From 8dece9ea7a12aa6ade3893c640183f6add84fe99 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Tue, 17 Aug 2010 10:50:26 +0000
Subject: [PATCH] LMS-1645 dynamix: parse timepoints correctly during dataset
upload
SVN: 17473
---
.../etl/dynamix/HCSImageFileExtractor.java | 53 ++++++++++++++++---
.../dynamix/HCSImageFileExtractorTest.java | 44 +++++++++++++++
2 files changed, 91 insertions(+), 6 deletions(-)
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractorTest.java
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 76f3e513e42..4361be170e0 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
@@ -17,8 +17,11 @@
package ch.systemsx.cisd.openbis.dss.etl.dynamix;
import java.io.File;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -28,7 +31,9 @@ import java.util.Set;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang.StringUtils;
+import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
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;
@@ -43,6 +48,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
*/
public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
{
+ private static final String DYNAMIX_TOKEN_SEPARATOR = "_";
+
private static final String POSITION_MAPPING_FILE_NAME = "pos2loc.tsv";
private final List<String> channelNames;
@@ -87,7 +94,7 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
*/
protected final Location tryGetPlateLocation(final String plateLocation)
{
- final String[] tokens = StringUtils.split(plateLocation, "_");
+ final String[] tokens = StringUtils.split(plateLocation, DYNAMIX_TOKEN_SEPARATOR);
Integer row = new Integer(tokens[0]);
Integer column = new Integer(tokens[1]);
return Location.tryCreateLocationFromRowAndColumn(row, column);
@@ -102,8 +109,8 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
@Override
protected final ImageFileInfo tryExtractImageInfo(File imageFile, SampleIdentifier datasetSample)
{
- final String baseName = FilenameUtils.getBaseName(imageFile.getPath());
- final String[] tokens = StringUtils.split(baseName, "_");
+ String baseName = FilenameUtils.getBaseName(imageFile.getPath());
+ String[] tokens = StringUtils.split(baseName, DYNAMIX_TOKEN_SEPARATOR);
if (tokens == null || tokens.length != 5)
{
if (operationLog.isDebugEnabled())
@@ -119,14 +126,48 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
// "left_dia_pos100_t20100227_152439.tif"
ImageFileInfo info = new ImageFileInfo();
// row_column - will be parsed later. It's unnecessary and should be refactored.
- info.setPlateLocationToken(wellLocation.getRow() + "_" + wellLocation.getColumn());
+ info.setPlateLocationToken(wellLocation.getRow() + DYNAMIX_TOKEN_SEPARATOR
+ + wellLocation.getColumn());
info.setWellLocationToken(null);
info.setChannelToken(tokens[1]);
+ long timepoint = getSecondsFromFirstMeasurement(imageFile, tokens);
+ info.setTimepointToken("" + timepoint);
+ return info;
+ }
+
+ private static long getSecondsFromFirstMeasurement(File imageFile, String[] tokens)
+ {
File[] images = imageFile.getParentFile().listFiles();
Arrays.sort(images);
- info.setTimepointToken("" + Arrays.asList(images).indexOf(imageFile));
- return info;
+ String firstMeasurementFilePath = images[0].getPath();
+
+ String firstMeasurementFileBaseName = FilenameUtils.getBaseName(firstMeasurementFilePath);
+ String[] firstMeasurementTokens =
+ StringUtils.split(firstMeasurementFileBaseName, DYNAMIX_TOKEN_SEPARATOR);
+
+ return getSecondsFromFirstMeasurement(tokens, firstMeasurementTokens);
+ }
+
+ @Private
+ static long getSecondsFromFirstMeasurement(String[] tokens, String[] firstMeasurementTokens)
+ {
+ Date firstMeasurementDate = parseDate(firstMeasurementTokens);
+ Date thisMeasurementDate = parseDate(tokens);
+ return (thisMeasurementDate.getTime() - firstMeasurementDate.getTime()) / 1000;
+ }
+
+ private static Date parseDate(String[] tokens)
+ {
+ // t20100227_152439 -> 20100227152439
+ String dateToken = tokens[3].substring(1) + tokens[4];
+ try
+ {
+ return new SimpleDateFormat("yyyymmddhhmmss").parse(dateToken);
+ } catch (ParseException ex)
+ {
+ throw new EnvironmentFailureException("Cannot parse the data in the file name: " + ex);
+ }
}
private WellLocation getWellLocation(File imageFile, final String[] tokens)
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractorTest.java
new file mode 100644
index 00000000000..338d9d5adae
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractorTest.java
@@ -0,0 +1,44 @@
+/*
+ * 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 org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.rinn.restrictions.Friend;
+
+/**
+ * Tests of {@link HCSImageFileExtractor}
+ *
+ * @author Tomasz Pylak
+ */
+@Friend(toClasses = HCSImageFileExtractor.class)
+public class HCSImageFileExtractorTest extends AssertJUnit
+{
+ @Test
+ public void testParseTimepoint()
+ {
+ String[] tokensThisMeasurement = new String[]
+ { "left", "dia", "pos100", "t20100227", "162542" };
+ String[] tokensFirstMeasurement = new String[]
+ { "left", "dia", "pos100", "t20100227", "152439" };
+ long secondsFromFirstMeasurement =
+ HCSImageFileExtractor.getSecondsFromFirstMeasurement(tokensThisMeasurement,
+ tokensFirstMeasurement);
+ assertEquals(3 + 60 + 3600, secondsFromFirstMeasurement);
+ }
+}
--
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