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| """Module for predicting a species list. | |
| Can be used to predict a species list using coordinates and weeks. | |
| """ | |
| import argparse | |
| import os | |
| import sys | |
| import config as cfg | |
| import model | |
| import utils | |
| def getSpeciesList(lat: float, lon: float, week: int, threshold=0.05, sort=False) -> list[str]: | |
| """Predict a species list. | |
| Uses the model to predict the species list for the given coordinates and filters by threshold. | |
| Args: | |
| lat: The latitude. | |
| lon: The longitude. | |
| week: The week of the year [1-48]. Use -1 for year-round. | |
| threshold: Only values above or equal to threshold will be shown. | |
| sort: If the species list should be sorted. | |
| Returns: | |
| A list of all eligible species. | |
| """ | |
| # Extract species from model | |
| pred = model.explore(lat, lon, week) | |
| # Make species list | |
| slist = [p[1] for p in pred if p[0] >= threshold] | |
| return sorted(slist) if sort else slist | |
| if __name__ == "__main__": | |
| # Parse arguments | |
| parser = argparse.ArgumentParser( | |
| description="Get list of species for a given location with BirdNET. Sorted by occurrence frequency." | |
| ) | |
| parser.add_argument( | |
| "--o", | |
| default="example/", | |
| help="Path to output file or folder. If this is a folder, file will be named 'species_list.txt'.", | |
| ) | |
| parser.add_argument("--lat", type=float, help="Recording location latitude.") | |
| parser.add_argument("--lon", type=float, help="Recording location longitude.") | |
| parser.add_argument( | |
| "--week", | |
| type=int, | |
| default=-1, | |
| help="Week of the year when the recording was made. Values in [1, 48] (4 weeks per month). Set -1 for year-round species list.", | |
| ) | |
| parser.add_argument("--threshold", type=float, default=0.05, help="Occurrence frequency threshold. Defaults to 0.05.") | |
| parser.add_argument( | |
| "--sortby", | |
| default="freq", | |
| help="Sort species by occurrence frequency or alphabetically. Values in ['freq', 'alpha']. Defaults to 'freq'.", | |
| ) | |
| args = parser.parse_args() | |
| # Set paths relative to script path (requested in #3) | |
| cfg.LABELS_FILE = os.path.join(os.path.dirname(os.path.abspath(sys.argv[0])), cfg.LABELS_FILE) | |
| cfg.MDATA_MODEL_PATH = os.path.join(os.path.dirname(os.path.abspath(sys.argv[0])), cfg.MDATA_MODEL_PATH) | |
| # Load eBird codes, labels | |
| cfg.LABELS = utils.readLines(cfg.LABELS_FILE) | |
| # Set output path | |
| cfg.OUTPUT_PATH = args.o | |
| if os.path.isdir(cfg.OUTPUT_PATH): | |
| cfg.OUTPUT_PATH = os.path.join(cfg.OUTPUT_PATH, "species_list.txt") | |
| # Set config | |
| cfg.LATITUDE, cfg.LONGITUDE, cfg.WEEK = args.lat, args.lon, args.week | |
| cfg.LOCATION_FILTER_THRESHOLD = args.threshold | |
| print(f"Getting species list for {cfg.LATITUDE}/{cfg.LONGITUDE}, Week {cfg.WEEK}...", end="", flush=True) | |
| # Get species list | |
| species_list = getSpeciesList( | |
| cfg.LATITUDE, cfg.LONGITUDE, cfg.WEEK, cfg.LOCATION_FILTER_THRESHOLD, False if args.sortby == "freq" else True | |
| ) | |
| print(f"Done. {len(species_list)} species on list.", flush=True) | |
| # Save species list | |
| with open(cfg.OUTPUT_PATH, "w") as f: | |
| for s in species_list: | |
| f.write(s + "\n") | |
| # A few examples to test | |
| # python3 species.py --o example/ --lat 42.5 --lon -76.45 --week -1 | |
| # python3 species.py --o example/species_list.txt --lat 42.5 --lon -76.45 --week 4 --threshold 0.05 --sortby alpha | |