From a1969d32a78b843ff91bd1dc4e68cd089cadb05e Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Wed, 28 Jul 2010 09:59:37 +0000
Subject: [PATCH] add: methods
IScreeningOpenbisServiceFacade.loadFeaturesForFatasetWellReferences() and
IScreeningOpenbisServiceFacade.loadFeaturesForPlateWells() to obtain the
feature vectors for a defined set of dataset well references change: minor
version of IDssServiceRpcScreening to 1
SVN: 17259
---
.../generic/server/FeatureTableBuilder.java | 106 ++++++++++++------
.../dss/generic/server/FeatureTableRow.java | 38 ++++---
...mageAnalysisMergedRowsReportingPlugin.java | 20 ++--
.../server/DssServiceRpcScreening.java | 77 ++++++++++---
.../api/v1/IDssServiceRpcScreening.java | 45 +++++++-
.../v1/IScreeningOpenbisServiceFacade.java | 98 +++++++++++++---
.../api/v1/ScreeningOpenbisServiceFacade.java | 92 ++++++++++++++-
.../FeatureVectorDatasetWellReference.java | 54 +++++++++
.../v1/dto/FeatureVectorWithDescription.java | 55 +++++++++
9 files changed, 488 insertions(+), 97 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDatasetWellReference.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorWithDescription.java
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 2a73c86937d..a72ecb55db5 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
@@ -30,6 +30,8 @@ import java.util.Map.Entry;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
@@ -50,6 +52,8 @@ public class FeatureTableBuilder
{
private ImgDatasetDTO dataSet;
+ private FeatureVectorDatasetWellReference reference;
+
private Map<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>> featureDefToValuesMap;
}
@@ -86,24 +90,35 @@ public class FeatureTableBuilder
this.featureNames = new HashSet<String>(featureNames);
}
+ /**
+ * 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 void addFeatureVectorsOfDataSet(String dataSetCode)
+ public Bundle addFeatureVectorsOfDataSet(String dataSetCode)
{
- ImgDatasetDTO dataSet = dao.tryGetDatasetByPermId(dataSetCode);
+ final ImgDatasetDTO dataSet = dao.tryGetDatasetByPermId(dataSetCode);
if (dataSet == null)
{
throw new UserFailureException("Unkown data set " + dataSetCode);
}
- Bundle bundle = new Bundle();
- List<ImgFeatureDefDTO> featureDefinitions = dao.listFeatureDefsByDataSetId(dataSet.getId());
+ final Bundle bundle = new Bundle();
+ final List<ImgFeatureDefDTO> featureDefinitions =
+ dao.listFeatureDefsByDataSetId(dataSet.getId());
bundle.dataSet = dataSet;
bundle.featureDefToValuesMap = new HashMap<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>>();
bundles.add(bundle);
for (ImgFeatureDefDTO featureDefinition : featureDefinitions)
{
- String featureName = featureDefinition.getName();
+ final String featureName = featureDefinition.getName();
if (featureNames.isEmpty() || featureNames.contains(featureName))
{
if (featureNameToIndexMap.containsKey(featureName) == false)
@@ -121,6 +136,7 @@ public class FeatureTableBuilder
bundle.featureDefToValuesMap.put(featureDefinition, featureValueSets);
}
}
+ return bundle;
}
/**
@@ -135,7 +151,7 @@ public class FeatureTableBuilder
/**
* Returns all features per well coordinates.
