/*
def choose_node_with_higher_cardinality(condensed_matrix,nodes,cutoff):
    """
    Returns the node in 'nodes' which has the bigger number of neighbours. One node
    is a neighbour of other if the distance between them is lower than the cutoff.
    The distances are stored in a condensed form distance matrix ('condensed_matrix') which
    represents a 'row_len' x 'row_len' symmetric square matrix.
    """
    neighbors = numpy.array([0]*len(nodes))
    len_nodes = len(nodes)
    nodes.sort()
    for i in range(len_nodes-1):
        inode = nodes[i]
        for j in range(i+1,len_nodes):
            #print inode, nodes[j],":",access_element(condensed_matrix, inode, nodes[j]-1, row_len)
            if condensed_matrix[inode,nodes[j]]<=cutoff: #access_element(condensed_matrix, inode, nodes[j]-1, row_len) <= cutoff:
                neighbors[i] += 1
                neighbors[j] += 1
        #print neighbors
    idx = neighbors.argmax()
    return (nodes[idx],neighbors[idx])
*/
static PyObject*  condensedMatrix_choose_node_with_higher_cardinality(CondensedMatrix* self, PyObject *args){
	// Parse all arguments
	PyObject *nodes_list,*cutoff_obj;

	if (!PyArg_ParseTuple(args, "OO",&nodes_list,&cutoff_obj)){
		PyErr_SetString(PyExc_RuntimeError, "Error parsing parameters.");
		return NULL;
	}

	// Convert to C types
	double cutoff = PyFloat_AsDouble((PyObject *)cutoff_obj);
	int len_nodes = PyList_Size((PyObject *)nodes_list);
	int* nodes = new int[len_nodes];
	for(int i = 0; i < len_nodes; ++i){
		nodes[i] = PyInt_AS_LONG(PyList_GET_ITEM((PyObject*) nodes_list,i));
	}
	//Do the job
	vector<int> neighbors(len_nodes,0);
	int inode,jnode,pos;
	double value;
	for (int i =0; i< len_nodes-1;++i){
		inode = nodes[i];
		for (int j = i+1; j< len_nodes;++j){
			jnode =nodes[j];
			pos = calc_vector_pos(inode,jnode,self);
			value =self->data[pos];
			if(value <= cutoff){
				neighbors[i] += 1;
				neighbors[j] += 1;
			}
		}
	}
	//Get index with maximum value
	int max =  *(max_element(neighbors.begin(),neighbors.end()));
	int index = 0;
	for (int i = 0; i< len_nodes-1;++i){
		if (neighbors[i]==max){
			index = i;
			break;
		}
	}

	PyObject* tuple = Py_BuildValue("(ii)", nodes[index],neighbors[index]);//PyTuple_Pack(2,nodes[index],neighbors[index]);
	delete [] nodes;
	return tuple;
}

/**
 * Returns an AmberSystem block as an array of ints.
 *
 * You have to free the thing you get back from this method!
 * Equivalent to: mol.blocks[block_name]
 */
int *get_block_as_int_array(PyObject *mol, const char *block_name, int *size)
{
  PyObject *block;
  if((block = get_block(mol, block_name)) == NULL)
  {
    // fprintf(stderr, "get_block_as_int_array: Couldn't find block %s\n", block_name);
    return NULL;
  }
  // Extract the list of integers from the AmberSystem
  Py_ssize_t block_length = PySequence_Size(block);
  *size = (int) block_length;
  int *data = (int*) malloc(sizeof(int) * (int) block_length);
  for(Py_ssize_t i = 0; i < block_length; i++)
    data[i] = PyInt_AS_LONG(PySequence_Fast_GET_ITEM(block, i));
  
  return data;
}

/*static*/ PyObject *
ColorAttribute_SetColor(PyObject *self, PyObject *args)
{
    ColorAttributeObject *obj = (ColorAttributeObject *)self;

    unsigned char *cvals = obj->data->GetColor();
    if(!PyArg_ParseTuple(args, "cccc", &cvals[0], &cvals[1], &cvals[2], &cvals[3]))
    {
        PyObject     *tuple;
        if(!PyArg_ParseTuple(args, "O", &tuple))
            return NULL;

        if(PyTuple_Check(tuple))
        {
            if(PyTuple_Size(tuple) != 4)
                return NULL;

