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Added Annotation dump program and fixed edfparser to make it work

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This commit is contained in:
Phil Olynyk 2019-08-04 21:49:17 -04:00
parent b80ae70525
commit b8b4acb804
7 changed files with 180 additions and 22 deletions
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32
anotDump.pro Normal file
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@ -0,0 +1,32 @@
#-------------------------------------------------
#
# Project created by pholynyk 2019Aug01T21:00:00
#
#-------------------------------------------------
message(Platform is $$QMAKESPEC )
CONFIG += c++11
CONFIG += rtti
CONFIG -= debug_and_release
QT += core widgets
TARGET = anotDump
TEMPLATE = app
QMAKE_TARGET_PRODUCT = anotDump
QMAKE_TARGET_COMPANY = The OSCAR Team
QMAKE_TARGET_COPYRIGHT = © 2019 The OSCAR Team
QMAKE_TARGET_DESCRIPTION = "OpenSource STR.edf Dumper"
VERSION = 0.5.0
SOURCES += \
anotDump/main.cpp \
dumpSTR/edfparser.cpp \
HEADERS += \
dumpSTR/common.h \
dumpSTR/edfparser.h \

123
anotDump/main.cpp Normal file
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@ -0,0 +1,123 @@
/* Dump the annotations of an edf file */
#include <QApplication>
// #include <iostream>
#include <QDebug>
typedef float EventDataType;
#include "../dumpSTR/edfparser.h"
// using namespace std;
void dumpHeader( const EDFHeaderQT hdr ) {
qDebug() << "EDF Header:";
qDebug() << "Version " << hdr.version << " Patient >" << hdr.patientident << "<";
qDebug() << "Recording >" << hdr.recordingident << "<";
qDebug() << "Date: " << hdr.startdate_orig.toString();
qDebug() << "Header size (bytes): " << hdr.num_header_bytes;
qDebug() << "EDF type: >" << hdr.reserved44 << "<";
qDebug() << "Duration(secs): " << hdr.duration_Seconds;
qDebug() << "Number of Signals: " << hdr.num_signals << "\n";
}
void ifprint( QString label, QString text) {
if ( text.isEmpty() )
return;
qDebug() << label << ": " << text;
return;
}
void dumpSignals( const QVector<EDFSignal> sigs ) {
int i = 1;
for (auto sig: sigs) {
qDebug() << "Signal #" << i++;
qDebug() << "Label: " << sig.label;
ifprint( "Transducer", sig.transducer_type );
ifprint( "Dimension", sig.physical_dimension );
qDebug() << "Physical min: " << sig.physical_minimum << " max: " << sig.physical_maximum;
qDebug() << "Digital min: " << sig.digital_minimum << " max: " << sig.digital_maximum;
qDebug() << "Gain: " << sig.gain << " Offset: " << sig.offset;
ifprint( "Pre-filter", sig.prefiltering );
qDebug() << "Sample Count: " << sig.sampleCnt;
qDebug() << "dataArray is at " << sig.dataArray << "\n";
}
}
int main(int argc, char *argv[]) {
// QString homeDocs = QStandardPaths::writableLocation(QStandardPaths::DocumentsLocation)+"/";
// QCoreApplication::setApplicationName(getAppName());
// QCoreApplication::setOrganizationName(getDeveloperName());
// QCoreApplication::setOrganizationDomain(getDeveloperDomain());
// int first = 0, last = 0;
// int firstSig = 1, lastSig = 0;
QApplication a(argc, argv);
QStringList args = a.arguments();
if ( args.size() < 2 ) {
qDebug() << args[0] << " needs a filename" ;
exit(1);
}
QString filename = args[args.size()-1];
bool showall = false; // brief = false;
for (int i = 1; i < args.size()-1; i++) {
// if (args[i] == "-f")
// first = args[++i].toInt();
// else if (args[i] == "-g")
// firstSig = args[++i].toInt();
// else if (args[i] == "-l")
// last = args[++i].toInt();
// else if (args[i] == "-m")
// lastSig = args[++i].toInt();
if (args[i] == "-a")
showall = true;
// else if (args[i] == "-b")
// brief = true;
}
EDFInfo edf;
QByteArray * buffer = edf.Open(filename);
if ( ! edf.Parse(buffer) )
exit(-1);
QDate d2 = edf.edfHdr.startdate_orig.date();
if (d2.year() < 2000) {
d2.setDate(d2.year() + 100, d2.month(), d2.day());
edf.edfHdr.startdate_orig.setDate(d2);
}
QDateTime date = edf.edfHdr.startdate_orig;
qDebug() << edf.filename << " starts at " << date.toString() << " with " << edf.GetNumSignals() << " signals" <<
" and " << edf.GetNumDataRecords() << " records";
// if (args.size() == 2) {
// exit(0);
// }
if (showall) {
dumpHeader( (edf.edfHdr) );
dumpSignals( (edf.edfsignals) );
}
// if ( brief )
// exit(0);
qDebug() << "File has " << edf.annotations.size() << "annotation vectors";
int vec = 1;
for (auto annoVec = edf.annotations.begin(); annoVec != edf.annotations.end(); annoVec++ ) {
qDebug() << "Vector " << vec++ << " has " << annoVec->size() << " annotations";
for (auto anno = annoVec->begin(); anno != annoVec->end(); anno++ ) {
qDebug() << "Offset: " << anno->offset << " Duration: " << anno->duration << " Text: " << anno->text;
}
}
}

