/usr/bin/ncl_convert2nc is in ncl-ncarg 6.4.0-9.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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#
# $Id: ncl_convert2nc,v 1.22 2010-04-05 22:37:28 dbrown Exp $
# Copyright (C) 2005
# University Corporation for Atmospheric Research
# All Rights Reserved
# File: ncl_convert2nc
# Author: Rick Grubin
# Original NCL code written by Dennis Shea
#
# National Center for Atmospheric Research
# POB 3000, Boulder, Colorado
# This script converts a NCL-supported file type (GRIB[1, 2], HDF, HDF-EOS) to a netCDF-formatted file.
# It can also convert between several NetCDF formats - classic, 64-bit offset, and NetCDF4 classic.
# In addition, it can be used to extract particular variables into a NetCDF file.
# It does not handle CCM data. See: http://www.cgd.ucar.edu/cms/ccm3/tools.
#
# This script determines what data type it was invoked with based on the suffix of the data
# file(s) provided to it. Data must be of a type supported by NCL. This information is
# provided to the NCL portion of this script for data-dependent processing.
#
# ncl_convert2nc inputFile [-i input_directory] [-o output_directory] [-v var1[,...]] [-c comment] [-d] [-h] [other_options]
# inputFile name of file [required]
# [-i input_directory] location of input file [default: current directory]
# [-o output_directory] location of output file [default: current directory]
# [-e extension] file type, defined by extension, to convert
# [-u [time_name]] name of the NCL-named time dimension to be UNLIMITED
# if time_name not specified NCL will attempt to find a suitable time dimension:
# if GRIB it will contain the substring "initial_time", otherwise "time" (any case);
# error will occur if the dimension found is not the left-most dimension
# [-U new_time_name] if -u is specified, will rename the NCL-named time dimension for netCDF
# [-sed sed1[,...]] GRIB files only; set single element dimensions [default: none]
# choices are initial_time, forecast_time, level, ensemble,
# probability, all, none"
# [-itime] GRIB files only; set initial time as a single element dimension
# (same as -sed initial_time)
# [-ftime] GRIB files only; set forecast time as a single element dimension
# (same as -sed forecast_time)
# [-tps] GRIB files only; remove suffix representing a time period (e.g. 2h)
# from statistically processed variables, leaving only type of
# processing as a suffix (e.g. _acc, _avg)
# [-v var1[,...]] user specified subset of variables [default: all variables]
# [-L] support for writing large (>2Gb) netCDF files [default: no largefile support]
# [-nc4c] output a NetCDF 4 classic format file
# [-cl compression_level] compression level 0 - 9 [ default 0 - only meaningful for NetCDF 4 output]
# [-th size_in_megabytes] theshold size: variables larger than specified size will be written incrementally
# in order to limit in-core memory requirements; 0 (the default) means no threshold
# -- ignored for variables that require a type conversion
# [-no-uc] turn off default conversion of unsigned integer types to corresponding signed types
# -- unsigned variables in the input will be skipped
# [-no-i64c] turn off default conversion of 64-bit integer types to double
# -- 64-bit integer types in the input will be skipped
# [-no-sc] turn off default conversion of string types to character
# -- string types in the input will be skipped
# [-no-aa] turn off default addition of the ncl_converted_from_type attribute
# when variable types are converted
# [-c comment] text to be included in netCDF file attribute [default: no comment]
# [-l] list information about each variable as it is copied
# [-d] upon exit: print contents of each netCDF file [like ncdump -h]
# [-B] <file> suppress informational messages; redirect messages to <file> if present [default: /dev/null]
# [-h] usage message
onintr CLEANUP
set progname = `basename $0`
if ($#argv < 1) then
goto USAGE
endif
# Location to write temporary files
set tmpdir = `ncargpath tmp`
if (! -w $tmpdir) then
echo "Temporary directory $tmpdir does not exist or is not writable; cannot proceed (check environment variable TMPDIR)"
exit(1)
endif
# Input and output directories default values
set valid_file = 0
set idirs = ()
set hasdirin = 0
set dirin = `pwd`
set dirout = `pwd`
#
# Default values for script commandline parameters for NCL commands
#
set dynamic_unlim_name = 0
set time_name = ""
set TIME_NAME = ""
unset tmnm_set
unset TMNM_set
unset vars
set nvars = 0
set ncdfcomment = ""
set ncdflrgf_t = "classic"
set ncdf_type = "nc3"
set compression_level = -1
set threshold_level = 0
set unsigned_to_signed = 1
set int64_to_double = 1
set string_to_char = 1
set add_attribute = 1
set list = 0
# Single Element Dimension variables
set seDims_t = ""
set singleElemDims = ""
set sed_n = 0
set sed_nt = 0
set sed_args = ""
set seds = ( '\(/'\\\"None\\\"'/\)' )
# Time Period Suffix variables
set tps = True
#
# Background/redirect mode
#
set fout = ""
set d_fout = "/dev/null"
set std_rd = ""
set f_rdir = ""
set redirect = 0
# Display resultant netCDF file when done
unset printonexit
# Suffix for all file arguments provided (default == none provided)
set have_esfx = 0
# Tell NCL to not echo its copyright notice
# This is not an advertised option
set noCN = ""
#
# First argument should be the input file(s); if it's not, exit.
# Check to see if the first argument contains a "-"
#
set hasdash = `echo $1 | awk '{print substr($0, 1, 1)}'`
if ("$hasdash" == "-") then
goto USAGE
endif
#
# Collect the file arguments, check them later -- need the "-i" ("dirin")
# argument prior to checking for unqualified full/partial pathnames.
#
# It's impossible to know if file arguments are valid at this point, so
# assume that if an argument has a "-" as its first character, it's an
# option and there are no (more) file arguments.
#
# NOTE: Bogus filenames are still *kept* at this point.
#
set nfiles = 0
set ifiles_t = ()
while ($#argv > 0)
set hasdash = `echo "$1" | awk '{print substr($0, 1, 1)}'`
if ("$hasdash" != "-") then
if ( x"$ifiles_t"x == "xx") then
set ifiles_t = ( "$1" )
else
set ifiles_t = ( "$ifiles_t" "$1" )
endif
@ nfiles += 1
shift
else
break
endif
end
#
# Parse options/arguments
#
while ($#argv > 0)
switch ("$1")
case "-i":
case "-in":
case "-input":
shift
set dirin = "$1"
set len = `echo "$dirin" | awk '{print length($0)}'`
if ($len > 0) then
shift
set hasdirin = 1
else
echo "${progname}: no input directory specified, defaulting to current directory."
endif
breaksw
case "-o":
case "-out":
case "-output":
shift
set dirout = "$1"
set len = `echo "$dirout" | awk '{print length($0)}'`
if ($len > 0) then
shift
else
echo "${progname}: no output directory specified, defaulting to current directory."
endif
breaksw
case "-e":
case "-ext":
case "-extension";
shift
set esfx = "$1"
set len = `echo $esfx | awk '{print length($0)}'`
if ($len > 0) then
set have_esfx = 1
shift
else
echo "${progname}: no file extension specified, ignoring."
