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+io/+HDF/hdf5read_main.m

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+% Call function without arguments for instructions on how to use it
+
+% Filename: $RCSfile: hdf5read_main.m,v $
+%
+% $Revision: 1.1 $  $Date: 2010/10/02 07:58:50 $
+% $Author:  $
+% $Tag: $
+%
+% Description:
+% Macro for reading HDF5 files written for example by the EIGER server
+% program cbd_server
+%
+% Note:
+% So far this is mainly a place holder for a thorough implementation. 
+%
+% Dependencies:
+% - image_read_set_default
+% - fopen_until_exists
+% - get_hdr_val
+%
+%
+% history:
+%
+% September 30th 2010: 1st version
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  Except where otherwise noted, this work is licensed under a          |
+%|  Creative Commons Attribution-NonCommercial-ShareAlike 4.0            |
+%|  International (CC BY-NC-SA 4.0) license.                             |
+%|                                                                       |
+%|  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
+%|                                                                       |
+%|       Author: CXS group, PSI                                          |
+%*-----------------------------------------------------------------------*
+% You may use this code with the following provisions:
+%
+% If the code is fully or partially redistributed, or rewritten in another
+%   computing language this notice should be included in the redistribution.
+%
+% If this code, or subfunctions or parts of it, is used for research in a 
+%   publication or if it is fully or partially rewritten for another 
+%   computing language the authors and institution should be acknowledged 
+%   in written form in the publication: “Data processing was carried out 
+%   using the “cSAXS matlab package” developed by the CXS group,
+%   Paul Scherrer Institut, Switzerland.” 
+%   Variations on the latter text can be incorporated upon discussion with 
+%   the CXS group if needed to more specifically reflect the use of the package 
+%   for the published work.
+%
+% A publication that focuses on describing features, or parameters, that
+%    are already existing in the code should be first discussed with the
+%    authors.
+%   
+% This code and subroutines are part of a continuous development, they 
+%    are provided “as they are” without guarantees or liability on part
+%    of PSI or the authors. It is the user responsibility to ensure its 
+%    proper use and the correctness of the results.
+
+function [frame,vararg_remain] = hdf5read_main(filename,varargin)
+import io.HDF.*
+import io.image_read
+import utils.fopen_until_exists
+import utils.get_hdr_val
+
+% 0: no debug information
+% 1: some feedback
+% 2: a lot of information
+debug_level = 0;
+
+% initialize return argument
+frame = struct('header',[], 'data',[]);
+
+
+% check minimum number of input arguments
+if (nargin < 1)
+    image_read_sub_help(mfilename,'h5');
+    error('At least the filename has to be specified as input parameter.');
+end
+
+% accept cell array with name/value pairs as well
+no_of_in_arg = nargin;
+if (nargin == 2)
+    if (isempty(varargin))
+        % ignore empty cell array
+        no_of_in_arg = no_of_in_arg -1;
+    else
+        if (iscell(varargin{1}))
+            % use a filled one given as first and only variable parameter
+            varargin = varargin{1};
+            no_of_in_arg = 1 + length(varargin);
+        end
+    end
+end
+
+% check number of input arguments
+if (rem(no_of_in_arg,2) ~= 1)
+    error('The optional parameters have to be specified as ''name'',value pairs');
+end
+    
+% set default values for the variable input arguments and parse the named
+% parameters: 
+vararg = cell(0,0);
+for ind = 1:2:length(varargin)
+    name = varargin{ind};
+    value = varargin{ind+1};
+    switch name
+        otherwise
+            % pass further arguments on to fopen_until_exists
+            vararg{end+1} = name;
+            vararg{end+1} = value;
+    end
+end
+
+
+% try to open the data file
+if (debug_level >= 1)
+    fprintf('Opening %s.\n',filename);
+end
+[fid,vararg_remain] = fopen_until_exists(filename,vararg);
+if (fid < 0)
+    return;
+end
+% close input data file
+fclose(fid);
+
+% get file header
+hdr = hdf5info(filename);
+
+% store part of the file header in the return argument
+frame.header = {};
+frame.header{end+1} = 'Exposure_time 1.0';
+% add the file modification date to the header
+dir_entry = dir(filename);
+frame.header{end+1} = [ 'DateTime ' dir_entry.date ];
+
+% read all data of first data set at once
+frame.data = hdf5read(hdr.GroupHierarchy(1).Groups(1).Datasets(1));
+
+if (debug_level >= 2)
+    fprintf('%dx%dx%dx%s data bytes read\n',...
+        size(fdat,1),size(fdat,2),size(fdat,3),size(fdat,4));
+end