public static Dictionary <uint, string> GetLabelWorkingSet(long group_id)
{
Dictionary <uint, string> labelWorkingSet = new Dictionary <uint, string>();
H5A.operator_t callBackMethod = DelegateMethod;
ArrayList attrNameArray = new ArrayList();
GCHandle nameArrayAlloc = GCHandle.Alloc(attrNameArray);
IntPtr ptrOnAllocArray = (IntPtr)nameArrayAlloc;
int status;
ulong beginAt = 0;
status = H5A.iterate(group_id, H5.index_t.CRT_ORDER, H5.iter_order_t.INC, ref beginAt, callBackMethod, ptrOnAllocArray);
for (int i = 0; i < attrNameArray.Count; i++)
{
string attr_name = Convert.ToString(attrNameArray[i]);
long attr_id = H5A.open(group_id, attr_name);
uint[] attr_value = { 0 };
GCHandle valueAlloc = GCHandle.Alloc(attr_value, GCHandleType.Pinned);
status = H5A.read(attr_id, H5T.NATIVE_UINT32, valueAlloc.AddrOfPinnedObject());
status = H5A.close(attr_id);
labelWorkingSet.Add(attr_value[0], attr_name);
}
status = H5G.close(group_id);
return(labelWorkingSet);
}
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 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>());
}
public static string GetAttributeValue(H5ObjectWithAttributes objectWithAttributes, string name)
{
if (objectWithAttributes is null)
{
throw new ArgumentNullException(nameof(objectWithAttributes));
}
if (name is null)
{
throw new ArgumentNullException(nameof(name));
}
H5AttributeId h5AttributeId = H5A.open(objectWithAttributes, name);
H5DataTypeId h5DataTypeId = H5A.getType(h5AttributeId);
if (H5T.isVariableString(h5DataTypeId))
{
VariableLengthString[] variableLengthStrings = new VariableLengthString[1];
H5A.read(h5AttributeId, h5DataTypeId, new H5Array <VariableLengthString> (variableLengthStrings));
H5T.close(h5DataTypeId);
H5A.close(h5AttributeId);
return(variableLengthStrings[0].ToString());
}
byte[] bytes = new byte[H5T.getSize(h5DataTypeId)];
H5A.read(h5AttributeId, h5DataTypeId, new H5Array <byte> (bytes));
H5T.close(h5DataTypeId);
H5A.close(h5AttributeId);
return(Encoding.ASCII.GetString(bytes));
}
public static string AttributeAsString(H5AttributeId _attributeId)
{
H5DataTypeId dataTypeId = H5A.getType(_attributeId);
bool isVariableLength = H5T.isVariableString(dataTypeId);
if (isVariableLength)
{
// Variable length string attribute
// NOTE: This section only works if the array length is 1
VariableLengthString[] value = new VariableLengthString[1];
H5A.read <VariableLengthString>(_attributeId, dataTypeId,
new H5Array <VariableLengthString>(value));
return(value[0].ToString());
}
else
{
// Make length smaller so null termination character is not read
int length = (int)H5T.getSize(dataTypeId) - 1;
// Fixed length string attribute
byte[] valueBytes = new byte[length];
H5A.read <byte>(_attributeId, dataTypeId, new H5Array <byte>(valueBytes));
string value = System.Text.ASCIIEncoding.ASCII.GetString(valueBytes);
return(value);
}
}
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);
}
public static int AttributeAsInt32(H5AttributeId _attributeId)
{
H5DataTypeId attributeType = H5T.copy(H5T.H5Type.NATIVE_INT);
int[] value = new int[1];
H5A.read <int>(_attributeId, attributeType, new H5Array <int>(value));
return(value[0]);
}
public void H5AreadTest2()
{
Assert.IsFalse(
H5A.read(Utilities.RandomInvalidHandle(),
Utilities.RandomInvalidHandle(), IntPtr.Zero) >= 0);
Assert.IsFalse(
H5A.read(Utilities.RandomInvalidHandle(),
H5T.NATIVE_DOUBLE, IntPtr.Zero) >= 0);
}
public static Double AttributeAsDouble(H5AttributeId _attributeId)
{
H5DataTypeId attributeType = H5T.copy(H5T.H5Type.NATIVE_DOUBLE);
double[] value = new double[1];
H5A.read <double>(_attributeId, attributeType, new H5Array <double>(value));
return(value[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($"Unknown Attribute: {key}", nameof(key));
}
dtypeId = H5A.get_type(attrId);
int size = H5T.get_size(dtypeId).ToInt32();
IntPtr iPtr = Marshal.AllocHGlobal(size);
int result = H5A.read(attrId, dtypeId, iPtr);
if (result < 0)
{
throw new IOException("Failed to read attribute");
}
if (H5T.equal(dtypeId, H5T.NATIVE_INT64) > 0)
{
var dest = new long[1];
Marshal.Copy(iPtr, dest, 0, 1);
Marshal.FreeHGlobal(iPtr);
return dest[0];
}
else // Must be a string...
{
var dest = new byte[size];
Marshal.Copy(iPtr, dest, 0, size);
Marshal.FreeHGlobal(iPtr);
return Encoding.ASCII.GetString(dest).TrimEnd((Char)0);
}
// return null;
}
finally
{
if (attrId > 0)
{
H5A.close(attrId);
}
if (dtypeId > 0)
{
H5T.close(dtypeId);
}
}
}));
}
}
private T[] ReadArray <T>(long size, H5AttributeId attId, H5DataTypeId typeId)
{
T[] v = new T[size];
if (size == 0)
{
return(v);
}
H5A.read <T>(attId, typeId, new H5Array <T>(v));
return(v);
}
protected T[] getAttribute <T>(H5AttributeId aid)
{
H5DataTypeId sv = H5A.getType(aid);
int size = H5T.getSize(sv);
var attValue = new T[size];
H5A.read <T>(aid, sv, new H5Array <T>(attValue));
return(attValue);
}
protected T[] ReadArray <T>(ulong size, int attId, int typeId)
{
T[] v = new T[size];
if (size == 0)
{
return(v);
}
GCHandle hnd = GCHandle.Alloc(v, GCHandleType.Pinned);
H5A.read(attId, typeId, hnd.AddrOfPinnedObject());
return(v);
}
static void ReadFile(string filePath)
{
var file = H5F.open(filePath, H5F.ACC_RDONLY);
var dataSet = H5D.open(file, "/group/dataset");
var dataSpace = H5D.get_space(dataSet);
var rank = H5S.get_simple_extent_ndims(dataSpace);
if (rank == 2)
{
var dims = new ulong[2];
H5S.get_simple_extent_dims(dataSpace, dims, null);
var data = new int[dims[0], dims[1]];
H5D.read(dataSet, H5T.NATIVE_INT, H5S.ALL, H5S.ALL, H5P.DEFAULT, new PinnedObject(data));
for (int i = 0; i < data.GetLength(0); ++i)
{
for (int j = 0; j < data.GetLength(1); ++j)
{
Write($"{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);
}
public static T ReadScalarNumericAttribute <T>(hid_t attribute) where T : struct
{
var space = H5A.get_space(attribute);
if (space < 0)
{
throw new Exception("Failed to get space");
}
if (H5S.get_simple_extent_type(space) != H5S.class_t.SCALAR)
{
H5S.close(space);
throw new Exception("Not a scalar data space");
}
H5S.close(space);
var type = H5A.get_type(attribute);
if (type < 0)
{
throw new Exception("Failed to get type");
}
var typeClass = H5T.get_class(type);
H5T.close(type);
if (typeClass != H5T.class_t.INTEGER && typeClass != H5T.class_t.FLOAT)
{
throw new Exception("Not an integral or floating point data type");
}
// TODO:
// Check if value can be cast to type of this attribute.
