Index (omero-renderer 5.5.11 API)

A B C D E F G H I L M N O P Q R S T U V X

A

add(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain: Adds a map context to the chain.
ALPHA_INDEX - Static variable in class omeis.providers.re.ColorsFactory: Index of the red component of a color.
alphalessRendering - Variable in class omeis.providers.re.Optimizations: We can do alphaless rendering
angle(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the angle between this vector and the specified argument, provided none of these vectors is the null vector.

B

base - Variable in class ome.util.mem.ReadOnlyByteArray: The original array.
BinaryMaskQuantizer - Class in omeis.providers.re.quantum: Quantization process for binary masks.
BinaryMaskQuantizer(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.BinaryMaskQuantizer: Creates a new strategy.
BIT - Static variable in class omeis.providers.re.data.PlaneFactory: Deprecated.
BLUE_INDEX - Static variable in class omeis.providers.re.ColorsFactory: Index of the red component of a color.
breakSharing() - Method in class ome.util.mem.Handle: Subclasses must call this method before forwarding any call that modifies the Body's state.
BYTE - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
ByteArray - Class in ome.util.mem: A read-write slice of a given array.
ByteArray(byte[], int, int) - Constructor for class ome.util.mem.ByteArray: Creates a read-write slice of base.
bytesPerPixel - Variable in class omeis.providers.re.data.Plane2D: How many bytes make up a pixel value.

C

call() - Method in interface omeis.providers.re.RenderingTask: Renders wavelength.
checkIndex(int) - Method in class ome.util.mem.ReadOnlyByteArray: Makes sure that i is in [0, length).
close() - Method in class omeis.providers.re.Renderer: Closes the buffer, cleaning up file state.
CodomainChain - Class in omeis.providers.re.codomain: Queues the contexts that define the spatial domain transformations that have to be applied to the image.
CodomainChain(int, int) - Constructor for class omeis.providers.re.codomain.CodomainChain: Creates a new chain.
CodomainChain(int, int, List<CodomainMapContext>) - Constructor for class omeis.providers.re.codomain.CodomainChain: Creates a new chain.
ColorsFactory - Class in omeis.providers.re: Utility class to determine the color usually associated to a specified channel depending on its emission wavelength.
ColorsFactory() - Constructor for class omeis.providers.re.ColorsFactory
computeLocationStats(Pixels, PixelBuffer, PlaneDef, int) - Method in class omeis.providers.re.metadata.StatsFactory: Helper object to determine the location of the pixels' values, the inputWindow i.e.
contains(double, double) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
contains(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
contains(Point2D) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
contains(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
contains(double, double) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
contains(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
contains(Point2D) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
contains(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
Copiable - Interface in ome.util.mem: Requires an implementing class to provide deep copies of its instances.
CopiableArray - Class in ome.util.mem: This abstract class provides an implementation of the Copiable interface.
CopiableArray(int) - Constructor for class ome.util.mem.CopiableArray: Creates a new instance.
copy() - Method in interface ome.util.mem.Copiable: Makes a copy of this object.
copy(int, int) - Method in class ome.util.mem.CopiableArray: Copies the Copiable from the specified position from into the specified position to.
copy() - Method in class ome.util.mem.CopiableArray: Implements the method as specified by Copiable.
copy() - Method in class ome.util.mem.Handle: Returns a deep copy of this object.
createPlane(PlaneDef, int, Pixels, PixelBuffer) - Static method in class omeis.providers.re.data.PlaneFactory: Factory method to fetch plane data and create an object to access it.

D

DECILE - Static variable in class omeis.providers.re.quantum.QuantumStrategy: Determines the number of sub-intervals of the [globalMin, globalMax] interval.
DEPTH_1BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 1-bit depth (=2^1-1) output interval.
DEPTH_2BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 2-bit depth (=2^2-1) output interval.
DEPTH_3BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 3-bit depth (=2^3-1) output interval.
DEPTH_4BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 4-bit depth (=2^4-1) output interval.
DEPTH_5BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 5-bit depth (=2^5-1) output interval.
DEPTH_6BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 6-bit depth (=2^6-1) output interval.
DEPTH_7BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 7-bit depth (=2^7-1) output interval.
DEPTH_8BIT - Static variable in class omeis.providers.re.quantum.QuantumFactory: Flag to select a 8-bit depth (=2^8-1) output interval.
diff(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the sum of this vector with the reciprocal of the specified argument.
direction - Variable in class ome.util.math.geom2D.Line: The unit vector that, given the Line.origin point, identifies this line.
directionX1 - Variable in class ome.util.math.geom2D.Segment: The end point of the segment's first element.
directionX2 - Variable in class ome.util.math.geom2D.Segment: The end point of the segment's second element.
distance(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the distance between this point and the specified argument.
dot(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calulates the dot product of this vector by the specified argument.
DOUBLE - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
DOUBLE_TYPE - Static variable in class omeis.providers.re.data.PlaneFactory: Deprecated.

