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|
# size_t, ptrdiff_t are defined in stdlib.h
cdef extern from "stdlib.h":
ctypedef long size_t
ctypedef long ptrdiff_t
# hdf5 version info.
cdef extern from "H5public.h":
ctypedef int herr_t
int H5get_libversion( unsigned int *majnum, unsigned int *minnum, unsigned int *relnum ) nogil
cdef extern from *:
ctypedef char* const_char_ptr "const char*"
# netcdf functions.
cdef extern from "netcdf.h":
ctypedef int nclong
ctypedef int nc_type
ctypedef struct nc_vlen_t:
size_t len # Length of VL data (in base type units)
void *p # Pointer to VL data
float NC_FILL_FLOAT
long NC_FILL_INT
double NC_FILL_DOUBLE
char NC_FILL_CHAR
long long NC_FILL_INT64
unsigned long NC_FILL_UINT
unsigned long long NC_FILL_UINT64
cdef enum:
NC_NAT # NAT = 'Not A Type' (c.f. NaN)
NC_BYTE # signed 1 byte integer
NC_CHAR # ISO/ASCII character
NC_SHORT # signed 2 byte integer
NC_INT # signed 4 byte integer
NC_LONG # deprecated, but required for backward compatibility.
NC_FLOAT # single precision floating point number
NC_DOUBLE # double precision floating point number
NC_UBYTE # unsigned 1 byte int
NC_USHORT # unsigned 2-byte int
NC_UINT # unsigned 4-byte int
NC_INT64 # signed 8-byte int
NC_UINT64 # unsigned 8-byte int
NC_STRING # string
NC_VLEN # used internally for vlen types
NC_OPAQUE # used internally for opaque types
NC_COMPOUND # used internally for compound types
NC_ENUM # used internally for enum types.
# Use these 'mode' flags for nc_open.
NC_NOWRITE # default is read only
NC_WRITE # read & write
# Use these 'mode' flags for nc_create.
NC_CLOBBER
NC_NOCLOBBER # Don't destroy existing file on create
NC_64BIT_OFFSET # Use large (64-bit) file offsets
NC_64BIT_DATA # Use cdf-5 format
NC_NETCDF4 # Use netCDF-4/HDF5 format
NC_CLASSIC_MODEL # Enforce strict netcdf-3 rules.
