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awips2/pythonPackages/scientific/Src/Scientific_netcdf.c
root 133dc97f67 Initial revision of AWIPS2 11.9.0-7p5 
Former-commit-id: 06a8b51d6d [formerly 9f19e3f712 [formerly 64fa9254b946eae7e61bbc3f513b7c3696c4f54f]]
Former-commit-id: 9f19e3f712
Former-commit-id: a02aeb236c
2012-01-06 08:55:05 -06:00

2287 lines
56 KiB
C
Executable file
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/*
* Objects representing netCDF files and variables.
*
* Written by Konrad Hinsen
* last revision: 2007-10-31
*/
#ifdef _WIN32
#define DLL_NETCDF
#endif
#include "Python.h"
#if defined(NUMPY)
#include "numpy/arrayobject.h"
#else
#if defined(NUMARRAY)
#include "numarray/arrayobject.h"
#else
#include "Numeric/arrayobject.h"
#endif
#endif
#include "netcdf.h"
#define _NETCDF_MODULE
#include "Scientific/netcdfmodule.h"
staticforward int
netcdf_file_init(PyNetCDFFileObject *self);
staticforward PyNetCDFVariableObject *
netcdf_variable_new(PyNetCDFFileObject *file, char *name, int id, int type,
int ndims, int *dimids, int nattrs);
/* Lock granting access to netCDF routines (netCDF isn't thread-safe) */
#ifdef WITH_THREAD
#include "pythread.h"
PyThread_type_lock netCDF_lock;
#define acquire_netCDF_lock() { PyThread_acquire_lock(netCDF_lock, 1); }
#define release_netCDF_lock() { PyThread_release_lock(netCDF_lock); }
#else
#define acquire_netCDF_lock() {}
#define release_netCDF_lock() {}
#endif
/* Typedef for Numeric/NumPy compatibility */
#if !defined(NUMPY)
typedef int npy_intp;
#endif
/* Set error string */
static void
netcdf_seterror(void)
{
char *error;
switch (ncerr) {
case NC_NOERR:
error = "No error";
break;
case NC_EBADID:
error = "Not a netCDF id";
break;
case NC_ENFILE:
error = "Too many netCDF files open";
break;
case NC_EEXIST:
error = "netCDF file exists && NC_NOCLOBBER";
break;
case NC_EINVAL:
error = "Invalid argument";
break;
case NC_EPERM:
error = "Write to read only";
break;
case NC_ENOTINDEFINE:
error = "Operation not allowed in data mode";
break;
case NC_EINDEFINE:
error = "Operation not allowed in define mode";
break;
case NC_EINVALCOORDS:
error = "Index exceeds dimension bound";
break;
case NC_EMAXDIMS:
error = "NC_MAX_DIMS exceeded";
break;
case NC_ENAMEINUSE:
error = "String match to name in use";
break;
case NC_ENOTATT:
error = "Attribute not found";
break;
case NC_EMAXATTS:
error = "NC_MAX_ATTRS exceeded";
break;
case NC_EBADTYPE:
error = "Not a netCDF data type or _FillValue type mismatch";
break;
case NC_EBADDIM:
error = "Invalid dimension id or name";
break;
case NC_EUNLIMPOS:
error = "NC_UNLIMITED in the wrong index";
break;
case NC_EMAXVARS:
error = "NC_MAX_VARS exceeded";
break;
case NC_ENOTVAR:
error = "Variable not found";
break;
case NC_EGLOBAL:
error = "Action prohibited on NC_GLOBAL varid";
break;
case NC_ENOTNC:
error = "Not a netCDF file";
break;
case NC_ESTS:
error = "In Fortran, string too short";
break;
case NC_EMAXNAME:
error = "NC_MAX_NAME exceeded";
break;
case NC_EUNLIMIT:
error = "NC_UNLIMITED size already in use";
break;
case NC_ENORECVARS:
error = "nc_rec op when there are no record vars";
break;
case NC_ECHAR:
error = "Attempt to convert between text & numbers";
break;
case NC_EEDGE:
error = "Edge+start exceeds dimension bound";
break;
case NC_ESTRIDE:
error = "Illegal stride";
break;
case NC_EBADNAME:
error = "Attribute or variable name contains illegal characters";
break;
case NC_ERANGE:
error = "Numeric conversion not representable";
break;
case NC_ENOMEM:
error = "Memory allocation (malloc) failure";
break;
case NC_EXDR:
error = "XDR error";
break;
default:
error = "Unknown error";
break;
}
PyErr_SetString(PyExc_IOError, error);
}
static void
netcdf_signalerror(int code)
{
static char buffer[200];
if (code != NC_NOERR) {
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
sprintf(buffer, "netcdf: %s", nc_strerror(code));
release_netCDF_lock();
Py_END_ALLOW_THREADS;
PyErr_SetString(PyExc_IOError, buffer);
}
}
/*
* Python equivalents to netCDF data types
*
* Caution: the following specification may not be fully portable.
* The comments indicate the correct netCDF specification. The assignment
* of Python types assumes that 'short' is 16-bit and 'int' is 32-bit.
*/
int data_types[] = {-1, /* not used */
#if defined(NUMPY)
PyArray_BYTE, /* signed 8-bit int */
#else
PyArray_SBYTE, /* signed 8-bit int */
#endif
PyArray_CHAR, /* 8-bit character */
PyArray_SHORT, /* 16-bit signed int */
PyArray_INT, /* 32-bit signed int */
PyArray_FLOAT, /* 32-bit IEEE float */
PyArray_DOUBLE /* 64-bit IEEE float */
};
/* Generic data type functions, similar to those in the netCDF 2 interface. */
static int
nc_put_att_any(int ncid, int varid, const char *name,
nc_type xtype, size_t len, const void *data)
{
switch (xtype) {
case NC_BYTE:
return nc_put_att_uchar(ncid, varid, name, xtype, len,
(unsigned char *)data);
break;
case NC_CHAR:
return nc_put_att_text(ncid, varid, name, len,
(char *)data);
break;
case NC_SHORT:
return nc_put_att_short(ncid, varid, name, xtype, len,
(short *)data);
break;
case NC_INT:
return nc_put_att_int(ncid, varid, name, xtype, len,
(int *)data);
break;
case NC_FLOAT:
return nc_put_att_float(ncid, varid, name, xtype, len,
(float *)data);
break;
case NC_DOUBLE:
return nc_put_att_double(ncid, varid, name, xtype, len,
(double *)data);
break;
default:
return NC_EINVAL;
}
}
static int
nc_put_var1_any(int ncid, int varid, nc_type xtype, const size_t *indexp,
const void *data)
{
switch (xtype) {
case NC_BYTE:
return nc_put_var1_uchar(ncid, varid, indexp, (unsigned char *)data);
break;
case NC_CHAR:
return nc_put_var1_text(ncid, varid, indexp, (char *)data);
break;
case NC_SHORT:
return nc_put_var1_short(ncid, varid, indexp, (short *)data);
break;
case NC_INT:
return nc_put_var1_int(ncid, varid, indexp, (int *)data);
break;
case NC_FLOAT:
return nc_put_var1_float(ncid, varid, indexp, (float *)data);
break;
case NC_DOUBLE:
return nc_put_var1_double(ncid, varid, indexp, (double *)data);
break;
default:
return NC_EINVAL;
}
}
static int
nc_put_vars_any(int ncid, int varid, nc_type xtype, const size_t start[],
const size_t count[], const ptrdiff_t stride[],
const void *data)
{
switch (xtype) {
case NC_BYTE:
return nc_put_vars_uchar(ncid, varid, start, count, stride,
(unsigned char *)data);
break;
case NC_CHAR:
return nc_put_vars_text(ncid, varid, start, count, stride,
(char *)data);
break;
case NC_SHORT:
