rmanach/covid-plotter
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rework on plots title, legend and name + generate html page with plots

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rmanach 2021-12-28 16:07:19 +01:00
parent a994f96eea
commit c0f024043b
5 changed files with 150 additions and 31 deletions
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3
.gitignore vendored
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@ -1,3 +1,4 @@
output
static/plots
data
build
.svn

4
README.md
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@ -24,4 +24,6 @@ python owid.py <country_trigram> <var_1> <var_2> <var..n>
python dress.py
```
**NOTE** : `-r` option is used to fetch update data
**NOTE** :
* `-r` option is used to fetch update data
* `dress.py` includes **--to-html** to generate html page with plots

98
drees.py
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@ -10,6 +10,7 @@ from typing import Any, Dict, List, Optional, OrderedDict, Tuple
import numpy as np
import requests
from jinja2 import Environment, FileSystemLoader, select_autoescape
from matplotlib import dates as md
from matplotlib import pyplot as plt
@ -20,7 +21,11 @@ DATE_FORMAT = "%Y-%m-%d"
DATA_URL = "https://data.drees.solidarites-sante.gouv.fr/api/records/1.0/search/?dataset=covid-19-resultats-par-age-issus-des-appariements-entre-si-vic-si-dep-et-vac-si&q=&rows=-1&facet=date&facet=vac_statut&facet=age"
DATA_REPOSITORY = "data"
OUTPUT_REPOSITORY = "output"
STATIC_REPOSITORY = "static"
OUTPUT_REPOSITORY = os.path.join(STATIC_REPOSITORY, "plots")
BUILD_REPOSITORY = "build"
MAIN_URL = "https://covid.thegux.fr/"
# cycler could be better, but for ages plots it's ok
AGE_COLORS = {
@ -41,9 +46,9 @@ class DreesEnum(bytes, Enum):
class Field(DreesEnum):
HC = (0, "hc")
SC = (1, "sc")
DC = (2, "dc")
HC = (0, "Hospitalisations")
SC = (1, "Soins critiques")
DC = (2, "Décés")
class VacStatus(DreesEnum):
@ -109,7 +114,7 @@ def get_enum_age(value):
def get_enum_field(value):
for field in Field:
if field.label == value:
if field.name.lower() == value:
return field.value
@ -141,9 +146,8 @@ def group_by_age_date(data: Dict[str, Any]) -> Dict[dt, Any]:
if vac_status not in dic_data_grouped[date][age]:
dic_data_grouped[date][age][vac_status] = OrderedDict()
for field in Field:
dic_data_grouped[date][age][vac_status][field.label] = row_fields[
field.label
]
field_name = field.name.lower()
dic_data_grouped[date][age][vac_status][field_name] = row_fields[field_name]
logging.info("data restructured")
return dic_data_grouped
@ -284,7 +288,7 @@ def analyse(np_data: np.ndarray, np_date: np.ndarray) -> None:
mean_vac_percent = np.round(
np.nanmean(np_percent_vac[:, age_group.value, field.value]) * 100, 2
)
print(f"{field.label} - {age_group.label} - vac : {mean_vac_percent}%")
print(f"{field.name} - {age_group.label} - vac : {mean_vac_percent}%")
logging.info("--- age by field and vac status mean percent ---")
for field in Field:
@ -297,22 +301,20 @@ def analyse(np_data: np.ndarray, np_date: np.ndarray) -> None:
percent_age_mean = np.round(
np.nanmean(np_percent_age[:, age_group.value]), 2
)
print(
f"age: {age_group.label} - field: {field.label} = {percent_age_mean}%"
)
print(f"age: {age_group.label} - field: {field.name} = {percent_age_mean}%")
percent_age_vac_mean = np.round(
np.nanmean(np_percent_age_vac[:, age_group.value]), 2
)
print(
