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minmax.c
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minmax.c
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// minmax.c-- genodsp operators dealing with minima and maxima
#include <stdlib.h>
#define true 1
#define false 0
#include <stdio.h>
#include <string.h>
#include <stdarg.h>
#include <math.h>
#include <float.h>
#include "utilities.h"
#include "genodsp_interface.h"
#include "minmax.h"
// miscellany
#define min_of(a,b) ((a <= b)? a: b)
#define noIndex ((u32) -1)
//----------
// [[-- a dsp operation function group, operating on the whole genome --]]
//
// See genodsp_interface.h, "headers for dsp operator function groups" for
// function descriptions and argument details.
//
//----------
//
// op_min_in_interval--
// Find the minimum value(s) in each of a set of intervals.
//
// The intervals are replaced by infinity everywhere except at their single
// trough position. Ties are broken by the position nearest the center of the
// interval. Any bases outside the intervals are also replaced by zeros.
//
//----------
// private dspop subtype
typedef struct dspop_minover
{
dspop common; // common elements shared with all operators
char* filename;
int originOne;
valtype infinityVal;
int debug;
} dspop_minover;
// op_min_in_interval_short--
void op_min_in_interval_short (char* name, int nameWidth, FILE* f, char* indent)
{
int nameFill = nameWidth-2 - strlen(name);
if (indent == NULL) indent = "";
if (nameFill > 0) fprintf (f, "%s%s:%*s", indent, name, nameFill+1, " ");
else fprintf (f, "%s%s: ", indent, name);
fprintf (f, "find the minimum value in each of a set of intervals\n");
}
// op_min_in_interval_usage--
void op_min_in_interval_usage (char* name, FILE* f, char* indent)
{
if (indent == NULL) indent = "";
// 3456789-123456789-123456789-123456789-123456789-123456789-123456789-123456789
fprintf (f, "%sFind the minimum value in each of a set of intervals. The intervals are\n", indent);
fprintf (f, "%sreplaced by infinity everywhere except at their single trough position. Ties\n", indent);
fprintf (f, "%sare broken by the position nearest the center of the interval. Any bases\n", indent);
fprintf (f, "%soutside the intervals are also replaced by infinity.\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%susage: %s <filename> [options]\n", indent, name);
fprintf (f, "%s --origin=one input intervals are origin-one, closed\n", indent);
fprintf (f, "%s --origin=zero input intervals are origin-zero, half-open\n", indent);
fprintf (f, "%s --infinity=<value> value to fill non-minima\n", indent);
fprintf (f, "%s (default is +inf)\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%sThe input intervals are required to be sorted along each chromosome, and\n", indent);
fprintf (f, "%snon-overlapping)\n", indent);
}
// op_min_in_interval_parse--
dspop* op_min_in_interval_parse (char* name, int _argc, char** _argv)
{
dspop_minover* op;
int argc = _argc;
char** argv = _argv;
char* arg, *argVal;
valtype tempVal;
// allocate and initialize our control record
op = (dspop_minover*) malloc (sizeof(dspop_minover));
if (op == NULL) goto cant_allocate;
op->common.atRandom = true;
op->filename = NULL;
op->originOne = (int) get_named_global ("originOne", false);
op->infinityVal = valtypeMax;
op->debug = false;
// parse arguments
while (argc > 0)
{
arg = argv[0];
argVal = strchr(arg,'=');
if (argVal != NULL) argVal++;
// --origin=one, --origin=zero
if ((strcmp (arg, "--origin=one") == 0)
|| (strcmp (arg, "--origin=1") == 0))
{ op->originOne = true; goto next_arg; }
if ((strcmp (arg, "--origin=zero") == 0)
|| (strcmp (arg, "--origin=0") == 0))
{ op->originOne = false; goto next_arg; }
// --infinity=<value>
if (strcmp_prefix (arg, "--infinity=") == 0)
{
tempVal = string_to_valtype (argVal);
op->infinityVal = tempVal;
goto next_arg;
}
// --debug arguments
if (strcmp (arg, "--debug") == 0)
{ op->debug = true; goto next_arg; }
// unknown -- argument
if (strcmp_prefix (arg, "--") == 0)
chastise ("[%s] Can't understand \"%s\"\n", name, arg);
// <filename>
