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MyTrace.m
d6981ee2fffaconfint-fix

MyTrace.m
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			% Class for XY data representation with labelling, plotting and
			% saving/loading functionality

			classdef MyTrace < handle & matlab.mixin.Copyable & matlab.mixin.SetGet
			properties (Access = public)
			x = []
			y = []

			name_x = 'x'
			name_y = 'y'
			unit_x = ''
			unit_y = ''

			file_name char

			% Array of MyMetadata objects with information about the trace.
			% The full metadata also contains information about the trace
			% properties like units etc.
			UserMetadata MyMetadata

			% Formatting options for the metadata
			metadata_opts cell

			% Data formatting options
			column_sep = '\t' % Data column separator
			line_sep = '\r\n' % Data line separator
			data_sep = 'Data' % Separator between metadata and data
			save_prec = 15 % Maximum digits of precision in saved data
			end

			properties (GetAccess = public, SetAccess = protected, ...
			NonCopyable = true)

			% Cell that contains the handles of Line objects the trace
			% is plotted in
			PlotLines = {}
			end

			properties (Dependent=true)
			label_x
			label_y
			end

			methods (Access = public)
			function this = MyTrace(varargin)
			P = MyClassParser(this);
			processInputs(P, this, varargin{:});
			end

			function delete(this)

			% Delete lines from all the axes the trace is plotted in
			cellfun(@delete, this.PlotLines);
			end

			%Defines the save function for the class.
			function save(this, filename, varargin)

			% Parse inputs for saving
			p = inputParser;
			addParameter(p, 'overwrite', false);
			parse(p, varargin{:});

			assert(ischar(filename) && isvector(filename), ...
			'''filename'' must be a character vector.')
			this.file_name = filename;

			% Create the file in the given folder
			stat = createFile(filename, 'overwrite', p.Results.overwrite);

			% Returns if the file is not created for some reason
			if ~stat
			warning('File not created, returned write_flag %i.', stat);
			return
			end

			% Create metadata header
			Mdt = getMetadata(this);

			save(Mdt, filename);

			% Write the data
			fileID = fopen(filename,'a');

			% Pads the vectors if they are not equal length
			diff = length(this.x)-length(this.y);
			if diff<0
			this.x = [this.x; zeros(-diff,1)];
			warning(['Zero padded x vector as the saved vectors ' ...
			'are not of the same length']);
			elseif diff>0
			this.y = [this.y; zeros(diff,1)];
			warning(['Zero padded y vector as the saved vectors ' ...
			'are not of the same length']);
			end

			% Save data in the more compact of fixed point and scientific
			% notation with trailing zeros removed.
			% If save_prec=15, we get %.15g\t%.15g\r\n
			% Formatting without column padding may look ugly but it
			% signigicantly reduces the file size.
			data_format_str = ...
			sprintf(['%%.%ig', this.column_sep, '%%.%ig', ...
			this.line_sep], this.save_prec, this.save_prec);

			fprintf(fileID, data_format_str, [this.x, this.y]');
			fclose(fileID);
			end

			function clearData(this)
			this.x = [];
			this.y = [];
			end

			%Plots the trace on the given axes, using the class variables to
			%define colors, markers, lines and labels. Takes all optional
			%parameters of the class as inputs.
			function plot(this, varargin)

			% Do nothing if there is no data in the trace
			if isDataEmpty(this)
			return
			end

			% Checks that x and y are the same size
			assert(validateData(this),...
			'The length of x and y must be identical to make a plot')

			% Parses inputs
			p = inputParser();
			p.KeepUnmatched = true;

			% Axes in which the trace should be plotted
			addOptional(p, 'Axes', [], @(x)assert(isaxes(x),...
			'Argument must be axes or uiaxes.'));

			addParameter(p, 'make_labels', true, @islogical);

			validateInterpreter = @(x) assert( ...
			ismember(x, {'none', 'tex', 'latex'}),...
			'Interpreter must be none, tex or latex');
			addParameter(p, 'Interpreter', 'latex', validateInterpreter);

			parse(p, varargin{:});

			line_opts = struct2namevalue(p.Unmatched);

