private static void ReadFile(string filePath)
{
var file = H5F.open(filePath, H5F.OpenMode.ACC_RDONLY);
var dataSet = H5D.open(file, "/group/dataset");
var fileSpace = H5D.getSpace(dataSet);
var rank = H5S.getSimpleExtentNDims(fileSpace);
WriteLine("Rank: {0}", rank);
var dims = H5S.getSimpleExtentDims(fileSpace);
Write("Dims:");
foreach (var d in dims)
{
Write(" {0}", d);
}
WriteLine();
H5S.close(fileSpace);
var ints = new int[1];
var intAttribute = H5A.openName(dataSet, "int");
H5A.read(intAttribute, H5A.getType(intAttribute), new H5Array <int>(ints));
WriteLine("int: {0}", ints[0]);
H5A.close(intAttribute);
var stringAttribute = H5A.openName(dataSet, "string");
var stringType = H5A.getType(stringAttribute);
var stringSize = H5T.getSize(stringType);
WriteLine("string length: {0}", stringSize);
var buffer = new byte[stringSize];
H5A.read(stringAttribute, stringType, new H5Array <byte>(buffer));
WriteLine("string: {0}", Encoding.ASCII.GetString(buffer));
H5T.close(stringType);
H5A.close(stringAttribute);
if (rank == 2)
{
var data = new int[dims[0], dims[1]];
H5D.read(dataSet, H5D.getType(dataSet), new H5Array <int>(data));
for (int i = 0; i < data.GetLength(0); ++i)
{
for (int j = 0; j < data.GetLength(1); ++j)
{
Write(" {0}", data[i, j]);
}
WriteLine();
}
}
H5D.close(dataSet);
H5F.close(file);
}
public AttributeValue GetAttribute(H5FileId fileId, string attributeName)
{
H5AttributeId attributeId = H5A.openName(fileId, attributeName); //根据属性名称得到属性Id
H5DataTypeId attributeType = H5A.getType(attributeId); //得到属性数据类型
int size = H5T.getSize(attributeType);
H5T.H5TClass typeClass = H5T.getClass(attributeType);
H5DataSpaceId spaceId = H5A.getSpace(attributeId);
long[] dims = H5S.getSimpleExtentDims(spaceId);
int rank = H5S.getSimpleExtentNDims(spaceId);
H5T.H5Type h5type;
Type dataType = null;
AttributeValue atrributeData = new AttributeValue();
atrributeData.dataValue = null;
atrributeData.valueType = DataValueType.EMPTY;
atrributeData.rank = rank;
switch (typeClass)
{
case H5T.H5TClass.FLOAT:
h5type = H5T.H5Type.NATIVE_FLOAT;
if (rank == 1)
{
float[] floatDatatmp = new float[dims[0]];
H5A.read(attributeId, new H5DataTypeId(h5type), new H5Array <float>(floatDatatmp));
atrributeData.dataValue = floatDatatmp;
}
else if (rank == 2)
{
float[,] floatDatatmp = new float[dims[0], dims[1]];
H5A.read(attributeId, new H5DataTypeId(h5type), new H5Array <float>(floatDatatmp));
atrributeData.dataValue = floatDatatmp;
}
atrributeData.valueType = DataValueType.FLOAT;
break;
case H5T.H5TClass.INTEGER:
h5type = H5T.H5Type.NATIVE_INT;
// int[,] intDatatmp = null;
if (rank == 1)
{
int[] intDatatmp = new int[dims[0]];
H5A.read(attributeId, new H5DataTypeId(h5type), new H5Array <int>(intDatatmp));
atrributeData.dataValue = intDatatmp;
}
else if (rank == 2)
{
int[,] intDatatmp = new int[dims[0], dims[1]];
H5A.read(attributeId, new H5DataTypeId(h5type), new H5Array <int>(intDatatmp));
atrributeData.dataValue = intDatatmp;
}
atrributeData.valueType = DataValueType.INT;
break;
case H5T.H5TClass.STRING:
h5type = H5T.H5Type.C_S1;
if (rank == 0)
{
string[] stringDatatmp = new string[1];
byte[] bytedata = new byte[255];
