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update dumpSTR to use the standard edfparser files

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This commit is contained in:
Phil Olynyk 2020-02-21 11:29:00 -05:00
parent a80134e7db
commit b4bbdd9a54
6 changed files with 39 additions and 534 deletions
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8
dumpSTR.pro
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@ -12,6 +12,8 @@ CONFIG -= debug_and_release
QT += core widgets QT += core widgets
DEFINES+=DUMPSTR
TARGET = dumpSTR TARGET = dumpSTR
TEMPLATE = app TEMPLATE = app
@ -24,9 +26,9 @@ VERSION = 0.5.0
SOURCES += \ SOURCES += \
dumpSTR/main.cpp \ dumpSTR/main.cpp \
dumpSTR/edfparser.cpp \ dumpSTR/edfparser.cpp
HEADERS += \ HEADERS += \
dumpSTR/common.h \ dumpSTR/SleepLib/common.h \
dumpSTR/edfparser.h \ dumpSTR/edfparser.h

0
dumpSTR/common.h → dumpSTR/SleepLib/common.h
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353
dumpSTR/edfparser.cpp
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@ -1,353 +0,0 @@
/* EDF Parser Implementation
*
* Copyright (c) 2019 The OSCAR Team
* Copyright (c) 2011-2018 Mark Watkins <mark@jedimark.net>
*
* This file is subject to the terms and conditions of the GNU General Public
* License. See the file COPYING in the main directory of the source code
* for more details. */
#include <QDateTime>
#include <QDebug>
#include <QFile>
#include <QMutexLocker>
#ifdef _MSC_VER
#include <QtZlib/zlib.h>
#else
#include <zlib.h>
#endif
#include "edfparser.h"
EDFInfo::EDFInfo()
{
filesize = 0;
datasize = 0;
signalPtr = nullptr;
hdrPtr = nullptr;
fileData = nullptr;
}
EDFInfo::~EDFInfo()
{
for (auto & s : edfsignals) {
if (s.dataArray)
delete [] s.dataArray;
}
// for (auto & a : annotations)
// delete a;
}
QByteArray * EDFInfo::Open(const QString & name)
{
if (hdrPtr != nullptr) {
qWarning() << "EDFInfo::Open() called with file already open " << name;
sleep(1);
return nullptr;
}
QFile fi(name);
if (!fi.open(QFile::ReadOnly)) {
qDebug() << "EDFInfo::Open() Couldn't open file " << name;
sleep(1);
return nullptr;
}
fileData = new QByteArray();
// if (name.endsWith(STR_ext_gz)) {
// *fileData = gUncompress(fi.readAll()); // Open and decompress file
// } else {
*fileData = fi.readAll(); // Open and read uncompressed file
// }
fi.close();
if (fileData->size() <= EDFHeaderSize) {
fileData->clear();
qDebug() << "EDFInfo::Open() File too short " << name;
sleep(1);
return nullptr;
}
filename = name;
return fileData;
}
bool EDFInfo::Parse(QByteArray * fileData )
{
bool ok;
if (fileData == nullptr) {
qWarning() << "EDFInfo::Parse() called without valid EDF data " << filename;
sleep(1);
return false;
}
hdrPtr = (EDFHeaderRaw *)(*fileData).constData();
signalPtr = (char *)(*fileData).constData() + EDFHeaderSize;
filesize = (*fileData).size();
pos = 0;
eof = false;
edfHdr.version = QString::fromLatin1(hdrPtr->version, 8).toLong(&ok);
if (!ok) {
qWarning() << "EDFInfo::Parse() Bad Version " << filename;
sleep(1);
return false;
}
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");
QDate d2 = edfHdr.startdate_orig.date();
if (d2.year() < 2000) {
d2.setDate(d2.year() + 100, d2.month(), d2.day());
edfHdr.startdate_orig.setDate(d2);
}
edfHdr.num_header_bytes = QString::fromLatin1(hdrPtr->num_header_bytes, 8).toLong(&ok);
if (!ok) {
qWarning() << "EDFInfo::Parse() Bad header byte count " << filename;
sleep(1);
return false;
}
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;
sleep(1);
return false;
}
edfHdr.duration_Seconds = QString::fromLatin1(hdrPtr->dur_data_records, 8).toDouble(&ok);
if (!ok) {
qWarning() << "EDFInfo::Parse() Bad duration " << filename;
sleep(1);
return false;
}
edfHdr.num_signals = QString::fromLatin1(hdrPtr->num_signals, 4).toLong(&ok);
if (!ok) {
qWarning() << "EDFInfo::Parse() Bad number of signals " << filename;
sleep(1);
return false;
}
datasize = filesize - EDFHeaderSize;
// Initialize fixed-size signal list.
