public BDFPoint(BDFEDFFileReader bdf)
{
_rec = 0;
_pt = 0;
_recSize = bdf.NSamp;
_sec = bdf.RecordDurationDouble;
_st = _sec / (double)_recSize;
}
static void Main(string[] args)
{
string fileName = @"C:\\Users\Jim\Desktop\Real datasets\S00xx-AP-20141107-1226\S0082-AP-20141107-1226.bdf";
BDFEDFFileReader bdf = new BDFEDFFileReader(new FileStream(fileName, FileMode.Open, FileAccess.Read));
Console.WriteLine("Opened BDF file " + fileName);
string s;
while (true)
{
Console.Write("Record number> ");
if ((s = Console.ReadLine()) == "") break;
BDFEDFRecord rec = bdf.read(Convert.ToInt32(s));
Console.WriteLine("Rec # = " + rec.RecordNumber.ToString("0"));
int[] status = bdf.getStatus();
Console.Write(HexDump(status, 12, 2));
}
}
public Window2()
{
Log.writeToLog("Starting FileConverter " + Utilities.getVersionNumber());
Microsoft.Win32.OpenFileDialog dlg = new Microsoft.Win32.OpenFileDialog();
dlg.Title = "Open Header file for conversion...";
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) { this.Close(); Environment.Exit(0); }
directory = System.IO.Path.GetDirectoryName(dlg.FileName);
head = (new HeaderFileReader(dlg.OpenFile())).read();
ED = head.Events;
bdf = new BDFEDFFileReader(
new FileStream(System.IO.Path.Combine(directory, head.BDFFile),
FileMode.Open, FileAccess.Read));
oldSR = bdf.NSamp / bdf.RecordDurationDouble;
oldNP = bdf.NSamp;
oldNS = bdf.RecordDurationDouble;
InitializeComponent();
this.MinHeight = SystemInformation.WorkingArea.Height - 240;
this.Title = "Convert " + System.IO.Path.GetFileNameWithoutExtension(dlg.FileName);
this.TitleLine.Text = head.Title + " - " + head.Date + " " + head.Time + " S=" + head.Subject.ToString("0000");
_EDEList = ED.Values.ToList<EventDictionaryEntry>();
listView1.SelectedItem = 0;
listView1.Focus();
listView1.ItemsSource = EDEList;
System.Windows.Data.Binding GVBinding = new System.Windows.Data.Binding();
GVBinding.Source = this;
GVBinding.NotifyOnSourceUpdated = true;
GVBinding.Path = new PropertyPath("GVList");
GVBinding.Mode = BindingMode.OneWay;
listView2.SetBinding(System.Windows.Controls.ListView.ItemsSourceProperty, GVBinding);
GVList = EDEList[0].GroupVars;
}
/// <summary>
/// Links all input Events to a particular dataset in order to make the timing of InputEvents relative
/// to the BDF file
/// </summary>
/// <param name="Head">HDR file reader for the dataset</param>
/// <param name="BDF">BDF file reader for the dataset</param>
public static void LinkEventsToDataset(Header.Header Head, BDFEDFFileReader BDF)
{
head = Head;
bdf = BDF;
}
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 Window2()
{
OpenFileDialog dlg = new OpenFileDialog();
dlg.Title = "Open Header file ...";
dlg.DefaultExt = ".hdr"; // Default file extension
dlg.Filter = "HDR Files (.hdr)|*.hdr"; // Filter files by extension
dlg.InitialDirectory = Properties.Settings.Default.LastDataset;
bool result = dlg.ShowDialog() == System.Windows.Forms.DialogResult.OK;
if (!result) Environment.Exit(0);
headerFileName = System.IO.Path.GetFileNameWithoutExtension(dlg.FileName);
directory = System.IO.Path.GetDirectoryName(dlg.FileName);
Properties.Settings.Default.LastDataset = directory;
CCIUtilities.Log.writeToLog("Starting ASCtoFMConverter " + CCIUtilities.Utilities.getVersionNumber());
head = (new HeaderFileReader(dlg.OpenFile())).read();
ED = head.Events;
bdf = new BDFEDFFileReader(
new FileStream(System.IO.Path.Combine(directory, head.BDFFile),
FileMode.Open, FileAccess.Read));
samplingRate = (int)((double)bdf.NSamp / bdf.RecordDurationDouble);
OpenPCommand.InputGestures.Add(
new KeyGesture(Key.O, ModifierKeys.Control | ModifierKeys.Shift, "Ctrl+Shift+O"));
SavePCommand.InputGestures.Add(
new KeyGesture(Key.S, ModifierKeys.Control, "Crtl+S"));
ProcessCommand.InputGestures.Add(
new KeyGesture(Key.P, ModifierKeys.Control, "Crtl+P"));
ExitCommand.InputGestures.Add(new KeyGesture(Key.Q, ModifierKeys.Control, "Crtl+Q"));
InitializeComponent();
//***** Set up menu commands and short cuts
CommandBinding cbOpenP = new CommandBinding(OpenPCommand, cbOpen_Execute, cbOpen_CanExecute);
this.CommandBindings.Add(cbOpenP);
