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niomodule.c
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/*******************************************************
* $Id: niomodule.c 16535 2016-06-17 23:24:19Z dbrown $
*******************************************************/
/*
* Objects representing NIO files and variables.
*
* David I. Brown
* Adapted from netcdfmodule.c which was
* Written by Konrad Hinsen
* last revision: 1998-3-14
*/
#ifndef PYNIO
#define PYNIO
#endif
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include "netcdf.h"
#include "Python.h"
#include "structmember.h"
#include "nio.h"
#include <numpy/arrayobject.h>
#include <sys/stat.h>
#include <unistd.h>
#include <limits.h>
/* Py_ssize_t for old Pythons */
/* This code is as recommended by: */
/* http://www.python.org/dev/peps/pep-0353/#conversion-guidelines */
#if PY_VERSION_HEX < 0x02050000 && !defined(PY_SSIZE_T_MIN)
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#endif
#define _NIO_MODULE
#include "niomodule.h"
/* Python 3.7 changes the unicode char* to const char* */
#if PY_MAJOR_VERSION >= 3 && PY_MINOR_VERSION >= 7
typedef const char py3_char;
#else
typedef char py3_char;
#endif
static PyObject* get_NioError(void);
static PyObject* get_NioFileType(void);
static PyObject* get_NioVariableType(void);
static PyObject* get_Niomodule(void);
static char* get_errbuf(void);
/* Converts unicode, bytes, or str to UTF8 unicode object.
* The ob argument can be unicode, bytes, or str;
*
* A new reference will always be returned.
* */
static PyObject* pystr_to_utf8(PyObject *ob) {
PyObject *bytes, *result;
int del_bytes = 0;
#if PY_MAJOR_VERSION >= 3
Py_ssize_t bytelen;
char *bytedata = NULL;
if (PyUnicode_Check(ob)) {
bytes = PyUnicode_AsUTF8String(ob);
del_bytes = 1;
}
else if (PyBytes_Check(ob)) {
bytes = ob;
del_bytes = 0;
} else {
del_bytes = 0;
PyErr_SetString(PyExc_ValueError, "argument is not a string type");
return NULL;
}
if (bytes) {
bytelen = PyBytes_Size(bytes);
bytedata = PyBytes_AsString(bytes);
result = PyUnicode_DecodeUTF8(bytedata, bytelen, "strict");
} else {
PyErr_SetString(PyExc_MemoryError, "creation of bytes failed");
return NULL;
}
#else
del_bytes = 0;
if (PyUnicode_Check(ob)) {
bytes = PyUnicode_AsUTF8String(ob);
} else if (PyString_Check(ob)) {
/* Make a copy of the string so that a new reference is returned */
bytes = PyString_FromString(PyString_AsString(ob));
} else {
PyErr_SetString(PyExc_ValueError, "argument is not a string type");
return NULL;
}
if (bytes) {
result = bytes;
} else {
PyErr_SetString(PyExc_MemoryError, "creation of bytes failed");
return NULL;
}
#endif
if (del_bytes) {
Py_XDECREF(bytes);
}
return result;
}
/* This will convert a Unicode/PyString to a UTF8 char* string.
*
* The resulting string must be free'd by the user.
*/
static py3_char* as_utf8_char_and_size(PyObject *ob, Py_ssize_t *size) {
char *result;
char *tempstr;
Py_ssize_t local_size;
PyObject *pystr = NULL;
#if PY_MAJOR_VERSION >= 3
tempstr = (char*) PyUnicode_AsUTF8AndSize(ob, &local_size);
#else
/* First, need to convert the object to UTF8 unicode/string object */
if (PyUnicode_Check(ob) || PyString_Check(ob)) {
pystr = pystr_to_utf8(ob);
} else {
PyErr_SetString(PyExc_ValueError, "argument is not a string type");
return NULL;
}
if (pystr) {
tempstr = PyString_AsString(pystr);
local_size = strlen(tempstr);
} else {
if (size) {
*size = 0;
}
PyErr_SetString(PyExc_ValueError, "creation of string failed");
return NULL;
}
#endif
/* create a copy of tempstr */
result = calloc(local_size + 1, sizeof(char));
if (result) {
strcpy(result, tempstr);
} else {
result = (char*) PyErr_NoMemory();
}
if (size) {
*size = local_size;
}
if (pystr) {
Py_XDECREF(pystr);
}
return (py3_char*) result;
}
static py3_char* as_utf8_char(PyObject *ob) {
return as_utf8_char_and_size(ob, NULL);
}
/* Converts a char* to a python string
*
* A new reference is always returned.
