From 62be1a06215075aca040bf6c84a54410682ffc8f Mon Sep 17 00:00:00 2001
From: gpawel <gpawel>
Date: Tue, 18 Dec 2012 16:39:04 +0000
Subject: [PATCH] SP-431 SOB-6: Allow custom image scaling of merged images
SVN: 27957
---
.../dss/etl/AbsoluteImageReference.java | 16 ++-
.../etl/dataaccess/ImagingDatasetLoader.java | 2 +-
.../ImageGenerationDescriptionFactory.java | 41 +++++-
.../server/images/ImageChannelsUtils.java | 71 +++++++---
.../dto/ImageGenerationDescription.java | 10 ++
.../images/dto/ImageTransformationParams.java | 26 +++-
.../detailviewers/ChannelChooser.java | 29 ++--
.../detailviewers/ChannelChooserPanel.java | 126 ++++++++++++++----
.../ChannelWidgetWithListener.java | 7 +-
.../MaterialReplicaSummaryComponent.java | 8 +-
.../UserDefinedRescalingSettingsDialog.java | 125 ++++++++++++-----
.../detailviewers/WellContentDialog.java | 5 +-
.../detailviewers/WellSearchGrid.java | 7 +-
.../dto/LogicalImageChannelsReference.java | 15 ++-
.../detailviewers/image/Image.java | 43 ++++--
.../client/web/public/screening-dictionary.js | 4 +-
.../server/logic/HCSImageDatasetLoader.java | 1 +
.../ImageSizeFeedingMaintenanceTaskTest.java | 4 +-
.../server/images/ImageChannelsUtilsTest.java | 15 ++-
.../server/DssServiceRpcScreeningTest.java | 8 +-
20 files changed, 427 insertions(+), 136 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
index 9283687317c..258036cb404 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
@@ -50,6 +50,8 @@ public class AbsoluteImageReference extends AbstractImageReference
private String singleChannelTransformationCodeOrNull;
+ private final String channelCodeOrNull;
+
/**
* @param contentNode is the original content before choosing the color component and the image
* ID
@@ -58,7 +60,8 @@ public class AbsoluteImageReference extends AbstractImageReference
String imageIdOrNull, ColorComponent colorComponentOrNull,
RequestedImageSize imageSize, ChannelColorRGB channelColor,
ImageTransfomationFactories imageTransfomationFactories,
- ImageLibraryInfo imageLibraryOrNull, String singleChannelTransformationCodeOrNull)
+ ImageLibraryInfo imageLibraryOrNull, String singleChannelTransformationCodeOrNull,
+ String channelCodeOrNull)
{
super(imageIdOrNull, colorComponentOrNull);
assert imageSize != null : "image size is null";
@@ -71,6 +74,7 @@ public class AbsoluteImageReference extends AbstractImageReference
this.imageTransfomationFactories = imageTransfomationFactories;
this.imageLibraryOrNull = imageLibraryOrNull;
this.singleChannelTransformationCodeOrNull = singleChannelTransformationCodeOrNull;
+ this.channelCodeOrNull = channelCodeOrNull;
}
/**
@@ -136,16 +140,24 @@ public class AbsoluteImageReference extends AbstractImageReference
return channelColor;
}
+ /**
+ * Returns the applied transformation code
+ */
public String tryGetSingleChannelTransformationCode()
{
return singleChannelTransformationCodeOrNull;
}
+ public String tryGetChannelCode()
+ {
+ return channelCodeOrNull;
+ }
+
public AbsoluteImageReference createWithoutColorComponent()
{
ColorComponent colorComponent = null;
return new AbsoluteImageReference(contentNode, uniqueId, tryGetImageID(), colorComponent,
imageSize, channelColor, imageTransfomationFactories, imageLibraryOrNull,
- singleChannelTransformationCodeOrNull);
+ singleChannelTransformationCodeOrNull, null);
}
}
\ No newline at end of file
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 794d196d34d..0b32b0a2501 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
@@ -177,7 +177,7 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
ImageLibraryInfo imageLibrary = tryGetImageLibrary(dataset, useNativeImageLibrary);
return new AbsoluteImageReference(contentNode, path, image.getImageID(), colorComponent,
imageSize, getColor(channel), imageTransfomationFactories, imageLibrary,
- image.tryGetSingleChannelTransformationCode());
+ image.tryGetSingleChannelTransformationCode(), channel.getCode());
}
private static ChannelColorRGB getColor(ImgChannelDTO channel)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImageGenerationDescriptionFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImageGenerationDescriptionFactory.java
index 26da2da889b..a750ad7f60e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImageGenerationDescriptionFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImageGenerationDescriptionFactory.java
@@ -27,11 +27,13 @@ import java.util.Map.Entry;
import javax.servlet.http.HttpServletRequest;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
import ch.systemsx.cisd.hcs.Location;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.DatasetAcquiredImagesReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageGenerationDescription;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.ImageServletUrlParameters;
/**
@@ -83,9 +85,44 @@ class ImageGenerationDescriptionFactory
String singleChannelTransformationCodeOrNull =
request.getParameter(ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM);
+
+ Map<String, String> transformationsPerChannel = extractTransformationsPerChannel(request);
+
return new ImageGenerationDescription(channelsToMerge,
- singleChannelTransformationCodeOrNull, overlayChannels, sessionId,
- thumbnailSizeOrNull);
+ singleChannelTransformationCodeOrNull, transformationsPerChannel, overlayChannels,
+ sessionId, thumbnailSizeOrNull);
+ }
+
+ private static Map<String, String> extractTransformationsPerChannel(HttpServletRequest request)
+ {
+ Map<String, String> transformationsPerChannel = new HashMap<String, String>();
+
+ Enumeration<?> params = request.getParameterNames();
+ while (params.hasMoreElements())
+ {
+ String paramName = (String) params.nextElement();
+ if (paramName
+ .startsWith(ScreeningConstants.ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM))
+ {
+ if (paramName
+ .equals(ScreeningConstants.ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM))
+ {
+ continue;
+ }
+
+ String channelCode =
+ paramName
+ .substring(ScreeningConstants.ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM
+ .length());
+ String transformationCode = request.getParameter(paramName);
+ if (StringUtils.isNotBlank(transformationCode))
+ {
+ transformationsPerChannel.put(channelCode, transformationCode);
