public void H5Aopen_by_idxTest1()
{
hid_t att = H5A.create(m_v2_test_file, "A", H5T.IEEE_F64LE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v2_test_file, "AA", H5T.IEEE_F64LE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.open_by_idx(m_v2_test_file, ".", H5.index_t.NAME,
H5.iter_order_t.NATIVE, 0);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.open_by_idx(m_v2_test_file, ".", H5.index_t.NAME,
H5.iter_order_t.NATIVE, 1);
Assert.IsTrue(att >= 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);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.open_by_idx(m_v0_test_file, ".", H5.index_t.NAME,
H5.iter_order_t.NATIVE, 0);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
}
public void H5Aget_info_by_idxTest1()
{
H5A.info_t info = new H5A.info_t();
hid_t att = H5A.create(m_v2_test_file, "A", H5T.IEEE_F64LE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v2_test_file, "B", H5T.IEEE_F64LE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
Assert.IsTrue(H5A.get_info_by_idx(m_v2_test_file, ".",
H5.index_t.NAME, H5.iter_order_t.NATIVE, 0,
ref info) >= 0);
Assert.IsTrue(H5A.get_info_by_idx(m_v2_test_file, ".",
H5.index_t.NAME, H5.iter_order_t.NATIVE, 1,
ref info) >= 0);
att = H5A.create(m_v0_test_file, "A", H5T.IEEE_F64LE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
Assert.IsTrue(H5A.get_info_by_idx(m_v0_test_file, ".",
H5.index_t.NAME, H5.iter_order_t.NATIVE, 0,
ref info) >= 0);
Assert.IsFalse(H5A.get_info_by_idx(m_v0_test_file, ".",
H5.index_t.NAME, H5.iter_order_t.NATIVE, 1,
ref info) >= 0);
}
public void H5Aget_info_by_nameTest1()
{
H5A.info_t info = new H5A.info_t();
hid_t att = H5A.create(m_v2_test_file, "A", H5T.IEEE_F64LE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v2_test_file, "B", H5T.IEEE_F64LE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
Assert.IsTrue(H5A.get_info_by_name(m_v2_test_file, ".", "A",
ref info) >= 0);
Assert.IsTrue(H5A.get_info_by_name(m_v2_test_file, ".", "B",
ref info) >= 0);
att = H5A.create(m_v0_test_file, "A", H5T.IEEE_F64LE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
Assert.IsTrue(H5A.get_info_by_name(m_v0_test_file, ".", "A",
ref info) >= 0);
Assert.IsFalse(H5A.get_info_by_name(m_v0_test_file, ".", "B",
ref info) >= 0);
}
public void H5AdeleteTest1()
{
hid_t att = H5A.create(m_v0_class_file, "DNA", H5T.IEEE_F32BE,
m_space_null);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v2_class_file, "DNA", H5T.IEEE_F32BE,
m_space_null);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v0_class_file, "DSA", H5T.IEEE_F32BE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v2_class_file, "DSA", H5T.IEEE_F32BE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
Assert.IsTrue(H5A.delete(m_v0_class_file, "DNA") >= 0);
Assert.IsTrue(H5A.delete(m_v0_class_file, "DSA") >= 0);
Assert.IsTrue(H5A.delete(m_v2_class_file, "DNA") >= 0);
Assert.IsTrue(H5A.delete(m_v2_class_file, "DSA") >= 0);
}
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 void H5AreadTest1()
{
double[] x = { Math.PI };
IntPtr buf = Marshal.AllocHGlobal(8);
hid_t att = H5A.create(m_v2_test_file, "A", H5T.IEEE_F64LE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.read(att, H5T.IEEE_F64BE, buf) >= 0);
Assert.IsTrue(H5A.read(att, H5T.NATIVE_DOUBLE, buf) >= 0);
Marshal.Copy(buf, x, 0, 1);
