[Calibrator] Allow use of custom charts #38

ijp-color-ui/src/main/resources/ij_plugins/color/ui/calibration/ColorCalibrator.fxml

@@ -25,7 +25,7 @@
 <?import javafx.geometry.*?>
 <?import javafx.scene.control.*?>
 <?import javafx.scene.layout.*?>
-<StackPane xmlns="http://javafx.com/javafx/10.0.1" xmlns:fx="http://javafx.com/fxml/1"
+<StackPane xmlns="http://javafx.com/javafx/16" xmlns:fx="http://javafx.com/fxml/1"
            fx:controller="ij_plugins.color.ui.calibration.ColorCalibratorUIController">
     <children>
         <GridPane fx:id="rootGridPane" hgap="10.0" vgap="10.0">
@@ -59,7 +59,7 @@
                         <MenuItem mnemonicParsing="false" text="Action 2"/>
                     </items>
                 </SplitMenuButton>
-                <HBox prefWidth="200.0" GridPane.columnSpan="2147483647" GridPane.rowIndex="4">
+                <HBox prefWidth="200.0" GridPane.columnSpan="2147483647" GridPane.rowIndex="5">
                     <children>
                         <Label id="ijp-separator" text="Actual Chart"/>
                         <Separator id="ijp-separator" valignment="TOP" HBox.hgrow="ALWAYS">
@@ -72,11 +72,11 @@
                         <Insets bottom="5.0" top="10.0"/>
                     </padding>
                 </HBox>
-                <Label id="ijp-label" text="Chip margin %" GridPane.rowIndex="5"/>
+                <Label id="ijp-label" text="Chip margin %" GridPane.rowIndex="6"/>
                 <Spinner fx:id="marginsSpinner" max="100" maxWidth="1.7976931348623157E308" min="0"
-                         GridPane.columnIndex="1" GridPane.rowIndex="5"/>
+                         GridPane.columnIndex="1" GridPane.rowIndex="6"/>
 