return nc_put_vars_short(ncid, varid, start, count, stride,
(short *)data);
break;
break;
case NC_INT:
return nc_put_vars_int(ncid, varid, start, count, stride,
(int *)data);
break;
break;
case NC_FLOAT:
return nc_put_vars_float(ncid, varid, start, count, stride,
(float *)data);
break;
break;
case NC_DOUBLE:
return nc_put_vars_double(ncid, varid, start, count, stride,
(double *)data);
break;
default:
return NC_EINVAL;
}
}
/* Utility functions */
static void
define_mode(PyNetCDFFileObject *file, int define_flag)
{
if (file->define != define_flag) {
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
if (file->define)
nc_enddef(file->id);
else
nc_redef(file->id);
release_netCDF_lock();
file->define = define_flag;
Py_END_ALLOW_THREADS;
}
}
static char
typecode(int type)
{
char t;
switch(type) {
#if defined(NUMPY)
case PyArray_STRING:
case PyArray_CHAR:
t = PyArray_CHARLTR;
break;
case PyArray_BYTE:
t = PyArray_BYTELTR;
break;
case PyArray_SHORT:
t = PyArray_SHORTLTR;
break;
case PyArray_INT:
t = PyArray_INTLTR;
break;
case PyArray_LONG:
t = PyArray_LONGLTR;
break;
case PyArray_FLOAT:
t = PyArray_FLOATLTR;
break;
case PyArray_DOUBLE:
t = PyArray_DOUBLELTR;
break;
#else
case PyArray_UBYTE:
t = 'b';
break;
case PyArray_SBYTE:
t = '1';
break;
case PyArray_CHAR:
t = 'c';
break;
case PyArray_SHORT:
t = 's';
break;
case PyArray_LONG:
t = 'l';
break;
case PyArray_INT:
t = 'i';
break;
case PyArray_FLOAT:
t = 'f';
break;
case PyArray_DOUBLE:
t = 'd';
break;
#endif
default:
t = ' ';
}
return t;
}
static nc_type
netcdf_type_from_code(char code)
{
int type;
switch(code) {
case 'c':
case 'S':
type = NC_CHAR;
break;
case 'b':
case 'B':
case '1':
type = NC_BYTE;
break;
case 's':
case 'h':
type = NC_SHORT;
break;
case 'i':
case 'l':
type = NC_INT;
break;
case 'f':
type = NC_FLOAT;
break;
case 'd':
type = NC_DOUBLE;
break;
default:
type = 0;
}
return type;
}
static int
netcdf_type_from_type(char array_type)
{
int type;
switch(array_type) {
#if !defined(NUMARRAY)
case PyArray_CHAR:
#if defined(NUMPY)
case PyArray_STRING:
#endif
type = NC_CHAR;
break;
#endif
case PyArray_UBYTE:
#if defined(NUMPY)
case PyArray_BYTE:
#else
case PyArray_SBYTE:
#endif
type = NC_BYTE;
break;
case PyArray_SHORT:
type = NC_SHORT;
break;
#if !defined(NUMARRAY)
case PyArray_INT:
#endif
case PyArray_LONG:
type = NC_INT;
break;
case PyArray_FLOAT:
type = NC_FLOAT;
break;
case PyArray_DOUBLE:
type = NC_DOUBLE;
break;
default:
type = 0;
}
return type;
}
static void
collect_attributes(int fileid, int varid, PyObject *attributes, int nattrs)
{
char name[MAX_NC_NAME];
nc_type type;
size_t length;
npy_intp lengthp;
int py_type;
int i;
for (i = 0; i < nattrs; i++) {
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
nc_inq_attname(fileid, varid, i, name);
nc_inq_att(fileid, varid, name, &type, &length);
lengthp = length;
release_netCDF_lock();
Py_END_ALLOW_THREADS;
py_type = data_types[type];
if (py_type == PyArray_CHAR) {
char *s = (char *)malloc((length+1)*sizeof(char));
if (s != NULL) {
PyObject *string;
*s = '\0';
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
nc_get_att_text(fileid, varid, name, s);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
s[length] = '\0';
string = PyString_FromString(s);
free(s);
if (string != NULL) {
PyDict_SetItemString(attributes, name, string);
Py_DECREF(string);
}
}
}
else {
#if defined(NUMPY)
PyObject *array = PyArray_SimpleNew(1, &lengthp, py_type);
#else
PyObject *array = PyArray_FromDims(1, &lengthp, py_type);
#endif
if (array != NULL) {
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ncattget(fileid, varid, name, ((PyArrayObject *)array)->data);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
array = PyArray_Return((PyArrayObject *)array);
if (array != NULL) {
PyDict_SetItemString(attributes, name, array);
Py_DECREF(array);
}
}
}
}
}
static int
set_attribute(int fileid, int varid, PyObject *attributes,
char *name, PyObject *value)
{
if (value == NULL) {
int ret;
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = nc_del_att(fileid, varid, name);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ret != NC_NOERR) {
netcdf_signalerror(ret);
return -1;
}
PyDict_DelItemString(attributes, name);
return 0;
}
else if (PyString_Check(value)) {
Py_ssize_t len = PyString_Size(value);
char *string = PyString_AsString(value);
int ret;
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = nc_put_att_text(fileid, varid, name, (size_t)len, string);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ret != NC_NOERR) {
netcdf_signalerror(ret);
return -1;
}
PyDict_SetItemString(attributes, name, value);
return 0;
}
else {
int ret;
PyArrayObject *array =
(PyArrayObject *)PyArray_ContiguousFromObject(value, PyArray_NOTYPE, 0, 1);
if (array != NULL) {
int len = (array->nd == 0) ? 1 : array->dimensions[0];
int type = netcdf_type_from_code(array->descr->type);
if (data_types[type] != array->descr->type_num) {
PyArrayObject *array2 = (PyArrayObject *)
PyArray_Cast(array, data_types[type]);
Py_DECREF(array);
array = array2;
if (array == NULL)
return -1;
}
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = nc_put_att_any(fileid, varid, name, type, len, array->data);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ret != NC_NOERR) {
netcdf_signalerror(ret);
return -1;
}
PyDict_SetItemString(attributes, name, (PyObject *)array);
return 0;
}
else
return -1;
}
}
static int
check_if_open(PyNetCDFFileObject *file, int mode)
{
/* mode: -1 read, 1 write, 0 other */
if (file == NULL || !file->open) {
PyErr_SetString(PyExc_IOError, "netcdf: file has been closed");
return 0;
}
else {
if (mode != 1 || file->write) {
return 1;
}
else {
PyErr_SetString(PyExc_IOError, "netcdf: write access to read-only file");
return 0;
}
}
}
/*
* NetCDFFile object
* (type declaration in netcdfmodule.h)
*/
/* Destroy file object */
static void
PyNetCDFFileObject_dealloc(PyNetCDFFileObject *self)
{
if (self->open)
PyNetCDFFile_Close(self);
Py_XDECREF(self->dimensions);
Py_XDECREF(self->variables);
Py_XDECREF(self->attributes);
Py_XDECREF(self->name);
Py_XDECREF(self->mode);
self->ob_type->tp_free((PyObject*)self);
}
/* Create file object */
static PyObject *
PyNetCDFFileObject_new(PyTypeObject *type, PyObject *args, PyObject *kwds)
{
PyNetCDFFileObject *self;
self = (PyNetCDFFileObject *)type->tp_alloc(type, 0);
if (self != NULL) {
self->dimensions = NULL;
self->variables = NULL;
self->attributes = NULL;
self->name = NULL;
self->mode = NULL;
}
return (PyObject *)self;
