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READ_NETCDF

READ_NETCDF

Name


read_netCDF.pro

Purpose


Read netCDF file into structure variable

Category


All levels of processing

Calling Sequence


read_netCDF, filename, data, attributes, status

Inputs


filename = filename for existing netCDF file

Outputs


data = structure variable for data read from netCDF file
attributes = array of strings of the attributes from the netCDF file
status = result status: 0 = OK_STATUS, -1 = BAD_PARAMS, -2 = BAD_FILE,
-3 = BAD_FILE_DATA, -4 = FILE_ALREADY_OPENED

Common Blocks


None

Procedure


Check for valid input parameters
Open the netCDF file
Create structures based on the netCDF definitions
Once structures are defined, then read the netCDF variables into the structure's data
Read the attributes into a string array
Close the netCDF file
NetCDF IDL Procedures / Process:
1. NCDF_OPEN: Open an existing netCDF file.
2. NCDF_INQUIRE: Call this function to find the format of the netCDF file.
3. NCDF_DIMINQ: Retrieve the names and sizes of dimensions in the file.
4. NCDF_VARINQ: Retrieve the names, types, and sizes of variables in the file.
5. NCDF_ATTINQ: Optionally, retrieve the types and lengths of attributes.
6. NCDF_ATTNAME: Optionally, retrieve attribute names.
7. NCDF_ATTGET: Optionally, retrieve the attributes.
8. NCDF_VARGET: Read the data from the variables.
9. NCDF_CLOSE: Close the file.

Modification History


9/20/1999 Tom Woods Original release of code, Version 1.00
12/3/1999 Tom Woods Removed BYTE array conversion to STRING
  $Log: read_netcdf.pro,v $
  Revision 1.1 2008/06/09 15:57:03 mankoff
  Initial revision
  Revision 1.1.1.1 2000/11/21 21:49:17 dlwoodra
  SEE Code Library Import
idver='$Id: read_netcdf.pro,v 1.1 2008/06/09 15:57:03 mankoff Exp mankoff $'
+
unction struct_name_cleanify, s_in
OMPILE_OPT IDL2, HIDDEN
  = s_in
  = STRJOIN(STRSPLIT(s,'-', /extract),'_')
  = STRJOIN(STRSPLIT(s,'.', /extract),'_dot_')
f (BYTE(s))[0] GE 48 AND (byte(s))[0] LE 57 then s = 'n_'+s ; starts with a number
eturn, s
nd
ro read_netCDF, filename, data, attributes, status
Generic "status" values
K_STATUS = 0
AD_PARAMS = -1
AD_FILE = -2
AD_FILE_DATA = -3
ILE_ALREADY_OPENED = -4
ebug_mode = 0 ; set to 1 if want to debug this procedure
check for valid parameters
tatus = BAD_PARAMS
f (n_params(0) lt 1) then begin
print, 'USAGE: read_netCDF, filename, data, attributes, status'

Return


ndif
f (n_params(0) lt 2) then begin
filename = ''
read, 'Enter filename for the existing netCDF file : ', filename
if (strlen(filename) lt 1) then return
ndif
tatus = OK_STATUS
f (debug_mode gt 2) and ( !d.name eq 'MAC' ) then begin
SEE_MAC_CODE = !dir + ':SEE DPS ?'
full_file = SEE_MAC_CODE + 'see_data:' + filename
ndif else begin
full_file = filename
ndelse
Open the netCDF file
1. NCDF_OPEN: Open an existing netCDF file.
f (debug_mode gt 0) then print, 'Opening ', filename, ' ...'
id = NCDF_OPEN( full_file, /NOWRITE )
Create structures based on the netCDF definitions
2. NCDF_INQUIRE: Call this function to find the format of the netCDF file.
3. NCDF_DIMINQ: Retrieve the names and sizes of dimensions in the file.
4. NCDF_VARINQ: Retrieve the names, types, and sizes of variables in the file.
inq = NCDF_INQUIRE( fid ) ; finq /str = ndims, nvars, ngatts, recdim
get dimension definitions first
get unlimited dimension (finq.recdim)

