public static double[][] ReadMesh(string fileName)
{
double[][] meshes = new double[3][];
string[] meshNames = { "x", "y", "z" };
H5FileId fileId = H5F.open(fileName, H5F.OpenMode.ACC_RDONLY);
for (int i = 0; i < meshNames.Length; i++)
{
H5DataSetId dsId = H5D.open(fileId, "/Mesh/" + meshNames[i]);
H5DataTypeId dtId = H5D.getType(dsId);
if (!H5T.equal(dtId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
}
float[] mesh = new float[H5D.getStorageSize(dsId) / H5T.getSize(dtId)];
H5D.read(dsId, dtId, new H5Array <float>(mesh));
meshes[i] = mesh.Select(x => (double)x * 1000.0).ToArray(); // m -> mm
H5D.close(dsId);
H5T.close(dtId);
}
H5F.close(fileId);
return(meshes);
}
public string GetFileApi(string source, string filename, string destination)
{
var fileId = H5F.open(source, H5F.OpenMode.ACC_RDONLY);
var datasetId = H5D.open(fileId, filename);
//var datasetTypeId = new H5DataTypeId(H5T.H5Type.NATIVE_OPAQUE);
//var space = H5D.getSpace(datasetId);
//var dims = H5S.getSimpleExtentDims(space);
var dataType = H5D.getType(datasetId);
long size = H5D.getStorageSize(datasetId);
var fileBytes = new byte[size];
var h5Array = new H5Array <byte>(fileBytes);
H5D.read(datasetId, dataType, h5Array);
H5D.close(datasetId);
H5F.close(fileId);
var outPath = Path.Combine(destination, filename);
File.WriteAllBytes(outPath, fileBytes);
return(destination);
}
private void ReadHDF5Mesh()
{
double[][] meshes = new double[3][];
string[] meshNames = { "phi", "r", "theta" };
H5FileId fileId = H5F.open(m_resultFile, H5F.OpenMode.ACC_RDONLY);
if (HDF5.ReadAttribute(m_resultFile, "/Mesh", "MeshType") != 2)
{
Console.WriteLine("Error: Invalid NF2FF mesh type in <{0}>", m_resultFile);
return;
}
for (int i = 0; i < meshNames.Length; i++)
{
H5DataSetId dsId = H5D.open(fileId, "/Mesh/" + meshNames[i]);
H5DataTypeId dtId = H5D.getType(dsId);
if (!H5T.equal(dtId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
}
float[] mesh = new float[H5D.getStorageSize(dsId) / H5T.getSize(dtId)];
H5D.read(dsId, dtId, new H5Array <float>(mesh));
meshes[i] = mesh.Select(x => (double)x).ToArray();
H5D.close(dsId);
H5T.close(dtId);
}
H5F.close(fileId);
m_theta = meshes[2];
m_phi = meshes[0];
}
public Dictionary <string, string> GetAttributes(string datasetName)
{
if (string.IsNullOrEmpty(datasetName) || !_datasetNames.Contains(datasetName))
{
return(null);
}
H5DataSetId datasetId = null;
H5GroupId groupId = null;
H5DataTypeId typeId = null;
H5DataSpaceId spaceId = null;
//H5PropertyListId psId = null;
try
{
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 == null)
{
return(null);
}
Dictionary <string, string> attValues = new Dictionary <string, string>();
typeId = H5D.getType(datasetId);
H5T.H5TClass type = H5T.getClass(typeId);
int tSize = H5T.getSize(typeId);
spaceId = H5D.getSpace(datasetId);
long[] dims = H5S.getSimpleExtentDims(spaceId);
long storageSize = H5D.getStorageSize(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");
int attrCount = H5A.getNumberOfAttributes(datasetId);
for (int i = 0; i < attrCount; i++)
{
string attName = H5A.getNameByIndex(datasetId, "/" + datasetName, H5IndexType.NAME, H5IterationOrder.NATIVE, (ulong)i);
attValues.Add(attName, ReadAttributeValue(datasetId, attName));
}
return(attValues);
}
finally
{
if (spaceId != null)
{
H5S.close(spaceId);
}
if (typeId != null)
{
H5T.close(typeId);
}
if (datasetId != null)
{
H5D.close(datasetId);
}
if (groupId != null)
{
H5G.close(groupId);
}
}
}
public void SimpleDataReadWrite()
{
// 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(TEST_FILE, H5F.CreateMode.ACC_TRUNC);
// Create a group in the file
H5GroupId groupId = H5G.create(fileId, "/simple");
// Prepare to create a data space for writing a 1-dimensional
// signed integer array.
const int RANK = 1;
long[] dims = new long[RANK];
const int SIZE = 12;
dims[0] = SIZE;
// Put descending ramp data in an array so that we can
// write it to the file.
int[] dset_data = new int[SIZE];
for (int i = 0; i < SIZE; i++)
{
dset_data[i] = SIZE - 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 the data set.
H5DataSetId dataSetId = H5D.create(fileId, "/arrayIntExample",
H5T.H5Type.NATIVE_INT, 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.
// Create the data set.
H5DataSetId scalarId = H5D.create(fileId, "/scalarIntExample",
H5T.H5Type.NATIVE_INT, spaceId);
int singleValue = 100;
H5D.writeScalar(scalarId,
new H5DataTypeId(H5T.H5Type.NATIVE_INT),
ref singleValue);
// Close everything down.
H5D.close(dataSetId);
H5D.close(scalarId);
H5S.close(spaceId);
H5G.close(groupId);
H5F.close(fileId);
Assert.IsTrue(System.IO.File.Exists(TEST_FILE));
fileId = H5F.open(TEST_FILE, H5F.OpenMode.ACC_RDONLY);
Assert.IsTrue(fileId.Id > 0);
groupId = H5G.open(fileId, "/simple");
Assert.IsTrue(groupId.Id > 0);
Assert.AreEqual(0, H5G.getNumObjects(groupId));
// Open the data set
dataSetId = H5D.open(fileId, "/arrayIntExample");
Assert.IsTrue(dataSetId.Id > 0);
long datasetsize = H5D.getStorageSize(dataSetId);
Assert.AreEqual(SIZE * sizeof(int), datasetsize);
// Read the integer data back from the data set
int[] readDataBack = new int[SIZE];
H5D.read(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT),
new H5Array <int>(readDataBack));
for (int i = 0; i < SIZE; i++)
{
Assert.AreEqual(SIZE - i, readDataBack[i]);
}
// Read back the single-int example
scalarId = H5D.open(fileId, "/scalarIntExample");
Assert.IsTrue(scalarId.Id > 0);
H5D.readScalar <int>(scalarId,
new H5DataTypeId(H5T.H5Type.NATIVE_INT),
ref singleValue);
Assert.AreEqual(100, singleValue);
H5D.close(dataSetId);
H5D.close(scalarId);
H5G.close(groupId);
H5F.close(fileId);
}