Switch to Era5t data (#29)

* Add paths and global variables in config

* Change lines to switch to ERA5T

* Add predict for xgboost model and modify add lags

* Modify unitary tests

pyro_risks/config.py

@@ -24,6 +24,7 @@
 TEST_FR_VIIRS_XLSX_FALLBACK: str = f"{DATA_FALLBACK}/test_data_VIIRS.xlsx"
 TEST_FR_VIIRS_JSON_FALLBACK: str = f"{DATA_FALLBACK}/test_data_VIIRS.json"
 TEST_FR_ERA5_2019_FALLBACK: str = f"{DATA_FALLBACK}/test_data_ERA5_2019.nc"
+TEST_FR_ERA5T_FALLBACK: str = f"{DATA_FALLBACK}/test_era5t_to_merge.nc"
 TEST_FWI_FALLBACK: str = f"{DATA_FALLBACK}/test_data_FWI.csv"
 TEST_FWI_TO_PREDICT: str = f"{DATA_FALLBACK}/fwi_test_to_predict.csv"
 TEST_ERA_TO_PREDICT: str = f"{DATA_FALLBACK}/era_test_to_predict.csv"
@@ -37,7 +38,30 @@
 CDS_API_KEY = os.getenv('CDS_API_KEY')
 
 RFMODEL_PATH: str = f"{DATA_FALLBACK}/pyrorisk_rfc_111220.pkl"
+RFMODEL_ERA5T_PATH: str = f"{DATA_FALLBACK}/pyrorisk_rfc_era5t_151220.pkl"
 XGBMODEL_PATH: str = f"{DATA_FALLBACK}/pyrorisk_xgb_091220.pkl"
+XGBMODEL_ERA5T_PATH: str = f"{DATA_FALLBACK}/pyrorisk_xgb_era5t_151220.pkl"
+
+FWI_VARS = ['fwi', 'ffmc', 'dmc', 'dc', 'isi', 'bui', 'dsr']
+WEATHER_VARS = [
+    'u10', 'v10', 'd2m', 't2m', 'fal', 'lai_hv', 'lai_lv', 'skt',
+    'asn', 'snowc', 'rsn', 'sde', 'sd', 'sf', 'smlt', 'stl1', 'stl2',
+    'stl3', 'stl4', 'slhf', 'ssr', 'str', 'sp', 'sshf', 'ssrd', 'strd', 'tsn', 'tp'
+]
+WEATHER_ERA5T_VARS = ['asn', 'd2m', 'e', 'es', 'fal', 'lai_hv', 'lai_lv', 'lblt',
+                      'licd', 'lict', 'lmld', 'lmlt', 'lshf', 'ltlt', 'pev', 'ro', 'rsn', 'sd', 'sf', 'skt',
+                      'slhf', 'smlt', 'sp', 'src', 'sro', 'sshf', 'ssr', 'ssrd', 'ssro', 'stl1', 'stl2', 'stl3',
+                      'stl4', 'str', 'strd', 'swvl1', 'swvl2', 'swvl3', 'swvl4', 't2m', 'tp', 'tsn', 'u10', 'v10']
+
+MODEL_ERA5T_VARS = ['str_max', 'str_mean', 'ffmc_min', 'str_min', 'ffmc_mean',
+                    'str_mean_lag1', 'str_max_lag1', 'str_min_lag1', 'isi_min',
+                    'ffmc_min_lag1', 'isi_mean', 'ffmc_mean_lag1', 'ffmc_std', 'ffmc_max',
+                    'isi_min_lag1', 'isi_mean_lag1', 'ffmc_max_lag1', 'asn_std', 'strd_max',
+                    'ssrd_min', 'strd_mean', 'isi_max', 'strd_min', 'd2m_min', 'asn_min',
+                    'ssr_min', 'ffmc_min_lag3', 'ffmc_std_lag1', 'lai_hv_mean_lag7',
+                    'str_max_lag3', 'str_mean_lag3', 'rsn_std_lag1', 'fwi_mean', 'ssr_mean',
+                    'ssrd_mean', 'swvl1_mean', 'rsn_std_lag3', 'isi_max_lag1', 'd2m_mean',
+                    'rsn_std']
 