endif
breaksw
case "-d"
set printonexit = 1
shift
breaksw
case "-u":
case "-unlim":
shift
if ("$1" =~ "-*" || "$1" == "") then
set dynamic_unlim_name = 1
echo "determining unlimited dimension dynamically"
set tmnm_set = 1
breaksw
endif
set time_name = "$1"
set len = `echo $time_name | awk '{print length($0)}'`
if ($len > 0) then
shift
set tmnm_set = 1
else
echo "${progname}: no NCL unlimited time dimension specified, ignoring."
endif
breaksw
case "-U":
shift
set TIME_NAME = "$1"
set len = `echo $TIME_NAME | awk '{print length($0)}'`
if ($len > 0) then
shift
set TMNM_set
else
echo "${progname}: no NCL-named time dimension specified for renaming, ignoring."
endif
breaksw
case "-itime"
@ sed_n = ($sed_n + 1)
set seDims_t = `echo $seDims_t "initial_time"`
shift
breaksw
case "-ftime"
@ sed_n = ($sed_n + 1)
set seDims_t = `echo $seDims_t "forecast_time"`
shift
breaksw
case "-sed":
case "-singleelemdims":
case "-singleElemDims":
shift
set sed_args = "$1"
# Determine number of args (count commas)
set sed_nt = `echo $* | awk -F, '{print NF}'`
if ($sed_nt == 0) then
echo "${progname}: no single element dimension(s) specified." ; echo
breaksw
endif
set sac = `echo $* | sed 's/, /,/g'`
set sa = $sac[1]
shift
set sedline = `echo $sa | sed 's/,/ /g'`
set seds = ( '\(/' )
set n = 1
while ($n < $sed_nt)
set i = `expr $n + 1`
set s = $sedline[$n]
set seds = ( $seds\\\"$s\\\"\',\' )
@ n = ($n + 1)
end
set s = $sedline[$n]
set seds = ( $seds\\\"$s\\\" )
breaksw
case "-tps":
case "-timeperiodsuffix":
case "-timePeriodSuffix":
case "-TimePeriodSuffix":
shift
set tps = False
breaksw
case "-v":
case "-var":
case "-vars":
case "-variable":
case "-variables":
shift
# Determine number of variables specified (count commas)
# set ncommas = `echo $* | tr -cd '\,' | wc -c`
# set ncommas = `echo $* | awk '{print(gsub(/,/, " "))}'`
set ncommas = `echo $* | awk -F, '{print NF - 1}'`
if ($ncommas == 0) then
# only one variable, or none?
set isopt = `echo $1 | grep -c '-'`
set isfile = `echo $1 | grep -c '\.'`
if ($isopt != 0 || $isfile != 0) then
echo "${progname}: warning: no variable(s) specified." ; echo
breaksw
endif
endif
set nvars = `expr $ncommas + 1`
# handle "space after commas" case
set psv = `echo $* | sed 's/, /,/g'`
set pvars = $psv[1]
shift
# Build array of variables as strings, quote so as to pass thru the shell
set vline = `echo $pvars | sed 's/,/ /g'`
set vars = ( '\(/' )
set n = 1
while ($n < $nvars)
set v = $vline[$n]
set vars = ( $vars\\\"$v\\\"\',\' )
@ n = ($n + 1)
end
# Catch the last variable
set vars = ( $vars\\\"$vline[$n]\\\"'/\)' )
breaksw
case "-L":
set ncdflrgf_t = "64bitoffset"
shift
breaksw
case "-nc4c":
set ncdf_type = "netcdf4classic"
shift
breaksw
case "-cl":
shift
set compression_level = $1
shift
breaksw
case "-th":
shift
set threshold_level = $1
shift
breaksw
case "-no-uc"
case "-no-unsigned-conversion"
set unsigned_to_signed = 0
shift
breaksw
case "-no-i64c"
case "-no-int64-conversion"
set int64_to_double = 0
shift
breaksw
case "-no-sc"
case "-no-string-conversion"
set string_to_char = 0
shift
breaksw
case "-no-aa"
case "-no-added-attributes"
set add_attribute = 0
shift
breaksw
case "-c":
case "-comment":
shift
set ncdfcomment = "$1"
shift
breaksw
case "-l":
case "-list":
set list = 1
shift
breaksw
case "-B":
case "-redirect":
set fout = $d_fout
shift
if ("$1" == "") then
# no redirection file specified, use default
set std_rd = ">&! $fout &"
set f_rdir = "$tmpdir/tmp$$.rdr"
set redirect = 1
breaksw
else
set hasdash = `echo "$1" | awk '{print substr($0, 1, 1)}'`
if ("$hasdash" != "-") then
set fout = "$1"
set std_rd = ">& $fout &"
set f_rdir = "$tmpdir/tmp$$.rdr"
set redirect = 1
shift
endif
endif
breaksw
case "-h":
case "-help":
case "--help":
goto USAGE
exit 0
breaksw
case "-Q":
case "-nocopyrightnotice":
case "-noCopyrightNotice":
shift
set noCN = "-Q"
breaksw
case "-*":
echo "${progname}: warning: '$1' is not a valid option, ignoring." ; echo
shift
breaksw
default:
echo "${progname}: warning: '$1' is not a valid argument, ignoring." ; echo
shift
breaksw
endsw
end
#
# If "-U" (rename NCL-name time dimension) was specified, "-u" (UNLIMITED dimension)
# had to also be specified.
#
#if ($?tmnm_set && ! $?TMNM_set) then
# echo "NCL-named time dimension '$time_name' specified for renaming, but"
# echo "new netCDF time dimension not named; ignoring '$time_name'."
#endif
if ($?TMNM_set && ! $?tmnm_set) then
echo "New netCDF time dimension '$TIME_NAME' specified but no NCL-named time"
echo "dimension to rename was specified; ignoring '$TIME_NAME'."
endif
#
# Single Element Dimensions
# set_nt has the count from the -sed option sed_n has count of -itime and -ftime
if ($sed_nt > 0 && $sed_n > 0) then
@ i = 1
while ($i <= $sed_n)
set seds = ( $seds\',\'\\\"$seDims_t[$i]\\\" )
@ i = ($i + 1)
end
else if ($sed_n > 0) then
@ i = 1
set seds = ( '\(/'\\\"$seDims_t[$i]\\\" )
@ i = ($i + 1)
while ($i <= $sed_n)
set seds = ( $seds\',\'\\\"$seDims_t[$i]\\\" )
@ i = ($i + 1)
end
else if ($sed_nt == 0) then
set seds = ( '\(/'\\\"none\\\" )
endif
set seds = ( $seds'/\)' )
#
# if the -nc4c option is set, it overrides the -L option
#
if ($ncdf_type != "nc3") then
set ncdflrgf_t = $ncdf_type
endif
#
# Split filenames into (full, relative) paths and filenames. This will
# ensure that file arguments entered with full/relative paths are properly
# accounted for. Files without a path will be assigned the value given
# with the "-i" switch (or its default if "-i" is not used).
#
# Check existence/readability of input file arguments; eliminate invalid entries.
# Guarantees a one-to-one correspondence between input and output file entries.
#
# No check is performed to determine if a file contains valid data; it is assumed
# that the user provides properly formatted data (regardless of filename).
#
set n = 1
set nbadf = 0
set ifiles = ()
set ifiles_r = ()
set ofiles = ()
set ftypes = ()
while ($n <= $nfiles)
