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 IEnumerable <OffsetInfo> GetCompoundInfo(Type type, bool ieee = false)
{
//Type t = typeof(T);
var strtype = H5T.copy(H5T.C_S1);
int strsize = (int)H5T.get_size(strtype);
int curSize = 0;
List <OffsetInfo> offsets = new List <OffsetInfo>();
foreach (var x in type.GetFields())
{
OffsetInfo oi = new OffsetInfo()
{
name = x.Name,
type = x.FieldType,
datatype = ieee ? GetDatatypeIEEE(x.FieldType) : GetDatatype(x.FieldType),
size = x.FieldType == typeof(string) ? stringLength(x) : Marshal.SizeOf(x.FieldType),
offset = 0 + curSize
};
if (oi.datatype == H5T.C_S1)
{
strtype = H5T.copy(H5T.C_S1);
H5T.set_size(strtype, new IntPtr(oi.size));
oi.datatype = strtype;
}
if (oi.datatype == H5T.STD_I64BE)
{
oi.size = oi.size * 2;
}
curSize = curSize + oi.size;
offsets.Add(oi);
}
H5T.close(strtype);
return(offsets);
}
public Dictionary <string, string> TryReadDataTable(string datasetName)
{
Dictionary <string, string> result = null;
var subDsDic = ds.GetSubDatasets();
if (subDsDic.Count > 0)
{
H5ID h5FileId = H5F.open(fileName, H5F.ACC_RDONLY);
H5ID datasetId = H5D.open(h5FileId, datasetName);
H5ID typeId = H5D.get_type(datasetId);
H5ID spaceId = H5D.get_space(datasetId);
if (H5T.get_class(typeId) == H5T.class_t.COMPOUND)
{
int numCount = H5T.get_nmembers(typeId);
var size = H5T.get_size(typeId);
byte[] buffer = new byte[size.ToInt32()];
GCHandle hnd = GCHandle.Alloc(buffer, GCHandleType.Pinned);
int ndims = H5S.get_simple_extent_ndims(spaceId);
if (ndims == 1)
{
result = new Dictionary <string, string>();
H5D.read(datasetId, typeId, H5S.ALL, H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
for (uint i = 0; i < numCount; i++)
{
string name = Marshal.PtrToStringAnsi(H5T.get_member_name(typeId, i));
int offset = H5T.get_member_offset(typeId, i).ToInt32();
H5ID subTypeId = H5T.get_member_type(typeId, i);
H5T.class_t typeClass = H5T.get_member_class(typeId, i);
string value = ReadBuffer(buffer, offset, typeClass, subTypeId);
result.Add(name, value);
H5T.close(subTypeId);
}
}
hnd.Free();
}
if (spaceId != 0)
{
H5S.close(spaceId);
}
if (typeId != 0)
{
H5T.close(typeId);
}
if (datasetId != 0)
{
H5D.close(datasetId);
}
if (h5FileId != 0)
{
H5F.close(h5FileId);
}
}
return(result);
}
private IntPtr CreateNativeArray(Array clrArray, long dtypeID)
{
var arraySize = clrArray.Length * ElementSize;
Array oneD;
if (clrArray.Rank > 1)
{
oneD = Array.CreateInstance(clrArray.ElementType(), clrArray.Length);
Buffer.BlockCopy(clrArray, 0, oneD, 0, arraySize);
}
else
{
oneD = clrArray;
}
var nativeSize = arraySize;
if (ClrType == typeof(byte))
{
nativeSize *= H5T.get_size(dtypeID).ToInt32();
}
var result = Marshal.AllocHGlobal(nativeSize);
if (ClrType == typeof(byte))
{
var maxLength = H5T.get_size(dtypeID).ToInt32();
string[] allStrings = (string[])oneD;
byte[] actualArray = new byte[maxLength * oneD.Length];
for (var i = 0; i < allStrings.Length; i++)
{
//return System.Text.Encoding.Default.GetString(slice);
byte[] bytes = Encoding.ASCII.GetBytes(allStrings[i] + '\0');
Buffer.BlockCopy(bytes, 0, actualArray, i * maxLength, bytes.Length);
}
Marshal.Copy(actualArray, 0, result, actualArray.Length);
}
else if (ClrType == typeof(double))
{
Marshal.Copy((double[])oneD, 0, result, oneD.Length);
}
else if (ClrType == typeof(float))