-                <HBox prefWidth="200.0" GridPane.columnSpan="2147483647" GridPane.rowIndex="6">
+                <HBox prefWidth="200.0" GridPane.columnSpan="2147483647" GridPane.rowIndex="7">
                     <children>
                         <Label id="ijp-separator" text="Calibration"/>
                         <Separator id="ijp-separator" valignment="TOP" HBox.hgrow="ALWAYS">
@@ -90,33 +90,33 @@
                     </padding>
                 </HBox>
                 <Label id="ijp-label" alignment="CENTER_RIGHT" text="Reference" GridPane.halignment="RIGHT"
-                       GridPane.rowIndex="7" GridPane.valignment="CENTER"/>
+                       GridPane.rowIndex="8" GridPane.valignment="CENTER"/>
                 <ChoiceBox fx:id="referenceColorSpaceChoiceBox" maxWidth="1.7976931348623157E308" prefWidth="150.0"
-                           GridPane.columnIndex="1" GridPane.rowIndex="7"/>
+                           GridPane.columnIndex="1" GridPane.rowIndex="8"/>
                 <CheckBox fx:id="enableExtraInfoCB" mnemonicParsing="false" text="Show extra info"
-                          GridPane.columnIndex="1" GridPane.rowIndex="9"/>
-                <Label id="ijp-label" text="Mapping method" GridPane.rowIndex="8"/>
+                          GridPane.columnIndex="1" GridPane.rowIndex="10"/>
+                <Label id="ijp-label" text="Mapping method" GridPane.rowIndex="9"/>
                 <ChoiceBox fx:id="mappingMethodChoiceBox" maxWidth="1.7976931348623157E308" prefWidth="150.0"
-                           GridPane.columnIndex="1" GridPane.rowIndex="8"/>
+                           GridPane.columnIndex="1" GridPane.rowIndex="9"/>
                 <Button fx:id="suggestCalibrationOptionsButton" mnemonicParsing="false" text="Sugget Options"
-                        GridPane.columnIndex="2" GridPane.rowIndex="7"/>
+                        GridPane.columnIndex="2" GridPane.rowIndex="8"/>
                 <Button id="ijp-button" fx:id="calibrateButton" contentDisplay="CENTER"
                         maxWidth="1.7976931348623157E308" mnemonicParsing="false" text="Calibrate"
-                        GridPane.columnIndex="1" GridPane.halignment="CENTER" GridPane.rowIndex="10">
+                        GridPane.columnIndex="1" GridPane.halignment="CENTER" GridPane.rowIndex="11">
                     <GridPane.margin>
                         <Insets bottom="5.0" top="5.0"/>
                     </GridPane.margin>
                 </Button>
                 <Button fx:id="applyToCurrentImageButton" maxWidth="1.7976931348623157E308" mnemonicParsing="false"
-                        text="Apply" GridPane.columnIndex="1" GridPane.rowIndex="12">
+                        text="Apply" GridPane.columnIndex="1" GridPane.rowIndex="13">
                     <padding>
                         <Insets bottom="5.0" top="5.0"/>
                     </padding>
                     <GridPane.margin>
                         <Insets bottom="5.0" top="5.0"/>
                     </GridPane.margin>
                 </Button>
-                <HBox prefWidth="200.0" GridPane.columnSpan="2147483647" GridPane.rowIndex="11">
+                <HBox prefWidth="200.0" GridPane.columnSpan="2147483647" GridPane.rowIndex="12">
                     <children>
                         <Label id="ijp-separator" text="Apply to Another Image"/>
                         <Separator id="ijp-separator" valignment="TOP" HBox.hgrow="ALWAYS">
@@ -130,7 +130,12 @@
                     </padding>
                 </HBox>
                 <Button fx:id="helpButton" maxWidth="1.7976931348623157E308" mnemonicParsing="false" text="Help"
-                        GridPane.columnIndex="2" GridPane.rowIndex="12"/>
+                        GridPane.columnIndex="2" GridPane.rowIndex="13"/>
+                <Label id="ijp-label" text="Info" GridPane.halignment="RIGHT" GridPane.rowIndex="4"
+                       GridPane.valignment="CENTER"/>
+                <Label id="ijp-label" fx:id="chartInfoLabel" text="???" GridPane.columnIndex="1" GridPane.rowIndex="4"/>
+                <Button fx:id="editChartButton" disable="true" maxWidth="1.7976931348623157E308" mnemonicParsing="false"
+                        text="Edit Chart" GridPane.columnIndex="2" GridPane.rowIndex="4"/>
             </children>
             <rowConstraints>
                 <RowConstraints minHeight="10.0"/>
@@ -146,6 +151,7 @@
                 <RowConstraints minHeight="10.0"/>
                 <RowConstraints minHeight="10.0"/>
                 <RowConstraints minHeight="10.0"/>
+                <RowConstraints minHeight="10.0"/>
             </rowConstraints>
             <columnConstraints>
                 <ColumnConstraints/>

ijp-color-ui/src/main/scala/ij_plugins/color/ui/calibration/ColorCalibratorUIController.scala

@@ -44,6 +44,8 @@ class ColorCalibratorUIController(
                                    private val imageTitleLabel: Label,
                                    private val chartTypeChoiceBox: ChoiceBox[ColorChartType],
                                    private val renderReferenceChartSplitButton: SplitMenuButton,
+                                   private val chartInfoLabel: Label,
+                                   private val editChartButton: Button,
                                    private val marginsSpinner: Spinner[java.lang.Integer],
                                    private val referenceColorSpaceChoiceBox: ChoiceBox[ReferenceColorSpace],
                                    private val enableExtraInfoCB: CheckBox,
@@ -91,6 +93,13 @@ class ColorCalibratorUIController(
     }
   )
 