			%If axes are not supplied get current
			if ~isempty(p.Results.Axes)
			Axes = p.Results.Axes;
			else
			Axes = gca();
			end

			ind = findLineInd(this, Axes);

			if ~isempty(ind) && any(ind)
			set(this.PlotLines{ind}, 'XData', this.x, 'YData', this.y);
			else
			this.PlotLines{end+1} = plot(Axes, this.x, this.y);
			ind = length(this.PlotLines);
			end

			% Sets the correct color and label options
			if ~isempty(line_opts)
			set(this.PlotLines{ind}, line_opts{:});
			end

			if p.Results.make_labels
			makeLabels(this, Axes, p.Results.Interpreter)
			end
			end

			% Add labels to the axes
			function makeLabels(this, Axes, interpreter)
			if exist('interpreter', 'var') == 0
			interpreter = 'latex';
			end

			xlabel(Axes, this.label_x, 'Interpreter', interpreter);
			ylabel(Axes, this.label_y, 'Interpreter', interpreter);
			set(Axes, 'TickLabelInterpreter', interpreter);
			end

			%If there is a line object from the trace in the figure, this sets
			%it to the appropriate visible setting.
			function setVisible(this, Axes, bool)
			if bool
			vis='on';
			else
			vis='off';
			end

			ind=findLineInd(this, Axes);
			if ~isempty(ind) && any(ind)
			set(this.PlotLines{ind},'Visible',vis)
			end
			end

			%Defines addition of two MyTrace objects
			function Sum=plus(this,b)
			checkArithmetic(this,b);

			Sum=MyTrace('x',this.x,'y',this.y+b.y, ...
			'unit_x',this.unit_x,'unit_y',this.unit_y, ...
			'name_x',this.name_x,'name_y',this.name_y);
			end

			%Defines subtraction of two MyTrace objects
			function Diff=minus(this,b)
			checkArithmetic(this,b);

			Diff=MyTrace('x',this.x,'y',this.y-b.y, ...
			'unit_x',this.unit_x,'unit_y',this.unit_y, ...
			'name_x',this.name_x,'name_y',this.name_y);
			end

			function [max_val,max_x]=max(this)
			assert(validateData(this),['MyTrace object must contain',...
			' nonempty data vectors of equal length to find the max'])
			[max_val,max_ind]=max(this.y);
			max_x=this.x(max_ind);
			end

			function fwhm=calcFwhm(this)
			assert(validateData(this),['MyTrace object must contain',...
			' nonempty data vectors of equal length to find the fwhm'])
			[~,~,fwhm,~]=findpeaks(this.y,this.x,'NPeaks',1);
			end

			function [mean_x,std_x,mean_y,std_y]=calcZScore(this)
			mean_x=mean(this.x);
			std_x=std(this.x);
			mean_y=mean(this.y);
			std_y=std(this.y);
			end

			% Integrates the trace numerically. Two possible ways to call the
			% function:
			%
			% integrate(Trace) - integrate the entire data
			% integrate(Trace, xmin, xmax) - integrate over [xmin, xmax]
			% integrate(Trace, ind) - integrate data with indices ind
			function area = integrate(this, varargin)
			assert(validateData(this), ['MyTrace object must contain',...
			' nonempty data vectors of equal length to integrate'])

			switch nargin()
			case 1

			% The function is called as integrate(Trace), integrate
			% the entire trace
			xvals = this.x;
			yvals = this.y;
			case 2

			% The function is called as integrate(Trace, ind)
			ind = varargin{1};
			xvals = this.x(ind);
			yvals = this.y(ind);
			case 3

			% The function is called as integrate(Trace,xmin,xmax)
			xmin = varargin{1};
			xmax = varargin{2};

			% Select all data points within the integration range
			ind = (this.x > xmin) & (this.x < xmax);
			xvals = this.x(ind);
			yvals = this.y(ind);

			% Add the two points corresponding to the interval ends
			% if the interval is within data range
			if xmin >= this.x(1)
			yb = interp1(this.x, this.y, xmin);
			xvals = [xmin; xvals];
			yvals = [yb; yvals];
			end

			if xmax <= this.x(end)
			yb = interp1(this.x, this.y, xmax);
			xvals = [xvals; xmax];
			yvals = [yvals; yb];
			end
			otherwise
			error(['Unrecognized function signature. Check ' ...
			'the function definition to see acceptable ' ...
			'input argument.'])
			end

