diff --git a/common/source/java/ch/systemsx/cisd/common/image/IntensityRescaling.java b/common/source/java/ch/systemsx/cisd/common/image/IntensityRescaling.java
index 8b868385436490efef52472e46279dcc3ca56ae4..41c0bd9f607c3730cc0e1c58a39c6555e879408c 100644
--- a/common/source/java/ch/systemsx/cisd/common/image/IntensityRescaling.java
+++ b/common/source/java/ch/systemsx/cisd/common/image/IntensityRescaling.java
@@ -438,38 +438,11 @@ public class IntensityRescaling
*/
public static BufferedImage rescaleIntensityLevelTo8Bits(BufferedImage image, Levels levels)
{
- final int width = image.getWidth();
- final int height = image.getHeight();
- final BufferedImage rescaledImage =
- new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
- WritableRaster rescaledRaster = rescaledImage.getRaster();
-
- final float dynamicRange = 255f / (levels.maxLevel - levels.minLevel);
-
- for (int y = 0; y < height; ++y)
- {
- for (int x = 0; x < width; ++x)
- {
- for (Channel channel : Channel.values())
- {
- int originalIntensity = (image.getRGB(x, y) >> channel.getShift()) & 0xff;
-
- // cut all intensities above the white point
- int intensity = Math.min(levels.maxLevel, originalIntensity);
- // cut all intensities below the black point and move the origin to 0
- intensity = Math.max(0, intensity - levels.minLevel);
- // normalize to [0, 1] and rescale to 8 bits
- intensity = (int) (0.5 + (intensity * dynamicRange));
-
- rescaledRaster.setSample(x, y, channel.getBand(), intensity);
- }
- }
- }
- return rescaledImage;
+ return rescaleIntensityLevelTo8Bits(image, levels, Channel.values());
}
public static BufferedImage rescaleIntensityLevelTo8Bits(BufferedImage image, Levels levels,
- Channel channel)
+ Channel... channels)
{
final int width = image.getWidth();
final int height = image.getHeight();
@@ -477,22 +450,16 @@ public class IntensityRescaling
new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
WritableRaster rescaledRaster = rescaledImage.getRaster();
- final float dynamicRange = 255f / (levels.maxLevel - levels.minLevel);
-
for (int y = 0; y < height; ++y)
{
for (int x = 0; x < width; ++x)
{
- int originalIntensity = (image.getRGB(x, y) >> channel.getShift()) & 0xff;
-
- // cut all intensities above the white point
- int intensity = Math.min(levels.maxLevel, originalIntensity);
- // cut all intensities below the black point and move the origin to 0
- intensity = Math.max(0, intensity - levels.minLevel);
- // normalize to [0, 1] and rescale to 8 bits
- intensity = (int) (0.5 + (intensity * dynamicRange));
-
- rescaledRaster.setSample(x, y, channel.getBand(), intensity);
+ for (Channel channel : channels)
+ {
+ int originalIntensity = (image.getRGB(x, y) >> channel.getShift()) & 0xff;
+ int rescaledIntensity = rescaleIntensity(originalIntensity, levels);
+ rescaledRaster.setSample(x, y, channel.getBand(), rescaledIntensity);
+ }
}
}
return rescaledImage;
@@ -510,25 +477,26 @@ public class IntensityRescaling
WritableRaster rescaledRaster = rescaledImage.getRaster();
final int[] pixelData = image.getPixelData();
- final float dynamicRange = 255f / (levels.maxLevel - levels.minLevel);
-
int offset = 0;
for (int y = 0; y < height; ++y)
{
for (int x = 0; x < width; ++x)
{
int originalIntensity = pixelData[offset++];
-
- // cut all intensities above the white point
- int intensity = Math.min(levels.maxLevel, originalIntensity);
- // cut all intensities below the black point and move the origin to 0
