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wavcorr.c
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wavcorr.c
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/*
wavcorr.c
*/
#include <Python.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
inline int min(int x, int y) { return (x < y)? x : y; }
inline int max(int x, int y) { return (x < y)? y : x; }
inline double hann(int i, int n) { return (1.0-cos(2.0*M_PI*i/n))/2.0; }
/* calcsims16: compute the similarity between two vectors. */
double calcsims16(int window, short* seq1, short* seq2)
{
int i;
double n1 = 0, n2 = 0, dot = 0;
for (i = 0; i < window; i++) {
double x1 = seq1[i]/32768.0;
double x2 = seq2[i]/32768.0;
n1 += x1*x1;
n2 += x2*x2;
dot += x1*x2;
}
return (n1*n2)? (dot/sqrt(n1*n2)) : 0;
}
/* autocorrs16: find the window that has the maximum similarity. */
int autocorrs16(double* psim, int window0, int window1, int length, short* seq)
{
if (window1 < window0) {
int x = window1;
window1 = window0;
window0 = x;
}
/* assert(window0 <= window1); */
int wmax = 0;
double smax = -1;
int w;
for (w = window0; w <= window1; w++) {
int w1 = window1 - (window1%w);
if (w1+w <= length) {
double s = calcsims16(w1, seq, seq+w);
if (smax < s) {
wmax = w;
smax = s;
}
}
}
*psim = smax;
return wmax;
}
/* autosplices16: find the window that has the maximum similarity. */
int autosplices16(double* psim, int window0, int window1,
int length1, short* seq1, int length2, short* seq2)
{
if (window1 < window0) {
int x = window1;
window1 = window0;
window0 = x;
}
/* assert(window0 <= window1); */
int wmax = 0;
double smax = -1;
int w;
for (w = window0; w <= window1; w++) {
if (w <= length1 && w <= length2) {
double s = calcsims16(w, seq1+length1-w, seq2);
if (smax < s) {
wmax = w;
smax = s;
}
}
}
*psim = smax;
return wmax;
}
/* psolas16: overlap-add two vectors. */
void psolas16(int outlen, short* out,
int length1, short* seq1,
int length2, short* seq2)
{
int i;
for (i = 0; i < outlen; i++) {
/* i < outlen ==> i*length/outlen < length */
double v = 0;
if (0 < length1) {
/* first half (decreasing) */
v += seq1[i*length1/outlen] * hann(i+outlen, outlen*2);
}
if (0 < length2) {
/* second half (increasing) */
v += seq2[i*length2/outlen] * hann(i, outlen*2);
}
out[i] = (short)v;
}
}
/* Python functions
*/
/* pycalcsims16(window, data1, offset1, data2, offset2); */
static PyObject* pycalcsims16(PyObject* self, PyObject* args)
{
int window;
PyObject* data1;
PyObject* data2;
int offset1;
int offset2;
if (!PyArg_ParseTuple(args, "iOiOi", &window,
&data1, &offset1, &data2, &offset2)) {
return NULL;
}
if (!PyString_CheckExact(data1) ||
!PyString_CheckExact(data2)) {
PyErr_SetString(PyExc_TypeError, "Must be string");
return NULL;
}
int length1 = PyString_Size(data1) / sizeof(short);
int length2 = PyString_Size(data2) / sizeof(short);
if (window < 0 ||
offset1 < 0 || length1 < offset1+window ||
offset2 < 0 || length2 < offset2+window) {
PyErr_SetString(PyExc_ValueError, "Invalid offset/window");
return NULL;
}
short* seq1 = (short*)PyString_AsString(data1);
short* seq2 = (short*)PyString_AsString(data2);
double sim = calcsims16(window, &seq1[offset1], &seq2[offset2]);
return PyFloat_FromDouble(sim);
}
/* pyautocorrs16(window0, window1, data, offset); */
static PyObject* pyautocorrs16(PyObject* self, PyObject* args)
{
int window0, window1;
PyObject* data;
int offset;
if (!PyArg_ParseTuple(args, "iiOi", &window0, &window1, &data, &offset)) {
