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($"H5A.create() returned ({id})");
}
}
H5Attribute rv = FromID(id);
if (default_ != null)
{
rv.Write(default_);
}
return(rv);
}
public string[] Column(long n)
{
using (H5Space file_space = SelectSlice(n, n + 1, axis: 1)) {
using (H5Space mem_space = H5Space.Create(1, new long[] { Dims[0] })) {
using (H5Type dtype = GetDType()) {
int slen = (int)dtype.Size;
byte[] buf = new byte[slen * mem_space.Length];
GCHandle pinnedArray = GCHandle.Alloc(buf, GCHandleType.Pinned);
int status = H5D.read(ID, dtype.ID, mem_space.ID, file_space.ID,
H5P.DEFAULT, pinnedArray.AddrOfPinnedObject());
pinnedArray.Free();
if (status < 0)
{
throw new H5LibraryException($"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 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})");
}
}
}
}
}
}