/* This function has all the knowledge about events in the various file types */
LOCAL void
read_neurofile_build_trigbuffer(transform_info_ptr tinfo) {
struct read_neurofile_storage *local_arg=(struct read_neurofile_storage *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
if (local_arg->triggers.buffer_start==NULL) {
growing_buf_allocate(&local_arg->triggers, 0);
} else {
growing_buf_clear(&local_arg->triggers);
}
if (args[ARGS_TRIGFILE].is_set) {
FILE * const triggerfile=(strcmp(args[ARGS_TRIGFILE].arg.s,"stdin")==0 ? stdin : fopen(args[ARGS_TRIGFILE].arg.s, "r"));
TRACEMS(tinfo->emethods, 1, "read_neurofile_build_trigbuffer: Reading event file\n");
if (triggerfile==NULL) {
ERREXIT1(tinfo->emethods, "read_neurofile_build_trigbuffer: Can't open trigger file >%s<\n", MSGPARM(args[ARGS_TRIGFILE].arg.s));
}
while (TRUE) {
long trigpoint;
char *description;
int const code=read_trigger_from_trigfile(triggerfile, tinfo->sfreq, &trigpoint, &description);
if (code==0) break;
push_trigger(&local_arg->triggers, trigpoint, code, description);
free_pointer((void **)&description);
}
if (triggerfile!=stdin) fclose(triggerfile);
} else {
TRACEMS(tinfo->emethods, 0, "read_neurofile_build_trigbuffer: No trigger source known.\n");
}
}
get_soi (j_decompress_ptr cinfo)
/* Process an SOI marker */
{
int i;
TRACEMS(cinfo, 1, JTRC_SOI);
if (cinfo->marker->saw_SOI)
ERREXIT(cinfo, JERR_SOI_DUPLICATE);
/* Reset all parameters that are defined to be reset by SOI */
for (i = 0; i < NUM_ARITH_TBLS; i++) {
cinfo->arith_dc_L[i] = 0;
cinfo->arith_dc_U[i] = 1;
cinfo->arith_ac_K[i] = 5;
}
cinfo->restart_interval = 0;
/* Set initial assumptions for colorspace etc */
cinfo->jpeg_color_space = JCS_UNKNOWN;
cinfo->CCIR601_sampling = FALSE; /* Assume non-CCIR sampling??? */
cinfo->saw_JFIF_marker = FALSE;
cinfo->density_unit = 0; /* set default JFIF APP0 values */
cinfo->X_density = 1;
cinfo->Y_density = 1;
cinfo->saw_Adobe_marker = FALSE;
cinfo->Adobe_transform = 0;
cinfo->marker->saw_SOI = TRUE;
return TRUE;
}
/* MDMSE: Process marked section end.
Issue an error if no marked section had started.
*/
int mdmse()
{
int retcode = 0; /* Return code: 0=same parse; 1=cancel special. */
if (mslevel) --mslevel;
else sgmlerr(26, (struct parse *)0, (UNCH *)0, (UNCH *)0);
if (msplevel) if (--msplevel==0) retcode = 1;
TRACEMS(0, retcode, mslevel, msplevel);
return retcode;
}
/*{{{ echo(transform_info_ptr tinfo) {*/
METHODDEF DATATYPE *
echo(transform_info_ptr tinfo) {
struct echo_storage *local_arg=(struct echo_storage *)tinfo->methods->local_storage;
if (local_arg->outfile==NULL) {
TRACEMS(tinfo->emethods, -1, local_arg->buf.buffer_start);
} else {
fputs(local_arg->buf.buffer_start, local_arg->outfile);
}
if (local_arg->outfile!=NULL) fflush(local_arg->outfile);
return tinfo->tsdata;
}
/*{{{ write_rec(transform_info_ptr tinfo) {*/
METHODDEF DATATYPE *
write_rec(transform_info_ptr tinfo) {
struct write_rec_storage *local_arg=(struct write_rec_storage *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
FILE *outfptr=local_arg->outfptr;
short *inbuf;
array myarray;
if (tinfo->itemsize!=1) {
ERREXIT(tinfo->emethods, "write_rec: Only itemsize=1 is supported.\n");
}
if (args[ARGS_CLOSE].is_set) {
write_rec_open_file(tinfo);
outfptr=local_arg->outfptr;
}
/*{{{ Write epoch*/
tinfo_array(tinfo, &myarray);
/* We read the data point by point, i.e. channels fastest */
array_transpose(&myarray);
/* Within the record, writing is non-interlaced, ie points fastest */
do {
do {
inbuf=local_arg->outbuf+local_arg->samples_per_record*myarray.current_element+local_arg->current_sample;
*inbuf= (short int)rint(array_scan(&myarray)/local_arg->resolution);
if (!local_arg->overflow_has_occurred && (*inbuf<local_arg->digmin || *inbuf>local_arg->digmax)) {
TRACEMS(tinfo->emethods, 0, "write_rec: Some output values exceed digitization bits!\n");
local_arg->overflow_has_occurred=TRUE;
}
#ifndef LITTLE_ENDIAN
Intel_int16(inbuf);
#endif
} while (myarray.message==ARRAY_CONTINUE);
if (++local_arg->current_sample>=local_arg->samples_per_record) {
if ((int)fwrite(local_arg->outbuf, sizeof(short), tinfo->nr_of_channels*local_arg->samples_per_record, outfptr)!=tinfo->nr_of_channels*local_arg->samples_per_record) {
ERREXIT(tinfo->emethods, "write_rec: Write error on data file.\n");
}
/* If nr_of_records was -1 (can only happen while appending),
* leave it that way */
if (local_arg->nr_of_records>=0) local_arg->nr_of_records++;
local_arg->current_sample=0L;
}
} while (myarray.message!=ARRAY_ENDOFSCAN);
/*}}} */
if (args[ARGS_CLOSE].is_set) write_rec_close_file(tinfo);
return tinfo->tsdata; /* Simply to return something `useful' */
}
/*{{{ subtract_init(transform_info_ptr tinfo)*/
METHODDEF void
subtract_init(transform_info_ptr tinfo) {
struct subtract_storage *local_arg=(struct subtract_storage *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
transform_info_ptr side_tinfo= &local_arg->side_tinfo;
local_arg->ttest=args[ARGS_TTEST].is_set;
if (args[ARGS_LEAVE_TPARAMETERS].is_set && !local_arg->ttest) {
TRACEMS(tinfo->emethods, 0, "subtract_init: Option -u given without -t. Adding -t...\n");
local_arg->ttest=TRUE;
}
if (args[ARGS_TYPE].is_set) {
local_arg->type=(enum subtract_types)args[ARGS_TYPE].arg.i;
} else {
local_arg->type=SUBTRACT_TYPE_SUBTRACT;
}
if (local_arg->type!=SUBTRACT_TYPE_SUBTRACT && local_arg->ttest) {
ERREXIT(tinfo->emethods, "subtract_init: T-test is only useful in subtract mode.\n");
}
side_tinfo->emethods=tinfo->emethods;
side_tinfo->methods= &local_arg->side_method;
select_readasc(side_tinfo);
growing_buf_init(&local_arg->side_argbuf);
growing_buf_allocate(&local_arg->side_argbuf, 0);
if (args[ARGS_CLOSE].is_set) {
growing_buf_appendstring(&local_arg->side_argbuf, "-c ");
}
if (args[ARGS_FROMEPOCH].is_set) {
#define BUFFER_SIZE 80
char buffer[BUFFER_SIZE];
snprintf(buffer, BUFFER_SIZE, "-f %ld ", args[ARGS_FROMEPOCH].arg.i);
growing_buf_appendstring(&local_arg->side_argbuf, buffer);
}
growing_buf_appendstring(&local_arg->side_argbuf, args[ARGS_SUBTRACTFILE].arg.s);
if (!local_arg->side_argbuf.can_be_freed || !setup_method(side_tinfo, &local_arg->side_argbuf)) {
ERREXIT(tinfo->emethods, "subtract_init: Error setting readasc arguments.\n");
}
(*side_tinfo->methods->transform_init)(side_tinfo);
side_tinfo->tsdata=NULL; /* We still have to fetch the data... */
tinfo->methods->init_done=TRUE;
}
GLOBAL void
jopen_backing_store (backing_store_ptr info, long total_bytes_needed)
{
char tracemsg[TEMP_NAME_LENGTH+40];
select_file_name(info->temp_name);
if ((info->temp_file = fopen(info->temp_name, RW_BINARY)) == NULL) {
/* hack to get around ERREXIT's inability to handle string parameters */
sprintf(tracemsg, "Failed to create temporary file %s", info->temp_name);
ERREXIT(methods, tracemsg);
}
info->read_backing_store = read_backing_store;
info->write_backing_store = write_backing_store;
info->close_backing_store = close_backing_store;
/* hack to get around TRACEMS' inability to handle string parameters */
sprintf(tracemsg, "Using temp file %s", info->temp_name);
TRACEMS(methods, 1, tracemsg);
}
/* MDMS: Process marked section start.
