public void Execute(object sender, DoWorkEventArgs e)
{
bw = (BackgroundWorker)sender;
bw.ReportProgress(0, "Starting ASC conversion");
CCIUtilities.Log.writeToLog("Started ASC conversion on records in " + headerFileName);
/***** Read electrode file *****/
ElectrodeInputFileStream etrFile = new ElectrodeInputFileStream(
new FileStream(System.IO.Path.Combine(directory, head.ElectrodeFile), FileMode.Open, FileAccess.Read));
/***** Open new FILMAN file *****/
SaveFileDialog dlg = new SaveFileDialog();
dlg.Title = "Save as FILMAN file ...";
dlg.AddExtension = true;
dlg.DefaultExt = ".fmn"; // Default file extension
dlg.Filter = "FILMAN Files (.fmn)|*.fmn"; // Filter files by extension
dlg.FileName = headerFileName;
dlg.InitialDirectory = ASCtoFMConverter.Properties.Settings.Default.LastDataset; //Use dataset default, but don't save if new location
bool? result = dlg.ShowDialog();
if (result == null || !(bool)result)
{
bw.ReportProgress(0, "Conversion cancelled before FM file created.");
e.Cancel = true;
return;
}
int newRecordLength = Convert.ToInt32(Math.Ceiling(FMRecLength * samplingRate / (double)decimation));
int FMRecordLengthInBDF = Convert.ToInt32(FMRecLength * samplingRate);
int GVCount = 6 + GVCopyAcross.Count;
bool PKCounterExists = false;
foreach (EpisodeDescription ed in specs)
{
PKDetectorEventCounterDescription pkd = ed.PKCounter;
if (pkd != null)
{
PKCounterExists = true;
pkd.assignedGVNumber = GVCount;
}
}
GVCount += PKCounterExists ? 3 : 0;
//NOTE: because we have to have the number of GVs (and Channels) available when we create the output stream,
// we have to separate the enumeration of GVs from the naming of GVs; this could be avoided by using lists
// rather than arrays for GVNames in FILMANOuputStream and having an actual Header entity for FILMAN files;
// one would then enter the GVNames (and Channel names) into the list before creating the ouput stream and have
// the constructor use the counts to get NG and NC; NA could also be an array that must be created before as a
// byte array, but this might be awkward
FMStream = new FILMANOutputStream(
File.Open(dlg.FileName, FileMode.Create, FileAccess.ReadWrite),
GVCount, 0, channels.Count,
newRecordLength,
FILMANFileStream.FILMANFileStream.Format.Real);
log = new LogFile(dlg.FileName + ".log.xml");
FMStream.IS = Convert.ToInt32((double)samplingRate / (double)decimation);
bigBuff = new double[bdf.NumberOfChannels - 1, FMStream.ND]; //have to dimension to BDF rather than FMStream
//in case we need for reference calculations
/***** Create FILMAN header records *****/
//First GV names:
//six for the standard generated
FMStream.GVNames(0, "Channel");
FMStream.GVNames(1, "Montage");
FMStream.GVNames(2, "NewGroupVariable");
FMStream.GVNames(3, "EpisodeNumber");
FMStream.GVNames(4, "EpisodeRecordNumber");
FMStream.GVNames(5, "SecondsFromStart");
//then the copied-across GVs
for (int n = 0; n < GVCopyAcross.Count; n++) FMStream.GVNames(n + 6, GVCopyAcross[n].Name);
//and last, the GVs from the counters
if (PKCounterExists) //if there are any PK counters, we'll need their GVs
{
FMStream.GVNames(GVCount - 3, "PK-rate");
FMStream.GVNames(GVCount - 2, "PK-velocity");
FMStream.GVNames(GVCount - 1, "PK-accel");
}
for (int j = 0; j < FMStream.NC; j++) //generate channel labels
{
string s = bdf.channelLabel(channels[j]);
ElectrodeFileStream.ElectrodeRecord p;
if (etrFile.etrPositions.TryGetValue(s, out p))
FMStream.ChannelNames(j, s.PadRight(16, ' ') + p.projectPhiTheta().ToString("0")); //add electrode location information, if available
else
FMStream.ChannelNames(j, s);
}
FMStream.Description(0, head.Title + " Date: " + head.Date + " " + head.Time +
" File: " + System.IO.Path.Combine(directory, System.IO.Path.GetFileNameWithoutExtension(head.BDFFile)));
StringBuilder sb = new StringBuilder("Subject: " + head.Subject.ToString());
if (head.Agent != 0) sb.Append(" Agent: " + head.Agent);
sb.Append(" Tech:");
foreach (string s in head.Technician) sb.Append(" " + s);
FMStream.Description(1, sb.ToString());
sb.Clear();
sb = sb.Append(specs[0].ToString());
for (int j = 1; j < specs.Length; j++) sb.Append("/ " + specs[j].ToString());
string str = sb.ToString();
int sl = str.Length;
int k;
if (sl < 72) { FMStream.Description(2, str); k = 3; }
else
{
FMStream.Description(2, str.Substring(0, 72));
if (sl < 144) { FMStream.Description(3, str.Substring(72)); k = 4; }
else
{
FMStream.Description(3, str.Substring(72, 72));
k = 5;
if (sl < 216) FMStream.Description(4, str.Substring(144));
else FMStream.Description(4, str.Substring(144, 72));
}
}
sb.Clear();
if (referenceGroups == null || referenceGroups.Count == 0) sb.Append("No reference");
else if (referenceGroups.Count == 1)
{
sb.Append("Single ref group with");
if (referenceGroups[0].Count >= FMStream.NC)
if (referenceChannels[0].Count == bdf.NumberOfChannels) sb.Append(" common average ref");
