public static double[, ,] ReadFieldData3D(string fileName)
{
H5FileId fileId = H5F.open(fileName, H5F.OpenMode.ACC_RDONLY);
H5DataSetId fDataSetId = H5D.open(fileId, "/FieldData/FD/f0");
H5DataTypeId fDataTypeId = H5D.getType(fDataSetId);
if (!H5T.equal(fDataTypeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
}
long[] dims = H5S.getSimpleExtentDims(H5D.getSpace(fDataSetId)).ToArray();
if (dims.Length != 3)
{
Console.WriteLine("Error: Invalid field data dimensions");
}
float[, ,] data = new float[dims[0], dims[1], dims[2]];
H5D.read(fDataSetId, fDataTypeId, new H5Array <float>(data));
// Reorder
double[, ,] fieldValues = new double[dims[2], dims[1], dims[0]];
for (int i = 0; i < dims[0]; i++)
{
for (int j = 0; j < dims[1]; j++)
{
for (int k = 0; k < dims[2]; k++)
{
fieldValues[k, j, i] = data[i, j, k];
}
}
}
return(fieldValues);
}
//Load weights from hdf5 file. Weights must be saved as a vector per layer
public static float[] loadH5(string path, string dsname)
{
//Get file id
var h5fid = H5F.open(path, H5F.OpenMode.ACC_RDONLY);
//Get dataset id
var h5did = H5D.open(h5fid, dsname);
//Dataset size
var h5space = H5D.getSpace(h5did);
var h5size = H5S.getSimpleExtentDims(h5space);
//Dataset size to array
var S = h5size.ToArray();
//Empty double array for the data
double[] data = new double[S[0]];
//Read the dataset
var h5array = new H5Array <double>(data);
var h5dtype = H5D.getType(h5did);
H5D.read(h5did, h5dtype, h5array);
//Convert to float
float[] newarray = new float[data.Length];
Parallel.For(0, data.Length, (k) =>
{
newarray[k] = (float)data[k];
});
return(newarray);
}
public void H5DreadTest1()
{
byte[] rdata = new byte[512];
hid_t mem_type = H5T.copy(H5T.C_S1);
Assert.IsTrue(H5T.set_size(mem_type, new IntPtr(2)) >= 0);
GCHandle hnd = GCHandle.Alloc(rdata, GCHandleType.Pinned);
Assert.IsTrue(H5D.read(m_v0_ascii_dset, mem_type, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject()) >= 0);
for (int i = 0; i < 256; ++i)
{
// H5T.FORTRAN_S1 is space (= ASCII dec. 32) padded
if (i != 32)
{
Assert.IsTrue(rdata[2 * i] == (byte)i);
}
else
{
Assert.IsTrue(rdata[64] == (byte)0);
}
Assert.IsTrue(rdata[2 * i + 1] == (byte)0);
}
hnd.Free();
Assert.IsTrue(H5T.close(mem_type) >= 0);
}
/// <summary>
/// Returns the entire matrix table
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="matName"></param>
/// <param name="rowIndex"></param>
/// <returns></returns>
public T[,] GetMatrix <T>(string matName)
{
var data = new T[Shape[0], Shape[1]];
// check that matrix exists
if (tables.ContainsKey(matName))
{
H5DataSetId matId;
tables.TryGetValue(matName, out matId);
H5DataTypeId matDataId = H5D.getType(matId);
H5DataSpaceId spaceId = H5S.create_simple(2, Shape);
var h5matrix = new H5Array <T>(data);
long[] start = { 0, 0 };
long[] count = { Shape[0], Shape[1] };
H5S.selectHyperslab(spaceId, H5S.SelectOperator.SET, start, count);
H5DataSpaceId readSpaceId = H5S.create_simple(2, count);
H5D.read(matId, matDataId, readSpaceId, spaceId, H5P.create(H5P.PropertyListClass.DATASET_XFER), h5matrix);
H5S.close(spaceId);
H5S.close(readSpaceId);
}
else
{
Console.WriteLine("table {0} not found in matrix file", matName);
}
return(data);
}
public string[] Column(long n)
{
using (H5Space file_space = SelectSlice(n, n + 1, axis: 1)) {
using (H5Space mem_space = H5Space.Create(1, new long[] { Dims[0] })) {
using (H5Type dtype = GetDType()) {
int slen = (int)dtype.Size;
