/*{{{ export_point(transform_info_ptr tinfo) {*/
METHODDEF DATATYPE *
export_point(transform_info_ptr tinfo) {
struct export_point_info *exp_info=(struct export_point_info *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
array_dump_format format=(args[ARGS_MATLAB].is_set ? ARRAY_MATLAB : ARRAY_ASCII);
int channel, itempart, i;
double *channelpos;
array myarray, newarray;
if (exp_info->pointno<0 || exp_info->pointno>=tinfo->nr_of_points) {
ERREXIT1(tinfo->emethods, "export_point: Point number %d is out of range.\n", MSGPARM(exp_info->pointno));
}
TRACEMS2(tinfo->emethods, 1, "export_point: Exporting point number %d to file %s\n", MSGPARM(exp_info->pointno), MSGPARM(args[ARGS_OFILE].arg.s));
if (args[ARGS_CLOSE].is_set) export_file_open(tinfo);
tinfo_array(tinfo, &myarray);
myarray.current_element=exp_info->pointno;
if (exp_info->channelcoords_to_display==0 && tinfo->itemsize==1) {
/*{{{ Don't need to build new array, just access tinfo*/
newarray=myarray;
array_transpose(&newarray);
array_setto_vector(&newarray); /* Select only one element */
array_transpose(&newarray);
/*}}} */
} else {
/*{{{ Build new array containing the data*/
newarray.nr_of_vectors=myarray.nr_of_vectors;
newarray.nr_of_elements=exp_info->channelcoords_to_display+tinfo->itemsize;
newarray.element_skip=1;
if (array_allocate(&newarray)==NULL) {
ERREXIT(tinfo->emethods, "export_point: Can't allocate output array\n");
}
for (channel=0; channel<tinfo->nr_of_channels; channel++) {
channelpos=tinfo->probepos+3*channel;
for (i=0; i<exp_info->channelcoords_to_display; i++) {
array_write(&newarray, channelpos[i]);
}
myarray.current_vector=channel;
for (itempart=0; itempart<tinfo->itemsize; itempart++) {
array_use_item(&myarray, itempart);
array_write(&newarray, READ_ELEMENT(&myarray));
}
}
/*}}} */
}
array_dump(exp_info->file, &newarray, format);
if (newarray.nr_of_elements>1) array_free(&newarray);
if (args[ARGS_CLOSE].is_set) export_file_close(tinfo);
return tinfo->tsdata;
}
int output_gamma()
{
int size = terms_prim;
int gamma_total_size = terms_prim;
array_write(&gamma_total_size, gamma_data_file, &gamma_[0][0]);
return 0;
}
/*{{{ recode(transform_info_ptr tinfo) {*/
METHODDEF DATATYPE *
recode(transform_info_ptr tinfo) {
struct recode_storage *local_arg=(struct recode_storage *)tinfo->methods->local_storage;
transform_info_ptr const tinfoptr=tinfo;
array myarray;
int itempart;
int shift, nrofshifts=1;
DATATYPE *save_tsdata;
tinfo_array(tinfoptr, &myarray); /* The channels are the vectors */
save_tsdata=myarray.start;
if (tinfoptr->data_type==FREQ_DATA) {
nrofshifts=tinfoptr->nrofshifts;
}
for (shift=0; shift<nrofshifts; shift++) {
myarray.start=save_tsdata+shift*tinfo->nroffreq*tinfo->nr_of_channels*tinfo->itemsize;
array_setreadwrite(&myarray);
for (itempart=local_arg->fromitem; itempart<=local_arg->toitem; itempart++) {
array_use_item(&myarray, itempart);
do {
if (local_arg->have_channel_list && !is_in_channellist(myarray.current_vector+1, local_arg->channel_list)) {
array_nextvector(&myarray);
continue;
}
do {
DATATYPE hold=READ_ELEMENT(&myarray);
struct blockdef *inblocks=local_arg->blockdefs;
while (inblocks!=NULL) {
if (isnan(inblocks->fromstart) && isnan(hold)) {
/* Recode NaN values */
hold=inblocks->tostart;
} else
if (hold>=inblocks->fromstart && hold<=inblocks->fromend) {
if (inblocks->fromend==inblocks->fromstart || inblocks->toend==inblocks->tostart) {
hold=inblocks->tostart;
} else {
hold=((hold-inblocks->fromstart)/(inblocks->fromend-inblocks->fromstart))*(inblocks->toend-inblocks->tostart)+inblocks->tostart;
}
break;
}
if (inblocks->last_block) break;
inblocks++;
}
array_write(&myarray, hold);
} while (myarray.message==ARRAY_CONTINUE);
} while (myarray.message==ARRAY_ENDOFVECTOR);
}
}
return tinfo->tsdata;
}
/*{{{ raw_fft(transform_info_ptr tinfo) {*/
METHODDEF DATATYPE *
raw_fft(transform_info_ptr tinfo) {
int i;
array myarray, fftarray;
long datasize, fftsize;
if (tinfo->itemsize==2) {
/*{{{ Do the inverse transform*/
if (tinfo->data_type==TIME_DATA) {
tinfo->nroffreq=tinfo->nr_of_points;
tinfo->nrofshifts=1;
}
datasize=tinfo->nroffreq;
fftsize=datasize-3;
for (i=0; fftsize>>=1; i++);
fftsize=1<<(i+2);
if (datasize!=fftsize/2+1 || tinfo->nrofshifts!=1) {
ERREXIT(tinfo->emethods, "raw_fft: Input spectra must have 2^n+1 frequencies, 2 items and 1 shift\n");
}
fftarray.nr_of_elements=fftsize;
fftarray.element_skip=1;
fftarray.nr_of_vectors=tinfo->nr_of_channels;
if (array_allocate(&fftarray)==NULL) {
ERREXIT(tinfo->emethods, "raw_fft: Error allocating memory\n");
}
/* We access tsdata as 1-item data already now (this makes copying easier) */
tinfo->itemsize=1;
tinfo->nr_of_points*=2;
tinfo->data_type=TIME_DATA;
tinfo_array(tinfo, &myarray);
do {
myarray.current_element=0;
myarray.current_vector=fftarray.current_vector;
realfft(ARRAY_ELEMENT(&myarray), fftsize, -1);
do {
array_write(&fftarray, array_scan(&myarray));
} while (fftarray.message==ARRAY_CONTINUE);
} while (fftarray.message==ARRAY_ENDOFVECTOR);
tinfo->nr_of_points=fftarray.nr_of_elements;
/*}}} */
} else {
/*{{{ rereference(transform_info_ptr tinfo)*/
METHODDEF DATATYPE *
rereference(transform_info_ptr tinfo) {
struct rereference_args_struct *rereference_args=(struct rereference_args_struct *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
int itempart;
transform_info_ptr const tinfoptr=tinfo;
array indata;
tinfo_array(tinfoptr, &indata);
array_transpose(&indata); /* Vector=map */
for (itempart=0; itempart<tinfoptr->itemsize-tinfoptr->leaveright; itempart++) {
array_use_item(&indata, itempart);
do {
DATATYPE mean=0;
int n=0;
do {
if (is_in_channellist(indata.current_element+1, rereference_args->refchannel_numbers)) {
mean+=array_scan(&indata);
n++;
} else {
array_advance(&indata);
}
} while (indata.message==ARRAY_CONTINUE);
mean/=n;
array_previousvector(&indata);
do {
if ((args[ARGS_EXCLUDEOTHER].is_set && !is_in_channellist(indata.current_element+1, rereference_args->refchannel_numbers))
|| is_in_channellist(indata.current_element+1, rereference_args->excludechannel_numbers)) {
array_advance(&indata);
} else {
array_write(&indata, READ_ELEMENT(&indata)-mean);
}
} while (indata.message==ARRAY_CONTINUE);
} while (indata.message!=ARRAY_ENDOFSCAN);
}
return tinfo->tsdata;
}
GLOBAL struct source_desc *
var_random_srcmodule(transform_info_ptr tinfo, char **args) {
int n_harmonics, n_noisedips, i, n_dipoles;
char **inargs=args;
DATATYPE *memptr;
float random_pos=0.0, random_moment=0.0;
double freq_default=0.1;
struct source_desc *sourcep;
struct dipole_desc *dipolep;
if (args==(char **)NULL) {
ERREXIT(tinfo->emethods, "var_random_srcmodule: Usage: var_random_dipoles ( n_harmonics n_noisedips )\n");
}
if (*inargs!=NULL) n_harmonics=atoi(*inargs++);
if (*inargs!=NULL) n_noisedips=atoi(*inargs++);
if (inargs-args!=2) {
ERREXIT(tinfo->emethods, "var_random_srcmodule: Need at least two arguments ( n_harmonics n_noisedips )\n");
}
n_dipoles=n_harmonics+n_noisedips;
if ((sourcep=(struct source_desc *)malloc(sizeof(struct source_desc)+(sizeof(struct dipole_desc)+3*3*sizeof(DATATYPE))*n_dipoles))==NULL) {
ERREXIT(tinfo->emethods, "var_random_srcmodule: Error allocating memory\n");
}
sourcep->nrofsources=n_dipoles;
dipolep=sourcep->dipoles=(struct dipole_desc *)(sourcep+1);
memptr=(DATATYPE *)(dipolep+n_dipoles);
for (i=0; i<n_dipoles; i++, dipolep++, memptr+=9) {
dipolep->position.start=memptr;
dipolep->dip_moment.start=memptr+3;
dipolep->initial_moment.start=memptr+6;
/*{{{ Read switchable options: FREQ_DEFAULT, RANDOM_POS, RANDOM_MOMENT keyword*/
if (*inargs!=NULL && strcmp(*inargs, "FREQ_DEFAULT")==0) {
if (*++inargs!=NULL) {
freq_default=atof(*inargs);
inargs++;
}
}
if (*inargs!=NULL && strcmp(*inargs, "RANDOM_POS")==0) {
if (*++inargs!=NULL) {
random_pos=atof(*inargs);
inargs++;
}
}
if (*inargs!=NULL && strcmp(*inargs, "RANDOM_MOMENT")==0) {
if (*++inargs!=NULL) {
random_moment=atof(*inargs);
inargs++;
}
}
/*}}} */
dipolep->position.nr_of_elements=dipolep->dip_moment.nr_of_elements=dipolep->initial_moment.nr_of_elements=3;
dipolep->position.nr_of_vectors=dipolep->dip_moment.nr_of_vectors=dipolep->initial_moment.nr_of_vectors=1;
dipolep->position.element_skip=dipolep->dip_moment.element_skip=dipolep->initial_moment.element_skip=1;
dipolep->position.vector_skip=dipolep->dip_moment.vector_skip=dipolep->initial_moment.vector_skip=3;
array_setreadwrite(&dipolep->position);
array_setreadwrite(&dipolep->dip_moment);
array_setreadwrite(&dipolep->initial_moment);
array_reset(&dipolep->position);
array_reset(&dipolep->dip_moment);
