omeis.providers.re

Class Renderer

java.lang.Object

omeis.providers.re.Renderer

public class Renderer
extends Object

Transforms raw image data into an RGB image that can be displayed on screen.

Every instance of this class works against a given pixels set within an OME Image (recall that an Image can have more than one pixels set) and holds the rendering environment for that pixels set. Said environment is composed of:

• Resources to access pixels raw data and metadata.
• Cached pixels metadata (statistic measurements).
• Settings that define the transformation context — that is, a specification of how raw data is to be transformed into an image that can be displayed on screen.
• Resources to apply the transformations defined by the transformation context to raw pixels.

This class delegates the actual rendering to a RenderingStrategy, which is selected depending on how transformed data is to be mapped into a color space.

Since:

OME2.2

Version:

2.2 (Internal version: $Revision$ $Date: 2005/07/05 16:13:52 $)

Author:

Jean-Marie Burel j.burel@dundee.ac.uk,
Andrea Falconi a.falconi@dundee.ac.uk

See Also:

RenderingDef, QuantumManager, CodomainChain, RenderingStrategy

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAX_CHANNELS The maximum number of channels.
static String	MODEL_GREYSCALE Identifies the type used to store model values.
static String	MODEL_HSB Identifies the type used to store model values.
static String	MODEL_RGB Identifies the type used to store model values.
static String	PHOTOMETRIC_MONOCHROME Deprecated.

Constructor Summary

Constructors

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.

Method Summary

Modifier and Type	Method and Description
void	close() Closes the buffer, cleaning up file state.
ChannelBinding[]	getChannelBindings() Returns an array containing the channel bindings.
List<ChannelBinding>	getChannelBindingsAsList() Returns a list containing the channel bindings.
CodomainChain	getCodomainChain(int channel) Returns the object that defines the sequence of spatial transformations to be applied to quantized data.
List	getCodomainMapContexts() Returns the list of codomain map contexts.
static int[]	getColorArray(ChannelBinding channel) Returns an array whose ascending indices represent the color components Red, Green and Blue.
int	getImageSize(PlaneDef pd) Returns the size, in bytes, of the RGBBuffer that would be rendered from the plane selected by pd.
Pixels	getMetadata() Returns the Pixels set the rendering engine is for.
Optimizations	getOptimizations() Returns the optimizations that the renderer currently has enabled.
Map<byte[],Integer>	getOverlays() Returns the current set of overlays to be rendered.
PixelBuffer	getPixels() Returns the object that allows to access the pixels raw data.
PixelsType	getPixelsType() Returns the pixels type.
double	getPixelsTypeLowerBound(int w) Returns the minimum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
double	getPixelsTypeUpperBound(int w) Returns the maximum value for that channels depending on the pixels type and the original range (globalmax, globalmin)
String	getPlaneDimsAsString(PlaneDef pd) Returns a string with the dimensions of the specified plane.
omeis.providers.re.QuantumManager	getQuantumManager() Returns the object that manages and allows to retrieve the objects that are used to quantize wavelength data.
RenderingDef	getRenderingDef() Returns the settings that define the transformation context.
List<List<Integer>>	getResolutionDescriptions() Returns the image's size information per resolution level.
int	getResolutionLevel() Retrieves the active resolution level.
int	getResolutionLevels() Retrieves the number of resolution levels that the backing pixels pyramid contains.
RenderingStats	getStats() Returns a RenderingStats object that the rendering strategy can use to track performance.
Dimension	getTileSize() Retrieves the tile size for the pixel store.
boolean	isPixelsTypeSigned() Returns true if the pixels type is signed, false otherwise.
RGBBuffer	render(PlaneDef pd) Renders the data selected by pd according to the current rendering settings.
int[]	renderAsPackedInt(PlaneDef pd, PixelBuffer newBuffer) Renders the data selected by pd according to the current rendering settings.
void	setActive(int w, boolean active) Makes a particular channel active or inactive.
void	setChannelLookupTable(int w, String lookupTable) Sets the lookup table associated to the channel.
void	setChannelWindow(int w, double start, double end) Sets the pixels intensity interval for the specified channel.
void	setCodomainInterval(int start, int end) Sets the codomain interval i.e. a sub-interval of [0, 255].
void	setDefaultT(int t) Sets the default timepoint index.
void	setDefaultZ(int z) Sets the index of the default focal section.
void	setModel(RenderingModel model) Specifies the model that dictates how transformed raw data has to be mapped onto a color space.
void	setOverlays(Map<byte[],Integer> overlays) Sets a map of overlays to be rendered.
void	setQuantizationMap(int w, Family family, double coefficient, boolean noiseReduction) Sets the mapping strategy for the specified channel.
void	setQuantumStrategy(int bitResolution) Sets the bit resolution.
void	setResolutionLevel(int resolutionLevel) Sets the active resolution level.
void	setRGBA(int w, int red, int green, int blue, int alpha) Sets the color associated to the specified channel.
void	updateQuantumManager() Updates the QuantumManager and configures it according to the current quantum definition.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MAX_CHANNELS

public static final int MAX_CHANNELS

The maximum number of channels.

