diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/CSVToCanonicalFeatureVector.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/CSVToCanonicalFeatureVector.java
new file mode 100644
index 0000000000000000000000000000000000000000..a098b039c5e7c7c1f4703ab12416a167037e0c14
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/CSVToCanonicalFeatureVector.java
@@ -0,0 +1,270 @@
+/*
+ * 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.dataaccess.fvec;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+
+import ch.systemsx.cisd.base.convert.NativeTaggedArray;
+import ch.systemsx.cisd.base.mdarray.MDDoubleArray;
+import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.common.geometry.Point;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureDefDTO;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureValuesDTO;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class CSVToCanonicalFeatureVector
+{
+ public static class CSVToCanonicalFeatureVectorConfiguration
+ {
+ private final String wellRowColumn;
+
+ private final String wellColumnColumn;
+
+ private final boolean isWellColumnAlphanumeric;
+
+ private final boolean isSplit;
+
+ public CSVToCanonicalFeatureVectorConfiguration(String wellRow, String wellColumn,
+ boolean wellColumnIsAlphanumeric)
+ {
+ this.wellRowColumn = wellRow;
+ this.wellColumnColumn = wellColumn;
+ this.isWellColumnAlphanumeric = wellColumnIsAlphanumeric;
+
+ isSplit = (false == wellRow.equals(wellColumn));
+ }
+
+ public String getWellRowColumn()
+ {
+ return wellRowColumn;
+ }
+
+ public String getWellColumnColumn()
+ {
+ return wellColumnColumn;
+ }
+
+ public boolean isWellColumnAlphanumeric()
+ {
+ return isWellColumnAlphanumeric;
+ }
+
+ public boolean isSplit()
+ {
+ return isSplit;
+ }
+ }
+
+ private final CSVToCanonicalFeatureVectorConfiguration configuration;
+
+ private final String[] header;
+
+ private final List<String[]> lines;
+
+ private final ArrayList<FeatureColumn> columns = new ArrayList<FeatureColumn>();
+
+ // Will be initialized during conversion
+ private int xColumn = -1;
+
+ private int yColumn = -1;
+
+ private int maxX = 0;
+
+ private int maxY = 0;
+
+ public CSVToCanonicalFeatureVector(DatasetFileLines fileLines,
+ CSVToCanonicalFeatureVectorConfiguration config)
+ {
+ this.configuration = config;
+ this.header = fileLines.getHeaderTokens();
+ this.lines = fileLines.getDataLines();
+ }
+
+ public ArrayList<CanonicalFeatureVector> convert()
+ {
+ initializeColumns();
+ readLines();
+
+ return convertColumnsToFeatureFectors();
+ }
+
+ private ArrayList<CanonicalFeatureVector> convertColumnsToFeatureFectors()
+ {
+ int[] dims =
+ { maxX + 1, maxY + 1 };
+
+ ArrayList<CanonicalFeatureVector> result = new ArrayList<CanonicalFeatureVector>();
+ for (FeatureColumn column : columns)
+ {
+ CanonicalFeatureVector featureVector = convertColumnToFeatureVector(dims, column);
+ result.add(featureVector);
+ }
+
+ return result;
+ }
+
+ private CanonicalFeatureVector convertColumnToFeatureVector(int[] dims, FeatureColumn column)
+ {
+ CanonicalFeatureVector featureVector = new CanonicalFeatureVector();
+ featureVector.setFeatureDef(new ImgFeatureDefDTO(column.name, column.name, 0));
+ byte[] valuesValues = convertColumnToByteArray(dims, column);
+ ImgFeatureValuesDTO values = new ImgFeatureValuesDTO(0., 0., valuesValues, 0);
+ featureVector.setValues(Collections.singletonList(values));
+ return featureVector;
+ }
+
+ private byte[] convertColumnToByteArray(int[] dims, FeatureColumn column)
+ {
+ MDDoubleArray doubleArray = new MDDoubleArray(dims);
+ for (Point loc : column.values.keySet())
+ {
+ Double value = column.values.get(loc);
+ doubleArray.set(value, loc.getX(), loc.getY());
+ }
+
+ return NativeTaggedArray.toByteArray(doubleArray);
+ }
+
+ private void readLines()
+ {
+ for (String[] line : lines)
+ {
+ readLine(line);
+ }
+ }
+
+ private void readLine(String[] line)
+ {
+ Point point = readPointFromLine(line);
+ for (FeatureColumn column : columns)
+ {
+ if ((true == column.isWellName) || (false == column.isNumeric))
+ {
+ continue;
+ }
+ try
+ {
+ column.values.put(point, Double.parseDouble(line[column.index]));
+ } catch (NumberFormatException ex)
+ {
+ // skip this column in the future
