source: issm/oecreview/Archive/13393-13976/ISSM-13748-13749.diff@ 13980

Last change on this file since 13980 was 13980, checked in by Mathieu Morlighem, 12 years ago

preparing oecreview for 13393-13976'
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[13980]1Index: ../trunk-jpl/src/c/python/python-binding.h
2===================================================================
3--- ../trunk-jpl/src/c/python/python-binding.h (revision 13748)
4+++ ../trunk-jpl/src/c/python/python-binding.h (revision 13749)
5@@ -1,7 +0,0 @@
6-#ifndef _PYTHON_BINDING_H_
7-#define _PYTHON_BINDING_H_
8-
9-#include "./io/pythonio.h"
10-#include "./include/python_macros.h"
11-
12-#endif
13Index: ../trunk-jpl/src/c/python/include/python_macros.h
14===================================================================
15--- ../trunk-jpl/src/c/python/include/python_macros.h (revision 13748)
16+++ ../trunk-jpl/src/c/python/include/python_macros.h (revision 13749)
17@@ -1,96 +0,0 @@
18-/* \file python_macros.h
19- * \brief: macros used for the python bindings
20- */
21-
22-#ifndef _PYTHON_MACROS_H_
23-#define _PYTHON_MACROS_H_
24-
25-/*Header {{{*/
26-
27-#ifdef HAVE_CONFIG_H
28- #include <config.h>
29-#else
30-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
31-#endif
32-/*}}}*/
33-
34-#ifdef _HAVE_PYTHON_
35-/* MODULEBOOT/MODULEEND {{{*/
36-
37-/*The following macros hide the error exception handling in a matlab module. Just put
38- * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions
39- * will be trapped*/
40-#define MODULEBOOT(); \
41- PyObject *output = PyTuple_New(NLHS); \
42- int nrhs = (int)PyTuple_Size(args); \
43- if(!output) return NULL;\
44- try{ \
45- IssmComm::SetComm(-1);
46-
47-#define MODULEEND(); }\
48- catch(ErrorException &exception){\
49- PyErr_SetString(PyExc_TypeError,exception.PythonReport()); \
50- return NULL;\
51- } \
52- catch (exception &e){\
53- PyErr_SetString(PyExc_TypeError,exprintf("Standard exception: %s\n",e.what()));\
54- return NULL;\
55- }\
56- catch(...){\
57- PyErr_SetString(PyExc_TypeError,"An unexpected error occurred");\
58- return NULL;\
59- }\
60- return output;
61-//}}}
62-#if _PYTHON_MAJOR_ >=3
63-/* WRAPPER 3.2 {{{*/
64-#define WRAPPER(modulename,...) \
65-\
66-static PyObject* modulename(PyObject* self,PyObject* args);\
67-static PyMethodDef modulename##_funcs[] = {\
68- {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\
69- {NULL,NULL,0,NULL}\
70-};\
71-\
72-static struct PyModuleDef modulename##module= {\
73- PyModuleDef_HEAD_INIT,\
74- #modulename, /* name of module */\
75- NULL, /* module documentation, may be NULL */\
76- -1, /* size of per-interpreter state of the module,\
77- or -1 if the module keeps state in global variables. */\
78- modulename##_funcs\
79-};\
80-\
81-PyMODINIT_FUNC PyInit_##modulename(void){\
82-\
83- import_array();\
84- return PyModule_Create(&modulename##module);\
85-}\
86-\
87-static PyObject* modulename(PyObject* self,PyObject* args)
88-/*}}}*/
89-#else
90-/* WRAPPER 2.7 {{{*/
91-#define WRAPPER(modulename,...) \
92-\
93-static PyObject* modulename(PyObject* self,PyObject* args);\
94-static PyMethodDef modulename##_funcs[] = {\
95- {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\
96- {NULL,NULL,0,NULL}\
97-};\
98-\
99-PyMODINIT_FUNC init##modulename(void){\
100-\
101- import_array();\
102- (void) Py_InitModule(#modulename, modulename##_funcs);\
103-}\
104-\
105-static PyObject* modulename(PyObject* self,PyObject* args)
106-/*}}}*/
107-#endif
108-/* CHECKARGUMENTS {{{*/
109-#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumPythonArguments(args, NRHS,functionpointer)
110-/*}}}*/
111-#endif
112-
113-#endif
114Index: ../trunk-jpl/src/c/python/io/pythonio.h
115===================================================================
116--- ../trunk-jpl/src/c/python/io/pythonio.h (revision 13748)
117+++ ../trunk-jpl/src/c/python/io/pythonio.h (revision 13749)
118@@ -1,43 +0,0 @@
119-/*\file pythonio.h
120- *\brief: I/O for ISSM in python mode
121- */
122-
123-#ifndef _PYTHON_IO_H_
124-#define _PYTHON_IO_H_
125-
126-#ifdef HAVE_CONFIG_H
127-#include <config.h>
128-#else
129-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
130-#endif
131-
132-#include "../../classes/classes.h"
133-#include "../../Container/Container.h"
134-#include "../../include/include.h"
135-
136-void WriteData(PyObject* py_tuple,int index, double* matrix, int M,int N);
137-void WriteData(PyObject* py_tuple,int index, int integer);
138-void WriteData(PyObject* py_tuple,int index, char* string);
139-void WriteData(PyObject* py_tuple,int index);
140-void WriteData(PyObject* py_tuple,int index, SeqMat<double>* matrix);
141-void WriteData(PyObject* py_tuple,int index, SeqVec<double>* vector);
142-void WriteData(PyObject* py_tuple,int index, BamgGeom* bamggeom);
143-void WriteData(PyObject* py_tuple,int index, BamgMesh* bamgmesh);
144-void WriteData(PyObject* py_tuple,int index, RiftStruct* riftstruct);
145-
146-void FetchData(double** pvector,int* pM,PyObject* py_ref);
147-void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_array);
148-void FetchData(int** pmatrix,int* pM,int *pN,PyObject* py_matrix);
149-void FetchData(char** pstring,PyObject* py_unicode);
150-void FetchData(double* pscalar,PyObject* py_float);
151-void FetchData(int* pinteger,PyObject* py_long);
152-void FetchData(bool* pbool,PyObject* py_boolean);
153-void FetchData(BamgGeom** bamggeom,PyObject* py_dict);
154-void FetchData(BamgMesh** bamgmesh,PyObject* py_dict);
155-void FetchData(BamgOpts** bamgopts,PyObject* py_dict);
156-void FetchData(Options** poptions,int istart, int nrhs,PyObject* py_tuple);
157-void FetchData(DataSet** pcontours,PyObject* py_list);
158-
159-int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void ));
160-
161-#endif /* _IO_H_ */
162Index: ../trunk-jpl/src/c/python/io/CheckNumPythonArguments.cpp
163===================================================================
164--- ../trunk-jpl/src/c/python/io/CheckNumPythonArguments.cpp (revision 13748)
165+++ ../trunk-jpl/src/c/python/io/CheckNumPythonArguments.cpp (revision 13749)
166@@ -1,35 +0,0 @@
167-/*!\file CheckNumPythonArguments.cpp:
168- * \brief: check number of arguments and report an usage error message.
169- */
170-
171-#ifdef HAVE_CONFIG_H
172- #include <config.h>
173-#else
174-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
175-#endif
176-
177-#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol
178-#define NO_IMPORT
179-
180-#include "../../toolkits/toolkits.h"
181-#include "../../shared/Exceptions/exceptions.h"
182-#include "../../include/include.h"
183-
184-int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void )){
185-
186- Py_ssize_t size=0;
187-
188- /*figure out size of tuple in input: */
189- size=PyTuple_Size(inputs);
190-
191- /*check on requested size: */
192- if (size==0){
193- function();
194- _error_("usage: see above");
195- }
196- else if (size!=NRHS ) {
197- function();
198- _error_("usage error.");
199- }
200- return 1;
201-}
202Index: ../trunk-jpl/src/c/python/io/FetchPythonData.cpp
203===================================================================
204--- ../trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 13748)
205+++ ../trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 13749)
206@@ -1,356 +0,0 @@
207-/*\file FetchData.cpp:
208- * \brief: general I/O interface to fetch data in python
209- */
210-
211-#ifdef HAVE_CONFIG_H
212- #include <config.h>
213-#else
214-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
215-#endif
216-
217-#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol
218-#define NO_IMPORT
219-
220-#include "../../toolkits/toolkits.h"
221-#include "../../include/include.h"
222-#include "../../shared/shared.h"
223-#include "../../io/io.h"
224-void FetchData(char** pstring,PyObject* py_string);
225-
226-/*Primitive data types*/
227-/*FUNCTION FetchData(double* pscalar,PyObject* py_float){{{*/
228-void FetchData(double* pscalar,PyObject* py_float){
229-
230- double scalar;
231-
232- /*return internal value: */
233- scalar=PyFloat_AsDouble(py_float);
234-
235- /*output: */
236- *pscalar=scalar;
237-}
238-/*}}}*/
239-/*FUNCTION FetchData(int* pinteger,PyObject* py_long){{{*/
240-void FetchData(int* pinteger, PyObject* py_long){
241-
242- int integer;
243-
244- /*return internal value: */
245- integer=(int)PyLong_AsLong(py_long);
246-
247- /*output: */
248- *pinteger=integer;
249-}
250-/*}}}*/
251-/*FUNCTION FetchData(bool* pboolean,PyObject* py_boolean){{{*/
252-void FetchData(bool* pboolean,PyObject* py_boolean){
253-
254- bool boolean;
255-
256- /*check this is indeed a subtype of long type: */
257- if(!PyBool_Check(py_boolean))_error_("expecting a boolean in input!");
258-
259- /*extract boolean: */
260- boolean=(bool)PyLong_AsLong(py_boolean);
261-
262- /*simple copy: */
263- *pboolean=boolean;
264-
265-}
266-/*}}}*/
267-/*FUNCTION FetchData(double** pmatrix,int* pM, int* pN, PyObject* py_matrix){{{*/
268-void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_matrix){
269-
270- /*output: */
271- double* dmatrix=NULL;
272- double* matrix=NULL;
273- int M,N;
274- int ndim;
275- npy_intp* dims=NULL;
276-
277- /*retrive dimensions: */
278- ndim=PyArray_NDIM((const PyArrayObject*)py_matrix);
279- if(ndim!=2)_error_("expecting an MxN matrix in input!");
280- dims=PyArray_DIMS((PyArrayObject*)py_matrix);
281- M=dims[0]; N=dims[1];
282-
283- if (M && N) {
284- /*retrieve internal value: */
285- dmatrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix);
286-
287- /*copy matrix: */
288- matrix=xNew<double>(M*N);
289- memcpy(matrix,dmatrix,(M*N)*sizeof(double));
290- }
291- else
292- matrix=NULL;
293-
294- /*output: */
295- if(pM)*pM=M;
296- if(pN)*pN=N;
297- if(pmatrix)*pmatrix=matrix;
298-}
299-/*}}}*/
300-/*FUNCTION FetchData(int** pmatrix,int* pM, int* pN, PyObject* py_matrix){{{*/
301-void FetchData(int** pmatrix,int* pM,int *pN,PyObject* py_matrix){
302-
303- /*output: */
304- double* dmatrix=NULL;
305- int* matrix=NULL;
306- int M,N;
307-
308- /*intermediary:*/
309- int i;
310- int ndim;
311- npy_intp* dims=NULL;
312-
313- /*retrive dimensions: */
314- ndim=PyArray_NDIM((const PyArrayObject*)py_matrix);
315- if(ndim!=2)_error_("expecting an MxN matrix in input!");
316- dims=PyArray_DIMS((PyArrayObject*)py_matrix);
317- M=dims[0]; N=dims[1];
318-
319- if (M && N) {
320- /*retrieve internal value: */
321- dmatrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix);
322-
323- /*transform into integer matrix: */
324- matrix=xNew<int>(M*N);
325- for(i=0;i<M*N;i++)matrix[i]=(int)dmatrix[i];
326- }
327- else
328- matrix=NULL;
329-
330- /*output: */
331- if(pM)*pM=M;
332- if(pN)*pN=N;
333- if(pmatrix)*pmatrix=matrix;
334-}
335-/*}}}*/
336-/*FUNCTION FetchData(double** pvector,int* pM, PyObject* py_vector){{{*/
337-void FetchData(double** pvector,int* pM,PyObject* py_vector){
338-
339- /*output: */
340- double* dvector=NULL;
341- double* vector=NULL;
342- int M;
343- int ndim;
344- npy_intp* dims=NULL;
345-
346- /*retrive dimensions: */
347- ndim=PyArray_NDIM((const PyArrayObject*)py_vector);
348- if(ndim!=1)_error_("expecting an Mx1 vector in input!");
349- dims=PyArray_DIMS((PyArrayObject*)py_vector);
350- M=dims[0];
351-
352- if (M) {
353- /*retrieve internal value: */
354- dvector=(double*)PyArray_DATA((PyArrayObject*)py_vector);
355-
356- /*copy vector: */
357- vector=xNew<double>(M);
358- memcpy(vector,dvector,(M)*sizeof(double));
359- }
360- else
361- vector=NULL;
362-
363- /*output: */
364- if(pM)*pM=M;
365- if(pvector)*pvector=vector;
366-}
367-/*}}}*/
368-
369-/*ISSM objects*/
370-/*FUNCTION FetchData(BamgGeom** pbamggeom,PyObject* py_dict){{{*/
371-void FetchData(BamgGeom** pbamggeom,PyObject* py_dict){
372-
373- /*Initialize output*/
374- BamgGeom* bamggeom=new BamgGeom();
375-
376- /*Fetch all fields*/
377- FetchData(&bamggeom->Vertices,&bamggeom->VerticesSize[0],&bamggeom->VerticesSize[1],PyDict_GetItemString(py_dict,"Vertices"));
378- FetchData(&bamggeom->Edges, &bamggeom->EdgesSize[0], &bamggeom->EdgesSize[1], PyDict_GetItemString(py_dict,"Edges"));
379- FetchData(&bamggeom->Corners, &bamggeom->CornersSize[0], &bamggeom->CornersSize[1], PyDict_GetItemString(py_dict,"Corners"));
380- FetchData(&bamggeom->RequiredVertices,&bamggeom->RequiredVerticesSize[0],&bamggeom->RequiredVerticesSize[1],PyDict_GetItemString(py_dict,"RequiredVertices"));
381- FetchData(&bamggeom->RequiredEdges, &bamggeom->RequiredEdgesSize[0], &bamggeom->RequiredEdgesSize[1], PyDict_GetItemString(py_dict,"RequiredEdges"));
382- FetchData(&bamggeom->CrackedEdges,&bamggeom->CrackedEdgesSize[0],&bamggeom->CrackedEdgesSize[1],PyDict_GetItemString(py_dict,"CrackedEdges"));
383- FetchData(&bamggeom->SubDomains,&bamggeom->SubDomainsSize[0],&bamggeom->SubDomainsSize[1],PyDict_GetItemString(py_dict,"SubDomains"));
384-
385- /*Assign output pointers:*/
386- *pbamggeom=bamggeom;
387-}
388-/*}}}*/
389-/*FUNCTION FetchData(BamgMesh** pbamgmesh,PyObject* py_dict){{{*/
390-void FetchData(BamgMesh** pbamgmesh,PyObject* py_dict){
391-
392- /*Initialize output*/
393- BamgMesh* bamgmesh=new BamgMesh();
394-
395- /*Fetch all fields*/
396- FetchData(&bamgmesh->Vertices,&bamgmesh->VerticesSize[0],&bamgmesh->VerticesSize[1],PyDict_GetItemString(py_dict,"Vertices"));
397- FetchData(&bamgmesh->Edges, &bamgmesh->EdgesSize[0], &bamgmesh->EdgesSize[1], PyDict_GetItemString(py_dict,"Edges"));
398- FetchData(&bamgmesh->Triangles, &bamgmesh->TrianglesSize[0], &bamgmesh->TrianglesSize[1], PyDict_GetItemString(py_dict,"Triangles"));
399- FetchData(&bamgmesh->CrackedEdges,&bamgmesh->CrackedEdgesSize[0],&bamgmesh->CrackedEdgesSize[1],PyDict_GetItemString(py_dict,"CrackedEdges"));
400- FetchData(&bamgmesh->VerticesOnGeomEdge,&bamgmesh->VerticesOnGeomEdgeSize[0],&bamgmesh->VerticesOnGeomEdgeSize[1],PyDict_GetItemString(py_dict,"VerticesOnGeomEdge"));
401- FetchData(&bamgmesh->VerticesOnGeomVertex,&bamgmesh->VerticesOnGeomVertexSize[0],&bamgmesh->VerticesOnGeomVertexSize[1],PyDict_GetItemString(py_dict,"VerticesOnGeomVertex"));
402- FetchData(&bamgmesh->EdgesOnGeomEdge, &bamgmesh->EdgesOnGeomEdgeSize[0], &bamgmesh->EdgesOnGeomEdgeSize[1], PyDict_GetItemString(py_dict,"EdgesOnGeomEdge"));
403- FetchData(&bamgmesh->IssmSegments,&bamgmesh->IssmSegmentsSize[0],&bamgmesh->IssmSegmentsSize[1],PyDict_GetItemString(py_dict,"IssmSegments"));
404-
405- /*Assign output pointers:*/
406- *pbamgmesh=bamgmesh;
407-}
408-/*}}}*/
409-/*FUNCTION FetchData(BamgOpts** pbamgopts,PyObject* py_dict){{{*/
410-void FetchData(BamgOpts** pbamgopts,PyObject* py_dict){
411-
412- /*Initialize output*/
413- BamgOpts* bamgopts=new BamgOpts();
414-
415- /*Fetch all fields*/
416- FetchData(&bamgopts->anisomax,PyDict_GetItemString(py_dict,"anisomax"));
417- FetchData(&bamgopts->cutoff,PyDict_GetItemString(py_dict,"cutoff"));
418- FetchData(&bamgopts->coeff,PyDict_GetItemString(py_dict,"coeff"));
419- FetchData(&bamgopts->errg,PyDict_GetItemString(py_dict,"errg"));
420- FetchData(&bamgopts->gradation,PyDict_GetItemString(py_dict,"gradation"));
421- FetchData(&bamgopts->Hessiantype,PyDict_GetItemString(py_dict,"Hessiantype"));
422- FetchData(&bamgopts->MaxCornerAngle,PyDict_GetItemString(py_dict,"MaxCornerAngle"));
423- FetchData(&bamgopts->maxnbv,PyDict_GetItemString(py_dict,"maxnbv"));
424- FetchData(&bamgopts->maxsubdiv,PyDict_GetItemString(py_dict,"maxsubdiv"));
425- FetchData(&bamgopts->Metrictype,PyDict_GetItemString(py_dict,"Metrictype"));
426- FetchData(&bamgopts->nbjacobi,PyDict_GetItemString(py_dict,"nbjacobi"));
427- FetchData(&bamgopts->nbsmooth,PyDict_GetItemString(py_dict,"nbsmooth"));
428- FetchData(&bamgopts->omega,PyDict_GetItemString(py_dict,"omega"));
429- FetchData(&bamgopts->power,PyDict_GetItemString(py_dict,"power"));
430- FetchData(&bamgopts->verbose,PyDict_GetItemString(py_dict,"verbose"));
431-
432- FetchData(&bamgopts->Crack,PyDict_GetItemString(py_dict,"Crack"));
433- FetchData(&bamgopts->geometricalmetric,PyDict_GetItemString(py_dict,"geometricalmetric"));
434- FetchData(&bamgopts->KeepVertices,PyDict_GetItemString(py_dict,"KeepVertices"));
435- FetchData(&bamgopts->splitcorners,PyDict_GetItemString(py_dict,"splitcorners"));
436-
437- FetchData(&bamgopts->hmin,PyDict_GetItemString(py_dict,"hmin"));
438- FetchData(&bamgopts->hmax,PyDict_GetItemString(py_dict,"hmax"));
439- FetchData(&bamgopts->hminVertices,&bamgopts->hminVerticesSize[0],&bamgopts->hminVerticesSize[1],PyDict_GetItemString(py_dict,"hminVertices"));
440- FetchData(&bamgopts->hmaxVertices,&bamgopts->hmaxVerticesSize[0],&bamgopts->hmaxVerticesSize[1],PyDict_GetItemString(py_dict,"hmaxVertices"));
441- FetchData(&bamgopts->hVertices,&bamgopts->hVerticesSize[0],&bamgopts->hVerticesSize[1],PyDict_GetItemString(py_dict,"hVertices"));
442- FetchData(&bamgopts->metric,&bamgopts->metricSize[0],&bamgopts->metricSize[1],PyDict_GetItemString(py_dict,"metric"));
443- FetchData(&bamgopts->field,&bamgopts->fieldSize[0],&bamgopts->fieldSize[1],PyDict_GetItemString(py_dict,"field"));
444- FetchData(&bamgopts->err,&bamgopts->errSize[0],&bamgopts->errSize[1],PyDict_GetItemString(py_dict,"err"));
445-
446- /*Additional checks*/
447- bamgopts->Check();
448-
449- /*Assign output pointers:*/
450- *pbamgopts=bamgopts;
451-}
452-/*}}}*/
453-/*FUNCTION FetchData(Options** poptions,int istart, int nrhs,PyObject* py_tuple){{{*/
454-void FetchData(Options** poptions,int istart, int nrhs,PyObject* py_tuple){
455-
456- char *name = NULL;
457- Option *option = NULL;
458-
459- /*Initialize output*/
460- Options* options=new Options();
461-
462- /*Fetch all options*/
463- for (int i=istart; i<nrhs; i=i+2){
464- if (!PyString_Check(PyTuple_GetItem(py_tuple,(Py_ssize_t)i))) _error_("Argument " << i+1 << " must be name of option");
465-
466- FetchData(&name,PyTuple_GetItem(py_tuple,(Py_ssize_t)i));
467- if(i+1 == nrhs) _error_("Argument " << i+2 << " must exist and be value of option \"" << name << "\".");
468-
469- _pprintLine_("FetchData for Options not implemented yet, ignoring option \"" << name << "\"!");
470-
471-// option=(Option*)OptionParse(name,&PyTuple_GetItem(py_tuple,(Py_ssize_t)(i+1)));
472-// options->AddOption(option);
473-// option=NULL;
474- }
475-
476- /*Assign output pointers:*/
477- *poptions=options;
478-}
479-/*}}}*/
480-/*FUNCTION FetchData(DataSet** pcontours,PyObject* py_list){{{*/
481-void FetchData(DataSet** pcontours,PyObject* py_list){
482-
483- int numcontours,test1,test2;
484- char *contourname = NULL;
485- DataSet *contours = NULL;
486- Contour<double> *contouri = NULL;
487- PyObject *py_dicti = NULL;
488- PyObject *py_item = NULL;
489-
490- if (PyString_Check(py_list)){
491- FetchData(&contourname,py_list);
492- contours=DomainOutlineRead<double>(contourname);
493- }
494- else if(PyList_Check(py_list)){
495-
496- contours=new DataSet(0);
497- numcontours=(int)PyList_Size(py_list);
498-
499- for(int i=0;i<numcontours;i++){
500-
501- contouri=xNew<Contour<double> >(1);
502- py_dicti=PyList_GetItem(py_list,(Py_ssize_t)i);
503-
504- py_item = PyDict_GetItemString(py_dicti,"nods");
505- if(!py_item) _error_("input structure does not have a 'nods' field");
506- FetchData(&contouri->nods,py_item);
507-
508- py_item = PyDict_GetItemString(py_dicti,"x");
509- if(!py_item) _error_("input structure does not have a 'x' field");
510- FetchData(&contouri->x,&test1,&test2,py_item);
511- if(test1!=contouri->nods || test2!=1) _error_("field x should be of size ["<<contouri->nods<<" 1]");
512-
513- py_item = PyDict_GetItemString(py_dicti,"y");
514- if(!py_item) _error_("input structure does not have a 'y' field");
515- FetchData(&contouri->y,&test1,&test2,py_item);
516- if(test1!=contouri->nods || test2!=1) _error_("field y should be of size ["<<contouri->nods<<" 1]");
517-
518- contours->AddObject(contouri);
519- }
520- }
521- else{
522- _error_("Contour is neither a string nor a structure and cannot be loaded");
523- }
524-
525- /*clean-up and assign output pointer*/
526- xDelete<char>(contourname);
527- *pcontours=contours;
528-}
529-/*}}}*/
530-
531-/*Python version dependent: */
532-#if _PYTHON_MAJOR_ >= 3
533-/*FUNCTION FetchData(char** pstring,PyObject* py_unicode){{{*/
534-void FetchData(char** pstring,PyObject* py_unicode){
535-
536- PyObject* py_bytes;
537- char* string=NULL;
538-
539- /*convert to bytes format: */
540- PyUnicode_FSConverter(py_unicode,&py_bytes);
541-
542- /*convert from bytes to string: */
543- string=PyBytes_AS_STRING(py_bytes);
544-
545- *pstring=string;
546-}
547-/*}}}*/
548-#else
549-/*FUNCTION FetchData(char** pstring,PyObject* py_string){{{*/
550-void FetchData(char** pstring,PyObject* py_string){
551-
552- char* string=NULL;
553-
554- /*extract internal string: */
555- string=PyString_AsString(py_string);
556-
557- /*copy string (note strlen does not include trailing NULL): */
558- *pstring=xNew<char>(strlen(string)+1);
559- memcpy(*pstring,string,(strlen(string)+1)*sizeof(char));
560-}
561-/*}}}*/
562-#endif
563Index: ../trunk-jpl/src/c/python/io/WritePythonData.cpp
564===================================================================
565--- ../trunk-jpl/src/c/python/io/WritePythonData.cpp (revision 13748)
566+++ ../trunk-jpl/src/c/python/io/WritePythonData.cpp (revision 13749)
567@@ -1,198 +0,0 @@
568-/* \file WriteData.c:
569- * \brief: general interface for writing data
570- */
571-
572-#ifdef HAVE_CONFIG_H
573- #include <config.h>
574-#else
575-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
576-#endif
577-
578-#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol
579-#define NO_IMPORT
580-
581-#include "../../toolkits/toolkits.h"
582-#include "../../include/include.h"
583-#include "../../modules/modules.h"
584-#include "../../Container/Container.h"
585-#include "../../shared/shared.h"
586-#include "../../io/io.h"
587-#include "../../EnumDefinitions/EnumDefinitions.h"
588-PyObject* PyArrayFromCopiedData(int dims[2],double* data);
589-PyObject* PyArrayFromCopiedData(int dimi,int dimj,double* data);
590-
591-/*Primitive data types*/
592-/*FUNCTION WriteData(PyObject* py_tuple,int index,int integer){{{*/
593-void WriteData(PyObject* py_tuple, int index, int integer){
594-
595- PyTuple_SetItem(py_tuple, index, PyInt_FromSsize_t((Py_ssize_t)integer));
596-
597-}/*}}}*/
598-/*FUNCTION WriteData(PyObject* py_tuple,int index,char* string){{{*/
599-void WriteData(PyObject* py_tuple, int index, char* string){
600-
601- PyTuple_SetItem(py_tuple, index, PyUnicode_FromString(string));
602-
603-}/*}}}*/
604-/*FUNCTION WriteData(PyObject* py_tuple,int index, double* matrix, int M, int N){{{*/
605-void WriteData(PyObject* tuple, int index, double* matrix, int M,int N){
606-
607- npy_intp dims[2]={0,0};
608- PyObject* array=NULL;
609-
610- dims[0]=(npy_intp)M;
611- dims[1]=(npy_intp)N;
612- array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,matrix);
613-
614- PyTuple_SetItem(tuple, index, array);
615-}/*}}}*/
616-/*FUNCTION WriteData(PyObject* py_tuple,int index){{{*/
617-void WriteData(PyObject* py_tuple, int index){
618-
619- PyTuple_SetItem(py_tuple, index, Py_None);
620-
621-}/*}}}*/
622-
623-/*ISSM objects*/
624-/*FUNCTION WriteData(PyObject* py_tuple,int index,BamgGeom* bamggeom){{{*/
625-void WriteData(PyObject* py_tuple,int index,BamgGeom* bamggeom){
626-
627- PyObject* dict=NULL;
628-
629- dict=PyDict_New();
630-
631- PyDict_SetItemString(dict,"Vertices",PyArrayFromCopiedData(bamggeom->VerticesSize,bamggeom->Vertices));
632- PyDict_SetItemString(dict,"Edges",PyArrayFromCopiedData(bamggeom->EdgesSize,bamggeom->Edges));
633- PyDict_SetItemString(dict,"TangentAtEdges",PyArrayFromCopiedData(bamggeom->TangentAtEdgesSize,bamggeom->TangentAtEdges));
634- PyDict_SetItemString(dict,"Corners",PyArrayFromCopiedData(bamggeom->CornersSize,bamggeom->Corners));
635- PyDict_SetItemString(dict,"RequiredVertices",PyArrayFromCopiedData(bamggeom->RequiredVerticesSize,bamggeom->RequiredVertices));
636- PyDict_SetItemString(dict,"RequiredEdges",PyArrayFromCopiedData(bamggeom->RequiredEdgesSize,bamggeom->RequiredEdges));
637- PyDict_SetItemString(dict,"CrackedEdges",PyArrayFromCopiedData(bamggeom->CrackedEdgesSize,bamggeom->CrackedEdges));
638- PyDict_SetItemString(dict,"SubDomains",PyArrayFromCopiedData(bamggeom->SubDomainsSize,bamggeom->SubDomains));
639-
640- PyTuple_SetItem(py_tuple, index, dict);
641-}
642-/*}}}*/
643-/*FUNCTION WriteData(PyObject* py_tuple,int index,BamgMesh* bamgmesh){{{*/
644-void WriteData(PyObject* py_tuple,int index,BamgMesh* bamgmesh){
645-
646- PyObject* dict=NULL;
647-
648- dict=PyDict_New();
649-
650- PyDict_SetItemString(dict,"Vertices",PyArrayFromCopiedData(bamgmesh->VerticesSize,bamgmesh->Vertices));
651- PyDict_SetItemString(dict,"Edges",PyArrayFromCopiedData(bamgmesh->EdgesSize,bamgmesh->Edges));
652- PyDict_SetItemString(dict,"Triangles",PyArrayFromCopiedData(bamgmesh->TrianglesSize,bamgmesh->Triangles));
653- PyDict_SetItemString(dict,"Quadrilaterals",PyArrayFromCopiedData(bamgmesh->QuadrilateralsSize,bamgmesh->Quadrilaterals));
654- PyDict_SetItemString(dict,"IssmEdges",PyArrayFromCopiedData(bamgmesh->IssmEdgesSize,bamgmesh->IssmEdges));
655- PyDict_SetItemString(dict,"IssmSegments",PyArrayFromCopiedData(bamgmesh->IssmSegmentsSize,bamgmesh->IssmSegments));
656- PyDict_SetItemString(dict,"VerticesOnGeomVertex",PyArrayFromCopiedData(bamgmesh->VerticesOnGeomVertexSize,bamgmesh->VerticesOnGeomVertex));
657- PyDict_SetItemString(dict,"VerticesOnGeomEdge",PyArrayFromCopiedData(bamgmesh->VerticesOnGeomEdgeSize,bamgmesh->VerticesOnGeomEdge));
658- PyDict_SetItemString(dict,"EdgesOnGeomEdge",PyArrayFromCopiedData(bamgmesh->EdgesOnGeomEdgeSize,bamgmesh->EdgesOnGeomEdge));
659- PyDict_SetItemString(dict,"SubDomains",PyArrayFromCopiedData(bamgmesh->SubDomainsSize,bamgmesh->SubDomains));
660- PyDict_SetItemString(dict,"SubDomainsFromGeom",PyArrayFromCopiedData(bamgmesh->SubDomainsFromGeomSize,bamgmesh->SubDomainsFromGeom));
661- PyDict_SetItemString(dict,"ElementConnectivity",PyArrayFromCopiedData(bamgmesh->ElementConnectivitySize,bamgmesh->ElementConnectivity));
662- PyDict_SetItemString(dict,"NodalConnectivity",PyArrayFromCopiedData(bamgmesh->NodalConnectivitySize,bamgmesh->NodalConnectivity));
663- PyDict_SetItemString(dict,"NodalElementConnectivity",PyArrayFromCopiedData(bamgmesh->NodalElementConnectivitySize,bamgmesh->NodalElementConnectivity));
664- PyDict_SetItemString(dict,"CrackedVertices",PyArrayFromCopiedData(bamgmesh->CrackedVerticesSize,bamgmesh->CrackedVertices));
665- PyDict_SetItemString(dict,"CrackedEdges",PyArrayFromCopiedData(bamgmesh->CrackedEdgesSize,bamgmesh->CrackedEdges));
666-
667- PyTuple_SetItem(py_tuple, index, dict);
668-}
669-/*}}}*/
670-/*FUNCTION WriteData(PyObject* py_tuple,int index,SeqMat<double>* matrix){{{*/
671-void WriteData(PyObject* py_tuple,int index,SeqMat<double>* matrix){
672-
673- int M,N;
674- double* buffer=NULL;
675- npy_intp dims[2]={0,0};
676- PyObject* array=NULL;
677-
678- buffer=matrix->ToSerial();
679- matrix->GetSize(&M,&N);
680- dims[0]=(npy_intp)M;
681- dims[1]=(npy_intp)N;
682- array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,buffer);
683-
684- PyTuple_SetItem(py_tuple, index, array);
685-
686-}/*}}}*/
687-/*FUNCTION WriteData(PyObject* py_tuple,int index,SeqVec<double>* vector){{{*/
688-void WriteData(PyObject* py_tuple,int index,SeqVec<double>* vector){
689-
690- int M;
691- double* buffer=NULL;
692- npy_intp dim=10;
693- PyObject* array=NULL;
694-
695- buffer=vector->ToMPISerial();
696- vector->GetSize(&M);
697- dim=(npy_intp)M;
698- array=PyArray_SimpleNewFromData(1,&dim,NPY_DOUBLE,buffer);
699-
700- PyTuple_SetItem(py_tuple, index, array);
701-}
702-/*}}}*/
703-/*FUNCTION WriteData(PyObject* py_tuple,int index,RiftStruct* riftstruct){{{*/
704-void WriteData(PyObject* py_tuple,int index,RiftStruct* riftstruct){
705-
706- int i;
707- PyObject* list=NULL;
708- PyObject* dict=NULL;
709-
710- list=PyList_New((Py_ssize_t)0);
711-
712- for (i=0; i<riftstruct->numrifts; i++) {
713- dict=PyDict_New();
714-
715- PyDict_SetItemString(dict,"numsegs" ,PyInt_FromSsize_t((Py_ssize_t)riftstruct->riftsnumsegments[i]));
716- PyDict_SetItemString(dict,"segments" ,PyArrayFromCopiedData(riftstruct->riftsnumsegments[i] ,3,riftstruct->riftssegments[i]));
717- PyDict_SetItemString(dict,"pairs" ,PyArrayFromCopiedData(riftstruct->riftsnumpairs[i] ,2,riftstruct->riftspairs[i]));
718- PyDict_SetItemString(dict,"tips" ,PyArrayFromCopiedData(1 ,2,&riftstruct->riftstips[2*i]));
719- PyDict_SetItemString(dict,"penaltypairs" ,PyArrayFromCopiedData(riftstruct->riftsnumpenaltypairs[i],7,riftstruct->riftspenaltypairs[i]));
720- PyDict_SetItemString(dict,"fill" ,PyInt_FromSsize_t((Py_ssize_t)IceEnum));
721- PyDict_SetItemString(dict,"friction" ,PyInt_FromSsize_t((Py_ssize_t)0));
722- PyDict_SetItemString(dict,"fraction" ,PyFloat_FromDouble(0.));
723- PyDict_SetItemString(dict,"fractionincrement",PyFloat_FromDouble(0.1));
724- PyDict_SetItemString(dict,"state" ,PyArrayFromCopiedData(riftstruct->riftsnumpenaltypairs[i],1,riftstruct->state[i]));
725-
726- PyList_Append(list, dict);
727- }
728-
729- PyTuple_SetItem(py_tuple, index, list);
730-}
731-/*}}}*/
732-
733-/*Utils*/
734-/*FUNCTION PyArrayFromCopiedData(int dims[2],double* data){{{*/
735-PyObject* PyArrayFromCopiedData(int dims[2],double* data){
736-
737- double* pydata;
738- npy_intp pydims[2]={0,0};
739-
740- /* note that PyArray_SimpleNewFromData does not copy the data, so that when the original
741- object (e.g. bamggeom,bamgmesh) is deleted, the data is gone. */
742-
743- pydims[0]=(npy_intp)dims[0];
744- pydims[1]=(npy_intp)dims[1];
745- pydata=xNew<IssmDouble>(dims[0]*dims[1]);
746- memcpy(pydata,data,dims[0]*dims[1]*sizeof(double));
747- return PyArray_SimpleNewFromData(2,pydims,NPY_DOUBLE,pydata);
748-}
749-/*}}}*/
750-/*FUNCTION PyArrayFromCopiedData(int dimi,int dimj,double* data){{{*/
751-PyObject* PyArrayFromCopiedData(int dimi,int dimj,double* data){
752-
753- double* pydata;
754- npy_intp pydims[2]={0,0};
755-
756- /* note that PyArray_SimpleNewFromData does not copy the data, so that when the original
757- object (e.g. bamggeom,bamgmesh) is deleted, the data is gone. */
758-
759- pydims[0]=(npy_intp)dimi;
760- pydims[1]=(npy_intp)dimj;
761- pydata=xNew<IssmDouble>(dimi*dimj);
762- memcpy(pydata,data,dimi*dimj*sizeof(double));
763- return PyArray_SimpleNewFromData(2,pydims,NPY_DOUBLE,pydata);
764-}
765-/*}}}*/
766Index: ../trunk-jpl/src/c/issm-binding.h
767===================================================================
768--- ../trunk-jpl/src/c/issm-binding.h (revision 13748)
769+++ ../trunk-jpl/src/c/issm-binding.h (revision 13749)
770@@ -1,18 +0,0 @@
771-#ifndef _ISSM_BINDING_H_
772-#define _ISSM_BINDING_H_
773-
774-#ifdef HAVE_CONFIG_H
775- #include <config.h>
776-#else
777-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
778-#endif
779-
780-#ifdef _HAVE_MATLAB_MODULES_
781-#include "./matlab/matlab-binding.h"
782-#endif
783-
784-#ifdef _HAVE_PYTHON_MODULES_
785-#include "./python/python-binding.h"
786-#endif
787-
788-#endif
789Index: ../trunk-jpl/src/c/matlab/include/matlab_macros.h
790===================================================================
791--- ../trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 13748)
792+++ ../trunk-jpl/src/c/matlab/include/matlab_macros.h (revision 13749)
793@@ -1,44 +0,0 @@
794-/* \file matlab macros.h
795- * \brief: macros used for the matlab bindings
796- */
797-
798-/*Header {{{*/
799-#ifndef _MATLAB_MACROS_H_
800-#define _MATLAB_MACROS_H_
801-
802-#ifdef HAVE_CONFIG_H
803- #include <config.h>
804-#else
805-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
806-#endif
807-/*}}}*/
808-
809-#ifdef _HAVE_MATLAB_
810-/* MODULEBOOT/MODULEEND {{{*/
811-
812-/*The following macros hide the error exception handling in a matlab module. Just put
813- * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions
814- * will be trapped*/
815-#define MODULEBOOT(); try{ \
816- IssmComm::SetComm(-1);
817-
818-#define MODULEEND(); }\
819- catch(ErrorException &exception){\
820- mexErrMsgTxt(exception.MatlabReport()); \
821- }\
822- catch (exception &e){\
823- mexErrMsgTxt(exprintf("Standard exception: %s\n",e.what()));\
824- }\
825- catch(...){\
826- mexErrMsgTxt("An unexpected error occurred");\
827- }
828-/*}}}*/
829-/* WRAPPER {{{*/
830-#define WRAPPER(modulename,...) void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
831-/*}}}*/
832-/* CHECKARGUMENTS {{{*/
833-#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,functionpointer)
834-/*}}}*/
835-#endif
836-
837-#endif
838Index: ../trunk-jpl/src/c/matlab/io/OptionParse.cpp
839===================================================================
840--- ../trunk-jpl/src/c/matlab/io/OptionParse.cpp (revision 13748)
841+++ ../trunk-jpl/src/c/matlab/io/OptionParse.cpp (revision 13749)
842@@ -1,203 +0,0 @@
843-/*\file OptionParse.c
844- *\brief: functions to parse the mex options.