{
Marshal.Copy((float[])oneD, 0, result, oneD.Length);
}
else if (ClrType == typeof(long))
{
Marshal.Copy((long[])oneD, 0, result, oneD.Length);
}
else
{
throw new ArgumentException("Unknown ClrType");
}
return(result);
}
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 float[] TryReadFactor(AbstractWarpDataset ds, string datasetName)
{
string dsPath = (ds.hdfOperator as Hdf5Operator).GetDatasetNames.Where(t => t.Contains(datasetName))
.FirstOrDefault();
float[] factor = null;
int h5FileId = H5F.open(ds.fileName, H5F.ACC_RDONLY);
int datasetId = H5D.open(h5FileId, dsPath);
int typeId = H5D.get_type(datasetId);
int spaceId = H5D.get_space(datasetId);
if (H5T.get_class(typeId) == H5T.class_t.FLOAT)
{
var size = H5T.get_size(typeId);
int rank = H5S.get_simple_extent_ndims(spaceId);
ulong[] dims = new ulong[rank];
int err = H5S.get_simple_extent_dims(spaceId, dims, null);
factor = new float[dims[0]];
GCHandle hnd = GCHandle.Alloc(factor, GCHandleType.Pinned);
H5D.read(datasetId, typeId, H5S.ALL, H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
}
if (spaceId != 0)
{
H5S.close(spaceId);
}
if (typeId != 0)
{
H5T.close(typeId);
}
if (datasetId != 0)
{
H5D.close(datasetId);
}
if (h5FileId != 0)
{
H5F.close(h5FileId);
}
return(factor);
}
public static IEnumerable ReadStrings(string filename, string dataset)
{
var f = H5F.open(filename, H5F.ACC_RDONLY);
if (f < 0)
{
throw new Exception("Could not open file: " + filename);
}
var dset = H5D.open(f, Encoding.ASCII.GetBytes(dataset), H5P.DEFAULT);
if (dset < 0)
{
throw new Exception("Could not open dataset: " + dataset);
}
var filetype = H5D.get_type(dset);
var sdim = H5T.get_size(filetype) + 1;
var space = H5D.get_space(dset);
var ndims = H5S.get_simple_extent_ndims(space);
ulong[] dims = new ulong[ndims];
H5S.get_simple_extent_dims(space, dims, null);
var memtype = H5T.copy(H5T.C_S1);
var status = H5T.set_size(memtype, sdim);
int len = (int)(dims[0] * (ulong)sdim * SIZEOF_CHAR);
byte[] buffer = new byte[len];
IntPtr ptr = Marshal.AllocHGlobal(len);
status = H5D.read(dset, memtype, H5S.ALL, H5S.ALL, H5P.DEFAULT, ptr);
Marshal.Copy(ptr, buffer, 0, len);
Marshal.FreeHGlobal(ptr);
string s = Encoding.ASCII.GetString(buffer);
return(s.Split(new char[] { '\0' }, StringSplitOptions.RemoveEmptyEntries));
}
/// <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);
}
public static string ReadUnicodeString(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);
var datasetId = H5D.open(groupId, name);
var typeId = H5D.get_type(datasetId);
var classId = H5T.get_class(typeId);
var order = H5T.get_order(typeId);
IntPtr size = H5T.get_size(typeId);
int strLen = (int)size;
var spaceId = H5D.get_space(datasetId);
hid_t count = H5S.get_simple_extent_npoints(spaceId);
IntPtr[] rdata = new IntPtr[count];
byte[] wdata = new byte[strLen];
GCHandle hnd = GCHandle.Alloc(rdata, GCHandleType.Pinned);
H5D.read(datasetId, datatype, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
for (int i = 0; i < strLen; i++)
{
Marshal.ReadByte(rdata[0], i);
}
Marshal.Copy(rdata[0], wdata, 0, strLen);
string s = Encoding.UTF8.GetString(wdata);
hnd.Free();
H5S.close(spaceId);
H5T.close(datatype);
H5D.close(datasetId);
return(s);
}
public static string[] LoadStringDataset(string filePath, string dataSetName)
{
