diff --git a/behavior/linearTrackBehavior.m b/behavior/linearTrackBehavior.m index 411ff1b..74cec65 100644 --- a/behavior/linearTrackBehavior.m +++ b/behavior/linearTrackBehavior.m @@ -43,8 +43,8 @@ addParameter(p, 'norm_zero_to_one', false, @islogical); % normalize linear coords 0-1 addParameter(p, 'maze_sizes', [], @isnumeric); % width of mazes in cm (must correspond with linear epochs) addParameter(p, 'split_linearize', false, @islogical); % make linear epoch by epoch -addParameter(p, 'remove_extra_fields', false, @islogical); % removes extra FMA syle fields 'positionTrials','run','positionTrialsRun' -addParameter(p, 'just_save_animal_behavior', false, @islogical); % true will only save animal behav file +addParameter(p, 'remove_extra_fields', true, @islogical); % removes extra FMA syle fields 'positionTrials','run','positionTrialsRun' +addParameter(p, 'just_save_animal_behavior', true, @islogical); % true will only save animal behav file addParameter(p, 'clean_tracker_jumps', false, @islogical); parse(p, varargin{:}); @@ -338,9 +338,7 @@ saveas(gcf, [basepath, filesep, [basename, '.linearTrackBehavior.fig']]); end -if remove_extra_fields - behavior = rmfield(behavior, {'positionTrials', 'run', 'positionTrialsRun', 'speedTh'}); -end +behavior = rmfield(behavior, {'positionTrials', 'run', 'positionTrialsRun', 'speedTh'}); %% Generate output variables if savemat diff --git a/tutorials/pipelineFiringMaps/pipelineFiringMaps.m b/tutorials/pipelineFiringMaps/pipelineFiringMaps.m index 2498399..9304f78 100644 --- a/tutorials/pipelineFiringMaps/pipelineFiringMaps.m +++ b/tutorials/pipelineFiringMaps/pipelineFiringMaps.m @@ -88,9 +88,6 @@ speed_smooth = get_SmoothedSpeed(behavior, MergePoints, epochs, orderKalmanVel, do_smooth, ... 'smoothing_width', smoothing_width, 'figopt', doPlot); behavior.speed_smooth = speed_smooth'; - if savedata - save(fullfile(basepath, [prefix, '.animal.behavior.mat']), 'behavior') % update behavior info - end end % use the smoothed speed? if use_smoothed_speed diff --git a/tutorials/pipelineThetaSequences.m b/tutorials/pipelineThetaSequences.m index c931182..3d2e8e9 100644 --- a/tutorials/pipelineThetaSequences.m +++ b/tutorials/pipelineThetaSequences.m @@ -75,9 +75,6 @@ run(diff(run,[],2)<0.5,:) = []; % remove run epochs lasting for less than 0.5s behavior.run = run; behavior.speed = speed(:,2)'; % replace old speed with this speed - - % I recommend saving the running epochs in the behavior file: - save(fullfile(basepath,[basename '.animal.behavior.mat']),'behavior'); end ok = InIntervals(thetacycles.timestamps,behavior.run);