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displayEventsProtocols.m
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displayEventsProtocols.m
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cleanUp
%% User input
params
recID = 'p108b';
for interval = 1:2
if interval == 1
noiseFile = fullfile(dataRepo,recFolder,recID, 'p108b_0019_sw1-5.abf');
targetFile = fullfile(dataRepo,recFolder,recID,'abf', 'algorithm_performance_data__amp0p3_sAmp0p05_n4000_RT0p5_sRT2p8_rho0_thr0p1_noiseScaleFactor1_smoothWindow1p5__11_Jan_2021_13_56_48_0001.abf');
targetRawFile = fullfile(dataRepo,recFolder,recID,'abf_raw', 'algorithm_performance_data__amp0p3_sAmp0p05_n4000_RT0p5_sRT2p8_rho0_thr0p1_noiseScaleFactor1_smoothWindow1p5__11_Jan_2021_13_56_48_0001.abf');
eventFileSim = fullfile(dataRepo,recFolder,recID,'mat_minis', 'algorithm_performance_data__amp0p3_sAmp0p05_n4000_RT0p5_sRT2p8_rho0_thr0p1_noiseScaleFactor1_smoothWindow1p5__11_Jan_2021_13_56_48.mat');
eventFileMiniAnalysis = fullfile(dataRepo,recFolder,recID,'mat_MA', 'algorithm_performance_data__amp0p3_sAmp0p05_n4000_RT0p5_sRT2p8_rho0_thr0p1_noiseScaleFactor1_smoothWindow1p5__11_Jan_2021_13_56_48_MiniAnalysis.mat');
eventFilepClampRaw = fullfile(dataRepo,recFolder,recID,'mat_pC_raw', 'algorithm_performance_data__amp0p3_sAmp0p05_n4000_RT0p5_sRT2p8_rho0_thr0p1_noiseScaleFactor1_smoothWindow1p5__11_Jan_2021_13_56_48_pClamp.mat');
elseif interval == 2
noiseFile = fullfile(dataRepo,recFolder,recID, 'p108b_0019_sw1-5.abf');
targetFile = fullfile(dataRepo,recFolder,recID,'abf', 'algorithm_performance_data__amp0p3_sAmp0p05_n8000_RT0p5_sRT2p8_rho0_thr0p1_noiseScaleFactor1_smoothWindow1p5__11_Jan_2021_13_57_31_0001.abf');
targetRawFile = fullfile(dataRepo,recFolder,recID,'abf_raw', 'algorithm_performance_data__amp0p3_sAmp0p05_n8000_RT0p5_sRT2p8_rho0_thr0p1_noiseScaleFactor1_smoothWindow1p5__11_Jan_2021_13_57_31_0001.abf');
eventFileSim = fullfile(dataRepo,recFolder,recID,'mat_minis', 'algorithm_performance_data__amp0p3_sAmp0p05_n8000_RT0p5_sRT2p8_rho0_thr0p1_noiseScaleFactor1_smoothWindow1p5__11_Jan_2021_13_57_31.mat');
eventFileMiniAnalysis = fullfile(dataRepo,recFolder,recID,'mat_MA', 'algorithm_performance_data__amp0p3_sAmp0p05_n8000_RT0p5_sRT2p8_rho0_thr0p1_noiseScaleFactor1_smoothWindow1p5__11_Jan_2021_13_57_31_MiniAnalysis.mat');
eventFilepClampRaw = fullfile(dataRepo,recFolder,recID,'mat_pC_raw', 'algorithm_performance_data__amp0p3_sAmp0p05_n8000_RT0p5_sRT2p8_rho0_thr0p1_noiseScaleFactor1_smoothWindow1p5__11_Jan_2021_13_57_31_pClamp.mat');
end
yRange = [-60.55 -53.45];
%% Load files
[noiseProperties, dt, sweepDuration] = loadabfWrap(noiseFile);
targetProperties = loadabfWrap(targetFile);
targetRawProperties = loadabfWrap(targetRawFile);
load(eventFileSim);
%% Get noise voltage traces