E

EllipseArea - Class in ome.util.math.geom2D: Represents an ellipse in the Euclidean space R².
EllipseArea(float, float, float, float) - Constructor for class ome.util.math.geom2D.EllipseArea: Creates a new instance.
endIO(int) - Method in class omeis.providers.re.RenderingStats: Notifies the end of pixels data retrieval for the specified wavelength (channel).
endMalloc() - Method in class omeis.providers.re.RenderingStats: Notifies the end of the allocation of an RGB memory buffers for the rendering process.
endRendering() - Method in class omeis.providers.re.RenderingStats: Notifies the end of the trasnformation of the raw pixels data.
equals(Object) - Method in class ome.util.math.geom2D.Line: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(Object) - Method in class ome.util.math.geom2D.PlanePoint: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
equals(double, double) - Method in class ome.util.math.geom2D.PlanePoint: Check to see if the point values are equal.
equals(double, double, double) - Method in class ome.util.math.geom2D.Segment: Performs an equality test based on a point on this line defined by k as in Segment.getPoint(double) and another given point.
equals(Object) - Method in class ome.util.math.geom2D.Segment: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
EXPONENTIAL - Static variable in class omeis.providers.re.quantum.QuantumFactory: Deprecated.
ExponentialMap - Class in omeis.providers.re.quantum: This class implements the QuantumMap interface.
ExponentialMap() - Constructor for class omeis.providers.re.quantum.ExponentialMap

F

FLOAT - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
FLOAT_TYPE - Static variable in class omeis.providers.re.data.PlaneFactory: Deprecated.

