Merge pull request #171 from JCSDA/feature/btj_extract_ACCoeff_NLTE_f…

…rom_BIN_to_NC

Enhance SpcCoeff_BIN2NC to Support Generation of Associated ACCoeff and NLTECoeff NetCDF Files during Binary to NetCDF Conversion

src/Coefficients/SpcCoeff/SpcCoeff_BIN2NC/SpcCoeff_BIN2NC.f90

@@ -35,27 +35,37 @@ PROGRAM SpcCoeff_BIN2NC
   INTEGER :: err_stat
   CHARACTER(256) :: msg
   CHARACTER(256) :: BIN_filename
-  CHARACTER(256) :: NC_filename
-  CHARACTER(256) :: answer
+  CHARACTER(256) :: NC_filename, tmp_filename
   CHARACTER(256) :: version_str
+  INTEGER :: n_args
 
   ! Program header
   CALL CRTM_Version(version_str)
   CALL Program_Message( PROGRAM_NAME, &
                         'Program to convert a CRTM SpcCoeff data file from Binary to netCDF format.', &
                         'CRTM Version: '//TRIM(version_str) )
 
-  ! Get the filenames
-  IF ( Big_Endian() ) THEN
-     WRITE(*,FMT='(/5x,"Enter the INPUT Binary [Big Endian] SpcCoeff filename : ")', ADVANCE='NO')
-  ELSE
-     WRITE(*,FMT='(/5x,"Enter the INPUT Binary [Little Endian] SpcCoeff filename : ")', ADVANCE='NO')
+  ! Get the filename                                                                                                                                                                                   ! Check for command line argument
+  n_args = COMMAND_ARGUMENT_COUNT()
+  IF ( n_args > 0 ) THEN
+     CALL GET_COMMAND_ARGUMENT(1, BIN_filename)
+     tmp_filename = BIN_filename(1:LEN_TRIM(BIN_filename) - 4)//".nc"
+     NC_filename = TRIM(ADJUSTL(tmp_filename))
+     PRINT *, "NC_filename:", NC_filename
+  ELSE     
+     ! Get the filenames
+     IF ( Big_Endian() ) THEN
+        WRITE(*,FMT='(/5x,"Enter the INPUT Binary [Big Endian] SpcCoeff filename : ")', ADVANCE='NO')
+     ELSE
+        WRITE(*,FMT='(/5x,"Enter the INPUT Binary [Little Endian] SpcCoeff filename : ")', ADVANCE='NO')
+     END IF
+     READ(*,'(a)') BIN_filename
+     BIN_filename = ADJUSTL(BIN_filename)
+     WRITE(*,FMT='(/5x,"Enter the OUTPUT netCDF SpcCoeff filename: ")', ADVANCE='NO')
+     READ(*,'(a)') NC_filename
+     NC_filename = ADJUSTL(NC_filename)
   END IF
-   READ(*,'(a)') BIN_filename
-  BIN_filename = ADJUSTL(BIN_filename)
-  WRITE(*,FMT='(/5x,"Enter the OUTPUT netCDF SpcCoeff filename: ")', ADVANCE='NO')
-  READ(*,'(a)') NC_filename
-  NC_filename = ADJUSTL(NC_filename)
+
 
   ! ...Sanity check that they're not the same
   IF ( bin_filename == nc_filename ) THEN

src/Coefficients/SpcCoeff/SpcCoeff_Binary_IO.f90

@@ -693,7 +693,7 @@ FUNCTION SpcCoeff_Binary_WriteFile( &
       CALL Write_Cleanup(); RETURN
     END IF
     ! ...Write the channel data
-    IF(SpcCoeff%Version > 2) THEN
+    IF(SpcCoeff%Version > 3) THEN
       WRITE( fid, IOSTAT=io_stat ) &
           SpcCoeff%Sensor_Channel            , &
           SpcCoeff%Polarization              , &
@@ -707,7 +707,7 @@ FUNCTION SpcCoeff_Binary_WriteFile( &
           SpcCoeff%Band_C2                   , &
           SpcCoeff%Cosmic_Background_Radiance, &
           SpcCoeff%Solar_Irradiance 
-    ELSE IF(SpcCoeff%Version < 3) THEN
+    ELSE IF(SpcCoeff%Version < 4) THEN
       WRITE( fid, IOSTAT=io_stat ) &
           SpcCoeff%Sensor_Channel            , &
           SpcCoeff%Polarization              , &

