Merge branch 'fix_1889' into 'develop'

Add "epsg" filename extension

Closes #1889

See merge request !709

.mailmap

@@ -54,6 +54,7 @@ Julien Malik <julien.malik@c-s.fr>                        Julien Malik <julien.m
 Julien Michel <julien.michel@cnes.fr>
 Julien Michel <julien.michel@cnes.fr>                     Julien Michel <julien.michel@c-s.fr>
 Julien Michel <julien.michel@cnes.fr>                     Julien Michel <julien.michel@orfeo-toolbox.org>
+Julien Osman <julien.osman@c-s.fr>
 Laurențiu Nicola <lnicola@dend.ro>                        Laurentiu Nicola <lnicola@dend.ro>
 Laurențiu Nicola <lnicola@dend.ro>                        Laurențiu Nicola <grayshade@gmail.com>
 Luc Hermitte <luc.hermitte@c-s.fr>                        Luc Hermitte <luc.hermitte@cnes.fr>

Data/Baseline/OTB/Images/ioTvExtendedFilenameToWriterOptions_FullOptions.txt

@@ -6,3 +6,7 @@
 BLOCKYSIZE=1024
 QUALITY=75
 TILED=YES
+1
+1 ; -99999
+1
+4326

Data/Baseline/OTB/Images/ioTvExtendedFilenameToWriterOptions_NoOptions.txt

@@ -3,3 +3,5 @@
 0
 1
 0
+0
+0

Documentation/Cookbook/rst/ExtendedFilenames.rst

@@ -323,6 +323,18 @@ The available syntax for boolean options are:
 
 -----------------------------------------------
 
+::
+
+    &epsg=<(int)value>
+
+-  To set the projection system of the output image.
+
+-  Provide the `EPSG code`_ of the desired projection.
+
+.. _EPSG code : https://en.wikipedia.org/wiki/EPSG_Geodetic_Parameter_Dataset
+
+-----------------------------------------------
+
 ::
 
    &multiwrite==<(bool)false>

Modules/IO/ExtendedFilename/include/otbExtendedFilenameToWriterOptions.h

 /*
  * Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
- * Copyright (C) 2018 CS Systemes d'Information (CS SI)
+ * Copyright (C) 2018-2020 CS Systemes d'Information (CS SI)
  *
  * This file is part of Orfeo Toolbox
  *
@@ -37,7 +37,13 @@ namespace otb
  * - &gdal:co:<KEY>=<VALUE> : the gdal creation option <KEY>
  * - streaming modes
  * - box
- * See http://wiki.orfeo-toolbox.org/index.php/ExtendedFileName
+ * - &bands=<BANDS_LIST> : to select a subset of bands from the output image
+ * - &nodata=<VALUE>/<VALUE:VALUE...> : to set specific nodata values
+ * - &multiwrite=<(bool)false> : to desactivate multi-writing
+ * - &epsg=<VALUE> : to set the spatial reference system
+ *
+ * See http://wiki.orfeo-toolbox.org/index.php/ExtendedFileName for
+ * more information
  *
  *  \sa ImageFileWriter
  *
@@ -76,6 +82,7 @@ public:
     std::pair<bool, double>      streamingSizeValue;
     std::pair<bool, std::string> box;
     std::pair<bool, std::string> bandRange;
+    std::pair<bool, unsigned int> srsValue;
     std::vector<std::string> optionList;
   };
 
@@ -111,6 +118,8 @@ public:
   bool        StreamingSizeValueIsSet() const;
   double      GetStreamingSizeValue() const;
   std::string GetBandRange() const;
+  bool        SrsValueIsSet() const;
+  unsigned int GetSrsValue() const;
 
   bool        BoxIsSet() const;
   std::string GetBox() const;

Modules/IO/ExtendedFilename/src/otbExtendedFilenameToWriterOptions.cxx

 /*
  * Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
- * Copyright (C) 2018 CS Systemes d'Information (CS SI)
+ * Copyright (C) 2018-2020 CS Systemes d'Information (CS SI)
  *
  * This file is part of Orfeo Toolbox
  *
@@ -52,8 +52,10 @@ ExtendedFilenameToWriterOptions::ExtendedFilenameToWriterOptions() : ExtendedFil
   m_Options.bandRange.first  = false;
   m_Options.bandRange.second = "";
 