*/
static PyObject* char_to_pystr(const char *s, Py_ssize_t len) {
PyObject *result = NULL;
#if PY_MAJOR_VERSION >= 3
result = PyUnicode_DecodeUTF8(s, len, "strict");
#else
result = PyString_FromStringAndSize(s, len);
#endif
return result;
}
static int is_string_type(PyObject *ob) {
int result;
#if PY_MAJOR_VERSION >= 3
result = PyUnicode_Check(ob) || PyBytes_Check(ob);
#else
result = PyUnicode_Check(ob) || PyString_Check(ob);
#endif
return result;
}
static PyObject* pystr_from_format(const char *format, ...) {
PyObject* result = NULL;
va_list arglist;
va_start(arglist, format);
#if PY_MAJOR_VERSION >= 3
PyObject *temp = PyUnicode_FromFormatV(format, arglist);
result = pystr_to_utf8(temp);
Py_XDECREF(temp);
#else
result = PyString_FromFormatV(format, arglist);
#endif
va_end(arglist);
return result;
}
static int dict_setitemstring(PyObject *d, const char *key, PyObject *val) {
PyObject *key_obj = char_to_pystr(key, strlen(key));
int success = 0;
success = PyDict_SetItem(d, key_obj, val);
Py_XDECREF(key_obj);
return success;
}
/* all doc strings defined within the C interface */
/* Nio.open_file.__doc__ */
static char *open_file_doc =
"\n\
Open a file containing data in a supported format for reading and/or writing.\
\n\n\
f = Nio.open_file(filepath, mode='r',options=None, history='')\n\n\
filepath -- path of file with data in a supported format. The path must end\n\
with an extension indicating the expected format of the file, whether or not\n\
it is part of the actual file name. Valid extensions include:\n\
.nc, .cdf, .netcdf, .nc3, .nc4, -- NetCDF\n\
.gr, .grb, .grib, .gr1, .grb1, .grib1, .gr2, .grb2, .grib2, -- GRIB\n\
.hd, .hdf -- HDF\n\
.he2, .he4, .hdfeos -- HDFEOS\n\
.he5, .hdfeos5 -- HDFEOS5\n\
.shp, .mif, .gmt, .rt1 -- shapefiles, other formats supported by GDAL OGR\n\
.ccm -- CCM history files\n\
Extensions are handled case-insensitvely, i.e.: .grib, .GRIB, and .Grib all\n\
indicate a GRIB file.\n\
mode -- access mode (optional):\n\
'r' -- open an existing file for reading\n\
'w','r+','rw','a' -- open an existing file for modification\n\
'c' -- create a new file open for writing\n\
options -- instance of NioOptions class used to specify format-specific\n\
options\n\
history -- a string specifying text to be appended to the file\'s global\n\
attribute. The attribute is created if it does not exist. Only valid\n\
if the file is open for writing\n\n\
Returns an NioFile object.\n\
";
/* Nio.options.__doc__ */
static char *options_doc =
"\n\
Return an NioOptions object for specifying format-specific options.\n\n\
opt = Nio.options()\n\
Assign 'opt' as the third (optional) argument to Nio.open_file.\n\
print opt.__doc__ to see valid options.\n\
";
/*
* opt = Nio.options()
* opt.__doc__
*/
static char *option_class_doc =
"\n\
NioOptions object\n\n\
Set options by assigning attributes to this object and then passing the\n\
object as an optional argument to Nio.open_file:\n\
opt.OptionName = value\n\
All option names and string option values are handled case-insensitively.\n\
\n\
Generic options:\n\
MaskedArrayMode -- Specify MaskedArray bahavior (string):\n\
'MaskedIfFillAtt' -- Return a masked array iff file variable has a\n\
_FillValue or a missing_value attribute (default).\n\
'MaskedNever' -- Never return a masked array for any variable.\n\
'MaskedAlways' -- Return a masked array for all variables.\n\
'MaskedIfFillAttAndValue' -- Return a masked array iff file variable has a\n\
_FillValue or a missing_value attribute and the returned data array\n\
actually contains 1 or more fill values.\n\
