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Start.m
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Start.m
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% DESCRIPTION
% Script to start the application. Conntains all the parametrs settings.
%
% NOTES:
%
% RELEASE VERSION: 0.6
%
% AUTHORS: Satya Arjunan ([email protected])
% Anton Shpak ([email protected])
%
% DATE: February 2020
%% include subfolders
addpath Lib
addpath Utils
addpath IO
addpath Analysers
addpath Entities
addpath Entities/Base
addpath Entities/Settings
addpath Entities/Signal
addpath Entities/Enums
%% load data
options = {'Parallel analyse csv files', 'Sequential analyse csv files',...
'Analyse a csv file'};
selection = listdlg('PromptString', 'What would you like to do?',...
'SelectionMode', 'single', 'ListString', options);
doubleFileSep = strcat(filesep, filesep);
% If analyse multiple files
if (selection == 1 | selection == 2)
% Select a folder containing all csv data files
folder = uigetdir(pwd, "Select folder containing csv data files");
% return if user pressed cancel button
if (folder == 0)
return
end
% Exit program if no csv files found in the folder
csv_files = dir(fullfile(folder, '*.csv'));
if (length(csv_files) == 0)
Log.ErrorMessage(0,...
strcat("Error: No csv files found in the selected folder, ",...
folder, ", exiting."));
return
end
% Analyse each csv file in the folder
% In parallel
if (selection == 1)
totalStartTime = Log.StartBlock(0,...
strcat("Started parallel KIC data analysis of ",...
num2str(length(csv_files)), " file(s)"));
parfor i = 1:length(csv_files)
fileFullName = strrep(strrep(string(fullfile(folder,...
csv_files(i).name)), doubleFileSep, filesep), filesep, doubleFileSep);
analyse_csv_file(fileFullName);
end
Log.EndBlock(totalStartTime, 0,...
strcat("Finished parallel KIC data analysis of ",...
num2str(length(csv_files)), " file(s)"));
% Sequentially
else
totalStartTime = Log.StartBlock(0,...
strcat("Started sequential KIC data analysis of ",...
num2str(length(csv_files)), " file(s)"));
for i = 1 : length(csv_files)
fileFullName = strrep(strrep(string(fullfile(folder,...
csv_files(i).name)), doubleFileSep, filesep), filesep, doubleFileSep);
analyse_csv_file(fileFullName);
end
Log.EndBlock(totalStartTime, 0,...
strcat("Finished sequential KIC data analysis of ",...
num2str(length(csv_files)), " file(s)"));
end
% If analyse a single file
elseif (selection == 3)
[file, folder] = uigetfile('*.csv');
% return if user pressed cancel button
if (file == 0)
return
end
fileFullName = strrep(strrep(string(fullfile(folder, file)), doubleFileSep, filesep),...
filesep, doubleFileSep);
[~, ~, fileExt] = fileparts(fileFullName);
if (~isequal(fileExt, ".csv"))
Log.ErrorMessage(0, "Error: Please, select a *.csv file");
return
end
analyse_csv_file(fileFullName);
% Return if cancelled file or folder selection
else
return
end
function analyse_csv_file(fileFullName)
clearvars -except fileFullName
%% start timer
fileStartTime = Log.StartBlock(1, strcat("Started analysis of one file '", fileFullName, "'"));
%% read data from file to table
tableData = FileReader.ReadFileToTable(fileFullName);
%% initialize Sampling
% Watch out - Sampling and Stimulation initialization order
Sampling.Init(mean(diff(table2array(tableData(:, 1)))));
% 1. SignalType:
%pulseDetection_signalType = SignalType.Calcium; % <--- PARAMETER
pulseDetection_signalType = SignalType.Voltage; % <--- PARAMETER
% 2. Stimulation parameters
% voltage example
