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K_PhaseWave_test.m
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K_PhaseWave_test.m
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classdef K_PhaseWave_test < matlab.unittest.TestCase
%
% clear;close all;clc; testCase=K_PhaseWave_test; res=testCase.run;disp(res);
%
%
% See also
% K_PhaseWave, K_PhaseHist, K_PhaseHist_test, K_plotLinearPhaseHist, ...
% K_plotCircPhaseHist_one
% TODO
properties
testdata1
testdata2
testdata3
end
methods (Test)
function simpleRun(testCase)
% testCase=K_PhaseWave_test; res=testCase.run('simpleRun');disp(res);
import matlab.unittest.constraints.IsEqualTo;
import matlab.unittest.constraints.RelativeTolerance;
import matlab.unittest.constraints.AbsoluteTolerance;
testCase = testCase.prep_testdata;
S = load(testCase.testdata1);
sRate = 1024;
newRate = 1024;
eeg = WaveformChan(S.IpsiEEG);
eegL = eeg.resample(1024);
wide = WaveformChan(S.ME1_LFP);
Wn = normalizedfreq(300,wide.SRate);
[b,a] = butter(5,Wn,'low');
fvtool(b,a,'Fs',wide.SRate);
close
lfp = wide;
lfp.Data = filtfilt(b,a,wide.Data);
high = WaveformChan(S.ME1_Unit);
thre = std(high.Data)*3;
buaL = high.getBUA('highpass thresholding',3,thre);
Wn = normalizedfreq([0.4 1.6],newRate);
[b, a] = butter(2, Wn,'bandpass');
fvtool(b,a,'Fs',newRate);
xlim([0 5]);ylim('auto');
assert(isstable(b,a));
close
%%
% *negate BUA for polarity*
%
% takes 0.8 min by Win
% MacBook cannot cope
[results,handles] = K_PhaseWave(eegL.Data, -buaL.Data, sRate, newRate, b, a);
%% unitrad
% testCase.verifyEqual(fieldnames(results.unitrad),{...
% 'axang';...
% 'axrad';...
% 'histN';...
% 'histnorm';...
% 'unitrad';...
% 'stats';...
% 'cmean';...
% 'rayl';...
% 'raylecdf';...
% 'vlen';...
% 'cvar';...
% 'cstd';...
% ...
% });
%
%
% testCase.verifyThat(results.unitrad.cmean, IsEqualTo(2.2609, ...
% 'Within', AbsoluteTolerance(0.0001)));
%
% testCase.verifyThat(results.unitrad.vlen, IsEqualTo(0.5965, ...
% 'Within', AbsoluteTolerance(0.0001)));
%
% testCase.verifyThat(results.unitrad.rayl, IsEqualTo(4.0034e-66, ...
% 'Within', AbsoluteTolerance(0.0001e-66)));
%
% testCase.verifyThat(results.unitrad.raylecdf, IsEqualTo(3.1961e-68, ...
% 'Within', AbsoluteTolerance(0.0001e-68)));
%
% testCase.verifyThat(results.unitrad.cstd, IsEqualTo(0.8983, ...
% 'Within', AbsoluteTolerance(0.0001)));
%
% testCase.verifyThat(results.unitrad.cvar, IsEqualTo(0.4035, ...
% 'Within', AbsoluteTolerance(0.0001)));
%% eegrad
% testCase.verifyEqual(fieldnames(results.eegrad),{...
% 'axang';...
% 'axrad';...
% 'histN';...
% 'histnorm';...
% 'rayl';...
% 'raylecdf';...
% 'cmean';...
% 'vlen';...
% ...
% });
%
% testCase.verifyThat(results.eegrad.rayl, IsEqualTo(2.7285e-203, ...
% 'Within', AbsoluteTolerance(0.01e-203)));%TODO unstable, AbsoluteTolerance(0.0001e-203) fails
%
% testCase.verifyThat(results.eegrad.raylecdf, IsEqualTo(1, ...
% 'Within', AbsoluteTolerance(0.0001)));
%
% testCase.verifyThat(results.eegrad.cmean, IsEqualTo(0.4419, ...