# Use these 'mode' flags for both nc_create and nc_open.
NC_SHARE # Share updates, limit caching
# The following flag currently is ignored, but use in
# nc_open() or nc_create() may someday support use of advisory
# locking to prevent multiple writers from clobbering a file
NC_LOCK # Use locking if available
# Default fill values, used unless _FillValue attribute is set.
# These values are stuffed into newly allocated space as appropriate.
# The hope is that one might use these to notice that a particular datum
# has not been set.
NC_FILL_BYTE
#NC_FILL_CHAR
NC_FILL_SHORT
#NC_FILL_INT
#NC_FILL_FLOAT
#NC_FILL_DOUBLE
NC_FILL_UBYTE
NC_FILL_USHORT
#NC_FILL_UINT
#NC_FILL_INT64
#NC_FILL_UINT64
# These represent the max and min values that can be stored in a
# netCDF file for their associated types. Recall that a C compiler
# may define int to be any length it wants, but a NC_INT is *always*
# a 4 byte signed int. On a platform with has 64 bit ints, there will
# be many ints which are outside the range supported by NC_INT. But
# since NC_INT is an external format, it has to mean the same thing
# everywhere.
NC_MAX_BYTE
NC_MIN_BYTE
NC_MAX_CHAR
NC_MAX_SHORT
NC_MIN_SHORT
NC_MAX_INT
NC_MIN_INT
NC_MAX_FLOAT
NC_MIN_FLOAT
NC_MAX_DOUBLE8
NC_MIN_DOUBLE
NC_MAX_UBYTE
NC_MAX_USHORT
NC_MAX_UINT
NC_MAX_INT64
NC_MIN_INT64
NC_MAX_UINT64
X_INT64_MAX
X_INT64_MIN
X_UINT64_MAX
# The above values are defaults.
# If you wish a variable to use a different value than the above
# defaults, create an attribute with the same type as the variable
# and the following reserved name. The value you give the attribute
# will be used as the fill value for that variable.
_FillValue
NC_FILL
NC_NOFILL
# Starting with version 3.6, there are different format netCDF
# files. 4.0 introduces the third one. These defines are only for
# the nc_set_default_format function.
NC_FORMAT_CLASSIC
NC_FORMAT_64BIT
NC_FORMAT_64BIT_OFFSET
NC_FORMAT_64BIT_DATA
NC_FORMAT_NETCDF4
NC_FORMAT_NETCDF4_CLASSIC
NC_FORMAT_NC3
NC_FORMAT_NC_HDF4
NC_FORMAT_NC_HDF5
NC_FORMAT_DAP2
NC_FORMAT_DAP4
NC_FORMAT_PNETCDF
NC_FORMAT_UNDEFINED
NC_SIZEHINT_DEFAULT
NC_ALIGN_CHUNK
# 'size' argument to ncdimdef for an unlimited dimension
NC_UNLIMITED
# attribute id to put/get a global attribute
NC_GLOBAL
# These maximums are enforced by the interface, to facilitate writing
# applications and utilities. However, nothing is statically allocated to
# these sizes internally.
NC_MAX_DIMS
NC_MAX_ATTRS
NC_MAX_VARS
NC_MAX_NAME
NC_MAX_VAR_DIMS
# Algorithms for netcdf-4 chunking.
NC_CHUNK_SEQ
NC_CHUNK_SUB
NC_CHUNK_SIZES
NC_CHUNKED
NC_CONTIGUOUS
# The netcdf version 3 functions all return integer error status.
# These are the possible values, in addition to certain
# values from the system errno.h.
NC_ISSYSERR
NC_NOERR
NC2_ERR
NC_EBADID
NC_ENFILE
NC_EEXIST
NC_EINVAL
NC_EPERM
NC_ENOTINDEFINE
NC_EINDEFINE
NC_EINVALCOORDS
NC_EMAXDIMS
NC_ENAMEINUSE
NC_ENOTATT
NC_EMAXATTS
NC_EBADTYPE
NC_EBADDIM
NC_EUNLIMPOS
NC_EMAXVARS
NC_ENOTVAR
NC_EGLOBAL
NC_ENOTNC
NC_ESTS
NC_EMAXNAME
NC_EUNLIMIT
NC_ENORECVARS
NC_ECHAR
NC_EEDGE
NC_ESTRIDE
NC_EBADNAME
# N.B. following must match value in ncx.h
NC_ERANGE # Math result not representable
NC_ENOMEM # Memory allocation (malloc) failure
