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EDFParser cleanup and .gz file handling fixes

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This commit is contained in:
Mark Watkins 2018-05-06 17:55:02 +10:00
parent 4dcf1a75fb
commit 0583675641
5 changed files with 93 additions and 118 deletions
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199
sleepyhead/SleepLib/loader_plugins/edfparser.cpp
View File

@ -9,6 +9,7 @@
#include <QDateTime>
#include <QDebug>
#include <QFile>
#include <QMutexLocker>
#include "zlib.h"
@ -22,16 +23,15 @@ EDFParser::EDFParser(QString name)
}
EDFParser::~EDFParser()
{
for (QVector<EDFSignal>::iterator s = edfsignals.begin(); s != edfsignals.end(); s++) {
if ((*s).data) { delete [](*s).data; }
for (auto & s : edfsignals) {
if (s.data) { delete [] s.data; }
}
if (buffer) { delete [] buffer; }
}
// Read a 16 bits integer
qint16 EDFParser::Read16()
{
if ((pos + 2) > filesize) {
if ((pos + 2) > datasize) {
eof = true;
return 0;
}
@ -49,8 +49,9 @@ qint16 EDFParser::Read16()
QString EDFParser::Read(unsigned n)
{
if ((pos + long(n)) > filesize) {
return "";
if ((pos + long(n)) > datasize) {
eof = true;
return QString();
}
QByteArray buf(&buffer[pos], n);
@ -61,25 +62,22 @@ QString EDFParser::Read(unsigned n)
bool EDFParser::Parse()
{
bool ok;
QString temp, temp2;
version = QString::fromLatin1(header.version, 8).toLong(&ok);
if (header == nullptr) {
qWarning() << "EDFParser::Parse() called without valid EDF data" << filename;
return false;
}
eof = false;
version = QString::fromLatin1(header->version, 8).toLong(&ok);
if (!ok) {
return false;
}
//patientident=QString::fromLatin1(header.patientident,80);
recordingident = QString::fromLatin1(header.recordingident, 80); // Serial number is in here..
recordingident = QString::fromLatin1(header->recordingident, 80); // Serial number is in here..
int snp = recordingident.indexOf("SRN=");
serialnumber.clear();
/*char * idx=index(header.recordingident,'=');
idx++;
for (int i=0;i<16;++i) {
if (*idx==0x20) break;
serialnumber+=*idx;
++idx;
} */
for (int i = snp + 4; i < recordingident.length(); i++) {
if (recordingident[i] == ' ') {
@ -89,7 +87,7 @@ bool EDFParser::Parse()
serialnumber += recordingident[i];
}
startdate_orig = QDateTime::fromString(QString::fromLatin1(header.datetime, 16), "dd.MM.yyHH.mm.ss");
startdate_orig = QDateTime::fromString(QString::fromLatin1(header->datetime, 16), "dd.MM.yyHH.mm.ss");
QDate d2 = startdate_orig.date();
@ -108,26 +106,26 @@ bool EDFParser::Parse()
//qDebug() << startDate.toString("yyyy-MM-dd HH:mm:ss");
num_header_bytes = QString::fromLatin1(header.num_header_bytes, 8).toLong(&ok);
num_header_bytes = QString::fromLatin1(header->num_header_bytes, 8).toLong(&ok);
if (!ok) {
return false;
}
//reserved44=QString::fromLatin1(header.reserved,44);
num_data_records = QString::fromLatin1(header.num_data_records, 8).toLong(&ok);
num_data_records = QString::fromLatin1(header->num_data_records, 8).toLong(&ok);
if (!ok) {
return false;
}
dur_data_record = (QString::fromLatin1(header.dur_data_records, 8).toDouble(&ok) * 1000.0L);
dur_data_record = (QString::fromLatin1(header->dur_data_records, 8).toDouble(&ok) * 1000.0L);
if (!ok) {
return false;
}
num_signals = QString::fromLatin1(header.num_signals, 4).toLong(&ok);
num_signals = QString::fromLatin1(header->num_signals, 4).toLong(&ok);
if (!ok) {
return false;
@ -142,47 +140,50 @@ bool EDFParser::Parse()
// Initialize fixed-size signal list.
edfsignals.resize(num_signals);
for (int i = 0; i < num_signals; i++) {
EDFSignal &sig = edfsignals[i];
for (auto & sig : edfsignals) {
sig.data = nullptr;
sig.label = Read(16);
signal_labels.push_back(sig.label);
signalList[sig.label].push_back(&sig);
signal.push_back(&sig);
if (eof) return false;
}
for (int i = 0; i < num_signals; i++) { edfsignals[i].transducer_type = Read(80); }
for (int i = 0; i < num_signals; i++) { edfsignals[i].physical_dimension = Read(8); }
for (int i = 0; i < num_signals; i++) { edfsignals[i].physical_minimum = Read(8).toDouble(&ok); }
for (int i = 0; i < num_signals; i++) { edfsignals[i].physical_maximum = Read(8).toDouble(&ok); }
for (int i = 0; i < num_signals; i++) { edfsignals[i].digital_minimum = Read(8).toDouble(&ok); }
for (int i = 0; i < num_signals; i++) {
EDFSignal &e = edfsignals[i];
e.digital_maximum = Read(8).toDouble(&ok);
e.gain = (e.physical_maximum - e.physical_minimum) / (e.digital_maximum - e.digital_minimum);
e.offset = 0;
for (auto & sig : edfsignals) { sig.transducer_type = Read(80); }
for (auto & sig : edfsignals) { sig.physical_dimension = Read(8); }
for (auto & sig : edfsignals) { sig.physical_minimum = Read(8).toDouble(&ok); }