src/Coefficients/SpcCoeff/SpcCoeff_IO.f90

@@ -26,8 +26,11 @@ MODULE SpcCoeff_IO
   USE SpcCoeff_netCDF_IO , ONLY: SpcCoeff_netCDF_InquireFile, &
                                  SpcCoeff_netCDF_ReadFile   , &
                                  SpcCoeff_netCDF_WriteFile
-  USE ACCoeff_netCDF_IO  , ONLY: ACCoeff_netCDF_ReadFile
-  USE NLTECoeff_netCDF_IO, ONLY: NLTECoeff_netCDF_ReadFile
+  USE ACCoeff_Define     , ONLY: ACCoeff_Associated
+  USE NLTECoeff_Define   , ONLY: NLTECoeff_Associated
+  USE ACCoeff_netCDF_IO  , ONLY: ACCoeff_netCDF_ReadFile, ACCoeff_netCDF_WriteFile
+  USE NLTECoeff_netCDF_IO, ONLY: NLTECoeff_netCDF_ReadFile, NLTECoeff_netCDF_WriteFile
+
   ! Disable implicit typing
   IMPLICIT NONE
 
@@ -820,26 +823,62 @@ FUNCTION SpcCoeff_Binary_to_netCDF( &
       END IF
     END IF
 
-    ! Read the substructure netCDF filenames
+
+    ! Read the substructure netCDF filenames 
     ! ...ACCoeff
     sub_filename = TRIM(spccoeff%Sensor_Id)//'.ACCoeff.nc'
     IF ( File_Exists(sub_filename) ) THEN
       err_stat = ACCoeff_netCDF_ReadFile( sub_filename, spccoeff%AC, Quiet = Quiet )
       IF ( err_stat /= SUCCESS ) THEN
-        msg = 'Error reading netCDF file '//TRIM(sub_filename)
+        msg = 'Error reading existing ACCoeff netCDF file '//TRIM(sub_filename)
         CALL Display_Message( ROUTINE_NAME, msg, err_stat )
         RETURN
       END IF
+    ELSE
+       IF ( ACCoeff_Associated(spccoeff%AC) ) THEN
+          !** there's no external file, but there's an ACCoeff structure
+          !** yoink the spccoeff%AC into sub_filename
+          err_stat = ACCoeff_netCDF_WriteFile( &
+               sub_filename      , &
+               spccoeff%AC       , &
+               Quiet   = Quiet   , &
+               Title   = "Earth, Platform, Space antenna efficiencies for "//trim(adjustl(spccoeff%sensor_id))//" for each fov, channel.", &
+               History = "Extracted from "//trim(adjustl(BIN_Filename))//" using "//trim(adjustl(ROUTINE_NAME))//" [email protected]" , &
+               Comment = ""  )
+          IF ( err_stat /= SUCCESS ) THEN
+             msg = 'Error creating ACCoeff netCDF file '//TRIM(sub_filename)
+             CALL Display_Message( ROUTINE_NAME, msg, err_stat )
+             RETURN
+          END IF
+       END IF
     END IF
+
     ! ...NLTECoeff
     sub_filename = TRIM(spccoeff%Sensor_Id)//'.NLTECoeff.nc'
     IF ( File_Exists(sub_filename) ) THEN
-      err_stat = NLTECoeff_netCDF_ReadFile( sub_filename, spccoeff%NC, Quiet = Quiet )
-      IF ( err_stat /= SUCCESS ) THEN
-        msg = 'Error reading netCDF file '//TRIM(sub_filename)
-        CALL Display_Message( ROUTINE_NAME, msg, err_stat )
-        RETURN
-      END IF
+       err_stat = NLTECoeff_netCDF_ReadFile( sub_filename, spccoeff%NC, Quiet = Quiet )
+       IF ( err_stat /= SUCCESS ) THEN
+          msg = 'Error reading netCDF file '//TRIM(sub_filename)
+          CALL Display_Message( ROUTINE_NAME, msg, err_stat )
+          RETURN
+       END IF
+    ELSE
+       IF ( NLTECoeff_Associated(spccoeff%NC) ) THEN
+          !** there's no external file, but there's an NLTECoeff structure
+          !** yoink the spccoeff%NC into sub_filename
+          err_stat = NLTECoeff_netCDF_WriteFile( &
+               sub_filename      , &
+               spccoeff%NC       , &
+               Quiet   = Quiet   , &
+               Title   = "NLTE Coefficients for "//TRIM(ADJUSTL(spccoeff%sensor_id))//"." , &
+               History = "Extracted from "//TRIM(ADJUSTL(BIN_Filename))//" using "//TRIM(ADJUSTL(ROUTINE_NAME))//" [email protected]" , &
+               Comment = ""  )
+          IF ( err_stat /= SUCCESS ) THEN
+             msg = 'Error creating NLTECoeff netCDF file '//TRIM(sub_filename)
+             CALL Display_Message( ROUTINE_NAME, msg, err_stat )
+             RETURN
+          END IF
+       END IF
     END IF
 
