The following commit has been merged in the master branch:
commit ee9ef082b050fcf1d4f6b54f05011a457f9931b1
Author: Andrei Zavada <[email protected]>
Date: Fri Apr 12 19:57:18 2013 +0300
parse and look at individual EDF patient_id fields (patch 1/2)
diff --git a/src/expdesign/recording.cc b/src/expdesign/recording.cc
index 704ba97..aa8ac62 100644
--- a/src/expdesign/recording.cc
+++ b/src/expdesign/recording.cc
@@ -130,7 +130,7 @@ CProfile (CSubject& J, const string& d, const
sigfile::SChannel& h,
// anchor zero page, get pagesize from edf^W CBinnedPower^W
either goes
time_t dima = F.start_time();
printf( "CProfile::CProfile(): adding %s of [%s, %s, %s] %zu
pages (%zu full, %zu in hypnogram) recorded %s",
- metrics::name(params.metric), F.subject(), F.session(),
F.episode(),
+ metrics::name(params.metric), F.id.c_str(),
F.session(), F.episode(),
M.total_pages(), M.full_pages(), M.hypnogram().pages(),
ctime( &dima));
if ( pz - pa != (int)M.full_pages() ) {
@@ -185,7 +185,7 @@ CProfile (CRecording& M,
pz = (size_t)difftime( M.F().end_time(), _0at) / _pagesize;
time_t dima = M.F().start_time();
printf( "CProfile::CProfile(): adding single recording %s of [%s, %s,
%s] %zu pages (%zu full, %zu in hypnogram) recorded %s",
- metrics::name(params.metric), M.F().subject(), M.F().session(),
M.F().episode(),
+ metrics::name(params.metric), M.F().id.c_str(),
M.F().session(), M.F().episode(),
M.total_pages(), M.full_pages(), M.hypnogram().pages(), ctime(
&dima));
if ( pz - pa != (int)M.full_pages() ) {
diff --git a/src/expdesign/recording.hh b/src/expdesign/recording.hh
index a0997d3..e197099 100644
--- a/src/expdesign/recording.hh
+++ b/src/expdesign/recording.hh
@@ -153,7 +153,7 @@ class CRecording {
const metrics::mc::SPPack&);
~CRecording ();
- const char* subject() const { return _source().subject(); }
+ const char* subject() const { return _source().name.c_str(); }
const char* session() const { return _source().session(); }
const char* episode() const { return _source().episode(); }
const char* channel() const { return
_source().channel_by_id(_sig_no); }
diff --git a/src/expdesign/tree-scanner.cc b/src/expdesign/tree-scanner.cc
index b1e9d23..e074779 100644
--- a/src/expdesign/tree-scanner.cc
+++ b/src/expdesign/tree-scanner.cc
@@ -151,16 +151,16 @@ register_intree_source( sigfile::CTypedSource&& F,
}
// refuse to register sources of wrong subjects
- if ( j_name != F().subject() ) {
- log_message( "%s: file belongs to subject \"%s\", is
misplaced here under subject \"%s\"\n",
- F().filename(), F().subject(),
j_name.c_str());
+ if ( j_name != F().id ) {
+ log_message( "%s: file belongs to subject %s (\"%s\"),
is misplaced here under subject \"%s\"\n",
+ F().filename(), F().id.c_str(),
F().name.c_str(), j_name.c_str());
return -1;
}
try {
- auto existing_group = group_of( F().subject());
+ auto existing_group = group_of( F().id.c_str());
if ( g_name != existing_group ) {
- log_message( "%s: subject \"%s\" belongs to a
different group (\"%s\")\n",
- F().filename(), F().subject(),
existing_group);
+ log_message( "%s: subject %s (\"%s\") belongs
to a different group (\"%s\")\n",
+ F().filename(), F().id.c_str(),
F().name.c_str(), existing_group);
return -1;
}
} catch (invalid_argument) {
@@ -189,8 +189,8 @@ register_intree_source( sigfile::CTypedSource&& F,
J = &*Ji;
// insert/update episode observing start/end times
- printf( "\nCExpDesign::register_intree_source( file: \"%s\", J:
\"%s\", E: \"%s\", D: \"%s\")\n",
