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author | MechCoder <manojkumarsivaraj334@gmail.com> | 2015-05-05 07:53:11 -0700 |
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committer | Xiangrui Meng <meng@databricks.com> | 2015-05-05 07:53:11 -0700 |
commit | 5ab652cdb8bef10214edd079502a7f49017579aa (patch) | |
tree | c41047fb05c22525d383b758dac0304d53f982c1 | |
parent | c6d1efba29a4235130024fee9f118e6b2cb89ce1 (diff) | |
download | spark-5ab652cdb8bef10214edd079502a7f49017579aa.tar.gz spark-5ab652cdb8bef10214edd079502a7f49017579aa.tar.bz2 spark-5ab652cdb8bef10214edd079502a7f49017579aa.zip |
[SPARK-7202] [MLLIB] [PYSPARK] Add SparseMatrixPickler to SerDe
Utilities for pickling and unpickling SparseMatrices using SerDe
Author: MechCoder <manojkumarsivaraj334@gmail.com>
Closes #5775 from MechCoder/spark-7202 and squashes the following commits:
7e689dc [MechCoder] [SPARK-7202] Add SparseMatrixPickler to SerDe
4 files changed, 72 insertions, 3 deletions
diff --git a/mllib/src/main/scala/org/apache/spark/mllib/api/python/PythonMLLibAPI.scala b/mllib/src/main/scala/org/apache/spark/mllib/api/python/PythonMLLibAPI.scala index 6237b64c8f..8e9a208d61 100644 --- a/mllib/src/main/scala/org/apache/spark/mllib/api/python/PythonMLLibAPI.scala +++ b/mllib/src/main/scala/org/apache/spark/mllib/api/python/PythonMLLibAPI.scala @@ -1015,6 +1015,61 @@ private[spark] object SerDe extends Serializable { } } + // Pickler for SparseMatrix + private[python] class SparseMatrixPickler extends BasePickler[SparseMatrix] { + + def saveState(obj: Object, out: OutputStream, pickler: Pickler): Unit = { + val s = obj.asInstanceOf[SparseMatrix] + val order = ByteOrder.nativeOrder() + + val colPtrsBytes = new Array[Byte](4 * s.colPtrs.length) + val indicesBytes = new Array[Byte](4 * s.rowIndices.length) + val valuesBytes = new Array[Byte](8 * s.values.length) + val isTransposed = if (s.isTransposed) 1 else 0 + ByteBuffer.wrap(colPtrsBytes).order(order).asIntBuffer().put(s.colPtrs) + ByteBuffer.wrap(indicesBytes).order(order).asIntBuffer().put(s.rowIndices) + ByteBuffer.wrap(valuesBytes).order(order).asDoubleBuffer().put(s.values) + + out.write(Opcodes.MARK) + out.write(Opcodes.BININT) + out.write(PickleUtils.integer_to_bytes(s.numRows)) + out.write(Opcodes.BININT) + out.write(PickleUtils.integer_to_bytes(s.numCols)) + out.write(Opcodes.BINSTRING) + out.write(PickleUtils.integer_to_bytes(colPtrsBytes.length)) + out.write(colPtrsBytes) + out.write(Opcodes.BINSTRING) + out.write(PickleUtils.integer_to_bytes(indicesBytes.length)) + out.write(indicesBytes) + out.write(Opcodes.BINSTRING) + out.write(PickleUtils.integer_to_bytes(valuesBytes.length)) + out.write(valuesBytes) + out.write(Opcodes.BININT) + out.write(PickleUtils.integer_to_bytes(isTransposed)) + out.write(Opcodes.TUPLE) + } + + def construct(args: Array[Object]): Object = { + if (args.length != 6) { + throw new PickleException("should be 6") + } + val order = ByteOrder.nativeOrder() + val colPtrsBytes = getBytes(args(2)) + val indicesBytes = getBytes(args(3)) + val valuesBytes = getBytes(args(4)) + val colPtrs = new Array[Int](colPtrsBytes.length / 4) + val rowIndices = new Array[Int](indicesBytes.length / 4) + val values = new Array[Double](valuesBytes.length / 