public static double[][] ReadMesh(string fileName)
{
double[][] meshes = new double[3][];
string[] meshNames = { "x", "y", "z" };
H5FileId fileId = H5F.open(fileName, H5F.OpenMode.ACC_RDONLY);
for (int i = 0; i < meshNames.Length; i++)
{
H5DataSetId dsId = H5D.open(fileId, "/Mesh/" + meshNames[i]);
H5DataTypeId dtId = H5D.getType(dsId);
if (!H5T.equal(dtId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
}
float[] mesh = new float[H5D.getStorageSize(dsId) / H5T.getSize(dtId)];
H5D.read(dsId, dtId, new H5Array <float>(mesh));
meshes[i] = mesh.Select(x => (double)x * 1000.0).ToArray(); // m -> mm
H5D.close(dsId);
H5T.close(dtId);
}
H5F.close(fileId);
return(meshes);
}
public static double ReadAttribute(string file, string dataSetOrGroup, string attribute)
{
double attr = Double.NaN;
try
{
H5FileId fileId = H5F.open(file, H5F.OpenMode.ACC_RDONLY);
H5ObjectInfo objectInfo = H5O.getInfoByName(fileId, dataSetOrGroup);
H5GroupId groupId = null;
H5DataSetId dataSetId = null;
H5AttributeId attrId;
if (objectInfo.objectType == H5ObjectType.GROUP)
{
groupId = H5G.open(fileId, dataSetOrGroup);
attrId = H5A.open(groupId, attribute);
}
else
{
dataSetId = H5D.open(fileId, dataSetOrGroup);
attrId = H5A.open(dataSetId, attribute);
}
H5DataTypeId attrTypeId = H5A.getType(attrId);
double[] dAttrs = new double[] { };
if (H5T.equal(attrTypeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
float[] fAttrs = new float[H5S.getSimpleExtentNPoints(H5A.getSpace(attrId))];
H5A.read(attrId, attrTypeId, new H5Array <float>(fAttrs));
dAttrs = (from f in fAttrs select(double) f).ToArray();
}
else if (H5T.equal(attrTypeId, H5T.copy(H5T.H5Type.NATIVE_DOUBLE)))
{
dAttrs = new double[H5S.getSimpleExtentNPoints(H5A.getSpace(attrId))];
H5A.read(attrId, attrTypeId, new H5Array <double>(dAttrs));
}
H5T.close(attrTypeId);
H5A.close(attrId);
if (groupId != null)
{
H5G.close(groupId);
}
if (dataSetId != null)
{
H5D.close(dataSetId);
}
H5F.close(fileId);
return((double)dAttrs[0]);
}
catch (HDFException e)
{
Console.WriteLine("Error: Unhandled HDF5 exception");
Console.WriteLine(e.Message);
}
return(attr);
}
public static double[, ,] ReadFieldData3D(string fileName)
{
H5FileId fileId = H5F.open(fileName, H5F.OpenMode.ACC_RDONLY);
H5DataSetId fDataSetId = H5D.open(fileId, "/FieldData/FD/f0");
H5DataTypeId fDataTypeId = H5D.getType(fDataSetId);
if (!H5T.equal(fDataTypeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
}
long[] dims = H5S.getSimpleExtentDims(H5D.getSpace(fDataSetId)).ToArray();
if (dims.Length != 3)
{
Console.WriteLine("Error: Invalid field data dimensions");
}
float[, ,] data = new float[dims[0], dims[1], dims[2]];
H5D.read(fDataSetId, fDataTypeId, new H5Array <float>(data));
// Reorder
double[, ,] fieldValues = new double[dims[2], dims[1], dims[0]];
for (int i = 0; i < dims[0]; i++)
{
for (int j = 0; j < dims[1]; j++)
{
for (int k = 0; k < dims[2]; k++)
{
fieldValues[k, j, i] = data[i, j, k];
}
}
}
return(fieldValues);
}
public void H5Dget_typeTest1()
{
hsize_t[] dims = { 1024, 2048 };
hid_t space = H5S.create_simple(3, dims, null);
hid_t dset = H5D.create(m_v0_test_file, "dset", H5T.STD_I16LE,
space);
Assert.IsTrue(dset >= 0);
