Hi Alois,
would you mind to simply push to the repository on Salsa. I need to
admit that while I like to help **a bit** with those NeuroDebian
packages the time I had to spent on it goes way beyond what I currently
can invest. So please be so kind to keep things as simple and smooth
for me.
Thanks a lot
Andreas.
On Mon, Nov 16, 2020 at 08:40:01AM +0100, Alois Schlögl wrote:
> Adrian is right. I want to make you aware of another patch set (see
> attachment) which I recommend to add.
>
>
> The patch is fixing an issue when importing an event file, and the sample
> rate in the event file does not match the data file.
>
>
> The patch set is currently maintained here
>
> https://git.ist.ac.at/alois.schloegl/sigviewer
>
> and corresponds to the last three patches (currently this 'git diff
> 7e26e4da 7303ba9d0' )
>
> The changes have been sent to the maintainer (Clemens Brunner), but there is
> no release yet.
>
>
> I can contact the maintainer, or submit another bug report. The easiest
> approach would be if you could just add the patch here.
>
>
> Alois
>
>
>
> On 11/14/20 11:08 PM, Adrian Bunk wrote:
> > On Sat, Nov 14, 2020 at 09:28:53PM +0100, Andreas Tille wrote:
> > > Control: tags -1 pending
> > > Control: tags 922571 pending
> > >
> > > Hi,
> > >
> > > I have moved sigviewer to Debian Med team[1], fixed the other bug and
> > > tried to build the new upstream version 0.6.4 but failed:
> > >
> > > ...
> > > g++ -c -pipe -g -O2 -fdebug-prefix-map=/build/sigviewer-0.6.4=.
> > > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> > > -D_FORTIFY_SOURCE=2 -std=gnu++11 -D_REENTRANT -Wall - Wextra -fPIC
> > > -DVERSION_MAJOR=0 -DVERSION_MINOR=6 -DVERSION_BUILD=4
> > > -DQT_NO_DEBUG_OUTPUT -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB
> > > -DQT_XML_LIB -DQT_CORE_LIB -I. -I/build/sigviewer-0.6.4/ external/include
> > > -Isrc -I/usr/include/x86_64-linux-gnu/qt5
> > > -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets
> > > -I/usr/include/x86_64-linux-gnu/qt5/QtGui
> > > -I/usr/include/x86_64-linux-gnu/qt5/ QtXml
> > > -I/usr/include/x86_64-linux-gnu/qt5/QtCore -Itmp/release -Itmp/release
> > > -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o
> > > tmp/release/undo_redo_gui_command.o src/gui_impl/commands/
> > > undo_redo_gui_command.cpp
> > > src/gui_impl/commands/open_file_gui_command.cpp: In member function 'void
> > > sigviewer::OpenFileGuiCommand::importEvents()':
> > > src/gui_impl/commands/open_file_gui_command.cpp:200:23: error:
> > > redeclaration of 'sigviewer::FileSignalReader* file_signal_reader'
> > > 200 | FileSignalReader* file_signal_reader =
> > > FileSignalReaderFactory::getInstance()->getHandler (file_path);
> > > | ^~~~~~~~~~~~~~~~~~
> > > src/gui_impl/commands/open_file_gui_command.cpp:185:23: note:
> > > 'sigviewer::FileSignalReader* file_signal_reader' previously declared here
> > > 185 | FileSignalReader* file_signal_reader =
> > > FileSignalReaderFactory::getInstance()->getHandler (file_path);
> > > | ^~~~~~~~~~~~~~~~~~
> > > make[1]: *** [Makefile:2576: tmp/release/open_file_gui_command.o] Error 1
> > >
> > >
> > > Any help would be welcome
> > This is from 0002-add-support-for-reading-GDF-formated-event-file.patch,
> > which seems to be upstream now - and adding the same code twice is what
> > failed.
> >
> > > Andreas.
