/******************************************************************************
 ** Filename: cluster.c
 ** Purpose:  Routines for clustering points in N-D space
 ** Author:   Dan Johnson
 ** History:  5/29/89, DSJ, Created.
 **
 ** (c) Copyright Hewlett-Packard Company, 1988.
 ** Licensed under the Apache License, Version 2.0 (the "License");
 ** you may not use this file except in compliance with the License.
 ** You may obtain a copy of the License at
 ** http://www.apache.org/licenses/LICENSE-2.0
 ** Unless required by applicable law or agreed to in writing, software
 ** distributed under the License is distributed on an "AS IS" BASIS,
 ** WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 ** See the License for the specific language governing permissions and
 ** limitations under the License.
 ******************************************************************************/
#include "const.h"
#include "cluster.h"
#include "emalloc.h"
#include "genericheap.h"
#include "helpers.h"
#include "kdpair.h"
#include "matrix.h"
#include "tprintf.h"
#include "danerror.h"
#include "freelist.h"
#include <math.h>

#define HOTELLING 1  // If true use Hotelling's test to decide where to split.
#define FTABLE_X 10  // Size of FTable.
#define FTABLE_Y 100  // Size of FTable.

// Table of values approximating the cumulative F-distribution for a confidence of 1%.
const double FTable[FTABLE_Y][FTABLE_X] = {
 {4052.19, 4999.52, 5403.34, 5624.62, 5763.65, 5858.97, 5928.33, 5981.10, 6022.50, 6055.85,},
  {98.502,  99.000,  99.166,  99.249,  99.300,  99.333,  99.356,  99.374,  99.388,  99.399,},
  {34.116,  30.816,  29.457,  28.710,  28.237,  27.911,  27.672,  27.489,  27.345,  27.229,},
  {21.198,  18.000,  16.694,  15.977,  15.522,  15.207,  14.976,  14.799,  14.659,  14.546,},
  {16.258,  13.274,  12.060,  11.392,  10.967,  10.672,  10.456,  10.289,  10.158,  10.051,},
  {13.745,  10.925,   9.780,   9.148,   8.746,   8.466,   8.260,   8.102,   7.976,   7.874,},
  {12.246,   9.547,   8.451,   7.847,   7.460,   7.191,   6.993,   6.840,   6.719,   6.620,},
  {11.259,   8.649,   7.591,   7.006,   6.632,   6.371,   6.178,   6.029,   5.911,   5.814,},
  {10.561,   8.022,   6.992,   6.422,   6.057,   5.802,   5.613,   5.467,   5.351,   5.257,},
  {10.044,   7.559,   6.552,   5.994,   5.636,   5.386,   5.200,   5.057,   4.942,   4.849,},
  { 9.646,   7.206,   6.217,   5.668,   5.316,   5.069,   4.886,   4.744,   4.632,   4.539,},
  { 9.330,   6.927,   5.953,   5.412,   5.064,   4.821,   4.640,   4.499,   4.388,   4.296,},
  { 9.074,   6.701,   5.739,   5.205,   4.862,   4.620,   4.441,   4.302,   4.191,   4.100,},
  { 8.862,   6.515,   5.564,   5.035,   4.695,   4.456,   4.278,   4.140,   4.030,   3.939,},
  { 8.683,   6.359,   5.417,   4.893,   4.556,   4.318,   4.142,   4.004,   3.895,   3.805,},
  { 8.531,   6.226,   5.292,   4.773,   4.437,   4.202,   4.026,   3.890,   3.780,   3.691,},
  { 8.400,   6.112,   5.185,   4.669,   4.336,   4.102,   3.927,   3.791,   3.682,   3.593,},
  { 8.285,   6.013,   5.092,   4.579,   4.248,   4.015,   3.841,   3.705,   3.597,   3.508,},
  { 8.185,   5.926,   5.010,   4.500,   4.171,   3.939,   3.765,   3.631,   3.523,   3.434,},
  { 8.096,   5.849,   4.938,   4.431,   4.103,   3.871,   3.699,   3.564,   3.457,   3.368,},
  { 8.017,   5.780,   4.874,   4.369,   4.042,   3.812,   3.640,   3.506,   3.398,   3.310,},
  { 7.945,   5.719,   4.817,   4.313,   3.988,   3.758,   3.587,   3.453,   3.346,   3.258,},
  { 7.881,   5.664,   4.765,   4.264,   3.939,   3.710,   3.539,   3.406,   3.299,   3.211,},
  { 7.823,   5.614,   4.718,   4.218,   3.895,   3.667,   3.496,   3.363,   3.256,   3.168,},
  { 7.770,   5.568,   4.675,   4.177,   3.855,   3.627,   3.457,   3.324,   3.217,   3.129,},
  { 7.721,   5.526,   4.637,   4.140,   3.818,   3.591,   3.421,   3.288,   3.182,   3.094,},
  { 7.677,   5.488,   4.601,   4.106,   3.785,   3.558,   3.388,   3.256,   3.149,   3.062,},
  { 7.636,   5.453,   4.568,   4.074,   3.754,   3.528,   3.358,   3.226,   3.120,   3.032,},
  { 7.598,   5.420,   4.538,   4.045,   3.725,   3.499,   3.330,   3.198,   3.092,   3.005,},
  { 7.562,   5.390,   4.510,   4.018,   3.699,   3.473,   3.305,   3.173,   3.067,   2.979,},
  { 7.530,   5.362,   4.484,   3.993,   3.675,   3.449,   3.281,   3.149,   3.043,   2.955,},
  { 7.499,   5.336,   4.459,   3.969,   3.652,   3.427,   3.258,   3.127,   3.021,   2.934,},
  { 7.471,   5.312,   4.437,   3.948,   3.630,   3.406,   3.238,   3.106,   3.000,   2.913,},
  { 7.444,   5.289,   4.416,   3.927,   3.611,   3.386,   3.218,   3.087,   2.981,   2.894,},
  { 7.419,   5.268,   4.396,   3.908,   3.592,   3.368,   3.200,   3.069,   2.963,   2.876,},
  { 7.396,   5.248,   4.377,   3.890,   3.574,   3.351,   3.183,   3.052,   2.946,   2.859,},
  { 7.373,   5.229,   4.360,   3.873,   3.558,   3.334,   3.167,   3.036,   2.930,   2.843,},
  { 7.353,   5.211,   4.343,   3.858,   3.542,   3.319,   3.152,   3.021,   2.915,   2.828,},
  { 7.333,   5.194,   4.327,   3.843,   3.528,   3.305,   3.137,   3.006,   2.901,   2.814,},
  { 7.314,   5.179,   4.313,   3.828,   3.514,   3.291,   3.124,   2.993,   2.888,   2.801,},
  { 7.296,   5.163,   4.299,   3.815,   3.501,   3.278,   3.111,   2.980,   2.875,   2.788,},
  { 7.280,   5.149,   4.285,   3.802,   3.488,   3.266,   3.099,   2.968,   2.863,   2.776,},
  { 7.264,   5.136,   4.273,   3.790,   3.476,   3.254,   3.087,   2.957,   2.851,   2.764,},
  { 7.248,   5.123,   4.261,   3.778,   3.465,   3.243,   3.076,   2.946,   2.840,   2.754,},
  { 7.234,   5.110,   4.249,   3.767,   3.454,   3.232,   3.066,   2.935,   2.830,   2.743,},
  { 7.220,   5.099,   4.238,   3.757,   3.444,   3.222,   3.056,   2.925,   2.820,   2.733,},
  { 7.207,   5.087,   4.228,   3.747,   3.434,   3.213,   3.046,   2.916,   2.811,   2.724,},
  { 7.194,   5.077,   4.218,   3.737,   3.425,   3.204,   3.037,   2.907,   2.802,   2.715,},
  { 7.182,   5.066,   4.208,   3.728,   3.416,   3.195,   3.028,   2.898,   2.793,   2.706,},
  { 7.171,   5.057,   4.199,   3.720,   3.408,   3.186,   3.020,   2.890,   2.785,   2.698,},
  { 7.159,   5.047,   4.191,   3.711,   3.400,   3.178,   3.012,   2.882,   2.777,   2.690,},
  { 7.149,   5.038,   4.182,   3.703,   3.392,   3.171,   3.005,   2.874,   2.769,   2.683,},
  { 7.139,   5.030,   4.174,   3.695,   3.384,   3.163,   2.997,   2.867,   2.762,   2.675,},
  { 7.129,   5.021,   4.167,   3.688,   3.377,   3.156,   2.990,   2.860,   2.755,   2.668,},
  { 7.119,   5.013,   4.159,   3.681,   3.370,   3.149,   2.983,   2.853,   2.748,   2.662,},
  { 7.110,   5.006,   4.152,   3.674,   3.363,   3.143,   2.977,   2.847,   2.742,   2.655,},
  { 7.102,   4.998,   4.145,   3.667,   3.357,   3.136,   2.971,   2.841,   2.736,   2.649,},
  { 7.093,   4.991,   4.138,   3.661,   3.351,   3.130,   2.965,   2.835,   2.730,   2.643,},
  { 7.085,   4.984,   4.132,   3.655,   3.345,   3.124,   2.959,   2.829,   2.724,   2.637,},
  { 7.077,   4.977,   4.126,   3.649,   3.339,   3.119,   2.953,   2.823,   2.718,   2.632,},
  { 7.070,   4.971,   4.120,   3.643,   3.333,   3.113,   2.948,   2.818,   2.713,   2.626,},
  { 7.062,   4.965,   4.114,   3.638,   3.328,   3.108,   2.942,   2.813,   2.708,   2.621,},
  { 7.055,   4.959,   4.109,   3.632,   3.323,   3.103,   2.937,   2.808,   2.703,   2.616,},
  { 7.048,   4.953,   4.103,   3.627,   3.318,   3.098,   2.932,   2.803,   2.698,   2.611,},
  { 7.042,   4.947,   4.098,   3.622,   3.313,   3.093,   2.928,   2.798,   2.693,   2.607,},
  { 7.035,   4.942,   4.093,   3.618,   3.308,   3.088,   2.923,   2.793,   2.689,   2.602,},
  { 7.029,   4.937,   4.088,   3.613,   3.304,   3.084,   2.919,   2.789,   2.684,   2.598,},
  { 7.023,   4.932,   4.083,   3.608,   3.299,   3.080,   2.914,   2.785,   2.680,   2.593,},
  { 7.017,   4.927,   4.079,   3.604,   3.295,   3.075,   2.910,   2.781,   2.676,   2.589,},
  { 7.011,   4.922,   4.074,   3.600,   3.291,   3.071,   2.906,   2.777,   2.672,   2.585,},
  { 7.006,   4.917,   4.070,   3.596,   3.287,   3.067,   2.902,   2.773,   2.668,   2.581,},
  { 7.001,   4.913,   4.066,   3.591,   3.283,   3.063,   2.898,   2.769,   2.664,   2.578,},
  { 6.995,   4.908,   4.062,   3.588,   3.279,   3.060,   2.895,   2.765,   2.660,   2.574,},
  { 6.990,   4.904,   4.058,   3.584,   3.275,   3.056,   2.891,   2.762,   2.657,   2.570,},
  { 6.985,   4.900,   4.054,   3.580,   3.272,   3.052,   2.887,   2.758,   2.653,   2.567,},
  { 6.981,   4.896,   4.050,   3.577,   3.268,   3.049,   2.884,   2.755,   2.650,   2.563,},
  { 6.976,   4.892,   4.047,   3.573,   3.265,   3.046,   2.881,   2.751,   2.647,   2.560,},
  { 6.971,   4.888,   4.043,   3.570,   3.261,   3.042,   2.877,   2.748,   2.644,   2.557,},
  { 6.967,   4.884,   4.040,   3.566,   3.258,   3.039,   2.874,   2.745,   2.640,   2.554,},
  { 6.963,   4.881,   4.036,   3.563,   3.255,   3.036,   2.871,   2.742,   2.637,   2.551,},
  { 6.958,   4.877,   4.033,   3.560,   3.252,   3.033,   2.868,   2.739,   2.634,   2.548,},
  { 6.954,   4.874,   4.030,   3.557,   3.249,   3.030,   2.865,   2.736,   2.632,   2.545,},
  { 6.950,   4.870,   4.027,   3.554,   3.246,   3.027,   2.863,   2.733,   2.629,   2.542,},
  { 6.947,   4.867,   4.024,   3.551,   3.243,   3.025,   2.860,   2.731,   2.626,   2.539,},
  { 6.943,   4.864,   4.021,   3.548,   3.240,   3.022,   2.857,   2.728,   2.623,   2.537,},
  { 6.939,   4.861,   4.018,   3.545,   3.238,   3.019,   2.854,   2.725,   2.621,   2.534,},
  { 6.935,   4.858,   4.015,   3.543,   3.235,   3.017,   2.852,   2.723,   2.618,   2.532,},
  { 6.932,   4.855,   4.012,   3.540,   3.233,   3.014,   2.849,   2.720,   2.616,   2.529,},
  { 6.928,   4.852,   4.010,   3.538,   3.230,   3.012,   2.847,   2.718,   2.613,   2.527,},
  { 6.925,   4.849,   4.007,   3.535,   3.228,   3.009,   2.845,   2.715,   2.611,   2.524,},
  { 6.922,   4.846,   4.004,   3.533,   3.225,   3.007,   2.842,   2.713,   2.609,   2.522,},
  { 6.919,   4.844,   4.002,   3.530,   3.223,   3.004,   2.840,   2.711,   2.606,   2.520,},
  { 6.915,   4.841,   3.999,   3.528,   3.221,   3.002,   2.838,   2.709,   2.604,   2.518,},
  { 6.912,   4.838,   3.997,   3.525,   3.218,   3.000,   2.835,   2.706,   2.602,   2.515,},
  { 6.909,   4.836,   3.995,   3.523,   3.216,   2.998,   2.833,   2.704,   2.600,   2.513,},
  { 6.906,   4.833,   3.992,   3.521,   3.214,   2.996,   2.831,   2.702,   2.598,   2.511,},
  { 6.904,   4.831,   3.990,   3.519,   3.212,   2.994,   2.829,   2.700,   2.596,   2.509,},
  { 6.901,   4.829,   3.988,   3.517,   3.210,   2.992,   2.827,   2.698,   2.594,   2.507,},
  { 6.898,   4.826,   3.986,   3.515,   3.208,   2.990,   2.825,   2.696,   2.592,   2.505,},
  { 6.895,   4.824,   3.984,   3.513,   3.206,   2.988,   2.823,   2.694,   2.590,   2.503}
};