noiseRawSweep = noiseProperties.sweep;
filtN.state = filtering.state;
filtN.nSweeps = noiseProperties.hd.lActualEpisodes;
filtN.excludedTimes = filtering.noiseExcludedTimes;
scaleFactorIndStart = strfind(targetRawFile,'noiseScaleFactor') + 16;
scaleFactorIndEnd = strfind(targetRawFile,'smoothWindow') - 2;
scaleFactor = targetRawFile(scaleFactorIndStart:scaleFactorIndEnd);
scaleFactor = strrep(scaleFactor, 'p', '.');
scaleFactor = str2double(scaleFactor);
[noiseSweep, ~, f2] = filterMinis(noiseRawSweep, dt, filtN, true);
close(f2);
noiseMean = mean(noiseSweep);
noiseSweep = (noiseSweep-noiseMean).*scaleFactor + noiseMean;
%% Estimate the baseline
time = (1:numel(noiseSweep)).*dt;
excludedInds = false(size(time));
excludedInds(round(excludedTimes./dt)+1) = true;
d = designFilterLP(0.05, 0.075, 0.5, 16, 1000/dt);
baseline = filtfilt(d, double(noiseSweep(~excludedInds)));
baselineInterp = interp1(time(~excludedInds), baseline, time, 'linear','extrap');
averagingWindowSize = 8000/dt;
baselineSmooth = movmean(baselineInterp, averagingWindowSize, 'EndPoints','shrink');
%figure; plot(time,baselineSmooth);
%% Get target and simulation voltage traces
targetSweep = targetProperties.sweep;
targetRawSweep = targetRawProperties.sweep;
simulationSweep = targetRawSweep - noiseSweep;
downwardShift = 0;
simulationSweepAdjusted = simulationSweep+baselineSmooth - (mean(simulationSweep+baselineSmooth) - mean(noiseSweep)) - downwardShift;
%% Position the noise target traces
downwardShift = 1.1;
detectionParameters.sampleInterval = noiseProperties.dt;
detectionParameters.smoothWindow = round(detectionParameters.smoothWindow/detectionParameters.sampleInterval);
waveform.estimate = false;
options.summaryPlot = false;
options.edit = false;
[~, ~, ~, ~, ~, noiseSweepSmooth] = detectMinis(noiseRawSweep, excludedTimes, detectionParameters, filtN, waveform, 4, options); %#ok<*ASGLU>
noiseSweepAdjusted = noiseSweepSmooth - 0.5*downwardShift;
targetSweepAdjusted = targetSweep - (mean(targetSweep) - mean(noiseSweep)) - 1.5*downwardShift;
%% Display voltage traces
lineWidth = 2;
% figure; plot(time,noiseSweep, 'b'); hold on
targetSweep1 = targetSweep - (mean(targetSweep) - mean(noiseSweep)) - 2.5*downwardShift;
fH = figure('Units', 'Normalized', 'Position', [0.005 0.06 0.99 0.83], 'GraphicsSmoothing','on');
set(0, 'DefaultFigureRenderer', 'painters');
%plot(time,targetSweep1, 'b', 'LineWidth',lineWidth); hold on
plot(time,targetSweep1, 'Color',matlabColours(8), 'LineWidth',lineWidth*(2/3)); hold on
targetSweep2 = targetSweep - (mean(targetSweep) - mean(noiseSweep)) - 3.5*downwardShift;
%plot(time,targetSweep2, 'b', 'LineWidth',lineWidth);
plot(time,targetSweep2, 'r', 'LineWidth',lineWidth*(2/3));
targetSweep3 = targetSweep - (mean(targetSweep) - mean(noiseSweep)) - 4.5*downwardShift;
