* While written in Java, the API is idiomatic for Matlab, i.e. values are returned as
* multi-dimensional arrays. For the get... and load... methods the first
* index will contain the actual data, while the second index will contain per-row annotations. For
* getFeatureMatrix, the third index contains per-column annotations. This allows
* simple access with Matlab's slicing operator, see doc of e.g.
* {@link #getFeatureMatrix(String, String, String[])}.
*
* A typical Matlab session looks like: * *
* % Add the API jar file to the classpath
* javaaddpath('/home/brinn/matlab/openbis_screening_api-batteries_included.jar')
* % Login to server
* OpenBISScreeningML.login('user', 'secret', 'https://www.infectome.org')
*
* % ...perform calls on the server...
*
* % Logout to close the session on the server
* OpenBISScreeningML.logout()
*
*
* Note: using this login your password will end up in the Matlab command history. An alternative
* that avoids this is to call the {@link ch.systemsx.cisd.openbis.generic.client.cli.Login} class.
* Logging in on the console will grant this class access to the openBIS server.
*
* To learn the API one needs to understand three basic notions: code, augmented code and perm id.
* Space, project, experiment, plate and well have their own code, which is unique only in
* the context of the parent.
* That's why one needs augmented code to point e.g. to one experiment, because two different
* projects can have experiments with the same code.
* Such an augmented code for experiment has a form of "/space-code/project-code/experiment-code".
* For plate it has a form of "/space-code/plate-code" (note that plate code is unique on the space
* level).
* The drawback of an augmented code is that it's not persistent. If someone e.g. moves the
* experiment from one space to the other augmented code of the experiment becomes invalid. That is
* why experiments, plates and datasets have perm id (permament identifier) which never
* change and allow to refer to them with one "magic" identifier, e.g. 20110516124520378-737166.
*
java.io.tmpdir is
* used.
*/
static File tempDir = new File(System.getProperty("java.io.tmpdir"));
static final String TEMP_DIR_PREFIX = "openbis_";
static final String TEMP_DIR_POSTFIX = "_temp_dir";
//
// Authentication methods
//
/**
* Login to the openBIS server given as url.
* * Matlab example: * *
* OpenBISScreeningML.login('user', 'secret', 'https://www.infectome.org')
*
*
* @param user The user id on the server
* @param password The password on the server
* @param url The URL, e.g. https://www.infectome.org
*/
public static void login(String user, String password, String url)
{
IScreeningOpenbisServiceFacade facade = facadeFactory.tryToCreate(user, password, url);
if (facade == null)
{
throw new RuntimeException("Login failed.");
}
init(facade);
}
private static void init(IScreeningOpenbisServiceFacade openBisFacade)
{
openbis = openBisFacade;
dataSetsDir = new File(tempDir, DATASETS_FOLDER);
if (dataSetsDir.isDirectory() == false && dataSetsDir.mkdirs() == false)
{
throw new RuntimeException("Couldn't create a data set directory.");
}
temporarySessionDir =
new File(tempDir, TEMP_DIR_PREFIX + System.currentTimeMillis() / 1000
+ TEMP_DIR_POSTFIX);
if (temporarySessionDir.mkdirs() == false)
{
throw new RuntimeException("Couldn't create a temporary directory.");
}
temporarySessionDir.deleteOnExit();
loadedImages = new HashMap();
experiments = openbis.listExperiments();
experimentCodeToExperimentMap.clear();
for (ExperimentIdentifier e : experiments)
{
experimentCodeToExperimentMap.put(e.getAugmentedCode(), e);
}
plates = openbis.listPlates();
plateCodeToPlateMap.clear();
experimentToPlateMap.clear();
for (Plate p : plates)
{
final String plateCode = p.getAugmentedCode();
plateCodeToPlateMap.put(plateCode, p);
final String experimentCode = p.getExperimentIdentifier().getAugmentedCode();
List experimentPlates = experimentToPlateMap.get(experimentCode);
if (experimentPlates == null)
{
experimentPlates = new ArrayList();
experimentToPlateMap.put(experimentCode, experimentPlates);
}
experimentPlates.add(p);
}
}
/**
* Logs out and closes the session on the server.
*
* Matlab example:
*
*
* OpenBISScreeningML.logout()
*
*/
public static void logout()
{
if (openbis == null)
{
return;
}
openbis.logout();
if (Login.OPENBIS_TOKEN_FILE.exists())
{
Login.OPENBIS_TOKEN_FILE.delete();
}
delete(temporarySessionDir);
openbis = null;
}
private static void delete(File file)
{
if (file.isDirectory())
{
File[] files = file.listFiles();
for (File child : files)
{
delete(child);
}
}
file.delete();
}
//
// Information methods
//
/**
* Lists all experiment.
*
* Matlab example:
*
*
* % Get the experiments
* exps = OpenBISScreeningML.listExperiments();
* % How many experiments do we have?
* length(exps)
* % Get all information about experiment 3
* exp3 = exps(3,:)
* % Get the perm ids for all experiments
* permids = exps(:,2)
*
*
* @return Each row contains information about one experiment:
*
* { experiment augmented code, experiment perm id, experiment space code,
* experiment project code, experiment code }
*/
public static Object[][] listExperiments()
{
checkLoggedIn();
final Object[][] result = new Object[experiments.size()][5];
for (int i = 0; i < experiments.size(); ++i)
{
final Object[] annotations =
new Object[]
{ experiments.get(i).getAugmentedCode(), experiments.get(i).getPermId(),
experiments.get(i).getSpaceCode(),
experiments.get(i).getProjectCode(),
experiments.get(i).getExperimentCode() };
System.arraycopy(annotations, 0, result[i], 0, annotations.length);
}
return result;
}
/**
* Lists all plates.
*
* Matlab example:
*
*
* % Get the plates
* plates = OpenBISScreeningML.listPlates();
* % How many plates do we have?
* length(plates)
* % Get all information about plate 2
* plate2 = plates(2,:)
* % Get the simple plate codes for all plates
* codes = plates(:,4)
*
*
* @return Each row contains information about one plate:
*
* { plate augmented code, plate perm id, plate space code, plate code,
* experiment augmented code, experiment perm id, experiment space code,
* experiment project code, experiment code }
*/
public static Object[][] listPlates()
{
checkLoggedIn();
return listPlates(plates);
}
/**
* Lists the plates of experiment.
*
* Matlab example:
*
*
* % Get the plates of experiment MYEXP in project PROJ of space SPACE
* plates = OpenBISScreeningML.listPlates('/SPACE/PROJ/MYEXP');
* % How many plates do we have?
* length(plates)
* % Get all information about plate 2
* plate2 = plates(2,:)
* % Get the augmented plate codes for all plates
* acodes = plates(:,1)
*
*
* @param experiment The augmented code of the experiment to list the plates for
* @return Each row contains information about one plate:
*
* { plate augmented code, plate perm id, plate space code, plate code,
* experiment augmented code, experiment perm id, experiment space code,
* experiment project code, experiment code }
*/
public static Object[][] listPlates(String experiment)
{
checkLoggedIn();
final List experimentPlates = experimentToPlateMap.get(experiment);
if (experimentPlates == null)
{
throw new RuntimeException("No experiment with that code found.");
}
return listPlates(experimentPlates);
}
/**
* Lists the plates of experiment and analysis procedure. Each returned plate has at
* least one data set with the specified analysis procedure.