8) + ByteBuffer.wrap(colPtrsBytes).order(order).asIntBuffer().get(colPtrs) + ByteBuffer.wrap(indicesBytes).order(order).asIntBuffer().get(rowIndices) + ByteBuffer.wrap(valuesBytes).order(order).asDoubleBuffer().get(values) + val isTransposed = args(5).asInstanceOf[Int] == 1 + new SparseMatrix( + args(0).asInstanceOf[Int], args(1).asInstanceOf[Int], colPtrs, rowIndices, values, + isTransposed) + } + } + // Pickler for SparseVector private[python] class SparseVectorPickler extends BasePickler[SparseVector] { @@ -1099,6 +1154,7 @@ private[spark] object SerDe extends Serializable { if (!initialized) { new DenseVectorPickler().register() new DenseMatrixPickler().register() + new SparseMatrixPickler().register() new SparseVectorPickler().register() new LabeledPointPickler().register() new RatingPickler().register() diff --git a/mllib/src/test/scala/org/apache/spark/mllib/api/python/PythonMLLibAPISuite.scala b/mllib/src/test/scala/org/apache/spark/mllib/api/python/PythonMLLibAPISuite.scala index db8ed62fa4..a629dba8a4 100644 --- a/mllib/src/test/scala/org/apache/spark/mllib/api/python/PythonMLLibAPISuite.scala +++ b/mllib/src/test/scala/org/apache/spark/mllib/api/python/PythonMLLibAPISuite.scala @@ -19,7 +19,7 @@ package org.apache.spark.mllib.api.python import org.scalatest.FunSuite -import org.apache.spark.mllib.linalg.{DenseMatrix, Matrices, Vectors} +import org.apache.spark.mllib.linalg.{DenseMatrix, Matrices, Vectors, SparseMatrix} import org.apache.spark.mllib.regression.LabeledPoint import org.apache.spark.mllib.recommendation.Rating @@ -77,6 +77,16 @@ class PythonMLLibAPISuite extends FunSuite { val emptyMatrix = Matrices.dense(0, 0, empty) val ne = SerDe.loads(SerDe.dumps(emptyMatrix)).asInstanceOf[DenseMatrix] assert(emptyMatrix == ne) + + val sm = new SparseMatrix(3, 2, Array(0, 1, 3), Array(1, 0, 2), Array(0.9, 1.2, 3.4)) + val nsm = SerDe.loads(SerDe.dumps(sm)).asInstanceOf[SparseMatrix] + assert(sm.toArray === nsm.toArray) + + val smt = new SparseMatrix( + 3, 3, Array(0, 2, 3, 5), Array(0, 2, 1, 0, 2), Array(0.9, 1.2, 3.4, 5.7, 8.9), + isTransposed=true) + val nsmt = SerDe.loads(SerDe.dumps(smt)).asInstanceOf[SparseMatrix] + assert(smt.toArray === nsmt.toArray) } test("pickle rating") { diff --git a/python/pyspark/mllib/linalg.py b/python/pyspark/mllib/linalg.py index a57c0b3ae0..9f3b0baf9f 100644 --- a/python/pyspark/mllib/linalg.py +++ b/python/pyspark/mllib/linalg.py @@ -755,7 +755,7 @@ class SparseMatrix(Matrix): return SparseMatrix, ( self.numRows, self.numCols, self.colPtrs.tostring(), self.rowIndices.tostring(), self.values.tostring(), - self.isTransposed) + int(self.isTransposed)) def __getitem__(self, indices): i, j = indices @@ -801,7 +801,7 @@ class SparseMatrix(Matrix): # TODO: More efficient implementation: def __eq__(self, other): - return np.all(self.toArray == other.toArray) + return np.all(self.toArray() == other.toArray()) class Matrices(object): diff --git a/python/pyspark/mllib/tests.py b/python/pyspark/mllib/tests.py index 1b008b93bc..1d9c6ebf3b 100644 --- a/python/pyspark/mllib/tests.py +++ b/python/pyspark/mllib/tests.py @@ -92,6 +92,9 @@ class VectorTests(MLlibTestCase): self._test_serialize(SparseVector(4, {1: 1, 3: 2})) self._test_serialize(SparseVector(3, {})) self._test_serialize(DenseMatrix(2, 3, range(6))) + sm1 = SparseMatrix( + 3, 4, [0, 2, 2, 4, 4], [1, 2, 1, 2], [1.0, 2.0, 4.0, 5.0]) + self._test_serialize(sm1) def test_dot(self): sv = SparseVector(4, {1: 1, 3: 2}) |