HDF5 Insert an Array Field into Compound Dataset

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Kat Lee
Kat Lee on 17 Feb 2022
Edited: Kat Lee on 17 Feb 2022
Long story in short, I am trying to save a structure as compound dataset
below long pasted code is a simplified demo code, most fields in my struct are numbers, however, there is one field (see FieldArray) that is an array
function h5ex_t_cmpdWArray
fileName = 'h5ex_t_cmpd.h5';
DIM0 = 5;
ADIM0 = 10;
dims = DIM0;
wdata.FieldA =int32([1153 ; 1184 ; 1027 ; 1313]);
wdata.FieldB ={'Exterior (static)', 'Intake',...
'Intake manifold', 'Exhaust manifold'};
wdata.FieldC =[53.23; 55.12; 130.55; 1252.89];
wdata.FieldD =[24.57; 22.95; 31.23; 84.11];
% NEW: 4x10
wdata.FieldArray = [randn(1,ADIM0);randn(1,ADIM0);randn(1,ADIM0);randn(1,ADIM0)];
%% Create a new file using the default properties.
file = H5F.create (fileName, 'H5F_ACC_TRUNC',...
%Create the required data types
intType =H5T.copy('H5T_NATIVE_INT');
sz(1) =H5T.get_size(intType);
strType = H5T.copy ('H5T_C_S1');
H5T.set_size (strType, 'H5T_VARIABLE');
sz(2) =H5T.get_size(strType);
sz(3) =H5T.get_size(doubleType);
sz(4) =H5T.get_size(doubleType);
% array size
base_type_id = H5T.copy('H5T_NATIVE_DOUBLE');
dimsArr = size(wdata.FieldArray);
arrayType = H5T.array_create(base_type_id, fliplr(dimsArr));
type_id = H5T.copy(base_type_id);
H5T.set_size(type_id, 16);
type_size = H5T.get_size(type_id);
%foo = H5T.get_size(arrayType);
sz(5) = type_size;
% Computer the offsets to each field. The first offset is always zero.
% Create the compound datatype for memory.
memtype = H5T.create ('H5T_COMPOUND', sum(sz));
H5T.insert (memtype,...
H5T.insert (memtype,...
'FieldB',offset(2), strType);
H5T.insert (memtype,...
'FieldC',offset(3), doubleType);
H5T.insert (memtype,...
'FieldD',offset(4), doubleType);
H5T.insert (memtype,...
'FieldArray',offset(5), type_id);
% Create the compound datatype for the file. Because the standard
% types we are using for the file may have different sizes than
% the corresponding native types, we must manually calculate the
% offset of each member.
filetype = H5T.create ('H5T_COMPOUND', sum(sz));
H5T.insert (filetype, 'FieldA', offset(1),intType);
H5T.insert (filetype, 'FieldB', offset(2), strType);
H5T.insert (filetype, 'FieldC',offset(3), doubleType);
H5T.insert (filetype, 'FieldD',offset(4), doubleType);
H5T.insert (filetype, 'FieldArray',offset(5), doubleType);
% Create dataspace. Setting maximum size to [] sets the maximum
% size to be the current size.
space = H5S.create_simple (1,fliplr( dims), []);
% Create the dataset and write the compound data to it.
dset = H5D.create (file, DATASET, filetype, space, 'H5P_DEFAULT');
H5D.write (dset, memtype, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', wdata);
% Close and release resources.
H5D.close (dset);
H5S.close (space);
H5T.close (filetype);
H5F.close (file);
The code errored out for line:
H5D.write (dset, memtype, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', wdata);
detail error see
Error using hdf5lib2
Attempted to transfer too many values to or from the library buffer.
Error in H5D.write (line 100)
H5ML.hdf5lib2('H5Dwrite', varargin{:});
Error in h5ex_t_cmpdWArray (line 112)
H5D.write (dset, memtype, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', wdata);
There are few questions I am confused about
  1. how to insert array into compound datatype
  2. how to write
Appreciate a lot

Answers (0)

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