G

get(int) - Method in class ome.util.mem.CopiableArray: Return the Copiable at the specified position.
get(int) - Method in class ome.util.mem.ReadOnlyByteArray: Reads the element at the index position within this slice.
getBody() - Method in class ome.util.mem.Handle: Returns a reference to the Body object that is currently paired up with this handle.
getBounds() - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
getBounds() - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
getBounds2D() - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
getBounds2D() - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
getChannelBindings() - Method in class omeis.providers.re.Renderer: Returns an array containing the channel bindings.
getChannelBindingsAsList() - Method in class omeis.providers.re.Renderer: Returns a list containing the channel bindings.
getCodomainChain(int) - Method in class omeis.providers.re.Renderer: Returns the object that defines the sequence of spatial transformations to be applied to quantized data.
getCodomainMapContexts() - Method in class omeis.providers.re.Renderer: Returns the list of codomain map contexts.
getColor(int, Channel) - Static method in class omeis.providers.re.ColorsFactory: Determines the color usually associated to the specified wavelength.
getColor(int, Channel, LogicalChannel) - Static method in class omeis.providers.re.ColorsFactory: Determines the color usually associated to the specified wavelength.
getColorArray(ChannelBinding) - Static method in class omeis.providers.re.Renderer: Returns an array whose ascending indices represent the color components Red, Green and Blue.
getContexts() - Method in class omeis.providers.re.codomain.CodomainChain: Returns a copy of the codomain context if any.
getCurveCoefficient() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the coefficient identifying a curve within a given family.
getData() - Method in class omeis.providers.re.data.Plane2D: Returns the pixel data that is used to back this Plane.
getFamily(String) - Method in class omeis.providers.re.quantum.QuantumFactory: Helper method to retrieve a Family enumeration from the database.
getFamily() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the mapping family.
getGlobalMax() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the maximum of all maxima.
getGlobalMin() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the minimum of all minima.
getImageSize(PlaneDef) - Method in class omeis.providers.re.Renderer: Returns the size, in bytes, of the RGBBuffer that would be rendered from the plane selected by pd.
getInputEnd() - Method in class omeis.providers.re.metadata.StatsFactory: Returns the input end.
getInputStart() - Method in class omeis.providers.re.metadata.StatsFactory: Returns the input start.
getIntervalEnd() - Method in class omeis.providers.re.codomain.CodomainChain: Returns the upper bound of the codomain interval.
getIntervalStart() - Method in class omeis.providers.re.codomain.CodomainChain: Returns the lower bound of the codomain interval.
getLocationStats() - Method in class omeis.providers.re.metadata.StatsFactory: Returns the statistics.
getMetadata() - Method in class omeis.providers.re.Renderer: Returns the Pixels set the rendering engine is for.
getMiddleRange(double) - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the range the values belongs to.
getNoiseReduction() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns true if the noise reduction algorithm is turned on, false if turned off.
getOptimizations() - Method in class omeis.providers.re.Renderer: Returns the optimizations that the renderer currently has enabled.
getOriginalGlobalMax() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the original maximum of all minima.
getOriginalGlobalMin() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the original minimum of all minima.
getOverlays() - Method in class omeis.providers.re.Renderer: Returns the current set of overlays to be rendered.
getPathIterator(AffineTransform) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
getPathIterator(AffineTransform, double) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
getPathIterator(AffineTransform) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
getPathIterator(AffineTransform, double) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
getPixels() - Method in class omeis.providers.re.Renderer: Returns the object that allows to access the pixels raw data.
getPixelsType() - Method in class omeis.providers.re.Renderer: Returns the pixels type.
getPixelsTypeLowerBound(int) - Method in class omeis.providers.re.Renderer: Returns the minimum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelsTypeMax() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the upper bound of the pixels range or 0 if the value couldn't be set.
getPixelsTypeMin() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the lower bound of the pixels range or 0 if the value couldn't be set.
getPixelsTypeUpperBound(int) - Method in class omeis.providers.re.Renderer: Returns the maximum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
getPixelValue(int, int) - Method in class omeis.providers.re.data.Plane2D: Returns the pixel intensity value of the pixel at (x1, x2).
getPixelValue(int) - Method in class omeis.providers.re.data.Plane2D: Returns the pixel intensity value of the pixel at a given offset within the backing buffer.
getPlaneDimsAsString(PlaneDef) - Method in class omeis.providers.re.Renderer: Returns a string with the dimensions of the specified plane.
getPoint(double) - Method in class ome.util.math.geom2D.Line: Returns the point of this line defined by k.
getPoint(double) - Method in class ome.util.math.geom2D.Segment: Returns the point of this line defined by k.
getPoints() - Method in class ome.util.math.geom2D.EllipseArea: Implemented as specified by the PlaneArea I/F.
getPoints() - Method in interface ome.util.math.geom2D.PlaneArea: Returns an array of PlanePoint contained in the PlaneArea.
getPoints() - Method in class ome.util.math.geom2D.RectangleArea: Implemented as specified by the PlaneArea I/F.
getQuantumManager() - Method in class omeis.providers.re.Renderer: Returns the object that manages and allows to retrieve the objects that are used to quantize wavelength data.
getRenderingDef() - Method in class omeis.providers.re.Renderer: Returns the settings that define the transformation context.
getResolutionDescriptions() - Method in class omeis.providers.re.Renderer: Returns the image's size information per resolution level.
getResolutionLevel() - Method in class omeis.providers.re.Renderer: Retrieves the active resolution level.
getResolutionLevels() - Method in class omeis.providers.re.Renderer: Retrieves the number of resolution levels that the backing pixels pyramid contains.
getSize() - Method in class ome.util.mem.CopiableArray: Returns the number of elements in the array.
getStats() - Method in class omeis.providers.re.Renderer: Returns a RenderingStats object that the rendering strategy can use to track performance.
getStats() - Method in class omeis.providers.re.RenderingStats: Returns a stats report ready to be written to the log file.
getStrategy(QuantumDef, Pixels) - Method in class omeis.providers.re.quantum.QuantumFactory: Returns a strategy to carry out the quantization process whose context is defined by pd.
getTileSize() - Method in class omeis.providers.re.Renderer: Retrieves the tile size for the pixel store.
getWavelength() - Method in exception omeis.providers.re.quantum.QuantizationException: Returns the index of the wavelength that couldn't be rendered.
getWindowEnd() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the upper bound of the input interval.
getWindowStart() - Method in class omeis.providers.re.quantum.QuantumStrategy: Returns the lower bound of the input interval.
GREEN_INDEX - Static variable in class omeis.providers.re.ColorsFactory: Index of the red component of a color.

