handyspark

by dvgodoy

dvgodoy /handyspark

HandySpark - bringing pandas-like capabilities to Spark dataframes

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HandySpark

Bringing pandas-like capabilities to Spark dataframes!

HandySpark is a package designed to improve PySpark user experience, especially when it comes to exploratory data analysis, including visualization capabilities!

It makes fetching data or computing statistics for columns really easy, returning pandas objects straight away.

It also leverages on the recently released pandas UDFs in Spark to allow for an out-of-the-box usage of common pandas functions in a Spark dataframe.

Moreover, it introduces the stratify operation, so users can perform more sophisticated analysis, imputation and outlier detection on stratified data without incurring in very computationally expensive groupby operations.

It brings the long missing capability of plotting data while retaining the advantage of performing distributed computation (unlike many tutorials on the internet, which just convert the whole dataset to pandas and then plot it - don't ever do that!).

Finally, it also extends evaluation metrics for binary classification, so you can easily choose which threshold to use!

Google Colab

Eager to try it out right away? Don't wait any longer!

Open the notebook directly on Google Colab and try it yourself:

Installation

To install HandySpark from PyPI, just type:

python
pip install handyspark

Documentation

You can find the full documentation here.

Here is a handy list of direct links to some classes, objects and methods used:

Quick Start

To use HandySpark, all you need to do is import the package and, after loading your data into a Spark dataframe, call the toHandy() method to get your own HandyFrame: ```python from pyspark.sql import SparkSession spark = SparkSession.builder.getOrCreate()

from handyspark import * sdf = spark.read.csv('./tests/rawdata/train.csv', header=True, inferSchema=True) hdf = sdf.toHandy() ```

Fetching and plotting data

Now you can easily fetch data as if you were using pandas, just use the cols object from your HandyFrame:

python
hdf.cols['Name'][:5]

It should return a pandas Series object:

0                              Braund, Mr. Owen Harris
1    Cumings, Mrs. John Bradley (Florence Briggs Th...
2                               Heikkinen, Miss. Laina
3         Futrelle, Mrs. Jacques Heath (Lily May Peel)
4                             Allen, Mr. William Henry
Name: Name, dtype: object

If you include a list of columns, it will return a pandas DataFrame.

Due to the distributed nature of data in Spark, it is only possible to fetch the top rows of any given HandyFrame.

Using cols you have access to several pandas-like column and DataFrame based methods implemented in Spark:

  • min / max / median / q1 / q3 / stddev / mode
  • nunique
  • value_counts
  • corr
  • hist
  • boxplot
  • scatterplot

For instance:

python
hdf.cols['Embarked'].value_counts(dropna=False)
S      644
C      168
Q       77
NaN      2
Name: Embarked, dtype: int64

You can also make some plots:

python
from matplotlib import pyplot as plt
fig, axs = plt.subplots(1, 4, figsize=(12, 4))
hdf.cols['Embarked'].hist(ax=axs[0])
hdf.cols['Age'].boxplot(ax=axs[1])
hdf.cols['Fare'].boxplot(ax=axs[2])
hdf.cols[['Fare', 'Age']].scatterplot(ax=axs[3])

cols plots

Handy, right (pun intended!)? But things can get even more interesting if you use stratify!

Stratify

Stratifying a HandyFrame means using a split-apply-combine approach. It will first split your HandyFrame according to the specified (discrete) columns, then it will apply some function to each stratum of data and finally combine the results back together.

This is better illustrated with an example - let's try the stratified version of our previous

value_counts
:
python
hdf.stratify(['Pclass']).cols['Embarked'].value_counts()
Pclass  Embarked
1       C            85
        Q             2
        S           127
2       C            17
        Q             3
        S           164
3       C            66
        Q            72
        S           353
Name: value_counts, dtype: int64

Cool, isn't it? Besides, under the hood, not a single group by operation was performed - everything is handled using filter clauses! So, no data shuffling!

What if you want to stratify on a column containing continuous values? No problem!

hdf.stratify(['Sex', Bucket('Age', 2)]).cols['Embarked'].value_counts()
Sex     Age                                Embarked
female  Age >= 0.4200 and Age < 40.2100    C            46
                                           Q            12
                                           S           154
        Age >= 40.2100 and Age <= 80.0000  C            15
                                           S            32
male    Age >= 0.4200 and Age < 40.2100    C            53
                                           Q            11
                                           S           287
        Age >= 40.2100 and Age <= 80.0000  C            16
                                           Q             5
                                           S            81
Name: value_counts, dtype: int64

You can use either Bucket or Quantile to discretize your data in any given number of bins!