//
// TODO:
// T[] value = new T[1];
// H5A.read(attribute, NumericTypeToHDF5Type<T>(), new PinnedObject(value));
object boxedValue = new T();
if (H5A.read(attribute, NumericTypeToHDF5Type <T>(), new PinnedObject(boxedValue)) < 0)
{
throw new Exception("Failed to read attribute");
}
return((T)boxedValue);
}
/// <summary>
/// Reads from the hdf file
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="_dataType"></param>
/// <param name="_attributeId"></param>
/// <returns></returns>
private static T ReadValue <T>(
Hdf5DataType _dataType,
Hdf5Identifier _attributeId)
{
T[] value = new T[1];
GCHandle arrayHandle = GCHandle.Alloc(value, GCHandleType.Pinned);
var dataType = H5T.copy(_dataType.NativeType.Value).ToId();
int result = H5A.read(_attributeId.Value, dataType.Value, arrayHandle.AddrOfPinnedObject());
arrayHandle.Free();
H5T.close(dataType.Value);
return(value[0]);
}
public static IEnumerable <string> ReadStringAttributes(hid_t groupId, string name)
{
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.NULLTERM);
//name = ToHdf5Name(name);
var datasetId = H5A.open(groupId, name);
hid_t spaceId = H5A.get_space(datasetId);
long count = H5S.get_simple_extent_npoints(spaceId);
H5S.close(spaceId);
IntPtr[] rdata = new IntPtr[count];
GCHandle hnd = GCHandle.Alloc(rdata, GCHandleType.Pinned);
H5A.read(datasetId, datatype, hnd.AddrOfPinnedObject());
var strs = new List <string>();
for (int i = 0; i < rdata.Length; ++i)
{
int len = 0;
while (Marshal.ReadByte(rdata[i], len) != 0)
{
++len;
}
byte[] buffer = new byte[len];
Marshal.Copy(rdata[i], buffer, 0, buffer.Length);
string s = Encoding.UTF8.GetString(buffer);
strs.Add(s);
H5.free_memory(rdata[i]);
}
hnd.Free();
H5T.close(datatype);
H5A.close(datasetId);
return(strs);
}
/// <summary>
/// Read the numeric value stored in this *attribute* specified by `T`.
/// </summary>
/// <remarks>
/// For reading a `string`, use `Reads()` instead!
/// </remarks>
public T Read <T>()
{
using (H5Type dtype = GetDType())
{
if (typeof(T) != dtype.PrimitiveType)
{
throw new InvalidCastException(dtype.PrimitiveType.ToString());
}
T[] buf = new T[1];
GCHandle pinnedArray = GCHandle.Alloc(buf, GCHandleType.Pinned);
int status = H5A.read(ID, dtype.ID, pinnedArray.AddrOfPinnedObject());
pinnedArray.Free();
if (status < 0)
{
throw new H5LibraryException($"H5A.read() returned ({status})");
}
return(buf[0]);
}
}
/// <summary>
/// Reads a string scalar attribute value.
/// Assumes that the parent object is already open.
/// </summary>
/// <param name="_objectId"></param>
/// <param name="_title"></param>
/// <returns></returns>
public static Hdf5Attribute GetStringAttribute(Hdf5Identifier _objectId, string _title)
{
int attributeId = 0;
int typeId = 0;
attributeId = H5A.open(_objectId.Value, _title);
typeId = H5A.get_type(attributeId);
var sizeData = H5T.get_size(typeId);
var size = sizeData.ToInt32();
byte[] strBuffer = new byte[size];
var aTypeMem = H5T.get_native_type(typeId, H5T.direction_t.ASCEND);
GCHandle pinnedArray = GCHandle.Alloc(strBuffer, GCHandleType.Pinned);
H5A.read(attributeId, aTypeMem, pinnedArray.AddrOfPinnedObject());
pinnedArray.Free();
H5T.close(aTypeMem);
string value = System.Text.Encoding.ASCII.GetString(strBuffer, 0, strBuffer.Length - 1);
var attribute = new Hdf5Attribute
{
Id = attributeId.ToId(),
Name = _title,
Value = value
};
if (attributeId > 0)
{
H5A.close(attributeId);
}
if (typeId > 0)
{
H5T.close(typeId);
}
return(attribute);
}
void FindAttribute(int i)
{
var attr_field = "FIELD_" + i + "_NAME";
var attr = H5A.open(Id, attr_field);
var dtype = H5A.getType(attr);
var size = H5T.getSize(dtype);
var mtype = H5T.create(H5T.CreateClass.STRING, size);
var buffer = new byte[size];
H5A.read(attr, mtype, new H5Array <byte>(buffer));
var attr_datatype = H5T.getMemberType(H5D.getType(Id), i);
var attr_size = H5T.getSize(attr_datatype);
var attr_class = H5T.getMemberClass(H5D.getType(Id), i).ToString();
var attr_name = Encoding.GetString(buffer).Replace('\0', ' ').Trim();
switch (attr_class)
{
case "STRING":
_attributes[i] = new StringAttribute(attr_name, attr_size);
break;
case "INTEGER":
_attributes[i] = new IntegerAttribute(attr_name, attr_size);
break;
case "FLOAT":
_attributes[i] = new FloatingPointAttribute(attr_name, attr_size);
break;
default:
throw new ArgumentException("Unknown attribute type " + attr_class, "attr_type");
}
}
public static Array ReadPrimitiveAttributes <T>(hid_t groupId, string name) //where T : struct
{
Type type = typeof(T);
var datatype = GetDatatype(type);
var attributeId = H5A.open(groupId, name);
var spaceId = H5A.get_space(attributeId);
int rank = H5S.get_simple_extent_ndims(spaceId);
ulong[] maxDims = new ulong[rank];
ulong[] dims = new ulong[rank];
hid_t memId = H5S.get_simple_extent_dims(spaceId, dims, maxDims);