'MaskedExplicit' -- Only mask values specified explicitly using options\n\
'ExplicitFillValues, MaskBelowValue, and/or MaskAboveValue;\n\
ignore fill value attributes associated with the variable.\n\
ExplicitFillValues -- A scalar value or a sequence of values to be masked in the\n\
return array. The first value becomes the fill_value attribute of the MaskedArray.\n\
Setting this option causes MaskedArrayMode to be set to 'MaskedExplicit'.\n\
MaskBelowValue -- A scalar value all values less than which are masked. However, if\n\
MaskAboveValue is less than MaskBelowValue, a range of of values become masked.\n\
Setting this option causes MaskedArrayMode to be set to 'MaskedExplicit'.\n\
MaskAboveValue -- A scalar value all values greater than which are masked. However, if\n\
MaskBelowValue is greater than MaskAboveValue, a range of of values become masked.\n\
Setting this option causes MaskedArrayMode to be set to 'MaskedExplicit'.\n\
UseAxisAttribute -- A boolean option that if set True when using extended subscripting,\n\
and if coordinate variables have the CF-compliant 'axis' attribute, expects the\n\
short names ('T','Z','Y' or 'X') instead of the actual coordinate names in the\n\
subscript specification.\n\
\n\
NetCDF file options:\n\
Format -- Specify the format of newly created files (string):\n\
'Classic' -- (default) standard file (generally file size < 2GB)\n\
'LargeFile' or '64BitOffset' -- (fixed-size variables or record\n\
elements of unlimited dimension variables each up to 4GB)\n\
'NetCDF4Classic' -- Classic mode NetCDF 4 file (uses HDF 5 as the\n\
underlying format but is restricted to features of the classic\n\
NetCDF data model).\n\
'NetCDF4' -- NetCDF 4 file (uses HDF 5 as the underlying format).\n\
CompressionLevel -- Specify the level of data compression on a scale\n\
of 0 - 9 (ignored unless Format is set to 'NetCDF4Classic' or 'NetCDF4').\n\
HeaderReserveSpace -- Reserve <int-value> extra bytes in the header\n\
of a file open for writing. Used to subsequently add dimensions,\n\
attributes, and variables to existing files efficiently.\n\
MissingToFillValue -- If set True (the default), create a virtual\n\
'_FillValue' attribute only for variables that have a\n\
'missing_value' but no '_FillValue'.\n\
PreFill -- If set True (the default), fill all elements of newly\n\
defined variables with a fill value. If set False, elements are\n\
undefined until data is written.\n\
SafeMode -- Close the file after each individual operation on the file.\n\
\n\
GRIB files options\n\
DefaultNCEPTable -- (GRIB 1 only) Specify the table to use in certain\n\
ambiguous cases:\n\
'Operational' -- (default) Use the NCEP operational parameter table\n\
'Reanalysis' -- Use the NCEP reanalysis parameter table\n\
InitialTimeCoordinateType -- Specify the type of the coordinate\n\
associated with initial_time (as opposed to forecast_time)\n\
dimensions:\n\
'Numeric' -- (default) use CF-compliant numeric coordinates\n\
'String' -- use date strings as the coordinates\n\
SingleElementDimensions -- Specify that dimensional types with only a\n\
single representative element be treated as full-fledged dimensions.\n\
'None' -- (default) no single element dimensions are created\n\
'All' -- all possible single element dimensions are created.\n\
The names of individual dimension types may be specified individually:\n\
'Initial_time', 'Forecast_time', 'Level', 'Ensemble', or 'Probability'.\n\
ThinnedGridInterpolation -- Specify the type of interpolation for\n\
thinned (GRIB 'quasi-regular') grids:\n\
