summarizeActivityStateTransitions.m

function T = summarizeActivityStateTransitions(rootDir, varargin)
% summarizeActivityStateTransitions  Pool activity-state transition results
% from many samples into one summary table and CSV.
%
% OPTIONAL NeuroSpikeX add-on. Recursively searches rootDir for the
% 'newActivityData_*.mat' files written by analyzeActivityStateTransitions.m
% and tabulates the four transition counts for each sample and comparison.
%
% USAGE
%   T = summarizeActivityStateTransitions('W:\...\MyExperiment');
%
% INPUT
%   rootDir - top folder to search recursively (e.g. a condition folder that
%             contains many sample folders).
%
% NAME-VALUE OPTIONS
%   'OutputFile' - CSV path (default <rootDir>/ActivityStateTransition_Summary.csv)
%
% OUTPUT
%   T - table with one row per newActivityData file: sample folder, comparison,
%       from/to timepoints, the four category counts, and the total classified.

    p = inputParser;
    p.addParameter('OutputFile', fullfile(rootDir,'ActivityStateTransition_Summary.csv'));
    p.parse(varargin{:});
    opt = p.Results;

    fprintf('Searching for newActivityData files under:\n  %s\n', rootDir);
    files = dir(fullfile(rootDir, '**', 'newActivityData_*.mat'));
    fprintf('Found %d file(s).\n', numel(files));

    T = table();
    for i = 1:numel(files)
        srcFile = fullfile(files(i).folder, files(i).name);
        S = load(srcFile);
        fn = fieldnames(S);
        hit = fn(contains(fn,'newActivityData','IgnoreCase',true));
        if isempty(hit)
            warning('No newActivityData variable in %s. Skipping.', srcFile);
            continue;
        end
        A = S.(hit{1});

        [fromTP, toTP, comparison] = inferComparison(A, files(i).name);
        sampleFolder = inferSampleFolder(files(i).folder);

        nStayedActive   = countCat(A, 'stayed_active');
        nBecameActive   = countCat(A, 'became_active');
        nBecameInactive = countCat(A, 'became_inactive');
        nStayedInactive = countCat(A, 'stayed_inactive');
        total = sum([nStayedActive nBecameActive nBecameInactive nStayedInactive], 'omitnan');

        row = table(string(sampleFolder), string(comparison), string(fromTP), string(toTP), ...
            nStayedActive, nBecameActive, nBecameInactive, nStayedInactive, total, string(srcFile), ...
            'VariableNames', {'sample_folder','comparison','from_timepoint','to_timepoint', ...
            'n_stayed_active','n_became_active','n_became_inactive','n_stayed_inactive', ...
            'total_classified_cells','source_file'});
        T = [T; row]; %#ok<AGROW>
    end

    if height(T) > 0
        T = sortrows(T, {'sample_folder','comparison'});
        writetable(T, opt.OutputFile);
        fprintf('Saved summary (%d rows):\n  %s\n', height(T), opt.OutputFile);
    else
        fprintf('No summary rows written.\n');
    end
end

%% ======================= local helpers =======================

function [fromTP, toTP, comparison] = inferComparison(A, fileName)
    fromTP = ''; toTP = ''; comparison = '';
    if isstruct(A)
        if isfield(A,'fromTag'), fromTP = char(A.fromTag); end
        if isfield(A,'toTag'),   toTP   = char(A.toTag);   end
        if isfield(A,'comparison'), comparison = char(A.comparison); end
    end
    if isempty(fromTP) || isempty(toTP)
        % Fall back to parsing "newActivityData_<from>_<to>.mat"
        tok = regexp(fileName, 'newActivityData_(.+?)_(.+)\.mat$', 'tokens', 'once');
        if ~isempty(tok)
            fromTP = tok{1}; toTP = tok{2};
        end
    end
    if isempty(comparison) && ~isempty(fromTP)
        comparison = sprintf('%s_to_%s', fromTP, toTP);
    end
end

function n = countCat(A, fieldName)
    n = NaN;
    if ~isstruct(A) || ~isfield(A, fieldName), return; end
    F = A.(fieldName);
    if isempty(F), n = 0; return; end
    if isstruct(F)
        if isfield(F,'numCells'), n = F.numCells; return; end
        if isfield(F,'cellNum'),  n = size(F.cellNum,1); return; end
    end
end

function sampleFolder = inferSampleFolder(folderStr)
% If results live in an 'AdditionalAnalyses' folder, the sample root is its
% parent; otherwise use the containing folder name.
    [parent, name] = fileparts(folderStr);
    if strcmpi(name, 'AdditionalAnalyses')
        [~, sampleFolder] = fileparts(parent);
    else
        sampleFolder = name;
    end
end