rapids/src/features/all_cleaning_individual/straw/main.py

import pandas as pd
import numpy as np
import math, sys

def straw_cleaning(sensor_data_files, provider):
    
    features = pd.read_csv(sensor_data_files["sensor_data"][0])

    # Impute selected features event
    impute_phone_features = provider["IMPUTE_PHONE_SELECTED_EVENT_FEATURES"]
    if 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].")
        
        phone_cols = [col for col in features if \
            col.startswith('phone_applications_foreground_rapids_') or
            col.startswith('phone_battery_rapids_') or
            col.startswith('phone_calls_rapids_') or
            col.startswith('phone_keyboard_rapids_') or
            col.startswith('phone_messages_rapids_') or
            col.startswith('phone_screen_rapids_') or
            col.startswith('phone_wifi_')]

        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"])

    # 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

    if not data_yield_column in features.columns:
        raise KeyError(f"RAPIDS provider needs to impute the selected event features based on {data_yield_column} column, please set config[PHONE_DATA_YIELD][PROVIDERS][RAPIDS][COMPUTE] to True and include 'ratiovalidyielded{data_yield_unit}' in [FEATURES].")
        
    features = features[features[data_yield_column] >= provider["DATA_YIELD_RATIO_THRESHOLD"]]

    # Remove cols if threshold of NaN values is passed
    features = features.loc[:, features.isna().sum() < provider["COLS_NAN_THRESHOLD"] * features.shape[0]]

    # Remove cols where variance is 0
    if provider["COLS_VAR_THRESHOLD"]:
        features.drop(features.std()[features.std() == 0].index.values, axis=1, inplace=True)
    
    # Drop highly correlated features - To-Do še en thershold var, ki je v config + kako se tretirajo NaNs?
    drop_corr_features = provider["DROP_HIGHLY_CORRELATED_FEATURES"]
    if drop_corr_features["COMPUTE"]:
        numerical_cols = features.select_dtypes(include=np.number).columns.tolist()

        cor_matrix = features[numerical_cols].corr(method='spearman').abs()

        upper_tri = cor_matrix.where(np.triu(np.ones(cor_matrix.shape), k=1).astype(np.bool))

        to_drop = [column for column in upper_tri.columns if any(upper_tri[column] > drop_corr_features["CORR_THRESHOLD"])]

        # Tukaj je še neka validacija s thresholdom, ampak ne razumem R kode "valid_pairs" 
        features.drop(to_drop, axis=1, inplace=True)

    # Remove rows if threshold of NaN values is passed
    min_count =  math.ceil((1 - provider["ROWS_NAN_THRESHOLD"]) * features.shape[1]) # min not nan values in row
    features.dropna(axis=0, thresh=min_count, inplace=True)

    return features

def impute(df, method='zero'):
    df.loc[:, df.isna().all()] = df.loc[:, df.isna().all()].fillna(0) # if column contains only NaN values impute it with 0
    return { # rest of the columns should be imputed with the selected method
        'zero': df.fillna(0),
        'mean': df.fillna(df.mean()),
        'median': df.fillna(df.median()),
        'k-nearest': None # To-Do
    }[method]