public void UpdateStringAttributeOnDataset()
{
string fileName = GetFilename("updatestringattributeondataset.h5");
Hdf5File file = Hdf5File.Create(fileName);
Hdf5Group group = file.Groups.Add("group");
List <Hdf5DimensionProperty> dimensionProps = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty prop = new Hdf5DimensionProperty {
CurrentSize = 1
};
dimensionProps.Add(prop);
Hdf5Dataset dataset = group.Datasets.Add("dataset1", Hdf5DataTypes.Int32, dimensionProps);
Hdf5Attribute attribute = dataset.Attributes.Add("attribute1", "test");
attribute.Value = "test2";
dataset.Attributes.Update(attribute);
file.Close();
file = new Hdf5File(fileName);
group = file.Groups[0];
dataset = group.Datasets[0];
attribute = dataset.Attributes[0];
Assert.AreEqual("test2", attribute.Value);
}
public void SetUInt64()
{
string filename = GetFilename("setuint64.h5");
Hdf5File file = Hdf5File.Create(filename);
List <Hdf5DimensionProperty> properties = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty property = new Hdf5DimensionProperty {
CurrentSize = 5
};
properties.Add(property);
Hdf5Dataset dataset = file.Datasets.Add("dataset1", Hdf5DataTypes.UInt64, properties);
Assert.IsNotNull(dataset);
UInt64[] value = { UInt64.MinValue, 1, 2, 3, UInt64.MaxValue };
dataset.SetData(value);
var array = dataset.GetData();
Assert.AreEqual(1, array.Rank);
Assert.AreEqual(5, array.GetLength(0));
Assert.AreEqual(UInt64.MinValue, array.GetValue(0));
Assert.AreEqual(UInt64.MaxValue, array.GetValue(4));
file.Close();
}
public void SetSingle()
{
string filename = GetFilename("setsingle.h5");
Hdf5File file = Hdf5File.Create(filename);
List <Hdf5DimensionProperty> properties = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty property = new Hdf5DimensionProperty {
CurrentSize = 5
};
properties.Add(property);
Hdf5Dataset dataset = file.Datasets.Add("dataset1", Hdf5DataTypes.Single, properties);
Assert.IsNotNull(dataset);
Single[] value = { Single.MinValue, -1.1f, 0.0f, -1.3f, Single.MaxValue };
dataset.SetData(value);
var array = dataset.GetData();
Assert.AreEqual(1, array.Rank);
Assert.AreEqual(5, array.GetLength(0));
Assert.AreEqual(Single.MinValue, array.GetValue(0));
Assert.AreEqual(Single.MaxValue, array.GetValue(4));
file.Close();
}
public void SetArrayDimensionMismatch1()
{
string filename = GetFilename("setarraydimensionmismatch1.h5");
Hdf5File file = Hdf5File.Create(filename);
List <Hdf5DimensionProperty> properties = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty property = new Hdf5DimensionProperty {
CurrentSize = 5
};
properties.Add(property);
Hdf5Dataset dataset = file.Datasets.Add("dataset1", Hdf5DataTypes.Int32, properties);
Assert.IsNotNull(dataset);
try
{
//2 dimensions sent, only one expected
Int32[,] value = { { 1, 2, 3, 4, 5 }, { 6, 7, 8, 9, 10 } };
dataset.SetData(value);
Assert.Fail("Exception was expected");
}
catch (Exception ex)
{
Assert.IsInstanceOf <Hdf5ArrayDimensionsMismatchException>(ex);
}
file.Close();
}
public void OpenDatasetInFile()
{
string filename = GetFilename("opendatasetinfile.h5");
Hdf5File file = Hdf5File.Create(filename);
List <Hdf5DimensionProperty> properties = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty property = new Hdf5DimensionProperty {
CurrentSize = 100
};
properties.Add(property);
Hdf5Dataset dataset = file.Datasets.Add("dataset1", Hdf5DataTypes.Int8, properties);
Assert.IsNotNull(dataset);
Assert.AreEqual(1, file.Datasets.Count);
file.Close();
file = new Hdf5File(filename);
dataset = file.Datasets[0];
Assert.IsNotNull(dataset);
Assert.AreEqual("dataset1", dataset.Name);
Assert.AreEqual(Hdf5DataTypes.Int8, dataset.DataType.Type);
file.Close();
}
public void SetDataMismatch()
{
