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 8163116a76861b48a653d4d183cc224f7ac4221c..c223a91b494bf99785198a7d522ed8c9a2faa82c 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
@@ -21,9 +21,9 @@ import java.awt.image.BufferedImage;
import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
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;
/**
@@ -46,15 +46,14 @@ public class AbsoluteImageReference extends AbstractImageReference
private BufferedImage image;
- private ImageChannelColor channelColor;
+ private ChannelColorRGB channelColor;
/**
* @param content is the original content before choosing the color component and the image ID
*/
public AbsoluteImageReference(IContent content, String uniqueId, String imageIdOrNull,
ColorComponent colorComponentOrNull, RequestedImageSize imageSize,
- ImageChannelColor channelColor,
- ImageTransfomationFactories imageTransfomationFactories,
+ ChannelColorRGB channelColor, ImageTransfomationFactories imageTransfomationFactories,
ImageLibraryInfo imageLibraryOrNull)
{
super(imageIdOrNull, colorComponentOrNull);
@@ -128,7 +127,7 @@ public class AbsoluteImageReference extends AbstractImageReference
return imageTransfomationFactories;
}
- public ImageChannelColor getChannelColor()
+ public ChannelColorRGB getChannelColor()
{
return channelColor;
}
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 08bb2096674d3bcb2ef0c2c8b529afe2cdb5b5ee..34114dc89d0bcc96b153fecb637a52e803717613 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
@@ -28,8 +28,8 @@ 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;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColor;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgExperimentDTO;
@@ -328,15 +328,52 @@ public class ImagingDatabaseHelper
Set<Integer> usedColorsIndieces = new HashSet<Integer>();
for (Channel channel : channels)
{
- ChannelColor channelColor = channel.tryGetChannelColor();
- if (channelColor != null)
+ ChannelColorRGB channelColorRGB = channel.tryGetChannelColor();
+ if (channelColorRGB != null)
{
+ ChannelColor channelColor = findNearestPlainChannelColor(channelColorRGB);
usedColorsIndieces.add(channelColor.getColorOrderIndex());
}
}
return usedColorsIndieces;
}
+ @Private
+ static ChannelColor findNearestPlainChannelColor(ChannelColorRGB color)
+ {
+ int r = color.getR();
+ int g = color.getG();
+ int b = color.getB();
+ int max = (r > g ? r : g);
+ max = (b > max ? b : max);
+
+ if (r == max)
+ {
+ if (r == g)
+ {
+ return ChannelColor.RED_GREEN;
+ } else if (r == b)
+ {
+ return ChannelColor.RED_BLUE;
+ } else
+ {
+ return ChannelColor.RED;
+ }
+ } else if (g == max)
+ {
+ if (g == b)
+ {
+ return ChannelColor.GREEN_BLUE;
+ } else
+ {
+ return ChannelColor.GREEN;
+ }
+ } else
+ {
+ return ChannelColor.BLUE;
+ }
+ }
+
private static int getSmallestUnused(Set<Integer> usedColorsIndieces)
{
int colorIndex = 0;
@@ -451,13 +488,13 @@ public class ImagingDatabaseHelper
private static ImgChannelDTO makeChannelDTO(Channel channel, ChannelOwner channelOwner)
{
- ChannelColor channelColor = channel.tryGetChannelColor();
+ ChannelColorRGB channelColor = channel.tryGetChannelColor();
assert channelColor != null : "channel color should be specified at this point";
- ImageChannelColor imageChannelColor = ImageChannelColor.valueOf(channelColor.name());
return new ImgChannelDTO(channel.getCode(), channel.tryGetDescription(),
channel.tryGetWavelength(), channelOwner.tryGetDatasetId(),
- channelOwner.tryGetExperimentId(), channel.getLabel(), imageChannelColor);
+ channelOwner.tryGetExperimentId(), channel.getLabel(), channelColor.getR(),
+ channelColor.getG(), channelColor.getB());
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingQueryDAO.java
index a8e6150f9eb98d6fc691901a720c5256535a929e..efcdad54081d47ac569a6284f37db0a9fdf81537 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingQueryDAO.java
@@ -70,8 +70,10 @@ public interface IImagingQueryDAO extends TransactionQuery, IImagingReadonlyQuer
@Select("insert into EXPERIMENTS (PERM_ID) values (?{1}) returning ID")
public long addExperiment(String experimentPermId);
- @Select("insert into CHANNELS (CODE, LABEL, DESCRIPTION, WAVELENGTH, DS_ID, EXP_ID, COLOR) values "
- + "(?{1.code}, ?{1.label}, ?{1.description}, ?{1.wavelength}, ?{1.datasetId}, ?{1.experimentId}, ?{1.dbChannelColor}) returning ID")
+ @Select("insert into CHANNELS (CODE, LABEL, DESCRIPTION, WAVELENGTH, DS_ID, EXP_ID, "
+ + "RED_CC, GREEN_CC, BLUE_CC) values "
+ + "(?{1.code}, ?{1.label}, ?{1.description}, ?{1.wavelength}, ?{1.datasetId}, ?{1.experimentId}, "
+ + "?{1.redColorComponent}, ?{1.greenColorComponent}, ?{1.blueColorComponent}) returning ID")
public long addChannel(ImgChannelDTO channel);
@Select("insert into CONTAINERS (PERM_ID, SPOTS_WIDTH, SPOTS_HEIGHT, EXPE_ID) values "
@@ -113,7 +115,8 @@ public interface IImagingQueryDAO extends TransactionQuery, IImagingReadonlyQuer
// updates
@Update("update CHANNELS "
- + "set DESCRIPTION = ?{1.description}, WAVELENGTH = ?{1.wavelength}, COLOR = ?{1.dbChannelColor} "
+ + "set DESCRIPTION = ?{1.description}, WAVELENGTH = ?{1.wavelength}, "
+ + "RED_CC = ?{1.redColorComponent}, GREEN_CC = ?{1.greenColorComponent}, BLUE_CC = ?{1.blueColorComponent}"
+ "where ID = ?{1.id}")
public void updateChannel(ImgChannelDTO channel);
}
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 909eb47f8109d96ce5a8735d06cfc8c6e38e2341..47671a22a7dc87bd5f9653589e60ba9b097e0ffb 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
@@ -32,12 +32,12 @@ import ch.systemsx.cisd.openbis.dss.etl.IContentRepository;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference.HCSChannelStackByLocationReference;
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;
@@ -135,10 +135,15 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
ColorComponent colorComponent = imageDTO.getColorComponent();
ImageTransfomationFactories imageTransfomationFactories =
createImageTransfomationFactories(imageDTO, channel);
- ImageChannelColor channelColor = ImageChannelColor.valueOf(channel.getDbChannelColor());
ImageLibraryInfo imageLibrary = tryGetImageLibrary(dataset, useNativeImageLibrary);
return new AbsoluteImageReference(content, path, imageDTO.getImageID(), colorComponent,
- imageSize, channelColor, imageTransfomationFactories, imageLibrary);
+ imageSize, getColor(channel), imageTransfomationFactories, imageLibrary);
+ }
+
+ private static ChannelColorRGB getColor(ImgChannelDTO channel)
+ {
+ return new ChannelColorRGB(channel.getRedColorComponent(),
+ channel.getGreenColorComponent(), channel.getBlueColorComponent());
}
private ImageTransfomationFactories createImageTransfomationFactories(ImgImageDTO imageDTO,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java
index 6330435e607263833405187f3999c40ad6fbf379..dbb5d610ccc02ce84545e4d22a054844f55154fe 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java
@@ -1,5 +1,8 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
+import java.awt.Color;
+
+import ch.systemsx.cisd.common.image.WavelengthColor;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
@@ -21,7 +24,7 @@ public final class Channel extends AbstractHashable
private Integer wavelength;
- private ChannelColor channelColorOrNull;
+ private ChannelColorRGB channelColorOrNull;
private ImageTransformation[] availableTransformations = new ImageTransformation[0];
@@ -31,7 +34,7 @@ public final class Channel extends AbstractHashable
*/
public Channel(String code, String label)
{
- this(code, label, null);
+ this(code, label, (ChannelColorRGB) null);
}
/**
@@ -39,6 +42,15 @@ public final class Channel extends AbstractHashable
* specified color.
