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Make linux compatible, add behavior-only session processing and add optional video background for tracking processing #19

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Make linux compatible, add behavior-only session processing and add optional video background for tracking processing #19

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c56c30d
Enhance behavior-only session processing and metadata handling
kushaangupta Oct 14, 2025
54b6ca7
Update ischar usage
kushaangupta Oct 14, 2025
a1aeea9
Update path separators
kushaangupta Oct 14, 2025
9abdae8
Restore backwards compatibility behavior-only mode to acqID and fix o…
kushaangupta Oct 15, 2025
8e0cfc8
Refactor code linting
kushaangupta Oct 15, 2025
1f00c2a
Support configurable digital and analog channel counts
kushaangupta Oct 19, 2025
6cfc30a
Add documentation for helper functions
kushaangupta Oct 19, 2025
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5 changes: 1 addition & 4 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,14 +1,11 @@
*.asv
*.pyc
*.mexa64
*.mexw64
*.mexmaci64
._*
behavior/dlc/Run_startdlc.bat
preProcessing/FilterM/FilterX.exp
preProcessing/FilterM/FilterX.lib
preProcessing/FilterM/FilterX.mexw64
preProcessing/FilterM/FilterX.exp
preProcessing/FilterM/FilterX.mexw64
preProcessing/FilterM/FilterX.lib
preProcessing/FilterM/FilterX.exp
spikeSorting/KiloSort1/CUDA/CUDA.xml
22 changes: 18 additions & 4 deletions behavior/general_behavior_file.m
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Expand Up @@ -20,6 +20,12 @@ function general_behavior_file(varargin)
% optitrack .csv file
% *_Behavior*.mat file from crcns_pfc-2_data
%
% OPTIONAL PARAMETERS:
% 'video_overlay' - logical, enable video overlay in manual_trackerjumps (default: false)
% 'clean_tracker_jumps' - logical, enable manual tracker jump cleaning GUI (default: true)
% 'convert_xy_to_cm' - logical, convert coordinates from pixels to cm (default: true)
% 'maze_sizes' - vector, maze dimensions in cm for coordinate conversion (required if convert_xy_to_cm=true)
%
% TODO:
% -make so you can choose (w/ varargin) which method to use (some sessions meet several)
% This will require making each method into a sub/local function
Expand All @@ -41,6 +47,7 @@ function general_behavior_file(varargin)
addParameter(p, 'clean_tracker_jumps', true, @islogical); % option to manually clean tracker jumps
addParameter(p, 'convert_xy_to_cm', true, @islogical); % option to convert xy to cm (best if used with clean_tracker_jumps)
addParameter(p, 'maze_sizes', [], @isvector); % list of maze sizes (x-dim, in cm) per non-sleep epoch (if same maze & cam pos over epochs use single number)
addParameter(p, 'video_overlay', false, @islogical); % option to overlay tracking on video frame in manual_trackerjumps

parse(p, varargin{:});
basepaths = p.Results.basepath;
Expand All @@ -54,12 +61,12 @@ function general_behavior_file(varargin)
clean_tracker_jumps = p.Results.clean_tracker_jumps;
convert_xy_to_cm = p.Results.convert_xy_to_cm;
maze_sizes = p.Results.maze_sizes;
video_overlay = p.Results.video_overlay;

if convert_xy_to_cm && isempty(maze_sizes)
error('Cannot run with "convert_xy_to_cm" option without providing maze_sizes.');
end


if ~iscell(basepaths)
basepaths = {basepaths};
end
Expand Down Expand Up @@ -152,14 +159,21 @@ function general_behavior_file(varargin)
epoch_df = epoch_df(epoch_df.environment ~= "sleep", :);
start = epoch_df.startTime;
stop = epoch_df.stopTime;
% make full paths using epoch_df.basepath and epoch_df.name
session_paths = cellfun(@(x,y) fullfile(x,y), ...
epoch_df.basepath, ...
epoch_df.name, ...
'UniformOutput', false);

good_idx = manual_trackerjumps(behavior.timestamps, ...
behavior.position.x, ...
behavior.position.y, ...
start, ...
stop, ...
basepath, ...
'darkmode', true);
session_paths, ...
'darkmode', true, ...
'video_overlay', p.Results.video_overlay);

behavior.position.x(~good_idx) = NaN;
behavior.position.y(~good_idx) = NaN;
Expand Down Expand Up @@ -598,9 +612,9 @@ function general_behavior_file(varargin)
source = 'basename.posTrials.mat';

% posTrials is sometimes moved
elseif exist([basepath, filesep, ['oldfiles\posTrials.mat']], 'file')
elseif exist([basepath, filesep, ['oldfiles', filesep, 'posTrials.mat']], 'file')
disp('detected posTrials.mat')
load([basepath, filesep, ['oldfiles\posTrials.mat']], 'posTrials');
load([basepath, filesep, ['oldfiles', filesep, 'posTrials.mat']], 'posTrials');
positions = [posTrials{1}; posTrials{2}];
[~, idx] = sort(positions(:, 1));
positions = positions(idx, :);
Expand Down
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