/* file: heaxml.c G. Moody 28 June 2010
Last revised: 11 December 2017
-------------------------------------------------------------------------------
heaxml: Convert a WFDB .hea (header) file to XML format
Copyright (C) 2010 George B. Moody
This program is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation; either version 2 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program; if not, see <http://www.gnu.org/licenses/>.
You may contact the author by e-mail (wfdb@physionet.org) or postal mail
(MIT Room E25-505A, Cambridge, MA 02139 USA). For updates to this software,
please visit PhysioNet (http://www.physionet.org/).
_______________________________________________________________________________
*/
#include <stdio.h>
#include <wfdb/wfdb.h>
#define WFDBXMLPROLOG "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" \
"<?xml-stylesheet type=\"text/xsl\"" \
" href=\"wfdb.xsl\"?>\n" \
"<!DOCTYPE wfdbrecord PUBLIC \"-//PhysioNet//DTD WFDB 1.0//EN\"" \
" \"http://physionet.org/physiobank/database/XML/wfdb.dtd\">\n"
char *token(char *p)
{
if (p) {
while (*p && *p != ' ' && *p != '\t' && *p != '\n')
p++; /* find whitespace */
while (*p && (*p == ' ' || *p == '\t' || *p == '\n'))
p++; /* find first non-whitespace */
if (*p == '\0') p = NULL;
}
return (p);
}
void output_xml(FILE *ofile, char *tag, char *p)
{
if (p) {
fprintf(ofile, "<%s>", tag);
while (*p) {
if (*p == '<') fprintf(ofile, "<");
else if (*p == '>') fprintf(ofile, ">");
else if (*p == '&') fprintf(ofile, "&");
else if (*p == '>') fprintf(ofile, ">");
else if (*p == '"') fprintf(ofile, """);
else if (*p == '\'') fprintf(ofile, "'");
else fprintf(ofile, "%c", *p);
p++;
}
fprintf(ofile, "</%s>\n", tag);
}
return;
}
int nsig;
FILE *ofile;
WFDB_Siginfo *s;
WFDB_Time t;
void process_start(char *tstring);
main(int argc, char **argv)
{
char *ofname, *info, *p, *pname, *record, *prog_name();
int i, in_msrec = 0, nsegments;
WFDB_Seginfo *seg, *sp;
pname = prog_name(argv[0]);
if (argc < 2) {
(void)fprintf(stderr, "usage: %s RECORD\n", pname);
exit(1);
}
record = argv[1];
/* Discover the number of signals defined in the header. */
if ((nsig = isigopen(record, NULL, 0)) < 0) exit(2);
/* The name of the output file is the record name with an
appended ".hea.xml". Any directory separators (/) in
the record name are replaced by hyphens (-) in the
output file name, so that the output file is always
written into the current directory. */
ofname = calloc(strlen(record)+9, sizeof(char));
strcpy(ofname, record);
for (p = ofname; *p; p++)
if (*p == '/') *p = '-';
strcat(ofname, ".hea.xml");
/* Open the output file and write the XML prolog. */
if ((ofile = fopen(ofname, "wt")) == NULL) {
fprintf(stderr, "%s: can't create %s\n", pname, ofname);
exit(3);
}
fprintf(ofile, WFDBXMLPROLOG);
/* Allocate storage for nsig signal information structures. */
if (nsig > 0 && (s = malloc(nsig * sizeof(WFDB_Siginfo))) == NULL) {
fprintf(stderr, "%s: insufficient memory\n", pname);
exit(4);
}
nsig = isigopen(record, s, -nsig);
(void)fprintf(ofile, "<wfdbrecord name=\"%s\">\n\n", record);
setgvmode(WFDB_LOWRES);
t = strtim("e");
if (nsig > 0 && (s[0].fmt == 0 || s[0].nsamp != 0) && s[0].nsamp != t) {
in_msrec = 1;
nsegments = getseginfo(&sp);
seg = calloc(nsegments, sizeof(WFDB_Seginfo));
for (i = 0; i < nsegments; i++)
seg[i] = sp[i];
sp = seg;
}
process_record();
if (in_msrec) {
static char *segname, nextts[30];
segname = calloc(strlen(record)+20, sizeof(char));
for (p = record + strlen(record) - 1; p > record && *p != '/'; p--)
;
*p = '\0';
/* If segment 0 has 0 samples, it's a layout segment, and the information
in it has already been output above, so skip it; otherwise, it's a
