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tkf on 09/05/08

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Last Edited at 09/05/08 06:23pm

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Example of Numpy/C API

/ Published in: C

Some macros are from the "Python Scripting for Computational Science" : http://folk.uio.no/hpl/scripting/

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/* dtlsmodule.c */
#include <math.h>
#include <stdio.h>

#include <Python.h>
#include "structmember.h"
#include <numpy/arrayobject.h>

/* ================================================================= MACROS */
#define QUOTE(s) # s   /* turn s into string "s" */
#define NDIM_CHECK(a, expected_ndim, rt_error)				\
  if (PyArray_NDIM(a) != expected_ndim) {				\
    PyErr_Format(PyExc_ValueError,					\
		 "%s array is %d-dimensional, but expected to be %d-dimensional", \
		 QUOTE(a), PyArray_NDIM(a), expected_ndim);		\
    return rt_error;							\
  }
#define DIM_CHECK(a, dim, expected_length, rt_error)			\
  if (dim > PyArray_NDIM(a)) {						\
    PyErr_Format(PyExc_ValueError,					\
		 "%s array has no %d dimension (max dim. is %d)",	\
		 QUOTE(a), dim, PyArray_NDIM(a));			\
    return rt_error;							\
  }									\
  if (PyArray_DIM(a, dim) != expected_length) {				\
    PyErr_Format(PyExc_ValueError,					\
		 "%s array has wrong %d-dimension=%d (expected %d)",	\
		 QUOTE(a), dim, PyArray_DIM(a, dim), expected_length);	\
    return rt_error;							\
  }
#define TYPE_CHECK(a, tp, rt_error)					\
  if (PyArray_TYPE(a) != tp) {						\
    PyErr_Format(PyExc_TypeError,					\
		 "%s array is not of correct type (%d)", QUOTE(a), tp); \
    return rt_error;							\
  }
#define CALLABLE_CHECK(func, rt_error)				\
  if (!PyCallable_Check(func)) {				\
    PyErr_Format(PyExc_TypeError,				\
		 "%s is not a callable function", QUOTE(func)); \
    return rt_error;						\
  }

#define DIND1(a, i) *((double *) PyArray_GETPTR1(a, i))
#define DIND2(a, i, j) *((double *) PyArray_GETPTR2(a, i, j))
#define DIND3(a, i, j, k) *((double *) Py_Array_GETPTR3(a, i, j, k))

#define IIND1(a, i) *((int *) PyArray_GETPTR1(a, i))
#define IIND2(a, i, j) *((int *) PyArray_GETPTR2(a, i, j))
#define IIND3(a, i, j, k) *((int *) Py_Array_GETPTR3(a, i, j, k))

#define DEF_PYARRAY_GETTER(funcname, selftype, valname)	\
  static PyObject *					\
  funcname(selftype *self, void *closure)		\
  {							\
    Py_INCREF(self->valname);				\
    return PyArray_Return(self->valname);		\
  }
#define DEF_PYARRAY_SETTER(funcname, selftype, valname, arraydim)	\
  static int								\
  funcname(selftype *self, PyObject *value, void *closure)		\
  {									\
    if (value == NULL) {						\
      PyErr_SetString( PyExc_TypeError,					\
		       "Cannot delete the last attribute");		\
      return -1;							\
    }									\
    if ( PyArray_Check(value) != 1 ){					\
      PyErr_Format( PyExc_ValueError,					\
		    "value is not of type numpy array");		\
      return -1;							\
    }									\
    if ( PyArray_NDIM(value) != arraydim ){				\
      PyErr_Format( PyExc_ValueError,					\
		    "value array's dimension %d != arraydim",		\
		    PyArray_NDIM(value));				\
      return -1;							\
    }									\
    if ( PyArray_TYPE(value) != NPY_DOUBLE ){				\
      PyErr_Format( PyExc_ValueError,					\
		    "value array is not of type 'Python float'");	\
      return -1;							\
    }									\
    Py_DECREF(self->valname);						\
    Py_INCREF(value);							\
    self->valname = (PyArrayObject *) value;				\
    return 0;								\
  }

/* ========================================================== DTLSys struct */
typedef struct {
  PyObject_HEAD
  PyArrayObject *wt;
  PyArrayObject *bs;
  PyArrayObject *xt;
} DTLSys;

