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This commit is contained in:
Phil Olynyk 2019-08-30 13:22:19 -04:00
parent 5ee8feb37c
commit 3055e1fe37
3 changed files with 139 additions and 132 deletions
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34
oscar/SleepLib/loader_plugins/edfparser.cpp
View File

@ -37,8 +37,8 @@ EDFInfo::EDFInfo()
EDFInfo::~EDFInfo() EDFInfo::~EDFInfo()
{ {
if ( fileData ) // if ( fileData )
delete fileData; // delete fileData;
for (auto & s : edfsignals) { for (auto & s : edfsignals) {
if (s.dataArray) if (s.dataArray)
@ -69,7 +69,7 @@ QByteArray * EDFInfo::Open(const QString & name)
} }
fi.close(); fi.close();
if (fileData->size() <= EDFHeaderSize) { if (fileData->size() <= EDFHeaderSize) {
delete fileData; fileData->clear();;
qDebug() << "EDFInfo::Open() File too short " << name; qDebug() << "EDFInfo::Open() File too short " << name;
sleep(1); sleep(1);
return nullptr; return nullptr;
@ -86,8 +86,7 @@ bool EDFInfo::parseHeader( EDFHeaderRaw *hdrPtr )
if (!ok) { if (!ok) {
qWarning() << "EDFInfo::Parse() Bad Version " << filename; qWarning() << "EDFInfo::Parse() Bad Version " << filename;
sleep(1); sleep(1);
delete fileData; fileData->clear();
fileData = nullptr;
return false; return false;
} }
@ -106,8 +105,7 @@ bool EDFInfo::parseHeader( EDFHeaderRaw *hdrPtr )
if (!ok) { if (!ok) {
qWarning() << "EDFInfo::Parse() Bad header byte count " << filename; qWarning() << "EDFInfo::Parse() Bad header byte count " << filename;
sleep(1); sleep(1);
delete fileData; fileData->clear();
fileData = nullptr;
return false; return false;
} }
edfHdr.reserved44=QString::fromLatin1(hdrPtr->reserved, 44).trimmed(); edfHdr.reserved44=QString::fromLatin1(hdrPtr->reserved, 44).trimmed();
@ -115,24 +113,21 @@ bool EDFInfo::parseHeader( EDFHeaderRaw *hdrPtr )
if (!ok) { if (!ok) {
qWarning() << "EDFInfo::Parse() Bad data record count " << filename; qWarning() << "EDFInfo::Parse() Bad data record count " << filename;
sleep(1); sleep(1);
delete fileData; fileData->clear();
fileData = nullptr;
return false; return false;
} }
edfHdr.duration_Seconds = QString::fromLatin1(hdrPtr->dur_data_records, 8).toDouble(&ok); edfHdr.duration_Seconds = QString::fromLatin1(hdrPtr->dur_data_records, 8).toDouble(&ok);
if (!ok) { if (!ok) {
qWarning() << "EDFInfo::Parse() Bad duration " << filename; qWarning() << "EDFInfo::Parse() Bad duration " << filename;
sleep(1); sleep(1);
delete fileData; fileData->clear();
fileData = nullptr;
return false; return false;
} }
edfHdr.num_signals = QString::fromLatin1(hdrPtr->num_signals, 4).toLong(&ok); edfHdr.num_signals = QString::fromLatin1(hdrPtr->num_signals, 4).toLong(&ok);
if (!ok) { if (!ok) {
qWarning() << "EDFInfo::Parse() Bad number of signals " << filename; qWarning() << "EDFInfo::Parse() Bad number of signals " << filename;
sleep(1); sleep(1);
delete fileData; fileData->clear();
fileData = nullptr;
return false; return false;
} }
return true; return true;
@ -172,8 +167,7 @@ bool EDFInfo::Parse(QByteArray * fileData )
if (eof) { if (eof) {
qWarning() << "EDFInfo::Parse() Early end of file " << filename; qWarning() << "EDFInfo::Parse() Early end of file " << filename;
sleep(1); sleep(1);