*/
public Channel(String code, String label, ChannelColor channelColorOrNull)
+ {
+ this(code, label, convertColor(channelColorOrNull));
+ }
+
+ /**
+ * Constructs a channel with a specified code and label. The channel will be presented in a
+ * specified color.
+ */
+ public Channel(String code, String label, ChannelColorRGB channelColorOrNull)
{
assert code != null : "code is null";
assert label != null : "label is null";
@@ -47,6 +59,15 @@ public final class Channel extends AbstractHashable
this.channelColorOrNull = channelColorOrNull;
}
+ private static ChannelColorRGB convertColor(ChannelColor plainChannelColorOrNull)
+ {
+ if (plainChannelColorOrNull == null)
+ {
+ return null;
+ }
+ return plainChannelColorOrNull.getRGB();
+ }
+
public String getCode()
{
return code;
@@ -72,7 +93,7 @@ public final class Channel extends AbstractHashable
* null only during dataset registration when default color should be used, afterwards
* never null.
*/
- public ChannelColor tryGetChannelColor()
+ public ChannelColorRGB tryGetChannelColor()
{
return channelColorOrNull;
}
@@ -85,20 +106,46 @@ public final class Channel extends AbstractHashable
// ------------------- setters -------------------
- /** Sets the description of the channel.Optional. */
+ /** Sets the description of the channel. Optional. */
public void setDescription(String description)
{
this.description = description;
}
- /** Sets the wavelength of the channel.Optional. */
+ /** Sets the wavelength of the light (in nanometers) used to acquire this channel. Optional. */
public void setWavelength(Integer wavelength)
{
this.wavelength = wavelength;
}
- /** Sets the color in which this channel will be displayed. */
+ /**
+ * Sets the wavelength of the light (in nanometers) used to acquire this channel.<br>
+ * Additionally sets the channel color. The color is calculated for display on a computer
+ * monitor on the basis of the given wavelength using Bruton's algorithm. See <a
+ * href="http://www.midnightkite.com/color.html">COLOR SCIENCE web page</a> for details.
+ * <p>
+ * Optional.
+ */
+ public void setWavelengthAndColor(Integer wavelength)
+ {
+ this.wavelength = wavelength;
+ Color color = WavelengthColor.getColorForWavelength(wavelength);
+ setChannelColorRGB(convertColor(color));
+ }
+
+ private ChannelColorRGB convertColor(Color color)
+ {
+ return new ChannelColorRGB(color.getRed(), color.getGreen(), color.getBlue());
+ }
+
+ /** Sets the plain color in which this channel will be displayed. */
public void setChannelColor(ChannelColor channelColor)
+ {
+ this.channelColorOrNull = convertColor(channelColor);
+ }
+
+ /** Sets RGB color in which this channel will be displayed. */
+ public void setChannelColorRGB(ChannelColorRGB channelColor)
{
this.channelColorOrNull = channelColor;
}
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 83dbe5c09beed3f0a8b3affbdb022327ba7ac13f..275b0fcfd15fd91c1fafa17fa936afa7a257fa8d 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
@@ -47,4 +47,25 @@ public enum ChannelColor
}
throw new IllegalStateException("Invalid color index: " + colorIndex + "!");
}
+
+ public ChannelColorRGB getRGB()
+ {
+ switch (this)
+ {
+ case RED:
+ return new ChannelColorRGB(255, 0, 0);
+ case GREEN:
+ return new ChannelColorRGB(0, 255, 0);
+ case BLUE:
+ return new ChannelColorRGB(0, 0, 255);
+ case RED_GREEN:
+ return new ChannelColorRGB(255, 255, 0);
+ case GREEN_BLUE:
+ return new ChannelColorRGB(0, 255, 255);
+ case RED_BLUE:
+ return new ChannelColorRGB(255, 0, 255);
+ default:
+ throw new IllegalStateException("unhandled enum " + this);
+ }
+ }
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorRGB.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorRGB.java
new file mode 100644
index 0000000000000000000000000000000000000000..b352a9e0485bf86a456afc9693c29ab33a75ce0b
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorRGB.java
@@ -0,0 +1,100 @@
+/*
+ * 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.dto.api.v1;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
+
+/**
+ * RGB color components specify the color in which channel should be displayed.
