Package ome.specification
Class XMLMockObjects
java.lang.Object
ome.specification.XMLMockObjects
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
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String[]The supported types of annotations.static final ArcTypeThe default type of an arc.static final BinningThe default binning value.static final IntegerThe number of bytes per pixels.static final NamingConventionThe default naming convention for columns.static final intThe default number of columns for a plate.static final StringThe default lot number of a component of a microscope.static final StringThe default manufacturer of a component of a microscope.static final StringThe default model of a component of a microscope.static final StringThe default serial number of a component of a microscope.static final CorrectionThe default objective's correction.static final DoubleThe default cut-in.static final DoubleThe default cut-out.static final ColorThe default color.static final DetectorTypeThe default type of a detector.static final DimensionOrderThe default dimension order.static final ExperimentTypeThe default type of a microscope.static final intThe default number of fields for a well.static final FilamentTypeThe default type of a filament.static final FilterTypeThe default objective's immersion.static final ImmersionThe default objective's immersion.protected InstrumentThe instrument used for the metadata.static final LaserMediumThe default type of a laser.static final LaserTypeThe default type of a laser.static final String[]The light sources to handle.static final DoubleThe default power of a light source.static final MediumThe default medium for the objective.static final MicrobeamManipulationTypeThe default type of a microbeam manipulation.static final MicroscopeTypeThe default type of a microscope.static final intThe number of detectors created.static final intThe number of dichroics created.static final intThe number of filters created.static final intThe number of objectives created.protected final OMERoot of the file.static final PixelTypeThe default pixels type.static final StringPoints used to create Polyline and Polygon shape.static final NamingConventionThe default naming convention for rows.static final intThe default number of rows for a plate.static final String[]The shapes to handle.static final IntegerThe default number of channels.static final IntegerThe default number of time-points.static final IntegerThe default number of pixels along the X-axis.static final IntegerThe default number of pixels along the Y-axis.static final IntegerThe default number of z-sections.static final StringThe default time. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionCreates and annotates an image.createAnnotation(String type, OMEModelObject object, int index) Create a comment annotation for the specified object.createBasicPlate(int index) Creates a basic plate.Creates a plate with1row,1column and1field.Creates a binary file.createBinData(int sizeX, int sizeY, int bpp) Creates a new object.createChannel(int index) Creates a channel.createDataset(int index) Creates a dataset.createDetector(int index) Creates a detector.createDetectorSettings(int ref) Creates a detector settings.createDichroic(int index) Creates a dichroic.createExperiment(int index) Creates an experiment.createExperimenter(int index) Creates an experimenter.createExperimentWithMicrobeam(int index) Creates an experiment with a microbeam.createFilter(int index, double cutIn, double cutOut) Creates a filter.createFilterSet(int index) Creates a filter set.createFullPopulatedPlate(int n) Creates and returns the root element.createImage(boolean metadata) Creates and returns the root element.createImage(int index) Creates a new image.createImage(int index, boolean metadata) Creates a new image.Creates a imaging environment.Creates an image with acquisition data.Creates an image with acquisition data.createImageWithExperiment(int index, boolean metadata, Experiment exp) Creates an image with a given experiment.Creates an image with ROI.createInstrument(boolean populate) Creates an instrument with filters, light sources etc.Creates a light path.createLightSource(String type, int index) Creates a light source of the specified type.createLightSourceSettings(int ref) Creates a light source settings.createMicrobeamManipulation(int index) Creates a microbeam manipulation.Creates a microscope.createObjective(int index) Creates an objective.createObjectiveSettings(int ref) Creates an objective settings.createPlane(int z, int c, int t) Creates a plane information object.createPlate(int numberOfPlates, int index, int numberOfPlateAcquisition) Creates a default platecreatePlate(int numberOfPlates, int index, int rows, int columns, int fields, int numberOfPlateAcquisition) Creates a populated plate with images.createPlate(int numberOfPlates, int index, int rows, int columns, int fields, int numberOfPlateAcquisition, boolean withMicrobeam) Creates a populated plate with images.createPlate(int numberOfScreens, int screenIndex, int numberOfPlates, int plateIndex, int rows, int columns, int fields, int numberOfPlateAcquisition) Creates a populated plate with images.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.createPopulatedPlate(int n) Creates a plate with1row,1column and1field.createPopulatedPlate(int n, int fields) Creates a plate with1row,1column andfieldsfield.createPopulatedPlate(int plates, int rows, int cols, int fields, int acqs) Creates several plates but no containing screen.createPopulatedPlate(int plates, int rows, int cols, int fields, int acqs, boolean withMicrobeam) Creates several plates but no containing screen.Creates one 2x2 plate of with a single well sample per well and one plate acquisition.createPopulatedScreen(int plates, int rows, int cols, int fields, int acqs) Creates a screen with several plates.createPopulatedScreen(int screens, int plates, int rows, int cols, int fields, int acqs) Creates several screens each with several plates.createPopulatedScreen(int screens, int plates, int rows, int cols, int fields, int acqs, boolean withMicrobeam) Creates several screens each with several plates.createProject(int index) Creates a project.createReagent(int index) Creates a reagent.createROI(int index, int z, int c, int t) Creates an ROI.createScreen(int index) Creates a screen.createShape(int index, String type, int z, int c, int t) Creates the specified type of shape.Creates a imaging environment.getRoot()Returns the root of the XML file.
