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($"H5D.read() returned ({status})");
}
string decoded = string1d.Enc.GetString(buf);
var rv = new string[mem_space.Length];
for (int i = 0; i < rv.Length; i++)
{
rv[i] = decoded.Substring(i * slen, slen).TrimEnd('\0');
}
return(rv);
}
}
}
}
internal static H5Attribute Create(hid_t loc_id, string name, Type primitive, object default_ = null)
{
if (primitive == null)
{
primitive = default_.GetType(); // may throw NullReferenceException, which is informational enough
}
int rank = 1;
long[] dims = new long[1] {
1
};
hid_t id;
using (H5Space space = H5Space.Create(rank, dims))
using (H5Type dtype = H5Type.Create(primitive))
{
if ((id = H5A.create(loc_id, name, dtype.ID, space.ID, H5P.DEFAULT, H5P.DEFAULT)) < 0)
{
throw new H5LibraryException($"H5A.create() returned ({id})");
}
}
H5Attribute rv = FromID(id);
if (default_ != null)
{
rv.Write(default_);
}
return(rv);
}
/// <summary>
/// Change the dimensions of the dataset to `new_dims`.
/// </summary>
public void Resize(params long[] new_dims)
{
if (!HasH5Pcreate)
{
throw new NotImplementedException($"cannot resize using hdf5 v{H5Library.LibVersion}");
}
using (H5Space space = GetSpace())
{
if (new_dims.Length != space.Rank)
{
throw new RankException($"{new_dims.Length} != {space.Rank}");
}
ulong[] extent = new ulong[space.Rank];
long[] maxdims = space.MaxDims;
for (int i = 0; i < new_dims.Length; i++)
{
if (!(0 <= new_dims[i] && (new_dims[i] <= maxdims[i] || maxdims[i] == H5Space.Unlimited)))
{
throw new IndexOutOfRangeException($"{new_dims[i]} > {maxdims[i]}");
}
extent[i] = (ulong)new_dims[i];
}
int status;
if ((status = H5D.set_extent(ID, extent)) < 0)
{
throw new H5LibraryException($"H5D.set_extent() returned ({status})");
}
}
}
protected H5Space GetSpace()
{
if (!(ID > 0))
{
throw new InvalidOperationException("operation on closed dataset");
}
return(H5Space.FromDataset(ID));
}
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($"H5D.read() returned ({status})");
}
}
}
}
}
}
/// <summary>
/// Create a new hdf5 `H5DataSet` at `loc_id`.
/// </summary>
/// <remarks>
/// `maxdims` may be `null` in which case it is set to `dims`.
/// </remarks>
internal static H5DataSet Create(hid_t loc_id, string key, int rank, long[] dims, long[] maxdims, Type primitive_type)
{
hid_t dcpl; // the 'dataset creation property list' controls chunking..
if (maxdims == null || dims.SequenceEqual(maxdims))
{
dcpl = H5P.DEFAULT;
}
else if (HasH5Pcreate)
{
// ..which is needed for later resizing:
var chunk = new ulong[rank];
// the chunk is of size 1 in each 'unlimited' dimension and of size 'maxdims'
// for all other dimensions (just like the 'SPECdata/Intensities' dataset):
for (int i = 0; i < rank; i++)
{
if (maxdims[i] == H5Space.Unlimited)
{
chunk[i] = 1UL;
}
else if (maxdims[i] > 0)
{
checked { chunk[i] = (ulong)maxdims[i]; }
}
else
{
throw new ArgumentException($"invalid value in parameter 'maxdims'");
}
}
dcpl = H5P.create(H5P.DATASET_CREATE);
H5P.set_chunk(dcpl, rank, chunk);
}
else
{
maxdims = dims;
dcpl = H5P.DEFAULT;
}
hid_t id;
using (H5Space space = H5Space.Create(rank, dims, maxdims))
using (H5Type dtype = H5Type.Create(primitive_type))
{
if ((id = H5D.create(loc_id, key, dtype.ID, space.ID, H5P.DEFAULT, dcpl, H5P.DEFAULT)) < 0)
{
throw new H5LibraryException($"H5D.create() returned ({id})");
}
}
return(FromID(id));
}
/// <summary>
/// Set the `value` at `index`.
