covid_map.py

import os
import json
import pandas as pd
import numpy as np
import geopandas as gpd
from pyspark.sql.types import *
from pyspark.sql import functions as F
from pyspark.sql import SparkSession
import matplotlib.pyplot as plt
from data import *
import findspark
from mpl_toolkits.axes_grid1 import make_axes_locatable
from config import MAPBOX_ACCESSTOKEN

from bokeh.io import output_file, show
from bokeh.models import GeoJSONDataSource
from bokeh.plotting import figure
from bokeh.sampledata.sample_geojson import geojson

findspark.init()
findspark.find()

def draw_fig(df=None, field='cumulative_cases', file_location='data/gpr_000b11a_e.shp', return_fig=False, create_json=False):

    data_df = df.copy()
    data_df.insert(1, "ID", [48, 59, 46, 13, 10, 12,
                             62, 61, 35, 11, 24, 47, 60], True)
    
    # get map data using geopandas
    print('reading shp file to make map data...')
    can = gpd.read_file(file_location)

    if create_json:
        can.to_file('data/canada.json', driver='GeoJSON')

    can_df = can.astype({'PRUID': 'int64'})

    # merge
    df_merged = pd.merge(can_df[['PRUID', 'geometry']], data_df[[
                         'ID', field, 'province']], left_on='PRUID', right_on='ID', how='left')
    df_merged = df_merged.dropna(subset=[field, 'geometry']).set_index('PRUID')
    df_merged = df_merged.drop(['ID'], axis=1)
    print(df_merged.head(14))

    # Convert geopandas to GeoJSON for plotly
    df_merged = df_merged.to_crs(epsg=4326)
    df_geo_json = df_merged.__geo_interface__

    print('preparing figure...')

    if return_fig:
        zmin = df_merged[field].min()
        zmax = df_merged[field].max()

        data = go.Choroplethmapbox(
            geojson=df_geo_json,
            locations=df_merged.index,
            z=df_merged[field],
            text=df_merged.province,
            colorbar=dict(thickness=20, ticklen=3),
            marker_line_width=1, marker_opacity=0.7, colorscale="Bluered",
            zmin=zmin, zmax=zmax,
            hovertemplate="<b>%{text}</b><br>" +
            "%{z}<br>" +
            "<extra></extra>")

        layout = go.Layout(
            mapbox1=dict(
                # domain={'x': [0, 1], 'y': [0, 1]},
                center=dict(lat=62.20, lon=-106.34),
                accesstoken=MAPBOX_ACCESSTOKEN,
                zoom=2),
            autosize=True,
            height=650,
            margin=dict(l=0, r=0, t=0, b=0))

        fig=go.Figure(data=data, layout=layout)
        fig.show()

        return fig

    else:
        z = df_merged[field]
        locations = df_merged.index
    
        return z, locations


if __name__ == "__main__":
    # spark = SparkSession.builder.appName('covid_19_cumulative').getOrCreate()
    # spark.sparkContext.setLogLevel("ERROR")
    # static_data = data_to_df('cumulative', spark)
    # df = static_data.toPandas()

    output_file("geojson.html")

    data = json.loads(geojson)
    for i in range(len(data['features'])):
        data['features'][i]['properties']['Color'] = ['blue', 'red'][i%2]

    geo_source = GeoJSONDataSource(geojson=json.dumps(data))

    TOOLTIPS = [
        ('Organisation', '@OrganisationName')
    ]

    p = figure(background_fill_color="lightgrey", tooltips=TOOLTIPS)
    p.circle(x='x', y='y', size=15, color='Color', alpha=0.7, source=geo_source)

    show(p)

    print('testing bokeh')