Class XMLMockObjects

java.lang.Object
ome.specification.XMLMockObjects

public class XMLMockObjects extends Object
Creates XML objects for the 2010-06 schema.
Since:
3.0-Beta4
Version:
3.0 (Internal version: $Revision: $Date: $)
Author:
Jean-Marie Burel      j.burel@dundee.ac.uk, Chris Allan      Chris Allan callan at blackcat dot ca
  • Field Details

    • DEFAULT_COLOR

      public static final Color DEFAULT_COLOR
      The default color.
    • LIGHTSOURCE_POWER

      public static final Double LIGHTSOURCE_POWER
      The default power of a light source.
    • COMPONENT_MODEL

      public static final String COMPONENT_MODEL
      The default model of a component of a microscope.
      See Also:
    • COMPONENT_MANUFACTURER

      public static final String COMPONENT_MANUFACTURER
      The default manufacturer of a component of a microscope.
      See Also:
    • COMPONENT_SERIAL_NUMBER

      public static final String COMPONENT_SERIAL_NUMBER
      The default serial number of a component of a microscope.
      See Also:
    • COMPONENT_LOT_NUMBER

      public static final String COMPONENT_LOT_NUMBER
      The default lot number of a component of a microscope.
      See Also:
    • LASER_TYPE

      public static final LaserType LASER_TYPE
      The default type of a laser.
    • ARC_TYPE

      public static final ArcType ARC_TYPE
      The default type of an arc.
    • FILAMENT_TYPE

      public static final FilamentType FILAMENT_TYPE
      The default type of a filament.
    • DETECTOR_TYPE

      public static final DetectorType DETECTOR_TYPE
      The default type of a detector.
    • CORRECTION

      public static final Correction CORRECTION
      The default objective's correction.
    • IMMERSION

      public static final Immersion IMMERSION
      The default objective's immersion.
    • FILTER_TYPE

      public static final FilterType FILTER_TYPE
      The default objective's immersion.
    • MICROSCOPE_TYPE

      public static final MicroscopeType MICROSCOPE_TYPE
      The default type of a microscope.
    • EXPERIMENT_TYPE

      public static final ExperimentType EXPERIMENT_TYPE
      The default type of a microscope.
    • MICROBEAM_MANIPULATION_TYPE

      public static final MicrobeamManipulationType MICROBEAM_MANIPULATION_TYPE
      The default type of a microbeam manipulation.
    • BINNING

      public static final Binning BINNING
      The default binning value.
    • MEDIUM

      public static final Medium MEDIUM
      The default medium for the objective.
    • LASER_MEDIUM

      public static final LaserMedium LASER_MEDIUM
      The default type of a laser.
    • SIZE_X

      public static final Integer SIZE_X
      The default number of pixels along the X-axis.
    • SIZE_Y

      public static final Integer SIZE_Y
      The default number of pixels along the Y-axis.
    • SIZE_Z

      public static final Integer SIZE_Z
      The default number of z-sections.
    • SIZE_C

      public static final Integer SIZE_C
      The default number of channels.
    • SIZE_T

      public static final Integer SIZE_T
      The default number of time-points.
    • BYTES_PER_PIXEL

      public static final Integer BYTES_PER_PIXEL
      The number of bytes per pixels.
    • ROWS

      public static final int ROWS
      The default number of rows for a plate.
      See Also:
    • COLUMNS

      public static final int COLUMNS
      The default number of columns for a plate.
      See Also:
    • FIELDS

      public static final int FIELDS
      The default number of fields for a well.
      See Also:
    • LIGHT_SOURCES

      public static final String[] LIGHT_SOURCES
      The light sources to handle.
    • SHAPES

      public static final String[] SHAPES
      The shapes to handle.
    • ANNOTATIONS

      public static final String[] ANNOTATIONS
      The supported types of annotations.
    • ROW_NAMING_CONVENTION

      public static final NamingConvention ROW_NAMING_CONVENTION
      The default naming convention for rows.
    • COLUMN_NAMING_CONVENTION

      public static final NamingConvention COLUMN_NAMING_CONVENTION
      The default naming convention for columns.
    • DIMENSION_ORDER

      public static final DimensionOrder DIMENSION_ORDER
      The default dimension order.
    • PIXEL_TYPE

      public static final PixelType PIXEL_TYPE
      The default pixels type.
    • NUMBER_OF_DECTECTORS

      public static final int NUMBER_OF_DECTECTORS
      The number of detectors created.
      See Also:
    • NUMBER_OF_OBJECTIVES

      public static final int NUMBER_OF_OBJECTIVES
      The number of objectives created.
      See Also:
    • NUMBER_OF_FILTERS

      public static final int NUMBER_OF_FILTERS
      The number of filters created.
      See Also:
    • NUMBER_OF_DICHROICS

      public static final int NUMBER_OF_DICHROICS
      The number of dichroics created.
      See Also:
    • POINTS

      public static final String POINTS
      Points used to create Polyline and Polygon shape.
      See Also:
    • TIME

      public static final String TIME
      The default time.
      See Also:
    • CUT_IN

      public static final Double CUT_IN
      The default cut-in.
    • CUT_OUT

      public static final Double CUT_OUT
      The default cut-out.
    • ome

      protected final OME ome
      Root of the file.
    • instrument

      protected Instrument instrument
      The instrument used for the metadata.
  • Constructor Details

