public static double ReadAttribute(string file, string dataSetOrGroup, string attribute)
{
double attr = Double.NaN;
try
{
H5FileId fileId = H5F.open(file, H5F.OpenMode.ACC_RDONLY);
H5ObjectInfo objectInfo = H5O.getInfoByName(fileId, dataSetOrGroup);
H5GroupId groupId = null;
H5DataSetId dataSetId = null;
H5AttributeId attrId;
if (objectInfo.objectType == H5ObjectType.GROUP)
{
groupId = H5G.open(fileId, dataSetOrGroup);
attrId = H5A.open(groupId, attribute);
}
else
{
dataSetId = H5D.open(fileId, dataSetOrGroup);
attrId = H5A.open(dataSetId, attribute);
}
H5DataTypeId attrTypeId = H5A.getType(attrId);
double[] dAttrs = new double[] { };
if (H5T.equal(attrTypeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
float[] fAttrs = new float[H5S.getSimpleExtentNPoints(H5A.getSpace(attrId))];
H5A.read(attrId, attrTypeId, new H5Array <float>(fAttrs));
dAttrs = (from f in fAttrs select(double) f).ToArray();
}
else if (H5T.equal(attrTypeId, H5T.copy(H5T.H5Type.NATIVE_DOUBLE)))
{
dAttrs = new double[H5S.getSimpleExtentNPoints(H5A.getSpace(attrId))];
H5A.read(attrId, attrTypeId, new H5Array <double>(dAttrs));
}
H5T.close(attrTypeId);
H5A.close(attrId);
if (groupId != null)
{
H5G.close(groupId);
}
if (dataSetId != null)
{
H5D.close(dataSetId);
}
H5F.close(fileId);
return((double)dAttrs[0]);
}
catch (HDFException e)
{
Console.WriteLine("Error: Unhandled HDF5 exception");
Console.WriteLine(e.Message);
}
return(attr);
}
private void Write(H5GroupId parent, string name, IEnumerable <IMeasurement> measurements)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] {
(long)measurements.Count()
});
// Set compression options for dataset
H5PropertyListId dataSetPropertyList = H5P.create(H5P.PropertyListClass.DATASET_CREATE);
H5P.setDeflate(dataSetPropertyList, NumericDataCompression);
H5P.setChunk(dataSetPropertyList, new long[] { (long)measurements.Count() });
H5DataSetId dataSetId = H5D.create(parent,
name,
measurement_t,
spaceId,
new H5PropertyListId(H5P.Template.DEFAULT),
dataSetPropertyList,
new H5PropertyListId(H5P.Template.DEFAULT));
MeasurementT[] ms = new MeasurementT[measurements.Count()];
int ilmCount = 0;
foreach (IMeasurement m in measurements)
{
MeasurementT mt = Convert(m);
ms[ilmCount++] = mt;
}
H5D.write <MeasurementT>(dataSetId, measurement_t, new H5Array <MeasurementT>(ms));
H5D.close(dataSetId);
H5S.close(spaceId);
}
// Function used with H5L.iterate
protected H5IterationResult Op_Func(H5GroupId id,
string objectName,
H5LinkInfo info, Object param)
{
H5ObjectInfo objInfo = H5O.getInfoByName(id, objectName);
string groupName = (string)param;
switch (objInfo.objectType)
{
case H5ObjectType.DATASET:
OnHdfObjInfoFound(objectName, HdfObjectType.Dataset, groupName);
break;
case H5ObjectType.GROUP:
GetHdfObjInfo(objectName);
break;
case H5ObjectType.NAMED_DATATYPE:
break;
case H5ObjectType.UNKNOWN:
break;
}
return(H5IterationResult.SUCCESS);
}
} // test_group_basics
/*
* Operator function.
*/
static int file_info(H5GroupId id, string objectName, Object param)
{
string str_param = (string)param;
Console.WriteLine("\t {0}: {1}", str_param, objectName);
return(0);
}
public EpochGroupIDs(H5GroupId group,
H5GroupId subGroups,
H5GroupId epochs)
{
GroupId = group;
SubGroupsId = subGroups;
EpochsId = epochs;
}
static void test_file_open()
{
try
{
// Output message about test being performed.
Console.Write("Testing file opening I/O");
// First ensure the file does not exist
File.Delete(FILE2);
// Try opening a non-existent file. This should fail.
try
{
H5FileId non_exist_file = H5F.open(FILE2, H5F.OpenMode.ACC_RDWR);
// should fail, but didn't, print out the error message.
Console.WriteLine("\ntest_file_open: Attempting to open a non-existent file.");
nerrors++;
}
catch (H5FopenException) { } // does nothing, it should fail
// Open the file.
H5FileId fileId = H5F.open(FILE1, H5F.OpenMode.ACC_RDWR);
// Create dataspace for the dataset in the file.
hssize_t[] dims = { 20 };
H5DataSpaceId dspace = H5S.create_simple(RANK, dims);
// Create a group.