if (op->filename == NULL)
{
op->filename = copy_string (arg);
goto next_arg;
}
// unknown argument
chastise ("[%s] Can't understand \"%s\"\n", name, arg);
next_arg:
argv++; argc--;
continue;
}
if (op->filename == NULL) goto filename_missing;
return (dspop*) op;
cant_allocate:
fprintf (stderr, "[%s] failed to allocate control record (%d bytes)\n",
name, (int) sizeof(dspop_minover));
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
filename_missing:
fprintf (stderr, "[%s] no filename was provided\n",
name);
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
}
// op_min_in_interval_free--
// op_min_in_interval_free--
void op_min_in_interval_free (dspop* _op)
{
dspop_minover* op = (dspop_minover*) _op;
if (op->filename != NULL) free (op->filename);
free (op);
}
// op_min_in_interval_apply--
void op_min_in_interval_apply
(arg_dont_complain(dspop* _op),
arg_dont_complain(char* vName),
arg_dont_complain(u32 vLen),
arg_dont_complain(valtype* _v))
{
dspop_minover* op = (dspop_minover*) _op;
char* filename = op->filename;
valtype infinityVal = op->infinityVal;
FILE* f;
char lineBuffer[1001];
char prevChrom[1001];
valtype* v = NULL;
char* chrom;
spec* chromSpec;
u32 start, end, o, prevEnd, adjStart, adjEnd;
valtype minVal, val;
u32 ix, chromIx, minIx, inset, maxInset;
int ok;
f = fopen (filename, "rt");
if (f == NULL) goto cant_open_file;
for (chromIx=0 ; chromsSorted[chromIx]!=NULL ; chromIx++)
{
chromSpec = chromsSorted[chromIx];
chromSpec->flag = false;
}
// read intervals and values and find the minima
if (op->originOne) o = 1;
else o = 0;
prevChrom[0] = 0;
chromSpec = NULL;
prevEnd = 0;
v = NULL;
while (true)
{
ok = read_interval (f, lineBuffer, sizeof(lineBuffer), -1,
&chrom, &start, &end, &val);
if (!ok) break;
if (val == 0.0) continue; // treat zero as a missing interval
// if this interval is on a different chromosome, finish the previous
// chromosome and then switch to this one
if (strcmp (chrom, prevChrom) != 0)
{
// clear any gap at the end of the previous chromosome
if (v != NULL)
{
if ((op->debug) && (prevEnd < chromSpec->length))
fprintf (stderr, "zeroing %s %u..%u\n", prevChrom, prevEnd, chromSpec->length-1);
for (ix=prevEnd ; ix<chromSpec->length ; ix++)
v[ix] = infinityVal;
}
v = NULL;
chromSpec = find_chromosome_spec (chrom);
if (chromSpec != NULL)
{
v = chromSpec->valVector;
prevEnd = 0;
if (chromSpec->flag) goto chrom_not_together;
}
strncpy (prevChrom, chrom, sizeof(prevChrom)-1);
}
// if the current chromosome is not of any interest, ignore this
// interval
if (chromSpec == NULL) continue;
// if this is the first interval on this chromosome, 'mark' the
// chromosome
if (!chromSpec->flag)
{
if (trackOperations) fprintf (stderr, "%s(%s)\n", op->common.name, chrom);
chromSpec->flag = true;
}
// validate the interval, and (if necessary) shift it onto the vector
start -= o;
adjStart = start;
adjEnd = end;
if (chromSpec->start == 0)
{
// if only length has been specified, we *reject* intervals beyond
// the end
if (end > chromSpec->length) goto chrom_too_short;
}
else
{
// if start and end have been specified, we *ignore* intervals, or
// portions of intervals, beyond the end
if (end <= chromSpec->start) continue;
adjEnd = end - chromSpec->start;
if (start <= chromSpec->start) adjStart = 0;
else adjStart = start - chromSpec->start;
if (adjStart >= chromSpec->length) continue;
if (adjEnd >= chromSpec->length) adjEnd = chromSpec->length;
}
// make sure intervals are in sorted order along the chromosome
if (adjStart < prevEnd)
goto intervals_out_of_order;
// clear any gap before this interval
if ((op->debug) && (prevEnd < adjStart))
fprintf (stderr, "zeroing %s %u..%u\n", chrom, prevEnd, adjStart-1);
for (ix=prevEnd ; ix<adjStart ; ix++)
v[ix] = infinityVal;
// find the minimum over this interval
minVal = v[adjStart];
minIx = adjStart;
maxInset = 0;
for (ix=adjStart+1 ; ix<adjEnd ; ix++)
{
if (v[ix] > minVal) continue;
if (v[ix] < minVal)
{
minVal = v[ix];
minIx = ix;
maxInset = min_of (minIx-adjStart,adjEnd-minIx);
continue;
}
// we have a tie, which min is closest to center?
