danforthcenter/plantcv: PlantCV v3.12.0

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 im