SE-287 dynamix: read mapping of positions to wells from the additional file

SVN: 17336

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

@@ -19,7 +19,9 @@ package ch.systemsx.cisd.openbis.dss.etl.dynamix;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Properties;
 import java.util.Set;
 
@@ -30,7 +32,9 @@ import ch.systemsx.cisd.bds.hcs.Location;
 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.dynamix.WellLocationMappingUtils.DynamixWellPosition;
 import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
 
 /**
  * Image extractor for DynamiX project - work in progress.
@@ -39,12 +43,17 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
  */
 public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
 {
+    private static final String POSITION_MAPPING_FILE_NAME = "pos2loc.tsv";
+
     private final List<String> channelNames;
 
+    private final Map<File/* mapping file */, Map<DynamixWellPosition, WellLocation>> wellLocationMapCache;
+
     public HCSImageFileExtractor(final Properties properties)
     {
         super(properties);
         this.channelNames = extractChannelNames(properties);
+        this.wellLocationMapCache = new HashMap<File, Map<DynamixWellPosition, WellLocation>>();
     }
 
     @Override
@@ -74,23 +83,14 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
 
     @Override
     /*
-     * Note: the right mapping for DynamiX project should be found, this one is just to fit all
-     * images on the 24x48 plate. Odd columns contain right position, even contain left position.
-     * @param plateLocation - format left_pos100
+     * @param plateLocation - format row_column
      */
     protected final Location tryGetPlateLocation(final String plateLocation)
     {
         final String[] tokens = StringUtils.split(plateLocation, "_");
-        boolean isLeft = (tokens[0].equalsIgnoreCase("left"));
-        Integer pos = Integer.parseInt(tokens[1].substring(3));
-        assert pos > 0 && pos <= 576 : "wrong position: " + pos;
-
-        int sideShift = isLeft ? 1 : 0;
-        int singleSidedMaxColumn = 24;
-        int row = ((pos - 1) / singleSidedMaxColumn);
-        int col = ((pos - 1) % singleSidedMaxColumn) * 2 + sideShift;
-
-        return new Location(col + 1, row + 1);
+        Integer row = new Integer(tokens[0]);
+        Integer column = new Integer(tokens[1]);
+        return Location.tryCreateLocationFromRowAndColumn(row, column);
     }
 
     @Override
@@ -114,10 +114,12 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
             }
             return null;
         }
+        WellLocation wellLocation = getWellLocation(imageFile, tokens);
+
         // "left_dia_pos100_t20100227_152439.tif"
         ImageFileInfo info = new ImageFileInfo();
-        // left_pos100
-        info.setPlateLocationToken(tokens[0] + "_" + tokens[2]);
+        // row_column - will be parsed later. It's unnecessary and should be refactored.
+        info.setPlateLocationToken(wellLocation.getRow() + "_" + wellLocation.getColumn());
         info.setWellLocationToken(null);
         info.setChannelToken(tokens[1]);
 
@@ -126,4 +128,30 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
         info.setTimepointToken("" + Arrays.asList(images).indexOf(imageFile));
         return info;
     }
+
+    private WellLocation getWellLocation(File imageFile, final String[] tokens)
+    {
+        Map<DynamixWellPosition, WellLocation> map = getWellLocationMapping(imageFile);
+        DynamixWellPosition wellPos =
+                WellLocationMappingUtils.parseWellPosition(tokens[0], tokens[2]);
+        return map.get(wellPos);
+    }
+
+    private Map<DynamixWellPosition, WellLocation> getWellLocationMapping(File imageFile)
+    {
+        File mappingFile = getMappingFile(imageFile);
+        Map<DynamixWellPosition, WellLocation> map = wellLocationMapCache.get(mappingFile);
+        if (map == null)
+        {
+            map = WellLocationMappingUtils.parseWellLocationMap(mappingFile);
+            wellLocationMapCache.put(mappingFile, map);
+        }
+        return map;
+    }
+
+    private static File getMappingFile(File imageFile)
+    {
+        File mappingDir = imageFile.getParentFile().getParentFile().getParentFile();
+        return new File(mappingDir, POSITION_MAPPING_FILE_NAME);
+    }
 }

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/WellLocationMappingUtils.java