//With much Help from: https://stackoverflow.com/questions/23295545/reading-string-array-from-a-hdf5-dataset
long fileId = H5F.open(filePath, H5F.ACC_RDONLY);
string longJoinedString;
int stringLength;
try {
long datasetId = H5D.open(fileId, dataSetName);
long spaceID = H5D.get_space(datasetId);
long dataType = H5D.get_type(datasetId);
int[] dimensions = GetDatasetDimensions(spaceID);
stringLength = (int)H5T.get_size(dataType);
byte[] buffer = new byte[dimensions[0] * stringLength];
GCHandle gch = GCHandle.Alloc(buffer, GCHandleType.Pinned);
try {
H5D.read(datasetId, dataType, H5S.ALL, H5S.ALL, H5P.DEFAULT, gch.AddrOfPinnedObject());
longJoinedString = Encoding.ASCII.GetString(buffer);
}
finally {
gch.Free();
H5D.close(dataType);
H5D.close(spaceID);
H5D.close(datasetId);
}
}
finally {
H5F.close(fileId);
}
return(longJoinedString.SplitInParts(stringLength).Select(ss => (string)(object)ss).ToArray());
}
private static string ReadDataString(hid_t fileLoc, string name)
{
hid_t dset = H5D.open(fileLoc, name);
hid_t type = H5D.get_type(dset);
// H5T.is_variable_str(type);
IntPtr size = H5T.get_size(type);
hid_t fspace = H5D.get_space(dset);
hid_t mem_type = H5T.copy(type);
H5T.set_size(mem_type, size);
byte[] buffer = new byte[size.ToInt32()];
GCHandle hnd = GCHandle.Alloc(buffer, GCHandleType.Pinned);
H5D.read(dset, mem_type, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
H5T.close(mem_type);
// remove the last "/0"
if (buffer[buffer.Length - 1] == 0)
{
byte[] buffer2 = new byte[buffer.Length - 1];
for (int i = 0; i < buffer2.Length; i++)
{
buffer2[i] = buffer[i];
}
return(ASCIIEncoding.ASCII.GetString(buffer2));
}
return(ASCIIEncoding.ASCII.GetString(buffer));
}
public static string ReadUnicodeString(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.SPACEPAD);
var datasetId = H5D.open(groupId, name);
var typeId = H5D.get_type(datasetId);
var classId = H5T.get_class(typeId);
var order = H5T.get_order(typeId);
IntPtr size = H5T.get_size(typeId);
int strLen = (int)size;
var spaceId = H5D.get_space(datasetId);
byte[] wdata = new byte[strLen];
//IntPtr ptr = new IntPtr();
GCHandle hnd = GCHandle.Alloc(wdata, GCHandleType.Pinned);
H5D.read(datasetId, datatype, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
//int len = 0;
//while (Marshal.ReadByte(ptr, len) != 0) { ++len; }
//byte[] name_buf = new byte[len];
//Marshal.Copy(ptr, name_buf, 0, len);
string s = Encoding.UTF8.GetString(wdata);
H5S.close(spaceId);
H5T.close(datatype);
H5D.close(datasetId);
return(s);
}
static void Main_Read(string[] args)
{
int DATA_ARRAY_LENGTH = 5;
//var h5 = H5F.open(@"E:\HDF5\HDF5DotNet-src\examples\CSharpExample\CSharpExample1\table.h5", H5F.ACC_RDONLY);
//var h5 = H5F.open(@"D:\test.h5", H5F.ACC_RDONLY);
//var h5 = H5F.open(@"E:\HDF5\Hdf5DotnetTools-master\ToolTest\bin\Debug\table.h5", H5F.ACC_RDONLY);
var h5 = H5F.open(@"E:\HDF5\test_gzip.h5", H5F.ACC_RDONLY);
var dataset = H5D.open(h5, "trans_detail/20160929");
var spaceid = H5D.get_space(dataset);
var npoints = H5S.get_simple_extent_npoints(spaceid);
//var dims = H5S.get_simple_extent_dims(spaceid);
int rank = H5S.get_simple_extent_ndims(spaceid);
// 是不是不能用自己的type
var dtype = H5D.get_type(dataset);
var dtcls = H5T.get_class(dtype);
var size = H5T.get_size(dtype);
var sz = Marshal.SizeOf(typeof(ComType));