}
/* Open file */
static int
open_netcdf_file(PyNetCDFFileObject *self, char *filename, char *mode)
{
int rw, share, ret;
rw = share = ret = 0;
if (strlen(mode) > 1) {
if (mode[1] == '+') rw = 1;
else if (mode[1] == 's') share = NC_SHARE;
else ret = -1;
}
if (strlen(mode) > 2) {
if (mode[2] == '+') rw = 1;
else if (mode[2] == 's') share = NC_SHARE;
else ret = -1;
}
if (ret == -1 || strlen(mode) > 3 ||
(mode[0] != 'r' && mode[0] != 'w' && mode[0] != 'a')) {
PyErr_SetString(PyExc_IOError, "netcdf: illegal mode specification");
return -1;
}
self->open = 0;
if (mode[0] == 'w') {
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = nc_create(filename, NC_CLOBBER|share, &self->id);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
self->define = 1;
self->write = 1;
if (ret == NC_NOERR) {
self->open = 1;
netcdf_file_init(self);
}
}
else if (mode[0] == 'a') {
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = nc_open(filename, NC_WRITE|share, &self->id);
self->define = 0;
if (ret == ENOENT) {
ret = nc_create(filename, NC_NOCLOBBER|share, &self->id);
self->define = 1;
}
release_netCDF_lock();
Py_END_ALLOW_THREADS;
self->write = 1;
if (ret == NC_NOERR) {
self->open = 1;
netcdf_file_init(self);
}
}
else if (mode[0] == 'r') {
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = nc_open(filename, rw ? (NC_WRITE|share) : (NC_NOWRITE|share),
&self->id);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
self->define = 0;
self->write = rw;
if (ret == NC_NOERR) {
self->open = 1;
netcdf_file_init(self);
}
}
else {
return -1;
}
if (ret != NC_NOERR) {
netcdf_signalerror(ret);
return -1;
}
self->name = PyString_FromString(filename);
self->mode = PyString_FromString(mode);
return 0;
}
static int
PyNetCDFFileObject_init(PyNetCDFFileObject *self,
PyObject *args, PyObject *kwds)
{
char *filename;
char *mode = NULL;
char *history = NULL;
if (!PyArg_ParseTuple(args, "s|ss:NetCDFFile", &filename, &mode, &history))
return -1;
if (mode == NULL)
mode = "r";
if (open_netcdf_file(self, filename, mode) < 0) {
return -1;
}
if (history != NULL)
PyNetCDFFile_AddHistoryLine(self, history);
return 0;
}
static PyNetCDFFileObject *
PyNetCDFFile_Open(char *filename, char *mode)
{
PyNetCDFFileObject *self = (PyNetCDFFileObject *)
PyNetCDFFileObject_new(&PyNetCDFFile_Type, NULL, NULL);
if (self == NULL)
return NULL;
if (open_netcdf_file(self, filename, mode) < 0) {
PyNetCDFFileObject_dealloc(self);
return NULL;
}
return self;
}
/* Create variables from file */
static int
netcdf_file_init(PyNetCDFFileObject *self)
{
int ndims, nvars, ngattrs, recdim;
int i;
self->dimensions = PyDict_New();
self->variables = PyDict_New();
self->attributes = PyDict_New();
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
nc_inq(self->id, &ndims, &nvars, &ngattrs, &recdim);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
self->recdim = recdim;
for (i = 0; i < ndims; i++) {
char name[MAX_NC_NAME];
unsigned long size;
PyObject *size_ob;
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
nc_inq_dim(self->id, i, name, &size);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (i == recdim)
PyDict_SetItemString(self->dimensions, name, Py_None);
else {
size_ob = PyInt_FromLong(size);
PyDict_SetItemString(self->dimensions, name, size_ob);
Py_DECREF(size_ob);
}
}
for (i = 0; i < nvars; i++) {
char name[MAX_NC_NAME];
nc_type datatype;
int ndimensions, nattrs;
int *dimids;
PyNetCDFVariableObject *variable;
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
nc_inq_varname(self->id, i, name);
nc_inq_vartype(self->id, i, &datatype);
nc_inq_varndims(self->id, i, &ndimensions);
nc_inq_varnatts(self->id, i, &nattrs);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ndimensions > 0) {
dimids = (int *)malloc(ndimensions*sizeof(int));
if (dimids == NULL) {
PyErr_NoMemory();
return 0;
}
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
nc_inq_vardimid(self->id, i, dimids);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
}
else
dimids = NULL;
variable = netcdf_variable_new(self, name, i, data_types[datatype],
ndimensions, dimids, nattrs);
if (variable != NULL) {
PyDict_SetItemString(self->variables, name, (PyObject *)variable);
Py_DECREF(variable);
}
else
free(dimids);
}
collect_attributes(self->id, NC_GLOBAL, self->attributes, ngattrs);
return 1;
}
/* Create dimension */
static int
PyNetCDFFile_CreateDimension(PyNetCDFFileObject *file, char *name, long size)
{
PyObject *size_ob;
int id, ret;
if (check_if_open(file, 1)) {
if (size == 0 && file->recdim != -1) {
PyErr_SetString(PyExc_IOError,
"netcdf: there is already an unlimited dimension");
return -1;
}
define_mode(file, 1);
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = nc_def_dim(file->id, name, (size == 0) ? NC_UNLIMITED : size, &id);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ret != NC_NOERR) {
netcdf_signalerror(ret);
return -1;
}
else {
if (size == 0) {
PyDict_SetItemString(file->dimensions, name, Py_None);
file->recdim = id;
}
else {
size_ob = PyInt_FromLong(size);
PyDict_SetItemString(file->dimensions, name, size_ob);
Py_DECREF(size_ob);
}
return 0;
}
}
else
return -1;
}
static PyObject *
PyNetCDFFileObject_new_dimension(PyNetCDFFileObject *self, PyObject *args)
{
char *name;
PyObject *size_ob;
long size;
if (!PyArg_ParseTuple(args, "sO", &name, &size_ob))
return NULL;
if (size_ob == Py_None)
size = 0;
else if (PyInt_Check(size_ob))
size = PyInt_AsLong(size_ob);
else {
PyErr_SetString(PyExc_TypeError, "size must be None or integer");
return NULL;
}
if (PyNetCDFFile_CreateDimension(self, name, size) == 0) {
Py_INCREF(Py_None);
return Py_None;
}
else
return NULL;
}
static char createDimension_doc[] = "";
/* Create variable */
static PyNetCDFVariableObject *
PyNetCDFFile_CreateVariable(PyNetCDFFileObject *file, char *name, int typecode,
char **dimension_names, int ndim)
{
int *dimids;
PyNetCDFVariableObject *variable;
int ntype, i, ret;
if (check_if_open(file, 1)) {
define_mode(file, 1);
if (ndim == 0)
dimids = NULL;
else {
dimids = (int *)malloc(ndim*sizeof(int));
if (dimids == NULL)
return (PyNetCDFVariableObject *)PyErr_NoMemory();
}
for (i = 0; i < ndim; i++) {
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
dimids[i] = ncdimid(file->id, dimension_names[i]);
ret = nc_inq_dimid(file->id, dimension_names[i], dimids+i);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ret != NC_NOERR) {
netcdf_signalerror(ret);
free(dimids);
return NULL;
}
