From 455ab7559bf5c20a7043ccb9ccee15443c349944 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 4 Aug 2010 11:04:54 +0000
Subject: [PATCH] SE-287 dynamix: read mapping of positions to wells from the
additional file
SVN: 17336
---
.../etl/dynamix/HCSImageFileExtractor.java | 58 +-
.../etl/dynamix/WellLocationMappingUtils.java | 151 +++
.../dynamix/WellLocationMappingUtilsTest.java | 62 +
.../cisd/openbis/dss/etl/dynamix/pos2loc.tsv | 1153 +++++++++++++++++
4 files changed, 1409 insertions(+), 15 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/WellLocationMappingUtils.java
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/WellLocationMappingUtilsTest.java
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/pos2loc.tsv
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java
index 88320361ef9..a3538845d5b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java
+++ b/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);
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/WellLocationMappingUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/WellLocationMappingUtils.java
new file mode 100644
index 00000000000..68d8100e1a4
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/WellLocationMappingUtils.java
@@ -0,0 +1,151 @@
+/*
+ * 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;
+ }
+ }
+
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/WellLocationMappingUtilsTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/WellLocationMappingUtilsTest.java
new file mode 100644
index 00000000000..e861742a58b
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/WellLocationMappingUtilsTest.java
@@ -0,0 +1,62 @@
+/*
+ * 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);
+
+ }
+
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/pos2loc.tsv b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/pos2loc.tsv
new file mode 100644
index 00000000000..b95b0be8f3a
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/pos2loc.tsv
@@ -0,0 +1,1153 @@
+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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+23 Right 1 47
+23 Left 1 48
+24 Right 2 47
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--
GitLab