var dtype_n = H5T.get_nmembers(dtype);
for (uint i = 0; i < dtype_n; ++i)
{
var x = H5T.get_member_name(dtype, i);
var x4 = Marshal.PtrToStringAnsi(x);
var y = H5T.get_member_type(dtype, i);
var z = H5T.get_class(y);
var x1 = H5T.get_member_offset(dtype, i);
var x3 = H5T.get_size(y);
Console.WriteLine(x4);
Console.WriteLine(z);
Console.WriteLine(x1);
//var x2 = Marshal.OffsetOf(typeof(ComType), x4).ToInt32();
//Console.WriteLine(x2);
Console.WriteLine(x3);
}
int ss1 = Marshal.SizeOf(typeof(ComType));
IntPtr p = Marshal.AllocHGlobal(ss1 * 11);
H5D.read(dataset, dtype, H5S.ALL, H5S.ALL, H5P.DEFAULT, p);
var s = Marshal.PtrToStructure(p, typeof(ComType));
Console.WriteLine(s);
var s2 = Marshal.PtrToStructure(p + ss1, typeof(ComType));
Console.WriteLine(s2);
var s3 = Marshal.PtrToStructure(p + ss1 * 4, typeof(ComType));
Console.WriteLine(s3);
var s4 = Marshal.PtrToStructure(p + ss1 * 5, typeof(ComType));
Console.WriteLine(s4);
var s6 = Marshal.PtrToStructure(p + ss1 * 10, typeof(ComType));
Console.WriteLine(s6);
}
public static string ReadUnicodeString(hid_t groupId, string name)
{
var datasetId = H5D.open(groupId, name);
var typeId = H5D.get_type(datasetId);
if (H5T.is_variable_str(typeId) > 0)
{
var spaceId = H5D.get_space(datasetId);
hid_t count = H5S.get_simple_extent_npoints(spaceId);
IntPtr[] rdata = new IntPtr[count];
GCHandle hnd = GCHandle.Alloc(rdata, GCHandleType.Pinned);
H5D.read(datasetId, typeId, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
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 stringPart = Encoding.UTF8.GetString(buffer);
attrStrings.Add(stringPart);
H5.free_memory(rdata[i]);
}
hnd.Free();
H5S.close(spaceId);
H5D.close(datasetId);
return(attrStrings[0]);
}
// Must be a non-variable length string.
int size = H5T.get_size(typeId).ToInt32();
IntPtr iPtr = Marshal.AllocHGlobal(size);
int result = H5D.read(datasetId, typeId, H5S.ALL, H5S.ALL,
H5P.DEFAULT, iPtr);
if (result < 0)
{
throw new IOException("Failed to read dataset");
}
var strDest = new byte[size];
Marshal.Copy(iPtr, strDest, 0, size);
Marshal.FreeHGlobal(iPtr);
H5D.close(datasetId);
return(Encoding.UTF8.GetString(strDest).TrimEnd((Char)0));
}
private string ReadBuffer(byte[] buffer, int offset, H5T.class_t typeClass, int typeId)
{
string result = string.Empty;
IntPtr dataSize = H5T.get_size(typeId);
H5T.order_t order = H5T.get_order(typeId);
byte[] temp = new byte[dataSize.ToInt32()];
Array.Copy(buffer, offset, temp, 0, dataSize.ToInt32());
if (order == H5T.order_t.BE && typeClass != H5T.class_t.STRING)
{
Array.Reverse(temp);
}
switch (typeClass)
{
case H5T.class_t.NO_CLASS:
break;
case H5T.class_t.INTEGER:
// H5T.Sign.TWOS_COMPLEMENT;
H5T.sign_t sign = H5T.get_sign(typeId);
switch (dataSize.ToInt32())
{
case 1:
result = ((double)BitConverter.ToChar(temp, 0)).ToString("G");
break;
case 2:
switch (sign)
{
case H5T.sign_t.SGN_2:
result = ((double)BitConverter.ToInt16(temp, 0)).ToString("G");
break;
case H5T.sign_t.NONE:
result = ((double)BitConverter.ToUInt16(temp, 0)).ToString("G");
break;
}
break;
case 4:
switch (sign)
{
case H5T.sign_t.SGN_2:
result = ((double)BitConverter.ToInt32(temp, 0)).ToString("G");
break;
case H5T.sign_t.NONE:
result = ((double)BitConverter.ToUInt32(temp, 0)).ToString("G");
break;
}
break;
case 8:
switch (sign)
{
