Author: bugman
Date: Fri Feb 25 14:24:59 2011
New Revision: 12625
URL: http://svn.gna.org/viewcvs/relax?rev=12625&view=rev
Log:
Removed numpy from the relaxation curve-fitting C module code.
This now expects Python lists as arguments. This should help with
incompatibilities between
different Python versions, as this seems to be due to the numpy C interface.
See for example
the thread started by Min-Kyu <min-kyu dott cho att vanderbilt dot edu>
https://mail.gna.org/public/relax-users/2011-02/msg00000.html (Message-id:
<001f01cbd24f$350042d0$9f00c870$@cho@vanderbilt.edu>).
Modified:
1.3/maths_fns/exponential.c
1.3/maths_fns/relax_fit.c
1.3/maths_fns/relax_fit.h
Modified: 1.3/maths_fns/exponential.c
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/exponential.c?rev=12625&r1=12624&r2=12625&view=diff
==============================================================================
--- 1.3/maths_fns/exponential.c (original)
+++ 1.3/maths_fns/exponential.c Fri Feb 25 14:24:59 2011
@@ -21,9 +21,6 @@
/* This include must come first */
#include <Python.h>
-
-/* The numpy array object header file, must come second */
-#include <numpy/arrayobject.h>
/* The header for all functions which will be called */
#include "relax_fit.h"
Modified: 1.3/maths_fns/relax_fit.c
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/relax_fit.c?rev=12625&r1=12624&r2=12625&view=diff
==============================================================================
--- 1.3/maths_fns/relax_fit.c (original)
+++ 1.3/maths_fns/relax_fit.c Fri Feb 25 14:24:59 2011
@@ -21,9 +21,6 @@
/* This include must come first */
#include <Python.h>
-/* The numpy array object header file, must come second */
-#include <numpy/arrayobject.h>
-
/* The header for all functions which will be called */
#include "relax_fit.h"
@@ -33,14 +30,15 @@
static PyObject *
setup(PyObject *self, PyObject *args, PyObject *keywords) {
- /* Python declarations */
+ /* Python object declarations */
PyObject *values_arg, *sd_arg, *relax_times_arg, *scaling_matrix_arg;
- extern PyArrayObject *numpy_values, *numpy_sd, *numpy_relax_times,
*numpy_scaling_matrix;
+ PyObject *element;
/* Normal declarations */
- extern double *values, *sd, *relax_times, *scaling_matrix;
+ extern double *params, *values, *sd, *relax_times, *scaling_matrix;
extern double relax_time_array;
extern int num_params, num_times;
+ int i;
/* The keyword list */
static char *keyword_list[] = {"num_params", "num_times", "values",
"sd", "relax_times", "scaling_matrix", NULL};
@@ -49,22 +47,54 @@
if (!PyArg_ParseTupleAndKeywords(args, keywords, "iiOOOO", keyword_list,
&num_params, &num_times, &values_arg, &sd_arg, &relax_times_arg,
&scaling_matrix_arg))
return NULL;
- Py_XDECREF(numpy_values);
- Py_XDECREF(numpy_sd);
- Py_XDECREF(numpy_relax_times);
- Py_XDECREF(numpy_scaling_matrix);
-
- /* Make the numpy arrays contiguous */
- numpy_values = (PyArrayObject *)
PyArray_ContiguousFromObject(values_arg, PyArray_DOUBLE, 1, 1);
- numpy_sd = (PyArrayObject *) PyArray_ContiguousFromObject(sd_arg,
PyArray_DOUBLE, 1, 1);
- numpy_relax_times = (PyArrayObject *)
PyArray_ContiguousFromObject(relax_times_arg, PyArray_DOUBLE, 1, 1);
- numpy_scaling_matrix = (PyArrayObject *)
PyArray_ContiguousFromObject(scaling_matrix_arg, PyArray_DOUBLE, 2, 2);
-
- /* Pointers to the numpy arrays */
- values = (double *) numpy_values->data;
- sd = (double *) numpy_sd->data;
- relax_times = (double *) numpy_relax_times->data;
- scaling_matrix = (double *) numpy_scaling_matrix->data;
+ /* Dynamic C arrays */
+ params = (double *) malloc(sizeof(double)*num_params);
+ values = (double *) malloc(sizeof(double)*num_times);
+ sd = (double *) malloc(sizeof(double)*num_times);
+ relax_times = (double *) malloc(sizeof(double)*num_times);
+ scaling_matrix = (double *) malloc(sizeof(double)*num_params);
+
+ /* Place the value elements into the C array */
+ for (i = 0; i < num_times; i++) {
+ /* Get the element */
+ element = PySequence_GetItem(values_arg, i);
+
+ /* Convert to a C double */
+ values[i] = PyFloat_AsDouble(element);
+ }
+
+ /* Place the sd elements into the C array */
+ for (i = 0; i < num_times; i++) {
+ /* Get the element */
+ element = PySequence_GetItem(sd_arg, i);
+
+ /* Convert to a C double */
+ sd[i] = PyFloat_AsDouble(element);
+ }
+
+ /* Place the relax_times elements into the C array */
+ for (i = 0; i < num_times; i++) {
+ /* Get the element */
