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I am getting duplicates when joining on two dataframes where one key is a decimal and the other is a string. It seems that Spark is converting the decimal to a string which results in a scientific notation expression, but then shows the original result in decimal form just fine. I found a workaround by converting to string directly, but this seems dangerous as duplicates are created without warning.
Is this a bug? How can I detect when this is happening?
Here's an demo in pyspark on Spark 2.4:
>>> from pyspark.sql.functions import *
>>> from pyspark.sql.types import *
>>> df1 = spark.createDataFrame([('a', 9223372034559809871), ('b', 9223372034559809771)], ['group', 'id_int'])
>>> df1=df1.withColumn('id',col('id_int').cast(DecimalType(38,0)))
>>>
>>> df1.show()
+-----+-------------------+-------------------+
|group| id_int| id|
+-----+-------------------+-------------------+
| a|9223372034559809871|9223372034559809871|
| b|9223372034559809771|9223372034559809771|
+-----+-------------------+-------------------+
>>>
>>> df2= spark.createDataFrame([(1, '9223372034559809871'), (2, '9223372034559809771')], ['value', 'id'])
>>> df2.show()
+-----+-------------------+
|value| id|
+-----+-------------------+
| 1|9223372034559809871|
| 2|9223372034559809771|
+-----+-------------------+
>>>
>>> df1.join(df2, ["id"]).show()
+-------------------+-----+-------------------+-----+
| id|group| id_int|value|
+-------------------+-----+-------------------+-----+
|9223372034559809871| a|9223372034559809871| 1|
|9223372034559809871| a|9223372034559809871| 2|
|9223372034559809771| b|9223372034559809771| 1|
|9223372034559809771| b|9223372034559809771| 2|
+-------------------+-----+-------------------+-----+
>>> df1.dtypes
[('group', 'string'), ('id_int', 'bigint'), ('id', 'decimal(38,0)')]
It's happenning because of the values (very very large) in the joining keys:
I tweaked the values in the joining condition and it's giving me the proper results :
from pyspark.sql.types import *
df1 = spark.createDataFrame([('a', 9223372034559809871), ('b', 9123372034559809771)],
['group', 'id_int'])
df1=df1.withColumn('id',col('id_int').cast(DecimalType(38,0)))
df2= spark.createDataFrame([(1, '9223372034559809871'), (2, '9123372034559809771')],
['value', 'id'])
df1.join(df2, df1["id"]==df2["id"],"inner").show()
I am trying to apply a user defined function to Window in PySpark. I have read that UDAF might be the way to to go, but I was not able to find anything concrete.
To give an example (taken from here: Xinh's Tech Blog and modified for PySpark):
from pyspark import SparkConf
from pyspark.sql import SparkSession
from pyspark.sql.window import Window
from pyspark.sql.functions import avg
spark = SparkSession.builder.master("local").config(conf=SparkConf()).getOrCreate()
a = spark.createDataFrame([[1, "a"], [2, "b"], [3, "c"], [4, "d"], [5, "e"]], ['ind', "state"])
customers = spark.createDataFrame([["Alice", "2016-05-01", 50.00],
["Alice", "2016-05-03", 45.00],
["Alice", "2016-05-04", 55.00],
["Bob", "2016-05-01", 25.00],
["Bob", "2016-05-04", 29.00],
["Bob", "2016-05-06", 27.00]],
["name", "date", "amountSpent"])
customers.show()
window_spec = Window.partitionBy("name").orderBy("date").rowsBetween(-1, 1)
result = customers.withColumn( "movingAvg", avg(customers["amountSpent"]).over(window_spec))
result.show()
I am applying avg which is already built into pyspark.sql.functions, but if instead of avg I wanted to use something of more complicated and write my own function, how would I do that?
Spark >= 3.0:
SPARK-24561 - User-defined window functions with pandas udf (bounded window) is a a work in progress. Please follow the related JIRA for details.
