Changeset 12112

Timestamp:

04/23/12 23:04:27 (13 years ago)

Author:

Eric.Larour

Message:

Finished python version of setmask.py and FlagElements.py
Also finished triangle.py, with addition of 2 python modules NodeConnectivity
and ElementConnectivity.

Location:

issm/trunk-jpl

Files:

• configs/config-macosx64-larour-nopetsc.sh (modified) (1 diff)
• src/c/python/io/FetchPythonData.cpp (modified) (1 diff)
• src/c/python/io/WritePythonData.cpp (modified) (1 diff)
• src/c/python/io/pythonio.h (modified) (4 diffs)
• src/m/model/mesh (modified) (1 prop)
• src/m/model/mesh/triangle.py (modified) (3 diffs)
• src/m/model/setmask.py (added)
• src/m/utils/Geometry/FlagElements.py (added)
• src/modules/ElementConnectivity/ElementConnectivity.cpp (modified) (3 diffs)
• src/modules/ElementConnectivity/ElementConnectivity.h (modified) (2 diffs)
• src/modules/NodeConnectivity/NodeConnectivity.cpp (modified) (3 diffs)
• src/modules/NodeConnectivity/NodeConnectivity.h (modified) (2 diffs)
• src/modules/TriMesh/TriMesh.cpp (modified) (1 diff)
• src/modules/python/Makefile.am (modified) (2 diffs)
• startup.py (modified) (1 diff)
• test/NightlyRun/test102.py (modified) (1 diff)

issm/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh

@@ -1 +1 @@
 #!/bin/sh
 
-pythonversion=2.7
+pythonversion=3.2
 
 ./configure \

issm/trunk-jpl/src/c/python/io/FetchPythonData.cpp

@@ -57 +57 @@
 }
 /*}}}*/
+/*FUNCTION FetchData(double** pmatrix,int* pM, int* pN, PyObject* py_matrix){{{1*/
+void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_matrix){
+
+        /*output: */
+        double* matrix=NULL;
+        int M,N;
+        int ndim;
+        npy_intp*  dims=NULL;
+
+        /*retrive dimensions: */
+        ndim=PyArray_NDIM((const PyArrayObject*)py_matrix);
+        if(ndim!=2)_error_("expecting an MxN matrix in input!");
+        dims=PyArray_DIMS((PyArrayObject*)py_matrix);
+        M=dims[0]; N=dims[1];
+        
+        /*retrieve internal value: */
+        matrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix);
+
+        /*output: */
+        if(pM)*pM=M;
+        if(pN)*pN=N;
+        if(pmatrix)*pmatrix=matrix;
+}
+/*}}}*/
 
 /*Python version dependent: */

issm/trunk-jpl/src/c/python/io/WritePythonData.cpp

@@ -64 +64 @@
 }
 /*}}}*/
+/*FUNCTION WriteData(PyObject* py_tuple,int index, double* matrix, int M, int N){{{1*/
+void WriteData(PyObject* tuple, int index, double* matrix, int M,int N){
+        
+        npy_intp dims[2]={0,0};
+        PyObject* array=NULL;
+        
+        dims[0]=(npy_intp)M;
+        dims[1]=(npy_intp)N;
+        array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,matrix);
+        
+        PyTuple_SetItem(tuple, index, array);
+
+}

issm/trunk-jpl/src/c/python/io/pythonio.h

@@ -21 +21 @@
 
 //void WriteData(PyObject* py_tuple,DataSet* dataset);
-//void WriteData(PyObject* py_tuple,double* matrix, int M,int N);
 //void WriteData(PyObject* py_tuple,int*    matrix, int M,int N);
 //void WriteData(PyObject* py_tuple,double* vector, int M);
@@ -28 +27 @@
 //void WriteData(PyObject* py_tuple,double scalar);
 //void WriteData(DataHandle* py_tuple,Parameters* parameters);
+void WriteData(PyObject* py_tuple, int index, double* matrix, int M,int N);
 void WriteData(PyObject* py_tuple, int index, char* string);
 void WriteData(PyObject* py_tuple, int index, Matrix* matrix);
@@ -34 +34 @@
 