regular segment, so process it. The initialization of i in the for
loop below tests for this. */
for (i = sp[0].nsamp ? 0 : 1; i < nsegments; i++) {
fprintf(stderr, "segment %d: %s\n", i, sp[i].recname);
if (strcmp("~", sp[i].recname) == 0) {
fprintf(ofile, "\n<segment name=\"gap_%d\">\n<gap>\n", i);
process_start(nextts);
fprintf(ofile, "<length>%ld</length></gap>\n", sp[i].nsamp);
}
else {
sprintf(segname, "%s/%s", record, sp[i].recname);
wfdbquit();
nsig = isigopen(segname, NULL, 0);
nsig = isigopen(segname, s, -nsig);
fprintf(ofile, "\n<segment name=\"%s\">\n", sp[i].recname);
setgvmode(WFDB_LOWRES);
t = strtim("e");
strcpy(nextts, mstimstr(-t));
process_record();
}
fprintf(ofile, "</segment>\n");
}
}
fprintf(ofile, "</wfdbrecord>\n");
exit(0);
}
void process_info(void)
{
char *info, *p;
if (info = getinfo((char *)NULL)) {
double age = -1.0;
char *sex = NULL;
fprintf(ofile, "\n<info>\n");
/* Find the first non-space in the first info string. */
for (p = info; *p && *p == ' '; p++)
;
if ('0' <= *p && *p <= '9') {
/* If the first token of the first info string is numeric, the
current .hea file does not have tagged info, and the first
and second tokens are the age and sex; and the second info
string (if present) contains the medications. Handle this
case first. */
sscanf(p, "%lf", &age);
if (age >= 0) fprintf(ofile, "<age>%g</age>\n", age);
p = token(p); /* go to the next token */
if (p && (*p == 'm' || *p == 'M')) sex = "M";
else if (p && (*p == 'f' || *p == 'F')) sex = "F";
if (sex) fprintf(ofile, "<sex>%s</sex>\n", sex);
/* If there are any more tokens, save them as 'extra' info. */
if (p = token(p))
output_xml(ofile, "extra", p);
if (info = getinfo((char *)NULL)) {
output_xml(ofile, "medication", info);
info = getinfo((char *)NULL);
}
}
/* process standard (tagged) info */
while (info) {
if (age < 0) {
if ((p = strstr(info, "age")) || (p = strstr(info, "Age"))) {
if (p = token(p)) {
sscanf(p, "%lf", &age);
if (age >= 0) fprintf(ofile, "<age>%g</age>\n", age);
}
/* Additional tagged data may follow age. Continue processing
the remainder of this info string below. */
if (!(info = token(p)))
/* If there is nothing else, get the next info if any. */
info = getinfo((char *)NULL);
}
}
if (sex == NULL) {
if (info &&
((p = strstr(info, "sex"))||(p = strstr(info, "Sex")))) {
if ((p = token(p)) && (*p == 'm' || *p == 'M')) sex = "M";
else if (p && (*p == 'f' || *p == 'F')) sex = "F";
if (sex) fprintf(ofile, "<sex>%s</sex>\n", sex);
/* Additional tagged data may follow sex. Continue processing
the remainder of this info string. */
if (!(info = token(p)))
/* If there is nothing else, get the next info if any. */
info = getinfo((char *)NULL);
}
}
/* Diagnoses may be present in more than one info string. */
if (info && *info &&
((p=strstr(info,"diagnos")) || (p=strstr(info,"Diagnos")))) {
if ((p = token(p)) == NULL)
/* If nothing follows the 'diagnosis' tag, assume the next info
is the diagnosis. */
p = getinfo((char *)NULL);
if (p) {
output_xml(ofile, "diagnosis", p);
/* This info has been consumed; get the next info if any. */
info = getinfo((char *)NULL);
continue;
}
}
if (info && *info &&
((p=strstr(info,"medication"))||(p=strstr(info,"Medication")))) {
if ((p = token(p)) == NULL)
/* If nothing follows the 'medication' tag, assume the next info
is the medication. */
p = getinfo((char *)NULL);
if (p) {
output_xml(ofile, "medication", p);
/* This info has been consumed; get the next info if any. */
info = getinfo((char *)NULL);
continue;
}
}
/* Process any info that was not identified above. */
if (info && *info)
output_xml(ofile, "other", info);
info = getinfo((char *)NULL);
}
fprintf(ofile, "</info>\n");
}
}
void process_start(char *p)
