Merge branch 'master' of gitlab-ssh.irstea.fr:remi.cresson/SimpleExtractionTools

include/otbMeanResampleImageFilter.hxx

@@ -43,15 +43,15 @@ MeanResampleImageFilter<TImage>
 
   // The new output image has the same origin
   ImagePointType origin = inputImage->GetOrigin();
-  origin[0] += 0.5 * inputImage->GetSignedSpacing()[0] * (m_StepX - 1);
-  origin[1] += 0.5 * inputImage->GetSignedSpacing()[1] * (m_StepY - 1);
+  origin[0] += 0.5 * inputImage->GetSpacing()[0] * (m_StepX - 1);
+  origin[1] += 0.5 * inputImage->GetSpacing()[1] * (m_StepY - 1);
   outputPtr->SetOrigin ( origin );
 
   // New spacing for the output image
-  ImageSpacingType spacing = inputImage->GetSignedSpacing();
+  ImageSpacingType spacing = inputImage->GetSpacing();
   spacing[0] *= m_StepX;
   spacing[1] *= m_StepY;
-  outputPtr->SetSignedSpacing (spacing);
+  outputPtr->SetSpacing (spacing);
 
   // New size for the output image
   ImageRegionType inRegion = inputImage->GetLargestPossibleRegion();

include/otbMosaicFromDirectoryHandler.h

+/*
+ * otbMosaicFromDirectoryHandler.h
+ *
+ *  Created on: 24 mars 2016
+ *      Author: cresson
+ */
+
+#ifndef MODULES_REMOTE_OTB_MosaicFromDirectoryHandler_INCLUDE_OTBMosaicFromDirectoryHandler_H_
+#define MODULES_REMOTE_OTB_MosaicFromDirectoryHandler_INCLUDE_OTBMosaicFromDirectoryHandler_H_
+
+#include "itkImageSource.h"
+#include "itkExceptionObject.h"
+#include "itkImageRegion.h"
+
+#include "otbStreamingSimpleMosaicFilter.h"
+
+#include "otbImageFileReader.h"
+#include "itkDirectory.h"
+#include "otbImageIOBase.h"
+#include "otbImageIOFactory.h"
+
+#include "otbMultiToMonoChannelExtractROI.h"
+#include "otbGenericRSResampleImageFilter.h"
+#include "itkNearestNeighborInterpolateImageFunction.h"
+
+namespace otb
+{
+/** \class MosaicFromDirectoryHandler
+ * \brief  This ImageSource produces an otb::image from multiple rasters
+ * stored in the m_Directory.
+ * TODO: Currently only .tif extension is supported. Might be nice to change it.
+ *
+ *
+ * \ingroup OTBMosaic
+ *
+ */
+template <class TOutputImage, class TReferenceImage>
+class ITK_EXPORT MosaicFromDirectoryHandler : public itk::ImageSource<TOutputImage>
+{
+public:
+  /** Standard class typedefs. */
+  typedef MosaicFromDirectoryHandler                    Self;
+  typedef itk::ImageSource<TOutputImage>                Superclass;
+  typedef itk::SmartPointer<Self>                       Pointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(MosaicFromDirectoryHandler, ImageSource);
+
+  /** Typedefs for output image */
+  typedef typename TOutputImage::SizeType               SizeType;
+  typedef typename TOutputImage::IndexType              IndexType;
+  typedef typename TOutputImage::SpacingType            SpacingType;
+  typedef typename TOutputImage::PointType              PointType;
+  typedef typename TOutputImage::RegionType             ImageRegionType;
+  typedef typename TOutputImage::InternalPixelType      OutputImagePixelType;
+
+  /** Typedefs for mosaic filter */
+  typedef otb::VectorImage<OutputImagePixelType>        InternalMaskImageType;
+  typedef otb::StreamingSimpleMosaicFilter<
+      InternalMaskImageType>                            MosaicFilterType;
+  typedef typename MosaicFilterType::Pointer            MosaicFilterPointerType;
+
+  /** Typedefs for image reader */
+  typedef otb::ImageFileReader<InternalMaskImageType>   ReaderType;
+  typedef typename ReaderType::Pointer                  ReaderPointerType;
+
+  /** Typedefs for casting the image */
+  typedef otb::MultiToMonoChannelExtractROI<
+      OutputImagePixelType, OutputImagePixelType>       CastFilterType;
+  typedef typename CastFilterType::Pointer              CastFilterPointerType;
+
+  /** Typedefs for image reprojection */
+  typedef otb::GenericRSResampleImageFilter<
+      InternalMaskImageType, InternalMaskImageType>     ResamplerType;
+  typedef typename ResamplerType::Pointer               ResamplerPointerType;
+  typedef itk::NearestNeighborInterpolateImageFunction<
+      InternalMaskImageType, double>                    NNInterpolatorType;
+
+  /** Input directory accessors */
+  itkGetMacro(Directory, std::string);
+  itkSetMacro(Directory, std::string);
+
+  /** Output parameters setters */
+  itkSetMacro(OutputSpacing, SpacingType);
+  itkSetMacro(OutputSize, SizeType);
+  itkSetMacro(OutputOrigin, PointType);
+  void SetReferenceImage(TReferenceImage * ptr){m_RefImagePtr = ptr;}
+  itkSetMacro(UseReferenceImage, bool);
+
+  /** Prepare image allocation at the first call of the pipeline processing */
+  virtual void GenerateOutputInformation(void);
+
+  /** Does the real work. */
+   virtual void GenerateData();
+
+protected:
+  MosaicFromDirectoryHandler();
+  virtual ~MosaicFromDirectoryHandler();
+
+  // Masks directory
+  std::string                       m_Directory;
+
+  // Output parameters
+  SpacingType                       m_OutputSpacing;
+  SizeType                          m_OutputSize;
+  PointType                         m_OutputOrigin;
+
+  // Internal filters
+  MosaicFilterPointerType           mosaicFilter;
+  CastFilterPointerType             castFilter;
+  std::vector<ReaderPointerType>    readers;
+  std::vector<ResamplerPointerType> resamplers;
+
+  // Reference image pointer
+  bool                              m_UseReferenceImage;
+  TReferenceImage *                 m_RefImagePtr;
+
+private:
+
+  MosaicFromDirectoryHandler(const Self &); //purposely not implemented
+  void operator =(const Self&); //purposely not implemented
+
+};
+
+} //namespace otb
+
+#ifndef OTB_MANUAL_INSTANTIATION
+#include <otbMosaicFromDirectoryHandler.txx>
+#endif
+
+#endif /* MODULES_REMOTE_OTB_MosaicFromDirectoryHandler_INCLUDE_OTBMosaicFromDirectoryHandler_H_ */

