public void WriteReadAndEditAttribute()
{
string filename = Path.Combine(folder, "WriteReadAndEditAttribute.H5");
try
{
var fileId = Hdf5.CreateFile(filename);
Assert.IsTrue(fileId > 0);
var groupId = Hdf5.CreateOrOpenGroup(fileId, "test");
DateTime nowTime = DateTime.Now;
Hdf5.WriteAttribute(groupId, "time", nowTime);
DateTime readTime = Hdf5.ReadAttribute <DateTime>(groupId, "time");
Assert.IsTrue(readTime == nowTime);
Hdf5.CloseFile(fileId);
fileId = Hdf5.OpenFile(filename, false);
readTime = Hdf5.ReadAttribute <DateTime>(groupId, "time");
Assert.IsTrue(readTime == nowTime);
nowTime = DateTime.Now;
Hdf5.WriteAttribute(groupId, "time", nowTime);
readTime = Hdf5.ReadAttribute <DateTime>(groupId, "time");
Assert.IsTrue(readTime == nowTime);
Hdf5.CloseFile(fileId);
fileId = Hdf5.OpenFile(filename, false);
readTime = Hdf5.ReadAttribute <DateTime>(groupId, "time");
Assert.IsTrue(readTime == nowTime);
Hdf5.CloseFile(fileId);
}
catch (Exception ex)
{
CreateExceptionAssert(ex);
}
}
public KamaAcquisitionFile(string filename, AcquisitionInterface acquisitionInterface, ILogger logger,
int eitDefaultChunkSize = 24000, int ecgDefaultChunkSize = 10)
{
FileName = filename;
Logger = logger;
EITDefaultChunkSize = eitDefaultChunkSize;
ECGDefaultChunkSize = ecgDefaultChunkSize;
RecordNumber = 1;
H5E.set_auto(H5E.DEFAULT, null, IntPtr.Zero);
fileId = Hdf5.CreateFile(filename);
groupRoot = fileId;
groupEIT = Hdf5.CreateOrOpenGroup(groupRoot, "eit");
ProcedureInformation = new ProcedureInformation(fileId, groupRoot, logger)
{
ProcedureDirectory = Path.GetDirectoryName(filename),
StartDateTime = DateTime.Now,
EndDateTime = DateTime.Now
};
SystemInformation = new SystemInformation(fileId, groupRoot, logger);
SystemInformation.SystemType = acquisitionInterface.ToString();
// InjectionGroup = new InjectionGroup(fileId, groupRoot);
CalibrationGroup = new CalibrationGroup(fileId, groupRoot, logger);
SystemEvents = new SystemEventGroup(fileId, groupRoot, logger);
RPosition = new RPositionGroup(fileId, groupRoot, logger);
Tags = new TagsGroup(fileId, groupRoot, logger);
UserEventsGroup = new UserEventsGroup(fileId, groupRoot, logger);
}
public void WriteAndReadAttribute()
{
string filename = Path.Combine(folder, "testAttribute.H5");
try
{
var fileId = Hdf5.CreateFile(filename);
Assert.IsTrue(fileId > 0);
var groupId = Hdf5.CreateOrOpenGroup(fileId, "test");
DateTime nowTime = DateTime.Now;
Hdf5.WriteAttribute(groupId, "time", nowTime);
Hdf5.WriteAttributes <DateTime>(groupId, "times", new List <DateTime> {
nowTime, nowTime.AddDays(1)
}.ToArray());
DateTime readTime = Hdf5.ReadAttribute <DateTime>(groupId, "time");
var allTimes = Hdf5.ReadAttributes <DateTime>(groupId, "times");
Assert.IsTrue(readTime == nowTime);
Assert.IsTrue(Hdf5.CloseFile(fileId) == 0);
}
catch (Exception ex)
{
CreateExceptionAssert(ex);
}
}
public void WriteAndReadStringAttribute()
{
string filename = Path.Combine(folder, "testAttributeString.H5");
try
{
var fileId = Hdf5.CreateFile(filename);
Assert.IsTrue(fileId > 0);
var groupId = Hdf5.CreateOrOpenGroup(fileId, "test");
string attrStr = "this is an attribute";
Hdf5.WriteAttribute(groupId, "time", attrStr);
string readStr = Hdf5.ReadAttribute <string>(groupId, "time_Non_Exist");