+ *
+ * @author Tomasz Pylak
+ */
+public class ChannelColorRGB implements ISerializable
+{
+ private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+
+ private int r, g, b;
+
+ @SuppressWarnings("unused")
+ private ChannelColorRGB()
+ {
+ }
+
+ public ChannelColorRGB(int r, int g, int b)
+ {
+ assert r >= 0 && r <= 255 : "invalid color " + r;
+ assert g >= 0 && g <= 255 : "invalid color " + g;
+ assert b >= 0 && b <= 255 : "invalid color " + b;
+
+ this.r = r;
+ this.g = g;
+ this.b = b;
+ }
+
+ public int getR()
+ {
+ return r;
+ }
+
+ public int getG()
+ {
+ return g;
+ }
+
+ public int getB()
+ {
+ return b;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "Color(r=" + r + ", g=" + g + ", b=" + b + ")";
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + b;
+ result = prime * result + g;
+ result = prime * result + r;
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ ChannelColorRGB other = (ChannelColorRGB) obj;
+ if (b != other.b)
+ return false;
+ if (g != other.g)
+ return false;
+ if (r != other.r)
+ return false;
+ return true;
+ }
+
+}
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 53fe43a2e3524a3a26c75492ae69769ffd99e677..e3f4e58a63edf799eb12ee3b2c6b177247bda689 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
@@ -118,16 +118,36 @@ abstract public class SimpleImageDataConfig
*/
public Channel createChannel(String channelCode)
{
- ChannelColor channelColor = getChannelColor(channelCode);
+ ChannelColorRGB channelColorOrNull = tryGetChannelColor(channelCode);
ImageTransformation[] availableTransformations =
getAvailableChannelTransformations(channelCode);
String label = channelCode;
String normalizedChannelCode = CodeNormalizer.normalize(channelCode);
- Channel channel = new Channel(normalizedChannelCode, label, channelColor);
+ Channel channel = new Channel(normalizedChannelCode, label, channelColorOrNull);
channel.setAvailableTransformations(availableTransformations);
return channel;
}
+ private ChannelColorRGB tryGetChannelColor(String channelCode)
+ {
+ ChannelColor channelColor = getChannelColor(channelCode);
+ ChannelColorRGB channelColorRGB = getChannelColorRGB(channelCode);
+ if (channelColorRGB != null && channelColor != null)
+ {
+ throw new IllegalStateException(String.format(
+ "Color for channel '%s' is specified in two ways: %s and %s", channelColor,
+ channelColorRGB));
+ }
+
+ if (channelColor != null)
+ {
+ return channelColor.getRGB();
+ } else
+ {
+ return channelColorRGB;
+ }
+ }
+
/**
* Sets available transformations which can be applied to images of the specified channel (on
* user's request).
@@ -143,14 +163,24 @@ abstract public class SimpleImageDataConfig
}
/**
- * Returns color for the specified channel. It will be used to display merged channels images.
+ * Has the same effect as {@link #getChannelColorRGB(String)}, but can return only plain colors.
+ */
+ public ChannelColor getChannelColor(String channelCode)
+ {
+ return null;
+ }
+
+ /**
+ * Returns RGB color for the specified channel. It will be used to display merged channels
+ * images.
* <p>
* Can be overridden in subclasses. It is ignored if {@link #createChannel(String)} is
- * overridden as well.
+ * overridden as well. One should not override {@link #getChannelColor(String)} and
+ * {@link #getChannelColorRGB(String)} at the same time.
* </p>
* By default returns null (the arbitrary color will be set).
*/
- public ChannelColor getChannelColor(String channelCode)
+ public ChannelColorRGB getChannelColorRGB(String channelCode)
{
return null;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ColorComponentImageChannelMerger.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ColorComponentImageChannelMerger.java
new file mode 100644
index 0000000000000000000000000000000000000000..ec1e8945328a8ea611daef31aa3bdaa197bf99e7
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ColorComponentImageChannelMerger.java
@@ -0,0 +1,103 @@
+/*
+ * 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.generic.server.images;
+
+import java.awt.Color;
+import java.awt.image.BufferedImage;
+import java.util.Arrays;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
+
+/**
+ * Handles the special case of merging image channels which in fact are encoded on the same image as
+ * different color components. It makes sense to use this class only for exactly two channels.
+ *
+ * @author Tomasz Pylak
+ */
+class ColorComponentImageChannelMerger
+{
+ public static BufferedImage mergeByExtractingComponents(BufferedImage[] images,
+ ColorComponent[] colorComponents)
+ {
+ assert images.length > 1 : "more than 1 image expected, but found: " + images.length;
+
+ BufferedImage newImage = createNewRGBImage(images[0]);
+ int width = newImage.getWidth();
+ int height = newImage.getHeight();
+ int colorBuffer[] = new int[4];
+ for (int y = 0; y < height; y++)
+ {
+ for (int x = 0; x < width; x++)
+ {
+ int mergedRGB = mergeRGBColor(images, colorComponents, x, y, colorBuffer);
+ newImage.setRGB(x, y, mergedRGB);
+ }
+ }
+ return newImage;
+ }
+
+ private static int mergeRGBColor(BufferedImage[] images, ColorComponent[] colorComponents,
+ int x, int y, int colorBuffer[])
+ {
+ Arrays.fill(colorBuffer, 0);
+ for (int index = 0; index < images.length; index++)
+ {
+ int rgb = images[index].getRGB(x, y);
+ Color singleColor = new Color(rgb, true);
+ setColorComponents(colorBuffer, singleColor, colorComponents[index]);
+ // merge alpha channel
+ colorBuffer[3] = Math.max(colorBuffer[3], singleColor.getAlpha());
+ }
+ return asRGB(colorBuffer);
+ }
+
+ private static void setColorComponents(int[] colorBuffer, Color singleColor,
+ ColorComponent colorComponent)
+ {
+ int index = getColorComponentIndex(colorComponent);
+ colorBuffer[index] = colorComponent.getComponent(singleColor);
+ }
+
+ private static int getColorComponentIndex(ColorComponent colorComponent)
+ {
+ switch (colorComponent)
+ {
+ case RED:
+ return 0;
+ case GREEN:
+ return 1;
+ case BLUE:
+ return 2;
+ default:
+ throw new IllegalStateException("Unknown color " + colorComponent);
+ }
+ }
+
+ private static int asRGB(int[] rgb)
+ {
+ return new Color(rgb[0], rgb[1], rgb[2], rgb[3]).getRGB();
+ }
+
+ // NOTE: drawing on this image will not preserve transparency - but we do not need it and the
+ // image is smaller
+ private static BufferedImage createNewRGBImage(BufferedImage bufferedImage)
+ {
+ return new BufferedImage(bufferedImage.getWidth(), bufferedImage.getHeight(),
+ BufferedImage.TYPE_INT_RGB);
+ }
+
+}
