The following commit has been merged in the master branch:
commit 99b1d5a023eee9df74b0e0d6f894516fc79435ad
Author: Andrei Zavada <[email protected]>
Date: Mon Jul 8 02:03:18 2013 +0300
WIP (<regex> not worky)
diff --git a/src/aghermann/expdesign/primaries.cc
b/src/aghermann/expdesign/primaries.cc
index e5245d4..13692fb 100644
--- a/src/aghermann/expdesign/primaries.cc
+++ b/src/aghermann/expdesign/primaries.cc
@@ -569,7 +569,7 @@ sync()
for ( auto &D : J.measurements )
for ( auto &E : D.second.episodes )
for ( auto &F : E.sources )
- F().write_ancillary_files();
+ F().save_ancillary_files();
}
diff --git a/src/aghermann/expdesign/tree-scanner.cc
b/src/aghermann/expdesign/tree-scanner.cc
index 9b98ab5..d581371 100644
--- a/src/aghermann/expdesign/tree-scanner.cc
+++ b/src/aghermann/expdesign/tree-scanner.cc
@@ -15,6 +15,7 @@
#include <string>
#include "common/alg.hh"
+#include "libsigfile/all.hh"
#include "primaries.hh"
@@ -246,11 +247,19 @@ agh::CExpDesign::
is_supported_source( sigfile::CTypedSource& F)
{
using namespace sigfile;
- CEDFFile::TSubtype subtype;
- return F.type() == CTypedSource::TType::edf and
- (subtype = static_cast<CEDFFile*>(&F()) -> subtype(),
- (subtype == CEDFFile::TSubtype::edf ||
- subtype == CEDFFile::TSubtype::edfplus_c));
+ union {
+ CEDFFile::TSubtype e;
+ CTSVFile::TSubtype t;
+ } u;
+ return (F.type() == CTypedSource::TType::edf and
+ (u.e = static_cast<CEDFFile*>(&F()) -> subtype(),
+ (u.e == CEDFFile::TSubtype::edf ||
+ u.e == CEDFFile::TSubtype::edfplus_c)))
+ or
+ (F.type() == CTypedSource::TType::ascii and
+ (u.t = static_cast<CTSVFile*>(&F()) -> subtype(),
+ (u.t == CTSVFile::TSubtype::csv ||
+ u.t == CTSVFile::TSubtype::tsv)));
}
namespace {
diff --git a/src/aghermann/model/ultradian-cycle.cc
b/src/aghermann/model/ultradian-cycle.cc
index 6f67194..106387b 100644
--- a/src/aghermann/model/ultradian-cycle.cc
+++ b/src/aghermann/model/ultradian-cycle.cc
@@ -15,6 +15,7 @@
#include "aghermann/globals.hh"
#include "aghermann/expdesign/recording.hh"
+#include "libsigproc/sigproc.hh"
#include "beersma.hh"
using namespace std;
diff --git a/src/aghermann/ui/mw/measurements_cb.cc
b/src/aghermann/ui/mw/measurements_cb.cc
index eeb3f8b..c2b2de1 100644
--- a/src/aghermann/ui/mw/measurements_cb.cc
+++ b/src/aghermann/ui/mw/measurements_cb.cc
@@ -9,6 +9,7 @@
* License: GPL
*/
+#include "libsigfile/source-base.hh"
#include "aghermann/ui/misc.hh"
#include "aghermann/ui/sf/sf.hh"
#include "mw.hh"
@@ -197,7 +198,7 @@ iSubjectTimelineEDFInfo_activate_cb(
const auto& F = J->using_episode->sources.front();
gtk_text_buffer_set_text(
ED.tEDFFileDetailsReport,
- F().details( 0|sigfile::CEDFFile::with_channels).c_str(), -1);
+ F().details(
0|sigfile::CSource::TDetails::with_channels).c_str(), -1);
gtk_window_set_title(
(GtkWindow*)ED.wEDFFileDetails,
snprintf_buf( "%s header", F().filename()));
diff --git a/src/libmetrics/psd.cc b/src/libmetrics/psd.cc
index b23cd55..9a1399a 100644
--- a/src/libmetrics/psd.cc
+++ b/src/libmetrics/psd.cc
@@ -13,6 +13,7 @@
*/
+#include <map>
#include <cassert>
