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edflib.c
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edflib.c
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/*
*****************************************************************************
*
* Copyright (c) 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018 Teunis van Beelen
* All rights reserved.
*
* email: teuniz@gmail.com
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY Teunis van Beelen ''AS IS'' AND ANY
* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL Teunis van Beelen BE LIABLE FOR ANY
* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*****************************************************************************
*/
/* compile with options "-D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE" */
#include "edflib.h"
#define EDFLIB_VERSION 113
#define EDFLIB_MAXFILES 64
#if defined(__APPLE__) || defined(__MACH__) || defined(__APPLE_CC__)
#define fopeno fopen
#else
#define fseeko fseeko64
#define ftello ftello64
#define fopeno fopen64
#endif
#ifdef _WIN32
#ifndef __MINGW32__
/* needed for visual c */
#undef fseeko
#define fseeko _fseeki64
#undef ftello
#define ftello _ftelli64
#undef fopeno
#define fopeno fopen
#endif
#endif
/* max size of annotationtext */
#define EDFLIB_WRITE_MAX_ANNOTATION_LEN 40
/* bytes in datarecord for EDF annotations, must be an integer multiple of three and two */
#define EDFLIB_ANNOTATION_BYTES 114
/* for writing only */
#define EDFLIB_MAX_ANNOTATION_CHANNELS 64
#define EDFLIB_ANNOT_MEMBLOCKSZ 1000
struct edfparamblock{
char label[17];
char transducer[81];
char physdimension[9];
double phys_min;
double phys_max;
int dig_min;
int dig_max;
char prefilter[81];
int smp_per_record;
char reserved[33];
double offset;
int buf_offset;
double bitvalue;
int annotation;
long long sample_pntr;
};
struct edfhdrblock{
FILE *file_hdl;
char path[1024];
int writemode;
char version[32];
char patient[81];
char recording[81];
char plus_patientcode[81];
char plus_gender[16];
char plus_birthdate[16];
char plus_patient_name[81];
char plus_patient_additional[81];
char plus_startdate[16];
char plus_admincode[81];
char plus_technician[81];
char plus_equipment[81];
char plus_recording_additional[81];
long long l_starttime;
int startdate_day;
int startdate_month;
int startdate_year;
int starttime_second;
int starttime_minute;
int starttime_hour;
char reserved[45];
int hdrsize;
int edfsignals;
long long datarecords;
int recordsize;
int annot_ch[EDFLIB_MAXSIGNALS];
int nr_annot_chns;
int mapped_signals[EDFLIB_MAXSIGNALS];
int edf;
int edfplus;
int bdf;
int bdfplus;
int discontinuous;
int signal_write_sequence_pos;
long long starttime_offset;
double data_record_duration;
long long long_data_record_duration;
int annots_in_file;
int annotlist_sz;
int total_annot_bytes;
int eq_sf;
char *wrbuf;
int wrbufsize;
struct edfparamblock *edfparam;
