From f7f6cf980f8bfd3614d94c1fe6d39bad45d97397 Mon Sep 17 00:00:00 2001
From: Jarek Sacha <jpsacha@gmail.com>
Date: Tue, 9 Nov 2021 08:50:59 -0500
Subject: [PATCH 1/3] Fix issue with incorrect computation of
 LinearNoInterceptCrossBand mapping #58

---
 .../regression/MappingFactory.scala           |  2 +-
 .../regression/MappingFactoryTest.scala       | 48 +++++++++++++++++++
 2 files changed, 49 insertions(+), 1 deletion(-)

diff --git a/ijp-color/src/main/scala/ij_plugins/color/calibration/regression/MappingFactory.scala b/ijp-color/src/main/scala/ij_plugins/color/calibration/regression/MappingFactory.scala
index a28e1de..6c421cd 100644
--- a/ijp-color/src/main/scala/ij_plugins/color/calibration/regression/MappingFactory.scala
+++ b/ijp-color/src/main/scala/ij_plugins/color/calibration/regression/MappingFactory.scala
@@ -133,7 +133,7 @@ object MappingFactory {
     require(rr.beta.length == 3, "Size of beta must be equal 3, got " + rr.beta.length)
 
     val alpha14 = new Array[Double](14)
-    alpha14(1) = rr.beta(0)
+    rr.beta.copyToArray(alpha14, 1)
 
     new CubicPolynomial(alpha14, Option(rr))
   }
diff --git a/ijp-color/src/test/scala/ij_plugins/color/calibration/regression/MappingFactoryTest.scala b/ijp-color/src/test/scala/ij_plugins/color/calibration/regression/MappingFactoryTest.scala
index c761727..47b53c9 100644
--- a/ijp-color/src/test/scala/ij_plugins/color/calibration/regression/MappingFactoryTest.scala
+++ b/ijp-color/src/test/scala/ij_plugins/color/calibration/regression/MappingFactoryTest.scala
@@ -66,6 +66,54 @@ class MappingFactoryTest extends AnyFlatSpec {
     cp.regressionResult.get.rSquared should be(0.9931 +- 0.0001)
   }
 
+  it should "createLinearNoInterceptXBand (for a band)" in {
+
+    // Values based on "IMG_0903_025p-crop.tif"
+    // Chip margin: 16
+    // Band: red (0)
+    // Chips with negative standard values excluded (21 of 24 chips used)
+
+    val standard = Array(126.91979030350699, 216.20834154788753, 65.59369249416655, 98.31654126463174,
+      118.2264657620243, 79.14341258243843, 242.05769847504052, 217.36207592151652, 88.1513891672125,
+      177.94611517624423, 252.25703548744028, 83.31632229886839, 204.2661490485881, 265.5540885367791,
+      204.39823118845072, 248.2796227241613, 201.91675592164282, 160.56106457681673, 117.76955679703373,
+      83.66445997737526, 49.37241240933231)
+    val observed = Array(
+      Array(50.0181598062954, 20.692493946731236, 6.2941888619854724),
+      Array(123.94199243379572, 60.84741488020177, 43.90668348045397),
+      Array(52.774739583333336, 48.147135416666664, 55.24609375),
+      Array(49.07827260458839, 45.76923076923077, 3.4116059379217276),
+      Array(80.11018131101812, 56.83682008368201, 76.83124128312413),
+      Array(70.71551724137932, 104.76867816091954, 77.96120689655173),
+      Array(129.9434832756632, 48.10957324106113, 6.1280276816609),
+      Array(122.0730198019802, 31.084158415841586, 27.407178217821784),
+      Array(34.896153846153844, 13.28974358974359, 25.8),
+      Array(111.19521912350598, 106.04780876494024, 0.0),
+      Array(159.51440329218107, 89.1673525377229, 0.0),
+      Array(42.25541619156214, 64.54161915621437, 4.850627137970354),
+      Array(101.95985832349469, 20.65289256198347, 14.334120425029516),
+      Array(166.38536585365853, 109.20487804878049, 0.0),
+      Array(118.84702907711757, 41.25031605562579, 65.6826801517067),
+      Array(160.03979057591624, 124.83769633507853, 102.07748691099476),
+      Array(130.071661237785, 99.51031487513572, 81.14332247557003),
+      Array(101.88004484304933, 76.65807174887892, 62.26569506726457),
+      Array(71.38675958188153, 50.54239256678281, 37.92566782810685),
+      Array(42.70169082125604, 29.83816425120773, 21.544685990338163),
+      Array(15.848180677540778, 5.183186951066499, 2.986198243412798)
+    )
+
+    val expectedResult = Array(0.0, 1.9724784162678572, -0.426914583530878, -0.1296547005685931, 0.0, 0.0, 0.0, 0.0,
+      0.0, 0.0, 0.0, 0.0, 0.0, 0.0)
+
+    val cp = MappingFactory.createLinearNoInterceptXBand(standard, observed)
+    val cpArray = cp.toArray
+
+    cpArray should be(expectedResult)
+
+    cp.regressionResult.isDefined should be(true)
+    cp.regressionResult.get.rSquared should be(0.991 +- 0.001)
+  }
+
   it should "createLinear" in {
     val observed = Array(1, 1.5, 2, 3, 4, 5, 7, 10)
     val standard =