+  m_Options.srsValue.first = false;
+
   m_Options.optionList = {"writegeom", "writerpctags", "multiwrite", "streaming:type",
-    "streaming:sizemode", "streaming:sizevalue", "nodata", "box", "bands"};
+    "streaming:sizemode", "streaming:sizevalue", "nodata", "box", "bands", "epsg"};
 }
 
 void ExtendedFilenameToWriterOptions::SetExtendedFileName(const char* extFname)
@@ -216,6 +218,34 @@ void ExtendedFilenameToWriterOptions::SetExtendedFileName(const std::string& ext
     }
   }
 
+  if (!map["epsg"].empty())
+  {
+	int code;
+	try
+	{
+	  code = std::stoi(map["epsg"]);
+	}
+	catch(const std::invalid_argument& e)
+	{
+	  itkWarningMacro("Invalid value ("
+                      << map["epsg"]
+                      << ") for Geographic coordinate reference system. Must be integer.");
+      code = 0;
+	}
+	if (code < 0)
+	{
+      itkWarningMacro("Invalid value ("
+		               << map["epsg"]
+		               << ") for Geographic coordinate reference system. Must be positive.");
+      code = 0;
+	}
+    if (code > 0)
+    {
+        m_Options.srsValue.first  = true;
+        m_Options.srsValue.second = (unsigned int) code;
+    }
+  }
+
   // Option Checking
   for (it = map.begin(); it != map.end(); it++)
   {
@@ -336,4 +366,14 @@ std::string ExtendedFilenameToWriterOptions::GetBandRange() const
   return m_Options.bandRange.second;
 }
 
+bool ExtendedFilenameToWriterOptions::SrsValueIsSet() const
+{
+	return m_Options.srsValue.first;
+}
+
+unsigned int ExtendedFilenameToWriterOptions::GetSrsValue() const
+{
+  return m_Options.srsValue.second;
+}
+
 } // end namespace otb

Modules/IO/ExtendedFilename/test/CMakeLists.txt

 #
 # Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
+# Copyright (C) 2020 CS Systemes d'Information (CS SI)
 #
 # This file is part of Orfeo Toolbox
 #
@@ -58,7 +59,7 @@ otb_add_test(NAME ioTvExtendedFilenameToReaderOptions_FullOptions COMMAND otbExt
   ${BASELINE}/ioTvExtendedFilenameToReaderOptions_FullOptions.txt
   ${TEMP}/ioTvExtendedFilenameToReaderOptions_FullOptions.txt
   otbExtendedFilenameToReaderOptions
-  /home/data/filename.tif?&geom=/home/dev/custom.geom&sdataidx=2&resol=4&skipcarto=On&bands=-23,:3,45:,-6:-6,234:-5&nodata=-99999
+  /home/data/filename.tif?&geom=/home/dev/custom.geom&sdataidx=2&resol=4&skipcarto=On&bands=-23,:3,45:,-6:-6,234:-5
   ${TEMP}/ioTvExtendedFilenameToReaderOptions_FullOptions.txt
   )
 
@@ -86,7 +87,7 @@ otb_add_test(NAME ioTvExtendedFilenameToWriterOptions_FullOptions COMMAND otbExt
   ${BASELINE}/ioTvExtendedFilenameToWriterOptions_FullOptions.txt
   ${TEMP}/ioTvExtendedFilenameToWriterOptions_FullOptions.txt
   otbExtendedFilenameToWriterOptions
-  /home/data/filename.tif?&writegeom=ON&gdal:co:QUALITY=75&gdal:co:TILED=YES&gdal:co:BLOCKYSIZE=1024
+  /home/data/filename.tif?&writegeom=ON&gdal:co:QUALITY=75&gdal:co:TILED=YES&gdal:co:BLOCKYSIZE=1024&nodata=-99999&epsg=4326
   ${TEMP}/ioTvExtendedFilenameToWriterOptions_FullOptions.txt
   )
 

