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129 changes: 129 additions & 0 deletions
129
mllib/src/main/scala/org/apache/spark/ml/feature/RFormulaParser.scala
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| /* | ||
| * 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. | ||
| */ | ||
|
|
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| package org.apache.spark.ml.feature | ||
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| import scala.util.parsing.combinator.RegexParsers | ||
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| import org.apache.spark.mllib.linalg.VectorUDT | ||
| import org.apache.spark.sql.types._ | ||
|
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| /** | ||
| * Represents a parsed R formula. | ||
| */ | ||
| private[ml] case class ParsedRFormula(label: ColumnRef, terms: Seq[Term]) { | ||
| /** | ||
| * Resolves formula terms into column names. A schema is necessary for inferring the meaning | ||
| * of the special '.' term. Duplicate terms will be removed during resolution. | ||
| */ | ||
| def resolve(schema: StructType): ResolvedRFormula = { | ||
| var includedTerms = Seq[String]() | ||
| terms.foreach { | ||
| case Dot => | ||
| includedTerms ++= simpleTypes(schema).filter(_ != label.value) | ||
| case ColumnRef(value) => | ||
| includedTerms :+= value | ||
| case Deletion(term: Term) => | ||
| term match { | ||
| case ColumnRef(value) => | ||
| includedTerms = includedTerms.filter(_ != value) | ||
| case Dot => | ||
| // e.g. "- .", which removes all first-order terms | ||
| val fromSchema = simpleTypes(schema) | ||
| includedTerms = includedTerms.filter(fromSchema.contains(_)) | ||
| case _: Deletion => | ||
| assert(false, "Deletion terms cannot be nested") | ||
| case _: Intercept => | ||
| } | ||
| case _: Intercept => | ||
| } | ||
| ResolvedRFormula(label.value, includedTerms.distinct) | ||
| } | ||
|
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| /** Whether this formula specifies fitting with an intercept term. */ | ||
| def hasIntercept: Boolean = { | ||
| var intercept = true | ||
| terms.foreach { | ||
| case Intercept(enabled) => | ||
| intercept = enabled | ||
| case Deletion(Intercept(enabled)) => | ||
| intercept = !enabled | ||
| case _ => | ||
| } | ||
| intercept | ||
| } | ||
|
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| // the dot operator excludes complex column types | ||
| private def simpleTypes(schema: StructType): Seq[String] = { | ||
| schema.fields.filter(_.dataType match { | ||
| case _: NumericType | StringType | BooleanType | _: VectorUDT => true | ||
| case _ => false | ||
| }).map(_.name) | ||
| } | ||
| } | ||
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| /** | ||
| * Represents a fully evaluated and simplified R formula. | ||
| */ | ||
| private[ml] case class ResolvedRFormula(label: String, terms: Seq[String]) | ||
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| /** | ||
| * R formula terms. See the R formula docs here for more information: | ||
| * http://stat.ethz.ch/R-manual/R-patched/library/stats/html/formula.html | ||
| */ | ||
| private[ml] sealed trait Term | ||
|
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| /* R formula reference to all available columns, e.g. "." in a formula */ | ||
| private[ml] case object Dot extends Term | ||
|
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| /* R formula reference to a column, e.g. "+ Species" in a formula */ | ||
| private[ml] case class ColumnRef(value: String) extends Term | ||
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| /* R formula intercept toggle, e.g. "+ 0" in a formula */ | ||
| private[ml] case class Intercept(enabled: Boolean) extends Term | ||
|
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| /* R formula deletion of a variable, e.g. "- Species" in a formula */ | ||
| private[ml] case class Deletion(term: Term) extends Term | ||
|
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| /** | ||
| * Limited implementation of R formula parsing. Currently supports: '~', '+', '-', '.'. | ||
| */ | ||
| private[ml] object RFormulaParser extends RegexParsers { | ||
| def intercept: Parser[Intercept] = | ||
| "([01])".r ^^ { case a => Intercept(a == "1") } | ||
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| def columnRef: Parser[ColumnRef] = | ||
| "([a-zA-Z]|\\.[a-zA-Z_])[a-zA-Z0-9._]*".r ^^ { case a => ColumnRef(a) } | ||
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| def term: Parser[Term] = intercept | columnRef | "\\.".r ^^ { case _ => Dot } | ||
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| def terms: Parser[List[Term]] = (term ~ rep("+" ~ term | "-" ~ term)) ^^ { | ||
| case op ~ list => list.foldLeft(List(op)) { | ||
| case (left, "+" ~ right) => left ++ Seq(right) | ||
| case (left, "-" ~ right) => left ++ Seq(Deletion(right)) | ||
| } | ||
| } | ||
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| def formula: Parser[ParsedRFormula] = | ||
| (columnRef ~ "~" ~ terms) ^^ { case r ~ "~" ~ t => ParsedRFormula(r, t) } | ||
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| def parse(value: String): ParsedRFormula = parseAll(formula, value) match { | ||
| case Success(result, _) => result | ||
| case failure: NoSuccess => throw new IllegalArgumentException( | ||
| "Could not parse formula: " + value) | ||
| } | ||
| } |
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53 changes: 53 additions & 0 deletions
53
mllib/src/main/scala/org/apache/spark/mllib/api/python/GaussianMixtureModelWrapper.scala
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,53 @@ | ||
| /* | ||
| * 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. | ||
| */ | ||
|
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| package org.apache.spark.mllib.api.python | ||
|
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| import java.util.{List => JList} | ||
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| import scala.collection.JavaConverters._ | ||
| import scala.collection.mutable.ArrayBuffer | ||
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| import org.apache.spark.SparkContext | ||
| import org.apache.spark.mllib.linalg.{Vector, Vectors, Matrix} | ||
| import org.apache.spark.mllib.clustering.GaussianMixtureModel | ||
|
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| /** | ||
| * Wrapper around GaussianMixtureModel to provide helper methods in Python | ||
| */ | ||
| private[python] class GaussianMixtureModelWrapper(model: GaussianMixtureModel) { | ||
| val weights: Vector = Vectors.dense(model.weights) | ||
| val k: Int = weights.size | ||
|
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| /** | ||
| * Returns gaussians as a List of Vectors and Matrices corresponding each MultivariateGaussian | ||
| */ | ||
| val gaussians: JList[Object] = { | ||
| val modelGaussians = model.gaussians | ||
| var i = 0 | ||
| var mu = ArrayBuffer.empty[Vector] | ||
| var sigma = ArrayBuffer.empty[Matrix] | ||
| while (i < k) { | ||
| mu += modelGaussians(i).mu | ||
| sigma += modelGaussians(i).sigma | ||
| i += 1 | ||
| } | ||
| List(mu.toArray, sigma.toArray).map(_.asInstanceOf[Object]).asJava | ||
| } | ||
|
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| def save(sc: SparkContext, path: String): Unit = model.save(sc, path) | ||
| } |
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