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morphology.c
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morphology.c
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// morphology.c-- genodsp operators performing Minkowkski morphology operations
#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 "morphology.h"
//----------
// [[-- 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_close--
// Perform a "close" operation, in the sense of Minkowski/morphology set
// operations on covered intervals.
//
// The incoming signal is first binarized (conceptually), and the result is
// 1 or 0 depending depending on whether a position is within the closure or
// not.
//
//----------
// private dspop subtype
typedef struct dspop_close
{
dspop common; // common elements shared with all operators
u32 closingLength;
int haveThreshold;
char* thresholdVarName;
valtype threshold;
valtype oneVal;
valtype zeroVal;
int debug;
} dspop_close;
// op_close_short--
void op_close_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, "apply interval closure (fill small gaps between intervals)\n");
}
// op_close_usage--
void op_close_usage (char* name, FILE* f, char* indent)
{
if (indent == NULL) indent = "";
// 3456789-123456789-123456789-123456789-123456789-123456789-123456789-123456789
fprintf (f, "%sCompute the morphological closure of the current set of intervals. This is\n", indent);
fprintf (f, "%sequivalent to \"filling\" short gaps between intervals.\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%sThe current signal is first binarized according to the given threshold; any\n", indent);
fprintf (f, "%slocations above the threshold are considered to be \"in\" the set. Closure is\n", indent);
fprintf (f, "%sthen performed, adding any short gaps into the set. The result is one for\n", indent);
fprintf (f, "%slocations in the resulting zet, zero otherwise. Note that short gaps at the\n", indent);
fprintf (f, "%send of chromosomes are NOT filled.\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%sStrictly speaking, the length parameter is twice the true closure length. For\n", indent);
fprintf (f, "%smore information on set morphology, see\n", indent);
fprintf (f, "%s en.wikipedia.org/wiki/Closing_(morphology).\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%susage: %s <length> [options]\n", indent, name);
fprintf (f, "%s <length> the \"length\" of closure; gaps of this length\n", indent);
fprintf (f, "%s or shorter will be filled\n", indent);
fprintf (f, "%s --threshold=<value> (T=) a binarization threshold; values above this\n", indent);
fprintf (f, "%s are considered to be \"in\" the incoming intervals\n", indent);
fprintf (f, "%s (default is 0.0)\n", indent);
fprintf (f, "%s <value> can be a named variable\n", indent);
fprintf (f, "%s --one=<value> (O=) value for locations in the closure\n", indent);
fprintf (f, "%s (default is 1.0)\n", indent);
fprintf (f, "%s --zero=<value> (Z=) value for locations not in the closure\n", indent);
fprintf (f, "%s (default is 0.0)\n", indent);
}
// op_close_parse--
dspop* op_close_parse (char* name, int _argc, char** _argv)
{
dspop_close* op;
int argc = _argc;
char** argv = _argv;
char* arg, *argVal;
valtype tempVal;
int haveLength;
// allocate and initialize our control record
op = (dspop_close*) malloc (sizeof(dspop_close));
if (op == NULL) goto cant_allocate;
op->common.atRandom = false;
op->closingLength = 0; // not used, user is required to set it
op->haveThreshold = false;
op->thresholdVarName = NULL;
op->threshold = 0.0;
op->oneVal = 1.0;
op->zeroVal = 0.0;
op->debug = false;
// parse arguments
haveLength = false;
while (argc > 0)
{
arg = argv[0];
argVal = strchr(arg,'=');
if (argVal != NULL) argVal++;
// --threshold=<variable> or T=<variable>
if ((strcmp_prefix (arg, "--threshold=") == 0)
|| (strcmp_prefix (arg, "T=") == 0)
|| (strcmp_prefix (arg, "--T=") == 0))
{
if (op->haveThreshold) goto more_than_one_threshold;
if (!try_string_to_valtype (argVal, &op->threshold))
op->thresholdVarName = copy_string (argVal);
else