Assert.IsTrue(x[0] == 0.0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v0_test_file, "A", H5T.IEEE_F64LE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.read(att, H5T.IEEE_F64BE, buf) >= 0);
Assert.IsTrue(H5A.read(att, H5T.NATIVE_DOUBLE, buf) >= 0);
Marshal.Copy(buf, x, 0, 1);
Assert.IsTrue(x[0] == 0.0);
Assert.IsTrue(H5A.close(att) >= 0);
Marshal.FreeHGlobal(buf);
}
/// <summary>
///
/// </summary>
/// <param name="_objectId"></param>
/// <param name="_attribute"></param>
public static void UpdateAttribute(Hdf5Identifier _objectId, Hdf5Attribute _attribute)
{
Hdf5Identifier attributeId = H5A.open(_objectId.Value, _attribute.Name).ToId();
if (attributeId.Value > 0)
{
Hdf5DataType type = TypeHelper.GetDataTypeFromAttribute(attributeId);
Hdf5DataTypes enumType = TypeHelper.GetDataTypesEnum(_attribute.Value.GetType());
if (type.Type == enumType)
{
if (enumType == Hdf5DataTypes.String)
{
H5A.close(attributeId.Value);
DeleteAttribute(_objectId, _attribute.Name);
Hdf5Attribute attribute = CreateAttribute(_objectId, _attribute.Name, _attribute.Value);
if (attribute != null)
{
_attribute.Id = attribute.Id;
_attribute.Name = attribute.Name;
_attribute.Value = attribute.Value;
}
}
else
{
WriteObjectValue(type, attributeId, _attribute.Value);
}
}
else
{
throw new Hdf5TypeMismatchException();
}
}
}
public static T ReadEnumAttribute <T>(hid_t hid, string key) where T : struct, IConvertible
{
var attribute = H5A.open(hid, key);
if (attribute < 0)
{
throw new ArgumentException(string.Format("Attribute {0} not found.", key));
}
var type = H5A.get_type(attribute);
if (type < 0)
{
H5A.close(attribute);
throw new Exception("H5A.get_type failed.");
}
var size = H5T.get_size(type).ToInt32();
if (size == 0)
{
H5T.close(type);
H5A.close(attribute);
throw new Exception("H5T.get_size failed.");
}
var unmanagedBuffer = new UnmanagedBuffer(size);
H5A.read(attribute, type, unmanagedBuffer);
H5T.close(type);
H5A.close(attribute);
return(unmanagedBuffer.ReadEnum <T>());
}
private bool setOMXFileAttributes()
{
// write OMX attributes
H5DataSpaceId dspace;
H5DataTypeId dtype;
H5AttributeId attr;
// OMX version
dspace = H5S.create(H5S.H5SClass.SCALAR);
dtype = H5T.copy(H5T.H5Type.C_S1); // string datatype
H5T.setSize(dtype, dllVersion[0].Length);
attr = H5A.create(fileId, omxVersionName, dtype, dspace);
ASCIIEncoding ascii = new ASCIIEncoding();
H5A.write(attr, dtype, new H5Array <System.Byte>(ascii.GetBytes(dllVersion[0])));
H5A.close(attr);
// OMX shape - only 2D tables
dspace = H5S.create_simple(1, new long[] { 2 });
dtype = H5T.copy(H5T.H5Type.NATIVE_INT);
attr = H5A.create(fileId, omxShapeAttr, dtype, dspace);
int[] shape = new int[2];
shape[0] = (int)Shape[0];
shape[1] = (int)Shape[1];
H5A.write <int>(attr, dtype, new H5Array <int>(shape));
H5S.close(dspace);
H5A.close(attr);
return(true);
}
private bool getOMXFileAttributes()
{
string version = "unknown";
// OMX Version
H5AttributeId verId = H5A.open(fileId, omxVersionName);
H5T.H5TClass verCl = H5T.getClass(H5A.getType(verId));
if (verCl.Equals(H5T.H5TClass.STRING))
{
Byte[] buff = getAttribute <byte>(verId);
ASCIIEncoding enc = new ASCIIEncoding();
version = enc.GetString(buff);
}
else if (verCl.Equals(H5T.H5TClass.FLOAT))
{
float[] buff = getAttribute <float>(verId);
version = buff.ToString();
// produces garbage - bail out from here...