% 'Within', AbsoluteTolerance(0.0001)));
%
% testCase.verifyThat(results.eegrad.vlen, IsEqualTo(0.0250, ...
% 'Within', AbsoluteTolerance(0.0001)));
%TODO
% 'threshold' option
end
function K_plotLinearPhaseHist_one(testCase)
% testCase=K_PhaseWave_test; res=testCase.run('K_plotLinearPhaseHist_one');disp(res);
testCase = testCase.prep_testdata;
S = load(testCase.testdata1);
sRate = 1/S.unite.interval;
newRate = 1024;
% make filter
getNF = @(freq, Fs) freq/(Fs/2);
[b, a] = butter(2, getNF([0.4, 1.6], newRate));
fvtool(b,a,'Fs',newRate);
xlim([0 5]);ylim('auto');
assert(isstable(b,a));
close
results = K_PhaseWave(eegL.Data, -buaL.Data, sRate, newRate, b,...
'PlotLinear',true,'PlotCirc',true);
hlin = K_plotLinearPhaseWave(results.unitrad.unitrad);
hlin = K_plotLinearPhaseWave(results.unitrad.unitrad, 'color', 'r',...
'plottype','line');
hlin = K_plotLinearPhaseWave(results.unitrad.unitrad, 'color', 'r',...
'plottype','bar');
testCase.verifyError(@()K_plotLinearPhaseHist(results.unitrad.unitrad, ...
'plottype','hoge'),...
'MATLAB:InputParser:ArgumentFailedValidation');
testCase.verifyError(@()K_plotLinearPhaseHist(results.unitrad.unitrad, ...
'Color','f'),...
'MATLAB:InputParser:ArgumentFailedValidation');
testCase.verifyError(@()K_plotLinearPhaseHist(results.unitrad.unitrad, ...
'Color',[0 0]),...
'MATLAB:InputParser:ArgumentFailedValidation');
hlin = K_plotLinearPhaseWave(results.unitrad.unitrad, 'color', 'r',...
'errorbar','std');
hlin = K_plotLinearPhaseWave(results.unitrad.unitrad, 'color', 'r',...
'Title','Neuron 1');
%TODO 'radiansallpoints'
% histc(?)
hlin = K_plotLinearPhaseWave(results.unitrad.unitrad, 'color', 'r',...
'XGrid','off');
hlin = K_plotLinearPhaseWave(results.unitrad.unitrad, 18, 'color', 'k',...
'plottype','bar');
hlin = K_plotLinearPhaseWave(results.unitrad.unitrad, 18, 'color', 'k',...
'rayleighecdf',results.unitrad.raylecdf);
%% axh
figure;
axh = subplot(2,1,1);
hlin = K_plotLinearPhaseWave(axh,results.unitrad.unitrad, 18, 'color', 'k',...
'plottype','bar');
close all
%% Event with no spike
nospk = false(size(S.onset.values));
[results,handles] = testCase.verifyWarning(@() K_PhaseHist(nospk, S.IpsiEEG.values, sRate,...
newRate, b, a,'plotECDF',true,'PlotLinear',true,'PlotCirc',true),...
'K:K_plotLinearPhaseHist:radians:empty');
hlin = testCase.verifyWarning(@() K_plotLinearPhaseWave(results.unitrad.unitrad),...
'K:K_plotLinearPhaseHist:radians:empty');
%TODO should it at least create axes?
%TODO what about circuler?
