Author: bugman
Date: Tue Mar 14 05:50:56 2006
New Revision: 2387
URL: http://svn.gna.org/viewcvs/relax?rev=2387&view=rev
Log:
A few modifications to try to eliminate the segfault.
Modified:
branches/c_modules/maths_fns/c_chi2.c
branches/c_modules/maths_fns/exponential.c
branches/c_modules/maths_fns/relax_fit.c
branches/c_modules/maths_fns/relax_fit.h
Modified: branches/c_modules/maths_fns/c_chi2.c
URL:
http://svn.gna.org/viewcvs/relax/branches/c_modules/maths_fns/c_chi2.c?rev=2387&r1=2386&r2=2387&view=diff
==============================================================================
--- branches/c_modules/maths_fns/c_chi2.c (original)
+++ branches/c_modules/maths_fns/c_chi2.c Tue Mar 14 05:50:56 2006
@@ -20,6 +20,15 @@
#include <stdio.h>
#include <math.h>
+
+/* This include must come first */
+#include <Python.h>
+
+/* The header for all functions which will be called */
+#include "relax_fit.h"
+
+/* The Numeric array object header file, must come second */
+#include <Numeric/arrayobject.h>
#define square(x) (x)*(x)
@@ -45,14 +54,14 @@
/* Declarations */
extern int *num_times;
- extern double *values, *sd;
+ extern PyArrayObject *values, *sd;
extern double back_calc[];
int i;
double chi2 = 0.0;
/* Loop over the time points and sum the chi-squared components */
- for (i = 0; i < (int)num_times; ++i) {
- chi2 = chi2 + square((values[i] - back_calc[i]) / sd[i]);
+ for (i = 0; i < *num_times; ++i) {
+ chi2 = chi2 + square((*(double *)values->data[i] -
back_calc[i]) / *(double *)sd->data[i]);
}
return chi2;
Modified: branches/c_modules/maths_fns/exponential.c
URL:
http://svn.gna.org/viewcvs/relax/branches/c_modules/maths_fns/exponential.c?rev=2387&r1=2386&r2=2387&view=diff
==============================================================================
--- branches/c_modules/maths_fns/exponential.c (original)
+++ branches/c_modules/maths_fns/exponential.c Tue Mar 14 05:50:56 2006
@@ -22,11 +22,11 @@
/* This include must come first */
#include <Python.h>
+/* The header for all functions which will be called */
+#include "relax_fit.h"
+
/* The Numeric array object header file, must come second */
#include <Numeric/arrayobject.h>
-
-/* The header for all functions which will be called */
-#include "relax_fit.h"
@@ -36,22 +36,21 @@
/* Declarations */
extern int *num_times;
- extern double *params, *relax_times;
+ extern PyArrayObject *params, *relax_times;
extern double back_calc[];
double Rx, I0;
int i;
/* Loop over the time points */
- /* for (i = 0; i < num_times; i++) { */
- for (i = 0; i < (int)num_times; i++) {
+ for (i = 0; i < *num_times; i++) {
/* Zero Rx value */
if (params[0] == 0.0)
back_calc[i] = 0.0;
/* Back calculate */
else
- back_calc[i] = params[1] * exp(-relax_times[i] * params[0]);
+ back_calc[i] = (double *)params->data[1] * exp(-(double
*)relax_times->data[i] * (double *)params->data[0]);
}
}
Modified: branches/c_modules/maths_fns/relax_fit.c
URL:
http://svn.gna.org/viewcvs/relax/branches/c_modules/maths_fns/relax_fit.c?rev=2387&r1=2386&r2=2387&view=diff
==============================================================================
--- branches/c_modules/maths_fns/relax_fit.c (original)
+++ branches/c_modules/maths_fns/relax_fit.c Tue Mar 14 05:50:56 2006
@@ -21,22 +21,24 @@
/* This include must come first */
#include <Python.h>
+/* The header for all functions which will be called */
+#include "relax_fit.h"
+
/* The Numeric array object header file, must come second */
#include <Numeric/arrayobject.h>
-/* The header for all functions which will be called */
-#include "relax_fit.h"
-
static PyObject *
setup(PyObject *self, PyObject *args, PyObject *keywords) {
+ /* Debugging */
+ printf("Setting up\n");
+
/* Python declarations */
PyObject *values_arg, *sd_arg, *relax_times_arg, *scaling_matrix_arg;
- extern PyArrayObject *numpy_values, *numpy_sd, *numpy_relax_times,
*numpy_scaling_matrix;
+ extern PyArrayObject *values, *sd, *relax_times, *scaling_matrix;
/* Normal declarations */
- extern double *values, *sd, *relax_times, *scaling_matrix;
extern double *relax_time_array;