throw new NotImplementedException();
}
else
{
throw new NotImplementedException();
}
//Console.WriteLine("omx version: {0}", version);
this.OmxVersion = version;
H5A.close(verId);
// matrix shape
H5AttributeId shId = H5A.open(fileId, omxShapeAttr);
H5T.H5TClass shCl = H5T.getClass(H5A.getType(shId));
if (shCl.Equals(H5T.H5TClass.INTEGER))
{
int[] shape = getAttribute <int>(shId);
this.Shape[0] = (long)shape[0];
this.Shape[1] = (long)shape[1];
}
else if (shCl.Equals(H5T.H5TClass.FLOAT))
{
float[] shape = getAttribute <float>(shId);
this.Shape[0] = (long)shape[0];
this.Shape[1] = (long)shape[1];
// returns garbage, bail out from here
throw new NotImplementedException();
}
else
{
throw new NotImplementedException();
}
H5A.close(shId);
return(true);
}
private static void WriteAttribute(H5ObjectWithAttributes target, string name, string value)
{
if (string.IsNullOrEmpty(name))
{
throw new ArgumentException("Name must not be empty (or null)", "name");
}
if (string.IsNullOrEmpty(value))
{
throw new ArgumentException("Value must not be empty or null", "value");
}
H5DataTypeId dtype;
byte[] strdata = EncodeStringData(value, out dtype);
H5DataSpaceId spaceId = H5S.create(H5S.H5SClass.SCALAR);
H5AttributeId attributeId = H5A.create(target, name, dtype, spaceId);
H5A.write(attributeId, dtype, new H5Array <byte>(strdata));
H5A.close(attributeId);
H5T.close(dtype);
H5S.close(spaceId);
}
/// <summary>
/// Reads the data from the specified attribute.
/// </summary>
/// <typeparam name="T">The data type.</typeparam>
/// <param name="locationId">The location ID.</param>
/// <param name="attributeName">The name of the attribute.</param>
/// <returns>Returns a set of type T which represents the read data.</returns>
public static T[] ReadAttribute <T>(long locationId, string attributeName)
{
long attributeId = -1;
T[] result;
try
{
attributeId = H5A.open(locationId, attributeName);
if (H5I.is_valid(attributeId) <= 0)
{
throw new Exception(ErrorMessage.IOHelper_CouldNotOpenAttribute);
}
result = IOHelper.Read <T>(attributeId, DataContainerType.Attribute);
}
finally
{
if (H5I.is_valid(attributeId) > 0)
{
H5A.close(attributeId);
}
}
return(result);
}
public static int WritePrimitiveAttribute <T>(hid_t groupId, string name, Array attributes, string datasetName = null) //where T : struct
{
var tmpId = groupId;
if (!string.IsNullOrWhiteSpace(datasetName))
{
var datasetId = H5D.open(groupId, datasetName);
if (datasetId > 0)
{
groupId = datasetId;
}
}
int rank = attributes.Rank;
ulong[] dims = Enumerable.Range(0, rank).Select(i =>
{ return((ulong)attributes.GetLength(i)); }).ToArray();
ulong[] maxDims = null;
var spaceId = H5S.create_simple(rank, dims, maxDims);
var datatype = GetDatatype(typeof(T));
var typeId = H5T.copy(datatype);
var attributeId = H5A.create(groupId, name, datatype, spaceId);
GCHandle hnd = GCHandle.Alloc(attributes, GCHandleType.Pinned);
var result = H5A.write(attributeId, datatype, hnd.AddrOfPinnedObject());
hnd.Free();
H5A.close(attributeId);
H5S.close(spaceId);
H5T.close(typeId);
if (tmpId != groupId)
{
H5D.close(groupId);
}
return(result);
}
private static void WriteFile(string filePath)
{
var file = H5F.create(filePath, H5F.CreateMode.ACC_TRUNC);
var group = H5G.create(file, "/group");
H5G.close(group);
const int RANK = 2;
const int DIM0 = 3;
const int DIM1 = 4;
var dims = new long[RANK] {
DIM0, DIM1
};
var dataSpace = H5S.create_simple(RANK, dims);
var dataSet = H5D.create(file, "/group/dataset", H5T.H5Type.NATIVE_INT, dataSpace);
H5S.close(dataSpace);
var data = new int[DIM0, DIM1]
{
{ 1, 2, 3, 4 },
{ 5, 6, 7, 8 },
{ 9, 10, 11, 12 }
};
H5D.write(dataSet, new H5DataTypeId(H5T.H5Type.NATIVE_INT), new H5Array <int>(data));
var dataType = new H5DataTypeId(H5T.H5Type.NATIVE_INT);
dataSpace = H5S.create(H5S.H5SClass.SCALAR);
var integerAttribute = H5A.create(dataSet, "int", dataType, dataSpace);
H5A.write(integerAttribute, dataType, new H5Array <int>(new int[1] {
42
}));
H5A.close(integerAttribute);
H5S.close(dataSpace);
//H5T.close(dataType); // Read-only.