%TODO K_plotLinearPhaseHist and
% K_plotCircPhaseHist_one/K_plotCircPhaseHist_group should be
% renamed as
% K_PhaseHist_plotLinear and
% K_PhaseHist_plotCircOne/K_PhaseHist_plotCircGroup
end
% function K_plotLinearPhaseHist_group(testCase)
% % testCase=K_PhaseWave_test; res=testCase.run('K_plotLinearPhaseHist_group');disp(res);
%
% testCase = testCase.prep_testdata;
%
% S1 = load(testCase.testdata1);
% S2 = load(testCase.testdata2);
% S3 = load(testCase.testdata3);
%
% S1.sRate = 1/S1.unite.interval;
% newRate = 1024;
%
% % make filter
% getNF = @(freq, Fs) freq/(Fs/2);
% [b, a] = butter(2, getNF([0.4, 1.6], newRate));
% fvtool(b,a,'Fs',newRate);
% xlim([0 5]);ylim('auto');
% assert(isstable(b,a));
% close
%
% results1 = K_PhaseHist(S1.onset.values, S1.IpsiEEG.values, 1/S1.unite.interval, newRate, b, a);
% results2 = K_PhaseHist(S2.onset.values, S2.IpsiEEG.values, 1/S2.unite.interval, newRate, b, a);
% results3 = K_PhaseHist(S3.onset.values, S3.IpsiEEG.values, 1/S3.unite.interval, newRate, b, a);
%
% radians = {results1.unitrad.unitrad,results2.unitrad.unitrad,results3.unitrad.unitrad};
%
% raylecdf = [results1.unitrad.raylecdf,results2.unitrad.raylecdf,results3.unitrad.raylecdf];
%
% h = K_plotLinearPhaseHist(radians,18);
%
% h = K_plotLinearPhaseHist(radians,18,'PlotType','bar');
%
% h = K_plotLinearPhaseHist(radians,18,'Errorbar','std');
%
% h = K_plotLinearPhaseHist(radians,18,'Errorbar','sem');
%
% h = K_plotLinearPhaseHist(radians,18,'PlotType','bar','Errorbar','std');
% h = K_plotLinearPhaseHist(radians,18,'PlotType','bar','Errorbar','sem');
%
% h = K_plotLinearPhaseHist(radians,18,'rayleighecdf',raylecdf);
%
%
%
% %% Identical three data
% radians2 = {results1.unitrad.unitrad,results1.unitrad.unitrad,results1.unitrad.unitrad};
%
% h = K_plotLinearPhaseHist(radians2,18,'Errorbar','std');
%
% h = K_plotLinearPhaseHist(radians2,18,'PlotType','bar','Errorbar','std');
%
% close all
% end
% function testCircularPhasePlot_one(testCase)
% % testCase=K_PhaseWave_test; res=testCase.run('testCircularPhasePlot_one');disp(res);
%
% testCase = testCase.prep_testdata;
%
% S = load(testCase.testdata1);
% sRate = 1/S.unite.interval;
% newRate = 1024;
%
% % make filter
% getNF = @(freq, Fs) freq/(Fs/2);
% [b, a] = butter(2, getNF([0.4, 1.6], newRate));
% fvtool(b,a,'Fs',newRate);
% xlim([0 5]);ylim('auto');
% assert(isstable(b,a));
% close
%
% [results,handles] = K_PhaseHist(S.onset.values, S.IpsiEEG.values, sRate,...
% newRate, b, a,'plotECDF',true,'PlotLinear',true,'PlotCirc',true);
%
% radians = results.unitrad.unitrad;
%
% hcirc = K_plotCircPhaseHist_one(radians);
%
% hcirc = K_plotCircPhaseHist_one(radians, 18, 'color', 'g');
%
% hcirc = K_plotCircPhaseHist_one(radians,'Direction','anti');
%
% hcirc = K_plotCircPhaseHist_one(radians,'ZeroPos','bottom');
%
% hcirc = K_plotCircPhaseHist_one(radians,'HistLimPercent',20);
%
% %% axh
% figure;
% axh = subplot(2,1,1);
% hcirc = K_plotCircPhaseHist_one(axh,radians);
%
% end
% function testCircularPhasePlot_group(testCase)
% % testCase=K_PhaseWave_test; res=testCase.run('testCircularPhasePlot_group');disp(res);
%
% testCase = testCase.prep_testdata;
%
% S1 = load(testCase.testdata1);
% S2 = load(testCase.testdata2);
% S3 = load(testCase.testdata3);
%
% S1.sRate = 1/S1.unite.interval;
% newRate = 1024;
%
% % make filter
% getNF = @(freq, Fs) freq/(Fs/2);
% [b, a] = butter(2, getNF([0.4, 1.6], newRate));
% fvtool(b,a,'Fs',newRate);
% xlim([0 5]);ylim('auto');
% assert(isstable(b,a));
