From b8b4acb8041876a0cf1343b8ff12157edb7e3023 Mon Sep 17 00:00:00 2001 From: Phil Olynyk Date: Sun, 4 Aug 2019 21:49:17 -0400 Subject: [PATCH] Added Annotation dump program and fixed edfparser to make it work --- anotDump.pro | 32 +++++ anotDump/main.cpp | 123 ++++++++++++++++++++ dumpSTR/edfparser.cpp | 14 ++- dumpSTR/edfparser.h | 4 +- dumpSTR/main.cpp | 3 +- oscar/SleepLib/loader_plugins/edfparser.cpp | 22 ++-- oscar/SleepLib/loader_plugins/edfparser.h | 4 +- 7 files changed, 180 insertions(+), 22 deletions(-) create mode 100644 anotDump.pro create mode 100644 anotDump/main.cpp diff --git a/anotDump.pro b/anotDump.pro new file mode 100644 index 00000000..1d671af5 --- /dev/null +++ b/anotDump.pro @@ -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 \ + diff --git a/anotDump/main.cpp b/anotDump/main.cpp new file mode 100644 index 00000000..de661796 --- /dev/null +++ b/anotDump/main.cpp @@ -0,0 +1,123 @@ +/* Dump the annotations of an edf file */ + +#include +// #include +#include + +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 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; + } + } + +} diff --git a/dumpSTR/edfparser.cpp b/dumpSTR/edfparser.cpp index 412477f2..687b3a42 100644 --- a/dumpSTR/edfparser.cpp +++ b/dumpSTR/edfparser.cpp @@ -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 * EDFInfo::ReadAnnotations(const char * data, int charLen) +QVector EDFInfo::ReadAnnotations(const char * data, int charLen) { - QVector * annoVec = new QVector; + QVector annoVec = QVector(); // Process event annotation record @@ -279,6 +280,7 @@ QVector * 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 * 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); diff --git a/dumpSTR/edfparser.h b/dumpSTR/edfparser.h index 83a27f5a..69eab21a 100644 --- a/dumpSTR/edfparser.h +++ b/dumpSTR/edfparser.h @@ -144,7 +144,7 @@ class EDFInfo // QVector< QVector > dataRecords; //! \brief Holds the datarecords - QVector< QVector * > annotations; //! \brief Holds the Annotaions for this EDF file + QVector< QVector > 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 * ReadAnnotations( const char * data, int charLen ); //! \brief Create an Annotaion vector from the signal values + QVector 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 diff --git a/dumpSTR/main.cpp b/dumpSTR/main.cpp index 1d44707f..54f2ac77 100644 --- a/dumpSTR/main.cpp +++ b/dumpSTR/main.cpp @@ -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) { diff --git a/oscar/SleepLib/loader_plugins/edfparser.cpp b/oscar/SleepLib/loader_plugins/edfparser.cpp index b12f5bea..bd95f777 100644 --- a/oscar/SleepLib/loader_plugins/edfparser.cpp +++ b/oscar/SleepLib/loader_plugins/edfparser.cpp @@ -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 * EDFInfo::ReadAnnotations(const char * data, int charLen) +QVector EDFInfo::ReadAnnotations(const char * data, int charLen) { - QVector * annoVec = new QVector; + QVector annoVec = QVector(); // Process event annotation record @@ -295,8 +295,8 @@ QVector * 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); diff --git a/oscar/SleepLib/loader_plugins/edfparser.h b/oscar/SleepLib/loader_plugins/edfparser.h index a54a8cb8..ba3e58dc 100644 --- a/oscar/SleepLib/loader_plugins/edfparser.h +++ b/oscar/SleepLib/loader_plugins/edfparser.h @@ -140,7 +140,7 @@ class EDFInfo QVector edfsignals; //! \brief Holds the EDFSignals contained in this edf file - QVector< QVector * > annotations; //! \brief Holds the Annotaions for this EDF file + QVector< QVector > 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 * ReadAnnotations( const char * data, int charLen ); //! \brief Create an Annotaion vector from the signal values + QVector 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