string filename = GetFilename("setdatamismatch.h5");
Hdf5File file = Hdf5File.Create(filename);
List <Hdf5DimensionProperty> properties = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty property = new Hdf5DimensionProperty {
CurrentSize = 3
};
properties.Add(property);
Hdf5Dataset dataset = file.Datasets.Add("dataset1", Hdf5DataTypes.Int8, properties);
Assert.IsNotNull(dataset);
try
{
Int32[] value = { 1, 2, 3 };
dataset.SetData(value);
Assert.Fail("Exception was expected");
}
catch (Exception ex)
{
Assert.IsInstanceOf <Hdf5TypeMismatchException>(ex);
}
file.Close();
}
public void SetDataNull()
{
string filename = GetFilename("setdatatnull.h5");
Hdf5File file = Hdf5File.Create(filename);
List <Hdf5DimensionProperty> properties = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty property = new Hdf5DimensionProperty {
CurrentSize = 100
};
properties.Add(property);
Hdf5Dataset dataset = file.Datasets.Add("dataset1", Hdf5DataTypes.Int8, properties);
Assert.IsNotNull(dataset);
try
{
sbyte[] value = null;
dataset.SetData(value);
Assert.Fail("Exception was expected");
}
catch (Exception ex)
{
Assert.IsInstanceOf <ArgumentNullException>(ex);
}
file.Close();
}
public void CreateAttributeTwiceOnDataset()
{
string fileName = GetFilename("createattributetwiceondataset.h5");
Hdf5File file = Hdf5File.Create(fileName);
Hdf5Group group = file.Groups.Add("test");
List <Hdf5DimensionProperty> dimensionProps = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty prop = new Hdf5DimensionProperty {
CurrentSize = 1
};
dimensionProps.Add(prop);
Hdf5Dataset dataset = group.Datasets.Add("dataset1", Hdf5DataTypes.Int32, dimensionProps);
dataset.Attributes.Add("attribute1", "test");
try
{
dataset.Attributes.Add("attribute1", "test2");
Assert.Fail("Should have thrown an exception");
}
catch (Exception ex)
{
file.Close();
Assert.IsInstanceOf <Hdf5AttributeAlreadyExistException>(ex);
}
}
public void UpdateAttributeWithMismatchOnDataset()
{
string fileName = GetFilename("updateattributewithmistmachondataset.h5");
Hdf5File file = Hdf5File.Create(fileName);
Hdf5Group group = file.Groups.Add("group");
List <Hdf5DimensionProperty> dimensionProps = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty prop = new Hdf5DimensionProperty {
CurrentSize = 1
};
dimensionProps.Add(prop);
Hdf5Dataset dataset = group.Datasets.Add("dataset1", Hdf5DataTypes.Int32, dimensionProps);
Hdf5Attribute attribute = dataset.Attributes.Add("attribute1", "test");
try
{
attribute.Value = 5;
dataset.Attributes.Update(attribute);
Assert.Fail("Should have thrown an exception");
}
catch (Exception ex)
{
file.Close();
Assert.IsInstanceOf <Hdf5TypeMismatchException>(ex);
}
}
public static Hdf5Dataset CreateDataset(
Hdf5Identifier _fileId,
Hdf5Path _parentPath,
string _name,
Hdf5DataTypes _datatype,
int _numberOfDimensions,
List <Hdf5DimensionProperty> _properties)
{
Hdf5Path path = _parentPath.Append(_name);
UInt64[] dimensionSize = new UInt64[_numberOfDimensions];
UInt64[] maxSize = null; // new UInt64[_numberOfDimensions];
int i = 0;
foreach (var property in _properties)
{
dimensionSize[i] = property.CurrentSize;
//if (property.MaximumSize == UInt64.MaxValue)
//{
// maxSize[i] = H5S.UNLIMITED;
//}
//else
//{
// maxSize[i] = property.MaximumSize;
//}
i++;
}
Hdf5Identifier dataspaceId = H5S.create_simple(_numberOfDimensions, dimensionSize, maxSize).ToId();
//TODO handle string datasets
Hdf5Identifier typeId = H5T.copy(TypeHelper.GetNativeType(_datatype).Value).ToId();
var status = H5T.set_order(typeId.Value, H5T.order_t.LE);
Hdf5Identifier datasetId = H5D.create(_fileId.Value, path.FullPath, typeId.Value, dataspaceId.Value).ToId();
Hdf5Dataset dataset = null;
if (datasetId.Value > 0)
