diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ColorRangeCalculator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ColorRangeCalculator.java
new file mode 100644
index 0000000000000000000000000000000000000000..19c53444bf871fe4ae6d38bb2de44ea13c29c186
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ColorRangeCalculator.java
@@ -0,0 +1,160 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.generic.server.plugins;
+
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import ch.systemsx.cisd.common.io.FileBasedContent;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+
+/**
+ * Helper methods and standalone program to calculate the range of brightness of a collection of
+ * images in grayscale.
+ *
+ * @author Tomasz Pylak
+ */
+public class ColorRangeCalculator
+{
+ /** Describes the minimal and maximal brightness of the pixel on the image. */
+ public static class ImagePixelsRange
+ {
+ private final int min, max;
+
+ public ImagePixelsRange(int min, int max)
+ {
+ this.min = min;
+ this.max = max;
+ }
+
+ public int getMin()
+ {
+ return min;
+ }
+
+ public int getMax()
+ {
+ return max;
+ }
+
+ public ImagePixelsRange createOverlap(ImagePixelsRange rangeOrNull)
+ {
+ if (rangeOrNull == null)
+ {
+ return this;
+ }
+ int newMin = Math.min(min, rangeOrNull.getMin());
+ int newMax = Math.max(max, rangeOrNull.getMax());
+ return new ImagePixelsRange(newMin, newMax);
+ }
+
+ @Override
+ public String toString()
+ {
+ return "[" + min + ", " + max + "]";
+ }
+ }
+
+ /**
+ * We should have converted 'globalRange' to [0,255] but instead a smaller range 'imageRange'
+ * has been converted to [0,255]. We have to squeeze 'imageRange' to a smaller range [a,b] (a >=
+ * 0, b <= 255) into which it would be mapped if globalRange would be used at the beginning.
+ */
+ public static ImagePixelsRange rescaleRange(ImagePixelsRange imageRange,
+ ImagePixelsRange globalRange)
+ {
+ double globalRangeLength = globalRange.getMax() - globalRange.getMin();
+ int min = (int) (255 * (imageRange.getMin() - globalRange.getMin()) / globalRangeLength);
+ int max = (int) (255 * (imageRange.getMax() - globalRange.getMin()) / globalRangeLength);
+ return new ImagePixelsRange(min, max);
+ }
+
+ public static ImagePixelsRange calculateOverlapRange(Collection<ImagePixelsRange> ranges)
+ {
+ ImagePixelsRange globalRange = null;
+ for (ImagePixelsRange imageRange : ranges)
+ {
+ globalRange = imageRange.createOverlap(globalRange);
+ }
+ return globalRange;
+ }
+
+ public static ImagePixelsRange calculatePixelsRange(BufferedImage bufferedImage,
+ int minRescaledColor, int maxRescaledColor)
+ {
+ int minColor = maxRescaledColor;
+ int maxColor = minRescaledColor;
+ for (int x = 0; x < bufferedImage.getWidth(); x++)
+ {
+ for (int y = 0; y < bufferedImage.getHeight(); y++)
+ {
+ int dominantColorComponent = bufferedImage.getRaster().getSample(x, y, 0);
+ if (dominantColorComponent >= minRescaledColor
+ && dominantColorComponent <= maxRescaledColor)
+ {
+ if (dominantColorComponent > maxColor)
+ {
+ maxColor = dominantColorComponent;
+ } else if (dominantColorComponent < minColor)
+ {
+ minColor = dominantColorComponent;
+ }
+ }
+ }
+ }
+ return new ImagePixelsRange(minColor, maxColor);
+ }
+
+ public static ImagePixelsRange calculatePixelsRange(List<File> imageFiles)
+ {
+ Collection<ImagePixelsRange> ranges =
+ new ArrayList<ColorRangeCalculator.ImagePixelsRange>();
+ for (File imageFile : imageFiles)
+ {
+ BufferedImage image =
+ ImageUtil.loadImage(new FileBasedContent(imageFile), null, null, null);
+ ImagePixelsRange range = calculatePixelsRange(image, 0, Integer.MAX_VALUE);
+ ranges.add(range);
+ }
+ return calculateOverlapRange(ranges);
+ }
+
+ public static void main(String[] args)
+ {
+ if (args.length == 0)
+ {
+ System.err.println("No files specified!");
+ System.exit(1);
+ }
+ List<File> imageFiles = new ArrayList<File>();
+ for (int i = 0; i < args.length; i++)
+ {
+ File imageFile = new File(args[i]);
+ if (imageFile.isFile() == false)
+ {
+ System.err.println("File does not exist: " + imageFile.getPath());
+ System.exit(1);
+ }
+ imageFiles.add(imageFile);
+ }
+ ImagePixelsRange range = calculatePixelsRange(imageFiles);
+ System.out.println(range.getMin() + " " + range.getMax());
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java
index 3c6240fe532e7bd96a4833c457c21a271795bfef..9b2692a8b7956143d1a10394d44870d1e290c023 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.dss.generic.server.plugins;
import java.awt.image.BufferedImage;
import java.io.File;
-import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -29,6 +28,7 @@ import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.etl.IContentRepository;