include/otbMosaicFromDirectoryHandler.txx

+/*
+ * otbMosaicFromDirectoryHandler.hxx
+ *
+ *  Created on: 24 mars 2016
+ *      Author: cresson
+ */
+
+#ifndef MODULES_REMOTE_OTB_MosaicFromDirectoryHandler_INCLUDE_OTBMosaicFromDirectoryHandler_HXX_
+#define MODULES_REMOTE_OTB_MosaicFromDirectoryHandler_INCLUDE_OTBMosaicFromDirectoryHandler_HXX_
+
+#include "otbMosaicFromDirectoryHandler.h"
+#include "otbImageFileWriter.h"
+
+namespace otb
+{
+
+template <class TOutputImage, class TReferenceImage>
+MosaicFromDirectoryHandler<TOutputImage, TReferenceImage>
+::MosaicFromDirectoryHandler()
+ {
+  mosaicFilter = MosaicFilterType::New();
+  castFilter = CastFilterType::New();
+  m_UseReferenceImage = false;
+  m_RefImagePtr = 0;
+ }
+
+template <class TOutputImage, class TReferenceImage>
+MosaicFromDirectoryHandler<TOutputImage, TReferenceImage>
+::~MosaicFromDirectoryHandler()
+{
+}
+
+template <class TOutputImage, class TReferenceImage>
+void
+MosaicFromDirectoryHandler<TOutputImage, TReferenceImage>
+::GenerateOutputInformation()
+ {
+  if (m_Directory[m_Directory.size()-1] != '/')
+    {
+    // If not, we add the separator
+    m_Directory.append("/");
+    }
+
+  // Get the list of files in the directory
+  itk::Directory::Pointer dir = itk::Directory::New();
+  if (!dir->Load(m_Directory.c_str()))
+    {
+    itkExceptionMacro(<< "Unable to browse directory " << m_Directory);
+    }
+
+  // Instanciate a new mosaic filter
+  mosaicFilter = MosaicFilterType::New();
+  mosaicFilter->SetGlobalWarningDisplay(false);
+  readers.clear();
+  resamplers.clear();
+
+  // Browse the directory
+  for (unsigned int i = 0; i < dir->GetNumberOfFiles(); i++)
+    {
+    const char *filename = dir->GetFile(i);
+    std::string sfilename(filename);
+    sfilename = m_Directory + sfilename;
+
+    // Try to read the file
+    otb::ImageIOBase::Pointer imageIO =
+        otb::ImageIOFactory::CreateImageIO(sfilename.c_str(),otb::ImageIOFactory::ReadMode);
+    if( imageIO.IsNotNull() )
+      {
+        // create reader
+        ReaderPointerType reader = ReaderType::New();
+        reader->SetFileName(sfilename);
+        reader->UpdateOutputInformation();
+
+        readers.push_back(reader);
+
+        if (m_UseReferenceImage)
+          {
+            ResamplerPointerType resampler = ResamplerType::New();
+            resampler->SetInput(reader->GetOutput());
+
+            // Setup transform through projRef and Keywordlist
+            SpacingType defSpacing = m_RefImagePtr->GetSignedSpacing();
+            defSpacing[0] *= 10;
+            defSpacing[1] *= 10;
+            resampler->SetDisplacementFieldSpacing(defSpacing);
+            resampler->SetInputKeywordList(reader->GetOutput()->GetImageKeywordlist());
+            resampler->SetInputProjectionRef(reader->GetOutput()->GetProjectionRef());
+            resampler->SetOutputKeywordList(m_RefImagePtr->GetImageKeywordlist());
+            resampler->SetOutputProjectionRef(m_RefImagePtr->GetProjectionRef());
+            resampler->SetOutputOrigin(m_RefImagePtr->GetOrigin());
+            resampler->SetOutputSpacing(m_RefImagePtr->GetSignedSpacing());
+            resampler->SetOutputSize(m_RefImagePtr->GetLargestPossibleRegion().GetSize());
+            resampler->SetOutputStartIndex(m_RefImagePtr->GetLargestPossibleRegion().GetIndex());
+
+            typename NNInterpolatorType::Pointer interpolator = NNInterpolatorType::New();
+            resampler->SetInterpolator(interpolator);
+
+            resamplers.push_back(resampler);
+
+            mosaicFilter->PushBackInput(resampler->GetOutput());
+          }
+        else
+          {
+            mosaicFilter->PushBackInput(reader->GetOutput());
+          }
+      }
+    else
+      {
+      //      itkWarningMacro(<<"Unable to read file " << sfilename);
+      }
+
+    }
+
+  if (m_UseReferenceImage)
+    {
+      mosaicFilter->SetOutputOrigin(m_RefImagePtr->GetOrigin());
+      mosaicFilter->SetOutputSpacing(m_RefImagePtr->GetSignedSpacing());
+      mosaicFilter->SetOutputSize(m_RefImagePtr->GetLargestPossibleRegion().GetSize());
+    }
+  else
+    {
+      mosaicFilter->SetOutputOrigin(m_OutputOrigin);
+      mosaicFilter->SetOutputSpacing(m_OutputSpacing);
+      mosaicFilter->SetOutputSize(m_OutputSize);
+    }
+  mosaicFilter->SetAutomaticOutputParametersComputation(false);
+
+  castFilter->SetInput(mosaicFilter->GetOutput());
+
+  castFilter->GraftOutput( this->GetOutput() );
+  castFilter->UpdateOutputInformation();
+  this->GraftOutput( castFilter->GetOutput() );
+ }
+
+template <class TOutputImage, class TReferenceImage>
+void
+MosaicFromDirectoryHandler<TOutputImage, TReferenceImage>
+::GenerateData()
+ {
+  castFilter->GraftOutput( this->GetOutput() );
+  castFilter->Update();
+  this->GraftOutput( castFilter->GetOutput() );
+ }
+
+} // end namespace otb
+
+#endif /* MODULES_REMOTE_OTB_MosaicFromDirectoryHandler_INCLUDE_OTBMosaicFromDirectoryHandler_HXX_ */