- F().filename(), F().subject(), F().episode(),
F().session());
+ printf( "\nCExpDesign::register_intree_source( file: \"%s\", J:
%s (\"%s\"), E: \"%s\", D: \"%s\")\n",
+ F().filename(), F().id.c_str(), F().name.c_str(),
F().episode(), F().session());
switch ( J->measurements[F().session()].add_one(
move(F), fft_params, swu_params, mc_params) )
{ // this will do it
case AGH_EPSEQADD_OVERLAP:
diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index 21c63a8..123cab6 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -41,7 +41,7 @@ template int sigfile::CEDFFile::export_original_( const
char*, const char*) cons
int
sigfile::CEDFFile::
-set_subject( const char* s)
+set_patient_id( const char* s)
{
memcpy( header.patient_id, agh::str::pad( s, 80).c_str(), 80);
return strlen(s) > 80;
@@ -265,7 +265,7 @@ CEDFFile (const char *fname_, TSubtype subtype_, int flags_,
_lay_out_header();
strncpy( header.version_number, version_string, 8);
- set_subject( "Mr. Fafa");
+ set_patient_id( "Fafa_1 M X Mr._Fafa");
set_recording_id( "Zzz");
set_comment( fname_);
set_start_time( time(NULL));
@@ -365,9 +365,9 @@ CEDFFile (CEDFFile&& rv)
_start_time = rv._start_time;
_end_time = rv._end_time;
- swap( _patient, rv._patient);
- swap( _episode, rv._episode);
- swap( _session, rv._session);
+ swap( _patient_id, rv._patient_id);
+ swap( _episode, rv._episode);
+ swap( _session, rv._session);
swap( channels, rv.channels);
@@ -512,6 +512,11 @@ _parse_header()
_get_next_field( header.data_record_size, 8);
_get_next_field( header.n_channels, 4);
+ if ( strncmp( header.version_number, version_string, 8) ) {
+ _status |= (bad_version | inoperable);
+ return -2;
+ }
+
_subtype =
(strncasecmp( header.reserved, "edf+c", 5) == 0)
? edfplus_c
@@ -519,11 +524,6 @@ _parse_header()
? edfplus_d
: edf;
- if ( strncmp( header.version_number, version_string, 8) ) {
- _status |= (bad_version | inoperable);
- return -2;
- }
-
size_t header_length;
header_length = n_data_records = data_record_size = n_channels
= 0;
@@ -542,7 +542,23 @@ _parse_header()
return -2;
}
- _patient = agh::str::trim( string (header.patient_id, 80));
+ _patient_id = agh::str::trim( string (header.patient_id, 80));
+
+ // sub-parse patient_id into SSubjectId struct
+ {
+ auto subfields = agh::str::tokens( _patient_id, " ");
+ if ( subfields.size() != 4 ) {
+ fprintf( stderr, "%s: Nonconforming
patient_id\n", filename());
+ SSubjectId::id = SSubjectId::name =
subfields.front();
+ SSubjectId::gender = TGender::unknown;
+ } else {
+ auto i = subfields.begin();
+ SSubjectId::id = *i++;
+ SSubjectId::gender =
SSubjectId::char_to_gender((*i++)[0]);
+ SSubjectId::dob = SSubjectId::str_to_dob(*i++);
+ SSubjectId::name = agh::str::join(
agh::str::tokens(*i++, "_"), " ");
+ }
+ }
// deal with episode and session
{
@@ -780,7 +796,7 @@ sigfile::CEDFFile::details( bool channels_too) const
" Record length\t: %zu sec\n",
filename(),
subtype_s(),
- subject(),
+ patient_id(),
agh::str::trim( string (header.recording_id,
80)).c_str(),
agh::str::trim( string (header.recording_date,
8)).c_str(),
agh::str::trim( string (header.recording_time,
8)).c_str(),
@@ -849,12 +865,11 @@ sigfile::CEDFFile::explain_edf_status( int status)
if ( status & time_unparsable )
recv.emplace_back( "* Time field ill-formed");
if ( status & nosession )
- recv.emplace_back(
- "* No session information in field RecordingID "
- "(expecting this to appear after "
- "episode designation followed by a comma)");