NC_EVARSIZE # One or more variable sizes violate format constraints
NC_EDIMSIZE # Invalid dimension size
NC_ETRUNC # NetCDFFile likely truncated or possibly corrupted
# The following was added in support of netcdf-4. Make all netcdf-4
# error codes < -100 so that errors can be added to netcdf-3 if
# needed.
NC4_FIRST_ERROR
NC_EHDFERR
NC_ECANTREAD
NC_ECANTWRITE
NC_ECANTCREATE
NC_EFILEMETA
NC_EDIMMETA
NC_EATTMETA
NC_EVARMETA
NC_ENOCOMPOUND
NC_EATTEXISTS
NC_ENOTNC4
NC_ESTRICTNC3
NC_ENOTNC3
NC_ENOPAR
NC_EPARINIT
NC_EBADGRPID
NC_EBADTYPID
NC_ETYPDEFINED
NC_EBADFIELD
NC_EBADCLASS
NC4_LAST_ERROR
NC_ENDIAN_NATIVE
NC_ENDIAN_LITTLE
NC_ENDIAN_BIG
const_char_ptr *nc_inq_libvers() nogil
const_char_ptr *nc_strerror(int ncerr)
int nc_create(char *path, int cmode, int *ncidp) nogil
int nc_open(char *path, int mode, int *ncidp) nogil
int nc_inq_path(int ncid, size_t *pathlen, char *path) nogil
int nc_inq_format_extended(int ncid, int *formatp, int* modep) nogil
int nc_inq_ncid(int ncid, char *name, int *grp_ncid) nogil
int nc_inq_grps(int ncid, int *numgrps, int *ncids) nogil
int nc_inq_grpname(int ncid, char *name) nogil
int nc_inq_grp_parent(int ncid, int *parent_ncid) nogil
int nc_inq_varids(int ncid, int *nvars, int *varids) nogil
int nc_inq_dimids(int ncid, int *ndims, int *dimids, int include_parents) nogil
int nc_def_grp(int parent_ncid, char *name, int *new_ncid) nogil
int nc_def_compound(int ncid, size_t size, char *name, nc_type *typeidp) nogil
int nc_insert_compound(int ncid, nc_type xtype, char *name,
size_t offset, nc_type field_typeid) nogil
int nc_insert_array_compound(int ncid, nc_type xtype, char *name,
size_t offset, nc_type field_typeid,
int ndims, int *dim_sizes) nogil
int nc_inq_type(int ncid, nc_type xtype, char *name, size_t *size) nogil
int nc_inq_compound(int ncid, nc_type xtype, char *name, size_t *size,
size_t *nfieldsp) nogil
int nc_inq_compound_name(int ncid, nc_type xtype, char *name) nogil
int nc_inq_compound_size(int ncid, nc_type xtype, size_t *size) nogil
int nc_inq_compound_nfields(int ncid, nc_type xtype, size_t *nfieldsp) nogil
int nc_inq_compound_field(int ncid, nc_type xtype, int fieldid, char *name,
size_t *offsetp, nc_type *field_typeidp, int *ndimsp,
int *dim_sizesp) nogil
int nc_inq_compound_fieldname(int ncid, nc_type xtype, int fieldid,
char *name) nogil
int nc_inq_compound_fieldindex(int ncid, nc_type xtype, char *name,
int *fieldidp) nogil
int nc_inq_compound_fieldoffset(int ncid, nc_type xtype, int fieldid,
size_t *offsetp) nogil
int nc_inq_compound_fieldtype(int ncid, nc_type xtype, int fieldid,
nc_type *field_typeidp) nogil
int nc_inq_compound_fieldndims(int ncid, nc_type xtype, int fieldid,
int *ndimsp) nogil
int nc_inq_compound_fielddim_sizes(int ncid, nc_type xtype, int fieldid,
int *dim_sizes) nogil
int nc_def_vlen(int ncid, char *name, nc_type base_typeid, nc_type *xtypep) nogil
int nc_inq_vlen(int ncid, nc_type xtype, char *name, size_t *datum_sizep,
nc_type *base_nc_typep) nogil
int nc_inq_user_type(int ncid, nc_type xtype, char *name, size_t *size,
nc_type *base_nc_typep, size_t *nfieldsp, int *classp) nogil
int nc_inq_typeids(int ncid, int *ntypes, int *typeids) nogil