H5GroupId groupId = H5G.create(fileId, GROUP_NAME);
// Create a dataset using file as location.
H5DataSetId dset1Id = H5D.create(fileId, DSET1_NAME, H5T.H5Type.NATIVE_INT, dspace);
// Create a dataset using group as location.
H5DataSetId dset2Id = H5D.create(groupId, DSET2_NAME, H5T.H5Type.NATIVE_SHORT, dspace);
// Close objects and files.
H5D.close(dset1Id);
H5D.close(dset2Id);
H5S.close(dspace);
H5G.close(groupId);
H5F.close(fileId);
Console.WriteLine("\t\t\t\tPASSED");
}
catch (HDFException anyHDF5E)
{
Console.WriteLine(anyHDF5E.Message);
nerrors++;
}
catch (System.Exception sysE)
{
Console.WriteLine(sysE.TargetSite);
Console.WriteLine(sysE.Message);
nerrors++;
}
} // test_file_open
private void GetGroupDatasetNames(string groupName)
{
H5GroupId h5GroupId = H5G.open(_h5FileId, groupName);
try
{
long dscount = H5G.getNumObjects(h5GroupId);
for (int i = 0; i < dscount; i++)
{
string objname = H5G.getObjectNameByIndex(h5GroupId, (ulong)i);
ObjectInfo objInfo = H5G.getObjectInfo(h5GroupId, objname, false);
switch (objInfo.objectType)
{
case H5GType.DATASET:
if (objInfo.objectType == H5GType.DATASET)
{
if (groupName == "/")
{
_datasetNames.Add(objname);
}
else
{
_datasetNames.Add(groupName + objname);
}
}
break;
case H5GType.GROUP:
if (groupName == "/")
{
GetGroupDatasetNames(objname + "/");
}
else
{
GetGroupDatasetNames(groupName + objname + "/");
}
break;
case H5GType.LINK:
break;
case H5GType.TYPE:
break;
default:
break;
}
}
}
finally
{
if (h5GroupId != null)
{
H5G.close(h5GroupId);
}
}
}
// Function used with H5L.iterate
static H5IterationResult MyH5LFunction(H5GroupId id,
string objectName,
H5LinkInfo info, Object param)
{
Console.WriteLine("The object name is {0}", objectName);
Console.WriteLine("The linkType is {0}", info.linkType);
Console.WriteLine("The object parameter is {0}", param);
return(H5IterationResult.SUCCESS);
}
public NeuralNetworkH5Loader(string h5File)
{
if (h5File is null)
{
throw new ArgumentNullException(nameof(h5File));
}
H5FileId = H5F.open(h5File, H5F.OpenMode.ACC_RDONLY);
H5GroupId = H5G.open(H5FileId, "/");
H5GroupIdModelWeights = H5G.open(H5GroupId, "model_weights");
}
// Generate string attribute
// GroupName: target group for the new attribute
// AttName: attribute name
// AttContent: content for the attribute, has to be a string
public static void StringAttributeGenerator(H5GroupId GroupName, string AttName, string AttContent)
{
char[] AttContentChar = AttContent.ToCharArray();
byte[] asciiStr = ASCIIEncoding.ASCII.GetBytes(AttContentChar);
int length = asciiStr.Length;
H5AttributeId attributeId = H5A.create(GroupName, AttName, H5T.create(H5T.CreateClass.STRING, length), H5S.create(H5S.H5SClass.SCALAR));
H5A.write(attributeId, H5T.create(H5T.CreateClass.STRING, length), new H5Array <byte>(asciiStr));
H5A.close(attributeId);
}
// Generate double attributes
// GroupName: target group for the new attribute
// AttName: attribute name
// AttContent: content for the attribute, has to be a single floating number, here 64bit double is used, to generate subgroups in Data
public static void DoubleAttributeGenerator(H5GroupId GroupName, string AttName, double AttContent)
{
double[] AttArray = new double[1] {
AttContent
};
long[] dims = new long[1];
dims[0] = AttArray.Length;
H5AttributeId attributeId = H5A.create(GroupName, AttName, H5T.copy(H5T.H5Type.NATIVE_DOUBLE), H5S.create_simple(1, dims));
H5A.write(attributeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT), new H5Array <double>(AttArray));
H5A.close(attributeId);
}
// Generate floating number attributes
// GroupName: target group for the new attribute
// AttName: attribute name
// AttContent: content for the attribute, has to be a single floating number, here 32bit floating number is used, consider using 64bit double if necessary
public static void NumberAttributeGenerator(H5GroupId GroupName, string AttName, float AttContent)
{
float[] AttArray = new float[1] {
AttContent
};
long[] dims = new long[1];
dims[0] = AttArray.Length;
H5AttributeId attributeId = H5A.create(GroupName, AttName, H5T.copy(H5T.H5Type.NATIVE_FLOAT), H5S.create_simple(1, dims));
H5A.write(attributeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT), new H5Array <float>(AttArray));
H5A.close(attributeId);
}
private void createHD5GroupObject(H5GroupId id, String name, ref HDF5GroupObject hdf5Obj)
{
hdf5Obj.GroupID = id;
hdf5Obj.GroupName = name;
long num = H5G.getNumObjects(hdf5Obj.GroupID);
// the items under the group
for (ulong i = 0; i < (ulong)num; i++)
{
String objName = H5G.getObjectNameByIndex(hdf5Obj.GroupID, i);
// get the link info.
