LMS-1546 create a default image extractor

SVN: 16676

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
 
 # ---------------------------------------------------------------------------

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java

+/*
+ * 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);
+    }
+}

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);
     }
 }