I'm working on the python with ctypes to call the c so file, but the c file define the structure with function pointer
// mem ==================================================================
typedef struct StdMemFunc
{
void* (*const malloc) (unsigned long size);
void (*const free) (void* ptr);
void* (*const realloc) (void* ptr, unsigned long size);
void* (*const calloc) (unsigned long count, unsigned long size);
void* (*const set) (void* ptr, int value, unsigned long num);
void* (*const copy) (void* dest, const void* src, unsigned long num);
}*StdMemFunc;
typedef struct StdLib
{
const uint32_t version;
bool (*const is_version_compatible) (uint32_t version, uint32_t func_mask);
void (*const delay) (int32_t milli_sec);
const StdMemFunc mem;
}*StdLib;
and mock the function in another file as below
void *std_malloc(unsigned long size)
{
return malloc(size);
}
void std_free(void *ptr)
{
free(ptr);
}
void *std_realloc(void *ptr, unsigned long size)
{
return realloc(ptr, size);
}
void *std_calloc(unsigned long count, unsigned long size)
{
return calloc(count, size);
}
void *std_memset(void *ptr, int value, unsigned long num)
{
return memset(ptr, value, num);
}
void *std_memcopy(void *dest, const void *src, unsigned long num)
{
return memcpy(dest, src, num);
}
struct StdMemFunc mem_func =
{
.malloc = std_malloc,
.free = std_free,
.realloc = std_realloc,
.calloc = std_calloc,
.set = std_memset,
.copy = std_memcopy
};
then the python need to call another method with std_lib as paramater, the std_lib with call mem->malloc() method in C part, so how to define the class in the python with ctypes?
I have tried the below one, but it was not work
class StdMemFunc(Structure):
_fields_ = [
("malloc", ctypes.CFUNCTYPE(c_void_p, c_ulong)),
("free", ctypes.CFUNCTYPE(None, c_void_p)),
("realloc", ctypes.CFUNCTYPE(c_void_p, c_void_p, c_ulong)),
("calloc", ctypes.CFUNCTYPE(c_void_p, c_ulong, c_ulong)),
("set", ctypes.CFUNCTYPE(c_void_p, c_void_p, c_int, c_ulong)),
("copy", ctypes.CFUNCTYPE(c_void_p, c_void_p, c_ulong))
]
class StdLib(Structure):
_fields_ = [
("version", c_uint32),
("is_version_compatible", c_bool),
("delay", c_void_p),
("mem", POINTER(StdMemFunc)),
]
libc_std_lib = CDLL('/home/linus/code/galileo/mock_std_lib.so')
std_lib = StdLib()
std_lib.mem.malloc = libc_std_lib.std_malloc
libc_modbus.modbus_create_server_station.argtypes = [POINTER(ModbusNodeDef), c_int, StdLib, PlcDrvAccessor]
libc_modbus.modbus_create_server_station.restype = POINTER(ModbusStation)
libc_modbus.modbus_create_server_station(node_def, node_num, std_lib, plc_drv_accessor)
It looks like there are two problems here:
The is_version_compatible and delay fields in the StdLib struct are functions, but you are defining them as constants.
You are not instantiating all the fields in the struct, meaning that the program might be trying to dereference a null pointer, as null pointers are the default value for pointer types.
The StdLib struct definition should look something like this:
class StdLib(Structure):
_fields_ = [
("version", c_uint32),
("is_version_compatible", CFUNCTYPE(POINTER(c_bool), c_uint32, _uint32)),
("delay", CFUNCTYPE(c_void_p, c_int32)),
("mem", POINTER(StdMemFunc)),
]
For the instantiation, I would do something like this:
libc_std_lib = CDLL('/home/linus/code/galileo/mock_std_lib.so')
std_mem_func = StdMemFunc(
libc_std_lib.std_malloc,
libc_std_lib.std_free,
libc_std_lib.std_realloc,
libc_std_lib.std_calloc,
libc_std_lib.std_set,
libc_std_lib.std_copy
)
std_lib = StdLib(
1,
reference_to_is_version_compatible_func,
reference_to_delay_func,
std_mem_func
)
Of course, you need to pass the correct params/function references to StdLib. Maybe you will need to mock the is_version_compatible and delay functions as well.