If already in special parse, bump the level counters and return
without parsing the declaration.
*/
struct parse *mdms(UNCH *tbuf, /* Work area for tokenization [NAMELEN+2]. */
struct parse *pcb) /* Parse control block for this parse. */
{
int key; /* Index of keyword in mslist. */
int ptype; /* Parameter token type. */
int pcbcode = 0; /* Parse code: 0=same; 2-4 per defines. */
if (++mslevel>TAGLVL) {
--mslevel;
sgmlerr(27, (struct parse *)0, ntoa(TAGLVL), (UNCH *)0);
}
/* If already in IGNORE mode, return without parsing parameters. */
if (msplevel) {++msplevel; return(pcb);}
parmno = 0; /* No parameters as yet. */
mdessv = es; /* Save es for checking entity nesting. */
pcbmd.newstate = pcbmdtk; /* First separator is optional. */
/* PARAMETERS: TEMP, RCDATA, CDATA, IGNORE, INCLUDE, or MDS. */
while ((ptype = parsemd(tbuf, NAMECASE, &pcblitp, NAMELEN))==NAS){
if ((key = mapsrch(mstab, tbuf+1))==0) {
sgmlerr(64, (struct parse *)0, ntoa(parmno), tbuf+1);
continue;
}
if (key==MSTEMP) continue; /* TEMP: for documentation. */
msplevel = 1; /* Special parse required. */
if (key>pcbcode) pcbcode = key; /* Update if higher priority. */
}
if (ptype!=MDS) {
NEWCC; /* Syntax error did REPEATCC. */
sgmlerr(97, (struct parse *)0, lex.m.dso, (UNCH *)0);
REPEATCC; /* 1st char of marked section. */
}
if (es!=mdessv) synerr(37, pcb);
TRACEMS(1, pcbcode, mslevel, msplevel);
if (pcbcode==MSIGNORE) pcb = &pcbmsi;
else if (pcbcode) {
pcb = pcbcode==MSCDATA ? &pcbmsc : (rcessv = es, &pcbmsrc);
}
return(pcb); /* Tell caller whether to change the parse. */
}
/*{{{ rereference_init(transform_info_ptr tinfo)*/
METHODDEF void
rereference_init(transform_info_ptr tinfo) {
struct rereference_args_struct *rereference_args=(struct rereference_args_struct *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
rereference_args->refchannel_numbers=expand_channel_list(tinfo, args[ARGS_REFCHANS].arg.s);
if (rereference_args->refchannel_numbers==NULL) {
ERREXIT(tinfo->emethods, "rereference_init: No reference channel was selected.\n");
}
if (args[ARGS_EXCLUDECHANS].is_set) {
rereference_args->excludechannel_numbers=expand_channel_list(tinfo, args[ARGS_EXCLUDECHANS].arg.s);
if (rereference_args->excludechannel_numbers==NULL) {
TRACEMS(tinfo->emethods, 0, "rereference_init: No exclude channels were actually selected!\n");
}
} else {
rereference_args->excludechannel_numbers=NULL;
}
tinfo->methods->init_done=TRUE;
}
/*{{{ get_mfxepoch(transform_info_ptr tinfo)*/
METHODDEF DATATYPE *
get_mfxepoch(transform_info_ptr tinfo) {
struct get_mfxepoch_storage *local_arg=(struct get_mfxepoch_storage *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
DATATYPE *newepoch;
int again=FALSE;
long epochlength;
if (local_arg->epochs--==0) return NULL;
do {
again=FALSE;
if ((newepoch=(DATATYPE *)mfx_getepoch(local_arg->fileptr, &epochlength, local_arg->beforetrig-local_arg->offset, local_arg->aftertrig+local_arg->offset, local_arg->trigname, args[ARGS_TRIGCODE].arg.i))==NULL) {
/* MFX_READERR4 is the normal end-of-file 'error' */
TRACEMS1(tinfo->emethods, (mfx_lasterr==MFX_READERR4 ? 1 : 0), "get_mfxepoch: mfx error >%s<\n", MSGPARM(mfx_errors[mfx_lasterr]));
/* If the error was due to the beforetrig time being too long, try to
* skip this epoch and try the next one */
if (mfx_lasterr==MFX_NEGSEEK) {
again=TRUE;
mfx_seektrigger(local_arg->fileptr, local_arg->trigname, args[ARGS_TRIGCODE].arg.i);
TRACEMS(tinfo->emethods, 1, "get_mfxepoch: Retrying...\n");
}
}
} while (again);
if (newepoch!=NULL) {
/* TOUCH TINFO ONLY IF GETEPOCH WAS SUCCESSFUL */
get_mfxinfo(local_arg->fileptr, tinfo);
tinfo->z_label=NULL;
tinfo->nr_of_points=epochlength;
tinfo->length_of_output_region=epochlength*tinfo->nr_of_channels;
tinfo->beforetrig=local_arg->beforetrig;
tinfo->aftertrig=tinfo->nr_of_points-tinfo->beforetrig;
tinfo->multiplexed=TRUE;
tinfo->sfreq=1.0/(local_arg->fileptr)->fileheader.sample_period;
tinfo->data_type=TIME_DATA;
tinfo->itemsize=1; /* Still, mfx doesn't support tuple data */
tinfo->leaveright=0;
tinfo->nrofaverages=1;
}
return newepoch;
}
LOCAL boolean
open_file_store (backing_store_ptr info, long total_bytes_needed)
{
short handle;
char tracemsg[TEMP_NAME_LENGTH+40];
select_file_name(info->temp_name);
if (jdos_open((short far *) & handle, (char far *) info->temp_name)) {
/* hack to get around TRACEMS' inability to handle string parameters */
sprintf(tracemsg, "Failed to create temporary file %s", info->temp_name);
ERREXIT(methods, tracemsg); /* jopen_backing_store will fail anyway */
return FALSE;
}
info->handle.file_handle = handle;
info->read_backing_store = read_file_store;
info->write_backing_store = write_file_store;
info->close_backing_store = close_file_store;
/* hack to get around TRACEMS' inability to handle string parameters */
sprintf(tracemsg, "Opened DOS file %d %s", handle, info->temp_name);
TRACEMS(methods, 1, tracemsg);
return TRUE; /* succeeded */
}
/*{{{ read_freiburg_init(transform_info_ptr tinfo) {*/
METHODDEF void
read_freiburg_init(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 stat statbuf;
/*{{{ Process options*/
local_arg->fromepoch=(args[ARGS_FROMEPOCH].is_set ? args[ARGS_FROMEPOCH].arg.i : 1);
local_arg->epochs=(args[ARGS_EPOCHS].is_set ? args[ARGS_EPOCHS].arg.i : -1);
/*}}} */
local_arg->channelnames=NULL;
local_arg->uV_per_bit=NULL;
growing_buf_init(&local_arg->segment_table); /* This sets buffer_start=NULL */
local_arg->nr_of_channels=0;
if (args[ARGS_CONTINUOUS].is_set) {
/*{{{ Open a continuous (sleep, Bernd Tritschler) file*/
FILE *infile;
local_arg->in_channels= &sleep_channels[0];
if (stat(args[ARGS_IFILE].arg.s, &statbuf)!= 0 || !S_ISREG(statbuf.st_mode)) {
/* File does not exist or isn't a regular file: Try BT format */
#ifdef __GNUC__
char co_name[strlen(args[ARGS_IFILE].arg.s)+4];
char coa_name[strlen(args[ARGS_IFILE].arg.s)+5];
#else
char co_name[MAX_PATHLEN];
char coa_name[MAX_PATHLEN];
#endif
char coa_buf[MAX_COALINE];
FILE *coafile;
strcpy(co_name, args[ARGS_IFILE].arg.s); strcat(co_name, ".co");
if((infile=fopen(co_name,"rb"))==NULL) {
ERREXIT1(tinfo->emethods, "read_freiburg_init: Can't open file %s\n", MSGPARM(co_name));
}
local_arg->infile=infile;
if (args[ARGS_REPAIR_OFFSET].is_set) {
fseek(infile, args[ARGS_REPAIR_OFFSET].arg.i, SEEK_SET);
} else {
if (read_struct((char *)&local_arg->btfile, sm_BT_file, infile)==0) {
ERREXIT1(tinfo->emethods, "read_freiburg_init: Header read error in file %s\n", MSGPARM(co_name));
}
# ifndef LITTLE_ENDIAN
change_byteorder((char *)&local_arg->btfile, sm_BT_file);
# endif
}
strcpy(coa_name, args[ARGS_IFILE].arg.s); strcat(coa_name, ".coa");
if((coafile=fopen(coa_name,"rb"))==NULL) {
TRACEMS1(tinfo->emethods, 0, "read_freiburg_init: No file %s found\n", MSGPARM(coa_name));