delete fileData; fileData->clear();
fileData = nullptr;
return false; return false;
} }
} }
@ -211,8 +205,7 @@ bool EDFInfo::Parse(QByteArray * fileData )
if (eof) { if (eof) {
qWarning() << "EDFInfo::Parse() Early end of file " << filename; qWarning() << "EDFInfo::Parse() Early end of file " << filename;
sleep(1); sleep(1);
delete fileData; fileData->clear();
fileData = nullptr;
return false; return false;
} }
@ -228,8 +221,7 @@ bool EDFInfo::Parse(QByteArray * fileData )
// so abort and let the user clean up the corrupted file themselves // so abort and let the user clean up the corrupted file themselves
qWarning() << "EDFInfo::Parse(): " << filename << " is too short!"; qWarning() << "EDFInfo::Parse(): " << filename << " is too short!";
sleep(1); sleep(1);
delete fileData; fileData->clear();
fileData = nullptr;
return false; return false;
} }
@ -256,8 +248,7 @@ bool EDFInfo::Parse(QByteArray * fileData )
} }
} }
} }
delete fileData; fileData->clear();
fileData = nullptr;
return true; return true;
} }
@ -282,6 +273,7 @@ EDFHeaderQT * EDFInfo::GetHeader( const QString & name)
if ( ! parseHeader( hdrPtr ) ) if ( ! parseHeader( hdrPtr ) )
return nullptr; return nullptr;
fileData->clear();
return & edfHdr; return & edfHdr;
} }

233
oscar/SleepLib/loader_plugins/resmed_loader.cpp
View File

@ -140,12 +140,12 @@ bool matchSignal(ChannelID ch, const QString & name)
} }
// This function parses a list of STR files and creates a date ordered map of individual records // This function parses a list of STR files and creates a date ordered map of individual records
void ResmedLoader::ParseSTR(Machine *mach, QMap<QDate, STRFile> & STRmap) void ResmedLoader::ParseSTR(Machine *mach, QMap<QDate, STRFile> & STRmap, QDate firstImport)
{ {
Q_UNUSED(mach) Q_UNUSED(mach)
QDateTime ignoreBefore = p_profile->session->ignoreOlderSessionsDate(); // QDateTime ignoreBefore = p_profile->session->ignoreOlderSessionsDate();
bool ignoreOldSessions = p_profile->session->ignoreOlderSessions(); // bool ignoreOldSessions = p_profile->session->ignoreOlderSessions();
int totalRecs = 0; int totalRecs = 0;
for (auto it=STRmap.begin(), end=STRmap.end(); it != end; ++it) { for (auto it=STRmap.begin(), end=STRmap.end(); it != end; ++it) {
@ -167,10 +167,15 @@ void ResmedLoader::ParseSTR(Machine *mach, QMap<QDate, STRFile> & STRmap)
QDate date = str.edfHdr.startdate_orig.date(); // each STR.edf record starts at 12 noon QDate date = str.edfHdr.startdate_orig.date(); // each STR.edf record starts at 12 noon
int size = str.GetNumDataRecords(); int size = str.GetNumDataRecords();
QDate lastDay = date.addDays(size-1);
qDebug() << "Parsing" << strfile << date.toString() << size << str.GetNumSignals(); qDebug() << "Parsing" << strfile << date.toString() << size << str.GetNumSignals();
qDebug() << "Last day is" << date.addDays(size-1).toString(); qDebug() << "Last day is" << lastDay;
sleep(1);
if ( lastDay < firstImport ) {
qDebug() << "LastDay before firstImport, skipping" << file.filename;
continue;
}
// ResMed and their consistent naming and spacing... :/ // ResMed and their consistent naming and spacing... :/
EDFSignal *maskon = str.lookupLabel("Mask On"); EDFSignal *maskon = str.lookupLabel("Mask On");