            PyErr_Clear();
            for(int i = 0; i < PyTuple_Size(tuple); ++i)
            {
                int c;
                PyObject *item = PyTuple_GET_ITEM(tuple, i);
                if(PyFloat_Check(item))
                    c = int(PyFloat_AS_DOUBLE(item));
                else if(PyInt_Check(item))
                    c = int(PyInt_AS_LONG(item));
                else if(PyLong_Check(item))
                    c = int(PyLong_AsDouble(item));
                else
                    c = 0;

                if(c < 0) c = 0;
                if(c > 255) c = 255;
                cvals[i] = (unsigned char)(c);
            }
        }
        else
            return NULL;
    }

    // Mark the color in the object as modified.
    obj->data->SelectColor();

    Py_INCREF(Py_None);
    return Py_None;
}

static PyObject *
SpiDev_writebytes(SpiDevObject *self, PyObject *args)
{
	int		status;
	uint16_t	ii, len;
	uint8_t	buf[SPIDEV_MAXPATH];
	PyObject	*list;

	if (!PyArg_ParseTuple(args, "O:write", &list))
		return NULL;

	if (!PyList_Check(list)) {
		PyErr_SetString(PyExc_TypeError, wrmsg);
		return NULL;
	}

	if ((len = PyList_GET_SIZE(list)) > SPIDEV_MAXPATH) {
		PyErr_SetString(PyExc_OverflowError, wrmsg);
		return NULL;
	}

	for (ii = 0; ii < len; ii++) {
		PyObject *val = PyList_GET_ITEM(list, ii);
		if (!PyInt_Check(val)) {
			PyErr_SetString(PyExc_TypeError, wrmsg);
			return NULL;
		}
		buf[ii] = (__u8)PyInt_AS_LONG(val);
	}

	status = write(self->fd, &buf[0], len);

	if (status < 0) {
		PyErr_SetFromErrno(PyExc_IOError);
		return NULL;
	}

	if (status != len) {
		perror("short write");
		return NULL;
	}

	Py_INCREF(Py_None);
	return Py_None;
}

static int
set_int(_UpdateCollectionPackageObject *self, PyObject *value, void *member_offset)
{
    long val;
    if (check_UpdateCollectionPackageStatus(self))
        return -1;
    if (PyLong_Check(value)) {
        val = PyLong_AsLong(value);
    } else if (PyInt_Check(value)) {
        val = PyInt_AS_LONG(value);
    } else {
        PyErr_SetString(PyExc_TypeError, "Number expected!");
        return -1;
    }
    cr_UpdateCollectionPackage *pkg = self->pkg;
    *((int *) ((size_t) pkg + (size_t) member_offset)) = (int) val;
    return 0;
}

      static unsigned BOOST_PYTHON_LONG_LONG extract(PyObject* intermediate)
      {
#if PY_VERSION_HEX < 0x03000000
          if (PyInt_Check(intermediate))
          {
              return numeric_cast<unsigned BOOST_PYTHON_LONG_LONG>(PyInt_AS_LONG(intermediate));
          }
          else
#endif
          {
              unsigned BOOST_PYTHON_LONG_LONG result = PyLong_AsUnsignedLongLong(intermediate);
              
              if (PyErr_Occurred())
                  throw_error_already_set();

              return result;
          }
      }

static INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
#if PY_VERSION_HEX < 0x03000000
    if (likely(PyInt_CheckExact(x) || PyInt_Check(x))) {
        long val = PyInt_AS_LONG(x);
        return (signed PY_LONG_LONG)val;
    } else
#endif
    if (likely(PyLong_CheckExact(x) || PyLong_Check(x))) {
        return PyLong_AsLongLong(x);
    } else {
        signed PY_LONG_LONG val;
        PyObject *tmp = __Pyx_PyNumber_Int(x);
        if (!tmp) return (signed PY_LONG_LONG)-1;
        val = __Pyx_PyInt_AsSignedLongLong(tmp);
        Py_DECREF(tmp);
        return val;
    }
}

