mirror of
https://github.com/Unidata/netcdf-c.git
synced 2024-12-21 08:39:46 +08:00
1475 lines
51 KiB
C
1475 lines
51 KiB
C
/* Copyright 2010-2018 University Corporation for Atmospheric
|
|
Research/Unidata. See COPYRIGHT file for more info. */
|
|
/**
|
|
* @file
|
|
* Functions for defining and inquiring about variables. @note The
|
|
* order of functions in this file affects the doxygen documentation.
|
|
*/
|
|
|
|
#include "config.h"
|
|
#include "netcdf.h"
|
|
#include "netcdf_filter.h"
|
|
#include "ncdispatch.h"
|
|
#include "nc4internal.h"
|
|
#include "netcdf_f.h"
|
|
#include "nc4internal.h"
|
|
|
|
/**
|
|
@defgroup variables Variables
|
|
|
|
Variables hold multi-dimensional arrays of data.
|
|
|
|
Variables for a netCDF dataset are defined when the dataset is
|
|
created, while the netCDF dataset is in define mode. Other
|
|
variables may be added later by reentering define mode. A netCDF
|
|
variable has a name, a type, and a shape, which are specified when
|
|
it is defined. A variable may also have values, which are
|
|
established later in data mode.
|
|
|
|
Ordinarily, the name, type, and shape are fixed when the variable
|
|
is first defined. The name may be changed, but the type and shape
|
|
of a variable cannot be changed. However, a variable defined in
|
|
terms of the unlimited dimension can grow without bound in that
|
|
dimension.
|
|
|
|
A netCDF variable in an open netCDF dataset is referred to by a
|
|
small integer called a variable ID.
|
|
|
|
Variable IDs reflect the order in which variables were defined
|
|
within a netCDF dataset. Variable IDs are 0, 1, 2,..., in the order
|
|
in which the variables were defined. A function is available for
|
|
getting the variable ID from the variable name and vice-versa.
|
|
|
|
@ref attributes may be associated with a variable to specify such
|
|
properties as units.
|
|
|
|
Operations supported on variables are:
|
|
- Create a variable, given its name, data type, and shape.
|
|
- Get a variable ID from its name.
|
|
- Get a variable's name, data type, shape, and number of attributes
|
|
from its ID.
|
|
- Put a data value into a variable, given variable ID, indices, and value.
|
|
- Put an array of values into a variable, given variable ID, corner
|
|
indices, edge lengths, and a block of values.
|
|
- Put a subsampled or mapped array-section of values into a variable,
|
|
given variable ID, corner indices, edge lengths, stride vector,
|
|
index mapping vector, and a block of values.
|
|
- Get a data value from a variable, given variable ID and indices.
|
|
- Get an array of values from a variable, given variable ID, corner
|
|
indices, and edge lengths.
|
|
- Get a subsampled or mapped array-section of values from a variable,
|
|
given variable ID, corner indices, edge lengths, stride vector, and
|
|
index mapping vector.
|
|
- Rename a variable.
|
|
|
|
@section language_types Data Types
|
|
|
|
NetCDF supported six atomic data types through version 3.6.0 (char,
|
|
byte, short, int, float, and double). Starting with version 4.0, many
|
|
new atomic and user defined data types are supported (unsigned int
|
|
types, strings, compound types, variable length arrays, enums,
|
|
opaque).
|
|
|
|
The additional data types are only supported in netCDF-4/HDF5
|
|
files. To create netCDF-4/HDF5 files, use the ::NC_NETCDF4 flag in
|
|
nc_create().
|
|
|
|
@section classic_types NetCDF-3 Classic and 64-Bit Offset Data Types
|
|
|
|
NetCDF-3 classic and 64-bit offset files support 6 atomic data types,
|
|
and none of the user defined datatype introduced in NetCDF-4.
|
|
|
|
The following table gives the netCDF-3 external data types and the
|
|
corresponding type constants for defining variables in the C
|
|
interface:
|
|
|
|
<table>
|
|
<tr><td>Type</td><td>C define</td><td>Bits</td></tr>
|
|
<tr><td>byte</td><td>::NC_BYTE</td><td>8</td></tr>
|
|
<tr><td>char</td><td>::NC_CHAR</td><td>8</td></tr>
|
|
<tr><td>short</td><td>::NC_SHORT</td><td>16</td></tr>
|
|
<tr><td>int</td><td>::NC_INT</td><td>32</td></tr>
|
|
<tr><td>float</td><td>::NC_FLOAT</td><td>32</td></tr>
|
|
<tr><td>double</td><td>::NC_DOUBLE</td><td>64</td></tr>
|
|
</table>
|
|
|
|
The first column gives the netCDF external data type, which is the
|
|
same as the CDL data type. The next column gives the corresponding C
|
|
pre-processor macro for use in netCDF functions (the pre-processor
|
|
macros are defined in the netCDF C header-file netcdf.h). The last
|
|
column gives the number of bits used in the external representation of
|
|
values of the corresponding type.
|
|
|
|
@section netcdf_4_atomic NetCDF-4 Atomic Data Types
|
|
|
|
NetCDF-4 files support all of the atomic data types from netCDF-3,
|
|
plus additional unsigned integer types, 64-bit integer types, and a
|
|
string type.
|
|
|
|
<table>
|
|
<tr><td>Type</td><td>C define</td><td>Bits
|
|
|
|
<tr><td>byte</td><td>::NC_BYTE</td><td>8</td></tr>
|
|
<tr><td>unsigned byte </td><td>::NC_UBYTE^</td><td> 8</td></tr>
|
|
<tr><td>char </td><td>::NC_CHAR </td><td>8</td></tr>
|
|
<tr><td>short </td><td>::NC_SHORT </td><td>16</td></tr>
|
|
<tr><td>unsigned short </td><td>::NC_USHORT^ </td><td>16</td></tr>
|
|
<tr><td>int </td><td>::NC_INT </td><td>32</td></tr>
|
|
<tr><td>unsigned int </td><td>::NC_UINT^ </td><td>32</td></tr>
|
|
<tr><td>unsigned long long </td><td>::NC_UINT64^ </td><td>64</td></tr>
|
|
<tr><td>long long </td><td>::NC_INT64^ </td><td>64</td></tr>
|
|
<tr><td>float </td><td>::NC_FLOAT </td><td>32</td></tr>
|
|
<tr><td>double </td><td>::NC_DOUBLE </td><td>64</td></tr>
|
|
<tr><td>char ** </td><td>::NC_STRING^ </td><td>string length + 1</td></tr>
|
|
</table>
|
|
|
|
^This type was introduced in netCDF-4, and is not supported in netCDF
|
|
classic or 64-bit offset format files, or in netCDF-4 files if they
|
|
are created with the ::NC_CLASSIC_MODEL flags.
|
|
*/
|
|
|
|
/** @{ */
|
|
/**
|
|
@name Defining Variables
|
|
|
|
Use these functions to define variables.
|
|
*/
|
|
/*! @{ */
|
|
|
|
/**
|
|
Define a new variable.
|
|
|
|
This function adds a new variable to an open netCDF dataset or group.
|
|
It returns (as an argument) a variable ID, given the netCDF ID,
|
|
the variable name, the variable type, the number of dimensions, and a
|
|
list of the dimension IDs.
|
|
|
|
@param ncid NetCDF or group ID, from a previous call to nc_open(),
|
|
nc_create(), nc_def_grp(), or associated inquiry functions such as
|
|
nc_inq_ncid().
|
|
@param name Variable @ref object_name.
|
|
@param xtype (Data
|
|
type)[https://docs.unidata.ucar.edu/nug/current/md_types.html#data_type]
|
|
of the variable.
|
|
@param ndims Number of dimensions for the variable. For example, 2
|
|
specifies a matrix, 1 specifies a vector, and 0 means the variable is
|
|
a scalar with no dimensions. Must not be negative or greater than the
|
|
predefined constant ::NC_MAX_VAR_DIMS. In netCDF-4/HDF5 files, may not
|
|
exceed the HDF5 maximum number of dimensions (32).