edfsignals.resize(edfHdr.num_signals);
// Now copy all the Signal descriptives into edfsignals
for (auto & sig : edfsignals) {
sig.dataArray = nullptr;
sig.label = ReadBytes(16);
signal_labels.push_back(sig.label);
signalList[sig.label].push_back(&sig);
if (eof) {
qWarning() << "EDFInfo::Parse() Early end of file " << filename;
sleep(1);
return false;
}
}
for (auto & sig : edfsignals) {
sig.transducer_type = ReadBytes(80).trimmed();
}
for (auto & sig : edfsignals) {
sig.physical_dimension = ReadBytes(8);
}
for (auto & sig : edfsignals) {
sig.physical_minimum = ReadBytes(8).toDouble(&ok);
}
for (auto & sig : edfsignals) {
sig.physical_maximum = ReadBytes(8).toDouble(&ok);
}
for (auto & sig : edfsignals) {
sig.digital_minimum = ReadBytes(8).toDouble(&ok);
}
for (auto & sig : edfsignals) {
sig.digital_maximum = ReadBytes(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 = ReadBytes(80).trimmed();
}
for (auto & sig : edfsignals) {
sig.sampleCnt = ReadBytes(8).toLong(&ok);
}
for (auto & sig : edfsignals) {
sig.reserved = ReadBytes(32).trimmed();
}
// could do it earlier, but it won't crash from > EOF Reads
if (eof) {
qWarning() << "EDFInfo::Parse() Early end of file " << filename;
sleep(1);
return false;
}
// Now check the file isn't truncated before allocating space for the values
long totalsize = 0;
for (auto & sig : edfsignals) {
if (edfHdr.num_data_records > 0) {
totalsize += sig.sampleCnt * edfHdr.num_data_records * 2;
}
}
if (totalsize > datasize) {
// Space required more than the remainder left to read,
// so abort and let the user clean up the corrupted file themselves
qWarning() << "EDFInfo::Parse(): " << filename << " is too short!";
sleep(1);
return false;
}
// allocate the arrays for the signal values
for (auto & sig : edfsignals) {
long samples = sig.sampleCnt * edfHdr.num_data_records;
if (edfHdr.num_data_records <= 0)
sig.dataArray = nullptr;
else
sig.dataArray = new qint16 [samples];
// qDebug() << "Allocated " << samples << " at " << sig.dataArray;
}
for (int recNo = 0; recNo < edfHdr.num_data_records; recNo++) {
for (auto & sig : edfsignals) {
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
for (int j=0;j<sig.sampleCnt;j++) { // Big endian safe
qint16 t=Read16();
sig.dataArray[recNo*sig.sampleCnt + j]=t;
}
}
}
}
return true;
}
// Parse the EDF file to get the annotations out of it.