else if (referenceChannels[0].Count == 1)
sb.Append(" ref channel " + referenceChannels[0][0].ToString("0") + "=" + bdf.channelLabel(referenceChannels[0][0]));
else sb.Append(" multiple ref channels=" + referenceChannels[0].Count.ToString("0"));
}
else // complex reference expression
{
sb.Append(" Multiple reference groups=" + referenceGroups.Count.ToString("0"));
}
FMStream.Description(k++, sb.ToString());
if (k < 6)
FMStream.Description(k, bdf.LocalRecordingId);
FMStream.writeHeader();
log.registerHeader(this);
EventFactory.Instance(ED);
int epiNo = 0; //found episode counter
//read in list of Events
bw.ReportProgress(0, "Reading Events, synchronizing clocks, and calculating Event offsets from BDF file");
List<InputEvent> EventList = new List<InputEvent>();
EventFileReader efr=new EventFileReader(
new FileStream(System.IO.Path.Combine(directory, head.EventFile),
FileMode.Open, FileAccess.Read));
InputEvent.LinkEventsToDataset(head, bdf); //link InputEvents to this specific dataset
foreach (InputEvent ie in efr)
{
EventList.Add(ie);
}
IEnumerator<InputEvent> EventEnumerator = EventList.GetEnumerator(); //Enumerator for stepping through Event file
//******** Synchronize clocks
//Need to synchronize clocks by setting the BDF.zeroTime value
//zeroTime is the time, according to the Event file clock, of the beginning of the BDF file (BioSemi clock)
if (ignoreStatus && offsetToFirstEvent < 0D) //cannot use Status markers to synchronize clocks, so
//use raw Event clock times as actual offsets from beginning of BDF file; in other words force all Events to be BDF-based
bdf.setZeroTime(0D); //this keeps it from throwing an error when "synchronizing"
else
{ //Need to find a covered (intrisic or extrinsic) Event to use as an indicial Event
bool found = false;
EventEnumerator.Reset();
if (syncToFirst || ignoreStatus)
while (!found && EventEnumerator.MoveNext())
{
if (EventEnumerator.Current.EDE.IsCovered) //have we found a covered Event?
{
if (ignoreStatus)
{
bdf.setZeroTime(EventEnumerator.Current.Time - offsetToFirstEvent);
found = true;
}
else
found = bdf.setZeroTime(EventEnumerator.Current);
}
}
else //sync to "middle" Event
{
int midRecord = bdf.NumberOfRecords / 2;
BDFLocFactory fac = new BDFLocFactory(bdf);
BDFLoc loc = fac.New();
loc.Rec = midRecord;
bdf.read(midRecord);
uint v1 = head.Mask & (uint)bdf.getStatusSample(loc);
uint v2;
InputEvent IE;
while ((v2 = (uint)bdf.getStatusSample(++loc) & head.Mask) == v1) ; //find next Status mark after mid point of file; v2 = GC
while (!found && EventEnumerator.MoveNext())
{
IE = EventEnumerator.Current;
if (IE.GC == v2)
{
bdf.setZeroTime(IE.Time - loc.ToSecs());
found = true;
}
}
}
if (!found)
{
log.Close();
FMStream.Close();
throw (new Exception("No valid synchronizing (covered) Event found; use manual synchronization"));
}
}
Log.writeToLog("\tinto FM file " + dlg.FileName);
foreach(InputEvent ie in EventList) //modify relativeTime field depending on type of Event
ie.setRelativeTime();
EventList = EventList.OrderBy(ev => ev.relativeTime).ToList(); //re-sort: minor order changes may occur
//Loop through each episode specification,
// then through the Event file to find any regions satisfying the specification,
// then create FILMAN records for each of these regions
//******** Episode specification loop
for (int i = 0; i < specs.Length; i++)
{
EpisodeDescription currentEpisode = specs[i];
FMStream.record.GV[2] = currentEpisode.GVValue; //set epispec GV value
if (currentEpisode.Exclude != null)
{
//Here we complete the ExclusionDescription for the given Episode specification
//by finding all the segemnts that must be excluded and
//calculating their From to To BDFPoints; this is done for each specification to
//permit different exclusion criteria for each EpisodeDescription
ExclusionDescription ed = currentEpisode.Exclude;
EventEnumerator.Reset();
EventDictionaryEntry startEDE = ed.startEvent;
bool t = ed.endEvent != null && ed.endEvent.GetType() == typeof(EventDictionaryEntry);
EventDictionaryEntry endEDE = null;
if(t)
endEDE = (EventDictionaryEntry)ed.endEvent;
while(EventEnumerator.MoveNext())
{
InputEvent ev = EventEnumerator.Current;
if (ev.Name == startEDE.Name)
{
BDFPoint b = new BDFPoint(bdf).FromSecs(bdf.timeFromBeginningOfFileTo(ev));
ed.From.Add(b);
if (t)
while (EventEnumerator.MoveNext())
{
ev = EventEnumerator.Current;
if (ev.Name == endEDE.Name)
{
ed.To.Add(new BDFPoint(bdf).FromSecs(bdf.timeFromBeginningOfFileTo(ev)));
break;
}
}
else
ed.To.Add(b);
}
}
}
// From here we loop through Event file until an Event is found that matches the
// current startEvent in spec[i]; from that point a matching endEvent is sought;
// episode is then processed; note that this implies that overlapping episodes are not
// generally permitted (in a given specification) except when caused by offsets.