op->threshold = string_to_valtype (argVal);
op->haveThreshold = true;
goto next_arg;
}
// --one=<value> or O=<value>
if ((strcmp_prefix (arg, "--one=") == 0)
|| (strcmp_prefix (arg, "O=") == 0)
|| (strcmp_prefix (arg, "--O=") == 0))
{
tempVal = string_to_valtype (argVal);
op->oneVal = tempVal;
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 argument
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);
// <length>
if (!haveLength)
{
op->closingLength = (u32) string_to_unitized_int (arg, /*thousands*/ true);
haveLength = true;
goto next_arg;
}
// unknown argument
chastise ("[%s] Can't understand \"%s\"\n", name, arg);
next_arg:
argv++; argc--;
continue;
}
if (!haveLength) goto length_missing;
return (dspop*) op;
cant_allocate:
fprintf (stderr, "[%s] failed to allocate control record (%d bytes)\n",
name, (int) sizeof(dspop_close));
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
more_than_one_threshold:
fprintf (stderr, "[%s] threshold specified more than once (at \"%s\")\n",
name, arg);
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
length_missing:
fprintf (stderr, "[%s] closing length was not provided\n", name);
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
}
// op_close_free--
void op_close_free (dspop* _op)
{
dspop_close* op = (dspop_close*) _op;
if (op->thresholdVarName != NULL) free (op->thresholdVarName);
free (op);
}
// op_close_apply--
void op_close_apply
(arg_dont_complain(dspop* _op),
arg_dont_complain(char* vName),
arg_dont_complain(u32 vLen),
arg_dont_complain(valtype* v))
{
dspop_close* op = (dspop_close*) _op;
valtype closingLength = op->closingLength;
valtype cutoffThresh = op->threshold;
valtype oneVal = op->oneVal;
valtype zeroVal = op->zeroVal;
int ok;
int inGap;
u32 gapStartIx = 0; // placate compiler
u32 ix, scanIx;
// if the threshold is a named variable, fetch it now; note that we copy
// the value from the named variable, then destroy our reference to the
// named variable
if (op->thresholdVarName != NULL)
{
ok = named_global_exists (op->thresholdVarName, &cutoffThresh);
if (!ok) goto no_threshold;
op->threshold = cutoffThresh;
fprintf (stderr, "[%s] using %s = " valtypeFmt " as threshold\n",
_op->name, op->thresholdVarName, cutoffThresh);
free (op->thresholdVarName);
op->thresholdVarName = NULL;
}
// process the vector, filling short gaps (and binarizing); note that we
// never fill the first gap because its "true" length is infinite (it
// includes everything on the number line before the start of the
// chromosome)
if (v[0] <= cutoffThresh) { gapStartIx = 0; inGap = true; }
else { v[0] = oneVal; inGap = false; }
for (ix=1 ; ix<vLen ; ix++)
{
if (v[ix] <= cutoffThresh) // new location is in a gap
{
if (inGap) continue;
gapStartIx = ix;
inGap = true;
}
else // new location is in an interval
{
v[ix] = oneVal;
if (!inGap) continue;
if ((gapStartIx == 0) || (ix - gapStartIx > closingLength))
{
if (op->debug) fprintf (stderr, "clear %u bp gap from %u..%u\n",
ix-gapStartIx, gapStartIx, ix);
for (scanIx=gapStartIx ; scanIx<ix ; scanIx++) v[scanIx] = zeroVal;
}
else
{
if (op->debug) fprintf (stderr, "fill %u bp gap from %u..%u\n",
ix-gapStartIx, gapStartIx, ix);
for (scanIx=gapStartIx ; scanIx<ix ; scanIx++) v[scanIx] = oneVal;
}
inGap = false;
}
}
// clear the final gap; we never fill it because its "true" length is
// infinite (it includes everything on the number line beyond the end of
// the chromosome)
if (inGap)
{
if (op->debug) fprintf (stderr, "clear %u bp gap from %u..%u\n",
vLen-gapStartIx, gapStartIx, vLen);
for (scanIx=gapStartIx ; scanIx<vLen ; scanIx++) v[scanIx] = zeroVal;
}
// success
return;
// failure
no_threshold:
fprintf (stderr, "[%s] attempt to use %s as threshold failed (no such variable)\n",
_op->name, op->thresholdVarName);
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_open--
// Perform a "open" operation, in the sense of Minkowski/morphology set
// operations on covered intervals.
//
// The incoming signal is first binarized (conceptually), and the result is
// 1 or 0 depending depending on whether a position is within the opened set
// or not.
