Merge branch 'sb_gdal_v3_1' into 'develop'

Update GDAL version in superbuild (3.1.0)

Closes #2052

See merge request orfeotoolbox/otb!715

Data/Baseline/OTB/Files/ioOtbVectorImageTestFORMOSAT2.1.txt

 ------ IMAGE --------
 Spacing [1, 1]
-Origin [0, 0]
+Origin [0.5, 0.5]
 Projection REF 
-GCP Projection GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0],UNIT["degree",0.0174532925199433],AUTHORITY["EPSG","4326"]]
+GCP Projection GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]
 GCP Count 4
 GCP[0] Id 1
 GCP[0] Info 
-GCP[0] Row 1
-GCP[0] Col 1
+GCP[0] Row 0.5
+GCP[0] Col 0.5
 GCP[0] X 1.05476
 GCP[0] Y 43.5896
 GCP[0] Z 0
 ----------------
 GCP[1] Id 2
 GCP[1] Info 
-GCP[1] Row 1
-GCP[1] Col 3000
+GCP[1] Row 0.5
+GCP[1] Col 2999.5
 GCP[1] X 1.41679
 GCP[1] Y 43.5219
 GCP[1] Z 0
 ----------------
 GCP[2] Id 3
 GCP[2] Info 
-GCP[2] Row 3000
-GCP[2] Col 3000
+GCP[2] Row 2999.5
+GCP[2] Col 2999.5
 GCP[2] X 1.32096
 GCP[2] Y 43.313
 GCP[2] Z 0
 ----------------
 GCP[3] Id 4
 GCP[3] Info 
-GCP[3] Row 3000
-GCP[3] Col 1
+GCP[3] Row 2999.5
+GCP[3] Col 0.5
 GCP[3] X 0.960095
 GCP[3] Y 43.3803
 GCP[3] Z 0

Data/Baseline/OTB/Files/ioOtbVectorImageTestFORMOSAT2.3.txt

------- IMAGE --------
-Spacing [1, 1]
-Origin [0.5, 0.5]
-Projection REF 
-GCP Projection GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]
-GCP Count 4
-GCP[0] Id 1
-GCP[0] Info 
-GCP[0] Row 0.5
-GCP[0] Col 0.5
-GCP[0] X 1.05476
-GCP[0] Y 43.5896
-GCP[0] Z 0
-----------------
-GCP[1] Id 2
-GCP[1] Info 
-GCP[1] Row 0.5
-GCP[1] Col 2999.5
-GCP[1] X 1.41679
-GCP[1] Y 43.5219
-GCP[1] Z 0
-----------------
-GCP[2] Id 3
-GCP[2] Info 
-GCP[2] Row 2999.5
-GCP[2] Col 2999.5
-GCP[2] X 1.32096
-GCP[2] Y 43.313
-GCP[2] Z 0
-----------------
-GCP[3] Id 4
-GCP[3] Info 
-GCP[3] Row 2999.5
-GCP[3] Col 0.5
-GCP[3] X 0.960095
-GCP[3] Y 43.3803
-GCP[3] Z 0
-----------------
-Geo Transform 
-Corners 
- UL[0] -> 0
- UL[1] -> 0
- UR[0] -> 3000
- UR[1] -> 0
- LL[0] -> 0
- LL[1] -> 3000
- LR[0] -> 3000
- LR[1] -> 3000

Data/Baseline/OTB/Files/ioOtbVectorImageTestFORMOSAT2.txt

 ------ IMAGE --------
 Spacing [1, 1]
-Origin [0, 0]
+Origin [0.5, 0.5]
 Projection REF 
-GCP Projection GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.2572235630016,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0],UNIT["degree",0.0174532925199433],AUTHORITY["EPSG","4326"]]
+GCP Projection GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]
 GCP Count 4
 GCP[0] Id 1
 GCP[0] Info 
-GCP[0] Row 1
-GCP[0] Col 1
+GCP[0] Row 0.5
+GCP[0] Col 0.5
 GCP[0] X 1.05476
 GCP[0] Y 43.5896
 GCP[0] Z 0
 ----------------
 GCP[1] Id 2
 GCP[1] Info 
-GCP[1] Row 1
-GCP[1] Col 3000
+GCP[1] Row 0.5
+GCP[1] Col 2999.5
 GCP[1] X 1.41679
 GCP[1] Y 43.5219
 GCP[1] Z 0
 ----------------
 GCP[2] Id 3
 GCP[2] Info 
-GCP[2] Row 3000
-GCP[2] Col 3000
+GCP[2] Row 2999.5
+GCP[2] Col 2999.5
 GCP[2] X 1.32096
 GCP[2] Y 43.313
 GCP[2] Z 0
 ----------------
 GCP[3] Id 4
 GCP[3] Info 
-GCP[3] Row 3000
-GCP[3] Col 1
+GCP[3] Row 2999.5
+GCP[3] Col 0.5
 GCP[3] X 0.960095
 GCP[3] Y 43.3803
 GCP[3] Z 0

