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detector.c
1126 lines (1028 loc) · 38 KB
/
detector.c
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/*
COPYRIGHT
Copyright (C) 2015 Kyle Briggs (kbrig035<at>uottawa.ca)
This file is part of CUSUM.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include"detector.h"
int64_t fit_events(configuration *config, io_struct *io, double *rawsignal, event *current_event, bessel *lpfilter, edge *current_edge, int64_t *error_summary, int64_t edgecount, timestruct *timestats)
{
int64_t lasttime = config->start;
int64_t last_end = config->start;
int64_t edgenum = 0;
int64_t edges;
int64_t index = 0;
time_t start_time;
time_t curr_time;
char progressmsg[STRLENGTH];
int64_t numevents = 0;
int64_t i;
int64_t typeswitch = 0;
time(&start_time);
while (current_edge)
{
#ifdef DEBUG
printf("Main Loop\n");
fflush(stdout);
#endif // DEBUG
snprintf(progressmsg,STRLENGTH*sizeof(char)," %"PRId64" events processed",numevents);
progressbar(edgenum, edgecount, progressmsg,difftime(time(&curr_time),start_time));
edges = get_next_event(current_event, current_edge, index);
if (edges == 0)
{
break;
}
edgenum += edges;
for (i=0; i<edges; i++)
{
current_edge = current_edge->next;
}
index++;
identify_step_events(current_event, config->stepfit_samples, config->subevent_minpoints, config->attempt_recovery);
filter_long_events(current_event, config->event_maxpoints);
filter_short_events(current_event, config->event_minpoints);
generate_trace(io->input, current_event, config->datatype, rawsignal, io->logfile, lpfilter, config->eventfilter, config->daqsetup, current_edge, last_end, config->start, config->subevent_minpoints, config->savegain, config->padding_wait, config->chimera_input);
last_end = current_event->finish;
count_crossing(current_event, config->intra_threshold, config->intra_hysteresis);
cusum(current_event, config->cusum_delta, config->cusum_min_threshold, config->cusum_max_threshold, config->subevent_minpoints, config->padding_wait, timestats, config->cusum_elasticity);
typeswitch += average_cusum_levels(current_event, config->subevent_minpoints, config->cusum_minstep, config->attempt_recovery, config->padding_wait);
step_response(current_event, config->usefilter || config->eventfilter ? 0.4/config->cutoff : 5, config->maxiters, config->cusum_minstep);
populate_event_levels(current_event);
calculate_level_noise(current_event, config->subevent_minpoints);
refine_event_estimates(current_event);
event_baseline(current_event, config->baseline_min, config->baseline_max);
event_max_blockage(current_event, config->cusum_minstep);
event_area(current_event, 1.0/config->samplingfreq);
print_event_signal(current_event->index, current_event, 1.0/config->samplingfreq*SECONDS_TO_MICROSECONDS,config->eventsfolder, config->print_bad);
print_event_line(io->events, io->rate, current_event, 1.0/config->samplingfreq, lasttime);
lasttime = current_event->start;
current_edge = current_edge->next;
edgenum++;
numevents++;
error_summary[current_event->type]++;
free_single_event(current_event);
#ifdef DEBUG
printf("Done\n");
fflush(stdout);
#endif // DEBUG
}
snprintf(progressmsg,STRLENGTH*sizeof(char)," %"PRId64" events processed",numevents);
progressbar(edgenum, edgecount, progressmsg,difftime(time(&curr_time),start_time));
return numevents;
}
void estimate_time_statistics(duration_struct *current_duration, timestruct *timestats, edge *current_edge)
{
duration_struct *head_duration = current_duration;
int64_t N = get_durations(current_duration, current_edge);
current_duration = head_duration;
double tempdur;
int swapped = 1;
