public async Task TestFullFileWriteRead()
{
string filename = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "test2.h5");
Console.WriteLine(filename);
if (File.Exists(filename))
{
File.Delete(filename);
}
kama = new KamaAcquisitionFile(filename, AcquisitionInterface.Simulator, Logger);
ProcedureInfo info = new ProcedureInfo
{
Age = 18,
FirstName = "Lior",
LastName = "Banai",
ExamDate = DateTime.Now,
Procedure = "test",
ProcedureID = "ID",
Patient = new PatientInfo()
};
kama.SavePatientInfo(info);
kama.UpdateSystemInformation("32423423", new[] { "11", "12" });
kama.SetProcedureInformation(info);
string data = File.ReadAllText(AcquisitionScanProtocolPath);
AcquisitionProtocolParameters parameters = AcquisitionProtocolParameters.FromJson(data);
await kama.StartLogging(parameters);
var ecgTask = WriteECGData(kama, 2, 1);
var eitTask = WriteEITData(parameters, kama, 5, 1);
var seTask = WriteSystemEvents(kama);
await Task.WhenAll(ecgTask, eitTask, seTask);
var ecgTestData = await ecgTask;
var eitsTestData = await eitTask;
kama.StopRecording();
await kama.StopProcedure();
using (KamaAcquisitionReadOnlyFile readFile = new KamaAcquisitionReadOnlyFile(filename))
{
readFile.ReadSystemInformation();
readFile.ReadProcedureInformation();
readFile.ReadPatientInformation();
Assert.IsTrue(readFile.PatientInformation.Equals(kama.PatientInfo));
Assert.IsTrue(readFile.ProcedureInformation.Equals(kama.ProcedureInformation));
Assert.IsTrue(readFile.SystemInformation.Equals(kama.SystemInformation));
readFile.ReadECGData();
readFile.ReadEITData();
Assert.IsTrue(readFile.EITs.SequenceEqual(eitsTestData));
readFile.ReadSystemEvents();
Assert.IsTrue(readFile.Events.Count == 100);
}
File.Delete(filename);
}
public async Task TestEventsWrite()
{
string filename = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "testEvents.h5");
Console.WriteLine(filename);
if (File.Exists(filename))
{
File.Delete(filename);
}
kama = new KamaAcquisitionFile(filename, AcquisitionInterface.Simulator, Logger);
ProcedureInfo info = new ProcedureInfo
{
Age = 18,
FirstName = "First",
LastName = "Last",
ExamDate = DateTime.Now,
Procedure = "test",
ProcedureID = "ID",
Patient = new PatientInfo()
};
kama.SavePatientInfo(info);
kama.UpdateSystemInformation("32423423", new[] { "11", "12" });
string data = File.ReadAllText(AcquisitionScanProtocolPath);
AcquisitionProtocolParameters parameters = AcquisitionProtocolParameters.FromJson(data);
await kama.StartLogging(parameters);
kama.StopRecording();
await kama.StopProcedure();
File.Delete(filename);
}
public Task StartLogging(AcquisitionProtocolParameters acquisitionProtocol)
{
EIT = new EIT(RecordNumber++, EITDefaultChunkSize, acquisitionProtocol.AsJson(), fileId, groupEIT, Logger);
//var acquisitionInformation = new AcquisitionInformation(acquisitionProtocol, fileId, groupEIT, Logger);
//acquisitionInformation.FlushDataAndCloseObject();
ECG = new ECG(fileId, groupRoot, ECGDefaultChunkSize, (int)acquisitionProtocol.ScanDescription.EcgParams.SampleRate, Logger);
SystemEvents.StartLogging();
RPosition.StartLogging();
Tags.StartLogging();
return(Task.CompletedTask);
}
private async Task <List <EITEntry> > WriteEITData(AcquisitionProtocolParameters parameters,
KamaAcquisitionFile file, int loop, int sleepsBetweenWritesMilliseconds)
{
var result = await Task.Factory.StartNew(() =>
{
Random random = new Random();
List <ElectrodeFrame> samples = new List <ElectrodeFrame>();
for (int index = 0; index < loop; index++)
{
ElectrodeFrame frame = new ElectrodeFrame();
frame.ComplexCurrentMatrix = Enumerable.Range(0, 2441)
.Select(i => ((float)random.NextDouble(), (float)random.NextDouble())).ToArray();
frame.ComplexVoltageMatrix = Enumerable.Range(0, 2441)
.Select(i => ((float)random.NextDouble(), (float)random.NextDouble())).ToArray();
frame.PacketId = (ulong)index;
var timestamp = DateTimeOffset.Now;
frame.timestamp = timestamp.ToUnixTimeMilliseconds();
ulong saturationMask = (ulong)random.Next();
saturationMask = (saturationMask << 32);
saturationMask = saturationMask | (ulong)random.Next();
frame.SaturationMask = saturationMask;
Thread.Sleep(sleepsBetweenWritesMilliseconds);
file.AppendElectrodeSample(frame);
samples.Add(frame);
}
EITEntry entry = new EITEntry
{
Configuration = parameters.AsJson(),
