Package qupath.lib.images.servers

Class LabeledImageServer.Builder

java.lang.Object

qupath.lib.images.servers.LabeledImageServer.Builder

Enclosing class:

LabeledImageServer

public static class LabeledImageServer.Builder
extends Object

Helper class for building a LabeledImageServer.

Constructor Summary

Constructors

Constructor	Description
Builder(ImageData<BufferedImage> imageData)	Create a Builder for a LabeledImageServer for the specified ImageData.

Method Summary

Modifier and Type	Method	Description
LabeledImageServer.Builder	addLabel(String pathClassName, int label)	Add a single label by classname, where the label represents the integer label used for annotations with the given classname.
LabeledImageServer.Builder	addLabel(String pathClassName, int label, Integer color)	Add a single label by classname, where the label represents the integer label used for annotations with the given classname.
LabeledImageServer.Builder	addLabel(PathClass pathClass, int label)	Add a single label by PathClass, where the label represents the integer label used for annotations with the given classification.
LabeledImageServer.Builder	addLabel(PathClass pathClass, int label, Integer color)	Add a single label by PathClass, where the label represents the integer label used for annotations with the given classification.
LabeledImageServer.Builder	addLabels(Map<PathClass,Integer> labelMap)	Add multiple labels by PathClass, where the key represents a PathClass and the value represents the integer label that should be used for annotations of the given class.
LabeledImageServer.Builder	addLabelsByName(Map<String,Integer> labelMap)	Add multiple labels by classname, where the key represents a classname and the value represents the integer label that should be used for annotations of the given class.
LabeledImageServer.Builder	addUnclassifiedLabel(int label)	Add a single label for objects that are unclassified, where the label represents the integer label used for annotations that have no classification set.
LabeledImageServer.Builder	addUnclassifiedLabel(int label, Integer color)	Add a single label for objects that are unclassified, where the label represents the integer label used for annotations that have no classification set.
LabeledImageServer.Builder	backgroundLabel(int label)	Specify the background label (0 by default).
LabeledImageServer.Builder	backgroundLabel(int label, Integer color)	Specify the background label (0 by default) and color.
LabeledImageServer	build()	Build the ImageServer with the requested parameters.
LabeledImageServer.Builder	downsample(double downsample)	Specify downsample factor.
LabeledImageServer.Builder	grayscale()	Use grayscale LUT, rather than deriving colors from classifications.
LabeledImageServer.Builder	grayscale(boolean grayscaleLut)	Optionally use grayscale LUT, rather than deriving colors from classifications.
LabeledImageServer.Builder	lineThickness(float thickness)	Thickness of boundary lines and line annotations, defined in terms of pixels at the resolution specified by the downsample value of the server.
LabeledImageServer.Builder	maxOutputChannelLimit(int maxChannels)	Specify the maximum number of output channels allowed before QuPath will throw an exception.
LabeledImageServer.Builder	multichannelOutput(boolean doMultichannel)	If true, the output image consists of multiple binary images concatenated as different channels, so that the channel number relates to a classification.
LabeledImageServer.Builder	setBoundaryLabel(String pathClassName, int label)	Set the classification and label to use for boundaries for classified areas.
LabeledImageServer.Builder	setBoundaryLabel(String pathClassName, int label, Integer color)	Set the classification and label to use for boundaries for classified areas.
LabeledImageServer.Builder	setBoundaryLabel(PathClass pathClass, int label)	Set the classification and label to use for boundaries for classified areas.
LabeledImageServer.Builder	setBoundaryLabel(PathClass pathClass, int label, Integer color)	Set the classification and label to use for boundaries for classified areas.
LabeledImageServer.Builder	shuffleInstanceLabels(boolean doShuffle)	Optionally request that instance labels are shuffled.
LabeledImageServer.Builder	tileSize(int tileSize)	Set tile width and height (square tiles).
LabeledImageServer.Builder	tileSize(int tileWidth, int tileHeight)	Set tile width and height.
LabeledImageServer.Builder	useAnnotations()	Use annotations for labels.
LabeledImageServer.Builder	useCellNuclei()	Use cells rather than annotations for labels, requesting the nucleus ROI where available.
LabeledImageServer.Builder	useCells()	Use cells rather than annotations for labels.
LabeledImageServer.Builder	useDetections()	Use detections rather than annotations for labels.
LabeledImageServer.Builder	useFilter(Predicate<PathObject> filter)	Use a custom method of selecting objects for inclusion.
LabeledImageServer.Builder	useInstanceLabels()	Request that unique labels are used for all objects, rather than classifications.
LabeledImageServer.Builder	useInstanceLabels(boolean instanceLabels)	Optionally request that unique labels are used for all objects, rather than classifications.
LabeledImageServer.Builder	useUniqueLabels()	Deprecated. in favor of useInstanceLabels()

Methods inherited from class java.lang.Object

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

Constructor Details

Builder

public Builder(ImageData<BufferedImage> imageData)

Create a Builder for a LabeledImageServer for the specified ImageData.