array_reset(&dipolep->initial_moment);
/* The parameter is the frequency relative to half the sampling frequency: */
dipolep->time[1]=M_PI*readval(tinfo, &inargs, freq_default);
if (dipolep->time[1]<=0) {
ERREXIT1(tinfo->emethods, "var_random_srcmodule: Frequency==%d\n", MSGPARM(dipolep->time[1]));
}
if (random_pos>0.0) {
float x, y, z;
sphere_random(random_pos, &x, &y, &z);
array_write(&dipolep->position, readval(tinfo, &inargs, x));
array_write(&dipolep->position, readval(tinfo, &inargs, y));
array_write(&dipolep->position, readval(tinfo, &inargs, z));
} else {
array_write(&dipolep->position, readval(tinfo, &inargs, 1));
array_write(&dipolep->position, readval(tinfo, &inargs, 1));
array_write(&dipolep->position, readval(tinfo, &inargs, 7.5));
}
if (random_moment>0.0) {
float x, y, z;
sphere_random(random_moment, &x, &y, &z);
array_write(&dipolep->dip_moment, readval(tinfo, &inargs, x));
array_write(&dipolep->dip_moment, readval(tinfo, &inargs, y));
array_write(&dipolep->dip_moment, readval(tinfo, &inargs, z));
} else {
array_write(&dipolep->dip_moment, readval(tinfo, &inargs, 1));
array_write(&dipolep->dip_moment, readval(tinfo, &inargs, 0));
array_write(&dipolep->dip_moment, readval(tinfo, &inargs, 0));
}
if (i<n_harmonics) {
/*{{{ Set harmonic behaviour*/
dipolep->time_function_init= &harmonic_time_init;
dipolep->time_function= &harmonic_time;
dipolep->time_function_exit= &harmonic_time_exit;
/*}}} */
} else {
/*{{{ Set noise behaviour*/
dipolep->time_function_init= &noise_time_init;
dipolep->time_function= &noise_time;
dipolep->time_function_exit= &noise_time_exit;
/*}}} */
}
}
return sourcep;
}
/*{{{ read_neurofile(transform_info_ptr tinfo) {*/
METHODDEF DATATYPE *
read_neurofile(transform_info_ptr tinfo) {
struct read_neurofile_storage *local_arg=(struct read_neurofile_storage *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
array myarray;
FILE *infile=local_arg->infile;
Bool not_correct_trigger=FALSE;
long trigger_point, file_start_point, file_end_point;
char *innamebuf;
int channel;
char *description=NULL;
if (local_arg->epochs--==0) return NULL;
tinfo->beforetrig=local_arg->beforetrig;
tinfo->aftertrig=local_arg->aftertrig;
tinfo->nr_of_points=local_arg->beforetrig+local_arg->aftertrig;
tinfo->nr_of_channels=local_arg->nr_of_channels;
tinfo->nrofaverages=1;
if (tinfo->nr_of_points<=0) {
ERREXIT1(tinfo->emethods, "read_neurofile: Invalid nr_of_points %d\n", MSGPARM(tinfo->nr_of_points));
}
/*{{{ Find the next window that fits into the actual data*/
/* This is just for the Continuous option (no trigger file): */
file_end_point=local_arg->current_point-1;
do {
if (args[ARGS_CONTINUOUS].is_set) {
/* Simulate a trigger at current_point+beforetrig */
file_start_point=file_end_point+1;
trigger_point=file_start_point+tinfo->beforetrig;
file_end_point=trigger_point+tinfo->aftertrig-1;
if (local_arg->points_in_file>0 && file_end_point>=local_arg->points_in_file) return NULL;
local_arg->current_trigger++;
local_arg->current_point+=tinfo->nr_of_points;
tinfo->condition=0;
} else
do {
tinfo->condition=read_neurofile_read_trigger(tinfo, &trigger_point, &description);
if (tinfo->condition==0) return NULL; /* No more triggers in file */
file_start_point=trigger_point-tinfo->beforetrig+local_arg->offset;
file_end_point=trigger_point+tinfo->aftertrig-1-local_arg->offset;
if (local_arg->trigcodes==NULL) {
not_correct_trigger=FALSE;
} else {
int trigno=0;
not_correct_trigger=TRUE;
while (local_arg->trigcodes[trigno]!=0) {
if (local_arg->trigcodes[trigno]==tinfo->condition) {
not_correct_trigger=FALSE;
break;
}
trigno++;
}
}
} while (not_correct_trigger || file_start_point<0 || (local_arg->points_in_file>0 && file_end_point>=local_arg->points_in_file));
} while (--local_arg->fromepoch>0);
if (description==NULL) {
TRACEMS3(tinfo->emethods, 1, "read_neurofile: Reading around tag %d at %d, condition=%d\n", MSGPARM(local_arg->current_trigger), MSGPARM(trigger_point), MSGPARM(tinfo->condition));
} else {
TRACEMS4(tinfo->emethods, 1, "read_neurofile: Reading around tag %d at %d, condition=%d, description=%s\n", MSGPARM(local_arg->current_trigger), MSGPARM(trigger_point), MSGPARM(tinfo->condition), MSGPARM(description));
}
/*{{{ Handle triggers within the epoch (option -T)*/
if (args[ARGS_TRIGTRANSFER].is_set) {
int trigs_in_epoch, code;
long trigpoint;
long const old_current_trigger=local_arg->current_trigger;
char *thisdescription;
/* First trigger entry holds file_start_point */
push_trigger(&tinfo->triggers, file_start_point, -1, NULL);
read_neurofile_reset_triggerbuffer(tinfo);
for (trigs_in_epoch=1; (code=read_neurofile_read_trigger(tinfo, &trigpoint, &thisdescription))!=0;) {
if (trigpoint>=file_start_point && trigpoint<=file_end_point) {
push_trigger(&tinfo->triggers, trigpoint-file_start_point, code, thisdescription);
trigs_in_epoch++;
}
}
push_trigger(&tinfo->triggers, 0, 0, NULL); /* End of list */
local_arg->current_trigger=old_current_trigger;
}
/*}}} */
fseek(infile, file_start_point*tinfo->nr_of_channels, SEEK_SET);
/*{{{ Configure myarray*/
myarray.element_skip=tinfo->itemsize=1;
tinfo->multiplexed=TRUE;
myarray.nr_of_elements=tinfo->nr_of_channels;
myarray.nr_of_vectors=tinfo->nr_of_points;
if (array_allocate(&myarray)==NULL ||
(tinfo->channelnames=(char **)malloc(tinfo->nr_of_channels*sizeof(char *)))==NULL ||
(innamebuf=(char *)malloc(local_arg->stringlength))==NULL ||
(tinfo->comment=(char *)malloc(strlen((char *)local_arg->seq.comment)+(1+17+1)))==NULL) {
ERREXIT(tinfo->emethods, "read_neurofile: Error allocating data\n");
}
/*}}} */
sprintf(tinfo->comment, "%s %02d/%02d/%02d,%02d:%02d:%02d", local_arg->seq.comment, local_arg->seq.month, local_arg->seq.day, local_arg->seq.year, local_arg->seq.hour, local_arg->seq.minute, local_arg->seq.second);
for (channel=0; channel<tinfo->nr_of_channels; channel++) {
strcpy(innamebuf, (char *)local_arg->seq.elnam[channel]);
tinfo->channelnames[channel]=innamebuf;
innamebuf+=strlen(innamebuf)+1;
}
do {
signed char exponent;
short delta;
if (fread(&exponent, sizeof(exponent), 1, infile)!=1) {
ERREXIT(tinfo->emethods, "read_neurofile: Error reading data\n");
}
delta=exponent;
exponent&=0x03;
if (exponent==0x03) {
delta>>=2;
} else {
delta=(delta&0xfffc)<<(exponent*2);
}
local_arg->last_values[myarray.current_element]+=delta;
array_write(&myarray, local_arg->last_values[myarray.current_element]*local_arg->factor);
} while (myarray.message!=ARRAY_ENDOFSCAN);
/*{{{ project(transform_info_ptr tinfo)*/
METHODDEF DATATYPE *
project(transform_info_ptr tinfo) {
struct project_args_struct *project_args=(struct project_args_struct *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
DATATYPE *retvalue=tinfo->tsdata;
array indata, scalars, *vectors= &project_args->vectors;
int itempart, itemparts=tinfo->itemsize-tinfo->leaveright;
if (project_args->project_mode==PROJECT_MODE_MULTIPLY) {
if (!(tinfo->nr_of_channels==vectors->nr_of_vectors
||(tinfo->nr_of_channels==1 && tinfo->itemsize==vectors->nr_of_vectors))) {
ERREXIT(tinfo->emethods, "project: Number of scalars and maps doesn't match!\n");
}
} else {
if (vectors->nr_of_elements!=tinfo->nr_of_channels) {
ERREXIT2(tinfo->emethods, "project: %d channels in epoch, but %d channels in project file.\n", MSGPARM(tinfo->nr_of_channels), MSGPARM(vectors->nr_of_elements));
}
}
array_reset(vectors);
tinfo_array(tinfo, &indata);
array_transpose(&indata); /* Vectors are maps */
/* Be sure that different output items are adjacent... */
scalars.nr_of_elements=vectors->nr_of_vectors;
switch (project_args->project_mode) {
case PROJECT_MODE_SCALAR:
scalars.nr_of_vectors=tinfo->nr_of_points;
scalars.element_skip=itemparts;
break;
case PROJECT_MODE_SSP:
case PROJECT_MODE_SSPS:
scalars.nr_of_vectors=1;
scalars.element_skip=1;
break;
case PROJECT_MODE_MULTIPLY:
scalars=indata;
if (tinfo->nr_of_channels!=vectors->nr_of_vectors) {
/* Ie, one channel and weights in the items: Convert from 1 element to
* itemsize elements */
scalars.element_skip=1;
scalars.nr_of_elements=tinfo->itemsize;
itemparts=1;
}
indata.element_skip=itemparts;
indata.nr_of_elements=vectors->nr_of_elements; /* New number of channels */
indata.nr_of_vectors=scalars.nr_of_vectors; /* New number of points */
if (array_allocate(&indata)==NULL) {
ERREXIT(tinfo->emethods, "project: Can't allocate new indata array\n");
}
break;
}
if (project_args->project_mode==PROJECT_MODE_MULTIPLY) {
array_transpose(vectors); /* Now the elements are the subspace dimensions */
for (itempart=0; itempart<itemparts; itempart++) {
array_use_item(&indata, itempart);