if (dimids[i] == file->recdim && i > 0) {
PyErr_SetString(PyExc_IOError,
"netcdf: unlimited dimension must be first");
free(dimids);
return NULL;
}
}
ntype = netcdf_type_from_code((char)typecode);
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = nc_def_var(file->id, name, ntype, ndim, dimids, &i);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ret != NC_NOERR) {
netcdf_signalerror(ret);
if (dimids != NULL)
free(dimids);
return NULL;
}
variable = netcdf_variable_new(file, name, i, data_types[ntype],
ndim, dimids, 0);
if (variable != NULL) {
PyDict_SetItemString(file->variables, name, (PyObject *)variable);
return variable;
}
else {
free(dimids);
return NULL;
}
}
else
return NULL;
}
static PyObject *
PyNetCDFFileObject_new_variable(PyNetCDFFileObject *self, PyObject *args)
{
PyNetCDFVariableObject *var;
char **dimension_names;
PyObject *item, *dim;
char *name;
Py_ssize_t len_dim;
int ndim;
char type;
int i;
if (!PyArg_ParseTuple(args, "scO!", &name, &type, &PyTuple_Type, &dim))
return NULL;
len_dim = PyTuple_Size(dim);
if (len_dim > INT_MAX) {
PyErr_SetString(PyExc_ValueError, "too many dimensions");
return NULL;
}
ndim = (int)len_dim;
if (ndim == 0)
dimension_names = NULL;
else {
dimension_names = (char **)malloc(ndim*sizeof(char *));
if (dimension_names == NULL) {
PyErr_SetString(PyExc_MemoryError, "out of memory");
return NULL;
}
}
for (i = 0; i < ndim; i++) {
item = PyTuple_GetItem(dim, (Py_ssize_t)i);
if (PyString_Check(item))
dimension_names[i] = PyString_AsString(item);
else {
PyErr_SetString(PyExc_TypeError, "dimension name must be a string");
free(dimension_names);
return NULL;
}
}
var = PyNetCDFFile_CreateVariable(self, name, type, dimension_names, ndim);
free(dimension_names);
return (PyObject *)var;
}
static char createVariable_doc[] = "";
/* Return a variable object referring to an existing variable */
static PyNetCDFVariableObject *
PyNetCDFFile_GetVariable(PyNetCDFFileObject *file, char *name)
{
return (PyNetCDFVariableObject *)PyDict_GetItemString(file->variables, name);
}
/* Synchronize output */
static int
PyNetCDFFile_Sync(PyNetCDFFileObject *file)
{
int ret;
if (check_if_open(file, 0)) {
define_mode(file, 0);
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = nc_sync(file->id);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ret == -1) {
netcdf_seterror();
return -1;
}
else
return 0;
}
else
return -1;
}
static PyObject *
PyNetCDFFileObject_sync(PyNetCDFFileObject *self, PyObject *args)
{
if (!PyArg_ParseTuple(args, ""))
return NULL;
if (PyNetCDFFile_Sync(self) == 0) {
Py_INCREF(Py_None);
return Py_None;
}
else
return NULL;
}
static char sync_doc[] = "";
static char flush_doc[] =
"ensures that all modified data is written to the file";
/* Close file */
static int
PyNetCDFFile_Close(PyNetCDFFileObject *file)
{
PyObject *name;
PyNetCDFVariableObject *variable;
int ret;
Py_ssize_t pos;
if (!check_if_open(file, 0))
return -1;
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = nc_close(file->id);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ret != NC_NOERR) {
netcdf_signalerror(ret);
ret = -1;
}
else
ret = 0;
file->open = 0;
pos = 0;
while (PyDict_Next(file->variables, &pos, &name, (PyObject **)&variable)) {
Py_DECREF(variable->file);
variable->file = NULL;
}
return ret;
}
static PyObject *
PyNetCDFFileObject_close(PyNetCDFFileObject *self, PyObject *args)
{
char *history = NULL;
if (!PyArg_ParseTuple(args, "|s", &history))
return NULL;
if (history != NULL)
PyNetCDFFile_AddHistoryLine(self, history);
if (PyNetCDFFile_Close(self) == 0) {
Py_INCREF(Py_None);
return Py_None;
}
else
return NULL;
}
static char close_doc[] = "";
/* Method table */
static PyMethodDef PyNetCDFFileObject_methods[] = {
{"close", (PyCFunction)PyNetCDFFileObject_close, 1, close_doc},
{"createDimension", (PyCFunction)PyNetCDFFileObject_new_dimension, 1,
createDimension_doc},
{"createVariable", (PyCFunction)PyNetCDFFileObject_new_variable, 1,
createVariable_doc},
{"sync", (PyCFunction)PyNetCDFFileObject_sync, 1, sync_doc},
{"flush", (PyCFunction)PyNetCDFFileObject_sync, 1, flush_doc},
{NULL, NULL} /* sentinel */
};
/* Attribute access */
static PyObject *
PyNetCDFFile_GetAttribute(PyNetCDFFileObject *self, char *name)
{
PyObject *value;
if (check_if_open(self, -1)) {
if (strcmp(name, "dimensions") == 0) {
Py_INCREF(self->dimensions);
return self->dimensions;
}
if (strcmp(name, "variables") == 0) {
Py_INCREF(self->variables);
return self->variables;
}
if (strcmp(name, "__dict__") == 0) {
Py_INCREF(self->attributes);
return self->attributes;
}
value = PyDict_GetItemString(self->attributes, name);
if (value != NULL) {
Py_INCREF(value);
return value;
}
else {
PyErr_Clear();
return Py_FindMethod(PyNetCDFFileObject_methods, (PyObject *)self, name);
}
}
else
return NULL;
}
static int
PyNetCDFFile_SetAttribute(PyNetCDFFileObject *self, char *name,
PyObject *value)
{
if (check_if_open(self, 1)) {
if (strcmp(name, "dimensions") == 0 ||
strcmp(name, "variables") == 0 ||
strcmp(name, "__dict__") == 0) {
PyErr_SetString(PyExc_TypeError, "object has read-only attributes");
return -1;
}
define_mode(self, 1);
return set_attribute(self->id, NC_GLOBAL, self->attributes, name, value);
}
else
return -1;
}
static int
PyNetCDFFile_SetAttributeString(PyNetCDFFileObject *self,
char *name, char *value)
{
PyObject *string = PyString_FromString(value);
if (string != NULL)
return PyNetCDFFile_SetAttribute(self, name, string);
else
return -1;
}
static int
PyNetCDFFile_AddHistoryLine(PyNetCDFFileObject *self, char *text)
{
static char *history = "history";
Py_ssize_t alloc, old, new, new_alloc;
PyStringObject *new_string;
PyObject *h = PyNetCDFFile_GetAttribute(self, history);
if (h == NULL) {
PyErr_Clear();
alloc = 0;
old = 0;
new = strlen(text);
}
else {
alloc = PyString_Size(h);
old = strlen(PyString_AsString(h));
new = old + strlen(text) + 1;
}
new_alloc = (new <= alloc) ? alloc : new + 500;
new_string = (PyStringObject *)PyString_FromStringAndSize(NULL, new_alloc);
if (new_string) {
char *s = new_string->ob_sval;
int len, ret;
memset(s, 0, new_alloc+1);
if (h == NULL)
len = -1;
else {
strcpy(s, PyString_AsString(h));
len = strlen(s);
s[len] = '\n';
}
strcpy(s+len+1, text);
ret = PyNetCDFFile_SetAttribute(self, history, (PyObject *)new_string);
Py_XDECREF(h);
Py_DECREF(new_string);
return ret;
}
else
return -1;
}
/* Printed representation */
static PyObject *
PyNetCDFFileObject_repr(PyNetCDFFileObject *file)
{
char buf[300];