/// </summary>
/// <remark>
/// The number of indices must match this dataset's rank.
/// </remark>
public void Set <T>(T value, params long[] index)
{
using (H5Space file_space = SelectPoint(index)) {
using (H5Space mem_space = H5Space.Create(1, new long[] { 1 })) {
using (H5Type dtype = GetDType()) {
T[] buf = new T[1];
buf[0] = value;
GCHandle pinnedArray = GCHandle.Alloc(buf, GCHandleType.Pinned);
int status = H5D.write(ID, dtype.ID, mem_space.ID, file_space.ID,
H5P.DEFAULT, pinnedArray.AddrOfPinnedObject());
pinnedArray.Free();
if (status < 0)
{
throw new H5LibraryException($"H5D.write() returned ({status})");
}
}
}
}
}
public string[] this[long m]
{
get
{
using (H5Space file_space = SelectSlice(m, m + 1)) {
using (H5Space mem_space = H5Space.Create(1, new long[] { Dims[1] })) {
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($"H5D.read() returned ({status})");
}
string decoded = string1d.Enc.GetString(buf);
var rv = new string[mem_space.Length];
for (int i = 0; i < rv.Length; i++)
{
rv[i] = decoded.Substring(i * slen, slen).TrimEnd('\0');
}
return(rv);
}
}
}
}
set
{
using (H5Space file_space = SelectSlice(m, m + 1)) {
using (H5Space mem_space = H5Space.Create(1, new long[] { Dims[1] })) {
using (H5Type dtype = GetDType()) {
if (value.Length > mem_space.Length)
{
throw new IndexOutOfRangeException($"can't hold array of length ({value.Length})");
}
int slen = (int)dtype.Size;
if (value.Any(s => s.Length > slen - 1))
{
throw new IndexOutOfRangeException($"string longer than ({slen})");
}
byte[] buf = new byte[slen * mem_space.Length];
for (int i = 0; i < value.Length; i++)
{
var bytes = string1d.Enc.GetBytes(value[i]);
Array.Copy(bytes, 0, buf, i * slen, bytes.Length);
}
GCHandle pinnedArray = GCHandle.Alloc(buf, GCHandleType.Pinned);
int status = H5D.write(ID, dtype.ID, mem_space.ID, file_space.ID,
H5P.DEFAULT, pinnedArray.AddrOfPinnedObject());
pinnedArray.Free();
if (status < 0)
{
throw new H5LibraryException($"H5D.write() returned ({status})");
}
}
}
}
}
}
/// <summary>
/// Load an existing dataset by `dset_id`.
/// </summary>
/// <remarks>
/// Creates and returns an `H5DataSet` of the appropriate `space` and `dtype`.
/// Throws `H5LibraryException` if `dset_id` is invalid.
/// </remarks>
internal static H5DataSet FromID(hid_t dset_id)
{
using (H5Space space = H5Space.FromDataset(dset_id)) {
using (H5Type dtype = H5Type.FromDataset(dset_id)) {
if (space.Rank == 1)
{
if (dtype.PrimitiveType == typeof(System.Double))
{
return(new dset1d <double>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.Single))
{
return(new dset1d <float>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.Byte))
{
return(new dset1d <byte>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.Int64))
{
return(new dset1d <long>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.Int32))
{
return(new dset1d <int>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.String))
{
return(new string1d(dset_id));
}
}
if (space.Rank == 2)
{
if (dtype.PrimitiveType == typeof(System.Double))
{
return(new dset2d <double>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.Single))
{
return(new dset2d <float>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.Byte))
{
return(new dset2d <byte>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.Int64))
{
return(new dset2d <long>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.Int32))
{
return(new dset2d <int>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.String))
{
return(new string2d(dset_id));
}
}
if (space.Rank == 3)
{
if (dtype.PrimitiveType == typeof(System.Double))
{
return(new dset3d <double>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.Single))
{
return(new dset3d <float>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.Byte))
{
return(new dset3d <byte>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.Int64))
{
return(new dset3d <long>(dset_id));
}
if (dtype.PrimitiveType == typeof(System.Int32))
{
return(new dset3d <int>(dset_id));
}
}
throw new NotImplementedException($"dataset<{dtype.PrimitiveType}> of rank ({space.Rank})");
}
}
}