H5A.read(attributeId, attributeType, new H5Array <byte>(bytedata));
//H5A.read(attributeId, new H5DataTypeId(h5type), new H5Array<string>(stringDatatmp));
stringDatatmp[0] = Encoding.Default.GetString(bytedata).Trim('\0');
atrributeData.dataValue = stringDatatmp;
}
else if (rank == 1)
{
string[] stringDatatmp = new string[dims[0]];
// string stringDatatmp = "";
// byte[] bytedata = new byte[255];
// byte[,] bytedata = new byte[2,255];
// H5DataTypeId memtype = H5T.copy(H5T.H5Type.C_S1);
//H5T.setVariableSize(memtype);
//H5T.setSize(attributeType, size);
// H5A.read(attributeId, memtype, new H5Array<string>(stringDatatmp));
// H5A.read(attributeId, new H5DataTypeId(h5type), new H5Array<string>(stringDatatmp));
// stringDatatmp[0] = Encoding.Default.GetString(bytedata).Trim('\0');
//string test = Encoding.Default.GetString(bytedata).Trim('\0');
// atrributeData.dataValue = stringDatatmp;
// VariableLengthString[] value = new VariableLengthString[1];
atrributeData.dataValue = stringDatatmp;
}
else if (rank == 2)
{
string[,] stringDatatmp = new string[dims[0], dims[1]];
//H5DataTypeId memtype = H5T.copy(H5T.H5Type.C_S1);
//H5T.setVariableSize(memtype);
//H5A.read(attributeId, memtype, new H5Array<string>(stringDatatmp));
atrributeData.dataValue = stringDatatmp;
}
atrributeData.valueType = DataValueType.STRING;
break;
default:
h5type = H5T.H5Type.C_S1;
break;
}
H5T.close(attributeType);
H5S.close(spaceId);
H5A.close(attributeId);
return(atrributeData);
}
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 AttributeValue GetAttribute(string attribXml, string attributeName, H5FileId fileId)
{
H5AttributeId attributeId = H5A.openName(fileId, attributeName); //根据属性名称得到属性Id
H5DataTypeId attributeType = H5A.getType(attributeId); //得到属性数据类型
H5T.H5TClass typeClass = H5T.getClass(attributeType);
H5DataSpaceId spaceId = H5A.getSpace(attributeId);
int rank = H5S.getSimpleExtentNDims(spaceId);
AttributeValue atrributeData = new AttributeValue();
string[] stringDatatmp = new string[1];
stringDatatmp[0] = "NULL";
XmlReaderSettings settings = new XmlReaderSettings();
settings.DtdProcessing = DtdProcessing.Ignore;
settings.ValidationType = ValidationType.None;
settings.ValidationEventHandler += settings_ValidationEventHandler;
settings.CheckCharacters = false;
StringReader xmlSr = ChangeXmlInGBCode(attribXml);
XmlReader reader = XmlReader.Create(xmlSr);
XmlDocument xml = new XmlDocument();
xml.Load(reader);
XmlNodeList node = xml.GetElementsByTagName("hdf5:Attribute");
foreach (XmlNode child in node)
{
if (child.OuterXml.Contains(attributeName))
{
stringDatatmp[0] = child.InnerText;
}
}
stringDatatmp[0] = stringDatatmp[0].Replace("\r\n", "");
stringDatatmp[0] = stringDatatmp[0].Trim();
atrributeData.dataValue = stringDatatmp;
switch (typeClass)
{
case H5T.H5TClass.FLOAT:
atrributeData.valueType = DataValueType.FLOAT;
break;
case H5T.H5TClass.INTEGER:
atrributeData.valueType = DataValueType.INT;
break;
case H5T.H5TClass.STRING:
atrributeData.valueType = DataValueType.STRING;
break;
default:
break;
}
atrributeData.rank = rank;
H5T.close(attributeType);
H5S.close(spaceId);
H5A.close(attributeId);
return(atrributeData);
}