Disclaimer: this is entirely untested, so I don't guarantee it will work.
The OP's code isn't quite reproducible, but I was able to get the same error message on the following line:
std_lib.mem.malloc = libc_std_lib.std_malloc
If I am following correctly, the OP wants to initialize the C structure with functions that are provided in C, but libc.std_lib.std_malloc isn't wrapped properly to do that. It is a function that wraps a C function that is callable from Python, not C.
ctypes function prototypes can be instantiated a number of ways, and the one that works is:
prototype(func_spec[, paramflags])
Returns a foreign function exported by a shared library. func_spec must be a 2-tuple
(name_or_ordinal, library). The first item is the name of the exported
function as string, or the ordinal of the exported function as small
integer. The second item is the shared library instance.
For example:
std_lib.mem.malloc = ctypes.CFUNCTYPE(ctypes.c_void_p, ctypes.c_ulong)(('std_malloc',libc_std_lib))
Here's a working set of files:
test.cpp
#include <stdlib.h>
#include <stdint.h>
#include <memory.h>
#include <stdio.h>
#ifdef _WIN32
# define API __declspec(dllexport)
#else
# define API
#endif
extern "C" {
typedef struct StdMemFunc {
void* (*const malloc)(unsigned long size);
void (*const free)(void* ptr);
void* (*const realloc)(void* ptr, unsigned long size);
void* (*const calloc)(unsigned long count, unsigned long size);
void* (*const set)(void* ptr, int value, unsigned long num);
void* (*const copy)(void* dest, const void* src, unsigned long num);
} *StdMemFuncPtr;
typedef struct StdLib {
const uint32_t version;
bool (*const is_version_compatible)(uint32_t version, uint32_t func_mask);
void (*const delay)(int32_t milli_sec);
const StdMemFunc mem;
} *StdLibPtr;
API void* std_malloc(unsigned long size) {
return malloc(size);
}
API void std_free(void* ptr) {
free(ptr);
}
API void* std_realloc(void* ptr, unsigned long size) {
return realloc(ptr, size);
}
API void* std_calloc(unsigned long count, unsigned long size) {
return calloc(count, size);
}
API void* std_memset(void* ptr, int value, unsigned long num) {
return memset(ptr, value, num);
}
API void* std_memcopy(void* dest, const void* src, unsigned long num) {
return memcpy(dest, src, num);
}
// A couple of test functions that accepts the initialized structure
// and calls sum of the function pointers.
API char* testit(StdLib* test) {
// This is how I debugged this, by comparing the *actual*
// function pointer value to the one received from Python.
// Once they matched the code worked.
printf("%p %p\n", std_malloc, test->mem.malloc);
char* p = static_cast<char*>(test->mem.malloc(10));
test->mem.set(p, 'A', 9);
p[9] = 0;
return p;
}
API void freeit(StdLib* test, char* p) {
test->mem.free(p);
}
}
test.py
import ctypes as ct
# prototypes
MALLOC = ct.CFUNCTYPE(ct.c_void_p,ct.c_ulong)
FREE = ct.CFUNCTYPE(None,ct.c_void_p)
REALLOC = ct.CFUNCTYPE(ct.c_void_p, ct.c_void_p, ct.c_ulong)
CALLOC = ct.CFUNCTYPE(ct.c_void_p, ct.c_ulong, ct.c_ulong)
SET = ct.CFUNCTYPE(ct.c_void_p,ct.c_void_p,ct.c_int,ct.c_ulong)
COPY = ct.CFUNCTYPE(ct.c_void_p, ct.c_void_p, ct.c_ulong)
class StdMemFunc(ct.Structure):
_fields_ = [("malloc", MALLOC),
("free", FREE),
("realloc", REALLOC),
("calloc", CALLOC),
("set", SET),
("copy", COPY)]
class StdLib(ct.Structure):
