Diffusion Instrument Control (confint-fix) Browse

MyPeakFinder.m
a1657a46897fconfint-fix

MyPeakFinder.m
View Options

			classdef MyPeakFinder < handle
			properties
			Trace;
			Peaks;
			end

			methods
			function this=MyPeakFinder(varargin)
			p=inputParser;
			addParameter(p,'Trace',MyTrace());
			parse(p,varargin{:})

			this.Trace=p.Results.Trace;
			this.Peaks=struct('Location',[],'Width',[],'Prominence',[],...
			'Value',[]);
			end

			%Checks if a peak exists within the given limits
			function bool=checkPeakExist(this,x_min,x_max)
			assert(isnumeric(x_min) & isnumeric(x_max),...
			'x_min and x_max must be numbers');
			assert(x_max>x_min,['x_max must be greater than x_min,',...
			' currently x_min is %e while x_max is %e'],x_min,x_max);
			bool=any([this.Peaks.Location]>x_min & [this.Peaks.Location]<x_max);
			end

			function searchPeaks(this,varargin)
			assert(validateData(this.Trace),...
			'The Trace is not valid for finding peaks, make sure a proper trace is loaded');
			p=inputParser;
			%Some validation functions
			ispositive=@(x) isnumeric(x) && isscalar(x) && (x > 0);
			isnumber=@(x) isnumeric(x) && isscalar(x);

			valid_sorts={'none','ascend','descend'};
			sortstrcheck=@(x) any(validatestring(x,valid_sorts));

			addParameter(p,'FindMinima',false);
			addParameter(p,'MinPeakDistance',0,ispositive);
			addParameter(p,'MinPeakHeight',-Inf,isnumber);
			addParameter(p,'MinPeakWidth',0,ispositive);
			addParameter(p,'MaxPeakWidth',Inf,ispositive);
			addParameter(p,'MinPeakProminence',0.1,isnumber);
			addParameter(p,'SortStr','none',sortstrcheck);
			addParameter(p,'Threshold',0);
			addParameter(p,'ClearPeaks',true);
			addParameter(p,'Limits',[min(this.Trace.x),max(this.Trace.x)])
			addParameter(p,'NPeaks',0);
			addParameter(p,'WidthReference','halfprom')
			parse(p,varargin{:});

			%Sets the indices to be searched
			x_lim=p.Results.Limits;
			ind=(this.Trace.x<x_lim(2)) & (this.Trace.x>x_lim(1));

			%Sets the minimum peak prominence, which is always normalized
			min_peak_prominence=p.Results.MinPeakProminence*...
			peak2peak(this.Trace.y(ind));

			%We must condition the Trace such that x is increasing and has
			%no NaNs
			nan_ind=isnan(this.Trace.x) \| isnan(this.Trace.y);
			this.Trace.x(nan_ind)=[];
			this.Trace.y(nan_ind)=[];
			ind(nan_ind)=[];

			if ~issorted(this.Trace.x)
			this.Trace.x=flipud(this.Trace.x);
			this.Trace.y=flipud(this.Trace.y);
			%If it is still not sorted, we sort it
			if ~issorted(this.Trace.x)
			'Sorting';
			[this.Trace.x,sort_ind]=sort(this.Trace.x);
			this.Trace.y=this.Trace.y(sort_ind);
			end
			end

			%If we are looking for minima, we invert the trace
			if p.Results.FindMinima
			y=-this.Trace.y;
			else
			y=this.Trace.y;
			end

			%As there is no way to tell it to look for infinite numbers of
			%peaks when you specify NPeaks, we only specify this parameter
			%if we need to
			if p.Results.NPeaks
			extra_args={'NPeaks',p.Results.NPeaks};
			else
			extra_args={};
			end