Assert.IsTrue(string.IsNullOrEmpty(readStr));
readStr = Hdf5.ReadAttribute <string>(groupId, "time");
Assert.IsTrue(readStr == attrStr);
Assert.IsTrue(H5G.close(groupId) == 0);
Assert.IsTrue(Hdf5.CloseFile(fileId) == 0);
ErrorCountExpected = 2;
}
catch (Exception ex)
{
CreateExceptionAssert(ex);
}
}
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);
}
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 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.CreateOrOpenGroup(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);
}
}
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.CreateOrOpenGroup(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);
}
}
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);
}
//[TestMethod]
public void ReadTable()
{
Hdf5.Settings.LowerCaseNaming = false;
Hdf5.Settings.EnableErrorReporting(true);
Hdf5Utils.LogWarning = (s) => Errors.Add(s);
Hdf5Utils.LogError = (s) => Errors.Add(s);
string filename = @"D:\h5\d.hdf5";
long fileId = -1;
try
{
fileId = Hdf5.OpenFile(filename, true);
var groupName = "/MODEL_STAGE[1]/RESULTS/ON_NODES/DISPLACEMENT/DATA";
var groupId = Hdf5.CreateOrOpenGroup(fileId, groupName);
TabularData <double> tableOfData = Hdf5.Read2DTable <double>(groupId, "STEP_0");
}
finally
{
if (fileId > 0)
{
Hdf5.CloseFile(fileId);
}
}
}
public void WriteAndReadAttributes()
{
string filename = Path.Combine(folder, "testAttributes.H5");
int[] intValues = new[] { 1, 2 };
double dblValue = 1.1;
string strValue = "test";
string[] strValues = new string[2] {
"test", "another test"
};
bool boolValue = true;
DateTime dateValue = new DateTime(1969, 1, 12);
var groupStr = "/test";
//string concatFunc(string x) => string.Concat(groupStr, "/", x);
string intName = nameof(intValues);
string dblName = nameof(dblValue);
string strName = nameof(strValue);
string strNames = nameof(strValues);
string boolName = nameof(boolValue);
string dateName = nameof(dateValue);
try
{
var fileId = Hdf5.CreateFile(filename);
Assert.IsTrue(fileId > 0);
var groupId = Hdf5.CreateOrOpenGroup(fileId, groupStr);
Hdf5.WriteAttributes <int>(groupId, intName, intValues);
Hdf5.WriteAttribute(groupId, dblName, dblValue);
Hdf5.WriteAttribute(groupId, strName, strValue);
Hdf5.WriteAttributes <string>(groupId, strNames, strValues);
Hdf5.WriteAttribute(groupId, boolName, boolValue);
Hdf5.WriteAttribute(groupId, dateName, dateValue);
H5G.close(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);
IEnumerable <int> readInts = (int[])Hdf5.ReadAttributes <int>(groupId, intName).result;
Assert.IsTrue(intValues.SequenceEqual(readInts));
double readDbl = Hdf5.ReadAttribute <double>(groupId, dblName);
Assert.IsTrue(dblValue == readDbl);
string readStr = Hdf5.ReadAttribute <string>(groupId, strName);
Assert.IsTrue(strValue == readStr);
IEnumerable <string> readStrs = (string[])Hdf5.ReadAttributes <string>(groupId, strNames).result;
Assert.IsTrue(strValues.SequenceEqual(readStrs));
bool readBool = Hdf5.ReadAttribute <bool>(groupId, boolName);
Assert.IsTrue(boolValue == readBool);
DateTime readDate = Hdf5.ReadAttribute <DateTime>(groupId, dateName);
Assert.IsTrue(dateValue == readDate);
H5G.close(groupId);
Hdf5.CloseFile(fileId);
}
catch (Exception ex)
{
CreateExceptionAssert(ex);
}
}
