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 030dbe2f8b3b748b93190dce70332197bd45960f..794413d82c2125fdfa5ad0d5e03aa0513084a605 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
@@ -23,6 +23,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
@@ -45,15 +46,14 @@ public class AbsoluteImageReference extends AbstractImageReference
private BufferedImage image;
- // This is an artificial value which helps to keep coloring channels constant. Starts with 0.
- // Unique for a given experiment or dataset (if channels are per dataset).
- private int channelIndex;
+ private ImageChannelColor channelColor;
/**
* @param content is the original content before choosing the color component and the page
*/
public AbsoluteImageReference(IContent content, String uniqueId, Integer pageOrNull,
- ColorComponent colorComponentOrNull, RequestedImageSize imageSize, int channelIndex,
+ ColorComponent colorComponentOrNull, RequestedImageSize imageSize,
+ ImageChannelColor channelColor,
ImageTransfomationFactories imageTransfomationFactories,
ImageLibraryInfo imageLibraryOrNull)
{
@@ -64,7 +64,7 @@ public class AbsoluteImageReference extends AbstractImageReference
this.content = content;
this.uniqueId = uniqueId;
this.imageSize = imageSize;
- this.channelIndex = channelIndex;
+ this.channelColor = channelColor;
this.imageTransfomationFactories = imageTransfomationFactories;
this.imageLibraryOrNull = imageLibraryOrNull;
}
@@ -128,16 +128,16 @@ public class AbsoluteImageReference extends AbstractImageReference
return imageTransfomationFactories;
}
- public int getChannelIndex()
+ public ImageChannelColor getChannelColor()
{
- return channelIndex;
+ return channelColor;
}
public AbsoluteImageReference createWithoutColorComponent()
{
ColorComponent colorComponent = null;
return new AbsoluteImageReference(content, uniqueId, tryGetPage(), colorComponent,
- imageSize, channelIndex, imageTransfomationFactories, imageLibraryOrNull);
+ imageSize, channelColor, imageTransfomationFactories, imageLibraryOrNull);
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java
index 9dc994cc37ad6880ec22344578b3ffa8dca8005b..ff2d2fbfc056fb4f1e12ebf0b4abeb1d3164b638 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java
@@ -17,9 +17,12 @@
package ch.systemsx.cisd.openbis.dss.etl;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Set;
+import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
@@ -237,7 +240,8 @@ public class ImagingDatabaseHelper
}
/** Logic to find or create channels */
- private static class ImagingChannelsCreator
+ @Private
+ static class ImagingChannelsCreator
{
private final IImagingQueryDAO dao;
@@ -290,22 +294,56 @@ public class ImagingDatabaseHelper
private Map<String, Long> createChannels(ChannelOwner channelOwner, List<Channel> channels)
{
- int colorIndex = 0;
Map<String, Long> map = new HashMap<String, Long>();
+ fillMissingChannelColors(channels);
for (Channel channel : channels)
{
- if (channel.tryGetChannelColor() == null)
- {
- ChannelColor channelColor = ChannelColor.createFromIndex(colorIndex);
- channel.setChannelColor(channelColor);
- colorIndex++;
- }
ImgChannelDTO channelDTO = createChannel(channel, channelOwner);
addChannel(map, channelDTO);
}
return map;
}
+ @Private
+ static void fillMissingChannelColors(List<Channel> channels)
+ {
+ Set<Integer> usedColorsIndieces = createUsedColorsIndiecesSet(channels);
+ for (Channel channel : channels)
+ {
+ if (channel.tryGetChannelColor() == null)
+ {
+ int colorIndex = getSmallestUnused(usedColorsIndieces);
+ ChannelColor color = ChannelColor.createFromIndex(colorIndex);
+ channel.setChannelColor(color);
+ usedColorsIndieces.add(colorIndex);
+ }
+ }
+ }
+
+ private static Set<Integer> createUsedColorsIndiecesSet(List<Channel> channels)
+ {
+ Set<Integer> usedColorsIndieces = new HashSet<Integer>();
+ for (Channel channel : channels)
+ {
+ ChannelColor channelColor = channel.tryGetChannelColor();
+ if (channelColor != null)
+ {
+ usedColorsIndieces.add(channelColor.getColorOrderIndex());
+ }
+ }
+ return usedColorsIndieces;
+ }
+
+ private static int getSmallestUnused(Set<Integer> usedColorsIndieces)
+ {
+ int colorIndex = 0;
+ while (usedColorsIndieces.contains(colorIndex))
+ {
+ colorIndex++;
+ }
+ return colorIndex;
+ }
+
private static void addChannel(Map<String, Long> map, ImgChannelDTO channelDTO)
{
map.put(channelDTO.getCode(), channelDTO.getId());