+ recv.emplace_back( "* No session information in field
RecordingID");
if ( status & non1020_channel )
recv.emplace_back( "* Channel designation not following the
10-20 system");
+ if ( status & nonconforming_patient_id )
+ recv.emplace_back( "* PatientId not conforming to section
2.1.3.3 of EDF spec");
if ( status & nonkemp_signaltype )
recv.emplace_back( "* Signal type not listed in Kemp et al");
if ( status & dup_channels )
diff --git a/src/libsigfile/edf.hh b/src/libsigfile/edf.hh
index e70c1d2..cd482e8 100644
--- a/src/libsigfile/edf.hh
+++ b/src/libsigfile/edf.hh
@@ -98,8 +98,8 @@ class CEDFFile
// identification
const char* filename() const
{ return _filename.c_str(); }
- const char* subject() const
- { return _patient.c_str(); }
+ const char* patient_id() const
+ { return _patient_id.c_str(); }
const char* recording_id() const
{ return header.recording_id; }
const char* comment() const
@@ -118,7 +118,7 @@ class CEDFFile
{ return n_data_records * data_record_size; }
// setters
- int set_subject( const char* s);
+ int set_patient_id( const char* s);
int set_recording_id( const char* s);
int set_episode( const char* s);
int set_session( const char* s);
@@ -484,22 +484,23 @@ class CEDFFile
enum TStatus : int {
- ok = 0,
- bad_header = (1 << 0),
- bad_version = (1 << 1),
- bad_numfld = (1 << 2),
- bad_recording = (1 << 3),
- date_unparsable = (1 << 4),
- time_unparsable = (1 << 5),
- nosession = (1 << 6),
- noepisode = (1 << 7),
- nonkemp_signaltype = (1 << 8),
- non1020_channel = (1 << 9),
- dup_channels = (1 << 11),
- nogain = (1 << 12),
- sysfail = (1 << 13),
- too_many_channels = (1 << 14),
- inoperable = (bad_header
+ ok = 0,
+ bad_header = (1 << 0),
+ bad_version = (1 << 1),
+ bad_numfld = (1 << 2),
+ bad_recording = (1 << 3),
+ date_unparsable = (1 << 4),
+ time_unparsable = (1 << 5),
+ nosession = (1 << 6),
+ noepisode = (1 << 7),
+ nonkemp_signaltype = (1 << 8),
+ non1020_channel = (1 << 9),
+ dup_channels = (1 << 11),
+ nogain = (1 << 12),
+ sysfail = (1 << 13),
+ too_many_channels = (1 << 14),
+ nonconforming_patient_id = (1 << 15),
+ inoperable = (bad_header
| bad_version
| bad_numfld
| bad_recording
@@ -517,7 +518,7 @@ class CEDFFile
time_t _start_time,
_end_time;
- string _patient,
+ string _patient_id, // this is trimmed, raw; parsed into SSubjectId
fields
// take care of file being named 'episode-1.edf'
_episode,
// loosely/possibly also use RecordingID as session
diff --git a/src/libsigfile/source-base.hh b/src/libsigfile/source-base.hh
index fc8ad43..45bed88 100644
--- a/src/libsigfile/source-base.hh
+++ b/src/libsigfile/source-base.hh
@@ -186,9 +186,81 @@ struct SFilterPack {
+// follow http://www.edfplus.info/specs/edfplus.html#datarecords, section
2.1.3.3
+struct SSubjectId {
+ string id,
+ name;
+ time_t dob;
+ enum class TGender : char {
+ unknown = 'X', male = 'M', female = 'F'
+ };
+ TGender gender;
+ static TGender char_to_gender( char x)
+ {
+ switch ( x ) {
+ case 'M':
+ case 'm':
+ return TGender::male;
+ case 'F':
+ case 'f':
+ return TGender::female;
+ default:
+ return TGender::unknown;
+ }
+ }
+ static int str_to_english_month( const string& s)
+ {
+ if ( strcasecmp( s.c_str(), "jan") == 0 )
+ return 0;
+ if ( strcasecmp( s.c_str(), "feb") == 0 )
+ return 1;
+ if ( strcasecmp( s.c_str(), "mar") == 0 )
+ return 2;
+ if ( strcasecmp( s.c_str(), "apr") == 0 )
+ return 3;
+ if ( strcasecmp( s.c_str(), "may") == 0 )
+ return 4;