{
dataset = new Hdf5Dataset(_fileId, datasetId, path.FullPath)
{
DataType = TypeHelper.GetDataTypeFromDataset(datasetId),
Dataspace = DataspaceHelper.GetDataspace(datasetId)
};
H5D.close(datasetId.Value);
}
H5T.close(typeId.Value);
FileHelper.FlushToFile(_fileId);
return(dataset);
}
public void DeleteAttributeOnDataset()
{
string fileName = GetFilename("deleteattributeondataset.h5");
Hdf5File file = Hdf5File.Create(fileName);
Hdf5Group group = file.Groups.Add("group1");
List <Hdf5DimensionProperty> dimensionProps = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty prop = new Hdf5DimensionProperty {
CurrentSize = 1
};
dimensionProps.Add(prop);
Hdf5Dataset dataset = group.Datasets.Add("dataset1", Hdf5DataTypes.Int32, dimensionProps);
dataset.Attributes.Add("attribute1", "test");
dataset.Attributes.Add("attribute2", 5);
Assert.AreEqual(2, dataset.Attributes.Count);
file.Close();
file = new Hdf5File(fileName);
group = file.Groups[0];
dataset = group.Datasets[0];
var attibutes = dataset.Attributes;
Assert.AreEqual(2, attibutes.Count);
var attribute1 = attibutes[0];
Assert.AreEqual("attribute1", attribute1.Name);
Assert.AreEqual("test", attribute1.Value);
var attribute2 = attibutes[1];
Assert.AreEqual("attribute2", attribute2.Name);
Assert.AreEqual(5, attribute2.Value);
dataset.Attributes.Delete(attribute1);
Assert.AreEqual(1, attibutes.Count);
attribute2 = attibutes[0];
Assert.AreEqual("attribute2", attribute2.Name);
Assert.AreEqual(5, attribute2.Value);
file.Close();
file = new Hdf5File(fileName);
group = file.Groups[0];
dataset = group.Datasets[0];
attibutes = dataset.Attributes;
Assert.AreEqual(1, attibutes.Count);
attribute2 = attibutes[0];
Assert.AreEqual("attribute2", attribute2.Name);
Assert.AreEqual(5, attribute2.Value);
}
private static Array SingleDimension(Hdf5Identifier _datasetIdentifer, Hdf5Dataset _dataset)
{
if (_dataset.DataType.Type == Hdf5DataTypes.Int8)
{
return(Read1DArray <sbyte>(_datasetIdentifer, _dataset));
}
if (_dataset.DataType.Type == Hdf5DataTypes.Int16)
{
return(Read1DArray <Int16>(_datasetIdentifer, _dataset));
}
if (_dataset.DataType.Type == Hdf5DataTypes.Int32)
{
return(Read1DArray <Int32>(_datasetIdentifer, _dataset));
}
if (_dataset.DataType.Type == Hdf5DataTypes.Int64)
{
return(Read1DArray <Int64>(_datasetIdentifer, _dataset));
}
if (_dataset.DataType.Type == Hdf5DataTypes.UInt8)
{
return(Read1DArray <byte>(_datasetIdentifer, _dataset));
}
if (_dataset.DataType.Type == Hdf5DataTypes.UInt16)
{
return(Read1DArray <UInt16>(_datasetIdentifer, _dataset));
}
if (_dataset.DataType.Type == Hdf5DataTypes.UInt32)
{
return(Read1DArray <UInt32>(_datasetIdentifer, _dataset));
}
if (_dataset.DataType.Type == Hdf5DataTypes.UInt64)
{
return(Read1DArray <UInt64>(_datasetIdentifer, _dataset));
}
if (_dataset.DataType.Type == Hdf5DataTypes.Single)
{
return(Read1DArray <Single>(_datasetIdentifer, _dataset));
}
if (_dataset.DataType.Type == Hdf5DataTypes.Double)
{
return(Read1DArray <Double>(_datasetIdentifer, _dataset));
}
return(null);
}
/// <summary>
/// Assumes that dataset already open
/// </summary>
/// <param name="_fileId"></param>
/// <param name="_datasetId"></param>
/// <param name="_fullPath"></param>
/// <returns></returns>
public static Hdf5Dataset LoadDataset(Hdf5Identifier _fileId, Hdf5Identifier _datasetId, string _fullPath)
{
Hdf5DataType datatype = TypeHelper.GetDataTypeFromDataset(_datasetId);
Hdf5Dataspace dataspace = DataspaceHelper.GetDataspace(_datasetId);
Hdf5Dataset dataset = new Hdf5Dataset(_fileId, _datasetId, _fullPath)
{
Dataspace = dataspace,
DataType = datatype
};
return(dataset);
}
/// <summary>
/// Assumes dataset is already open
