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Published September 10, 2020 | Version v3.10.0
Software Open

danforthcenter/plantcv: PlantCV v3.10.0

Creators

  • 1. @danforthcenter
  • 2. Donald Danforth Plant Science Center
  • 3. Washington State University
  • 4. Machine Learning and Sensing Lab
  • 5. Mockler Lab

Description

3.10 updates:

  • Integration with GitHub actions.
    • More specifically, makes the deploy packaging Actions job dependent on the proceeding build job. I.e. we should only upload packages to PyPI if tests pass.
  • Update plantcv.auto_crop to allow users to separately parameterize the padding.
    • This edit allows users to add custom padding to the top, bottom, left, and right of a cropped image. 'padding_x' and 'padding_y' can both accept tuples (optionally)
  • Modified the Dockerfile to install dependencies (other than OpenCV) from the requirements.txt file (Dockerfile had previously hardcoded dependencies for PlantCV). The Docker container is now built with the correct dependencies each time without manually updating the Dockerfile.
  • Python multiprocessing was local parallelization (i.e. computing took place where the program plantcv-workflow.py was run). This functionality is maintained by using the dask.distributed LocalCluster option. However, using dask-jobqueue, we now support remote, distributed computing using cluster options available through dask-jobqueue, currently: HTCondorCluster, LSFCluster, MoabCluster, OARCluster, PBSCluster, SGECluster, and SLURMCluster.
  • Add and revise testing to bring code coverage to 100%!
  • Added plantcv.morphology.fill_segments
    • This function propogates the labels of a segmented skeleton to fill a mask, using a watershed algorithm. Data about the area of each filled segments automatically gets store to Outputs.
  • Added a photosynthesis sub-package
    • Refactored plantcv.fluor_fvfm which is now plantcv.photosynthesis.analyze_fvfm to be consistent with the naming of other analysis functions. Also fixed a bug within this function. Previously, the function returned the Fm image to users. Now corrected so that Fv/Fm image is getting returned.
      • Added support for CropReported fluorescence image data. This was achieved by adding a new function, called plantcv.photosynthesis.read_cropreporter, that reads in, reshapes, and pulls out fdark, fmin, and fmax from a .DAT file which also utilizing the metadata recorded about image data in the corresponding .INF file.

Version 3.10 breaking changes:

  • Refactored plantcv.fluor_fvfm which is now plantcv.photosynthesis.analyze_fvfm to be consistent with the naming of other analysis functions. Input parameters are unchanged.

Files

danforthcenter/plantcv-v3.10.0.zip

Files (82.3 MB)

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Additional details

Related works

Is supplement to
https://github.com/danforthcenter/plantcv/tree/v3.10.0 (URL)