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);
}
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);
}
}
private static bool IsHDF5String(hid_t fileLoc, string name)
{
hid_t dset = H5D.open(fileLoc, name);
hid_t type = H5D.get_type(dset);
H5T.class_t cl = H5T.get_class(type);
return(cl == H5T.class_t.STRING);
}
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);
}
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 bool WriteScalarNumericAttribute <T>(hid_t attribute, T value, hid_t type) 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 attributeType = H5A.get_type(attribute);
if (attributeType < 0)
{
throw new Exception("Failed to get type");
}
var attributeTypeClass = H5T.get_class(attributeType);
H5T.close(attributeType);
if (attributeTypeClass != H5T.class_t.INTEGER && attributeTypeClass != 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.
object boxedValue = value;
H5A.write(attribute, type, new PinnedObject(boxedValue));
return(true);
}
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 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);
}
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 bool WriteFixedStringAttribute(hid_t attribute, string value, bool utf8)
{
if (value == null)
{
throw new ArgumentNullException("value");
}
var space = H5A.get_space(attribute);
if (space < 0)
{
throw new Exception("Failed to get data 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);
if (typeClass != H5T.class_t.STRING)
{
H5T.close(type);
throw new Exception("Not a string attribute");
}
var isVariableString = H5T.is_variable_str(type);
H5T.close(type);
if (isVariableString < 0)
{
throw new Exception("H5T.is_variable_str failed");
}
if (isVariableString > 0)
{
throw new Exception("Not a fixed string attribute");
}
// TODO: Do we really need to create a new memory type here?
var bytes = value.ToBytes(utf8);
var memType = CreateFixedStringType(bytes, utf8);
// TODO: type or memType here?
H5A.write(attribute, memType, new PinnedObject(bytes));
H5T.close(memType);
return(true);
}
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);
}
}
}
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);
}
}
}
private static List <HDF5info> ScanInfo(hid_t gId, List <HDF5info> fields, string fullname)
{
IntPtr MAX_NAME = new IntPtr(1024);
System.Text.StringBuilder group_name = new System.Text.StringBuilder();
System.Text.StringBuilder member_name = new System.Text.StringBuilder();
IntPtr len = H5I.get_name(gId, group_name, MAX_NAME);
hsize_t nobj = new hsize_t();
H5G.get_num_objs(gId, ref nobj);
for (int i = 0; i < (int)nobj; i++)
{
member_name = new System.Text.StringBuilder();
member_name.Capacity = 1024;
IntPtr len2 = H5G.get_objname_by_idx(gId, (ulong)i, member_name, MAX_NAME);
int objtype = H5G.get_objtype_by_idx(gId, (ulong)i);
if (objtype == 0) //group
{
hid_t gId2 = H5G.open(gId, member_name.ToString());
fields = ScanInfo(gId2, fields, string.Format("{0}/{1}", fullname, member_name));
}
else if (objtype == 1) //Object is a dataset.
{
HDF5info hDF5Info = new HDF5info();
hid_t dset = H5D.open(gId, member_name.ToString());
hid_t fspace = H5D.get_space(dset);
hid_t count = H5S.get_simple_extent_ndims(fspace);
hid_t type = H5D.get_type(dset);
hDF5Info.HDFclass = getH5Tstring(type);
hDF5Info.field = string.Format("{0}/{1}", fullname, member_name);
if (H5T.get_class(type) == H5T.class_t.STRING)
{
hDF5Info.description = nirs.io.ReadDataString(gId, string.Format("{0}", member_name));
}
else if (H5T.get_class(type) == H5T.class_t.FLOAT |