array_use_item(&scalars, itempart);
do {
/*{{{ Build the signal subspace vector*/
do {
array_write(&indata, array_multiply(vectors, &scalars, MULT_SAMESIZE));
} while (indata.message==ARRAY_CONTINUE);
/*}}} */
} while (indata.message!=ARRAY_ENDOFSCAN);
}
array_transpose(vectors);
} else {
if (array_allocate(&scalars)==NULL) {
ERREXIT(tinfo->emethods, "project: Can't allocate scalars array\n");
}
for (itempart=0; itempart<itemparts; itempart++) {
array_use_item(&indata, itempart);
if (project_args->project_mode==PROJECT_MODE_SCALAR) {
array_use_item(&scalars, itempart);
}
do {
/*{{{ Calculate the projection scalars*/
do {
/* With all vectors in turn: */
DATATYPE product=0.0;
do {
if (project_args->channel_list!=NULL && !is_in_channellist(vectors->current_element+1, project_args->channel_list)) {
array_advance(vectors);
array_advance(&indata);
} else {
product+=array_scan(&indata)*array_scan(vectors);
}
} while (vectors->message==ARRAY_CONTINUE);
array_write(&scalars, product);
if (scalars.message==ARRAY_CONTINUE) array_previousvector(&indata);
} while (scalars.message==ARRAY_CONTINUE);
/*}}} */
switch (project_args->project_mode) {
case PROJECT_MODE_SCALAR:
break;
case PROJECT_MODE_SSP:
/*{{{ Build the signal subspace vector*/
array_transpose(vectors); /* Now the elements are the subspace dimensions */
array_previousvector(&indata);
do {
array_write(&indata, array_multiply(vectors, &scalars, MULT_VECTOR));
} while (indata.message==ARRAY_CONTINUE);
array_transpose(vectors);
/*}}} */
break;
case PROJECT_MODE_SSPS:
/*{{{ Subtract the signal subspace vector*/
array_transpose(vectors); /* Now the elements are the subspace dimensions */
array_previousvector(&indata);
do {
array_write(&indata, READ_ELEMENT(&indata)-array_multiply(vectors, &scalars, MULT_VECTOR));
} while (indata.message==ARRAY_CONTINUE);
array_transpose(vectors);
/*}}} */
break;
default:
/* Can't happen, just to keep the compiler happy... */
ERREXIT(tinfo->emethods, "project: This cannot happen!\n");
break;
}
} while (indata.message!=ARRAY_ENDOFSCAN);
}
}
/*{{{ Prepare tinfo to reflect the data structure returned*/
switch (project_args->project_mode) {
case PROJECT_MODE_SCALAR:
if (args[ARGS_USE_CHANNELS].is_set) {
tinfo->nr_of_channels=vectors->nr_of_vectors;
tinfo->itemsize=itemparts;
} else {
tinfo->nr_of_channels=1;
tinfo->itemsize=itemparts*vectors->nr_of_vectors;
}
tinfo->length_of_output_region=scalars.nr_of_elements*scalars.element_skip*scalars.nr_of_vectors;
tinfo->leaveright=0;
tinfo->multiplexed=TRUE;
if (tinfo->channelnames!=NULL) {
free_pointer((void **)&tinfo->channelnames[0]);
free_pointer((void **)&tinfo->channelnames);
}
free_pointer((void **)&tinfo->probepos);
create_channelgrid(tinfo);
retvalue=scalars.start;
break;
case PROJECT_MODE_SSP:
case PROJECT_MODE_SSPS:
array_free(&scalars);
retvalue=tinfo->tsdata;
break;
case PROJECT_MODE_MULTIPLY:
/* Note that we don't free `scalars' because it just points to the original tsdata! */
/* Have to set this correctly so that copy_channelinfo works... */
tinfo->nr_of_channels=indata.nr_of_elements;
copy_channelinfo(tinfo, project_args->save_side_tinfo.channelnames, project_args->save_side_tinfo.probepos);
tinfo->nr_of_points=indata.nr_of_vectors;
tinfo->itemsize=indata.element_skip;
tinfo->length_of_output_region=tinfo->nr_of_channels*tinfo->nr_of_points*tinfo->itemsize;
retvalue=indata.start;
tinfo->multiplexed=TRUE;
break;
}
/*}}} */
return retvalue;
}
int main(int argc, char **argv) {
FILE *fp;
surfspline_desc sspline;
int err, npoints, itempart=0;
int binary_output=FALSE, matlab_output=FALSE, mtv_output=FALSE, interpolate_only=FALSE;
float fbuf, external_value=0.0;
DATATYPE f, x, y, xmin, xmax, ymin, ymax, xstep, ystep;
array index;
pid_t pid;
char outname[L_tmpnam], inname[L_tmpnam], **inargs, *infile;
/*{{{ Read command line args*/
for (inargs=argv+1; inargs-argv<argc && **inargs=='-'; inargs++) {
switch(inargs[0][1]) {
case 'B':
binary_output=TRUE;
break;
case 'I':
if (inargs[0][2]!='\0') {
itempart=atoi(*inargs+2);
}
break;
case 'i':
interpolate_only=TRUE;
if (inargs[0][2]!='\0') {
external_value=atof(*inargs+2);
}
break;
case 'M':
matlab_output=TRUE;
break;
case 'm':
mtv_output=TRUE;
break;
default:
fprintf(stderr, "%s: Ignoring unknown option %s\n", argv[0], *inargs);
continue;
}
}
if (argc-(inargs-argv)!=3) {
fprintf(stderr, "Usage: %s array_filename degree npoints\n"
"Options:\n"
" -Iitem: Use item number item as z-axis (2+item'th column); default: 0\n"
" -i[value]: Interpolate only; set external values to value (default: 0.0)\n"
" -B: Binary output (gnuplot floats)\n"
" -M: Matlab output (x, y vectors and z matrix)\n"
" -m: Plotmtv output\n"
, argv[0]);
return -1;
}
infile= *inargs++;
if ((fp=fopen(infile, "r"))==NULL) {
fprintf(stderr, "Can't open %s\n", infile);
return -2;
}
array_undump(fp, &sspline.inpoints);
fclose(fp);
if (sspline.inpoints.message==ARRAY_ERROR) {
fprintf(stderr, "Error in array_undump\n");
return -3;
}
if (sspline.inpoints.nr_of_elements<3+itempart) {
fprintf(stderr, "Not enough columns in array %s\n", *(inargs-1));
return -3;
}
sspline.degree=atoi(*inargs++);;
npoints=atoi(*inargs++);
/*}}} */
/*{{{ Get the index of qhull point pairs by running qhull*/
tmpnam(outname); tmpnam(inname);
if ((pid=fork())==0) { /* I'm the child */
#define LINEBUF_SIZE 128
char linebuf[LINEBUF_SIZE];
array tmp_array;
/*{{{ Dump xy positions to tmp file inname*/
tmp_array.nr_of_elements=2;
tmp_array.nr_of_vectors=sspline.inpoints.nr_of_vectors;
tmp_array.element_skip=1;
if (array_allocate(&tmp_array)==NULL) {
fprintf(stderr, "Error allocating tmp_array\n");
return -4;
}
array_reset(&sspline.inpoints);
do {
array_write(&tmp_array, array_scan(&sspline.inpoints));
array_write(&tmp_array, array_scan(&sspline.inpoints));
array_nextvector(&sspline.inpoints);
} while (tmp_array.message!=ARRAY_ENDOFSCAN);
if ((fp=fopen(inname, "w"))==NULL) {
fprintf(stderr, "Can't open %s\n", inname);
return -5;
}
array_dump(fp, &tmp_array, ARRAY_ASCII);
fclose(fp);
array_free(&tmp_array);
/*}}} */
snprintf(linebuf, LINEBUF_SIZE, "qhull C0 i b <%s >%s", inname, outname);
execl("/bin/sh", "sh", "-c", linebuf, 0);
#undef LINEBUF_SIZE
} else {
wait(NULL);
}
unlink(inname);
if ((fp=fopen(outname, "r"))==NULL) {
fprintf(stderr, "Can't open %s\n", outname);
return -6;
}
array_undump(fp, &index);
fclose(fp);
unlink(outname);
/*}}} */
/*{{{ Find min, max and mean coordinates*/
array_transpose(&sspline.inpoints);
array_reset(&sspline.inpoints);
xmin=array_min(&sspline.inpoints);
ymin=array_min(&sspline.inpoints);
array_reset(&sspline.inpoints);
xmax=array_max(&sspline.inpoints);
ymax=array_max(&sspline.inpoints);
array_reset(&sspline.inpoints);
xmean=array_mean(&sspline.inpoints);
ymean=array_mean(&sspline.inpoints);
xstep=(xmax-xmin)/npoints;
ystep=(ymax-ymin)/npoints;
array_transpose(&sspline.inpoints);
array_reset(&sspline.inpoints);
/*}}} */
/*{{{ Copy itempart to 3rd location if necessary*/
/* Note: For this behavior it is essential that array_surfspline
* will accept vectors of any size >=3 and only process the first three
* elements ! */
if (itempart>0) {
DATATYPE hold;
do {
sspline.inpoints.current_element=2+itempart;
hold=READ_ELEMENT(&sspline.inpoints);
sspline.inpoints.current_element=2;
WRITE_ELEMENT(&sspline.inpoints, hold);
array_nextvector(&sspline.inpoints);
} while (sspline.inpoints.message!=ARRAY_ENDOFSCAN);
}
/*}}} */
/*{{{ Do surface spline*/
if ((err=array_surfspline(&sspline))!=0) {
fprintf(stderr, "Error %d in array_surfspline\n", err);
return err;
}
xmin-=xstep; xmax+=2*xstep;
ymin-=ystep; ymax+=2*ystep;
if (binary_output) {
/*{{{ Gnuplot binary output*/
int n_xval=(xmax-xmin)/xstep+1, n; /* Number of x values */
fbuf=n_xval;
fwrite(&fbuf, sizeof(float), 1, stdout);
for (fbuf=xmin, n=0; n<n_xval; fbuf+=xstep, n++) { /* x values */
fwrite(&fbuf, sizeof(float), 1, stdout);
}
for (y=ymin; y<=ymax; y+=ystep) {
fbuf=y; fwrite(&fbuf, sizeof(float), 1, stdout);
for (x=xmin, n=0; n<n_xval; x+=xstep, n++) {
if (interpolate_only && !is_inside(&index, &sspline.inpoints, x, y)) {
f=external_value;
} else {
f=array_fsurfspline(&sspline, x, y);
}
fbuf=f; fwrite(&fbuf, sizeof(float), 1, stdout);
}
}
/*}}} */
} else if (matlab_output) {
/*{{{ Matlab output*/
array xm, ym, zm;
xm.nr_of_elements=ym.nr_of_elements=1;
xm.nr_of_vectors=zm.nr_of_elements=(xmax-xmin)/xstep+1;
ym.nr_of_vectors=zm.nr_of_vectors=(ymax-ymin)/ystep+1;
xm.element_skip=ym.element_skip=zm.element_skip=1;
array_allocate(&xm); array_allocate(&ym); array_allocate(&zm);