//************* Event file loop
EventEnumerator.Reset();
bool found;
do
{
if (bw.CancellationPending) //look for cancellation first
{
bw.ReportProgress(0, "Conversion canceled with " + FMStream.NR.ToString("0") +
" records in " + (FMStream.NR / FMStream.NC).ToString("0") + " recordsets generated.");
FMStream.Close();
log.Close();
e.Cancel = true;
return;
}
InputEvent startEvent = null;
InputEvent endEvent = null;
double startTime;
double endTime = 0;
found = findNextMark(currentEpisode.Start, EventEnumerator, true, out startTime, out startEvent) &&
findNextMark(currentEpisode.End, EventEnumerator, false, out endTime, out endEvent);
if (found || startTime >= 0D && specs[i].useEOF)
{ //use EOF
//***************** FILMAN record loop
startTime += currentEpisode.Start._offset;
endTime += currentEpisode.End._offset;
bw.ReportProgress(0, "Found episode " + (++epiNo).ToString("0") +
" from " + startTime.ToString("0.000") +
" to " + endTime.ToString("0.000"));
int maxNumberOfFMRecs = (int)Math.Floor((endTime - startTime) / FMRecLength);
log.openFoundEpisode(epiNo, startTime, endTime, maxNumberOfFMRecs);
BDFPoint startBDFPoint = new BDFPoint(bdf);
startBDFPoint.FromSecs(startTime);
BDFPoint endBDFPoint = new BDFPoint(startBDFPoint);
/***** Get group variables for this record *****/
FMStream.record.GV[3] = epiNo;
if (startEvent != null) //exclude BOF
{
int GrVar = 6; //Load up group variables, based on the start Event
foreach (GVEntry gve in GVCopyAcross)
{
int j = startEvent.GetIntValueForGVName(gve.Name);
FMStream.record.GV[GrVar++] = j < 0 ? 0 : j; //use zero to indicate "No value"
}
}
/***** Process each FILMAN record *****/
int actualNumberOfFMRecs = 0;
for (int rec = 1; rec <= maxNumberOfFMRecs; rec++)
{
endBDFPoint += FMRecordLengthInBDF; //update end point
if (currentEpisode.Exclude == null || !currentEpisode.Exclude.IsExcluded(startBDFPoint, endBDFPoint)) //is not excluded:
{
FMStream.record.GV[4] = ++actualNumberOfFMRecs; //Record number in this episode
FMStream.record.GV[5] = Convert.ToInt32(Math.Ceiling(startBDFPoint.ToSecs())); //Approximate seconds since start of BDF file
//calculate start and end times for this record: use BDFPoint values to assure accuracy;
//avoids problem if FMRecordLength is not exactly represented in double
startTime = startBDFPoint.ToSecs();
endTime = endBDFPoint.ToSecs();
//*****Count PK Events in this record*****
if (PKCounterExists)
{
for (int j = GVCount - 3; j < GVCount; j++) FMStream.record.GV[j] = 0; //zero out as default
if(currentEpisode.PKCounter!=null)
{
PKDetectorEventCounterDescription pkd = currentEpisode.PKCounter;
double[] v = pkd.countMatchingEvents(startTime, startTime + FMRecLength, EventList);
FMStream.record.GV[GVCount - 3] = Convert.ToInt32(1000D * v[0]); //make per thousand to nave useful integer
FMStream.record.GV[GVCount - 2] = Convert.ToInt32(v[1]);
FMStream.record.GV[GVCount - 1] = Convert.ToInt32(v[2]);
}
}
createFILMANRecord(startBDFPoint, endBDFPoint);
}
startBDFPoint = endBDFPoint; //move start point forward
}
log.closeFoundEpisode(actualNumberOfFMRecs);
}
} while (found && !(currentEpisode.Start.MatchesType("Beginning of file") == true)); //next Event, if any
} //next spec
e.Result = new int[] { FMStream.NR, FMStream.NR / FMStream.NC };
FMStream.Close();
log.Close();
Log.writeToLog("Completed ASC conversion with " + FMStream.NR.ToString("0") + " FM records created");
}
public MainWindow()
{
bool r;
do //first get HDR file and open BDF file
{
OpenFileDialog dlg = new OpenFileDialog();
dlg.Title = "Open Header of dataset to be edited...";
dlg.DefaultExt = ".hdr"; // Default file extension
dlg.Filter = "HDR Files (.hdr)|*.hdr"; // Filter files by extension
Nullable<bool> result = dlg.ShowDialog();
if (result == null || result == false) Environment.Exit(0);
directory = System.IO.Path.GetDirectoryName(dlg.FileName); //will use to find other files in dataset
headerFileName = System.IO.Path.GetFileNameWithoutExtension(dlg.FileName);
header = (new HeaderFileReader(dlg.OpenFile())).read();
