Package ome.specification
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 Summary
Fields Modifier and Type Field Description static String[]
ANNOTATIONS
The supported types of annotations.static ArcType
ARC_TYPE
The default type of an arc.static Binning
BINNING
The default binning value.static Integer
BYTES_PER_PIXEL
The number of bytes per pixels.static NamingConvention
COLUMN_NAMING_CONVENTION
The default naming convention for columns.static int
COLUMNS
The default number of columns for a plate.static String
COMPONENT_LOT_NUMBER
The default lot number of a component of a microscope.static String
COMPONENT_MANUFACTURER
The default manufacturer of a component of a microscope.static String
COMPONENT_MODEL
The default model of a component of a microscope.static String
COMPONENT_SERIAL_NUMBER
The default serial number of a component of a microscope.static Correction
CORRECTION
The default objective's correction.static Double
CUT_IN
The default cut-in.static Double
CUT_OUT
The default cut-out.static Color
DEFAULT_COLOR
The default color.static DetectorType
DETECTOR_TYPE
The default type of a detector.static DimensionOrder
DIMENSION_ORDER
The default dimension order.static ExperimentType
EXPERIMENT_TYPE
The default type of a microscope.static int
FIELDS
The default number of fields for a well.static FilamentType
FILAMENT_TYPE
The default type of a filament.static FilterType
FILTER_TYPE
The default objective's immersion.static Immersion
IMMERSION
The default objective's immersion.protected Instrument
instrument
The instrument used for the metadata.static LaserMedium
LASER_MEDIUM
The default type of a laser.static LaserType
LASER_TYPE
The default type of a laser.static String[]
LIGHT_SOURCES
The light sources to handle.static Double
LIGHTSOURCE_POWER
The default power of a light source.static Medium
MEDIUM
The default medium for the objective.static MicrobeamManipulationType
MICROBEAM_MANIPULATION_TYPE
The default type of a microbeam manipulation.static MicroscopeType
MICROSCOPE_TYPE
The default type of a microscope.static int
NUMBER_OF_DECTECTORS
The number of detectors created.static int
NUMBER_OF_DICHROICS
The number of dichroics created.static int
NUMBER_OF_FILTERS
The number of filters created.static int
NUMBER_OF_OBJECTIVES
The number of objectives created.protected OME
ome
Root of the file.static PixelType
PIXEL_TYPE
The default pixels type.static String
POINTS
Points used to create Polyline and Polygon shape.static NamingConvention
ROW_NAMING_CONVENTION
The default naming convention for rows.static int
ROWS
The default number of rows for a plate.static String[]
SHAPES
The shapes to handle.static Integer
SIZE_C
The default number of channels.static Integer
SIZE_T
The default number of time-points.static Integer
SIZE_X
The default number of pixels along the X-axis.static Integer
SIZE_Y
The default number of pixels along the Y-axis.static Integer
SIZE_Z
The default number of z-sections.static String
TIME
The default time.
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Constructor Summary
Constructors Constructor Description XMLMockObjects()
Creates a new instance.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description OME
createAnnotatedImage()
Creates and annotates an image.Annotation
createAnnotation(String type, OMEModelObject object, int index)
Create a comment annotation for the specified object.Plate
createBasicPlate(int index)
Creates a basic plate.OME
createBasicPlateWithReagent()
Creates a plate with1
row,1
column and1
field.BinaryFile
createBinaryFile()
Creates a binary file.BinData
createBinData(int sizeX, int sizeY, int bpp)
Creates a new object.Channel
createChannel(int index)
Creates a channel.Dataset
createDataset(int index)
Creates a dataset.Detector
createDetector(int index)
Creates a detector.DetectorSettings
createDetectorSettings(int ref)
Creates a detector settings.Dichroic
createDichroic(int index)
Creates a dichroic.Experiment
createExperiment(int index)
Creates an experiment.Experimenter
createExperimenter(int index)
Creates an experimenter.Experiment
createExperimentWithMicrobeam(int index)
Creates an experiment with a microbeam.Filter
createFilter(int index, double cutIn, double cutOut)
Creates a filter.FilterSet
createFilterSet(int index)
Creates a filter set.OME
createFullPopulatedPlate(int n)
OME
createImage()
Creates and returns the root element.OME
createImage(boolean metadata)
Creates and returns the root element.Image
createImage(int index)
Creates a new image.Image
createImage(int index, boolean metadata)
Creates a new image.ImagingEnvironment
createImageEnvironment()
Creates a imaging environment.OME
createImageWithAcquisitionData()
Creates an image with acquisition data.OME
createImageWithAnnotatedAcquisitionData()
Creates an image with acquisition data.Image
createImageWithExperiment(int index, boolean metadata, Experiment exp)
