From 762d31ddf4d5342b871dc607f8a2a7ae5802a7d7 Mon Sep 17 00:00:00 2001
From: Jonathan Lambrechts <jonathan.lambrechts@uclouvain.be>
Date: Thu, 31 Oct 2013 15:58:06 +0000
Subject: [PATCH] python : transparent conversion from numpy vector to
fullMatrix(in place when possible)
---
CMakeLists.txt | 40 ++++++----
Common/GmshConfig.h.in | 1 +
wrappers/gmshpy/gmshCommon.i | 1 +
wrappers/gmshpy/gmshGeo.i | 1 +
wrappers/gmshpy/gmshMesh.i | 1 +
wrappers/gmshpy/gmshNumeric.i | 1 +
wrappers/gmshpy/gmshPost.i | 1 +
wrappers/gmshpy/gmshSolver.i | 1 +
wrappers/gmshpy/gmshtypemaps.i | 129 +++++++++++++++++++++++++++++++++
9 files changed, 163 insertions(+), 13 deletions(-)
create mode 100644 wrappers/gmshpy/gmshtypemaps.i
diff --git a/CMakeLists.txt b/CMakeLists.txt
index aff6ab2830..e4a2f61307 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -61,6 +61,7 @@ opt(MSVC_STATIC_RUNTIME "Enable static Visual C++ runtime" OFF)
opt(MUMPS "Enable MUMPS sparse direct linear solver" OFF)
opt(NATIVE_FILE_CHOOSER "Enable native file chooser in GUI" ${DEFAULT})
opt(NETGEN "Enable Netgen 3D frontal mesh generator" ${DEFAULT})
+opt(NUMPY "Enable conversion between fullMatrix and numpy array (requires SWIG)" OFF)
opt(OCC "Enable Open CASCADE geometrical models" ${DEFAULT})
opt(ONELAB "Enable OneLab solver interface" ${DEFAULT})
opt(ONELAB_METAMODEL "Enable OneLab metamodels (experimental)" ${DEFAULT})
@@ -1052,6 +1053,29 @@ if(ENABLE_ACIS)
endif(ACIS_LIB)
endif(ENABLE_ACIS)
+if(ENABLE_WRAP_PYTHON)
+ find_package(SWIG)
+ find_package(PythonLibs)
+ if(SWIG_FOUND AND PYTHONLIBS_FOUND)
+ message(STATUS "Found SWIG version " ${SWIG_VERSION})
+ string(SUBSTRING ${SWIG_VERSION} 0 1 SWIG_MAJOR_VERSION)
+ if(SWIG_MAJOR_VERSION EQUAL 1)
+ message(WARNING "Python bindings require SWIG >= 2: disabling Python")
+ else(SWIG_MAJOR_VERSION EQUAL 1)
+ set_config_option(HAVE_PYTHON "Python")
+ endif(SWIG_MAJOR_VERSION EQUAL 1)
+ endif(SWIG_FOUND AND PYTHONLIBS_FOUND)
+endif(ENABLE_WRAP_PYTHON)
+
+if(HAVE_PYTHON)
+ if(ENABLE_NUMPY)
+ find_path(NUMPY_INC "numpyconfig.h" HINTS ${PYTHON_INCLUDE_PATH} PATH_SUFFIXES /numpy)
+ if(NUMPY_INC)
+ set_config_option(HAVE_NUMPY "Numpy")
+ endif(NUMPY_INC)
+ endif(ENABLE_NUMPY)
+endif(HAVE_PYTHON)
+
check_function_exists(vsnprintf HAVE_VSNPRINTF)
if(NOT HAVE_VSNPRINTF AND NOT ENABLE_BUILD_IOS)
set_config_option(HAVE_NO_VSNPRINTF "NoVsnprintf")
@@ -1576,19 +1600,9 @@ else(APPLE AND ENABLE_OS_SPECIFIC_INSTALL)
set(CPACK_GENERATOR TGZ)
endif(APPLE AND ENABLE_OS_SPECIFIC_INSTALL)
-if(ENABLE_WRAP_PYTHON)
- find_package(SWIG)
- find_package(PythonLibs)
- if(SWIG_FOUND AND PYTHONLIBS_FOUND)
- message(STATUS "Found SWIG version " ${SWIG_VERSION})
- string(SUBSTRING ${SWIG_VERSION} 0 1 SWIG_MAJOR_VERSION)
- if(SWIG_MAJOR_VERSION EQUAL 1)
- message(WARNING "Python bindings require SWIG >= 2: disabling Python")
- else(SWIG_MAJOR_VERSION EQUAL 1)
- add_subdirectory(wrappers/gmshpy)
- endif(SWIG_MAJOR_VERSION EQUAL 1)
- endif(SWIG_FOUND AND PYTHONLIBS_FOUND)
-endif(ENABLE_WRAP_PYTHON)
+if (HAVE_PYTHON)
+ add_subdirectory(wrappers/gmshpy)
+endif(HAVE_PYTHON)
if(ENABLE_WRAP_JAVA)
if(NOT HAVE_BLAS OR NOT HAVE_LAPACK)
diff --git a/Common/GmshConfig.h.in b/Common/GmshConfig.h.in
index 1edfc74682..cf3c81d219 100644