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 9f7fbec58a0ce82d6f0c37d6d0ccc3a7398d37a2..1f8e4b3bd1cd1c1e98fdf6f14f0d688b5f0d38ba 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 +23,6 @@ import java.awt.image.BufferedImage;
import java.awt.image.RenderedImage;
import java.io.File;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.List;
import org.apache.log4j.Logger;
@@ -33,6 +32,7 @@ import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.bds.hcs.Location;
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.common.io.ByteArrayBasedContent;
import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.common.logging.LogCategory;
@@ -43,6 +43,7 @@ import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.etl.IImagingLoaderStrategy;
import ch.systemsx.cisd.openbis.dss.etl.ImagingLoaderStrategyFactory;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
import ch.systemsx.cisd.openbis.dss.generic.server.ResponseContentStream;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.DatasetAcquiredImagesReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference;
@@ -51,7 +52,6 @@ import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageTransformatio
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;
@@ -449,6 +449,7 @@ public class ImageChannelsUtils
operationLog.debug("Load original image: " + (System.currentTimeMillis() - start));
}
+
// resized the image if necessary
RequestedImageSize requestedSize = imageReference.getRequestedSize();
@@ -645,21 +646,57 @@ public class ImageChannelsUtils
// this method always returns RGB images, even if the input was in grayscale
private static BufferedImage mergeImages(List<ImageWithReference> images)
{
- assert images.size() > 1 : "more than 1 image expected, but found: " + images.size();
+ BufferedImage[] bufferedImages = new BufferedImage[images.size()];
+ Color[] colors = new Color[images.size()];
+ for (int i = 0; i < images.size(); i++)
+ {
+ ImageWithReference image = images.get(i);
+ bufferedImages[i] = image.getBufferedImage();
+ colors[i] = getColor(image);
+ }
- BufferedImage newImage = createNewRGBImage(images.get(0).getBufferedImage());
- int width = newImage.getWidth();
- int height = newImage.getHeight();
- int colorBuffer[] = new int[4];
- for (int y = 0; y < height; y++)
+ ColorComponent[] colorComponents = tryExtractColorComponent(images);
+ if (colorComponents != null)
{
- for (int x = 0; x < width; x++)
+ return ColorComponentImageChannelMerger.mergeByExtractingComponents(bufferedImages,
+ colorComponents);
+ } else
+ {
+ return MixColors.mixImages(bufferedImages, colors, false, 0);
+ }
+ }
+
+ private static Color getColor(ImageWithReference image)
+ {
+ return getColor(image.getReference().getChannelColor());
+ }
+
+ private static Color getColor(ChannelColorRGB color)
+ {
+ return new Color(color.getR(), color.getG(), color.getB());
+ }
+
+ private static ColorComponent[] tryExtractColorComponent(List<ImageWithReference> images)
+ {
+ ColorComponent[] components = new ColorComponent[images.size()];
+ int i = 0;
+ for (ImageWithReference image : images)
+ {
+ ColorComponent colorComponent = image.getReference().tryGetColorComponent();
+ if (colorComponent == null)
{
- int mergedRGB = mergeRGBColor(images, x, y, colorBuffer);
- newImage.setRGB(x, y, mergedRGB);
+ if (i == 0)
+ {
+ return null;
+ } else
+ {
+ throw new IllegalStateException(
+ "Some images have color component set and some have it unset.");
+ }
}
+ components[i++] = colorComponent;
}
- return newImage;
+ return components;
}
private static void drawOverlay(BufferedImage image, ImageWithReference overlayImage)
@@ -728,63 +765,6 @@ public class ImageChannelsUtils
return image.getBufferedImage().getColorModel().hasAlpha();
}
- private static int mergeRGBColor(List<ImageWithReference> images, int x, int y,
- int colorBuffer[])
- {
- Arrays.fill(colorBuffer, 0);
- for (int index = 0; index < images.size(); index++)
- {
- ImageWithReference image = images.get(index);
- int rgb = image.getBufferedImage().getRGB(x, y);
- Color singleColor = new Color(rgb, true);
- AbsoluteImageReference imageReference = image.getReference();
- setColorComponents(colorBuffer, singleColor, imageReference);
- // merge alpha channel
- colorBuffer[3] = Math.max(colorBuffer[3], singleColor.getAlpha());
- }
- return asRGB(colorBuffer);
- }
-
- private static void setColorComponents(int[] colorBuffer, Color singleColor,
- AbsoluteImageReference imageReference)
- {
- ColorComponent colorComponent = imageReference.tryGetColorComponent();
- if (colorComponent != null)
- {
- int index = getColorComponentIndex(colorComponent);
- colorBuffer[index] = colorComponent.getComponent(singleColor);
- } else
- {
- ImageChannelColor channelColor = imageReference.getChannelColor();
- setColorComponentsForChannelIndex(colorBuffer, singleColor, channelColor);
- }
- }
-
- private static int getColorComponentIndex(ColorComponent colorComponent)
- {
- switch (colorComponent)
- {
- case RED:
- return 0;
- case GREEN:
- return 1;
- case BLUE:
- return 2;
- default:
- throw new IllegalStateException("Unknown color " + colorComponent);
- }
- }
-
- private static void setColorComponentsForChannelIndex(int[] colorBuffer, Color singleColor,
- ImageChannelColor channelColor)
- {
- int maxIngredient = extractMaxColorIngredient(singleColor);
- for (int i : getRGBColorIndexes(channelColor))
- {
- colorBuffer[i] = Math.max(colorBuffer[i], maxIngredient);
- }
- }
-
// --------- common
private EnvironmentFailureException createImageNotFoundException(
@@ -817,44 +797,6 @@ public class ImageChannelsUtils
return newImage;
}
- // NOTE: drawing on this image will not preserve transparency - but we do not need it and the
- // image is smaller
- private static BufferedImage createNewRGBImage(RenderedImage bufferedImage)
- {
- BufferedImage newImage =
- new BufferedImage(bufferedImage.getWidth(), bufferedImage.getHeight(),
- BufferedImage.TYPE_INT_RGB);
- return newImage;
- }
-
- // 0=R, 1=G, 2=B, 3=RG, 4=RB, 5=GB
- private static int[] getRGBColorIndexes(ImageChannelColor channelColor)
- {
- switch (channelColor)
- {
- case RED:
- return new int[]
- { 0 };
- case GREEN:
- return new int[]
- { 1 };
- case BLUE:
- return new int[]
- { 2 };
- case RED_GREEN:
- return new int[]
- { 0, 1 };
- case RED_BLUE:
- return new int[]
- { 0, 2 };
- case GREEN_BLUE:
- return new int[]
- { 1, 2 };
- default:
- throw new IllegalStateException("not possible");
- }
- }
-
// We reset all ingredients besides the one which is specified by color component.