Spark >= 2.4:
SPARK-22239 - User-defined window functions with pandas udf (unbounded window) introduced support for Pandas based window functions with unbounded windows. General structure is
return_type: DataType
#pandas_udf(return_type, PandasUDFType.GROUPED_AGG)
def f(v):
return ...
w = (Window
.partitionBy(grouping_column)
.rowsBetween(Window.unboundedPreceding, Window.unboundedFollowing))
df.withColumn('foo', f('bar').over(w))
Please see the doctests and the unit tests for detailed examples.
Spark < 2.4
You cannot. Window functions require UserDefinedAggregateFunction or equivalent object, not UserDefinedFunction, and it is not possible to define one in PySpark.
However, in PySpark 2.3 or later, you can define vectorized pandas_udf, which can be applied on grouped data. You can find a working example Applying UDFs on GroupedData in PySpark (with functioning python example). While Pandas don't provide direct equivalent of window functions, there are expressive enough to implement any window-like logic, especially with pandas.DataFrame.rolling. Furthermore function used with GroupedData.apply can return arbitrary number of rows.
You can also call Scala UDAF from PySpark Spark: How to map Python with Scala or Java User Defined Functions?.
UDFs can be applied to Window now as of Spark 3.0.0.
https://spark.apache.org/docs/3.1.2/api/python/reference/api/pyspark.sql.functions.pandas_udf.html
Extract from the documentation:
from pyspark.sql import Window
#pandas_udf("double")
def mean_udf(v: pd.Series) -> float:
return v.mean()
df = spark.createDataFrame(
[(1, 1.0), (1, 2.0), (2, 3.0), (2, 5.0), (2, 10.0)], ("id", "v"))
w = Window.partitionBy('id').orderBy('v').rowsBetween(-1, 0)
df.withColumn('mean_v', mean_udf("v").over(w)).show()
+---+----+------+
| id| v|mean_v|
+---+----+------+
| 1| 1.0| 1.0|
| 1| 2.0| 1.5|
| 2| 3.0| 3.0|
| 2| 5.0| 4.0|
| 2|10.0| 7.5|
+---+----+------+
How do I handle categorical data with spark-ml and not spark-mllib ?
Thought the documentation is not very clear, it seems that classifiers e.g. RandomForestClassifier, LogisticRegression, have a featuresCol argument, which specifies the name of the column of features in the DataFrame, and a labelCol argument, which specifies the name of the column of labeled classes in the DataFrame.
Obviously I want to use more than one feature in my prediction, so I tried using the VectorAssembler to put all my features in a single vector under featuresCol.
However, the VectorAssembler only accepts numeric types, boolean type, and vector type (according to the Spark website), so I can't put strings in my features vector.
How should I proceed?
I just wanted to complete Holden's answer.
Since Spark 2.3.0,OneHotEncoder has been deprecated and it will be removed in 3.0.0. Please use OneHotEncoderEstimator instead.