'Cubic' -- (cubic) use cubic interpolation\n\
'Linear' -- use linear interpolation\n\n\
";
static char *niofile_type_doc =
"\n\
NioFile object\n\n\
Given:\n\
f = Nio.open_file(filepath, mode='r', options=None, history='',format='')\n\
\n\
To see summary of file contents, including all attributes:\n\
print f\n\
Assign global attributes to writable files or groups using:\n\
f.global_att = global_att_value\n\
Attributes:\n\
name -- the name of the file or group\n\
dimensions -- dictionary of dimension lengths with dimension name keys\n\
variables -- dictionary of variable objects with variable name keys\n\
attributes -- dictionary of global file or group attributes with attribute name keys\n\
(the following are applicable for advanced formats NetCDF4 and HDF5 only)\n\
groups -- dictionary of groups with group name keys\n\
ud_types -- dictionary of user-defined data type definitions with data type name keys\n\
chunk_dimensions -- dictionary of chunking dimension sizes with dimension name keys\n\
parent -- reference to the parent group, parent file for the root group, or None for a file\n\
path -- the path of a group relative to the root group ('/'), or the file path for a file\n\
Methods:\n\
close(history='') -- close the file\n\
create_dimension(name, length) -- create a dimension in the file\n\
create_variable(name, type, dimensions) -- create a variable in the file\n\
unlimited(dimension_name) -- returns True if dimension_name refers to an unlimited dimension; False otherwise\n\
(the following are applicable for advanced formats NetCDF4 and HDF5 only)\n\
create_group(name) -- create a group in the file or group.\n\
create_vlen(name,type,dimensions) -- create a variable length array variable in the file or group.\n\
create_compound(name,type,dimensions) -- create a compound variable with the given type and dimensions.\n\
create_compound_type(name, type) -- create a user-defined compound type; with member names, sizes\n\
and types as defined in the type sequence argument.\n\
";
/* NioFile object method doc strings */
/*
* f = Nio.open_file(..)
* f.close.__doc__
* f.create_dimension.__doc__
* f.create_chunk_dimension.__doc__
* f.create_variable.__doc__
* f.create_group.__doc__
*/
static char *close_doc =
"\n\
Close a file, ensuring all modifications are up-to-date if open for writing.\
\n\n\
f.close([history])\n\
history -- optional string appended to the global 'history' attribute\n\
before closing a writable file. The attribute is created if it does not\n\
already exist.\n\
Read or write access attempts on the file object after closing\n\
raise an exception.\n\
";
static char *create_dimension_doc =
"\nCreate a new dimension with the given name and length in a writable file.\n\n\
f.create_dimension(name,length)\n\
name -- a string specifying the dimension name.\n\
length -- a positive integer specifying the dimension length. If set to\n\
None or 0, specifies the unlimited dimension.\n";
static char *create_chunk_dimension_doc =
"\nCreate a chunking size for a dimension that has been defined but not yet used in a writable file.\n\
The size must be no larger than the dimension size; once set it cannot be changed.\n\
f.create_chunk_dimension(name,length)\n\
name -- a string specifying the dimension name.\n\
length -- a positive integer specifying the dimension length. If set to\n\
None or 0, it will be reset to 1.\n";
static char *create_variable_doc =
"\n\
Create a new variable with given name, type, and dimensions in a writable file.\
\n\n\
f.create_variable(name,type,dimensions)\n\
