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randomWalk.m
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randomWalk.m
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classdef randomWalk < matlab.mixin.Copyable
properties (GetAccess = 'public', SetAccess = 'private')
positions
journal
oldPositions
name char = ''
end
properties
segment = struct('byAnisotropy',[],...
'cluster',[],'thread',[],'other',[])
pixelSize double = 1
stepTime double = 1
timeUnit char = 'us'
spaceUnit char = 'nm'
voltageZoom = [800, 900, 1000, 2000, 3000, 4000, 5000, ...
6000, 7000, 8000, 9000, 10000, 11000, 12000];
pixelScale = [20.904 23.517 26.13 52.26 78.39 104.52 130.65 156.78 ...
182.91 209.04 235.17 261.3 287.43 313.56];
end
properties (Access = private)
originalPositions
end
methods
function d = dimension(obj)
d = size(obj.steps,2);
end
function n = stepsNumber(obj)
n = size(obj.steps,1);
end
function T = duration(obj,unit)
t = obj.stepTime*obj.stepsNumber;
T = changeTimeUnit(t,unit);
display(sprintf('La caminata tiene una duracion de %.3g ( %s )',T,unit))
end
function out = x(obj)
out = obj.pixelSize*obj.positions(:,1);
end
function out = t(obj)
out = obj.stepTime*(0:length(obj.positions)-1);
end
function out = y(obj)
if dimension(obj)> 1
out = obj.pixelSize*obj.positions(:,2);
end
end
function out = z(obj)
if dimension(obj)> 2
out = obj.pixelSize*obj.positions(:,3);
end
end
function out = XY(obj)
if dimension(obj)> 1
out = obj.pixelSize*obj.positions(:,1:2);
end
end
function varargout = plot(obj,varargin)
fig = figure;
if numel(varargin) == 0
if dimension(obj) == 1
pt = plot(obj.t,obj.x);
xlabel(['tiempo ( ' obj.timeUnit ' )']);
ylabel(['x ( ' obj.spaceUnit ' )']);
elseif dimension(obj) == 2
pt = plot(obj.x,obj.y);
xlabel(['x ( ' obj.spaceUnit ' )']);
ylabel(['y ( ' obj.spaceUnit ' )']);
elseif dimension(obj) == 3
pt = plot3(obj.x,obj.y,obj.z);
xlabel(['x ( ' obj.spaceUnit ' )']);
ylabel(['y ( ' obj.spaceUnit ' )']);
zlabel(['z ( ' obj.spaceUnit ' )']);
end
elseif numel(varargin) == 1
switch varargin{1}
case 'x'
pt = plot(obj.t,obj.x);
xlabel(['tiempo ( ' obj.timeUnit ' )']);
ylabel(['x ( ' obj.spaceUnit ' )']);
case 'y'
pt = plot(obj.t,obj.y);
xlabel(['tiempo ( ' obj.timeUnit ' )']);
ylabel(['y ( ' obj.spaceUnit ' )']);
case 'z'
pt = plot(obj.t,obj.z);
xlabel(['tiempo ( ' obj.timeUnit ' )']);
ylabel(['z ( ' obj.spaceUnit ' )']);
case 'XY'
pt = plot(obj.x,obj.y);
xlabel(['x ( ' obj.spaceUnit ' )']);
ylabel(['y ( ' obj.spaceUnit ' )']);
case 'XZ'
pt = plot(obj.x,obj.z);
xlabel(['x ( ' obj.spaceUnit ' )']);
ylabel(['z ( ' obj.spaceUnit ' )']);
case 'YZ'
pt = plot(obj.y,obj.z);
xlabel(['x ( ' obj.spaceUnit ' )']);
ylabel(['y ( ' obj.spaceUnit ' )']);
case 'msd'
pt = plot(0:obj.stepsNumber,obj.msd(1));
xlabel(['tiempo ( ' obj.timeUnit ' )']);
ylabel(sprintf('msd ( %s^{2} )',obj.spaceUnit));
otherwise
warning('No se puede plotear lo que desea')
end
elseif numel(varargin)>1
if ischar(varargin{1})
switch varargin{1}
case 'msd'
if isnumeric(varargin{2}) && varargin{2} <= 1
pt = plot(obj.stepTime*(0:numel(obj.msd(varargin{2}))-1),obj.msd(varargin{2}));
xlabel(['tiempo ( ' obj.timeUnit ' )']);
ylabel(sprintf('msd ( %s^{2} )',obj.spaceUnit));
end
otherwise
end
end
end
set(pt,'LineStyle','-','Marker','.')
