Merge pull request #1 from Azure/master

feat: ONNX model inference on Spark (microsoft#1152)

build.sbt

@@ -8,8 +8,6 @@ import scala.xml.transform.{RewriteRule, RuleTransformer}
 import BuildUtils._
 import xerial.sbt.Sonatype._
 
-import java.nio.file.Files
-
 val condaEnvName = "mmlspark"
 val sparkVersion = "3.1.2"
 name := "mmlspark"
@@ -41,7 +39,7 @@ val dependencies = coreDependencies ++ extraDependencies
 
 def txt(e: Elem, label: String): String = "\"" + e.child.filter(_.label == label).flatMap(_.text).mkString + "\""
 
-val omittedDeps = Set(s"spark-core_${scalaMajorVersion}", s"spark-mllib_${scalaMajorVersion}", "org.scala-lang")
+val omittedDeps = Set(s"spark-core_$scalaMajorVersion", s"spark-mllib_$scalaMajorVersion", "org.scala-lang")
 // skip dependency elements with a scope
 
 def pomPostFunc(node: XmlNode): scala.xml.Node = {
@@ -67,7 +65,7 @@ pomPostProcess := pomPostFunc
 val speechResolver = "Speech" at "https://mmlspark.blob.core.windows.net/maven/"
 
 val getDatasetsTask = TaskKey[Unit]("getDatasets", "download datasets used for testing")
-val datasetName = "datasets-2020-08-27.tgz"
+val datasetName = "datasets-2021-07-27.tgz"
 val datasetUrl = new URL(s"https://mmlspark.blob.core.windows.net/installers/$datasetName")
 val datasetDir = settingKey[File]("The directory that holds the dataset")
 ThisBuild / datasetDir := {
@@ -196,7 +194,7 @@ ThisBuild / publishMavenStyle := true
 
 lazy val core = (project in file("core"))
   .enablePlugins(BuildInfoPlugin && SbtPlugin)
-  .settings((settings ++ Seq(
+  .settings(settings ++ Seq(
     libraryDependencies ++= dependencies,
     buildInfoKeys ++= Seq[BuildInfoKey](
       datasetDir,
@@ -207,48 +205,51 @@ lazy val core = (project in file("core"))
     ),
     name := "mmlspark-core",
     buildInfoPackage := "com.microsoft.ml.spark.build",
-  )): _*)
+  ): _*)
 
 lazy val deepLearning = (project in file("deep-learning"))
   .enablePlugins(SbtPlugin)
-  .dependsOn(core % "test->test;compile->compile")
-  .settings((settings ++ Seq(
-    libraryDependencies += ("com.microsoft.cntk" % "cntk" % "2.4"),
+  .dependsOn(core % "test->test;compile->compile", opencv % "test->test;compile->compile")
+  .settings(settings ++ Seq(
+    libraryDependencies ++= Seq(
+      "com.microsoft.cntk" % "cntk" % "2.4",
+      "com.microsoft.onnxruntime" % "onnxruntime_gpu" % "1.8.1"
+    ),
     name := "mmlspark-deep-learning",
-  )): _*)
+  ): _*)
 
 lazy val lightgbm = (project in file("lightgbm"))
   .enablePlugins(SbtPlugin)
   .dependsOn(core % "test->test;compile->compile")
-  .settings((settings ++ Seq(
+  .settings(settings ++ Seq(
     libraryDependencies += ("com.microsoft.ml.lightgbm" % "lightgbmlib" % "3.2.110"),
     name := "mmlspark-lightgbm"
-  )): _*)
+  ): _*)
 
 lazy val vw = (project in file("vw"))
   .enablePlugins(SbtPlugin)
   .dependsOn(core % "test->test;compile->compile")
-  .settings((settings ++ Seq(
+  .settings(settings ++ Seq(
     libraryDependencies += ("com.github.vowpalwabbit" % "vw-jni" % "8.9.1"),
     name := "mmlspark-vw"
-  )): _*)
+  ): _*)
 
 lazy val cognitive = (project in file("cognitive"))
   .enablePlugins(SbtPlugin)
   .dependsOn(core % "test->test;compile->compile")
-  .settings((settings ++ Seq(
+  .settings(settings ++ Seq(
     libraryDependencies += ("com.microsoft.cognitiveservices.speech" % "client-sdk" % "1.14.0"),
     resolvers += speechResolver,
     name := "mmlspark-cognitive"
-  )): _*)
+  ): _*)
 
