Diffusion Instrument Control (confint-fix) Browse

MyMetadata.m
7d66b42abcd4confint-fix

MyMetadata.m
View Options

			% MyMetadata stores parameter-value pairs grouped by fields. MyMetadata can
			% be saved and read in a readable text format.
			% 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.
			% If instantiated as MyMetadata(load_path)
			% then the content is loaded from file

			classdef MyMetadata < dynamicprops
			properties (Access=public)
			% Header sections are separated by [hdr_spec,hdr_spec,hdr_spec]
			hdr_spec='=='
			% Data starts from the line next to [hdr_spec,end_header,hdr_spec]
			end_header='Data'
			% 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
			end

			properties (Access=private)
			PropHandles %Used to store the handles of the dynamic properties
			end

			properties (Dependent=true)
			field_names
			end

			methods
			function [this,varargout]=MyMetadata(varargin)
			P=MyClassParser(this);

			if mod(length(varargin),2)==1
			% odd number of elements in varargin - interpret the first
			% element as file name and the rest as name-value pairs
			load_path=varargin{1};
			assert(ischar(load_path)&&isvector(load_path),...
			'''file_name'' must be a vector of characters');
			processInputs(P, this, varargin{2:end});
			else
			% Parse varargin as a list of name-value pairs
			processInputs(P, this, varargin{:});
			load_path=[];
			end

			this.PropHandles=struct();

			if ~isempty(load_path)
			varargout{1}=load(this, load_path);
			end
			end

			%Fields are added using this command. The field is a property of
			%the class, populated by the parameters with their values and
			%string specifications for later printing
			function addField(this, field_name)
			assert(isvarname(field_name),...
			'Field name must be a valid MATLAB variable name.');
			assert(~ismember(field_name, this.field_names),...
			['Field with name ',field_name,' already exists.']);

			this.PropHandles.(field_name)=addprop(this,field_name);
			this.PropHandles.(field_name).SetAccess='protected';
			% Dynamic properties must not be copyable, copying of
			% MyMetadata objects is handled by dedicated overloaded method
			this.PropHandles.(field_name).NonCopyable=true;
			this.(field_name)=struct();
			end

			%Deletes a named field
			function deleteField(this, field_name)
			assert(isvarname(field_name),...
			'Field name must be a valid MATLAB variable name.');
			assert(ismember(field_name,this.field_names),...
			['Attemped to delete field ''',field_name ...
			,''' that does not exist.']);
			% Delete dynamic property from the class
			delete(this.PropHandles.(field_name));
			% Erase entry in PropHandles
			this.PropHandles=rmfield(this.PropHandles,field_name);
			end

			%Clears the object of all fields
			function clearFields(this)
			cellfun(@(x) deleteField(this, x), this.field_names)
			end


			% Copy all the fields of another Metadata object to this object
			function addMetadata(this, Metadata)
			assert(isa(Metadata,'MyMetadata'),...
			'Input must be of class MyMetadata, current input is %s',...
			class(Metadata));
			assert(~any(ismember(this.field_names,Metadata.field_names)),...
			['The metadata being added contain fields with the same ',...
			'name. This conflict must be resolved before adding'])
			for i=1:length(Metadata.field_names)
			fn=Metadata.field_names{i};
			addField(this,fn);
			param_names=fieldnames(Metadata.(fn));
			cellfun(@(x) addParam(this,fn,x,Metadata.(fn).(x).value,...
			'fmt_spec', Metadata.(fn).(x).fmt_spec,...
			'comment', Metadata.(fn).(x).comment),...
			param_names);
			end
			end

			%Adds a parameter to a specified field. The field must be created
			%first.
			function addParam(this, field_name, param_name, value, varargin)
			assert(ischar(field_name),'Field name must be a char');
			assert(isprop(this,field_name),...
			'%s is not a field, use addField to add it',param_name);
			assert(ischar(param_name),'Parameter name must be a char');

			p=inputParser();
			% Format specifier for printing the value
			addParameter(p,'fmt_spec','',@ischar);
			% Comment to be added to the line
			addParameter(p,'comment','',@ischar);
			addParameter(p,'SubStruct',struct('type',{},'subs',{}),...
			@isstruct)
			parse(p,varargin{:});

			S=p.Results.SubStruct;
			comment=p.Results.comment;

