From 63dad82e4c658a092acb7aa0628cebfe58ea9968 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 8 Oct 2014 10:03:52 +0000
Subject: [PATCH] SSDM-946: Javadoc added.
SVN: 32562
---
.../cisd/common/image/IntensityRescaling.java | 5 +++
.../server/images/ImageChannelsUtils.java | 31 +++++++++++++++++--
.../server/images/ImageLoadingHelper.java | 6 +++-
3 files changed, 38 insertions(+), 4 deletions(-)
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 d15f37f59f8..b65965212d6 100644
--- a/common/source/java/ch/systemsx/cisd/common/image/IntensityRescaling.java
+++ b/common/source/java/ch/systemsx/cisd/common/image/IntensityRescaling.java
@@ -337,6 +337,11 @@ public class IntensityRescaling
}
+ /**
+ * Converts a {@link BufferedImage} instance into a {@link Pixels} instance.
+ *
+ * @author Franz-Josef Elmer
+ */
public static interface IImageToPixelsConverter
{
public Pixels convert(BufferedImage image);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
index 69806d4922e..5ebe9160033 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
@@ -70,8 +70,12 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.Color
/**
* Utility classes to create an image of a specified size containing one channel or a subset of all
* channels.
+ * <p>
+ * In autumn 2014 this class went throw a bigger refactoring in order to make the code more understandable.
+ * The images created by this class are the result of little processing pipelines.
*
* @author Tomasz Pylak
+ * @author Franz-Josef Elmer
*/
public class ImageChannelsUtils
{
@@ -91,6 +95,10 @@ public class ImageChannelsUtils
public BufferedImage create(AbsoluteImageReference imageContent);
}
+ /**
+ * Data class which contains an {@link AbsoluteImageReference} and its corresponding image
+ * which is often no longer the unchanged image from {@link AbsoluteImageReference#getUnchangedImage()}.
+ */
private static class ImageWithReference
{
private BufferedImage image;
@@ -386,9 +394,17 @@ public class ImageChannelsUtils
return null;
}
/**
- * @param threshold
- * @param useMergedChannelsTransformation sometimes we can have a single image which contain all
- * channels merged. In this case a different transformation will be applied to it.
+ * Calculates from the specified image reference (i.e. image file content and meta data from imaging database)
+ * an 8-bit colored gray image for display purposes. This is done by the following steps:
+ * <ol>
+ * <li>Load the unchanged image from the file content. This done by {@link ImageUtil#loadUnchangedImage(IHierarchicalContentNode, String, String, String, ch.systemsx.cisd.imagereaders.IReadParams)}.
+ * <li>Re-scale intensities to 8-bit if at least one color component has more than 8 bit. This is done by {@link IntensityRescaling}.
+ * <li>Re-size to the requested size. This is done by {@link ImageUtil#rescale(BufferedImage, int, int, boolean, boolean, ch.systemsx.cisd.common.image.IntensityRescaling.IImageToPixelsConverter)}.
+ * <li>Extract the color component, if specified.
+ * <li>Apply any transformation as revealed from the imaging database. This can include user-specified intensity ranges.
+ * If there is no transformation in the imaging database {@link AutoRescaleIntensityImageTransformerFactory} is used.
+ * <li>Finally the gray image is colored by the corresponding channel color.
+ * </ol>
*/
private static BufferedImage calculateAndTransformSingleImageForDisplay(
AbsoluteImageReference imageReference, ImageTransformationParams transformationInfo,
@@ -475,6 +491,15 @@ public class ImageChannelsUtils
}
}
+ /**
+ * Creates a colored image by merging at least two gray images. This done by the following steps:
+ * <ol>
+ * <li>The images are loaded a processed similar to {@link #calculateAndTransformSingleImageForDisplay(AbsoluteImageReference, ImageTransformationParams, Float)}.
+ * <li>The processed images (colored gray 8-bit images) are merged.
+ * <li>The merged image is transformed either by a transformation found in imaging database or
+ * by an intensity range re-scaling transformation.
+ * </ol>
+ */
private static BufferedImage mergeChannels(List<AbsoluteImageReference> imageReferences,
ImageTransformationParams transformationInfo,
IImageTransformerFactory mergedChannelTransformationOrNull)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageLoadingHelper.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageLoadingHelper.java
index 2ed25e31b94..9c7700e7b52 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageLoadingHelper.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageLoadingHelper.java
@@ -36,7 +36,11 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
/**
- * Helper class for loading images using an {@link IImagingLoaderStrategy}.
+ * Helper class for loading images using an {@link IImagingLoaderStrategy}. Actually this class
+ * doesn't load images but it creates {@link AbsoluteImageReference} instances which contain lazily loaded images
+ * and meta data from the imaging database.
+ * <p>
+ * This code has been refactored out of {@link ImageChannelsUtils} in autumn 2014.
*
* @author Franz-Josef Elmer
*/
--
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