Uses of Class
ome.model.core.Pixels

Packages that use Pixels

Package	Description
ome.api	Contains the central verbs of the Omero System.
ome.formats
ome.formats.importer.util
ome.io.bioformats
ome.io.nio	New Input/Output handling for the OMERO server This includes interfaces/classes for the input and output handling of data within the OMERO server.
ome.logic	The central repository of implementations which will be accessible through this server.
ome.model.core
ome.model.display
ome.model.roi
ome.services	Base services package for OMERO API services This includes classes that implement OMERO API services described as interfaces in the OMERO Common component.
ome.services.pixeldata
ome.util	Utilities for all of OMERO.
omeis.providers.re	Red-Green-Blue (RGB) data structures and Image Rendering Service This package provides basic data structures to represent an RGB pixel set and provide a service for the rendering of this pixel set.
omeis.providers.re.data	Provides classes needed to define XY planes within a dynamic 3D context.
omeis.providers.re.metadata
omeis.providers.re.quantum

Uses of Pixels in ome.api

Methods in ome.api that return Pixels

Modifier and Type	Method and Description
Pixels	IPixels.retrievePixDescription(long pixelsId) Retrieves the pixels metadata with the following objects pre-linked: pixels.pixelsType pixels.pixelsDimensions pixels.channels pixels.channnels.statsInfo pixels.channnels.colorComponent pixels.channnels.logicalChannel pixels.channnels.logicalChannel.photometricInterpretation
Pixels	RawPixelsStore.save()

Methods in ome.api with parameters of type Pixels

Modifier and Type	Method and Description
RenderingDef	IRenderingSettings.createNewRenderingDef(Pixels pixels) Creates a new rendering definition object along with its sub-objects.
void	IRenderingSettings.resetDefaults(RenderingDef def, Pixels pixels) Resets the given rendering settings to those that are specified by the rendering engine intelligent pretty good image (PG) logic for the pixels set linked to that set of rendering settings.
RenderingDef	IRenderingSettings.resetDefaultsNoSave(RenderingDef def, Pixels pixels) Resets the given rendering settings to those that are specified by the rendering engine intelligent pretty good image (PG) logic for the pixels set linked to that set of rendering settings.
boolean	IRenderingSettings.sanityCheckPixels(Pixels pFrom, Pixels pTo) Checks if the specified sets of pixels are compatible.

Uses of Pixels in ome.formats

Methods in ome.formats that return types with arguments of type Pixels

Modifier and Type	Method and Description
List<Pixels>	OMEROMetadataStore.saveToDB(FilesetJobLink link) Saves the current object graph to the database.

Uses of Pixels in ome.formats.importer.util

Methods in ome.formats.importer.util that return Pixels

Modifier and Type	Method and Description
Pixels	TinyImportFixture.getPixels()

Uses of Pixels in ome.io.bioformats

Constructors in ome.io.bioformats with parameters of type Pixels

Constructor and Description
BfPyramidPixelBuffer(Pixels pixels, String filePath, boolean write) We may want a constructor that takes the id of an imported file or that takes a File object?
BfPyramidPixelBuffer(TileSizes sizes, Pixels pixels, String filePath, boolean write) Full constructor taking a TileSizes implementation which defines how large the pyramid tiles will be.
BfPyramidPixelBuffer(TileSizes sizes, Pixels pixels, String filePath, boolean write, boolean init)