*/
- public List<FeatureTableRow> getFeatureTableRows()
+ public List<FeatureTableRow> createFeatureTableRows()
{
List<FeatureTableRow> rows = new ArrayList<FeatureTableRow>();
for (Bundle bundle : bundles)
@@ -143,40 +159,64 @@ public class FeatureTableBuilder
String dataSetCode = bundle.dataSet.getPermId();
ImgContainerDTO container = dao.getContainerById(bundle.dataSet.getContainerId());
SampleIdentifier identifier = service.tryToGetSampleIdentifier(container.getPermId());
- for (int rowIndex = 1; rowIndex <= container.getNumberOfRows(); rowIndex++)
+ if (bundle.reference == null)
{
- for (int colIndex = 1; colIndex <= container.getNumberOfColumns(); colIndex++)
+ for (int rowIndex = 1; rowIndex <= container.getNumberOfRows(); rowIndex++)
{
- FeatureTableRow row = new FeatureTableRow();
- rows.add(row);
- row.setDataSetCode(dataSetCode);
- row.setPlateIdentifier(identifier);
- row.setRowIndex(rowIndex);
- row.setColumnIndex(colIndex);
- float[] valueArray = new float[featureNameToIndexMap.size()];
- Arrays.fill(valueArray, Float.NaN);
- for (Entry<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>> entry : bundle.featureDefToValuesMap
- .entrySet())
+ for (int colIndex = 1; colIndex <= container.getNumberOfColumns(); colIndex++)
{
- ImgFeatureDefDTO featureDefinition = entry.getKey();
- List<ImgFeatureValuesDTO> featureValueSets = entry.getValue();
- // We take only the first set of feature value sets
- ImgFeatureValuesDTO featureValueDTO = featureValueSets.get(0);
- PlateFeatureValues featureValues = featureValueDTO.getValues();
- if (rowIndex > featureValues.getGeometry().getNumberOfRows()
- || colIndex > featureValues.getGeometry().getNumberOfColumns())
- {
- break;
- }
- Integer index = featureNameToIndexMap.get(featureDefinition.getName());
- assert index != null : "No index for feature "
- + featureDefinition.getName();
- valueArray[index] = featureValues.getForWellLocation(rowIndex, colIndex);
+ final FeatureTableRow row =
+ createFeatureTableRow(bundle.featureDefToValuesMap, dataSetCode,
+ identifier, null, new WellPosition(rowIndex,
+ colIndex));
+ rows.add(row);
}
- row.setFeatureValues(valueArray);
}
+ } else
+ {
+ final FeatureTableRow row =
+ createFeatureTableRow(bundle.featureDefToValuesMap, dataSetCode,
+ identifier, bundle.reference, bundle.reference.getWellPosition());
+ rows.add(row);
+
}
}
return rows;
}
+
+ private FeatureTableRow createFeatureTableRow(
+ Map<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>> featureDefToValuesMap,
+ String dataSetCode, SampleIdentifier identifier,
+ FeatureVectorDatasetWellReference reference, WellPosition wellPosition)
+ {
+ FeatureTableRow row = new FeatureTableRow();
+ row.setDataSetCode(dataSetCode);
+ row.setPlateIdentifier(identifier);
+ row.setReference(reference);
+ row.setWellPosition(wellPosition);
+ float[] valueArray = new float[featureNameToIndexMap.size()];
+ Arrays.fill(valueArray, Float.NaN);
+ for (Entry<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>> entry : featureDefToValuesMap
+ .entrySet())
+ {
+ ImgFeatureDefDTO featureDefinition = entry.getKey();
+ List<ImgFeatureValuesDTO> featureValueSets = entry.getValue();
+ // We take only the first set of feature value sets
+ ImgFeatureValuesDTO featureValueDTO = featureValueSets.get(0);
+ PlateFeatureValues featureValues = featureValueDTO.getValues();
+ if (wellPosition.getWellRow() > featureValues.getGeometry().getNumberOfRows()
+ || wellPosition.getWellColumn() > featureValues.getGeometry()
+ .getNumberOfColumns())
+ {
+ break;
+ }
+ Integer index = featureNameToIndexMap.get(featureDefinition.getName());
+ assert index != null : "No index for feature " + featureDefinition.getName();
+ valueArray[index] =
+ featureValues.getForWellLocation(wellPosition.getWellRow(), wellPosition
+ .getWellColumn());
+ }
+ row.setFeatureValues(valueArray);
+ return row;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableRow.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableRow.java
index dd1a3bfd84e..010240425d8 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableRow.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableRow.java
@@ -17,10 +17,12 @@
package ch.systemsx.cisd.openbis.dss.generic.server;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
/**
* Bean for a row in a table of feature vectors. Each row is specified by data set code, plate
- * identifier, well coordinates and and array of feature values. Double.NaN is used for unknown
+ * identifier, well position and and array of feature values. Double.NaN is used for unknown
* feature value in this array.
