lfi2cdf: new option: '-c or --compress' to compress data

tools/lfi2cdf/src/lfi2cdf.f90

 subroutine  LFI2CDFMAIN(hinfile,iiflen,ooutname,houtfile,ioflen,hvarlist,ivlen,olfi2cdf,olfilist,ohdf5,omerge,nb_levels,&
-                        oreduceprecision)
+                        oreduceprecision,ocompress,compress_level)
   USE mode_util
   IMPLICIT NONE 
   INTEGER :: iiflen, ioflen, ivlen
@@ -7,8 +7,9 @@ subroutine  LFI2CDFMAIN(hinfile,iiflen,ooutname,houtfile,ioflen,hvarlist,ivlen,o
   CHARACTER(LEN=iiflen) :: hinfile
   CHARACTER(LEN=ioflen) :: houtfile
   CHARACTER(LEN=ivlen)  :: hvarlist
-  LOGICAL :: ooutname, olfi2cdf, olfilist, ohdf5, omerge, oreduceprecision
-  
+  LOGICAL :: ooutname, olfi2cdf, olfilist, ohdf5, omerge, oreduceprecision, ocompress
+  INTEGER :: compress_level
+
   INTEGER :: ibuflen
   INTEGER :: ilu
   INTEGER :: inaf, ji
@@ -44,7 +45,7 @@ subroutine  LFI2CDFMAIN(hinfile,iiflen,ooutname,houtfile,ioflen,hvarlist,ivlen,o
      !Standard treatment (one LFI file only)
      IF (.not.omerge) THEN
        CALL parse_lfi(ilu,hvarlist,inaf,tzreclist,ibuflen)
-       CALL def_ncdf(tzreclist,inaf,oreduceprecision,icdf_id,omerge)
+       CALL def_ncdf(tzreclist,inaf,oreduceprecision,icdf_id,omerge,ocompress,compress_level)
        CALL fill_ncdf(ilu,icdf_id,tzreclist,inaf,ibuflen)
      ELSE
      !Treat several LFI files and merge into 1 NC file
@@ -57,7 +58,7 @@ subroutine  LFI2CDFMAIN(hinfile,iiflen,ooutname,houtfile,ioflen,hvarlist,ivlen,o
 
        !Read 1st LFI file
        CALL parse_lfi(ilu,hvarlist,inaf,tzreclist,ibuflen,current_level)
-       CALL def_ncdf(tzreclist,inaf,oreduceprecision,icdf_id,omerge)
+       CALL def_ncdf(tzreclist,inaf,oreduceprecision,icdf_id,omerge,ocompress,compress_level)
 
        DO current_level = first_level,last_level
          print *,'Treating level ',current_level

tools/lfi2cdf/src/mode_util.f90

@@ -274,12 +274,14 @@ CONTAINS
     END IF
   END SUBROUTINE HANDLE_ERR
 
-  SUBROUTINE def_ncdf(tpreclist,knaf,oreduceprecision,kcdf_id,omerge)
+  SUBROUTINE def_ncdf(tpreclist,knaf,oreduceprecision,kcdf_id,omerge,ocompress,compress_level)
     TYPE(workfield),DIMENSION(:),INTENT(INOUT) :: tpreclist
     INTEGER,                     INTENT(IN) :: knaf
     LOGICAL,                     INTENT(IN) :: oreduceprecision
     INTEGER,                     INTENT(OUT):: kcdf_id
     LOGICAL,                     INTENT(IN) :: omerge
+    LOGICAL,                     INTENT(IN) :: ocompress
+    INTEGER,                     INTENT(IN) :: compress_level
 