% close
%
% results1 = K_PhaseHist(S1.onset.values, S1.IpsiEEG.values, 1/S1.unite.interval, newRate, b, a);
% results2 = K_PhaseHist(S2.onset.values, S2.IpsiEEG.values, 1/S2.unite.interval, newRate, b, a);
% results3 = K_PhaseHist(S3.onset.values, S3.IpsiEEG.values, 1/S3.unite.interval, newRate, b, a);
%
% radians = {results1.unitrad.unitrad,results2.unitrad.unitrad,results3.unitrad.unitrad};
%
% raylecdf = [results1.unitrad.raylecdf,results2.unitrad.raylecdf,results3.unitrad.raylecdf];
%
% h = K_plotCircPhaseHist_group(radians);
%
% h = K_plotCircPhaseHist_group(radians,'Groupmean','on');
%
%
% h = K_plotCircPhaseHist_group(radians,'Direction','anti');
%
% h = K_plotCircPhaseHist_group(radians,'ZeroPos','bottom');
%
% h = K_plotCircPhaseHist_group(radians,'ZeroPos','right','Direction','anti');
%
% end
% function testECDF(testCase)
% %TODO
% end
%
%
% function testBadFilter(testCase)
% % testCase=K_PhaseWave_test; res=testCase.run('testBadFilter');disp(res);
%
% testCase = testCase.prep_testdata;
%
% S = load(testCase.testdata1);
% sRate = 1/S.unite.interval;
% newRate = 1024;
%
% % make filter
% getNF = @(freq, Fs) freq/(Fs/2);
% [b, a] = butter(2, getNF([0.4, 1.6], newRate));
% fvtool(b,a,'Fs',newRate);
% xlim([0 5]);ylim('auto');
% assert(isstable(b,a));
% close
%
% results = K_PhaseHist(S.onset.values, S.IpsiEEG.values, sRate, newRate, b, a);
%
% testCase.verifyEqual(fieldnames(results),{...
% 'unitrad';...
% 'eegrad';...
% 'eegpwelch';...
% 'eegpwelchLow';...
% 'ue_lres';...
% 'ue_hres';...
% ...
% });
%
% testCase.verifyEqual(fieldnames(results.unitrad),{...
% 'axang';...
% 'axrad';...
% 'histN';...
% 'histnorm';...
% 'unitrad';...
% 'stats';...
% 'cmean';...
% 'rayl';...
% 'raylecdf';...
% 'vlen';...
% 'cvar';...
% 'cstd';...
% ...
% });
%
%
% results = K_PhaseHist(S.onset.values, S.IpsiEEG.values, sRate, newRate, b, a);
%
%
%
% %TODO how to validate the results?
% % examine results?
% % examine plot?
%
%
% end
end
methods
function testCase = prep_testdata(testCase)
startdir = fileparts(which('startup'));
endind = regexp(startdir,regexptranslate('escape','Private_Dropbox'),'end');
if ~isempty(endind)
testCase.testdata1 = fullfile(startdir(1:endind),...
'Kouichi MATLAB data','thalamus','S potentials','HF pauser',...
'PC','SWA','kjx021i01_i02_spliced.mat');
testCase.testdata2 = fullfile(startdir(1:endind),...
'Kouichi MATLAB data','thalamus','S potentials','HF pauser',...
'PC','SWA','kjx040e01e02spliced.mat'); %TODO for group analysis
testCase.testdata3 = fullfile(startdir(1:endind),...
'Kouichi MATLAB data','thalamus','S potentials','HF pauser',...
'PC','SWA','kjx019f02@300-828.mat'); %TODO for group analysis
else
error('move to the folder "%s"',fullfile('Kouichi MATLAB data','thalamus'))
end
end
end
end
function local
%K_PhaseHist_script
clear;close all;clc;
load('Z:\Dropbox\Private_Dropbox\Kouichi MATLAB data\thalamus\S potentials\HF pauser\PC\SWA\kjx021i01_i02_spliced.mat');
srate = 1/unite.interval;
smalle_ts= EventChan(smalle.values, 0, srate, 'smalle');
eegw_ts = WaveformChan(IpsiEEG.values, 0, srate, 'eeg');
unite_ts = EventChan(unite.values, 0, srate, 'unite');
onset_ts = EventChan(onset.values, 0, srate, 'onset');
newRate = 1024;
% make filter
getNF = @(freq, srate) freq/(srate/2);
[b, a] = butter(2, getNF([0.4, 1.6], newRate));
[results] = K_PhaseHist(onset_ts.Data, eegw_ts.Data, srate, newRate, b, a);
[results, handles] = K_PhaseHist(onset_ts.Data, eegw_ts.Data, srate, newRate, b, a,...
