Provided by: libpdl-netcdf-perl_4.24-1build4_amd64 
NAME
PDL::NetCDF - Object-oriented interface between NetCDF files and PDL objects.
Perl extension to allow interface to NetCDF portable binary gridded files via PDL objects.
SYNOPSIS
use PDL;
use PDL::NetCDF;
use PDL::Char;
my $ncobj = PDL::NetCDF->new ("test.nc", {REVERSE_DIMS => 1, PDL_BAD => 1}); # New file
my $pdl = pdl [[1, 2, 3], [4, 5, 6]];
# Specify variable name to put PDL in, plus names of the dimensions. Dimension
# lengths are taken from the PDL, in this case, dim1 = 2 and dim2 = 3.
$ncobj->put ('var1', ['dim1', 'dim2'], $pdl);
# or for netcdf4 files
# $ncobj->put ('var1', ['dim1', 'dim2'], $pdl, {DEFLATE => 9, _FillValue => -999});
# get the deflate level (for any fileformat)
my ($deflate, $shuffle) = $ncobj->getDeflateShuffle('var1');
# $pdlout = [[1, 2, 3], [4, 5, 6]]
my $pdlout = $ncobj->get ('var1');
# Store textual NetCDF arrays using perl strings: (This is a bit primitive, but works)
my $str = "Station1 Station2 Station3 ";
$obj->puttext('textvar', ['n_station', 'n_string'], [3,10], $str);
my $outstr = $obj->gettext('textvar');
# $outstr = "Station1 Station2 Station3 "
# Now textual NetCDF arrays can be stored with PDL::Char style PDLs. This is much
# more natural and flexible than the above method.
$str = PDL::Char->new (['Station1', 'Station2', 'Station3']);
$obj->put ('stations', ['dim_station', 'dim_charlen'], $str);
$outstr = $obj->get('stations');
print $outstr;
# Prints: ['Station1', 'Station2', 'Station3']
# For more info on PDL::Char variables see PDL::Char(3), or perldoc PDL::Char
# $dim1size = 2
my $dim1size = $ncobj->dimsize('dim1');
# A slice of the netCDF variable.
# [0,0] is the starting point, [1,2] is the count.
# $slice = [1,2]
my $slice = $ncobj->get ('var1', [0,0], [1,2]);
# Attach a double attribute of size 3 to var1
$ncobj->putatt (double([1,2,3]), 'double_attribute', 'var1');
# $attr1 = [1,2,3]
my $attr1 = $ncobj->getatt ('double_attribute', 'var1');
# $type = PDL::double
my $type = $ncobj->getvariabletype('var1');
# Write a textual, global attribute. 'attr_name' is the attribute name.
$ncobj->putatt ('The text of the global attribute', 'attr_name');
# $attr2 = 'The text of the global attribute'
my $attr2 = $ncobj->getatt ('attr_name');
# Close the netCDF file. The file is also automatically closed in a DESTROY block
# when it passes out of scope. This just makes is explicit.
$ncobj->close;
For (much) more information on NetCDF, see
http://www.unidata.ucar.edu/packages/netcdf/index.html
Also see the test file, test.pl in this distribution for some working examples.
DESCRIPTION
This is the PDL interface to the Unidata NetCDF library. It uses the netCDF version 3
library to make a subset of netCDF functionality available to PDL users in a clean,
object-oriented interface.
Another NetCDF perl interface, which allows access to the entire range of netCDF
functionality (but in a non-object-oriented style which uses perl arrays instead of PDLs)
is available through Unidata at http://www.unidata.ucar.edu/packages/netcdf/index.html).
The NetCDF standard allows N-dimensional binary data to be efficiently stored, annotated
and exchanged between many platforms.
When one creates a new netCDF object, this object is associated with one netCDF file.
FUNCTIONS
isNetcdf4
Check if compiled against netcdf4
Arguments: none
if (PDL::NetCDF::isNetcdf4) {
# open netcdf4 file
}
defaultFormat
Get or change the default format when creating a netcdf-file. This can be overwritten by
the NC_FORMAT option for new. Possible values are: PDL::NetCDF::NC_FORMAT_CLASSIC,
PDL::NetCDF::NC_FORMAT_64BIT, PDL::NetCDF::NC_FORMAT_NETCDF4,
PDL::NetCDF::NC_FORMAT_NETCDF4_CLASSIC
Arguments:
1) new format (constant)
Return:
old format as one of the NC_FORMAT_* constants
new
Create an object representing a netCDF file.
Arguments:
1) The name of the file.
