Install latest release
pip install cppcpyutils
Install dev version
pip install git+https://github.com/CougPhenomics/cppcpyutils.git
There are two components to the package:
At the top of a PlantCV workflow starts with:
#!/usr/bin/env python import os import argparse import cppcpyutils as cppc from plantcv import plantcv as pcv
In the workflow you will need to assign
cppc.pixelresolution to the pixel resolution of the camera you are analyzing.
The main user facing function is
cppc.roi.iterate_rois() which will run a loop through each roi and save to the PlantCV Outputs for each plant.
You have some options for which outputs to compute and save but plant_area (in mm2) and shape dimensions are always saved. Optionally you can save greenness index (
gi) with a pseudocolor image, all color information (
hist) with the histogram saved, or just hsv (
hue) with a hue pseudocolor image