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lvq_pak.c
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lvq_pak.c
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/************************************************************************
* *
* Program packages 'lvq_pak' and 'som_pak' : *
* *
* lvq_pak.c *
* -very general routines needed in many places *
* *
* Version 3.2 *
* Date: 21 Aug 1995 *
* *
* NOTE: This program package is copyrighted in the sense that it *
* may be used for scientific purposes. The package as a whole, or *
* parts thereof, cannot be included or used in any commercial *
* application without written permission granted by its producents. *
* No programs contained in this package may be copied for commercial *
* distribution. *
* *
* All comments concerning this program package may be sent to the *
* e-mail address 'lvq@cochlea.hut.fi'. *
* *
************************************************************************/
#include <stdio.h>
#include <string.h>
#include <time.h>
#include <stdlib.h>
#ifndef NO_BACKGROUND_SNAP
#include <unistd.h>
#endif
#include <math.h>
#include <float.h>
#include "lvq_pak.h"
#include "datafile.h"
/* find_winner_euc - finds the winning entry (1 nearest neighbour) in
codebook using euclidean distance. Information about the winning
entry is saved in the winner_info structure. Return 1 (the number
of neighbours) when successful and 0 when winner could not be found
(for example, all components of data vector have been masked off) */
int find_winner_euc(struct entries *codes, struct data_entry *sample,
struct winner_info *win, int knn)
{
struct data_entry *codetmp;
int dim, i, masked;
float diffsf, diff, difference;
eptr p;
dim = codes->dimension;
win->index = -1;
win->winner = NULL;
win->diff = -1.0;
/* Go through all code vectors */
codetmp = rewind_entries(codes, &p);
diffsf = FLT_MAX;
while (codetmp != NULL) {
difference = 0.0;
masked = 0;
/* Compute the distance between codebook and input entry */
for (i = 0; i < dim; i++)
{
if ((sample->mask != NULL) && (sample->mask[i] != 0))
{
masked++;
continue; /* ignore vector components that have 1 in mask */
}
diff = codetmp->points[i] - sample->points[i];
difference += diff * diff;
if (difference > diffsf) break;
}
if (masked == dim)
return 0; /* can't calculate winner, empty data vector */
/* If distance is smaller than previous distances */
if (difference < diffsf) {
win->winner = codetmp;
win->index = p.index;
win->diff = difference;
diffsf = difference;
}
codetmp = next_entry(&p);
}
if (win->index < 0)
ifverbose(3)
fprintf(stderr, "find_winner_euc: can't find winner\n");
return 1; /* number of neighbours */
}
int find_winner_euc2(struct entries *codes, struct data_entry *sample,
struct winner_info *win, int knn)
{
struct data_entry *codetmp;
int dim, i;
float diffsf, diff, difference, *s, *c;
eptr p;
if (sample->mask != NULL)
return find_winner_euc(codes, sample, win, knn);
dim = codes->dimension;
win->index = -1;
win->winner = NULL;
win->diff = -1.0;
/* Go through all code vectors */
codetmp = rewind_entries(codes, &p);
diffsf = FLT_MAX;
while (codetmp != NULL) {
difference = 0.0;
/* Compute the distance between codebook and input entry */
c = codetmp->points; s = sample->points;
for (i = 0; i < dim; i++)
{
diff = *c++ - *s++;
difference += diff * diff;
}
/* If distance is smaller than previous distances */
if (difference < diffsf) {
win->winner = codetmp;
win->index = p.index;
win->diff = difference;
diffsf = difference;
}
codetmp = next_entry(&p);
}
if (win->index < 0)
ifverbose(3)
fprintf(stderr, "find_winner_euc: can't find winner\n");
return 1; /* number of neighbours */
}
/* find_winner_knn - finds the winning entrys (k nearest neighbours)