 lazy val opencv = (project in file("opencv"))
   .enablePlugins(SbtPlugin)
   .dependsOn(core % "test->test;compile->compile")
-  .settings((settings ++ Seq(
+  .settings(settings ++ Seq(
     libraryDependencies += ("org.openpnp" % "opencv" % "3.2.0-1"),
     name := "mmlspark-opencv"
-  )): _*)
+  ): _*)
 
 lazy val root = (project in file("."))
   .aggregate(core, deepLearning, cognitive, vw, lightgbm, opencv)
@@ -297,15 +298,15 @@ pgpPassphrase := Some(Secrets.pgpPassword.toCharArray)
 pgpSecretRing := {
   val temp = File.createTempFile("secret", ".asc")
   new PrintWriter(temp) {
-    write(Secrets.pgpPrivate);
+    write(Secrets.pgpPrivate)
     close()
   }
   temp
 }
 pgpPublicRing := {
   val temp = File.createTempFile("public", ".asc")
   new PrintWriter(temp) {
-    write(Secrets.pgpPublic);
+    write(Secrets.pgpPublic)
     close()
   }
   temp

core/src/main/python/mmlspark/core/serialize/java_params_patch.py

@@ -6,6 +6,7 @@
 from pyspark.ml.common import _to_java_object_rdd, _java2py
 import pyspark
 from pyspark.ml import PipelineModel
+from pyspark.sql.types import DataType
 
 
 @staticmethod
@@ -21,7 +22,7 @@ def __get_class(clazz):
         """
         Loads Python class from its name.
         """
-        parts = clazz.split('.')
+        parts = clazz.split(".")
         module = ".".join(parts[:-1])
         m = __import__(module)
         for comp in parts[1:]:
@@ -41,8 +42,7 @@ def __get_class(clazz):
     elif hasattr(py_type, "_from_java"):
         py_stage = py_type._from_java(java_stage)
     else:
-        raise NotImplementedError("This Java stage cannot be loaded into Python currently: %r"
-                                  % stage_name)
+        raise NotImplementedError("This Java stage cannot be loaded into Python currently: %r" % stage_name)
     return py_stage
 
 
@@ -68,6 +68,8 @@ def _mml_py2java(sc, obj):
         pass
     elif isinstance(obj, (int, float, bool, bytes, str)):
         pass
+    elif isinstance(obj, DataType):
+        obj = sc._jvm.org.apache.spark.sql.types.DataType.fromJson(obj.json())
     else:
         data = bytearray(PickleSerializer().dumps(obj))
         obj = sc._jvm.org.apache.spark.ml.python.MLSerDe.loads(data)

core/src/main/scala/com/microsoft/ml/spark/core/schema/ImageSchemaUtils.scala

@@ -20,11 +20,10 @@ object ImageSchemaUtils {
         StructField("data", BinaryType, true) :: Nil)
   }
 
-  val ImageSchemaNullable = StructType(StructField("image", ColumnSchemaNullable, true) :: Nil)
+  val ImageSchemaNullable: StructType = StructType(StructField("image", ColumnSchemaNullable, nullable = true) :: Nil)
 
   def isImage(dataType: DataType): Boolean = {
-    dataType == ImageSchema.columnSchema ||
-      dataType == ColumnSchemaNullable
+    DataType.equalsStructurally(dataType, ImageSchema.columnSchema, ignoreNullability = true)
   }
 
   def isImage(dataType: StructField): Boolean = {

core/src/main/scala/com/microsoft/ml/spark/explainers/BreezeUtils.scala → core/src/main/scala/com/microsoft/ml/spark/core/utils/BreezeUtils.scala

@@ -1,10 +1,10 @@
 // Copyright (C) Microsoft Corporation. All rights reserved.
 // Licensed under the MIT License. See LICENSE in project root for information.
 
-package com.microsoft.ml.spark.explainers
+package com.microsoft.ml.spark.core.utils
 
-import breeze.linalg.{DenseVector => BDV, SparseVector => BSV, Vector => BV, DenseMatrix => BDM}
-import org.apache.spark.ml.linalg.{Vector, Vectors, Matrix, Matrices}
+import org.apache.spark.ml.linalg.{Matrices, Matrix, Vector, Vectors}
+import breeze.linalg.{DenseVector => BDV, DenseMatrix => BDM, SparseVector => BSV, Vector => BV}
 
 object BreezeUtils {
   implicit class SparkVectorCanConvertToBreeze(sv: Vector) {

