public void CombinesParameters()
{
var measurements = new List<IMeasurement> { new Measurement(1, "V") };
var data = new OutputData(measurements, new Measurement(1, "Hz"), false);
var s1 = new RenderedStimulus("stim1", new Dictionary<string, object>()
{
{"key1", "value"},
{"key2", 5}
}, data);
var s2 = new RenderedStimulus("stim2", new Dictionary<string, object>()
{
{"key1", "value"},
{"key2", 2},
{"key3", 0}
}, data);
var combine = new CombinedStimulus("CombinedStimulus", new Dictionary<string, object>(), new List<IStimulus>() {s1, s2}, CombinedStimulus.Add);
var expected = new Dictionary<string, object>();
expected["stim0_stimulusID"] = "stim1";
expected["stim0_key1"] = "value";
expected["stim0_key2"] = 5;
expected["stim1_stimulusID"] = "stim2";
expected["stim1_key1"] = "value";
expected["stim1_key2"] = 2;
expected["stim1_key3"] = 0;
Assert.That(combine.Parameters, Is.EqualTo(expected));
}
public void EnumeratesDataBlocks(
[Values(100, 500, 1000, 5000)] double blockMilliseconds,
[Values(1000, 5000, 10000)] double sampleRateHz
)
{
var parameters = new Dictionary <string, object>();
var sampleRate = new Measurement((decimal)sampleRateHz, "Hz");
IOutputData data = new OutputData(Enumerable.Range(0, (int)TimeSpan.FromSeconds(3).Samples(new Measurement((decimal)sampleRateHz, "Hz")))
.Select(i => new Measurement(i, "units")).ToList(),
sampleRate,
false);
var s = new RenderedStimulus((string)"RenderedStimulus", (IDictionary <string, object>)parameters, data);
var blockSpan = TimeSpan.FromMilliseconds(blockMilliseconds);
IEnumerator <IOutputData> iter = s.DataBlocks(blockSpan).GetEnumerator();
while (iter.MoveNext())
{
var cons = data.SplitData(blockSpan);
data = cons.Rest;
Assert.That(iter.Current.Duration, Is.EqualTo(cons.Head.Duration));
Assert.That(iter.Current.Data, Is.EqualTo(cons.Head.Data));
}
}
public void ShouldPushOutputDataConfigurationToStimuli()
{
var e = new Epoch(UNUSED_PROTOCOL_ID);
var dev = new UnitConvertingExternalDevice("name", "co", new Measurement(0m, "units"));
const string units = "units";
var data = new OutputData(Enumerable.Repeat(new Measurement(0, units), 100), new Measurement(10, "Hz"));
var s = new RenderedStimulus((string)"stimID", (IDictionary <string, object>) new Dictionary <string, object>(), (IOutputData)data);
e.Stimuli[dev] = s;
var configuration = new List <IPipelineNodeConfiguration>();
var config = new Dictionary <string, object>();
config["key"] = "value";
configuration.Add(new PipelineNodeConfiguration("NODE1", config));
var outputTime = DateTimeOffset.Now;
e.DidOutputData(dev, outputTime, data.Duration, configuration);
var expected = configuration;
Assert.That(e.Stimuli[dev].OutputConfigurationSpans.First().Nodes, Is.EqualTo(expected));
Assert.That(e.Stimuli[dev].OutputConfigurationSpans.First().Time, Is.EqualTo(data.Duration));
}
public void OutputPipelineContinuity(
[Values(1000, 5000, 10000, 15000, 20000)] double sampleRate,
[Values(0.1, 0.5, 1, 5)] double blockDurationSeconds
)
{
const double epochDuration = 2; //seconds
var srate = new Measurement((decimal) sampleRate, "Hz");
var daq = new TestDAQController();
var outStream = new DAQOutputStream("OUT")
{
SampleRate = srate,
MeasurementConversionTarget = "V"
};
var inStream = new DAQInputStream("IN")
{
SampleRate = srate,
MeasurementConversionTarget = "V"
};
var controller = new Controller() { Clock = daq, DAQController = daq };
var dev = new UnitConvertingExternalDevice("dev", "co", controller, new Measurement(0, "V"))
{
Clock = daq,
MeasurementConversionTarget = "V",
OutputSampleRate = srate,
InputSampleRate = srate
};
dev.BindStream(outStream).BindStream(inStream);
// Setup Epoch
var e = new Epoch("OutputPipelineContinuity");
var nSamples = (int)TimeSpan.FromSeconds(epochDuration).Samples(srate);
IList<IMeasurement> stimData = (IList<IMeasurement>) Enumerable.Range(0, nSamples)
.Select(i => new Measurement((decimal) (8 * Math.Sin(((double)i) / (nSamples / 10.0))), "V") as IMeasurement)
.ToList();
IOutputData stimOutputData = new OutputData(stimData, srate);
var stim = new RenderedStimulus((string) "RenderedStimulus", (IDictionary<string, object>) new Dictionary<string, object>(),
stimOutputData);
e.Stimuli[dev] = stim;
e.Responses[dev] = new Response();
e.Backgrounds[dev] = new Background(new Measurement(0, "V"), srate);
controller.EnqueueEpoch(e);
var blockSpan = TimeSpan.FromSeconds(blockDurationSeconds);
foreach (var stimBlock in stim.DataBlocks(blockSpan))
{
var cons = stimOutputData.SplitData(blockSpan);
var expected = cons.Head.Data;
stimOutputData = cons.Rest;
Assert.That(stimBlock.Data, Is.EqualTo(expected));
}
}
public void OutputPipelineContinuity(
[Values(1000, 5000, 10000, 15000, 20000)] double sampleRate,
[Values(0.1, 0.5, 1, 5)] double blockDurationSeconds
)
{
const double epochDuration = 2; //seconds
var srate = new Measurement((decimal) sampleRate, "Hz");
var daq = new TestDAQController();
var outStream = new DAQOutputStream("OUT")
{
SampleRate = srate,
MeasurementConversionTarget = "V"
};
var controller = new Controller() { Clock = daq, DAQController = daq };
var dev = new UnitConvertingExternalDevice("dev", "co", controller, new Measurement(0, "V"))
{
Clock = daq,
MeasurementConversionTarget = "V"
};
dev.BindStream(outStream);
// Setup Epoch
var e = new Epoch("OutputPipelineContinuity");
var nSamples = (int)TimeSpan.FromSeconds(epochDuration).Samples(srate);