duration_struct *lptr = NULL;
while (swapped)
{
swapped = 0;
current_duration = head_duration;
while (current_duration->next != lptr)
{
if (current_duration->duration > current_duration->next->duration)
{
tempdur = current_duration->duration;
current_duration->duration = current_duration->next->duration;
current_duration->next->duration = tempdur;
swapped = 1;
}
current_duration = current_duration->next;
}
lptr = current_duration;
}
current_duration = head_duration;
int64_t i25 = N/4;
int64_t i75 = 3*N/4;
double alpha = 1.09861; //10th/90th percentile for tanh sigmoid
int64_t i = 0;
while (i < i25)
{
current_duration = current_duration->next;
i++;
}
timestats->t25 = (double) current_duration->duration;
while (i < i75)
{
current_duration = current_duration->next;
i++;
}
timestats->t75 = (double) current_duration->duration;
timestats->t50 = 0.5*(timestats->t25 + timestats->t75);
timestats->tsig = (timestats->t75 - timestats->t25)/(2.0*alpha);
}
int64_t get_durations(duration_struct *current_duration, edge *current_edge)
{
#ifdef DEBUG
printf("Next Duration\n");
fflush(stdout);
#endif // DEBUG
int64_t N = 0;
int64_t start;
int64_t finish;
while (current_edge->next)
{
while (current_edge->type != 0 && current_edge->next) //if for some reason there are multiple of the same type in a row, skip them.
{
current_edge = current_edge->next;
}
start = current_edge->location;
while (current_edge->type != 1 && current_edge->next) //if for some reason there are multiple of the same type in a row, skip them.
{
current_edge = current_edge->next;
}
finish = current_edge->location;
if (finish > start)
{
current_duration = add_duration(current_duration, log10((double) (finish-start)));
N++;
}
}
return N;
}
void count_crossing(event *current, double intra_threshold, double intra_hysteresis)
{
#ifdef DEBUG
printf("Count Crossings\n");
fflush(stdout);
#endif // DEBUG
current->intra_edges = initialize_edges();
if (!current->signal)
{
return;
}
int64_t i = 0;
int64_t length = current->length + current->padding_after + current->padding_before;
double sign;
double down_threshold;
double up_threshold;
int state = 0;
int64_t num_crossings = 0;
double *signal = current->signal;
double baseline = current->local_baseline;
intra_threshold *= current->local_stdev;
intra_hysteresis *= current->local_stdev;
edge *current_edge = current->intra_edges;
sign = signum(signal[0]); //get the sign of the average so that we can properly invert the signal
if (length <=0 )
{
printf("read length is zero or less, cannot process\n");
current->intracrossings = 0;
return;
}
down_threshold = baseline - intra_threshold;//current thresholds for detection of downspikes and upspikes can be different
up_threshold = baseline - intra_threshold + intra_hysteresis;
for (i=0; i<length; i++)
{
if (signal[i]*sign < down_threshold && state == 0) //if we are open pore state and detect a downspike
{
state = 1;
current_edge = add_edge(current_edge, i, state, current->local_stdev, current->local_baseline);
num_crossings++;
}
else if (signal[i]*sign > up_threshold && state == 1) //blocked state and detect an upspike
{
state = 0;
current_edge = add_edge(current_edge, i, state, current->local_stdev, current->local_baseline);
num_crossings++;
}
}
current->intracrossings = num_crossings;
}
edge *find_edges(configuration *config, io_struct *io, signal_struct *sig, baseline_struct *baseline_stats, bessel *lpfilter, edge *current_edge, edge *head_edge)
{
#ifdef DEBUG
printf("Find edges\n");
fflush(stdout);
#endif // DEBUG
fprintf(io->logfile, "<----RUN LOG BEGINS---->\n\n");