// The result is the rgb value with only one component which is non-zero.
private static int extractSingleComponent(int rgb, ColorComponent colorComponent)
@@ -862,15 +804,14 @@ public class ImageChannelsUtils
return colorComponent.extractSingleComponent(rgb).getRGB();
}
- // returns the max ingredient for the color
- private static int extractMaxColorIngredient(Color c)
- {
- return Math.max(Math.max(c.getBlue(), c.getGreen()), c.getRed());
- }
-
- private static int asRGB(int[] rgb)
+ // NOTE: drawing on this image will not preserve transparency - but we do not need it and the
+ // image is smaller
+ private static BufferedImage createNewRGBImage(RenderedImage bufferedImage)
{
- return new Color(rgb[0], rgb[1], rgb[2], rgb[3]).getRGB();
+ BufferedImage newImage =
+ new BufferedImage(bufferedImage.getWidth(), bufferedImage.getHeight(),
+ BufferedImage.TYPE_INT_RGB);
+ return newImage;
}
private static IContent createPngContent(BufferedImage image, String nameOrNull)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannel.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannel.java
index c3fd5d26526a66cc195801196bc392a859a145d3..09aadd1a26856d97c4f120f0fd2c22f90b49afd5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannel.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannel.java
@@ -40,8 +40,6 @@ public class ImageChannel implements ISerializable
private Integer wavelength;
- private ImageChannelColor channelColor;
-
private List<ImageTransformationInfo> availableImageTransformations;
// GWT only
@@ -51,17 +49,15 @@ public class ImageChannel implements ISerializable
}
public ImageChannel(String code, String label, String description, Integer wavelength,
- ImageChannelColor channelColor,
List<ImageTransformationInfo> availableImageTransformations)
{
assert code != null;
-// assert availableImageTransformations != null;
+ // assert availableImageTransformations != null;
this.code = code;
this.label = label;
this.description = description;
this.wavelength = wavelength;
- this.channelColor = channelColor;
this.availableImageTransformations = availableImageTransformations;
}
@@ -85,14 +81,6 @@ public class ImageChannel implements ISerializable
return label;
}
- /**
- * @return color for the specified channel which will be used to display merged channels images.
- */
- public ImageChannelColor getChannelColor()
- {
- return channelColor;
- }
-
public List<ImageTransformationInfo> getAvailableImageTransformations()
{
return availableImageTransformations;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
index 82f86cadad718d11f995dfca1dd9229ec6e27f04..68804831108a91535dd01208c65f614ebc8a7b19 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
@@ -25,7 +25,6 @@ import ch.systemsx.cisd.common.utilities.MD5ChecksumCalculator;
import ch.systemsx.cisd.openbis.generic.shared.basic.utils.GroupByMap;
import ch.systemsx.cisd.openbis.generic.shared.basic.utils.IGroupKeyExtractor;
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.ImageChannelStack;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageTransformationInfo;
@@ -205,12 +204,10 @@ public class HCSDatasetLoader implements IImageDatasetLoader
private ImageChannel convert(ImgChannelDTO channelDTO)
{
- ImageChannelColor imageChannelColor =
- ImageChannelColor.valueOf(channelDTO.getDbChannelColor());
List<ImageTransformationInfo> availableImageTransformations =
convertTransformations(availableImageTransformationsMap.get(channelDTO.getId()));
return new ImageChannel(channelDTO.getCode(), channelDTO.getLabel(),
- channelDTO.getDescription(), channelDTO.getWavelength(), imageChannelColor,
+ channelDTO.getDescription(), channelDTO.getWavelength(),
availableImageTransformations);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
index 1c30c8fba51c8bbfc857e28eb89fe50db7c98069..d82c3f1d454e000e3251f0c1e5049ff2f10cc972 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
@@ -19,7 +19,6 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.ResultColumn;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
/**
* @author Tomasz Pylak
@@ -46,9 +45,15 @@ public class ImgChannelDTO extends AbstractImgIdentifiable
@ResultColumn("EXP_ID")
private Long experimentIdOrNull;
- /** Value for the {@link ImageChannelColor} enum. Not null. */
- @ResultColumn("COLOR")
- private String channelColor;
+ /** RGB color components specify the color in which channel should be displayed. Not null. */
+ @ResultColumn("RED_CC")
+ private int redColorComponent;
+
+ @ResultColumn("GREEN_CC")
+ private int greenColorComponent;
+
+ @ResultColumn("BLUE_CC")
+ private int blueColorComponent;
// EODSQL only
@SuppressWarnings("unused")
@@ -58,8 +63,7 @@ public class ImgChannelDTO extends AbstractImgIdentifiable
}
public ImgChannelDTO(String code, String descriptionOrNull, Integer wavelengthOrNull,
- Long datasetIdOrNull, Long experimentIdOrNull, String label,
- ImageChannelColor channelColor)
+ Long datasetIdOrNull, Long experimentIdOrNull, String label, int r, int g, int b)
{
assert (datasetIdOrNull == null && experimentIdOrNull != null)
|| (datasetIdOrNull != null && experimentIdOrNull == null);
@@ -69,7 +73,10 @@ public class ImgChannelDTO extends AbstractImgIdentifiable
this.wavelengthOrNull = wavelengthOrNull;
this.datasetIdOrNull = datasetIdOrNull;
this.experimentIdOrNull = experimentIdOrNull;
- this.channelColor = channelColor.name();
+
+ this.redColorComponent = r;
+ this.greenColorComponent = g;
+ this.blueColorComponent = b;
}
public String getCode()
@@ -133,14 +140,33 @@ public class ImgChannelDTO extends AbstractImgIdentifiable
this.experimentIdOrNull = experimentId;
}
- /** Can be converted to {@link ImageChannelColor}. */
- public String getDbChannelColor()
+ public int getRedColorComponent()
+ {
+ return redColorComponent;