IList<IMeasurement> stimData = (IList<IMeasurement>) Enumerable.Range(0, nSamples)
.Select(i => new Measurement((decimal) (8 * Math.Sin(((double)i) / (nSamples / 10.0))), "V") as IMeasurement)
.ToList();
IOutputData stimOutputData = new OutputData(stimData, srate);
var stim = new RenderedStimulus((string) "RenderedStimulus", (IDictionary<string, object>) new Dictionary<string, object>(),
stimOutputData);
e.Stimuli[dev] = stim;
e.Responses[dev] = new Response();
e.Background[dev] = new Epoch.EpochBackground(new Measurement(0, "V"), srate);
controller.EnqueueEpoch(e);
controller.NextEpoch();
var blockSpan = TimeSpan.FromSeconds(blockDurationSeconds);
foreach (var stimBlock in stim.DataBlocks(blockSpan))
{
var cons = stimOutputData.SplitData(blockSpan);
var expected = cons.Head.Data;
stimOutputData = cons.Rest;
Assert.That(stimBlock.Data, Is.EqualTo(expected));
}
}
public void HoldsStimulusID()
{
var parameters = new Dictionary <string, object>();
const string stimID = "my.ID";
var measurements = new List <IMeasurement> {
new Measurement(1, "V")
};
var data = new OutputData(measurements, new Measurement(1, "Hz"), false);
var s = new RenderedStimulus((string)stimID, (IDictionary <string, object>)parameters, (IOutputData)data);
Assert.That(s.StimulusID, Is.EqualTo(stimID));
}
public void HoldsParameters()
{
var parameters = new Dictionary <string, object>();
parameters["key1"] = "value1";
parameters["key2"] = 2;
var measurements = new List <IMeasurement> {
new Measurement(1, "V")
};
var data = new OutputData(measurements, new Measurement(1, "Hz"), false);
var s = new RenderedStimulus((string)"RenderedStimulus", (IDictionary <string, object>)parameters, (IOutputData)data);
Assert.That(s.Parameters, Is.EqualTo(parameters));
}
public void MarksAsNotLastIfMoreBlocks()
{
var parameters = new Dictionary <string, object>();
var sampleRate = new Measurement(1000, "Hz");
IOutputData data = new OutputData(Enumerable.Range(0, 1000).Select(i => new Measurement(i, "units")).ToList(),
sampleRate,
true);
var s = new RenderedStimulus((string)"RenderedStimulus", (IDictionary <string, object>)parameters, data);
var block = TimeSpan.FromMilliseconds(100);
IEnumerator <IOutputData> iter = s.DataBlocks(block).GetEnumerator();
Assert.True(iter.MoveNext());
Assert.False(iter.Current.IsLast);
}
/// <summary>
/// Matlab-friendly factory method to run a single Epoch.
/// </summary>
/// <remarks>Constructs an Epoch with homogenous stimulus ID, sample rate and units, then runs the
/// constructed Epoch.
/// </remarks>
///
/// <param name="protocolID">Protocol ID of the constructed Epoch</param>
/// <param name="parameters">Protocol parameters of the constructed Epoch</param>
/// <param name="stimulusID">Stimulus plugin ID for all constructed stimuli</param>
/// <param name="stimulusSampleRate">Simulus sample rate for all constructed stimuli</param>
/// <param name="stimuli">Simulus data for output devices</param>
/// <param name="backgrounds">Backgrounds for output devices</param>
/// <param name="responses">Devices from which to record Responses</param>
/// <param name="persistor">EpochPersistor to persist Epoch</param>
public void RunEpoch(
string protocolID,
IDictionary <string, object> parameters,
string stimulusID,
Measurement stimulusSampleRate,
IDictionary <ExternalDeviceBase, IEnumerable <IMeasurement> > stimuli,
IDictionary <ExternalDeviceBase, IMeasurement> backgrounds,
IEnumerable <ExternalDeviceBase> responses,
EpochPersistor persistor)
{
var epoch = new Epoch(protocolID,
parameters);
foreach (var dev in stimuli.Keys)
{
var data = new OutputData(stimuli[dev],
stimulusSampleRate,
true);
var stim = new RenderedStimulus(stimulusID,
(IDictionary <string, object>) new Dictionary <string, object> {
{ "data", data }
},
(IOutputData)data);
epoch.Stimuli[dev] = stim;
}
foreach (var dev in responses)
{
epoch.Responses[dev] = new Response();
}
foreach (var dev in backgrounds.Keys)
{
epoch.Background[dev] = new Epoch.EpochBackground(backgrounds[dev], stimulusSampleRate);
}
RunEpoch(epoch, persistor);
}
public void ShouldThrowForDurationMismatch()
{
const double sampleRateHz = 100d;
var parameters = new Dictionary<string, object>();
var sampleRate = new Measurement((decimal)sampleRateHz, "Hz");
IOutputData data = new OutputData(Enumerable.Range(0, (int)TimeSpan.FromSeconds(3).Samples(new Measurement((decimal)sampleRateHz, "Hz")))
.Select(i => new Measurement(i, "units")).ToList(),
sampleRate,
false);
var s1 = new RenderedStimulus("stim1", new Dictionary<string, object>(), data);
var s2 = new RenderedStimulus("stim2", new Dictionary<string, object>(), data.SplitData(data.Duration - TimeSpan.FromSeconds(0.1)).Head);
Assert.That(() => new CombinedStimulus("CombinedStimulus", new Dictionary<string, object>(), new List<IStimulus>() { s1, s2 }, CombinedStimulus.Add), Throws.TypeOf(typeof(ArgumentException)));
}
public void HoldsParameters()
{
var parameters = new Dictionary<string, object>();
parameters["key1"] = "value1";
parameters["key2"] = 2;
var measurements = new List<IMeasurement> {new Measurement(1, "V")};
var data = new OutputData(measurements, new Measurement(1, "Hz"), false);
var s = new RenderedStimulus((string) "RenderedStimulus", (IDictionary<string, object>) parameters, (IOutputData) data);
Assert.That(s.Parameters, Is.EqualTo(parameters));
}
