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MyMetadata.m
67fbb905ba3aconfint-fix

MyMetadata.m
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			% MyMetadata stores parameter-value pairs and can be saved in a readable
			% format.
			%
			% Metadata parameters can be strings, numerical values or cells, as well as
			% any arrays and structures of such with arbitrary nesting. Sub-indices are
			% automatically expanded when saving.

			classdef MyMetadata < handle & matlab.mixin.CustomDisplay & ...
			matlab.mixin.SetGet & matlab.mixin.Copyable

			properties (Access = public)

			% Header sections are separated by [hdr_spec, title, hdr_spec]
			title = ''
			hdr_spec = '=='

			% Columns are separated by this symbol (space-tab by default)
			column_sep = ' \t'

			% Comments start from this symbol
			comment_sep = '%'
			line_sep = '\r\n'

			% Limit for column padding. Variables which take more space than
			% this limit are ignored when calculating the padding length.
			pad_lim = 15

			% Metadata parameter values
			ParamList = struct()

			% Options for metadata parameters
			ParamOptList = struct()
			end

			methods (Access = public)

			function this = MyMetadata(varargin)
			P = MyClassParser(this);
			processInputs(P, this, varargin{:});
			end

			% Adds a new metadata parameter.
			function addParam(this, param_name, value, varargin)
			assert(isvarname(param_name), ['Parameter name must be a ' ...
			'valid variable name.']);

			p = inputParser();

			% Format specifier for printing the value
			addParameter(p, 'format', '', @ischar);

			% Comment to be added to the line
			addParameter(p, 'comment', '', @ischar);

			addParameter(p, 'SubStruct', struct('type',{},'subs',{}),...
			@isstruct)
			parse(p, varargin{:});

			% Make sure that the comment does not contain new line or
			% carriage return characters, which would mess up formating
			% when saving the metadata
			[comment, is_mod] = toSingleLine(p.Results.comment);
			this.ParamOptList.(param_name).comment = comment;

			if is_mod
			warning(['Comment string for ''%s'' has been ' ...
			'converted to single line.'], param_name);
			end

			this.ParamOptList.(param_name).format = p.Results.format;

			S = p.Results.SubStruct;
			if isempty(S)
			this.ParamList.(param_name) = value;
			else

			% Initialize property with an empty variable of the same
			% class as value, this is important if SubStruct is an
			% array index.
			this.ParamList.(param_name) = ...
			feval([class(value),'.empty']);

			% Construct full subscript reference with respect to 'this'
			S = [struct('type', '.', 'subs', param_name), S];

			% Assign the value of parameter
			this.ParamList = subsasgn(this.ParamList, S, value);
			end
			end

			function bool = isparam(this, param_name)
			bool = isfield(this.ParamList, param_name);
			end

			% Alias for addParam that is useful to ensure the correspondence
			% between metadata parameter names and object property names.
			function addObjProp(this, Obj, tag, varargin)
			addParam(this, tag, Obj.(tag), varargin{:});
			end

			% Print metadata in a readable form
			function str = mdt2str(this)

			% Make the function spannable over arrays
			if isempty(this)
			str = '';
			return
			elseif length(this) > 1
			str_arr = arrayfun(@mdt2str, this, 'UniformOutput', false);

			% Add an extra line between sections
			str = strjoin(str_arr, this(1).line_sep);
			return
			end

			cs = this.column_sep;
			ls = this.line_sep;

			% Make the output string. Start by printing the title.
			str = sprintf([this.hdr_spec, this.title, this.hdr_spec, ls]);

			% Compose the list of parameter names expanded over subscripts
			% except for those which are already character arrays
			par_names = fieldnames(this.ParamList);

			if isempty(par_names)
			return
			end

			% Expand parameters over subscripts, except for the arrays of
			% characters
			exp_par_names = cell(1, length(par_names));
			max_nm_arr = zeros(1, length(par_names));

			for i = 1:length(par_names)

			% Expand parameter subscripts
			exp_par_names{i} = printSubs( ...
			this.ParamList.(par_names{i}), ...
			'own_name', par_names{i}, ...
			'expansion_test', @(y) ~ischar(y));

			% Max name length for this parameter including subscripts
			max_nm_arr(i) = max(cellfun(@(x) length(x), ...
			exp_par_names{i}));
			end

			% Calculate width of the name column
			name_pad_length = max(max_nm_arr);

			% Compose a list of parameter values converted to char strings
			val_strs = cell(1, length(par_names));

			% Width of the values column will be the maximum parameter
			% string width
			for i = 1:length(par_names)
			tmp_nm = par_names{i};

			% Iterate over parameter indices
			for j = 1:length(exp_par_names{i})
			tmp_exp_nm = exp_par_names{i}{j};
			TmpS = str2substruct(tmp_exp_nm);