+ }
+ }
+ }
+
+ return transformationsPerChannel;
}
private static List<DatasetAcquiredImagesReference> getOverlayChannels(
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 e1b839ff3e4..8f5fb1cac20 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
@@ -23,7 +23,9 @@ import java.awt.image.BufferedImage;
import java.awt.image.RenderedImage;
import java.io.File;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import org.apache.log4j.Logger;
@@ -119,8 +121,8 @@ public class ImageChannelsUtils
RequestedImageSize imageSize = new RequestedImageSize(thumbnailSizeOrNull, false);
image =
calculateBufferedImage(imageChannels,
- params.tryGetSingleChannelTransformationCode(), contentProvider,
- imageSize);
+ params.tryGetSingleChannelTransformationCode(),
+ params.tryGetTransformationsPerChannel(), contentProvider, imageSize);
}
RequestedImageSize overlaySize = calcOverlaySize(image, thumbnailSizeOrNull);
@@ -158,11 +160,13 @@ public class ImageChannelsUtils
createImageChannelsUtils(imagesReference, contentProvider, imageSize,
singleChannelTransformationCodeOrNull);
boolean mergeAllChannels = utils.isMergeAllChannels(imagesReference);
- List<AbsoluteImageReference> imageContents =
- utils.fetchImageContents(imagesReference, mergeAllChannels, true);
ImageTransformationParams transformationInfo =
- new ImageTransformationParams(true, mergeAllChannels, null);
- return calculateSingleImagesForDisplay(imageContents, transformationInfo, 0.0f);
+ new ImageTransformationParams(true, mergeAllChannels, null,
+ new HashMap<String, String>());
+ List<AbsoluteImageReference> imageContents =
+ utils.fetchImageContents(imagesReference, mergeAllChannels, true,
+ transformationInfo);
+ return calculateSingleImagesForDisplay(imageContents, transformationInfo, 0.0f, null);
}
private static RequestedImageSize getSize(BufferedImage img, boolean highQuality)
@@ -203,6 +207,7 @@ public class ImageChannelsUtils
private static BufferedImage calculateBufferedImage(
DatasetAcquiredImagesReference imageChannels,
String singleChannelTransformationCodeOrNull,
+ Map<String, String> transformationsPerChannels,
IHierarchicalContentProvider contentProvider, RequestedImageSize imageSizeLimit)
{
ImageChannelsUtils imageChannelsUtils =
@@ -212,7 +217,7 @@ public class ImageChannelsUtils
imageChannelsUtils.isMergeAllChannels(imageChannels);
ImageTransformationParams transformationInfo =
new ImageTransformationParams(true, useMergedChannelsTransformation,
- singleChannelTransformationCodeOrNull);
+ singleChannelTransformationCodeOrNull, transformationsPerChannels);
return imageChannelsUtils.calculateBufferedImage(imageChannels, transformationInfo);
}
@@ -234,7 +239,7 @@ public class ImageChannelsUtils
{
boolean mergeAllChannels = isMergeAllChannels(imageChannels);
List<AbsoluteImageReference> imageContents =
- fetchImageContents(imageChannels, mergeAllChannels, false);
+ fetchImageContents(imageChannels, mergeAllChannels, false, transformationInfo);
return calculateBufferedImage(imageContents, transformationInfo);
}
@@ -247,10 +252,11 @@ public class ImageChannelsUtils
* @param skipNonExisting if true references to non-existing images are ignored, otherwise an
* exception is thrown
* @param mergeAllChannels true if all existing channel images should be merged
+ * @param transformationInfo
*/
private List<AbsoluteImageReference> fetchImageContents(
DatasetAcquiredImagesReference imagesReference, boolean mergeAllChannels,
- boolean skipNonExisting)
+ boolean skipNonExisting, ImageTransformationParams transformationInfo)
{
List<String> channelCodes = imagesReference.getChannelCodes(getAllChannelCodes());
List<AbsoluteImageReference> images = new ArrayList<AbsoluteImageReference>();
@@ -272,7 +278,8 @@ public class ImageChannelsUtils
}
// Optimization for a case where all channels are on one image
- if (mergeAllChannels)
+ if (mergeAllChannels
+ && (false == shouldApplySingleChannelsTransformations(transformationInfo)))
{
AbsoluteImageReference allChannelsImageReference =
tryCreateAllChannelsImageReference(images);
@@ -285,6 +292,19 @@ public class ImageChannelsUtils
return images;
}
+ private boolean shouldApplySingleChannelsTransformations(
+ ImageTransformationParams transformationInfo)
+ {
+ if (transformationInfo == null
+ || transformationInfo.tryGetTransformationCodeForChannels() == null
+ || transformationInfo.tryGetTransformationCodeForChannels().size() == 0)
+ {
+ return false;
+ }
+
+ return true;
+ }
+
private static IImagingDatasetLoader createImageAccessor(
DatasetAcquiredImagesReference imagesReference,
IHierarchicalContentProvider contentProvider)
@@ -309,7 +329,7 @@ public class ImageChannelsUtils
.getRepresentativeImageReferences(wellLocationOrNull);
BufferedImage image =
calculateBufferedImage(imageReferences, new ImageTransformationParams(true, true,
- null));
+ null, new HashMap<String, String>()));
String name = createFileName(datasetCode, wellLocationOrNull, imageSizeLimitOrNull);
return createResponseContentStream(image, name);
}
@@ -369,17 +389,19 @@ public class ImageChannelsUtils
new ImageChannelsUtils(imageLoaderStrategy, imageSizeLimitOrNull,
singleChannelImageTransformationCodeOrNull);
boolean mergeAllChannels = imageChannelsUtils.isMergeAllChannels(imagesReference);
+ ImageTransformationParams transformationInfo =
+ new ImageTransformationParams(transform, mergeAllChannels,
+ singleChannelImageTransformationCodeOrNull, new HashMap<String, String>());
+
List<AbsoluteImageReference> imageContents =
- imageChannelsUtils.fetchImageContents(imagesReference, mergeAllChannels, false);
+ imageChannelsUtils.fetchImageContents(imagesReference, mergeAllChannels, false,
+ transformationInfo);
IHierarchicalContentNode contentNode = tryGetRawContent(convertToPng, imageContents);
if (contentNode != null)
{
return contentNode;
}
- ImageTransformationParams transformationInfo =
- new ImageTransformationParams(transform, mergeAllChannels,
- singleChannelImageTransformationCodeOrNull);
BufferedImage image = calculateBufferedImage(imageContents, transformationInfo);
return createPngContent(image, null);
}
@@ -541,7 +563,7 @@ public class ImageChannelsUtils
{
// We do not transform single images here.