long[] lengths = dims.Select(d => Convert.ToInt64(d)).ToArray();
Array attributes = Array.CreateInstance(type, lengths);
var typeId = H5A.get_type(attributeId);
var mem_type = H5T.copy(datatype);
if (datatype == H5T.C_S1)
{
H5T.set_size(datatype, new IntPtr(2));
}
var propId = H5A.get_create_plist(attributeId);
memId = H5S.create_simple(rank, dims, maxDims);
GCHandle hnd = GCHandle.Alloc(attributes, GCHandleType.Pinned);
H5A.read(attributeId, datatype, hnd.AddrOfPinnedObject());
hnd.Free();
H5A.close(typeId);
H5A.close(attributeId);
H5S.close(spaceId);
return(attributes);
}
private string GetModelConfig()
{
long fileId = H5F.open(this.fileName, H5F.ACC_RDONLY);
long attrId = H5A.open(fileId, @"model_config");
long typeId = H5A.get_type(attrId);
long spaceId = H5A.get_space(attrId);
long count = H5S.get_simple_extent_npoints(spaceId);
H5S.close(spaceId);
IntPtr[] dest = new IntPtr[count];
GCHandle handle = GCHandle.Alloc(dest, GCHandleType.Pinned);
H5A.read(attrId, typeId, handle.AddrOfPinnedObject());
var attrStrings = new List <string>();
for (int i = 0; i < dest.Length; ++i)
{
int attrLength = 0;
while (Marshal.ReadByte(dest[i], attrLength) != 0)
{
++attrLength;
}
byte[] buffer = new byte[attrLength];
Marshal.Copy(dest[i], buffer, 0, buffer.Length);
string stringPart = Encoding.UTF8.GetString(buffer);
attrStrings.Add(stringPart);
H5.free_memory(dest[i]);
}
handle.Free();
return(attrStrings.ToArray().ToString());
}
/// <summary>
/// Read the string value stored in this *attribute*.
/// </summary>
public string Reads()
{
using (H5Type dtype = GetDType())
{
if (typeof(System.String) != dtype.PrimitiveType)
{
throw new InvalidCastException(dtype.PrimitiveType.ToString());
}
long slen = dtype.Size;
byte[] buf = new byte[slen];
GCHandle pinnedArray = GCHandle.Alloc(buf, GCHandleType.Pinned);
int status = H5A.read(ID, dtype.ID, pinnedArray.AddrOfPinnedObject());
pinnedArray.Free();
if (status < 0)
{
throw new H5LibraryException($"H5A.read() returned ({status})");
}
string decoded = System.Text.Encoding.ASCII.GetString(buf);
return(decoded.TrimEnd('\0'));
}
}
private static void ReadFile(string filePath)
{
var file = H5F.open(filePath, H5F.OpenMode.ACC_RDONLY);
var dataSet = H5D.open(file, "/group/dataset");
var fileSpace = H5D.getSpace(dataSet);
var rank = H5S.getSimpleExtentNDims(fileSpace);
WriteLine("Rank: {0}", rank);
var dims = H5S.getSimpleExtentDims(fileSpace);
Write("Dims:");
foreach (var d in dims)
{
Write(" {0}", d);
}
WriteLine();
H5S.close(fileSpace);
var ints = new int[1];
var intAttribute = H5A.openName(dataSet, "int");
H5A.read(intAttribute, H5A.getType(intAttribute), new H5Array <int>(ints));
WriteLine("int: {0}", ints[0]);
H5A.close(intAttribute);
var stringAttribute = H5A.openName(dataSet, "string");
var stringType = H5A.getType(stringAttribute);
var stringSize = H5T.getSize(stringType);
WriteLine("string length: {0}", stringSize);
var buffer = new byte[stringSize];
H5A.read(stringAttribute, stringType, new H5Array <byte>(buffer));
WriteLine("string: {0}", Encoding.ASCII.GetString(buffer));
H5T.close(stringType);
H5A.close(stringAttribute);
if (rank == 2)
{
var data = new int[dims[0], dims[1]];
H5D.read(dataSet, H5D.getType(dataSet), new H5Array <int>(data));
for (int i = 0; i < data.GetLength(0); ++i)
{
for (int j = 0; j < data.GetLength(1); ++j)
{
Write(" {0}", data[i, j]);
}
WriteLine();
}
}
H5D.close(dataSet);
H5F.close(file);
}
} // test_attr_basic_write
static void test_attr_basic_read()
{
try
{
Console.Write("Testing basic reading attribute functions");
// Make an integer type object to use in various calls (instead of copying like in test_attr_basic_write)
H5DataTypeId inttype = new H5DataTypeId(H5T.H5Type.NATIVE_INT);
// Open file
H5FileId fileId = H5F.open(FILE_NAME, H5F.OpenMode.ACC_RDWR);
// Open dataset DSET1_NAME.
H5DataSetId dsetId = H5D.open(fileId, DSET1_NAME);
// Verify the correct number of attributes.
H5ObjectInfo oinfo = H5O.getInfo(dsetId);
if (oinfo.nAttributes != 2)
{
Console.WriteLine("\ntest_attr_basic_read: incorrect number of attributes: read {0} - should be {1}",
oinfo.nAttributes, 2);
nerrors++;
}
// Open first attribute for the dataset.
H5AttributeId attrId = H5A.open(dsetId, D1ATTR1_NAME);
// Read attribute data.
int[] read_data1 = new int[3];
H5A.read(attrId, inttype, new H5Array <int>(read_data1));
// Verify values read in.
int[] attr_data1 = new int[] { 512, -234, 98123 }; /* Test data for 1st attribute */
int ii;
for (ii = 0; ii < ATTR1_DIM; ii++)
{
if (attr_data1[ii] != read_data1[ii])
{
Console.WriteLine("\ntest_attr_basic_read:check2: read value differs from input: read {0} - input {1}", read_data1[ii], attr_data1[ii]);
nerrors++;
}
}
H5A.close(attrId);
// Open second attribute for the dataset.
attrId = H5A.open(dsetId, D1ATTR2_NAME);
// Read attribute data.