private static Controller SetupController(double sampleRate, out Epoch e, out IExternalDevice dev0, out RenderedStimulus stim1, out IExternalDevice dev1, out RenderedStimulus stim2, out IList<IMeasurement> stimData, int nChannels)
{
Converters.Clear();
Converters.Register("V", "V",
// just an identity conversion for now, to pass Validate()
(IMeasurement m) => m);
var streamNameMap = new Dictionary<string, string>();
streamNameMap["Out0"] = "In0";
if (nChannels > 1)
streamNameMap["Out1"] = "In1";
Controller controller = new Parser().ParseConfiguration(Resources.LowGainConfig);
var daq = (SimulationDAQController)controller.DAQController;
daq.Clock = daq;
foreach (var stream in daq.Streams)
{
stream.SampleRate = new Measurement((decimal) sampleRate, "Hz");
}
daq.SimulationRunner += (output, timestep) =>
{
var input = new ConcurrentDictionary<IDAQInputStream, IInputData>();
Parallel.ForEach(output, (kv) =>
{
var outData = kv.Value;
var outStream = kv.Key;
var inStream = daq.InputStreams.Where((s) =>
s.Name == streamNameMap[outStream.Name]).First();
var data = outData.DataWithUnits("V").Data;
var inData = new InputData(data,
outData.SampleRate,
DateTimeOffset.Now)
.DataWithNodeConfiguration("SimulationController",daq.Configuration);
input[inStream] = inData;
}
);
return input;
};
var protocolParams = new Dictionary<string, object>(1);
protocolParams["key1"] = "value1";
e = new Epoch("LowGainSimulation", protocolParams);
dev0 = controller.GetDevice("Device0");
dev1 = controller.GetDevice("Device1");
if (nChannels == 1)
{
dev1.UnbindStream(dev1.Streams.Values.First().Name);
}
stimData = Enumerable.Range(0, (int)(10 * sampleRate))
.Select(i => new Measurement(i, -3, "V") as IMeasurement)
.ToList();
var srate = new Measurement((decimal) sampleRate, "Hz");
stim1 = new RenderedStimulus((string) "RenderedStimulus",
(IDictionary<string, object>) new Dictionary<string, object>(),
(IOutputData) new OutputData(stimData, srate, false));
stim2 = new RenderedStimulus((string) "RenderedStimulus",
(IDictionary<string, object>) new Dictionary<string, object>(),
(IOutputData) new OutputData(stimData, srate, false));
e.Stimuli[dev0] = stim1;
if (nChannels > 1)
e.Stimuli[dev1] = stim2;
e.Responses[dev0] = new Response();
if (nChannels > 1)
e.Responses[dev1] = new Response();
e.Background[dev1] = new Epoch.EpochBackground(new Measurement(0, "V"), srate);
e.Background[dev0] = new Epoch.EpochBackground(new Measurement(0, "V"), srate);
return controller;
}
private static Epoch CreateTestEpoch(out ExternalDeviceBase dev1, out ExternalDeviceBase dev2)
{
dev1 = new UnitConvertingExternalDevice("dev1", "man1", new Measurement(0, "V"));
dev2 = new UnitConvertingExternalDevice("dev2", "man2", new Measurement(0, "V"));
var stream1 = new DAQInputStream("Stream1");
var stream2 = new DAQInputStream("Stream2");
var stimParameters = new Dictionary<string, object>();
stimParameters["param1"] = 1;
stimParameters["param2"] = 2;
var srate = new Measurement(1000, "Hz");
List<Measurement> samples =
Enumerable.Range(0, 10000).Select(i => new Measurement((decimal)Math.Sin((double)i / 100), "V")).ToList();
var stimData = new OutputData(samples, srate, false);
var stim1 = new RenderedStimulus("RenderedStimulus", stimParameters, stimData);
var stim2 = new RenderedStimulus("RenderedStimulus", stimParameters, stimData)
{
ShouldDataBePersisted = true
};
var protocolParameters = new Dictionary<string, object>
{
{"one", 1},
{"two", "second"},
{"three", 5.55}
};
var epoch = new TestEpoch("protocol.banana", protocolParameters);
epoch.Stimuli[dev1] = stim1;
epoch.Stimuli[dev2] = stim2;
DateTimeOffset start = DateTimeOffset.Now;
epoch.SetStartTime(Maybe<DateTimeOffset>.Yes(start));
epoch.Backgrounds[dev1] = new Background(new Measurement(0, "V"), new Measurement(1000, "Hz"));
epoch.Backgrounds[dev2] = new Background(new Measurement(1, "V"), new Measurement(1000, "Hz"));
epoch.Responses[dev1] = new Response();
epoch.Responses[dev2] = new Response();
var streamConfig = new Dictionary<string, object>();
streamConfig["configParam1"] = 1;
var devConfig = new Dictionary<string, object>();
devConfig["configParam2"] = 2;
IInputData responseData1 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream1, streamConfig)
.DataWithExternalDeviceConfiguration(dev1, devConfig);
IInputData responseData2 = new InputData(samples, srate, start + TimeSpanExtensions.FromSamples((uint) samples.Count, srate))
.DataWithStreamConfiguration(stream1, streamConfig)
.DataWithExternalDeviceConfiguration(dev1, devConfig);
IInputData responseData3 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream2, streamConfig)
.DataWithExternalDeviceConfiguration(dev2, devConfig);
IInputData responseData4 = new InputData(samples, srate, start + TimeSpanExtensions.FromSamples((uint)samples.Count, srate))
.DataWithStreamConfiguration(stream2, streamConfig)
.DataWithExternalDeviceConfiguration(dev2, devConfig);
epoch.Responses[dev1].AppendData(responseData1);
epoch.Responses[dev1].AppendData(responseData2);
epoch.Responses[dev2].AppendData(responseData3);
epoch.Responses[dev2].AppendData(responseData4);
epoch.Properties.Add("prop1", 5);
epoch.Properties.Add("prop2", "banana");
epoch.Keywords.Add("word1");
epoch.Keywords.Add("word2");
return epoch;
}
public void ShouldAllowNumericEpochParameters()
{
if (File.Exists("..\\..\\..\\ShouldAllowNumericEpochParameters.h5"))
{
File.Delete("..\\..\\..\\ShouldAllowNumericEpochParameters.h5");
