Xmipp

Python Binding (Text borrowed from http://www.tutorialspoint.com/python/python_further_extensions.htm)

Any code that you write using any compiled language like C, C++ or Java can be integrated or imported into a Python script. This code is considered as an "extension". A Python extension module is nothing more than a normal C library. On Unix machines, writting extensions, usually requires installing a developer-specific package such as python2.5-dev.

For your first look at a Python extension module, you'll be grouping your code into three parts:

  • The C functions you want to expose as the interface from your module.
  • A table mapping the names of your functions as Python developers will see them to C functions inside the extension module.
  • An initialization function.

The C functions:

The signatures of the C implementations of your functions will always take one of the following three forms:

static PyObject *MyFunction( PyObject *self, PyObject *args );

static PyObject *MyFunctionWithKeywords(PyObject *self,
                                 PyObject *args,
                                 PyObject *kw);

static PyObject *MyFunctionWithNoArgs( PyObject *self );

Each one of the preceding declarations returns a Python object. There's no such thing as a void function in Python as there is in C. If you don't want your functions to return a value, return the C equivalent of Python's None value. The Python headers define a macro, Py_RETURN_NONE, that does this for us.

The names of your C functions can be whatever you like as they will never be seen outside of the extension module. So they would be defined as static function.

Your C functions usually are named by combining the Python module and function names together, as shown here:

static PyObject * FileName _isImage(PyObject *obj, PyObject *args, PyObject *kwargs) 
{ 
    if (isImage(FileName _Value(obj))) 
        Py_RETURN_TRUE; 
    else 
        Py_RETURN_FALSE; 
}

This would be a Python function called isImage inside of the module FileName. You'll be putting pointers to your C functions into the method table for the module that usually comes next in your source code.

The method mapping table:

This method table is a simple array of PyMethodDef structures. That structure looks something like this:

struct PyMethodDef {
   char *ml_name;
   PyCFunction ml_meth;
   int ml_flags;
   char *ml_doc;
};

Here is the description of the members of this structure:

ml_name: This is the name of the function as the Python interpreter will present it when it is used in Python programs.

ml_meth: This must be the address to a function that has any one of the signatures described in previous seection.

ml_flags: This tells the interpreter which of the three signatures ml_meth is using.

This flag will usually have a value of METH_VARARGS.

This flag can be bitwise or'ed with METH_KEYWORDS if you want to allow keyword arguments into your function.

This can also have a value of METH_NOARGS that indicates you don't want to accept any arguments.

ml_doc: This is the docstring for the function, which could be NULL if you don't feel like writing one

This table needs to be terminated with a sentinel that consists of NULL and 0 values for the appropriate members.

Example:

static PyMethodDef FileName_methods[] =
    {
        { "compose", (PyCFunction) FileName_compose, METH_VARARGS,
          "Compose from root, number and extension OR prefix with number @" },
        { "composeBlock", (PyCFunction) FileName_composeBlock, METH_VARARGS,
          "Compose from blockname, number, root and extension" },
        { NULL } /* Sentinel */
    };

The initialization function:

The last part of your extension module is the initialization function. This function is called by the Python interpreter when the module is loaded. It's required that the function be named initModule, where Module is the name of the module (the name is initxmipp in our case).

Your C initialization function generally has the following overall structure:

PyMODINIT _FUNC initModule() { Py_InitModule3(func, module_methods, "docstring..."); }

Here is the description of Py_InitModule3 function:

func: This is the function to be exported.

module_methods: This is the mapping table name defined above.

docstring: This is the comment you want to give in your extension.

Example:

PyMODINIT_FUNC initxmipp(void)
{
    //Initialize module variable
    PyObject* module;
    module = Py_InitModule3("xmipp", xmipp_methods,
                            "Xmipp module as a Python extension.");

...
}

All together

A simple example that makes use of all the above concepts:

#include <Python.h>

static PyObject* helloworld(PyObject* self)
{
    return Py_BuildValue("s", "Hello, Python extensions!!");
}

static char helloworld_docs[] =
    "helloworld( ): Any message you want to put here!!\n";

static PyMethodDef helloworld_funcs[] = {
    {"helloworld", (PyCFunction)helloworld, 
     METH_NOARGS, helloworld_docs},
    {NULL}
};

void inithelloworld(void)
{
    Py_InitModule3("helloworld", helloworld_funcs,
                   "Extension module example!");
}

Passing Function Parameters:

Most of the time you will add functions to an existing module. For example, the following function, that accepts some number of parameters, would be defined like this:

static PyObject *module_func(PyObject *self, PyObject *args) {
   /* Parse args and do something interesting here. */
   Py_RETURN_NONE;
}

The method table containing an entry for the new function would look like this:

static PyMethodDef module_methods[] = {

   { "func", module_func, METH_VARARGS, "help message" },
   { NULL, NULL, 0, NULL }
};

You can use API PyArg_ParseTuple function to extract the arguments from the one PyObject pointer passed into your C function.

