analyzeT1Transitions.m

% This function is meant to be run on a cluster to convert the output of
% the Epi-Scale simulation into a matlab-interpretable format.

% Flags
% 1: Made datafile for label
% 2: Datafile already exists
% -1: Did not find raw data

% Usage:
% analyzeT1Transitions(coreNumber [uint8 = 1], settings [struct = getSettings],
%    path [string = pwd], analysis [uint8 = 2])
% where:
% coreNumber [uint8] indicates the number of cores to be used
% settings [struct] indicates the settings object for the analysis. This
%       defaults to the object generated by getSettings. Empty set means
%       default settings are used.
% path [string] indicates the path for the analysis. This defaults to the
%       current directory.
% analysis [uint8] indicates the type of analysis to be conducted. This
%       defaults to a full analysis (2). The following are the types:
%         1: Convert data into .mat files
%         2: Extract T1 transition frequency (requires 1)
% force [logical] determines whether to force recalculation of quantities.
%         empty: Default to settings
%         0: Do not force anything
%         1: Force T1 transition analysis
%         2: Force T1 transition analysis and data processing

function flag = analyzeT1Transitions(varargin)
%% Input parsing
% Define the input parser
p = inputParser;
addOptional(p,'coreNumber', 1,     @(x) validateattributes(x, {'numeric'}, {'>=',1,'<=',12}));
addOptional(p,'path',       pwd,   @ischar);
addOptional(p,'settings',   [],    @(x) isempty(x) || isstruct(x));
addOptional(p,'analysis',   2,     @(x) any(x==[1,2]));
addOptional(p,'force',      [],    @(x) any(x==[0,1,2]));

% Parse inputs
parse(p,varargin{:});

coreNumber = p.Results.coreNumber;
settings = p.Results.settings;
path = p.Results.path;
analysis = p.Results.analysis;

% Prepare workspace
delete(gcp('nocreate'))
cd(path);
if isempty(settings)
    settings = prepareWorkspace;
else
    settings = prepareWorkspace(settings);
end

% Override force
if ~isempty(p.Results.force)
    settings.force = p.Results.force;
end

labels = importData(settings);

%% Processes all files listed in the spreadsheet
flag_convert = zeros(length(labels), 1);
flag_analyze = zeros(length(labels), 1);

if coreNumber == 1
    for k = 1:length(labels) %randperm(length(labels))
        flag_convert(k) = saveSimulation(labels{k}, settings);
        if analysis == 2
            flag_analyze(k) = extractT1Transitions(labels{k}, settings);
        end
    end
else
    parpool(coreNumber)
    parfor k = 1:length(labels)
        flag_convert(k) = saveSimulation(labels{k}, settings);
        if analysis == 2
            flag_analyze(k) = extractT1Transitions(labels{k}, settings);
        end
    end
    delete(gcp('nocreate'))
end

flag = [flag_convert, flag_analyze];