diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
index 050450642423419764aa02943ab7fba51676afff..2400cc8bd383735c82a41d0d5a7835f87aff78c1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
@@ -18,14 +18,14 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collections;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import java.util.Map.Entry;
+import java.util.Set;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
@@ -49,12 +49,11 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFe
*/
public class FeatureTableBuilder
{
- private static final class Bundle
+ // stores all feature vectors of one dataset
+ private static final class DatasetFeaturesBundle
{
private ImgDatasetDTO dataSet;
- private FeatureVectorDatasetWellReference reference;
-
private Map<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>> featureDefToValuesMap;
}
@@ -62,67 +61,142 @@ public class FeatureTableBuilder
private final IEncapsulatedOpenBISService service;
- private final List<Bundle> bundles;
+ private final List<DatasetFeaturesBundle> bundles;
private final Map<CodeAndLabel, Integer> featureCodeLabelToIndexMap;
private final Set<String> featureCodes;
-
+
private final boolean useAllFeatures;
+ /** fetches all features of specified wells */
+ public static WellFeatureCollection fetchWellFeatures(
+ List<FeatureVectorDatasetWellReference> references, IImagingReadonlyQueryDAO dao,
+ IEncapsulatedOpenBISService service)
+ {
+ return fetchWellFeatures(references, new ArrayList<String>(), dao, service);
+ }
+
/**
- * Creates an instance for specified DAO and openBIS service.
+ * fetches specified features of specified wells
+ *
+ * @param featureCodes empty list means no filtering.
*/
- public FeatureTableBuilder(IImagingReadonlyQueryDAO dao, IEncapsulatedOpenBISService service)
+ public static WellFeatureCollection fetchWellFeatures(
+ List<FeatureVectorDatasetWellReference> references, List<String> featureCodes,
+ IImagingReadonlyQueryDAO dao, IEncapsulatedOpenBISService service)
{
- this(Collections.<String> emptyList(), dao, service);
+ FeatureTableBuilder builder = new FeatureTableBuilder(featureCodes, dao, service);
+ Set<String> datasetCodes = extractDatasetCodes(references);
+ for (String datasetCode : datasetCodes)
+ {
+ builder.addFeatureVectorsOfDataSet(datasetCode);
+ }
+ List<FeatureTableRow> features = builder.createFeatureTableRows(references);
+ return new WellFeatureCollection(features, builder.getCodesAndLabels());
+ }
+
+ /**
+ * fetches specified features of all wells
+ *
+ * @param featureCodes empty list means no filtering.
+ */
+ public static WellFeatureCollection fetchDatasetFeatures(List<String> datasetCodes,
+ List<String> featureCodes, IImagingReadonlyQueryDAO dao,
+ IEncapsulatedOpenBISService service)
+ {
+ FeatureTableBuilder builder = new FeatureTableBuilder(featureCodes, dao, service);
+ for (String datasetCode : datasetCodes)
+ {
+ builder.addFeatureVectorsOfDataSet(datasetCode);
+ }
+ List<FeatureTableRow> features = builder.createFeatureTableRows();
+ return new WellFeatureCollection(features, builder.getCodesAndLabels());
+ }
+
+ public static class WellFeatureCollection
+ {
+ private final List<FeatureTableRow> features;
+
+ private final List<CodeAndLabel> featureNames;
+
+ public WellFeatureCollection(List<FeatureTableRow> features, List<CodeAndLabel> featureNames)
+ {
+ this.features = features;
+ this.featureNames = featureNames;
+ }
+
+ public List<FeatureTableRow> getFeatures()
+ {
+ return features;
+ }
+
+ public List<CodeAndLabel> getFeatureCodesAndLabels()
+ {
+ return featureNames;
+ }
+
+ public List<String> getFeatureCodes()
+ {
+ List<String> codes = new ArrayList<String>();
+ for (CodeAndLabel codeAndTitle : featureNames)
+ {
+ codes.add(codeAndTitle.getCode());
+ }
+ return codes;
+ }
+
+ public List<String> getFeatureLabels()
+ {
+ List<String> labels = new ArrayList<String>();
+ for (CodeAndLabel codeAndTitle : featureNames)
+ {
+ labels.add(codeAndTitle.getLabel());
+ }
+ return labels;
+ }
+ }
+
+ private static Set<String> extractDatasetCodes(
+ List<FeatureVectorDatasetWellReference> references)
+ {
+ Set<String> datasetCodes = new HashSet<String>();
+ for (FeatureVectorDatasetWellReference ref : references)
+ {
+ datasetCodes.add(ref.getDatasetCode());
+ }
+ return datasetCodes;
}
/**
* Creates an instance for specified DAO and openBIS service but filters on specified features.