The first argument to PyArg_ParseTuple is the args argument. This is the object you'll be parsing. The second argument is a format string describing the arguments as you expect them to appear. Each argument is represented by one or more characters in the format string as follows.

static PyObject *module_func(PyObject *self, PyObject *args) {
   int i;
   double d;
   char *s;

   if (!PyArg_ParseTuple(args, "ids", &i, &d, &s)) {
      return NULL;
   }
   
   /* Do something interesting here. */
   Py_RETURN_NONE;
}

Compiling the new version of your module and importing it will enable you to invoke the new function with any number of arguments of any type:

module.func(1, "three", 2.0)
module.func(s="three", d=2.0, i=1)

The PyArg _ParseTuple Function:

Here is a list of format codes for PyArg _ParseTuple function:

Code C type Meaning
c char A Python string of length 1 becomes a C char.
d double A Python float becomes a C double.
f float A Python float becomes a C float.
i int A Python int becomes a C int.
l long A Python int becomes a C long.
L long long A Python int becomes a C long long
O PyObject* Gets non-NULL borrowed reference to Python argument.
s char* Python string without embedded nulls to C char*.
s# char*+int Any Python string to C address and length.
t# char*+int Read-only single-segment buffer to C address and length.
u Py_UNICODE* Python Unicode without embedded nulls to C.
u# Py_UNICODE*+int Any Python Unicode C address and length.
w# char*+int Read/write single-segment buffer to C address and length.
z char* Like s, also accepts None (sets C char* to NULL).
z# char*+int Like s#, also accepts None (sets C char* to NULL).
(...) as per ... A Python sequence is treated as one argument per item.
\   The following arguments are optional.
:   Format end, followed by function name for error messages.
;   Format end, followed by entire error message text.

Returning Values:

Py_BuildValue takes in a format string much like PyArg _ParseTuple does. Instead of passing in the addresses of the values you're building, you pass in the actual values. Here's an example showing how to implement an add function:

static PyObject *foo_add(PyObject *self, PyObject *args) {
   int a;
   int b;

   if (!PyArg_ParseTuple(args, "ii", &a, &b)) {
      return NULL;
   }
   return Py_BuildValue("i", a + b);
}

This is what it would look like if implemented in Python:

def add(a, b):
   return (a + b)

You can return two values from your function as follows, this would be cauptured using a list in Python.

static PyObject *foo_add_subtract(PyObject *self, PyObject *args) {
   int a;
   int b;

   if (!PyArg_ParseTuple(args, "ii", &a, &b)) {
      return NULL;
   }
   return Py_BuildValue("ii", a + b, a - b);
}

This is what it would look like if implemented in Python:

def add_subtract(a, b):
   return (a + b, a - b)

Calling Python (+numpy) from C:

Here is an example code to perform the sum of two volumes in Python:

#include <data/xmipp_image.h>

#include <Python.h>
#include <numpy/ndarrayobject.h>

void myImport_array()
{
    import_array();
}

int main()
{
 try {
 time_config();

 Image<double> I;
 I.read("/home/coss/temp/BPV_Project/BPV_scale_filtered_windowed.vol");
 ProcessorTimeStamp t0;
 const MultidimArray<double> &mI=I();
 annotate_processor_time(&t0);
 double retval=0.0;
 FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mI)
 retval+=DIRECT_MULTIDIM_ELEM(mI,n)+DIRECT_MULTIDIM_ELEM(mI,n);
     std::cout << elapsed_time(t0,false) << std::endl;
 std::cout << "In C++: " << retval << std::endl;

 std::cout << "Initializing Python\n";
 annotate_processor_time(&t0);
 Py_Initialize();
 myImport_array();
     std::cout << elapsed_time(t0,false) << std::endl;

 // Create numpy array in Python with I()
 std::cout << "Creating numpy array\n";
 annotate_processor_time(&t0);
 npy_intp dim[3];
 dim[0]=ZSIZE(I());
 dim[1]=YSIZE(I());
 dim[2]=XSIZE(I());
 PyObject *pyI=PyArray_SimpleNewFromData(3, dim, NPY_DOUBLE, (void *)MULTIDIM_ARRAY(I()));
     std::cout << elapsed_time(t0,false) << std::endl;

 // Import testPython
 std::cout << "Importing module\n";
 annotate_processor_time(&t0);
 PyObject* pName = PyString_FromString("testPython"); // Import testPython
 PyObject* pModule = PyImport_Import(pName);
 Py_DECREF(pName);
     std::cout << elapsed_time(t0,false) << std::endl;

 // Call sum
 std::cout << "Calling sum\n";
 annotate_processor_time(&t0);
 PyObject *arglist = Py_BuildValue("OO", pyI, pyI);
 PyObject *pFunc = PyObject_GetAttrString(pModule, "sum");
 PyObject *result = PyObject_CallObject(pFunc, arglist);
     std::cout << elapsed_time(t0,false) << std::endl;
 std::cout << "In Python: " << PyFloat_AsDouble(result) << std::endl;
 } catch (XmippError e)
 {
 std::cout << e << std::endl;
 }
 return 0;
}

You have to compile with

xmipp_compile -i myCode.cpp --python

And the Python code is

def sum(I1,I2):
   retval=I1.sum()+I2.sum()
   return retval