From b4bbdd9a546a033b71096887a9f5c776222df503 Mon Sep 17 00:00:00 2001 From: Phil Olynyk Date: Fri, 21 Feb 2020 11:29:00 -0500 Subject: [PATCH] update dumpSTR to use the standard edfparser files --- dumpSTR.pro | 8 +- dumpSTR/{ => SleepLib}/common.h | 0 dumpSTR/edfparser.cpp | 354 +------------------- dumpSTR/edfparser.h | 176 +--------- dumpSTR/main.cpp | 27 +- oscar/SleepLib/loader_plugins/edfparser.cpp | 8 + 6 files changed, 39 insertions(+), 534 deletions(-) rename dumpSTR/{ => SleepLib}/common.h (100%) mode change 100644 => 120000 dumpSTR/edfparser.cpp mode change 100644 => 120000 dumpSTR/edfparser.h 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 - * - * 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 -#include -#include -#include -#ifdef _MSC_VER -#include -#else -#include -#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 EDFInfo::ReadAnnotations(const char * data, int charLen) -{ - QVector annoVec = QVector(); - - // 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 - * - * 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 -#include -#include -#include -#include - -// #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 - \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 edfsignals; //! \brief Holds the EDFSignals contained in this edf file - -// QVector< QVector > dataRecords; //! \brief Holds the datarecords - - QVector< QVector > annotations; //! \brief Holds the Annotaions for this EDF file - - QStringList signal_labels; //! \brief An by-name indexed into the EDFSignal data - - QHash > signalList; //! \brief ResMed sometimes re-uses the SAME signal name - -// the following could be private - private: - QVector 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 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();