Added Annotation dump program and fixed edfparser to make it work

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 \
+

anotDump/main.cpp

@@ -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;
+        }
+    }
+	
+}

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<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);
+            text = QString::fromUtf8(textStart, textLen);
-            annoVec->push_back( Annotation( offset, duration, text) );
+            annoVec.push_back( Annotation( offset, duration, text) );
             if (pos >= charLen) {
                 qDebug() << "Short EDF Annotations record";
         //      sleep(1);

dumpSTR/edfparser.h

@@ -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
 

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) {

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.patientident=QString::fromLatin1(hdrPtr->patientident,80).trimmed();
-    edfHdr.recordingident = QString::fromLatin1(hdrPtr->recordingident, 80); // Serial number is in here..
+    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);
+            text = QString::fromUtf8(textStart, textLen);
-            annoVec->push_back( Annotation( offset, duration, text) );
+            annoVec.push_back( Annotation( offset, duration, text) );
             if (pos >= charLen) {
                 qDebug() << "Short EDF Annotations record";
         //      sleep(1);

oscar/SleepLib/loader_plugins/edfparser.h

@@ -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