From 15aabc4a5e966fd40e5cd38b8f03c1ef748664bf Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 2 Nov 2015 11:30:34 +0000
Subject: [PATCH] SSDM-2710: Extending
MaximumIntensityProjectionGenerationAlgorithm by allowing to use thumbnails
as image sources if available.
SVN: 34957
---
.../dss/etl/Hdf5ThumbnailGenerator.java | 2 +-
.../dto/api/IImageGenerationAlgorithm.java | 8 +-
.../api/impl/EmptyImageCreationAlgorithm.java | 4 +-
...ntensityProjectionGenerationAlgorithm.java | 92 ++++++++++++++++++-
...ImagingDataSetRegistrationTransaction.java | 2 +-
...sityProjectionGenerationAlgorithmTest.java | 4 +-
6 files changed, 99 insertions(+), 13 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
index 9ba79c9b523..0ea50170d90 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
@@ -300,7 +300,7 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
return Status.OK;
}
- private String createThumbnailPath(ImageFileInfo plateImage, String channelCode)
+ public static String createThumbnailPath(ImageFileInfo plateImage, String channelCode)
{
StringBuilder newImagePath = new StringBuilder();
if (plateImage.hasWellLocation())
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IImageGenerationAlgorithm.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IImageGenerationAlgorithm.java
index 2a00f8b6d65..3dad3085540 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IImageGenerationAlgorithm.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IImageGenerationAlgorithm.java
@@ -3,6 +3,7 @@ package ch.systemsx.cisd.openbis.dss.etl.dto.api;
import java.awt.image.BufferedImage;
import java.util.List;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
import ch.systemsx.cisd.openbis.dss.etl.IImageProvider;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
@@ -16,7 +17,8 @@ public interface IImageGenerationAlgorithm
/**
* Creates thumbnails for the specified data set info.
*/
- public List<BufferedImage> generateImages(ImageDataSetInformation information, IImageProvider imageProvider);
+ public List<BufferedImage> generateImages(ImageDataSetInformation information,
+ List<IDataSet> thumbnailDatasets, IImageProvider imageProvider);
/**
* Returns the code of the data set to be registered containing these representative thumbnails.
@@ -25,8 +27,8 @@ public interface IImageGenerationAlgorithm
/**
* Returns the thumbnail file name for the specified index. The index specifies the corresponding
- * image returned by {@link #generateImages(ImageDataSetInformation, IImageProvider)}.
- * Note, all file names generated by this method have to different.
+ * image returned by {@link #generateImages(ImageDataSetInformation, List, IImageProvider)}.
+ * Note, all file names generated by this method have to be different.
*/
public String getImageFileName(int index);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/EmptyImageCreationAlgorithm.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/EmptyImageCreationAlgorithm.java
index 2e2bd6fbcb6..ac7f0e41309 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/EmptyImageCreationAlgorithm.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/EmptyImageCreationAlgorithm.java
@@ -5,6 +5,7 @@ import java.io.Serializable;
import java.util.Collections;
import java.util.List;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
import ch.systemsx.cisd.openbis.dss.etl.IImageProvider;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.IImageGenerationAlgorithm;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
@@ -21,7 +22,8 @@ public class EmptyImageCreationAlgorithm implements IImageGenerationAlgorithm, S
}
@Override
- public List<BufferedImage> generateImages(ImageDataSetInformation information, IImageProvider imageProvider)
+ public List<BufferedImage> generateImages(ImageDataSetInformation information,
+ List<IDataSet> thumbnailDatasets, IImageProvider imageProvider)
{
return Collections.emptyList();
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithm.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithm.java
index e3f11abeb47..daa1dc24683 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithm.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithm.java
@@ -11,7 +11,13 @@ import java.util.List;
import java.util.Map;
import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.impl.DataSet;
import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode;
+import ch.systemsx.cisd.openbis.common.io.hierarchical_content.DefaultFileBasedHierarchicalContentFactory;
+import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent;
+import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode;
+import ch.systemsx.cisd.openbis.dss.etl.Hdf5ThumbnailGenerator;
import ch.systemsx.cisd.openbis.dss.etl.IImageProvider;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
@@ -19,6 +25,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.IImageGenerationAlgorithm;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
@@ -56,6 +63,8 @@ public class MaximumIntensityProjectionGenerationAlgorithm implements IImageGene
private int width;
private int height;
+
+ private boolean useThumbnails;
/**
* Creates an instance for the specified data set type. The generated image will have the same size as
@@ -94,6 +103,15 @@ public class MaximumIntensityProjectionGenerationAlgorithm implements IImageGene
this.height = height;
this.filename = filename;
}
+
+ /**
+ * Uses thumbnails (if present) instead of original images.