im_unlimited = finq.recdim ; = -1 if undefined, otherwise index into dim array
f ( finq.ndims gt 0 ) then begin
dimstr = ' '
dimsize = 0L
dim_name = strarr( finq.ndims )
dim_size = lonarr( finq.ndims )
for k=0,finq.ndims-1 do begin
NCDF_DIMINQ, fid, k, dimstr, dimsize
dim_name[k] = dimstr
dim_size[k] = dimsize
endfor
ndif
get variable definitions next
also determine nested structure levels, max. dimension, and command dimension value
LIMITATION: 6 dimensions allowed per variable
netCDF does not really define unsigned variable types
Have internal structure definition for tracking variables / structures
name = name from netCDF file
var_name = name from structure definition (last word after last '.')
type = data type value (same values as used by size())
natts = number of attributes for this variable
ndims = number of dimensions in "dim"
dim = dimension index into dim_size[]
nest_level = nest level of structures (number of '.' in name)
nest_name = structure name (nested)
nest_id = index to first case of structure name (nested)
nest_cnt = index of variable within a single structure (nested)
ptr = data variable pointer
str_ptr = structure pointer (if first case of new structure)

ar_inq1 = { name : " ", var_name : " ", type : 0, natts : 0L, ndims : 0L, dim: lonarr(8), nest_level : 0, $
nest_name: strarr(6), nest_id : lonarr(6), nest_cnt : lonarr(6), ptr : PTR_NEW(), str_ptr : PTRARR(6) }
ar_inq = replicate( var_inq1, finq.nvars )
ax_level = 0 ; track max structure nest level while getting variable definitions
ax_dim = 1 ; track max base structure dimension required
as_common_dim = 1 ; assume TRUE to start out, any conflict makes it FALSE
sort out first the dimensions and attribute numbers
check for max. dim needed for base structure
and if should have base structure array (if all the same last dim)
or k=0, finq.nvars-1 do begin
var_def = NCDF_VARINQ( fid, k )
var_inq[k].ndims = var_def.ndims
var_inq[k].natts = var_def.natts
if (var_def.ndims gt 0) then begin
for j=0, var_def.ndims-1 do var_inq[k].dim[j] = var_def.dim[j]
endif
if (var_def.ndims gt 0) then begin
lastdim = dim_size[ var_def.dim[var_def.ndims-1] ]
if (lastdim gt max_dim) then max_dim = lastdim
if (var_inq[k].dim[var_inq[k].ndims-1] ne var_inq[0].dim[var_inq[0].ndims-1]) then has_common_dim = 0
endif else has_common_dim = 0
ndfor
f (debug_mode gt 0) then begin
print, ' '
if (has_common_dim) then print, 'Array dimension for base structure = ', strtrim(max_dim, 2) $
else print, 'Single structure element will be defined - max dim. seen though is ', strtrim(max_dim, 2)
ndif
f (has_common_dim eq 0) then max_dim = 1 ; make single-element structure only
tr_dim_limit = 1 ; define limit for converting BYTE array into STRING
f (has_common_dim) then str_dim_limit = 2
now define variables
or k=0, finq.nvars-1 do begin
var_def = NCDF_VARINQ( fid, k )
var_inq[k].name = var_def.name
case strupcase(var_def.datatype) of
'BYTE': begin
theType = 1 ; use size() definitions for data type numbers
; if (var_def.ndims ge str_dim_limit) then begin
; if (debug_mode gt 0) then print, 'Forcing STRING type for ', var_def.name
; theType = 7
; endif
end
'CHAR': begin
theType = 7 ; expect STRING type
if (debug_mode gt 0) then print, 'STRING type for ', var_def.name
end
'SHORT': theType = 2
'LONG': theType = 3
'DOUBLE': theType = 5
else: theType = 4 ; default is FLOAT
endcase
;
; set up structure variable definitions, assume nest level 0 before looking for '.'
; increase nest_level for each '.' found and fill in nest_name, nest_id[], nest_cnt[]
;
var_inq[k].type = theType
var_inq[k].nest_level = 0
for ii=0,5 do begin
var_inq[k].nest_name[ii] = ''
var_inq[k].nest_id[ii] = 0
var_inq[k].nest_cnt[ii] = 0
endfor
var_inq[k].nest_id[0] = 0
if (k eq 0) then var_inq[k].nest_cnt[0] = 0 $
else var_inq[k].nest_cnt[0] = var_inq[k-1].nest_cnt[0] + 1
dotpos = 0
while (dotpos ge 0) do begin
lastpos = dotpos
dotpos = strpos( var_def.name, '.', lastpos )
if (dotpos ge 0) then begin
var_inq[k].nest_level = var_inq[k].nest_level + 1
nn = var_inq[k].nest_level
if (nn gt max_level) then max_level = nn
if (nn gt 5) then begin
print, 'ERROR: write_netCDF can not handle more than 4 nested structures !'
print, 'Aborting...'
NCDF_CONTROL, fid, /ABORT
status = BAD_FILE_DATA