name -- a string specifying the variable name.\n\
type -- a type identifier. The following are currently supported:\n\
'd' -- 64 bit real\n\
'f' -- 32 bit real\n\
'l' -- 32 bit integer\n\
'L' -- 32 bit unsigned integer\n\
'q' -- 64 bit integer\n\
'Q' -- 64 bit unsigned integer\n\
'h' -- 16 bit integer\n\
'H' -- 16 bit unsigned integer\n\
'b' -- 8 bit integer\n\
'B' -- 8 bit unsigned integer\n\
'S1','c' -- character\n\
dimensions -- a tuple of dimension names (strings), previously defined\n\
";
static char *create_group_doc =
"\n\
Create a new group with given name in a writable file.\
\n\n\
f.create_group(name)\n\
name -- a string specifying the group name.\n\
";
static char *create_vlen_doc =
"\n\
Create a new variable length array variable with given name in a writable file.\
\n\n\
f.create_vlen(name,type,dimensions)\n\
name -- a string specifying the vlen variable name.\n\
type -- the variable type.\n\
dimensions -- the dimensions of the vlen variable.\n\
";
static char *create_compound_type_doc =
"\n\
Create a new compound variable type with given name in a writable file.\
\n\n\
f.create_compound_type(name,type)\n\
name -- a string specifying the compound type name.\n\
type -- a sequence containing the name, type, and number of elements for each member of the compound type\n\
";
static char *create_compound_doc =
"\n\
Create a new compound variable with given name in a writable file.\
\n\n\
f.create_compound(name,type,dimensions)\n\
name -- a string specifying the compound variable name.\n\
type -- the variable type.\n\
dimensions -- the dimensions of the compound variable.\n\
";
static char *unlimited_doc =
"\n\
Returns True or False depending on whether the named dimension is unlimited.\n\n\
f.unlimited(name)\n\
name -- a string specifying the dimension name to be queried for the unlimited property.\n\
";
static char *niovariable_type_doc =
"\n\
NioVariable object\n\n\
Given \n\
v = f.variables['varname']\n\
Get summary of variable contents using:\n\
print v\n\
Assign variable attributes for writable files using, e.g:\n\
v.units = 'meters'\n\
Get or assign variable values using slicing syntax:\n\
val = v[:]\n\
assigns all elements of variable to 'val', retaining dimensionality;\n\
val = v[0,:]\n\
assigns one element of the first dimension and all elements of the remaining dimensions.\n\
Attributes:\n\
rank -- a scalar value indicating the number of dimensions\n\
shape -- a tuple containing the number of elements in each dimension\n\
dimensions -- a tuple containing the dimensions names in order\n\
attributes -- a dictionary of variable attributes with attribute name keys\n\
size -- a scalar value indicating the size in bytes of the variable\n\
name -- the name of the variable\n\
parent -- reference to the group or file to which the variable belongs\n\
path -- the path of the variable relative to the root group ('/')\n\
Methods:\n\
assign_value(value) -- assign a value to a variable in the file.\n\
get_value() -- retrieve the value of a variable in the file.\n\
typecode() -- return a character code representing the variable's type.\n\
set_option(option,value) -- set certain options.\n\
";
/* NioVariable object method doc strings */
/*
* v = f.variables['varname']
* v.assign_value.__doc__
* v.get_value.__doc__
* v.typecode.__doc__
*/
static char *assign_value_doc =
"\n\
Assign a value to a variable in the file.\n\n\
v = f.variables['varname']\n\
v.assign_value(value)\n\
value - a NumPy array or a Python sequence of values that are coercible\n\
to the type of variable 'v'.\n\