if (xm.message==ARRAY_ERROR || ym.message==ARRAY_ERROR || zm.message==ARRAY_ERROR) {
fprintf(stderr, "Error allocating output arrays\n");
return -7;
}
x=xmin; do {
array_write(&xm, x);
x+=xstep;
} while (xm.message!=ARRAY_ENDOFSCAN);
y=ymin; do {
array_write(&ym, y);
x=xmin; do {
if (interpolate_only && !is_inside(&index, &sspline.inpoints, x, y)) {
f=external_value;
} else {
f=array_fsurfspline(&sspline, x, y);
}
array_write(&zm, f);
x+=xstep;
} while (zm.message==ARRAY_CONTINUE);
y+=ystep;
} while (zm.message!=ARRAY_ENDOFSCAN);
array_dump(stdout, &xm, ARRAY_MATLAB);
array_dump(stdout, &ym, ARRAY_MATLAB);
array_dump(stdout, &zm, ARRAY_MATLAB);
array_free(&xm); array_free(&ym); array_free(&zm);
/*}}} */
} else if (mtv_output) {
/*{{{ Plotmtv output*/
array zm;
DATATYPE zmin=FLT_MAX, zmax= -FLT_MAX;
zm.nr_of_elements=(xmax-xmin)/xstep+1;
zm.nr_of_vectors=(ymax-ymin)/ystep+1;
zm.element_skip=1;
array_allocate(&zm);
if (zm.message==ARRAY_ERROR) {
fprintf(stderr, "Error allocating output arrays\n");
return -7;
}
y=ymin; do {
x=xmin; do {
if (interpolate_only && !is_inside(&index, &sspline.inpoints, x, y)) {
f=external_value;
} else {
f=array_fsurfspline(&sspline, x, y);
}
array_write(&zm, f);
if (f<zmin) zmin=f;
if (f>zmax) zmax=f;
x+=xstep;
} while (zm.message==ARRAY_CONTINUE);
y+=ystep;
} while (zm.message!=ARRAY_ENDOFSCAN);
/*{{{ Print file header*/
printf(
"# Output of Spline_Gridder (C) Bernd Feige 1995\n\n"
"$ DATA=CONTOUR\n\n"
"%% toplabel = \"Spline_Gridder output\"\n"
"%% subtitle = \"File: %s\"\n\n"
"%% interp = 0\n"
"%% contfill = on\n"
"%% meshplot = off\n\n"
"%% xmin = %g xmax = %g\n"
"%% ymin = %g ymax = %g\n"
"%% zmin = %g zmax = %g\n"
"%% nx = %d\n"
"%% ny = %d\n"
, infile,
xmin, xmax,
ymin, ymax,
zmin, zmax,
zm.nr_of_elements,
zm.nr_of_vectors);
/*}}} */
array_dump(stdout, &zm, ARRAY_MATLAB);
array_free(&zm);
/*}}} */
} else {
/*{{{ Gnuplot output*/
for (x=xmin; x<=xmax; x+=xstep) {
for (y=ymin; y<=ymax; y+=ystep) {
if (interpolate_only && !is_inside(&index, &sspline.inpoints, x, y)) {
f=external_value;
} else {
f=array_fsurfspline(&sspline, x, y);
}
printf("%g %g %g\n", x, y, f);
}
printf("\n");
}
/*}}} */
}
/*}}} */
return 0;
}
GLOBAL void
array_copy(array *array1, array *array2) {
do {
array_write(array2, array_scan(array1));
} while (array1->message!=ARRAY_ENDOFSCAN && array2->message!=ARRAY_ENDOFSCAN);
}
/* freiburg_get_segment returns 0 on success and -1 on out-of-input-bounds */
LOCAL int
freiburg_get_segment(transform_info_ptr tinfo, array *toarray) {
struct read_freiburg_storage *local_arg=(struct read_freiburg_storage *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
/* Well, again... It appears that at some time, there was a bug in KL's
* programs resulting in ZEROES inserted before every new block, ie every
* 513 data points... No indication of that in the header (`blockluecke' or
* such, still don't know what that value means)... End of broadcast... */
do {
/* If this is FALSE at the start, it will never become TRUE... */
int everything_was_zero=args[ARGS_ZEROCHECK].is_set;
/* NOTE: The first time through, the values in last_values_buf are not
* initialized. It should be assumed that the values in the very first point
* read are NOT marked as differences, but with BT's Nxxx files, it's
* different at the start of a `Block' if there was saturation as well... */
short *in_last_values_buf=local_arg->last_values_buf;
const Bool no_last_values=local_arg->no_last_values;
do {
short oldword= *in_last_values_buf;
int nextchar=fgetc(local_arg->infile);
unsigned short word;
DATATYPE floatval;
if (nextchar==EOF) return -1;
if (nextchar&0x0080 || no_last_values) {
/* data is a whole short */
word=(((unsigned int)nextchar)<<8)+(((unsigned int)fgetc(local_arg->infile))&0x00ff);
if ((word&0x4000)==0) {
word&=0x7fff; /* Make positive if bit 14 clear */
}
} else {
/* data is relative to oldword */
unsigned short byte=(unsigned short)nextchar;
if (byte&0x0040) {
/* Negative difference */
byte|=0xffc0;
} else {
/* Positive difference */
byte&=0x003f;
}
word=(unsigned short)((short)oldword+(short)byte); /* Signed addition */
}
if (word!=0) everything_was_zero=FALSE;
*(unsigned short *)in_last_values_buf=word;
floatval= *in_last_values_buf++;
if (local_arg->uV_per_bit!=NULL) floatval*=local_arg->uV_per_bit[toarray->current_element];
array_write(toarray, floatval);
} while (toarray->message==ARRAY_CONTINUE);
if (everything_was_zero) {
array_previousvector(toarray);
local_arg->zero_idiotism_encountered=TRUE;
} else {
break;
}
} while (TRUE);
local_arg->current_point++;
local_arg->no_last_values=FALSE;
return 0;
}
METHODDEF DATATYPE *
read_freiburg(transform_info_ptr tinfo) {
struct read_freiburg_storage *local_arg=(struct read_freiburg_storage *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
struct freiburg_channels_struct *in_channels=local_arg->in_channels;
array myarray;
FILE *infile;
int i, point, channel;
int trial_not_accepted;
long length_of_data;
short header[FREIBURG_HEADER_LENGTH/sizeof(short)];
char const *last_sep=strrchr(args[ARGS_IFILE].arg.s, PATHSEP);
char const *last_component=(last_sep==NULL ? args[ARGS_IFILE].arg.s : last_sep+1);
char comment[MAX_COMMENTLEN];
tinfo->nrofaverages=1;
if (args[ARGS_CONTINUOUS].is_set) {
/*{{{ Read an epoch from a continuous file*/
infile=local_arg->infile;
if (local_arg->epochs--==0) return NULL;
/*{{{ Configure myarray*/
myarray.element_skip=tinfo->itemsize=1;
myarray.nr_of_vectors=tinfo->nr_of_points=local_arg->epochlength;
myarray.nr_of_elements=tinfo->nr_of_channels=local_arg->nr_of_channels;
if (array_allocate(&myarray)==NULL) {
ERREXIT(tinfo->emethods, "read_freiburg: Error allocating data\n");
}
tinfo->multiplexed=TRUE;
/*}}} */
do {
do {
if (local_arg->segment_table.buffer_start!=NULL && local_arg->current_point%SEGMENT_LENGTH==0) {
int const segment=local_arg->current_point/SEGMENT_LENGTH;
long const nr_of_segments=local_arg->segment_table.current_length/sizeof(long);
if (segment>=nr_of_segments) {
array_free(&myarray);
return NULL;
}
fseek(infile, ((long *)local_arg->segment_table.buffer_start)[segment], SEEK_SET);
local_arg->no_last_values=TRUE;
}
if (freiburg_get_segment(tinfo, &myarray)!=0) {
array_free(&myarray);
return NULL;
}
} while (myarray.message!=ARRAY_ENDOFSCAN);
} while (--local_arg->fromepoch>0);
snprintf(comment, MAX_COMMENTLEN, "%s %s %02d/%02d/%04d,%02d:%02d:%02d", (local_arg->continuous_type==SLEEP_BT_TYPE ? "sleep_BT" : "sleep_KL"), last_component, local_arg->btfile.start_month, local_arg->btfile.start_day, local_arg->btfile.start_year, local_arg->btfile.start_hour, local_arg->btfile.start_minute, local_arg->btfile.start_second);
tinfo->sfreq=local_arg->sfreq;
/*}}} */
} else
/*{{{ Read an epoch from a single (epoched or averaged) file*/
do { /* Return here if trial was not accepted */
trial_not_accepted=FALSE;
if (local_arg->epochs--==0 || (local_arg->average_mode && local_arg->current_trigger>=1)) return NULL;
if (local_arg->average_mode) {
/*{{{ Prepare reading an averaged file*/
if((infile=fopen(args[ARGS_IFILE].arg.s,"rb"))==NULL) {
ERREXIT1(tinfo->emethods, "read_freiburg: Can't open file %s\n", MSGPARM(args[ARGS_IFILE].arg.s));
}
fseek(infile, 0, SEEK_END);
length_of_data=ftell(infile)-FREIBURG_HEADER_LENGTH;
local_arg->current_trigger++;
snprintf(comment, MAX_COMMENTLEN, "Freiburg-avg %s", last_component);
/*}}} */
} else {
/*{{{ Build pathname of the single trial to read*/
/* A directory name was given. */
char const * const expnumber=args[ARGS_IFILE].arg.s+strlen(args[ARGS_IFILE].arg.s)-2;
#ifdef __GNUC__
#define NEWFILENAME_SIZE (strlen(args[ARGS_IFILE].arg.s)+strlen(last_component)+20)
#else
#define NEWFILENAME_SIZE MAX_PATHLEN
#endif
char newfilename[NEWFILENAME_SIZE];
do { /* Files from which only the parameter part exists are rejected */
int div100=local_arg->current_trigger/100, mod100=local_arg->current_trigger%100;
snprintf(newfilename, NEWFILENAME_SIZE, "%s%c%s%02d%c%c%s%02d%02d", args[ARGS_IFILE].arg.s, PATHSEP, last_component, div100, PATHSEP, tolower(expnumber[-1]), expnumber, div100, mod100);
TRACEMS1(tinfo->emethods, 1, "read_freiburg: Constructed filename %s\n", MSGPARM(newfilename));
if((infile=fopen(newfilename,"rb"))==NULL) {
if (local_arg->current_trigger==0) {
ERREXIT1(tinfo->emethods, "read_freiburg: Can't open file %s\n", MSGPARM(newfilename));
} else {
return NULL;
}
}
fseek(infile, 0, SEEK_END);
length_of_data=ftell(infile)-FREIBURG_HEADER_LENGTH;
local_arg->current_trigger++;
} while (length_of_data==0 || --local_arg->fromepoch>0);