#include <unistd.h>
diff --git a/src/libsigfile/Makefile.am b/src/libsigfile/Makefile.am
index 9fad844..b861ba6 100644
--- a/src/libsigfile/Makefile.am
+++ b/src/libsigfile/Makefile.am
@@ -19,7 +19,8 @@ libsigfile_la_SOURCES := \
tsv.cc \
tsv.hh \
page.cc \
- page.hh
+ page.hh \
+ all.hh
libsigfile_la_LDFLAGS := \
-avoid-version \
diff --git a/src/libmetrics/all.hh b/src/libsigfile/all.hh
similarity index 56%
copy from src/libmetrics/all.hh
copy to src/libsigfile/all.hh
index 2645064..d24074c 100644
--- a/src/libmetrics/all.hh
+++ b/src/libsigfile/all.hh
@@ -1,21 +1,20 @@
/*
- * File name: libmetrics/all.hh
+ * File name: libsigfile/all.hh
* Project: Aghermann
* Author: Andrei Zavada <[email protected]>
*
- * Initial version: 2013-05-23
+ * Initial version: 2013-07-07
*
* Purpose:
*
* License: GPL
*/
-#ifndef AGH_LIBMETRICS_ALL_H_
-#define AGH_LIBMETRICS_ALL_H_
+#ifndef AGH_LIBSIGFILE_ALL_H_
+#define AGH_LIBSIGFILE_ALL_H_
-#include "psd.hh"
-#include "mc.hh"
-#include "swu.hh"
+#include "edf.hh"
+#include "tsv.hh"
#endif
diff --git a/src/libsigfile/edf-io.cc b/src/libsigfile/edf-io.cc
index ee4fce5..d88f239 100644
--- a/src/libsigfile/edf-io.cc
+++ b/src/libsigfile/edf-io.cc
@@ -63,99 +63,6 @@ get_region_original_smpl( const int h,
-valarray<TFloat>
-CEDFFile::
-get_region_filtered_smpl( const int h,
- const size_t smpla, const size_t smplz) const
-{
- valarray<TFloat> recp =
- get_region_original_smpl( h, smpla, smplz);
- if ( recp.size() == 0 )
- return valarray<TFloat> (0);
- // and zeromean
- recp -= (recp.sum() / recp.size());
-
- const SSignal& H = operator[](h);
-
- // artifacts
- size_t this_samplerate = H.samples_per_record / data_record_size;
- for ( auto &A : H.artifacts() ) {
- size_t Aa = A.a * this_samplerate,
- Az = A.z * this_samplerate;
- if ( unlikely (Aa >= smplz) )
- break;
- size_t run = (Az - Aa),
- window = min( run, this_samplerate),
- t;
- if ( unlikely (Az > smplz) )
- run = smplz - Aa;
- valarray<TFloat>
- W (run);
-
- if ( run > window ) {
- // construct a vector of multipliers using an INVERTED
windowing function on the
- // first and last windows of the run
- size_t t0;
- for ( t = 0; t < window/2; ++t )
- W[t] = (1 -
sigproc::winf[(size_t)H.artifacts.dampen_window_type]( t, window));
- t0 = run-window; // start of the last window but one
- for ( t = window/2; t < window; ++t )
- W[t0 + t] = (1 -
sigproc::winf[(size_t)H.artifacts.dampen_window_type]( t, window));
- // AND, connect mid-first to mid-last windows (at
lowest value of the window)
- TFloat minimum =
sigproc::winf[(size_t)H.artifacts.dampen_window_type]( window/2, window);
- W[ slice(window/2, run-window, 1) ] =
- (1. - minimum);
- } else // run is shorter than samplerate (1 sec)
- for ( t = 0; t < window; ++t )
- W[t] = (1 -
sigproc::winf[(size_t)H.artifacts.dampen_window_type]( t, window));
-
- // now gently apply the multiplier vector onto the artifacts
- recp[ slice(Aa, run, 1) ] *= (W * (TFloat)H.artifacts.factor);
- }
-
- // filters
- if ( H.filters.low_pass_cutoff > 0. && H.filters.high_pass_cutoff > 0.