};
static struct edf_annotationblock{
long long onset;
char duration[16];
char annotation[EDFLIB_MAX_ANNOTATION_LEN + 1];
} *annotationslist[EDFLIB_MAXFILES];
static struct edf_write_annotationblock{
long long onset;
long long duration;
char annotation[EDFLIB_WRITE_MAX_ANNOTATION_LEN + 1];
} *write_annotationslist[EDFLIB_MAXFILES];
static int edf_files_open=0;
static struct edfhdrblock *hdrlist[EDFLIB_MAXFILES];
static struct edfhdrblock * edflib_check_edf_file(FILE *, int *);
static int edflib_is_integer_number(char *);
static int edflib_is_number(char *);
static long long edflib_get_long_duration(char *);
static int edflib_get_annotations(struct edfhdrblock *, int, int);
static int edflib_is_duration_number(char *);
static int edflib_is_onset_number(char *);
static long long edflib_get_long_time(char *);
static int edflib_write_edf_header(struct edfhdrblock *);
static void edflib_latin1_to_ascii(char *, int);
static void edflib_latin12utf8(char *, int);
static void edflib_remove_padding_trailing_spaces(char *);
static int edflib_atoi_nonlocalized(const char *);
static double edflib_atof_nonlocalized(const char *);
static int edflib_sprint_number_nonlocalized(char *, double);
/*
static int edflib_sprint_int_number_nonlocalized(char *, int, int, int);
*/
static int edflib_sprint_ll_number_nonlocalized(char *, long long, int, int);
static int edflib_fprint_int_number_nonlocalized(FILE *, int, int, int);
static int edflib_fprint_ll_number_nonlocalized(FILE *, long long, int, int);
static int edflib_write_tal(struct edfhdrblock *, FILE *);
int edflib_is_file_used(const char *path)
{
int i;
for(i=0; i<EDFLIB_MAXFILES; i++)
{
if(hdrlist[i]!=NULL)
{
if(!(strcmp(path, hdrlist[i]->path)))
{
return 1;
}
}
}
return 0;
}
int edflib_get_number_of_open_files()
{
return edf_files_open;
}
int edflib_get_handle(int file_number)
{
int i, file_count=0;
for(i=0; i<EDFLIB_MAXFILES; i++)
{
if(hdrlist[i]!=NULL)
{
if(file_count++ == file_number)
{
return i;
}
}
}
return -1;
}
int edfopen_file_readonly(const char *path, struct edf_hdr_struct *edfhdr, int read_annotations)
{
int i, j,
channel,
edf_error;
FILE *file;
struct edfhdrblock *hdr;
if(read_annotations<0)
{
edfhdr->filetype = EDFLIB_INVALID_READ_ANNOTS_VALUE;
return -1;
}
if(read_annotations>2)
{
edfhdr->filetype = EDFLIB_INVALID_READ_ANNOTS_VALUE;
return -1;
}
memset(edfhdr, 0, sizeof(struct edf_hdr_struct));
if(edf_files_open>=EDFLIB_MAXFILES)
{
edfhdr->filetype = EDFLIB_MAXFILES_REACHED;
return -1;
}
for(i=0; i<EDFLIB_MAXFILES; i++)
{
if(hdrlist[i]!=NULL)
{
if(!(strcmp(path, hdrlist[i]->path)))
{
edfhdr->filetype = EDFLIB_FILE_ALREADY_OPENED;
return -1;
}
}
}
file = fopeno(path, "rb");
if(file==NULL)
{
edfhdr->filetype = EDFLIB_NO_SUCH_FILE_OR_DIRECTORY;
return -1;
}
hdr = edflib_check_edf_file(file, &edf_error);
if(hdr==NULL)
{
edfhdr->filetype = edf_error;
fclose(file);