var str = "Hello, world!";
var strBytes = Encoding.ASCII.GetBytes(str);
// There is a H5T.get_cset, but there does not seem to be a way of setting the character encoding, i.e. set_cset.
dataType = H5T.copy(H5T.H5Type.C_S1);
H5T.setSize(dataType, strBytes.Length);
dataSpace = H5S.create(H5S.H5SClass.SCALAR);
var stringAttribute = H5A.create(dataSet, "string", dataType, dataSpace);
H5A.write(stringAttribute, dataType, new H5Array <byte>(strBytes));
H5A.close(stringAttribute);
H5S.close(dataSpace);
H5T.close(dataType);
H5D.close(dataSet);
H5F.close(file);
}
public static (int success, hid_t CreatedgroupId) WriteStringAttributes(hid_t groupId, string name, IEnumerable <string> strs, string datasetName = null)
{
hid_t tmpId = groupId;
if (!string.IsNullOrWhiteSpace(datasetName))
{
hid_t datasetId = H5D.open(groupId, datasetName);
if (datasetId > 0)
{
groupId = datasetId;
}
}
// create UTF-8 encoded attributes
hid_t datatype = H5T.create(H5T.class_t.STRING, H5T.VARIABLE);
H5T.set_cset(datatype, H5T.cset_t.UTF8);
H5T.set_strpad(datatype, H5T.str_t.SPACEPAD);
int strSz = strs.Count();
hid_t spaceId = H5S.create_simple(1,
new ulong[] { (ulong)strSz }, null);
var attributeId = H5A.create(groupId, name, datatype, spaceId);
GCHandle[] hnds = new GCHandle[strSz];
IntPtr[] wdata = new IntPtr[strSz];
int cntr = 0;
foreach (string str in strs)
{
hnds[cntr] = GCHandle.Alloc(
Encoding.UTF8.GetBytes(str),
GCHandleType.Pinned);
wdata[cntr] = hnds[cntr].AddrOfPinnedObject();
cntr++;
}
var hnd = GCHandle.Alloc(wdata, GCHandleType.Pinned);
var result = H5A.write(attributeId, datatype, hnd.AddrOfPinnedObject());
hnd.Free();
for (int i = 0; i < strSz; ++i)
{
hnds[i].Free();
}
H5A.close(attributeId);
H5S.close(spaceId);
H5T.close(datatype);
if (tmpId != groupId)
{
H5D.close(groupId);
}
return(result, attributeId);
}
public override void Dispose()
{
base.Dispose();
if (ID > 0)
{
ID = H5A.close(ID);
}
}
public static bool WriteStringAttribute(hid_t hid, string key, string value, bool utf8 = true, bool variable = true)
{
if (H5A.exists(hid, key) == 0)
{
// Attribute doesn't exist.