in codebook using euclidean distance. Information about the winning
entry is saved in the winner_info structures provided by the
caller. Return k (the number of neighbours) when successful and 0
when winner could not be found (for example, all components of data
vector have been masked off) */
int find_winner_knn(struct entries *codes, struct data_entry *sample,
struct winner_info *win, int knn)
{
struct data_entry *codetmp;
int dim, i, j, masked;
float difference, diff;
eptr p;
if (knn == 1) /* might be a little faster */
return find_winner_euc(codes, sample, win, 1);
dim = codes->dimension;
for (i = 0; i < knn; i++)
{
win[i].index = -1;
win[i].winner = NULL;
win[i].diff = FLT_MAX;
}
/* Go through all code vectors */
codetmp = rewind_entries(codes, &p);
while (codetmp != NULL) {
difference = 0.0;
masked = 0;
/* Compute the distance between codebook and input entry */
for (i = 0; i < dim; i++)
{
/* pitaisiko ottaa huomioon myos codebookissa olevat?? */
if ((sample->mask != NULL) && (sample->mask[i] != 0))
{
masked++;
continue; /* ignore vector components that have 1 in mask */
}
diff = codetmp->points[i] - sample->points[i];
difference += diff * diff;
if (difference > win[knn-1].diff) break;
}
if (masked == dim)
return 0;
/* If distance is smaller than previous distances */
for (i = 0; (i < knn) && (difference > win[i].diff); i++);
if (i < knn)
{
for (j = knn - 1; j > i; j--)
{
win[j].diff = win[j - 1].diff;
win[j].index = win[j - 1].index;
win[j].winner = win[j - 1].winner;
}
win[i].diff = difference;
win[i].index = p.index;
win[i].winner = codetmp;
}
codetmp = next_entry(&p);
}
if (win->index < 0)
ifverbose(3)
fprintf(stderr, "find_winner_knn: can't find winner\n");
return knn; /* number of neighbours */
}
int find_winner_knn2(struct entries *codes, struct data_entry *sample,
struct winner_info *win, int knn)
{
struct data_entry *codetmp;
int dim, i, j;
float difference, diff, *s, *c;
eptr p;
if (sample->mask != NULL)
return find_winner_knn(codes, sample, win, knn);
if (knn == 1) /* might be a little faster */
return find_winner_euc2(codes, sample, win, 1);
dim = codes->dimension;
for (i = 0; i < knn; i++)
{
win[i].index = -1;
win[i].winner = NULL;
win[i].diff = FLT_MAX;
}
/* Go through all code vectors */
codetmp = rewind_entries(codes, &p);
while (codetmp != NULL) {
difference = 0.0;
/* Compute the distance between codebook and input entry */
c = codetmp->points; s = sample->points;
for (i = 0; i < dim; i++)
{
diff = *c++ - *s++;
difference += diff * diff;
}
/* If distance is smaller than previous distances */
for (i = 0; (i < knn) && (difference > win[i].diff); i++);
if (i < knn)
{
for (j = knn - 1; j > i; j--)
{
win[j].diff = win[j - 1].diff;
win[j].index = win[j - 1].index;
win[j].winner = win[j - 1].winner;
}
win[i].diff = difference;
win[i].index = p.index;
win[i].winner = codetmp;
}
codetmp = next_entry(&p);
}
if (win->index < 0)
ifverbose(3)
fprintf(stderr, "find_winner_knn: can't find winner\n");
return knn; /* number of neighbours */
}
/* vector_dist_euc - compute distance between two vectors is euclidean
metric. Returns < 0 if distance couldn't be calculated (all components
were masked off */
float vector_dist_euc(struct data_entry *v1, struct data_entry *v2, int dim)
{
float diff, difference;
int i, masked = 0;
difference = 0.0;
for (i = 0; i < dim; i++)
{
if (((v1->mask != NULL) && (v1->mask[i] != 0)) ||
((v2->mask != NULL) && (v2->mask[i] != 0)))
{
masked++;
/* ignore vector components that have 1 in mask */
}
else
{
diff = v1->points[i] - v2->points[i];
difference += diff * diff;
}
}
if (masked == dim)
return -1;
return sqrt(difference);
}