Data/Baseline/OTB/Files/ioOtbVectorImageTestSpot5.1.txt

 ------ IMAGE --------
 Spacing [1, 1]
-Origin [0, 0]
+Origin [0.5, 0.5]
 Projection REF 
-GCP Projection GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0],UNIT["degree",0.0174532925199433],AUTHORITY["EPSG","4326"]]
+GCP Projection GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]
 GCP Count 4
 GCP[0] Id 1
 GCP[0] Info 
-GCP[0] Row 1
-GCP[0] Col 1
+GCP[0] Row 0.5
+GCP[0] Col 0.5
 GCP[0] X 51.1515
 GCP[0] Y 36.0442
 GCP[0] Z 0
 ----------------
 GCP[1] Id 2
 GCP[1] Info 
-GCP[1] Row 1
-GCP[1] Col 6000
+GCP[1] Row 0.5
+GCP[1] Col 5999.5
 GCP[1] X 51.8029
 GCP[1] Y 35.9172
 GCP[1] Z 0
 ----------------
 GCP[2] Id 3
 GCP[2] Info 
-GCP[2] Row 6000
-GCP[2] Col 6000
+GCP[2] Row 5999.5
+GCP[2] Col 5999.5
 GCP[2] X 51.6467
 GCP[2] Y 35.3907
 GCP[2] Z 0
 ----------------
 GCP[3] Id 4
 GCP[3] Info 
-GCP[3] Row 6000
-GCP[3] Col 1
+GCP[3] Row 5999.5
+GCP[3] Col 0.5
 GCP[3] X 50.9995
 GCP[3] Y 35.5173
 GCP[3] Z 0
@@ -46,3 +46,4 @@ Corners
  LL[1] -> 6000
  LR[0] -> 6000
  LR[1] -> 6000
+

Data/Baseline/OTB/Files/ioOtbVectorImageTestSpot5.3.txt

------- IMAGE --------
-Spacing [1, 1]
-Origin [0.5, 0.5]
-Projection REF 
-GCP Projection GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]
-GCP Count 4
-GCP[0] Id 1
-GCP[0] Info 
-GCP[0] Row 0.5
-GCP[0] Col 0.5
-GCP[0] X 51.1515
-GCP[0] Y 36.0442
-GCP[0] Z 0
-----------------
-GCP[1] Id 2
-GCP[1] Info 
-GCP[1] Row 0.5
-GCP[1] Col 5999.5
-GCP[1] X 51.8029
-GCP[1] Y 35.9172
-GCP[1] Z 0
-----------------
-GCP[2] Id 3
-GCP[2] Info 
-GCP[2] Row 5999.5
-GCP[2] Col 5999.5
-GCP[2] X 51.6467
-GCP[2] Y 35.3907
-GCP[2] Z 0
-----------------
-GCP[3] Id 4
-GCP[3] Info 
-GCP[3] Row 5999.5
-GCP[3] Col 0.5
-GCP[3] X 50.9995
-GCP[3] Y 35.5173
-GCP[3] Z 0
-----------------
-Geo Transform 
-Corners 
- UL[0] -> 0
- UL[1] -> 0
- UR[0] -> 6000
- UR[1] -> 0
- LL[0] -> 0
- LL[1] -> 6000
- LR[0] -> 6000
- LR[1] -> 6000

Data/Baseline/OTB/Files/ioOtbVectorImageTestSpot5.txt

 ------ IMAGE --------
 Spacing [1, 1]
-Origin [0, 0]
+Origin [0.5, 0.5]
 Projection REF 
-GCP Projection GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.2572235629972,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0],UNIT["degree",0.0174532925199433],AUTHORITY["EPSG","4326"]]
+GCP Projection GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]
 GCP Count 4
 GCP[0] Id 1
 GCP[0] Info 
-GCP[0] Row 1
-GCP[0] Col 1
+GCP[0] Row 0.5
+GCP[0] Col 0.5
 GCP[0] X 51.1515
 GCP[0] Y 36.0442
 GCP[0] Z 0
 ----------------
 GCP[1] Id 2
 GCP[1] Info 
-GCP[1] Row 1
-GCP[1] Col 6000
+GCP[1] Row 0.5
+GCP[1] Col 5999.5
 GCP[1] X 51.8029
 GCP[1] Y 35.9172
 GCP[1] Z 0
 ----------------
 GCP[2] Id 3
 GCP[2] Info 
-GCP[2] Row 6000
-GCP[2] Col 6000
+GCP[2] Row 5999.5
+GCP[2] Col 5999.5
 GCP[2] X 51.6467
 GCP[2] Y 35.3907
 GCP[2] Z 0
 ----------------
 GCP[3] Id 4
 GCP[3] Info 
-GCP[3] Row 6000
-GCP[3] Col 1
+GCP[3] Row 5999.5
+GCP[3] Col 0.5
 GCP[3] X 50.9995
 GCP[3] Y 35.5173
 GCP[3] Z 0