--- a/Common/GmshConfig.h.in
+++ b/Common/GmshConfig.h.in
@@ -39,6 +39,7 @@
#cmakedefine HAVE_MUMPS
#cmakedefine HAVE_NATIVE_FILE_CHOOSER
#cmakedefine HAVE_NETGEN
+#cmakedefine HAVE_NUMPY
#cmakedefine HAVE_NO_INTPTR_T
#cmakedefine HAVE_NO_SOCKLEN_T
#cmakedefine HAVE_NO_STDINT_H
diff --git a/wrappers/gmshpy/gmshCommon.i b/wrappers/gmshpy/gmshCommon.i
index 47f02845dc..1efbdca9bd 100644
--- a/wrappers/gmshpy/gmshCommon.i
+++ b/wrappers/gmshpy/gmshCommon.i
@@ -5,6 +5,7 @@
%include std_vector.i
%include std_map.i
%include cpointer.i
+%import "gmshtypemaps.i"
%{
#include "GmshConfig.h"
diff --git a/wrappers/gmshpy/gmshGeo.i b/wrappers/gmshpy/gmshGeo.i
index a44493370a..da667b3997 100644
--- a/wrappers/gmshpy/gmshGeo.i
+++ b/wrappers/gmshpy/gmshGeo.i
@@ -4,6 +4,7 @@
%include std_string.i
%include std_list.i
%include std_vector.i
+%import "gmshtypemaps.i"
%{
#include "GmshConfig.h"
diff --git a/wrappers/gmshpy/gmshMesh.i b/wrappers/gmshpy/gmshMesh.i
index 38836cae21..c35f1392a6 100644
--- a/wrappers/gmshpy/gmshMesh.i
+++ b/wrappers/gmshpy/gmshMesh.i
@@ -2,6 +2,7 @@
%module gmshMesh
%include std_string.i
%include std_list.i
+%import "gmshtypemaps.i"
%{
#include "GmshConfig.h"
diff --git a/wrappers/gmshpy/gmshNumeric.i b/wrappers/gmshpy/gmshNumeric.i
index 7f564e759e..9fca5e851b 100644
--- a/wrappers/gmshpy/gmshNumeric.i
+++ b/wrappers/gmshpy/gmshNumeric.i
@@ -3,6 +3,7 @@
%include std_string.i
%include std_vector.i
+%import "gmshtypemaps.i"
%{
#include "GmshConfig.h"
diff --git a/wrappers/gmshpy/gmshPost.i b/wrappers/gmshpy/gmshPost.i
index 46ad08d599..d30cc19dba 100644
--- a/wrappers/gmshpy/gmshPost.i
+++ b/wrappers/gmshpy/gmshPost.i
@@ -4,6 +4,7 @@
%include std_string.i
%include std_vector.i
%include std_map.i
+%import "gmshtypemaps.i"
%{
#include "GmshConfig.h"
diff --git a/wrappers/gmshpy/gmshSolver.i b/wrappers/gmshpy/gmshSolver.i
index 20b8e64462..2743ac5be8 100644
--- a/wrappers/gmshpy/gmshSolver.i
+++ b/wrappers/gmshpy/gmshSolver.i
@@ -3,6 +3,7 @@
%include std_string.i
%include std_vector.i
%include std_complex.i
+%import "gmshtypemaps.i"
%{
#include "GmshConfig.h"
diff --git a/wrappers/gmshpy/gmshtypemaps.i b/wrappers/gmshpy/gmshtypemaps.i
new file mode 100644
index 0000000000..fbc81f41c2
--- /dev/null
+++ b/wrappers/gmshpy/gmshtypemaps.i
@@ -0,0 +1,129 @@
+%fragment("fullMatrixConversionInit", "init") {
+ %#ifdef HAVE_NUMPY
+ import_array();
+ %#endif
+}
+
+%fragment("fullMatrixConversion", "header", fragment="fullMatrixConversionInit") {
+ %#include "fullMatrix.h"
+ %#include "GmshConfig.h"
+ %#ifdef HAVE_NUMPY
+ %#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+ %#include <numpy/arrayobject.h>
+ %#if NPY_API_VERSION < 0x00000007
+ %#define NPY_ARRAY_FARRAY NPY_FARRAY
+ %#endif
+ %#endif
+ fullMatrix<double> *pySequenceToFullMatrixDouble(PyObject *o) {
+ fullMatrix<double> *fm;
+ if (!PySequence_Check(o))
+ return NULL;
+ long int nRow = PySequence_Length(o);
+ for (int i = 0; i < PySequence_Length(o); ++i) {
+ PyObject *l = PySequence_GetItem(o, i);
+ long int nCol = PySequence_Length(l);
+ if (i == 0)
+ fm = new fullMatrix<double>(nRow, nCol);
+ else if (nCol != fm->size2()) {
+ delete fm;
+ return NULL;
+ }
+ for (int j = 0; j < nCol; ++j) {
+ PyObject *v = PySequence_GetItem(l, j);