*
* @author Franz-Josef Elmer
@@ -28,13 +30,13 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
public class FeatureTableRow
{
private String dataSetCode;
+
+ private FeatureVectorDatasetWellReference reference;
private SampleIdentifier plateIdentifier;
- private int rowIndex;
-
- private int columnIndex;
-
+ private WellPosition wellPosition;
+
private float[] featureValues;
public final String getDataSetCode()
@@ -47,34 +49,34 @@ public class FeatureTableRow
this.dataSetCode = dataSetCode;
}
- public final SampleIdentifier getPlateIdentifier()
+ public FeatureVectorDatasetWellReference getReference()
{
- return plateIdentifier;
+ return reference;
}
- public final void setPlateIdentifier(SampleIdentifier plateIdentifier)
+ public void setReference(FeatureVectorDatasetWellReference reference)
{
- this.plateIdentifier = plateIdentifier;
+ this.reference = reference;
}
- public final int getRowIndex()
+ public final SampleIdentifier getPlateIdentifier()
{
- return rowIndex;
+ return plateIdentifier;
}
- public final void setRowIndex(int rowIndex)
+ public final void setPlateIdentifier(SampleIdentifier plateIdentifier)
{
- this.rowIndex = rowIndex;
+ this.plateIdentifier = plateIdentifier;
}
- public final int getColumnIndex()
+ public void setWellPosition(WellPosition wellPosition)
{
- return columnIndex;
+ this.wellPosition = wellPosition;
}
-
- public final void setColumnIndex(int columnIndex)
+
+ public final WellPosition getWellPosition()
{
- this.columnIndex = columnIndex;
+ return wellPosition;
}
public final float[] getFeatureValues()
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 532a4194888..05407fbf021 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
@@ -50,14 +50,17 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractDatastorePlu
IReportingPluginTask
{
private static final long serialVersionUID = 1L;
-
+
private static final String DATA_SET_CODE_TITLE = "Data Set Code";
+
private static final String PLATE_IDENTIFIER_TITLE = "Plate Identifier";
+
private static final String ROW_TITLE = "Row";
+
private static final String COLUMN_TITLE = "Column";
-
+
private IEncapsulatedOpenBISService service;
-
+
private IImagingQueryDAO dao;
public ImageAnalysisMergedRowsReportingPlugin(Properties properties, File storeRoot)
@@ -72,7 +75,7 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractDatastorePlu
this.service = service;
this.dao = dao;
}
-
+
public TableModel createReport(List<DatasetDescription> datasets)
{
FeatureTableBuilder featureTableBuilder = new FeatureTableBuilder(getDAO(), getService());
@@ -82,7 +85,7 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractDatastorePlu
featureTableBuilder.addFeatureVectorsOfDataSet(dataSetCode);
}
List<String> featureNames = featureTableBuilder.getFeatureNames();
- List<FeatureTableRow> rows = featureTableBuilder.getFeatureTableRows();
+ List<FeatureTableRow> rows = featureTableBuilder.createFeatureTableRows();
SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
builder.addHeader(DATA_SET_CODE_TITLE);
builder.addHeader(PLATE_IDENTIFIER_TITLE);
@@ -97,8 +100,9 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractDatastorePlu
List<ISerializableComparable> values = new ArrayList<ISerializableComparable>();
values.add(new StringTableCell(row.getDataSetCode()));
values.add(new StringTableCell(row.getPlateIdentifier().toString()));
- values.add(new StringTableCell(PlateUtils.translateRowNumberIntoLetterCode(row.getRowIndex())));
- values.add(new IntegerTableCell(row.getColumnIndex()));
+ values.add(new StringTableCell(PlateUtils.translateRowNumberIntoLetterCode(row
+ .getWellPosition().getWellRow())));
+ values.add(new IntegerTableCell(row.getWellPosition().getWellColumn()));
float[] featureValues = row.getFeatureValues();
StringTableCell nullValue = new StringTableCell("");
for (float value : featureValues)
@@ -124,7 +128,7 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractDatastorePlu
}
return dao;
}
-
+
private IEncapsulatedOpenBISService getService()
{
if (service == null)
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 f80115e6129..f1970227f39 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
@@ -51,6 +51,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDatasetIdentifier;
@@ -72,6 +74,11 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
IDssServiceRpcScreening
{
+ /**
+ * The minor version of this service.