     INTEGER :: status
     INTEGER :: ji
@@ -383,6 +385,12 @@ CONTAINS
 
        END SELECT
 
+       ! Compress data (costly operation for the CPU)
+       IF (ocompress .AND. invdims>0) THEN
+         status = NF90_DEF_VAR_DEFLATE(kcdf_id,tpreclist(ji)%id,1,1,compress_level)
+         IF (status /= NF90_NOERR) CALL HANDLE_ERR(status,__LINE__)
+       END IF
+
        ! GRID attribute definition
        status = NF90_PUT_ATT(kcdf_id,tpreclist(ji)%id,'GRID',tpreclist(ji)%grid)
        IF (status /= NF90_NOERR) CALL HANDLE_ERR(status,__LINE__)

tools/lfi2cdf/src/newmain.c

@@ -5,7 +5,7 @@
 
 #define BUFSIZE 4096
 
-extern lfi2cdfmain_(char*, int*, int *, char*, int*, char*, int*, int*, int*, int*, int*, int*, int*);
+extern lfi2cdfmain_(char*, int*, int *, char*, int*, char*, int*, int*, int*, int*, int*, int*, int*, int*, int*);
 
 char *cleancomma(char *varlist)
 {
@@ -33,6 +33,7 @@ int main(int argc, char **argv)
   int merge_flag, nb_levels;
   int reduceprecision_flag;
   int outname_flag;
+  int compress_flag, compress_level;
   char *cmd, *infile;
   int c;
   char buff[BUFSIZE];
@@ -53,6 +54,7 @@ int main(int argc, char **argv)
   list_flag = 0;
   hdf5_flag = 0;
   reduceprecision_flag = 0;
+  compress_flag = 0;
   p = buff;
   *p = '\0';
 
@@ -65,6 +67,7 @@ int main(int argc, char **argv)
 
     static struct option long_options[] = {
       {"cdf4",             no_argument,       0, '4' },
+      {"compress",         required_argument, 0, 'c' },
       {"list",             no_argument,       0, 'l' },
       {"merge",            required_argument, 0, 'm' },
       {"output",           required_argument, 0, 'o' },
@@ -73,7 +76,7 @@ int main(int argc, char **argv)
       {0,                  0,                 0,  0  }
     };
 
-    c = getopt_long(argc, argv, "4lm:o:rv:",
+    c = getopt_long(argc, argv, "4c:lm:o:rv:",
 		    long_options, &option_index);
     if (c == -1)
       break;
@@ -85,6 +88,14 @@ int main(int argc, char **argv)
 	printf(" with arg %s", optarg);
       printf("\n");
       break;
+    case 'c':
+      compress_flag = 1;
+      compress_level = atoi(optarg);
+      if(compress_level<1 || compress_level>9) {
+        printf("Error: compression level should in the 1 to 9 interval\n");
+        exit(EXIT_FAILURE);
+      }
+      break;
     case '4':
       hdf5_flag = 1;
       break;
@@ -124,7 +135,7 @@ int main(int argc, char **argv)
   }
 
   if (optind == argc) {
-    printf("usage : lfi2cdf [--cdf4 -4] [-l] [-v --var var1[,...]] [-r --reduce-precision] [-m --merge number_of_z_levels] [-o --output output-file.nc] input-file.lfi\n");
+    printf("usage : lfi2cdf [--cdf4 -4] [-l] [-v --var var1[,...]] [-r --reduce-precision] [-m --merge number_of_z_levels] [-o --output output-file.nc] [-c --compress compression_level] input-file.lfi\n");
     printf("        cdf2lfi [-o --output output-file.lfi] input-file.nc\n");
     exit(EXIT_FAILURE);
   } 
@@ -156,13 +167,19 @@ int main(int argc, char **argv)
     olen = strlen(outfile);
   }
 
+  /* Compression flag only supported if using netCDF4 */
+  if (hdf5_flag==0 && compress_flag==1) {
+	  compress_flag = 0;
+	  printf("Warning: compression is forced to disable (only supported from netCDF4).\n");
+  }
+
   /*
   printf("cmd=%s; inputfile=%s(%d); outputfile=%s(%d); varlistclean=%s with size : %d\n", cmd, 
          infile, ilen, outfile, olen, varlist, varlistlen);
   */
 
   lfi2cdfmain_(infile, &ilen, &outname_flag, outfile, &olen, varlist, &varlistlen, &l2c_flag, &list_flag, &hdf5_flag, &merge_flag,
-		       &nb_levels, &reduceprecision_flag);
+		       &nb_levels, &reduceprecision_flag, &compress_flag, &compress_level);
 
   exit(EXIT_SUCCESS);
 }