CommandBinding cbSaveP = new CommandBinding(SavePCommand, cbSave_Execute, validParams_CanExecute);
this.CommandBindings.Add(cbSaveP);
CommandBinding cbProcess = new CommandBinding(ProcessCommand, ConvertFM_Click, validParams_CanExecute);
this.CommandBindings.Add(cbProcess);
CommandBinding cbExit = new CommandBinding(ExitCommand, Done_Click, cbExit_CanExecute);
this.CommandBindings.Add(cbExit);
this.MinHeight = SystemInformation.WorkingArea.Height - 240;
this.EpisodeEntries.Items.Add(new EpisodeDescriptionEntry(head, this)); //include initial episode description
this.Title = "Convert " + headerFileName;
this.TitleLine.Text = head.Title + " - " + head.Date + " " + head.Time + " S=" + head.Subject.ToString("0000");
if (head.GroupVars != null)
{
System.Windows.Data.Binding GVBinding = new System.Windows.Data.Binding();
GVBinding.Source = this;
GVBinding.NotifyOnSourceUpdated = true;
GVBinding.Path = new PropertyPath("GVList");
GVBinding.Mode = BindingMode.OneWay;
listView2.SetBinding(System.Windows.Controls.ListView.ItemsSourceProperty, GVBinding);
GVList = head.GroupVars.Values.ToList<GVEntry>();
}
else
GVList = new List<GVEntry>(0);
this.Activate();
}
static void Main(string[] args)
{
List<eventTime> eventList = new List<eventTime>();
Console.Write("Degree of fit desired: ");
int degree = Convert.ToInt32(Console.ReadLine());
BDFEDFFileReader bdf = new BDFEDFFileReader(new FileStream(@"C:\\Users\Jim\Desktop\PK detector data\S9998-AP-20150210-1205_PKcubes.bdf", FileMode.Open, FileAccess.Read));
Console.WriteLine("Opened BDF file");
double[] d = bdf.readAllChannelData(5);
int N = d.Length;
double n = (double)N;
Console.WriteLine(d[0].ToString() + " " + d[1].ToString() + " " + d[100].ToString());
removeTrend(d, degree);
Console.WriteLine(d[0].ToString() + " " + d[1].ToString() + " " + d[100].ToString());
double[] V = new double[filterN];
double c1 = 12D / (double)(filterN * (filterN - 1) * (filterN + 1));
double offset = ((double)filterN - 1D) / 2D;
for (int i = 0; i < filterN; i++) V[i] = c1 * ((double)i - offset);
List<double> filtered = new List<double>(64);
byte[] marker = new byte[N];
bool inEvent = false;
int eventLength = 0;
double sign = 1D;
for (int i = 0; i < N; i++)
{
double s = 0;
for (int j = 0; j < filterN; j++)
{
int index = i + j - filterN / 2;
if (index < 0) //handle start-up
s += V[j] * d[0]; //repeat first value to its left
else if (index >= N) //handle end
s += V[j] * d[N - 1]; //repeat last value to its right
else //usual case
s += V[j] * d[index];
}
if (Math.Abs(s) > threshold) //above threshold?
{
if (!inEvent) //found beginning of new event
{
sign = s > 0D ? 1D : -1D;
eventLength = 0;
inEvent = true;
}
filtered.Add(s - sign * threshold);
eventLength++;
}
else //below threshold
if (inEvent) //are we just exiting an event?
{
if (eventLength > minimumLength) //event counts only if longer than minimum length
{
eventTime e = new eventTime();
e.time = i - eventLength;
e.length = eventLength;
e.sign = sign;
e.filteredSignal = filtered;
filtered = new List<double>(64); //need new filtered array
eventList.Add(e);
}
else
filtered.Clear();
inEvent = false;
}
}
int dataLength;
double t;
eventTime et0;
eventTime et1;
double t0 = (double)filterN / (2D * SR);
for (int i = 0; i < eventList.Count - 1; i++)
{
et0 = eventList[i];
et1 = eventList[i + 1];
dataLength = Math.Min(et1.time - et0.time, 16000);
double max = double.MinValue;
for (int p = et0.time; p < et0.time + et0.length; p++) max = Math.Max(max, Math.Abs(d[p]));
et0.A = et0.sign * max; //correct sign of displacement; could be max sign*Abs(displacement)
et0.C = d[et0.time]; //estimate of initial offset
et0.B = et0.C; //current actual "baseline"
et0.a = 4D; //typical alpha
et0.b = 0.04; //typical beta
t = t0; //half filterN / SR
if (et0.foundFit = fitSignal(d, et0.time, dataLength, ref et0.A, ref et0.B, ref et0.C, ref et0.a, ref et0.b, ref t))
et0.time += (int)(t * SR);
Console.WriteLine();
Console.WriteLine(et0.time.ToString("0") + " (" + LM.Result.ToString() + ", " + LM.Iterations.ToString("0") +
", " + LM.ChiSquare.ToString("0.0") + ", " + LM.normalizedStandardErrorOfFit.ToString("0.00") + "): ");
