API: prefer use of immutable IndexedSeq instead of Array #72

ijp-color/src/main/scala/ij_plugins/color/calibration/chart/ChartFrame.scala

@@ -44,14 +44,14 @@ object ChartFrame {
  */
 class ChartFrame(
   refOutline: IndexedSeq[Point2D],
-  refChipOutlines: IndexedSeq[Seq[Point2D]],
+  refChipOutlines: IndexedSeq[IndexedSeq[Point2D]],
   final val alignmentTransform: PerspectiveTransform /*= new PerspectiveTransform()*/
 ) {
 
   require(refOutline.length == 4, s"The reference outline must have 4 points, got ${refOutline.length}.")
 
   private val _referenceOutline: IndexedSeq[Point2D]  = deepCopy(refOutline)
-  private val _chipOutlines: IndexedSeq[Seq[Point2D]] = refChipOutlines.map(deepCopy)
+  private val _chipOutlines: IndexedSeq[IndexedSeq[Point2D]] = refChipOutlines.map(deepCopy)
 
   /**
    * Outline of the reference chart as a sequence of 4 corner points: top-left, top-right, bottom-right, bottom-left.
@@ -61,7 +61,7 @@ class ChartFrame(
   /**
    * Outlines of the reference chips. OOutlines are polygons, may have 3 or more vertices.
    */
-  final def referenceChipOutlines: IndexedSeq[Seq[Point2D]] = _chipOutlines.map(deepCopy)
+  final def referenceChipOutlines: IndexedSeq[IndexedSeq[Point2D]] = _chipOutlines.map(deepCopy)
 
   /**
    * Creates a copy of this chart that has its chip outline aligned to given ROI.

ijp-color/src/main/scala/ij_plugins/color/calibration/chart/ColorChip.scala

@@ -1,6 +1,6 @@
 /*
  * Image/J Plugins
- * Copyright (C) 2002-2021 Jarek Sacha
+ * Copyright (C) 2002-2022 Jarek Sacha
  * Author's email: jpsacha at gmail dot com
  *
  * This library is free software; you can redistribute it and/or
@@ -54,7 +54,7 @@ object ColorChip {
     new ColorChip(
       name,
       color,
-      List(
+      IndexedSeq(
         point2D(column + margin, row + margin),
         point2D(column + 1 - margin, row + margin),
         point2D(column + 1 - margin, row + 1 - margin),
@@ -74,4 +74,4 @@ object ColorChip {
  * @param outline
  *   outline describing the chip and its location.
  */
-class ColorChip(val name: String, val color: Lab, val outline: Seq[Point2D])
+class ColorChip(val name: String, val color: Lab, val outline: IndexedSeq[Point2D])

ijp-color/src/main/scala/ij_plugins/color/calibration/chart/GridChartFrame.scala

@@ -1,6 +1,6 @@
 /*
  * Image/J Plugins
- * Copyright (C) 2002-2021 Jarek Sacha
+ * Copyright (C) 2002-2022 Jarek Sacha
  * Author's email: jpsacha at gmail dot com
  *
  * This library is free software; you can redistribute it and/or
@@ -30,12 +30,12 @@ import java.awt.geom.Point2D
 import scala.collection.compat.immutable.ArraySeq
 
 object GridChartFrame {
-  private def createChipOutlines(nbColumns: Int, nbRows: Int, chipMargin: Double): IndexedSeq[Seq[Point2D]] = {
+  private def createChipOutlines(nbColumns: Int, nbRows: Int, chipMargin: Double): IndexedSeq[IndexedSeq[Point2D]] = {
     require(nbColumns > 0)
     require(nbRows > 0)
 
     for {
-      row    <- 0 until nbRows
+      row <- 0 until nbRows
       column <- 0 until nbColumns
     } yield {
       Seq(

ijp-color/src/main/scala/ij_plugins/color/calibration/regression/Regression.scala

