private void GetAllFileAttributes()
{
//所有Attributes的键
ArrayList arrayList = new ArrayList();
GCHandle handle = GCHandle.Alloc(arrayList);
ulong n = 0;
// the callback is defined in H5ATest.cs
H5A.operator_t cb = (int location_id, IntPtr attr_name, ref H5A.info_t ainfo, IntPtr op_data) =>
{
GCHandle hnd = (GCHandle)op_data;
ArrayList al = (hnd.Target as ArrayList);
int len = 0;
while (Marshal.ReadByte(attr_name, len) != 0)
{
++len;
}
byte[] buf = new byte[len];
Marshal.Copy(attr_name, buf, 0, len);
al.Add(Encoding.UTF8.GetString(buf));
return(0);
};
H5A.iterate(_h5FileId, H5.index_t.NAME, H5.iter_order_t.NATIVE, ref n, cb, (IntPtr)handle);
handle.Free();
foreach (string attributeName in arrayList)
{
_fileAttrs.Add(attributeName, ReadAttributeValue(_h5FileId, attributeName));
}
}
public static Dictionary <uint, string> GetLabelWorkingSet(long group_id)
{
Dictionary <uint, string> labelWorkingSet = new Dictionary <uint, string>();
H5A.operator_t callBackMethod = DelegateMethod;
ArrayList attrNameArray = new ArrayList();
GCHandle nameArrayAlloc = GCHandle.Alloc(attrNameArray);
IntPtr ptrOnAllocArray = (IntPtr)nameArrayAlloc;
int status;
ulong beginAt = 0;
status = H5A.iterate(group_id, H5.index_t.CRT_ORDER, H5.iter_order_t.INC, ref beginAt, callBackMethod, ptrOnAllocArray);
for (int i = 0; i < attrNameArray.Count; i++)
{
string attr_name = Convert.ToString(attrNameArray[i]);
long attr_id = H5A.open(group_id, attr_name);
uint[] attr_value = { 0 };
GCHandle valueAlloc = GCHandle.Alloc(attr_value, GCHandleType.Pinned);
status = H5A.read(attr_id, H5T.NATIVE_UINT32, valueAlloc.AddrOfPinnedObject());
status = H5A.close(attr_id);
labelWorkingSet.Add(attr_value[0], attr_name);
}
status = H5G.close(group_id);
return(labelWorkingSet);
}
public void H5AiterateTest1()
{
hid_t att = H5A.create(m_v2_test_file, "IEEE_F32BE",
H5T.IEEE_F32BE, m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v2_test_file, "IEEE_F64BE", H5T.IEEE_F64BE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v2_test_file, "NATIVE_B8", H5T.NATIVE_B8,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
ArrayList al = new ArrayList();
GCHandle hnd = GCHandle.Alloc(al);
IntPtr op_data = (IntPtr)hnd;
hsize_t n = 0;
// the callback is defined in H5ATest.cs
H5A.operator_t cb = DelegateMethod;
Assert.IsTrue(H5A.iterate(m_v2_test_file, H5.index_t.NAME,
H5.iter_order_t.NATIVE, ref n, cb, op_data) >= 0);
// we should have 3 elements in the array list
Assert.IsTrue(al.Count == 3);
att = H5A.create(m_v0_test_file, "IEEE_F32BE",
H5T.IEEE_F32BE, m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v0_test_file, "IEEE_F64BE", H5T.IEEE_F64BE,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
att = H5A.create(m_v0_test_file, "NATIVE_B8", H5T.NATIVE_B8,
m_space_scalar);
Assert.IsTrue(att >= 0);
Assert.IsTrue(H5A.close(att) >= 0);
al.Clear();
n = 0;
Assert.IsTrue(H5A.iterate(m_v0_test_file, H5.index_t.NAME,
H5.iter_order_t.NATIVE, ref n, cb, op_data) >= 0);
// we should have 3 elements in the array list
Assert.IsTrue(al.Count == 3);
hnd.Free();
}
public void H5AiterateTest2()
{
ArrayList al = new ArrayList();
GCHandle hnd = GCHandle.Alloc(al);
IntPtr op_data = (IntPtr)hnd;
hsize_t n = 0;
// the callback is defined in H5ATest.cs
H5A.operator_t cb = DelegateMethod;
Assert.IsFalse(
H5A.iterate(Utilities.RandomInvalidHandle(),
H5.index_t.NAME, H5.iter_order_t.NATIVE, ref n,
cb, op_data) >= 0);
hnd.Free();
}
/// <summary>
/// Loads all attributes on an object into the supplied attributes collection.