byte[] buf = new byte[slen * mem_space.Length];
GCHandle pinnedArray = GCHandle.Alloc(buf, GCHandleType.Pinned);
int status = H5D.read(ID, dtype.ID, mem_space.ID, file_space.ID,
H5P.DEFAULT, pinnedArray.AddrOfPinnedObject());
pinnedArray.Free();
if (status < 0)
{
throw new H5LibraryException($"H5D.read() returned ({status})");
}
string decoded = string1d.Enc.GetString(buf);
var rv = new string[mem_space.Length];
for (int i = 0; i < rv.Length; i++)
{
rv[i] = decoded.Substring(i * slen, slen).TrimEnd('\0');
}
return(rv);
}
}
}
}
public static double[,] ReadFieldData2D(string file, string dataSet)
{
H5FileId fileId = H5F.open(file, H5F.OpenMode.ACC_RDONLY);
H5DataSetId fDataSetId = H5D.open(fileId, dataSet);
H5DataTypeId fDataTypeId = H5D.getType(fDataSetId);
long[] dims = H5S.getSimpleExtentDims(H5D.getSpace(fDataSetId)).ToArray();
double[,] data = new double[dims[0], dims[1]];
H5D.read(fDataSetId, fDataTypeId, new H5Array <double>(data));
double[,] fieldValues = new double[dims[1], dims[0]];
for (int i = 0; i < dims[1]; i++)
{
for (int j = 0; j < dims[0]; j++)
{
fieldValues[i, j] = (double)data[j, i];
}
}
H5T.close(fDataTypeId);
H5D.close(fDataSetId);
H5F.close(fileId);
return(fieldValues);
}
public static double[][] ReadMesh(string fileName)
{
double[][] meshes = new double[3][];
string[] meshNames = { "x", "y", "z" };
H5FileId fileId = H5F.open(fileName, H5F.OpenMode.ACC_RDONLY);
for (int i = 0; i < meshNames.Length; i++)
{
H5DataSetId dsId = H5D.open(fileId, "/Mesh/" + meshNames[i]);
H5DataTypeId dtId = H5D.getType(dsId);
if (!H5T.equal(dtId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
}
float[] mesh = new float[H5D.getStorageSize(dsId) / H5T.getSize(dtId)];
H5D.read(dsId, dtId, new H5Array <float>(mesh));
meshes[i] = mesh.Select(x => (double)x * 1000.0).ToArray(); // m -> mm
H5D.close(dsId);
H5T.close(dtId);
}
H5F.close(fileId);
return(meshes);
}
public void H5DreadTest2()
{
hid_t mem_type = H5T.create(H5T.class_t.STRING, H5T.VARIABLE);
Assert.IsTrue(H5T.set_cset(mem_type, H5T.cset_t.UTF8) >= 0);
Assert.IsTrue(H5T.set_strpad(mem_type, H5T.str_t.NULLTERM) >= 0);
hid_t fspace = H5D.get_space(m_v0_utf8_dset);
Assert.IsTrue(fspace >= 0);
hssize_t count = H5S.get_simple_extent_npoints(fspace);
Assert.IsTrue(count > 0);
Assert.IsTrue(H5S.close(fspace) >= 0);
IntPtr[] rdata = new IntPtr[count];
GCHandle hnd = GCHandle.Alloc(rdata, GCHandleType.Pinned);
Assert.IsTrue(H5D.read(m_v0_utf8_dset, mem_type, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject()) >= 0);
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);
Assert.IsTrue(s == ((string)m_utf8strings[i]));
Assert.IsTrue(H5.free_memory(rdata[i]) >= 0);
}
Assert.IsTrue(H5D.read(m_v2_utf8_dset, mem_type, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject()) >= 0);
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);
Assert.IsTrue(s == ((string)m_utf8strings[i]));
Assert.IsTrue(H5.free_memory(rdata[i]) >= 0);
}
hnd.Free();
}
private static double[,] ReadDataArray(hid_t fileLoc, string name, bool transpose = false)
{
hid_t dset = H5D.open(fileLoc, name);
hid_t fspace = H5D.get_space(dset);
hid_t count = H5S.get_simple_extent_ndims(fspace);
hid_t type = H5D.get_type(dset);
hsize_t[] dims = new hsize_t[count];
hsize_t[] maxdims = new hsize_t[count];
H5S.get_simple_extent_dims(fspace, dims, maxdims);
H5S.close(fspace);
byte[] rdata = new byte[dims[0] * dims[1] * 8];