|
|
@param dimidsp Vector of ndims dimension IDs corresponding to the
|
|
variable dimensions. For classic model netCDF files, if the ID of the
|
|
unlimited dimension is included, it must be first. This argument is
|
|
ignored if ndims is 0. For expanded model netCDF4/HDF5 files, there
|
|
may be any number of unlimited dimensions, and they may be used in any
|
|
element of the dimids array.
|
|
@param varidp Pointer to location for the returned variable ID.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EBADID Bad ncid.
|
|
@return ::NC_ENOTINDEFINE Not in define mode.
|
|
@return ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3 netcdf-4 file.
|
|
@return ::NC_EMAXVARS NC_MAX_VARS exceeded [Not enforced after 4.5.0]
|
|
@return ::NC_EBADTYPE Bad type.
|
|
@return ::NC_EINVAL Invalid input.
|
|
@return ::NC_ENAMEINUSE Name already in use.
|
|
@return ::NC_EPERM Attempt to create object in read-only file.
|
|
|
|
@section nc_def_var_example Example
|
|
|
|
Here is an example using nc_def_var to create a variable named rh of
|
|
type double with three dimensions, time, lat, and lon in a new netCDF
|
|
dataset named foo.nc:
|
|
|
|
@code
|
|
#include <netcdf.h>
|
|
...
|
|
int status;
|
|
int ncid;
|
|
int lat_dim, lon_dim, time_dim;
|
|
int rh_id;
|
|
int rh_dimids[3];
|
|
...
|
|
status = nc_create("foo.nc", NC_NOCLOBBER, &ncid);
|
|
if (status != NC_NOERR) handle_error(status);
|
|
...
|
|
|
|
status = nc_def_dim(ncid, "lat", 5L, &lat_dim);
|
|
if (status != NC_NOERR) handle_error(status);
|
|
status = nc_def_dim(ncid, "lon", 10L, &lon_dim);
|
|
if (status != NC_NOERR) handle_error(status);
|
|
status = nc_def_dim(ncid, "time", NC_UNLIMITED, &time_dim);
|
|
if (status != NC_NOERR) handle_error(status);
|
|
...
|
|
|
|
rh_dimids[0] = time_dim;
|
|
rh_dimids[1] = lat_dim;
|
|
rh_dimids[2] = lon_dim;
|
|
status = nc_def_var (ncid, "rh", NC_DOUBLE, 3, rh_dimids, &rh_id);
|
|
if (status != NC_NOERR) handle_error(status);
|
|
@endcode
|
|
|
|
@author Glenn Davis, Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc_def_var(int ncid, const char *name, nc_type xtype,
|
|
int ndims, const int *dimidsp, int *varidp)
|
|
{
|
|
NC* ncp;
|
|
int stat = NC_NOERR;
|
|
|
|
if ((stat = NC_check_id(ncid, &ncp)))
|
|
return stat;
|
|
TRACE(nc_def_var);
|
|
return ncp->dispatch->def_var(ncid, name, xtype, ndims,
|
|
dimidsp, varidp);
|
|
}
|
|
|
|
/**
|
|
Set the fill value for a variable.
|
|
|
|
@note For netCDF classic, 64-bit offset, and CDF5 formats, it is
|
|
allowed (but not good practice) to set the fill value after data
|
|
have been written to the variable. In this case, unless the
|
|
variable has been completely specified (without gaps in the data),
|
|
any existing filled values will not be recognized as fill values by
|
|
applications reading the data. Best practice is to set the fill
|
|
value after the variable has been defined, but before any data have
|
|
been written to that variable. In NetCDF-4 files, this is enforced
|
|
by the HDF5 library. For netCDF-4 files, an error is returned if
|
|
the user attempts to set the fill value after writing data to the
|
|
variable.
|
|
|
|
@param ncid NetCDF ID, from a previous call to nc_open() or
|
|
nc_create().
|
|
@param varid Variable ID.
|
|
@param no_fill Set to ::NC_NOFILL to turn off fill mode for this
|
|
variable. Set to ::NC_FILL (the default) to turn on fill mode for
|
|
the variable.
|
|
@param fill_value the fill value to be used for this variable. Must
|
|
be the same type as the variable. This must point to enough free
|
|
memory to hold one element of the data type of the variable. (For
|
|
example, an ::NC_INT will require 4 bytes for it's fill value,
|
|
which is also an ::NC_INT.)
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EBADID Bad ID.
|
|
@return ::NC_ENOTINDEFINE Not in define mode. This is returned for
|
|
netCDF classic, 64-bit offset, or 64-bit data files, or for
|
|
netCDF-4 files, when they were created with ::NC_CLASSIC_MODEL flag by
|
|
nc_creae().
|
|
@return ::NC_EPERM Attempt to create object in read-only file.
|
|
@return ::NC_ELATEDEF (NetCDF-4 only). Returned when user attempts
|
|
to set fill value after data are written.
|
|
@return ::NC_EGLOBAL Attempt to set fill value on NC_GLOBAL.
|
|
|
|
Warning: Using a vlen type as the fill value may lead to a memory
|
|
leak.
|
|
|
|
@section nc_def_var_fill_example Example
|
|
|
|
In this example from libsrc4/tst_vars.c, a variable is defined, and
|
|
the fill mode turned off. Then nc_inq_fill() is used to check that
|
|
the setting is correct. Then some data are written to the
|
|
variable. Since the data that are written do not cover the full
|
|
extent of the variable, the missing values will just be random. If
|
|
fill value mode was turned on, the missing values would get the
|
|
fill value.
|
|
|
|
@code
|
|
#define DIM7_LEN 2
|
|
#define DIM7_NAME "dim_7_from_Indiana"
|
|
#define VAR7_NAME "var_7_from_Idaho"
|
|
#define NDIMS 1
|
|
int dimids[NDIMS];
|
|
size_t index[NDIMS];
|
|
int varid;
|
|
int no_fill;
|
|
unsigned short ushort_data = 42, ushort_data_in, fill_value_in;
|
|
|
|
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
|
|
if (nc_def_dim(ncid, DIM7_NAME, DIM7_LEN, &dimids[0])) ERR;
|
|
if (nc_def_var(ncid, VAR7_NAME, NC_USHORT, NDIMS, dimids,
|
|
&varid)) ERR;
|
|
if (nc_def_var_fill(ncid, varid, 1, NULL)) ERR;
|
|
|
|
if (nc_inq_var_fill(ncid, varid, &no_fill, &fill_value_in)) ERR;
|
|
if (!no_fill) ERR;
|
|
|
|
index[0] = 1;
|
|
if (nc_put_var1_ushort(ncid, varid, index, &ushort_data)) ERR;
|
|
|
|
index[0] = 0;
|
|
if (nc_get_var1_ushort(ncid, varid, index, &ushort_data_in)) ERR;
|
|
|
|
if (nc_close(ncid)) ERR;
|
|
@endcode
|
|
@author Glenn Davis, Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc_def_var_fill(int ncid, int varid, int no_fill, const void *fill_value)
|
|
{
|
|
NC* ncp;
|
|
int stat = NC_check_id(ncid,&ncp);
|
|
if(stat != NC_NOERR) return stat;
|
|
|
|
/* Using NC_GLOBAL is illegal, as this API has no provision for
|
|
* specifying the type of the fillvalue, it must of necessity be
|
|
* using the type of the variable to interpret the bytes of the
|
|
* fill_value argument. */
|
|
if (varid == NC_GLOBAL) return NC_EGLOBAL;
|
|
|
|
return ncp->dispatch->def_var_fill(ncid,varid,no_fill,fill_value);
|
|
}
|
|
|
|
/**
|
|
Set the zlib compression and shuffle settings for a variable in an
|
|
netCDF/HDF5 file.
|
|
|
|
This function must be called after nc_def_var and before nc_enddef
|
|
or any functions which writes data to the file.
|
|
|
|
Deflation and shuffle are only available for HDF5 files. Attempting
|
|
to set them on non-HDF5 files will return ::NC_ENOTNC4.
|
|
|
|
Deflation and shuffle require chunked data. If this function is
|
|
called on a variable with contiguous data, then the data is changed
|
|
to chunked data, with default chunksizes. Use nc_def_var_chunking()
|
|
to tune performance with user-defined chunksizes.