+ column.isNumeric = false;
+ }
+ }
+
+ if (point.getX() > maxX)
+ {
+ maxX = point.getX();
+ }
+
+ if (point.getY() > maxY)
+ {
+ maxY = point.getY();
+ }
+ }
+
+ private Point readPointFromLine(String[] line)
+ {
+ int x, y;
+ if (configuration.isSplit())
+ {
+ String xString = line[xColumn];
+ String yString = line[yColumn];
+ if (configuration.isWellColumnAlphanumeric())
+ {
+ Location loc =
+ Location.tryCreateLocationFromSplitMatrixCoordinate(xString, yString);
+ x = loc.getX();
+ y = loc.getY();
+ } else
+ {
+ x = Integer.parseInt(xString);
+ y = Integer.parseInt(yString);
+ }
+ } else
+ {
+ Location loc = Location.tryCreateLocationFromMatrixCoordinate(line[xColumn]);
+ x = loc.getX();
+ y = loc.getY();
+ }
+
+ // Well-locations are 1-offset; we need 0-offset to put into an matrix
+ Point point = new Point(x - 1, y - 1);
+ return point;
+ }
+
+ private void initializeColumns()
+ {
+ for (int i = 0; i < header.length; ++i)
+ {
+ String headerName = header[i];
+ boolean isWellName;
+ if (configuration.getWellRowColumn().equals(headerName))
+ {
+ xColumn = i;
+ isWellName = true;
+ } else if (configuration.getWellColumnColumn().equals(headerName))
+ {
+ yColumn = i;
+ isWellName = true;
+ } else
+ {
+ isWellName = false;
+ }
+ FeatureColumn featureColumn = new FeatureColumn(i, headerName, isWellName);
+ columns.add(featureColumn);
+ }
+
+ if (false == configuration.isSplit())
+ {
+ yColumn = xColumn;
+ }
+
+ if (xColumn < 0 || yColumn < 0)
+ {
+ throw new IllegalArgumentException("Could not parse data set");
+ }
+ }
+
+ private static class FeatureColumn
+ {
+ private final int index;
+
+ private final String name;
+
+ private final boolean isWellName;
+
+ private final HashMap<Point, Double> values;
+
+ // this may change during the course of reading the file
+ private boolean isNumeric = true;
+
+ private FeatureColumn(int index, String name, boolean isWellName)
+ {
+ this.index = index;
+ this.name = name;
+ this.isWellName = isWellName;
+ values = new HashMap<Point, Double>();
+ }
+ }
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/CSVToCanonicalFeatureVectorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/CSVToCanonicalFeatureVectorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..50dc7016355628299bb6725afbf9f8e23f93f199
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/fvec/CSVToCanonicalFeatureVectorTest.java
@@ -0,0 +1,94 @@
+/*
+ * 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.dataaccess.fvec;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import com.csvreader.CsvReader;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.fvec.CSVToCanonicalFeatureVector.CSVToCanonicalFeatureVectorConfiguration;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class CSVToCanonicalFeatureVectorTest extends AssertJUnit
+{
+ @Test
+ public void testConversion()
+ {
+ try
+ {
+ CSVToCanonicalFeatureVectorConfiguration config =
+ new CSVToCanonicalFeatureVectorConfiguration("WellName", "WellName", true);
+ CSVToCanonicalFeatureVector convertor =
+ new CSVToCanonicalFeatureVector(getDatasetFileLines(), config);
+ convertor.convert();
+ } catch (IOException ex)
+ {
+ fail(ex.getMessage());
+ }
+ }
+
+ /**
+ * Return the tabular data as a DatasetFileLines.
+ */
+ protected DatasetFileLines getDatasetFileLines() throws IOException
+ {
+ File file =
+ new File(
+ "sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/CP037-1df.csv");
+ CsvReader reader = getCsvReader(file);
+ List<String[]> lines = new ArrayList<String[]>();
+ while (reader.readRecord())
+ {
+ lines.add(reader.getValues());
+ }
+
+ return new DatasetFileLines(file, "test", lines);
+
+ }
+
+ /**
+ * Get a CsvReader for parsing a tabular data file.
+ */
+ protected CsvReader getCsvReader(File file) throws IOException
+ {
+ if (file.isFile() == false)
+ {
+ throw new UserFailureException(file + " does not exist or is not a file.");
+ }
+ FileInputStream fileInputStream = new FileInputStream(file);
+
+ CsvReader csvReader = new CsvReader(fileInputStream, Charset.defaultCharset());
+ csvReader.setDelimiter(';');
+ csvReader.setSkipEmptyRecords(true);
+ csvReader.setUseComments(true);
+ csvReader.setComment('#');
+
+ return csvReader;
+ }
+}