/** define the variance which will be used as a minimum variance for any
  dimension of any feature. Since most features are calculated from numbers
  with a precision no better than 1 in 128, the variance should never be
  less than the square of this number for parameters whose range is 1. */
#define MINVARIANCE     0.0004

/** define the absolute minimum number of samples which must be present in
  order to accurately test hypotheses about underlying probability
  distributions.  Define separately the minimum samples that are needed
  before a statistical analysis is attempted; this number should be
  equal to MINSAMPLES but can be set to a lower number for early testing
  when very few samples are available. */
#define MINSAMPLESPERBUCKET 5
#define MINSAMPLES    (MINBUCKETS * MINSAMPLESPERBUCKET)
#define MINSAMPLESNEEDED  1

/** define the size of the table which maps normalized samples to
  histogram buckets.  Also define the number of standard deviations
  in a normal distribution which are considered to be significant.
  The mapping table will be defined in such a way that it covers
  the specified number of standard deviations on either side of
  the mean.  BUCKETTABLESIZE should always be even. */
#define BUCKETTABLESIZE   1024
#define NORMALEXTENT    3.0

struct TEMPCLUSTER {
  CLUSTER *Cluster;
  CLUSTER *Neighbor;
};

typedef tesseract::KDPairInc<float, TEMPCLUSTER*> ClusterPair;
typedef tesseract::GenericHeap<ClusterPair> ClusterHeap;

struct STATISTICS {
  FLOAT32 AvgVariance;
  FLOAT32 *CoVariance;
  FLOAT32 *Min;                  // largest negative distance from the mean
  FLOAT32 *Max;                  // largest positive distance from the mean
};

struct BUCKETS {
  DISTRIBUTION Distribution;     // distribution being tested for
  uinT32 SampleCount;            // # of samples in histogram
  FLOAT64 Confidence;            // confidence level of test
  FLOAT64 ChiSquared;            // test threshold
  uinT16 NumberOfBuckets;        // number of cells in histogram
  uinT16 Bucket[BUCKETTABLESIZE];// mapping to histogram buckets
  uinT32 *Count;                 // frequency of occurrence histogram
  FLOAT32 *ExpectedCount;        // expected histogram
};

struct CHISTRUCT{
  uinT16 DegreesOfFreedom;
  FLOAT64 Alpha;
  FLOAT64 ChiSquared;
};

// For use with KDWalk / MakePotentialClusters
struct ClusteringContext {
  ClusterHeap *heap;  // heap used to hold temp clusters, "best" on top
  TEMPCLUSTER *candidates;  // array of potential clusters
  KDTREE *tree;  // kd-tree to be searched for neighbors
  inT32 next;  // next candidate to be used
};

typedef FLOAT64 (*DENSITYFUNC) (inT32);
typedef FLOAT64 (*SOLVEFUNC) (CHISTRUCT *, double);

#define Odd(N) ((N)%2)
#define Mirror(N,R) ((R) - (N) - 1)
#define Abs(N) ( ( (N) < 0 ) ? ( -(N) ) : (N) )

//--------------Global Data Definitions and Declarations----------------------
/** the following variables describe a discrete normal distribution
  which is used by NormalDensity() and NormalBucket().  The
  constant NORMALEXTENT determines how many standard
  deviations of the distribution are mapped onto the fixed
  discrete range of x.  x=0 is mapped to -NORMALEXTENT standard
  deviations and x=BUCKETTABLESIZE is mapped to
  +NORMALEXTENT standard deviations. */
#define SqrtOf2Pi     2.506628275
static const FLOAT64 kNormalStdDev = BUCKETTABLESIZE / (2.0 * NORMALEXTENT);
static const FLOAT64 kNormalVariance =
    (BUCKETTABLESIZE * BUCKETTABLESIZE) / (4.0 * NORMALEXTENT * NORMALEXTENT);
static const FLOAT64 kNormalMagnitude =
    (2.0 * NORMALEXTENT) / (SqrtOf2Pi * BUCKETTABLESIZE);
static const FLOAT64 kNormalMean = BUCKETTABLESIZE / 2;

/** define lookup tables used to compute the number of histogram buckets
  that should be used for a given number of samples. */
#define LOOKUPTABLESIZE   8
#define MAXDEGREESOFFREEDOM MAXBUCKETS

static const uinT32 kCountTable[LOOKUPTABLESIZE] = {
  MINSAMPLES, 200, 400, 600, 800, 1000, 1500, 2000
};  // number of samples

static const uinT16 kBucketsTable[LOOKUPTABLESIZE] = {
  MINBUCKETS, 16, 20, 24, 27, 30, 35, MAXBUCKETS
};  // number of buckets

/*-------------------------------------------------------------------------
          Private Function Prototypes
--------------------------------------------------------------------------*/
void CreateClusterTree(CLUSTERER *Clusterer);

void MakePotentialClusters(ClusteringContext *context, CLUSTER *Cluster,
                           inT32 Level);

CLUSTER *FindNearestNeighbor(KDTREE *Tree,
                             CLUSTER *Cluster,
                             FLOAT32 *Distance);

CLUSTER *MakeNewCluster(CLUSTERER *Clusterer, TEMPCLUSTER *TempCluster);

inT32 MergeClusters (inT16 N,
register PARAM_DESC ParamDesc[],
register inT32 n1,
register inT32 n2,
register FLOAT32 m[],
register FLOAT32 m1[], register FLOAT32 m2[]);

void ComputePrototypes(CLUSTERER *Clusterer, CLUSTERCONFIG *Config);

PROTOTYPE *MakePrototype(CLUSTERER *Clusterer,
                         CLUSTERCONFIG *Config,
                         CLUSTER *Cluster);

PROTOTYPE *MakeDegenerateProto(uinT16 N,
                               CLUSTER *Cluster,
                               STATISTICS *Statistics,
                               PROTOSTYLE Style,
                               inT32 MinSamples);

PROTOTYPE *TestEllipticalProto(CLUSTERER *Clusterer,
                               CLUSTERCONFIG *Config,
                               CLUSTER *Cluster,
                               STATISTICS *Statistics);

PROTOTYPE *MakeSphericalProto(CLUSTERER *Clusterer,
                              CLUSTER *Cluster,
                              STATISTICS *Statistics,
                              BUCKETS *Buckets);

PROTOTYPE *MakeEllipticalProto(CLUSTERER *Clusterer,
                               CLUSTER *Cluster,
                               STATISTICS *Statistics,
                               BUCKETS *Buckets);

PROTOTYPE *MakeMixedProto(CLUSTERER *Clusterer,
                          CLUSTER *Cluster,
                          STATISTICS *Statistics,
                          BUCKETS *NormalBuckets,
                          FLOAT64 Confidence);

void MakeDimRandom(uinT16 i, PROTOTYPE *Proto, PARAM_DESC *ParamDesc);

void MakeDimUniform(uinT16 i, PROTOTYPE *Proto, STATISTICS *Statistics);

STATISTICS *ComputeStatistics (inT16 N,
PARAM_DESC ParamDesc[], CLUSTER * Cluster);

PROTOTYPE *NewSphericalProto(uinT16 N,
                             CLUSTER *Cluster,
                             STATISTICS *Statistics);

PROTOTYPE *NewEllipticalProto(inT16 N,
                              CLUSTER *Cluster,
                              STATISTICS *Statistics);

PROTOTYPE *NewMixedProto(inT16 N, CLUSTER *Cluster, STATISTICS *Statistics);

PROTOTYPE *NewSimpleProto(inT16 N, CLUSTER *Cluster);

BOOL8 Independent (PARAM_DESC ParamDesc[],
inT16 N, FLOAT32 * CoVariance, FLOAT32 Independence);

BUCKETS *GetBuckets(CLUSTERER* clusterer,
                    DISTRIBUTION Distribution,
                    uinT32 SampleCount,
                    FLOAT64 Confidence);

BUCKETS *MakeBuckets(DISTRIBUTION Distribution,
                     uinT32 SampleCount,
                     FLOAT64 Confidence);

uinT16 OptimumNumberOfBuckets(uinT32 SampleCount);

FLOAT64 ComputeChiSquared(uinT16 DegreesOfFreedom, FLOAT64 Alpha);

FLOAT64 NormalDensity(inT32 x);

FLOAT64 UniformDensity(inT32 x);

FLOAT64 Integral(FLOAT64 f1, FLOAT64 f2, FLOAT64 Dx);

void FillBuckets(BUCKETS *Buckets,
                 CLUSTER *Cluster,
                 uinT16 Dim,
                 PARAM_DESC *ParamDesc,
                 FLOAT32 Mean,
                 FLOAT32 StdDev);

uinT16 NormalBucket(PARAM_DESC *ParamDesc,
                    FLOAT32 x,
                    FLOAT32 Mean,
                    FLOAT32 StdDev);

uinT16 UniformBucket(PARAM_DESC *ParamDesc,
                     FLOAT32 x,
                     FLOAT32 Mean,
                     FLOAT32 StdDev);

BOOL8 DistributionOK(BUCKETS *Buckets);

void FreeStatistics(STATISTICS *Statistics);

void FreeBuckets(BUCKETS *Buckets);

void FreeCluster(CLUSTER *Cluster);

uinT16 DegreesOfFreedom(DISTRIBUTION Distribution, uinT16 HistogramBuckets);

int NumBucketsMatch(void *arg1,   // BUCKETS *Histogram,
                    void *arg2);  // uinT16 *DesiredNumberOfBuckets);

int ListEntryMatch(void *arg1, void *arg2);

void AdjustBuckets(BUCKETS *Buckets, uinT32 NewSampleCount);

void InitBuckets(BUCKETS *Buckets);

int AlphaMatch(void *arg1,   // CHISTRUCT *ChiStruct,
               void *arg2);  // CHISTRUCT *SearchKey);

CHISTRUCT *NewChiStruct(uinT16 DegreesOfFreedom, FLOAT64 Alpha);

FLOAT64 Solve(SOLVEFUNC Function,
              void *FunctionParams,
              FLOAT64 InitialGuess,
              FLOAT64 Accuracy);

FLOAT64 ChiArea(CHISTRUCT *ChiParams, FLOAT64 x);

BOOL8 MultipleCharSamples(CLUSTERER *Clusterer,
                          CLUSTER *Cluster,
                          FLOAT32 MaxIllegal);

double InvertMatrix(const float* input, int size, float* inv);

//--------------------------Public Code--------------------------------------
/**
 * This routine creates a new clusterer data structure,
 * initializes it, and returns a pointer to it.
 *
 * @param SampleSize  number of dimensions in feature space
 * @param ParamDesc description of each dimension
 * @return  pointer to the new clusterer data structure
 * @note Exceptions:  None
 * @note History: 5/29/89, DSJ, Created.
 */
CLUSTERER *
MakeClusterer (inT16 SampleSize, const PARAM_DESC ParamDesc[]) {
  CLUSTERER *Clusterer;
  int i;

  // allocate main clusterer data structure and init simple fields
  Clusterer = (CLUSTERER *) Emalloc (sizeof (CLUSTERER));
  Clusterer->SampleSize = SampleSize;
  Clusterer->NumberOfSamples = 0;
  Clusterer->NumChar = 0;

  // init fields which will not be used initially
  Clusterer->Root = NULL;
  Clusterer->ProtoList = NIL_LIST;

  // maintain a copy of param descriptors in the clusterer data structure
  Clusterer->ParamDesc =
    (PARAM_DESC *) Emalloc (SampleSize * sizeof (PARAM_DESC));
  for (i = 0; i < SampleSize; i++) {
    Clusterer->ParamDesc[i].Circular = ParamDesc[i].Circular;
    Clusterer->ParamDesc[i].NonEssential = ParamDesc[i].NonEssential;
    Clusterer->ParamDesc[i].Min = ParamDesc[i].Min;
    Clusterer->ParamDesc[i].Max = ParamDesc[i].Max;
    Clusterer->ParamDesc[i].Range = ParamDesc[i].Max - ParamDesc[i].Min;
    Clusterer->ParamDesc[i].HalfRange = Clusterer->ParamDesc[i].Range / 2;
    Clusterer->ParamDesc[i].MidRange =
      (ParamDesc[i].Max + ParamDesc[i].Min) / 2;
  }

  // allocate a kd tree to hold the samples
  Clusterer->KDTree = MakeKDTree (SampleSize, ParamDesc);

  // Initialize cache of histogram buckets to minimize recomputing them.
  for (int d = 0; d < DISTRIBUTION_COUNT; ++d) {
    for (int c = 0; c < MAXBUCKETS + 1 - MINBUCKETS; ++c)
      Clusterer->bucket_cache[d][c] = NULL;
  }

  return Clusterer;
}                                // MakeClusterer

/**
 * This routine creates a new sample data structure to hold
 * the specified feature.  This sample is added to the clusterer
 * data structure (so that it knows which samples are to be
 * clustered later), and a pointer to the sample is returned to
 * the caller.
 *
 * @param Clusterer clusterer data structure to add sample to
 * @param Feature feature to be added to clusterer
 * @param CharID  unique ident. of char that sample came from
 *
 * @return    Pointer to the new sample data structure
 * @note Exceptions:  ALREADYCLUSTERED  MakeSample can't be called after
 *    ClusterSamples has been called
 * @note History: 5/29/89, DSJ, Created.
 */
SAMPLE* MakeSample(CLUSTERER * Clusterer, const FLOAT32* Feature,
                   inT32 CharID) {
  SAMPLE *Sample;
  int i;

  // see if the samples have already been clustered - if so trap an error
  if (Clusterer->Root != NULL)
    DoError (ALREADYCLUSTERED,
      "Can't add samples after they have been clustered");