} else {
while (!feof(coafile)) {
Bool repeat;
fgets(coa_buf, MAX_COALINE-1, coafile);
do {
repeat=FALSE;
if (strncmp(coa_buf, "Channel_Table ", 14)==0) {
int havechannels=0, stringlength=0;
long tablepos=ftell(coafile);
char *innames;
while (!feof(coafile)) {
char *eol;
fgets(coa_buf, MAX_COALINE-1, coafile);
if (!isdigit(*coa_buf)) break;
if (strncmp(coa_buf, "0 0 ", 4)==0) {
/* Empty channel descriptors: Don't generate channelnames */
} else {
for (eol=coa_buf+strlen(coa_buf)-1; eol>=coa_buf && (*eol=='\n' || *eol=='\r'); eol--) *eol='\0';
/* This includes 1 for the zero at the end: */
stringlength+=strlen(strrchr(coa_buf, ' '));
}
havechannels++;
}
if (havechannels==0) continue; /* Channel table is unuseable */
local_arg->nr_of_channels=havechannels;
innames=NULL;
if ((stringlength!=0 &&
((local_arg->channelnames=(char **)malloc(havechannels*sizeof(char *)))==NULL ||
(innames=(char *)malloc(stringlength))==NULL)) ||
(local_arg->uV_per_bit=(float *)malloc(havechannels*sizeof(float)))==NULL) {
ERREXIT(tinfo->emethods, "read_freiburg_init: Error allocating .coa memory\n");
}
fseek(coafile, tablepos, SEEK_SET);
havechannels=0;
while (!feof(coafile)) {
char *eol;
fgets(coa_buf, MAX_COALINE-1, coafile);
if (!isdigit(*coa_buf)) break;
for (eol=coa_buf+strlen(coa_buf)-1; eol>=coa_buf && (*eol=='\n' || *eol=='\r'); eol--) *eol='\0';
if (innames!=NULL) {
strcpy(innames, strrchr(coa_buf, ' ')+1);
local_arg->channelnames[havechannels]=innames;
innames+=strlen(innames)+1;
}
/* The sensitivity in .coa files is given as nV/Bit */
local_arg->uV_per_bit[havechannels]=atoi(strchr(coa_buf, ' ')+1)/1000.0;
if (local_arg->uV_per_bit[havechannels]==0.0) {
local_arg->uV_per_bit[havechannels]=0.086;
TRACEMS1(tinfo->emethods, 1, "read_freiburg_init: Sensitivity for channel %d set to 86 nV/Bit\n", MSGPARM(havechannels));
}
havechannels++;
}
repeat=TRUE;
} else if (strncmp(coa_buf, SEGMENT_TABLE_STRING, strlen(SEGMENT_TABLE_STRING))==0) {
long current_offset=0;
char *inbuf=coa_buf;
Bool havesomething=FALSE;
growing_buf_allocate(&local_arg->segment_table, 0);
while (!feof(coafile)) {
int const nextchar=fgetc(coafile);
if (nextchar=='\r' || nextchar=='\n' || nextchar==' ') {
if (havesomething) {
*inbuf = '\0';
current_offset+=atoi(coa_buf);
growing_buf_append(&local_arg->segment_table, (char *)¤t_offset, sizeof(long));
inbuf=coa_buf;
havesomething=FALSE;
}
if (nextchar=='\n') break;
} else {
*inbuf++ = nextchar;
havesomething=TRUE;
}
}
repeat=FALSE;
}
} while (repeat);
}
fclose(coafile);
if (local_arg->uV_per_bit==NULL) {
TRACEMS1(tinfo->emethods, 0, "read_freiburg_init: No channel table found in file %s\n", MSGPARM(coa_name));
}
if (local_arg->segment_table.buffer_start==NULL) {
TRACEMS1(tinfo->emethods, 0, "read_freiburg_init: No segment table found in file %s\n", MSGPARM(coa_name));
}
/* Determine the exact number of points in file: Start with the previous
* segment and add the last segment. */
fstat(fileno(infile),&statbuf);
//printf("File size is %ld\n", statbuf.st_size);
//printf("Last segment (EOF) at %ld\n", ((long *)local_arg->segment_table.buffer_start)[local_arg->segment_table.current_length/sizeof(long)-1]);
while (local_arg->segment_table.current_length>=1 && ((long *)local_arg->segment_table.buffer_start)[local_arg->segment_table.current_length/sizeof(long)-1]>=statbuf.st_size) {
//printf("%ld - Removing last segment!\n", ((long *)local_arg->segment_table.buffer_start)[local_arg->segment_table.current_length/sizeof(long)-1]);
local_arg->segment_table.current_length--;
}
/* Size without the last segment */
tinfo->points_in_file=(local_arg->segment_table.current_length/sizeof(long)-1)*SEGMENT_LENGTH;
/* Count the points in the last segment */
{
array myarray;
int length_of_last_segment=0;
myarray.element_skip=tinfo->itemsize=1;
myarray.nr_of_vectors=1;
myarray.nr_of_elements=local_arg->nr_of_channels;
if (array_allocate(&myarray)==NULL) {
ERREXIT(tinfo->emethods, "read_freiburg_init: Error allocating myarray\n");
}
fseek(infile, ((long *)local_arg->segment_table.buffer_start)[local_arg->segment_table.current_length/sizeof(long)-1], SEEK_SET);
//printf("Seeking to %ld\n", ((long *)local_arg->segment_table.buffer_start)[local_arg->segment_table.current_length/sizeof(long)-1]);
tinfo->nr_of_channels=local_arg->nr_of_channels; /* This is used by freiburg_get_segment_init! */
freiburg_get_segment_init(tinfo);
while (freiburg_get_segment(tinfo, &myarray)==0) length_of_last_segment++;
freiburg_get_segment_free(tinfo);
tinfo->points_in_file+=length_of_last_segment;
TRACEMS1(tinfo->emethods, 1, "read_freiburg_init: Last segment has %ld points\n",length_of_last_segment);
array_free(&myarray);
}
}
if (local_arg->channelnames==NULL && local_arg->btfile.text[0]=='\0') {
local_arg->in_channels= &goeppi_channels[0];
TRACEMS(tinfo->emethods, 0, "read_freiburg_init: Assuming Goeppingen style setup!\n");
}
local_arg->continuous_type=SLEEP_BT_TYPE;
TRACEMS(tinfo->emethods, 1, "read_freiburg_init: Opened file in BT format\n");
} else {
if((infile=fopen(args[ARGS_IFILE].arg.s,"rb"))==NULL) {
ERREXIT1(tinfo->emethods, "read_freiburg_init: Can't open file %s\n", MSGPARM(args[ARGS_IFILE].arg.s));
}
if (args[ARGS_REPAIR_OFFSET].is_set) {
fseek(infile, args[ARGS_REPAIR_OFFSET].arg.i, SEEK_SET);
} else {
if (read_struct((char *)&local_arg->btfile, sm_BT_file, infile)==0) {
ERREXIT1(tinfo->emethods, "read_freiburg_init: Header read error in file %s\n", MSGPARM(args[ARGS_IFILE].arg.s));
}
# ifdef LITTLE_ENDIAN
change_byteorder((char *)&local_arg->btfile, sm_BT_file);
# endif
}
local_arg->continuous_type=SLEEP_KL_TYPE;
/* Year and day are swapped in KL format with respect to BT format... */
{short buf=local_arg->btfile.start_year; local_arg->btfile.start_year=local_arg->btfile.start_day; local_arg->btfile.start_day=buf;}
/* Well, sometimes or most of the time, in KL files the sampling interval
* was not set correctly... */
if (!args[ARGS_SFREQ].is_set && local_arg->btfile.sampling_interval_us!=9765 && local_arg->btfile.sampling_interval_us!=9766) {
TRACEMS1(tinfo->emethods, 0, "read_freiburg_init: sampling_interval_us was %d, corrected!\n", MSGPARM(local_arg->btfile.sampling_interval_us));
local_arg->btfile.sampling_interval_us=9766;
}
TRACEMS(tinfo->emethods, 1, "read_freiburg_init: Opened file in KL format\n");
}
if (args[ARGS_REPAIR_CHANNELS].is_set) local_arg->btfile.nr_of_channels=args[ARGS_REPAIR_CHANNELS].arg.i;
tinfo->nr_of_channels=local_arg->btfile.nr_of_channels;
if (tinfo->nr_of_channels<=0 || tinfo->nr_of_channels>MAX_NUMBER_OF_CHANNELS_IN_EP) {
ERREXIT1(tinfo->emethods, "read_freiburg_init: Impossible: %d channels?\n", MSGPARM(tinfo->nr_of_channels));
}
if (local_arg->nr_of_channels==0) {