'plotECDF', true);
[results] = K_PhaseHist(onset_ts.Data, eegw_ts.Data, srate, newRate, b, a,...
'plotLinear', true);
[results] = K_PhaseHist(onset_ts.Data, eegw_ts.Data, srate, newRate, b, a,...
'plotCirc', true);
u = results.unitrad;
%method plotPhaseHist
[results] = onset_ts.plotPhaseHist(eegw_ts, 'plotECDF', true); %TODO to be implemented into a test case
% threshold
[results] = onset_ts.plotPhaseHist(eegw_ts, 'threshold', [0.02, 0.25], 'plotECDF', true);
%% transform [-pi, pi] to [0, 4*pi]
twopi = @(x) circshift(repmat(x, 2, 1), round(size(x, 1)/2));
ang2rad = @(x) x * pi /180;
rad2ang = @(x) x/pi*180;
%% plot linear phase histogram
ax(1) = subplot('Position', [0.13, 0.11, 0.775, 0.75]);
ax(2) = subplot('Position', [0.13, 0.87, 0.775, 0.10]);
x = twopi(u.axrad);
x = round(rad2ang(unwrap([x(end);x;x(1)]))); % 2 cylces + alpha
y = twopi(u.histnorm*100);
y = [y(end); y; y(1)]; % 2 cylces + alpha
lh1= plot(ax(1), x, y, 'LineWidth', 2);
xtic = cellfun(@(x) [num2str(x), '?'], num2cell(0:90:720), 'UniformOutput', false);
set(ax(1), 'TickDir', 'out', 'Box', 'off',...
'XTick', 0:90:720, 'XTickLabel', xtic,...
'XLim', [0, 720]);
hold(ax(1)) % doesn't work
lh2= plot(ax(1),[90:90:720;90:90:720], ylim(ax(1))', 'Color', [0.5 0.5 0.5]);
uistack (lh2, 'bottom');
xlabel(ax(1),'Phase');
ylabel(ax(1), 'Firing Probabiliy per 10? [%]');
%% subplot for cosine curve
x2 = linspace(0, 720, 1440);
y2 = cos(ang2rad(x2));
plot(ax(2), x2, y2, 'Color' , 'k', 'LineWidth', 2);
set(ax(2), 'Visible', 'off', 'XLim', [0, 720], 'YLim', [-1.1, 1.1]);
%% plot linear phase histogram
h = K_plotLinearPhaseHist(u.unitrad, 72);
%% plot circular phase histogram
% h = CircularPlotSingle_KCN(cmean, veclen, radians, color1, axh, omitcircles, zero_pos, direction)
% h = K_circularPlot_oneCell(u.unitrad);
% h = K_circularPlot_oneCell(u.unitrad, 'Color', 'g',...
% 'zeropos', 'bottom', 'dir', 'anti');
% h = K_circularPlot_oneCell(gca, u.unitrad);
% h = K_circularPlot_oneCell(u.unitrad, 'Histbin', 36);
% h = K_circularPlot_oneCell(u.unitrad, 'Histbin', 36, 'HistLimPercent', 12);
% h = K_circularPlot_oneCell(u.unitrad, 'Histbin', 36, 'HistLimPercent', 0);
%% built-in plots
rose(u.unitrad)
pol = polar(u.unitrad,ones(size(u.unitrad)));
set(pol, 'LineStyle', 'none', 'Marker', 'o')
circ_plot(u.unitrad, 'pretty');
circ_plot(u.unitrad, 'hist');
circ_plot(u.unitrad, 'density');
%%
datacell = [fieldnames(results)';...
struct2cell(results)'];
data = cell2dataset(datacell, 'ObsName', {'kjx021i'})
openvar('data');
datacell(2, 11)
end