  // allocate the new sample and initialize it
  Sample = (SAMPLE *) Emalloc (sizeof (SAMPLE) +
    (Clusterer->SampleSize -
    1) * sizeof (FLOAT32));
  Sample->Clustered = FALSE;
  Sample->Prototype = FALSE;
  Sample->SampleCount = 1;
  Sample->Left = NULL;
  Sample->Right = NULL;
  Sample->CharID = CharID;

  for (i = 0; i < Clusterer->SampleSize; i++)
    Sample->Mean[i] = Feature[i];

  // add the sample to the KD tree - keep track of the total # of samples
  Clusterer->NumberOfSamples++;
  KDStore (Clusterer->KDTree, Sample->Mean, (char *) Sample);
  if (CharID >= Clusterer->NumChar)
    Clusterer->NumChar = CharID + 1;

  // execute hook for monitoring clustering operation
  // (*SampleCreationHook)( Sample );

  return (Sample);
}                                // MakeSample

/**
 * This routine first checks to see if the samples in this
 * clusterer have already been clustered before; if so, it does
 * not bother to recreate the cluster tree.  It simply recomputes
 * the prototypes based on the new Config info.
 *
 * If the samples have not been clustered before, the
 * samples in the KD tree are formed into a cluster tree and then
 * the prototypes are computed from the cluster tree.
 *
 * In either case this routine returns a pointer to a
 * list of prototypes that best represent the samples given
 * the constraints specified in Config.
 *
 * @param Clusterer data struct containing samples to be clustered
 * @param Config  parameters which control clustering process
 *
 * @return Pointer to a list of prototypes
 * @note Exceptions:  None
 * @note History: 5/29/89, DSJ, Created.
 */
LIST ClusterSamples(CLUSTERER *Clusterer, CLUSTERCONFIG *Config) {
  //only create cluster tree if samples have never been clustered before
  if (Clusterer->Root == NULL)
    CreateClusterTree(Clusterer);

  //deallocate the old prototype list if one exists
  FreeProtoList (&Clusterer->ProtoList);
  Clusterer->ProtoList = NIL_LIST;

  //compute prototypes starting at the root node in the tree
  ComputePrototypes(Clusterer, Config);
  // We don't need the cluster pointers in the protos any more, so null them
  // out, which makes it safe to delete the clusterer.
  LIST proto_list = Clusterer->ProtoList;
  iterate(proto_list) {
    PROTOTYPE *proto = reinterpret_cast<PROTOTYPE *>(first_node(proto_list));
    proto->Cluster = NULL;
  }
  return Clusterer->ProtoList;
}                                // ClusterSamples

/**
 * This routine frees all of the memory allocated to the
 * specified data structure.  It will not, however, free
 * the memory used by the prototype list.  The pointers to
 * the clusters for each prototype in the list will be set
 * to NULL to indicate that the cluster data structures no
 * longer exist.  Any sample lists that have been obtained
 * via calls to GetSamples are no longer valid.
 * @param Clusterer pointer to data structure to be freed
 * @return None
 * @note Exceptions:  None
 * @note History: 6/6/89, DSJ, Created.
 */
void FreeClusterer(CLUSTERER *Clusterer) {
  if (Clusterer != NULL) {
    memfree (Clusterer->ParamDesc);
    if (Clusterer->KDTree != NULL)
      FreeKDTree (Clusterer->KDTree);
    if (Clusterer->Root != NULL)
      FreeCluster (Clusterer->Root);
    // Free up all used buckets structures.
    for (int d = 0; d < DISTRIBUTION_COUNT; ++d) {
      for (int c = 0; c < MAXBUCKETS + 1 - MINBUCKETS; ++c)
        if (Clusterer->bucket_cache[d][c] != NULL)
          FreeBuckets(Clusterer->bucket_cache[d][c]);
    }

    memfree(Clusterer);
  }
}                                // FreeClusterer

/**
 * This routine frees all of the memory allocated to the
 * specified list of prototypes.  The clusters which are
 * pointed to by the prototypes are not freed.
 * @param ProtoList pointer to list of prototypes to be freed
 * @return None
 * @note Exceptions:  None
 * @note History: 6/6/89, DSJ, Created.
 */
void FreeProtoList(LIST *ProtoList) {
  destroy_nodes(*ProtoList, FreePrototype);
}                                // FreeProtoList

/**
 * This routine deallocates the memory consumed by the specified
 * prototype and modifies the corresponding cluster so that it
 * is no longer marked as a prototype.  The cluster is NOT
 * deallocated by this routine.
 * @param arg prototype data structure to be deallocated
 * @return None
 * @note Exceptions: None
 * @note History: 5/30/89, DSJ, Created.
 */
void FreePrototype(void *arg) {  //PROTOTYPE     *Prototype)
  PROTOTYPE *Prototype = (PROTOTYPE *) arg;

  // unmark the corresponding cluster (if there is one
  if (Prototype->Cluster != NULL)
    Prototype->Cluster->Prototype = FALSE;

  // deallocate the prototype statistics and then the prototype itself
  if (Prototype->Distrib != NULL)
    memfree (Prototype->Distrib);
  if (Prototype->Mean != NULL)
    memfree (Prototype->Mean);
  if (Prototype->Style != spherical) {
    if (Prototype->Variance.Elliptical != NULL)
      memfree (Prototype->Variance.Elliptical);
    if (Prototype->Magnitude.Elliptical != NULL)
      memfree (Prototype->Magnitude.Elliptical);
    if (Prototype->Weight.Elliptical != NULL)
      memfree (Prototype->Weight.Elliptical);
  }
  memfree(Prototype);
}                                // FreePrototype

/**
 * This routine is used to find all of the samples which
 * belong to a cluster.  It starts by removing the top
 * cluster on the cluster list (SearchState).  If this cluster is
 * a leaf it is returned.  Otherwise, the right subcluster
 * is pushed on the list and we continue the search in the
 * left subcluster.  This continues until a leaf is found.
 * If all samples have been found, NULL is returned.
 * InitSampleSearch() must be called
 * before NextSample() to initialize the search.
 * @param SearchState ptr to list containing clusters to be searched
 * @return  Pointer to the next leaf cluster (sample) or NULL.
 * @note Exceptions:  None
 * @note History: 6/16/89, DSJ, Created.
 */
CLUSTER *NextSample(LIST *SearchState) {
  CLUSTER *Cluster;

  if (*SearchState == NIL_LIST)
    return (NULL);
  Cluster = (CLUSTER *) first_node (*SearchState);
  *SearchState = pop (*SearchState);
  while (TRUE) {
    if (Cluster->Left == NULL)
      return (Cluster);
    *SearchState = push (*SearchState, Cluster->Right);
    Cluster = Cluster->Left;
  }
}                                // NextSample

/**
 * This routine returns the mean of the specified
 * prototype in the indicated dimension.
 * @param Proto prototype to return mean of
 * @param Dimension dimension whose mean is to be returned
 * @return  Mean of Prototype in Dimension
 * @note Exceptions: none
 * @note History: 7/6/89, DSJ, Created.
 */
FLOAT32 Mean(PROTOTYPE *Proto, uinT16 Dimension) {
  return (Proto->Mean[Dimension]);
}                                // Mean

/**
 * This routine returns the standard deviation of the
 * prototype in the indicated dimension.
 * @param Proto   prototype to return standard deviation of
 * @param Dimension dimension whose stddev is to be returned
 * @return  Standard deviation of Prototype in Dimension
 * @note Exceptions: none
 * @note History: 7/6/89, DSJ, Created.
 */
FLOAT32 StandardDeviation(PROTOTYPE *Proto, uinT16 Dimension) {
  switch (Proto->Style) {
    case spherical:
      return ((FLOAT32) sqrt ((double) Proto->Variance.Spherical));
    case elliptical:
      return ((FLOAT32)
        sqrt ((double) Proto->Variance.Elliptical[Dimension]));
    case mixed:
      switch (Proto->Distrib[Dimension]) {
        case normal:
          return ((FLOAT32)
            sqrt ((double) Proto->Variance.Elliptical[Dimension]));
        case uniform:
        case D_random:
          return (Proto->Variance.Elliptical[Dimension]);
        case DISTRIBUTION_COUNT:
          ASSERT_HOST(!"Distribution count not allowed!");
      }
  }
  return 0.0f;
}                                // StandardDeviation


/*---------------------------------------------------------------------------
            Private Code
----------------------------------------------------------------------------*/
/**
 * This routine performs a bottoms-up clustering on the samples
 * held in the kd-tree of the Clusterer data structure.  The
 * result is a cluster tree.  Each node in the tree represents
 * a cluster which conceptually contains a subset of the samples.
 * More precisely, the cluster contains all of the samples which
 * are contained in its two sub-clusters.  The leaves of the
 * tree are the individual samples themselves; they have no
 * sub-clusters.  The root node of the tree conceptually contains
 * all of the samples.
 * @param Clusterer data structure holdings samples to be clustered
 * @return  None (the Clusterer data structure is changed)
 * @note Exceptions:  None
 * @note History: 5/29/89, DSJ, Created.
 */
void CreateClusterTree(CLUSTERER *Clusterer) {
  ClusteringContext context;
  ClusterPair HeapEntry;
  TEMPCLUSTER *PotentialCluster;

  // each sample and its nearest neighbor form a "potential" cluster
  // save these in a heap with the "best" potential clusters on top
  context.tree = Clusterer->KDTree;
  context.candidates = (TEMPCLUSTER *)
    Emalloc(Clusterer->NumberOfSamples * sizeof(TEMPCLUSTER));
  context.next = 0;
  context.heap = new ClusterHeap(Clusterer->NumberOfSamples);
  KDWalk(context.tree, (void_proc)MakePotentialClusters, &context);

  // form potential clusters into actual clusters - always do "best" first
  while (context.heap->Pop(&HeapEntry)) {
    PotentialCluster = HeapEntry.data;

    // if main cluster of potential cluster is already in another cluster
    // then we don't need to worry about it
    if (PotentialCluster->Cluster->Clustered) {
      continue;
    }

    // if main cluster is not yet clustered, but its nearest neighbor is
    // then we must find a new nearest neighbor
    else if (PotentialCluster->Neighbor->Clustered) {
      PotentialCluster->Neighbor =
        FindNearestNeighbor(context.tree, PotentialCluster->Cluster,
                            &HeapEntry.key);
      if (PotentialCluster->Neighbor != NULL) {
        context.heap->Push(&HeapEntry);
      }
    }

    // if neither cluster is already clustered, form permanent cluster
    else {
      PotentialCluster->Cluster =
          MakeNewCluster(Clusterer, PotentialCluster);
      PotentialCluster->Neighbor =
          FindNearestNeighbor(context.tree, PotentialCluster->Cluster,
                              &HeapEntry.key);
      if (PotentialCluster->Neighbor != NULL) {
        context.heap->Push(&HeapEntry);
      }
    }
  }

  // the root node in the cluster tree is now the only node in the kd-tree
  Clusterer->Root = (CLUSTER *) RootOf(Clusterer->KDTree);

  // free up the memory used by the K-D tree, heap, and temp clusters
  FreeKDTree(context.tree);
  Clusterer->KDTree = NULL;
  delete context.heap;
  memfree(context.candidates);
}                                // CreateClusterTree

/**
 * This routine is designed to be used in concert with the
 * KDWalk routine.  It will create a potential cluster for
 * each sample in the kd-tree that is being walked.  This
 * potential cluster will then be pushed on the heap.
 * @param context  ClusteringContext (see definition above)
 * @param Cluster  current cluster being visited in kd-tree walk
 * @param Level  level of this cluster in the kd-tree
 */
void MakePotentialClusters(ClusteringContext *context,
                           CLUSTER *Cluster, inT32 Level) {
  ClusterPair HeapEntry;
  int next = context->next;
  context->candidates[next].Cluster = Cluster;
  HeapEntry.data = &(context->candidates[next]);
  context->candidates[next].Neighbor =
      FindNearestNeighbor(context->tree,
                          context->candidates[next].Cluster,
                          &HeapEntry.key);
  if (context->candidates[next].Neighbor != NULL) {
    context->heap->Push(&HeapEntry);
    context->next++;
  }
}                                // MakePotentialClusters

/**
 * This routine searches the specified kd-tree for the nearest
 * neighbor of the specified cluster.  It actually uses the
 * kd routines to find the 2 nearest neighbors since one of them
 * will be the original cluster.  A pointer to the nearest
 * neighbor is returned, if it can be found, otherwise NULL is
 * returned.  The distance between the 2 nodes is placed
 * in the specified variable.
 * @param Tree    kd-tree to search in for nearest neighbor
 * @param Cluster cluster whose nearest neighbor is to be found
 * @param Distance  ptr to variable to report distance found
 * @return  Pointer to the nearest neighbor of Cluster, or NULL
 * @note Exceptions: none
 * @note History: 5/29/89, DSJ, Created.
 *  7/13/89, DSJ, Removed visibility of kd-tree node data struct
 */
CLUSTER *
FindNearestNeighbor(KDTREE * Tree, CLUSTER * Cluster, FLOAT32 * Distance)
#define MAXNEIGHBORS  2
#define MAXDISTANCE   MAX_FLOAT32
{
  CLUSTER *Neighbor[MAXNEIGHBORS];
  FLOAT32 Dist[MAXNEIGHBORS];
  int NumberOfNeighbors;
  inT32 i;
  CLUSTER *BestNeighbor;

  // find the 2 nearest neighbors of the cluster
  KDNearestNeighborSearch(Tree, Cluster->Mean, MAXNEIGHBORS, MAXDISTANCE,
                          &NumberOfNeighbors, (void **)Neighbor, Dist);

  // search for the nearest neighbor that is not the cluster itself
  *Distance = MAXDISTANCE;
  BestNeighbor = NULL;
  for (i = 0; i < NumberOfNeighbors; i++) {
    if ((Dist[i] < *Distance) && (Neighbor[i] != Cluster)) {
      *Distance = Dist[i];
      BestNeighbor = Neighbor[i];
    }
  }
  return BestNeighbor;
}                                // FindNearestNeighbor

