Redefined cleaning steps after revision

notes
Primoz 2022-09-22 13:45:51 +00:00
parent 247d758cb7
commit 19aa8707c0
1 changed files with 22 additions and 18 deletions

View File

@ -19,6 +19,7 @@ def straw_cleaning(sensor_data_files, provider):
excluded_columns = ['local_segment', 'local_segment_label', 'local_segment_start_datetime', 'local_segment_end_datetime']
# (1) FILTER_OUT THE ROWS THAT DO NOT HAVE THE TARGET COLUMN AVAILABLE
if config['PARAMS_FOR_ANALYSIS']['TARGET']['COMPUTE']:
target = config['PARAMS_FOR_ANALYSIS']['TARGET']['LABEL'] # get target label from config
@ -36,9 +37,16 @@ def straw_cleaning(sensor_data_files, provider):
# because of the lack of the availability. Secondly, there's a high importance that features data frame is checked if and NaN
# values still exist.
# (2) PARTIAL IMPUTATION: IMPUTE DATA DEPENDEND ON THE FEATURES GROUP (e.g., phone or E4 features)
# (2) REMOVE COLS IF THEIR NAN THRESHOLD IS PASSED (should be <= if even all NaN columns must be preserved - this solution now drops columns with all NaN rows)
# TODO: determine the threshold at which the column should be removed because of too many Nans.
features = features.loc[:, features.isna().sum() < provider["COLS_NAN_THRESHOLD"] * features.shape[0]]
# (3.1) QUALITY CHECK (DATA YIELD COLUMN) which determines if the row stays or not (if either E4 or phone is low quality the row is useless - TODO: determine threshold)
# Here, the imputation is still not executed - only quality check
impute_phone_features = provider["IMPUTE_PHONE_SELECTED_EVENT_FEATURES"]
if impute_phone_features["COMPUTE"]:
if True: #impute_phone_features["COMPUTE"]:
if not 'phone_data_yield_rapids_ratiovalidyieldedminutes' in features.columns:
raise KeyError("RAPIDS provider needs to impute the selected event features based on phone_data_yield_rapids_ratiovalidyieldedminutes column, please set config[PHONE_DATA_YIELD][PROVIDERS][RAPIDS][COMPUTE] to True and include 'ratiovalidyieldedminutes' in [FEATURES].")
@ -55,7 +63,9 @@ def straw_cleaning(sensor_data_files, provider):
mask = features['phone_data_yield_rapids_ratiovalidyieldedminutes'] > impute_phone_features['MIN_DATA_YIELDED_MINUTES_TO_IMPUTE']
features.loc[mask, phone_cols] = impute(features[mask][phone_cols], method=impute_phone_features["TYPE"].lower())
# ??? Drop rows with the value of data_yield_column less than data_yield_ratio_threshold ???
print(features[features['phone_data_yield_rapids_ratiovalidyieldedminutes'] > impute_phone_features['MIN_DATA_YIELDED_MINUTES_TO_IMPUTE']][phone_cols])
# ??? Drop rows with the value of data_yield_column less than data_yield_ratio_threshold ???
data_yield_unit = provider["DATA_YIELD_FEATURE"].split("_")[3].lower()
data_yield_column = "phone_data_yield_rapids_ratiovalidyielded" + data_yield_unit
@ -65,10 +75,13 @@ def straw_cleaning(sensor_data_files, provider):
if provider["DATA_YIELD_RATIO_THRESHOLD"]:
features = features[features[data_yield_column] >= provider["DATA_YIELD_RATIO_THRESHOLD"]]
# (3) REMOVE COLS IF THEIR NAN THRESHOLD IS PASSED (should be <= if even all NaN columns must be preserved - this solution now drops columns with all NaN rows)
features = features.loc[:, features.isna().sum() < provider["COLS_NAN_THRESHOLD"] * features.shape[0]]
# (3.2) (optional) DOES ROW CONSIST OF ENOUGH NON-NAN VALUES? Possible some of these examples could still pass previous condition but not this one?
# (4) REMOVE COLS WHERE VARIANCE IS 0
# (4) IMPUTATION: IMPUTE DATA WITH KNN METHOD
# - no other input restriction for this method except that rows are full enough and have reasonably high quality as assessed by data yield
# (5) REMOVE COLS WHERE VARIANCE IS 0
if provider["COLS_VAR_THRESHOLD"]:
features.drop(features.std()[features.std() == 0].index.values, axis=1, inplace=True)
@ -77,7 +90,7 @@ def straw_cleaning(sensor_data_files, provider):
if esm not in features:
features[esm] = esm_cols[esm]
# (5) DROP HIGHLY CORRELATED FEATURES
# (6) DROP HIGHLY CORRELATED FEATURES
drop_corr_features = provider["DROP_HIGHLY_CORRELATED_FEATURES"]
if drop_corr_features["COMPUTE"]:
@ -92,7 +105,7 @@ def straw_cleaning(sensor_data_files, provider):
features.drop(to_drop, axis=1, inplace=True)
# (6) Remove rows if threshold of NaN values is passed
# (7) Remove rows if threshold of NaN values is passed
min_count = math.ceil((1 - provider["ROWS_NAN_THRESHOLD"]) * features.shape[1]) # minimal not nan values in row
features.dropna(axis=0, thresh=min_count, inplace=True)
@ -101,20 +114,11 @@ def straw_cleaning(sensor_data_files, provider):
sns.heatmap(features.isna(), cbar=False)
plt.savefig(f'features_nans_bf_knn.png', bbox_inches='tight')
## (7) STANDARDIZATION
## (8) STANDARDIZATION
if provider["STANDARDIZATION"]:
features.loc[:, ~features.columns.isin(excluded_columns)] = StandardScaler().fit_transform(features.loc[:, ~features.columns.isin(excluded_columns)])
# (8) KNN IMPUTATION
impute_cols = [col for col in features.columns if col not in excluded_columns]
features[impute_cols] = impute(features[impute_cols], method="knn")
# (9) STANDARDIZATION AGAIN
if provider["STANDARDIZATION"]:
features.loc[:, ~features.columns.isin(excluded_columns)] = StandardScaler().fit_transform(features.loc[:, ~features.columns.isin(excluded_columns)])
sns.set(rc={"figure.figsize":(16, 8)})
sns.heatmap(features.isna(), cbar=False)