/* ============================================================ Declaration */
static void       DTLSys_dealloc(DTLSys* self);
static PyObject * DTLSys_new(PyTypeObject *type, PyObject *args, PyObject *kwds);
static int        DTLSys_init(DTLSys *self, PyObject *args, PyObject *kwds);

static PyMemberDef DTLSys_members[] = {
    {NULL}  /* Sentinel */
};

static PyObject * DTLSys_get_wt(DTLSys *self,                  void *closure);
static int        DTLSys_set_wt(DTLSys *self, PyObject *value, void *closure);
static PyObject * DTLSys_get_bs(DTLSys *self,                  void *closure);
static int        DTLSys_set_bs(DTLSys *self, PyObject *value, void *closure);
static PyObject * DTLSys_get_xt(DTLSys *self,                  void *closure);
static int        DTLSys_set_xt(DTLSys *self, PyObject *value, void *closure);

static PyGetSetDef DTLSys_getseters[] = {
    {"wt", (getter)DTLSys_get_wt, (setter)DTLSys_set_wt, "Matrix", NULL},
    {"bs", (getter)DTLSys_get_bs, (setter)DTLSys_set_bs, "Vector", NULL},
    {"xt", (getter)DTLSys_get_xt, (setter)DTLSys_set_xt, "Vector time sequence", NULL},
    {NULL}  /* Sentinel */
};

static int       _DTLSys_check_sys_conf(DTLSys *self);
static PyObject * DTLSys_check_sys_conf(DTLSys *self);
static PyObject * DTLSys_make_tms(DTLSys *self, PyObject *args);

static PyMethodDef DTLSys_methods[] = {
  {"check_sys_conf", (PyCFunction)DTLSys_check_sys_conf, METH_NOARGS, "Check if system config is correct"},
  {"make_tms", (PyCFunction)DTLSys_make_tms, METH_VARARGS, "Make TiMe Series"},
  {NULL}  /* Sentinel */
};

static PyTypeObject DTLSysType = {
    PyObject_HEAD_INIT(NULL)
    0,				/*ob_size*/
    "dtls.DTLSys",		/*tp_name*/
    sizeof(DTLSys),             /*tp_basicsize*/
    0,				/*tp_itemsize*/
    (destructor)DTLSys_dealloc, /*tp_dealloc*/
    0,				/*tp_print*/
    0,				/*tp_getattr*/
    0,				/*tp_setattr*/
    0,				/*tp_compare*/
    0,				/*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 | Py_TPFLAGS_BASETYPE,	/*tp_flags*/
    "DTLSys objects",           /* tp_doc */
    0,				/* tp_traverse */
    0,				/* tp_clear */
    0,				/* tp_richcompare */
    0,				/* tp_weaklistoffset */
    0,				/* tp_iter */
    0,				/* tp_iternext */
    DTLSys_methods,             /* tp_methods */
    DTLSys_members,             /* tp_members */
    DTLSys_getseters,           /* tp_getset */
    0,				/* tp_base */
    0,				/* tp_dict */
    0,				/* tp_descr_get */
    0,				/* tp_descr_set */
    0,				/* tp_dictoffset */
    (initproc)DTLSys_init,      /* tp_init */
    0,				/* tp_alloc */
    DTLSys_new,                 /* tp_new */
};

static PyMethodDef module_methods[] = {
    {NULL}  /* Sentinel */
};

#ifndef PyMODINIT_FUNC	/* declarations for DLL import/export */
#define PyMODINIT_FUNC void
#endif
PyMODINIT_FUNC
initdtls(void) 
{
  PyObject* m;
  if (PyType_Ready(&DTLSysType) < 0){ return; }

m = Py_InitModule3("dtls", module_methods,
		     "Example module that creates an extension type.");
  if (m == NULL){ return; }

Py_INCREF(&DTLSysType);
  PyModule_AddObject(m, "DTLSys", (PyObject *)&DTLSysType);
  import_array();   /* required NumPy initialization */
}

/* ================================================================= Define */
static void
DTLSys_dealloc(DTLSys* self)
{
  Py_XDECREF(self->wt);
  Py_XDECREF(self->bs);
  Py_XDECREF(self->xt);
  self->ob_type->tp_free((PyObject*)self);
}

static PyObject *
DTLSys_new(PyTypeObject *type, PyObject *args, PyObject *kwds)
{
  DTLSys *self;
  npy_intp wt_dims[2] = {0,0};
  npy_intp bs_dims[1] = {0};
  npy_intp xt_dims[2] = {0,0};

self = (DTLSys *)type->tp_alloc(type, 0);
  if (self != NULL) {
    self->wt = (PyArrayObject *) PyArray_SimpleNew(2, wt_dims, NPY_DOUBLE);
    if (self->wt == NULL){ Py_DECREF(self); return NULL; }
    self->bs = (PyArrayObject *) PyArray_SimpleNew(1, bs_dims, NPY_DOUBLE);
    if (self->bs == NULL){ Py_DECREF(self); return NULL; }
    self->xt = (PyArrayObject *) PyArray_SimpleNew(2, xt_dims, NPY_DOUBLE);
    if (self->xt == NULL){ Py_DECREF(self); return NULL; }
  }

return (PyObject *)self;
}

static int
DTLSys_init(DTLSys *self, PyObject *args, PyObject *kwds)
{
  PyArrayObject *wt, *bs, *tmp;
  int t_max;
  npy_intp xt_dims[2] = {0,0};