printf("Locating events in %"PRId64" samples (%g s):... \n",config->finish - config->start, (double) (config->finish - config->start)/(double) config->samplingfreq);
fprintf(io->logfile, "Locating events...\n ");
fflush(stdout);
double baseline;
double badbaseline = 0;
double goodbaseline = 0;
int64_t read;
int64_t pos;
int endflag;
endflag = 0;
read = 0;
pos = 0;
char progressmsg[STRLENGTH];
time_t start_time;
time_t curr_time;
time(&start_time);
for (pos = config->start; pos < config->finish; pos += read)
{
snprintf(progressmsg,STRLENGTH*sizeof(char)," %.2f seconds processed (%d%% good)",(pos-config->start)/(double) config->samplingfreq, pos > config->start ? (int) (100.0 * (pos-config->start - badbaseline)/(double) (pos-config->start)) : 0);
progressbar(pos-config->start,config->finish-config->start,progressmsg,difftime(time(&curr_time),start_time));
read = read_current(io->input, sig->signal, sig->rawsignal, pos, intmin(config->readlength,config->finish - pos), config->datatype, config->daqsetup, config->savegain, config->chimera_input);
if (read < config->readlength || feof(io->input))
{
endflag = 1;
}
if (config->usefilter)
{
filter_signal(sig->signal, sig->paddedsignal, lpfilter, read);
}
gauss_histogram(sig->signal, baseline_stats, read);
if (isnan(baseline_stats->mean) || isnan(baseline_stats->stdev))
{
baseline_stats->mean = 0;
baseline_stats->stdev = 0;
}
baseline = baseline_stats->mean;
output_baseline_stats(io->baselinefile, baseline_stats, pos, config->samplingfreq);
if (baseline < config->baseline_min || baseline > config->baseline_max || d_abs(baseline_stats->stdev) < EPS)
{
badbaseline += read;
}
else
{
goodbaseline += read;
current_edge = detect_edges(sig->signal, baseline, read, current_edge, config->threshold, baseline_stats->stdev, config->hysteresis, pos, config->event_direction);
}
if (endflag)
{
pos += read;
break;
}
memset(sig->signal,'0',(config->readlength)*sizeof(double));
}
snprintf(progressmsg,STRLENGTH*sizeof(char)," %.2f seconds processed (%d%% good)",(pos-config->start)/(double) config->samplingfreq, pos > config->start ? (int) (100.0 * (pos-config->start - badbaseline)/(double) (pos-config->start)) : 100);
progressbar(pos-config->start,config->finish-config->start,progressmsg,difftime(time(&curr_time),start_time));
printf("\nRead %g seconds of good baseline\nRead %g seconds of bad baseline\n", goodbaseline/(double) config->samplingfreq, badbaseline / (double) config->samplingfreq);
fprintf(io->logfile, "\nRead %g seconds of good baseline\nRead %g seconds of bad baseline\n", goodbaseline/(double) config->samplingfreq, badbaseline / (double) config->samplingfreq);
current_edge = head_edge;
if (!current_edge || current_edge->type == HEAD)
{
printf("No signals found, exiting\n");
fprintf(io->logfile, "No signals found, exiting\n");
pause_and_exit(8);
}
current_edge = head_edge;
return current_edge;
}
int64_t get_next_event_start(edge *current_edge)
{
while (current_edge->type != 0 && current_edge->next) //if for some reason there are multiple of the same type in a row, skip them.
{
current_edge = current_edge->next;
}
return current_edge->location;
}
int64_t get_next_event(event *current_event, edge *current_edge, int64_t index)
{
#ifdef DEBUG
printf("Next Event\n");
fflush(stdout);
#endif // DEBUG
int64_t edges = 0;
int64_t start;
int64_t finish;
while (current_edge->type != 0 && current_edge->next) //if for some reason there are multiple of the same type in a row, skip them.
{
current_edge = current_edge->next;
edges++;
}
start = current_edge->location;
while (current_edge->type != 1 && current_edge->next) //if for some reason there are multiple of the same type in a row, skip them.