    • XMLMockObjects

      public XMLMockObjects()
      Creates a new instance.
  • Method Details

    • createDetector

      public Detector createDetector(int index)
      Creates a detector.
      Parameters:
      index - The index of the detector in the file.
      Returns:
      See above.
    • createFilterSet

      public FilterSet createFilterSet(int index)
      Creates a filter set.
      Parameters:
      index - The index of the filter set in the file.
      Returns:
      See above.
    • createMicroscope

      public Microscope createMicroscope()
      Creates a microscope.
      Returns:
      See above.
    • createDichroic

      public Dichroic createDichroic(int index)
      Creates a dichroic.
      Parameters:
      index - The index of the dichroic in the file.
      Returns:
      See above.
    • createObjective

      public Objective createObjective(int index)
      Creates an objective.
      Parameters:
      index - The index of the objective in the file.
      Returns:
      See above.
    • createFilter

      public Filter createFilter(int index, double cutIn, double cutOut)
      Creates a filter.
      Parameters:
      index - The index of the objective in the file.
      cutIn - The cut in value.
      cutOut - The cut out value.
      Returns:
      See above.
    • createLightSource

      public LightSource createLightSource(String type, int index)
      Creates a light source of the specified type.
      Parameters:
      type - The type of light source to create.
      index - The index of the light source in the file.
      Returns:
      See above.
    • createBinData

      public BinData createBinData(int sizeX, int sizeY, int bpp)
      Creates a new object.
      Parameters:
      sizeX - The number of pixels along the X-axis.
      sizeY - The number of pixels along the Y-axis.
      bpp - The number of bytes per pixels.
      Returns:
      See above.
    • createLightPath

      public LightPath createLightPath()
      Creates a light path.
      Returns:
      See above.
    • createImageEnvironment

      public ImagingEnvironment createImageEnvironment()
      Creates a imaging environment.
      Returns:
      See above.
    • createStageLabel

      public StageLabel createStageLabel()
      Creates a imaging environment.
      Returns:
      See above.
    • createLightSourceSettings

      public LightSourceSettings createLightSourceSettings(int ref)
      Creates a light source settings.
      Parameters:
      ref - Reference to the light source.
      Returns:
      See above.
    • createMicrobeamManipulation

      public MicrobeamManipulation createMicrobeamManipulation(int index)
      Creates a microbeam manipulation.
      Parameters:
      index - The index in the file.
      Returns:
      See above.
    • createExperimenter

      public Experimenter createExperimenter(int index)
      Creates an experimenter.
      Parameters:
      index - The index of the Experimenter.
      Returns:
      See above.
    • createExperiment

      public Experiment createExperiment(int index)
      Creates an experiment.
      Parameters:
      index - The index in the file.
      Returns:
      See above.
    • createExperimentWithMicrobeam

      public Experiment createExperimentWithMicrobeam(int index)
      Creates an experiment with a microbeam.
      Parameters:
      index - The index in the file.
      Returns:
      See above.
    • createDetectorSettings

      public DetectorSettings createDetectorSettings(int ref)
      Creates a detector settings.
      Parameters:
      ref - Reference to the detector.
      Returns:
      See above.
    • createObjectiveSettings

      public ObjectiveSettings createObjectiveSettings(int ref)
      Creates an objective settings.
      Parameters:
      ref - Reference to the objective.
      Returns:
      See above.
    • createBinaryFile

      public BinaryFile createBinaryFile()
      Creates a binary file.
      Returns:
      See above.
    • createShape

      public Shape createShape(int index, String type, int z, int c, int t)
      Creates the specified type of shape.
      Parameters:
      index - The index of the shape in the file.
      type - The type of shape to create.
      z - The selected z-section.
      c - The selected channel.
      t - The selected time-point.
      Returns:
      See above.
    • createROI

      public ROI createROI(int index, int z, int c, int t)
      Creates an ROI.
      Parameters:
      index - The index of the ROI in the file.
      z - The selected z-section.
      c - The selected channel.
      t - The selected time-point.
    • getRoot

