fiji.plugin.trackmate.action

Class LabelImgExporter

java.lang.Object

fiji.plugin.trackmate.action.AbstractTMAction

fiji.plugin.trackmate.action.LabelImgExporter

All Implemented Interfaces:

TrackMateAction

public class LabelImgExporter
extends AbstractTMAction

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	LabelImgExporter.Factory
static class	LabelImgExporter.LabelIdPainting Specifies how spots will be labeled in the exported label image.
static class	LabelImgExporter.SpotAsDotWriter<T extends RealType<T>>
static class	LabelImgExporter.SpotRoiWriter<T extends RealType<T>>
static interface	LabelImgExporter.SpotWriter Interface for classes that can 'write' a spot into a label image.

Field Summary

Fields

Modifier and Type	Field and Description
static String	INFO_TEXT
static String	KEY
static String	NAME

Fields inherited from class fiji.plugin.trackmate.action.AbstractTMAction

logger

Constructor Summary

Constructors

Constructor and Description
LabelImgExporter()

Method Summary

Modifier and Type	Method and Description
static ij.ImagePlus	createLabelImagePlus(Model model, ij.ImagePlus imp, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labelIdPainting) Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
static ij.ImagePlus	createLabelImagePlus(Model model, ij.ImagePlus imp, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labelIdPainting, Logger logger) Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
static ij.ImagePlus	createLabelImagePlus(Model model, int[] dimensions, double[] calibration, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labelIdPainting) Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
static ij.ImagePlus	createLabelImagePlus(Model model, int[] dimensions, double[] calibration, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labelIdPainting, Logger logger) Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
static ij.ImagePlus	createLabelImagePlus(TrackMate trackmate, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labeIdPainting) Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
static ij.ImagePlus	createLabelImagePlus(TrackMate trackmate, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labelIdPainting, Logger logger) Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
static Img<FloatType>	createLabelImg(Model model, long[] dimensions, double[] calibration, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labelIdPainting) Creates a new label Img of FloatType where the spots of the specified model are painted with their shape, with their track ID as pixel value.
static Img<FloatType>	createLabelImg(Model model, long[] dimensions, double[] calibration, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labelIdPainting, Logger logger) Creates a new label Img of FloatType where the spots of the specified model are painted with their shape, with an ID pixel value.
static <T extends RealType<T> & NativeType<T>> ImgPlus<T>	createLabelImg(SpotCollection spots, long[] dimensions, double[] calibration, boolean exportSpotsAsDots, LabelImgExporter.LabelIdPainting labelIdPainting, T outputType, Logger logger) Creates a new label ImgPlus of FloatType where the spots are painted with an ID.
void	execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame gui) Executes this action within an application specified by the parameters.

Methods inherited from class fiji.plugin.trackmate.action.AbstractTMAction

setLogger

Methods inherited from class java.lang.Object

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

Field Detail

INFO_TEXT

public static final String INFO_TEXT

See Also:

Constant Field Values

KEY

public static final String KEY

See Also:

Constant Field Values

NAME

public static final String NAME

See Also:

Constant Field Values

Constructor Detail

LabelImgExporter

public LabelImgExporter()

Method Detail

execute

public void execute(TrackMate trackmate,
                    SelectionModel selectionModel,
                    DisplaySettings displaySettings,
                    Frame gui)

Description copied from interface: TrackMateAction

Executes this action within an application specified by the parameters.

Parameters:

trackmate - the TrackMate instance to use to execute the action.

selectionModel - the SelectionModel currently used in the application,

displaySettings - the DisplaySettings used to render the views in the application.

gui - the user-interface parent window.

createLabelImagePlus

public static final ij.ImagePlus createLabelImagePlus(TrackMate trackmate,
                                                      boolean exportSpotsAsDots,
                                                      boolean exportTracksOnly,
                                                      LabelImgExporter.LabelIdPainting labeIdPainting)

Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.