Return


endif
newname = strmid(var_def.name, lastpos, dotpos-lastpos)
var_inq[k].nest_name[nn] = newname
if (k eq 0) then k1=0 else k1 = k - 1
if (k ne 0) and ( var_inq[k1].nest_level ge nn ) and (var_inq[k1].nest_name[nn] eq newname) then begin
var_inq[k].nest_cnt[nn-1] = var_inq[k].nest_cnt[nn-1] - 1
var_inq[k].nest_id[nn] = var_inq[k1].nest_id[nn]
var_inq[k].nest_cnt[nn] = var_inq[k1].nest_cnt[nn] + 1
endif else begin
var_inq[k].nest_id[nn] = k
var_inq[k].nest_cnt[nn] = 0
endelse
dotpos = dotpos + 1
endif
endwhile
var_inq[k].var_name = strmid( var_def.name, lastpos, strlen(var_def.name) - lastpos )
;
; now define variable and save as PTR
; uses dumb dimension rules :
; ndim_var = ndim_total - 1 for base structure being an array
; if (CHAR) then ndim_var = ndim_var - 1 for string definitions
;
ndim_array = var_inq[k].ndims
if (has_common_dim) then ndim_array = ndim_array - 1
if (var_inq[k].type eq 7) then ndim_array = ndim_array - 1
if (ndim_array lt 0) then ndim_array = 0
case ndim_array of
0: begin
case var_inq[k].type of
1: theData = 0B
2: theData = 0
3: theData = 0L
5: theData = 0.0D0
7: theData = ''
else: theData = 0.0
endcase
end
1: begin
case var_inq[k].type of
1: theData = bytarr( dim_size[ var_inq[k].dim[0] ] )
2: theData = intarr( dim_size[ var_inq[k].dim[0] ] )
3: theData = lonarr( dim_size[ var_inq[k].dim[0] ] )
5: theData = dblarr( dim_size[ var_inq[k].dim[0] ] )
7: theData = strarr( dim_size[ var_inq[k].dim[1] ] ) ; offset 1 Dim for char array
else: theData = fltarr( dim_size[ var_inq[k].dim[0] ] )
endcase
end
2: begin
case var_inq[k].type of
1: theData = bytarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ] )
2: theData = intarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ] )
3: theData = lonarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ] )
5: theData = dblarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ] )
7: theData = strarr( dim_size[ var_inq[k].dim[1] ], dim_size[ var_inq[k].dim[2] ] )
else: theData = fltarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ] )
endcase
end
3: begin
case var_inq[k].type of
1: theData = bytarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ], $
dim_size[ var_inq[k].dim[2] ] )
2: theData = intarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ], $
dim_size[ var_inq[k].dim[2] ] )
3: theData = lonarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ], $
dim_size[ var_inq[k].dim[2] ] )
5: theData = dblarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ], $
dim_size[ var_inq[k].dim[2] ] )
7: theData = strarr( dim_size[ var_inq[k].dim[1] ], dim_size[ var_inq[k].dim[2] ], $
dim_size[ var_inq[k].dim[3] ] ) ; offset 1 Dim for char array
else: theData = fltarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ], $
dim_size[ var_inq[k].dim[2] ] )
endcase
end
4: begin
case var_inq[k].type of
1: theData = bytarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ], $
dim_size[ var_inq[k].dim[2] ], dim_size[ var_inq[k].dim[3] ] )
2: theData = intarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ], $
dim_size[ var_inq[k].dim[2] ], dim_size[ var_inq[k].dim[3] ] )
3: theData = lonarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ], $
dim_size[ var_inq[k].dim[2] ], dim_size[ var_inq[k].dim[3] ] )
5: theData = dblarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ], $
dim_size[ var_inq[k].dim[2] ], dim_size[ var_inq[k].dim[3] ] )
7: theData = strarr( dim_size[ var_inq[k].dim[1] ], dim_size[ var_inq[k].dim[2] ], $
dim_size[ var_inq[k].dim[3] ], dim_size[ var_inq[k].dim[4] ] )
else: theData = fltarr( dim_size[ var_inq[k].dim[0] ], dim_size[ var_inq[k].dim[1] ], $
dim_size[ var_inq[k].dim[2] ], dim_size[ var_inq[k].dim[3] ] )
endcase
end
else: begin
print, 'ERROR: read_netCDF can only handle 4 dimensions for arrays'
print, 'Aborting...'
NCDF_CONTROL, fid, /ABORT
status = BAD_FILE_DATA