StartDateTime = DateTimeOffset.FromUnixTimeMilliseconds(samples.First().timestamp).DateTime,
EndDateTime = DateTimeOffset.FromUnixTimeMilliseconds(samples.Last().timestamp).DateTime,
VoltagesReal = new float[samples.Count, samples[0].ComplexVoltageMatrix.Length],
VoltagesIm = new float[samples.Count, samples[0].ComplexVoltageMatrix.Length],
CurrentsIm = new float[samples.Count, samples[0].ComplexVoltageMatrix.Length],
CurrentsReal = new float[samples.Count, samples[0].ComplexVoltageMatrix.Length],
Saturation = new ulong[samples.Count, 1],
Timestamps = new long[samples.Count, 1]
};
for (var i = 0; i < samples.Count; i++)
{
ElectrodeFrame electrodeFrame = samples[i];
for (int j = 0; j < electrodeFrame.ComplexVoltageMatrix.Length; j++)
{
entry.VoltagesReal[i, j] = electrodeFrame.ComplexVoltageMatrix[j].Re;
entry.VoltagesIm[i, j] = electrodeFrame.ComplexVoltageMatrix[j].Im;
}
for (int j = 0; j < electrodeFrame.ComplexCurrentMatrix.Length; j++)
{
entry.CurrentsReal[i, j] = electrodeFrame.ComplexCurrentMatrix[j].Re;
entry.CurrentsIm[i, j] = electrodeFrame.ComplexCurrentMatrix[j].Im;
}
entry.Saturation[i, 0] = electrodeFrame.SaturationMask;
entry.Timestamps[i, 0] = electrodeFrame.timestamp;
}
return(entry);
});
return(new List <EITEntry>
{
result
});
}
public async Task CreatePatientInfoTest()
{
string data = File.ReadAllText(AcquisitionScanProtocolPath);
string filename = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "h5test.h5");
kama = new KamaAcquisitionFile(filename, AcquisitionInterface.Simulator, Logger);
CreatePatientDetails(kama);
UpdateSystemInformation(kama);
AcquisitionProtocolParameters parameters = AcquisitionProtocolParameters.FromJson(data);
await kama.StartLogging(parameters);
string lineVoltage, lineCurrent, lineEcg;
string directory = AppDomain.CurrentDomain.BaseDirectory;
string voltagePath = Path.Combine(directory, voltage);
string currentPath = Path.Combine(directory, current);
using StreamReader srVoltage = new StreamReader(voltagePath);
using StreamReader srCurrent = new StreamReader(currentPath);
int i = 0;
while (!string.IsNullOrEmpty(lineVoltage = await srVoltage.ReadLineAsync()) &&
!string.IsNullOrEmpty(lineCurrent = await srCurrent.ReadLineAsync()))
{
ElectrodeFrame sample = new ElectrodeFrame();
var itemsVoltage = lineVoltage.Split(',', StringSplitOptions.RemoveEmptyEntries);
var itemsCurrent = lineCurrent.Split(',', StringSplitOptions.RemoveEmptyEntries);
sample.timestamp = long.Parse(itemsCurrent.First());
sample.SaturationMask = Convert.ToUInt64(itemsCurrent.Skip(1).Take(1).Single().Trim(), 16);
var evenvals = itemsCurrent.Skip(2).Where((c, i) => i % 2 == 0).Select(float.Parse);
var oddvals = itemsCurrent.Skip(2).Where((c, i) => i % 2 != 0).Select(float.Parse);
sample.ComplexCurrentMatrix = evenvals.Zip(oddvals).Select(itm => (itm.First, itm.Second)).ToArray();
evenvals = itemsVoltage.Skip(2).Where((c, i) => i % 2 == 0).Select(float.Parse);
oddvals = itemsVoltage.Skip(2).Where((c, i) => i % 2 != 0).Select(float.Parse);
sample.ComplexVoltageMatrix = evenvals.Zip(oddvals).Select(itm => (itm.First, itm.Second)).ToArray();
kama.AppendElectrodeSample(sample);
}
using StreamReader srEcg = new StreamReader(ecg);
var filteredFrameData = new List <List <float> > {
new List <float>(), new List <float>()
};
var frameData = new List <List <float> > {
new List <float>(), new List <float>()
};
var timestamps = new List <long>();
while (!string.IsNullOrEmpty(lineEcg = await srEcg.ReadLineAsync()))
{
var items = lineEcg.Split(",", StringSplitOptions.RemoveEmptyEntries);
var c1 = float.Parse(items[0]);
var c2 = float.Parse(items[1]);
var time = long.Parse(items[2]);
var c1_filtered = float.Parse(items[4]);
var c2_filtered = float.Parse(items[5]);
frameData[0].Add(c1);
frameData[1].Add(c2);
filteredFrameData[0].Add(c1_filtered);
filteredFrameData[1].Add(c2_filtered);
timestamps.Add(time);
}
ECGFrame frame = new ECGFrame(filteredFrameData, frameData, timestamps[0], 0);
kama.AppendEcgSample(frame);
await kama.StopProcedure();
var fileId = Hdf5.OpenFile(filename);
Stopwatch st = Stopwatch.StartNew();
var readback = Hdf5.ReadDatasetToArray <float>(fileId, "/eit/d1/voltages.re");
st.Stop();
Console.WriteLine("read time: " + st.ElapsedMilliseconds);
Hdf5.CloseFile(fileId);
File.Delete(filename);
}