snprintf(comment, MAX_COMMENTLEN, "Freiburg-raw %s", last_component);
/*}}} */
}
/*{{{ Read the 64-Byte header*/
fseek(infile, 0, SEEK_SET);
fread(header, 1, FREIBURG_HEADER_LENGTH, infile);
for (i=0; i<18; i++) {
# ifdef LITTLE_ENDIAN
Intel_int16((uint16_t *)&header[i]);
# endif
TRACEMS2(tinfo->emethods, 3, "read_freiburg: Header %02d: %d\n", MSGPARM(i), MSGPARM(header[i]));
}
/*}}} */
if (local_arg->average_mode) {
if ((length_of_data/sizeof(short))%local_arg->nr_of_channels!=0) {
ERREXIT2(tinfo->emethods, "read_freiburg: length_of_data=%d does not fit with nr_of_channels=%d\n", MSGPARM(length_of_data), MSGPARM(local_arg->nr_of_channels));
}
tinfo->nr_of_points=(length_of_data/sizeof(short))/local_arg->nr_of_channels;
local_arg->sfreq=(args[ARGS_SFREQ].is_set ? args[ARGS_SFREQ].arg.d : 200.0); /* The most likely value */
} else {
local_arg->nr_of_channels=header[14];
/* Note: In a lot of experiments, one point MORE is available in the data
* than specified in the header, but this occurs erratically. We could only
* check for this during decompression, but that's probably too much fuss. */
tinfo->nr_of_points=header[16]/header[15];
local_arg->sfreq=(args[ARGS_SFREQ].is_set ? args[ARGS_SFREQ].arg.d : 1000.0/header[15]);
}
tinfo->sfreq=local_arg->sfreq;
/*{{{ Parse arguments that can be in seconds*/
local_arg->offset=(args[ARGS_OFFSET].is_set ? gettimeslice(tinfo, args[ARGS_OFFSET].arg.s) : 0);
/*}}} */
tinfo->beforetrig= -local_arg->offset;
tinfo->aftertrig=tinfo->nr_of_points+local_arg->offset;
/*{{{ Configure myarray*/
myarray.element_skip=tinfo->itemsize=1;
myarray.nr_of_vectors=tinfo->nr_of_points;
myarray.nr_of_elements=tinfo->nr_of_channels=local_arg->nr_of_channels;
if (array_allocate(&myarray)==NULL) {
ERREXIT(tinfo->emethods, "read_freiburg: Error allocating data\n");
}
tinfo->multiplexed=TRUE;
/*}}} */
fseek(infile, FREIBURG_HEADER_LENGTH, SEEK_SET);
if (local_arg->average_mode) {
/*{{{ Read averaged epoch*/
for (point=0; point<tinfo->nr_of_points; point++) {
#ifdef __GNUC__
short buffer[tinfo->nr_of_channels];
#else
short buffer[MAX_NR_OF_CHANNELS];
#endif
if ((int)fread(buffer, sizeof(short), tinfo->nr_of_channels, infile)!=tinfo->nr_of_channels) {
ERREXIT1(tinfo->emethods, "read_freiburg: Error reading data point %d\n", MSGPARM(point));
}
for (channel=0; channel<tinfo->nr_of_channels; channel++) {
# ifdef LITTLE_ENDIAN
Intel_int16((uint16_t *)&buffer[channel]);
# endif
array_write(&myarray, (DATATYPE)buffer[channel]);
}
}
/*}}} */
} else {
/*{{{ Read compressed single trial*/
# ifdef DISPLAY_ADJECTIVES
char *adjektiv_ende=strchr(((char *)header)+36, ' ');
if (adjektiv_ende!=NULL) *adjektiv_ende='\0';
printf("Single trial: nr_of_points=%d, nr_of_channels=%d, Adjektiv=%s\n", tinfo->nr_of_points, tinfo->nr_of_channels, ((char *)header)+36);
# endif
local_arg->infile=infile;
do {
if (freiburg_get_segment(tinfo, &myarray)!=0) {
TRACEMS1(tinfo->emethods, 0, "read_freiburg: Decompression out of bounds for trial %d - skipped\n", MSGPARM(local_arg->current_trigger-1));
array_free(&myarray);
trial_not_accepted=TRUE;
break;
}
} while (myarray.message!=ARRAY_ENDOFSCAN);
/*}}} */
}
fclose(infile);
} while (trial_not_accepted);
/*}}} */
/*{{{ Look for a Freiburg channel setup for this number of channels*/
/* Force create_channelgrid to really allocate the channel info anew.
* Otherwise, free_tinfo will free someone else's data ! */
tinfo->channelnames=NULL; tinfo->probepos=NULL;
if (local_arg->channelnames!=NULL) {
copy_channelinfo(tinfo, local_arg->channelnames, NULL);
} else {
while (in_channels->nr_of_channels!=0 && in_channels->nr_of_channels!=tinfo->nr_of_channels) in_channels++;
if (in_channels->nr_of_channels==0) {
TRACEMS1(tinfo->emethods, 1, "read_freiburg: Don't have a setup for %d channels.\n", MSGPARM(tinfo->nr_of_channels));
} else {
copy_channelinfo(tinfo, in_channels->channelnames, NULL);
}
}
create_channelgrid(tinfo); /* Create defaults for any missing channel info */
/*}}} */
if ((tinfo->comment=(char *)malloc(strlen(comment)+1))==NULL) {
ERREXIT(tinfo->emethods, "read_freiburg: Error allocating comment memory\n");
}
strcpy(tinfo->comment, comment);
if (local_arg->zero_idiotism_warned==FALSE && local_arg->zero_idiotism_encountered) {
TRACEMS(tinfo->emethods, 0, "read_freiburg: All-zero data points have been encountered and omitted!\n");
local_arg->zero_idiotism_warned=TRUE;
}
tinfo->z_label=NULL;
tinfo->tsdata=myarray.start;
tinfo->length_of_output_region=tinfo->nr_of_channels*tinfo->nr_of_points;
tinfo->leaveright=0;
tinfo->data_type=TIME_DATA;
return tinfo->tsdata;
}
/*{{{ project_init(transform_info_ptr tinfo)*/
METHODDEF void
project_init(transform_info_ptr tinfo) {
struct project_args_struct *project_args=(struct project_args_struct *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
transform_info_ptr side_tinfo= &project_args->side_tinfo;
array *vectors= &project_args->vectors;
growing_buf buf;
#define BUFFER_SIZE 80
char buffer[BUFFER_SIZE];
side_tinfo->methods= &project_args->methods;
side_tinfo->emethods=tinfo->emethods;
select_readasc(side_tinfo);
growing_buf_init(&buf);
growing_buf_allocate(&buf, 0);
if (args[ARGS_FROMEPOCH].is_set) {
snprintf(buffer, BUFFER_SIZE, "-f %ld ", args[ARGS_FROMEPOCH].arg.i);
growing_buf_appendstring(&buf, buffer);
}
if (args[ARGS_EPOCHS].is_set) {
project_args->epochs=args[ARGS_EPOCHS].arg.i;
if (project_args->epochs<=0) {
ERREXIT(tinfo->emethods, "project_init: The number of epochs must be positive.\n");
}
} else {
project_args->epochs=1;
}
snprintf(buffer, BUFFER_SIZE, "-e %d ", project_args->epochs);
growing_buf_appendstring(&buf, buffer);
growing_buf_appendstring(&buf, args[ARGS_PROJECTFILE].arg.s);
if (!buf.can_be_freed || !setup_method(side_tinfo, &buf)) {
ERREXIT(tinfo->emethods, "project_init: Error setting readasc arguments.\n");
}
project_args->points=(args[ARGS_POINTS].is_set ? args[ARGS_POINTS].arg.i : 1);
project_args->nr_of_item=(args[ARGS_NROFITEM].is_set ? args[ARGS_NROFITEM].arg.i : 0);
project_args->orthogonalize_vectors_first=args[ARGS_ORTHOGONALIZE].is_set;
if (args[ARGS_SUBSPACE].is_set) {
project_args->project_mode=PROJECT_MODE_SSP;
} else if (args[ARGS_SUBTRACT_SUBSPACE].is_set) {
project_args->project_mode=PROJECT_MODE_SSPS;
} else if (args[ARGS_MULTIPLY].is_set) {
project_args->project_mode=PROJECT_MODE_MULTIPLY;
} else {
project_args->project_mode=PROJECT_MODE_SCALAR;
}
if (args[ARGS_CHANNELNAMES].is_set) {
project_args->channel_list=expand_channel_list(tinfo, args[ARGS_CHANNELNAMES].arg.s);
if (project_args->channel_list==NULL) {
ERREXIT(tinfo->emethods, "project_init: Zero channels were selected by -N!\n");
}
} else {
project_args->channel_list=NULL;
}
(*side_tinfo->methods->transform_init)(side_tinfo);
/*{{{ Read first project_file epoch and allocate vectors array accordingly*/
if ((side_tinfo->tsdata=(*side_tinfo->methods->transform)(side_tinfo))==NULL) {
ERREXIT(tinfo->emethods, "project_init: Can't get the first project epoch.\n");
}
if (project_args->project_mode==PROJECT_MODE_MULTIPLY) {
/* Save channel names and positions for later */
project_args->save_side_tinfo.nr_of_channels=side_tinfo->nr_of_channels;
copy_channelinfo(&project_args->save_side_tinfo, side_tinfo->channelnames, side_tinfo->probepos);
}
if (project_args->points==0) project_args->points=side_tinfo->nr_of_points;
if (project_args->points>side_tinfo->nr_of_points) {
ERREXIT1(tinfo->emethods, "project_init: There are only %d points in the project_file epoch.\n", MSGPARM(side_tinfo->nr_of_points));
}
if (args[ARGS_AT_XVALUE].is_set) {
project_args->nr_of_point=find_pointnearx(side_tinfo, (DATATYPE)atof(args[ARGS_NROFPOINT].arg.s));
} else {
project_args->nr_of_point=gettimeslice(side_tinfo, args[ARGS_NROFPOINT].arg.s);
}
vectors->nr_of_vectors=project_args->epochs*project_args->points;
vectors->nr_of_elements=side_tinfo->nr_of_channels;
vectors->element_skip=1;
if (array_allocate(vectors)==NULL) {
ERREXIT(tinfo->emethods, "project_init: Error allocating vectors memory\n");
}
/*}}} */
do {
/*{{{ Copy [points] vectors from project_file to vectors array*/
array indata;
int point;
if (vectors->nr_of_elements!=side_tinfo->nr_of_channels) {
ERREXIT(side_tinfo->emethods, "project_init: Varying channel numbers in project file!\n");
}
if (project_args->nr_of_point>=side_tinfo->nr_of_points) {
ERREXIT2(side_tinfo->emethods, "project_init: nr_of_point=%d, nr_of_points=%d\n", MSGPARM(project_args->nr_of_point), MSGPARM(side_tinfo->nr_of_points));
}
if (project_args->nr_of_item>=side_tinfo->itemsize) {