#
# Was a URL provided? This requires an OPeNDAP-enabled NCL. If
# it's a URL, don't bother verifying the file suffix.
#
set http = `echo "$ifiles_t[$n]" | awk '{print index($0, "http")}'`
if ($http > 0) then
set dir = `dirname "$ifiles_t[$n]"`
#set $if = `echo $ifiles_t[$n] | awk -F\/ '{print $NF}'`
set if = `basename "$ifiles_t[$n]"`
set of = "$if:r"
if ( x"$idirs"x == "xx") then
set idirs = ( "$dir" )
else
set idirs = ( "$idirs" "$dir" )
endif
if ( x"$ifiles"x == "xx") then
set ifiles = ( "$if" )
else
set ifiles = ( "$ifiles" "$if" )
endif
if ( x"$ofiles"x == "xx") then
set ofiles = ( "$of" )
else
set ofiles = ( "$ofiles" "$of" )
endif
# No definitive way to verify file type
set ftypes = ( $ftypes "OPeNDAP" )
# Keep the name of the file actually specified on the command line
if (x"$ifiles_r"x == "xx") then
set ifiles_r = ( "$ifiles_t[$n]" )
else
set ifiles_r = ( "$ifiles_r" "$ifiles_t[$n]" )
endif
@ n += 1
continue
endif
set valid_file = 0
set t = "$ifiles_t[$n]"
set fil = `basename "$t"`
if ($hasdirin == 1) then
set dir = "$dirin"
else
set dir = `dirname "$ifiles_t[$n]"`
endif
set relpath = `echo "$dir" | grep -c '.'`
set haspath = `echo "$dir" | grep -c '/'`
# Does the file exist, and is it readble, as named?
# Must account for different data directory if specified
# If an input file already has an extension, ignore "-e"
# for that file.
set sfx = "$fil"
if ( "$sfx" !~ *\.* ) then
set sfx = ""
else
while ("$sfx" =~ *\.*)
set sfx = "$sfx:e"
end
endif
set sfxlen = `echo "$sfx" | awk '{print length($0)}'`
if (((-e "$ifiles_t[$n]") && (-r "$ifiles_t[$n]")) \
|| ((-e "$dirin/$ifiles_t[$n]") && (-r "$dirin/$ifiles_t[$n]"))) then
if ($have_esfx == 1) then
set psfx = "$esfx"
set fil = "$fil"."$psfx"
endif
if ($sfxlen == 0) then
if ($have_esfx == 1) then
set psfx = "$esfx"
else
goto VALID_FILE
endif
else
set psfx = "$fil:e"
endif
# Does the file have a suffix (delineated by a ".") or
# was a suffix specified via command-line options? If
# yes, does the suffix indicate requested data type?
set lsfx = `echo "$psfx" | tr '[A-Z]' '[a-z]'`
switch ($lsfx)
case nc:
case cdf:
case nc3:
case nc4:
case netcdf:
set ftype = "NETCDF"
set if = "$fil"
set of = "$if:r"
set valid_file = 1
goto VALID_FILE
breaksw
case gr:
case gr1:
case grb:
case grib:
case grb1:
case grib1:
case gr2:
case grb2:
case grib2:
set ftype = "GRIB"
set if = "$fil"
set of = "$if:r"
set valid_file = 1
goto VALID_FILE
breaksw
case hdf:
case h4:
set ftype = "HDF"
set if = "$fil"
set of = "$if:r"
set valid_file = 1
goto VALID_FILE
breaksw
case hdfeos:
case he2:
case he4:
set ftype = "HDFEOS"
set if = "$fil"
set of = "$if:r"
set valid_file = 1
goto VALID_FILE
breaksw
case hdf5:
case h5:
set ftype = "HDF5"
set if = "$fil"
set of = "$if:r"
set valid_file = 1
goto VALID_FILE
breaksw
case hdfeos5:
case he5:
set ftype = "HDFEOS5"
set if = "$fil"
set of = "$if:r"
set valid_file = 1
goto VALID_FILE
breaksw
case ccm:
echo "${progname}: file '${fil}': CCM files not supported. Please use: ccm2nc"
echo " Download at: http://www.cgd.ucar.edu/cms/ccm3/tools"
echo
@ nbadf += 1
@ n += 1
continue
breaksw
case shp:
case mif:
case gmt:
case rt1: # The possible TIGER suffixes...
case rt2:
case rt3:
case rt4:
case rt5:
case rt6:
case rt7:
case rt8:
case rt9:
case rta:
case rtb:
case rtc:
case rte:
case rth:
case rti:
case rtm:
case rtp:
case rtr:
case rts:
case rtt:
case rtu:
case rtz:
set ftype = "OGR"
set if = "$fil"
set of = "$if:r"
set valid_file = 1
goto VALID_FILE
breaksw
default:
echo "${progname}: filetype '${lsfx}' not supported."
echo
@ nbadf += 1
@ n += 1
continue
breaksw
endsw
else
# The file, as named, doesn't exist or isn't readable.
# Check existence/readability as an incomplete file name
# (ex.: 'ruc.grb' ==> 'ruc' exists). This emulates NCL's
# 'addfile()' functionality. If found, keep it as input.
set tf = "$ifiles_t[$n]"
if ($have_esfx == 1) then
if (( (-e "$tf:r"."$esfx") && (-r "$tf:r"."$esfx")) \
|| ( (-e "$dirin/$tf:r"."$esfx") && (-r "$dirin/$tf:r"."$esfx"))) then
set psfx = "$esfx"
set if = "$tf"
set of = "$tf":r
endif
else
if ( !( ((-e "$tf:r") && (-r "$tf:r")) \
|| ((-e "$dirin/$tf:r") && (-r "$dirin/$tf:r")) ) ) then
goto VALID_FILE
endif
endif
if ($sfxlen == 0) then
goto VALID_FILE
else
set psfx = "$sfx"
endif
set lsfx = `echo $psfx | tr '[A-Z]' '[a-z]'`
set tf = "$fil"
switch ($lsfx)
case nc:
case cdf:
case nc3:
case nc4:
case netcdf:
set ftype = "NETCDF"
set if = "$tf"
set of = "$if:r"
set valid_file = 1
goto VALID_FILE
breaksw
case gr:
case gr1:
case grb:
case grib:
case grb1:
case grib1:
case gr2:
case grb2:
case grib2:
set ftype = "GRIB"
set if = "$tf:r".$lsfx
set of = "$tf:r"
echo if " " of
set valid_file = 1
goto VALID_FILE
breaksw
case hdf:
case h4:
set ftype = "HDF"
set if = "$tf:r".$lsfx
set of = "$tf:r"
set valid_file = 1
goto VALID_FILE
breaksw
case hdf5:
case h5:
set ftype = "HDF5"
set if = "$tf:r".$lsfx
set of = "$tf:r"
set valid_file = 1
goto VALID_FILE
breaksw
case hdfeos:
case he2:
case he4:
set ftype = "HDFEOS"
set if = "$tf:r".$lsfx
set of = "$tf:r"
set valid_file = 1
goto VALID_FILE
breaksw
case hdfeos5:
case he5:
set ftype = "HDFEOS5"
set if = "$tf:r".$lsfx
set of = "$tf:r"
set valid_file = 1
goto VALID_FILE
breaksw
case ccm:
echo "${progname}: file '${fil}': CCM files not supported. Please use: ccm2nc"
echo " Download at: http://www.cgd.ucar.edu/cms/ccm3/tools"
echo
@ nbadf += 1
@ n += 1
continue
breaksw
case shp:
case mif:
case gmt:
case rt1: # The possible TIGER suffixes...