Creates an image with a given experiment.OME
createImageWithROI()
Creates an image with ROI.Instrument
createInstrument(boolean populate)
Creates an instrument with filters, light sources etc.LightPath
createLightPath()
Creates a light path.LightSource
createLightSource(String type, int index)
Creates a light source of the specified type.LightSourceSettings
createLightSourceSettings(int ref)
Creates a light source settings.MicrobeamManipulation
createMicrobeamManipulation(int index)
Creates a microbeam manipulation.Microscope
createMicroscope()
Creates a microscope.Objective
createObjective(int index)
Creates an objective.ObjectiveSettings
createObjectiveSettings(int ref)
Creates an objective settings.Plane
createPlane(int z, int c, int t)
Creates a plane information object.Plate
createPlate(int numberOfPlates, int index, int numberOfPlateAcquisition)
Creates a default platePlate
createPlate(int numberOfPlates, int index, int rows, int columns, int fields, int numberOfPlateAcquisition)
Creates a populated plate with images.Plate
createPlate(int numberOfPlates, int index, int rows, int columns, int fields, int numberOfPlateAcquisition, boolean withMicrobeam)
Creates a populated plate with images.Plate
createPlate(int numberOfScreens, int screenIndex, int numberOfPlates, int plateIndex, int rows, int columns, int fields, int numberOfPlateAcquisition)
Creates a populated plate with images.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.OME
createPopulatedPlate(int n)
Creates a plate with1
row,1
column and1
field.OME
createPopulatedPlate(int n, int fields)
Creates a plate with1
row,1
column andfields
field.OME
createPopulatedPlate(int plates, int rows, int cols, int fields, int acqs)
Creates several plates but no containing screen.OME
createPopulatedPlate(int plates, int rows, int cols, int fields, int acqs, boolean withMicrobeam)
Creates several plates but no containing screen.OME
createPopulatedScreen()
Creates one 2x2 plate of with a single well sample per well and one plate acquisition.OME
createPopulatedScreen(int plates, int rows, int cols, int fields, int acqs)
Creates a screen with several plates.OME
createPopulatedScreen(int screens, int plates, int rows, int cols, int fields, int acqs)
Creates several screens each with several plates.OME
createPopulatedScreen(int screens, int plates, int rows, int cols, int fields, int acqs, boolean withMicrobeam)
Creates several screens each with several plates.Project
createProject(int index)
Creates a project.Reagent
createReagent(int index)
Creates a reagent.ROI
createROI(int index, int z, int c, int t)
Creates an ROI.Screen
createScreen(int index)
Creates a screen.Shape
createShape(int index, String type, int z, int c, int t)
Creates the specified type of shape.StageLabel
createStageLabel()
Creates a imaging environment.OME
getRoot()
Returns the root of the XML file.
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Field Detail
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DEFAULT_COLOR
public static final Color DEFAULT_COLOR
The default color.
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LIGHTSOURCE_POWER
public static final Double LIGHTSOURCE_POWER
The default power of a light source.
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COMPONENT_MODEL
public static final String COMPONENT_MODEL
The default model of a component of a microscope.- See Also:
- Constant Field Values
-
COMPONENT_MANUFACTURER
public static final String COMPONENT_MANUFACTURER
The default manufacturer of a component of a microscope.- See Also:
- Constant Field Values
-
COMPONENT_SERIAL_NUMBER
public static final String COMPONENT_SERIAL_NUMBER
The default serial number of a component of a microscope.- See Also:
- Constant Field Values
-
COMPONENT_LOT_NUMBER
public static final String COMPONENT_LOT_NUMBER
The default lot number of a component of a microscope.- See Also:
- Constant Field Values
-
LASER_TYPE
public static final LaserType LASER_TYPE
The default type of a laser.
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ARC_TYPE
public static final ArcType ARC_TYPE
The default type of an arc.
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FILAMENT_TYPE
public static final FilamentType FILAMENT_TYPE
The default type of a filament.
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DETECTOR_TYPE
public static final DetectorType DETECTOR_TYPE
The default type of a detector.
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CORRECTION
public static final Correction CORRECTION
The default objective's correction.
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IMMERSION
public static final Immersion IMMERSION
The default objective's immersion.
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FILTER_TYPE
public static final FilterType FILTER_TYPE
The default objective's immersion.