*
* Matlab example:
*
*
* % Get all plates having data sets with analysis procedure 'PROC' in the experiment MYEXP in project PROJ of space SPACE
* plates = OpenBISScreeningML.listPlates('/SPACE/PROJ/MYEXP', 'PROC');
* % Get all information about plate 2
* plate2 = plates(2,:)
* % Get the augmented plate codes for all plates
* acodes = plates(:,1)
*
*
* @param experiment The augmented code of the experiment to list the plates for
* @param analysisProcedure The analysis procedure
* @return Each row contains information about one plate:
*
* { plate augmented code, plate perm id, plate space code, plate code,
* experiment augmented code, experiment perm id, experiment space code,
* experiment project code, experiment code }
*/
public static Object[][] listPlates(String experiment, String analysisProcedure)
{
checkLoggedIn();
ExperimentIdentifier experimentIdentifier = getExperimentIdentifierOrFail(experiment);
List resultPlates = openbis.listPlates(experimentIdentifier, analysisProcedure);
return listPlates(resultPlates);
}
private static Object[][] listPlates(final List list)
{
final Object[][] result = new Object[list.size()][9];
for (int i = 0; i < list.size(); ++i)
{
final Object[] annotations =
new Object[]
{ list.get(i).getAugmentedCode(), plates.get(i).getPermId(),
list.get(i).tryGetSpaceCode(), plates.get(i).getPlateCode(),
list.get(i).getExperimentIdentifier().getAugmentedCode(),
list.get(i).getExperimentIdentifier().getPermId(),
list.get(i).getExperimentIdentifier().getSpaceCode(),
list.get(i).getExperimentIdentifier().getProjectCode(),
list.get(i).getExperimentIdentifier().getExperimentCode(), };
System.arraycopy(annotations, 0, result[i], 0, annotations.length);
}
return result;
}
/**
* Returns an alphabetically sorted list of analysis procedure codes of all data sets of a
* specified experiment.
*
* Matlab example:
*
*
* % Get the analysis procedures for experiment MYEXP in project PROJ of space SPACE
* analysisProcedures = OpenBISScreeningML.listAnalysisProcedures('/SPACE/PROJ/MYEXP');
* % How many analysis procedures do we have?
* length(analysisProcedures)
* % Get all the analysis procedure codes
* acodes = analysisProcedures(:,1)
*
*
* @param experiment The augmented code of the experiment to list analysis procedures for
* @return Each row contains information about one analysis procedure:
*
* { analysis procedure code }
*/
public static Object[][] listAnalysisProcedures(String experiment)
{
checkLoggedIn();
ExperimentIdentifier experimentIdentifier = getExperimentIdentifierOrFail(experiment);
List proceduresList = openbis.listAnalysisProcedures(experimentIdentifier);
return listAnalysisProcedures(proceduresList);
}
private static Object[][] listAnalysisProcedures(final List list)
{
final Object[][] result = new Object[list.size()][1];
for (int i = 0; i < list.size(); ++i)
{
result[i][0] = list.get(i);
}
return result;
}
/**
* Returns the properties of specified well for specified plate.
*
* Matlab example:
*
*
* % Get properties for well A03 of plate P005 in space SPACE
* properties = OpenBISScreeningML.getWellProperties('/SPACE/P005', 1, 3)
* % Get property type code of first property
* properties(1,1)
* % Get property value of first property
* properties(1,2)
*
*
* @param augmentedPlateCode The augmented plate code
* @param row The row in the plate to get the well properties for
* @param column The column in the plate to get the well properties for
* @return A two dimensional array where the first column contains the property codes and the
* second column the corresponding property values.
*/
public static Object[][] getWellProperties(String augmentedPlateCode, int row, int column)
{
checkLoggedIn();
WellPosition wellPosition = new WellPosition(row, column);
WellIdentifier wellIdentifier = getWell(augmentedPlateCode, wellPosition);
Map wellProperties = openbis.getWellProperties(wellIdentifier);
return listProperties(wellProperties);
}
/**
* Updates properties of specified well for specified plate.
*
* Matlab example:
*
*
* % Updates properties DESCRIPTION and NUMBER for well A03 of plate P005 in space SPACE
* properties = {'DESCRIPTION' 'hello example'; 'NUMBER' 3.14}
* OpenBISScreeningML.updateWellProperties('/SPACE/P005', 1, 3, properties)
*
*
* @param augmentedPlateCode The augmented plate code
* @param row The row in the plate to get the well properties for
* @param column The column in the plate to get the well properties for
* @param properties A two dimensional array where the first column contains the property codes
* and the second column the corresponding property values.
*/
public static void updateWellProperties(String augmentedPlateCode, int row, int column,
Object[][] properties)
{
checkLoggedIn();
WellPosition wellPosition = new WellPosition(row, column);
WellIdentifier wellIdentifier = getWell(augmentedPlateCode, wellPosition);
openbis.updateWellProperties(wellIdentifier, createMap(properties));
}
private static WellIdentifier getWell(String augmentedPlateCode, WellPosition wellPosition)
{
Plate plate = getPlate(augmentedPlateCode);
List wells = openbis.listPlateWells(plate);
for (WellIdentifier wellIdentifier : wells)
{
if (wellIdentifier.getWellPosition().equals(wellPosition))
{
return wellIdentifier;
}
}
throw new RuntimeException("Plate '" + augmentedPlateCode + "' has no well at "
+ wellPosition + ".");
}
/**
* Fetches metadata of the image datasets for the specified plate.
*
* Matlab example:
*
*
* % Get the metadata of image datasets of plate P005 from space SPACE
* imagesMetadata = OpenBISScreeningML.getImagesMetadata('/SPACE/P005');
* % How many image datasets do we have? Usually there will be just one.
* length(imagesMetadata)
* % What is the number of tiles in the first image dataset?
* imagesMetadata(1, 3)
*
*
* @param augmentedPlateCode The augmented plate code.
* @return { images width, images height, number of tiles in the well,
* number of tiles rows, number of tiles columns, number of plate rows, number of plate columns }
* .
*/
public static Object[][] getImagesMetadata(String augmentedPlateCode)
{
checkLoggedIn();
final Plate plateId = getPlate(augmentedPlateCode);
final List imageDatasets = listRawImageDatasets(plateId);
final List metaList = openbis.listImageMetadata(imageDatasets);
Object[][] result = new Object[metaList.size()][];
for (int i = 0; i < metaList.size(); ++i)
{
ImageDatasetMetadata meta = metaList.get(i);
ImageDatasetReference imageDatasetReference = imageDatasets.get(i);
Geometry plateGeometry = imageDatasetReference.getPlateGeometry();
result[i] =
new Object[]
{ meta.getWidth(), meta.getHeight(), meta.getNumberOfTiles(),
meta.getTilesRows(), meta.getTilesCols(),
plateGeometry.getNumberOfRows(), plateGeometry.getNumberOfColumns() };
}
return result;
}
/**
* Lists all channels measured in experiment.
*
* Matlab example:
*
*
* % Get the channels of experiment MYEXP in project PROJ of space SPACE
* channels = OpenBISScreeningML.listChannels('/SPACE/PROJ/MYEXP');
* % How many channels do we have?
* length(channels)
* % What is the name of channel 1?
* channels(1)
*
*
* @param experiment The augmented code of the experiment to list the channels for
* @return Each row contains information about one channel. Currently the only information
* available is the channel name.
*/
public static Object[][] listChannels(String experiment)
{
checkLoggedIn();
final List experimentPlates = experimentToPlateMap.get(experiment);
if (experimentPlates == null)
{
throw new RuntimeException("No experiment with that code found.");
}
if (experimentPlates.isEmpty())
{
return new Object[0][];
}
final List imageDatasets =
openbis.listRawImageDatasets(experimentPlates);
if (imageDatasets.isEmpty())
{
return new Object[0][];
}
return extractChannels(imageDatasets.get(0));
}
private static List getChannelCodes(final List meta)
{
return meta.get(0).getChannelCodes();
}
/**
* Lists all features computed for experiment using specified analysis procedure.
