A B C D E F G I J L M N O P R S T V W X

A

ANNOTATIONS - Static variable in class ome.specification.XMLMockObjects

The supported types of annotations.

ARC_TYPE - Static variable in class ome.specification.XMLMockObjects

The default type of an arc.

B

BIG_ENDIAN_ATTRIBUTE - Static variable in class ome.specification.XMLWriter

Identifies the BigEndian attribute.

BIN_DATA_TAG - Static variable in class ome.specification.XMLWriter

Identifies the BinData tag.

BINNING - Static variable in class ome.specification.XMLMockObjects

The default binning value.

BYTES_PER_PIXEL - Static variable in class ome.specification.XMLMockObjects

The number of bytes per pixels.

C

COLUMN_NAMING_CONVENTION - Static variable in class ome.specification.XMLMockObjects

The default naming convention for columns.

COLUMNS - Static variable in class ome.specification.XMLMockObjects

The default number of columns for a plate.

COMPONENT_LOT_NUMBER - Static variable in class ome.specification.XMLMockObjects

The default lot number of a component of a microscope.

COMPONENT_MANUFACTURER - Static variable in class ome.specification.XMLMockObjects

The default manufacturer of a component of a microscope.

COMPONENT_MODEL - Static variable in class ome.specification.XMLMockObjects

The default model of a component of a microscope.

COMPONENT_SERIAL_NUMBER - Static variable in class ome.specification.XMLMockObjects

The default serial number of a component of a microscope.

COMPRESSION_ATTRIBUTE - Static variable in class ome.specification.XMLWriter

Identifies the Compression attribute.

CORRECTION - Static variable in class ome.specification.XMLMockObjects

The default objective's correction.

createAnnotatedImage() - Method in class ome.specification.XMLMockObjects

Creates and annotates an image.

createAnnotation(String, OMEModelObject, int) - Method in class ome.specification.XMLMockObjects

Create a comment annotation for the specified object.

createBasicPlate(int) - Method in class ome.specification.XMLMockObjects

Creates a basic plate.

createBasicPlateWithReagent() - Method in class ome.specification.XMLMockObjects

Creates a plate with 1 row, 1 column and 1 field.

createBinaryFile() - Method in class ome.specification.XMLMockObjects

Creates a binary file.

createBinData(int, int, int) - Method in class ome.specification.XMLMockObjects

Creates a new object.

createChannel(int) - Method in class ome.specification.XMLMockObjects

Creates a channel.

createDataset(int) - Method in class ome.specification.XMLMockObjects

Creates a dataset.

createDetector(int) - Method in class ome.specification.XMLMockObjects

Creates a detector.

createDetectorSettings(int) - Method in class ome.specification.XMLMockObjects

Creates a detector settings.

createDichroic(int) - Method in class ome.specification.XMLMockObjects

Creates a dichroic.

createExperiment(int) - Method in class ome.specification.XMLMockObjects

Creates an experiment.

createExperimenter(int) - Method in class ome.specification.XMLMockObjects

Creates an experimenter.

createExperimentWithMicrobeam(int) - Method in class ome.specification.XMLMockObjects

Creates an experiment with a microbeam.

createFilter(int, double, double) - Method in class ome.specification.XMLMockObjects

Creates a filter.

createFilterSet(int) - Method in class ome.specification.XMLMockObjects

Creates a filter set.

createFullPopulatedPlate(int) - Method in class ome.specification.XMLMockObjects

Creates a plate with XMLMockObjects.ROWS rows, XMLMockObjects.COLUMNS columns and XMLMockObjects.FIELDS field.

createImage(int, boolean) - Method in class ome.specification.XMLMockObjects

Creates a new image.

createImage(int) - Method in class ome.specification.XMLMockObjects

Creates a new image.

createImage() - Method in class ome.specification.XMLMockObjects

Creates and returns the root element.