      public OME getRoot()
      Returns the root of the XML file.
      Returns:
      See above.
    • createProject

      public Project createProject(int index)
      Creates a project.
      Parameters:
      index - The index of the project.
      Returns:
      See above.
    • createDataset

      public Dataset createDataset(int index)
      Creates a dataset.
      Parameters:
      index - The index of the dataset.
      Returns:
      See above.
    • createScreen

      public Screen createScreen(int index)
      Creates a screen.
      Parameters:
      index - The index of the screen.
      Returns:
      See above.
    • createBasicPlate

      public Plate createBasicPlate(int index)
      Creates a basic plate.
      Parameters:
      index - The index of the plate.
      Returns:
      See above.
    • createPlate

      public Plate createPlate(int numberOfPlates, int index, int numberOfPlateAcquisition)
      Creates a default plate
      Parameters:
      numberOfPlates - The total number of plates.
      index - The index of the plate.
      numberOfPlateAcquisition - The number of plate acquisition to add.
      Returns:
      See above.
    • createPlate

      public Plate createPlate(int numberOfPlates, int index, int rows, int columns, int fields, int numberOfPlateAcquisition)
      Creates a populated plate with images.
      Parameters:
      numberOfPlates - The total number of plates.
      index - The index of the plate.
      rows - The number of rows.
      columns - The number of columns.
      fields - The number of fields.
      numberOfPlateAcquisition - The number of plate acquisition to add.
      Returns:
      See above.
    • createPlate

      public Plate createPlate(int numberOfPlates, int index, int rows, int columns, int fields, int numberOfPlateAcquisition, boolean withMicrobeam)
      Creates a populated plate with images.
      Parameters:
      numberOfPlates - The total number of plates.
      index - The index of the plate.
      rows - The number of rows.
      columns - The number of columns.
      fields - The number of fields.
      numberOfPlateAcquisition - The number of plate acquisition to add.
      withMicrobeam - Whether the experiment should contain a microbeam
      Returns:
      See above.
    • createPlate

      public Plate createPlate(int numberOfScreens, int screenIndex, int numberOfPlates, int plateIndex, int rows, int columns, int fields, int numberOfPlateAcquisition)
      Creates a populated plate with images.
      Parameters:
      numberOfScreens - The total number of screens.
      screenIndex - The index of the screen.
      numberOfPlates - The total number of plates.
      plateIndex - The index of the plate.
      rows - The number of rows.
      columns - The number of columns.
      fields - The number of fields.
      numberOfPlateAcquisition - The number of plate acquisition to add.
      Returns:
      See above.
    • createPlate

      public Plate createPlate(int numberOfScreens, int screenIndex, int numberOfPlates, int plateIndex, int rows, int columns, int fields, int numberOfPlateAcquisition, boolean withMicrobeam)
      Creates a populated plate with images.
      Parameters:
      numberOfScreens - The total number of screens.
      screenIndex - The index of the screen.
      numberOfPlates - The total number of plates.
      plateIndex - The index of the plate.
      rows - The number of rows.
      columns - The number of columns.
      fields - The number of fields.
      numberOfPlateAcquisition - The number of plate acquisition to add.
      withMicrobeam - Whether the experiment should contain a microbeam
      Returns:
      See above.
    • createPlane

      public Plane createPlane(int z, int c, int t)
      Creates a plane information object.
      Parameters:
      z - The z-section.
      c - The channel.
      t - The time-point.
      Returns:
      See above.
    • createImage

      public Image createImage(int index, boolean metadata)
      Creates a new image.
      Parameters:
      index - The identifier of the image.
      metadata - Pass true to create channel with acquisition metadata, false otherwise.
      Returns:
      See above.
    • createChannel

      public Channel createChannel(int index)
      Creates a channel.
      Parameters:
      index - The index in the file.
      Returns:
      See above.
    • createImage

      public Image createImage(int index)
      Creates a new image.
      Parameters:
      index - The identifier of the image.
      Returns:
      See above.
    • createInstrument

      public Instrument createInstrument(boolean populate)
      Creates an instrument with filters, light sources etc.
      Parameters:
      populate - Pass true to populate the instrument, false otherwise.
      Returns:
      See above.
    • createReagent

      public Reagent createReagent(int index)
      Creates a reagent.
      Parameters:
      index - The index in the file.
      Returns:
      See above.
    • createAnnotation

      public Annotation createAnnotation(String type, OMEModelObject object, int index)
      Create a comment annotation for the specified object.
      Parameters:
      type - The type of annotation to create.
      object - The object to link the annotation to.
      index - The index of the annotation.
      Returns:
      See above.
    • createImage

