mirror of
https://github.com/c-sooyoung/fold_slice.git
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243 lines
8.5 KiB
Matlab
243 lines
8.5 KiB
Matlab
%SAVE2HDF5 saves matlab data to a Hierarchical Data Format file (hdf5)
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%
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% filename... full path to file, including file extension
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% data... matlab structure or array or link
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% data_name... needed if input data is not a matlab structure, needs
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% to be given as name/value pair
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%
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% *optional*
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% overwrite... replace existing file if it exists
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% gpath... specify the group to which you want to append the data
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% (only if data is an array); default root ('/')
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% Attributes... structure of attributes; will be appended to current
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% gpath
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% comp... compression level; default 0 (no compression)
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% creator... attribute in root; default 'ptycho_recons'
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%
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%
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% If you want to save a structure, everything declared within an 'Attributes'
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% fieldname will be treated as an attribute to the current group.
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% If you want to add attributes to a dataset, you have to define your
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% data within .Value and your attributes within .Attributes.
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%
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% A simple structure could look like:
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% h5_struc = [];
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% h5_struc.probe_mask = ones(256,256);
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% h5_struc.Attributes.probe_id = 1;
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% h5_struc.measurement.n0.diff = fmag(:,:,1);
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% h5_struc.measurement.n0.Attributes.detector = 0;
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% h5_struc.measurement.n1.diff.Value = fmag(:,:,2);
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% h5_struc.measurement.n1.diff.Attributes.slice = 2;
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%
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% fmag(:,:,1) will be written to dataset 'diff' in group '/measurement/n0'
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% fmag(:,:,2) with attribute 'slice' will be written to dataset 'diff' in
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% group '/measurement/n1'
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%
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%
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% EXAMPLES:
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% -) if data is a matlab structure:
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% save2hdf5('./awesome_file.h5', data);
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% save2hdf5('./awesome_file.h5', data, 'overwrite', true);
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%
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%
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% -) if data is a matlab array:
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% save2hdf5('./awesome_file.h5', data, 'data_name', data_name);
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% save2hdf5('./awesome_file.h5', data, 'data_name', 'my_dataset',...
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% 'gpath', 'group1/group2', 'Attributes', attr_struc);
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%
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% -) if data is a link:
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% currently, only external links ('ext') and internal soft links
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% ('int_soft') are supported
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%
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% external links have to be specified by a single string with
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% 3 sections: '<link_type>:<file_path>:<target_object>'
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%
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% e.g.: 'ext:./awesome_file2.h5:/data'
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% save2hdf5('./awesome_file.h5',...
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% 'ext:./awesome_file2.h5:/data', 'data_name', data_name)
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%
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% will create a link called $data_name to dataset (or group) '/data'
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% in './awesome_file2.h5'
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%
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% internal links have to be specified by a single string with
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% 2 sections: '<link_type>:<target_object>'
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%
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% e.g.: 'int_soft:/data'
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% save2hdf5('./awesome_file.h5',...
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% 'int_soft:/data', 'data_name', data_name, 'gpath', 'g1/g2')
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%
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% will create a link called $data_name to dataset (or group) '/data'
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% in '/g1/g2'
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%
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%
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% Please notice that structures are not supported as attributes, i.e.
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% h5_struc = [];
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% h5_struc.attr.probe.probe_id = 1;
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%
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% save2hdf5('./awesome_file.h5', h5_struc)
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%
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% will crash!
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%
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%
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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function save2hdf5( filename, data, varargin)
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import io.HDF.*
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% take care of input arguments
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overwrite = false;
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gpath_full = '';
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attr = [];
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data_name = '';
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comp = 0;
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creator = 'ptycho_recons';
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iscopy = false;
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extend_dim = 0;
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extendable = false;
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extend_offset = 0;
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extend_maxdims = 0;
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vararg = cell(0,0);
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% parse the variable input arguments vararg = cell(0,0);
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if ~isempty(varargin)
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for ind = 1:2:length(varargin)
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name = varargin{ind};
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value = varargin{ind+1};
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switch lower(name)
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case 'data_name'
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data_name = value;
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case 'overwrite'
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overwrite = value;
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case 'gpath'
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gpath_full = value;
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case 'attr'
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attr = value;
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case 'comp'
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comp = value;
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case 'creator'
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creator = value;
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case 'iscopy'
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iscopy = value;
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case 'extend_dim'
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extend_dim = value;
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case 'extendable'
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extendable = value;
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case 'extend_offset'
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extend_offset = value;
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case 'extend_maxdims'
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extend_maxdims = value;
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otherwise
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vararg{end+1} = name;
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vararg{end+1} = value;
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end
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end
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end
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if ~isstruct(data)
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full_data = false;
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else
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full_data = true;
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end
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if ~isstruct(data) && isempty(data_name)
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data_name = inputname(2);
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if isempty(data_name)
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error('Please specify the data_name.')
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end
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end
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if extendable && extend_dim
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error('Extending the dimension of an unlimited dataset is currently not supported.');
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end
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plist = 'H5P_DEFAULT';
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%%% create file if it does not exist
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if exist(filename, 'file')&&~overwrite
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fileID = H5F.open(filename,'H5F_ACC_RDWR',plist);
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else
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fileID = H5F.create(filename,'H5F_ACC_TRUNC','H5P_DEFAULT','H5P_DEFAULT');
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if ~iscopy
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write_attribute(fileID, filename, 'filename');
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write_attribute(fileID, creator,'creator');
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write_attribute(fileID, datestr(now),'file_time');
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end
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end
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if full_data
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%%%%%%%%%%%%%%%%%%%%%%%%%
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%%% data as structure %%%
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%%%%%%%%%%%%%%%%%%%%%%%%%
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add_content(data, fileID, plist, comp, overwrite)
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else
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%%%%%%%%%%%%%%%%%%%%%
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%%% data as array %%%
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%%%%%%%%%%%%%%%%%%%%%
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% prepare group handles
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if ~isempty(gpath_full)
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gpath = strsplit(rm_delimiter(gpath_full), '/');
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gid = add_groups(fileID, gpath, plist, false);
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else
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gid{1} = fileID;
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end
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% write data to file
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write_dataset(data, gid{end}, data_name, plist, comp, overwrite, [], extend_dim, extendable, extend_offset, extend_maxdims);
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% append attributes
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if ~isempty(attr)
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attr_fn = fieldnames(attr);
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for ii=1:length(attr_fn)
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write_attribute(gid{end}, attr.(attr_fn{ii}), attr_fn{ii}, true);
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end
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end
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end
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% close handles
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H5F.close(fileID);
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end
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