return -1;
}
if(hdr->discontinuous)
{
edfhdr->filetype = EDFLIB_FILE_IS_DISCONTINUOUS;
free(hdr->edfparam);
free(hdr);
fclose(file);
return -1;
}
hdr->writemode = 0;
for(i=0; i<EDFLIB_MAXFILES; i++)
{
if(hdrlist[i]==NULL)
{
hdrlist[i] = hdr;
edfhdr->handle = i;
break;
}
}
if((hdr->edf)&&(!(hdr->edfplus)))
{
edfhdr->filetype = EDFLIB_FILETYPE_EDF;
}
if(hdr->edfplus)
{
edfhdr->filetype = EDFLIB_FILETYPE_EDFPLUS;
}
if((hdr->bdf)&&(!(hdr->bdfplus)))
{
edfhdr->filetype = EDFLIB_FILETYPE_BDF;
}
if(hdr->bdfplus)
{
edfhdr->filetype = EDFLIB_FILETYPE_BDFPLUS;
}
edfhdr->edfsignals = hdr->edfsignals - hdr->nr_annot_chns;
edfhdr->file_duration = hdr->long_data_record_duration * hdr->datarecords;
edfhdr->startdate_day = hdr->startdate_day;
edfhdr->startdate_month = hdr->startdate_month;
edfhdr->startdate_year = hdr->startdate_year;
edfhdr->starttime_hour = hdr->starttime_hour;
edfhdr->starttime_second = hdr->starttime_second;
edfhdr->starttime_minute = hdr->starttime_minute;
edfhdr->starttime_subsecond = hdr->starttime_offset;
edfhdr->datarecords_in_file = hdr->datarecords;
edfhdr->datarecord_duration = hdr->long_data_record_duration;
annotationslist[edfhdr->handle] = NULL;
hdr->annotlist_sz = 0;
hdr->annots_in_file = 0;
edfhdr->annotations_in_file = 0LL;
if((!(hdr->edfplus))&&(!(hdr->bdfplus)))
{
strcpy(edfhdr->patient, hdr->patient);
strcpy(edfhdr->recording, hdr->recording);
edfhdr->patientcode[0] = 0;
edfhdr->gender[0] = 0;
edfhdr->birthdate[0] = 0;
edfhdr->patient_name[0] = 0;
edfhdr->patient_additional[0] = 0;
edfhdr->admincode[0] = 0;
edfhdr->technician[0] = 0;
edfhdr->equipment[0] = 0;
edfhdr->recording_additional[0] = 0;
}
else
{
edfhdr->patient[0] = 0;
edfhdr->recording[0] = 0;
strcpy(edfhdr->patientcode, hdr->plus_patientcode);
strcpy(edfhdr->gender, hdr->plus_gender);
strcpy(edfhdr->birthdate, hdr->plus_birthdate);
strcpy(edfhdr->patient_name, hdr->plus_patient_name);
strcpy(edfhdr->patient_additional, hdr->plus_patient_additional);
strcpy(edfhdr->admincode, hdr->plus_admincode);
strcpy(edfhdr->technician, hdr->plus_technician);
strcpy(edfhdr->equipment, hdr->plus_equipment);
strcpy(edfhdr->recording_additional, hdr->plus_recording_additional);
if((read_annotations==EDFLIB_READ_ANNOTATIONS)||(read_annotations==EDFLIB_READ_ALL_ANNOTATIONS))
{
if(edflib_get_annotations(hdr, edfhdr->handle, read_annotations))
{
edfhdr->filetype = EDFLIB_FILE_CONTAINS_FORMAT_ERRORS;
fclose(file);
free(hdr->edfparam);
hdr->edfparam = NULL;
free(hdr);
hdr = NULL;
hdrlist[edfhdr->handle] = NULL;
free(annotationslist[edfhdr->handle]);
annotationslist[edfhdr->handle] = NULL;
return -1;
}
}
edfhdr->annotations_in_file = hdr->annots_in_file;
}
strcpy(hdr->path, path);
edf_files_open++;
j = 0;
for(i=0; i<hdr->edfsignals; i++)
{
if(!(hdr->edfparam[i].annotation))
{
hdr->mapped_signals[j++] = i;
}
}
for(i=0; i<edfhdr->edfsignals; i++)
{