/// Assumes that the object is already open.
/// </summary>
/// <param name="_attributes"></param>
public static void LoadAttributes(
Hdf5Attributes _attributes)
{
ulong n = 0;
AbstractHdf5Object obj = _attributes.ParentObject;
int id = H5A.iterate(obj.Id.Value, H5.index_t.NAME, H5.iter_order_t.NATIVE, ref n,
delegate(int _id, IntPtr _namePtr, ref H5A.info_t _ainfo, IntPtr _data)
{
string attributeName = Marshal.PtrToStringAnsi(_namePtr);
var attributeId = H5A.open(_id, attributeName).ToId();
if (attributeId.Value > 0)
{
var attributeTypeId = H5A.get_type(attributeId.Value).ToId();
var type = TypeHelper.GetDataTypeByType(attributeTypeId);
if (attributeTypeId.Value > 0)
{
Hdf5Attribute attribute = null;
if (type.NativeType.Value == H5T.C_S1)
{
attribute = GetStringAttribute(obj.Id, attributeName);
}
else
{
attribute = GetAttribute(attributeId, attributeName, type);
}
if (attribute != null)
{
_attributes.Add(attribute);
}
H5T.close(attributeTypeId.Value);
}
H5A.close(attributeId.Value);
}
return(0);
}, new IntPtr());
}
static void Main(string[] args)
{
try
{
// We will write and read an int array of this length.
const int DATA_ARRAY_LENGTH = 12;
// Rank is the number of dimensions of the data array.
const int RANK = 1;
// Create an HDF5 file.
// The enumeration type H5F.CreateMode provides only the legal
// creation modes. Missing H5Fcreate parameters are provided
// with default values.
H5FileId fileId = H5F.create("myCSharp.h5",
H5F.CreateMode.ACC_TRUNC);
// Create a HDF5 group.
H5GroupId groupId = H5G.create(fileId, "/cSharpGroup");
H5GroupId subGroup = H5G.create(groupId, "mySubGroup");
// Close the subgroup.
H5G.close(subGroup);
// Prepare to create a data space for writing a 1-dimensional
// signed integer array.
long[] dims = new long[RANK];
dims[0] = DATA_ARRAY_LENGTH;
// Put descending ramp data in an array so that we can
// write it to the file.
int[] dset_data = new int[DATA_ARRAY_LENGTH];
for (int i = 0; i < DATA_ARRAY_LENGTH; i++)
{
dset_data[i] = DATA_ARRAY_LENGTH - i;
}
// Create a data space to accommodate our 1-dimensional array.
// The resulting H5DataSpaceId will be used to create the
// data set.
H5DataSpaceId spaceId = H5S.create_simple(RANK, dims);
// Create a copy of a standard data type. We will use the
// resulting H5DataTypeId to create the data set. We could
// have used the HST.H5Type data directly in the call to
// H5D.create, but this demonstrates the use of H5T.copy
// and the use of a H5DataTypeId in H5D.create.
H5DataTypeId typeId = H5T.copy(H5T.H5Type.NATIVE_INT);
// Find the size of the type
int typeSize = H5T.getSize(typeId);
Console.WriteLine("typeSize is {0}", typeSize);
// Set the order to big endian
H5T.setOrder(typeId, H5T.Order.BE);
// Set the order to little endian
H5T.setOrder(typeId, H5T.Order.LE);
// Create the data set.
H5DataSetId dataSetId = H5D.create(fileId, "/csharpExample",
typeId, spaceId);
// Write the integer data to the data set.
H5D.write(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT),
new H5Array <int>(dset_data));
// If we were writing a single value it might look like this.