hid_t mem_type = H5T.copy(H5T.NATIVE_DOUBLE);
H5T.set_size(mem_type, new IntPtr(8));
GCHandle hnd = GCHandle.Alloc(rdata, GCHandleType.Pinned);
H5D.read(dset, mem_type, H5S.ALL,
H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
H5T.close(mem_type);
if (transpose)
{
double[,] val = new double[dims[1], dims[0]];
int cnt = 0;
for (int i = 0; i < (int)dims[0]; i++)
{
for (int j = 0; j < (int)dims[1]; j++)
{
val[j, i] = BitConverter.ToDouble(rdata, cnt * 8);
cnt++;
}
}
return(val);
}
else
{
double[,] val = new double[dims[0], dims[1]];
int cnt = 0;
for (int i = 0; i < (int)dims[0]; i++)
{
for (int j = 0; j < (int)dims[1]; j++)
{
val[i, j] = BitConverter.ToDouble(rdata, cnt * 8);
cnt++;
}
}
return(val);
}
}
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 success, IEnumerable <string> result) ReadStrings(long groupId, string name, string alternativeName)
{
long 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 = H5D.open(groupId, Hdf5Utils.NormalizedName(name));
if (datasetId < 0) //does not exist?
{
datasetId = H5D.open(groupId, Hdf5Utils.NormalizedName(alternativeName));
}
if (datasetId <= 0)
{
Hdf5Utils.LogError?.Invoke($"Error reading {groupId}. Name:{name}. AlternativeName:{alternativeName}");
return(false, Array.Empty <string>());
}
long spaceId = H5D.get_space(datasetId);
long count = H5S.get_simple_extent_npoints(spaceId);
H5S.close(spaceId);
var strs = new List <string>();
if (count >= 0)
{
IntPtr[] rdata = new IntPtr[count];
GCHandle hnd = GCHandle.Alloc(rdata, GCHandleType.Pinned);
H5D.read(datasetId, datatype, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
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);
H5D.close(datasetId);
return(true, strs);
}
/// <summary>
/// WARNING: ADVANCED USE ONLY!! Loads a 2D generic dataset from an H5 file.
/// The generic loaders only loads data in non-Unity friendly types, such as bytes, uints, longs etc...
/// You'll have to know the correct cast to retrieve usable data.
///
/// Created With help from https://github.com/LiorBanai/HDF5-CSharp/blob/master/HDF5-CSharp/Hdf5Dataset.cs
/// </summary>
/// <param name="filePath"></param>
/// <param name="datasetName"></param>
/// <typeparam name="T"></typeparam>
/// <returns></returns>
/// <exception cref="FileNotFoundException"></exception>
static T[,] Load2DDataset <T>(string filePath, string datasetName)
{
if (!File.Exists(filePath))
{
throw new FileNotFoundException($"Loading dataset {datasetName} from file that doesn't exist {filePath}");
}
long fileId = H5F.open(filePath, H5F.ACC_RDONLY);
T[,] resultArray = new T[2, 2];
try {
ulong[] start = { 0, 0 };
ulong[] count = { 0, 0 };
long datasetId = H5D.open(fileId, datasetName);
var datatype = H5D.get_type(datasetId);
var spaceId = H5D.get_space(datasetId);
int rank = H5S.get_simple_extent_ndims(spaceId);
ulong[] maxDims = new ulong[rank];
ulong[] dims = new ulong[rank];
H5S.get_simple_extent_dims(spaceId, dims, maxDims);
count[0] = dims[0];
count[1] = dims[1];
// Define file hyperslab.
long status = H5S.select_hyperslab(spaceId, H5S.seloper_t.SET, start, null, count, null);
// Define the memory dataspace.
resultArray = new T[dims[0], dims[1]];
var memId = H5S.create_simple(rank, dims, null);
// Define memory hyperslab.
status = H5S.select_hyperslab(memId, H5S.seloper_t.SET, start, null,
count, null);
// Read data from hyperslab in the file into the hyperslab in
// memory and display.