What about plotting it? Yes, HandySpark can handle that as well!

hdf.stratify(['Sex', Bucket('Age', 2)]).cols['Embarked'].hist(figsize=(8, 6))

stratified hist

Handling missing data

HandySpark makes it very easy to spot and fill missing values. To figure if there are any missing values, just use isnull:

python
hdf.isnull(ratio=True)
PassengerId    0.000000
Survived       0.000000
Pclass         0.000000
Name           0.000000
Sex            0.000000
Age            0.198653
SibSp          0.000000
Parch          0.000000
Ticket         0.000000
Fare           0.000000
Cabin          0.771044
Embarked       0.002245
Name: missing(ratio), dtype: float64

Ok, now you know there are 3 columns with missing values:

Age
,
Cabin
and
Embarked
. It's time to fill those values up! But, let's skip
Cabin
, which has 77% of its values missing!

So,

Age
is a continuous variable, while
Embarked
is a categorical variable. Let's start with the latter:
hdf_filled = hdf.fill(categorical=['Embarked'])

HandyFrame has a fill method which takes up to 3 arguments: - categorical: a list of categorical variables - continuous: a list of continuous variables - strategy: which strategy to use for each one of the continuous variables (either

mean
or
median
)

Categorical variables use a

mode
strategy by default.

But you do not need to stick with the basics anymore... you can fancy it up using stratify together with fill:

python
hdf_filled = hdf_filled.stratify(['Pclass', 'Sex']).fill(continuous=['Age'], strategy=['mean'])

How do you know which values are being used? Simple enough:

python
hdf_filled.statistics_
{'Age': {'Pclass == "1" and Sex == "female"': 34.61176470588235,
  'Pclass == "1" and Sex == "male"': 41.28138613861386,
  'Pclass == "2" and Sex == "female"': 28.722972972972972,
  'Pclass == "2" and Sex == "male"': 30.74070707070707,
  'Pclass == "3" and Sex == "female"': 21.75,
  'Pclass == "3" and Sex == "male"': 26.507588932806325},
 'Embarked': 'S'}

There you go! The filter clauses and the corresponding imputation values!

But there is more - once you're with your imputation procedure, why not generate a custom transformer to do that for you, either on your test set or in production?

You only need to call the imputer method of the transformer object that every HandyFrame has:

python
imputer = hdf_filled.transformers.imputer()

In the example above, imputer is now a full-fledged serializable PySpark transformer! What does that mean? You can use it in your pipeline and save / load at will :-)

Detecting outliers

Second only to the problem of missing data, outliers can pose a challenge for training machine learning models.

HandyFrame to the rescue, with its outliers method:

hdf_filled.outliers(method='tukey', k=3.)
PassengerId      0.0
Survived         0.0
Pclass           0.0
Age              1.0
SibSp           12.0
Parch          213.0
Fare            53.0
dtype: float64

Currently, only Tukey's method is available. This method takes an optional k argument, which you can set to larger values (like 3) to allow for a more loose detection.

The good thing is, now we can take a peek at the data by plotting it:

from matplotlib import pyplot as plt
fig, axs = plt.subplots(1, 4, figsize=(16, 4))
hdf_filled.cols['Parch'].hist(ax=axs[0])
hdf_filled.cols['SibSp'].hist(ax=axs[1])
hdf_filled.cols['Age'].boxplot(ax=axs[2], k=3)
hdf_filled.cols['Fare'].boxplot(ax=axs[3], k=3)

outliers

Let's focus on the

Fare
column - what can we do about it? Well, we could use Tukey's fences to, er... fence the outliers :-)
hdf_fenced = hdf_filled.fence(['Fare'])

Which values were used, you ask?

python
hdf_fenced.fences_
{'Fare': [-26.0105, 64.4063]}

It works quite similarly to the fill method and, I hope you guessed, it also gives you the ability to create the corresponding custom transformer :-)

fencer = hdf_fenced.transformers.fencer()

You can also use Mahalanobis distance to identify outliers in a multi-dimensional space, given a critical value (usually 99.9%, but you are free to have either more restriced or relaxed threshold).