case rt2:
case rt3:
case rt4:
case rt5:
case rt6:
case rt7:
case rt8:
case rt9:
case rta:
case rtb:
case rtc:
case rte:
case rth:
case rti:
case rtm:
case rtp:
case rtr:
case rts:
case rtt:
case rtu:
case rtz:
set ftype = "OGR"
set if = "$tf:r".$lsfx
set of = "$tf:r"
set valid_file = 1
goto VALID_FILE
breaksw
endsw
endif
# Is the file valid -- i.e., it exists/is readable, and has a valid name?
# If not, skip it, else set values for input/output filenames, and input
# directory. Output directory is set by "-o" or assumed to be the current
# working directory (default).
VALID_FILE:
# if ($?valid_file) then
if ($valid_file == 0) then
echo "${progname}: file '$tf' not readable, does not contain recognized data, or doesn't exist, skipping."
echo
@ nbadf += 1
@ n += 1
continue
else
if (($haspath == 1) || ($relpath == 1)) then
if ( x"$idirs"x == "xx") then
set idirs = ( "$dir" )
else
set idirs = ( "$idirs" "$dir" )
endif
else
if ( x"$idirs"x == "xx") then
set idirs = ( "$dirin" )
else
set idirs = ( "$idirs" "$dir" )
endif
endif
if ( x"$ifiles"x == "xx") then
set ifiles = ( "$if" )
else
set ifiles = ( "$ifiles" "$if" )
endif
if ( x"$ofiles"x == "xx") then
set ofiles = ( "$of" )
else
set ofiles = ( "$ofiles" "$of" )
endif
set ftypes = ( $ftypes $ftype )
endif
# Keep the name of the file actually specified on the command line
if (x"$ifiles_r"x == "xx") then
set ifiles_r = ( "$ifiles_t[$n]" )
else
set ifiles_r = ( "$ifiles_r" "$ifiles_t[$n]" )
endif
@ n += 1
end
unset ifiles_t
# Account for any discarded files
@ nfiles -= $nbadf
#
# Create temporary file to hold NCL script
#
set tmpfile = `date "+%s"`
set tmpfile = `printf "%x" $tmpfile`
set tmp_nclf = "$tmpdir/tmp$$-$tmpfile.ncl"
#echo $tmp_nclf
/bin/rm $tmp_nclf >& /dev/null
cat << 'EOF_NCL' >! $tmp_nclf
;***************************************************
; GRIB, GRIB2, HDF, HDF-EOS to netcdf
;***************************************************
;
; ncl_convert2nc inputFile
; [-i input_directory]
; [-o output_directory]
; [-e extension]
; [-u time_name]
; [-U new_time_name]
; [-sed sed1[,...]]
; [-tps]
; [-v var1[,...]]
; [-L]
; [-c comment]
; [-d]
; [-B] <file>
; [-h]
;
; inputFile name of GRIB/HDF/HDF-EOS file [required]
; [-i input_directory] location of input file [default: current directory]
; [-o output_directory] location of output file [default: current directory]
; [-e extension] file type, defined by extension, to convert
; [-u time_name] name of the NCL-named time dimension to be UNLIMITED
; [-U new_time_name] if -u is specified, will rename the NCL-named time dimension for netCDF
; [-sed sed1[,...]] set single element time record dimensions [default: None]
; GRIB files only; choices are Initial_time, Forecast_time, Level,
; Ensemble, Probability, All, None
; [-tps] GRIB files only; remove suffix representing a time period (e.g. 2h)
; from statistically processed variables, leaving only type of
; processing as a suffix (e.g. _acc, _avg)
; [-v var1[,...]] user specified subset of variables [default: all variables]
; ncl_filedump can be used to determine desired variable names
; [-L] support for writing large (>2Gb) netCDF files [default: no largefile support]"
; [-c comment] text to be included in netCDF file attribute [default: no comment]
; [-d] upon exit: print contents each netCDF file [like ncdump -h]
; [-B] <file> suppress informational messages; redirect messages to <file> if present [default: /dev/null]
; [-h] this usage message
;
; Sample Usage
; (1) ncl_convert2nc U12345.grb
; => U12345.nc [location current directory]
;
; (2) ncl_convert2nc U12345 -e grb -t
; => apply ".grb" extension to input file(s)
; => time coordinate type set to "string"
;
; (3) ncl_convert2nc U12345.hdf -i /my/input
; [/my/input/U12345]
; => U12345.nc [location current directory]
;
; (4) ncl_convert2nc U12345.hdfeos -i /my/input -o /my/output
; => /my/output/U12345.nc
;
; (5) ncl_convert2nc U12345.grb -i /my/input -o /my/output
; => /my/output/U12345.nc
;
; (6) ncl_convert2nc U12345.hdf -c 'Data Support Section: ds124.1'
; => /my/output/U12345.nc [includes file attribute "ds124.1"]
;
; (7) ncl_convert2nc U12345.grb -o /my/output \
; -v gridlat_236,gridlon_236,PRES_236_SFC,NCPCP_236_SFC_acc1h
; => /my/output/U12345.nc [contains 4 variables only]
;
; (8) ncl_convert2nc U12345.grb -v gridlat_236,gridlon_236,PRES_236_SFC -L
; => U12345.nc [location current directory]
; [contains only three variables]
; [supports large files (>2Gb) for netCDF]
;
; (9) ncl_convert2nc U78677.grb -u initial_time0_hours
; => double initial_time0_hours(initial_time0_hours) ; UNLIMITED
; => initial_time0_hours:units = "hours since 1800-01-01 00:00"
; => float D_GDS4_HYBL_123(initial_time0_hours, lv_HYBL3, g4_lat_1, g4_lon_2) ;
;
; (10) ncl_convert2nc U78677.grb -u initial_time0_hours -U time
; => double time(time) ; ; UNLIMITED
; => time:units = "hours since 1800-01-01 00:00" ;
; => float D_GDS4_HYBL_123(time, lv_HYBL3, g4_lat_1, g4_lon_2) ;
;
; (11) ncl_convert2nc U78677.grb -sed initial_time,forecast_time
; => set Single Element Dimensions 'initial_time' and 'forecast_time'
;
; (12) ncl_convert2nc U12345.he5 -i /my/input -o /my/output
; => /my/output/U12345.nc
;
;
;***************************************************
; Multiple files
; The driver shell script gets the expanded file
; names and invokes this script, one file at a time
;***************************************************
; Sample usage of the NCL script:
; (a) ncl 'fili="U12345.grb"' anyFile2nc.ncl_v1
; (b) ncl 'fili="U12345.hdf"' -t
; (c) ncl 'fili="U12345.hdfeos"' ncDump=True anyFile2nc.ncl_v1
; (d) ncl 'fili="U12345.grb"' 'filo=Ugrib' anyFile2nc.ncl_v1
; (e) ncl 'fili="U12345.hdf"' 'diri="/my/input"' anyFile2nc.ncl_v1
; (f) ncl 'fili="U12345.hdfeos"' 'diri="/my/input"' 'diro="/my/output"' anyFile2nc.ncl_v1
; (g) ncl 'fili="U12345.grb"' 'diri="/my/input"' \
; 'diro="/my/output"'\
; 'comment="Data Support Section: ds124.1"' anyFile2nc.ncl_v1
; (h) ncl 'fili="U12345.grb"' 'varSelect=(/"gridlat_236","gridlon_236", \
; "PRES_236_SFC,"NCPCP_236_SFC_acc1h"/) anyFile2nc.ncl_v1
; (h) ncl 'fili="U12345.grb"' 'varSelect=(/"gridlat_236","gridlon_236", \
; "PRES_236_SFC/) -L anyFile2nc.ncl_v1
; (i) ncl 'fili="U78677.hdf"' -u "forecast_time0_hours"
; (j) ncl 'fili="U78677.hdfeos"' -u "initial_time0_hours -U time"
; (k) ncl 'fili="U78677.grb"' 'singleElemDims=(/"forecast_time", "initial_time"/)
; (l) ncl 'fili="U78677.he5"' -u "initial_time0_hours -U time"
;***************************************************
begin
; debug = True
debug = False
;***************************************************
; fili is *required*
;***************************************************
if (.not. isvar("fili")) then
print(pname + ": REQUIRED input file name(s) missing, exiting.")
