//------------------------------------------------------------------------- // filename: conv_sleep_annot.c // version: 1.0 // authors: G. Clifford, with much help from P. Hayton, N. Townsend 2001 // (C) authors, under the GNU pulic license //------------------------------------------------------------------------- // description: Program to convert the MIT Polysomnographic slp annotations // files produced by rdann into floating point numbers that represent the // sleep continuum, and patient ailments. // // Expects 2 arguments - the slp file you want to convert and the annotation // file you want to record the converted // // To compile : gcc -Wall conv_sleep_annot.c -o conv_sleep_annot -lm // e.g. // rdann -r slp01a -a st > slp01a.ascii // conv_sleep_annot slp01a.ascii file.out // // // Reads in MIT polysomographic DB annotations and writes them out // in a new format: (float)time float(sleep_ann) float(arousal/condition) // where sleep_ann and arousal/condition = /* -1 W subject is awake 0 R REM sleep 1 1 sleep stage 1 2 2 sleep stage 2 2 2 sleep stage 3 4 4 sleep stage 4 -0.1 No label in 3rd column -2 H Hypopnea -0.2 HA Hypopnea with arousal -3 OA Obstructive apnea -0.3 X Obstructive apnea with arousal -4 CA Central apnea -0.4 CAA Central apnea with arousal -5 L Leg movements -0.5 LA Leg movements with arousal -0.6 A Unspecified arousal -10 MT Movement time In theory, the arousals will only manifest in the 3rd column - this is to show that the sleep stage may give misleading information about the arousal (plot the third column and one sees that any values between -0.1 and -0.6 mean that the patient experienced an arousal of between 5-30s in this 30s window. Classification: Based on Mayela's feedback: Classifying outside stages 1-4, awake and REM sleep is more difficult: REM sleep is indistinguishable from Awake when using EEG only and has therefore been given a classification between stage 1 and W. Movement in MT usually causes a strong EEG artefact so this is placed at the end of the list. Assuming that the analysis is based on the EEG, only the categories 'with arousal' are those that can be associated with a specific sleep stage: Awake. Therefore these are clustered together and placed near 0. An hypopnea or an apnoea can occur at any sleep stage, including REM sleep. Leg movements are only noticeable in EMG signals from the leg. An arousal can occur with no apparent reason. Normal subjects experience about 15 arousals during the night. Arousals caused by OSA are short in duration (3-20 seconds). The labels are time stamped in seconds (the period is 30 seconds _FROM_ the time) */ #include #include #include #include #include // user defined values #define sample_freq 250 // file pointers declared FILE *fptr_in; FILE *fptr_out; #define MAX_LINE_LEN 460000 #define TRUE 1 #define FALSE 0 #define YES 1 #define NO 0 #define samp_freq 250 char* scanline (char **ptr, char *buffer, int max) { int n=0; char *start = buffer; if (**ptr == '\0') return NULL; while (**ptr != '\n' && n < max) { *buffer = **ptr; if (**ptr == '\0') return start; (*ptr)++; buffer++; n++; } *buffer = **ptr; (*ptr)++; buffer++; *buffer='\0'; return start; } int scanstring (char **ptr, char *buffer) { int n=0; if (**ptr == '\0') return FALSE; // Skip whitespace while (**ptr == ' ' || **ptr == '\n') (*ptr)++; // Copy until the next space is found while (**ptr != '\n' && **ptr != ' ' && **ptr != '\0') { *buffer = **ptr; if (**ptr == '\0') return TRUE; (*ptr)++; buffer++; n++; } (*ptr)++; *buffer='\0'; return TRUE; } char *parse_line(FILE *fp, char *line, int max_len, char *parts, char **part, int *n_parts, char** text_stream) { char *cp; char *result; int in_white; int in_quote; int k; // If fp == NULL, we scan from the text stream instead if (fp) result = fgets(line, max_len, fp); else if (text_stream != NULL) result = scanline(text_stream, line, max_len); else result = 0; if (result) { cp = &line[0]; in_white = YES; in_quote = NO; *n_parts = 0; k = 0; while (*cp != '\0') { if (in_quote) { if (*cp == '"') { in_quote = NO; in_white = YES; parts[k++] = '\0'; } else parts[k++] = *cp; } /* else if ((*cp == '"') && in_white) { */ /* in_quote = YES; */ /* part[(*n_parts)++] = &parts[k]; */ /* } */ else if (*cp == '%') { /* ignore comments */ *cp = '\0'; continue; } else if ((*cp == ' ') || (*cp == '\t') || (*cp == ':') || (*cp == '\n')) { if (!in_white) { in_white = YES; if (*n_parts) parts[k++] = '\0'; } } else { if (in_white) part[(*n_parts)++] = &parts[k]; parts[k++] = *cp; in_white = NO; } cp++; } if (!in_white && *n_parts) parts[k] = '\0'; } return result; } int main(int argc, char *argv[]) { char *part[MAX_LINE_LEN/2]; char line[MAX_LINE_LEN]; char parts[3*MAX_LINE_LEN/2+1]; int n_parts; float time_s; int time_int; // if we have less than 2 arguments (executable+file to read) if (argc < 3) { printf("\n Usage: %s \n", argv[0]); exit(0); } // open record (1st argument of executable) for input and check // if it can be opened if ( !(fptr_out = fopen(argv[2],"w")) ) { fprintf(stderr, "\n Error: cannot open record %s\n",argv[2]); exit(0); } if ( !(fptr_in = fopen(argv[1],"r")) ) { fprintf(stderr, "\n Error: cannot open record %s\n",argv[1]); exit(0); } // loop over the data until the end of the file while (parse_line(fptr_in, line, MAX_LINE_LEN, parts, part, &n_parts, NULL)) { /* fprintf(stderr,"%d parts : last part is %s\n",n_parts,part[n_parts-1]); */ time_int = atoi(part[4]); // time_float = atof(part[5]); time_s = time_int/samp_freq; // printf("%i\n",time_int); if (n_parts < 10) fprintf(stderr,"-20"); // error else if (n_parts-1 == 9) { // label state - if there is no other label third column is 0 if (!strcmp(part[9],"W")) fprintf(fptr_out,"%f -1 -0.1\n",time_s); else if (!strcmp(part[9],"1")) fprintf(fptr_out,"%f 1 -0.1\n",time_s); else if (!strcmp(part[9],"2")) fprintf(fptr_out,"%f 2 -0.1\n",time_s); else if (!strcmp(part[9],"3")) fprintf(fptr_out,"%f 3 -0.1\n",time_s); else if (!strcmp(part[9],"4")) fprintf(fptr_out,"%f 4 -0.1\n",time_s); else if (!strcmp(part[9],"R")) fprintf(fptr_out,"%f 0 -0.1\n",time_s); else if (!strcmp(part[9],"H")) fprintf(fptr_out,"%f -2 -0.1\n",time_s); else if (!strcmp(part[9],"HA")) fprintf(fptr_out,"%f -0.2 -0.1\n",time_s); else if (!strcmp(part[9],"OA")) fprintf(fptr_out,"%f -3 -0.1\n",time_s); else if (!strcmp(part[9],"X")) fprintf(fptr_out,"%f -0.3 -0.1\n",time_s); else if (!strcmp(part[9],"CA")) fprintf(fptr_out,"%f -4 -0.1\n",time_s); else if (!strcmp(part[9],"CAA")) fprintf(fptr_out,"%f -0.4 -0.1\n",time_s); else if (!strcmp(part[9],"L")) fprintf(fptr_out,"%f -5 -0.1\n",time_s); else if (!strcmp(part[9],"LA")) fprintf(fptr_out,"%f -0.5 -0.1\n",time_s); else if (!strcmp(part[9],"A")) fprintf(fptr_out,"%f -0.6 -0.1\n",time_s); else if (!strcmp(part[9],"MT")) fprintf(fptr_out,"%f -10 -0.1\n",time_s); else fprintf(fptr_out,"%f -21\n",time_s); // error } else if (n_parts-1 > 9) { // OR label sleep state and arousal level //* == arousal -- only relevant annot if (!strcmp(part[9],"W")) fprintf(fptr_out,"%f 0 ",time_s); else if (!strcmp(part[9],"1")) fprintf(fptr_out,"%f 1 ",time_s); else if (!strcmp(part[9],"2")) fprintf(fptr_out,"%f 2 ",time_s); else if (!strcmp(part[9],"3")) fprintf(fptr_out,"%f 3 ",time_s); else if (!strcmp(part[9],"4")) fprintf(fptr_out,"%f 4 ",time_s); else if (!strcmp(part[9],"R")) fprintf(fptr_out,"%f 0 ",time_s); else if (!strcmp(part[9],"H")) fprintf(fptr_out,"%f -2 ",time_s); else if (!strcmp(part[9],"HA")) fprintf(fptr_out,"%f -0.1 ",time_s);//* else if (!strcmp(part[9],"OA")) fprintf(fptr_out,"%f -3 ",time_s); else if (!strcmp(part[9],"X")) fprintf(fptr_out,"%f -0.3 ",time_s); //* else if (!strcmp(part[9],"CA")) fprintf(fptr_out,"%f -4 ",time_s); else if (!strcmp(part[9],"CAA")) fprintf(fptr_out,"%f -0.4 ",time_s);//* else if (!strcmp(part[9],"L")) fprintf(fptr_out,"%f -5 ",time_s); else if (!strcmp(part[9],"LA")) fprintf(fptr_out,"%f -0.5 ",time_s);//* else if (!strcmp(part[9],"A")) fprintf(fptr_out,"%f -0.6 ",time_s); //* else if (!strcmp(part[9],"MT")) fprintf(fptr_out,"%f -10 ",time_s); else fprintf(fptr_out,"%f -21 ",time_s); // error // label specific awareness level if (!strcmp(part[10],"W")) fprintf(fptr_out,"-1\n"); else if (!strcmp(part[10],"1")) fprintf(fptr_out,"1\n"); else if (!strcmp(part[10],"2")) fprintf(fptr_out,"2\n"); else if (!strcmp(part[10],"3")) fprintf(fptr_out,"3\n"); else if (!strcmp(part[10],"4")) fprintf(fptr_out,"4\n"); else if (!strcmp(part[10],"R")) fprintf(fptr_out,"0\n"); else if (!strcmp(part[10],"H")) fprintf(fptr_out,"-2\n"); else if (!strcmp(part[10],"HA")) fprintf(fptr_out,"-0.2\n"); //* else if (!strcmp(part[10],"OA")) fprintf(fptr_out,"-3\n"); else if (!strcmp(part[10],"X")) fprintf(fptr_out,"-0.3\n"); //* else if (!strcmp(part[10],"CA")) fprintf(fptr_out,"-4\n"); else if (!strcmp(part[10],"CAA")) fprintf(fptr_out,"0.4\n");//* else if (!strcmp(part[10],"L")) fprintf(fptr_out,"-5\n"); else if (!strcmp(part[10],"LA")) fprintf(fptr_out,"-0.5\n"); //* else if (!strcmp(part[10],"A")) fprintf(fptr_out,"-0.6\n"); //* else if (!strcmp(part[10],"MT")) fprintf(fptr_out,"-10\n"); else fprintf(fptr_out,"%f -5\n",time_s); // error // else fprintf(fptr_out,"%f -22\n",time_s); // error } // else if (n_parts-1 > 10) // { // } else fprintf(fptr_out,"%f -100\n",time_s); // big error //fprintf(stdout,"%i %s %i\n",time_int,part[n_parts-1], n_parts-1); } return(1); }