Truncate Stim+EEG files to the end of stimulation data

Author: tstenner

Directory.Build.props

@@ -3,11 +3,8 @@
 		<Authors>Tristan Stenner</Authors>
 		<Company>IMPS UKSH Kiel</Company>
 		<Product>NEDF Reader</Product>
-		<Version>1.1.4</Version>
+		<Version>1.1.5</Version>
 		<PackageLicenseExpression>GPL-3.0-or-later</PackageLicenseExpression>
-		<BaseIntermediateOutputPath>$(SolutionDir)\obj\$(MSBuildProjectName)\</BaseIntermediateOutputPath>
-		<OutputPath>$(SolutionDir)bin\$(Configuration)</OutputPath>
-		<PublishDir>..\pub</PublishDir>
 		<TargetFramework>netcoreapp3.1</TargetFramework>
 		<LangVersion>8</LangVersion>
 	</PropertyGroup>

nedfbvaddin/NedfDataReader.cs

@@ -75,8 +75,8 @@ void IEEGRawFileReader.CreateStorageEntries(
 			try
 			{
 				var props = ComponentFactory.CreateChangeProperties();
-				using var file = new NedfFile(filename, (warning)=>MessageBox.Show(filename, warning));
-				var dataName = "Tristans Raw Data";
+				using var file = new NedfFile(filename, (warning)=>MessageBox.Show(warning, filename));
+				string dataName = "Tristans Raw Data";
 				var markers = file.GetMarkerPairs().ToList();
 				if (markers.Count > file.NSample / 10)
 					dataName = "Corrupt Data File";
@@ -85,7 +85,7 @@ void IEEGRawFileReader.CreateStorageEntries(
 					{
 						var m = ComponentFactory.CreateChangeMarker();
 						m.Channel = -1;
-						(var pos, var val) = pair;
+						(uint pos, var val) = pair;
 						m.Position = pos;
 						m.Points = 1;
 						m.Type = "Stimulus";

nedfbvaddin/nedfbvaddin.csproj

@@ -1,7 +1,8 @@
 <?xml version="1.0" encoding="utf-8"?>
 <Project Sdk="Microsoft.NET.Sdk">
 	<PropertyGroup>
-		<TargetFrameworks>net48</TargetFrameworks>
+		<TargetFramework>net48</TargetFramework>
+		<OutputPath>C:\Vision\Analyzer2\</OutputPath>
 	</PropertyGroup>
 	<ItemGroup>
 		<ProjectReference Include="..\nedfreader\nedfreader.csproj" />

nedfreader/NedfFile.cs

@@ -70,8 +70,8 @@ public sealed class NedfFile : IDisposable
 		public readonly NedfHeader hdr;
 		public readonly string headerxml;
 		private readonly FileStream infile;
-		public readonly uint NSampleStimPerEEG;
-		public uint NSample => hdr.EEGSettings.NumberOfRecordsOfEEG;
+		public readonly uint NSampleStimPerEEG = 0;
+		public uint NSample;
 		public uint SFreq => hdr.EEGSettings.EEGSamplingRate;
 		public uint NChan => hdr.EEGSettings.TotalNumberOfChannels;
 		public uint NAcc => hdr.NumberOfChannelsOfAccelerometer;
@@ -87,11 +87,14 @@ public NedfFile(string dataFile, Action<string> suspiciousFileCallback = null)
 			if (dataFile is null)
 				throw new ArgumentNullException(nameof(dataFile));
 			infile = new FileStream(dataFile, FileMode.Open, FileAccess.Read);
-			headerxml = Encoding.UTF8.GetString(new BinaryReader(infile).ReadBytes(10240)).Trim('\0');
-
-			if (headerxml[0] != '<')
+			const int headersize = 10240;
+			byte[] buf = new byte[headersize];
+			infile.Read(buf, 0, headersize);
+			if (buf[0] != '<')
 				throw new ArgumentException($"'{dataFile}' does not begin with an xml header");
 
+			headerxml = Encoding.UTF8.GetString(buf).Trim('\0');
+
 			// The XML 1.0 spec contains a list of valid characters for tag names:
 			// https://www.w3.org/TR/2008/REC-xml-20081126/#NT-NameChar
 			// Older NIC versions allowed any character in the root tag name, so we have to sanitize the "xml" to avoid parse errors
@@ -109,6 +112,8 @@ public NedfFile(string dataFile, Action<string> suspiciousFileCallback = null)
 			if ((hdr.AdditionalChannelStatus ?? "OFF") != "OFF")
 				throw new ArgumentException($"Unexpected value for AdditionalChannelStatus: {hdr.AdditionalChannelStatus}");
 
+			NSample = hdr.EEGSettings.NumberOfRecordsOfEEG;
+
 			string eegunits = hdr.EEGSettings.EEGUnits ?? "nV";
 			if (eegunits != "nV")
 				throw new ArgumentException($"Unknown EEG unit {eegunits ?? "null"}");
@@ -120,7 +125,10 @@ public NedfFile(string dataFile, Action<string> suspiciousFileCallback = null)
 					SuspiciousFileCallback?.Invoke("Data files recorded by NIC 2.0.8 with stimulation channels are broken, proceed at your own risk!");
 				uint numstimrec = node.NumberOfRecordsOfStimulation;
 				if (numstimrec < 2 * NSample)
-					throw new Exception($"Can't handle intermittent stimulation data {numstimrec} records, expected {2 * NSample}");
+				{
+					SuspiciousFileCallback?.Invoke($"Intermittent stimulation data {numstimrec} <= {2 * NSample}, EEG data will be truncated.");
+					NSample = numstimrec / 2;
+				}
 				uint stimsrate = node.StimulationSamplingRate;
 				if (stimsrate != 1000)
 					throw new Exception($"Unexpected stimulation sampling rate ({stimsrate}!=1000)");