public Hdf5ElementBase(string name, Hdf5ElementType type, Hdf5ElementBase parent, long id, bool isLazyLoading)
{
Name = name;
Type = type;
Parent = parent;
IsLazyLoading = isLazyLoading;
Id = id;
}
public static bool ItemExists(long groupId, string groupName, Hdf5ElementType type)
{
switch (type)
{
case Hdf5ElementType.Group:
case Hdf5ElementType.Dataset:
return(H5L.exists(groupId, NormalizedName(groupName)) > 0);
case Hdf5ElementType.Attribute:
return(H5A.exists(groupId, NormalizedName(groupName)) > 0);
default:
throw new ArgumentOutOfRangeException(nameof(type), type, null);
}
}
private static long GetId(long parentId, string name, long dataType, long spaceId, Hdf5ElementType type)
{
string normalizedName = NormalizedName(name);
bool exists = ItemExists(parentId, normalizedName, type);
if (exists)
{
LogMessage($"{normalizedName} already exists", Hdf5LogLevel.Debug);
if (!Hdf5.Settings.OverrideExistingData)
{
if (Hdf5.Settings.ThrowOnError)
{
throw new Hdf5Exception($"{normalizedName} already exists");
}
return(-1);
}
}
var datasetId = -1L;
switch (type)
{
case Hdf5ElementType.Unknown:
break;
case Hdf5ElementType.Group:
case Hdf5ElementType.Dataset:
if (exists)
{
H5L.delete(parentId, normalizedName);
// datasetId = H5D.open(parentId, normalizedName);
}
datasetId = H5D.create(parentId, normalizedName, dataType, spaceId);
break;
case Hdf5ElementType.Attribute:
if (exists)
{
H5A.delete(parentId, normalizedName);
}
datasetId = H5A.create(parentId, normalizedName, dataType, spaceId);
break;
default:
throw new ArgumentOutOfRangeException(nameof(type), type, null);
}
if (datasetId == -1L)
{
string error = $"Unable to create dataset for {normalizedName}";
LogMessage($"{normalizedName} already exists", Hdf5LogLevel.Error);
if (Hdf5.Settings.ThrowOnError)
{
throw new Hdf5Exception(error);
}
}
return(datasetId);
}
public Hdf5Element(string name, Hdf5ElementType type, Hdf5ElementBase parent, long id, bool isLazyLoading) : base(name, type, parent, id, isLazyLoading)
{
Children = new List <Hdf5Element>();
}
internal static (List <Hdf5Element> tree, List <Hdf5Element> flat) ReadFileStructure(string fileName)
{
var attributes = new List <Hdf5AttributeElement>();
var elements = new List <Hdf5Element>();
var structure = new List <Hdf5Element>();
if (!File.Exists(fileName))
{
Hdf5Utils.LogError?.Invoke($"File {fileName} does not exist");
return(structure, elements);
}
long fileId = H5F.open(fileName, H5F.ACC_RDONLY);
if (fileId < 0)
{
Hdf5Utils.LogError?.Invoke($"Could not open file {fileName}");
return(structure, elements);
}
try
{
StringBuilder filePath = new StringBuilder(260);
H5F.get_name(fileId, filePath, new IntPtr(260));
ulong idx = 0;
bool reEnableErrors = Settings.ErrorLoggingEnable;
Settings.EnableErrorReporting(false);
H5L.iterate(fileId, H5.index_t.NAME, H5.iter_order_t.INC, ref idx, Callback,
Marshal.StringToHGlobalAnsi("/"));
Settings.EnableErrorReporting(reEnableErrors);
}
catch (Exception e)
{
Hdf5Utils.LogError?.Invoke($"Error during reading file structure of {fileName}. Error:{e}");
}
finally
{
if (fileId > 0)
{
H5F.close(fileId);
}
}
int Callback(long elementId, IntPtr intPtrName, ref H5L.info_t info, IntPtr intPtrUserData)
{
ulong idx2 = 0;
long groupId = -1;
long datasetId = -1;
H5O.type_t objectType;
var name = Marshal.PtrToStringAnsi(intPtrName);
var userData = Marshal.PtrToStringAnsi(intPtrUserData);
var fullName = CombinePath(userData, name);
Hdf5ElementType elementType = Hdf5ElementType.Unknown;
// this is necessary, since H5Oget_info_by_name is slow because it wants verbose object header data
// and H5G_loc_info is not directly accessible
// only chance is to modify source code (H5Oget_info_by_name)
groupId = (H5L.exists(elementId, name) >= 0) ? H5G.open(elementId, name) : -1L;
if (H5I.is_valid(groupId) > 0)
{
objectType = H5O.type_t.GROUP;
elementType = Hdf5ElementType.Group;
}
else
{
datasetId = H5D.open(elementId, name);
if ((H5I.is_valid(datasetId) > 0))
{
objectType = H5O.type_t.DATASET;
elementType = Hdf5ElementType.Dataset;
}
else
{
objectType = H5O.type_t.UNKNOWN;
elementType = Hdf5ElementType.Group;
}
}
var parent = elements.FirstOrDefault(e =>
{
var index = fullName.LastIndexOf("/", StringComparison.Ordinal);
var partial = fullName.Substring(0, index);
return(partial.Equals(e.Name));
});
if (parent == null)
{
var element = new Hdf5Element(fullName, elementType, null, attributes, elementId, false);
attributes.Clear();
structure.Add(element);
elements.Add(element);
}
else
{
var element = new Hdf5Element(fullName, elementType, parent, attributes, elementId, false);
attributes.Clear();
parent.AddChild(element);
elements.Add(element);
}
if (objectType == H5O.type_t.GROUP)
{
H5L.iterate(groupId, H5.index_t.NAME, H5.iter_order_t.INC, ref idx2, Callback,
Marshal.StringToHGlobalAnsi(fullName));
}
// clean up
if (H5I.is_valid(groupId) > 0)
{
H5G.close(groupId);
}
if (H5I.is_valid(datasetId) > 0)
{
H5D.close(datasetId);
}
return(0);
}
int AttributeCallback(long location_id, IntPtr attr_name, ref H5A.info_t ainfo, IntPtr op_data)
{
var name = Marshal.PtrToStringAnsi(attr_name);
var att = ReadStringAttributes(location_id, name, String.Empty);
if (att.success && att.items.Any())
{
attributes.Add(new Hdf5AttributeElement(name, att.items.First()));
}
//var typeId = H5A.get_type(location_id);
//H5T.class_t classType = H5T.get_class(location_id);
//var cset = H5T.get_cset(location_id);
//var padd = H5T.get_strpad(location_id);
return(0);
}
return(structure, elements);
}
public Hdf5Element(string name, Hdf5ElementType type, Hdf5ElementBase parent, List <Hdf5AttributeElement> attributes, long id, bool isLazyLoading) : base(name, type, parent, id, isLazyLoading)
{
Children = new List <Hdf5Element>();
Attributes = attributes.ToList();
}