//linfo = H5L.getInfo(groupID, objName);
ObjectInfo objInfo = H5G.getObjectInfo(hdf5Obj.GroupID, objName, true);
if (objInfo.objectType == H5GType.GROUP)
{
String pathName = "/" + name + "/" + objName;
if (name.CompareTo("/") == 0)
{
pathName = "/" + objName;
}
H5GroupId groupID = null;
try
{
groupID = H5G.open(hdf5Obj.GroupID, pathName);
HDF5GroupObject subObj = new HDF5GroupObject();
subObj.ShortName = objName;
createHD5GroupObject(groupID, pathName, ref subObj);
hdf5Obj.SubGroups.Add(subObj);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
if (groupID != null)
{
H5G.close(groupID);
}
}
}
else
if (objInfo.objectType == H5GType.DATASET)
{
String pathName = "/" + name + "/" + objName;
HD5DataSetObject dataObject = new HD5DataSetObject();
dataObject.ShortName = objName;
createHD5DataObject(hdf5Obj.GroupID, pathName, ref dataObject);
hdf5Obj.Datasets.Add(dataObject);
}
}
}
private void createHD5DataObject(H5GroupId h5GroupId, string pathName, ref HD5DataSetObject dataObject)
{
H5DataSetId datasetid = null;
H5DataSpaceId spaceid = null;
H5DataTypeId dataTypeid = null;
try
{
dataObject.GroupId = h5GroupId;
datasetid = H5D.open(h5GroupId, pathName);
dataObject.DatasetID = datasetid;
dataObject.DatasetName = pathName;
spaceid = H5D.getSpace(datasetid);
var dims = H5S.getSimpleExtentDims(spaceid);
dataTypeid = H5D.getType(datasetid);
dataObject.Dim = dims.Length;
HDF5DotNet.H5T.H5TClass classType = H5T.getClass(dataTypeid);
int size = H5T.getSize(dataTypeid);
H5T.Sign sign = H5T.Sign.TWOS_COMPLEMENT;
if (classType == H5T.H5TClass.INTEGER)
{
sign = H5T.getSign(dataTypeid);
}
//var rank = H5S.getSimpleExtentNDims(space);
//var statu = H5S.getSimpleExtentDims(space);
Boolean bString = H5T.isVariableString(dataTypeid);
//String name = H5T.getMemberName(dataType, 0);
// var type2 = H5T.getNativeType(dataType, H5T.Direction.DEFAULT);
Type type = getTypeof(classType, size, sign);
dataObject.DataType = type;
dataObject.Data = readData(dataObject);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
}
finally{
if (datasetid != null)
{
H5D.close(datasetid);
}
if (spaceid != null)
{
H5S.close(spaceid);
}
if (dataTypeid != null)
{
H5T.close(dataTypeid);
}
}
}
private void Write(H5GroupId parent, string name, double d)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] {
1
});
H5DataSetId dataSetId = H5D.create(parent, name, H5T.H5Type.NATIVE_DOUBLE, spaceId);
double data = d;
H5D.writeScalar <double>(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_DOUBLE), ref data);
H5D.close(dataSetId);
H5S.close(spaceId);
}
private void Write(H5GroupId parent, string name, ulong ul)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] {
1
});
H5DataSetId dataSetId = H5D.create(parent, name, H5T.H5Type.NATIVE_ULLONG, spaceId);
ulong data = ul;
H5D.writeScalar <ulong>(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_ULLONG), ref data);
H5D.close(dataSetId);
H5S.close(spaceId);
}
private static H5GroupId CreateGroupIfNoneExists(H5FileId fileId, string path)
{
H5GroupId group = null;
if (H5L.Exists(fileId, path))
{
group = H5G.open(fileId, path);
}
else
{
group = H5G.create(fileId, path);
}
return(group);
}
private void Write(H5GroupId parent, string name, IMeasurement m)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] {
(long)1
});
H5DataSetId dataSetId = H5D.create(parent, name, measurement_t, spaceId);
MeasurementT mt = Convert(m);
H5D.writeScalar <MeasurementT>(dataSetId, measurement_t, ref mt);
H5D.close(dataSetId);
H5S.close(spaceId);
}
public override void Serialize(Epoch e, string fileTag)
{
if (!e.StartTime)
{
throw new PersistanceException("Epoch must have a start time.");
}
if (CurrentEpochGroupID == null)
{
throw new InvalidOperationException("Cannot serialize an Epoch without an open EpochGroup. Call BeginEpochGroup before attempting to serialize an Epoch.");