*
* Matlab example:
*
*
* % Get the features of experiment MYEXP in project PROJ of space SPACE
* features = OpenBISScreeningML.listFeatures('/SPACE/PROJ/MYEXP', []);
* % Get the features of experiment MYEXP in project PROJ of space SPACE which are computed
* % with analysis procedure AP-4711
* features = OpenBISScreeningML.listFeatures('/SPACE/PROJ/MYEXP', 'AP-4711');
* % How many features do we have?
* length(features)
* % What is the name of features 1?
* features(1)
*
*
* @param experiment The augmented code of the experiment to list the features for
* @param analysisProcedureOrNull The analysis procedure used to filter the result. That is, the
* result is restricted to feature vector data sets with a value of property
* ANALYSIS_PROCEDURE as specified. If null (or
* [] in MatLab) no restriction applies.
* @return Each row contains information about one feature. Currently the only information
* available is the feature name.
*/
public static Object[][] listFeatures(String experiment, String analysisProcedureOrNull)
{
checkLoggedIn();
final List experimentPlates = experimentToPlateMap.get(experiment);
if (experimentPlates == null)
{
throw new RuntimeException("No experiment with that code found.");
}
if (experimentPlates.isEmpty())
{
return new Object[0][];
}
final List featureDatasets =
openbis.listFeatureVectorDatasets(experimentPlates, analysisProcedureOrNull);
if (featureDatasets.isEmpty())
{
return new Object[0][];
}
List featureCodes = openbis.listAvailableFeatureCodes(featureDatasets);
Collections.sort(featureCodes);
Object[][] result = new Object[featureCodes.size()][1];
for (int i = 0; i < result.length; ++i)
{
result[i][0] = featureCodes.get(i);
}
return result;
}
/**
* Loads data sets for specified plate code. For each data set the path to the root of the data
* set is returned. If it is possible the path points directly into the data set store. No data
* is copied. Otherwise the data is retrieved from the data store server.
* If the same dataset is loaded for the second time in one session it will be immediately
* returned from the local cache.
*
* Matlab example:
*
*
* % Load all data sets of plate P005 in space SPACE
* dsinfo = OpenBISScreeningML.loadDataSets('/SPACE/P005', 'HCS_ANALYSIS_CELL_FEATURES_CC_MAT', '/mount/openbis-store')
* % Get the data set codes
* dsinfo(:,1)
* % Get root path of first data set (assuming there is at least one)
* dsginfo(1,2)
* % Get the properties for the first data set
* props = dsginfo(1,3)
* % Get property key of first property
* props(1,1)
* % Get property value of first property
* props(1,2)
*
*
* @param augmentedPlateCode The augmented plate code.
* @param dataSetTypeCodePattern only datasets of the type which matches the specified pattern
* will be returned. To fetch all datasets specify ".*".
* @param overrideStoreRootPathOrNull A path, in the context of the local file system mounts, to
* the DSS' store root. If null, paths are returned in the context of the DSS' file
* system mounts.
* @return Each row contains information about one data set:
*
* { data set code, data set root path, { {key1, value1}, {key2, value2} ...} }
*/
public static Object[][] loadDataSets(String augmentedPlateCode, String dataSetTypeCodePattern,
String overrideStoreRootPathOrNull)
{
return loadDataSets(augmentedPlateCode, dataSetTypeCodePattern, new Object[0][],
overrideStoreRootPathOrNull);
}
/**
* Loads data sets for specified plate code. For each data set the path to the root of the data
* set is returned. If it is possible the path points directly into the data set store. No data
* is copied. Otherwise the data is retrieved from the data store server.
* If the same dataset is loaded for the second time in one session it will be immediately
* returned from the local cache.
*
* Matlab example:
*
*
* % Load all data sets of plate P005 in space SPACE
* properties = {'ANALYSIS_PROCEDURE' 'AX87'}
* dsinfo = OpenBISScreeningML.loadDataSets('/SPACE/P005', 'HCS_ANALYSIS_CELL_FEATURES_CC_MAT', properties, '/mount/openbis-store')
* % Get the data set codes
* dsinfo(:,1)
* % Get root path of first data set (assuming there is at least one)
* dsinfo(1,2)
* % Get the properties for the first data set
* props = dsinfo(1,3)
* % Get property key of first property
* props(1,1)
* % Get property value of first property
* props(1,2)
*
*
* @param augmentedPlateCode The augmented plate code.
* @param dataSetTypeCodePattern only data sets of the type which matches the specified pattern
* will be returned. To fetch all data sets specify ".*".
* @param properties Only data set with specified property values will be returned. This is a
* two dimensional array where the first column contains the property codes and the
* second column the corresponding property values.
* @return Each row contains information about one data set:
* @param overrideStoreRootPathOrNull A path, in the context of the local file system mounts, to
* the DSS' store root. If null, paths are returned in the context of the DSS' file
* system mounts.
*
* { data set code, data set root path, { {key1, value1}, {key2, value2} ...} }
*/
public static Object[][] loadDataSets(String augmentedPlateCode,
final String dataSetTypeCodePattern, final Object[][] properties,
String overrideStoreRootPathOrNull)
{
checkLoggedIn();
Plate plateIdentifier = getPlate(augmentedPlateCode);
List dataSets =
openbis.getFullDataSets(plateIdentifier, new AndDataSetFilter(
new TypeBasedDataSetFilter(dataSetTypeCodePattern),
new PropertiesBasedDataSetFilter(createMap(properties))));
Object[][] result = new Object[dataSets.size()][];
try
{
for (int i = 0; i < dataSets.size(); i++)
{
DataSet dataSet = dataSets.get(i);
String code = dataSet.getCode();
File file = new File(dataSetsDir, code);
if (file.exists() == false)
{
file =
dataSet.getLinkOrCopyOfContents(overrideStoreRootPathOrNull,
dataSetsDir);
}
Object[][] dataSetProperties = listProperties(dataSet.getProperties());
result[i] = new Object[]
{ code, file.getPath(), dataSetProperties };
}
return result;
} catch (Exception ex)
{
throw new RuntimeException("Loading data sets for plate '" + augmentedPlateCode
+ "' failed: " + ex, ex);
}
}
/**
* Loads file/folder of specified data set and specified file/folder path inside the data set.
* If it is possible the path points directly into the data set store. No data is copied.
* Otherwise the data is retrieved from the data store server.
*
* Matlab example:
*
*
* % List all data sets of plate P005 in space SPACE. The query is restricted to data sets
* % of a type starting with HCS_IMAGE
* files = OpenBISScreeningML.listDataSetsFiles('/SPACE/P005', 'HCS_IMAGE.*')
* % Load from the first data set (assuming at least one data set found) the third file/folder
* % (assuming at least three files/folders)
* file = OpenBISScreeningML.loadDataSetFile(files(1,1), files(1,2,3), [])
*
*
* @param dataSetCode The code of the data set.
* @param pathInDataSet Path inside the data set pointing to the file/folder which should be
* down loaded. Use '/' if all files are requested.
* @param overrideStoreRootPathOrNull A path, in the context of the local file system mounts, to
* the DSS' store root. If null, paths are returned in the context of the DSS' file
* system mounts.
* @return path to the down loaded file/folder.
*/
public static Object loadDataSetFile(String dataSetCode, String pathInDataSet,
String overrideStoreRootPathOrNull)
{
checkLoggedIn();
IDataSetDss dataSet = openbis.getDataSet(dataSetCode);
return dataSet.getLinkOrCopyOfContent(overrideStoreRootPathOrNull, temporarySessionDir,
pathInDataSet).toString();
}
/**
* Lists all files of all data sets for specifies plate and data set type code matching
* specified regular expression pattern.