f"age: {age_group.label} - status: vac - field: {field.label} = {percent_age_vac_mean}%"
f"age: {age_group.label} - status: vac - field: {field.name} = {percent_age_vac_mean}%"
)
percent_age_unvac_mean = np.round(
np.nanmean(np_percent_age_unvac[:, age_group.value]), 2
)
print(
f"age: {age_group.label} - status: unvac - field: {field.label} = {percent_age_unvac_mean}%"
f"age: {age_group.label} - status: unvac - field: {field.name} = {percent_age_unvac_mean}%"
)
@ -324,7 +326,8 @@ def plot_bar_age_percent_vac_status_by_field(
) -> None:
fig, ax = get_plot_fig(figsize=(22, 8), locator=md.WeekdayLocator())
bottom = np_data_vac_status[:, 0]
title = "vac" if is_vac else "no vac"
suffix = "vac" if is_vac else "unvac"
title = "Vaccinés" if is_vac else "Non vaccinés"
for age_group in AgeGroup:
percents_age = np_data_vac_status[:, age_group.value]
if age_group.value > 0:
@ -351,7 +354,7 @@ def plot_bar_age_percent_vac_status_by_field(
)
save_and_close_fig(
fig,
os.path.join(OUTPUT_REPOSITORY, f"age_percent_{title}_{field.label}"),
os.path.join(OUTPUT_REPOSITORY, f"age_percent_{suffix}_{field.name.lower()}"),
has_legend=False,
)
@ -385,13 +388,13 @@ def plot_cumulative_field(
np_cumulate_unvac: np.ndarray = np.cumsum(
np_data_unvac[:, age_group.value, field.value], axis=0
)
plt.plot(np_date, np_cumulate_vac, label=f"{age_group.label} vac")
plt.plot(np_date, np_cumulate_unvac, label=f"{age_group.label} no vac")
plt.plot(np_date, np_cumulate_vac, label=f"{age_group.label} Vaccinés")
plt.plot(np_date, np_cumulate_unvac, label=f"{age_group.label} Non vaccinés")
plt.title(f"nombre de {field.label} cumulé par age")
plt.title(f"{field.label} cumulés par âge")
plt.xlabel("date")
save_and_close_fig(
fig, os.path.join(OUTPUT_REPOSITORY, f"cumulative_{field.label}")
fig, os.path.join(OUTPUT_REPOSITORY, f"cumulative_{field.name.lower()}")
)
@ -411,11 +414,13 @@ def plot_fields_by_age_vac(
)
plt.xlabel("date")
plt.ylabel("nombre")
plt.title(f"{age_group.label}ans - {vac_status.label}")
plt.title(f"{age_group.label} - {vac_status.label}")
save_and_close_fig(
fig,
os.path.join(OUTPUT_REPOSITORY, f"all_{age_group.label}_{vac_status.label}"),
os.path.join(
OUTPUT_REPOSITORY, f"all_{age_group.name.lower()}_{vac_status.name.lower()}"
),
)
@ -440,8 +445,10 @@ def plot_bar_data_by_age_field(
unvac_percent = np.round(
np_percent_unvac[idx_date, age_group.value, field.value] * 100, 2
)
bar_vac = ax.bar(idx_date, vac_percent, color="b", label="vac")
ax.bar(idx_date, unvac_percent, bottom=vac_percent, color="r", label="no vac")
bar_vac = ax.bar(idx_date, vac_percent, color="b", label="Vaccinés")
ax.bar(
idx_date, unvac_percent, bottom=vac_percent, color="r", label="Non vaccinés"
)
ax.bar_label(
bar_vac, label_type="edge", color="black", fontsize="7", fmt="%.0f"
)
@ -458,11 +465,14 @@ def plot_bar_data_by_age_field(
for idx, d in enumerate(np_date.astype(dt))
],
)
plt.legend(["vac", "no vac"], loc="upper right", frameon=True)
plt.legend(["Vaccinés", "Non vaccinés"], loc="upper right", frameon=True)
save_and_close_fig(
fig,
os.path.join(OUTPUT_REPOSITORY, f"vac_percent_{age_group.label}_{field.label}"),
os.path.join(
OUTPUT_REPOSITORY,
f"vac_percent_{age_group.name.lower()}_{field.name.lower()}",
),
has_legend=False,
)
@ -489,6 +499,27 @@ def get_age_field_args() -> List[Tuple[AgeGroup, Field]]:
return pool_args
def generate_html_page() -> None:
logging.info("generating html page with plots...")