This method is the only way to assign a scalar value. There is no way to\n\
indicate a slice. For array variables direct assignment using slicing\n\
syntax is more flexible.\n\
";
static char *get_value_doc =
"\n\
Retrieve the value of a variable in the file.\n\n\
v = f.variables['varname']\n\
val = v.get_value()\n\
'val' is returned as a NumPy array.\n\
This method is the only way to retrieve the scalar value from a file.\n\
There is no way to indicate a slice. For array variables direct assignment\n\
using slicing syntax is more flexible.\n\
";
static char *typecode_doc =
"\n\
Return a character code representing the variable's type.\n\n\
v = f.variables['varname']\n\
t = v.typecode()\n\
Return variable 't' will be one of the following:\n\
'd' -- 64 bit real\n\
'f' -- 32 bit real\n\
'i' -- 32 bit integer\n\
'I' -- 32 bit unsigned integer\n\
'l' -- 32 or 64 bit integer (platform dependent)\n\
'L' -- 32 or 64 bit unsigned integer (platform dependent)\n\
'q' -- 64 bit integer\n\
'Q' -- 64 bit unsigned integer\n\
'h' -- 16 bit integer\n\
'H' -- 16 bit unsigned integer\n\
'b' -- 8 bit integer\n\
'B' -- 8 bit unsigned integer\n\
'S1', 'c' -- character\n\
'S' -- string\n\
'v' -- Vlen\n\
'x' -- Cmpound\n\
";
static void
NioVariableObject_dealloc(NioVariableObject *self);
static void
NioFileObject_dealloc(NioFileObject *self);
/*
* global used in NclMultiDValData
*/
short NCLnoPrintElem = 0;
size_t NCLtotalVariables = 0;
size_t NCLtotalGroups = 0;
static int nio_file_init(NioFileObject *self);
static NioFileObject* nio_read_group(NioFileObject* file,
NclFileGrpNode *grpnode);
static NioFileObject* nio_create_group(NioFileObject* file, NrmQuark gname);
static NioVariableObject* nio_read_advanced_variable(NioFileObject* file,
NclFileVarNode* varnode, int id);
static NioVariableObject *nio_variable_new(NioFileObject *file, char *name,
int id, int type, int ndims, NrmQuark *qdims, int nattrs);
void _convertObj2COMPOUND(PyObject* pyobj, obj* listids,
NclFileCompoundRecord *comprec, ng_size_t n_dims, ng_size_t curdim,
ng_usize_t* counter);
#if PY_MAJOR_VERSION < 3
static char err_buf[256];
static PyObject *Niomodule; /* the Nio Module object */
/* Error object and error messages for nio-specific errors */
static PyObject *NIOError;
#endif
static char *nio_errors[] = { "No Error", /* 0 */
"Not a NIO id", "Too many NIO files open", "NIO file exists && NC_NOCLOBBER",
"Invalid Argument", "Write to read only",
"Operation not allowed in data mode",
"Operation not allowed in define mode", "Coordinates out of Domain",
"MAX_NC_DIMS exceeded", "String match to name in use",
"Attribute not found", "MAX_NC_ATTRS exceeded", "Not a NIO data type",
"Invalid dimension id", "NC_UNLIMITED in the wrong index",
"MAX_NC_VARS exceeded", "Variable not found",
"Action prohibited on NC_GLOBAL varid", "Not an NIO supported file",
"In Fortran, string too short", "MAX_NC_NAME exceeded",
"NC_UNLIMITED size already in use", /* 22 */
"Memory allocation error", "attempt to set read-only attributes",
"invalid mode specification", "", "", "", "", "", "", "XDR error" /* 32 */
};
static void nio_seterror(int nio_ncerr) {
if (nio_ncerr != 0) {
char *error = "Unknown error";
if (nio_ncerr > 0 && nio_ncerr <= 32) {
error = nio_errors[nio_ncerr];
}
PyErr_SetString(get_NioError(), error);
}
}
/*
* Python equivalents to NIO data types
*
* Attention: the following specification may not be fully portable.
* The comments indicate the correct NIO specification. The assignment
* of Python types assumes that 'short' is 16-bit and 'int' is 32-bit.
