Module io.scif.labeling

Package io.scif.labeling

Interface LabelingIOService

All Superinterfaces:

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

All Known Implementing Classes:

DefaultLabelingIOService

public interface LabelingIOService
extends net.imagej.ImageJService

A service to easily access a load/save functionality for JSON-based labeling data files. Basic support for primitive types and JSON standard types is already included. For non-primitive types, a codec must be set and the class must be given as an argument to the methods.

Author:

Tom Burke

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 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

Method Detail

load

<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

Throws:

IOException

save

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

Throws:

IOException

loadWithMetadata

<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

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

Type Parameters:

T - the label value

I - IntegerType for the pixel value

S - Class of the meta data

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

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

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

Type Parameters:

T - the label value

I - IntegerType for the pixel value

S - Class of the meta data

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)

Throws:

IOException - on file read fail

saveWithMetaData

<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

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).

Type Parameters:

T - the label value

I - IntegerType for the pixel value

S - Class of the meta data

Parameters:

imgLabeling - the imglabeling object that needs to be serialized

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

Throws:

IOException

saveWithMetaData

<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

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).

Type Parameters:

T - the label value

I - IntegerType for the pixel value

S - Class of the meta data

Parameters:

imgLabeling - the imglabeling object that needs to be serialized

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

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

Throws:

IOException