List<ImageWithReference> images =
- calculateSingleImagesForDisplay(imageReferences, null, null);
+ calculateSingleImagesForDisplay(imageReferences, null, null, transformationInfo);
BufferedImage mergedImage = mergeImages(images);
// NOTE: even if we are not merging all the channels but just few of them we use the
// merged-channel transformation
@@ -626,10 +648,12 @@ public class ImageChannelsUtils
/**
* @param transformationInfoOrNull if null all transformations (including image-level) will be
* skipped
+ * @param transformationInfo
*/
private static List<ImageWithReference> calculateSingleImagesForDisplay(
List<AbsoluteImageReference> imageReferences,
- ImageTransformationParams transformationInfoOrNull, Float threshold)
+ ImageTransformationParams transformationInfoOrNull, Float threshold,
+ ImageTransformationParams transformationInfoForMergingOrNull)
{
List<ImageWithReference> images = new ArrayList<ImageWithReference>();
for (AbsoluteImageReference imageRef : imageReferences)
@@ -640,6 +664,19 @@ public class ImageChannelsUtils
image =
calculateAndTransformSingleImageForDisplay(imageRef,
transformationInfoOrNull, threshold);
+ } else if (transformationInfoForMergingOrNull != null
+ && null != transformationInfoForMergingOrNull
+ .tryGetTransformationCodeForChannel(imageRef.tryGetChannelCode()))
+ {
+ String transformationCode =
+ transformationInfoForMergingOrNull
+ .tryGetTransformationCodeForChannel(imageRef.tryGetChannelCode());
+ image =
+ calculateAndTransformSingleImageForDisplay(
+ imageRef,
+ new ImageTransformationParams(transformationInfoForMergingOrNull
+ .isApplyNonImageLevelTransformation(), false,
+ transformationCode, null), threshold);
} else
{
// NOTE: here we skip image level transformations as well
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageGenerationDescription.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageGenerationDescription.java
index 88579d5892f..3cf10a5b86e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageGenerationDescription.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageGenerationDescription.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.dss.generic.server.images.dto;
import java.util.List;
+import java.util.Map;
import ch.systemsx.cisd.hcs.Location;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference.HCSChannelStackByLocationReference;
@@ -34,6 +35,8 @@ public class ImageGenerationDescription
private final String singleChannelTransformationCodeOrNull;
+ private final Map<String, String> transformationsPerChannelOrNull;
+
private final List<DatasetAcquiredImagesReference> overlayChannels;
private final String sessionId;
@@ -43,11 +46,13 @@ public class ImageGenerationDescription
public ImageGenerationDescription(DatasetAcquiredImagesReference imageChannelsOrNull,
String singleChannelTransformationCodeOrNull,
+ Map<String, String> transformationsPerChannelOrNull,
List<DatasetAcquiredImagesReference> overlayChannels, String sessionId,
Size thumbnailSizeOrNull)
{
this.imageChannelsOrNull = imageChannelsOrNull;
this.singleChannelTransformationCodeOrNull = singleChannelTransformationCodeOrNull;
+ this.transformationsPerChannelOrNull = transformationsPerChannelOrNull;
this.overlayChannels = overlayChannels;
this.sessionId = sessionId;
this.thumbnailSizeOrNull = thumbnailSizeOrNull;
@@ -63,6 +68,11 @@ public class ImageGenerationDescription
return singleChannelTransformationCodeOrNull;
}
+ public Map<String, String> tryGetTransformationsPerChannel()
+ {
+ return transformationsPerChannelOrNull;
+ }
+
public List<DatasetAcquiredImagesReference> getOverlayChannels()
{
return overlayChannels;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageTransformationParams.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageTransformationParams.java
index 4450df0b274..bfbcbfdb20c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageTransformationParams.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageTransformationParams.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.dss.generic.server.images.dto;
+import java.util.Map;
+
/**
* Describes which image transformations should be applied. Note that image-level transformation is
* always applied for single channels.
@@ -35,12 +37,16 @@ public class ImageTransformationParams
*/
private final String singleChannelTransformationCodeOrNull;
+ private Map<String, String> transformationsPerChannel;
+
public ImageTransformationParams(boolean applyNonImageLevelTransformation,
- boolean useMergedChannelsTransformation, String singleChannelTransformationCodeOrNull)
+ boolean useMergedChannelsTransformation, String singleChannelTransformationCodeOrNull,
+ Map<String, String> transformationsPerChannel)
{
this.applyNonImageLevelTransformation = applyNonImageLevelTransformation;
this.useMergedChannelsTransformation = useMergedChannelsTransformation;
this.singleChannelTransformationCodeOrNull = singleChannelTransformationCodeOrNull;
+ this.transformationsPerChannel = transformationsPerChannel;
}
public boolean isApplyNonImageLevelTransformation()
@@ -57,4 +63,22 @@ public class ImageTransformationParams
{
return singleChannelTransformationCodeOrNull;
}
+
+ public String tryGetTransformationCodeForChannel(String channelCode)
+ {
+ if (channelCode == null || transformationsPerChannel == null)
+ {
+ return null;
+ }
+ return transformationsPerChannel.get(channelCode);
+ }
+
+ public Map<String, String> tryGetTransformationCodeForChannels()
+ {
+ if (transformationsPerChannel == null)
+ {
+ return null;
+ }
+ return transformationsPerChannel;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooser.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooser.java
index 849d86e9916..9b42e61d8b8 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooser.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooser.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
@@ -53,6 +54,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageResolutio
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageChannel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageTransformationInfo;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.AnalysisProcedureCriteria;
/**
@@ -95,7 +97,7 @@ class ChannelChooser
private String imageTransformationCodeOrNull;
- private IntensityRange rangeOrNull;