 //void FetchData(DataSet** pdataset,PyObject* py_ref);
-//void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_ref);
 //void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref);
 //void FetchData(int** pmatrix,int* pM,int *pN,PyObject* py_ref);
@@ -47 +46 @@
 //void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref);
 //void FetchData(Parameters** pparameters, DataHandle py_ref);
+void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_array);
 void FetchData(char** pstring,PyObject* py_unicode);
 void FetchData(double* pscalar,PyObject* py_float);

issm/trunk-jpl/src/m/model/mesh

@@ +1 @@
+__pycache__
 Makefile.in
 Makefile

@@ +1 @@
+__pycache__
 Makefile.in
 Makefile

issm/trunk-jpl/src/m/model/mesh/triangle.py

@@ -1 @@
-from TriMesh import *
 from numpy import *
+import TriMesh as tm
+import NodeConnectivity as nc
+import ElementConnectivity as ec
 
 def triangle(md, domainname, resolution,riftname=''):
@@ -32 +34 @@
 
         #Mesh using TriMesh
-        [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,riftname,area)
+        [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=tm.TriMesh(domainname,riftname,area)
 
         #Fill in rest of fields:
@@ -46 +48 @@
 
         #Now, build the connectivity tables for this mesh.
-        print "Node: NodeConnectivity not implemented yet!"
-        #md.mesh.vertexconnectivity = NodeConnectivity((md.mesh.elements), (md.mesh.numberofvertices))
-        print "Node: ElementConnectivity not implemented yet!"
-        #md.mesh.elementconnectivity = ElementConnectivity((md.mesh.elements), (md.mesh.vertexconnectivity))
+        [md.mesh.vertexconnectivity]= nc.NodeConnectivity(md.mesh.elements, md.mesh.numberofvertices)
+        [md.mesh.elementconnectivity] = ec.ElementConnectivity(md.mesh.elements, md.mesh.vertexconnectivity)
 
         #type of model

issm/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.cpp

@@ -5 +5 @@
 #include "./ElementConnectivity.h"
 
-void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){
+WRAPPER(ElementConnectivity){
 
         /*inputs: */
@@ -19 +19 @@
         MODULEBOOT();
 
-        /*checks on arguments on the matlab side: */
-        CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&ElementConnectivityUsage);
+        /*checks on arguments: */
+        CHECKARGUMENTS(NLHS,NRHS,&ElementConnectivityUsage);
         
         /*Input datasets: */
@@ -32 +32 @@
         WriteData(ELEMENTCONNECTIVITY,elementconnectivity,nel,3);
 
-        /*Free ressources: */
-        xfree((void**)&elements);
-        xfree((void**)&nodeconnectivity);
-
         /*end module: */
         MODULEEND();

issm/trunk-jpl/src/modules/ElementConnectivity/ElementConnectivity.h

@@ -6 +6 @@
 #define _ELEMENTCONNECTIVITY_H
 
-/* local prototypes: */
-void ElementConnectivityUsage(void);
+#ifdef HAVE_CONFIG_H
+        #include <config.h>
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
 
+/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/
+#ifdef _HAVE_PYTHON_
+#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol
+#endif
+
+/*Header files: */
 #include "../../c/include/globals.h"
+#include "../../c/toolkits/toolkits.h"
+#include "../../c/include/include.h"
 #include "../../c/modules/modules.h"
 #include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
 #include "../../c/issm-binding.h"
+#include "../../c/io/io.h"
+#include "../../c/EnumDefinitions/EnumDefinitions.h"
+
+#ifdef _HAVE_MATLAB_MODULES_
+/* serial input macros: */
+/* serial input macros: */
+#define ELEMENTS (mxArray*)prhs[0]
+#define NODECONNECTIVITY (mxArray*)prhs[1]
+/* serial output macros: */
+#define ELEMENTCONNECTIVITY (mxArray**)&plhs[0]
+#endif
+
+#ifdef _HAVE_PYTHON_MODULES_
+/* serial input macros: */
+/* serial input macros: */
+#define ELEMENTS PyTuple_GetItem(args,0)
+#define NODECONNECTIVITY PyTuple_GetItem(args,1)
+/* serial output macros: */
+#define ELEMENTCONNECTIVITY output,0
+#endif
 
 #undef __FUNCT__ 
 #define __FUNCT__  "ElementConnectivity"
-
-/* serial input macros: */
-#define ELEMENTS (mxArray*)prhs[0]
-#define NODECONNECTIVITY (mxArray*)prhs[1]
-
-/* serial output macros: */
-#define ELEMENTCONNECTIVITY (mxArray**)&plhs[0]
 
 /* serial arg counts: */
@@ -31 +55 @@
 #define NRHS  2
 
+/* local prototypes: */
+void ElementConnectivityUsage(void);
+
 #endif  /* _ELEMENTCONNECTIVITY_H */

issm/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.cpp

@@ -5 +5 @@
 #include "./NodeConnectivity.h"
 
