diff --git a/dumpSTR.pro b/dumpSTR.pro
index 2e3aaa39..2ed676ce 100644
--- a/dumpSTR.pro
+++ b/dumpSTR.pro
@@ -12,6 +12,8 @@ CONFIG -= debug_and_release
QT += core widgets
+DEFINES+=DUMPSTR
+
TARGET = dumpSTR
TEMPLATE = app
@@ -24,9 +26,9 @@ VERSION = 0.5.0
SOURCES += \
dumpSTR/main.cpp \
- dumpSTR/edfparser.cpp \
+ dumpSTR/edfparser.cpp
HEADERS += \
- dumpSTR/common.h \
- dumpSTR/edfparser.h \
+ dumpSTR/SleepLib/common.h \
+ dumpSTR/edfparser.h
diff --git a/dumpSTR/common.h b/dumpSTR/SleepLib/common.h
similarity index 100%
rename from dumpSTR/common.h
rename to dumpSTR/SleepLib/common.h
diff --git a/dumpSTR/edfparser.cpp b/dumpSTR/edfparser.cpp
deleted file mode 100644
index ad62946f..00000000
--- a/dumpSTR/edfparser.cpp
+++ /dev/null
@@ -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];
-}
-
diff --git a/dumpSTR/edfparser.cpp b/dumpSTR/edfparser.cpp
new file mode 120000
index 00000000..0cf82530
--- /dev/null
+++ b/dumpSTR/edfparser.cpp
@@ -0,0 +1 @@
+../oscar/SleepLib/loader_plugins/edfparser.cpp
\ No newline at end of file
diff --git a/dumpSTR/edfparser.h b/dumpSTR/edfparser.h
deleted file mode 100644
index 69eab21a..00000000
--- a/dumpSTR/edfparser.h
+++ /dev/null
@@ -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
diff --git a/dumpSTR/edfparser.h b/dumpSTR/edfparser.h
new file mode 120000
index 00000000..9296f3c2
--- /dev/null
+++ b/dumpSTR/edfparser.h
@@ -0,0 +1 @@
+../oscar/SleepLib/loader_plugins/edfparser.h
\ No newline at end of file
diff --git a/dumpSTR/main.cpp b/dumpSTR/main.cpp
index c8024de6..4f3e54db 100644
--- a/dumpSTR/main.cpp
+++ b/dumpSTR/main.cpp
@@ -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[]) {
// QString homeDocs = QStandardPaths::writableLocation(QStandardPaths::DocumentsLocation)+"/";
@@ -77,14 +89,23 @@ int main(int argc, char *argv[]) {
lastSig = args[++i].toInt();
else if (args[i] == "-a")
showall = true;
- else if (args[i] == "-b")
+ else if (args[i] == "-s")
brief = true;
+ else if ((args[i] == "-?") || (args[i] == "-h")) {
+ usage();
+ exit(0);
+ }
}
EDFInfo str;
- QByteArray * buffer = str.Open(filename);
- if ( ! str.Parse(buffer) )
+ if ( ! str.Open(filename) ) {
+ qDebug() << "Failed to open" << filename;
exit(-1);
+ }
+ if ( ! str.Parse() ) {
+ qDebug() << "Parsing failed on" << filename;
+ 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 62ed45e7..6d21fb9a 100644
--- a/oscar/SleepLib/loader_plugins/edfparser.cpp
+++ b/oscar/SleepLib/loader_plugins/edfparser.cpp
@@ -68,11 +68,15 @@ bool EDFInfo::Open(const QString & name)
return false;
}
// fileData = new QByteArray();
+#ifndef DUMPSTR
if (name.endsWith(STR_ext_gz)) {
fileData = gUncompress(fi.readAll()); // Open and decompress file
} else {
fileData = fi.readAll(); // Open and read uncompressed file
}
+#else
+ fileData = fi.readAll(); // Open and read uncompressed file
+#endif
fi.close();
if (fileData.size() <= EDFHeaderSize) {
fileData.clear();;
@@ -280,11 +284,15 @@ EDFHeaderQT * EDFInfo::GetHeader( const QString & name)
return nullptr;
}
// fileData = new QByteArray();
+#ifndef DUMPSTR
if (name.endsWith(STR_ext_gz)) {
fileData = gUncompress(fi.read(sizeof(EDFHeaderRaw))); // Open and decompress file
} else {
fileData = fi.read(sizeof(EDFHeaderRaw)); // Open and read uncompressed file
}
+#else
+ fileData = fi.read(sizeof(EDFHeaderRaw)); // Open and read uncompressed file
+#endif
fi.close();
filename = name;
hdrPtr = (EDFHeaderRaw *)fileData.constData();