;
+
+    typename TImage::RegionType inPatchRegion(index, patchSize);
+
+    if (inPtr->GetLargestPossibleRegion().IsInside(inPatchRegion))
+    {
+      // Fill patch
+      PropagateRequestedRegion<TImage>(inPtr, inPatchRegion);
+
+      typename itk::ImageRegionConstIterator<TImage> inIt (inPtr, inPatchRegion);
+      for (inIt.GoToBegin(); !inIt.IsAtEnd(); ++inIt)
+      {
+        dist.Update(inIt.Get());
+      }
+      return true;
+    }
+  }
+  return false;
+
+}
+
+
+} // namespace tf
+} // namespace otb

include/otbTensorflowSamplingUtils.h

+/*=========================================================================
+
+  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.
+
+=========================================================================*/
+#ifndef MODULES_REMOTE_OTBTF_INCLUDE_OTBTENSORFLOWSAMPLINGUTILS_H_
+#define MODULES_REMOTE_OTBTF_INCLUDE_OTBTENSORFLOWSAMPLINGUTILS_H_
+
+#include "otbTensorflowCommon.h"
+#include "vnl/vnl_vector.h"
+
+namespace otb
+{
+namespace tf
+{
+
+template<class TImage>
+class Distribution
+{
+public:
+  typedef typename TImage::PixelType ValueType;
+  typedef vnl_vector<float> CountsType;
+
+  Distribution(unsigned int nClasses){
+    m_NbOfClasses = nClasses;
+    m_Dist = CountsType(nClasses, 0);
+
+  }
+  Distribution(unsigned int nClasses, float fillValue){
+    m_NbOfClasses = nClasses;
+    m_Dist = CountsType(nClasses, fillValue);
+
+  }
+  Distribution(){
+    m_NbOfClasses = 2;
+    m_Dist = CountsType(m_NbOfClasses, 0);
+  }
+  Distribution(const Distribution & other){
+    m_Dist = other.Get();
+    m_NbOfClasses = m_Dist.size();
+  }
+  ~Distribution(){}
+
+  void Update(const typename TImage::PixelType & pixel)
+  {
+    m_Dist[pixel]++;
+  }
+
+  void Update(const Distribution & other)
+  {
+    const CountsType otherDist = other.Get();
+    for (unsigned int c = 0 ; c < m_NbOfClasses ; c++)
+      m_Dist[c] += otherDist[c];
+  }
+
+  CountsType Get() const
+  {
+    return m_Dist;
+  }
+
+  CountsType GetNormalized() const
+  {
+    const float invNorm = 1.0 / std::sqrt(dot_product(m_Dist, m_Dist));
+    const CountsType normalizedDist = invNorm * m_Dist;
+    return normalizedDist;
+  }
+
+  float Cosinus(const Distribution & other) const
+  {
+    return dot_product(other.GetNormalized(), GetNormalized());
+  }
+
+  std::string ToString()
+  {
+    std::stringstream ss;
+    ss << "\n";
+    for (unsigned int c = 0 ; c < m_NbOfClasses ; c++)
+      ss << "\tClass #" << c << " : " << m_Dist[c] << "\n";
+    return ss.str();
+  }
+
+private:
+  unsigned int m_NbOfClasses;
+  CountsType m_Dist;
+};
+
+// Update the distribution of the patch located at the specified location
+template<class TImage, class TDistribution>
+bool UpdateDistributionFromPatch(const typename TImage::Pointer inPtr,
+    typename TImage::PointType point, typename TImage::SizeType patchSize,
+    TDistribution & dist);
+
+} // namesapce tf
+} // namespace otb
+
+#include "otbTensorflowSamplingUtils.cxx"
+
+#endif /* MODULES_REMOTE_OTBTF_INCLUDE_OTBTENSORFLOWSAMPLINGUTILS_H_ */