+ */
+ private static final int MINOR_VERSION = 1;
+
private IImagingQueryDAO dao;
public DssServiceRpcScreening(String storeRootDir)
@@ -203,17 +210,59 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
new FeatureTableBuilder(featureNames, getDAO(), getOpenBISService());
builder.addFeatureVectorsOfDataSet(dataset.getDatasetCode());
List<String> existingFeatureNames = builder.getFeatureNames();
- List<FeatureTableRow> featureTableRows = builder.getFeatureTableRows();
+ List<FeatureTableRow> featureTableRows = builder.createFeatureTableRows();
List<FeatureVector> featureVectors = new ArrayList<FeatureVector>();
for (FeatureTableRow featureTableRow : featureTableRows)
{
- featureVectors.add(new FeatureVector(new WellPosition(
- featureTableRow.getRowIndex(), featureTableRow.getColumnIndex()),
- featureTableRow.getFeatureValuesAsDouble()));
+ featureVectors.add(new FeatureVector(featureTableRow.getWellPosition(), featureTableRow
+ .getFeatureValuesAsDouble()));
}
return new FeatureVectorDataset(dataset, existingFeatureNames, featureVectors);
}
+ public List<FeatureVectorWithDescription> loadFeaturesForDatasetWellReferences(
+ String sessionToken, List<FeatureVectorDatasetWellReference> datasetWellReferences,
+ List<String> featureNames)
+ {
+ assertDataSetsAreAccessible(sessionToken, datasetWellReferences);
+ final FeatureTableBuilder builder =
+ createFeatureTableBuilder(datasetWellReferences, featureNames);
+ return createFeatureVectorList(builder);
+ }
+
+ private List<FeatureVectorWithDescription> createFeatureVectorList(
+ final FeatureTableBuilder builder)
+ {
+ final List<String> featureNames = builder.getFeatureNames();
+ final List<FeatureTableRow> featureTableRows = builder.createFeatureTableRows();
+ final List<FeatureVectorWithDescription> result =
+ new ArrayList<FeatureVectorWithDescription>(featureTableRows.size());
+ for (FeatureTableRow featureTableRow : featureTableRows)
+ {
+ result.add(createFeatureVector(featureTableRow, featureNames));
+ }
+ return result;
+ }
+
+ private FeatureVectorWithDescription createFeatureVector(FeatureTableRow featureTableRow,
+ final List<String> featureNames)
+ {
+ return new FeatureVectorWithDescription(featureTableRow.getReference(), featureNames,
+ featureTableRow.getFeatureValuesAsDouble());
+ }
+
+ private FeatureTableBuilder createFeatureTableBuilder(
+ List<FeatureVectorDatasetWellReference> plateWellReferences, List<String> featureNames)
+ {
+ final FeatureTableBuilder builder =
+ new FeatureTableBuilder(featureNames, getDAO(), getOpenBISService());
+ for (FeatureVectorDatasetWellReference datasetWellReference : plateWellReferences)
+ {
+ builder.addFeatureVectorsOfDataSet(datasetWellReference);
+ }
+ return builder;
+ }
+
public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences)
{
Map<String, IHCSImageDatasetLoader> imageLoadersMap =
@@ -353,16 +402,6 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return dataset.getDataSetType().getCode().equals(ScreeningConstants.IMAGE_DATASET_TYPE);
}
- public int getMajorVersion()
- {
- return 1;
- }
-
- public int getMinorVersion()
- {
- return 0;
- }
-
private List<ImgFeatureDefDTO> getFeatureDefinitions(IDatasetIdentifier identifier)
{
ImgDatasetDTO dataSet = getDAO().tryGetDatasetByPermId(identifier.getDatasetCode());
@@ -393,4 +432,14 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return dao;
}
+ public int getMajorVersion()
+ {
+ return MAJOR_VERSION;
+ }
+
+ public int getMinorVersion()
+ {
+ return MINOR_VERSION;
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
index 90367ede094..e2d61d81763 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
@@ -22,6 +22,8 @@ import java.util.List;
import ch.systemsx.cisd.common.api.IRpcService;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
@@ -34,21 +36,52 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageRef
*/
public interface IDssServiceRpcScreening extends IRpcService
{
+ /**
+ * The major version of this service.
+ */
+ public static final int MAJOR_VERSION = 1;
+
/**
* For a given set of feature vector data sets provide the list of all available features. This
* is just the name of the feature. If for different data sets different sets of features are
* available, provide the union of the features of all data sets.
*/
- List<String> listAvailableFeatureNames(String sessionToken,
+ public List<String> listAvailableFeatureNames(String sessionToken,
List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
/**
- * For a given set of data sets and a set of features (given by their name), provide the feature
- * matrix. Each column in that matrix is one feature, each row is one well in one data set.
+ * Conceptually, for a given list of data well references (i.e. specified wells on specified
+ * feature vector data sets) and a set of features (given by their name) provide the feature
+ * matrix. In this matrix, each column is one feature, each row is one well in one data set.
+ * <p>
+ * Physically, the result is delivered as a list of feature vector datasets. Each entry in this
+ * list corresponds to one well in one dataset.
+ *
+ * @return The list of {@link FeatureVectorDataset}s, each element corresponds to one of the
+ * <var>featureDatasets</var>.
*/
- List<FeatureVectorDataset> loadFeatures(String sessionToken,
+ public List<FeatureVectorDataset> loadFeatures(String sessionToken,
List<FeatureVectorDatasetReference> featureDatasets, List<String> featureNames);
+ /**
+ * Conceptually, for a given list of dataset well references (i.e. specified wells on specified
+ * feature vector data sets) and a set of features (given by their name) provide the feature
+ * matrix. In this matrix, each column is one feature, each row is one well in one data set.
+ * <p>
+ * Physically, the result is delivered as a list of feature vectors. Each entry in this list
+ * corresponds to one well in one dataset.
+ *
+ * @return The list of {@link FeatureVectorWithDescription}s, each element corresponds to one of
+ * the <var>datasetWellReferences</var>. <b>Note that the order of the returned ist is
+ * <i>not</i> guaranteed to be the same as the order of the list
+ * <var>datasetWellReferences</var>. Use
+ * {@link FeatureVectorWithDescription#getDatasetWellReference()} to find the
+ * corresponding dataset / well.</b>
+ */
+ public List<FeatureVectorWithDescription> loadFeaturesForDatasetWellReferences(
+ String sessionToken, List<FeatureVectorDatasetWellReference> datasetWellReferences,
+ List<String> featureNames);
+
/**
* Provide images for a given list of image references (given by data set code, well position,
* channel and tile). The result is encoded into one stream, which consist of multiple blocks in
@@ -56,13 +89,13 @@ public interface IDssServiceRpcScreening extends IRpcService
* encoded as one long number. The number of blocks is equal to the number of specified
* references and the order of blocks corresponds to the order of image references.
*/
- InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences);
+ public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences);
/**
* For a given set of image data sets, provide all image channels that have been acquired and
* the available (natural) image size(s).
*/
- List<ImageDatasetMetadata> listImageMetadata(String sessionToken,
+ public List<ImageDatasetMetadata> listImageMetadata(String sessionToken,
List<? extends IImageDatasetIdentifier> imageDatasets);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
index 5c9d28df3d3..40201e86a1b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
@@ -23,6 +23,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisS
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDatasetIdentifier;
@@ -45,66 +47,128 @@ public interface IScreeningOpenbisServiceFacade
/**
* Return the session token for this authenticated user.
*/
- public abstract String getSessionToken();
+ public String getSessionToken();
/** Closes connection with the server. After calling this method this facade cannot be used. */
- public abstract void logout();
+ public void logout();
/**
* Return the list of all visible plates assigned to any experiment, along with their
* hierarchical context (space, project, experiment).
*/
- public abstract List<Plate> listPlates();
+ public List<Plate> listPlates();
/**
- * Return the list of all visible experiments, along with their
- * hierarchical context (space, project).
+ * Return the list of all visible experiments, along with their hierarchical context (space,
+ * project).
*/
- public abstract List<ExperimentIdentifier> listExperiments();
+ public List<ExperimentIdentifier> listExperiments();
/**
* For a given set of plates provides the list of all connected data sets containing feature
* vectors.
*/
- public abstract List<FeatureVectorDatasetReference> listFeatureVectorDatasets(
+ public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(
List<? extends PlateIdentifier> plates);
/**
* For a given set of plates provides the list of all connected data sets containing images.
*/
- public abstract List<ImageDatasetReference> listImageDatasets(
- List<? extends PlateIdentifier> plates);
+ public List<ImageDatasetReference> listImageDatasets(List<? extends PlateIdentifier> plates);
/**
* For the given <var>experimentIdentifier</var> find all plate locations that are connected to
* the specified <var>materialIdentifier</var>. If <code>findDatasets == true</code>, find also
* the connected image and image analysis data sets for the relevant plates.
+ * <p>
+ * For how to get the feature vectors, see
+ * {@link #convertToFeatureVectorDatasetWellIdentifier(List)}.
*/
public List<PlateWellReferenceWithDatasets> listPlateWells(
ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier,
boolean findDatasets);
-
+
+ /**
+ * Converts the given list of {@link PlateWellReferenceWithDatasets} into a list of
+ * {@link FeatureVectorDatasetWellReference}.