channel = hdr->mapped_signals[i];
strcpy(edfhdr->signalparam[i].label, hdr->edfparam[channel].label);
strcpy(edfhdr->signalparam[i].transducer, hdr->edfparam[channel].transducer);
strcpy(edfhdr->signalparam[i].physdimension, hdr->edfparam[channel].physdimension);
strcpy(edfhdr->signalparam[i].prefilter, hdr->edfparam[channel].prefilter);
edfhdr->signalparam[i].smp_in_file = hdr->edfparam[channel].smp_per_record * hdr->datarecords;
edfhdr->signalparam[i].phys_max = hdr->edfparam[channel].phys_max;
edfhdr->signalparam[i].phys_min = hdr->edfparam[channel].phys_min;
edfhdr->signalparam[i].dig_max = hdr->edfparam[channel].dig_max;
edfhdr->signalparam[i].dig_min = hdr->edfparam[channel].dig_min;
edfhdr->signalparam[i].smp_in_datarecord = hdr->edfparam[channel].smp_per_record;
}
return 0;
}
int edfclose_file(int handle)
{
struct edf_write_annotationblock *annot2;
int i, j, k, n, p, err,
datrecsize,
nmemb;
long long offset,
datarecords;
char str[EDFLIB_ANNOTATION_BYTES * 2];
struct edfhdrblock *hdr;
if(handle<0)
{
return -1;
}
if(handle>=EDFLIB_MAXFILES)
{
return -1;
}
if(hdrlist[handle]==NULL)
{
return -1;
}
hdr = hdrlist[handle];
if(hdr->writemode)
{
if(hdr->datarecords == 0LL)
{
err = edflib_write_edf_header(hdr);
if(err)
{
fclose(hdr->file_hdl);
free(hdr->edfparam);
free(hdr->wrbuf);
free(hdr);
hdrlist[handle] = NULL;
free(write_annotationslist[handle]);
write_annotationslist[handle] = NULL;
edf_files_open--;
return err;
}
for(k=0; k<hdr->annots_in_file; k++)
{
annot2 = write_annotationslist[handle] + k;
p = edflib_fprint_ll_number_nonlocalized(hdr->file_hdl, (hdr->datarecords * hdr->long_data_record_duration) / EDFLIB_TIME_DIMENSION, 0, 1);
if(hdr->long_data_record_duration % EDFLIB_TIME_DIMENSION)
{
fputc('.', hdr->file_hdl);
p++;
p += edflib_fprint_ll_number_nonlocalized(hdr->file_hdl, (hdr->datarecords * hdr->long_data_record_duration) % EDFLIB_TIME_DIMENSION, 7, 0);
}
fputc(20, hdr->file_hdl);
fputc(20, hdr->file_hdl);
p += 2;
for(; p<hdr->total_annot_bytes; p++)
{
fputc(0, hdr->file_hdl);
}
hdr->datarecords++;
}
}
if(hdr->datarecords<100000000LL)
{
fseeko(hdr->file_hdl, 236LL, SEEK_SET);
p = edflib_fprint_int_number_nonlocalized(hdr->file_hdl, (int)(hdr->datarecords), 0, 0);
if(p < 2)
{
fputc(' ', hdr->file_hdl);
}
}
datarecords = 0LL;
offset = (long long)((hdr->edfsignals + hdr->nr_annot_chns + 1) * 256);
datrecsize = hdr->total_annot_bytes;
for(i=0; i<hdr->edfsignals; i++)
{
if(hdr->edf)
{
offset += (long long)(hdr->edfparam[i].smp_per_record * 2);
datrecsize += (hdr->edfparam[i].smp_per_record * 2);
}
else
{
offset += (long long)(hdr->edfparam[i].smp_per_record * 3);
datrecsize += (hdr->edfparam[i].smp_per_record * 3);
}
}
j = 0;
for(k=0; k<hdr->annots_in_file; k++)
{
annot2 = write_annotationslist[handle] + k;
p = 0;
if(j==0) // first annotation signal
{
if(fseeko(hdr->file_hdl, offset, SEEK_SET))
{
break;
}