To get the outliers for a subset of columns (only numerical columns are considered!):

outliers = hdf_filled.cols[['Age', 'Fare', 'SibSp']].get_outliers(critical_value=.90)

Let's take a look at the first 5 outliers found:

outliers.cols[:][:5]

outliers

What if you want to discard these sample? You just need to call

remove_outliers
:
hdf_without_outliers = hdf_filled.cols[['Age', 'Fare', 'SibSp']].remove_outliers(critical_value=0.90)

Evaluating your model!

You cleaned your data, you trained your classification model, you fine-tuned it and now you want to evaluate it, right?

from pyspark.ml.feature import VectorAssembler
from pyspark.ml.classification import RandomForestClassifier
from pyspark.ml.pipeline import Pipeline
from pyspark.ml.evaluation import BinaryClassificationEvaluator

assem = VectorAssembler(inputCols=['Fare', 'Pclass', 'Age'], outputCol='features') rf = RandomForestClassifier(featuresCol='features', labelCol='Survived', numTrees=20) pipeline = Pipeline(stages=[assem, rf]) model = pipeline.fit(hdf_fenced)

predictions = model.transform(hdf_fenced) evaluator = BinaryClassificationEvaluator(labelCol='Survived') evaluator.evaluate(predictions)

Then you realize evaluators only give you

areaUnderROC
and
areaUnderPR
. How about plotting ROC or PR curves? How about finding a threshold that suits your needs for False Positive or False negatives?

HandySpark extends the BinaryClassificationMetrics object to take DataFrames and output all your evaluation needs!

bcm = BinaryClassificationMetrics(predictions, scoreCol='probability', labelCol='Survived')

Now you can plot the curves...

from matplotlib import pyplot as plt
fig, axs = plt.subplots(1, 2, figsize=(12, 4))
bcm.plot_roc_curve(ax=axs[0])
bcm.plot_pr_curve(ax=axs[1])

curves

...or get metrics for every threshold...

bcm.getMetricsByThreshold().toPandas()[100:105]

metrics

...or the confusion matrix for the threshold you chose:

bcm.print_confusion_matrix(.572006)

cm

Pandas and more pandas!

With HandySpark you can feel almost as if you were using traditional pandas :-)

To gain access to the whole suite of available pandas functions, you need to leverage the pandas object of your HandyFrame:

python
some_ports = hdf_fenced.pandas['Embarked'].isin(values=['C', 'Q'])
some_ports
Column(Embarked,)`'>

In the example above, HandySpark treats the

Embarked
column as if it were a pandas Series and, therefore, you may call its isin method!

But, remember Spark has lazy evaluation, so the result is a column expression which leverages the power of pandas UDFs (provived that PyArrow is installed, otherwise it will fall back to traditional UDFs).

The only thing left to do is to actually assign the results to a new column, right? ```python hdffenced = hdffenced.assign(iscorq=someports)

What's in there?

hdf_fenced.cols['iscor_q'][:5] ```

0     True
1    False
2    False
3     True
4     True
Name: is_c_or_q, dtype: bool

You got that right! HandyFrame has a very convenient assign method, just like in pandas!

It does not get much easier than that :-) There are several column methods available already: - betweeen / betweentime - isin - isna / isnull - notna / notnull - abs - clip / cliplower / clipupper - replace - round / truncate - tzconvert / tz_localize

And this is not all! Both specialized str and dt objects from pandas are available as well!

For instance, if you want to find if a given string contains another substring?

col_mrs = hdf_fenced.pandas['Name'].str.find(sub='Mrs.')
hdf_fenced = hdf_fenced.assign(is_mrs=col_mrs > 0)

is mrs

There are many, many more available methods:

  1. String methods:
  2. contains
  3. startswith / endswitch
  4. match
  5. isalpha / isnumeric / isalnum / isdigit / isdecimal / isspace
  6. islower / isupper / istitle
  7. replace
  8. repeat
  9. join
  10. pad
  11. slice / slice_replace
  12. strip / lstrip / rstrip
  13. wrap / center / ljust / rjust
  14. translate
  15. get
  16. normalize
  17. lower / upper / capitalize / swapcase / title
  18. zfill
  19. count
  20. find / rfind
  21. len

