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MyTrace.m
c5d3f5d51f5cconfint-fix

MyTrace.m
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			% Class for XY data representation with labelling, plotting and
			% saving/loading functionality
			% If instantiated as MyTrace(load_path) then
			% the content is loaded from file

			classdef MyTrace < handle & matlab.mixin.Copyable & matlab.mixin.SetGet
			properties (Access=public)
			x=[];
			y=[];
			name_x='x';
			name_y='y';
			unit_x='';
			unit_y='';
			% MyMetadata storing information about how the trace was taken
			MeasHeaders
			file_name='';
			uid='';

			% Data column and line separators
			column_sep = '\t'
			line_sep='\r\n'

			%Cell that contains handles the trace is plotted in
			hlines={};
			end

			properties (Dependent=true)
			%MyMetadata containing the MeasHeaders and
			%information about the trace
			Metadata

			label_x
			label_y
			end

			methods (Access=public)
			function this=MyTrace(varargin)
			P=MyClassParser(this);
			% options for MeasHeaders
			addParameter(P, 'metadata_opts',{},@iscell);

			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});
			this.file_name=load_path;
			else
			% Parse varargin as a list of name-value pairs
			processInputs(P, this, varargin{:});
			load_path=[];
			end

			this.MeasHeaders=MyMetadata(P.Results.metadata_opts{:});

			if ~isempty(load_path)
			load(this, load_path);
			end
			end

			%Defines the save function for the class. Note that this is only
			%used when we want to write only the data with its associated
			%trace, rather than just the trace. To write just the trace with
			%fewer input checks, use the writeData function.
			function save(this, varargin)
			%Parse inputs for saving
			p=inputParser;
			addParameter(p,'save_prec',15);
			addParameter(p,'overwrite',false);

			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
			fname=varargin{1};
			assert(ischar(fname)&&isvector(fname),...
			'''filename'' must be a vector of characters');
			this.file_name=fname;
			parse(p,varargin{2:end});
			else
			% Parse varargin as a list of name-value pairs and take
			% file name from the class property
			fname=this.file_name;
			parse(p,varargin{:});
			end

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

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

			%We now write the data to the file
			writeData(this, fname, 'save_prec', p.Results.save_prec);
			end

			%Writes the data to a file. This is separated so that other
			%programs can write to the file from the outside. We circumvent the
			%checks for the existence of the file here, assuming it is done
			%outside.
			function writeData(this, fullfilename, varargin)
			p=inputParser;
			addRequired(p,'fullfilename',@ischar);
			addParameter(p,'save_prec',15);
			parse(p,fullfilename,varargin{:});

			fullfilename=p.Results.fullfilename;
			save_prec=p.Results.save_prec;

			%Writes the metadata header
			save(this.Metadata,fullfilename);

			fileID=fopen(fullfilename,'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 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 looks ugly but makes
			%files significantly smaller
			data_format_str=sprintf(['%%.%ig',this.column_sep,'%%.%ig',...
			this.line_sep],save_prec,save_prec);
			fprintf(fileID, data_format_str,[this.x, this.y]');
			fclose(fileID);
			end

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

			function load(this, file_path, varargin)
			p=inputParser;
			addParameter(p,'hdr_spec',...
			this.MeasHeaders.hdr_spec,@ischar);
			addParameter(p,'end_header',...
			this.MeasHeaders.end_header,@ischar);
			parse(p,varargin{:});

			this.MeasHeaders.hdr_spec=p.Results.hdr_spec;
			this.MeasHeaders.end_header=p.Results.end_header;

			if ~exist(file_path,'file')
			error('File does not exist, please choose a different load path')
			end

			%Read metadata. We get the line number we want to read
			%the main data from as an output.
			end_line_no=load(this.MeasHeaders, file_path);

			%Tries to assign units and names and then delete the Info field
			%from MeasHeaders
			try
			this.unit_x=this.MeasHeaders.Info.Unit1.value;
			this.unit_y=this.MeasHeaders.Info.Unit2.value;
			this.name_x=this.MeasHeaders.Info.Name1.value;
			this.name_y=this.MeasHeaders.Info.Name2.value;
			deleteField(this.MeasHeaders,'Info');
			catch
			warning(['No metadata found. No units or labels assigned',...
			' when loading trace from %s'],file_path)
			this.name_x='x';
			this.name_y='y';
			this.unit_x='x';
			this.unit_y='y';
			end

			%Reads x and y data
			data_array=dlmread(file_path, this.column_sep, ...
			end_line_no,0);
			this.x=data_array(:,1);
			this.y=data_array(:,2);

			this.file_name=file_path;
			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)
			%Checks that x and y are the same size
			assert(validatePlot(this),...
			'The length of x and y must be identical to make a plot')
			%Parses inputs
			p=inputParser();

