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).
Related
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;
}
I am writing a C function that takes a Python tuple of ints as an argument.
static PyObject* lcs(PyObject* self, PyObject *args) {
int *data;
if (!PyArg_ParseTuple(args, "(iii)", &data)) {
....
}
}
I am able to convert a tuple of a fixed length (here 3) but how to get a C array from a tuple of any length?
import lcs
lcs.lcs((1,2,3,4,5,6)) #<- C should receive it as {1,2,3,4,5,6}
EDIT:
Instead of a tuple I can pass a string with numbers separated by ';'. Eg '1;2;3;4;5;6' and separate them to the array in C code. But I dont think it is a proper way of doing that.
static PyObject* lcs(PyObject* self, PyObject *args) {
char *data;
if (!PyArg_ParseTuple(args, "s", &data)) {
....
}
int *idata;
//get ints from data(string) and place them in idata(array of ints)
}
Use PyArg_VaParse: https://docs.python.org/2/c-api/arg.html#PyArg_VaParse
It works with va_list, where you can retrieve a variable number of arguments.
More info here: http://www.cplusplus.com/reference/cstdarg/va_list/
And as it's a tuple you can use the tuple functions: https://docs.python.org/2/c-api/tuple.html like PyTuple_Size and PyTuple_GetItem
Here's there's a example of how to use it: Python extension module with variable number of arguments
Let me know if it helps you.
Not sure if this is what you're looking for, but
you could write a C function that takes a variable number of arguments, using va_list and va_start.
A tutorial is here: http://www.cprogramming.com/tutorial/c/lesson17.html
I think I have found a solution:
static PyObject* lcs(PyObject* self, PyObject *args) {
PyObject *py_tuple;
int len;
int *c_array;
if (!PyArg_ParseTuple(args, "O", &py_tuple)) {
return NULL;
}
len = PyTuple_Size(py_tuple);
c_array= malloc(len*4);
while (len--) {
c_array[len] = (int) PyInt_AsLong(PyTuple_GetItem(py_tuple, len));
// c_array is our array of ints
}
}
This answer was posted as an edit to the question Python tuple to C array by the OP Piotr Dabkowski under CC BY-SA 3.0.
I have a c++ class written and I am using SWIG to make a Python version of my class. I would like to overload the constructor so that it can take in Python lists. For example:
>>> import example
>>> a = example.Array([1,2,3,4])
I was attempting to use the typemap feature in swig, but the scope of typemap does not include code in extend
Here is a similar example to what I have...
%typemap(in) double[]
{
if (!PyList_Check($input))
return NULL;
int size = PyList_Size($input);
int i = 0;
$1 = (double *) malloc((size+1)*sizeof(double));
for (i = 0; i < size; i++)
{
PyObject *o = PyList_GetItem($input,i);
if (PyNumber_Check(o))
$1[i] = PyFloat_AsDouble(o);
else
{
PyErr_SetString(PyExc_TypeError,"list must contain numbers");
free($1);
return NULL;
}
}
$1[i] = 0;
}
%include "Array.h"
%extend Array
{
Array(double lst[])
{
Array *a = new Array();
...
/* do stuff with lst[] */
...
return a;
}
}
I know the typemap is working correctly (I wrote a small test function that just prints out elements in the double[]).
I attempted putting the typemap inside the extend clause, but that did not solve the problem.
Maybe there is another way to use Python Lists inside of the extend, but I could not find any examples.
Thanks for the help in advance.
You're really close: instead of a double lst[], extend with std::list<double>:
%include "std_list.i" // or std_vector.i
%include "Array.h"
%extend Array
{
Array(const std::list<double>& numbers) {
Array* arr = new Array;
...put numbers list items in "arr", then
return a; // interpreter will take ownership
}
}
SWIG should automatically convert the Python list to the std::list.
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.)
If I'm trying to overload an embedded Python function so that the second argument can be a long or an Object, is there a standard way to do it? Is this it?
What I'm trying now (names changed to protect the innocent):
bool UseLongVar2 = true;
if (!PyArg_ParseTuple(args, "ll:foo", &LongVar1, &LongVar2))
{
PyErr_Clear();
if (!PyArg_ParseTuple(args, "lO&:foo", &LongVar1, convertObject, &Object))
{
UseLongVar2 = false;
return NULL;
}
}
What I normally do is have two C functions that take the different arguments. The "python-facing" function's job is to parse out the arguments, call the appropriate C function, and build the return value if any.
This is pretty common when, for example, you want to allow both byte and Unicode strings.
Here is an example of what I mean.
// Silly example: get the length of a string, supporting Unicode and byte strings
static PyObject* getlen_py(PyObject *self, PyObject *args)
{
// Unpack our argument (error handling omitted...)
PyObject *arg = NULL;
PyArg_UnpackTuple(args, "getlen", 1, 1, arg) ;
if ( PyUnicode_Check(arg) )
{
// It's a Unicode string
return PyInt_FromLong(getlen_w(PyUnicode_AS_UNICODE(arg))) ;
}
else
{
// It's a byte string
return PyInt_FromLong(getlen_a(PyString_AS_STRING(arg))) ;
}
}