return(variable ? CreateOrOverwriteVariableStringAttribute(hid, key, new string[] { value }, utf8)
: CreateOrOverwriteFixedStringAttribute(hid, key, value, utf8));
}
else
{
var attribute = H5A.open(hid, key);
if (attribute < 0)
{
return(false);
}
var type = H5A.get_type(attribute);
if (type < 0)
{
H5A.close(attribute);
return(false);
}
var typeClass = H5T.get_class(type);
if (typeClass == H5T.class_t.NO_CLASS)
{
H5T.close(type);
H5T.close(attribute);
return(false);
}
if (typeClass != H5T.class_t.STRING)
{
H5T.close(type);
H5T.close(attribute);
throw new ArgumentException("H5T.get_class(type) != H5T.class_t.STRING");
}
utf8 = H5T.get_cset(type) == H5T.cset_t.UTF8;
bool ok;
if (H5T.is_variable_str(type) > 0)
{
ok = CreateOrOverwriteVariableStringAttribute(hid, key, new string[] { value }, utf8);
}
else
{
ok = CreateOrOverwriteFixedStringAttribute(hid, key, value, utf8);
}
H5T.close(type);
H5T.close(attribute);
return(ok);
}
}
public static bool WriteScalarNumericAttribute <T>(hid_t hid, string key, T value, hid_t type) where T : struct
{
if (key == null)
{
throw new ArgumentNullException("key");
}
var exists = H5A.exists(hid, key);
if (exists < 0)
{
throw new Exception("H5A.exists failed");
}
if (exists == 0)
{
var space = H5S.create(H5S.class_t.SCALAR);
if (space < 0)
{
throw new Exception("Failed to create scalar space");
}
var attribute = H5A.create(hid, key, type, space);
if (attribute < 0)
{
H5S.close(space);
throw new Exception(string.Format("Failed to create attribute \"{0}\"", key));
}
H5S.close(space);
object boxedValue = value;
H5A.write(attribute, type, new PinnedObject(boxedValue));
H5A.close(attribute);
return(true);
}
else
{
var attribute = H5A.open(hid, key);
if (attribute < 0)
{
throw new Exception(string.Format("Failed to open attribute \"{0}\"", key));
}
try
{
return(WriteScalarNumericAttribute(attribute, value, type));
}
finally
{
H5A.close(attribute);
}
}
}
public static bool WriteFixedStringAttribute(hid_t hid, string key, string value, bool utf8)
{
var exists = H5A.exists(hid, key);
if (exists < 0)
{
throw new Exception("H5A.exists failed");
}
if (exists == 0) // Attribute doesn't exist
{
var bytes = value.ToBytes(utf8);
var type = CreateFixedStringType(bytes, utf8);
var space = H5S.create(H5S.class_t.SCALAR);
if (space < 0)
{
H5T.close(type);
throw new Exception("Failed to create scalar space");
}
var attribute = H5A.create(hid, key, type, space);
if (attribute < 0)
{
H5S.close(space);
H5T.close(type);
throw new Exception(string.Format("Failed to create attribute \"{0}\"", key));
}
H5A.write(attribute, type, new PinnedObject(bytes));
H5A.close(attribute);
H5S.close(space);
H5T.close(type);
return(true);
}
else
{
var attribute = H5A.open(hid, key);
if (attribute < 0)
{
throw new Exception(string.Format("Failed to open attribute \"{0}\"", key));
}
try
{
return(WriteFixedStringAttribute(attribute, value, utf8));
}
finally
{
H5A.close(attribute);
}
}
}
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);
}
}
}));
}
}
// Generate string attribute
// GroupName: target group for the new attribute
// AttName: attribute name
// AttContent: content for the attribute, has to be a string
public static void StringAttributeGenerator(H5GroupId GroupName, string AttName, string AttContent)
{
char[] AttContentChar = AttContent.ToCharArray();
byte[] asciiStr = ASCIIEncoding.ASCII.GetBytes(AttContentChar);
int length = asciiStr.Length;
H5AttributeId attributeId = H5A.create(GroupName, AttName, H5T.create(H5T.CreateClass.STRING, length), H5S.create(H5S.H5SClass.SCALAR));
H5A.write(attributeId, H5T.create(H5T.CreateClass.STRING, length), new H5Array <byte>(asciiStr));
H5A.close(attributeId);
}