GCHandle handle = GCHandle.Alloc(resultArray, GCHandleType.Pinned);
try {
H5D.read(datasetId, datatype, memId, spaceId,
H5P.DEFAULT, handle.AddrOfPinnedObject());
}
finally {
handle.Free();
H5S.close(status);
H5S.close(memId);
H5S.close(spaceId);
H5D.close(datatype);
H5D.close(datasetId);
}
}
finally {
H5F.close(fileId);
}
return(resultArray);
}
void LoadRowData()
{
var dtype = H5D.getType(Id);
var size = H5T.getSize(dtype);
_row_data = new byte[FindNumberOfRows(), size];
H5D.read(Id, dtype, new H5Array <byte>(_row_data));
//TODO: Does this work with more than one row? Dunno. Probs not.
}
/// <summary>
/// 重写数据集的值（去条带的数据）
/// </summary>
/// <typeparam name="T">数据类型</typeparam>
/// <param name="dataSetName">数据集的名称</param>
/// <param name="dataTypeId">数据集的类型ID</param>
/// <param name="values">去条带之后数据</param>
/// <param name="BrandNo">在数据集的维度从0开始</param>
private void ReWriteDataSet <T>(string dataSetName, H5DataTypeId dataTypeId, T[] values, int BrandNo)
{
H5FileId _h5FileId = null;
H5DataSetId dataSetId = null;
H5DataSpaceId spaceid = null;
try
{
_h5FileId = H5F.open(fileName, H5F.OpenMode.ACC_RDWR);
//先找出含有指定波段的数据集
dataSetId = H5D.open(_h5FileId, dataSetName);
spaceid = H5D.getSpace(dataSetId);
long[] dims = H5S.getSimpleExtentDims(spaceid); //得到数据数组的大小，比如[3,1800,2048]
int rank = H5S.getSimpleExtentNDims(spaceid); //得到数据数组的维数，比如3
H5S.close(spaceid);
//根据数据集的名字获取数据集的ID
int size = 0;
if (rank == 0)
{
size = 1;
}
else if (rank == 1)
{
size = Convert.ToInt32(dims[0]);
}
else if (rank == 2)
{
size = Convert.ToInt32(dims[0] * dims[1]);
}
else if (rank == 3)
{
size = Convert.ToInt32(dims[0] * dims[1] * dims[2]);
}
T[] v = new T[size];
//从数据集中读取原始数据
H5D.read <T>(dataSetId, dataTypeId, new H5Array <T>(v));
//将波段校正后的数据读取赋给相应的波段
for (int i = BrandNo; i < values.Length; i++)
{
v[i] = values[i];
}
H5D.write <T>(dataSetId, dataTypeId, new H5Array <T>(v));
}
catch (Exception e)
{
throw new Exception(e.Message);
}
finally
{
H5D.close(dataSetId);
H5F.close(_h5FileId);
}
}
private mData[] ReadData()
{
Console.WriteLine("Reading H5 file {0}...", filename);
H5FileId fileId = H5F.open(filename, H5F.OpenMode.ACC_RDONLY);
H5DataSetId dataSetId = H5D.open(fileId, dataSetName);
mData[] readDataBack = new mData[count];
H5D.read(dataSetId, new H5DataTypeId(H5T.H5Type.STD_REF_OBJ), new H5Array <mData>(readDataBack));
H5D.close(dataSetId);
H5F.close(fileId);
return(readDataBack);
}
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($"string-vlen: {ReadStringAttribute(dataSet, "string-vlen")}");
H5D.close(dataSet);
H5F.close(file);
}
public static int[,] GetIntDataset(long dataset_id_inp, int rows_inp, int cols_inp)
{
int status;
int[,] dataArray_out = new int[rows_inp, cols_inp];
GCHandle buf = GCHandle.Alloc(dataArray_out, GCHandleType.Pinned);
status = H5D.read(dataset_id_inp, H5T.NATIVE_INT, H5S.ALL, H5S.ALL, H5P.DEFAULT, buf.AddrOfPinnedObject());
H5D.close(dataset_id_inp);
return(dataArray_out);
}
private T[] ReadArray <T>(int size, H5DataSetId dsId, H5DataTypeId typeId, int bandIndex, int outSize)
{
T[] v = new T[size];
H5D.read <T>(dsId, typeId, new H5Array <T>(v));
T[] outdata = new T[outSize];
int index = bandIndex * outSize;
for (int i = 0; i < outdata.Length; i++)
{