// int singleValue = 100;
// H5D.writeScalar(dataSetId,
// new H5DataTypeId(H5T.H5Type.NATIVE_INT),
// ref singleValue);
// Create an integer array to receive the read data.
int[] readDataBack = new int[DATA_ARRAY_LENGTH];
// Read the integer data back from the data set
H5D.read(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT),
new H5Array <int>(readDataBack));
// Echo the data
for (int i = 0; i < DATA_ARRAY_LENGTH; i++)
{
Console.WriteLine(readDataBack[i]);
}
// Close all the open resources.
H5D.close(dataSetId);
// Reopen and close the data sets to show that we can.
dataSetId = H5D.open(fileId, "/csharpExample");
H5D.close(dataSetId);
dataSetId = H5D.open(groupId, "/csharpExample");
H5D.close(dataSetId);
H5T.close(typeId);
H5G.close(groupId);
// Get H5O info
H5ObjectInfo objectInfo = H5O.getInfoByName(fileId,
"/csharpExample");
Console.WriteLine("header.space.message is {0}",
objectInfo.header.space.message);
Console.WriteLine("fileNumber is {0}", objectInfo.fileNumber);
Console.WriteLine("address is {0}", objectInfo.address);
Console.WriteLine("type is {0}",
objectInfo.objectType.ToString());
Console.WriteLine("reference count is {0}",
objectInfo.referenceCount);
Console.WriteLine("modification time is {0}",
objectInfo.modificationTime);
Console.WriteLine("birth time is {0}",
objectInfo.birthTime);
Console.WriteLine("access time is {0}",
objectInfo.accessTime);
Console.WriteLine("change time is {0}",
objectInfo.changeTime);
Console.WriteLine("number of attributes is {0}",
objectInfo.nAttributes);
Console.WriteLine("header version is {0}",
objectInfo.header.version);
Console.WriteLine("header nMessages is {0}",
objectInfo.header.nMessages);
Console.WriteLine("header nChunks is {0}",
objectInfo.header.nChunks);
Console.WriteLine("header flags is {0}",
objectInfo.header.flags);
H5LinkInfo linkInfo = H5L.getInfo(fileId, "/cSharpGroup");
Console.WriteLine(
"address: {0:x}, charSet: {1}, creationOrder: {2}",
linkInfo.address, linkInfo.charSet, linkInfo.creationOrder);
Console.WriteLine("linkType: {0}, softLinkSizeOrUD: {1}",
linkInfo.linkType, linkInfo.softLinkSizeOrUD);
// Reopen the group id to show that we can.
groupId = H5G.open(fileId, "/cSharpGroup");
// Use H5L.iterate to visit links
H5LIterateCallback myDelegate;
myDelegate = MyH5LFunction;
ulong linkNumber = 0;
H5IterationResult result =
H5L.iterate(groupId, H5IndexType.NAME,
H5IterationOrder.INCREASING,
ref linkNumber, myDelegate, 0);
// Create some attributes
H5DataTypeId attributeType = H5T.copy(H5T.H5Type.NATIVE_INT);
long[] attributeDims = new long[1];
const int RAMP_LENGTH = 5;
attributeDims[0] = RAMP_LENGTH;
int[] ascendingRamp = new int[RAMP_LENGTH] {
1, 2, 3, 4, 5
};
int[] descendingRamp = new int[RAMP_LENGTH] {
5, 4, 3, 2, 1
};
int[] randomData = new int[RAMP_LENGTH] {
3, 123, 27, 6, 1
};
int[] readBackRamp = new int[RAMP_LENGTH];
// Call set buffer using H5Memory
// Allocate memory from "C" runtime heap (not garbage collected)
H5Memory typeConversionBuffer = new H5Memory(new IntPtr(DATA_ARRAY_LENGTH));
H5Memory backgroundBuffer = new H5Memory(new IntPtr(DATA_ARRAY_LENGTH));
// Set the property list type conversion and background buffers.