local_arg->nr_of_channels=tinfo->nr_of_channels;
} else {
if (local_arg->nr_of_channels!=tinfo->nr_of_channels) {
ERREXIT2(tinfo->emethods, "read_freiburg_init: Setup has %d channels, but the file has %d!\n", MSGPARM(local_arg->nr_of_channels), MSGPARM(tinfo->nr_of_channels));
}
}
local_arg->sfreq=(args[ARGS_SFREQ].is_set ? args[ARGS_SFREQ].arg.d : 1.0e6/local_arg->btfile.sampling_interval_us);
tinfo->sfreq=local_arg->sfreq;
if (tinfo->sfreq<=0.0 || tinfo->sfreq>MAX_POSSIBLE_SFREQ) {
ERREXIT1(tinfo->emethods, "read_freiburg_init: Impossible: sfreq=%gHz?\n", MSGPARM(tinfo->sfreq));
}
/*{{{ Parse arguments that can be in seconds*/
tinfo->nr_of_points=gettimeslice(tinfo, args[ARGS_NCHANNELS].arg.s);
if (tinfo->nr_of_points<=0) {
/* Read the whole file as one epoch */
TRACEMS1(tinfo->emethods, 1, "read_freiburg_init: Reading %ld points\n",tinfo->points_in_file);
tinfo->nr_of_points=tinfo->points_in_file;
}
local_arg->offset=(args[ARGS_OFFSET].is_set ? gettimeslice(tinfo, args[ARGS_OFFSET].arg.s) : 0);
local_arg->epochlength=tinfo->nr_of_points;
/*}}} */
tinfo->beforetrig= -local_arg->offset;
tinfo->aftertrig=tinfo->nr_of_points+local_arg->offset;
/*}}} */
} else {
local_arg->in_channels= &freiburg_channels[0];
local_arg->current_trigger=0;
if (stat(args[ARGS_IFILE].arg.s, &statbuf)!=0) {
ERREXIT1(tinfo->emethods, "read_freiburg_init: Can't stat file %s\n", MSGPARM(args[ARGS_IFILE].arg.s));
}
local_arg->nr_of_channels=atoi(args[ARGS_NCHANNELS].arg.s);
/* average mode if the name does not belong to a directory */
local_arg->average_mode= !S_ISDIR(statbuf.st_mode);
tinfo->nr_of_channels=MAX_NUMBER_OF_CHANNELS_IN_EP;
}
freiburg_get_segment_init(tinfo);
local_arg->current_point=0;
tinfo->methods->init_done=TRUE;
}
/* This function has all the knowledge about events in the various file types */
LOCAL void
read_synamps_build_trigbuffer(transform_info_ptr tinfo) {
struct read_synamps_storage * const local_arg=(struct read_synamps_storage *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
if (local_arg->triggers.buffer_start==NULL) {
growing_buf_allocate(&local_arg->triggers, 0);
} else {
growing_buf_clear(&local_arg->triggers);
}
if (args[ARGS_TRIGFILE].is_set) {
FILE * const triggerfile=(strcmp(args[ARGS_TRIGFILE].arg.s,"stdin")==0 ? stdin : fopen(args[ARGS_TRIGFILE].arg.s, "r"));
TRACEMS(tinfo->emethods, 1, "read_synamps_build_trigbuffer: Reading event file\n");
if (triggerfile==NULL) {
ERREXIT1(tinfo->emethods, "read_synamps_build_trigbuffer: Can't open trigger file >%s<\n", MSGPARM(args[ARGS_TRIGFILE].arg.s));
}
while (TRUE) {
long trigpoint;
char *description;
int const code=read_trigger_from_trigfile(triggerfile, tinfo->sfreq, &trigpoint, &description);
if (code==0) break;
push_trigger(&local_arg->triggers, trigpoint, code, description);
free_pointer((void **)&description);
}
if (triggerfile!=stdin) fclose(triggerfile);
} else {
switch(local_arg->SubType) {
case NST_CONTINUOUS:
case NST_SYNAMPS: {
/*{{{ Read the events header and array*/
/* We handle errors through setting errormessage, because we want to continue
* with a warning if we are in continuous mode or read from an event file */
TEEG TagType;
EVENT2 event;
TRACEMS(tinfo->emethods, 1, "read_synamps_build_trigbuffer: Reading event table\n");
fseek(local_arg->SCAN,local_arg->EEG.EventTablePos,SEEK_SET);
/* Here we face two evils in one header: Coding enums as chars and
* allowing longs at odd addresses. Well... */
if (read_struct((char *)&TagType, sm_TEEG, local_arg->SCAN)==1) {
# ifndef LITTLE_ENDIAN
change_byteorder((char *)&TagType, sm_TEEG);
# endif
if (TagType.Teeg==TEEG_EVENT_TAB1 || TagType.Teeg==TEEG_EVENT_TAB2) {
/*{{{ Read the event table*/
struct_member * const sm_EVENT=(TagType.Teeg==TEEG_EVENT_TAB1 ? sm_EVENT1 : sm_EVENT2);
int ntags, tag;
ntags=TagType.Size/sm_EVENT[0].offset; /* sm_EVENT[0].offset is the size of the structure in file. */
for (tag=0; tag<ntags; tag++) {
long trigger_position=0;
int TrigVal=0, KeyPad=0, KeyBoard=0;
enum NEUROSCAN_ACCEPTVALUES Accept=(enum NEUROSCAN_ACCEPTVALUES)0;
if (read_struct((char *)&event, sm_EVENT, local_arg->SCAN)==0) {
ERREXIT(tinfo->emethods, "read_synamps_build_trigbuffer: Can't read an event table entry.\n");
break;
}
# ifndef LITTLE_ENDIAN
change_byteorder((char *)&event, sm_EVENT);
# endif
trigger_position=offset2point(tinfo,event.Offset);
TrigVal=event.StimType &0xff;
KeyBoard=event.KeyBoard&0xf;
KeyPad=Event_KeyPad_value(event);
Accept=Event_Accept_value(event);
if (!args[ARGS_NOREJECTED].is_set || Accept!=NAV_REJECT) {
read_synamps_push_keys(tinfo, trigger_position, TrigVal, KeyPad, KeyBoard, Accept);
}
}
/*}}} */
} else {
ERREXIT1(tinfo->emethods, "read_synamps_build_trigbuffer: Unknown tag type %d.\n", MSGPARM(TagType.Teeg));
}
} else {
ERREXIT(tinfo->emethods, "read_synamps_build_trigbuffer: Can't read the event table header.\n");
}
/*}}} */
}
break;
case NST_CONT0: {
/*{{{ CONT0: Two trailing marker channels*/
long current_triggerpoint=0;
unsigned short *pdata;
TRACEMS(tinfo->emethods, 1, "read_synamps_build_trigbuffer: Analyzing CONT0 marker channels\n");
while (current_triggerpoint<local_arg->EEG.NumSamples) {
int TrigVal=0, KeyPad=0, KeyBoard=0;
enum NEUROSCAN_ACCEPTVALUES Accept=(enum NEUROSCAN_ACCEPTVALUES)0;
read_synamps_seek_point(tinfo, current_triggerpoint);
pdata=(unsigned short *)local_arg->buffer+current_triggerpoint-local_arg->first_point_in_buffer+local_arg->nchannels;
TrigVal =pdata[0]&0xff;
KeyBoard=pdata[1]&0xf; if (KeyBoard>13) KeyBoard=0;
if (TrigVal!=0 || KeyBoard!=0) {
read_synamps_push_keys(tinfo, current_triggerpoint, TrigVal, KeyPad, KeyBoard, Accept);
current_triggerpoint++;
while (current_triggerpoint<local_arg->EEG.NumSamples) {
int This_TrigVal, This_KeyBoard;
read_synamps_seek_point(tinfo, current_triggerpoint);
pdata=(unsigned short *)local_arg->buffer+current_triggerpoint-local_arg->first_point_in_buffer+local_arg->nchannels;
This_TrigVal =pdata[0]&0xff;
This_KeyBoard=pdata[1]&0xf; if (This_KeyBoard>13) This_KeyBoard=0;
if (This_TrigVal!=TrigVal || This_KeyBoard!=KeyBoard) break;
current_triggerpoint++;
}
}
}
/*}}} */
}
break;
case NST_DCMES: {
/*{{{ DC-MES: Single, leading marker channel*/
long current_triggerpoint=0;
unsigned short *pdata;
TRACEMS(tinfo->emethods, 1, "read_synamps_build_trigbuffer: Analyzing DCMES marker channel\n");
while (current_triggerpoint<local_arg->EEG.NumSamples) {
int TrigVal=0, KeyPad=0, KeyBoard=0;
enum NEUROSCAN_ACCEPTVALUES Accept=(enum NEUROSCAN_ACCEPTVALUES)0;
read_synamps_seek_point(tinfo, current_triggerpoint);
pdata=(unsigned short *)local_arg->buffer+current_triggerpoint-local_arg->first_point_in_buffer;
TrigVal= *pdata&0xff;
KeyBoard=(*pdata>>8)&0xf; if (KeyBoard>13) KeyBoard=0;
if (TrigVal!=0 || KeyBoard!=0) {