+ }
+
+ public void setRedColorComponent(int redColorComponent)
+ {
+ this.redColorComponent = redColorComponent;
+ }
+
+ public int getGreenColorComponent()
+ {
+ return greenColorComponent;
+ }
+
+ public void setGreenColorComponent(int greenColorComponent)
+ {
+ this.greenColorComponent = greenColorComponent;
+ }
+
+ public int getBlueColorComponent()
{
- return channelColor;
+ return blueColorComponent;
}
- public void setDbChannelColor(String channelColor)
+ public void setBlueColorComponent(int blueColorComponent)
{
- this.channelColor = channelColor;
+ this.blueColorComponent = blueColorComponent;
}
}
diff --git a/screening/source/sql/imaging/postgresql/015/schema-015.sql b/screening/source/sql/imaging/postgresql/015/schema-015.sql
index ecb4508d3c86687590bb578c4bf33aea4797d6c0..98efd99752f4375e11f44dd403f25bf78012fdf9 100644
--- a/screening/source/sql/imaging/postgresql/015/schema-015.sql
+++ b/screening/source/sql/imaging/postgresql/015/schema-015.sql
@@ -100,7 +100,11 @@ CREATE TABLE CHANNELS (
LABEL NAME NOT NULL,
DESCRIPTION DESCRIPTION,
WAVELENGTH INTEGER,
- COLOR CHANNEL_COLOR NOT NULL,
+
+ -- RGB color components specify the color in which channel should be displayed
+ RED_CC INTEGER NOT NULL,
+ GREEN_CC INTEGER NOT NULL,
+ BLUE_CC INTEGER NOT NULL,
DS_ID TECH_ID,
EXP_ID TECH_ID,
diff --git a/screening/source/sql/imaging/postgresql/migration/migration-014-015.sql b/screening/source/sql/imaging/postgresql/migration/migration-014-015.sql
index 6515c17a8e29fecd4879055dc9b234daef1d1088..63e17fcf493a69c1c6accd1d76b392d86079131d 100644
--- a/screening/source/sql/imaging/postgresql/migration/migration-014-015.sql
+++ b/screening/source/sql/imaging/postgresql/migration/migration-014-015.sql
@@ -1,7 +1,9 @@
--- Migration from 014 to 015
+-- Migration from 014 to 015, sprint 116
alter table IMAGE_TRANSFORMATIONS add column IS_DEFAULT BOOLEAN_CHAR NOT NULL DEFAULT 'F';
+-- allow to define a default image transformation
+
CREATE OR REPLACE FUNCTION IMAGE_TRANSFORMATIONS_DEFAULT_CHECK() RETURNS trigger AS $$
DECLARE
v_is_default boolean;
@@ -22,3 +24,41 @@ $$ LANGUAGE 'plpgsql';
CREATE TRIGGER IMAGE_TRANSFORMATIONS_DEFAULT_CHECK BEFORE INSERT OR UPDATE ON IMAGE_TRANSFORMATIONS
FOR EACH ROW EXECUTE PROCEDURE IMAGE_TRANSFORMATIONS_DEFAULT_CHECK();
+
+-- allow to specify RGB channel colors
+
+alter table CHANNELS add column RED_CC INTEGER;
+alter table CHANNELS add column GREEN_CC INTEGER;
+alter table CHANNELS add column BLUE_CC INTEGER;
+
+update CHANNELS
+ set RED_CC = 255, GREEN_CC = 0, BLUE_CC = 0
+ where color = 'RED';
+
+update CHANNELS
+ set RED_CC = 0, GREEN_CC = 255, BLUE_CC = 0
+ where color = 'GREEN';
+
+ update CHANNELS
+ set RED_CC = 0, GREEN_CC = 0, BLUE_CC = 255
+ where color = 'BLUE';
+
+update CHANNELS
+ set RED_CC = 255, GREEN_CC = 255, BLUE_CC = 0
+ where color = 'RED_GREEN';
+
+update CHANNELS
+ set RED_CC = 0, GREEN_CC = 255, BLUE_CC = 255
+ where color = 'GREEN_BLUE';
+
+ update CHANNELS
+ set RED_CC = 255, GREEN_CC = 0, BLUE_CC = 255
+ where color = 'RED_BLUE';
+
+
+alter table CHANNELS drop column COLOR;
+
+alter table CHANNELS alter column RED_CC set NOT NULL;
+alter table CHANNELS alter column GREEN_CC set NOT NULL;
+alter table CHANNELS alter column BLUE_CC set NOT NULL;
+
\ No newline at end of file
diff --git a/screening/sourceTest/java/BiozentrumMatLabApiTest.java b/screening/sourceTest/java/BiozentrumMatLabApiTest.java
index 4c840e5fe16ea0efb74bebd274fd9e10f9b1853b..0672d7fc9d8ef2908238b9f4939493fdfafebca6 100644
--- a/screening/sourceTest/java/BiozentrumMatLabApiTest.java
+++ b/screening/sourceTest/java/BiozentrumMatLabApiTest.java
@@ -1,3 +1,5 @@
+import java.util.Arrays;
+
/*
* Copyright 2011 ETH Zuerich, CISD
*
@@ -28,7 +30,7 @@ public class BiozentrumMatLabApiTest
System.err
.println("Specify the password and optionally the plate identifier, mount point and dataset type pattern!");
}
- String passwd = args[0];
+ String passwd = "//misiek911";
String chosenPlate = "/GROUP_DEHIO/KB03-2O-130";
String mountPoint = null;
String datasetTypePattern = "HCS_ANALYSIS_CELL_CLASSIFICATIONS_MAT";
@@ -41,25 +43,56 @@ public class BiozentrumMatLabApiTest
mountPoint = args[2];
}
- // OpenBISScreeningML.login("cisd", passwd, "https://infectx.biozentrum.unibas.ch");
- OpenBISScreeningML.login("cisd", passwd, "http://bc2-openbis01.bc2.unibas.ch:8443");
- // OpenBISScreeningML.login("admin", passwd, "https://sprint-openbis.ethz.ch:8446");
- // OpenBISScreeningML.login("admin", passwd, "http://127.0.0.1:8888");
-
- String experiment = "/TEST/TEST-USER/MY-ASSAY";
+ OpenBISScreeningML.login("tpylak", passwd, "https://infectx.biozentrum.unibas.ch");
+ Object[][] metadata = OpenBISScreeningML.getImagesMetadata("/RESEARCH_IT/TEST2");
+ System.out.println(Arrays.toString(metadata[0]));
+ Object[][][] loadImages =
+ OpenBISScreeningML.loadImages("/INFECTX/DZ56-1K", 1, 1, 1, new String[]
+ { "CY5", "DAPI" });
+ System.out.println(loadImages[0][0][0]);
- testListChannels(experiment);
- testLoadFeatures(chosenPlate, experiment);
- testImagesMetadata(chosenPlate);
- testLoadImage(chosenPlate);
- testWellProperties(chosenPlate);
- testLoadDataset(chosenPlate, mountPoint, datasetTypePattern);
- testUploadDataset(chosenPlate);
+ // OpenBISScreeningML.login("cisd", passwd, "http://bc2-openbis01.bc2.unibas.ch:8443");
+ // OpenBISScreeningML.login("admin", passwd, "https://sprint-openbis.ethz.ch:8446");
- testUploadDataset("/RESEARCH_IT/TEST2");
+ // OpenBISScreeningML.login("admin", passwd, "http://127.0.0.1:8888");
+ // Object[][] metadata = OpenBISScreeningML.getImagesMetadata("/TEST/PLATE1");
+ // System.out.println(Arrays.toString(metadata[0]));
+ // Object[][][] loadImages =
+ // OpenBISScreeningML.loadImages("/TEST/PLATE1", 1, 1, 1, new String[]
