cppcpyutils

Utilities for image processing pipelines at the Compact Plants Phenomics Center at Washingtion State University - Pullman. Pipelines are designed around PlantCV

Installation

Install latest release

pip install cppcpyutils

Install dev version

pip install git+https://github.com/CougPhenomics/cppcpyutils.git

Use

There are two components to the package:

1. A command line interface to download images from the LemnaTec database which is documented here
2. A python package that wraps some commonly used processes in the PlantCV workflows. The API reference is here

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