Module io.scif.labeling

Package io.scif.labeling

Class DefaultLabelingIOService

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

org.scijava.service.AbstractService

io.scif.labeling.DefaultLabelingIOService

All Implemented Interfaces:

LabelingIOService, Comparable<org.scijava.Prioritized>, net.imagej.ImageJService, org.scijava.Contextual, org.scijava.Disposable, org.scijava.Identifiable, org.scijava.Initializable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.plugin.HasPluginInfo, org.scijava.plugin.RichPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Prioritized, org.scijava.service.Service, org.scijava.Versioned

public class DefaultLabelingIOService
extends org.scijava.service.AbstractService
implements LabelingIOService

Constructor Summary

Constructors

Constructor	Description
DefaultLabelingIOService()

Method Summary

Modifier and Type	Method	Description
<T,I extends net.imglib2.type.numeric.IntegerType<I>> net.imglib2.roi.labeling.ImgLabeling<T,I>	load(String file, Class<T> labelType, Class<I> backingType)
<S,T,I extends net.imglib2.type.numeric.IntegerType<I>> Container<S,T,I>	loadWithMetadata(String file, Class<S> metadataType, Class<T> labelType, Class<I> backingType)	Load a labeling container from the given file path as string.
<S,T,I extends net.imglib2.type.numeric.IntegerType<I>> Container<S,T,I>	loadWithMetadata(String file, LongFunction<T> idToLabel, Class<S> metadataClazz)	Load a labeling container from the given file path as string.
<T,I extends net.imglib2.type.numeric.IntegerType<I>> void	save(net.imglib2.roi.labeling.ImgLabeling<T,I> imgLabeling, String file)
<S,T,I extends net.imglib2.type.numeric.IntegerType<I>> void	saveWithMetaData(net.imglib2.roi.labeling.ImgLabeling<T,I> imgLabeling, String file, ToLongFunction<T> labelToId, S metadata)	Save an ImgLabelingContainer in the file-path, transforming it into a JSON file and an image.
<S,T,I extends net.imglib2.type.numeric.IntegerType<I>> void	saveWithMetaData(net.imglib2.roi.labeling.ImgLabeling<T,I> imgLabeling, String file, S metadata)	Save an ImgLabelingContainer in the file-path, transforming it into a JSON file and an image.

Methods inherited from class org.scijava.service.AbstractService

getContext, setContext, toString

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

getInfo, getPriority, setInfo, setPriority

Methods inherited from class org.scijava.AbstractContextual

context

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.scijava.Contextual

context, getContext, setContext

Methods inherited from interface org.scijava.Disposable

dispose

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier, log

Methods inherited from interface org.scijava.service.Service

initialize, registerEventHandlers

Methods inherited from interface org.scijava.Versioned

getVersion

Constructor Detail

DefaultLabelingIOService

public DefaultLabelingIOService()

Method Detail

load

public <T,I extends net.imglib2.type.numeric.IntegerType<I>> net.imglib2.roi.labeling.ImgLabeling<T,I> load(String file,
                                                                                                                        Class<T> labelType,
                                                                                                                        Class<I> backingType)
                                                                                                                 throws IOException

Specified by:

load in interface LabelingIOService

Throws:

IOException

loadWithMetadata

public <S,T,I extends net.imglib2.type.numeric.IntegerType<I>> Container<S,T,I> loadWithMetadata(String file,
                                                                                                                         Class<S> metadataType,
                                                                                                                         Class<T> labelType,
                                                                                                                         Class<I> backingType)
                                                                                                                  throws IOException

Description copied from interface: LabelingIOService

Load a labeling container from the given file path as string. The file path must point to the JSON file containing the labeling data.

Specified by:

loadWithMetadata in interface LabelingIOService

Type Parameters:

S - Class of the meta data

T - the label value

I - IntegerType for the pixel value

Parameters:

file - The path to the file

metadataType - the metadata class

Returns:

a container object holding the ImgLabeling (as well as an optional source mapping)

Throws:

IOException - on file read fail

loadWithMetadata

public <S,T,I extends net.imglib2.type.numeric.IntegerType<I>> Container<S,T,I> loadWithMetadata(String file,
                                                                                                                         LongFunction<T> idToLabel,
                                                                                                                         Class<S> metadataClazz)

Description copied from interface: LabelingIOService

Load a labeling container from the given file path as string. The file path must point to the JSON file containing the labeling data.

Specified by:

loadWithMetadata in interface LabelingIOService

Type Parameters:

S - Class of the meta data

T - the label value

I - IntegerType for the pixel value

Parameters:

file - The path to the file

idToLabel - a function transforming the label of type T into something else

metadataClazz - the metadata class

Returns:

a container object holding the ImgLabeling (as well as an optional source mapping)

save

public <T,I extends net.imglib2.type.numeric.IntegerType<I>> void save(net.imglib2.roi.labeling.ImgLabeling<T,I> imgLabeling,
                                                                             String file)
                                                                      throws IOException

Specified by:

save in interface LabelingIOService

Throws:

IOException

saveWithMetaData

public <S,T,I extends net.imglib2.type.numeric.IntegerType<I>> void saveWithMetaData(net.imglib2.roi.labeling.ImgLabeling<T,I> imgLabeling,
                                                                                                 String file,
                                                                                                 S metadata)
                                                                                          throws IOException

Description copied from interface: LabelingIOService

Save an ImgLabelingContainer in the file-path, transforming it into a JSON file and an image. The path must contain the filename (ending does not matter).

Specified by:

saveWithMetaData in interface LabelingIOService

Type Parameters:

S - Class of the meta data

T - the label value

I - IntegerType for the pixel value

Parameters:

imgLabeling - the imglabeling object that needs to be serialized

file - the path pointing to the file, including the filename

Throws:

IOException

saveWithMetaData

public <S,T,I extends net.imglib2.type.numeric.IntegerType<I>> void saveWithMetaData(net.imglib2.roi.labeling.ImgLabeling<T,I> imgLabeling,
                                                                                                 String file,
                                                                                                 ToLongFunction<T> labelToId,
                                                                                                 S metadata)
                                                                                          throws IOException

Description copied from interface: LabelingIOService

Save an ImgLabelingContainer in the file-path, transforming it into a JSON file and an image. The path must contain the filename (ending does not matter).

Specified by:

saveWithMetaData in interface LabelingIOService

Type Parameters:

S - Class of the meta data

T - the label value

I - IntegerType for the pixel value

Parameters:

imgLabeling - the imglabeling object that needs to be serialized

file - the path pointing to the file, including the filename

labelToId - a function to convert the type T to a long value.

Throws:

IOException