Develop Reference

Return data from struct using Numpy Array

I am writing Python C-extensions to a library and wish to return data as an Numpy Array. The library has a function that returns data from a sensor into a C structure. I would like to take the data from that structure and return it as a Numpy Array.
The structure definition in the library:
typedef struct rs_extrinsics
{
float rotation[9]; /* column-major 3x3 rotation matrix */
float translation[3]; /* 3 element translation vector, in meters */
} rs_extrinsics;
The function prototype:
void rs_get_device_extrinsics(const rs_device * device, rs_stream from_stream, rs_stream to_stream, rs_extrinsics * extrin, rs_error ** error);
Here is my code that is just trying to return the first value for now:
static PyObject *get_device_extrinsics(PyObject *self, PyObject *args)
{
PyArrayObject *result;
int dimensions = 12;
rs_stream from_stream;
rs_stream to_stream;
rs_extrinsics extrin;
if (!PyArg_ParseTuple(args, "iiffffffffffff", &from_stream, &to_stream, &extrin)) {
return NULL;
}
result = (PyArrayObject *) PyArray_FromDims(1, &dimensions, PyArray_DOUBLE);
if (result == NULL) {
return NULL;
}
rs_get_device_extrinsics(dev, from_stream, to_stream, &extrin, &e);
check_error();
result[0] = extrin.rotation[0];
return PyArray_Return(result);
}
I get the following error on compile:
error: assigning to 'PyArrayObject' (aka 'struct tagPyArrayObject_fields') from incompatible type 'float'
result[0] = extrin.rotation[0];
^ ~~~~~~~~~~~~~~~~~~

PyArrayObject, apart from data, have multiple fields:
typedef struct PyArrayObject {
PyObject_HEAD
char *data;
int nd;
npy_intp *dimensions;
npy_intp *strides;
PyObject *base;
PyArray_Descr *descr;
int flags;
PyObject *weakreflist;
} PyArrayObject;
You should get your data field data from your PyArrayObjects. Like this: result->data[index]; Also you need to cast your data to proper type indicated by result->descr->type character code. Also dims, you are passing to PyArray constructor should be of type npy_intp *, not int. Type of array in your case should be NPY_DOUBLE.
If you are calling your function from python (are you?), you better just passing list object from Python and use PyList C API to manage float sequence.
PyObject*list_of_floats;
PyArg_ParseTuple(args, "iiO", &from_stream, &to_stream, &list_of_floats);

Python C Wrapper Memory Leak

I am moderately experienced in python and C but new to writing python modules as wrappers on C functions. For a project I needed one function named "score" to run much faster than I was able to get in python so I coded it in C and literally just want to be able to call it from python. It takes in a python list of integers and I want the C function to get an array of integers, the length of that array, and then return an integer back to python. Here is my current (working) solution.
static PyObject *module_score(PyObject *self, PyObject *args) {
int i, size, value, *gene;
PyObject *seq, *data;
/* Parse the input tuple */
if (!PyArg_ParseTuple(args, "O", &data))
return NULL;
seq = PySequence_Fast(data, "expected a sequence");
size = PySequence_Size(seq);
gene = (int*) PyMem_Malloc(size * sizeof(int));
for (i = 0; i < size; i++)
gene[i] = PyInt_AsLong(PySequence_Fast_GET_ITEM(seq, i));
/* Call the external C function*/
value = score(gene, size);
PyMem_Free(gene);
/* Build the output tuple */
PyObject *ret = Py_BuildValue("i", value);
return ret;
}
This works but seems to leak memory and at a rate I can't ignore. I made sure that the leak is happening in the shown function by temporarily making the score function just return 0 and still saw the leaking behavior. I had thought that the call to PyMem_Free should take care of the PyMem_Malloc'ed storage but my current guess is that something in this function is getting allocated and retained on each call since the leaking behavior is proportional to the number of calls to this function. Am I not doing the sequence to array conversion correctly or am I possibly returning the ending value inefficiently? Any help is appreciated.

seq is a new Python object so you will need delete that object. You should check if seq is NULL, too.
Something like (untested):
static PyObject *module_score(PyObject *self, PyObject *args) {
int i, size, value, *gene;
long temp;
PyObject *seq, *data;
/* Parse the input tuple */
if (!PyArg_ParseTuple(args, "O", &data))
return NULL;
if (!(seq = PySequence_Fast(data, "expected a sequence")))
return NULL;
size = PySequence_Size(seq);
gene = (int*) PyMem_Malloc(size * sizeof(int));
for (i = 0; i < size; i++) {
temp = PyInt_AsLong(PySequence_Fast_GET_ITEM(seq, i));
if (temp == -1 && PyErr_Occurred()) {
Py_DECREF(seq);
PyErr_SetString(PyExc_ValueError, "an integer value is required");
return NULL;
}
/* Do whatever you need to verify temp will fit in an int */
gene[i] = (int*)temp;
}
/* Call the external C function*/
value = score(gene, size);
PyMem_Free(gene);
Py_DECREF(seq):
/* Build the output tuple */
PyObject *ret = Py_BuildValue("i", value);
return ret;
}