			%Making sure that the comment does not
			%contain new line or carriage return characters, which would
			%mess up formating when saving metadata

			newline_smb={sprintf('\n'),sprintf('\r')}; %#ok<SPRINTFN>

			if contains(comment, newline_smb)
			warning(['Comment string for ''%s'' must not contain ',...
			'''\\n'' and ''\\r'' symbols, replacing them ',...
			'with space.'], param_name);
			comment=replace(comment, newline_smb,' ');
			end

			this.(field_name).(param_name).comment=comment;

			if isempty(S)
			% Assign value directly
			this.(field_name).(param_name).value=value;
			else
			% Assign using subref structure
			tmp=feval([class(value),'.empty']);
			this.(field_name).(param_name).value=subsasgn(tmp,S,value);
			end

			this.(field_name).(param_name).fmt_spec=p.Results.fmt_spec;
			end

			function save(this, filename, varargin)
			createFile(filename, varargin{:});
			for i=1:length(this.field_names)
			printField(this, this.field_names{i}, filename);
			end
			printEndMarker(this, filename);
			end

			function printField(this, field_name, filename, varargin)
			%Takes optional inputs
			p=inputParser();
			addParameter(p,'title',field_name);
			parse(p,varargin{:});
			title_str=p.Results.title;

			ParStruct=this.(field_name);

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

			%Expand parameters over subscripts, except for the character
			%arrays
			exp_par_names=cell(1, length(par_names));
			maxnmarr=zeros(1, length(par_names));
			for i=1:length(par_names)
			tmpval=ParStruct.(par_names{i}).value;
			exp_par_names{i}=printSubs(tmpval, ...
			'own_name', par_names{i}, ...
			'expansion_test',@(y) ~ischar(y));

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

			%Calculate width of the name column
			name_pad_length=min(max(maxnmarr), this.pad_lim);

			%Compose list of parameter values converted to char strings
			par_strs=cell(1, length(par_names));
			%Width of the values column will be the maximum parameter
			%string width
			val_pad_length=0;
			for i=1:length(par_names)
			TmpPar=ParStruct.(par_names{i});
			for j=1:length(exp_par_names{i})
			tmpnm=exp_par_names{i}{j};
			TmpS=str2substruct(tmpnm);
			if isempty(TmpS)
			tmpval=TmpPar.value;
			else
			tmpval=subsref(TmpPar.value, TmpS);
			end

			%Do check to detect unsupported data type
			if ischar(tmpval)&&~isvector(tmpval)&&~isempty(tmpval)
			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.'],tmpnm)
			% Flatten
			tmpval=tmpval(:);
			end

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

			if isempty(TmpPar.fmt_spec)
			% Convert to string with format specifier
			% extracted from the varaible calss
			par_strs{i}{j}=var2str(tmpval);
			else
			par_strs{i}{j}=sprintf(TmpPar.fmt_spec, tmpval);
			end
			% Find maximum length to determine the colum width,
			% but, for beauty, do not account for variables with
			% excessively long value strings
			tmplen=length(par_strs{i}{j});
			if (val_pad_length<tmplen)&&(tmplen<=this.pad_lim)
			val_pad_length=tmplen;
			end
			end
			end

			fileID=fopen(filename,'a');
			%Prints the header separator
			fprintf(fileID,[this.hdr_spec, title_str,...
			this.hdr_spec, this.line_sep]);

			cs=this.column_sep;
			ls=this.line_sep;
			data_fmt_spec=[sprintf('%%-%is',name_pad_length),...
			cs, sprintf('%%-%is',val_pad_length)];

			for i=1:length(par_names)
			%Capitalize first letter of comment
			if ~isempty(ParStruct.(par_names{i}).comment)
			fmt_comment=[this.comment_sep,' '...
			upper(ParStruct.(par_names{i}).comment(1)),...
			ParStruct.(par_names{i}).comment(2:end)];
			else
			fmt_comment='';
			end

			for j=1:length(exp_par_names{i})
			if j==1
			% Print comment in the first line
			fprintf(fileID, [data_fmt_spec,cs,'%s',ls],...
			exp_par_names{i}{j},par_strs{i}{j},fmt_comment);
			else
			fprintf(fileID, [data_fmt_spec,ls],...
			exp_par_names{i}{j}, par_strs{i}{j});
			end
			end
			end

			%Prints an extra line separator at the end
			fprintf(fileID, ls);
			fclose(fileID);
			end

			%Print terminator that separates header from data
			function printEndMarker(this, filename)
			fileID=fopen(filename,'a');
			fprintf(fileID,...
			[this.hdr_spec, this.end_header, ...
			this.hdr_spec, this.line_sep]);
			fclose(fileID);
			end