+ *
+ * @see #listPlateWells(ExperimentIdentifier, MaterialIdentifier, boolean)
+ * @see #loadFeaturesForDatasetWellReferences(List, List)
+ */
+ public List<FeatureVectorDatasetWellReference> convertToFeatureVectorDatasetWellIdentifier(
+ List<PlateWellReferenceWithDatasets> plateWellReferenceWithDataSets);
+
/**
* Converts a given list of dataset codes to dataset identifiers which can be used in other API
* calls.
*/
- public abstract List<IDatasetIdentifier> getDatasetIdentifiers(List<String> datasetCodes);
+ public List<IDatasetIdentifier> getDatasetIdentifiers(List<String> datasetCodes);
/**
* For a given set of feature vector data sets provides the list of all available features. This
* is just the name of the feature. If for different data sets different sets of features are
* available, provides the union of the feature names of all data sets.
*/
- public abstract List<String> listAvailableFeatureNames(
+ public List<String> listAvailableFeatureNames(
List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
/**
- * For a given set of data sets and a set of features (given by their name), provide all the
- * feature vectors.
+ * Conceptually, for a given list of dataset well references (i.e. specified wells on specified
+ * feature vector data sets) and a set of features (given by their name) provide the feature
+ * matrix. In this matrix, each column is one feature, each row is one well in one data set.
+ * <p>
+ * Physically, the result is delivered as a list of feature vector datasets. Each entry in this
+ * list corresponds to one well in one dataset.
+ *
+ * @return The list of {@link FeatureVectorDataset}s, each element corresponds to one of the
+ * <var>featureDatasets</var>.
*/
- public abstract List<FeatureVectorDataset> loadFeatures(
+ public List<FeatureVectorDataset> loadFeatures(
List<FeatureVectorDatasetReference> featureDatasets, List<String> featureNames);
+ /**
+ * Conceptually, for a given list of dataset well references (i.e. specified wells on specified
+ * feature vector data sets) and a set of features (given by their name) provide the feature
+ * matrix. In this matrix, each column is one feature, each row is one well in one data set.
+ * <p>
+ * Physically, the result is delivered as a list of feature vectors. Each entry in this list
+ * corresponds to one well in one dataset.
+ *
+ * @param datasetWellReferences The references for datasets / wells to get the feature vectors
+ * for.
+ * @param featureNamesOrNull The names of the features to build the feature vectors from, or
+ * <code>null</code>, if all available features should be included. Note that for an
+ * empty list as well all features will be included.
+ * @return The list of {@link FeatureVectorWithDescription}s, each element corresponds to one of
+ * the <var>datasetWellReferences</var>. <b>Note that the order of the returned list is
+ * <i>not</i> guaranteed to be the same as the order of the list
+ * <var>datasetWellReferences</var>. Use
+ * {@link FeatureVectorWithDescription#getDatasetWellReference()} to find the
+ * corresponding dataset / well.</b>
+ */
+ public List<FeatureVectorWithDescription> loadFeaturesForDatasetWellReferences(
+ List<FeatureVectorDatasetWellReference> datasetWellReferences,
+ List<String> featureNamesOrNull);
+
+ /**
+ * For the given <var>experimentIdentifier</var> find all plate locations that are connected to
+ * the specified <var>materialIdentifier</var> and load the feature vectors for the given
+ * <var>featureNamesOrNull</var> if not <code>null</code>, or all available features otherwise.
+ *
+ * @param experimentIdentifer The identifier of the experiment to get the feature vectors for
+ * @param materialIdentifier The identifier of the material contained in the wells to get the
+ * feature vectors for.
+ * @param featureNamesOrNull The names of the features to build the feature vectors from, or
+ * <code>null</code>, if all available features should be included. Note that for an
+ * empty list as well all features will be included.
+ * @return The list of {@link FeatureVectorWithDescription}s found in the given
+ * <var>experimentIdentifer</var> and connected with the given
+ * <var>materialIdentifier</var>.
+ */
+ public List<FeatureVectorWithDescription> loadFeaturesForPlateWells(
+ ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier,
+ List<String> featureNamesOrNull);
+
/**
* Saves images for a given list of image references (given by data set code, well position,
* channel and tile) in the provided output streams. Output streams will not be closed
@@ -114,14 +178,14 @@ public interface IScreeningOpenbisServiceFacade
* @throws IOException when reading images from the server or writing them to the output streams
* fails
*/
- public abstract void loadImages(List<PlateImageReference> imageReferences,
+ public void loadImages(List<PlateImageReference> imageReferences,
IImageOutputStreamProvider outputStreamProvider) throws IOException;
/**
* For a given set of image data sets, provide all image channels that have been acquired and
* the available (natural) image size(s).