formatFigure(fig)
set(fig,'Name',obj.name)
if nargout == 1
varargout{1} = fig;
end
end
function varargout = plotAngular(obj,varargin)
varargout{:} = plotAngular(obj.XY,varargin{:});
end
function plotTheoreticalMSD(obj,type,fraction)
t = obj.stepTime*(0:numel(obj.msd(fraction))-1);
if ischar(type)
if strcmpi(type,'free') || strcmpi(type,'linear') || strcmpi(type,'brownian')
values = {'D',obj.D,'d',obj.dimension};
elseif strcmpi(type,'drift') || strcmpi(type,'quadratic')
values = {'D',obj.D,'d',obj.dimension,'v',obj.v};
elseif strcmpi(type,'correlated') || strcmpi(type,'directed')
values = {'D',obj.D,'d',obj.dimension,'rho',obj.meanCosine};
elseif strcmpi(type,'telegraph')
values = {'D',obj.D,'d',obj.dimension,'lambda',-log(obj.meanCosine)/2};
elseif strcmpi(type,'confined')
values = {'D',obj.D,'d',obj.dimension,'Ro',obj.radius};
else
error('Tipo no reconocido')
end
else
error('Tipo tiene formato incorrecto')
end
plotTheoreticalMSD(t,type,values)
set(gcf,'Name',obj.name)
end
function out = radius(obj)
out = obj.pixelSize*sqrt(sum(diag(cov(obj.positions,1))));
end
function out = anisotropy(obj)
eigCov = cov(obj.positions(:,1:2));
out = min(eigCov)/max(eigCov);
end
function varargout = plotScatter(obj,varargin)
if nargout>0
if nargin>1
varargout{1} = plotScatter(obj.pixelSize*obj.positions,varargin{:});
else
varargout{1} = plotScatter(obj.pixelSize*obj.positions);
end
else
if nargin>1
plotScatter(obj.pixelSize*obj.positions,varargin{:})
else
plotScatter(obj.pixelSize*obj.positions)
end
end
end
function obj = setPixelSize(obj)
voltage = obj.journal.ExperimentParameters('Voltage full scale');
voltIndex = (obj.voltageZoom == voltage);
obj.pixelSize = obj.pixelScale(voltIndex);
end
function obj = setStepTime(obj)
obj.stepTime = obj.journal.ParametersForTracking('Period')*...
obj.journal.ParametersForTracking('Rperiods')*...
obj.journal.ParametersForTracking('Z-Period');
end
function obj = setUnits(obj)
try
obj.timeUnit = obj.journal.timeUnit;
catch
end
end
function obj = setName(obj)
[~,fName,~] = fileparts(obj.journal.Path);
obj.name = fName;
end
function out = steps(obj,varargin)
if numel(varargin) == 0
out = obj.pixelSize*diff(obj.positions);
elseif numel(varargin) == 1
switch varargin{1}
case 'x'
out = diff(obj.x);
case 'y'
out = diff(obj.y);
case 'z'
out = diff(obj.z);
case 'XY'
out = diff(obj.XY);
otherwise
end
else
warning('No se puede calcular')
end
end
function out = stepLength(obj,varargin)
norm = @(x) sqrt(sum(x.^2,2));
if numel(varargin) == 1
out = norm(obj.steps(varargin{1}));
elseif numel(varargin) == 0
out = norm(obj.steps);
end
end
function out = stepAngle(obj)
[out ,~] = cart2pol(obj.x,obj.y);
end
function out = D(obj,varargin)
% D es el coeficiente de difusion y es igual a var(pasos)/2
if numel(varargin) == 0
out = 1e6*sum(var(obj.steps))/(2*obj.dimension*obj.stepTime);
elseif numel(varargin) == 1
d = size(obj.steps(varargin{1}),2);
out = 1e6*sum(var(obj.steps(varargin{1})))/(2*d*obj.stepTime);
end
disp(sprintf('D = %.2g ( nm^{2}/s )',out))
end
function out = stepVariance(obj,varargin)
if numel(varargin) == 0
out = var(obj.steps);
elseif numel(varargin) == 1
out = var(obj.steps(varargin{1}));
end
end
function obj = removeZeroLengthStep(obj,varargin)
if numel(varargin) == 0
isZeroLength = (obj.stepLength == 0);
obj.removePoints([false; isZeroLength])
else
isZeroLength = (obj.stepLength(varargin{:}) == 0);
obj.removePoints([false; isZeroLength])
end
end
function out = v(obj,varargin)
norm = @(x) sqrt(sum(x.^2,2));
% v es el coeficiente de difusion y es igual a var(pasos)/2
if numel(varargin) == 0
out = 1e6*norm(obj.meanStep)/obj.stepTime;
elseif numel(varargin) == 1
out = 1e6*norm(obj.meanStep(varargin{1}))/obj.stepTime;
end
disp(sprintf('v = %.2g ( nm/s )',out))
end
function out = meanStep(obj,varargin)
if numel(varargin) == 0
out = mean(obj.steps);
elseif numel(varargin) == 1
out = mean(obj.steps(varargin{1}));
end
end
function out = meanCosine(obj)
angle = stepAngle(obj);
r = mean(exp(1i*diff(angle)));
out = real(r)/sqrt(r*r');
end
function obj = removePoints(obj,pointsIndex)
if numel(obj.originalPositions) == 0;
obj.originalPositions = obj.positions;
end
obj.oldPositions = obj.positions;
obj.positions(pointsIndex,:) = [];
end
function obj = restoreOldPositions(obj)
obj.positions = obj.oldPositions;
obj.oldPositions = [];
end
function obj = restoreOriginalPositions(obj)
obj.positions = obj.originalPositions;
end
function out = msd(obj,fraction)
out = msd(obj.positions,fraction);
end
function sref = subsref(obj,s)
% obj(i) is equivalent to obj.positions(i)
sref = copy(obj);
switch s(1).type
case '.'
sref = builtin('subsref',sref,s);
case '()'
if length(s) < 2
sref.positions = builtin('subsref',sref.positions,s);
sref.segment = struct('byAnisotropy',[],...