core/src/main/scala/com/microsoft/ml/spark/explainers/KernelSHAPBase.scala

@@ -5,7 +5,7 @@ package com.microsoft.ml.spark.explainers
 import breeze.linalg.{*, DenseMatrix => BDM, DenseVector => BDV}
 import com.microsoft.ml.spark.codegen.Wrappable
 import com.microsoft.ml.spark.core.schema.DatasetExtensions
-import com.microsoft.ml.spark.explainers.BreezeUtils._
+import com.microsoft.ml.spark.core.utils.BreezeUtils._
 import com.microsoft.ml.spark.logging.BasicLogging
 import org.apache.spark.ml.Transformer
 import org.apache.spark.ml.linalg.SQLDataTypes.VectorType

core/src/main/scala/com/microsoft/ml/spark/explainers/KernelSHAPSampler.scala

@@ -4,7 +4,7 @@
 package com.microsoft.ml.spark.explainers
 
 import breeze.linalg.{sum, DenseVector => BDV}
-import com.microsoft.ml.spark.explainers.BreezeUtils._
+import com.microsoft.ml.spark.core.utils.BreezeUtils._
 import org.apache.commons.math3.util.CombinatoricsUtils.{binomialCoefficientDouble => comb}
 import org.apache.spark.ml.linalg.Vector
 

core/src/main/scala/com/microsoft/ml/spark/explainers/LIMEBase.scala

@@ -6,7 +6,7 @@ package com.microsoft.ml.spark.explainers
 import breeze.linalg.{*, DenseMatrix => BDM, DenseVector => BDV}
 import com.microsoft.ml.spark.codegen.Wrappable
 import com.microsoft.ml.spark.core.schema.DatasetExtensions
-import com.microsoft.ml.spark.explainers.BreezeUtils._
+import com.microsoft.ml.spark.core.utils.BreezeUtils._
 import com.microsoft.ml.spark.logging.BasicLogging
 import org.apache.spark.injections.UDFUtils
 import org.apache.spark.ml.Transformer

core/src/main/scala/com/microsoft/ml/spark/explainers/LIMESampler.scala

@@ -6,7 +6,7 @@ package com.microsoft.ml.spark.explainers
 import breeze.linalg.{BitVector, axpy, norm, DenseVector => BDV}
 import breeze.stats.distributions.RandBasis
 import org.apache.spark.ml.linalg.Vector
-import com.microsoft.ml.spark.explainers.BreezeUtils._
+import com.microsoft.ml.spark.core.utils.BreezeUtils._
 
 private[explainers] trait LIMESampler[TObservation] extends Sampler[TObservation, Vector] {
   def sample: (TObservation, Vector, Double) = {

core/src/main/scala/com/microsoft/ml/spark/explainers/Sampler.scala

@@ -5,7 +5,7 @@ package com.microsoft.ml.spark.explainers
 
 import breeze.linalg.{norm, DenseVector => BDV}
 import breeze.stats.distributions.RandBasis
-import com.microsoft.ml.spark.explainers.BreezeUtils._
+import com.microsoft.ml.spark.core.utils.BreezeUtils._
 import com.microsoft.ml.spark.explainers.RowUtils.RowCanGetAsDouble
 import com.microsoft.ml.spark.lime.{Superpixel, SuperpixelData}
 import org.apache.spark.ml.linalg.{Vector, Vectors}
@@ -152,6 +152,8 @@ private[explainers] class LIMETabularSampler(val instance: Row, val featureStats
         (instance.get(i), 1d)
       case (_: ContinuousFeatureStats, i) =>
         (instance.getAsDouble(i), instance.getAsDouble(i))
+      case (_, _) =>
+        throw new NotImplementedError("invalid state")
     }.unzip
 
     (Row.fromSeq(identityRow), Vectors.dense(identityState.toArray), 0d)

core/src/main/scala/com/microsoft/ml/spark/lime/LIME.scala

@@ -164,10 +164,10 @@ trait LIMEBase extends LIMEParams with ComplexParamsWritable {
 
 }
 
-@deprecated("Please use 'com.microsoft.ml.spark.explainers.VectorLIME'.", since="1.0.0-RC3")
+@deprecated("Please use 'com.microsoft.ml.spark.explainers.VectorLIME'.", since="1.0.0-rc3")
 object TabularLIME extends ComplexParamsReadable[TabularLIME]
 