H5T.get_class(type) == H5T.class_t.INTEGER)
{
hsize_t[] dims = new hsize_t[count];
hsize_t[] maxdims = new hsize_t[count];
H5S.get_simple_extent_dims(fspace, dims, maxdims);
if (dims.Length == 1 & dims[0] == 1)
{
var val = nirs.io.ReadDataValue(gId, string.Format("{0}", member_name));
hDF5Info.description = string.Format("{0}", val);
}
else if (dims.Length == 1 & dims[0] > 1)
{
hDF5Info.description = string.Format("Vector <{0} x 1>", dims[0]);
}
else
{
hDF5Info.description = string.Format("Array <{0} x {1}>", dims[0], dims[1]);
if (hDF5Info.field.Contains("dataTimeSeries") & dims[0] > dims[1])
{
hDF5Info.description += " TRANSPOSE WARNING ";
}
if (hDF5Info.field.Contains("Pos") & dims[1] != 3)
{
hDF5Info.description += " TRANSPOSE WARNING ";
}
if (hDF5Info.field.Contains("stim") & hDF5Info.field.Contains("data") & dims[1] != 3)
{
hDF5Info.description += " TRANSPOSE WARNING ";
}
}
}
else
{
hDF5Info.description = "";
}
fields.Add(hDF5Info);
}
}
H5G.close(gId);
return(fields);
}
private static string getH5Tstring(hid_t typeT)
{
// TODO
return(String.Format("{0}", H5T.get_class(typeT)));
}
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);
}
private List <float[]> ReadDataSetToSingle(AbstractWarpDataset srcbandpro, int[] bands)
{
List <float[]> datas = new List <float[]>();
var prjBands = PrjBandTable.GetPrjBands(srcbandpro);
H5ID h5FileId = H5F.open(srcbandpro.fileName, H5F.ACC_RDONLY);
foreach (int index in bands)
{
//Single[] data = new Single[srcSize.Width * srcSize.Height];
var bandIndex = prjBands[index - 1].DataSetIndex;
string dsName = "CALChannel" + bandIndex.ToString("00");
H5ID datasetId = H5D.open(h5FileId, dsName);
if (datasetId <= 0)
{
throw new ArgumentNullException(string.Format("FY4辐射定标，未找到名称为{0}的数据.",
"CALChannel" + index.ToString("00")));
}
H5ID typeId = H5D.get_type(datasetId);
H5ID spaceId = H5D.get_space(datasetId);
if (H5T.get_class(typeId) == H5T.class_t.FLOAT)
{
int rank = H5S.get_simple_extent_ndims(spaceId);
ulong[] dims = new ulong[rank];
ulong[] maxDims = new ulong[rank];
H5S.get_simple_extent_dims(spaceId, dims, maxDims);
float[] buffer = new float[dims[0]];
GCHandle hnd = GCHandle.Alloc(buffer, GCHandleType.Pinned);
H5D.read(datasetId, typeId, H5S.ALL, H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
if (buffer.Any(t => t > Math.Pow(10, 10) || t < -Math.Pow(10, 10)))
{
for (int i = 0; i < buffer.Length; i++)
{
var t = BitConverter.GetBytes(buffer[i]);
Array.Reverse(t);
buffer[i] = BitConverter.ToSingle(t, 0);
}
}
datas.Add(buffer);
}
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(datas);
}
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);
}
private int depth_first(HObject parentObject, int nTotal)
{
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject}): start");
int nelems;
string fullPath = null;
string ppath = null;
long gid = -1;
H5Group pgroup = (H5Group)parentObject;
ppath = pgroup.getPath();
if (ppath == null)
{
fullPath = HObject.SEPARATOR;
}
else
{
fullPath = ppath + pgroup.getName() + HObject.SEPARATOR;
}
nelems = 0;
try
{
gid = pgroup.open();
var info = new H5G.info_t();
H5G.get_info(gid, ref info);
nelems = (int)info.nlinks;
}
catch (Exception ex)
{
nelems = -1;
Hdf5Utils.LogError?.Invoke($"depth_first({parentObject}): H5Gget_info(gid {gid}) failure: {ex}");
}
if (nelems <= 0)
{
pgroup.close(gid);
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject}): nelems <= 0");
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject}): finish");
return(nTotal);
}
// since each call of H5.H5Gget_objname_by_idx() takes about one second.
