HDF5 in MATLAB

author:

Paul Kienzle, NIST

Note

Editor’s Note: These files were copied directly from an older version of the NeXus documentation (DocBook) and have not been checked that they will run under current Matlab versions.

input.dat

This is the same data used with HDF5 in Python.

17.92608    1037
17.92591    1318
17.92575    1704
17.92558    2857
17.92541    4516
17.92525    9998
17.92508    23819
17.92491    31662
17.92475    40458
17.92458    49087
17.92441    56514
17.92425    63499
17.92408    66802
17.92391    66863
17.92375    66599
17.92358    66206
17.92341    65747
17.92325    65250
17.92308    64129
17.92291    63044
17.92275    60796
17.92258    56795
17.92241    51550
17.92225    43710
17.92208    29315
17.92191    19782
17.92175    12992
17.92158    6622
17.92141    4198
17.92125    2248
17.92108    1321

writing data

basic_writer.m: Write a NeXus HDF5 file using Matlab

% Writes a NeXus HDF5 file using matlab

disp 'Write a NeXus HDF5 file'
filename = 'prj_test.nexus.hdf5';
timestamp = '2010-10-18T17:17:04-0500';

% read input data
A = load('input.dat');
mr = A(:,1);
I00 = int32(A(:,2));

% clear out old file, if it exists

delete(filename);

% using the simple h5 interface, there is no way to create a group without
% first creating a dataset; creating the dataset creates all intervening
% groups.

% store x
h5create(filename,'/entry/mr_scan/mr',[length(mr)]);
h5write(filename,'/entry/mr_scan/mr',mr);
h5writeatt(filename,'/entry/mr_scan/mr','units','degrees');
h5writeatt(filename,'/entry/mr_scan/mr','long_name','USAXS mr (degrees)');

% store y
h5create(filename,'/entry/mr_scan/I00',[length(I00)],'DataType','int32');
h5write(filename,'/entry/mr_scan/I00',I00);
h5writeatt(filename,'/entry/mr_scan/I00','units','counts');
h5writeatt(filename,'/entry/mr_scan/I00','long_name','USAXS I00 (counts)');

% indicate that we are plotting y vs. x
h5writeatt(filename,'/','default','entry');
h5writeatt(filename,'/entry','default','mr_scan');
h5writeatt(filename,'/entry/mr_scan','signal','I00');
h5writeatt(filename,'/entry/mr_scan','axes','mr_scan');
h5writeatt(filename,'/entry/mr_scan','mr_scan_indices', int32(0));

% add NeXus metadata
h5writeatt(filename,'/','file_name',filename);
h5writeatt(filename,'/','file_time',timestamp);
h5writeatt(filename,'/','instrument','APS USAXS at 32ID-B');
h5writeatt(filename,'/','creator','basic_writer.m');
h5writeatt(filename,'/','NeXus_version','4.3.0');
h5writeatt(filename,'/','HDF5_Version','1.6'); % no 1.8 features used in this example
h5writeatt(filename,'/entry','NX_class','NXentry');
h5writeatt(filename,'/entry/mr_scan','NX_class','NXdata');


h5disp(filename);

reading data

basic_reader.m: Read a NeXus HDF5 file using Matlab

% Reads NeXus HDF5 file and print the contents

filename = 'prj_test.nexus.hdf5';
root = h5info(filename,'/');
attrs = root.Attributes;
for i = 1:length(attrs)
    fprintf('%s: %s\n', attrs(i).Name, attrs(i).Value);
end
mr = h5read(filename,'/entry/mr_scan/mr');
i00 = h5read(filename, '/entry/mr_scan/I00');
fprintf('#\t%s\t%s\n','mr','I00');
for i = 1:length(mr)
    fprintf('%d\t%g\t%d\n', i, mr(i), i00(i));
end

writing data file with links

writer_2_1.m: Write a NeXus HDF5 file with links

% Writes a simple NeXus HDF5 file with links
% according to the example from Figure 2.1 in the Design chapter

filename = 'writer_2_1.hdf5';

% read input data
A = load('input.dat');
two_theta = A(:,1);
counts = int32(A(:,2));