for (auto & sig : edfsignals) { sig.physical_maximum = Read(8).toDouble(&ok); }
for (auto & sig : edfsignals) { sig.digital_minimum = Read(8).toDouble(&ok); }
for (auto & sig : edfsignals) { sig.digital_maximum = Read(8).toDouble(&ok);
sig.gain = (sig.physical_maximum - sig.physical_minimum) / (sig.digital_maximum - sig.digital_minimum);
sig.offset = 0;
}
for (auto & sig : edfsignals) { sig.prefiltering = Read(80); }
for (auto & sig : edfsignals) { sig.nr = Read(8).toLong(&ok); }
for (auto & sig : edfsignals) { sig.reserved = Read(32); }
for (int i = 0; i < num_signals; i++) { edfsignals[i].prefiltering = Read(80); }
// could do it earlier, but it won't crash from > EOF Reads
if (eof) return false;
for (int i = 0; i < num_signals; i++) { edfsignals[i].nr = Read(8).toLong(&ok); }
for (int i = 0; i < num_signals; i++) { edfsignals[i].reserved = Read(32); }
// Now check the file isn't truncated before allocating all the memory
long allocsize = 0;
for (auto & sig : edfsignals) {
if (num_data_records > 0) {
allocsize += sig.nr * num_data_records * 2;
}
}
if (allocsize > (datasize - pos)) {
// Space required more than the remainder left to read,
// so abort and let the user clean up the corrupted file themselves
qWarning() << "EDFParser::Parse():" << filename << " is truncated!";
return false;
}
// allocate the buffers
for (int i = 0; i < num_signals; i++) {
//qDebug//cout << "Reading signal " << signals[i]->label << endl;
EDFSignal &sig = edfsignals[i];
for (auto & sig : edfsignals) {
long recs = sig.nr * num_data_records;
if (num_data_records < 0) {
if (num_data_records <= 0) {
sig.data = nullptr;
continue;
}
@ -191,9 +192,9 @@ bool EDFParser::Parse()
sig.pos = 0;
}
for (int x = 0; x < num_data_records; x++) {
for (int i = 0; i < num_signals; i++) {
EDFSignal &sig = edfsignals[i];
for (auto & sig : edfsignals) {
#ifdef Q_LITTLE_ENDIAN
// Intel x86, etc..
memcpy((char *)&sig.data[sig.pos], (char *)&buffer[pos], sig.nr * 2);
@ -211,84 +212,58 @@ bool EDFParser::Parse()
return true;
}
QByteArray gUncompress(const QByteArray &data);
bool EDFParser::Open(const QString & name)
{
if (buffer != nullptr) {
qWarning() << "EDFParser::Open() called with buffer already initialized";
qWarning() << "EDFParser::Open() called with file already open" << name;
return false;
}
if (name.endsWith(STR_ext_gz)) {
// Open and decempress file to buffer
filename = name.mid(0, -3);
// Get file length from inside gzip file
QFile fi(name);
if (!fi.open(QFile::ReadOnly) || !fi.seek(fi.size() - 4)) {
goto badfile;
}
unsigned char ch[4];
fi.read((char *)ch, 4);
filesize = ch[0] | (ch [1] << 8) | (ch[2] << 16) | (ch[3] << 24);
datasize = filesize - EDFHeaderSize;
if (datasize < 0) {
goto badfile;
}
EDFMutex.lock();
// Open gzip file for reading
gzFile f = gzopen(name.toLatin1(), "rb");
if (!f) {
EDFMutex.unlock();
goto badfile;
}
// Decompressed header and data block
gzread(f, (char *)&header, EDFHeaderSize);
buffer = new char [datasize];
gzread(f, buffer, datasize);
gzclose(f);
EDFMutex.unlock();
} else {
// Open and read uncompressed file
QFile f(name);
if (!f.open(QIODevice::ReadOnly)) {
goto badfile;
}
filename = name;
filesize = f.size();
datasize = filesize - EDFHeaderSize;
if (datasize < 0) {
goto badfile;
}
f.read((char *)&header, EDFHeaderSize);
buffer = new char [datasize];
f.read(buffer, datasize);
f.close();
QFile fi(name);
if (!fi.open(QFile::ReadOnly)) {
goto badfile;
}
if (name.endsWith(STR_ext_gz)) {
filename = name.mid(0, -3); // DoubleCheck: why am I cropping the extension? this is used for debugging
// Open and decempress file
data = gUncompress(fi.readAll());
} else {
// Open and read uncompressed file
filename = name;
data = fi.readAll();
}
fi.close();
filesize = data.size();
if (filesize > EDFHeaderSize) {
header = (EDFHeader *)data.constData();
//memcpy((char *)&header, (char *)data.constData(), sizeof(EDFHeader));
buffer = (char *)data.constData() + EDFHeaderSize;
datasize = filesize - EDFHeaderSize;
} else goto badfile;
pos = 0;
return true;
badfile:
filesize = 0;
datasize = 0;
buffer = nullptr;
header = nullptr;
data.clear();
qDebug() << "EDFParser::Open() Couldn't open file" << name;
return false;
}
EDFSignal *EDFParser::lookupLabel(const QString & name, int index)
{
QHash<QString, QList<EDFSignal *> >::iterator it = signalList.find(name);
auto it = signalList.find(name);
if (it == signalList.end()) return nullptr;
if (index >= it.value().size()) return nullptr;
@ -296,4 +271,4 @@ EDFSignal *EDFParser::lookupLabel(const QString & name, int index)
return it.value()[index];
}
QMutex EDFParser::EDFMutex;
//QMutex EDFParser::EDFMutex;