read_synamps_push_keys(tinfo, current_triggerpoint, TrigVal, KeyPad, KeyBoard, Accept);
current_triggerpoint++;
while (current_triggerpoint<local_arg->EEG.NumSamples) {
int This_TrigVal, This_KeyBoard;
read_synamps_seek_point(tinfo, current_triggerpoint);
pdata=(unsigned short *)local_arg->buffer+current_triggerpoint-local_arg->first_point_in_buffer;
This_TrigVal= *pdata&0xff;
This_KeyBoard=(*pdata>>8)&0xf; if (This_KeyBoard>13) This_KeyBoard=0;
if (This_TrigVal!=TrigVal || This_KeyBoard!=KeyBoard) break;
current_triggerpoint++;
}
}
}
/*}}} */
}
break;
default:
break;
}
}
/*{{{ write_synamps_init(transform_info_ptr tinfo) {*/
METHODDEF void
write_synamps_init(transform_info_ptr tinfo) {
struct write_synamps_storage *local_arg=(struct write_synamps_storage *)tinfo->methods->local_storage;
transform_argument *args=tinfo->methods->arguments;
double xmin, xmax, ymin, ymax;
int NoOfChannels=tinfo->nr_of_channels;
int channel;
growing_buf_init(&local_arg->triggers);
local_arg->output_format=(args[ARGS_OUTPUTFORMAT].is_set ? (enum output_formats)args[ARGS_OUTPUTFORMAT].arg.i : FORMAT_EEGFILE);
local_arg->SCAN=fopen(args[ARGS_OFILE].arg.s, "r+b");
if (!args[ARGS_APPEND].is_set || local_arg->SCAN==NULL) { /* target does not exist*/
/*{{{ Create file*/
if (local_arg->SCAN!=NULL) fclose(local_arg->SCAN);
/*{{{ Calculate the span in x-y channel positions*/
xmin=ymin= FLT_MAX;
xmax=ymax= -FLT_MAX;
for (channel=0; channel<tinfo->nr_of_channels; channel++) {
const double this_x=tinfo->probepos[3*channel], this_y=tinfo->probepos[3*channel+1];
if (this_x>xmax) xmax=this_x;
if (this_x<xmin) xmin=this_x;
if (this_y>ymax) ymax=this_y;
if (this_y<ymin) ymin=this_y;
}
if (xmax==xmin) {
xmax+=0.5;
xmin-=0.5;
}
if (ymax==ymin) {
ymax+=0.5;
ymin-=0.5;
}
/*}}} */
if ((local_arg->SCAN=fopen(args[ARGS_OFILE].arg.s, "wb"))==NULL) {
ERREXIT1(tinfo->emethods, "write_synamps_init: Can't open %s\n", MSGPARM(args[ARGS_OFILE].arg.s));
}
/*{{{ Many settings, taken from example files...*/
strcpy(local_arg->EEG.rev, "Version 3.0");
local_arg->EEG.AdditionalFiles=local_arg->EEG.NextFile=local_arg->EEG.PrevFile=0;
switch (local_arg->output_format) {
case FORMAT_EEGFILE:
local_arg->EEG.review = 1;
local_arg->EEG.savemode=NSM_EEGF;
local_arg->EEG.type = NTY_EPOCHED;
local_arg->EEG.ContinousType=0;
local_arg->EEG.nsweeps=local_arg->EEG.compsweeps=local_arg->EEG.acceptcnt=0;
break;
case FORMAT_CNTFILE:
local_arg->EEG.review = 1;
local_arg->EEG.savemode=NSM_CONT;
local_arg->EEG.type = 0;
local_arg->EEG.ContinousType=NST_SYNAMPS-NST_CONT0;
local_arg->EEG.nsweeps=1;
local_arg->EEG.compsweeps=local_arg->EEG.acceptcnt=0;
break;
case FORMAT_AVGFILE:
local_arg->EEG.review = 0;
local_arg->EEG.savemode=NSM_AVGD;
local_arg->EEG.type = NTY_AVERAGED;
local_arg->EEG.ContinousType=0;
local_arg->EEG.nsweeps=local_arg->EEG.compsweeps=local_arg->EEG.acceptcnt=(tinfo->nrofaverages>0 ? tinfo->nrofaverages : 1);
break;
}
/* Since the comment can be of arbitrary length and thus also larger than the
* rest of the header, we should limit ourselves to the size of the id field */
strncpy(local_arg->EEG.id, tinfo->comment, sizeof(local_arg->EEG.id));
/* The date is coded in the comment, and read_synamps appends the date and time
* from the corresponding fields and the contents of the id field, so that
* the comment2time reader could be confused by the two date/time fields if we
* would not somehow invalidate remnants of the date field here... */
{char *slash;
while ((slash=strchr(local_arg->EEG.id, '/'))!=NULL) {
*slash='|';
}
}
strcpy(local_arg->EEG.oper, "Unspecified");
strcpy(local_arg->EEG.doctor, "Unspecified");
strcpy(local_arg->EEG.referral, "Unspecified");
strcpy(local_arg->EEG.hospital, "Unspecified");
strcpy(local_arg->EEG.patient, "Unspecified");
local_arg->EEG.age = 0;
local_arg->EEG.sex = 'U';
local_arg->EEG.hand = 'U';
strcpy(local_arg->EEG.med, "Unspecified");
strcpy(local_arg->EEG.category, "Unspecified");
strcpy(local_arg->EEG.state, "Unspecified");
strcpy(local_arg->EEG.label, "Unspecified");
{short dd, mm, yy, yyyy, hh, mi, ss;
if (comment2time(tinfo->comment, &dd, &mm, &yy, &yyyy, &hh, &mi, &ss)) {
char buffer[16]; /* Must be long enough to fit date (10) and time (12) +1 */
/* This is necessary because the date field was devised for 2-digit years.
* With 4-digit years it uses all 10 bytes and the trailing zero
* does not fit in any more. */
snprintf(buffer, 16, "%02d/%02d/%04d", mm, dd, yyyy);
strncpy(local_arg->EEG.date, buffer, sizeof(local_arg->EEG.date));
snprintf(buffer, 16, "%02d:%02d:%02d", hh, mi, ss);
strncpy(local_arg->EEG.time, buffer, sizeof(local_arg->EEG.time));
}
}
local_arg->EEG.rejectcnt = 0;
local_arg->EEG.pnts=(tinfo->data_type==FREQ_DATA ? tinfo->nroffreq : tinfo->nr_of_points);
local_arg->EEG.nchannels=NoOfChannels;
local_arg->EEG.avgupdate=1;
local_arg->EEG.domain=(tinfo->data_type==FREQ_DATA ? 1 : 0);
local_arg->EEG.variance=0;
local_arg->EEG.rate=(uint16_t)rint(tinfo->sfreq);
if (tinfo->data_type==FREQ_DATA) {
/* I know that this field is supposed to contain the taper window size in %,
but we need some way to store basefreq and 'rate' is only integer... */
local_arg->EEG.SpectWinLength=tinfo->basefreq;
}
if (local_arg->EEG.rate==0) {
local_arg->EEG.rate=1;
TRACEMS(tinfo->emethods, 0, "write_synamps_init: Rate was zero, corrected to 1!\n");
}
local_arg->EEG.scale=3.4375; /* This is a common sensitivity factor, used if sensitivities for channels are zero */
local_arg->EEG.veogcorrect=0;
local_arg->EEG.heogcorrect=0;
local_arg->EEG.aux1correct=0;
local_arg->EEG.aux2correct=0;
local_arg->EEG.veogtrig=15; /* Trigger threshold in percent of the maximum */
local_arg->EEG.heogtrig=10;
local_arg->EEG.aux1trig=10;
local_arg->EEG.aux2trig=10;
local_arg->EEG.veogchnl=find_channel_number(tinfo, "VEOG");
local_arg->EEG.heogchnl=find_channel_number(tinfo, "HEOG");
local_arg->EEG.veogdir=0; /* 0=positive, 1=negative */
local_arg->EEG.veog_n=10; /* "Number of points per waveform", really: minimum acceptable # averages */
local_arg->EEG.heog_n=10;
local_arg->EEG.veogmaxcnt=(int16_t)rint(0.3*tinfo->sfreq); /* "Number of observations per point", really: event window size in points */
local_arg->EEG.heogmaxcnt=(int16_t)rint(0.5*tinfo->sfreq);
local_arg->EEG.AmpSensitivity=10; /* External Amplifier gain */
local_arg->EEG.baseline=0;
local_arg->EEG.reject=0;
local_arg->EEG.trigtype=2; /* 2=Port */
local_arg->EEG.trigval=255; /* Hold */
local_arg->EEG.dir=0; /* Invert (negative up)=0 */
local_arg->EEG.dispmin= -1; /* displayed y range */
local_arg->EEG.dispmax= +1;
local_arg->EEG.DisplayXmin=local_arg->EEG.AutoMin=local_arg->EEG.rejstart=local_arg->EEG.offstart=local_arg->EEG.xmin= -tinfo->beforetrig/tinfo->sfreq;