static int
set_num(_PackageObject *self, PyObject *value, void *member_offset)
{
    gint64 val;
    if (check_PackageStatus(self))
        return -1;
    if (PyLong_Check(value)) {
        val = (gint64) PyLong_AsLong(value);
    } else if (PyInt_Check(value)) {
        val = (gint64) PyInt_AS_LONG(value);
    } else {
        PyErr_SetString(PyExc_TypeError, "Number expected!");
        return -1;
    }
    cr_Package *pkg = self->package;
    *((gint64 *) ((size_t) pkg + (size_t) member_offset)) = val;
    return 0;
}

static PyArrayObject * 
PyGSL_PyArray_generate_gsl_matrix_view(PyObject *src,
				      int array_type,
				      int argnum)
{
     PyObject *tmp;
     PyArrayObject *a_array = NULL;

     PyGSL_array_index_t dimensions[2];
     int i;

     FUNC_MESS_BEGIN();     
     if(!PySequence_Check(src) || PySequence_Size(src) != 2){
	  sprintf(pygsl_error_str, "I need a sequence of two elements as argument number % 3d",
		  argnum);
	 PyErr_SetString(PyExc_TypeError, pygsl_error_str);
	 return NULL;

     }

     for(i = 0; i<2; i++){
	  tmp = PyNumber_Int(PySequence_GetItem(src, i));
	  if(!tmp){
	       sprintf(pygsl_error_str, "I could not convert argument number % 3d. for dimension %3d to an integer.",
		       argnum, i);
	       PyErr_SetString(PyExc_TypeError, pygsl_error_str);
	       return NULL;
	  }
	  dimensions[i] = PyInt_AS_LONG(tmp);
	  Py_DECREF(tmp);
	  if(dimensions[i] <= 0){
	       sprintf(pygsl_error_str, "Argument number % 3d is % 10ld< 0. Its the size of the vector and thus must be positive!",
		       argnum, (long)dimensions[i]);
	       PyErr_SetString(PyExc_TypeError, pygsl_error_str);
	       return NULL;
	  }

     }     
     a_array = (PyArrayObject *) PyGSL_New_Array(2, dimensions, array_type);
     if(NULL == a_array){
	  return NULL;
     }
     return a_array;
}

static PyObject* condensedMatrix_get_neighbors_for_node(CondensedMatrix* self, PyObject *args){
	// Parse all arguments
	PyObject *nodes_left_list, *node_obj,*cutoff_obj;

	if (!PyArg_ParseTuple(args, "OOO",&node_obj,&nodes_left_list,&cutoff_obj)){
		PyErr_SetString(PyExc_RuntimeError, "Error parsing parameters.");
		return NULL;
	}

	// Convert to C types
	int node = (int) PyInt_AsLong((PyObject *)node_obj);
	double cutoff = PyFloat_AsDouble((PyObject *)cutoff_obj);
	int len_nodes_left = PyList_Size((PyObject *)nodes_left_list);
	int* nodes_left = new int[len_nodes_left];
	for(int i = 0; i < len_nodes_left; ++i){
		nodes_left[i] = PyInt_AS_LONG(PyList_GET_ITEM((PyObject*) nodes_left_list,i));
	}

	// Do the job
	vector<int> neighbours;
	int pos,j;
	for(int i = 0; i < len_nodes_left; ++i){
		j = nodes_left[i];
		if(node<j){
			pos = calc_vector_pos(node,j,self);
			if(self->data[pos]<=cutoff){
				neighbours.push_back(j);
			}
		}
		if(node>j){
			pos = calc_vector_pos(j,node,self);
			if(self->data[pos]<=cutoff){
				neighbours.push_back(j);
			}
		}
	}

	int neigh_len = neighbours.size();
	npy_intp dims[1] = {neigh_len};
	int* neighbours_data = new int[neigh_len];
	copy(&(neighbours[0]),&(neighbours[0]) + neigh_len,neighbours_data);
	delete [] nodes_left;
	return PyArray_SimpleNewFromData(1,dims,NPY_INT,neighbours_data);
}

static void
w_object(PyObject *v, WFILE *p)
{
	int i, n;

	p->depth++;