sprintf(buf, "<%s netCDF file '%.256s', mode '%.10s' at %lx>",
file->open ? "open" : "closed",
PyString_AsString(file->name),
PyString_AsString(file->mode),
(long)file);
return PyString_FromString(buf);
}
/* Type definition */
statichere PyTypeObject PyNetCDFFile_Type = {
PyObject_HEAD_INIT(NULL)
0, /*ob_size*/
"NetCDFFile", /*tp_name*/
sizeof(PyNetCDFFileObject), /*tp_basicsize*/
0, /*tp_itemsize*/
/* methods */
(destructor)PyNetCDFFileObject_dealloc, /*tp_dealloc*/
0, /*tp_print*/
(getattrfunc)PyNetCDFFile_GetAttribute, /*tp_getattr*/
(setattrfunc)PyNetCDFFile_SetAttribute, /*tp_setattr*/
0, /*tp_compare*/
(reprfunc)PyNetCDFFileObject_repr, /*tp_repr*/
0, /*tp_as_number*/
0, /*tp_as_sequence*/
0, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
0, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT, /*tp_flags*/
"NetCDFFile(filename, mode, history_line)\n\nopens a netCDF file\n",
/* tp_doc */
0, /* tp_traverse */
0, /* tp_clear */
0, /* tp_richcompare */
0, /* tp_weaklistoffset */
0, /* tp_iter */
0, /* tp_iternext */
PyNetCDFFileObject_methods, /* tp_methods */
0, /* tp_members */
0, /* tp_getset */
0, /* tp_base */
0, /* tp_dict */
0, /* tp_descr_get */
0, /* tp_descr_set */
0, /* tp_dictoffset */
(initproc)PyNetCDFFileObject_init, /* tp_init */
0, /* tp_alloc */
PyNetCDFFileObject_new, /* tp_new */
};
/*
* NetCDFVariable object
* (type declaration in netcdfmodule.h)
*/
/* Destroy variable object */
static void
PyNetCDFVariableObject_dealloc(PyNetCDFVariableObject *self)
{
if (self->dimids != NULL)
free(self->dimids);
if (self->dimensions != NULL)
free(self->dimensions);
if (self->name != NULL)
free(self->name);
Py_XDECREF(self->file);
Py_XDECREF(self->attributes);
self->ob_type->tp_free((PyObject*)self);
}
/* Create variable object */
static PyNetCDFVariableObject *
netcdf_variable_new(PyNetCDFFileObject *file, char *name, int id, int type,
int ndims, int *dimids, int nattrs)
{
PyNetCDFVariableObject *self;
int recdim;
int i;
if (check_if_open(file, -1)) {
self = PyObject_NEW(PyNetCDFVariableObject, &PyNetCDFVariable_Type);
if (self == NULL)
return NULL;
self->file = file;
Py_INCREF(file);
self->id = id;
self->type = type;
self->nd = ndims;
self->dimids = dimids;
self->unlimited = 0;
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
nc_inq_unlimdim(file->id, &recdim);
self->dimensions = (size_t *)malloc(ndims*sizeof(size_t));
if (self->dimensions != NULL) {
for (i = 0; i < ndims; i++)
nc_inq_dimlen(file->id, dimids[i], &self->dimensions[i]);
if (ndims > 0 && self->dimids[0] == self->file->recdim)
self->unlimited = 1;
}
release_netCDF_lock();
Py_END_ALLOW_THREADS;
self->name = (char *)malloc(strlen(name)+1);
if (self->name != NULL)
strcpy(self->name, name);
self->attributes = PyDict_New();
collect_attributes(file->id, self->id, self->attributes, nattrs);
return self;
}
else
return NULL;
}
/* Return value */
static PyObject *
PyNetCDFVariableObject_value(PyNetCDFVariableObject *self, PyObject *args)
{
PyNetCDFIndex *indices;
if (!PyArg_ParseTuple(args, ""))
return NULL;
if (self->nd == 0)
indices = NULL;
else
indices = PyNetCDFVariable_Indices(self);
return PyArray_Return(PyNetCDFVariable_ReadAsArray(self, indices));
}
/* Assign value */
static PyObject *
PyNetCDFVariableObject_assign(PyNetCDFVariableObject *self, PyObject *args)
{
PyObject *value;
PyNetCDFIndex *indices;
if (!PyArg_ParseTuple(args, "O", &value))
return NULL;
if (self->nd == 0)
indices = NULL;
else
indices = PyNetCDFVariable_Indices(self);
if (PyNetCDFVariable_WriteArray(self, indices, value) < 0)
return NULL;
Py_INCREF(Py_None);
return Py_None;
}
/* Return typecode */
static PyObject *
PyNetCDFVariableObject_typecode(PyNetCDFVariableObject *self, PyObject *args)
{
char t;
if (!PyArg_ParseTuple(args, ""))
return NULL;
t = typecode(self->type);
return PyString_FromStringAndSize(&t, (Py_ssize_t)1);
}
/* Method table */
static PyMethodDef PyNetCDFVariableObject_methods[] = {
{"assignValue", (PyCFunction)PyNetCDFVariableObject_assign, 1},
{"getValue", (PyCFunction)PyNetCDFVariableObject_value, 1},
{"typecode", (PyCFunction)PyNetCDFVariableObject_typecode, 1},
{NULL, NULL} /* sentinel */
};
/* Attribute access */
static int
PyNetCDFVariable_GetRank(PyNetCDFVariableObject *var)
{
return var->nd;
}
static size_t *
PyNetCDFVariable_GetShape(PyNetCDFVariableObject *var)
{
int i;
if (check_if_open(var->file, -1)) {
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
for (i = 0; i < var->nd; i++)
nc_inq_dimlen(var->file->id, var->dimids[i], &var->dimensions[i]);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
return var->dimensions;
}
else
return NULL;
}
static PyObject *
PyNetCDFVariable_GetAttribute(PyNetCDFVariableObject *self, char *name)
{
PyObject *value;
if (strcmp(name, "shape") == 0) {
PyObject *tuple;
int i;
if (check_if_open(self->file, -1)) {
PyNetCDFVariable_GetShape(self);
tuple = PyTuple_New((Py_ssize_t)self->nd);
for (i = 0; i < self->nd; i++)
PyTuple_SetItem(tuple, (Py_ssize_t)i,
PyInt_FromLong(self->dimensions[i]));
return tuple;
}
else
return NULL;
}
if (strcmp(name, "dimensions") == 0) {
PyObject *tuple;
char name[MAX_NC_NAME];
int i;
if (check_if_open(self->file, -1)) {
tuple = PyTuple_New((Py_ssize_t)self->nd);
for (i = 0; i < self->nd; i++) {
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
nc_inq_dimname(self->file->id, self->dimids[i], name);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
PyTuple_SetItem(tuple, (Py_ssize_t)i, PyString_FromString(name));
}
return tuple;
}
else
return NULL;
}
if (strcmp(name, "__dict__") == 0) {
Py_INCREF(self->attributes);
return self->attributes;
}
value = PyDict_GetItemString(self->attributes, name);
if (value != NULL) {
Py_INCREF(value);
return value;
}
else {
PyErr_Clear();
return Py_FindMethod(PyNetCDFVariableObject_methods, (PyObject *)self,name);
}
}
static int
PyNetCDFVariable_SetAttribute(PyNetCDFVariableObject *self,
char *name, PyObject *value)
{
if (check_if_open(self->file, 1)) {
if (strcmp(name, "shape") == 0 ||
strcmp(name, "dimensions") == 0 ||
strcmp(name, "__dict__") == 0) {
PyErr_SetString(PyExc_TypeError, "object has read-only attributes");
return -1;
}
define_mode(self->file, 1);
return set_attribute(self->file->id, self->id, self->attributes,
name, value);
}
else
return -1;
}
static int
PyNetCDFVariable_SetAttributeString(PyNetCDFVariableObject *self,
char *name, char *value)
{
PyObject *string = PyString_FromString(value);