*
* Matlab example:
*
*
* % List all data sets of plate P005 in space SPACE. The query is restricted to data sets
* % of a type starting with HCS_IMAGE
* files = OpenBISScreeningML.listDataSetsFiles('/SPACE/P005', 'HCS_IMAGE.*')
* % Codes of all found data sets
* files(:,1)
* % Code of third data set (assuming at least three data sets found)
* files(3,1)
* % Files of third data set (assuming at least three data sets found)
* files(3,2,:)
*
*
* @param augmentedPlateCode The augmented plate code.
* @param dataSetTypeCodePattern only data sets of the type which matches the specified pattern
* will be returned. To fetch all data sets specify ".*".
* @return {data set code, file/folder paths}
*/
public static Object[][][] listDataSetsFiles(String augmentedPlateCode,
String dataSetTypeCodePattern)
{
checkLoggedIn();
Plate plateIdentifier = getPlate(augmentedPlateCode);
List dataSets =
openbis.getDataSets(plateIdentifier, new TypeBasedDataSetFilter(
dataSetTypeCodePattern));
Object[][][] result = new Object[dataSets.size()][][];
for (int i = 0; i < dataSets.size(); i++)
{
IDataSetDss dataSet = dataSets.get(i);
FileInfoDssDTO[] fileInfos = dataSet.listFiles("/", true);
String code = dataSet.getCode();
result[i] = new Object[2][];
result[i][0] = new Object[]
{ code };
result[i][1] = new Object[fileInfos.length];
for (int j = 0; j < fileInfos.length; j++)
{
FileInfoDssDTO fileInfo = fileInfos[j];
result[i][1][j] = fileInfo.getPathInDataSet();
}
}
return result;
}
/**
* Uploads specified data set for specified plate. The data set code will be returned.
*
* Matlab example:
*
*
* % Upload data set /path/to/my-data-set with properties DESCRIPTION and NUMBER for
* % plate P005 in space SPACE
* properties = {'DESCRIPTION' 'hello example'; 'NUMBER' 3.14}
* datasetcode = OpenBISScreeningML.uploadDataSet('/SPACE/P005', '/path/to/my-data-set', 'HCS_IMAGE', properties)
*
*
* @param augmentedPlateCode The augmented plate code.
* @param dataSetFilePath Path to the data set file/folder to be uploaded.
* @param dataSetType Data set type.
* @param dataSetProperties A two dimensional array where the first column contains the property
* codes and the second column the corresponding property values.
*/
public static Object uploadDataSet(String augmentedPlateCode, String dataSetFilePath,
String dataSetType, Object[][] dataSetProperties)
{
checkLoggedIn();
Plate plateIdentifier = getPlate(augmentedPlateCode);
File dataSetFile = new File(dataSetFilePath);
if (dataSetFile.exists() == false)
{
throw new RuntimeException("Unknown data set file path '" + dataSetFilePath + "'.");
}
try
{
Map map = createMap(dataSetProperties);
IDataSetDss dataSet =
openbis.putDataSet(plateIdentifier, dataSetFile, new NewDataSetMetadataDTO(
dataSetType, map));
return dataSet.getCode();
} catch (Exception ex)
{
throw new RuntimeException("Couldn't upload data set for plate '" + augmentedPlateCode
+ "'.", ex);
}
}
/**
* Uploads specified data set for specified plate. The data set code will be returned.
*
* Matlab example:
*
*
* % Upload data set /path/to/my-data-set with properties DESCRIPTION and NUMBER for
* % plate P005 in space SPACE
* % with data set 201007091122-928 as the parent
* properties = {'DESCRIPTION' 'hello example'; 'NUMBER' 3.14}
* parents = {'201007091122-928' }
* datasetcode = OpenBISScreeningML.uploadDataSetForPlateAndParents('/SPACE/P005', parents, '/path/to/my-data-set', 'HCS_IMAGE', properties)
*
*
* @param augmentedPlateCode The augmented plate code.
* @param parentDataSetCodeObjects The codes of the parents of this data set
* @param dataSetFilePath Path to the data set file/folder to be uploaded.
* @param dataSetType Data set type.
* @param dataSetProperties A two dimensional array where the first column contains the property
* codes and the second column the corresponding property values.
*/
public static Object uploadDataSetForPlateAndParents(String augmentedPlateCode,
Object[] parentDataSetCodeObjects, String dataSetFilePath, String dataSetType,
Object[][] dataSetProperties)
{
checkLoggedIn();
Plate plateIdentifier = getPlate(augmentedPlateCode);
List dataSetCodes = createStringList(parentDataSetCodeObjects);
File dataSetFile = new File(dataSetFilePath);
if (dataSetFile.exists() == false)
{
throw new RuntimeException("Unknown data set file path '" + dataSetFilePath + "'.");
}
try
{
Map map = createMap(dataSetProperties);
IDataSetDss dataSet =
openbis.putDataSet(plateIdentifier, dataSetFile, new NewDataSetMetadataDTO(
dataSetType, map, dataSetCodes));
return dataSet.getCode();
} catch (Exception ex)
{
throw new RuntimeException("Couldn't upload data set for plate '" + augmentedPlateCode
+ "'.", ex);
}
}
/**
* Uploads a data set to the specified experiment, setting the data set parents. The data set
* code will be returned.
*
* Matlab example:
*
*
* % Upload data set /path/to/my-data-set (with property DESCRIPTION)
* % to experiment E103 in project PROJECT and space SPACE,
* % with data set 201007091122-928 as the parent
* properties = {'DESCRIPTION' 'hello example' }
* parents = {'201007091122-928' }
* datasetcode = OpenBISScreeningML.uploadDataSetForExperimentAndParents('/SPACE/PROJECT/E103', parents, '/path/to/my-data-set', 'HCS_IMAGE', properties)
*
*
* @param augmentedExperimentCode The augmented experiment code.
* @param parentDataSetCodeObjects The codes of the parents of this data set
* @param dataSetFilePath Path to the data set file/folder to be uploaded.
* @param dataSetType Data set type.
* @param dataSetProperties A two dimensional array where the first column contains the property
* codes and the second column the corresponding property values.
*/
public static Object uploadDataSetForExperimentAndParents(String augmentedExperimentCode,
Object[] parentDataSetCodeObjects, String dataSetFilePath, String dataSetType,
Object[][] dataSetProperties)
{
checkLoggedIn();
ExperimentIdentifier experimentIdentifier =
getExperimentIdentifierOrFail(augmentedExperimentCode);
List dataSetCodes = createStringList(parentDataSetCodeObjects);
File dataSetFile = new File(dataSetFilePath);
if (dataSetFile.exists() == false)
{
throw new RuntimeException("Unknown data set file path '" + dataSetFilePath + "'.");
}
try
{
Map map = createMap(dataSetProperties);
IDataSetDss dataSet =
openbis.putDataSet(experimentIdentifier, dataSetFile,
new NewDataSetMetadataDTO(dataSetType, map, dataSetCodes));
return dataSet.getCode();
} catch (Exception ex)
{
throw new RuntimeException("Couldn't upload data set for experiment '"
+ augmentedExperimentCode + "' and parents '"
+ Arrays.toString(parentDataSetCodeObjects) + "'.", ex);
}
}
private static Map createMap(Object[][] properties)
{
Map map = new HashMap();
for (Object[] objects : properties)
{
if (objects.length == 2)
{
Object value = objects[1];
map.put(objects[0].toString(), value == null ? null : value.toString());
}
}
return map;
}
private static List createStringList(Object[] identifiers)
{
List list = new ArrayList();
for (Object identifier : identifiers)
{
list.add(identifier.toString());
}
return list;
}
//
// Images
//
/**
* Loads the TIFF images for the given well location, all tiles and all channels and stores them
* in temporary files. The temporary files will be removed automatically when the Java Virtual
* Machine exits.