+/*
+ * Copyright 2010 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.dynamix;
+
+import java.io.File;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import ch.systemsx.cisd.common.annotation.BeanProperty;
+import ch.systemsx.cisd.common.parser.TabFileLoader;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
+
+/**
+ * Utility methods to map DynamiX specific position to well location.
+ * 
+ * @author Tomasz Pylak
+ */
+class WellLocationMappingUtils
+{
+    public static Map<DynamixWellPosition, WellLocation> parseWellLocationMap(File mappingFile)
+    {
+        final TabFileLoader<MappingEntry> parser =
+                new TabFileLoader<MappingEntry>(MappingEntry.class);
+        List<MappingEntry> mappingEntries = parser.load(mappingFile);
+        return createMapping(mappingEntries);
+    }
+
+    public static DynamixWellPosition parseWellPosition(String sideToken, String posToken)
+    {
+        String posNumber = posToken.substring("pos".length());
+        return new DynamixWellPosition(new Integer(posNumber), isRight(sideToken));
+    }
+
+    private static Map<DynamixWellPosition, WellLocation> createMapping(
+            List<MappingEntry> mappingEntries)
+    {
+        Map<DynamixWellPosition, WellLocation> mapping =
+                new HashMap<DynamixWellPosition, WellLocation>();
+        for (MappingEntry entry : mappingEntries)
+        {
+            DynamixWellPosition wellPos = parseWellPosition(entry.getSide(), entry.getPosition());
+
+            int row = new Integer(entry.getRow());
+            int col = new Integer(entry.getColumn());
+            WellLocation wellLoc = new WellLocation(row, col);
+
+            mapping.put(wellPos, wellLoc);
+        }
+        return mapping;
+    }
+
+    private static boolean isRight(String sideToken)
+    {
+        return sideToken.equalsIgnoreCase("Right");
+    }
+
+    public static class MappingEntry extends AbstractHashable
+    {
+        private String position;
+
+        private String side;
+
+        private String row;
+
+        private String column;
+
+        public String getPosition()
+        {
+            return position;
+        }
+
+        @BeanProperty(label = "position")
+        public void setPosition(String position)
+        {
+            this.position = position;
+        }
+
+        public String getSide()
+        {
+            return side;
+        }
+
+        @BeanProperty(label = "Side")
+        public void setSide(String side)
+        {
+            this.side = side;
+        }
+
+        public String getRow()
+        {
+            return row;
+        }
+
+        @BeanProperty(label = "row")
+        public void setRow(String row)
+        {
+            this.row = row;
+        }
+
+        public String getColumn()
+        {
+            return column;
+        }
+
+        @BeanProperty(label = "column")
+        public void setColumn(String column)
+        {
+            this.column = column;
+        }
+    }
+
+    static class DynamixWellPosition extends AbstractHashable
+    {
+        private final int position;
+
+        private final boolean isRight;
+
+        public DynamixWellPosition(int position, boolean isRight)
+        {
+            this.position = position;
+            this.isRight = isRight;
+        }
+
+        public int getPosition()
+        {
+            return position;
+        }
+
+        public boolean isRight()
+        {
+            return isRight;
+        }
+    }
+
+}

screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/WellLocationMappingUtilsTest.java

+/*
+ * Copyright 2010 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.dynamix;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Map;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.dss.etl.dynamix.WellLocationMappingUtils.DynamixWellPosition;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
+
+/**
+ * Tests of {@link WellLocationMappingUtils}
+ * 
+ * @author Tomasz Pylak
+ */
+public class WellLocationMappingUtilsTest extends AssertJUnit
+{
+    @Test
+    public void testMapping() throws IOException
+    {
+        Map<DynamixWellPosition, WellLocation> map =
+                WellLocationMappingUtils.parseWellLocationMap(new File(
+                        "sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/pos2loc.tsv"));
+        DynamixWellPosition pos = new DynamixWellPosition(100, true);
+
+        WellLocation wellLocation = map.get(pos);
+        assertEquals(wellLocation.getRow(), 5);
+        assertEquals(wellLocation.getColumn(), 17);
+    }
+
+    @Test
+    public void testPositionParsing() throws IOException
+    {
+        DynamixWellPosition expectedPos = new DynamixWellPosition(100, true);
+        DynamixWellPosition pos = WellLocationMappingUtils.parseWellPosition("Right", "100");
+        assertEquals(expectedPos, pos);
+
+        expectedPos = new DynamixWellPosition(5, false);
+        pos = WellLocationMappingUtils.parseWellPosition("Left", "5");
+        assertEquals(expectedPos, pos);
+
+    }
+
+}

screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/pos2loc.tsv

+position	side	row	column
+1	Right	1	3
+1	Left	1	4
+2	Right	1	5
+2	Left	1	6
+3	Right	1	7
+3	Left	1	8
+4	Right	1	9
+4	Left	1	10
+5	Right	1	11
+5	Left	1	12
+6	Right	1	13
+6	Left	1	14
+7	Right	1	15
+7	Left	1	16
+8	Right	1	17
+8	Left	1	18
+9	Right	1	19
+9	Left	1	20
+10	Right	1	21
+10	Left	1	22
+11	Right	1	23
+11	Left	1	24
+12	Right	1	25
+12	Left	1	26
+13	Right	1	27
+13	Left	1	28
+14	Right	1	29
+14	Left	1	30
+15	Right	1	31
+15	Left	1	32
+16	Right	1	33
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+41	Left	2	14
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+43	Right	2	9
+43	Left	2	10
+44	Right	2	7
+44	Left	2	8
+45	Right	2	5
+45	Left	2	6
+46	Right	2	3
+46	Left	2	4
+47	Right	3	3
+47	Left	3	4
+48	Right	3	5
+48	Left	3	6
+49	Right	3	7
+49	Left	3	8
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\ No newline at end of file