p += edflib_sprint_ll_number_nonlocalized(str, (datarecords * hdr->long_data_record_duration) / EDFLIB_TIME_DIMENSION, 0, 1);
if(hdr->long_data_record_duration % EDFLIB_TIME_DIMENSION)
{
str[p++] = '.';
n = edflib_sprint_ll_number_nonlocalized(str + p, (datarecords * hdr->long_data_record_duration) % EDFLIB_TIME_DIMENSION, 7, 0);
p += n;
}
str[p++] = 20;
str[p++] = 20;
str[p++] = 0;
}
n = edflib_sprint_ll_number_nonlocalized(str + p, annot2->onset / 10000LL, 0, 1);
p += n;
if(annot2->onset % 10000LL)
{
str[p++] = '.';
n = edflib_sprint_ll_number_nonlocalized(str + p, annot2->onset % 10000LL, 4, 0);
p += n;
}
if(annot2->duration>=0LL)
{
str[p++] = 21;
n = edflib_sprint_ll_number_nonlocalized(str + p, annot2->duration / 10000LL, 0, 0);
p += n;
if(annot2->duration % 10000LL)
{
str[p++] = '.';
n = edflib_sprint_ll_number_nonlocalized(str + p, annot2->duration % 10000LL, 4, 0);
p += n;
}
}
str[p++] = 20;
for(i=0; i<EDFLIB_WRITE_MAX_ANNOTATION_LEN; i++)
{
if(annot2->annotation[i]==0)
{
break;
}
str[p++] = annot2->annotation[i];
}
str[p++] = 20;
for(; p<EDFLIB_ANNOTATION_BYTES; p++)
{
str[p] = 0;
}
nmemb = fwrite(str, EDFLIB_ANNOTATION_BYTES, 1, hdr->file_hdl);
if(nmemb != 1)
{
break;
}
j++;
if(j >= hdr->nr_annot_chns)
{
j = 0;
offset += datrecsize;
datarecords++;
if(datarecords>=hdr->datarecords)
{
break;
}
}
}
free(write_annotationslist[handle]);
}
else
{
free(annotationslist[handle]);
}
fclose(hdr->file_hdl);
free(hdr->edfparam);
free(hdr->wrbuf);
free(hdr);
hdrlist[handle] = NULL;
edf_files_open--;
return 0;
}
long long edfseek(int handle, int edfsignal, long long offset, int whence)
{
long long smp_in_file;
int channel;
if(handle<0)
{
return -1;
}
if(handle>=EDFLIB_MAXFILES)
{
return -1;
}
if(hdrlist[handle]==NULL)
{
return -1;
}
if(edfsignal<0)
{
return -1;
}
if(hdrlist[handle]->writemode)
{
return -1;
}
if(edfsignal>=(hdrlist[handle]->edfsignals - hdrlist[handle]->nr_annot_chns))
{
return -1;
}
channel = hdrlist[handle]->mapped_signals[edfsignal];
smp_in_file = hdrlist[handle]->edfparam[channel].smp_per_record * hdrlist[handle]->datarecords;
if(whence==EDFSEEK_SET)
{
hdrlist[handle]->edfparam[channel].sample_pntr = offset;
}
if(whence==EDFSEEK_CUR)
{
hdrlist[handle]->edfparam[channel].sample_pntr += offset;
}
if(whence==EDFSEEK_END)
{
hdrlist[handle]->edfparam[channel].sample_pntr =
(hdrlist[handle]->edfparam[channel].smp_per_record * hdrlist[handle]->datarecords) + offset;
}
if(hdrlist[handle]->edfparam[channel].sample_pntr > smp_in_file)
{
hdrlist[handle]->edfparam[channel].sample_pntr = smp_in_file;
}
if(hdrlist[handle]->edfparam[channel].sample_pntr < 0LL)
{
hdrlist[handle]->edfparam[channel].sample_pntr = 0LL;
}
return hdrlist[handle]->edfparam[channel].sample_pntr;
}
long long edftell(int handle, int edfsignal)
{
int channel;
if(handle<0)
{
return -1;
}
if(handle>=EDFLIB_MAXFILES)
{
return -1;
}
if(hdrlist[handle]==NULL)
