The following commit has been merged in the master branch:
commit 37b6bb69e5fe50218c9558b0341e254c8e000b77
Author: Andrei Zavada <[email protected]>
Date: Wed Apr 17 19:36:38 2013 +0300
initial support for EDF annotations
diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index efcdd4e..d3ee19f 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -111,6 +111,9 @@ const char version_string[8] = {'0',' ',' ',' ', ' ',' ','
',' '};
}
+const char* sigfile::CEDFFile::SSignal::edf_annotations_label = "EDF
Annotations";
+
+
sigfile::CEDFFile::
CEDFFile (const string& fname_, int flags_)
: CSource (fname_, flags_)
@@ -676,6 +679,8 @@ _parse_header()
for ( auto &H : channels ) {
_get_next_field( H.header.physical_min, 8);
+ if ( H.label == SSignal::edf_annotations_label )
+ continue;
if ( sscanf( H.header.physical_min, "%8lg",
&H.physical_min) != 1 ) {
_status |= bad_numfld;
@@ -685,6 +690,8 @@ _parse_header()
}
for ( auto &H : channels ) {
_get_next_field( H.header.physical_max, 8);
+ if ( H.label == SSignal::edf_annotations_label )
+ continue;
if ( sscanf( H.header.physical_max, "%8lg",
&H.physical_max) != 1 ) {
_status |= bad_numfld;
@@ -695,6 +702,8 @@ _parse_header()
for ( auto &H : channels ) {
_get_next_field( H.header.digital_min, 8);
+ if ( H.label == SSignal::edf_annotations_label )
+ continue;
if ( sscanf( H.header.digital_min, "%8d",
&H.digital_min) != 1 ) {
_status |= bad_numfld;
@@ -704,6 +713,8 @@ _parse_header()
}
for ( auto &H : channels ) {
_get_next_field( H.header.digital_max, 8);
+ if ( H.label == SSignal::edf_annotations_label )
+ continue;
if ( sscanf( H.header.digital_max, "%8d",
&H.digital_max) != 1 ) {
_status |= bad_numfld;
@@ -712,9 +723,12 @@ _parse_header()
}
}
- for ( auto &H : channels )
+ for ( auto &H : channels ) {
+ if ( H.label == SSignal::edf_annotations_label )
+ continue;
H.filtering_info.assign(
agh::str::trim( string
(_get_next_field( H.header.filtering_info, 80), 80)));
+ }
for ( auto &H : channels ) {
char *tail;
@@ -742,42 +756,49 @@ _parse_header()
// calculate gain
for ( auto &H : channels )
- if ( H.physical_max <= H.physical_min ||
- H.digital_max <= H.digital_min ) {
- _status |= nogain;
- if ( not (flags() & no_field_consistency_check) )
- return -2;
- } else
- H.scale =
- (H.physical_max - H.physical_min) /
- (H.digital_max - H.digital_min );
+ if ( H.label == SSignal::edf_annotations_label )
+ ;
+ else
+ if ( H.physical_max <= H.physical_min ||
+ H.digital_max <= H.digital_min ) {
+ _status |= nogain;
+ if ( not (flags() & no_field_consistency_check)
)
+ return -2;
+ } else
+ H.scale =
+ (H.physical_max - H.physical_min) /
+ (H.digital_max - H.digital_min );
- // determine signal type
+ // determine & validate signal types
i = 0;
for ( auto &H : channels ) {
- // try parsing as "type channel" first
- string parsable (H.label);
- char *_1 = strtok( &parsable[0], " :,./"),
- *_2 = strtok( NULL, " :,./");
- if ( _2 ) {
- H.signal_type_s = _1;
- H.signal_type = SChannel::figure_signal_type(_1);
- H.label.assign( _2); // .channel overwritten
- // it only has a channel name
- } else {
- H.signal_type_s = SChannel::kemp_signal_types[
- H.signal_type =
SChannel::signal_type_of_channel( H.label) ];
-
- if ( not H.label.follows_system1020() ) { // in case
there are duplicate labels, rewrite
- DEF_UNIQUE_CHARP (_);
- if ( asprintf( &_, "%zu:<%s>", i,
H.label.c_str()) ) {}
- H.label.assign( _);
- _status |= non1020_channel;
+ if ( H.label == SSignal::edf_annotations_label )
+ ;
+ else {
+ // try parsing as "type channel" first
+ string parsable (H.label);
+ char *_1 = strtok( &parsable[0], " :,./"),
+ *_2 = strtok( NULL, " :,./");
+ if ( _2 ) {
+ H.signal_type_s = _1;
+ H.signal_type =
SChannel::figure_signal_type(_1);
+ H.label.assign( _2); // .channel overwritten
+ // it only has a channel name
+ } else {
+ H.signal_type_s = SChannel::kemp_signal_types[
+ H.signal_type =
SChannel::signal_type_of_channel( H.label) ];
+
+ if ( not H.label.follows_system1020() ) { //
in case there are duplicate labels, rewrite
+ DEF_UNIQUE_CHARP (_);
+ if ( asprintf( &_, "%zu:<%s>", i,
H.label.c_str()) ) {}
+ H.label.assign( _);
+ _status |= non1020_channel;
+ }
}
+ if ( H.signal_type == SChannel::TType::other )
+ _status |= nonkemp_signaltype;
}
- if ( H.signal_type == SChannel::TType::other )
- _status |= nonkemp_signaltype;
++i;
}
@@ -804,6 +825,50 @@ _parse_header()
+
+int
+sigfile::CEDFFile::
+_extract_embedded_annotations()
+{
+ auto S = find( channels.begin(), channels.end(),
SSignal::edf_annotations_label);
+ if ( S == channels.end() )
+ return 0;
+ auto& AH = *S;
+
+ // hand-picked from get_signal_original
+ size_t r_cnt = n_data_records * AH.data_record_size * 2;
+
+ size_t alen = r_cnt * AH.samples_per_record * 2;
+ char* abuf = (char*)malloc( alen);
+ while ( r_cnt-- )
+ memcpy( &abuf[ r_cnt * H.samples_per_record ],
+
+ (char*)_mmapping + header_length
+ + r_cnt * _total_samples_per_record * 2 // full records
before
+ + H._at, // offset to
our samples
+
+ H.samples_per_record * 2); // our precious ones
+
+ // walk it and pick up annotations
+ size_t ai = 0;
+// while ( index( abuf+ai, 20) )
+ // for ( size_t i = 0; i < alen; ++i )
+ // for ( size_t k = i; k < alen-1; ++k )
+ // if ( abuf[k ] == (char)21 &&
+ // abuf[i+1] == (char)20 )
+ // ;
+
+ free(tmp);
+
+ return 0;
+}
+
+
+
+
+
+
+
string
sigfile::CEDFFile::details( bool channels_too) const
{
diff --git a/src/libsigfile/edf.hh b/src/libsigfile/edf.hh
index c80e5f2..9943fd1 100644
--- a/src/libsigfile/edf.hh
+++ b/src/libsigfile/edf.hh
@@ -406,6 +406,7 @@ class CEDFFile
// channels
struct SSignal {
+ static const char* edf_annotations_label;
struct SEDFSignalHeader {
char *label ,// [16],
*transducer_type ,// [80],
@@ -534,6 +535,7 @@ class CEDFFile
void _lay_out_header();
int _parse_header();
+ int _extract_embedded_annotations();
size_t header_length,
_fsize,
--
Sleep experiment manager
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