|
|
|
|
If this function is called on a scalar variable, ::NC_EINVAL is
|
|
returned. Only chunked variables may use filters.
|
|
|
|
Zlib compression cannot be used with szip compression. If this
|
|
function is called on a variable which already has szip compression
|
|
turned on, ::NC_EINVAL is returned.
|
|
|
|
@note Parallel I/O reads work with compressed data. Parallel I/O
|
|
writes work with compressed data in netcdf-c-4.7.4 and later
|
|
releases, using hdf5-1.10.3 and later releases. Using the zlib,
|
|
shuffle (or any other) filter requires that collective access be
|
|
used with the variable. Turning on deflate and/or shuffle for a
|
|
variable in a file opened for parallel I/O will automatically
|
|
switch the access for that variable to collective access.
|
|
|
|
@note The HDF5 manual has this to say about shuffle:
|
|
|
|
The shuffle filter de-interlaces a block of data by reordering
|
|
the bytes. All the bytes from one consistent byte position of
|
|
each data element are placed together in one block; all bytes
|
|
from a second consistent byte position of each data element are
|
|
placed together a second block; etc. For example, given three
|
|
data elements of a 4-byte datatype stored as 012301230123,
|
|
shuffling will re-order data as 000111222333. This can be a
|
|
valuable step in an effective compression algorithm because the
|
|
bytes in each byte position are often closely related to each
|
|
other and putting them together can increase the compression
|
|
ratio.
|
|
|
|
As implied above, the primary value of the shuffle filter lies
|
|
in its coordinated use with a compression filter; it does not
|
|
provide data compression when used alone. When the shuffle
|
|
filter is applied to a dataset immediately prior to the use of a
|
|
compression filter, the compression ratio achieved is often
|
|
superior to that achieved by the use of a compression filter
|
|
without the shuffle filter.
|
|
|
|
@note The shuffle and deflate flags are ambiguous.
|
|
|
|
In most cases, if the shuffle or deflate flag is zero, then it is interpreted
|
|
to mean that shuffle or deflate should not be set. However, if the variable
|
|
already has shuffle or deflate turned on, then it is unclear if a flag
|
|
value of zero means leave the state as it is, or if it means
|
|
that it should be turned off. Since currently no other filters can be
|
|
disabled, it is assumed here that a zero value means to leave the
|
|
state as it is.
|
|
|
|
@param ncid NetCDF or group ID, from a previous call to nc_open(),
|
|
nc_create(), nc_def_grp(), or associated inquiry functions such as
|
|
nc_inq_ncid().
|
|
@param varid Variable ID
|
|
@param shuffle True to turn on the shuffle filter. The shuffle
|
|
filter can assist with the compression of data by changing the byte
|
|
order in the data stream. It makes no sense to use the shuffle
|
|
filter without setting a deflate level.
|
|
@param deflate True to turn on deflation for this variable.
|
|
@param deflate_level A number between 0 (no compression) and 9
|
|
(maximum compression).
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EBADID Bad ncid.
|
|
@return ::NC_ENOTVAR Invalid variable ID.
|
|
@return ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
|
|
not netCDF-4/HDF5.
|
|
@return ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
|
|
netcdf-4 file.
|
|
@return ::NC_ELATEDEF Too late to change settings for this variable.
|
|
@return ::NC_ENOTINDEFINE Not in define mode.
|
|
@return ::NC_EPERM File is read only.
|
|
@return ::NC_ESTRICTNC3 Attempting to create netCDF-4 type var in
|
|
classic model file
|
|
@return ::NC_EHDFERR Error returned by HDF5 layer.
|
|
@return ::NC_EINVAL Invalid input. Deflate can't be set unless
|
|
variable storage is NC_CHUNK.
|
|
|
|
@section nc_def_var_deflate_example Example
|
|
|
|
Here is an example from /examples/C/simple_xy_nc4_wr.c using
|
|
nc_def_var_deflate to create a variable and then turn on the shuffle
|
|
filter and compression.
|
|
|
|
@code
|
|
#include <netcdf.h>
|
|
#define NDIMS 2
|
|
#define NX 6
|
|
#define NY 12
|
|
|
|
int ncid, x_dimid, y_dimid, varid;
|
|
int dimids[NDIMS];
|
|
int shuffle, deflate, deflate_level;
|
|
int data_out[NX][NY];
|
|
int x, y, retval;
|
|
|
|
shuffle = NC_SHUFFLE;
|
|
deflate = 1;
|
|
deflate_level = 1;
|
|
...
|
|
if ((retval = nc_create(FILE_NAME, NC_NETCDF4, &ncid)))
|
|
ERR(retval);
|
|
|
|
if ((retval = nc_def_dim(ncid, "x", NX, &x_dimid)))
|
|
ERR(retval);
|
|
if ((retval = nc_def_dim(ncid, "y", NY, &y_dimid)))
|
|
ERR(retval);
|
|
|
|
dimids[0] = x_dimid;
|
|
dimids[1] = y_dimid;
|
|
|
|
if ((retval = nc_def_var(ncid, "data", NC_INT, NDIMS,
|
|
dimids, &varid)))
|
|
ERR(retval);
|
|
|
|
...
|
|
|
|
if ((retval = nc_def_var_deflate(ncid, varid, shuffle, deflate,
|
|
deflate_level)))
|
|
ERR(retval);
|
|
...
|
|
@endcode
|
|
@author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc_def_var_deflate(int ncid, int varid, int shuffle, int deflate, int deflate_level)
|
|
{
|
|
NC* ncp;
|
|
int stat = NC_check_id(ncid,&ncp);
|
|
if(stat != NC_NOERR) return stat;
|
|
return ncp->dispatch->def_var_deflate(ncid,varid,shuffle,deflate,deflate_level);
|
|
}
|
|
|
|
/**
|
|
Turn on quantization for a variable.
|
|
|
|
The data are quantized by setting unneeded bits to zeros or ones
|
|
so that they may compress well. BitGroom sets bits alternately to 1/0,
|
|
while BitRound and Granular BitRound (GBR) round (more) bits to zeros
|
|
Quantization is lossy (data are irretrievably altered), and it
|
|
improves the compression ratio provided by a subsequent lossless
|
|
compression filter. Quantization alone will not reduce the data size.
|
|
Lossless compression like zlib must also be used (see nc_def_var_deflate()).
|
|
|
|
Producers of large datasets may find that using quantize with
|
|
compression will result in significant improvent in the final data
|
|
size.
|
|
|
|
A notable feature of all the quantization algorithms is data remain
|
|
in IEEE754 format afterwards. Therefore quantization algorithms do
|
|
nothing when data are read.
|
|
|
|
Quantization is only available for variables of type NC_FLOAT or
|
|
NC_DOUBLE. Attempts to set quantization for other variable
|
|
types return an error (NC_EINVAL).
|
|
|
|
Variables that use quantize will have added an attribute with name
|
|
NC_QUANTIZE_[ALGORITHM_NAME]_ATT_NAME, which will contain the
|
|
number of significant digits. Users should not delete or change this
|
|
attribute. This is the only record that quantize has been applied
|
|
to the data.
|
|
|
|
Quantization is not applied to values equal to the value of the
|
|
_FillValue attribute, if any. If the _FillValue attribute is not
|
|
set, then quantization is not applied to values matching the
|
|
default fill value.
|
|
|
|
Quantization may be applied to scalar variables.
|
|
|
|
When type conversion takes place during a write, then it occurs
|
|
before quantization is applied. For example, if nc_put_var_double()
|
|
is called on a variable of type NC_FLOAT, which has quantize
|
|
turned on, then the data are first converted from double to float,
|
|
then quantization is applied to the float values.
|
|
|
|
As with the deflate settings, quantize settings may only be
|
|
modified before the first call to nc_enddef(). Once nc_enddef() is
|
|
called for the file, quantize settings for any variable in the file
|
|
may not be changed.