*
- * @param featureCodes And empty list means no filtering.
+ * @param featureCodes empty list means no filtering.
*/
- public FeatureTableBuilder(List<String> featureCodes, IImagingReadonlyQueryDAO dao,
+ FeatureTableBuilder(List<String> featureCodes, IImagingReadonlyQueryDAO dao,
IEncapsulatedOpenBISService service)
{
this.dao = dao;
this.service = service;
- bundles = new ArrayList<Bundle>();
+ bundles = new ArrayList<DatasetFeaturesBundle>();
featureCodeLabelToIndexMap = new LinkedHashMap<CodeAndLabel, Integer>();
this.featureCodes = new LinkedHashSet<String>(featureCodes);
this.useAllFeatures = featureCodes.isEmpty();
}
- /**
- * Adds feature vectors for specified data set, marking the well position.
- */
- public Bundle addFeatureVectorsOfDataSet(FeatureVectorDatasetWellReference reference)
- {
- final Bundle bundle = addFeatureVectorsOfDataSet(reference.getDatasetCode());
- bundle.reference = reference;
- return bundle;
- }
-
/**
* Adds feature vectors for specified data set.
*/
- public Bundle addFeatureVectorsOfDataSet(String dataSetCode)
+ DatasetFeaturesBundle addFeatureVectorsOfDataSet(String dataSetCode)
{
final ImgDatasetDTO dataSet = dao.tryGetDatasetByPermId(dataSetCode);
if (dataSet == null)
{
throw new UserFailureException("Unkown data set " + dataSetCode);
}
- final Bundle bundle = new Bundle();
- final List<ImgFeatureDefDTO> featureDefinitions =
- dao.listFeatureDefsByDataSetId(dataSet.getId());
+ final DatasetFeaturesBundle bundle = new DatasetFeaturesBundle();
final Map<String, ImgFeatureDefDTO> featureCodeToDefMap =
- new LinkedHashMap<String, ImgFeatureDefDTO>();
- for (ImgFeatureDefDTO def : featureDefinitions)
- {
- featureCodeToDefMap.put(def.getCode(), def);
- }
+ createFeatureCodeToDefMap(dao, dataSet);
bundle.dataSet = dataSet;
bundle.featureDefToValuesMap = new HashMap<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>>();
bundles.add(bundle);
@@ -138,8 +212,8 @@ public class FeatureTableBuilder
CodeAndLabel codeAndLabel = getCodeAndLabel(featureDefinition);
if (featureCodeLabelToIndexMap.containsKey(codeAndLabel) == false)
{
- featureCodeLabelToIndexMap.put(codeAndLabel,
- new Integer(featureCodeLabelToIndexMap.size()));
+ featureCodeLabelToIndexMap.put(codeAndLabel, new Integer(
+ featureCodeLabelToIndexMap.size()));
}
List<ImgFeatureValuesDTO> featureValueSets =
dao.getFeatureValues(featureDefinition);
@@ -154,50 +228,92 @@ public class FeatureTableBuilder
return bundle;
}
+ private static Map<String, ImgFeatureDefDTO> createFeatureCodeToDefMap(
+ IImagingReadonlyQueryDAO dao, final ImgDatasetDTO dataSet)
+ {
+ final List<ImgFeatureDefDTO> featureDefinitions =
+ dao.listFeatureDefsByDataSetId(dataSet.getId());
+ final Map<String, ImgFeatureDefDTO> featureCodeToDefMap =
+ new LinkedHashMap<String, ImgFeatureDefDTO>();
+ for (ImgFeatureDefDTO def : featureDefinitions)
+ {
+ featureCodeToDefMap.put(def.getCode(), def);
+ }
+ return featureCodeToDefMap;
+ }
+
/**
- * Returns all feature codes/labels found. If the feature code list in the constructor is not empty the
- * result will a list where the codes are a subset of this list.
+ * Returns all feature codes/labels found. If the feature code list in the constructor is not
+ * empty the result will a list where the codes are a subset of this list.
*/
- public List<CodeAndLabel> getCodesAndLabels()
+ List<CodeAndLabel> getCodesAndLabels()
{
return new ArrayList<CodeAndLabel>(featureCodeLabelToIndexMap.keySet());
}
/**
- * Returns all features per well coordinates.
+ * Returns all features for previously loaded datasets. Features for all plate wells are
+ * returned.
