Position processing

MATLAB pipeline that turns raw Vicon .c3d motion-capture files into the position data needed for beam-pattern analysis: microphone positions, maze geometry, and the bat flight trajectory, all in the Vicon global coordinate frame (mm).

This is the position half of the Vicon + Avisoft pipeline. Its two data outputs — the per-session mic position file and the per-trial bat_pos file — are later used in Beam pattern analysis.

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Run it

Entry point: run_position_processing.m or master_position_processing.mlx (run either one). Set the config block at the top, then run:

date_data           = '20260623';      % capture date, yyyyMMdd
batID               = 'batA125';       % which bat
Mic_marker_distance = 35;              % mm from base marker to actual mic
floating_mic_ids    = [5 8 10 11 13 16];  % mic numbers that are movable, not wall-mounted

Path requirement: both this folder and position_processing\landmark must be on the MATLAB path (Home → Set Path → Add Folder).

The 5 steps:

1. Mic positions — mic_landmarks() builds (or reuses) the per-session mic landmark file from raw .c3d captures, then extract_mic_location() extrapolates the actual mic position and pointing vector.
2. Maze structure — extract_maze_structure() reads y-maze_layout.json.
3. Bat trajectory — extract_bat_pos() pulls the bat marker track from the selected trial .c3d.
4. Save bat_pos — save_bat_pos() writes a Beampattern_analysis-ready .mat (see Outputs).
5. Plot — plot_bat_trajectory() draws 3D / top / side / time / speed figures. Plotting only; it writes no data.

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Folders & outputs

Folder	What's in it
Mic_positions\	Final computed mic files only: extract_mic_location.m writes mic_pos_<date>.csv/.mat (actual mic position + pointing vector, plus mic_loc/mic_vec aliases for Beampattern_analysis). The raw <date>_mic_loc landmark files live in landmark\mic_landmark_output\.
Bat_Position\	Per-trial bat_pos files: <batID>_<date>_<trial>_bat_pos.mat.
plot\	Saved figures / trajectory images only. No data files.
landmark\	Step-1 mic-landmark sub-pipeline (fixed + floating passes). Writes its raw <date>_mic_loc.csv/.mat into landmark\mic_landmark_output\. Has its own README.md.
y-maze_layout.json	Maze landmark coordinates (walls, start line, take-off perch).
archive\, ezc3d_matlab\, legacy\	Superseded material and the ezc3d .c3d reader dependency.

bat_pos.mat contents (what Beampattern_analysis loads)

bat_pos (1×1 cell → [n_frames × 3], NaNs preserved), markers, frame_rate, maze, tp_position, lp_position, bat_marker_idx, selection_method, source_file.

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Key functions

• run_position_processing.m — top-level driver (steps 1–5 above).
• extract_mic_location.m — mic landmark file → actual mic position + pointing vector; writes to Mic_positions\.
• extract_maze_structure.m — parses y-maze_layout.json.
• extract_bat_pos.m — bat marker trajectory from a trial .c3d.
• save_bat_pos.m — writes the bat_pos .mat to Bat_Position\.
• plot_bat_trajectory.m — all diagnostic figures.
• landmark\ — the mic-landmark sub-pipeline (see its README).

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Downstream

Beampattern_analysis's bp_proc.m loads the Bat_Position\*.mat track and the Mic_positions\ mic file (via the mic_loc / mic_vec aliases). Not produced here on purpose: mic_gain and mic_vh (recorder/calibration values) — merge those in on the audio side.