*/
- public abstract List<ImageDatasetMetadata> listImageMetadata(
+ public List<ImageDatasetMetadata> listImageMetadata(
List<? extends IImageDatasetIdentifier> imageDatasets);
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
index 5d1f7593dd9..628bb60df76 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
@@ -19,6 +19,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServ
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDatasetIdentifier;
@@ -29,6 +31,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
/**
* A client side facade of openBIS and Datastore Server API.
@@ -61,6 +64,8 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
private final DataStoreMultiplexer<FeatureVectorDatasetReference> featureVectorDataSetReferenceMultiplexer;
+ private final DataStoreMultiplexer<FeatureVectorDatasetWellReference> featureVectorDataSetWellReferenceMultiplexer;
+
private final DataStoreMultiplexer<IImageDatasetIdentifier> metaDataMultiplexer;
private final String sessionToken;
@@ -130,6 +135,8 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
new DataStoreMultiplexer<IFeatureVectorDatasetIdentifier>(dssServiceCache);
featureVectorDataSetReferenceMultiplexer =
new DataStoreMultiplexer<FeatureVectorDatasetReference>(dssServiceCache);
+ featureVectorDataSetWellReferenceMultiplexer =
+ new DataStoreMultiplexer<FeatureVectorDatasetWellReference>(dssServiceCache);
}
/**
@@ -250,6 +257,89 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
return result;
}
+ public List<FeatureVectorDatasetWellReference> convertToFeatureVectorDatasetWellIdentifier(
+ List<PlateWellReferenceWithDatasets> plateWellReferenceWithDataSets)
+ {
+ final List<FeatureVectorDatasetWellReference> result =
+ new ArrayList<FeatureVectorDatasetWellReference>(plateWellReferenceWithDataSets
+ .size());
+ for (PlateWellReferenceWithDatasets plateWellRef : plateWellReferenceWithDataSets)
+ {
+ for (FeatureVectorDatasetReference fvdr : plateWellRef
+ .getFeatureVectorDatasetReferences())
+ {
+ result.add(createFVDatasetReference(fvdr, plateWellRef.getWellPosition()));
+ }
+ }
+ return result;
+ }
+
+ private FeatureVectorDatasetWellReference createFVDatasetReference(
+ FeatureVectorDatasetReference fvdr, WellPosition wellPosition)
+ {
+ return new FeatureVectorDatasetWellReference(fvdr.getDatasetCode(), fvdr
+ .getDatastoreServerUrl(), fvdr.getPlate(), fvdr.getPlateGeometry(), fvdr
+ .getRegistrationDate(), fvdr.getParentImageDataset(), wellPosition);
+ }
+
+ public List<FeatureVectorWithDescription> loadFeaturesForDatasetWellReferences(
+ final List<FeatureVectorDatasetWellReference> datasetWellReferences,
+ final List<String> featureNamesOrNull)
+ {
+ final List<String> featureNames =
+ (isEmpty(featureNamesOrNull)) ? listAvailableFeatureNames(datasetWellReferences)
+ : featureNamesOrNull;
+
+ final List<FeatureVectorWithDescription> result =
+ new ArrayList<FeatureVectorWithDescription>();
+ featureVectorDataSetWellReferenceMultiplexer.process(datasetWellReferences,
+ new IReferenceHandler<FeatureVectorDatasetWellReference>()
+ {
+ public void handle(IDssServiceRpcScreening dssService,
+ List<FeatureVectorDatasetWellReference> references)
+ {
+ result.addAll(dssService.loadFeaturesForDatasetWellReferences(
+ sessionToken, references, featureNames));
+ }
+ });
+ return result;
+ }
+
+ private boolean isEmpty(final List<String> featureNamesOrNull)
+ {
+ return featureNamesOrNull == null || featureNamesOrNull.isEmpty();
+ }
+
+ public List<FeatureVectorWithDescription> loadFeaturesForPlateWells(
+ ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier,
+ List<String> featureNamesOrNull)
+ {
+ final List<PlateWellReferenceWithDatasets> plateWellRefs =
+ listPlateWells(experimentIdentifer, materialIdentifier, true);
+ final List<String> featureNames =
+ (isEmpty(featureNamesOrNull)) ? listAvailableFeatureNamesForPlateWells(plateWellRefs)
+ : featureNamesOrNull;
+ final List<FeatureVectorDatasetWellReference> datasetWellReferences =
+ convertToFeatureVectorDatasetWellIdentifier(plateWellRefs);
+ return loadFeaturesForDatasetWellReferences(datasetWellReferences, featureNames);
+ }
+
+ private List<String> listAvailableFeatureNamesForPlateWells(
+ final List<PlateWellReferenceWithDatasets> plateWellRefs)
+ {
+ final List<String> featureNames;
+ final List<FeatureVectorDatasetReference> featureVectorDatasetReferences =
+ new ArrayList<FeatureVectorDatasetReference>(plateWellRefs.size());
+ for (PlateWellReferenceWithDatasets plateWellRef : plateWellRefs)
+ {
+ featureVectorDatasetReferences.addAll(plateWellRef.getFeatureVectorDatasetReferences());
+ }
+ final List<String> availableFeatureNames =
+ listAvailableFeatureNames(featureVectorDatasetReferences);
+ featureNames = availableFeatureNames;
+ return featureNames;
+ }
+
/**
* An interface to provide mapping between image references and output streams where the images
* should be saved.