H5PropertyListId myPropertyListId =
H5P.create(H5P.PropertyListClass.DATASET_XFER);
H5P.setBuffer(myPropertyListId,
typeConversionBuffer, backgroundBuffer);
// Test use of vlen
// Create a vlen data type
H5DataTypeId tid1 = H5T.vlenCreate(H5T.H5Type.NATIVE_UINT);
H5DataSetId vDataSetId = H5D.create(fileId, "/vlenTest", tid1,
spaceId);
// Create a jagged array of integers.
hvl_t[] vlArray = new hvl_t[DATA_ARRAY_LENGTH];
// HDF5 variable length data types require the use of void
// pointers. C# requires that sections of code that deal
// directly with pointer be marked
// as unsafe.
unsafe
{
for (int i = 0; i < DATA_ARRAY_LENGTH; i++)
{
IntPtr ptr = new IntPtr((i + 1) * sizeof(int));
// Allocate memory that is not garbage collected.
vlArray[i].p = H5CrtHeap.Allocate(
new IntPtr((i + 1) * sizeof(int))
).ToPointer();
// Fill the array with integers = the row number
int *intPointer = (int *)vlArray[i].p;
for (int j = 0; j < i + 1; j++)
{
intPointer[j] = (int)i;
}
if (IntPtr.Size == 8)
{
vlArray[i].len = (ulong)i + 1;
}
else
{
vlArray[i].len = (uint)i + 1;
}
}
// Write the variable length data
H5D.write(vDataSetId, tid1,
new H5Array <hvl_t>(vlArray));
// Create an array to read back the array.
hvl_t[] vlReadBackArray = new hvl_t[DATA_ARRAY_LENGTH];
// Read the array back
H5D.read(vDataSetId, tid1, new H5Array <hvl_t>(vlReadBackArray));
// Write the data to the console
for (int i = 0; i < DATA_ARRAY_LENGTH; i++)
{
int *iPointer = (int *)vlReadBackArray[i].p;
for (int j = 0; j < i + 1; j++)
{
Console.WriteLine(iPointer[j]);
}
}
// Reclaim the memory that read allocated
H5D.vlenReclaim(tid1, spaceId, new H5PropertyListId(H5P.Template.DEFAULT),
new H5Array <hvl_t>(vlReadBackArray));
// Now read it back again using our own memory manager
//H5AllocateCallback allocDelegate = new H5AllocCallback(userAlloc);
H5FreeCallback freeDelegate = new H5FreeCallback(userFree);
H5PropertyListId memManagerPlist = H5P.create(H5P.PropertyListClass.DATASET_XFER);
unsafe
{
H5P.setVlenMemManager(memManagerPlist, userAlloc, IntPtr.Zero,
freeDelegate, IntPtr.Zero);
}
// Read the array back
H5D.read(vDataSetId, tid1,
new H5DataSpaceId(H5S.H5SType.ALL),
new H5DataSpaceId(H5S.H5SType.ALL),
memManagerPlist,
new H5Array <hvl_t>(vlReadBackArray));
// Write the data to the console
for (int i = 0; i < DATA_ARRAY_LENGTH; i++)
{
int *iPointer = (int *)vlReadBackArray[i].p;
for (int j = 0; j < i + 1; j++)
{
Console.WriteLine(iPointer[j]);
}
}
// Reclaim the memory that read allocated using our free routines
H5D.vlenReclaim(tid1, spaceId, memManagerPlist,
new H5Array <hvl_t>(vlReadBackArray));
}
H5S.close(spaceId);
H5DataSpaceId attributeSpace =
H5S.create_simple(1, attributeDims);
H5AttributeId attributeId =
H5A.create(groupId, "ascendingRamp", attributeType, attributeSpace);
int offset = H5T.getOffset(attributeType);
Console.WriteLine("Offset is {0}", offset);
H5DataTypeId float32BE = H5T.copy(H5T.H5Type.IEEE_F32BE);
H5T.Norm norm = H5T.getNorm(float32BE);
Console.WriteLine("Norm is {0}", norm);
int precision = H5T.getPrecision(float32BE);
Console.WriteLine("Precision is {0}", precision);
H5FloatingBitFields bitFields = H5T.getFields(float32BE);
Console.WriteLine("getFields: sign bit position: {0}", bitFields.signBitPosition);
Console.WriteLine("getFields: exponent bit position: {0}", bitFields.exponentBitPosition);
Console.WriteLine("getFields: number of exponent bits: {0}", bitFields.nExponentBits);
Console.WriteLine("getFields: mantissa bit position: {0} ", bitFields.mantissaBitPosition);
Console.WriteLine("getFields: number of mantissa bits: {0}", bitFields.nMantissaBits);
Console.Write("{0}", bitFields);
// Write to an attribute
H5A.write <int>(attributeId, attributeType,
new H5Array <int>(ascendingRamp));
// Read from an attribute
H5A.read <int>(attributeId, attributeType,
new H5Array <int>(readBackRamp));
// Echo results
Console.WriteLine("ramp elements are: ");
foreach (int rampElement in readBackRamp)
{
Console.WriteLine(" {0}", rampElement);
}
H5A.close(attributeId);
// Create and write two more attributes.