*/
#if 0
int data_types[] =
{ -1, /* not used */
NPY_BYTE, /* signed 8-bit int */
NPY_CHAR, /* 8-bit character */
NPY_SHORT, /* 16-bit signed int */
NPY_INT, /* 32-bit signed int */
NPY_FLOAT, /* 32-bit IEEE float */
NPY_DOUBLE /* 64-bit IEEE float */
};
#endif
int data_type(NclBasicDataTypes ntype) {
switch (ntype) {
case NCL_short:
return NPY_SHORT;
case NCL_ushort:
return NPY_USHORT;
case NCL_int:
return NPY_INT; /* netcdf 3.x has only a long type */
case NCL_uint:
return NPY_UINT; /* netcdf 3.x has only a long type */
case NCL_long:
return NPY_LONG;
case NCL_ulong:
return NPY_ULONG;
case NCL_int64:
return NPY_LONGLONG;
case NCL_uint64:
return NPY_ULONGLONG;
case NCL_float:
return NPY_FLOAT;
case NCL_double:
return NPY_DOUBLE;
case NCL_byte:
return NPY_BYTE;
case NCL_ubyte:
return NPY_UBYTE;
case NCL_char:
return NPY_CHAR;
case NCL_logical:
return NPY_BOOL;
case NCL_string:
return NPY_STRING;
/* case NCL_vlen:
return NPY_VLEN;
case NCL_compound:
return NPY_COMPOUND;
case NCL_enum:
return NPY_ENUM;
case NCL_opaque:
return NPY_OPAQUE;
case NCL_reference:
return NPY_REFERENCE;
case NCL_list:
return NPY_LIST;
case NCL_listarray:
return NPY_LISTARRAY;
*/
case NCL_vlen:
case NCL_compound:
case NCL_enum:
case NCL_opaque:
case NCL_reference:
case NCL_list:
case NCL_listarray:
return NPY_OBJECT;
default:
return NPY_NOTYPE;
}
return NPY_NOTYPE;
}
/* Utility functions */
static void define_mode(NioFileObject *file, int define_flag) {
if (file->define != define_flag) {
#if 0
if (file->define)
ncendef(file->id);
else
ncredef(file->id);
#endif
file->define = define_flag;
}
}
static char *
typecode(int type) {
static char buf[3];
memset(buf, 0, 3);
switch (type) {
case NPY_BOOL:
buf[0] = NPY_BOOLLTR;
break;
case NPY_BYTE:
buf[0] = NPY_BYTELTR;
break;
case NPY_UBYTE:
buf[0] = NPY_UBYTELTR;
break;
case NPY_SHORT:
buf[0] = NPY_SHORTLTR;
break;
case NPY_USHORT:
buf[0] = NPY_USHORTLTR;
break;
case NPY_INT:
buf[0] = NPY_INTLTR;
break;
case NPY_UINT:
buf[0] = NPY_UINTLTR;
break;
case NPY_LONG:
buf[0] = NPY_LONGLTR;
break;
case NPY_ULONG:
buf[0] = NPY_ULONGLTR;
break;
case NPY_LONGLONG:
buf[0] = NPY_LONGLONGLTR;
break;
case NPY_ULONGLONG:
buf[0] = NPY_ULONGLONGLTR;
break;
case NPY_FLOAT:
buf[0] = NPY_FLOATLTR;
break;
case NPY_DOUBLE:
buf[0] = NPY_DOUBLELTR;
break;
case NPY_STRING:
buf[0] = NPY_STRINGLTR;
break;
#if 0
case NPY_CHAR:
buf[0] = NPY_STRINGLTR;
break;
#else
case NPY_CHAR:
buf[0] = NPY_CHARLTR;
break;
#endif
case NPY_VLEN:
buf[0] = NPY_VLENLTR;
break;
case NPY_COMPOUND:
buf[0] = NPY_COMPOUNDLTR;
break;
case NPY_ENUM:
buf[0] = NPY_ENUMLTR;
break;
case NPY_OPAQUE:
buf[0] = NPY_OPAQUELTR;
break;
case NPY_LIST:
buf[0] = NPY_LISTLTR;
break;
case NPY_LISTARRAY:
buf[0] = NPY_LISTARRAYLTR;
break;
case NPY_REFERENCE:
buf[0] = NPY_REFERENCELTR;
break;
default:
buf[0] = ' ';
break;
}
return &buf[0];
}
static NrmQuark nio_type_from_code(int code) {
NrmQuark type;
switch ((char) code) {
case 'c':
type = NrmStringToQuark("character");
break;
case 'S':
type = NrmStringToQuark("string");
break;
case '1':
case 'b':
type = NrmStringToQuark("byte");
break;
case 'B':
type = NrmStringToQuark("ubyte");
break;
case 'h':
type = NrmStringToQuark("short");
break;
case 'H':
type = NrmStringToQuark("ushort");
break;
case 'i':
type = NrmStringToQuark("integer");
break;
case 'I':
type = NrmStringToQuark("uint");
break;