updateFlag = header.Events.ContainsKey("**ArtifactBegin"); //indicates that we are editing a dataset that has already been edited for artifacts
bdf = new BDFEDFFileReader(new FileStream(System.IO.Path.Combine(directory, header.BDFFile),
FileMode.Open, FileAccess.Read));
//make list of candidate EEG channels, so that channel selection window can use it
BDFLength = (double)bdf.NumberOfRecords * bdf.RecordDuration;
string trans = bdf.transducer(0); //here we assumne that channel 0 is an EEG channel
for (int i = 0; i < bdf.NumberOfChannels - 1; i++) //exclude Status channel
if (bdf.transducer(i) == trans) EEGChannels.Add(i);
Window1 w = new Window1(this); //open channel selection and file approval window
r = (bool)w.ShowDialog();
} while (r == false);
InitializeComponent();
Log.writeToLog("Starting EEGArtifactEditor " + Assembly.GetExecutingAssembly().GetName().Version.ToString() +
" on dataset " + headerFileName);
ViewerGrid.Width = BDFLength;
try
{
//process Events in current dataset; we have to do this now in case this is an update situation, but don't have to when we finish
Event.EventFactory.Instance(header.Events); // set up the factory, based on this Event dictionary
//and read them in
EventFileReader efr = new EventFileReader(
new FileStream(System.IO.Path.Combine(directory, header.EventFile),
FileMode.Open, FileAccess.Read)); // open Event file
foreach (InputEvent ie in efr)// read in all Events into list
events.Add(new OutputEvent(ie));
efr.Close(); //now events is list of Events in the dataset
//now set zeroTime for this BDF file, after finding an appropriate (non-"naked") Event
bool ok = false;
foreach (OutputEvent ev in events)
if (header.Events[ev.Name].IsCovered)
{
bdf.setZeroTime(ev);
ok = true;
break;
}
if (!ok)
{
ErrorWindow ew = new ErrorWindow();
ew.Message = "Unable to find a covered Event in this dataset on which to synchronize clocks. Exiting.";
ew.ShowDialog();
Log.writeToLog("Unable to synchronize clocks.");
this.Close();
}
if (updateFlag) //re-editing this dataset for artifacts
{
Event.EventFactory.Instance(header.Events); // set up the factory, based on this Event dictionary
//and read them in
OutputEvent ev;
int i = 0;
double left;
while (i < events.Count)
{
ev = events[i];
if (ev.Name == "**ArtifactBegin")
{
left = bdf.timeFromBeginningOfFileTo(ev);
events.Remove(ev);
while (i < events.Count)
{
ev = events[i];
if (ev.Name == "**ArtifactEnd")
{
MarkerCanvas.createMarkRegion(left, bdf.timeFromBeginningOfFileTo(ev));
events.Remove(ev);
break;
}
if (ev.Name == "**ArtifactBegin")
throw (new Exception("Unmatched artifact Event in Event file " +
System.IO.Path.Combine(directory, header.EventFile)));
i++;
}
}
else
i++;
}
}
//initialize the individual channel canvases
foreach (int chan in selectedEEGChannels)
{
ChannelCanvas cc = new ChannelCanvas(this, chan);
currentChannelList.Add(cc);
ViewerCanvas.Children.Add(cc);
ViewerCanvas.Children.Add(cc.offScaleRegions);
}
Title = headerFileName; //set window title
BDFFileInfo.Content = bdf.ToString();
HDRFileInfo.Content = header.ToString();
ElectrodeInputFileStream eif = new ElectrodeInputFileStream(
new FileStream(System.IO.Path.Combine(directory, header.ElectrodeFile),
FileMode.Open, FileAccess.Read)); //open Electrode file
electrodes = eif.etrPositions;
//initialize vertical gridline array; never more than 18
for (int i = 0; i < 18; i++)
{
Line l = new Line();
Grid.SetRow(l, 0);
Grid.SetColumn(l, 0);
l.Y1 = 0D;
l.HorizontalAlignment = HorizontalAlignment.Left;
l.VerticalAlignment = VerticalAlignment.Stretch;
l.IsHitTestVisible = false;
l.Stroke = Brushes.LightBlue;
l.Visibility = Visibility.Hidden;
Panel.SetZIndex(l, int.MaxValue);
VerticalGrid.Children.Add(l);
gridlines[i] = l;
}
//Initialize timer
timer.AutoReset = true;
timer.Elapsed += new ElapsedEventHandler(timer_Elapsed);
//Initialize channel information popup
Color c1 = Color.FromArgb(0xFF, 0xF8, 0xF8, 0xF8);
Color c2 = Color.FromArgb(0xFF, 0xC8, 0xC8, 0xC8);
popupTB.Background = new LinearGradientBrush(c1, c2, 45D);
popupTB.Foreground = Brushes.Black;
popupTB.Padding = new Thickness(4D);
Border b = new Border();