+ private Map<String, IntensityRange> rangesOrNull;
public ChannelChooser(LogicalImageReference basicImage, IChanneledViewerFactory viewerFactory,
IDefaultChannelState defaultChannelState)
@@ -109,7 +111,7 @@ class ChannelChooser
this.imageTransformationCodeOrNull =
tryGetInitialImageTransformationCode(defaultChannelState, basicChannelCodes,
basicImage.getImagetParameters());
- this.rangeOrNull = tryGetInitialIntensityRange(defaultChannelState, basicChannelCodes);
+ this.rangesOrNull = tryGetInitialIntensityRange(defaultChannelState, basicChannelCodes);
this.defaultChannelState = defaultChannelState;
this.selectedOverlayChannels = new HashSet<ImageDatasetChannel>();
}
@@ -126,7 +128,7 @@ class ChannelChooser
{
LogicalImageChannelsReference state =
new LogicalImageChannelsReference(basicImage, basicChannelCodes,
- imageTransformationCodeOrNull, rangeOrNull, selectedOverlayChannels);
+ imageTransformationCodeOrNull, rangesOrNull, selectedOverlayChannels);
LayoutContainer view =
viewerFactory.create(state,
@@ -337,12 +339,12 @@ class ChannelChooser
public void selectionChanged(List<String> newlySelectedChannels,
@SuppressWarnings("hiding")
String imageTransformationCodeOrNull, @SuppressWarnings("hiding")
- IntensityRange rangeOrNull)
+ Map<String, IntensityRange> rangesOrNull)
{
basicChannelCodes = newlySelectedChannels;
ChannelChooser.this.imageTransformationCodeOrNull =
imageTransformationCodeOrNull;
- ChannelChooser.this.rangeOrNull = rangeOrNull;
+ ChannelChooser.this.rangesOrNull = rangesOrNull;
refresh();
}
});
@@ -387,9 +389,10 @@ class ChannelChooser
IDefaultChannelState defaultChannelState, List<String> channels,
ImageDatasetParameters imageParameters)
{
- if (imageParameters != null && channels.size() == 1)
+ if (imageParameters != null)
{
- String channel = channels.get(0);
+ String channel =
+ channels.size() == 1 ? channels.get(0) : ScreeningConstants.MERGED_CHANNELS;
String initialTransformation = defaultChannelState.tryGetDefaultTransformation(channel);
if (ChannelChooserPanel.DEFAULT_TRANSFORMATION_CODE.equals(initialTransformation))
{
@@ -417,17 +420,17 @@ class ChannelChooser
return null;
}
- private static IntensityRange tryGetInitialIntensityRange(
+ private static Map<String, IntensityRange> tryGetInitialIntensityRange(
IDefaultChannelState defaultChannelState, List<String> channels)
{
- if (channels.size() == 1)
+ Map<String, IntensityRange> ranges = new HashMap<String, IntensityRange>();
+
+ for (String channel : channels)
{
- String channel = channels.get(0);
IntensityRange rangeOrNull = defaultChannelState.tryGetIntensityRange(channel);
-
- return rangeOrNull;
+ ranges.put(channel, rangeOrNull);
}
- return null;
+ return ranges;
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooserPanel.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooserPanel.java
index 0012c3edaeb..80f78a9deeb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooserPanel.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooserPanel.java
@@ -74,7 +74,7 @@ public class ChannelChooserPanel extends LayoutContainer
public static interface ChannelSelectionListener
{
void selectionChanged(List<String> channels, String imageTransformationCodeOrNull,
- IntensityRange rangeOrNull);
+ Map<String, IntensityRange> rangesOrNull);
}
public static final String DEFAULT_TRANSFORMATION_CODE = "$DEFAULT$";
@@ -126,29 +126,37 @@ public class ChannelChooserPanel extends LayoutContainer
@Override
public void handleEvent(BaseEvent be)
{
- String channelCode = getSelectedValues().get(0);
+ List<LabeledItem<String>> channelCodes = getSelectedLabeledValues();
InternalImageTransformationInfo selectedTransformation =
transformationsComboBox.getSimpleValue().getItem();
String transformationCode = selectedTransformation.getCode();
- defaultChannelState.setDefaultTransformation(channelCode, transformationCode);
+ defaultChannelState.setDefaultTransformation(getChannelCode(channelCodes),
+ transformationCode);
changeTransformationSettingsButtonVisibility(true, false);
- IntensityRange intensityRange =
- defaultChannelState.tryGetIntensityRange(channelCode);
+ Map<String, IntensityRange> intensityRanges = new HashMap<String, IntensityRange>();
+ for (LabeledItem<String> channelCode : channelCodes)
+ {
+ intensityRanges.put(channelCode.getItem(),
+ defaultChannelState.tryGetIntensityRange(channelCode.getItem()));
+ }
notifySelectionListeners(getSelectedValues(),
- tryGetSelectedTransformationCode(false), intensityRange);
+ tryGetSelectedTransformationCode(false), intensityRanges);
String updatedTooltip = selectedTransformation.getLabel();
if (ScreeningConstants.USER_DEFINED_RESCALING_CODE
.equalsIgnoreCase(transformationCode))
{
- updatedTooltip +=
- " ["
- + (intensityRange == null ? "undefined" : intensityRange
- .getBlackPoint()
- + " - "
- + intensityRange.getWhitePoint()) + "]";
- ChannelChooserPanel.this.intensitiesPerChannel.put(channelCode, intensityRange);
+ /*
+ * TODO updatedTooltip += " [" + (intensityRange == null ? "undefined" :
+ * intensityRange .getBlackPoint() + " - " + intensityRange.getWhitePoint()) +
+ * "]";
+ */
+ for (Map.Entry<String, IntensityRange> rangeEntry : intensityRanges.entrySet())
+ {
+ ChannelChooserPanel.this.intensitiesPerChannel.put(rangeEntry.getKey(),
+ rangeEntry.getValue());
+ }
}
transformationsComboBox.setToolTip(updatedTooltip);
}
@@ -192,7 +200,7 @@ public class ChannelChooserPanel extends LayoutContainer
UserDefinedRescalingSettingsDialog dialog =
new UserDefinedRescalingSettingsDialog(messageProvider,
intensitiesPerChannel, defaultChannelState,
- getSelectedValues().get(0));
+ getSelectedLabeledValues());
dialog.addListener(Events.OnChange, transformationSelection);
dialog.show();
}
@@ -207,6 +215,16 @@ public class ChannelChooserPanel extends LayoutContainer
updateChannelSelection(selectedChannelsOrNull);
}
+ private final static String getChannelCode(List<LabeledItem<String>> selection)
+ {
+ if (selection.size() == 1)
+ {
+ return selection.get(0).getItem();
+ }
+
+ return ScreeningConstants.MERGED_CHANNELS;
+ }
+
private SimpleModelComboBox<String> createChannelsComboBox()
{
SimpleModelComboBox<String> comboBox =
@@ -287,6 +305,50 @@ public class ChannelChooserPanel extends LayoutContainer
return channels;
}
+ /**
+ * @return the current channel selection. If all channels are selected, returns whole list of
+ * channels.