Modules/IO/ExtendedFilename/test/otbExtendedFilenameToWriterOptionsTest.cxx

 /*
  * Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
+ * Copyright (C) 2020 CS Systemes d'Information (CS SI)
  *
  * This file is part of Orfeo Toolbox
  *
@@ -45,10 +46,25 @@ int otbExtendedFilenameToWriterOptions(int itkNotUsed(argc), char* argv[])
 
   file << helper->gdalCreationOptionsIsSet() << std::endl;
   if (helper->gdalCreationOptionsIsSet())
+  {
     for (unsigned int i = 0; i < helper->GetgdalCreationOptions().size(); i++)
     {
       file << helper->GetgdalCreationOptions()[i] << std::endl;
     }
+  }
+
+  file << helper->NoDataValueIsSet() << std::endl;
+  if (helper->NoDataValueIsSet())
+  {
+    for (auto const& nodata_kv : helper->GetNoDataList())
+    {
+      file << nodata_kv.first << " ; " << nodata_kv.second << "\n";
+    }
+  }
+
+  file << helper->SrsValueIsSet() << std::endl;
+  if (helper->SrsValueIsSet())
+	  file << helper->GetSrsValue() << std::endl;
 
   return EXIT_SUCCESS;
 }

Modules/IO/IOGDAL/include/otbGDALImageIO.h

 /*
  * Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
- * Copyright (C) 2018 CS Systemes d'Information (CS SI)
+ * Copyright (C) 2018-2020 CS Systemes d'Information (CS SI)
  *
  * This file is part of Orfeo Toolbox
  *
@@ -30,6 +30,7 @@
 #include "otbImageIOBase.h"
 
 #include "OTBIOGDALExport.h"
+#include "otbSpatialReference.h"
 
 namespace otb
 {
@@ -197,6 +198,9 @@ public:
 
   itkGetMacro(NbBands, int);
 
+  /** Set the projection system from EPSG code */
+  void SetEpsgCode(const unsigned int wellKnownCRS);
+
 protected:
   /**
    * Constructor.
@@ -246,9 +250,10 @@ private:
   /** GDAL parameters. */
   typedef itk::SmartPointer<GDALDatasetWrapper> GDALDatasetWrapperPointer;
   GDALDatasetWrapperPointer                     m_Dataset;
+  unsigned int                                  m_epsgCode;
 
   GDALDataTypeWrapper* m_PxType;
-  /** Nombre d'octets par pixel */
+  /** Number of bytes per pixel */
   int m_BytePerPixel;
 
   bool GDALInfoReportCorner(const char* corner_name, double x, double y, double& dfGeoX, double& dfGeoY) const;

Modules/IO/IOGDAL/src/otbGDALImageIO.cxx

 /*
  * Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
- * Copyright (C) 2018 CS Systemes d'Information (CS SI)
+ * Copyright (C) 2018-2020 CS Systemes d'Information (CS SI)
  *
  * This file is part of Orfeo Toolbox
  *
@@ -116,6 +116,8 @@ GDALImageIO::GDALImageIO()
   m_ResolutionFactor  = 0;
   m_BytePerPixel      = 0;
   m_WriteRPCTags      = false;
+
+  m_epsgCode          = 0;
 }
 
 GDALImageIO::~GDALImageIO()
@@ -405,6 +407,11 @@ std::vector<std::string> GDALImageIO::GetOverviewsInfo()
   return desc;
 }
 
+void GDALImageIO::SetEpsgCode(const unsigned int epsgCode)
+{
+  m_epsgCode = epsgCode;
+}
+
 void GDALImageIO::InternalReadImageInformation()
 {
   itk::ExposeMetaData<unsigned int>(this->GetMetaDataDictionary(), MetaDataKey::ResolutionFactor, m_ResolutionFactor);
@@ -1165,6 +1172,13 @@ void GDALImageIO::Write(const void* buffer)
     lFirstColumn = 0;
   }
 