&&
- H.filters.low_pass_order > 0 && H.filters.high_pass_order > 0 ) {
- auto tmp (exstrom::band_pass(
- recp, this_samplerate,
- H.filters.high_pass_cutoff,
H.filters.low_pass_cutoff,
- H.filters.low_pass_order, true));
- recp = tmp;
- } else {
- if ( H.filters.low_pass_cutoff > 0. && H.filters.low_pass_order
> 0 ) {
- auto tmp (exstrom::low_pass(
- recp, this_samplerate,
- H.filters.low_pass_cutoff,
H.filters.low_pass_order, true));
- recp = tmp;
- }
- if ( H.filters.high_pass_cutoff > 0. &&
H.filters.high_pass_order > 0 ) {
- auto tmp (exstrom::high_pass(
- recp, this_samplerate,
- H.filters.high_pass_cutoff,
H.filters.high_pass_order, true));
- recp = tmp;
- }
- }
-
- switch ( H.filters.notch_filter ) {
- case SFilterPack::TNotchFilter::at50Hz:
- recp = exstrom::band_stop( recp, this_samplerate,
- 48, 52, 1, true);
- break;
- case SFilterPack::TNotchFilter::at60Hz:
- recp = exstrom::band_stop( recp, this_samplerate,
- 58, 62, 1, true);
- break;
- case SFilterPack::TNotchFilter::none:
- default:
- break;
- }
-
- // filters happen to append samples, so
- return move(recp[ slice (0, smplz-smpla, 1)]);
-}
-
-
-
int
diff --git a/src/libsigfile/edf.cc b/src/libsigfile/edf.cc
index 5d188a5..281cb3e 100644
--- a/src/libsigfile/edf.cc
+++ b/src/libsigfile/edf.cc
@@ -176,10 +176,7 @@ CEDFFile (const string& fname_, const int flags_)
_extract_embedded_annotations();
- // ancillary files:
- if ( flags_ & sigfile::CSource::no_ancillary_files )
- ;
- else
+ if ( not (flags_ & CSource::no_ancillary_files) )
load_ancillary_files();
}
diff --git a/src/libsigfile/edf.hh b/src/libsigfile/edf.hh
index b376675..589bd72 100644
--- a/src/libsigfile/edf.hh
+++ b/src/libsigfile/edf.hh
@@ -22,7 +22,6 @@
#include <map>
#include <stdexcept>
-#include "libsigproc/sigproc.hh"
#include "channel.hh"
#include "source-base.hh"
@@ -199,9 +198,6 @@ class CEDFFile
h, 0, n_data_records *
operator[](h).samples_per_record); }
valarray<TFloat>
- get_region_filtered_smpl( int, size_t, size_t) const;
-
- valarray<TFloat>
get_signal_filtered( const int h) const
{ return get_region_filtered_smpl(
h, 0, n_data_records *
operator[](h).samples_per_record); }
@@ -258,9 +254,6 @@ class CEDFFile
// reporting & misc
- void write_ancillary_files();
-
- enum TEdfDetails { with_channels = 1, with_annotations = 2 };
string details( int which) const;
sigproc::TWinType af_dampen_window_type; // master copy
diff --git a/src/libsigfile/source-base.cc b/src/libsigfile/source-base.cc
index 59dc3aa..b826290 100644
--- a/src/libsigfile/source-base.cc
+++ b/src/libsigfile/source-base.cc
@@ -12,12 +12,14 @@
#include <fstream>
#include "common/string.hh"
+#include "libsigproc/sigproc.hh"
#include "source-base.hh"
using namespace std;
+using namespace sigfile;
void
-sigfile::SArtifacts::
+SArtifacts::
mark_artifact( const double aa, const double az)
{
if ( aa >= az )
@@ -38,7 +40,7 @@ mark_artifact( const double aa, const double az)
void
-sigfile::SArtifacts::
+SArtifacts::
clear_artifact( const double aa, const double az)
{
auto A = obj.begin();
@@ -66,7 +68,7 @@ clear_artifact( const double aa, const double az)
float
__attribute__ ((pure))
-sigfile::SArtifacts::
+SArtifacts::
region_dirty_fraction( const double ra, const double rz) const
{
size_t dirty = 0;
@@ -95,7 +97,7 @@ region_dirty_fraction( const double ra, const double rz) const
