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rINSTCONTROL/@MyTrace/MyTrace.m
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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='';
% 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
%We now write the data to the file
writeData(this, fname, 'save_prec', p.Results.save_prec);
else
warning('File not created, returned write_flag %i',stat);
end
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 look 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)
% Do nothing if there is no data in the trace
if isempty(this)
return
end
%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(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(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
% Picks every n-th element from the trace,
% performing a running average first if opt=='avg'
function downsample(this, n, opt)
n0=ceil(n/2);
if nargin()==3 && (strcmpi(opt,'average') || strcmpi(opt,'vg'))
% 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, 'Endpoints', 'shrink');
this.x=this.x(n0:n:end);
this.y=tmpy(n0:n:end);
else
% Downsample without averaging
this.x=this.x(n0:n:end);
this.y=this.y(n0:n:end);
end
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(this, b)
assert(isa(this,'MyTrace') && isa(b,'MyTrace'),...
['Both objects must be of type MyTrace to add,',...
'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 MyTrace classes must have the same units for arithmetic')
assert(length(this.x)==length(this.y)==...
length(this.x)==length(this.y),...
'The length of x and y must be equal for arithmetic');
assert(all(this.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 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
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
%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','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
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