local_arg->EEG.DisplayXmax=local_arg->EEG.AutoMax=local_arg->EEG.rejstop=local_arg->EEG.offstop=local_arg->EEG.xmax= tinfo->aftertrig/tinfo->sfreq;
local_arg->EEG.zmin=0.0;
local_arg->EEG.zmax=0.1;
strcpy(local_arg->EEG.ref, "A1-A2");
strcpy(local_arg->EEG.screen, "--------");
local_arg->EEG.CalMode=2;
local_arg->EEG.CalMethod=0;
local_arg->EEG.CalUpdate=1;
local_arg->EEG.CalBaseline=0;
local_arg->EEG.CalSweeps=5;
local_arg->EEG.CalAttenuator=1;
local_arg->EEG.CalPulseVolt=1;
local_arg->EEG.CalPulseStart=0;
local_arg->EEG.CalPulseStop=0;
local_arg->EEG.CalFreq=10;
strcpy(local_arg->EEG.taskfile, "--------");
strcpy(local_arg->EEG.seqfile, "--------"); /* Otherwise tries to read a seqfile */
local_arg->EEG.HeadGain=150;
local_arg->EEG.FspFValue=2.5;
local_arg->EEG.FspBlockSize=200;
local_arg->EEG.fratio=1.0;
local_arg->EEG.minor_rev=12; /* Necessary ! Otherwise a different file structure is assumed... */
local_arg->EEG.eegupdate=1;
local_arg->EEG.xscale=local_arg->EEG.yscale=0;
local_arg->EEG.xsize=40;
local_arg->EEG.ysize=20;
local_arg->EEG.ACmode=0;
local_arg->EEG.XScaleValue=XSCALEVALUE;
local_arg->EEG.XScaleInterval=XSCALEINTERVAL;
local_arg->EEG.YScaleValue=YSCALEVALUE;
local_arg->EEG.YScaleInterval=YSCALEINTERVAL;
local_arg->EEG.ScaleToolX1=20;
local_arg->EEG.ScaleToolY1=170;
local_arg->EEG.ScaleToolX2=23.1535;
local_arg->EEG.ScaleToolY2=153.87;
local_arg->EEG.port=715;
local_arg->EEG.NumSamples=0;
local_arg->EEG.FilterFlag=0;
local_arg->EEG.LowCutoff=4;
local_arg->EEG.LowPoles=2;
local_arg->EEG.HighCutoff=50;
local_arg->EEG.HighPoles=2;
local_arg->EEG.FilterType=3;
local_arg->EEG.FilterDomain=1;
local_arg->EEG.SnrFlag=0;
local_arg->EEG.CoherenceFlag=0;
local_arg->EEG.ContinousSeconds=4;
local_arg->EEG.ChannelOffset=sizeof(int16_t);
local_arg->EEG.AutoCorrectFlag=0;
local_arg->EEG.DCThreshold='F';
/*}}} */
/*{{{ Write SETUP structure*/
# ifndef LITTLE_ENDIAN
change_byteorder((char *)&local_arg->EEG, sm_SETUP);
# endif
write_struct((char *)&local_arg->EEG, sm_SETUP, local_arg->SCAN);
# ifndef LITTLE_ENDIAN
change_byteorder((char *)&local_arg->EEG, sm_SETUP);
# endif
/*}}} */
if ((local_arg->Channels=(ELECTLOC *)calloc(NoOfChannels,sizeof(ELECTLOC)))==NULL) {
ERREXIT(tinfo->emethods, "write_synamps_init: Error allocating Channels list\n");
}
for (channel=0; channel<NoOfChannels; channel++) {
/*{{{ Settings in the channel structure*/
strncpy(local_arg->Channels[channel].lab, tinfo->channelnames[channel],sizeof(local_arg->Channels[channel].lab));
local_arg->Channels[channel].reference=0;
local_arg->Channels[channel].skip=0;
local_arg->Channels[channel].reject=0;
local_arg->Channels[channel].display=1;
local_arg->Channels[channel].bad=0;
local_arg->Channels[channel].n=(local_arg->output_format==FORMAT_AVGFILE ? local_arg->EEG.acceptcnt : (local_arg->output_format==FORMAT_CNTFILE ? 0 : 1));
local_arg->Channels[channel].avg_reference=0;
local_arg->Channels[channel].ClipAdd=0;
local_arg->Channels[channel].x_coord= (tinfo->probepos[3*channel ]-xmin)/(xmax-xmin)*RANGE_TO_COVER+XOFFSET;
local_arg->Channels[channel].y_coord=((ymax-tinfo->probepos[3*channel+1])/(ymax-ymin)*RANGE_TO_COVER+YOFFSET)/3;
local_arg->Channels[channel].veog_wt=0;
local_arg->Channels[channel].veog_std=0;
local_arg->Channels[channel].heog_wt=0;
local_arg->Channels[channel].heog_std=0;
local_arg->Channels[channel].baseline=0;
local_arg->Channels[channel].Filtered=0;
local_arg->Channels[channel].sensitivity=204.8/args[ARGS_CONVFACTOR].arg.d; /* This arranges for conv_factor to act as the expected product before integer truncation */
local_arg->Channels[channel].Gain=5;
local_arg->Channels[channel].HiPass=0; /* 0=DC */
local_arg->Channels[channel].LoPass=4;
local_arg->Channels[channel].Page=0;
local_arg->Channels[channel].Size=0;
local_arg->Channels[channel].Impedance=0;
local_arg->Channels[channel].PhysicalChnl=channel; /* Channel mapping */
local_arg->Channels[channel].Rectify=0;
local_arg->Channels[channel].calib=1.0;
/*}}} */
/*{{{ Write ELECTLOC struct*/
# ifndef LITTLE_ENDIAN
change_byteorder((char *)&local_arg->Channels[channel], sm_ELECTLOC);
# endif
write_struct((char *)&local_arg->Channels[channel], sm_ELECTLOC, local_arg->SCAN);
# ifndef LITTLE_ENDIAN
change_byteorder((char *)&local_arg->Channels[channel], sm_ELECTLOC);
# endif
/*}}} */
}
local_arg->SizeofHeader = ftell(local_arg->SCAN);
TRACEMS2(tinfo->emethods, 1, "write_synamps_init: Creating file %s, format `%s'\n", MSGPARM(args[ARGS_OFILE].arg.s), MSGPARM(neuroscan_subtype_names[NEUROSCAN_SUBTYPE(&local_arg->EEG)]));
/*}}} */
} else {
/*{{{ Append to file*/
enum NEUROSCAN_SUBTYPES SubType;
if (read_struct((char *)&local_arg->EEG, sm_SETUP, local_arg->SCAN)==0) {
ERREXIT(tinfo->emethods, "write_synamps_init: Can't read file header.\n");
}
# ifndef LITTLE_ENDIAN
change_byteorder((char *)&local_arg->EEG, sm_SETUP);
# endif
NoOfChannels = local_arg->EEG.nchannels;
/*{{{ Allocate channel header*/
if ((local_arg->Channels=(ELECTLOC *)malloc(NoOfChannels*sizeof(ELECTLOC)))==NULL) {
ERREXIT(tinfo->emethods, "write_synamps_init: Error allocating Channels list\n");
}
/*}}} */
for (channel=0; channel<NoOfChannels; channel++) {
if (read_struct((char *)&local_arg->Channels[channel], sm_ELECTLOC, local_arg->SCAN)==0) {
ERREXIT(tinfo->emethods, "write_synamps_init: Can't read channel headers.\n");
}
# ifndef LITTLE_ENDIAN
change_byteorder((char *)&local_arg->Channels[channel], sm_ELECTLOC);
# endif
}
local_arg->SizeofHeader = ftell(local_arg->SCAN);
SubType=NEUROSCAN_SUBTYPE(&local_arg->EEG);
switch (SubType) {
case NST_EPOCHS:
if (local_arg->output_format!=FORMAT_EEGFILE) {
TRACEMS(tinfo->emethods, 0, "write_synamps_init: Appending to epoch file, discarding option -c\n");
local_arg->output_format=FORMAT_EEGFILE;
}
fseek(local_arg->SCAN, 0, SEEK_END);
break;
case NST_CONTINUOUS:
case NST_SYNAMPS: {
TEEG TagType;
EVENT1 event;
if (local_arg->output_format!=FORMAT_CNTFILE) {
TRACEMS(tinfo->emethods, 0, "write_synamps_init: Appending to continuous file, assuming option -c\n");
local_arg->output_format=FORMAT_CNTFILE;
}
fseek(local_arg->SCAN, local_arg->EEG.EventTablePos, SEEK_SET);
/* Here we face two evils in one header: Coding enums as chars and
* allowing longs at odd addresses. Well... */
if (1==read_struct((char *)&TagType, sm_TEEG, local_arg->SCAN)) {
# ifndef LITTLE_ENDIAN
change_byteorder((char *)&TagType, sm_TEEG);
# endif
if (TagType.Teeg==TEEG_EVENT_TAB1) {
/*{{{ Read the event table*/
int tag;
int const ntags=TagType.Size/sm_EVENT1[0].offset; /* sm_EVENT1[0].offset is sizeof(EVENT1) in the file. */
for (tag=0; tag<ntags; tag++) {
if (1!=read_struct((char *)&event, sm_EVENT1, local_arg->SCAN)) {
ERREXIT(tinfo->emethods, "write_synamps_init: Can't read an event table entry.\n");
break;