//
//----------
// private dspop subtype
typedef struct dspop_open
{
dspop common; // common elements shared with all operators
u32 openingLength;
int haveThreshold;
char* thresholdVarName;
valtype threshold;
valtype oneVal;
valtype zeroVal;
} dspop_open;
// op_open_short--
void op_open_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, "apply interval opening (remove small intervals)\n");
}
// op_open_usage--
void op_open_usage (char* name, FILE* f, char* indent)
{
if (indent == NULL) indent = "";
// 3456789-123456789-123456789-123456789-123456789-123456789-123456789-123456789
fprintf (f, "%sCompute the morphological opening of the current set of intervals. This is\n", indent);
fprintf (f, "%sequivalent to \"removing\" short intervals.\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%sThe current signal is first binarized according to the given threshold; any\n", indent);
fprintf (f, "%slocations above the threshold are considered to be \"in\" the set. Opening is\n", indent);
fprintf (f, "%sthen performed, removing any short intervals from the set. The result is one\n", indent);
fprintf (f, "%sfor locations in the resulting zet, zero otherwise.\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%sStrictly speaking, the length parameter is twice the true opening length. For\n", indent);
fprintf (f, "%smore information on set morphology, see\n", indent);
fprintf (f, "%s en.wikipedia.org/wiki/Opening_(morphology).\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%susage: %s <length> [options]\n", indent, name);
fprintf (f, "%s <length> the \"length\" of opening; intervals of this\n", indent);
fprintf (f, "%s length or shorter will be removed\n", indent);
fprintf (f, "%s --threshold=<value> (T=) a binarization threshold; values above this\n", indent);
fprintf (f, "%s are considered to be \"in\" the incoming intervals\n", indent);
fprintf (f, "%s (default is 0.0)\n", indent);
fprintf (f, "%s <value> can be a named variable\n", indent);
fprintf (f, "%s --one=<value> (O=) value for locations in the opened set\n", indent);
fprintf (f, "%s (default is 1.0)\n", indent);
fprintf (f, "%s --zero=<value> (Z=) value for locations not in the opened set\n", indent);
fprintf (f, "%s (default is 0.0)\n", indent);
}
// op_open_parse--
dspop* op_open_parse (char* name, int _argc, char** _argv)
{
dspop_open* op;
int argc = _argc;
char** argv = _argv;
char* arg, *argVal;
valtype tempVal;
int haveLength;
// allocate and initialize our control record
op = (dspop_open*) malloc (sizeof(dspop_open));
if (op == NULL) goto cant_allocate;
op->common.atRandom = false;
op->openingLength = 0; // not used, user is required to set it
op->haveThreshold = false;
op->thresholdVarName = NULL;
op->threshold = 0.0;
op->oneVal = 1.0;
op->zeroVal = 0.0;
// parse arguments
haveLength = false;
while (argc > 0)
{
arg = argv[0];
argVal = strchr(arg,'=');
if (argVal != NULL) argVal++;
// --threshold=<variable> or T=<variable>
if ((strcmp_prefix (arg, "--threshold=") == 0)
|| (strcmp_prefix (arg, "T=") == 0)
|| (strcmp_prefix (arg, "--T=") == 0))
{
if (op->haveThreshold) goto more_than_one_threshold;
if (!try_string_to_valtype (argVal, &op->threshold))
op->thresholdVarName = copy_string (argVal);
else
op->threshold = string_to_valtype (argVal);
op->haveThreshold = true;
goto next_arg;
}
// --one=<value> or O=<value>
if ((strcmp_prefix (arg, "--one=") == 0)
|| (strcmp_prefix (arg, "O=") == 0)
|| (strcmp_prefix (arg, "--O=") == 0))
{
tempVal = string_to_valtype (argVal);
op->oneVal = tempVal;
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;
}
// unknown -- argument
if (strcmp_prefix (arg, "--") == 0)
chastise ("[%s] Can't understand \"%s\"\n", name, arg);
// <length>
if (!haveLength)
{
op->openingLength = (u32) string_to_unitized_int (arg, /*thousands*/ true);
haveLength = true;
goto next_arg;
}
// unknown argument
chastise ("[%s] Can't understand \"%s\"\n", name, arg);
next_arg:
argv++; argc--;
continue;
}
if (!haveLength) goto length_missing;
return (dspop*) op;
cant_allocate:
fprintf (stderr, "[%s] failed to allocate control record (%d bytes)\n",
name, (int) sizeof(dspop_open));