|
|
|
|
Use of quantization is fully backwards compatible with existing
|
|
versions and packages that can read compressed netCDF data. A
|
|
variable which has been quantized is readable to older versions of
|
|
the netCDF libraries, and to netCDF-Java.
|
|
|
|
For more information about quantization and the BitGroom filter,
|
|
see @ref quantize.
|
|
|
|
@note Users new to quantization should start with Granular Bit
|
|
Round, which results in the best compression. The Bit Groom
|
|
algorithm is not as effective when compressing, but is faster than
|
|
Granular Bit Round. The Bit Round algorithm accepts a number of
|
|
bits to maintain, rather than a number of decimal digits, and is
|
|
provided for users who are already performing some bit-based
|
|
quantization, and wish to turn this task over to the netCDF
|
|
library.
|
|
|
|
@param ncid File ID.
|
|
@param varid Variable ID. ::NC_GLOBAL may not be used.
|
|
@param quantize_mode Quantization mode. May be ::NC_NOQUANTIZE or
|
|
::NC_QUANTIZE_BITGROOM or ::NC_QUANTIZE_GRANULARBR or
|
|
::NC_QUANTIZE_BITROUND.
|
|
@param nsd Number of significant digits (either decimal or binary).
|
|
May be any integer from 1 to ::NC_QUANTIZE_MAX_FLOAT_NSD (for variables
|
|
of type ::NC_FLOAT) or ::NC_QUANTIZE_MAX_DOUBLE_NSD (for variables
|
|
of type ::NC_DOUBLE) for mode ::NC_QUANTIZE_BITGROOM and mode
|
|
::NC_QUANTIZE_GRANULARBR. May be any integer from 1 to
|
|
::NC_QUANTIZE_MAX_FLOAT_NSB (for variables of type ::NC_FLOAT) or
|
|
::NC_QUANTIZE_MAX_DOUBLE_NSB (for variables of type ::NC_DOUBLE)
|
|
for mode ::NC_QUANTIZE_BITROUND. Ignored if quantize_mode = NC_NOQUANTIZE.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EGLOBAL Can't use ::NC_GLOBAL with this function.
|
|
@return ::NC_EBADID Bad ncid.
|
|
@return ::NC_ENOTVAR Invalid variable ID.
|
|
@return ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
|
|
not netCDF-4/HDF5.
|
|
@return ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
|
|
netcdf-4 file.
|
|
@return ::NC_ELATEDEF Too late to change settings for this variable.
|
|
@return ::NC_EINVAL Invalid input.
|
|
@author Charlie Zender, Ed Hartnett
|
|
*/
|
|
int
|
|
nc_def_var_quantize(int ncid, int varid, int quantize_mode, int nsd)
|
|
{
|
|
NC* ncp;
|
|
int stat = NC_check_id(ncid,&ncp);
|
|
if(stat != NC_NOERR) return stat;
|
|
|
|
/* Using NC_GLOBAL is illegal. */
|
|
if (varid == NC_GLOBAL) return NC_EGLOBAL;
|
|
return ncp->dispatch->def_var_quantize(ncid,varid,quantize_mode,nsd);
|
|
}
|
|
|
|
/**
|
|
Set checksum for a var.
|
|
|
|
This function must be called after nc_def_var and before nc_enddef
|
|
or any functions which writes data to the file.
|
|
|
|
Checksums require chunked data. If this function is called on a
|
|
variable with contiguous data, then the data is changed to chunked
|
|
data, with default chunksizes. Use nc_def_var_chunking() to tune
|
|
performance with user-defined chunksizes.
|
|
|
|
@note Parallel I/O reads work with fletcher32 encoded
|
|
data. Parallel I/O writes work with fletcher32 in netcdf-c-4.7.4
|
|
and later releases, using hdf5-1.10.2 and later releases. Using the
|
|
fletcher32 (or any) filter requires that collective access be used
|
|
with the variable. Turning on fletcher32 for a variable in a file
|
|
opened for parallel I/O will automatically switch the access for
|
|
that variable to collective access.
|
|
|
|
@param ncid NetCDF or group ID, from a previous call to nc_open(),
|
|
nc_create(), nc_def_grp(), or associated inquiry functions such as
|
|
nc_inq_ncid().
|
|
@param varid Variable ID
|
|
@param fletcher32 True to turn on Fletcher32 checksums for this
|
|
variable.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EBADID Bad ncid.
|
|
@return ::NC_ENOTVAR Invalid variable ID.
|
|
@return ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
|
|
not netCDF-4/HDF5.
|
|
@return ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
|
|
netcdf-4 file.
|
|
@return ::NC_ELATEDEF Too late to change settings for this variable.
|
|
@return ::NC_EINVAL Invalid input
|
|
@author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc_def_var_fletcher32(int ncid, int varid, int fletcher32)
|
|
{
|
|
NC* ncp;
|
|
int stat = NC_check_id(ncid,&ncp);
|
|
if(stat != NC_NOERR) return stat;
|
|
return ncp->dispatch->def_var_fletcher32(ncid,varid,fletcher32);
|
|
}
|
|
|
|
/**
|
|
Define storage and, if chunked storage is used, chunking parameters
|
|
for a variable
|
|
|
|
The storage may be set to NC_CONTIGUOUS, NC_COMPACT, or NC_CHUNKED.
|
|
|
|
Contiguous storage means the variable is stored as one block of
|
|
data in the file. This is the default storage.
|
|
|
|
Compact storage means the variable is stored in the header record
|
|
of the file. This can have large performance benefits on HPC system
|
|
running many processors. Compact storage is only available for
|
|
variables whose data are 64 KB or less. Attempting to turn on
|
|
compact storage for a variable that is too large will result in the
|
|
::NC_EVARSIZE error.
|
|
|
|
Chunked storage means the data are stored as chunks, of
|
|
user-configurable size. Chunked storage is required for variable
|
|
with one or more unlimted dimensions, or variable which use
|
|
compression, or any other filter.
|
|
|
|
The total size of a chunk must be less than 4 GiB. That is, the
|
|
product of all chunksizes and the size of the data (or the size of
|
|
nc_vlen_t for VLEN types) must be less than 4 GiB.
|
|
|
|
This function may only be called after the variable is defined, but
|
|
before nc_enddef is called. Once the chunking parameters are set for a
|
|
variable, they cannot be changed.
|
|
|
|
@note Scalar variables may have a storage of NC_CONTIGUOUS or
|
|
NC_COMPACT. Attempts to set chunking on a scalare variable will
|
|
cause ::NC_EINVAL to be returned. Only non-scalar variables can
|
|
have chunking.
|
|
|
|
@param ncid NetCDF ID, from a previous call to nc_open() or
|
|
nc_create().
|
|
@param varid Variable ID.
|
|
@param storage If ::NC_CONTIGUOUS or ::NC_COMPACT, then contiguous
|
|
or compact storage is used for this variable. Variables with one or
|
|
more unlimited dimensions cannot use contiguous or compact
|
|
storage. If contiguous or compact storage is turned on, the
|
|
chunksizes parameter is ignored. If ::NC_CHUNKED, then chunked
|
|
storage is used for this variable. Chunk sizes may be specified
|
|
with the chunksizes parameter or default sizes will be used if that
|
|
parameter is NULL.
|
|
@param chunksizesp A pointer to an array list of chunk sizes. The
|
|
array must have one chunksize for each dimension of the variable. If
|
|
::NC_CONTIGUOUS storage is set, then the chunksizes parameter is
|
|
ignored. Ignored if NULL.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EBADID Bad ID.
|
|
@return ::NC_ENOTNC4 Not a netCDF-4 file.
|
|
@return ::NC_ELATEDEF This variable has already been the subject of
|
|
a nc_enddef call. In netCDF-4 files nc_enddef will be called
|
|
automatically for any data read or write. Once nc_enddef has been
|
|
called after the nc_def_var call for a variable, it is impossible
|
|
to set the chunking for that variable.
|
|
@return ::NC_ENOTINDEFINE Not in define mode. This is returned for
|
|
netCDF classic or 64-bit offset files, or for netCDF-4 files, when
|
|
they wwere created with ::NC_CLASSIC_MODEL flag by nc_create().