inset = min_of (ix-adjStart,adjEnd-ix);
if (inset > maxInset)
{
minIx = ix;
maxInset = inset;
}
}
if (op->debug)
fprintf (stderr, "minimum over %s %u..%u is " valtypeFmt " at %u\n",
chrom, adjStart, adjEnd-1, minVal, minIx);
// clear the interval, except for the min
for (ix=adjStart ; ix<adjEnd ; ix++)
{ if (ix != minIx) v[ix] = infinityVal; }
prevEnd = adjEnd;
}
// clear any gap at the end of the last chromosome observed
if (v != NULL)
{
if ((op->debug) && (prevEnd < chromSpec->length))
fprintf (stderr, "zeroing %s %u..%u\n", prevChrom, prevEnd, chromSpec->length-1);
for (ix=prevEnd ; ix<chromSpec->length ; ix++)
v[ix] = infinityVal;
}
// clear any chromosomes that weren't observed in the incoming set
for (chromIx=0 ; chromsSorted[chromIx]!=NULL ; chromIx++)
{
chromSpec = chromsSorted[chromIx];
if (chromSpec->flag) continue;
chrom = chromSpec->chrom;
v = chromSpec->valVector;
start = 0;
end = chromSpec->length;
if (trackOperations)
fprintf (stderr, "%s(%s,absent)\n", op->common.name, chrom);
if (op->debug)
fprintf (stderr, "zeroing (all of) %s %u..%u\n",
chrom, chromSpec->start+start, chromSpec->start+end-1);
for (ix=start ; ix<end ; ix++)
v[ix] = infinityVal;
}
// success
fclose (f);
return;
//////////
// failure exits
//////////
cant_open_file:
fprintf (stderr, "[%s] can't open \"%s\" for reading\n",
op->common.name, filename);
exit (EXIT_FAILURE);
chrom_too_short:
fprintf (stderr, "[%s] in \"%s\", %s %d %d is beyond the end of the chromosome (L=%d)\n",
op->common.name, filename, chrom, start, end, chromSpec->length);
exit (EXIT_FAILURE);
chrom_not_together:
fprintf (stderr, "[%s] in \"%s\", not all intervals on %s are together (%d..%d begins new group)\n",
op->common.name, filename, chrom, start, end);
exit (EXIT_FAILURE);
intervals_out_of_order:
fprintf (stderr, "[%s] in \"%s\", intervals on %s are not sorted (%d..%d after %d)\n",
op->common.name, filename, chrom, start, end, chromSpec->start+prevEnd);
exit (EXIT_FAILURE);
}
//----------
// [[-- a dsp operation function group, operating on the whole genome --]]
//
// See genodsp_interface.h, "headers for dsp operator function groups" for
// function descriptions and argument details.
//
//----------
//
// op_max_in_interval--
// Find the maximum value(s) in each of a set of intervals.
//
// The intervals are replaced by zeros everywhere except at their single peak
// position. Ties are broken by the position nearest the center of the
// interval. Any bases outside the intervals are also replaced by zeros.