+ */
+ public List<LabeledItem<String>> getSelectedLabeledValues()
+ {
+ LabeledItem<String> comboBoxValue;
+ if (channelsComboBox.getSelectedIndex() == -1)
+ {
+ comboBoxValue = null;
+ } else
+ {
+ comboBoxValue = channelsComboBox.getSimpleValue();
+ }
+
+ if (comboBoxValue == null)
+ {
+ return Collections.<LabeledItem<String>> emptyList();
+ }
+ if (ScreeningConstants.MERGED_CHANNELS.equals(comboBoxValue.getItem()))
+ {
+ // multiple channel selection
+ return getMergedChannelLabeledSelection();
+ } else
+ {
+ // single channel selection
+ return Collections.singletonList(comboBoxValue);
+ }
+ }
+
+ private List<LabeledItem<String>> getMergedChannelLabeledSelection()
+ {
+ List<LabeledItem<String>> channels = new ArrayList<LabeledItem<String>>();
+ for (CheckBox cb : getAllCheckBoxes())
+ {
+ if (cb.getValue() == true)
+ {
+ channels.add(new LabeledItem<String>(cb.getValueAttribute(), cb.getBoxLabel()));
+ }
+ }
+
+ return channels;
+ }
+
private void addChannelsForParameters(ImageDatasetParameters imageParameters)
{
addChannelToComboBox(new LabeledItem<String>(MERGED_CHANNELS, MERGED_CHANNELS));
@@ -312,6 +374,8 @@ public class ChannelChooserPanel extends LayoutContainer
transformationsForChannel.addAll(imageParameters
.getAvailableImageTransformationsFor(code));
+ intensitiesPerChannel.put(code, defaultChannelState.tryGetIntensityRange(code));
+
if (codeAdded)
{
// also add a checkBockbox for the channel
@@ -408,7 +472,7 @@ public class ChannelChooserPanel extends LayoutContainer
updateTransformationComboBox();
notifySelectionListeners(selection, tryGetSelectedTransformationCode(false),
- tryGetSelectedIntensityRange());
+ tryGetSelectedIntensityRanges());
}
public String tryGetSelectedTransformationCode(boolean force)
@@ -428,16 +492,21 @@ public class ChannelChooserPanel extends LayoutContainer
return transformCode(code);
}
- public IntensityRange tryGetSelectedIntensityRange()
+ public Map<String, IntensityRange> tryGetSelectedIntensityRanges()
{
- List<String> selectedValues = getSelectedValues();
- if (selectedValues != null && selectedValues.size() > 0)
+ List<LabeledItem<String>> selectedValues = getSelectedLabeledValues();
+ if (selectedValues != null)
{
- return intensitiesPerChannel.get(getSelectedValues().get(0));
- } else
- {
- return null;
+ Map<String, IntensityRange> ranges = new HashMap<String, IntensityRange>();
+ for (LabeledItem<String> channelCode : selectedValues)
+ {
+ ranges.put(channelCode.getItem(), intensitiesPerChannel.get(channelCode.getItem()));
+ }
+
+ return ranges;
}
+
+ return null;
}
private static String transformCode(String code)
@@ -452,11 +521,11 @@ public class ChannelChooserPanel extends LayoutContainer
}
private void notifySelectionListeners(List<String> selection,
- String imageTransformationCodeOrNull, IntensityRange rangeOrNull)
+ String imageTransformationCodeOrNull, Map<String, IntensityRange> rangesOrNull)
{
for (ChannelSelectionListener listener : channelSelectionListeners)
{
- listener.selectionChanged(selection, imageTransformationCodeOrNull, rangeOrNull);
+ listener.selectionChanged(selection, imageTransformationCodeOrNull, rangesOrNull);
}
}
@@ -569,6 +638,15 @@ public class ChannelChooserPanel extends LayoutContainer
selectTransformation(selectedValues.get(0));
setTransformationsVisible(true);
+ } else if (selectedValues.size() > 0)
+ {
+ model.add(DEFAULT_TRANSFORMATION);
+ model.add(convertToLabeledItem(new InternalImageTransformationInfo(
+ ScreeningConstants.USER_DEFINED_RESCALING_CODE, "User defined",
+ "User defined intensity rescaling", "", false)));
+ transformationsComboBox.add(model);
+ selectTransformation(ScreeningConstants.MERGED_CHANNELS);
+ setTransformationsVisible(true);
} else
{
setTransformationsVisible(false);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelWidgetWithListener.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelWidgetWithListener.java
index 0e83909df37..c7e5615bc47 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelWidgetWithListener.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelWidgetWithListener.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
import java.util.List;
+import java.util.Map;
import com.extjs.gxt.ui.client.widget.LayoutContainer;
import com.google.gwt.user.client.ui.Widget;
@@ -40,7 +41,7 @@ public class ChannelWidgetWithListener implements ChannelChooserPanel.ChannelSel
interface ISimpleChanneledViewerFactory
{
Widget create(List<String> channelCodes, String imageTransformationCodeOrNull,
- IntensityRange rangeOrNull);
+ Map<String, IntensityRange> rangesOrNull);
}
public ChannelWidgetWithListener(final ISimpleChanneledViewerFactory viewerFactory)
@@ -56,12 +57,12 @@ public class ChannelWidgetWithListener implements ChannelChooserPanel.ChannelSel
@Override
public void selectionChanged(List<String> channelNames, String imageTransformationCodeOrNull,
- IntensityRange rangeOrNull)
+ Map<String, IntensityRange> rangesOrNull)
{
if (channelNames != null)
{
GuiUtils.replaceLastItem(container,
- viewerFactory.create(channelNames, imageTransformationCodeOrNull, rangeOrNull));
+ viewerFactory.create(channelNames, imageTransformationCodeOrNull, rangesOrNull));
}
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryComponent.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryComponent.java
index fc2bcda9326..7b1538095b4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryComponent.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryComponent.java
@@ -59,11 +59,11 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.d
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.utils.PropertiesUtil;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReplicaImage;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.AnalysisProcedureCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchCriteria;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
/**
* Component which for a specified material and experiment presents 1. feature vectors (detailed and
@@ -347,17 +347,17 @@ public class MaterialReplicaSummaryComponent
{
@Override
public Widget create(List<String> channels, String imageTransformationCodeOrNull,
- IntensityRange rangeOrNull)
+ Map<String, IntensityRange> rangesOrNull)
{
return WellContentDialog.createImageViewerForChannel(screeningViewContext,
image, oneImageSizeFactorPx, channels, imageTransformationCodeOrNull,
- rangeOrNull);
+ rangesOrNull);
}
};
ChannelWidgetWithListener widgetWithListener = new ChannelWidgetWithListener(viewerFactory);
widgetWithListener.selectionChanged(channelChooser.getSelectedValues(),
channelChooser.tryGetSelectedTransformationCode(false),
- channelChooser.tryGetSelectedIntensityRange());
