Merge branch 'develop' into small_region_merging

CMake/OTBModuleEnablement.cmake

@@ -196,6 +196,8 @@ foreach(otb-module ${OTB_MODULES_ALL})
   if(OTB_MODULE_${otb-module}_ACTIVATION_OPTION
      AND NOT ${OTB_MODULE_${otb-module}_ACTIVATION_OPTION})
      otb_module_disable("${otb-module}" "${OTB_MODULE_${otb-module}_ACTIVATION_OPTION}")
+  elseif(OTB_MODULE_${otb-module}_IS_DEPRECATED AND NOT OTB_USE_DEPRECATED)
+     otb_module_disable("${otb-module}" "OTB_USE_DEPRECATED")
   endif()
 endforeach()
 

CMake/OTBModuleMacros.cmake

@@ -69,6 +69,9 @@ macro(otb_module _name)
     elseif("${arg}" MATCHES "^ENABLE_SHARED$")
       set(_doing "")
       set(OTB_MODULE_${otb-module}_ENABLE_SHARED 1)
+    elseif("${arg}" MATCHES "^DEPRECATED$")
+      set(_doing "")
+      set(OTB_MODULE_${otb-module}_IS_DEPRECATED 1)
     elseif("${arg}" MATCHES "^[A-Z][A-Z][A-Z]$")
       set(_doing "")
       message(AUTHOR_WARNING "Unknown argument [${arg}]")
@@ -221,6 +224,7 @@ macro(otb_module_impl)
     generate_export_header(${otb-module}
       EXPORT_FILE_NAME ${_export_header_file}
       EXPORT_MACRO_NAME ${otb-module}_EXPORT
+      DEPRECATED_MACRO_NAME ${otb-module}_DEPRECATED
       NO_EXPORT_MACRO_NAME ${otb-module}_HIDDEN
       STATIC_DEFINE OTB_STATIC )
     install(FILES

Documentation/Cookbook/rst/AdvancedUse.rst

@@ -3,8 +3,8 @@ Advanced Use
 
 This section describes advanced configuration options and tricks.
 
-Environment variables that affects Orfeo ToolBox
-------------------------------------------------
+Environment variables that affect Orfeo ToolBox
+-----------------------------------------------
 
 The following environment variables are parsed by Orfeo ToolBox. Note
 that they only affect default values, and that settings in extended

Modules/Core/ImageBase/include/otbImageIOBase.h

@@ -208,7 +208,7 @@ public:
 
   /** Convenience method returns the IOPixelType as a string. This can be
    * used for writing output files. */
-  std::string GetPixelTypeAsString(IOPixelType) const;
+  static std::string GetPixelTypeAsString(IOPixelType);
 
   /** Enums used to specify write style: whether binary or ASCII. Some
    * subclasses use this, some ignore it. */
@@ -255,11 +255,11 @@ public:
 
   /** Convenience method returns the FileType as a string. This can be
    * used for writing output files. */
-  std::string GetFileTypeAsString(FileType) const;
+  static std::string GetFileTypeAsString(FileType);
 
   /** Convenience method returns the ByteOrder as a string. This can be
    * used for writing output files. */
-  std::string GetByteOrderAsString(ByteOrder) const;
+  static std::string GetByteOrderAsString(ByteOrder);
 
   /** Type for representing size of bytes, and or positions along a file */
   typedef std::streamoff SizeType;

Modules/Core/ImageBase/src/otbImageIOBase.cxx

@@ -709,7 +709,7 @@ unsigned int ImageIOBase::GetComponentSize() const
   return 0;
 }
 
-std::string ImageIOBase::GetFileTypeAsString(FileType t) const
+std::string ImageIOBase::GetFileTypeAsString(FileType t)
 {
   std::string s;
   switch(t)
@@ -724,7 +724,7 @@ std::string ImageIOBase::GetFileTypeAsString(FileType t) const
     }
 }
 
-std::string ImageIOBase::GetByteOrderAsString(ByteOrder t) const
+std::string ImageIOBase::GetByteOrderAsString(ByteOrder t)
 {
   std::string s;
   switch(t)
@@ -778,7 +778,7 @@ std::string ImageIOBase::GetComponentTypeAsString(IOComponentType t)
     }
 }
 
