ea_command_line_run.m

function [] = ea_command_line_run(varargin)
% This function is called when lead has multiple inputs. These inputs are
% the patient directories and leadfigure handles with their values. Then,
% the specified command is executed via ea_run without a UI.
%
% For example, to run Segment normalization:
% lead dbs -normalize_checkbox -normmethod 2 /path/to/patient/directory

switch varargin{1}
    case {'dbs', '-d', 'd'}
        h = lead_dbs;
        leadprod = 'dbs';
    case {'connectome', 'conn', '-c', 'c'}
        h = lead_connectome;
        leadprod = 'connectome';
end

set(h, 'Visible', 'off'); drawnow;
handles = guihandles(h);

% reset all checkboxes to 0
handles_names = fieldnames(handles);
for i = 1:length(handles_names)
    if isprop(handles.(handles_names{i}), 'Style') && strcmp(handles.(handles_names{i}).Style,'checkbox')
        handles.(handles_names{i}).Value = 0;
    end
end

tryBIDS = false; % flag to try BIDS import when calling with -process
dirs = {};

for i = 2:nargin
    switch varargin{i}(1) % first character of str
        case filesep % directory
            patient_dir = varargin{i};
            if isfolder(patient_dir)
                dirs{end+1} = patient_dir;
            else
                error([patient_dir ' is not a folder'])
            end
        case '-' % option
            opt = varargin{i}(2:end);
            if isfield(handles, opt)
                set(handles.(opt),'Value',1); % set default option to 1
            elseif strcmp(opt,'process')
                % run basic lead dbs pipeline with defaults
                handles.coreg_checkbox.Value = 1;
                handles.coregmrmethod.Value = 1;
                handles.normalize_checkbox.Value = 1;
                handles.normmethod.Value = 9;
                handles.scrf.Value = 1;
                handles.scrfmask.Value = 2;
                handles.doreconstruction.Value = 1;
                handles.reconmethod.Value = 3;
                tryBIDS = true;
            else
                error(['Unrecognized field: ' opt])
            end
        otherwise
            set(handles.(opt),'Value',str2double(varargin{i}));
    end
end

options = ea_handles2options(handles);
options.uipatdirs = dirs;
options.leadprod = leadprod;
setappdata(h,'handles',handles);
options.leadfigure = h;

% dont show pop up methods
umachine = load(ea_prefspath('mat'));
machine = umachine.machine;
machine.methods_show = 0;
save(ea_prefspath('mat'),'machine');

% run
ea_run('run',options);

% restore previous pop up config
machine.methods_show = umachine.machine.methods_show;
save(ea_prefspath('mat'),'machine');

set(h, 'Visible', 'on'); drawnow; % make gui visible so that close request function is executed
close(h)