+ channelChooser.tryGetSelectedIntensityRanges());
ImageDatasetParameters imageParameters = image.tryGetImageDataset().getImageParameters();
channelChooser.addSelectionChangedListener(widgetWithListener);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/UserDefinedRescalingSettingsDialog.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/UserDefinedRescalingSettingsDialog.java
index 654640cb3a7..dca1d7a9e45 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/UserDefinedRescalingSettingsDialog.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/UserDefinedRescalingSettingsDialog.java
@@ -16,6 +16,9 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import com.extjs.gxt.ui.client.event.BaseEvent;
@@ -27,6 +30,7 @@ import com.extjs.gxt.ui.client.widget.button.Button;
import com.google.gwt.user.client.ui.Grid;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.IntegerField;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.LabeledItem;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
@@ -36,46 +40,77 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange
*/
public class UserDefinedRescalingSettingsDialog extends Dialog
{
- private final Label labelMin;
+ private static class SingleChannelIntesityRange
+ {
+ private final LabeledItem<String> channelCode;
+
+ private final Label labelMin;
+
+ private final Label labelMax;
+
+ private final IntegerField minTextField;
- private final Label labelMax;
+ private final IntegerField maxTextField;
- private final IntegerField minTextField;
+ public SingleChannelIntesityRange(IMessageProvider messageProvider,
+ LabeledItem<String> channelCode)
+ {
+ this.channelCode = channelCode;
+ labelMin =
+ new Label(messageProvider.getMessage(Dict.RESCALING_DIALOG_MIN,
+ channelCode.getLabel()));
+ labelMax =
+ new Label(messageProvider.getMessage(Dict.RESCALING_DIALOG_MAX,
+ channelCode.getLabel()));
+ minTextField =
+ new IntegerField(messageProvider.getMessage(Dict.RESCALING_DIALOG_MIN,
+ channelCode), true);
+ maxTextField =
+ new IntegerField(messageProvider.getMessage(Dict.RESCALING_DIALOG_MAX,
+ channelCode), true);
+ }
+ }
- private final IntegerField maxTextField;
+ private final List<SingleChannelIntesityRange> intensitiesPerChannel;
private final IMessageProvider messageProvider;
private final IDefaultChannelState defaultChannelState;
- private final String channelCode;
+ private final List<LabeledItem<String>> channelCodes;
public UserDefinedRescalingSettingsDialog(IMessageProvider messageProvider,
Map<String, IntensityRange> intensitiesPerChannel,
- IDefaultChannelState defaultChannelState, String channelCode)
+ IDefaultChannelState defaultChannelState, List<LabeledItem<String>> channelCodes)
{
super();
this.messageProvider = messageProvider;
this.defaultChannelState = defaultChannelState;
- this.channelCode = channelCode;
+ this.channelCodes = channelCodes;
setHeading(this.messageProvider.getMessage(Dict.TITLE_USER_DEFINED_RESCALING_DIALOG));
setButtons(Dialog.OKCANCEL);
- labelMin = new Label(this.messageProvider.getMessage(Dict.RESCALING_DIALOG_MIN));
- labelMax = new Label(this.messageProvider.getMessage(Dict.RESCALING_DIALOG_MAX));
- minTextField =
- new IntegerField(messageProvider.getMessage(Dict.RESCALING_DIALOG_MIN), true);
- maxTextField =
- new IntegerField(messageProvider.getMessage(Dict.RESCALING_DIALOG_MAX), true);
+
+ this.intensitiesPerChannel = new ArrayList<SingleChannelIntesityRange>(channelCodes.size());
+ for (LabeledItem<String> channelCode : channelCodes)
+ {
+ this.intensitiesPerChannel.add(new SingleChannelIntesityRange(messageProvider,
+ channelCode));
+ }
setInitialValues(intensitiesPerChannel);
- Grid grid = new Grid(2, 2);
- grid.setWidget(0, 0, labelMin);
- grid.setWidget(0, 1, minTextField);
- grid.setWidget(1, 0, labelMax);
- grid.setWidget(1, 1, maxTextField);
+ Grid grid = new Grid(channelCodes.size() * 2, 2);
+ int counter = 0;
+ for (SingleChannelIntesityRange scir : this.intensitiesPerChannel)
+ {
+ grid.setWidget(2 * counter, 0, scir.labelMin);
+ grid.setWidget(2 * counter, 1, scir.minTextField);
+ grid.setWidget(2 * counter + 1, 0, scir.labelMax);
+ grid.setWidget(2 * counter + 1, 1, scir.maxTextField);
+ counter++;
+ }
add(grid);
@@ -94,14 +129,17 @@ public class UserDefinedRescalingSettingsDialog extends Dialog
private void setInitialValues(Map<String, IntensityRange> intensitiesPerChannel)
{
- minTextField.setValue(0);
- maxTextField.setValue(65535);
-
- IntensityRange range = intensitiesPerChannel.get(channelCode);
- if (range != null)
+ for (SingleChannelIntesityRange scir : this.intensitiesPerChannel)
{
- minTextField.setValue(range.getBlackPoint());
- maxTextField.setValue(range.getWhitePoint());
+ scir.minTextField.setValue(0);
+ scir.maxTextField.setValue(65535);
+
+ IntensityRange range = intensitiesPerChannel.get(scir.channelCode.getItem());
+ if (range != null)
+ {
+ scir.minTextField.setValue(range.getBlackPoint());
+ scir.maxTextField.setValue(range.getWhitePoint());
+ }
}
}
@@ -111,7 +149,7 @@ public class UserDefinedRescalingSettingsDialog extends Dialog
if (button.getItemId().equals(Dialog.OK))
{
button.disable();
- if (minTextField.isValid() && maxTextField.isValid())
+ if (areIntensitiesValid())
{
super.onButtonPressed(button);
updateIntensityRescaling();
@@ -128,23 +166,40 @@ public class UserDefinedRescalingSettingsDialog extends Dialog
}
}
+ private boolean areIntensitiesValid()
+ {
+ for (SingleChannelIntesityRange scir : intensitiesPerChannel)
+ {
+ if ((false == scir.minTextField.isValid()) || (false == scir.maxTextField.isValid()))
+ {
+ return false;
+ }
+ }
+
+ return true;
+ }
+
public void updateIntensityRescaling()
{
- IntensityRange result = null;
+ Map<String, IntensityRange> result = new HashMap<String, IntensityRange>();
try
{
- int min = Integer.parseInt(minTextField.getValue().toString());
- int max = Integer.parseInt(maxTextField.getValue().toString());
+ for (SingleChannelIntesityRange scir : intensitiesPerChannel)
+ {
+ int min = Integer.parseInt(scir.minTextField.getValue().toString());
+ int max = Integer.parseInt(scir.maxTextField.getValue().toString());
- result = new IntensityRange(min, max);
- } catch (NumberFormatException e)
- {
- }
+ result.put(scir.channelCode.getItem(), new IntensityRange(min, max));
+ }
- if (result != null)
+ for (LabeledItem<String> channelCode : channelCodes)
+ {
+ defaultChannelState.setIntensityRange(channelCode.getItem(),
+ result.get(channelCode.getItem()));
+ }
+ } catch (NumberFormatException e)
{
- defaultChannelState.setIntensityRange(channelCode, result);
}
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
index 519c872bd93..e7ecaddeaf6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.