-void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){
+WRAPPER(NodeConnectivity){
 
         /*inputs: */
         double* elements=NULL;
-        int     nel,nods;
+        int     nel;
+        int     nods;
 
         /*outputs: */
@@ -18 +19 @@
         MODULEBOOT();
 
-        /*checks on arguments on the matlab side: */
-        CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&NodeConnectivityUsage);
+        /*checks on arguments: */
+        CHECKARGUMENTS(NLHS,NRHS,&NodeConnectivityUsage);
         
         /*Input datasets: */
@@ -31 +32 @@
         WriteData(CONNECTIVITY,connectivity,nods,width);
 
-        /*Free ressources: */
-        xfree((void**)&elements);
-
         /*end module: */
         MODULEEND();

issm/trunk-jpl/src/modules/NodeConnectivity/NodeConnectivity.h

@@ -6 +6 @@
 #define _NODECONNECTIVITY_H
 
-/* local prototypes: */
-void NodeConnectivityUsage(void);
+#ifdef HAVE_CONFIG_H
+        #include <config.h>
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
 
+/*Very important definition in case we are compiling a python module!: needs to come before header files inclusion*/
+#ifdef _HAVE_PYTHON_
+#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol
+#endif
+
+/*Header files: */
 #include "../../c/include/globals.h"
+#include "../../c/toolkits/toolkits.h"
+#include "../../c/include/include.h"
 #include "../../c/modules/modules.h"
 #include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
 #include "../../c/issm-binding.h"
+#include "../../c/io/io.h"
+#include "../../c/EnumDefinitions/EnumDefinitions.h"
+
+#ifdef _HAVE_MATLAB_MODULES_
+/* serial input macros: */
+#define ELEMENTS (mxArray*)prhs[0]
+#define NUMNODES (mxArray*)prhs[1]
+/* serial output macros: */
+#define CONNECTIVITY (mxArray**)&plhs[0]
+#endif
+
+#ifdef _HAVE_PYTHON_MODULES_
+/* serial input macros: */
+#define ELEMENTS PyTuple_GetItem(args,0)
+#define NUMNODES PyTuple_GetItem(args,1)
+/* serial output macros: */
+#define CONNECTIVITY output,0
+#endif
 
 #undef __FUNCT__ 
 #define __FUNCT__  "NodeConnectivity"
-
-/* serial input macros: */
-#define ELEMENTS (mxArray*)prhs[0]
-#define NUMNODES (mxArray*)prhs[1]
-
-/* serial output macros: */
-#define CONNECTIVITY (mxArray**)&plhs[0]
 
 /* serial arg counts: */
@@ -31 +53 @@
 #define NRHS  2
 
+/* local prototypes: */
+void NodeConnectivityUsage(void);
+
 #endif  /* _NODECONNECTIVITY_H */

issm/trunk-jpl/src/modules/TriMesh/TriMesh.cpp

@@ -26 +26 @@
         MODULEBOOT();
 
-        /*checks on arguments on the matlab side: */
+        /*checks on arguments: */
         CHECKARGUMENTS(NLHS,NRHS,&TriMeshUsage);
         

issm/trunk-jpl/src/modules/python/Makefile.am

@@ -3 +3 @@
 #Bin programs {{{1
 if MODULES
-bin_PROGRAMS = TriMesh
+bin_PROGRAMS = TriMesh \
+                           NodeConnectivity \
+                           ElementConnectivity
 endif 
 #}}}
@@ -26 +28 @@
 #}}}
 #Bin sources {{{1
+ElementConnectivity_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\
+                          ../ElementConnectivity/ElementConnectivity.h
+
+NodeConnectivity_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\
+                                                                                ../NodeConnectivity/NodeConnectivity.h
+
 TriMesh_SOURCES = ../TriMesh/TriMesh.cpp\
                           ../TriMesh/TriMesh.h

issm/trunk-jpl/startup.py

@@ -83 +83 @@
 from private import *
 from triangle import *
+from setmask import *
 
 #}}}

issm/trunk-jpl/test/NightlyRun/test102.py

@@ -1 +1 @@
 from model import *
 from triangle import *
+from setmask import *
 
 md=model();
 md=triangle(md,'../Exp/Square.exp',150000);
+md=setmask(md,'all','');

@@ +1 @@
+__pycache__
 Makefile.in
 Makefile