b.BorderThickness = new Thickness(1);
b.CornerRadius = new CornerRadius(4);
b.BorderBrush = Brushes.Tomato;
b.Margin = new Thickness(0, 0, 24, 24); //allows drop shadow to show up
b.Effect = new DropShadowEffect();
b.Child = popupTB;
channelPopup.Placement = PlacementMode.MousePoint;
channelPopup.AllowsTransparency = true;
channelPopup.Child = b;
//Initialize FOV slider
FOV.Maximum = Math.Log10(BDFLength);
FOV.Value = 1D;
FOVMax.Text = BDFLength.ToString("0");
//Note file always uses the "main" orginal dataset name, which should be the BDFFile name; this keeps notes from all levels of
//processing in the same place
noteFilePath = System.IO.Path.Combine(directory, System.IO.Path.GetFileNameWithoutExtension(header.BDFFile) + ".notes.txt");
}
catch (Exception ex)
{
ErrorWindow ew = new ErrorWindow();
ew.Message = "Error in EEGArtifactEditor initialization" + ex.Message;
ew.ShowDialog();
this.Close(); //exit
}
//from here on the program is GUI-event driven
}
public void Execute(object sender, DoWorkEventArgs e)
{
bw = (BackgroundWorker)sender;
bw.ReportProgress(0, "Starting FMConverter");
CCIUtilities.Log.writeToLog("Starting FMConverter on records in " + directory);
/***** Read electrode file *****/
ElectrodeInputFileStream etrFile = new ElectrodeInputFileStream(
new FileStream(Path.Combine(directory, eventHeader.ElectrodeFile), FileMode.Open, FileAccess.Read));
/***** Open FILMAN file *****/
SaveFileDialog dlg = new SaveFileDialog();
dlg.Title = "Save as FILMAN file ...";
dlg.AddExtension = true;
dlg.DefaultExt = ".fmn"; // Default file extension
dlg.Filter = "FILMAN Files (.fmn)|*.fmn"; // Filter files by extension
dlg.FileName=Path.GetFileNameWithoutExtension(eventHeader.BDFFile);
Nullable<bool> result = dlg.ShowDialog();
if (result == null || !(bool)result)
{
e.Result = new int[] { 0, 0 };
return;
}
samplingRate = BDF.NSamp / BDF.RecordDuration;
offsetInPts = Convert.ToInt32(offset * samplingRate);
newRecordLength = Convert.ToInt32(Math.Ceiling(length * samplingRate / (float)decimation));
FMStream = new FILMANOutputStream(
File.Open(dlg.FileName, FileMode.Create, FileAccess.ReadWrite),
GV.Count + 2, EDE.ancillarySize, channels.Count,
newRecordLength,
FILMANFileStream.FILMANFileStream.Format.Real);
log = new LogFile(dlg.FileName + ".log.xml");
FMStream.IS = Convert.ToInt32( (double)samplingRate/(double)decimation);
bigBuff = new float[BDF.NumberOfChannels - 1, FMStream.ND]; //have to dimension to BDF rather than FMStream
//in case we need for reference calculations
/***** Create FILMAN header records *****/
FMStream.GVNames(0, "Channel");
FMStream.GVNames(1, "Montage");
int i = 2;
foreach (GVEntry gv in GV) FMStream.GVNames(i++, gv.Name); //generate group variable names
for (i = 0; i < FMStream.NC; i++) //generate channel labels
{
string s = BDF.channelLabel(channels[i]);
ElectrodeFileStream.ElectrodeRecord p;
if (etrFile.etrPositions.TryGetValue(s, out p)) //add electrode location information, if available
FMStream.ChannelNames(i, s.PadRight(16, ' ') + p.projectPhiTheta().ToString("0"));
else
FMStream.ChannelNames(i, s);
}
FMStream.Description(0, eventHeader.Title + " Date: " + eventHeader.Date + " " + eventHeader.Time);
FMStream.Description(1, "File: " + Path.Combine(directory, Path.GetFileNameWithoutExtension(eventHeader.BDFFile)));
StringBuilder sb = new StringBuilder("Subject: " + eventHeader.Subject.ToString());
if (eventHeader.Agent != 0) sb.Append(" Agent: " + eventHeader.Agent);
sb.Append(" Tech:");
foreach (string s in eventHeader.Technician) sb.Append(" " + s);
FMStream.Description(2, sb.ToString());
sb = new StringBuilder("Event="+EDE.Name);
sb.Append(" Offset=" + offset.ToString("0.00"));
sb.Append(" Length=" + length.ToString("0.00"));
if (referenceGroups == null || referenceGroups.Count == 0) sb.Append(" No reference");
else if (referenceGroups.Count == 1)
{
sb.Append(" Single ref group with");
if (referenceGroups[0].Count >= FMStream.NC)
if (referenceChannels[0].Count == BDF.NumberOfChannels) sb.Append(" common average ref");
else if (referenceChannels[0].Count == 1)
