/// <summary>
/// Open a H5Group at `location` relative to the hdf5 root group,
/// creating subgroups as necessary.
/// </summary>
public H5Group MakeGroups(string location)
{
location = location.Trim('/');
H5Group tmp, node = null;
foreach (string subloc in location.Split('/'))
{
if (node == null)
{
node = Root.SubGroup(subloc, create: true);
}
else
{
// note: if we could rely on the GC, we
// wouldn't need a temporary variable..
tmp = node.SubGroup(subloc, create: true);
node.Dispose();
node = tmp;
}
}
// re-open the group for its '.Key' set to our 'location'..
node.Dispose();
node = Root.SubGroup(location);
return(node);
}
protected H5File(hid_t fid, string path, string mode)
: base(fid)
{
Path = path;
Mode = mode;
Root = H5Group.Open(ID, key: "/", writable: mode != "r");
}
/// <summary>
/// Access the sub-Group given by `key` relative to this Group.
/// If the sub-Group does not exist and `create = false` (default),
/// a `KeyNotFoundException` is thrown.
/// An attempt to create multiple groups or to write a readonly-file
/// will throw an `InvalidOperationException`.
/// </summary>
public H5Group SubGroup(string key, bool create = false)
{
if (H5Link.Exists(ID, key))
{
return(H5Group.Open(ID, key, IsWritable));
}
if (create)
{
return(CreateGroup(key));
}
else
{
throw new KeyNotFoundException(key);
}
}
/// <summary>
/// Automagically fill data fields with their Hdf5 implementations.
/// </summary>
private void Initialize(H5Group grp)
{
var collectedH5Attrs = new Dictionary <string, H5Attribute>();
foreach (object attr in this.GetType().GetCustomAttributes(inherit: true))
{
if (attr.GetType() == typeof(AttributeAttribute))
{
string name = ((AttributeAttribute)attr).name;
try
{
collectedH5Attrs.Add(name, grp.GetAttribute(name));
}
catch (KeyNotFoundException)
{
Type primitive = ((AttributeAttribute)attr).primitive;
object default_ = ((AttributeAttribute)attr).default_;
if (primitive == null && default_ == null)
{
continue;
}
collectedH5Attrs.Add(name, grp.SetAttribute(name, primitive, default_));
}
}
}
var pendingAttrs = new List <Tuple <string, Type, object> >();
var flags = BindingFlags.NonPublic | BindingFlags.Public | BindingFlags.Instance | BindingFlags.FlattenHierarchy;
foreach (FieldInfo dsetInfo in this.GetType().GetFields(flags))
{
// skip fields that don't interest us here..
if (!dsetInfo.FieldType.IsSubclassOf(typeof(H5DataSet)))
{
continue;
}
// ..as well as those that have been already defined:
if (!(dsetInfo.GetValue(this) == null))
{
continue;
}
// set default dataset creation parameters..
string key = dsetInfo.Name;
bool readonli = false;
Match match = Regex.Match(dsetInfo.FieldType.Name, @".*([1-3])d");
int rank = Int32.Parse(match.Groups[1].Value);
long[] dims = new long[rank];
long[] maxdims = new long[rank];
dims.Fill <long>(1L);
maxdims.Fill <long>(-1L); // use H5S.UNLIMITED on all dimensions
// ..which may be overridden by Attributes:
pendingAttrs.Clear();
foreach (object attr in dsetInfo.GetCustomAttributes(inherit: false))
{
if (attr.GetType() == typeof(LocationAttribute))
{
key = ((LocationAttribute)attr).key;
}
else if (attr.GetType() == typeof(ReadonlyAttribute))
{
readonli = true;
}
else if (attr.GetType() == typeof(ShapeAttribute))
{
dims = ((ShapeAttribute)attr).dims;
}
else if (attr.GetType() == typeof(MaximumShapeAttribute))
{
maxdims = ((MaximumShapeAttribute)attr).dims;
}
else if (attr.GetType() == typeof(AttributeAttribute))
{
pendingAttrs.Add(new Tuple <string, Type, object>(
((AttributeAttribute)attr).name,
((AttributeAttribute)attr).primitive,
((AttributeAttribute)attr).default_
));
}
}
// initialize the dataset..
H5DataSet dset;
if (H5Link.Exists(grp.ID, key))
{
dset = grp[key];
}
else if (readonli)
{
continue;
}
else
{
Type dtype, field_type = dsetInfo.FieldType;
if (field_type.IsGenericType)
{
dtype = field_type.GenericTypeArguments[0];
}
else if (field_type == typeof(string1d))
{
dtype = typeof(string);
}
else if (field_type == typeof(string2d))
{
dtype = typeof(string);
}
else
{
throw new NotImplementedException(field_type.ToString());
}
dset = grp.CreateDataset(key, rank, dims, dtype, maxdims);
}
// add pending hdf5 attributes..
foreach (var tup in pendingAttrs)
{
string name = tup.Item1;
Type primitive = tup.Item2;
object default_ = tup.Item3;
try
{
collectedH5Attrs.Add(name, dset.GetAttribute(name));
}
catch (KeyNotFoundException)
{
if (primitive == null && default_ == null)
{
continue;
}
collectedH5Attrs.Add(name, dset.SetAttribute(name, primitive, default_));
}
}
// finally, set this instance's field to the new object.
// Note that, even if `dset` is declared as `object`, it will be
// of type `field.FieldType`:
dsetInfo.SetValue(this, dset);
}
Attr = new ReadOnlyDictionary <string, H5Attribute>(collectedH5Attrs);
}
public H5Object(H5Group group)
{
Attr = new ReadOnlyDictionary <string, H5Attribute>(new Dictionary <string, H5Attribute>());
Initialize(group);
}