QVector<Annotation> EDFInfo::ReadAnnotations(const char * data, int charLen)
{
QVector<Annotation> annoVec = QVector<Annotation>();
// Process event annotation record
long pos = 0;
double offset;
double duration;
while (pos < charLen) {
QString text;
bool sign, ok;
char c = data[pos];
if ((c != '+') && (c != '-')) // Annotaion must start with a +/- sign
break;
sign = (data[pos++] == '+');
text = "";
c = data[pos];
do { // collect the offset
text += c;
pos++;
c = data[pos];
} while ((c != AnnoSep) && (c != AnnoDurMark)); // a duration is optional
offset = text.toDouble(&ok);
if (!ok) {
qDebug() << "Faulty offset in annotation record ";
// sleep(1);
break;
}
if (!sign)
offset = -offset;
duration = -1.0; // This indicates no duration supplied
// First entry
if (data[pos] == AnnoDurMark) { // get duration.(preceded by decimal 21 byte)
pos++;
text = "";
do { // collect the duration
text += data[pos];
pos++;
} while ((data[pos] != AnnoSep) && (pos < charLen)); // separator code
duration = text.toDouble(&ok);
if (!ok) {
qDebug() << "Faulty duration in annotation record ";
// sleep(1);
break;
}
}
while ((data[pos] == AnnoSep) && (pos < charLen)) {
text = "";
int textLen = 0;
pos++;
const char * textStart = &data[pos];
if (data[pos] == AnnoEnd)
break;
if (data[pos] == AnnoSep) {
pos++;
break;
}
do { // collect the annotation text
pos++; // officially UTF-8 is allowed here, so don't mangle it
textLen++;
} while ((data[pos] != AnnoSep) && (pos < charLen)); // separator code
text = QString::fromUtf8(textStart, textLen);
annoVec.push_back( Annotation( offset, duration, text) );
if (pos >= charLen) {
qDebug() << "Short EDF Annotations record";
// sleep(1);
break;
}
}
while ((pos < charLen) && (data[pos] == AnnoEnd))
pos++;
if (pos >= charLen)
break;
}
return annoVec;
}
// Read a 16 bits integer
qint16 EDFInfo::Read16()
{
if ((pos + 2) > datasize) {
eof = true;
return 0;
}
#ifdef Q_LITTLE_ENDIAN // Intel, etc...
qint16 res = *(qint16 *)&signalPtr[pos];
#else // ARM, PPC, etc..
qint16 res = quint8(signalPtr[pos]) | (qint8(signalPtr[pos+1]) << 8);
#endif
pos += 2;
return res;
}
QString EDFInfo::ReadBytes(unsigned n)
{
if ((pos + long(n)) > datasize) {
eof = true;
return QString();
}
QByteArray buf(&signalPtr[pos], n);
pos+=n;
return buf.trimmed();
}
EDFSignal *EDFInfo::lookupLabel(const QString & name, int index)
{
auto it = signalList.find(name);
if (it == signalList.end())
return nullptr;
if (index >= it.value().size())
return nullptr;
return it.value()[index];
}

1
dumpSTR/edfparser.cpp Symbolic link
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@ -0,0 +1 @@
../oscar/SleepLib/loader_plugins/edfparser.cpp

175
dumpSTR/edfparser.h
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@ -1,175 +0,0 @@
/* EDF Parser Header
*
* Copyright (c) 2019 The OSCAR Team
* Copyright (c) 2011-2018 Mark Watkins <mark@jedimark.net>
*
* This file is subject to the terms and conditions of the GNU General Public
* License. See the file COPYING in the main directory of the source code
* for more details. */
#ifndef EDFPARSER_H
#define EDFPARSER_H
#include <QString>
#include <QVector>
#include <QHash>
#include <QList>
#include <QDateTime>
// #include "SleepLib/common.h"
typedef float EventDataType;
const QString STR_ext_EDF = "edf";
const QString STR_ext_gz = ".gz";
const char AnnoSep = 20;
const char AnnoDurMark = 21;
const char AnnoEnd = 0;
/*! \struct EDFHeader
\brief Represents the EDF+ header structure, used as a place holder while processing the text data.