createImage(boolean) - Method in class ome.specification.XMLMockObjects

Creates and returns the root element.

createImageEnvironment() - Method in class ome.specification.XMLMockObjects

Creates a imaging environment.

createImageWithAcquisitionData() - Method in class ome.specification.XMLMockObjects

Creates an image with acquisition data.

createImageWithAnnotatedAcquisitionData() - Method in class ome.specification.XMLMockObjects

Creates an image with acquisition data.

createImageWithExperiment(int, boolean, Experiment) - Method in class ome.specification.XMLMockObjects

Creates an image with a given experiment.

createImageWithROI() - Method in class ome.specification.XMLMockObjects

Creates an image with ROI.

createInstrument(boolean) - Method in class ome.specification.XMLMockObjects

Creates an instrument with filters, light sources etc.

createLightPath() - Method in class ome.specification.XMLMockObjects

Creates a light path.

createLightSource(String, int) - Method in class ome.specification.XMLMockObjects

Creates a light source of the specified type.

createLightSourceSettings(int) - Method in class ome.specification.XMLMockObjects

Creates a light source settings.

createMicrobeamManipulation(int) - Method in class ome.specification.XMLMockObjects

Creates a microbeam manipulation.

createMicroscope() - Method in class ome.specification.XMLMockObjects

Creates a microscope.

createObjective(int) - Method in class ome.specification.XMLMockObjects

Creates an objective.

createObjectiveSettings(int) - Method in class ome.specification.XMLMockObjects

Creates an objective settings.

createPlane(int, int, int) - Method in class ome.specification.XMLMockObjects

Creates a plane information object.

createPlate(int, int, int) - Method in class ome.specification.XMLMockObjects

Creates a default plate

createPlate(int, int, int, int, int, int) - Method in class ome.specification.XMLMockObjects

Creates a populated plate with images.

createPlate(int, int, int, int, int, int, boolean) - Method in class ome.specification.XMLMockObjects

Creates a populated plate with images.

createPlate(int, int, int, int, int, int, int, int) - Method in class ome.specification.XMLMockObjects

Creates a populated plate with images.

createPlate(int, int, int, int, int, int, int, int, boolean) - Method in class ome.specification.XMLMockObjects

Creates a populated plate with images.

createPopulatedPlate(int) - Method in class ome.specification.XMLMockObjects

Creates a plate with 1 row, 1 column and 1field.

createPopulatedPlate(int, int) - Method in class ome.specification.XMLMockObjects

Creates a plate with 1 row, 1 column and fieldsfield.

createPopulatedPlate(int, int, int, int, int) - Method in class ome.specification.XMLMockObjects

Creates several plates but no containing screen.

createPopulatedPlate(int, int, int, int, int, boolean) - Method in class ome.specification.XMLMockObjects

Creates several plates but no containing screen.

createPopulatedScreen(int, int, int, int, int, int) - Method in class ome.specification.XMLMockObjects

Creates several screens each with several plates.

createPopulatedScreen(int, int, int, int, int, int, boolean) - Method in class ome.specification.XMLMockObjects

Creates several screens each with several plates.

createPopulatedScreen(int, int, int, int, int) - Method in class ome.specification.XMLMockObjects

Creates a screen with several plates.

createPopulatedScreen() - Method in class ome.specification.XMLMockObjects

Creates one 2x2 plate of with a single well sample per well and one plate acquisition.

createProject(int) - Method in class ome.specification.XMLMockObjects

Creates a project.

createReagent(int) - Method in class ome.specification.XMLMockObjects

Creates a reagent.

createROI(int, int, int, int) - Method in class ome.specification.XMLMockObjects

Creates an ROI.

createScreen(int) - Method in class ome.specification.XMLMockObjects

Creates a screen.

createShape(int, String, int, int, int) - Method in class ome.specification.XMLMockObjects

Creates the specified type of shape.

createStageLabel() - Method in class ome.specification.XMLMockObjects

Creates a imaging environment.