14
dumpSTR/edfparser.cpp
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@ -125,7 +125,7 @@ bool EDFInfo::Parse(QByteArray * fileData )
sleep(1);
return false;
}
datasize = filesize - edfHdr.num_header_bytes;
datasize = filesize - EDFHeaderSize;
// Initialize fixed-size signal list.
edfsignals.resize(edfHdr.num_signals);
@ -206,7 +206,8 @@ bool EDFInfo::Parse(QByteArray * fileData )
}
for (int recNo = 0; recNo < edfHdr.num_data_records; recNo++) {
for (auto & sig : edfsignals) {
if ( sig.label.contains("ANNOTATIONS") ) {
if ( sig.label.contains("Annotation") ) {
// qDebug() << "Rec " << recNo << " Anno @ " << pos << " starts with " << signalPtr[pos];
annotations.push_back(ReadAnnotations( (char *)&signalPtr[pos], sig.sampleCnt*2));
pos += sig.sampleCnt * 2;
} else { // it's got genuine 16-bit values
@ -221,9 +222,9 @@ bool EDFInfo::Parse(QByteArray * fileData )
}
// Parse the EDF file to get the annotations out of it.
QVector<Annotation> * EDFInfo::ReadAnnotations(const char * data, int charLen)
QVector<Annotation> EDFInfo::ReadAnnotations(const char * data, int charLen)
{
QVector<Annotation> * annoVec = new QVector<Annotation>;
QVector<Annotation> annoVec = QVector<Annotation>();
// Process event annotation record
@ -279,6 +280,7 @@ QVector<Annotation> * EDFInfo::ReadAnnotations(const char * data, int charLen)
}
while ((data[pos] == AnnoSep) && (pos < charLen)) {
text = "";
int textLen = 0;
pos++;
const char * textStart = &data[pos];
@ -292,8 +294,8 @@ QVector<Annotation> * EDFInfo::ReadAnnotations(const char * data, int charLen)
pos++; // officially UTF-8 is allowed here, so don't mangle it
textLen++;
} while ((data[pos] != AnnoSep) && (pos < charLen)); // separator code
text.fromUtf8(textStart, textLen);
annoVec->push_back( Annotation( offset, duration, text) );
text = QString::fromUtf8(textStart, textLen);
annoVec.push_back( Annotation( offset, duration, text) );
if (pos >= charLen) {
qDebug() << "Short EDF Annotations record";
// sleep(1);

4
dumpSTR/edfparser.h
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@ -144,7 +144,7 @@ class EDFInfo
// QVector< QVector<qint16> > dataRecords; //! \brief Holds the datarecords
QVector< QVector<Annotation> * > annotations; //! \brief Holds the Annotaions for this EDF file
QVector< QVector<Annotation> > annotations; //! \brief Holds the Annotaions for this EDF file
QStringList signal_labels; //! \brief An by-name indexed into the EDFSignal data
@ -152,7 +152,7 @@ class EDFInfo
// the following could be private
private:
QVector<Annotation> * ReadAnnotations( const char * data, int charLen ); //! \brief Create an Annotaion vector from the signal values
QVector<Annotation> ReadAnnotations( const char * data, int charLen ); //! \brief Create an Annotaion vector from the signal values
QString ReadBytes(unsigned n); //! \brief Read n bytes of 8 bit data from the EDF+ data stream

3
dumpSTR/main.cpp
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@ -82,7 +82,8 @@ int main(int argc, char *argv[]) {
EDFInfo str;
QByteArray * buffer = str.Open(filename);
str.Parse(buffer);
if ( ! str.Parse(buffer) )
exit(-1);
QDate d2 = str.edfHdr.startdate_orig.date();
if (d2.year() < 2000) {