unsigned long
-sigfile::SArtifacts::
+SArtifacts::
dirty_signature() const
{
string sig ("a");
@@ -107,10 +109,9 @@ dirty_signature() const
unsigned long
-sigfile::SFilterPack::
+SFilterPack::
dirty_signature() const
{
-// DEF_UNIQUE_CHARP (tmp);
char *tmp;
ASPRINTF( &tmp, "%g%d%g%d%d",
low_pass_cutoff, low_pass_order, high_pass_cutoff,
high_pass_order, (int)notch_filter);
@@ -124,7 +125,7 @@ dirty_signature() const
int
-sigfile::CSource::
+CSource::
load_ancillary_files()
{
int retval = 0;
@@ -207,7 +208,7 @@ load_ancillary_files()
int
-sigfile::CSource::
+CSource::
save_ancillary_files()
{
int retval = 0;
@@ -280,7 +281,7 @@ CSource (CSource&& rv)
tuple<string, string, int>
-sigfile::CSource::
+CSource::
figure_session_and_episode()
{
int status = 0;
@@ -329,6 +330,105 @@ figure_session_and_episode()
+
+
+
+
+valarray<TFloat>
+CSource::
+get_region_filtered_smpl( const int h,
+ const size_t smpla, const size_t smplz) const
+{
+ valarray<TFloat> recp =
+ get_region_original_smpl( h, smpla, smplz);
+ if ( recp.size() == 0 )
+ return valarray<TFloat> (0);
+ // and zeromean
+ recp -= (recp.sum() / recp.size());
+
+ size_t this_samplerate = samplerate(h);
+
+ // artifacts
+ const auto& AA = artifacts(h);
+ for ( const auto& A : AA() ) {
+ size_t Aa = A.a * this_samplerate,
+ Az = A.z * this_samplerate;
+ if ( unlikely (Aa >= smplz) )
+ break;
+ size_t run = (Az - Aa),
+ window = min( run, this_samplerate),
+ t;
+ if ( unlikely (Az > smplz) )
+ run = smplz - Aa;
+ valarray<TFloat>
+ W (run);
+
+ if ( run > window ) {
+ // construct a vector of multipliers using an INVERTED
windowing function on the
+ // first and last windows of the run
+ size_t t0;
+ for ( t = 0; t < window/2; ++t )
+ W[t] = (1 -
sigproc::winf[(size_t)AA.dampen_window_type]( t, window));
+ t0 = run-window; // start of the last window but one
+ for ( t = window/2; t < window; ++t )
+ W[t0 + t] = (1 -
sigproc::winf[(size_t)AA.dampen_window_type]( t, window));
+ // AND, connect mid-first to mid-last windows (at
lowest value of the window)
+ TFloat minimum =
sigproc::winf[(size_t)AA.dampen_window_type]( window/2, window);
+ W[ slice(window/2, run-window, 1) ] =
+ (1. - minimum);
+ } else // run is shorter than samplerate (1 sec)
+ for ( t = 0; t < window; ++t )
+ W[t] = (1 -
sigproc::winf[(size_t)AA.dampen_window_type]( t, window));
+
+ // now gently apply the multiplier vector onto the artifacts
+ recp[ slice(Aa, run, 1) ] *= (W * (TFloat)AA.factor);
+ }
+
+ // filters
+ const auto& ff = filters(h);
+ if ( ff.low_pass_cutoff > 0. && ff.high_pass_cutoff > 0. &&
+ ff.low_pass_order > 0 && ff.high_pass_order > 0 ) {
+ auto tmp (exstrom::band_pass(
+ recp, this_samplerate,
+ ff.high_pass_cutoff, ff.low_pass_cutoff,
+ ff.low_pass_order, true));
+ recp = tmp;
+ } else {
+ if ( ff.low_pass_cutoff > 0. && ff.low_pass_order > 0 ) {
+ auto tmp (exstrom::low_pass(
+ recp, this_samplerate,
+ ff.low_pass_cutoff,
ff.low_pass_order, true));
+ recp = tmp;
+ }
+ if ( ff.high_pass_cutoff > 0. && ff.high_pass_order > 0 ) {
+ auto tmp (exstrom::high_pass(
+ recp, this_samplerate,
+ ff.high_pass_cutoff,
ff.high_pass_order, true));
+ recp = tmp;
+ }
+ }
+
+ switch ( ff.notch_filter ) {
+ case SFilterPack::TNotchFilter::at50Hz:
+ recp = exstrom::band_stop( recp, this_samplerate,
+ 48, 52, 1, true); // hardcoded
numerals spotted!