 

src/Coefficients/SpcCoeff/SpcCoeff_Inspect/SpcCoeff_Inspect.f90

@@ -1,7 +1,7 @@
 !
 ! SpcCoeff_Inspect
 !
-! Program to inspect the contents of a CRTM Binary format SpcCoeff file.
+! Program to inspect the contents of a CRTM SpcCoeff file (binary or netCDF)
 !
 !
 ! CREATION HISTORY:
@@ -19,7 +19,7 @@ PROGRAM SpcCoeff_Inspect
   USE Message_Handler   , ONLY: SUCCESS, FAILURE, Program_Message, Display_Message
   USE SpcCoeff_Define   , ONLY: SpcCoeff_type, SpcCoeff_Destroy, &
                                 Inspect => SpcCoeff_Inspect
-  USE SpcCoeff_Binary_IO, ONLY: SpcCoeff_Binary_ReadFile
+  USE SpcCoeff_IO, ONLY: SpcCoeff_ReadFile
   ! Disable implicit typing
   IMPLICIT NONE
 
@@ -36,6 +36,7 @@ PROGRAM SpcCoeff_Inspect
   CHARACTER(256) :: filename, msg
   INTEGER :: n_args
   TYPE(SpcCoeff_type) :: sc
+  LOGICAL :: is_nc, is_bin
 
   ! Generate a string containing the SpcCoeff release for info
   WRITE(msg,'(i10)') sc%Release
@@ -44,7 +45,7 @@ PROGRAM SpcCoeff_Inspect
   ! Output program header
   CALL Program_Message( PROGRAM_NAME, &
                         'Program to display the contents of a CRTM '//&
-                        'Binary format R'//TRIM(ADJUSTL(msg))//' SpcCoeff '//&
+                        'Binary/netCDF format R'//TRIM(ADJUSTL(msg))//' SpcCoeff '//&
                         'file to stdout.', &
                         '$Revision$' )
 
@@ -53,7 +54,7 @@ PROGRAM SpcCoeff_Inspect
   IF ( n_args > 0 ) THEN 
     CALL GET_COMMAND_ARGUMENT(1, filename) 
   ELSE 
-    WRITE( *,FMT='(/5x,"Enter the Binary SpcCoeff filename: ")',ADVANCE='NO' ) 
+    WRITE( *,FMT='(/5x,"Enter the SpcCoeff filename: ")',ADVANCE='NO' ) 
     READ( *,'(a)' ) filename 
   END IF
   filename = ADJUSTL(filename)
@@ -62,10 +63,19 @@ PROGRAM SpcCoeff_Inspect
     CALL Display_Message( PROGRAM_NAME, msg, FAILURE ); STOP
   END IF
 