{
current_edge = current_edge->next;
edges++;
}
finish = current_edge->location;
if (finish > start)
{
current_event = add_event(current_event, start, finish, index, current_edge->local_stdev, current_edge->local_baseline);
}
return edges;
}
void calculate_level_noise(event *current, int64_t minpoints)
{
#ifdef DEBUG
printf("Noise\n");
fflush(stdout);
#endif // DEBUG
if (current->type == CUSUM || current->type == STEPRESPONSE)
{
cusumlevel *level = current->first_level;
int64_t start = minpoints;
while (level)
{
if (minpoints + 2 > level->length)
{
level->stdev = 0;
}
else
{
level->stdev = sqrt(signal_variance(¤t->signal[start], level->length - minpoints));
}
start += level->length;
level = level->next;
}
}
}
void identify_step_events(event *current, int64_t stepfit_samples, int64_t subevent_minpoints, int attempt_recovery)
{
#ifdef DEBUG
printf("Step Events\n");
fflush(stdout);
#endif // DEBUG
if (current->length < stepfit_samples || current->length < subevent_minpoints)
{
if (attempt_recovery || stepfit_samples)
{
current->type = STEPRESPONSE;
}
else
{
current->type = TOOSHORT;
}
}
}
void filter_long_events(event *current, int64_t maxpoints)
{
#ifdef DEBUG
printf("Long Filter\n");
fflush(stdout);
#endif // DEBUG
if (current->length > maxpoints)
{
current->type = TOOLONG;
}
}
void filter_short_events(event *current, int64_t minpoints)
{
#ifdef DEBUG
printf("Short Filter\n");
fflush(stdout);
#endif // DEBUG
if (current->length < minpoints)
{
current->type = TOOSHORT;
}
}
int64_t average_cusum_levels(event *current, int64_t subevent_minpoints, double cusum_minstep, int attempt_recovery, int64_t padding_wait)
{
#ifdef DEBUG
printf("Average CUSUM levels\n");
fflush(stdout);
#endif // DEBUG
if (current->type == CUSUM)
{
cusum_minstep *= current->local_stdev;
edge *first_edge = current->first_edge;
edge *current_edge = first_edge;
double baseline = signal_average(current->signal, current->padding_before);
double lastlevel = baseline;
int64_t j, nStates = 0;
int64_t typeswitch = 0;
int passflag = 1;
int64_t anchor = 0;
int64_t prev_anchor = anchor;
double average;
double residual = 0;
int64_t totallength = current->length + current->padding_before + current->padding_after;
int64_t levels = 0;
while (current_edge)
{
levels++;
current_edge = current_edge->next;
}
current_edge = first_edge;
while (current_edge)
{
if (nStates <= levels - 1)
{
average = signal_average(¤t->signal[anchor + subevent_minpoints], current_edge->location - anchor - subevent_minpoints);
}
else
{
average = signal_average(¤t->signal[anchor + padding_wait + subevent_minpoints], current_edge->location - anchor - padding_wait - subevent_minpoints);
}
if (d_abs(average - lastlevel) < cusum_minstep && passflag == 0)
{
anchor = prev_anchor;
passflag = 1;
continue;
}
passflag = 0;
lastlevel = average;
for (j=anchor; j<current_edge->location; j++)
{
current->filtered_signal[j] = average;
}
prev_anchor = anchor;
anchor = current_edge->location;
current_edge = current_edge->next;
}
residual = (current->signal[0]-current->filtered_signal[0])*(current->signal[0]-current->filtered_signal[0]);
for (j=1; j<totallength; j++)
{
if (signum(current->filtered_signal[j] - current->filtered_signal[j-1]) != 0)
{
nStates++;
}
residual += (current->signal[j]-current->filtered_signal[j])*(current->signal[j]-current->filtered_signal[j]);
}
current->residual = sqrt(residual / totallength);
nStates++;
if (nStates < 3)
{
if (attempt_recovery)
{
current->type = STEPRESPONSE;
typeswitch = 1;
}
else
{
current->type = BADLEVELS;
}
}
current_edge = first_edge;