See Also:

Constant Field Values

MODEL_GREYSCALE

public static final String MODEL_GREYSCALE

Identifies the type used to store model values.

See Also:

Constant Field Values

MODEL_RGB

public static final String MODEL_RGB

Identifies the type used to store model values.

See Also:

Constant Field Values

MODEL_HSB

public static final String MODEL_HSB

Identifies the type used to store model values.

See Also:

Constant Field Values

PHOTOMETRIC_MONOCHROME

@Deprecated
public static final String PHOTOMETRIC_MONOCHROME

Deprecated.

Identifies the type used to store photometric interpretation values.

See Also:

Constant Field Values

Constructor Detail

Renderer

public 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.

Parameters:

quantumFactory - a populated quantum factory.

renderingModels - an enumerated list of all rendering models.

pixelsObj - Pixels object.

renderingDefObj - Rendering definition object.

bufferObj - PixelBuffer object.

luts - the available lookup tables.

Throws:

NullPointerException - If null parameters are passed.

Method Detail

setModel

public void setModel(RenderingModel model)

Specifies the model that dictates how transformed raw data has to be mapped onto a color space. This class delegates the actual rendering to a RenderingStrategy, which is selected depending on that model. So setting the model also results in changing the rendering strategy.

Parameters:

model - Identifies the color space model.

setDefaultZ

public void setDefaultZ(int z)

Sets the index of the default focal section. This index is used to define a default plane.

Parameters:

z - The stack index.

See Also:

setDefaultT(int)

setDefaultT

public void setDefaultT(int t)

Sets the default timepoint index. This index is used to define a default plane.

Parameters:

t - The timepoint index.

See Also:

setDefaultZ(int)

setOverlays

public void setOverlays(Map<byte[],Integer> overlays)

Sets a map of overlays to be rendered.

Parameters:

overlays - Overlay to color map.

getOverlays

public Map<byte[],Integer> getOverlays()

Returns the current set of overlays to be rendered.

Returns:

Overlay to color map.

updateQuantumManager

public void updateQuantumManager()

Updates the QuantumManager and configures it according to the current quantum definition.

render

public RGBBuffer render(PlaneDef pd)
                 throws IOException,
                        QuantizationException

Renders the data selected by pd according to the current rendering settings. The passed argument selects a plane orthogonal to one of the X, Y, or Z axes. How many wavelengths are rendered and what color model is used depends on the current rendering settings.

Parameters:

pd - Selects a plane orthogonal to one of the X, Y, or Z axes.

Returns:

An RGB image ready to be displayed on screen.

Throws:

IOException - If an error occurred while trying to pull out data from the pixels data repository.

QuantizationException - If an error occurred while quantizing the pixels raw data.

NullPointerException - If pd is null.

renderAsPackedInt

public int[] renderAsPackedInt(PlaneDef pd,
                               PixelBuffer newBuffer)
                        throws IOException,
                               QuantizationException

Renders the data selected by pd according to the current rendering settings. The passed argument selects a plane orthogonal to one of the X, Y, or Z axes. How many wavelengths are rendered and what color model is used depends on the current rendering settings.

Parameters:

pd - Selects a plane orthogonal to one of the X, Y, or Z axes.

newBuffer - The pixel buffer to use in place of the one currently defined in the renderer. This will not change the state of the Renderer. If null is passed the existing pixel buffer will be used.

Returns:

An RGB image ready to be displayed on screen.

Throws:

IOException - If an error occurred while trying to pull out data from the pixels data repository.

QuantizationException - If an error occurred while quantizing the pixels raw data.

NullPointerException - If pd is null.

getImageSize

public int getImageSize(PlaneDef pd)

Returns the size, in bytes, of the RGBBuffer that would be rendered from the plane selected by pd. Note that the returned value also depends on the current rendering strategy which is selected by the setModel method. So a subsequent invocation of this method may return a different value if the setModel method has been called since the first call to this method.

Parameters:

pd - Selects a plane orthogonal to one of the X, Y, or Z axes.

Returns:

See above.

Throws:

NullPointerException - If pd is null.

getPlaneDimsAsString

public String getPlaneDimsAsString(PlaneDef pd)

Returns a string with the dimensions of the specified plane. The returned string has the format AxB, where A is the number of pixels on the X1-axis and B the the number of pixels on the the X2-axis. The X1-axis is the X-axis in the case of an XY or XZ plane. Otherwise it is the Z-axis — ZY plane. The X2-axis is the Y-axis in the case of an XY or ZY plane. Otherwise it is the Z-axis — XZ plane.

Parameters:

pd - Selects a plane orthogonal to one of the X, Y, or Z axes.

Returns:

See above.

Throws:

NullPointerException - If pd is null.

getChannelBindings

public ChannelBinding[] getChannelBindings()

Returns an array containing the channel bindings. The dimension of the array equals the number of channels.