*/
- public List<FeatureTableRow> createFeatureTableRows()
+ List<FeatureTableRow> createFeatureTableRows()
{
List<FeatureTableRow> rows = new ArrayList<FeatureTableRow>();
- for (Bundle bundle : bundles)
+ for (DatasetFeaturesBundle bundle : bundles)
{
String dataSetCode = bundle.dataSet.getPermId();
ImgContainerDTO container = dao.getContainerById(bundle.dataSet.getContainerId());
SampleIdentifier identifier = service.tryToGetSampleIdentifier(container.getPermId());
- if (bundle.reference == null)
+ for (int rowIndex = 1; rowIndex <= container.getNumberOfRows(); rowIndex++)
{
- for (int rowIndex = 1; rowIndex <= container.getNumberOfRows(); rowIndex++)
+ for (int colIndex = 1; colIndex <= container.getNumberOfColumns(); colIndex++)
{
- for (int colIndex = 1; colIndex <= container.getNumberOfColumns(); colIndex++)
- {
- final FeatureTableRow row =
- createFeatureTableRow(bundle.featureDefToValuesMap, dataSetCode,
- identifier, null, new WellPosition(rowIndex, colIndex));
- rows.add(row);
- }
+ final FeatureTableRow row =
+ createFeatureTableRow(bundle.featureDefToValuesMap, dataSetCode,
+ identifier, null, new WellPosition(rowIndex, colIndex));
+ rows.add(row);
}
- } else
- {
- final FeatureTableRow row =
- createFeatureTableRow(bundle.featureDefToValuesMap, dataSetCode,
- identifier, bundle.reference, bundle.reference.getWellPosition());
- rows.add(row);
+ }
+ }
+ return rows;
+ }
+ /**
+ * Returns all features for the specified wells in previously loaded datasets.
+ */
+ private List<FeatureTableRow> createFeatureTableRows(
+ List<FeatureVectorDatasetWellReference> references)
+ {
+ Map<String/* dataset code */, DatasetFeaturesBundle> bundleMap = createBundleMap(bundles);
+ List<FeatureTableRow> rows = new ArrayList<FeatureTableRow>();
+ for (FeatureVectorDatasetWellReference reference : references)
+ {
+ String dataSetCode = reference.getDatasetCode();
+ DatasetFeaturesBundle bundle = bundleMap.get(dataSetCode);
+ if (bundle == null)
+ {
+ throw new IllegalStateException("Dataset has not been loaded: " + dataSetCode);
}
+ ImgContainerDTO container = dao.getContainerById(bundle.dataSet.getContainerId());
+ SampleIdentifier identifier = service.tryToGetSampleIdentifier(container.getPermId());
+ final FeatureTableRow row =
+ createFeatureTableRow(bundle.featureDefToValuesMap, dataSetCode, identifier,
+ reference, reference.getWellPosition());
+ rows.add(row);
}
return rows;
}
+ private static HashMap<String, DatasetFeaturesBundle> createBundleMap(
+ List<DatasetFeaturesBundle> bundles)
+ {
+ HashMap<String, DatasetFeaturesBundle> map = new HashMap<String, DatasetFeaturesBundle>();
+ for (DatasetFeaturesBundle bundle : bundles)
+ {
+ map.put(bundle.dataSet.getPermId(), bundle);
+ }
+ return map;
+ }
+
private FeatureTableRow createFeatureTableRow(
Map<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>> featureDefToValuesMap,
String dataSetCode, SampleIdentifier identifier,
@@ -227,13 +343,13 @@ public class FeatureTableBuilder
Integer index = featureCodeLabelToIndexMap.get(getCodeAndLabel(featureDefinition));
assert index != null : "No index for feature " + featureDefinition.getCode();
valueArray[index] =
- featureValues.getForWellLocation(wellPosition.getWellRow(), wellPosition
- .getWellColumn());
+ featureValues.getForWellLocation(wellPosition.getWellRow(),
+ wellPosition.getWellColumn());
}
row.setFeatureValues(valueArray);
return row;
}
-
+
private CodeAndLabel getCodeAndLabel(final ImgFeatureDefDTO featureDefinition)
{
return new CodeAndLabel(featureDefinition.getCode(), featureDefinition.getLabel());
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
index 68b258f71310dc3b304e2b5f5332266503e228e5..2cb872ff7e233cd4d192a27b0af6a54e05205fb1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
@@ -18,8 +18,10 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
+import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableBuilder.WellFeatureCollection;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
@@ -83,10 +85,11 @@ public class TabularDataGraphServlet extends AbstractTabularDataGraphServlet
private void initialize()
{
- final FeatureTableBuilder tableBuilder = new FeatureTableBuilder(dao, service);
- tableBuilder.addFeatureVectorsOfDataSet(dataSetCode);
+ WellFeatureCollection featureCollection =
+ FeatureTableBuilder.fetchDatasetFeatures(Arrays.asList(dataSetCode),
+ new ArrayList<String>(), dao, service);
- List<CodeAndLabel> featureCodeAndLabels = tableBuilder.getCodesAndLabels();
