Add group reading operations (Resolve #9) (#14)

* Add group reading operations & examples
* update README.md

Author: cd10kfsu

CMakeLists.txt

@@ -154,6 +154,7 @@ endif()
 # test nc Fast I/O lib
 if (BUILD_FAST_IO AND HAS_NC)
     cda_add_test(test_ncio  test_ncio  ${CMAKE_SOURCE_DIR}/test-fast "Test passed")
+    cda_add_test(test_ncio_group  test_ncio_group  ${CMAKE_SOURCE_DIR}/test-fast "Test passed")
 endif()
 
 # test hdf5 Fast I/O lib

README.md

@@ -1,4 +1,4 @@
-#  F90GIO Release v2.0.3
+#  F90GIO Release v2.1
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7729468.svg)](https://doi.org/10.5281/zenodo.7729468)
 [![GitHub Clones](https://img.shields.io/badge/dynamic/json?color=blue&label=Unique%20clone%20since%2009/13/2023&query=uniques&url=https://gist.githubusercontent.com/cd10kfsu/10a9cdaa0d1d14b12e1f58bcef5e56c3/raw/clone.json&logo=github)](https://github.com/MShawon/github-clone-count-badge)
 [![build_gfortran](https://github.com/cd10kfsu/F90GIO/actions/workflows/build_gfortran.yml/badge.svg)](https://github.com/cd10kfsu/F90GIO/actions/workflows/build_gfortran.yml)

libsrc/fast/nc/m_ncio.f90

@@ -9,7 +9,7 @@ MODULE m_ncio
                     NF90_DOUBLE, NF90_FLOAT, NF90_INT, NF90_SHORT, NF90_BYTE, &
                     NF90_UNLIMITED, &
                     NF90_Open, NF90_Close, &
-                    NF90_inquire, NF90_Inq_Varid, NF90_Inquire_Variable, &
+                    NF90_inquire, NF90_Inq_Ncid, NF90_Inq_Varid, NF90_Inquire_Variable, &
                     NF90_Inq_DimID, NF90_Inquire_Dimension, &
                     NF90_Get_Var, NF90_Put_Var, &
                     NF90_Create, NF90_Def_dim, NF90_Def_Var, NF90_Enddef, NF90_reDef, &
@@ -22,6 +22,9 @@ MODULE m_ncio
 ! open/close file
   PUBLIC :: nc_get_fid, nc_close_fid
 
+! get group id
+  PUBLIC :: nc_get_gid
+
 ! Create new file/dim/var
   PUBLIC :: nc_create_file, nc_create_dim, nc_create_var
 
@@ -42,9 +45,11 @@ MODULE m_ncio
   PUBLIC :: nc_fndvar, nc_fnddim
 
 ! read ND vars
+  PUBLIC :: nc_rdvar
   PUBLIC :: nc_rdvar1d, nc_rdvar2d, nc_rdvar3d, nc_rdvar4d
 
 ! write ND vars
+  PUBLIC :: nc_wrtvar
   PUBLIC :: nc_wrtvar1d, nc_wrtvar2d, nc_wrtvar3d, nc_wrtvar4d
 
 ! low-level Read 1D
@@ -82,6 +87,17 @@ MODULE m_ncio
     MODULE PROCEDURE nc_rdatt_r4, nc_rdatt_r8
   END INTERFACE
 
+  INTERFACE nc_rdvar
+    MODULE PROCEDURE nc_rdvar1d_i1, nc_rdvar1d_i2, nc_rdvar1d_i4
+    MODULE PROCEDURE nc_rdvar1d_r4, nc_rdvar1d_r8
+    MODULE PROCEDURE nc_rdvar2d_i1, nc_rdvar2d_i2, nc_rdvar2d_i4
+    MODULE PROCEDURE nc_rdvar2d_r4, nc_rdvar2d_r8
+    MODULE PROCEDURE nc_rdvar3d_i1, nc_rdvar3d_i2, nc_rdvar3d_i4
+    MODULE PROCEDURE nc_rdvar3d_r4, nc_rdvar3d_r8
+    MODULE PROCEDURE nc_rdvar4d_i1, nc_rdvar4d_i2, nc_rdvar4d_i4
+    MODULE PROCEDURE nc_rdvar4d_r4, nc_rdvar4d_r8
+  END INTERFACE
+
   INTERFACE nc_rdvar1d
     MODULE PROCEDURE nc_rdvar1d_i1, nc_rdvar1d_i2, nc_rdvar1d_i4
     MODULE PROCEDURE nc_rdvar1d_r4, nc_rdvar1d_r8
@@ -102,6 +118,17 @@ MODULE m_ncio
     MODULE PROCEDURE nc_rdvar4d_r4, nc_rdvar4d_r8
   END INTERFACE
 