}
var gID = new Guid("{2F2719F7-4A8C-4C22-9698-BE999DBC5385}");
using (var exp = new EpochHDF5Persistor("..\\..\\..\\ShouldAllowNumericEpochParameters.h5", null, () => gID)
)
{
var time = new DateTimeOffset(1000, TimeSpan.Zero);
var guid = new Guid("053C64D4-ED7A-4128-AA43-ED115716A97D");
var props = new Dictionary <string, object>();
props["int"] = 2;
props["float"] = 2.0f;
props["double"] = 2.0d;
props["decimal"] = 2.0m;
props["array"] = new[] { 1.0, 2.0, 3.0 };
props["short"] = (short)2;
props["unit16"] = (UInt16)1;
props["uint32"] = (UInt32)2;
props["byte"] = (byte)1;
props["bool"] = true;
const string protocolID = "Epoch.Fixture";
Dictionary <string, object> parameters = props;
dev1 = new UnitConvertingExternalDevice(dev1Name, "DEVICECO", new Measurement(0, "V"));
dev2 = new UnitConvertingExternalDevice(dev2Name, "DEVICECO", new Measurement(0, "V"));
var stream1 = new DAQInputStream("Stream1");
var stream2 = new DAQInputStream("Stream2");
var stimParameters = new Dictionary <string, object>();
stimParameters[param1] = value1;
stimParameters[param2] = value2;
var srate = new Measurement(1000, "Hz");
List <Measurement> samples =
Enumerable.Range(0, 10000).Select(i => new Measurement((decimal)Math.Sin((double)i / 100), "V")).
ToList();
var stimData = new OutputData(samples, srate, false);
var stim1 = new RenderedStimulus("RenderedStimulus", stimParameters, stimData);
//.Data does not need to be persisted
var stim2 = new RenderedStimulus("RenderedStimulus", stimParameters, stimData);
//.Data does not need to be persisted
var e = new Epoch(protocolID, parameters);
e.Stimuli[dev1] = stim1;
e.Stimuli[dev2] = stim2;
DateTimeOffset start = DateTimeOffset.Parse("1/11/2011 6:03:29 PM -08:00");
// Do this to match the XML stored in the EpochXML.txt resource
e.StartTime = Maybe <DateTimeOffset> .Yes(start);
e.Background[dev1] = new Epoch.EpochBackground(new Measurement(0, "V"), new Measurement(1000, "Hz"));
e.Background[dev2] = new Epoch.EpochBackground(new Measurement(1, "V"), new Measurement(1000, "Hz"));
e.Responses[dev1] = new Response();
e.Responses[dev2] = new Response();
var streamConfig = new Dictionary <string, object>();
streamConfig[param1] = value1;
var devConfig = new Dictionary <string, object>();
devConfig[param2] = value2;
IInputData responseData1 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream1, streamConfig)
.DataWithExternalDeviceConfiguration(dev1, devConfig);
IInputData responseData2 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream2, streamConfig)
.DataWithExternalDeviceConfiguration(dev2, devConfig);
e.Responses[dev1].AppendData(responseData1);
e.Responses[dev2].AppendData(responseData2);
e.Keywords.Add(kw1);
e.Keywords.Add(kw2);
exp.BeginEpochGroup("label", "source identifier", new[] { "keyword1", "keyword2" }, props, guid,
time);
exp.Serialize(e);
exp.EndEpochGroup();
exp.Close();
}
H5.Close();
Approvals.VerifyFile("..\\..\\..\\ShouldAllowNumericEpochParameters.h5");
}
public void Setup()
{
const string protocolID = "Epoch.Fixture";
var parameters = new Dictionary <string, object>();
parameters[param1] = value1;
parameters[param2] = value2;
dev1 = new UnitConvertingExternalDevice(dev1Name, "DEVICECO", new Measurement(0, "V"));
dev2 = new UnitConvertingExternalDevice(dev2Name, "DEVICECO", new Measurement(0, "V"));
var stream1 = new DAQInputStream("Stream1");
var stream2 = new DAQInputStream("Stream2");
var stimParameters = new Dictionary <string, object>();
stimParameters[param1] = value1;
stimParameters[param2] = value2;
var srate = new Measurement(1000, "Hz");
List <Measurement> samples =
Enumerable.Range(0, 10000).Select(i => new Measurement((decimal)Math.Sin((double)i / 100), "V")).ToList();
var stimData = new OutputData(samples, srate, false);
var stim1 = new RenderedStimulus("RenderedStimulus", stimParameters, stimData);
//.Data does not need to be persisted
var stim2 = new RenderedStimulus("RenderedStimulus", stimParameters, stimData);
//.Data does not need to be persisted
var e = new Epoch(protocolID, parameters);
e.Stimuli[dev1] = stim1;
e.Stimuli[dev2] = stim2;
DateTimeOffset start = DateTimeOffset.Parse("1/11/2011 6:03:29 PM -08:00");
// Do this to match the XML stored in the EpochXML.txt resource
e.StartTime = Maybe <DateTimeOffset> .Yes(start);
e.Background[dev1] = new Epoch.EpochBackground(new Measurement(0, "V"), new Measurement(1000, "Hz"));
e.Background[dev2] = new Epoch.EpochBackground(new Measurement(1, "V"), new Measurement(1000, "Hz"));
e.Responses[dev1] = new Response();
e.Responses[dev2] = new Response();
var streamConfig = new Dictionary <string, object>();
streamConfig[param1] = value1;
var devConfig = new Dictionary <string, object>();
devConfig[param2] = value2;
IInputData responseData1 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream1, streamConfig)
.DataWithExternalDeviceConfiguration(dev1, devConfig);
IInputData responseData2 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream2, streamConfig)
.DataWithExternalDeviceConfiguration(dev2, devConfig);
e.Responses[dev1].AppendData(responseData1);
e.Responses[dev2].AppendData(responseData2);
e.Keywords.Add(kw1);
e.Keywords.Add(kw2);
testEpoch = e;
}
public void ShouldAllowLongStringEpochParameters()
{
if (File.Exists("..\\..\\..\\ShouldAllowLongStringEpochParameters.h5"))
{
File.Delete("..\\..\\..\\ShouldAllowLongStringEpochParameters.h5");