Console.WriteLine(et0.A.ToString("0.0") + " " + et0.B.ToString("0.0") + " " + et0.C.ToString("0.0") +
" " + et0.a.ToString("0.000") + " " + et0.b.ToString("0.00000") + " " + t.ToString("0.000") + " ");
NVector Sp = LM.parameterStandardError;
Console.WriteLine(Sp[0].ToString("0.00") + " " + Sp[1].ToString("0.00") + " " + Sp[2].ToString("0.00") +
" " + Sp[3].ToString("0.0000") + " " + Sp[4].ToString("0.000000") + " " + Sp[5].ToString("0.0000") + " ");
}
et0 = eventList[eventList.Count - 1];
dataLength = Math.Min(N - et0.time, 16000);
et0.A = et0.sign * 5000D; //correct sign of displacement; could be max sign*Abs(displacement)
et0.C = d[et0.time]; //estimate of initial offset
et0.B = et0.C;
et0.a = 4D;
et0.b = 0.05;
t = 0.25;
if (et0.foundFit = fitSignal(d, et0.time, dataLength, ref et0.A, ref et0.B, ref et0.C, ref et0.a, ref et0.b, ref t))
et0.time += (int)(t * SR);
Console.WriteLine(et0.time.ToString("0") + " (" + LM.Result.ToString() + ", " + LM.Iterations.ToString("0") +
", " + LM.ChiSquare.ToString("0.0") + "): " + et0.A.ToString("0.0") + " " + et0.B.ToString("0.0") + " " + et0.C.ToString("0.0") +
" " + et0.a.ToString("0.000") + " " + et0.b.ToString("0.00000") + " " + t.ToString("0.000") + " ");
Console.WriteLine("Total events found = " + eventList.Count.ToString("0"));
ConsoleKeyInfo cki = Console.ReadKey();
}
public MainWindow()
{
OpenFileDialog dlg = new OpenFileDialog();
dlg.Title = "Open Header file ...";
dlg.DefaultExt = ".hdr"; // Default file extension
dlg.Filter = "HDR Files (.hdr)|*.hdr"; // Filter files by extension
dlg.InitialDirectory = Properties.Settings.Default.LastDataset;
DialogResult result = dlg.ShowDialog();
if (result != System.Windows.Forms.DialogResult.OK) Environment.Exit(0);
directory = System.IO.Path.GetDirectoryName(dlg.FileName);
Properties.Settings.Default.LastDataset = directory;
headerFileName = System.IO.Path.GetFileNameWithoutExtension(dlg.FileName);
CCIUtilities.Log.writeToLog("Starting PKDetectorAnalyzer " + CCIUtilities.Utilities.getVersionNumber() +
" on " + headerFileName);
head = (new HeaderFileReader(dlg.OpenFile())).read();
bdf = new BDFEDFFileReader(
new FileStream(System.IO.Path.Combine(directory, head.BDFFile),
FileMode.Open, FileAccess.Read));
for (int i = 0; i < bdf.NumberOfChannels; i++) //first see if this file has standard transducer labels
if (bdf.transducer(i) == "Analog Input Box")
channels.Add(new channelOptions(i, bdf.channelLabel(i))); //if it does, use them as channel choices
if (channels.Count == 0) //if it does not, then show all channels
for (int i = 0; i < bdf.NumberOfChannels; i++)
channels.Add(new channelOptions(i, bdf.channelLabel(i)));
AnalogChannelCount = channels.Count;
OpenPCommand.InputGestures.Add(
new KeyGesture(Key.O, ModifierKeys.Control | ModifierKeys.Shift, "Ctrl+Shift+O"));
SavePCommand.InputGestures.Add(
new KeyGesture(Key.S, ModifierKeys.Control, "Crtl+S"));
ProcessCommand.InputGestures.Add(
new KeyGesture(Key.P, ModifierKeys.Control, "Crtl+P"));
ExitCommand.InputGestures.Add(new KeyGesture(Key.Q, ModifierKeys.Control, "Crtl+Q"));
InitializeComponent();
//***** Set up menu commands and short cuts
CommandBinding cbOpenP = new CommandBinding(OpenPCommand, cbOpen_Execute, cbOpen_CanExecute);
this.CommandBindings.Add(cbOpenP);
CommandBinding cbSaveP = new CommandBinding(SavePCommand, cbSave_Execute, validParams_CanExecute);
this.CommandBindings.Add(cbSaveP);
CommandBinding cbProcess = new CommandBinding(ProcessCommand, ProcessChannels_Click, validParams_CanExecute);
this.CommandBindings.Add(cbProcess);
CommandBinding cbExit = new CommandBinding(ExitCommand, Quit_Click, cbExit_CanExecute);
this.CommandBindings.Add(cbExit);
//***** Set up defaults and other housekeeping
Title = headerFileName;
TitleLine.Text = directory + System.IO.Path.DirectorySeparatorChar + headerFileName;
FNExtension.Text = "PKDetection";
DataContext = this;
ChannelItem ci = new ChannelItem(this);
ChannelEntries.Items.Add(ci);
ci.Channel.SelectedIndex = 0;
Process.IsEnabled = true; //have to reenable here -- like checkError(); values are guarenteed valid however
this.Activate();
}