%plot(time,targetSweep3, 'b', 'LineWidth',lineWidth);
plot(time,targetSweep3, 'm', 'LineWidth',lineWidth*(2/3));
plot(time, simulationSweepAdjusted, 'k', 'LineWidth',lineWidth);
plot(time, noiseSweepAdjusted, 'k', 'LineWidth',lineWidth);
plot(time, targetSweepAdjusted, 'k', 'LineWidth',lineWidth);
%yRange = ylim;
ylim(yRange);
%% Get event info
load(eventFileSim);
fileOrder = str2double(targetFile(end-4));
allTrue = performance{fileOrder}(1,:);
%% Mark simulated and noise events
shift = 0.2;
xLim = xlim;
yLim = ylim;
allTrueInds = find(allTrue);
for iEvent = 1:numel(allTrueInds)
plot([time(allTrueInds(iEvent)) time(allTrueInds(iEvent))],[yLim(2)-2*downwardShift yLim(2)] + shift, 'g:', 'LineWidth',2);
% plot([time(allTrueInds(iEvent)) time(allTrueInds(iEvent))],[yLim(2)-3.5*downwardShift yLim(2)-2.5*downwardShift] + shift, 'g:', 'LineWidth',1);
plot([time(allTrueInds(iEvent)) time(allTrueInds(iEvent))],[yLim(2)-7*downwardShift yLim(2)-2.5*downwardShift] + shift, 'g:', 'LineWidth',2);
end
for iEvent = 1:numel(falseI)
% plot([time(falseI(iEvent)) time(falseI(iEvent))],[yLim(2)-3.5*downwardShift yLim(2)-2*downwardShift] + shift, 'c:', 'LineWidth',1);
plot([time(falseI(iEvent)) time(falseI(iEvent))],[yLim(2)-7*downwardShift yLim(2)-2*downwardShift] + shift, 'c:', 'LineWidth',2);
end
for iEvent = 1:numel(allTrueInds)
ciplot([yLim(2) yLim(2)] -2*downwardShift + shift, [yLim(2) yLim(2)] + shift, [time(allTrueInds(iEvent))-5 time(allTrueInds(iEvent))+5], [230 255 230]./255, 1);
% ciplot([yLim(2) yLim(2)] -3.5*downwardShift + shift, [yLim(2) yLim(2)] -2.5*downwardShift + shift, [time(allTrueInds(iEvent))-5 time(allTrueInds(iEvent))+5], 'g', 0.1);
ciplot([yLim(2) yLim(2)] -7*downwardShift + shift, [yLim(2) yLim(2)] -2.5*downwardShift + shift, [time(allTrueInds(iEvent))-5 time(allTrueInds(iEvent))+5], [230 255 230]./255, 1);
end
for iEvent = 1:numel(falseI)
% ciplot([yLim(2) yLim(2)] -3.5*downwardShift + shift, [yLim(2) yLim(2)] -2*downwardShift + shift, [time(falseI(iEvent))-5 time(falseI(iEvent))+5], 'c', 0.1);
p = ciplot([yLim(2) yLim(2)] -7*downwardShift + shift, [yLim(2) yLim(2)] -2*downwardShift + shift, [time(falseI(iEvent))-5 time(falseI(iEvent))+5], [230 255 255]./255, 1);
end
set(gca, 'Children', flipud(get(gca, 'Children')))
%% Mark detected events by minis
markerSize = 20;
lineWidth = 1.25;
markerFaceColourHits = 'none';
markerFaceColourFA = 'none';
truePositive = performance{fileOrder}(4,:);
pHit = plot(time(logical(truePositive)), targetSweep1(logical(truePositive)),...
'g^', 'MarkerFaceColor',markerFaceColourHits, 'MarkerEdgeColor',matlabColours(9), 'MarkerSize',markerSize, 'Linewidth',lineWidth);
falsePositive = performance{fileOrder}(6,:);
pFA = plot(time(logical(falsePositive)), targetSweep1(logical(falsePositive)),...
