static void ReadFile(string filePath)
{
var file = Hdf5.OpenFile(filePath, true);
var group = Hdf5.CreateOrOpenGroup(file, "group");
var(ok, rawData) = Hdf5.ReadDataset <int>(group, "dataset");
if (ok)
{
var data = (int[, ])rawData;
for (int i = 0; i < data.GetLength(0); ++i)
{
for (int j = 0; j < data.GetLength(1); ++j)
{
Write($"{data[i, j],3}");
}
WriteLine();
}
}
//var dataSet = H5D.open(group, "dataset");
//var hello = Hdf5.ReadUnicodeString(dataSet, "string");
//H5D.close(dataSet);
//WriteLine($"string: {hello}");
Hdf5.CloseGroup(group);
Hdf5.CloseFile(file);
}
public void WriteAndReadGroupsWithDataset()
{
string filename = Path.Combine(folder, "testGroups.H5");
try
{
var fileId = Hdf5.CreateFile(filename);
Assert.IsTrue(fileId > 0);
var dset = dsets.First();
var groupId = H5G.create(fileId, Hdf5Utils.NormalizedName("/A")); ///B/C/D/E/F/G/H
Hdf5.WriteDataset(groupId, Hdf5Utils.NormalizedName("test"), dset);
var subGroupId = Hdf5.CreateOrOpenGroup(groupId, Hdf5Utils.NormalizedName("C"));
var subGroupId2 = Hdf5.CreateOrOpenGroup(groupId, Hdf5Utils.NormalizedName("/D")); // will be saved at the root location
dset = dsets.Skip(1).First();
Hdf5.WriteDataset(subGroupId, Hdf5Utils.NormalizedName("test2"), dset);
Hdf5.CloseGroup(subGroupId);
Hdf5.CloseGroup(subGroupId2);
Hdf5.CloseGroup(groupId);
groupId = H5G.create(fileId, Hdf5Utils.NormalizedName("/A/B")); ///B/C/D/E/F/G/H
dset = dsets.Skip(1).First();
Hdf5.WriteDataset(groupId, Hdf5Utils.NormalizedName("test"), dset);
Hdf5.CloseGroup(groupId);
groupId = Hdf5.CreateGroupRecursively(fileId, Hdf5Utils.NormalizedName("A/B/C/D/E/F/I"));
Hdf5.CloseGroup(groupId);
Hdf5.CloseFile(fileId);
fileId = Hdf5.OpenFile(filename);
Assert.IsTrue(fileId > 0);
fileId = Hdf5.OpenFile(filename);
groupId = H5G.open(fileId, Hdf5Utils.NormalizedName("/A/B"));
double[,] dset2 = (double[, ])Hdf5.ReadDataset <double>(groupId, Hdf5Utils.NormalizedName("test")).result;
CompareDatasets(dset, dset2);
Assert.IsTrue(Hdf5.CloseGroup(groupId) >= 0);
groupId = H5G.open(fileId, Hdf5Utils.NormalizedName("/A/C"));
dset2 = (double[, ])Hdf5.ReadDataset <double>(groupId, Hdf5Utils.NormalizedName("test2")).result;
CompareDatasets(dset, dset2);
Assert.IsTrue(Hdf5.CloseGroup(groupId) >= 0);
bool same = dset == dset2;
dset = dsets.First();
dset2 = (double[, ])Hdf5.ReadDataset <double>(fileId, Hdf5Utils.NormalizedName("/A/test")).result;
CompareDatasets(dset, dset2);
Assert.IsTrue(Hdf5Utils.ItemExists(fileId, Hdf5Utils.NormalizedName("A/B/C/D/E/F/I"), DataTypes.Hdf5ElementType.Dataset));
Assert.IsTrue(Hdf5.CloseFile(fileId) == 0);
}
catch (Exception ex)
{
CreateExceptionAssert(ex);
}
}
public static void save_weights_to_hdf5_group(long f, List <ILayer> layers)
{
List <string> layerName = new List <string>();
foreach (var layer in layers)
{
layerName.Add(layer.Name);
}
save_attributes_to_hdf5_group(f, "layer_names", layerName.ToArray());
Hdf5.WriteAttribute(f, "backend", "tensorflow");
Hdf5.WriteAttribute(f, "keras_version", "2.5.0");
long g = 0, crDataGroup = 0;
List <IVariableV1> weights = new List <IVariableV1>();
//List<IVariableV1> weight_values = new List<IVariableV1>();
List <string> weight_names = new List <string>();
foreach (var layer in layers)
{
weight_names = new List <string>();
g = Hdf5.CreateOrOpenGroup(f, Hdf5Utils.NormalizedName(layer.Name));
weights = _legacy_weights(layer);
//weight_values= keras.backend.batch_get_value(weights);
foreach (var weight in weights)
{
weight_names.Add(weight.Name);
}
save_attributes_to_hdf5_group(g, "weight_names", weight_names.ToArray());
Tensor tensor = null;
foreach (var(name, val) in zip(weight_names, weights))
{
tensor = val.AsTensor();
if (name.IndexOf("/") > 1)
{
crDataGroup = Hdf5.CreateOrOpenGroup(g, Hdf5Utils.NormalizedName(name.Split('/')[0]));
WriteDataset(crDataGroup, name.Split('/')[1], tensor);
Hdf5.CloseGroup(crDataGroup);
}
else
{
WriteDataset(crDataGroup, name, tensor);
}
tensor = null;
}
