diff --git a/screening/dist/etc/service.properties b/screening/dist/etc/service.properties
index fa6fce88ca4f5a0529dd93d6102025a54197e167..fb363b46c7be2e6e2516a43c8eee78ce55f50516 100644
--- a/screening/dist/etc/service.properties
+++ b/screening/dist/etc/service.properties
@@ -241,7 +241,7 @@ merged-channels-images.storage-processor.channel-names = green, blue
merged-channels-images.storage-processor.well_geometry = 3x3
merged-channels-images.storage-processor.file-extractor = ch.systemsx.cisd.openbis.dss.etl.lmc.HCSImageFileExtractor
merged-channels-images.storage-processor.data-source = imaging-db
-# Available values: RED, BLUE or GREEN
+# Available values: RED, GREEN or BLUE
merged-channels-images.storage-processor.extract-single-image-channels = GREEN, BLUE
# ---------------------------------------------------------------------------
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
new file mode 100644
index 0000000000000000000000000000000000000000..83968201db4a6175d66cf2ed956cc9cad378d081
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
@@ -0,0 +1,146 @@
+/*
+ * Copyright 2008 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.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+import java.util.Set;
+
+import ch.systemsx.cisd.bds.hcs.Geometry;
+import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.filesystem.FileOperations;
+import ch.systemsx.cisd.openbis.dss.etl.AbstractHCSImageFileExtractor;
+import ch.systemsx.cisd.openbis.dss.etl.AcquiredPlateImage;
+import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ColorComponent;
+
+/**
+ * Generic <code>IHCSImageFileExtractor</code> implementation.
+ *
+ * @author Tomasz Pylak
+ */
+public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
+{
+ private static final String[] IMAGE_EXTENSIONS = new String[]
+ { "tif", "tiff", "jpg", "jpeg", "gif", "png" };
+
+ private final List<String> channelNames;
+
+ private final List<ColorComponent> channelColorComponentsOrNull;
+
+ private final Geometry wellGeometry;
+
+ public HCSImageFileExtractor(final Properties properties)
+ {
+ super(properties);
+ this.channelNames = extractChannelNames(properties);
+ this.channelColorComponentsOrNull = tryGetChannelComponents(properties);
+ checkChannelsAndColorComponents();
+ this.wellGeometry = getWellGeometry(properties);
+ }
+
+ private void checkChannelsAndColorComponents()
+ {
+ if (channelColorComponentsOrNull != null
+ && channelColorComponentsOrNull.size() != channelNames.size())
+ {
+ throw ConfigurationFailureException.fromTemplate(
+ "There should be exactly one color component for each channel name."
+ + " Correct the list of values for '%s' property.",
+ AbstractHCSImageFileExtractor.EXTRACT_SINGLE_IMAGE_CHANNELS_PROPERTY);
+ }
+ }
+
+ /**
+ * Extracts the well location from given <var>value</var>, following the convention adopted
+ * here.<br>
+ * Here is a numbering example for a 3x3 plate:<br>
+ * 1 4 7<br>
+ * 2 5 8<br>
+ * 3 6 9<br>
+ * <p>
+ * Returns <code>null</code> if the operation fails.
+ * </p>
+ */
+ @Override
+ protected final Location tryGetWellLocation(final String wellLocation)
+ {
+ try
+ {
+ int tileNumber = Integer.parseInt(wellLocation);
+ Location letterLoc = Location.tryCreateLocationFromPosition(tileNumber, wellGeometry);
+ // transpose rows with columns
+ return new Location(letterLoc.getY(), letterLoc.getX());
+ } catch (final NumberFormatException ex)
+ {
+ // Nothing to do here. Rest of the code can handle this.
