C_arraytest.c

/* A file to test imorting C modules for handling arrays to Python */

#include "Python.h"
#include "numpy/arrayobject.h"
#include "C_arraytest.h"
#include <math.h>

/* #### Globals #################################### */

/* ==== Set up the methods table ====================== */
static PyMethodDef _C_arraytestMethods[] = {
	{"vecfcn1", vecfcn1, METH_VARARGS},
	{"vecsq", vecsq, METH_VARARGS},
	{"rowx2", rowx2, METH_VARARGS},
	{"rowx2_v2", rowx2, METH_VARARGS},
	{"matsq", matsq, METH_VARARGS},
	{"contigmat", contigmat, METH_VARARGS},
	{"intfcn1", intfcn1, METH_VARARGS},
	{NULL, NULL}     /* Sentinel - marks the end of this structure */
};

/* ==== Initialize the C_test functions ====================== */
// Module name must be _C_arraytest in compile and linked 
void init_C_arraytest()  {
	(void) Py_InitModule("_C_arraytest", _C_arraytestMethods);
	import_array();  // Must be present for NumPy.  Called first after above line.
}

/* #### Vector Extensions ############################## */

/* ==== vector function - manipulate vector in place ======================
    Multiply the input by 2 x dfac and put in output
    Interface:  vecfcn1(vec1, vec2, str1, d1)
                vec1, vec2 are NumPy vectors, 
                str1 is Python string, d1 is Python float (double)
                Returns integer 1 if successful                */
static PyObject *vecfcn1(PyObject *self, PyObject *args)
{
	PyArrayObject *vecin, *vecout;  // The python objects to be extracted from the args
	double *cin, *cout;             // The C vectors to be created to point to the 
	                                //   python vectors, cin and cout point to the row
	                                //   of vecin and vecout, respectively
	int i,j,n;
	const char *str;
	double dfac;
	
	/* Parse tuples separately since args will differ between C fcns */
	if (!PyArg_ParseTuple(args, "O!O!sd", &PyArray_Type, &vecin,
		&PyArray_Type, &vecout, &str, &dfac))  return NULL;
	if (NULL == vecin)  return NULL;
	if (NULL == vecout)  return NULL;
	
	// Print out input string
	printf("Input string: %s\n", str);
	
	/* Check that objects are 'double' type and vectors
	     Not needed if python wrapper function checks before call to this routine */
	if (not_doublevector(vecin)) return NULL;
	if (not_doublevector(vecout)) return NULL;
	
	/* Change contiguous arrays into C * arrays   */
	cin=pyvector_to_Carrayptrs(vecin);
	cout=pyvector_to_Carrayptrs(vecout);
	
	/* Get vector dimension. */
	n=vecin->dimensions[0];
	
	/* Operate on the vectors  */
	for ( i=0; i<n; i++)  {
			cout[i]=2.0*dfac*cin[i];
	}
		
	return Py_BuildValue("i", 1);
}

/* ==== Square vector components & multiply by a float =========================
    Returns a NEW  NumPy vector array
    interface:  vecsq(vec1, x1)
                vec1 is NumPy vector, x1 is Python float (double)
                returns a NumPy vector                                        */
static PyObject *vecsq(PyObject *self, PyObject *args)  {
	PyArrayObject *vecin, *vecout;
	double *cin, *cout, dfactor;   // The C vectors to be created to point to the 
	                               //   python vectors, cin and cout point to the row
	                               //   of vecin and vecout, respectively
	int i,j,n,m, dims[2];
	
	/* Parse tuples separately since args will differ between C fcns */
	if (!PyArg_ParseTuple(args, "O!d", 
		&PyArray_Type, &vecin, &dfactor))  return NULL;
	if (NULL == vecin)  return NULL;
	
	/* Check that object input is 'double' type and a vector
	   Not needed if python wrapper function checks before call to this routine */
	if (not_doublevector(vecin)) return NULL;
	
	/* Get the dimension of the input */
	n=dims[0]=vecin->dimensions[0];
	
	/* Make a new double vector of same dimension */
	vecout=(PyArrayObject *) PyArray_FromDims(1,dims,NPY_DOUBLE);
		