hid_t type = H5D.get_type(dset);
Assert.IsTrue(type >= 0);
Assert.IsTrue(H5T.equal(type, H5T.STD_I16LE) > 0);
Assert.IsTrue(H5T.close(type) >= 0);
Assert.IsTrue(H5D.close(dset) >= 0);
dset = H5D.create(m_v2_test_file, "dset", H5T.STD_I16LE,
space);
Assert.IsTrue(dset >= 0);
type = H5D.get_type(dset);
Assert.IsTrue(type >= 0);
Assert.IsTrue(H5T.equal(type, H5T.STD_I16LE) > 0);
Assert.IsTrue(H5T.close(type) >= 0);
Assert.IsTrue(H5D.close(dset) >= 0);
Assert.IsTrue(H5S.close(space) >= 0);
}
public object this[string key]
{
get
{
return(Host.With <object>((objId) =>
{
long attrId = 0;
long dtypeId = 0;
try
{
attrId = H5A.open(objId, key);
if (attrId < 0)
{
throw new ArgumentException($"Unknown Attribute: {key}", nameof(key));
}
dtypeId = H5A.get_type(attrId);
int size = H5T.get_size(dtypeId).ToInt32();
IntPtr iPtr = Marshal.AllocHGlobal(size);
int result = H5A.read(attrId, dtypeId, iPtr);
if (result < 0)
{
throw new IOException("Failed to read attribute");
}
if (H5T.equal(dtypeId, H5T.NATIVE_INT64) > 0)
{
var dest = new long[1];
Marshal.Copy(iPtr, dest, 0, 1);
Marshal.FreeHGlobal(iPtr);
return dest[0];
}
else // Must be a string...
{
var dest = new byte[size];
Marshal.Copy(iPtr, dest, 0, size);
Marshal.FreeHGlobal(iPtr);
return Encoding.ASCII.GetString(dest).TrimEnd((Char)0);
}
// return null;
}
finally
{
if (attrId > 0)
{
H5A.close(attrId);
}
if (dtypeId > 0)
{
H5T.close(dtypeId);
}
}
}));
}
}
public static (long DatasetId, bool IsNew) OpenOrCreateDataset(long locationId, string datasetPath, long datasetTypeId, Func <long> createDatasetCallback)
{
Contract.Requires(createDatasetCallback != null);
long datasetId = -1;
long datasetTypeId_actual = -1;
bool isNew;
try
{
if (IOHelper.CheckLinkExists(locationId, datasetPath))
{
datasetId = H5D.open(locationId, datasetPath);
datasetTypeId_actual = H5D.get_type(datasetId);
if (H5T.equal(datasetTypeId_actual, datasetTypeId) <= 0)
{
throw new Exception($"{ ErrorMessage.IOHelper_DataTypeMismatch } Dataset: '{ datasetPath }'.");
}
isNew = false;
}
else
{
datasetId = createDatasetCallback.Invoke();
isNew = true;
}
if (H5I.is_valid(datasetId) <= 0)
{
throw new Exception($"{ ErrorMessage.IOHelper_CouldNotOpenOrCreateDataset } Dataset: '{ datasetPath }'.");
}
}
finally
{
if (H5I.is_valid(datasetTypeId_actual) > 0)
{
H5T.close(datasetTypeId_actual);
}
}
return(datasetId, isNew);
}
public static (long AttributeId, bool IsNew) OpenOrCreateAttribute(long locationId, string name, long attributeTypeId, Func <long> createAttributeCallback)
{
long attributeId = -1;
long attributeTypeId_actual = -1;
bool isNew;
try
{
if (H5A.exists(locationId, name) > 0)
{
attributeId = H5A.open(locationId, name);
attributeTypeId_actual = H5A.get_type(attributeId);
if (H5T.equal(attributeTypeId_actual, attributeTypeId) <= 0)
{
throw new Exception($"{ ErrorMessage.IOHelper_DataTypeMismatch } Attribute: '{ name }'.");
}
isNew = false;
}
else
{
attributeId = createAttributeCallback.Invoke();
isNew = true;
}
if (H5I.is_valid(attributeId) <= 0)
{
throw new Exception($"{ ErrorMessage.IOHelper_CouldNotOpenOrCreateAttribute } Attribute: '{ name }'.");
}
}
finally
{
if (H5I.is_valid(attributeTypeId_actual) > 0)
