Small Changes

- Fixed a bug that would resulted in triggers with similar trigger
numbers but unequal timings to be removed.
- Added an option that has the tool offset the trigger onset in
Presentation software generated logs due to Pauses (Presentation time is
paused during the pauses so results in asynchrony.

EDFPlusCheckerEngine/Engine/Actions/ActionCompareTriggers.cs

@@ -55,7 +55,7 @@ public override string Act()
                         // same triggernumber, unequal timing.
                         else
                         {
-                            if (this.EqNumberUneqTiming_RemoveRec && !RemoveList.Contains(EDFPlusTriggers[j]))
+                            if (this.EqNumberUneqTiming_RemoveRec && !RemoveList2.Contains(EDFPlusTriggers[j])&&!RemoveList.Contains(EDFPlusTriggers[j]))
                                 RemoveList2.Add(EDFPlusTriggers[j]);
                         }
                     }
@@ -64,7 +64,7 @@ public override string Act()
                         // different triggernumber, equal timing.
                         if (Map[i].SameTiming(EDFPlusTriggers[j], ErrorMargin))
                         {   
-                            if (this.UneqNumberEqTiming_RemoveRec && !RemoveList.Contains(EDFPlusTriggers[j]))
+                            if (this.UneqNumberEqTiming_RemoveRec && !RemoveList.Contains(EDFPlusTriggers[j]) && !RemoveList2.Contains(EDFPlusTriggers[j]))
                                 RemoveList.Add(EDFPlusTriggers[j]);
                         }
                         // different triggernumber, different timing.
@@ -136,6 +136,11 @@ public override string Act()
 
             Control.Log(Environment.NewLine, PrintInConsole);
 
+            foreach (Trigger trig in RemoveList2)
+            {
+                RemoveList.Add(trig);
+            }            
+
             //fill control variable with the differences
             Control.DifferenceBetweenFiles = new DifferenceFile(AddList, RemoveList);         
 

EDFPlusCheckerEngine/Engine/Actions/ActionOpenFiles.cs

@@ -39,11 +39,12 @@ public override string Act()
                     Control.EDFPlusHandle.ReadTALsToMemory();
             }
             else
-                throw new ActionCannotDoWhatDoBeDo("Couldn't find file: " + @EDFFileName); 
+                throw new ActionCannotDoWhatDoBeDo("Couldn't find or access file: " + @EDFFileName); 
 
             if (File.Exists(@PresentationLogFilename))
                 Control.PresentationLogHandle = new PresentationLogFile(this.Control, @PresentationLogFilename);
-
+            else
+                throw new ActionCannotDoWhatDoBeDo("Couldn't find or access file: " + @PresentationLogFilename); 
             Active = false;
 
             string Description = "Action: Opened File(s): ";

EDFPlusCheckerEngine/Engine/Controller.cs

@@ -35,6 +35,7 @@ public bool HasLogFiles
         public int[] TriggerNumbersToIgnore = new int[0];
         public int TriggerNumberLowerLimit = 0;
         public int TriggerNumberUpperLimit = 9999;
+        public bool CorrectForPauses;
 
         private StreamWriter ApplicationLogFile;
 

EDFPlusCheckerEngine/Engine/FileHandles/PresentationLogFile.cs

@@ -26,7 +26,7 @@ public Trigger[] Triggers {
             get {
                 if(_Triggers == null)
                 {
-                    _Triggers = GetTriggers(Owner.TriggerNumbersToIgnore, Owner.TriggerNumberLowerLimit, Owner.TriggerNumberUpperLimit);
+                    _Triggers = GetTriggers(Owner.TriggerNumbersToIgnore, Owner.TriggerNumberLowerLimit, Owner.TriggerNumberUpperLimit, Owner.CorrectForPauses);
                 }
                 return _Triggers;
             } 
@@ -39,20 +39,38 @@ public string[] GetDataColumn(string header)
             return Data[IndexOfColumn].ToArray<string>();
         }
 