Return


end
endcase
var_inq[k].ptr = PTR_NEW( theData )
ndfor
f (debug_mode gt 0) then begin
print, ' '
nvar = n_elements( var_inq )
print, 'Indx Lvl -- 0 1 ID 2 3--< 0 1 CT 2 3 > NAME'
for jj=0,nvar-1 do print, jj, var_inq[jj].nest_level, var_inq[jj].nest_id[0:3], var_inq[jj].nest_cnt[0:3], $
var_inq[jj].name, form="(10I4,' ',A)"
stop, 'Check out var_inq and dim_name, dim_size...'
ndif
define structures based on var and dim definitions from netCDF file
using anonymous structure name with CREATE_STRUCT()
start with largest nest level and work down to zero level
store higher level structures as PTR (in var_inq[XX].str_ptr)
search backwards in variables for structure definitions
  assume structure variables are grouped together
or nn=max_level,0,-1 do begin
for k=0, finq.nvars-1 do begin
;
; check if new structure found (same nest level as "nn" and cnt = 0)
; if new, then ss = CREATE_STRUCT( tag, value ) for first parameter and
; then ss = CREATE_STRUCT( ss, tag, value ) for other parameters
;
if (k eq 0) then firstzero = var_inq[k].nest_cnt[nn] eq 0 $
else firstzero = (var_inq[k].nest_cnt[nn] eq 0) and $
( (var_inq[k-1].nest_cnt[nn] ne 0) or (var_inq[k-1].nest_id[nn] ne var_inq[k].nest_id[nn]) )
if (var_inq[k].nest_level ge nn) and (firstzero) then begin
if (nn lt var_inq[k].nest_level) then begin
              ;; ss = CREATE_STRUCT( var_inq[k].nest_name[nn+1], *(var_inq[k].str_ptr[nn+1]) )
              ss = CREATE_STRUCT( struct_name_cleanify(var_inq[k].nest_name[nn+1]), *(var_inq[k].str_ptr[nn+1]) )
endif else begin
              ;; ss = CREATE_STRUCT( var_inq[k].var_name, *(var_inq[k].ptr) )
              ss = CREATE_STRUCT( struct_name_cleanify(var_inq[k].var_name), *(var_inq[k].ptr) )
endelse
k1 = k
for kk=k+1, finq.nvars-1 do begin
k2 = kk
if ( var_inq[k2].nest_level ge nn ) and ( var_inq[k2].nest_id[nn] eq var_inq[k].nest_id[nn] ) and $
( var_inq[k2].nest_cnt[nn] eq (var_inq[k1].nest_cnt[nn] + 1) ) then begin
if (nn lt var_inq[kk].nest_level) then begin
                      ;; ss = CREATE_STRUCT( ss, var_inq[kk].nest_name[nn+1], *(var_inq[kk].str_ptr[nn+1]) )
                      ss = CREATE_STRUCT( ss, struct_name_cleanify(var_inq[kk].nest_name[nn+1]), *(var_inq[kk].str_ptr[nn+1]) )
endif else begin
                      ;; ss = CREATE_STRUCT( ss, var_inq[kk].var_name, *(var_inq[kk].ptr) )
                      ss = CREATE_STRUCT( ss, struct_name_cleanify(var_inq[kk].var_name), *(var_inq[kk].ptr) )
endelse
k1 = k2
endif
endfor
;
; store new structure as PTR
; if BASE structure, then replicate for all data reading later
var_inq[k].str_ptr[nn] = PTR_NEW( ss )
if (nn eq 0) then begin
data = replicate( ss, max_dim )
endif
if (debug_mode gt 0) then begin
if (nn gt 0) then print, k, nn, ' Structure defined for ', var_inq[k].nest_name[nn] $
else print, k, nn, ' Base Structure defined as '
help, ss, /struct
endif
endif
endfor
ndfor
f (debug_mode gt 0) then begin
print, ' '
print, '"data" array size is ', strtrim(max_dim,2)
stop, 'Check out structure definitions in data...'
ndif
Once structures are defined, then read the netCDF variables into "data"
8. NCDF_VARGET: Read the data from the variables.
or k=0, finq.nvars-1 do begin
case var_inq[k].nest_level of
0: begin