+ }
+ return null;
+ }
+
+ @Override
+ protected final List<File> listImageFiles(final File directory)
+ {
+ return FileOperations.getInstance().listFiles(directory, IMAGE_EXTENSIONS, true);
+ }
+
+ @Override
+ protected final List<AcquiredPlateImage> getImages(String channelStr, Location plateLocation,
+ Location wellLocation, String imageRelativePath)
+ {
+ List<AcquiredPlateImage> images = new ArrayList<AcquiredPlateImage>();
+ checkChannelsAndColorComponents();
+
+ if (channelColorComponentsOrNull != null)
+ {
+ for (int i = 0; i < channelColorComponentsOrNull.size(); i++)
+ {
+ ColorComponent colorComponent = channelColorComponentsOrNull.get(i);
+ String channelName = channelNames.get(i);
+ images.add(createImage(plateLocation, wellLocation, imageRelativePath, channelName,
+ colorComponent));
+ }
+ } else
+ {
+ ensureChannelExist(channelStr);
+ images
+ .add(createImage(plateLocation, wellLocation, imageRelativePath, channelStr,
+ null));
+ }
+ return images;
+ }
+
+ private void ensureChannelExist(String channelName)
+ {
+ if (channelNames.indexOf(channelName.toUpperCase()) == -1)
+ {
+ throw UserFailureException.fromTemplate(
+ "Channel '%s' is not one of: %s. Change the configuration.", channelName,
+ channelNames);
+ }
+ }
+
+ @Override
+ protected Set<Channel> getAllChannels()
+ {
+ return createChannels(channelNames);
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/lmc/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/lmc/HCSImageFileExtractor.java
index ae348077d1b45383ea363dba31dc0d0d4cc4ac7c..d6c744738c6a2ffe51bef4c57323264373abe3ed 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/lmc/HCSImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/lmc/HCSImageFileExtractor.java
@@ -16,131 +16,17 @@
package ch.systemsx.cisd.openbis.dss.etl.lmc;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
import java.util.Properties;
-import java.util.Set;
-
-import ch.systemsx.cisd.bds.hcs.Geometry;
-import ch.systemsx.cisd.bds.hcs.Location;
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.filesystem.FileOperations;
-import ch.systemsx.cisd.openbis.dss.etl.AbstractHCSImageFileExtractor;
-import ch.systemsx.cisd.openbis.dss.etl.AcquiredPlateImage;
-import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ColorComponent;
/**
* A <code>IHCSImageFileExtractor</code> implementation suitable for <i>LMC</i>.
*
* @author Tomasz Pylak
*/
-public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
+public class HCSImageFileExtractor extends ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractor
{
- private static final String[] IMAGE_EXTENSIONS = new String[]
- { "tif", "tiff", "jpg", "jpeg", "gif", "png" };
-
- private final List<String> channelNames;
-
- private final List<ColorComponent> channelColorComponentsOrNull;
-
- private final Geometry wellGeometry;
-
public HCSImageFileExtractor(final Properties properties)
{
super(properties);
- this.channelNames = extractChannelNames(properties);
- this.channelColorComponentsOrNull = tryGetChannelComponents(properties);
- checkChannelsAndColorComponents();
- this.wellGeometry = getWellGeometry(properties);
- }
-
- private void checkChannelsAndColorComponents()
- {
- if (channelColorComponentsOrNull != null
- && channelColorComponentsOrNull.size() != channelNames.size())
- {
- throw ConfigurationFailureException.fromTemplate(
- "There should be exactly one color component for each channel name."
- + " Correct the list of values for '%s' property.",
- AbstractHCSImageFileExtractor.EXTRACT_SINGLE_IMAGE_CHANNELS_PROPERTY);
- }
- }
-
- /**
- * Extracts the well location from given <var>value</var>, following the convention adopted
- * here.<br>
- * Here is a numbering example for a 3x3 plate:<br>
- * 1 4 7<br>
- * 2 5 8<br>
- * 3 6 9<br>
- * <p>
- * Returns <code>null</code> if the operation fails.
- * </p>
- */
- @Override
- protected final Location tryGetWellLocation(final String wellLocation)
- {
- try
- {
- int tileNumber = Integer.parseInt(wellLocation);
- Location letterLoc = Location.tryCreateLocationFromPosition(tileNumber, wellGeometry);
- // transpose rows with columns
- return new Location(letterLoc.getY(), letterLoc.getX());
- } catch (final NumberFormatException ex)
- {
- // Nothing to do here. Rest of the code can handle this.
- }
- return null;
- }
-
- @Override
- protected final List<File> listImageFiles(final File directory)
- {
- return FileOperations.getInstance().listFiles(directory, IMAGE_EXTENSIONS, true);
- }
-
- @Override
- protected final List<AcquiredPlateImage> getImages(String channelStr, Location plateLocation,
- Location wellLocation, String imageRelativePath)
- {
- List<AcquiredPlateImage> images = new ArrayList<AcquiredPlateImage>();
- checkChannelsAndColorComponents();
-
- if (channelColorComponentsOrNull != null)
- {
- for (int i = 0; i < channelColorComponentsOrNull.size(); i++)
- {
- ColorComponent colorComponent = channelColorComponentsOrNull.get(i);
- String channelName = channelNames.get(i);
- images.add(createImage(plateLocation, wellLocation, imageRelativePath, channelName,
- colorComponent));
- }
- } else
- {
- ensureChannelExist(channelStr);
- images
- .add(createImage(plateLocation, wellLocation, imageRelativePath, channelStr,
- null));
- }
- return images;
- }
-
- private void ensureChannelExist(String channelName)
- {
- if (channelNames.indexOf(channelName.toUpperCase()) == -1)
- {
- throw UserFailureException.fromTemplate(
- "Channel '%s' is not one of: %s. Change the configuration.", channelName,
- channelNames);
- }
- }
-
- @Override
- protected Set<Channel> getAllChannels()
- {
- return createChannels(channelNames);
}
}