\note More information on the EDF+ file format can be obtained from http://edfplus.info
*/
struct EDFHeaderRaw {
char version[8];
char patientident[80];
char recordingident[80];
char datetime[16];
char num_header_bytes[8];
char reserved[44];
char num_data_records[8];
char dur_data_records[8];
char num_signals[4];
}
#ifndef _MSC_VER
__attribute__((packed))
#endif
;
const int EDFHeaderSize = sizeof(EDFHeaderRaw);
/*! \struct EDFHeaderQT
\brief Contains the QT version of the EDF header information
*/
struct EDFHeaderQT {
public:
long version;
QString patientident;
QString recordingident;
QDateTime startdate_orig;
long num_header_bytes;
QString reserved44;
long num_data_records;
double duration_Seconds;
int num_signals;
};
/*! \struct EDFSignal
\brief Contains information about a single EDF+ Signal
\note More information on the EDF+ file format can be obtained from http://edfplus.info
*/
struct EDFSignal {
public:
QString label; //! \brief Name of this Signal
QString transducer_type; //! \brief Tranducer Type (source of the data, usually blank)
QString physical_dimension; //! \brief The units of measurements represented by this signal
EventDataType physical_minimum; //! \brief The minimum limits of the ungained data
EventDataType physical_maximum; //! \brief The maximum limits of the ungained data
EventDataType digital_minimum; //! \brief The minimum limits of the data with gain and offset applied
EventDataType digital_maximum; //! \brief The maximum limits of the data with gain and offset applied
EventDataType gain; //! \brief Raw integer data is multiplied by this value
EventDataType offset; //! \brief This value is added to the raw data
QString prefiltering; //! \brief Any prefiltering methods used (usually blank)
long sampleCnt; //! \brief Number of samples per record
QString reserved; //! \brief Reserved (usually blank)
qint16 * dataArray; //! \brief Offset in record to the signals sample data
};
/*! \class Annotation
\author Phil Olynyk
\brief Hold the annotation text from an EDF file
*/
class Annotation
{
public:
Annotation() { duration = -1.0; };
Annotation( double off, double dur, QString tx ) {
offset = off;
duration = dur;
text = tx;
};
virtual ~Annotation() {};
double offset;
double duration;
QString text;
};
/*! \class EDFInfo
\author Phil Olynyk
\author Mark Watkins <mark@jedimark.net>
\brief Parse an EDF+ data file into a list of EDFSignal's
\note More information on the EDF+ file format can be obtained from http://edfplus.info
*/
class EDFInfo
{
public:
//! \brief Constructs an EDFParser object, opening the filename if one supplied
EDFInfo();
virtual ~EDFInfo();
virtual QByteArray * Open(const QString & name); //! \brief Open the EDF+ file, and read it's header
virtual bool Parse(QByteArray * fileData); //! \brief Parse the EDF+ file into the EDFheaderQT. Must call Open(..) first.
virtual EDFSignal *lookupLabel(const QString & name, int index=0); //! \brief Return a ptr to the i'th signal with that name
virtual long GetNumSignals() { return edfHdr.num_signals; } //! \brief Returns the number of signals contained in this EDF file
virtual long GetNumDataRecords() { return edfHdr.num_data_records; } //! \brief Returns the number of data records contained per signal.
virtual double GetDuration() { return edfHdr.duration_Seconds; } //! \brief Returns the duration represented by this EDF file
virtual QString GetPatient() { return edfHdr.patientident; } //! \brief Returns the patientid field from the EDF header
// The data members follow
QString filename; //! \brief For debug and error messages
EDFHeaderQT edfHdr; //! \brief The header in a QT friendly form
QVector<EDFSignal> edfsignals; //! \brief Holds the EDFSignals contained in this edf file
// QVector< QVector<qint16> > dataRecords; //! \brief Holds the datarecords
QVector< QVector<Annotation> > annotations; //! \brief Holds the Annotaions for this EDF file
QStringList signal_labels; //! \brief An by-name indexed into the EDFSignal data
QHash<QString, QList<EDFSignal *> > signalList; //! \brief ResMed sometimes re-uses the SAME signal name
// the following could be private
private:
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
qint16 Read16(); //! \brief Read 16 bit word of data from the EDF+ data stream
//! \brief This is the array holding the EDF file data
QByteArray * fileData;
//! \brief The EDF+ files header structure, used as a place holder while processing the text data.