% clear out old file, if it exists
delete(filename);

% store x
h5create(filename,'/entry/instrument/detector/two_theta',[length(two_theta)]);
h5write(filename,'/entry/instrument/detector/two_theta',two_theta);
h5writeatt(filename,'/entry/instrument/detector/two_theta','units','degrees');

% store y
h5create(filename,'/entry/instrument/detector/counts',[length(counts)],'DataType','int32');
h5write(filename,'/entry/instrument/detector/counts',counts);
h5writeatt(filename,'/entry/instrument/detector/counts','units','counts');

% create group NXdata with links to detector
% note: requires the additional file h5link.m
h5link(filename,'/entry/instrument/detector/two_theta','/entry/data/two_theta');
h5link(filename,'/entry/instrument/detector/counts','/entry/data/counts');

% indicate that we are plotting y vs. x
h5writeatt(filename,'/','default','entry');
h5writeatt(filename,'/entry','default','data');
h5writeatt(filename,'/entry/data','signal','counts');
h5writeatt(filename,'/entry/data','axes','two_theta');
h5writeatt(filename,'/entry/data','two_theta_indices',int32(0));

% add NeXus metadata
h5writeatt(filename,'/','file_name',filename);
h5writeatt(filename,'/','file_time',timestamp);
h5writeatt(filename,'/','instrument','APS USAXS at 32ID-B');
h5writeatt(filename,'/','creator','writer_2_1.m');
h5writeatt(filename,'/','NeXus_version','4.3.0');
h5writeatt(filename,'/','HDF5_Version','1.6'); % no 1.8 features used in this example
h5writeatt(filename,'/entry','NX_class','NXentry');
h5writeatt(filename,'/entry/instrument','NX_class','NXinstrument');
h5writeatt(filename,'/entry/instrument/detector','NX_class','NXdetector');
h5writeatt(filename,'/entry/data','NX_class','NXdata');

% show structure of the file that was created
h5disp(filename);

h5link.m: support module for creating NeXus-style HDF5 hard links

function h5link(filename, from, to)
%H5LINK Create link to an HDF5 dataset.
%   H5LINK(FILENAME,SOURCE,TARGET) creates an HDF5 link from the
%   dataset at location SOURCE to a dataset at location TARGET.  All
%   intermediate groups in the path to target are created.
%
%   Example:  create a link from /hello/world to /goodbye/world
%      h5create('myfile.h5','/hello/world',[100 200]);
%      h5link('myfile.h5','/hello/world','/goodbye/world');
%      hgdisp('myfile.h5');
%
%   See also: h5create, h5read, h5write, h5info, h5disp

% split from and to into group/dataset
idx = strfind(from,'/');
from_path = from(1:idx(end)-1);
from_data = from(idx(end)+1:end);
idx = strfind(to,'/');
to_path = to(1:idx(end)-1);
to_data = to(idx(end)+1:end);
  
% open the HDF file
fid = H5F.open(filename,'H5F_ACC_RDWR','H5P_DEFAULT');
  
% create target group if it doesn't already exist
create_intermediate = H5P.create('H5P_LINK_CREATE');
H5P.set_create_intermediate_group(create_intermediate, 1);
try
    H5G.create(fid,to_path,create_intermediate,'H5P_DEFAULT','H5P_DEFAULT');
catch
end
H5P.close(create_intermediate);

% open groups and create link
from_id = H5G.open(fid, from_path);
to_id = H5G.open(fid, to_path);
H5L.create_hard(from_id, from_data, to_id, to_data, 'H5P_DEFAULT','H5P_DEFAULT');

% close all
H5G.close(from_id);
H5G.close(to_id);
H5F.close(fid);
end

Downloads

file	description
input.dat	two-column text data file, also used in other examples
basic_writer.m	writes a NeXus HDF5 file using input.dat
basic_reader.m	reads the NeXus HDF5 file written by basic_writer.m
h5link.m	support module for creating NeXus-style HDF5 hard links
writer_2_1.m	like basic_writer.m but stores data in /entry/instrument/detector and then links to NXdata group