return NULL;
}
if (!PyString_CheckExact(data)) {
PyErr_SetString(PyExc_TypeError, "Must be string");
return NULL;
}
int length = PyString_Size(data) / sizeof(short);
if (window0 < 0 || window1 < 0 ||
offset < 0 || length < offset+window0 || length < offset+window1) {
PyErr_SetString(PyExc_ValueError, "Invalid offset/window");
return NULL;
}
short* seq = (short*)PyString_AsString(data);
double smax = 0;
int wmax = autocorrs16(&smax, window0, window1, length-offset, &seq[offset]);
PyObject* tuple;
{
PyObject* v1 = PyInt_FromLong(wmax);
PyObject* v2 = PyFloat_FromDouble(smax);
tuple = PyTuple_Pack(2, v1, v2);
Py_DECREF(v1);
Py_DECREF(v2);
}
return tuple;
}
/* pyautosplices16(window0, window1, data1, data2); */
static PyObject* pyautosplices16(PyObject* self, PyObject* args)
{
int window0, window1;
PyObject* data1;
PyObject* data2;
if (!PyArg_ParseTuple(args, "iiOO", &window0, &window1, &data1, &data2)) {
return NULL;
}
if (!PyString_CheckExact(data1) ||
!PyString_CheckExact(data2)) {
PyErr_SetString(PyExc_TypeError, "Must be string");
return NULL;
}
int length1 = PyString_Size(data1) / sizeof(short);
int length2 = PyString_Size(data2) / sizeof(short);
if (window0 < 0 || window1 < 0 ||
length1 < window0 || length1 < window1 ||
length2 < window0 || length2 < window1) {
PyErr_SetString(PyExc_ValueError, "Invalid offset/window");
return NULL;
}
short* seq1 = (short*)PyString_AsString(data1);
short* seq2 = (short*)PyString_AsString(data2);
double smax = 0;
int wmax = autosplices16(&smax, window0, window1, length1, seq1, length2, seq2);
PyObject* tuple;
{
PyObject* v1 = PyInt_FromLong(wmax);
PyObject* v2 = PyFloat_FromDouble(smax);
tuple = PyTuple_Pack(2, v1, v2);
Py_DECREF(v1);
Py_DECREF(v2);
}
return tuple;
}
/* pypsolas16(outlen,
offset1, window1, data1,
offset2, window2, data2); */
static PyObject* pypsolas16(PyObject* self, PyObject* args)
{
int outlen;
int offset1, offset2;
int window1, window2;
PyObject* data1;
PyObject* data2;
if (!PyArg_ParseTuple(args, "iiiOiiO", &outlen,
&offset1, &window1, &data1,
&offset2, &window2, &data2)) {
return NULL;
}
if (!PyString_CheckExact(data1) ||
!PyString_CheckExact(data2)) {
PyErr_SetString(PyExc_TypeError, "Must be string");
return NULL;
}
int length1 = PyString_Size(data1) / sizeof(short);
int length2 = PyString_Size(data2) / sizeof(short);
if (window1 < 0 || window2 < 0 ||
offset1 < 0 || length1 < offset1+window1 ||
offset2 < 0 || length2 < offset2+window2) {
PyErr_SetString(PyExc_ValueError, "Invalid offset/window");
return NULL;
}
if (outlen <= 0) {
PyErr_SetString(PyExc_ValueError, "Invalid outlen");
return NULL;
}
short* out = (short*) PyMem_Malloc(sizeof(short)*outlen);
if (out == NULL) return PyErr_NoMemory();
short* seq1 = (short*)PyString_AsString(data1);
short* seq2 = (short*)PyString_AsString(data2);
psolas16(outlen, out, window1, &seq1[offset1], window2, &seq2[offset2]);
PyObject* obj = PyString_FromStringAndSize((char*)out, sizeof(short)*outlen);
PyMem_Free(out);
return obj;
}
/* Module initialization */
PyMODINIT_FUNC
initwavcorr(void)
{
static PyMethodDef functions[] = {
{ "calcsims16", (PyCFunction)pycalcsims16, METH_VARARGS,
"calcsims16"
},
{ "autocorrs16", (PyCFunction)pyautocorrs16, METH_VARARGS,
"autocorrs16"
},
{ "autosplices16", (PyCFunction)pyautosplices16, METH_VARARGS,
"autosplices16"
},
{ "psolas16", (PyCFunction)pypsolas16, METH_VARARGS,
"psolas16"
},
{NULL, NULL},
};
Py_InitModule3("wavcorr", functions, "wavcorr");
}