Commit bd7e1872 authored by Chris Jewell's avatar Chris Jewell
Browse files

Added insample7 summary to summary_longformat.xlsx

parent 5a862f51
......@@ -194,7 +194,7 @@ def run_pipeline(global_config, results_directory, cli_options):
# DSTL Summary
rf.transform(
[[process_data, insample14, medium_term, next_generation_matrix]],
[[process_data, insample7, insample14, medium_term, next_generation_matrix]],
rf.formatter(),
wd("summary_longformat.xlsx"),
)(summary_longformat)
......
......@@ -76,9 +76,10 @@ def summary_longformat(input_files, output_file):
csv file.
:param input_files: a list of filenames [data_pkl,
insample14_pkl,
medium_term_pred_pkl,
ngm_pkl]
insample7_nc
insample14_nc,
medium_term_pred_nc,
ngm_nc]
:param output_file: the output CSV with columns `[date,
location,value_name,value,q0.025,q0.975]`
"""
......@@ -97,11 +98,18 @@ def summary_longformat(input_files, output_file):
insample_df = xarray2summarydf(
insample["events"][..., 2].reset_coords(drop=True)
)
insample_df["value_name"] = "insample7_Cases"
df = pd.concat([df, insample_df], axis="index")
insample = xarray.open_dataset(input_files[2])
insample_df = xarray2summarydf(
insample["events"][..., 2].reset_coords(drop=True)
)
insample_df["value_name"] = "insample14_Cases"
df = pd.concat([df, insample_df], axis="index")
# Medium term incidence
medium_term = xarray.open_dataset(input_files[2])
medium_term = xarray.open_dataset(input_files[3])
medium_df = xarray2summarydf(
medium_term["events"][..., 2].reset_coords(drop=True)
)
......@@ -121,7 +129,7 @@ def summary_longformat(input_files, output_file):
df = pd.concat([df, prev_df], axis="index")
# Rt
ngms = xarray.load_dataset(input_files[3])["ngm"]
ngms = xarray.load_dataset(input_files[4])["ngm"]
rt = ngms.sum(dim="dest")
rt = rt.rename({"src": "location"})
rt_summary = xarray2summarydf(rt)
......@@ -144,3 +152,33 @@ def summary_longformat(input_files, output_file):
value=df["value"],
quantiles={q: df[q] for q in quantiles},
).to_excel(output_file, index=False)
if __name__ == "__main__":
import os
import argparse
parser = argparse.ArgumentParser()
parser.add_argument(
"--output", "-o", type=str, required=True, help="Output file"
)
parser.add_argument(
"resultsdir",
type=str,
help="Results directory",
)
args = parser.parse_args()
input_files = [
os.path.join(args.resultsdir, d)
for d in [
"pipeline_data.pkl",
"insample7.nc",
"insample14.nc",
"medium_term.nc",
"ngm.nc",
]
]
summary_longformat(input_files, args.output)
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