case H5T.sign_t.SGN_2:
result = ((double)BitConverter.ToInt64(temp, 0)).ToString("G");
break;
case H5T.sign_t.NONE:
result = ((double)BitConverter.ToUInt64(temp, 0)).ToString("G");
break;
}
break;
}
break;
case H5T.class_t.FLOAT:
switch (dataSize.ToInt32())
{
case 4:
{
result = BitConverter.ToSingle(temp, 0).ToString("G");
break;
}
case 8:
{
result = BitConverter.ToDouble(temp, 0).ToString("G");
break;
}
}
break;
case H5T.class_t.STRING:
{
GCHandle handler = GCHandle.Alloc(temp, GCHandleType.Pinned);
var str = Marshal.PtrToStringAnsi(handler.AddrOfPinnedObject());
handler.Free();
result = str;
break;
}
default:
break;
}
return(result);
}
public static Hdf5DataType GetDataTypeByType(Hdf5Identifier _typeId)
{
var typeClass = H5T.get_class(_typeId.Value);
var typeSize = (int)H5T.get_size(_typeId.Value);
var typeSign = H5T.get_sign(_typeId.Value);
var typeOrder = H5T.get_order(_typeId.Value);
Hdf5DataType dt = new Hdf5DataType
{
Id = _typeId,
Size = typeSize,
};
if (typeOrder == H5T.order_t.BE)
{
dt.ByteOrder = Hdf5ByteOrder.BigEndian;
}
else if (typeOrder == H5T.order_t.LE)
{
dt.ByteOrder = Hdf5ByteOrder.LittleEndian;
}
else if (typeOrder == H5T.order_t.ONE)
{
dt.ByteOrder = Hdf5ByteOrder.None;
}
if (typeClass == H5T.class_t.INTEGER)
{
if (typeSign == H5T.sign_t.NONE)
{
if (typeSize == 1)
{
dt.Type = Hdf5DataTypes.UInt8;
dt.NativeType = H5T.NATIVE_UINT8.ToId();
}
else if (typeSize == 2)
{
dt.Type = Hdf5DataTypes.UInt16;
dt.NativeType = H5T.NATIVE_UINT16.ToId();
}
else if (typeSize == 4)
{
dt.Type = Hdf5DataTypes.UInt32;
dt.NativeType = H5T.NATIVE_UINT32.ToId();
}
else if (typeSize == 8)
{
dt.Type = Hdf5DataTypes.UInt64;
dt.NativeType = H5T.NATIVE_UINT64.ToId();
}
}
else
{
if (typeSize == 1)
{
dt.Type = Hdf5DataTypes.Int8;
dt.NativeType = H5T.NATIVE_INT8.ToId();
}
else if (typeSize == 2)
{
dt.Type = Hdf5DataTypes.Int16;
dt.NativeType = H5T.NATIVE_INT16.ToId();
}
else if (typeSize == 4)
{
dt.Type = Hdf5DataTypes.Int32;
dt.NativeType = H5T.NATIVE_INT32.ToId();
}
else if (typeSize == 8)
{
dt.Type = Hdf5DataTypes.Int64;
dt.NativeType = H5T.NATIVE_INT64.ToId();
}
}
}
else if (typeClass == H5T.class_t.FLOAT)
{
if (typeSize == 4)
{
dt.Type = Hdf5DataTypes.Single;
dt.NativeType = H5T.NATIVE_FLOAT.ToId();
}
else if (typeSize == 8)
{
dt.Type = Hdf5DataTypes.Double;
dt.NativeType = H5T.NATIVE_DOUBLE.ToId();
}
}
else if (typeClass == H5T.class_t.STRING)
{
dt.Type = Hdf5DataTypes.String;
dt.NativeType = H5T.C_S1.ToId();
}
return(dt);
}
public static IEnumerable <OffsetInfo> GetCompoundInfo(Type type, bool ieee = false)
{
//Type t = typeof(T);
var strtype = H5T.copy(H5T.C_S1);
int strsize = (int)H5T.get_size(strtype);
int curSize = 0;
List <OffsetInfo> offsets = new List <OffsetInfo>();
foreach (var x in type.GetFields())
{
var fldType = x.FieldType;
OffsetInfo oi = new OffsetInfo()
{
name = x.Name,
type = fldType,
datatype = ieee ? GetDatatypeIEEE(fldType) : GetDatatype(fldType),
size = fldType == typeof(string) ? StringLength(x) : Marshal.SizeOf(fldType),
offset = 0 + curSize
};
if (oi.datatype == H5T.C_S1)
{
strtype = H5T.copy(H5T.C_S1);
H5T.set_size(strtype, new IntPtr(oi.size));
oi.datatype = strtype;
}
if (oi.datatype == H5T.STD_I64BE)
{
oi.size = oi.size * 2;
}
curSize = curSize + oi.size;
offsets.Add(oi);
}
/* poging om ook properties te bewaren.