return typeswitch;
}
return 0;
}
void populate_event_levels(event *current)
{
#ifdef DEBUG
printf("Populate Levels\n");
fflush(stdout);
#endif // DEBUG'
if (current->type == CUSUM || current->type == STEPRESPONSE)
{
int64_t i;
int64_t eventlength = current->length;
int64_t padding = current->padding_before + current->padding_after;
double *filtered_signal = current->filtered_signal;
double lastlevel = filtered_signal[0];
int64_t anchor = 0;
int64_t numlevels = 0;
current->first_level = initialize_levels();
cusumlevel *current_level = current->first_level;
for (i=0; i<eventlength + padding; i++)
{
if (signum(lastlevel - filtered_signal[i]) != 0)
{
current_level = add_cusum_level(current_level, lastlevel, i-anchor);
anchor = i;
lastlevel = filtered_signal[i];
numlevels++;
}
}
current_level = add_cusum_level(current_level, lastlevel, i-anchor);
numlevels++;
current->numlevels = numlevels;
if (numlevels < 3)
{
current->type = BADLEVELS;
}
}
}
void event_max_blockage(event *current, double minstep)
{
#ifdef DEBUG
printf("Max Blockage\n");
fflush(stdout);
#endif // DEBUG
if (current->type == CUSUM || current->type == STEPRESPONSE)
{
minstep *= current->local_stdev;
cusumlevel *current_level = current->first_level;
double baseline = 0.5*(current->baseline_before + current->baseline_after);
double blockage;
double maxblockage = 0;
double minblockage = DBL_MAX;
int minfound = 0;
int64_t maxsamples = 0;
int64_t minsamples = 0;
while (current_level)
{
blockage = d_abs(baseline - current_level->current);
if (blockage > maxblockage)
{
maxblockage = blockage;
maxsamples = current_level->length;
}
if (blockage < minblockage && blockage > minstep)
{
minblockage = blockage;
minsamples = current_level->length;
minfound = 1;
}
current_level = current_level->next;
}
current->max_blockage = maxblockage;
current->max_length = maxsamples;
current->min_blockage = minblockage;
current->min_length = minsamples;
if (!minfound)
{
current->type = BADBASELINE;
}
}
}
void refine_event_estimates(event *current)
{
#ifdef DEBUG
printf("Refine\n");
fflush(stdout);
#endif // DEBUG
if (current->type == CUSUM || current->type == STEPRESPONSE)
{
cusumlevel *level = current->first_level;
int64_t newstart = current->start + level->length - current->padding_before;
current->padding_before = level->length;
while (level)
{
if (level->next)
{
level = level->next;
}
else
{
break;
}
}
int64_t newfinish = current->finish - level->length + current->padding_after;
current->padding_after = level->length;
current->start = newstart;
current->finish = newfinish;
current->length = newfinish - newstart;
}
}
double get_cusum_threshold(int64_t length, double minthreshold, double maxthreshold, double sigma, double mun)
{
#ifdef DEBUG
printf("Get Threshold\n");
fflush(stdout);
#endif // DEBUG
length *= 2;
double arlmin;
double mindif;
double h;
int sign;
int oldsign;
double arl;
double threshold = minthreshold;
arlmin = ARL(length, sigma, mun, minthreshold);
oldsign = signum(arlmin);
mindif = d_abs(arlmin);
for (h = minthreshold; h<maxthreshold; h += 0.5)
{
arl = ARL(length, sigma, mun, h);
sign = signum(arl);
if (sign != oldsign)
{
threshold = h;
break;
}
else if (d_abs(arl) < mindif)
{
mindif = d_abs(arl);
threshold = h;
}
}
return threshold;
}
void cusum(event *current_event, double delta, double minthreshold, double maxthreshold, int64_t subevent_minpoints, int64_t padding_wait, timestruct *timestats, double elasticity)
{
#ifdef DEBUG
printf("cusum\n");
fflush(stdout);
#endif // DEBUG
if (current_event->type == CUSUM)
{
if (elasticity > 0)