	/* Change contiguous arrays into C *arrays   */
	cin=pyvector_to_Carrayptrs(vecin);
	cout=pyvector_to_Carrayptrs(vecout);
	
	/* Do the calculation. */
	for ( i=0; i<n; i++)  {
			cout[i]= dfactor*cin[i]*cin[i];
	}
		
	return PyArray_Return(vecout);
}

/* #### Vector Utility functions ######################### */

/* ==== Make a Python Array Obj. from a PyObject, ================
     generates a double vector w/ contiguous memory which may be a new allocation if
     the original was not a double type or contiguous 
  !! Must DECREF the object returned from this routine unless it is returned to the
     caller of this routines caller using return PyArray_Return(obj) or
     PyArray_BuildValue with the "N" construct   !!!
*/
PyArrayObject *pyvector(PyObject *objin)  {
	return (PyArrayObject *) PyArray_ContiguousFromObject(objin,
		NPY_DOUBLE, 1,1);
}
/* ==== Create 1D Carray from PyArray ======================
    Assumes PyArray is contiguous in memory.             */
double *pyvector_to_Carrayptrs(PyArrayObject *arrayin)  {
	int i,n;
	
	n=arrayin->dimensions[0];
	return (double *) arrayin->data;  /* pointer to arrayin data as double */
}
/* ==== Check that PyArrayObject is a double (Float) type and a vector ==============
    return 1 if an error and raise exception */ 
int  not_doublevector(PyArrayObject *vec)  {
	if (vec->descr->type_num != NPY_DOUBLE || vec->nd != 1)  {
		PyErr_SetString(PyExc_ValueError,
			"In not_doublevector: array must be of type Float and 1 dimensional (n).");
		return 1;  }
	return 0;
}

/* #### Matrix Extensions ############################## */

/* ==== Row x 2 function - manipulate matrix in place ======================
    Multiply the 2nd row of the input by 2 and put in output
    interface:  rowx2(mat1, mat2)
                mat1 and mat2 are NumPy matrices
                Returns integer 1 if successful                        */
static PyObject *rowx2(PyObject *self, PyObject *args)
{
	PyArrayObject *matin, *matout;  // The python objects to be extracted from the args
	double **cin, **cout;           // The C matrices to be created to point to the 
	                                //   python matrices, cin and cout point to the rows
	                                //   of matin and matout, respectively
	int i,j,n,m;
	
	/* Parse tuples separately since args will differ between C fcns */
	if (!PyArg_ParseTuple(args, "O!O!", &PyArray_Type, &matin,
		&PyArray_Type, &matout))  return NULL;
	if (NULL == matin)  return NULL;
	if (NULL == matout)  return NULL;
	
	/* Check that objects are 'double' type and matrices
	     Not needed if python wrapper function checks before call to this routine */
	if (not_doublematrix(matin)) return NULL;
	if (not_doublematrix(matout)) return NULL;
		
	/* Change contiguous arrays into C ** arrays (Memory is Allocated!) */
	cin=pymatrix_to_Carrayptrs(matin);
	cout=pymatrix_to_Carrayptrs(matout);
	
	/* Get matrix dimensions. */
	n=matin->dimensions[0];
	m=matin->dimensions[1];
	
	/* Operate on the matrices  */
	for ( i=0; i<n; i++)  {
		for ( j=0; j<m; j++)  {
			if (i==1) cout[i][j]=2.0*cin[i][j];
	}  }
		
	/* Free memory, close file and return */
	free_Carrayptrs(cin);
	free_Carrayptrs(cout);
	return Py_BuildValue("i", 1);
}
/* ==== Row x 2 function- Version 2. - manipulate matrix in place ======================
    Multiply the 2nd row of the input by 2 and put in output
    interface:  rowx2(mat1, mat2)
                mat1 and mat2 are NumPy matrices
                Returns integer 1 if successful
    Uses the utility function pymatrix to make NumPy C objects from PyObjects
*/
static PyObject *rowx2_v2(PyObject *self, PyObject *args)
{
	PyObject *Pymatin, *Pymatout;   // The python objects to be extracted from the args
	PyArrayObject *matin, *matout;  // The python array objects to be extracted from python objects
	double **cin, **cout;           // The C matrices to be created to point to the 
	                                //   python matrices, cin and cout point to the rows
	                                //   of matin and matout, respectively
	int i,j,n,m;
	