845- */
846-#ifdef HAVE_CONFIG_H
847- #include <config.h>
848-#else
849-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
850-#endif
851-
852-#include <cstring>
853-#include <mex.h>
854-#include "../../shared/shared.h"
855-#include "../../io/io.h"
856-#include "../../include/include.h"
857-#include "./matlabio.h"
858-
859-GenericOption<double>* OptionDoubleParse( char* name, const mxArray* prhs[]){ /*{{{*/
860-
861- GenericOption<double> *odouble = NULL;
862-
863- /*check and parse the name */
864- odouble=new GenericOption<double>();
865- odouble->name =xNew<char>(strlen(name)+1);
866- memcpy(odouble->name,name,(strlen(name)+1)*sizeof(char));
867- FetchData(&odouble->value,prhs[0]);
868- odouble->numel=1;
869- odouble->ndims=1;
870- odouble->size=NULL;
871-
872- return(odouble);
873-}/*}}}*/
874-GenericOption<double*>* OptionDoubleArrayParse( char* name, const mxArray* prhs[]){ /*{{{*/
875-
876- GenericOption<double*> *odouble = NULL;
877-
878- /*check and parse the name */
879- odouble=new GenericOption<double*>();
880- odouble->name =xNew<char>(strlen(name)+1);
881- memcpy(odouble->name,name,(strlen(name)+1)*sizeof(char));
882-
883- /*check and parse the value */
884- if (!mxIsClass(prhs[0],"double")){
885- _error_("Value of option \"" << odouble->name << "\" must be class \"double\", not class \"" << mxGetClassName(prhs[0]) <<"\".");
886- }
887- FetchData(&odouble->value,&odouble->numel,&odouble->ndims,&odouble->size,prhs[0]);
888-
889- return(odouble);
890-}/*}}}*/
891-GenericOption<bool*>* OptionLogicalParse( char* name, const mxArray* prhs[]){ /*{{{*/
892-
893- GenericOption<bool*> *ological = NULL;
894-
895- /*check and parse the name */
896- ological=new GenericOption<bool*>();
897- ological->name =xNew<char>(strlen(name)+1);
898- memcpy(ological->name,name,(strlen(name)+1)*sizeof(char));
899-
900- /*check and parse the value */
901- if (!mxIsClass(prhs[0],"logical")){
902- _error_("Value of option \"" << ological->name << "\" must be class \"logical\", not class \"" << mxGetClassName(prhs[0]) <<"\".");
903- }
904- FetchData(&ological->value,&ological->numel,&ological->ndims,&ological->size,prhs[0]);
905-
906- return(ological);
907-}/*}}}*/
908-GenericOption<char*>* OptionCharParse( char* name, const mxArray* prhs[]){ /*{{{*/
909-
910- GenericOption<char*> *ochar = NULL;
911-
912- /*check and parse the name */
913- ochar=new GenericOption<char*>();
914- ochar->name =xNew<char>(strlen(name)+1);
915- memcpy(ochar->name,name,(strlen(name)+1)*sizeof(char));
916-
917- /*check and parse the value */
918- if (!mxIsClass(prhs[0],"char")){
919- _error_("Value of option \"" << ochar->name << "\" must be class \"char\", not class \"" << mxGetClassName(prhs[0]) <<"\".");
920- }
921- FetchData(&ochar->value,&ochar->numel,&ochar->ndims,&ochar->size,prhs[0]);
922-
923- return(ochar);
924-}/*}}}*/
925-GenericOption<Options**>* OptionStructParse( char* name, const mxArray* prhs[]){ /*{{{*/
926-
927- int i;
928- char namei[161];
929- Option* option = NULL;
930- GenericOption<Options**> *ostruct = NULL;
931- const mwSize *ipt = NULL;
932- const mxArray *structi;
933- mwIndex sindex;
934-
935- /*check and parse the name */
936- ostruct=new GenericOption<Options**>();
937- ostruct->name =xNew<char>(strlen(name)+1);
938- memcpy(ostruct->name,name,(strlen(name)+1)*sizeof(char));
939-
940- /*check and parse the value */
941- if (!mxIsClass(prhs[0],"struct")){
942- _error_("Value of option \"" << ostruct->name << "\" must be class \"struct\", not class \"" << mxGetClassName(prhs[0]) <<"\".");
943- }
944- ostruct->numel=mxGetNumberOfElements(prhs[0]);
945- ostruct->ndims=mxGetNumberOfDimensions(prhs[0]);
946- ipt =mxGetDimensions(prhs[0]);
947- ostruct->size =xNew<int>(ostruct->ndims);
948- for (i=0; i<ostruct->ndims; i++) ostruct->size[i]=(int)ipt[i];
949- if (ostruct->numel) ostruct->value=xNew<Options*>(ostruct->numel);
950-
951- /*loop through and process each element of the struct array */
952- for (sindex=0; sindex<ostruct->numel; sindex++) {
953- ostruct->value[sindex]=new Options;
954-
955- /*loop through and process each field for the element */
956- for (i=0; i<mxGetNumberOfFields(prhs[0]); i++) {
957- sprintf(namei,"%s.%s",name,mxGetFieldNameByNumber(prhs[0],i));
958- structi=mxGetFieldByNumber(prhs[0],sindex,i);
959-
960- option=(Option*)OptionParse(namei,&structi);
961- ostruct->value[sindex]->AddObject((Object*)option);
962- option=NULL;
963- }
964- }
965-
966- return(ostruct);
967-}/*}}}*/
968-GenericOption<Options*>* OptionCellParse( char* name, const mxArray* prhs[]){ /*{{{*/
969-
970- int i;
971- int *dims;
972- char namei[161];
973- char cstr[81];
974- GenericOption<Options*> *ocell = NULL;
975- Option *option = NULL;
976- const mwSize *ipt = NULL;
977- const mxArray *celli;
978- mwIndex cindex;
979-
980- /*check and parse the name */
981- ocell=new GenericOption<Options*>();
982- ocell->name =xNew<char>(strlen(name)+1);
983- memcpy(ocell->name,name,(strlen(name)+1)*sizeof(char));
984-
985- /*check and parse the value */
986- if (!mxIsClass(prhs[0],"cell")){
987- _error_("Value of option \"" << ocell->name << "\" must be class \"cell\", not class \"" << mxGetClassName(prhs[0]) <<"\".");
988- }
989-
990- ocell->numel=mxGetNumberOfElements(prhs[0]);
991- ocell->ndims=mxGetNumberOfDimensions(prhs[0]);
992- ipt =mxGetDimensions(prhs[0]);
993- ocell->size =xNew<int>(ocell->ndims);
994- for (i=0; i<ocell->ndims; i++) ocell->size[i]=(int)ipt[i];
995- ocell->value=new Options;
996-
997- /*loop through and process each element of the cell array */
998- dims=xNew<int>(ocell->ndims);
999- for (cindex=0; cindex<ocell->numel; cindex++) {
1000- ColumnWiseDimsFromIndex(dims,(int)cindex,ocell->size,ocell->ndims);
1001- StringFromDims(cstr,dims,ocell->ndims);
1002- #ifdef _INTEL_WIN_
1003- _snprintf(namei,161,"%s%s",name,cstr);
1004- #else
1005- snprintf(namei,161,"%s%s",name,cstr);
1006- #endif
1007- celli=mxGetCell(prhs[0],cindex);
1008-
1009- option=(Option*)OptionParse(namei,&celli);
1010- ocell->value->AddObject((Object*)option);
1011- option=NULL;
1012- }
1013- xDelete<int>(dims);
1014-
1015- return(ocell);
1016-}/*}}}*/
1017-Option* OptionParse(char* name, const mxArray* prhs[]){ /*{{{*/
1018-
1019- Option *option = NULL;
1020- mxArray *lhs[1];
1021-
1022- /*parse the value according to the matlab data type */
1023- if (mxIsClass(prhs[0],"double") && (mxGetNumberOfElements(prhs[0])==1))
1024- option=(Option*)OptionDoubleParse(name,prhs);
1025- else if(mxIsClass(prhs[0],"double") && (mxGetNumberOfElements(prhs[0])!=1))
1026- option=(Option*)OptionDoubleArrayParse(name,prhs);
1027- else if(mxIsClass(prhs[0],"logical"))
1028- option=(Option*)OptionLogicalParse(name,prhs);
1029- else if(mxIsClass(prhs[0],"char"))
1030- option=(Option*)OptionCharParse(name,prhs);
1031- else if(mxIsClass(prhs[0],"struct"))
1032- option=(Option*)OptionStructParse(name,prhs);
1033- else if(mxIsClass(prhs[0],"cell"))
1034- option=(Option*)OptionCellParse(name,prhs);
1035- else {
1036- _pprintLine_(" Converting value of option \"" << name << "\" from unrecognized class \"" << mxGetClassName(prhs[0]) << "\" to class \"" << "struct" << "\".");
1037- if (!mexCallMATLAB(1,lhs,1,(mxArray**)prhs,"struct")) {
1038- option=(Option*)OptionStructParse(name,(const mxArray**)lhs);
1039- mxDestroyArray(lhs[0]);
1040- }
1041- else _error_("Second argument value of option \""<< name <<"\" is of unrecognized class \""<< mxGetClassName(prhs[0]) <<"\".");
1042- }
1043-
1044- return(option);
1045-}/*}}}*/
1046Index: ../trunk-jpl/src/c/matlab/io/MatlabMatrixToSeqMat.cpp
1047===================================================================
1048--- ../trunk-jpl/src/c/matlab/io/MatlabMatrixToSeqMat.cpp (revision 13748)
1049+++ ../trunk-jpl/src/c/matlab/io/MatlabMatrixToSeqMat.cpp (revision 13749)
1050@@ -1,29 +0,0 @@
1051-/*!\file MatlabMatrixToSeqMat.cpp
1052- */
1053-
1054-/*Headers:*/
1055-/*{{{*/
1056-#ifdef HAVE_CONFIG_H
1057- #include <config.h>
1058-#else
1059-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
1060-#endif
1061-
1062-#include <mex.h>
1063-#include <stdio.h>
1064-#include <string.h>
1065-#include "../../toolkits/toolkits.h"
1066-#include "../../shared/shared.h"
1067-#include "./matlabio.h"
1068-
1069-/*}}}*/
1070-
1071-SeqMat<double>* MatlabMatrixToSeqMat(const mxArray* dataref){
1072-
1073- SeqMat<double>* output=NULL;
1074-
1075- output=new SeqMat<double>();
1076- MatlabMatrixToDoubleMatrix(&output->matrix,&output->M,&output->N,dataref);
1077- return output;
1078-
1079-}
1080Index: ../trunk-jpl/src/c/matlab/io/MatlabVectorToPetscVec.cpp
1081===================================================================
1082--- ../trunk-jpl/src/c/matlab/io/MatlabVectorToPetscVec.cpp (revision 13748)
1083+++ ../trunk-jpl/src/c/matlab/io/MatlabVectorToPetscVec.cpp (revision 13749)
1084@@ -1,108 +0,0 @@
1085-/* \file MatlabVectorToPetscVector.cpp
1086- * \brief: convert a sparse or dense matlab vector to a serial Petsc vector:
1087- */
1088-
1089-#ifdef HAVE_CONFIG_H
1090- #include <config.h>
1091-#else
1092-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
1093-#endif
1094-
1095-/*Petsc includes: */
1096-#include "petscmat.h"
1097-#include "petscvec.h"
1098-#include "petscksp.h"
1099-
1100-/*Matlab includes: */
1101-#include "mex.h"
1102-
1103-#include "../../shared/shared.h"
1104-#include "matlabio.h"
1105-
1106-PetscVec* MatlabVectorToPetscVec(const mxArray* mxvector){
1107-
1108- int dummy;
1109- PetscVec* vector=new PetscVec();
1110-
1111- MatlabVectorToPetscVec(&vector->vector,&dummy, mxvector);
1112-
1113- return vector;
1114-}
1115-
1116-int MatlabVectorToPetscVec(Vec* pvector,int* pvector_rows,const mxArray* mxvector){
1117-
1118- int rows, cols;
1119- double* mxvector_ptr=NULL;
1120- int ierr;
1121- int i,j;
1122-
1123- /*output: */
1124- Vec vector=NULL;
1125-
1126- /*matlab indices: */
1127- mwIndex* ir=NULL;
1128- mwIndex* jc=NULL;
1129- double* pr=NULL;
1130- int count;
1131- int nnz;
1132- int nz;
1133-
1134- /*petsc indices: */
1135- int* idxm=NULL;
1136-
1137- /*Ok, first check if we are dealing with a sparse or full vector: */
1138- if (mxIsSparse(mxvector)){
1139-
1140- /*Dealing with sparse vector: recover size first: */
1141- mxvector_ptr=(double*)mxGetPr(mxvector);
1142- rows=mxGetM(mxvector);
1143- cols=mxGetN(mxvector);
1144- nnz=mxGetNzmax(mxvector);
1145- nz=(int)((double)nnz/(double)rows);
1146-
1147- ierr=VecCreateSeq(PETSC_COMM_SELF,rows,&vector);CHKERRQ(ierr);
1148-
1149- /*Now, get ir,jc and pr: */
1150- pr=mxGetPr(mxvector);
1151- ir=mxGetIr(mxvector);
1152- jc=mxGetJc(mxvector);
1153-
1154- /*Now, start inserting data into sparse vector: */
1155- count=0;
1156- for(i=0;i<cols;i++){
1157- for(j=0;j<(jc[i+1]-jc[i]);j++){
1158- VecSetValue(vector,ir[count],pr[count],INSERT_VALUES);
1159- count++;
1160- }
1161- }
1162-
1163- }
1164- else{
1165-
1166- /*Dealing with dense vector: recover pointer and size: */
1167- mxvector_ptr=(double*)mxGetPr(mxvector);
1168- rows=mxGetM(mxvector);
1169- cols=mxGetN(mxvector);
1170-
1171- /*Create serial vector: */
1172- ierr=VecCreateSeq(PETSC_COMM_SELF,rows,&vector);CHKERRQ(ierr);
1173-
1174- /*Insert mxvector_ptr values into petsc vector: */
1175- idxm=xNew<int>(rows);
1176-
1177- for(i=0;i<rows;i++)idxm[i]=i;
1178-
1179- ierr=VecSetValues(vector,rows,idxm,mxvector_ptr,INSERT_VALUES);CHKERRQ(ierr);
1180-
1181- }
1182-
1183- /*Assemble vector: */
1184- VecAssemblyBegin(vector);
1185- VecAssemblyEnd(vector);
1186-
1187- /*Assign output pointer: */
1188- *pvector=vector;
1189- *pvector_rows=rows;
1190-
1191- return 1;
1192-}
1193Index: ../trunk-jpl/src/c/matlab/io/MatlabVectorToDoubleVector.cpp
1194===================================================================
1195--- ../trunk-jpl/src/c/matlab/io/MatlabVectorToDoubleVector.cpp (revision 13748)
1196+++ ../trunk-jpl/src/c/matlab/io/MatlabVectorToDoubleVector.cpp (revision 13749)
1197@@ -1,94 +0,0 @@
1198-/* \file MatlabVectorToDoubleVector.cpp
1199- * \brief: convert a sparse or dense matlab vector to a serial vector:
1200- */
1201-
1202-#ifdef HAVE_CONFIG_H
1203- #include <config.h>
1204-#else
1205-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
1206-#endif
1207-
1208-#include <string.h>
1209-
1210-/*Matlab includes: */
1211-#include "mex.h"
1212-
1213-#include "../../shared/shared.h"
1214-
1215-int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector){
1216-
1217- int rows,cols;
1218- double* mxvector_ptr=NULL;
1219- int ierr;
1220- int i,j;
1221-
1222- /*output: */
1223- double* vector=NULL;
1224-
1225- /*matlab indices: */
1226- mwIndex* ir=NULL;
1227- mwIndex* jc=NULL;
1228- double* pr=NULL;
1229- int count;
1230- int nnz;
1231- int nz;
1232-
1233- /*Ok, first check if we are dealing with a sparse or full vector: */
1234- if (mxIsSparse(mxvector)){
1235-
1236- /*Dealing with sparse vector: recover size first: */
1237- mxvector_ptr=(double*)mxGetPr(mxvector);
1238- rows=mxGetM(mxvector);
1239- cols=mxGetN(mxvector);
1240- nnz=mxGetNzmax(mxvector);
1241-
1242- /*Check that input is actualy a vector*/
1243- if (cols!=1) _error_("input vector of size " << rows << "x" << cols << " should have only one column");
1244-
1245- nz=(int)((double)nnz/(double)rows);
1246-
1247- if(rows){
1248- vector=xNewZeroInit<double>(rows);
1249-
1250- /*Now, get ir,jc and pr: */
1251- pr=mxGetPr(mxvector);
1252- ir=mxGetIr(mxvector);
1253- jc=mxGetJc(mxvector);
1254-
1255- /*Now, start inserting data into sparse vector: */
1256- count=0;
1257- for(i=0;i<cols;i++){
1258- for(j=0;j<(jc[i+1]-jc[i]);j++){
1259- vector[ir[count]]=pr[count];
1260- count++;
1261- }
1262- }
1263- }
1264-
1265- }
1266- else{
1267-
1268- /*Dealing with dense vector: recover pointer and size: */
1269- mxvector_ptr=(double*)mxGetPr(mxvector);
1270- rows=mxGetM(mxvector);
1271- cols=mxGetN(mxvector);
1272-
1273- /*Check that input is actualy a vector*/
1274- if (cols!=1) _error_("input vector of size " << rows << "x" << cols << " should have only one column");
1275-
1276- /*allocate and memcpy*/
1277- if(rows){
1278- vector=xNew<double>(rows);
1279- memcpy(vector,mxvector_ptr,rows*sizeof(double));
1280- }
1281- else{
1282- vector=NULL;
1283- }
1284- }
1285-
1286- /*Assign output pointer: */
1287- *pvector=vector;
1288- *pvector_rows=rows;
1289-
1290- return 1;
1291-}
1292Index: ../trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp
1293===================================================================
1294--- ../trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp (revision 13748)
1295+++ ../trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp (revision 13749)
1296@@ -1,693 +0,0 @@
1297-/*\file FetchData.cpp:
1298- * \brief: general I/O interface to fetch data in matlab
1299- */
1300-
1301-#ifdef HAVE_CONFIG_H
1302- #include <config.h>
1303-#else
1304-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
1305-#endif
1306-
1307-#include <mex.h>
1308-#include "../../shared/shared.h"
1309-#include "../../include/include.h"
1310-#include "./matlabio.h"
1311-
1312-/*Primitive data types*/
1313-/*FUNCTION FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){{{*/
1314-void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){
1315-
1316- double* outmatrix=NULL;
1317- int outmatrix_rows,outmatrix_cols;
1318-
1319- if(mxIsEmpty(dataref) ){
1320- /*Nothing to pick up. Just initialize matrix pointer to NULL: */
1321- outmatrix_rows=0;
1322- outmatrix_cols=0;
1323- outmatrix=NULL;
1324- }
1325- else if( mxIsClass(dataref,"double") ||
1326- mxIsClass(dataref,"single") ||
1327- mxIsClass(dataref,"int16") ||
1328- mxIsClass(dataref,"int8") ||
1329- mxIsClass(dataref,"uint8")){
1330- /*Check dataref is not pointing to NaN: */
1331- if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){
1332- outmatrix_rows=0;
1333- outmatrix_cols=0;
1334- outmatrix=NULL;
1335- }
1336- else{
1337- if(!mxIsClass(dataref,"double") && !mxIsClass(dataref,"single")){
1338- _printLine_("Warning: converting matlab data from '" << mxGetClassName(dataref) << "' to 'double'");
1339- }
1340- /*Convert matlab matrix to double* matrix: */
1341- MatlabMatrixToDoubleMatrix(&outmatrix,&outmatrix_rows,&outmatrix_cols,dataref);
1342- }
1343- }
1344- else{
1345- /*This is an error: we don't have the correct input!: */
1346- _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
1347- }
1348-
1349- /*Assign output pointers:*/
1350- *pmatrix=outmatrix;
1351- if (pM)*pM=outmatrix_rows;
1352- if (pN)*pN=outmatrix_cols;
1353-
1354-}
1355-/*}}}*/
1356-/*FUNCTION FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){{{*/
1357-void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){
1358-
1359- int outmatrix_numel,outmatrix_ndims;
1360- double *outmatrix = NULL;
1361- int *outmatrix_size = NULL;
1362-
1363- if(mxIsEmpty(dataref) ){
1364- /*Nothing to pick up. Just initialize matrix pointer to NULL: */
1365- outmatrix_numel = 0;
1366- outmatrix_ndims = 0;
1367- outmatrix_size = NULL;
1368- outmatrix = NULL;
1369- }
1370- else if( mxIsClass(dataref,"double") ||
1371- mxIsClass(dataref,"single") ||
1372- mxIsClass(dataref,"int16") ||
1373- mxIsClass(dataref,"int8") ||
1374- mxIsClass(dataref,"uint8")){
1375-
1376- /*Check dataref is not pointing to NaN: */
1377- if (mxIsNaN(*(mxGetPr(dataref))) && (mxGetNumberOfElements(dataref)==1)){
1378- outmatrix_numel = 0;
1379- outmatrix_ndims = 0;
1380- outmatrix_size = NULL;
1381- outmatrix = NULL;
1382- }
1383- else{
1384- if(!mxIsClass(dataref,"double") && !mxIsClass(dataref,"single")){
1385- _printLine_("Warning: converting matlab data from '" << mxGetClassName(dataref) << "' to 'double'");
1386- }
1387- /*Convert matlab n-dim array to double* matrix: */
1388- MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref);
1389- }
1390- }
1391- else{
1392- /*This is an error: we don't have the correct input!: */
1393- _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
1394- }
1395-
1396- /*Assign output pointers:*/
1397- *pmatrix=outmatrix;
1398- if (pnumel)*pnumel=outmatrix_numel;
1399- if (pndims)*pndims=outmatrix_ndims;
1400- if (psize )*psize =outmatrix_size;
1401- else xDelete<int>(outmatrix_size);
1402-
1403-}
1404-/*}}}*/
1405-/*FUNCTION FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref){{{*/
1406-void FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref){
1407-
1408- int i,outmatrix_rows,outmatrix_cols;
1409- double *doublematrix=NULL;
1410- int *outmatrix=NULL;
1411-
1412- if(mxIsEmpty(dataref) ){
1413- /*Nothing to pick up. Just initialize matrix pointer to NULL: */
1414- outmatrix_rows=0;
1415- outmatrix_cols=0;
1416- outmatrix=NULL;
1417- }
1418- else if( mxIsClass(dataref,"double") ||
1419- mxIsClass(dataref,"single") ||
1420- mxIsClass(dataref,"int16") ||
1421- mxIsClass(dataref,"int8") ||
1422- mxIsClass(dataref,"uint8")){
1423-
1424- /*Check dataref is not pointing to NaN: */
1425- if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){
1426- outmatrix_rows=0;
1427- outmatrix_cols=0;
1428- outmatrix=NULL;
1429- }
1430- else{
1431- if(!mxIsClass(dataref,"double") && !mxIsClass(dataref,"single")){
1432- _printLine_("Warning: converting matlab data from '" << mxGetClassName(dataref) << "' to 'double'");
1433- }
1434- /*Convert matlab matrix to double* matrix: */
1435- MatlabMatrixToDoubleMatrix(&doublematrix,&outmatrix_rows,&outmatrix_cols,dataref);
1436-
1437- /*Convert double matrix into integer matrix: */
1438- outmatrix=xNew<int>(outmatrix_rows*outmatrix_cols);
1439- for(i=0;i<outmatrix_rows*outmatrix_cols;i++)outmatrix[i]=(int)doublematrix[i];
1440- }
1441- }
1442- else{
1443- /*This is an error: we don't have the correct input!: */
1444- _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
1445- }
1446-
1447- /*Assign output pointers:*/
1448- *pmatrix=outmatrix;
1449- if (pM)*pM=outmatrix_rows;
1450- if (pN)*pN=outmatrix_cols;
1451-}
1452-/*}}}*/
1453-/*FUNCTION FetchData(bool** pmatrix,int* pM,int *pN,const mxArray* dataref){{{*/
1454-void FetchData(bool** pmatrix,int* pM,int *pN,const mxArray* dataref){
1455-
1456- int i,outmatrix_rows,outmatrix_cols;
1457- double *doublematrix=NULL;
1458- bool *outmatrix=NULL;
1459-
1460- if(mxIsEmpty(dataref) ){
1461- /*Nothing to pick up. Just initialize matrix pointer to NULL: */
1462- outmatrix_rows=0;
1463- outmatrix_cols=0;
1464- outmatrix=NULL;
1465- }
1466- else if (mxIsClass(dataref,"double") ){
1467-
1468- /*Check dataref is not pointing to NaN: */
1469- if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){
1470- outmatrix_rows=0;
1471- outmatrix_cols=0;
1472- outmatrix=NULL;
1473- }
1474- else{
1475-
1476- /*Convert matlab matrix to double* matrix: */
1477- MatlabMatrixToDoubleMatrix(&doublematrix,&outmatrix_rows,&outmatrix_cols,dataref);
1478-
1479- /*Convert double matrix into integer matrix: */
1480- outmatrix=xNew<bool>(outmatrix_rows*outmatrix_cols);
1481- for(i=0;i<outmatrix_rows;i++)outmatrix[i]=(bool)doublematrix[i];
1482- }
1483- }
1484- else{
1485- /*This is an error: we don't have the correct input!: */
1486- _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
1487- }
1488-
1489- /*Assign output pointers:*/
1490- *pmatrix=outmatrix;
1491- if (pM)*pM=outmatrix_rows;
1492- if (pN)*pN=outmatrix_cols;
1493-}
1494-/*}}}*/
1495-/*FUNCTION FetchData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){{{*/
1496-void FetchData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){
1497-
1498- int i;
1499- int outmatrix_numel,outmatrix_ndims;
1500- int* outmatrix_size=NULL;
1501- double* doublematrix=NULL;
1502- bool* outmatrix=NULL;
1503-
1504- if(mxIsEmpty(dataref) ){
1505- /*Nothing to pick up. Just initialize matrix pointer to NULL: */
1506- outmatrix_numel=0;
1507- outmatrix_ndims=0;
1508- outmatrix_size =NULL;
1509- outmatrix=NULL;
1510- }
1511- else if (mxIsClass(dataref,"logical") ){
1512-
1513- /*Check dataref is not pointing to NaN: */
1514- if ( mxIsNaN(*((bool*)mxGetData(dataref))) && (mxGetNumberOfElements(dataref)==1) ){
1515- outmatrix_numel=0;
1516- outmatrix_ndims=0;
1517- outmatrix_size =NULL;
1518- outmatrix=NULL;
1519- }
1520- else{
1521-
1522- /*Convert matlab n-dim array to bool* matrix: */
1523- MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref);
1524- }
1525- }
1526- else if (mxIsClass(dataref,"double") ){
1527-
1528- /*Check dataref is not pointing to NaN: */
1529- if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetNumberOfElements(dataref)==1) ){
1530- outmatrix_numel=0;
1531- outmatrix_ndims=0;
1532- outmatrix_size =NULL;
1533- outmatrix=NULL;
1534- }
1535- else{
1536-
1537- /*Convert matlab n-dim array to double* matrix: */
1538- MatlabNArrayToNArray(&doublematrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref);
1539-
1540- /*Convert double matrix into bool matrix: */
1541- outmatrix=xNew<bool>(outmatrix_numel);
1542- for(i=0;i<outmatrix_numel;i++)outmatrix[i]=(bool)doublematrix[i];
1543- xDelete<double>(doublematrix);
1544- }
1545- }
1546- else{
1547- /*This is an error: we don't have the correct input!: */
1548- _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
1549- }
1550-
1551- /*Assign output pointers:*/
1552- *pmatrix=outmatrix;
1553- if (pnumel)*pnumel=outmatrix_numel;
1554- if (pndims)*pndims=outmatrix_ndims;
1555- if (psize )*psize =outmatrix_size;
1556- else xDelete<int>(outmatrix_size);
1557-
1558-}
1559-/*}}}*/
1560-/*FUNCTION FetchData(double** pvector,int* pM,const mxArray* dataref){{{*/
1561-void FetchData(double** pvector,int* pM,const mxArray* dataref){
1562-
1563- double* outvector=NULL;
1564- int outvector_rows;
1565-
1566- if(mxIsEmpty(dataref)){
1567- /*Nothing to pick up. Just initialize matrix pointer to NULL: */
1568- outvector_rows=0;
1569- outvector=NULL;
1570- }
1571- else if (mxIsClass(dataref,"double") ){
1572-
1573- /*Convert matlab vector to double* vector: */
1574- MatlabVectorToDoubleVector(&outvector,&outvector_rows,dataref);
1575-
1576- }
1577- else{
1578- /*This is an error: we don't have the correct input!: */
1579- _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
1580- }
1581-
1582- /*Assign output pointers:*/
1583- *pvector=outvector;
1584- if (pM)*pM=outvector_rows;
1585-}
1586-/*}}}*/
1587-/*FUNCTION FetchData(int** pvector,int* pM,const mxArray* dataref){{{*/
1588-void FetchData(int** pvector,int* pM,const mxArray* dataref){
1589-
1590- int i;
1591- double *doublevector = NULL;
1592- int *outvector = NULL;
1593- int outvector_rows;
1594-
1595- if(mxIsEmpty(dataref)){
1596- /*Nothing to pick up. Just initialize matrix pointer to NULL: */
1597- outvector_rows=0;
1598- outvector=NULL;
1599- }
1600- else if (mxIsClass(dataref,"double") ){
1601-
1602- /*Convert matlab vector to double* vector: */
1603- MatlabVectorToDoubleVector(&doublevector,&outvector_rows,dataref);
1604-
1605- /*Convert double vector into integer vector: */
1606- outvector=xNew<int>(outvector_rows);
1607- for(i=0;i<outvector_rows;i++)outvector[i]=(int)doublevector[i];
1608- }
1609- else{
1610- /*This is an error: we don't have the correct input!: */
1611- _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
1612- }
1613-
1614- /*Assign output pointers:*/
1615- *pvector=outvector;
1616- if (pM)*pM=outvector_rows;
1617-}
1618-/*}}}*/
1619-/*FUNCTION FetchData(bool** pvector,int* pM,const mxArray* dataref){{{*/
1620-void FetchData(bool** pvector,int* pM,const mxArray* dataref){
1621-
1622- int i;
1623- double *doublevector = NULL;
1624- bool *outvector = NULL;
1625- int outvector_rows;
1626-
1627- if(mxIsEmpty(dataref)){
1628- /*Nothing to pick up. Just initialize matrix pointer to NULL: */
1629- outvector_rows=0;
1630- outvector=NULL;
1631- }
1632- else if (mxIsClass(dataref,"double") ){
1633-
1634- /*Convert matlab vector to double* vector: */
1635- MatlabVectorToDoubleVector(&doublevector,&outvector_rows,dataref);
1636-
1637- /*Convert double vector into integer vector: */
1638- outvector=xNew<bool>(outvector_rows);
1639- for(i=0;i<outvector_rows;i++)outvector[i]=(bool)doublevector[i];
1640- }
1641- else{
1642- /*This is an error: we don't have the correct input!: */
1643- _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
1644- }
1645-
1646- /*Assign output pointers:*/
1647- *pvector=outvector;
1648- if (pM)*pM=outvector_rows;
1649-}
1650-/*}}}*/
1651-/*FUNCTION FetchData(float** pvector,int* pM,const mxArray* dataref){{{*/
1652-void FetchData(float** pvector,int* pM,const mxArray* dataref){
1653-
1654- int i;
1655- double *doublevector = NULL;
1656- float *outvector = NULL;
1657- int outvector_rows;
1658-
1659- if(mxIsEmpty(dataref)){
1660- /*Nothing to pick up. Just initialize matrix pointer to NULL: */
1661- outvector_rows=0;
1662- outvector=NULL;
1663- }
1664- else if (mxIsClass(dataref,"double") ){
1665-
1666- /*Convert matlab vector to double* vector: */
1667- MatlabVectorToDoubleVector(&doublevector,&outvector_rows,dataref);
1668-
1669- /*Convert double vector into float vector: */
1670- outvector=xNew<float>(outvector_rows);
1671- for(i=0;i<outvector_rows;i++)outvector[i]=(float)doublevector[i];
1672- }
1673- else{
1674- /*This is an error: we don't have the correct input!: */
1675- _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
1676- }
1677-
1678- /*Assign output pointers:*/
1679- *pvector=outvector;
1680- if (pM)*pM=outvector_rows;
1681-}
1682-/*}}}*/
1683-/*FUNCTION FetchData(char** pstring,const mxArray* dataref){{{*/
1684-void FetchData(char** pstring,const mxArray* dataref){
1685-
1686- char* outstring=NULL;
1687-
1688- /*Ok, the string should be coming directly from the matlab workspace: */
1689- if (!mxIsClass(dataref,"char")){
1690- _error_("input data_type is not a string!");
1691- }
1692- else{
1693- /*Recover the string:*/
1694- int stringlen;
1695-
1696- stringlen = mxGetM(dataref)*mxGetN(dataref)+1;
1697- outstring =xNew<char>(stringlen);
1698- mxGetString(dataref,outstring,stringlen);
1699- }
1700-
1701- /*Assign output pointers:*/
1702- *pstring=outstring;
1703-}/*}}}*/
1704-/*FUNCTION FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){{{*/
1705-void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){
1706-
1707- int outmatrix_numel,outmatrix_ndims;
1708- int* outmatrix_size=NULL;
1709- char* outmatrix=NULL;
1710-
1711- if(mxIsEmpty(dataref) ){
1712- /*Nothing to pick up. Just initialize matrix pointer to NULL: */
1713- outmatrix_numel=0;
1714- outmatrix_ndims=0;
1715- outmatrix_size =NULL;
1716- outmatrix=NULL;
1717- }
1718- else if (mxIsClass(dataref,"char") ){
1719-
1720- /*Convert matlab n-dim array to char* matrix: */
1721- MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref);
1722- }
1723- else{
1724- /*This is an error: we don't have the correct input!: */
1725- _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
1726- }
1727-
1728- /*Assign output pointers:*/
1729- *pmatrix=outmatrix;
1730- if (pnumel)*pnumel=outmatrix_numel;
1731- if (pndims)*pndims=outmatrix_ndims;
1732- if (psize )*psize =outmatrix_size;
1733- else xDelete<int>(outmatrix_size);
1734-
1735-}
1736-/*}}}*/
1737-/*FUNCTION FetchData(double* pscalar,const mxArray* dataref){{{*/
1738-void FetchData(double* pscalar,const mxArray* dataref){
1739-
1740- double scalar;
1741-
1742- if (!mxIsClass(dataref,"double")){
1743- _error_("input data_type is not a double!");
1744- }
1745- else{
1746- /*Recover the double: */
1747- scalar=mxGetScalar(dataref);
1748- }
1749-
1750- /*Assign output pointers:*/
1751- *pscalar=scalar;
1752-}
1753-/*}}}*/
1754-/*FUNCTION FetchData(int* pinteger,const mxArray* dataref){{{*/
1755-void FetchData(int* pinteger,const mxArray* dataref){
1756-
1757- int integer;
1758-
1759- if (!mxIsClass(dataref,"double")){
1760- _error_("input data_type is not a scalar!");
1761- }
1762- else{
1763- /*Recover the double: */
1764- integer=(int)mxGetScalar(dataref);
1765- }
1766-
1767- /*Assign output pointers:*/
1768- *pinteger=integer;
1769-}
1770-/*}}}*/
1771-/*FUNCTION FetchData(bool* pboolean,const mxArray* dataref){{{*/
1772-void FetchData(bool* pboolean,const mxArray* dataref){
1773-
1774- bool* mxbool_ptr=NULL;
1775-
1776- if (mxIsClass(dataref,"logical")){
1777- if(mxGetM(dataref)!=1) _error_("input data is not of size 1x1");
1778- if(mxGetN(dataref)!=1) _error_("input data is not of size 1x1");
1779- mxbool_ptr=mxGetLogicals(dataref);
1780- }
1781- else{
1782- _error_("input data_type is not a bool!");
1783- }
1784-
1785- *pboolean=*mxbool_ptr;
1786-}
1787-/*}}}*/
1788-
1789-/*ISSM objects*/
1790-/*FUNCTION FetchData(Matrix<double>** pmatrix,const mxArray* dataref){{{*/
1791-void FetchData(Matrix<double>** pmatrix,const mxArray* dataref){
1792-
1793- Matrix<double>* outmatrix=NULL;
1794- int dummy=0;
1795-
1796- if (mxIsClass(dataref,"double") ){
1797-
1798- /*Convert matlab matrix to matrix: */
1799- outmatrix=MatlabMatrixToMatrix(dataref);
1800-
1801- }
1802- else{
1803- /*This is an error: we don't have the correct input!: */
1804- _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
1805- }
1806-
1807- /*Assign output pointers:*/
1808- *pmatrix=outmatrix;
1809-}
1810-/*}}}*/
1811-/*FUNCTION FetchData(Vector<double>** pvector,const mxArray* dataref){{{*/
1812-void FetchData(Vector<double>** pvector,const mxArray* dataref){
1813-
1814- Vector<double>* vector=NULL;
1815- int dummy;
1816-
1817- if(mxIsEmpty(dataref)){
1818- /*Nothing to pick up. Just initialize matrix pointer to NULL: */
1819- vector=new Vector<double>(0);
1820- }
1821- else if (mxIsClass(dataref,"double") ){
1822-
1823- /*Convert matlab vector to petsc vector: */
1824- vector=MatlabVectorToVector(dataref);
1825- }
1826- else{
1827- /*This is an error: we don't have the correct input!: */
1828- _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
1829- }
1830-
1831- /*Assign output pointers:*/
1832- *pvector=vector;
1833-}
1834-/*}}}*/
1835-/*FUNCTION FetchData(BamgGeom** pbamggeom,const mxArray* dataref){{{*/
1836-void FetchData(BamgGeom** pbamggeom,const mxArray* dataref){
1837-
1838- /*Initialize output*/
1839- BamgGeom* bamggeom=new BamgGeom();
1840-
1841- /*Fetch all fields*/
1842- FetchData(&bamggeom->Vertices,&bamggeom->VerticesSize[0],&bamggeom->VerticesSize[1],mxGetAssignedField(dataref,0,"Vertices"));
1843- FetchData(&bamggeom->Edges, &bamggeom->EdgesSize[0], &bamggeom->EdgesSize[1], mxGetAssignedField(dataref,0,"Edges"));
1844- FetchData(&bamggeom->Corners, &bamggeom->CornersSize[0], &bamggeom->CornersSize[1], mxGetAssignedField(dataref,0,"Corners"));
1845- FetchData(&bamggeom->RequiredVertices,&bamggeom->RequiredVerticesSize[0],&bamggeom->RequiredVerticesSize[1],mxGetAssignedField(dataref,0,"RequiredVertices"));
1846- FetchData(&bamggeom->RequiredEdges, &bamggeom->RequiredEdgesSize[0], &bamggeom->RequiredEdgesSize[1], mxGetAssignedField(dataref,0,"RequiredEdges"));
1847- FetchData(&bamggeom->CrackedEdges,&bamggeom->CrackedEdgesSize[0],&bamggeom->CrackedEdgesSize[1],mxGetAssignedField(dataref,0,"CrackedEdges"));
1848- FetchData(&bamggeom->SubDomains,&bamggeom->SubDomainsSize[0],&bamggeom->SubDomainsSize[1],mxGetAssignedField(dataref,0,"SubDomains"));
1849-
1850- /*Assign output pointers:*/
1851- *pbamggeom=bamggeom;
1852-}
1853-/*}}}*/
1854-/*FUNCTION FetchData(BamgMesh** pbamgmesh,const mxArray* dataref){{{*/
1855-void FetchData(BamgMesh** pbamgmesh,const mxArray* dataref){
1856-
1857- /*Initialize output*/
1858- BamgMesh* bamgmesh=new BamgMesh();
1859-
1860- /*Fetch all fields*/
1861- FetchData(&bamgmesh->Vertices,&bamgmesh->VerticesSize[0],&bamgmesh->VerticesSize[1],mxGetAssignedField(dataref,0,"Vertices"));
1862- FetchData(&bamgmesh->Edges, &bamgmesh->EdgesSize[0], &bamgmesh->EdgesSize[1], mxGetAssignedField(dataref,0,"Edges"));
1863- FetchData(&bamgmesh->Triangles, &bamgmesh->TrianglesSize[0], &bamgmesh->TrianglesSize[1], mxGetAssignedField(dataref,0,"Triangles"));
1864- FetchData(&bamgmesh->CrackedEdges,&bamgmesh->CrackedEdgesSize[0],&bamgmesh->CrackedEdgesSize[1],mxGetAssignedField(dataref,0,"CrackedEdges"));
1865- FetchData(&bamgmesh->VerticesOnGeomEdge,&bamgmesh->VerticesOnGeomEdgeSize[0],&bamgmesh->VerticesOnGeomEdgeSize[1],mxGetAssignedField(dataref,0,"VerticesOnGeomEdge"));
1866- FetchData(&bamgmesh->VerticesOnGeomVertex,&bamgmesh->VerticesOnGeomVertexSize[0],&bamgmesh->VerticesOnGeomVertexSize[1],mxGetAssignedField(dataref,0,"VerticesOnGeomVertex"));
1867- FetchData(&bamgmesh->EdgesOnGeomEdge, &bamgmesh->EdgesOnGeomEdgeSize[0], &bamgmesh->EdgesOnGeomEdgeSize[1], mxGetAssignedField(dataref,0,"EdgesOnGeomEdge"));
1868- FetchData(&bamgmesh->IssmSegments,&bamgmesh->IssmSegmentsSize[0],&bamgmesh->IssmSegmentsSize[1],mxGetAssignedField(dataref,0,"IssmSegments"));
1869-
1870- /*Assign output pointers:*/
1871- *pbamgmesh=bamgmesh;
1872-}
1873-/*}}}*/
1874-/*FUNCTION FetchData(BamgOpts** pbamgopts,const mxArray* dataref){{{*/
1875-void FetchData(BamgOpts** pbamgopts,const mxArray* dataref){
1876-
1877- /*Initialize output*/
1878- BamgOpts* bamgopts=new BamgOpts();
1879-
1880- /*Fetch all fields*/
1881- FetchData(&bamgopts->anisomax,mxGetField(dataref,0,"anisomax"));
1882- FetchData(&bamgopts->cutoff,mxGetField(dataref,0,"cutoff"));
1883- FetchData(&bamgopts->coeff,mxGetField(dataref,0,"coeff"));
1884- FetchData(&bamgopts->errg,mxGetField(dataref,0,"errg"));
1885- FetchData(&bamgopts->gradation,mxGetField(dataref,0,"gradation"));
1886- FetchData(&bamgopts->Hessiantype,mxGetField(dataref,0,"Hessiantype"));
1887- FetchData(&bamgopts->MaxCornerAngle,mxGetField(dataref,0,"MaxCornerAngle"));
1888- FetchData(&bamgopts->maxnbv,mxGetField(dataref,0,"maxnbv"));
1889- FetchData(&bamgopts->maxsubdiv,mxGetField(dataref,0,"maxsubdiv"));
1890- FetchData(&bamgopts->Metrictype,mxGetField(dataref,0,"Metrictype"));
1891- FetchData(&bamgopts->nbjacobi,mxGetField(dataref,0,"nbjacobi"));
1892- FetchData(&bamgopts->nbsmooth,mxGetField(dataref,0,"nbsmooth"));
1893- FetchData(&bamgopts->omega,mxGetField(dataref,0,"omega"));
1894- FetchData(&bamgopts->power,mxGetField(dataref,0,"power"));
1895- FetchData(&bamgopts->verbose,mxGetField(dataref,0,"verbose"));
1896-
1897- FetchData(&bamgopts->Crack,mxGetField(dataref,0,"Crack"));
1898- FetchData(&bamgopts->geometricalmetric,mxGetField(dataref,0,"geometricalmetric"));
1899- FetchData(&bamgopts->KeepVertices,mxGetField(dataref,0,"KeepVertices"));
1900- FetchData(&bamgopts->splitcorners,mxGetField(dataref,0,"splitcorners"));
1901-
1902- FetchData(&bamgopts->hmin,mxGetField(dataref,0,"hmin"));
1903- FetchData(&bamgopts->hmax,mxGetField(dataref,0,"hmax"));
1904- FetchData(&bamgopts->hminVertices,&bamgopts->hminVerticesSize[0],&bamgopts->hminVerticesSize[1],mxGetField(dataref,0,"hminVertices"));
1905- FetchData(&bamgopts->hmaxVertices,&bamgopts->hmaxVerticesSize[0],&bamgopts->hmaxVerticesSize[1],mxGetField(dataref,0,"hmaxVertices"));
1906- FetchData(&bamgopts->hVertices,&bamgopts->hVerticesSize[0],&bamgopts->hVerticesSize[1],mxGetField(dataref,0,"hVertices"));
1907- FetchData(&bamgopts->metric,&bamgopts->metricSize[0],&bamgopts->metricSize[1],mxGetField(dataref,0,"metric"));
1908- FetchData(&bamgopts->field,&bamgopts->fieldSize[0],&bamgopts->fieldSize[1],mxGetField(dataref,0,"field"));
1909- FetchData(&bamgopts->err,&bamgopts->errSize[0],&bamgopts->errSize[1],mxGetField(dataref,0,"err"));
1910-
1911- /*Additional checks*/
1912- bamgopts->Check();
1913-
1914- /*Assign output pointers:*/
1915- *pbamgopts=bamgopts;
1916-}
1917-/*}}}*/
1918-/*FUNCTION FetchData(Options** poptions,const mxArray** pdataref){{{*/
1919-void FetchData(Options** poptions,int istart, int nrhs,const mxArray** pdataref){
1920-
1921- char *name = NULL;
1922- Option *option = NULL;
1923-
1924- /*Initialize output*/
1925- Options* options=new Options();
1926-
1927- /*Fetch all options*/
1928- for (int i=istart; i<nrhs; i=i+2){
1929- if (!mxIsClass(pdataref[i],"char")) _error_("Argument " << i+1 << " must be name of option");
1930-
1931- FetchData(&name,pdataref[i]);
1932- if(i+1 == nrhs) _error_("Argument " << i+2 << " must exist and be value of option \"" << name << "\".");
1933-
1934- option=(Option*)OptionParse(name,&pdataref[i+1]);
1935- options->AddOption(option);
1936- option=NULL;
1937- }
1938-
1939- /*Assign output pointers:*/
1940- *poptions=options;
1941-}
1942-/*}}}*/
1943-/*FUNCTION FetchData(DataSet** pcontours,const mxArray* dataref){{{*/
1944-void FetchData(DataSet** pcontours,const mxArray* dataref){
1945-
1946- int numcontours,index,test1,test2;
1947- char *contourname = NULL;
1948- DataSet *contours = NULL;
1949- Contour<double> *contouri = NULL;
1950-
1951- if (mxIsClass(dataref,"char")){
1952- FetchData(&contourname,dataref);
1953- contours=DomainOutlineRead<double>(contourname);
1954- }
1955- else if(mxIsClass(dataref,"struct")){
1956-
1957- contours=new DataSet(0);
1958- numcontours=mxGetNumberOfElements(dataref);
1959-
1960- for(int i=0;i<numcontours;i++){
1961-
1962- contouri=xNew<Contour<double> >(1);
1963-
1964- index = mxGetFieldNumber(dataref,"nods");
1965- if(index==-1) _error_("input structure does not have a 'nods' field");
1966- FetchData(&contouri->nods,mxGetFieldByNumber(dataref,i,index));
1967-
1968- index = mxGetFieldNumber(dataref,"x");
1969- if(index==-1) _error_("input structure does not have a 'x' field");
1970- FetchData(&contouri->x,&test1,&test2,mxGetFieldByNumber(dataref,i,index));
1971- if(test1!=contouri->nods || test2!=1) _error_("field x should be of size ["<<contouri->nods<<" 1]");
1972-
1973- index = mxGetFieldNumber(dataref,"y");
1974- if(index==-1) _error_("input structure does not have a 'y' field");
1975- FetchData(&contouri->y,&test1,&test2,mxGetFieldByNumber(dataref,i,index));
1976- if(test1!=contouri->nods || test2!=1) _error_("field y should be of size ["<<contouri->nods<<" 1]");
1977-
1978- contours->AddObject(contouri);
1979- }
1980- }
1981- else{
1982- _error_("Contour is neither a string nor a structure and cannot be loaded ("<<mxGetClassName(dataref)<<" not supported)");
1983- }
1984-
1985- /*clean-up and assign output pointer*/
1986- xDelete<char>(contourname);
1987- *pcontours=contours;
1988-}
1989-/*}}}*/
1990Index: ../trunk-jpl/src/c/matlab/io/CheckNumMatlabArguments.cpp
1991===================================================================
1992--- ../trunk-jpl/src/c/matlab/io/CheckNumMatlabArguments.cpp (revision 13748)
1993+++ ../trunk-jpl/src/c/matlab/io/CheckNumMatlabArguments.cpp (revision 13749)
1994@@ -1,30 +0,0 @@
1995-/*!\file CheckNumMatlabArguments.cpp:
1996- * \brief: check number of arguments and report an usage error message.