Uses of Pixels in ome.io.nio

Methods in ome.io.nio with parameters of type Pixels

Modifier and Type	Method and Description
PixelBuffer	PixelsService._getPixelBuffer(Pixels pixels, boolean write)
protected long	SimpleBackOff.calculate(Pixels pixels)
protected int	SimpleBackOff.countTiles(Pixels pixels)
PixelBuffer	PixelsService.createPixelBuffer(Pixels pixels) Creates a PixelBuffer for a given pixels set.
protected BfPyramidPixelBuffer	PixelsService.createPyramidPixelBuffer(Pixels pixels, String filePath, boolean write) Helper method to properly log any exceptions raised by Bio-Formats.
protected PixelBuffer	PixelsService.createRomioPixelBuffer(String pixelsFilePath, Pixels pixels, boolean allowModification) Helper method to properlty create a RomioPixelBuffer.
IFormatReader	PixelsService.getBfReader(Pixels pixels) Short-cut in the FS case where we know that we are dealing with a FS-lite file, and want to retrieve the actual file as opposed to a pyramid or anything else.
String	FilePathResolver.getOriginalFilePath(AbstractFileSystemService service, Pixels pixels) Retrieves the original file path for a given set of pixels.
protected String	PixelsService.getOriginalFilePath(Pixels pixels) Retrieves the original file path for a given set of pixels.
PixelBuffer	PixelsService.getPixelBuffer(Pixels pixels) Deprecated. In the future callers should use the more descriptive PixelsService.getPixelBuffer(Pixels, boolean).
PixelBuffer	PixelsService.getPixelBuffer(Pixels pixels, boolean write) Returns a pixel buffer for a given set of pixels.
protected int	PixelsService.getSeries(Pixels pixels) Retrieves the series for a given set of pixels.
protected void	PixelsService.handleMissingPyramid(Pixels pixels, String pixelsPyramidFilePath) If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.
protected void	PixelsService.handleMissingStatsInfo(Pixels pixels) If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.
StatsInfo[]	PixelsService.makePyramid(Pixels pixels) Creates a pixels pyramid for a given set of pixels.
boolean	PixelsService.requiresPixelsPyramid(Pixels pixels) Returns whether a pyramid should be used for the given Pixels.
void	BackOff.throwMissingPyramidException(String msg, Pixels pixels)
void	SimpleBackOff.throwMissingPyramidException(String msg, Pixels pixels)

Constructors in ome.io.nio with parameters of type Pixels

Constructor and Description
InMemoryPlanarPixelBuffer(Pixels pixels, byte[][][][] planes) Constructs an in memory pixel buffer based on a defined dimensionality.
RomioPixelBuffer(String path, Pixels pixels) Creates a new instance.
RomioPixelBuffer(String path, Pixels pixels, boolean permitModification) Creates a new instance, with manual setting of RomioPixelBuffer.permitModification.

Uses of Pixels in ome.logic

Methods in ome.logic that return Pixels

Modifier and Type	Method and Description
Pixels	PixelsImpl.retrievePixDescription(long pixId)

Methods in ome.logic with parameters of type Pixels

Modifier and Type	Method and Description
RenderingDef	RenderingSettingsImpl.createNewRenderingDef(Pixels pixels) Implemented as specified by the IRenderingSettings I/F
void	RenderingSettingsImpl.resetDefaults(RenderingDef def, Pixels pixels) Implemented as specified by the IRenderingSettings I/F
RenderingDef	RenderingSettingsImpl.resetDefaultsNoSave(RenderingDef def, Pixels pixels) Implemented as specified by the IRenderingSettings I/F
boolean	RenderingSettingsImpl.sanityCheckPixels(Pixels pFrom, Pixels pTo) Implemented as specified by the IRenderingSettings I/F

Uses of Pixels in ome.model.core

Fields in ome.model.core declared as Pixels

Modifier and Type	Field and Description
protected Pixels	Channel.pixels
protected Pixels	PlaneInfo.pixels
protected Pixels	Pixels.relatedTo

Fields in ome.model.core with type parameters of type Pixels

Modifier and Type	Field and Description
protected List<Pixels>	Image.pixels

Methods in ome.model.core that return Pixels

Modifier and Type	Method and Description
Pixels	PixelsOriginalFileMap.child()
Pixels	Channel.getPixels() Many-to-one field ome.model.core.Channel.pixels (ome.model.core.Pixels)
Pixels	PlaneInfo.getPixels() Many-to-one field ome.model.core.PlaneInfo.pixels (ome.model.core.Pixels)
Pixels	Image.getPixels(int index) Gets the ome.model.core.Pixels at the given index.
Pixels	Image.getPrimaryPixels() Gets the first element of pixels which can be interpreted as the primary or default element in some situations.
Pixels	Pixels.getRelatedTo() Many-to-one field ome.model.core.Pixels.relatedTo (ome.model.core.Pixels)
Pixels	Pixels.newInstance()
Pixels	Pixels.proxy()
Pixels	Image.setPixels(int index, Pixels element) Sets the ome.model.core.Pixels at the given index.
Pixels	Image.setPrimaryPixels(Pixels element) Swaps the first element of pixels with the first instance of the given element.