+  renderReferenceChartSplitButton.disable <== !model.referenceChartDefined
+
+  editChartButton.onAction = _ => model.onEditChart()
+  editChartButton.disable <== !model.referenceChartEditEnabled
+
+  chartInfoLabel.text <== model.chartInfoText
+
   // Actual chart
   marginsSpinner.valueFactory = new IntegerSpinnerValueFactory(0, 49) {
     value = model.chipMarginPercent()

ijp-color-ui/src/main/scala/ij_plugins/color/ui/calibration/ColorCalibratorUIModel.scala

@@ -22,12 +22,14 @@
 
 package ij_plugins.color.ui.calibration
 
+import ij.gui.GenericDialog
 import ij.measure.ResultsTable
 import ij.plugin.BrowserLauncher
 import ij.{ImagePlus, Prefs}
 import ij_plugins.color.calibration.chart.{ColorChartType, ColorCharts, GridColorChart, ReferenceColorSpace}
 import ij_plugins.color.calibration.regression.MappingMethod
 import ij_plugins.color.calibration.{CorrectionRecipe, renderReferenceChart}
+import ij_plugins.color.converter.ReferenceWhite
 import ij_plugins.color.ui.calibration.tasks.{ApplyToCurrentImageTask, CalibrateTask, SuggestCalibrationOptionsTask}
 import ij_plugins.color.ui.util.LiveChartROI
 import javafx.beans.property.ReadOnlyBooleanProperty
@@ -36,6 +38,7 @@ import org.scalafx.extras.{BusyWorker, ShowMessage, onFX}
 import scalafx.beans.property._
 import scalafx.stage.Window
 
+import java.io.File
 import java.util.concurrent.Future
 
 object ColorCalibratorUIModel {
@@ -124,16 +127,27 @@ class ColorCalibratorUIModel(val image: ImagePlus, parentWindow: Window) extends
   referenceChartType.onChange { (_, _, _) =>
     recreateReferenceChart()
   }
-  val chipMarginPercent = new ObjectProperty[Integer](this, "chipMargin", 20)
-  chipMarginPercent.onChange { (_, _, _) =>
-    recreateReferenceChart()
-  }
 
   // This is a derived value that needs to be updated when UI selections change: `referenceChartType` and `chipMarginPercent`
   private val referenceChartOptionWrapper = new ReadOnlyObjectWrapper[Option[GridColorChart]](this, "chart", None)
   val referenceChartOption: ReadOnlyObjectProperty[Option[GridColorChart]] =
     referenceChartOptionWrapper.readOnlyProperty
 
+  private val referenceChartDefinedWrapper = new ReadOnlyBooleanWrapper()
+  val referenceChartDefined: ReadOnlyBooleanProperty = referenceChartDefinedWrapper.readOnlyProperty
+
+  private val referenceChartEditEnabledWrapper = new ReadOnlyBooleanWrapper()
+  val referenceChartEditEnabled: ReadOnlyBooleanProperty = referenceChartEditEnabledWrapper.readOnlyProperty
+
+  private var customChartOption: Option[GridColorChart] = None
+
+  val chartInfoText = new StringProperty("???")
+
+  val chipMarginPercent = new ObjectProperty[Integer](this, "chipMargin", 20)
+  chipMarginPercent.onChange { (_, _, _) =>
+    recreateReferenceChart()
+  }
+
   val mappingMethod = new ObjectProperty[MappingMethod](this, "mappingMethod", MappingMethod.LinearCrossBand)
   val clipReferenceRGB = new BooleanProperty(this, "clipReferenceRGB", true)
   val showExtraInfo = new BooleanProperty(this, "showExtraInfo", false)
@@ -155,14 +169,29 @@ class ColorCalibratorUIModel(val image: ImagePlus, parentWindow: Window) extends
     p.getReadOnlyProperty
   }
 