H5A.read(attrId, inttype, new H5Array <int>(read_data1));
// Verify values read in.
int[] attr_data2 = new int[] { 256, 11945, -22107 }; // Data to test second attribute of dataset.
for (ii = 0; ii < ATTR1_DIM; ii++)
{
if (attr_data2[ii] != read_data1[ii])
{
Console.WriteLine("\ntest_attr_basic_read: check3: read value differs from input: read {0} - input {1}", read_data1[ii], attr_data2[ii]);
nerrors++;
}
}
// Close the attribute and dataset.
H5A.close(attrId);
H5D.close(dsetId);
/* Checking group's attribute */
// Open the group.
H5GroupId groupId = H5G.open(fileId, GROUP1_NAME);
// Verify the correct number of attributes for this group.
oinfo = H5O.getInfo(groupId);
if (oinfo.nAttributes != 1)
{
Console.WriteLine("\ntest_attr_basic_read: incorrect number of attributes: read {0} - should be {1}",
oinfo.nAttributes, 1);
nerrors++;
}
// Open the attribute for the group.
attrId = H5A.open(groupId, GATTR_NAME);
// Read attribute information.
int[,] read_data2 = new int[GATTR_DIM1, GATTR_DIM2];
H5A.read(attrId, new H5DataTypeId(H5T.H5Type.NATIVE_INT), new H5Array <int>(read_data2));
// Verify values read in.
int jj;
for (ii = 0; ii < GATTR_DIM1; ii++)
{
for (jj = 0; jj < GATTR_DIM2; jj++)
{
if (gattr_data[ii, jj] != read_data2[ii, jj])
{
Console.WriteLine("\ntest_attr_basic_read: check4: read value differs from input: read {0} - input {1}", read_data2[ii, jj], gattr_data[ii, jj]);
nerrors++;
}
}
}
// Close attribute, group, and file.
H5A.close(attrId);
H5G.close(groupId);
H5F.close(fileId);
Console.WriteLine("\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_basic_read
public static string ReadStringAttribute(hid_t hid, string key)
{
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 typeClass = H5T.get_class(type);
if (typeClass != H5T.class_t.STRING)
{
H5T.close(type);
throw new Exception("Not a string attribute");
}
var utf8 = H5T.get_cset(type) == H5T.cset_t.UTF8;
var ascii = H5T.get_cset(type) == H5T.cset_t.ASCII;
if (!utf8 && !ascii)
{
H5T.close(type);
H5A.close(attribute);
throw new Exception("Neither ASCII nor UTF8.");
}
var isVariableString = H5T.is_variable_str(type);
if (isVariableString < 0)
{
H5T.close(type);
H5A.close(attribute);
throw new Exception("H5T.is_variable_str failed");
}
if (isVariableString > 0)
{
var space = H5A.get_space(attribute);
if (space < 0)
{
H5T.close(type);
H5A.close(attribute);
throw new Exception("H5A.get_space failed.");
}
hid_t count = H5S.get_simple_extent_npoints(space);
var rdata = new IntPtr[count];
H5A.read(attribute, type, new PinnedObject(rdata));
var attrStrings = new List <string>();
for (int i = 0; i < rdata.Length; ++i)
{
int attrLength = 0;
while (Marshal.ReadByte(rdata[i], attrLength) != 0)
{
++attrLength;
}
byte[] buffer = new byte[attrLength];
Marshal.Copy(rdata[i], buffer, 0, buffer.Length);
string part = utf8 ? Encoding.UTF8.GetString(buffer)
: Encoding.ASCII.GetString(buffer);
attrStrings.Add(part);
H5.free_memory(rdata[i]);
}
H5S.close(space);
H5T.close(type);
H5A.close(attribute);
return(attrStrings[0]);
}
// Must be a non-variable length string.
var size = H5T.get_size(type).ToInt32();
var unmanagedBuffer = new UnmanagedBuffer(size);
int result = H5A.read(attribute, type, unmanagedBuffer);
if (result < 0)
{
H5T.close(type);
H5D.close(attribute);
throw new IOException("Failed to read attribute.");
}
var bytes = new byte[size];
unmanagedBuffer.CopyTo(bytes, 0, bytes.Length);
H5T.close(type);
H5A.close(attribute);
var value = utf8 ? Encoding.UTF8.GetString(bytes)
: Encoding.ASCII.GetString(bytes);
return(value.TrimEnd('\0'));
}
} // test_attr_compound_write
static void test_attr_compound_read()
{
try
{
Console.Write("Testing read attribute with compound datatype");
// Open file.
H5FileId fileId = H5F.open(COMP_FNAME, H5F.OpenMode.ACC_RDWR);
// Open the dataset.
H5DataSetId dsetId = H5D.open(fileId, DSET1_NAME);
// Verify the correct number of attributes for this dataset.
H5ObjectInfo oinfo = H5O.getInfo(dsetId);
if (oinfo.nAttributes != 1)
{
Console.WriteLine("\ntest_attr_basic_read: incorrect number of attributes: read {0} - should be {1}",
oinfo.nAttributes, 1);
nerrors++;
}
// Open first attribute for the dataset.
H5AttributeId attrId = H5A.openByIndex(dsetId, ".", H5IndexType.CRT_ORDER, H5IterationOrder.INCREASING, 0);
// Verify dataspace.
H5DataSpaceId spaceId = H5A.getSpace(attrId);
int rank = H5S.getSimpleExtentNDims(spaceId);
if (rank != ATTR4_RANK)
{
Console.WriteLine("\ntest_attr_compound_read: incorrect rank = {0} - should be {1}", rank, ATTR4_RANK);
nerrors++;
}
long[] dims = H5S.getSimpleExtentDims(spaceId);
if (dims[0] != ATTR4_DIM1)
{
Console.WriteLine("\ntest_attr_compound_read: incorrect dim[0] = {0} - should be {1}", dims[0], ATTR4_DIM1);
nerrors++;
}
if (dims[1] != ATTR4_DIM2)
{
Console.WriteLine("\ntest_attr_compound_read: incorrect dim[1] = {0} - should be {1}", dims[1], ATTR4_DIM2);
nerrors++;
}
// Close dataspace.
H5S.close(spaceId);
// Verify datatype of the attribute.