-  ! Read the binary data file
-  err_stat = SpcCoeff_Binary_ReadFile( filename, sc )
+  ! Check if filename ends in ".nc"
+  is_nc = (INDEX(TRIM(filename), '.nc') == LEN_TRIM(filename) - 2)
+
+  ! Check if filename ends in ".bin"
+  is_bin = (INDEX(TRIM(filename), '.bin') == LEN_TRIM(filename) - 3)
+
+  err_stat = FAILURE
+  ! Read the data file
+  If (is_bin) err_stat = SpcCoeff_ReadFile( filename, sc )
+  IF (is_nc)  err_stat = SpcCoeff_ReadFile( filename, sc, netCDF=.TRUE. )
+
   IF ( err_stat /= SUCCESS ) THEN
-    msg = 'Error reading Binary SpcCoeff file '//TRIM(filename)
+    msg = 'Error reading SpcCoeff file '//TRIM(filename)
     CALL Display_Message( PROGRAM_NAME, msg, FAILURE ); STOP
   END IF
 

src/Coefficients/SpcCoeff/SpcCoeff_NC2BIN/SpcCoeff_NC2BIN.f90

@@ -36,28 +36,37 @@ PROGRAM SpcCoeff_NC2BIN
   INTEGER :: err_stat
   CHARACTER(256) :: msg, version_str
   CHARACTER(256) :: nc_filename
-  CHARACTER(256) :: bin_filename
-  CHARACTER(256) :: answer
-  INTEGER :: version
+  CHARACTER(256) :: bin_filename, tmp_filename
+  INTEGER :: n_args
 
   ! Program header
   CALL CRTM_Version (version_str)
   CALL Program_Message( PROGRAM_NAME, &
                         'Program to convert a CRTM SpcCoeff data file '//&
                         'from netCDF to Binary format.', &
                         'CRTM Version:'//trim(version_str) )
-
-  ! Get the filenames
-  WRITE(*,FMT='(/5x,"Enter the INPUT netCDF SpcCoeff filename : ")', ADVANCE='NO')
-  READ(*,'(a)') nc_filename
-  nc_filename = ADJUSTL(nc_filename)
-  WRITE(*,FMT='(/5x,"Enter the OUTPUT Binary SpcCoeff filename: ")', ADVANCE='NO')
-  READ(*,'(a)') bin_filename
-  bin_filename = ADJUSTL(bin_filename)
-  ! ...Sanity check that they're not the same
-  IF ( bin_filename == nc_filename ) THEN
-    msg = 'SpcCoeff netCDF and Binary filenames are the same!'
-    CALL Display_Message( PROGRAM_NAME, msg, FAILURE ); STOP
+
+  ! Get the filename
+  n_args = COMMAND_ARGUMENT_COUNT()
+  IF ( n_args > 0 ) THEN
+     CALL GET_COMMAND_ARGUMENT(1, nc_filename)
+     !** automatically generate the binary filename based on the command line netcdf filename
+     tmp_filename = nc_filename(1:LEN_TRIM(nc_filename) - 3)//".bin"
+     bin_filename = TRIM(ADJUSTL(tmp_filename))  
+     PRINT *, "Output filename:", bin_filename
+  ELSE      
+     ! Get the filenames
+     WRITE(*,FMT='(/5x,"Enter the INPUT netCDF SpcCoeff filename : ")', ADVANCE='NO')
+     READ(*,'(a)') nc_filename
+     nc_filename = ADJUSTL(nc_filename)
+     WRITE(*,FMT='(/5x,"Enter the OUTPUT Binary SpcCoeff filename: ")', ADVANCE='NO')
+     READ(*,'(a)') bin_filename
+     bin_filename = ADJUSTL(bin_filename)
+     ! ...Sanity check that they're not the same
+     IF ( bin_filename == nc_filename ) THEN
+        msg = 'SpcCoeff netCDF and Binary filenames are the same!'
+        CALL Display_Message( PROGRAM_NAME, msg, FAILURE ); STOP
+     END IF
   END IF
 
