tree-disk-rings 0.6.0

A package for tree disk rings detection in images

Tree Disk Rings

A Python package for analyzing tree rings in cross-sectional images. Originally forked from hmarichal93/cstrd_ipol.

Installation

pip install tree-disk-rings

Usage

Python API

import treediskrings

# Configure the analyzer
treediskrings.configure(
    input_image="input/tree-disk4.png",
    cx=1204,
    cy=1264,
    save_results=True,
)

# Run the analysis
(
    img_in,          # Original input image
    img_pre,         # Preprocessed image
    devernay_edges,  # Detected edges
    devernay_curves_f,  # Filtered curves
    devernay_curves_s,  # Smoothed curves
    devernay_curves_c,  # Connected curves
    devernay_curves_p,  # Final processed curves
) = treediskrings.run()

Command Line Interface (CLI)

Basic usage:

tree-disk-rings --input_image input/tree-disk4.png --cx 1204 --cy 1264

Save intermediate results:

tree-disk-rings --input_image input/tree-disk4.png --cx 1204 --cy 1264 --save_results

Advanced usage with custom parameters:

tree-disk-rings \
    --input_image input/F02c.png \
    --cx 1204 \
    --cy 1264 \
    --output_dir custom_output/ \
    --sigma 4.0 \
    --th_low 10 \
    --th_high 25 \
    --min_chain_length 2 \
    --save_results \
    --debug

CLI Arguments

Argument	Type	Required	Default	Description
--input_image	str	Yes	-	Path to input image
--cx	int	Yes	-	Pith x-coordinate
--cy	int	Yes	-	Pith y-coordinate
--output_dir	str	No	./output	Output directory path
--sigma	float	No	3.0	Gaussian kernel parameter for edge detection
--th_low	float	No	5.0	Low threshold for gradient magnitude
--th_high	float	No	20.0	High threshold for gradient magnitude
--height	int	No	0	Height after resizing (0 to keep original)
--width	int	No	0	Width after resizing (0 to keep original)
--alpha	float	No	30.0	Collinearity threshold in degrees. Defines the maximum allowable angle between an edge's direction and its gradient.
--nr	int	No	360	Number of rays
--min_chain_length	int	No	2	Minimum chain length
--debug	flag	No	False	Enable debug mode
--save_results	flag	No	False	Save intermediate images, labelme and config file

Development

Setting up Development Environment

1. Create and activate virtual environment:

poetry config virtualenvs.in-project true
poetry env use python

poetry install
eval $(poetry env activate)

2. Running tests:

pytest

3. Compile the external C code:

cd ./externals/devernay_1.0 && make clean && make