Merge branch '1442-export-to-image' into 'devel_15.1.x'

neutral color is used in color extractor

See merge request !1264

CHANGELOG

@@ -4,6 +4,8 @@ minerva (15.1.2) stable; urgency=medium
   * Bug fix: export to SBML failed if reactant/product line had length=0
   * Bug fix: downloading submap from big project as a map quite often resulted
     in error (#1440)
+  * Bug fix: colors for values in exported image were incorrect for
+    intermediate values, like 0.5 (#1442)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 7 Jan 2021 15:00:00 +0200
 

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java

@@ -170,7 +170,7 @@ public abstract class AbstractImageGenerator {
     this.level = params.getLevel();
     this.scale = params.getScale();
 
-    colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor(), params.getSimpleColor());
+    colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor(), params.getSimpleColor(), params.getNeutralColor());
 
     // set border frame extended by a margin
     border = new Rectangle2D.Double(params.getX() - SINGLE_FRAME_MARGIN, params.getY() - SINGLE_FRAME_MARGIN,
@@ -383,7 +383,7 @@ public abstract class AbstractImageGenerator {
     this.graphics = graphics;
   }
 
-/**
+  /**
    * Saves generated image into file.
    *
    * @param fileName
@@ -400,7 +400,7 @@ public abstract class AbstractImageGenerator {
     saveToFileImplementation(fileName);
   }
 
-    /**
+  /**
    * Saves generated image from {@link #getGraphics()} into file.
    *
    * @param fileName
@@ -700,6 +700,8 @@ public abstract class AbstractImageGenerator {
 
     private Color simpleColor = Color.BLACK;
 
+    private Color neutralColor = Color.WHITE;
+
     /**
      * @param scale
      *          scale to set
@@ -1090,9 +1092,21 @@ public abstract class AbstractImageGenerator {
     }
 
     public Params colorExtractor(ColorExtractor colorExtractor) {
-      return minColor(colorExtractor.getMinColor()).maxColor(colorExtractor.getMaxColor())
-          .simpleColor(colorExtractor.getSimpleColor());
+      return minColor(colorExtractor.getMinColor())
+          .maxColor(colorExtractor.getMaxColor())
+          .simpleColor(colorExtractor.getSimpleColor())
+          .neutralColor(colorExtractor.getNeutralColor());
     }
 
+    public Params neutralColor(Color neutralColor) {
+      this.neutralColor  = neutralColor;
+      return this;
+    }
+
+    public Color getNeutralColor() {
+      return this.neutralColor;
+    }
+
+
   }
 }
\ No newline at end of file

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java

@@ -48,8 +48,10 @@ public class ImageGenerators {
     try {
       availableGenerators = new ArrayList<Pair<String, Class<? extends AbstractImageGenerator>>>();
       Model model = new ModelFullIndexed(null);
-      AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().model(model).width(1)
-          .minColor(Color.WHITE).maxColor(Color.WHITE).height(1);
+      AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().model(model).width(1).height(1)
+          .minColor(Color.WHITE)
+          .maxColor(Color.WHITE)
+          .neutralColor(Color.WHITE);
       generatorInstances = new ArrayList<>();
       generatorInstances.add(new PngImageGenerator(params));
       generatorInstances.add(new PdfImageGenerator(params));

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java

@@ -25,7 +25,7 @@ public class ConverterTest extends GraphicsTestFunctions {
 
   @Test
   public void test() {
-    ColorExtractor colorExtractor = new ColorExtractor(Color.BLUE, Color.RED, Color.BLUE);
+    ColorExtractor colorExtractor = new ColorExtractor(Color.BLUE, Color.RED, Color.BLUE, Color.WHITE);
     new BioEntityConverterImpl(new BottomSquareCompartment("id1"), colorExtractor);
     new BioEntityConverterImpl(new TopSquareCompartment("id2"), colorExtractor);
     new BioEntityConverterImpl(new LeftSquareCompartment("id3"), colorExtractor);

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java

@@ -27,7 +27,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
 
 public class BioEntityConverterImplTest extends GraphicsTestFunctions {
 
-  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
 
   @AfterClass
   public static void tearDownAfterClass() throws Exception {

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverterTest.java

@@ -23,7 +23,7 @@ import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 
 public class PathwayCompartmentConverterTest extends GraphicsTestFunctions {
 