public void H5AiterateTest1()
{
hid_t att = H5A.create(m_v2_test_file, "IEEE_F32BE",
H5T.IEEE_F32BE, m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v2_test_file, "IEEE_F64BE", H5T.IEEE_F64BE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v2_test_file, "NATIVE_B8", H5T.NATIVE_B8,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
ArrayList al = new ArrayList();
GCHandle hnd = GCHandle.Alloc(al);
IntPtr op_data = (IntPtr)hnd;
hsize_t n = 0;
// the callback is defined in H5ATest.cs
H5A.operator_t cb = DelegateMethod;
Assert.IsTrue(H5A.iterate(m_v2_test_file, H5.index_t.NAME,
H5.iter_order_t.NATIVE, ref n, cb, op_data) >= 0);
// we should have 3 elements in the array list
Assert.IsTrue(al.Count == 3);
att = H5A.create(m_v0_test_file, "IEEE_F32BE",
H5T.IEEE_F32BE, m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v0_test_file, "IEEE_F64BE", H5T.IEEE_F64BE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v0_test_file, "NATIVE_B8", H5T.NATIVE_B8,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
al.Clear();
n = 0;
Assert.IsTrue(H5A.iterate(m_v0_test_file, H5.index_t.NAME,
H5.iter_order_t.NATIVE, ref n, cb, op_data) >= 0);
// we should have 3 elements in the array list
Assert.IsTrue(al.Count == 3);
hnd.Free();
}
// Generate double attributes
// GroupName: target group for the new attribute
// AttName: attribute name
// AttContent: content for the attribute, has to be a single floating number, here 64bit double is used, to generate subgroups in Data
public static void DoubleAttributeGenerator(H5GroupId GroupName, string AttName, double AttContent)
{
double[] AttArray = new double[1] {
AttContent
};
long[] dims = new long[1];
dims[0] = AttArray.Length;
H5AttributeId attributeId = H5A.create(GroupName, AttName, H5T.copy(H5T.H5Type.NATIVE_DOUBLE), H5S.create_simple(1, dims));
H5A.write(attributeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT), new H5Array <double>(AttArray));
H5A.close(attributeId);
}
// Generate floating number attributes
// GroupName: target group for the new attribute
// AttName: attribute name
// AttContent: content for the attribute, has to be a single floating number, here 32bit floating number is used, consider using 64bit double if necessary
public static void NumberAttributeGenerator(H5GroupId GroupName, string AttName, float AttContent)
{
float[] AttArray = new float[1] {
AttContent
};
long[] dims = new long[1];
dims[0] = AttArray.Length;
H5AttributeId attributeId = H5A.create(GroupName, AttName, H5T.copy(H5T.H5Type.NATIVE_FLOAT), H5S.create_simple(1, dims));
H5A.write(attributeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT), new H5Array <float>(AttArray));
H5A.close(attributeId);
}
static void test_attr_plist()
{
try
{
Console.Write("Testing attribute property lists");
hssize_t[] dims = { 256, 512 };
const string PLST_FILE_NAME = ("tattr_plist.h5");
hssize_t[] dims1 = { SPACE1_DIM1, SPACE1_DIM2, SPACE1_DIM3 };
hssize_t[] dims2 = { ATTR1_DIM };
// Create file.
H5FileId fileId = H5F.create(PLST_FILE_NAME, H5F.CreateMode.ACC_TRUNC);
// Create dataspace for dataset.
H5DataSpaceId space1_Id = H5S.create_simple(SPACE1_RANK, dims1);
// Create a dataset.
H5DataSetId dsetId = H5D.create(fileId, DSET1_NAME, H5T.H5Type.NATIVE_UCHAR, space1_Id);
// Create dataspace for attribute.
H5DataSpaceId space2_Id = H5S.create_simple(ATTR1_RANK, dims2);
// Create default property list for attribute.
H5PropertyListId plist
= H5P.create(H5P.PropertyListClass.ATTRIBUTE_CREATE);
// Create an attribute for the dataset using the property list.
H5AttributeId attrId = H5A.create(dsetId, ATTR1_NAME, new H5DataTypeId(H5T.H5Type.NATIVE_INT), space2_Id, plist);
// Close all objects.