+ */
+ public MaximumIntensityProjectionGenerationAlgorithm useThumbnails()
+ {
+ useThumbnails = true;
+ return this;
+ }
@Override
public String getDataSetTypeCode()
@@ -102,13 +120,15 @@ public class MaximumIntensityProjectionGenerationAlgorithm implements IImageGene
}
@Override
- public List<BufferedImage> generateImages(ImageDataSetInformation information, IImageProvider imageProvider)
+ public List<BufferedImage> generateImages(ImageDataSetInformation information,
+ List<IDataSet> thumbnailDatasets, IImageProvider imageProvider)
{
ImageDataSetStructure structure = information.getImageDataSetStructure();
ImageLibraryInfo library = structure.getImageStorageConfiguraton().tryGetImageLibrary();
List<ImageFileInfo> images = structure.getImages();
Map<String, ChannelAndColorComponent> channelsByCode = getChannelsByCode(structure);
File incomingDirectory = information.getIncomingDirectory();
+ File thumbnailDataSet = tryFindMatchingThumbnailDataSet(information, thumbnailDatasets);
int maxIntensity = 0;
for (ImageFileInfo imageFileInfo : images)
{
@@ -116,10 +136,10 @@ public class MaximumIntensityProjectionGenerationAlgorithm implements IImageGene
{
continue;
}
- String imagePath = imageFileInfo.getImageRelativePath();
- ChannelAndColorComponent channelAndColorComponent = channelsByCode.get(imageFileInfo.getChannelCode());
- String identifier = imageFileInfo.tryGetUniqueStringIdentifier();
- BufferedImage image = loadImage(imageProvider, incomingDirectory, imagePath, identifier, library);
+ String channelCode = imageFileInfo.getChannelCode();
+ ChannelAndColorComponent channelAndColorComponent = channelsByCode.get(channelCode);
+ BufferedImage image = loadImage(imageProvider, library, images, incomingDirectory,
+ thumbnailDataSet, imageFileInfo, channelCode);
image = ImageChannelsUtils.rescaleIfNot8Bit(image, 0f, channelAndColorComponent.channel.tryGetChannelColor());
image = ImageChannelsUtils.extractChannel(image, channelAndColorComponent.colorComponent);
image = ImageChannelsUtils.transformGrayToColor(image, channelAndColorComponent.channel.tryGetChannelColor());
@@ -150,6 +170,68 @@ public class MaximumIntensityProjectionGenerationAlgorithm implements IImageGene
}
}
+ private BufferedImage loadImage(IImageProvider imageProvider, ImageLibraryInfo library,
+ List<ImageFileInfo> images, File incomingDirectory,
+ File thumbnailDataSet, ImageFileInfo imageFileInfo, String channelCode)
+ {
+ String imagePath = imageFileInfo.getImageRelativePath();
+ String identifier = imageFileInfo.tryGetUniqueStringIdentifier();
+ BufferedImage image = null;
+ if (thumbnailDataSet != null && useThumbnails)
+ {
+ IHierarchicalContent content = new DefaultFileBasedHierarchicalContentFactory()
+ .asHierarchicalContent(thumbnailDataSet, null);
+ String thumbnailPath = Hdf5ThumbnailGenerator.createThumbnailPath(imageFileInfo, channelCode);
+ IHierarchicalContentNode rootNode = content.getRootNode();
+ String containerPath = rootNode.getChildNodes().get(0).getRelativePath();
+ IHierarchicalContentNode node = content.tryGetNode(containerPath + "/" + thumbnailPath + ".png");
+ if (node != null)
+ {
+ image = imageProvider.getImage(node, images.get(0).tryGetUniqueStringIdentifier(), null);
+ }
+ }
+ if (image == null)
+ {