|
|
@return ::NC_EPERM Attempt to create object in read-only file.
|
|
@return ::NC_EBADCHUNK Returns if the chunk size specified for a
|
|
variable is larger than the length of the dimensions associated with
|
|
variable.
|
|
@return ::NC_EVARSIZE Compact storage attempted for variable bigger
|
|
than 64 KB.
|
|
@return ::NC_EINVAL Attempt to set contiguous or compact storage
|
|
for var with one or more unlimited dimensions, or chunking for a
|
|
scalar var.
|
|
|
|
@section nc_def_var_chunking_example Example
|
|
|
|
In this example from libsrc4/tst_vars2.c, chunksizes are set with
|
|
nc_var_def_chunking, and checked with nc_var_inq_chunking.
|
|
|
|
@code
|
|
printf("**** testing chunking...");
|
|
{
|
|
#define NDIMS5 1
|
|
#define DIM5_NAME "D5"
|
|
#define VAR_NAME5 "V5"
|
|
#define DIM5_LEN 1000
|
|
|
|
int dimids[NDIMS5], dimids_in[NDIMS5];
|
|
int varid;
|
|
int ndims, nvars, natts, unlimdimid;
|
|
nc_type xtype_in;
|
|
char name_in[NC_MAX_NAME + 1];
|
|
int data[DIM5_LEN], data_in[DIM5_LEN];
|
|
size_t chunksize[NDIMS5] = {5};
|
|
size_t chunksize_in[NDIMS5];
|
|
int storage_in;
|
|
int i, d;
|
|
|
|
for (i = 0; i < DIM5_LEN; i++)
|
|
data[i] = i;
|
|
|
|
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
|
|
if (nc_def_dim(ncid, DIM5_NAME, DIM5_LEN, &dimids[0])) ERR;
|
|
if (nc_def_var(ncid, VAR_NAME5, NC_INT, NDIMS5, dimids, &varid)) ERR;
|
|
if (nc_def_var_chunking(ncid, varid, NC_CHUNKED, chunksize)) ERR;
|
|
if (nc_put_var_int(ncid, varid, data)) ERR;
|
|
|
|
if (nc_inq_var_chunking(ncid, varid, &storage_in, chunksize_in)) ERR;
|
|
for (d = 0; d < NDIMS5; d++)
|
|
if (chunksize[d] != chunksize_in[d]) ERR;
|
|
if (storage_in != NC_CHUNKED) ERR;
|
|
@endcode
|
|
@author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc_def_var_chunking(int ncid, int varid, int storage, const size_t *chunksizesp)
|
|
{
|
|
NC* ncp;
|
|
int stat = NC_check_id(ncid, &ncp);
|
|
if(stat != NC_NOERR) return stat;
|
|
return ncp->dispatch->def_var_chunking(ncid, varid, storage,
|
|
chunksizesp);
|
|
}
|
|
|
|
/**
|
|
Define endianness of a variable.
|
|
|
|
With this function the endianness (i.e. order of bits in integers) can
|
|
be changed on a per-variable basis. By default, the endianness is the
|
|
same as the default endianness of the platform. But with
|
|
nc_def_var_endianness the endianness can be explicitly set for a
|
|
variable.
|
|
|
|
Warning: this function is only defined if the type of the variable
|
|
is an atomic integer or float type.
|
|
|
|
This function may only be called after the variable is defined, but
|
|
before nc_enddef is called.
|
|
|
|
@param ncid NetCDF ID, from a previous call to nc_open() or
|
|
nc_create().
|
|
|
|
@param varid Variable ID.
|
|
|
|
@param endian ::NC_ENDIAN_NATIVE to select the native endianness of
|
|
the platform (the default), ::NC_ENDIAN_LITTLE to use
|
|
little-endian, ::NC_ENDIAN_BIG to use big-endian.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EBADID Bad ID.
|
|
@return ::NC_ENOTNC4 Not a netCDF-4 file.
|
|
@return ::NC_ELATEDEF This variable has already been the subject of a
|
|
nc_enddef call. In netCDF-4 files nc_enddef will be called
|
|
automatically for any data read or write. Once nc_enddef has been
|
|
called after the nc_def_var call for a variable, it is impossible to
|
|
set the chunking for that variable.
|
|
@return ::NC_ENOTINDEFINE Not in define mode. This is returned for
|
|
netCDF classic or 64-bit offset files, or for netCDF-4 files, when
|
|
they wwere created with ::NC_CLASSIC_MODEL flag by nc_create().
|
|
@return ::NC_EPERM Attempt to create object in read-only file.
|
|
|
|
@section nc_def_var_endian_example Example
|
|
|
|
In this example from libsrc4/tst_vars2.c, a variable is created, and
|
|
the endianness set to ::NC_ENDIAN_BIG.
|
|
|
|
@code
|
|
#define NDIMS4 1
|
|
#define DIM4_NAME "Joe"
|
|
#define VAR_NAME4 "Ed"
|
|
#define DIM4_LEN 10
|
|
{
|
|
int dimids[NDIMS4], dimids_in[NDIMS4];
|
|
int varid;
|
|
int ndims, nvars, natts, unlimdimid;
|
|
nc_type xtype_in;
|
|
char name_in[NC_MAX_NAME + 1];
|
|
int data[DIM4_LEN], data_in[DIM4_LEN];
|
|
int endian_in;
|
|
int i;
|
|
|
|
for (i = 0; i < DIM4_LEN; i++)
|
|
data[i] = i;
|
|
|
|
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
|
|
if (nc_def_dim(ncid, DIM4_NAME, DIM4_LEN, &dimids[0])) ERR;
|
|
if (dimids[0] != 0) ERR;
|
|
if (nc_def_var(ncid, VAR_NAME4, NC_INT, NDIMS4, dimids, &varid)) ERR;
|
|
if (nc_def_var_endian(ncid, varid, NC_ENDIAN_BIG)) ERR;
|
|
@endcode
|
|
@author Ed Hartnett
|
|
*/
|
|
int
|
|
nc_def_var_endian(int ncid, int varid, int endian)
|
|
{
|
|
NC* ncp;
|
|
int stat = NC_check_id(ncid,&ncp);
|
|
if(stat != NC_NOERR) return stat;
|
|
return ncp->dispatch->def_var_endian(ncid,varid,endian);
|
|
}
|
|
|
|
/**
|
|
* Set szip compression settings on a variable. Szip is an
|
|
* implementation of the extended-Rice lossless compression algorithm;
|
|
* it is reported to provide fast and effective compression. Szip is
|
|
* only available to netCDF if HDF5 was built with szip support.
|
|
*
|
|
* SZIP compression cannot be applied to variables with any
|
|
* user-defined type.
|
|
*
|
|
* If zlib compression has already be turned on for a variable, then
|
|
* this function will return ::NC_EINVAL.
|
|
*
|
|
* To learn the szip settings for a variable, use nc_inq_var_szip().
|
|
*
|
|
* @note The options_mask parameter may be either ::NC_SZIP_EC (entropy
|
|
* coding) or ::NC_SZIP_NN (nearest neighbor):
|
|
* * The entropy coding method is best suited for data that has been
|
|
* processed. The EC method works best for small numbers.
|
|
* * The nearest neighbor coding method preprocesses the data then the
|
|
* applies EC method as above.
|
|
*
|
|
* For more information about HDF5 and szip, see
|
|
* https://support.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetSzip
|
|
* and
|
|
* https://support.hdfgroup.org/doc_resource/SZIP/index.html.
|
|
*
|
|
* @param ncid File ID.
|
|
* @param varid Variable ID.
|
|
* @param options_mask The options mask. Can be ::NC_SZIP_EC or
|
|
* ::NC_SZIP_NN.
|
|
* @param pixels_per_block Pixels per block. Must be even and not
|
|
* greater than 32, with typical values being 8, 10, 16, or 32. This
|
|
* parameter affects compression ratio; the more pixel values vary,
|
|
* the smaller this number should be to achieve better performance. If
|
|
* pixels_per_block is bigger than the total number of elements in a
|
|
* dataset chunk, ::NC_EINVAL will be returned.
