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2026-09-18 00:09:10 +09:00 · 2026-08-07 15:56:42 +09:00
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+%HDF5_CP_FILE copy HDF files
+%   orig_filename...        source file
+%   duplicate_filename...   target file
+%
+%   *optional*              given as name/value pair
+%   groups...               groups to copy; either string or cell of
+%                           strings; default: everything in root 
+%   copy_type...            'deep', 'normal' or 'shallow' copy; 
+%                           'shallow' creates external links in target file; 
+%                           'normal' is similar to linux 'cp' command; 
+%                           'deep' dereferences all internal and external links; 
+%                           default: 'shallow'
+%
+%   EXAMPLES:
+%       hdf5_cp_file('./test.h5', './test_new.h5')
+%       hdf5_cp_file('./test.h5', './test_new.h5', 'copy_type', 'deep');
+%   
+% 
+
+%*-----------------------------------------------------------------------*
+%|                                                                       |
+%|  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 hdf5_cp_file(orig_filename, duplicate_filename, varargin)
+import io.HDF.*
+% take care of input arguments
+groups = [];
+copy_type = 'shallow';
+
+% parse the variable input arguments vararg = cell(0,0);
+if ~isempty(varargin)
+    for ind = 1:2:length(varargin)
+        name = varargin{ind};
+        value = varargin{ind+1};
+        switch lower(name)
+            case 'groups'
+                groups = value;
+            case 'copy_type'
+                copy_type = value;
+        end
+    end
+end
+
+switch copy_type
+    case 'shallow'
+        if isempty(groups)
+            % if no groups are specified, use h5info to get all datasets and groups
+            % from root
+            h = h5info(orig_filename, '/');
+            lng = length(h.Groups);
+            lnd = length(h.Datasets);
+            lna = length(h.Attributes);
+            
+            groups = cell([1 lng+lnd]);
+            attributes = [];
+            
+            for ii=1:lng
+                groups{ii} = h.Groups(ii).Name;
+            end
+            for ii=1:lnd
+                groups{ii+lng} = h.Datasets(ii).Name;
+            end
+            for ii=1:lna
+                attributes.(h.Attributes(ii).Name) = h.Attributes(ii).Value;
+                if iscell(h.Attributes(ii).Value)
+                    attributes.(h.Attributes(ii).Name) = attributes.(h.Attributes(ii).Name){1};
+                end
+            end
+        else
+            attributes = [];
+        end
+        
+        
+        s = [];
+        if iscell(groups)
+            for ii=1:length(groups)
+                subgrps = strsplit(rm_delimiter(groups{ii}), '/');
+                s = setfield(s, subgrps{:}, ['ext:' orig_filename ':' groups{ii}]);
+            end
+        else
+            s.groups = ['ext:' orig_filename ':' groups];
+        end
+        
+        % append attributes
+        if ~isempty(attributes)
+            s.Attributes = attributes;
+        end
+        
+        save2hdf5(duplicate_filename, s, 'overwrite', true, 'iscopy', true);
+        
+    case 'deep'
+        s = io.HDF.hdf5_load(orig_filename, '-ca');
+        save2hdf5(duplicate_filename, s, 'overwrite', true, 'iscopy', true);
+        
+    case 'normal'
+        copyfile(orig_filename, duplicate_filename)
+        
+    otherwise
+        error('Unknown copy type!')
+end
+
+end