* foreach (var x in type.GetProperties(BindingFlags.NonPublic | BindingFlags.Instance | BindingFlags.Public))
* {
* bool saveProperty = false;
* bool isNotPublic = x.PropertyType.Attributes != TypeAttributes.Public;
* foreach (Attribute attr in Attribute.GetCustomAttributes(x))
* {
* var legAttr = attr as Hdf5SaveAttribute;
* var kind = legAttr?.SaveKind;
* bool saveAndPrivateProp = isNotPublic && kind == Hdf5Save.Save;
* bool doNotSaveProp = (kind == Hdf5Save.DoNotSave) ;
* if (saveAndPrivateProp && !doNotSaveProp)
* {
* saveProperty = true;
* continue;
* }
*
* }
* if (!saveProperty)
* continue;
* var propType = x.PropertyType;
* OffsetInfo oi = new OffsetInfo()
* {
* name = x.Name,
* type = propType,
* datatype = ieee ? GetDatatypeIEEE(propType) : GetDatatype(propType),
* size = propType == typeof(string) ? stringLength(x) : Marshal.SizeOf(propType),
* offset = 0 + curSize
* };
* if (oi.datatype == H5T.C_S1)
* {
* strtype = H5T.copy(H5T.C_S1);
* H5T.set_size(strtype, new IntPtr(oi.size));
* oi.datatype = strtype;
* }
* if (oi.datatype == H5T.STD_I64BE)
* oi.size = oi.size * 2;
* curSize = curSize + oi.size;
*
* offsets.Add(oi);
* }*/
H5T.close(strtype);
return(offsets);
}
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'));
}
public static IEnumerable <OffsetInfo> GetCompoundInfo(Type type, bool ieee = false)
{
//Type t = typeof(T);
var strtype = H5T.copy(H5T.C_S1);
int strsize = (int)H5T.get_size(strtype);
int curSize = 0;
List <OffsetInfo> offsets = new List <OffsetInfo>();
foreach (var x in type.GetFields())
{
//var fldType = x.FieldType;
//OffsetInfo oi = new OffsetInfo()
//{
// name = x.Name,
// type = fldType,
// datatype = ieee ? GetDatatypeIEEE(fldType) : GetDatatype(fldType),
// size = fldType == typeof(string) ? StringLength(x) : Marshal.SizeOf(fldType),
// offset = 0 + curSize
//};
var fldType = x.FieldType;
var marshallAsAttribute = type.GetMember(x.Name).Select(m => m.GetCustomAttribute <MarshalAsAttribute>()).FirstOrDefault();
OffsetInfo oi = new OffsetInfo()
{
name = x.Name,
type = fldType,
datatype = !fldType.IsArray ? ieee ? GetDatatypeIEEE(fldType) : GetDatatype(fldType)
: H5T.array_create(ieee ? GetDatatypeIEEE(fldType.GetElementType()) : GetDatatype(fldType.GetElementType()), (uint)fldType.GetArrayRank(), Enumerable.Range(0, fldType.GetArrayRank()).Select(i => (ulong)marshallAsAttribute.SizeConst).ToArray()),
size = fldType == typeof(string) ? StringLength(x) : !fldType.IsArray ? Marshal.SizeOf(fldType) : Marshal.SizeOf(fldType.GetElementType()) * marshallAsAttribute.SizeConst,
offset = 0 + curSize
};
if (oi.datatype == H5T.C_S1)
{
strtype = H5T.copy(H5T.C_S1);
H5T.set_size(strtype, new IntPtr(oi.size));
oi.datatype = strtype;
}
if (oi.datatype == H5T.STD_I64BE)
{
oi.size = oi.size * 2;
}
curSize = curSize + oi.size;
offsets.Add(oi);
}
/* poging om ook properties te bewaren.