   ! Perform the conversion (no change to version)

src/Coefficients/SpcCoeff/SpcCoeff_netCDF_IO.f90

@@ -598,7 +598,7 @@ FUNCTION SpcCoeff_netCDF_WriteFile( &
       CALL Write_Cleanup(); RETURN
     END IF
     ! ...Polarization angle variable
-    IF( SpcCoeff%Version > 2 ) THEN
+    IF( SpcCoeff%Version > 3 ) THEN
       NF90_Status = NF90_INQ_VARID( FileId,POLANGLE_VARNAME,VarId )
       IF ( NF90_Status /= NF90_NOERR ) THEN
         msg = 'Error inquiring '//TRIM(Filename)//' for '//POLANGLE_VARNAME//&
@@ -983,7 +983,7 @@ FUNCTION SpcCoeff_netCDF_ReadFile( &
       CALL Read_Cleanup(); RETURN
     END IF
     ! ...Polarization angle variable
-    IF ( SpcCoeff%Version > 2 ) THEN
+    IF ( SpcCoeff%Version > 3 ) THEN
       nf90_status = NF90_INQ_VARID( fileid,POLANGLE_VARNAME,varid )
       IF ( nf90_status /= NF90_NOERR ) THEN
         msg = 'Error inquiring '//TRIM(Filename)//' for '//POLANGLE_VARNAME//&
@@ -1591,24 +1591,29 @@ FUNCTION CreateFile( &
       msg = 'Error writing '//POLARIZATION_VARNAME//' variable attributes to '//TRIM(Filename)
       CALL Create_Cleanup(); RETURN
     END IF
-    ! ...Polarization angle variable
-    nf90_status = NF90_DEF_VAR( FileID, &
-                                POLANGLE_VARNAME, &
-                                POLANGLE_TYPE, &
-                                dimIDs=(/n_channels_dimid/), &
-                                varID=variD )
-    IF ( nf90_status /= NF90_NOERR ) THEN
-      msg = 'Error defining '//POLANGLE_VARNAME//' variable in '//&
-            TRIM(Filename)//' - '//TRIM(NF90_STRERROR( nf90_status ))
-      CALL Create_Cleanup(); RETURN
-    END IF
-    put_status(1) = NF90_PUT_ATT( FileID,varid,LONGNAME_ATTNAME   ,POLANGLE_LONGNAME    )
-    put_status(2) = NF90_PUT_ATT( FileID,varid,DESCRIPTION_ATTNAME,POLANGLE_DESCRIPTION )
-    put_status(3) = NF90_PUT_ATT( FileID,varid,UNITS_ATTNAME      ,POLANGLE_UNITS       )
-    put_status(4) = NF90_PUT_ATT( FileID,varid,FILLVALUE_ATTNAME  ,POLANGLE_FILLVALUE   )
-    IF ( ANY(put_status /= NF90_NOERR) ) THEN
-      msg = 'Error writing '//POLANGLE_VARNAME//' variable attributes to '//TRIM(Filename)
-      CALL Create_Cleanup(); RETURN
+
+    IF ( PRESENT(VERSION) ) THEN
+       IF (VERSION > 3) THEN 
+          ! ...Polarization angle variable
+          nf90_status = NF90_DEF_VAR( FileID, &
+               POLANGLE_VARNAME, &
+               POLANGLE_TYPE, &
+               dimIDs=(/n_channels_dimid/), &
+               varID=variD )
+          IF ( nf90_status /= NF90_NOERR ) THEN
+             msg = 'Error defining '//POLANGLE_VARNAME//' variable in '//&
+                  TRIM(Filename)//' - '//TRIM(NF90_STRERROR( nf90_status ))
+             CALL Create_Cleanup(); RETURN
+          END IF
+          put_status(1) = NF90_PUT_ATT( FileID,varid,LONGNAME_ATTNAME   ,POLANGLE_LONGNAME    )
+          put_status(2) = NF90_PUT_ATT( FileID,varid,DESCRIPTION_ATTNAME,POLANGLE_DESCRIPTION )
+          put_status(3) = NF90_PUT_ATT( FileID,varid,UNITS_ATTNAME      ,POLANGLE_UNITS       )
+          put_status(4) = NF90_PUT_ATT( FileID,varid,FILLVALUE_ATTNAME  ,POLANGLE_FILLVALUE   )
+          IF ( ANY(put_status /= NF90_NOERR) ) THEN
+             msg = 'Error writing '//POLANGLE_VARNAME//' variable attributes to '//TRIM(Filename)
+             CALL Create_Cleanup(); RETURN
+          END IF
+       END IF
     END IF
     ! ...Channel_Flag variable
     nf90_status = NF90_DEF_VAR( FileID, &