			%Adds time header
			%Second optional argument is the name of the field, i.e
			%addTimeField(this, 'TimeField')
			function addTimeField(this, t_field_name)
			if nargin()>1
			assert(ischar(t_field_name)&&isvector(t_field_name),...
			'Time field name must be a character vector')
			else
			t_field_name='Time';
			end

			if ismember(t_field_name, this.field_names)
			deleteField(this, t_field_name)
			end

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

			function n_end_header=load(this, filename)
			%Before we load, we clear all existing fields
			clearFields(this);

			fileID=fopen(filename,'r');

			title_exp=[this.hdr_spec,'(\w.*)',this.hdr_spec];

			%Loop initialization
			line_no=0;
			curr_title='';

			%Loop continues until we reach the next header or we reach
			%the end of the file
			while ~feof(fileID)
			line_no=line_no+1;
			%Grabs the current line
			curr_line=fgetl(fileID);
			%Gives an error if the file is empty, i.e. fgetl returns -1
			if curr_line==-1
			error('Tried to read empty file. Aborting.')
			end
			%Skips if current line is empty
			if isempty(curr_line)
			continue
			end

			title_token=regexp(curr_line,title_exp,'once','tokens');
			%If we find a title, first check if it is the specified
			%end header. Then change the title if a title was found,
			%then if no title was found, put the data under the current
			%title.
			if ismember(this.end_header, title_token)
			break
			elseif ~isempty(title_token)
			% Apply genvarname for sefety in case the title string
			% is not a proper variable name
			curr_title=genvarname(title_token{1});
			addField(this, curr_title);
			%This runs if there was no match for the header regular
			%expression, i.e. the current line is not a filed
			%separator, and the current line is not empty. We then
			%add this line to the current field (curr_title), possibly
			%iterating over the parameter subscripts.
			elseif ~isempty(curr_title)
			% First separate the comment if present
			tmp=regexp(curr_line,this.comment_sep,'split','once');
			if length(tmp)>1
			% the line has comment
			comment_str=tmp{2};
			else
			comment_str='';
			end
			% Then process name-value pair. Regard everything after
			% the first column separator as value.
			tmp=regexp(tmp{1},this.column_sep,'split','once');

			if length(tmp)<2
			% Ignore the line if a name-value pair is not found
			continue
			else
			% Attempt convertion of value to number
			val=str2doubleHedged(strtrim(tmp{2}));
			end

			% Infer the variable name and subscript reference
			try
			[S, name]=str2substruct(strtrim(tmp{1}));
			catch
			name='';
			end

			if isempty(name)
			% Ignore the line if variable name is not missing
			continue
			elseif ismember(name, fieldnames(this.(curr_title)))
			% If the variable name already presents among
			% parameters, add new subscript value
			this.(curr_title).(name).value= ...
			subsasgn(this.(curr_title).(name).value,S,val);
			else
			% Add new parameter with comment
			addParam(this, curr_title, name, val,...
			'SubStruct', S, 'comment', comment_str);
			end
			end
			end
			fclose(fileID);
			if isempty(this.field_names)
			warning('No metadata found, continuing without metadata.')
			n_end_header=1;
			else
			n_end_header=line_no;
			end
			end

			% Need a custom copy method as the one provided by
			% matlab.mixin.Copyable does not re-create the handles of dynamic
			% properties stored in this.PropHandles
			function NewMet=copy(this)
			NewMet=MyMetadata();
			Mc=metaclass(NewMet);

			% Copy static public non-dependent properties
			for i=1:length(Mc.PropertyList)
			TmpProp=Mc.PropertyList(i);
			if strcmpi(TmpProp.GetAccess,'public') && ...
			strcmpi(TmpProp.SetAccess,'public') && ...
			~TmpProp.Dependent
			NewMet.(TmpProp.Name)=this.(TmpProp.Name);
			end
			end

			% Copy dynamic properties
			addMetadata(NewMet, this);
			end
			end


			%% Set and Get methods

			methods
			function field_names=get.field_names(this)
			field_names=fieldnames(this.PropHandles);
			end

			end
			end

rINSTCONTROL/@MyMetadata/MyMetadata.m7d66b42abcd4confint-fix

MyMetadata.mView Options

rINSTCONTROL/@MyMetadata/MyMetadata.m
7d66b42abcd4confint-fix

MyMetadata.m
View Options