From 34a889db857f8752a0a78dcedec75ac6cd6cd48d Mon Sep 17 00:00:00 2001 From: Yu ISHIKAWA Date: Fri, 17 Jul 2015 18:30:04 -0700 Subject: [SPARK-7879] [MLLIB] KMeans API for spark.ml Pipelines I Implemented the KMeans API for spark.ml Pipelines. But it doesn't include clustering abstractions for spark.ml (SPARK-7610). It would fit for another issues. And I'll try it later, since we are trying to add the hierarchical clustering algorithms in another issue. Thanks. [SPARK-7879] KMeans API for spark.ml Pipelines - ASF JIRA https://issues.apache.org/jira/browse/SPARK-7879 Author: Yu ISHIKAWA Closes #6756 from yu-iskw/SPARK-7879 and squashes the following commits: be752de [Yu ISHIKAWA] Add assertions a14939b [Yu ISHIKAWA] Fix the dashed line's length in pyspark.ml.rst 4c61693 [Yu ISHIKAWA] Remove the test about whether "features" and "prediction" columns exist or not in Python fb2417c [Yu ISHIKAWA] Use getInt, instead of get f397be4 [Yu ISHIKAWA] Switch the comparisons. ca78b7d [Yu ISHIKAWA] Add the Scala docs about the constraints of each parameter. effc650 [Yu ISHIKAWA] Using expertSetParam and expertGetParam c8dc6e6 [Yu ISHIKAWA] Remove an unnecessary test 19a9d63 [Yu ISHIKAWA] Include spark.ml.clustering to python tests 1abb19c [Yu ISHIKAWA] Add the statements about spark.ml.clustering into pyspark.ml.rst f8338bc [Yu ISHIKAWA] Add the placeholders in Python 4a03003 [Yu ISHIKAWA] Test for contains in Python 6566c8b [Yu ISHIKAWA] Use `get`, instead of `apply` 288e8d5 [Yu ISHIKAWA] Using `contains` to check the column names 5a7d574 [Yu ISHIKAWA] Renamce `validateInitializationMode` to `validateInitMode` and remove throwing exception 97cfae3 [Yu ISHIKAWA] Fix the type of return value of `KMeans.copy` e933723 [Yu ISHIKAWA] Remove the default value of seed from the Model class 978ee2c [Yu ISHIKAWA] Modify the docs of KMeans, according to mllib's KMeans 2ec80bc [Yu ISHIKAWA] Fit on 1 line e186be1 [Yu ISHIKAWA] Make a few variables, setters and getters be expert ones b2c205c [Yu ISHIKAWA] Rename the method `getInitializationSteps` to `getInitSteps` and `setInitializationSteps` to `setInitSteps` in Scala and Python f43f5b4 [Yu ISHIKAWA] Rename the method `getInitializationMode` to `getInitMode` and `setInitializationMode` to `setInitMode` in Scala and Python 3cb5ba4 [Yu ISHIKAWA] Modify the description about epsilon and the validation 4fa409b [Yu ISHIKAWA] Add a comment about the default value of epsilon 2f392e1 [Yu ISHIKAWA] Make some variables `final` and Use `IntParam` and `DoubleParam` 19326f8 [Yu ISHIKAWA] Use `udf`, instead of callUDF 4d2ad1e [Yu ISHIKAWA] Modify the indentations 0ae422f [Yu ISHIKAWA] Add a test for `setParams` 4ff7913 [Yu ISHIKAWA] Add "ml.clustering" to `javacOptions` in SparkBuild.scala 11ffdf1 [Yu ISHIKAWA] Use `===` and the variable 220a176 [Yu ISHIKAWA] Set a random seed in the unit testing 92c3efc [Yu ISHIKAWA] Make the points for a test be fewer c758692 [Yu ISHIKAWA] Modify the parameters of KMeans in Python 6aca147 [Yu ISHIKAWA] Add some unit testings to validate the setter methods 687cacc [Yu ISHIKAWA] Alias mllib.KMeans as MLlibKMeans in KMeansSuite.scala a4dfbef [Yu ISHIKAWA] Modify the last brace and indentations 5bedc51 [Yu ISHIKAWA] Remve an extra new line 444c289 [Yu ISHIKAWA] Add the validation for `runs` e41989c [Yu ISHIKAWA] Modify how to validate `initStep` 7ea133a [Yu ISHIKAWA] Change how to validate `initMode` 7991e15 [Yu ISHIKAWA] Add a validation for `k` c2df35d [Yu ISHIKAWA] Make `predict` private 93aa2ff [Yu ISHIKAWA] Use `withColumn` in `transform` d3a79f7 [Yu ISHIKAWA] Remove the inhefited docs e9532e1 [Yu ISHIKAWA] make `parentModel` of KMeansModel private 8559772 [Yu ISHIKAWA] Remove the `paramMap` parameter of KMeans 6684850 [Yu ISHIKAWA] Rename `initializationSteps` to `initSteps` 99b1b96 [Yu ISHIKAWA] Rename `initializationMode` to `initMode` 79ea82b [Yu ISHIKAWA] Modify the parameters of KMeans docs 6569bcd [Yu ISHIKAWA] Change how to set the default values with `setDefault` 20a795a [Yu ISHIKAWA] Change how to set the default values with `setDefault` 11c2a12 [Yu ISHIKAWA] Limit the imports badb481 [Yu ISHIKAWA] Alias spark.mllib.{KMeans, KMeansModel} f80319a [Yu ISHIKAWA] Rebase mater branch and add copy methods 85d92b1 [Yu ISHIKAWA] Add `KMeans.setPredictionCol` aa9469d [Yu ISHIKAWA] Fix a python test suite error caused by python 3.x c2d6bcb [Yu ISHIKAWA] ADD Java test suites of the KMeans API for spark.ml Pipeline 598ed2e [Yu ISHIKAWA] Implement the KMeans API for spark.ml Pipelines in Python 63ad785 [Yu ISHIKAWA] Implement the KMeans API for spark.ml Pipelines in Scala --- python/pyspark/ml/clustering.py | 206 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 206 insertions(+) create mode 100644 python/pyspark/ml/clustering.py (limited to 'python/pyspark/ml/clustering.py') diff --git a/python/pyspark/ml/clustering.py b/python/pyspark/ml/clustering.py new file mode 100644 index 0000000000..b5e9b6549d --- /dev/null +++ b/python/pyspark/ml/clustering.py @@ -0,0 +1,206 @@ +# +# Licensed to the Apache Software Foundation (ASF) under one or more +# contributor license agreements. See the NOTICE file distributed with +# this work for additional information regarding copyright ownership. +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +from pyspark.ml.util import keyword_only +from pyspark.ml.wrapper import JavaEstimator, JavaModel +from pyspark.ml.param.shared import * +from pyspark.mllib.common import inherit_doc +from pyspark.mllib.linalg import _convert_to_vector + +__all__ = ['KMeans', 'KMeansModel'] + + +class KMeansModel(JavaModel): + """ + Model fitted by KMeans. + """ + + def clusterCenters(self): + """Get the cluster centers, represented as a list of NumPy arrays.""" + return [c.toArray() for c in self._call_java("clusterCenters")] + + +@inherit_doc +class KMeans(JavaEstimator, HasFeaturesCol, HasMaxIter, HasSeed): + """ + K-means Clustering + + >>> from pyspark.mllib.linalg import Vectors + >>> data = [(Vectors.dense([0.0, 0.0]),), (Vectors.dense([1.0, 1.0]),), + ... (Vectors.dense([9.0, 8.0]),), (Vectors.dense([8.0, 9.0]),)] + >>> df = sqlContext.createDataFrame(data, ["features"]) + >>> kmeans = KMeans().setK(2).setSeed(1).setFeaturesCol("features") + >>> model = kmeans.fit(df) + >>> centers = model.clusterCenters() + >>> len(centers) + 2 + >>> transformed = model.transform(df).select("features", "prediction") + >>> rows = transformed.collect() + >>> rows[0].prediction == rows[1].prediction + True + >>> rows[2].prediction == rows[3].prediction + True + """ + + # a placeholder to make it appear in the generated doc + k = Param(Params._dummy(), "k", "number of clusters to create") + epsilon = Param(Params._dummy(), "epsilon", + "distance threshold within which " + + "we've consider centers to have converged") + runs = Param(Params._dummy(), "runs", "number of runs of the algorithm to execute in parallel") + initMode = Param(Params._dummy(), "initMode", + "the initialization algorithm. This can be either \"random\" to " + + "choose random points as initial cluster centers, or \"k-means||\" " + + "to use a parallel variant of k-means++") + initSteps = Param(Params._dummy(), "initSteps", "steps for k-means initialization mode") + + @keyword_only + def __init__(self, k=2, maxIter=20, runs=1, epsilon=1e-4, initMode="k-means||", initStep=5): + super(KMeans, self).