22
oscar/SleepLib/loader_plugins/edfparser.cpp
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@ -92,10 +92,10 @@ bool EDFInfo::Parse(QByteArray * fileData )
return false;
}
edfHdr.patientident=QString::fromLatin1(hdrPtr->patientident,80);
edfHdr.recordingident = QString::fromLatin1(hdrPtr->recordingident, 80); // Serial number is in here..
edfHdr.patientident=QString::fromLatin1(hdrPtr->patientident,80).trimmed();
edfHdr.recordingident = QString::fromLatin1(hdrPtr->recordingident, 80).trimmed(); // Serial number is in here..
edfHdr.startdate_orig = QDateTime::fromString(QString::fromLatin1(hdrPtr->datetime, 16), "dd.MM.yyHH.mm.ss");
// This conversion will fail in 2086 after when the spec calls for the year to be 'yy' instead of digits
// This conversion will fail in 2084 after when the spec calls for the year to be 'yy' instead of digits
// The solution is left for the afflicted - it won't be me!
QDate d2 = edfHdr.startdate_orig.date();
if (d2.year() < 2000) {
@ -109,7 +109,7 @@ bool EDFInfo::Parse(QByteArray * fileData )
sleep(1);
return false;
}
edfHdr.reserved44=QString::fromLatin1(hdrPtr->reserved, 44);
edfHdr.reserved44=QString::fromLatin1(hdrPtr->reserved, 44).trimmed();
edfHdr.num_data_records = QString::fromLatin1(hdrPtr->num_data_records, 8).toLong(&ok);
if (!ok) {
qWarning() << "EDFInfo::Parse() Bad data record count " << filename;
@ -199,17 +199,17 @@ bool EDFInfo::Parse(QByteArray * fileData )
// allocate the arrays for the signal values
for (auto & sig : edfsignals) {
long recs = sig.sampleCnt * edfHdr.num_data_records;
long samples = sig.sampleCnt * edfHdr.num_data_records;
if (edfHdr.num_data_records <= 0) {
sig.dataArray = nullptr;
continue;
}
sig.dataArray = new qint16 [recs];
sig.dataArray = new qint16 [samples];
// sig.pos = 0;
}
for (int recNo = 0; recNo < edfHdr.num_data_records; recNo++) {
for (auto & sig : edfsignals) {
if ( sig.label.contains("ANNOTATIONS") ) {
if ( sig.label.contains("Annotations") ) {
annotations.push_back(ReadAnnotations( (char *)&signalPtr[pos], sig.sampleCnt*2));
pos += sig.sampleCnt * 2;
} else { // it's got genuine 16-bit values
@ -224,9 +224,9 @@ bool EDFInfo::Parse(QByteArray * fileData )
}
// Parse the EDF file to get the annotations out of it.
QVector<Annotation> * EDFInfo::ReadAnnotations(const char * data, int charLen)
QVector<Annotation> EDFInfo::ReadAnnotations(const char * data, int charLen)
{
QVector<Annotation> * annoVec = new QVector<Annotation>;
QVector<Annotation> annoVec = QVector<Annotation>();
// Process event annotation record
@ -295,8 +295,8 @@ QVector<Annotation> * EDFInfo::ReadAnnotations(const char * data, int charLen)
pos++; // officially UTF-8 is allowed here, so don't mangle it
textLen++;
} while ((data[pos] != AnnoSep) && (pos < charLen)); // separator code
text.fromUtf8(textStart, textLen);
annoVec->push_back( Annotation( offset, duration, text) );
text = QString::fromUtf8(textStart, textLen);
annoVec.push_back( Annotation( offset, duration, text) );
if (pos >= charLen) {
qDebug() << "Short EDF Annotations record";
// sleep(1);

4
oscar/SleepLib/loader_plugins/edfparser.h
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@ -140,7 +140,7 @@ class EDFInfo
QVector<EDFSignal> edfsignals; //! \brief Holds the EDFSignals contained in this edf file
QVector< QVector<Annotation> * > annotations; //! \brief Holds the Annotaions for this EDF file
QVector< QVector<Annotation> > annotations; //! \brief Holds the Annotaions for this EDF file
QStringList signal_labels; //! \brief An by-name indexed into the EDFSignal data
@ -148,7 +148,7 @@ class EDFInfo
// the following could be private
private:
QVector<Annotation> * ReadAnnotations( const char * data, int charLen ); //! \brief Create an Annotaion vector from the signal values
QVector<Annotation> ReadAnnotations( const char * data, int charLen ); //! \brief Create an Annotaion vector from the signal values
QString ReadBytes(unsigned n); //! \brief Read n bytes of 8 bit data from the EDF+ data stream