> > cu
> > Adrian
> diff --git a/src/file_handling_impl/biosig_reader.cpp
> b/src/file_handling_impl/biosig_reader.cpp
> index 41fce69..42c12ae 100644
> --- a/src/file_handling_impl/biosig_reader.cpp
> +++ b/src/file_handling_impl/biosig_reader.cpp
> @@ -121,10 +121,6 @@ QString BioSigReader::open (QString const& file_name)
> QString BioSigReader::loadFixedHeader(const QString& file_name)
> {
> QMutexLocker locker (&biosig_access_lock_);
> - char *c_file_name = new char[file_name.length() + 1];
> - strcpy (c_file_name, file_name.toLocal8Bit ().data());
> - c_file_name[file_name.length()] = '\0';
> -
> tzset();
>
> if(biosig_header_==NULL)
> @@ -134,7 +130,7 @@ QString BioSigReader::loadFixedHeader(const QString&
> file_name)
> biosig_header_->FLAG.OVERFLOWDETECTION = 1;
> }
>
> - biosig_header_ = sopen(c_file_name, "r", biosig_header_ );
> + biosig_header_ = sopen(file_name.toStdString().c_str(), "r",
> biosig_header_ );
>
> basic_header_ = QSharedPointer<BasicHeader>
> (new BiosigBasicHeader (biosig_header_, file_name));
> @@ -145,8 +141,6 @@ QString BioSigReader::loadFixedHeader(const QString&
> file_name)
> destructHDR(biosig_header_);
> biosig_header_ = NULL;
>
> - delete[] c_file_name;
> -
> qDebug() << "File doesn't exist.";
> QMessageBox msgBox;
> msgBox.setIcon(QMessageBox::Warning);
> @@ -167,17 +161,11 @@ QString BioSigReader::loadFixedHeader(const QString&
> file_name)
> destructHDR(biosig_header_);
> biosig_header_ = NULL;
>
> - delete[] c_file_name;
> -
> return "file not supported";
> }
>
> convert2to4_eventtable(biosig_header_);
>
> - delete[] c_file_name;
> -
> - c_file_name = NULL;
> -
> basic_header_->setNumberEvents(biosig_header_->EVENT.N);
>
> if (biosig_header_->EVENT.SampleRate)
> diff --git a/src/gui_impl/commands/open_file_gui_command.cpp
> b/src/gui_impl/commands/open_file_gui_command.cpp
> index 094e1d9..d7ed693 100644
> --- a/src/gui_impl/commands/open_file_gui_command.cpp
> +++ b/src/gui_impl/commands/open_file_gui_command.cpp
> @@ -2,7 +2,7 @@
> // Licensed under the GNU General Public License (GPL)
> // https://www.gnu.org/licenses/gpl
>
> -
> +#include <biosig.h>
> #include "open_file_gui_command.h"
> #include "gui_impl/gui_helper_functions.h"
>
> @@ -182,26 +182,85 @@ void OpenFileGuiCommand::importEvents ()
> if (file_path.isEmpty())
> return;
>
> - FileSignalReader* file_signal_reader =
> FileSignalReaderFactory::getInstance()->getHandler (file_path);
> - if (file_signal_reader != 0) {
> - QList<QSharedPointer<SignalEvent const> > events =
> file_signal_reader->getEvents ();
> - QSharedPointer<EventManager> event_manager =
> applicationContext()->getCurrentFileContext()->getEventManager();
> - QList<QSharedPointer<QUndoCommand> > creation_commands;
> - foreach (QSharedPointer<SignalEvent const> event, events) {
> - QSharedPointer<QUndoCommand> creation_command (new
> NewEventUndoCommand (event_manager, event));
> - creation_commands.append (creation_command);
> - }
> - MacroUndoCommand* macro_command = new MacroUndoCommand
> (creation_commands);
> - applicationContext()->getCurrentCommandExecuter()->executeCommand
> (macro_command);
> - delete file_signal_reader;
> - return;
> - }
> + QList<QSharedPointer<SignalEvent const> > events;
> + QSharedPointer<EventManager> event_manager =
> applicationContext()->getCurrentFileContext()->getEventManager();
> + double sampleRate = event_manager->getSampleRate();
> + std::set<EventType> types = event_manager->getEventTypes();
> + int numberChannels =
> applicationContext()->getCurrentFileContext()->getChannelManager().getNumberChannels();
> +
> + // try reading event file through biosig
> + HDRTYPE* evtHDR = sopen(file_path.toStdString().c_str(), "r", NULL );
> + if (!serror2(evtHDR)) {
> + /* Note: evtSampleRate and transition rate can be NaN,
> + indicating sample rate is not specified in event file
> + */
> + double evtSampleRate = biosig_get_eventtable_samplerate(evtHDR);
> + double transition_rate = sampleRate / evtSampleRate;
> + size_t NumEvents = biosig_get_number_of_events(evtHDR);
> + for (size_t k = 0; k < NumEvents; k++) {
> + uint16_t typ; uint32_t pos; uint16_t chn; uint32_t dur;