CUT_IN - Static variable in class ome.specification.XMLMockObjects

The default cut-in.

CUT_OUT - Static variable in class ome.specification.XMLMockObjects

The default cut-out.

D

DEFAULT_COLOR - Static variable in class ome.specification.XMLMockObjects

The default color.

DETECTOR_TYPE - Static variable in class ome.specification.XMLMockObjects

The default type of a detector.

DIMENSION_ORDER - Static variable in class ome.specification.XMLMockObjects

The default dimension order.

DIMENSION_ORDER_ATTRIBUTE - Static variable in class ome.specification.XMLWriter

Identifies the DimensionOrder attribute.

E

EXPERIMENT_TYPE - Static variable in class ome.specification.XMLMockObjects

The default type of a microscope.

F

FIELDS - Static variable in class ome.specification.XMLMockObjects

The default number of fields for a well.

FILAMENT_TYPE - Static variable in class ome.specification.XMLMockObjects

The default type of a filament.

FILTER_TYPE - Static variable in class ome.specification.XMLMockObjects

The default objective's immersion.

G

getRoot() - Method in class ome.specification.XMLMockObjects

Returns the root of the XML file.

I

ID_ATTRIBUTE - Static variable in class ome.specification.XMLWriter

Identifies the ID attribute.

IMAGE_TAG - Static variable in class ome.specification.XMLWriter

Identifies the Image tag.

IMMERSION - Static variable in class ome.specification.XMLMockObjects

The default objective's immersion.

instrument - Variable in class ome.specification.XMLMockObjects

The instrument used for the metadata.

isValidFile(File, File) - Method in class ome.specification.OmeValidator

Validate the specified file

isValidFile(File, StreamSource[]) - Method in class ome.specification.OmeValidator

Validate the specified file

J

JAXP_SCHEMA_LANGUAGE - Static variable in class ome.specification.OmeValidator

Path the schema language.

JAXP_SCHEMA_SOURCE - Static variable in class ome.specification.OmeValidator

The source.

L

LASER_MEDIUM - Static variable in class ome.specification.XMLMockObjects

The default type of a laser.

LASER_TYPE - Static variable in class ome.specification.XMLMockObjects

The default type of a laser.

LENGTH_ATTRIBUTE - Static variable in class ome.specification.XMLWriter

Identifies the Length attribute.

LIGHT_SOURCES - Static variable in class ome.specification.XMLMockObjects

The light sources to handle.

LIGHTSOURCE_POWER - Static variable in class ome.specification.XMLMockObjects

The default power of a light source.

M

MEDIUM - Static variable in class ome.specification.XMLMockObjects

The default medium for the objective.

MICROBEAM_MANIPULATION_TYPE - Static variable in class ome.specification.XMLMockObjects

The default type of a microbeam manipulation.

MICROSCOPE_TYPE - Static variable in class ome.specification.XMLMockObjects

The default type of a microscope.

N

NAME_ATTRIBUTE - Static variable in class ome.specification.XMLWriter

Identifies the Name attribute.

NUMBER_OF_DECTECTORS - Static variable in class ome.specification.XMLMockObjects

The number of detectors created.

NUMBER_OF_DICHROICS - Static variable in class ome.specification.XMLMockObjects

The number of dichroics created.

NUMBER_OF_FILTERS - Static variable in class ome.specification.XMLMockObjects

The number of filters created.

NUMBER_OF_OBJECTIVES - Static variable in class ome.specification.XMLMockObjects

The number of objectives created.

O

ome - Variable in class ome.specification.XMLMockObjects

Root of the file.

ome.specification - package ome.specification

OME_TAG - Static variable in class ome.specification.XMLWriter

Identifies the OME tag.