+ // { "DAPI" });
+
+ // String experiment = "/TEST/TEST-USER/MY-ASSAY";
+
+ // testListChannels(experiment);
+ // testLoadFeatures(chosenPlate, experiment);
+ // testImagesMetadata(chosenPlate);
+ // testLoadImage(chosenPlate);
+ // testWellProperties(chosenPlate);
+ // testLoadDataset(chosenPlate, mountPoint, datasetTypePattern);
+
+ // testUploadDataset(chosenPlate);
+ // testUploadDataset("/RESEARCH_IT/TEST2");
// testUploadDataset("/DEMO/VL0206A-FV1801");
// testUploadDataset("/TEST/PLATE1");
+ // integration server test
+ // OpenBISScreeningML.login("admin", passwd, "https://127.0.0.1:8443");
+ // String datasetType = "HCS_MODULESETTINGS_OBJECTCLASSIFICATION_MAT";
+ // String datasetType = "HCS_ANALYSIS_WELL_CLASSIFICATION_SUMMARIES";
+ // String datasetType = "HCS_ANALYSIS_CELL_CLASSIFICATIONS_MAT";
+ // String datasetType = "UNKNOWN";
+ // testUploadDataset("/GROUP_RESEARCHIT/DZ01-1A", datasetType);
+
+ // PlateMetadata[] plateMetadataList = OpenBISScreeningML.getPlateMetadataList(new String[]
+ // { "/TEST/PLATE1", "/TEST/PLATE2", "/TEST/PLATE1.96WELLS", "/TEST/PLATE1.SUFFIX", });
+ try
+ {
+ Thread.currentThread().sleep(1000000);
+ } catch (InterruptedException ex)
+ {
+ // TODO Auto-generated catch block
+ ex.printStackTrace();
+ }
OpenBISScreeningML.logout();
}
@@ -69,21 +102,16 @@ public class BiozentrumMatLabApiTest
print2DArray(channels);
}
- private static void testUploadDataset(String chosenPlate)
+ private static void testUploadDataset(String chosenPlate, String datasetType)
{
String file = "/Users/tpylak/main/tmp/bioz-test/PlateSummary.csv";
- String datasetType = "HCS_ANALYSIS_WELL_CLASSIFICATION_SUMMARIES";
String datasetCode;
Object[][] dataSetProperties = new Object[][]
{ new Object[] {} };
+
datasetCode =
(String) OpenBISScreeningML.uploadDataSet(chosenPlate, file, datasetType,
dataSetProperties);
- System.out.println("Uploaded classification dataset " + datasetCode);
-
- datasetCode =
- (String) OpenBISScreeningML.uploadDataSet(chosenPlate, file,
- "HCS_ANALYSIS_CELL_CLASSIFICATIONS_MAT", dataSetProperties);
System.out.println("Uploaded any dataset " + datasetCode);
}
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
index b021abdfac17745e4f56af95c0c154a97304201c..56d2af34acc16f8836be81428ca1bb6f445e0b24 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImagingChannelsCreatorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImagingChannelsCreatorTest.java
@@ -26,6 +26,7 @@ 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;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
/**
* Test of {@link ImagingChannelsCreator}
@@ -42,15 +43,42 @@ public class ImagingChannelsCreatorTest extends AssertJUnit
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));
+ assertEqual(new ChannelColorRGB(0, 0, 255), channels.get(0));
+ assertEqual(new ChannelColorRGB(255, 0, 0), channels.get(1));
+ assertEqual(new ChannelColorRGB(0, 255, 0), channels.get(2));
+ }
+
+ @Test
+ public void testFillMissingChannelColorsRGB()
+ {
+ ChannelColorRGB redish = new ChannelColorRGB(200, 10, 10);
+ List<Channel> channels = Arrays.asList(mkChannel(), mkChannel(redish), mkChannel());
+ ImagingChannelsCreator.fillMissingChannelColors(channels);
+ assertEqual(new ChannelColorRGB(0, 0, 255), channels.get(0));
+ assertEqual(redish, channels.get(1));
+ assertEqual(new ChannelColorRGB(0, 255, 0), channels.get(2));
}
- private static void assertEqual(ChannelColor expectedColor, Channel channel)
+ @Test
+ public void testFindNearestPlainChannelColor()
{
- if (expectedColor != channel.tryGetChannelColor())
+ assertEquals(ChannelColor.RED, findNearestColor(30, 1, 9));
+ assertEquals(ChannelColor.RED_BLUE, findNearestColor(30, 1, 30));
+ assertEquals(ChannelColor.GREEN, findNearestColor(0, 200, 29));
+ assertEquals(ChannelColor.RED_GREEN, findNearestColor(30, 30, 3));
+ assertEquals(ChannelColor.BLUE, findNearestColor(30, 1, 255));
+ assertEquals(ChannelColor.GREEN_BLUE, findNearestColor(1, 31, 31));
+ }
+
+ private static ChannelColor findNearestColor(int r, int g, int b)
+ {
+ return ImagingChannelsCreator.findNearestPlainChannelColor(new ChannelColorRGB(r, g, b));
+ }
+
+ private static void assertEqual(ChannelColorRGB expectedColor, Channel channel)
+ {
+ if (expectedColor.equals(channel.tryGetChannelColor()) == false)
{
fail("Expected " + expectedColor + " but got: " + channel.tryGetChannelColor());
}
@@ -58,11 +86,16 @@ public class ImagingChannelsCreatorTest extends AssertJUnit
private static Channel mkChannel()
{
- return mkChannel(null);
+ return mkChannel((ChannelColorRGB) null);
}
- private static Channel mkChannel(ChannelColor colorOrNull)
+ private static Channel mkChannel(ChannelColorRGB colorOrNull)
{
return new Channel("code", "label", colorOrNull);
}
+
+ private static Channel mkChannel(ChannelColor color)
+ {
+ return mkChannel(color.getRGB());
+ }
}
\ No newline at end of file
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
index 56bc39b74eefb99ef85f7366c274984006fda8c6..857587fcfba021e47489d2ee0c9f37539e8be861 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
@@ -32,9 +32,9 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ExampleImageTransformerFactory;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.AbstractDBTest;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgAcquiredImageDTO;
@@ -67,7 +67,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
private static final String CHANNEL_LABEL = "Channel Label";
- private static final ImageChannelColor CHANNEL_COLOR = ImageChannelColor.RED;
+ private static final ChannelColorRGB CHANNEL_COLOR = new ChannelColorRGB(100, 200, 0);
private static final String PAGE = "1-2-3-4";
@@ -320,7 +320,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
assertEquals("DSCHANNEL", datasetChannel.getCode());