@ -189,12 +194,12 @@ void ResmedLoader::ParseSTR(Machine *mach, QMap<QDate, STRFile> & STRmap)
emit setProgressValue(++currentRec); emit setProgressValue(++currentRec);
QCoreApplication::processEvents(); QCoreApplication::processEvents();
if (ignoreOldSessions) { // if (ignoreOldSessions) {
if (date < ignoreBefore.date()) { if (date < firstImport) {
qDebug() << "Skipping" << date.toString() << "Before" << ignoreBefore.date().toString(); // qDebug() << "Skipping" << date.toString() << "Before" << ignoreBefore.date().toString();
continue; continue;
} }
} // }
auto rit = resdayList.find(date); auto rit = resdayList.find(date);
if (rit != resdayList.end()) { if (rit != resdayList.end()) {
@ -221,8 +226,8 @@ void ResmedLoader::ParseSTR(Machine *mach, QMap<QDate, STRFile> & STRmap)
rit = resdayList.insert(date, ResMedDay()); rit = resdayList.insert(date, ResMedDay());
qDebug() << "Setting up STRRecord for" << date.toString(); // qDebug() << "Setting up STRRecord for" << date.toString();
sleep(1); // sleep(1);
STRRecord &R = rit.value().str; STRRecord &R = rit.value().str;
uint timestamp = QDateTime(date,QTime(12,0,0)).toTime_t(); uint timestamp = QDateTime(date,QTime(12,0,0)).toTime_t();
@ -591,12 +596,12 @@ void ResmedLoader::ParseSTR(Machine *mach, QMap<QDate, STRFile> & STRmap)
if ((sig = str.lookupLabel("S.Tube"))) { if ((sig = str.lookupLabel("S.Tube"))) {
R.s_Tube = EventDataType(sig->dataArray[rec]) * sig->gain + sig->offset; R.s_Tube = EventDataType(sig->dataArray[rec]) * sig->gain + sig->offset;
} }
qDebug() << "Finished" << date.toString(); // qDebug() << "Finished" << date.toString();
sleep(1); // sleep(1);
} }
} }
qDebug() << "Finished ParseSTR"; // qDebug() << "Finished ParseSTR";
sleep(3); // sleep(3);
} }
ResmedLoader::ResmedLoader() { ResmedLoader::ResmedLoader() {
@ -648,6 +653,46 @@ bool ResmedLoader::Detect(const QString & givenpath)
return true; return true;
} }
QHash<QString, QString> parseIdentLine( const QString line, MachineInfo * info)
{
QHash<QString, QString> hash;
if (!line.isEmpty()) {
QString key = line.section(" ", 0, 0).section("#", 1);
QString value = line.section(" ", 1);
if (key == "SRN") { // Serial Number
info->serial = value;
} else if (key == "PNA") { // Product Name
value.replace("_"," ");
if (value.contains(STR_ResMed_S9)) {
value.replace(STR_ResMed_S9, "");
info->series = STR_ResMed_S9;
} else if (value.contains(STR_ResMed_AirSense10)) {
value.replace(STR_ResMed_AirSense10, "");
info->series = STR_ResMed_AirSense10;
} else if (value.contains(STR_ResMed_AirCurve10)) {
value.replace(STR_ResMed_AirCurve10, "");
info->series = STR_ResMed_AirCurve10;
}
value.replace("(","");
value.replace(")","");
if (value.contains("Adapt", Qt::CaseInsensitive)) {
if (!value.contains("VPAP")) {
value.replace("Adapt", QObject::tr("VPAP Adapt"));
}
}
info->model = value.trimmed();
} else if (key == "PCD") { // Product Code
info->modelnumber = value;
}
hash[key] = value;
}
return hash;
}
MachineInfo ResmedLoader::PeekInfo(const QString & path) MachineInfo ResmedLoader::PeekInfo(const QString & path)
{ {
@ -665,39 +710,7 @@ MachineInfo ResmedLoader::PeekInfo(const QString & path)
// Parse # entries into idmap. // Parse # entries into idmap.