Parameters:

imageData -

Method Details

useDetections

public LabeledImageServer.Builder useDetections()

Use detections rather than annotations for labels. The default is to use annotations.

Returns:

See Also:

• useAnnotations()

useCells

public LabeledImageServer.Builder useCells()

Use cells rather than annotations for labels. The default is to use annotations.

Returns:

See Also:

• useAnnotations()

useCellNuclei

public LabeledImageServer.Builder useCellNuclei()

Use cells rather than annotations for labels, requesting the nucleus ROI where available. The default is to use annotations.

Returns:

See Also:

• useAnnotations()

useAnnotations

public LabeledImageServer.Builder useAnnotations()

Use annotations for labels. This is the default.

Returns:

See Also:

• useDetections()

useFilter

public LabeledImageServer.Builder useFilter(Predicate<PathObject> filter)

Use a custom method of selecting objects for inclusion. The default is to use annotations.

Parameters:

filter - the filter that determines whether an object will be included or not

Returns:

See Also:

• useAnnotations()

grayscale

public LabeledImageServer.Builder grayscale()

Use grayscale LUT, rather than deriving colors from classifications. This can streamline import in software that automatically converts paletted images to RGB.

Returns:

Since:

v0.4.0

See Also:

• grayscale(boolean)

grayscale

public LabeledImageServer.Builder grayscale(boolean grayscaleLut)

Optionally use grayscale LUT, rather than deriving colors from classifications. This can streamline import in software that automatically converts paletted images to RGB.

Parameters:

grayscaleLut -

Returns:

Since:

v0.4.0

See Also:

• grayscale()

downsample

public LabeledImageServer.Builder downsample(double downsample)

Specify downsample factor. This is very important because it defines the resolution at which shapes will be drawn and the line thickness is determined.

Parameters:

downsample -

Returns:

tileSize

public LabeledImageServer.Builder tileSize(int tileSize)

Set tile width and height (square tiles).

Parameters:

tileSize -

Returns:

tileSize

public LabeledImageServer.Builder tileSize(int tileWidth,
 int tileHeight)

Set tile width and height.

Parameters:

tileWidth -

tileHeight -

Returns:

lineThickness

public LabeledImageServer.Builder lineThickness(float thickness)

Thickness of boundary lines and line annotations, defined in terms of pixels at the resolution specified by the downsample value of the server.

Parameters:

thickness -

Returns:

useUniqueLabels

@Deprecated
public LabeledImageServer.Builder useUniqueLabels()

Deprecated.

in favor of useInstanceLabels()

Returns:

useInstanceLabels

public LabeledImageServer.Builder useInstanceLabels()

Request that unique labels are used for all objects, rather than classifications. If this flag is set, all other label requests are ignored.

Returns:

See Also:

• useInstanceLabels(boolean)
• shuffleInstanceLabels(boolean)

useInstanceLabels

public LabeledImageServer.Builder useInstanceLabels(boolean instanceLabels)

Optionally request that unique labels are used for all objects, rather than classifications. If this flag is set, all other label requests are ignored.

Parameters:

instanceLabels -

Returns:

Since:

v0.4.0

See Also:

• useInstanceLabels()
• shuffleInstanceLabels(boolean)

shuffleInstanceLabels

public LabeledImageServer.Builder shuffleInstanceLabels(boolean doShuffle)

Optionally request that instance labels are shuffled. Default is true. Only has an effect if useInstanceLabels(boolean) is called with true.

Parameters:

doShuffle -

Returns:

Since:

v0.4.0

See Also:

• useInstanceLabels()
• useInstanceLabels(boolean)

multichannelOutput

public LabeledImageServer.Builder multichannelOutput(boolean doMultichannel)

If true, the output image consists of multiple binary images concatenated as different channels, so that the channel number relates to a classification. If false, the output image is a single-channel indexed image so that each pixel value relates to a classification. Indexed images are much more efficient, but are unable to support more than one classification per pixel.