H5DataTypeId typeId = H5A.getType(attrId);
H5T.H5TClass t_class = H5T.getClass(typeId);
if (t_class != H5T.H5TClass.COMPOUND)
{
Console.WriteLine("test_compound_dtypes: H5T.getMemberClass and H5T.getClass return different classes for the same type.");
nerrors++;
}
int nfields = H5T.getNMembers(typeId);
if (nfields != 3)
{
Console.WriteLine("test_compound_dtypes: H5T.getMemberClass and H5T.getClass return different classes for the same type.");
nerrors++;
}
// Check name against this list
string[] memb_names = { ATTR4_FIELDNAME1, ATTR4_FIELDNAME2, ATTR4_FIELDNAME3 };
int[] memb_offsets = { 0, 1, 5 }; // list of member offsets
H5DataTypeId mtypeId; // member type
H5T.H5TClass memb_cls1; // member classes retrieved different ways
string memb_name; // member name
int memb_idx; // member index
int memb_offset, idx; // member offset, loop index
// how to handle int versus uint for memb_idx and idx???
// For each member, check its name, class, index, and size.
for (idx = 0; idx < nfields; idx++)
{
// Get the type of the ith member to test other functions later.
mtypeId = H5T.getMemberType(typeId, idx);
// Get the name of the ith member.
memb_name = H5T.getMemberName(typeId, idx);
if (memb_name != memb_names[idx])
{
Console.WriteLine("test_compound_dtypes: incorrect member name, {0}, for member no {1}", memb_name, idx);
nerrors++;
}
// Get the class of the ith member and then verify the class.
memb_cls1 = H5T.getMemberClass(typeId, idx);
if (memb_cls1 != H5T.H5TClass.INTEGER)
{
Console.WriteLine("test_compound_dtypes: incorrect class, {0}, for member no {1}", memb_cls1, idx);
nerrors++;
}
// Get member's index back using its name and verify it.
memb_idx = H5T.getMemberIndex(typeId, memb_name);
if (memb_idx != idx)
{
Console.WriteLine("test_attr_compound_read: H5T.getMemberName and/or H5T.getMemberIndex returned false values.");
nerrors++;
}
// Get member's offset and verify it.
memb_offset = H5T.getMemberOffset(typeId, idx);
if (memb_offset != memb_offsets[idx])
{
Console.WriteLine("test_attr_compound_read: H5T.getMemberOffset returned incorrect value - {0}, should be {1}", memb_offset, memb_offsets[idx]);
nerrors++;
}
// Get member's size and verify it.
int tsize = H5T.getSize(mtypeId);
switch (idx)
{
case 0:
if (tsize != H5T.getSize(H5T.H5Type.STD_U8LE))
{
Console.WriteLine("test_attr_compound_read: H5T.getSize returned incorrect value.");
nerrors++;
}
break;
case 1:
if (tsize != H5T.getSize(H5T.H5Type.NATIVE_INT))
{
Console.WriteLine("test_attr_compound_read: H5T.getSize returned incorrect value.");
nerrors++;
}
break;
case 2:
if (tsize != H5T.getSize(H5T.H5Type.STD_I64BE))
{
Console.WriteLine("test_attr_compound_read: H5T.getSize returned incorrect value.");
nerrors++;
}
break;
default:
Console.WriteLine("test_attr_compound_read: We should only have 3 members.");
nerrors++;
break;
} // end switch
// Close current member type.
H5T.close(mtypeId);
} // end for
// Prepare the check array to verify read data. It should be the same as the attr_data4 array
// in the previous test function test_attr_compound_write.
attr4_struct[,] check = new attr4_struct[ATTR4_DIM1, ATTR4_DIM2];
// Initialize the dataset
int ii, jj, nn;
for (ii = nn = 0; ii < ATTR4_DIM1; ii++)
{
for (jj = 0; jj < ATTR4_DIM2; jj++)
{
check[ii, jj].c = 't';
check[ii, jj].i = nn++;
check[ii, jj].l = (ii * 10 + jj * 100) * nn;
}
}
// Read attribute information.
attr4_struct[,] read_data4 = new attr4_struct[ATTR4_DIM1, ATTR4_DIM2];
H5A.read(attrId, typeId, new H5Array <attr4_struct>(read_data4));
// Verify values read in.
for (ii = 0; ii < ATTR4_DIM1; ii++)
{
for (jj = 0; jj < ATTR4_DIM2; jj++)
{
if ((check[ii, jj].c != read_data4[ii, jj].c) ||
(check[ii, jj].i != read_data4[ii, jj].i) ||
(check[ii, jj].l != read_data4[ii, jj].l))
{
Console.WriteLine("test_attr_compound_read: Incorrect read data: {0}, should be {1}", read_data4[ii, jj], check[ii, jj]);
nerrors++;
}
}
}
// Close resources.
H5T.close(typeId);
H5A.close(attrId);
H5D.close(dsetId);
H5F.close(fileId);
Console.WriteLine("\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_compound_read
static void Main(string[] args)
{
try
{
// We will write and read an int array of this length.
const int DATA_ARRAY_LENGTH = 12;
// Rank is the number of dimensions of the data array.
const int RANK = 1;
// Create an HDF5 file.
// The enumeration type H5F.CreateMode provides only the legal
// creation modes. Missing H5Fcreate parameters are provided
// with default values.
H5FileId fileId = H5F.create("myCSharp.h5",
H5F.CreateMode.ACC_TRUNC);
// Create a HDF5 group.
H5GroupId groupId = H5G.create(fileId, "/cSharpGroup");
H5GroupId subGroup = H5G.create(groupId, "mySubGroup");
// Close the subgroup.
H5G.close(subGroup);
// Prepare to create a data space for writing a 1-dimensional
// signed integer array.
long[] dims = new long[RANK];
dims[0] = DATA_ARRAY_LENGTH;
// Put descending ramp data in an array so that we can
// write it to the file.
int[] dset_data = new int[DATA_ARRAY_LENGTH];
for (int i = 0; i < DATA_ARRAY_LENGTH; i++)
{
dset_data[i] = DATA_ARRAY_LENGTH - i;
}
// Create a data space to accommodate our 1-dimensional array.
// The resulting H5DataSpaceId will be used to create the
// data set.
H5DataSpaceId spaceId = H5S.create_simple(RANK, dims);
// Create a copy of a standard data type. We will use the
// resulting H5DataTypeId to create the data set. We could
// have used the HST.H5Type data directly in the call to
// H5D.create, but this demonstrates the use of H5T.copy
// and the use of a H5DataTypeId in H5D.create.
H5DataTypeId typeId = H5T.copy(H5T.H5Type.NATIVE_INT);
// Find the size of the type
int typeSize = H5T.getSize(typeId);
Console.WriteLine("typeSize is {0}", typeSize);
// Set the order to big endian
H5T.setOrder(typeId, H5T.Order.BE);
// Set the order to little endian
H5T.setOrder(typeId, H5T.Order.LE);
// Create the data set.
H5DataSetId dataSetId = H5D.create(fileId, "/csharpExample",
typeId, spaceId);
// Write the integer data to the data set.