{
delta += 0.5 * elasticity * (1 + tanh((log10(current_event->length) - timestats->t50)/timestats->tsig));
}
current_event->delta = delta;
delta *= current_event->local_stdev;
double baseline = current_event->local_baseline;
double *signal = current_event->signal;
int64_t length = current_event->length + current_event->padding_before + current_event->padding_after;
current_event->first_edge = initialize_edges();
edge *first_edge = current_event->first_edge;
edge *current_edge = first_edge;
double threshold = minthreshold;
int64_t anchor = 0;//initial position
double mean = signal[anchor];//initial mean value guess
double variance = 0;//initial variance estimation
double logp = 0;//log-likelihood ratio for positive jumps
double logn = 0;//log-likelihood ratio for negative jumps
double stdev = sqrt(signal_variance(signal, current_event->padding_before));
double jumpsizestdev = delta/stdev;
int64_t k = 0;//loop index
int64_t numjumps = 0;
int64_t jumppos = 0;
int64_t jumpneg = 0;
double varM = signal[0];
double varS = 0;
double oldVarM;
threshold = get_cusum_threshold(length, minthreshold, maxthreshold, jumpsizestdev, -1.0*jumpsizestdev/2.0);
current_event->threshold = threshold;
double *cpos;//cumulative log-likelihood for positive jumps
cpos = calloc_and_check(length, sizeof(double),"Cannot allocate cpos");
cpos[0] = 0;
double *cneg;//cumulative log-likelihood for negative jumps
cneg = calloc_and_check(length, sizeof(double),"Cannot allocate cneg");
cneg[0] = 0;
double *gpos;//decision function for positive jumps
gpos = calloc_and_check(length, sizeof(double),"Cannot allocate gpos");
gpos[0] = 0;
double *gneg;//decision function for negative jumps
gneg = calloc_and_check(length, sizeof(double),"Cannot allocate cneg");
gneg[0] = 0;
while (k<length-1)
{
k++;
if (padding_wait > 0 && k-anchor < subevent_minpoints && signal[k]*signum(signal[k]) > baseline*signum(baseline) && numjumps > 1)
{
break;
}
mean = ((k-anchor) * mean + signal[k])/(double) (k+1-anchor);
oldVarM = varM;
varM = varM + (signal[k] - varM) / (double) (k+1-anchor);
varS = varS + (signal[k] - oldVarM) * (signal[k] - varM);
variance = varS / (double) (k - anchor);
logp = delta/variance*(signal[k]-mean-delta/2);
logn = -delta/variance*(signal[k]-mean+delta/2);
cpos[k] = cpos[k-1] + logp;
cneg[k] = cneg[k-1] + logn;
gpos[k] = my_max(gpos[k-1] + logp, 0);
gneg[k] = my_max(gneg[k-1] + logn, 0);
if (gpos[k] > threshold || gneg[k] > threshold)
{
if (gpos[k] > threshold)
{
jumppos = anchor + locate_min(&cpos[anchor], k+1-anchor);
if (jumppos - current_edge->location > subevent_minpoints && length - jumppos > subevent_minpoints)
{
current_edge = add_edge(current_edge, jumppos, 1, 0, 0);
numjumps++;
}
}
if (gneg[k] > threshold)
{
jumpneg = anchor + locate_min(&cneg[anchor], k+1-anchor);
if (jumpneg - current_edge->location > subevent_minpoints && length - jumpneg > subevent_minpoints)
{
current_edge = add_edge(current_edge, jumpneg, -1, 0, 0);
numjumps++;
}
}
anchor = k;
mean = 0;
variance = 0;
memset(cpos,'0',length*sizeof(double));
memset(cneg,'0',length*sizeof(double));
memset(gpos,'0',length*sizeof(double));
memset(gneg,'0',length*sizeof(double));
mean = signal[anchor];
varM = signal[anchor];
varS = 0;
}
}
current_edge = add_edge(current_edge, length, 1, 0, 0);
free(cpos);
free(cneg);
free(gpos);
free(gneg);
}
}
void event_area(event *current_event, double timestep)
{
#ifdef DEBUG
printf("Area\n");
fflush(stdout);
#endif // DEBUG
if (current_event->type == CUSUM || current_event->type == STEPRESPONSE)
{
int64_t i;