+ if ( strcasecmp( s.c_str(), "jun") == 0 )
+ return 5;
+ if ( strcasecmp( s.c_str(), "jul") == 0 )
+ return 6;
+ if ( strcasecmp( s.c_str(), "aug") == 0 )
+ return 7;
+ if ( strcasecmp( s.c_str(), "sep") == 0 )
+ return 8;
+ if ( strcasecmp( s.c_str(), "oct") == 0 )
+ return 9;
+ if ( strcasecmp( s.c_str(), "nov") == 0 )
+ return 10;
+ if ( strcasecmp( s.c_str(), "dec") == 0 )
+ return 11;
+ else
+ return -1;
+ }
+ static time_t str_to_dob( const string& s)
+ {
+ struct tm t;
+ memset( &t, '\0', sizeof (t));
+
+ // strptime( s, "%d-", &t); // will suck in non-US
locales, so
+ auto ff = agh::str::tokens(s, "-");
+ if ( ff.size() != 3 )
+ return (time_t)0;
+ auto f = ff.begin();
+ try {
+ t.tm_mday = stoi( *f++);
+ t.tm_mon = str_to_english_month(*f++);
+ t.tm_year = 1900 + stoi(*f);
+ return mktime( &t);
+ } catch (...) {
+ return (time_t)0;
+ }
+ }
+};
+
-class CSource {
+class CSource : public SSubjectId {
friend class CTypedSource;
protected:
string _filename;
@@ -216,7 +288,7 @@ class CSource {
{
return _filename.c_str();
}
- virtual const char* subject() const = 0;
+ virtual const char* patient_id() const = 0;
virtual const char* recording_id() const = 0;
virtual const char* comment() const = 0;
// probably parsed out of recording_id
@@ -280,7 +352,7 @@ class CSource {
}
// setters
- virtual int set_subject( const char*) = 0;
+ virtual int set_patient_id( const char*) = 0;
virtual int set_recording_id( const char*) = 0;
virtual int set_episode( const char*) = 0;
virtual int set_session( const char*) = 0;
diff --git a/src/metrics/mc.cc b/src/metrics/mc.cc
index f4e5afc..26c5e5f 100644
--- a/src/metrics/mc.cc
+++ b/src/metrics/mc.cc
@@ -162,7 +162,7 @@ export_tsv( const string& fname) const
fprintf( f, "## Subject: %s; Session: %s, Episode: %s recorded %.*s;
Channel: %s\n"
"## Total EEG Microcontinuity course (%zu %zu-sec pages) from
%g up to %g Hz in bins of %g Hz\n"
"#Page\t",
- _using_F().subject(), _using_F().session(),
_using_F().episode(),
+ _using_F().name.c_str(), _using_F().session(),
_using_F().episode(),
(int)strlen(asctime_)-1, asctime_,
_using_F().channel_by_id(_using_sig_no),
pages(), Pp.pagesize, Pp.freq_from, Pp.freq_from +
Pp.bandwidth * bins(), Pp.bandwidth);
@@ -196,7 +196,7 @@ export_tsv( size_t bin,
fprintf( f, "## Microcontinuity profile of\n"
"## Subject: %s; Session: %s, Episode: %s recorded %.*s;
Channel: %s\n"
"## Course (%zu %zu-sec pages) in range %g-%g Hz\n",
- _using_F().subject(), _using_F().session(),
_using_F().episode(),
+ _using_F().name.c_str(), _using_F().session(),
_using_F().episode(),
(int)strlen(asctime_)-1, asctime_,
_using_F().channel_by_id(_using_sig_no),
pages(), Pp.pagesize, Pp.freq_from, Pp.freq_from + (bin+1) *
Pp.bandwidth);
diff --git a/src/metrics/page-metrics-base.cc b/src/metrics/page-metrics-base.cc
index d7aab1a..3064806 100644
--- a/src/metrics/page-metrics-base.cc
+++ b/src/metrics/page-metrics-base.cc
@@ -217,7 +217,7 @@ export_tsv( const string& fname) const
char *asctime_ = asctime( localtime( &sttm));
fprintf( f, "## Subject: %s; Session: %s, Episode: %s recorded %.*s;
Channel: %s\n"
"#Page\t",
- _using_F().subject(), _using_F().session(),
_using_F().episode(),
+ _using_F().name.c_str(), _using_F().session(),
_using_F().episode(),
(int)strlen(asctime_)-1, asctime_,
_using_F().channel_by_id(_using_sig_no));
diff --git a/src/metrics/psd.cc b/src/metrics/psd.cc
index 214b479..6137127 100644
--- a/src/metrics/psd.cc
+++ b/src/metrics/psd.cc