}
var groupName = "epoch-" + e.ProtocolID + "-" + GuidGenerator();
H5GroupId epochID = H5G.create(CurrentEpochGroupID.EpochsId, groupName); //epochGroupMetadata
log.DebugFormat("Serializing Epoch to HDF5 {0}", groupName);
WriteAttribute(epochID, "protocolID", e.ProtocolID);
// WriteEpochStart and duration
WriteAttribute(epochID, startTimeOffsetName, ((DateTimeOffset)e.StartTime).Offset.TotalHours); //TimeZone.CurrentTimeZone.GetUtcOffset(((DateTimeOffset)e.StartTime).DateTime).TotalHours);
WriteAttribute(epochID, startTimeUtcName, ((DateTimeOffset)e.StartTime).Ticks);
WriteAttribute(epochID, "durationSeconds", ((TimeSpan)e.Duration).TotalSeconds);
if (fileTag != null)
{
WriteAttribute(epochID, "fileTag", fileTag);
}
//Write keywords
WriteKeywords(epochID, e.Keywords);
// WriteBackground
Write(epochID, "background", e.Background);
// WriteProtocolParams
WriteDictionary(epochID, "protocolParameters", e.ProtocolParameters);
// WriteStimulus
WriteStimuli(epochID, "stimuli", e.Stimuli);
// WriteResponse
WriteResponses(epochID, "responses", e.Responses);
H5G.close(epochID);
H5F.flush(fileId);
}
/// <summary>
/// 得到所有数据集合名，未对异常进行处理
/// </summary>
private void getDatasetNames()
{
H5GroupId groupId = H5G.open(_fileId, "/");
long dscount = H5G.getNumObjects(groupId);
for (int ii = 0; ii < dscount; ++ii)
{
String v = H5G.getObjectNameByIndex(groupId, (ulong)ii);
_datasetNames.Add(v);
}
if (groupId != null)
{
H5G.close(groupId);
}
}
public static H5FileId InitializeHDF(int numpos, int height, int width, UInt16[,,] datacube, string fullpath)
{
// write in HDF5 (.h5) format
// generate standard groups
H5FileId fileId = H5F.create(fullpath,
H5F.CreateMode.ACC_TRUNC);
//H5FileId fileId = H5F.create("D:/2017/Pixelated Camera/CameraSoftware/FileFormat/Test/test5.emd",
//H5F.CreateMode.ACC_TRUNC);
//NumberAttributeGenerator(fileId, "voltage", Convert.ToSingle(300));
//H5GroupId dataGroup = H5G.create(fileId, "/data"); //dash is required for root group
H5GroupId userGroup = H5G.create(fileId, "/user");
H5GroupId micGroup = H5G.create(fileId, "/microscope");
H5GroupId sampleGroup = H5G.create(fileId, "/sample");
H5GroupId commentGroup = H5G.create(fileId, "/comments");
// generate attributes for user group, all attributes are sting
StringAttributeGenerator(userGroup, "user", "Chenyu Zhang");
StringAttributeGenerator(userGroup, "email", "*****@*****.**");
StringAttributeGenerator(userGroup, "institution", "UW-Madison");
StringAttributeGenerator(userGroup, "department", "Materials Science and Engineering");
// generate attributes for microscope group
StringAttributeGenerator(micGroup, "voltage units", "kV");
NumberAttributeGenerator(micGroup, "voltage", Convert.ToSingle(300));
StringAttributeGenerator(micGroup, "wavelength units", "nm");
NumberAttributeGenerator(micGroup, "wavelength", Convert.ToSingle(0.00197));
// generate attributes for sample group
StringAttributeGenerator(sampleGroup, "material", "STO");
StringAttributeGenerator(sampleGroup, "preparation", "Mechanical polishing and ion milling");
StringAttributeGenerator(sampleGroup, "Zone Axis", "[1][0][0]");
// Write 3D data cube to the file
WriteDataCube(fileId, datacube);
// close groups and file
H5G.close(userGroup);
H5G.close(micGroup);
H5G.close(sampleGroup);
H5G.close(commentGroup);
//H5G.close(dataGroup);
H5F.close(fileId);
return(fileId);
}
public static void WriteDataCube(H5FileId fileId, UInt16[,,] datacube)
{
H5GroupId dataGroup = H5G.create(fileId, "/data");
H5GroupId dataSubGroup = H5G.create(dataGroup, "DEsoftware");
long[] dims = new long[3] {
datacube.GetLength(0), datacube.GetLength(1), datacube.GetLength(2)
};
H5DataSpaceId spaceId = H5S.create_simple(3, dims);
H5DataTypeId typeId = H5T.copy(H5T.H5Type.NATIVE_USHORT);
H5DataSetId dataSetId = H5D.create(dataSubGroup, "data",
typeId, spaceId);