while (!f.atEnd()) { while (!f.atEnd()) {
QString line = f.readLine().trimmed(); QString line = f.readLine().trimmed();
QHash<QString, QString> hash = parseIdentLine( line, & info );
if (!line.isEmpty()) {
QString key = line.section(" ", 0, 0).section("#", 1);
QString value = line.section(" ", 1);
if (key == "SRN") { // Serial Number
info.serial = value;
} else if (key == "PNA") { // Product Name
value.replace("_"," ");
if (value.contains(STR_ResMed_S9)) {
value.replace(STR_ResMed_S9, "");
info.series = STR_ResMed_S9;
} else if (value.contains(STR_ResMed_AirSense10)) {
value.replace(STR_ResMed_AirSense10, "");
info.series = STR_ResMed_AirSense10;
} else if (value.contains(STR_ResMed_AirCurve10)) {
value.replace(STR_ResMed_AirCurve10, "");
info.series = STR_ResMed_AirCurve10;
}
value.replace("(","");
value.replace(")","");
if (value.contains("Adapt", Qt::CaseInsensitive)) {
if (!value.contains("VPAP")) {
value.replace("Adapt", QObject::tr("VPAP Adapt"));
}
}
info.model = value.trimmed();
} else if (key == "PCD") { // Product Code
info.modelnumber = value;
}
}
} }
return info; return info;
@ -948,7 +961,7 @@ EDFduration getEDFDuration(const QString & filename)
/////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////
// Sorted EDF files that need processing into date records according to ResMed noon split // Sorted EDF files that need processing into date records according to ResMed noon split
/////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////
int ResmedLoader::scanFiles(Machine * mach, const QString & datalog_path) int ResmedLoader::scanFiles(Machine * mach, const QString & datalog_path, QDate firstImport)
{ {
QTime time; QTime time;
@ -988,8 +1001,8 @@ int ResmedLoader::scanFiles(Machine * mach, const QString & datalog_path)
QFileInfoList dirlist = dir.entryInfoList(); QFileInfoList dirlist = dir.entryInfoList();
int dirlistSize = dirlist.size(); int dirlistSize = dirlist.size();
QDateTime ignoreBefore = p_profile->session->ignoreOlderSessionsDate(); // QDateTime ignoreBefore = p_profile->session->ignoreOlderSessionsDate();
bool ignoreOldSessions = p_profile->session->ignoreOlderSessions(); // bool ignoreOldSessions = p_profile->session->ignoreOlderSessions();
// Scan for any sub folders and create files lists // Scan for any sub folders and create files lists
for (int i = 0; i < dirlistSize ; i++) { for (int i = 0; i < dirlistSize ; i++) {
@ -1004,13 +1017,13 @@ int ResmedLoader::scanFiles(Machine * mach, const QString & datalog_path)
continue; continue;
} }
} else if (len == 8) { // test directory date } else if (len == 8) { // test directory date
if (ignoreOldSessions) { // if (ignoreOldSessions) {
QDateTime dirDate = QDateTime().fromString(filename, "yyyyMMdd"); QDate dirDate = QDate().fromString(filename, "yyyyMMdd");
if (dirDate.date() < ignoreBefore.date()) { if (dirDate < firstImport) {
qDebug() << "Skipping directory - ignore before " << filename; qDebug() << "Skipping directory - ignore before " << filename;
continue; continue;
} }
} // }
} else { } else {
qDebug() << "Skipping directory - bad name size " << filename; qDebug() << "Skipping directory - bad name size " << filename;
continue; continue;
@ -1079,10 +1092,10 @@ int ResmedLoader::scanFiles(Machine * mach, const QString & datalog_path)
date = date.addDays(-1); date = date.addDays(-1);
} }
if (ignoreOldSessions) { // if (ignoreOldSessions) {
if (date < ignoreBefore.date()) if (date < firstImport)
continue; continue;
} // }
// Chop off the .gz component if it exists, it's not needed at this stage // Chop off the .gz component if it exists, it's not needed at this stage
if (filename.endsWith(STR_ext_gz)) { if (filename.endsWith(STR_ext_gz)) {
@ -1630,48 +1643,50 @@ bool parseIdentTGT( QString path, MachineInfo * info, QHash<QString, QString> &
// Parse # entries into idmap. // Parse # entries into idmap.
