Author: varioustoxins
Date: Fri Apr 7 08:33:34 2006
New Revision: 2455
URL: http://svn.gna.org/viewcvs/relax?rev=2455&view=rev
Log:
removed memory leak in fitting functions c module
edward at nmr-relax.com
https://gna.org/bugs/index.php?func=detailitem&item_id=5602
https://gna.org/bugs/index.php?func=detailitem&item_id=5473
Modified:
1.2/maths_fns/c_chi2.c
1.2/maths_fns/exponential.c
1.2/maths_fns/relax_fit.c
1.2/maths_fns/relax_fit.h
Modified: 1.2/maths_fns/c_chi2.c
URL:
http://svn.gna.org/viewcvs/relax/1.2/maths_fns/c_chi2.c?rev=2455&r1=2454&r2=2455&view=diff
==============================================================================
--- 1.2/maths_fns/c_chi2.c (original)
+++ 1.2/maths_fns/c_chi2.c Fri Apr 7 08:33:34 2006
@@ -24,7 +24,7 @@
#define square(x) (x)*(x)
-double chi2(void) {
+double chi2(double *values, double *sd, double *back_calc, int num_times) {
/* Function to calculate the chi-squared value.
The chi-sqared equation
@@ -43,10 +43,6 @@
The chi-squared value is returned.
*/
- /* Declarations */
- extern int num_times;
- extern double *values, *sd;
- extern double back_calc[];
int i;
double chi2 = 0.0;
Modified: 1.2/maths_fns/exponential.c
URL:
http://svn.gna.org/viewcvs/relax/1.2/maths_fns/exponential.c?rev=2455&r1=2454&r2=2455&view=diff
==============================================================================
--- 1.2/maths_fns/exponential.c (original)
+++ 1.2/maths_fns/exponential.c Fri Apr 7 08:33:34 2006
@@ -30,14 +30,11 @@
-void exponential(void) {
+void exponential(double *params, double *relax_times, double *back_calc, int
num_times) {
/* Function to back calculate the peak intensities.
*/
/* Declarations */
- extern int num_times;
- extern double *params, *relax_times;
- extern double back_calc[];
double Rx, I0;
int i;
Modified: 1.2/maths_fns/relax_fit.c
URL:
http://svn.gna.org/viewcvs/relax/1.2/maths_fns/relax_fit.c?rev=2455&r1=2454&r2=2455&view=diff
==============================================================================
--- 1.2/maths_fns/relax_fit.c (original)
+++ 1.2/maths_fns/relax_fit.c Fri Apr 7 08:33:34 2006
@@ -27,26 +27,35 @@
/* The header for all functions which will be called */
#include "relax_fit.h"
-
+/* functions for chi2 and exponential */
+#include "c_chi2.h"
+#include "exponential.h"
static PyObject *
setup(PyObject *self, PyObject *args, PyObject *keywords) {
/* Python declarations */
PyObject *values_arg, *sd_arg, *relax_times_arg, *scaling_matrix_arg;
- PyArrayObject *numpy_values, *numpy_sd, *numpy_relax_times,
*numpy_scaling_matrix;
+ extern PyArrayObject *numpy_values, *numpy_sd, *numpy_relax_times,
*numpy_scaling_matrix;
/* Normal declarations */
extern double *values, *sd, *relax_times, *scaling_matrix;
extern double relax_time_array;
extern int num_params, num_times;
-
+
/* The keyword list */
static char *keyword_list[] = {"num_params", "num_times", "values",
"sd", "relax_times", "scaling_matrix", NULL};
/* Parse the function arguments */
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 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);
@@ -59,10 +68,8 @@
relax_times = (double *) numpy_relax_times->data;
scaling_matrix = (double *) numpy_scaling_matrix->data;
- /* Increment the reference count for the python object None */
+ /* Return nothing */
Py_INCREF(Py_None);
-
- /* Return nothing */
return Py_None;
}
@@ -77,8 +84,8 @@
/* Declarations */
PyObject *arg1;
- extern PyArrayObject *numpy_params;
- double chi2(void);
+ PyArrayObject *numpy_params;
+ double* params;
/* Parse the function arguments, the only argument should be the
parameter array */
@@ -92,13 +99,11 @@
params = (double *) numpy_params->data;
/* Back calculated the peak intensities */
- exponential();
-
- /* Deallocate the memory used by the parameters */
+ exponential(params, relax_times, back_calc, num_times);
+
Py_DECREF(numpy_params);
-
/* Calculate and return the chi-squared value */
- return Py_BuildValue("f", chi2());
+ return Py_BuildValue("f", chi2(values,sd,back_calc,num_times));
}
@@ -108,13 +113,14 @@
/* Declarations */
PyObject *arg1;
- extern PyArrayObject *numpy_params;
+ PyArrayObject *numpy_params;
/* 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))
@@ -127,20 +133,19 @@
params = (double *) numpy_params->data;
/* Back calculated the peak intensities */
- exponential();
+ exponential(params, relax_times, back_calc, num_times);
/* Test code (convert aaa to a Numeric array */
- aaa_numpy = (PyArrayObject *) PyArray_FromDims(1, &num_params,
PyArray_DOUBLE);
- aaa_pointer = (double *) aaa_numpy->data;
+ /* 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 Numeric array */
- for (i = 0; i < 2; i++)
- aaa_pointer[i] = aaa[i];
-
- /* Deallocate the memory used by the parameters */
+ /*for (i = 0; i < 2; i++)
+ aaa_pointer[i] = aaa[i];*/
+
Py_DECREF(numpy_params);
-
return NULL;
return PyArray_Return(aaa_numpy);
}
Modified: 1.2/maths_fns/relax_fit.h
URL:
http://svn.gna.org/viewcvs/relax/1.2/maths_fns/relax_fit.h?rev=2455&r1=2454&r2=2455&view=diff
==============================================================================
--- 1.2/maths_fns/relax_fit.h (original)
+++ 1.2/maths_fns/relax_fit.h Fri Apr 7 08:33:34 2006
@@ -41,11 +41,12 @@
double *sd;
/* Variables sent to 'func', 'dfunc', and 'd2func' during optimisation */
-PyArrayObject *numpy_params;
+/*PyArrayObject *numpy_params;*/
/* Pointers to contiguous PyArrayObjects */
double *values, *sd, *relax_times, *scaling_matrix;
-double *params;
+/*double *params;*/
+
/* Variables used for storage during the function calls of optimisation */
double back_calc[MAXTIMES];
r2455 - in /1.2/maths_fns: c_chi2.c exponential.c relax_fit.c relax_fit.h