os.makedirs(BUILD_REPOSITORY, exist_ok=True)
env = Environment(
loader=FileSystemLoader("templates"), autoescape=select_autoescape()
)
template = env.get_template("index.template.html")
data = template.render(
**{
"fields": Field,
"ages": AgeGroup,
"status": VacStatus,
"static": os.path.join(MAIN_URL, STATIC_REPOSITORY),
"src": DATA_URL,
}
)
with open(os.path.join(BUILD_REPOSITORY, "index.html"), "w") as f:
f.write(data)
logging.info("html page build")
if __name__ == "__main__":
"""
This script aims to plot DRESS data
@ -517,13 +548,18 @@ if __name__ == "__main__":
"--no-plot",
action="store_true",
default=False,
help="redownload data for updates",
help="no plot data",
)
parser.add_argument(
"-th",
"--to-html",
action="store_true",
default=False,
help="create an html with the plots",
)
args = parser.parse_args()
os.makedirs(OUTPUT_REPOSITORY, exist_ok=True)
dic_data: Dict[str, Any] = get_data(
file_path=os.path.join(DATA_REPOSITORY, "dress.json"), refresh=args.refresh
)
@ -533,6 +569,7 @@ if __name__ == "__main__":
analyse(np_data, np_date)
if not args.no_plot:
os.makedirs(OUTPUT_REPOSITORY, exist_ok=True)
plot_fields_args = get_age_vac_args()
f_fields = partial(plot_fields_by_age_vac, np_data, np_date)
plot_vac_percent_age_args = get_age_field_args()
@ -544,3 +581,6 @@ if __name__ == "__main__":
for field in Field:
plot_cumulative_field(np_data, np_date, field)
plot_bar_age_percent_by_field(np_data, np_date, field)
if args.to_html:
generate_html_page()

31
static/css/index.css Normal file
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@ -0,0 +1,31 @@
.main-container {
display: flex;
flex-direction: column;
flex-wrap: nowrap;
justify-content: center;
text-align: center;
}
.plot-container {
display: flex;
flex-direction: row;
justify-content: center;
align-items: center;
flex-wrap: wrap;
}
.plot-item {
flex: 0 1 33%
}
.img-bars {
width: 1500px;
height: 500px;
border: solid
}
img {
width: 100%;
height: 100%;
object-fit: contain;
}

45
templates/index.template.html Normal file
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@ -0,0 +1,45 @@
<!DOCTYPE html>
<html>
<head>
<title>Covid data extraction from DRESS dataset</title>
<meta charset="UTF-8">
<meta name="keywords" content="thegux, covid">
<link rel="stylesheet" href="{{ static }}/css/index.css">
<meta name="description" content="A simple page to share some useful data about covid 19">
</head>
<body>
<div class="main-container">
<h1>Thegux covid-19</h1>
<div>source : <a href="{{ src }}">Data DRESS</a></div>
<h3>Hospitalisations/Soins critiques/Décés par status vaccinal groupés par tranches d'âges</h3>
{% for field in fields %}
<img src="{{ static }}/plots/age_percent_vac_{{ field.name.lower() }}.png"/>
<img src="{{ static }}/plots/age_percent_unvac_{{ field.name.lower() }}.png"/>
{% endfor %}
<h3>Hospitalisations/Soins critiques/Décés par tranches d'âges groupés par status vaccinal</h3>
{% for age in ages %}
{% for field in fields %}
<img src="{{ static }}/plots/vac_percent_{{ age.name.lower() }}_{{ field.name.lower() }}.png"/>
{% endfor %}
{% endfor %}
<h3>Hospitalisations/Soins critiques/Décés par tranches d'âges et status vaccinal</h3>
<div class="plot-container">
{% for age in ages %}
{% for vac_status in status %}
<div class="plot-item">
<img src="{{ static }}/plots/all_{{ age.name.lower() }}_{{ vac_status.name.lower() }}.png"/>
</div>
{% endfor %}
{% endfor %}
</div>
<h3>Hospitalisations/Soins critiques/Décés cumulés par tranches d'âges et status vaccinal</h3>
<div class="plot-container">
{% for field in fields %}
<div class="plot-item">
<img src="{{ static }}/plots/cumulative_{{ field.name.lower() }}.png"/>
</div>
{% endfor %}
</div>
</div>
</body>
</html>