Changeset: 521aa4d78816 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=521aa4d78816
Modified Files:
configure.ag
monetdb5/extras/pyapi/Tests/pyapi00.malC
monetdb5/extras/pyapi/pyapi.c
Branch: pyapi
Log Message:
Python Integration: NumPy arrays part 1
diffs (205 lines):
diff --git a/configure.ag b/configure.ag
--- a/configure.ag
+++ b/configure.ag
@@ -2279,7 +2279,7 @@ if test "x$enable_pyintegration" != xno;
enable_pyintegration=no
disable_pyintegration="(python-config command not
found)"
fi
- elif libpy_CFLAGS=`$PYCMD --includes ` && libpy_LIBS=`$PYCMD
--ldflags`; then
+ elif libpy_CFLAGS=`\`$PYCMD --exec-prefix\`/bin/python -c "from
distutils.sysconfig import get_python_inc; import numpy; print ' -I' +
get_python_inc() + ' -I' + numpy.get_include();"` && libpy_LIBS=`$PYCMD
--ldflags`; then
have_libpy=yes
AC_DEFINE(HAVE_LIBPY, 1, [Define if we can link to python])
AC_SUBST(libpy_CFLAGS, $libpy_CFLAGS)
diff --git a/monetdb5/extras/pyapi/Tests/pyapi00.malC
b/monetdb5/extras/pyapi/Tests/pyapi00.malC
--- a/monetdb5/extras/pyapi/Tests/pyapi00.malC
+++ b/monetdb5/extras/pyapi/Tests/pyapi00.malC
@@ -12,7 +12,7 @@ bat.append(b,1189641421);
io.print(b);
-r:bat[:oid,:int] := pyapi.eval(nil:ptr,"int(arg1/1000)",b);
+r:bat[:oid,:int] := pyapi.eval(nil:ptr,"r=[e**2 for e in arg1]\nreturn
([numpy.asarray(r)])",b);
io.print(r);
diff --git a/monetdb5/extras/pyapi/pyapi.c b/monetdb5/extras/pyapi/pyapi.c
--- a/monetdb5/extras/pyapi/pyapi.c
+++ b/monetdb5/extras/pyapi/pyapi.c
@@ -21,7 +21,9 @@
#undef _POSIX_C_SOURCE
#include <Python.h>
-// other headers
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+#include <numpy/arrayobject.h>
+
#include <string.h>
const char* pyapi_enableflag = "embedded_py";
@@ -64,16 +66,12 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
size_t pos;
char* rcall = NULL;
size_t rcalllen;
- size_t ret_rows = 0;
- //int ret_cols = 0; /* int because pci->retc is int, too*/
str *args;
- //int evalErr;
char *msg = MAL_SUCCEED;
BAT *b = NULL;
- BUN cnt;
node * argnode;
int seengrp = FALSE;
- PyObject *pArgs; // this is going to be the parameter tuple
+ PyObject *pArgs, *pResult; // this is going to be the parameter tuple
if (!PyAPIEnabled()) {
throw(MAL, "pyapi.eval",
@@ -106,7 +104,6 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
argnode = argnode->next;
}
}
- pArgs = PyTuple_New(pci->argc - pci->retc + 2);
// the first unknown argument is the group, we don't really care for
the rest.
for (i = pci->retc + 2; i < pci->argc; i++) {
@@ -121,10 +118,12 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
}
}
+ // create function argument tuple, we pass a tuple of numpy arrays
+ pArgs = PyTuple_New(pci->argc-(pci->retc + 2));
+
// for each input column (BAT):
for (i = pci->retc + 2; i < pci->argc; i++) {
- PyObject *varlist = NULL;
- size_t j;
+ PyObject *vararray = NULL;
// turn scalars into one-valued BATs
// TODO: also do this for Python? Or should scalar values be
'simple' variables?
@@ -149,19 +148,14 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
}
}
- varlist = PyList_New(BATcount(b));
switch (ATOMstorage(getColumnType(getArgType(mb,pci,i)))) {
case TYPE_int:
- // BAT_TO_INTSXP(b, int, varvalue);
- for (j = 0; j < BATcount(b); j++) {
- int v = ((int*) Tloc(b,
BUNfirst(b)))[j];
- //if ( v == int_nil)
- //
PyList_SET_ITEM(varlist, j, );
- //else
- // TODO: use numpy arrays here,
readonly, ignore NULLs for now?
- PyList_SET_ITEM(varlist, j,
PyInt_FromLong(v));
- }
+ // yeah yeah yeah
+ vararray = PyArray_New(&PyArray_Type, 1, (npy_intp[1])
{BATcount(b)}, NPY_INT32, NULL,
+ (int*) Tloc(b, BUNfirst(b)), 0,
NPY_ARRAY_CARRAY || !NPY_ARRAY_WRITEABLE, NULL);
break;
+ // TODO: handle NULLs!
