def __init__(self,
fips,
n_years=2,
n_samples=250,
suppression_policy=(0.35, 0.5, 0.75, 1),
skip_plots=False,
output_percentiles=(5, 25, 32, 50, 75, 68, 95),
generate_report=True):
self.fips = fips
self.t_list = np.linspace(0, 365 * n_years, 365 * n_years)
self.skip_plots = skip_plots
self.county_metadata = load_data.load_county_metadata_by_fips(fips)
self.output_percentiles = output_percentiles
self.n_samples = n_samples
self.n_years = n_years
self.t0 = fit_results.load_t0(fips)
self.date_generated = datetime.datetime.utcnow().isoformat()
self.suppression_policy = suppression_policy
self.summary = copy.deepcopy(self.__dict__)
self.summary.pop('t_list')
self.generate_report = generate_report
self.all_outputs = {}
self.output_file_report = os.path.join(
OUTPUT_DIR, self.county_metadata['state'], 'reports',
f"{self.county_metadata['state']}__{self.county_metadata['county']}__{self.fips}__ensemble_projections.pdf"
)
self.output_file_data = os.path.join(
OUTPUT_DIR, self.county_metadata['state'], 'data',
f"{self.county_metadata['state']}__{self.county_metadata['county']}__{self.fips}__ensemble_projections.json"
)
def __init__(
self,
fips,
n_years=0.5,
n_samples=250,
suppression_policy=(0.35, 0.5, 0.75, 1),
skip_plots=False,
output_percentiles=(5, 25, 32, 50, 75, 68, 95),
generate_report=True,
run_mode=RunMode.DEFAULT,
min_hospitalization_threshold=5,
hospitalization_to_confirmed_case_ratio=1 / 4,
):
self.fips = fips
self.agg_level = AggregationLevel.COUNTY if len(fips) == 5 else AggregationLevel.STATE
self.t_list = np.linspace(0, int(365 * n_years), int(365 * n_years) + 1)
self.skip_plots = skip_plots
self.run_mode = RunMode(run_mode)
self.hospitalizations_for_state = None
self.min_hospitalization_threshold = min_hospitalization_threshold
self.hospitalization_to_confirmed_case_ratio = hospitalization_to_confirmed_case_ratio
if self.agg_level is AggregationLevel.COUNTY:
self.county_metadata = load_data.load_county_metadata_by_fips(fips)
self.state_abbr = us.states.lookup(self.county_metadata["state"]).abbr
self.state_name = us.states.lookup(self.county_metadata["state"]).name
self.output_file_report = get_run_artifact_path(self.fips, RunArtifact.ENSEMBLE_REPORT)
self.output_file_data = get_run_artifact_path(self.fips, RunArtifact.ENSEMBLE_RESULT)
else:
self.state_abbr = us.states.lookup(self.fips).abbr
self.state_name = us.states.lookup(self.fips).name
self.output_file_report = None
self.output_file_data = get_run_artifact_path(self.fips, RunArtifact.ENSEMBLE_RESULT)
os.makedirs(os.path.dirname(self.output_file_data), exist_ok=True)
if self.output_file_report:
os.makedirs(os.path.dirname(self.output_file_report), exist_ok=True)
self.output_percentiles = output_percentiles
self.n_samples = n_samples
self.n_years = n_years
# TODO: Will be soon replaced with loaders for all the inferred params.
# self.t0 = fit_results.load_t0(fips)
self.date_generated = datetime.datetime.utcnow().isoformat()
self.suppression_policy = suppression_policy
self.summary = copy.deepcopy(self.__dict__)
self.summary.pop("t_list")
self.generate_report = generate_report
self.suppression_policies = None
self.override_params = dict()
self.init_run_mode()
self.all_outputs = {}
def __init__(self, fips, model_ensemble, county_outputs, filename, summary, xlim=(0, 360)):
self.fips = fips
self.county_outputs = county_outputs
self.model_ensemble = model_ensemble
self.county_metadata = load_data.load_county_metadata_by_fips(fips)
self.summary = summary
timeseries = combined_datasets.get_timeseries_for_fips(
fips, columns=[CommonFields.CASES, CommonFields.DEATHS], min_range_with_some_value=True
)
self.county_case_data = timeseries.data
self.report = PDFReport(filename=filename)
self.xlim = xlim
def __init__(self,
fips,
model_ensemble,
county_outputs,
filename,
summary,
xlim=(0, 360)):
self.fips = fips
self.county_outputs = county_outputs
self.model_ensemble = model_ensemble
self.county_metadata = load_data.load_county_metadata_by_fips(fips)
self.summary = summary
_county_case_data = load_data.load_county_case_data()
self.county_case_data = _county_case_data[_county_case_data['fips'] ==
fips]
self.report = PDFReport(filename=filename)
self.xlim = xlim
def get_run_artifact_path(fips, artifact, output_dir=None) -> str:
"""
Get an artifact path for a given locale and artifact type.