+  // Initialize reference chart
   recreateReferenceChart()
 
   def recreateReferenceChart(): Unit = {
     val chartOpt =
-      ColorCharts
-        .withColorChartType(referenceChartType.value)
-        .map(c => c.copyWithNewChipMargin(chipMarginPercent.value / 100d))
+      (
+        if (referenceChartType.value != ColorChartType.Custom) {
+          ColorCharts.withColorChartType(referenceChartType.value)
+        } else {
+          customChartOption
+        }
+        ).map(c => c.copyWithNewChipMargin(chipMarginPercent.value / 100d))
+
     referenceChartOptionWrapper.value = chartOpt
+
+    referenceChartDefinedWrapper.value = referenceChartOptionWrapper.value.isDefined
+
+    referenceChartEditEnabledWrapper.value = referenceChartType.value == ColorChartType.Custom
+
+    chartInfoText.value =
+      referenceChartOptionWrapper.value
+        .map(c => s"${c.nbColumns} x ${c.nbRows}, ${c.refWhite}")
+        .getOrElse("Chart not defined")
   }
 
   private def currentChart: GridColorChart = {
@@ -230,6 +259,61 @@ class ColorCalibratorUIModel(val image: ImagePlus, parentWindow: Window) extends
     }
   }
 
+  def onEditChart(): Unit = {
+
+    val _nbRows = customChartOption.map(_.nbRows).getOrElse(5)
+    val _nbColumns = customChartOption.map(_.nbColumns).getOrElse(6)
+    val _refWhite = customChartOption.map(_.refWhite).getOrElse(ReferenceWhite.D50)
+    val _defaultPath = ""
+
+    val gd = new GenericDialog("Edit Custom Reference Chart") {
+      addMessage("Chart Layout")
+      addNumericField("Rows", _nbRows, 0, 3, "")
+      addNumericField("Columns", _nbColumns, 0, 3, "")
+      addChoice("Reference White", ReferenceWhite.values.map(_.toString).toArray, _refWhite.toString)
+      addFileField("Reference values file", _defaultPath)
+    }
+
+    gd.showDialog()
+
+    if (gd.wasOKed()) {
+      val nbRows = {
+        val v = gd.getNextNumber
+        math.max(1, math.round(v).toInt)
+      }
+
+      val nbCols = {
+        val v = gd.getNextNumber
+        math.max(1, math.round(v).toInt)
+      }
+
+      val refWhite: ReferenceWhite = {
+        val v = gd.getNextChoice
+        ReferenceWhite.withName(v)
+      }
+
+      val filePath = gd.getNextString
+      val file = new File(filePath)
+
+      val chips = ColorCharts.loadReferenceValues(file)
+
+      val chart = new GridColorChart(
+        s"Custom - ${file.getName}",
+        nbColumns = nbCols,
+        nbRows = nbRows,
+        chips = chips,
+        chipMargin = 0.2,
+        refWhite = refWhite
+      )
+
+      customChartOption = Option(chart)
+      recreateReferenceChart()
+    } else {
+      //
+    }
+
+  }
+
   def onSuggestCalibrationOptions(): Unit = busyWorker.doTask("onSuggestCalibrationOptions") {
     new SuggestCalibrationOptionsTask(currentChart, image, Option(parentWindow))
   }

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

@@ -39,6 +39,8 @@ case object ColorChartType extends Enum[ColorChartType] {
 
   case object ImageScienceColorGaugeMatte extends ColorChartType("Image Science ColorGauge Matte")
 
+  case object Custom extends ColorChartType("Custom")
+
   /** All refined reference color spaces. */
   val values: immutable.IndexedSeq[ColorChartType] = findValues
 }

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

@@ -22,18 +22,21 @@
 
 package ij_plugins.color.calibration.chart
 
+import ij.measure.ResultsTable
 import ij_plugins.color.converter.ColorTriple.Lab
-import ij_plugins.color.converter.ReferenceWhite
+import ij_plugins.color.converter.{ColorTriple, ReferenceWhite}
+
+import java.io.File
 