H5D.write(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT),
new H5Array <int>(dset_data));
// If we were writing a single value it might look like this.
// int singleValue = 100;
// H5D.writeScalar(dataSetId,
// new H5DataTypeId(H5T.H5Type.NATIVE_INT),
// ref singleValue);
// Create an integer array to receive the read data.
int[] readDataBack = new int[DATA_ARRAY_LENGTH];
// Read the integer data back from the data set
H5D.read(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT),
new H5Array <int>(readDataBack));
// Echo the data
for (int i = 0; i < DATA_ARRAY_LENGTH; i++)
{
Console.WriteLine(readDataBack[i]);
}
// Close all the open resources.
H5D.close(dataSetId);
// Reopen and close the data sets to show that we can.
dataSetId = H5D.open(fileId, "/csharpExample");
H5D.close(dataSetId);
dataSetId = H5D.open(groupId, "/csharpExample");
H5D.close(dataSetId);
H5T.close(typeId);
H5G.close(groupId);
// Get H5O info
H5ObjectInfo objectInfo = H5O.getInfoByName(fileId,
"/csharpExample");
Console.WriteLine("header.space.message is {0}",
objectInfo.header.space.message);
Console.WriteLine("fileNumber is {0}", objectInfo.fileNumber);
Console.WriteLine("address is {0}", objectInfo.address);
Console.WriteLine("type is {0}",
objectInfo.objectType.ToString());
Console.WriteLine("reference count is {0}",
objectInfo.referenceCount);
Console.WriteLine("modification time is {0}",
objectInfo.modificationTime);
Console.WriteLine("birth time is {0}",
objectInfo.birthTime);
Console.WriteLine("access time is {0}",
objectInfo.accessTime);
Console.WriteLine("change time is {0}",
objectInfo.changeTime);
Console.WriteLine("number of attributes is {0}",
objectInfo.nAttributes);
Console.WriteLine("header version is {0}",
objectInfo.header.version);
Console.WriteLine("header nMessages is {0}",
objectInfo.header.nMessages);
Console.WriteLine("header nChunks is {0}",
objectInfo.header.nChunks);
Console.WriteLine("header flags is {0}",
objectInfo.header.flags);
H5LinkInfo linkInfo = H5L.getInfo(fileId, "/cSharpGroup");
Console.WriteLine(
"address: {0:x}, charSet: {1}, creationOrder: {2}",
linkInfo.address, linkInfo.charSet, linkInfo.creationOrder);
Console.WriteLine("linkType: {0}, softLinkSizeOrUD: {1}",
linkInfo.linkType, linkInfo.softLinkSizeOrUD);
// Reopen the group id to show that we can.
groupId = H5G.open(fileId, "/cSharpGroup");
// Use H5L.iterate to visit links
H5LIterateCallback myDelegate;
myDelegate = MyH5LFunction;
ulong linkNumber = 0;
H5IterationResult result =
H5L.iterate(groupId, H5IndexType.NAME,
H5IterationOrder.INCREASING,
ref linkNumber, myDelegate, 0);
// Create some attributes
H5DataTypeId attributeType = H5T.copy(H5T.H5Type.NATIVE_INT);
long[] attributeDims = new long[1];
const int RAMP_LENGTH = 5;
attributeDims[0] = RAMP_LENGTH;
int[] ascendingRamp = new int[RAMP_LENGTH] {
1, 2, 3, 4, 5
};
int[] descendingRamp = new int[RAMP_LENGTH] {
5, 4, 3, 2, 1
};
int[] randomData = new int[RAMP_LENGTH] {
3, 123, 27, 6, 1
};
int[] readBackRamp = new int[RAMP_LENGTH];
// Call set buffer using H5Memory
// Allocate memory from "C" runtime heap (not garbage collected)
H5Memory typeConversionBuffer = new H5Memory(new IntPtr(DATA_ARRAY_LENGTH));
H5Memory backgroundBuffer = new H5Memory(new IntPtr(DATA_ARRAY_LENGTH));
// Set the property list type conversion and background buffers.
H5PropertyListId myPropertyListId =
H5P.create(H5P.PropertyListClass.DATASET_XFER);
H5P.setBuffer(myPropertyListId,
typeConversionBuffer, backgroundBuffer);
// Test use of vlen
// Create a vlen data type
H5DataTypeId tid1 = H5T.vlenCreate(H5T.H5Type.NATIVE_UINT);
H5DataSetId vDataSetId = H5D.create(fileId, "/vlenTest", tid1,
spaceId);
// Create a jagged array of integers.
hvl_t[] vlArray = new hvl_t[DATA_ARRAY_LENGTH];
// HDF5 variable length data types require the use of void
// pointers. C# requires that sections of code that deal
// directly with pointer be marked
// as unsafe.
unsafe
{
for (int i = 0; i < DATA_ARRAY_LENGTH; i++)
{
IntPtr ptr = new IntPtr((i + 1) * sizeof(int));
// Allocate memory that is not garbage collected.
vlArray[i].p = H5CrtHeap.Allocate(
new IntPtr((i + 1) * sizeof(int))
).ToPointer();
// Fill the array with integers = the row number
int *intPointer = (int *)vlArray[i].p;
for (int j = 0; j < i + 1; j++)
{
intPointer[j] = (int)i;
}
if (IntPtr.Size == 8)
{
vlArray[i].len = (ulong)i + 1;
}
else
{
vlArray[i].len = (uint)i + 1;
}
}
// Write the variable length data
H5D.write(vDataSetId, tid1,
new H5Array <hvl_t>(vlArray));
// Create an array to read back the array.