1997- */
1998-
1999-#ifdef HAVE_CONFIG_H
2000- #include <config.h>
2001-#else
2002-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
2003-#endif
2004-
2005-#include "../../shared/Exceptions/exceptions.h"
2006-#include "../../include/include.h"
2007-#include "mex.h"
2008-
2009-int CheckNumMatlabArguments(int nlhs,int NLHS, int nrhs,int NRHS, const char* __FUNCT__, void (*function)( void )){
2010-
2011- /*checks on arguments on the matlab side: */
2012- if (nrhs==0 && nlhs==0) {
2013- /*unless NLHS=0 and NRHS=0, we are just asking for documentation: */
2014- if (NRHS==0 && NLHS==0)return 1;
2015- /* special case: */
2016- function();
2017- _error_("usage: see above");
2018- }
2019- else if (nlhs!=NLHS || nrhs!=NRHS ) {
2020- function();
2021- _error_("usage error.");
2022- }
2023- return 1;
2024-}
2025Index: ../trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp
2026===================================================================
2027--- ../trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp (revision 13748)
2028+++ ../trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp (revision 13749)
2029@@ -1,390 +0,0 @@
2030-/* \file WriteData.c:
2031- * \brief: general interface for writing data
2032- */
2033-
2034-#ifdef HAVE_CONFIG_H
2035- #include <config.h>
2036-#else
2037-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
2038-#endif
2039-
2040-#include <mex.h>
2041-#include "../../include/include.h"
2042-#include "../../shared/shared.h"
2043-#include "./matlabio.h"
2044-
2045-/*Primitive data types*/
2046-/*FUNCTION WriteData(mxArray** pdataref,double* matrix, int M,int N){{{*/
2047-void WriteData(mxArray** pdataref,double* matrix, int M,int N){
2048-
2049- mxArray *dataref = NULL;
2050- double *tmatrix = NULL;
2051-
2052- if(matrix){
2053- /*create the matlab matrixwith Matlab's memory manager */
2054- tmatrix=(double*)mxMalloc(M*N*sizeof(double));
2055- for(int i=0;i<M;i++){
2056- for(int j=0;j<N;j++){
2057- tmatrix[j*M+i]=matrix[i*N+j];
2058- }
2059- }
2060- dataref = mxCreateDoubleMatrix(0,0,mxREAL);
2061- mxSetM(dataref,(mwSize)M);
2062- mxSetN(dataref,(mwSize)N);
2063- mxSetPr(dataref,(double*)tmatrix);
2064- }
2065- else{
2066- dataref = mxCreateDoubleMatrix(0,0,mxREAL);
2067- }
2068- *pdataref=dataref;
2069-}
2070-/*}}}*/
2071-/*FUNCTION WriteData(mxArray** pdataref,int* matrix, int M,int N){{{*/
2072-void WriteData(mxArray** pdataref,int* matrix, int M,int N){
2073-
2074- mxArray* dataref = NULL;
2075- double* tmatrix = NULL;
2076-
2077- if(matrix){
2078- /*convert to double matrix using Matlab's memory manager*/
2079- double* tmatrix=(double*)mxMalloc(M*N*sizeof(double));
2080- for(int i=0;i<M;i++){
2081- for(int j=0;j<N;j++){
2082- tmatrix[j*M+i]=(double)matrix[i*N+j];
2083- }
2084- }
2085- dataref = mxCreateDoubleMatrix(0,0,mxREAL);
2086- mxSetM(dataref,(mwSize)M);
2087- mxSetN(dataref,(mwSize)N);
2088- mxSetPr(dataref,(double*)tmatrix);
2089- }
2090- else{
2091- dataref = mxCreateDoubleMatrix(0,0,mxREAL);
2092- }
2093- *pdataref=dataref;
2094-}
2095-/*}}}*/
2096-/*FUNCTION WriteData(mxArray** pdataref,double* vector, int M){{{*/
2097-void WriteData(mxArray** pdataref,double* vector, int M){
2098-
2099- mxArray* dataref = NULL;
2100- double* vector_matlab = NULL;
2101-
2102- if(vector){
2103-
2104- /*create the matlab vector with Matlab's memory manager */
2105- vector_matlab=(double*)mxMalloc(M*sizeof(double));
2106- for(int i=0;i<M;i++) vector_matlab[i]=vector[i];
2107- dataref = mxCreateDoubleMatrix(0,0,mxREAL);
2108- mxSetM(dataref,(mwSize)M);
2109- mxSetN(dataref,(mwSize)1);
2110- mxSetPr(dataref,vector_matlab);
2111- }
2112- else{
2113- dataref = mxCreateDoubleMatrix(0,0,mxREAL);
2114- }
2115-
2116- *pdataref=dataref;
2117-}
2118-/*}}}*/
2119-/*FUNCTION WriteData(mxArray** pdataref,double scalar){{{*/
2120-void WriteData(mxArray** pdataref,double scalar){
2121-
2122- *pdataref=mxCreateDoubleScalar(scalar);
2123-}
2124-/*}}}*/
2125-/*FUNCTION WriteData(mxArray** pdataref,int integer){{{*/
2126-void WriteData(mxArray** pdataref,int integer){
2127-
2128- *pdataref=mxCreateDoubleScalar((double)integer);
2129-
2130-}
2131-/*}}}*/
2132-/*FUNCTION WriteData(mxArray** pdataref,int boolean){{{*/
2133-void WriteData(mxArray** pdataref,bool boolean){
2134-
2135- *pdataref=mxCreateDoubleScalar((double)boolean);
2136-
2137-}
2138-/*}}}*/
2139-/*FUNCTION WriteData(mxArray** pdataref,char* string){{{*/
2140-void WriteData(mxArray** pdataref,char* string){
2141-
2142- *pdataref=mxCreateString(string);
2143-}
2144-/*}}}*/
2145-/*FUNCTION WriteData(mxArray** pdataref){{{*/
2146-void WriteData(mxArray** pdataref){
2147-
2148- ;
2149-
2150-}
2151-/*}}}*/
2152-
2153-/*ISSM objects*/
2154-/*FUNCTION WriteData(mxArray** pdataref,BamgGeom* bamggeom){{{*/
2155-void WriteData(mxArray** pdataref,BamgGeom* bamggeom){
2156-
2157- /*Intermediary*/
2158- int i;
2159- mxArray *dataref = NULL;
2160- const int numfields = 8;
2161- const char *fnames[numfields];
2162- mwSize ndim = 2;
2163- mwSize dimensions[2] = {1,1};
2164-
2165- /*Initialize field names*/
2166- i=0;
2167- fnames[i++] = "Vertices";
2168- fnames[i++] = "Edges";
2169- fnames[i++] = "TangentAtEdges";
2170- fnames[i++] = "Corners";
2171- fnames[i++] = "RequiredVertices";
2172- fnames[i++] = "RequiredEdges";
2173- fnames[i++] = "CrackedEdges";
2174- fnames[i++] = "SubDomains";
2175- _assert_(i==numfields);
2176-
2177- /*Initialize Matlab structure*/
2178- dataref=mxCreateStructArray(ndim,dimensions,numfields,fnames);
2179-
2180- /*set each matlab each field*/
2181- i=0;
2182- i++; SetStructureField(dataref,"Vertices", bamggeom->VerticesSize[0], bamggeom->VerticesSize[1], bamggeom->Vertices);
2183- i++; SetStructureField(dataref,"Edges", bamggeom->EdgesSize[0], bamggeom->EdgesSize[1], bamggeom->Edges);
2184- i++; SetStructureField(dataref,"TangentAtEdges", bamggeom->TangentAtEdgesSize[0], bamggeom->TangentAtEdgesSize[1], bamggeom->TangentAtEdges);
2185- i++; SetStructureField(dataref,"Corners", bamggeom->CornersSize[0], bamggeom->CornersSize[1], bamggeom->Corners);
2186- i++; SetStructureField(dataref,"RequiredVertices",bamggeom->RequiredVerticesSize[0],bamggeom->RequiredVerticesSize[1],bamggeom->RequiredVertices);
2187- i++; SetStructureField(dataref,"RequiredEdges", bamggeom->RequiredEdgesSize[0], bamggeom->RequiredEdgesSize[1], bamggeom->RequiredEdges);
2188- i++; SetStructureField(dataref,"CrackedEdges", bamggeom->CrackedEdgesSize[0], bamggeom->CrackedEdgesSize[1], bamggeom->CrackedEdges);
2189- i++; SetStructureField(dataref,"SubDomains", bamggeom->SubDomainsSize[0], bamggeom->SubDomainsSize[1], bamggeom->SubDomains);
2190- _assert_(i==numfields);
2191-
2192- /*Assign output*/
2193- *pdataref=dataref;
2194-}
2195-/*}}}*/
2196-/*FUNCTION WriteData(mxArray** pdataref,BamgMesh* bamgmesh){{{*/
2197-void WriteData(mxArray** pdataref,BamgMesh* bamgmesh){
2198-
2199- /*Intermediary*/
2200- int i;
2201- mxArray *dataref = NULL;
2202- const int numfields = 16;
2203- const char *fnames[numfields];
2204- mwSize ndim = 2;
2205- mwSize dimensions[2] = {1,1};
2206-
2207- /*Initialize field names*/
2208- i=0;
2209- fnames[i++] = "Vertices";
2210- fnames[i++] = "Edges";
2211- fnames[i++] = "Triangles";
2212- fnames[i++] = "Quadrilaterals";
2213- fnames[i++] = "IssmEdges";
2214- fnames[i++] = "IssmSegments";
2215- fnames[i++] = "VerticesOnGeomVertex";
2216- fnames[i++] = "VerticesOnGeomEdge";
2217- fnames[i++] = "EdgesOnGeomEdge";
2218- fnames[i++] = "SubDomains";
2219- fnames[i++] = "SubDomainsFromGeom";
2220- fnames[i++] = "ElementConnectivity";
2221- fnames[i++] = "NodalConnectivity";
2222- fnames[i++] = "NodalElementConnectivity";
2223- fnames[i++] = "CrackedVertices";
2224- fnames[i++] = "CrackedEdges";
2225- _assert_(i==numfields);
2226-
2227- /*Initialize Matlab structure*/
2228- dataref=mxCreateStructArray(ndim,dimensions,numfields,fnames);
2229-
2230- /*set each matlab each field*/
2231- i=0;
2232- i++; SetStructureField(dataref,"Vertices",bamgmesh->VerticesSize[0], bamgmesh->VerticesSize[1],bamgmesh->Vertices);
2233- i++; SetStructureField(dataref,"Edges", bamgmesh->EdgesSize[0],bamgmesh->EdgesSize[1], bamgmesh->Edges);
2234- i++; SetStructureField(dataref,"Triangles", bamgmesh->TrianglesSize[0],bamgmesh->TrianglesSize[1], bamgmesh->Triangles);
2235- i++; SetStructureField(dataref,"Quadrilaterals",bamgmesh->QuadrilateralsSize[0], bamgmesh->QuadrilateralsSize[1],bamgmesh->Quadrilaterals);
2236- i++; SetStructureField(dataref,"IssmEdges", bamgmesh->IssmEdgesSize[0],bamgmesh->IssmEdgesSize[1], bamgmesh->IssmEdges);
2237- i++; SetStructureField(dataref,"IssmSegments",bamgmesh->IssmSegmentsSize[0], bamgmesh->IssmSegmentsSize[1],bamgmesh->IssmSegments);
2238- i++; SetStructureField(dataref,"VerticesOnGeomVertex",bamgmesh->VerticesOnGeomVertexSize[0],bamgmesh->VerticesOnGeomVertexSize[1], bamgmesh->VerticesOnGeomVertex);
2239- i++; SetStructureField(dataref,"VerticesOnGeomEdge",bamgmesh->VerticesOnGeomEdgeSize[0],bamgmesh->VerticesOnGeomEdgeSize[1], bamgmesh->VerticesOnGeomEdge);
2240- i++; SetStructureField(dataref,"EdgesOnGeomEdge", bamgmesh->EdgesOnGeomEdgeSize[0], bamgmesh->EdgesOnGeomEdgeSize[1],bamgmesh->EdgesOnGeomEdge);
2241- i++; SetStructureField(dataref,"SubDomains",bamgmesh->SubDomainsSize[0], bamgmesh->SubDomainsSize[1],bamgmesh->SubDomains);
2242- i++; SetStructureField(dataref,"SubDomainsFromGeom", bamgmesh->SubDomainsFromGeomSize[0], bamgmesh->SubDomainsFromGeomSize[1],bamgmesh->SubDomainsFromGeom);
2243- i++; SetStructureField(dataref,"ElementConnectivity",bamgmesh->ElementConnectivitySize[0],bamgmesh->ElementConnectivitySize[1], bamgmesh->ElementConnectivity);
2244- i++; SetStructureField(dataref,"NodalConnectivity",bamgmesh->NodalConnectivitySize[0],bamgmesh->NodalConnectivitySize[1], bamgmesh->NodalConnectivity);
2245- i++; SetStructureField(dataref,"NodalElementConnectivity", bamgmesh->NodalElementConnectivitySize[0], bamgmesh->NodalElementConnectivitySize[1],bamgmesh->NodalElementConnectivity);
2246- i++; SetStructureField(dataref,"CrackedVertices", bamgmesh->CrackedVerticesSize[0],bamgmesh->CrackedVerticesSize[1], bamgmesh->CrackedVertices);
2247- i++; SetStructureField(dataref,"CrackedEdges",bamgmesh->CrackedEdgesSize[0], bamgmesh->CrackedEdgesSize[1],bamgmesh->CrackedEdges);
2248- _assert_(i==numfields);
2249-
2250- /*Assign output*/
2251- *pdataref=dataref;
2252-}
2253-/*}}}*/
2254-/*FUNCTION WriteData(mxArray** pdataref,SeqMat<double>* matrix){{{*/
2255-void WriteData(mxArray** pdataref,SeqMat<double>* matrix){
2256-
2257- int i,j;
2258- int rows,cols;
2259- mxArray *dataref = NULL;
2260- double *matrix_ptr = NULL;
2261- double *tmatrix_ptr = NULL;
2262-
2263- if(matrix){
2264-
2265- matrix_ptr=matrix->ToSerial();
2266- matrix->GetSize(&rows,&cols);
2267-
2268- /*Now transpose the matrix and allocate with Matlab's memory manager: */
2269- tmatrix_ptr=(double*)mxMalloc(rows*cols*sizeof(double));
2270- for(i=0;i<rows;i++){
2271- for(j=0;j<cols;j++){
2272- tmatrix_ptr[j*rows+i]=matrix_ptr[i*cols+j];
2273- }
2274- }
2275-
2276- /*create matlab matrix: */
2277- dataref=mxCreateDoubleMatrix(0,0,mxREAL);
2278- mxSetM(dataref,rows);
2279- mxSetN(dataref,cols);
2280- mxSetPr(dataref,tmatrix_ptr);
2281-
2282- /*Free ressources:*/
2283- xDelete<double>(matrix_ptr);
2284- }
2285- else{
2286- dataref = mxCreateDoubleMatrix(0,0,mxREAL);
2287- }
2288-
2289- *pdataref=dataref;
2290-}
2291-/*}}}*/
2292-/*FUNCTION WriteData(mxArray** pdataref,SeqVec<double>* vector){{{*/
2293-void WriteData(mxArray** pdataref,SeqVec<double>* vector){
2294-
2295- mxArray* dataref=NULL;
2296- double* vector_ptr=NULL;
2297- double* vector_matlab=NULL;
2298- int rows;
2299-
2300- if(vector){
2301- /*call toolkit routine: */
2302- vector_ptr=vector->ToMPISerial();
2303- vector->GetSize(&rows);
2304-
2305- /*now create the matlab vector with Matlab's memory manager */
2306- vector_matlab=(double*)mxMalloc(rows*sizeof(double));
2307- for(int i=0;i<rows;i++) vector_matlab[i]=vector_ptr[i];
2308-
2309- dataref = mxCreateDoubleMatrix(0,0,mxREAL);
2310- mxSetM(dataref,rows);
2311- mxSetN(dataref,1);
2312- mxSetPr(dataref,vector_matlab);
2313- }
2314- else{
2315- dataref = mxCreateDoubleMatrix(0,0,mxREAL);
2316- }
2317-
2318- /*Clean-up and return*/
2319- xDelete<double>(vector_ptr);
2320- *pdataref=dataref;
2321-}
2322-/*}}}*/
2323-/*FUNCTION WriteData(mxArray** pdataref,RiftStruct* riftstruct){{{*/
2324-void WriteData(mxArray** pdataref,RiftStruct* riftstruct){
2325-
2326- /*Intermediary*/
2327- int i;
2328- mxArray *dataref = NULL;
2329- const int numfields = 10;
2330- const char *fnames[numfields];
2331- mwSize ndim = 2;
2332- mwSize dimensions[2] = {1,1};
2333-
2334- /*Initialize field names*/
2335- i=0;
2336- fnames[i++] = "numsegs";
2337- fnames[i++] = "segments";
2338- fnames[i++] = "pairs";
2339- fnames[i++] = "tips";
2340- fnames[i++] = "penaltypairs";
2341- fnames[i++] = "fill";
2342- fnames[i++] = "friction";
2343- fnames[i++] = "fraction";
2344- fnames[i++] = "fractionincrement";
2345- fnames[i++] = "state";
2346- _assert_(i==numfields);
2347-
2348- /*Initialize matlab structure of dimension numrifts*/
2349- dimensions[0]=riftstruct->numrifts;
2350- dataref=mxCreateStructArray(ndim,dimensions,numfields,fnames);
2351-
2352- /*set each matlab each field*/
2353- for(int i=0;i<riftstruct->numrifts;i++){
2354- SetStructureFieldi(dataref,i,"numsegs" ,riftstruct->riftsnumsegments[i]);
2355- SetStructureFieldi(dataref,i,"segments" ,riftstruct->riftsnumsegments[i] ,3,riftstruct->riftssegments[i]);
2356- SetStructureFieldi(dataref,i,"pairs" ,riftstruct->riftsnumpairs[i] ,2,riftstruct->riftspairs[i]);
2357- SetStructureFieldi(dataref,i,"tips" ,1 ,2,&riftstruct->riftstips[2*i]);
2358- SetStructureFieldi(dataref,i,"penaltypairs" ,riftstruct->riftsnumpenaltypairs[i],7,riftstruct->riftspenaltypairs[i]);
2359- SetStructureFieldi(dataref,i,"fill" ,IceEnum);
2360- SetStructureFieldi(dataref,i,"friction" ,0);
2361- SetStructureFieldi(dataref,i,"fraction" ,0.);
2362- SetStructureFieldi(dataref,i,"fractionincrement",0.1);
2363- SetStructureFieldi(dataref,i,"state" ,riftstruct->riftsnumpenaltypairs[i],1,riftstruct->state[i]);
2364- }
2365-
2366- /*Assign output*/
2367- *pdataref=dataref;
2368-}
2369-/*}}}*/
2370-
2371-/*Toolkit*/
2372-/*FUNCTION SetStructureField{{{*/
2373-void SetStructureField(mxArray* dataref,const char* fieldname,int M,int N,double* fieldpointer){
2374-
2375- mxArray* field = NULL;
2376-
2377- /*Convert field*/
2378- WriteData(&field,fieldpointer,M,N);
2379-
2380- /*Assign to structure*/
2381- mxSetField(dataref,0,fieldname,field);
2382-}
2383-/*}}}*/
2384-/*FUNCTION SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int M,int N,double* fieldpointer){{{*/
2385-void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int M,int N,double* fieldpointer){
2386-
2387- mxArray* field = NULL;
2388-
2389- /*Convert field*/
2390- WriteData(&field,fieldpointer,M,N);
2391-
2392- /*Assign to structure*/
2393- mxSetField(dataref,i,fieldname,field);
2394-}
2395-/*}}}*/
2396-/*FUNCTION SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int field){{{*/
2397-void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int fieldin){
2398-
2399- mxArray* field = NULL;
2400-
2401- /*Convert field*/
2402- WriteData(&field,fieldin);
2403-
2404- /*Assign to structure*/
2405- mxSetField(dataref,i,fieldname,field);
2406-}
2407-/*}}}*/
2408-/*FUNCTION SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,double field){{{*/
2409-void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,double fieldin){
2410-
2411- mxArray* field = NULL;
2412-
2413- /*Convert field*/
2414- WriteData(&field,fieldin);
2415-
2416- /*Assign to structure*/
2417- mxSetField(dataref,i,fieldname,field);
2418-}
2419-/*}}}*/
2420Index: ../trunk-jpl/src/c/matlab/io/mxGetAssignedField.cpp
2421===================================================================
2422--- ../trunk-jpl/src/c/matlab/io/mxGetAssignedField.cpp (revision 13748)
2423+++ ../trunk-jpl/src/c/matlab/io/mxGetAssignedField.cpp (revision 13749)
2424@@ -1,45 +0,0 @@
2425-/*!\file: mxGetAssignedField.c:
2426- * \brief: abstract interface on parallel side for i/o, so it ressembles the serial i/o.
2427- *
2428- * In serial mode, this routine takes care of returning the field coming
2429- * from the model. If largesize is 1, we are running out of core models in
2430- * matlab, and we need to call the subsref private method from the model object
2431- * in order to correctly load the data from disk.
2432- */
2433-
2434-#ifdef HAVE_CONFIG_H
2435-#include <config.h>
2436-#else
2437-#error "Cannot compile without HAVE_CONFIG_H symbol! run configure first!"
2438-#endif
2439-
2440-#include "mex.h"
2441-
2442-mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number,const char* field){
2443-
2444- //output
2445- mxArray* mxfield=NULL;
2446-
2447- //input
2448- mxArray *inputs[2];
2449- mxArray *pindex = NULL;
2450- const char *fnames[2];
2451- mwSize ndim = 2;
2452- mwSize onebyone[2] = {1,1};
2453-
2454- //We want to call the subsasgn method, and get the returned array.This ensures that if we are running
2455- //large sized problems, the data is truly loaded from disk by the model subsasgn class method.