			%We now search for the peaks using the specified parameters
			[pks,locs,wdth,prom]=findpeaks(y(ind),...
			this.Trace.x(ind),...
			'MinPeakDistance',p.Results.MinPeakDistance,...
			'MinPeakheight',p.Results.MinPeakHeight,...
			'MinPeakWidth',p.Results.MinPeakWidth,...
			'MaxPeakWidth',p.Results.MaxPeakWidth,...
			'SortStr',p.Results.SortStr,...
			'MinPeakProminence',min_peak_prominence,...
			'Threshold',p.Results.Threshold,...
			'WidthReference',p.Results.WidthReference,...
			extra_args{:});

			%We invert the results back if we are looking for minima.
			if p.Results.FindMinima
			pks=-pks;
			prom=-prom;
			end

			PeakStruct=struct('Value',num2cell(pks),...
			'Location',num2cell(locs),...
			'Width',num2cell(wdth),...
			'Prominence',num2cell(prom));

			%If the clearpeaks flag is set, we delete the previous peaks.
			if p.Results.ClearPeaks
			clearPeaks(this);
			this.Peaks=PeakStruct;
			else
			this.Peaks=[this.Peaks;PeakStruct];
			end
			end

			function loadTrace(this,fullfilename)
			%Finds type of file
			[~,~,ext]=fileparts(fullfilename);

			switch ext
			case '.txt'
			load(this.Trace,fullfilename);
			case '.mat'
			DataStruct=load(fullfilename);
			fields=fieldnames(DataStruct);

			%We try to find which vectors are x and y for the data,
			%first we find the two longest vectors in the .mat file
			%and use these
			vec_length=structfun(@(x) length(x), DataStruct);
			[~,sort_ind]=sort(vec_length,'descend');
			vec_names=fields(sort_ind(1:2));

			%Now we do some basic conditioning of these vectors:
			%Make column vectors and remove NaNs.
			vec{1}=DataStruct.(vec_names{1})(:);
			vec{2}=DataStruct.(vec_names{2})(:);

			%If there is a start and stopindex, cut down the
			%longest vector to size.
			if ismember('startIndex',fields) && ...
			ismember('stopIndex',fields)
			[~,ind]=max(cellfun(@(x) length(x), vec));
			vec{ind}=vec{ind}(DataStruct.startIndex:...
			DataStruct.stopIndex);
			end

			nan_ind=isnan(vec{1}) \| isnan(vec{2});
			vec{1}(nan_ind)=[];
			vec{2}(nan_ind)=[];

			%We find what x is by looking for a sorted vector
			ind_x=cellfun(@(x) issorted(x,'monotonic'),vec);

			this.Trace.x=vec{ind_x};
			this.Trace.y=vec{~ind_x};

			if ismember('offsetFrequency',fields)
			this.Trace.x=this.Trace.x+DataStruct.offsetFrequency;
			end
			otherwise
			error('File type %s is not supported',ext)
			end
			end

			function fitAllPeaks(this,varargin)
			p=inputParser;
			addParameter(p,'FitNames',{'Gorodetsky2000'});
			addParameter(p,'base_dir',pwd);
			addParameter(p,'session_name','placeholder');
			addParameter(p,'filename','placeholder');
			addParameter(p,'fit_width',16)
			parse(p,varargin{:});

			fit_names=p.Results.FitNames;

			%We instantiate the MyFit objects used for the fitting
			Fits=struct();
			for i=1:length(fit_names)
			Fits.(fit_names{i})=launchFit(fit_names{i},...
			'enable_gui',0,'enable_plot',0);
			Fits.(fit_names{i}).base_dir=p.Results.base_dir;
			Fits.(fit_names{i}).session_name=p.Results.session_name;
			Fits.(fit_names{i}).filename=...
			[p.Results.filename,'_',fit_names{i}];
			end