> + gdf_time timestamp;
> + const char *desc;
> + biosig_get_nth_event(evtHDR, k, &typ, &pos, &chn, &dur,
> ×tamp, &desc);
> +
> + if (transition_rate > 0) {
> + pos = lround(pos*transition_rate);
> + dur = lround(dur*transition_rate);
> + }
>
> - std::fstream file;
> - file.open(file_path.toStdString());
> + if (typ <= 254 && do_not_show_warning_message == false) {
> + QMessageBox msgBox;
> + msgBox.setText("Currently customized event text cannot be
> properly imported.");
> + msgBox.setIcon(QMessageBox::Warning);
> + msgBox.addButton(QMessageBox::Ok);
> + msgBox.addButton(QMessageBox::Cancel);
> + msgBox.setDefaultButton(QMessageBox::Cancel);
> + QCheckBox* dontShowCheckBox = new QCheckBox("Don't show this
> message again");
> + msgBox.setCheckBox(dontShowCheckBox);
> + int32_t userReply = msgBox.exec();
> + if (userReply == QMessageBox::Ok) {
> + if(dontShowCheckBox->checkState() == Qt::Checked) {
> + QSettings settings;
> + settings.setValue("DoNotShowWarningMessage", true);
> + do_not_show_warning_message = true;
> + }
> + }
> + else if (userReply == QMessageBox::Cancel) {
> + if(dontShowCheckBox->checkState() == Qt::Checked) {
> + QSettings settings;
> + settings.setValue("DoNotShowWarningMessage", true);
> + do_not_show_warning_message = true;
> + }
> + destructHDR(evtHDR);
> + return;
> + }
> + }
> +
> + /* biosig uses a 1-based channel index, and 0 refers to all
> channels,
> + sigviewer uses a 0-based indexing, and -1 indicates all
> channels */
> + //boundary check & error handling
> + if (pos > event_manager->getMaxEventPosition()
> + || pos + dur > event_manager->getMaxEventPosition()
> + || chn > numberChannels
> + || !types.count(typ))
> + continue;
>
> - if (file.is_open())
> + QSharedPointer<SignalEvent> event =
> QSharedPointer<SignalEvent>(new SignalEvent(pos,
> + typ, sampleRate, -1, chn-1, dur));
> +
> + events << event;
> + }
> + sclose(evtHDR);
> + destructHDR(evtHDR);
> + } else
> {
> + // if the file can not be read with biosig, try this approach
> + destructHDR(evtHDR);
> +#if BIOSIG_VERSION<10903
> + std::fstream file;
> + file.open(file_path.toStdString());
> +
> + if (file.is_open()) {
> std::string line;
> std::getline(file, line);
>
> @@ -211,13 +270,6 @@ void OpenFileGuiCommand::importEvents ()
> return;
> }
>
> - QList<QSharedPointer<SignalEvent const> > events;
> - QSharedPointer<EventManager> event_manager
> - =
> applicationContext()->getCurrentFileContext()->getEventManager();
> - double sampleRate = event_manager->getSampleRate();
> - std::set<EventType> types = event_manager->getEventTypes();
> - int numberChannels =
> applicationContext()->getCurrentFileContext()->getChannelManager().getNumberChannels();
> -
> while (std::getline(file, line))
> {
> QStringList Qline = QString::fromStdString(line).split(',');
> @@ -274,22 +326,25 @@ void OpenFileGuiCommand::importEvents ()
>
> events << event;
> }
> -
> -
> - QList<QSharedPointer<QUndoCommand> > creation_commands;
> - foreach (QSharedPointer<SignalEvent const> event, events)
> - {
> - QSharedPointer<QUndoCommand> creation_command (new
> NewEventUndoCommand (event_manager, event));
> - creation_commands.append (creation_command);
> - }
> - MacroUndoCommand* macro_command = new MacroUndoCommand
> (creation_commands);
> - applicationContext()->getCurrentCommandExecuter()->executeCommand
> (macro_command);
> }
> else
> {
> +#endif
> QMessageBox::critical(0, file_path, tr("Cannot open file.\nIs the
> target file open in another application?"));
> return;
> +#if BIOSIG_VERSION<10903
> + }
> +#endif
> + }
> +
> + QList<QSharedPointer<QUndoCommand> > creation_commands;
> + foreach (QSharedPointer<SignalEvent const> event, events)
> + {
> + QSharedPointer<QUndoCommand> creation_command (new
> NewEventUndoCommand (event_manager, event));
> + creation_commands.append (creation_command);
> }
> + MacroUndoCommand* macro_command = new MacroUndoCommand
> (creation_commands);
> + applicationContext()->getCurrentCommandExecuter()->executeCommand
> (macro_command);
> }
>
> //-------------------------------------------------------------------------
--
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