2456- inputs[0]=(mxArray*)pmxa_array; //this is the model
2457-
2458- //create index structure used in the assignment (index.type='.' and index.subs='x' for field x for ex)
2459- fnames[0] = "type";
2460- fnames[1] = "subs";
2461- pindex=mxCreateStructArray( ndim,onebyone,2,fnames);
2462- mxSetField( pindex, 0, "type",mxCreateString("."));
2463- mxSetField( pindex, 0, "subs",mxCreateString(field));
2464- inputs[1]=pindex;
2465-
2466- mexCallMATLAB( 1, &mxfield, 2, (mxArray**)inputs, "subsref");
2467-
2468- return mxfield;
2469-}
2470Index: ../trunk-jpl/src/c/matlab/io/MatlabMatrixToDoubleMatrix.cpp
2471===================================================================
2472--- ../trunk-jpl/src/c/matlab/io/MatlabMatrixToDoubleMatrix.cpp (revision 13748)
2473+++ ../trunk-jpl/src/c/matlab/io/MatlabMatrixToDoubleMatrix.cpp (revision 13749)
2474@@ -1,130 +0,0 @@
2475-/* \file MatlabMatrixToDoubleMatrix.cpp
2476- * \brief: convert a sparse or dense matlab matrix to a double* pointer
2477- */
2478-
2479-#ifdef HAVE_CONFIG_H
2480- #include <config.h>
2481-#else
2482-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
2483-#endif
2484-
2485-/*Matlab includes: */
2486-#include "mex.h"
2487-#include "../../shared/shared.h"
2488-
2489-int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){
2490-
2491- int i,j,count,rows,cols;
2492-
2493- /*output: */
2494- double* matrix=NULL;
2495-
2496- /*matlab indices: */
2497- mwIndex* ir=NULL;
2498- mwIndex* jc=NULL;
2499-
2500- /*Ok, first check if we are dealing with a sparse or full matrix: */
2501- if (mxIsSparse(mxmatrix)){
2502-
2503- /*Dealing with sparse matrix: recover size first: */
2504- double* pmxmatrix=(double*)mxGetPr(mxmatrix);
2505- rows=mxGetM(mxmatrix);
2506- cols=mxGetN(mxmatrix);
2507-
2508- if(rows*cols){
2509- matrix=xNewZeroInit<double>(rows*cols);
2510-
2511- /*Now, get ir,jc and pr: */
2512- ir=mxGetIr(mxmatrix);
2513- jc=mxGetJc(mxmatrix);
2514-
2515- /*Now, start inserting data into double* matrix: */
2516- count=0;
2517- for(i=0;i<cols;i++){
2518- for(j=0;j<(jc[i+1]-jc[i]);j++){
2519- matrix[rows*ir[count]+i]=pmxmatrix[count];
2520- count++;
2521- }
2522- }
2523- }
2524-
2525- }
2526- else if(mxIsClass(mxmatrix,"double")){
2527- /*Dealing with dense matrix: recover pointer and size: */
2528- double* pmxmatrix=(double*)mxGetPr(mxmatrix);
2529- rows=mxGetM(mxmatrix);
2530- cols=mxGetN(mxmatrix);
2531-
2532- /*Create serial matrix: */
2533- if(rows*cols){
2534- matrix=xNewZeroInit<double>(rows*cols);
2535-
2536- for(i=0;i<rows;i++){
2537- for(j=0;j<cols;j++){
2538- matrix[cols*i+j]=(double)pmxmatrix[rows*j+i];
2539- }
2540- }
2541- }
2542- }
2543- else if(mxIsClass(mxmatrix,"single")){
2544- /*Dealing with dense matrix: recover pointer and size: */
2545- float *pmxmatrix=(float*)mxGetPr(mxmatrix);
2546- rows=mxGetM(mxmatrix);
2547- cols=mxGetN(mxmatrix);
2548-
2549- /*Create serial matrix: */
2550- if(rows*cols){
2551- matrix=xNewZeroInit<double>(rows*cols);
2552-
2553- for(i=0;i<rows;i++){
2554- for(j=0;j<cols;j++){
2555- matrix[cols*i+j]=(double)pmxmatrix[rows*j+i];
2556- }
2557- }
2558- }
2559- }
2560- else if(mxIsClass(mxmatrix,"int16")){
2561- /*Dealing with dense matrix: recover pointer and size: */
2562- short int *pmxmatrix=(short*)mxGetPr(mxmatrix);
2563- rows=mxGetM(mxmatrix);
2564- cols=mxGetN(mxmatrix);
2565-
2566- /*Create serial matrix: */
2567- if(rows*cols){
2568- matrix=xNewZeroInit<double>(rows*cols);
2569-
2570- for(i=0;i<rows;i++){
2571- for(j=0;j<cols;j++){
2572- matrix[cols*i+j]=(double)pmxmatrix[rows*j+i];
2573- }
2574- }
2575- }
2576- }
2577- else if(mxIsClass(mxmatrix,"uint8")){
2578- /*Dealing with dense matrix: recover pointer and size: */
2579- char *pmxmatrix=(char*)mxGetPr(mxmatrix);
2580- rows=mxGetM(mxmatrix);
2581- cols=mxGetN(mxmatrix);
2582-
2583- /*Create serial matrix: */
2584- if(rows*cols){
2585- matrix=xNewZeroInit<double>(rows*cols);
2586-
2587- for(i=0;i<rows;i++){
2588- for(j=0;j<cols;j++){
2589- matrix[cols*i+j]=(double)pmxmatrix[rows*j+i];
2590- }
2591- }
2592- }
2593- }
2594- else{
2595- _error_("Matlab matrix type Not implemented yet");
2596- }
2597-
2598- /*Assign output pointer: */
2599- *pmatrix=matrix;
2600- *pmatrix_rows=rows;
2601- *pmatrix_cols=cols;
2602-
2603- return 1;
2604-}
2605Index: ../trunk-jpl/src/c/matlab/io/MatlabVectorToVector.cpp
2606===================================================================
2607--- ../trunk-jpl/src/c/matlab/io/MatlabVectorToVector.cpp (revision 13748)
2608+++ ../trunk-jpl/src/c/matlab/io/MatlabVectorToVector.cpp (revision 13749)
2609@@ -1,39 +0,0 @@
2610-/*!\file MatlabVectorToVector.cpp
2611- */
2612-
2613-/*Headers:*/
2614-/*{{{*/
2615-#ifdef HAVE_CONFIG_H
2616- #include <config.h>
2617-#else
2618-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
2619-#endif
2620-
2621-#include <mex.h>
2622-#include <stdio.h>
2623-#include <string.h>
2624-#include "./matlabio.h"
2625-#include "../../classes/classes.h"
2626-#include "../../shared/shared.h"
2627-#include "../../Container/Container.h"
2628-#include "../../include/include.h"
2629-#include "../../toolkits/toolkits.h"
2630-
2631-/*}}}*/
2632-
2633-Vector<double>* MatlabVectorToVector(const mxArray* mxvector){
2634-
2635- int dummy;
2636- Vector<double>* vector=NULL;
2637-
2638- /*allocate vector object: */
2639- vector=new Vector<double>();
2640-
2641- #ifdef _HAVE_PETSC_
2642- vector->pvector=MatlabVectorToPetscVec(mxvector);
2643- #else
2644- vector->svector=MatlabVectorToSeqVec(mxvector);
2645- #endif
2646-
2647- return vector;
2648-}
2649Index: ../trunk-jpl/src/c/matlab/io/MatlabMatrixToPetscMat.cpp
2650===================================================================
2651--- ../trunk-jpl/src/c/matlab/io/MatlabMatrixToPetscMat.cpp (revision 13748)
2652+++ ../trunk-jpl/src/c/matlab/io/MatlabMatrixToPetscMat.cpp (revision 13749)
2653@@ -1,123 +0,0 @@
2654-/* \file MatlabMatrixToPetscMatrix.cpp
2655- * \brief: convert a sparse or dense matlab matrix to a serial Petsc matrix:
2656- */
2657-
2658-#ifdef HAVE_CONFIG_H
2659- #include <config.h>
2660-#else
2661-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
2662-#endif
2663-#include "../../shared/shared.h"
2664-
2665-/*Petsc includes: */
2666-#include "petscmat.h"
2667-#include "petscvec.h"
2668-#include "petscksp.h"
2669-
2670-/*Matlab includes: */
2671-#include "mex.h"
2672-#include "matlabio.h"
2673-
2674-PetscMat* MatlabMatrixToPetscMat(const mxArray* mxmatrix){
2675-
2676- int dummy;
2677- PetscMat* matrix=new PetscMat();
2678-
2679- MatlabMatrixToPetscMat(&matrix->matrix, &dummy, &dummy, mxmatrix);
2680-
2681- return matrix;
2682-}
2683-int MatlabMatrixToPetscMat(Mat* pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){
2684-
2685- int rows, cols;
2686- double *mxmatrix_ptr = NULL;
2687- double *tmatrix = NULL;
2688- int ierr;
2689- int i,j;
2690-
2691- /*output: */
2692- Mat matrix = NULL;
2693-
2694- /*matlab indices: */
2695- mwIndex *ir = NULL;
2696- mwIndex *jc = NULL;
2697- double *pr = NULL;
2698- int count;
2699- int nnz;
2700- int nz;
2701-
2702- /*petsc indices: */
2703- int *idxm = NULL;
2704- int *idxn = NULL;
2705-
2706- /*Ok, first check if we are dealing with a sparse or full matrix: */
2707- if (mxIsSparse(mxmatrix)){
2708-
2709- /*Dealing with sparse matrix: recover size first: */
2710- mxmatrix_ptr=(double*)mxGetPr(mxmatrix);
2711- rows=mxGetM(mxmatrix);
2712- cols=mxGetN(mxmatrix);
2713- nnz=mxGetNzmax(mxmatrix);
2714- if(rows){
2715- nz=(int)((double)nnz/(double)rows);
2716- }
2717- else{
2718- nz=0;
2719- }
2720-
2721- ierr=MatCreateSeqAIJ(PETSC_COMM_SELF,rows,cols,nz,PETSC_NULL,&matrix);CHKERRQ(ierr);
2722-
2723- /*Now, get ir,jc and pr: */
2724- pr=mxGetPr(mxmatrix);
2725- ir=mxGetIr(mxmatrix);
2726- jc=mxGetJc(mxmatrix);
2727-
2728- /*Now, start inserting data into sparse matrix: */
2729- count=0;
2730- for(i=0;i<cols;i++){
2731- for(j=0;j<(jc[i+1]-jc[i]);j++){
2732- MatSetValue(matrix,ir[count],i,pr[count],INSERT_VALUES);
2733- count++;
2734- }
2735- }
2736- }
2737- else{
2738- /*Dealing with dense matrix: recover pointer and size: */
2739- mxmatrix_ptr=(double*)mxGetPr(mxmatrix);
2740- rows=mxGetM(mxmatrix);
2741- cols=mxGetN(mxmatrix);
2742-
2743- /*transpose, as Petsc now does not allows MAT_COLUMN_ORIENTED matrices in MatSetValues: */
2744- tmatrix=xNew<double>(rows*cols);
2745- for(i=0;i<cols;i++){
2746- for(j=0;j<rows;j++){
2747- *(tmatrix+rows*i+j)=*(mxmatrix_ptr+cols*j+i);
2748- }
2749- }
2750-
2751- /*Create serial matrix: */
2752- ierr=MatCreateSeqDense(PETSC_COMM_SELF,rows,cols,NULL,&matrix);CHKERRQ(ierr);
2753-
2754- /*Insert mxmatrix_ptr values into petsc matrix: */
2755- idxm=xNew<int>(rows);
2756- idxn=xNew<int>(cols);
2757-
2758- for(i=0;i<rows;i++)idxm[i]=i;
2759- for(i=0;i<cols;i++)idxn[i]=i;
2760-
2761- ierr=MatSetValues(matrix,rows,idxm,cols,idxn,tmatrix,INSERT_VALUES); CHKERRQ(ierr);
2762-
2763- xDelete<double>(tmatrix);
2764- }
2765-
2766- /*Assemble matrix: */
2767- MatAssemblyBegin(matrix,MAT_FINAL_ASSEMBLY);
2768- MatAssemblyEnd(matrix,MAT_FINAL_ASSEMBLY);
2769-
2770- /*Assign output pointer: */
2771- *pmatrix=matrix;
2772- if(pmatrix_rows) *pmatrix_rows=rows;
2773- if(pmatrix_cols) *pmatrix_cols=cols;
2774-
2775- return 1;
2776-}
2777Index: ../trunk-jpl/src/c/matlab/io/matlabio.h
2778===================================================================
2779--- ../trunk-jpl/src/c/matlab/io/matlabio.h (revision 13748)
2780+++ ../trunk-jpl/src/c/matlab/io/matlabio.h (revision 13749)
2781@@ -1,93 +0,0 @@
2782-/*\file matlabio.h
2783- *\brief: I/O for ISSM in matlab mode
2784- */
2785-
2786-#ifndef _MATLAB_IO_H_
2787-#define _MATLAB_IO_H_
2788-
2789-#ifdef HAVE_CONFIG_H
2790-#include <config.h>
2791-#else
2792-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
2793-#endif
2794-
2795-#include <mex.h>
2796-#include "../../classes/classes.h"
2797-#include "../../Container/Container.h"
2798-#include "../../include/include.h"
2799-
2800-void WriteData(mxArray** pdataref,SeqMat<double>* matrix);
2801-void WriteData(mxArray** pdataref,double* matrix, int M,int N);
2802-void WriteData(mxArray** pdataref,int* matrix, int M,int N);
2803-void WriteData(mxArray** pdataref,SeqVec<double>* vector);
2804-void WriteData(mxArray** pdataref,double* vector, int M);
2805-void WriteData(mxArray** pdataref,int integer);
2806-void WriteData(mxArray** pdataref,bool boolean);
2807-void WriteData(mxArray** pdataref,double scalar);
2808-void WriteData(mxArray** pdataref,char* string);
2809-void WriteData(mxArray** pdataref);
2810-void WriteData(mxArray** pdataref,BamgGeom* bamggeom);
2811-void WriteData(mxArray** pdataref,BamgMesh* bamgmesh);
2812-void WriteData(mxArray** pdataref,RiftStruct* riftstruct);
2813-
2814-void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref);
2815-void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref);
2816-void FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref);
2817-void FetchData(bool** pmatrix,int* pM,int *pN,const mxArray* dataref);
2818-void FetchData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref);
2819-void FetchData(Matrix<double>** pmatrix,const mxArray* dataref);
2820-void FetchData(int** pvector,int* pM,const mxArray* dataref);
2821-void FetchData(float** pvector,int* pM,const mxArray* dataref);
2822-void FetchData(double** pvector,int* pM,const mxArray* dataref);
2823-void FetchData(bool** pvector,int* pM,const mxArray* dataref);
2824-void FetchData(Vector<double>** pvector,const mxArray* dataref);
2825-void FetchData(char** pstring,const mxArray* dataref);
2826-void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref);
2827-void FetchData(double* pscalar,const mxArray* dataref);
2828-void FetchData(int* pinteger,const mxArray* dataref);
2829-void FetchData(bool* pbool,const mxArray* dataref);
2830-void FetchData(BamgGeom** bamggeom,const mxArray* dataref);
2831-void FetchData(BamgMesh** bamgmesh,const mxArray* dataref);
2832-void FetchData(BamgOpts** bamgopts,const mxArray* dataref);
2833-void FetchData(Options** poptions,int istart, int nrhs,const mxArray** pdataref);
2834-void FetchData(DataSet** pcontours,const mxArray* dataref);
2835-
2836-Option* OptionParse(char* name, const mxArray* prhs[]);
2837-GenericOption<double>* OptionDoubleParse( char* name, const mxArray* prhs[]);
2838-GenericOption<double*>* OptionDoubleArrayParse( char* name, const mxArray* prhs[]);
2839-GenericOption<bool*>* OptionLogicalParse( char* name, const mxArray* prhs[]);
2840-GenericOption<char*>* OptionCharParse( char* name, const mxArray* prhs[]);
2841-GenericOption<Options**>* OptionStructParse( char* name, const mxArray* prhs[]);
2842-GenericOption<Options*>* OptionCellParse( char* name, const mxArray* prhs[]);
2843-
2844-mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number, const char* field);
2845-void SetStructureField(mxArray* dataref,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer);
2846-void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer);
2847-void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int field);
2848-void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,double field);
2849-int CheckNumMatlabArguments(int nlhs,int NLHS, int nrhs,int NRHS, const char* THISFUNCTION, void (*function)( void ));
2850-
2851-/*Matlab to Matrix routines: */
2852-Matrix<double>* MatlabMatrixToMatrix(const mxArray* mxmatrix);
2853-Vector<double>* MatlabVectorToVector(const mxArray* mxvector);
2854-
2855-/*Matlab to double* routines: */
2856-int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector);
2857-int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix);
2858-int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix);
2859-int MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix);
2860-int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix);
2861-
2862-/*Matlab to SeqMat routines: */
2863-SeqMat<double>* MatlabMatrixToSeqMat(const mxArray* dataref);
2864-SeqVec<double>* MatlabVectorToSeqVec(const mxArray* dataref);
2865-
2866-/*Matlab to Petsc routines: */
2867-#ifdef _HAVE_PETSC_
2868-int MatlabMatrixToPetscMat(Mat* matrix,int* prows,int* pcols, const mxArray* mxmatrix);
2869-PetscMat* MatlabMatrixToPetscMat(const mxArray* mxmatrix);
2870-int MatlabVectorToPetscVec(Vec* pvector,int* pvector_rows,const mxArray* mxvector);
2871-PetscVec* MatlabVectorToPetscVec(const mxArray* mxvector);
2872-#endif
2873-
2874-#endif /* _IO_H_ */
2875Index: ../trunk-jpl/src/c/matlab/io/MatlabVectorToSeqVec.cpp
2876===================================================================
2877--- ../trunk-jpl/src/c/matlab/io/MatlabVectorToSeqVec.cpp (revision 13748)
2878+++ ../trunk-jpl/src/c/matlab/io/MatlabVectorToSeqVec.cpp (revision 13749)
2879@@ -1,29 +0,0 @@
2880-/*!\file MatlabVectorToSeqVec.cpp
2881- */
2882-
2883-/*Headers:*/
2884-/*{{{*/
2885-#ifdef HAVE_CONFIG_H
2886- #include <config.h>
2887-#else
2888-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
2889-#endif
2890-
2891-#include <mex.h>
2892-#include <stdio.h>
2893-#include <string.h>
2894-#include "../../toolkits/toolkits.h"
2895-#include "../../shared/shared.h"
2896-#include "./matlabio.h"
2897-
2898-/*}}}*/
2899-
2900-SeqVec<double>* MatlabVectorToSeqVec(const mxArray* dataref){
2901-
2902- SeqVec<double>* output=NULL;
2903-
2904- output=new SeqVec<double>();
2905- MatlabVectorToDoubleVector(&output->vector,&output->M,dataref);
2906- return output;
2907-
2908-}
2909Index: ../trunk-jpl/src/c/matlab/io/MatlabNArrayToNArray.cpp
2910===================================================================
2911--- ../trunk-jpl/src/c/matlab/io/MatlabNArrayToNArray.cpp (revision 13748)
2912+++ ../trunk-jpl/src/c/matlab/io/MatlabNArrayToNArray.cpp (revision 13749)
2913@@ -1,251 +0,0 @@
2914-/* \file MatlabNArrayToNArray.cpp
2915- * \brief: convert a sparse or dense matlab n-dimensional array to cpp n-dimensional array
2916- */
2917-
2918-#ifdef HAVE_CONFIG_H
2919- #include <config.h>
2920-#else
2921-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
2922-#endif
2923-
2924-#include "../../shared/shared.h"
2925-#include "../../include/include.h"
2926-
2927-#include <mex.h>
2928-
2929-/*FUNCTION MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){{{*/
2930-int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){
2931-
2932- int i,j,rows,cols;
2933- int numel,ndims;
2934- int *size,*dims;
2935- double* mxmatrix_ptr=NULL;
2936- const mwSize* ipt=NULL;
2937-
2938- /*output: */
2939- double* matrix=NULL;
2940-
2941- /*matlab indices: */
2942- mwIndex *ir = NULL;
2943- mwIndex *jc = NULL;
2944- double *pr = NULL;
2945- int count;
2946-
2947- /*get Matlab matrix information: */
2948- numel=mxGetNumberOfElements(mxmatrix);
2949- ndims=mxGetNumberOfDimensions(mxmatrix);
2950- ipt =mxGetDimensions(mxmatrix);
2951- size =xNew<int>(ndims);
2952- for (i=0;i<ndims;i++) size[i]=(int)ipt[i];
2953-
2954- /*Ok, first check if we are dealing with a sparse or full matrix: */
2955- if (mxIsSparse(mxmatrix)){
2956-
2957- /*Dealing with sparse matrix: recover size first: */
2958- rows = mxGetM(mxmatrix);
2959- cols = mxGetN(mxmatrix);
2960-
2961- matrix=xNewZeroInit<double>(rows*cols);
2962-
2963- /*Now, get ir,jc and pr: */
2964- ir = mxGetIr(mxmatrix);
2965- jc = mxGetJc(mxmatrix);
2966- pr = mxGetPr(mxmatrix);
2967-
2968- /*Now, start inserting data into double* matrix: */
2969- count=0;
2970- for(i=0;i<cols;i++){
2971- for(j=0;j<(jc[i+1]-jc[i]);j++){
2972- *(matrix+rows*ir[count]+i)=pr[count];
2973- count++;
2974- }
2975- }
2976-
2977- }
2978- else{
2979-
2980- /*Dealing with dense matrix: recover pointer and size: */
2981- mxmatrix_ptr=(double*)mxGetPr(mxmatrix);
2982-
2983- /*Create serial matrix: */
2984- matrix=xNewZeroInit<double>(numel);
2985-
2986- dims=xNew<int>(ndims);
2987- for(i=0;i<numel;i++){
2988- ColumnWiseDimsFromIndex(dims,i,size,ndims);
2989- j = IndexFromRowWiseDims(dims,size,ndims);
2990- matrix[j]=(double)mxmatrix_ptr[i];
2991- }
2992- xDelete<int>(dims);
2993- }
2994-
2995- /*Assign output pointer: */
2996- *pmatrix = matrix;
2997- *pmatrix_numel = numel;
2998- *pmatrix_ndims = ndims;
2999- *pmatrix_size = size;
3000-
3001- return 1;
3002-}
3003-/*}}}*/
3004-/*FUNCTION MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){{{*/
3005-int MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){
3006-
3007- int i,j,rows,cols;
3008- int numel,ndims;
3009- int *size,*dims;
3010- bool* mxmatrix_ptr=NULL;
3011- const mwSize* ipt=NULL;
3012-
3013- /*output: */
3014- bool* matrix=NULL;
3015-
3016- /*matlab indices: */
3017- mwIndex *ir = NULL;
3018- mwIndex *jc = NULL;
3019- bool *pm = NULL;
3020- int count;
3021-
3022- /*get Matlab matrix information: */
3023- numel = mxGetNumberOfElements(mxmatrix);
3024- ndims = mxGetNumberOfDimensions(mxmatrix);
3025- ipt = mxGetDimensions(mxmatrix);
3026- size = xNew<int>(ndims);
3027- for (i=0;i<ndims;i++) size[i]=(int)ipt[i];
3028-
3029- /*Ok, first check if we are dealing with a sparse or full matrix: */
3030- if (mxIsSparse(mxmatrix)){
3031-
3032- /*Dealing with sparse matrix: recover size first: */
3033- rows=mxGetM(mxmatrix);
3034- cols=mxGetN(mxmatrix);
3035- matrix=xNewZeroInit<bool>(rows*cols);
3036-
3037- /*Now, get ir,jc and pm: */
3038- ir=mxGetIr(mxmatrix);
3039- jc=mxGetJc(mxmatrix);
3040- pm=(bool*)mxGetData(mxmatrix);
3041-
3042- /*Now, start inserting data into bool* matrix: */
3043- count=0;
3044- for(i=0;i<cols;i++){
3045- for(j=0;j<(jc[i+1]-jc[i]);j++){
3046- matrix[rows*ir[count]+i]=pm[count];
3047- count++;
3048- }
3049- }
3050- }
3051- else{
3052-
3053- /*Dealing with dense matrix: recover pointer and size: */
3054- mxmatrix_ptr=(bool*)mxGetData(mxmatrix);
3055-
3056- /*Create serial matrix: */
3057- matrix=xNew<bool>(numel);
3058- dims=xNew<int>(ndims);
3059- for(i=0;i<numel;i++){
3060- ColumnWiseDimsFromIndex(dims,i,size,ndims);
3061- j=IndexFromRowWiseDims(dims,size,ndims);
3062- matrix[j]=(bool)mxmatrix_ptr[i];
3063- }
3064- xDelete<int>(dims);
3065- }
3066-
3067- /*Assign output pointer: */
3068- *pmatrix = matrix;
3069- *pmatrix_numel = numel;
3070- *pmatrix_ndims = ndims;
3071- *pmatrix_size = size;
3072-
3073- return 1;
3074-}
3075-/*}}}*/
3076-/*FUNCTION MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){{{*/
3077-int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){
3078-
3079- int i,j,rows,cols;
3080- int numel,ndims;
3081- int *size , *dims;
3082- mxChar *mxmatrix_ptr = NULL;
3083- const mwSize *ipt = NULL;
3084-
3085- /*output: */
3086- char* matrix=NULL;
3087-
3088- /*matlab indices: */
3089- mwIndex *ir = NULL;
3090- mwIndex *jc = NULL;
3091- char *pm = NULL;
3092- int count;
3093-
3094- /*get Matlab matrix information: */
3095- numel = mxGetNumberOfElements(mxmatrix);
3096- ndims = mxGetNumberOfDimensions(mxmatrix);
3097- ipt = mxGetDimensions(mxmatrix);
3098- size = xNew<int>(ndims);
3099- for (i=0;i<ndims;i++) size[i]=(int)ipt[i];
3100-
3101- /*Ok, first check if we are dealing with a sparse or full matrix: */
3102- if (mxIsSparse(mxmatrix)){
3103-
3104- /*Dealing with sparse matrix: recover size first: */
3105- rows = mxGetM(mxmatrix);
3106- cols = mxGetN(mxmatrix);
3107- matrix=xNew<char>(rows*cols);
3108-
3109- /*Now, get ir,jc and pm: */
3110- ir = mxGetIr(mxmatrix);
3111- jc = mxGetJc(mxmatrix);
3112- pm = (char*)mxGetData(mxmatrix);
3113-
3114- /*Now, start inserting data into char* matrix: */
3115- count=0;
3116- for(i=0;i<cols;i++){
3117- for(j=0;j<(jc[i+1]-jc[i]);j++){
3118- matrix[rows*ir[count]+i]=(char)pm[count];
3119- count++;
3120- }
3121- }
3122- }
3123- else{
3124- /*Dealing with dense matrix: recover pointer and size: */
3125- mxmatrix_ptr=mxGetChars(mxmatrix);
3126-
3127- /*Create serial matrix: */
3128- matrix=xNew<char>(numel+1);
3129- matrix[numel]='\0';
3130-
3131- /*looping code adapted from Matlab example explore.c: */
3132- int elements_per_page = size[0] * size[1];
3133- /* total_number_of_pages = size[2] x size[3] x ... x size[N-1] */
3134- int total_number_of_pages = 1;
3135- for (i=2; i<ndims; i++) {
3136- total_number_of_pages *= size[i];
3137- }
3138-
3139- i=0;
3140- for (int page=0; page < total_number_of_pages; page++) {
3141- int row;
3142- /* On each page, walk through each row. */
3143- for (row=0; row<size[0]; row++) {
3144- int column;
3145- j = (page * elements_per_page) + row;
3146-
3147- /* Walk along each column in the current row. */
3148- for (column=0; column<size[1]; column++) {
3149- *(matrix+i++)=(char)*(mxmatrix_ptr+j);
3150- j += size[0];
3151- }
3152- }
3153- }
3154- }
3155-
3156- /*Assign output pointer: */
3157- *pmatrix = matrix;
3158- *pmatrix_numel = numel;
3159- *pmatrix_ndims = ndims;
3160- *pmatrix_size = size;
3161-
3162- return 1;
3163-}
3164-/*}}}*/
3165Index: ../trunk-jpl/src/c/matlab/io/MatlabMatrixToMatrix.cpp
3166===================================================================
3167--- ../trunk-jpl/src/c/matlab/io/MatlabMatrixToMatrix.cpp (revision 13748)
3168+++ ../trunk-jpl/src/c/matlab/io/MatlabMatrixToMatrix.cpp (revision 13749)
3169@@ -1,39 +0,0 @@
3170-/*!\file MatlabMatrixToMatrix.cpp
3171- */
3172-
3173-/*Headers:*/
3174-/*{{{*/
3175-#ifdef HAVE_CONFIG_H
3176- #include <config.h>
3177-#else
3178-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
3179-#endif
3180-
3181-#include <mex.h>
3182-#include <stdio.h>
3183-#include <string.h>
3184-#include "./matlabio.h"
3185-#include "../../classes/classes.h"
3186-#include "../../shared/shared.h"
3187-#include "../../Container/Container.h"
3188-#include "../../include/include.h"
3189-#include "../../toolkits/toolkits.h"
3190-
3191-/*}}}*/
3192-
3193-Matrix<double>* MatlabMatrixToMatrix(const mxArray* mxmatrix){
3194-
3195- int dummy;
3196- Matrix<double>* matrix=NULL;
3197-
3198- /*allocate matrix object: */
3199- matrix=new Matrix<double>();
3200-
3201- #ifdef _HAVE_PETSC_
3202- matrix->pmatrix=MatlabMatrixToPetscMat(mxmatrix);
3203- #else
3204- matrix->smatrix=MatlabMatrixToSeqMat(mxmatrix);
3205- #endif
3206-
3207- return matrix;
3208-}
3209Index: ../trunk-jpl/src/c/toolkits/python/pythonincludes.h
3210===================================================================
3211--- ../trunk-jpl/src/c/toolkits/python/pythonincludes.h (revision 13748)
3212+++ ../trunk-jpl/src/c/toolkits/python/pythonincludes.h (revision 13749)
3213@@ -1,24 +0,0 @@
3214-/* \file pythonincludes.h
3215- * \brief all includes for PYTHON layer
3216- */
3217-
3218-#ifndef _PYTHON_INCLUDES_H_
3219-#define _PYTHON_INCLUDES_H_
3220-
3221-#ifdef HAVE_CONFIG_H
3222- #include <config.h>
3223-#else
3224-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
3225-#endif
3226-
3227-#if _PYTHON_MAJOR_ == 2
3228-#undef NPY_NO_DEPRECATED_API
3229-#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
3230-#else
3231-#define NPY_NO_DEPRECATED_API
3232-#endif
3233-
3234-#include "Python.h"
3235-#include "arrayobject.h"
3236-
3237-#endif
3238Index: ../trunk-jpl/src/c/toolkits/toolkits.h
3239===================================================================
3240--- ../trunk-jpl/src/c/toolkits/toolkits.h (revision 13748)
3241+++ ../trunk-jpl/src/c/toolkits/toolkits.h (revision 13749)
3242@@ -11,10 +11,6 @@
3243 #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
3244 #endif
3245
3246-#ifdef _HAVE_PYTHON_
3247-#include "./python/pythonincludes.h"
3248-#endif
3249-
3250 #ifdef _HAVE_PETSC_
3251 #include "./petsc/petscincludes.h"
3252 #endif
3253@@ -30,5 +26,4 @@
3254 #include "./triangle/triangleincludes.h"
3255 #include "./toolkitsenums.h"
3256 #include "./issm/issmtoolkit.h"
3257-
3258 #endif
3259Index: ../trunk-jpl/src/c/Makefile.am
3260===================================================================
3261--- ../trunk-jpl/src/c/Makefile.am (revision 13748)
3262+++ ../trunk-jpl/src/c/Makefile.am (revision 13749)
3263@@ -1,4 +1,4 @@
3264-AM_CPPFLAGS = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@
3265+AM_CPPFLAGS = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ @BOOSTINCL@
3266
3267 EXEEXT=$(ISSMEXT)
3268
3269@@ -8,15 +8,6 @@
3270 if SHAREDLIBS
3271 lib_LTLIBRARIES = libISSMCore.la libISSMOverload.la libISSM.la
3272 endif
3273-if PYTHON
3274-lib_LIBRARIES += libISSMPython.a
3275-endif
3276-if MATLAB
3277-if SHAREDLIBS
3278-lib_LTLIBRARIES += libISSMMatlab.la
3279-endif
3280-lib_LIBRARIES += libISSMMatlab.a
3281-endif
3282 if WRAPPERS
3283 if SHAREDLIBS
3284 lib_LTLIBRARIES += libISSMWrappers.la
3285@@ -763,36 +754,6 @@
3286 metis_sources= ./toolkits/metis/patches/metispatches.h\
3287 ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp
3288 #}}}
3289-#Python sources {{{
3290-python_sources= ./python/io/pythonio.h\
3291- ./python/python-binding.h\
3292- ./python/io/WritePythonData.cpp\
3293- ./python/io/CheckNumPythonArguments.cpp\
3294- ./python/io/FetchPythonData.cpp
3295-
3296-#}}}
3297-#Matlab sources {{{
3298-matlab_sources= ./toolkits/matlab/matlabincludes.h\
3299- ./matlab/matlab-binding.h\
3300- ./matlab/io/matlabio.h\
3301- ./matlab/io/MatlabNArrayToNArray.cpp\
3302- ./matlab/io/CheckNumMatlabArguments.cpp\
3303- ./matlab/io/mxGetAssignedField.cpp\
3304- ./matlab/io/WriteMatlabData.cpp\
3305- ./matlab/io/FetchMatlabData.cpp\
3306- ./matlab/io/OptionParse.cpp\
3307- ./matlab/io/MatlabMatrixToMatrix.cpp\
3308- ./matlab/io/MatlabVectorToVector.cpp\
3309- ./matlab/io/MatlabVectorToDoubleVector.cpp\
3310- ./matlab/io/MatlabMatrixToDoubleMatrix.cpp\
3311- ./matlab/io/MatlabMatrixToSeqMat.cpp\
3312- ./matlab/io/MatlabVectorToSeqVec.cpp
3313-#}}}
3314-#Matlab and Petsc sources {{{
3315-matlabpetsc_sources= ./matlab/io/MatlabMatrixToPetscMat.cpp\
3316- ./matlab/io/MatlabVectorToPetscVec.cpp
3317-
3318-#}}}
3319 #Wrappers sources{{{
3320 wrapper_sources= ./shared/Threads/issm_threads.h\
3321 ./shared/Threads/LaunchThread.cpp\
3322@@ -944,12 +905,6 @@
3323 issm_sources += $(metis_sources)
3324 endif
3325
3326-if PETSC
3327-if MATLAB
3328-issm_sources += $(matlabpetsc_sources)
3329-endif
3330-endif
3331-
3332 if KRIGING
3333 issm_sources += $(pkriging_sources)
3334 endif
3335@@ -986,19 +941,6 @@
3336 endif
3337 endif
3338
3339-if PYTHON
3340-libISSMPython_a_SOURCES = $(python_sources)
3341-libISSMPython_a_CXXFLAGS= $(ALLCXXFLAGS)
3342-endif
3343-
3344-if MATLAB
3345-libISSMMatlab_a_SOURCES = $(matlab_sources)
3346-libISSMMatlab_a_CXXFLAGS= $(ALLCXXFLAGS)
3347-if SHAREDLIBS
3348-libISSMMatlab_la_SOURCES = $(libISSMMatlab_a_SOURCES)
3349-endif
3350-endif
3351-
3352 if VERSION
3353 AM_LDFLAGS =
3354 else
3355Index: ../trunk-jpl/src/wrappers/python/include/wrapper_macros.h
3356===================================================================
3357--- ../trunk-jpl/src/wrappers/python/include/wrapper_macros.h (revision 0)
3358+++ ../trunk-jpl/src/wrappers/python/include/wrapper_macros.h (revision 13749)
3359@@ -0,0 +1,92 @@
3360+/* \file python_macros.h
3361+ * \brief: macros used for the python bindings
3362+ */
3363+
3364+#ifndef _PY_WRAPPER_MACROS_H_
3365+#define _PY_WRAPPER_MACROS_H_
3366+
3367+#ifdef HAVE_CONFIG_H
3368+ #include <config.h>
3369+#else
3370+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
3371+#endif
3372+
3373+#ifdef _HAVE_PYTHON_
3374+/* MODULEBOOT/MODULEEND {{{*/
3375+
3376+/*The following macros hide the error exception handling in a matlab module. Just put
3377+ * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions
3378+ * will be trapped*/
3379+#define MODULEBOOT(); \
3380+ PyObject *output = PyTuple_New(NLHS); \
3381+ int nrhs = (int)PyTuple_Size(args); \
3382+ if(!output) return NULL;\
3383+ try{ \
3384+ IssmComm::SetComm(-1);
3385+
3386+#define MODULEEND(); }\
3387+ catch(ErrorException &exception){\
3388+ PyErr_SetString(PyExc_TypeError,exception.PythonReport()); \
3389+ return NULL;\
3390+ } \
3391+ catch (exception &e){\
3392+ PyErr_SetString(PyExc_TypeError,exprintf("Standard exception: %s\n",e.what()));\
3393+ return NULL;\
3394+ }\
3395+ catch(...){\
3396+ PyErr_SetString(PyExc_TypeError,"An unexpected error occurred");\
3397+ return NULL;\
3398+ }\
3399+ return output;
3400+//}}}
3401+#if _PYTHON_MAJOR_ >=3
3402+/* WRAPPER 3.2 {{{*/
3403+#define WRAPPER(modulename,...) \
3404+\
3405+static PyObject* modulename(PyObject* self,PyObject* args);\
3406+static PyMethodDef modulename##_funcs[] = {\
3407+ {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\
3408+ {NULL,NULL,0,NULL}\
3409+};\
3410+\
3411+static struct PyModuleDef modulename##module= {\
3412+ PyModuleDef_HEAD_INIT,\
3413+ #modulename, /* name of module */\
3414+ NULL, /* module documentation, may be NULL */\
3415+ -1, /* size of per-interpreter state of the module,\
3416+ or -1 if the module keeps state in global variables. */\
3417+ modulename##_funcs\
3418+};\
3419+\
3420+PyMODINIT_FUNC PyInit_##modulename(void){\
3421+\
3422+ import_array();\
3423+ return PyModule_Create(&modulename##module);\
3424+}\
3425+\
3426+static PyObject* modulename(PyObject* self,PyObject* args)
3427+/*}}}*/
3428+#else
3429+/* WRAPPER 2.7 {{{*/
3430+#define WRAPPER(modulename,...) \
3431+\
3432+static PyObject* modulename(PyObject* self,PyObject* args);\
3433+static PyMethodDef modulename##_funcs[] = {\
3434+ {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\
3435+ {NULL,NULL,0,NULL}\
3436+};\
3437+\
3438+PyMODINIT_FUNC init##modulename(void){\
3439+\
3440+ import_array();\
3441+ (void) Py_InitModule(#modulename, modulename##_funcs);\
3442+}\
3443+\
3444+static PyObject* modulename(PyObject* self,PyObject* args)
3445+/*}}}*/
3446+#endif
3447+/* CHECKARGUMENTS {{{*/
3448+#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumPythonArguments(args, NRHS,functionpointer)
3449+/*}}}*/
3450+#endif
3451+#endif
3452Index: ../trunk-jpl/src/wrappers/python/io/pythonio.h
3453===================================================================
3454--- ../trunk-jpl/src/wrappers/python/io/pythonio.h (revision 0)
3455+++ ../trunk-jpl/src/wrappers/python/io/pythonio.h (revision 13749)
3456@@ -0,0 +1,48 @@
3457+/*\file pythonio.h
3458+ *\brief: I/O for ISSM in python mode
3459+ */
3460+
3461+#ifndef _PYTHON_IO_H_
3462+#define _PYTHON_IO_H_
3463+
3464+#ifdef HAVE_CONFIG_H
3465+#include <config.h>
3466+#else
3467+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
3468+#endif
3469+
3470+#include "../include/pythonincludes.h"
3471+#include "../../c/classes/classes.h"
3472+#include "../../c/Container/Container.h"
3473+#include "../../c/include/include.h"
3474+
3475+void WriteData(PyObject* py_tuple,int index, double* matrix, int M,int N);
3476+void WriteData(PyObject* py_tuple,int index, int integer);
3477+void WriteData(PyObject* py_tuple,int index, char* string);
3478+void WriteData(PyObject* py_tuple,int index);
3479+void WriteData(PyObject* py_tuple,int index, SeqMat<double>* matrix);
3480+void WriteData(PyObject* py_tuple,int index, SeqVec<double>* vector);
3481+void WriteData(PyObject* py_tuple,int index, BamgGeom* bamggeom);
3482+void WriteData(PyObject* py_tuple,int index, BamgMesh* bamgmesh);
3483+void WriteData(PyObject* py_tuple,int index, RiftStruct* riftstruct);
3484+
3485+void FetchData(double** pvector,int* pM,PyObject* py_ref);
3486+void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_array);
3487+void FetchData(int** pmatrix,int* pM,int *pN,PyObject* py_matrix);
3488+void FetchData(char** pstring,PyObject* py_unicode);
3489+void FetchData(double* pscalar,PyObject* py_float);
3490+void FetchData(int* pinteger,PyObject* py_long);
3491+void FetchData(bool* pbool,PyObject* py_boolean);
3492+void FetchData(BamgGeom** bamggeom,PyObject* py_dict);
3493+void FetchData(BamgMesh** bamgmesh,PyObject* py_dict);
3494+void FetchData(BamgOpts** bamgopts,PyObject* py_dict);
3495+void FetchData(Options** poptions,int istart, int nrhs,PyObject* py_tuple);
3496+void FetchData(DataSet** pcontours,PyObject* py_list);
3497+
3498+int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void ));
3499+
3500+/*Utils*/
3501+PyObject* PyArrayFromCopiedData(int dims[2],double* data);
3502+PyObject* PyArrayFromCopiedData(int dimi,int dimj,double* data);
3503+
3504+#endif /* _IO_H_ */
3505Index: ../trunk-jpl/src/wrappers/python/io/CheckNumPythonArguments.cpp
3506===================================================================
3507--- ../trunk-jpl/src/wrappers/python/io/CheckNumPythonArguments.cpp (revision 0)
3508+++ ../trunk-jpl/src/wrappers/python/io/CheckNumPythonArguments.cpp (revision 13749)
3509@@ -0,0 +1,29 @@
3510+/*!\file CheckNumPythonArguments.cpp:
3511+ * \brief: check number of arguments and report an usage error message.