sb.Append(" ref channel " + referenceChannels[0][0].ToString("0") + "=" + BDF.channelLabel(referenceChannels[0][0]));
else sb.Append(" multiple ref channels=" + referenceChannels[0].Count.ToString("0"));
}
else // complex reference expression
{
sb.Append(" Multiple reference groups=" + referenceGroups.Count.ToString("0"));
}
FMStream.Description(3, sb.ToString());
sb = new StringBuilder("#Group vars=" + GV.Count.ToString("0"));
if (anc) sb.Append(" Ancillary=" + FMStream.NA.ToString("0"));
sb.Append(" #Channels=" + FMStream.NC.ToString("0"));
sb.Append(" #Samples=" + FMStream.ND.ToString("0"));
sb.Append(" Samp rate=" + FMStream.IS.ToString("0"));
FMStream.Description(4, sb.ToString());
FMStream.Description(5, BDF.LocalRecordingId);
FMStream.writeHeader();
log.registerHeader(this);
/***** Open Event file for reading *****/
EventFactory.Instance(eventHeader.Events); // set up the factory
EventFileReader EventFR = new EventFileReader(
new FileStream(Path.Combine(directory, eventHeader.EventFile), FileMode.Open, FileAccess.Read));
BDFLoc stp = BDF.LocationFactory.New();
if (!EDE.intrinsic)
if (risingEdge) threshold = EDE.channelMin + (EDE.channelMax - EDE.channelMin) * threshold;
else threshold = EDE.channelMax - (EDE.channelMax - EDE.channelMin) * threshold;
nominalT = BDF.LocationFactory.New(); //nominal Event time based on Event.Time
actualT = BDF.LocationFactory.New(); //actual Event time in Status channel
//Note: these should be the same if the two clocks run the same rate (BioSemi DAQ and computer)
/***** MAIN LOOP *****/
foreach (InputEvent ie in EventFR) //Loop through Event file
{
bw.ReportProgress(0, "Processing event " + ie.Index.ToString("0")); //Report progress
if (ie.Name == EDE.Name) // Event match found in Event file
{
if (findEvent(ref stp, ie))
createFILMANRecord(stp, ie); //Create FILMAN recordset around this found point
}
}
e.Result = new int[] { FMStream.NR, FMStream.NR / FMStream.NC };
FMStream.Close();
EventFR.Close();
log.Close();
}
public void Execute(object sender, DoWorkEventArgs e)
{
bw = (BackgroundWorker)sender;
bw.ReportProgress(0, "Starting BDFConverter");
CCIUtilities.Log.writeToLog("Starting BDFConverter on records in " + directory);
/***** Read electrode file *****/
ElectrodeInputFileStream etrFile = new ElectrodeInputFileStream(
new FileStream(Path.Combine(directory, eventHeader.ElectrodeFile), FileMode.Open, FileAccess.Read));
/***** Open BDF file *****/
Microsoft.Win32.SaveFileDialog dlg = new Microsoft.Win32.SaveFileDialog();
dlg.Title = "Save as BDF file ...";
dlg.AddExtension = true;
dlg.DefaultExt = ".bdf"; // Default file extension
dlg.Filter = "BDF Files (.bdf)|*.bdf"; // Filter files by extension
dlg.FileName = Path.GetFileNameWithoutExtension(eventHeader.BDFFile);
bool? result = dlg.ShowDialog();
if (result == false)
{
e.Result = new int[] { 0, 0 };
return;
}
samplingRate = BDF.NSamp / BDF.RecordDuration; //Old sampling rate; exact as number of samples and duration are always an exact multiple
oldOffsetInPts = Convert.ToInt32(offset * samplingRate);
int newSamplingRate = (int)((double)samplingRate / (double)decimation + 0.5); //Make best estimate possible with integers
newOffsetInPts = Convert.ToInt32(offset * newSamplingRate);
newRecordLength = length * newSamplingRate; //new record length must be exact multiple of the sampling rate in BDF
newStatus = new int[newRecordLength];
status = new int[BDF.NSamp];
GV0 = GV[0];
BDFWriter = new BDFEDFFileWriter(File.Open(dlg.FileName, FileMode.Create, FileAccess.ReadWrite),
channels.Count + 1, /* Extra channel will have group variable value in it */
length, /* Record length in seconds, must be integer */
newSamplingRate,
true);
log = new LogFile(dlg.FileName + ".log.xml");
bigBuff = new float[BDF.NumberOfChannels - 1, newRecordLength]; //have to dimension to old channels rather than new
//in case we need for reference calculations later
/***** Create BDF header record *****/
BDFWriter.LocalRecordingId = BDF.LocalRecordingId;
BDFWriter.LocalSubjectId = BDF.LocalSubjectId;
int chan;
for (int i = 0; i < channels.Count; i++)