ERREXIT2(side_tinfo->emethods, "project_init: nr_of_item=%d, itemsize=%d\n", MSGPARM(project_args->nr_of_item), MSGPARM(side_tinfo->itemsize));
}
for (point=0; point<project_args->points; point++) {
tinfo_array(side_tinfo, &indata);
array_transpose(&indata); /* Vector = map */
if (vectors->nr_of_elements!=indata.nr_of_elements) {
ERREXIT(side_tinfo->emethods, "project_init: vector size doesn't match\n");
}
indata.current_vector=project_args->nr_of_point+point;
array_setto_vector(&indata);
array_use_item(&indata, project_args->nr_of_item);
array_copy(&indata, vectors);
}
/*}}} */
free_tinfo(side_tinfo);
} while ((side_tinfo->tsdata=(*side_tinfo->methods->transform)(side_tinfo))!=NULL);
if (vectors->message!=ARRAY_ENDOFSCAN) {
ERREXIT1(tinfo->emethods, "project_init: Less than %d epochs in project file\n", MSGPARM(vectors->nr_of_vectors));
}
/*{{{ Set unused channels to zero if requested*/
if (args[ARGS_ZERO_UNUSEDCOEFFICIENTS].is_set) {
if (project_args->channel_list!=NULL) {
do {
do {
if (is_in_channellist(vectors->current_element+1, project_args->channel_list)) {
array_advance(vectors);
} else {
array_write(vectors, 0.0);
}
} while (vectors->message==ARRAY_CONTINUE);
} while (vectors->message!=ARRAY_ENDOFSCAN);
} else {
ERREXIT(tinfo->emethods, "project_init: Option -z only makes sense in combination with -N!\n");
}
}
/*}}} */
/*{{{ De-mean vectors if requested*/
if (args[ARGS_CORRELATION].is_set) {
do {
DATATYPE mean=0.0;
int nrofaverages=0;
do {
if (project_args->channel_list!=NULL && !is_in_channellist(vectors->current_element+1, project_args->channel_list)) {
array_advance(vectors);
} else {
mean+=array_scan(vectors);
nrofaverages++;
}
} while (vectors->message==ARRAY_CONTINUE);
mean/=nrofaverages;
array_previousvector(vectors);
do {
array_write(vectors, READ_ELEMENT(vectors)-mean);
} while (vectors->message==ARRAY_CONTINUE);
} while (vectors->message!=ARRAY_ENDOFSCAN);
}
/*}}} */
/*{{{ Orthogonalize vectors if requested*/
if (project_args->orthogonalize_vectors_first) {
array_make_orthogonal(vectors);
if (vectors->message==ARRAY_ERROR) {
ERREXIT(tinfo->emethods, "project_init: Error orthogonalizing projection vectors\n");
}
}
/*}}} */
if (!args[ARGS_NONORMALIZATION].is_set) {
/*{{{ Normalize vectors*/
do {
DATATYPE length=0.0;
do {
if (project_args->channel_list!=NULL && !is_in_channellist(vectors->current_element+1, project_args->channel_list)) {
array_advance(vectors);
} else {
const DATATYPE hold=array_scan(vectors);
length+=hold*hold;
}
} while (vectors->message==ARRAY_CONTINUE);
length=sqrt(length);
array_previousvector(vectors);
if (length==0.0) {
ERREXIT1(tinfo->emethods, "project_init: Vector %d has zero length !\n", MSGPARM(vectors->current_vector));
}
array_scale(vectors, 1.0/length);
} while (vectors->message!=ARRAY_ENDOFSCAN);
/*}}} */
}
/*{{{ Dump vectors if requested*/
if (args[ARGS_DUMPVECTORS].is_set) {
FILE * const fp=fopen(args[ARGS_DUMPVECTORS].arg.s, "w");
if (fp==NULL) {
ERREXIT1(tinfo->emethods, "project_init: Error opening output file >%s<.\n", MSGPARM(args[ARGS_DUMPVECTORS].arg.s));
}
array_transpose(vectors); /* We want one vector to be one column */
array_dump(fp, vectors, ARRAY_MATLAB);
array_transpose(vectors);
fclose(fp);
}
/*}}} */
(*side_tinfo->methods->transform_exit)(side_tinfo);
free_methodmem(side_tinfo);
growing_buf_free(&buf);
tinfo->methods->init_done=TRUE;
}
LOCAL void noise_time(struct dipole_desc *dipole) {
double scale=((double)rand())/(RAND_MAX/2)-1;
do {
array_write(&dipole->dip_moment, array_scan(&dipole->initial_moment)*scale);
} while (dipole->dip_moment.message==ARRAY_CONTINUE);
}
void array_fill( array *arr, const void *src )
{
int i;
for ( i = 0; i < arr->length; i++ )
array_write( arr, i, src );
}
/*{{{ read_synamps_get_singlepoint(transform_info_ptr tinfo, array *toarray) {*/
LOCAL int
read_synamps_get_singlepoint(transform_info_ptr tinfo, array *toarray) {
struct read_synamps_storage *local_arg=(struct read_synamps_storage *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
if (local_arg->current_point>=local_arg->EEG.NumSamples) return -1;
read_synamps_seek_point(tinfo, local_arg->current_point);
switch(local_arg->SubType) {
case NST_DCMES: {
/* DC-MES data is unsigned, and the marker channel is skipped: */
unsigned short *pdata=(unsigned short *)local_arg->buffer+local_arg->current_point-local_arg->first_point_in_buffer+1;
int channel=0;
do {
*pdata^=0x8000; /* Exclusive or to convert to signed... */
if (args[ARGS_NOBADCHANS].is_set && local_arg->Channels[channel].bad) {
toarray->message=ARRAY_CONTINUE;
} else {
array_write(toarray, NEUROSCAN_CONVSHORT(&local_arg->Channels[channel], *((signed short *)pdata)));
}
pdata+=local_arg->EEG.ChannelOffset/local_arg->bytes_per_sample;
channel++;
} while (toarray->message==ARRAY_CONTINUE);
}
break;
case NST_CONT0:
case NST_CONTINUOUS:
case NST_SYNAMPS: {
int channel=0;
do {
DATATYPE val;
if (args[ARGS_NOBADCHANS].is_set && local_arg->Channels[channel].bad) {
toarray->message=ARRAY_CONTINUE;
} else {
if (local_arg->bytes_per_sample==2) {
int16_t * const pdata=((int16_t *)local_arg->buffer)+local_arg->current_point-local_arg->first_point_in_buffer+channel;
# ifndef LITTLE_ENDIAN
Intel_int16(pdata);
# endif
val=NEUROSCAN_CONVSHORT(&local_arg->Channels[channel],*pdata);
} else if (local_arg->bytes_per_sample==4) {
int32_t * const pdata=((int32_t *)local_arg->buffer)+local_arg->current_point-local_arg->first_point_in_buffer+channel;
# ifndef LITTLE_ENDIAN
Intel_int32(pdata);
# endif
val=NEUROSCAN_CONVSHORT(&local_arg->Channels[channel],*pdata);
} else {
ERREXIT(tinfo->emethods, "read_synamps: Unknown bytes_per_sample\n");
}
array_write(toarray, val);
}
channel++;
} while (toarray->message==ARRAY_CONTINUE);
}
break;
default:
ERREXIT1(tinfo->emethods, "read_synamps_get_singlepoint: Format `%s' is not yet supported\n", MSGPARM(neuroscan_subtype_names[local_arg->SubType]));
break;
}
local_arg->current_point++;
return 0;
}
/*{{{ normalize_channelbox(transform_info_ptr tinfo) {*/
METHODDEF DATATYPE *
normalize_channelbox(transform_info_ptr tinfo) {
struct normalize_channelbox_storage *local_arg=(struct normalize_channelbox_storage *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
transform_info_ptr const tinfoptr=tinfo;
int channel, xmaxchan, xminchan, ymaxchan, yminchan, zmaxchan, zminchan;
DATATYPE value, value2, xmax, ymax, zmax, xmin, ymin, zmin, xmid, ymid, zmid;
DATATYPE tval[9];
double phi;
array myarray, t;
local_arg->view_from_left=FALSE;
/*{{{ Construct array myarray*/
myarray.start=(DATATYPE *)tinfoptr->probepos;
myarray.nr_of_elements=3;
myarray.nr_of_vectors=tinfoptr->nr_of_channels;
myarray.vector_skip=3;
myarray.element_skip=1;
array_setreadwrite_double(&myarray);
/*}}} */
/*{{{ Swap x and y if data set is 'Roma' (x=left->right)*/
if (strncmp(tinfo->comment, "Roma ", 5)==0) {
/* This is the trace that vp2mfx leaves in Roma files. Though generality
* lacks, this seems unavoidable in this module */
array_reset(&myarray);
do {
value=array_scan(&myarray);
value2=array_scan(&myarray);
myarray.current_element=0;
array_write(&myarray, value2);
array_write(&myarray, -value);
array_advance(&myarray);
} while (myarray.message!=ARRAY_ENDOFSCAN);
}
/*}}} */
/*{{{ Find min and max values of the box*/
array_reset(&myarray);
xmax=xmin=array_scan(&myarray);
ymax=ymin=array_scan(&myarray);
zmax=zmin=array_scan(&myarray);
xmaxchan=xminchan=ymaxchan=yminchan=zmaxchan=zminchan=0;
channel=1;
do {
value=array_scan(&myarray);
if (value>xmax) { xmax=value; xmaxchan=channel; }
if (value<xmin) { xmin=value; xminchan=channel; }
value=array_scan(&myarray);
if (value>ymax) { ymax=value; ymaxchan=channel; }
if (value<ymin) { ymin=value; yminchan=channel; }
value=array_scan(&myarray);
if (value>zmax) { zmax=value; zmaxchan=channel; }
if (value<zmin) { zmin=value; zminchan=channel; }
channel++;
} while (myarray.message!=ARRAY_ENDOFSCAN);
# ifdef DEBUG
printf("zmaxchan=%s, xmaxchan=%s\n", tinfoptr->channelnames[zmaxchan], tinfoptr->channelnames[xmaxchan]);
# endif
/*}}} */
/*{{{ Subtract midpoint*/
xmid=(xmax+xmin)/2; ymid=(ymax+ymin)/2; zmid=(zmax+zmin)/2;
# ifdef DEBUG
printf("xmid=%g, ymid=%g, zmid=%g\n", xmid, ymid, zmid);
# endif
array_reset(&myarray);
do {
array_write(&myarray, READ_ELEMENT(&myarray)-xmid);
array_write(&myarray, READ_ELEMENT(&myarray)-ymid);
array_write(&myarray, READ_ELEMENT(&myarray)-zmid);
} while (myarray.message!=ARRAY_ENDOFSCAN);
/*}}} */
/*{{{ Construct array t to be used for rotations*/
t.start=tval;
t.nr_of_elements=3;
t.nr_of_vectors=3;
t.element_skip=1;
t.vector_skip=3;
array_setreadwrite(&t);
/*}}} */