3512+ */
3513+
3514+#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol
3515+#define NO_IMPORT
3516+
3517+#include "./pythonio.h"
3518+#include "../../c/shared/Exceptions/exceptions.h"
3519+#include "../../c/include/include.h"
3520+
3521+int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void )){
3522+
3523+ Py_ssize_t size=0;
3524+
3525+ /*figure out size of tuple in input: */
3526+ size=PyTuple_Size(inputs);
3527+
3528+ /*check on requested size: */
3529+ if (size==0){
3530+ function();
3531+ _error_("usage: see above");
3532+ }
3533+ else if (size!=NRHS ) {
3534+ function();
3535+ _error_("usage error.");
3536+ }
3537+ return 1;
3538+}
3539Index: ../trunk-jpl/src/wrappers/python/io/FetchPythonData.cpp
3540===================================================================
3541--- ../trunk-jpl/src/wrappers/python/io/FetchPythonData.cpp (revision 0)
3542+++ ../trunk-jpl/src/wrappers/python/io/FetchPythonData.cpp (revision 13749)
3543@@ -0,0 +1,354 @@
3544+/*\file FetchData.cpp:
3545+ * \brief: general I/O interface to fetch data in python
3546+ */
3547+
3548+#ifdef HAVE_CONFIG_H
3549+ #include <config.h>
3550+#else
3551+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
3552+#endif
3553+
3554+#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol
3555+#define NO_IMPORT
3556+
3557+#include "./pythonio.h"
3558+#include "../../c/include/include.h"
3559+#include "../../c/shared/shared.h"
3560+
3561+/*Primitive data types*/
3562+/*FUNCTION FetchData(double* pscalar,PyObject* py_float){{{*/
3563+void FetchData(double* pscalar,PyObject* py_float){
3564+
3565+ double scalar;
3566+
3567+ /*return internal value: */
3568+ scalar=PyFloat_AsDouble(py_float);
3569+
3570+ /*output: */
3571+ *pscalar=scalar;
3572+}
3573+/*}}}*/
3574+/*FUNCTION FetchData(int* pinteger,PyObject* py_long){{{*/
3575+void FetchData(int* pinteger, PyObject* py_long){
3576+
3577+ int integer;
3578+
3579+ /*return internal value: */
3580+ integer=(int)PyLong_AsLong(py_long);
3581+
3582+ /*output: */
3583+ *pinteger=integer;
3584+}
3585+/*}}}*/
3586+/*FUNCTION FetchData(bool* pboolean,PyObject* py_boolean){{{*/
3587+void FetchData(bool* pboolean,PyObject* py_boolean){
3588+
3589+ bool boolean;
3590+
3591+ /*check this is indeed a subtype of long type: */
3592+ if(!PyBool_Check(py_boolean))_error_("expecting a boolean in input!");
3593+
3594+ /*extract boolean: */
3595+ boolean=(bool)PyLong_AsLong(py_boolean);
3596+
3597+ /*simple copy: */
3598+ *pboolean=boolean;
3599+
3600+}
3601+/*}}}*/
3602+/*FUNCTION FetchData(double** pmatrix,int* pM, int* pN, PyObject* py_matrix){{{*/
3603+void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_matrix){
3604+
3605+ /*output: */
3606+ double* dmatrix=NULL;
3607+ double* matrix=NULL;
3608+ int M,N;
3609+ int ndim;
3610+ npy_intp* dims=NULL;
3611+
3612+ /*retrive dimensions: */
3613+ ndim=PyArray_NDIM((const PyArrayObject*)py_matrix);
3614+ if(ndim!=2)_error_("expecting an MxN matrix in input!");
3615+ dims=PyArray_DIMS((PyArrayObject*)py_matrix);
3616+ M=dims[0]; N=dims[1];
3617+
3618+ if (M && N) {
3619+ /*retrieve internal value: */
3620+ dmatrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix);
3621+
3622+ /*copy matrix: */
3623+ matrix=xNew<double>(M*N);
3624+ memcpy(matrix,dmatrix,(M*N)*sizeof(double));
3625+ }
3626+ else
3627+ matrix=NULL;
3628+
3629+ /*output: */
3630+ if(pM)*pM=M;
3631+ if(pN)*pN=N;
3632+ if(pmatrix)*pmatrix=matrix;
3633+}
3634+/*}}}*/
3635+/*FUNCTION FetchData(int** pmatrix,int* pM, int* pN, PyObject* py_matrix){{{*/
3636+void FetchData(int** pmatrix,int* pM,int *pN,PyObject* py_matrix){
3637+
3638+ /*output: */
3639+ double* dmatrix=NULL;
3640+ int* matrix=NULL;
3641+ int M,N;
3642+
3643+ /*intermediary:*/
3644+ int i;
3645+ int ndim;
3646+ npy_intp* dims=NULL;
3647+
3648+ /*retrive dimensions: */
3649+ ndim=PyArray_NDIM((const PyArrayObject*)py_matrix);
3650+ if(ndim!=2)_error_("expecting an MxN matrix in input!");
3651+ dims=PyArray_DIMS((PyArrayObject*)py_matrix);
3652+ M=dims[0]; N=dims[1];
3653+
3654+ if (M && N) {
3655+ /*retrieve internal value: */
3656+ dmatrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix);
3657+
3658+ /*transform into integer matrix: */
3659+ matrix=xNew<int>(M*N);
3660+ for(i=0;i<M*N;i++)matrix[i]=(int)dmatrix[i];
3661+ }
3662+ else
3663+ matrix=NULL;
3664+
3665+ /*output: */
3666+ if(pM)*pM=M;
3667+ if(pN)*pN=N;
3668+ if(pmatrix)*pmatrix=matrix;
3669+}
3670+/*}}}*/
3671+/*FUNCTION FetchData(double** pvector,int* pM, PyObject* py_vector){{{*/
3672+void FetchData(double** pvector,int* pM,PyObject* py_vector){
3673+
3674+ /*output: */
3675+ double* dvector=NULL;
3676+ double* vector=NULL;
3677+ int M;
3678+ int ndim;
3679+ npy_intp* dims=NULL;
3680+
3681+ /*retrive dimensions: */
3682+ ndim=PyArray_NDIM((const PyArrayObject*)py_vector);
3683+ if(ndim!=1)_error_("expecting an Mx1 vector in input!");
3684+ dims=PyArray_DIMS((PyArrayObject*)py_vector);
3685+ M=dims[0];
3686+
3687+ if (M) {
3688+ /*retrieve internal value: */
3689+ dvector=(double*)PyArray_DATA((PyArrayObject*)py_vector);
3690+
3691+ /*copy vector: */
3692+ vector=xNew<double>(M);
3693+ memcpy(vector,dvector,(M)*sizeof(double));
3694+ }
3695+ else
3696+ vector=NULL;
3697+
3698+ /*output: */
3699+ if(pM)*pM=M;
3700+ if(pvector)*pvector=vector;
3701+}
3702+/*}}}*/
3703+
3704+/*ISSM objects*/
3705+/*FUNCTION FetchData(BamgGeom** pbamggeom,PyObject* py_dict){{{*/
3706+void FetchData(BamgGeom** pbamggeom,PyObject* py_dict){
3707+
3708+ /*Initialize output*/
3709+ BamgGeom* bamggeom=new BamgGeom();
3710+
3711+ /*Fetch all fields*/
3712+ FetchData(&bamggeom->Vertices,&bamggeom->VerticesSize[0],&bamggeom->VerticesSize[1],PyDict_GetItemString(py_dict,"Vertices"));
3713+ FetchData(&bamggeom->Edges, &bamggeom->EdgesSize[0], &bamggeom->EdgesSize[1], PyDict_GetItemString(py_dict,"Edges"));
3714+ FetchData(&bamggeom->Corners, &bamggeom->CornersSize[0], &bamggeom->CornersSize[1], PyDict_GetItemString(py_dict,"Corners"));
3715+ FetchData(&bamggeom->RequiredVertices,&bamggeom->RequiredVerticesSize[0],&bamggeom->RequiredVerticesSize[1],PyDict_GetItemString(py_dict,"RequiredVertices"));
3716+ FetchData(&bamggeom->RequiredEdges, &bamggeom->RequiredEdgesSize[0], &bamggeom->RequiredEdgesSize[1], PyDict_GetItemString(py_dict,"RequiredEdges"));
3717+ FetchData(&bamggeom->CrackedEdges,&bamggeom->CrackedEdgesSize[0],&bamggeom->CrackedEdgesSize[1],PyDict_GetItemString(py_dict,"CrackedEdges"));
3718+ FetchData(&bamggeom->SubDomains,&bamggeom->SubDomainsSize[0],&bamggeom->SubDomainsSize[1],PyDict_GetItemString(py_dict,"SubDomains"));
3719+
3720+ /*Assign output pointers:*/
3721+ *pbamggeom=bamggeom;
3722+}
3723+/*}}}*/
3724+/*FUNCTION FetchData(BamgMesh** pbamgmesh,PyObject* py_dict){{{*/
3725+void FetchData(BamgMesh** pbamgmesh,PyObject* py_dict){
3726+
3727+ /*Initialize output*/
3728+ BamgMesh* bamgmesh=new BamgMesh();
3729+
3730+ /*Fetch all fields*/
3731+ FetchData(&bamgmesh->Vertices,&bamgmesh->VerticesSize[0],&bamgmesh->VerticesSize[1],PyDict_GetItemString(py_dict,"Vertices"));
3732+ FetchData(&bamgmesh->Edges, &bamgmesh->EdgesSize[0], &bamgmesh->EdgesSize[1], PyDict_GetItemString(py_dict,"Edges"));
3733+ FetchData(&bamgmesh->Triangles, &bamgmesh->TrianglesSize[0], &bamgmesh->TrianglesSize[1], PyDict_GetItemString(py_dict,"Triangles"));
3734+ FetchData(&bamgmesh->CrackedEdges,&bamgmesh->CrackedEdgesSize[0],&bamgmesh->CrackedEdgesSize[1],PyDict_GetItemString(py_dict,"CrackedEdges"));
3735+ FetchData(&bamgmesh->VerticesOnGeomEdge,&bamgmesh->VerticesOnGeomEdgeSize[0],&bamgmesh->VerticesOnGeomEdgeSize[1],PyDict_GetItemString(py_dict,"VerticesOnGeomEdge"));
3736+ FetchData(&bamgmesh->VerticesOnGeomVertex,&bamgmesh->VerticesOnGeomVertexSize[0],&bamgmesh->VerticesOnGeomVertexSize[1],PyDict_GetItemString(py_dict,"VerticesOnGeomVertex"));
3737+ FetchData(&bamgmesh->EdgesOnGeomEdge, &bamgmesh->EdgesOnGeomEdgeSize[0], &bamgmesh->EdgesOnGeomEdgeSize[1], PyDict_GetItemString(py_dict,"EdgesOnGeomEdge"));
3738+ FetchData(&bamgmesh->IssmSegments,&bamgmesh->IssmSegmentsSize[0],&bamgmesh->IssmSegmentsSize[1],PyDict_GetItemString(py_dict,"IssmSegments"));
3739+
3740+ /*Assign output pointers:*/
3741+ *pbamgmesh=bamgmesh;
3742+}
3743+/*}}}*/
3744+/*FUNCTION FetchData(BamgOpts** pbamgopts,PyObject* py_dict){{{*/
3745+void FetchData(BamgOpts** pbamgopts,PyObject* py_dict){
3746+
3747+ /*Initialize output*/
3748+ BamgOpts* bamgopts=new BamgOpts();
3749+
3750+ /*Fetch all fields*/
3751+ FetchData(&bamgopts->anisomax,PyDict_GetItemString(py_dict,"anisomax"));
3752+ FetchData(&bamgopts->cutoff,PyDict_GetItemString(py_dict,"cutoff"));
3753+ FetchData(&bamgopts->coeff,PyDict_GetItemString(py_dict,"coeff"));
3754+ FetchData(&bamgopts->errg,PyDict_GetItemString(py_dict,"errg"));
3755+ FetchData(&bamgopts->gradation,PyDict_GetItemString(py_dict,"gradation"));
3756+ FetchData(&bamgopts->Hessiantype,PyDict_GetItemString(py_dict,"Hessiantype"));
3757+ FetchData(&bamgopts->MaxCornerAngle,PyDict_GetItemString(py_dict,"MaxCornerAngle"));
3758+ FetchData(&bamgopts->maxnbv,PyDict_GetItemString(py_dict,"maxnbv"));
3759+ FetchData(&bamgopts->maxsubdiv,PyDict_GetItemString(py_dict,"maxsubdiv"));
3760+ FetchData(&bamgopts->Metrictype,PyDict_GetItemString(py_dict,"Metrictype"));
3761+ FetchData(&bamgopts->nbjacobi,PyDict_GetItemString(py_dict,"nbjacobi"));
3762+ FetchData(&bamgopts->nbsmooth,PyDict_GetItemString(py_dict,"nbsmooth"));
3763+ FetchData(&bamgopts->omega,PyDict_GetItemString(py_dict,"omega"));
3764+ FetchData(&bamgopts->power,PyDict_GetItemString(py_dict,"power"));
3765+ FetchData(&bamgopts->verbose,PyDict_GetItemString(py_dict,"verbose"));
3766+
3767+ FetchData(&bamgopts->Crack,PyDict_GetItemString(py_dict,"Crack"));
3768+ FetchData(&bamgopts->geometricalmetric,PyDict_GetItemString(py_dict,"geometricalmetric"));
3769+ FetchData(&bamgopts->KeepVertices,PyDict_GetItemString(py_dict,"KeepVertices"));
3770+ FetchData(&bamgopts->splitcorners,PyDict_GetItemString(py_dict,"splitcorners"));
3771+
3772+ FetchData(&bamgopts->hmin,PyDict_GetItemString(py_dict,"hmin"));
3773+ FetchData(&bamgopts->hmax,PyDict_GetItemString(py_dict,"hmax"));
3774+ FetchData(&bamgopts->hminVertices,&bamgopts->hminVerticesSize[0],&bamgopts->hminVerticesSize[1],PyDict_GetItemString(py_dict,"hminVertices"));
3775+ FetchData(&bamgopts->hmaxVertices,&bamgopts->hmaxVerticesSize[0],&bamgopts->hmaxVerticesSize[1],PyDict_GetItemString(py_dict,"hmaxVertices"));
3776+ FetchData(&bamgopts->hVertices,&bamgopts->hVerticesSize[0],&bamgopts->hVerticesSize[1],PyDict_GetItemString(py_dict,"hVertices"));
3777+ FetchData(&bamgopts->metric,&bamgopts->metricSize[0],&bamgopts->metricSize[1],PyDict_GetItemString(py_dict,"metric"));
3778+ FetchData(&bamgopts->field,&bamgopts->fieldSize[0],&bamgopts->fieldSize[1],PyDict_GetItemString(py_dict,"field"));
3779+ FetchData(&bamgopts->err,&bamgopts->errSize[0],&bamgopts->errSize[1],PyDict_GetItemString(py_dict,"err"));
3780+
3781+ /*Additional checks*/
3782+ bamgopts->Check();
3783+
3784+ /*Assign output pointers:*/
3785+ *pbamgopts=bamgopts;
3786+}
3787+/*}}}*/
3788+/*FUNCTION FetchData(Options** poptions,int istart, int nrhs,PyObject* py_tuple){{{*/
3789+void FetchData(Options** poptions,int istart, int nrhs,PyObject* py_tuple){
3790+
3791+ char *name = NULL;
3792+ Option *option = NULL;
3793+
3794+ /*Initialize output*/
3795+ Options* options=new Options();
3796+
3797+ /*Fetch all options*/
3798+ for (int i=istart; i<nrhs; i=i+2){
3799+ if (!PyString_Check(PyTuple_GetItem(py_tuple,(Py_ssize_t)i))) _error_("Argument " << i+1 << " must be name of option");
3800+
3801+ FetchData(&name,PyTuple_GetItem(py_tuple,(Py_ssize_t)i));
3802+ if(i+1 == nrhs) _error_("Argument " << i+2 << " must exist and be value of option \"" << name << "\".");
3803+
3804+ _pprintLine_("FetchData for Options not implemented yet, ignoring option \"" << name << "\"!");
3805+
3806+// option=(Option*)OptionParse(name,&PyTuple_GetItem(py_tuple,(Py_ssize_t)(i+1)));
3807+// options->AddOption(option);
3808+// option=NULL;
3809+ }
3810+
3811+ /*Assign output pointers:*/
3812+ *poptions=options;
3813+}
3814+/*}}}*/
3815+/*FUNCTION FetchData(DataSet** pcontours,PyObject* py_list){{{*/
3816+void FetchData(DataSet** pcontours,PyObject* py_list){
3817+
3818+ int numcontours,test1,test2;
3819+ char *contourname = NULL;
3820+ DataSet *contours = NULL;
3821+ Contour<double> *contouri = NULL;
3822+ PyObject *py_dicti = NULL;
3823+ PyObject *py_item = NULL;
3824+
3825+ if (PyString_Check(py_list)){
3826+ FetchData(&contourname,py_list);
3827+ contours=DomainOutlineRead<double>(contourname);
3828+ }
3829+ else if(PyList_Check(py_list)){
3830+
3831+ contours=new DataSet(0);
3832+ numcontours=(int)PyList_Size(py_list);
3833+
3834+ for(int i=0;i<numcontours;i++){
3835+
3836+ contouri=xNew<Contour<double> >(1);
3837+ py_dicti=PyList_GetItem(py_list,(Py_ssize_t)i);
3838+
3839+ py_item = PyDict_GetItemString(py_dicti,"nods");
3840+ if(!py_item) _error_("input structure does not have a 'nods' field");
3841+ FetchData(&contouri->nods,py_item);
3842+
3843+ py_item = PyDict_GetItemString(py_dicti,"x");
3844+ if(!py_item) _error_("input structure does not have a 'x' field");
3845+ FetchData(&contouri->x,&test1,&test2,py_item);
3846+ if(test1!=contouri->nods || test2!=1) _error_("field x should be of size ["<<contouri->nods<<" 1]");
3847+
3848+ py_item = PyDict_GetItemString(py_dicti,"y");
3849+ if(!py_item) _error_("input structure does not have a 'y' field");
3850+ FetchData(&contouri->y,&test1,&test2,py_item);
3851+ if(test1!=contouri->nods || test2!=1) _error_("field y should be of size ["<<contouri->nods<<" 1]");
3852+
3853+ contours->AddObject(contouri);
3854+ }
3855+ }
3856+ else{
3857+ _error_("Contour is neither a string nor a structure and cannot be loaded");
3858+ }
3859+
3860+ /*clean-up and assign output pointer*/
3861+ xDelete<char>(contourname);
3862+ *pcontours=contours;
3863+}
3864+/*}}}*/
3865+
3866+/*Python version dependent: */
3867+#if _PYTHON_MAJOR_ >= 3
3868+/*FUNCTION FetchData(char** pstring,PyObject* py_unicode){{{*/
3869+void FetchData(char** pstring,PyObject* py_unicode){
3870+
3871+ PyObject* py_bytes;
3872+ char* string=NULL;
3873+
3874+ /*convert to bytes format: */
3875+ PyUnicode_FSConverter(py_unicode,&py_bytes);
3876+
3877+ /*convert from bytes to string: */
3878+ string=PyBytes_AS_STRING(py_bytes);
3879+
3880+ *pstring=string;
3881+}
3882+/*}}}*/
3883+#else
3884+/*FUNCTION FetchData(char** pstring,PyObject* py_string){{{*/
3885+void FetchData(char** pstring,PyObject* py_string){
3886+
3887+ char* string=NULL;
3888+
3889+ /*extract internal string: */
3890+ string=PyString_AsString(py_string);
3891+
3892+ /*copy string (note strlen does not include trailing NULL): */
3893+ *pstring=xNew<char>(strlen(string)+1);
3894+ memcpy(*pstring,string,(strlen(string)+1)*sizeof(char));
3895+}
3896+/*}}}*/
3897+#endif
3898Index: ../trunk-jpl/src/wrappers/python/io/WritePythonData.cpp
3899===================================================================
3900--- ../trunk-jpl/src/wrappers/python/io/WritePythonData.cpp (revision 0)
3901+++ ../trunk-jpl/src/wrappers/python/io/WritePythonData.cpp (revision 13749)
3902@@ -0,0 +1,194 @@
3903+/* \file WriteData.c:
3904+ * \brief: general interface for writing data
3905+ */
3906+
3907+#ifdef HAVE_CONFIG_H
3908+ #include <config.h>
3909+#else
3910+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
3911+#endif
3912+
3913+#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol
3914+#define NO_IMPORT
3915+
3916+#include "./pythonio.h"
3917+#include "../../c/include/include.h"
3918+#include "../../c/Container/Container.h"
3919+#include "../../c/shared/shared.h"
3920+#include "../../c/EnumDefinitions/EnumDefinitions.h"
3921+
3922+/*Primitive data types*/
3923+/*FUNCTION WriteData(PyObject* py_tuple,int index,int integer){{{*/
3924+void WriteData(PyObject* py_tuple, int index, int integer){
3925+
3926+ PyTuple_SetItem(py_tuple, index, PyInt_FromSsize_t((Py_ssize_t)integer));
3927+
3928+}/*}}}*/
3929+/*FUNCTION WriteData(PyObject* py_tuple,int index,char* string){{{*/
3930+void WriteData(PyObject* py_tuple, int index, char* string){
3931+
3932+ PyTuple_SetItem(py_tuple, index, PyUnicode_FromString(string));
3933+
3934+}/*}}}*/
3935+/*FUNCTION WriteData(PyObject* py_tuple,int index, double* matrix, int M, int N){{{*/
3936+void WriteData(PyObject* tuple, int index, double* matrix, int M,int N){
3937+
3938+ npy_intp dims[2]={0,0};
3939+ PyObject* array=NULL;
3940+
3941+ dims[0]=(npy_intp)M;
3942+ dims[1]=(npy_intp)N;
3943+ array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,matrix);
3944+
3945+ PyTuple_SetItem(tuple, index, array);
3946+}/*}}}*/
3947+/*FUNCTION WriteData(PyObject* py_tuple,int index){{{*/
3948+void WriteData(PyObject* py_tuple, int index){
3949+
3950+ PyTuple_SetItem(py_tuple, index, Py_None);
3951+
3952+}/*}}}*/
3953+
3954+/*ISSM objects*/
3955+/*FUNCTION WriteData(PyObject* py_tuple,int index,BamgGeom* bamggeom){{{*/
3956+void WriteData(PyObject* py_tuple,int index,BamgGeom* bamggeom){
3957+
3958+ PyObject* dict=NULL;
3959+
3960+ dict=PyDict_New();
3961+
3962+ PyDict_SetItemString(dict,"Vertices",PyArrayFromCopiedData(bamggeom->VerticesSize,bamggeom->Vertices));
3963+ PyDict_SetItemString(dict,"Edges",PyArrayFromCopiedData(bamggeom->EdgesSize,bamggeom->Edges));
3964+ PyDict_SetItemString(dict,"TangentAtEdges",PyArrayFromCopiedData(bamggeom->TangentAtEdgesSize,bamggeom->TangentAtEdges));
3965+ PyDict_SetItemString(dict,"Corners",PyArrayFromCopiedData(bamggeom->CornersSize,bamggeom->Corners));
3966+ PyDict_SetItemString(dict,"RequiredVertices",PyArrayFromCopiedData(bamggeom->RequiredVerticesSize,bamggeom->RequiredVertices));
3967+ PyDict_SetItemString(dict,"RequiredEdges",PyArrayFromCopiedData(bamggeom->RequiredEdgesSize,bamggeom->RequiredEdges));
3968+ PyDict_SetItemString(dict,"CrackedEdges",PyArrayFromCopiedData(bamggeom->CrackedEdgesSize,bamggeom->CrackedEdges));
3969+ PyDict_SetItemString(dict,"SubDomains",PyArrayFromCopiedData(bamggeom->SubDomainsSize,bamggeom->SubDomains));
3970+
3971+ PyTuple_SetItem(py_tuple, index, dict);
3972+}
3973+/*}}}*/
3974+/*FUNCTION WriteData(PyObject* py_tuple,int index,BamgMesh* bamgmesh){{{*/
3975+void WriteData(PyObject* py_tuple,int index,BamgMesh* bamgmesh){
3976+
3977+ PyObject* dict=NULL;
3978+
3979+ dict=PyDict_New();
3980+
3981+ PyDict_SetItemString(dict,"Vertices",PyArrayFromCopiedData(bamgmesh->VerticesSize,bamgmesh->Vertices));
3982+ PyDict_SetItemString(dict,"Edges",PyArrayFromCopiedData(bamgmesh->EdgesSize,bamgmesh->Edges));
3983+ PyDict_SetItemString(dict,"Triangles",PyArrayFromCopiedData(bamgmesh->TrianglesSize,bamgmesh->Triangles));
3984+ PyDict_SetItemString(dict,"Quadrilaterals",PyArrayFromCopiedData(bamgmesh->QuadrilateralsSize,bamgmesh->Quadrilaterals));
3985+ PyDict_SetItemString(dict,"IssmEdges",PyArrayFromCopiedData(bamgmesh->IssmEdgesSize,bamgmesh->IssmEdges));
3986+ PyDict_SetItemString(dict,"IssmSegments",PyArrayFromCopiedData(bamgmesh->IssmSegmentsSize,bamgmesh->IssmSegments));
3987+ PyDict_SetItemString(dict,"VerticesOnGeomVertex",PyArrayFromCopiedData(bamgmesh->VerticesOnGeomVertexSize,bamgmesh->VerticesOnGeomVertex));
3988+ PyDict_SetItemString(dict,"VerticesOnGeomEdge",PyArrayFromCopiedData(bamgmesh->VerticesOnGeomEdgeSize,bamgmesh->VerticesOnGeomEdge));
3989+ PyDict_SetItemString(dict,"EdgesOnGeomEdge",PyArrayFromCopiedData(bamgmesh->EdgesOnGeomEdgeSize,bamgmesh->EdgesOnGeomEdge));
3990+ PyDict_SetItemString(dict,"SubDomains",PyArrayFromCopiedData(bamgmesh->SubDomainsSize,bamgmesh->SubDomains));
3991+ PyDict_SetItemString(dict,"SubDomainsFromGeom",PyArrayFromCopiedData(bamgmesh->SubDomainsFromGeomSize,bamgmesh->SubDomainsFromGeom));
3992+ PyDict_SetItemString(dict,"ElementConnectivity",PyArrayFromCopiedData(bamgmesh->ElementConnectivitySize,bamgmesh->ElementConnectivity));
3993+ PyDict_SetItemString(dict,"NodalConnectivity",PyArrayFromCopiedData(bamgmesh->NodalConnectivitySize,bamgmesh->NodalConnectivity));
3994+ PyDict_SetItemString(dict,"NodalElementConnectivity",PyArrayFromCopiedData(bamgmesh->NodalElementConnectivitySize,bamgmesh->NodalElementConnectivity));
3995+ PyDict_SetItemString(dict,"CrackedVertices",PyArrayFromCopiedData(bamgmesh->CrackedVerticesSize,bamgmesh->CrackedVertices));
3996+ PyDict_SetItemString(dict,"CrackedEdges",PyArrayFromCopiedData(bamgmesh->CrackedEdgesSize,bamgmesh->CrackedEdges));
3997+
3998+ PyTuple_SetItem(py_tuple, index, dict);
3999+}
4000+/*}}}*/
4001+/*FUNCTION WriteData(PyObject* py_tuple,int index,SeqMat<double>* matrix){{{*/
4002+void WriteData(PyObject* py_tuple,int index,SeqMat<double>* matrix){
4003+
4004+ int M,N;
4005+ double* buffer=NULL;
4006+ npy_intp dims[2]={0,0};
4007+ PyObject* array=NULL;
4008+
4009+ buffer=matrix->ToSerial();
4010+ matrix->GetSize(&M,&N);
4011+ dims[0]=(npy_intp)M;
4012+ dims[1]=(npy_intp)N;
4013+ array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,buffer);
4014+
4015+ PyTuple_SetItem(py_tuple, index, array);
4016+
4017+}/*}}}*/
4018+/*FUNCTION WriteData(PyObject* py_tuple,int index,SeqVec<double>* vector){{{*/
4019+void WriteData(PyObject* py_tuple,int index,SeqVec<double>* vector){
4020+
4021+ int M;
4022+ double* buffer=NULL;
4023+ npy_intp dim=10;
4024+ PyObject* array=NULL;
4025+
4026+ buffer=vector->ToMPISerial();
4027+ vector->GetSize(&M);
4028+ dim=(npy_intp)M;
4029+ array=PyArray_SimpleNewFromData(1,&dim,NPY_DOUBLE,buffer);
4030+
4031+ PyTuple_SetItem(py_tuple, index, array);
4032+}
4033+/*}}}*/
4034+/*FUNCTION WriteData(PyObject* py_tuple,int index,RiftStruct* riftstruct){{{*/
4035+void WriteData(PyObject* py_tuple,int index,RiftStruct* riftstruct){
4036+
4037+ int i;
4038+ PyObject* list=NULL;
4039+ PyObject* dict=NULL;
4040+
4041+ list=PyList_New((Py_ssize_t)0);
4042+
4043+ for (i=0; i<riftstruct->numrifts; i++) {
4044+ dict=PyDict_New();
4045+
4046+ PyDict_SetItemString(dict,"numsegs" ,PyInt_FromSsize_t((Py_ssize_t)riftstruct->riftsnumsegments[i]));
4047+ PyDict_SetItemString(dict,"segments" ,PyArrayFromCopiedData(riftstruct->riftsnumsegments[i] ,3,riftstruct->riftssegments[i]));
4048+ PyDict_SetItemString(dict,"pairs" ,PyArrayFromCopiedData(riftstruct->riftsnumpairs[i] ,2,riftstruct->riftspairs[i]));
4049+ PyDict_SetItemString(dict,"tips" ,PyArrayFromCopiedData(1 ,2,&riftstruct->riftstips[2*i]));
4050+ PyDict_SetItemString(dict,"penaltypairs" ,PyArrayFromCopiedData(riftstruct->riftsnumpenaltypairs[i],7,riftstruct->riftspenaltypairs[i]));
4051+ PyDict_SetItemString(dict,"fill" ,PyInt_FromSsize_t((Py_ssize_t)IceEnum));
4052+ PyDict_SetItemString(dict,"friction" ,PyInt_FromSsize_t((Py_ssize_t)0));
4053+ PyDict_SetItemString(dict,"fraction" ,PyFloat_FromDouble(0.));
4054+ PyDict_SetItemString(dict,"fractionincrement",PyFloat_FromDouble(0.1));
4055+ PyDict_SetItemString(dict,"state" ,PyArrayFromCopiedData(riftstruct->riftsnumpenaltypairs[i],1,riftstruct->state[i]));
4056+
4057+ PyList_Append(list, dict);
4058+ }
4059+
4060+ PyTuple_SetItem(py_tuple, index, list);
4061+}
4062+/*}}}*/
4063+
4064+/*Utils*/
4065+/*FUNCTION PyArrayFromCopiedData(int dims[2],double* data){{{*/
4066+PyObject* PyArrayFromCopiedData(int dims[2],double* data){
4067+
4068+ double* pydata;
4069+ npy_intp pydims[2]={0,0};
4070+
4071+ /* note that PyArray_SimpleNewFromData does not copy the data, so that when the original
4072+ object (e.g. bamggeom,bamgmesh) is deleted, the data is gone. */
4073+
4074+ pydims[0]=(npy_intp)dims[0];
4075+ pydims[1]=(npy_intp)dims[1];
4076+ pydata=xNew<IssmDouble>(dims[0]*dims[1]);
4077+ memcpy(pydata,data,dims[0]*dims[1]*sizeof(double));
4078+ return PyArray_SimpleNewFromData(2,pydims,NPY_DOUBLE,pydata);
4079+}
4080+/*}}}*/
4081+/*FUNCTION PyArrayFromCopiedData(int dimi,int dimj,double* data){{{*/
4082+PyObject* PyArrayFromCopiedData(int dimi,int dimj,double* data){
4083+
4084+ double* pydata;
4085+ npy_intp pydims[2]={0,0};
4086+
4087+ /* note that PyArray_SimpleNewFromData does not copy the data, so that when the original
4088+ object (e.g. bamggeom,bamgmesh) is deleted, the data is gone. */
4089+
4090+ pydims[0]=(npy_intp)dimi;
4091+ pydims[1]=(npy_intp)dimj;
4092+ pydata=xNew<IssmDouble>(dimi*dimj);
4093+ memcpy(pydata,data,dimi*dimj*sizeof(double));
4094+ return PyArray_SimpleNewFromData(2,pydims,NPY_DOUBLE,pydata);
4095+}
4096+/*}}}*/
4097Index: ../trunk-jpl/src/wrappers/python/Makefile.am
4098===================================================================
4099--- ../trunk-jpl/src/wrappers/python/Makefile.am (revision 13748)
4100+++ ../trunk-jpl/src/wrappers/python/Makefile.am (revision 13749)
4101@@ -1,7 +1,28 @@
4102-AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@
4103+AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@
4104
4105 EXEEXT=$(PYTHONWRAPPEREXT)
4106
4107+#python io{{{
4108+lib_LIBRARIES = libISSMPython.a
4109+if SHAREDLIBS
4110+lib_LTLIBRARIES = libISSMPython.la
4111+else
4112+ lib_LTLIBRARIES =
4113+endif
4114+
4115+io_sources= ./include/pythonincludes.h\
4116+ ./io/pythonio.h\
4117+ ./io/WritePythonData.cpp\
4118+ ./io/CheckNumPythonArguments.cpp\
4119+ ./io/FetchPythonData.cpp
4120+
4121+ALLCXXFLAGS= -fPIC -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS)
4122+libISSMPython_a_SOURCES = $(io_sources)
4123+libISSMPython_a_CXXFLAGS= $(ALLCXXFLAGS)
4124+if SHAREDLIBS
4125+libISSMPython_la_SOURCES = $(io_sources)
4126+endif
4127+#}}}
4128 #Wrappers {{{
4129 if WRAPPERS
4130 lib_LTLIBRARIES = BamgConvertMesh.la\
4131@@ -37,9 +58,9 @@
4132 AM_LDFLAGS += -avoid-version
4133 endif
4134 if SHAREDLIBS
4135-deps += ../../c/libISSMPython.la
4136+deps += ./libISSMPython.la
4137 else
4138-deps += ../../c/libISSMPython.a
4139+deps += ./libISSMPython.a
4140 AM_LDFLAGS += --no-warnings
4141 endif
4142
4143Index: ../trunk-jpl/src/wrappers/Scotch/Scotch.h
4144===================================================================
4145--- ../trunk-jpl/src/wrappers/Scotch/Scotch.h (revision 13748)
4146+++ ../trunk-jpl/src/wrappers/Scotch/Scotch.h (revision 13749)
4147@@ -12,7 +12,7 @@
4148 #include "../../c/modules/modules.h"
4149 #include "../../c/Container/Container.h"
4150 #include "../../c/shared/shared.h"
4151-#include "../../c/issm-binding.h"
4152+#include "../bindings.h"
4153
4154 #undef __FUNCT__
4155 #define __FUNCT__ "Scotch"
4156Index: ../trunk-jpl/src/wrappers/NodeConnectivity/NodeConnectivity.h
4157===================================================================
4158--- ../trunk-jpl/src/wrappers/NodeConnectivity/NodeConnectivity.h (revision 13748)
4159+++ ../trunk-jpl/src/wrappers/NodeConnectivity/NodeConnectivity.h (revision 13749)
4160@@ -26,7 +26,7 @@
4161 #include "../../c/modules/modules.h"
4162 #include "../../c/Container/Container.h"
4163 #include "../../c/shared/shared.h"
4164-#include "../../c/issm-binding.h"
4165+#include "../bindings.h"
4166 #include "../../c/io/io.h"
4167 #include "../../c/EnumDefinitions/EnumDefinitions.h"
4168
4169Index: ../trunk-jpl/src/wrappers/BamgConvertMesh/BamgConvertMesh.h
4170===================================================================
4171--- ../trunk-jpl/src/wrappers/BamgConvertMesh/BamgConvertMesh.h (revision 13748)
4172+++ ../trunk-jpl/src/wrappers/BamgConvertMesh/BamgConvertMesh.h (revision 13749)
4173@@ -20,7 +20,7 @@
4174 #include "../../c/modules/modules.h"
4175 #include "../../c/Container/Container.h"
4176 #include "../../c/shared/shared.h"
4177-#include "../../c/issm-binding.h"
4178+#include "../bindings.h"
4179 #include "../../c/io/io.h"
4180
4181 #undef __FUNCT__
4182Index: ../trunk-jpl/src/wrappers/KMLOverlay/KMLOverlay.h
4183===================================================================
4184--- ../trunk-jpl/src/wrappers/KMLOverlay/KMLOverlay.h (revision 13748)
4185+++ ../trunk-jpl/src/wrappers/KMLOverlay/KMLOverlay.h (revision 13749)
4186@@ -20,7 +20,7 @@
4187 #include "../../c/modules/modules.h"
4188 #include "../../c/Container/Container.h"
4189 #include "../../c/shared/shared.h"
4190-#include "../../c/issm-binding.h"
4191+#include "../bindings.h"
4192
4193 #undef __FUNCT__
4194 #define __FUNCT__ "KMLOverlay"
4195Index: ../trunk-jpl/src/wrappers/ContourToNodes/ContourToNodes.h
4196===================================================================
4197--- ../trunk-jpl/src/wrappers/ContourToNodes/ContourToNodes.h (revision 13748)
4198+++ ../trunk-jpl/src/wrappers/ContourToNodes/ContourToNodes.h (revision 13749)
4199@@ -20,7 +20,7 @@
4200 #include "../../c/modules/modules.h"
4201 #include "../../c/Container/Container.h"
4202 #include "../../c/shared/shared.h"
4203-#include "../../c/issm-binding.h"
4204+#include "../bindings.h"
4205
4206 #undef __FUNCT__
4207 #define __FUNCT__ "ContourToNodes"
4208Index: ../trunk-jpl/src/wrappers/HoleFiller/HoleFiller.h
4209===================================================================
4210--- ../trunk-jpl/src/wrappers/HoleFiller/HoleFiller.h (revision 13748)
4211+++ ../trunk-jpl/src/wrappers/HoleFiller/HoleFiller.h (revision 13749)
4212@@ -20,7 +20,7 @@
4213 #include "../../c/modules/modules.h"
4214 #include "../../c/Container/Container.h"
4215 #include "../../c/shared/shared.h"
4216-#include "../../c/issm-binding.h"
4217+#include "../bindings.h"
4218
4219 #undef __FUNCT__
4220 #define __FUNCT__ "HoleFiller"
4221Index: ../trunk-jpl/src/wrappers/MeshProfileIntersection/MeshProfileIntersection.h
4222===================================================================
4223--- ../trunk-jpl/src/wrappers/MeshProfileIntersection/MeshProfileIntersection.h (revision 13748)
4224+++ ../trunk-jpl/src/wrappers/MeshProfileIntersection/MeshProfileIntersection.h (revision 13749)
4225@@ -20,7 +20,7 @@
4226 #include "../../c/modules/modules.h"
4227 #include "../../c/Container/Container.h"
4228 #include "../../c/shared/shared.h"
4229-#include "../../c/issm-binding.h"
4230+#include "../bindings.h"
4231
4232 #undef __FUNCT__
4233 #define __FUNCT__ "MeshProfileIntersection"
4234Index: ../trunk-jpl/src/wrappers/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h
4235===================================================================
4236--- ../trunk-jpl/src/wrappers/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h (revision 13748)
4237+++ ../trunk-jpl/src/wrappers/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h (revision 13749)
4238@@ -20,7 +20,7 @@
4239 #include "../../c/modules/modules.h"
4240 #include "../../c/Container/Container.h"
4241 #include "../../c/shared/shared.h"
4242-#include "../../c/issm-binding.h"
4243+#include "../bindings.h"
4244
4245 #undef __FUNCT__
4246 #define __FUNCT__ "InterpFromMeshToMesh3d"
4247Index: ../trunk-jpl/src/wrappers/Ll2xy/Ll2xy.h
4248===================================================================
4249--- ../trunk-jpl/src/wrappers/Ll2xy/Ll2xy.h (revision 13748)
4250+++ ../trunk-jpl/src/wrappers/Ll2xy/Ll2xy.h (revision 13749)
4251@@ -20,7 +20,7 @@
4252 #include "../../c/modules/modules.h"
4253 #include "../../c/Container/Container.h"
4254 #include "../../c/shared/shared.h"
4255-#include "../../c/issm-binding.h"
4256+#include "../bindings.h"
4257
4258 #undef __FUNCT__
4259 #define __FUNCT__ "Ll2xy"
4260Index: ../trunk-jpl/src/wrappers/BamgMesher/BamgMesher.h
4261===================================================================
4262--- ../trunk-jpl/src/wrappers/BamgMesher/BamgMesher.h (revision 13748)
4263+++ ../trunk-jpl/src/wrappers/BamgMesher/BamgMesher.h (revision 13749)
4264@@ -20,7 +20,7 @@
4265 #include "../../c/modules/modules.h"
4266 #include "../../c/Container/Container.h"
4267 #include "../../c/shared/shared.h"
4268-#include "../../c/issm-binding.h"
4269+#include "../bindings.h"
4270
4271 #undef __FUNCT__
4272 #define __FUNCT__ "BamgMesher"
4273Index: ../trunk-jpl/src/wrappers/InterpFromGridToMesh/InterpFromGridToMesh.h
4274===================================================================
4275--- ../trunk-jpl/src/wrappers/InterpFromGridToMesh/InterpFromGridToMesh.h (revision 13748)
4276+++ ../trunk-jpl/src/wrappers/InterpFromGridToMesh/InterpFromGridToMesh.h (revision 13749)
4277@@ -20,7 +20,7 @@
4278 #include "../../c/modules/modules.h"
4279 #include "../../c/Container/Container.h"
4280 #include "../../c/shared/shared.h"
4281-#include "../../c/issm-binding.h"
4282+#include "../bindings.h"
4283
4284 #undef __FUNCT__
4285 #define __FUNCT__ "InterpFromGridToMesh"
4286Index: ../trunk-jpl/src/wrappers/InterpFromMeshToGrid/InterpFromMeshToGrid.h
4287===================================================================
4288--- ../trunk-jpl/src/wrappers/InterpFromMeshToGrid/InterpFromMeshToGrid.h (revision 13748)
4289+++ ../trunk-jpl/src/wrappers/InterpFromMeshToGrid/InterpFromMeshToGrid.h (revision 13749)
4290@@ -20,7 +20,7 @@
4291 #include "../../c/modules/modules.h"
4292 #include "../../c/Container/Container.h"
4293 #include "../../c/shared/shared.h"
4294-#include "../../c/issm-binding.h"
4295+#include "../bindings.h"
4296
4297 #undef __FUNCT__
4298 #define __FUNCT__ "InterpFromMeshToGrid"
4299Index: ../trunk-jpl/src/wrappers/KMLFileRead/KMLFileRead.h
4300===================================================================
4301--- ../trunk-jpl/src/wrappers/KMLFileRead/KMLFileRead.h (revision 13748)
4302+++ ../trunk-jpl/src/wrappers/KMLFileRead/KMLFileRead.h (revision 13749)
4303@@ -20,7 +20,7 @@
4304 #include "../../c/modules/modules.h"
4305 #include "../../c/Container/Container.h"
4306 #include "../../c/shared/shared.h"
4307-#include "../../c/issm-binding.h"
4308+#include "../bindings.h"
4309
4310 #undef __FUNCT__
4311 #define __FUNCT__ "KMLFileRead"
4312Index: ../trunk-jpl/src/wrappers/Shp2Kml/Shp2Kml.h
4313===================================================================
4314--- ../trunk-jpl/src/wrappers/Shp2Kml/Shp2Kml.h (revision 13748)
4315+++ ../trunk-jpl/src/wrappers/Shp2Kml/Shp2Kml.h (revision 13749)
4316@@ -20,7 +20,7 @@
4317 #include "../../c/modules/modules.h"
4318 #include "../../c/Container/Container.h"
4319 #include "../../c/shared/shared.h"
4320-#include "../../c/issm-binding.h"
4321+#include "../bindings.h"
4322
4323 #undef __FUNCT__
4324 #define __FUNCT__ "Shp2Kml"
4325Index: ../trunk-jpl/src/wrappers/AverageFilter/AverageFilter.h
