[SPARK-1752][MLLIB] Standardize text format for vectors and labeled points

We should standardize the text format used to represent vectors and labeled points. The proposed formats are the following:

1. dense vector: `[v0,v1,..]`
2. sparse vector: `(size,[i0,i1],[v0,v1])`
3. labeled point: `(label,vector)`

where "(..)" indicates a tuple and "[...]" indicate an array. `loadLabeledPoints` is added to pyspark's `MLUtils`. I didn't add `loadVectors` to pyspark because `RDD.saveAsTextFile` cannot stringify dense vectors in the proposed format automatically.

`MLUtils#saveLabeledData` and `MLUtils#loadLabeledData` are deprecated. Users should use `RDD#saveAsTextFile` and `MLUtils#loadLabeledPoints` instead. In Scala, `MLUtils#loadLabeledPoints` is compatible with the format used by `MLUtils#loadLabeledData`.

CC: @mateiz, @srowen

Author: Xiangrui Meng <meng@databricks.com>

Closes #685 from mengxr/labeled-io and squashes the following commits:

2d1116a [Xiangrui Meng] make loadLabeledData/saveLabeledData deprecated since 1.0.1
297be75 [Xiangrui Meng] change LabeledPoint.parse to LabeledPointParser.parse to maintain binary compatibility
d6b1473 [Xiangrui Meng] Merge branch 'master' into labeled-io
56746ea [Xiangrui Meng] replace # by .
623a5f0 [Xiangrui Meng] merge master
f06d5ba [Xiangrui Meng] add docs and minor updates
640fe0c [Xiangrui Meng] throw SparkException
5bcfbc4 [Xiangrui Meng] update test to add scientific notations
e86bf38 [Xiangrui Meng] remove NumericTokenizer
050fca4 [Xiangrui Meng] use StringTokenizer
6155b75 [Xiangrui Meng] merge master
f644438 [Xiangrui Meng] remove parse methods based on eval from pyspark
a41675a [Xiangrui Meng] python loadLabeledPoint uses Scala's implementation
ce9a475 [Xiangrui Meng] add deserialize_labeled_point to pyspark with tests
e9fcd49 [Xiangrui Meng] add serializeLabeledPoint and tests
aea4ae3 [Xiangrui Meng] minor updates
810d6df [Xiangrui Meng] update tokenizer/parser implementation
7aac03a [Xiangrui Meng] remove Scala parsers
c1885c1 [Xiangrui Meng] add headers and minor changes
b0c50cb [Xiangrui Meng] add customized parser
d731817 [Xiangrui Meng] style update
63dc396 [Xiangrui Meng] add loadLabeledPoints to pyspark
ea122b5 [Xiangrui Meng] Merge branch 'master' into labeled-io
cd6c78f [Xiangrui Meng] add __str__ and parse to LabeledPoint
a7a178e [Xiangrui Meng] add stringify to pyspark's Vectors
5c2dbfa [Xiangrui Meng] add parse to pyspark's Vectors
7853f88 [Xiangrui Meng] update pyspark's SparseVector.__str__
e761d32 [Xiangrui Meng] make LabelPoint.parse compatible with the dense format used before v1.0 and deprecate loadLabeledData and saveLabeledData
9e63a02 [Xiangrui Meng] add loadVectors and loadLabeledPoints
19aa523 [Xiangrui Meng] update toString and add parsers for Vectors and LabeledPoint

1 files changed, 50 insertions, 19 deletions

diff --git a/python/pyspark/mllib/util.py b/python/pyspark/mllib/util.py
index 0e5f4520b9..e24c144f45 100644
--- a/python/pyspark/mllib/util.py
+++ b/python/pyspark/mllib/util.py
@@ -19,7 +19,10 @@ import numpy as np
 
 from pyspark.mllib.linalg import Vectors, SparseVector
 from pyspark.mllib.regression import LabeledPoint
-from pyspark.mllib._common import _convert_vector
+from pyspark.mllib._common import _convert_vector, _deserialize_labeled_point
+from pyspark.rdd import RDD
+from pyspark.serializers import NoOpSerializer
+
 
 
 class MLUtils:
@@ -105,24 +108,18 @@ class MLUtils:
         >>> examples = MLUtils.loadLibSVMFile(sc, tempFile.name).collect()
         >>> multiclass_examples = MLUtils.loadLibSVMFile(sc, tempFile.name, True).collect()
         >>> tempFile.close()
-        >>> examples[0].label
-        1.0
-        >>> examples[0].features.size
-        6
-        >>> print examples[0].features
-        [0: 1.0, 2: 2.0, 4: 3.0]
-        >>> examples[1].label
-        0.0
-        >>> examples[1].features.size
-        6
-        >>> print examples[1].features
-        []
-        >>> examples[2].label
-        0.0
-        >>> examples[2].features.size
-        6
-        >>> print examples[2].features
-        [1: 4.0, 3: 5.0, 5: 6.0]
+        >>> type(examples[0]) == LabeledPoint
+        True
+        >>> print examples[0]
+        (1.0,(6,[0,2,4],[1.0,2.0,3.0]))
+        >>> type(examples[1]) == LabeledPoint
+        True
+        >>> print examples[1]
+        (0.0,(6,[],[]))
+        >>> type(examples[2]) == LabeledPoint
+        True
+        >>> print examples[2]
+        (0.0,(6,[1,3,5],[4.0,5.0,6.0]))
         >>> multiclass_examples[1].label
         -1.0
         """
@@ -158,6 +155,40 @@ class MLUtils:
         lines.saveAsTextFile(dir)
 
 
+    @staticmethod
+    def loadLabeledPoints(sc, path, minPartitions=None):
+        """
+        Load labeled points saved using RDD.saveAsTextFile.
+
+        @param sc: Spark context
+        @param path: file or directory path in any Hadoop-supported file
+                     system URI
+        @param minPartitions: min number of partitions
+        @return: labeled data stored as an RDD of LabeledPoint
+
+        >>> from tempfile import NamedTemporaryFile
+        >>> from pyspark.mllib.util import MLUtils
+        >>> examples = [LabeledPoint(1.1, Vectors.sparse(3, [(0, -1.23), (2, 4.56e-7)])), \
+                        LabeledPoint(0.0, Vectors.dense([1.01, 2.02, 3.03]))]
+        >>> tempFile = NamedTemporaryFile(delete=True)
+        >>> tempFile.close()
+        >>> sc.parallelize(examples, 1).saveAsTextFile(tempFile.name)
+        >>> loaded = MLUtils.loadLabeledPoints(sc, tempFile.name).collect()
+        >>> type(loaded[0]) == LabeledPoint
+        True
+        >>> print examples[0]
+        (1.1,(3,[0,2],[-1.23,4.56e-07]))
+        >>> type(examples[1]) == LabeledPoint
+        True
+        >>> print examples[1]
+        (0.0,[1.01,2.02,3.03])
+        """
+        minPartitions = minPartitions or min(sc.defaultParallelism, 2)
+        jSerialized = sc._jvm.PythonMLLibAPI().loadLabeledPoints(sc._jsc, path, minPartitions)
+        serialized = RDD(jSerialized, sc, NoOpSerializer())
+        return serialized.map(lambda bytes: _deserialize_labeled_point(bytearray(bytes)))
+
+
 def _test():
     import doctest
     from pyspark.context import SparkContext