float vector_dist_euc2(struct data_entry *v1, struct data_entry *v2, int dim)
{
float diff, difference, *x1, *x2;
int i;
if ((v1->mask != NULL) || (v2->mask != NULL))
return vector_dist_euc(v1, v2, dim);
difference = 0.0;
for (x1 = v1->points, x2 = v2->points, i = 0; i < dim; i++)
{
diff = *x1++ - *x2++;
difference += diff * diff;
}
return sqrt(difference);
}
/* adapt_vector - move a codebook vector towards another vector */
void adapt_vector(struct data_entry *codetmp, struct data_entry *sample,
int dim, float alpha)
{
int i;
for (i = 0; i < dim; i++)
if ((sample->mask != NULL) && (sample->mask[i] != 0))
continue; /* ignore vector components that have 1 in mask */
else
codetmp->points[i] += alpha *
(sample->points[i] - codetmp->points[i]);
}
void adapt_vector2(struct data_entry *codetmp, struct data_entry *sample,
int dim, float alpha)
{
int i;
float *c, *s;
if (sample->mask != NULL)
adapt_vector(codetmp, sample, dim, alpha);
c = codetmp->points; s = sample->points;
for (i = 0; i < dim; i++, c++)
*c += alpha * (*s++ - *c);
}
/*******************************************************************
* Routines for general usage *
*******************************************************************/
/* package errors */
int lvq_errno;
void errormsg(char *msg)
{
fprintf(stderr, "%s\n", msg);
}
/* My own free routine */
void ofree(void *data)
{
if (data != NULL)
free(data);
}
/* oalloc - my malloc allocation routine with some error checking. Not
used much any more as it exits if an error occurs. */
void *oalloc(unsigned int len)
{
void *tmp;
if ((tmp = malloc(len)) == NULL) {
fprintf(stderr, "Can't allocate memory");
exit(-1);
}
return(tmp);
}
/* orealloc - my realloc allocation routine with some error
checking. Not used much any more as it exits if an error occurs. */
void *orealloc(void *po, unsigned int len)
{
void *tmp;
if ((tmp = realloc(po, len)) == NULL) {
fprintf(stderr, "Can't reallocate memory");
exit(-1);
}
return(tmp);
}
/* Print dots indicating that a job is in progress */
void mprint(long rlen)
{
#ifndef time_t
#define time_t long
#endif
static time_t startt, prevt;
time_t currt;
static long totlen = 0;
long t1, t2;
int i;
currt=time(NULL);
if (!totlen) {
totlen=rlen;
startt=currt;
fprintf(stderr, " ");
for (i=0; i<10; i++) fprintf(stderr, "------");
}
if (currt!=prevt || !rlen) {
t1=currt-startt;
if (rlen!=totlen) t2=(currt-startt)*(float)totlen/(totlen-rlen);
else t2=0;
if (t2>9999) {
t1/=60;
t2/=60;
i=0;
} else i=1;
fprintf(stderr, "\r%4u/%4u %4s ", (int)t1, (int)t2, i?"sec.":"min.");
if (totlen) {
i=(int) (60*(float)(totlen-rlen)/totlen);
while (i--) fprintf(stderr, ".");
}
fflush(stderr);
prevt=currt;
}
if (!rlen) totlen=0;
}
static unsigned long next = 1;
#ifndef RND_MAX
#define RND_MAX 32767L
#endif
/* May define my own random generator */
void osrand(int i)
{
next = i;
}
long orand()
{
return((int) ((next = (next * 23) % 100000001) % RND_MAX));
}
/* init_random - initialize own random number generator with seed.
If seed is 0, uses current time as seed. */
void init_random(int seed)
{
if (!seed)
osrand((int) time(NULL));
else
osrand(seed);
}
int verbose_level = 1;
int verbose(int level)
{
if (level >= 0) {
verbose_level = level;
}
return(verbose_level);
}
int silent(int level)
{
static int silent_level = 0;
if (level >= 0) {
silent_level = level;
}
return(silent_level);
}
int use_fixed(int level)
{
static int fixed_level = 0;
if (level >= 0) {
fixed_level = level;
}
return(fixed_level);
}
int use_weights(int level)
{
static int weights_level = 0;
if (level >= 0) {
weights_level = level;
}
return(weights_level);
}
/* ostrdup - return a pointer to a duplicate of string str. If no memory
for new string cannot be allocated, return NULL. */
