seminal-root-angle 0.0.6

Extract seminal root angle from rhizobox images

Seminal root angle extraction

Used for high-throughput phenotyping of rhizobox images.

Install

The latest version is available via PyPI (https://pypi.org/project/seminal-root-angle) for convenient installation with pip

pip install seminal-root-angle

Example usage

Assuming the following folder structure:

output
data
├── photos
│   ├── photo1.JPG
│   ├── photo2.JPG
│   └── ....
├── root_segmentations
│   ├── photo1.png
│   ├── photo2.png
│   └── ....
└── seed_segmentations
    ├── photo1.png
    └── photo2.png
    └── ....

Then the angles can be extracted to the output/angles.csv with the following python code:

from seminal_root_angle.extract import extract_all_angles
extract_all_angles(root_seg_dir='data/root_segmentations',
                   im_dataset_dir='data/photos',
                   seed_seg_dir='data/seed_segmentations',
                   max_seed_points_per_im=2,
                   debug_image_dir='output/debug_images',
                   output_csv_path='output/angles.csv',
                   error_csv_path='output/errors.csv')