if ( !PyArg_ParseTuple( args, "O!O!i:DTLSys.init",
			  &PyArray_Type, &wt,
			  &PyArray_Type, &bs,
			  &t_max)
       ) {
    return -1; /* PyArg_ParseTuple has raised an exception */
  } 
  if ( wt==NULL || bs==NULL ) {
    printf("getting args failed\n"); return -1;
  }
  if ( t_max < 0 ) {
    printf("t_max (3rd arg) must be positive int\n"); return -1;
  }

xt_dims[0] = PyArray_DIM(wt,0);
  xt_dims[1] = t_max;
  self->xt = (PyArrayObject *) PyArray_SimpleNew(2, xt_dims, NPY_DOUBLE);
  if (self->xt == NULL){ 
    printf("creating %dx%d array failed\n", (int)xt_dims[0], (int)xt_dims[1]);
    return -1;
  }

tmp = self->wt; Py_INCREF(wt); self->wt = wt; Py_DECREF(tmp);
  tmp = self->bs; Py_INCREF(bs); self->bs = bs; Py_DECREF(tmp);

if( _DTLSys_check_sys_conf(self) != 0 ){
    PyErr_Clear();
    printf("DTLSys config is not correct!\n");
  }
  return 0;
}

DEF_PYARRAY_GETTER( DTLSys_get_wt, DTLSys, wt )
DEF_PYARRAY_SETTER( DTLSys_set_wt, DTLSys, wt, 2 )
DEF_PYARRAY_GETTER( DTLSys_get_bs, DTLSys, bs )
DEF_PYARRAY_SETTER( DTLSys_set_bs, DTLSys, bs, 1 )
DEF_PYARRAY_GETTER( DTLSys_get_xt, DTLSys, xt )
DEF_PYARRAY_SETTER( DTLSys_set_xt, DTLSys, xt, 2 )

static int
_DTLSys_check_sys_conf(DTLSys *self)
{
  int vecsize;

NDIM_CHECK(self->wt, 2, -1); TYPE_CHECK(self->wt, NPY_DOUBLE, -1);
  NDIM_CHECK(self->bs, 1, -1); TYPE_CHECK(self->bs, NPY_DOUBLE, -1);

vecsize = PyArray_DIM(self->wt,0);
  if (vecsize != PyArray_DIM(self->wt,1) ) {
    PyErr_Format( PyExc_ValueError, "self.wt must be square");
    return -1;
  }
  if (vecsize != PyArray_DIM(self->bs,0) ) {
    PyErr_Format( PyExc_ValueError, "self.bs and self.wt[0] must be same shape");
    return -1;
  }
  if (vecsize != PyArray_DIM(self->xt,0) ) {
    PyErr_Format( PyExc_ValueError, "self.xt[,0] and self.wt[0] must be same shape");
    return -1;
  }
  return 0;
}

static PyObject *
DTLSys_check_sys_conf(DTLSys *self)
{
  if( _DTLSys_check_sys_conf(self) != 0 ){
    PyErr_Clear();
    Py_RETURN_FALSE;
  }
  Py_RETURN_TRUE;
}

static PyObject *
DTLSys_make_tms(DTLSys *self, PyObject *args)
{
  int vecsize, t_max, i, j, t;
  if( _DTLSys_check_sys_conf(self) != 0 ){
    return NULL;
  }
  vecsize = PyArray_DIM(self->wt,0);
  t_max   = PyArray_DIM(self->xt,1);

for (t = 1; t < t_max; t++) {
    for (i = 0; i < vecsize; i++) {
      DIND2(self->xt,i,t) = DIND1(self->bs,i);
      for (j = 0; j < vecsize; j++) {
	DIND2(self->xt,i,t) += DIND2(self->wt,i,j) * DIND2(self->xt,j,t-1);
      }
    }
  }
  return Py_BuildValue("");  /* return None */
}

/*
# setup.py
# build command : python setup.py build build_ext --inplace
from numpy.distutils.core import setup, Extension
import os, numpy

name = 'dtls'
sources = ['dtlsmodule.c']

include_dirs = [
    numpy.get_include()
    ]

setup( name = name,
       include_dirs = include_dirs,
       ext_modules = [Extension(name, sources)]
       )
*/

/*
# test code
import scipy, pylab
import dtls

t_max = 200
rot = 5.0 * 2.0 * scipy.pi / t_max
wt = scipy.array([
    [  scipy.cos(rot), scipy.sin(rot) ],
    [ -scipy.sin(rot), scipy.cos(rot) ]
    ])
wt *= 0.99
bs = scipy.array([0.,0.])

a=dtls.DTLSys( wt, bs, t_max )
a.xt[0,0] = 0
a.xt[1,0] = 1
a.make_tms()

pylab.clf()
pylab.plot(a.xt[0],a.xt[1], 'o-')

# Check calculation
print (scipy.dot( a.wt, a.xt[:,0] ) + a.bs) - a.xt[:,1]
*/

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