/**
 * This routine creates a new permanent cluster from the
 * clusters specified in TempCluster.  The 2 clusters in
 * TempCluster are marked as "clustered" and deleted from
 * the kd-tree.  The new cluster is then added to the kd-tree.
 * @param Clusterer current clustering environment
 * @param TempCluster potential cluster to make permanent
 * @return Pointer to the new permanent cluster
 * @note Exceptions:  none
 * @note History: 5/29/89, DSJ, Created.
 *    7/13/89, DSJ, Removed visibility of kd-tree node data struct
 */
CLUSTER *MakeNewCluster(CLUSTERER *Clusterer, TEMPCLUSTER *TempCluster) {
  CLUSTER *Cluster;

  // allocate the new cluster and initialize it
  Cluster = (CLUSTER *) Emalloc(
      sizeof(CLUSTER) + (Clusterer->SampleSize - 1) * sizeof(FLOAT32));
  Cluster->Clustered = FALSE;
  Cluster->Prototype = FALSE;
  Cluster->Left = TempCluster->Cluster;
  Cluster->Right = TempCluster->Neighbor;
  Cluster->CharID = -1;

  // mark the old clusters as "clustered" and delete them from the kd-tree
  Cluster->Left->Clustered = TRUE;
  Cluster->Right->Clustered = TRUE;
  KDDelete(Clusterer->KDTree, Cluster->Left->Mean, Cluster->Left);
  KDDelete(Clusterer->KDTree, Cluster->Right->Mean, Cluster->Right);

  // compute the mean and sample count for the new cluster
  Cluster->SampleCount =
      MergeClusters(Clusterer->SampleSize, Clusterer->ParamDesc,
                    Cluster->Left->SampleCount, Cluster->Right->SampleCount,
                    Cluster->Mean, Cluster->Left->Mean, Cluster->Right->Mean);

  // add the new cluster to the KD tree
  KDStore(Clusterer->KDTree, Cluster->Mean, Cluster);
  return Cluster;
}                                // MakeNewCluster

/**
 * This routine merges two clusters into one larger cluster.
 * To do this it computes the number of samples in the new
 * cluster and the mean of the new cluster.  The ParamDesc
 * information is used to ensure that circular dimensions
 * are handled correctly.
 * @param N # of dimensions (size of arrays)
 * @param ParamDesc array of dimension descriptions
 * @param n1, n2  number of samples in each old cluster
 * @param m array to hold mean of new cluster
 * @param m1, m2  arrays containing means of old clusters
 * @return  The number of samples in the new cluster.
 * @note Exceptions:  None
 * @note History: 5/31/89, DSJ, Created.
 */
inT32 MergeClusters(inT16 N,
                    PARAM_DESC ParamDesc[],
                    inT32 n1,
                    inT32 n2,
                    FLOAT32 m[],
                    FLOAT32 m1[], FLOAT32 m2[]) {
  inT32 i, n;

  n = n1 + n2;
  for (i = N; i > 0; i--, ParamDesc++, m++, m1++, m2++) {
    if (ParamDesc->Circular) {
      // if distance between means is greater than allowed
      // reduce upper point by one "rotation" to compute mean
      // then normalize the mean back into the accepted range
      if ((*m2 - *m1) > ParamDesc->HalfRange) {
        *m = (n1 * *m1 + n2 * (*m2 - ParamDesc->Range)) / n;
        if (*m < ParamDesc->Min)
          *m += ParamDesc->Range;
      }
      else if ((*m1 - *m2) > ParamDesc->HalfRange) {
        *m = (n1 * (*m1 - ParamDesc->Range) + n2 * *m2) / n;
        if (*m < ParamDesc->Min)
          *m += ParamDesc->Range;
      }
      else
        *m = (n1 * *m1 + n2 * *m2) / n;
    }
    else
      *m = (n1 * *m1 + n2 * *m2) / n;
  }
  return n;
}                                // MergeClusters

/**
 * This routine decides which clusters in the cluster tree
 * should be represented by prototypes, forms a list of these
 * prototypes, and places the list in the Clusterer data
 * structure.
 * @param Clusterer data structure holding cluster tree
 * @param Config    parameters used to control prototype generation
 * @return  None
 * @note Exceptions:  None
 * @note History: 5/30/89, DSJ, Created.
 */
void ComputePrototypes(CLUSTERER *Clusterer, CLUSTERCONFIG *Config) {
  LIST ClusterStack = NIL_LIST;
  CLUSTER *Cluster;
  PROTOTYPE *Prototype;

  // use a stack to keep track of clusters waiting to be processed
  // initially the only cluster on the stack is the root cluster
  if (Clusterer->Root != NULL)
    ClusterStack = push (NIL_LIST, Clusterer->Root);

  // loop until we have analyzed all clusters which are potential prototypes
  while (ClusterStack != NIL_LIST) {
    // remove the next cluster to be analyzed from the stack
    // try to make a prototype from the cluster
    // if successful, put it on the proto list, else split the cluster
    Cluster = (CLUSTER *) first_node (ClusterStack);
    ClusterStack = pop (ClusterStack);
    Prototype = MakePrototype(Clusterer, Config, Cluster);
    if (Prototype != NULL) {
      Clusterer->ProtoList = push (Clusterer->ProtoList, Prototype);
    }
    else {
      ClusterStack = push (ClusterStack, Cluster->Right);
      ClusterStack = push (ClusterStack, Cluster->Left);
    }
  }
}                                // ComputePrototypes

/**
 * This routine attempts to create a prototype from the
 * specified cluster that conforms to the distribution
 * specified in Config.  If there are too few samples in the
 * cluster to perform a statistical analysis, then a prototype
 * is generated but labelled as insignificant.  If the
 * dimensions of the cluster are not independent, no prototype
 * is generated and NULL is returned.  If a prototype can be
 * found that matches the desired distribution then a pointer
 * to it is returned, otherwise NULL is returned.
 * @param Clusterer data structure holding cluster tree
 * @param Config  parameters used to control prototype generation
 * @param Cluster cluster to be made into a prototype
 * @return  Pointer to new prototype or NULL
 * @note Exceptions:  None
 * @note History: 6/19/89, DSJ, Created.
 */
PROTOTYPE *MakePrototype(CLUSTERER *Clusterer,
                         CLUSTERCONFIG *Config,
                         CLUSTER *Cluster) {
  STATISTICS *Statistics;
  PROTOTYPE *Proto;
  BUCKETS *Buckets;

  // filter out clusters which contain samples from the same character
  if (MultipleCharSamples (Clusterer, Cluster, Config->MaxIllegal))
    return NULL;

  // compute the covariance matrix and ranges for the cluster
  Statistics =
      ComputeStatistics(Clusterer->SampleSize, Clusterer->ParamDesc, Cluster);

  // check for degenerate clusters which need not be analyzed further
  // note that the MinSamples test assumes that all clusters with multiple
  // character samples have been removed (as above)
  Proto = MakeDegenerateProto(
      Clusterer->SampleSize, Cluster, Statistics, Config->ProtoStyle,
      (inT32) (Config->MinSamples * Clusterer->NumChar));
  if (Proto != NULL) {
    FreeStatistics(Statistics);
    return Proto;
  }
  // check to ensure that all dimensions are independent
  if (!Independent(Clusterer->ParamDesc, Clusterer->SampleSize,
                   Statistics->CoVariance, Config->Independence)) {
    FreeStatistics(Statistics);
    return NULL;
  }

  if (HOTELLING && Config->ProtoStyle == elliptical) {
    Proto = TestEllipticalProto(Clusterer, Config, Cluster, Statistics);
    if (Proto != NULL) {
      FreeStatistics(Statistics);
      return Proto;
    }
  }

  // create a histogram data structure used to evaluate distributions
  Buckets = GetBuckets(Clusterer, normal, Cluster->SampleCount,
                       Config->Confidence);

  // create a prototype based on the statistics and test it
  switch (Config->ProtoStyle) {
    case spherical:
      Proto = MakeSphericalProto(Clusterer, Cluster, Statistics, Buckets);
      break;
    case elliptical:
      Proto = MakeEllipticalProto(Clusterer, Cluster, Statistics, Buckets);
      break;
    case mixed:
      Proto = MakeMixedProto(Clusterer, Cluster, Statistics, Buckets,
                             Config->Confidence);
      break;
    case automatic:
      Proto = MakeSphericalProto(Clusterer, Cluster, Statistics, Buckets);
      if (Proto != NULL)
        break;
      Proto = MakeEllipticalProto(Clusterer, Cluster, Statistics, Buckets);
      if (Proto != NULL)
        break;
      Proto = MakeMixedProto(Clusterer, Cluster, Statistics, Buckets,
                             Config->Confidence);
      break;
  }
  FreeStatistics(Statistics);
  return Proto;
}                                // MakePrototype

/**
 * This routine checks for clusters which are degenerate and
 * therefore cannot be analyzed in a statistically valid way.
 * A cluster is defined as degenerate if it does not have at
 * least MINSAMPLESNEEDED samples in it.  If the cluster is
 * found to be degenerate, a prototype of the specified style
 * is generated and marked as insignificant.  A cluster is
 * also degenerate if it does not have at least MinSamples
 * samples in it.
 *
 * If the cluster is not degenerate, NULL is returned.
 *
 * @param N   number of dimensions
 * @param Cluster   cluster being analyzed
 * @param Statistics  statistical info about cluster
 * @param Style   type of prototype to be generated
 * @param MinSamples  minimum number of samples in a cluster
 * @return  Pointer to degenerate prototype or NULL.
 * @note Exceptions:  None
 * @note History: 6/20/89, DSJ, Created.
 *    7/12/89, DSJ, Changed name and added check for 0 stddev.
 *    8/8/89, DSJ, Removed check for 0 stddev (handled elsewhere).
 */
PROTOTYPE *MakeDegenerateProto(  //this was MinSample
                               uinT16 N,
                               CLUSTER *Cluster,
                               STATISTICS *Statistics,
                               PROTOSTYLE Style,
                               inT32 MinSamples) {
  PROTOTYPE *Proto = NULL;

  if (MinSamples < MINSAMPLESNEEDED)
    MinSamples = MINSAMPLESNEEDED;

  if (Cluster->SampleCount < MinSamples) {
    switch (Style) {
      case spherical:
        Proto = NewSphericalProto (N, Cluster, Statistics);
        break;
      case elliptical:
      case automatic:
        Proto = NewEllipticalProto (N, Cluster, Statistics);
        break;
      case mixed:
        Proto = NewMixedProto (N, Cluster, Statistics);
        break;
    }
    Proto->Significant = FALSE;
  }
  return (Proto);
}                                // MakeDegenerateProto

/**
 * This routine tests the specified cluster to see if **
 * there is a statistically significant difference between
 * the sub-clusters that would be made if the cluster were to
 * be split. If not, then a new prototype is formed and
 * returned to the caller. If there is, then NULL is returned
 * to the caller.
 * @param Clusterer data struct containing samples being clustered
 * @param Config provides the magic number of samples that make a good cluster
 * @param Cluster   cluster to be made into an elliptical prototype
 * @param Statistics  statistical info about cluster
 * @return Pointer to new elliptical prototype or NULL.
 */
PROTOTYPE *TestEllipticalProto(CLUSTERER *Clusterer,
                               CLUSTERCONFIG *Config,
                               CLUSTER *Cluster,
                               STATISTICS *Statistics) {
  // Fraction of the number of samples used as a range around 1 within
  // which a cluster has the magic size that allows a boost to the
  // FTable by kFTableBoostMargin, thus allowing clusters near the
  // magic size (equal to the number of sample characters) to be more
  // likely to stay together.
  const double kMagicSampleMargin = 0.0625;
  const double kFTableBoostMargin = 2.0;

  int N = Clusterer->SampleSize;
  CLUSTER* Left = Cluster->Left;
  CLUSTER* Right = Cluster->Right;
  if (Left == NULL || Right == NULL)
    return NULL;
  int TotalDims = Left->SampleCount + Right->SampleCount;
  if (TotalDims < N + 1 || TotalDims < 2)
    return NULL;
  const int kMatrixSize = N * N * sizeof(FLOAT32);
  FLOAT32* Covariance = reinterpret_cast<FLOAT32 *>(Emalloc(kMatrixSize));
  FLOAT32* Inverse = reinterpret_cast<FLOAT32 *>(Emalloc(kMatrixSize));
  FLOAT32* Delta = reinterpret_cast<FLOAT32*>(Emalloc(N * sizeof(FLOAT32)));
  // Compute a new covariance matrix that only uses essential features.
  for (int i = 0; i < N; ++i) {
    int row_offset = i * N;
    if (!Clusterer->ParamDesc[i].NonEssential) {
      for (int j = 0; j < N; ++j) {
        if (!Clusterer->ParamDesc[j].NonEssential)
          Covariance[j + row_offset] = Statistics->CoVariance[j + row_offset];
        else
          Covariance[j + row_offset] = 0.0f;
      }
    } else {
      for (int j = 0; j < N; ++j) {
        if (i == j)
          Covariance[j + row_offset] = 1.0f;
        else
          Covariance[j + row_offset] = 0.0f;
      }
    }
  }
  double err = InvertMatrix(Covariance, N, Inverse);
  if (err > 1) {
    tprintf("Clustering error: Matrix inverse failed with error %g\n", err);
  }
  int EssentialN = 0;
  for (int dim = 0; dim < N; ++dim) {
    if (!Clusterer->ParamDesc[dim].NonEssential) {
      Delta[dim] = Left->Mean[dim] - Right->Mean[dim];
      ++EssentialN;
    } else {
      Delta[dim] = 0.0f;
    }
  }
  // Compute Hotelling's T-squared.
  double Tsq = 0.0;
  for (int x = 0; x < N; ++x) {
    double temp = 0.0;
    for (int y = 0; y < N; ++y) {
      temp += Inverse[y + N*x] * Delta[y];
    }
    Tsq += Delta[x] * temp;
  }
  memfree(Covariance);
  memfree(Inverse);
  memfree(Delta);
  // Changed this function to match the formula in
  // Statistical Methods in Medical Research p 473
  // By Peter Armitage, Geoffrey Berry, J. N. S. Matthews.
  // Tsq *= Left->SampleCount * Right->SampleCount / TotalDims;
  double F = Tsq * (TotalDims - EssentialN - 1) / ((TotalDims - 2)*EssentialN);
  int Fx = EssentialN;
  if (Fx > FTABLE_X)
    Fx = FTABLE_X;
  --Fx;
  int Fy = TotalDims - EssentialN - 1;
  if (Fy > FTABLE_Y)
    Fy = FTABLE_Y;
  --Fy;
  double FTarget = FTable[Fy][Fx];
  if (Config->MagicSamples > 0 &&
      TotalDims >= Config->MagicSamples * (1.0 - kMagicSampleMargin) &&
      TotalDims <= Config->MagicSamples * (1.0 + kMagicSampleMargin)) {
    // Give magic-sized clusters a magic FTable boost.
    FTarget += kFTableBoostMargin;
  }
  if (F < FTarget) {
    return NewEllipticalProto (Clusterer->SampleSize, Cluster, Statistics);
  }
  return NULL;
}