- intensity = Math.max(0, intensity - levels.minLevel);
- // normalize to [0, 1] and rescale to 8 bits
- intensity = (int) (0.5 + (intensity * dynamicRange));
-
- rescaledRaster.setSample(x, y, 0, intensity);
+ rescaledRaster.setSample(x, y, 0, rescaleIntensity(originalIntensity, levels));
}
}
return rescaledImage;
}
+
+ private static int rescaleIntensity(int originalIntensity, Levels levels)
+ {
+ // cut all intensities above the white point
+ int intensity = Math.min(levels.maxLevel, originalIntensity);
+ // cut all intensities below the black point and move the origin to 0
+ intensity = Math.max(0, intensity - levels.minLevel);
+ // normalize to [0, 1] and rescale to 8 bits
+ int range = levels.maxLevel - levels.minLevel;
+ return (255 * intensity + range / 2) / range;
+ }
}
\ No newline at end of file
diff --git a/common/source/java/ch/systemsx/cisd/common/image/MixColors.java b/common/source/java/ch/systemsx/cisd/common/image/MixColors.java
index f980fca442bae1fc72084719a3f3ecdbc73c0fb1..a82b3a93204c135080b8e2a8f7e91115a2883a3a 100644
--- a/common/source/java/ch/systemsx/cisd/common/image/MixColors.java
+++ b/common/source/java/ch/systemsx/cisd/common/image/MixColors.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.common.image;
import java.awt.Color;
import java.awt.image.BufferedImage;
+import org.apache.commons.lang.time.StopWatch;
import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.logging.LogCategory;
@@ -302,6 +303,8 @@ public class MixColors
{
assert colors.length == images.length : "number of colors and images do not match";
+ StopWatch stopWatch = new StopWatch();
+ stopWatch.start();
ColorMergingAlgorithm mergeColorsAlgorithm =
createColorMergingAlgorithm(quadratic, saturationEnhancementFactor, images);
@@ -335,6 +338,7 @@ public class MixColors
}
}
}
+ operationLog.info("MIXING " + images.length + " images (" + width + "x" + height + ") took " + stopWatch);
return new MixedImageWithWhitePoint(mixed, whitePointColor);
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/image/IntensityRescalingTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/image/IntensityRescalingTest.java
index 19d835b3503ca1655f36b6ac6a2a38bfcbe71636..fa4eac274d610bd24a0f977502cbbeddd59c1eb6 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/image/IntensityRescalingTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/image/IntensityRescalingTest.java
@@ -18,8 +18,14 @@ package ch.systemsx.cisd.common.image;
import static org.testng.AssertJUnit.assertEquals;
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.image.BufferedImage;
+
import org.testng.annotations.Test;
+import ch.systemsx.cisd.common.image.IntensityRescaling.Channel;
+import ch.systemsx.cisd.common.image.IntensityRescaling.GrayscalePixels;
import ch.systemsx.cisd.common.image.IntensityRescaling.Levels;
/**
@@ -29,7 +35,7 @@ import ch.systemsx.cisd.common.image.IntensityRescaling.Levels;
public class IntensityRescalingTest
{
- public void testRegularCaseOfIntensityRescaling()
+ public void testComputeLevelsRegularCaseOfIntensityRescaling()
{
int[] histogramArray =
new int[]
@@ -41,7 +47,7 @@ public class IntensityRescalingTest
}
@Test
- public void testBorderCaseOfIntensityRescaling()
+ public void testComputeLevelsBorderCaseOfIntensityRescaling()
{
Levels result = IntensityRescaling.computeLevels(14, new int[]
{ 1098, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1 });