if (string != NULL)
return PyNetCDFVariable_SetAttribute(self, name, string);
else
return -1;
}
/* Subscripting */
static Py_ssize_t
PyNetCDFVariableObject_length(PyNetCDFVariableObject *self)
{
if (self->nd > 0)
return (Py_ssize_t)self->dimensions[0];
else
return (Py_ssize_t)0;
}
static PyNetCDFIndex *
PyNetCDFVariable_Indices(PyNetCDFVariableObject *var)
{
PyNetCDFIndex *indices =
(PyNetCDFIndex *)malloc(var->nd*sizeof(PyNetCDFIndex));
int i;
if (indices != NULL)
for (i = 0; i < var->nd; i++) {
indices[i].start = 0;
indices[i].stop = var->dimensions[i];
indices[i].stride = 1;
indices[i].item = 0;
}
else
PyErr_SetString(PyExc_MemoryError, "out of memory");
return indices;
}
static PyArrayObject *
PyNetCDFVariable_ReadAsArray(PyNetCDFVariableObject *self,
PyNetCDFIndex *indices)
{
npy_intp *dims;
PyArrayObject *array;
int i, d;
int nitems;
int error = 0;
d = 0;
nitems = 1;
if (!check_if_open(self->file, -1)) {
free(indices);
return NULL;
}
define_mode(self->file, 0);
if (self->nd == 0)
dims = NULL;
else {
dims = (npy_intp *)malloc(self->nd*sizeof(npy_intp));
if (dims == NULL) {
free(indices);
return (PyArrayObject *)PyErr_NoMemory();
}
}
for (i = 0; i < self->nd; i++) {
error = error || (indices[i].stride <= 0);
if (indices[i].start < 0)
indices[i].start += self->dimensions[i];
if (indices[i].start < 0)
indices[i].start = 0;
if (indices[i].start > self->dimensions[i])
indices[i].start = self->dimensions[i];
if (indices[i].item != 0)
indices[i].stop = indices[i].start + 1;
else {
if (indices[i].stop < 0)
indices[i].stop += self->dimensions[i];
if (indices[i].stop < 0)
indices[i].stop = 0;
if (indices[i].stop > self->dimensions[i])
indices[i].stop = self->dimensions[i];
dims[d] = (indices[i].stop-indices[i].start-1)/indices[i].stride+1;
if (dims[d] < 0)
dims[d] = 0;
nitems *= dims[d];
d++;
}
}
if (error) {
PyErr_SetString(PyExc_IndexError, "illegal index");
if (dims != NULL)
free(dims);
if (indices != NULL)
free(indices);
return NULL;
}
#if defined(NUMPY)
array = (PyArrayObject *)PyArray_SimpleNew (d, dims, self->type);
#else
array = (PyArrayObject *)PyArray_FromDims(d, dims, self->type);
#endif
if (array != NULL && nitems > 0) {
if (self->nd == 0) {
long zero = 0;
int ret;
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = ncvarget1(self->file->id, self->id, &zero, array->data);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ret == -1) {
netcdf_seterror();
Py_DECREF(array);
array = NULL;
}
}
else {
long *start;
long *count;
long *stride;
start = (long *)malloc(self->nd*sizeof(long));
count = (long *)malloc(self->nd*sizeof(long));
stride = (long *)malloc(self->nd*sizeof(long));
if (start != NULL && count != NULL && stride != NULL) {
int ret;
for (i = 0; i < self->nd; i++) {
start[i] = indices[i].start;
stride[i] = indices[i].stride;
count[i] = (indices[i].stop-indices[i].start-1)/indices[i].stride+1;
}
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = ncvargetg(self->file->id, self->id, start, count, stride, NULL,
array->data);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ret == -1) {
netcdf_seterror();
Py_DECREF(array);
array = NULL;
}
}
if (start != NULL)
free(start);
if (count != NULL)
free(count);
if (stride != NULL)
free(stride);
}
}
free(dims);
free(indices);
return array;
}
static PyStringObject *
PyNetCDFVariable_ReadAsString(PyNetCDFVariableObject *self)
{
if (self->type != PyArray_CHAR || self->nd != 1) {
PyErr_SetString(PyExc_IOError, "netcdf: not a string variable");
return NULL;
}
if (check_if_open(self->file, -1)) {
int ret;
char *temp;
PyObject *string;
define_mode(self->file, 0);
temp = (char *)malloc((self->dimensions[0]+1)*sizeof(char));
if (temp == NULL)
return (PyStringObject *)PyErr_NoMemory();
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = nc_get_var_text(self->file->id, self->id, temp);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ret != NC_NOERR) {
netcdf_signalerror(ret);
string = NULL;
}
else {
temp[self->dimensions[0]] = '\0';
string = PyString_FromString(temp);
}
free(temp);
return (PyStringObject *)string;
}
else
return NULL;
}
#include "time.h"
static int
PyNetCDFVariable_WriteArray(PyNetCDFVariableObject *self,
PyNetCDFIndex *indices, PyObject *value)
{
int *dims;
PyArrayObject *array;
int i, j, d;
int nitems;
int error = 0;
int ret = 0;
d = 0;
nitems = 1;
if (!check_if_open(self->file, 1)) {
free(indices);
return -1;
}
if (self->nd == 0)
dims = NULL;
else {
dims = (int *)malloc(self->nd*sizeof(int));
if (dims == NULL) {
free(indices);
PyErr_SetString(PyExc_MemoryError, "out of memory");
return -1;
}
}
define_mode(self->file, 0);
for (i = 0; i < self->nd; i++) {
error = error || (indices[i].stride <= 0);
if (indices[i].start < 0)
indices[i].start += self->dimensions[i];
if (indices[i].start < 0)
indices[i].start = 0;
if (indices[i].stop < 0)
indices[i].stop += self->dimensions[i];
if (indices[i].stop < 0)
indices[i].stop = 0;
if (i > 0 || !self->unlimited) {
if (indices[i].start > self->dimensions[i])
indices[i].start = self->dimensions[i];
if (indices[i].stop > self->dimensions[i])
indices[i].stop = self->dimensions[i];
}
if (indices[i].item == 0) {
dims[d] = (indices[i].stop-indices[i].start-1)/indices[i].stride+1;
if (dims[d] < 0)
dims[d] = 0;
nitems *= dims[d];
d++;
}
else
indices[i].stop = indices[i].start + 1;
}
if (error) {
PyErr_SetString(PyExc_IndexError, "illegal index");
free(dims);
free(indices);
return -1;
}
array = (PyArrayObject *)PyArray_ContiguousFromObject(value, self->type,
0, d);
if (array != NULL) {
if (self->nd == 0) {
size_t zero = 0;
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
error = nc_put_var1_any(self->file->id, self->id,
netcdf_type_from_type(self->type), &zero,
array->data);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (error != NC_NOERR) {
netcdf_signalerror(ret);
ret = -1;
}
}
else {
size_t *start;
size_t *count, *count1;
ptrdiff_t *stride;
size_t *current;
char *loop;
long repeat = 1;
int lastloop = 0;
start = (size_t *)malloc(self->nd*sizeof(size_t));
count = (size_t *)malloc(self->nd*sizeof(size_t));
count1 = (size_t *)malloc(self->nd*sizeof(size_t));
stride = (ptrdiff_t *)malloc(self->nd*sizeof(ptrdiff_t));
current = (size_t *)malloc(self->nd*sizeof(size_t));
loop = (char *)malloc(self->nd*sizeof(char));
if (start != NULL && count != NULL && count1 != NULL
&& stride != NULL && current != NULL && loop != NULL) {
for (i = 0; i < self->nd; i++) {
start[i] = indices[i].start;
stride[i] = indices[i].stride;