'cluster',[],'thread',[],'other',[]);
return
else
sref = builtin('subsref',sref,s);
end
case '{}'
error('randomWalk:subsref',...
'Not a supported subscripted reference')
end
end
function obj = segmentByAnisotropy(obj,varargin)
if isempty(obj.segment.byAnisotropy)
obj.segment.byAnisotropy = segmentByAnisotropy(obj.XY,varargin{:});
else
warning('Ya existen segmentos por anisotropia')
end
% out = obj.segment.byAnisotropy;
end
function obj = segmentCluster(obj,varargin)
if isempty(obj.segment.cluster)
obj.segment.cluster = segmentCluster(obj.XY,varargin{:});
else
warning('Ya existen cúmulos')
end
end
function obj = segmentThread(obj,varargin)
if isempty(obj.segment.thread)
obj.segment.thread = segmentThread(obj.XY,varargin{:});
else
warning('Ya existen filamentos')
end
% out = obj.segment.thread;
end
end
methods %de los segmentos
% function seg_out = getSegment(obj,varargin)
% if nargin > 1
%
% else
% seg_out(obj.segmentos.Nsegmentos) = subcaminata;
% k = 1;
% for i = 1:size(obj.segmentos.Segment,1)
% rang_seg = obj.segmentos.Segment{i,1};
% for j = 1:obj.segmentos.Nsegmentos(rang_seg)
% ind_seg = obj.segmentos.Segment{i,2}(j);
% seg_out(k) = subcaminata(obj.pasos(ind_seg:ind_seg+rang_seg,:),ind_seg);
% k = k + 1;
% end
% end
% end
% end
% function out = msd(obj,varargin)
%
% if nargin>1
% frac = 4;
% rango = 1:obj.Npasos;
% for i = 1:numel(varargin)
% switch varargin{i}
% case 'Segmentos'
% out = cellfun(@MeanSD,obj.getSegment,'UniformOutput',false);
% case 'Clusters'
% out = cellfun(@MeanSD,obj.getCluster,'UniformOutput',false);
% case 'Fraccion'
% frac = varargin{i+1};
% case 'Rango'
% rango = varargin{i+1}:varargin{i+2};
% end
% end
% out = MeanSD(obj.pasos(rango,:),frac);
% else
% out = MeanSD(obj.pasos,4);
% end
%
% end
%
% function out = D(obj,varargin)
%
% end
end
methods %%constructor
%
function obj = randomWalk(val)
if nargin > 0
if ischar(val)
[pathstr,name,~] = fileparts(val);
val = fullfile(pathstr,[name '.txt']);
val = regexprep(val,{'/','\\'},filesep);
end
if ismatrix(val) && isnumeric(val)
if size(val,1)<size(val,2)
obj.positions = val';
else
obj.positions = val;
end
elseif ischar(val) && exist(val,'file') == 2
try
obj.positions = importWalk(fullfile(pathstr,[name '.txt']));
catch
[FileName,PathName,~] = uigetfile;
filePath = fullfile(PathName,FileName);
obj.positions = importWalk(filePath);
end
try
obj.journal = importJournal(fullfile(pathstr,[name '.jrn']));
obj.setUnits();
obj.setPixelSize();
obj.setStepTime();
obj.setName();
catch
warning('No se encontro el journal en el directorio')
end
else
error('No se pudo generar la caminata')
end
else
try
try
[FileName,PathName,~] = uigetfile('.txt');
filePath = fullfile(PathName,FileName);
obj.positions = importWalk(filePath);
try
[pathstr,name,~] = fileparts(filePath);
obj.journal = importJournal(fullfile(pathstr,[name '.jrn']));
catch
warning('No se encontro el journal en el directorio')
end
catch
warning('No se pudo importar la caminata')
end
obj.setUnits();
obj.setPixelSize();
obj.setStepTime();
obj.setName();
catch
warning('Se creo una caminata vacia')
end
end
end
% function addSegment(obj,varargin)
% if nargin == 2
% obj.segmentos = varargin{1};
% else
% if obj.segmentos.isempty
% foo_seg = segmento(segmentacion_j(obj.pasos));
% obj.segmentos = foo_seg;
% end
% end
% end
end
end
function out = changeTimeUnit(time,unit)
% CHANGETIMEUNITS cambia de microsegundos a segundo o minutos
switch unit
case 'us'
out = time;
case 's'
out = time/1e6;
case 'min'
out = time/6e7;
otherwise
warning('Unidad no valida')
end
end