+
// TODO: implement other types
default:
msg = createException(MAL, "pyapi.eval", "unknown
argument type ");
@@ -169,7 +163,7 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
}
BBPunfix(b->batCacheid);
- PyTuple_SetItem(pArgs, ai++, varlist);
+ PyTuple_SetItem(pArgs, ai++, vararray);
}
pos = 0;
@@ -192,20 +186,19 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
#endif
// parse the code and create the function
- // TODO: do this in a temporary namespace, how?
+ // TODO: do this in a temporary namespace? Later...
+
// TODO: actually include user code
- // TODO: use numpy arrays for columns!
- // TODO: How do we make nice indentation so it parses? Force user code
to use level-1 indentation?
+ // TODO: Indent user code: Search for newline-tab, if there, add tabs,
if not, add single space in front of every line. Thanks Sjoerd!
{
int pyret;
- PyObject *pFunc, *pModule, *pResult;
-
+ PyObject *pFunc, *pModule;
+ // TODO: check whether this succeeds
pModule = PyImport_Import(PyString_FromString("__main__"));
- pyret = PyRun_SimpleString("def pyfun(x):\n print(x)\n return
list(([e+1 for e in x],1))");
+ pyret = PyRun_SimpleString("def pyfun(x):\n import numpy as
np\n r=[e+1 for e in x]\n return ([np.asarray(r)])");
pFunc = PyObject_GetAttrString(pModule, "pyfun");
if (pyret != 0 || !pModule || !pFunc ||
!PyCallable_Check(pFunc)) {
- // TODO: include parsed code
msg = createException(MAL, "pyapi.eval", "could not
parse Python code %s", rcall);
goto wrapup; // shudder
}
@@ -213,8 +206,8 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
// TODO: use other interface, here we can assign each value. We
know how many params there will be
// this is it
pResult = PyObject_CallObject(pFunc, pArgs);
- if (!pResult || !PyList_Check(pResult) ||
!PyList_Size(pResult)) {
- msg = createException(MAL, "pyapi.eval", "invalid
result object");
+ if (!pResult || !PyList_Check(pResult) || PyList_Size(pResult)
!= pci->retc) {
+ msg = createException(MAL, "pyapi.eval", "Invalid
result object. Need list of size %d containing numpy arrays", pci->retc);
goto wrapup;
}
// delete the function again
@@ -223,12 +216,33 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
// collect the return values
for (i = 0; i < pci->retc; i++) {
+ PyObject * pColO = PyList_GetItem(pResult, i);
int bat_type = ATOMstorage(getColumnType(getArgType(mb,pci,i)));
- cnt = (BUN) ret_rows;
switch (bat_type) {
case TYPE_int: {
- // TODO
+ int *p;
+ BUN j;
+ // this only copies if it has to
+ PyArrayObject* pCol = (PyArrayObject*)
PyArray_FromAny(pColO,
+ PyArray_DescrFromType(NPY_INT32), 1, 1,
NPY_ARRAY_CARRAY | NPY_ARRAY_FORCECAST, NULL);
+ //size_t cnt = pCol->dimensions[0];
+ size_t cnt = 5;
+ // TODO: get actual length from array
+
+ // TODO null rewriting, we are guaranteed to be able to
write to this
+ // TODO: only accepted masked array as output?
+ // TODO check whether the length of our output
+
+ /* We would like to simply pass over the BAT from numpy,
+ * but cannot due to malloc/free incompatibility */
+ b = BATnew(TYPE_void, TYPE_int, cnt, TRANSIENT);
+ BATseqbase(b, 0); b->T->nil = 0; b->T->nonil = 1;
b->tkey = 0;
+ b->tsorted = 0; b->trevsorted = 0;
+ p = (int*) Tloc(b, BUNfirst(b));
\
+ for( j =0; j< cnt; j++, p++){
+ *p = (int) PyArray_GETPTR1(pCol, j);
+ }
break;
}
// TODO: implement other types
@@ -239,7 +253,6 @@ str PyAPIeval(MalBlkPtr mb, MalStkPtr st
bat_type);
goto wrapup;
}
- BATsetcount(b, cnt);
// bat return
if (isaBatType(getArgType(mb,pci,i))) {
@@ -265,7 +278,9 @@ str PyAPIprelude(void *ret) {
MT_lock_set(&pyapiLock, "pyapi.evaluate");
/* startup internal Python environment */
if (!pyapiInitialized) {
+ char* iar = NULL;
Py_Initialize();
+ import_array1(iar);
pyapiInitialized++;
}
MT_lock_unset(&pyapiLock, "pyapi.evaluate");
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