/**
 * This routine tests the specified cluster to see if it can
 * be approximated by a spherical normal distribution.  If it
 * can be, then a new prototype is formed and returned to the
 * caller.  If it can't be, then NULL is returned to the caller.
 * @param Clusterer data struct containing samples being clustered
 * @param Cluster   cluster to be made into a spherical prototype
 * @param Statistics  statistical info about cluster
 * @param Buckets   histogram struct used to analyze distribution
 * @return  Pointer to new spherical prototype or NULL.
 * @note Exceptions:  None
 * @note History: 6/1/89, DSJ, Created.
 */
PROTOTYPE *MakeSphericalProto(CLUSTERER *Clusterer,
                              CLUSTER *Cluster,
                              STATISTICS *Statistics,
                              BUCKETS *Buckets) {
  PROTOTYPE *Proto = NULL;
  int i;

  // check that each dimension is a normal distribution
  for (i = 0; i < Clusterer->SampleSize; i++) {
    if (Clusterer->ParamDesc[i].NonEssential)
      continue;

    FillBuckets (Buckets, Cluster, i, &(Clusterer->ParamDesc[i]),
      Cluster->Mean[i],
      sqrt ((FLOAT64) (Statistics->AvgVariance)));
    if (!DistributionOK (Buckets))
      break;
  }
  // if all dimensions matched a normal distribution, make a proto
  if (i >= Clusterer->SampleSize)
    Proto = NewSphericalProto (Clusterer->SampleSize, Cluster, Statistics);
  return (Proto);
}                                // MakeSphericalProto

/**
 * This routine tests the specified cluster to see if it can
 * be approximated by an elliptical normal distribution.  If it
 * can be, then a new prototype is formed and returned to the
 * caller.  If it can't be, then NULL is returned to the caller.
 * @param Clusterer data struct containing samples being clustered
 * @param Cluster   cluster to be made into an elliptical prototype
 * @param Statistics  statistical info about cluster
 * @param Buckets   histogram struct used to analyze distribution
 * @return  Pointer to new elliptical prototype or NULL.
 * @note Exceptions:  None
 * @note History: 6/12/89, DSJ, Created.
 */
PROTOTYPE *MakeEllipticalProto(CLUSTERER *Clusterer,
                               CLUSTER *Cluster,
                               STATISTICS *Statistics,
                               BUCKETS *Buckets) {
  PROTOTYPE *Proto = NULL;
  int i;

  // check that each dimension is a normal distribution
  for (i = 0; i < Clusterer->SampleSize; i++) {
    if (Clusterer->ParamDesc[i].NonEssential)
      continue;

    FillBuckets (Buckets, Cluster, i, &(Clusterer->ParamDesc[i]),
      Cluster->Mean[i],
      sqrt ((FLOAT64) Statistics->
      CoVariance[i * (Clusterer->SampleSize + 1)]));
    if (!DistributionOK (Buckets))
      break;
  }
  // if all dimensions matched a normal distribution, make a proto
  if (i >= Clusterer->SampleSize)
    Proto = NewEllipticalProto (Clusterer->SampleSize, Cluster, Statistics);
  return (Proto);
}                                // MakeEllipticalProto

/**
 * This routine tests each dimension of the specified cluster to
 * see what distribution would best approximate that dimension.
 * Each dimension is compared to the following distributions
 * in order: normal, random, uniform.  If each dimension can
 * be represented by one of these distributions,
 * then a new prototype is formed and returned to the
 * caller.  If it can't be, then NULL is returned to the caller.
 * @param Clusterer data struct containing samples being clustered
 * @param Cluster   cluster to be made into a prototype
 * @param Statistics  statistical info about cluster
 * @param NormalBuckets histogram struct used to analyze distribution
 * @param Confidence  confidence level for alternate distributions
 * @return  Pointer to new mixed prototype or NULL.
 * @note Exceptions:  None
 * @note History: 6/12/89, DSJ, Created.
 */
PROTOTYPE *MakeMixedProto(CLUSTERER *Clusterer,
                          CLUSTER *Cluster,
                          STATISTICS *Statistics,
                          BUCKETS *NormalBuckets,
                          FLOAT64 Confidence) {
  PROTOTYPE *Proto;
  int i;
  BUCKETS *UniformBuckets = NULL;
  BUCKETS *RandomBuckets = NULL;

  // create a mixed proto to work on - initially assume all dimensions normal*/
  Proto = NewMixedProto (Clusterer->SampleSize, Cluster, Statistics);

  // find the proper distribution for each dimension
  for (i = 0; i < Clusterer->SampleSize; i++) {
    if (Clusterer->ParamDesc[i].NonEssential)
      continue;

    FillBuckets (NormalBuckets, Cluster, i, &(Clusterer->ParamDesc[i]),
      Proto->Mean[i],
      sqrt ((FLOAT64) Proto->Variance.Elliptical[i]));
    if (DistributionOK (NormalBuckets))
      continue;

    if (RandomBuckets == NULL)
      RandomBuckets =
        GetBuckets(Clusterer, D_random, Cluster->SampleCount, Confidence);
    MakeDimRandom (i, Proto, &(Clusterer->ParamDesc[i]));
    FillBuckets (RandomBuckets, Cluster, i, &(Clusterer->ParamDesc[i]),
      Proto->Mean[i], Proto->Variance.Elliptical[i]);
    if (DistributionOK (RandomBuckets))
      continue;

    if (UniformBuckets == NULL)
      UniformBuckets =
        GetBuckets(Clusterer, uniform, Cluster->SampleCount, Confidence);
    MakeDimUniform(i, Proto, Statistics);
    FillBuckets (UniformBuckets, Cluster, i, &(Clusterer->ParamDesc[i]),
      Proto->Mean[i], Proto->Variance.Elliptical[i]);
    if (DistributionOK (UniformBuckets))
      continue;
    break;
  }
  // if any dimension failed to match a distribution, discard the proto
  if (i < Clusterer->SampleSize) {
    FreePrototype(Proto);
    Proto = NULL;
  }
  return (Proto);
}                                // MakeMixedProto

/**
 * This routine alters the ith dimension of the specified
 * mixed prototype to be D_random.
 * @param i index of dimension to be changed
 * @param Proto prototype whose dimension is to be altered
 * @param ParamDesc description of specified dimension
 * @return  None
 * @note Exceptions:  None
 * @note History: 6/20/89, DSJ, Created.
 */
void MakeDimRandom(uinT16 i, PROTOTYPE *Proto, PARAM_DESC *ParamDesc) {
  Proto->Distrib[i] = D_random;
  Proto->Mean[i] = ParamDesc->MidRange;
  Proto->Variance.Elliptical[i] = ParamDesc->HalfRange;

  // subtract out the previous magnitude of this dimension from the total
  Proto->TotalMagnitude /= Proto->Magnitude.Elliptical[i];
  Proto->Magnitude.Elliptical[i] = 1.0 / ParamDesc->Range;
  Proto->TotalMagnitude *= Proto->Magnitude.Elliptical[i];
  Proto->LogMagnitude = log ((double) Proto->TotalMagnitude);

  // note that the proto Weight is irrelevant for D_random protos
}                                // MakeDimRandom

/**
 * This routine alters the ith dimension of the specified
 * mixed prototype to be uniform.
 * @param i index of dimension to be changed
 * @param Proto   prototype whose dimension is to be altered
 * @param Statistics  statistical info about prototype
 * @return  None
 * @note Exceptions:  None
 * @note History: 6/20/89, DSJ, Created.
 */
void MakeDimUniform(uinT16 i, PROTOTYPE *Proto, STATISTICS *Statistics) {
  Proto->Distrib[i] = uniform;
  Proto->Mean[i] = Proto->Cluster->Mean[i] +
    (Statistics->Min[i] + Statistics->Max[i]) / 2;
  Proto->Variance.Elliptical[i] =
    (Statistics->Max[i] - Statistics->Min[i]) / 2;
  if (Proto->Variance.Elliptical[i] < MINVARIANCE)
    Proto->Variance.Elliptical[i] = MINVARIANCE;

  // subtract out the previous magnitude of this dimension from the total
  Proto->TotalMagnitude /= Proto->Magnitude.Elliptical[i];
  Proto->Magnitude.Elliptical[i] =
    1.0 / (2.0 * Proto->Variance.Elliptical[i]);
  Proto->TotalMagnitude *= Proto->Magnitude.Elliptical[i];
  Proto->LogMagnitude = log ((double) Proto->TotalMagnitude);

  // note that the proto Weight is irrelevant for uniform protos
}                                // MakeDimUniform

/**
 * This routine searches the cluster tree for all leaf nodes
 * which are samples in the specified cluster.  It computes
 * a full covariance matrix for these samples as well as
 * keeping track of the ranges (min and max) for each
 * dimension.  A special data structure is allocated to
 * return this information to the caller.  An incremental
 * algorithm for computing statistics is not used because
 * it will not work with circular dimensions.
 * @param N number of dimensions
 * @param ParamDesc array of dimension descriptions
 * @param Cluster cluster whose stats are to be computed
 * @return  Pointer to new data structure containing statistics
 * @note Exceptions:  None
 * @note History: 6/2/89, DSJ, Created.
 */
STATISTICS *
ComputeStatistics (inT16 N, PARAM_DESC ParamDesc[], CLUSTER * Cluster) {
  STATISTICS *Statistics;
  int i, j;
  FLOAT32 *CoVariance;
  FLOAT32 *Distance;
  LIST SearchState;
  SAMPLE *Sample;
  uinT32 SampleCountAdjustedForBias;

  // allocate memory to hold the statistics results
  Statistics = (STATISTICS *) Emalloc (sizeof (STATISTICS));
  Statistics->CoVariance = (FLOAT32 *) Emalloc (N * N * sizeof (FLOAT32));
  Statistics->Min = (FLOAT32 *) Emalloc (N * sizeof (FLOAT32));
  Statistics->Max = (FLOAT32 *) Emalloc (N * sizeof (FLOAT32));

  // allocate temporary memory to hold the sample to mean distances
  Distance = (FLOAT32 *) Emalloc (N * sizeof (FLOAT32));

  // initialize the statistics
  Statistics->AvgVariance = 1.0;
  CoVariance = Statistics->CoVariance;
  for (i = 0; i < N; i++) {
    Statistics->Min[i] = 0.0;
    Statistics->Max[i] = 0.0;
    for (j = 0; j < N; j++, CoVariance++)
      *CoVariance = 0;
  }
  // find each sample in the cluster and merge it into the statistics
  InitSampleSearch(SearchState, Cluster);
  while ((Sample = NextSample (&SearchState)) != NULL) {
    for (i = 0; i < N; i++) {
      Distance[i] = Sample->Mean[i] - Cluster->Mean[i];
      if (ParamDesc[i].Circular) {
        if (Distance[i] > ParamDesc[i].HalfRange)
          Distance[i] -= ParamDesc[i].Range;
        if (Distance[i] < -ParamDesc[i].HalfRange)
          Distance[i] += ParamDesc[i].Range;
      }
      if (Distance[i] < Statistics->Min[i])
        Statistics->Min[i] = Distance[i];
      if (Distance[i] > Statistics->Max[i])
        Statistics->Max[i] = Distance[i];
    }
    CoVariance = Statistics->CoVariance;
    for (i = 0; i < N; i++)
      for (j = 0; j < N; j++, CoVariance++)
        *CoVariance += Distance[i] * Distance[j];
  }
  // normalize the variances by the total number of samples
  // use SampleCount-1 instead of SampleCount to get an unbiased estimate
  // also compute the geometic mean of the diagonal variances
  // ensure that clusters with only 1 sample are handled correctly
  if (Cluster->SampleCount > 1)
    SampleCountAdjustedForBias = Cluster->SampleCount - 1;
  else
    SampleCountAdjustedForBias = 1;
  CoVariance = Statistics->CoVariance;
  for (i = 0; i < N; i++)
  for (j = 0; j < N; j++, CoVariance++) {
    *CoVariance /= SampleCountAdjustedForBias;
    if (j == i) {
      if (*CoVariance < MINVARIANCE)
        *CoVariance = MINVARIANCE;
      Statistics->AvgVariance *= *CoVariance;
    }
  }
  Statistics->AvgVariance = (float)pow((double)Statistics->AvgVariance,
                                       1.0 / N);

  // release temporary memory and return
  memfree(Distance);
  return (Statistics);
}                                // ComputeStatistics

/**
 * This routine creates a spherical prototype data structure to
 * approximate the samples in the specified cluster.
 * Spherical prototypes have a single variance which is
 * common across all dimensions.  All dimensions are normally
 * distributed and independent.
 * @param N number of dimensions
 * @param Cluster cluster to be made into a spherical prototype
 * @param Statistics  statistical info about samples in cluster
 * @return  Pointer to a new spherical prototype data structure
 * @note Exceptions:  None
 * @note History: 6/19/89, DSJ, Created.
 */
PROTOTYPE *NewSphericalProto(uinT16 N,
                             CLUSTER *Cluster,
                             STATISTICS *Statistics) {
  PROTOTYPE *Proto;