|
|
*
|
|
* @returns ::NC_NOERR No error.
|
|
* @returns ::NC_EBADID Bad ncid.
|
|
* @returns ::NC_ENOTVAR Invalid variable ID.
|
|
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
|
|
* not netCDF-4/HDF5.
|
|
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
|
|
* @returns ::NC_ENOTINDEFINE Not in define mode.
|
|
* @returns ::NC_EINVAL Invalid input, or zlib filter already applied
|
|
* to this var.
|
|
* @author Ed Hartnett
|
|
*/
|
|
int
|
|
nc_def_var_szip(int ncid, int varid, int options_mask, int pixels_per_block)
|
|
{
|
|
int ret;
|
|
|
|
/* This will cause H5Pset_szip to be called when the var is
|
|
* created. */
|
|
unsigned int params[2];
|
|
params[0] = options_mask;
|
|
params[1] = pixels_per_block;
|
|
if ((ret = nc_def_var_filter(ncid, varid, HDF5_FILTER_SZIP, 2, params)))
|
|
return ret;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/** @} */
|
|
|
|
/**
|
|
@name Rename a Variable
|
|
|
|
Rename a variable.
|
|
*/
|
|
/** @{ */
|
|
|
|
/**
|
|
Rename a variable.
|
|
|
|
This function changes the name of a netCDF variable in an open netCDF
|
|
file or group. You cannot rename a variable to have the name of any existing
|
|
variable.
|
|
|
|
For classic format, 64-bit offset format, and netCDF-4/HDF5 with
|
|
classic mode, if the new name is longer than the old name, the netCDF
|
|
dataset must be in define mode.
|
|
|
|
For netCDF-4/HDF5 files, renaming the variable changes the order of
|
|
the variables in the file. The renamed variable becomes the last
|
|
variable in the file.
|
|
|
|
@param ncid NetCDF or group ID, from a previous call to nc_open(),
|
|
nc_create(), nc_def_grp(), or associated inquiry functions such as
|
|
nc_inq_ncid().
|
|
|
|
@param varid Variable ID
|
|
|
|
@param name New name of the variable.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EBADID Bad ncid.
|
|
@return ::NC_ENOTVAR Invalid variable ID.
|
|
@return ::NC_EBADNAME Bad name.
|
|
@return ::NC_EMAXNAME Name is too long.
|
|
@return ::NC_ENAMEINUSE Name in use.
|
|
@return ::NC_ENOMEM Out of memory.
|
|
|
|
@section nc_rename_var_example Example
|
|
|
|
Here is an example using nc_rename_var to rename the variable rh to
|
|
rel_hum in an existing netCDF dataset named foo.nc:
|
|
|
|
@code
|
|
#include <netcdf.h>
|
|
...
|
|
int status;
|
|
int ncid;
|
|
int rh_id;
|
|
...
|
|
status = nc_open("foo.nc", NC_WRITE, &ncid);
|
|
if (status != NC_NOERR) handle_error(status);
|
|
...
|
|
status = nc_redef(ncid);
|
|
if (status != NC_NOERR) handle_error(status);
|
|
status = nc_inq_varid (ncid, "rh", &rh_id);
|
|
if (status != NC_NOERR) handle_error(status);
|
|
status = nc_rename_var (ncid, rh_id, "rel_hum");
|
|
if (status != NC_NOERR) handle_error(status);
|
|
status = nc_enddef(ncid);
|
|
if (status != NC_NOERR) handle_error(status);
|
|
@endcode
|
|
@author Glenn Davis, Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
nc_rename_var(int ncid, int varid, const char *name)
|
|
{
|
|
NC* ncp;
|
|
int stat = NC_check_id(ncid, &ncp);
|
|
if(stat != NC_NOERR) return stat;
|
|
TRACE(nc_rename_var);
|
|
return ncp->dispatch->rename_var(ncid, varid, name);
|
|
}
|
|
/** @} */
|
|
|
|
/**
|
|
@internal Does a variable have a record dimension?
|
|
|
|
@param ncid File ID.
|
|
@param varid Variable ID.
|
|
@param nrecs Pointer that gets number of records.
|
|
|
|
@return 0 if not a record var, 1 if it is.
|
|
*/
|
|
int
|
|
NC_is_recvar(int ncid, int varid, size_t* nrecs)
|
|
{
|
|
int status = NC_NOERR;
|
|
int unlimid;
|
|
int ndims;
|
|
int dimset[NC_MAX_VAR_DIMS];
|
|
|
|
status = nc_inq_unlimdim(ncid,&unlimid);
|
|
if(status != NC_NOERR) return 0; /* no unlimited defined */
|
|
status = nc_inq_varndims(ncid,varid,&ndims);
|
|
if(status != NC_NOERR) return 0; /* no unlimited defined */
|
|
if(ndims == 0) return 0; /* scalar */
|
|
status = nc_inq_vardimid(ncid,varid,dimset);
|
|
if(status != NC_NOERR) return 0; /* no unlimited defined */
|
|
status = nc_inq_dim(ncid,dimset[0],NULL,nrecs);
|
|
if(status != NC_NOERR) return 0;
|
|
return (dimset[0] == unlimid ? 1: 0);
|
|
}
|
|
|
|
/**
|
|
@internal Get the number of record dimensions for a variable and an
|
|
array that identifies which of a variable's dimensions are record
|
|
dimensions. Intended to be used instead of NC_is_recvar(), which
|
|
doesn't work for netCDF-4 variables which have multiple unlimited
|
|
dimensions or an unlimited dimension that is not the first of a
|
|
variable's dimensions.
|
|
|
|
@param ncid File ID.
|
|
@param varid Variable ID.
|
|
@param nrecdimsp Pointer that gets number of record dims.
|
|
@param is_recdim Pointer that gets 1 if there is one or more record
|
|
dimensions, 0 if not.
|
|
|
|
@return 0 if not a record var, 1 if it is.
|
|
|
|
Example use:
|
|
@code
|
|
int nrecdims;
|
|
int is_recdim[NC_MAX_VAR_DIMS];
|
|
...
|
|
status = NC_inq_recvar(ncid,varid,&nrecdims,is_recdim);
|
|
isrecvar = (nrecdims > 0);
|
|
@endcode
|
|
*/
|
|
int
|
|
NC_inq_recvar(int ncid, int varid, int* nrecdimsp, int *is_recdim)
|
|
{
|
|
int status = NC_NOERR;
|
|
int unlimid;
|
|
int nvardims;
|
|
int dimset[NC_MAX_VAR_DIMS];
|
|
int dim;
|
|
int nrecdims = 0;
|
|
|
|
status = nc_inq_varndims(ncid,varid,&nvardims);
|
|
if(status != NC_NOERR) return status;
|
|
if(nvardims == 0) return NC_NOERR; /* scalars have no dims */
|
|
for(dim = 0; dim < nvardims; dim++)
|
|
is_recdim[dim] = 0;
|
|
status = nc_inq_unlimdim(ncid, &unlimid);
|
|
if(status != NC_NOERR) return status;
|
|
if(unlimid == -1) return status; /* no unlimited dims for any variables */
|
|
#ifdef USE_NETCDF4
|
|
{
|
|
int nunlimdims;
|
|
int *unlimids;
|
|
int recdim;
|
|
status = nc_inq_unlimdims(ncid, &nunlimdims, NULL); /* for group or file, not variable */
|
|
if(status != NC_NOERR) return status;
|
|
if(nunlimdims == 0) return status;
|
|
|
|
if (!(unlimids = malloc(nunlimdims * sizeof(int))))
|
|
return NC_ENOMEM;
|
|
status = nc_inq_unlimdims(ncid, &nunlimdims, unlimids); /* for group or file, not variable */
|
|
if(status != NC_NOERR) {
|
|
free(unlimids);
|
|
return status;
|
|
}
|
|
status = nc_inq_vardimid(ncid, varid, dimset);
|
|
if(status != NC_NOERR) {
|
|
free(unlimids);
|
|
return status;
|
|
}
|
|
for (dim = 0; dim < nvardims; dim++) { /* netCDF-4 rec dims need not be first dim for a rec var */
|
|
for(recdim = 0; recdim < nunlimdims; recdim++) {
|
|
if(dimset[dim] == unlimids[recdim]) {
|
|
is_recdim[dim] = 1;
|
|
nrecdims++;
|
|
}
|
|
}
|
|
}
|
|
free(unlimids);
|
|
}
|
|
#else
|
|
status = nc_inq_vardimid(ncid, varid, dimset);
|
|
if(status != NC_NOERR) return status;
|
|
if(dimset[0] == unlimid) {
|
|
is_recdim[0] = 1;
|
|
nrecdims++;
|
|
}
|
|
#endif /* USE_NETCDF4 */
|
|
if(nrecdimsp) *nrecdimsp = nrecdims;
|
|
return status;
|
|
}
|
|
|
|
/* Ok to use NC pointers because
|
|
all IOSP's will use that structure,
|
|
but not ok to use e.g. NC_Var pointers
|
|
because they may be different structure
|
|
entirely.
