Perform preprocessing operations from pandas on Spark dataframe

Question

I have a rather large CSV so I am using AWS EMR to read the data into a Spark dataframe to perform some operations. I have a pandas function that does some simple preprocessing:

def clean_census_data(df):
    """
    This function cleans the dataframe and drops columns that contain 70% NaN values
    """
    # Replace None or 0 with np.nan
    df = df.replace('None', np.nan)
    # Replace weird numbers
    df = df.replace(-666666666.0, np.nan)
    
    # Drop columns that contain 70% NaN or 0 values
    df = df.loc[:, df.isnull().mean() < .7]
    
    
    return df

I want to apply this function onto a Spark dataframe, but the functions are not the same. I am not familiar with Spark and performing these rather simple operations in pandas is not obvious to me how to perform the same operations in Spark. I know I can convert a Spark dataframe into pandas, but that does not seem very efficient.

Asked By: justanewb

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Source

Answer 1

Native Spark functions can do such aggregation for every column.
The following dataframe contains the percentage of nulls, nans and zeros.

df2 = df1.select(
    [(F.count(F.when(F.isnan(c) | F.isnull(c) | (F.col(c) == 0), c))
     / F.count(F.lit(1))).alias(c) 
     for c in df1.columns]
)

With an example:

from pyspark.sql import functions as F
df1 = spark.createDataFrame(
    [(1000, 0, None),
     (None, 2, None),
     (None, 3, 2222),
     (None, 4, 2233),
     (None, 5, 2244)],
    ['c1', 'c2', 'c3'])

df2 = df1.select(
    [(F.count(F.when(F.isnan(c) | F.isnull(c) | (F.col(c) == 0), c))
     / F.count(F.lit(1))).alias(c) 
     for c in df1.columns]
)
df2.show()
# +---+---+---+
# | c1| c2| c3|
# +---+---+---+
# |0.8|0.2|0.4|
# +---+---+---+

What remains is just selecting the columns from df1:

df = df1.select([c for c in df1.columns if df2.head()[c] < .7])
df.show()
# +---+----+
# | c2|  c3|
# +---+----+
# |  0|null|
# |  2|null|
# |  3|2222|
# |  4|2233|
# |  5|2244|
# +---+----+

The percentage is calculated based on this condition, change it according to your needs:
F.isnan(c) | F.isnull(c) | (F.col(c) == 0)

This would replace None with np.nan:
df.fillna(np.nan)

This would replace specified value with np.nan:
df.replace(-666666666, np.nan)

Answered By: ZygD

Answer 2

First answer, so please be kind. This function should work with pyspark dataframes instead of pandas dataframes, and should give you similar results:

def clean_census_data(df):
    """
    This function cleans the dataframe and drops columns that contain 70% NaN values
    """
    # Replace None or 0 with np.nan
    df = df.replace('None', None)

    # Replace weird numbers
    df = df.replace(-666666666.0, None)

    # Drop columns that contain 70% NaN or 0 values
    selection_dict = df.select([(count(when(isnan(c) | col(c).isNull() | (col(c).cast('int') == 0), c))/count(c) > .7).alias(c) for c in df.columns]).first().asDict()
    columns_to_remove = [name for name, is_selected in selection_dict.items() if is_selected]
    df = df.drop(*columns_to_remove)

    return df

Attention: The resulting dataframe contains None instead of np.nan.

Answered By: KnutKiesel

Perform preprocessing operations from pandas on Spark dataframe

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