Python C API: Parse args of string and integer in C

Refering to http://mail.python.org/pipermail/python-dev/2009-June/090210.html
AND http://dan.iel.fm/posts/python-c-extensions/
and here is other places i searched regarding my question:
http://article.gmane.org/gmane.comp.python.general/424736
http://joyrex.spc.uchicago.edu/bookshelves/python/cookbook/pythoncook-CHP-16-SECT-3.html
http://docs.python.org/2/c-api/sequence.html#PySequence_Check
Python extension module with variable number of arguments
I am inexperienced in Python/C API.
I have the following code:
sm_int_list = (1,20,3)
c_int_array = (ctypes.c_int * len(sm_int_list))(*sm_int_list)
sm_str_tuple = ('some','text', 'here')
On the C extension side, i have done something like this:
static PyObject* stuff_here(PyObject *self, PyObject *args)
{
char* input;
int *i1, *i2;
char *s1, *s2;
// args = (('some','text', 'here'), [1,20,3], ('some','text', 'here'), [1,20,3])
**PyArg_ParseTuple(args, "(s#:):#(i:)#(s#:):#(i:)#", &s1, &i1, &s2, &i2)**;
/*stuff*/
}
such that:
stuff.here(('some','text', 'here'), [1,20,3], ('some','text', 'here'), [1,20,3])
returns data in the same form as args after some computation.
I would like to know the PyArg_ParseTuple expression, is it the proper way to parse
an array of varying string
an array of integers
UPDATE NEW
Is this the correct way?:
static PyObject* stuff_here(PyObject *self, PyObject *args)
unsigned int tint[], cint[];
ttotal=0, ctotal=0;
char *tstr, *cstr;
int *t_counts, *c_counts;
Py_ssize_t size;
PyObject *t_str1, *t_int1, *c_str2, *c_int2; //the C var that takes in the py variable value
PyObject *tseq, cseq;
int t_seqlen=0, c_seqlen=0;
if (!PyArg_ParseTuple(args, "OOiOOi", &t_str1, &t_int1, &ttotal, &c_str2, &c_int2, &ctotal))
{
return NULL;
}
if (!PySequence_Check(tag_str1) && !PySequence_Check(cat_str2)) return NULL;
else:
{
//All things t
tseq = PySequence_Fast(t_str1, "iterable");
t_seqlen = PySequence_Fast_GET_SIZE(tseq);
t_counts = PySequence_Fast(t_int1);
//All things c
cseq = PySequence_Fast(c_str2);
c_seqlen = PySequence_Fast_GET_SIZE(cseq);
c_counts = PySequence_Fast(c_int2);
//Make c arrays of all things tag and cat
for (i=0; i<t_seqlen; i++)
{
tstr[i] = PySequence_Fast_GET_ITEM(tseq, i);
tcounts[i] = PySequence_Fast_GET_ITEM(t_counts, i);
}
for (i=0; i<c_seqlen; i++)
{
cstr[i] = PySequence_Fast_GET_ITEM(cseq, i);
ccounts[i] = PySequence_Fast_GET_ITEM(c_counts, i);
}
}
OR
PyArg_ParseTuple(args, "(s:)(i:)(s:)(i:)", &s1, &i1, &s2, &i2)
And then again while returning,
Py_BuildValue("sisi", arr_str1,arr_int1,arr_str2,arr_int2) ??
Infact if someone could in detail clarify the various PyArg_ParseTuple function that would be of great benefit. the Python C API, as i find it in the documentation, is not exactly a tutorial on things to do.

You can use PyArg_ParseTuple to parse a real tuple, that has a fixed structure. Especially the number of items in the subtuples cannot change.
As the 2.7.5 documentation says, your format "(s#:):#(i:)#(s#:):#(i:)#" is wrong since : cannot occur in nested parenthesis. The format "(sss)(iii)(sss)(iii)", along with total of 12 pointer arguments should match your arguments. Likewise for Py_BuildValue you can use the same format string (which creates 4 tuples within 1 tuple), or "(sss)[iii](sss)[iii]" if the type matters (this makes the integers to be in lists instead of tuples).

