public void WriteAndOverrideChunkedDataset()
{
var data = CreateDataset();
string filename = Path.Combine(folder, "testOverrideChunks.H5");
string groupName = "/test";
string datasetName = "Data";
//create
var fileId = Hdf5.CreateFile(filename);
Assert.IsTrue(fileId > 0);
var groupId = Hdf5.CreateOrOpenGroup(fileId, groupName);
Assert.IsTrue(groupId >= 0);
using (var chunkedDset = new ChunkedDataset <double>(datasetName, groupId))
{
chunkedDset.AppendOrCreateDataset(data);
}
Hdf5.CloseFile(fileId);
//read
fileId = Hdf5.OpenFile(filename);
var dataRead = Hdf5.ReadDatasetToArray <double>(fileId, string.Concat(groupName, "/", datasetName));
Hdf5.CloseFile(fileId);
CompareDatasets(dataRead.result as double[, ], data);
}
public void WriteAndReadChunckedDataset2()
{
string filename = Path.Combine(folder, "testChunks2.H5");
string groupName = "/test";
string datasetName = "Data";
try
{
var fileId = Hdf5.CreateFile(filename);
Assert.IsTrue(fileId > 0);
var groupId = Hdf5.CreateGroup(fileId, groupName);
Assert.IsTrue(groupId >= 0);
//var chunkSize = new ulong[] { 5, 5 };
using (var chunkedDset = new ChunkedDataset <double>(datasetName, groupId))
{
foreach (var ds in dsets)
{
chunkedDset.AppendOrCreateDataset(ds);
}
;
}
Hdf5.CloseFile(fileId);
}
catch (Exception ex)
{
CreateExceptionAssert(ex);
}
try
{
var fileId = Hdf5.OpenFile(filename);
//var groupId = H5G.open(fileId, groupName);
//var dset = Hdf5.ReadDatasetToArray<double>(groupId, datasetName);
var dset = Hdf5.ReadDatasetToArray <double>(fileId, string.Concat(groupName, "/", datasetName));
Assert.IsTrue(dset.result.Rank == dsets.First().Rank);
var xSum = dsets.Select(d => d.GetLength(0)).Sum();
Assert.IsTrue(xSum == dset.result.GetLength(0));
var testRange = Enumerable.Range(0, 30).Select(t => (double)t);
// get every 5th element in the matrix
var x0Range = dset.result.Cast <double>().Where((d, i) => i % 5 == 0);
Assert.IsTrue(testRange.SequenceEqual(x0Range));
Hdf5.CloseFile(fileId);
}
catch (Exception ex)
{
CreateExceptionAssert(ex);
}
}
//[TestMethod]
public void TestRead()
{
//string filename = @"D:\Data\9_pig.h5";
string filename = @"c:\kalpa\test.h5";
//string filename = @"d:\data\test2400.h5";
var fileId = Hdf5.OpenFile(filename);
Stopwatch st = Stopwatch.StartNew();
var ds = Hdf5.ReadDatasetToArray <float>(fileId, "/eit/d1/voltages.im");
st.Stop();
Console.WriteLine(ds.result.Length);
Console.WriteLine("read time im: " + st.ElapsedMilliseconds);
st.Restart();
ds = Hdf5.ReadDatasetToArray <float>(fileId, "/eit/d1/voltages.re");
st.Stop();
Console.WriteLine(ds.result.Length);
Console.WriteLine("read time re: " + st.ElapsedMilliseconds);
Hdf5.CloseFile(fileId);
}
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);
}