//
//----------
// private dspop subtype
typedef struct dspop_maxover
{
dspop common; // common elements shared with all operators
char* filename;
int originOne;
valtype zeroVal;
int debug;
} dspop_maxover;
// op_max_in_interval_short--
void op_max_in_interval_short (char* name, int nameWidth, FILE* f, char* indent)
{
int nameFill = nameWidth-2 - strlen(name);
if (indent == NULL) indent = "";
if (nameFill > 0) fprintf (f, "%s%s:%*s", indent, name, nameFill+1, " ");
else fprintf (f, "%s%s: ", indent, name);
fprintf (f, "find the maximum value in each of a set of intervals\n");
}
// op_max_in_interval_usage--
void op_max_in_interval_usage (char* name, FILE* f, char* indent)
{
if (indent == NULL) indent = "";
// 3456789-123456789-123456789-123456789-123456789-123456789-123456789-123456789
fprintf (f, "%sFind the maximum value in each of a set of intervals. The intervals are\n", indent);
fprintf (f, "%sreplaced by zeros everywhere except at their single peak position. Ties are\n", indent);
fprintf (f, "%sbroken by the position nearest the center of the interval. Any bases\n", indent);
fprintf (f, "%soutside the intervals are also replaced by zeros.\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%susage: %s <filename> [options]\n", indent, name);
fprintf (f, "%s --origin=one input intervals are origin-one, closed\n", indent);
fprintf (f, "%s --origin=zero input intervals are origin-zero, half-open\n", indent);
fprintf (f, "%s --zero=<value> (Z=) zero value to fill non-maxima\n", indent);
fprintf (f, "%s (default is 0.0)\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%sThe input intervals are required to be sorted along each chromosome, and\n", indent);
fprintf (f, "%snon-overlapping)\n", indent);
}
// op_max_in_interval_parse--
dspop* op_max_in_interval_parse (char* name, int _argc, char** _argv)
{
dspop_maxover* op;
int argc = _argc;
char** argv = _argv;
char* arg, *argVal;
valtype tempVal;
// allocate and initialize our control record
op = (dspop_maxover*) malloc (sizeof(dspop_maxover));
if (op == NULL) goto cant_allocate;
op->common.atRandom = true;
op->filename = NULL;
op->originOne = (int) get_named_global ("originOne", false);
op->zeroVal = 0.0;
op->debug = false;
// parse arguments
while (argc > 0)
{
arg = argv[0];
argVal = strchr(arg,'=');
if (argVal != NULL) argVal++;
// --origin=one, --origin=zero
if ((strcmp (arg, "--origin=one") == 0)
|| (strcmp (arg, "--origin=1") == 0))
{ op->originOne = true; goto next_arg; }
if ((strcmp (arg, "--origin=zero") == 0)
|| (strcmp (arg, "--origin=0") == 0))
{ op->originOne = false; goto next_arg; }
// --zero=<value> or Z=<value>
if ((strcmp_prefix (arg, "--zero=") == 0)
|| (strcmp_prefix (arg, "Z=") == 0)
|| (strcmp_prefix (arg, "--Z=") == 0))
{
tempVal = string_to_valtype (argVal);
op->zeroVal = tempVal;
goto next_arg;
}
// --debug arguments
if (strcmp (arg, "--debug") == 0)
{ op->debug = true; goto next_arg; }
// unknown -- argument
if (strcmp_prefix (arg, "--") == 0)
chastise ("[%s] Can't understand \"%s\"\n", name, arg);
// <filename>
if (op->filename == NULL)
{
op->filename = copy_string (arg);
goto next_arg;
}
// unknown argument
chastise ("[%s] Can't understand \"%s\"\n", name, arg);
next_arg:
argv++; argc--;
continue;
}
if (op->filename == NULL) goto filename_missing;
return (dspop*) op;
cant_allocate:
fprintf (stderr, "[%s] failed to allocate control record (%d bytes)\n",
name, (int) sizeof(dspop_maxover));
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
filename_missing:
fprintf (stderr, "[%s] no filename was provided\n",