-std::string ImageIOBase::GetPixelTypeAsString(IOPixelType t) const
+std::string ImageIOBase::GetPixelTypeAsString(IOPixelType t)
 {
   std::string s;
   switch(t)
@@ -805,7 +805,7 @@ std::string ImageIOBase::GetPixelTypeAsString(IOPixelType t) const
       return (s = "complex");
     case UNKNOWNPIXELTYPE:
     default:
-      itkExceptionMacro ("Unknown pixel type: " << t);
+      return (s = "unknown");
     }
 }
 
@@ -1325,13 +1325,13 @@ void ImageIOBase::PrintSelf(std::ostream& os, itk::Indent indent) const
   Superclass::PrintSelf(os, indent);
 
   os << indent << "FileName: " << m_FileName << std::endl;
-  os << indent << "FileType: " << this->GetFileTypeAsString(m_FileType) << std::endl;
-  os << indent << "ByteOrder: " << this->GetByteOrderAsString(m_ByteOrder) << std::endl;
+  os << indent << "FileType: " << ImageIOBase::GetFileTypeAsString(m_FileType) << std::endl;
+  os << indent << "ByteOrder: " << ImageIOBase::GetByteOrderAsString(m_ByteOrder) << std::endl;
   os << indent << "IORegion: " << std::endl;
   m_IORegion.Print(os, indent.GetNextIndent());
   os << indent << "Number of Components/Pixel: " << m_NumberOfComponents << "\n";
-  os << indent << "Pixel Type: " << this->GetPixelTypeAsString(m_PixelType) << std::endl;
-  os << indent << "Component Type: " << this->GetComponentTypeAsString(m_ComponentType)
+  os << indent << "Pixel Type: " << ImageIOBase::GetPixelTypeAsString(m_PixelType) << std::endl;
+  os << indent << "Component Type: " << ImageIOBase::GetComponentTypeAsString(m_ComponentType)
      << std::endl;
   os << indent << "Dimensions: ( ";
   for (unsigned int i=0; i < m_NumberOfDimensions; i++)

Modules/Detection/ObjectDetection/include/otbDescriptorsListSampleGenerator.h

@@ -183,7 +183,6 @@ private:
 
   bool IsInsideWithNeighborhoodRadius(const RegionType& region, const ContinuousIndexType &index) const
     {
-    typedef typename RegionType::IndexType     IndexType;
     typedef typename IndexType::IndexValueType IndexValueType;
     typedef typename ContinuousIndexType::ValueType ContinuousIndexValueType;
 

Modules/Detection/ObjectDetection/include/otbObjectDetectionClassifier.h

@@ -194,7 +194,6 @@ private:
   bool
   IsInsideWithNeighborhoodRadius(const RegionType& region, const ContinuousIndexType &index) const
     {
-    typedef typename RegionType::IndexType     IndexType;
     typedef typename IndexType::IndexValueType IndexValueType;
 
     for(unsigned int i=0; i<ImageDimension; ++i)

Modules/Feature/Descriptors/include/otbImageToSIFTKeyPointSetFilter.hxx

@@ -58,7 +58,7 @@ ImageToSIFTKeyPointSetFilter<TInputImage, TOutputPointSet>
   m_GradientMagnitudeThreshold = 0.2;
 
   m_ExpandFilter = ExpandFilterType::New();
-  
+
   const double HistogramGaussianWeights[73] = {
     2.3771112282795414e-07, 3.8860734758633732e-07, 6.2655544995978937e-07, 9.9631120821413786e-07,
     1.5624909838697011e-06, 2.4167238265599128e-06, 3.6865788528530121e-06,
@@ -82,9 +82,9 @@ ImageToSIFTKeyPointSetFilter<TInputImage, TOutputPointSet>
     2.4167238265599128e-06, 1.5624909838697011e-06, 9.9631120821413786e-07,
     6.2655544995978937e-07, 3.8860734758633732e-07, 2.3771112282795414e-07
   };
-  
+
   m_HistogramGaussianWeights = std::vector<double>(HistogramGaussianWeights,HistogramGaussianWeights+73);
-  
+
   m_Offsets[0][0]=-1;
   m_Offsets[0][1]=-1;
   m_Offsets[1][0]=-1;
@@ -896,9 +896,7 @@ void
 ImageToSIFTKeyPointSetFilter<TInputImage, TOutputPointSet>
 ::PrintSelf(std::ostream& os, itk::Indent indent) const
 {
-
-  typedef itk::ProcessObject                                     ProcessObjectType;
-  const OutputPointSetType* output = dynamic_cast<const OutputPointSetType*>(this->ProcessObjectType::GetOutput(0));
+  const OutputPointSetType* output = dynamic_cast<const OutputPointSetType*>(this->Superclass::ProcessObjectType::GetOutput(0));
 