*
* Matlab example:
*
*
* % Load the images for all channels of well B10 of plate P005 in space SPACE
* imginfo = OpenBISScreeningML.loadImages('/SPACE/P005', 2, 10)
* % Get the plate-well descriptions of all locations
* imginfo(2,:,3)
* % Show the third image (assuming there are at least three images)
* imtool(imginfo(1,3))
*
*
* @param plate The augmented plate code
* @param row The row in the plate to get the images for
* @param col The column in the plate to get the images for
* @return { names of TIFF files, image annotation }
*
* Each of names of TIFF files and image annotation is a
* vector of length of the number of images.
*
* image annotation contains
* { channel name, tile number, plate well description,
* plate augmented code, plate perm id, plate space code, plate code, row, column,
* experiment augmented code, experiment perm id, experiment space code,
* experiment project code, experiment code, data set code }
*/
public static Object[][][] loadImages(String plate, int row, int col)
{
return loadImages(plate, row, col, (String[]) null);
}
/**
* Loads the TIFF images for the given well location, tile number, and all channels and stores
* them in temporary files. The temporary files will be removed automatically when the Java
* Virtual Machine exits.
*
* Matlab example:
*
*
* % Load the images for all channels of well B10 and tile 3 of plate P005 in space SPACE
* imginfo = OpenBISScreeningML.loadImages('/SPACE/P005', 2, 10, 3)
* % Get the plate-well descriptions of all locations
* imginfo(2,:,3)
* % Show the third image (assuming there are at least three images)
* imtool(imginfo(1,3))
*
*
* @param plate The augmented plate code
* @param row The row in the plate to get the images for
* @param col The column in the plate to get the images for
* @param tile The tile number. Starts with 0.
* @return { names of TIFF files, image annotation }
*
* Each of names of TIFF files and image annotation is a
* vector of length of the number of images.
*
* image annotation contains
* { channel name, tile number, plate well description,
* plate augmented code, plate perm id, plate space code, plate code, row, column,
* experiment augmented code, experiment perm id, experiment space code,
* experiment project code, experiment code, data set code }
*/
public static Object[][][] loadImages(String plate, int row, int col, int tile)
{
return loadImages(plate, row, col, tile, (String[]) null);
}
/**
* Loads the TIFF images for the given well location, list of channels, and all tiles and stores
* them in temporary files. The temporary files will be removed automatically when the Java
* Virtual Machine exits.
*
* Matlab example:
*
*
* % Load the images for channel DAPI of well H10 of plate P005 in space SPACE
* imginfo=OpenBISScreeningML.loadImages('/SPACE/P005', 8, 10, 'DAPI')
* % Get the channel names and tile numbers of all locations
* imginfo(2,:,1:2)
* % Show the second image (assuming there are at least two images)
* imtool(imginfo(1,2))
*
*
* @param plate The augmented plate code
* @param row The row in the plate to get the images for
* @param col The column in the plate to get the images for
* @param channels The names of the channels to get the images for
* @return { names of TIFF files, image annotation }
*
* Each of names of TIFF files and image annotation is a
* vector of length of the number of images.
*
* image annotation contains
* { channel name, tile number, plate well description,
* plate augmented code, plate perm id, plate space code, plate code, row, column,
* experiment augmented code, experiment perm id, experiment space code,
* experiment project code, experiment code, data set code }
*/
public static Object[][][] loadImages(String plate, int row, int col, String[] channels)
{
return loadRawImages(plate, row, col, channels, createAllTilesIterator());
}
/**
* Has the same effect as {@link #loadImages(String, int, int, String[])}, but instead of
* loading raw images loads their segmentation results if available.
*
* @param objectNamesOrNull The names of the segmentation objects to get the images for. If
* null (or [] in MatLab) no restriction applies.
* @param analysisProcedureOrNull The analysis procedure used to filter the result. That is, the
* result is restricted to feature vector data sets with a value of property
* ANALYSIS_PROCEDURE as specified. If null (or
* [] in MatLab) no restriction applies.
*/
public static Object[][][] loadSegmentationImages(String plate, int row, int col,
String[] objectNamesOrNull, String analysisProcedureOrNull)
{
return loadSegmentationImages(plate, row, col, objectNamesOrNull, createAllTilesIterator(),
analysisProcedureOrNull);
}
private static ITileNumberIterable createAllTilesIterator()
{
return new ITileNumberIterable()
{
private int maximumNumberOfTiles;
public void setMaximumNumberOfTiles(int numberOfTiles)
{
this.maximumNumberOfTiles = numberOfTiles;
}
public int getMaximumNumberOfTiles()
{
return maximumNumberOfTiles;
}
public Iterator iterator()
{
return new Iterator()
{
private int index;
public boolean hasNext()
{
return index < maximumNumberOfTiles;
}
public Integer next()
{
return index++;
}
public void remove()
{
throw new UnsupportedOperationException();
}
};
}
};
}
/**
* Loads the TIFF images for the given well location, tile number, and list of channels and
* stores them in temporary files. The temporary files will be removed automatically when the
* Java Virtual Machine exits.
*
* Matlab example:
*
*
* % Load the images for channel DAPI of well H10 and tile 3 of plate P005 in space SPACE
* imginfo=OpenBISScreeningML.loadImages('/SPACE/P005', 8, 10, 3, 'DAPI')
* % Get the channel names of all locations
* imginfo(2,:,1)
* % Show the second image (assuming there are at least two images)
* imtool(imginfo(1,2))
*
*
* @param plate The augmented plate code
* @param row The row in the plate to get the images for
* @param col The column in the plate to get the images for
* @param tile The tile number. Starts with 0.
* @param channels The names of the channels to get the images for
* @return { names of TIFF files, image annotation }
*
* Each of names of TIFF files and image annotation is a
* vector of length of the number of images.
*
* image annotation contains
* { channel name, tile number, plate well description,
* plate augmented code, plate perm id, plate space code, plate code, row, column,
* experiment augmented code, experiment perm id, experiment space code,
* experiment project code, experiment code, data set code }
*/
public static Object[][][] loadImages(String plate, int row, int col, final int tile,
String[] channels)
{
return loadRawImages(plate, row, col, channels, createSingleTileIterator(tile));
}
/**
* Has the same effect as {@link #loadImages(String, int, int, int, String[])}, but instead of
* loading raw images loads their segmentation results if available.
*
* @param objectNamesOrNull The names of the segmentation objects to get the images for. If
* null (or [] in MatLab) no restriction applies.
* @param analysisProcedureOrNull The analysis procedure used to filter the result. That is, the
* result is restricted to feature vector data sets with a value of property
* ANALYSIS_PROCEDURE as specified. If null (or
* [] in MatLab) no restriction applies.