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="_datasetIdentifer"></param>
/// <param name="_dataset"></param>
/// <returns></returns>
public static T[] Read1DArray <T>(Hdf5Identifier _datasetIdentifer, Hdf5Dataset _dataset)
{
T[] dataArray = new T[_dataset.Dataspace.DimensionProperties[0].CurrentSize];
GCHandle arrayHandle = GCHandle.Alloc(dataArray, GCHandleType.Pinned);
var dataType = H5T.copy(_dataset.DataType.NativeType.Value).ToId();
int result = H5D.read(
_datasetIdentifer.Value,
dataType.Value,
H5S.ALL,
H5S.ALL,
H5P.DEFAULT,
arrayHandle.AddrOfPinnedObject());
arrayHandle.Free();
H5T.close(dataType.Value);
return(dataArray);
}
public void Set2DuInt64()
{
string filename = GetFilename("set2duint64.h5");
Hdf5File file = Hdf5File.Create(filename);
List <Hdf5DimensionProperty> properties = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty property1 = new Hdf5DimensionProperty {
CurrentSize = 2
};
properties.Add(property1);
Hdf5DimensionProperty property2 = new Hdf5DimensionProperty {
CurrentSize = 3
};
properties.Add(property2);
Hdf5Dataset dataset = file.Datasets.Add("dataset1", Hdf5DataTypes.UInt64, properties);
Assert.IsNotNull(dataset);
UInt64[,] value = { { UInt64.MinValue, 0, UInt64.MaxValue }, { UInt64.MaxValue, 0, UInt64.MinValue } };
dataset.SetData(value);
var array = dataset.GetData();
Assert.AreEqual(2, array.Rank);
Assert.AreEqual(2, array.GetLength(0));
Assert.AreEqual(3, array.GetLength(1));
Assert.AreEqual(UInt64.MinValue, array.GetValue(0, 0));
Assert.AreEqual(0, array.GetValue(0, 1));
Assert.AreEqual(UInt64.MaxValue, array.GetValue(0, 2));
Assert.AreEqual(UInt64.MaxValue, array.GetValue(1, 0));
Assert.AreEqual(0, array.GetValue(1, 1));
Assert.AreEqual(UInt64.MinValue, array.GetValue(1, 2));
file.Close();
}
public void CreateAttributeOnDataset()
{
string fileName = GetFilename("createattributeondataset.h5");
Hdf5File file = Hdf5File.Create(fileName);
Hdf5Group group = file.Groups.Add("group1");
List <Hdf5DimensionProperty> dimensionProps = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty prop = new Hdf5DimensionProperty {
CurrentSize = 1
};
dimensionProps.Add(prop);
Hdf5Dataset dataset = group.Datasets.Add("dataset1", Hdf5DataTypes.Int32, dimensionProps);
dataset.Attributes.Add("attribute1", "test");
dataset.Attributes.Add("attribute2", 5);
Assert.AreEqual(2, dataset.Attributes.Count);
file.Close();
}
public static void Write2DArray <T>(Hdf5Dataset _dataset, T[,] _array)
{
if (_dataset.Dataspace.NumberOfDimensions != 2)
{
throw new Hdf5ArrayDimensionsMismatchException();
}
if ((ulong)_array.GetLength(0) != _dataset.Dataspace.DimensionProperties[0].CurrentSize)
{
throw new Hdf5ArraySizeMismatchException();
}
if ((ulong)_array.GetLength(1) != _dataset.Dataspace.DimensionProperties[1].CurrentSize)
{
throw new Hdf5ArraySizeMismatchException();
}
var datasetId = H5O.open(_dataset.FileId.Value, _dataset.Path.FullPath).ToId();
GCHandle arrayHandle = GCHandle.Alloc(_array, GCHandleType.Pinned);
var typeId = H5T.copy(_dataset.DataType.NativeType.Value).ToId();
int result = H5D.write(
datasetId.Value,
typeId.Value,
H5S.ALL,
H5S.ALL,
H5P.DEFAULT,
arrayHandle.AddrOfPinnedObject());
arrayHandle.Free();
H5T.close(typeId.Value);
H5O.close(datasetId.Value);
FileHelper.FlushToFile(_dataset.FileId);
}
public void CreateDatasetInGroup()
{
string filename = GetFilename("createdatasetingroup.h5");
Hdf5File file = Hdf5File.Create(filename);
Hdf5Group group = file.Groups.Add("group1");
List <Hdf5DimensionProperty> properties = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty property = new Hdf5DimensionProperty {
CurrentSize = 100
};
properties.Add(property);
Hdf5Dataset dataset = group.Datasets.Add("dataset1", Hdf5DataTypes.Int8, properties);