char *ostrdup(char *str)
{
char *tmp;
int len;
/* allocate mem for duplicate */
len = strlen(str);
if (len < 0)
return NULL;
tmp = malloc(sizeof(char) * (len + 1));
if (tmp == NULL)
{
fprintf(stderr, "ostrdup: Can't allocate mem.\n");
perror("ostrdup");
return NULL;
}
/* copy string */
strcpy(tmp, str);
return(tmp);
}
/*******************************************************************
* Routines to get the parameter values *
*******************************************************************/
static int no_parameters = -1;
int parameters_left(void)
{
return(no_parameters);
}
long oatoi(char *str, long def)
{
if (str == (char *) NULL)
return(def);
else
return(atol(str));
}
float oatof(char *str, float def)
{
if (str == (char *) NULL)
return(def);
else
return((float) atof(str));
}
char *extract_parameter(int argc, char **argv, char *param, int when)
{
int i = 0;
if (no_parameters == -1)
no_parameters = argc - 1;
while ((i < argc) && (strcmp(param, argv[i]))) {
i++;
}
if ((i <= argc - 1) && (when == OPTION2))
{
no_parameters -= 1;
return "";
}
if (i < argc-1) {
no_parameters -= 2;
return(argv[i+1]);
}
else {
if (when == ALWAYS) {
fprintf(stderr, "Can't find asked option %s\n", param);
exit(-1);
}
}
return((char *) NULL);
}
/* global_options - handle some options that are common to all
programs. Also read some environment variables. */
int global_options(int argc, char **argv)
{
char *s;
/* set program name */
setprogname(argv[0]);
#ifndef NO_PIPED_COMMANDS
/* command for compressing */
s = getenv("LVQSOM_COMPRESS_COMMAND");
if (s)
compress_command = s;
s = extract_parameter(argc, argv, "-compress_cmd", OPTION);
if (s)
compress_command = s;
/* command for uncompressing */
s = getenv("LVQSOM_UNCOMPRESS_COMMAND");
if (s)
uncompress_command = s;
s = extract_parameter(argc, argv, "-uncompress_cmd", OPTION);
if (s)
uncompress_command = s;
#endif /* NO_PIPED_COMMANDS */
/* string that identifies a vector component to be ignored in files */
s = getenv("LVQSOM_MASK_STR");
if (s)
masked_string = s;
s = extract_parameter(argc, argv, "-mask_str", OPTION);
if (s)
masked_string = s;
if (extract_parameter(argc, argv, "-version", OPTION2))
fprintf(stderr, "Version: %s\n", get_version());
verbose(oatoi(extract_parameter(argc, argv, VERBOSE, OPTION), 1));
return 0;
}
/* save_snapshot - save a snapshot of the codebook */
int save_snapshot(struct teach_params *teach, long iter)
{
struct entries *codes = teach->codes;
struct snapshot_info *shot = teach->snapshot;
struct data_entry *entry;
eptr p;
char filename[1024]; /* hope this is enough */
struct file_info *fi = NULL;
int retcode = 0;
int bg = shot->flags & SNAPFLAG_BACKGROUND;
int ko = shot->flags & SNAPFLAG_KEEPOPEN;
shot->counter++;
if (ko) {
if ((fi = shot->fi) == NULL)
{
if ((shot->fi = open_file(shot->filename, "w")) == NULL)
return 1;
fi = shot->fi;
}
else
fi = shot->fi;
}
#ifndef NO_BACKGROUND_SNAP
if (bg)
{
if (shot->pid > 0)
{
int statptr;
if (!(shot->flags & SNAPFLAG_NOWAIT))
{
/* fprintf(stderr, "Snap: waiting for pid %d\n", (int)shot->pid); */
/* wait for previous child before forking a new one */
waitpid(shot->pid, &statptr, 0);
shot->pid = -1;
}
}
if ((shot->pid = fork()) < 0)
{
perror("save_snapshot(background):");
return 1;
}
if (shot->pid == 0)
{
/* fprintf(stderr, "saving snapshot\n"); */
}
else
{
/* fprintf(stderr, "forked pid %d\n", (int)shot->pid); */
return 0;
}
}
#endif /* NO_BACKGROUND_SNAP */
if (fi == NULL)
{
/* make filename */
sprintf(filename, shot->filename, iter);
if ((fi = open_file(filename, "w")) == NULL)
return 1;
}
if (ko)
fprintf(fi2fp(fi), "#start %d\n", shot->counter);
if (write_header(fi, codes))
{
fprintf(stderr, "save_snapshot: Error writing headers\n");