In Scala:
import org.apache.spark.ml.Pipeline
import org.apache.spark.ml.feature.{OneHotEncoderEstimator, StringIndexer}
val df = Seq((0, "a", 1), (1, "b", 2), (2, "c", 3), (3, "a", 4), (4, "a", 4), (5, "c", 3)).toDF("id", "category1", "category2")
val indexer = new StringIndexer().setInputCol("category1").setOutputCol("category1Index")
val encoder = new OneHotEncoderEstimator()
.setInputCols(Array(indexer.getOutputCol, "category2"))
.setOutputCols(Array("category1Vec", "category2Vec"))
val pipeline = new Pipeline().setStages(Array(indexer, encoder))
pipeline.fit(df).transform(df).show
// +---+---------+---------+--------------+-------------+-------------+
// | id|category1|category2|category1Index| category1Vec| category2Vec|
// +---+---------+---------+--------------+-------------+-------------+
// | 0| a| 1| 0.0|(2,[0],[1.0])|(4,[1],[1.0])|
// | 1| b| 2| 2.0| (2,[],[])|(4,[2],[1.0])|
// | 2| c| 3| 1.0|(2,[1],[1.0])|(4,[3],[1.0])|
// | 3| a| 4| 0.0|(2,[0],[1.0])| (4,[],[])|
// | 4| a| 4| 0.0|(2,[0],[1.0])| (4,[],[])|
// | 5| c| 3| 1.0|(2,[1],[1.0])|(4,[3],[1.0])|
// +---+---------+---------+--------------+-------------+-------------+
In Python:
from pyspark.ml import Pipeline
from pyspark.ml.feature import StringIndexer, OneHotEncoderEstimator
df = spark.createDataFrame([(0, "a", 1), (1, "b", 2), (2, "c", 3), (3, "a", 4), (4, "a", 4), (5, "c", 3)], ["id", "category1", "category2"])
indexer = StringIndexer(inputCol="category1", outputCol="category1Index")
inputs = [indexer.getOutputCol(), "category2"]
encoder = OneHotEncoderEstimator(inputCols=inputs, outputCols=["categoryVec1", "categoryVec2"])
pipeline = Pipeline(stages=[indexer, encoder])
pipeline.fit(df).transform(df).show()
# +---+---------+---------+--------------+-------------+-------------+
# | id|category1|category2|category1Index| categoryVec1| categoryVec2|
# +---+---------+---------+--------------+-------------+-------------+
# | 0| a| 1| 0.0|(2,[0],[1.0])|(4,[1],[1.0])|
# | 1| b| 2| 2.0| (2,[],[])|(4,[2],[1.0])|
# | 2| c| 3| 1.0|(2,[1],[1.0])|(4,[3],[1.0])|
# | 3| a| 4| 0.0|(2,[0],[1.0])| (4,[],[])|
# | 4| a| 4| 0.0|(2,[0],[1.0])| (4,[],[])|
# | 5| c| 3| 1.0|(2,[1],[1.0])|(4,[3],[1.0])|
# +---+---------+---------+--------------+-------------+-------------+
Since Spark 1.4.0, MLLib also supplies OneHotEncoder feature, which maps a column of label indices to a column of binary vectors, with at most a single one-value.
This encoding allows algorithms which expect continuous features, such as Logistic Regression, to use categorical features
Let's consider the following DataFrame:
val df = Seq((0, "a"),(1, "b"),(2, "c"),(3, "a"),(4, "a"),(5, "c"))
.toDF("id", "category")
The first step would be to create the indexed DataFrame with the StringIndexer:
import org.apache.spark.ml.feature.StringIndexer
val indexer = new StringIndexer()
.setInputCol("category")
.setOutputCol("categoryIndex")
.fit(df)
val indexed = indexer.transform(df)
indexed.show
// +---+--------+-------------+
// | id|category|categoryIndex|
// +---+--------+-------------+
// | 0| a| 0.0|
// | 1| b| 2.0|
// | 2| c| 1.0|
// | 3| a| 0.0|
// | 4| a| 0.0|
// | 5| c| 1.0|
// +---+--------+-------------+
You can then encode the categoryIndex with OneHotEncoder :
import org.apache.spark.ml.feature.OneHotEncoder
val encoder = new OneHotEncoder()
.setInputCol("categoryIndex")
.setOutputCol("categoryVec")
val encoded = encoder.transform(indexed)
encoded.select("id", "categoryVec").show
// +---+-------------+
// | id| categoryVec|
// +---+-------------+
// | 0|(2,[0],[1.0])|
// | 1| (2,[],[])|
// | 2|(2,[1],[1.0])|
// | 3|(2,[0],[1.0])|
// | 4|(2,[0],[1.0])|
// | 5|(2,[1],[1.0])|
// +---+-------------+
I am going to provide an answer from another perspective, since I was also wondering about categorical features with regards to tree-based models in Spark ML (not MLlib), and the documentation is not that clear how everything works.
When you transform a column in your dataframe using pyspark.ml.feature.StringIndexer extra meta-data gets stored in the dataframe that specifically marks the transformed feature as a categorical feature.