4326===================================================================
4327--- ../trunk-jpl/src/wrappers/AverageFilter/AverageFilter.h (revision 13748)
4328+++ ../trunk-jpl/src/wrappers/AverageFilter/AverageFilter.h (revision 13749)
4329@@ -20,7 +20,7 @@
4330 #include "../../c/modules/modules.h"
4331 #include "../../c/Container/Container.h"
4332 #include "../../c/shared/shared.h"
4333-#include "../../c/issm-binding.h"
4334+#include "../bindings.h"
4335
4336 #undef __FUNCT__
4337 #define __FUNCT__ "AverageFilter"
4338Index: ../trunk-jpl/src/wrappers/TriMeshProcessRifts/TriMeshProcessRifts.h
4339===================================================================
4340--- ../trunk-jpl/src/wrappers/TriMeshProcessRifts/TriMeshProcessRifts.h (revision 13748)
4341+++ ../trunk-jpl/src/wrappers/TriMeshProcessRifts/TriMeshProcessRifts.h (revision 13749)
4342@@ -20,7 +20,7 @@
4343 #include "../../c/modules/modules.h"
4344 #include "../../c/Container/Container.h"
4345 #include "../../c/shared/shared.h"
4346-#include "../../c/issm-binding.h"
4347+#include "../bindings.h"
4348
4349 #undef __FUNCT__
4350 #define __FUNCT__ "TriMeshProcessRifts"
4351Index: ../trunk-jpl/src/wrappers/Exp2Kml/Exp2Kml.h
4352===================================================================
4353--- ../trunk-jpl/src/wrappers/Exp2Kml/Exp2Kml.h (revision 13748)
4354+++ ../trunk-jpl/src/wrappers/Exp2Kml/Exp2Kml.h (revision 13749)
4355@@ -20,7 +20,7 @@
4356 #include "../../c/modules/modules.h"
4357 #include "../../c/Container/Container.h"
4358 #include "../../c/shared/shared.h"
4359-#include "../../c/issm-binding.h"
4360+#include "../bindings.h"
4361
4362 #undef __FUNCT__
4363 #define __FUNCT__ "Exp2Kml"
4364Index: ../trunk-jpl/src/wrappers/Kml2Exp/Kml2Exp.h
4365===================================================================
4366--- ../trunk-jpl/src/wrappers/Kml2Exp/Kml2Exp.h (revision 13748)
4367+++ ../trunk-jpl/src/wrappers/Kml2Exp/Kml2Exp.h (revision 13749)
4368@@ -20,7 +20,7 @@
4369 #include "../../c/modules/modules.h"
4370 #include "../../c/Container/Container.h"
4371 #include "../../c/shared/shared.h"
4372-#include "../../c/issm-binding.h"
4373+#include "../bindings.h"
4374
4375 #undef __FUNCT__
4376 #define __FUNCT__ "Kml2Exp"
4377Index: ../trunk-jpl/src/wrappers/PointCloudFindNeighbors/PointCloudFindNeighbors.h
4378===================================================================
4379--- ../trunk-jpl/src/wrappers/PointCloudFindNeighbors/PointCloudFindNeighbors.h (revision 13748)
4380+++ ../trunk-jpl/src/wrappers/PointCloudFindNeighbors/PointCloudFindNeighbors.h (revision 13749)
4381@@ -20,7 +20,7 @@
4382 #include "../../c/modules/modules.h"
4383 #include "../../c/Container/Container.h"
4384 #include "../../c/shared/shared.h"
4385-#include "../../c/issm-binding.h"
4386+#include "../bindings.h"
4387
4388 #undef __FUNCT__
4389 #define __FUNCT__ "PointCloudFindNeighbors"
4390Index: ../trunk-jpl/src/wrappers/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h
4391===================================================================
4392--- ../trunk-jpl/src/wrappers/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h (revision 13748)
4393+++ ../trunk-jpl/src/wrappers/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h (revision 13749)
4394@@ -20,7 +20,7 @@
4395 #include "../../c/modules/modules.h"
4396 #include "../../c/Container/Container.h"
4397 #include "../../c/shared/shared.h"
4398-#include "../../c/issm-binding.h"
4399+#include "../bindings.h"
4400
4401 #undef __FUNCT__
4402 #define __FUNCT__ "PropagateFlagsFromConnectivity"
4403Index: ../trunk-jpl/src/wrappers/include/issm-binding.h
4404===================================================================
4405--- ../trunk-jpl/src/wrappers/include/issm-binding.h (revision 0)
4406+++ ../trunk-jpl/src/wrappers/include/issm-binding.h (revision 13749)
4407@@ -0,0 +1,18 @@
4408+#ifndef _ISSM_BINDING_H_
4409+#define _ISSM_BINDING_H_
4410+
4411+#ifdef HAVE_CONFIG_H
4412+ #include <config.h>
4413+#else
4414+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
4415+#endif
4416+
4417+#ifdef _HAVE_MATLAB_MODULES_
4418+#include "../matlab/include/matlab-macros.h"
4419+#endif
4420+
4421+#ifdef _HAVE_PYTHON_MODULES_
4422+#include "../python/include/python-macros.h"
4423+#endif
4424+
4425+#endif
4426Index: ../trunk-jpl/src/wrappers/bindings.h
4427===================================================================
4428--- ../trunk-jpl/src/wrappers/bindings.h (revision 0)
4429+++ ../trunk-jpl/src/wrappers/bindings.h (revision 13749)
4430@@ -0,0 +1,22 @@
4431+#ifndef _BINDINGS_H_
4432+#define _BINDINGS_H_
4433+
4434+#ifdef HAVE_CONFIG_H
4435+ #include <config.h>
4436+#else
4437+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
4438+#endif
4439+
4440+#ifdef _HAVE_MATLAB_MODULES_
4441+#include "./matlab/include/matlabincludes.h"
4442+#include "./matlab/include/wrapper_macros.h"
4443+#include "./matlab/io/matlabio.h"
4444+#endif
4445+
4446+#ifdef _HAVE_PYTHON_MODULES_
4447+#include "./python/include/pythonincludes.h"
4448+#include "./python/include/wrapper_macros.h"
4449+#include "./python/io/pythonio.h"
4450+#endif
4451+
4452+#endif
4453Index: ../trunk-jpl/src/wrappers/TriaSearch/TriaSearch.h
4454===================================================================
4455--- ../trunk-jpl/src/wrappers/TriaSearch/TriaSearch.h (revision 13748)
4456+++ ../trunk-jpl/src/wrappers/TriaSearch/TriaSearch.h (revision 13749)
4457@@ -19,7 +19,7 @@
4458 #include "../../c/modules/modules.h"
4459 #include "../../c/Container/Container.h"
4460 #include "../../c/shared/shared.h"
4461-#include "../../c/issm-binding.h"
4462+#include "../bindings.h"
4463
4464 #undef __FUNCT__
4465 #define __FUNCT__ "TriaSearch"
4466Index: ../trunk-jpl/src/wrappers/InternalFront/InternalFront.h
4467===================================================================
4468--- ../trunk-jpl/src/wrappers/InternalFront/InternalFront.h (revision 13748)
4469+++ ../trunk-jpl/src/wrappers/InternalFront/InternalFront.h (revision 13749)
4470@@ -18,7 +18,7 @@
4471
4472 #include "../../c/include/globals.h"
4473 #include "../../c/shared/shared.h"
4474-#include "../../c/issm-binding.h"
4475+#include "../bindings.h"
4476 #include "../../c/io/io.h"
4477
4478 #undef __FUNCT__
4479Index: ../trunk-jpl/src/wrappers/MeshPartition/MeshPartition.h
4480===================================================================
4481--- ../trunk-jpl/src/wrappers/MeshPartition/MeshPartition.h (revision 13748)
4482+++ ../trunk-jpl/src/wrappers/MeshPartition/MeshPartition.h (revision 13749)
4483@@ -20,7 +20,7 @@
4484 #include "../../c/modules/modules.h"
4485 #include "../../c/Container/Container.h"
4486 #include "../../c/shared/shared.h"
4487-#include "../../c/issm-binding.h"
4488+#include "../bindings.h"
4489
4490 #undef __FUNCT__
4491 #define __FUNCT__ "MeshPartition"
4492Index: ../trunk-jpl/src/wrappers/InterpFromMesh2d/InterpFromMesh2d.h
4493===================================================================
4494--- ../trunk-jpl/src/wrappers/InterpFromMesh2d/InterpFromMesh2d.h (revision 13748)
4495+++ ../trunk-jpl/src/wrappers/InterpFromMesh2d/InterpFromMesh2d.h (revision 13749)
4496@@ -20,7 +20,7 @@
4497 #include "../../c/modules/modules.h"
4498 #include "../../c/Container/Container.h"
4499 #include "../../c/shared/shared.h"
4500-#include "../../c/issm-binding.h"
4501+#include "../bindings.h"
4502
4503 #undef __FUNCT__
4504 #define __FUNCT__ "InterpFromMesh2d"
4505Index: ../trunk-jpl/src/wrappers/ElementConnectivity/ElementConnectivity.h
4506===================================================================
4507--- ../trunk-jpl/src/wrappers/ElementConnectivity/ElementConnectivity.h (revision 13748)
4508+++ ../trunk-jpl/src/wrappers/ElementConnectivity/ElementConnectivity.h (revision 13749)
4509@@ -23,7 +23,7 @@
4510 #include "../../c/modules/modules.h"
4511 #include "../../c/Container/Container.h"
4512 #include "../../c/shared/shared.h"
4513-#include "../../c/issm-binding.h"
4514+#include "../bindings.h"
4515 #include "../../c/io/io.h"
4516 #include "../../c/EnumDefinitions/EnumDefinitions.h"
4517
4518Index: ../trunk-jpl/src/wrappers/Kriging/Kriging.h
4519===================================================================
4520--- ../trunk-jpl/src/wrappers/Kriging/Kriging.h (revision 13748)
4521+++ ../trunk-jpl/src/wrappers/Kriging/Kriging.h (revision 13749)
4522@@ -19,7 +19,7 @@
4523 #include "../../c/include/globals.h"
4524 #include "../../c/modules/modules.h"
4525 #include "../../c/shared/shared.h"
4526-#include "../../c/issm-binding.h"
4527+#include "../bindings.h"
4528
4529 #undef __FUNCT__
4530 #define __FUNCT__ "Kriging"
4531Index: ../trunk-jpl/src/wrappers/EnumToString/EnumToString.h
4532===================================================================
4533--- ../trunk-jpl/src/wrappers/EnumToString/EnumToString.h (revision 13748)
4534+++ ../trunk-jpl/src/wrappers/EnumToString/EnumToString.h (revision 13749)
4535@@ -21,7 +21,7 @@
4536 #include "../../c/modules/modules.h"
4537 #include "../../c/Container/Container.h"
4538 #include "../../c/shared/shared.h"
4539-#include "../../c/issm-binding.h"
4540+#include "../bindings.h"
4541
4542 #undef __FUNCT__
4543 #define __FUNCT__ "EnumToString"
4544Index: ../trunk-jpl/src/wrappers/StringToEnum/StringToEnum.h
4545===================================================================
4546--- ../trunk-jpl/src/wrappers/StringToEnum/StringToEnum.h (revision 13748)
4547+++ ../trunk-jpl/src/wrappers/StringToEnum/StringToEnum.h (revision 13749)
4548@@ -21,7 +21,7 @@
4549 #include "../../c/modules/modules.h"
4550 #include "../../c/Container/Container.h"
4551 #include "../../c/shared/shared.h"
4552-#include "../../c/issm-binding.h"
4553+#include "../bindings.h"
4554
4555 #undef __FUNCT__
4556 #define __FUNCT__ "StringToEnum"
4557Index: ../trunk-jpl/src/wrappers/matlab/include/wrapper_macros.h
4558===================================================================
4559--- ../trunk-jpl/src/wrappers/matlab/include/wrapper_macros.h (revision 0)
4560+++ ../trunk-jpl/src/wrappers/matlab/include/wrapper_macros.h (revision 13749)
4561@@ -0,0 +1,42 @@
4562+/* \file matlab macros.h
4563+ * \brief: macros used for the matlab bindings
4564+ */
4565+
4566+#ifndef _MATLAB_MACROS_H_
4567+#define _MATLAB_MACROS_H_
4568+
4569+#ifdef HAVE_CONFIG_H
4570+ #include <config.h>
4571+#else
4572+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
4573+#endif
4574+
4575+#ifdef _HAVE_MATLAB_
4576+/* MODULEBOOT/MODULEEND {{{*/
4577+
4578+/*The following macros hide the error exception handling in a matlab module. Just put
4579+ * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions
4580+ * will be trapped*/
4581+#define MODULEBOOT(); try{ \
4582+ IssmComm::SetComm(-1);
4583+
4584+#define MODULEEND(); }\
4585+ catch(ErrorException &exception){\
4586+ mexErrMsgTxt(exception.MatlabReport()); \
4587+ }\
4588+ catch (exception &e){\
4589+ mexErrMsgTxt(exprintf("Standard exception: %s\n",e.what()));\
4590+ }\
4591+ catch(...){\
4592+ mexErrMsgTxt("An unexpected error occurred");\
4593+ }
4594+/*}}}*/
4595+/* WRAPPER {{{*/
4596+#define WRAPPER(modulename,...) void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
4597+/*}}}*/
4598+/* CHECKARGUMENTS {{{*/
4599+#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,functionpointer)
4600+/*}}}*/
4601+#endif
4602+
4603+#endif
4604Index: ../trunk-jpl/src/wrappers/matlab/io/MatlabMatrixToSeqMat.cpp
4605===================================================================
4606--- ../trunk-jpl/src/wrappers/matlab/io/MatlabMatrixToSeqMat.cpp (revision 0)
4607+++ ../trunk-jpl/src/wrappers/matlab/io/MatlabMatrixToSeqMat.cpp (revision 13749)
4608@@ -0,0 +1,25 @@
4609+/*!\file MatlabMatrixToSeqMat.cpp
4610+ */
4611+
4612+/*Headers:*/
4613+#ifdef HAVE_CONFIG_H
4614+ #include <config.h>
4615+#else
4616+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
4617+#endif
4618+
4619+#include <stdio.h>
4620+#include <string.h>
4621+#include "./matlabio.h"
4622+#include "../../c/toolkits/toolkits.h"
4623+#include "../../c/shared/shared.h"
4624+
4625+SeqMat<double>* MatlabMatrixToSeqMat(const mxArray* dataref){
4626+
4627+ SeqMat<double>* output=NULL;
4628+
4629+ output=new SeqMat<double>();
4630+ MatlabMatrixToDoubleMatrix(&output->matrix,&output->M,&output->N,dataref);
4631+ return output;
4632+
4633+}
4634Index: ../trunk-jpl/src/wrappers/matlab/io/MatlabVectorToPetscVec.cpp
4635===================================================================
4636--- ../trunk-jpl/src/wrappers/matlab/io/MatlabVectorToPetscVec.cpp (revision 0)
4637+++ ../trunk-jpl/src/wrappers/matlab/io/MatlabVectorToPetscVec.cpp (revision 13749)
4638@@ -0,0 +1,106 @@
4639+/* \file MatlabVectorToPetscVector.cpp
4640+ * \brief: convert a sparse or dense matlab vector to a serial Petsc vector:
4641+ */
4642+
4643+#ifdef HAVE_CONFIG_H
4644+ #include <config.h>
4645+#else
4646+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
4647+#endif
4648+
4649+/*Petsc includes: */
4650+#include <petscmat.h>
4651+#include <petscvec.h>
4652+#include <petscksp.h>
4653+
4654+/*Matlab includes: */
4655+#include "./matlabio.h"
4656+#include "../../c/shared/shared.h"
4657+
4658+PetscVec* MatlabVectorToPetscVec(const mxArray* mxvector){
4659+
4660+ int dummy;
4661+ PetscVec* vector=new PetscVec();
4662+
4663+ MatlabVectorToPetscVec(&vector->vector,&dummy, mxvector);
4664+
4665+ return vector;
4666+}
4667+
4668+int MatlabVectorToPetscVec(Vec* pvector,int* pvector_rows,const mxArray* mxvector){
4669+
4670+ int rows, cols;
4671+ double* mxvector_ptr=NULL;
4672+ int ierr;
4673+ int i,j;
4674+
4675+ /*output: */
4676+ Vec vector=NULL;
4677+
4678+ /*matlab indices: */
4679+ mwIndex* ir=NULL;
4680+ mwIndex* jc=NULL;
4681+ double* pr=NULL;
4682+ int count;
4683+ int nnz;
4684+ int nz;
4685+
4686+ /*petsc indices: */
4687+ int* idxm=NULL;
4688+
4689+ /*Ok, first check if we are dealing with a sparse or full vector: */
4690+ if (mxIsSparse(mxvector)){
4691+
4692+ /*Dealing with sparse vector: recover size first: */
4693+ mxvector_ptr=(double*)mxGetPr(mxvector);
4694+ rows=mxGetM(mxvector);
4695+ cols=mxGetN(mxvector);
4696+ nnz=mxGetNzmax(mxvector);
4697+ nz=(int)((double)nnz/(double)rows);
4698+
4699+ ierr=VecCreateSeq(PETSC_COMM_SELF,rows,&vector);CHKERRQ(ierr);
4700+
4701+ /*Now, get ir,jc and pr: */
4702+ pr=mxGetPr(mxvector);
4703+ ir=mxGetIr(mxvector);
4704+ jc=mxGetJc(mxvector);
4705+
4706+ /*Now, start inserting data into sparse vector: */
4707+ count=0;
4708+ for(i=0;i<cols;i++){
4709+ for(j=0;j<(jc[i+1]-jc[i]);j++){
4710+ VecSetValue(vector,ir[count],pr[count],INSERT_VALUES);
4711+ count++;
4712+ }
4713+ }
4714+
4715+ }
4716+ else{
4717+
4718+ /*Dealing with dense vector: recover pointer and size: */
4719+ mxvector_ptr=(double*)mxGetPr(mxvector);
4720+ rows=mxGetM(mxvector);
4721+ cols=mxGetN(mxvector);
4722+
4723+ /*Create serial vector: */
4724+ ierr=VecCreateSeq(PETSC_COMM_SELF,rows,&vector);CHKERRQ(ierr);
4725+
4726+ /*Insert mxvector_ptr values into petsc vector: */
4727+ idxm=xNew<int>(rows);
4728+
4729+ for(i=0;i<rows;i++)idxm[i]=i;
4730+
4731+ ierr=VecSetValues(vector,rows,idxm,mxvector_ptr,INSERT_VALUES);CHKERRQ(ierr);
4732+
4733+ }
4734+
4735+ /*Assemble vector: */
4736+ VecAssemblyBegin(vector);
4737+ VecAssemblyEnd(vector);
4738+
4739+ /*Assign output pointer: */
4740+ *pvector=vector;
4741+ *pvector_rows=rows;
4742+
4743+ return 1;
4744+}
4745Index: ../trunk-jpl/src/wrappers/matlab/io/OptionParse.cpp
4746===================================================================
4747--- ../trunk-jpl/src/wrappers/matlab/io/OptionParse.cpp (revision 0)
4748+++ ../trunk-jpl/src/wrappers/matlab/io/OptionParse.cpp (revision 13749)
4749@@ -0,0 +1,201 @@
4750+/*\file OptionParse.c
4751+ *\brief: functions to parse the mex options.
4752+ */
4753+#ifdef HAVE_CONFIG_H
4754+ #include <config.h>
4755+#else
4756+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
4757+#endif
4758+
4759+#include <cstring>
4760+#include "./matlabio.h"
4761+#include "../../c/shared/shared.h"
4762+#include "../../c/io/io.h"
4763+
4764+GenericOption<double>* OptionDoubleParse( char* name, const mxArray* prhs[]){ /*{{{*/
4765+
4766+ GenericOption<double> *odouble = NULL;
4767+
4768+ /*check and parse the name */
4769+ odouble=new GenericOption<double>();
4770+ odouble->name =xNew<char>(strlen(name)+1);
4771+ memcpy(odouble->name,name,(strlen(name)+1)*sizeof(char));
4772+ FetchData(&odouble->value,prhs[0]);
4773+ odouble->numel=1;
4774+ odouble->ndims=1;
4775+ odouble->size=NULL;
4776+
4777+ return(odouble);
4778+}/*}}}*/
4779+GenericOption<double*>* OptionDoubleArrayParse( char* name, const mxArray* prhs[]){ /*{{{*/
4780+
4781+ GenericOption<double*> *odouble = NULL;
4782+
4783+ /*check and parse the name */
4784+ odouble=new GenericOption<double*>();
4785+ odouble->name =xNew<char>(strlen(name)+1);
4786+ memcpy(odouble->name,name,(strlen(name)+1)*sizeof(char));
4787+
4788+ /*check and parse the value */
4789+ if (!mxIsClass(prhs[0],"double")){
4790+ _error_("Value of option \"" << odouble->name << "\" must be class \"double\", not class \"" << mxGetClassName(prhs[0]) <<"\".");
4791+ }
4792+ FetchData(&odouble->value,&odouble->numel,&odouble->ndims,&odouble->size,prhs[0]);
4793+
4794+ return(odouble);
4795+}/*}}}*/
4796+GenericOption<bool*>* OptionLogicalParse( char* name, const mxArray* prhs[]){ /*{{{*/
4797+
4798+ GenericOption<bool*> *ological = NULL;
4799+
4800+ /*check and parse the name */
4801+ ological=new GenericOption<bool*>();
4802+ ological->name =xNew<char>(strlen(name)+1);
4803+ memcpy(ological->name,name,(strlen(name)+1)*sizeof(char));
4804+
4805+ /*check and parse the value */
4806+ if (!mxIsClass(prhs[0],"logical")){
4807+ _error_("Value of option \"" << ological->name << "\" must be class \"logical\", not class \"" << mxGetClassName(prhs[0]) <<"\".");
4808+ }
4809+ FetchData(&ological->value,&ological->numel,&ological->ndims,&ological->size,prhs[0]);
4810+
4811+ return(ological);
4812+}/*}}}*/
4813+GenericOption<char*>* OptionCharParse( char* name, const mxArray* prhs[]){ /*{{{*/
4814+
4815+ GenericOption<char*> *ochar = NULL;
4816+
4817+ /*check and parse the name */
4818+ ochar=new GenericOption<char*>();
4819+ ochar->name =xNew<char>(strlen(name)+1);
4820+ memcpy(ochar->name,name,(strlen(name)+1)*sizeof(char));
4821+
4822+ /*check and parse the value */
4823+ if (!mxIsClass(prhs[0],"char")){
4824+ _error_("Value of option \"" << ochar->name << "\" must be class \"char\", not class \"" << mxGetClassName(prhs[0]) <<"\".");
4825+ }
4826+ FetchData(&ochar->value,&ochar->numel,&ochar->ndims,&ochar->size,prhs[0]);
4827+
4828+ return(ochar);
4829+}/*}}}*/
4830+GenericOption<Options**>* OptionStructParse( char* name, const mxArray* prhs[]){ /*{{{*/
4831+
4832+ int i;
4833+ char namei[161];
4834+ Option* option = NULL;
4835+ GenericOption<Options**> *ostruct = NULL;
4836+ const mwSize *ipt = NULL;
4837+ const mxArray *structi;
4838+ mwIndex sindex;
4839+
4840+ /*check and parse the name */
4841+ ostruct=new GenericOption<Options**>();
4842+ ostruct->name =xNew<char>(strlen(name)+1);
4843+ memcpy(ostruct->name,name,(strlen(name)+1)*sizeof(char));
4844+
4845+ /*check and parse the value */
4846+ if (!mxIsClass(prhs[0],"struct")){
4847+ _error_("Value of option \"" << ostruct->name << "\" must be class \"struct\", not class \"" << mxGetClassName(prhs[0]) <<"\".");
4848+ }
4849+ ostruct->numel=mxGetNumberOfElements(prhs[0]);
4850+ ostruct->ndims=mxGetNumberOfDimensions(prhs[0]);
4851+ ipt =mxGetDimensions(prhs[0]);
4852+ ostruct->size =xNew<int>(ostruct->ndims);
4853+ for (i=0; i<ostruct->ndims; i++) ostruct->size[i]=(int)ipt[i];
4854+ if (ostruct->numel) ostruct->value=xNew<Options*>(ostruct->numel);
4855+
4856+ /*loop through and process each element of the struct array */
4857+ for (sindex=0; sindex<ostruct->numel; sindex++) {
4858+ ostruct->value[sindex]=new Options;
4859+
4860+ /*loop through and process each field for the element */
4861+ for (i=0; i<mxGetNumberOfFields(prhs[0]); i++) {
4862+ sprintf(namei,"%s.%s",name,mxGetFieldNameByNumber(prhs[0],i));
4863+ structi=mxGetFieldByNumber(prhs[0],sindex,i);
4864+
4865+ option=(Option*)OptionParse(namei,&structi);
4866+ ostruct->value[sindex]->AddObject((Object*)option);
4867+ option=NULL;
4868+ }
4869+ }
4870+
4871+ return(ostruct);
4872+}/*}}}*/
4873+GenericOption<Options*>* OptionCellParse( char* name, const mxArray* prhs[]){ /*{{{*/
4874+
4875+ int i;
4876+ int *dims;
4877+ char namei[161];
4878+ char cstr[81];
4879+ GenericOption<Options*> *ocell = NULL;
4880+ Option *option = NULL;
4881+ const mwSize *ipt = NULL;
4882+ const mxArray *celli;
4883+ mwIndex cindex;
4884+
4885+ /*check and parse the name */
4886+ ocell=new GenericOption<Options*>();
4887+ ocell->name =xNew<char>(strlen(name)+1);
4888+ memcpy(ocell->name,name,(strlen(name)+1)*sizeof(char));
4889+
4890+ /*check and parse the value */
4891+ if (!mxIsClass(prhs[0],"cell")){
4892+ _error_("Value of option \"" << ocell->name << "\" must be class \"cell\", not class \"" << mxGetClassName(prhs[0]) <<"\".");
4893+ }
4894+
4895+ ocell->numel=mxGetNumberOfElements(prhs[0]);
4896+ ocell->ndims=mxGetNumberOfDimensions(prhs[0]);
4897+ ipt =mxGetDimensions(prhs[0]);
4898+ ocell->size =xNew<int>(ocell->ndims);
4899+ for (i=0; i<ocell->ndims; i++) ocell->size[i]=(int)ipt[i];
4900+ ocell->value=new Options;
4901+
4902+ /*loop through and process each element of the cell array */
4903+ dims=xNew<int>(ocell->ndims);
4904+ for (cindex=0; cindex<ocell->numel; cindex++) {
4905+ ColumnWiseDimsFromIndex(dims,(int)cindex,ocell->size,ocell->ndims);
4906+ StringFromDims(cstr,dims,ocell->ndims);
4907+ #ifdef _INTEL_WIN_
4908+ _snprintf(namei,161,"%s%s",name,cstr);
4909+ #else
4910+ snprintf(namei,161,"%s%s",name,cstr);
4911+ #endif
4912+ celli=mxGetCell(prhs[0],cindex);
4913+
4914+ option=(Option*)OptionParse(namei,&celli);
4915+ ocell->value->AddObject((Object*)option);
4916+ option=NULL;
4917+ }
4918+ xDelete<int>(dims);
4919+
4920+ return(ocell);
4921+}/*}}}*/
4922+Option* OptionParse(char* name, const mxArray* prhs[]){ /*{{{*/
4923+
4924+ Option *option = NULL;
4925+ mxArray *lhs[1];
4926+
4927+ /*parse the value according to the matlab data type */
4928+ if (mxIsClass(prhs[0],"double") && (mxGetNumberOfElements(prhs[0])==1))
4929+ option=(Option*)OptionDoubleParse(name,prhs);
4930+ else if(mxIsClass(prhs[0],"double") && (mxGetNumberOfElements(prhs[0])!=1))
4931+ option=(Option*)OptionDoubleArrayParse(name,prhs);
4932+ else if(mxIsClass(prhs[0],"logical"))
4933+ option=(Option*)OptionLogicalParse(name,prhs);
4934+ else if(mxIsClass(prhs[0],"char"))
4935+ option=(Option*)OptionCharParse(name,prhs);
4936+ else if(mxIsClass(prhs[0],"struct"))
4937+ option=(Option*)OptionStructParse(name,prhs);
4938+ else if(mxIsClass(prhs[0],"cell"))
4939+ option=(Option*)OptionCellParse(name,prhs);
4940+ else {
4941+ _pprintLine_(" Converting value of option \"" << name << "\" from unrecognized class \"" << mxGetClassName(prhs[0]) << "\" to class \"" << "struct" << "\".");
4942+ if (!mexCallMATLAB(1,lhs,1,(mxArray**)prhs,"struct")) {
4943+ option=(Option*)OptionStructParse(name,(const mxArray**)lhs);
4944+ mxDestroyArray(lhs[0]);
4945+ }
4946+ else _error_("Second argument value of option \""<< name <<"\" is of unrecognized class \""<< mxGetClassName(prhs[0]) <<"\".");
4947+ }
4948+
4949+ return(option);
4950+}/*}}}*/
4951Index: ../trunk-jpl/src/wrappers/matlab/io/CheckNumMatlabArguments.cpp
4952===================================================================
4953--- ../trunk-jpl/src/wrappers/matlab/io/CheckNumMatlabArguments.cpp (revision 0)
4954+++ ../trunk-jpl/src/wrappers/matlab/io/CheckNumMatlabArguments.cpp (revision 13749)
4955@@ -0,0 +1,23 @@
4956+/*!\file CheckNumMatlabArguments.cpp:
4957+ * \brief: check number of arguments and report an usage error message.
4958+ */
4959+
4960+#include "./matlabio.h"
4961+#include "../../c/shared/Exceptions/exceptions.h"
4962+
4963+int CheckNumMatlabArguments(int nlhs,int NLHS, int nrhs,int NRHS, const char* THISFUNCTION, void (*function)( void )){
4964+
4965+ /*checks on arguments on the matlab side: */
4966+ if (nrhs==0 && nlhs==0) {
4967+ /*unless NLHS=0 and NRHS=0, we are just asking for documentation: */
4968+ if (NRHS==0 && NLHS==0)return 1;
4969+ /* special case: */
4970+ function();
4971+ _error_("usage: see above");
4972+ }
4973+ else if (nlhs!=NLHS || nrhs!=NRHS ) {
4974+ function();
4975+ _error_("usage error.");
4976+ }
4977+ return 1;
4978+}
4979Index: ../trunk-jpl/src/wrappers/matlab/io/FetchMatlabData.cpp
4980===================================================================
4981--- ../trunk-jpl/src/wrappers/matlab/io/FetchMatlabData.cpp (revision 0)
4982+++ ../trunk-jpl/src/wrappers/matlab/io/FetchMatlabData.cpp (revision 13749)
4983@@ -0,0 +1,691 @@
4984+/*\file FetchData.cpp:
4985+ * \brief: general I/O interface to fetch data in matlab
4986+ */
4987+
4988+#ifdef HAVE_CONFIG_H
4989+ #include <config.h>
4990+#else
4991+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
4992+#endif
4993+
4994+#include "./matlabio.h"
4995+#include "../../c/shared/shared.h"
4996+
4997+/*Primitive data types*/
4998+/*FUNCTION FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){{{*/
4999+void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){
5000+
5001+ double* outmatrix=NULL;
5002+ int outmatrix_rows,outmatrix_cols;
5003+
5004+ if(mxIsEmpty(dataref) ){
5005+ /*Nothing to pick up. Just initialize matrix pointer to NULL: */
5006+ outmatrix_rows=0;
5007+ outmatrix_cols=0;
5008+ outmatrix=NULL;
5009+ }
5010+ else if( mxIsClass(dataref,"double") ||
5011+ mxIsClass(dataref,"single") ||
5012+ mxIsClass(dataref,"int16") ||
5013+ mxIsClass(dataref,"int8") ||
5014+ mxIsClass(dataref,"uint8")){
5015+ /*Check dataref is not pointing to NaN: */
5016+ if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){
5017+ outmatrix_rows=0;
5018+ outmatrix_cols=0;
5019+ outmatrix=NULL;
5020+ }
5021+ else{
5022+ if(!mxIsClass(dataref,"double") && !mxIsClass(dataref,"single")){
5023+ _printLine_("Warning: converting matlab data from '" << mxGetClassName(dataref) << "' to 'double'");
5024+ }
5025+ /*Convert matlab matrix to double* matrix: */
5026+ MatlabMatrixToDoubleMatrix(&outmatrix,&outmatrix_rows,&outmatrix_cols,dataref);
5027+ }
5028+ }
5029+ else{
5030+ /*This is an error: we don't have the correct input!: */
5031+ _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
5032+ }
5033+
5034+ /*Assign output pointers:*/
5035+ *pmatrix=outmatrix;
5036+ if (pM)*pM=outmatrix_rows;
5037+ if (pN)*pN=outmatrix_cols;
5038+
5039+}
5040+/*}}}*/
5041+/*FUNCTION FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){{{*/
5042+void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){
5043+
5044+ int outmatrix_numel,outmatrix_ndims;
5045+ double *outmatrix = NULL;
5046+ int *outmatrix_size = NULL;
5047+
5048+ if(mxIsEmpty(dataref) ){
5049+ /*Nothing to pick up. Just initialize matrix pointer to NULL: */
5050+ outmatrix_numel = 0;
5051+ outmatrix_ndims = 0;
5052+ outmatrix_size = NULL;
5053+ outmatrix = NULL;
5054+ }
5055+ else if( mxIsClass(dataref,"double") ||
5056+ mxIsClass(dataref,"single") ||
5057+ mxIsClass(dataref,"int16") ||
5058+ mxIsClass(dataref,"int8") ||
5059+ mxIsClass(dataref,"uint8")){
5060+
5061+ /*Check dataref is not pointing to NaN: */
5062+ if (mxIsNaN(*(mxGetPr(dataref))) && (mxGetNumberOfElements(dataref)==1)){
5063+ outmatrix_numel = 0;
5064+ outmatrix_ndims = 0;
5065+ outmatrix_size = NULL;
5066+ outmatrix = NULL;
5067+ }
5068+ else{
5069+ if(!mxIsClass(dataref,"double") && !mxIsClass(dataref,"single")){
5070+ _printLine_("Warning: converting matlab data from '" << mxGetClassName(dataref) << "' to 'double'");
5071+ }
5072+ /*Convert matlab n-dim array to double* matrix: */
5073+ MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref);
5074+ }
5075+ }
5076+ else{
5077+ /*This is an error: we don't have the correct input!: */
5078+ _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
5079+ }
5080+
5081+ /*Assign output pointers:*/
5082+ *pmatrix=outmatrix;
5083+ if (pnumel)*pnumel=outmatrix_numel;
5084+ if (pndims)*pndims=outmatrix_ndims;
5085+ if (psize )*psize =outmatrix_size;
5086+ else xDelete<int>(outmatrix_size);
5087+
5088+}
5089+/*}}}*/
5090+/*FUNCTION FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref){{{*/
5091+void FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref){
5092+
5093+ int i,outmatrix_rows,outmatrix_cols;
5094+ double *doublematrix=NULL;
5095+ int *outmatrix=NULL;
5096+
5097+ if(mxIsEmpty(dataref) ){
5098+ /*Nothing to pick up. Just initialize matrix pointer to NULL: */
5099+ outmatrix_rows=0;
5100+ outmatrix_cols=0;
5101+ outmatrix=NULL;
5102+ }
5103+ else if( mxIsClass(dataref,"double") ||
5104+ mxIsClass(dataref,"single") ||
5105+ mxIsClass(dataref,"int16") ||
5106+ mxIsClass(dataref,"int8") ||
5107+ mxIsClass(dataref,"uint8")){
5108+
5109+ /*Check dataref is not pointing to NaN: */
5110+ if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){
5111+ outmatrix_rows=0;
5112+ outmatrix_cols=0;
5113+ outmatrix=NULL;
5114+ }
5115+ else{
5116+ if(!mxIsClass(dataref,"double") && !mxIsClass(dataref,"single")){
5117+ _printLine_("Warning: converting matlab data from '" << mxGetClassName(dataref) << "' to 'double'");
5118+ }
5119+ /*Convert matlab matrix to double* matrix: */
5120+ MatlabMatrixToDoubleMatrix(&doublematrix,&outmatrix_rows,&outmatrix_cols,dataref);
5121+
5122+ /*Convert double matrix into integer matrix: */
5123+ outmatrix=xNew<int>(outmatrix_rows*outmatrix_cols);
5124+ for(i=0;i<outmatrix_rows*outmatrix_cols;i++)outmatrix[i]=(int)doublematrix[i];
5125+ }
5126+ }
5127+ else{
5128+ /*This is an error: we don't have the correct input!: */
5129+ _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
5130+ }
5131+
5132+ /*Assign output pointers:*/
5133+ *pmatrix=outmatrix;
5134+ if (pM)*pM=outmatrix_rows;
5135+ if (pN)*pN=outmatrix_cols;
5136+}
5137+/*}}}*/
5138+/*FUNCTION FetchData(bool** pmatrix,int* pM,int *pN,const mxArray* dataref){{{*/
5139+void FetchData(bool** pmatrix,int* pM,int *pN,const mxArray* dataref){
5140+
5141+ int i,outmatrix_rows,outmatrix_cols;
5142+ double *doublematrix=NULL;
5143+ bool *outmatrix=NULL;
5144+
5145+ if(mxIsEmpty(dataref) ){
5146+ /*Nothing to pick up. Just initialize matrix pointer to NULL: */
5147+ outmatrix_rows=0;
5148+ outmatrix_cols=0;
5149+ outmatrix=NULL;
5150+ }
5151+ else if (mxIsClass(dataref,"double") ){
5152+
5153+ /*Check dataref is not pointing to NaN: */
5154+ if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){
5155+ outmatrix_rows=0;
5156+ outmatrix_cols=0;
5157+ outmatrix=NULL;
5158+ }
5159+ else{
5160+
5161+ /*Convert matlab matrix to double* matrix: */
5162+ MatlabMatrixToDoubleMatrix(&doublematrix,&outmatrix_rows,&outmatrix_cols,dataref);
5163+
5164+ /*Convert double matrix into integer matrix: */
5165+ outmatrix=xNew<bool>(outmatrix_rows*outmatrix_cols);
5166+ for(i=0;i<outmatrix_rows;i++)outmatrix[i]=(bool)doublematrix[i];
5167+ }
5168+ }
5169+ else{
5170+ /*This is an error: we don't have the correct input!: */
5171+ _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
5172+ }
5173+
5174+ /*Assign output pointers:*/
5175+ *pmatrix=outmatrix;
5176+ if (pM)*pM=outmatrix_rows;
5177+ if (pN)*pN=outmatrix_cols;
5178+}
5179+/*}}}*/
5180+/*FUNCTION FetchData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){{{*/
5181+void FetchData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){
5182+
5183+ int i;
5184+ int outmatrix_numel,outmatrix_ndims;
5185+ int* outmatrix_size=NULL;
5186+ double* doublematrix=NULL;
5187+ bool* outmatrix=NULL;
5188+
5189+ if(mxIsEmpty(dataref) ){
5190+ /*Nothing to pick up. Just initialize matrix pointer to NULL: */
5191+ outmatrix_numel=0;
5192+ outmatrix_ndims=0;
5193+ outmatrix_size =NULL;
5194+ outmatrix=NULL;
5195+ }
5196+ else if (mxIsClass(dataref,"logical") ){
5197+
5198+ /*Check dataref is not pointing to NaN: */
5199+ if ( mxIsNaN(*((bool*)mxGetData(dataref))) && (mxGetNumberOfElements(dataref)==1) ){
5200+ outmatrix_numel=0;
5201+ outmatrix_ndims=0;
5202+ outmatrix_size =NULL;
5203+ outmatrix=NULL;
5204+ }
5205+ else{
5206+
5207+ /*Convert matlab n-dim array to bool* matrix: */
5208+ MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref);
5209+ }
5210+ }
5211+ else if (mxIsClass(dataref,"double") ){
5212+
5213+ /*Check dataref is not pointing to NaN: */
5214+ if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetNumberOfElements(dataref)==1) ){
5215+ outmatrix_numel=0;
5216+ outmatrix_ndims=0;
5217+ outmatrix_size =NULL;
5218+ outmatrix=NULL;
5219+ }
5220+ else{
5221+
5222+ /*Convert matlab n-dim array to double* matrix: */
5223+ MatlabNArrayToNArray(&doublematrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref);
5224+
5225+ /*Convert double matrix into bool matrix: */
5226+ outmatrix=xNew<bool>(outmatrix_numel);
5227+ for(i=0;i<outmatrix_numel;i++)outmatrix[i]=(bool)doublematrix[i];
5228+ xDelete<double>(doublematrix);
5229+ }
5230+ }
5231+ else{
5232+ /*This is an error: we don't have the correct input!: */
5233+ _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
5234+ }
5235+
5236+ /*Assign output pointers:*/
5237+ *pmatrix=outmatrix;
5238+ if (pnumel)*pnumel=outmatrix_numel;
5239+ if (pndims)*pndims=outmatrix_ndims;
5240+ if (psize )*psize =outmatrix_size;
5241+ else xDelete<int>(outmatrix_size);
5242+
5243+}
5244+/*}}}*/
5245+/*FUNCTION FetchData(double** pvector,int* pM,const mxArray* dataref){{{*/
5246+void FetchData(double** pvector,int* pM,const mxArray* dataref){
5247+
5248+ double* outvector=NULL;
5249+ int outvector_rows;
5250+
5251+ if(mxIsEmpty(dataref)){
5252+ /*Nothing to pick up. Just initialize matrix pointer to NULL: */
5253+ outvector_rows=0;
5254+ outvector=NULL;
5255+ }
5256+ else if (mxIsClass(dataref,"double") ){
5257+
5258+ /*Convert matlab vector to double* vector: */
5259+ MatlabVectorToDoubleVector(&outvector,&outvector_rows,dataref);
5260+
5261+ }
5262+ else{
5263+ /*This is an error: we don't have the correct input!: */
