semvec/pypi-packages huggingface dataset:
tree-disk-pith-detector 0.1.1
A package for tree disk pith detection in images
Requires Python: >=3.7

# Tree Disk Pith Detection

[![PyPI - Version](https://img.shields.io/pypi/v/tree-disk-pith-detector)](https://pypi.org/project/tree-disk-pith-detector/)

A Python package for analyzing tree rings in cross-sectional images. Originally forked from [hmarichal93/apd](https://github.com/hmarichal93/apd).

## Installation

```bash
pip install tree-disk-pith-detector
```

## Usage

### Python API

```python
import treediskpithdetector

# Configure the analyzer
treediskpithdetector.configure(
    input_image="input/tree-disk4.png",
    save_results=True,
)

# Run the detection
(
    img_in,          # Original input image
    img_pre,         # Preprocessed image
    pith,  # Center of the tree disk
) = treediskpithdetector.run()
```

### Command Line Interface (CLI)

Basic usage:
```bash
tree-disk-pith-detector --input_image ./input/tree-disk3.png --new_shape 640 --debug
```

Save intermediate results:
```bash
tree-disk-pith-detector --input_image ./input/tree-disk3.png --new_shape 640 --debug --method apd_pcl --save_results
```

Advanced usage with custom parameters:
```bash
tree-disk-pith-detector \
    --input_image input/tree-disk3.png \
    --cx 1204 \
    --cy 1264 \
    --output_dir custom_output/ \
    --sigma 4.0 \
    --th_low 10 \
    --th_high 25 \
    --save_results \
    --debug
```

## CLI Arguments

| Argument | Type | Required | Default | Description |
|----------|------|----------|---------|-------------|
| `--input_image` | str | Yes | - | Input image file path |
| `--output_dir` | str | Yes | - | Output directory path |
| `--method` | str | No | apd | Detection method to use. Choices are apd, apd_pcl, or apd_dl |
| `--model_path` | str | No | - | Path to the weights file (required if using apd_dl method) |
| `--percent_lo` | float | No | 0.7 | percent_lo parameter for the algorithm |
| `--st_w` | int | No | 3 | st_w parameter for the algorithm |
| `--lo_w` | int | No | 3 | lo_w parameter for the algorithm |
| `--st_sigma` | float | No | 1.2 | st_sigma parameter for the algorithm |
| `--new_shape` | int | No | 0 | New shape for resizing the input image. If 0, no resizing is done |
| `--debug` | flag | No | False | Enable debug mode to save intermediate images and outputs |
| `--save_results` | flag | No | False | Save intermediate images, labelme and config file |

## Development

### Setting up Development Environment

1. Clone the repository:
```bash
git clone https://github.com/tuke307/tree-disk-pith-detector.git
cd tree-disk-pith-detector
```

2. Create and activate virtual environment:
```bash
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate
```

3. Install development dependencies:
```bash
pip install -r requirements.txt
```

4. Install the package in editable mode:
```bash
pip install -e .
```

5. fetch dataset
```bash
python fetch_dataset.py
```

6. Download pretrained model
```bash
python fetch_pretrained_model.py
```
gff-to-genbank 0.1.0
Script to convert from GFF to Genbank
Requires Python: >=3.8

# gff-to-genbank

Convert GFF file to GenBank file format while extracting the sequences between the annotated regions

Original script written by Brad Chapman and Hsiao Yi - <https://github.com/chapmanb/bcbb/blob/master/gff/Scripts/gff/gff_to_genbank.py>

Edited by Kartik Chundru to crop the FASTA sequence between the first and last annotated regions.

Edited by Cornelius Roemer to make it work with BioPython 1.81 and to allow compound CDS features. Made pip installable at <https://pypi.org/project/gff-to-genbank/>

## Usage

Installation:

```bash
pip install gff-to-genbank
```

```bash
gff-to-genbank <gff_file> <fasta_file>
```

Output is written to stdout, so you'll want to redirect it to a file.

## Dependencies

- BioPython - https://biopython.org/
- BCBio - https://github.com/chapmanb/bcbb

## Development

Set new version:

```bash
hatch version <new_version>
```

Publishing to PyPi:

```bash
hatch build
hatch publish
```
odoo12-addon-sale-product-name-description 12.0.1.0.0
Only code, name and attributes in product description.
Requires Python: >=3.5

.. image:: https://img.shields.io/badge/licence-AGPL--3-blue.svg
	:target: http://www.gnu.org/licenses/agpl
	:alt: License: AGPL-3

=============================
Sale Product Name Description
=============================

Only code, name and attributes in product description.


Installation
============

To install this module, you need to:

#. Just install the module


Configuration
=============

To configure this module, you need to:

#. No configuration needed


Usage
=====

To use this module, you need to:

#. No special usage instructions needed.


ROADMAP
=======

[ Enumerate known caveats and future potential improvements.
  It is mostly intended for end-users, and can also help
  potential new contributors discovering new features to implement. ]

* ...


Bug Tracker
===========

Bugs and errors are managed in `issues of GitHub <https://github.com/sygel-technology/REPOSITORY/issues>`_.
In case of problems, please check if your problem has already been
reported. If you are the first to discover it, help us solving it by indicating
a detailed description `here <https://github.com/sygel-technology/REPOSITORY/issues/new>`_.

Do not contact contributors directly about support or help with technical issues.


Credits
=======

Authors
~~~~~~~

* Sygel


Contributors
~~~~~~~~~~~~

* Manuel Regidor <manuel.regidor@sygel.es>


Maintainer
~~~~~~~~~~

This module is maintained by Sygel.


This module is part of the `Sygel/REPOSITORY <https://github.com/sygel-technology/repository>`_.

To contribute to this module, please visit https://github.com/sygel-technology.