*/
public static Object[][][] loadSegmentationImages(String plate, int row, int col,
final int tile, String[] objectNamesOrNull, String analysisProcedureOrNull)
{
return loadSegmentationImages(plate, row, col, objectNamesOrNull,
createSingleTileIterator(tile), analysisProcedureOrNull);
}
private static ITileNumberIterable createSingleTileIterator(final int tile)
{
return new ITileNumberIterable()
{
public void setMaximumNumberOfTiles(int numberOfTiles)
{
if (tile >= numberOfTiles)
{
throw new IllegalArgumentException("Tile number " + tile
+ " is not less than number of tiles " + numberOfTiles + ".");
}
}
public int getMaximumNumberOfTiles()
{
return 1;
}
public Iterator iterator()
{
return new Iterator()
{
private boolean delivered;
public boolean hasNext()
{
return delivered == false;
}
public Integer next()
{
delivered = true;
return tile;
}
public void remove()
{
throw new UnsupportedOperationException();
}
};
}
};
}
/**
* Lists all segmentation objects for the plate.
*
* Matlab example:
*
*
* % Get the segmentation objects of plate P005 in space SPACE.
* segmentationObjects = OpenBISScreeningML.listSegmentationObjects('/SPACE/P005', []);
* % Get the segmentation objects of plate P005 in space SPACE for data sets calculated
* % with analysis procedure AP-42.
* segmentationObjects = OpenBISScreeningML.listSegmentationObjects('/SPACE/P005', 'AP-42');
* % How many segmentation objects do we have?
* length(segmentationObjects)
* % What is the name of segmentation objects 1?
* segmentationObjects(1)
*
*
* @param plate augmented code of the plate
* @param analysisProcedureOrNull The analysis procedure used to filter the result. That is, the
* result is restricted to feature vector data sets with a value of property
* ANALYSIS_PROCEDURE as specified. If null (or
* [] in MatLab) no restriction applies.
* @return Each row contains information about one segmentation object. Currently the only
* information available is the segmentation object name.
*/
public static Object[][] listSegmentationObjects(String plate, String analysisProcedureOrNull)
{
checkLoggedIn();
Plate plateId = getPlate(plate);
final List imageDatasets =
listSegmentationImageDatasets(plateId, analysisProcedureOrNull);
if (imageDatasets.isEmpty())
{
return new Object[0][];
}
return extractChannels(imageDatasets.get(0));
}
private static Object[][] extractChannels(ImageDatasetReference imageDatasetReference)
{
final List meta =
openbis.listImageMetadata(Arrays.asList(imageDatasetReference));
if (meta.isEmpty())
{
return new Object[0][];
}
final List channels = getChannelCodes(meta);
Object[][] result = new Object[channels.size()][1];
for (int i = 0; i < result.length; ++i)
{
result[i][0] = channels.get(i);
}
return result;
}
private static Object[][][] loadRawImages(String plate, int row, int col, String[] channels,
ITileNumberIterable tileNumberIterable)
{
checkLoggedIn();
final Plate plateId = getPlate(plate);
final List imageDatasets = listRawImageDatasets(plateId);
return loadImages(plateId, imageDatasets, row, col, channels, tileNumberIterable);
}
private static Object[][][] loadSegmentationImages(String plate, int row, int col,
String[] channelsOrNull, ITileNumberIterable tileNumberIterable,
String analysisProcedureOrNull)
{
checkLoggedIn();
final Plate plateId = getPlate(plate);
final List imageDatasets =
listSegmentationImageDatasets(plateId, analysisProcedureOrNull);
return loadImages(plateId, imageDatasets, row, col, channelsOrNull, tileNumberIterable);
}
private static Object[][][] loadImages(Plate plate, List imageDatasets,
int row, int col, String[] channelsOrNull, ITileNumberIterable tileNumberIterable)
{
final List meta = openbis.listImageMetadata(imageDatasets);
if (meta.isEmpty())
{
return new Object[][][]
{ new Object[0][], new Object[0][] };
}
final List imageChannels;
if (channelsOrNull == null || channelsOrNull.length == 0)
{
imageChannels = getChannelCodes(meta);
} else
{
imageChannels = Arrays.asList(channelsOrNull);
}
final List imageReferencesAndFiles =
new ArrayList(imageDatasets.size());
final Object[][][] result = new Object[2][][];
tileNumberIterable.setMaximumNumberOfTiles(meta.get(0).getNumberOfTiles());
int numberOfTiles = tileNumberIterable.getMaximumNumberOfTiles();
result[0] = new Object[imageDatasets.size() * imageChannels.size() * numberOfTiles][1];
result[1] = new Object[imageDatasets.size() * imageChannels.size() * numberOfTiles][15];
int resultIdx = 0;
for (ImageDatasetReference ds : imageDatasets)
{
for (String channel : imageChannels)
{
for (Integer tile : tileNumberIterable)
{
final PlateImageReference ref =
new PlateImageReference(row, col, tile, channel, ds);
final File imageFile = createImageFileName(plate, ref);
imageReferencesAndFiles.add(new ImageReferenceAndFile(ref, imageFile));
result[0][resultIdx][0] = imageFile.getPath();
PlateIdentifier plateIdentifier = ds.getPlate();
ExperimentIdentifier expIdentifier = ds.getExperimentIdentifier();
final Object[] annotations =
new Object[]
{ channel, tile,
createPlateWellDescription(plateIdentifier, row, col),
plateIdentifier.getAugmentedCode(),
plateIdentifier.getPermId(),
plateIdentifier.tryGetSpaceCode(),
plateIdentifier.getPlateCode(), row, col,
expIdentifier.getAugmentedCode(),
expIdentifier.getPermId(), expIdentifier.getSpaceCode(),
expIdentifier.getProjectCode(),
expIdentifier.getExperimentCode(), ds.getPermId(), };
System.arraycopy(annotations, 0, result[1][resultIdx], 0, annotations.length);
resultIdx++;
}
}
}
try
{
loadImages(imageReferencesAndFiles);
} catch (IOException ex)
{
throw new RuntimeException(ex);
}
return result;
}
private static List listRawImageDatasets(final Plate plateId)
{
return openbis.listRawImageDatasets(Arrays.asList(plateId));
}
private static List listSegmentationImageDatasets(final Plate plateId,
String analysisProcedureOrNull)
{
return openbis.listSegmentationImageDatasets(Arrays.asList(plateId),
analysisProcedureOrNull);
}
/**
* Saves images for a given list of image references (given by data set code, well position,
* channel and tile) and files.
*
* @throws IOException when reading images from the server or writing them to the files fails
*/
private static void loadImages(List imageReferencesAndFiles)
throws IOException
{
List imageReferences = new ArrayList();
final Map imageRefToFileMap =
new HashMap();
for (ImageReferenceAndFile imageReferenceAndFile : imageReferencesAndFiles)
{
PlateImageReference imageReference = imageReferenceAndFile.getImageReference();
File file = loadedImages.get(imageReference);
if (file == null)
{
imageReferences.add(imageReference);
imageRefToFileMap.put(imageReference, imageReferenceAndFile);
}
}
try
{
openbis.loadImages(imageReferences, new IImageOutputStreamProvider()
{
public OutputStream getOutputStream(PlateImageReference imageReference)
throws IOException
{
return imageRefToFileMap.get(imageReference).open();
}
}, false);
} finally
{
Collection values = imageRefToFileMap.values();
for (ImageReferenceAndFile imageReferenceAndFile : values)
{
imageReferenceAndFile.close();
PlateImageReference imageReference = imageReferenceAndFile.getImageReference();
loadedImages.put(imageReference, imageReferenceAndFile.getImageFile());
}
}
}
private static File createImageFileName(Plate plate, PlateImageReference image)
{
final WellPosition well = image.getWellPosition();
File imageDir = new File(temporarySessionDir, "images");
imageDir.mkdirs();
final File f =
new File(imageDir, "img_" + plate.getPlateCode() + "_" + image.getDatasetCode()
+ "_row" + well.getWellRow() + "_col" + well.getWellColumn() + "_"
+ image.getChannel() + "_tile" + image.getTile() + ".tiff");
f.deleteOnExit();
return f;
}
//
// Feature matrix
//
/**
* Returns the feature matrix of the specified features for all locations in
* experiment (a location is one well position in one feature vector data set) in
* experiment connected to gene in [0], location annotations
* in [1] and feature annotation in [2].