-@deprecated("Please use 'com.microsoft.ml.spark.explainers.VectorLIME'.", since="1.0.0-RC3")
+@deprecated("Please use 'com.microsoft.ml.spark.explainers.VectorLIME'.", since="1.0.0-rc3")
 class TabularLIME(val uid: String) extends Estimator[TabularLIMEModel]
   with LIMEParams with Wrappable with ComplexParamsWritable with BasicLogging {
   logClass()
@@ -200,10 +200,10 @@ class TabularLIME(val uid: String) extends Estimator[TabularLIMEModel]
   }
 }
 
-@deprecated("Please use 'com.microsoft.ml.spark.explainers.VectorLIME'.", since="1.0.0-RC3")
+@deprecated("Please use 'com.microsoft.ml.spark.explainers.VectorLIME'.", since="1.0.0-rc3")
 object TabularLIMEModel extends ComplexParamsReadable[TabularLIMEModel]
 
-@deprecated("Please use 'com.microsoft.ml.spark.explainers.VectorLIME'.", since="1.0.0-RC3")
+@deprecated("Please use 'com.microsoft.ml.spark.explainers.VectorLIME'.", since="1.0.0-rc3")
 class TabularLIMEModel(val uid: String) extends Model[TabularLIMEModel]
   with LIMEBase with Wrappable with BasicLogging {
   logClass()
@@ -256,15 +256,15 @@ class TabularLIMEModel(val uid: String) extends Model[TabularLIMEModel]
 
 }
 
-@deprecated("Please use 'com.microsoft.ml.spark.explainers.ImageLIME'.", since="1.0.0-RC3")
+@deprecated("Please use 'com.microsoft.ml.spark.explainers.ImageLIME'.", since="1.0.0-rc3")
 object ImageLIME extends ComplexParamsReadable[ImageLIME]
 
 /** Distributed implementation of
   * Local Interpretable Model-Agnostic Explanations (LIME)
   *
   * https://arxiv.org/pdf/1602.04938v1.pdf
   */
-@deprecated("Please use 'com.microsoft.ml.spark.explainers.ImageLIME'.", since="1.0.0-RC3")
+@deprecated("Please use 'com.microsoft.ml.spark.explainers.ImageLIME'.", since="1.0.0-rc3")
 class ImageLIME(val uid: String) extends Transformer with LIMEBase
   with Wrappable with HasModifier with HasCellSize with BasicLogging {
   logClass()

core/src/main/scala/com/microsoft/ml/spark/lime/TextLIME.scala

@@ -25,7 +25,7 @@ object TextLIME extends ComplexParamsReadable[TextLIME]
   *
   * https://arxiv.org/pdf/1602.04938v1.pdf
   */
-@deprecated("Please use 'com.microsoft.ml.spark.explainers.TextLIME'.", since="1.0.0-RC3")
+@deprecated("Please use 'com.microsoft.ml.spark.explainers.TextLIME'.", since="1.0.0-rc3")
 class TextLIME(val uid: String) extends Model[TextLIME]
   with LIMEBase with Wrappable with BasicLogging {
   logClass()

core/src/main/scala/com/microsoft/ml/spark/stages/MiniBatchTransformer.scala

@@ -8,7 +8,8 @@ import com.microsoft.ml.spark.logging.BasicLogging
 import org.apache.spark.ml.Transformer
 import org.apache.spark.ml.param._
 import org.apache.spark.ml.util.{DefaultParamsReadable, DefaultParamsWritable, Identifiable}
-import org.apache.spark.sql.catalyst.encoders.RowEncoder
+import org.apache.spark.sql.catalyst.encoders.{ExpressionEncoder, RowEncoder}
+import org.apache.spark.sql.catalyst.expressions.GenericRowWithSchema
 import org.apache.spark.sql.types._
 import org.apache.spark.sql.{DataFrame, Dataset, Row}
 
@@ -30,16 +31,20 @@ trait MiniBatchBase extends Transformer with DefaultParamsWritable with Wrappabl
 
   def transform(dataset: Dataset[_]): DataFrame = {
     logTransform[DataFrame]({
+      val outputSchema = transformSchema(dataset.schema)
+      implicit val outputEncoder: ExpressionEncoder[Row] = RowEncoder(outputSchema)
       dataset.toDF().mapPartitions { it =>
         if (it.isEmpty) {
           it
         } else {
-          getBatcher(it).map(listOfRows => Row.fromSeq(transpose(listOfRows.map(r => r.toSeq))))
+          getBatcher(it).map {
+            listOfRows =>
+              new GenericRowWithSchema(transpose(listOfRows.map(r => r.toSeq)).toArray, outputSchema)
+          }
         }
-      }(RowEncoder(transformSchema(dataset.schema)))
+      }
     })
   }
-
 }
 