count[i] = (indices[i].stop-indices[i].start-1)/indices[i].stride+1;
count1[i] = count[i];
current[i] = 0;
loop[i] = 0;
}
for (i = array->nd-1, j = self->nd-1; i >= 0 && j >= 0; i--, j--) {
while (j >= 0 && indices[j].item)
j--;
if (j < 0) {
ret = -1;
break;
}
if (array->dimensions[i] != count[j]) {
if (self->unlimited && j == 0
&& indices[j].stop == self->dimensions[j]
&& array->dimensions[i] > count[j]) {
count[j] = array->dimensions[i];
count1[j] = array->dimensions[i];
}
else
ret = -1;
}
}
if (i == -1) {
lastloop = -1;
while (j >= 0) {
loop[j] = !indices[j].item;
if (loop[j]) {
if (lastloop < 0)
lastloop = j;
repeat *= count[j];
count1[j] = 1;
}
j--;
}
}
else
ret = -1;
if (ret == -1)
PyErr_SetString(PyExc_ValueError, "shapes are not aligned");
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
error = NC_NOERR;
while (repeat--) {
error = nc_put_vars_any(self->file->id, self->id,
netcdf_type_from_type(self->type),
start, count1, stride, array->data);
if (error != NC_NOERR)
break;
if (lastloop >= 0) {
for (i = lastloop; i >= 0; i--) {
while (!loop[i] && i >= 0)
i--;
if (i >= 0) {
start[i] += stride[i];
if (++current[i] != count[i])
break;
start[i] -= count[i]*stride[i];
current[i] = 0;
}
}
}
}
if (self->unlimited)
error = nc_inq_dimlen(self->file->id, self->dimids[0],
&self->dimensions[0]);
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (error != NC_NOERR) {
netcdf_signalerror(error);
ret = -1;
}
}
if (start != NULL)
free(start);
if (count != NULL)
free(count);
if (count1 != NULL)
free(count1);
if (stride != NULL)
free(stride);
if (current != NULL)
free(current);
if (loop != NULL)
free(loop);
}
Py_DECREF(array);
free(dims);
free(indices);
return ret;
}
else {
free(dims);
free(indices);
return -1;
}
}
static int
PyNetCDFVariable_WriteString(PyNetCDFVariableObject *self,
PyStringObject *value)
{
if (self->type != PyArray_CHAR || self->nd != 1) {
PyErr_SetString(PyExc_IOError, "netcdf: not a string variable");
return -1;
}
if (PyString_Size((PyObject *)value) > self->dimensions[0]) {
PyErr_SetString(PyExc_ValueError, "string too long");
return -1;
}
if (check_if_open(self->file, 1)) {
int ret;
define_mode(self->file, 0);
Py_BEGIN_ALLOW_THREADS;
acquire_netCDF_lock();
ret = nc_put_var_text(self->file->id, self->id,
PyString_AsString((PyObject *)value));
release_netCDF_lock();
Py_END_ALLOW_THREADS;
if (ret != NC_NOERR) {
netcdf_signalerror(ret);
return -1;
}
return 0;
}
else
return -1;
}
static PyObject *
PyNetCDFVariableObject_item(PyNetCDFVariableObject *self, Py_ssize_t i)
{
PyNetCDFIndex *indices;
if (self->nd == 0) {
PyErr_SetString(PyExc_TypeError, "Not a sequence");
return NULL;
}
indices = PyNetCDFVariable_Indices(self);
if (indices != NULL) {
indices[0].start = i;
indices[0].stop = i+1;
indices[0].item = 1;
return PyArray_Return(PyNetCDFVariable_ReadAsArray(self, indices));
}
return NULL;
}
static PyObject *
PyNetCDFVariableObject_slice(PyNetCDFVariableObject *self,
Py_ssize_t low, Py_ssize_t high)
{
PyNetCDFIndex *indices;
if (self->nd == 0) {
PyErr_SetString(PyExc_TypeError, "Not a sequence");
return NULL;
}
indices = PyNetCDFVariable_Indices(self);
if (indices != NULL) {
indices[0].start = low;
indices[0].stop = high;
return PyArray_Return(PyNetCDFVariable_ReadAsArray(self, indices));
}
return NULL;
}
static PyObject *
PyNetCDFVariableObject_subscript(PyNetCDFVariableObject *self, PyObject *index)
{
PyNetCDFIndex *indices;
if (PyInt_Check(index)) {
int i = PyInt_AsLong(index);
return PyNetCDFVariableObject_item(self, i);
}
if (self->nd == 0) {
PyErr_SetString(PyExc_TypeError, "Not a sequence");
return NULL;
}
indices = PyNetCDFVariable_Indices(self);
if (indices != NULL) {
if (PySlice_Check(index)) {
PySlice_GetIndices((PySliceObject *)index,
(Py_ssize_t)self->dimensions[0],
&indices->start, &indices->stop, &indices->stride);
return PyArray_Return(PyNetCDFVariable_ReadAsArray(self, indices));
}
if (PyTuple_Check(index)) {
int ni;
Py_ssize_t len_dim = PyTuple_Size(index);
if (len_dim > INT_MAX) {
PyErr_SetString(PyExc_ValueError, "too many dimensions");
return NULL;
}
ni = (int)len_dim;
if (ni <= self->nd) {
int i, d;
d = 0;
for (i = 0; i < ni; i++) {
PyObject *subscript = PyTuple_GetItem(index, (Py_ssize_t)i);
if (PyInt_Check(subscript)) {
int n = PyInt_AsLong(subscript);
indices[d].start = n;
indices[d].stop = n+1;
indices[d].item = 1;
d++;
}
else if (PySlice_Check(subscript)) {
PySlice_GetIndices((PySliceObject *)subscript, self->dimensions[d],
&indices[d].start, &indices[d].stop,
&indices[d].stride);
d++;
}
else if (subscript == Py_Ellipsis) {
d = self->nd - ni + i + 1;
}
else {
PyErr_SetString(PyExc_TypeError, "illegal subscript type");
free(indices);
return NULL;
}
}
return PyArray_Return(PyNetCDFVariable_ReadAsArray(self, indices));
}
else {
PyErr_SetString(PyExc_IndexError, "too many subscripts");
free(indices);
return NULL;
}
}
PyErr_SetString(PyExc_TypeError, "illegal subscript type");
free(indices);
}
return NULL;
}
static int
PyNetCDFVariableObject_ass_item(PyNetCDFVariableObject *self,
Py_ssize_t i, PyObject *value)
{
PyNetCDFIndex *indices;
if (value == NULL) {
PyErr_SetString(PyExc_ValueError, "Can't delete elements.");
return -1;
}
if (self->nd == 0) {
PyErr_SetString(PyExc_TypeError, "Not a sequence");
return -1;
}
indices = PyNetCDFVariable_Indices(self);
if (indices != NULL) {
indices[0].start = i;
indices[0].stop = i+1;
indices[0].item = 1;
return PyNetCDFVariable_WriteArray(self, indices, value);
}
return -1;
}
static int
PyNetCDFVariableObject_ass_slice(PyNetCDFVariableObject *self,
Py_ssize_t low, Py_ssize_t high,
PyObject *value)
{
PyNetCDFIndex *indices;
if (value == NULL) {
PyErr_SetString(PyExc_ValueError, "Can't delete elements.");
return -1;
}
if (self->nd == 0) {
PyErr_SetString(PyExc_TypeError, "Not a sequence");
return -1;
}
if (low < -(long)self->dimensions[0])
low = -self->dimensions[0];
if (low < 0)
low += self->dimensions[0];
if (high < low)
high = low;
if (self->unlimited && self->dimids[0] == self->file->recdim) {
if (high > self->dimensions[0])
high = self->dimensions[0];
}
indices = PyNetCDFVariable_Indices(self);
if (indices != NULL) {
indices[0].start = low;
indices[0].stop = high;
return PyNetCDFVariable_WriteArray(self, indices, value);
}
return -1;
}
static int
PyNetCDFVariableObject_ass_subscript(PyNetCDFVariableObject *self,
PyObject *index, PyObject *value)
{
PyNetCDFIndex *indices;
if (PyInt_Check(index)) {