+ if (PyNumber_Check(v)) {
+ (*fm)(i, j) = (float) PyFloat_AsDouble(v);
+ }
+ else {
+ delete fm;
+ return NULL;
+ }
+ }
+ }
+ return fm;
+ }
+
+ fullMatrix<double> *objToFullMatrixRO(PyObject *obj, bool &newMatrix, PyObject *&tmpObject)
+ {
+ fullMatrix<double> *fm = NULL;
+ SWIG_ConvertPtr(obj,(void **) &fm, SWIGTYPE_p_fullMatrixT_double_t, 1);
+ if (fm)
+ return fm;
+ %#ifdef HAVE_NUMPY
+ PyArrayObject *array = (PyArrayObject*)obj;
+ if (PyArray_Check(array) && PyArray_ISFARRAY_RO(array) && PyArray_NDIM(array) == 2) {
+ newMatrix = true;
+ return new fullMatrix<double>((double*)PyArray_DATA(array), PyArray_DIM(array, 0), PyArray_DIM(array, 1));
+ }
+ if ((tmpObject = PyArray_FROMANY(obj, NPY_DOUBLE, 2, 2, NPY_ARRAY_FARRAY))) {
+ array = (PyArrayObject*)tmpObject;
+ newMatrix = true;
+ return new fullMatrix<double>((double*)PyArray_DATA(array), PyArray_DIM(array, 0), PyArray_DIM(array, 1));
+ }
+ %#endif
+ if ((fm = pySequenceToFullMatrixDouble(obj)))
+ newMatrix = true;
+ return fm;
+ }
+
+ fullMatrix<double> *objToFullMatrixRW(PyObject *obj, bool &newMatrix)
+ {
+ fullMatrix<double> *fm = NULL;
+ SWIG_ConvertPtr(obj,(void **) &fm, SWIGTYPE_p_fullMatrixT_double_t, 1);
+ if (fm)
+ return fm;
+ %#ifdef HAVE_NUMPY
+ PyArrayObject *array = (PyArrayObject*)obj;
+ if (PyArray_Check(array) && PyArray_ISFARRAY(array) && PyArray_NDIM(array) == 2) {
+ newMatrix = true;
+ return new fullMatrix<double>((double*)PyArray_DATA(array), PyArray_DIM(array, 0), PyArray_DIM(array, 1));
+ }
+ %#endif
+ return NULL;
+ }
+}
+
+%typemap(in, fragment="fullMatrixConversion") const fullMatrix<double> &(PyObject *tmpObject = NULL, bool newMatrix = false){
+ $1 = objToFullMatrixRO($input, newMatrix, tmpObject);
+ if (!$1) {
+ PyErr_Format(PyExc_TypeError, "cannot convert argument %i to a fullMatrix<double>", $argnum);
+ SWIG_fail;
+ }
+}
+%typemap(freearg) const fullMatrix<double> &{
+ if (tmpObject$argnum) Py_DECREF(tmpObject$argnum);
+ if (newMatrix$argnum && $1) delete $1;
+}
+
+%typemap(in, fragment="fullMatrixConversion") fullMatrix<double> &(bool newMatrix = false){
+ $1 = objToFullMatrixRW($input, newMatrix);
+ if (!$1) {
+ PyErr_Format(PyExc_TypeError, "cannot convert argument %i to a writable fullMatrix<double>", $argnum);
+ SWIG_fail;
+ }
+}
+%typemap(freearg) fullMatrix<double> &{
+ if (newMatrix$argnum && $1) delete $1;
+}
+
+%typemap(in, fragment="fullMatrixConversion") const fullMatrix<double> *(PyObject *tmpObject = NULL, bool newMatrix = false){
+ $1 = objToFullMatrixRO($input, newMatrix, tmpObject);
+ if (!$1) {
+ PyErr_Format(PyExc_TypeError, "cannot convert argument %i to a fullMatrix<double>", $argnum);
+ SWIG_fail;
+ }
+}
+%typemap(freearg) const fullMatrix<double> *{
+ if (tmpObject$argnum) Py_DECREF(tmpObject$argnum);
+ if (newMatrix$argnum && $1) delete $1;
+}
+
+%typemap(in, fragment="fullMatrixConversion") fullMatrix<double> *(bool newMatrix = false){
+ $1 = objToFullMatrixRW($input, newMatrix);
+ if (!$1) {
+ PyErr_Format(PyExc_TypeError, "cannot convert argument %i to a writable fullMatrix<double>", $argnum);
+ SWIG_fail;
+ }
+}
+%typemap(freearg) fullMatrix<double> *{
+ if (newMatrix$argnum && $1) delete $1;
+}
--
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