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
more_than_one_threshold:
fprintf (stderr, "[%s] threshold specified more than once (at \"%s\")\n",
name, arg);
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
length_missing:
fprintf (stderr, "[%s] opening length was not provided\n", name);
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
}
// op_open_free--
void op_open_free (dspop* _op)
{
dspop_open* op = (dspop_open*) _op;
if (op->thresholdVarName != NULL) free (op->thresholdVarName);
free (op);
}
// op_open_apply--
void op_open_apply
(arg_dont_complain(dspop* _op),
arg_dont_complain(char* vName),
arg_dont_complain(u32 vLen),
arg_dont_complain(valtype* v))
{
dspop_open* op = (dspop_open*) _op;
valtype openingLength = op->openingLength;
valtype cutoffThresh = op->threshold;
valtype oneVal = op->oneVal;
valtype zeroVal = op->zeroVal;
int ok;
int inInterval;
u32 intervalStartIx = 0; // placate compiler
u32 ix, scanIx;
// if the threshold is a named variable, fetch it now; note that we copy
// the value from the named variable, then destroy our reference to the
// named variable
if (op->thresholdVarName != NULL)
{
ok = named_global_exists (op->thresholdVarName, &cutoffThresh);
if (!ok) goto no_threshold;
op->threshold = cutoffThresh;
fprintf (stderr, "[%s] using %s = " valtypeFmt " as threshold\n",
_op->name, op->thresholdVarName, cutoffThresh);
free (op->thresholdVarName);
op->thresholdVarName = NULL;
}
// process the vector, clearing short intervals (and binarizing)
if (v[0] > cutoffThresh) { intervalStartIx = 0; inInterval = true; }
else { v[0] = zeroVal; inInterval = false; }
for (ix=1 ; ix<vLen ; ix++)
{
if (v[ix] > cutoffThresh) // new location is in an interval
{
if (inInterval) continue;
intervalStartIx = ix;
inInterval = true;
}
else // new location is in a gap
{
v[ix] = zeroVal;
if (!inInterval) continue;
if (ix - intervalStartIx > openingLength)
{ for (scanIx=intervalStartIx ; scanIx<ix ; scanIx++) v[scanIx] = oneVal; }
else
{ for (scanIx=intervalStartIx ; scanIx<ix ; scanIx++) v[scanIx] = zeroVal; }
inInterval = false;
}
}
// fill or clear the final interval
if (inInterval)
{
if (vLen - intervalStartIx > openingLength)
{ for (scanIx=intervalStartIx ; scanIx<vLen ; scanIx++) v[scanIx] = oneVal; }
else
{ for (scanIx=intervalStartIx ; scanIx<vLen ; scanIx++) v[scanIx] = zeroVal; }
}
// success
return;
// failure
no_threshold:
fprintf (stderr, "[%s] attempt to use %s as threshold failed (no such variable)\n",
_op->name, op->thresholdVarName);
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_dilate--
// Perform a "dilation" operation, in the sense of Minkowski/morphology set
// operations on covered intervals.
//
// The incoming signal is first binarized (conceptually), and the result is
// 1 or 0 depending depending on whether a position is within the dilation set
// or not.
//
//----------
// private dspop subtype
typedef struct dspop_dilate
{
dspop common; // common elements shared with all operators
u32 dilationLength;
u32 leftDilation;
u32 rightDilation;
int haveThreshold;
char* thresholdVarName;
valtype threshold;
valtype oneVal;
valtype zeroVal;
int debug;
} dspop_dilate;
// op_dilate_short--
void op_dilate_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, "apply interval dilation (widen intervals)\n");
}
// op_dilate_usage--
void op_dilate_usage (char* name, FILE* f, char* indent)
{
if (indent == NULL) indent = "";
// 3456789-123456789-123456789-123456789-123456789-123456789-123456789-123456789
fprintf (f, "%sCompute the morphological dilation of the current set of intervals. This is\n", indent);
fprintf (f, "%sequivalent to widening intervals.\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%sThe current signal is first binarized according to the given threshold; any\n", indent);
fprintf (f, "%slocations above the threshold are considered to be \"in\" the set. Dilation is\n", indent);
fprintf (f, "%sthen performed, widening any intervals in the set. The result is one for\n", indent);
fprintf (f, "%slocations in the resulting zet, zero otherwise.\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%sWe assume that the signal is equivalent to a zero beyond the left and right\n", indent);
fprintf (f, "%sends of the vector.\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%sStrictly speaking, the length parameter is twice the true dilation length.\n", indent);
fprintf (f, "%sFor more information on set morphology, see\n", indent);
fprintf (f, "%s en.wikipedia.org/wiki/Dilation_(morphology).\n", indent);
fprintf (f, "%s\n", indent);
fprintf (f, "%susage: %s <length> [options]\n", indent, name);
fprintf (f, "%s <length> the \"length\" of dilation; intervals will be\n", indent);
fprintf (f, "%s widened by this amount, half on each side\n", indent);
fprintf (f, "%s --threshold=<value> (T=) a binarization threshold; values above this\n", indent);
fprintf (f, "%s are considered to be \"in\" the incoming intervals\n", indent);
fprintf (f, "%s (default is 0.0)\n", indent);
fprintf (f, "%s <value> can be a named variable\n", indent);
fprintf (f, "%s --one=<value> (O=) value for locations in the dilation set\n", indent);
fprintf (f, "%s (default is 1.0)\n", indent);
fprintf (f, "%s --zero=<value> (Z=) value for locations not in the dilation set\n", indent);
fprintf (f, "%s (default is 0.0)\n", indent);
fprintf (f, "%s --left=<length> intervals will be widened by this amount, only on\n", indent);
fprintf (f, "%s the left side\n", indent);
fprintf (f, "%s --right=<length> intervals will be widened by this amount, only on\n", indent);
fprintf (f, "%s the right side\n", indent);
}
// op_dilate_parse--
dspop* op_dilate_parse (char* name, int _argc, char** _argv)
{
dspop_dilate* op;
int argc = _argc;
char** argv = _argv;
char* arg, *argVal;
valtype tempVal;
int haveLength;
// allocate and initialize our control record
op = (dspop_dilate*) malloc (sizeof(dspop_dilate));
if (op == NULL) goto cant_allocate;
op->common.atRandom = false;
op->dilationLength = 0; // not used, user is required to set it
op->leftDilation = 0;
op->rightDilation = 0;
op->haveThreshold = false;
op->thresholdVarName = NULL;
op->threshold = 0.0;
op->oneVal = 1.0;
op->zeroVal = 0.0;
op->debug = false;
// parse arguments
haveLength = false;
while (argc > 0)
{
arg = argv[0];
argVal = strchr(arg,'=');
if (argVal != NULL) argVal++;
// --threshold=<variable> or T=<variable>
if ((strcmp_prefix (arg, "--threshold=") == 0)
|| (strcmp_prefix (arg, "T=") == 0)
|| (strcmp_prefix (arg, "--T=") == 0))
{
if (op->haveThreshold) goto more_than_one_threshold;
if (!try_string_to_valtype (argVal, &op->threshold))
op->thresholdVarName = copy_string (argVal);
else
op->threshold = string_to_valtype (argVal);
op->haveThreshold = true;
goto next_arg;
}
// --one=<value> or O=<value>
if ((strcmp_prefix (arg, "--one=") == 0)
|| (strcmp_prefix (arg, "O=") == 0)
|| (strcmp_prefix (arg, "--O=") == 0))
{
tempVal = string_to_valtype (argVal);
op->oneVal = tempVal;
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;
}
// --left=<length> or --right=<length>
if (strcmp_prefix (arg, "--left=") == 0)
{
if (strcmp_suffix (argVal, "-1") == 0)
{
char* tempStr = copy_string (argVal);
tempStr[strlen(tempStr)-strlen("-1")] = 0;
op->leftDilation = string_to_unitized_int(tempStr,/*thousands*/true) - 1;
free(tempStr);
}
else
{
op->leftDilation = string_to_unitized_int(argVal,/*thousands*/true);
}
goto next_arg;
}
if (strcmp_prefix (arg, "--right=") == 0)
{
if (strcmp_suffix (argVal, "-1") == 0)
{
char* tempStr = copy_string (argVal);
tempStr[strlen(tempStr)-strlen("-1")] = 0;
op->rightDilation = string_to_unitized_int(tempStr,/*thousands*/true) - 1;
free(tempStr);
}
else
{
op->rightDilation = string_to_unitized_int(argVal,/*thousands*/true);
}
goto next_arg;
}
// --debug argument
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);
// <length>
if (!haveLength)
{
op->dilationLength = (u32) string_to_unitized_int (arg, /*thousands*/ true);
haveLength = true;
goto next_arg;
}
// unknown argument
chastise ("[%s] Can't understand \"%s\"\n", name, arg);
next_arg:
argv++; argc--;
continue;
}
// user has to specify the length, OR specify a left-only or right-only
// length
if (haveLength)
{
if ((op->leftDilation != 0) || (op->rightDilation != 0)) goto more_than_one_length;