-  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
   PathwayCompartmentConverter converter = new PathwayCompartmentConverter(colorExtractor);
 
   @Test

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverterTest.java

@@ -25,7 +25,7 @@ public class SquareCompartmentConverterTest extends GraphicsTestFunctions {
 
   Logger logger = LogManager.getLogger();
 
-  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
   SquareCompartmentConverter converter = new SquareCompartmentConverter(colorExtractor);
 
   @Test

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverterTest.java

@@ -22,7 +22,7 @@ public class ComplexConverterTest extends GraphicsTestFunctions {
   
   Logger logger = LogManager.getLogger();
 
-  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+  private ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
 
   @Before
   public void setUp() throws Exception {

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexSbgnConverterTest.java

@@ -21,7 +21,7 @@ import lcsb.mapviewer.model.map.species.field.StructuralState;
 
 public class ComplexSbgnConverterTest extends GraphicsTestFunctions {
 
-  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+  private ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
 
   @Test
   public void testDrawStructuralState() throws Exception {

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverterTest.java

@@ -19,7 +19,7 @@ import lcsb.mapviewer.model.map.species.Protein;
 public class ProteinConverterTest extends GraphicsTestFunctions {
   Logger logger = LogManager.getLogger();
 
-  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
 
   @Before
   public void setUp() throws Exception {

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinSbgnConverterTest.java

@@ -20,7 +20,7 @@ import lcsb.mapviewer.model.map.species.field.StructuralState;
 
 public class ProteinSbgnConverterTest extends GraphicsTestFunctions {
 
-  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
 
   @Test
   public void testDrawStructuralState() throws Exception {

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverterTest.java

@@ -23,7 +23,7 @@ import lcsb.mapviewer.model.map.species.SimpleMolecule;
 public class SimpleMoleculeConverterTest extends GraphicsTestFunctions {
   Logger logger = LogManager.getLogger();
 
-  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
 
   private BufferedImage bi;
   private Graphics2D graphics;

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeSbgnConverterTest.java

@@ -21,7 +21,7 @@ import lcsb.mapviewer.model.map.species.SimpleMolecule;
 public class SimpleMoleculeSbgnConverterTest extends GraphicsTestFunctions {
   Logger logger = LogManager.getLogger();
 
-  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
 
   private BufferedImage bi;
   private Graphics2D graphics;

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java

@@ -34,7 +34,7 @@ import lcsb.mapviewer.model.map.species.field.*;
 public class SpeciesConverterTest extends GraphicsTestFunctions {
   Logger logger = LogManager.getLogger(SpeciesConverterTest.class);
 
-  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
 
   @Before
   public void setUp() throws Exception {

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesGenericConverterTests.java

@@ -34,7 +34,7 @@ public class SpeciesGenericConverterTests extends GraphicsTestFunctions {
 
   Logger logger = LogManager.getLogger();
 
-  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
 
   private Element species;
 

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java

@@ -34,7 +34,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
 
 public class ReactionConverterTest extends GraphicsTestFunctions {
 
-  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+  ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
 
   @Before
   public void setUp() throws Exception {

model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java

@@ -28,7 +28,7 @@ public class ClearColorModelCommand extends ModelCommand {
   public ClearColorModelCommand(Model model) {
     super(model);
     colorModelCommand = new ColorModelCommand(model, new ArrayList<>(),
-        new ColorExtractor(Color.WHITE, Color.WHITE, Color.WHITE));
+        new ColorExtractor(Color.WHITE, Color.WHITE, Color.WHITE, Color.WHITE));
   }
 
   @Override

model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java

 package lcsb.mapviewer.commands;
 
-import java.awt.*;
+import java.awt.Color;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.map.layout.ColorSchema;
@@ -20,12 +20,14 @@ public class ColorExtractor {
   private Color minColor;
 
   /**
-   * Color that should be used for maxvalues of {@link ColorSchema#value}.
+   * Color that should be used for max values of {@link ColorSchema#value}.
    */
   private Color maxColor;
 
   private Color simpleColor;
 