}
var gID = new Guid("{2F2719F7-4A8C-4C22-9698-BE999DBC5385}");
using (
var exp = new EpochHDF5Persistor("..\\..\\..\\ShouldAllowLongStringEpochParameters.h5", null, () => gID)
)
{
var time = new DateTimeOffset(1000, TimeSpan.Zero);
var guid = new Guid("053C64D4-ED7A-4128-AA43-ED115716A97D");
var props = new Dictionary <string, object>();
props["key1"] =
"1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890";
//100 elements
props["key2"] = 2;
const string protocolID = "Epoch.Fixture";
Dictionary <string, object> parameters = props;
dev1 = new UnitConvertingExternalDevice(dev1Name, "DEVICECO", new Measurement(0, "V"));
dev2 = new UnitConvertingExternalDevice(dev2Name, "DEVICECO", new Measurement(0, "V"));
var stream1 = new DAQInputStream("Stream1");
var stream2 = new DAQInputStream("Stream2");
var stimParameters = new Dictionary <string, object>();
stimParameters[param1] = value1;
stimParameters[param2] = value2;
var srate = new Measurement(1000, "Hz");
List <Measurement> samples =
Enumerable.Range(0, 10000).Select(i => new Measurement((decimal)Math.Sin((double)i / 100), "mV")).
ToList();
var stimData = new OutputData(samples, srate, false);
var stim1 = new RenderedStimulus("RenderedStimulus", stimParameters, stimData);
//.Data does not need to be persisted
var stim2 = new RenderedStimulus("RenderedStimulus", stimParameters, stimData);
//.Data does not need to be persisted
var e = new Epoch(protocolID, parameters);
e.Stimuli[dev1] = stim1;
e.Stimuli[dev2] = stim2;
DateTimeOffset start = DateTimeOffset.Parse("1/11/2011 6:03:29 PM -08:00");
// Do this to match the XML stored in the EpochXML.txt resource
e.StartTime = Maybe <DateTimeOffset> .Yes(start);
e.Background[dev1] = new Epoch.EpochBackground(new Measurement(0, "V"), new Measurement(1000, "Hz"));
e.Background[dev2] = new Epoch.EpochBackground(new Measurement(1, "V"), new Measurement(1000, "Hz"));
e.Responses[dev1] = new Response();
e.Responses[dev2] = new Response();
var streamConfig = new Dictionary <string, object>();
streamConfig[param1] = value1;
var devConfig = new Dictionary <string, object>();
devConfig[param2] = value2;
IInputData responseData1 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream1, streamConfig)
.DataWithExternalDeviceConfiguration(dev1, devConfig);
IInputData responseData2 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream2, streamConfig)
.DataWithExternalDeviceConfiguration(dev2, devConfig);
e.Responses[dev1].AppendData(responseData1);
e.Responses[dev2].AppendData(responseData2);
e.Keywords.Add(kw1);
e.Keywords.Add(kw2);
exp.BeginEpochGroup("label", "source identifier", new[] { "keyword1", "keyword2" }, props, guid,
time);
exp.Serialize(e);
exp.EndEpochGroup(time.AddMilliseconds(100));
exp.Close();
}
H5.Close();
var startInfo = new ProcessStartInfo(@"..\..\..\..\..\..\externals\HDF5\bin\h5dump",
@" --xml ..\..\..\ShouldAllowLongStringEpochParameters.h5");
startInfo.RedirectStandardOutput = true;
startInfo.UseShellExecute = false;
Process proc = Process.Start(startInfo);
Approvals.VerifyXml(proc.StandardOutput.ReadToEnd());
}
public void MarksAsNotLastIfMoreBlocks()
{
var parameters = new Dictionary<string, object>();
var sampleRate = new Measurement(1000, "Hz");
IOutputData data = new OutputData(Enumerable.Range(0, 1000).Select(i => new Measurement(i, "units")).ToList(),
sampleRate,
true);
var s = new RenderedStimulus((string) "RenderedStimulus", (IDictionary<string, object>) parameters, data);
var block = TimeSpan.FromMilliseconds(100);
IEnumerator<IOutputData> iter = s.DataBlocks(block).GetEnumerator();
Assert.True(iter.MoveNext());
Assert.False(iter.Current.IsLast);
}
public void HoldsStimulusID()
{
var parameters = new Dictionary<string, object>();
const string stimID = "my.ID";
var measurements = new List<IMeasurement> { new Measurement(1, "V") };
var data = new OutputData(measurements, new Measurement(1, "Hz"), false);
var s = new RenderedStimulus((string) stimID, (IDictionary<string, object>) parameters, (IOutputData) data);
Assert.That(s.StimulusID, Is.EqualTo(stimID));
}
public void ShouldAllowLongStringEpochParameters()
{
if (File.Exists("..\\..\\..\\ShouldAllowLongStringEpochParameters.h5"))
File.Delete("..\\..\\..\\ShouldAllowLongStringEpochParameters.h5");
var gID = new Guid("{2F2719F7-4A8C-4C22-9698-BE999DBC5385}");
using (
var exp = new EpochHDF5Persistor("..\\..\\..\\ShouldAllowLongStringEpochParameters.h5", null, () => gID)
)
{
var time = new DateTimeOffset(1000, TimeSpan.Zero);
var guid = new Guid("053C64D4-ED7A-4128-AA43-ED115716A97D");
var props = new Dictionary<string, object>();
props["key1"] =
"1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890";
//100 elements
props["key2"] = 2;
const string protocolID = "Epoch.Fixture";
Dictionary<string, object> parameters = props;
dev1 = new UnitConvertingExternalDevice(dev1Name, "DEVICECO", new Measurement(0, "V"));
dev2 = new UnitConvertingExternalDevice(dev2Name, "DEVICECO", new Measurement(0, "V"));
var stream1 = new DAQInputStream("Stream1");
var stream2 = new DAQInputStream("Stream2");
var stimParameters = new Dictionary<string, object>();
stimParameters[param1] = value1;
stimParameters[param2] = value2;
var srate = new Measurement(1000, "Hz");
List<Measurement> samples =
Enumerable.Range(0, 10000).Select(i => new Measurement((decimal) Math.Sin((double) i/100), "mV")).