/*{{{ rotate zmaxchan about the x axis by its angle to the y axis (maximize y)*/
/* By this rotation, the z component of zmaxchan is removed. */
array_reset(&t);
myarray.current_vector=zmaxchan;
myarray.current_element=1;
value=array_scan(&myarray); /* y value */
value2=READ_ELEMENT(&myarray); /* z value */
value/=sqrt(value*value+value2*value2);
phi=(value2>0 ? -acos(value) : acos(value));
# ifdef DEBUG
printf("z=%g, cos phi=%g=%g, phi=%g\n", value2, value, cos(phi), phi);
# endif
array_write(&t, 1.0);
array_write(&t, 0.0);
array_write(&t, 0.0);
array_write(&t, 0.0);
array_write(&t, cos(phi));
array_write(&t, sin(phi));
array_write(&t, 0.0);
array_write(&t, -sin(phi));
array_write(&t, cos(phi));
array_transpose(&t);
array_reset(&myarray);
do {
DATATYPE x, y, z;
x=array_multiply(&t, &myarray, MULT_SAMESIZE);
y=array_multiply(&t, &myarray, MULT_SAMESIZE);
z=array_multiply(&t, &myarray, MULT_SAMESIZE);
array_previousvector(&myarray);
array_write(&myarray, x);
array_write(&myarray, y);
array_write(&myarray, z);
} while (myarray.message!=ARRAY_ENDOFSCAN);
/*}}} */
/*{{{ rotate zmaxchan about the z axis by its angle to the y axis (maximize y)*/
/* Now remove the x component of zmaxchan. Coordinates should be 0, z, 0 */
array_reset(&t);
myarray.current_element=0;
myarray.current_vector=zmaxchan;
value2=array_scan(&myarray); /* x value */
value=READ_ELEMENT(&myarray); /* y value */
value/=sqrt(value*value+value2*value2);
phi=(value2>0 ? -acos(value) : acos(value));
# ifdef DEBUG
printf("z=%g, cos phi=%g=%g, phi=%g\n", value2, value, cos(phi), phi);
# endif
array_write(&t, cos(phi));
array_write(&t, sin(phi));
array_write(&t, 0.0);
array_write(&t, -sin(phi));
array_write(&t, cos(phi));
array_write(&t, 0.0);
array_write(&t, 0.0);
array_write(&t, 0.0);
array_write(&t, 1.0);
if (value2<0.0) array_transpose(&t);
array_reset(&myarray);
do {
DATATYPE x, y, z;
x=array_multiply(&t, &myarray, MULT_SAMESIZE);
y=array_multiply(&t, &myarray, MULT_SAMESIZE);
z=array_multiply(&t, &myarray, MULT_SAMESIZE);
array_previousvector(&myarray);
array_write(&myarray, x);
array_write(&myarray, y);
array_write(&myarray, z);
} while (myarray.message!=ARRAY_ENDOFSCAN);
/*}}} */
/*{{{ rotate xmaxchan about the y axis by its angle to the x axis (maximize x)*/
/* This is the only rotation that will leave zmaxchan at its position */
array_reset(&t);
myarray.current_element=0;
myarray.current_vector=(args[ARGS_DECIDE_LEFTRIGHT].is_set && ymid>0.0 ? local_arg->view_from_left=TRUE,xminchan : xmaxchan);
value=array_scan(&myarray); /* x value */
array_advance(&myarray);
value2=READ_ELEMENT(&myarray); /* z value */
value/=sqrt(value*value+value2*value2);
phi=(value2>0 ? -acos(value) : acos(value));
# ifdef DEBUG
printf("z=%g, cos phi=%g=%g, phi=%g\n", value2, value, cos(phi), phi);
# endif
array_write(&t, cos(phi));
array_write(&t, 0.0);
array_write(&t, -sin(phi));
array_write(&t, 0.0);
array_write(&t, 1.0);
array_write(&t, 0.0);
array_write(&t, sin(phi));
array_write(&t, 0.0);
array_write(&t, cos(phi));
if (value2<0.0) array_transpose(&t);
array_reset(&myarray);
do {
DATATYPE x, y, z;
x=array_multiply(&t, &myarray, MULT_SAMESIZE);
y=array_multiply(&t, &myarray, MULT_SAMESIZE);
z=array_multiply(&t, &myarray, MULT_SAMESIZE);
array_previousvector(&myarray);
array_write(&myarray, x);
array_write(&myarray, y);
array_write(&myarray, z);
} while (myarray.message!=ARRAY_ENDOFSCAN);
/*}}} */
return tinfo->tsdata;
}
/*{{{ trim(transform_info_ptr tinfo) {*/
METHODDEF DATATYPE *
trim(transform_info_ptr tinfo) {
struct trim_storage *local_arg=(struct trim_storage *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
int item, shift, nrofshifts=1;
long nr_of_input_ranges,nr_of_ranges;
long output_points;
long rangeno, current_output_point=0;
const Bool collapse=args[ARGS_COLLAPSE].is_set || args[ARGS_COLLAPSE_Q].is_set;
const DATATYPE collapse_quantile=(args[ARGS_COLLAPSE].is_set&&args[ARGS_COLLAPSE].arg.i==COLLAPSE_BY_MEDIAN ? 0.5 : (args[ARGS_COLLAPSE_Q].is_set ? args[ARGS_COLLAPSE_Q].arg.d/100.0 : 0.0));
array myarray, newarray;
DATATYPE *oldtsdata;
DATATYPE *new_xdata=NULL;
growing_buf ranges, tokenbuf;
growing_buf triggers;
growing_buf_init(&ranges);
growing_buf_init(&tokenbuf);
growing_buf_init(&triggers);
if (tinfo->data_type==FREQ_DATA) {
tinfo->nr_of_points=tinfo->nroffreq;
nrofshifts=tinfo->nrofshifts;
}
/*{{{ Parse the ranges argument */
nr_of_input_ranges=growing_buf_count_tokens(&local_arg->rangearg);
if (nr_of_input_ranges<=0 || nr_of_input_ranges%2!=0) {
ERREXIT(tinfo->emethods, "trim: Need an even number of arguments >=2\n");
}
nr_of_input_ranges/=2;
output_points=0;
growing_buf_allocate(&ranges, 0);
growing_buf_allocate(&tokenbuf, 0);
growing_buf_get_firsttoken(&local_arg->rangearg,&tokenbuf);
while (tokenbuf.current_length>0) {
struct range thisrange;
if (args[ARGS_USE_CHANNEL].is_set) {
int const channel=find_channel_number(tinfo,args[ARGS_USE_CHANNEL].arg.s);
if (channel>=0) {
DATATYPE const minval=get_value(tokenbuf.buffer_start, NULL);
growing_buf_get_nexttoken(&local_arg->rangearg,&tokenbuf);
DATATYPE const maxval=get_value(tokenbuf.buffer_start, NULL);
array indata;
tinfo_array(tinfo, &indata);
indata.current_vector=channel;
thisrange.offset= -1; /* Marks no start recorded yet */
do {
DATATYPE const currval=indata.read_element(&indata);
if (currval>=minval && currval<=maxval) {
if (thisrange.offset== -1) {
thisrange.offset=indata.current_element;
thisrange.length= 1;
} else {
thisrange.length++;
}
} else {
if (thisrange.offset!= -1) {
growing_buf_append(&ranges, (char *)&thisrange, sizeof(struct range));
output_points+=(collapse ? 1 : thisrange.length);
thisrange.offset= -1;
}
}
array_advance(&indata);
} while (indata.message==ARRAY_CONTINUE);
if (thisrange.offset!= -1) {
growing_buf_append(&ranges, (char *)&thisrange, sizeof(struct range));
output_points+=(collapse ? 1 : thisrange.length);
}
} else {
ERREXIT1(tinfo->emethods, "set xdata_from_channel: Unknown channel name >%s<\n", MSGPARM(args[ARGS_USE_CHANNEL].arg.s));
}
} else {
if (args[ARGS_USE_XVALUES].is_set) {
if (tinfo->xdata==NULL) create_xaxis(tinfo, NULL);
thisrange.offset=decode_xpoint(tinfo, tokenbuf.buffer_start);
growing_buf_get_nexttoken(&local_arg->rangearg,&tokenbuf);
thisrange.length=decode_xpoint(tinfo, tokenbuf.buffer_start)-thisrange.offset+1;
} else {
thisrange.offset=gettimeslice(tinfo, tokenbuf.buffer_start);
growing_buf_get_nexttoken(&local_arg->rangearg,&tokenbuf);
thisrange.length=gettimeslice(tinfo, tokenbuf.buffer_start);
if (thisrange.length==0) {
thisrange.length=tinfo->nr_of_points-thisrange.offset;
}
}
if (thisrange.length<=0) {
ERREXIT1(tinfo->emethods, "trim: length is %d but must be >0.\n", MSGPARM(thisrange.length));
}
growing_buf_append(&ranges, (char *)&thisrange, sizeof(struct range));
output_points+=(collapse ? 1 : thisrange.length);
}
growing_buf_get_nexttoken(&local_arg->rangearg,&tokenbuf);
}
/*}}} */
nr_of_ranges=ranges.current_length/sizeof(struct range);
if (nr_of_ranges==0) {
TRACEMS(tinfo->emethods, 0, "trim: No valid ranges selected, rejecting epoch.\n");
return NULL;
}
TRACEMS2(tinfo->emethods, 1, "trim: nr_of_ranges=%ld, output_points=%ld\n", MSGPARM(nr_of_ranges), MSGPARM(output_points));
newarray.nr_of_vectors=tinfo->nr_of_channels*nrofshifts;
newarray.nr_of_elements=output_points;
newarray.element_skip=tinfo->itemsize;
if (array_allocate(&newarray)==NULL) {
ERREXIT(tinfo->emethods, "trim: Error allocating memory.\n");
}
oldtsdata=tinfo->tsdata;
if (tinfo->xdata!=NULL) {
/* Store xchannelname at the end of xdata, as in create_xaxis(); otherwise we'll have
* a problem after free()'ing xdata... */
new_xdata=(DATATYPE *)malloc(output_points*sizeof(DATATYPE)+strlen(tinfo->xchannelname)+1);
if (new_xdata==NULL) {
ERREXIT(tinfo->emethods, "trim: Error allocating xdata memory.\n");
}
}
if (tinfo->triggers.buffer_start!=NULL) {
struct trigger trig= *(struct trigger *)tinfo->triggers.buffer_start;
growing_buf_allocate(&triggers, 0);
/* Record the file position... */
if (collapse) {
/* Make triggers in subsequent append() work as expected at least with
* continuous reading */
trig.position=local_arg->current_epoch*nr_of_ranges;
trig.code= -1;
}
growing_buf_append(&triggers, (char *)&trig, sizeof(struct trigger));
}
for (rangeno=0; rangeno<nr_of_ranges; rangeno++) {
struct range *rangep=((struct range *)(ranges.buffer_start))+rangeno;
long const old_startpoint=(rangep->offset>0 ? rangep->offset : 0);
long const new_startpoint=(rangep->offset<0 ? -rangep->offset : 0);
/*{{{ Transfer the data*/