while (!f.atEnd()) { while (!f.atEnd()) {
QString line = f.readLine().trimmed(); QString line = f.readLine().trimmed();
QHash<QString, QString> hash = parseIdentLine( line, info );
idmap.unite(hash);
if (!line.isEmpty()) { // if (!line.isEmpty()) {
QString key = line.section(" ", 0, 0).section("#", 1); // QString key = line.section(" ", 0, 0).section("#", 1);
QString value = line.section(" ", 1); // QString value = line.section(" ", 1);
//
if (key == "SRN") { // Serial Number // if (key == "SRN") { // Serial Number
info->serial = value; // info->serial = value;
qDebug() << "Serial # is >" << value << "<"; // qDebug() << "Serial # is >" << value << "<";
continue; // continue;
//
} else if (key == "PNA") { // Product Name // } else if (key == "PNA") { // Product Name
qDebug() << "Prouct Name is >" << value << "<"; // qDebug() << "Prouct Name is >" << value << "<";
value.replace("_"," "); // value.replace("_"," ");
if (value.contains(STR_ResMed_S9)) { // if (value.contains(STR_ResMed_S9)) {
value.replace(STR_ResMed_S9, ""); // value.replace(STR_ResMed_S9, "");
info->series = STR_ResMed_S9; // info->series = STR_ResMed_S9;
} else if (value.contains(STR_ResMed_AirSense10)) { // } else if (value.contains(STR_ResMed_AirSense10)) {
value.replace(STR_ResMed_AirSense10, ""); // value.replace(STR_ResMed_AirSense10, "");
info->series = STR_ResMed_AirSense10; // info->series = STR_ResMed_AirSense10;
} else if (value.contains(STR_ResMed_AirCurve10)) { // } else if (value.contains(STR_ResMed_AirCurve10)) {
value.replace(STR_ResMed_AirCurve10, ""); // value.replace(STR_ResMed_AirCurve10, "");
info->series = STR_ResMed_AirCurve10; // info->series = STR_ResMed_AirCurve10;
} // }
value.replace("(",""); // value.replace("(","");
value.replace(")",""); // value.replace(")","");
//
if (value.contains("Adapt", Qt::CaseInsensitive)) { // if (value.contains("Adapt", Qt::CaseInsensitive)) {
if (!value.contains("VPAP")) { // if (!value.contains("VPAP")) {
value.replace("Adapt", QObject::tr("VPAP Adapt")); // value.replace("Adapt", QObject::tr("VPAP Adapt"));
} // }
} // }
info->model = value.trimmed(); // info->model = value.trimmed();
continue; // continue;
//
} else if (key == "PCD") { // Product Code // } else if (key == "PCD") { // Product Code
qDebug() << "Prouct Code is >" << value << "<"; // qDebug() << "Prouct Code is >" << value << "<";
info->modelnumber = value; // info->modelnumber = value;
continue; // continue;
} // }
//
idmap[key] = value; // idmap[key] = value;
} // }
} }
f.close(); f.close();
@ -1973,7 +1988,7 @@ int ResmedLoader::Open(const QString & dirpath)
// Build a Date map of all records in STR.edf files, populating ResDayList // Build a Date map of all records in STR.edf files, populating ResDayList
/////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////
ParseSTR(mach, STRmap ); // , firstImportDay); ParseSTR(mach, STRmap, firstImportDay);
// We are done with the Parsed STR EDF objects, so delete them // We are done with the Parsed STR EDF objects, so delete them
for (auto it=STRmap.begin(), end=STRmap.end(); it != end; ++it) { for (auto it=STRmap.begin(), end=STRmap.end(); it != end; ++it) {
@ -2026,7 +2041,7 @@ int ResmedLoader::Open(const QString & dirpath)
qDebug() << "Starting scan of DATALOG"; qDebug() << "Starting scan of DATALOG";
sleep(1); sleep(1);
scanFiles(mach, datalogPath ); // , firstImportDay); scanFiles(mach, datalogPath, firstImportDay);
if (isAborted()) if (isAborted())
return 0; return 0;
@ -2206,11 +2221,11 @@ bool ResmedLoader::LoadCSL(Session *sess, const QString & path)
// Process event annotation records // Process event annotation records
qDebug() << "File has " << edf.annotations.size() << "annotation vectors"; qDebug() << "File has " << edf.annotations.size() << "annotation vectors";
int vec = 1; // int vec = 1;
