combine_nests.py

import glob
import os
import re
import sys
from zipfile import ZIP_DEFLATED
from zipfile import ZipFile

import geopandas
import pandas as pd
import tools


def get_site(path):
    path = os.path.basename(path)
    regex = re.compile("(\\w+)_\\d+.*_processed_nests")
    return regex.match(path).group(1)


def load_shapefile(x):
    shp = geopandas.read_file(x)
    # Force correct types
    # Empty shape files don't see to maintain provided types
    # when written and loaded
    shp = shp.astype({
        'nest_id': 'int',
        'Site': 'str',
        'Year': 'str',
        'xmean': 'float',
        'ymean': 'float',
        'first_obs': 'str',
        'last_obs': 'str',
        'num_obs': 'int',
        'species': 'str',
        'sum_top1': 'float',
        'num_top1': 'int',
        'bird_match': 'str'
    })
    shp["site"] = get_site(x)
    return shp


def combine(paths):
    """Take prediction shapefiles and wrap into a single file"""
    shapefiles = []
    for x in paths:
        try:
            shapefiles.append(load_shapefile(x))
        except:
            print(f"Mistructured file path: {x}. File not added to processed_nests.shp")
    summary = geopandas.GeoDataFrame(pd.concat(shapefiles, ignore_index=True), crs=shapefiles[0].crs)

    return summary


if __name__ == "__main__":
    working_dir = tools.get_working_dir()
    nests_path = f"{working_dir}/processed_nests/"
    output_path = f"{working_dir}/everwatch-workflow/App/Zooniverse/data/"

    nest_files = sys.argv[1:]
    # write output to zooniverse app
    df = combine(nest_files)
    df.to_file(os.path.join(output_path, "nest_detections_processed.shp"))

    # Zip the shapefile for storage efficiency
    with ZipFile(os.path.join(output_path, "nest_detections_processed.zip"), 'w', ZIP_DEFLATED) as zip:
        for ext in ['cpg', 'dbf', 'prj', 'shp', 'shx']:
            focal_file = os.path.join(output_path, f"nest_detections_processed.{ext}")
            file_name = os.path.basename(focal_file)
            zip.write(focal_file, arcname=file_name)
            os.remove(focal_file)