*
* Matlab example:
*
*
* % Get feature matrix for experiment /SPACE/PROJ/MYEXP for locations connected to GENENAME
* fmatrix = OpenBISScreeningML.getFeatureMatrix('/SPACE/PROJ/MYEXP', 'GENENAME', [], []);
* % Get feature matrix for features F1, F2 and F3 for
* % experiment /SPACE/PROJ/MYEXP for locations connected to GENENAME
* fmatrix = OpenBISScreeningML.getFeatureMatrix('/SPACE/PROJ/MYEXP', 'GENENAME', [], {'F1' 'F2' 'F3'));
* % Get feature matrix for features F1 and F2 for experiment /SPACE/PROJ/MYEXP for locations
* % connected to GENENAME calculated with analysis procedure AP-42.
* fmatrix = OpenBISScreeningML.getFeatureMatrix('/SPACE/PROJ/MYEXP', 'GENENAME', 'AP-42', {'F1' 'F2'));
* % Get the feature vector for the second location (assuming that there are at least two locations)
* % of third data set (assuming that there are at least three data sets)
* fmatrix(1,:,2,3)
* % Get the values of the fourth feature for all locations (assuming that there are at least 4 features)
* % of third data set (assuming that there are at least three data sets)
* fmatrix(1,4,:,3)
* % Get code of the fourth feature (assuming that there are at least 4 features)
* fmatrix(3,4)
* % Get the plate-well descriptions for the second location (assuming that there are at least two locations)
* % of third data set (assuming that there are at least three data sets)
* fmatrix(2,2,3,:)
*
*
* @param experiment The augmented experiment code
* @param gene The gene code (stored as material code in openBIS, usually it is gene id)
* @param analysisProcedureOrNull The code of the analysis procedure used to calculate requested
* features. That is, the result is restricted to feature vector data sets with a
* value of property ANALYSIS_PROCEDURE as specified. If
* null (or [] in MatLab) no restriction applies.
* @param featuresOrNull The codes of the features to contain the feature matrix. Unknown
* feature codes will be ignored. If null (or [] in MatLab)
* all features are returned.
* @return a four dimensional matrix. The first dimension denotes the type in the following
* order: {feature matrix, annotations per location, feature codes}. The
* other dimensions depend on the value of the first dimension:
*
* - feature matrix: 2. dimension is feature vector, 3. dimension is location number,
* 4. dimension is data set number. If for a particular location and a particular data
* set the corresponding feature value does not exists
NaN will be
* returned. - annotations: 2. dimension is location number, 3. dimension is data set
* number, 4. dimension is location annotations in the following order:
{plate
* well description, plate augmented code, plate perm id, plate space code, plate code,
* row, column, experiment augmented code, experiment perm id, experiment space code,
* experiment project code, experiment code, data set code, data set type} -
* feature codes: 2. dimension is feature codes in alphabetical order. 3. and 4.
* dimension are meaningless (i.e. they have length one)
*
*/
public static Object[][][][] getFeatureMatrix(String experiment, String gene,
String analysisProcedureOrNull, String[] featuresOrNull)
{
checkLoggedIn();
final ExperimentIdentifier experimentId = experimentCodeToExperimentMap.get(experiment);
if (experimentId == null)
{
throw new RuntimeException("No experiment with that code found.");
}
final List experimentPlates = experimentToPlateMap.get(experiment);
if (experimentPlates == null || experimentPlates.isEmpty())
{
return new Object[][][][]
{ new Object[0][][], new Object[0][][], new Object[0][][] };
}
final List featureVectors =
openbis.loadFeaturesForPlateWells(experimentId, new MaterialIdentifier(
MaterialTypeIdentifier.GENE, gene), analysisProcedureOrNull,
(featuresOrNull == null) ? null : Arrays.asList(featuresOrNull));
return getFeatureMatrix(featureVectors);
}
/**
* Returns the feature matrix of the specified features for all locations (a location is one
* well position in one feature vector data set) in experiment connected to
* gene in [0], location annotations in [1] and feature
* annotation in [2].
*
* Matlab example:
*
*
* % Get feature matrix for GENENAME
* fmatrix = OpenBISScreeningML.getFeatureMatrix('GENENAME', [], []);
* % Get feature matrix for features FEATURE1, FEATURE2 and FEATURE3 for GENENAME
* fmatrix = OpenBISScreeningML.getFeatureMatrix('GENENAME', [], {'FEATURE1' 'FEATURE2' 'FEATURE3'});
* % Get feature matrix for features FEATURE1 and FEATURE2 for GENENAME
* % computed with analysis procedure AP-42
* fmatrix = OpenBISScreeningML.getFeatureMatrix('GENENAME', 'AP-42', {'FEATURE1' 'FEATURE2'});
* % Get the feature vector for the second location (assuming that there are at least two locations)
* % of third data set (assuming that there are at least three data sets)
* fmatrix(1,:,2,3)
* % Get the values of the fourth feature for all locations (assuming that there are at least 4 features)
* % of third data set (assuming that there are at least three data sets)
* fmatrix(1,4,:,3)
* % Get code of the fourth feature (assuming that there are at least 4 features)
* fmatrix(3,4)
* % Get the plate-well descriptions for the second location (assuming that there are at least two locations)
* % of third data set (assuming that there are at least three data sets)
* fmatrix(2,2,3,:)
*
*
* @param gene The gene code (stored as material code in openBIS, usually it is gene id)
* @param analysisProcedureOrNull The code of the analysis procedure used to calculate requested
* features. That is, the result is restricted to feature vector data sets with a
* value of property ANALYSIS_PROCEDURE as specified. If
* null (or [] in MatLab) no restriction applies.
* @param featuresOrNull The codes of the features to contain the feature matrix. Unknown
* feature codes will be ignored. If null (or [] in MatLab)
* all features are returned.
* @return a four dimensional matrix. The first dimension denotes the type in the following
* order: {feature matrix, annotations per location, feature codes}. The
* other dimensions depend on the value of the first dimension:
*
* - feature matrix: 2. dimension is feature vector, 3. dimension is location number,
* 4. dimension is data set number. If for a particular location and a particular data
* set the corresponding feature value does not exists
NaN will be
* returned. - annotations: 2. dimension is location number, 3. dimension is data set
* number, 4. dimension is location annotations in the following order:
{plate
* well description, plate augmented code, plate perm id, plate space code, plate code,
* row, column, experiment augmented code, experiment perm id, experiment space code,
* experiment project code, experiment code, data set code, data set type} -
* feature codes: 2. dimension is feature codes in alphabetical order. 3. and 4.