int nc_put_att(int ncid, int varid, char *name, nc_type xtype,
size_t len, void *op) nogil
int nc_get_att(int ncid, int varid, char *name, void *ip) nogil
int nc_get_att_string(int ncid, int varid, char *name, char **ip) nogil
int nc_put_att_string(int ncid, int varid, char *name, size_t len, const char **op) nogil
int nc_def_opaque(int ncid, size_t size, char *name, nc_type *xtypep) nogil
int nc_inq_opaque(int ncid, nc_type xtype, char *name, size_t *sizep) nogil
int nc_put_att_opaque(int ncid, int varid, char *name,
size_t len, void *op) nogil
int nc_get_att_opaque(int ncid, int varid, char *name,
void *ip) nogil
int nc_put_cmp_att_opaque(int ncid, nc_type xtype, int fieldid,
char *name, size_t len, void *op) nogil
int nc_get_cmp_att_opaque(int ncid, nc_type xtype, int fieldid,
char *name, void *ip) nogil
int nc_put_var1(int ncid, int varid, size_t *indexp,
void *op) nogil
int nc_get_var1(int ncid, int varid, size_t *indexp,
void *ip) nogil
int nc_put_vara(int ncid, int varid, size_t *startp,
size_t *countp, void *op) nogil
int nc_get_vara(int ncid, int varid, size_t *startp,
size_t *countp, void *ip) nogil
int nc_put_vars(int ncid, int varid, size_t *startp,
size_t *countp, ptrdiff_t *stridep,
void *op) nogil
int nc_get_vars(int ncid, int varid, size_t *startp,
size_t *countp, ptrdiff_t *stridep,
void *ip) nogil
int nc_put_varm(int ncid, int varid, size_t *startp,
size_t *countp, ptrdiff_t *stridep,
ptrdiff_t *imapp, void *op) nogil
int nc_get_varm(int ncid, int varid, size_t *startp,
size_t *countp, ptrdiff_t *stridep,
ptrdiff_t *imapp, void *ip) nogil
int nc_put_var(int ncid, int varid, void *op) nogil
int nc_get_var(int ncid, int varid, void *ip) nogil
int nc_def_var_deflate(int ncid, int varid, int shuffle, int deflate,
int deflate_level) nogil
int nc_def_var_fletcher32(int ncid, int varid, int fletcher32) nogil
int nc_inq_var_fletcher32(int ncid, int varid, int *fletcher32p) nogil
int nc_def_var_chunking(int ncid, int varid, int contiguous, size_t *chunksizesp) nogil
int nc_def_var_fill(int ncid, int varid, int no_fill, void *fill_value) nogil
int nc_def_var_endian(int ncid, int varid, int endian) nogil
int nc_inq_var_chunking(int ncid, int varid, int *contiguousp, size_t *chunksizesp) nogil
int nc_inq_var_deflate(int ncid, int varid, int *shufflep,
int *deflatep, int *deflate_levelp) nogil
int nc_inq_var_fill(int ncid, int varid, int *no_fill, void *fill_value) nogil
int nc_inq_var_endian(int ncid, int varid, int *endianp) nogil
int nc_set_fill(int ncid, int fillmode, int *old_modep) nogil
int nc_set_default_format(int format, int *old_formatp) nogil
int nc_redef(int ncid) nogil
int nc_enddef(int ncid) nogil
int nc_sync(int ncid) nogil
int nc_abort(int ncid) nogil
int nc_close(int ncid) nogil
int nc_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp) nogil
int nc_inq_ndims(int ncid, int *ndimsp) nogil
int nc_inq_nvars(int ncid, int *nvarsp) nogil
int nc_inq_natts(int ncid, int *nattsp) nogil
int nc_inq_unlimdim(int ncid, int *unlimdimidp) nogil
int nc_inq_unlimdims(int ncid, int *nunlimdimsp, int *unlimdimidsp) nogil
int nc_inq_format(int ncid, int *formatp) nogil
int nc_def_dim(int ncid, char *name, size_t len, int *idp) nogil