_fields_ = [("version", ct.c_uint32),
# Note these two fields were function pointers as well.
# Declared correctly now.
("is_version_compatible", ct.CFUNCTYPE(ct.c_bool, ct.c_uint32, ct.c_uint32)),
("delay", ct.CFUNCTYPE(None, ct.c_int32)),
("mem", StdMemFunc)]
dll = ct.CDLL('./test')
dll.testit.argtypes = ct.POINTER(StdLib),
dll.testit.restype = ct.POINTER(ct.c_char)
dll.freeit.argtypes = ct.POINTER(StdLib), ct.c_char_p
dll.freeit.restype = None
lib = StdLib()
lib.mem.malloc = MALLOC(('std_malloc', dll))
lib.mem.realloc = REALLOC(('std_realloc', dll))
lib.mem.calloc = CALLOC(('std_calloc', dll))
lib.mem.free = FREE(('std_free', dll))
lib.mem.set = SET(('std_memset', dll))
lib.mem.copy = COPY(('std_memcopy', dll))
p = dll.testit(lib)
# One way to access the data in the returned pointer is to slice it to the known length
print(p[:10])
# If known to be null-terminated, can also cast to c_char_p, which expects
# null-terminated data, and extract the value.
print(ct.cast(p,ct.c_char_p).value)
dll.freeit(lib,p)
Output:
b'AAAAAAAAA\x00'
b'AAAAAAAAA'
I am working on my Project which implies the use of Empirical Mode Decomposition in C++ for EEG Signals. The input Data is Eigen::MatrixXd, where the rows are the Channels and the columns are the samples.
I did not found a good C++ library for EMD so I want to use a Python one (dsatools). I have downloaded the package through Pip installer from the setup.py file on Xubuntu... so it's a system package now.
the problem is that the program can't read the module.
this is the code:
std::vector <Eigen::MatrixXd> DataAquisition::EMD (Eigen::MatrixXd array, int order, int iterations, int locality) {
std::vector <Eigen::MatrixXd> IMFs;
for (int i = 0; i < array.rows(); i++) {
Eigen::MatrixXd Kanals = array.row(i);
Eigen::MatrixXd IMFs_Cpp;
Py_Initialize();
//PyRun_SimpleString("from dsatools._base._imf_decomposition import * ");
PyObject* sys_path = PySys_GetObject("path");
PyObject* ProgrammName = PyUnicode_FromString("/home/user/Schreibtisch/mne-cpp-main/applications/mne_bci/MNE-BCI-QT/dsatools-master/dsatools/_base/_imf_decomposition/_emd.py");
PyList_Append(sys_path, ProgrammName);
PyObject* pModuleString = PyUnicode_FromString ((char*)"_emd.py");
PyObject* pModule = PyImport_Import(pModuleString);
PyObject* pFunction = PyObject_GetAttrString(pModule,(char*)"emd");
//PyObject* pDict = PyModule_GetDict(pModule);
//PyObject* pFunc = PyDict_GetItemString(pDict, (char*)"emd");
if (PyCallable_Check(pFunction))
{
PyObject* Signal = Py_BuildValue("(d)",(double*)Kanals.data());
PyObject* Order = Py_BuildValue("(i)",order);
PyObject* method = Py_BuildValue("(z)",(char*)"cubic");
PyObject* max_itter = Py_BuildValue("(i)",iterations);
PyObject* args = PyTuple_Pack(4,Signal,Order,method,max_itter);
PyErr_Print();
PyObject* IMFs_Py = PyObject_CallObject(pFunction,args);
PyErr_Print();
if (PyArray_Check(IMFs_Py))
std::cout << "EMD Output is NOT Array \n";
PyArrayObject *np_ret = reinterpret_cast <PyArrayObject*> (IMFs_Py);
int Rows = PyArray_SHAPE(np_ret)[0];
int Cols = PyArray_SHAPE(np_ret)[1];
double* c_out = reinterpret_cast<double*>(PyArray_DATA(np_ret));
Eigen::MatrixXd IMFs_Cpp = Eigen::Map <Eigen::MatrixXd> (c_out,Rows,Cols);
IMFs.push_back(IMFs_Cpp);
}
else
std::cout << "Python did not call the function \n";
Py_Finalize();
}
return IMFs;}
this is how the code in Python should look like and I just want to call the emd function:
I'm figuring out the Python/C API for a more complex task. Initially, I wrote a simple example of adding two ndarrays of shape = (2,3) and type = float32.
I am able to pass two numpy arrays into c functions, read their dimensions and data and perform custom addion on data. But when I try to wrap the resulting data using PyArray_SimpleNewFromData, code hangs (returns NULL?)