EDFHeaderRaw *hdrPtr;
//! \brief This is the array of signal descriptors and values
char *signalPtr;
long filesize;
long datasize;
long pos;
bool eof;
};
#endif // EDFPARSER_H

1
dumpSTR/edfparser.h Symbolic link
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@ -0,0 +1 @@
../oscar/SleepLib/loader_plugins/edfparser.h

27
dumpSTR/main.cpp
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@ -45,6 +45,18 @@ void dumpSignals( const QVector<EDFSignal> sigs ) {
} }
} }
void usage() {
qDebug() << "dumpSTR [ options ] filename";
qDebug() << "Options";
qDebug() << "\t-a Show all";
qDebug() << "\t-f ### First day";
qDebug() << "\t-l ### Last day";
qDebug() << "\t-g ### First signal";
qDebug() << "\t-m ### Last signal";
qDebug() << "\t-s Signal list only";
qDebug() << "\t-h or -? This help message";
}
int main(int argc, char *argv[]) { int main(int argc, char *argv[]) {
// QString homeDocs = QStandardPaths::writableLocation(QStandardPaths::DocumentsLocation)+"/"; // QString homeDocs = QStandardPaths::writableLocation(QStandardPaths::DocumentsLocation)+"/";
@ -77,14 +89,23 @@ int main(int argc, char *argv[]) {
lastSig = args[++i].toInt(); lastSig = args[++i].toInt();
else if (args[i] == "-a") else if (args[i] == "-a")
showall = true; showall = true;
else if (args[i] == "-b") else if (args[i] == "-s")
brief = true; brief = true;
else if ((args[i] == "-?") || (args[i] == "-h")) {
usage();
exit(0);
}
} }
EDFInfo str; EDFInfo str;
QByteArray * buffer = str.Open(filename); if ( ! str.Open(filename) ) {
if ( ! str.Parse(buffer) ) qDebug() << "Failed to open" << filename;
exit(-1); exit(-1);
}
if ( ! str.Parse() ) {
qDebug() << "Parsing failed on" << filename;
exit(-1);
}
QDate d2 = str.edfHdr.startdate_orig.date(); QDate d2 = str.edfHdr.startdate_orig.date();
if (d2.year() < 2000) { if (d2.year() < 2000) {

8
oscar/SleepLib/loader_plugins/edfparser.cpp
View File

@ -68,11 +68,15 @@ bool EDFInfo::Open(const QString & name)
return false; return false;
} }
// fileData = new QByteArray(); // fileData = new QByteArray();
#ifndef DUMPSTR
if (name.endsWith(STR_ext_gz)) { if (name.endsWith(STR_ext_gz)) {
fileData = gUncompress(fi.readAll()); // Open and decompress file fileData = gUncompress(fi.readAll()); // Open and decompress file
} else { } else {
fileData = fi.readAll(); // Open and read uncompressed file fileData = fi.readAll(); // Open and read uncompressed file
} }
#else
fileData = fi.readAll(); // Open and read uncompressed file
#endif
fi.close(); fi.close();
if (fileData.size() <= EDFHeaderSize) { if (fileData.size() <= EDFHeaderSize) {
fileData.clear();; fileData.clear();;
@ -280,11 +284,15 @@ EDFHeaderQT * EDFInfo::GetHeader( const QString & name)
return nullptr; return nullptr;
} }
// fileData = new QByteArray(); // fileData = new QByteArray();
#ifndef DUMPSTR
if (name.endsWith(STR_ext_gz)) { if (name.endsWith(STR_ext_gz)) {
fileData = gUncompress(fi.read(sizeof(EDFHeaderRaw))); // Open and decompress file fileData = gUncompress(fi.read(sizeof(EDFHeaderRaw))); // Open and decompress file
} else { } else {
fileData = fi.read(sizeof(EDFHeaderRaw)); // Open and read uncompressed file fileData = fi.read(sizeof(EDFHeaderRaw)); // Open and read uncompressed file
} }
#else
fileData = fi.read(sizeof(EDFHeaderRaw)); // Open and read uncompressed file
#endif
fi.close(); fi.close();
filename = name; filename = name;
hdrPtr = (EDFHeaderRaw *)fileData.constData(); hdrPtr = (EDFHeaderRaw *)fileData.constData();