Changeset 25

Timestamp:

05/22/07 01:01:01 (2 years ago)

Author:

emuller

Message:

--with-nrnpython optional python binary, conditional numpy support in nrnpython

Files:

• branches/pygetsetcall/configure.in (modified) (1 diff)
• branches/pygetsetcall/m4/nrnpython.m4 (modified) (6 diffs)
• branches/pygetsetcall/src/nrnpython/nrnpy_hoc.cpp (modified) (6 diffs)
• branches/pygetsetcall/src/nrnpython/setup.py.in (modified) (2 diffs)

branches/pygetsetcall/configure.in

@@ -441 +441 @@
-
-if test "$exec_prefix" = "NONE" ; then
-
+
+
+
-fi
-

branches/pygetsetcall/m4/nrnpython.m4

@@ -2 +2 @@
-        dnl determine configuration if able to  run python
-        ac_nrn_pyconf_val=""
-python
+$4
-print distutils.sysconfig.get_config_var('[$2]')"`
-        if test $? != 0 ; then
@@ -59 +59 @@
-
-        AC_ARG_WITH([nrnpython],
-
+=[desired python binary]
-                        [Python interpreter can be used (default is NO)
-Probably need to set PYLIBDIR to find libpython...
@@ -67 +67 @@
-        )
-
+        if test "$ac_nrn_python" = "yes" ; then
+                ac_nrn_python="python"
+        fi
+
+
-        if test "$ac_nrn_python" != "no" ; then
+                
-                AC_MSG_CHECKING([nrnpython configuration])
-                NRN_DEFINE(USE_PYTHON,1,[define if Python available])
-                if test "$PYVER" = "" ; then
-
+,$ac_nrn_python
-                        PYVER=python${xxx}
-                fi
-                if test "$PYINCDIR" = "" ; then
-
+,$ac_nrn_python
-                        if test "$xxx" = "" ; then
-                                PYINCDIR="$HOME/python/include/${PYVER}"
@@ -83 +89 @@
-                fi
-                if test "$EXTRAPYLIBS" = "" ; then
-
+,$ac_nrn_python
-                fi
-                if test "$PYLIB" = "" ; then
-                        case "$host_os" in
-                        darwin*)
-
+,$ac_nrn_python
-                                PYLIB="$xxx"
-                                PYLIBLINK="$PYLIB"
-                                ;;
-                        *)
-
+,$ac_nrn_python
-                                PYLINKFORSHARED="$xxx"                          
-
+,$ac_nrn_python
-                                if test "$xxx" = "" ; then
-                                        PYLIBDIR="$HOME/python/lib"
@@ -110 +116 @@
-                NRNPYTHON_DEP="../nrnpython/libnrnpython.la"
-                NRNPYTHON_INCLUDES="-I${PYINCDIR}"
+
+                CMD="import numpy;print numpy.__path__@<:@0@:>@ + '''/core/include''' "
+                PYTHON_NUMPY_INCLUDE=`${ac_nrn_python} -c "${CMD}"`
+
+                if test "$PYTHON_NUMPY_INCLUDE" != ""; then
+                        HAVE_NUMPY="yes"
+                        NRNPYTHON_INCLUDES="${NRNPYTHON_INCLUDES} -I${PYTHON_NUMPY_INCLUDE}"
+                        NRNPYTHON_DEFINES="-DWITH_NUMPY"
+                else
+                        HAVE_NUMPY="no"
+                        NRNPYTHON_DEFINES="-UWITH_NUMPY"
+                fi
+
+                build_nrnpython=yes
+
-                build_nrnpython=yes
-                AC_NRN_RUNPYTHON
@@ -117 +138 @@
-        AC_SUBST(NRNPYTHON_DEP)
-        AC_SUBST(NRNPYTHON_INCLUDES)
+        AC_SUBST(NRNPYTHON_DEFINES)
+
-
-]) dnl end of AC_NRN_PYTHON