Returns:

See above.

getCodomainMapContexts

public List getCodomainMapContexts()

Returns the list of codomain map contexts. One per channel.

Returns:

See above.

getChannelBindingsAsList

public List<ChannelBinding> getChannelBindingsAsList()

Returns a list containing the channel bindings. The dimension of the array equals the number of channels.

Returns:

See above.

getRenderingDef

public RenderingDef getRenderingDef()

Returns the settings that define the transformation context. That is, a specification of how raw data is to be transformed into an image that can be displayed on screen.

Returns:

See above.

getQuantumManager

public omeis.providers.re.QuantumManager getQuantumManager()

Returns the object that manages and allows to retrieve the objects that are used to quantize wavelength data.

Returns:

See above.

getPixels

public PixelBuffer getPixels()

Returns the object that allows to access the pixels raw data.

Returns:

See above.

getMetadata

public Pixels getMetadata()

Returns the Pixels set the rendering engine is for.

Returns:

See above.

getPixelsType

public PixelsType getPixelsType()

Returns the pixels type.

Returns:

A pixels type enumeration object.

getCodomainChain

public CodomainChain getCodomainChain(int channel)

Returns the object that defines the sequence of spatial transformations to be applied to quantized data.

Parameters:

channel -

Returns:

See above.

getStats

public RenderingStats getStats()

Returns a RenderingStats object that the rendering strategy can use to track performance. A new stats object is created upon each invocation of the render method.

Returns:

The stats object.

setQuantumStrategy

public void setQuantumStrategy(int bitResolution)

Sets the bit resolution.

Parameters:

bitResolution - The value to set.

setCodomainInterval

public void setCodomainInterval(int start,
                                int end)

Sets the codomain interval i.e. a sub-interval of [0, 255].

Parameters:

start - The lower bound of the interval.

end - The upper bound of the interval.

setChannelWindow

public void setChannelWindow(int w,
                             double start,
                             double end)

Sets the pixels intensity interval for the specified channel.

Parameters:

w - The channel index.

start - The lower bound of the interval.

end - The upper bound of the interval.

setQuantizationMap

public void setQuantizationMap(int w,
                               Family family,
                               double coefficient,
                               boolean noiseReduction)

Sets the mapping strategy for the specified channel.

Parameters:

w - The channel index.

family - The mapping family.

coefficient - The coefficient identifying a curve in the family.

noiseReduction - Pass true to select the noiseReduction algorithm, false otherwise.

setRGBA

public void setRGBA(int w,
                    int red,
                    int green,
                    int blue,
                    int alpha)

Sets the color associated to the specified channel.

Parameters:

w - The channel index.

red - The red component of the color.

green - The green component of the color.

blue - The blue component of the color.

alpha - The alpha component of the color.

setChannelLookupTable

public void setChannelLookupTable(int w,
                                  String lookupTable)

Sets the lookup table associated to the channel.

Parameters:

w - The selected channel.

lookupTable - The lookup table.

setActive

public void setActive(int w,
                      boolean active)

Makes a particular channel active or inactive.

Parameters:

w - the wavelength index to toggle.

active - true to set the channel active or false to set the channel inactive.

getOptimizations

public Optimizations getOptimizations()

Returns the optimizations that the renderer currently has enabled.

Returns:

See above.

close

public void close()

Closes the buffer, cleaning up file state.

Throws:

IOException - if an I/O error occurs.

getColorArray

public static int[] getColorArray(ChannelBinding channel)

Returns an array whose ascending indices represent the color components Red, Green and Blue.

Parameters:

channel - the color to decompose into an array.

Returns:

See above.

isPixelsTypeSigned

public boolean isPixelsTypeSigned()

Returns true if the pixels type is signed, false otherwise.

Returns:

See above.

getPixelsTypeLowerBound

public double getPixelsTypeLowerBound(int w)

Returns the minimum value for that channels depending on the pixels type and the original range (globalmax, globalmin)

Parameters:

w - The channel index.

Returns:

See above.

getPixelsTypeUpperBound

public double getPixelsTypeUpperBound(int w)

Returns the maximum value for that channels depending on the pixels type and the original range (globalmax, globalmin)

Parameters:

w - The channel index.

Returns:

See above.

setResolutionLevel

public void setResolutionLevel(int resolutionLevel)

Sets the active resolution level.

Parameters:

resolutionLevel - The resolution level to be used by the renderer.

getResolutionLevel

public int getResolutionLevel()

Retrieves the active resolution level.

Returns:

The active resolution level.

getResolutionLevels

public int getResolutionLevels()

Retrieves the number of resolution levels that the backing pixels pyramid contains.

Returns:

The number of resolution levels. This value does not necessarily indicate either the presence or absence of a pixels pyramid.

getResolutionDescriptions

public List<List<Integer>> getResolutionDescriptions()

Returns the image's size information per resolution level.

Returns:

See above.

getTileSize

public Dimension getTileSize()

Retrieves the tile size for the pixel store.

Returns:

The dimension of the tile or null if the pixel buffer is not tiled.