name);
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
}
// op_max_in_interval_free--
// op_max_in_interval_free--
void op_max_in_interval_free (dspop* _op)
{
dspop_maxover* op = (dspop_maxover*) _op;
if (op->filename != NULL) free (op->filename);
free (op);
}
// op_max_in_interval_apply--
void op_max_in_interval_apply
(arg_dont_complain(dspop* _op),
arg_dont_complain(char* vName),
arg_dont_complain(u32 vLen),
arg_dont_complain(valtype* _v))
{
dspop_maxover* op = (dspop_maxover*) _op;
char* filename = op->filename;
valtype zeroVal = op->zeroVal;
FILE* f;
char lineBuffer[1001];
char prevChrom[1001];
valtype* v = NULL;
char* chrom;
spec* chromSpec;
u32 start, end, o, prevEnd, adjStart, adjEnd;
valtype maxVal, val;
u32 ix, chromIx, maxIx, inset, maxInset;
int ok;
f = fopen (filename, "rt");
if (f == NULL) goto cant_open_file;
for (chromIx=0 ; chromsSorted[chromIx]!=NULL ; chromIx++)
{
chromSpec = chromsSorted[chromIx];
chromSpec->flag = false;
}
// read intervals and values and find the maxima
if (op->originOne) o = 1;
else o = 0;
prevChrom[0] = 0;
chromSpec = NULL;
prevEnd = 0;
v = NULL;
while (true)
{
ok = read_interval (f, lineBuffer, sizeof(lineBuffer), -1,
&chrom, &start, &end, &val);
if (!ok) break;
if (val == 0.0) continue; // treat zero as a missing interval
// if this interval is on a different chromosome, finish the previous
// chromosome and then switch to this one
if (strcmp (chrom, prevChrom) != 0)
{
// clear any gap at the end of the previous chromosome
if (v != NULL)
{
if ((op->debug) && (prevEnd < chromSpec->length))
fprintf (stderr, "zeroing %s %u..%u\n", prevChrom, prevEnd, chromSpec->length-1);
for (ix=prevEnd ; ix<chromSpec->length ; ix++)
v[ix] = zeroVal;
}
v = NULL;
chromSpec = find_chromosome_spec (chrom);
if (chromSpec != NULL)
{
v = chromSpec->valVector;
prevEnd = 0;
if (chromSpec->flag) goto chrom_not_together;
}
strncpy (prevChrom, chrom, sizeof(prevChrom)-1);
}
// if the current chromosome is not of any interest, ignore this
// interval
if (chromSpec == NULL) continue;
// if this is the first interval on this chromosome, 'mark' the
// chromosome
if (!chromSpec->flag)
{
if (trackOperations) fprintf (stderr, "%s(%s)\n", op->common.name, chrom);
chromSpec->flag = true;
}
// validate the interval, and (if necessary) shift it onto the vector
start -= o;
adjStart = start;
adjEnd = end;
if (chromSpec->start == 0)
{
// if only length has been specified, we *reject* intervals beyond
// the end
if (end > chromSpec->length) goto chrom_too_short;
}
else
{
// if start and end have been specified, we *ignore* intervals, or
// portions of intervals, beyond the end
if (end <= chromSpec->start) continue;
adjEnd = end - chromSpec->start;
if (start <= chromSpec->start) adjStart = 0;
else adjStart = start - chromSpec->start;
if (adjStart >= chromSpec->length) continue;
if (adjEnd >= chromSpec->length) adjEnd = chromSpec->length;
}
// make sure intervals are in sorted order along the chromosome
if (adjStart < prevEnd)
goto intervals_out_of_order;
// clear any gap before this interval
if ((op->debug) && (prevEnd < adjStart))
fprintf (stderr, "zeroing %s %u..%u\n", chrom, prevEnd, adjStart-1);
for (ix=prevEnd ; ix<adjStart ; ix++)
v[ix] = zeroVal;
// find the maximum over this interval
maxVal = v[adjStart];
maxIx = adjStart;
maxInset = 0;
for (ix=adjStart+1 ; ix<adjEnd ; ix++)
{
if (v[ix] < maxVal) continue;
if (v[ix] > maxVal)
{
maxVal = v[ix];
maxIx = ix;
maxInset = min_of (maxIx-adjStart,adjEnd-maxIx);
continue;
}
// we have a tie, which max is closest to center?