// 1,000,000 calls take 12 days. Instead of calling it in a loop,
// we use only one call to get all the information, which takes about
// two seconds
int[] objTypes = new int[nelems];
//long[] fNos = new long[nelems];
//long[] objRefs = new long[nelems];
string[] objNames = new string[nelems];
H5L.info_t[] infos = new H5L.info_t[nelems];
try
{
int i = 0;
int callback(long group, IntPtr name, ref H5L.info_t info, IntPtr op_data)
{
string realName = Marshal.PtrToStringAuto(name);
objTypes[i] = (int)info.type;
objNames[i] = realName;
infos[i] = info;
return(i++);
}
ulong pos = 0;
H5L.iterate(gid, indexType, indexOrder, ref pos, callback, IntPtr.Zero);
//for (ulong i = 0; i < (ulong)nelems; i++)
//{
// H5G.info_t info = new H5G.info_t();
// H5G.get_info_by_idx(fid, fullPath, indexType, indexOrder, i, ref info);
// infos[i] = info;
//}
// H5.H5Gget_obj_info_full(fid, fullPath, objNames, objTypes, null, fNos, objRefs, indexType, indexOrder);
}
catch (Exception ex)
{
Hdf5Utils.LogError?.Invoke($"depth_first({parentObject}): failure: {ex}");
Hdf5Utils.LogError?.Invoke($"depth_first({parentObject}): finish");
return(nTotal);
}
int nStart = getStartMembers();
int nMax = getMaxMembers();
string obj_name;
int obj_type;
// Iterate through the file to see members of the group
for (int i = 0; i < nelems; i++)
{
obj_name = objNames[i];
obj_type = objTypes[i];
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject}): obj_name={obj_name}, obj_type={obj_type}");
if (obj_name == null)
{
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject}): continue after null obj_name");
continue;
}
nTotal++;
if (nMax > 0)
{
if ((nTotal - nStart) >= nMax)
{
break; // loaded enough objects
}
}
bool skipLoad = (nTotal > 0) && (nTotal < nStart);
// create a new group
if (obj_type == HDF5Constants.H5O_TYPE_GROUP)
{
H5Group g = new H5Group(this, obj_name, fullPath, pgroup);
pgroup.addToMemberList(g);
// detect and stop loops
// a loop is detected if there exists object with the same
// object ID by tracing path back up to the root.
bool hasLoop = false;
H5Group tmpObj = (H5Group)parentObject;
while (tmpObj != null)
{
if (tmpObj.equalsOID(new IntPtr((int)infos[i].u.address)) && (tmpObj.getPath() != null))
{
hasLoop = true;
break;
}
else
{
tmpObj = (H5Group)tmpObj.getParent();
}
}
// recursively go through the next group
// stops if it has loop.
if (!hasLoop)
{
nTotal = depth_first(g, nTotal);
}
}
else if (skipLoad)
{
continue;
}
else if (obj_type == HDF5Constants.H5O_TYPE_DATASET)
{
long did = -1;
long tid = -1;
H5T.class_t tclass = H5T.class_t.NO_CLASS;
try
{
did = H5D.open(fid, fullPath + obj_name, HDF5Constants.H5P_DEFAULT);
if (did >= 0)
{
tid = H5D.get_type(did);
tclass = H5T.get_class(tid);
if ((tclass == HDF5Constants.H5T_ARRAY) || (tclass == HDF5Constants.H5T_VLEN))
{
// for ARRAY, the type is determined by the base type
long btid = H5T.get_super(tid);
tclass = H5T.get_class(btid);
try
{
H5T.close(btid);
}
catch (Exception ex)
{
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject})[{i}] dataset {obj_name} H5Tclose(btid {btid}) failure: {ex}");
}
}
}
else
{
Hdf5Utils.LogError?.Invoke($"depth_first({parentObject})[{i}] {obj_name} dataset open failure");
}
}
catch (Exception ex)
{
Hdf5Utils.LogError?.Invoke($"depth_first({parentObject})[{i}] {obj_name} dataset access failure: {ex}");
}
finally
{
try
{
H5T.close(tid);
}
catch (Exception ex)
{
Hdf5Utils.LogError?.Invoke($"depth_first({parentObject})[{i}] dataset {obj_name} H5Tclose(tid {tid}) failure: {ex}");
}
try
{
H5D.close(did);
}
catch (Exception ex)
{
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject})[{i}] dataset {obj_name} H5Dclose(did {did}) failure: {ex}");
}
}
//todo:
//Dataset d = null;
//if (tclass == HDF5Constants.H5T_COMPOUND)
//{
// // create a new compound dataset
// d = new H5CompoundDS(this, obj_name, fullPath, oid); // deprecated!
//}
//else
//{
// // create a new scalar dataset
// d = new H5ScalarDS(this, obj_name, fullPath, oid); // deprecated!
//}
// pgroup.addToMemberList(d);
}
else if (obj_type == HDF5Constants.H5O_TYPE_NAMED_DATATYPE)
{
//Datatype t = new H5Datatype(this, obj_name, fullPath, oid); // deprecated!
//pgroup.addToMemberList(t);
}
else if (obj_type == HDF5Constants.H5O_TYPE_UNKNOWN)
{
//H5Link link = new H5Link(this, obj_name, fullPath, oid);
// pgroup.addToMemberList(link);
continue; // do the next one, if the object is not identified.
}
} // ( i = 0; i < nelems; i++)
pgroup.close(gid);
Hdf5Utils.LogInfo?.Invoke($"depth_first({parentObject}): finish");
return(nTotal);
}
