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rknng_lib.cpp
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rknng_lib.cpp
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/*******************************************************************************
*
* This file is part of RKNNG software.
* Copyright (C) 2015-2018 Sami Sieranoja
*
* RKNNG is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version. You should have received a copy
* of the GNU Lesser General Public License along with RKNNG.
* If not, see <http://www.gnu.org/licenses/lgpl.html>.
*******************************************************************************/
#include <Python.h>
#include <math.h>
#include <numpy/arrayobject.h>
#include <stdio.h>
#define m(x0) (*(npy_float64 *)((PyArray_DATA(py_m) + (x0)*PyArray_STRIDES(py_m)[0])))
#define m_shape(i) (py_m->dimensions[(i)])
#define r(x0, x1) \
(*(npy_float64 *)((PyArray_DATA(py_r) + (x0)*PyArray_STRIDES(py_r)[0] + \
(x1)*PyArray_STRIDES(py_r)[1])))
#define r_shape(i) (py_r->dimensions[(i)])
#define v(x0, x1) \
(*(npy_float64 *)((PyArray_DATA(py_v) + (x0)*PyArray_STRIDES(py_v)[0] + \
(x1)*PyArray_STRIDES(py_v)[1])))
#define v_shape(i) (py_v->dimensions[(i)])
#define F(x0, x1) \
(*(npy_float64 *)((PyArray_DATA(py_F) + (x0)*PyArray_STRIDES(py_F)[0] + \
(x1)*PyArray_STRIDES(py_F)[1])))
#define F_shape(i) (py_F->dimensions[(i)])
#include "timer.h"
#include "util.h"
#include "globals.h"
#include "dataset.h"
#include "knngraph.h"
kNNGraph *g_ground_truth;
#include "recall.h"
#include "rp_div.h"
#include "brute_force.h"
extern "C" {
void test_rknn_lib() {
DataSet *DS = loadStringData("data/birkbeckU.txt");
debugStringDataset(DS);
}
void printDSVec(kNNGraph *knng, int id) {
DataSet *DS = (DataSet *)knng->DS;
printf("id:%d [%f, %f]\n", id, DS->data[id][0], DS->data[id][1]);
}
float knng_dist(kNNGraph *knng, int p1, int p2) {
DataSet *DS = (DataSet *)knng->DS;
return distance(DS, p1, p2);
}
PyObject *knng2py(kNNGraph *knng) {
// Convert kNN graph to python format
printf("knng2py size=%d\n",knng->size);
PyObject *pyknng = PyList_New(knng->size);
for (int i = 0; i < knng->size; i++) {
PyObject *col = PyList_New(2);
PyObject *nnlist = PyList_New(knng->k);
PyObject *distlist = PyList_New(knng->k);
for (int nn_i = 0; nn_i < knng->k; nn_i++) {
int idx = (int)get_kNN_item_id(knng, i, nn_i);
float dist = get_kNN_item_dist(knng, i, nn_i);
PyList_SetItem(nnlist, nn_i, Py_BuildValue("i", idx));
PyList_SetItem(distlist, nn_i, Py_BuildValue("f", dist));
}
PyList_SetItem(col, 0, nnlist);
PyList_SetItem(col, 1, distlist);
PyList_SetItem(pyknng, i, col);
}
return pyknng;
}
// For generic distance function defined in python
PyObject *__rpdiv_knng_generic(PyObject *py_v, int k, int w, float nndes, float delta, int maxiter) {
PyObject *pysize = PyObject_GetAttrString(py_v, "size");
DataSet *DS = (DataSet *)safemalloc(sizeof(DataSet));
DS->size = PyLong_AsLong(pysize);
DS->dimensionality = 0;
DS->type = T_CUSTOMDF;
DS->pydf = PyObject_GetAttrString(py_v, "distance");
kNNGraph *knng = rpdiv_create_knng(DS, DS, k, w, delta, nndes, maxiter);
PyObject *pyknng = knng2py(knng);
return pyknng;
}
// For vector data
PyObject *__rpdiv_knng(PyArrayObject *py_v, int k, int w, float nndes, float delta, int maxiter, int dtype) {
int N = py_v->dimensions[0];
int D = py_v->dimensions[1];
g_options.minkowski_p=1.0;
// Convert input from python to C data structure
// printf("N=%d D=%d\n",N,D);
DataSet *DS = init_DataSet(N, D);
DS->distance_type = dtype;
for (int i = 0; i < N; i++) {
for (int j = 0; j < D; j++) {
set_val(DS, i, j, v(i, j));
}
}
kNNGraph *knng = rpdiv_create_knng(DS, DS, k, w, delta, nndes, maxiter);
PyObject *pyknng = knng2py(knng);
return pyknng;
}
kNNGraph *get_knng(const char *infn, int k, int data_type, int algo, float endcond,
float nndes_start, int W, int dfunc) {
g_options.distance_type = dfunc;
DataSet *DS;
if (data_type == 1) {
DS = read_ascii_dataset(infn);
} else if (data_type == 2) {
DS = loadStringData(infn);
} else {
printf("Incorrect data type:%d\n", data_type);
}
kNNGraph *knng;
DS->distance_type = dfunc;
g_timer.tick();
if (algo == 0) {
knng = rpdiv_create_knng(DS, DS, k, W, endcond, nndes_start, 100);
} else if (algo == 9) {
knng = brute_force_search(DS, k);
}
// debugVecGraph(DS,knng,0);
// debugStringGraph(DS,knng,0);
knng->DS = (void *)DS;
printf("time=%fs\n", g_timer.get_time());
return knng;
}
float get_elapsed_time() { return g_timer.get_time(); }
}