Using HDF5DotNet, can anyone point me at example code, which will open an hdf5 file, extract the contents of a dataset, and print the contents to standard output?
So far I have the following:
H5.Open();
var h5 = H5F.open("example.h5", H5F.OpenMode.ACC_RDONLY);
var dataset = H5D.open(h5, "/Timings/aaPCBTimes");
var space = H5D.getSpace(dataset);
var size = H5S.getSimpleExtentDims(space);
Then it gets a bit confusing.
I actually want to do some processing on the contents of the dataset but I think once I have dump to standard output I can work it out from there.
UPDATE: I've hacked around this sufficient to solve my own problem. I failed to realise a dataset was a multi-array - I thought it was more like a db table. In the unlikely event anyone is interested,
double[,] dataArray = new double[size[0], 6];
var wrapArray = new H5Array<double>(dataArray);
var dataType = H5D.getType(d);
H5D.read(dataset, dataType, wrapArray);
Console.WriteLine(dataArray[0, 0]);
Answer
Try this:
using System;
using HDF5DotNet;
namespace CSharpExample1
{
class Program
{
// 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;
}
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", 0);
H5GroupId subGroup = H5G.create(groupId, "mySubGroup", 0);
// Demonstrate getObjectInfo
ObjectInfo info = H5G.getObjectInfo(fileId, "/cSharpGroup", true);
Console.WriteLine("cSharpGroup header size is {0}", info.headerSize);
Console.WriteLine("cSharpGroup nlinks is {0}", info.nHardLinks);
Console.WriteLine("cSharpGroup fileno is {0} {1}",
info.fileNumber[0], info.fileNumber[1]);
Console.WriteLine("cSharpGroup objno is {0} {1}",
info.objectNumber[0], info.objectNumber[1]);
Console.WriteLine("cSharpGroup type is {0}", info.objectType);
H5G.close(subGroup);
// Prepare to create a data space for writing a 1-dimensional
// signed integer array.
ulong[] dims = new ulong[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
uint 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);
H5S.close(spaceId);
H5T.close(typeId);
H5G.close(groupId);
//int x = 10;
//H5T.enumInsert<int>(typeId, "myString", ref x);
//H5G.close(groupId);
H5GIterateDelegate myDelegate;
myDelegate = myFunction;
int x = 9;
int index = H5G.iterate(fileId, "/cSharpGroup",
myDelegate, x, 0);
// Reopen the group id to show that we can.
groupId = H5G.open(fileId, "/cSharpGroup");
H5G.close(groupId);
H5F.close(fileId);
// Reopen and reclose the file.
H5FileId openId = H5F.open("myCSharp.h5",
H5F.OpenMode.ACC_RDONLY);
H5F.close(openId);
}
// This catches all the HDF exception classes. Because each call
// generates 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();
}
}
}