+  private Color neutralColor;
+
   /**
    * Default constructor.
    * 
@@ -36,13 +38,14 @@ public class ColorExtractor {
    *          Color that should be used for max values of
    *          {@link ColorSchema#value}
    */
-  public ColorExtractor(Color minColor, Color maxColor, Color simpleColor) {
-    if (minColor == null || maxColor == null || simpleColor == null) {
+  public ColorExtractor(Color minColor, Color maxColor, Color simpleColor, Color neutralColor) {
+    if (minColor == null || maxColor == null || simpleColor == null || neutralColor == null) {
       throw new InvalidArgumentException("Parameters cannot be null");
     }
     this.minColor = minColor;
     this.maxColor = maxColor;
     this.simpleColor = simpleColor;
+    this.neutralColor = neutralColor;
   }
 
   /**
@@ -72,17 +75,40 @@ public class ColorExtractor {
    * @return color for the double value
    */
   protected Color getColorForValue(Double value) {
+    int maxRed = maxColor.getRed();
+    int maxGreen = maxColor.getGreen();
+    int maxBlue = maxColor.getBlue();
+
+    int minRed = minColor.getRed();
+    int minGreen = minColor.getGreen();
+    int minBlue = minColor.getBlue();
+
+    int neutralRed = neutralColor.getRed();
+    int neutralGreen = neutralColor.getGreen();
+    int neutralBlue = neutralColor.getBlue();
+
     if (value > 0) {
       double ratio = value;
-      return new Color((int) (maxColor.getRed() * ratio), (int) (maxColor.getGreen() * ratio),
-          (int) (maxColor.getBlue() * ratio));
+      int red = getColorForRatio(neutralRed, maxRed, ratio);
+      int green = getColorForRatio(neutralGreen, maxGreen, ratio);
+      int blue = getColorForRatio(neutralBlue, maxBlue, ratio);
+      return new Color(red, green, blue);
     }
     if (value < 0) {
       double ratio = -value;
-      return new Color((int) (minColor.getRed() * ratio), (int) (minColor.getGreen() * ratio),
-          (int) (minColor.getBlue() * ratio));
+      int red = getColorForRatio(neutralRed, minRed, ratio);
+      int green = getColorForRatio(neutralGreen, minGreen, ratio);
+      int blue = getColorForRatio(neutralBlue, minBlue, ratio);
+      return new Color(red, green, blue);
     }
-    return Color.WHITE;
+    return neutralColor;
+  }
+
+  private int getColorForRatio(int neutralRed, int maxRed, double ratio) {
+    int red = (int) Math.round(neutralRed + (maxRed - neutralRed) * ratio);
+    red = Math.max(0, red);
+    red = Math.min(255, red);
+    return red;
   }
 
   /**
@@ -104,4 +130,8 @@ public class ColorExtractor {
   public Color getSimpleColor() {
     return simpleColor;
   }
+
+  public Color getNeutralColor() {
+    return neutralColor;
+  }
 }

model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java

@@ -13,6 +13,7 @@ import lcsb.mapviewer.commands.properties.AllPropertyCommandTests;
     AllLayoutTests.class,
     AllPropertyCommandTests.class,
     ClearColorModelCommandTest.class,
+    ColorExtractorTest.class,
     ColorModelCommandTest.class,
     CopyCommandTest.class,
     CreateHierarchyCommandTest.class,

model-command/src/test/java/lcsb/mapviewer/commands/ColorExtractorTest.java

+package lcsb.mapviewer.commands;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.Color;
+
+import org.junit.Test;
+
+public class ColorExtractorTest {
+  ColorExtractor extractor = new ColorExtractor(Color.GREEN, Color.BLUE, Color.RED, Color.YELLOW);
+
+  @Test
+  public void testZeroColor() {
+    assertEquals(Color.YELLOW, extractor.getColorForValue(0.0001));
+    assertEquals(Color.YELLOW, extractor.getColorForValue(0.0));
+  }
+
+  @Test
+  public void testMaxColor() {
+    assertEquals(Color.BLUE, extractor.getColorForValue(1.0));
+    assertEquals(Color.BLUE, extractor.getColorForValue(0.99999));
+  }
+
+  @Test
+  public void testMinColor() {
+    assertEquals(Color.GREEN, extractor.getColorForValue(-1.0));
+    assertEquals(Color.GREEN, extractor.getColorForValue(-0.99999));
+  }
+
+  @Test
+  public void testColorForNotNormalizedValue() {
+    assertEquals(Color.GREEN, extractor.getColorForValue(-10.0));
+    assertEquals(Color.BLUE, extractor.getColorForValue(10.0));
+  }
+
+}