{
chan = channels[i];
BDFWriter.channelLabel(i, BDF.channelLabel(chan));
BDFWriter.transducer(i, BDF.transducer(chan));
BDFWriter.dimension(i, BDF.dimension(chan));
BDFWriter.pMax(i, BDF.pMax(chan));
BDFWriter.pMin(i, BDF.pMin(chan));
BDFWriter.dMax(i, BDF.dMax(chan));
BDFWriter.dMin(i, BDF.dMin(chan));
BDFWriter.prefilter(i, BDF.prefilter(chan));
}
chan = channels.Count;
BDFWriter.channelLabel(chan, GV0.Name); //Make entries for old Status channel
BDFWriter.transducer(chan, "None");
BDFWriter.dimension(chan, "");
BDFWriter.pMax(chan, 262143);
BDFWriter.pMin(chan, -262144);
BDFWriter.dMax(chan, 262143);
BDFWriter.dMin(chan, -262144);
BDFWriter.prefilter(chan, "None");
log.registerHeader(this);
/***** Open Event file for reading *****/
EventFactory.Instance(eventHeader.Events); // set up the factory
EventFileReader EventFR = new EventFileReader(
new FileStream(Path.Combine(directory, eventHeader.EventFile), FileMode.Open, FileAccess.Read));
BDFLoc stp = BDF.LocationFactory.New();
BDFLoc lastEvent = BDF.LocationFactory.New();
if (!EDE.intrinsic) //set threshold
if (risingEdge) threshold = EDE.channelMin + (EDE.channelMax - EDE.channelMin) * threshold;
else threshold = EDE.channelMax - (EDE.channelMax - EDE.channelMin) * threshold;
nominalT = BDF.LocationFactory.New(); //nominal Event time based on Event.Time
actualT = BDF.LocationFactory.New(); //actual Event time in Status channel
//Note: these should be the same if the two clocks run the same rate (DAQ and computer)
/***** MAIN LOOP *****/
foreach (InputEvent ie in EventFR) //Loop through Event file
{
bw.ReportProgress(0, "Processing event " + ie.Index.ToString("0")); //Report progress
if (ie.Name == EDE.Name) // Event match found in Event file
{
if(findEvent(ref stp, ie))
if (allSamps) //this is a continuous copy, not Event generated episodic conversion
{
runBDFtoEvent(lastEvent, ref stp, ie);
lastEvent = BDF.LocationFactory.New();
}
else createBDFRecord(stp, ie); //Create BDF recordset around this point; i.e. Event generated episodic conversion
}
}
if (allSamps) //copy out to end of file
{
stp.Rec = BDF.NumberOfRecords;
stp.Pt = 0;
runBDFtoEvent(lastEvent, ref stp, null);
}
e.Result = new int[] { BDFWriter.NumberOfRecords, BDFWriter.NumberOfRecords };
BDFWriter.Close();
EventFR.Close();
log.Close();
}
public MainWindow()
{
Log.writeToLog("Starting DatasetReviewer " + Assembly.GetExecutingAssembly().GetName().Version.ToString());
do
{
bool r;
do
{
System.Windows.Forms.OpenFileDialog dlg = new System.Windows.Forms.OpenFileDialog();
dlg.Title = "Open Header file to be displayed...";
dlg.DefaultExt = ".hdr"; // Default file extension
dlg.Filter = "HDR Files (.hdr)|*.hdr"; // Filter files by extension
bool result = dlg.ShowDialog() == System.Windows.Forms.DialogResult.OK;
if (!result) Environment.Exit(0);
directory = System.IO.Path.GetDirectoryName(dlg.FileName); //will use to find other files in dataset
headerFileName = System.IO.Path.GetFileNameWithoutExtension(dlg.FileName);
try
{
head = (new HeaderFileReader(dlg.OpenFile())).read();
}
catch (Exception e)
{
r = false; //loop around again
ErrorWindow ew = new ErrorWindow();
ew.Message = "Error reading Header file: " + e.Message;
continue;
}
ED = head.Events;
try
{
bdf = new BDFEDFFileStream.BDFEDFFileReader(
new FileStream(System.IO.Path.Combine(directory, head.BDFFile),
FileMode.Open, FileAccess.Read));
}
catch (Exception e)
{
r = false; //loop around again
ErrorWindow ew = new ErrorWindow();
ew.Message = "Error reading BDF file header: " + e.Message;
ew.ShowDialog();
continue;
}
BDFLength = (double)bdf.NumberOfRecords * bdf.RecordDurationDouble;
Window1 w = new Window1(this);
r = (bool)w.ShowDialog();
} while (r == false);
Log.writeToLog(" on dataset " + headerFileName);
if (includeANAs)
{
foreach (EventDictionaryEntry ede in ED.Values) // add ANA channels that are referenced by extrinsic Events
{
if (ede.IsCovered && ede.IsExtrinsic)
{
int chan = bdf.ChannelNumberFromLabel(ede.channelName);
if (!channelList.Contains(chan)) //don't enter duplicate
channelList.Add(chan);
}
}
}
