link trajectories skipped (or do not appear for) a number of frames
linkSkippedFrames(trackll, tolerance, maxSkip, cores = 1)
| tolerance | Distance tolerance level measured in pixels after the frame skip. |
|---|---|
| maxSkip | Maximum number of frames a trajectory can skip. |
| trackll | A list of track lists. |
| cores | Number of cores used for parallel computation. This can be the cores on a workstation, or on a cluster. Tip: each core will be assigned to read in a file when paralleled. |
linked trackll
Given user input for a tolerance level to limit how far the next point after the skip can deviate from the last point in pixel distance and a maximum number of frame skips possible, all trajectories falling within these parameters are automatically linked, renamed, and ordered accordingly. For a maxSkip example, if the maxSkip for a trajectory ending in frame 7 was 3, the next linked trajectory can start up to a maximum frame of 11.
Although not required, in order for the output to have a frame record column (recommended), the input must have one as well.
The naming scheme for each linked track is as follows:
[Last five characters of the file name].[Start frame #].[Length].[Track #]. [# of links]
Track List: [full name of input file]
Track: [Last five characters of the file name].[Start frame].[Length]. [Track].[# of links]. [Index in overall list (will differ from Track # when merging)]
(Note: The last five characters of the file name, excluding the extension, cannot contain '.')
folder=system.file('extdata','SWR1',package='sojourner') trackll=createTrackll(folder=folder, input=3)#> #> Reading ParticleTracker file: SWR1_WT_140mW_image6.csv ... #> #> mage6 read and processed. #> #> Process complete.#Basic function call of linkSkippedFrames trackll.linked <- linkSkippedFrames(trackll, tolerance = 5, maxSkip = 10)#> #> Linking mage6 ... #> #> 156 links found in mage6 #> #> Process complete.