+  INTERFACE nc_wrtvar
+    MODULE PROCEDURE nc_wrtvar1d_i1, nc_wrtvar1d_i2, nc_wrtvar1d_i4
+    MODULE PROCEDURE nc_wrtvar1d_r4, nc_wrtvar1d_r8
+    MODULE PROCEDURE nc_wrtvar2d_i1, nc_wrtvar2d_i2, nc_wrtvar2d_i4
+    MODULE PROCEDURE nc_wrtvar2d_r4, nc_wrtvar2d_r8
+    MODULE PROCEDURE nc_wrtvar3d_i1, nc_wrtvar3d_i2, nc_wrtvar3d_i4
+    MODULE PROCEDURE nc_wrtvar3d_r4, nc_wrtvar3d_r8
+    MODULE PROCEDURE nc_wrtvar4d_i1, nc_wrtvar4d_i2, nc_wrtvar4d_i4
+    MODULE PROCEDURE nc_wrtvar4d_r4, nc_wrtvar4d_r8
+  END INTERFACE
+
   INTERFACE nc_wrtvar1d
     MODULE PROCEDURE nc_wrtvar1d_i1, nc_wrtvar1d_i2, nc_wrtvar1d_i4
     MODULE PROCEDURE nc_wrtvar1d_r4, nc_wrtvar1d_r8
@@ -144,6 +171,7 @@ MODULE m_ncio
     INTEGER(i1) :: gendim  = 8
     INTEGER(i1) :: genvar  = 9
     INTEGER(i1) :: endgen  = 10
+    INTEGER(i1) :: gid     = 11
     INTEGER(i1) :: undef  = 127 ! max positive for signed 8-byte int
   END TYPE 
   TYPE(t_errcode),SAVE,PRIVATE:: errcode
@@ -246,6 +274,24 @@ SUBROUTINE nc_close_fid(fid)
 
 END SUBROUTINE nc_close_fid
 
+!--------------------------------------------------------------------------------
+! group operations
+!--------------------------------------------------------------------------------
+SUBROUTINE nc_get_gid(fid, gname, gid)
+  IMPLICIT NONE
+
+  INTEGER(i4),INTENT(IN) :: fid
+  CHARACTER(*),INTENT(IN) :: gname
+  INTEGER(i4),INTENT(OUT) :: gid
+  INTEGER(i4) :: istat
+
+  istat = nf90_inq_ncid(fid, trim(gname), gid)
+  if (istat /= NF90_NOERR) then
+     write(lout_log,*) "[err] nc_close_fid::Fail to get group id =",fid, "for var:", trim(gname)
+     call mystop(errcode%gid)
+  end if
+
+END SUBROUTINE nc_get_gid
 
 !--------------------------------------------------------------------------------
 ! create vars

test-fast/CMakeLists.txt

@@ -8,6 +8,16 @@ if (BUILD_FAST_IO AND HAS_NC)
     target_link_libraries(${EXE} ${TESTLIBS})
     set_target_properties(${EXE}
         PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/test-fast)
+
+    set(EXE test_ncio_group)
+    set(TESTSRC test_ncio_group.f90)
+    set(TESTLIBS ncio $ENV{NC_LIBS})
+    add_executable(${EXE} ${TESTSRC})
+#target_include_directories(${EXE} PRIVATE "$<BUILD_INTERFACE:${CMAKE_Fortran_MODULE_DIRECTORY}>")
+    target_link_libraries(${EXE} ${TESTLIBS})
+    set_target_properties(${EXE}
+        PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/test-fast)
+ 
 endif()
 
 if (BUILD_FAST_IO AND HAS_H5)

test-fast/profile_has_groups.nc4

@@ -0,0 +1,61 @@
+PROGRAM test_ncio_group
+  USE iso_fortran_env, ONLY: r8 =>real64, r4 =>real32
+  USE m_ncio,   ONLY: nc_get_fid, nc_get_gid, nc_close_fid, nc_rddim, nc_rdatt, &
+                      nc_rdvar
+  use netcdf
+  IMPLICIT NONE
+
+  CHARACTER(256) :: obsinfile
+
+  INTEGER :: fid, gid
+  INTEGER :: nx   ! Location
+  REAL(r4),ALLOCATABLE :: alon1d(:), alat1d(:)  ! nx
+  REAL(r4),ALLOCATABLE :: hofx0_waterTemperature(:) ! nx
+  REAL(r4) :: rFillValue
+
+!-------------------------------------------------------------------------------
+! Open the nc file 
+
+  obsinfile = "profile_has_groups.nc4"
+  WRITE(6,*) "[msg] ioda_read::obsinfile=", trim(obsinfile)
+  CALL nc_get_fid(trim(obsinfile), fid)
+  
+!-------------------------------------------------------------------------------
+! read global dimension
+  CALL nc_rddim(fid, "Location", nx)
+  WRITE(6,*) "[msg] ioda_read::Location=", nx
+
+! read group "MetaData"
+  CALL nc_get_gid(fid, "MetaData", gid)
+  ALLOCATE(alon1d(nx),alat1d(nx))
+  CALL nc_rdvar(gid, "longitude", alon1d)
+  WRITE(6,*) "[msg] ioda_read::MetaData - longitude: min, max=", &
+             minval(alon1d), maxval(alon1d)
+  CALL nc_rdvar(gid, "latitude",  alat1d)
+  WRITE(6,*) "[msg] ioda_read::MetaData - latitude: min, max=", &
+             minval(alat1d), maxval(alat1d)
+  CALL nc_rdatt(gid, "latitude", "_FillValue", rFillValue)
+  WRITE(6,*) "[msg] ioda_read::MetaData - latitude: _FillValue =", rFillValue
+
+  ! [FIXME]: currently no way to read string attributes using netcdf-fortran
+  !  	float longitude(Location) ;
+  !		longitude:_FillValue = -3.368795e+38f ;
+  !		string longitude:units = "degrees_east" ;
+
+! read another group "hofx0"
+  CALL nc_get_gid(fid, "hofx0", gid)
+  ALLOCATE(hofx0_waterTemperature(nx))
+  CALL nc_rdvar(gid, "waterTemperature",hofx0_waterTemperature)
+  WRITE(6,*) "[msg] ioda_read::hofx0 - waterTemperature: min, max=", &
+             minval(hofx0_waterTemperature), maxval(hofx0_waterTemperature)
+
+!-------------------------------------------------------------------------------
+! Close the nc file 
+
+  CALL nc_close_fid(fid)
+
+  WRITE(6,*) "Test passed"
+
+END PROGRAM
+
+