hvl_t[] vlReadBackArray = new hvl_t[DATA_ARRAY_LENGTH];
// Read the array back
H5D.read(vDataSetId, tid1, new H5Array <hvl_t>(vlReadBackArray));
// Write the data to the console
for (int i = 0; i < DATA_ARRAY_LENGTH; i++)
{
int *iPointer = (int *)vlReadBackArray[i].p;
for (int j = 0; j < i + 1; j++)
{
Console.WriteLine(iPointer[j]);
}
}
// Reclaim the memory that read allocated
H5D.vlenReclaim(tid1, spaceId, new H5PropertyListId(H5P.Template.DEFAULT),
new H5Array <hvl_t>(vlReadBackArray));
// Now read it back again using our own memory manager
//H5AllocateCallback allocDelegate = new H5AllocCallback(userAlloc);
H5FreeCallback freeDelegate = new H5FreeCallback(userFree);
H5PropertyListId memManagerPlist = H5P.create(H5P.PropertyListClass.DATASET_XFER);
unsafe
{
H5P.setVlenMemManager(memManagerPlist, userAlloc, IntPtr.Zero,
freeDelegate, IntPtr.Zero);
}
// Read the array back
H5D.read(vDataSetId, tid1,
new H5DataSpaceId(H5S.H5SType.ALL),
new H5DataSpaceId(H5S.H5SType.ALL),
memManagerPlist,
new H5Array <hvl_t>(vlReadBackArray));
// Write the data to the console
for (int i = 0; i < DATA_ARRAY_LENGTH; i++)
{
int *iPointer = (int *)vlReadBackArray[i].p;
for (int j = 0; j < i + 1; j++)
{
Console.WriteLine(iPointer[j]);
}
}
// Reclaim the memory that read allocated using our free routines
H5D.vlenReclaim(tid1, spaceId, memManagerPlist,
new H5Array <hvl_t>(vlReadBackArray));
}
H5S.close(spaceId);
H5DataSpaceId attributeSpace =
H5S.create_simple(1, attributeDims);
H5AttributeId attributeId =
H5A.create(groupId, "ascendingRamp", attributeType, attributeSpace);
int offset = H5T.getOffset(attributeType);
Console.WriteLine("Offset is {0}", offset);
H5DataTypeId float32BE = H5T.copy(H5T.H5Type.IEEE_F32BE);
H5T.Norm norm = H5T.getNorm(float32BE);
Console.WriteLine("Norm is {0}", norm);
int precision = H5T.getPrecision(float32BE);
Console.WriteLine("Precision is {0}", precision);
H5FloatingBitFields bitFields = H5T.getFields(float32BE);
Console.WriteLine("getFields: sign bit position: {0}", bitFields.signBitPosition);
Console.WriteLine("getFields: exponent bit position: {0}", bitFields.exponentBitPosition);
Console.WriteLine("getFields: number of exponent bits: {0}", bitFields.nExponentBits);
Console.WriteLine("getFields: mantissa bit position: {0} ", bitFields.mantissaBitPosition);
Console.WriteLine("getFields: number of mantissa bits: {0}", bitFields.nMantissaBits);
Console.Write("{0}", bitFields);
// Write to an attribute
H5A.write <int>(attributeId, attributeType,
new H5Array <int>(ascendingRamp));
// Read from an attribute
H5A.read <int>(attributeId, attributeType,
new H5Array <int>(readBackRamp));
// Echo results
Console.WriteLine("ramp elements are: ");
foreach (int rampElement in readBackRamp)
{
Console.WriteLine(" {0}", rampElement);
}
H5A.close(attributeId);
// Create and write two more attributes.
attributeId = H5A.createByName(groupId, ".", "descendingRamp",
attributeType, attributeSpace);
H5A.write <int>(attributeId, attributeType,
new H5Array <int>(descendingRamp));
H5A.close(attributeId);
attributeId = H5A.createByName(groupId, ".",
"randomData", attributeType,
attributeSpace);
H5A.write <int>(attributeId, attributeType,
new H5Array <int>(randomData));
// Read back the attribute data
H5A.read <int>(attributeId, attributeType,
new H5Array <int>(readBackRamp));
Console.WriteLine("ramp elements are: ");
foreach (int rampElement in readBackRamp)
{
Console.WriteLine(" {0}", rampElement);
}
H5A.close(attributeId);
// Iterate through the attributes.
long position = 0;
H5AIterateCallback attributeDelegate;
attributeDelegate = MyH5AFunction;
H5ObjectInfo groupInfo = H5O.getInfo(groupId);
Console.WriteLine(
"fileNumber: {0}, total space: {1}, referceCount: {2}, modification time: {3}",
groupInfo.fileNumber, groupInfo.header.space.total,
groupInfo.referenceCount, groupInfo.modificationTime);
// While iterating, collect the names of all the attributes.
ArrayList attributeNames = new ArrayList();
H5A.iterate(groupId, H5IndexType.CRT_ORDER,
H5IterationOrder.INCREASING,
ref position, attributeDelegate,
(object)attributeNames);
// Write out the names of the attributes
foreach (string attributeName in attributeNames)
{
Console.WriteLine("attribute name is {0}", attributeName);
}
// Demonstrate H5A.openName
attributeId = H5A.openName(groupId, "descendingRamp");
Console.WriteLine("got {0} by name", H5A.getName(attributeId));
H5A.close(attributeId);
// Demonstrate H5A.getNameByIndex
string secondAttribute = H5A.getNameByIndex(groupId, ".",
H5IndexType.CRT_ORDER, H5IterationOrder.INCREASING, 1);
Console.WriteLine("second attribute is named {0}",
secondAttribute);
// Demonstrate H5G.getInfo
H5GInfo gInfo = H5G.getInfo(groupId);
Console.WriteLine(
"link storage: {0}, max creation order: {1}, nLinks: {2}",
gInfo.linkStorageType, gInfo.maxCreationOrder, gInfo.nLinks);
// Demonstrate H5A.getSpace
//attributeId = H5A.openByName(groupId, ".", "descendingRamp");
attributeId = H5A.open(groupId, "descendingRamp");
H5DataSpaceId rampSpaceId = H5A.getSpace(attributeId);
H5S.close(rampSpaceId);
// Demonstrate H5A.getType
H5DataTypeId rampTypeId = H5A.getType(attributeId);
Console.WriteLine("size of ramp data type is {0} bytes.",
H5T.getSize(rampTypeId));
H5T.close(rampTypeId);
// Demonstrate H5A.getInfo
H5AttributeInfo rampInfo = H5A.getInfo(attributeId);
Console.WriteLine(
"characterset: {0}, creationOrder: {1}, creationOrderValid: {2}, dataSize: {3}",
rampInfo.characterSet, rampInfo.creationOrder,
rampInfo.creationOrderValid, rampInfo.dataSize);
// Demonstrate H5A.Delete
H5A.Delete(groupId, "descendingRamp");
//H5A.DeleteByName(groupId, ".", "descendingRamp");
// Iterate through the attributes to show that the deletion
// was successful.
position = 0;
ArrayList namesAfterDeletion = new ArrayList();
H5A.iterate(groupId, H5IndexType.CRT_ORDER,
H5IterationOrder.DECREASING, ref position,
attributeDelegate,
(object)namesAfterDeletion);
H5G.close(groupId);
H5F.close(fileId);
// Reopen and reclose the file.