{
if (*p == '[') {
int day = -1, month = -1, year = -1;
double hour = -1.0, minute = -1.0, second = -1.0;
fprintf(ofile, "<start>\n");
sscanf(p+1, "%lf:%lf:%lf %d/%d/%d",
&hour, &minute, &second, &day, &month, &year);
if (year >= 0) {
if (year < 100) year += 1900;
if (year < 1975) year += 100;
fprintf(ofile, "<year>%d</year>\n", year);
}
if (month > 0) fprintf(ofile, "<month>%d</month>\n", month);
if (day > 0) fprintf(ofile, "<day>%d</day>\n", day);
if (second < 0) { /* incomplete start time in MM:SS or SS format */
if (minute < 0) { second = hour; hour = -1; } /* SS format */
else { second = minute; minute = hour; hour = -1; } /* MM:SS */
}
if (hour >= 0) fprintf(ofile, "<hour>%g</hour>\n", hour);
if (minute >= 0) fprintf(ofile, "<minute>%g</minute>\n", minute);
if (second >= 0) fprintf(ofile, "<second>%g</second>\n", second);
fprintf(ofile, "</start>\n");
}
}
int process_record(void)
{
char *p;
double cfreq, sfreq;
int i, skew;
FILE *ifile;
/* Process and output info. */
process_info();
/* Output the <start> section if the starting time is specified. */
process_start(mstimstr(0L));
if (nsig < 1 || t > 0L)
(void)fprintf(ofile, "<length>%ld</length>\n", t);
else if (s[0].fmt && (ifile = fopen(s[0].fname, "rb")) &&
(fseek(ifile, 0L, 2) == 0)) {
int framesize = 0;
long nbytes = ftell(ifile) - wfdbgetstart(0);
fclose(ifile);
for (i = 0; i < nsig && s[i].group == 0; i++)
framesize += s[i].spf;
switch (s[0].fmt) {
case 8:
case 80:
t = nbytes / framesize;
break;
default:
case 16:
case 61:
case 160:
t = nbytes / (2*framesize);
break;
case 212:
t = (2L * nbytes) / (3*framesize);
break;
case 310:
case 311:
t = (3L * nbytes) / (4*framesize);
break;
}
(void)fprintf(ofile, "<length>%ld</length>\n", t);
}
(void)fprintf(ofile, "<samplingfrequency>%.12g</samplingfrequency>\n",
sfreq = sampfreq(NULL));
(void)fprintf(ofile, "<signals>%d</signals>\n", nsig);
cfreq = getcfreq();
if (sfreq != cfreq) {
double basecount = getbasecount();
fprintf(ofile, "<counterfrequency");
if (basecount > 0.0) fprintf(ofile, " basecount=\"%g\"", basecount);
fprintf(ofile, ">%.12g</counterfrequency>\n", cfreq);
}
if (nsig > 0) {
for (i = 0; i < nsig; i++) {
if (i == 0 || s[i].group != s[i-1].group) {
long plen;
if (i > 0) fprintf(ofile, "</signalfile>\n\n");
fprintf(ofile, "<signalfile>\n<filename>%s</filename>\n\n",
s[i].fmt ? s[i].fname : "[none]");
if (plen = wfdbgetstart(i))
fprintf(ofile, "<preamblelength>%ld</preamblelength>\n", plen);
}
fprintf(ofile, "<signal>\n<description>%s</description>\n",
s[i].desc);
fprintf(ofile, "<gain>%.12g</gain>\n",
s[i].gain == 0. ? WFDB_DEFGAIN : s[i].gain);
fprintf(ofile, "<units>%s</units>\n",
s[i].units ? s[i].units : "mV");
fprintf(ofile, "<initialvalue>%d</initialvalue>\n", s[i].initval);
fprintf(ofile, "<storageformat>%d</storageformat>\n", s[i].fmt);
if (s[i].spf > 1)
fprintf(ofile,"<samplesperframe>%d</samplesperframe>\n", s[i].spf);
if (skew = wfdbgetskew(i))
fprintf(ofile, "<skew>%d</skew>\n", skew);
fprintf(ofile, "<blocksize>%d</blocksize>\n", s[i].bsize);
fprintf(ofile, "<adcresolution>%d</adcresolution>\n", s[i].adcres);
fprintf(ofile, "<adczero>%d</adczero>\n", s[i].adczero);
fprintf(ofile, "<baseline>%d</baseline>\n", s[i].baseline);
fprintf(ofile, "<checksum>%d</checksum>\n", s[i].cksum);
fprintf(ofile, "</signal>\n\n");
}
}
if (nsig > 0) fprintf(ofile, "</signalfile>\n\n");
return (0);
}
char *prog_name(s)
char *s;
{
char *p = s + strlen(s);
#ifdef MSDOS
while (p >= s && *p != '\\' && *p != ':') {
if (*p == '.')
*p = '\0'; /* strip off extension */
if ('A' <= *p && *p <= 'Z')
*p += 'a' - 'A'; /* convert to lower case */
p--;
}
#else
while (p >= s && *p != '/')
p--;
#endif
return (p+1);
}