Compute area of selected scouts

process_scout_area.m

function varargout = process_scout_area( varargin )
% PROCESS_SCOUTAREA: Computes the area of selected scouts

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
% 
% Copyright (c)2000-2018 University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
% 
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
%
% For more information type "brainstorm license" at command prompt.
% =============================================================================@
%
% Authors: Martin Cousineau, 2018

eval(macro_method);
end


%% ===== GET DESCRIPTION =====
function sProcess = GetDescription() %#ok<DEFNU>
    % Description the process
    sProcess.Comment     = 'Compute scout area';
    sProcess.Category    = 'Custom';
    sProcess.SubGroup    = 'External';
    sProcess.Index       = 400;
    sProcess.Description = '';
    % Definition of the input accepted by this process
    sProcess.InputTypes  = {'data', 'results', 'timefreq', 'matrix'};
    sProcess.OutputTypes = {'data', 'results', 'timefreq', 'matrix'};
    sProcess.nInputs     = 1;
    sProcess.nMinFiles   = 1;
    % === CSV OUTPUT FILE
    SelectOptions = {...
        '', ...                               % Filename
        '', ...                               % FileFormat
        'save', ...                           % Dialog type: {open,save}
        'Save output...', ...                 % Window title
        'ExportData', ...                     % LastUsedDir: {ImportData,ImportChannel,ImportAnat,ExportChannel,ExportData,ExportAnat,ExportProtocol,ExportImage,ExportScript}
        'single', ...                         % Selection mode: {single,multiple}
        'files', ...                          % Selection mode: {files,dirs,files_and_dirs}
        {{'.csv'}, 'ASCII: Comma-separated (*.csv)',  'ASCII-CSV'}, ...
        ''};
    sProcess.options.csvfile.Comment = 'Output CSV file: ';
    sProcess.options.csvfile.Type    = 'filename';
    sProcess.options.csvfile.Value   = SelectOptions;
    % === SCOUTS
    sProcess.options.scouts.Comment = '';
    sProcess.options.scouts.Type    = 'scout';
    sProcess.options.scouts.Value   = {};
end


%% ===== FORMAT COMMENT =====
function Comment = FormatComment(sProcess) %#ok<DEFNU>
    Comment = sProcess.Comment;
end


%% ===== RUN =====
function sInputs = Run(sProcess, sInputs) %#ok<DEFNU>
    subjects = {};
    scouts   = {};
    areas    = [];
    nOutputs = 0;

    % Parse inputs
    if ~isempty(sProcess.options.csvfile.Value)
        csvFile = sProcess.options.csvfile.Value{1};
    else
        bst_report('Error', sProcess, sInputs, 'No output file specified.');
        return;
    end
    if ~isempty(sProcess.options.scouts.Value) && ~isempty(sProcess.options.scouts.Value{2})
        selectedAtlas  = sProcess.options.scouts.Value{1};
        selectedScouts = sProcess.options.scouts.Value{2};
    else
        bst_report('Error', sProcess, sInputs, 'No selected scout.');
        return;
    end

    for iInput = 1:length(sInputs)
        % Load basic subject information
        sInput = sInputs(iInput);
        subject = sInput.SubjectName;
        sSubject = bst_get('Subject', subject);
        if ismember(subject, subjects)
            disp(['Warning: subject ' subject ' already computed, skipping...']);
            continue;
        end
        
        % Find selected atlas
        foundAtlas = 0;
        if ~isempty(sSubject.iCortex)
            SurfaceFile = sSubject.Surface(sSubject.iCortex).FileName;
            sSurf = bst_memory('LoadSurface', SurfaceFile);
            for iAtlas = 1:length(sSurf.Atlas)
                if strcmpi(sSurf.Atlas(iAtlas).Name, selectedAtlas)
                    foundAtlas = iAtlas;
                    break;
                end
            end
        end
        if foundAtlas == 0
            bst_report('Error', sProcess, sInput, ['Could not find atlas for subject ' subject]);
            continue;
        end
        
        % Find selected scouts
        sScouts = sSurf.Atlas(foundAtlas).Scouts;
        for iSelScout = 1:length(selectedScouts)
            foundScout = 0;
            for iScout = 1:length(sScouts)
                if strcmpi(sScouts(iScout).Label, selectedScouts{iSelScout})
                    foundScout = iScout;
                    break;
                end
            end
            
            if foundScout == 0
                bst_report('Error', sProcess, sInput, ['Could not find scout ' selectedScouts{iSelScout} ' for subject ' subject]);
                continue;
            end
            
            % Compute area
            allVertices = unique([sScouts(foundScout).Vertices]);
            totalArea = sum(sSurf.VertArea(allVertices)) * 100 * 100;
            nOutputs = nOutputs + 1;
            subjects{nOutputs} = subject;
            scouts{nOutputs}   = selectedScouts{iSelScout};
            areas(nOutputs)    = totalArea;
        end
    end
    
    % Save output
    fid = fopen(csvFile, 'w') ;
    fprintf(fid, 'atlas,subject,scout,area\n');
    for iOutput = 1:nOutputs
        fprintf(fid, '%s,%s,%s,%f\n', selectedAtlas, subjects{iOutput}, scouts{iOutput}, areas(iOutput));
    end
    fclose(fid);
end