From f835535fc77bc54c74db8a9a38442209a6fadd4b Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 22 Jun 2010 09:26:34 +0000
Subject: [PATCH] LMS-1584 Convert Genedata feature vectors to the canonical
form.
SVN: 16652
---
...enedataFormatToCanonicalFeatureVector.java | 257 ++++++++++++++++++
1 file changed, 257 insertions(+)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/GenedataFormatToCanonicalFeatureVector.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/GenedataFormatToCanonicalFeatureVector.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/GenedataFormatToCanonicalFeatureVector.java
new file mode 100644
index 00000000000..4db30d31dec
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/GenedataFormatToCanonicalFeatureVector.java
@@ -0,0 +1,257 @@
+/*
+ * 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.featurevector;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.StringTokenizer;
+
+import org.apache.commons.lang.StringUtils;
+
+import ch.systemsx.cisd.base.mdarray.MDDoubleArray;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+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;
+
+/**
+ * Converts currentFeature vectors from the Genedata currentFeature vector file format to
+ * CanonicaFeatureVector objects.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class GenedataFormatToCanonicalFeatureVector
+{
+ private final String layerPrefix;
+
+ private final List<String> lines;
+
+ private final ArrayList<FeatureParser> features = new ArrayList<FeatureParser>();
+
+ public GenedataFormatToCanonicalFeatureVector(List<String> lines, String layerPrefix)
+ {
+ this.layerPrefix = layerPrefix;
+ this.lines = lines;
+ }
+
+ public ArrayList<CanonicalFeatureVector> convert()
+ {
+ readLines();
+
+ return convertFeaturesToFeatureFectors();
+ }
+
+ private ArrayList<CanonicalFeatureVector> convertFeaturesToFeatureFectors()
+ {
+ ArrayList<CanonicalFeatureVector> result = new ArrayList<CanonicalFeatureVector>();
+ for (FeatureParser feature : features)
+ {
+ CanonicalFeatureVector featureVector = convertFeatureToFeatureVector(feature);
+ result.add(featureVector);
+ }
+
+ return result;
+ }
+
+ private CanonicalFeatureVector convertFeatureToFeatureVector(FeatureParser feature)
+ {
+ int[] dims =
+ { feature.numberOfRows, feature.numberOfColumns };
+
+ CanonicalFeatureVector featureVector = new CanonicalFeatureVector();
+ featureVector.setFeatureDef(new ImgFeatureDefDTO(feature.name, feature.name, 0));
+ MDDoubleArray valuesValues = convertColumnToByteArray(dims, feature);
+ ImgFeatureValuesDTO values = new ImgFeatureValuesDTO(0., 0., valuesValues, 0);
+ featureVector.setValues(Collections.singletonList(values));
+ return featureVector;
+ }
+
+ private MDDoubleArray convertColumnToByteArray(int[] dims, FeatureParser feature)
+ {
+ MDDoubleArray doubleArray = new MDDoubleArray(dims);
+ for (Point loc : feature.values.keySet())
+ {
+ Double value = feature.values.get(loc);
+ doubleArray.set(value, loc.getX(), loc.getY());
+ }
+
+ return doubleArray;
+ }
+
+ private void readLines()
+ {
+ String featureName = null;
+ ArrayList<String> featureLines = new ArrayList<String>();
+
+ // Don't need to do anything with the barcode, just make sure it is there
+ extractBarCode(lines.get(0).trim());
+
+ for (int i = 1; i < lines.size(); i++)
+ {
+ String line = lines.get(i).trim();
+
+ if (StringUtils.isEmpty(line))
+ {
+ continue;
+ }
+ // If the line starts with the layer prefix, this is a new feature
+ if (line.startsWith(getLayerPrefix()))
+ {
+ // End the old feature
+ if (false == featureLines.isEmpty())
+ {
+ createFeature(featureName, featureLines);
+ }
+
+ // begin the new feature
+ featureName = extractLayer(line, i);
+ featureLines = new ArrayList<String>();
+ } else
+ {
+ featureLines.add(line);
+ }
+ }
+ // End the last feature
+ createFeature(featureName, featureLines);
+ }
+
+ private FeatureParser createFeature(String name, ArrayList<String> featureLines)
+ {
+ FeatureParser feature = new FeatureParser(name, featureLines);
+ feature.parse();
+ features.add(feature);
+ return feature;
+ }
+
+ private String extractBarCode(String firstLine)
+ {
+ int indexOfEqual = firstLine.indexOf('=');
+ if (indexOfEqual < 0)
+ {
+ throw error(0, firstLine, "Missing '='");
+ }
+ return firstLine.substring(indexOfEqual + 1).trim();
+ }
+
+ private String extractLayer(String line, int lineIndex)
+ {
+ String layer = line.substring(getLayerPrefix().length());
+ if (layer.endsWith(">") == false)
+ {
+ throw error(lineIndex, line, "Missing '>' at the end");
+ }
+ return layer.substring(0, layer.length() - 1);
+ }
+
+ private String getLayerPrefix()
+ {
+ return layerPrefix;
+ }
+
+ private UserFailureException error(int lineIndex, String line, String reason)
+ {
+ return new UserFailureException("Error in line " + lineIndex + 1 + ": " + reason + ": "
+ + line);
+ }
+
+ /**
+ * Class for parsing features from the Genedata format.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+ private static class FeatureParser
+ {
+ private final String name;
+
+ private final ArrayList<String> lines;
+
+ private final ArrayList<String> rowLetters;
+
+ private final int numberOfColumns;
+
+ private final HashMap<Point, Double> values;
+
+ // this is not known until we complete processing
+ private int numberOfRows = 0;
+
+ private FeatureParser(String name, ArrayList<String> lines)
+ {
+ this.name = name;
+ this.lines = lines;
+ this.numberOfColumns = computeNumberOfColumns(lines);
+ values = new HashMap<Point, Double>();
+ rowLetters = new ArrayList<String>();
+ }
+
+ /**
+ * Parse the header to get the number of columns
+ */
+ private int computeNumberOfColumns(List<String> aList)
+ {
+ StringTokenizer tokenizer = new StringTokenizer(aList.get(0));
+ return tokenizer.countTokens();
+ }
+
+ public void parse()
+ {
+ // skip the first line, the header, since the only information it contains is the number
+ // of columns
+ for (int i = 1; i < lines.size(); ++i)
+ {
+ pasrseLine(lines.get(i), i);
+ }
+ numberOfRows = rowLetters.size();
+ }
+
+ public void pasrseLine(String line, int lineIndex)
+ {
+ StringTokenizer tokenizer = new StringTokenizer(line);
+ int countTokens = tokenizer.countTokens();
+ if (countTokens != numberOfColumns + 1)
+ {
+ throw error(lineIndex, line, "Inconsistent number of features: Expected "
+ + numberOfColumns + " but was " + (countTokens - 1));
+ }
+
+ String rowLetter = tokenizer.nextToken();
+ if (rowLetters.contains(rowLetter) == false)
+ {
+ rowLetters.add(rowLetter);
+ }
+
+ for (int i = 0; tokenizer.hasMoreTokens(); ++i)
+ {
+ String token = tokenizer.nextToken();
+ Point point = new Point(rowLetters.size() - 1, i);
+ try
+ {
+ values.put(point, Double.parseDouble(token));
+ } catch (NumberFormatException ex)
+ {
+ }
+ }
+ }
+
+ private UserFailureException error(int lineIndex, String line, String reason)
+ {
+ return new UserFailureException("Error in line " + lineIndex + 1 + ": " + reason + ": "
+ + line);
+ }
+ }
+}
--
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