}
# ifndef LITTLE_ENDIAN
change_byteorder((char *)&event, sm_EVENT1);
# endif
{
int const TrigVal=event.StimType &0xff;
int const KeyBoard=event.KeyBoard&0xf;
int const KeyPad=Event_KeyPad_value(event);
int const Accept=Event_Accept_value(event);
int code=TrigVal-KeyPad+neuroscan_accept_translation[Accept];
if (code==0) {
code= -((KeyBoard+1)<<4);
}
push_trigger(&local_arg->triggers,offset2point(tinfo, event.Offset),code,NULL);
}
}
/*}}} */
} else {
ERREXIT(tinfo->emethods, "write_synamps_init: Type 2 events are not yet supported.\n");
}
} else {
ERREXIT(tinfo->emethods, "write_synamps_init: Can't read the event table header.\n");
}
fseek(local_arg->SCAN, local_arg->EEG.EventTablePos, SEEK_SET);
}
break;
default:
ERREXIT1(tinfo->emethods, "write_synamps: Cannot append to file type `%s'\n", MSGPARM(neuroscan_subtype_names[SubType]));
break;
}
/* Conformance to the incoming epochs is checked in write_synamps */
TRACEMS1(tinfo->emethods, 1, "write_synamps_init: Appending to file %s\n", MSGPARM(args[ARGS_OFILE].arg.s));
/*}}} */
}
tinfo->methods->init_done=TRUE;
}
jinit_downsampler( j_compress_ptr cinfo )
{
my_downsample_ptr downsample;
int ci;
jpeg_component_info *compptr;
boolean smoothok = TRUE;
int h_in_group, v_in_group, h_out_group, v_out_group;
downsample = ( my_downsample_ptr )
( *cinfo->mem->alloc_small )( ( j_common_ptr ) cinfo, JPOOL_IMAGE,
SIZEOF( my_downsampler ) );
cinfo->downsample = ( struct jpeg_downsampler * ) downsample;
downsample->pub.start_pass = start_pass_downsample;
downsample->pub.downsample = sep_downsample;
downsample->pub.need_context_rows = FALSE;
if( cinfo->CCIR601_sampling )
{
ERREXIT( cinfo, JERR_CCIR601_NOTIMPL );
}
/* Verify we can handle the sampling factors, and set up method pointers */
for( ci = 0, compptr = cinfo->comp_info; ci < cinfo->num_components;
ci++, compptr++ )
{
/* Compute size of an "output group" for DCT scaling. This many samples
* are to be converted from max_h_samp_factor * max_v_samp_factor pixels.
*/
h_out_group = ( compptr->h_samp_factor * compptr->DCT_h_scaled_size ) /
cinfo->min_DCT_h_scaled_size;
v_out_group = ( compptr->v_samp_factor * compptr->DCT_v_scaled_size ) /
cinfo->min_DCT_v_scaled_size;
h_in_group = cinfo->max_h_samp_factor;
v_in_group = cinfo->max_v_samp_factor;
downsample->rowgroup_height[ci] = v_out_group; /* save for use later */
if( h_in_group == h_out_group && v_in_group == v_out_group )
{
#ifdef INPUT_SMOOTHING_SUPPORTED
if( cinfo->smoothing_factor )
{
downsample->methods[ci] = fullsize_smooth_downsample;
downsample->pub.need_context_rows = TRUE;
}
else
#endif
downsample->methods[ci] = fullsize_downsample;
}
else if( h_in_group == h_out_group * 2 &&
v_in_group == v_out_group )
{
smoothok = FALSE;
downsample->methods[ci] = h2v1_downsample;
}
else if( h_in_group == h_out_group * 2 &&
v_in_group == v_out_group * 2 )
{
#ifdef INPUT_SMOOTHING_SUPPORTED
if( cinfo->smoothing_factor )
{
downsample->methods[ci] = h2v2_smooth_downsample;
downsample->pub.need_context_rows = TRUE;
}
else
#endif
downsample->methods[ci] = h2v2_downsample;
}
else if( ( h_in_group % h_out_group ) == 0 &&
( v_in_group % v_out_group ) == 0 )
{
smoothok = FALSE;
downsample->methods[ci] = int_downsample;
downsample->h_expand[ci] = ( UINT8 )( h_in_group / h_out_group );
downsample->v_expand[ci] = ( UINT8 )( v_in_group / v_out_group );
}
else
{
ERREXIT( cinfo, JERR_FRACT_SAMPLE_NOTIMPL );
}
}
#ifdef INPUT_SMOOTHING_SUPPORTED
if( cinfo->smoothing_factor && !smoothok )
{
TRACEMS( cinfo, 0, JTRC_SMOOTH_NOTIMPL );
}
#endif
}
GLOBAL void
jinit_downsampler(j_compress_ptr cinfo)
{
my_downsample_ptr downsample;
int ci;
jpeg_component_info *compptr;
boolean smoothok = TRUE;
downsample = (my_downsample_ptr)
(*cinfo->mem->alloc_small)((j_common_ptr) cinfo, JPOOL_IMAGE,
SIZEOF(my_downsampler));
cinfo->downsample = (struct jpeg_downsampler *) downsample;
downsample->pub.start_pass = start_pass_downsample;
downsample->pub.downsample = sep_downsample;
downsample->pub.need_context_rows = FALSE;
if(cinfo->CCIR601_sampling)
{
ERREXIT(cinfo, JERR_CCIR601_NOTIMPL);
}
/* Verify we can handle the sampling factors, and set up method pointers */
for(ci = 0, compptr = cinfo->comp_info; ci < cinfo->num_components;
ci++, compptr++)
{
if(compptr->h_samp_factor == cinfo->max_h_samp_factor &&
compptr->v_samp_factor == cinfo->max_v_samp_factor)
{
#ifdef INPUT_SMOOTHING_SUPPORTED
if(cinfo->smoothing_factor)
{
downsample->methods[ci] = fullsize_smooth_downsample;
downsample->pub.need_context_rows = TRUE;
}
else
#endif
downsample->methods[ci] = fullsize_downsample;
}
else if(compptr->h_samp_factor * 2 == cinfo->max_h_samp_factor &&
compptr->v_samp_factor == cinfo->max_v_samp_factor)
{
smoothok = FALSE;
downsample->methods[ci] = h2v1_downsample;
}
else if(compptr->h_samp_factor * 2 == cinfo->max_h_samp_factor &&
compptr->v_samp_factor * 2 == cinfo->max_v_samp_factor)
{
#ifdef INPUT_SMOOTHING_SUPPORTED
if(cinfo->smoothing_factor)
{
downsample->methods[ci] = h2v2_smooth_downsample;
downsample->pub.need_context_rows = TRUE;
}
else
#endif
downsample->methods[ci] = h2v2_downsample;
}
else if((cinfo->max_h_samp_factor % compptr->h_samp_factor) == 0 &&
(cinfo->max_v_samp_factor % compptr->v_samp_factor) == 0)
{
smoothok = FALSE;
downsample->methods[ci] = int_downsample;
}
else
{
ERREXIT(cinfo, JERR_FRACT_SAMPLE_NOTIMPL);
}
}
#ifdef INPUT_SMOOTHING_SUPPORTED
if(cinfo->smoothing_factor && !smoothok)
{
TRACEMS(cinfo, 0, JTRC_SMOOTH_NOTIMPL);
}
#endif
}
/*{{{ write_vitaport_exit(transform_info_ptr tinfo) {*/
METHODDEF void
write_vitaport_exit(transform_info_ptr tinfo) {
struct write_vitaport_storage *local_arg=(struct write_vitaport_storage *)tinfo->methods->local_storage;
int channel, NoOfChannels=local_arg->fileheader.knum;
long point;
long const channellen=local_arg->total_points*sizeof(uint16_t);
long const hdlen=local_arg->fileheader.hdlen;
uint16_t checksum=0;
local_arg->fileheaderII.dlen=hdlen+NoOfChannels*channellen;
/*{{{ Write the file headers*/
# ifdef LITTLE_ENDIAN
change_byteorder((char *)&local_arg->fileheader, sm_vitaport_fileheader);
change_byteorder((char *)&local_arg->fileheaderII, sm_vitaportII_fileheader);
change_byteorder((char *)&local_arg->fileext, sm_vitaportII_fileext);
# endif
write_struct((char *)&local_arg->fileheader, sm_vitaport_fileheader, local_arg->outfile);
write_struct((char *)&local_arg->fileheaderII, sm_vitaportII_fileheader, local_arg->outfile);
write_struct((char *)&local_arg->fileext, sm_vitaportII_fileext, local_arg->outfile);
/*}}} */
for (channel=0; channel<NoOfChannels; channel++) {
/*{{{ Write a channel header*/
/* This is the factor as we'd like to have it... */
float factor=((float)(local_arg->channelmax[channel]> -local_arg->channelmin[channel] ? local_arg->channelmax[channel] : -local_arg->channelmin[channel]))/SHRT_MAX;