'r^', 'MarkerFaceColor',markerFaceColourFA, 'MarkerSize',markerSize, 'Linewidth',lineWidth);
falseNegative = performance{fileOrder}(5,:);
pMiss = plot(time(logical(falseNegative)), targetSweep1(logical(falseNegative)), 'ro', 'MarkerSize',markerSize, 'Linewidth',lineWidth);
trueNegative = performance{fileOrder}(7,:);
pCR = plot(time(logical(trueNegative)), targetSweep1(logical(trueNegative)), 'x', 'Color',matlabColours(11), 'MarkerSize',markerSize+5, 'Linewidth',lineWidth*2); %#ok<*NASGU>
%% Mark detected events by Mini Analysis
load(eventFileMiniAnalysis);
truePositive = performance{fileOrder}(4,:);
plot(time(logical(truePositive)), targetSweep2(logical(truePositive)),...
'g^', 'MarkerFaceColor',markerFaceColourHits, 'MarkerEdgeColor',matlabColours(9), 'MarkerSize',markerSize, 'Linewidth',lineWidth);
falsePositive = performance{fileOrder}(6,:);
plot(time(logical(falsePositive)), targetSweep2(logical(falsePositive)),...
'r^', 'MarkerFaceColor',markerFaceColourFA, 'MarkerSize',markerSize, 'Linewidth',lineWidth);
falseNegative = performance{fileOrder}(5,:);
plot(time(logical(falseNegative)), targetSweep2(logical(falseNegative)), 'ro', 'MarkerSize',markerSize, 'Linewidth',lineWidth);
trueNegative = performance{fileOrder}(7,:);
plot(time(logical(trueNegative)), targetSweep2(logical(trueNegative)), 'x', 'Color',matlabColours(11), 'MarkerSize',markerSize+5, 'Linewidth',lineWidth*2);
%% Mark detected events in unsmoothed data by pClamp
load(eventFilepClampRaw);
truePositive = performance{fileOrder}(4,:);
plot(time(logical(truePositive)), targetSweep3(logical(truePositive)),...
'g^', 'MarkerFaceColor',markerFaceColourHits, 'MarkerEdgeColor',matlabColours(9), 'MarkerSize',markerSize, 'Linewidth',lineWidth, 'Linewidth',lineWidth);
falsePositive = performance{fileOrder}(6,:);
plot(time(logical(falsePositive)), targetSweep3(logical(falsePositive)),...
'r^', 'MarkerFaceColor',markerFaceColourFA, 'MarkerSize',markerSize, 'Linewidth',lineWidth);
falseNegative = performance{fileOrder}(5,:);
plot(time(logical(falseNegative)), targetSweep3(logical(falseNegative)), 'ro', 'MarkerSize',markerSize, 'Linewidth',lineWidth);
trueNegative = performance{fileOrder}(7,:);
pCR = plot(time(logical(trueNegative)), targetSweep3(logical(trueNegative)), 'x', 'Color',matlabColours(11), 'MarkerSize',markerSize+5, 'Linewidth',lineWidth*2);
hold off
%legend([pHit pFA pMiss], {'Hit','False alarm','Miss'});
%legend boxoff
%% Save trace chunk images
[abfFilePath, imageFileName] = fileparts(targetFile);
recordingPath = fileparts(abfFilePath);
loopSize = 2000; %ms
%imageLoop(fH, loopSize, time, recordingPath, imageFileName, yLim);
imageChunk(fH, getChunkTimes(), recordingPath, imageFileName, yLim);
%% Tidy and save the figure
%legend([pHit pFA pMiss], {'Hit','False alarm','Miss'});
%legend boxoff
yWindowSize = 4.2;
yShift = 0.25;
yLim = yRange;
xLim = [0 time(end)];
ax1 = axesProperties({}, 1, 'normal', 'off', 'w', 'Calibri', 12, 4/3, 2, [0.005 0], 'out',...
'off', 'w', {}, xLim, xticks,...