H

Handle - Class in ome.util.mem: Provides the basic machinery to share the same logical state across objects with different identities.
Handle(Copiable) - Constructor for class ome.util.mem.Handle: Subclasses use this constructor to specify the Body instance this handle will be paired up with.
hasEmissionData(LogicalChannel) - Static method in class omeis.providers.re.ColorsFactory: Returns true if the channel has emission metadata, false otherwise.
hashCode() - Method in class ome.util.math.geom2D.Line: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class ome.util.math.geom2D.PlanePoint: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hashCode() - Method in class ome.util.math.geom2D.Segment: Overridden to reflect equality of abstract values (data object) as opposite to object identity.
hasMapContext() - Method in class omeis.providers.re.codomain.CodomainChain: Returns true if some transformations need to be applied, false otherwise.

I

in(PixelsType, String[]) - Static method in class omeis.providers.re.data.PlaneFactory: A static helper method to check if a type is one of the elements in an array.
initPixelsRange(Pixels) - Method in class omeis.providers.re.metadata.StatsFactory: Determines the minimum and maximum corresponding to the passed pixels.
INT - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
INT16 - Static variable in class omeis.providers.re.data.PlaneFactory: Deprecated.
INT32 - Static variable in class omeis.providers.re.data.PlaneFactory: Deprecated.
INT8 - Static variable in class omeis.providers.re.data.PlaneFactory: Deprecated.
intersects(double, double, double, double) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
intersects(Rectangle2D) - Method in class ome.util.math.geom2D.EllipseArea: Required by the Shape I/F.
intersects(double, double, double, double) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
intersects(Rectangle2D) - Method in class ome.util.math.geom2D.RectangleArea: Required by the Shape I/F.
isAlphalessRendering() - Method in class omeis.providers.re.Optimizations: Returns true if the alphaless rendering optimization is enabled, and false if it is not.
isNoiseReduction() - Method in class omeis.providers.re.metadata.StatsFactory: Returns true if the flag is on, false otherwise.
isPixelsTypeSigned() - Method in class omeis.providers.re.Renderer: Returns true if the pixels type is signed, false otherwise.
isPrimaryColorEnabled() - Method in class omeis.providers.re.Optimizations: Returns true if the primary color optimization is enabled, and false if it is not.
isTypeSigned(PixelsType) - Static method in class omeis.providers.re.data.PlaneFactory: A static helper method to retrieve pixel byte signage.
isXYPlanar() - Method in class omeis.providers.re.data.Plane2D: Returns true if the plane is an XY-plane, false otherwise.

L

length - Variable in class ome.util.mem.ReadOnlyByteArray: The length of the slice.
lies(PlanePoint) - Method in class ome.util.math.geom2D.Line: Tells whether the specified point lies on this line.
lies(PlanePoint, boolean) - Method in class ome.util.math.geom2D.Line: Tells whether the specified point lies on this line and within the specified orientation.
lies(double, double) - Method in class ome.util.math.geom2D.Segment: Tells whether a specified point lies on this line.
Line - Class in ome.util.math.geom2D: An orientated line in the Euclidean space R².
Line(PlanePoint, PlanePoint) - Constructor for class ome.util.math.geom2D.Line: Creates a new object to represent the line passing through the o and p points.
Line(PlanePoint, PlanePoint, PlanePoint) - Constructor for class ome.util.math.geom2D.Line: Creates a new object to represent the line passing through o and having direction pq.
LINEAR - Static variable in class omeis.providers.re.quantum.QuantumFactory: Deprecated.
LOGARITHMIC - Static variable in class omeis.providers.re.quantum.QuantumFactory: Deprecated.
LogarithmicMap - Class in omeis.providers.re.quantum: This class implements the QuantumMap interface.
LogarithmicMap() - Constructor for class omeis.providers.re.quantum.LogarithmicMap
LONG - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.

