Implement nonLin slightly differently

encoder/src/main/scala/org/clulab/scala_transformers/encoder/Encoder.scala

@@ -1,13 +1,12 @@
 package org.clulab.scala_transformers.encoder
 
 import ai.onnxruntime.{OnnxTensor, OrtEnvironment, OrtSession}
-import org.clulab.scala_transformers.encoder.math.Mathematics
 import org.clulab.scala_transformers.encoder.math.Mathematics.{Math, MathMatrix}
 
 import java.io.DataInputStream
 import java.util.{HashMap => JHashMap}
 
-class Encoder(val encoderEnvironment: OrtEnvironment, val encoderSession: OrtSession, nonLin: Option[NonLinearity] = None) {
+class Encoder(val encoderEnvironment: OrtEnvironment, val encoderSession: OrtSession, nonLinOpt: Option[NonLinearity] = None) {
   /**
     * Runs the inference using a transformer encoder over a batch of sentences
     *
@@ -21,18 +20,11 @@ class Encoder(val encoderEnvironment: OrtEnvironment, val encoderSession: OrtSes
     val result: OrtSession.Result = encoderSession.run(inputs)
     val outputs = Math.fromResult(result)
 
-    if(nonLin.isDefined) {
-      for (matrix <- outputs) {
-        for (i <- 0 until Math.rows(matrix)) {
-          val row = Math.row(matrix, i)
-          for (j <- 0 until Math.cols(matrix)) {
-            val orig = Math.get(row, j)
-            Math.set(row, j, nonLin.get.compute(orig))
-          }
-        }
+    nonLinOpt.foreach { nonLin =>
+      outputs.foreach { matrix =>
+        Math.map(matrix, nonLin.compute)
       }
     }
-
     outputs
   }
 

encoder/src/main/scala/org/clulab/scala_transformers/encoder/NonLinearity.scala

@@ -1,15 +1,13 @@
 package org.clulab.scala_transformers.encoder
 
-import org.clulab.scala_transformers.encoder.math.EjmlMath.MathValue
-
-import java.lang
+import org.clulab.scala_transformers.encoder.math.Mathematics.MathValue
 
 trait NonLinearity {
   def compute(input: MathValue): MathValue
 }
 
-class ReLU extends NonLinearity {
+object ReLU extends NonLinearity {
   override def compute(input: MathValue): MathValue = {
-    lang.Float.max(0, input)
+    scala.math.max(0, input)
   }
 }

encoder/src/main/scala/org/clulab/scala_transformers/encoder/math/EjmlMath.scala

@@ -100,6 +100,17 @@ object EjmlMath extends Math {
     new FMatrixRMaj(rows, cols)
   }
 
+  override def map(matrix: MathRowMatrix, f: MathValue => MathValue): Unit = {
+    val iterator = matrix.iterator(true, 0, 0, matrix.getNumRows, matrix.getNumCols)
+
+    while (iterator.hasNext) {
+      val oldValue = iterator.next()
+      val newValue = f(oldValue)
+
+      iterator.set(newValue)
+    }
+  }
+
   def row(matrix: MathRowMatrix, index: Int): MathRowVector = {
     val result = SimpleMatrix.wrap(matrix).rows(index, index + 1).getMatrix[FMatrixRMaj]
 

encoder/src/main/scala/org/clulab/scala_transformers/encoder/math/Math.scala

@@ -13,6 +13,7 @@ trait Math {
   def inplaceMatrixAddition(matrix: MathRowMatrix, colVector: MathColVector): Unit
   def inplaceMatrixAddition(matrix: MathRowMatrix, rowIndex: Int, rowVector: MathRowVector): Unit
 //  def rowVectorAddition(leftRowVector: MathRowVector, rightRowVector: MathRowVector): MathRowVector
+  def map(matrix: MathRowMatrix, f: MathValue => MathValue): Unit
   def mul(leftMatrix: MathRowMatrix, rightMatrix: MathRowMatrix): MathRowMatrix
   def rows(matrix: MathRowMatrix): Int
   def cols(matrix: MathRowMatrix): Int

encoder/src/main/scala/org/clulab/scala_transformers/encoder/math/Mathematics.scala

@@ -7,6 +7,7 @@ object Mathematics {
   // val Math = CommonsMath
   // val Math = CluMath
 
+  type MathValue = Math.MathValue
   type MathMatrix = Math.MathRowMatrix
   type MathColVector = Math.MathColVector
   type MathRowVector = Math.MathRowVector