{
H5T.close(attributeTypeId_actual);
}
}
return(attributeId, isNew);
}
public void H5Aget_typeTest1()
{
hid_t att = H5A.create(m_v2_test_file, "A", H5T.IEEE_F64LE,
m_space_scalar);
Assert.IsTrue(att >= 0);
hid_t type = H5A.get_type(att);
Assert.IsTrue(type >= 0);
Assert.IsTrue(H5T.equal(type, H5T.IEEE_F64LE) > 0);
Assert.IsTrue(H5T.close(type) >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v0_test_file, "A", H5T.IEEE_F64LE,
m_space_scalar);
Assert.IsTrue(att >= 0);
type = H5A.get_type(att);
Assert.IsTrue(type >= 0);
Assert.IsTrue(H5T.equal(type, H5T.IEEE_F64LE) > 0);
Assert.IsTrue(H5T.close(type) >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
}
private void ReadHDF5Mesh()
{
double[][] meshes = new double[3][];
string[] meshNames = { "phi", "r", "theta" };
H5FileId fileId = H5F.open(m_resultFile, H5F.OpenMode.ACC_RDONLY);
if (HDF5.ReadAttribute(m_resultFile, "/Mesh", "MeshType") != 2)
{
Console.WriteLine("Error: Invalid NF2FF mesh type in <{0}>", m_resultFile);
return;
}
for (int i = 0; i < meshNames.Length; i++)
{
H5DataSetId dsId = H5D.open(fileId, "/Mesh/" + meshNames[i]);
H5DataTypeId dtId = H5D.getType(dsId);
if (!H5T.equal(dtId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
}
float[] mesh = new float[H5D.getStorageSize(dsId) / H5T.getSize(dtId)];
H5D.read(dsId, dtId, new H5Array <float>(mesh));
meshes[i] = mesh.Select(x => (double)x).ToArray();
H5D.close(dsId);
H5T.close(dtId);
}
H5F.close(fileId);
m_theta = meshes[2];
m_phi = meshes[0];
}
public static Type GetTypeFromHdfTypeId(long typeId)
{
long typeId_reference = -1;
Type type = null;
type = null;
if (H5T.equal(typeId, H5T.NATIVE_UINT8) > 0)
{
type = typeof(Byte);
}
else if (H5T.equal(typeId, H5T.NATIVE_INT8) > 0)
{
type = typeof(SByte);
}
else if (H5T.equal(typeId, H5T.NATIVE_UINT16) > 0)
{
type = typeof(UInt16);
}
else if (H5T.equal(typeId, H5T.NATIVE_INT16) > 0)
{
type = typeof(Int16);
}
else if (H5T.equal(typeId, H5T.NATIVE_UINT32) > 0)
{
type = typeof(UInt32);
}
else if (H5T.equal(typeId, H5T.NATIVE_INT32) > 0)
{
type = typeof(Int32);
}
else if (H5T.equal(typeId, H5T.NATIVE_UINT64) > 0)
{
type = typeof(UInt64);
}
else if (H5T.equal(typeId, H5T.NATIVE_INT64) > 0)
{
type = typeof(Int64);
}
else if (H5T.equal(typeId, H5T.NATIVE_FLOAT) > 0)
{
type = typeof(Single);
}
else if (H5T.equal(typeId, H5T.NATIVE_DOUBLE) > 0)
{
type = typeof(Double);
}
else if (H5T.equal(typeId, typeId_reference = TypeConversionHelper.GetHdfTypeIdFromType(typeof(string))) > 0)
{
type = typeof(string);
}
else if (H5T.equal(typeId, typeId_reference = TypeConversionHelper.GetHdfTypeIdFromType(typeof(hdf_aggregate_function_t))) > 0)
{
type = typeof(hdf_aggregate_function_t);
}
else if (H5T.equal(typeId, typeId_reference = TypeConversionHelper.GetHdfTypeIdFromType(typeof(hdf_tag_t))) > 0)
{
type = typeof(hdf_tag_t);
}
else if (H5T.equal(typeId, typeId_reference = TypeConversionHelper.GetHdfTypeIdFromType(typeof(hdf_transfer_function_t))) > 0)
{
type = typeof(hdf_transfer_function_t);
}
if (H5I.is_valid(typeId_reference) > 0)
{
H5T.close(typeId_reference);
}
if (type == null)
{
throw new NotSupportedException();
}
return(type);
}