			%We fit the peaks
			for i=1:length(this.Peaks)
			%First extract the data around the peak
			[x_fit,y_fit]=extractPeak(this,i,p.Results.fit_width);

			for j=1:length(fit_names)
			Fits.(fit_names{j}).Data.x=x_fit;
			Fits.(fit_names{j}).Data.y=y_fit;
			genInitParams(Fits.(fit_names{j}));
			fitTrace(Fits.(fit_names{j}));
			saveParams(Fits.(fit_names{j}),...
			'save_user_params',false,...
			'save_gof',true);
			end
			end

			fprintf('Finished fitting peaks \n');
			end

			function [x_peak,y_peak]=extractPeak(this,peak_no,ext_width)
			loc=this.Peaks(peak_no).Location;
			w=this.Peaks(peak_no).Width;
			ind=(loc-ext_width/2*w<this.Trace.x) &...
			(loc+ext_width/2*w>this.Trace.x);
			x_peak=this.Trace.x(ind)-loc;
			y_peak=this.Trace.y(ind);
			end

			function save(this,varargin)
			%Parse inputs for saving
			p=inputParser;
			addParameter(p,'filename','placeholder',@ischar);
			addParameter(p,'save_dir',pwd,@ischar);
			addParameter(p,'overwrite_flag',false);
			addParameter(p,'save_prec',15);
			parse(p,varargin{:});

			%Assign shorter names
			filename=p.Results.filename;
			save_dir=p.Results.save_dir;
			overwrite_flag=p.Results.overwrite_flag;
			save_prec=p.Results.save_prec;

			%Puts together the full file name
			fullfilename=fullfile([save_dir,filename,'.txt']);

			%Creates the file in the given folder
			write_flag=createFile(fullfilename,'overwrite',overwrite_flag);

			%Returns if the file is not created for some reason
			if ~write_flag; return; end

			col_names={'Value','Location','Width','Prominence'};
			n_columns=length(col_names);
			%Finds appropriate column width
			cw=max([cellfun(@(x) length(x),col_names), save_prec+7]);
			cw_vec=repmat(cw,1,4);

			pre_fmt_str=repmat('%%%is\\t',1,n_columns);
			fmt_str=sprintf([pre_fmt_str,'\r\n'],cw_vec);

			fileID=fopen(fullfilename,'w');
			fprintf(fileID,fmt_str,col_names{:});

			pre_fmt_str_nmb=repmat('%%%i.15e\\t',1,n_columns);
			%Removes the tab at the end
			pre_fmt_str_nmb((end-2):end)=[];

			nmb_fmt_str=sprintf([pre_fmt_str_nmb,'\r\n'],cw_vec);

			fprintf(fileID,nmb_fmt_str,...
			[[this.Peaks.Value];[this.Peaks.Location];...
			[this.Peaks.Width];[this.Peaks.Prominence]]);
			fclose(fileID);
			end

			function loadPeaks(this,fullfilename)
			assert(ischar(fullfilename),...
			'File name must be a char, currently it is a %s',...
			class(fullfilename));
			if ~exist(fullfilename,'file')
			error('File named ''%s'' does not exist, choose a different file',...
			fullfilename);
			end

			LoadStruct=importdata(fullfilename);
			headers=regexp(LoadStruct.textdata{1},'\s(\w)\s*','Tokens');
			this.Peaks=struct(headers{1}{1},num2cell(LoadStruct.data(:,1)),...
			headers{2}{1},num2cell(LoadStruct.data(:,2)),...
			headers{3}{1},num2cell(LoadStruct.data(:,3)),...
			headers{4}{1},num2cell(LoadStruct.data(:,4)));

			end

			function clearPeaks(this)
			this.Peaks=struct('Location',[],'Width',[],'Prominence',[],...
			'Value',[]);
			end
			end
			end

rINSTCONTROL/@MyPeakFinder/MyPeakFinder.ma1657a46897fconfint-fix

MyPeakFinder.mView Options

rINSTCONTROL/@MyPeakFinder/MyPeakFinder.m
a1657a46897fconfint-fix

MyPeakFinder.m
View Options