M

makeNew(int) - Method in class ome.util.mem.CopiableArray: Creates a new array of the speficied size.
MAX - Static variable in class omeis.providers.re.quantum.QuantumStrategy: Maximum value (255) allowed for the upper bound of the codomain interval.
MAX_CHANNELS - Static variable in class omeis.providers.re.Renderer: The maximum number of channels.
MIN - Static variable in class omeis.providers.re.quantum.QuantumStrategy: Minimum value (0) allowed for the lower bound of the codomain interval.
MODEL_GREYSCALE - Static variable in class omeis.providers.re.Renderer: Identifies the type used to store model values.
MODEL_HSB - Static variable in class omeis.providers.re.Renderer: Identifies the type used to store model values.
MODEL_RGB - Static variable in class omeis.providers.re.Renderer: Identifies the type used to store model values.

N

newBlueColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new Blue Color object.
newGreenColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new Green Color object.
newGreyColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new Grey Color object.
newRedColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new Red Color object.
newWhiteColor() - Static method in class omeis.providers.re.ColorsFactory: Creates a new White Color object.
NOISE_REDUCTION - Static variable in class omeis.providers.re.quantum.QuantumFactory: Default value.
norm() - Method in class ome.util.math.geom2D.PlanePoint: Calculates the Euclidian norm of this vector.
normalize() - Method in class ome.util.math.geom2D.PlanePoint: Calculates the unit vector of this vector, provided this is not the null vector.

O

offset - Variable in class ome.util.mem.ReadOnlyByteArray: Marks the start of the slice.
ome.util.math.geom2D - package ome.util.math.geom2D: Plane geometry data structures for OMERO
ome.util.mem - package ome.util.mem: Dynamic object instance and state management for OMERO
omeis.providers.re - package omeis.providers.re
omeis.providers.re.codomain - package omeis.providers.re.codomain
omeis.providers.re.data - package omeis.providers.re.data
omeis.providers.re.metadata - package omeis.providers.re.metadata
omeis.providers.re.quantum - package omeis.providers.re.quantum
onBoundaries(double, double) - Method in class ome.util.math.geom2D.EllipseArea: Implemented as specified by the PlaneArea I/F.
onBoundaries(double, double) - Method in interface ome.util.math.geom2D.PlaneArea: Controls if a specified point is on the boundary of the PlaneArea.
onBoundaries(double, double) - Method in class ome.util.math.geom2D.RectangleArea: Implemented as specified by the PlaneArea I/F.
onWindowChange() - Method in class omeis.providers.re.quantum.BinaryMaskQuantizer
onWindowChange() - Method in class omeis.providers.re.quantum.Quantization_32_bit: The input window size changed, re-map the values.
onWindowChange() - Method in class omeis.providers.re.quantum.Quantization_8_16_bit: The input window size changed, rebuild the LUT.
onWindowChange() - Method in class omeis.providers.re.quantum.Quantization_float: The input window size changed, re-map the values.
onWindowChange() - Method in class omeis.providers.re.quantum.QuantumStrategy: Notifies when the input interval has changed or the mapping strategy has changed.
Optimizations - Class in omeis.providers.re: A container for any potential optimizations that the renderer can enable based on the data and rendering settings it has been fed.
Optimizations() - Constructor for class omeis.providers.re.Optimizations
origin - Variable in class ome.util.math.geom2D.Line: The origin point of the line.
originX1 - Variable in class ome.util.math.geom2D.Segment: The origin of the segment's first element.
originX2 - Variable in class ome.util.math.geom2D.Segment: The origin of the segment's first element.

P

PHOTOMETRIC_MONOCHROME - Static variable in class omeis.providers.re.Renderer: Deprecated.
pixels - Variable in class omeis.providers.re.quantum.QuantumStrategy: The pixels this strategy is for.
Plane2D - Class in omeis.providers.re.data
Plane2D(PlaneDef, Pixels, PixelData) - Constructor for class omeis.providers.re.data.Plane2D: Constructor that sub-classes must call.
PlaneArea - Interface in ome.util.math.geom2D: Interface that all areas of the Euclidean space R² must implement.
planeDef - Variable in class omeis.providers.re.data.Plane2D: The type of plane.
PlaneFactory - Class in omeis.providers.re.data: Encapsulates access to the image raw data.
PlaneFactory() - Constructor for class omeis.providers.re.data.PlaneFactory
PlanePoint - Class in ome.util.math.geom2D: Represents a point in the Euclidean space R².
PlanePoint(double, double) - Constructor for class ome.util.math.geom2D.PlanePoint: Creates a new instance.
POLYNOMIAL - Static variable in class omeis.providers.re.quantum.QuantumFactory: Deprecated.
PolynomialMap - Class in omeis.providers.re.quantum: This class implements the QuantumMap interface.
PolynomialMap() - Constructor for class omeis.providers.re.quantum.PolynomialMap
primaryColorEnabled - Variable in class omeis.providers.re.Optimizations: The channel bindings are only "primary" colors.