-        private Trigger[] GetTriggers( int[] triggersToIgnore, int lowerTriggerLimit, int upperTriggerLimit)
+        private Trigger[] GetTriggers( int[] triggersToIgnore, int lowerTriggerLimit, int upperTriggerLimit, bool CorrectForPauses = true)
         {
            string[] CodeColumn = GetDataColumn("Code");
            string[] TimingColumn = GetDataColumn("Time");
            string[] UncertaintyColumn = GetDataColumn("Uncertainty");
-
+            string[] EventTypeColumn = new string[0];
+            string[] DurationColumn = new string[0];
+
+           if (CorrectForPauses)
+           {
+               EventTypeColumn = GetDataColumn("Event Type");
+               DurationColumn = GetDataColumn("Duration");
+           }
+
            if(CodeColumn.Length != TimingColumn.Length || TimingColumn.Length != UncertaintyColumn.Length)
                 throw new ActionCannotDoWhatDoBeDo("Something fishy going on with the length of the columns in the Presentation file " + this.FileName);
 
            List<Trigger> Result = new List<Trigger>(CodeColumn.Length);
+           int PauseOffset = 0;
 
            for (int i = 0; i < CodeColumn.Length; i++)
            {
                int TriggerNumber = -1;
+
+               if (CorrectForPauses && EventTypeColumn[i] == "Pause")
+               {
+                   int PauseDuration;
+                   if (!int.TryParse(DurationColumn[i], out PauseDuration))
+                       throw new ActionCannotDoWhatDoBeDo("Something fishy going on with PresentationLog Event Type of Duration column");
+                   PauseOffset += PauseDuration;
+               }
+
                if (int.TryParse(CodeColumn[i], out TriggerNumber) && TriggerNumber <= upperTriggerLimit && TriggerNumber >= lowerTriggerLimit && !triggersToIgnore.Contains(TriggerNumber))
                {
                    int OnsetTimeOneTenth = -9999;
@@ -61,7 +79,7 @@ private Trigger[] GetTriggers( int[] triggersToIgnore, int lowerTriggerLimit, in
                    if (!int.TryParse(TimingColumn[i], out OnsetTimeOneTenth) || !int.TryParse(UncertaintyColumn[i], out UncertaintyOneTenth))
                        throw new ActionCannotDoWhatDoBeDo("Something fishy going on with PresentationLog OnsetTime (TIME column)");
 
-                   double OnsetTime = ((double) OnsetTimeOneTenth)/10000;
+                   double OnsetTime = ((double)OnsetTimeOneTenth + PauseOffset) / 10000;
                    double Uncertainty = ((double) UncertaintyOneTenth)/10000;
                    Result.Add(new Trigger(OnsetTime, Uncertainty, TriggerNumber));
                }

EDFPlusCheckerEngine/Engine/TimeFrameConverter.cs

@@ -12,6 +12,9 @@ public class TimeFrameConverter
         public Controller Control;
 
         private double[,] TimeStamps;
+        private int[,] NumberStamps;
+
+        public int NumberOfTries;
 
         //EEGtime_missing_marker = ( (Prestime_missing_marker - PresentationFirst) * (AnalyzerLast- AnalyzerFirst) / (PresentationLast - PresentationFirst) ) + AnalyzerFirst
         public bool TimeConvertTriggers(Trigger[] mapFrom, out Trigger[] mapToo)
@@ -32,22 +35,25 @@ public bool TimeConvertTriggers(Trigger[] mapFrom, out Trigger[] mapToo)
             return true;
         }
 
-        public string ToString()
+        public override string ToString()
         {
             StringBuilder Description = new StringBuilder();
-            Description.Append("Time Conversion Target:\t");
-            Description.AppendLine(Math.Round(TimeStamps[0, 0], 3) + "s and " + Math.Round(TimeStamps[0, 1], 3) + "s");
-            Description.Append("Time Conversion Source:\t");
-            Description.AppendLine(Math.Round(TimeStamps[1, 0], 3) + "s and " + Math.Round(TimeStamps[1, 1], 3) + "s");
+            Description.Append("Time Conversion Logged File:\t");
+            Description.AppendLine(String.Format("{0:0.000}s ({1}) and {2:0.000}s ({3})", TimeStamps[0, 0], NumberStamps[0, 0], TimeStamps[0, 1], NumberStamps[0, 1]));
+            Description.Append("Time Conversion Recording File:\t");
+            Description.AppendLine(String.Format("{0:0.000}s ({1}) and {2:0.000}s ({3})", TimeStamps[1, 0], NumberStamps[1, 0], TimeStamps[1, 1], NumberStamps[1, 1]));
+            Description.AppendLine("Number of attempts: " + this.NumberOfTries);
             return Description.ToString();
         }
 
         public bool FindTimeConversion(Trigger[] mapFrom, Trigger[] mapToo, int verificationWindowSize, double errorMargin)
         {
             double[,] TempTimeStamps = new double[2, 2];
-
+            int[,] TempNumberStamps = new int[2, 2];
             bool TimeConversionFound = false;
 