attributeId = H5A.createByName(groupId, ".", "descendingRamp",
attributeType, attributeSpace);
H5A.write <int>(attributeId, attributeType,
new H5Array <int>(descendingRamp));
H5A.close(attributeId);
attributeId = H5A.createByName(groupId, ".",
"randomData", attributeType,
attributeSpace);
H5A.write <int>(attributeId, attributeType,
new H5Array <int>(randomData));
// Read back the attribute data
H5A.read <int>(attributeId, attributeType,
new H5Array <int>(readBackRamp));
Console.WriteLine("ramp elements are: ");
foreach (int rampElement in readBackRamp)
{
Console.WriteLine(" {0}", rampElement);
}
H5A.close(attributeId);
// Iterate through the attributes.
long position = 0;
H5AIterateCallback attributeDelegate;
attributeDelegate = MyH5AFunction;
H5ObjectInfo groupInfo = H5O.getInfo(groupId);
Console.WriteLine(
"fileNumber: {0}, total space: {1}, referceCount: {2}, modification time: {3}",
groupInfo.fileNumber, groupInfo.header.space.total,
groupInfo.referenceCount, groupInfo.modificationTime);
// While iterating, collect the names of all the attributes.
ArrayList attributeNames = new ArrayList();
H5A.iterate(groupId, H5IndexType.CRT_ORDER,
H5IterationOrder.INCREASING,
ref position, attributeDelegate,
(object)attributeNames);
// Write out the names of the attributes
foreach (string attributeName in attributeNames)
{
Console.WriteLine("attribute name is {0}", attributeName);
}
// Demonstrate H5A.openName
attributeId = H5A.openName(groupId, "descendingRamp");
Console.WriteLine("got {0} by name", H5A.getName(attributeId));
H5A.close(attributeId);
// Demonstrate H5A.getNameByIndex
string secondAttribute = H5A.getNameByIndex(groupId, ".",
H5IndexType.CRT_ORDER, H5IterationOrder.INCREASING, 1);
Console.WriteLine("second attribute is named {0}",
secondAttribute);
// Demonstrate H5G.getInfo
H5GInfo gInfo = H5G.getInfo(groupId);
Console.WriteLine(
"link storage: {0}, max creation order: {1}, nLinks: {2}",
gInfo.linkStorageType, gInfo.maxCreationOrder, gInfo.nLinks);
// Demonstrate H5A.getSpace
//attributeId = H5A.openByName(groupId, ".", "descendingRamp");
attributeId = H5A.open(groupId, "descendingRamp");
H5DataSpaceId rampSpaceId = H5A.getSpace(attributeId);
H5S.close(rampSpaceId);
// Demonstrate H5A.getType
H5DataTypeId rampTypeId = H5A.getType(attributeId);
Console.WriteLine("size of ramp data type is {0} bytes.",
H5T.getSize(rampTypeId));
H5T.close(rampTypeId);
// Demonstrate H5A.getInfo
H5AttributeInfo rampInfo = H5A.getInfo(attributeId);
Console.WriteLine(
"characterset: {0}, creationOrder: {1}, creationOrderValid: {2}, dataSize: {3}",
rampInfo.characterSet, rampInfo.creationOrder,
rampInfo.creationOrderValid, rampInfo.dataSize);
// Demonstrate H5A.Delete
H5A.Delete(groupId, "descendingRamp");
//H5A.DeleteByName(groupId, ".", "descendingRamp");
// Iterate through the attributes to show that the deletion
// was successful.