			% Axes in which log should be plotted
			addOptional(p, 'plot_axes', [], @(x)assert( ...
			isa(x,'matlab.graphics.axis.Axes')\|\|...
			isa(x,'matlab.ui.control.UIAxes'),...
			'Argument must be axes or uiaxes.'));

			validateColor=@(x) assert(iscolor(x),...
			'Input must be a valid color. See iscolor function');
			addParameter(p,'Color','b',validateColor);

			validateMarker=@(x) assert(ismarker(x),...
			'Input must be a valid marker. See ismarker function');
			addParameter(p,'Marker','none',validateMarker);

			validateLine=@(x) assert(isline(x),...
			'Input must be a valid linestyle. See isline function');
			addParameter(p,'LineStyle','-',validateLine);

			addParameter(p,'MarkerSize',6,...
			@(x) validateattributes(x,{'numeric'},{'positive'}));
			addParameter(p,'make_labels',false,@islogical);

			interpreters={'none','tex','latex'};
			validateInterpreter=@(x) assert(contains(x,interpreters),...
			'Interpreter must be none, tex or latex');
			addParameter(p,'Interpreter','latex',validateInterpreter);
			parse(p,varargin{:});

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

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

			%Sets the correct color and label options
			set(this.hlines{ind},'Color',p.Results.Color,'LineStyle',...
			p.Results.LineStyle,'Marker',p.Results.Marker,...
			'MarkerSize',p.Results.MarkerSize);

			if p.Results.make_labels
			interpreter=p.Results.Interpreter;
			xlabel(plot_axes,this.label_x,'Interpreter',interpreter);
			ylabel(plot_axes,this.label_y,'Interpreter',interpreter);
			set(plot_axes,'TickLabelInterpreter',interpreter);
			end
			end

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

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

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

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

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

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

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

			%Integrates the trace numerically
			function area=integrate(this,varargin)
			assert(validatePlot(this),['MyTrace object must contain',...
			' nonempty data vectors of equal length to integrate'])

			%Input parser for optional inputs
			p=inputParser;
			%Default is to use all the data in the trace
			addOptional(p,'ind',true(1,length(this.x)));
			parse(p,varargin{:});
			ind=p.Results.ind;

			%Integrates the data contained in the indexed part.
			area=trapz(this.x(ind),this.y(ind));
			end

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

			%Checks if the data can be plotted
			function bool=validatePlot(this)
			bool=~isempty(this.x) && ~isempty(this.y)...
			&& length(this.x)==length(this.y);
			end

			function hline=getLineHandle(this,ax)
			ind=findLineInd(this,ax);
			if ~isempty(ind)
			hline=this.hlines{ind};
			else
			hline=[];
			end
			end
			end

			methods (Access=private)
			%Checks if arithmetic can be done with MyTrace objects.
			function checkArithmetic(a,b)
			assert(isa(a,'MyTrace') && isa(b,'MyTrace'),...
			['Both objects must be of type MyTrace to add,',...
			'here they are type %s and %s'],class(a),class(b));
			assert(strcmp(a.unit_x, b.unit_x) && strcmp(a.unit_y,b.unit_y),...
			'The MyTrace classes must have the same units for arithmetic');
			assert(length(a.x)==length(a.y) && length(a.x)==length(a.y),...
			'The length of x and y must be equal for arithmetic');
			assert(all(a.x==b.x),...
			'The MyTrace objects must have identical x-axis for arithmetic')
			end

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

			%Set and get methods
			methods
			%Set function for MeasHeaders
			function set.MeasHeaders(this, MeasHeaders)
			assert(isa(MeasHeaders,'MyMetadata'),...
			['MeasHeaders must be an instance of MyMetadata, ',...
			'it is %s'],class(MeasHeaders));
			this.MeasHeaders=MeasHeaders;
			end

			%Set function for x, checks if it is a vector of doubles.
			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
			%generates a new UID for the trace
			function set.y(this, y)
			assert(isnumeric(y),...
			'Data must be of class double');
			this.y=y(:);
			this.uid=genUid(); %#ok<MCSUP>
			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

			function set.file_name(this, file_name)
			assert(ischar(file_name),'File path must be a char, not a %s',...
			class(file_name));
			this.file_name=file_name;
			end

			function set.uid(this, uid)
			assert(ischar(uid),'UID must be a char, not a %s',...
			class(uid));
			this.uid=uid;
			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

			%Generates the full metadata of the trace
			function Metadata=get.Metadata(this)
			%First we update the trace information
			Metadata=MyMetadata();
			addField(Metadata,'Info');
			addParam(Metadata,'Info','uid',this.uid);
			addParam(Metadata,'Info','Name1',this.name_x);
			addParam(Metadata,'Info','Name2',this.name_y);
			addParam(Metadata,'Info','Unit1',this.unit_x);
			addParam(Metadata,'Info','Unit2',this.unit_y);

			addMetadata(Metadata,this.MeasHeaders);
			end
			end
			end

rINSTCONTROL/@MyTrace/MyTrace.mc5d3f5d51f5cconfint-fix

MyTrace.mView Options

rINSTCONTROL/@MyTrace/MyTrace.m
c5d3f5d51f5cconfint-fix

MyTrace.m
View Options