@@ -267,7 +267,7 @@ export_tsv( const string& fname) const
fprintf( f, "## Subject: %s; Session: %s, Episode: %s recorded %.*s;
Channel: %s\n"
"## Total spectral power course (%zu %zu-sec pages) up to %g
Hz in bins of %g Hz\n"
"#Page\t",
- _using_F().subject(), _using_F().session(),
_using_F().episode(),
+ _using_F().name.c_str(), _using_F().session(),
_using_F().episode(),
(int)strlen(asctime_)-1, asctime_,
_using_F().channel_by_id(_using_sig_no),
pages(), Pp.pagesize, _bins*Pp.binsize, Pp.binsize);
@@ -303,7 +303,7 @@ export_tsv( float from, float upto,
fprintf( f, "PSD profile of\n"
"## Subject: %s; Session: %s, Episode: %s recorded %.*s;
Channel: %s\n"
"## Course (%zu %zu-sec pages) in range %g-%g Hz\n",
- _using_F().subject(), _using_F().session(),
_using_F().episode(),
+ _using_F().name.c_str(), _using_F().session(),
_using_F().episode(),
(int)strlen(asctime_)-1, asctime_,
_using_F().channel_by_id(_using_sig_no),
pages(), Pp.pagesize, from, upto);
diff --git a/src/metrics/swu.cc b/src/metrics/swu.cc
index 36a1312..0c8cafd 100644
--- a/src/metrics/swu.cc
+++ b/src/metrics/swu.cc
@@ -155,7 +155,7 @@ export_tsv( const string& fname) const
fprintf( f, "## Subject: %s; Session: %s, Episode: %s recorded %.*s;
Channel: %s\n"
"## SWU course (%zu %zu-sec pages)\n"
"#Page\tSWU\n",
- _using_F().subject(), _using_F().session(),
_using_F().episode(),
+ _using_F().name.c_str(), _using_F().session(),
_using_F().episode(),
(int)strlen(asctime_)-1, asctime_,
_using_F().channel_by_id(_using_sig_no),
pages(), Pp.pagesize);
diff --git a/src/tools/edfcat.cc b/src/tools/edfcat.cc
index 62b814e..108810f 100644
--- a/src/tools/edfcat.cc
+++ b/src/tools/edfcat.cc
@@ -390,7 +390,7 @@ exec_prune( const SOperation::SObject& obj)
F.data_record_size,
F.n_data_records);
- G.set_subject( F.subject());
+ G.set_patient_id( F.patient_id());
string tmp = F.recording_id();
G.set_recording_id( tmp.c_str());
tmp = F.comment();
diff --git a/src/ui/mw/admit-one.cc b/src/ui/mw/admit-one.cc
index db595fa..9f597b5 100644
--- a/src/ui/mw/admit-one.cc
+++ b/src/ui/mw/admit-one.cc
@@ -36,7 +36,7 @@ dnd_maybe_admit_one( const char* fname)
snprintf_buf( "File: <i>%s</i>", fname);
gtk_label_set_markup( lEdfImportCaption, __buf__);
- snprintf_buf( "<b>%s</b>", (*Fp)().subject());
+ snprintf_buf( "<b>%s</b> (%s)", (*Fp)().id.c_str(),
(*Fp)().name.c_str());
gtk_label_set_markup( lEdfImportSubject, __buf__);
} catch ( exception& ex) {
@@ -55,7 +55,7 @@ dnd_maybe_admit_one( const char* fname)
try {
gtk_entry_set_text(
eEdfImportGroupEntry,
- ED->group_of( (*Fp)().subject()));
+ ED->group_of( (*Fp)().id.c_str()));
gtk_widget_set_sensitive( (GtkWidget*)eEdfImportGroup, FALSE);
} catch (invalid_argument ex) {
for ( auto &i : AghGG ) {
@@ -109,7 +109,7 @@ dnd_maybe_admit_one( const char* fname)
dest_path = g_strdup_printf( "%s/%s/%s/%s",
ED->session_dir().c_str(),
selected_group,
- (*Fp)().subject(),
+ (*Fp)().id.c_str(),
selected_session);
dest = g_strdup_printf( "%s/%s.edf",
dest_path,
diff --git a/src/ui/mw/construct.cc b/src/ui/mw/construct.cc
index 72d2658..ef0f36b 100644
--- a/src/ui/mw/construct.cc
+++ b/src/ui/mw/construct.cc
@@ -639,7 +639,6 @@ SExpDesignUIWidgets ()
(GCallback)gtk_tree_view_expand_all,
NULL);
G_CONNECT_2 (tvGlobalAnnotations, row, activated);
- FAFA;
int c = 0;
for ( auto column : {"Recording", "Page(s)", "Channel", "Type",
"Label"} ) {
--
Sleep experiment manager
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