int nc_inq_dimid(int ncid, char *name, int *idp) nogil
int nc_inq_dim(int ncid, int dimid, char *name, size_t *lenp) nogil
int nc_inq_dimname(int ncid, int dimid, char *name) nogil
int nc_inq_dimlen(int ncid, int dimid, size_t *lenp) nogil
int nc_rename_dim(int ncid, int dimid, char *name) nogil
int nc_inq_att(int ncid, int varid, char *name,
nc_type *xtypep, size_t *lenp) nogil
int nc_inq_attid(int ncid, int varid, char *name, int *idp) nogil
int nc_inq_atttype(int ncid, int varid, char *name, nc_type *xtypep) nogil
int nc_inq_attlen(int ncid, int varid, char *name, size_t *lenp) nogil
int nc_inq_attname(int ncid, int varid, int attnum, char *name) nogil
int nc_copy_att(int ncid_in, int varid_in, char *name, int ncid_out, int varid_out)
int nc_rename_att(int ncid, int varid, char *name, char *newname) nogil
int nc_del_att(int ncid, int varid, char *name) nogil
int nc_put_att_text(int ncid, int varid, char *name,
size_t len, char *op) nogil
int nc_get_att_text(int ncid, int varid, char *name, char *ip) nogil
int nc_def_var(int ncid, char *name, nc_type xtype, int ndims,
int *dimidsp, int *varidp) nogil
int nc_inq_var(int ncid, int varid, char *name, nc_type *xtypep,
int *ndimsp, int *dimidsp, int *nattsp) nogil
int nc_inq_varid(int ncid, char *name, int *varidp) nogil
int nc_inq_varname(int ncid, int varid, char *name) nogil
int nc_inq_vartype(int ncid, int varid, nc_type *xtypep) nogil
int nc_inq_varndims(int ncid, int varid, int *ndimsp) nogil
int nc_inq_vardimid(int ncid, int varid, int *dimidsp) nogil
int nc_inq_varnatts(int ncid, int varid, int *nattsp) nogil
int nc_rename_var(int ncid, int varid, char *name) nogil
int nc_free_vlen(nc_vlen_t *vl) nogil
int nc_free_vlens(size_t len, nc_vlen_t *vl) nogil
int nc_free_string(size_t len, char **data) nogil
int nc_get_chunk_cache(size_t *sizep, size_t *nelemsp, float *preemptionp) nogil
int nc_set_chunk_cache(size_t size, size_t nelems, float preemption) nogil
int nc_set_var_chunk_cache(int ncid, int varid, size_t size, size_t nelems, float preemption) nogil
int nc_get_var_chunk_cache(int ncid, int varid, size_t *sizep, size_t *nelemsp, float *preemptionp) nogil
int nc_def_enum(int ncid, nc_type base_typeid, char *name, nc_type *typeidp) nogil
int nc_insert_enum(int ncid, nc_type xtype, char *name, void *value) nogil
int nc_inq_enum(int ncid, nc_type xtype, char *name, nc_type *base_nc_typep,\
size_t *base_sizep, size_t *num_membersp) nogil
int nc_inq_enum_member(int ncid, nc_type xtype, int idx, char *name, void *value) nogil
int nc_inq_enum_ident(int ncid, nc_type xtype, long long value, char *identifier) nogil
cdef extern from "mpi-compat.h":
pass
# taken from numpy.pxi in numpy 1.0rc2.
cdef extern from "numpy/arrayobject.h":
ctypedef int npy_intp
ctypedef extern class numpy.ndarray [object PyArrayObject]:
pass
npy_intp PyArray_SIZE(ndarray arr) nogil
npy_intp PyArray_ISCONTIGUOUS(ndarray arr) nogil
npy_intp PyArray_ISALIGNED(ndarray arr) nogil
void* PyArray_DATA(ndarray) nogil
char* PyArray_BYTES(ndarray) nogil
npy_intp* PyArray_STRIDES(ndarray) nogil
void import_array()
include "parallel_support_imports.pxi"
# Compatibility shims
cdef extern from "netcdf-compat.h":