NCDF_VARGET, fid, k, value
if ( var_inq[k].type eq 7 ) then $
data.(var_inq[k].nest_cnt[0]) = string( value ) $
else data.(var_inq[k].nest_cnt[0]) = value
end
1: begin
NCDF_VARGET, fid, k, value
if ( var_inq[k].type eq 7 ) then $
data.(var_inq[k].nest_cnt[0]).(var_inq[k].nest_cnt[1]) = string( value ) $
else data.(var_inq[k].nest_cnt[0]).(var_inq[k].nest_cnt[1]) = value
end
2: begin
NCDF_VARGET, fid, k, value
if ( var_inq[k].type eq 7 ) then $
data.(var_inq[k].nest_cnt[0]).(var_inq[k].nest_cnt[1]).(var_inq[k].nest_cnt[2]) = string( value ) $
else data.(var_inq[k].nest_cnt[0]).(var_inq[k].nest_cnt[1]).(var_inq[k].nest_cnt[2]) = value
end
3: begin
NCDF_VARGET, fid, k, value
if ( var_inq[k].type eq 7 ) then $
data.(var_inq[k].nest_cnt[0]).(var_inq[k].nest_cnt[1]).(var_inq[k].nest_cnt[2]).(var_inq[k].nest_cnt[3]) = string( value ) $
else data.(var_inq[k].nest_cnt[0]).(var_inq[k].nest_cnt[1]).(var_inq[k].nest_cnt[2]).(var_inq[k].nest_cnt[3]) = value
end
else: begin
print, 'ERROR: read_netCDF can only process 4 nested structures'
print, ' data is lost for ', var_inq[k].name
end
endcase
ndfor
now define "attributes" as string array and read attributes from the netCDF file
5. NCDF_ATTINQ: Optionally, retrieve the types and lengths of attributes.
6. NCDF_ATTNAME: Optionally, retrieve attribute names.
7. NCDF_ATTGET: Optionally, retrieve the attributes.
LIMITATION: limit attributes with more than 1 parameter are compressed into single string
R = string( [ 13B ] )
um_att = 0L
finq.ngatts = number of GLOBAL attributes from NCDF_INQUIRE earlier
f (finq.ngatts gt 0) then num_att = finq.ngatts + 1
or k=0, finq.nvars-1 do if (var_inq[k].natts gt 0) then num_att = num_att + var_inq[k].natts + 1
f ( num_att gt 0 ) then begin
attributes = strarr( num_att )
acnt = 0L
;
; do global variables first
;
if ( finq.ngatts gt 0) then begin
attributes[acnt] = 'GLOBAL:' ; + CR
acnt = acnt + 1
for jj=0,finq.ngatts-1 do begin
att_name = NCDF_ATTNAME( fid, /GLOBAL, jj )
NCDF_ATTGET, fid, /GLOBAL, att_name, att_value
att_str = string( att_value )
n_str = n_elements(att_str)
if (n_str gt 1) then begin
new_str = ''
for ii=0,n_str-1 do new_str = new_str + ' ' + strtrim(att_str[ii],2)
att_str = new_str
endif
attributes[acnt] = ' ' + att_name + ' = ' + att_str ; + CR
acnt = acnt + 1
endfor
endif
for k=0, finq.nvars-1 do begin
if (var_inq[k].natts gt 0) then begin
attributes[acnt] = var_inq[k].name + ':' ; + CR
acnt = acnt + 1
for jj=0,var_inq[k].natts-1 do begin
att_name = NCDF_ATTNAME( fid, k, jj )
NCDF_ATTGET, fid, k, att_name, att_value
att_str = string( att_value )
n_str = n_elements(att_str)
if (n_str gt 1) then begin
new_str = ''
for ii=0,n_str-1 do new_str = new_str + ' ' + strtrim(att_str[ii],2)
att_str = new_str
endif
attributes[acnt] = ' ' + att_name + ' = ' + att_str ; + CR
acnt = acnt + 1
endfor
endif
endfor
ndif else begin
attributes = "NONE"
ndelse
Close the netCDF file
9. NCDF_CLOSE: Close the file.
CDF_CLOSE, fid
Free up Pointers before exiting
or k=0, finq.nvars-1 do begin
if PTR_VALID( var_inq[k].ptr ) then PTR_FREE, var_inq[k].ptr
for jj=0,5 do if PTR_VALID( var_inq[k].str_ptr[jj] ) then PTR_FREE, var_inq[k].str_ptr[jj]
ndfor
eturn
nd



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