  22. Date / Datetime methods:

  23. isleapyear / ismonthend / ismonthstart / isquarterend / isquarterstart / isyearend / isyearstart

  24. strftime

  25. tz / time / tzconvert / tzlocalize

  26. day / dayofweek / dayofyear / daysinmonth / daysinmonth

  27. hour / microsecond / minute / nanosecond / second

  28. week / weekday / weekday_name

  29. month / quarter / year / weekofyear

  30. date

  31. ceil / floor / round

  32. normalize

Your own functions

The sky is the limit! You can create regular Python functions and use assign to create new columns :-)

No need to worry about turning them into pandas UDFs - everything is handled by HandySpark under the hood!

The arguments of your function (or

lambda
) should have the names of the columns you want to use. For instance, to take the
log
of
Fare
:
import numpy as np
hdf_fenced = hdf_fenced.assign(logFare=lambda Fare: np.log(Fare + 1))

logfare

You can also use multiple columns:

hdf_fenced = hdf_fenced.assign(fare_times_age=lambda Fare, Age: Fare * Age)

Even though the result is kinda pointless, it will work :-)

Keep in mind that the return type, that is, the column type of the new column, will be the same as the first column used (

Fare
, in the example).

What if you want to return something of a different type?! No worries! You only need to wrap your function with the desired return type. An example should make this more clear:

from pyspark.sql.types import StringType

hdf_fenced = hdf_fenced.assign(str_fare=StringType.ret(lambda Fare: Fare.map('${:,.2f}'.format)))

hdf_fenced.cols['str_fare'][:5]

0    $65.66
1    $53.10
2    $26.55
3    $65.66
4    $65.66
Name: str_fare, dtype: object

Basically, we imported the desired output type - StringType - and used its extended method ret to wrap our

lambda
function that formats our numeric
Fare
column into a string.

It is also possible to create a more complex type, like an array of doubles:

from pyspark.sql.types import ArrayType, DoubleType

def make_list(Fare): return Fare.apply(lambda v: [v, v*2])

hdf_fenced = hdf_fenced.assign(fare_list=ArrayType(DoubleType()).ret(make_list))

hdf_fenced.cols['fare_list'][:5]

0           [7.25, 14.5]
1    [71.2833, 142.5666]
2         [7.925, 15.85]
3          [53.1, 106.2]
4           [8.05, 16.1]
Name: fare_list, dtype: object

OK, so, what happened here?

  1. First, we imported the necessary types, ArrayType and DoubleType, since we are building a function that returns a list of doubles.
  2. We actually built the function - notice that we call apply straight from Fare, which is treated as a pandas Series under the hood.
  3. We wrap the function with the return type
    ArrayType(DoubleType())
    by invoking the extended method
    ret
    .
  4. Finally, we assign it to a new column name, and that's it!

Nicer exceptions

Now, suppose you make a mistake while creating your function... if you have used Spark for a while, you already realized that, when an exception is raised, it will be loooong, right?

To help you with that, HandySpark analyzes the error message and parses it nicely for you at the very top of the error message, in bold red:

exception

Safety first

HandySpark wants to protect your cluster and network, so it implements a safety whenever you perform an operation that are going to retrieve ALL data from your HandyFrame, like

collect
or
toPandas
.

How does that work? Every time a HandyFrame has one of these methods called, it will output up to the safety limit, which has a default of 1,000 elements.

safety on

Do you want to set a different safety limit for your HandyFrame?

safety limit

What if you want to retrieve everything nonetheless?! You can invoke the safety_off method prior to the actual method you want to call and you get a one-time unlimited result.

safety off

Don't feel like Handy anymore?

To get back your original Spark dataframe, you only need to call notHandy to make it not handy again:

hdf_fenced.notHandy()
DataFrame[PassengerId: int, Survived: int, Pclass: int, Name: string, Sex: string, Age: double, SibSp: int, Parch: int, Ticket: string, Fare: double, Cabin: string, Embarked: string, logFare: double, is_c_or_q: boolean]

Comments, questions, suggestions, bugs

DISCLAIMER: this is a project under development, so it is likely you'll run into bugs/problems.

So, if you find any bugs/problems, please open an issue or submit a pull request.

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