{
return -1;
}
if(edfsignal<0)
{
return -1;
}
if(hdrlist[handle]->writemode)
{
return -1;
}
if(edfsignal>=(hdrlist[handle]->edfsignals - hdrlist[handle]->nr_annot_chns))
{
return -1;
}
channel = hdrlist[handle]->mapped_signals[edfsignal];
return hdrlist[handle]->edfparam[channel].sample_pntr;
}
void edfrewind(int handle, int edfsignal)
{
int channel;
if(handle<0)
{
return;
}
if(handle>=EDFLIB_MAXFILES)
{
return;
}
if(hdrlist[handle]==NULL)
{
return;
}
if(edfsignal<0)
{
return;
}
if(hdrlist[handle]->writemode)
{
return;
}
if(edfsignal>=(hdrlist[handle]->edfsignals - hdrlist[handle]->nr_annot_chns))
{
return;
}
channel = hdrlist[handle]->mapped_signals[edfsignal];
hdrlist[handle]->edfparam[channel].sample_pntr = 0LL;
}
int edfread_physical_samples(int handle, int edfsignal, int n, double *buf)
{
int bytes_per_smpl=2,
tmp,
i,
channel;
double phys_bitvalue,
phys_offset;
long long smp_in_file,
offset,
sample_pntr,
smp_per_record,
jump;
struct edfhdrblock *hdr;
union {
unsigned int one;
signed int one_signed;
unsigned short two[2];
signed short two_signed[2];
unsigned char four[4];
} var;
FILE *file;
if(handle<0)
{
return -1;
}
if(handle>=EDFLIB_MAXFILES)
{
return -1;
}
if(hdrlist[handle]==NULL)
{
return -1;
}
if(edfsignal<0)
{
return -1;
}
if(hdrlist[handle]->writemode)
{
return -1;
}
if(edfsignal>=(hdrlist[handle]->edfsignals - hdrlist[handle]->nr_annot_chns))
{
return -1;
}
channel = hdrlist[handle]->mapped_signals[edfsignal];
if(n<0LL)
{
return -1;
}
if(n==0LL)
{
return 0LL;
}
hdr = hdrlist[handle];
if(hdr->edf)
{
bytes_per_smpl = 2;
}
if(hdr->bdf)
{
bytes_per_smpl = 3;
}
smp_in_file = hdr->edfparam[channel].smp_per_record * hdr->datarecords;
if((hdr->edfparam[channel].sample_pntr + n) > smp_in_file)
{
n = smp_in_file - hdr->edfparam[channel].sample_pntr;
if(n==0)
{
return 0LL;
}
if(n<0)
{
return -1;
}
}
file = hdr->file_hdl;
offset = hdr->hdrsize;
offset += (hdr->edfparam[channel].sample_pntr / hdr->edfparam[channel].smp_per_record) * hdr->recordsize;
offset += hdr->edfparam[channel].buf_offset;
offset += ((hdr->edfparam[channel].sample_pntr % hdr->edfparam[channel].smp_per_record) * bytes_per_smpl);
fseeko(file, offset, SEEK_SET);
sample_pntr = hdr->edfparam[channel].sample_pntr;
smp_per_record = hdr->edfparam[channel].smp_per_record;
jump = hdr->recordsize - (smp_per_record * bytes_per_smpl);
phys_bitvalue = hdr->edfparam[channel].bitvalue;
phys_offset = hdr->edfparam[channel].offset;
if(hdr->edf)
{
for(i=0; i<n; i++)
{
if(!(sample_pntr%smp_per_record))
{
if(i)
{
fseeko(file, jump, SEEK_CUR);
}
}
var.four[0] = fgetc(file);
tmp = fgetc(file);
if(tmp==EOF)
{
return -1;
}
var.four[1] = tmp;
buf[i] = phys_bitvalue * (phys_offset + (double)var.two_signed[0]);
sample_pntr++;
}
}
if(hdr->bdf)
{
for(i=0; i<n; i++)
{
if(!(sample_pntr%smp_per_record))
{
if(i)
{
fseeko(file, jump, SEEK_CUR);
}
}
var.four[0] = fgetc(file);