mdftracks

R package for reading and writing MTrackJ Data Format (.mdf) files

https://github.com/burgerga/mdftracks

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 3 DOI reference(s) in README
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Links to: science.org, zenodo.org
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Low similarity (13.7%) to scientific vocabulary

Keywords

file-format r tracking

Last synced: 6 months ago · JSON representation ·

Repository

R package for reading and writing MTrackJ Data Format (.mdf) files

Basic Info

Host: GitHub
Owner: burgerga
License: gpl-3.0
Language: R
Default Branch: master
Homepage: https://cran.r-project.org/package=mdftracks
Size: 85.9 KB

Statistics

Stars: 1
Watchers: 2
Forks: 1
Open Issues: 2
Releases: 2

Topics

file-format r tracking

Created over 9 years ago · Last pushed about 2 years ago

Metadata Files

Readme Changelog Contributing License Citation

README.Rmd

---
title: mdftracks
output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```


[![R-CMD-check](https://github.com/burgerga/mdftracks/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/burgerga/mdftracks/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/burgerga/mdftracks/branch/master/graph/badge.svg)](https://app.codecov.io/gh/burgerga/mdftracks?branch=master)
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/mdftracks)](https://cran.r-project.org/package=mdftracks)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4692671.svg)](https://doi.org/10.5281/zenodo.4692671)


## Overview

mdftracks reads and writes **[MTrackJ](https://imagescience.org/meijering/software/mtrackj/) Data Files** ([`.mdf`](https://imagescience.org/meijering/software/mtrackj/format/)).
Supports clusters, 2D data, and channel information. If desired, generates
unique track identifiers based on cluster and id data from the `.mdf` file.

## Installation

```{r, eval=F}
install.packages('mdftracks')
```

### Development version

To get a bug fix or to use a feature from the development version, you can install the development version from GitHub.

```{r, eval=F}
# install.packages("remotes")
remotes::install_github("burgerga/mdftracks")

```


## Usage

First load the package with 
```{r}
library(mdftracks)
```

### Reading 3D data

```{r}
mdf.file <- system.file("extdata", "example.mdf", package = 'mdftracks')
data <- read.mdf(mdf.file)
head(data, 10)
```

### Dropping the z-coordinate for 2D data

```{r}
data <- read.mdf(mdf.file, drop.Z = T)
head(data, 10)
```

### Writing data in `(id, t, x, y, z)` format (e.g., from [celltrackR](https://github.com/ingewortel/celltrackR))

```{r}
library('celltrackR')
tracks.df <- as.data.frame(TCells)
```

```{r, collapse=FALSE}
head(tracks.df, 10)
write.mdf(head(tracks.df, 10), pos.columns = c(3,4))
```

### Writing data with cluster, channel, and point information

```{r, collapse=FALSE}
print(mdftracks.example.data)
write.mdf(mdftracks.example.data, cluster.column = 'cl', id.column = 'id',  
          pos.columns = letters[24:26], channel.column = 'ch', 
          point.column = "p")
```

For more information, please consult the package documentation.

Owner

Name: Gerhard Burger
Login: burgerga
Kind: user
Location: Gouda
Company: Leiden University

Website: https://www.universiteitleiden.nl/en/staffmembers/gerhard-burger
Repositories: 8
Profile: https://github.com/burgerga

Assistant Professor / Open Source Enthusiast

Citation (CITATION.cff)

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.5.0
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "mdftracks" in publications use:'
type: software
license: GPL-3.0-only
title: 'mdftracks: Read and Write ''MTrackJ Data Files'''
version: 0.2.1.9000
abstract: '''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.'
authors:
- family-names: Burger
  given-names: Gerhard
  email: burger.ga@gmail.com
  orcid: https://orcid.org/0000-0003-1062-5576
repository: https://CRAN.R-project.org/package=mdftracks
repository-code: https://github.com/burgerga/mdftracks
url: https://github.com/burgerga/mdftracks
contact:
- family-names: Burger
  given-names: Gerhard
  email: burger.ga@gmail.com
  orcid: https://orcid.org/0000-0003-1062-5576
keywords:
- file-format
- r
- tracking
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2023'
  institution:
    name: R Foundation for Statistical Computing
  version: '>= 2.10'
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2023'
- type: software
  title: tools
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Suggests
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2023'
  institution:
    name: R Foundation for Statistical Computing
- type: software
  title: tibble
  abstract: 'tibble: Simple Data Frames'
  notes: Suggests
  url: https://tibble.tidyverse.org/
  repository: https://CRAN.R-project.org/package=tibble
  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2023'
- type: software
  title: spelling
  abstract: 'spelling: Tools for Spell Checking in R'
  notes: Suggests
  url: https://docs.ropensci.org/spelling/
  repository: https://CRAN.R-project.org/package=spelling
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
  - family-names: Hester
    given-names: Jim
    email: james.hester@rstudio.com
  year: '2023'

GitHub Events

Total

Last Year

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 53
Total Committers: 1
Avg Commits per committer: 53.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Gerhard Burger	b**a@g**m	53

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Last synced: 6 months ago

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Total issues: 5
Total pull requests: 0
Average time to close issues: about 2 months
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Total pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
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Average time to close pull requests: N/A
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Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
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burgerga (5)

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Total packages: 1
Total downloads:
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Total docker downloads: 42,005

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 3
Total maintainers: 1

cran.r-project.org: mdftracks

Read and Write 'MTrackJ Data Files'

Homepage: https://github.com/burgerga/mdftracks
Documentation: http://cran.r-project.org/web/packages/mdftracks/mdftracks.pdf
License: GPL-3 | file LICENSE
Latest release: 0.2.2
published about 2 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 223 Last month
Docker Downloads: 42,005

Rankings

Forks count: 28.8%

Dependent packages count: 29.8%

Stargazers count: 31.7%

Dependent repos count: 35.5%

Average: 37.5%

Downloads: 61.9%

Maintainers (1)

burger.ga@gmail.com

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 2.10 depends
spelling * suggests
testthat * suggests
tibble * suggests
tools * suggests

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actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
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mdftracks

Science Score: 67.0%

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README.Rmd

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