stimuliPeriod_ms = 1000; % <--- PARAMETER
stimuliNumber = 10; % <--- PARAMETER
stimulationStart_ms = 5000; % <--- PARAMETER
stimulusPulseDuration_ms = 7.5;
%% calcium example
%stimuliPeriod_ms = 1670; % <--- PARAMETER
%stimuliNumber = 9; % <--- PARAMETER
%stimulationStart_ms = 5000; % <--- PARAMETER
%stimulusPulseDuration_ms = 7.5;
% 3. PulseDetection Parameters
% threshold to detect pulses
pulseDetection_thresholdPercentage = 20; % <--- PARAMETER
% part of signal at start to ignore
pulseDetection_numberOfSecondsAtStartToIgnore = 0; % <--- PARAMETER
% specify params for false pulses removal
pulseDetection_removeFalsePulses_PeakThresholdPercentage = 25;
pulseDetection_removeFalsePulses_DurationThresholdPercentage = 25;
% specify params for wavelet for Upstroke Detection
pulseDetection_denoise_waveletName = "bior"; % use biorthogonal wavelet
pulseDetection_denoise_waveletNumber = 6.8;
pulseDetection_denoise_waveletThresholdRule = "Hard";
% 4. PulseAnalysis Parameters
% specify APDs to be calculated
pulseAnalysis_apDurations = [30 50 75 90 95]; % <--- PARAMETER
pulseAnalysis_apdIsEndPointApproximatedSymbol = "*";
pulseAnalysis_pulseStartOnStimulusDetectionDelta_ms = 30; % <--- PARAMETER
pulseAnalysis_pulseStartOnStimulusDetectionSymbol = "^";
pulseAnalysis_pulseStartPointType = PulseStartPointType.ActivationPoint; % <--- PARAMETER
%PulseStartPointType.UpstrokeStart
%PulseStartPointType.UpstrokeEnd
% 5. Visualization Parameters
visualize_showVisualizedCells = false; % <--- PARAMETER
visualize_saveVisualizedCellsToFiles = true;% <--- PARAMETER
% 6. Quality Control Parameters
qc_isQC_Required = true; % <--- PARAMETER
qc_SNR_Threshold = 10; % <--- PARAMETER
qc_writeFiguresToQCReportFile = true; % <--- PARAMETER
qc_checkForSNR = true; % <--- PARAMETER
qc_checkForNoPulsesDetected = true; % <--- PARAMETER
qc_checkForPulsesMissingStimuli = false; % <--- PARAMETER (TODO)
qc_checkForPulsesSpanMoreThanOneStimilus = false;% <--- PARAMETER (TODO)
%% initialize parameters
Stimulation.Init(stimulationStart_ms, stimuliPeriod_ms, stimulusPulseDuration_ms, stimuliNumber);
pulseDetectionParameters = PulseDetectionParameters(pulseDetection_thresholdPercentage, pulseDetection_numberOfSecondsAtStartToIgnore, pulseDetection_signalType,...
pulseDetection_removeFalsePulses_PeakThresholdPercentage, pulseDetection_removeFalsePulses_DurationThresholdPercentage,...
pulseDetection_denoise_waveletName, pulseDetection_denoise_waveletNumber, pulseDetection_denoise_waveletThresholdRule);
pulseAnalysisParameters = PulseAnalysisParameters(pulseAnalysis_apDurations, pulseAnalysis_apdIsEndPointApproximatedSymbol,...
pulseAnalysis_pulseStartOnStimulusDetectionDelta_ms, pulseAnalysis_pulseStartOnStimulusDetectionSymbol,...
pulseAnalysis_pulseStartPointType);
visualizationParameters = VisualizationParameters(visualize_showVisualizedCells, visualize_saveVisualizedCellsToFiles);
qcParameters = QCParameters(qc_isQC_Required, qc_SNR_Threshold, qc_writeFiguresToQCReportFile, qc_checkForSNR, qc_checkForNoPulsesDetected, qc_checkForPulsesMissingStimuli, qc_checkForPulsesSpanMoreThanOneStimilus);
% initialize Global Parameters
Parameters.Init(pulseDetectionParameters, pulseAnalysisParameters, visualizationParameters, qcParameters);
%% run analysis
wellAnalyser = WellAnalyser(tableData);
wellAnalyser.StartAnalysis();
%% end timer
Log.EndBlock(fileStartTime, 1, strcat("Completed analysis of one file: processed ", num2str(length(wellAnalyser.Well.Cells)), " cells from file '", fileFullName, "'"));
end