`ijtiff`

[rorynolan]

Summary

• What does this package do? (explain in 50 words or less):
  Correctly import TIFF files that were saved from ImageJ and write TIFF files than can be correctly read by ImageJ. Full support for TIFF files with floating point (real-numbered) pixels. Also supports text image I/O.

• Paste the full DESCRIPTION file inside a code block below:

Package: ijtiff
Type: Package
Title: TIFF I/O for 'ImageJ' Users
Version: 0.1.0
Authors@R: c(person("Rory", "Nolan", email = "rorynoolan@gmail.com", 
                    role = c("aut", "cre", "cph")),
             person("Sergi", "Padilla-Parra", email = "spadilla@well.ox.ac.uk", 
                    role = "ths"))
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Description: Correctly import TIFF files that were saved from 'ImageJ' and write 
    TIFF files than can be correctly read by 'ImageJ'. Full support for TIFF files
    with floating point (real-numbered) pixels. Also supports text image I/O.
License: GPL-3
SystemRequirements: libtiff
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.4.0)
RoxygenNote: 6.0.1
URL: https://www.github.com/rorynolan/ijtiff
BugReports: https://www.github.com/rorynolan/ijtiff/issues
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
Imports: checkmate,
    RSAGA,
    magrittr,
    filesstrings (>= 2.0.0),
    stringr,
    purrr,
    Rcpp,
    tiff,
    fields,
    grDevices,
    readr,
    abind
Suggests: knitr,
    testthat,
    rmarkdown,
    covr
LinkingTo: Rcpp

• URL for the package (the development repository, not a stylized html page):
  https://www.github.com/rorynolan/ijtiff
• Please indicate which category or categories from our package fit policies this package falls under *and why(? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):

[e.g., "data extraction, because the package parses a scientific data file format"]
Data extraction, because the package can import (correctly) a common type of TIFF file that is not currently well-supported in R.

• Who is the target audience?
  R users who also use ImageJ, or who collaborate with people who use ImageJ.
• Are there other R packages that accomplish the same thing? If so, how does
  yours differ or meet our criteria for best-in-category?
  There's another R package for TIFF I/O, but it does not interface well with ImageJ (which I would argue is very important). It's also not actively maintained (I'm not getting responses when I file an issue).
•   If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

Requirements

Confirm each of the following by checking the box. This package:

• [ y] does not violate the Terms of Service of any service it interacts with.
• [ y] has a CRAN and OSI accepted license.
• [ y] contains a README with instructions for installing the development version.
• [ y] includes documentation with examples for all functions.
• [ y] contains a vignette with examples of its essential functions and uses.
• [ y] has a test suite.
• [ y] has continuous integration, including reporting of test coverage, using services such as Travis CI, Coeveralls and/or CodeCov.
• [ y] I agree to abide by ROpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

Publication options

• [ y] Do you intend for this package to go on CRAN?
• [ y] Do you wish to automatically submit to the Journal of Open Source Software? If so:
  • [y ] The package has an obvious research application according to JOSS's definition.
  • [ y] The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • [ y] The package is deposited in a long-term repository with the DOI: 10.5281/zenodo.1068230
  • (Do not submit your package separately to JOSS)
• [n ] Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
  • The package is novel and will be of interest to the broad readership of the journal.
  • The manuscript describing the package is no longer than 3000 words.
  • You intend to archive the code for the package in a long-term repository which meets the requirements of the journal.
  • (Please do not submit your package separately to Methods in Ecology and Evolution)

Detail

• [ y] Does R CMD check (or devtools::check()) succeed? Paste and describe any errors or warnings:

• [ y] Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:

• If this is a resubmission following rejection, please explain the change in circumstances:

• If possible, please provide recommendations of reviewers - those with experience with similar packages and/or likely users of your package - and their GitHub user names:
  Andrzej K. Oleś (aoles)

[sckott]

Thank you for your submission @rorynolan 😸

It's a good fit for rOpenSci - and we'll assign an editor asap

[sckott]

(@rorynolan is there a way to instal ImageJ on osx 10.13 (High Sierra), seems I don't need it to run your pkg, but still curious)

[sckott]

Editor checks:

• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has a CRAN or OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

Editor comments

Thanks for your submission @rorynolan !!

Goodpractice output for you and reviewers to consider:

It is good practice to

  ✖ write unit tests for all functions, and all package code
    in general. 72% of code lines are covered by test cases.

    src/common.c:21:NA
    src/common.c:22:NA
    src/common.c:59:NA
    src/common.c:60:NA
    src/common.c:61:NA
    ... and 196 more lines

  ✖ avoid calling setwd(), it changes the global environment.
    If you need it, consider using on.exit() to restore the working
    directory.

    R/write.R:37:13
    R/write.R:38:5
    tests/testthat/test_graphics.R:5:11
    tests/testthat/test_graphics.R:6:3
    tests/testthat/test_io.R:4:11
    ... and 18 more lines

Seeking reviewers now 🕐

---

Reviewers: @jeroen @jonclayden
Due date: 2018-01-18

[rorynolan]

Hi @sckott,
To install ImageJ for Mac, head to https://imagej.net/Fiji/Downloads and download Fiji. Fiji stands for "Fiji Is Just ImageJ," but what it really is is ImageJ packaged up nicely with some add-ons which is easy to install. Kind of like a version of R that comes with the tidyverse installed.
To any potential reviewers, with regard to the goodpractice output, I've covered as much of the code lines as I can, and you'll notice that wherever I've used setwd(), I do indeed use on.exit() to restore the working directory.
Thanks for your selfless work.
Rory

[sckott]

ah right! i totally forgot about fiji - i did use it in the past, but forgot. thanks for the help

[sckott]

still seeking reviewers 🕐