	/* Parse tuples separately since args will differ between C fcns */
	if (!PyArg_ParseTuple(args, "OO", &Pymatin, &Pymatout))  return NULL;
	if (NULL == Pymatin)  return NULL;
	if (NULL == Pymatout)  return NULL;
	
	/* Convert Python Objects to Python Array Objects */
	matin= pymatrix(Pymatin);
	matout= pymatrix(Pymatout);
	
	/* Check that objects are 'double' type and matrices
	     Not needed if python wrapper function checks before call to this routine */
	if (not_doublematrix(matin)) return NULL;
	if (not_doublematrix(matout)) return NULL;
		
	/* Change contiguous arrays into C ** arrays (Memory is Allocated!) */
	cin=pymatrix_to_Carrayptrs(matin);
	cout=pymatrix_to_Carrayptrs(matout);
	
	/* Get matrix dimensions. */
	n=matin->dimensions[0];
	m=matin->dimensions[1];
	
	/* Operate on the matrices  */
	for ( i=0; i<n; i++)  {
		for ( j=0; j<m; j++)  {
			if (i==1) cout[i][j]=2.0*cin[i][j];
	}  }
	
	/* Free memory, close file and return */
	free_Carrayptrs(cin);
	free_Carrayptrs(cout);
	return Py_BuildValue("i", 1);
}
/* ==== Square matrix components function & multiply by int and float =========
    Returns a NEW NumPy array
    interface:  matsq(mat1, i1, d1)
                mat1 is NumPy matrix, i1 is Python integer, d1 is Python float (double)
                returns a NumPy matrix                                        */
static PyObject *matsq(PyObject *self, PyObject *args)
{
	PyArrayObject *matin, *matout;
	double **cin, **cout, dfactor;
	int i,j,n,m, dims[2], ifactor;
	
	/* Parse tuples separately since args will differ between C fcns */
	if (!PyArg_ParseTuple(args, "O!id", 
		&PyArray_Type, &matin, &ifactor, &dfactor))  return NULL;
	if (NULL == matin)  return NULL;
	
	/* Check that object input is 'double' type and a matrix
	   Not needed if python wrapper function checks before call to this routine */
	if (not_doublematrix(matin)) return NULL;
	
	/* Get the dimensions of the input */
	n=dims[0]=matin->dimensions[0];
	m=dims[1]=matin->dimensions[1];
	
	/* Make a new double matrix of same dims */
	matout=(PyArrayObject *) PyArray_FromDims(2,dims,NPY_DOUBLE);
		
	/* Change contiguous arrays into C ** arrays (Memory is Allocated!) */
	cin=pymatrix_to_Carrayptrs(matin);
	cout=pymatrix_to_Carrayptrs(matout);
	
	/* Do the calculation. */
	for ( i=0; i<n; i++)  {
		for ( j=0; j<m; j++)  {
			cout[i][j]= ifactor*dfactor*cin[i][j]*cin[i][j];
	}  }
		
	/* Free memory, close file and return */
	free_Carrayptrs(cin);
	free_Carrayptrs(cout);
	return PyArray_Return(matout);
}

/* ==== Operate on Matrix components as contiguous memory =========================
  Shows how to access the array data as a contiguous block of memory. Used, for example,
  in matrix classes implemented as contiquous memory rather than as n arrays of 
  pointers to the data "rows"
  
    Returns a NEW NumPy array
    interface:  contigmat(mat1, x1)
                mat1 is NumPy matrix, x1 is Python float (double)
                returns a NumPy matrix                                        */
static PyObject *contigmat(PyObject *self, PyObject *args)
{
	PyArrayObject *matin, *matout;
	double *cin, *cout, x1;     // Pointers to the contiguous data in the matrices to
	                            // be used by C (e.g. passed to a program that uses
	                            // matrix classes implemented as contiquous memory rather
	                            // than as n arrays of pointers to the data "rows"
	int i,j,n,m, dims[2], ncomps;  // ncomps=n*m=total number of matrix components in mat1
	