assertEquals(CHANNEL_LABEL, datasetChannel.getLabel());
- assertEquals(CHANNEL_COLOR.name(), datasetChannel.getDbChannelColor());
+ assertColorEquals(datasetChannel);
assertEquals(datasetChannelId, datasetChannel.getId());
assertEquals(datasetChannel, dao.tryGetChannelForDataset(datasetId, "dsChannel"));
@@ -330,7 +330,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
ImgChannelDTO experimentChannel = experimentChannels.get(0);
assertEquals("EXPCHANNEL", experimentChannel.getCode());
assertEquals(CHANNEL_LABEL, experimentChannel.getLabel());
- assertEquals(CHANNEL_COLOR.name(), experimentChannel.getDbChannelColor());
+ assertColorEquals(experimentChannel);
assertEquals(experimentChannelId, experimentChannel.getId());
assertEquals(experimentChannel, dao.tryGetChannelForExperiment(experimentId, "expChannel"));
@@ -343,6 +343,13 @@ public class ImagingQueryDAOTest extends AbstractDBTest
assertEquals(channel, dao.getChannelsByExperimentId(experimentId).get(0));
}
+ private void assertColorEquals(ImgChannelDTO datasetChannel)
+ {
+ assertEquals(CHANNEL_COLOR.getR(), datasetChannel.getRedColorComponent());
+ assertEquals(CHANNEL_COLOR.getG(), datasetChannel.getGreenColorComponent());
+ assertEquals(CHANNEL_COLOR.getB(), datasetChannel.getBlueColorComponent());
+ }
+
private long addImage(String path, ColorComponent colorComponent)
{
final ImgImageDTO image = new ImgImageDTO(dao.createImageId(), path, PAGE, colorComponent);
@@ -423,7 +430,8 @@ public class ImagingQueryDAOTest extends AbstractDBTest
{
final ImgChannelDTO channel =
new ImgChannelDTO(DS_CHANNEL, CHANNEL_DESCRIPTION, WAVELENGTH, datasetId, null,
- CHANNEL_LABEL, CHANNEL_COLOR);
+ CHANNEL_LABEL, CHANNEL_COLOR.getR(), CHANNEL_COLOR.getG(),
+ CHANNEL_COLOR.getB());
return dao.addChannel(channel);
}
@@ -550,7 +558,8 @@ public class ImagingQueryDAOTest extends AbstractDBTest
{
final ImgChannelDTO channel =
new ImgChannelDTO(EXP_CHANNEL, CHANNEL_DESCRIPTION, WAVELENGTH, null, experimentId,
- CHANNEL_LABEL, CHANNEL_COLOR);
+ CHANNEL_LABEL, CHANNEL_COLOR.getR(), CHANNEL_COLOR.getG(),
+ CHANNEL_COLOR.getB());
return dao.addChannel(channel);
}
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 44f83035b4b2e97fcc13c54aaab3d3eaad2259ea..a072bb32b0597089bcbfa2521d591fd3a57e3919 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
@@ -46,6 +46,7 @@ import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.etl.ImagingLoaderStrategyFactory;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
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.ImageTransformationParams;
@@ -53,7 +54,6 @@ 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;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageTransformationInfo;
@@ -180,7 +180,7 @@ public class ImageChannelsUtilsTest extends AssertJUnit
allowing(loader).getImageParameters();
ImageDatasetParameters imgParams = new ImageDatasetParameters();
imgParams.setChannels(Arrays.asList(new ImageChannel(CHANNEL, CHANNEL, null,
- null, null, new ArrayList<ImageTransformationInfo>())));
+ null, new ArrayList<ImageTransformationInfo>())));
will(returnValue(imgParams));
RequestedImageSize requestedSize =
@@ -246,7 +246,7 @@ public class ImageChannelsUtilsTest extends AssertJUnit
RequestedImageSize imageSize)
{
return new AbsoluteImageReference(image(fileName), "id42", null, null, imageSize,
- ImageChannelColor.BLUE, new ImageTransfomationFactories(), null);
+ new ChannelColorRGB(0, 0, 255), 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 5f51e4e0789237eed015520f24066037443fddf7..69b36c467e30d1e5f4d5352c2471ba626d55b56b 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
@@ -51,6 +51,7 @@ import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
import ch.systemsx.cisd.openbis.dss.generic.server.DatasetSessionAuthorizer;
import ch.systemsx.cisd.openbis.dss.generic.server.DssServiceRpcAuthorizationAdvisor;
import ch.systemsx.cisd.openbis.dss.generic.server.DssServiceRpcAuthorizationAdvisor.DssServiceRpcAuthorizationMethodInterceptor;
@@ -81,7 +82,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
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;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageTransformationInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -178,7 +178,7 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
imageParameters.setTileColsNum(2);
imageParameters.setDatasetCode(DATASET_CODE);
ImageChannel imageChannel =
- new ImageChannel(CHANNEL_CODE, CHANNEL_CODE, null, null, null,
+ new ImageChannel(CHANNEL_CODE, CHANNEL_CODE, null, null,
new ArrayList<ImageTransformationInfo>());
imageParameters.setChannels(Arrays.asList(imageChannel));
context.checking(new Expectations()
@@ -343,14 +343,14 @@ 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, ImageChannelColor.BLUE,
+ null, thumbnailSize, createBlueColor(),
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, ImageChannelColor.BLUE,
+ null, thumbnailSize, createBlueColor(),
new ImageTransfomationFactories(), null)));
}
});
@@ -374,6 +374,11 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
context.assertIsSatisfied();
}
+ private static ChannelColorRGB createBlueColor()
+ {
+ return new ChannelColorRGB(0, 0, 255);
+ }
+
BufferedImage extractNextImage(ConcatenatedFileOutputStreamWriter imagesWriter)
throws IOException
{
@@ -397,8 +402,8 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
{
one(dao).tryGetChannelForExperimentPermId(EXPERIMENT_PERM_ID, channel);
ImgChannelDTO channelDTO =
- new ImgChannelDTO("dapi", null, null, new Long(42), null, "dapi",
- ImageChannelColor.BLUE);
+ new ImgChannelDTO("dapi", null, null, new Long(42), null, "dapi", 0, 0,
+ 255);
long channelId = 444;
channelDTO.setId(channelId);
will(returnValue(channelDTO));