Methods in ome.model.core that return types with arguments of type Pixels

Modifier and Type	Method and Description
protected List<Pixels>	Image.getPixels() returns pixels .
Iterator<Pixels>	Image.iteratePixels() should be used rather than accessing the pixels set directly.
Iterator<Pixels>	OriginalFile.linkedPixelsIterator() provides an iterator over the parent values of the pixelsFileMaps.
List<Pixels>	OriginalFile.linkedPixelsList() produces a List-copy of the underlying collection.
Collection<Pixels>	Image.unmodifiablePixels() Returns an unmodifiable collection-view

Methods in ome.model.core with parameters of type Pixels

Modifier and Type	Method and Description
void	Image.addPixels(Pixels target) use instead of setPixels .
Set<PixelsOriginalFileMap>	OriginalFile.findPixelsOriginalFileMap(Pixels target) find all ome.model.core.PixelsOriginalFileMap which have the argument as their child.
void	PixelsOriginalFileMap.link(OriginalFile parent, Pixels child)
PixelsOriginalFileMap	OriginalFile.linkPixels(Pixels addition) Adds a ome.model.core.PixelsOriginalFileMap to pixelsFileMaps .
void	Image.removePixels(Pixels target) removes a single element from this set and makes the inverse call on ome.model.core.Pixels
Pixels	Image.setPixels(int index, Pixels element) Sets the ome.model.core.Pixels at the given index.
void	Channel.setPixels(Pixels pixels)
void	PlaneInfo.setPixels(Pixels pixels)
Pixels	Image.setPrimaryPixels(Pixels element) Swaps the first element of pixels with the first instance of the given element.
void	Pixels.setRelatedTo(Pixels relatedTo)
void	OriginalFile.unlinkPixels(Pixels removal) unlinks all ome.model.core.Pixels instances from this instance.

Method parameters in ome.model.core with type arguments of type Pixels

Modifier and Type	Method and Description
void	Image.addPixelsSet(Collection<Pixels> targets) use like addPixels.
void	Image.removePixelsSet(Collection<Pixels> targets) use like removePixels
protected void	Image.setPixels(List<Pixels> pixels) setter for pixels should be avoided.

Constructors in ome.model.core with parameters of type Pixels

Constructor and Description
Channel(LogicalChannel _logicalChannel, Pixels _pixels)
PlaneInfo(Pixels _pixels, Integer _theZ, Integer _theC, Integer _theT)

Uses of Pixels in ome.model.display

Fields in ome.model.display declared as Pixels

Modifier and Type	Field and Description
protected Pixels	RenderingDef.pixels
protected Pixels	Thumbnail.pixels

Methods in ome.model.display that return Pixels

Modifier and Type	Method and Description
Pixels	RenderingDef.getPixels() Many-to-one field ome.model.display.RenderingDef.pixels (ome.model.core.Pixels)
Pixels	Thumbnail.getPixels() Many-to-one field ome.model.display.Thumbnail.pixels (ome.model.core.Pixels)

Methods in ome.model.display with parameters of type Pixels

Modifier and Type	Method and Description
void	RenderingDef.setPixels(Pixels pixels)
void	Thumbnail.setPixels(Pixels pixels)

Constructors in ome.model.display with parameters of type Pixels

Constructor and Description
RenderingDef(Pixels _pixels, Integer _defaultZ, Integer _defaultT, RenderingModel _model, QuantumDef _quantization)
Thumbnail(Pixels _pixels, String _mimeType, Integer _sizeX, Integer _sizeY)

Uses of Pixels in ome.model.roi

Fields in ome.model.roi declared as Pixels

Modifier and Type	Field and Description
protected Pixels	Mask.pixels

Methods in ome.model.roi that return Pixels

Modifier and Type	Method and Description
Pixels	Mask.getPixels() Many-to-one field ome.model.roi.Mask.pixels (ome.model.core.Pixels)

Methods in ome.model.roi with parameters of type Pixels

Modifier and Type	Method and Description
void	Mask.setPixels(Pixels pixels)