import java.util.Collections;
import java.util.List;
+import java.util.Map;
import com.extjs.gxt.ui.client.Style.HorizontalAlignment;
import com.extjs.gxt.ui.client.Style.Scroll;
@@ -172,7 +173,7 @@ public class WellContentDialog extends ImageDialog
public static Widget createImageViewerForChannel(
final IViewContext<IScreeningClientServiceAsync> viewContext,
final WellContent wellImage, int imageSizePx, List<String> channels,
- String imageTransformationCodeOrNull, IntensityRange rangeOrNull)
+ String imageTransformationCodeOrNull, Map<String, IntensityRange> rangesOrNull)
{
final ImageDatasetEnrichedReference imageDataset = tryGetImageDataset(wellImage);
if (imageDataset == null)
@@ -210,7 +211,7 @@ public class WellContentDialog extends ImageDialog
new LogicalImageReference(imageDataset, locationOrNull);
LogicalImageChannelsReference channelReferences =
LogicalImageChannelsReference.createWithoutOverlays(wellImages, channels,
- imageTransformationCodeOrNull, rangeOrNull);
+ imageTransformationCodeOrNull, rangesOrNull);
LayoutContainer staticTilesGrid =
LogicalImageViewer.createTilesGrid(channelReferences, sessionId, imageSizePx,
clickHandler, null);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java
index 76abc4000ed..961bd58e11d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.
import java.util.Arrays;
import java.util.Date;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import com.extjs.gxt.ui.client.store.ListStore;
@@ -639,18 +640,18 @@ public class WellSearchGrid extends TypedTableGrid<WellContent> implements
@Override
public Widget create(List<String> channels,
String imageTransformationCodeOrNull,
- IntensityRange rangeOrNull)
+ Map<String, IntensityRange> rangesOrNull)
{
return WellContentDialog.createImageViewerForChannel(
getViewContext(), entity, IMAGE_SIZE_PX, channels,
- imageTransformationCodeOrNull, rangeOrNull);
+ imageTransformationCodeOrNull, rangesOrNull);
}
};
ChannelWidgetWithListener widgetWithListener =
new ChannelWidgetWithListener(viewerFactory);
widgetWithListener.selectionChanged(channelChooser.getSelectedValues(),
channelChooser.tryGetSelectedTransformationCode(false),
- channelChooser.tryGetSelectedIntensityRange());
+ channelChooser.tryGetSelectedIntensityRanges());
ImageDatasetParameters imageParameters = images.getImageParameters();
channelChooser.addSelectionChangedListener(widgetWithListener);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/LogicalImageChannelsReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/LogicalImageChannelsReference.java
index 87034aefc2d..71e4f79a1e5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/LogicalImageChannelsReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/LogicalImageChannelsReference.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.
import java.util.HashSet;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
@@ -31,10 +32,10 @@ public class LogicalImageChannelsReference
{
public static LogicalImageChannelsReference createWithoutOverlays(
LogicalImageReference basicImage, List<String> channels,
- String imageTransformationCodeOrNull, IntensityRange rangeOrNull)
+ String imageTransformationCodeOrNull, Map<String, IntensityRange> rangesOrNull)
{
return new LogicalImageChannelsReference(basicImage, channels,
- imageTransformationCodeOrNull, rangeOrNull, new HashSet<ImageDatasetChannel>());
+ imageTransformationCodeOrNull, rangesOrNull, new HashSet<ImageDatasetChannel>());
}
// ----
@@ -45,18 +46,18 @@ public class LogicalImageChannelsReference
private final String imageTransformationCodeOrNull;
- private final IntensityRange rangeOrNull;
+ private final Map<String, IntensityRange> rangesOrNull;
private final Set<ImageDatasetChannel> overlayChannels;
public LogicalImageChannelsReference(LogicalImageReference basicImage, List<String> channels,
- String imageTransformationCodeOrNull, IntensityRange rangeOrNull,
+ String imageTransformationCodeOrNull, Map<String, IntensityRange> rangesOrNull,
Set<ImageDatasetChannel> overlayChannels)
{
this.basicImage = basicImage;
this.channels = channels;
this.imageTransformationCodeOrNull = imageTransformationCodeOrNull;
- this.rangeOrNull = rangeOrNull;
+ this.rangesOrNull = rangesOrNull;
this.overlayChannels = overlayChannels;
}
@@ -80,8 +81,8 @@ public class LogicalImageChannelsReference
return imageTransformationCodeOrNull;
}
- public IntensityRange tryGetIntensityRange()
+ public Map<String, IntensityRange> tryGetIntensityRanges()
{
- return rangeOrNull;
+ return rangesOrNull;
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/image/Image.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/image/Image.java
index 27b95c867b8..099f9b31fac 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/image/Image.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/image/Image.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.image;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import com.extjs.gxt.ui.client.widget.LayoutContainer;
@@ -62,20 +63,46 @@ public class Image extends LayoutContainer
if (getInitializer().getChannelReferences().tryGetImageTransformationCode() != null)
{
- String suffix = "";
if (ScreeningConstants.USER_DEFINED_RESCALING_CODE.equalsIgnoreCase(getInitializer()
.getChannelReferences().tryGetImageTransformationCode()))
{
- IntensityRange range =
- getInitializer().getChannelReferences().tryGetIntensityRange();
- if (range != null)
+ Map<String, IntensityRange> rangesOrNull =
+ getInitializer().getChannelReferences().tryGetIntensityRanges();
+ if (rangesOrNull != null)
{
- suffix = "(" + range.getBlackPoint() + "," + range.getWhitePoint() + ")";
+ for (Map.Entry<String, IntensityRange> range : rangesOrNull.entrySet())
+ {
+ String suffix = "";
+ if (range.getValue() != null)
+ {
+ suffix =
+ "(" + range.getValue().getBlackPoint() + ","
+ + range.getValue().getWhitePoint() + ")";
+ }
+
+ if (rangesOrNull.size() == 1)
+ {
+ url.addParameter(
+ ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM,
+ getInitializer().getChannelReferences()
+ .tryGetImageTransformationCode() + suffix);
+ } else
+ {
+ url.addParameter(
+ ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM
+ + range.getKey(), getInitializer()