inset = min_of (ix-adjStart,adjEnd-ix);
if (inset > maxInset)
{
maxIx = ix;
maxInset = inset;
}
}
if (op->debug)
fprintf (stderr, "maximum over %s %u..%u is " valtypeFmt " at %u\n",
chrom, adjStart, adjEnd-1, maxVal, maxIx);
// clear the interval, except for the max
for (ix=adjStart ; ix<adjEnd ; ix++)
{ if (ix != maxIx) v[ix] = zeroVal; }
prevEnd = adjEnd;
}
// clear any gap at the end of the last chromosome observed
if (v != NULL)
{
if ((op->debug) && (prevEnd < chromSpec->length))
fprintf (stderr, "zeroing %s %u..%u\n", prevChrom, prevEnd, chromSpec->length-1);
for (ix=prevEnd ; ix<chromSpec->length ; ix++)
v[ix] = zeroVal;
}
// clear any chromosomes that weren't observed in the incoming set
for (chromIx=0 ; chromsSorted[chromIx]!=NULL ; chromIx++)
{
chromSpec = chromsSorted[chromIx];
if (chromSpec->flag) continue;
chrom = chromSpec->chrom;
v = chromSpec->valVector;
start = 0;
end = chromSpec->length;
if (trackOperations)
fprintf (stderr, "%s(%s,absent)\n", op->common.name, chrom);
if (op->debug)
fprintf (stderr, "zeroing (all of) %s %u..%u\n",
chrom, chromSpec->start+start, chromSpec->start+end-1);
for (ix=start ; ix<end ; ix++)
v[ix] = zeroVal;
}
// success
fclose (f);
return;
//////////
// failure exits
//////////
cant_open_file:
fprintf (stderr, "[%s] can't open \"%s\" for reading\n",
op->common.name, filename);
exit (EXIT_FAILURE);
chrom_too_short:
fprintf (stderr, "[%s] in \"%s\", %s %d %d is beyond the end of the chromosome (L=%d)\n",
op->common.name, filename, chrom, start, end, chromSpec->length);
exit (EXIT_FAILURE);
chrom_not_together:
fprintf (stderr, "[%s] in \"%s\", not all intervals on %s are together (%d..%d begins new group)\n",
op->common.name, filename, chrom, start, end);
exit (EXIT_FAILURE);
intervals_out_of_order:
fprintf (stderr, "[%s] in \"%s\", intervals on %s are not sorted (%d..%d after %d)\n",
op->common.name, filename, chrom, start, end, chromSpec->start+prevEnd);
exit (EXIT_FAILURE);
}
//----------
// [[-- a dsp operation function group, operating on a single chromosome --]]
//
// See genodsp_interface.h, "headers for dsp operator function groups" for
// function descriptions and argument details.
//
//----------
//
// op_local_minima--
// Apply a trough-finder (more of a local minima finder). Any entry equal to
// to the minimum (in the window centered at that entry) is kept. All entries
// that aren't the minimum are cleared.