			% Integrates the data using the trapezoidal method
			area = trapz(xvals, yvals);
			end

			% Picks every n-th element from the trace,
			% performing a running average first if opt=='avg'
			function NewTrace = downsample(this, n, opt)
			n0 = ceil(n/2);

			if exist('opt', 'var') && ...
			(strcmpi(opt,'average') \|\| strcmpi(opt,'avg'))

			% Compute moving average with 'shrink' option so that the
			% total number of samples is preserved. Endpoints will be
			% discarded by starting the indexing from n0.
			tmpy = movmean(this.y, n, 'Endpoints', 'shrink');

			new_x = this.x(n0:n:end);
			new_y = tmpy(n0:n:end);
			else

			% Downsample without averaging
			new_x = this.x(n0:n:end);
			new_y = this.y(n0:n:end);
			end

			NewTrace = MyTrace('x', new_x, 'y', new_y, ...
			'unit_x',this.unit_x,'unit_y',this.unit_y, ...
			'name_x',this.name_x,'name_y',this.name_y);
			end

			%Checks if the object is empty
			function bool = isDataEmpty(this)
			bool = isempty(this.x) && isempty(this.y);
			end

			%Checks if the data can be processed as a list of {x, y} values,
			%e.g. integrated over x or plotted
			function bool = validateData(this)
			bool =~isempty(this.x) && ~isempty(this.y)...
			&& length(this.x)==length(this.y);
			end

			function Line = getLine(this, Ax)
			ind = findLineInd(this, Ax);
			if ~isempty(ind)
			Line = this.PlotLines{ind};
			else
			Line = [];
			end
			end
			end

			methods (Access = public, Static = true)

			% Load trace from file
			function Trace = load(filename, varargin)
			assert(exist(filename, 'file') ~= 0, ['File does not ' ...
			'exist, please choose a different load path.'])

			% Extract data formatting
			p = inputParser();
			p.KeepUnmatched = true;
			addParameter(p, 'FormatSource', {}, @(x) isa(x,'MyTrace'));
			addParameter(p, 'metadata_opts', {}, @iscell);
			parse(p, varargin{:});

			if ~ismember('FormatSource', p.UsingDefaults)
			Fs = p.Results.FormatSource;

			% Take formatting from the source object
			mdt_opts = Fs.metadata_opts;
			trace_opts = { ...
			'column_sep', Fs.column_sep, ...
			'line_sep', Fs.line_sep, ...
			'data_sep', Fs.data_sep, ...
			'save_prec', Fs.save_prec, ...
			'metadata_opts', Fs.metadata_opts};
			else

			% Formatting is either default or was suppled explicitly
			mdt_opts = p.Results.metadata_opts;
			trace_opts = varargin;
			end

			% Load metadata and convert from array to structure
			[Mdt, n_end_line] = MyMetadata.load(filename, mdt_opts{:});

			Info = titleref(Mdt, 'Info');
			if ~isempty(Info) && isparam(Info, 'Type')
			class_name = Info.ParamList.Type;
			else
			class_name = 'MyTrace';
			end

			% Instantiate an appropriate type of Trace
			Trace = feval(class_name, trace_opts{:}); %#ok<FVAL>

			setMetadata(Trace, Mdt);

			% Reads x and y data
			data_array = dlmread(filename, Trace.column_sep, n_end_line,0);
			Trace.x = data_array(:,1);
			Trace.y = data_array(:,2);

			Trace.file_name = filename;
			end
			end

			methods (Access = protected)

			% Generate metadata that includes measurement headers and
			% information about trace. This function is used in place of 'get'
			% method so it can be overloaded in a subclass.
			function Mdt = getMetadata(this)

			% Make a field with the information about the trace
			Info = MyMetadata('title', 'Info');
			addParam(Info, 'Type', class(this));
			addParam(Info, 'Name1', this.name_x);
			addParam(Info, 'Name2', this.name_y);
			addParam(Info, 'Unit1', this.unit_x);
			addParam(Info, 'Unit2', this.unit_y);

			% Make a separator for the bulk of trace data
			DataSep = MyMetadata('title', this.data_sep);

			Mdt = [Info, this.UserMetadata, DataSep];

			% Ensure uniform formatting
			if ~isempty(this.metadata_opts)
			set(Mdt, this.metadata_opts{:});
			end
			end