H5FileId openId = H5F.open("myCSharp.h5",
H5F.OpenMode.ACC_RDONLY);
H5F.close(openId);
// Set the function to be called on error.
unsafe
{
H5AutoCallback myErrorDelegate = new H5AutoCallback(myErrorFunction);
H5E.setAuto(0, myErrorDelegate, IntPtr.Zero);
}
// Uncomment the next line if you want to generate an error to
// test H5E.setAuto
// H5G.open(openId, "noGroup");
}
// This catches all the HDF exception classes. Because each call
// generates a unique exception, different exception can be handled
// separately. For example, to catch open errors we could have used
// catch (H5FopenException openException).
catch (HDFException e)
{
Console.WriteLine(e.Message);
}
Console.WriteLine("Processing complete!");
Console.ReadLine();
}
static void test_attr_basic_write()
{
try
{
Console.Write("Testing Basic Scalar Attribute Writing Functions");
// Create a new file using H5F_ACC_TRUNC access,
// default file creation properties, and default file
// access properties.
H5FileId fileId = H5F.create(FILE_NAME, H5F.CreateMode.ACC_TRUNC);
// Copy datatype for use.
H5DataTypeId typeId = H5T.copy(H5T.H5Type.NATIVE_INT);
// Open the root group.
H5GroupId groupId = H5G.open(fileId, "/");
// Create dataspace for attribute.
hssize_t[] gdims = { GATTR_DIM1, GATTR_DIM2 };
H5DataSpaceId gspace_Id = H5S.create_simple(GATTR_RANK, gdims);
// Create an attribute for the group.
H5AttributeId attrId = H5A.create(groupId, RGATTR_NAME, typeId, gspace_Id);
H5A.close(attrId);
H5G.close(groupId);
// Create a group in this file.
groupId = H5G.create(fileId, GROUP1_NAME);
// Create an attribute for group /Group1.
attrId = H5A.create(groupId, GATTR_NAME, typeId, gspace_Id);
H5A.write(attrId, typeId, new H5Array <int>(gattr_data));
// Create the dataspace.
hssize_t[] dims1 = { SPACE1_DIM1, SPACE1_DIM2 };
H5DataSpaceId space1_Id = H5S.create_simple(SPACE1_RANK, dims1);
// Create a dataset using default properties.
H5DataSetId dsetId = H5D.create(fileId, DSET1_NAME, H5T.H5Type.NATIVE_UCHAR, space1_Id);
// Close objects and file.
H5A.close(attrId);
H5D.close(dsetId);
H5G.close(groupId);
H5F.close(fileId);
// Open the file again.
fileId = H5F.open(FILE_NAME, H5F.OpenMode.ACC_RDWR);
// Open the root group.
groupId = H5G.open(fileId, "/");
// Open attribute again.
attrId = H5A.open(groupId, RGATTR_NAME);
// Close attribute and root group.
H5A.close(attrId);
H5G.close(groupId);
// Open dataset.
dsetId = H5D.open(fileId, DSET1_NAME);
// Create the dataspace for dataset's attribute.
hssize_t[] attdims = { ATTR1_DIM };
H5DataSpaceId attspaceId = H5S.create_simple(ATTR1_RANK, attdims);
// Create an attribute for the dataset.
attrId = H5A.create(dsetId, D1ATTR1_NAME, typeId, attspaceId);
// Try to create the same attribute again (should fail.)
try
{
H5AttributeId attr_twice = H5A.create(dsetId, D1ATTR1_NAME, typeId, attspaceId);
// should fail, but didn't, print an error message.
Console.WriteLine("\ntest_attr_basic_write: Attempting to create an existing attribute.");
nerrors++;
}
catch (HDFException) { } // does nothing, it should fail
// Write attribute information.
int[] attr_data1 = new int[] { 512, -234, 98123 }; /* Test data for 1st attribute */
H5A.write(attrId, typeId, new H5Array <int>(attr_data1));
// Create another attribute for the dataset.
H5AttributeId attr2Id = H5A.create(dsetId, D1ATTR2_NAME, typeId, attspaceId);
// Write attribute information.
int[] attr_data2 = new int[] { 256, 11945, -22107 };
H5A.write(attr2Id, typeId, new H5Array <int>(attr_data2));
// Read attribute information immediately, without closing attribute.
int[] read_data1 = new int[3];
H5A.read(attrId, typeId, new H5Array <int>(read_data1));
// Verify values read in.
int ii;
for (ii = 0; ii < ATTR1_DIM; ii++)
{
if (attr_data1[ii] != read_data1[ii])
{
Console.WriteLine("\ntest_attr_basic_write: check1: read value differs from input: read {0} - input {1}", read_data1[ii], attr_data1[ii]);
nerrors++;
}
}
// Close attributes.
H5A.close(attrId);
H5A.close(attr2Id);
// Open attribute again and verify its name.
attrId = H5A.openIndex(dsetId, 0);
string attr_name = H5A.getName(attrId);
if (attr_name != D1ATTR1_NAME)
{
Console.WriteLine("\ntest_attr_basic_write: attribute name incorrect: is {0} - should be {1}", attr_name, D1ATTR1_NAME);
nerrors++;
}
// Close attribute.
H5A.close(attrId);
// Open the second attribute again and verify its name.
attr2Id = H5A.openIndex(dsetId, 1);
attr_name = H5A.getName(attr2Id);
if (attr_name != D1ATTR2_NAME)
{
Console.WriteLine("\ntest_attr_basic_write: attribute name incorrect: is {0} - should be {1}", attr_name, D1ATTR2_NAME);
nerrors++;
}
// Close all objects.
H5A.close(attr2Id);
H5S.close(space1_Id);
H5S.close(gspace_Id);
H5D.close(dsetId);
H5F.close(fileId);
Console.WriteLine("\tPASSED");
} // end try block
catch (HDFException anyHDF5E)
{
Console.WriteLine(anyHDF5E.Message);
nerrors++;
}
catch (System.Exception sysE)
{
Console.WriteLine(sysE.TargetSite);
Console.WriteLine(sysE.Message);
nerrors++;
}
} // test_attr_basic_write
static void ReadFile(string filePath)
{
var file = H5F.open(filePath, H5F.ACC_RDONLY);
IterateObjects(file);
var group = H5G.open(file, "group");
IterateObjects(group);
H5G.close(group);
var dataSet = H5D.open(file, "/group/dataset");
IterateObjects(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 true
//double pi = 0.0; // Won't work
object pi = 0.0;
H5A.read(doubleAttribute, H5T.NATIVE_DOUBLE, new PinnedObject(pi));
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($"string-vlen: {ReadStringAttribute(dataSet, "string-vlen")}");
WriteLine($"boolean-8-bit-enum: {ReadEnumAttribute<Boolean>(dataSet, "boolean-8-bit-enum")}");
H5D.close(dataSet);
H5F.close(file);
}