 MODEL_VARIABLES = ['ffmc_min', 'str_mean', 'str_min', 'str_max', 'ffmc_mean', 'isi_min',
                    'ffmc_min_lag1', 'strd_mean', 'isi_mean', 'strd_min', 'strd_max',
@@ -48,6 +72,7 @@
                    'strd_min_lag1', 'ffmc_min_lag3', 'ffmc_std_lag1', 'strd_mean_lag1',
                    'rsn_mean_lag1', 'fwi_mean', 'isi_max_lag1', 'sd_max', 'strd_max_lag1',
                    'rsn_mean', 'snowc_std_lag7', 'stl1_std_lag3']
+
 TRAIN_SELECTED_DEP = ['Aisne', 'Alpes-Maritimes', 'Ardèche', 'Ariège', 'Aude', 'Aveyron',
                       'Cantal', 'Eure', 'Eure-et-Loir', 'Gironde', 'Haute-Corse', 'Hautes-Pyrénées',
                       'Hérault', 'Indre', 'Landes', 'Loiret', 'Lozère', 'Marne', 'Oise',

pyro_risks/datasets/era_fwi_viirs.py

@@ -1,9 +1,10 @@
 import logging
 import pandas as pd
 
-from pyro_risks.datasets import NASAFIRMS_VIIRS, ERA5Land
+from pyro_risks.datasets import NASAFIRMS_VIIRS, ERA5Land, ERA5T
 from pyro_risks.datasets.utils import get_intersection_range
 from pyro_risks.datasets.fwi import GwisFwi
+from pyro_risks import config as cfg
 
 __all__ = ["MergedEraFwiViirs"]
 
@@ -28,19 +29,15 @@ def process_dataset_to_predict(fwi, era):
 
     # Group fwi dataframe by day and department and compute min, max, mean, std
     agg_fwi_df = fwi_df.groupby(['day', 'nom'])[
-        'fwi', 'ffmc', 'dmc', 'dc', 'isi', 'bui', 'dsr'
-    ].agg(['min', 'max', 'mean', 'std']).reset_index()
+        cfg.FWI_VARS].agg(['min', 'max', 'mean', 'std']).reset_index()
     agg_fwi_df.columns = ['day', 'nom'] + \
         [x[0] + '_' + x[1] for x in agg_fwi_df.columns if x[1] != '']
 
     logger.info("Finished aggregationg of FWI")
 
     # Group weather dataframe by day and department and compute min, max, mean, std
     agg_wth_df = weather.groupby(['time', 'nom'])[
-        'u10', 'v10', 'd2m', 't2m', 'fal', 'lai_hv', 'lai_lv', 'skt',
-        'asn', 'snowc', 'rsn', 'sde', 'sd', 'sf', 'smlt', 'stl1', 'stl2',
-        'stl3', 'stl4', 'slhf', 'ssr', 'str', 'sp', 'sshf', 'ssrd', 'strd', 'tsn', 'tp'
-    ].agg(['min', 'max', 'mean', 'std']).reset_index()
+        cfg.WEATHER_ERA5T_VARS].agg(['min', 'max', 'mean', 'std']).reset_index()
     agg_wth_df.columns = ['day', 'nom'] + \
         [x[0] + '_' + x[1] for x in agg_wth_df.columns if x[1] != '']
 
@@ -75,7 +72,7 @@ def __init__(self, era_source_path=None, viirs_source_path=None, fwi_source_path
             viirs_source_path (str, optional): Viirs data source path. Defaults to None.
             fwi_source_path (str, optional): Fwi data source path. Defaults to None.
         """
-        weather = ERA5Land(era_source_path)
+        weather = ERA5T(era_source_path)  # ERA5Land(era_source_path)
         nasa_firms = NASAFIRMS_VIIRS(viirs_source_path)
 
         # Time span selection
@@ -100,17 +97,13 @@ def __init__(self, era_source_path=None, viirs_source_path=None, fwi_source_path
 
         # Group fwi dataframe by day and department and compute min, max, mean, std
         agg_fwi_df = fwi_df.groupby(['day', 'departement'])[
-            'fwi', 'ffmc', 'dmc', 'dc', 'isi', 'bui', 'dsr'
-        ].agg(['min', 'max', 'mean', 'std']).reset_index()
+            cfg.FWI_VARS].agg(['min', 'max', 'mean', 'std']).reset_index()
         agg_fwi_df.columns = ['day', 'departement'] + \
             [x[0] + '_' + x[1] for x in agg_fwi_df.columns if x[1] != '']
 
         # Group weather dataframe by day and department and compute min, max, mean, std
         agg_wth_df = weather.groupby(['time', 'nom'])[
-            'u10', 'v10', 'd2m', 't2m', 'fal', 'lai_hv', 'lai_lv', 'skt',
-            'asn', 'snowc', 'rsn', 'sde', 'sd', 'sf', 'smlt', 'stl1', 'stl2',
-            'stl3', 'stl4', 'slhf', 'ssr', 'str', 'sp', 'sshf', 'ssrd', 'strd', 'tsn', 'tp'
-        ].agg(['min', 'max', 'mean', 'std']).reset_index()
+            cfg.WEATHER_ERA5T_VARS].agg(['min', 'max', 'mean', 'std']).reset_index()
         agg_wth_df.columns = ['day', 'departement'] + \
             [x[0] + '_' + x[1] for x in agg_wth_df.columns if x[1] != '']
 

pyro_risks/models/predict.py

@@ -1,9 +1,10 @@
 import joblib
 from urllib.request import urlopen
+import xgboost
 
 from pyro_risks import config as cfg
 from pyro_risks.datasets.fwi import get_fwi_data_for_predict
-from pyro_risks.datasets.ERA5 import get_data_era5land_for_predict
+from pyro_risks.datasets.ERA5 import get_data_era5land_for_predict, get_data_era5t_for_predict
 from pyro_risks.datasets.era_fwi_viirs import process_dataset_to_predict
 from pyro_risks.models.score_v0 import add_lags
 