'off', 'w', {}, yLim, yticks);
[abfFilePath, imageFileName] = fileparts(targetFile);
recordingPath = fileparts(abfFilePath);
figFileName = [imageFileName '_interv_' num2str(xLim(1)) '_' num2str(xLim(2))...
'_voltage_range_' num2str(yLim(1)) '_' num2str(yLim(2))];
set(fH, 'Name',figFileName);
voltageTraceFolder = [recordingPath filesep 'traces'];
if ~exist(voltageTraceFolder, 'file')
mkdir(voltageTraceFolder);
end
figFileName = [voltageTraceFolder filesep figFileName];
label = [0 0];
margin = [0 0];
width = 15-label(1)-margin(1);
height = 1.5*15-label(2)-margin(2);
paperSize = resizeFig(fH, ax1, width, height, label, margin, 0);
%exportFig(fH, [figFileName '.png'],'-dpng','-r300', paperSize);
%exportFig(fH, [figFileName '.eps'],'-depsc','-r1200', paperSize);
hgsave(gcf, [figFileName '.fig']);
end
close all
%% Local functions
function [fileProperties, dt, sweepDuration] = loadabfWrap(filename)
fileProperties = loadABF(filename);
dt = fileProperties.dt;
sweepDuration = (length(fileProperties.sweep)*dt - dt)/fileProperties.hd.lActualEpisodes;
end
function imageLoop(fH, loopSize, time, recordingPath, imageFileName, yLim) %#ok<*DEFNU>
nChunks = ceil(time(end)/loopSize);
for iChunk = 1:nChunks
if iChunk == nChunks
chunkTime = [(iChunk-1)*loopSize time(end)];
else
chunkTime = [(iChunk-1)*loopSize iChunk*loopSize];
end
xlim(chunkTime);
xLim = xlim;
figFileName = [imageFileName '_time_interval_' num2str(xLim(1)) '_' num2str(xLim(2))...
'_voltage_range_' num2str(yLim(1)) '_' num2str(yLim(2))];
set(fH, 'Name',figFileName);
voltageTraceFolder = [recordingPath filesep 'traces'];
if ~exist(voltageTraceFolder, 'file')
mkdir(voltageTraceFolder);
end
figFileName = [voltageTraceFolder filesep figFileName]; %#ok<*AGROW>
saveas(fH, [figFileName '.png'], 'png');
end
end
function chunkTimes = getChunkTimes()
%chunkTimes = [26850 28250];
%chunkTimes = [26940 27670];
%chunkTimes = [12100 13400];
chunkTimes = [12570 13350];
end
function imageChunk(fH, chunkTimes, recordingPath, imageFileName, yLim)
%legend boxoff
for iChunk = 1:size(chunkTimes,1)
xlim(chunkTimes(iChunk,:));
xLim = xlim;
figFileName = [imageFileName '_interv_' num2str(xLim(1)) '_' num2str(xLim(2))...
'_voltage_range_' num2str(yLim(1)) '_' num2str(yLim(2))];
set(fH, 'Name',figFileName);
voltageTraceFolder = [recordingPath filesep 'traces'];
if ~exist(voltageTraceFolder, 'file')
mkdir(voltageTraceFolder);
end
figFileName = [voltageTraceFolder filesep figFileName]; %#ok<*AGROW>
label = [0 0];
margin = [0 0];
width = ((chunkTimes(iChunk,2)-chunkTimes(iChunk,1))/1000)*60-label(1)-margin(1);
height = 2*15-label(2)-margin(2);
paperSize = resizeFig(fH, gca, width, height, label, margin, 0);
%savefig(fH, [figFileName '.fig'], 'compact');
set(gca, 'Box', 'off');
set(gca, 'TickLength', [0; 0]);
exportFig(fH, [figFileName '.png'],'-dpng','-r300', paperSize);
exportFig(fH, [figFileName '.eps'],'-depsc','-r1200', paperSize);
end
end