//
//----------
// private dspop subtype
typedef struct dspop_localmin
{
dspop common; // common elements shared with all operators
u32 neighborhood;
valtype infinityVal;
} dspop_localmin;
// op_local_minima_short--
void op_local_minima_short (char* name, int nameWidth, FILE* f, char* indent)
{
int nameFill = nameWidth-2 - strlen(name);
if (indent == NULL) indent = "";
if (nameFill > 0) fprintf (f, "%s%s:%*s", indent, name, nameFill+1, " ");
else fprintf (f, "%s%s: ", indent, name);
fprintf (f, "find local minima\n");
}
// op_local_minima_usage--
void op_local_minima_usage (char* name, FILE* f, char* indent)
{
if (indent == NULL) indent = "";
// 3456789-123456789-123456789-123456789-123456789-123456789-123456789-123456789
fprintf (f, "%sIdentify local minima. Any entry *not* equal to the minimum over the\n", indent);
fprintf (f, "%sneighborhood centered at that entry is set to infinity. Input values beyond\n", indent);
fprintf (f, "%sthe ends of the vector are not considered.\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%susage: %s [options]\n", indent, name);
fprintf (f, "%s --neighborhood=<length> (N=) size of neighborhood\n", indent);
fprintf (f, "%s (default is 3)\n", indent);
fprintf (f, "%s (if this is not odd, it will be increased by 1)\n", indent);
fprintf (f, "%s --infinity=<value> value to fill non-minima\n", indent);
fprintf (f, "%s (default is +inf)\n", indent);
}
// op_local_minima_parse--
dspop* op_local_minima_parse (char* name, int _argc, char** _argv)
{
dspop_localmin* op;
int argc = _argc;
char** argv = _argv;
char* arg, *argVal;
int tempInt;
valtype tempVal;
// allocate and initialize our control record
op = (dspop_localmin*) malloc (sizeof(dspop_localmin));
if (op == NULL) goto cant_allocate;
op->common.atRandom = false;
op->neighborhood = 3;
op->infinityVal = valtypeMax;
// parse arguments
while (argc > 0)
{
arg = argv[0];
argVal = strchr(arg,'=');
if (argVal != NULL) argVal++;
// --neighborhood=<length> or N=<length>
if ((strcmp_prefix (arg, "--neighborhood=") == 0)
|| (strcmp_prefix (arg, "N=") == 0)
|| (strcmp_prefix (arg, "--N=") == 0))
{
tempInt = string_to_unitized_int (argVal, /*thousands*/ true);
if (tempInt == 0)
chastise ("[%s] neighborhood can't be zero (\"%s\")\n", name, arg);
if (tempInt < 0)
chastise ("[%s] neighborhood can't be negative (\"%s\")\n", name, arg);
if (tempInt < 3)
{
fprintf (stderr, "[%s] WARNING: raising neighborhood from %d to %d\n",
name, tempInt, 3);
tempInt = 3;
}
if ((tempInt & 1) == 0)
{
fprintf (stderr, "[%s] WARNING: raising neighborhood from %d to %d\n",
name, tempInt, tempInt+1);
tempInt++;
}
op->neighborhood = (u32) tempInt;
goto next_arg;
}
// --infinity=<value>
if (strcmp_prefix (arg, "--infinity=") == 0)
{
tempVal = string_to_valtype (argVal);
op->infinityVal = tempVal;
goto next_arg;
}
// unknown -- argument
if (strcmp_prefix (arg, "--") == 0)
chastise ("[%s] Can't understand \"%s\"\n", name, arg);
// unknown argument
chastise ("[%s] Can't understand \"%s\"\n", name, arg);
next_arg:
argv++; argc--;
continue;
}
return (dspop*) op;
cant_allocate:
fprintf (stderr, "[%s] failed to allocate control record (%d bytes)\n",
name, (int) sizeof(dspop_localmin));
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
}
// op_local_minima_free--
void op_local_minima_free (dspop* op)
{
free (op);
}
// op_local_minima_apply--
void op_local_minima_apply
(arg_dont_complain(dspop* _op),
arg_dont_complain(char* vName),
arg_dont_complain(u32 vLen),
arg_dont_complain(valtype* v))
{
dspop_localmin* op = (dspop_localmin*) _op;
u32 neighborhood = op->neighborhood;
valtype infinityVal = op->infinityVal;
valtype* s = get_scratch_vector();
valtype val;
u32 hOff, ix, wIx, wStart, wEnd;
// find the local minima
hOff = (neighborhood - 1) / 2;
for (ix=0 ; ix<vLen ; ix++)
{
if (ix < hOff) wStart = 0;