PlantCV v3.8.0

• Fixed a few missing pages and broken links within the documentation.
• Add plantcv.hyperspectral.analyze_index
  • This function now accepts min/maximum bin labels, or can auto-calculate bins based on image data range.
  • Collects frequency data for all integrated indices (mean, median, std, frequency).
  • Optionally plots a histogram of frequency values.
• Add links to source code throughout documentation pages. This allows users to more easily find the raw, source code for those interested in learning more of the mechanics of a function than the documentation page provides.
• Adds a border_width parameter to plantcv.within_frame.
  • Allows the user to specify how many pixels from the image edge they want to consider for detecting out-of-frame objects.
  • The default is 1 px, which maintains the previous default behavior.
• Made some updates to the documentation based on usage on Windows.
• Update dependencies in requirements.txt
• Add plantcv.roi.roi2mask which allows user to create a binary mask from any contour.
• Added plantcv.plantcv.visualize.colorspaces which
  • Used to quickly view all potential colorspaces, that are often used for thresholding/object segmentation steps.
  • Plots out an image will all potential colorspaces, labeled with which colorspace each is, next to the original image.
• Add indices to the plantcv.hyperspectral.extract_index function
  • Add PRI (Photochemical reflectance index)
  • Add ARI (anthocyanin reflectance index)
  • Add ACI (anthocyanin content index)
• Add and update plantcv.hyperspectral.analyze_spectral function
  • Was storing out information, mainly about the global statistics like the maximum reflectance value for the entire datacube.
  • Average reflectance per band was the only per-band measurement that we had been doing but really most of the stats could be per-band rather than global.
• Modify various .npz test data files in code tests (avoid using Numpy object arrays and the pickle module)
• In plantcv.transform.create_color_card_mask() the exclude input option required users to input excluded color chip IDs in descending numerical order.
• Adds plantcv.threshold.saturation function for masking saturated pixels.
  • Any channel at or above a certain threshold
  • All channels at or above a certain threshold.
  • The user can also pick this threshold (default = 255).