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MICROSCOPE_TYPE
public static final MicroscopeType MICROSCOPE_TYPE
The default type of a microscope.
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EXPERIMENT_TYPE
public static final ExperimentType EXPERIMENT_TYPE
The default type of a microscope.
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MICROBEAM_MANIPULATION_TYPE
public static final MicrobeamManipulationType MICROBEAM_MANIPULATION_TYPE
The default type of a microbeam manipulation.
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BINNING
public static final Binning BINNING
The default binning value.
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MEDIUM
public static final Medium MEDIUM
The default medium for the objective.
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LASER_MEDIUM
public static final LaserMedium LASER_MEDIUM
The default type of a laser.
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SIZE_X
public static final Integer SIZE_X
The default number of pixels along the X-axis.
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SIZE_Y
public static final Integer SIZE_Y
The default number of pixels along the Y-axis.
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SIZE_Z
public static final Integer SIZE_Z
The default number of z-sections.
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SIZE_C
public static final Integer SIZE_C
The default number of channels.
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SIZE_T
public static final Integer SIZE_T
The default number of time-points.
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BYTES_PER_PIXEL
public static final Integer BYTES_PER_PIXEL
The number of bytes per pixels.
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ROWS
public static final int ROWS
The default number of rows for a plate.- See Also:
- Constant Field Values
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COLUMNS
public static final int COLUMNS
The default number of columns for a plate.- See Also:
- Constant Field Values
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FIELDS
public static final int FIELDS
The default number of fields for a well.- See Also:
- Constant Field Values
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LIGHT_SOURCES
public static final String[] LIGHT_SOURCES
The light sources to handle.
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SHAPES
public static final String[] SHAPES
The shapes to handle.
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ANNOTATIONS
public static final String[] ANNOTATIONS
The supported types of annotations.
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ROW_NAMING_CONVENTION
public static final NamingConvention ROW_NAMING_CONVENTION
The default naming convention for rows.
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COLUMN_NAMING_CONVENTION
public static final NamingConvention COLUMN_NAMING_CONVENTION
The default naming convention for columns.
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DIMENSION_ORDER
public static final DimensionOrder DIMENSION_ORDER
The default dimension order.
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PIXEL_TYPE
public static final PixelType PIXEL_TYPE
The default pixels type.
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NUMBER_OF_DECTECTORS
public static final int NUMBER_OF_DECTECTORS
The number of detectors created.- See Also:
- Constant Field Values
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NUMBER_OF_OBJECTIVES
public static final int NUMBER_OF_OBJECTIVES
The number of objectives created.- See Also:
- Constant Field Values
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NUMBER_OF_FILTERS
public static final int NUMBER_OF_FILTERS
The number of filters created.- See Also:
- Constant Field Values
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NUMBER_OF_DICHROICS
public static final int NUMBER_OF_DICHROICS
The number of dichroics created.- See Also:
- Constant Field Values
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POINTS
public static final String POINTS
Points used to create Polyline and Polygon shape.- See Also:
- Constant Field Values
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TIME
public static final String TIME
The default time.- See Also:
- Constant Field Values
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CUT_IN
public static final Double CUT_IN
The default cut-in.
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CUT_OUT
public static final Double CUT_OUT
The default cut-out.
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ome
protected final OME ome
Root of the file.
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instrument
protected Instrument instrument
The instrument used for the metadata.
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Method Detail
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createDetector
public Detector createDetector(int index)
Creates a detector.- Parameters:
index
- The index of the detector in the file.- Returns:
- See above.
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createFilterSet
public FilterSet createFilterSet(int index)
Creates a filter set.- Parameters:
index
- The index of the filter set in the file.- Returns:
- See above.
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createMicroscope
public Microscope createMicroscope()
Creates a microscope.- Returns:
- See above.
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createDichroic
public Dichroic createDichroic(int index)
Creates a dichroic.- Parameters:
index
- The index of the dichroic in the file.- Returns:
- See above.
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createObjective
public Objective createObjective(int index)
Creates an objective.- Parameters:
index
- The index of the objective in the file.- Returns:
- See above.
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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.
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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.
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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.
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createLightPath
public LightPath createLightPath()
Creates a light path.- Returns:
- See above.
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createImageEnvironment
public ImagingEnvironment createImageEnvironment()
Creates a imaging environment.- Returns:
- See above.
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createStageLabel
public StageLabel createStageLabel()
Creates a imaging environment.- Returns:
- See above.
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createLightSourceSettings
public LightSourceSettings createLightSourceSettings(int ref)
Creates a light source settings.- Parameters:
ref
- Reference to the light source.- Returns:
- See above.