What is the proper usage of PyArg_ParseTuple

I am using what seems to be the exact usgae of PyArg_ParseTuple, yet the code is still failing to work. I am using python 2.7
This is my C code for the Python Extension I am writing:
static PyObject* tpp(PyObject* self, PyObject* args)
{
PyObject* obj;
PyObject* seq;
int i, len;
PyObject* item;
int arrayValue, temp;
if (!PyArg_ParseTuple(args, "O", &obj)){
printf("Item is not a list\n");
return NULL;
}
seq = PySequence_Fast(obj, "expected a sequence");
len = PySequence_Size(obj);
arrayValue = -5;
printf("[\n");
for (i = 0; i < len; i++) {
item = PySequence_Fast_GET_ITEM(seq, i);
// printf("%d : %d, PyArg: ", item, *item);
// PyArg_ParseTuple(item, "I", &temp);
PyObject* objectsRepresentation = PyObject_Repr(item);
const char* s = PyString_AsString(objectsRepresentation);
printf("%s\n", s);
PyObject* objType = PyObject_Type(item);
PyObject* objTypeString = PyObject_Repr(objType);
const char* sType = PyString_AsString(objTypeString);
printf("%s\n", sType);
if (PyArg_ParseTuple(item, "i", &arrayValue) != 0){
printf("%d\n", arrayValue);
printf("horray!\n");
}
}
Py_DECREF(seq);
printf("]\n");
printf("Item is a list!\n");
Py_RETURN_NONE;
}
Then I just build the extension and go to the terminal
import et
and then
et.tpp([1,2])
fails to print the line
if (PyArg_ParseTuple(item, "i", &arrayValue) != 0){
printf("%d\n", arrayValue);
printf("horray!\n");
}
I checked the type, as you can see in the code, of the elements in the list, and it prints 'int'. Yet for some reason PyArg_ParseTuple is having errors.
I need to be able to access information from lists in python to copy some data, pass it to my C code elsewhere, and then return the result to python.
Thank you so much!

The answer is to use long PyInt_AsLong(PyObject *io)
"long PyInt_AsLong(PyObject *io) Will first attempt to cast the object to a PyIntObject, if it is not already one, and then return its value. If there is an error, -1 is returned, and the caller should check PyErr_Occurred() to find out whether there was an error, or whether the value just happened to be -1."
This is from http://docs.python.org/2/c-api/int.html That is the official c python int objects documentation which has all relevant methods.
Unfortunately this returns only a long value. However, a simple cast should suffice if the expected values will be small.

PyArg_ParseTuple() is about parsing tuples only, as the name suggests. In your code, item is an int, not a tuple. In order to convert an int object to a C value, you need to use arrayValue = PyInt_AsLong(item). Note that it returns a C long, not an int, so you should declare arrayValue as a long.
(EDIT: previously I mentioned PyInt_FromLong by mistake.)

Python/SWIG: Output an array

I am trying to output an array of values from a C function wrapped using SWIG for Python. The way I am trying to do is using the following typemap.
Pseudo code:
int oldmain() {
float *output = {0,1};
return output;
}
Typemap:
%typemap(out) float* {
int i;
$result = PyList_New($1_dim0);
for (i = 0; i < $1_dim0; i++) {
PyObject *o = PyFloat_FromDouble((double) $1[i]);
PyList_SetItem($result,i,o);
}
}
My code compiles well, but it hangs when I run access this function (with no more ways to debug it).
Any suggestions on where I am going wrong?
Thanks.

The easiest way to allow the length to vary is to add another output parameter that tells you the size of the array too:
%module test
%include <stdint.i>
%typemap(in,numinputs=0,noblock=1) size_t *len {
size_t templen;
$1 = &templen;
}
%typemap(out) float* oldmain {
int i;
$result = PyList_New(templen);
for (i = 0; i < templen; i++) {
PyObject *o = PyFloat_FromDouble((double)$1[i]);
PyList_SetItem($result,i,o);
}
}
%inline %{
float *oldmain(size_t *len) {
static float output[] = {0.f, 1.f, 2, 3, 4};
*len = sizeof output/sizeof *output;
return output;
}
%}
This is modified from this answer to add size_t *len which can be used to return the length of the array at run time. The typemap completely hides that output from the Python wrapper though and instead uses it in the %typemap(out) instead of a fixed size to control the length of the returned list.

This should get you going:
/* example.c */
float * oldmain() {
static float output[] = {0.,1.};
return output;
}
You are returning a pointer here, and swig has no idea about the size of it. Plain $1_dim0 would not work, so you would have to hard code or do some other magic. Something like this:
/* example.i */
%module example
%{
/* Put header files here or function declarations like below */
extern float * oldmain();
%}
%typemap(out) float* oldmain {
int i;
//$1, $1_dim0, $1_dim1
$result = PyList_New(2);
for (i = 0; i < 2; i++) {
PyObject *o = PyFloat_FromDouble((double) $1[i]);
PyList_SetItem($result,i,o);
}
}
%include "example.c"
Then in python you should get:
>> import example
>> example.oldmain()
[0.0, 1.0]
When adding typemaps you may find -debug-tmsearch very handy, i.e.
swig -python -debug-tmsearch example.i
Should clearly indicate that your typemap is used when looking for a suitable 'out' typemap for float *oldmain. Also if you just like to access c global variable array you can do the same trick using typemap for varout instead of just out.