case 'l':
type = NrmStringToQuark("long");
break;
case 'L':
type = NrmStringToQuark("ulong");
break;
case 'q':
type = NrmStringToQuark("int64");
break;
case 'Q':
type = NrmStringToQuark("uint64");
break;
case 'f':
type = NrmStringToQuark("float");
break;
case 'd':
type = NrmStringToQuark("double");
break;
case '?':
type = NrmStringToQuark("logical");
break;
case 'v':
type = NrmStringToQuark("list");
break;
case 'x':
type = NrmStringToQuark("compound");
break;
case 'O':
type = NrmStringToQuark("object");
break;
default:
type = NrmNULLQUARK;
}
return type;
}
static void collect_attributes(void *fileid, int varid, PyObject *attributes,
int nattrs) {
NclFile file = (NclFile) fileid;
NclFileAttInfoList *att_list = NULL;
NclFAttRec *att;
NclFVarRec *fvar = NULL;
char *name;
npy_intp length;
int py_type;
int i;
if (varid > -1) {
att_list = file->file.var_att_info[varid];
fvar = file->file.var_info[varid];
}
for (i = 0; i < nattrs; i++) {
NclMultiDValData md;
if (varid < 0) {
att = file->file.file_atts[i];
name = NrmQuarkToString(att->att_name_quark);
md = _NclFileReadAtt(file, att->att_name_quark, NULL);
} else if (!(att_list && fvar)) {
PyErr_SetString(get_NioError(),
"internal attribute or file variable error");
return;
} else {
att = att_list->the_att;
name = NrmQuarkToString(att->att_name_quark);
md = _NclFileReadVarAtt(file, fvar->var_name_quark,
att->att_name_quark, NULL);
att_list = att_list->next;
}
if (att->data_type == NCL_string) {
PyObject *string = NULL;
char *satt = NrmQuarkToString(*((NrmQuark *) md->multidval.val));
if (satt != NULL) {
string = char_to_pystr(satt, strlen(satt));
} else {
string = char_to_pystr("", strlen(""));
}
if (string != NULL) {
dict_setitemstring(attributes, name, string);
Py_DECREF(string);
}
} else {
PyObject *array;
length = (npy_intp) md->multidval.totalelements;
py_type = data_type(att->data_type);
/* following three if clauses are temporary until these types are actually supported */
if (py_type == NPY_REFERENCE) {
py_type = NPY_LONG;
}
if (py_type == NPY_COMPOUND) {
py_type = NPY_LONG;
}
if (py_type == NPY_ENUM) {
py_type = NPY_LONG;
}
array = PyArray_SimpleNew(1, &length, py_type);
if (array != NULL) {
memcpy(PyArray_BYTES((PyArrayObject *) array),
md->multidval.val,
(size_t) length * md->multidval.type->type_class.size);
array = PyArray_Return((PyArrayObject *) array);
if (array != NULL) {
dict_setitemstring(attributes, name, array);
Py_DECREF(array);
}
}
}
}
}
static int set_attribute(NioFileObject *file, int varid, PyObject *attributes,
char *name, PyObject *value) {
NclFile nfile = (NclFile) file->id;
NhlErrorTypes ret;
NclMultiDValData md = NULL;
PyArrayObject *array = NULL;
if (!value || value == Py_None) {
/* delete attribute */
if (varid == NC_GLOBAL) {
ret = _NclFileDeleteAtt(nfile, NrmStringToQuark(name));
} else {
ret = _NclFileDeleteVarAtt(nfile,
nfile->file.var_info[varid]->var_name_quark,
NrmStringToQuark(name));
}
PyObject_DelItemString(attributes, name);
return 0;
}
if (is_string_type(value)) {
ng_size_t len_dims = 1;
NrmQuark *qval = malloc(sizeof(NrmQuark));
py3_char* utf8 = as_utf8_char(value);
qval[0] = NrmStringToQuark(utf8);
free(utf8);
md = _NclCreateMultiDVal(NULL, NULL, Ncl_MultiDValData, 0, (void*) qval,
NULL, 1, &len_dims, TEMPORARY, NULL,
(NclTypeClass) nclTypestringClass);
} else {
ng_size_t dim_sizes = 1;
int n_dims;