__init__() + self._java_obj = self._new_java_obj("org.apache.spark.ml.clustering.KMeans", self.uid) + self.k = Param(self, "k", "number of clusters to create") + self.epsilon = Param(self, "epsilon", + "distance threshold within which " + + "we've consider centers to have converged") + self.runs = Param(self, "runs", "number of runs of the algorithm to execute in parallel") + self.seed = Param(self, "seed", "random seed") + self.initMode = Param(self, "initMode", + "the initialization algorithm. This can be either \"random\" to " + + "choose random points as initial cluster centers, or \"k-means||\" " + + "to use a parallel variant of k-means++") + self.initSteps = Param(self, "initSteps", "steps for k-means initialization mode") + self._setDefault(k=2, maxIter=20, runs=1, epsilon=1e-4, initMode="k-means||", initSteps=5) + kwargs = self.__init__._input_kwargs + self.setParams(**kwargs) + + def _create_model(self, java_model): + return KMeansModel(java_model) + + @keyword_only + def setParams(self, k=2, maxIter=20, runs=1, epsilon=1e-4, initMode="k-means||", initSteps=5): + """ + setParams(self, k=2, maxIter=20, runs=1, epsilon=1e-4, initMode="k-means||", initSteps=5): + + Sets params for KMeans. + """ + kwargs = self.setParams._input_kwargs + return self._set(**kwargs) + + def setK(self, value): + """ + Sets the value of :py:attr:`k`. + + >>> algo = KMeans().setK(10) + >>> algo.getK() + 10 + """ + self._paramMap[self.k] = value + return self + + def getK(self): + """ + Gets the value of `k` + """ + return self.getOrDefault(self.k) + + def setEpsilon(self, value): + """ + Sets the value of :py:attr:`epsilon`. + + >>> algo = KMeans().setEpsilon(1e-5) + >>> abs(algo.getEpsilon() - 1e-5) < 1e-5 + True + """ + self._paramMap[self.epsilon] = value + return self + + def getEpsilon(self): + """ + Gets the value of `epsilon` + """ + return self.getOrDefault(self.epsilon) + + def setRuns(self, value): + """ + Sets the value of :py:attr:`runs`. + + >>> algo = KMeans().setRuns(10) + >>> algo.getRuns() + 10 + """ + self._paramMap[self.runs] = value + return self + + def getRuns(self): + """ + Gets the value of `runs` + """ + return self.getOrDefault(self.runs) + + def setInitMode(self, value): + """ + Sets the value of :py:attr:`initMode`. + + >>> algo = KMeans() + >>> algo.getInitMode() + 'k-means||' + >>> algo = algo.setInitMode("random") + >>> algo.getInitMode() + 'random' + """ + self._paramMap[self.initMode] = value + return self + + def getInitMode(self): + """ + Gets the value of `initMode` + """ + return self.getOrDefault(self.initMode) + + def setInitSteps(self, value): + """ + Sets the value of :py:attr:`initSteps`. + + >>> algo = KMeans().setInitSteps(10) + >>> algo.getInitSteps() + 10 + """ + self._paramMap[self.initSteps] = value + return self + + def getInitSteps(self): + """ + Gets the value of `initSteps` + """ + return self.getOrDefault(self.initSteps) + + +if __name__ == "__main__": + import doctest + from pyspark.context import SparkContext + from pyspark.sql import SQLContext + globs = globals().copy() + # The small batch size here ensures that we see multiple batches, + # even in these small test examples: + sc = SparkContext("local[2]", "ml.clustering tests") + sqlContext = SQLContext(sc) + globs['sc'] = sc + globs['sqlContext'] = sqlContext + (failure_count, test_count) = doctest.testmod(globs=globs, optionflags=doctest.ELLIPSIS) + sc.stop() + if failure_count: + exit(-1) -- cgit v1.2.3