+ break;
+ case SFilterPack::TNotchFilter::at60Hz:
+ recp = exstrom::band_stop( recp, this_samplerate,
+ 58, 62, 1, true);
+ break;
+ case SFilterPack::TNotchFilter::none:
+ default:
+ break;
+ }
+
+ // filters happen to append samples, so
+ return move(recp[ slice (0, smplz-smpla, 1)]);
+}
+
+
+
+
// Local Variables:
// Mode: c++
// indent-tabs-mode: 8
diff --git a/src/libsigfile/source-base.hh b/src/libsigfile/source-base.hh
index 8a8acdf..1141059 100644
--- a/src/libsigfile/source-base.hh
+++ b/src/libsigfile/source-base.hh
@@ -238,7 +238,11 @@ class CSource {
: _filename (fname_),
_status (0),
_flags (flags_)
- {}
+ {
+ // if ( not (_flags & no_ancillary_files) )
+ // load_ancillary_files();
+ /// defer until, at least, n_channels is known
+ }
CSource( CSource&&);
virtual ~CSource()
{
@@ -250,6 +254,7 @@ class CSource {
int flags() const { return _flags; }
virtual string explain_status() const = 0;
+ enum TDetails { with_channels = 1, with_annotations = 2 };
virtual string details( int which_details) const = 0;
// identification
@@ -355,7 +360,7 @@ class CSource {
// filtered
virtual valarray<TFloat>
- get_region_filtered_smpl( int, size_t, size_t) const = 0;
+ get_region_filtered_smpl( int, size_t, size_t) const;
valarray<TFloat>
get_region_filtered_sec( const int h,
diff --git a/src/libsigfile/tsv.cc b/src/libsigfile/tsv.cc
index 733869d..0f125e4 100644
--- a/src/libsigfile/tsv.cc
+++ b/src/libsigfile/tsv.cc
@@ -13,7 +13,7 @@
#include <sys/stat.h>
#include <unistd.h>
#include <fcntl.h>
-#include <fstream>
+#include <regex.h>
#include <sstream>
#include <list>
#include <stdexcept>
@@ -59,15 +59,13 @@ CTSVFile (const string& fname_, const int flags_)
if ( stst == -1 )
throw invalid_argument (explain_status(_status |=
TStatus::sysfail));
}
- _fd = open( fname_.c_str(), O_RDWR);
- if ( _fd == -1 )
+ _f = fopen( fname_.c_str(), "r");
+ if ( !_f )
throw invalid_argument (explain_status(_status |=
TStatus::sysfail));
// parse header
if ( _parse_header() ) { // creates channels list
if ( not (flags_ &
sigfile::CSource::no_field_consistency_check) ) {
- close( _fd);
- _fd = -1;
throw invalid_argument (explain_status(_status)); //
_status set in _parse_header()
} else
fprintf( stderr, "CTSVFile::CTSVFile(\"%s\") Warning:
parse header failed, but proceeding anyway\n", fname_.c_str());
@@ -76,8 +74,7 @@ CTSVFile (const string& fname_, const int flags_)
_read_data();
- // ancillary files:
- if ( not (flags_ & sigfile::CSource::no_ancillary_files) )
+ if ( not (flags_ & CSource::no_ancillary_files) )
load_ancillary_files();
}
@@ -93,8 +90,8 @@ CTSVFile (const string& fname_, const TSubtype subtype_,
const int flags_,
_subtype (subtype_),
_samplerate (samplerate_)
{
- _fd = open( fname_.c_str(), O_RDWR | O_CREAT | O_TRUNC, S_IRUSR |
S_IWUSR | S_IRGRP);
- if ( _fd == -1 ) {
+ _f = fopen( fname_.c_str(), "r");
+ if ( !_f ) {
fprintf( stderr, "CTSVFile::CTSVFile(\"%s\"): Failed to open
file for writing\n", fname_.c_str());
throw invalid_argument (explain_status(_status |=
TStatus::sysfail));
}
@@ -139,20 +136,16 @@ CTSVFile (CTSVFile&& rv)
swap( channels, rv.channels);
swap( common_annotations, rv.common_annotations);
- _fd = rv._fd;
- rv._fd = -1;
+ _f = rv._f;
+ rv._f = nullptr;
}
CTSVFile::
~CTSVFile ()
{
- if ( _fd != -1 ) {
- close( _fd);
-
- if ( not (flags() & sigfile::CSource::no_ancillary_files) )