+ .getChannelReferences().tryGetImageTransformationCode()
+ + suffix);
+ }
+
+ }
}
+ } else
+ {
+ url.addParameter(
+ ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM,
+ getInitializer().getChannelReferences().tryGetImageTransformationCode());
}
- url.addParameter(ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM,
- getInitializer().getChannelReferences().tryGetImageTransformationCode()
- + suffix);
}
addImageTransformerSignature(url, getInitializer().getChannelReferences());
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js
index b47d96e6c8f..24f0567e29e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js
@@ -142,8 +142,8 @@ RESOLUTION_CHOOSER_DEFAULT: "Default",
RESOLUTION_CHOOSER_RESOLUTION: "{0}x{1}",
TITLE_USER_DEFINED_RESCALING_DIALOG: "Set rescaling parameters",
-RESCALING_DIALOG_MIN: "black point: ",
-RESCALING_DIALOG_MAX: "white point: ",
+RESCALING_DIALOG_MIN: "{0} black point: ",
+RESCALING_DIALOG_MAX: "{0} white point: ",
// LAST LINE: KEEP IT AT THE END
lastline: "" // we need a line without a comma
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoader.java
index e068c430b37..0942ad3d12c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoader.java
@@ -303,6 +303,7 @@ class HCSImageDatasetLoader extends PlateDatasetLoader
DataStore dataStore = externalData.getDataStore();
DataSetType dataSetType = externalData.getDataSetType();
String dataSetTypeCodeOrNull = dataSetType == null ? null : dataSetType.getCode();
+
return new ImageDatasetReference(externalData.getCode(), dataSetTypeCodeOrNull,
getDataStoreUrlFromDataStore(dataStore), createPlateIdentifier(externalData),
createExperimentIdentifier(externalData), extractPlateGeometry(externalData),
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTaskTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTaskTest.java
index 949f4a09471..4ae052c1388 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTaskTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTaskTest.java
@@ -28,9 +28,9 @@ import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent;
import ch.systemsx.cisd.common.logging.BufferedAppender;
import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize;
@@ -57,7 +57,7 @@ public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
public MockAbsoluteImageReference(int width, int height)
{
super(null, null, null, null, new RequestedImageSize(null, false), null,
- new ImageTransfomationFactories(), null, null);
+ new ImageTransfomationFactories(), null, null, null);
this.width = width;
this.height = height;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
index ceac2fb6ed1..eec32f3828b 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
@@ -38,10 +38,10 @@ import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.base.image.IImageTransformer;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode;
-import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode;
import ch.systemsx.cisd.imagereaders.ImageReaderConstants;
import ch.systemsx.cisd.imagereaders.ImageReadersTestHelper;
+import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode;
+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.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.etl.ImagingLoaderStrategyFactory;
@@ -136,7 +136,7 @@ public class ImageChannelsUtilsTest extends AssertJUnit
private ImageTransformationParams createSingleChannelTransformationParams()
{
- return new ImageTransformationParams(true, false, null);
+ return new ImageTransformationParams(true, false, null, new HashMap<String, String>());
}
@Test
@@ -226,8 +226,10 @@ public class ImageChannelsUtilsTest extends AssertJUnit
});
BufferedImage image =
- createImageChannelsUtils(null).calculateBufferedImage(imageRef,
- new ImageTransformationParams(true, false, transformationCode));
+ createImageChannelsUtils(null).calculateBufferedImage(
+ imageRef,
+ new ImageTransformationParams(true, false, transformationCode,
+ new HashMap<String, String>()));
assertEquals("e00 f00 f00 e00\n" + "f00 c00 c00 f00\n" + "f00 c00 c00 f00\n"
+ "e00 f00 f00 e00\n", getImageContentDescription(image));
@@ -247,7 +249,8 @@ public class ImageChannelsUtilsTest extends AssertJUnit
RequestedImageSize imageSize)
{
return new AbsoluteImageReference(image(fileName), "id42", null, null, imageSize,
- new ChannelColorRGB(0, 0, 255), new ImageTransfomationFactories(), null, null);
+ new ChannelColorRGB(0, 0, 255), new ImageTransfomationFactories(), null, null,
+ "ch2");
}
private ImageChannelsUtils createImageChannelsUtils(Size thumbnailSizeOrNull)
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
index 085064a35e8..e88cabc523c 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
@@ -456,14 +456,14 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
new Location(1, 1)), thumbnailSize, null);
will(returnValue(new AbsoluteImageReference(image("img1.jpg"), "img1", null,
null, thumbnailSize, createBlueColor(),
- new ImageTransfomationFactories(), null, null)));
+ new ImageTransfomationFactories(), null, null, CHANNEL_CODE)));
one(imageLoader).tryGetImage(
CHANNEL_CODE,
ImageChannelStackReference.createHCSFromLocations(new Location(3, 1),
new Location(2, 1)), thumbnailSize, null);
will(returnValue(new AbsoluteImageReference(image("img1.gif"), "img1", null,
null, thumbnailSize, createBlueColor(),
- new ImageTransfomationFactories(), null, null)));
+ new ImageTransfomationFactories(), null, null, CHANNEL_CODE)));
}
});
}
@@ -590,7 +590,7 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
new Location(1, 1)), thumbnailSize, null);
will(returnValue(new AbsoluteImageReference(image("img1.jpg"), "img1", null,
null, thumbnailSize, createBlueColor(),
- new ImageTransfomationFactories(), null, null)));
+ new ImageTransfomationFactories(), null, null, CHANNEL_CODE)));
one(imageLoader).tryGetImage(
CHANNEL_CODE,
@@ -598,7 +598,7 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
new Location(2, 1)), thumbnailSize, null);
will(returnValue(new AbsoluteImageReference(image("img1.png"), "img1", null,
null, thumbnailSize, createBlueColor(),
- new ImageTransfomationFactories(), null, null)));
+ new ImageTransfomationFactories(), null, null, CHANNEL_CODE)));
}
});
--
GitLab