danforthcenter/plantcv: 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.roi2contour which allows user to create a binary mask from any contour. Added plantcv.plantcv.visualize.colorspacese 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)