	/* Parse tuples separately since args will differ between C fcns */
	if (!PyArg_ParseTuple(args, "O!d", 
		&PyArray_Type, &matin, &x1))  return NULL;
	if (NULL == matin)  return NULL;
	
	/* Check that object input is 'double' type and a matrix
	   Not needed if python wrapper function checks before call to this routine */
	if (not_doublematrix(matin)) return NULL;
	
	/* Get the dimensions of the input */
	n=dims[0]=matin->dimensions[0];
	m=dims[1]=matin->dimensions[1];
	ncomps=n*m;
	
	/* Make a new double matrix of same dims */
	matout=(PyArrayObject *) PyArray_FromDims(2,dims,NPY_DOUBLE);
		
	/* Change contiguous arrays into C * arrays pointers to PyArrayObject data */
	cin=pyvector_to_Carrayptrs(matin);
	cout=pyvector_to_Carrayptrs(matout);
	
	/* Do the calculation. */
	printf("In contigmat, cout (as contiguous memory) =\n");
	for ( i=0; i<ncomps; i++)  {
		cout[i]= cin[i]-x1;
		printf("%e ",cout[i]);
	}
	printf("\n");
		
	return PyArray_Return(matout);
}

/* #### Matrix Utility functions ######################### */

/* ==== Make a Python Array Obj. from a PyObject, ================
     generates a double matrix w/ contiguous memory which may be a new allocation if
     the original was not a double type or contiguous 
  !! Must DECREF the object returned from this routine unless it is returned to the
     caller of this routines caller using return PyArray_Return(obj) or
     PyArray_BuildValue with the "N" construct   !!!
*/
PyArrayObject *pymatrix(PyObject *objin)  {
	return (PyArrayObject *) PyArray_ContiguousFromObject(objin,
		NPY_DOUBLE, 2,2);
}
/* ==== Create Carray from PyArray ======================
    Assumes PyArray is contiguous in memory.
    Memory is allocated!                                    */
double **pymatrix_to_Carrayptrs(PyArrayObject *arrayin)  {
	double **c, *a;
	int i,n,m;
	
	n=arrayin->dimensions[0];
	m=arrayin->dimensions[1];
	c=ptrvector(n);
	a=(double *) arrayin->data;  /* pointer to arrayin data as double */
	for ( i=0; i<n; i++)  {
		c[i]=a+i*m;  }
	return c;
}
/* ==== Allocate a double *vector (vec of pointers) ======================
    Memory is Allocated!  See void free_Carray(double ** )                  */
double **ptrvector(long n)  {
	double **v;
	v=(double **)malloc((size_t) (n*sizeof(double)));
	if (!v)   {
		printf("In **ptrvector. Allocation of memory for double array failed.");
		exit(0);  }
	return v;
}
/* ==== Free a double *vector (vec of pointers) ========================== */ 
void free_Carrayptrs(double **v)  {
	free((char*) v);
}
/* ==== Check that PyArrayObject is a double (Float) type and a matrix ==============
    return 1 if an error and raise exception */ 
int  not_doublematrix(PyArrayObject *mat)  {
	if (mat->descr->type_num != NPY_DOUBLE || mat->nd != 2)  {
		PyErr_SetString(PyExc_ValueError,
			"In not_doublematrix: array must be of type Float and 2 dimensional (n x m).");
		return 1;  }
	return 0;
}

/* #### Integer 2D Array Extensions ############################## */

/* ==== Integer function - manipulate integer 2D array in place ======================
    Replace >=0 integer with 1 and < 0 integer with 0 and put in output
    interface:  intfcn1(int1, afloat)
                int1 is a NumPy integer 2D array, afloat is a Python float
                Returns integer 1 if successful                        */
static PyObject *intfcn1(PyObject *self, PyObject *args)
{
	PyArrayObject *intin, *intout;  // The python objects to be extracted from the args
	int **cin, **cout;              // The C integer 2D arrays to be created to point to the 
	                                //   python integer 2D arrays, cin and cout point to the rows
	                                //   of intin and intout, respectively
	int i,j,n,m, dims[2];
	double afloat;
	