} while (channelList.Count == 0);
InitializeComponent();
//initialize the individual channel graphs
foreach (int i in channelList)
{
ChannelGraph pg = new ChannelGraph(this, i);
GraphCanvas.Children.Add(pg);
}
Title = headerFileName; //set window title
BDFFileInfo.Content = bdf.ToString();
HDRFileInfo.Content = head.ToString();
Event.EventFactory.Instance(head.Events); // set up the factory
EventFileReader efr = null;
try
{
efr = new EventFileReader(
new FileStream(System.IO.Path.Combine(directory, head.EventFile),
FileMode.Open, FileAccess.Read)); // open Event file
bool z = false;
foreach (Event.InputEvent ie in efr)// read in all Events into dictionary
{
if (ie.IsNaked)
events.Add(ie);
else if (events.Count(e => e.GC == ie.GC) == 0) //quietly skip duplicates
{
if (!z) //use first found covered Event to synchronize clocks
z = bdf.setZeroTime(ie);
events.Add(ie);
}
}
efr.Close(); //now events is Dictionary of Events in the dataset; lookup by GC
}
catch (Exception e)
{
ErrorWindow ew = new ErrorWindow();
ew.Message = "Error reading Event file : " + e.Message + ". Exiting DatasetReviewer.";
ew.ShowDialog();
Log.writeToLog(Environment.NewLine + e.StackTrace);
Environment.Exit(0);
}
try
{
ElectrodeInputFileStream eif = new ElectrodeInputFileStream(
new FileStream(System.IO.Path.Combine(directory, head.ElectrodeFile),
FileMode.Open, FileAccess.Read)); //open Electrode file
electrodes = eif.etrPositions; //read 'em in
}
catch (Exception e)
{
ErrorWindow ew = new ErrorWindow();
ew.Message = "Error reading Electrode file : " + e.Message + ". Exitting DatasetReviewer.";
ew.ShowDialog();
Log.writeToLog(Environment.NewLine + e.StackTrace);
Environment.Exit(0);
}
EventMarkers.Width = BDFLength;
eventTB = new TextBlock(new Run("Events"));
Canvas.SetBottom(eventTB, ScrollBarSize + 13D);
//initialize gridline array
for (int i = 0; i < 18; i++)
{
Line l = new Line();
Grid.SetRow(l, 0);
Grid.SetColumn(l, 0);
Grid.SetColumnSpan(l, 2);
l.Y1 = 0D;
l.HorizontalAlignment = HorizontalAlignment.Left;
l.VerticalAlignment = VerticalAlignment.Stretch;
l.IsHitTestVisible = false;
l.Stroke = Brushes.LightBlue;
l.Visibility = Visibility.Hidden;
Panel.SetZIndex(l, int.MinValue);
MainFrame.Children.Add(l);
gridlines[i] = l;
}
//Initialize timer
timer.AutoReset = true;
timer.Elapsed += new ElapsedEventHandler(timer_Elapsed);
//Initialize channel information popup
Color c1 = Color.FromArgb(0xFF, 0xF8, 0xF8, 0xF8);
Color c2 = Color.FromArgb(0xFF, 0xC8, 0xC8, 0xC8);
popupTB.Background = new LinearGradientBrush(c1, c2, 45D);
popupTB.Foreground = Brushes.Black;
popupTB.Padding = new Thickness(4D);
Border b = new Border();
b.BorderThickness = new Thickness(1);
b.CornerRadius = new CornerRadius(4);
b.BorderBrush = Brushes.Tomato;
b.Margin = new Thickness(0, 0, 24, 24); //allows drop shadow to show up
b.Effect = new DropShadowEffect();
b.Child = popupTB;
channelPopup.Placement = PlacementMode.MousePoint;
channelPopup.AllowsTransparency = true;
channelPopup.Child = b;
//Initialize Event information popup
eventPopupTB.Background = new LinearGradientBrush(c1, c2, 45D);
eventPopupTB.Foreground = Brushes.Black;
eventPopupTB.Padding = new Thickness(4D);
b = new Border();
b.BorderThickness = new Thickness(1);
b.CornerRadius = new CornerRadius(4);
b.BorderBrush = Brushes.Tomato;
b.Margin = new Thickness(0, 0, 24, 24); //allows drop shadow to show up
b.Effect = new DropShadowEffect();
b.Child = eventPopupTB;
eventPopup.Placement = PlacementMode.MousePoint;
eventPopup.AllowsTransparency = true;
eventPopup.Child = b;
//Initialize FOV slider
FOV.Maximum = Math.Log10(BDFLength);
FOV.Value = 1D;
FOVMax.Text = BDFLength.ToString("0");
//Initialize Event selector
bool first = true;
foreach (EventDictionaryEntry e in head.Events.Values)
{
MenuItem mi = (MenuItem)EventSelector.FindResource("EventMenuItem");
mi.Header = e.Name;
if (first)
{
mi.IsChecked = true;
first = false;
}
EventSelector.Items.Add(mi);
}
noteFilePath = System.IO.Path.Combine(directory,System.IO.Path.ChangeExtension(head.BDFFile,".notes.txt"));
//from here on the program is GUI-event driven
}