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 2c87c40a4627f4d729b956b9a0b8b50fa2b7fcfe..cbd95afbdcc3e1099df46b56b32fa0174d82cfd2 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
@@ -34,6 +34,7 @@ import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackR
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference.MicroscopyChannelStackByLocationReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.HCSDatasetLoader;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
@@ -130,10 +131,10 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
ColorComponent colorComponent = imageDTO.getColorComponent();
ImageTransfomationFactories imageTransfomationFactories =
createImageTransfomationFactories(imageDTO, channel);
- int channelIndex = getChannelIndex(channel);
+ ImageChannelColor channelColor = ImageChannelColor.valueOf(channel.getDbChannelColor());
ImageLibraryInfo imageLibrary = tryGetImageLibrary(dataset, useNativeImageLibrary);
return new AbsoluteImageReference(content, path, imageDTO.getPage(), colorComponent,
- imageSize, channelIndex, imageTransfomationFactories, imageLibrary);
+ imageSize, channelColor, imageTransfomationFactories, imageLibrary);
}
private ImageTransfomationFactories createImageTransfomationFactories(ImgImageDTO imageDTO,
@@ -157,20 +158,6 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
return imageTransformerFactory;
}
- private int getChannelIndex(ImgChannelDTO chosenChannel)
- {
- int index = 0;
- for (ImgChannelDTO channel : channels)
- {
- if (channel.getId() == chosenChannel.getId())
- {
- return index;
- }
- index++;
- }
- throw new IllegalStateException("Channel not found: " + chosenChannel);
- }
-
private ImgChannelDTO tryLoadChannel(String chosenChannelCode)
{
// first we check if there are some channels defined at the dataset level (even for HCS one
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColor.java
index 0a10cf74204457afb80fbb0b4cc9d82472cf340e..83dbe5c09beed3f0a8b3affbdb022327ba7ac13f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColor.java
@@ -9,6 +9,8 @@ public enum ChannelColor
{
BLUE(0), GREEN(1), RED(2), RED_GREEN(3), RED_BLUE(4), GREEN_BLUE(5);
+ private static final int MAX_COLOR = calcMaxColorIndex();
+
// If no mapping between channels and colors has been provided then channels get consecutive
// colors. This field determines the order in which colors are assigned.
// It is important for backward compatibility as well.
@@ -19,6 +21,16 @@ public enum ChannelColor
this.orderIndex = orderIndex;
}
+ private static int calcMaxColorIndex()
+ {
+ int max = 0;
+ for (ChannelColor color : values())
+ {
+ max = Math.max(max, color.getColorOrderIndex());
+ }
+ return max;
+ }
+
public int getColorOrderIndex()
{
return orderIndex;
@@ -28,7 +40,7 @@ public enum ChannelColor
{
for (ChannelColor color : values())
{
- if (color.getColorOrderIndex() == colorIndex)
+ if (color.getColorOrderIndex() == colorIndex % (MAX_COLOR + 1))
{
return color;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
index 1ff5f95da8eb40b5b74ca83632315190fbb0775b..3e3cdcb00e166f621eee07b5a94bb4ce8189f13e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
@@ -84,7 +84,7 @@ abstract public class SimpleImageDataConfig
*/
public Channel createChannel(String channelCode)
{
- ChannelColor channelColor = getChannelColor(channelCode);
+ ChannelColor channelColor = getChannelColor(channelCode.toUpperCase());
return new Channel(channelCode, channelCode, channelColor);
}
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 e3576dc8aad670fd1847b6b8180ac92ab2627c87..885dcb76fd12b0371a4b43c50529b7720ee65678 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
@@ -51,6 +51,7 @@ import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageGenerationDes
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
@@ -712,8 +713,8 @@ public class ImageChannelsUtils
colorBuffer[index] = colorComponent.getComponent(singleColor);
} else
{
- int channelIndex = imageReference.getChannelIndex();
- setColorComponentsForChannelIndex(colorBuffer, singleColor, channelIndex);
+ ImageChannelColor channelColor = imageReference.getChannelColor();
+ setColorComponentsForChannelIndex(colorBuffer, singleColor, channelColor);
}
}
@@ -733,9 +734,9 @@ public class ImageChannelsUtils
}
private static void setColorComponentsForChannelIndex(int[] colorBuffer, Color singleColor,
- int channelIndex)