8
sleepyhead/SleepLib/loader_plugins/edfparser.h
View File

@ -123,8 +123,6 @@ class EDFParser
//! \brief ResMed likes to use the SAME signal name
QHash<QString, QList<EDFSignal *> > signalList;
QList<EDFSignal *> signal;
EDFSignal *lookupLabel(const QString & name, int index=0);
//! \brief Returns the number of signals contained in this EDF file
@ -144,7 +142,8 @@ class EDFParser
char *buffer;
//! \brief The EDF+ files header structure, used as a place holder while processing the text data.
EDFHeader header;
EDFHeader *header;
QByteArray data;
QString filename;
long filesize;
@ -164,7 +163,8 @@ class EDFParser
qint64 startdate;
qint64 enddate;
QString reserved44;
static QMutex EDFMutex;
// static QMutex EDFMutex;
bool eof;
};

1
sleepyhead/SleepLib/loader_plugins/resmed_loader.cpp
View File

@ -2488,7 +2488,6 @@ int ResmedLoader::Open(const QString & dirpath)
QFileInfoList flist = dir.entryInfoList();
QDate date;
int size = flist.size();
// Add any STR_Backup versions to the file list
for (auto & fi : flist) {
filename = fi.fileName();

2
sleepyhead/logger.cpp
View File

@ -66,7 +66,7 @@ void initializeLogger()
bool b = otherThreadPool->tryStart(logger);
qInstallMessageHandler(MyOutputHandler);
if (b) {
qWarning() << "Started logging thread";
qDebug() << "Started logging thread";
} else {
qWarning() << "Logging thread did not start correctly";
}

1
sleepyhead/mainwindow.cpp
View File

@ -249,6 +249,7 @@ void MainWindow::logMessage(QString msg)
void MainWindow::closeEvent(QCloseEvent * event)
{
Q_UNUSED(event);
static bool runonce = false;
if (!runonce) {
if (AppSetting->removeCardReminder()) {