diff --git a/screening/.classpath b/screening/.classpath
index c02a69ae620240b1f757651bd92614b6eca14657..314d7bc3a608d1dfee5cf1486f3d9996ce55d894 100644
--- a/screening/.classpath
+++ b/screening/.classpath
@@ -47,5 +47,6 @@
<classpathentry kind="lib" path="/libraries/sybit-image-viewer/image-viewer.jar"/>
<classpathentry kind="lib" path="/libraries/jython/jython.jar" sourcepath="/libraries/jython/src.zip"/>
<classpathentry kind="lib" path="/libraries/hibernate/hibernate3.jar" sourcepath="/libraries/hibernate/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/bioformats/bioformats.jar" sourcepath="/libraries/bioformats/bioformats_src.zip"/>
<classpathentry kind="output" path="targets/www/WEB-INF/classes"/>
</classpath>
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java
new file mode 100644
index 0000000000000000000000000000000000000000..86171607e97f2174c21137bf661012243fc8cb3e
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java
@@ -0,0 +1,158 @@
+/*
+ * 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.biozentrum;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeSet;
+
+import loci.formats.IFormatReader;
+import loci.formats.ImageReader;
+import loci.formats.gui.BufferedImageReader;
+import loci.formats.in.DefaultMetadataOptions;
+import loci.formats.in.MetadataLevel;
+import loci.formats.in.MetadataOptions;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Location;
+
+/**
+ * @author Kaloyan Enimanev
+ */
+public class ImageMetadataExtractor
+{
+
+ static final String POSITION_X_PROP = "stage-position-x";
+
+ static final String POSITION_Y_PROP = "stage-position-y";
+
+ public static Map<String, Object> extractMetadata(File imageFile)
+ {
+ HashMap<String, Object> result = new HashMap<String, Object>();
+ // initialize the reader
+ IFormatReader reader = new BufferedImageReader(new ImageReader());
+ MetadataOptions metaOptions = new DefaultMetadataOptions(MetadataLevel.ALL);
+ reader.setMetadataOptions(metaOptions);
+
+ try
+ {
+ reader.setId(imageFile.getAbsolutePath());
+ nullSafeAddAll(result, reader.getGlobalMetadata());
+ nullSafeAddAll(result, reader.getSeriesMetadata());
+ } catch (Exception ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ } finally
+ {
+ close(reader);
+ }
+
+ return result;
+ }
+
+ /**
+ * @param tileToMetadataMap mapping from tile number to image metadata
+ */
+ public static Map<Integer/* tile number */, Location> tryGetTileMapping(
+ Map<Integer/* tile number */, Map<String/* name */, Object/* value */>> tileToMetadataMap)
+ {
+ Set<Number> xCoords = new TreeSet<Number>();
+ Set<Number> yCoords = new TreeSet<Number>();
+ for (Map<String, Object> metadata : tileToMetadataMap.values())
+ {
+ xCoords.add(extractXCoord(metadata));
+ yCoords.add(extractYCoord(metadata));
+ }
+
+ List<Number> sortedXCoords = new ArrayList<Number>(xCoords);
+ List<Number> sortedYCoords = new ArrayList<Number>(yCoords);
+
+ Map<Integer, Location> result = new HashMap<Integer, Location>();
+ for (Entry<Integer, Map<String, Object>> entry : tileToMetadataMap.entrySet())
+ {
+ Integer tileNumber = entry.getKey();
+ Location location = extractLocation(entry.getValue(), sortedXCoords, sortedYCoords);
+ result.put(tileNumber, location);
+ }
+ return result;
+ }
+
+ private static void nullSafeAddAll(HashMap<String, Object> accumulator,
+ Hashtable<String, Object> toAdd)
+ {
+ if (toAdd != null)
+ {
+ accumulator.putAll(toAdd);
+ }
+
+ }
+
+ private static void close(IFormatReader reader)
+ {
+ try
+ {
+ reader.close();
+ } catch (Exception ex)
+ {
+ // do not throw exception
+ }
+ }
+
+ private static Location extractLocation(Map<String, Object> metadata, List<Number> xCoords,
+ List<Number> yCoords)
+ {
+ Number x = extractXCoord(metadata);
+ Number y = extractYCoord(metadata);
+
+ int locationX = xCoords.indexOf(x);
+ int locationY = yCoords.indexOf(y);
+
+ Location location = new Location(locationY, locationX);
+ return location;
+ }
+
+ private static Number extractXCoord(Map<String, Object> metadata)
+ {
+ return extractNumber(metadata, POSITION_X_PROP);
+ }
+
+ private static Number extractYCoord(Map<String, Object> metadata)
+ {
+ return extractNumber(metadata, POSITION_Y_PROP);
+ }
+
+ private static Number extractNumber(Map<String, Object> metadata, String propName)
+ {
+ String numberAsString = (String) metadata.get(propName);
+ try
+ {
+ return Double.valueOf(numberAsString);
+ } catch (NumberFormatException nfe)
+ {
+ throw UserFailureException.fromTemplate(
+ "Cannot parse number for property %s with value %s", propName, numberAsString);
+ }
+ }
+
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..cc52ffe1cc9227bdaaafb4b0ceb5138117e0491b
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractorTest.java
@@ -0,0 +1,179 @@
+/*
+ * 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.biozentrum;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Location;
+
+/**
+ * @author Kaloyan Enimanev
+ */
+public class ImageMetadataExtractorTest extends AssertJUnit
+{
+
+ public final String FILE_NAME =
+ "./sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/demo.tif";
+
+ @Test
+ public void testMetaDataExtraction() throws Exception
+ {
+ File imageFile = new File(FILE_NAME);
+ Map<String, Object> metaData = ImageMetadataExtractor.extractMetadata(imageFile);
+ List<String> sortedKeys = new ArrayList<String>(metaData.keySet());
+ Collections.sort(sortedKeys);
+
+ StringBuilder output = new StringBuilder();
+ for (String key : sortedKeys)
+ {
+ Object value = metaData.get(key);
+ output.append(key + ": " + value);
+ output.append("\n");
+ }
+
+ assertEquals(
+ "<prop id=\"Description\" type=\"string\" value=\"Experiment base name:ME20101116METADATA03&#13;&#10;Experiment set:ME20101116METADATA03&#13;&#10;Plate Screen&#13;&#10;Exposure: 10 ms&#13;&#10;Binning: 1 x 1&#13;&#10;Region: 1392 x 1040, offset at (0, 0)&#13;&#10;Acquired from Photometrics&#13;&#10;Subtract: Off&#13;&#10;Shading: Off&#13;&#10;Digitizer: 20 MHz&#13;&#10;Gain: Gain 1 (1x)&#13;&#10;Camera Shutter: Always Open&#13;&#10;Clear Count: 2&#13;&#10;Clear Mode: CLEAR PRE SEQUENCE&#13;&#10;Frames to Average: 1&#13;&#10;Trigger Mode: Normal (TIMED)&#13;&#10;Temperature: -29.95&#13;&#10;\">\n"
+ + "<prop id=\"stage-label\" type=\"string\" value=\"F09: Site 1\">\n"
+ + "ApplicationName: MetaMorph\n"
+ + "ApplicationVersion: 3.1.0.79\n"
+ + "Binning: 1 x 1\n"
+ + "BitsPerSample: 16\n"
+ + "Camera Bit Depth: 12\n"
+ + "Camera Shutter: Always Open\n"
+ + "Clear Count: 2\n"
+ + "Clear Mode: CLEAR PRE SEQUENCE\n"
+ + "Compression: Uncompressed\n"
+ + "DateTime: 20101121 16:52:52.986\n"
+ + "Digitizer: 20 MHz\n"
+ + "Experiment base name: ME20101116METADATA03\n"
+ + "Experiment set: ME20101116METADATA03\n"
+ + "Exposure: 10 ms\n"
+ + "Frames to Average: 1\n"
+ + "Gain: Gain 1 (1x)\n"
+ + "ImageLength: 1040\n"
+ + "ImageWidth: 1392\n"
+ + "ImageXpress Micro Filter Cube: Texas Red\n"
+ + "ImageXpress Micro Objective: 10X S Fluor\n"
+ + "ImageXpress Micro Shutter: Closed\n"
+ + "Laser focus score: 36.4006\n"
+ + "MetaDataPhotometricInterpretation: Monochrome\n"
+ + "MetaDataVersion: 1\n"
+ + "NewSubfileType: 2\n"
+ + "NumberOfChannels: 1\n"
+ + "PhotometricInterpretation: BlackIsZero\n"
+ + "Region: 1392 x 1040, offset at (0, 0)\n"
+ + "SamplesPerPixel: 1\n"
+ + "Shading: Off\n"
+ + "Software: MetaSeries\n"
+ + "Subtract: Off\n"
+ + "Temperature: -29.95\n"
+ + "Trigger Mode: Normal (TIMED)\n"
+ + "X position for position #1: 73296.5\n"
+ + "Y position for position #1: 25554.2\n"
+ + "_IllumSetting_: Cy3\n"
+ + "_MagNA_: 0.5\n"
+ + "_MagRI_: 1\n"
+ + "_MagSetting_: 10X S Fluor\n"
+ + "acquisition-time-local: 20101121 16:52:52.986\n"
+ + "autoscale-max-percent: 0\n"
+ + "autoscale-min-percent: 0\n"
+ + "autoscale-state: off\n"
+ + "bits-per-pixel: 16\n"
+ + "camera-binning-x: 1\n"
+ + "camera-binning-y: 1\n"
+ + "camera-chip-offset-x: 0\n"
+ + "camera-chip-offset-y: 0\n"
+ + "gamma: 1\n"
+ + "gray-calibration-curve-fit-algorithm: 4\n"
+ + "gray-calibration-max: -1\n"
+ + "gray-calibration-min: -1\n"
+ + "gray-calibration-units: \n"
+ + "gray-calibration-values: \n"
+ + "image-name: Cy3\n"
+ + "look-up-table-name: Set By Wavelength\n"
+ + "look-up-table-type: by-wavelength\n"
+ + "modification-time-local: 20101121 16:52:53.50\n"
+ + "number-of-planes: 1\n"
+ + "photonegative-mode: off\n"
+ + "pixel-size-x: 1392\n"
+ + "pixel-size-y: 1040\n"
+ + "plane-guid: {70EAFB69-A568-464E-9EE2-4479767F96EF}\n"
+ + "plane-type: plane\n"
+ + "scale-max: 1058\n"
+ + "scale-min: 96\n"
+ + "spatial-calibration-state: on\n"
+ + "spatial-calibration-units: um\n"
+ + "spatial-calibration-x: 0.645\n"
+ + "spatial-calibration-y: 0.645\n"
+ + "stage-label: F09 : Site 1\n"
+ + "stage-position-x: 73296.5\n"
+ + "stage-position-y: 25554.2\n"
+ + "threshold-color: 4080ff\n"
+ + "threshold-high: 65535\n"
+ + "threshold-low: 0\n"
+ + "threshold-state: ThresholdOff\n"
+ + "timestamp 0: 2010-11-21T16:52:52\n"
+ + "wavelength: 624\n" + "z-position: 11145.7\n" + "zoom-percent: 50\n",
+ output.toString());
+ }
+
+ @Test
+ public void testTileMapping() throws Exception
+ {
+ Map<Integer, Map<String, Object>> tileMetadata =
+ new HashMap<Integer, Map<String, Object>>();
+
+ tileMetadata.put(1, createTileMetadata(1, 1));
+ tileMetadata.put(2, createTileMetadata(2, 2));
+ tileMetadata.put(3, createTileMetadata(3, 3));
+ tileMetadata.put(4, createTileMetadata(1, 2));
+ tileMetadata.put(5, createTileMetadata(3, 2));
+
+ Map<Integer, Location> locations = ImageMetadataExtractor.tryGetTileMapping(tileMetadata);
+
+ assertLocation(0, 0, 1, locations);
+ assertLocation(1, 1, 2, locations);
+ assertLocation(2, 2, 3, locations);
+ assertLocation(0, 1, 4, locations);
+ assertLocation(2, 1, 5, locations);
+
+ }
+
+ private void assertLocation(int column, int row, int tileNumber, Map<Integer, Location> locations)
+ {
+ Location location = locations.get(tileNumber);
+ assertEquals(column, location.getColumn());
+ assertEquals(row, location.getRow());
+ }
+
+ private Map<String, Object> createTileMetadata(double x, double y)
+ {
+ Map<String, Object> metadata = new HashMap<String, Object>();
+ metadata.put(ImageMetadataExtractor.POSITION_X_PROP, String.valueOf(x));
+ metadata.put(ImageMetadataExtractor.POSITION_Y_PROP, String.valueOf(y));
+ return metadata;
+ }
+
+}