- write_ancillary_files();
- }
+ if ( not (flags() & sigfile::CSource::no_ancillary_files) )
+ save_ancillary_files();
}
@@ -166,18 +159,33 @@ _parse_header()
size_t n_channels;
// 1. read metadata
- do {
-
- } while ();
+
+ regex_t RE;
+ assert (0 == regcomp( &RE, "^#\\W*(\\w+)\\W*(:|=)\\", REG_EXTENDED));
+ regmatch_t M[1+2];
+
+ size_t n = 4096;
+ char *line = (char*)malloc( n);
+ while ( getline( &line, &n, _f) > 0 ) {
+ if ( regexec( &RE, line, 1+2, M, 0) == 0 ) {
+ metadata[string (line, M[1].rm_so, M[1].rm_eo)] =
+ string (line, M[2].rm_so, M[2].rm_eo);
+ printf( "matched metadata [%s] = %s\n", string (line,
M[1].rm_so, M[1].rm_eo).c_str(), string (line, M[2].rm_so, M[2].rm_eo).c_str());
+ } else
+ if ( line[0] != '#' )
+ break; // end of header
+ }
+ free( (void*)line);
// 2. pick essential bits
// 3. deal with episode and session
-
- tie( _session, _episode, parsed_successfully) =
- figure_session_and_episode( _recording_id, _filename);
-
+ int parsed_with_issues;
+ tie( _session, _episode, parsed_with_issues) =
+ figure_session_and_episode();
+ if ( parsed_with_issues )
+ _status |= (nosession | noepisode);
// are channels unique?
for ( auto &H : channels )
@@ -209,6 +217,13 @@ _read_data()
+int
+CTSVFile::
+put_region_smpl( int, const valarray<TFloat>&, size_t) const
+{
+
+ return 0;
+}
string
@@ -219,81 +234,33 @@ details( const int which) const
if ( _status & bad_header )
recv << "Bad header, or no file\n";
else {
- size_t n_dicontinuities = 0;
- double prev_offset = NAN, cur_offset;
- for ( size_t r = 1; r < _record_offsets.size(); ++r ) {
- cur_offset = _record_offsets[r] - _record_offsets[r-1];
- if ( isfinite(prev_offset) and cur_offset !=
prev_offset )
- ++n_dicontinuities;
- prev_offset = cur_offset;
- }
- char *outp;
- ASPRINTF( &outp,
- "File\t: %s\n"
- " subtype\t: %s\n"
- " PatientID\t: %s\n"
- " RecordingID\t: %s\n"
- " Date\t: %s\n"
- " Time\t: %s\n"
- " # of channels\t: %zu\n"
- " # of records\t: %zu\n"
- " Record size\t: %g sec\n"
- " # of discontinuities\t: %zu\n"
- " # of embedded annotations\t: %zu\n",
- filename(),
- subtype_s(),
- patient_id(),
- recording_id.c_str(),
- recording_date, 8)).c_str(),
- trim( string (header.recording_time, 8)).c_str(),
- channels.size(),
- n_data_records,
- data_record_size,
- n_dicontinuities,
- common_annotations.size());
- recv << outp;
- free( outp);
+ char b[20];
+ recv << agh::str::sasprintf(
+ "File\t: %s\n"
+ " subtype\t: %s\n"
+ " PatientID\t: %s\n"
+ " RecordingID\t: %s\n"
+ " Start time\t: %s\n"
+ " Duration\t: %s\n"
+ " # of channels\t: %zu\n"
+ " Sample rate\t: %zu\n",
+ filename(),
+ subtype_s(),
+ patient_id(),
+ recording_id(),
+ (strftime( b, 20, "%F %T", localtime(&_start_time)), b),
+ agh::str::dhms( recording_time()).c_str(),
+ channels.size(),
+ _samplerate);
if ( which & with_channels ) {
size_t i = 0;
- for ( auto &H : channels ) {
- ASPRINTF( &outp,
- " Channel %zu:\n"
- " Label\t: %s\n"
- " Transducer type\t: %s\n"
- " Physical dimension\t: %s\n"
- " Physical min\t: % g\n"
- " Physical max\t: % g\n"
- " Digital min\t: % d\n"
- " Digital max\t: % d\n"
- " Filtering info\t: %s\n"
- " Samples/rec\t: %zu\n"
- " Scale\t: %g\n"
- " (reserved)\t: %s\n",
- ++i,
- trim( string (H.header.label,
16)).c_str(),
- H.transducer_type.c_str(),
- H.physical_dim.c_str(),
- H.physical_min,
- H.physical_max,
- H.digital_min,