Parameters:

trackmate - the trackmate instance from which we takes the spots to paint. The label image will have the same calibration, name and dimension from the input image stored in the trackmate settings. The output label image will have the same size that of this input image, except for the number of channels, which will be 1.

exportSpotsAsDots - if true, spots will be painted as single dots. If false they will be painted with their shape.

exportTracksOnly - if true, only the spots belonging to visible tracks will be painted. If false, spots not belonging to a track will be painted with a unique ID, different from the track IDs and different for each spot.

labeIdPainting - specifies how to paint the label ID of spots.

Returns:

a new ImagePlus.

createLabelImagePlus

public static final ij.ImagePlus createLabelImagePlus(TrackMate trackmate,
                                                      boolean exportSpotsAsDots,
                                                      boolean exportTracksOnly,
                                                      LabelImgExporter.LabelIdPainting labelIdPainting,
                                                      Logger logger)

Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.

Parameters:

trackmate - the trackmate instance from which we takes the spots to paint. The label image will have the same calibration, name and dimension from the input image stored in the trackmate settings. The output label image will have the same size that of this input image, except for the number of channels, which will be 1.

exportSpotsAsDots - if true, spots will be painted as single dots instead their shape.

exportTracksOnly - if true, only the spots belonging to visible tracks will be painted. If false, spots not belonging to a track will be painted with a unique ID, different from the track IDs and different for each spot.

labelIdPainting - specifies how to paint the label ID of spots.

logger - a Logger instance, to report progress of the export process.

Returns:

a new ImagePlus.

createLabelImagePlus

public static final ij.ImagePlus createLabelImagePlus(Model model,
                                                      ij.ImagePlus imp,
                                                      boolean exportSpotsAsDots,
                                                      boolean exportTracksOnly,
                                                      LabelImgExporter.LabelIdPainting labelIdPainting)

Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.

Parameters:

model - the model from which we takes the spots to paint.

imp - a source image to read calibration, name and dimension from. The output label image will have the same size that of this source image, except for the number of channels, which will be 1.

exportSpotsAsDots - if true, spots will be painted as single dots instead their shape.

exportTracksOnly - if true, only the spots belonging to visible tracks will be painted. If false, spots not belonging to a track will be painted with a unique ID, different from the track IDs and different for each spot.

labelIdPainting - specifies how to paint the label ID of spots.

Returns:

a new ImagePlus.

createLabelImagePlus

public static final ij.ImagePlus createLabelImagePlus(Model model,
                                                      ij.ImagePlus imp,
                                                      boolean exportSpotsAsDots,
                                                      boolean exportTracksOnly,
                                                      LabelImgExporter.LabelIdPainting labelIdPainting,
                                                      Logger logger)

Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.

Parameters:

model - the model from which we takes the spots to paint.

imp - a source image to read calibration, name and dimension from. The output label image will have the same size that of this source image, except for the number of channels, which will be 1.

exportSpotsAsDots - if true, spots will be painted as single dots instead their shape.

exportTracksOnly - if true, only the spots belonging to visible tracks will be painted. If false, spots not belonging to a track will be painted with a unique ID, different from the track IDs and different for each spot.

labelIdPainting - specifies how to paint the label ID of spots.

logger - a Logger instance, to report progress of the export process.

Returns:

a new ImagePlus.

createLabelImagePlus

public static final ij.ImagePlus createLabelImagePlus(Model model,
                                                      int[] dimensions,
                                                      double[] calibration,
                                                      boolean exportSpotsAsDots,
                                                      boolean exportTracksOnly,
                                                      LabelImgExporter.LabelIdPainting labelIdPainting)

Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.

Parameters:

model - the model from which we takes the spots to paint.

dimensions - the desired dimensions of the output image (width, height, nZSlices, nFrames) as a 4 element long array. Spots outside these dimensions are ignored.

exportSpotsAsDots - if true, spots will be painted as single dots instead their shape.

exportTracksOnly - if true, only the spots belonging to visible tracks will be painted. If false, spots not belonging to a track will be painted with a unique ID, different from the track IDs and different for each spot.

labelIdPainting - specifies how to paint the label ID of spots.