exit
end if
;***************************************************
; The following are optional command line variables
;***************************************************
if (.not. isvar("diri")) then
diri = "./" ; default input dir
else
diri = diri + "/"
end if
if (.not. isvar("diro")) then
diro = "./" ; default output dir
else
diro = diro + "/"
end if
if (.not. isvar("comment")) then
comment = "" ; comment option
end if
iFileName = diri + fili
;***************************************************
; if the file starts with "http" check that it points to a valid URL
;***************************************************
if (ftype .eq. "OPeNDAP") then
if (.not. isfilepresent(iFileName)) then
print(iFileName + " is not accessible: exiting")
exit()
end if
end if
;***************************************************
; Specify that COARDS style output desired
; NOTE: [not yet implemented]
;***************************************************
;;setfileoption(f, "COARDS", True) ; place holder
;***************************************************
; Specify the type of time coordinate
; [default is 'numeric'] [obsolete]
;
; Specify the type(s) of time record dimension
; NOTE: valid for GRIB files only
;***************************************************
if (ftype .eq. "GRIB") then
; setfileoption(f, "InitialTimeCoordinateType", "numeric")
sed = singleElemDims
if (debug) then
print("Setting file option: SingleElementDimensions: " + sed)
end if
setfileoption("grib", "SingleElementDimensions", sed)
tps = timePeriodSuffix
if (debug) then
print("Setting file option: TimePeriodSuffix: " + tps)
end if
setfileoption("grib", "TimePeriodSuffix", tps)
end if
;***************************************************
;
; Specify the type(s) of time record dimension
; NOTE: valid for GRIB files only
;***************************************************
time_dim_substring = "time"
if (ftype .eq. "GRIB") then
; setfileoption(f, "InitialTimeCoordinateType", "numeric")
sed = singleElemDims
if (debug) then
print("Setting file option: SingleElementDimensions: " + sed)
end if
setfileoption("grib", "SingleElementDimensions", sed)
tps = timePeriodSuffix
if (debug) then
print("Setting file option: TimePeriodSuffix: " + tps)
end if
setfileoption("grib", "TimePeriodSuffix", tps)
if (dynamic_unlim_name .eq. 1) then
time_dim_substring = "initial_time"
end if
end if
;***************************************************
; open file with appropriate extension
;***************************************************
f = addfile(iFileName, "r") ; suffix ok
;***************************************************
; Get all the global [file] attributes. These will
; be copied to the output file.
; NOTE: GRIB files will return "missing"
;***************************************************
fInAtts = getvaratts( f )
;***************************************************
; Get *all* variables names on the file
; or
; Specify a subset of variables. All variable names,
; including coordinate variable names, must be
; specified.
;***************************************************
;***************************************************
; Get *all* variables names on the file
; or
; Specify a subset of variables. All variable names,
; including coordinate variable names, must be
; specified.
;***************************************************
if (.not. isvar("nvars")) then
fVarNames = getfilevarnames(f) ; all files names
else
fVarNames = vars ; user specified variables
end if
nfNames = dimsizes(fVarNames)
if (debug) then
print(nfNames)
print(fVarNames)
end if
;***************************************************
; open output netcdf file
; Set for 'large file' or netCDFclassic support if specified
;***************************************************
netcdfSizeType = ncdfSize
setfileoption("netcdf", "format", netcdfSizeType)
osuffix = ".nc"
if (netcdfSizeType .eq. "netcdf4classic") then
osuffix = ".nc4"
if (ncdfCompLevel .gt. -1) then
setfileoption("netcdf", "CompressionLevel", ncdfCompLevel)
end if
end if
ncFileName = diro + filo + osuffix
ofile_i = str_get_field(systemfunc("ls -iL " + ncFileName + " 2>/dev/null"),1," ")
ifile_i = str_get_field(systemfunc("ls -iL " + iFileName + " 2>/dev/null" ),1," ")
if (.not. ismissing(ofile_i) .and. .not. ismissing(ifile_i) .and. ofile_i .eq. ifile_i) then
ncFileName = ncFileName + ".nc"
end if
system("/bin/rm -f '" + ncFileName + "'") ; remove pre-existing file (if any)
fnc = addfile(ncFileName, "c") ; "c"reate the netCDF file
;***************************************************
; define file options [version a033 and beyond]
;***************************************************
setfileoption(fnc, "prefill", False)
setfileoption(fnc, "suppressclose", True)
setfileoption(fnc, "definemode", True)
;***********************************************
; assign standard file attributes [Sample]
;***********************************************
fAtt = True
title = "NCL: convert-" + ftype + "-to-netCDF"
fAtt@title = title
if (ftype .eq. "GRIB") then
fAtt@grib_source = fili
end if
if (ftype .eq. "NETCDF") then
fAtt@netcdf_source = fili
end if
if (ftype .eq. "HDF") then
fAtt@hdf_source = fili
end if
if (ftype .eq. "HDFEOS") then
fAtt@hdfeos_source = fili
end if
if (ftype .eq. "HDFEOS5") then
fAtt@hdfeos5_source = fili
end if
fAtt@Conventions = "None"
fAtt@system = systemfunc("uname -a")
fAtt@NCL_Version = get_ncl_version()
fAtt@creation_date = systemfunc ("date")
if (comment .ne. "") then
fAtt@comment = comment
end if
;***********************************************
; copy input file attributes to output file
;***********************************************
if (.not. all(ismissing(fInAtts))) then
do i = 0, dimsizes(fInAtts) - 1
fAtt@$fInAtts(i)$ = f@$fInAtts(i)$
end do
end if
fileattdef(fnc, fAtt)
;************************************************
; If the file contains no readable variables then
; it is necessary to quit here