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Field Details
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DEFAULT_COLOR
The default color. -
LIGHTSOURCE_POWER
The default power of a light source. -
COMPONENT_MODEL
The default model of a component of a microscope.- See Also:
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COMPONENT_MANUFACTURER
The default manufacturer of a component of a microscope.- See Also:
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COMPONENT_SERIAL_NUMBER
The default serial number of a component of a microscope.- See Also:
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COMPONENT_LOT_NUMBER
The default lot number of a component of a microscope.- See Also:
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LASER_TYPE
The default type of a laser. -
ARC_TYPE
The default type of an arc. -
FILAMENT_TYPE
The default type of a filament. -
DETECTOR_TYPE
The default type of a detector. -
CORRECTION
The default objective's correction. -
IMMERSION
The default objective's immersion. -
FILTER_TYPE
The default objective's immersion. -
MICROSCOPE_TYPE
The default type of a microscope. -
EXPERIMENT_TYPE
The default type of a microscope. -
MICROBEAM_MANIPULATION_TYPE
The default type of a microbeam manipulation. -
BINNING
The default binning value. -
MEDIUM
The default medium for the objective. -
LASER_MEDIUM
The default type of a laser. -
SIZE_X
The default number of pixels along the X-axis. -
SIZE_Y
The default number of pixels along the Y-axis. -
SIZE_Z
The default number of z-sections. -
SIZE_C
The default number of channels. -
SIZE_T
The default number of time-points. -
BYTES_PER_PIXEL
The number of bytes per pixels. -
ROWS
public static final int ROWSThe default number of rows for a plate.- See Also:
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COLUMNS
public static final int COLUMNSThe default number of columns for a plate.- See Also:
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FIELDS
public static final int FIELDSThe default number of fields for a well.- See Also:
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LIGHT_SOURCES
The light sources to handle. -
SHAPES
The shapes to handle. -
ANNOTATIONS
The supported types of annotations. -
ROW_NAMING_CONVENTION
The default naming convention for rows. -
COLUMN_NAMING_CONVENTION
The default naming convention for columns. -
DIMENSION_ORDER
The default dimension order. -
PIXEL_TYPE
The default pixels type. -
NUMBER_OF_DECTECTORS
public static final int NUMBER_OF_DECTECTORSThe number of detectors created.- See Also:
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NUMBER_OF_OBJECTIVES
public static final int NUMBER_OF_OBJECTIVESThe number of objectives created.- See Also:
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NUMBER_OF_FILTERS
public static final int NUMBER_OF_FILTERSThe number of filters created.- See Also:
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NUMBER_OF_DICHROICS
public static final int NUMBER_OF_DICHROICSThe number of dichroics created.- See Also:
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POINTS
Points used to create Polyline and Polygon shape.- See Also:
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TIME
The default time.- See Also:
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CUT_IN
The default cut-in. -
CUT_OUT
The default cut-out. -
ome
Root of the file. -
instrument
The instrument used for the metadata.
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Constructor Details
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XMLMockObjects
public XMLMockObjects()Creates a new instance.
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Method Details
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createDetector
Creates a detector.- Parameters:
index- The index of the detector in the file.- Returns:
- See above.
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createFilterSet
Creates a filter set.- Parameters:
index- The index of the filter set in the file.- Returns:
- See above.
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createMicroscope
Creates a microscope.- Returns:
- See above.
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createDichroic
Creates a dichroic.- Parameters:
index- The index of the dichroic in the file.- Returns:
- See above.
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createObjective
Creates an objective.- Parameters:
index- The index of the objective in the file.- Returns:
- See above.
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createFilter
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.
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createLightSource
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.
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createBinData
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.