// create attribute emd_group_type for dataSubGroup, which is required to have value 1
int par = 1;
long[] attdims = new long[1];
int[] AttArray = new int[1] {
par
};
dims[0] = AttArray.Length;
H5AttributeId attributeId = H5A.create(dataSubGroup, "emd_group_type", H5T.copy(H5T.H5Type.NATIVE_UCHAR), H5S.create_simple(1, dims));
H5A.write(attributeId, H5T.copy(H5T.H5Type.NATIVE_INT), new H5Array <int>(AttArray));
H5A.close(attributeId);
// write datacube to "data", which contains whole 3D datacube
H5D.write <ushort>(dataSetId, typeId, new H5Array <ushort>(datacube));
// create three more array for three dimensions
long[] dim1 = new long[1] {
datacube.GetLength(0)
};
double[] dimarray = new double [datacube.GetLength(0)];
spaceId = H5S.create_simple(3, dim1);
typeId = H5T.copy(H5T.H5Type.NATIVE_DOUBLE);
dataSetId = H5D.create(dataSubGroup, "dim1", typeId, spaceId);
H5D.write <double>(dataSetId, typeId, new H5Array <double>(dimarray));
H5S.close(spaceId);
H5T.close(typeId);
H5D.close(dataSetId);
H5G.close(dataGroup);
H5G.close(dataSubGroup);
}
public static List <string> GetChildGroupNames(H5GroupId _groupId)
{
List <string> names = new List <string>();
ulong count = (ulong)H5G.getNumObjects(_groupId);;
for (ulong i = 0; i < count; i++)
{
string name = H5G.getObjectNameByIndex(_groupId, i);
ObjectInfo info = H5G.getObjectInfo(_groupId, name, false);
if (info.objectType == H5GType.GROUP)
{
names.Add(name);
}
}
return(names);
}
/// <summary>
/// 得到所有文件属性名，未对异常进行处理
/// </summary>
private void getFileAttributeNames()
{
H5GroupId groupId = H5G.open(_fileId, "/");
int attCount = H5A.getNumberOfAttributes(groupId);
for (int ii = 0; ii < attCount; ++ii)
{
String attName = H5A.getNameByIndex(groupId, "/", H5IndexType.NAME, H5IterationOrder.NATIVE, (ulong)ii);
if (attName != null)
{
_fileAttributeNames.Add(attName);
}
}
if (groupId != null)
{
H5G.close(groupId);
}
}
private static H5DataSetId CreateDatasetIfNoneExists(H5FileId fileId, string setName, int dim1, H5DataTypeId dataType)
{
H5DataSetId dataSetId = null;
char[] sep = { '/' };
string[] strings = setName.Split(sep);
string path = "/";
for (int x = 0; x < strings.Length - 1; x++)
{
path += strings[x] + "/";
H5GroupId groupId = CreateGroupIfNoneExists(fileId, path);
}
long[] dims = new long[] {
dim1
};
long[] maxDims = new long[] {
-1
};
if (H5L.Exists(fileId, setName))
{
dataSetId = H5D.open(fileId, setName);
H5D.setExtent(dataSetId, dims);
}
else
{
H5PropertyListId linkp = H5P.create(H5P.PropertyListClass.LINK_CREATE);
H5PropertyListId accessp = H5P.create(H5P.PropertyListClass.DATASET_ACCESS);
H5PropertyListId createp = H5P.create(H5P.PropertyListClass.DATASET_CREATE);
H5P.setChunk(createp, dims);
H5P.setDeflate(createp, 1);
H5DataSpaceId sId = H5S.create_simple(1, dims, maxDims);
dataSetId = H5D.create(fileId, setName, dataType, sId, linkp, createp, accessp);
}
return(dataSetId);
}
private void WriteConfigurationSpans(H5GroupId gID, IEnumerable <IConfigurationSpan> configurationSpans)
{
var spansId = H5G.create(gID, DATA_CONFIGURATION_SPANS_GROUP);
uint i = 0;
var totalTime = TimeSpan.Zero;
foreach (var configSpan in configurationSpans)
{
var spanId = H5G.create(spansId, DATA_CONFIGURATION_SPAN_PREFIX + i++);
WriteAttribute(spanId, "startTimeSeconds", totalTime.TotalSeconds);
totalTime += configSpan.Time;
WriteAttribute(spanId, "timeSpanSeconds", configSpan.Time.TotalSeconds);
foreach (var nodeConfig in configSpan.Nodes)
{
WriteDictionary(spanId, nodeConfig.Name, nodeConfig.Configuration);
}
}
}
private static T[,] Read2DArray <T>(H5GroupId fileId, string dataSetName)
{
var dataset = H5D.open(fileId, dataSetName);
var space = H5D.getSpace(dataset);
var dims = H5S.getSimpleExtentDims(space);
var dataType = H5D.getType(dataset);
if (typeof(T) == typeof(string))
{
// this will also need a string hack...