2) optional: A hashref containing options. Currently defined are:
TEMPLATE:
An existing netCDF object for a file with
identical layout. This allows one to read in many similar netCDF
files without incurring the overhead of reading in all variable
and dimension names and IDs each time. Caution: Undefined
weirdness may occur if you pass the netCDF object from a dissimilar
file!
MODE:
use sysopen file-opening arguments, O_RDONLY, O_RDWR, O_CREAT, O_EXCL
when used, this will overwrite the '>file.nc' type of opening
see L<perlopentut> for usage of O_RDONLY...
REVERSE_DIMS:
this will turn the order of the dimension-names of
netcdf-files. Even with this option the 'put' function will write
variables in FORTRAN order (as before) and will reverse the
dimension names so they fit this order. With this option, the
'putslice' function will write variables in the same way as 'put'.
You should use this option if your planning to work with other
netcdf-programs (ncview, NCL) or if you are planning to combine
putslice and slice. You should _not_ use this option, if you need
compatibility to older versions of PDL::NetCDF.
NC_FORMAT:
set the file format for a new netcdf file, see defaultFormat()
SLOW_CHAR_FETCH:
If this option is set, then a 'get' into a PDL::Char will be done
one string at a time instead of all text data at once. This
is necessary if there are NULLs (hex 0) values embedded in the string
arrays. This takes longer, but gives the correct results. If
the fetch of a string array yields only the first element, try setting
this option.
PDL_BAD:
_FillValue's or missing_values are translated to bad-pdls.
Example:
my $nc = PDL::NetCDF->new ("file1.nc", {REVERSE_DIMS => 1, PDL_BAD => 1});
...
foreach my $ncfile (@a_bunch_of_similar_format_netcdf_files) {
$nc = PDL::NetCDF->new("file2.nc", {TEMPLATE => $nc}); # These calls to 'new' are *much* faster
...
}
# opening using MODE
use Fcntl; # define O_CREAT...
# opening a completely new file (deleting if it exists!)
my $newnc = PDL::NetCDF->new ("file2.nc", {MODE => O_CREAT|O_RDWR,
REVERSE_DIMS => 1, NC_FORMAT => PDL::NetCDF::NC_FORMAT_NETCDF4});
# opening existing file for reading and writing
$nc = PDL::NetCDF->new ("file2.nc", {MODE => O_RDWR}
REVERSE_DIMS => 1});
# opening existing file for reading only
$nc = PDL::NetCDF->new ("file2.nc", {MODE => O_RDONLY,
REVERSE_DIMS => 1});
If this file exists and you want to write to it, prepend the name with the '>' character:
">name.nc"
Returns: The netCDF object. Barfs if there is an error.
getFormat
Get the format of a netcdf file
Arguments: none
Returns: @ integer equal to one of the PDL::NetCDF::NC_FORMAT_* constants.
put
Put a PDL matrix to a netCDF variable.
Arguments:
1) The name of the variable to create
2) A reference to a list of dimension names for this variable
3) The PDL to put. It must have the same number of dimensions as specified in the
dimension name list.
4) Optional options hashref: {SHUFFLE => 1, DEFLATE => 7, COMPRESS => 0, _FillValue =>
-32767}
Returns: None.
my $pdl = pdl [[1, 2, 3], [4, 5, 6]];
# Specify variable name to put PDL in, plus names of the dimensions. Dimension
# lengths are taken from the PDL, in this case, dim1 = 2 and dim2 = 3.
$ncobj->put ('var1', ['dim1', 'dim2'], $pdl);
# Now textual NetCDF arrays can be stored with PDL::Char style PDLs.
$str = PDL::Char->new (['Station1', 'Station2', 'Station3']);
$obj->put ('stations', ['dim_station', 'dim_charlen'], $str);
$outstr = $obj->get('stations');
print $outstr;
# Prints: ['Station1', 'Station2', 'Station3']
# For more info on PDL::Char variables see PDL::Char(3), or perldoc PDL::Char
putslice
Put a PDL matrix to a slice of a NetCDF variable
Arguments:
1) The name of the variable to create
2) A reference to a list of dimension names for this variable
3) A reference to a list of dimensions for this variable
4) A reference to a list which specifies the N dimensional starting point of the slice.
5) A reference to a list which specifies the N dimensional count of the slice.
6) The PDL to put. It must conform to the size specified by the 4th and 5th
arguments. The 2nd and 3rd argument are optional if the variable is already
defined in the netcdf object.
