Merge pull request #15 from rkwi/anuga_py3

Cythonizing calc_grid_values_ext
stoiver · Nov 26, 2019 · 117e83a · 117e83a
2 parents 688d11b + 2fd5b5d
commit 117e83a
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Showing 3 changed files with 51 additions and 94 deletions.
diff --git a/anuga/file_conversion/calc_grid_values_ext.c → anuga/file_conversion/calc_grid_values.c b/anuga/file_conversion/calc_grid_values_ext.c → anuga/file_conversion/calc_grid_values.c
@@ -1,11 +1,5 @@
-#include "Python.h"
-#include "numpy/arrayobject.h"
 #include <stdio.h>
 #include <math.h>
-//#include <malloc.h>
-
-#define DDATA(p) ((double*)(((PyArrayObject *)p)->data))
-#define IDATA(p) ((long*)(((PyArrayObject *)p)->data))
 
 #define MIN(a, b) (((a)<=(b))?(a):(b))
 #define MAX(a, b) (((a)>(b))?(a):(b))
@@ -405,89 +399,3 @@ void _calc_grid_values( double *x, double *y, double *norms,
 	}
 
 }
-
-static PyObject *calc_grid_values( PyObject *self, PyObject *args )
-{
-	int i, ok, num_tri, num_vert, ncol, nrow, num_norms, num_grid_val;
-	long *volumes; 
-	double nodata_val;
-    double cell_size;
-	double *x, *y;
-    double *norms;
-	double *result;
-	double *grid_val;
-	PyObject *pyobj_x;
-    PyObject *pyobj_y;
-    PyObject *pyobj_norms;
-	PyObject *pyobj_volumes;
-	PyObject *pyobj_result;
-	PyObject *pyobj_grid_val;
-
-	ok = PyArg_ParseTuple( args, "iiddOOOOOO",
-				&nrow,
-				&ncol,
-                &cell_size,
-				&nodata_val, 
-				&pyobj_x,
-                &pyobj_y,
-                &pyobj_norms,
-				&pyobj_volumes, 
-				&pyobj_result,
-				&pyobj_grid_val );
-
-
-
-
-	if( !ok ){
-		fprintf( stderr, "calc_grid_values: argument parsing error\n" );
-		exit(1);
-	}
-
-	// get data from python objects
-	x = DDATA( pyobj_x );
-    y = DDATA( pyobj_y );
-    norms    = DDATA( pyobj_norms );
-	result	 = DDATA( pyobj_result );
-	grid_val = DDATA( pyobj_grid_val );
-	volumes  = IDATA( pyobj_volumes );
-
-
-	num_tri  = ((PyArrayObject*)pyobj_volumes)->dimensions[0];
-	num_vert = ((PyArrayObject*)pyobj_x)->dimensions[0];
-    num_norms = ((PyArrayObject*)pyobj_norms)->dimensions[0];
-    num_grid_val = ((PyArrayObject*)pyobj_grid_val)->dimensions[0];
-
-    //printf("==== %d %d %d %d %d \n",num_norms,num_tri,num_vert,nrow,ncol);
-
-	// init triangle array
-	init_norms( x,y, norms, volumes, num_tri );
-
-
-
-        //printf("+++ %d\n",nrow*ncol);
-	// evaluate grid
-	for ( i = 0 ; i < nrow*ncol; i++ ) 
-		grid_val[i] = nodata_val;
-
-
-
-	_calc_grid_values( x,y, norms, num_vert, volumes, num_tri, \
-				    cell_size, nrow, ncol,   	\
-				    result, grid_val );
-
-
-	return Py_BuildValue("");
-}
-
-static PyMethodDef calc_grid_values_ext_methods[] = {
-	{"calc_grid_values", calc_grid_values, METH_VARARGS},
-	{NULL, NULL}
-};
-
-void initcalc_grid_values_ext( )
-{
-	(void) Py_InitModule( "calc_grid_values_ext", calc_grid_values_ext_methods );
-
-	import_array( );
-}
-
diff --git a/anuga/file_conversion/calc_grid_values_ext.pyx b/anuga/file_conversion/calc_grid_values_ext.pyx
@@ -0,0 +1,45 @@
+#cython: wraparound=False, boundscheck=False, cdivision=True, profile=False, nonecheck=False, overflowcheck=False, cdivision_warnings=False, unraisable_tracebacks=False
+import cython
+
+# import both numpy and the Cython declarations for numpy
+import numpy as np
+cimport numpy as np
+
+# declare the interface to the C code
+cdef extern from "calc_grid_values.c":
+	void _calc_grid_values(double* x, double* y, double* norms, int num_vert, long* volumes, int num_tri, double cell_size, int nrow, int ncol, double* vertex_val, double* grid_val)
+	void init_norms(double* x, double* y, double* norms, long* volumes, int num_tri)
+
+
+def calc_grid_values(int nrow, int ncol,\
+                    double cell_size,\
+                    double nodata_val,\
+                    np.ndarray[double, ndim=1, mode="c"] x not None,\
+                    np.ndarray[double, ndim=1, mode="c"] y not None,\
+                    np.ndarray[double, ndim=1, mode="c"] norms not None,\
+                    np.ndarray[long, ndim=2, mode="c"] volumes not None,\
+                    np.ndarray[double, ndim=1, mode="c"] result not None,\
+                    np.ndarray[double, ndim=1, mode="c"] grid_val not None):
+
+	cdef int i, num_tri, num_vert, num_norms, num_grid_val
+
+	num_tri = volumes.shape[0]
+	num_vert = x.shape[0]
+	num_norms = norms.shape[0]
+	num_grid_val = grid_val.shape[0]
+
+	init_norms(&x[0], &y[0], &norms[0], &volumes[0,0], num_tri)
+
+	for i in xrange(nrow*ncol):
+		grid_val[i] = nodata_val
+
+	_calc_grid_values(&x[0], &y[0],\
+                    &norms[0],\
+                    num_vert,\
+                    &volumes[0,0],\
+                    num_tri,\
+                    cell_size,\
+                    nrow,\
+                    ncol,\
+                    &result[0],\
+                    &grid_val[0])
diff --git a/anuga/file_conversion/setup.py b/anuga/file_conversion/setup.py
@@ -4,6 +4,9 @@
 import sys
 
 from os.path import join
+from Cython.Build import cythonize
+import Cython.Compiler.Options
+Cython.Compiler.Options.annotate = True
 
 def configuration(parent_package='',top_path=None):
 
@@ -18,9 +21,10 @@ def configuration(parent_package='',top_path=None):
     util_dir = join('..','utilities')
 
     config.add_extension('calc_grid_values_ext',
-                         sources=['calc_grid_values_ext.c'],
+                         sources=['calc_grid_values_ext.pyx'],
                          include_dirs=[util_dir])
-
+
+    config.ext_modules = cythonize(config.ext_modules, annotate=True)
 
     return config