@@ -362,7 +452,7 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
}
- private static interface IReferenceHandler<R extends IDatasetIdentifier>
+ private interface IReferenceHandler<R extends IDatasetIdentifier>
{
public void handle(IDssServiceRpcScreening dssService, List<R> references);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDatasetWellReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDatasetWellReference.java
new file mode 100644
index 00000000000..c5673dc0570
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDatasetWellReference.java
@@ -0,0 +1,54 @@
+/*
+ * 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.plugin.screening.shared.api.v1.dto;
+
+import java.util.Date;
+
+/**
+ * Reference to one well in a feature vector dataset.
+ *
+ * @author Bernd Rinn
+ */
+public class FeatureVectorDatasetWellReference extends FeatureVectorDatasetReference
+{
+ private static final long serialVersionUID = 1L;
+
+ private final WellPosition wellPosition;
+
+ public FeatureVectorDatasetWellReference(String datasetCode, String datastoreServerUrl,
+ PlateIdentifier plate, Geometry plateGeometry, Date registrationDate,
+ IImageDatasetIdentifier imageDatasetIdentifier, WellPosition wellPosition)
+ {
+ super(datasetCode, datastoreServerUrl, plate, plateGeometry, registrationDate,
+ imageDatasetIdentifier);
+ this.wellPosition = wellPosition;
+ }
+
+ /**
+ * Returns the well position of this reference.
+ */
+ public WellPosition getWellPosition()
+ {
+ return wellPosition;
+ }
+
+ @Override
+ public String toString()
+ {
+ return super.toString() + " " + wellPosition.toString();
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorWithDescription.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorWithDescription.java
new file mode 100644
index 00000000000..74a099f456e
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorWithDescription.java
@@ -0,0 +1,55 @@
+package ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto;
+
+import java.io.Serializable;
+import java.util.List;
+
+/**
+ * Feature vectors of one well in one feature vector dataset.
+ *
+ * @author Bernd Rinn
+ */
+public class FeatureVectorWithDescription extends FeatureVector implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private final FeatureVectorDatasetWellReference datasetWellReference;
+
+ private final List<String> featureNames;
+
+ public FeatureVectorWithDescription(FeatureVectorDatasetWellReference dataset,
+ List<String> featureNames, double[] values)
+ {
+ super(dataset.getWellPosition(), values);
+ this.datasetWellReference = dataset;
+ this.featureNames = featureNames;
+ }
+
+ /**
+ * Identifier of the dataset and well of this feature vector.
+ */
+ public FeatureVectorDatasetWellReference getDatasetWellReference()
+ {
+ return datasetWellReference;
+ }
+
+ /**
+ * Names (and implicitly order) of the features present in each feature vector.
+ */
+ public List<String> getFeatureNames()
+ {
+ return featureNames;
+ }
+
+ @Override
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append("datasetCode: " + datasetWellReference.getDatasetCode());
+ sb.append(", storeUrl: " + datasetWellReference.getDatastoreServerUrl());
+ sb.append("\n\tfeatures: " + featureNames);
+ sb.append("\n");
+ sb.append(super.toString());
+ return sb.toString();
+ }
+
+}
\ No newline at end of file
--
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