Returns:

a new ImagePlus.

createLabelImagePlus

public static final ij.ImagePlus createLabelImagePlus(Model model,
                                                      int[] dimensions,
                                                      double[] calibration,
                                                      boolean exportSpotsAsDots,
                                                      boolean exportTracksOnly,
                                                      LabelImgExporter.LabelIdPainting labelIdPainting,
                                                      Logger logger)

Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.

Parameters:

model - the model from which we takes the spots to paint.

dimensions - the desired dimensions of the output image (width, height, nZSlices, nFrames) as a 4 element int array. Spots outside these dimensions are ignored.

exportSpotsAsDots - if true, spots will be painted as single dots instead their shape.

exportTracksOnly - if true, only the spots belonging to visible tracks will be painted. If false, spots not belonging to a track will be painted with a unique ID, different from the track IDs and different for each spot.

labelIdPainting - specifies how to paint the label ID of spots.

logger - a Logger instance, to report progress of the export process.

Returns:

a new ImagePlus.

createLabelImg

public static final Img<FloatType> createLabelImg(Model model,
                                                  long[] dimensions,
                                                  double[] calibration,
                                                  boolean exportSpotsAsDots,
                                                  boolean exportTracksOnly,
                                                  LabelImgExporter.LabelIdPainting labelIdPainting)

Creates a new label Img of FloatType where the spots of the specified model are painted with their shape, with their track ID as pixel value.

Parameters:

model - the model from which we takes the spots to paint.

dimensions - the desired dimensions of the output image (width, height, nZSlices, nFrames) as a 4 element long array. Spots outside these dimensions are ignored.

exportSpotsAsDots - if true, spots will be painted as single dots instead their shape.

exportTracksOnly - if true, only the spots belonging to visible tracks will be painted. If false, spots not belonging to a track will be painted with a unique ID, different from the track IDs and different for each spot.

labelIdPainting - specifies how to paint the label ID of spots.

Returns:

a new Img.

createLabelImg

public static final Img<FloatType> createLabelImg(Model model,
                                                  long[] dimensions,
                                                  double[] calibration,
                                                  boolean exportSpotsAsDots,
                                                  boolean exportTracksOnly,
                                                  LabelImgExporter.LabelIdPainting labelIdPainting,
                                                  Logger logger)

Creates a new label Img of FloatType where the spots of the specified model are painted with their shape, with an ID pixel value.

Parameters:

model - the model from which we takes the spots to paint.

dimensions - the desired dimensions of the output image (width, height, nZSlices, nFrames) as a 4 element long array. Spots outside these dimensions are ignored.

exportSpotsAsDots - if true, spots will be painted as single dots instead their shape.

exportTracksOnly - if true, only the spots belonging to visible tracks will be painted. If false, spots not belonging to a track will be painted with a unique ID, different from the track IDs and different for each spot.

labelIdPainting - specifies how to paint the label ID of spots.

logger - a Logger instance, to report progress of the export process.

Returns:

a new Img.

createLabelImg

public static <T extends RealType<T> & NativeType<T>> ImgPlus<T> createLabelImg(SpotCollection spots,
                                                                                long[] dimensions,
                                                                                double[] calibration,
                                                                                boolean exportSpotsAsDots,
                                                                                LabelImgExporter.LabelIdPainting labelIdPainting,
                                                                                T outputType,
                                                                                Logger logger)

Creates a new label ImgPlus of FloatType where the spots are painted with an ID. All visible spots are painted, whether they are in a track or not.

Parameters:

spots - the spots to paint.

dimensions - the desired dimensions of the output image (width, height, nZSlices, nFrames) as a 4 element long array. Spots outside these dimensions are ignored.

exportSpotsAsDots - if true, spots will be painted as single dots instead of their shape.

labelIdPainting - specifies how to paint the label ID of spots. The LabelImgExporter.LabelIdPainting.LABEL_IS_TRACK_ID is not supported and defaults to LabelImgExporter.LabelIdPainting.LABEL_IS_SPOT_ID.

logger - a Logger instance, to report progress of the export process.

Returns:

a new ImgPlus.