  Proto = NewSimpleProto (N, Cluster);

  Proto->Variance.Spherical = Statistics->AvgVariance;
  if (Proto->Variance.Spherical < MINVARIANCE)
    Proto->Variance.Spherical = MINVARIANCE;

  Proto->Magnitude.Spherical =
    1.0 / sqrt ((double) (2.0 * PI * Proto->Variance.Spherical));
  Proto->TotalMagnitude = (float)pow((double)Proto->Magnitude.Spherical,
                                     (double) N);
  Proto->Weight.Spherical = 1.0 / Proto->Variance.Spherical;
  Proto->LogMagnitude = log ((double) Proto->TotalMagnitude);

  return (Proto);
}                                // NewSphericalProto

/**
 * This routine creates an elliptical prototype data structure to
 * approximate the samples in the specified cluster.
 * Elliptical prototypes have a variance for each dimension.
 * All dimensions are normally distributed and independent.
 * @param N number of dimensions
 * @param Cluster cluster to be made into an elliptical prototype
 * @param Statistics  statistical info about samples in cluster
 * @return  Pointer to a new elliptical prototype data structure
 * @note Exceptions:  None
 * @note History: 6/19/89, DSJ, Created.
 */
PROTOTYPE *NewEllipticalProto(inT16 N,
                              CLUSTER *Cluster,
                              STATISTICS *Statistics) {
  PROTOTYPE *Proto;
  FLOAT32 *CoVariance;
  int i;

  Proto = NewSimpleProto (N, Cluster);
  Proto->Variance.Elliptical = (FLOAT32 *) Emalloc (N * sizeof (FLOAT32));
  Proto->Magnitude.Elliptical = (FLOAT32 *) Emalloc (N * sizeof (FLOAT32));
  Proto->Weight.Elliptical = (FLOAT32 *) Emalloc (N * sizeof (FLOAT32));

  CoVariance = Statistics->CoVariance;
  Proto->TotalMagnitude = 1.0;
  for (i = 0; i < N; i++, CoVariance += N + 1) {
    Proto->Variance.Elliptical[i] = *CoVariance;
    if (Proto->Variance.Elliptical[i] < MINVARIANCE)
      Proto->Variance.Elliptical[i] = MINVARIANCE;

    Proto->Magnitude.Elliptical[i] =
      1.0 / sqrt ((double) (2.0 * PI * Proto->Variance.Elliptical[i]));
    Proto->Weight.Elliptical[i] = 1.0 / Proto->Variance.Elliptical[i];
    Proto->TotalMagnitude *= Proto->Magnitude.Elliptical[i];
  }
  Proto->LogMagnitude = log ((double) Proto->TotalMagnitude);
  Proto->Style = elliptical;
  return (Proto);
}                                // NewEllipticalProto

/**
 * This routine creates a mixed prototype data structure to
 * approximate the samples in the specified cluster.
 * Mixed prototypes can have different distributions for
 * each dimension.  All dimensions are independent.  The
 * structure is initially filled in as though it were an
 * elliptical prototype.  The actual distributions of the
 * dimensions can be altered by other routines.
 * @param N number of dimensions
 * @param Cluster cluster to be made into a mixed prototype
 * @param Statistics  statistical info about samples in cluster
 * @return  Pointer to a new mixed prototype data structure
 * @note Exceptions:  None
 * @note History: 6/19/89, DSJ, Created.
 */
PROTOTYPE *NewMixedProto(inT16 N, CLUSTER *Cluster, STATISTICS *Statistics) {
  PROTOTYPE *Proto;
  int i;

  Proto = NewEllipticalProto (N, Cluster, Statistics);
  Proto->Distrib = (DISTRIBUTION *) Emalloc (N * sizeof (DISTRIBUTION));

  for (i = 0; i < N; i++) {
    Proto->Distrib[i] = normal;
  }
  Proto->Style = mixed;
  return (Proto);
}                                // NewMixedProto

/**
 * This routine allocates memory to hold a simple prototype
 * data structure, i.e. one without independent distributions
 * and variances for each dimension.
 * @param N number of dimensions
 * @param Cluster cluster to be made into a prototype
 * @return  Pointer to new simple prototype
 * @note Exceptions:  None
 * @note History: 6/19/89, DSJ, Created.
 */
PROTOTYPE *NewSimpleProto(inT16 N, CLUSTER *Cluster) {
  PROTOTYPE *Proto;
  int i;

  Proto = (PROTOTYPE *) Emalloc (sizeof (PROTOTYPE));
  Proto->Mean = (FLOAT32 *) Emalloc (N * sizeof (FLOAT32));

  for (i = 0; i < N; i++)
    Proto->Mean[i] = Cluster->Mean[i];
  Proto->Distrib = NULL;

  Proto->Significant = TRUE;
  Proto->Merged = FALSE;
  Proto->Style = spherical;
  Proto->NumSamples = Cluster->SampleCount;
  Proto->Cluster = Cluster;
  Proto->Cluster->Prototype = TRUE;
  return (Proto);
}                                // NewSimpleProto

/**
 * This routine returns TRUE if the specified covariance
 * matrix indicates that all N dimensions are independent of
 * one another.  One dimension is judged to be independent of
 * another when the magnitude of the corresponding correlation
 * coefficient is
 * less than the specified Independence factor.  The
 * correlation coefficient is calculated as: (see Duda and
 * Hart, pg. 247)
 * coeff[ij] = stddev[ij] / sqrt (stddev[ii] * stddev[jj])
 * The covariance matrix is assumed to be symmetric (which
 * should always be true).
 * @param ParamDesc descriptions of each feature space dimension
 * @param N number of dimensions
 * @param CoVariance  ptr to a covariance matrix
 * @param Independence  max off-diagonal correlation coefficient
 * @return  TRUE if dimensions are independent, FALSE otherwise
 * @note Exceptions:  None
 * @note History: 6/4/89, DSJ, Created.
 */
BOOL8
Independent (PARAM_DESC ParamDesc[],
inT16 N, FLOAT32 * CoVariance, FLOAT32 Independence) {
  int i, j;
  FLOAT32 *VARii;                // points to ith on-diagonal element
  FLOAT32 *VARjj;                // points to jth on-diagonal element
  FLOAT32 CorrelationCoeff;

  VARii = CoVariance;
  for (i = 0; i < N; i++, VARii += N + 1) {
    if (ParamDesc[i].NonEssential)
      continue;

    VARjj = VARii + N + 1;
    CoVariance = VARii + 1;
    for (j = i + 1; j < N; j++, CoVariance++, VARjj += N + 1) {
      if (ParamDesc[j].NonEssential)
        continue;

      if ((*VARii == 0.0) || (*VARjj == 0.0))
        CorrelationCoeff = 0.0;
      else
        CorrelationCoeff =
          sqrt (sqrt (*CoVariance * *CoVariance / (*VARii * *VARjj)));
      if (CorrelationCoeff > Independence)
        return (FALSE);
    }
  }
  return (TRUE);
}                                // Independent

/**
 * This routine returns a histogram data structure which can
 * be used by other routines to place samples into histogram
 * buckets, and then apply a goodness of fit test to the
 * histogram data to determine if the samples belong to the
 * specified probability distribution.  The routine keeps
 * a list of bucket data structures which have already been
 * created so that it minimizes the computation time needed
 * to create a new bucket.
 * @param clusterer  which keeps a bucket_cache for us.
 * @param Distribution  type of probability distribution to test for
 * @param SampleCount number of samples that are available
 * @param Confidence  probability of a Type I error
 * @return  Bucket data structure
 * @note Exceptions: none
 * @note History: Thu Aug  3 12:58:10 1989, DSJ, Created.
 */
BUCKETS *GetBuckets(CLUSTERER* clusterer,
                    DISTRIBUTION Distribution,
                    uinT32 SampleCount,
                    FLOAT64 Confidence) {
  // Get an old bucket structure with the same number of buckets.
  uinT16 NumberOfBuckets = OptimumNumberOfBuckets(SampleCount);
  BUCKETS *Buckets =
      clusterer->bucket_cache[Distribution][NumberOfBuckets - MINBUCKETS];

  // If a matching bucket structure is not found, make one and save it.
  if (Buckets == NULL) {
    Buckets = MakeBuckets(Distribution, SampleCount, Confidence);
    clusterer->bucket_cache[Distribution][NumberOfBuckets - MINBUCKETS] =
        Buckets;
  } else {
    // Just adjust the existing buckets.
    if (SampleCount != Buckets->SampleCount)
      AdjustBuckets(Buckets, SampleCount);
    if (Confidence != Buckets->Confidence) {
      Buckets->Confidence = Confidence;
      Buckets->ChiSquared = ComputeChiSquared(
          DegreesOfFreedom(Distribution, Buckets->NumberOfBuckets),
          Confidence);
    }
    InitBuckets(Buckets);
  }
  return Buckets;
}                                // GetBuckets

/**
 * This routine creates a histogram data structure which can
 * be used by other routines to place samples into histogram
 * buckets, and then apply a goodness of fit test to the
 * histogram data to determine if the samples belong to the
 * specified probability distribution.  The buckets are
 * allocated in such a way that the expected frequency of
 * samples in each bucket is approximately the same.  In
 * order to make this possible, a mapping table is
 * computed which maps "normalized" samples into the
 * appropriate bucket.
 * @param Distribution  type of probability distribution to test for
 * @param SampleCount number of samples that are available
 * @param Confidence  probability of a Type I error
 * @return Pointer to new histogram data structure
 * @note Exceptions:  None
 * @note History: 6/4/89, DSJ, Created.
 */
BUCKETS *MakeBuckets(DISTRIBUTION Distribution,
                     uinT32 SampleCount,
                     FLOAT64 Confidence) {
  const DENSITYFUNC DensityFunction[] =
    { NormalDensity, UniformDensity, UniformDensity };
  int i, j;
  BUCKETS *Buckets;
  FLOAT64 BucketProbability;
  FLOAT64 NextBucketBoundary;
  FLOAT64 Probability;
  FLOAT64 ProbabilityDelta;
  FLOAT64 LastProbDensity;
  FLOAT64 ProbDensity;
  uinT16 CurrentBucket;
  BOOL8 Symmetrical;

  // allocate memory needed for data structure
  Buckets = reinterpret_cast<BUCKETS*>(Emalloc(sizeof(BUCKETS)));
  Buckets->NumberOfBuckets = OptimumNumberOfBuckets(SampleCount);
  Buckets->SampleCount = SampleCount;
  Buckets->Confidence = Confidence;
  Buckets->Count = reinterpret_cast<uinT32*>(
      Emalloc(Buckets->NumberOfBuckets * sizeof(uinT32)));
  Buckets->ExpectedCount = reinterpret_cast<FLOAT32*>(
      Emalloc(Buckets->NumberOfBuckets * sizeof(FLOAT32)));

  // initialize simple fields
  Buckets->Distribution = Distribution;
  for (i = 0; i < Buckets->NumberOfBuckets; i++) {
    Buckets->Count[i] = 0;
    Buckets->ExpectedCount[i] = 0.0;
  }

  // all currently defined distributions are symmetrical
  Symmetrical = TRUE;
  Buckets->ChiSquared = ComputeChiSquared(
      DegreesOfFreedom(Distribution, Buckets->NumberOfBuckets), Confidence);

  if (Symmetrical) {
    // allocate buckets so that all have approx. equal probability
    BucketProbability = 1.0 / (FLOAT64) (Buckets->NumberOfBuckets);

    // distribution is symmetric so fill in upper half then copy
    CurrentBucket = Buckets->NumberOfBuckets / 2;
    if (Odd (Buckets->NumberOfBuckets))
      NextBucketBoundary = BucketProbability / 2;
    else
      NextBucketBoundary = BucketProbability;

    Probability = 0.0;
    LastProbDensity =
      (*DensityFunction[(int) Distribution]) (BUCKETTABLESIZE / 2);
    for (i = BUCKETTABLESIZE / 2; i < BUCKETTABLESIZE; i++) {
      ProbDensity = (*DensityFunction[(int) Distribution]) (i + 1);
      ProbabilityDelta = Integral (LastProbDensity, ProbDensity, 1.0);
      Probability += ProbabilityDelta;
      if (Probability > NextBucketBoundary) {
        if (CurrentBucket < Buckets->NumberOfBuckets - 1)
          CurrentBucket++;
        NextBucketBoundary += BucketProbability;
      }
      Buckets->Bucket[i] = CurrentBucket;
      Buckets->ExpectedCount[CurrentBucket] +=
        (FLOAT32) (ProbabilityDelta * SampleCount);
      LastProbDensity = ProbDensity;
    }
    // place any leftover probability into the last bucket
    Buckets->ExpectedCount[CurrentBucket] +=
      (FLOAT32) ((0.5 - Probability) * SampleCount);

    // copy upper half of distribution to lower half
    for (i = 0, j = BUCKETTABLESIZE - 1; i < j; i++, j--)
      Buckets->Bucket[i] =
        Mirror(Buckets->Bucket[j], Buckets->NumberOfBuckets);

    // copy upper half of expected counts to lower half
    for (i = 0, j = Buckets->NumberOfBuckets - 1; i <= j; i++, j--)
      Buckets->ExpectedCount[i] += Buckets->ExpectedCount[j];
  }
  return Buckets;
}                                // MakeBuckets

/**
 * This routine computes the optimum number of histogram
 * buckets that should be used in a chi-squared goodness of
 * fit test for the specified number of samples.  The optimum
 * number is computed based on Table 4.1 on pg. 147 of
 * "Measurement and Analysis of Random Data" by Bendat & Piersol.
 * Linear interpolation is used to interpolate between table
 * values.  The table is intended for a 0.05 level of
 * significance (alpha).  This routine assumes that it is
 * equally valid for other alpha's, which may not be true.
 * @param SampleCount number of samples to be tested
 * @return Optimum number of histogram buckets
 * @note Exceptions: None
 * @note History: 6/5/89, DSJ, Created.
 */
uinT16 OptimumNumberOfBuckets(uinT32 SampleCount) {
  uinT8 Last, Next;
  FLOAT32 Slope;

  if (SampleCount < kCountTable[0])
    return kBucketsTable[0];

  for (Last = 0, Next = 1; Next < LOOKUPTABLESIZE; Last++, Next++) {
    if (SampleCount <= kCountTable[Next]) {
      Slope = (FLOAT32) (kBucketsTable[Next] - kBucketsTable[Last]) /
          (FLOAT32) (kCountTable[Next] - kCountTable[Last]);
      return ((uinT16) (kBucketsTable[Last] +
          Slope * (SampleCount - kCountTable[Last])));
    }
  }
  return kBucketsTable[Last];
}                                // OptimumNumberOfBuckets