 /** Enumeration of some common color charts. */
 object ColorCharts {
 
   /**
-   * GretagMacbeth ColorChecker with values measured by Robin D. Myers, average of two charts manufactured 2002-10.
-   *
-   * Illuminant D65.
-   * [[http://www.rmimaging.com/spectral_library/Reflective/Charts-Calibration/ColorChecker_2002-10_averaged.ss3.zip]]
-   */
+    * GretagMacbeth ColorChecker with values measured by Robin D. Myers, average of two charts manufactured 2002-10.
+    *
+    * Illuminant D65.
+    * [[http://www.rmimaging.com/spectral_library/Reflective/Charts-Calibration/ColorChecker_2002-10_averaged.ss3.zip]]
+    */
   val GretagMacbethColorChecker = new GridColorChart(
     ColorChartType.GretagMacbethColorChecker.name,
     6,
@@ -162,4 +165,51 @@ object ColorCharts {
     require(colorChartType != null, "'colorChartType' cannot be null.")
     values.find(_.name == colorChartType.name)
   }
+
+  /**
+    * Load chart reference values from a CSV file represented in CIE L*a*b* color space.
+    *
+    * The file is expected to have at least 4 columns: "SAMPLE_NAME", "LAB_L", "LAB_A", "LAB_B".
+    * Any additional columns will be ignored.
+    *
+    * Example of a file with 4 chips:
+    *
+    * {{{
+    * SAMPLE_NAME,LAB_L,LAB_A,LAB_B
+    * 1,38.675,12.907,14.358,19.306
+    * 2,65.750,19.811,17.790,26.626
+    * 3,50.373,-3.646,-22.360,22.656
+    * 4,43.697,-13.342,22.858,26.466
+    * }}}
+    *
+    * @return list of tuples representing chip name and reference value in CIE L*a*b*
+    */
+  def loadReferenceValues(file: File): List[(String, ColorTriple.Lab)] = {
+    require(file.exists(), "File must exist: " + file.getCanonicalPath)
+    val rt = ResultsTable.open(file.getCanonicalPath)
+
+    val headingName = "SAMPLE_NAME"
+    val headingL = "LAB_L"
+    val headingA = "LAB_A"
+    val headingB = "LAB_B"
+
+    require(rt.columnExists(headingName))
+    require(rt.columnExists(headingL))
+    require(rt.columnExists(headingA))
+    require(rt.columnExists(headingB))
+
+    val chips =
+      (0 until rt.size())
+        .map { r =>
+          val name = rt.getStringValue(headingName, r)
+          val l = rt.getValue(headingL, r)
+          val a = rt.getValue(headingA, r)
+          val b = rt.getValue(headingB, r)
+
+          (name, ColorTriple.Lab(l, a, b))
+        }
+        .toList
+
+    chips
+  }
 }

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

@@ -58,17 +58,21 @@ final class GridColorChart(
   require(chipMargin >= 0 && chipMargin < 0.5, "Margin value must at least 0 but less than 0.5, got " + chipMargin)
   require(nbColumns > 0)
   require(nbRows > 0)
-  require(nbColumns * nbRows == chips.size)
+  require(
+    nbColumns * nbRows == chips.size,
+    "Number of chips must equal number of columns times number of rows. " +
+      s"Expecting ${nbColumns * nbRows}, got ${chips.size}."
+  )
   require(chips.size == enabled.size)
   require(refWhite != null)
   require(alignmentTransform != null)
 
   /**
-   * Construct chart with all chips enabled.
-   *
-   * @param name      chart's name
-   * @param nbColumns number of columns
-   * @param nbRows    number of rows
+    * Construct chart with all chips enabled.
+    *
+    * @param name      chart's name
+    * @param nbColumns number of columns
+    * @param nbRows    number of rows
    * @param chips     chip names and CIE L*a*b* / D65 color values, row by row, starting at (0,0) or top left corner.
    */
   def this(