			% Get the indexed value of parameter
			TmpS = [struct('type','.','subs', tmp_nm), TmpS]; %#ok<AGROW>
			tmp_val = subsref(this.ParamList, TmpS);

			%Do the check to detect unsupported data type
			if ischar(tmp_val) && ~isvector(tmp_val) && ...
			~isempty(tmp_val)
			warning(['Argument ''%s'' is a multi-dimensional ',...
			'character array. It will be converted to ',...
			'single string during saving. Use cell',...
			'arrays to save data as a set of separate ',...
			'strings.'], tmp_exp_nm)

			% Flatten
			tmp_val = tmp_val(:);
			end

			% Check for new line symbols in strings
			if (ischar(tmp_val) \|\| isstring(tmp_val)) && ...
			any(ismember({newline, sprintf('\r')},tmp_val))
			warning(['String values must not contain ' ...
			'''\\n'' and ''\\r'' symbols, replacing ' ...
			'them with '' ''.']);

			tmp_val = replace(tmp_val, ...
			{newline, sprintf('\r')}, ' ');
			end

			if isfield(this.ParamOptList, tmp_nm)
			format = this.ParamOptList.(tmp_nm).format;
			else
			format = '';
			end

			if isempty(format)

			% Convert to string with format specifier
			% extracted from the varaible calss
			val_strs{i}{j} = var2str(tmp_val);
			else
			val_strs{i}{j} = sprintf(format, tmp_val);
			end
			end
			end

			% Find the maximum string length to determine the colum width,
			% but, for beauty, exclude excessively long value strings
			val_str_len = cellfun(@length, [val_strs{:}]);
			if max(val_str_len)-min(val_str_len)<=this.pad_lim
			val_pad_length = max(val_str_len);
			else
			val_pad_length = min(val_str_len)+this.pad_lim;
			end

			par_format = [sprintf('%%-%is', name_pad_length),...
			cs, sprintf('%%-%is', val_pad_length)];

			% Print parameters
			for i = 1:length(par_names)

			% Capitalize the first letter of comment
			if isfield(this.ParamOptList, par_names{i})
			comment = this.ParamOptList.(par_names{i}).comment;
			else
			comment = '';
			end

			if ~isempty(comment)
			fmt_comment = [this.comment_sep, ' '...
			upper(comment(1)), comment(2:end)];
			else
			fmt_comment = '';
			end

			% Iterate over the parameter subscripts
			for j = 1:length(exp_par_names{i})
			if j == 1

			% Print the comment in the first line
			str = [str, ...
			sprintf([par_format, cs, '%s', ls], ...
			exp_par_names{i}{j}, val_strs{i}{j}, ...
			fmt_comment)]; %#ok<AGROW>
			else
			str = [str, sprintf([par_format, ls],...
			exp_par_names{i}{j}, val_strs{i}{j})]; %#ok<AGROW>
			end
			end
			end
			end

			% Save metadata to a file
			function save(this, filename, varargin)
			p = inputParser();
			addParameter(p, 'overwrite', false, @islogical)
			parse(p, varargin{:});

			if p.Results.overwrite

			% Open and delete any existing content of the file
			fileID = fopen(filename, 'w');
			else

			% Open for appending
			fileID = fopen(filename, 'a');
			end

			fprintf(fileID, '%s', mdt2str(this));
			fclose(fileID);
			end

			% Select objects with titles listed in varargin from the array
			function SubArr = titleref(this, varargin)
			ind = ismember({this.title}, varargin);
			SubArr = this(ind);
			end

			% Remove objects with titles listed in varargin from the array
			function SubArr = rmtitle(this, varargin)
			ind = ~ismember({this.title}, varargin);
			SubArr = this(ind);
			end
			end

			methods (Access = public, Static = true)

			% Create metadata indicating the present moment of time
			function TimeMdt = time(varargin)
			TimeMdt = MyMetadata(varargin{:});

			if isempty(TimeMdt.title)
			TimeMdt.title = 'Time';
			end

			dv = datevec(datetime('now'));
			addParam(TimeMdt, 'Year', dv(1), 'format', '%i');
			addParam(TimeMdt, 'Month', dv(2), 'format', '%i');
			addParam(TimeMdt, 'Day', dv(3), 'format', '%i');
			addParam(TimeMdt, 'Hour', dv(4), 'format', '%i');
			addParam(TimeMdt, 'Minute', dv(5), 'format', '%i');
			addParam(TimeMdt, 'Second', floor(dv(6)), 'format', '%i');
			addParam(TimeMdt, 'Millisecond',...
			round(1000*(dv(6)-floor(dv(6)))), 'format', '%i');
			end