outdata[i] = v[i + index];
}
return(outdata);
}
public string this[long m, long n]
{
get
{
using (H5Space file_space = SelectPoint(m, n)) {
using (H5Space mem_space = H5Space.Create(1, new long[] { 1 })) {
using (H5Type dtype = GetDType()) {
long slen = dtype.Size;
byte[] buf = new byte[slen];
GCHandle pinnedArray = GCHandle.Alloc(buf, GCHandleType.Pinned);
int status = H5D.read(ID, dtype.ID, mem_space.ID, file_space.ID,
H5P.DEFAULT, pinnedArray.AddrOfPinnedObject());
pinnedArray.Free();
if (status < 0)
{
throw new H5LibraryException($"H5D.read() returned ({status})");
}
string decoded = string1d.Enc.GetString(buf);
return(decoded.TrimEnd('\0'));
}
}
}
}
set
{
using (H5Space file_space = SelectPoint(m, n)) {
using (H5Space mem_space = H5Space.Create(1, new long[] { 1 })) {
using (H5Type dtype = GetDType()) {
long slen = dtype.Size;
if (value.Length > slen - 1)
{
throw new IndexOutOfRangeException($"string longer than ({slen})");
}
byte[] buf = new byte[slen];
Array.Copy(string1d.Enc.GetBytes(value), buf, value.Length);
GCHandle pinnedArray = GCHandle.Alloc(buf, GCHandleType.Pinned);
int status = H5D.write(ID, dtype.ID, mem_space.ID, file_space.ID,
H5P.DEFAULT, pinnedArray.AddrOfPinnedObject());
pinnedArray.Free();
if (status < 0)
{
throw new H5LibraryException($"H5D.read() returned ({status})");
}
}
}
}
}
}
/// <summary>
/// Reads an n-dimensional dataset.
/// </summary>
/// <typeparam name="T">Generic parameter strings or primitive type</typeparam>
/// <param name="groupId">id of the group. Can also be a file Id</param>
/// <param name="name">name of the dataset</param>
/// <returns>The n-dimensional dataset</returns>
public static Array ReadDatasetToArray <T>(hid_t groupId, string name) //where T : struct
{
var datatype = GetDatatype(typeof(T));
var datasetId = H5D.open(groupId, name);
var spaceId = H5D.get_space(datasetId);
int rank = H5S.get_simple_extent_ndims(spaceId);
long count = H5S.get_simple_extent_npoints(spaceId);
Array dset;
Type type = typeof(T);
if (rank >= 0 && count >= 0)
{
int rankChunk;
ulong[] maxDims = new ulong[rank];
ulong[] dims = new ulong[rank];
ulong[] chunkDims = new ulong[rank];
hid_t memId = H5S.get_simple_extent_dims(spaceId, dims, maxDims);
long[] lengths = dims.Select(d => Convert.ToInt64(d)).ToArray();
dset = Array.CreateInstance(type, lengths);
var typeId = H5D.get_type(datasetId);
var mem_type = H5T.copy(datatype);
if (datatype == H5T.C_S1)
{
H5T.set_size(datatype, new IntPtr(2));
}
var propId = H5D.get_create_plist(datasetId);
if (H5D.layout_t.CHUNKED == H5P.get_layout(propId))
{
rankChunk = H5P.get_chunk(propId, rank, chunkDims);
}
memId = H5S.create_simple(rank, dims, maxDims);
GCHandle hnd = GCHandle.Alloc(dset, GCHandleType.Pinned);
H5D.read(datasetId, datatype, memId, spaceId,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
}
else
{
dset = Array.CreateInstance(type, new long[1] {
0
});
}
H5D.close(datasetId);
H5S.close(spaceId);
return(dset);
}
/// <summary>
/// 读取指定数据集，未对异常进行处理
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="datasetName"></param>
/// <param name="bandN"></param>
/// <param name="bandH"></param>
/// <param name="bandW"></param>
/// <returns></returns>
public T[] ReadDataArray <T>(String datasetName, ref int bandN, ref int bandH, ref int bandW)