for (auto annoVec = edf.annotations.begin(); annoVec != edf.annotations.end(); annoVec++ ) { for (auto annoVec = edf.annotations.begin(); annoVec != edf.annotations.end(); annoVec++ ) {
qDebug() << "Vector " << vec++ << " has " << annoVec->size() << " annotations"; // qDebug() << "Vector " << vec++ << " has " << annoVec->size() << " annotations";
for (auto anno = annoVec->begin(); anno != annoVec->end(); anno++ ) { for (auto anno = annoVec->begin(); anno != annoVec->end(); anno++ ) {
qDebug() << "Offset: " << anno->offset << " Duration: " << anno->duration << " Text: " << anno->text; // qDebug() << "Offset: " << anno->offset << " Duration: " << anno->duration << " Text: " << anno->text;
double tt = edf.startdate + qint64(anno->offset*1000.0); double tt = edf.startdate + qint64(anno->offset*1000.0);
if ( ! anno->text.isEmpty()) { if ( ! anno->text.isEmpty()) {
@ -2228,7 +2243,7 @@ bool ResmedLoader::LoadCSL(Session *sess, const QString & path)
} else { } else {
qDebug() << "Split csr event flag in " << edf.filename; qDebug() << "Split csr event flag in " << edf.filename;
} }
} else if (anno->text != "recording starts") { } else if (anno->text != "Recording starts") {
qDebug() << "Unobserved ResMed CSL annotation field: " << anno->text; qDebug() << "Unobserved ResMed CSL annotation field: " << anno->text;
} }
} }
@ -2283,11 +2298,11 @@ bool ResmedLoader::LoadEVE(Session *sess, const QString & path)
// Process event annotation records // Process event annotation records
qDebug() << "File has " << edf.annotations.size() << "annotation vectors"; qDebug() << "File has " << edf.annotations.size() << "annotation vectors";
int vec = 1; // int vec = 1;
for (auto annoVec = edf.annotations.begin(); annoVec != edf.annotations.end(); annoVec++ ) { for (auto annoVec = edf.annotations.begin(); annoVec != edf.annotations.end(); annoVec++ ) {
qDebug() << "Vector " << vec++ << " has " << annoVec->size() << " annotations"; // qDebug() << "Vector " << vec++ << " has " << annoVec->size() << " annotations";
for (auto anno = annoVec->begin(); anno != annoVec->end(); anno++ ) { for (auto anno = annoVec->begin(); anno != annoVec->end(); anno++ ) {
qDebug() << "Offset: " << anno->offset << " Duration: " << anno->duration << " Text: " << anno->text; // qDebug() << "Offset: " << anno->offset << " Duration: " << anno->duration << " Text: " << anno->text;
double tt = edf.startdate + qint64(anno->offset*1000.0); double tt = edf.startdate + qint64(anno->offset*1000.0);
if ( ! anno->text.isEmpty()) { if ( ! anno->text.isEmpty()) {
@ -2317,7 +2332,7 @@ bool ResmedLoader::LoadEVE(Session *sess, const QString & path)
if (sess->checkInside(tt)) if (sess->checkInside(tt))
CA->AddEvent(tt, anno->duration); CA->AddEvent(tt, anno->duration);
} else { } else {
if (anno->text != "recording starts") { if (anno->text != "Recording starts") {
qDebug() << "Unobserved ResMed annotation field: " << anno->text; qDebug() << "Unobserved ResMed annotation field: " << anno->text;
} }
} }

4
oscar/SleepLib/loader_plugins/resmed_loader.h
View File

@ -349,10 +349,10 @@ class ResmedLoader : public CPAPLoader
protected: protected:
//! \brief The STR.edf file is a unique edf file with many signals //! \brief The STR.edf file is a unique edf file with many signals
void ParseSTR(Machine *, QMap<QDate, STRFile> &); void ParseSTR(Machine *, QMap<QDate, STRFile> &, QDate);
//! \brief Scan for new files to import, group into sessions and add to task que //! \brief Scan for new files to import, group into sessions and add to task que
int scanFiles(Machine * mach, const QString & datalog_path); int scanFiles(Machine * mach, const QString & datalog_path, QDate firstImport);
//! \brief Write a backup copy to the backup path //! \brief Write a backup copy to the backup path
QString backup(const QString & file, const QString & backup_path); QString backup(const QString & file, const QString & backup_path);