+            this.NumberOfTries = 1;
+
             //Initiate search starting from the tops.
             for (int i = 0; i < mapToo.Length; i++)
             {
@@ -63,14 +69,24 @@ public bool FindTimeConversion(Trigger[] mapFrom, Trigger[] mapToo, int verifica
                                 {
                                     TempTimeStamps[0, 0] = mapFrom[j].ApproximateOnsetInSeconds;
                                     TempTimeStamps[0, 1] = mapFrom[b].ApproximateOnsetInSeconds;
+
+                                    TempNumberStamps[0, 0] = mapFrom[j].TriggerNumber;
+                                    TempNumberStamps[0, 1] = mapFrom[b].TriggerNumber;
+
                                     TempTimeStamps[1, 0] = mapToo[i].ApproximateOnsetInSeconds;
                                     TempTimeStamps[1, 1] = mapToo[a].ApproximateOnsetInSeconds;
 
+                                    TempNumberStamps[1, 0] = mapFrom[i].TriggerNumber;
+                                    TempNumberStamps[1, 1] = mapFrom[a].TriggerNumber;
+
                                     if (FindVerificationWindow(mapFrom, mapToo, verificationWindowSize, errorMargin, TempTimeStamps))
                                     {
                                         this.TimeStamps = TempTimeStamps;
+                                        this.NumberStamps = TempNumberStamps;
                                         return true;
                                     }
+                                    else
+                                        this.NumberOfTries++;
                                 }
                             }
                         }

EDFPlusCheckerGUI/ConfigurationWindow/ParseTriggerPage.xaml

@@ -80,8 +80,13 @@
         </GroupBox>
 
         <GroupBox Header="Log File (Presentation)" Grid.Row="4" FontSize="12" Margin="5" Padding="5">
-            <Label VerticalContentAlignment="Center" HorizontalContentAlignment="Center" Content="Presentation-Log event codes are ignored if they do not parse into integers. "/>
+            <StackPanel Orientation="Vertical" VerticalAlignment="Center" >
+                <Label VerticalContentAlignment="Center" HorizontalContentAlignment="Center" Content="Presentation-Log event codes are ignored if they do not parse into integers. "/>
+                <CheckBox Margin="5" x:Name="CorrectForPausesCheckbox" Content="Correct for Pauses in trigger onsets." HorizontalAlignment="Center" IsChecked="True"/>
+            </StackPanel>
+
         </GroupBox>
+
     </Grid>
 </src:ConfigurationPageBase>
 

EDFPlusCheckerGUI/ConfigurationWindow/ParseTriggerPage.xaml.cs

@@ -69,6 +69,7 @@ public override bool ConfigureEngine(out string possibleErrorMessage)
                     Engine.TriggerNumberLowerLimit = TriggerLowerLimit;
                     Engine.TriggerNumberUpperLimit = TriggerUpperLimit;
                     Engine.TriggerNumbersToIgnore = IgnoreTriggers_int;
+                    Engine.CorrectForPauses = CorrectForPausesCheckbox.IsChecked == true;
                 }
 
             }

EDFPlusCheckerGUI/MainEDFPlusCheckerWindow.xaml.cs

@@ -71,7 +71,7 @@ protected void MyBackGroundWorker_RunWorkerCompleted(object sender, RunWorkerCom
             else
             {
                 StatusTextBox.Text = "An error has occured! The background worker has crashed!";
-                throw new Exception("The background worker has crashed!", e.Error);
+                throw new Exception("The background worker has crashed!", e.Error.InnerException);
             }
             ExitButton.IsEnabled = true;
             StartButton.IsEnabled = false;