extern int *num_params, *num_times;
@@ -48,20 +50,29 @@
if (!PyArg_ParseTupleAndKeywords(args, keywords, "iiOOOO", keyword_list,
&num_params, &num_times, &values_arg, &sd, &relax_times_arg,
&scaling_matrix_arg))
return NULL;
+ /* Debugging */
+ printf("Function args have been parsed\n");
+
/* Make the Numeric 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 Numeric 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;
+ values = (PyArrayObject *) PyArray_ContiguousFromObject(values_arg,
PyArray_DOUBLE, 1, 1);
+ sd = (PyArrayObject *) PyArray_ContiguousFromObject(sd_arg,
PyArray_DOUBLE, 1, 1);
+ relax_times = (PyArrayObject *)
PyArray_ContiguousFromObject(relax_times_arg, PyArray_DOUBLE, 1, 1);
+ scaling_matrix = (PyArrayObject *)
PyArray_ContiguousFromObject(scaling_matrix_arg, PyArray_DOUBLE, 2, 2);
+
+ /* Debugging */
+ printf("Py_INCREF\n");
+
+ /* ??? */
+ Py_INCREF(Py_None);
+ Py_INCREF(values);
+ Py_INCREF(sd);
+ Py_INCREF(relax_times);
+ Py_INCREF(scaling_matrix);
+
+ /* Debugging */
+ printf("Finished setup\n");
/* Return nothing */
- Py_INCREF(Py_None);
return Py_None;
}
@@ -74,9 +85,13 @@
* calculated
*/
+ /* Debugging */
+ printf("Inside func\n");
+
/* Declarations */
PyObject *arg1;
- extern PyArrayObject *numpy_params;
+ extern PyArrayObject *params;
+ extern double *params;
double chi2(void);
@@ -85,14 +100,14 @@
return NULL;
/* Convert the Numeric array to be contiguous */
- numpy_params = (PyArrayObject *) PyArray_ContiguousFromObject(arg1,
PyArray_DOUBLE, 1, 1);
-
- /* Pointers to the Numeric arrays */
- params = (double *) numpy_params->data;
+ params = (PyArrayObject *) PyArray_ContiguousFromObject(arg1,
PyArray_DOUBLE, 1, 1);
/* Back calculated the peak intensities */
exponential();
+ /* ??? */
+ Py_INCREF(params);
+
/* Calculate and return the chi-squared value */
return Py_BuildValue("f", chi2());
}
@@ -104,7 +119,8 @@
/* Declarations */
PyObject *arg1;
- extern PyArrayObject *numpy_params;
+ extern PyArrayObject *params;
+ extern double *params;
/* Temp Declarations */
PyArrayObject *aaa_numpy;
@@ -117,10 +133,7 @@
return NULL;
/* Convert the Numeric array to be contiguous */
- numpy_params = (PyArrayObject *) PyArray_ContiguousFromObject(arg1,
PyArray_DOUBLE, 1, 1);
-
- /* Pointers to the Numeric arrays */
- params = (double *) numpy_params->data;
+ params = (PyArrayObject *) PyArray_ContiguousFromObject(arg1,
PyArray_DOUBLE, 1, 1);
/* Back calculated the peak intensities */
exponential();
@@ -128,8 +141,7 @@
/* Test code (convert aaa to a Numeric 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;
+ aaa_numpy = (PyArrayObject *) PyArray_FromDims(1, (int *) *num_params,
PyArray_DOUBLE);
/* Fill the Numeric array */
for (i = 0; i < 2; i++)
@@ -155,11 +167,11 @@
extern int *num_times;
int i;
- PyObject *back_calc_py = PyList_New((int)num_times);
+ PyObject *back_calc_py = PyList_New(*num_times);
assert(PyList_Check(back_calc_py));
/* Copy the values out of the C array into the Python array */
- for (i = 0; i < (int)num_times; i++)
+ for (i = 0; i < *num_times; i++)
PyList_SetItem(back_calc_py, i, Py_BuildValue("f", back_calc[i]));
/* Return the Numeric array */
Modified: branches/c_modules/maths_fns/relax_fit.h
URL:
http://svn.gna.org/viewcvs/relax/branches/c_modules/maths_fns/relax_fit.h?rev=2387&r1=2386&r2=2387&view=diff
==============================================================================
--- branches/c_modules/maths_fns/relax_fit.h (original)
+++ branches/c_modules/maths_fns/relax_fit.h Tue Mar 14 05:50:56 2006
@@ -36,16 +36,11 @@
/****************************************/
/* Variables sent to the setup function to be stored for later use */
-PyArrayObject *numpy_values, *numpy_sd, *numpy_relax_times,
*numpy_scaling_matrix;
+PyArrayObject *values, *sd, *relax_times, *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;
+PyArrayObject *params;
/* Variables used for storage during the function calls of optimisation */
double back_calc[MAXTIMES];
r2387 - in /branches/c_modules/maths_fns: c_chi2.c exponential.c relax_fit.c relax_fit.h