From 4bc3bb29a4b6ab24b6b7e1f8df26414c41c80ace Mon Sep 17 00:00:00 2001
From: Jeremy Freeman <the.freeman.lab@gmail.com>
Date: Fri, 1 Aug 2014 22:33:25 -0700
Subject: [PATCH] StatCounter on NumPy arrays [PYSPARK][SPARK-2012]
These changes allow StatCounters to work properly on NumPy arrays, to fix the issue reported here (https://issues.apache.org/jira/browse/SPARK-2012).
If NumPy is installed, the NumPy functions ``maximum``, ``minimum``, and ``sqrt``, which work on arrays, are used to merge statistics. If not, we fall back on scalar operators, so it will work on arrays with NumPy, but will also work without NumPy.
New unit tests added, along with a check for NumPy in the tests.
Author: Jeremy Freeman <the.freeman.lab@gmail.com>
Closes #1725 from freeman-lab/numpy-max-statcounter and squashes the following commits:
fe973b1 [Jeremy Freeman] Avoid duplicate array import in tests
7f0e397 [Jeremy Freeman] Refactored check for numpy
8e764dd [Jeremy Freeman] Explicit numpy imports
875414c [Jeremy Freeman] Fixed indents
1c8a832 [Jeremy Freeman] Unit tests for StatCounter with NumPy arrays
176a127 [Jeremy Freeman] Use numpy arrays in StatCounter
---
python/pyspark/statcounter.py | 21 +++++++++++++--------
python/pyspark/tests.py | 24 ++++++++++++++++++++++++
2 files changed, 37 insertions(+), 8 deletions(-)
diff --git a/python/pyspark/statcounter.py b/python/pyspark/statcounter.py
index e287bd3da1..1e597d64e0 100644
--- a/python/pyspark/statcounter.py
+++ b/python/pyspark/statcounter.py
@@ -20,6 +20,13 @@
import copy
import math
+try:
+ from numpy import maximum, minimum, sqrt
+except ImportError:
+ maximum = max
+ minimum = min
+ sqrt = math.sqrt
+
class StatCounter(object):
@@ -39,10 +46,8 @@ class StatCounter(object):
self.n += 1
self.mu += delta / self.n
self.m2 += delta * (value - self.mu)
- if self.maxValue < value:
- self.maxValue = value
- if self.minValue > value:
- self.minValue = value
+ self.maxValue = maximum(self.maxValue, value)
+ self.minValue = minimum(self.minValue, value)
return self
@@ -70,8 +75,8 @@ class StatCounter(object):
else:
self.mu = (self.mu * self.n + other.mu * other.n) / (self.n + other.n)
- self.maxValue = max(self.maxValue, other.maxValue)
- self.minValue = min(self.minValue, other.minValue)
+ self.maxValue = maximum(self.maxValue, other.maxValue)
+ self.minValue = minimum(self.minValue, other.minValue)
self.m2 += other.m2 + (delta * delta * self.n * other.n) / (self.n + other.n)
self.n += other.n
@@ -115,14 +120,14 @@ class StatCounter(object):
# Return the standard deviation of the values.
def stdev(self):
- return math.sqrt(self.variance())
+ return sqrt(self.variance())
#
# Return the sample standard deviation of the values, which corrects for bias in estimating the
# variance by dividing by N-1 instead of N.
#
def sampleStdev(self):
- return math.sqrt(self.sampleVariance())
+ return sqrt(self.sampleVariance())
def __repr__(self):
return ("(count: %s, mean: %s, stdev: %s, max: %s, min: %s)" %
diff --git a/python/pyspark/tests.py b/python/pyspark/tests.py
index c29deb9574..16fb5a9256 100644
--- a/python/pyspark/tests.py
+++ b/python/pyspark/tests.py
@@ -38,12 +38,19 @@ from pyspark.serializers import read_int
from pyspark.shuffle import Aggregator, InMemoryMerger, ExternalMerger
_have_scipy = False
+_have_numpy = False
try:
import scipy.sparse
_have_scipy = True
except:
# No SciPy, but that's okay, we'll skip those tests
pass
+try:
+ import numpy as np
+ _have_numpy = True
+except:
+ # No NumPy, but that's okay, we'll skip those tests
+ pass
SPARK_HOME = os.environ["SPARK_HOME"]
@@ -914,9 +921,26 @@ class SciPyTests(PySparkTestCase):
self.assertEqual(expected, observed)
+@unittest.skipIf(not _have_numpy, "NumPy not installed")
+class NumPyTests(PySparkTestCase):
+ """General PySpark tests that depend on numpy """
+
+ def test_statcounter_array(self):
+ x = self.sc.parallelize([np.array([1.0,1.0]), np.array([2.0,2.0]), np.array([3.0,3.0])])
+ s = x.stats()
+ self.assertSequenceEqual([2.0,2.0], s.mean().tolist())
+ self.assertSequenceEqual([1.0,1.0], s.min().tolist())
+ self.assertSequenceEqual([3.0,3.0], s.max().tolist())
+ self.assertSequenceEqual([1.0,1.0], s.sampleStdev().tolist())
+
+
if __name__ == "__main__":
if not _have_scipy:
print "NOTE: Skipping SciPy tests as it does not seem to be installed"
+ if not _have_numpy:
+ print "NOTE: Skipping NumPy tests as it does not seem to be installed"
unittest.main()
if not _have_scipy:
print "NOTE: SciPy tests were skipped as it does not seem to be installed"
+ if not _have_numpy:
+ print "NOTE: NumPy tests were skipped as it does not seem to be installed"
--
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