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createLightPath
Creates a light path.- Returns:
- See above.
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createImageEnvironment
Creates a imaging environment.- Returns:
- See above.
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createStageLabel
Creates a imaging environment.- Returns:
- See above.
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createLightSourceSettings
Creates a light source settings.- Parameters:
ref- Reference to the light source.- Returns:
- See above.
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createMicrobeamManipulation
Creates a microbeam manipulation.- Parameters:
index- The index in the file.- Returns:
- See above.
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createExperimenter
Creates an experimenter.- Parameters:
index- The index of the Experimenter.- Returns:
- See above.
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createExperiment
Creates an experiment.- Parameters:
index- The index in the file.- Returns:
- See above.
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createExperimentWithMicrobeam
Creates an experiment with a microbeam.- Parameters:
index- The index in the file.- Returns:
- See above.
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createDetectorSettings
Creates a detector settings.- Parameters:
ref- Reference to the detector.- Returns:
- See above.
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createObjectiveSettings
Creates an objective settings.- Parameters:
ref- Reference to the objective.- Returns:
- See above.
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createBinaryFile
Creates a binary file.- Returns:
- See above.
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createShape
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.
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createROI
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.
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getRoot
Returns the root of the XML file.- Returns:
- See above.
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createProject
Creates a project.- Parameters:
index- The index of the project.- Returns:
- See above.
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createDataset
Creates a dataset.- Parameters:
index- The index of the dataset.- Returns:
- See above.
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createScreen
Creates a screen.- Parameters:
index- The index of the screen.- Returns:
- See above.
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createBasicPlate
Creates a basic plate.- Parameters:
index- The index of the plate.- Returns:
- See above.
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createPlate
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.
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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.
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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.
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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.
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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.
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createPlane
Creates a plane information object.- Parameters:
z- The z-section.c- The channel.t- The time-point.- Returns:
- See above.
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createImage
Creates a new image.- Parameters:
index- The identifier of the image.metadata- Passtrueto create channel with acquisition metadata,falseotherwise.- Returns:
- See above.
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createChannel
Creates a channel.- Parameters:
index- The index in the file.- Returns:
- See above.
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createImage
Creates a new image.- Parameters:
index- The identifier of the image.- Returns:
- See above.
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createInstrument
Creates an instrument with filters, light sources etc.- Parameters:
populate- Passtrueto populate the instrument,falseotherwise.- Returns:
- See above.
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createReagent
Creates a reagent.- Parameters:
index- The index in the file.- Returns:
- See above.
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createAnnotation
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.
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createImage
Creates and returns the root element. Creates an image w/o metadata.- Returns:
- See above.
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createImage
Creates and returns the root element.- Parameters:
metadata- Passtrueto create an image with metadata,falsew/o/- Returns:
- See above.
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createAnnotatedImage
Creates and annotates an image. The following types of annotations are added: TagAnnotation, TermAnnotation, BooleanAnnotation, LongAnnotation, CommentAnnotation.- Returns:
- See above.
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createImageWithAcquisitionData
Creates an image with acquisition data.- Returns:
- See above.
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createImageWithAnnotatedAcquisitionData
Creates an image with acquisition data.- Returns:
- See above.
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createImageWithExperiment
Creates an image with a given experiment. The Image is not added to ome.- Returns:
- See above.
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createImageWithROI
Creates an image with ROI.- Returns:
- See above.
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createPopulatedPlate
Creates a plate with1row,1column and1field. The plate will have images with acquisition data but no plate acquisition data if the passed value is0otherwise will havenplate acquisitions.- Parameters:
n- The number of plate acquisition.- Returns:
- See above
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createPopulatedPlate
Creates a plate with1row,1column andfieldsfield. The plate will have images with acquisition data but no plate acquisition data if the passed value is0otherwise will havenplate acquisitions.- Parameters:
n- The number of plate acquisition.fields- The number of fields.- Returns:
- See above
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createPopulatedPlate
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.
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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.
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createPopulatedScreen
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.
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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.
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createPopulatedScreen
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.
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createPopulatedScreen
Creates one 2x2 plate of with a single well sample per well and one plate acquisition. -
createBasicPlateWithReagent
Creates a plate with1row,1column and1field. This plate will be added to a screen and the well linked to a reagent.- Returns:
- See above
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createFullPopulatedPlate
Creates a plate withROWSrows,COLUMNScolumns andFIELDSfield. The plate will have images with acquisition data but no plate acquisition data.- Parameters:
n- The number of plate acquisition.- Returns:
- See above
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