source: branches/2886_SymRegGrammarEnumeration/ExpressionClustering/Flann.cs @ 15991

using System;
using System.Collections.Generic;
using System.Linq;
using System.Runtime.InteropServices;
using System.Text;
using System.Threading.Tasks;

namespace ExpressionClustering {
  // /* file flann_example.c */
  // # include "flann.h"
  // # include <stdio.h>
  // # include <assert.h>
  //   /* Function that reads a dataset */
  //   float* read_points(char* filename, int* rows, int* cols);
  //   int main(int argc, char** argv) {
  //     int rows, cols;
  //     int t_rows, t_cols;
  //     float speedup;
  //     /* read dataset points from file dataset.dat */
  //     float* dataset = read_points("dataset.dat", &rows, &cols);
  //     float* testset = read_points("testset.dat", &t_rows, &t_cols);
  //     /* points in dataset and testset should have the same dimensionality */
  //     assert(cols == t_cols);
  //     /* number of nearest neighbors to search */
  //     int nn = 3;
  //     /* allocate memory for the nearest-neighbors indices */
  //     int* result = (int*)malloc(t_rows * nn * sizeof(int));
  //     /* allocate memory for the distances */
  //     float* dists = (float*)malloc(t_rows * nn * sizeof(float));
  // /* index parameters are stored here */
  // struct FLANNParameters p = DEFAULT_FLANN_PARAMETERS;
  // p.algorithm = FLANN_INDEX_AUTOTUNED; /* or FLANN_INDEX_KDTREE, FLANN_INDEX_KMEANS, ... /*
  // p.target_precision = 0.9; /* want 90% target precision */
  // /* compute the 3 nearest-neighbors of each point in the testset */
  // flann_find_nearest_neighbors(dataset, rows, cols, testset, t_rows,
  // result, dists, nn, &p);
  // ...
  // free(dataset);
  // free(testset);
  // free(result);
  // free(dists);
  // return 0;
  // }

  public static class Flann {

    public enum flann_algorithm_t {
      FLANN_INDEX_LINEAR = 0,
      FLANN_INDEX_KDTREE = 1,
      FLANN_INDEX_KMEANS = 2,
      FLANN_INDEX_COMPOSITE = 3,
      FLANN_INDEX_KDTREE_SINGLE = 3,
      FLANN_INDEX_SAVED = 254,
      FLANN_INDEX_AUTOTUNED = 255
    };


    public enum flann_centers_init_t {
      FLANN_CENTERS_RANDOM = 0,
      FLANN_CENTERS_GONZALES = 1,
      FLANN_CENTERS_KMEANSPP = 2
    };

    public enum flann_log_level_t {
      FLANN_LOG_NONE = 0,
      FLANN_LOG_FATAL = 1,
      FLANN_LOG_ERROR = 2,
      FLANN_LOG_WARN = 3,
      FLANN_LOG_INFO = 4
    };

    public enum flann_distance_t {
      FLANN_DIST_EUCLIDEAN = 1, // squared euclidean distance
      FLANN_DIST_MANHATTAN = 2,
      FLANN_DIST_MINKOWSKI = 3,
      FLANN_DIST_HIST_INTERSECT = 5,
      FlANN_DIST_HELLINGER = 6,
      FLANN_DIST_CHI_SQUARE = 7, // chi-square
      FLANN_DIST_KULLBACK_LEIBLER = 8, // kullback-leibler divergence
    };

    public struct FLANNParameters {
      public flann_algorithm_t algorithm; /* the algorithm to use */

      /* search time parameters */
      public int checks;                /* how many leafs (features) to check in one search */
      public float cb_index;            /* cluster boundary index. Used when searching the kmeans tree */
      public float eps;

      /*  kdtree index parameters */
      public int trees;                 /* number of randomized trees to use (for kdtree) */
      public int leaf_max_size;

      /* kmeans index parameters */
      public int branching;             /* branching factor (for kmeans tree) */
      public int iterations;            /* max iterations to perform in one kmeans cluetering (kmeans tree) */
      public flann_centers_init_t centers_init;  /* algorithm used for picking the initial cluster centers for kmeans tree */

      /* autotuned index parameters */
      public float target_precision;    /* precision desired (used for autotuning, -1 otherwise) */
      public float build_weight;        /* build tree time weighting factor */
      public float memory_weight;       /* index memory weigthing factor */
      public float sample_fraction;     /* what fraction of the dataset to use for autotuning */

      public uint table_number_;
      public uint key_size_;
      public uint multi_probe_level_;

      /* other parameters */
      public flann_log_level_t log_level;    /* determines the verbosity of each flann function */
      public long random_seed;            /* random seed to use */
    };

    // struct FLANNParameters DEFAULT_FLANN_PARAMETERS = {
    // FLANN_INDEX_KDTREE,
    // 32, 0.2f, 0.0f,
    // 4, 4,
    // 32, 11, FLANN_CENTERS_RANDOM,
    // 0.9f, 0.01f, 0, 0.1f,
    // FLANN_LOG_NONE, 0
    // };


    public static FLANNParameters DEFAULT_FLANN_PARAMETERS = new FLANNParameters() {
      algorithm = flann_algorithm_t.FLANN_INDEX_KDTREE,
      checks = 32,
      cb_index = 0.2f,
      trees = 4,
      branching = 32,
      iterations = 11,
      centers_init = flann_centers_init_t.FLANN_CENTERS_RANDOM,
      target_precision = 0.9f,
      build_weight = 0.01f,
      memory_weight = 0,
      sample_fraction = 0.1f,
      log_level = flann_log_level_t.FLANN_LOG_NONE,
      random_seed = 0,
    };


    [DllImport("flann-1.7.1.dll")]
    public static extern int flann_find_nearest_neighbors(float[] dataset, int rows, int cols, float[] testset, int t_rows, int[] result, float[] dist, int nn, ref FLANNParameters flann_params);

    [DllImport("flann-1.7.1.dll")]
    public static extern IntPtr flann_build_index(float[] dataset, int rows, int cols, ref float speedup, ref FLANNParameters flann_params);

    [DllImport("flann-1.7.1.dll")]
    public static extern int flann_find_nearest_neighbors_index(IntPtr index_id, float[] testset, int trows, int[] indices, float[] dists, int nn, int checks, ref FLANNParameters flann_params);

    [DllImport("flann-1.7.1.dll")]
    public static extern void flann_set_distance_type(flann_distance_t distance_type, int order);

    [DllImport("flann-1.7.1.dll")]
    public static extern int flann_compute_cluster_centers(float[] dataset, int rows, int cols, int clusters, float[] result, ref FLANNParameters flann_params);

    public static int FindClusters(List<double[]> dataset, out List<int> results, out List<double> distances, int nClusters) {
      var _nRows = dataset.Count;
      var _dists = new float[_nRows];
      var _result = new int[_nRows];
      var _dim = dataset.First().Length;
      FLANNParameters p = DEFAULT_FLANN_PARAMETERS;
      p.algorithm = flann_algorithm_t.FLANN_INDEX_LINEAR;
      p.centers_init = flann_centers_init_t.FLANN_CENTERS_RANDOM;
      p.target_precision = 0.9f;
      p.log_level = flann_log_level_t.FLANN_LOG_INFO;
      // copy training set
      var _ds = new float[dataset.Count * _dim];
      var i = 0;
      foreach (var e in dataset) {
        for (int d = 0; d < _dim; d++) {
          _ds[i++] = (float)e[d];
        }
      }

      flann_set_distance_type(flann_distance_t.FLANN_DIST_EUCLIDEAN, 0);

      float[] centers = new float[nClusters * _dim];
      int actualClusters = flann_compute_cluster_centers(_ds, rows: dataset.Count, cols: _dim, clusters: nClusters, result: centers, flann_params: ref p);

      var res = flann_find_nearest_neighbors(centers, actualClusters, _dim, _ds, _nRows, _result, _dists, 1, ref p);


      distances = _dists.Select(fi => (double)fi).ToList();
      results = _result.ToList();
      return res;
    }

    public static int FindNearestNeighbours(List<double[]> dataset, List<double[]> queryset, out List<int> results, out List<double> distances, int nearestNeighbours = 3) {
      var _nn = nearestNeighbours;
      var _tRows = queryset.Count;
      var _dists = new float[_nn * _tRows];
      var _result = new int[_nn * _tRows];
      var _dim = dataset.First().Length;
      FLANNParameters p = DEFAULT_FLANN_PARAMETERS;
      p.algorithm = flann_algorithm_t.FLANN_INDEX_LINEAR;
      p.centers_init = flann_centers_init_t.FLANN_CENTERS_RANDOM;
      p.target_precision = 0.9f;
      p.log_level = flann_log_level_t.FLANN_LOG_INFO;
      // copy training set
      var _ds = new float[dataset.Count * _dim];
      var i = 0;
      for (int d = 0; d < _dim; d++) {
        foreach (var e in dataset) {
          _ds[i++] = (float)e[d];
        }
      }

      flann_set_distance_type(flann_distance_t.FLANN_DIST_EUCLIDEAN, 0);

      // int nClusters = 100;
      // float[] centers = new float[nClusters * _dim];
      // flann_compute_cluster_centers(_ds, rows: dataset.Count, cols: _dim, clusters: nClusters, result: centers, flann_params: ref p);


      // for each point in the training set find the nearest cluster

      // float speedup = -1.0f;
      // _ds must be a rows × cols matrix stored in row-major order (one feature on each row)                         
      //var index = flann_build_index(_ds, rows: dataset.Count, cols: _dim, speedup: ref speedup, flann_params: ref p);


      // copy testset
      var _testset = new float[_tRows * _dim];
      i = 0;
      for (int d = 0; d < _dim; d++) {
        foreach (var e in queryset) {
          _testset[i++] = (float)e[d];
        }
      }

      //var res = flann_find_nearest_neighbors_index(index, _testset, _tRows, _result, _dists, _nn, 10, ref p);


      var res =
        flann_find_nearest_neighbors(
          _ds, dataset.Count, _dim,
        _testset, _tRows,
        _result, _dists, _nn, ref p);


      distances = _dists.Select(fi => (double)fi).ToList();
      results = _result.ToList();
      return res;
    }
  }
}