   Superclass::PrintSelf(os, indent);
   os << indent << "Number of octaves: " << m_OctavesNumber << std::endl;

Modules/Filtering/ChangeDetection/include/otbKullbackLeiblerSupervizedDistanceImageFilter.hxx

@@ -57,12 +57,6 @@ KullbackLeiblerSupervizedDistance<TInput1, TInput2, TInputROIImage, TOutput>
            const typename TInput2::ImageType * img2,
            const TInputROIImage * imgROI)
 {
-  typedef ROIdataConversion<typename TInput1::ImageType, TInputROIImage>
-  ROIConversionType1;
-
-  typedef itk::ConstNeighborhoodIterator<
-      typename ROIConversionType1::OutputImageType> ROIInputType1;
-
   typename ROIConversionType1::Pointer conversion1 = ROIConversionType1::New();
   conversion1->SetInputImage(img1);
   conversion1->SetROIImage(imgROI);

Modules/Filtering/Path/include/otbCompacityPathFunction.hxx

@@ -43,8 +43,6 @@ typename CompacityPathFunction<TInputPath,
 CompacityPathFunction<TInputPath, TOutput>
 ::Evaluate(const PathType& path) const
 {
-  typedef double RealType;
-
   VertexListPointer vertexList;
   VertexType        cindex;
   VertexType        IndexOut;

Modules/Filtering/Path/include/otbOrientationPathFunction.hxx

@@ -44,8 +44,6 @@ typename OrientationPathFunction<TInputPath,
 OrientationPathFunction<TInputPath, TOutput>
 ::Evaluate(const PathType& path) const
 {
-  typedef double RealType;
-
   VertexListPointer vertexList;
   VertexType        cindex;
   VertexType        IndexOut;

Modules/Filtering/VectorDataRendering/include/otbMapnikAdapter.h

@@ -61,7 +61,7 @@ typedef Image32 image_32;
 
 namespace otb
 {
-namespace mapnik_otb
+namespace [[deprecated]] mapnik_otb
 {
 // this should be removed once mapnik support for version < 2.0 is dropped.
 // should be around 01/2013.

Modules/Filtering/VectorDataRendering/include/otbVectorDataStyle.h

@@ -42,10 +42,12 @@ namespace otb
  *
  * \sa VectorDataToMapFilter
  *
+ * \deprecated
+ *
  * \ingroup OTBVectorDataRendering
  */
 
-class ITK_EXPORT VectorDataStyle : public itk::LightObject
+class [[deprecated]] VectorDataStyle : public itk::LightObject
 {
 public:
   /** Standard class typedefs. */

Modules/Filtering/VectorDataRendering/include/otbVectorDataToMapFilter.h

@@ -68,12 +68,13 @@ namespace otb
    * otb::Image< itk::RGBAPixel<InternalPixelType> >,
    * otb::Image< itk::RGBPixel<InternalPixelType> >.
    *
- *
- * \ingroup OTBVectorDataRendering
+   * \deprecated
+   *
+   * \ingroup OTBVectorDataRendering
    */
 
 template <class TVectorData, class TImage>
-class ITK_EXPORT VectorDataToMapFilter : public itk::ImageSource<TImage>
+class [[deprecated]] VectorDataToMapFilter : public itk::ImageSource<TImage>
 {
 public:
   /** Standard class typedefs. */

Modules/Filtering/VectorDataRendering/otb-module.cmake

@@ -37,6 +37,8 @@ otb_module(OTBVectorDataRendering
     OTBVectorDataIO
     OTBImageBase
 
+  DEPRECATED
+
   DESCRIPTION
     "${DOCUMENTATION}"
 )

Modules/IO/IOGDAL/src/otbGDALImageIO.cxx

@@ -1313,7 +1313,7 @@ void GDALImageIO::InternalWriteImageInformation(const void* buffer)
       }
     else
       {
-      itkExceptionMacro(<< "This complex type is not defined :" << this->GetPixelTypeAsString(this->GetPixelType()) );
+      itkExceptionMacro(<< "This complex type is not defined :" << ImageIOBase::GetPixelTypeAsString(this->GetPixelType()) );
       }
     }
   else

