python利用geopandas库和pandas在anaconda的jupter notebook下生成疫情演变图-python-泓源视野

python利用geopandas库和pandas在anaconda的jupter notebook下生成疫情演变图



法国新冠病毒发展演变图 从2020年03月18日至2020年11月8日 考验你机器性能的时候到了,因为本图超过100m 请耐心等待加载……… &…

python利用geopandas库和pandas在anaconda的jupter notebook下生成疫情演变图插图

demo-covid.ipynb 利用这个生成演变图:目录下需要新建一个img文件夹


from IPython.display import HTML import requests import zipfile import io from datetime import timedelta, date import matplotlib import matplotlib.pyplot as plt from mpl_toolkits.axes_grid1 import make_axes_locatable import pandas as pd import geopandas as gpd import contextily as ctx from PIL import Image

COVID-19 evolution in French departments

Visualize evolution of the number of people hospitalized in French departments due to COVID-19 infection

In [1]:
%load_ext lab_black%matplotlib inline
In [2]:
from IPython.display import HTMLimport requestsimport zipfileimport iofrom datetime import timedelta, dateimport matplotlibimport matplotlib.pyplot as pltfrom mpl_toolkits.axes_grid1 import make_axes_locatableimport pandas as pdimport geopandas as gpdimport contextily as ctxfrom PIL import Image

COVID data are open data from the French open data portal

In [3]:
url_dep = ""covid_url = ( "")filter_dep = ["971", "972", "973", "974", "976"] # only metropolitan Francefigsize = (15, 15)tile_zoom = 7frame_duration = 500 # in ms

Load French departements data into a GeoPandas GeoSeries

More information on these geographical open data can be found here:

In [4]:
local_path = "tmp/"r = requests.get(url_dep)z = zipfile.ZipFile(io.BytesIO(r.content))z.extractall(path=local_path)filenames = [ y for y in sorted(z.namelist()) for ending in ["dbf", "prj", "shp", "shx"] if y.endswith(ending)]dbf, prj, shp, shx = [filename for filename in filenames]fr = gpd.read_file(local_path + shp) # + encoding="utf-8" if = "epsg:4326" # {'init': 'epsg:4326'}met = fr.query("code_insee not in @filter_dep")met.set_index("code_insee", inplace=True)met = met["geometry"]

Load the map tile with contextily

In [5]:
w, s, e, n = met.total_boundsbck, ext = ctx.bounds2img(w, s, e, n, zoom=tile_zoom, ll=True)

Plot function to save image at a given date (title)

In [6]:
def save_img(df, title, img_name, vmin, vmax): gdf = gpd.GeoDataFrame(df, crs={"init": "epsg:4326"}) gdf_3857 = gdf.to_crs(epsg=3857) # web mercator f, ax = plt.subplots(figsize=figsize) ax.imshow( bck, extent=ext, interpolation="sinc", aspect="equal" ) # load background map divider = make_axes_locatable(ax) cax = divider.append_axes( "right", size="5%", pad=0.1 ) # GeoPandas trick to adjust the legend bar gdf_3857.plot( column="hosp", # Number of people currently hospitalized ax=ax, cax=cax, alpha=0.75, edgecolor="k", legend=True,"magma_r"), vmin=vmin, vmax=vmax, ) ax.set_axis_off() ax.get_xaxis().set_visible(False) ax.get_yaxis().set_visible(False) ax.set_title(title, fontsize=25) plt.savefig(img_name, bbox_inches="tight") # pad_inches=-0.1 to remove border plt.close(f)

Load COVID data into a pandas DataFrame

In [7]:
cov = pd.read_csv(covid_url, sep=";", index_col=2, parse_dates=True,)cov = cov.query("sexe == 0") # sum of male/femalecov = cov.query("dep not in @filter_dep")cov.dropna(inplace=True)cov.head()

Add geometry data to COVID DataFrame

In [8]:
cov["geometry"] = cov["dep"].map(met)

Parse recorded days and save one image for each day

In [9]:
def daterange(date1, date2): for n in range(int((date2 - date1).days) + 1): yield date1 + timedelta(n)

Create the folder img at the root of the notebook

In [10]:
vmax = cov.hosp.max()for i, dt in enumerate(daterange(cov.index.min(), cov.index.max())): title = dt.strftime("%d-%b-%Y") df = cov.query("jour == @dt") df = df.drop_duplicates(subset=["dep"], keep="first") img_name = "img/" + str(i) + ".png" save_img(df, title, img_name, 0, vmax)

Compile images in animated gif

In [11]:
frames = []for i, dt in enumerate(daterange(cov.index.min(), cov.index.max())): name = "img/" + str(i) + ".png" frames.append([0].save( "covid.gif", format="GIF", append_images=frames[1:], save_all=True, duration=frame_duration, loop=0,)from IPython.display import HTMLHTML("<img src='covid.gif'>")
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