@@ -59,17 +59,13 @@ object Regression {
   /**
     * Compute linear fit coefficient `s = A*o` if `noIntercept` is true or `s = A*o + b` if `noIntercept` is `false`.
     *
-    * @param standard
-    * array of expected output values.
-    * @param observation
-    * array of input values
-    * @param noIntercept
-    * true means the model is to be estimated without an intercept term
-    * @return
-    * linear fit coefficients
+    * @param standard    array of expected output values.
+    * @param observation array of input values
+    * @param noIntercept true means the model is to be estimated without an intercept term
+    * @return linear fit coefficients
     */
   def regression(standard: Array[Double],
-                 observation: IndexedSeq[IndexedSeq[Double]],
+                 observation: Array[Array[Double]],
                  noIntercept: Boolean
                 ): Regression.Result = {
     require(standard != null, "Argument `standard` cannot be null.")
@@ -86,7 +82,7 @@ object Regression {
 
     val regression = new OLSMultipleLinearRegression()
     regression.setNoIntercept(noIntercept)
-    regression.newSampleData(standard, toArrayArray(observation))
+    regression.newSampleData(standard, observation)
     Regression.Result(
       numberOfSamples = standard.length,
       beta = regression.estimateRegressionParameters,
@@ -97,6 +93,21 @@ object Regression {
     )
   }
 
+  /**
+    * Compute linear fit coefficient `s = A*o` if `noIntercept` is true or `s = A*o + b` if `noIntercept` is `false`.
+    *
+    * @param standard    array of expected output values.
+    * @param observation array of input values
+    * @param noIntercept true means the model is to be estimated without an intercept term
+    * @return linear fit coefficients
+    */
+  def regression(standard: Array[Double],
+                 observation: IndexedSeq[IndexedSeq[Double]],
+                 noIntercept: Boolean
+                ): Regression.Result = {
+    regression(standard, toArrayArray(observation), noIntercept)
+  }
+
   /**
     * Compute linear fit coefficients that map observations to a reference: `s = A*[o, 1]`.
     *
@@ -110,4 +121,8 @@ object Regression {
   def createLinear(standard: Array[Double], observation: IndexedSeq[IndexedSeq[Double]]): Regression.Result = {
     regression(standard, observation, noIntercept = false)
   }
+
+  def createLinear(standard: Array[Double], observation: Array[Array[Double]]): Regression.Result = {
+    regression(standard, observation, noIntercept = false)
+  }
 }

ijp-color/src/main/scala/ij_plugins/color/util/PerspectiveTransform.scala

@@ -1,6 +1,6 @@
 /*
  * Image/J Plugins
- * Copyright (C) 2002-2021 Jarek Sacha
+ * Copyright (C) 2002-2022 Jarek Sacha
  * Author's email: jpsacha at gmail dot com
  *
  * This library is free software; you can redistribute it and/or
@@ -317,6 +317,27 @@ object PerspectiveTransform {
     )
   }
 
+  def quadToQuad(points1: IndexedSeq[Point2D], points2: IndexedSeq[Point2D]): PerspectiveTransform = {
+    quadToQuad(
+      points1(0).getX,
+      points1(0).getY,
+      points1(1).getX,
+      points1(1).getY,
+      points1(2).getX,
+      points1(2).getY,
+      points1(3).getX,
+      points1(3).getY,
+      points2(0).getX,
+      points2(0).getY,
+      points2(1).getX,
+      points2(1).getY,
+      points2(2).getX,
+      points2(2).getY,
+      points2(3).getX,
+      points2(3).getY
+    )
+  }
+
   private final val PERSPECTIVE_DIVIDE_EPSILON: Double = 1.0e-10
 }
 
@@ -806,12 +827,11 @@ final class PerspectiveTransform(
    * @throws java.lang.IllegalArgumentException
    *   if ptSrc is null
    */
-  def transform(points: Seq[Point2D]): immutable.Seq[Point2D] = {
+  def transform(points: IndexedSeq[Point2D]): immutable.IndexedSeq[Point2D] = {
     require(points != null, "The input argument 'points' may not be null.")
     // Conversion `toList` to achieve Scala 2.12 compatibility
     points
       .map(p => transform(p))
-      .toList
   }
 
   /**