+  // If needed, set the coordinate reference
+  if (m_epsgCode != 0)
+  {
+    auto spatialReference = SpatialReference::FromEPSG(m_epsgCode);
+    m_Dataset->GetDataSet()->SetProjection(spatialReference.ToWkt().c_str());
+  }
+
   // Convert buffer from void * to unsigned char *
   // unsigned char *p = static_cast<unsigned char*>( const_cast<void *>(buffer));
   // printDataBuffer(p,  m_PxType->pixType, m_NbBands, 10*2); // Buffer incorrect

Modules/IO/ImageIO/include/otbImageFileWriter.h

 /*
  * Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
+ * Copyright (C) 2020 CS Systemes d'Information (CS SI)
  *
  * This file is part of Orfeo Toolbox
  *
@@ -57,7 +58,7 @@ namespace otb
  * \sa ImageFileReader
  * \sa ImageSeriesReader
  * \sa ImageIOBase
- * \sa ExtendedFilenameToReaderOptions
+ * \sa ExtendedFilenameToWriterOptions
  *
  * \ingroup OTBImageIO
  */

Modules/IO/ImageIO/include/otbImageFileWriter.hxx

 /*
  * Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
- * Copyright (C) 2018 CS Systemes d'Information (CS SI)
+ * Copyright (C) 2018-2020 CS Systemes d'Information (CS SI)
  *
  * This file is part of Orfeo Toolbox
  *
@@ -421,7 +421,7 @@ void ImageFileWriter<TInputImage>::GenerateOutputInformation(void)
 
   // Manage extended filename
   if ((strcmp(m_ImageIO->GetNameOfClass(), "GDALImageIO") == 0) &&
-      (m_FilenameHelper->gdalCreationOptionsIsSet() || m_FilenameHelper->WriteRPCTagsIsSet() || m_FilenameHelper->NoDataValueIsSet()))
+      (m_FilenameHelper->gdalCreationOptionsIsSet() || m_FilenameHelper->WriteRPCTagsIsSet() || m_FilenameHelper->NoDataValueIsSet() || m_FilenameHelper->SrsValueIsSet()))
   {
     typename GDALImageIO::Pointer imageIO = dynamic_cast<GDALImageIO*>(m_ImageIO.GetPointer());
 
@@ -438,6 +438,8 @@ void ImageFileWriter<TInputImage>::GenerateOutputInformation(void)
     imageIO->SetWriteRPCTags(m_FilenameHelper->GetWriteRPCTags());
     if (m_FilenameHelper->NoDataValueIsSet())
       imageIO->SetNoDataList(m_FilenameHelper->GetNoDataList());
+    if  (m_FilenameHelper->SrsValueIsSet())
+	  imageIO->SetEpsgCode(m_FilenameHelper->GetSrsValue());
   }
 
 

Modules/IO/ImageIO/test/CMakeLists.txt

 #
 # Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
+# Copyright (C) 2020 CS Systemes d'Information (CS SI)
 #
 # This file is part of Orfeo Toolbox
 #
@@ -910,6 +911,13 @@ otb_add_test(NAME ioTvImageFileWriterPNG2BSQ COMMAND otbImageIOTestDriver
   otbImageFileWriterTest
   ${INPUTDATA}/cthead1.png
   ${TEMP}/ioImageFileWriterPNG2BSQ_cthead1.hdr )
+  
+otb_add_test(NAME ioTvImageFileWriterTIF2TIF COMMAND otbImageIOTestDriver
+  --compare-image ${EPSILON_9}   ${BASELINE}/ioTvImageFileWriterTIF2TIFOutput.tif
+  ${TEMP}/ioImageFileWriterTIF2TIF_QB_Toulouse_Ortho_PAN.tif
+  otbImageFileWriterTest
+  ${INPUTDATA}/QB_Toulouse_Ortho_PAN.tif
+  ${TEMP}/ioImageFileWriterTIF2TIF_QB_Toulouse_Ortho_PAN.tif?epsg=4326 )
 
 otb_add_test(NAME ioTvCompareWritingComplexImage_TIF COMMAND otbImageIOTestDriver
   otbCompareWritingComplexImageTest