int i = PyInt_AsLong(index);
return PyNetCDFVariableObject_ass_item(self, i, value);
}
if (value == NULL) {
PyErr_SetString(PyExc_ValueError, "Can't delete elements.");
return -1;
}
if (self->nd == 0) {
PyErr_SetString(PyExc_TypeError, "Not a sequence");
return -1;
}
indices = PyNetCDFVariable_Indices(self);
if (indices != NULL) {
if (PySlice_Check(index)) {
PySlice_GetIndices((PySliceObject *)index, self->dimensions[0],
&indices->start, &indices->stop, &indices->stride);
return PyNetCDFVariable_WriteArray(self, indices, value);
}
if (PyTuple_Check(index)) {
int ni;
Py_ssize_t len_dim = PyTuple_Size(index);
if (len_dim > INT_MAX) {
PyErr_SetString(PyExc_ValueError, "too many dimensions");
return -1;
}
ni = (int)len_dim;
if (ni <= self->nd) {
int i, d;
d = 0;
for (i = 0; i < ni; i++) {
PyObject *subscript = PyTuple_GetItem(index, (Py_ssize_t)i);
if (PyInt_Check(subscript)) {
int n = PyInt_AsLong(subscript);
indices[d].start = n;
indices[d].stop = n+1;
indices[d].item = 1;
d++;
}
else if (PySlice_Check(subscript)) {
PySlice_GetIndices((PySliceObject *)subscript, self->dimensions[d],
&indices[d].start, &indices[d].stop,
&indices[d].stride);
d++;
}
else if (subscript == Py_Ellipsis) {
d = self->nd - ni + i + 1;
}
else {
PyErr_SetString(PyExc_TypeError, "illegal subscript type");
free(indices);
return -1;
}
}
return PyNetCDFVariable_WriteArray(self, indices, value);
}
else {
PyErr_SetString(PyExc_IndexError, "too many subscripts");
free(indices);
return -1;
}
}
PyErr_SetString(PyExc_TypeError, "illegal subscript type");
free(indices);
}
return -1;
}
/* Type definition */
static PyObject *
PyNetCDFVariableObject_error1(PyNetCDFVariableObject *self,
PyNetCDFVariableObject *other)
{
PyErr_SetString(PyExc_TypeError, "can't add netCDF variables");
return NULL;
}
static PyObject *
PyNetCDFVariableObject_error2(PyNetCDFVariableObject *self, Py_ssize_t n)
{
PyErr_SetString(PyExc_TypeError, "can't multiply netCDF variables");
return NULL;
}
static PySequenceMethods PyNetCDFVariableObject_as_sequence = {
(lenfunc)PyNetCDFVariableObject_length, /*sq_length*/
(binaryfunc)PyNetCDFVariableObject_error1, /*nb_add*/
(ssizeargfunc)PyNetCDFVariableObject_error2, /*nb_multiply*/
(ssizeargfunc)PyNetCDFVariableObject_item, /*sq_item*/
(ssizessizeargfunc)PyNetCDFVariableObject_slice, /*sq_slice*/
(ssizeobjargproc)PyNetCDFVariableObject_ass_item, /*sq_ass_item*/
(ssizessizeobjargproc)PyNetCDFVariableObject_ass_slice, /*sq_ass_slice*/
};
static PyMappingMethods PyNetCDFVariableObject_as_mapping = {
(lenfunc)PyNetCDFVariableObject_length, /*mp_length*/
(binaryfunc)PyNetCDFVariableObject_subscript, /*mp_subscript*/
(objobjargproc)PyNetCDFVariableObject_ass_subscript, /*mp_ass_subscript*/
};
statichere PyTypeObject PyNetCDFVariable_Type = {
PyObject_HEAD_INIT(NULL)
0, /*ob_size*/
"NetCDFVariable", /*tp_name*/
sizeof(PyNetCDFVariableObject), /*tp_basicsize*/
0, /*tp_itemsize*/
/* methods */
(destructor)PyNetCDFVariableObject_dealloc, /*tp_dealloc*/
0, /*tp_print*/
(getattrfunc)PyNetCDFVariable_GetAttribute, /*tp_getattr*/
(setattrfunc)PyNetCDFVariable_SetAttribute, /*tp_setattr*/
0, /*tp_compare*/
0, /*tp_repr*/
0, /*tp_as_number*/
&PyNetCDFVariableObject_as_sequence, /*tp_as_sequence*/
&PyNetCDFVariableObject_as_mapping, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
0, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT, /*tp_flags*/
"NetCDF Variable", /* tp_doc */
};
/* Table of functions defined in the module */
static PyMethodDef netcdf_methods[] = {
{NULL, NULL} /* sentinel */
};
/* Module initialization */
DL_EXPORT(void)
initScientific_netcdf(void)
{
PyObject *m;
static void *PyNetCDF_API[PyNetCDF_API_pointers];
/* Initialize netcdf variables */
ncopts = 0;
/* Initialize type objects */
PyNetCDFFile_Type.tp_new = PyType_GenericNew;
if (PyType_Ready(&PyNetCDFFile_Type) < 0)
return;
PyNetCDFVariable_Type.tp_new = PyType_GenericNew;
if (PyType_Ready(&PyNetCDFVariable_Type) < 0)
return;
/* Create netCDF lock */
#ifdef WITH_THREAD
netCDF_lock = PyThread_allocate_lock();
#endif
/* Create the module and add the functions */
m = Py_InitModule("Scientific_netcdf", netcdf_methods);
/* Import the array module */
import_array();
/* Initialize C API pointer array and store in module */
PyNetCDF_API[PyNetCDFFile_Type_NUM] = (void *)&PyNetCDFFile_Type;
PyNetCDF_API[PyNetCDFVariable_Type_NUM] = (void *)&PyNetCDFVariable_Type;
PyNetCDF_API[PyNetCDFFile_Open_NUM] = (void *)&PyNetCDFFile_Open;
PyNetCDF_API[PyNetCDFFile_Close_NUM] = (void *)&PyNetCDFFile_Close;
PyNetCDF_API[PyNetCDFFile_Sync_NUM] = (void *)&PyNetCDFFile_Sync;
PyNetCDF_API[PyNetCDFFile_CreateDimension_NUM] =
(void *)&PyNetCDFFile_CreateDimension;
PyNetCDF_API[PyNetCDFFile_CreateVariable_NUM] =
(void *)&PyNetCDFFile_CreateVariable;
PyNetCDF_API[PyNetCDFFile_GetVariable_NUM] =
(void *)&PyNetCDFFile_GetVariable;
PyNetCDF_API[PyNetCDFVariable_GetRank_NUM] =
(void *)&PyNetCDFVariable_GetRank;
PyNetCDF_API[PyNetCDFVariable_GetShape_NUM] =
(void *)&PyNetCDFVariable_GetShape;
PyNetCDF_API[PyNetCDFVariable_Indices_NUM] =
(void *)&PyNetCDFVariable_Indices;
PyNetCDF_API[PyNetCDFVariable_ReadAsArray_NUM] =
(void *)&PyNetCDFVariable_ReadAsArray;
PyNetCDF_API[PyNetCDFVariable_ReadAsString_NUM] =
(void *)&PyNetCDFVariable_ReadAsString;
PyNetCDF_API[PyNetCDFVariable_WriteArray_NUM] =
(void *)&PyNetCDFVariable_WriteArray;
PyNetCDF_API[PyNetCDFVariable_WriteString_NUM] =
(void *)&PyNetCDFVariable_WriteString;
PyNetCDF_API[PyNetCDFFile_GetAttribute_NUM] =
(void *)&PyNetCDFFile_GetAttribute;
PyNetCDF_API[PyNetCDFFile_SetAttribute_NUM] =
(void *)&PyNetCDFFile_SetAttribute;
PyNetCDF_API[PyNetCDFFile_SetAttributeString_NUM] =
(void *)&PyNetCDFFile_SetAttributeString;
PyNetCDF_API[PyNetCDFVariable_GetAttribute_NUM] =
(void *)&PyNetCDFVariable_GetAttribute;
PyNetCDF_API[PyNetCDFVariable_SetAttribute_NUM] =
(void *)&PyNetCDFVariable_SetAttribute;
PyNetCDF_API[PyNetCDFVariable_SetAttributeString_NUM] =
(void *)&PyNetCDFVariable_SetAttributeString;
PyNetCDF_API[PyNetCDFFile_AddHistoryLine_NUM] =
(void *)&PyNetCDFFile_AddHistoryLine;
PyModule_AddObject(m, "_C_API",
PyCObject_FromVoidPtr((void *)PyNetCDF_API, NULL));
/* Add the netCDF file type object */
Py_INCREF(&PyNetCDFFile_Type);
PyModule_AddObject(m, "NetCDFFile", (PyObject *)&PyNetCDFFile_Type);
/* Check for errors */
if (PyErr_Occurred())
Py_FatalError("can't initialize module Scientific_netcdf");
}
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