Hdf5.CloseGroup(g);
weight_names = null;
}
weights = null;
// weight_values = null;
}
public void WriteAndReadPrimitives()
{
string filename = Path.Combine(folder, "testPrimitives.H5");
int intValue = 2;
double dblValue = 1.1;
string strValue = "test";
bool boolValue = true;
var groupStr = "/test";
string concatFunc(string x) => string.Concat(groupStr, "/", x);
Dictionary <string, List <string> > attributes = new Dictionary <string, List <string> >();
try
{
var fileId = Hdf5.CreateFile(filename);
Assert.IsTrue(fileId > 0);
var groupId = Hdf5.CreateGroup(fileId, groupStr);
Hdf5.WriteOneValue(groupId, concatFunc(nameof(intValue)), intValue, attributes);
Hdf5.WriteOneValue(groupId, concatFunc(nameof(dblValue)), dblValue, attributes);
Hdf5.WriteOneValue(groupId, concatFunc(nameof(strValue)), strValue, attributes);
Hdf5.WriteOneValue(groupId, concatFunc(nameof(boolValue)), boolValue, attributes);
Hdf5.CloseGroup(groupId);
Hdf5.CloseFile(fileId);
}
catch (Exception ex)
{
CreateExceptionAssert(ex);
}
try
{
var fileId = Hdf5.OpenFile(filename);
Assert.IsTrue(fileId > 0);
var groupId = H5G.open(fileId, groupStr);
int readInt = Hdf5.ReadOneValue <int>(groupId, concatFunc(nameof(intValue)));
Assert.IsTrue(intValue == readInt);
double readDbl = Hdf5.ReadOneValue <double>(groupId, concatFunc(nameof(dblValue)));
Assert.IsTrue(dblValue == readDbl);
string readStr = Hdf5.ReadOneValue <string>(groupId, concatFunc(nameof(strValue)));
Assert.IsTrue(strValue == readStr);
bool readBool = Hdf5.ReadOneValue <bool>(groupId, concatFunc(nameof(boolValue)));
Assert.IsTrue(boolValue == readBool);
H5G.close(groupId);
Hdf5.CloseFile(fileId);
}
catch (Exception ex)
{
CreateExceptionAssert(ex);
}
}
public void Dispose()
{
try
{
if (!Disposed)
{
Hdf5.CloseGroup(GroupId);
}
}
catch (Exception)
{
//nothing
}
}
public void Dispose()
{
try
{
if (!Disposed)
{
Hdf5.CloseGroup(GroupId);
}
}
catch (Exception e)
{
Logger.LogError(e, $"Error closing RPosition group: {e.Message}");
}
}
public void Dispose()
{
try
{
if (!Disposed)
{
Hdf5.CloseGroup(GroupId);
Disposed = true;
}
}
catch (Exception e)
{
Logger?.LogError($"Error closing file: {e}");
}
}
public void Dispose()
{
try
{
if (!Disposed)
{
UnFiltered.Dispose();
Filtered.Dispose();
Timestamps.Dispose();
PacketIds?.Dispose();
EcgSamplesData.Dispose();
EcgTaskWriter.Dispose();
Hdf5.CloseGroup(GroupId);
Disposed = true;
}
}
catch (Exception e)
{
Logger.LogError($"Error during dispose of ECG: {e.Message}");
}
}
static void WriteFile(string filePath)
{
var file = Hdf5.CreateFile(filePath);
var group = Hdf5.CreateOrOpenGroup(file, "group");
Hdf5.WriteDataset(group, "dataset",
new int[, ]
{
{ 1, 2, 3, 4 },
{ 5, 6, 7, 8 },
{ 9, 10, 11, 12 }
});
var hello = "早上好！";
Hdf5.WriteStringAttribute(group, "string", hello, "dataset");
Hdf5.CloseGroup(group);
Hdf5.CloseFile(file);
}
public async Task <(bool, string)> StopProcedure()
{
if (!File.Exists(FileName))
{
string msg = $"File {FileName} does not exist";
Logger?.LogWarning(msg);
return(false, msg);
}
if (FileClosed)
{
return(GeneralUtils.CheckFileSize(FileName));
}
FileClosed = true;
Logger?.LogInformation("Stop Procedure called");
ProcedureInformation.EndDateTime = DateTime.Now;
if (RecordingInProgress)
{
StopRecording();
}
await CloseHandles();
Hdf5.Flush(groupRoot, H5F.scope_t.GLOBAL);
Hdf5.CloseGroup(groupEIT);
Hdf5.CloseGroup(groupRoot);
long result = Hdf5.CloseFile(fileId);
if (result >= 0)
{
Logger?.LogInformation("Stop Procedure H5 File closed");
}
else
{
Logger?.LogError("Cannot close H5 File: " + result);
}
return(GeneralUtils.CheckFileSize(FileName));
}
public void Dispose()
{
try
{
if (!Disposed)
{
VoltagesReal.Dispose();
VoltagesIm.Dispose();
CurrentsReal?.Dispose();
CurrentsIm.Dispose();
Saturation.Dispose();
Timestamps.Dispose();
PacketIds?.Dispose();
ElectrodeTaskWriter.Dispose();
Hdf5.CloseGroup(GroupId);
Disposed = true;
}
}
catch (Exception e)
{
Logger.LogError($"Error during dispose of EIT: {e.Message}");
}
}