T[,] dataArray = new T[dims[0], 2];
return(dataArray);
}
else
{
T[,] dataArray = new T[dims[0], dims[1]];
var wrapArray = new H5Array <T>(dataArray);
H5D.read(dataset, dataType, wrapArray);
return(dataArray);
}
}
public void GetHdfObjInfo(string groupName)
{
H5GroupId groupId = H5G.open(m_fileId, groupName);
H5LIterateCallback myDelegate;
myDelegate = Op_Func;
ulong linkNumber = 0;
int attriNum = H5A.getNumberOfAttributes(groupId);
for (int i = 0; i < attriNum; i++)
{
string attriName = H5A.getNameByIndex(groupId, groupName, H5IndexType.CRT_ORDER, H5IterationOrder.NATIVE, (ulong)i);
OnHdfObjInfoFound(attriName, HdfObjectType.Attribute, groupName);
}
H5L.iterate(groupId, H5IndexType.NAME, H5IterationOrder.NATIVE, ref linkNumber, myDelegate, groupName);
H5G.close(groupId);
}
/// <summary>
/// 暂时不用
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="fileId"></param>
/// <param name="datasetName"></param>
/// <param name="groupName"></param>
/// <param name="datasetOut"></param>
/// <param name="rowIndex"></param>
/// <param name="rowcount"></param>
/// <param name="colcount"></param>
public void GetDataset <T>(H5FileId fileId, string datasetName, string groupName, T[,] datasetOut, int rowIndex, int rowcount, int colcount)
{
H5GroupId groupId = H5G.open(fileId, groupName);
H5DataSetId dataSetId = H5D.open(groupId, datasetName /*"EV_Emissive"*/);
H5DataTypeId tid0 = H5D.getType(dataSetId);
H5DataSpaceId spaceid = H5D.getSpace(dataSetId);
long[] start = new long[2];
start[0] = rowIndex;
start[1] = 0;
long[] count = new long[2];
count[0] = rowcount;
count[1] = colcount;
H5S.selectHyperslab(spaceid, H5S.SelectOperator.SET, start, count);
//long[] dimes = new long[2];
//dimes[0] = 1;
//dimes[1] = 8192;
H5DataSpaceId simpleSpaceid = H5S.create_simple(2, count);
H5PropertyListId listid = new H5PropertyListId(H5P.Template.DEFAULT);
H5DataTypeId tid1 = new H5DataTypeId(H5T.H5Type.NATIVE_INT);//数据类型
// Read the array back
//int[,] dataSet = new int[cout[0], cout[1]];
H5D.read(dataSetId, tid1, simpleSpaceid, spaceid, listid, new H5Array <T>(datasetOut));
H5S.close(simpleSpaceid);
H5S.close(spaceid);
H5T.close(tid0);
H5D.close(dataSetId);
H5G.close(groupId);
}
private void WriteResponses(H5GroupId parent, string name, IDictionary <IExternalDevice, Response> dict)
{
H5GroupId dictId = H5G.create(parent, name);
foreach (var ed in dict.Keys)
{
Response r = dict[ed];
H5GroupId rId = H5G.create(dictId, ed.Name);
WriteAttribute(rId, "deviceName", ed.Name);
WriteAttribute(rId, "deviceManufacturer", ed.Manufacturer);
WriteAttribute(rId, "inputTimeUTC", r.InputTime.ToUniversalTime().ToString());
WriteAttribute(rId, "sampleRate", r.SampleRate.QuantityInBaseUnit);
WriteAttribute(rId, "sampleRateUnits", r.SampleRate.BaseUnit);
Write(rId, "data", r.Data);
WriteResponseDataConfigurationSpans(rId, r);
H5G.close(rId);
}
H5G.close(dictId);
}
private void WriteResponses(H5GroupId parent, string name, IDictionary<IExternalDevice, Response> dict)
{
H5GroupId dictId = H5G.create(parent, name);
foreach (var ed in dict.Keys)
{
Response r = dict[ed];
H5GroupId rId = H5G.create(dictId, ed.Name);
WriteAttribute(rId, "deviceName", ed.Name);
WriteAttribute(rId, "deviceManufacturer", ed.Manufacturer);
WriteAttribute(rId, "inputTimeUTC", r.InputTime.ToUniversalTime().ToString());
WriteAttribute(rId, "sampleRate", r.SampleRate.QuantityInBaseUnit);
WriteAttribute(rId, "sampleRateUnits", r.SampleRate.BaseUnit);
Write(rId, "data", r.Data);
WriteResponseDataConfigurationSpans(rId, r);
H5G.close(rId);
}
H5G.close(dictId);
}
private void Write(H5GroupId parent, string name, string str)
