Batlab: Julia-Based Chirp Processing

Setup

1. Install Julia, Jupyter Notebook, and IJulia.
2. Clone this repository: git@github.com:NSagan271/batlab-chirp-processing.git. Before doing so, you will have to add your SSH key to Github.
3. Run cd batlab-chirp-processing.
4. Run git submodule init and git submodule update. This will clone the BatlabJuliaUtils library into a folder of the same name.
5. Install the required packages (make sure you're in the batlab-chirp-processing directory, AKA the root directory of this repository.
   • On the command line, type julia. Then, hit the ] key.
   • Type add Plots, and then press Enter.
   • Do the same for using Printf, MAT, Statistics, Roots, DataInterpolations, DSP, and WAV.
   • Run activate ./BatlabJuliaUtils.
   • Press Backspace to exit package mode, and CTRL+d to exit the Julia command line.
6. Go to matlab_utils and use tdms_to_mat.m to convert some bat audio TDMS files to MAT files. It is recommended you start off with Pu166_01 and Gr116_01, and save the MAT files in the batlab-chirp-processing/data directory.
7. Copy all mic position files to data.
8. Make a subdirectory of data called centroid and copy all relevant centroid data files to that directory.
9. Go to jupyter_notebooks and run either jupyter notebook or jupyter lab from the command line. When prompted, opt to use a Julia kernel. The file Walkthrough.ipynb contains a tutorial for estimating bat vocalizations given the audio data.
   • If jupyter lab doesn't work, then here are some alternatives that might work: python3 -m jupyterlab, python3 -m jupyter lab, python3 -m notebook.

Notebooks

1. Walkthrough.ipynb: contains a tutorial for estimating bat vocalizations given the audio data. You should look at this notebook before anything else.
2. SaveChirpsMAT.ipynb: contains code for saving various computed values (e.g., estimated vocalizations and vocalization times) to MAT files.
3. ValidateCentroidData.ipynb: a short notebook to sanity-check whether the centroid data looks reasonable, i.e., whether the chirps reach the microphones closest to the bat first.

Documentation: Julia Code

Documentation for the BatlabJuliaUtils library can be found online here.

Transformer-Based Imputation and Signal Boosting

Coming soon!