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Published April 23, 2021 | Version v3.12.0
Software Open

danforthcenter/plantcv: PlantCV v3.12.0

Creators

  • 1. @danforthcenter
  • 2. Donald Danforth Plant Science Center
  • 3. @danforthcenter @GatorSense
  • 4. Washington State University
  • 5. Oklahoma State University
  • 6. Mockler Lab

Description

PlantCVVersion 3.12 Updates

  • Updated the pcv.apply_mask(), changed the rgb_img parameter to img since the function is now able to handle grayscale, NIR, and hyperspectral data.
  • Add json datatype check in the add_observation method.
  • Started to move some internal code within functions across the package to start using a debug module rather than having repetitive code for plotting/printing debugging images.
  • Extend the pcv.cluster_contours_splitimg functionality to grayscale images.
  • Added a bounding parameter to pcv.clustered_contours() function so circles can be turned on or off (default behavior as on).
  • Added a pcv.deprecation_warning function for warning statements internal use within functions.
    • Add a "verbose" variable to pcv.params such that users have the option to turn off (deprecation) warnings by setting it to "False".
  • Update and resolve a bug within the random_sample utility function so that it works as intended on datasets with subdirectories.
  • Added a new method (save_results) to the Outputs class. outputs.save_results supports two output formats, JSON and CSV. The code from plantcv.print_results was moved to the save_results method and a deprecation warning is now printed via print_results. When run with outformat = "json", outputs.save_results has the same functionality as plantcv.print_results. When run with outformat = "csv", a single CSV table in "long" format is produced that is compatible with use in R. CSV format is useful for a user who runs workflows only in Jupyter or wants to utilize data for testing from Jupyter. The output format JSON must be used for parallel workflows as before.
    • Users will need to migrate workflows from pcv.print_results(args.result) to pcv.outputs.save_results(args.result) before pcv.print_results is removed.
  • Addition of RGB2CMYK function to PlantCV to allow the conversion of images from the RGB colour space to CMYK colour space and split the channels.
  • Updated the way PlantCV handles subdaily timestamps for parallelization. Now will work with months and days even where there are no years.

Version 3.11.0 breaking changes

  • pcv.apply_mask(), changed the rgb_img parameter to img
  • pcv.cluster_contours_splitimg, changed the rgb_img parameter to img

Files

danforthcenter/plantcv-v3.12.0.zip

Files (87.5 MB)

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Additional details

Related works

Is supplement to
https://github.com/danforthcenter/plantcv/tree/v3.12.0 (URL)