;************************************************
if (all(ismissing(fVarNames))) then
print(iFileName + " contains no variables readable by NCL: converting global attributes only")
delete(f)
exit()
end if
;***********************************************
; predefine the file's dimension names, sizes
; and types
;***********************************************
dimNames = getvardims(f)
ind_ncl_scalar = ind(dimNames .eq. "ncl_scalar")
if (.not. ismissing(ind_ncl_scalar)) then
has_scalar_dim = True
else
has_scalar_dim = False
end if
dimSizes = getfiledimsizes(f)
dimUnlim = new(dimsizes(dimNames), "logical")
dimUnlim = False
;***********************************************
; file variable to make dimension as UNLIMITED
;***********************************************
if (time_name .ne. "") then
if (any(dimNames .eq. time_name)) then
tu_dim = ind(dimNames .eq. time_name)
dimUnlim(tu_dim) = True
if (TIME_NAME .ne. "") then
dimNames(tu_dim) = TIME_NAME
end if
end if
else if (dynamic_unlim_name .ne. 0) then
if ((ftype .eq. "GRIB") .and. \
(.not. (ismissing(all(str_match_ind(dimNames,"ensemble"))) .and. \
ismissing(all(str_match_ind(dimNames,"probability"))))))
print("Dimensions left of the initial_time dimension exist; initial_time dimension cannot be unlimited")
else
dim_ind = str_match_ind_ic(dimNames,time_dim_substring)
if (.not. any(ismissing(dim_ind))) then
max_ind = maxind(dimSizes(dim_ind))
unlim_ind = dim_ind(max_ind)
dimUnlim(unlim_ind) = True
if (TIME_NAME .ne. "") then
time_name = dimNames(unlim_ind)
dimNames(unlim_ind) = TIME_NAME
end if
end if
delete(dim_ind)
end if
end if
end if
;
; if there is a scalar dimension then it should be the first one listed
;
if (has_scalar_dim) then
if (ind_ncl_scalar .eq. 0) then
filedimdef(fnc, dimNames(1:), dimSizes(1:), dimUnlim(1:))
else
endix = dimsizes(dimNames) - 2
do i = ind_ncl_scalar, endix
dimNames(i) = dimNames(i+1)
dimSizes(i) = dimSizes(i+1)
dimUnlim(i) = dimUnlim(i+1)
end do
filedimdef(fnc, dimNames(:endix), dimSizes(:endix), dimUnlim(:endix))
end if
else
filedimdef(fnc, dimNames, dimSizes, dimUnlim)
end if
if (debug) then
print(dimNames)
print(dimSizes)
print(dimUnlim)
end if
;***************************************************
; optionally, create new names for the output netcdf
; file. Add variable renaming later.
;***************************************************
ncVarNames = fVarNames ; default: netCDF names <==> NCL names
if (time_name .ne. "" .and. TIME_NAME .ne. "") then
if (any(ncVarNames .eq. time_name)) then
tu_dim = ind(ncVarNames .eq. time_name)
ncVarNames(tu_dim) = TIME_NAME
end if
end if
;***********************************************
; determine the type of each variable
;***********************************************
varType = getfilevartypes(f, fVarNames)
long_size = sizeof(1L)
enumeric_types = (/"ubyte","ushort","uint","ulong","uint64","int64","string"/)
convert_types = (/"byte","short","integer","long","double","double","character"/)
str_to_c_ix = 6
uint_to_sint_max_ix = 3
if (long_size .eq. 8) then
convert_types(3) = "double"
end if
do_conversion = new(nfNames,logical)
do_conversion = False
str_dim_names = new(nfNames,string)
num_strings = 0
;***********************************************
; loop over each variable: skip variables of type
; string [not allowed by netCDF v3.6.x]
; (1) define name, type and dimension names
; (2) rather than read in the variable [could be
; big and slow], read each attribute of a
; variable and assign to a dummy variable
;***********************************************
do i = 0, nfNames - 1
if (debug) then
print(" ")
print(i + " ncl_name = " + fVarNames(i))
print(i + " ncl_type = " + varType(i))
print(i + " dim_names " + getfilevardims(f, fVarNames(i)))
end if
en_ix = ind(varType(i) .eq. enumeric_types)
create_attribute = False
old_type = varType(i)
if (.not. ismissing(en_ix)) then
new_type = convert_types(en_ix)
;
; note that no actual conversion is required when going from unsigned to signed integers, but clearly a conversion is
; required to go to double from integer
;
if (en_ix .eq. str_to_c_ix) then
if (string_to_char .eq. 0) then
print ("Classic model NetCDF does not support string types: " + fVarNames(i) + " will be skipped")
do_conversion(i) = _Missing
else
print ("Classic model NetCDF does not support string types, converting " + fVarNames(i) + " to a character array")
print("Dimension 'ncl_strlen_" + num_strings + "' will be added")
do_conversion(i) = True
if (add_attribute .eq. 1) then
create_attribute = True
end if
dim_name = "ncl_strlen_" + num_strings
num_strings = num_strings + 1
dim_size = max(strlen(f->$fVarNames(i)$))
filedimdef(fnc, dim_name, dim_size, False)
str_dim_names(i) = dim_name
end if
end if
if (new_type .eq. "double") then
if (int64_to_double .eq. 0) then
print ("Classic model NetCDF does not support 64bit integer types: " + fVarNames(i) + " will be skipped")
do_conversion = _Missing
else
print ("Classic model NetCDF does not support 64bit integer types, converting " + fVarNames(i) + " to double")
do_conversion(i) = True
if (add_attribute .eq. 1) then
create_attribute = True
end if
end if
else
if (en_ix .le. uint_to_sint_max_ix) then
if (unsigned_to_signed .eq. 0) then
print ("Classic mode NetCDf does not support unsigned integer types: " + fVarNames(i) + " will be skipped")
do_conversion(i) = _Missing
else
print ("Classic mode NetCDf does not support unsigned integer types: " + fVarNames(i) + " will be written as type " + new_type)
if (add_attribute .eq. 1) then
create_attribute = True
end if
end if
end if
end if
varType(i) = new_type
end if
if (.not. ismissing(do_conversion(i))) then ; netCDF (currently no strings)
; predefine variable
dimVarNames = getfilevardims(f, fVarNames(i))
if (TIME_NAME .ne. "") then
if (any(dimVarNames .eq. time_name)) then
tu_dim = ind(dimVarNames .eq. time_name)
dimVarNames(tu_dim) = TIME_NAME
end if
end if
if (do_conversion(i) .and. varType(i) .eq. "character") then