To replicate the issue, create three files: mymath.c, setup.py, test.py in a folder as follows and run test.py (it runs setup.py to compile and install the module and then runs a simple test).
I'm using python in windows, inside an anaconda environment. I'm new to the Python/C API. So, any help would be much appreciated.
// mymath.c
#include <Python.h>
#include <stdio.h>
#include "numpy/arrayobject.h"
#include "numpy/npy_math.h"
#include <math.h>
#include <omp.h>
/*
C functions
*/
float* arr_add(float* d1, float* d2, int M, int N){
float * result = (float *) malloc(sizeof(float)*M*N);
for (int m=0; m<M; m++)
for (int n=0; n<N; n++)
result [m*N+ n] = d1[m*N+ n] + d2[m*N+ n];
return result;
}
/*
Unwrap apply and wrap pyObjects
*/
void capsule_cleanup(PyObject *capsule) {
void *memory = PyCapsule_GetPointer(capsule, NULL);
free(memory);
}
// add two 2d arrays (float32)
static PyObject *arr_add_fn(PyObject *self, PyObject *args)
{
PyArrayObject *arr1, *arr2;
if (!PyArg_ParseTuple(args, "OO", &arr1, &arr2))
return NULL;
// get data as flat list
float *d1, *d2;
d1 = (float *) arr1->data;
d2 = (float *) arr2->data;
int M, N;
M = (int)arr1->dimensions[0];
N = (int)arr1->dimensions[1];
printf("Dimensions, %d, %d \n\n", M,N);
PyObject *result, *capsule;
npy_intp dim[2];
dim[0] = M;
dim[1] = N;
float * d3 = arr_add(d1, d2, M, N);
result = PyArray_SimpleNewFromData(2, dim, NPY_FLOAT, (void *)d3);
if (result == NULL)
return NULL;
// -----------This is not executed. code hangs--------------------
for (int m=0; m<M; m++)
for (int n=0; n<N; n++)
printf("%f \n", d3[m*N+n]);
capsule = PyCapsule_New(d3, NULL, capsule_cleanup);
PyArray_SetBaseObject((PyArrayObject *) result, capsule);
return result;
}
/*
Bundle functions into module
*/
static PyMethodDef MyMethods [] ={
{"arr_add", arr_add_fn, METH_VARARGS, "Array Add two numbers"},
{NULL,NULL,0,NULL}
};
/*
Create module
*/
static struct PyModuleDef mymathmodule = {
PyModuleDef_HEAD_INIT,
"mymath", "My doc of mymath", -1, MyMethods
};
PyMODINIT_FUNC PyInit_mymath(void){
return PyModule_Create(&mymathmodule);
}
# setup.py
from distutils.core import setup, Extension
import numpy
module1 = Extension('mymath',
sources = ['mymath.c'],
# define_macros = [('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
include_dirs=[numpy.get_include()],
extra_compile_args = ['-fopenmp'],
extra_link_args = ['-lgomp'])
setup (name = 'mymath',
version = '1.0',
description = 'My math',
ext_modules = [module1])
# test.py
import os
os.system("python .\setup.py install")
import numpy as np
import mymath
a = np.arange(6,dtype=np.float32).reshape(2,3)
b = np.arange(6,dtype=np.float32).reshape(2,3)
c = mymath.arr_add(a,b)
print(c)
I have a few values defined as symbolic constants in my header file:
#define NONE 0x00
#define SYM 0x11
#define SEG 0x43
...
The names of these values represent a certain type of data.
Now in my current implementation of my module I put all these symbolic links into an array
static unsigned char TYPES[] = { NONE, SYM, SEG, ...}
And add the positions of the types in the array as int constants in the module.
PyMODINIT_FUNC initShell(void)
{
PyObject *m;
m= Py_InitModule3("Sample", sample_Methods,"Sample Modules");
if (m == NULL)
return;
...
PyModule_AddIntConstant(m, "NONE", 0);
PyModule_AddIntConstant(m, "SYM", 1);
PyModule_AddIntConstant(m, "SEG", 2);
...