	if (p->depth > MAX_MARSHAL_STACK_DEPTH) {
		p->error = 2;
	}
	else if (v == NULL) {
		w_byte(TYPE_NULL, p);
	}
	else if (v == Py_None) {
		w_byte(TYPE_NONE, p);
	}
	else if (v == PyExc_StopIteration) {
		w_byte(TYPE_STOPITER, p);
	}
	else if (v == Py_Ellipsis) {
	        w_byte(TYPE_ELLIPSIS, p);
	}
	else if (v == Py_False) {
	        w_byte(TYPE_FALSE, p);
	}
	else if (v == Py_True) {
	        w_byte(TYPE_TRUE, p);
	}
	else if (PyInt_Check(v)) {
		long x = PyInt_AS_LONG((PyIntObject *)v);
#if SIZEOF_LONG > 4
		long y = Py_ARITHMETIC_RIGHT_SHIFT(long, x, 31);
		if (y && y != -1) {
			w_byte(TYPE_INT64, p);
			w_long64(x, p);
		}
		else
#endif
			{
			w_byte(TYPE_INT, p);
			w_long(x, p);
		}
	}
	else if (PyLong_Check(v)) {

static PyObject *
Text3DObject_SetPosition(PyObject *self, PyObject *args)
{
    Text3DObjectObject *obj = (Text3DObjectObject *)self;

    double *dvals = obj->data->GetPosition();
    if(!PyArg_ParseTuple(args, "ddd", &dvals[0], &dvals[1], &dvals[2]))
    {
        PyObject     *tuple;
        if(!PyArg_ParseTuple(args, "O", &tuple))
            return NULL;

        if(PyTuple_Check(tuple))
        {
            if(PyTuple_Size(tuple) != 3)
                return NULL;

            PyErr_Clear();
            for(int i = 0; i < PyTuple_Size(tuple); ++i)
            {
                PyObject *item = PyTuple_GET_ITEM(tuple, i);
                if(PyFloat_Check(item))
                    dvals[i] = PyFloat_AS_DOUBLE(item);
                else if(PyInt_Check(item))
                    dvals[i] = double(PyInt_AS_LONG(item));
                else if(PyLong_Check(item))
                    dvals[i] = PyLong_AsDouble(item);
                else
                    dvals[i] = 0.;
            }
        }
        else
            return NULL;
    }

    // Mark the position in the object as modified.
    obj->data->SelectPosition();

/*CUSTOM*/
    UpdateAnnotationHelper(obj->data);

    Py_INCREF(Py_None);
    return Py_None;
}

static void *PyDateToINT64(JSOBJ _obj, JSONTypeContext *tc, void *outValue, size_t *_outLen)
{
  PyObject *obj = (PyObject *) _obj;
  PyObject *date, *ord;
  int y, m, d, days;

  y = PyDateTime_GET_YEAR(obj);
  m = PyDateTime_GET_MONTH(obj);
  d = PyDateTime_GET_DAY(obj);

  date = PyDate_FromDate(y, m, 1);
  ord = PyObject_CallMethod(date, "toordinal", NULL);
  days = PyInt_AS_LONG(ord) - EPOCH_ORD + d - 1;
  Py_DECREF(date);
  Py_DECREF(ord);
  *( (JSINT64 *) outValue) = ((JSINT64) days * 86400);

  return NULL;
}

static int
test_dict_inner(int count)
{
	Py_ssize_t pos = 0, iterations = 0;
	int i;
	PyObject *dict = PyDict_New();
	PyObject *v, *k;

	if (dict == NULL)
		return -1;

	for (i = 0; i < count; i++) {
		v = PyInt_FromLong(i);
		PyDict_SetItem(dict, v, v);
		Py_DECREF(v);
	}

	while (PyDict_Next(dict, &pos, &k, &v)) {
		PyObject *o;
		iterations++;

		i = PyInt_AS_LONG(v) + 1;
		o = PyInt_FromLong(i);
		if (o == NULL)
			return -1;
		if (PyDict_SetItem(dict, k, o) < 0) {
			Py_DECREF(o);
			return -1;
		}
		Py_DECREF(o);
	}