position = 0;
ArrayList namesAfterDeletion = new ArrayList();
H5A.iterate(groupId, H5IndexType.CRT_ORDER,
H5IterationOrder.DECREASING, ref position,
attributeDelegate,
(object)namesAfterDeletion);
H5G.close(groupId);
H5F.close(fileId);
// Reopen and reclose the file.
H5FileId openId = H5F.open("myCSharp.h5",
H5F.OpenMode.ACC_RDONLY);
H5F.close(openId);
// Set the function to be called on error.
unsafe
{
H5AutoCallback myErrorDelegate = new H5AutoCallback(myErrorFunction);
H5E.setAuto(0, myErrorDelegate, IntPtr.Zero);
}
// Uncomment the next line if you want to generate an error to
// test H5E.setAuto
// H5G.open(openId, "noGroup");
}
// This catches all the HDF exception classes. Because each call
// generates a unique exception, different exception can be handled
// separately. For example, to catch open errors we could have used
// catch (H5FopenException openException).
catch (HDFException e)
{
Console.WriteLine(e.Message);
}
Console.WriteLine("Processing complete!");
Console.ReadLine();
}
public Dictionary <string, string> GetDatasetAttributes(string originalDatasetName)
{
H5DataSetId datasetId = 0;
H5GroupId groupId = 0;
H5DataTypeId typeId = 0;
H5DataSpaceId spaceId = 0;
try
{
if (_h5FileId < 0)
{
return(null);
}
string datasetName = GetDatasetFullNames(originalDatasetName, _h5FileId);
if (string.IsNullOrEmpty(datasetName))
{
return(null);
}
int groupIndex = datasetName.LastIndexOf('/');
if (groupIndex == -1)
{
datasetId = H5D.open(_h5FileId, datasetName);
}
else
{
string groupName = datasetName.Substring(0, groupIndex + 1);
string dsName = datasetName.Substring(groupIndex + 1);
groupId = H5G.open(_h5FileId, groupName);
datasetId = H5D.open(groupId, dsName);
}
if (datasetId == 0)
{
return(null);
}
Dictionary <string, string> attValues = new Dictionary <string, string>();
typeId = H5D.get_type(datasetId);
H5T.class_t type = H5T.get_class(typeId);
IntPtr tSize = H5T.get_size(typeId);
spaceId = H5D.get_space(datasetId);
int length = H5S.get_simple_extent_ndims(spaceId);
ulong[] dims = new ulong[length];
H5S.get_simple_extent_dims(spaceId, dims, null);
ulong storageSize = H5D.get_storage_size(datasetId);
attValues.Add("DataSetName", datasetName);
attValues.Add("DataType", type.ToString());
attValues.Add("DataTypeSize", tSize.ToString() + "Byte");
attValues.Add("Dims", String.Join("*", dims));
attValues.Add("StorageSize", storageSize.ToString() + "Byte");
//所有Attributes的键
ArrayList arrayList = new ArrayList();
GCHandle handle = GCHandle.Alloc(arrayList);
ulong n = 0;
// the callback is defined in H5ATest.cs
H5A.operator_t cb = (int location_id, IntPtr attr_name, ref H5A.info_t ainfo, IntPtr op_data) =>
{
GCHandle hnd = (GCHandle)op_data;
ArrayList al = (hnd.Target as ArrayList);
int len = 0;
while (Marshal.ReadByte(attr_name, len) != 0)
{
++len;
}
byte[] buf = new byte[len];
Marshal.Copy(attr_name, buf, 0, len);
al.Add(Encoding.UTF8.GetString(buf));
return(0);
};
H5A.iterate(datasetId, H5.index_t.NAME, H5.iter_order_t.NATIVE, ref n, cb, (IntPtr)handle);
handle.Free();
foreach (string attName in arrayList)
{
attValues.Add(attName, ReadAttributeValue(datasetId, attName));
}
return(attValues);
}
finally
{
if (spaceId != 0)
{
H5S.close(spaceId);
}
if (typeId != 0)
{