@@ -50,7 +56,7 @@ public class IntensityRescalingTest
}
@Test
- public void testBorderCaseOfIntensityRescalingOtherWay()
+ public void testComputeLevelsBorderCaseOfIntensityRescalingOtherWay()
{
Levels result = IntensityRescaling.computeLevels(14, new int[]
{ 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 19876 });
@@ -59,12 +65,87 @@ public class IntensityRescalingTest
}
@Test
- public void testAnotherBorderCase()
+ public void testComputeLevelsAnotherBorderCase()
{
Levels result = IntensityRescaling.computeLevels(14, new int[]
{ 19876, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 });
assertEquals(0, result.minLevel);
assertEquals(1, result.maxLevel);
}
+
+ @Test
+ public void testRescaleIntensityLevelTo8BitsForRGBExampleAndTwoColors()
+ {
+ BufferedImage image = new BufferedImage(6, 5, BufferedImage.TYPE_INT_RGB);
+ Graphics graphics = image.getGraphics();
+ graphics.setColor(Color.ORANGE);
+ graphics.fillRect(0, 0, 4, 3);
+ graphics.setColor(Color.PINK);
+ graphics.fillRect(1, 1, 4, 3);
+
+ BufferedImage rescaledImage = IntensityRescaling.rescaleIntensityLevelTo8Bits(image, new Levels(75, 190),
+ Channel.GREEN, Channel.BLUE);
+
+ ImageHistogram histogram = ImageHistogram.calculateHistogram(rescaledImage);
+
+ assertEquals("[0=30]", renderHistogram(histogram.getRedHistogram()));
+ assertEquals("[0=12, 222=12, 255=6]", renderHistogram(histogram.getGreenHistogram()));
+ assertEquals("[0=18, 222=12]", renderHistogram(histogram.getBlueHistogram()));
+ }
-}
+ @Test
+ public void testRescaleIntensityLevelTo8BitsForRGBExampleAndAllColors()
+ {
+ BufferedImage image = new BufferedImage(6, 5, BufferedImage.TYPE_INT_RGB);
+ Graphics graphics = image.getGraphics();
+ graphics.setColor(Color.ORANGE);
+ graphics.fillRect(0, 0, 4, 3);
+ graphics.setColor(Color.PINK);
+ graphics.fillRect(1, 1, 4, 3);
+
+ BufferedImage rescaledImage = IntensityRescaling.rescaleIntensityLevelTo8Bits(image, new Levels(75, 190));
+
+ ImageHistogram histogram = ImageHistogram.calculateHistogram(rescaledImage);
+
+ assertEquals("[0=12, 255=18]", renderHistogram(histogram.getRedHistogram()));
+ assertEquals("[0=12, 222=12, 255=6]", renderHistogram(histogram.getGreenHistogram()));
+ assertEquals("[0=18, 222=12]", renderHistogram(histogram.getBlueHistogram()));
+ }
+
+ @Test
+ public void testRescaleIntensityLevelTo8BitsForGrayExample()
+ {
+ BufferedImage image = new BufferedImage(6, 5, BufferedImage.TYPE_BYTE_GRAY);
+ Graphics graphics = image.getGraphics();
+ graphics.setColor(Color.DARK_GRAY);
+ graphics.fillRect(0, 0, 4, 3);
+ graphics.setColor(Color.LIGHT_GRAY);
+ graphics.fillRect(1, 1, 4, 3);
+
+ BufferedImage rescaledImage = IntensityRescaling.rescaleIntensityLevelTo8Bits(
+ new GrayscalePixels(image), new Levels(75, 200));
+
+ ImageHistogram histogram = ImageHistogram.calculateHistogram(rescaledImage);
+
+ assertEquals("[0=18, 239=12]", renderHistogram(histogram.getRedHistogram()));
+ assertEquals("[0=18, 239=12]", renderHistogram(histogram.getGreenHistogram()));
+ assertEquals("[0=18, 239=12]", renderHistogram(histogram.getBlueHistogram()));
+ }
+
+ private String renderHistogram(int[] histogram)
+ {
+ StringBuilder builder = new StringBuilder();
+ for (int i = 0; i < histogram.length; i++)
+ {
+ int value = histogram[i];
+ if (value > 0)
+ {
+ if (builder.length() > 0)
+ {
+ builder.append(", ");
+ }
+ builder.append(i).append("=").append(value);
+ }
+ }
+ return "[" + builder.toString() + "]";
+ }}