H5S.close(space1_Id);
H5S.close(space2_Id);
H5P.close(plist);
H5A.close(attrId);
H5D.close(dsetId);
H5F.close(fileId);
Console.WriteLine("\t\t\tPASSED");
}
catch (HDFException anyHDF5E)
{
Console.WriteLine(anyHDF5E.Message);
nerrors++;
}
catch (System.Exception sysE)
{
Console.WriteLine(sysE.TargetSite);
Console.WriteLine(sysE.Message);
nerrors++;
}
} // test_attr_plist
static void ReadFile(string filePath)
{
var file = H5F.open(filePath, H5F.ACC_RDONLY);
var dataSet = H5D.open(file, "/group/dataset");
var dataSpace = H5D.get_space(dataSet);
var rank = H5S.get_simple_extent_ndims(dataSpace);
if (rank == 2)
{
var dims = new ulong[2];
H5S.get_simple_extent_dims(dataSpace, dims, null);
var data = new int[dims[0], dims[1]];
H5D.read(dataSet, H5T.NATIVE_INT, H5S.ALL, H5S.ALL, H5P.DEFAULT, new PinnedObject(data));
for (int i = 0; i < data.GetLength(0); ++i)
{
for (int j = 0; j < data.GetLength(1); ++j)
{
Write($"{data[i,j],3}");
}
WriteLine();
}
}
H5S.close(dataSpace);
var doubleAttribute = H5A.open(dataSet, "double");
#if false
double pi = 0.0;
var handle = GCHandle.Alloc(pi, GCHandleType.Pinned);
H5A.read(doubleAttribute, H5T.NATIVE_DOUBLE, handle.AddrOfPinnedObject());
handle.Free();
WriteLine($"PI = {pi}");
#else
var values = new double[1];
H5A.read(doubleAttribute, H5T.NATIVE_DOUBLE, new PinnedObject(values));
WriteLine($"PI = {values[0]}");
#endif
H5A.close(doubleAttribute);
WriteLine($"string: {ReadStringAttribute(dataSet, "string")}");
WriteLine($"string-ascii: {ReadStringAttribute(dataSet, "string-ascii")}");
WriteLine($"string-vlen: {ReadStringAttribute(dataSet, "string-vlen")}");
H5D.close(dataSet);
H5F.close(file);
}
private void AttributeCreateProcedure()
{
string name = Thread.CurrentThread.Name;
hid_t space = H5S.create(H5S.class_t.NULL);
Assert.IsTrue(space >= 0);
Assert.IsTrue(
H5A.close(H5A.create(m_shared_file_id, name, H5T.STD_I32BE,
space)) >= 0);
Assert.IsTrue(H5S.close(space) >= 0);
}
private static void WriteAttribute(H5ObjectWithAttributes target, string name, long value)
{
H5DataTypeId dtype = H5T.copy(H5T.H5Type.NATIVE_LLONG);
H5DataSpaceId spaceId = H5S.create(H5S.H5SClass.SCALAR);
H5AttributeId attributeId = H5A.create(target, name, dtype, spaceId);
H5A.write(attributeId, dtype, new H5Array <long>(new[] { value }));
H5A.close(attributeId);
H5T.close(dtype);
H5S.close(spaceId);
}
public static unsafe void Add(ContainerType container, long fileId, string groupName, string elementName, long typeId, void *dataPtr, long spaceId, long cpl = 0, long apl = 0)
{
long res;
long groupId;
if (H5L.exists(fileId, groupName) > 0)
{
groupId = H5G.open(fileId, groupName);
}
else
{
groupId = H5G.create(fileId, groupName);
}
long id;
if (container == ContainerType.Dataset)
{
id = H5D.create(groupId, Encoding.UTF8.GetBytes(elementName), typeId, spaceId, dcpl_id: cpl, dapl_id: apl);
if (id == -1)
{
throw new Exception("Could not create dataset.");
}
if ((int)dataPtr != 0)
{
res = H5D.write(id, typeId, spaceId, H5S.ALL, 0, new IntPtr(dataPtr));
}
res = H5D.close(id);
}
else
{
id = H5A.create(groupId, Encoding.UTF8.GetBytes(elementName), typeId, spaceId, acpl_id: cpl);
if (id == -1)
{
throw new Exception("Could not create attribute.");
}
if ((int)dataPtr != 0)
{
res = H5A.write(id, typeId, new IntPtr(dataPtr));
}
res = H5A.close(id);
}
res = H5G.close(groupId);
}
private static void WriteAttribute(H5ObjectWithAttributes target, string name, double[] value)
{
H5DataTypeId dtype = H5T.copy(H5T.H5Type.NATIVE_DOUBLE);
H5DataSpaceId spaceId = H5S.create_simple(1, new[] { value.LongCount() });
H5AttributeId attributeId = H5A.create(target, name, dtype, spaceId);
H5A.write(attributeId, dtype, new H5Array <double>(value));
H5A.close(attributeId);
H5T.close(dtype);
H5S.close(spaceId);
}
