Package ch.systemsx.cisd.openbis.dss.etl.dto.api.v2

Interface IImagingDatasetFactory

public interface IImagingDatasetFactory

Factory for defining image and feature vector datasets.

Method Summary

Modifier and Type	Method	Description
IFeaturesBuilder	createFeaturesBuilder()	Allows to define feature vectors of one image analysis dataset.
DataSetRegistrationDetails<FeatureVectorDataSetInformation>	createFeatureVectorDatasetDetails(IFeaturesBuilder featureBuilder)	Creates feature vector dataset details by using the specified builder.
DataSetRegistrationDetails<FeatureVectorDataSetInformation>	createFeatureVectorDatasetDetails(java.lang.String csvFilePath, java.util.Properties properties)	Creates feature vector dataset details by parsing the specified CSV file.
DataSetRegistrationDetails<ImageDataSetInformation>	createImageRegistrationDetails(SimpleImageDataConfig imageDataSet, java.io.File incomingDatasetFolder)	Deprecated.
java.lang.String	figureGeometry(DataSetRegistrationDetails<ImageDataSetInformation> registrationDetails)	Utility method to find out the plate geometry by looking for which wells images are available.
boolean	registerImageDataset(DataSetRegistrationDetails<ImageDataSetInformation> imageDatasetDetails, java.io.File incomingDatasetFolder, ch.systemsx.cisd.etlserver.registrator.v2.DataSetRegistrationService<ImageDataSetInformation> service)	Deprecated.
boolean	registerImageDataset(SimpleImageDataConfig imageDataSet, java.io.File incomingDatasetFolder, ch.systemsx.cisd.etlserver.registrator.v2.DataSetRegistrationService<ImageDataSetInformation> service)	A convenience method to register the specified image dataset in a separate transaction.

Method Detail

createImageRegistrationDetails

@Deprecated
DataSetRegistrationDetails<ImageDataSetInformation> createImageRegistrationDetails(SimpleImageDataConfig imageDataSet,
                                                                                   java.io.File incomingDatasetFolder)

Deprecated.

Creates image dataset details. Used if
1. more then one dataset is created in one transaction and using registerImageDataset(ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig, java.io.File, ch.systemsx.cisd.etlserver.registrator.v2.DataSetRegistrationService<ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation>) is not sufficient or
2. SimpleImageDataConfig is not sufficient to describe the dataset and further modifications on the dataset detail object are required.

registerImageDataset

boolean registerImageDataset(SimpleImageDataConfig imageDataSet,
                             java.io.File incomingDatasetFolder,
                             ch.systemsx.cisd.etlserver.registrator.v2.DataSetRegistrationService<ImageDataSetInformation> service)

A convenience method to register the specified image dataset in a separate transaction.

Parameters:

imageDataSet - simple dataset specification

registerImageDataset

@Deprecated
boolean registerImageDataset(DataSetRegistrationDetails<ImageDataSetInformation> imageDatasetDetails,
                             java.io.File incomingDatasetFolder,
                             ch.systemsx.cisd.etlserver.registrator.v2.DataSetRegistrationService<ImageDataSetInformation> service)

Deprecated.

A convenience method to register the specified image dataset in a separate transaction.

Parameters:

imageDatasetDetails - advanced dataset specification

createFeaturesBuilder

IFeaturesBuilder createFeaturesBuilder()

Allows to define feature vectors of one image analysis dataset. Used to define a dataset details with createFeatureVectorDatasetDetails(IFeaturesBuilder).

createFeatureVectorDatasetDetails

DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorDatasetDetails(IFeaturesBuilder featureBuilder)

Creates feature vector dataset details by using the specified builder.

createFeatureVectorDatasetDetails

DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorDatasetDetails(java.lang.String csvFilePath,
                                                                                              java.util.Properties properties)
                                                                                       throws java.io.IOException

Creates feature vector dataset details by parsing the specified CSV file.

CSV format can be configured with following properties:

   # Separator character between headers and row cells.
   separator = ,
   ignore-comments = true
   # Header of the column denoting the row of a well.
   well-name-row = row
   # Header of the column denoting the column of a well.
   well-name-col = col
   well-name-col-is-alphanum = true
 

Throws:

java.io.IOException - if file cannot be parsed

figureGeometry

java.lang.String figureGeometry(DataSetRegistrationDetails<ImageDataSetInformation> registrationDetails)

Utility method to find out the plate geometry by looking for which wells images are available.

Returns:

a constant which can be used as a vocabulary term value for $PLATE_GEOMETRY property of a plate/

Throws:

ch.systemsx.cisd.common.exceptions.UserFailureException - if all available geometries in openBIS are too small (there is a well outside).