H5T.close(typeId);
}
if (datasetId != 0)
{
H5D.close(datasetId);
}
if (groupId != 0)
{
H5G.close(groupId);
}
}
}
internal static (List <Hdf5Element> tree, List <Hdf5Element> flat) ReadFileStructure(string fileName)
{
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;
ulong attId = 0;
H5A.iterate(groupId, H5.index_t.NAME, H5.iter_order_t.INC, ref attId, AttributeCallback, Marshal.StringToHGlobalAnsi("/"));
}
else
{
datasetId = H5D.open(elementId, name);
if ((H5I.is_valid(datasetId) > 0))
{
objectType = H5O.type_t.DATASET;
elementType = Hdf5ElementType.Dataset;
ulong attId = 0;
H5A.iterate(groupId, H5.index_t.NAME, H5.iter_order_t.INC, ref attId, AttributeCallback, Marshal.StringToHGlobalAnsi("/"));
}
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, elementId, false);
structure.Add(element);
elements.Add(element);
}
else
{
var element = new Hdf5Element(fullName, elementType, parent, elementId, false);
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);
}
return(structure, elements);
}
static void test_attr_iterate()
{
try
{
Console.Write("Testing attribute iteration");
// Open the file.
H5FileId fileId = H5F.open(FILE_NAME, H5F.OpenMode.ACC_RDWR);
// Create a dataspace.
H5DataSpaceId spaceId = H5S.create(H5S.H5SClass.SCALAR);
// Create a new dataset using default properties.
const string DSET2_NAME = ("Dataset2");
H5DataSetId dsetId = H5D.create(fileId, DSET2_NAME, H5T.H5Type.NATIVE_INT, spaceId);
// Close dataspace.
H5S.close(spaceId);
// Verify the correct number of attributes.
H5ObjectInfo oinfo = H5O.getInfo(dsetId);
if (oinfo.nAttributes != 0)
{
Console.WriteLine("\ntest_attr_iterate: incorrect number of attributes: read {0} - should be {1}",
oinfo.nAttributes, 1);
nerrors++;
}
// Iterate through the attributes.
hssize_t position = 0;
H5AIterateCallback attributeCallback;
attributeCallback = MyH5AFunction;
H5ObjectInfo groupInfo = H5O.getInfo(dsetId);
// While iterating, collect the names of all the attributes.
ArrayList attributeNames = new ArrayList();
Console.WriteLine();
Console.WriteLine("\tIterating through attributes:");
H5A.iterate(dsetId, H5IndexType.CRT_ORDER,
H5IterationOrder.INCREASING,
ref position, attributeCallback,
(object)attributeNames);
// Close dataset.
H5D.close(dsetId);
// Open existing dataset with attributes.
dsetId = H5D.open(fileId, DSET1_NAME);
// Iterate through the attributes of dataset DSET1_NAME.
position = 0;
attributeCallback = MyH5AFunction;
groupInfo = H5O.getInfo(dsetId);
// While iterating, collect the names of all the attributes.
attributeNames = new ArrayList();
H5A.iterate(dsetId, H5IndexType.CRT_ORDER,
H5IterationOrder.INCREASING,
ref position, attributeCallback,
(object)attributeNames);
// Verify the correct number of attributes.
oinfo = H5O.getInfo(dsetId);
if (oinfo.nAttributes != 2)
{
Console.WriteLine("\ntest_attr_iterate: incorrect number of attributes: read {0} - should be {1}",
oinfo.nAttributes, 2);
nerrors++;
}
// Close dataset and file.
H5D.close(dsetId);
H5F.close(fileId);
Console.WriteLine("\tPASSED");
}
catch (HDFException anyHDF5E)
{
Console.WriteLine(anyHDF5E.Message);
nerrors++;
}
catch (System.Exception sysE)
{
Console.WriteLine(sysE.TargetSite);
Console.WriteLine(sysE.Message);
nerrors++;
}
}