/**
 * This routine computes the chi-squared value which will
 * leave a cumulative probability of Alpha in the right tail
 * of a chi-squared distribution with the specified number of
 * degrees of freedom.  Alpha must be between 0 and 1.
 * DegreesOfFreedom must be even.  The routine maintains an
 * array of lists.  Each list corresponds to a different
 * number of degrees of freedom.  Each entry in the list
 * corresponds to a different alpha value and its corresponding
 * chi-squared value.  Therefore, once a particular chi-squared
 * value is computed, it is stored in the list and never
 * needs to be computed again.
 * @param DegreesOfFreedom  determines shape of distribution
 * @param Alpha probability of right tail
 * @return Desired chi-squared value
 * @note Exceptions: none
 * @note History: 6/5/89, DSJ, Created.
 */
FLOAT64
ComputeChiSquared (uinT16 DegreesOfFreedom, FLOAT64 Alpha)
#define CHIACCURACY     0.01
#define MINALPHA  (1e-200)
{
  static LIST ChiWith[MAXDEGREESOFFREEDOM + 1];

  CHISTRUCT *OldChiSquared;
  CHISTRUCT SearchKey;

  // limit the minimum alpha that can be used - if alpha is too small
  //      it may not be possible to compute chi-squared.
  Alpha = ClipToRange(Alpha, MINALPHA, 1.0);
  if (Odd (DegreesOfFreedom))
    DegreesOfFreedom++;

  /* find the list of chi-squared values which have already been computed
     for the specified number of degrees of freedom.  Search the list for
     the desired chi-squared. */
  SearchKey.Alpha = Alpha;
  OldChiSquared = (CHISTRUCT *) first_node (search (ChiWith[DegreesOfFreedom],
    &SearchKey, AlphaMatch));

  if (OldChiSquared == NULL) {
    OldChiSquared = NewChiStruct (DegreesOfFreedom, Alpha);
    OldChiSquared->ChiSquared = Solve (ChiArea, OldChiSquared,
      (FLOAT64) DegreesOfFreedom,
      (FLOAT64) CHIACCURACY);
    ChiWith[DegreesOfFreedom] = push (ChiWith[DegreesOfFreedom],
      OldChiSquared);
  }
  else {
    // further optimization might move OldChiSquared to front of list
  }

  return (OldChiSquared->ChiSquared);

}                                // ComputeChiSquared

/**
 * This routine computes the probability density function
 * of a discrete normal distribution defined by the global
 * variables kNormalMean, kNormalVariance, and kNormalMagnitude.
 * Normal magnitude could, of course, be computed in terms of
 * the normal variance but it is precomputed for efficiency.
 * @param x number to compute the normal probability density for
 * @note Globals:
 *    kNormalMean mean of a discrete normal distribution
 *    kNormalVariance variance of a discrete normal distribution
 *    kNormalMagnitude  magnitude of a discrete normal
 *distribution
 * @return  The value of the normal distribution at x.
 * @note Exceptions: None
 * @note History: 6/4/89, DSJ, Created.
 */
FLOAT64 NormalDensity(inT32 x) {
  FLOAT64 Distance;

  Distance = x - kNormalMean;
  return kNormalMagnitude * exp(-0.5 * Distance * Distance / kNormalVariance);
}                                // NormalDensity

/**
 * This routine computes the probability density function
 * of a uniform distribution at the specified point.  The
 * range of the distribution is from 0 to BUCKETTABLESIZE.
 * @param x number to compute the uniform probability density for
 * @return The value of the uniform distribution at x.
 * @note Exceptions: None
 * @note History: 6/5/89, DSJ, Created.
 */
FLOAT64 UniformDensity(inT32 x) {
  static FLOAT64 UniformDistributionDensity = (FLOAT64) 1.0 / BUCKETTABLESIZE;

  if ((x >= 0.0) && (x <= BUCKETTABLESIZE))
    return UniformDistributionDensity;
  else
    return (FLOAT64) 0.0;
}                                // UniformDensity

/**
 * This routine computes a trapezoidal approximation to the
 * integral of a function over a small delta in x.
 * @param f1  value of function at x1
 * @param f2  value of function at x2
 * @param Dx  x2 - x1 (should always be positive)
 * @return Approximation of the integral of the function from x1 to x2.
 * @note Exceptions: None
 * @note History: 6/5/89, DSJ, Created.
 */
FLOAT64 Integral(FLOAT64 f1, FLOAT64 f2, FLOAT64 Dx) {
  return (f1 + f2) * Dx / 2.0;
}                                // Integral

/**
 * This routine counts the number of cluster samples which
 * fall within the various histogram buckets in Buckets.  Only
 * one dimension of each sample is examined.  The exact meaning
 * of the Mean and StdDev parameters depends on the
 * distribution which is being analyzed (this info is in the
 * Buckets data structure).  For normal distributions, Mean
 * and StdDev have the expected meanings.  For uniform and
 * random distributions the Mean is the center point of the
 * range and the StdDev is 1/2 the range.  A dimension with
 * zero standard deviation cannot be statistically analyzed.
 * In this case, a pseudo-analysis is used.
 * @param Buckets histogram buckets to count samples
 * @param Cluster cluster whose samples are being analyzed
 * @param Dim dimension of samples which is being analyzed
 * @param ParamDesc description of the dimension
 * @param Mean  "mean" of the distribution
 * @param StdDev  "standard deviation" of the distribution
 * @return None (the Buckets data structure is filled in)
 * @note Exceptions: None
 * @note History: 6/5/89, DSJ, Created.
 */
void FillBuckets(BUCKETS *Buckets,
                 CLUSTER *Cluster,
                 uinT16 Dim,
                 PARAM_DESC *ParamDesc,
                 FLOAT32 Mean,
                 FLOAT32 StdDev) {
  uinT16 BucketID;
  int i;
  LIST SearchState;
  SAMPLE *Sample;

  // initialize the histogram bucket counts to 0
  for (i = 0; i < Buckets->NumberOfBuckets; i++)
    Buckets->Count[i] = 0;

  if (StdDev == 0.0) {
    /* if the standard deviation is zero, then we can't statistically
       analyze the cluster.  Use a pseudo-analysis: samples exactly on
       the mean are distributed evenly across all buckets.  Samples greater
       than the mean are placed in the last bucket; samples less than the
       mean are placed in the first bucket. */

    InitSampleSearch(SearchState, Cluster);
    i = 0;
    while ((Sample = NextSample (&SearchState)) != NULL) {
      if (Sample->Mean[Dim] > Mean)
        BucketID = Buckets->NumberOfBuckets - 1;
      else if (Sample->Mean[Dim] < Mean)
        BucketID = 0;
      else
        BucketID = i;
      Buckets->Count[BucketID] += 1;
      i++;
      if (i >= Buckets->NumberOfBuckets)
        i = 0;
    }
  }
  else {
    // search for all samples in the cluster and add to histogram buckets
    InitSampleSearch(SearchState, Cluster);
    while ((Sample = NextSample (&SearchState)) != NULL) {
      switch (Buckets->Distribution) {
        case normal:
          BucketID = NormalBucket (ParamDesc, Sample->Mean[Dim],
            Mean, StdDev);
          break;
        case D_random:
        case uniform:
          BucketID = UniformBucket (ParamDesc, Sample->Mean[Dim],
            Mean, StdDev);
          break;
        default:
          BucketID = 0;
      }
      Buckets->Count[Buckets->Bucket[BucketID]] += 1;
    }
  }
}                                // FillBuckets

/**
 * This routine determines which bucket x falls into in the
 * discrete normal distribution defined by kNormalMean
 * and kNormalStdDev.  x values which exceed the range of
 * the discrete distribution are clipped.
 * @param ParamDesc used to identify circular dimensions
 * @param x value to be normalized
 * @param Mean  mean of normal distribution
 * @param StdDev  standard deviation of normal distribution
 * @return Bucket number into which x falls
 * @note Exceptions: None
 * @note History: 6/5/89, DSJ, Created.
 */
uinT16 NormalBucket(PARAM_DESC *ParamDesc,
                    FLOAT32 x,
                    FLOAT32 Mean,
                    FLOAT32 StdDev) {
  FLOAT32 X;

  // wraparound circular parameters if necessary
  if (ParamDesc->Circular) {
    if (x - Mean > ParamDesc->HalfRange)
      x -= ParamDesc->Range;
    else if (x - Mean < -ParamDesc->HalfRange)
      x += ParamDesc->Range;
  }

  X = ((x - Mean) / StdDev) * kNormalStdDev + kNormalMean;
  if (X < 0)
    return 0;
  if (X > BUCKETTABLESIZE - 1)
    return ((uinT16) (BUCKETTABLESIZE - 1));
  return (uinT16) floor((FLOAT64) X);
}                                // NormalBucket

/**
 * This routine determines which bucket x falls into in the
 * discrete uniform distribution defined by
 * BUCKETTABLESIZE.  x values which exceed the range of
 * the discrete distribution are clipped.
 * @param ParamDesc used to identify circular dimensions
 * @param x value to be normalized
 * @param Mean  center of range of uniform distribution
 * @param StdDev  1/2 the range of the uniform distribution
 * @return Bucket number into which x falls
 * @note Exceptions: None
 * @note History: 6/5/89, DSJ, Created.
 */
uinT16 UniformBucket(PARAM_DESC *ParamDesc,
                     FLOAT32 x,
                     FLOAT32 Mean,
                     FLOAT32 StdDev) {
  FLOAT32 X;

  // wraparound circular parameters if necessary
  if (ParamDesc->Circular) {
    if (x - Mean > ParamDesc->HalfRange)
      x -= ParamDesc->Range;
    else if (x - Mean < -ParamDesc->HalfRange)
      x += ParamDesc->Range;
  }

  X = ((x - Mean) / (2 * StdDev) * BUCKETTABLESIZE + BUCKETTABLESIZE / 2.0);
  if (X < 0)
    return 0;
  if (X > BUCKETTABLESIZE - 1)
    return (uinT16) (BUCKETTABLESIZE - 1);
  return (uinT16) floor((FLOAT64) X);
}                                // UniformBucket

/**
 * This routine performs a chi-square goodness of fit test
 * on the histogram data in the Buckets data structure.  TRUE
 * is returned if the histogram matches the probability
 * distribution which was specified when the Buckets
 * structure was originally created.  Otherwise FALSE is
 * returned.
 * @param Buckets   histogram data to perform chi-square test on
 * @return TRUE if samples match distribution, FALSE otherwise
 * @note Exceptions: None
 * @note History: 6/5/89, DSJ, Created.
 */
BOOL8 DistributionOK(BUCKETS *Buckets) {
  FLOAT32 FrequencyDifference;
  FLOAT32 TotalDifference;
  int i;

  // compute how well the histogram matches the expected histogram
  TotalDifference = 0.0;
  for (i = 0; i < Buckets->NumberOfBuckets; i++) {
    FrequencyDifference = Buckets->Count[i] - Buckets->ExpectedCount[i];
    TotalDifference += (FrequencyDifference * FrequencyDifference) /
      Buckets->ExpectedCount[i];
  }

  // test to see if the difference is more than expected
  if (TotalDifference > Buckets->ChiSquared)
    return FALSE;
  else
    return TRUE;
}                                // DistributionOK

/**
 * This routine frees the memory used by the statistics
 * data structure.
 * @param Statistics  pointer to data structure to be freed
 * @return None
 * @note Exceptions: None
 * @note History: 6/5/89, DSJ, Created.
 */
void FreeStatistics(STATISTICS *Statistics) {
  memfree (Statistics->CoVariance);
  memfree (Statistics->Min);
  memfree (Statistics->Max);
  memfree(Statistics);
}                                // FreeStatistics

/**
 * This routine properly frees the memory used by a BUCKETS.
 *
 * @param buckets  pointer to data structure to be freed
 */
void FreeBuckets(BUCKETS *buckets) {
  Efree(buckets->Count);
  Efree(buckets->ExpectedCount);
  Efree(buckets);
}                                // FreeBuckets

/**
 * This routine frees the memory consumed by the specified
 * cluster and all of its subclusters.  This is done by
 * recursive calls to FreeCluster().
 *
 * @param Cluster pointer to cluster to be freed
 *
 * @return None
 *
 * @note Exceptions: None
 * @note History: 6/6/89, DSJ, Created.
 */
void FreeCluster(CLUSTER *Cluster) {
  if (Cluster != NULL) {
    FreeCluster (Cluster->Left);
    FreeCluster (Cluster->Right);
    memfree(Cluster);
  }
}                                // FreeCluster

/**
 * This routine computes the degrees of freedom that should
 * be used in a chi-squared test with the specified number of
 * histogram buckets.  The result is always rounded up to
 * the next even number so that the value of chi-squared can be
 * computed more easily.  This will cause the value of
 * chi-squared to be higher than the optimum value, resulting
 * in the chi-square test being more lenient than optimum.
 * @param Distribution    distribution being tested for
 * @param HistogramBuckets  number of buckets in chi-square test
 * @return The number of degrees of freedom for a chi-square test
 * @note Exceptions: none
 * @note History: Thu Aug  3 14:04:18 1989, DSJ, Created.
 */
uinT16 DegreesOfFreedom(DISTRIBUTION Distribution, uinT16 HistogramBuckets) {
  static uinT8 DegreeOffsets[] = { 3, 3, 1 };

  uinT16 AdjustedNumBuckets;

  AdjustedNumBuckets = HistogramBuckets - DegreeOffsets[(int) Distribution];
  if (Odd (AdjustedNumBuckets))
    AdjustedNumBuckets++;
  return (AdjustedNumBuckets);