double area = 0;
int64_t padding = current_event->padding_before;
int64_t length = current_event->length;
double *signal = current_event->signal;
double baseline = 0.5 * (current_event->baseline_before + current_event->baseline_after);
for (i=padding; i<padding+length; i++)
{
area += (signal[i] - baseline) * timestep;
}
current_event->area = d_abs(area);
current_event->average_blockage = current_event->area/(current_event->length*timestep);
}
}
void event_baseline(event *current_event, double baseline_min, double baseline_max)
{
#ifdef DEBUG
printf("Baseline\n");
fflush(stdout);
#endif // DEBUG
if (current_event->type == CUSUM || current_event->type == STEPRESPONSE)
{
double stdev;
double baseline_before = 0;
int64_t baseline_before_length = 0;
double baseline_after = 0;
double *signal = current_event->signal;
cusumlevel *current_level = current_event->first_level;
baseline_before = current_level->current;
baseline_before_length = current_level->length;
while (current_level->next)
{
current_level = current_level->next;
}
baseline_after = current_level->current;
stdev = sqrt(signal_variance(signal, baseline_before_length));
if (d_abs(baseline_before - baseline_after) > 2.5 * stdev || baseline_before > baseline_max || baseline_after > baseline_max || baseline_before < baseline_min || baseline_after < baseline_min)
{
current_event->type = BADBASELINE;
}
current_event->baseline_before = baseline_before;
current_event->baseline_after = baseline_after;
int64_t i;
int64_t length = current_event->length + current_event->padding_before + current_event->padding_after;
double maxdeviation = 0;
double deviation;
double baseline = 0.5 * (baseline_before + baseline_after);
for (i=0; i<length; i++)
{
deviation = d_abs(current_event->signal[i] - baseline);
if (deviation > maxdeviation)
{
maxdeviation = deviation;
}
}
current_event->maxdeviation = maxdeviation;
}
}
void generate_trace(FILE *input, event *current, int datatype, void *rawsignal, FILE *logfile, bessel *lpfilter, int eventfilter, chimera *daqsetup, edge *current_edge, int64_t last_end, int64_t start, int64_t subevent_minpoints, double savegain, int64_t padding_wait, chimera_file *chimera_input)
{
#ifdef DEBUG
printf("Generate Trace\n");
fflush(stdout);
#endif // DEBUG
if (current->type != TOOLONG)
{
int64_t filter_order = 0;
int64_t filter_padding = 0;
int64_t padding = intmin(500, current->length);
if (lpfilter)
{
filter_order = lpfilter->order;
filter_padding = lpfilter->padding;
padding = 100 * 2.0 / lpfilter->cutoff;
}
int64_t position;
int64_t read;
int64_t next_start = get_next_event_start(current_edge);
current->padding_before = padding;
current->padding_after = padding + padding_wait;
if (current->start - start < current->padding_before)
{
current->padding_before = current->start - start;
}
if (current->start - current->padding_before < last_end)
{
current->padding_before = current->start - last_end;
}
if (current->padding_after + current->finish > next_start && current->finish != next_start)
{
current->padding_after = next_start - current->finish;
}
position = current->start - current->padding_before;
if (position > current->start || current->padding_before < subevent_minpoints || current->padding_after < subevent_minpoints || current->start - current->padding_before < last_end)
{
current->type = BADPADDING;
return;
}
current->paddedsignal = calloc_and_check(current->length + current->padding_before + current->padding_after + 2*(filter_order + filter_padding),sizeof(double),"Cannot allocate event signal array");