if (old_startpoint<tinfo->nr_of_points
/* Skip this explicitly if no "real" point needs copying (length confined within negative offset)
* since otherwise an endless loop can result as the stop conditions below look at the array
* states and no array is touched... */
&& new_startpoint<rangep->length)
for (item=0; item<tinfo->itemsize; item++) {
array_use_item(&newarray, item);
for (shift=0; shift<nrofshifts; shift++) {
tinfo_array(tinfo, &myarray);
array_use_item(&myarray, item);
do {
DATATYPE sum=0.0;
long reached_length=new_startpoint;
myarray.current_element= old_startpoint;
if (collapse) {
newarray.current_element=current_output_point;
newarray.message=ARRAY_CONTINUE; /* Otherwise the loop below may finish promptly... */
if (args[ARGS_COLLAPSE].is_set)
switch (args[ARGS_COLLAPSE].arg.i) {
case COLLAPSE_BY_HIGHEST:
sum= -FLT_MAX;
break;
case COLLAPSE_BY_LOWEST:
sum= FLT_MAX;
break;
default:
break;
}
} else {
newarray.current_element=current_output_point+new_startpoint;
}
if (collapse && collapse_quantile>0.0) {
array helparray=myarray;
helparray.ringstart=ARRAY_ELEMENT(&myarray);
helparray.current_element=helparray.current_vector=0;
helparray.nr_of_vectors=1;
helparray.nr_of_elements=rangep->length;
sum=array_quantile(&helparray,collapse_quantile);
myarray.message=ARRAY_CONTINUE;
} else
do {
if (reached_length>=rangep->length) break;
if (args[ARGS_COLLAPSE].is_set) {
DATATYPE const hold=array_scan(&myarray);
switch (args[ARGS_COLLAPSE].arg.i) {
case COLLAPSE_BY_SUMMATION:
case COLLAPSE_BY_AVERAGING:
sum+=hold;
break;
case COLLAPSE_BY_HIGHEST:
if (hold>sum) sum=hold;
break;
case COLLAPSE_BY_LOWEST:
if (hold<sum) sum=hold;
break;
default:
break;
}
} else {
array_write(&newarray, array_scan(&myarray));
}
reached_length++;
} while (newarray.message==ARRAY_CONTINUE && myarray.message==ARRAY_CONTINUE);
if (collapse) {
if (args[ARGS_COLLAPSE].is_set && args[ARGS_COLLAPSE].arg.i==COLLAPSE_BY_AVERAGING && item<tinfo->itemsize-tinfo->leaveright) sum/=reached_length;
array_write(&newarray, sum);
}
if (newarray.message==ARRAY_CONTINUE) {
array_nextvector(&newarray);
}
if (myarray.message==ARRAY_CONTINUE) {
array_nextvector(&myarray);
}
} while (myarray.message==ARRAY_ENDOFVECTOR);
tinfo->tsdata+=myarray.nr_of_vectors*myarray.nr_of_elements*myarray.element_skip;
}
tinfo->tsdata=oldtsdata;
}
/*}}} */
if (new_xdata!=NULL) {
/*{{{ Transfer xdata*/
DATATYPE sum=0.0;
long reached_length=new_startpoint;
long point, newpoint;
if (collapse) {
newpoint=current_output_point;
} else {
newpoint=current_output_point+new_startpoint;
}
for (point=old_startpoint;
point<tinfo->nr_of_points && reached_length<rangep->length;
point++) {
if (collapse) {
sum+=tinfo->xdata[point];
} else {
new_xdata[newpoint]=tinfo->xdata[point];
newpoint++;
}
reached_length++;
}
if (collapse) {
/* Summation of x axis values does not appear to make sense, so we always average: */
new_xdata[newpoint]=sum/reached_length;
}
/*}}} */
/* Save xchannelname to the end of new_xdata */
strcpy((char *)(new_xdata+output_points),tinfo->xchannelname);
}
if (tinfo->triggers.buffer_start!=NULL) {
/* Collect triggers... */
struct trigger *intrig=(struct trigger *)tinfo->triggers.buffer_start+1;
while (intrig->code!=0) {
if (intrig->position>=old_startpoint && intrig->position<old_startpoint+rangep->length) {
struct trigger trig= *intrig;
if (collapse) {
trig.position=current_output_point;
} else {
trig.position=intrig->position-old_startpoint+current_output_point;
}
growing_buf_append(&triggers, (char *)&trig, sizeof(struct trigger));
}
intrig++;
}
}
current_output_point+=(collapse ? 1 : rangep->length);
}
if (new_xdata!=NULL) {
free(tinfo->xdata);
tinfo->xdata=new_xdata;
tinfo->xchannelname=(char *)(new_xdata+output_points);
}
if (tinfo->triggers.buffer_start!=NULL) {
struct trigger trig;
/* Write end marker */
trig.position=0;
trig.code=0;
growing_buf_append(&triggers, (char *)&trig, sizeof(struct trigger));
growing_buf_free(&tinfo->triggers);
tinfo->triggers=triggers;
}
tinfo->multiplexed=FALSE;
tinfo->nr_of_points=output_points;
if (tinfo->data_type==FREQ_DATA) {
tinfo->nroffreq=tinfo->nr_of_points;
} else {
tinfo->beforetrig-=((struct range *)(ranges.buffer_start))->offset;
tinfo->aftertrig=output_points-tinfo->beforetrig;
}
tinfo->length_of_output_region=tinfo->nr_of_points*tinfo->nr_of_channels*tinfo->itemsize*nrofshifts;
local_arg->current_epoch++;
growing_buf_free(&tokenbuf);
growing_buf_free(&ranges);
return newarray.start;
}
int main(int argc, char *argv[]) {
int i=1, start=0, end=0, freqno;
DATATYPE *new_tsdata, hold;
array D;
OPT_DTYPE ax, bx, cx, fa, fb, fc, xmin, sumsq, weight, sumweight, ave, min_power, optimize_arg, *points;
optimize_struct ostruct;
struct minfunc_struct mfs;
struct transform_info_struct firsttinfo;
transform_info_ptr tinfo, tinfo_next;
struct transform_methods_struct methods[2];
struct external_methods_struct emethod;
tinfo= &firsttinfo;
/*{{{ Process command line*/
while (*argv[1]=='-') {
switch (argv[1][1]) {
}
argv++; argc--;
}
if (argc!=3) {
fprintf(stderr, "Usage: %s ascdatafile outfile\n"
, argv[0]);
return 1;
}
if (start<0) start=0;
if (end<=0) end=start;
/*}}} */
clear_external_methods(&emethod);
firsttinfo.methods= methods;
firsttinfo.emethods= &emethod;
/*{{{ Read all data sets*/
select_readasc(tinfo);
(*tinfo->methods->transform_defaults)(tinfo);
firsttinfo.filename=argv[1];
firsttinfo.epochs= -1; firsttinfo.fromepoch=1;
(*tinfo->methods->transform_init)(tinfo);
if (start!=0) {
while (i<start) {
(*tinfo->methods->transform)(tinfo);
i++;
}
}
while ((end==0 || i<=end) && (*tinfo->methods->transform)(tinfo)!=NULL) {
if ((tinfo_next=malloc(sizeof(struct transform_info_struct)))==NULL) {
ERREXIT(&emethod, "similarity: Error malloc'ing tinfo struct\n");
}
*(tinfo_next)=firsttinfo;
tinfo_next->previous=tinfo;
tinfo_next->next=NULL;
tinfo->next=tinfo_next;
tinfo=tinfo_next;
i++;
}
/* The last tinfo structure was allocated in vein, throw away */
tinfo=tinfo->previous;
free(tinfo->next);
tinfo->next=NULL;
(*firsttinfo.methods->transform_exit)(&firsttinfo);
/*}}} */
points=malloc(2*firsttinfo.nr_of_channels*sizeof(OPT_DTYPE));
for (freqno=0; freqno<firsttinfo.nr_of_channels; freqno++) {
/*{{{ Construct symmetrical function*/
sumweight=ave=0.0;
min_power=1e10;
for (i=0, tinfo= &firsttinfo; tinfo!=NULL; tinfo=tinfo->next, i++) {
tinfo_array(tinfo, &D);
array_transpose(&D);
array_reset(&D);
D.current_vector=freqno;
D.current_element=i;
hold=array_readelement(&D);
D.current_element=0;
do {
points[D.current_element*2]=100*channel_distance(tinfo, i, D.current_element);
points[D.current_element*2+1]=array_scan(&D)/hold;
} while (D.message==ARRAY_CONTINUE);
ostruct.function= &minfunc;
mfs.nr_of_points=firsttinfo.nr_of_channels;
mfs.points=points;
ostruct.fixed_args=(void *)&mfs;
ostruct.num_opt_args=1;
ostruct.opt_args=(void *)&optimize_arg;
ax=0.1; bx=12;
opt_mnbrak(&ostruct, &ax, &bx, &cx, &fa, &fb, &fc);
sumsq=opt_brent(&ostruct, ax, bx, cx, 1e-4, &xmin);
# ifdef VERBOSE
printf("%d %g %g %g\n", i, xmin, sumsq, hold);
# endif
weight= 1.0/sumsq;
sumweight+=weight;
ave+=weight*xmin;
if (hold<min_power) min_power=hold;
}
ave/=sumweight;
# ifdef VERBOSE
printf("Consensus: %g %g\n", ave, min_power);
# endif
/*}}} */
/*{{{ Subtract symmetrical function*/
for (i=0, tinfo= &firsttinfo; tinfo!=NULL; tinfo=tinfo->next, i++) {
tinfo_array(tinfo, &D);
array_transpose(&D);
array_reset(&D);
D.current_vector=freqno;
D.current_element=0;
do {
hold= min_power*distfun(100*channel_distance(tinfo, i, D.current_element), ave);
array_write(&D, array_readelement(&D)-hold);
} while (D.message==ARRAY_CONTINUE);
}
/*}}} */
}
free(points);
/*{{{ Write all data sets*/
tinfo= &firsttinfo;
select_extract_item(tinfo); /* Output real part only */
(*tinfo->methods->transform_defaults)(tinfo);
tinfo->methods->local_storage=(void *)0;
(*tinfo->methods->transform_init)(tinfo);
tinfo->methods++;
select_writeasc(tinfo);
(*tinfo->methods->transform_defaults)(tinfo);
tinfo->outfname=argv[2];
tinfo->methods->local_storage=(void *)1;
(*tinfo->methods->transform_init)(tinfo);
for (; tinfo!=NULL; tinfo=tinfo->next) {
tinfo->outfptr=firsttinfo.outfptr;
tinfo->methods=methods;
if ((new_tsdata=(*tinfo->methods->transform)(tinfo))==NULL) {
ERREXIT(tinfo->emethods, "extract_item failed !\n");
}
free(tinfo->tsdata);
tinfo->tsdata=new_tsdata;
tinfo->methods++;
(*tinfo->methods->transform)(tinfo);
}
tinfo= &firsttinfo;
tinfo->methods=methods;
(*tinfo->methods->transform_exit)(tinfo);
tinfo->methods++;
(*tinfo->methods->transform_exit)(tinfo);
/*}}} */
return 0;
}