When you print the dataframe you will see a numeric value (which is an index that corresponds with one of your categorical values) and if you look at the schema you will see that your new transformed column is of type double. However, this new column you created with pyspark.ml.feature.StringIndexer.transform is not just a normal double column, it has extra meta-data associated with it that is very important. You can inspect this meta-data by looking at the metadata property of the appropriate field in your dataframe's schema (you can access the schema objects of your dataframe by looking at yourdataframe.schema)
This extra metadata has two important implications:
When you call .fit() when using a tree based model, it will scan the meta-data of your dataframe and recognize fields that you encoded as categorical with transformers such as pyspark.ml.feature.StringIndexer (as noted above there are other transformers that will also have this effect such as pyspark.ml.feature.VectorIndexer). Because of this, you DO NOT have to one-hot encode your features after you have transformed them with StringIndxer when using tree-based models in spark ML (however, you still have to perform one-hot encoding when using other models that do not naturally handle categoricals like linear regression, etc.).
Because this metadata is stored in the data frame, you can use pyspark.ml.feature.IndexToString to reverse the numeric indices back to the original categorical values (which are often strings) at any time.
There is a component of the ML pipeline called StringIndexer you can use to convert your strings to Double's in a reasonable way. http://spark.apache.org/docs/latest/api/scala/index.html#org.apache.spark.ml.feature.StringIndexer has more documentation, and http://spark.apache.org/docs/latest/ml-guide.html shows how to construct pipelines.
I use the following method for oneHotEncoding a single column in a Spark dataFrame:
def ohcOneColumn(df, colName, debug=False):
colsToFillNa = []
if debug: print("Entering method ohcOneColumn")
countUnique = df.groupBy(colName).count().count()
if debug: print(countUnique)
collectOnce = df.select(colName).distinct().collect()
for uniqueValIndex in range(countUnique):
uniqueVal = collectOnce[uniqueValIndex][0]
if debug: print(uniqueVal)
newColName = str(colName) + '_' + str(uniqueVal) + '_TF'
df = df.withColumn(newColName, df[colName]==uniqueVal)
colsToFillNa.append(newColName)
df = df.drop(colName)
df = df.na.fill(False, subset=colsToFillNa)
return df
I use the following method for oneHotEncoding Spark dataFrames:
from pyspark.sql.functions import col, countDistinct, approxCountDistinct
from pyspark.ml.feature import StringIndexer
from pyspark.ml.feature import OneHotEncoderEstimator
def detectAndLabelCat(sparkDf, minValCount=5, debug=False, excludeCols=['Target']):
if debug: print("Entering method detectAndLabelCat")
newDf = sparkDf
colList = sparkDf.columns
for colName in sparkDf.columns:
uniqueVals = sparkDf.groupBy(colName).count()
if debug: print(uniqueVals)
countUnique = uniqueVals.count()
dtype = str(sparkDf.schema[colName].dataType)
#dtype = str(df.schema[nc].dataType)
if (colName in excludeCols):
if debug: print(str(colName) + ' is in the excluded columns list.')
elif countUnique == 1:
newDf = newDf.drop(colName)
if debug:
print('dropping column ' + str(colName) + ' because it only contains one unique value.')
#end if debug
#elif (1==2):
elif ((countUnique < minValCount) | (dtype=="String") | (dtype=="StringType")):
if debug:
print(len(newDf.columns))
oldColumns = newDf.columns
newDf = ohcOneColumn(newDf, colName, debug=debug)
if debug:
print(len(newDf.columns))
newColumns = set(newDf.columns) - set(oldColumns)
print('Adding:')
print(newColumns)
for newColumn in newColumns:
if newColumn in newDf.columns:
try:
newUniqueValCount = newDf.groupBy(newColumn).count().count()
print("There are " + str(newUniqueValCount) + " unique values in " + str(newColumn))
except:
print('Uncaught error discussing ' + str(newColumn))
#else:
# newColumns.remove(newColumn)
print('Dropping:')
print(set(oldColumns) - set(newDf.columns))
else:
if debug: print('Nothing done for column ' + str(colName))
#end if countUnique == 1, elif countUnique other condition
#end outer for
return newDf
You can cast a string column type in a spark data frame to a numerical data type using the cast function.