|
|
*/
|
|
|
|
/**
|
|
@internal
|
|
Find the length of a type. This is how much space is required by
|
|
the in memory to hold one element of this type.
|
|
|
|
@param type A netCDF atomic type.
|
|
|
|
@return Length of the type in bytes, or -1 if type not found.
|
|
@author Ed Hartnett
|
|
*/
|
|
int
|
|
nctypelen(nc_type type)
|
|
{
|
|
switch(type){
|
|
case NC_CHAR :
|
|
return ((int)sizeof(char));
|
|
case NC_BYTE :
|
|
return ((int)sizeof(signed char));
|
|
case NC_SHORT :
|
|
return ((int)sizeof(short));
|
|
case NC_INT :
|
|
return ((int)sizeof(int));
|
|
case NC_FLOAT :
|
|
return ((int)sizeof(float));
|
|
case NC_DOUBLE :
|
|
return ((int)sizeof(double));
|
|
|
|
/* These can occur in netcdf-3 code */
|
|
case NC_UBYTE :
|
|
return ((int)sizeof(unsigned char));
|
|
case NC_USHORT :
|
|
return ((int)(sizeof(unsigned short)));
|
|
case NC_UINT :
|
|
return ((int)sizeof(unsigned int));
|
|
case NC_INT64 :
|
|
return ((int)sizeof(signed long long));
|
|
case NC_UINT64 :
|
|
return ((int)sizeof(unsigned long long));
|
|
#ifdef USE_NETCDF4
|
|
case NC_STRING :
|
|
return ((int)sizeof(char*));
|
|
#endif /*USE_NETCDF4*/
|
|
|
|
default:
|
|
return -1;
|
|
}
|
|
}
|
|
|
|
/**
|
|
@internal
|
|
Find the length of a type. Redundant over nctypelen() above.
|
|
|
|
@param xtype an nc_type.
|
|
|
|
@author Dennis Heimbigner
|
|
*/
|
|
size_t
|
|
NC_atomictypelen(nc_type xtype)
|
|
{
|
|
size_t sz = 0;
|
|
switch(xtype) {
|
|
case NC_NAT: sz = 0; break;
|
|
case NC_BYTE: sz = sizeof(signed char); break;
|
|
case NC_CHAR: sz = sizeof(char); break;
|
|
case NC_SHORT: sz = sizeof(short); break;
|
|
case NC_INT: sz = sizeof(int); break;
|
|
case NC_FLOAT: sz = sizeof(float); break;
|
|
case NC_DOUBLE: sz = sizeof(double); break;
|
|
case NC_INT64: sz = sizeof(signed long long); break;
|
|
case NC_UBYTE: sz = sizeof(unsigned char); break;
|
|
case NC_USHORT: sz = sizeof(unsigned short); break;
|
|
case NC_UINT: sz = sizeof(unsigned int); break;
|
|
case NC_UINT64: sz = sizeof(unsigned long long); break;
|
|
#ifdef USE_NETCDF4
|
|
case NC_STRING: sz = sizeof(char*); break;
|
|
#endif
|
|
default: break;
|
|
}
|
|
return sz;
|
|
}
|
|
|
|
/**
|
|
@internal
|
|
Get the type name.
|
|
|
|
@param xtype an nc_type.
|
|
|
|
@author Dennis Heimbigner
|
|
*/
|
|
char *
|
|
NC_atomictypename(nc_type xtype)
|
|
{
|
|
char* nm = NULL;
|
|
switch(xtype) {
|
|
case NC_NAT: nm = "undefined"; break;
|
|
case NC_BYTE: nm = "byte"; break;
|
|
case NC_CHAR: nm = "char"; break;
|
|
case NC_SHORT: nm = "short"; break;
|
|
case NC_INT: nm = "int"; break;
|
|
case NC_FLOAT: nm = "float"; break;
|
|
case NC_DOUBLE: nm = "double"; break;
|
|
case NC_INT64: nm = "int64"; break;
|
|
case NC_UBYTE: nm = "ubyte"; break;
|
|
case NC_USHORT: nm = "ushort"; break;
|
|
case NC_UINT: nm = "uint"; break;
|
|
case NC_UINT64: nm = "uint64"; break;
|
|
#ifdef USE_NETCDF4
|
|
case NC_STRING: nm = "string"; break;
|
|
#endif
|
|
default: break;
|
|
}
|
|
return nm;
|
|
}
|
|
|
|
/**
|
|
@internal
|
|
Get the shape of a variable.
|
|
|
|
@param ncid NetCDF ID, from a previous call to nc_open() or
|
|
nc_create().
|
|
@param varid Variable ID.
|
|
@param ndims Number of dimensions for this var.
|
|
@param shape Pointer to pre-allocated array that gets the size of
|
|
each dimension.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EBADID Bad ncid.
|
|
@return ::NC_ENOTVAR Bad varid.
|
|
|
|
@author Dennis Heimbigner
|
|
*/
|
|
int
|
|
NC_getshape(int ncid, int varid, int ndims, size_t* shape)
|
|
{
|
|
int dimids[NC_MAX_VAR_DIMS];
|
|
int i;
|
|
int status = NC_NOERR;
|
|
|
|
if ((status = nc_inq_vardimid(ncid, varid, dimids)))
|
|
return status;
|
|
for(i = 0; i < ndims; i++)
|
|
if ((status = nc_inq_dimlen(ncid, dimids[i], &shape[i])))
|
|
break;
|
|
|
|
return status;
|
|
}
|
|
|
|
/**
|
|
@internal Check the start, count, and stride parameters for gets
|
|
and puts, and handle NULLs.
|
|
|
|
@param ncid The file ID.
|
|
@param varid The variable ID.
|
|
@param start Pointer to start array. If NULL ::NC_EINVALCOORDS will
|
|
be returned for non-scalar variable.
|
|
@param count Pointer to pointer to count array. If *count is NULL,
|
|
an array of the correct size will be allocated, and filled with
|
|
counts that represent the full extent of the variable. In this
|
|
case, the memory must be freed by the caller.
|
|
@param stride Pointer to pointer to stride array. If NULL, stide is
|
|
ignored. If *stride is NULL an array of the correct size will be
|
|
allocated, and filled with ones. In this case, the memory must be
|
|
freed by the caller.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EBADID Bad ncid.
|
|
@return ::NC_ENOTVAR Variable not found.
|
|
@return ::NC_ENOMEM Out of memory.
|
|
@return ::NC_EINVALCOORDS Missing start array.
