% 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);