Parameters
----------
fips: str
State or county fips code. Can also be a 2 character state abbreviation.
If arbitrary string (e.g. for tests) then passed through
artifact: RunArtifact
The artifact type to retrieve the pointer for.
output_dir: str or NoneType
Output directory to obtain the path for.
Returns
-------
path: str
Location of the artifact.
"""
state_obj = us.states.lookup(fips[:2])
if len(fips) == 5:
agg_level = AggregationLevel.COUNTY
county = load_data.load_county_metadata_by_fips(fips)["county"]
elif len(fips) == 2:
agg_level = AggregationLevel.STATE
else:
agg_level = None
artifact = RunArtifact(artifact)
output_dir = output_dir or OUTPUT_DIR
if artifact is RunArtifact.RT_INFERENCE_REPORT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
REPORTS_FOLDER(output_dir, state_obj.name),
f"Rt_results__{state_obj.name}__{county}__{fips}.pdf",
)
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir),
"reports",
f"Rt_results__{state_obj.name}__{fips}.pdf",
)
elif artifact is RunArtifact.RT_SMOOTHING_REPORT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
REPORTS_FOLDER(output_dir, state_obj.name),
f"Rt_smoothing__{state_obj.name}__{county}__{fips}.pdf",
)
elif agg_level is AggregationLevel.STATE:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir),
"reports",
f"Rt_smoothing__{state_obj.name}__{fips}.pdf",
)
else: # For tests
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir),
"reports",
f"Rt_smoothing__{state_obj.name}__{fips}.pdf",
)
elif artifact is RunArtifact.RT_INFERENCE_RESULT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
DATA_FOLDER(output_dir, state_obj.name),
f"Rt_results__{state_obj.name}__{county}__{fips}.json",
)
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir),
"data",
f"Rt_results__{state_obj.name}__{fips}.json",
)
elif artifact is RunArtifact.MLE_FIT_REPORT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
REPORTS_FOLDER(output_dir, state_obj.name),
f"mle_fit_results__{state_obj.name}__{county}__{fips}.pdf",
)
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir),
"reports",
f"mle_fit_results__{state_obj.name}__{fips}.pdf",
)
elif artifact is RunArtifact.MLE_FIT_RESULT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir),
"data",
f"mle_fit_results__{state_obj.name}_counties.json",
)
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir),
"data",
f"mle_fit_results__{state_obj.name}_state_only.json",
)
elif artifact is RunArtifact.MLE_FIT_MODEL:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
DATA_FOLDER(output_dir, state_obj.name),
f"mle_fit_model__{state_obj.name}__{county}__{fips}.pkl",
)
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir),
"data",
f"mle_fit_model__{state_obj.name}_state_only.pkl",
)
elif artifact is RunArtifact.ENSEMBLE_RESULT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
DATA_FOLDER(output_dir, state_obj.name),
f"ensemble_projections__{state_obj.name}__{county}__{fips}.json",
)
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir),
"data",
f"ensemble_projections__{state_obj.name}__{fips}.json",
)
elif artifact is RunArtifact.ENSEMBLE_REPORT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
REPORTS_FOLDER(output_dir, state_obj.name),
f"ensemble_projections__{state_obj.name}__{county}__{fips}.pdf",
)
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir),
"reports",
f"ensemble_projections__{state_obj.name}__{fips}.pdf",
)
elif artifact is RunArtifact.WEB_UI_RESULT:
path = os.path.join(WEB_UI_FOLDER(output_dir), f"{fips}.__INTERVENTION_IDX__.json")
elif artifact is RunArtifact.WHITELIST_RESULT:
path = os.path.join(output_dir, "api_whitelist.json")
elif artifact is RunArtifact.BACKTEST_RESULT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
REPORTS_FOLDER(output_dir, state_obj.name),
f"backtest_results__{state_obj.name}__{county}__{fips}.pdf",
)
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir),
"reports",
f"backtest_results__{state_obj.name}__{fips}.pdf",
)
else:
raise ValueError(f"No paths available for artifact {RunArtifact}")
os.makedirs(os.path.dirname(path), exist_ok=True)
return path
def get_run_artifact_path(fips, artifact, output_dir=None):
"""
Get an artifact path for a given locale and artifact type.