|
|
@author Ed Hartnett
|
|
*/
|
|
int
|
|
NC_check_nulls(int ncid, int varid, const size_t *start, size_t **count,
|
|
ptrdiff_t **stride)
|
|
{
|
|
int varndims;
|
|
int stat;
|
|
|
|
if ((stat = nc_inq_varndims(ncid, varid, &varndims)))
|
|
return stat;
|
|
|
|
/* For non-scalar vars, start is required. */
|
|
if (!start && varndims)
|
|
return NC_EINVALCOORDS;
|
|
|
|
/* If count is NULL, assume full extent of var. */
|
|
if (!*count)
|
|
{
|
|
if (!(*count = malloc(varndims * sizeof(size_t))))
|
|
return NC_ENOMEM;
|
|
if ((stat = NC_getshape(ncid, varid, varndims, *count)))
|
|
{
|
|
free(*count);
|
|
*count = NULL;
|
|
return stat;
|
|
}
|
|
}
|
|
|
|
/* If stride is NULL, do nothing, if *stride is NULL use all
|
|
* 1s. */
|
|
if (stride && !*stride)
|
|
{
|
|
int i;
|
|
|
|
if (!(*stride = malloc(varndims * sizeof(ptrdiff_t))))
|
|
return NC_ENOMEM;
|
|
for (i = 0; i < varndims; i++)
|
|
(*stride)[i] = 1;
|
|
}
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/**
|
|
@name Free String Resources
|
|
|
|
Use this functions to free resources associated with ::NC_STRING
|
|
data.
|
|
*/
|
|
/*! @{ */
|
|
/**
|
|
Free string space allocated by the library.
|
|
|
|
When you read string type the library will allocate the storage
|
|
space for the data. This storage space must be freed, so pass the
|
|
pointer back to this function, when you're done with the data, and
|
|
it will free the string memory.
|
|
|
|
@param len The number of character arrays in the array.
|
|
@param data The pointer to the data array.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@author Ed Hartnett
|
|
*/
|
|
int
|
|
nc_free_string(size_t len, char **data)
|
|
{
|
|
int i;
|
|
for (i = 0; i < len; i++)
|
|
free(data[i]);
|
|
return NC_NOERR;
|
|
}
|
|
/** @} */
|
|
|
|
/**
|
|
@name Variables Chunk Caches
|
|
|
|
Use these functions to change the variable chunk cache settings.
|
|
*/
|
|
/*! @{ */
|
|
/**
|
|
Change the cache settings for a chunked variable. This function allows
|
|
users to control the amount of memory used in the per-variable chunk
|
|
cache at the HDF5 level. Changing the chunk cache only has effect
|
|
until the file is closed. Once re-opened, the variable chunk cache
|
|
returns to its default value.
|
|
|
|
Current cache settings for each var may be obtained with
|
|
nc_get_var_chunk_cache().
|
|
|
|
Default values for these settings may be changed for the whole file
|
|
with nc_set_chunk_cache().
|
|
|
|
@param ncid NetCDF or group ID, from a previous call to nc_open(),
|
|
nc_create(), nc_def_grp(), or associated inquiry functions such as
|
|
nc_inq_ncid().
|
|
@param varid Variable ID
|
|
@param size The total size of the raw data chunk cache, in bytes.
|
|
@param nelems The number of chunk slots in the raw data chunk cache.
|
|
@param preemption The preemption, a value between 0 and 1 inclusive
|
|
that indicates how much chunks that have been fully read are favored
|
|
for preemption. A value of zero means fully read chunks are treated no
|
|
differently than other chunks (the preemption is strictly LRU) while a
|
|
value of one means fully read chunks are always preempted before other
|
|
chunks.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EBADID Bad ncid.
|
|
@return ::NC_ENOTVAR Invalid variable ID.
|
|
@return ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
|
|
netcdf-4 file.
|
|
@return ::NC_EINVAL Invalid input
|
|
|
|
@section nc_def_var_chunk_cache_example Example
|
|
|
|
In this example from nc_test4/tst_coords.c, a variable is defined, and
|
|
the chunk cache settings are changed for that variable.
|
|
|
|
@code
|
|
printf("**** testing setting cache values for coordinate variables...");
|
|
{
|
|
#define RANK_1 1
|
|
#define DIM0_NAME "d0"
|
|
#define CACHE_SIZE 1000000
|
|
#define CACHE_NELEMS 1009
|
|
#define CACHE_PREEMPTION .90
|
|
|
|
int ncid, dimid, varid;
|
|
char name_in[NC_MAX_NAME + 1];
|
|
|
|
if (nc_create(FILE_NAME, NC_CLASSIC_MODEL|NC_NETCDF4, &ncid)) ERR;
|
|
if (nc_def_dim(ncid, DIM0_NAME, NC_UNLIMITED, &dimid)) ERR;
|
|
if (nc_def_var(ncid, DIM0_NAME, NC_DOUBLE, 1, &dimid, &varid)) ERR;
|
|
if (nc_set_var_chunk_cache(ncid, varid, CACHE_SIZE, CACHE_NELEMS, CACHE_PREEMPTION)) ERR;
|
|
if (nc_close(ncid)) ERR;
|
|
|
|
...
|
|
}
|
|
SUMMARIZE_ERR;
|
|
@endcode
|
|
@author Ed Hartnett
|
|
*/
|
|
int
|
|
nc_set_var_chunk_cache(int ncid, int varid, size_t size, size_t nelems,
|
|
float preemption)
|
|
{
|
|
NC* ncp;
|
|
int stat = NC_check_id(ncid, &ncp);
|
|
if(stat != NC_NOERR) return stat;
|
|
return ncp->dispatch->set_var_chunk_cache(ncid, varid, size,
|
|
nelems, preemption);
|
|
}
|
|
|
|
/**
|
|
Get the per-variable chunk cache settings from the HDF5
|
|
layer. These settings may be changed with nc_set_var_chunk_cache().
|
|
|
|
See nc_set_chunk_cache() for a full discussion of these settings.
|
|
|
|
@param ncid NetCDF or group ID, from a previous call to nc_open(),
|
|
nc_create(), nc_def_grp(), or associated inquiry functions such as
|
|
nc_inq_ncid().
|
|
@param varid Variable ID
|
|
@param sizep The total size of the raw data chunk cache, in bytes,
|
|
will be put here. @ref ignored_if_null.
|
|
@param nelemsp The number of chunk slots in the raw data chunk
|
|
cache hash table will be put here. @ref ignored_if_null.
|
|
@param preemptionp The preemption will be put here. The preemtion
|
|
value is between 0 and 1 inclusive and indicates how much chunks
|
|
that have been fully read are favored for preemption. A value of
|
|
zero means fully read chunks are treated no differently than other
|
|
chunks (the preemption is strictly LRU) while a value of one means
|
|
fully read chunks are always preempted before other chunks. @ref
|
|
ignored_if_null.
|
|
|
|
@return ::NC_NOERR No error.
|
|
@return ::NC_EBADID Bad ncid.
|
|
@return ::NC_ENOTVAR Invalid variable ID.
|
|
@return ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
|
|
netcdf-4 file.
|
|
@return ::NC_EINVAL Invalid input
|
|
@author Ed Hartnett
|
|
*/
|
|
int
|
|
nc_get_var_chunk_cache(int ncid, int varid, size_t *sizep, size_t *nelemsp,
|
|
float *preemptionp)
|
|
{
|
|
NC* ncp;
|
|
int stat = NC_check_id(ncid, &ncp);
|
|
if(stat != NC_NOERR) return stat;
|
|
return ncp->dispatch->get_var_chunk_cache(ncid, varid, sizep,
|
|
nelemsp, preemptionp);
|
|
}
|
|
|
|
#ifndef USE_NETCDF4
|
|
/* Make sure the fortran API is defined, even if it only returns errors */
|
|
|
|
int
|
|
nc_set_chunk_cache_ints(int size, int nelems, int preemption)
|
|
{
|
|
return NC_ENOTBUILT;
|
|
}
|
|
|
|
int
|
|
nc_get_chunk_cache_ints(int *sizep, int *nelemsp, int *preemptionp)
|
|
{
|
|
return NC_ENOTBUILT;
|
|
}
|
|
|
|
int
|
|
nc_set_var_chunk_cache_ints(int ncid, int varid, int size, int nelems,
|
|
int preemption)
|
|
{
|
|
return NC_ENOTBUILT;
|
|
}
|
|
|
|
int
|
|
nc_get_var_chunk_cache_ints(int ncid, int varid, int *sizep,
|
|
int *nelemsp, int *preemptionp)
|
|
{
|
|
return NC_ENOTBUILT;
|
|
}
|
|
|
|
#endif /*USE_NETCDF4*/
|
|
|
|
/** @} */
|
|
/** @} */
|