branches/pygetsetcall/src/nrnpython/nrnpy_hoc.cpp

@@ -5 +5 @@
-#include <ivoc.h>
-#include <ocjump.h>
+
+#ifdef WITH_NUMPY
+
+// needed for C extension using NumPy
+#define PY_ARRAY_UNIQUE_SYMBOL _nrnpy_arrayu
+
+
+// Numeric Python header
+#include "numpy/arrayobject.h"
+
+#endif // WITH_NUMPY
+
-
-extern "C" {
@@ -402 +414 @@
-//printf("hocobj_getattro %s\n", n);
-
-        # return None by default
-        PyObject* result = 0;
-
@@ -410 +421 @@
-        if (self->type_ == 1 && !self->ho_) {
-                Py_DECREF(name);
-
+
+
+
-        }
-        Symbol* sym = getsym(n, self->ho_);
@@ -722 +735 @@
-};
-
+#ifdef WITH_NUMPY
+
+
+static PyObject* PyObj_FromNrnObj(Object* obj) {
+
+  if (obj==NULL) {
+    printf("Warning: PyObj_FromNrnObj obj NULL\n");
+    //return null;
+    Py_INCREF(Py_None);
+    return Py_None;
+  }
+  
+
+  if (is_obj_type(obj,"Vector")) {
+    // we can deal with vectors
+    Vect* v = (Vect*)obj->u.this_pointer;
+    PyArrayObject*array = NULL;
+    int i,n = v->capacity();
+
+    array = (PyArrayObject*)PyArray_FromDims(1,&n,PyArray_DOUBLE);
+    for (i=0;i<n;i++) {
+      *(double*)(array->data + i*array->strides[0]) = (*v)[i];
+    }
+
+    return (PyObject*)array;
+
+  }
+
+  printf("Warning: PyObj_FromNrnObj cannot handle obj type, returning NULL\n");
+  //return NULL;
+  Py_INCREF(Py_None);
+  return Py_None;
+  
+}
+
+
+
+
+
+static int hocobj_tonumpy(PyObject* self, PyObject* args) {
+
+
+  if (!PyArg_ParseTuple(args, "")) {
+    return NULL;
+  }
+
+  PyArrayObject* array = NULL;
+
+
+  if (self->type_ == 2 || self->type_ == 3) {
+
+    Symbol* sym = self->sym_;
+
+    if (!sym) {
+      PyErr_SetString(PyExc_RuntimeError, "sym==NULL");
+      return NULL;
+    }
+
+    if (sym->type == VAR) {
+
+      if (ISARRAY(sym)) {
+
+        // Make a numpy array from an ndim NEURON array
+
+        int total = hoc_total_array(sym);
+        PyArrayObject* array = NULL;
+        int i;
+
+        Arrayinfo* a = sym->arayinfo;
+        double* p = OPVAL(sym);
+          
+        if (a) {
+          PyObject* pDims = PyList_New(a->nsub);
+
+          for (i= a->nsub-1;i>=0;--i) {
+            PyList_SetItem(pDims,i,PyInt_FromLong(a->sub[i]));
+          }
+
+          // first contiguous, then reshape
+          array = (PyArrayObject*)PyArray_FromDims(1,&total,PyArray_DOUBLE);
+          if (array==NULL) {
+            PyErr_SetString(PyExc_RuntimeError,"hoc.get hoc error allocating array.");
+            return NULL;
+          }
+
+          // fill array memory
+
+          for (i=0;i<total;i++) {
+            *(double*)(array->data + i*array->strides[0]) = p[i];
+          }
+
+          // return shaped array
+
+          pObj = (PyObject*)PyArray_Reshape(array,pDims);
+          // throw away pDims
+          Py_DECREF(pDims);
+
+        }
+
+      }
+      else {
+        // VAR is not an array
+
+        pObj = PyFloat_FromDouble(*OPVAL(sym));
+      }
+
+    }
+    else if (sym->type == OBJECTVAR) {
+
+      if (ISARRAY(sym)) {
+
+        // create numpy array of type 'O' (PyObjects) from NEURON OBJREF array
+
+        int total = hoc_total_array(sym);
+        PyArrayObject* array = NULL;
+        int i;
+
+        Arrayinfo* a = sym->arayinfo;
+
+        if (a) {
+          PyObject* pDims = PyList_New(a->nsub);
+
+          for (i= a->nsub-1;i>=0;--i) {
+            PyList_SetItem(pDims,i,PyInt_FromLong(a->sub[i]));
+          }
+
+
+          // first contiguous, then reshape
+
+          array = (PyArrayObject*)PyArray_FromDims(1,&total,PyArray_OBJECT);
+          if (array==NULL) {
+            PyErr_SetString(PyExc_RuntimeError,"hoc.get hoc error allocating array.");
+            return NULL;
+          }
+
+          // fill array memory
+
+          for (i=0;i<total;i++) {
+            *(PyObject**)(array->data + i*array->strides[0]) = PyObj_FromNrnObj(OPOBJ(sym)[i]);
+          }
+
+          // return shaped array
+
+          pObj = (PyObject*)PyArray_Reshape(array,pDims);
+          // throw away pDims
+          Py_DECREF(pDims);
+              
+          if (pObj==NULL) {
+            PyErr_SetString(PyExc_RuntimeError,"hoc.get hoc error reshaping array.");
+            return NULL;
+          }
+
+
+        }
+
+      }
+      else {
+        // return single object
+        pObj = PyObj_FromNrnObj(OPOBJ(sym)[0]);
+      }
+
+
+  }
+  else {
+    PyErr_SetString(PyExc_TypeError, "not a compound type");
+    return NULL;
+  }
+
+}
+
+
+
+
+static PyMethodDef hocobj_methods[] = {
+  {"toarray",hocobj_tonumpy,METH_VARARGS,"toarray(self) returns a numpy array of self."},
+  {NULL, NULL, 0, NULL}
+};
+
+
+#else
+
-static PyMethodDef hocobj_methods[] = {
-        {NULL, NULL, 0, NULL}
-};
+
+
+#endif //WITH_NUMPY
-
-static PyMemberDef hocobj_members[] = {
@@ -759 +956 @@
-    0,                         /* tp_iter */
-    0,                         /* tp_iternext */
-0,//
+
-    0,//hocobj_members,             /* tp_members */
-    0,                         /* tp_getset */
@@ -784 +981 @@
-//printf("AddObject HocObject\n");
-        PyModule_AddObject(m, "HocObject", (PyObject*)hocobject_type);
+
+#ifdef WITH_NUMPY
+
+        // setup for numpy
+        import_array();
+
+#endif // WITH_NUMPY
+
+
-        nrnpy_nrn();
-}

branches/pygetsetcall/src/nrnpython/setup.py.in

@@ -20 +20 @@
-        print "Warning: Old numpy found and not being used.  Please upgrade your version of numpy to > 1.0rc1"
-    else:
-
-
+    
+    
-
-
@@ -46 +46 @@
-        "readline"
-      ],
-numpy_include_path
+[numpy_include_path]
-      define_macros=defines
-    )