}
And when calling functions I have to do something like :
static PyObject *py_samplefunction(PyObject *self, PyObject *args, PyObject *kwargs) {
int type;
if (!PyArg_ParseTuple(args,kwargs,"i",&type)
return NULL;
int retc;
retc = sample_function(TYPES[type]);
return Py_BuildValue("i", retc);
}
I'm not very happy with this hack and I think it is very prone to errors and so I'm basically looking for a solution which eliminates the array and allows for direct use of the constants in a function call. Any tips?
Edit
Using PyModule_AddIntMacro(m, SEG); and calling sample function as such, solves it:
static PyObject *py_samplefunction(PyObject *self, PyObject *args, PyObject *kwargs) {
int type;
if (!PyArg_ParseTuple(args,kwargs,"i",&type)
return NULL;
int retc;
retc = sample_function((unsigned char) type);
return Py_BuildValue("i", retc);
}
Why not just add the constants to the module ?
PyModule_AddIntMacro(m, SYM);
What would be the C equivalent to this python code?
Thanks.
data = gather_me_some_data()
# where data = [ (metic, datapoints), ... ]
# and datapoints = [ (timestamp, value), ... ]
serialized_data = cPickle.dumps(data, protocol=-1)
length_prefix = struct.pack("!L", len(serialized_data))
message = length_prefix + serialized_data
C doesn't supports direct serialization mechanism because in C you can't get type information at run-time. You must yourself inject some type info at run-time and then construct required object by that type info. So define all your possible structs:
typedef struct {
int myInt;
float myFloat;
unsigned char myData[MY_DATA_SIZE];
} MyStruct_1;
typedef struct {
unsigned char myUnsignedChar;
double myDouble;
} MyStruct_2;
Then define enum which collects info about what structs in total you have:
typedef enum {
ST_MYSTRUCT_1,
ST_MYSTRUCT_2
} MyStructType;
Define helper function which lets to determine any struct size:
int GetStructSize(MyStructType structType) {
switch (structType) {
case ST_MYSTRUCT_1:
return sizeof(MyStruct_1);
case ST_MYSTRUCT_2:
return sizeof(MyStruct_2);
default:
// OOPS no such struct in our pocket
return 0;
}
}
Then define serialize function:
void BinarySerialize(
MyStructType structType,
void * structPointer,
unsigned char * serializedData) {
int structSize = GetStructSize(structType);
if (structSize != 0) {
// copy struct metadata to serialized bytes
memcpy(serializedData, &structType, sizeof(structType));
// copy struct itself
memcpy(serializedData+sizeof(structType), structPointer, structSize);
}
}
And de-serialization function:
void BinaryDeserialize(
MyStructType structTypeDestination,
void ** structPointer,
unsigned char * serializedData)
{
// get source struct type
MyStructType structTypeSource;
memcpy(&structTypeSource, serializedData, sizeof(structTypeSource));
// get source struct size
int structSize = GetStructSize(structTypeSource);
if (structTypeSource == structTypeDestination && structSize != 0) {
*structPointer = malloc(structSize);
memcpy(*structPointer, serializedData+sizeof(structTypeSource), structSize);
}
}
Serialization usage example:
MyStruct_2 structInput = {0x69, 0.1};
MyStruct_1 * structOutput_1 = NULL;
MyStruct_2 * structOutput_2 = NULL;
unsigned char testSerializedData[SERIALIZED_DATA_MAX_SIZE] = {0};
// serialize structInput
BinarySerialize(ST_MYSTRUCT_2, &structInput, testSerializedData);
// try to de-serialize to something
BinaryDeserialize(ST_MYSTRUCT_1, &structOutput_1, testSerializedData);
BinaryDeserialize(ST_MYSTRUCT_2, &structOutput_2, testSerializedData);
// determine which object was de-serialized
// (plus you will get code-completion support about object members from IDE)
if (structOutput_1 != NULL) {
// do something with structOutput_1
free(structOutput_1);
}
else if (structOutput_2 != NULL) {
// do something with structOutput_2
free(structOutput_2);
}
I think this is most simple serialization approach in C. But it has some problems:
struct must not have pointers, because you will never know how much memory one needs to allocate when serializing pointers and from where/how to serialize data into pointers.
this example has issues with system endianess - you need to be careful about how data is stored in memory - in big-endian or little-endian fashion and reverse bytes if needed [when casting char * to integal type such as enum] (...or refactor code to be more portable).
If you can use C++, there is the PicklingTools library