Type: Package
Title: Read and Write 'MTrackJ Data Files'
Version: 0.2.2
Description: 'MTrackJ' is an 'ImageJ' plugin for motion tracking and analysis (see https://imagescience.org/meijering/software/mtrackj/). This package reads and writes 'MTrackJ Data Files' ('.mdf', see https://imagescience.org/meijering/software/mtrackj/format/). It supports 2D data and read/writes cluster, point, and channel information. If desired, generates track identifiers that are unique over the clusters. See the project page for more information and examples.
License: GPL-3 | file LICENSE
LazyData: TRUE
Depends: R (≥ 2.10)
URL: https://github.com/burgerga/mdftracks
BugReports: https://github.com/burgerga/mdftracks/issues
RoxygenNote: 7.2.3
Config/testthat/edition: 3
Encoding: UTF-8
Suggests: testthat, tools, tibble, spelling
Language: en-US
NeedsCompilation: no
Packaged: 2023-12-24 12:42:43 UTC; burge
Author: Gerhard Burger ORCID iD [aut, cre]
Maintainer: Gerhard Burger <burger.ga@gmail.com>
Repository: CRAN
Date/Publication: 2024-01-08 10:00:06 UTC

mdftracks: Read and Write 'MTrackJ Data Files'

Description

'MTrackJ' is an 'ImageJ' plugin for motion tracking and analysis (see https://imagescience.org/meijering/software/mtrackj/). This package reads and writes 'MTrackJ Data Files' ('.mdf', see https://imagescience.org/meijering/software/mtrackj/format/). It supports 2D data and read/writes cluster, point, and channel information. If desired, generates track identifiers that are unique over the clusters. See the project page for more information and examples.

Author(s)

Maintainer: Gerhard Burger burger.ga@gmail.com (ORCID)

See Also

MTrackJ Data Format

Example data to show mdftracks functionality

Description

Example data to show mdftracks functionality

Usage

mdftracks.example.data

Format

A data frame with 10 rows and 9 variables

cl

track cluster

id

track identifier (in cluster)

p

point in track (not necessarily the same as frame number)

x

x-coordinate of point

y

y-coordinate of point

z

z-coordinate of point

t

time of point

ch

track channel

uid

track identifier (unique over clusters)

Source

Self-generated

Read an MTrackJ Data File (.mdf)

Description

Reads an MTrackJ Data File (.mdf) file in a data.frame.

Usage

read.mdf(
  file,
  drop.Z = F,
  include.point.numbers = FALSE,
  include.channel = F,
  generate.unique.ids = F,
  text,
  fileEncoding = ""
)

Arguments

file

MTrackJ Data File (.mdf) file with tracking data.

drop.Z

drop z-coordinate (for 2D data)

include.point.numbers

include the point numbers in the mdf file (NB these can be different from the time/frame points)

include.channel

include channel information

generate.unique.ids

combine cluster and id columns to get unique ids

text

character string: if file is not supplied and this is, then data are read from the value of text via a text connection. Notice that a literal string can be used to include (small) data sets within R code.

fileEncoding

character string: if non-empty declares the encoding to be used on a file (not a connection) so the character data can be re-encoded as they are written. See base::file().

See Also

MTrackJ Data Format

Other mdftracks functions: write.mdf()

Examples

read.mdf(system.file("extdata", "example.mdf", package = 'mdftracks'))

Write an MTrackJ Data File (.mdf)

Description

Writes a data.frame with tracking information as an MTrackJ Data File (.mdf) file. Allows flexible column specification, and to avoid errors the column mapping used for writing is reported back to the user. Writing tracking data in 'id time x y z' format, for example, from the celltrackR package, doesn't require additional arguments.

Usage

write.mdf(
  x,
  file = "",
  cluster.column = NA,
  id.column = 1,
  time.column = 2,
  scale.time = 1,
  pos.columns = c(3, 4, 5),
  channel.column = NA,
  point.column = NA,
  default.channel = 1,
  fileEncoding = ""
)

Arguments

x

the data.frame with track information.

file

either a character string naming a file or a connection open for writing. "" indicates output to the console.

cluster.column

index or name of the column that contains the cluster ID.

id.column

index or name of the column that contains the track ID (either the id in the cluster or a unique id).

time.column

index or name of the column that contains elapsed time

scale.time

a value by which to multiply each time point. Useful for changing units, or specifying the time between positions if the time is given in frames.

pos.columns

vector containing indices or names of the columns that contain the spatial coordinates. If this vector has two entries, the data is assumed to be 2D and the z coordinate is set to 1.0.

channel.column

index or name of the column that contains channel information. If there is no channel column default.channel will be used.

point.column

index or name of the column that contains point ID. If there is no point column, points will be numbered automatically (NB points are not necessarily the same as frames).

default.channel

channel to be used if channel.column is not specified.

fileEncoding

character string: if non-empty declares the encoding to be used on a file (not a connection) so the character data can be re-encoded as they are written. See base::file().

See Also

MTrackJ Data Format

celltrackR

Other mdftracks functions: read.mdf()

Examples

## Not run: 
# Output to file
write.mdf(mdftracks.example.data, '~/example.mdf', id.column = 'uid',
          time.column = 't', pos.columns = letters[24:26])

## End(Not run)

# Output to stdout with cluster column
write.mdf(mdftracks.example.data, cluster.column = 'cl',
          id.column = 'id', time.column = 't', pos.columns = letters[24:26])

# Output to stdout using data in (id, t, x, y, z) format
write.mdf(mdftracks.example.data[, c('uid', 't', letters[24:26])])