      public OME createImage()
      Creates and returns the root element. Creates an image w/o metadata.
      Returns:
      See above.
    • createImage

      public OME createImage(boolean metadata)
      Creates and returns the root element.
      Parameters:
      metadata - Pass true to create an image with metadata, false w/o/
      Returns:
      See above.
    • createAnnotatedImage

      public OME createAnnotatedImage()
      Creates and annotates an image. The following types of annotations are added: TagAnnotation, TermAnnotation, BooleanAnnotation, LongAnnotation, CommentAnnotation.
      Returns:
      See above.
    • createImageWithAcquisitionData

      public OME createImageWithAcquisitionData()
      Creates an image with acquisition data.
      Returns:
      See above.
    • createImageWithAnnotatedAcquisitionData

      public OME createImageWithAnnotatedAcquisitionData()
      Creates an image with acquisition data.
      Returns:
      See above.
    • createImageWithExperiment

      public Image createImageWithExperiment(int index, boolean metadata, Experiment exp)
      Creates an image with a given experiment. The Image is not added to ome.
      Returns:
      See above.
    • createImageWithROI

      public OME createImageWithROI()
      Creates an image with ROI.
      Returns:
      See above.
    • createPopulatedPlate

      public OME createPopulatedPlate(int n)
      Creates a plate with 1 row, 1 column and 1field. The plate will have images with acquisition data but no plate acquisition data if the passed value is 0 otherwise will have n plate acquisitions.
      Parameters:
      n - The number of plate acquisition.
      Returns:
      See above
    • createPopulatedPlate

      public OME createPopulatedPlate(int n, int fields)
      Creates a plate with 1 row, 1 column and fieldsfield. The plate will have images with acquisition data but no plate acquisition data if the passed value is 0 otherwise will have n plate acquisitions.
      Parameters:
      n - The number of plate acquisition.
      fields - The number of fields.
      Returns:
      See above
    • createPopulatedPlate

      public OME createPopulatedPlate(int plates, int rows, int cols, int fields, int acqs)
      Creates several plates but no containing screen.
      Parameters:
      plates - The number of plates to create.
      rows - The number of rows for plate.
      cols - The number of columns for plate.
      fields - The number of fields.
      acqs - The number of plate acquisitions.
      Returns:
      See above.
    • createPopulatedPlate

      public OME createPopulatedPlate(int plates, int rows, int cols, int fields, int acqs, boolean withMicrobeam)
      Creates several plates but no containing screen.
      Parameters:
      plates - The number of plates to create.
      rows - The number of rows for plate.
      cols - The number of columns for plate.
      fields - The number of fields.
      acqs - The number of plate acquisitions.
      withMicrobeam - Whether the experiment should contain a microbeam
      Returns:
      See above.
    • createPopulatedScreen

      public OME createPopulatedScreen(int screens, int plates, int rows, int cols, int fields, int acqs)
      Creates several screens each with several plates.
      Parameters:
      screens - The number of screens to create.
      plates - The number of plates to create.
      rows - The number of rows for plate.
      cols - The number of columns for plate.
      fields - The number of fields.
      acqs - The number of plate acquisitions.
      Returns:
      See above.
    • createPopulatedScreen

      public OME createPopulatedScreen(int screens, int plates, int rows, int cols, int fields, int acqs, boolean withMicrobeam)
      Creates several screens each with several plates.
      Parameters:
      screens - The number of screens to create.
      plates - The number of plates to create.
      rows - The number of rows for plate.
      cols - The number of columns for plate.
      fields - The number of fields.
      acqs - The number of plate acquisitions.
      withMicrobeam - Whether the experiment should contain a microbeam
      Returns:
      See above.
    • createPopulatedScreen

      public OME createPopulatedScreen(int plates, int rows, int cols, int fields, int acqs)
      Creates a screen with several plates.
      Parameters:
      plates - The number of plates to create.
      rows - The number of rows for plate.
      cols - The number of columns for plate.
      fields - The number of fields.
      acqs - The number of plate acquisitions.
      Returns:
      See above.
    • createPopulatedScreen

      public OME createPopulatedScreen()
      Creates one 2x2 plate of with a single well sample per well and one plate acquisition.
    • createBasicPlateWithReagent

      public OME createBasicPlateWithReagent()
      Creates a plate with 1 row, 1 column and 1 field. This plate will be added to a screen and the well linked to a reagent.
      Returns:
      See above
    • createFullPopulatedPlate

      public OME createFullPopulatedPlate(int n)
      Creates a plate with ROWS rows, COLUMNS columns and FIELDS field. The plate will have images with acquisition data but no plate acquisition data.
      Parameters:
      n - The number of plate acquisition.
      Returns:
      See above