dim_names = new(dimsizes(dimVarNames) + 1, string)
dim_names(:dimsizes(dimVarNames) - 1) = dimVarNames
dim_names(dimsizes(dim_names) -1) = str_dim_names(i)
delete(dimVarNames)
dimVarNames = dim_names
delete(dim_names)
end if
filevardef(fnc, ncVarNames(i), varType(i), dimVarNames)
delete(dimVarNames)
varAtts = getfilevaratts(f, fVarNames(i))
if (.not. all(ismissing(varAtts))) then
nAtts = dimsizes(varAtts)
dumAtts = new (1, varType(i)) ; dummy to attach varAtts
delete(dumAtts@_FillValue) ; delete auto assigned _FillValue
do j = 0, nAtts - 1
att_val = f->$fVarNames(i)$@$varAtts(j)$
att_en_ix = ind(typeof(att_val) .eq. enumeric_types)
if (.not. ismissing(att_en_ix) .and. att_en_ix .lt. 5) then
if (convert_types(att_en_ix) .eq. "double") then
tmp_att_val = todouble(att_val)
else
tmp_att_val = tosigned(att_val)
end if
delete(att_val)
att_val = tmp_att_val
delete(tmp_att_val)
end if
dumAtts@$varAtts(j)$ = att_val
delete(att_val)
end do
if (create_attribute) then
dumAtts@NCL_converted_from_type = old_type
end if
if (debug) then ; can lead to much output
print(varAtts)
print(nAtts)
print(dumAtts)
end if
; define variable attributes
filevarattdef(fnc, ncVarNames(i) , dumAtts)
delete(dumAtts)
end if
delete(varAtts)
end if
end do
setfileoption(fnc, "definemode", False) ; not necessary
;***************************************************************************************
; Write *only* data values to predefined locations. If the variable exceeds a *
; certain size, perform the operation in a loop to save on core memory. There *
; is no way to get the size of a type in NCL (!!!). The approach used could be *
; inefficient if the leftmost dimensions have more elements than the rightmost. *
; Hopefully that is a rare occurence -- certainly it would be very rare in GRIB files. *
;***************************************************************************************
threshold_size = threshold_level * 1000000
do i = 0, nfNames - 1
if (.not. ismissing(do_conversion(i))) then
if (debug) then
print("write loop: i = " + i + " " + fVarNames(i))
end if
dsizes = getfilevardimsizes(f,fVarNames(i))
type_size = 1
if (varType(i) .eq. "double") then
type_size = 8
else if (varType(i) .eq. "short") then
type_size = 2
else if (varType(i) .ne. "byte" .and. varType(i) .ne. "character") then
type_size = 4
end if
end if
end if
tsize = product(dsizes) * type_size
if (debug.or.verbose) then
print(fVarNames(i) + " : " + tsize + " (size in bytes) : " + dimsizes(dsizes) + " (number of dimensions)")
end if
ndims = dimsizes(dsizes)
; no special handling for ndims greater than 6 or less than 3 or if doing a type conversion
;
if (do_conversion(i)) then
if (varType(i) .eq. "character") then
tmp_char = stringtocharacter ( (/ f->$fVarNames(i)$ /) )
tmp_size = dimsizes(tmp_char)
if (dimsizes(tmp_size) .eq. 1) then
fnc->$ncVarNames(i)$(0,:) = (/ tmp_char(:tmp_size-2) /)
else
fnc->$ncVarNames(i)$ = (/ tmp_char(:,:tmp_size(1)-2) /)
end if
delete(tmp_size)
delete(tmp_char)
else
fnc->$ncVarNames(i)$ = todouble ( (/ f->$fVarNames(i)$ /) )
end if
else if (threshold_size .eq. 0 .or. tsize .lt. threshold_size .or. ndims .gt. 7 .or. ndims .lt. 3) then
fnc->$ncVarNames(i)$ = (/ f->$fVarNames(i)$ /)
else
if (ndims .eq. 7) then
if (tsize / dsizes(0) .lt. threshold_size) then
do j = 0, dsizes(0) - 1
if (debug) then
print("copying " + fVarNames(i) + "(" + j + ",:,:,:,:,:,:)")
end if
fnc->$ncVarNames(i)$(j,:,:,:,:,:,:) = (/ f->$fVarNames(i)$(j,:,:,:,:,:,:) /)
end do
else
do j = 0, dsizes(0) - 1
do k = 0, dsizes(1) -1
if (debug) then
print("copying " + fVarNames(i) + "(" + j + "," + k + ",:,:,:,:,:)")
end if
fnc->$ncVarNames(i)$(j,k,:,:,:,:,:) = (/ f->$fVarNames(i)$(j,k,:,:,:,:,:) /)
end do
end do
end if
end if
if (ndims .eq. 6) then
if (tsize / dsizes(0) .lt. threshold_size) then
do j = 0, dsizes(0) - 1
if (debug) then
print("copying " + fVarNames(i) + "(" + j + ",:,:,:,:,:)")
end if
fnc->$ncVarNames(i)$(j,:,:,:,:,:) = (/ f->$fVarNames(i)$(j,:,:,:,:,:) /)
end do
else
do j = 0, dsizes(0) - 1
do k = 0, dsizes(1) - 1
if (debug) then
print("copying " + fVarNames(i) + "(" + j + "," + k + ",:,:,:,:)")
end if
fnc->$ncVarNames(i)$(j,k,:,:,:,:) = (/ f->$fVarNames(i)$(j,k,:,:,:,:) /)
end do
end do
end if
end if
if (ndims .eq. 5) then
if (tsize / dsizes(0) .lt. threshold_size) then
do j = 0, dsizes(0) - 1
if (debug) then
print("copying " + fVarNames(i) + "(" + j + ",:,:,:,:)")
end if
fnc->$ncVarNames(i)$(j,:,:,:,:) = (/ f->$fVarNames(i)$(j,:,:,:,:) /)
end do
else
do j = 0, dsizes(0) - 1
do k = 0, dsizes(1) -1
if (debug) then
print("copying " + fVarNames(i) + "(" + j + "," + k + ",:,:,:)")
end if
fnc->$ncVarNames(i)$(j,k,:,:,:) = (/ f->$fVarNames(i)$(j,k,:,:,:) /)
end do
end do
end if
end if
if (ndims .eq. 4) then
if (tsize / dsizes(0) .lt. threshold_size) then
do j = 0, dsizes(0) - 1
if (debug) then
print("copying " + fVarNames(i) + "(" + j + ",:,:,:)")
end if
fnc->$ncVarNames(i)$(j,:,:,:) = (/ f->$fVarNames(i)$(j,:,:,:) /)
end do
else
do j = 0, dsizes(0) - 1
do k = 0, dsizes(1) -1
if (debug) then
print("copying " + fVarNames(i) + "(" + j + "," + k + ",:,:)")
end if
fnc->$ncVarNames(i)$(j,k,:,:) = (/ f->$fVarNames(i)$(j,k,:,:) /)
end do
end do
end if
end if
if (ndims .eq. 3) then
if (tsize / dsizes(0) .lt. threshold_size) then
do j = 0, dsizes(0) - 1
if (debug) then
print("copying " + fVarNames(i) + "(" + j + ",:,:)")
end if
fnc->$ncVarNames(i)$(j,:,:) = (/ f->$fVarNames(i)$(j,:,:) /)
end do
else
do j = 0, dsizes(0) - 1
do k = 0, dsizes(1) -1
if (debug) then
print("copying " + fVarNames(i) + "(" + j + "," + k + ",:)")
end if
fnc->$ncVarNames(i)$(j,k,:) = (/ f->$fVarNames(i)$(j,k,:) /)
end do
end do
end if
end if
end if
end if
delete(dsizes)
end if
end do
delete(f) ; not necessary
end
'EOF_NCL'
#
# Loop over input file(s), executing NCL script
#
set n = 1
while ($n <= $nfiles)
if ("$redirect" == 0) then
echo "Processing file: $ifiles_r[$n]..."