	/* Parse tuples separately since args will differ between C fcns */
	if (!PyArg_ParseTuple(args, "O!d", 
		&PyArray_Type, &intin, &afloat))  return NULL;
	if (NULL == intin)  return NULL;
	
	printf("In intfcn1, the input Python float = %e, a C double\n",afloat);
	
	/* Check that object input is int type and a 2D array
	   Not needed if python wrapper function checks before call to this routine */
	if (not_int2Darray(intin)) return NULL;
	
	/* Get the dimensions of the input */
	n=dims[0]=intin->dimensions[0];
	m=dims[1]=intin->dimensions[1];
	
	/* Make a new int array of same dims */
	intout=(PyArrayObject *) PyArray_FromDims(2,dims,NPY_LONG);
		
	/* Change contiguous arrays into C ** arrays (Memory is Allocated!) */
	cin=pyint2Darray_to_Carrayptrs(intin);
	cout=pyint2Darray_to_Carrayptrs(intout);
	
	/* Do the calculation. */
	for ( i=0; i<n; i++)  {
		for ( j=0; j<m; j++)  {
			if (cin[i][j] >= 0)  {
				cout[i][j]= 1;  }
			else  {
				cout[i][j]= 0;  }
	}  }
	
	printf("In intfcn1, the output array is,\n\n");

	for ( i=0; i<n; i++)  {
		for ( j=0; j<m; j++)  {
			printf("%d ",cout[i][j]);
		}
		printf("\n");
	}
	printf("\n");
		
	/* Free memory, close file and return */
	free_Cint2Darrayptrs(cin);
	free_Cint2Darrayptrs(cout);
	return PyArray_Return(intout);
}
/* #### Integer Array Utility functions ######################### */

/* ==== Make a Python int Array Obj. from a PyObject, ================
     generates a 2D integer array w/ contiguous memory which may be a new allocation if
     the original was not an integer type or contiguous 
  !! Must DECREF the object returned from this routine unless it is returned to the
     caller of this routines caller using return PyArray_Return(obj) or
     PyArray_BuildValue with the "N" construct   !!!
*/
PyArrayObject *pyint2Darray(PyObject *objin)  {
	return (PyArrayObject *) PyArray_ContiguousFromObject(objin,
		NPY_LONG, 2,2);
}
/* ==== Create integer 2D Carray from PyArray ======================
    Assumes PyArray is contiguous in memory.
    Memory is allocated!                                    */
int **pyint2Darray_to_Carrayptrs(PyArrayObject *arrayin)  {
	int **c, *a;
	int i,n,m;
	
	n=arrayin->dimensions[0];
	m=arrayin->dimensions[1];
	c=ptrintvector(n);
	a=(int *) arrayin->data;  /* pointer to arrayin data as int */
	for ( i=0; i<n; i++)  {
		c[i]=a+i*m;  }
	return c;
}
/* ==== Allocate a a *int (vec of pointers) ======================
    Memory is Allocated!  See void free_Carray(int ** )                  */
int **ptrintvector(long n)  {
	int **v;
	v=(int **)malloc((size_t) (n*sizeof(int)));
	if (!v)   {
		printf("In **ptrintvector. Allocation of memory for int array failed.");
		exit(0);  }
	return v;
}
/* ==== Free an int *vector (vec of pointers) ========================== */ 
void free_Cint2Darrayptrs(int **v)  {
	free((char*) v);
}
/* ==== Check that PyArrayObject is an int (integer) type and a 2D array ==============
    return 1 if an error and raise exception
    Note:  Use NY_LONG for NumPy integer array, not NP_INT      */ 
int  not_int2Darray(PyArrayObject *mat)  {
	if (mat->descr->type_num != NPY_LONG || mat->nd != 2)  {
		PyErr_SetString(PyExc_ValueError,
			"In not_int2Darray: array must be of type int and 2 dimensional (n x m).");
		return 1;  }
	return 0;
}







// EOF