ToList();
var stimData = new OutputData(samples, srate, false);
var stim1 = new RenderedStimulus("RenderedStimulus", stimParameters, stimData);
//.Data does not need to be persisted
var stim2 = new RenderedStimulus("RenderedStimulus", stimParameters, stimData);
//.Data does not need to be persisted
var e = new Epoch(protocolID, parameters);
e.Stimuli[dev1] = stim1;
e.Stimuli[dev2] = stim2;
DateTimeOffset start = DateTimeOffset.Parse("1/11/2011 6:03:29 PM -08:00");
// Do this to match the XML stored in the EpochXML.txt resource
e.StartTime = Maybe<DateTimeOffset>.Yes(start);
e.Background[dev1] = new Epoch.EpochBackground(new Measurement(0, "V"), new Measurement(1000, "Hz"));
e.Background[dev2] = new Epoch.EpochBackground(new Measurement(1, "V"), new Measurement(1000, "Hz"));
e.Responses[dev1] = new Response();
e.Responses[dev2] = new Response();
var streamConfig = new Dictionary<string, object>();
streamConfig[param1] = value1;
var devConfig = new Dictionary<string, object>();
devConfig[param2] = value2;
IInputData responseData1 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream1, streamConfig)
.DataWithExternalDeviceConfiguration(dev1, devConfig);
IInputData responseData2 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream2, streamConfig)
.DataWithExternalDeviceConfiguration(dev2, devConfig);
e.Responses[dev1].AppendData(responseData1);
e.Responses[dev2].AppendData(responseData2);
e.Keywords.Add(kw1);
e.Keywords.Add(kw2);
exp.BeginEpochGroup("label", "source identifier", new[] {"keyword1", "keyword2"}, props, guid,
time);
exp.Serialize(e);
exp.EndEpochGroup(time.AddMilliseconds(100));
exp.Close();
}
H5.Close();
var startInfo = new ProcessStartInfo(@"..\..\..\..\..\..\externals\HDF5\bin\h5dump",
@" --xml ..\..\..\ShouldAllowLongStringEpochParameters.h5");
startInfo.RedirectStandardOutput = true;
startInfo.UseShellExecute = false;
Process proc = Process.Start(startInfo);
Approvals.VerifyXml(proc.StandardOutput.ReadToEnd());
}
public void LastDataIsLast()
{
var parameters = new Dictionary<string, object>();
var sampleRate = new Measurement(1000, "Hz");
IOutputData data = new OutputData(Enumerable.Range(0, 1000).Select(i => new Measurement(i, "units")).ToList(),
sampleRate,
false);
var s1 = new RenderedStimulus("stim1", new Dictionary<string, object>(), data);
var s2 = new RenderedStimulus("stim2", new Dictionary<string, object>(), data);
var combine = new CombinedStimulus("CombinedStimulus", new Dictionary<string, object>(), new List<IStimulus>() { s1, s2 }, CombinedStimulus.Add);
var block = TimeSpan.FromMilliseconds(100);
IEnumerator<IOutputData> iter = combine.DataBlocks(block).GetEnumerator();
IOutputData current = null;
while (iter.MoveNext())
{
current = iter.Current;
}
Assert.That(current.IsLast, Is.True);
}
public void ShouldAllowNumericEpochParameters()
{
if (File.Exists("..\\..\\..\\ShouldAllowNumericEpochParameters.h5"))
File.Delete("..\\..\\..\\ShouldAllowNumericEpochParameters.h5");
var gID = new Guid("{2F2719F7-4A8C-4C22-9698-BE999DBC5385}");
using (var exp = new EpochHDF5Persistor("..\\..\\..\\ShouldAllowNumericEpochParameters.h5", null, () => gID)
)
{
var time = new DateTimeOffset(1000, TimeSpan.Zero);
var guid = new Guid("053C64D4-ED7A-4128-AA43-ED115716A97D");
var props = new Dictionary<string, object>();
props["int"] = 2;
props["float"] = 2.0f;
props["double"] = 2.0d;
props["decimal"] = 2.0m;
props["array"] = new[] {1.0, 2.0, 3.0};
props["short"] = (short) 2;
props["unit16"] = (UInt16) 1;
props["uint32"] = (UInt32) 2;
props["byte"] = (byte) 1;
props["bool"] = true;
const string protocolID = "Epoch.Fixture";
Dictionary<string, object> parameters = props;
dev1 = new UnitConvertingExternalDevice(dev1Name, "DEVICECO", new Measurement(0, "V"));
dev2 = new UnitConvertingExternalDevice(dev2Name, "DEVICECO", new Measurement(0, "V"));
var stream1 = new DAQInputStream("Stream1");
var stream2 = new DAQInputStream("Stream2");
var stimParameters = new Dictionary<string, object>();
stimParameters[param1] = value1;
stimParameters[param2] = value2;
var srate = new Measurement(1000, "Hz");
List<Measurement> samples =
Enumerable.Range(0, 10000).Select(i => new Measurement((decimal) Math.Sin((double) i/100), "V")).
