从HDF5文件读取单个元素

Question

Could you please provide me with an example of reading a single element from HDF5 file using HDF5DotNet library. I know how to read the full array into the memory and select the necessary element by index. The problem that I don't want to read the full array and would like to use the H5S.selectElements method ( http://hdf5.net/api/M_HDF5DotNet_H5S_selectElements_4_9e6f2387.aspx ).
So far I've created the following:

H5.Open();
H5FileId fileId = H5F.open(this.filePath, H5F.OpenMode.ACC_RDONLY);
var dSet = H5D.open(fileId, "/Link");
var dSpace = H5D.getSpace(dSet);
var dDims = H5S.getSimpleExtentDims(dSpace);
var dType = H5D.getType(dSet);

H5S.selectElements(dSpace, H5S.SelectOperator.SET, InpPtr numElements,long [] coord);

I can not figure out how to define the numElements parameter and coord of the element (I have 3 dimensional array).

Answer 1

Using the HDF5 support doc

Assuming your DataSet is As Follows: (2D for simplicity explaining how the parameters work)

1 2 3
4 5 6
7 8 9

And you wanted to select the 6 and only the 6 . That means that you want one element located in the second row and the third column. (One Indexed).

That means that you will need a 1 by 2 array of points in the selection array. (Zero Indexed).

1 2

If you wanted to select the 7 also, then the selection array would look like this. (Zero Indexed).

1 2 2 0

The related calls would be:

H5S.selectElements(dSpace, H5S.SelectOperator.SET, 1, new long [] { 1, 2 });
H5S.selectElements(dSpace, H5S.SelectOperator.SET, 2, new long [] { 1, 2, 2, 0 });

---

Translating to a 3D dataspace, we just add an extra value to the selection array.

That is:

1 2 0

Will select the point (2,3,1)

If you wanted to select a second value, then the selection array would look like this. (Zero Indexed).

1 2 0 1 2 1

Will select the points (2,3,1), (2,3,2).

The related calls would be:

H5S.selectElements(dSpace, H5S.SelectOperator.SET, 1, new long [] { 1, 2, 0 });
H5S.selectElements(dSpace, H5S.SelectOperator.SET, 2, new long [] { 1, 2, 0, 1, 2, 1 });

Note : That I have never used HDF5, describing call based on documentation, so there may be errors.

Answer 2

Using HDFql in C#, reading one particular element of a three dimensional dataset can be done as follows (assume that the dataset is called my_dataset and the element to read is at position 2, 3 and 5 in the first, second and third dimension respectively):

HDFql.Execute("SELECT FROM my_dataset(2, 3, 5)");

From there, you can retrieve the element by doing the following (assume that my_dataset is of datatype integer):

HDFql.CursorFirst();
System.Console.WriteLine("Element is " + HDFql.CursorGetInt());

Answer 3

I've found another approach to solve the problem - using H5S.selectHyperslab method. Maybe it's not so elegant but it seems to work fine.

H5.Open();
H5FileId fileId = H5F.open(this.filePath, H5F.OpenMode.ACC_RDONLY);
var dSet = H5D.open(fileId, "/Link");
var dSpace = H5D.getSpace(dSet);
var dDims = H5S.getSimpleExtentDims(dSpace);
var dType = H5D.getType(dSet);
//E.g. to extract the value with coordinates [0,1,0]:
H5DataSpaceId memspaceid = H5S.create_simple(1, new long[] { 1, 1, 1 });
H5S.selectHyperslab(memspaceid, H5S.SelectOperator.SET, new long[] { 0, 1, 0 }, new long[] { 1, 1, 1 });
H5S.selectHyperslab(dSpace, H5S.SelectOperator.SET, new long[] { 0, 1, 0 }, new long[] { 1, 1, 1 });

//array to read data
double[] readDataBank = new double[1];
H5DataTypeId typeId = new H5DataTypeId(H5T.H5Type.NATIVE_DOUBLE);
H5D.read(dSet, dType, memspaceid, dSpace,new H5PropertyListId(new H5P.Template()), new H5Array<double>(readDataBank));