From 913ca45cfa7dee8b23b356a03239c7176479756a Mon Sep 17 00:00:00 2001
From: gpawel <gpawel>
Date: Mon, 5 Nov 2012 13:58:48 +0000
Subject: [PATCH] SP-354 BIS-238 : SOB-6 : Setting image scaling parameters
does not work.
SVN: 27493
---
.../etl/dataaccess/ImagingDatasetLoader.java | 30 ++++++++++++++++++-
.../etl/dto/ImageTransfomationFactories.java | 19 +++++++++++-
.../server/images/ImageChannelsUtils.java | 27 +++++++++++------
3 files changed, 65 insertions(+), 11 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java
index e356f48035a..6f1103cf731 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java
@@ -27,9 +27,9 @@ import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.hcs.Location;
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.hcs.Location;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.etl.PrefixedImage;
@@ -197,6 +197,15 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
getAvailableImageTransformationsForChannel(channel);
imageTransfomationFactories.setForChannel(singleChannelMap);
+ ImgImageTransformationDTO defaultTransformationOrNull =
+ tryGetDefaultTransformation(channel);
+ if (defaultTransformationOrNull != null)
+ {
+ imageTransfomationFactories.setDefaultTransformation(
+ defaultTransformationOrNull.getCode(),
+ defaultTransformationOrNull.getImageTransformerFactory());
+ }
+
imageTransfomationFactories.setForImage(imageDTO.tryGetImageTransformerFactory());
return imageTransfomationFactories;
}
@@ -219,6 +228,25 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
return singleChannelMap;
}
+ private ImgImageTransformationDTO tryGetDefaultTransformation(ImgChannelDTO channel)
+ {
+ List<ImgImageTransformationDTO> availableImageTransformations =
+ availableImageTransformationsMap.get(channel.getId());
+
+ if (availableImageTransformations != null)
+ {
+ for (ImgImageTransformationDTO transformation : availableImageTransformations)
+ {
+ if (transformation.getIsDefault())
+ {
+ return transformation;
+ }
+ }
+ }
+
+ return null;
+ }
+
private IImageTransformerFactory tryGetImageTransformerFactoryForMergedChannels()
{
IImageTransformerFactory imageTransformerFactory = dataset.tryGetImageTransformerFactory();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java
index 43caf51acac..b47fa281993 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java
@@ -36,11 +36,17 @@ public class ImageTransfomationFactories
// individual transformation for the image
private IImageTransformerFactory image;
+ // default channel transformation
+ private IImageTransformerFactory defaultTransformationOrNull;
+
+ // default channel transformation code
+ private String defaultTransformationCodeOrNull;
+
public IImageTransformerFactory tryGetForChannel(String transformationCodeOrNull)
{
if (transformationCodeOrNull == null)
{
- return null;
+ return defaultTransformationOrNull;
}
return singleChannelMap.get(transformationCodeOrNull);
}
@@ -56,6 +62,13 @@ public class ImageTransfomationFactories
this.singleChannelMap = singleChannelMap;
}
+ public void setDefaultTransformation(String defaultTransformationCodeOrNull,
+ IImageTransformerFactory defaultTransformationOrNull)
+ {
+ this.defaultTransformationCodeOrNull = defaultTransformationCodeOrNull;
+ this.defaultTransformationOrNull = defaultTransformationOrNull;
+ }
+
public void setForMergedChannels(IImageTransformerFactory transformerFactoryForMergedChannels)
{
this.mergedChannels = transformerFactoryForMergedChannels;
@@ -71,4 +84,8 @@ public class ImageTransfomationFactories
this.image = transformerFactoryForImage;
}
+ public String tryGetDefaultTransformationCode()
+ {
+ return defaultTransformationCodeOrNull;
+ }
}
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 efa301db78e..f8dcf80438f 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
@@ -32,12 +32,12 @@ import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.image.MixColors;
-import ch.systemsx.cisd.openbis.common.io.ByteArrayBasedContentNode;
-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.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.hcs.Location;
+import ch.systemsx.cisd.openbis.common.io.ByteArrayBasedContentNode;
+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.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageDatasetLoaderFactory;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
@@ -570,14 +570,23 @@ public class ImageChannelsUtils
if (transformationInfo.isUseMergedChannelsTransformation())
{
channelLevelTransformationOrNull = transfomations.tryGetForMerged();
- } else if (transformationInfo.tryGetSingleChannelTransformationCode() != null
- && (false == transformationInfo.tryGetSingleChannelTransformationCode().equals(
- imageReference.tryGetSingleChannelTransformationCode())))
+ } else
{
- channelLevelTransformationOrNull =
- transfomations.tryGetForChannel(transformationInfo
- .tryGetSingleChannelTransformationCode());
+ String channelTransformationCode =
+ transformationInfo.tryGetSingleChannelTransformationCode() == null ? transfomations
+ .tryGetDefaultTransformationCode() : transformationInfo
+ .tryGetSingleChannelTransformationCode();
+
+ if (channelTransformationCode != null
+ && (false == channelTransformationCode.equals(imageReference
+ .tryGetSingleChannelTransformationCode())))
+ {
+ channelLevelTransformationOrNull =
+ transfomations.tryGetForChannel(transformationInfo
+ .tryGetSingleChannelTransformationCode());
+ }
}
+
return applyImageTransformation(resultImage, channelLevelTransformationOrNull);
}
--
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