7) Optional options: {DEFLATE => 7, SHUFFLE => 0/1, _FillValue => -32767} will use
gzip compression (level 7)
on that variable and shuffle will not/will use the shuffle filter. These options are
only valid for netcdf4 files. If you are unsure, test with
($nc->getFormat >= PDL::NetCDF::NC_FORMAT::NC_FORMAT_NETCDF4)
In addition, netcdf4 does not allow changing the _FillValue attribute
after the variable has been put/putslice'd. Therefore, the _FillValue
can be set with an option to put/putslice.
Returns: None.
my $pdl = pdl [[1, 2, 3], [4, 5, 6]];
# Specify variable name to put PDL in, plus names of the dimensions. Dimension
# lengths are taken from the PDL, in this case, dim1 = 2 and dim2 = 3.
$ncobj->putslice ('var1', ['dim1', 'dim2', 'dim3'], [2,3,3], [0,0,0], [2,3,1], $pdl);
$ncobj->putslice ('var1', [], [], [0,0,2], [2,3,1], $pdl);
my $pdl2 = $ncobj->get('var1');
print $pdl2;
[
[
[ 1 9.96921e+36 1]
[ 2 9.96921e+36 2]
[ 3 9.96921e+36 3]
]
[
[ 4 9.96921e+36 4]
[ 5 9.96921e+36 5]
[ 6 9.96921e+36 6]
]
]
note that the netcdf missing value (not 0) is filled in.
sync
Synchronize the data to the disk. Use this if you want to read the file from another
process without closing the file. This makes only sense after put, puttext, putslice,
putatt operations
Returns: nothing. Barfs on error.
$ncobj->sync
get
Get a PDL matrix from a netCDF variable.
Arguments:
1) The name of the netCDF variable to fetch. If this is the only argument, then the
entire variable will be returned.
To fetch a slice of the netCDF variable, optional 2nd and 3rd arguments must be specified:
2) A pdl which specifies the N dimensional starting point of the slice.
3) A pdl which specifies the N dimensional count of the slice.
Also, an options hashref may be passed. The option 'NOCOMPRESS' tells PDL::NetCDF to
*not* try to uncompress an compressed variable. See the COMPRESS option on 'put' and
'putslice' for more info. The option 'PDL_BAD' tells PDL::NetCDF to translate _FillValue
or missing_value attributes to bad-values, e.g. NaN's.
Returns: The PDL representing the netCDF variable. Barfs on error.
# A slice of the netCDF variable.
# [0,0] is the starting point, [1,2] is the count.
my $slice = $ncobj->get ('var1', [0,0], [1,2], {NOCOMPRESS => 1, PDL_BAD => 1});
# If var1 contains this: [[1, 2, 3], [4, 5, 6]]
# Then $slice contains: [1,2] (Size '1' dimensions are eliminated).
putatt
putatt -- Attach a numerical or textual attribute to a NetCDF variable or the entire file.
Arguments:
1) The attribute. Either: A one dimensional PDL (perhaps containing only one number) or
a string.
2) The name to give the attribute in the netCDF file. Many attribute names have pre-
defined meanings. See the netCDF documentation for more details.
3) Optionally, you may specify the name of the pre-defined netCDF variable to associate
this attribute with. If this is left off, the attribute is a global one, pertaining to
the entire netCDF file.
Returns: Nothing. Barfs on error.
# Attach a double attribute of size 3 to var1
$ncobj->putatt (double([1,2,3]), 'double_attribute', 'var1');
# Write a textual, global attribute. 'attr_name' is the attribute name.
$ncobj->putatt ('The text of the global attribute', 'attr_name');
getatt
Get an attribute from a netCDF object.
Arguments:
1) The name of the attribute (a text string).
2) The name of the variable this attribute is attached to. If this argument is not
specified, this function returns a global attribute of the input name.
# Get a global attribute
my $attr2 = $ncobj->getatt ('attr_name');
# Get an attribute associated with the variable 'var1'
my $attr1 = $ncobj->getatt ('double_attribute', 'var1');
getDeflateShuffle
Get the deflate level and the shuffle flag for a variable.
Can be called on all files, although only netcdf4 files support shuffle and deflate.
Arguments:
1) The name of the variable.
Returns:
($deflate, $shuffle)
my ($deflate, $shuffle) = $nc->getDeflateShuffle('varName');
getvariabletype
Get a type of a variable from a netCDF object.
Arguments:
1) The name of the variable.
Returns: PDL::type or undef, when variable not defined
# Get a type
my $type = $ncobj->getvariabletype ('var1');
puttext
Put a perl text string into a multi-dimensional NetCDF array.
Arguments:
1) The name of the variable to be created (a text string).