int nc_rename_grp(int grpid, char *name) nogil
int nc_set_alignment(int threshold, int alignment)
int nc_get_alignment(int *threshold, int *alignment)
int nc_rc_set(char* key, char* value) nogil
const_char_ptr *nc_rc_get(char* key)
int nc_open_mem(const char *path, int mode, size_t size, void* memory, int *ncidp) nogil
int nc_create_mem(const char *path, int mode, size_t initialize, int *ncidp) nogil
ctypedef struct NC_memio:
size_t size
void* memory
int flags
int nc_close_memio(int ncid, NC_memio* info) nogil
# Quantize shims
int nc_def_var_quantize(int ncid, int varid, int quantize_mode, int nsd) nogil
int nc_inq_var_quantize(int ncid, int varid, int *quantize_modep, int *nsdp) nogil
# Filter shims
int nc_inq_filter_avail(int ncid, unsigned filterid) nogil
int nc_def_var_szip(int ncid, int varid, int options_mask,
int pixels_per_bloc) nogil
int nc_inq_var_szip(int ncid, int varid, int *options_maskp,
int *pixels_per_blockp) nogil
int nc_def_var_zstandard(int ncid, int varid, int level) nogil
int nc_inq_var_zstandard(int ncid, int varid, int* hasfilterp, int *levelp) nogil
int nc_def_var_bzip2(int ncid, int varid, int level) nogil
int nc_inq_var_bzip2(int ncid, int varid, int* hasfilterp, int *levelp) nogil
int nc_def_var_blosc(int ncid, int varid, unsigned subcompressor, unsigned level,
unsigned blocksize, unsigned addshuffle) nogil
int nc_inq_var_blosc(int ncid, int varid, int* hasfilterp, unsigned* subcompressorp,
unsigned* levelp, unsigned* blocksizep,
unsigned* addshufflep) nogil
# Parallel shims
int nc_create_par(char *path, int cmode, MPI_Comm comm, MPI_Info info, int *ncidp) nogil
int nc_open_par(char *path, int mode, MPI_Comm comm, MPI_Info info, int *ncidp) nogil
int nc_var_par_access(int ncid, int varid, int par_access) nogil
cdef enum:
HAS_RENAME_GRP
HAS_NC_INQ_PATH
HAS_NC_INQ_FORMAT_EXTENDED
HAS_NC_OPEN_MEM
HAS_NC_CREATE_MEM
HAS_CDF5_FORMAT
HAS_PARALLEL_SUPPORT
HAS_PARALLEL4_SUPPORT
HAS_PNETCDF_SUPPORT
HAS_SZIP_SUPPORT
HAS_QUANTIZATION_SUPPORT
HAS_ZSTANDARD_SUPPORT
HAS_BZIP2_SUPPORT
HAS_BLOSC_SUPPORT
HAS_SET_ALIGNMENT
HAS_NCFILTER
HAS_NCRCSET
NC_NOQUANTIZE
NC_QUANTIZE_BITGROOM
NC_QUANTIZE_GRANULARBR
NC_QUANTIZE_BITROUND
H5Z_FILTER_SZIP
H5Z_FILTER_ZSTD
H5Z_FILTER_BZIP2
H5Z_FILTER_BLOSC
NC_COLLECTIVE
NC_INDEPENDENT
NC_MPIIO
NC_MPIPOSIX
NC_PNETCDF
# Declarations for handling complex numbers
cdef extern from "nc_complex/nc_complex.h":
bint pfnc_var_is_complex(int ncid, int varid) nogil
bint pfnc_var_is_complex_type(int ncid, int varid) nogil
int pfnc_get_complex_dim(int ncid, int* nc_dim) nogil
int pfnc_inq_var_complex_base_type(int ncid, int varid, int* nc_typeid) nogil
int pfnc_inq_varndims (int ncid, int varid, int *ndimsp) nogil
int pfnc_inq_vardimid (int ncid, int varid, int *dimidsp) nogil
int pfnc_def_var(int ncid, char *name, nc_type xtype, int ndims,
int *dimidsp, int *varidp) nogil
int pfnc_get_vars(int ncid, int varid, size_t *startp,
size_t *countp, ptrdiff_t *stridep,
void *ip) nogil
int pfnc_put_vars(int ncid, int varid, size_t *startp,
size_t *countp, ptrdiff_t *stridep,
void *op) nogil
cdef enum:
PFNC_DOUBLE_COMPLEX
PFNC_DOUBLE_COMPLEX_DIM
PFNC_FLOAT_COMPLEX
PFNC_FLOAT_COMPLEX_DIM
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