Q

qDef - Variable in class omeis.providers.re.quantum.QuantumStrategy: Reference to a quantumDef object.
Quantization_32_bit - Class in omeis.providers.re.quantum: Quantization process.
Quantization_32_bit(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.Quantization_32_bit: Creates a new strategy.
Quantization_8_16_bit - Class in omeis.providers.re.quantum: Quantization process.
Quantization_8_16_bit(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.Quantization_8_16_bit: Creates a new strategy.
Quantization_float - Class in omeis.providers.re.quantum: Quantization process.
Quantization_float(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.Quantization_float: Creates a new strategy.
QuantizationException - Exception in omeis.providers.re.quantum: This exception is thrown during the quantization process if something goes wrong.
QuantizationException() - Constructor for exception omeis.providers.re.quantum.QuantizationException: Creates a new exception.
QuantizationException(String) - Constructor for exception omeis.providers.re.quantum.QuantizationException: Constructs a new exception with the specified detail message.
QuantizationException(Throwable) - Constructor for exception omeis.providers.re.quantum.QuantizationException: Constructs a new exception with the specified cause.
QuantizationException(String, Throwable) - Constructor for exception omeis.providers.re.quantum.QuantizationException: Constructs a new exception with the specified detail message and cause.
quantize(double) - Method in class omeis.providers.re.quantum.BinaryMaskQuantizer: Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.Quantization_32_bit: Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.Quantization_8_16_bit: Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.Quantization_float: Implemented as specified in QuantumStrategy.
quantize(double) - Method in class omeis.providers.re.quantum.QuantumStrategy: Maps a value from [windowStart, windowEnd] to a value in the codomain interval.
QuantumFactory - Class in omeis.providers.re.quantum: Factory to create objects to carry out quantization for a given context.
QuantumFactory(List<Family>) - Constructor for class omeis.providers.re.quantum.QuantumFactory: Default constructor.
QuantumMap - Interface in omeis.providers.re.quantum: Provides methods to map value.
QuantumStrategy - Class in omeis.providers.re.quantum: Subclasses Work on explicit pixel types.
QuantumStrategy(QuantumDef, Pixels) - Constructor for class omeis.providers.re.quantum.QuantumStrategy: Creates a new instance.

R

ReadOnlyByteArray - Class in ome.util.mem: A read-only slice of a given array.
ReadOnlyByteArray(byte[], int, int) - Constructor for class ome.util.mem.ReadOnlyByteArray: Creates a read-only slice of base.
RectangleArea - Class in ome.util.math.geom2D: Represents a rectangle in the Euclidean space R².
RectangleArea() - Constructor for class ome.util.math.geom2D.RectangleArea: Constructs a new RectangleAreaAdapter whose top-left corner is (0, 0) and whose width and height are both zero.
RectangleArea(int, int, int, int) - Constructor for class ome.util.math.geom2D.RectangleArea: Constructs a new RectangleAreaAdapter whose top-left corner is specified as (x, y) and whose width and height are specified by the arguments of the same name.
RED_INDEX - Static variable in class omeis.providers.re.ColorsFactory: Index of the red component of a color.
remove() - Method in class omeis.providers.re.codomain.CodomainChain: Removes all CodomainMapContexts except the identity and resets the interval.
remove(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain: Removes a map context from the chain.
render(PlaneDef) - Method in class omeis.providers.re.Renderer: Renders the data selected by pd according to the current rendering settings.
renderAsPackedInt(PlaneDef, PixelBuffer) - Method in class omeis.providers.re.Renderer: Renders the data selected by pd according to the current rendering settings.
Renderer - Class in omeis.providers.re: Transforms raw image data into an RGB image that can be displayed on screen.
Renderer(QuantumFactory, List<RenderingModel>, Pixels, RenderingDef, PixelBuffer, LutProvider) - Constructor for class omeis.providers.re.Renderer: Creates a new instance to render the specified pixels set and get this new instance ready for rendering.
RenderingStats - Class in omeis.providers.re: Exposes methods to time the various steps in the rendering process and provides a stats report.
RenderingStats(Renderer, PlaneDef) - Constructor for class omeis.providers.re.RenderingStats: Creates a new instance.
RenderingTask - Interface in omeis.providers.re: This interface represents a rendering operation task.