2) A reference to a perl list of dimension names to use in creating this NetCDF array.
3) A reference to a perl list of dimension lengths.
4) A perl string to put into the netCDF array. If the NetCDF array is 3 x 10, then the
string must
have 30 charactars.
5) Optional nc4 options: {DEFLATE => 7, SHUFFLE => 0}
my $str = "Station1 Station2 Station3 ";
$obj->puttext('textvar', ['n_station', 'n_string'], [3,10], $str);
gettext
Get a multi-dimensional NetCDF array into a perl string.
Arguments:
1) The name of the NetCDF variable.
my $outstr = $obj->gettext('textvar');
dimsize
Get the size of a dimension from a netCDF object.
Arguments:
1) The name of the dimension.
Returns: The size of the dimension.
my $dim1size = $ncobj->dimsize('dim1');
close
Close a NetCDF object, writing out the file.
Arguments: None
Returns: Nothing
This closing of the netCDF file can be done explicitly though the 'close' method.
Alternatively, a DESTROY block does an automatic close whenever the netCDF object passes
out of scope.
$ncobj->close();
getdimensionnames ([$varname])
Get all the dimension names from an open NetCDF object. If a variable name is specified,
just return dimension names for *that* variable.
Arguments: none
Returns: An array reference of dimension names
my $varlist = $ncobj->getdimensionnames();
foreach(@$varlist){
print "Found dim $_\n";
}
getattributenames
Get the attribute names for a given variable from an open NetCDF object.
Arguments: Optional variable name, with no arguments it will return the objects global
netcdf attributes.
Returns: An array reference of attribute names
my $attlist = $ncobj->getattributenames('var1');
getvariablenames
Get all the variable names for an open NetCDF object.
Arguments:
none.
Returns: An array reference of variable names
my $varlist = $ncobj->getvariablenames();
setrec
Set up a 'record' of several 1D netCDF variables with the same dimension. Once this is
set up, quick reading/writing of one element from all variables can be put/get from/to a
perl list.
Arguments:
1) The names of all the netCDF variables to group into a record
Returns:
A record name to use in future putrec/getrec calls
my $rec = $ncobj->setrec('var1', 'var2', 'var3');
getrec
Gets a 'record' (one value from each of several 1D netCDF variables) previously set up
using 'setrec'. These values are returned in a perl list.
Arguments:
1) The name of the record set up in 'setrec'.
2) The index to fetch.
Returns:
A perl list of all values. Note that these variables
can be of different types: float, double, integer, string.
my @rec = $ncobj->getrec($rec, 5);
putrec
Puts a 'record' (one value from each of several 1D netCDF variables) previously set up
using 'setrec'. These values are supplied as a perl list reference.
Arguments:
1) The name of the record set up in 'setrec'.
2) The index to set.
3) A perl list ref containing the values.
Returns:
None.
$ncobj->putrec($rec, 5, \@values);
WRITING NetCDF-FILES EFFICIENTLY
Writing several variables to NetCDF-files can take a long time. When a new variable is
attached by "put" to a file, the attribute header has to be written. This might force the
internal netcdf-library to restructure the complete file, and thus might take very much
IO-resources. By pre-defining the dimensions, attributes, and variables, much time can be
saved. Essentially the rule of thumb is to define and write the data in the order it will
be laid out in the file. Talking PDL::NetCDF, this means the following:
Open the netcdf file
my $nc = new PDL::NetCDF('test.nc', {MODE => O_CREAT|O_RDWR,
REVERSE_DIMS => 1});
Write the global attributes
$nc->putatt (double([1,2,3]), 'double_attribute');
Define all variables, make use of the NC_UNLIMITED dimension
# here it is possible to choose float/double/short/long
$pdl_init = long ([]);
for (my $i=0; $i<$it; $i++) {
my $out2 = $nc->putslice("VAR$i",
['x','y','z','t'],
[150,100,20,PDL::NetCDF::NC_UNLIMITED()],
[0,0,0,0],[1,0,0,0],$pdl_init);
}
Write the variable-attributes
$nc->putatt ("var-attr", 'attribute', 'VAR0');
Write data with putslice
$nc->putslice("VAR5",[],[],[0,0,0,0],[$datapdl->dims],$datapdl);
AUTHOR
Doug Hunt, dhunt\@ucar.edu.
CONTRIBUTORS
Heiko Klein, heiko.klein\@met.no Edward Baudrez, Royal Meteorological Institute of
Belgium, edward.baudrez\@meteo.be Ed J (mohawk2), etj@cpan.org
SEE ALSO
perl(1), PDL(1), netcdf(3).