5264+ _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
5265+ }
5266+
5267+ /*Assign output pointers:*/
5268+ *pvector=outvector;
5269+ if (pM)*pM=outvector_rows;
5270+}
5271+/*}}}*/
5272+/*FUNCTION FetchData(int** pvector,int* pM,const mxArray* dataref){{{*/
5273+void FetchData(int** pvector,int* pM,const mxArray* dataref){
5274+
5275+ int i;
5276+ double *doublevector = NULL;
5277+ int *outvector = NULL;
5278+ int outvector_rows;
5279+
5280+ if(mxIsEmpty(dataref)){
5281+ /*Nothing to pick up. Just initialize matrix pointer to NULL: */
5282+ outvector_rows=0;
5283+ outvector=NULL;
5284+ }
5285+ else if (mxIsClass(dataref,"double") ){
5286+
5287+ /*Convert matlab vector to double* vector: */
5288+ MatlabVectorToDoubleVector(&doublevector,&outvector_rows,dataref);
5289+
5290+ /*Convert double vector into integer vector: */
5291+ outvector=xNew<int>(outvector_rows);
5292+ for(i=0;i<outvector_rows;i++)outvector[i]=(int)doublevector[i];
5293+ }
5294+ else{
5295+ /*This is an error: we don't have the correct input!: */
5296+ _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
5297+ }
5298+
5299+ /*Assign output pointers:*/
5300+ *pvector=outvector;
5301+ if (pM)*pM=outvector_rows;
5302+}
5303+/*}}}*/
5304+/*FUNCTION FetchData(bool** pvector,int* pM,const mxArray* dataref){{{*/
5305+void FetchData(bool** pvector,int* pM,const mxArray* dataref){
5306+
5307+ int i;
5308+ double *doublevector = NULL;
5309+ bool *outvector = NULL;
5310+ int outvector_rows;
5311+
5312+ if(mxIsEmpty(dataref)){
5313+ /*Nothing to pick up. Just initialize matrix pointer to NULL: */
5314+ outvector_rows=0;
5315+ outvector=NULL;
5316+ }
5317+ else if (mxIsClass(dataref,"double") ){
5318+
5319+ /*Convert matlab vector to double* vector: */
5320+ MatlabVectorToDoubleVector(&doublevector,&outvector_rows,dataref);
5321+
5322+ /*Convert double vector into integer vector: */
5323+ outvector=xNew<bool>(outvector_rows);
5324+ for(i=0;i<outvector_rows;i++)outvector[i]=(bool)doublevector[i];
5325+ }
5326+ else{
5327+ /*This is an error: we don't have the correct input!: */
5328+ _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
5329+ }
5330+
5331+ /*Assign output pointers:*/
5332+ *pvector=outvector;
5333+ if (pM)*pM=outvector_rows;
5334+}
5335+/*}}}*/
5336+/*FUNCTION FetchData(float** pvector,int* pM,const mxArray* dataref){{{*/
5337+void FetchData(float** pvector,int* pM,const mxArray* dataref){
5338+
5339+ int i;
5340+ double *doublevector = NULL;
5341+ float *outvector = NULL;
5342+ int outvector_rows;
5343+
5344+ if(mxIsEmpty(dataref)){
5345+ /*Nothing to pick up. Just initialize matrix pointer to NULL: */
5346+ outvector_rows=0;
5347+ outvector=NULL;
5348+ }
5349+ else if (mxIsClass(dataref,"double") ){
5350+
5351+ /*Convert matlab vector to double* vector: */
5352+ MatlabVectorToDoubleVector(&doublevector,&outvector_rows,dataref);
5353+
5354+ /*Convert double vector into float vector: */
5355+ outvector=xNew<float>(outvector_rows);
5356+ for(i=0;i<outvector_rows;i++)outvector[i]=(float)doublevector[i];
5357+ }
5358+ else{
5359+ /*This is an error: we don't have the correct input!: */
5360+ _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
5361+ }
5362+
5363+ /*Assign output pointers:*/
5364+ *pvector=outvector;
5365+ if (pM)*pM=outvector_rows;
5366+}
5367+/*}}}*/
5368+/*FUNCTION FetchData(char** pstring,const mxArray* dataref){{{*/
5369+void FetchData(char** pstring,const mxArray* dataref){
5370+
5371+ char* outstring=NULL;
5372+
5373+ /*Ok, the string should be coming directly from the matlab workspace: */
5374+ if (!mxIsClass(dataref,"char")){
5375+ _error_("input data_type is not a string!");
5376+ }
5377+ else{
5378+ /*Recover the string:*/
5379+ int stringlen;
5380+
5381+ stringlen = mxGetM(dataref)*mxGetN(dataref)+1;
5382+ outstring =xNew<char>(stringlen);
5383+ mxGetString(dataref,outstring,stringlen);
5384+ }
5385+
5386+ /*Assign output pointers:*/
5387+ *pstring=outstring;
5388+}/*}}}*/
5389+/*FUNCTION FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){{{*/
5390+void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){
5391+
5392+ int outmatrix_numel,outmatrix_ndims;
5393+ int* outmatrix_size=NULL;
5394+ char* outmatrix=NULL;
5395+
5396+ if(mxIsEmpty(dataref) ){
5397+ /*Nothing to pick up. Just initialize matrix pointer to NULL: */
5398+ outmatrix_numel=0;
5399+ outmatrix_ndims=0;
5400+ outmatrix_size =NULL;
5401+ outmatrix=NULL;
5402+ }
5403+ else if (mxIsClass(dataref,"char") ){
5404+
5405+ /*Convert matlab n-dim array to char* matrix: */
5406+ MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref);
5407+ }
5408+ else{
5409+ /*This is an error: we don't have the correct input!: */
5410+ _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
5411+ }
5412+
5413+ /*Assign output pointers:*/
5414+ *pmatrix=outmatrix;
5415+ if (pnumel)*pnumel=outmatrix_numel;
5416+ if (pndims)*pndims=outmatrix_ndims;
5417+ if (psize )*psize =outmatrix_size;
5418+ else xDelete<int>(outmatrix_size);
5419+
5420+}
5421+/*}}}*/
5422+/*FUNCTION FetchData(double* pscalar,const mxArray* dataref){{{*/
5423+void FetchData(double* pscalar,const mxArray* dataref){
5424+
5425+ double scalar;
5426+
5427+ if (!mxIsClass(dataref,"double")){
5428+ _error_("input data_type is not a double!");
5429+ }
5430+ else{
5431+ /*Recover the double: */
5432+ scalar=mxGetScalar(dataref);
5433+ }
5434+
5435+ /*Assign output pointers:*/
5436+ *pscalar=scalar;
5437+}
5438+/*}}}*/
5439+/*FUNCTION FetchData(int* pinteger,const mxArray* dataref){{{*/
5440+void FetchData(int* pinteger,const mxArray* dataref){
5441+
5442+ int integer;
5443+
5444+ if (!mxIsClass(dataref,"double")){
5445+ _error_("input data_type is not a scalar!");
5446+ }
5447+ else{
5448+ /*Recover the double: */
5449+ integer=(int)mxGetScalar(dataref);
5450+ }
5451+
5452+ /*Assign output pointers:*/
5453+ *pinteger=integer;
5454+}
5455+/*}}}*/
5456+/*FUNCTION FetchData(bool* pboolean,const mxArray* dataref){{{*/
5457+void FetchData(bool* pboolean,const mxArray* dataref){
5458+
5459+ bool* mxbool_ptr=NULL;
5460+
5461+ if (mxIsClass(dataref,"logical")){
5462+ if(mxGetM(dataref)!=1) _error_("input data is not of size 1x1");
5463+ if(mxGetN(dataref)!=1) _error_("input data is not of size 1x1");
5464+ mxbool_ptr=mxGetLogicals(dataref);
5465+ }
5466+ else{
5467+ _error_("input data_type is not a bool!");
5468+ }
5469+
5470+ *pboolean=*mxbool_ptr;
5471+}
5472+/*}}}*/
5473+
5474+/*ISSM objects*/
5475+/*FUNCTION FetchData(Matrix<double>** pmatrix,const mxArray* dataref){{{*/
5476+void FetchData(Matrix<double>** pmatrix,const mxArray* dataref){
5477+
5478+ Matrix<double>* outmatrix=NULL;
5479+ int dummy=0;
5480+
5481+ if (mxIsClass(dataref,"double") ){
5482+
5483+ /*Convert matlab matrix to matrix: */
5484+ outmatrix=MatlabMatrixToMatrix(dataref);
5485+
5486+ }
5487+ else{
5488+ /*This is an error: we don't have the correct input!: */
5489+ _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
5490+ }
5491+
5492+ /*Assign output pointers:*/
5493+ *pmatrix=outmatrix;
5494+}
5495+/*}}}*/
5496+/*FUNCTION FetchData(Vector<double>** pvector,const mxArray* dataref){{{*/
5497+void FetchData(Vector<double>** pvector,const mxArray* dataref){
5498+
5499+ Vector<double>* vector=NULL;
5500+ int dummy;
5501+
5502+ if(mxIsEmpty(dataref)){
5503+ /*Nothing to pick up. Just initialize matrix pointer to NULL: */
5504+ vector=new Vector<double>(0);
5505+ }
5506+ else if (mxIsClass(dataref,"double") ){
5507+
5508+ /*Convert matlab vector to petsc vector: */
5509+ vector=MatlabVectorToVector(dataref);
5510+ }
5511+ else{
5512+ /*This is an error: we don't have the correct input!: */
5513+ _error_("Input parameter of class " << mxGetClassName(dataref) << " not supported yet");
5514+ }
5515+
5516+ /*Assign output pointers:*/
5517+ *pvector=vector;
5518+}
5519+/*}}}*/
5520+/*FUNCTION FetchData(BamgGeom** pbamggeom,const mxArray* dataref){{{*/
5521+void FetchData(BamgGeom** pbamggeom,const mxArray* dataref){
5522+
5523+ /*Initialize output*/
5524+ BamgGeom* bamggeom=new BamgGeom();
5525+
5526+ /*Fetch all fields*/
5527+ FetchData(&bamggeom->Vertices,&bamggeom->VerticesSize[0],&bamggeom->VerticesSize[1],mxGetAssignedField(dataref,0,"Vertices"));
5528+ FetchData(&bamggeom->Edges, &bamggeom->EdgesSize[0], &bamggeom->EdgesSize[1], mxGetAssignedField(dataref,0,"Edges"));
5529+ FetchData(&bamggeom->Corners, &bamggeom->CornersSize[0], &bamggeom->CornersSize[1], mxGetAssignedField(dataref,0,"Corners"));
5530+ FetchData(&bamggeom->RequiredVertices,&bamggeom->RequiredVerticesSize[0],&bamggeom->RequiredVerticesSize[1],mxGetAssignedField(dataref,0,"RequiredVertices"));
5531+ FetchData(&bamggeom->RequiredEdges, &bamggeom->RequiredEdgesSize[0], &bamggeom->RequiredEdgesSize[1], mxGetAssignedField(dataref,0,"RequiredEdges"));
5532+ FetchData(&bamggeom->CrackedEdges,&bamggeom->CrackedEdgesSize[0],&bamggeom->CrackedEdgesSize[1],mxGetAssignedField(dataref,0,"CrackedEdges"));
5533+ FetchData(&bamggeom->SubDomains,&bamggeom->SubDomainsSize[0],&bamggeom->SubDomainsSize[1],mxGetAssignedField(dataref,0,"SubDomains"));
5534+
5535+ /*Assign output pointers:*/
5536+ *pbamggeom=bamggeom;
5537+}
5538+/*}}}*/
5539+/*FUNCTION FetchData(BamgMesh** pbamgmesh,const mxArray* dataref){{{*/
5540+void FetchData(BamgMesh** pbamgmesh,const mxArray* dataref){
5541+
5542+ /*Initialize output*/
5543+ BamgMesh* bamgmesh=new BamgMesh();
5544+
5545+ /*Fetch all fields*/
5546+ FetchData(&bamgmesh->Vertices,&bamgmesh->VerticesSize[0],&bamgmesh->VerticesSize[1],mxGetAssignedField(dataref,0,"Vertices"));
5547+ FetchData(&bamgmesh->Edges, &bamgmesh->EdgesSize[0], &bamgmesh->EdgesSize[1], mxGetAssignedField(dataref,0,"Edges"));
5548+ FetchData(&bamgmesh->Triangles, &bamgmesh->TrianglesSize[0], &bamgmesh->TrianglesSize[1], mxGetAssignedField(dataref,0,"Triangles"));
5549+ FetchData(&bamgmesh->CrackedEdges,&bamgmesh->CrackedEdgesSize[0],&bamgmesh->CrackedEdgesSize[1],mxGetAssignedField(dataref,0,"CrackedEdges"));
5550+ FetchData(&bamgmesh->VerticesOnGeomEdge,&bamgmesh->VerticesOnGeomEdgeSize[0],&bamgmesh->VerticesOnGeomEdgeSize[1],mxGetAssignedField(dataref,0,"VerticesOnGeomEdge"));
5551+ FetchData(&bamgmesh->VerticesOnGeomVertex,&bamgmesh->VerticesOnGeomVertexSize[0],&bamgmesh->VerticesOnGeomVertexSize[1],mxGetAssignedField(dataref,0,"VerticesOnGeomVertex"));
5552+ FetchData(&bamgmesh->EdgesOnGeomEdge, &bamgmesh->EdgesOnGeomEdgeSize[0], &bamgmesh->EdgesOnGeomEdgeSize[1], mxGetAssignedField(dataref,0,"EdgesOnGeomEdge"));
5553+ FetchData(&bamgmesh->IssmSegments,&bamgmesh->IssmSegmentsSize[0],&bamgmesh->IssmSegmentsSize[1],mxGetAssignedField(dataref,0,"IssmSegments"));
5554+
5555+ /*Assign output pointers:*/
5556+ *pbamgmesh=bamgmesh;
5557+}
5558+/*}}}*/
5559+/*FUNCTION FetchData(BamgOpts** pbamgopts,const mxArray* dataref){{{*/
5560+void FetchData(BamgOpts** pbamgopts,const mxArray* dataref){
5561+
5562+ /*Initialize output*/
5563+ BamgOpts* bamgopts=new BamgOpts();
5564+
5565+ /*Fetch all fields*/
5566+ FetchData(&bamgopts->anisomax,mxGetField(dataref,0,"anisomax"));
5567+ FetchData(&bamgopts->cutoff,mxGetField(dataref,0,"cutoff"));
5568+ FetchData(&bamgopts->coeff,mxGetField(dataref,0,"coeff"));
5569+ FetchData(&bamgopts->errg,mxGetField(dataref,0,"errg"));
5570+ FetchData(&bamgopts->gradation,mxGetField(dataref,0,"gradation"));
5571+ FetchData(&bamgopts->Hessiantype,mxGetField(dataref,0,"Hessiantype"));
5572+ FetchData(&bamgopts->MaxCornerAngle,mxGetField(dataref,0,"MaxCornerAngle"));
5573+ FetchData(&bamgopts->maxnbv,mxGetField(dataref,0,"maxnbv"));
5574+ FetchData(&bamgopts->maxsubdiv,mxGetField(dataref,0,"maxsubdiv"));
5575+ FetchData(&bamgopts->Metrictype,mxGetField(dataref,0,"Metrictype"));
5576+ FetchData(&bamgopts->nbjacobi,mxGetField(dataref,0,"nbjacobi"));
5577+ FetchData(&bamgopts->nbsmooth,mxGetField(dataref,0,"nbsmooth"));
5578+ FetchData(&bamgopts->omega,mxGetField(dataref,0,"omega"));
5579+ FetchData(&bamgopts->power,mxGetField(dataref,0,"power"));
5580+ FetchData(&bamgopts->verbose,mxGetField(dataref,0,"verbose"));
5581+
5582+ FetchData(&bamgopts->Crack,mxGetField(dataref,0,"Crack"));
5583+ FetchData(&bamgopts->geometricalmetric,mxGetField(dataref,0,"geometricalmetric"));
5584+ FetchData(&bamgopts->KeepVertices,mxGetField(dataref,0,"KeepVertices"));
5585+ FetchData(&bamgopts->splitcorners,mxGetField(dataref,0,"splitcorners"));
5586+
5587+ FetchData(&bamgopts->hmin,mxGetField(dataref,0,"hmin"));
5588+ FetchData(&bamgopts->hmax,mxGetField(dataref,0,"hmax"));
5589+ FetchData(&bamgopts->hminVertices,&bamgopts->hminVerticesSize[0],&bamgopts->hminVerticesSize[1],mxGetField(dataref,0,"hminVertices"));
5590+ FetchData(&bamgopts->hmaxVertices,&bamgopts->hmaxVerticesSize[0],&bamgopts->hmaxVerticesSize[1],mxGetField(dataref,0,"hmaxVertices"));
5591+ FetchData(&bamgopts->hVertices,&bamgopts->hVerticesSize[0],&bamgopts->hVerticesSize[1],mxGetField(dataref,0,"hVertices"));
5592+ FetchData(&bamgopts->metric,&bamgopts->metricSize[0],&bamgopts->metricSize[1],mxGetField(dataref,0,"metric"));
5593+ FetchData(&bamgopts->field,&bamgopts->fieldSize[0],&bamgopts->fieldSize[1],mxGetField(dataref,0,"field"));
5594+ FetchData(&bamgopts->err,&bamgopts->errSize[0],&bamgopts->errSize[1],mxGetField(dataref,0,"err"));
5595+
5596+ /*Additional checks*/
5597+ bamgopts->Check();
5598+
5599+ /*Assign output pointers:*/
5600+ *pbamgopts=bamgopts;
5601+}
5602+/*}}}*/
5603+/*FUNCTION FetchData(Options** poptions,const mxArray** pdataref){{{*/
5604+void FetchData(Options** poptions,int istart, int nrhs,const mxArray** pdataref){
5605+
5606+ char *name = NULL;
5607+ Option *option = NULL;
5608+
5609+ /*Initialize output*/
5610+ Options* options=new Options();
5611+
5612+ /*Fetch all options*/
5613+ for (int i=istart; i<nrhs; i=i+2){
5614+ if (!mxIsClass(pdataref[i],"char")) _error_("Argument " << i+1 << " must be name of option");
5615+
5616+ FetchData(&name,pdataref[i]);
5617+ if(i+1 == nrhs) _error_("Argument " << i+2 << " must exist and be value of option \"" << name << "\".");
5618+
5619+ option=(Option*)OptionParse(name,&pdataref[i+1]);
5620+ options->AddOption(option);
5621+ option=NULL;
5622+ }
5623+
5624+ /*Assign output pointers:*/
5625+ *poptions=options;
5626+}
5627+/*}}}*/
5628+/*FUNCTION FetchData(DataSet** pcontours,const mxArray* dataref){{{*/
5629+void FetchData(DataSet** pcontours,const mxArray* dataref){
5630+
5631+ int numcontours,index,test1,test2;
5632+ char *contourname = NULL;
5633+ DataSet *contours = NULL;
5634+ Contour<double> *contouri = NULL;
5635+
5636+ if (mxIsClass(dataref,"char")){
5637+ FetchData(&contourname,dataref);
5638+ contours=DomainOutlineRead<double>(contourname);
5639+ }
5640+ else if(mxIsClass(dataref,"struct")){
5641+
5642+ contours=new DataSet(0);
5643+ numcontours=mxGetNumberOfElements(dataref);
5644+
5645+ for(int i=0;i<numcontours;i++){
5646+
5647+ contouri=xNew<Contour<double> >(1);
5648+
5649+ index = mxGetFieldNumber(dataref,"nods");
5650+ if(index==-1) _error_("input structure does not have a 'nods' field");
5651+ FetchData(&contouri->nods,mxGetFieldByNumber(dataref,i,index));
5652+
5653+ index = mxGetFieldNumber(dataref,"x");
5654+ if(index==-1) _error_("input structure does not have a 'x' field");
5655+ FetchData(&contouri->x,&test1,&test2,mxGetFieldByNumber(dataref,i,index));
5656+ if(test1!=contouri->nods || test2!=1) _error_("field x should be of size ["<<contouri->nods<<" 1]");
5657+
5658+ index = mxGetFieldNumber(dataref,"y");
5659+ if(index==-1) _error_("input structure does not have a 'y' field");
5660+ FetchData(&contouri->y,&test1,&test2,mxGetFieldByNumber(dataref,i,index));
5661+ if(test1!=contouri->nods || test2!=1) _error_("field y should be of size ["<<contouri->nods<<" 1]");
5662+
5663+ contours->AddObject(contouri);
5664+ }
5665+ }
5666+ else{
5667+ _error_("Contour is neither a string nor a structure and cannot be loaded ("<<mxGetClassName(dataref)<<" not supported)");
5668+ }
5669+
5670+ /*clean-up and assign output pointer*/
5671+ xDelete<char>(contourname);
5672+ *pcontours=contours;
5673+}
5674+/*}}}*/
5675Index: ../trunk-jpl/src/wrappers/matlab/io/MatlabVectorToDoubleVector.cpp
5676===================================================================
5677--- ../trunk-jpl/src/wrappers/matlab/io/MatlabVectorToDoubleVector.cpp (revision 0)
5678+++ ../trunk-jpl/src/wrappers/matlab/io/MatlabVectorToDoubleVector.cpp (revision 13749)
5679@@ -0,0 +1,93 @@
5680+/* \file MatlabVectorToDoubleVector.cpp
5681+ * \brief: convert a sparse or dense matlab vector to a serial vector:
5682+ */
5683+
5684+#ifdef HAVE_CONFIG_H
5685+ #include <config.h>
5686+#else
5687+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
5688+#endif
5689+
5690+#include <string.h>
5691+
5692+/*Matlab includes: */
5693+#include "./matlabio.h"
5694+#include "../../c/shared/shared.h"
5695+
5696+int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector){
5697+
5698+ int rows,cols;
5699+ double* mxvector_ptr=NULL;
5700+ int ierr;
5701+ int i,j;
5702+
5703+ /*output: */
5704+ double* vector=NULL;
5705+
5706+ /*matlab indices: */
5707+ mwIndex* ir=NULL;
5708+ mwIndex* jc=NULL;
5709+ double* pr=NULL;
5710+ int count;
5711+ int nnz;
5712+ int nz;
5713+
5714+ /*Ok, first check if we are dealing with a sparse or full vector: */
5715+ if (mxIsSparse(mxvector)){
5716+
5717+ /*Dealing with sparse vector: recover size first: */
5718+ mxvector_ptr=(double*)mxGetPr(mxvector);
5719+ rows=mxGetM(mxvector);
5720+ cols=mxGetN(mxvector);
5721+ nnz=mxGetNzmax(mxvector);
5722+
5723+ /*Check that input is actualy a vector*/
5724+ if (cols!=1) _error_("input vector of size " << rows << "x" << cols << " should have only one column");
5725+
5726+ nz=(int)((double)nnz/(double)rows);
5727+
5728+ if(rows){
5729+ vector=xNewZeroInit<double>(rows);
5730+
5731+ /*Now, get ir,jc and pr: */
5732+ pr=mxGetPr(mxvector);
5733+ ir=mxGetIr(mxvector);
5734+ jc=mxGetJc(mxvector);
5735+
5736+ /*Now, start inserting data into sparse vector: */
5737+ count=0;
5738+ for(i=0;i<cols;i++){
5739+ for(j=0;j<(jc[i+1]-jc[i]);j++){
5740+ vector[ir[count]]=pr[count];
5741+ count++;
5742+ }
5743+ }
5744+ }
5745+
5746+ }
5747+ else{
5748+
5749+ /*Dealing with dense vector: recover pointer and size: */
5750+ mxvector_ptr=(double*)mxGetPr(mxvector);
5751+ rows=mxGetM(mxvector);
5752+ cols=mxGetN(mxvector);
5753+
5754+ /*Check that input is actualy a vector*/
5755+ if (cols!=1) _error_("input vector of size " << rows << "x" << cols << " should have only one column");
5756+
5757+ /*allocate and memcpy*/
5758+ if(rows){
5759+ vector=xNew<double>(rows);
5760+ memcpy(vector,mxvector_ptr,rows*sizeof(double));
5761+ }
5762+ else{
5763+ vector=NULL;
5764+ }
5765+ }
5766+
5767+ /*Assign output pointer: */
5768+ *pvector=vector;
5769+ *pvector_rows=rows;
5770+
5771+ return 1;
5772+}
5773Index: ../trunk-jpl/src/wrappers/matlab/io/WriteMatlabData.cpp
5774===================================================================
5775--- ../trunk-jpl/src/wrappers/matlab/io/WriteMatlabData.cpp (revision 0)
5776+++ ../trunk-jpl/src/wrappers/matlab/io/WriteMatlabData.cpp (revision 13749)
5777@@ -0,0 +1,388 @@
5778+/* \file WriteData.c:
5779+ * \brief: general interface for writing data
5780+ */
5781+
5782+#ifdef HAVE_CONFIG_H
5783+ #include <config.h>
5784+#else
5785+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
5786+#endif
5787+
5788+#include "./matlabio.h"
5789+#include "../../c/shared/shared.h"
5790+
5791+/*Primitive data types*/
5792+/*FUNCTION WriteData(mxArray** pdataref,double* matrix, int M,int N){{{*/
5793+void WriteData(mxArray** pdataref,double* matrix, int M,int N){
5794+
5795+ mxArray *dataref = NULL;
5796+ double *tmatrix = NULL;
5797+
5798+ if(matrix){
5799+ /*create the matlab matrixwith Matlab's memory manager */
5800+ tmatrix=(double*)mxMalloc(M*N*sizeof(double));
5801+ for(int i=0;i<M;i++){
5802+ for(int j=0;j<N;j++){
5803+ tmatrix[j*M+i]=matrix[i*N+j];
5804+ }
5805+ }
5806+ dataref = mxCreateDoubleMatrix(0,0,mxREAL);
5807+ mxSetM(dataref,(mwSize)M);
5808+ mxSetN(dataref,(mwSize)N);
5809+ mxSetPr(dataref,(double*)tmatrix);
5810+ }
5811+ else{
5812+ dataref = mxCreateDoubleMatrix(0,0,mxREAL);
5813+ }
5814+ *pdataref=dataref;
5815+}
5816+/*}}}*/
5817+/*FUNCTION WriteData(mxArray** pdataref,int* matrix, int M,int N){{{*/
5818+void WriteData(mxArray** pdataref,int* matrix, int M,int N){
5819+
5820+ mxArray* dataref = NULL;
5821+ double* tmatrix = NULL;
5822+
5823+ if(matrix){
5824+ /*convert to double matrix using Matlab's memory manager*/
5825+ double* tmatrix=(double*)mxMalloc(M*N*sizeof(double));
5826+ for(int i=0;i<M;i++){
5827+ for(int j=0;j<N;j++){
5828+ tmatrix[j*M+i]=(double)matrix[i*N+j];
5829+ }
5830+ }
5831+ dataref = mxCreateDoubleMatrix(0,0,mxREAL);
5832+ mxSetM(dataref,(mwSize)M);
5833+ mxSetN(dataref,(mwSize)N);
5834+ mxSetPr(dataref,(double*)tmatrix);
5835+ }
5836+ else{
5837+ dataref = mxCreateDoubleMatrix(0,0,mxREAL);
5838+ }
5839+ *pdataref=dataref;
5840+}
5841+/*}}}*/
5842+/*FUNCTION WriteData(mxArray** pdataref,double* vector, int M){{{*/
5843+void WriteData(mxArray** pdataref,double* vector, int M){
5844+
5845+ mxArray* dataref = NULL;
5846+ double* vector_matlab = NULL;
5847+
5848+ if(vector){
5849+
5850+ /*create the matlab vector with Matlab's memory manager */
5851+ vector_matlab=(double*)mxMalloc(M*sizeof(double));
5852+ for(int i=0;i<M;i++) vector_matlab[i]=vector[i];
5853+ dataref = mxCreateDoubleMatrix(0,0,mxREAL);
5854+ mxSetM(dataref,(mwSize)M);
5855+ mxSetN(dataref,(mwSize)1);
5856+ mxSetPr(dataref,vector_matlab);
5857+ }
5858+ else{
5859+ dataref = mxCreateDoubleMatrix(0,0,mxREAL);
5860+ }
5861+
5862+ *pdataref=dataref;
5863+}
5864+/*}}}*/
5865+/*FUNCTION WriteData(mxArray** pdataref,double scalar){{{*/
5866+void WriteData(mxArray** pdataref,double scalar){
5867+
5868+ *pdataref=mxCreateDoubleScalar(scalar);
5869+}
5870+/*}}}*/
5871+/*FUNCTION WriteData(mxArray** pdataref,int integer){{{*/
5872+void WriteData(mxArray** pdataref,int integer){
5873+
5874+ *pdataref=mxCreateDoubleScalar((double)integer);
5875+
5876+}
5877+/*}}}*/
5878+/*FUNCTION WriteData(mxArray** pdataref,int boolean){{{*/
5879+void WriteData(mxArray** pdataref,bool boolean){
5880+
5881+ *pdataref=mxCreateDoubleScalar((double)boolean);
5882+
5883+}
5884+/*}}}*/
5885+/*FUNCTION WriteData(mxArray** pdataref,char* string){{{*/
5886+void WriteData(mxArray** pdataref,char* string){
5887+
5888+ *pdataref=mxCreateString(string);
5889+}
5890+/*}}}*/
5891+/*FUNCTION WriteData(mxArray** pdataref){{{*/
5892+void WriteData(mxArray** pdataref){
5893+
5894+ ;
5895+
5896+}
5897+/*}}}*/
5898+
5899+/*ISSM objects*/
5900+/*FUNCTION WriteData(mxArray** pdataref,BamgGeom* bamggeom){{{*/
5901+void WriteData(mxArray** pdataref,BamgGeom* bamggeom){
5902+
5903+ /*Intermediary*/
5904+ int i;
5905+ mxArray *dataref = NULL;
5906+ const int numfields = 8;
5907+ const char *fnames[numfields];
5908+ mwSize ndim = 2;
5909+ mwSize dimensions[2] = {1,1};
5910+
5911+ /*Initialize field names*/
5912+ i=0;
5913+ fnames[i++] = "Vertices";
5914+ fnames[i++] = "Edges";
5915+ fnames[i++] = "TangentAtEdges";
5916+ fnames[i++] = "Corners";
5917+ fnames[i++] = "RequiredVertices";
5918+ fnames[i++] = "RequiredEdges";
5919+ fnames[i++] = "CrackedEdges";
5920+ fnames[i++] = "SubDomains";
5921+ _assert_(i==numfields);
5922+
5923+ /*Initialize Matlab structure*/
5924+ dataref=mxCreateStructArray(ndim,dimensions,numfields,fnames);
5925+
5926+ /*set each matlab each field*/
5927+ i=0;
5928+ i++; SetStructureField(dataref,"Vertices", bamggeom->VerticesSize[0], bamggeom->VerticesSize[1], bamggeom->Vertices);
5929+ i++; SetStructureField(dataref,"Edges", bamggeom->EdgesSize[0], bamggeom->EdgesSize[1], bamggeom->Edges);
5930+ i++; SetStructureField(dataref,"TangentAtEdges", bamggeom->TangentAtEdgesSize[0], bamggeom->TangentAtEdgesSize[1], bamggeom->TangentAtEdges);
5931+ i++; SetStructureField(dataref,"Corners", bamggeom->CornersSize[0], bamggeom->CornersSize[1], bamggeom->Corners);
5932+ i++; SetStructureField(dataref,"RequiredVertices",bamggeom->RequiredVerticesSize[0],bamggeom->RequiredVerticesSize[1],bamggeom->RequiredVertices);
5933+ i++; SetStructureField(dataref,"RequiredEdges", bamggeom->RequiredEdgesSize[0], bamggeom->RequiredEdgesSize[1], bamggeom->RequiredEdges);
5934+ i++; SetStructureField(dataref,"CrackedEdges", bamggeom->CrackedEdgesSize[0], bamggeom->CrackedEdgesSize[1], bamggeom->CrackedEdges);
5935+ i++; SetStructureField(dataref,"SubDomains", bamggeom->SubDomainsSize[0], bamggeom->SubDomainsSize[1], bamggeom->SubDomains);
5936+ _assert_(i==numfields);
5937+
5938+ /*Assign output*/
5939+ *pdataref=dataref;
5940+}
5941+/*}}}*/
5942+/*FUNCTION WriteData(mxArray** pdataref,BamgMesh* bamgmesh){{{*/
5943+void WriteData(mxArray** pdataref,BamgMesh* bamgmesh){
5944+
5945+ /*Intermediary*/
5946+ int i;
5947+ mxArray *dataref = NULL;
5948+ const int numfields = 16;
5949+ const char *fnames[numfields];
5950+ mwSize ndim = 2;
5951+ mwSize dimensions[2] = {1,1};
5952+
5953+ /*Initialize field names*/
5954+ i=0;
5955+ fnames[i++] = "Vertices";
5956+ fnames[i++] = "Edges";
5957+ fnames[i++] = "Triangles";
5958+ fnames[i++] = "Quadrilaterals";
5959+ fnames[i++] = "IssmEdges";
5960+ fnames[i++] = "IssmSegments";
5961+ fnames[i++] = "VerticesOnGeomVertex";
5962+ fnames[i++] = "VerticesOnGeomEdge";
5963+ fnames[i++] = "EdgesOnGeomEdge";
5964+ fnames[i++] = "SubDomains";
5965+ fnames[i++] = "SubDomainsFromGeom";
5966+ fnames[i++] = "ElementConnectivity";
5967+ fnames[i++] = "NodalConnectivity";
5968+ fnames[i++] = "NodalElementConnectivity";
5969+ fnames[i++] = "CrackedVertices";
5970+ fnames[i++] = "CrackedEdges";
5971+ _assert_(i==numfields);
5972+
5973+ /*Initialize Matlab structure*/
5974+ dataref=mxCreateStructArray(ndim,dimensions,numfields,fnames);
5975+
5976+ /*set each matlab each field*/
5977+ i=0;
5978+ i++; SetStructureField(dataref,"Vertices",bamgmesh->VerticesSize[0], bamgmesh->VerticesSize[1],bamgmesh->Vertices);
5979+ i++; SetStructureField(dataref,"Edges", bamgmesh->EdgesSize[0],bamgmesh->EdgesSize[1], bamgmesh->Edges);
5980+ i++; SetStructureField(dataref,"Triangles", bamgmesh->TrianglesSize[0],bamgmesh->TrianglesSize[1], bamgmesh->Triangles);
5981+ i++; SetStructureField(dataref,"Quadrilaterals",bamgmesh->QuadrilateralsSize[0], bamgmesh->QuadrilateralsSize[1],bamgmesh->Quadrilaterals);
5982+ i++; SetStructureField(dataref,"IssmEdges", bamgmesh->IssmEdgesSize[0],bamgmesh->IssmEdgesSize[1], bamgmesh->IssmEdges);
5983+ i++; SetStructureField(dataref,"IssmSegments",bamgmesh->IssmSegmentsSize[0], bamgmesh->IssmSegmentsSize[1],bamgmesh->IssmSegments);
5984+ i++; SetStructureField(dataref,"VerticesOnGeomVertex",bamgmesh->VerticesOnGeomVertexSize[0],bamgmesh->VerticesOnGeomVertexSize[1], bamgmesh->VerticesOnGeomVertex);
5985+ i++; SetStructureField(dataref,"VerticesOnGeomEdge",bamgmesh->VerticesOnGeomEdgeSize[0],bamgmesh->VerticesOnGeomEdgeSize[1], bamgmesh->VerticesOnGeomEdge);
5986+ i++; SetStructureField(dataref,"EdgesOnGeomEdge", bamgmesh->EdgesOnGeomEdgeSize[0], bamgmesh->EdgesOnGeomEdgeSize[1],bamgmesh->EdgesOnGeomEdge);
5987+ i++; SetStructureField(dataref,"SubDomains",bamgmesh->SubDomainsSize[0], bamgmesh->SubDomainsSize[1],bamgmesh->SubDomains);
5988+ i++; SetStructureField(dataref,"SubDomainsFromGeom", bamgmesh->SubDomainsFromGeomSize[0], bamgmesh->SubDomainsFromGeomSize[1],bamgmesh->SubDomainsFromGeom);
5989+ i++; SetStructureField(dataref,"ElementConnectivity",bamgmesh->ElementConnectivitySize[0],bamgmesh->ElementConnectivitySize[1], bamgmesh->ElementConnectivity);
5990+ i++; SetStructureField(dataref,"NodalConnectivity",bamgmesh->NodalConnectivitySize[0],bamgmesh->NodalConnectivitySize[1], bamgmesh->NodalConnectivity);
5991+ i++; SetStructureField(dataref,"NodalElementConnectivity", bamgmesh->NodalElementConnectivitySize[0], bamgmesh->NodalElementConnectivitySize[1],bamgmesh->NodalElementConnectivity);
5992+ i++; SetStructureField(dataref,"CrackedVertices", bamgmesh->CrackedVerticesSize[0],bamgmesh->CrackedVerticesSize[1], bamgmesh->CrackedVertices);
5993+ i++; SetStructureField(dataref,"CrackedEdges",bamgmesh->CrackedEdgesSize[0], bamgmesh->CrackedEdgesSize[1],bamgmesh->CrackedEdges);
5994+ _assert_(i==numfields);
5995+
5996+ /*Assign output*/
5997+ *pdataref=dataref;
5998+}
5999+/*}}}*/
6000+/*FUNCTION WriteData(mxArray** pdataref,SeqMat<double>* matrix){{{*/
6001+void WriteData(mxArray** pdataref,SeqMat<double>* matrix){
6002+
6003+ int i,j;
6004+ int rows,cols;
6005+ mxArray *dataref = NULL;
6006+ double *matrix_ptr = NULL;
6007+ double *tmatrix_ptr = NULL;
6008+
6009+ if(matrix){
6010+
6011+ matrix_ptr=matrix->ToSerial();
6012+ matrix->GetSize(&rows,&cols);
6013+
6014+ /*Now transpose the matrix and allocate with Matlab's memory manager: */
6015+ tmatrix_ptr=(double*)mxMalloc(rows*cols*sizeof(double));
6016+ for(i=0;i<rows;i++){
6017+ for(j=0;j<cols;j++){
6018+ tmatrix_ptr[j*rows+i]=matrix_ptr[i*cols+j];
6019+ }
6020+ }
6021+
6022+ /*create matlab matrix: */
6023+ dataref=mxCreateDoubleMatrix(0,0,mxREAL);
6024+ mxSetM(dataref,rows);
6025+ mxSetN(dataref,cols);
6026+ mxSetPr(dataref,tmatrix_ptr);
6027+
6028+ /*Free ressources:*/
6029+ xDelete<double>(matrix_ptr);
6030+ }
6031+ else{
6032+ dataref = mxCreateDoubleMatrix(0,0,mxREAL);
6033+ }
6034+
6035+ *pdataref=dataref;
6036+}
6037+/*}}}*/
6038+/*FUNCTION WriteData(mxArray** pdataref,SeqVec<double>* vector){{{*/
6039+void WriteData(mxArray** pdataref,SeqVec<double>* vector){
6040+
6041+ mxArray* dataref=NULL;
6042+ double* vector_ptr=NULL;
6043+ double* vector_matlab=NULL;
6044+ int rows;
6045+
6046+ if(vector){
6047+ /*call toolkit routine: */
6048+ vector_ptr=vector->ToMPISerial();
6049+ vector->GetSize(&rows);
6050+
6051+ /*now create the matlab vector with Matlab's memory manager */
6052+ vector_matlab=(double*)mxMalloc(rows*sizeof(double));
6053+ for(int i=0;i<rows;i++) vector_matlab[i]=vector_ptr[i];
6054+
6055+ dataref = mxCreateDoubleMatrix(0,0,mxREAL);
6056+ mxSetM(dataref,rows);
6057+ mxSetN(dataref,1);
6058+ mxSetPr(dataref,vector_matlab);
6059+ }
6060+ else{
6061+ dataref = mxCreateDoubleMatrix(0,0,mxREAL);
6062+ }
6063+
6064+ /*Clean-up and return*/
6065+ xDelete<double>(vector_ptr);
6066+ *pdataref=dataref;
6067+}
6068+/*}}}*/
6069+/*FUNCTION WriteData(mxArray** pdataref,RiftStruct* riftstruct){{{*/
6070+void WriteData(mxArray** pdataref,RiftStruct* riftstruct){
6071+
6072+ /*Intermediary*/
6073+ int i;
6074+ mxArray *dataref = NULL;
6075+ const int numfields = 10;
6076+ const char *fnames[numfields];
6077+ mwSize ndim = 2;
6078+ mwSize dimensions[2] = {1,1};
6079+
6080+ /*Initialize field names*/
6081+ i=0;
6082+ fnames[i++] = "numsegs";
6083+ fnames[i++] = "segments";
6084+ fnames[i++] = "pairs";
6085+ fnames[i++] = "tips";
6086+ fnames[i++] = "penaltypairs";
6087+ fnames[i++] = "fill";
6088+ fnames[i++] = "friction";
6089+ fnames[i++] = "fraction";
6090+ fnames[i++] = "fractionincrement";
6091+ fnames[i++] = "state";
6092+ _assert_(i==numfields);
6093+
6094+ /*Initialize matlab structure of dimension numrifts*/
6095+ dimensions[0]=riftstruct->numrifts;
6096+ dataref=mxCreateStructArray(ndim,dimensions,numfields,fnames);
6097+
6098+ /*set each matlab each field*/
6099+ for(int i=0;i<riftstruct->numrifts;i++){
6100+ SetStructureFieldi(dataref,i,"numsegs" ,riftstruct->riftsnumsegments[i]);
6101+ SetStructureFieldi(dataref,i,"segments" ,riftstruct->riftsnumsegments[i] ,3,riftstruct->riftssegments[i]);
6102+ SetStructureFieldi(dataref,i,"pairs" ,riftstruct->riftsnumpairs[i] ,2,riftstruct->riftspairs[i]);
6103+ SetStructureFieldi(dataref,i,"tips" ,1 ,2,&riftstruct->riftstips[2*i]);
6104+ SetStructureFieldi(dataref,i,"penaltypairs" ,riftstruct->riftsnumpenaltypairs[i],7,riftstruct->riftspenaltypairs[i]);
6105+ SetStructureFieldi(dataref,i,"fill" ,IceEnum);
6106+ SetStructureFieldi(dataref,i,"friction" ,0);
6107+ SetStructureFieldi(dataref,i,"fraction" ,0.);
6108+ SetStructureFieldi(dataref,i,"fractionincrement",0.1);
6109+ SetStructureFieldi(dataref,i,"state" ,riftstruct->riftsnumpenaltypairs[i],1,riftstruct->state[i]);
6110+ }
6111+
6112+ /*Assign output*/
6113+ *pdataref=dataref;
6114+}
6115+/*}}}*/
6116+
6117+/*Toolkit*/
6118+/*FUNCTION SetStructureField{{{*/
6119+void SetStructureField(mxArray* dataref,const char* fieldname,int M,int N,double* fieldpointer){
6120+
6121+ mxArray* field = NULL;
6122+
6123+ /*Convert field*/
6124+ WriteData(&field,fieldpointer,M,N);
6125+
6126+ /*Assign to structure*/
6127+ mxSetField(dataref,0,fieldname,field);
6128+}
6129+/*}}}*/
6130+/*FUNCTION SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int M,int N,double* fieldpointer){{{*/
6131+void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int M,int N,double* fieldpointer){
6132+
6133+ mxArray* field = NULL;
6134+
6135+ /*Convert field*/
6136+ WriteData(&field,fieldpointer,M,N);
6137+
6138+ /*Assign to structure*/
6139+ mxSetField(dataref,i,fieldname,field);
6140+}
6141+/*}}}*/
6142+/*FUNCTION SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int field){{{*/
6143+void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int fieldin){
6144+
6145+ mxArray* field = NULL;
6146+
6147+ /*Convert field*/
6148+ WriteData(&field,fieldin);
6149+
6150+ /*Assign to structure*/
6151+ mxSetField(dataref,i,fieldname,field);
6152+}
6153+/*}}}*/
6154+/*FUNCTION SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,double field){{{*/
6155+void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,double fieldin){
6156+
6157+ mxArray* field = NULL;
6158+
6159+ /*Convert field*/
6160+ WriteData(&field,fieldin);
6161+
6162+ /*Assign to structure*/
6163+ mxSetField(dataref,i,fieldname,field);
6164+}
6165+/*}}}*/
6166Index: ../trunk-jpl/src/wrappers/matlab/io/mxGetAssignedField.cpp
6167===================================================================
6168--- ../trunk-jpl/src/wrappers/matlab/io/mxGetAssignedField.cpp (revision 0)
6169+++ ../trunk-jpl/src/wrappers/matlab/io/mxGetAssignedField.cpp (revision 13749)
6170@@ -0,0 +1,39 @@
6171+/*!\file: mxGetAssignedField.c:
6172+ * \brief: abstract interface on parallel side for i/o, so it ressembles the serial i/o.