S

scalar(double) - Method in class ome.util.math.geom2D.PlanePoint: Multiplies this vector by the specified scalar.
scale(double) - Method in class ome.util.math.geom2D.EllipseArea: Implemented as specified by the PlaneArea I/F.
scale(double) - Method in interface ome.util.math.geom2D.PlaneArea: Resets the bounding Rectangle of the planeArea according to the specified scaling factor.
scale(double) - Method in class ome.util.math.geom2D.RectangleArea: Implemented as specified by the PlaneArea I/F.
Segment - Class in ome.util.math.geom2D: A segment in the Euclidean space R².
Segment(double, double, double, double) - Constructor for class ome.util.math.geom2D.Segment: Creates a new instance.
set(int, byte) - Method in class ome.util.mem.ByteArray: Writes value into the element at the index position within this slice.
set(int, byte[]) - Method in class ome.util.mem.ByteArray: Copies the values in buf into this slice, starting from index.
set(int, int, InputStream) - Method in class ome.util.mem.ByteArray: Writes up to maxLength bytes from the supplied stream into this slice, starting from index.
set(Copiable, int) - Method in class ome.util.mem.CopiableArray: Replaces the element at the specified position with the specified Copiable.
setActive(int, boolean) - Method in class omeis.providers.re.Renderer: Makes a particular channel active or inactive.
setAlphalessRendering(boolean) - Method in class omeis.providers.re.Optimizations: Enable or disable the alphaless rendering optimization.
setBounds(int, int, int, int) - Method in class ome.util.math.geom2D.EllipseArea: Implemented as specified in the PlaneArea I/F.
setBounds(int, int, int, int) - Method in interface ome.util.math.geom2D.PlaneArea: Sets the bounding Rectangle of the planeArea to the specified x, y, width, and height.
setBounds(int, int, int, int) - Method in class ome.util.math.geom2D.RectangleArea: Implemented as specified by the PlaneArea I/F.
setChannelLookupTable(int, String) - Method in class omeis.providers.re.Renderer: Sets the lookup table associated to the channel.
setChannelWindow(int, double, double) - Method in class omeis.providers.re.Renderer: Sets the pixels intensity interval for the specified channel.
setCodomainInterval(int, int) - Method in class omeis.providers.re.Renderer: Sets the codomain interval i.e.
setDefaultT(int) - Method in class omeis.providers.re.Renderer: Sets the default timepoint index.
setDefaultZ(int) - Method in class omeis.providers.re.Renderer: Sets the index of the default focal section.
setExtent(double, double) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the maximum range of the input window.
setInterval(int, int) - Method in class omeis.providers.re.codomain.CodomainChain: Sets the codomain interval.
setMap(QuantumMap) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the quantum map.
setMapping(Family, double, boolean) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the selected family, the curve coefficient and the noise reduction flag.
setModel(RenderingModel) - Method in class omeis.providers.re.Renderer: Specifies the model that dictates how transformed raw data has to be mapped onto a color space.
setOverlays(Map<byte[], Integer>) - Method in class omeis.providers.re.Renderer: Sets a map of overlays to be rendered.
setPrimaryColorEnabled(boolean) - Method in class omeis.providers.re.Optimizations: Enable or disable the primary color optimization.
setQuantizationMap(Family, double, boolean) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the selected family, the curve coefficient and the noise reduction flag and rebuilds the look-up table.
setQuantizationMap(int, Family, double, boolean) - Method in class omeis.providers.re.Renderer: Sets the mapping strategy for the specified channel.
setQuantumStrategy(int) - Method in class omeis.providers.re.Renderer: Sets the bit resolution.
setResolutionLevel(int) - Method in class omeis.providers.re.Renderer: Sets the active resolution level.
setRGBA(int, int, int, int, int) - Method in class omeis.providers.re.Renderer: Sets the color associated to the specified channel.
setWavelength(int) - Method in exception omeis.providers.re.quantum.QuantizationException: Sets the index of the wavelength that couldn't be rendered.
setWindow(double, double) - Method in class omeis.providers.re.quantum.QuantumStrategy: Sets the input window interval.
SHORT - Static variable in class omeis.providers.re.data.PlaneFactory: Identifies the type used to store pixel values.
signed - Variable in class omeis.providers.re.data.Plane2D: The sign of the type
sizeX - Variable in class omeis.providers.re.data.Plane2D: Number of pixels along the X-axis.
sizeY - Variable in class omeis.providers.re.data.Plane2D: Number of pixels along the Y-axis.
slice - Variable in class omeis.providers.re.data.Plane2D: The slice we're working with
startIO(int) - Method in class omeis.providers.re.RenderingStats: Notifies the start of pixels data retrieval for the specified wavelength (channel).
startMalloc() - Method in class omeis.providers.re.RenderingStats: Notifies the start of the allocation of an RGB memory buffer for the rendering process.
startRendering() - Method in class omeis.providers.re.RenderingStats: Notifies the start of the trasnformation of the raw pixels data.
StatsFactory - Class in omeis.providers.re.metadata: Computes two types of statistics: The PixelsStats and the location stats.
StatsFactory() - Constructor for class omeis.providers.re.metadata.StatsFactory
stop() - Method in class omeis.providers.re.RenderingStats: Notifies this object that the rendering process has finished.
sum(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the sum of this vector with the specified argument.