Modules/IO/IOONERA/src/otbONERAImageIO.cxx

@@ -384,13 +384,13 @@ void ONERAImageIO::InternalReadImageInformation()
   otbMsgDebugMacro(<< "Driver to read: ONERA");
   otbMsgDebugMacro(<< "         Read  file         : " << m_FileName);
   otbMsgDebugMacro(<< "         Size               : " << m_Dimensions[0] << "," << m_Dimensions[1]);
-  otbMsgDebugMacro(<< "         PixelType          : " << this->GetPixelTypeAsString(this->GetPixelType()));
-  otbMsgDebugMacro(<< "         ComponentType      : " << this->GetComponentTypeAsString(this->GetComponentType()));
+  otbMsgDebugMacro(<< "         PixelType          : " << ImageIOBase::GetPixelTypeAsString(this->GetPixelType()));
+  otbMsgDebugMacro(<< "         ComponentType      : " << ImageIOBase::GetComponentTypeAsString(this->GetComponentType()));
   otbMsgDebugMacro(<< "         ComponentSize      : " << this->GetComponentSize());
   otbMsgDebugMacro(<< "         NumberOfComponents : " << this->GetNumberOfComponents());
   otbMsgDebugMacro(<< "         BytePerPixel       : " << m_BytePerPixel);
-  otbMsgDebugMacro(<< "         Host byte order    : " << this->GetByteOrderAsString(m_ByteOrder));
-  otbMsgDebugMacro(<< "         File byte order    : " << this->GetByteOrderAsString(m_FileByteOrder));
+  otbMsgDebugMacro(<< "         Host byte order    : " << ImageIOBase::GetByteOrderAsString(m_ByteOrder));
+  otbMsgDebugMacro(<< "         File byte order    : " << ImageIOBase::GetByteOrderAsString(m_FileByteOrder));
 
   delete [] sHeader;
 }
@@ -595,7 +595,7 @@ void ONERAImageIO::InternalWriteImageInformation()
     otbMsgDebugMacro(<< "         ComponentType      : " << this->GetComponentType());
     otbMsgDebugMacro(<< "         NumberOfComponents : " << this->GetNumberOfComponents());
     otbMsgDebugMacro(<< "         BytePerPixel       : " << m_BytePerPixel);
-    otbMsgDebugMacro(<< "         Host byte order    : " << this->GetByteOrderAsString(m_ByteOrder));
+    otbMsgDebugMacro(<< "         Host byte order    : " << ImageIOBase::GetByteOrderAsString(m_ByteOrder));
 }
 
 } // end namespace otb

Modules/IO/IORAD/src/otbRADImageIO.cxx

@@ -618,8 +618,8 @@ void RADImageIO::WriteImageInformation()
   m_HeaderFile << "TYPECODAGE ";
 
   std::string lExtension;
-  std::string lStringPixelType = itksys::SystemTools::UpperCase(this->GetPixelTypeAsString(m_PixelType));
-  std::string lStringComponentType = itksys::SystemTools::UpperCase(this->GetComponentTypeAsString(this->GetComponentType()));
+  std::string lStringPixelType = itksys::SystemTools::UpperCase(ImageIOBase::GetPixelTypeAsString(m_PixelType));
+  std::string lStringComponentType = itksys::SystemTools::UpperCase(ImageIOBase::GetComponentTypeAsString(this->GetComponentType()));
 
   if (lStringPixelType == "SCALAR")
     {

Modules/IO/ImageIO/include/otbImageFileReader.hxx

@@ -889,7 +889,7 @@ ImageFileReader<TOutputImage, ConvertPixelTraits>
     std::ostringstream msg;
     msg <<"Couldn't convert component type: "
         << std::endl << "    "
-        << m_ImageIO->GetComponentTypeAsString(m_ImageIO->GetComponentType())
+        << ImageIOBase::GetComponentTypeAsString(m_ImageIO->GetComponentType())
         << std::endl << "to one of: "
         << std::endl << "    " << typeid(unsigned char).name()
         << std::endl << "    " << typeid(char).name()

Modules/OBIA/RCC8/include/otbRCC8GraphFileWriter.h

@@ -88,12 +88,13 @@ public:
   typedef typename InputGraphType::VertexDescriptorType VertexDescriptorType;
   typedef typename InputGraphType::RCC8ValueType        RCC8ValueType;
   typedef typename VertexType::AttributesMapType        AttributesMapType;
+  typedef typename AttributesMapType::iterator          IteratorType;
 
   /** Set the filename */
   itkSetStringMacro(FileName);
   /** Get the filename */
   itkGetStringMacro(FileName);
-  
+
   using Superclass::SetInput;
   /**
    * Set the input graph.