6173+ *
6174+ * In serial mode, this routine takes care of returning the field coming
6175+ * from the model. If largesize is 1, we are running out of core models in
6176+ * matlab, and we need to call the subsref private method from the model object
6177+ * in order to correctly load the data from disk.
6178+ */
6179+
6180+#include "./matlabio.h"
6181+
6182+mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number,const char* field){
6183+
6184+ //output
6185+ mxArray* mxfield=NULL;
6186+
6187+ //input
6188+ mxArray *inputs[2];
6189+ mxArray *pindex = NULL;
6190+ const char *fnames[2];
6191+ mwSize ndim = 2;
6192+ mwSize onebyone[2] = {1,1};
6193+
6194+ //We want to call the subsasgn method, and get the returned array.This ensures that if we are running
6195+ //large sized problems, the data is truly loaded from disk by the model subsasgn class method.
6196+ inputs[0]=(mxArray*)pmxa_array; //this is the model
6197+
6198+ //create index structure used in the assignment (index.type='.' and index.subs='x' for field x for ex)
6199+ fnames[0] = "type";
6200+ fnames[1] = "subs";
6201+ pindex=mxCreateStructArray( ndim,onebyone,2,fnames);
6202+ mxSetField( pindex, 0, "type",mxCreateString("."));
6203+ mxSetField( pindex, 0, "subs",mxCreateString(field));
6204+ inputs[1]=pindex;
6205+
6206+ mexCallMATLAB( 1, &mxfield, 2, (mxArray**)inputs, "subsref");
6207+
6208+ return mxfield;
6209+}
6210Index: ../trunk-jpl/src/wrappers/matlab/io/MatlabMatrixToDoubleMatrix.cpp
6211===================================================================
6212--- ../trunk-jpl/src/wrappers/matlab/io/MatlabMatrixToDoubleMatrix.cpp (revision 0)
6213+++ ../trunk-jpl/src/wrappers/matlab/io/MatlabMatrixToDoubleMatrix.cpp (revision 13749)
6214@@ -0,0 +1,130 @@
6215+/* \file MatlabMatrixToDoubleMatrix.cpp
6216+ * \brief: convert a sparse or dense matlab matrix to a double* pointer
6217+ */
6218+
6219+#ifdef HAVE_CONFIG_H
6220+ #include <config.h>
6221+#else
6222+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
6223+#endif
6224+
6225+/*Matlab includes: */
6226+#include "./matlabio.h"
6227+#include "../../c/shared/shared.h"
6228+
6229+int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){
6230+
6231+ int i,j,count,rows,cols;
6232+
6233+ /*output: */
6234+ double* matrix=NULL;
6235+
6236+ /*matlab indices: */
6237+ mwIndex* ir=NULL;
6238+ mwIndex* jc=NULL;
6239+
6240+ /*Ok, first check if we are dealing with a sparse or full matrix: */
6241+ if (mxIsSparse(mxmatrix)){
6242+
6243+ /*Dealing with sparse matrix: recover size first: */
6244+ double* pmxmatrix=(double*)mxGetPr(mxmatrix);
6245+ rows=mxGetM(mxmatrix);
6246+ cols=mxGetN(mxmatrix);
6247+
6248+ if(rows*cols){
6249+ matrix=xNewZeroInit<double>(rows*cols);
6250+
6251+ /*Now, get ir,jc and pr: */
6252+ ir=mxGetIr(mxmatrix);
6253+ jc=mxGetJc(mxmatrix);
6254+
6255+ /*Now, start inserting data into double* matrix: */
6256+ count=0;
6257+ for(i=0;i<cols;i++){
6258+ for(j=0;j<(jc[i+1]-jc[i]);j++){
6259+ matrix[rows*ir[count]+i]=pmxmatrix[count];
6260+ count++;
6261+ }
6262+ }
6263+ }
6264+
6265+ }
6266+ else if(mxIsClass(mxmatrix,"double")){
6267+ /*Dealing with dense matrix: recover pointer and size: */
6268+ double* pmxmatrix=(double*)mxGetPr(mxmatrix);
6269+ rows=mxGetM(mxmatrix);
6270+ cols=mxGetN(mxmatrix);
6271+
6272+ /*Create serial matrix: */
6273+ if(rows*cols){
6274+ matrix=xNewZeroInit<double>(rows*cols);
6275+
6276+ for(i=0;i<rows;i++){
6277+ for(j=0;j<cols;j++){
6278+ matrix[cols*i+j]=(double)pmxmatrix[rows*j+i];
6279+ }
6280+ }
6281+ }
6282+ }
6283+ else if(mxIsClass(mxmatrix,"single")){
6284+ /*Dealing with dense matrix: recover pointer and size: */
6285+ float *pmxmatrix=(float*)mxGetPr(mxmatrix);
6286+ rows=mxGetM(mxmatrix);
6287+ cols=mxGetN(mxmatrix);
6288+
6289+ /*Create serial matrix: */
6290+ if(rows*cols){
6291+ matrix=xNewZeroInit<double>(rows*cols);
6292+
6293+ for(i=0;i<rows;i++){
6294+ for(j=0;j<cols;j++){
6295+ matrix[cols*i+j]=(double)pmxmatrix[rows*j+i];
6296+ }
6297+ }
6298+ }
6299+ }
6300+ else if(mxIsClass(mxmatrix,"int16")){
6301+ /*Dealing with dense matrix: recover pointer and size: */
6302+ short int *pmxmatrix=(short*)mxGetPr(mxmatrix);
6303+ rows=mxGetM(mxmatrix);
6304+ cols=mxGetN(mxmatrix);
6305+
6306+ /*Create serial matrix: */
6307+ if(rows*cols){
6308+ matrix=xNewZeroInit<double>(rows*cols);
6309+
6310+ for(i=0;i<rows;i++){
6311+ for(j=0;j<cols;j++){
6312+ matrix[cols*i+j]=(double)pmxmatrix[rows*j+i];
6313+ }
6314+ }
6315+ }
6316+ }
6317+ else if(mxIsClass(mxmatrix,"uint8")){
6318+ /*Dealing with dense matrix: recover pointer and size: */
6319+ char *pmxmatrix=(char*)mxGetPr(mxmatrix);
6320+ rows=mxGetM(mxmatrix);
6321+ cols=mxGetN(mxmatrix);
6322+
6323+ /*Create serial matrix: */
6324+ if(rows*cols){
6325+ matrix=xNewZeroInit<double>(rows*cols);
6326+
6327+ for(i=0;i<rows;i++){
6328+ for(j=0;j<cols;j++){
6329+ matrix[cols*i+j]=(double)pmxmatrix[rows*j+i];
6330+ }
6331+ }
6332+ }
6333+ }
6334+ else{
6335+ _error_("Matlab matrix type Not implemented yet");
6336+ }
6337+
6338+ /*Assign output pointer: */
6339+ *pmatrix=matrix;
6340+ *pmatrix_rows=rows;
6341+ *pmatrix_cols=cols;
6342+
6343+ return 1;
6344+}
6345Index: ../trunk-jpl/src/wrappers/matlab/io/MatlabMatrixToPetscMat.cpp
6346===================================================================
6347--- ../trunk-jpl/src/wrappers/matlab/io/MatlabMatrixToPetscMat.cpp (revision 0)
6348+++ ../trunk-jpl/src/wrappers/matlab/io/MatlabMatrixToPetscMat.cpp (revision 13749)
6349@@ -0,0 +1,122 @@
6350+/* \file MatlabMatrixToPetscMatrix.cpp
6351+ * \brief: convert a sparse or dense matlab matrix to a serial Petsc matrix:
6352+ */
6353+
6354+#ifdef HAVE_CONFIG_H
6355+ #include <config.h>
6356+#else
6357+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
6358+#endif
6359+#include "../../c/shared/shared.h"
6360+
6361+/*Petsc includes: */
6362+#include <petscmat.h>
6363+#include <petscvec.h>
6364+#include <petscksp.h>
6365+
6366+/*Matlab includes: */
6367+#include "./matlabio.h"
6368+
6369+PetscMat* MatlabMatrixToPetscMat(const mxArray* mxmatrix){
6370+
6371+ int dummy;
6372+ PetscMat* matrix=new PetscMat();
6373+
6374+ MatlabMatrixToPetscMat(&matrix->matrix, &dummy, &dummy, mxmatrix);
6375+
6376+ return matrix;
6377+}
6378+int MatlabMatrixToPetscMat(Mat* pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){
6379+
6380+ int rows, cols;
6381+ double *mxmatrix_ptr = NULL;
6382+ double *tmatrix = NULL;
6383+ int ierr;
6384+ int i,j;
6385+
6386+ /*output: */
6387+ Mat matrix = NULL;
6388+
6389+ /*matlab indices: */
6390+ mwIndex *ir = NULL;
6391+ mwIndex *jc = NULL;
6392+ double *pr = NULL;
6393+ int count;
6394+ int nnz;
6395+ int nz;
6396+
6397+ /*petsc indices: */
6398+ int *idxm = NULL;
6399+ int *idxn = NULL;
6400+
6401+ /*Ok, first check if we are dealing with a sparse or full matrix: */
6402+ if (mxIsSparse(mxmatrix)){
6403+
6404+ /*Dealing with sparse matrix: recover size first: */
6405+ mxmatrix_ptr=(double*)mxGetPr(mxmatrix);
6406+ rows=mxGetM(mxmatrix);
6407+ cols=mxGetN(mxmatrix);
6408+ nnz=mxGetNzmax(mxmatrix);
6409+ if(rows){
6410+ nz=(int)((double)nnz/(double)rows);
6411+ }
6412+ else{
6413+ nz=0;
6414+ }
6415+
6416+ ierr=MatCreateSeqAIJ(PETSC_COMM_SELF,rows,cols,nz,PETSC_NULL,&matrix);CHKERRQ(ierr);
6417+
6418+ /*Now, get ir,jc and pr: */
6419+ pr=mxGetPr(mxmatrix);
6420+ ir=mxGetIr(mxmatrix);
6421+ jc=mxGetJc(mxmatrix);
6422+
6423+ /*Now, start inserting data into sparse matrix: */
6424+ count=0;
6425+ for(i=0;i<cols;i++){
6426+ for(j=0;j<(jc[i+1]-jc[i]);j++){
6427+ MatSetValue(matrix,ir[count],i,pr[count],INSERT_VALUES);
6428+ count++;
6429+ }
6430+ }
6431+ }
6432+ else{
6433+ /*Dealing with dense matrix: recover pointer and size: */
6434+ mxmatrix_ptr=(double*)mxGetPr(mxmatrix);
6435+ rows=mxGetM(mxmatrix);
6436+ cols=mxGetN(mxmatrix);
6437+
6438+ /*transpose, as Petsc now does not allows MAT_COLUMN_ORIENTED matrices in MatSetValues: */
6439+ tmatrix=xNew<double>(rows*cols);
6440+ for(i=0;i<cols;i++){
6441+ for(j=0;j<rows;j++){
6442+ *(tmatrix+rows*i+j)=*(mxmatrix_ptr+cols*j+i);
6443+ }
6444+ }
6445+
6446+ /*Create serial matrix: */
6447+ ierr=MatCreateSeqDense(PETSC_COMM_SELF,rows,cols,NULL,&matrix);CHKERRQ(ierr);
6448+
6449+ /*Insert mxmatrix_ptr values into petsc matrix: */
6450+ idxm=xNew<int>(rows);
6451+ idxn=xNew<int>(cols);
6452+
6453+ for(i=0;i<rows;i++)idxm[i]=i;
6454+ for(i=0;i<cols;i++)idxn[i]=i;
6455+
6456+ ierr=MatSetValues(matrix,rows,idxm,cols,idxn,tmatrix,INSERT_VALUES); CHKERRQ(ierr);
6457+
6458+ xDelete<double>(tmatrix);
6459+ }
6460+
6461+ /*Assemble matrix: */
6462+ MatAssemblyBegin(matrix,MAT_FINAL_ASSEMBLY);
6463+ MatAssemblyEnd(matrix,MAT_FINAL_ASSEMBLY);
6464+
6465+ /*Assign output pointer: */
6466+ *pmatrix=matrix;
6467+ if(pmatrix_rows) *pmatrix_rows=rows;
6468+ if(pmatrix_cols) *pmatrix_cols=cols;
6469+
6470+ return 1;
6471+}
6472Index: ../trunk-jpl/src/wrappers/matlab/io/MatlabVectorToVector.cpp
6473===================================================================
6474--- ../trunk-jpl/src/wrappers/matlab/io/MatlabVectorToVector.cpp (revision 0)
6475+++ ../trunk-jpl/src/wrappers/matlab/io/MatlabVectorToVector.cpp (revision 13749)
6476@@ -0,0 +1,31 @@
6477+/*!\file MatlabVectorToVector.cpp
6478+ */
6479+
6480+/*Headers:*/
6481+#ifdef HAVE_CONFIG_H
6482+ #include <config.h>
6483+#else
6484+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
6485+#endif
6486+#include <stdio.h>
6487+#include <string.h>
6488+#include "./matlabio.h"
6489+#include "../../c/shared/shared.h"
6490+#include "../../c/toolkits/toolkits.h"
6491+
6492+Vector<double>* MatlabVectorToVector(const mxArray* mxvector){
6493+
6494+ int dummy;
6495+ Vector<double>* vector=NULL;
6496+
6497+ /*allocate vector object: */
6498+ vector=new Vector<double>();
6499+
6500+ #ifdef _HAVE_PETSC_
6501+ vector->pvector=MatlabVectorToPetscVec(mxvector);
6502+ #else
6503+ vector->svector=MatlabVectorToSeqVec(mxvector);
6504+ #endif
6505+
6506+ return vector;
6507+}
6508Index: ../trunk-jpl/src/wrappers/matlab/io/MatlabMatrixToMatrix.cpp
6509===================================================================
6510--- ../trunk-jpl/src/wrappers/matlab/io/MatlabMatrixToMatrix.cpp (revision 0)
6511+++ ../trunk-jpl/src/wrappers/matlab/io/MatlabMatrixToMatrix.cpp (revision 13749)
6512@@ -0,0 +1,31 @@
6513+/*!\file MatlabMatrixToMatrix.cpp
6514+ */
6515+
6516+#ifdef HAVE_CONFIG_H
6517+ #include <config.h>
6518+#else
6519+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
6520+#endif
6521+
6522+#include <stdio.h>
6523+#include <string.h>
6524+#include "./matlabio.h"
6525+#include "../../c/shared/shared.h"
6526+#include "../../c/toolkits/toolkits.h"
6527+
6528+Matrix<double>* MatlabMatrixToMatrix(const mxArray* mxmatrix){
6529+
6530+ int dummy;
6531+ Matrix<double>* matrix=NULL;
6532+
6533+ /*allocate matrix object: */
6534+ matrix=new Matrix<double>();
6535+
6536+ #ifdef _HAVE_PETSC_
6537+ matrix->pmatrix=MatlabMatrixToPetscMat(mxmatrix);
6538+ #else
6539+ matrix->smatrix=MatlabMatrixToSeqMat(mxmatrix);
6540+ #endif
6541+
6542+ return matrix;
6543+}
6544Index: ../trunk-jpl/src/wrappers/matlab/io/MatlabNArrayToNArray.cpp
6545===================================================================
6546--- ../trunk-jpl/src/wrappers/matlab/io/MatlabNArrayToNArray.cpp (revision 0)
6547+++ ../trunk-jpl/src/wrappers/matlab/io/MatlabNArrayToNArray.cpp (revision 13749)
6548@@ -0,0 +1,250 @@
6549+/* \file MatlabNArrayToNArray.cpp
6550+ * \brief: convert a sparse or dense matlab n-dimensional array to cpp n-dimensional array
6551+ */
6552+
6553+#ifdef HAVE_CONFIG_H
6554+ #include <config.h>
6555+#else
6556+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
6557+#endif
6558+
6559+#include "./matlabio.h"
6560+#include "../../c/shared/shared.h"
6561+#include "../../c/include/include.h"
6562+
6563+/*FUNCTION MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){{{*/
6564+int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){
6565+
6566+ int i,j,rows,cols;
6567+ int numel,ndims;
6568+ int *size,*dims;
6569+ double* mxmatrix_ptr=NULL;
6570+ const mwSize* ipt=NULL;
6571+
6572+ /*output: */
6573+ double* matrix=NULL;
6574+
6575+ /*matlab indices: */
6576+ mwIndex *ir = NULL;
6577+ mwIndex *jc = NULL;
6578+ double *pr = NULL;
6579+ int count;
6580+
6581+ /*get Matlab matrix information: */
6582+ numel=mxGetNumberOfElements(mxmatrix);
6583+ ndims=mxGetNumberOfDimensions(mxmatrix);
6584+ ipt =mxGetDimensions(mxmatrix);
6585+ size =xNew<int>(ndims);
6586+ for (i=0;i<ndims;i++) size[i]=(int)ipt[i];
6587+
6588+ /*Ok, first check if we are dealing with a sparse or full matrix: */
6589+ if (mxIsSparse(mxmatrix)){
6590+
6591+ /*Dealing with sparse matrix: recover size first: */
6592+ rows = mxGetM(mxmatrix);
6593+ cols = mxGetN(mxmatrix);
6594+
6595+ matrix=xNewZeroInit<double>(rows*cols);
6596+
6597+ /*Now, get ir,jc and pr: */
6598+ ir = mxGetIr(mxmatrix);
6599+ jc = mxGetJc(mxmatrix);
6600+ pr = mxGetPr(mxmatrix);
6601+
6602+ /*Now, start inserting data into double* matrix: */
6603+ count=0;
6604+ for(i=0;i<cols;i++){
6605+ for(j=0;j<(jc[i+1]-jc[i]);j++){
6606+ *(matrix+rows*ir[count]+i)=pr[count];
6607+ count++;
6608+ }
6609+ }
6610+
6611+ }
6612+ else{
6613+
6614+ /*Dealing with dense matrix: recover pointer and size: */
6615+ mxmatrix_ptr=(double*)mxGetPr(mxmatrix);
6616+
6617+ /*Create serial matrix: */
6618+ matrix=xNewZeroInit<double>(numel);
6619+
6620+ dims=xNew<int>(ndims);
6621+ for(i=0;i<numel;i++){
6622+ ColumnWiseDimsFromIndex(dims,i,size,ndims);
6623+ j = IndexFromRowWiseDims(dims,size,ndims);
6624+ matrix[j]=(double)mxmatrix_ptr[i];
6625+ }
6626+ xDelete<int>(dims);
6627+ }
6628+
6629+ /*Assign output pointer: */
6630+ *pmatrix = matrix;
6631+ *pmatrix_numel = numel;
6632+ *pmatrix_ndims = ndims;
6633+ *pmatrix_size = size;
6634+
6635+ return 1;
6636+}
6637+/*}}}*/
6638+/*FUNCTION MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){{{*/
6639+int MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){
6640+
6641+ int i,j,rows,cols;
6642+ int numel,ndims;
6643+ int *size,*dims;
6644+ bool* mxmatrix_ptr=NULL;
6645+ const mwSize* ipt=NULL;
6646+
6647+ /*output: */
6648+ bool* matrix=NULL;
6649+
6650+ /*matlab indices: */
6651+ mwIndex *ir = NULL;
6652+ mwIndex *jc = NULL;
6653+ bool *pm = NULL;
6654+ int count;
6655+
6656+ /*get Matlab matrix information: */
6657+ numel = mxGetNumberOfElements(mxmatrix);
6658+ ndims = mxGetNumberOfDimensions(mxmatrix);
6659+ ipt = mxGetDimensions(mxmatrix);
6660+ size = xNew<int>(ndims);
6661+ for (i=0;i<ndims;i++) size[i]=(int)ipt[i];
6662+
6663+ /*Ok, first check if we are dealing with a sparse or full matrix: */
6664+ if (mxIsSparse(mxmatrix)){
6665+
6666+ /*Dealing with sparse matrix: recover size first: */
6667+ rows=mxGetM(mxmatrix);
6668+ cols=mxGetN(mxmatrix);
6669+ matrix=xNewZeroInit<bool>(rows*cols);
6670+
6671+ /*Now, get ir,jc and pm: */
6672+ ir=mxGetIr(mxmatrix);
6673+ jc=mxGetJc(mxmatrix);
6674+ pm=(bool*)mxGetData(mxmatrix);
6675+
6676+ /*Now, start inserting data into bool* matrix: */
6677+ count=0;
6678+ for(i=0;i<cols;i++){
6679+ for(j=0;j<(jc[i+1]-jc[i]);j++){
6680+ matrix[rows*ir[count]+i]=pm[count];
6681+ count++;
6682+ }
6683+ }
6684+ }
6685+ else{
6686+
6687+ /*Dealing with dense matrix: recover pointer and size: */
6688+ mxmatrix_ptr=(bool*)mxGetData(mxmatrix);
6689+
6690+ /*Create serial matrix: */
6691+ matrix=xNew<bool>(numel);
6692+ dims=xNew<int>(ndims);
6693+ for(i=0;i<numel;i++){
6694+ ColumnWiseDimsFromIndex(dims,i,size,ndims);
6695+ j=IndexFromRowWiseDims(dims,size,ndims);
6696+ matrix[j]=(bool)mxmatrix_ptr[i];
6697+ }
6698+ xDelete<int>(dims);
6699+ }
6700+
6701+ /*Assign output pointer: */
6702+ *pmatrix = matrix;
6703+ *pmatrix_numel = numel;
6704+ *pmatrix_ndims = ndims;
6705+ *pmatrix_size = size;
6706+
6707+ return 1;
6708+}
6709+/*}}}*/
6710+/*FUNCTION MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){{{*/
6711+int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){
6712+
6713+ int i,j,rows,cols;
6714+ int numel,ndims;
6715+ int *size , *dims;
6716+ mxChar *mxmatrix_ptr = NULL;
6717+ const mwSize *ipt = NULL;
6718+
6719+ /*output: */
6720+ char* matrix=NULL;
6721+
6722+ /*matlab indices: */
6723+ mwIndex *ir = NULL;
6724+ mwIndex *jc = NULL;
6725+ char *pm = NULL;
6726+ int count;
6727+
6728+ /*get Matlab matrix information: */
6729+ numel = mxGetNumberOfElements(mxmatrix);
6730+ ndims = mxGetNumberOfDimensions(mxmatrix);
6731+ ipt = mxGetDimensions(mxmatrix);
6732+ size = xNew<int>(ndims);
6733+ for (i=0;i<ndims;i++) size[i]=(int)ipt[i];
6734+
6735+ /*Ok, first check if we are dealing with a sparse or full matrix: */
6736+ if (mxIsSparse(mxmatrix)){
6737+
6738+ /*Dealing with sparse matrix: recover size first: */
6739+ rows = mxGetM(mxmatrix);
6740+ cols = mxGetN(mxmatrix);
6741+ matrix=xNew<char>(rows*cols);
6742+
6743+ /*Now, get ir,jc and pm: */
6744+ ir = mxGetIr(mxmatrix);
6745+ jc = mxGetJc(mxmatrix);
6746+ pm = (char*)mxGetData(mxmatrix);
6747+
6748+ /*Now, start inserting data into char* matrix: */
6749+ count=0;
6750+ for(i=0;i<cols;i++){
6751+ for(j=0;j<(jc[i+1]-jc[i]);j++){
6752+ matrix[rows*ir[count]+i]=(char)pm[count];
6753+ count++;
6754+ }
6755+ }
6756+ }
6757+ else{
6758+ /*Dealing with dense matrix: recover pointer and size: */
6759+ mxmatrix_ptr=mxGetChars(mxmatrix);
6760+
6761+ /*Create serial matrix: */
6762+ matrix=xNew<char>(numel+1);
6763+ matrix[numel]='\0';
6764+
6765+ /*looping code adapted from Matlab example explore.c: */
6766+ int elements_per_page = size[0] * size[1];
6767+ /* total_number_of_pages = size[2] x size[3] x ... x size[N-1] */
6768+ int total_number_of_pages = 1;
6769+ for (i=2; i<ndims; i++) {
6770+ total_number_of_pages *= size[i];
6771+ }
6772+
6773+ i=0;
6774+ for (int page=0; page < total_number_of_pages; page++) {
6775+ int row;
6776+ /* On each page, walk through each row. */
6777+ for (row=0; row<size[0]; row++) {
6778+ int column;
6779+ j = (page * elements_per_page) + row;
6780+
6781+ /* Walk along each column in the current row. */
6782+ for (column=0; column<size[1]; column++) {
6783+ *(matrix+i++)=(char)*(mxmatrix_ptr+j);
6784+ j += size[0];
6785+ }
6786+ }
6787+ }
6788+ }
6789+
6790+ /*Assign output pointer: */
6791+ *pmatrix = matrix;
6792+ *pmatrix_numel = numel;
6793+ *pmatrix_ndims = ndims;
6794+ *pmatrix_size = size;
6795+
6796+ return 1;
6797+}
6798+/*}}}*/
6799Index: ../trunk-jpl/src/wrappers/matlab/io/MatlabVectorToSeqVec.cpp
6800===================================================================
6801--- ../trunk-jpl/src/wrappers/matlab/io/MatlabVectorToSeqVec.cpp (revision 0)
6802+++ ../trunk-jpl/src/wrappers/matlab/io/MatlabVectorToSeqVec.cpp (revision 13749)
6803@@ -0,0 +1,20 @@
6804+/*!\file MatlabVectorToSeqVec.cpp
6805+ */
6806+
6807+/*Headers:*/
6808+#include <mex.h>
6809+#include <stdio.h>
6810+#include <string.h>
6811+#include "./matlabio.h"
6812+#include "../../c/toolkits/toolkits.h"
6813+#include "../../c/shared/shared.h"
6814+
6815+SeqVec<double>* MatlabVectorToSeqVec(const mxArray* dataref){
6816+
6817+ SeqVec<double>* output=NULL;
6818+
6819+ output=new SeqVec<double>();
6820+ MatlabVectorToDoubleVector(&output->vector,&output->M,dataref);
6821+ return output;
6822+
6823+}
6824Index: ../trunk-jpl/src/wrappers/matlab/io/matlabio.h
6825===================================================================
6826--- ../trunk-jpl/src/wrappers/matlab/io/matlabio.h (revision 0)
6827+++ ../trunk-jpl/src/wrappers/matlab/io/matlabio.h (revision 13749)
6828@@ -0,0 +1,93 @@
6829+/*\file matlabio.h
6830+ *\brief: I/O for ISSM in matlab mode
6831+ */
6832+
6833+#ifndef _MATLAB_IO_H_
6834+#define _MATLAB_IO_H_
6835+
6836+#ifdef HAVE_CONFIG_H
6837+#include <config.h>
6838+#else
6839+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
6840+#endif
6841+
6842+#include "../include/matlabincludes.h"
6843+#include "../../c/classes/classes.h"
6844+#include "../../c/Container/Container.h"
6845+#include "../../c/include/include.h"
6846+
6847+void WriteData(mxArray** pdataref,SeqMat<double>* matrix);
6848+void WriteData(mxArray** pdataref,double* matrix, int M,int N);
6849+void WriteData(mxArray** pdataref,int* matrix, int M,int N);
6850+void WriteData(mxArray** pdataref,SeqVec<double>* vector);
6851+void WriteData(mxArray** pdataref,double* vector, int M);
6852+void WriteData(mxArray** pdataref,int integer);
6853+void WriteData(mxArray** pdataref,bool boolean);
6854+void WriteData(mxArray** pdataref,double scalar);
6855+void WriteData(mxArray** pdataref,char* string);
6856+void WriteData(mxArray** pdataref);
6857+void WriteData(mxArray** pdataref,BamgGeom* bamggeom);
6858+void WriteData(mxArray** pdataref,BamgMesh* bamgmesh);
6859+void WriteData(mxArray** pdataref,RiftStruct* riftstruct);
6860+
6861+void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref);
6862+void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref);
6863+void FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref);
6864+void FetchData(bool** pmatrix,int* pM,int *pN,const mxArray* dataref);
6865+void FetchData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref);
6866+void FetchData(Matrix<double>** pmatrix,const mxArray* dataref);
6867+void FetchData(int** pvector,int* pM,const mxArray* dataref);
6868+void FetchData(float** pvector,int* pM,const mxArray* dataref);
6869+void FetchData(double** pvector,int* pM,const mxArray* dataref);
6870+void FetchData(bool** pvector,int* pM,const mxArray* dataref);
6871+void FetchData(Vector<double>** pvector,const mxArray* dataref);
6872+void FetchData(char** pstring,const mxArray* dataref);
6873+void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref);
6874+void FetchData(double* pscalar,const mxArray* dataref);
6875+void FetchData(int* pinteger,const mxArray* dataref);
6876+void FetchData(bool* pbool,const mxArray* dataref);
6877+void FetchData(BamgGeom** bamggeom,const mxArray* dataref);
6878+void FetchData(BamgMesh** bamgmesh,const mxArray* dataref);
6879+void FetchData(BamgOpts** bamgopts,const mxArray* dataref);
6880+void FetchData(Options** poptions,int istart, int nrhs,const mxArray** pdataref);
6881+void FetchData(DataSet** pcontours,const mxArray* dataref);
6882+
6883+Option* OptionParse(char* name, const mxArray* prhs[]);
6884+GenericOption<double>* OptionDoubleParse( char* name, const mxArray* prhs[]);
6885+GenericOption<double*>* OptionDoubleArrayParse( char* name, const mxArray* prhs[]);
6886+GenericOption<bool*>* OptionLogicalParse( char* name, const mxArray* prhs[]);
6887+GenericOption<char*>* OptionCharParse( char* name, const mxArray* prhs[]);
6888+GenericOption<Options**>* OptionStructParse( char* name, const mxArray* prhs[]);
6889+GenericOption<Options*>* OptionCellParse( char* name, const mxArray* prhs[]);
6890+
6891+mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number, const char* field);
6892+void SetStructureField(mxArray* dataref,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer);
6893+void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer);
6894+void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,int field);
6895+void SetStructureFieldi(mxArray* dataref,int i,const char* fieldname,double field);
6896+int CheckNumMatlabArguments(int nlhs,int NLHS, int nrhs,int NRHS, const char* THISFUNCTION, void (*function)( void ));
6897+
6898+/*Matlab to Matrix routines: */
6899+Matrix<double>* MatlabMatrixToMatrix(const mxArray* mxmatrix);
6900+Vector<double>* MatlabVectorToVector(const mxArray* mxvector);
6901+
6902+/*Matlab to double* routines: */
6903+int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector);
6904+int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix);
6905+int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix);
6906+int MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix);
6907+int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix);
6908+
6909+/*Matlab to SeqMat routines: */
6910+SeqMat<double>* MatlabMatrixToSeqMat(const mxArray* dataref);
6911+SeqVec<double>* MatlabVectorToSeqVec(const mxArray* dataref);
6912+
6913+/*Matlab to Petsc routines: */
6914+#ifdef _HAVE_PETSC_
6915+int MatlabMatrixToPetscMat(Mat* matrix,int* prows,int* pcols, const mxArray* mxmatrix);
6916+PetscMat* MatlabMatrixToPetscMat(const mxArray* mxmatrix);
6917+int MatlabVectorToPetscVec(Vec* pvector,int* pvector_rows,const mxArray* mxvector);
6918+PetscVec* MatlabVectorToPetscVec(const mxArray* mxvector);
6919+#endif
6920+
6921+#endif /* _IO_H_ */
6922Index: ../trunk-jpl/src/wrappers/matlab/Makefile.am
6923===================================================================
6924--- ../trunk-jpl/src/wrappers/matlab/Makefile.am (revision 13748)
6925+++ ../trunk-jpl/src/wrappers/matlab/Makefile.am (revision 13749)
6926@@ -1,10 +1,40 @@
6927-AM_CPPFLAGS = @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ @ADOLCINCL@
6928+AM_CPPFLAGS = @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@
6929
6930 EXEEXT=$(MATLABWRAPPEREXT)
6931
6932+#matlab io{{{
6933+lib_LIBRARIES = libISSMMatlab.a
6934+if SHAREDLIBS
6935+lib_LTLIBRARIES = libISSMMatlab.la
6936+else
6937+lib_LTLIBRARIES =
6938+endif
6939+
6940+io_sources= ./include/matlabincludes.h\
6941+ ./io/matlabio.h\
6942+ ./io/MatlabNArrayToNArray.cpp\
6943+ ./io/CheckNumMatlabArguments.cpp\
6944+ ./io/mxGetAssignedField.cpp\
6945+ ./io/WriteMatlabData.cpp\
6946+ ./io/FetchMatlabData.cpp\
6947+ ./io/OptionParse.cpp\
6948+ ./io/MatlabMatrixToMatrix.cpp\
6949+ ./io/MatlabVectorToVector.cpp\
6950+ ./io/MatlabVectorToDoubleVector.cpp\
6951+ ./io/MatlabMatrixToDoubleMatrix.cpp\
6952+ ./io/MatlabMatrixToSeqMat.cpp\
6953+ ./io/MatlabVectorToSeqVec.cpp
6954+
6955+ALLCXXFLAGS= -fPIC -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS)
6956+libISSMMatlab_a_SOURCES = $(io_sources)
6957+libISSMMatlab_a_CXXFLAGS= $(ALLCXXFLAGS)
6958+if SHAREDLIBS
6959+libISSMMatlab_la_SOURCES = $(io_sources)
6960+endif
6961+#}}}
6962 #Wrappers {{{
6963 if WRAPPERS
6964-lib_LTLIBRARIES = AverageFilter.la\
6965+lib_LTLIBRARIES += AverageFilter.la\
6966 BamgMesher.la\
6967 BamgConvertMesh.la\
6968 BamgTriangulate.la\
6969@@ -45,7 +75,6 @@
6970 Kml2Exp.la
6971 endif
6972 endif
6973-
6974 #}}}
6975 #Flags and libraries {{{
6976 #if SHAREDLIBS
6977@@ -67,9 +96,9 @@
6978 AM_LDFLAGS += -avoid-version
6979 endif
6980 if SHAREDLIBS
6981-deps += ../../c/libISSMMatlab.la
6982+deps += ./libISSMMatlab.la
6983 else
6984-deps += ../../c/libISSMMatlab.a
6985+deps += ./libISSMMatlab.a
6986 AM_LDFLAGS += --no-warnings
6987 endif
6988
6989Index: ../trunk-jpl/src/wrappers/BamgTriangulate/BamgTriangulate.h
6990===================================================================
6991--- ../trunk-jpl/src/wrappers/BamgTriangulate/BamgTriangulate.h (revision 13748)
6992+++ ../trunk-jpl/src/wrappers/BamgTriangulate/BamgTriangulate.h (revision 13749)
6993@@ -20,7 +20,7 @@
6994 #include "../../c/modules/modules.h"
6995 #include "../../c/Container/Container.h"
6996 #include "../../c/shared/shared.h"
6997-#include "../../c/issm-binding.h"
6998+#include "../bindings.h"
6999
7000 #undef __FUNCT__
7001 #define __FUNCT__ "BamgTriangulate"
7002Index: ../trunk-jpl/src/wrappers/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h
7003===================================================================
7004--- ../trunk-jpl/src/wrappers/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h (revision 13748)
7005+++ ../trunk-jpl/src/wrappers/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h (revision 13749)
7006@@ -23,7 +23,7 @@
7007 #include "../../c/modules/modules.h"
7008 #include "../../c/Container/Container.h"
7009 #include "../../c/shared/shared.h"
7010-#include "../../c/issm-binding.h"
7011+#include "../bindings.h"
7012 #include "../../c/io/io.h"
7013 #include "../../c/EnumDefinitions/EnumDefinitions.h"
7014
7015Index: ../trunk-jpl/src/wrappers/ContourToMesh/ContourToMesh.h
7016===================================================================
7017--- ../trunk-jpl/src/wrappers/ContourToMesh/ContourToMesh.h (revision 13748)
7018+++ ../trunk-jpl/src/wrappers/ContourToMesh/ContourToMesh.h (revision 13749)
7019@@ -23,7 +23,7 @@
7020 #include "../../c/modules/modules.h"
7021 #include "../../c/Container/Container.h"
7022 #include "../../c/shared/shared.h"
7023-#include "../../c/issm-binding.h"
7024+#include "../bindings.h"
7025 #include "../../c/io/io.h"
7026 #include "../../c/EnumDefinitions/EnumDefinitions.h"
7027
7028Index: ../trunk-jpl/src/wrappers/Xy2ll/Xy2ll.h
7029===================================================================
7030--- ../trunk-jpl/src/wrappers/Xy2ll/Xy2ll.h (revision 13748)
7031+++ ../trunk-jpl/src/wrappers/Xy2ll/Xy2ll.h (revision 13749)
7032@@ -20,7 +20,7 @@
7033 #include "../../c/modules/modules.h"
7034 #include "../../c/Container/Container.h"
7035 #include "../../c/shared/shared.h"
7036-#include "../../c/issm-binding.h"
7037+#include "../bindings.h"
7038
7039 #undef __FUNCT__
7040 #define __FUNCT__ "Xy2ll"
7041Index: ../trunk-jpl/src/wrappers/KMLMeshWrite/KMLMeshWrite.h
7042===================================================================
7043--- ../trunk-jpl/src/wrappers/KMLMeshWrite/KMLMeshWrite.h (revision 13748)
7044+++ ../trunk-jpl/src/wrappers/KMLMeshWrite/KMLMeshWrite.h (revision 13749)
7045@@ -20,7 +20,7 @@
7046 #include "../../c/modules/modules.h"
7047 #include "../../c/Container/Container.h"
7048 #include "../../c/shared/shared.h"
7049-#include "../../c/issm-binding.h"
7050+#include "../bindings.h"
7051
7052 #undef __FUNCT__
7053 #define __FUNCT__ "KMLMeshWrite"
7054Index: ../trunk-jpl/src/wrappers/TriMesh/TriMesh.h
7055===================================================================
7056--- ../trunk-jpl/src/wrappers/TriMesh/TriMesh.h (revision 13748)
7057+++ ../trunk-jpl/src/wrappers/TriMesh/TriMesh.h (revision 13749)
7058@@ -23,7 +23,7 @@
7059 #include "../../c/modules/modules.h"
7060 #include "../../c/Container/Container.h"
7061 #include "../../c/shared/shared.h"
7062-#include "../../c/issm-binding.h"
7063+#include "../bindings.h"
7064 #include "../../c/io/io.h"
7065 #include "../../c/EnumDefinitions/EnumDefinitions.h"
7066
7067Index: ../trunk-jpl/src/wrappers/Chaco/Chaco.h
7068===================================================================
7069--- ../trunk-jpl/src/wrappers/Chaco/Chaco.h (revision 13748)
7070+++ ../trunk-jpl/src/wrappers/Chaco/Chaco.h (revision 13749)
7071@@ -24,7 +24,7 @@
7072 #include "../../c/modules/modules.h"
7073 #include "../../c/Container/Container.h"
7074 #include "../../c/shared/shared.h"
7075-#include "../../c/issm-binding.h"
7076+#include "../bindings.h"
7077
7078 #undef __FUNCT__
7079 #define __FUNCT__ "Chaco"
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