ToList();
var stimData = new OutputData(samples, srate, false);
var stim1 = new RenderedStimulus("RenderedStimulus", stimParameters, stimData);
//.Data does not need to be persisted
var stim2 = new RenderedStimulus("RenderedStimulus", stimParameters, stimData);
//.Data does not need to be persisted
var e = new Epoch(protocolID, parameters);
e.Stimuli[dev1] = stim1;
e.Stimuli[dev2] = stim2;
DateTimeOffset start = DateTimeOffset.Parse("1/11/2011 6:03:29 PM -08:00");
// Do this to match the XML stored in the EpochXML.txt resource
e.StartTime = Maybe<DateTimeOffset>.Yes(start);
e.Background[dev1] = new Epoch.EpochBackground(new Measurement(0, "V"), new Measurement(1000, "Hz"));
e.Background[dev2] = new Epoch.EpochBackground(new Measurement(1, "V"), new Measurement(1000, "Hz"));
e.Responses[dev1] = new Response();
e.Responses[dev2] = new Response();
var streamConfig = new Dictionary<string, object>();
streamConfig[param1] = value1;
var devConfig = new Dictionary<string, object>();
devConfig[param2] = value2;
IInputData responseData1 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream1, streamConfig)
.DataWithExternalDeviceConfiguration(dev1, devConfig);
IInputData responseData2 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream2, streamConfig)
.DataWithExternalDeviceConfiguration(dev2, devConfig);
e.Responses[dev1].AppendData(responseData1);
e.Responses[dev2].AppendData(responseData2);
e.Keywords.Add(kw1);
e.Keywords.Add(kw2);
exp.BeginEpochGroup("label", "source identifier", new[] {"keyword1", "keyword2"}, props, guid,
time);
exp.Serialize(e);
exp.EndEpochGroup();
exp.Close();
}
H5.Close();
Approvals.VerifyFile("..\\..\\..\\ShouldAllowNumericEpochParameters.h5");
}
public void ShouldSetStreamBackgroundOnStop(
[Values(10000, 20000)] double sampleRate
)
{
Converters.Clear();
Converters.Register("V", "V",
// just an identity conversion for now, to pass Validate()
(IMeasurement m) => m);
HekaDAQInputStream.RegisterConverters();
HekaDAQOutputStream.RegisterConverters();
Assert.That(HekaDAQController.AvailableControllers().Count(), Is.GreaterThan(0));
foreach (var daq in HekaDAQController.AvailableControllers())
{
const double epochDuration = 1; //s
//Configure DAQ
daq.InitHardware();
try
{
daq.SampleRate = new Measurement((decimal)sampleRate, "Hz");
var controller = new Controller();
controller.Clock = daq.Clock;
controller.DAQController = daq;
const decimal expectedBackgroundVoltage = -3.2m;
var expectedBackground = new Measurement(expectedBackgroundVoltage, "V");
var dev0 = new UnitConvertingExternalDevice("Device0", "Manufacturer", controller, expectedBackground)
{
MeasurementConversionTarget = "V",
OutputSampleRate = daq.SampleRate,
InputSampleRate = daq.SampleRate
};
dev0.BindStream(daq.GetStreams("ao0").First() as IDAQOutputStream);
dev0.BindStream(daq.GetStreams("ai0").First() as IDAQInputStream);
dev0.Clock = daq.Clock;
controller.DiscardedEpoch += (c, args) => Console.WriteLine("Discarded epoch: " + args.Epoch);
// Setup Epoch
var e = new Epoch("HekaIntegration");
var nSamples = (int)TimeSpanExtensions.Samples(TimeSpan.FromSeconds(epochDuration), daq.SampleRate);
IList<IMeasurement> stimData = (IList<IMeasurement>)Enumerable.Range(0, nSamples)
.Select(i => new Measurement((decimal)(8 * Math.Sin(((double)i) / (nSamples / 10.0))), "V") as IMeasurement)
.ToList();
var stim = new RenderedStimulus((string) "RenderedStimulus", (IDictionary<string, object>) new Dictionary<string, object>(),
(IOutputData) new OutputData(stimData, daq.SampleRate, false));
e.Stimuli[dev0] = stim;
e.Responses[dev0] = new Response();
e.Backgrounds[dev0] = new Background(expectedBackground, daq.SampleRate);
//Run single epoch
var fakeEpochPersistor = new FakeEpochPersistor();
controller.RunEpoch(e, fakeEpochPersistor);
Thread.Sleep(TimeSpan.FromMilliseconds(100)); //allow DAC to settle
var actual = ((HekaDAQController)controller.DAQController).ReadStreamAsync(
daq.GetStreams("ai0").First() as IDAQInputStream);
//Should be within +/- 0.025 volts
Assert.That(actual.Data.First().QuantityInBaseUnits, Is.InRange(expectedBackground.QuantityInBaseUnits - (decimal)0.025,
expectedBackground.QuantityInBaseUnits + (decimal)0.025));
}
finally
{
if (daq.IsHardwareReady)
daq.CloseHardware();
}
}
}
public void Setup()
{
const string protocolID = "Epoch.Fixture";
var parameters = new Dictionary<string, object>();
parameters[param1] = value1;
parameters[param2] = value2;
dev1 = new UnitConvertingExternalDevice(dev1Name, "DEVICECO", new Measurement(0, "V"));
dev2 = new UnitConvertingExternalDevice(dev2Name, "DEVICECO", new Measurement(0, "V"));
var stream1 = new DAQInputStream("Stream1");
var stream2 = new DAQInputStream("Stream2");
var stimParameters = new Dictionary<string, object>();
stimParameters[param1] = value1;
stimParameters[param2] = value2;
var srate = new Measurement(1000, "Hz");
var samples = Enumerable.Range(0, 1000).Select(i => new Measurement((decimal)Math.Sin((double)i / 100), "V")).ToList();