+ ImageChannelColor channelColor)
{
- for (int i : getRGBColorIndexes(channelIndex))
+ for (int i : getRGBColorIndexes(channelColor))
{
colorBuffer[i] = Math.max(colorBuffer[i], extractMaxColorIngredient(singleColor));
}
@@ -783,23 +784,27 @@ public class ImageChannelsUtils
return newImage;
}
- // 0=B, 1=G, 2=R, 3=RG, 4=RB, 5=GB
- private static int[] getRGBColorIndexes(int channelIndex)
+ // 0=R, 1=G, 2=B, 3=RG, 4=RB, 5=GB
+ private static int[] getRGBColorIndexes(ImageChannelColor channelColor)
{
- switch (channelIndex % 6)
+ switch (channelColor)
{
- case 0:
- case 1:
- case 2:
+ case RED:
+ return new int[]
+ { 0 };
+ case GREEN:
+ return new int[]
+ { 1 };
+ case BLUE:
return new int[]
- { 2 - (channelIndex % 6) };
- case 3:
+ { 2 };
+ case RED_GREEN:
return new int[]
{ 0, 1 };
- case 4:
+ case RED_BLUE:
return new int[]
{ 0, 2 };
- case 5:
+ case GREEN_BLUE:
return new int[]
{ 1, 2 };
default:
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImagingChannelsCreatorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImagingChannelsCreatorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..b021abdfac17745e4f56af95c0c154a97304201c
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImagingChannelsCreatorTest.java
@@ -0,0 +1,68 @@
+/*
+ * 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.etl;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseHelper.ImagingChannelsCreator;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColor;
+
+/**
+ * Test of {@link ImagingChannelsCreator}
+ *
+ * @author Tomasz Pylak
+ */
+@Friend(toClasses = ImagingChannelsCreator.class)
+public class ImagingChannelsCreatorTest extends AssertJUnit
+{
+ @Test
+ public void testFillMissingChannelColors()
+ {
+ List<Channel> channels =
+ Arrays.asList(mkChannel(), mkChannel(ChannelColor.RED), mkChannel());
+ ImagingChannelsCreator.fillMissingChannelColors(channels);
+
+ assertEqual(ChannelColor.BLUE, channels.get(0));
+ assertEqual(ChannelColor.RED, channels.get(1));
+ assertEqual(ChannelColor.GREEN, channels.get(2));
+
+ }
+
+ private static void assertEqual(ChannelColor expectedColor, Channel channel)
+ {
+ if (expectedColor != channel.tryGetChannelColor())
+ {
+ fail("Expected " + expectedColor + " but got: " + channel.tryGetChannelColor());
+ }
+ }
+
+ private static Channel mkChannel()
+ {
+ return mkChannel(null);
+ }
+
+ private static Channel mkChannel(ChannelColor colorOrNull)
+ {
+ return new Channel("code", "label", colorOrNull);
+ }
+}
\ No newline at end of file
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 eb2a160d7cbf03b2cfae696c68449ef8f914a765..69614af24fa68e4fba014e08b42fad28dc61d397 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
@@ -48,6 +48,7 @@ import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtilTest;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannel;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
/**
@@ -218,8 +219,8 @@ public class ImageChannelsUtilsTest extends AssertJUnit
private static AbsoluteImageReference createAbsoluteImageReference(String fileName,
RequestedImageSize imageSize)
{
- return new AbsoluteImageReference(image(fileName), "id42", null, null, imageSize, 0,
- new ImageTransfomationFactories(), null);
+ return new AbsoluteImageReference(image(fileName), "id42", null, null, imageSize,
+ ImageChannelColor.BLUE, new ImageTransfomationFactories(), null);
}
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 cd6cb792052dee44963a18c47beeed4cf55b6fd4..a000c7a6bd13993c2a92d7eadcef6831fe731ab3 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
@@ -335,13 +335,15 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
ImageChannelStackReference.createHCSFromLocations(new Location(3, 1),
new Location(1, 1)), thumbnailSize);
will(returnValue(new AbsoluteImageReference(image("img1.jpg"), "img1", null,
- null, thumbnailSize, 0, new ImageTransfomationFactories(), null)));
+ null, thumbnailSize, ImageChannelColor.BLUE,
+ new ImageTransfomationFactories(), null)));
one(imageLoader).tryGetImage(
channel,
ImageChannelStackReference.createHCSFromLocations(new Location(3, 1),
new Location(2, 1)), thumbnailSize);
will(returnValue(new AbsoluteImageReference(image("img1.gif"), "img1", null,
- null, thumbnailSize, 0, new ImageTransfomationFactories(), null)));
+ null, thumbnailSize, ImageChannelColor.BLUE,
+ new ImageTransfomationFactories(), null)));
}
});