3. Setup - ashleyblawas/respdetect GitHub Wiki

First, you will need to identify three different paths to direct MATLAB to the tools and data on your local machine. The three paths you will need to identify are where you are storing the:

  1. respdetect tools (from this repository),
  2. DTAG tools (dtagtools can be cloned from: https://github.com/stacyderuiter/dtagtools.git), and
  3. DTAG data (ending in the two letter species name, e.g. gm for short-finned pilot whale, where your prh folder lives).

Open the paths.txt file in the respository and the three path lines to your respective paths. Below is an example of what these paths look like on my local machine. Do note that if you are working with the test DTAG data provided with this repository, your DTAG data path will be tests\ + the two letter species name of interest (either gm or mn).

An example of the paths.txt file.

Now you are ready for Step 1 of main.m which is the main script to run respdetect and can be found in the respdetect folder.

When you run this section, you will first be prompted to navigate to and select the paths.txt file.

 

This file should be living in the main repository folder. Next, this section will open a window in the prh folder in your DTAG data path and will allow you to choose one or multiple prh files (hold down Ctrl to select multiple files).

 

 

In addition to a prh folder containing your prh files, respdetect expects several other folders to exist where it will save your outputs. When you run Step 1 of main.m folders named breaths, diving, figs, metadata, and movement will be created in your DTAG data path, if they don’t already exist, to store data outputs and relevant figures.

After running Step 1, your data_path should point to a folder that looks like this:

data_path (e.g. C:\Users\ashle\Dropbox\Ashley\Graduate\Manuscripts\respdetect\tests\gm)
|
└───breaths
└───diving
└───figs
└───metadata
└───movement
└───prh
    |
    └─── gm08_143bprh.mat