			% Load metadata into the trace
			function setMetadata(this, Mdt)

			Info = titleref(Mdt, 'Info');
			if ~isempty(Info)
			if isparam(Info, 'Unit1')
			this.unit_x = Info.ParamList.Unit1;
			end

			if isparam(Info, 'Unit2')
			this.unit_y = Info.ParamList.Unit2;
			end

			if isparam(Info, 'Name1')
			this.name_x = Info.ParamList.Name1;
			end

			if isparam(Info, 'Name2')
			this.name_y = Info.ParamList.Name2;
			end

			% Remove the metadata containing trace properties
			Mdt = rmtitle(Mdt, 'Info');
			else
			warning(['No trace metadata found. No units or labels ' ...
			'assigned when loading trace from %s.'], filename);
			end

			% Remove the empty data separator field
			Mdt = rmtitle(Mdt, this.data_sep);

			% Store the remainder as user metadata
			this.UserMetadata = Mdt;
			end

			%Checks if arithmetic can be done with MyTrace objects.
			function checkArithmetic(this, b)
			assert(isa(this,'MyTrace') && isa(b,'MyTrace'),...
			['Both objects must be of type MyTrace ,',...
			'here they are type %s and %s'],class(this),class(b));

			assert(strcmp(this.unit_x, b.unit_x) && ...
			strcmp(this.unit_y,b.unit_y),...
			'The trace objects do not have the same units')

			assert(length(this.x)==length(this.y), ['The length of x ' ...
			'and y in the first argument are not equal']);

			assert(length(b.x)==length(b.y), ['The length of x and y ' ...
			'in the second argument are not equal']);

			assert(all(this.x==b.x),...
			'The trace objects do not have identical x-axis ')
			end

			% Finds the hline handle that is plotted in the specified axes
			function ind = findLineInd(this, Axes)
			if ~isempty(this.PlotLines)
			ind = cellfun(@(x) ismember(x, findall(Axes, ...
			'Type','Line')), this.PlotLines);
			else
			ind = [];
			end
			end

			% Overload the standard copy() method to create a deep copy,
			% i.e. when handle properties are copied recursively
			function Copy = copyElement(this)
			Copy = copyElement@matlab.mixin.Copyable(this);

			% Copy metadata
			Copy.UserMetadata = copy(this.UserMetadata);
			end
			end

			%% Set and get methods

			methods

			%Set function for x, checks if it is a vector of doubles and
			%reshapes into a column vector
			function set.x(this, x)
			assert(isnumeric(x),...
			'Data must be of class double');
			this.x=x(:);
			end

			%Set function for y, checks if it is a vector of doubles and
			%reshapes into a column vector
			function set.y(this, y)
			assert(isnumeric(y),...
			'Data must be of class double');
			this.y=y(:);
			end

			%Set function for unit_x, checks if input is a string.
			function set.unit_x(this, unit_x)
			assert(ischar(unit_x),'Unit must be a char, not a %s',...
			class(unit_x));
			this.unit_x=unit_x;
			end

			%Set function for unit_y, checks if input is a string
			function set.unit_y(this, unit_y)
			assert(ischar(unit_y),'Unit must be a char, not a %s',...
			class(unit_y));
			this.unit_y=unit_y;
			end

			%Set function for name_x, checks if input is a string
			function set.name_x(this, name_x)
			assert(ischar(name_x),'Name must be a char, not a %s',...
			class(name_x));
			this.name_x=name_x;
			end

			%Set function for name_y, checks if input is a string
			function set.name_y(this, name_y)
			assert(ischar(name_y),'Name must be a char, not a %s',...
			class(name_y));
			this.name_y=name_y;
			end

			%Get function for label_x, creates label from name_x and unit_x.
			function label_x=get.label_x(this)
			label_x=sprintf('%s (%s)', this.name_x, this.unit_x);
			end

			%Get function for label_y, creates label from name_y and unit_y.
			function label_y=get.label_y(this)
			label_y=sprintf('%s (%s)', this.name_y, this.unit_y);
			end
			end
			end

rINSTCONTROL/@MyTrace/MyTrace.md6981ee2fffaconfint-fix

MyTrace.mView Options

rINSTCONTROL/@MyTrace/MyTrace.m
d6981ee2fffaconfint-fix

MyTrace.m
View Options