From 6eddb57658dcbbc7f0ef31d437acd1ef4fb58c28 Mon Sep 17 00:00:00 2001
From: Jarek Sacha <jpsacha@gmail.com>
Date: Tue, 9 Nov 2021 08:53:19 -0500
Subject: [PATCH 2/3] Fixed spelling mistake in UI #59

---
 .../ij_plugins/color/ui/calibration/ColorCalibrator.fxml        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ijp-color-ui/src/main/resources/ij_plugins/color/ui/calibration/ColorCalibrator.fxml b/ijp-color-ui/src/main/resources/ij_plugins/color/ui/calibration/ColorCalibrator.fxml
index 5d6430e..1e30047 100644
--- a/ijp-color-ui/src/main/resources/ij_plugins/color/ui/calibration/ColorCalibrator.fxml
+++ b/ijp-color-ui/src/main/resources/ij_plugins/color/ui/calibration/ColorCalibrator.fxml
@@ -97,7 +97,7 @@
                 <ChoiceBox fx:id="mappingMethodChoiceBox" maxWidth="1.7976931348623157E308" prefWidth="150.0"
                            GridPane.columnIndex="1" GridPane.rowIndex="11"/>
                 <Button fx:id="suggestCalibrationOptionsButton" maxWidth="1.7976931348623157E308"
-                        mnemonicParsing="false" text="Sugget Options" GridPane.columnIndex="2" GridPane.rowIndex="10"/>
+                        mnemonicParsing="false" text="Suggest Options" GridPane.columnIndex="2" GridPane.rowIndex="10"/>
                 <Button id="ijp-button" fx:id="calibrateButton" contentDisplay="CENTER"
                         maxWidth="1.7976931348623157E308" mnemonicParsing="false" text="Calibrate"
                         GridPane.columnIndex="1" GridPane.halignment="CENTER" GridPane.rowIndex="13">

From cffbdfed260519e374874de98fb04d6da57dc4ce Mon Sep 17 00:00:00 2001
From: Jarek Sacha <jpsacha@gmail.com>
Date: Tue, 9 Nov 2021 09:01:22 -0500
Subject: [PATCH 3/3] Add clear indication in ImageJ status that batch
 processing completed

---
 .../scala/ij_plugins/color/ui/util/batch/BatchProcessing.scala  | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/ijp-color-ui/src/main/scala/ij_plugins/color/ui/util/batch/BatchProcessing.scala b/ijp-color-ui/src/main/scala/ij_plugins/color/ui/util/batch/BatchProcessing.scala
index d4d8e93..a2f0daa 100644
--- a/ijp-color-ui/src/main/scala/ij_plugins/color/ui/util/batch/BatchProcessing.scala
+++ b/ijp-color-ui/src/main/scala/ij_plugins/color/ui/util/batch/BatchProcessing.scala
@@ -136,6 +136,8 @@ class BatchProcessing(override val parentWindow: Option[Window]) extends ShowMes
         }
       if (abort.get()) {
         IJ.showStatus(title + " - batch processing aborted by user.")
+      } else {
+        IJ.showStatus(title + " - competed.")
       }
 
       //      onFX {progressStatus.close()}