{
if (string.IsNullOrEmpty(name))
throw new ArgumentException("Name must not be empty (or null)", "name");
if (string.IsNullOrEmpty(str))
throw new ArgumentException("Value must not be empty or null", "value");
H5DataTypeId dtype;
byte[] data = EncodeStringData(str, out dtype);
H5DataSpaceId spaceId = H5S.create_simple(1, new long[] { 1 });
H5DataSetId dataSetId = H5D.create(parent, name, dtype, spaceId);
H5D.write(dataSetId, string_t, new H5Array<byte>(data));
H5D.close(dataSetId);
H5S.close(spaceId);
}
private void Write(H5GroupId parent, string name, IDictionary<IExternalDevice, Epoch.EpochBackground> background)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] { (long)background.Keys.Count });
H5DataSetId dataSetId = H5D.create(parent, name, extdevmeasurement_t, spaceId);
ExtdevBackgroundMeasurementT[] emts = new ExtdevBackgroundMeasurementT[background.Keys.Count];
int count = 0;
foreach (var ed in background.Keys)
{
IMeasurement m = background[ed].Background;
IMeasurement sr = background[ed].SampleRate;
emts[count] = Convert(ed, m, sr);
count++;
}
H5D.write<ExtdevBackgroundMeasurementT>(dataSetId, extdevmeasurement_t, new H5Array<ExtdevBackgroundMeasurementT>(emts));
H5D.close(dataSetId);
H5S.close(spaceId);
}
public Group(Container container, string groupname)
{
_groupname = groupname;
_group_id = H5G.open((H5LocId)container.Id, groupname);
}
private void WriteDictionary(H5GroupId parent, string name, IDictionary<string, object> dict)
{
if (name == null)
throw new ArgumentException("Dictionary name may not be null", "name");
H5GroupId dictId = H5G.create(parent, name);
try
{
// Make a local copy of Keys
var keys = dict.Keys.Select(k => k).ToList();
foreach (var key in keys)
{
if(!dict.ContainsKey(key))
{
log.WarnFormat("Dictionary value for key {0} missing during persistence. This likely means someone else modified the dictionary while it was being persisted.", key);
continue;
}
var value = dict[key];
if(value == null)
{
WriteAttribute(dictId, key, "<null>");
}
else if (value is double[])
{
WriteAttribute(dictId, key, (double[])value);
}
else if (value is IMeasurement)
{
var measurement = value as IMeasurement;
WriteAttribute(dictId, key + "_quantity", measurement.Quantity);
WriteAttribute(dictId, key + "_units", measurement.DisplayUnit);
WriteAttribute(dictId, key, measurement.ToString());
}
else if (value is decimal)
{
WriteAttribute(dictId, key, (decimal)value);
}
else if (value is double)
{
WriteAttribute(dictId, key, (double)value);
}
else if (value is long)
{
WriteAttribute(dictId, key, (long)value);
}
else if (value is float)
{
WriteAttribute(dictId, key, (float)value);
}
else if (value is int)
{
WriteAttribute(dictId, key, (int)value);
}
else if (value is short)
{
WriteAttribute(dictId, key, (short) value);
}
else if (value is byte)
{
short tmp = (byte)value;
WriteAttribute(dictId, key, tmp);
}
else if (value is UInt16)
{
int tmp = (UInt16) value;
WriteAttribute(dictId, key, tmp);
}
else if (value is UInt32)
{
long tmp = (UInt32) value;
WriteAttribute(dictId, key, tmp);
}
else if (value is bool)
{
WriteAttribute(dictId, key, (bool)value);
}
else if (value is string)
{
WriteAttribute(dictId, key, (string)value);
}
else
{
log.WarnFormat("Dictionary value ({0} : {1}) is of usupported type. Falling back to string representation.", key, value);
WriteAttribute(dictId, key, String.Format("{0}", value));
}
}
}
finally
{
H5G.close(dictId);
}
}
public EpochGroupIDs(H5GroupId group,
H5GroupId subGroups,
H5GroupId epochs)
{
GroupId = group;
SubGroupsId = subGroups;
EpochsId = epochs;
}
} // test_group_basics
/*
* Operator function.