include/otbVectorDataToLabelImageCustomFilter.hxx

@@ -119,7 +119,7 @@ VectorDataToLabelImageCustomFilter<TVectorData, TOutputImage>
 ::SetOutputParametersFromImage(const ImageBaseType * src)
  {
   this->SetOutputOrigin ( src->GetOrigin() );
-  this->SetOutputSignedSpacing ( src->GetSignedSpacing() );
+  this->SetOutputSpacing ( src->GetSignedSpacing() );
   this->SetOutputSize ( src->GetLargestPossibleRegion().GetSize() );
   otb::ImageMetadataInterfaceBase::Pointer imi = otb::ImageMetadataInterfaceFactory::CreateIMI(src->GetMetaDataDictionary());
   this->SetOutputProjectionRef(imi->GetProjectionRef());
@@ -144,7 +144,7 @@ VectorDataToLabelImageCustomFilter<TVectorData, TOutputImage>
   outputPtr->SetLargestPossibleRegion(outputLargestPossibleRegion);
 
   // Set spacing and origin
-  outputPtr->SetSignedSpacing(m_OutputSpacing);
+  outputPtr->SetSpacing(m_OutputSpacing);
   outputPtr->SetOrigin(m_OutputOrigin);
 
   itk::MetaDataDictionary& dict = outputPtr->GetMetaDataDictionary();
@@ -295,8 +295,8 @@ VectorDataToLabelImageCustomFilter<TVectorData, TOutputImage>::GenerateData()
   this->GetOutput()->TransformIndexToPhysicalPoint(bufferIndexOrigin, bufferOrigin);
   geoTransform[0] = bufferOrigin[0];
   geoTransform[3] = bufferOrigin[1];
-  geoTransform[1] = this->GetOutput()->GetSignedSpacing()[0];
-  geoTransform[5] = this->GetOutput()->GetSignedSpacing()[1];
+  geoTransform[1] = this->GetOutput()->GetSpacing()[0];
+  geoTransform[5] = this->GetOutput()->GetSpacing()[1];
 
   // FIXME: Here component 1 and 4 should be replaced by the orientation parameters
   geoTransform[2] = 0.;

otb-module.cmake

@@ -8,6 +8,7 @@ otb_module(SimpleExtractionTools
 	OTBImageBase
 	OTBImageIO
 	OTBStatistics
+        OTBMosaic
 	
   TEST_DEPENDS
     OTBTestKernel