			% Create basic metadata typically used in newly acquired instrument
			% traces
			function AcqMdt = acq(instr_name)

			% Add the name of acquisition instrument
			AcqInstrMdt = MyMetadata('title', 'AcquisitionInstrument');
			addParam(AcqInstrMdt, 'Name', instr_name);

			% Add field indicating the time when the trace was acquired
			TimeMdt = MyMetadata.time('title', 'AcquisitionTime');

			AcqMdt = [AcqInstrMdt, TimeMdt];
			end

			% Load metadata from file. Return all the entries found and
			% the number of the last line read.
			function [MdtArr, n_end_line] = load(filename, varargin)
			fileID = fopen(filename, 'r');

			MasterMdt = MyMetadata(varargin{:});

			% Loop initialization
			MdtArr = MyMetadata.empty();
			line_no = 0;

			% Loop continues until we reach the next header or we reach
			% the end of the file
			while ~feof(fileID)

			% Grabs the current line
			curr_line = fgetl(fileID);

			% Give a warning if the file is empty, i.e. if fgetl
			% returns -1
			if curr_line == -1
			disp(['Read empty file ', filename, '.']);
			break
			end

			% Skips if the current line is empty
			if isempty(deblank(curr_line))
			line_no = line_no+1;
			continue
			end

			S = parseLine(MasterMdt, curr_line);

			switch S.type
			case 'title'

			% Add new a new metadata to the output list
			TmpMdt = MyMetadata(varargin{:}, 'title', S.match);
			MdtArr = [MdtArr, TmpMdt]; %#ok<AGROW>
			case 'paramval'

			% Add a new parameter-value pair to the current
			% metadata
			[name, value, format, comment, Subs] = S.match{:};

			if ~isparam(TmpMdt, name)

			% Add new parameter
			addParam(TmpMdt, name, value, ...
			'format', format, 'SubStruct', Subs, ...
			'comment', comment);
			else

			% Assign the value to a new subscript of
			% an existing parameter
			Subs = [substruct('.', name), Subs]; %#ok<AGROW>
			TmpMdt.ParamList = subsasgn( ...
			TmpMdt.ParamList, Subs, value);
			end
			otherwise

			% Exit
			break
			end

			% Increment the counter
			line_no = line_no+1;
			end

			n_end_line = line_no;
			fclose(fileID);
			end
			end

			methods (Access = protected)

			% Parse string and determine the type of string
			function S = parseLine(this, str)
			S = struct( ...
			'type', '', ... % title, paramval, other
			'match', []); % parsed output

			% Check if the line contains a parameter - value pair.
			% First separate the comment if present
			pv_token = regexp(str, this.comment_sep, 'split', 'once');

			if length(pv_token)>1
			comment = pv_token{2}; % There is a comment
			else
			comment = ''; % There is no comment
			end

			% Then process name-value pair. Regard everything after
			% the first column separator as value.
			pv_token = regexp(pv_token{1}, this.column_sep, 'split', ...
			'once');

			% Remove leading and trailing blanks
			pv_token = strtrim(pv_token);

			if length(pv_token)>=2

			% A candidate for parameter-value pair is found. Infer
			% the variable name and subscript reference.
			[Subs, name] = str2substruct(pv_token{1});

			if isvarname(name)

			% Attempt converting the value to a number
			[value, format] = str2doubleHedged(pv_token{2});

			S.type = 'paramval';
			S.match = {name, value, format, comment, Subs};
			return
			end
			end

			% Check if the line contains a title
			title_exp = [this.hdr_spec, '(\w.*)', this.hdr_spec];
			title_token = regexp(str, title_exp, 'once', 'tokens');

			if ~isempty(title_token)

			% Title expression found
			S.type = 'title';
			S.match = title_token{1};
			return
			end

			% No match found
			S.type = 'other';
			S.match = {};
			end

			% Make custom footer for command line display
			% (see matlab.mixin.CustomDisplay)
			function str = getFooter(this)
			if length(this) == 1

			% For a single object display its properties
			str = ['Content:', newline, newline, ...
			replace(mdt2str(this), sprintf(this.line_sep), ...
			newline)];
			elseif length(this) > 1

			% For a non-empty array of objects display titles
			str = sprintf('\tTitles:\n\n');

			for i = 1:length(this)
			str = [str, sprintf('%i\t%s\n', i, this(i).title)]; %#ok<AGROW>
			end

			str = [str, newline];
			else

			% For an empty array display nothing
			str = '';
			end
			end
			end
			end

rINSTCONTROL/@MyMetadata/MyMetadata.m67fbb905ba3aconfint-fix

MyMetadata.mView Options

rINSTCONTROL/@MyMetadata/MyMetadata.m
67fbb905ba3aconfint-fix

MyMetadata.m
View Options