Parameters
----------
fips: str
State or county fips code. Can also be a 2 character state abbreviation.
artifact: RunArtifact
The artifact type to retrieve the pointer for.
output_dir: str or NoneType
Output directory to obtain the path for.
Returns
-------
path: str
Location of the artifact.
"""
state_obj = us.states.lookup(fips[:2])
if len(fips) == 5:
agg_level = AggregationLevel.COUNTY
county = load_data.load_county_metadata_by_fips(fips)['county']
else:
agg_level = AggregationLevel.STATE
artifact = RunArtifact(artifact)
output_dir = output_dir or OUTPUT_DIR
if artifact is RunArtifact.RT_INFERENCE_REPORT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
REPORTS_FOLDER(output_dir, state_obj.name),
f'Rt_results__{state_obj.name}__{county}__{fips}.pdf')
else:
path = os.path.join(STATE_SUMMARY_FOLDER(output_dir), 'reports',
f'Rt_results__{state_obj.name}__{fips}.pdf')
elif artifact is RunArtifact.RT_INFERENCE_RESULT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
DATA_FOLDER(output_dir, state_obj.name),
f'Rt_results__{state_obj.name}__{county}__{fips}.json')
else:
path = os.path.join(STATE_SUMMARY_FOLDER(output_dir), 'data',
f'Rt_results__{state_obj.name}__{fips}.json')
elif artifact is RunArtifact.MLE_FIT_REPORT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
REPORTS_FOLDER(output_dir, state_obj.name),
f'mle_fit_results__{state_obj.name}__{county}__{fips}.pdf')
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir), 'reports',
f'mle_fit_results__{state_obj.name}__{fips}.pdf')
elif artifact is RunArtifact.MLE_FIT_RESULT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir), 'data',
f'mle_fit_results__{state_obj.name}_counties.json')
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir), 'data',
f'mle_fit_results__{state_obj.name}_state_only.json')
elif artifact is RunArtifact.MLE_FIT_MODEL:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
DATA_FOLDER(output_dir, state_obj.name),
f'mle_fit_model__{state_obj.name}__{county}__{fips}.pkl')
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir), 'data',
f'mle_fit_model__{state_obj.name}_state_only.pkl')
elif artifact is RunArtifact.ENSEMBLE_RESULT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
DATA_FOLDER(output_dir, state_obj.name),
f'ensemble_projections__{state_obj.name}__{county}__{fips}.json'
)
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir), 'data',
f'ensemble_projections__{state_obj.name}__{fips}.json')
elif artifact is RunArtifact.ENSEMBLE_REPORT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
REPORTS_FOLDER(output_dir, state_obj.name),
f'ensemble_projections__{state_obj.name}__{county}__{fips}.pdf'
)
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir), 'reports',
f'ensemble_projections__{state_obj.name}__{fips}.pdf')
elif artifact is RunArtifact.WEB_UI_RESULT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
WEB_UI_FOLDER(output_dir), 'county',
f'{state_obj.abbr}.{fips}.__INTERVENTION_IDX__.json')
else:
path = os.path.join(WEB_UI_FOLDER(output_dir), 'state',
f'{state_obj.abbr}.__INTERVENTION_IDX__.json')
elif artifact is RunArtifact.WHITELIST_RESULT:
path = os.path.join(output_dir, 'api_whitelist.json')
elif artifact is RunArtifact.BACKTEST_RESULT:
if agg_level is AggregationLevel.COUNTY:
path = os.path.join(
REPORTS_FOLDER(output_dir, state_obj.name),
f'backtest_results__{state_obj.name}__{county}__{fips}.pdf')
else:
path = os.path.join(
STATE_SUMMARY_FOLDER(output_dir), 'reports',
f'backtest_results__{state_obj.name}__{fips}.pdf')
else:
raise ValueError(f'No paths available for artifact {RunArtifact}')
os.makedirs(os.path.dirname(path), exist_ok=True)
return path