T

toString() - Method in class omeis.providers.re.codomain.CodomainChain: Overrides the toString method.
transform(int) - Method in class omeis.providers.re.codomain.CodomainChain: Applies the transformation.
transform(int, double) - Method in class omeis.providers.re.quantum.ExponentialMap: Implemented as specified in QuantumMap.
transform(double, double) - Method in class omeis.providers.re.quantum.ExponentialMap: Implemented as specified in QuantumMap.
transform(float, double) - Method in class omeis.providers.re.quantum.ExponentialMap: Implemented as specified in QuantumMap.
transform(int, double) - Method in class omeis.providers.re.quantum.LogarithmicMap: Implemented as specified in QuantumMap.
transform(double, double) - Method in class omeis.providers.re.quantum.LogarithmicMap: Implemented as specified in QuantumMap.
transform(float, double) - Method in class omeis.providers.re.quantum.LogarithmicMap: Implemented as specified in QuantumMap.
transform(int, double) - Method in class omeis.providers.re.quantum.PolynomialMap: Implemented as specified in QuantumMap.
transform(double, double) - Method in class omeis.providers.re.quantum.PolynomialMap: Implemented as specified in QuantumMap.
transform(float, double) - Method in class omeis.providers.re.quantum.PolynomialMap: Implemented as specified in QuantumMap.
transform(int, double) - Method in interface omeis.providers.re.quantum.QuantumMap: Maps the specified value.
transform(double, double) - Method in interface omeis.providers.re.quantum.QuantumMap: Maps the specified value.
transform(float, double) - Method in interface omeis.providers.re.quantum.QuantumMap: Maps the specified value.

U

UINT16 - Static variable in class omeis.providers.re.data.PlaneFactory: Deprecated.
UINT32 - Static variable in class omeis.providers.re.data.PlaneFactory: Deprecated.
UINT8 - Static variable in class omeis.providers.re.data.PlaneFactory: Deprecated.
update(CodomainMapContext) - Method in class omeis.providers.re.codomain.CodomainChain: Updates a map context in the chain.
updateQuantumManager() - Method in class omeis.providers.re.Renderer: Updates the QuantumManager and configures it according to the current quantum definition.

V

valueMapper - Variable in class omeis.providers.re.quantum.QuantumStrategy: Reference to the value mapper.
vec(PlanePoint) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the vector associated to this point and the specified argument.
vec(double, double) - Method in class ome.util.math.geom2D.PlanePoint: Calculates the vector associated to this point and the specified argument.

X

x1 - Variable in class ome.util.math.geom2D.PlanePoint: The first element.
x2 - Variable in class ome.util.math.geom2D.PlanePoint: The second element.

A B C D E F G H I L M N O P Q R S T U V X