current->signal = ¤t->paddedsignal[filter_order + filter_padding];
current->filtered_signal = calloc_and_check(current->length + current->padding_before + current->padding_after,sizeof(double),"Cannot allocate event filtered signal array");
if (fseeko64(input,(off64_t) position*2*sizeof(double),SEEK_SET))
{
printf("Cannot locate file position at sample %" PRId64 "\n",position);
fprintf(logfile,"Cannot locate file position at sample %" PRId64 "\n",position);
fflush(logfile);
pause_and_exit(17);
}
read = read_current(input, current->signal, rawsignal, position, current->length + current->padding_before + current->padding_after, datatype, daqsetup, savegain, chimera_input);
if (read != current->length + current->padding_before + current->padding_after)
{
printf("Unable to read %" PRId64 " samples for event %" PRId64 ": obtained %" PRId64 "\n",current->length + + current->padding_before + current->padding_after,current->index,read);
fprintf(logfile,"Unable to read %" PRId64 " samples for event %" PRId64 ": obtained %" PRId64 "\n",current->length + + current->padding_before + current->padding_after,current->index,read);
fflush(logfile);
current->type = BADTRACE;
}
if (eventfilter)
{
filter_signal(current->signal, current->paddedsignal, lpfilter, read);
}
}
}
edge *detect_edges(double *signal, double baseline, int64_t length, edge *current, double threshold, double stdev, double hysteresis, int64_t position, int event_direction)
{
#ifdef DEBUG
printf("Detect Edges\n");
fflush(stdout);
#endif // DEBUG
int64_t i = 0;
double sign;
double down_threshold;
double up_threshold;
int state = 0;
threshold *= stdev;
hysteresis *= stdev;
sign = signum(baseline); //get the sign of the average so that we can properly invert the signal
baseline *= sign;
if (length <=0 )
{
printf("read length is zero or less, cannot process\n");
return NULL;
}
if (event_direction == 0)
{
down_threshold = baseline - threshold;//current thresholds for detection of downspikes and upspikes can be different
up_threshold = baseline - threshold + hysteresis;
for (i=0; i<length; i++)
{
if (signal[i]*sign < down_threshold && state == 0) //if we are open pore state and detect a downspike
{
current = add_edge(current, i+position, state, stdev, baseline);
state = 1;
}
else if (signal[i]*sign > up_threshold && state == 1) //blocked state and detect an upspike
{
current = add_edge(current, i+position, state, stdev, baseline);
state = 0;
}
}
}
else
{
up_threshold = baseline + threshold;
down_threshold = baseline + threshold - hysteresis;//current thresholds for detection of downspikes and upspikes can be different
for (i=0; i<length; i++)
{
if (signal[i]*sign > up_threshold && state == 0) //if we are open pore state and detect a downspike
{
current = add_edge(current, i+position, state, stdev, baseline);
state = 1;
}
else if (signal[i]*sign < down_threshold && state == 1) //blocked state and detect an upspike
{
current = add_edge(current, i+position, state, stdev, baseline);
state = 0;
}
}
}
return current;
}
void gauss_histogram(double *signal, baseline_struct *baseline, int64_t length)
{
#ifdef DEBUG
printf("Gauss Histogram\n");
fflush(stdout);
#endif // DEBUG
double *histogram = baseline->histogram;
double baseline_min = baseline->baseline_min;
double baseline_max = baseline->baseline_max;
double delta = baseline->delta;
int64_t numbins = baseline->numbins;
int64_t i;
for (i=0; i<numbins; i++)
{
histogram[i] = 0;
}
for (i=0; i<length; i++)
{
if (signal[i] > baseline_min && signal[i] < baseline_max)
{
histogram[(int64_t) ((signal[i]-baseline_min)/delta)] += 1;