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createMicrobeamManipulation
public MicrobeamManipulation createMicrobeamManipulation(int index)
Creates a microbeam manipulation.- Parameters:
index
- The index in the file.- Returns:
- See above.
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createExperimenter
public Experimenter createExperimenter(int index)
Creates an experimenter.- Parameters:
index
- The index of the Experimenter.- Returns:
- See above.
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createExperiment
public Experiment createExperiment(int index)
Creates an experiment.- Parameters:
index
- The index in the file.- Returns:
- See above.
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createExperimentWithMicrobeam
public Experiment createExperimentWithMicrobeam(int index)
Creates an experiment with a microbeam.- Parameters:
index
- The index in the file.- Returns:
- See above.
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createDetectorSettings
public DetectorSettings createDetectorSettings(int ref)
Creates a detector settings.- Parameters:
ref
- Reference to the detector.- Returns:
- See above.
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createObjectiveSettings
public ObjectiveSettings createObjectiveSettings(int ref)
Creates an objective settings.- Parameters:
ref
- Reference to the objective.- Returns:
- See above.
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createBinaryFile
public BinaryFile createBinaryFile()
Creates a binary file.- Returns:
- See above.
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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.
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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.
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getRoot
public OME getRoot()
Returns the root of the XML file.- Returns:
- See above.
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createProject
public Project createProject(int index)
Creates a project.- Parameters:
index
- The index of the project.- Returns:
- See above.
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createDataset
public Dataset createDataset(int index)
Creates a dataset.- Parameters:
index
- The index of the dataset.- Returns:
- See above.
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createScreen
public Screen createScreen(int index)
Creates a screen.- Parameters:
index
- The index of the screen.- Returns:
- See above.
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createBasicPlate
public Plate createBasicPlate(int index)
Creates a basic plate.- Parameters:
index
- The index of the plate.- Returns:
- See above.
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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.
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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
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.
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createImage
public Image createImage(int index, boolean metadata)
Creates a new image.- Parameters:
index
- The identifier of the image.metadata
- Passtrue
to create channel with acquisition metadata,false
otherwise.- Returns:
- See above.
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createChannel
public Channel createChannel(int index)
Creates a channel.- Parameters:
index
- The index in the file.- Returns:
- See above.
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createImage
public Image createImage(int index)
Creates a new image.- Parameters:
index
- The identifier of the image.- Returns:
- See above.
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createInstrument
public Instrument createInstrument(boolean populate)
Creates an instrument with filters, light sources etc.- Parameters:
populate
- Passtrue
to populate the instrument,false
otherwise.- Returns:
- See above.
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createReagent
public Reagent createReagent(int index)
Creates a reagent.- Parameters:
index
- The index in the file.- Returns:
- See above.
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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.
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createImage
public OME createImage()
Creates and returns the root element. Creates an image w/o metadata.- Returns:
- See above.
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createImage
public OME createImage(boolean metadata)
Creates and returns the root element.- Parameters:
metadata
- Passtrue
to create an image with metadata,false
w/o/- Returns:
- See above.
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createAnnotatedImage
public OME 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
public OME createImageWithAcquisitionData()
Creates an image with acquisition data.- Returns:
- See above.
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createImageWithAnnotatedAcquisitionData
public OME createImageWithAnnotatedAcquisitionData()
Creates an image with acquisition data.- Returns:
- See above.
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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.
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createImageWithROI
public OME createImageWithROI()
Creates an image with ROI.- Returns:
- See above.
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createPopulatedPlate
public OME createPopulatedPlate(int n)
Creates a plate with1
row,1
column and1
field. The plate will have images with acquisition data but no plate acquisition data if the passed value is0
otherwise will haven
plate acquisitions.- Parameters:
n
- The number of plate acquisition.- Returns:
- See above
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createPopulatedPlate
public OME createPopulatedPlate(int n, int fields)
Creates a plate with1
row,1
column andfields
field. The plate will have images with acquisition data but no plate acquisition data if the passed value is0
otherwise will haven
plate acquisitions.- Parameters:
n
- The number of plate acquisition.fields
- The number of fields.- Returns:
- See above
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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.
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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
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.
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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
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.
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createPopulatedScreen
public OME createPopulatedScreen()
Creates one 2x2 plate of with a single well sample per well and one plate acquisition.
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createBasicPlateWithReagent
public OME createBasicPlateWithReagent()
Creates a plate with1
row,1
column and1
field. This plate will be added to a screen and the well linked to a reagent.- Returns:
- See above
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