Uses of Pixels in ome.services

Methods in ome.services that return Pixels

Modifier and Type	Method and Description
Pixels	RenderingBean.getPixels() Implemented as specified by the RenderingEngine interface.
Pixels	ThumbnailCtx.getPixels(long pixelsId) Retrieves the Pixels object for a given Pixels ID.
Pixels	RawPixelsBean.save()

Methods in ome.services with parameters of type Pixels

Modifier and Type	Method and Description
Dimension	ThumbnailCtx.calculateXYWidths(Pixels pixels, int longestSide) Calculates the ratio of the two sides of a Pixel set and returns the X and Y widths based on the longest side maintaining aspect ratio.
Thumbnail	ThumbnailCtx.createThumbnailMetadata(Pixels pixels, Dimension dimensions) Creates metadata for a thumbnail of a given set of pixels set and X-Y dimensions.
String	OmeroFilePathResolver.getOriginalFilePath(AbstractFileSystemService service, Pixels pixels)

Uses of Pixels in ome.services.pixeldata

Methods in ome.services.pixeldata that return Pixels

Modifier and Type	Method and Description
protected Pixels	PixelDataHandler.getPixels(Long id, ServiceFactory sf)

Uses of Pixels in ome.util

Methods in ome.util with parameters of type Pixels

Modifier and Type	Method and Description
static Validation	Validator.valid(Pixels pixels)

Uses of Pixels in omeis.providers.re

Methods in omeis.providers.re that return Pixels

Modifier and Type	Method and Description
Pixels	Renderer.getMetadata() Returns the Pixels set the rendering engine is for.
Pixels	RenderingEngine.getPixels() Returns the Pixels set the Rendering engine is for.

Constructors in omeis.providers.re with parameters of type Pixels

Constructor and Description
Renderer(QuantumFactory quantumFactory, List<RenderingModel> renderingModels, Pixels pixelsObj, RenderingDef renderingDefObj, PixelBuffer bufferObj, List<File> luts) Creates a new instance to render the specified pixels set and get this new instance ready for rendering.

Uses of Pixels in omeis.providers.re.data

Methods in omeis.providers.re.data with parameters of type Pixels

Modifier and Type	Method and Description
static Plane2D	PlaneFactory.createPlane(PlaneDef planeDef, int channel, Pixels pixels, PixelBuffer buffer) Factory method to fetch plane data and create an object to access it.

Constructors in omeis.providers.re.data with parameters of type Pixels

Constructor and Description
Plane2D(PlaneDef pDef, Pixels pixels, PixelData data) Constructor that sub-classes must call.

Uses of Pixels in omeis.providers.re.metadata

Methods in omeis.providers.re.metadata with parameters of type Pixels

Modifier and Type	Method and Description
void	StatsFactory.computeLocationStats(Pixels metadata, PixelBuffer pixelsData, PlaneDef pd, int index) Helper object to determine the location of the pixels' values, the inputWindow i.e.
double[]	StatsFactory.initPixelsRange(Pixels metadata) Determines the minimum and maximum corresponding to the passed pixels.

Uses of Pixels in omeis.providers.re.quantum

Fields in omeis.providers.re.quantum declared as Pixels

Modifier and Type	Field and Description
protected Pixels	QuantumStrategy.pixels The pixels this strategy is for.

Methods in omeis.providers.re.quantum with parameters of type Pixels

Modifier and Type	Method and Description
QuantumStrategy	QuantumFactory.getStrategy(QuantumDef qd, Pixels pixels) Returns a strategy to carry out the quantization process whose context is defined by pd.

Constructors in omeis.providers.re.quantum with parameters of type Pixels

Constructor and Description
BinaryMaskQuantizer(QuantumDef qd, Pixels pixels) Creates a new strategy.
Quantization_32_bit(QuantumDef qd, Pixels pixels) Creates a new strategy.
Quantization_8_16_bit(QuantumDef qd, Pixels pixels) Creates a new strategy.
Quantization_float(QuantumDef qd, Pixels pixels) Creates a new strategy.
QuantumStrategy(QuantumDef qd, Pixels pixels) Creates a new instance.