close_file(shot->fi);
shot->fi = NULL;
return 1;
}
/* open file for writing */
ifverbose(3)
fprintf(stderr, "saving snapshot: file '%s', type '%s'\n", filename,
get_str_by_id(snapshot_list, shot->type));
fprintf(fi2fp(fi), "#SNAPSHOT FILE\n#iterations: %ld/%ld\n",
iter, teach->length);
for (entry = rewind_entries(codes, &p); entry != NULL; entry = next_entry(&p))
{
if (write_entry(fi, codes, entry))
{
fprintf(stderr, "save_entries: Error writing entry, aborting\n");
retcode = 1;
break;
}
}
if (ko)
{
fprintf(fi2fp(fi), "#end\n");
fflush(fi2fp(fi));
}
else
close_file(fi);
#ifndef NO_BACKGROUND_SNAP
if (bg)
exit(retcode);
else
#endif
return(retcode);
}
/* get_snapshot - allocate and initialize snapshot info */
struct snapshot_info *get_snapshot(char *filename, long interval, int type)
{
struct snapshot_info *shot;
int len = 0;
shot = malloc(sizeof(struct snapshot_info));
if (shot == NULL)
{
fprintf(stderr, "get_snapshot: Can't allocate structure\n");
perror("get_snapshot");
return NULL;
}
shot->flags = 0;
shot->fi = NULL;
#ifndef NO_BACKGROUND_SNAP
shot->pid = -1;
#endif
shot->counter = 0;
shot->data = NULL;
/* allocate room for string */
shot->filename = NULL;
if (filename)
{
len = strlen(filename);
if ((shot->filename = malloc(len + 1)) == NULL)
{
fprintf(stderr, "get_snapshot: Can't allocate mem for string\n");
perror("get_snapshot");
free(shot);
return NULL;
}
else
strcpy(shot->filename, filename);
}
if (len > 0)
if (shot->filename[len - 1] == '&')
{
shot->filename[len - 1] = '\0';
shot->flags |= SNAPFLAG_BACKGROUND;
}
shot->interval = interval;
shot->type = type;
switch (type)
{
case SNAPSHOT_KEEPOPEN:
shot->flags |= SNAPFLAG_KEEPOPEN;
shot->flags &= (~SNAPFLAG_NOWAIT);
break;
#ifndef NO_BACKGROUND_SNAP
case SNAPSHOT_ASYNC:
shot->flags |= SNAPFLAG_BACKGROUND;
break;
case SNAPSHOT_ASYNC_NOWAIT:
shot->flags |= SNAPFLAG_BACKGROUND|SNAPFLAG_NOWAIT;
break;
#endif
default:
break;
}
ifverbose(2)
fprintf(stderr, "snapshot: filename: '%s', interval: %ld, type: %s\n",
shot->filename, shot->interval, get_str_by_id(snapshot_list, type));
return shot;
}
/* free_snapshot - deallocate snapshot info */
void free_snapshot(struct snapshot_info *shot)
{
if (shot)
{
if (shot->filename)
free(shot->filename);
if (shot->fi)
close_file(shot->fi);
#ifndef NO_BACKGROUND_SNAP
if ((shot->pid > 0) && (!(shot->flags & SNAPFLAG_NOWAIT)))
{
int statptr;
waitpid(shot->pid, &statptr, 0);
shot->pid = -1;
}
#endif /* NO_BACKGROUND_SNAP */
free(shot);
}
}
/* get_type_by_id - search typelist for id */
struct typelist *get_type_by_id(struct typelist *types, int id)
{
for (;types->str; types++)
if (types->id == id)
break;
return types;
}
/* get_type_by_str - search typelist for string */
struct typelist *get_type_by_str(struct typelist *types, char *str)
{
for (;types->str; types++)
if (str) /* NULL str gets the last item */
if (strcasecmp(types->str, str) == 0)
break;
return types;
}
/* ------- different alpha functions -------------- */
/* alpha functions */
struct typelist alpha_list[] = {
{ALPHA_LINEAR, "linear", linear_alpha},
{ALPHA_INVERSE_T, "inverse_t", inverse_t_alpha},
{ALPHA_UNKNOWN, NULL, NULL}}; /* default */
/* linearly decreasing alpha */
float linear_alpha(long iter, long length, float alpha)
{
return (alpha * (float) (length - iter) / (float) length);
}
#ifndef INV_ALPHA_CONSTANT
#define INV_ALPHA_CONSTANT 100.0
#endif /* INV_ALPHA_CONSTANT */
float inv_alpha_constant = INV_ALPHA_CONSTANT;
float inverse_t_alpha(long iter, long length, float alpha)
{
float c;
c = length / inv_alpha_constant;
return (alpha * c / (c + iter));
}
/* print_lines */
int print_lines(FILE *fp, char **lines)
{
char *line;
while ((line = *lines++))
fputs(line, fp);
return 0;
}