+ List<CodeAndLabel> featureCodeAndLabels = featureCollection.getFeatureCodesAndLabels();
int headerTokensLength = featureCodeAndLabels.size() + 3;
headerLabels = new String[headerTokensLength];
headerLabels[0] = WELL_NAME_COLUMN;
@@ -106,7 +109,7 @@ public class TabularDataGraphServlet extends AbstractTabularDataGraphServlet
lines = new ArrayList<String[]>();
- final List<FeatureTableRow> rows = tableBuilder.createFeatureTableRows();
+ final List<FeatureTableRow> rows = featureCollection.getFeatures();
for (FeatureTableRow row : rows)
{
String[] line = new String[headerTokensLength];
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
index 2651d27379774e094d761b4ca84088aff1086c6e..1777e782a4130882ee8b7a54b8d8aa023e4dad35 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
@@ -22,6 +22,7 @@ import java.util.List;
import java.util.Properties;
import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableBuilder;
+import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableBuilder.WellFeatureCollection;
import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableRow;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
@@ -79,14 +80,14 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractDatastorePlu
public TableModel createReport(List<DatasetDescription> datasets)
{
- FeatureTableBuilder featureTableBuilder = new FeatureTableBuilder(getDAO(), getService());
- for (DatasetDescription datasetDescription : datasets)
- {
- String dataSetCode = datasetDescription.getDatasetCode();
- featureTableBuilder.addFeatureVectorsOfDataSet(dataSetCode);
- }
- List<CodeAndLabel> codeAndLabels = featureTableBuilder.getCodesAndLabels();
- List<FeatureTableRow> rows = featureTableBuilder.createFeatureTableRows();
+ List<String> datasetCodes = extractDatasetCodes(datasets);
+ ArrayList<String> featureCodes = new ArrayList<String>(); // fetch all
+ WellFeatureCollection featuresCollection =
+ FeatureTableBuilder.fetchDatasetFeatures(datasetCodes, featureCodes, getDAO(),
+ getService());
+
+ List<CodeAndLabel> codeAndLabels = featuresCollection.getFeatureCodesAndLabels();
+ List<FeatureTableRow> rows = featuresCollection.getFeatures();
SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
builder.addHeader(DATA_SET_CODE_TITLE);
builder.addHeader(PLATE_IDENTIFIER_TITLE);
@@ -121,6 +122,16 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractDatastorePlu
return builder.getTableModel();
}
+ private static List<String> extractDatasetCodes(List<DatasetDescription> datasets)
+ {
+ List<String> datasetCodes = new ArrayList<String>();
+ for (DatasetDescription datasetDescription : datasets)
+ {
+ datasetCodes.add(datasetDescription.getDatasetCode());
+ }
+ return datasetCodes;
+ }
+
private IImagingReadonlyQueryDAO getDAO()
{
synchronized (this)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index aeae8f6b4fb3bc6cfc180cb86b4eb34f1572001e..f0b29b0f271e046633ba7e96746ac2fec4629311 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -20,6 +20,7 @@ import java.awt.image.BufferedImage;
import java.io.File;
import java.io.InputStream;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
@@ -37,10 +38,11 @@ import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageDatasetLoaderFactory;
import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
+import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDssServiceRpc;
import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableBuilder;
+import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableBuilder.WellFeatureCollection;
import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableRow;
-import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
@@ -173,8 +175,9 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
Size imageSize = getImageSize(dataset, imageAccessor);
PlateImageParameters params = imageAccessor.getImageParameters();
int tilesNumber = params.getTileColsNum() * params.getTileRowsNum();
- return new ImageDatasetMetadata(dataset, params.getChannelsCodes(), params
- .getChannelsLabels(), tilesNumber, imageSize.getWidth(), imageSize.getHeight());
+ return new ImageDatasetMetadata(dataset, params.getChannelsCodes(),
+ params.getChannelsLabels(), tilesNumber, imageSize.getWidth(),
+ imageSize.getHeight());
}
private static Size getImageSize(IImageDatasetIdentifier dataset,
@@ -235,20 +238,18 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