- H.digital_max,
- H.filtering_info.c_str(),
- H.samples_per_record,
- H.scale,
- H.reserved.c_str());
- recv << outp;
- free( outp);
- }
- }
-
- if ( which & with_annotations ) {
- recv << "Embedded annotations (" <<
common_annotations.size() << "):\n";
- for ( auto &A : common_annotations )
- recv << ' '
- << A.span.a << '\t'
- << A.span.z << '\t'
- << A.label << endl;
+ for ( auto &H : channels )
+ recv << agh::str::sasprintf(
+ " Channel %zu:\n"
+ " Label\t: %s\n",
+ ++i,
+ H.ucd.name());
}
}
@@ -308,15 +275,13 @@ details( const int which) const
string
CTSVFile::
-explain_edf_status( const int status)
+explain_status( const int status)
{
list<string> recv;
if ( status & sysfail )
recv.emplace_back( "* stat or fopen error");
if ( status & bad_header )
recv.emplace_back( "* Ill-formed header");
- if ( status & bad_version )
- recv.emplace_back( "* Bad Version signature (i.e., not an EDF
file)");
if ( status & missing_patient_id )
recv.emplace_back( "* Missing PatientId");
if ( status & bad_numfld )
@@ -337,18 +302,10 @@ explain_edf_status( const int status)
recv.emplace_back( "* Signal type not listed in Kemp et al");
if ( status & dup_channels )
recv.emplace_back( "* Duplicate channel names");
- if ( status & nogain )
- recv.emplace_back( "* Physical or Digital Min value greater
than Max");
if ( status & too_many_channels )
recv.emplace_back( string("* Number of channels grearter than
") + to_string(max_channels));
- if ( status & file_truncated )
- recv.emplace_back( "* File truncated");
- if ( status & trailing_junk )
- recv.emplace_back( "* File has trailing junk");
if ( status & extra_patientid_subfields )
recv.emplace_back( "* Extra subfields in PatientId");
- if ( status & recognised_channel_conflicting_type )
- recv.emplace_back( "* Explicitly specified signal type does not
match type of known channel name");
return join(recv, "\n");
}
diff --git a/src/libsigfile/tsv.hh b/src/libsigfile/tsv.hh
index 3812e3d..991f2c7 100644
--- a/src/libsigfile/tsv.hh
+++ b/src/libsigfile/tsv.hh
@@ -21,6 +21,7 @@
#include <list>
#include <map>
#include <stdexcept>
+#include <fstream>
#include "libsigproc/sigproc.hh"
#include "channel.hh"
@@ -204,16 +205,14 @@ class CTSVFile
// signal data extractors
valarray<TFloat>
- get_region_original_smpl( int, size_t, size_t) const;
+ get_region_original_smpl( const int h, const size_t sa, const size_t
sz) const
+ { return operator[](h).data[ slice (sa, sz-sa, 1) ];}
valarray<TFloat>
get_signal_original( const int h) const // there is a
CSource::get_signal_original already, but this one is a little better
{ return get_region_original_smpl( h, 0,
channels.front().data.size()); }
valarray<TFloat>
- get_region_filtered_smpl( int, size_t, size_t) const;
-
- valarray<TFloat>
get_signal_filtered( const int h) const
{ return get_region_filtered_smpl( h, 0,
channels.front().data.size()); }
@@ -260,10 +259,7 @@ class CTSVFile
// reporting & misc
- void write_ancillary_files();
-
- enum TTsvDetails { with_channels = 1, with_annotations = 2 };
- string details( int which) const;
+ string details( int which_details) const;
sigproc::TWinType af_dampen_window_type; // master copy
@@ -376,7 +372,7 @@ class CTSVFile
time_t _start_time,
_end_time;
- int _fd;
+ FILE *_f;
int _parse_header();
int _read_data();
--
Sleep experiment manager
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