{
H5DataSetId datasetId = null;
H5DataSpaceId spaceId = null;
H5DataTypeId typeId = null;
long[] dims = null;
if (!String.IsNullOrEmpty(datasetName) && _datasetNames.Contains(datasetName))
{
datasetId = H5D.open(_fileId, datasetName);
spaceId = H5D.getSpace(datasetId);
dims = H5S.getSimpleExtentDims(spaceId);
if (dims.Length == 2)
{
bandN = 1;
bandH = (int)dims[0];
bandW = (int)dims[1];
}
else if (dims.Length == 3)
{
bandN = (int)dims[0];
bandH = (int)dims[1];
bandW = (int)dims[2];
}
typeId = H5D.getType(datasetId);
typeId = H5T.getNativeType(typeId, H5T.Direction.DEFAULT);
T[] dv = new T[bandN * bandH * bandW];
H5D.read <T>(datasetId, typeId, new H5Array <T>(dv));
if (typeId != null)
{
H5T.close(typeId);
}
if (spaceId != null)
{
H5S.close(spaceId);
}
if (datasetId != null)
{
H5D.close(datasetId);
}
return(dv);
}
else
{
throw new Exception("未查到指定数据集！");
}
}
public static IEnumerable <T> ReadCompounds <T>(hid_t groupId, string name) where T : struct
{
Type type = typeof(T);
hid_t typeId = 0;
// open dataset
var datasetId = H5D.open(groupId, name);
typeId = CreateType(type);
var compoundSize = Marshal.SizeOf(type);
/*
* Get dataspace and allocate memory for read buffer.
*/
var spaceId = H5D.get_space(datasetId);
int rank = H5S.get_simple_extent_ndims(spaceId);
ulong[] dims = new ulong[rank];
var ndims = H5S.get_simple_extent_dims(spaceId, dims, null);
int rows = Convert.ToInt32(dims[0]);
byte[] bytes = new byte[rows * compoundSize];
// Read the data.
GCHandle hnd = GCHandle.Alloc(bytes, GCHandleType.Pinned);
IntPtr hndAddr = hnd.AddrOfPinnedObject();
H5D.read(datasetId, typeId, spaceId, H5S.ALL, H5P.DEFAULT, hndAddr);
int counter = 0;
IEnumerable <T> strcts = Enumerable.Range(1, rows).Select(i =>
{
byte[] select = new byte[compoundSize];
Array.Copy(bytes, counter, select, 0, compoundSize);
T s = fromBytes <T>(select);
counter = counter + compoundSize;
return(s);
});
/*
* Close and release resources.
*/
H5D.vlen_reclaim(typeId, spaceId, H5P.DEFAULT, hndAddr);
hnd.Free();
H5D.close(datasetId);
H5S.close(spaceId);
H5T.close(typeId);
return(strcts);
}
public static T[,] ReadDataset <T>(int groupId, string name, ulong beginIndex, ulong endIndex) where T : struct
{
ulong[] start = { 0, 0 }, stride = null, count = { 0, 0 },
block = null, offsetOut = new ulong[] { 0, 0 };
var datatype = GetDatatype(typeof(T));
name = ToHdf5Name(name);
var datasetId = H5D.open(groupId, name);
var spaceId = H5D.get_space(datasetId);
int rank = H5S.get_simple_extent_ndims(spaceId);
ulong[] maxDims = new ulong[rank];
ulong[] dims = new ulong[rank];
ulong[] chunkDims = new ulong[rank];
var memId_n = H5S.get_simple_extent_dims(spaceId, dims, maxDims);
start[0] = beginIndex;
start[1] = 0;
count[0] = endIndex - beginIndex;
count[1] = dims[1];
var status = H5S.select_hyperslab(spaceId, H5S.seloper_t.SET, start, stride, count, block);
// Define the memory dataspace.
T[,] dset = new T[count[0], count[1]];
var memId = H5S.create_simple(rank, count, null);
// Define memory hyperslab.
status = H5S.select_hyperslab(memId, H5S.seloper_t.SET, offsetOut, null,
count, null);
/*
* Read data from hyperslab in the file into the hyperslab in
* memory and display.