if (strncmp(local_arg->channelheaders[channel].kname, VP_MARKERCHANNEL_NAME, 6)==0) {
strcpy(local_arg->channelheaders[channel].kunit, "mrk");
local_arg->channelheaders[channel].datype=VP_DATYPE_MARKER;
/* Since the marker channel is read without the conversion factors,
* set the conversion to 1.0 for this channel */
local_arg->channelheaders[channel].mulfac=local_arg->channelheaders[channel].divfac=1;
local_arg->channelheaders[channel].offset=0;
} else {
float const logdiff=log(factor)-TARGET_LOG_SHORTVAL;
local_arg->channelheaders[channel].offset=0;
if (logdiff<0) {
/*{{{ Factor is small: Better to fix divfac and calculate mulfac after that*/
double const divfac=exp(-logdiff);
if (divfac>SHRT_MAX) {
local_arg->channelheaders[channel].divfac=SHRT_MAX;
} else {
local_arg->channelheaders[channel].divfac=(unsigned short)divfac;
}
/* The +1 takes care that we never get below the `ideal' factor computed above. */
local_arg->channelheaders[channel].mulfac=(unsigned short)(factor*local_arg->channelheaders[channel].divfac+1);
if (local_arg->channelheaders[channel].mulfac==0) {
local_arg->channelheaders[channel].mulfac=1;
local_arg->channelheaders[channel].divfac=(unsigned short)(1.0/factor-1);
}
/*}}} */
} else {
/*{{{ Factor is large: Better to fix mulfac and calculate divfac after that*/
double const mulfac=exp(logdiff);
if (mulfac>SHRT_MAX) {
local_arg->channelheaders[channel].mulfac=SHRT_MAX;
} else {
local_arg->channelheaders[channel].mulfac=(unsigned short)mulfac;
}
/* The -1 takes care that we never get below the `ideal' factor computed above. */
local_arg->channelheaders[channel].divfac=(unsigned short)(local_arg->channelheaders[channel].mulfac/factor-1);
if (local_arg->channelheaders[channel].divfac==0) {
local_arg->channelheaders[channel].mulfac=(unsigned short)(factor+1);
local_arg->channelheaders[channel].divfac=1;
}
/*}}} */
}
}
/* Now see which factor we actually got constructed */
factor=((float)local_arg->channelheaders[channel].mulfac)/local_arg->channelheaders[channel].divfac;
local_arg->channelheadersII[channel].doffs=channel*channellen;
local_arg->channelheadersII[channel].dlen=channellen;
# ifdef LITTLE_ENDIAN
change_byteorder((char *)&local_arg->channelheaders[channel], sm_vitaport_channelheader);
change_byteorder((char *)&local_arg->channelheadersII[channel], sm_vitaportIIrchannelheader);
# endif
write_struct((char *)&local_arg->channelheaders[channel], sm_vitaport_channelheader, local_arg->outfile);
write_struct((char *)&local_arg->channelheadersII[channel], sm_vitaportIIrchannelheader, local_arg->outfile);
# ifdef LITTLE_ENDIAN
change_byteorder((char *)&local_arg->channelheaders[channel], sm_vitaport_channelheader);
change_byteorder((char *)&local_arg->channelheadersII[channel], sm_vitaportIIrchannelheader);
# endif
/*}}} */
}
fwrite(&checksum, sizeof(checksum), 1, local_arg->outfile);
TRACEMS(tinfo->emethods, 1, "write_vitaport_exit: Copying channels to output file...\n");
/* We close and re-open the channel file because buffering is much more
* efficient at least with DJGPP if the file is either only read or written */
fclose(local_arg->channelfile);
if ((local_arg->channelfile=fopen(local_arg->channelfilename, "rb"))==NULL) {
ERREXIT1(tinfo->emethods, "write_vitaport_exit: Can't open temp file %s\n", MSGPARM(local_arg->channelfilename));
}
for (channel=0; channel<NoOfChannels; channel++) {
/*{{{ Copy a channel to the target file */
float const factor=((float)local_arg->channelheaders[channel].mulfac)/local_arg->channelheaders[channel].divfac;
unsigned short const offset=local_arg->channelheaders[channel].offset;
for (point=0; point<local_arg->total_points; point++) {
DATATYPE dat;
int16_t s;
fseek(local_arg->channelfile, (point*NoOfChannels+channel)*sizeof(DATATYPE), SEEK_SET);
if (fread(&dat, sizeof(DATATYPE), 1, local_arg->channelfile)!=1) {
ERREXIT(tinfo->emethods, "write_vitaport_exit: Error reading temp file.\n");
}
s= (int16_t)rint(dat/factor)-offset;
# ifdef LITTLE_ENDIAN
Intel_int16((uint16_t *)&s);
# endif
if (fwrite(&s, sizeof(s), 1, local_arg->outfile)!=1) {
ERREXIT(tinfo->emethods, "write_vitaport_exit: Write error.\n");
}
}
/*}}} */
}
fclose(local_arg->channelfile);
unlink(local_arg->channelfilename);
if (local_arg->triggers.current_length!=0) {
long tagno, n_events;
uint32_t length, trigpoint;
int const nevents=local_arg->triggers.current_length/sizeof(struct trigger);
struct vitaport_idiotic_multiplemarkertablenames *markertable_entry;
/* Try to keep a security space of at least 20 free events */
for (markertable_entry=markertable_names; markertable_entry->markertable_name!=NULL && markertable_entry->idiotically_fixed_length<nevents+20; markertable_entry++);
if (markertable_entry->markertable_name==NULL) {
if ((markertable_entry-1)->idiotically_fixed_length<=nevents) {
/* Drop the requirement for at least 20 free events */
markertable_entry--;
} else {
/* No use... */
ERREXIT1(tinfo->emethods, "write_vitaport_exit: %d events wouldn't fit into the fixed-length VITAGRAPH marker tables!\nBlame the Vitaport people!\n", MSGPARM(nevents));
}
}
n_events=markertable_entry->idiotically_fixed_length;
fwrite(markertable_entry->markertable_name, 1, VP_TABLEVAR_LENGTH, local_arg->outfile);
length=n_events*sizeof(length);
#ifdef LITTLE_ENDIAN
Intel_int32((uint32_t *)&length);
#endif
fwrite(&length, sizeof(length), 1, local_arg->outfile);
for (tagno=0; tagno<n_events; tagno++) {
if (tagno<nevents) {
struct trigger * const intrig=((struct trigger *)local_arg->triggers.buffer_start)+tagno;
/* Trigger positions are given in ms units */
trigpoint=(long)rint(intrig->position*1000.0/local_arg->sfreq);
/* Make trigpoint uneven if code%2==1 */
trigpoint=trigpoint-trigpoint%2+(intrig->code-1)%2;
} else {
trigpoint= -1;
}
#ifdef LITTLE_ENDIAN
Intel_int32((uint32_t *)&trigpoint);
#endif
fwrite(&trigpoint, sizeof(trigpoint), 1, local_arg->outfile);
}
for (; tagno<n_events; tagno++) {
trigpoint= -1;
#ifdef LITTLE_ENDIAN
Intel_int32((uint32_t *)&trigpoint);
#endif
fwrite(&trigpoint, sizeof(trigpoint), 1, local_arg->outfile);
}
}
fclose(local_arg->outfile);
/*{{{ Free memory*/
free_pointer((void **)&local_arg->channelfilename);
free_pointer((void **)&local_arg->channelmax);
free_pointer((void **)&local_arg->channelmin);
free_pointer((void **)&local_arg->channelheaders);
free_pointer((void **)&local_arg->channelheadersII);
if (local_arg->triggers.buffer_start!=NULL) {
clear_triggers(&local_arg->triggers);
growing_buf_free(&local_arg->triggers);
}
/*}}} */
tinfo->methods->init_done=FALSE;
}
/*{{{ 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;
}
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;
}