+ image = loadImage(imageProvider, incomingDirectory, imagePath, identifier, library);
+ }
+ return image;
+ }
+
+ private File tryFindMatchingThumbnailDataSet(ImageDataSetInformation information, List<IDataSet> thumbnailDatasets)
+ {
+ ThumbnailsInfo thumbnailsInfos = information.getThumbnailsInfos();
+ if (thumbnailsInfos != null)
+ {
+ for (String permId : thumbnailsInfos.getThumbnailPhysicalDatasetsPermIds())
+ {
+ Size dimension = thumbnailsInfos.tryGetDimension(permId);
+ if (dimension != null && (dimension.getWidth() == width || dimension.getHeight() == height))
+ {
+ IDataSet thumbnailDataSet = tryFindDataSetByPermId(thumbnailDatasets, permId);
+ if (thumbnailDataSet instanceof DataSet)
+ {
+ return ((DataSet<?>) thumbnailDataSet).getDataSetStagingFolder();
+ }
+ }
+ }
+ }
+ return null;
+ }
+
+
+
+ private IDataSet tryFindDataSetByPermId(List<IDataSet> dataSets, String permId)
+ {
+ for (IDataSet dataSet : dataSets)
+ {
+ if (dataSet.getDataSetCode().equals(permId))
+ {
+ return dataSet;
+ }
+ }
+ return null;
+ }
+
@Private BufferedImage loadImage(IImageProvider imageProvider, File incomingDirectory, String imagePath,
String identifier, ImageLibraryInfo library)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java
index d626cd91230..40751157131 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java
@@ -384,7 +384,7 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
{
return;
}
- List<BufferedImage> images = algorithm.generateImages(imageDataSetInformation, imageCache);
+ List<BufferedImage> images = algorithm.generateImages(imageDataSetInformation, thumbnailDatasets, imageCache);
if (images.size() > 0)
{
IDataSet representative = createNewDataSet(algorithm.getDataSetTypeCode());
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithmTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithmTest.java
index 572c124b62f..4eec12b4793 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithmTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithmTest.java
@@ -186,7 +186,7 @@ public class MaximumIntensityProjectionGenerationAlgorithmTest extends AbstractF
Channel channel2 = new Channel("CI2", "i2", new ChannelColorRGB(0, 120, 180));
structure.setChannels(Arrays.asList(channel1, channel2));
- List<BufferedImage> generatedImages = generationAlgorithm.generateImages(information, DUMMY_IMAGE_PROVIDER);
+ List<BufferedImage> generatedImages = generationAlgorithm.generateImages(information, null, DUMMY_IMAGE_PROVIDER);
assertEquals("[incoming/images/i1.png: i1 [lib (reader: reader)], "
+ "incoming/images/i2.png: i2 [lib (reader: reader)]]", generationAlgorithm.recorder.toString());
@@ -208,7 +208,7 @@ public class MaximumIntensityProjectionGenerationAlgorithmTest extends AbstractF
Channel channel2 = new Channel("CI3", "i3", new ChannelColorRGB(0, 120, 180));
structure.setChannels(Arrays.asList(channel1, channel2));
- List<BufferedImage> generatedImages = generationAlgorithm.generateImages(information, DUMMY_IMAGE_PROVIDER);
+ List<BufferedImage> generatedImages = generationAlgorithm.generateImages(information, null, DUMMY_IMAGE_PROVIDER);
assertEquals("[incoming/images/i2.png: i2 [lib (reader: reader)], "
+ "incoming/images/i3.png: i3 [lib (reader: reader)]]", generationAlgorithm.recorder.toString());
--
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