+ element = PySequence_GetItem(relax_times_arg, i);
+
+ /* Convert to a C double */
+ relax_times[i] = PyFloat_AsDouble(element);
+ }
+
+ /* Place the scaling matrix elements into the C array */
+ for (i = 0; i < num_params; i++) {
+ /* Get the element */
+ element = PySequence_GetItem(values_arg, i);
+
+ /* Convert to a C double */
+ scaling_matrix[i] = PyFloat_AsDouble(element);
+ }
+
+ /* Reference counting */
+ Py_XDECREF(values);
+ Py_XDECREF(sd);
+ Py_XDECREF(relax_times);
+ Py_XDECREF(scaling_matrix);
/* Return nothing */
Py_INCREF(Py_None);
@@ -81,25 +111,30 @@
*/
/* Declarations */
- PyObject *arg1;
- PyArrayObject *numpy_params;
- double* params;
-
+ PyObject *params_arg;
+ PyObject *element;
+ extern double *params;
+ int i;
/* Parse the function arguments, the only argument should be the
parameter array */
- if (!PyArg_ParseTuple(args, "O", &arg1))
+ if (!PyArg_ParseTuple(args, "O", ¶ms_arg))
return NULL;
- /* Convert the numpy array to be contiguous */
- numpy_params = (PyArrayObject *) PyArray_ContiguousFromObject(arg1,
PyArray_DOUBLE, 1, 1);
-
- /* Pointers to the numpy arrays */
- params = (double *) numpy_params->data;
+ /* Place the parameter array elements into the C array */
+ for (i = 0; i < num_params; i++) {
+ /* Get the element */
+ element = PySequence_GetItem(params_arg, i);
+
+ /* Convert to a C double */
+ params[i] = PyFloat_AsDouble(element);
+ }
/* Back calculated the peak intensities */
exponential(params, relax_times, back_calc, num_times);
- Py_DECREF(numpy_params);
+ /* Reference counting */
+ Py_DECREF(params_arg);
+
/* Calculate and return the chi-squared value */
return Py_BuildValue("f", chi2(values,sd,back_calc,num_times));
}
@@ -110,42 +145,22 @@
/* Function for calculating and returning the chi-squared gradient. */
/* Declarations */
- PyObject *arg1;
- PyArrayObject *numpy_params;
+ PyObject *params_arg;
/* Temp Declarations */
- PyArrayObject *aaa_numpy;
double aaa[MAXPARAMS] = {1.0, 2.0};
- double *aaa_pointer;
int i;
double* params;
/* Parse the function arguments, the only argument should be the
parameter array */
- if (!PyArg_ParseTuple(args, "O", &arg1))
+ if (!PyArg_ParseTuple(args, "O", ¶ms_arg))
return NULL;
-
- /* Convert the numpy array to be contiguous */
- numpy_params = (PyArrayObject *) PyArray_ContiguousFromObject(arg1,
PyArray_DOUBLE, 1, 1);
-
- /* Pointers to the numpy arrays */
- params = (double *) numpy_params->data;
/* Back calculated the peak intensities */
exponential(params, relax_times, back_calc, num_times);
-
- /* Test code (convert aaa to a numpy array */
- /* aaa_numpy = (PyArrayObject *) PyArray_FromDimsAndData(1, num_params,
PyArray_DOUBLE, aaa_pointer); */
- /*aaa_numpy = (PyArrayObject *) PyArray_FromDims(1, &num_params,
PyArray_DOUBLE);
- aaa_pointer = (double *) aaa_numpy->data;*/
-
- /* Fill the numpy array */
- /*for (i = 0; i < 2; i++)
- aaa_pointer[i] = aaa[i];*/
-
- Py_DECREF(numpy_params);
+ Py_DECREF(params);
return NULL;
- return PyArray_Return(aaa_numpy);
}
static PyObject *
@@ -192,7 +207,4 @@
initrelax_fit(void)
{
(void) Py_InitModule("relax_fit", relax_fit_methods);
-
- /* Import the numpy array module. This is essential. */
- import_array();
-}
+}
Modified: 1.3/maths_fns/relax_fit.h
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/relax_fit.h?rev=12625&r1=12624&r2=12625&view=diff
==============================================================================
--- 1.3/maths_fns/relax_fit.h (original)
+++ 1.3/maths_fns/relax_fit.h Fri Feb 25 14:24:59 2011
@@ -19,11 +19,6 @@
*/
-/* Required for the Python/C API??? */
-
-#define PY_ARRAY_UNIQUE_SYMBOL numarray
-
-
/* The maximum number of parameters for this function */
#define MAXPARAMS 3
@@ -36,18 +31,10 @@
/****************************************/
/* Variables sent to the setup function to be stored for later use */
-PyArrayObject *numpy_values, *numpy_sd, *numpy_relax_times,
*numpy_scaling_matrix;
int num_params, num_times;
-double *sd;
-/* Variables sent to 'func', 'dfunc', and 'd2func' during optimisation */
-/*PyArrayObject *numpy_params;*/
-
-/* Pointers to contiguous PyArrayObjects */
-double *values, *sd, *relax_times, *scaling_matrix;
-/*double *params;*/
-
+/* Pointers to PyObjects */
+double *params, *values, *sd, *relax_times, *scaling_matrix;
/* Variables used for storage during the function calls of optimisation */
double back_calc[MAXTIMES];
-
r12625 - in /1.3/maths_fns: exponential.c relax_fit.c relax_fit.h