* dimension are meaningless (i.e. they have length one)
*
*/
public static Object[][][][] getFeatureMatrix(String gene, String analysisProcedureOrNull,
String[] featuresOrNull)
{
checkLoggedIn();
final List featureVectors =
openbis.loadFeaturesForPlateWells(new MaterialIdentifier(
MaterialTypeIdentifier.GENE, gene), analysisProcedureOrNull,
(featuresOrNull == null) ? null : Arrays.asList(featuresOrNull));
return getFeatureMatrix(featureVectors);
}
private static Object[][][][] getFeatureMatrix(
final List featureVectors)
{
final Object[][][][] result = new Object[3][][][];
if (featureVectors.isEmpty())
{
return result;
}
List featureCodes = getFeatureCodes(featureVectors);
Map featureCodeToIndexMap = new HashMap();
result[2] = new Object[featureCodes.size()][1][1];
for (int i = 0; i < featureCodes.size(); ++i)
{
String code = featureCodes.get(i);
result[2][i][0][0] = code;
featureCodeToIndexMap.put(code, i);
}
IndexSet dataSetCodes = new IndexSet();
IndexSet wellPositions = new IndexSet();
for (FeatureVectorWithDescription featureVector : featureVectors)
{
WellPosition wellPosition = featureVector.getWellPosition();
wellPositions.add(wellPosition);
dataSetCodes.add(featureVector.getDatasetWellReference().getDatasetCode());
}
result[0] = new Object[featureCodes.size()][wellPositions.size()][dataSetCodes.size()];
result[1] = new Object[wellPositions.size()][dataSetCodes.size()][14];
for (FeatureVectorWithDescription vector : featureVectors)
{
WellPosition wellPosition = vector.getWellPosition();
int wellIndex = wellPositions.getIndex(wellPosition);
int[] featureIndexes = createFeatureIndexes(vector, featureCodeToIndexMap);
FeatureVectorDatasetWellReference dataSetRef = vector.getDatasetWellReference();
int dataSetIndex = dataSetCodes.getIndex(dataSetRef.getDatasetCode());
copyFeatureValuesInto(result, wellIndex, dataSetIndex, featureIndexes, vector);
copyAnnotationsInto(result, wellIndex, dataSetIndex, dataSetRef, vector);
}
return replaceFeatureNullValuesByNaN(result);
}
/**
* Returns the feature matrix of the specified features for all locations (a location is one
* well position in one feature vector data set) of all feature vector data sets created by
* specified analysis procedure of the given plate in [0], location
* annotations in [1] and feature annotation in [2].
*
* Matlab example:
*
*
* % Get feature matrix for PLATECODE
* fmatrix = OpenBISScreeningML.getFeatureMatrixForPlate('PLATECODE', [], []);
* % Get feature matrix for features FEATURE1, FEATURE2 and FEATURE3 for PLATECODE.
* fmatrix = OpenBISScreeningML.getFeatureMatrixForPlate('PLATECODE', [], {'FEATURE1' 'FEATURE2' 'FEATURE3'});
* % Get feature matrix for features FEATURE1 and FEATURE2 for PLATECODE calculated by analysis procedure AP-42.
* fmatrix = OpenBISScreeningML.getFeatureMatrixForPlate('PLATECODE', 'AP-42', {'FEATURE1' 'FEATURE2'});
* % Get the feature vector for the second location (assuming that there are at least two locations)
* % of third data set (assuming that there are at least three data sets)
* fmatrix(1,:,2,3)
* % Get the values of the fourth feature for all locations (assuming that there are at least 4 features)
* % of third data set (assuming that there are at least three data sets)
* fmatrix(1,4,:,3)
* % Get code of the fourth feature (assuming that there are at least 4 features)
* fmatrix(3,4)
* % Get the plate-well descriptions for the second location (assuming that there are at least two locations)
* % of third data set (assuming that there are at least three data sets)
* fmatrix(2,2,3,:)
*
*
* @param plate augmented code of the plate for which features should be loaded
* @param analysisProcedureOrNull The code of the analysis procedure used to calculate requested
* features. That is, the result is restricted to feature vector data sets with a
* value of property ANALYSIS_PROCEDURE as specified. If
* null (or [] in MatLab) no restriction applies.
* @param featuresOrNull The codes of the features to contain the feature matrix. Unknown
* feature codes will be ignored. If null (or [] in MatLab)
* all features are returned.
* @return a four dimensional matrix. The first dimension denotes the type in the following
* order: {feature matrix, annotations per location, feature codes}. The
* other dimensions depend on the value of the first dimension:
*
* - feature matrix: 2. dimension is feature vector, 3. dimension is location number,
* 4. dimension is data set number. If for a particular location and a particular data
* set the corresponding feature value does not exists
NaN will be
* returned. - annotations: 2. dimension is location number, 3. dimension is data set
* number, 4. dimension is location annotations in the following order:
{plate
* well description, plate augmented code, plate perm id, plate space code, plate code,
* row, column, experiment augmented code, experiment perm id, experiment space code,
* experiment project code, experiment code, data set code, data set type} -
* feature codes: 2. dimension is feature codes in alphabetical order. 3. and 4.
* dimension are meaningless (i.e. they have length one)
*
*/
public static Object[][][][] getFeatureMatrixForPlate(String plate,
String analysisProcedureOrNull, String[] featuresOrNull)
{
checkLoggedIn();
final List dataSets =
openbis.loadFeaturesForPlates(
Arrays.asList(PlateIdentifier.createFromAugmentedCode(plate)),
(featuresOrNull == null) ? null : Arrays.asList(featuresOrNull),
analysisProcedureOrNull);
final Object[][][][] result = new Object[3][][][];
if (dataSets.isEmpty())
{
return result;
}
List featureCodes = getFeatureCodes(dataSets);
Map featureCodeToIndexMap = new HashMap();
result[2] = new Object[featureCodes.size()][1][1];
for (int i = 0; i < featureCodes.size(); ++i)
{
String code = featureCodes.get(i);
result[2][i][0][0] = code;
featureCodeToIndexMap.put(code, i);
}
IndexSet wellPositions = new IndexSet();
for (FeatureVectorDataset dataSet : dataSets)
{
List featureVectors = dataSet.getFeatureVectors();
for (FeatureVector featureVector : featureVectors)
{
WellPosition wellPosition = featureVector.getWellPosition();
wellPositions.add(wellPosition);
}
}
int numberOfDataSets = dataSets.size();
result[0] = new Object[featureCodes.size()][wellPositions.size()][numberOfDataSets];
result[1] = new Object[wellPositions.size()][numberOfDataSets][14];
for (int dataSetIndex = 0; dataSetIndex < numberOfDataSets; dataSetIndex++)
{
FeatureVectorDataset dataSet = dataSets.get(dataSetIndex);
FeatureVectorDatasetReference dataSetRef = dataSet.getDataset();
int[] featureIndexes = createFeatureIndexes(dataSet, featureCodeToIndexMap);
for (FeatureVector vector : dataSet.getFeatureVectors())
{
WellPosition wellPosition = vector.getWellPosition();
int wellIndex = wellPositions.getIndex(wellPosition);
copyFeatureValuesInto(result, wellIndex, dataSetIndex, featureIndexes, vector);
copyAnnotationsInto(result, wellIndex, dataSetIndex, dataSetRef, vector);
}
}
return replaceFeatureNullValuesByNaN(result);
}
private static Object[][][][] replaceFeatureNullValuesByNaN(final Object[][][][] result)
{
Double nan = Double.NaN;
for (int i = 0; i < result[0].length; i++)
{
Object[][] r0i = result[0][i];
for (int j = 0; j < r0i.length; j++)
{
Object[] r0ij = r0i[j];
for (int k = 0; k < r0ij.length; k++)
{
if (r0ij[k] == null)
{
r0ij[k] = nan;
}
}
}
}
return result;
}
private static int[] createFeatureIndexes(IFeatureCodesProvider dataSet,
Map featureCodeToIndexMap)
{
List codes = dataSet.getFeatureCodes();
int[] featureIndexes = new int[codes.size()];
for (int i = 0; i < featureIndexes.length; i++)
{
featureIndexes[i] = featureCodeToIndexMap.get(codes.get(i));
}
return featureIndexes;
}
private static void copyFeatureValuesInto(final Object[][][][] result, int wellIndex,
int dataSetIndex, int[] featureIndexes, FeatureVector vector)
{
List