from pyspark.sql import SQLContext
from pyspark.sql.types import DoubleType, IntegerType
sqlContext = SQLContext(sc)
dataset = sqlContext.read.format('com.databricks.spark.csv').options(header='true').load('./data/titanic.csv')
dataset = dataset.withColumn("Age", dataset["Age"].cast(DoubleType()))
dataset = dataset.withColumn("Survived", dataset["Survived"].cast(IntegerType()))
In the above example, we read in a csv file as a data frame, cast the default string datatypes into integer and double, and overwrite the original data frame. We can then use the VectorAssembler to merge the features in a single vector and apply your favorite Spark ML algorithm.
I have a dataframe resulting from a sql query
df1 = sqlContext.sql("select * from table_test")
I need to convert this dataframe to libsvm format so that it can be provided as an input for
pyspark.ml.classification.LogisticRegression
I tried to do the following. However, this resulted in the following error as I'm using spark 1.5.2
df1.write.format("libsvm").save("data/foo")
Failed to load class for data source: libsvm
I wanted to use MLUtils.loadLibSVMFile instead. I'm behind a firewall and can't directly pip install it. So I downloaded the file, scp-ed it and then manually installed it. Everything seemed to work fine but I still get the following error
import org.apache.spark.mllib.util.MLUtils
No module named org.apache.spark.mllib.util.MLUtils
Question 1: Is my above approach to convert dataframe to libsvm format in the right direction.
Question 2: If "yes" to question 1, how to get MLUtils working. If "no", what is the best way to convert dataframe to libsvm format
I would act like that (it's just an example with an arbitrary dataframe, I don't know how your df1 is done, focus is on data transformations):
This is my way to convert dataframe to libsvm format:
# ... your previous imports
from pyspark.mllib.util import MLUtils
from pyspark.mllib.regression import LabeledPoint
# A DATAFRAME
>>> df.show()
+---+---+---+
| _1| _2| _3|
+---+---+---+
| 1| 3| 6|
| 4| 5| 20|
| 7| 8| 8|
+---+---+---+
# FROM DATAFRAME TO RDD
>>> c = df.rdd # this command will convert your dataframe in a RDD
>>> print (c.take(3))
[Row(_1=1, _2=3, _3=6), Row(_1=4, _2=5, _3=20), Row(_1=7, _2=8, _3=8)]
# FROM RDD OF TUPLE TO A RDD OF LABELEDPOINT
>>> d = c.map(lambda line: LabeledPoint(line[0],[line[1:]])) # arbitrary mapping, it's just an example
>>> print (d.take(3))
[LabeledPoint(1.0, [3.0,6.0]), LabeledPoint(4.0, [5.0,20.0]), LabeledPoint(7.0, [8.0,8.0])]
# SAVE AS LIBSVM
>>> MLUtils.saveAsLibSVMFile(d, "/your/Path/nameFolder/")
What you will see on the "/your/Path/nameFolder/part-0000*" files is:
1.0 1:3.0 2:6.0
4.0 1:5.0 2:20.0
7.0 1:8.0 2:8.0
See here for LabeledPoint docs
I had to do this for it to work
D.map(lambda line: LabeledPoint(line[0],[line[1],line[2]]))
If you want to convert sparse vectors to a 'sparse' libsvm which is more efficient, try this:
from pyspark.ml.linalg import Vectors
from pyspark.mllib.linalg import Vectors as MLLibVectors
from pyspark.mllib.regression import LabeledPoint
from pyspark.mllib.util import MLUtils
df = spark.createDataFrame([
(0, Vectors.sparse(5, [(1, 1.0), (3, 7.0)])),
(1, Vectors.sparse(5, [(1, 1.0), (3, 7.0)])),
(1, Vectors.sparse(5, [(1, 1.0), (3, 7.0)]))
], ["label", "features"])
df.show()
# +-----+-------------------+
# |label| features|
# +-----+-------------------+
# | 0|(5,[1,3],[1.0,7.0])|
# | 1|(5,[1,3],[1.0,7.0])|
# | 1|(5,[1,3],[1.0,7.0])|
# +-----+-------------------+
MLUtils.saveAsLibSVMFile(df.rdd.map(lambda x: LabeledPoint(x.label, MLLibVectors.fromML(x.features))), './libsvm')
I am working with data extracted from SFDC using simple-salesforce package.