var stimData = new OutputData(samples, srate, false);
RenderedStimulus stim1 = new RenderedStimulus((string) "RenderedStimulus", (IDictionary<string, object>) stimParameters, (IOutputData) stimData); //.Data does not need to be persisted
RenderedStimulus stim2 = new RenderedStimulus((string) "RenderedStimulus", (IDictionary<string, object>) stimParameters, (IOutputData) stimData); //.Data does not need to be persisted
Epoch e = new Epoch(protocolID, parameters);
e.Stimuli[dev1] = stim1;
e.Stimuli[dev2] = stim2;
var start = DateTimeOffset.Parse("1/11/2011 6:03:29 PM -08:00");
// Do this to match the XML stored in the EpochXML.txt resource
e.StartTime = Maybe<DateTimeOffset>.Yes(start);
e.Background[dev1] = new Epoch.EpochBackground(new Measurement(0, "V"), new Measurement(1000, "Hz"));
e.Background[dev2] = new Epoch.EpochBackground(new Measurement(1, "V"), new Measurement(1000, "Hz"));
e.Responses[dev1] = new Response();
e.Responses[dev2] = new Response();
var streamConfig = new Dictionary<string, object>();
streamConfig[param1] = value1;
var devConfig = new Dictionary<string, object>();
devConfig[param2] = value2;
var responseData1 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream1, streamConfig)
.DataWithExternalDeviceConfiguration(dev1, devConfig);
var responseData2 = new InputData(samples, srate, start)
.DataWithStreamConfiguration(stream2, streamConfig)
.DataWithExternalDeviceConfiguration(dev2, devConfig);
e.Responses[dev1].AppendData(responseData1);
e.Responses[dev2].AppendData(responseData2);
e.Keywords.Add(kw1);
e.Keywords.Add(kw2);
testEpoch = e;
}
public void SetUp()
{
const int srate = 1000;
IList<IMeasurement> list = Enumerable.Range(0, srate * 2).Select(i => new Measurement(i, "V") as IMeasurement).ToList();
var data = new OutputData(list, new Measurement(srate, "Hz"));
var stim1 = new RenderedStimulus("stim1", new Dictionary<string, object>(), data);
stream1 = new StimulusOutputDataStream(stim1, TimeSpan.FromSeconds(0.1));
var stim2 = new RenderedStimulus("stim2", new Dictionary<string, object>(), data);
stream2 = new StimulusOutputDataStream(stim2, TimeSpan.FromSeconds(0.1));
seqData = data.Concat(data);
seqStream = new SequenceOutputDataStream();
seqStream.Add(stream1);
seqStream.Add(stream2);
}
public void MultipleEpochs(
[Values(1000, 5000, 10000, 20000)] double sampleRate
)
{
Epoch e;
IExternalDevice dev0;
RenderedStimulus stim1;
IExternalDevice dev1;
RenderedStimulus stim2;
IList<IMeasurement> stimData;
var controller = SetupController(sampleRate, out e, out dev0, out stim1, out dev1, out stim2, out stimData, 2);
controller.RunEpoch(e, new FakeEpochPersistor());
var inputData = e.Responses[dev0].Data;
const double MAX_VOLTAGE_DIFF = 0.001;
int failures = inputData.Select((t, i) => t.QuantityInBaseUnit - stimData[i].QuantityInBaseUnit)
.Count(dif => Math.Abs(dif) > (decimal) MAX_VOLTAGE_DIFF);
Assert.AreEqual(0, failures);
e = new Epoch("LowGainSimulation");
dev0 = controller.GetDevice("Device0");
dev1 = controller.GetDevice("Device1");
var srate = new Measurement((decimal) sampleRate, "Hz");
stim1 = new RenderedStimulus((string) "RenderedStimulus",
(IDictionary<string, object>) new Dictionary<string, object>(),
(IOutputData) new OutputData(stimData, srate, false));
stim2 = new RenderedStimulus((string) "RenderedStimulus",
(IDictionary<string, object>) new Dictionary<string, object>(),
(IOutputData) new OutputData(stimData, srate, false));
e.Stimuli[dev0] = stim1;
e.Stimuli[dev1] = stim2;
e.Responses[dev0] = new Response();
e.Responses[dev1] = new Response();
e.Background[dev1] = new Epoch.EpochBackground(new Measurement(0, "V"), srate);
e.Background[dev0] = new Epoch.EpochBackground(new Measurement(0, "V"), srate);
Assert.DoesNotThrow(() => controller.RunEpoch(e, new FakeEpochPersistor()));
inputData = e.Responses[dev0].Data;
failures = inputData.Select((t, i) => t.QuantityInBaseUnit - stimData[i].QuantityInBaseUnit)
.Count(dif => Math.Abs(dif) > (decimal) MAX_VOLTAGE_DIFF);
Assert.AreEqual(0, failures);
}
public void EnumeratesDataBlocks(
[Values(100, 500, 1000, 5000)] double blockMilliseconds,
[Values(1000, 5000, 10000)] double sampleRateHz
)
{
var parameters = new Dictionary<string, object>();
var sampleRate = new Measurement((decimal)sampleRateHz, "Hz");
IOutputData data = new OutputData(Enumerable.Range(0, (int)TimeSpan.FromSeconds(3).Samples(new Measurement((decimal)sampleRateHz, "Hz")))
.Select(i => new Measurement(i, "units")).ToList(),
sampleRate,
false);
var s = new RenderedStimulus((string) "RenderedStimulus", (IDictionary<string, object>) parameters, data);
var blockSpan = TimeSpan.FromMilliseconds(blockMilliseconds);
IEnumerator<IOutputData> iter = s.DataBlocks(blockSpan).GetEnumerator();
while (iter.MoveNext())
{
var cons = data.SplitData(blockSpan);
data = cons.Rest;
Assert.That(iter.Current.Duration, Is.EqualTo(cons.Head.Duration));
Assert.That(iter.Current.Data, Is.EqualTo(cons.Head.Data));
}
}