OmeValidator - Class in ome.specification

Provides methods to validate OME instance documents against

OmeValidator() - Constructor for class ome.specification.OmeValidator

P

parseFile(File) - Method in class ome.specification.OmeValidator

Parses the specified file and returns the document.

parseFile(File, File) - Method in class ome.specification.OmeValidator

Parses the specified file and returns the document.

parseFileWithStreamArray(File, StreamSource[]) - Method in class ome.specification.OmeValidator

Parses the specified file and returns the document.

parseFileWithStreamArrayToSdtErr(File, StreamSource[]) - Method in class ome.specification.OmeValidator

Parses the specified file and returns the document.

PIXEL_TYPE - Static variable in class ome.specification.XMLMockObjects

The default pixels type.

PIXELS_TAG - Static variable in class ome.specification.XMLWriter

Identifies the Pixels tag.

PIXELS_TYPE_ATTRIBUTE - Static variable in class ome.specification.XMLWriter

Identifies the PixelType attribute.

POINTS - Static variable in class ome.specification.XMLMockObjects

Points used to create Polyline and Polygon shape.

R

resolveResource(String, String, String, String, String) - Method in class ome.specification.SchemaResolver

Resolves known namespace locations to their appropriate jar resource

ROW_NAMING_CONVENTION - Static variable in class ome.specification.XMLMockObjects

The default naming convention for rows.

ROWS - Static variable in class ome.specification.XMLMockObjects

The default number of rows for a plate.

S

SchemaResolver - Class in ome.specification

A resolver for Schema locations that pulls them from jar resources.

SchemaResolver() - Constructor for class ome.specification.SchemaResolver

SHAPES - Static variable in class ome.specification.XMLMockObjects

The shapes to handle.

SIZE_C - Static variable in class ome.specification.XMLMockObjects

The default number of channels.

SIZE_C_ATTRIBUTE - Static variable in class ome.specification.XMLWriter

Identifies the SizeC attribute.

SIZE_T - Static variable in class ome.specification.XMLMockObjects

The default number of time-points.

SIZE_T_ATTRIBUTE - Static variable in class ome.specification.XMLWriter

Identifies the SizeT attribute.

SIZE_X - Static variable in class ome.specification.XMLMockObjects

The default number of pixels along the X-axis.

SIZE_X_ATTRIBUTE - Static variable in class ome.specification.XMLWriter

Identifies the SizeX attribute.

SIZE_Y - Static variable in class ome.specification.XMLMockObjects

The default number of pixels along the Y-axis.

SIZE_Y_ATTRIBUTE - Static variable in class ome.specification.XMLWriter

Identifies the SizeY attribute.

SIZE_Z - Static variable in class ome.specification.XMLMockObjects

The default number of z-sections.

SIZE_Z_ATTRIBUTE - Static variable in class ome.specification.XMLWriter

Identifies the SizeZ attribute.

T

TIME - Static variable in class ome.specification.XMLMockObjects

The default time.

V

validateFile(File, StreamSource[]) - Method in class ome.specification.OmeValidator

Validate the specified file Any validation errors thrown as an exception.

validateFile(File, File) - Method in class ome.specification.OmeValidator

validateFileToStdError(File, StreamSource[]) - Method in class ome.specification.OmeValidator

Validate the specified file Any validation errors are sent to StdErr, not thrown as an exception.

W

W3C_XML_SCHEMA - Static variable in class ome.specification.OmeValidator

W3C.

writeFile(File, OME) - Method in class ome.specification.XMLWriter

Writes the data to the file.

writeFile(File, OME, boolean) - Method in class ome.specification.XMLWriter

Writes the data to the file.

X

XMLMockObjects - Class in ome.specification

Creates XML objects for the 2010-06 schema.

XMLMockObjects() - Constructor for class ome.specification.XMLMockObjects

Creates a new instance.

XMLWriter - Class in ome.specification

Methods to write the XML tags to the files.

XMLWriter() - Constructor for class ome.specification.XMLWriter

Creates a new instance.

A B C D E F G I J L M N O P R S T V W X