I am using Python3 for scripting and Spark 1.5.2.
I created an rdd containing the following data:
[('Id', 'a0w1a0000003xB1A'), ('PackSize', 1.0), ('Name', 'A')]
[('Id', 'a0w1a0000003xAAI'), ('PackSize', 1.0), ('Name', 'B')]
[('Id', 'a0w1a00000xB3AAI'), ('PackSize', 30.0), ('Name', 'C')]
...
This data is in RDD called v_rdd
My schema looks like this:
StructType(List(StructField(Id,StringType,true),StructField(PackSize,StringType,true),StructField(Name,StringType,true)))
I am trying to create DataFrame out of this RDD:
sqlDataFrame = sqlContext.createDataFrame(v_rdd, schema)
I print my DataFrame:
sqlDataFrame.printSchema()
And get the following:
+--------------------+--------------------+--------------------+
| Id| PackSize| Name|
+--------------------+--------------------+--------------------+
|[Ljava.lang.Objec...|[Ljava.lang.Objec...|[Ljava.lang.Objec...|
|[Ljava.lang.Objec...|[Ljava.lang.Objec...|[Ljava.lang.Objec...|
|[Ljava.lang.Objec...|[Ljava.lang.Objec...|[Ljava.lang.Objec...|
I am expecting to see actual data, like this:
+------------------+------------------+--------------------+
| Id|PackSize| Name|
+------------------+------------------+--------------------+
|a0w1a0000003xB1A | 1.0| A |
|a0w1a0000003xAAI | 1.0| B |
|a0w1a00000xB3AAI | 30.0| C |
Can you please help me identify what I am doing wrong here.
My Python script is long, I am not sure it would be convenient for people to sift through it, so I posted only parts I am having issue with.
Thank a ton in advance!
Hey could you next time provide a working example. That would be easier.
The way how your RDD is presented is basically weird to create a DataFrame. This is how you create a DF according to Spark Documentation.
>>> l = [('Alice', 1)]
>>> sqlContext.createDataFrame(l).collect()
[Row(_1=u'Alice', _2=1)]
>>> sqlContext.createDataFrame(l, ['name', 'age']).collect()
[Row(name=u'Alice', age=1)]
So concerning your example you can create your desired output like this way:
# Your data at the moment
data = sc.parallelize([
[('Id', 'a0w1a0000003xB1A'), ('PackSize', 1.0), ('Name', 'A')],
[('Id', 'a0w1a0000003xAAI'), ('PackSize', 1.0), ('Name', 'B')],
[('Id', 'a0w1a00000xB3AAI'), ('PackSize', 30.0), ('Name', 'C')]
])
# Convert to tuple
data_converted = data.map(lambda x: (x[0][1], x[1][1], x[2][1]))
# Define schema
schema = StructType([
StructField("Id", StringType(), True),
StructField("Packsize", StringType(), True),
StructField("Name", StringType(), True)
])
# Create dataframe
DF = sqlContext.createDataFrame(data_converted, schema)
# Output
DF.show()
+----------------+--------+----+
| Id|Packsize|Name|
+----------------+--------+----+
|a0w1a0000003xB1A| 1.0| A|
|a0w1a0000003xAAI| 1.0| B|
|a0w1a00000xB3AAI| 30.0| C|
+----------------+--------+----+
Hope this helps