private FeatureVectorDataset createFeatureVectorDataset(String sessionToken,
FeatureVectorDatasetReference dataset, List<String> featureCodes)
{
- FeatureTableBuilder builder =
- new FeatureTableBuilder(featureCodes, getDAO(), getOpenBISService());
- builder.addFeatureVectorsOfDataSet(dataset.getDatasetCode());
- List<FeatureTableRow> featureTableRows = builder.createFeatureTableRows();
+ WellFeatureCollection datasetFeatures =
+ FeatureTableBuilder.fetchDatasetFeatures(Arrays.asList(dataset.getDatasetCode()),
+ featureCodes, getDAO(), getOpenBISService());
List<FeatureVector> featureVectors = new ArrayList<FeatureVector>();
- for (FeatureTableRow featureTableRow : featureTableRows)
+ for (FeatureTableRow featureTableRow : datasetFeatures.getFeatures())
{
WellPosition wellPosition = featureTableRow.getWellPosition();
double[] values = featureTableRow.getFeatureValuesAsDouble();
featureVectors.add(new FeatureVector(wellPosition, values));
}
- List<String> codes = getCodes(builder);
- List<String> labels = getLabels(builder);
- return new FeatureVectorDataset(dataset, codes, labels, featureVectors);
+ return new FeatureVectorDataset(dataset, datasetFeatures.getFeatureCodes(),
+ datasetFeatures.getFeatureLabels(), featureVectors);
}
private List<String> normalize(List<String> names)
@@ -266,16 +267,17 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
List<String> featureNames)
{
checkDatasetsAuthorizationForIDatasetIdentifier(sessionToken, datasetWellReferences);
- final FeatureTableBuilder builder =
- createFeatureTableBuilder(datasetWellReferences, normalize(featureNames));
- return createFeatureVectorList(builder);
+ WellFeatureCollection features =
+ FeatureTableBuilder.fetchWellFeatures(datasetWellReferences, featureNames, dao,
+ getOpenBISService());
+ return createFeatureVectorList(features);
}
private List<FeatureVectorWithDescription> createFeatureVectorList(
- final FeatureTableBuilder builder)
+ final WellFeatureCollection features)
{
- final List<String> featureCodes = getCodes(builder);
- final List<FeatureTableRow> featureTableRows = builder.createFeatureTableRows();
+ final List<String> featureCodes = features.getFeatureCodes();
+ final List<FeatureTableRow> featureTableRows = features.getFeatures();
final List<FeatureVectorWithDescription> result =
new ArrayList<FeatureVectorWithDescription>(featureTableRows.size());
for (FeatureTableRow featureTableRow : featureTableRows)
@@ -285,28 +287,6 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return result;
}
- private List<String> getCodes(FeatureTableBuilder builder)
- {
- List<CodeAndLabel> featureCodesAndLabels = builder.getCodesAndLabels();
- List<String> codes = new ArrayList<String>();
- for (CodeAndLabel codeAndTitle : featureCodesAndLabels)
- {
- codes.add(codeAndTitle.getCode());
- }
- return codes;
- }
-
- private List<String> getLabels(FeatureTableBuilder builder)
- {
- List<CodeAndLabel> featureCodesAndLabels = builder.getCodesAndLabels();
- List<String> labels = new ArrayList<String>();
- for (CodeAndLabel codeAndTitle : featureCodesAndLabels)
- {
- labels.add(codeAndTitle.getLabel());
- }
- return labels;
- }
-
private FeatureVectorWithDescription createFeatureVector(FeatureTableRow featureTableRow,
final List<String> featureCodes)
{
@@ -314,18 +294,6 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
featureTableRow.getFeatureValuesAsDouble());
}
- private FeatureTableBuilder createFeatureTableBuilder(
- List<FeatureVectorDatasetWellReference> plateWellReferences, List<String> featureCodes)
- {
- final FeatureTableBuilder builder =
- new FeatureTableBuilder(featureCodes, getDAO(), getOpenBISService());
- for (FeatureVectorDatasetWellReference datasetWellReference : plateWellReferences)
- {
- builder.addFeatureVectorsOfDataSet(datasetWellReference);
- }
- return builder;
- }
-
public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences)
{
checkDatasetsAuthorizationForIDatasetIdentifier(sessionToken, imageReferences);
@@ -381,8 +349,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
{
ImageChannelStackReference channelStackReference =
ImageChannelStackReference.createFromLocations(wellLocation, tileLocation);
- return ImageChannelsUtils.getImage(imageAccessor, channelStackReference, imageRef
- .getChannel(), null);
+ return ImageChannelsUtils.getImage(imageAccessor, channelStackReference,
+ imageRef.getChannel(), null);
} catch (EnvironmentFailureException e)
{
operationLog.error("Error reading image.", e);