Assert.IsNotNull(dataset);
Assert.AreEqual(0, file.Datasets.Count);
Assert.AreEqual(1, group.Datasets.Count);
file.Close();
}
public void Set2DArraySizeMismatch2()
{
string filename = GetFilename("set2darraysizemismatch2.h5");
Hdf5File file = Hdf5File.Create(filename);
List <Hdf5DimensionProperty> properties = new List <Hdf5DimensionProperty>();
Hdf5DimensionProperty property1 = new Hdf5DimensionProperty {
CurrentSize = 3
};
properties.Add(property1);
Hdf5DimensionProperty property2 = new Hdf5DimensionProperty {
CurrentSize = 5
};
properties.Add(property2);
Hdf5Dataset dataset = file.Datasets.Add("dataset1", Hdf5DataTypes.Int32, properties);
Assert.IsNotNull(dataset);
try
{
//Only 3x4
Int32[,] value = { { 1, 2, 3 }, { 4, 5, 6, }, { 7, 8, 9, }, { 10, 11, 12, } };
dataset.SetData(value);
Assert.Fail("Exception was expected");
}
catch (Exception ex)
{
Assert.IsInstanceOf <Hdf5ArraySizeMismatchException>(ex);
}
file.Close();
}
public static Hdf5Dataset CreateDatasetAddToDatasets(
ReadonlyNamedItemList <Hdf5Dataset> _datasets,
Hdf5Identifier _fileId,
Hdf5Path _parentPath,
string _name,
Hdf5DataTypes _datatype,
int _numberOfDimensions,
List <Hdf5DimensionProperty> _properties)
{
Hdf5Dataset dataset = CreateDataset(
_fileId,
_parentPath,
_name,
_datatype,
_numberOfDimensions,
_properties);
if (dataset != null)
{
_datasets.Add(dataset);
}
return(dataset);
}
public static Array GetData(Hdf5Dataset _dataset)
{
var id = H5O.open(_dataset.FileId.Value, _dataset.Path.FullPath).ToId();
if (id.Value > 0)
{
Array a = null;
if (_dataset.Dataspace.NumberOfDimensions == 1)
{
a = SingleDimension(id, _dataset);
}
else if (_dataset.Dataspace.NumberOfDimensions == 2)
{
a = TwoDimension(id, _dataset);
}
H5O.close(id.Value);
return(a);
}
return(null);
}
public static Hdf5Dataset CreateDataset(
Hdf5Identifier _fileId,
Hdf5Path _parentPath,
string _name,
Hdf5DataTypes _datatype,
int _numberOfDimensions,
List <Hdf5DimensionProperty> _properties,
Hdf5CompressionProperty _compressionProperty = null)
{
Hdf5Path path = _parentPath.Append(_name);
UInt64[] dimensionSize = new UInt64[_numberOfDimensions];
UInt64[] maxSize = null; // new UInt64[_numberOfDimensions];
if (_numberOfDimensions != _properties.Count ||
(_compressionProperty != null && _numberOfDimensions != _compressionProperty.ChunkDimensions.Length))
{
throw new Hdf5ArrayDimensionsMismatchException();
}
int i = 0;
foreach (var property in _properties)
{
dimensionSize[i] = property.CurrentSize;
if (_compressionProperty != null && _compressionProperty.ChunkDimensions[i] > property.CurrentSize)
{
throw new Hdf5ArraySizeMismatchException();
}
i++;
}
Hdf5Identifier dataspaceId = H5S.create_simple(_numberOfDimensions, dimensionSize, maxSize).ToId();
//TODO handle string datasets
Hdf5Identifier typeId = H5T.copy(TypeHelper.GetNativeType(_datatype).Value).ToId();
var status = H5T.set_order(typeId.Value, H5T.order_t.LE);
var plist_id = _compressionProperty != null?H5P.create(H5P.DATASET_CREATE) : 0;
if (plist_id != 0)
{
H5P.set_chunk(plist_id, _compressionProperty.ChunkDimensions.Length, _compressionProperty.ChunkDimensions);
H5P.set_deflate(plist_id, _compressionProperty.CompressionLevel);
}
Hdf5Identifier datasetId = H5D.create(_fileId.Value, path.FullPath, typeId.Value, dataspaceId.Value, dcpl_id: plist_id).ToId();
Hdf5Dataset dataset = null;
if (datasetId.Value > 0)
{
dataset = new Hdf5Dataset(_fileId, datasetId, path.FullPath)
{
DataType = TypeHelper.GetDataTypeFromDataset(datasetId),
Dataspace = DataspaceHelper.GetDataspace(datasetId)
};
H5D.close(datasetId.Value);
}
H5T.close(typeId.Value);
if (plist_id != 0)
{
H5P.close(plist_id);
}
FileHelper.FlushToFile(_fileId);
return(dataset);
}