*/
GCHandle hnd = GCHandle.Alloc(dset, GCHandleType.Pinned);
H5D.read(datasetId, datatype, memId, spaceId,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
hnd.Free();
H5D.close(datasetId);
H5S.close(spaceId);
H5S.close(memId);
return(dset);
}
/// <summary>
/// Returns mapping index - assumes that matrices are square and uses first dimension as the map size
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="mapName">Name of index map</param>
public T[] GetMapping <T>(string mapName)
{
var mapData = new T[Shape[0]];
// check that index map exists
if (indexMaps.ContainsKey(mapName))
{
H5DataSetId mapId;
indexMaps.TryGetValue(mapName, out mapId);
H5D.read(mapId, H5D.getType(mapId), new H5Array <T>(mapData));
}
else
{
Console.WriteLine("index map {0} not found in file", mapName);
}
return(mapData);
}
public static T[,] Read2DArray <T>(this H5FileId fileId, string dataSetName)
{
var dataset = H5D.open(fileId, dataSetName);
var space = H5D.getSpace(dataset);
var dims = H5S.getSimpleExtentDims(space);
var dataType = H5D.getType(dataset);
if (typeof(T) == typeof(string))
{
// this will also need a string hack...
}
T[,] dataArray = new T[dims[0], dims[1]];
var wrapArray = new H5Array <T>(dataArray);
H5D.read(dataset, dataType, wrapArray);
return(dataArray);
}
public static IEnumerable <string> ReadStrings(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 = H5D.open(groupId, name);
hid_t spaceId = H5D.get_space(datasetId);
long count = H5S.get_simple_extent_npoints(spaceId);
H5S.close(spaceId);
var strs = new List <string>();
if (count >= 0)
{
IntPtr[] rdata = new IntPtr[count];
GCHandle hnd = GCHandle.Alloc(rdata, GCHandleType.Pinned);
H5D.read(datasetId, datatype, H5S.ALL, H5S.ALL,
H5P.DEFAULT, hnd.AddrOfPinnedObject());
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);
H5D.close(datasetId);
return(strs);
}
//Reading and Printing Methods
private static double[] GetDoubleDataSet(H5FileId dataFile, string path)
{
if (H5L.Exists(dataFile, path))
{
H5DataSetId dataSet = H5D.open(dataFile, path);
H5DataSpaceId space = H5D.getSpace(dataSet);
long[] size2 = H5S.getSimpleExtentDims(space);
long count = size2[0];
double[] dataArray = new double[count];
H5Array <double> wrapArray = new H5Array <double>(dataArray);
H5DataTypeId tid1 = H5D.getType(dataSet);
H5D.read(dataSet, tid1, wrapArray);
return(dataArray);
}
return(null);
}
public static void GetDataSet <T> (H5FileOrGroupId groupOrFileId, string name, out T[,,,] array, int width, int height, int depth, int number)
{
if (groupOrFileId is null)
{
throw new ArgumentNullException(nameof(groupOrFileId));
}
if (name is null)
{
throw new ArgumentNullException(nameof(name));
}
H5DataSetId h5DataSetId = H5D.open(groupOrFileId, name);
H5DataTypeId h5DataTypeId = H5D.getType(h5DataSetId);
array = new T[height, width, depth, number];
H5D.read(h5DataSetId, h5DataTypeId, new H5Array <T> (array));
H5T.close(h5DataTypeId);
H5D.close(h5DataSetId);
}
public static void GetDataSet <T> (H5FileOrGroupId groupOrFileId, string name, out T[] array, int length)
{
if (groupOrFileId is null)
{
throw new ArgumentNullException(nameof(groupOrFileId));
}
if (name is null)
{
throw new ArgumentNullException(nameof(name));
}
array = new T[length];
H5DataSetId h5DataSetId = H5D.open(groupOrFileId, name);
H5DataTypeId h5DataTypeId = H5D.getType(h5DataSetId);
H5D.read(h5DataSetId, h5DataTypeId, new H5Array <T> (array));
H5T.close(h5DataTypeId);
H5D.close(h5DataSetId);
}
private static int[] GetInt32DataSet(H5FileId dataFile, string path)
{
if (H5L.Exists(dataFile, path))
{
var dataSet = H5D.open(dataFile, path);
var space = H5D.getSpace(dataSet);
var size2 = H5S.getSimpleExtentDims(space);
long count = size2[0];
var dataArray = new Int32[count];
var wrapArray = new H5Array <Int32>(dataArray);
H5DataTypeId tid1 = H5D.getType(dataSet);
H5D.read(dataSet, tid1, wrapArray);
return(dataArray);
}
return(null);
}