@@ -28,10 +29,13 @@ def __init__(self, which='RF'):
             which (str, optional): Can be 'RF' for random forest or 'XGB' for xgboost. Defaults to 'RF'.
         """
         if which == 'RF':
-            self.model_path = cfg.RFMODEL_PATH
+            self.model_path = cfg.RFMODEL_ERA5T_PATH
         elif which == 'XGB':
-            self.model_path = cfg.XGBMODEL_PATH
+            self.model_path = cfg.XGBMODEL_ERA5T_PATH
+        else:
+            raise ValueError("Model can be only of type RF or XGB")
         self.model = joblib.load(urlopen(self.model_path))
+        self._model_type = which
 
     def get_input(self, day):
         """Returns for a given day data to feed into the model.
@@ -45,12 +49,15 @@ def get_input(self, day):
         Returns:
             pd.DataFrame
         """
-        model_cols = cfg.MODEL_VARIABLES
+        model_cols = cfg.MODEL_ERA5T_VARS
         fwi = get_fwi_data_for_predict(day)
-        era = get_data_era5land_for_predict(day)
+        era = get_data_era5t_for_predict(day)
         res_test = process_dataset_to_predict(fwi, era)
         res_test = res_test.rename({'nom': 'departement'}, axis=1)
-        res_lags = add_lags(res_test, res_test.drop(['day', 'departement'], axis=1).columns)
+        # Add lags only for columns on which model was trained on
+        cols_lags = ['_'.join(x.split('_')[:-1]) for x in cfg.MODEL_ERA5T_VARS if '_lag' in x]
+        res_lags = add_lags(res_test, cols_lags)
+        # Select only rows corresponding to day
         to_predict = res_lags.loc[res_lags['day'] == day]
         to_predict = to_predict.drop('day', axis=1).set_index('departement')
         # Some NaN due to the aggregations on departments with only one line (variables with std)
@@ -68,9 +75,15 @@ def predict(self, day, country='France'):
             country (str, optional): Defaults to 'France'.
 
         Returns:
-            dict: keys are departements and values model probability predictions for label 1 (fire)
+            dict: keys are departements, values dictionaries whose keys are score and explainability
+            and values probability predictions for label 1 (fire) and feature contributions to predictions
+            respectively
         """
         sample = self.get_input(day)
-        predictions = self.model.predict_proba(sample.values)
-        res = dict(zip(sample.index, predictions[:, 1].round(3)))
+        if self._model_type == 'RF':
+            predictions = self.model.predict_proba(sample.values)
+            res = dict(zip(sample.index, predictions[:, 1].round(3)))
+        elif self._model_type == 'XGB':
+            predictions = self.model.predict(xgboost.DMatrix(sample))
+            res = dict(zip(sample.index, predictions.round(3)))
         return {x: {'score': res[x], 'explainability': None} for x in res}

test/test_datasets.py

@@ -428,11 +428,12 @@ def test_era5t(self):
 
     def test_MergedEraFwiViirs(self):
         ds = era_fwi_viirs.MergedEraFwiViirs(
-            era_source_path=cfg.TEST_FR_ERA5_2019_FALLBACK,
+            era_source_path=cfg.TEST_FR_ERA5T_FALLBACK,
             viirs_source_path=None,
             fwi_source_path=cfg.TEST_FWI_FALLBACK,
         )
         self.assertIsInstance(ds, pd.DataFrame)
+        self.assertTrue(len(ds) > 0)
 
     def test_call_era5land(self):
         with tempfile.TemporaryDirectory() as tmp:

test/test_models.py

@@ -79,13 +79,13 @@ def test_xgb_model(self):
     def test_pyrorisk(self):
         pr = predict.PyroRisk(which='RF')
         self.assertEqual(pr.model.n_estimators, 500)
-        self.assertEqual(pr.model_path, cfg.RFMODEL_PATH)
+        self.assertEqual(pr.model_path, cfg.RFMODEL_ERA5T_PATH)
         res = pr.get_input('2020-05-05')
         self.assertIsInstance(res, pd.DataFrame)
-        self.assertEqual(res.shape, (93, 41))
+        self.assertEqual(res.shape, (93, 40))
         preds = pr.predict('2020-05-05')
         self.assertEqual(len(preds), 93)
-        self.assertEqual(preds['Ardennes'], {'score': 0.11, 'explainability': None})
+        self.assertEqual(preds['Ardennes'], {'score': 0.246, 'explainability': None})
 
 
 if __name__ == "__main__":