if ($?vars) then
eval ncl $noCN -n 'pname=\"$progname\"' 'ftype=\"$ftypes[$n]\"' 'fili=\""$ifiles[$n]"\"' 'diri=\"'$idirs[$n]'\"' 'diro=\""$dirout"\"' 'filo=\""$ofiles[$n]"\"' nvars=$nvars vars=$vars 'ncdfSize=\""$ncdflrgf_t"\"' ncdfCompLevel=$compression_level threshold_level=$threshold_level unsigned_to_signed=$unsigned_to_signed int64_to_double=$int64_to_double string_to_char=$string_to_char add_attribute=$add_attribute singleElemDims=$seds 'timePeriodSuffix=$tps' dynamic_unlim_name=$dynamic_unlim_name 'time_name=\""$time_name"\"' 'TIME_NAME=\""$TIME_NAME"\"' 'comment=\""$ncdfcomment"\"' verbose=$list $tmp_nclf
else
eval ncl $noCN -n 'pname=\"$progname\"' 'ftype=\"$ftypes[$n]\"' 'fili=\""$ifiles[$n]"\"' 'diri=\""$idirs[$n]"\"' 'diro=\""$dirout"\"' 'filo=\""$ofiles[$n]"\"' 'ncdfSize=\""$ncdflrgf_t"\"' ncdfCompLevel=$compression_level threshold_level=$threshold_level unsigned_to_signed=$unsigned_to_signed int64_to_double=$int64_to_double string_to_char=$string_to_char add_attribute=$add_attribute singleElemDims=$seds 'timePeriodSuffix=$tps' dynamic_unlim_name=$dynamic_unlim_name 'time_name=\""$time_name"\"' 'TIME_NAME=\""$TIME_NAME"\"' 'comment=\""$ncdfcomment"\"' verbose=$list $tmp_nclf
endif
else
# redirection requested
(echo "Processing file: $ifiles_r[$n]..." >&! $f_rdir)
if ($?vars) then
(eval ncl $noCN -n 'pname=\"$progname\"' 'ftype=\"$ftypes[$n]\"' 'fili=\""$ifiles[$n]"\"' 'diri=\""$idirs[$n]"\"' 'diro=\""$dirout"\"' 'filo=\""$ofiles[$n]"\"' nvars=$nvars vars=$vars 'ncdfSize=\""$ncdflrgf_t"\"' ncdfCompLevel=$compression_level threshold_level=$threshold_level unsigned_to_signed=$unsigned_to_signed int64_to_double=$int64_to_double string_to_char=$string_to_char add_attribute=$add_attribute singleElemDims=$seds 'timePeriodSuffix=$tps' dynamic_unlim_name=$dynamic_unlim_name 'time_name=\""$time_name"\"' 'TIME_NAME=\""$TIME_NAME"\"' 'comment=\""$ncdfcomment"\"' verbose=$list $tmp_nclf >! $fout) >&! $f_rdir
else
(eval ncl $noCN -n 'pname=\"$progname\"' 'ftype=\"$ftypes[$n]\"' 'fili=\""$ifiles[$n]"\"' 'diri=\""$idirs[$n]"\"' 'diro=\""$dirout"\"' 'filo=\""$ofiles[$n]"\"' 'ncdfSize=\""$ncdflrgf_t"\"' ncdfCompLevel=$compression_level threshold_level=$threshold_level unsigned_to_signed=$unsigned_to_signed int64_to_double=$int64_to_double string_to_char=$string_to_char add_attribute=$add_attribute singleElemDims=$seds 'timePeriodSuffix=$tps' dynamic_unlim_name=$dynamic_unlim_name 'time_name=\""$time_name"\"' 'TIME_NAME=\""$TIME_NAME"\"' 'comment=\""$ncdfcomment"\"' verbose=$list $tmp_nclf >! $fout) >&! $f_rdir
endif
endif
# Display output if requested.
echo
if ($?printonexit) then
set fdump = `which ncl_filedump`
if ($? != 0) then
set fdump = `which ncdump`
if ($? != 0) then
echo "Can't locate 'ncl_filedump' or 'ncdump' to display output file."
endif
else
if (-e $dirout/$ofiles[$n].nc) then
echo " Displaying $dirout/$ofiles[$n].nc"
sleep 2
$fdump -c "$dirout/$ofiles[$n].nc"
echo ; echo
endif
endif
endif
INCR:
@ n += 1
if (($n > $#ifiles) || ($n > $#ofiles)) then
break
endif
end
#
# Clean up
#
#echo $tmp_nclf
if ("$redirect" == 0) then
/bin/rm -f $tmp_nclf
endif
/bin/rm -f $f_rdir
exit 0
CLEANUP:
/bin/rm -f $tmp_nclf
/bin/rm -f $f_rdir
exit 1
USAGE:
echo "${progname} inputFile(s) OPTIONS"
echo " inputFile(s) name(s) of data file(s) [required]"
echo " [valid types: GRIB1 GRIB2 HDF HDF-EOS netCDF shapefile]"
echo " [-i input_directory] location of input file(s) [default: current directory]"
echo " [-o output_directory] location of output file(s) [default: current directory]"
echo " [-e extension] file type, defined by extension, to convert [example: grb]"
echo " [-u [time_name]] name of the NCL-named time dimension to be UNLIMITED"
echo " if time_name not specified NCL will attempt to find a suitable time dimension:"
echo " if GRIB it will contain the substring "initial_time", otherwise "time" (any case);"
echo " error will occur if the dimension found is not the left-most dimension"
echo " [-U new_time_name] if -u is specified: new name of UNLIMITED variable and dimension"
echo " [-sed sed1[,...]] GRIB files only; set single element dimensions [default: none]"
echo " choices are initial_time, forecast_time, level, ensemble,"
echo " probability, all, none"
echo " [-itime] GRIB files only; set initial time as a single element dimension"
echo " (same as -sed initial_time)"
echo " [-ftime] GRIB files only; set forecast time as a single element dimension"
echo " (same as -sed forecast_time)"
echo " [-tps] GRIB files only; remove suffix representing a time period (e.g. 2h)"
echo " from statistically processed variables, leaving only type of"
echo " processing as a suffix (e.g. _acc, _avg)"
echo " [-v var1[,...]] user specified subset of variables [default: all variables]"
echo " ncl_filedump can be used to determine desired variable names"
echo " [-L] support for writing large (>2Gb) netCDF files [default: no largefile support]"
echo " [-nc4c] output a NetCDF 4 classic format file"
echo " [-cl compression_level] compression level 0 - 9 [ default 0 - only meaningful for NetCDF 4 output]"
echo " [-th size_in_megabytes] theshold size: variables larger than specified size will be written incrementally"
echo " in order to limit in-core memory requirements; 0 (the default) means no threshold"
echo " -- ignored for variables that require a type conversion"
echo " [-no-uc] turn off default conversion of unsigned integer types to corresponding signed types"
echo " -- unsigned variables in the input will be skipped"
echo " [-no-i64c] turn off default conversion of 64-bit integer types to double"
echo " -- 64-bit integer types in the input will be skipped"
echo " [-no-sc] turn off default conversion of string types to character"
echo " -- string types in the input will be skipped"
echo " [-no-aa] turn off default addition of the 'ncl_converted_from_type' attribute"
echo " when variable types are converted"
echo " [-c comment] text to be included in netCDF file attribute [default: no comment]"
echo " [-l] list some information about each variable as it is copied"
echo " [-d] upon exit: print contents of each netCDF file [like ncdump -h]"
echo " [-B] <file> suppress informational messages; redirect messages to <file> if present"
echo " [default: /dev/null]"
echo " [-h] this usage message"
|