Documentation/Cookbook/rst/CompilingOTBFromSource.rst

@@ -29,7 +29,7 @@ process:
     +------------------------------------------------------------------+-----------------------+----------------------------+--------------------------+
     | `ITK <http://www.itk.org>`_                                      | Yes                   | 4.6.0                      | 4.13.1                   |
     +------------------------------------------------------------------+-----------------------+----------------------------+--------------------------+
-    | `GDAL <http://www.gdal.org>`_                                    | Yes                   | 2.0                        | 2.4.1                    |
+    | `GDAL <http://www.gdal.org>`_                                    | Yes                   | 2.4.1                      | 3.1.0                    |
     +------------------------------------------------------------------+-----------------------+----------------------------+--------------------------+
     | `OSSIM <http://www.ossim.org>`_                                  | Yes                   | 1.8.20-3                   | 1.8.20                   |
     +------------------------------------------------------------------+-----------------------+----------------------------+--------------------------+

SuperBuild/CMake/External_gdal.cmake

@@ -148,8 +148,8 @@ endif()
 
 ExternalProject_Add(GDAL
   PREFIX GDAL
-  URL "http://download.osgeo.org/gdal/3.0.2/gdal-3.0.2.tar.gz"
-  URL_MD5 8a31507806b26f070858558aaad42277
+  URL "http://download.osgeo.org/gdal/3.1.0/gdal-3.1.0.tar.gz"
+  URL_MD5 bda0f002cd63b51c8d2f1b1400daffa9
   SOURCE_DIR ${GDAL_SB_SRC}
   BINARY_DIR ${GDAL_SB_SRC}
   INSTALL_DIR ${SB_INSTALL_PREFIX}

SuperBuild/patches/GDAL/gdal-3-ioheaderconflict-win.diff

+diff -burN gdal_orig/apps/gdaltransform.cpp gdal/apps/gdaltransform.cpp 
+--- gdal_orig/apps/gdaltransform.cpp	2020-05-28 13:20:16.124465749 +0200
++++ gdal/apps/gdaltransform.cpp	2020-05-28 13:26:47.563450287 +0200
+@@ -47,7 +47,9 @@
+ #include "commonutils.h"
+ 
+ #ifdef _WIN32
+-#include <io.h>
++// We need the io.h file from system but io.h from geos conflicts with io.h from system
++//#include <io.h>
++#include <corecrt_io.h>
+ #else
+ #include <unistd.h>
+ #endif
+diff -burN gdal_orig/apps/gdallocationinfo.cpp gdal/apps/gdallocationinfo.cpp 
+--- gdal_orig/apps/gdallocationinfo.cpp	2020-05-28 13:20:16.124465749 +0200
++++ gdal/apps/gdallocationinfo.cpp	2020-05-28 13:26:58.719601480 +0200
+@@ -36,7 +36,9 @@
+ #include <vector>
+ 
+ #ifdef _WIN32
+-#include <io.h>
++// We need the io.h file from system but io.h from geos conflicts with io.h from system
++//#include <io.h>
++#include <corecrt_io.h>
+ #else
+ #include <unistd.h>
+ #endif

SuperBuild/patches/GDAL/gdal-4-fixhdf5-win.diff

---- gdal-2.4.1_orig/frmts/hdf5/makefile.vc	2019-03-15 13:30:02.000000000 +0100
-+++ gdal-2.4.1/frmts/hdf5/makefile.vc	2019-04-05 17:43:22.356322797 +0200
-@@ -7,7 +7,7 @@
- 
- PLUGIN_DLL 	=	gdal_HDF5.dll
- 
--EXTRAFLAGS 	= 	-I$(HDF5_DIR)\include -DWIN32 -D_HDF5USEDLL_ 
-+EXTRAFLAGS 	= 	-I$(HDF5_DIR)\include -DWIN32 -DH5_BUILT_AS_DYNAMIC_LIB 
- 
- !IF "$(HDF5_PLUGIN)" == "YES"
- EXTRAFLAGS = $(EXTRAFLAGS) -DHDF5_PLUGIN

SuperBuild/patches/GDAL/nmake_gdal_extra.opt.in

@@ -109,6 +109,10 @@ NETCDF_INC_DIR = @SB_INSTALL_PREFIX_NATIVE@\include
 NETCDF_HAS_NC4 = YES
 NETCDF_HAS_HDF4 = YES
 
+# Needed to define H5_BUILT_AS_DYNAMIC_LIB for windows compilation 
+# scenarios where it is not exported on the target (non-CMake builds)
+HDF5_H5_IS_DLL = YES
+
 # Binding list. One or several in the following list
 # csharp, java, python
 BINDINGS=python