* foreach (var x in type.GetProperties(BindingFlags.NonPublic | BindingFlags.Instance | BindingFlags.Public))
* {
* bool saveProperty = false;
* bool isNotPublic = x.PropertyType.Attributes != TypeAttributes.Public;
* foreach (Attribute attr in Attribute.GetCustomAttributes(x))
* {
* var legAttr = attr as Hdf5SaveAttribute;
* var kind = legAttr?.SaveKind;
* bool saveAndPrivateProp = isNotPublic && kind == Hdf5Save.Save;
* bool doNotSaveProp = (kind == Hdf5Save.DoNotSave) ;
* if (saveAndPrivateProp && !doNotSaveProp)
* {
* saveProperty = true;
* continue;
* }
*
* }
* if (!saveProperty)
* continue;
* var propType = x.PropertyType;
* OffsetInfo oi = new OffsetInfo()
* {
* name = x.Name,
* type = propType,
* datatype = ieee ? GetDatatypeIEEE(propType) : GetDatatype(propType),
* size = propType == typeof(string) ? stringLength(x) : Marshal.SizeOf(propType),
* offset = 0 + curSize
* };
* if (oi.datatype == H5T.C_S1)
* {
* strtype = H5T.copy(H5T.C_S1);
* H5T.set_size(strtype, new IntPtr(oi.size));
* oi.datatype = strtype;
* }
* if (oi.datatype == H5T.STD_I64BE)
* oi.size = oi.size * 2;
* curSize = curSize + oi.size;
*
* offsets.Add(oi);
* }*/
H5T.close(strtype);
return(offsets);
}
private object GetAttributeValue(int _h5FileId, string attributeName)
{
H5AttributeId attId = H5A.open(_h5FileId, attributeName);
if (attId == 0)
{
return(null);
}
H5DataTypeId typeId = 0;
H5DataTypeId dtId = 0;
H5A.info_t attInfo = new H5A.info_t();
H5DataSpaceId spaceId = 0;
H5DataTypeId oldTypeId = 0;
object retObject = null;
try
{
typeId = H5A.get_type(attId);
H5A.get_info(attId, ref attInfo);
dtId = H5A.get_type(attId);
spaceId = H5A.get_space(attId);
IntPtr dataSize = H5T.get_size(dtId);
//
oldTypeId = typeId;
typeId = H5T.get_native_type(typeId, H5T.direction_t.DEFAULT);
H5T.class_t typeClass = H5T.get_class(typeId);
int ndims = H5S.get_simple_extent_ndims(spaceId);
ulong[] dims = new ulong[ndims];
H5S.get_simple_extent_dims(spaceId, dims, null);
ulong dimSize = 1;
if (dims.Length == 0)
{
dimSize = 1;
}
else
{
foreach (ulong dim in dims)
{
dimSize *= dim;
}
}
switch (typeClass)
{
case H5T.class_t.NO_CLASS:
break;
case H5T.class_t.INTEGER:
// H5T.Sign.TWOS_COMPLEMENT;
H5T.sign_t sign = H5T.get_sign(oldTypeId);
switch (dataSize.ToInt32())
{
case 1:
retObject = ReadArray <byte>(dimSize, attId, typeId);
break;
case 2:
switch (sign)
{
case H5T.sign_t.SGN_2:
retObject = ReadArray <Int16>(dimSize, attId, typeId);
break;
case H5T.sign_t.NONE:
retObject = ReadArray <UInt16>(dimSize, attId, typeId);
break;
}
break;
case 4:
switch (sign)
{
case H5T.sign_t.SGN_2:
retObject = ReadArray <Int32>(dimSize, attId, typeId);
break;
case H5T.sign_t.NONE:
retObject = ReadArray <UInt32>(dimSize, attId, typeId);
break;
}
break;
case 8:
switch (sign)
{
case H5T.sign_t.SGN_2:
retObject = ReadArray <Int64>(dimSize, attId, typeId);
break;
case H5T.sign_t.NONE:
retObject = ReadArray <UInt64>(dimSize, attId, typeId);
break;
}
break;
}
break;