	Py_DECREF(dict);

	if (iterations != count) {
		PyErr_SetString(
			TestError,
			"test_dict_iteration: dict iteration went wrong ");
		return -1;
	} else {
		return 0;
	}
}

static PyObject *
grp_getgrgid(PyObject *self, PyObject *pyo_id)
{
    PyObject *py_int_id;
    unsigned int gid;
    struct group *p;

    py_int_id = PyNumber_Int(pyo_id);
    if (!py_int_id)
	    return NULL;
    gid = PyInt_AS_LONG(py_int_id);
    Py_DECREF(py_int_id);

    if ((p = getgrgid(gid)) == NULL) {
	PyErr_Format(PyExc_KeyError, "getgrgid(): gid not found: %d", gid);
        return NULL;
    }
    return mkgrent(p);
}

int        s_pyvpi_systfdata_settype(s_pyvpi_systfdata *self, PyObject *value, void *closure)
{
    //Check type, it must be vpiSysTask,vpiSysFunc.
    int tmp;
    if(!PyInt_Check(value)){
        PyErr_SetString(VpiError,
                        "The value must be vpiSys[Task,Func].");
        return -1;
    }
    tmp = PyInt_AS_LONG(value);
    if(tmp != vpiSysTask &&
       tmp != vpiSysFunc) {
        PyErr_SetString(VpiError,
                        "The value must be vpiSys[Task,Func].");
        return -1;
    }
    self->_vpi_systfdata.type = tmp;
    return 0;
}

static PyObject *
builtin_videomode(PyObject *self, PyObject *args)
{
	PyObject *v = NULL;

	if (!PyArg_UnpackTuple(args, "inb", 1, 1, &v))
		return NULL;
	
	if (!PyInt_CheckExact(v))
		return NULL;

	switch(PyInt_AS_LONG(v))	{
	case 0:	set80x25();		break;
	case 1: set640x480x16();	break;
	case 2: set320x200x256();	break;
	}
	Py_INCREF(Py_True);
	return Py_True;
}

static PyObject *
builtin_inb(PyObject *self, PyObject *args)
{
	PyObject *v = NULL;

	if (!PyArg_UnpackTuple(args, "inb", 1, 1, &v))
		return NULL;
	
	if (!PyInt_CheckExact(v)) {
		/* ERROR */
		return NULL;
	} else {
		unsigned short port = PyInt_AS_LONG(v);
		unsigned char data = in(port);
		PyObject *result = PyInt_FromLong(data);

		return result;
	}
}

static PyObject*
test_list_api(PyObject *self)
{
	PyObject* list;
	int i;

	/* SF bug 132008:  PyList_Reverse segfaults */
#define NLIST 30
	list = PyList_New(NLIST);
	if (list == (PyObject*)NULL)
		return (PyObject*)NULL;
	/* list = range(NLIST) */
	for (i = 0; i < NLIST; ++i) {
		PyObject* anint = PyInt_FromLong(i);
		if (anint == (PyObject*)NULL) {
			Py_DECREF(list);
			return (PyObject*)NULL;
		}
		PyList_SET_ITEM(list, i, anint);
	}
	/* list.reverse(), via PyList_Reverse() */
	i = PyList_Reverse(list);   /* should not blow up! */
	if (i != 0) {
		Py_DECREF(list);
		return (PyObject*)NULL;
	}
	/* Check that list == range(29, -1, -1) now */
	for (i = 0; i < NLIST; ++i) {
		PyObject* anint = PyList_GET_ITEM(list, i);
		if (PyInt_AS_LONG(anint) != NLIST-1-i) {
			PyErr_SetString(TestError,
			                "test_list_api: reverse screwed up");
			Py_DECREF(list);
			return (PyObject*)NULL;
		}
	}
	Py_DECREF(list);
#undef NLIST

	Py_INCREF(Py_None);
	return Py_None;
}

/* adapted from Python source, floatobject.c:convert_to_double */
int
convert_to_double(PyObject *obj, double *dbl)
{
    if (PyFloat_Check(obj)) {
        *dbl = PyFloat_AS_DOUBLE(obj);
#ifndef IS_PY3K
    } else if (PyInt_Check(obj)) {
        *dbl = (double)PyInt_AS_LONG(obj);
#endif
    } else if (PyLong_Check(obj)) {
        *dbl = PyLong_AsDouble(obj);
        if (*dbl == -1.0 && PyErr_Occurred()) {
            return 0;
        }
    } else {
        PyErr_SetString(PyExc_ValueError, "Expected a number");
        return 0;
    }
    return 1;
}