deformablemesh.io

Class TrackMateAdapter

java.lang.Object

deformablemesh.io.TrackMateAdapter

public class TrackMateAdapter
extends Object

A utility class for using TrackMate files.

Constructor Summary

Constructors

Constructor and Description
TrackMateAdapter()

Method Summary

Modifier and Type	Method and Description
static List<Track>	applyTracking(List<Track> tracks, MeshImageStack mis, Path trackMateFile) Takes the provided Tracks for the provided image file and attempts to link them based on associated positions.
static List<Track>	createSpotList(Model model, MeshImageStack geometry)
static double[]	getCenterRealCoordinates(DeformableMesh3D mesh, MeshImageStack stack) Uses the same algorithm that is used to get the real coordinates for spot/track generation.
static List<Track>	importTrackMateFile(MeshImageStack mis, Path trackMateFile)
static List<Track>	importTrackMateFile(Path image, Path trackMateFile) Overload in case the image hasn't been loaded yet.
static void	main(String[] args)
static void	saveAsTrackMateFile(MeshImageStack stack, List<Track> tracks, Path destination)

Methods inherited from class java.lang.Object

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

Constructor Detail

TrackMateAdapter

public TrackMateAdapter()

Method Detail

applyTracking

public static List<Track> applyTracking(List<Track> tracks,
                                        MeshImageStack mis,
                                        Path trackMateFile)

Takes the provided Tracks for the provided image file and attempts to link them based on associated positions. First all of the spots are loaded from the trackmate file, each spot is associated with a mesh based on the center of mass positions. If a mesh is associated to a spat, it is added to a track related to the spots track id. This will return an intersection of mesh tracks and trackmate spots.

Parameters:

tracks - The collection of tracks that will be mapped using the trackmate file tracks.

mis - Image that tracks geometry is based on.

trackMateFile - xml file that tracking information is loaded from.

Returns:

A new set of tracks with meshs from the original tracks link based on information from the trackmate file.

importTrackMateFile

public static List<Track> importTrackMateFile(Path image,
                                              Path trackMateFile)

Overload in case the image hasn't been loaded yet.

Parameters:

image - path to the associated image.

trackMateFile - path to a trackmate xml file.

Returns:

Spherical meshes based on the position and radius of the spots found in the trackmate file. The meshes are linked into tracks based on the TrackModel#trackIDOf(Spot spot)

getCenterRealCoordinates

public static double[] getCenterRealCoordinates(DeformableMesh3D mesh,
                                                MeshImageStack stack)

Uses the same algorithm that is used to get the real coordinates for spot/track generation. the values are [0, width*px_width), [0, height*px_height), [0, depth*px_depth)

Parameters:

mesh -

stack -

Returns:

createSpotList

public static List<Track> createSpotList(Model model,
                                         MeshImageStack geometry)

importTrackMateFile

public static List<Track> importTrackMateFile(MeshImageStack mis,
                                              Path trackMateFile)

saveAsTrackMateFile

public static void saveAsTrackMateFile(MeshImageStack stack,
                                       List<Track> tracks,
                                       Path destination)
                                throws IOException

Throws:

IOException

main

public static void main(String[] args)
                 throws IOException

Throws:

IOException