case H5T.class_t.FLOAT:
switch (dataSize.ToInt32())
{
case 4:
retObject = ReadArray <float>(dimSize, attId, typeId);
break;
case 8:
retObject = ReadArray <double>(dimSize, attId, typeId);
break;
}
break;
case H5T.class_t.STRING:
ulong size = attInfo.data_size;
byte[] chars = ReadArray <byte>(size, attId, typeId);
retObject = Encoding.ASCII.GetString(chars);
break;
default:
break;
}
return(retObject);
}
finally
{
if (spaceId != 0)
{
H5S.close(spaceId);
}
if (attId != 0)
{
H5A.close(attId);
}
if (oldTypeId != 0)
{
H5T.close(oldTypeId);
}
if (typeId != 0)
{
H5T.close(typeId);
}
if (dtId != 0)
{
H5T.close(dtId);
}
}
}
public Dictionary <string, string> GetDatasetAttributes(string originalDatasetName)
{
H5DataSetId datasetId = 0;
H5GroupId groupId = 0;
H5DataTypeId typeId = 0;
H5DataSpaceId spaceId = 0;
try
{
if (_h5FileId < 0)
{
return(null);
}
string datasetName = GetDatasetFullNames(originalDatasetName, _h5FileId);
if (string.IsNullOrEmpty(datasetName))
{
return(null);
}
int groupIndex = datasetName.LastIndexOf('/');
if (groupIndex == -1)
{
datasetId = H5D.open(_h5FileId, datasetName);
}
else
{
string groupName = datasetName.Substring(0, groupIndex + 1);
string dsName = datasetName.Substring(groupIndex + 1);
groupId = H5G.open(_h5FileId, groupName);
datasetId = H5D.open(groupId, dsName);
}
if (datasetId == 0)
{
return(null);
}
Dictionary <string, string> attValues = new Dictionary <string, string>();
typeId = H5D.get_type(datasetId);
H5T.class_t type = H5T.get_class(typeId);
IntPtr tSize = H5T.get_size(typeId);
spaceId = H5D.get_space(datasetId);
int length = H5S.get_simple_extent_ndims(spaceId);
ulong[] dims = new ulong[length];
H5S.get_simple_extent_dims(spaceId, dims, null);
ulong storageSize = H5D.get_storage_size(datasetId);
attValues.Add("DataSetName", datasetName);
attValues.Add("DataType", type.ToString());
attValues.Add("DataTypeSize", tSize.ToString() + "Byte");
attValues.Add("Dims", String.Join("*", dims));
attValues.Add("StorageSize", storageSize.ToString() + "Byte");
//所有Attributes的键
ArrayList arrayList = new ArrayList();
GCHandle handle = GCHandle.Alloc(arrayList);
ulong n = 0;
// the callback is defined in H5ATest.cs
H5A.operator_t cb = (int location_id, IntPtr attr_name, ref H5A.info_t ainfo, IntPtr op_data) =>
{
GCHandle hnd = (GCHandle)op_data;
ArrayList al = (hnd.Target as ArrayList);
int len = 0;
while (Marshal.ReadByte(attr_name, len) != 0)
{
++len;
}
byte[] buf = new byte[len];
Marshal.Copy(attr_name, buf, 0, len);
al.Add(Encoding.UTF8.GetString(buf));
return(0);
};
H5A.iterate(datasetId, H5.index_t.NAME, H5.iter_order_t.NATIVE, ref n, cb, (IntPtr)handle);
handle.Free();
foreach (string attName in arrayList)
{
attValues.Add(attName, ReadAttributeValue(datasetId, attName));
}
return(attValues);
}
finally
{
if (spaceId != 0)
{
H5S.close(spaceId);
}
if (typeId != 0)
{
H5T.close(typeId);
}
if (datasetId != 0)
{
H5D.close(datasetId);
}
if (groupId != 0)
{
H5G.close(groupId);
}
}
}