}                                // DegreesOfFreedom

/**
 * This routine is used to search a list of histogram data
 * structures to find one with the specified number of
 * buckets.  It is called by the list search routines.
 * @param arg1 current histogram being tested for a match
 * @param arg2 match key
 * @return TRUE if arg1 matches arg2
 * @note Exceptions: none
 * @note History: Thu Aug  3 14:17:33 1989, DSJ, Created.
 */
int NumBucketsMatch(void *arg1,    // BUCKETS *Histogram,
                    void *arg2) {  // uinT16 *DesiredNumberOfBuckets)
  BUCKETS *Histogram = (BUCKETS *) arg1;
  uinT16 *DesiredNumberOfBuckets = (uinT16 *) arg2;

  return (*DesiredNumberOfBuckets == Histogram->NumberOfBuckets);

}                                // NumBucketsMatch

/**
 * This routine is used to search a list for a list node
 * whose contents match Key.  It is called by the list
 * delete_d routine.
 * @return TRUE if ListNode matches Key
 * @note Exceptions: none
 * @note History: Thu Aug  3 14:23:58 1989, DSJ, Created.
 */
int ListEntryMatch(void *arg1,    //ListNode
                   void *arg2) {  //Key
  return (arg1 == arg2);

}                                // ListEntryMatch

/**
 * This routine multiplies each ExpectedCount histogram entry
 * by NewSampleCount/OldSampleCount so that the histogram
 * is now adjusted to the new sample count.
 * @param Buckets histogram data structure to adjust
 * @param NewSampleCount  new sample count to adjust to
 * @return none
 * @note Exceptions: none
 * @note History: Thu Aug  3 14:31:14 1989, DSJ, Created.
 */
void AdjustBuckets(BUCKETS *Buckets, uinT32 NewSampleCount) {
  int i;
  FLOAT64 AdjustFactor;

  AdjustFactor = (((FLOAT64) NewSampleCount) /
    ((FLOAT64) Buckets->SampleCount));

  for (i = 0; i < Buckets->NumberOfBuckets; i++) {
    Buckets->ExpectedCount[i] *= AdjustFactor;
  }

  Buckets->SampleCount = NewSampleCount;

}                                // AdjustBuckets

/**
 * This routine sets the bucket counts in the specified histogram
 * to zero.
 * @param Buckets histogram data structure to init
 * @return none
 * @note Exceptions: none
 * @note History: Thu Aug  3 14:31:14 1989, DSJ, Created.
 */
void InitBuckets(BUCKETS *Buckets) {
  int i;

  for (i = 0; i < Buckets->NumberOfBuckets; i++) {
    Buckets->Count[i] = 0;
  }

}                                // InitBuckets

/**
 * This routine is used to search a list of structures which
 * hold pre-computed chi-squared values for a chi-squared
 * value whose corresponding alpha field matches the alpha
 * field of SearchKey.
 *
 * It is called by the list search routines.
 *
 * @param arg1 chi-squared struct being tested for a match
 * @param arg2 chi-squared struct that is the search key
 * @return TRUE if ChiStruct's Alpha matches SearchKey's Alpha
 * @note Exceptions: none
 * @note History: Thu Aug  3 14:17:33 1989, DSJ, Created.
 */
int AlphaMatch(void *arg1,    //CHISTRUCT                             *ChiStruct,
               void *arg2) {  //CHISTRUCT                             *SearchKey)
  CHISTRUCT *ChiStruct = (CHISTRUCT *) arg1;
  CHISTRUCT *SearchKey = (CHISTRUCT *) arg2;

  return (ChiStruct->Alpha == SearchKey->Alpha);

}                                // AlphaMatch

/**
 * This routine allocates a new data structure which is used
 * to hold a chi-squared value along with its associated
 * number of degrees of freedom and alpha value.
 *
 * @param DegreesOfFreedom  degrees of freedom for new chi value
 * @param Alpha     confidence level for new chi value
 * @return none
 * @note Exceptions: none
 * @note History: Fri Aug  4 11:04:59 1989, DSJ, Created.
 */
CHISTRUCT *NewChiStruct(uinT16 DegreesOfFreedom, FLOAT64 Alpha) {
  CHISTRUCT *NewChiStruct;

  NewChiStruct = (CHISTRUCT *) Emalloc (sizeof (CHISTRUCT));
  NewChiStruct->DegreesOfFreedom = DegreesOfFreedom;
  NewChiStruct->Alpha = Alpha;
  return (NewChiStruct);

}                                // NewChiStruct

/**
 * This routine attempts to find an x value at which Function
 * goes to zero (i.e. a root of the function ).  It will only
 * work correctly if a solution actually exists and there
 * are no extrema between the solution and the InitialGuess.
 * The algorithms used are extremely primitive.
 *
 * @param Function  function whose zero is to be found
 * @param FunctionParams  arbitrary data to pass to function
 * @param InitialGuess  point to start solution search at
 * @param Accuracy  maximum allowed error
 * @return Solution of function ( x for which f(x) = 0 ).
 * @note Exceptions: none
 * @note History: Fri Aug  4 11:08:59 1989, DSJ, Created.
 */
FLOAT64
Solve (SOLVEFUNC Function,
void *FunctionParams, FLOAT64 InitialGuess, FLOAT64 Accuracy)
#define INITIALDELTA    0.1
#define  DELTARATIO     0.1
{
  FLOAT64 x;
  FLOAT64 f;
  FLOAT64 Slope;
  FLOAT64 Delta;
  FLOAT64 NewDelta;
  FLOAT64 xDelta;
  FLOAT64 LastPosX, LastNegX;

  x = InitialGuess;
  Delta = INITIALDELTA;
  LastPosX = MAX_FLOAT32;
  LastNegX = -MAX_FLOAT32;
  f = (*Function) ((CHISTRUCT *) FunctionParams, x);
  while (Abs (LastPosX - LastNegX) > Accuracy) {
    // keep track of outer bounds of current estimate
    if (f < 0)
      LastNegX = x;
    else
      LastPosX = x;

    // compute the approx. slope of f(x) at the current point
    Slope =
      ((*Function) ((CHISTRUCT *) FunctionParams, x + Delta) - f) / Delta;

    // compute the next solution guess */
    xDelta = f / Slope;
    x -= xDelta;

    // reduce the delta used for computing slope to be a fraction of
    //the amount moved to get to the new guess
    NewDelta = Abs (xDelta) * DELTARATIO;
    if (NewDelta < Delta)
      Delta = NewDelta;

    // compute the value of the function at the new guess
    f = (*Function) ((CHISTRUCT *) FunctionParams, x);
  }
  return (x);

}                                // Solve

/**
 * This routine computes the area under a chi density curve
 * from 0 to x, minus the desired area under the curve.  The
 * number of degrees of freedom of the chi curve is specified
 * in the ChiParams structure.  The desired area is also
 * specified in the ChiParams structure as Alpha ( or 1 minus
 * the desired area ).  This routine is intended to be passed
 * to the Solve() function to find the value of chi-squared
 * which will yield a desired area under the right tail of
 * the chi density curve.  The function will only work for
 * even degrees of freedom.  The equations are based on
 * integrating the chi density curve in parts to obtain
 * a series that can be used to compute the area under the
 * curve.
 * @param ChiParams contains degrees of freedom and alpha
 * @param x   value of chi-squared to evaluate
 * @return Error between actual and desired area under the chi curve.
 * @note Exceptions: none
 * @note History: Fri Aug  4 12:48:41 1989, DSJ, Created.
 */
FLOAT64 ChiArea(CHISTRUCT *ChiParams, FLOAT64 x) {
  int i, N;
  FLOAT64 SeriesTotal;
  FLOAT64 Denominator;
  FLOAT64 PowerOfx;

  N = ChiParams->DegreesOfFreedom / 2 - 1;
  SeriesTotal = 1;
  Denominator = 1;
  PowerOfx = 1;
  for (i = 1; i <= N; i++) {
    Denominator *= 2 * i;
    PowerOfx *= x;
    SeriesTotal += PowerOfx / Denominator;
  }
  return ((SeriesTotal * exp (-0.5 * x)) - ChiParams->Alpha);

}                                // ChiArea

/**
 * This routine looks at all samples in the specified cluster.
 * It computes a running estimate of the percentage of the
 * charaters which have more than 1 sample in the cluster.
 * When this percentage exceeds MaxIllegal, TRUE is returned.
 * Otherwise FALSE is returned.  The CharID
 * fields must contain integers which identify the training
 * characters which were used to generate the sample.  One
 * integer is used for each sample.  The NumChar field in
 * the Clusterer must contain the number of characters in the
 * training set.  All CharID fields must be between 0 and
 * NumChar-1.  The main function of this routine is to help
 * identify clusters which need to be split further, i.e. if
 * numerous training characters have 2 or more features which are
 * contained in the same cluster, then the cluster should be
 * split.
 *
 * @param Clusterer data structure holding cluster tree
 * @param Cluster   cluster containing samples to be tested
 * @param MaxIllegal  max percentage of samples allowed to have
 *        more than 1 feature in the cluster
 * @return TRUE if the cluster should be split, FALSE otherwise.
 * @note Exceptions: none
 * @note History: Wed Aug 30 11:13:05 1989, DSJ, Created.
 * 2/22/90, DSJ, Added MaxIllegal control rather than always
 * splitting illegal clusters.
 */
BOOL8
MultipleCharSamples (CLUSTERER * Clusterer,
CLUSTER * Cluster, FLOAT32 MaxIllegal)
#define ILLEGAL_CHAR    2
{
  static BOOL8 *CharFlags = NULL;
  static inT32 NumFlags = 0;
  int i;
  LIST SearchState;
  SAMPLE *Sample;
  inT32 CharID;
  inT32 NumCharInCluster;
  inT32 NumIllegalInCluster;
  FLOAT32 PercentIllegal;

  // initial estimate assumes that no illegal chars exist in the cluster
  NumCharInCluster = Cluster->SampleCount;
  NumIllegalInCluster = 0;

  if (Clusterer->NumChar > NumFlags) {
    if (CharFlags != NULL)
      memfree(CharFlags);
    NumFlags = Clusterer->NumChar;
    CharFlags = (BOOL8 *) Emalloc (NumFlags * sizeof (BOOL8));
  }

  for (i = 0; i < NumFlags; i++)
    CharFlags[i] = FALSE;

  // find each sample in the cluster and check if we have seen it before
  InitSampleSearch(SearchState, Cluster);
  while ((Sample = NextSample (&SearchState)) != NULL) {
    CharID = Sample->CharID;
    if (CharFlags[CharID] == FALSE) {
      CharFlags[CharID] = TRUE;
    }
    else {
      if (CharFlags[CharID] == TRUE) {
        NumIllegalInCluster++;
        CharFlags[CharID] = ILLEGAL_CHAR;
      }
      NumCharInCluster--;
      PercentIllegal = (FLOAT32) NumIllegalInCluster / NumCharInCluster;
      if (PercentIllegal > MaxIllegal) {
        destroy(SearchState);
        return (TRUE);
      }
    }
  }
  return (FALSE);

}                                // MultipleCharSamples

/**
 * Compute the inverse of a matrix using LU decomposition with partial pivoting.
 * The return value is the sum of norms of the off-diagonal terms of the
 * product of a and inv. (A measure of the error.)
 */
double InvertMatrix(const float* input, int size, float* inv) {
  // Allocate memory for the 2D arrays.
  GENERIC_2D_ARRAY<double> U(size, size, 0.0);
  GENERIC_2D_ARRAY<double> U_inv(size, size, 0.0);
  GENERIC_2D_ARRAY<double> L(size, size, 0.0);

  // Initialize the working matrices. U starts as input, L as I and U_inv as O.
  int row;
  int col;
  for (row = 0; row < size; row++) {
    for (col = 0; col < size; col++) {
      U[row][col] = input[row*size + col];
      L[row][col] = row == col ? 1.0 : 0.0;
      U_inv[row][col] = 0.0;
    }
  }

  // Compute forward matrix by inversion by LU decomposition of input.
  for (col = 0; col < size; ++col) {
    // Find best pivot
    int best_row = 0;
    double best_pivot = -1.0;
    for (row = col; row < size; ++row) {
      if (Abs(U[row][col]) > best_pivot) {
        best_pivot = Abs(U[row][col]);
        best_row = row;
      }
    }
    // Exchange pivot rows.
    if (best_row != col) {
      for (int k = 0; k < size; ++k) {
        double tmp = U[best_row][k];
        U[best_row][k] = U[col][k];
        U[col][k] = tmp;
        tmp = L[best_row][k];
        L[best_row][k] = L[col][k];
        L[col][k] = tmp;
      }
    }
    // Now do the pivot itself.
    for (row = col + 1; row < size; ++row) {
      double ratio = -U[row][col] / U[col][col];
      for (int j = col; j < size; ++j) {
        U[row][j] += U[col][j] * ratio;
      }
      for (int k = 0; k < size; ++k) {
        L[row][k] += L[col][k] * ratio;
      }
    }
  }
  // Next invert U.
  for (col = 0; col < size; ++col) {
    U_inv[col][col] = 1.0 / U[col][col];
    for (row = col - 1; row >= 0; --row) {
      double total = 0.0;
      for (int k = col; k > row; --k) {
        total += U[row][k] * U_inv[k][col];
      }
      U_inv[row][col] = -total / U[row][row];
    }
  }
  // Now the answer is U_inv.L.
  for (row = 0; row < size; row++) {
    for (col = 0; col < size; col++) {
      double sum = 0.0;
      for (int k = row; k < size; ++k) {
        sum += U_inv[row][k] * L[k][col];
      }
      inv[row*size + col] = sum;
    }
  }
  // Check matrix product.
  double error_sum = 0.0;
  for (row = 0; row < size; row++) {
    for (col = 0; col < size; col++) {
      double sum = 0.0;
      for (int k = 0; k < size; ++k) {
        sum += input[row*size + k] * inv[k *size + col];
      }
      if (row != col) {
        error_sum += Abs(sum);
      }
    }
  }
  return error_sum;
}