Parameters:

doMultichannel -

Returns:

backgroundLabel

public LabeledImageServer.Builder backgroundLabel(int label)

Specify the background label (0 by default).

Parameters:

label -

Returns:

backgroundLabel

public LabeledImageServer.Builder backgroundLabel(int label,
 Integer color)

Specify the background label (0 by default) and color.

Parameters:

label -

color -

Returns:

addLabelsByName

public LabeledImageServer.Builder addLabelsByName(Map<String,Integer> labelMap)

Add multiple labels by classname, where the key represents a classname and the value represents the integer label that should be used for annotations of the given class.

Parameters:

labelMap -

Returns:

addLabels

public LabeledImageServer.Builder addLabels(Map<PathClass,Integer> labelMap)

Add multiple labels by PathClass, where the key represents a PathClass and the value represents the integer label that should be used for annotations of the given class.

Parameters:

labelMap -

Returns:

addLabel

public LabeledImageServer.Builder addLabel(String pathClassName,
 int label)

Add a single label by classname, where the label represents the integer label used for annotations with the given classname.

Parameters:

pathClassName -

label -

Returns:

addLabel

public LabeledImageServer.Builder addLabel(String pathClassName,
 int label,
 Integer color)

Add a single label by classname, where the label represents the integer label used for annotations with the given classname.

Parameters:

pathClassName -

label - the indexed image pixel value or channel number for the given classification

color - the color of the lookup table used with any indexed image

Returns:

addLabel

public LabeledImageServer.Builder addLabel(PathClass pathClass,
 int label)

Add a single label by PathClass, where the label represents the integer label used for annotations with the given classification.

Parameters:

pathClass -

label - the indexed image pixel value or channel number for the given classification

Returns:

addLabel

public LabeledImageServer.Builder addLabel(PathClass pathClass,
 int label,
 Integer color)

Add a single label by PathClass, where the label represents the integer label used for annotations with the given classification.

Parameters:

pathClass -

label - the indexed image pixel value or channel number for the given classification

color - the color of the lookup table used with any indexed image

Returns:

addUnclassifiedLabel

public LabeledImageServer.Builder addUnclassifiedLabel(int label,
 Integer color)

Add a single label for objects that are unclassified, where the label represents the integer label used for annotations that have no classification set.

Parameters:

label - the indexed image pixel value or channel number without a classification

color - the color of the lookup table used with any indexed image

Returns:

addUnclassifiedLabel

public LabeledImageServer.Builder addUnclassifiedLabel(int label)

Add a single label for objects that are unclassified, where the label represents the integer label used for annotations that have no classification set.

Parameters:

label - the indexed image pixel value or channel number without a classification

Returns:

setBoundaryLabel

public LabeledImageServer.Builder setBoundaryLabel(PathClass pathClass,
 int label)

Set the classification and label to use for boundaries for classified areas.

Parameters:

pathClass -

label - the indexed image pixel value or channel number for the given classification

Returns:

setBoundaryLabel

public LabeledImageServer.Builder setBoundaryLabel(PathClass pathClass,
 int label,
 Integer color)

Set the classification and label to use for boundaries for classified areas.

Parameters:

pathClass -

label - the indexed image pixel value or channel number for the given classification

color - the color of the lookup table used with any indexed image

Returns:

setBoundaryLabel

public LabeledImageServer.Builder setBoundaryLabel(String pathClassName,
 int label)

Set the classification and label to use for boundaries for classified areas.

Parameters:

pathClassName -

label - the indexed image pixel value or channel number for the given classification

Returns:

setBoundaryLabel

public LabeledImageServer.Builder setBoundaryLabel(String pathClassName,
 int label,
 Integer color)

Set the classification and label to use for boundaries for classified areas.

Parameters:

pathClassName -

label - the indexed image pixel value or channel number for the given classification

color - the color of the lookup table used with any indexed image

Returns:

maxOutputChannelLimit

public LabeledImageServer.Builder maxOutputChannelLimit(int maxChannels)

Specify the maximum number of output channels allowed before QuPath will throw an exception. This is used to guard against inadvertently requesting a labelled image that would have an infeasibly large number of output channels, most commonly with useInstanceLabels().

Parameters:

maxChannels - the maximum supported channels; set (cautiously!) ≤ 0 to ignore the limit entirely.

Returns:

build

public LabeledImageServer build()

Build the ImageServer with the requested parameters.

Returns: