[LMS-2085] extend raw image dropbox to use image metadata : Added image...

[LMS-2085] extend raw image dropbox to use image metadata : Added image metadata parsing + tile location detection

SVN: 20429

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>

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java

+/*
+ * 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);
+        }
+    }
+
+}

screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractorTest.java

+/*
+ * 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&amp;#13;&amp;#10;Experiment set:ME20101116METADATA03&amp;#13;&amp;#10;Plate Screen&amp;#13;&amp;#10;Exposure: 10 ms&amp;#13;&amp;#10;Binning: 1 x 1&amp;#13;&amp;#10;Region: 1392 x 1040, offset at (0, 0)&amp;#13;&amp;#10;Acquired from Photometrics&amp;#13;&amp;#10;Subtract: Off&amp;#13;&amp;#10;Shading: Off&amp;#13;&amp;#10;Digitizer: 20 MHz&amp;#13;&amp;#10;Gain: Gain 1 (1x)&amp;#13;&amp;#10;Camera Shutter: Always Open&amp;#13;&amp;#10;Clear Count: 2&amp;#13;&amp;#10;Clear Mode: CLEAR PRE SEQUENCE&amp;#13;&amp;#10;Frames to Average: 1&amp;#13;&amp;#10;Trigger Mode: Normal (TIMED)&amp;#13;&amp;#10;Temperature: -29.95&amp;#13;&amp;#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;
+    }
+
+}