import ch.systemsx.cisd.openbis.dss.etl.dynamix.IntensityRangeReductionFactory;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.ColorRangeCalculator.ImagePixelsRange;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageEnrichedDTO;
@@ -63,45 +63,6 @@ public class DynamixWellBrightnessEqualizerProcessingPlugin extends
this.maxRescaledColor = PropertyUtils.getInt(properties, "max-color", 16384 - 1);
}
- /** Describes the minimal and maximal brightness of the pixel on the image. */
- private static class ImagePixelsRange
- {
- private final int min, max;
-
- public ImagePixelsRange(int min, int max)
- {
- this.min = min;
- this.max = max;
- }
-
- public int getMin()
- {
- return min;
- }
-
- public int getMax()
- {
- return max;
- }
-
- public ImagePixelsRange createOverlap(ImagePixelsRange rangeOrNull)
- {
- if (rangeOrNull == null)
- {
- return this;
- }
- int newMin = Math.min(min, rangeOrNull.getMin());
- int newMax = Math.max(max, rangeOrNull.getMax());
- return new ImagePixelsRange(newMin, newMax);
- }
-
- @Override
- public String toString()
- {
- return "[" + min + ", " + max + "]";
- }
- }
-
@Override
protected IImageTransformerFactoryProvider getTransformationProvider(
List<ImgImageEnrichedDTO> spotImages, IContentRepository contentRepository)
@@ -115,47 +76,14 @@ public class DynamixWellBrightnessEqualizerProcessingPlugin extends
for (ImgImageEnrichedDTO image : spotImages)
{
BufferedImage bufferedImage = loadImage(contentRepository, image);
- ImagePixelsRange imageRange = calculatePixelsRange(bufferedImage);
+ ImagePixelsRange imageRange =
+ ColorRangeCalculator.calculatePixelsRange(bufferedImage, minRescaledColor,
+ maxRescaledColor);
rangeMap.put(image, imageRange);
}
return createImageTransformerFactoryProvider(rangeMap);
}
- private static ImagePixelsRange calculateOverlapRange(Collection<ImagePixelsRange> ranges)
- {
- ImagePixelsRange globalRange = null;
- for (ImagePixelsRange imageRange : ranges)
- {
- globalRange = imageRange.createOverlap(globalRange);
- }
- return globalRange;
- }
-
- private ImagePixelsRange calculatePixelsRange(BufferedImage bufferedImage)
- {
- int minColor = maxRescaledColor;
- int maxColor = minRescaledColor;
- for (int x = 0; x < bufferedImage.getWidth(); x++)
- {
- for (int y = 0; y < bufferedImage.getHeight(); y++)
- {
- int dominantColorComponent = bufferedImage.getRaster().getSample(x, y, 0);
- if (dominantColorComponent >= minRescaledColor
- && dominantColorComponent <= maxRescaledColor)
- {
- if (dominantColorComponent > maxColor)
- {
- maxColor = dominantColorComponent;
- } else if (dominantColorComponent < minColor)
- {
- minColor = dominantColorComponent;
- }
- }
- }
- }
- return new ImagePixelsRange(minColor, maxColor);
- }
-
// --- DynamiX specific part ----------------
private static BufferedImage loadImage(IContentRepository contentRepository,
@@ -169,14 +97,16 @@ public class DynamixWellBrightnessEqualizerProcessingPlugin extends
private static IImageTransformerFactoryProvider createImageTransformerFactoryProvider(
final Map<ImgImageEnrichedDTO, ImagePixelsRange> rangeMap)
{
- final ImagePixelsRange globalRange = calculateOverlapRange(rangeMap.values());
+ final ImagePixelsRange globalRange =
+ ColorRangeCalculator.calculateOverlapRange(rangeMap.values());
return new IImageTransformerFactoryProvider()
{
public IImageTransformerFactory tryGetTransformationFactory(
ImgImageEnrichedDTO image)
{
ImagePixelsRange imageRange = rangeMap.get(image);
- ImagePixelsRange rescaledRange = rescaleRange(imageRange, globalRange);
+ ImagePixelsRange rescaledRange =
+ ColorRangeCalculator.rescaleRange(imageRange, globalRange);
operationLog.info(image.getFilePath() + " global: " + globalRange + ", local: "
+ imageRange + ", rescaled: " + rescaledRange);
return new IntensityRangeReductionFactory(rescaledRange.getMin(),
@@ -184,19 +114,4 @@ public class DynamixWellBrightnessEqualizerProcessingPlugin extends
}
};
}
-
- /**
- * We should have converted 'globalRange' to [0,255] but instead a smaller range 'imageRange'
- * has been converted to [0,255]. We have to squeeze 'imageRange' to a smaller range [a,b] (a >=
- * 0, b <= 255) into which it would be mapped if globalRange would be used at the beginning.
- */
- private static ImagePixelsRange rescaleRange(ImagePixelsRange imageRange,
- ImagePixelsRange globalRange)
- {
- double globalRangeLength = globalRange.getMax() - globalRange.getMin();
- int min = (int) (255 * (imageRange.getMin() - globalRange.getMin()) / globalRangeLength);
- int max = (int) (255 * (imageRange.getMax() - globalRange.getMin()) / globalRangeLength);
- return new ImagePixelsRange(min, max);
- }
-
}