 object DynamicMiniBatchTransformer extends DefaultParamsReadable[DynamicMiniBatchTransformer]
@@ -203,15 +208,20 @@ class FlattenBatch(val uid: String)
 
   override def transform(dataset: Dataset[_]): DataFrame = {
     logTransform[DataFrame]({
+      val outputSchema = transformSchema(dataset.schema)
+      implicit val outputEncoder: ExpressionEncoder[Row] = RowEncoder(outputSchema)
+
       dataset.toDF().mapPartitions(it =>
         it.flatMap { rowOfLists =>
-          val transposed = transpose(
+          val transposed: Seq[Seq[Any]] = transpose(
             (0 until rowOfLists.length)
               .filterNot(rowOfLists.isNullAt)
               .map(rowOfLists.getSeq))
-          transposed.map(Row.fromSeq)
+          transposed.map {
+            values => new GenericRowWithSchema(values.toArray, outputSchema)
+          }
         }
-      )(RowEncoder(transformSchema(dataset.schema)))
+      )
     })
   }
 

core/src/test/scala/com/microsoft/ml/spark/core/test/base/TestBase.scala

@@ -238,12 +238,21 @@ abstract class TestBase extends FunSuite with BeforeAndAfterEachTestData with Be
     }
   }
 
-  def breezeVectorEq[T: Field: ClassTag](tol: Double)(implicit normImpl: Impl[T, Double]): Equality[BDV[T]] =
+  def breezeVectorEq[T: Field](tol: Double)(implicit normImpl: Impl[T, Double]): Equality[BDV[T]] =
     (a: BDV[T], b: Any) => {
       b match {
         case p: BDV[T @unchecked] =>
           a.length == p.length && norm(a - p) < tol
         case _ => false
       }
     }
+
+  def mapEq[K, V: Equality]: Equality[Map[K, V]] = {
+    (a: Map[K, V], b: Any) => {
+      b match {
+        case m: Map[K @unchecked, V @unchecked] => a.keySet == m.keySet && a.keySet.forall(key => a(key) === m(key))
+        case _ => false
+      }
+    }
+  }
 }

core/src/test/scala/com/microsoft/ml/spark/explainers/split1/SamplerSuite.scala

@@ -6,7 +6,7 @@ package com.microsoft.ml.spark.explainers.split1
 import breeze.linalg.{DenseMatrix => BDM, DenseVector => BDV}
 import breeze.stats.distributions.RandBasis
 import breeze.stats.{mean, stddev}
-import com.microsoft.ml.spark.explainers.BreezeUtils._
+import com.microsoft.ml.spark.core.utils.BreezeUtils._
 import com.microsoft.ml.spark.explainers._
 import com.microsoft.ml.spark.io.image.ImageUtils
 import com.microsoft.ml.spark.lime.{Superpixel, SuperpixelData}

core/src/test/scala/com/microsoft/ml/spark/explainers/split1/TabularLIMEExplainerSuite.scala

@@ -6,7 +6,7 @@ package com.microsoft.ml.spark.explainers.split1
 import breeze.linalg.{DenseVector => BDV}
 import com.microsoft.ml.spark.core.test.base.TestBase
 import com.microsoft.ml.spark.core.test.fuzzing.{TestObject, TransformerFuzzing}
-import com.microsoft.ml.spark.explainers.BreezeUtils._
+import com.microsoft.ml.spark.core.utils.BreezeUtils._
 import com.microsoft.ml.spark.explainers.{LocalExplainer, TabularLIME}
 import org.apache.spark.ml.classification.{LogisticRegression, LogisticRegressionModel}
 import org.apache.spark.ml.feature.{OneHotEncoder, StringIndexer, VectorAssembler}

core/src/test/scala/com/microsoft/ml/spark/explainers/split1/TabularSHAPExplainerSuite.scala

@@ -5,7 +5,7 @@ package com.microsoft.ml.spark.explainers.split1
 
 import com.microsoft.ml.spark.core.test.base.TestBase
 import com.microsoft.ml.spark.core.test.fuzzing.{TestObject, TransformerFuzzing}
-import com.microsoft.ml.spark.explainers.BreezeUtils._
+import com.microsoft.ml.spark.core.utils.BreezeUtils._
 import com.microsoft.ml.spark.explainers.{LocalExplainer, TabularSHAP}
 import org.apache.spark.ml.classification.{LogisticRegression, LogisticRegressionModel}
 import org.apache.spark.ml.feature.{OneHotEncoder, StringIndexer, VectorAssembler}