}
else // if (!haveLength)
{
if ((op->leftDilation == 0) && (op->rightDilation == 0)) goto length_missing;
}
return (dspop*) op;
cant_allocate:
fprintf (stderr, "[%s] failed to allocate control record (%d bytes)\n",
name, (int) sizeof(dspop_dilate));
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
more_than_one_threshold:
fprintf (stderr, "[%s] threshold specified more than once (at \"%s\")\n",
name, arg);
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
length_missing:
fprintf (stderr, "[%s] dilation length was not provided\n", name);
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
more_than_one_length:
fprintf (stderr, "[%s] dilation length was provided in more than one way\n", name);
exit(EXIT_FAILURE);
return NULL; // (never reaches here)
}
// op_dilate_free--
void op_dilate_free (dspop* _op)
{
dspop_dilate* op = (dspop_dilate*) _op;
if (op->thresholdVarName != NULL) free (op->thresholdVarName);
free (op);
}
// op_dilate_apply--
void op_dilate_apply
(arg_dont_complain(dspop* _op),
arg_dont_complain(char* vName),
arg_dont_complain(u32 vLen),
arg_dont_complain(valtype* v))
{
dspop_dilate* op = (dspop_dilate*) _op;
valtype dilationLength = op->dilationLength;
valtype cutoffThresh = op->threshold;
valtype oneVal = op->oneVal;
valtype zeroVal = op->zeroVal;
int ok;
int inInterval;
u32 leftDilation, rightDilation;
u32 gapStartIx, leftIx, rightIx, ix, scanIx;
// if the threshold is a named variable, fetch it now; note that we copy
// the value from the named variable, then destroy our reference to the
// named variable
if (op->thresholdVarName != NULL)
{
ok = named_global_exists (op->thresholdVarName, &cutoffThresh);
if (!ok) goto no_threshold;
op->threshold = cutoffThresh;
fprintf (stderr, "[%s] using %s = " valtypeFmt " as threshold\n",
_op->name, op->thresholdVarName, cutoffThresh);
free (op->thresholdVarName);
op->thresholdVarName = NULL;
}
// process the vector, widening intervals (and binarizing); note that
// locations in intervals are binarized immediately; locations in gaps
// are not binarized until we have determined the start and end of the gap
if ((op->leftDilation == 0) && (op->rightDilation == 0))
{
leftDilation = dilationLength / 2;
rightDilation = dilationLength - leftDilation;
}
else
{
leftDilation = op->leftDilation;
rightDilation = op->rightDilation;
}
gapStartIx = 0;
inInterval = (v[0] > cutoffThresh);
if (inInterval) v[0] = oneVal;
for (ix=1 ; ix<vLen ; ix++)
{
if (v[ix] <= cutoffThresh) // new location is in a gap
{
if (!inInterval) continue;
// we've encountered the start of a new gap; record the start
gapStartIx = ix;
inInterval = false;
}
else // new location is in an interval
{
v[ix] = oneVal;
if (inInterval) continue;
// we've encountered the start of a new interval; set and/or clear
// items to narrow the gap between this interval and the last
if (op->debug) fprintf (stderr, "%u bp gap from %u..%u\n",
ix-gapStartIx, gapStartIx, ix);
if (gapStartIx == 0)
{
// gap is at left edge, so there's no fill on the gap's left
if (ix <= leftDilation)
{
// left-extension of new interval reaches left edge
if (op->debug)
{
fprintf (stderr, " narrowed gap is -%u..%u\n", leftDilation-ix, 0);
fprintf (stderr, " set %u..%u\n", 0, ix);
}
for (scanIx=0 ; scanIx<ix ; scanIx++) v[scanIx] = oneVal;
}
else
{
// left-extension of new interval leaves a gap at left edge
leftIx = ix - leftDilation;
if (op->debug)
{
fprintf (stderr, " narrowed gap is %u..%u\n", 0, leftIx);
fprintf (stderr, " clear %u..%u\n", 0, leftIx);
fprintf (stderr, " set %u..%u\n", leftIx, ix);
}
for (scanIx=0 ; scanIx<leftIx ; scanIx++) v[scanIx] = zeroVal;
for ( ; scanIx<ix ; scanIx++) v[scanIx] = oneVal;
}
}
else
{
rightIx = gapStartIx + rightDilation;
leftIx = (ix <= leftDilation)? 0 : ix - leftDilation;
if (op->debug) fprintf (stderr, " narrowed gap is %u..%u\n", rightIx, leftIx);
if (rightIx >= leftIx)
{
// right-extension of previous interval and left-extension
// of new interval overlap (or abut), so gap disappears
if (op->debug)
fprintf (stderr, " set %u..%u\n", gapStartIx, ix);
for (scanIx=gapStartIx ; scanIx<ix ; scanIx++) v[scanIx] = oneVal;
}
else
{