*/
static int file_info(H5GroupId id, string objectName, Object param)
{
Console.WriteLine("The object name is {0}", objectName);
return 0;
}
private void WriteConfigurationSpans(H5GroupId gID, IEnumerable<IConfigurationSpan> configurationSpans)
{
var spansId = H5G.create(gID, DATA_CONFIGURATION_SPANS_GROUP);
uint i = 0;
var totalTime = TimeSpan.Zero;
foreach (var configSpan in configurationSpans)
{
var spanId = H5G.create(spansId, DATA_CONFIGURATION_SPAN_PREFIX + i++);
WriteAttribute(spanId, "startTimeSeconds", totalTime.TotalSeconds);
totalTime += configSpan.Time;
WriteAttribute(spanId, "timeSpanSeconds", configSpan.Time.TotalSeconds);
foreach (var nodeConfig in configSpan.Nodes)
{
WriteDictionary(spanId, nodeConfig.Name, nodeConfig.Configuration);
}
}
}
private void Write(H5GroupId parent, string name, IDictionary<IExternalDevice, Measurement> dict)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] { (long)dict.Keys.Count });
H5DataSetId dataSetId = H5D.create(parent, name, extdevmeasurement_t, spaceId);
ExtdevMeasurementT[] emts = new ExtdevMeasurementT[dict.Keys.Count];
int count = 0;
foreach (var ed in dict.Keys)
{
IMeasurement m = dict[ed];
emts[count] = Convert(ed, m);
count++;
}
H5D.write<ExtdevMeasurementT>(dataSetId, extdevmeasurement_t, new H5Array<ExtdevMeasurementT>(emts));
H5D.close(dataSetId);
H5S.close(spaceId);
}
private void Write(H5GroupId parent, string name, ulong ul)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] { 1 });
H5DataSetId dataSetId = H5D.create(parent, name, H5T.H5Type.NATIVE_ULLONG, spaceId);
ulong data = ul;
H5D.writeScalar<ulong>(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_ULLONG), ref data);
H5D.close(dataSetId);
H5S.close(spaceId);
}
private void WriteResponseDataConfigurationSpans(H5GroupId rId, Response r)
{
WriteConfigurationSpans(rId, r.DataConfigurationSpans);
}
private void Write(H5GroupId parent, string name, double d)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] { 1 });
H5DataSetId dataSetId = H5D.create(parent, name, H5T.H5Type.NATIVE_DOUBLE, spaceId);
double data = d;
H5D.writeScalar<double>(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_DOUBLE), ref data);
H5D.close(dataSetId);
H5S.close(spaceId);
}
private void WriteStimulusDataConfigurationSpans(H5GroupId sId, IStimulus s)
{
WriteConfigurationSpans(sId, s.OutputConfigurationSpans);
}
// Function used with
static int myFunction(H5GroupId id, string objectName, Object param)
{
Console.WriteLine("The object name is {0}", objectName);
Console.WriteLine("The object parameter is {0}", param);
return 0;
}
private void Write(H5GroupId parent, string name, IMeasurement m)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] { (long)1 });
H5DataSetId dataSetId = H5D.create(parent, name, measurement_t, spaceId);
MeasurementT mt = Convert(m);
H5D.writeScalar<MeasurementT>(dataSetId, measurement_t, ref mt);
H5D.close(dataSetId);
H5S.close(spaceId);
}
private void Write(H5GroupId parent, string name, IEnumerable<IMeasurement> measurements)
{
H5DataSpaceId spaceId = H5S.create_simple(1, new long[1] { (long)measurements.Count() });
// Set compression options for dataset
H5PropertyListId dataSetPropertyList = H5P.create(H5P.PropertyListClass.DATASET_CREATE);
H5P.setDeflate(dataSetPropertyList, NumericDataCompression);
H5P.setChunk(dataSetPropertyList, new long[] {(long)measurements.Count()});
H5DataSetId dataSetId = H5D.create(parent,
name,
measurement_t,
spaceId,
new H5PropertyListId(H5P.Template.DEFAULT),
dataSetPropertyList,
new H5PropertyListId(H5P.Template.DEFAULT));
MeasurementT[] ms = new MeasurementT[measurements.Count()];
int ilmCount = 0;
foreach (IMeasurement m in measurements)
{
MeasurementT mt = Convert(m);
ms[ilmCount++] = mt;
}
H5D.write<MeasurementT>(dataSetId, measurement_t, new H5Array<MeasurementT>(ms));
H5D.close(dataSetId);
H5S.close(spaceId);
}
private void WriteStimuli(H5GroupId parent, string name, IDictionary<IExternalDevice, IStimulus> dict)
{
H5GroupId dictId = H5G.create(parent, name);
foreach (var ed in dict.Keys)
{
var s = dict[ed];
H5GroupId sId = H5G.create(dictId, ed.Name);
WriteAttribute(sId, "deviceName", ed.Name);
WriteAttribute(sId, "deviceManufacturer", ed.Manufacturer);
WriteAttribute(sId, "stimulusID", s.StimulusID);
WriteAttribute(sId, "stimulusUnits", s.Units);
WriteDictionary(sId, "parameters", s.Parameters);
WriteStimulusDataConfigurationSpans(sId, s);
H5G.close(sId);
}
H5G.close(dictId);
}
