diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..c5587fb --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,19 @@ +# Read the Docs configuration file for MkDocs projects +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Set the version of Python and other tools you might need +build: + os: ubuntu-22.04 + tools: + python: "3.11" + +mkdocs: + configuration: mkdocs.yml + +# Optionally declare the Python requirements required to build your docs +python: + install: + - requirements: docs/requirements.txt diff --git a/docs/CODE_OF_CONDUCT.md b/docs/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..deb3b69 --- /dev/null +++ b/docs/CODE_OF_CONDUCT.md @@ -0,0 +1,137 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of + any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, + without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement, Noah Fahlgren +[nfahlgren@danforthcenter.org](mailto:nfahlgren@danforthcenter.org) and +Malia Gehan [mgehan@danforthcenter.org](mailto:mgehan@danforthcenter.org). +Alternatively, information about contacting the Danforth Center Human Resources +department (including anonymous reporting) can be found at +[https://www.danforthcenter.org/about-us/accountability/][accountability]. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.1, available at +[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + +Community Impact Guidelines were inspired by +[Mozilla's code of conduct enforcement ladder][Mozilla CoC]. + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at +[https://www.contributor-covenant.org/translations][translations]. + +[homepage]: https://www.contributor-covenant.org +[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html +[Mozilla CoC]: https://github.com/mozilla/diversity +[FAQ]: https://www.contributor-covenant.org/faq +[translations]: https://www.contributor-covenant.org/translations +[accountability]: https://www.danforthcenter.org/about-us/accountability diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md new file mode 100644 index 0000000..4d1482a --- /dev/null +++ b/docs/CONTRIBUTING.md @@ -0,0 +1,19 @@ +# Contrbution to PlantCV-Annotate + +!!! note + PlantCV-Annotate is an add-on package to PlantCV so please first refer to the main package's [contributing guide](https://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) for the majority of the information on what and how to contribute to either project (including but not limited to reporting bugs, requesting new features, add/revise documentation, and adding tutorials). + +## Overview Of What To Contribute to PlantCV-Annotate vs. Other Packages + +This document aims to give an overview of what to contribute to PlantCV-Annotate, and guidelines to +decide which repository is the most appropriate place for new features. Please +[create an issue in GitHub](https://github.com/danforthcenter/plantcv-annotate/issues) assuming one +does not already exist. + +Functions in the Annotate toolbox are considered lower throughput, since they +usually involve interacting with data on a per-image basis, compared to tools from the main PlantCV +package which aim to build modularly into workflows that can be batch processed. + +Data annotation is helpful when downstream analysis steps include machine learning or deep learning, +but it's also helpful for tuning computer vision algorithm approaches by ground truthing a +dataset with annotation and comparing results from the two methods. diff --git a/docs/Points.md b/docs/Points.md new file mode 100644 index 0000000..a1fd3a4 --- /dev/null +++ b/docs/Points.md @@ -0,0 +1,49 @@ +## Interactive Point Annotation Tool + +Using [Jupyter Notebooks](jupyter.md) it is possible to interactively click to collect coordinates from an image, which can be used in various downstream applications. Left click on the image to collect a point. Right click removes the +closest collected point. + +**plantcv.annotate.Points**(*img, figsize=(12,6), label="dafault"*) + +**returns** interactive image class + +- **Parameters:** + - img - Image data + - figsize - Interactive plot figure size (default = (12,6)) + - label - The current label (default = "default") + +- **Attributes:** + - coords - dictionary of all coordinates per group label + - events - includes right and left click events + - count - dictionary that save the counts of different groups (labels) + - label - the current label + - sample_labels - list of all sample labels, one to one with coordinates collected + - view_all - flag indicating whether or not to view all labels + - color - current color + - colors - all used colors + - figsize - size of the interactive plotting figure + +- **Context:** + - Used to define a list of coordinates of interest. + - +- **Example use:** + - (pcv.roi.multi) + - (pcv.roi.custom) + + +```python +import plantcv.plantcv as pcv +import plantcv.annotate as an + +# Create an instance of the Points class +marker = an.Points(img=img, figsize=(12,6)) + +# Click on the plotted image to collect coordinates + +# Use the identified coordinates to create a custom polygon ROI +roi = pcv.roi.custom(img=img, vertices=marker.coords['default']) + +``` + + +**Source Code:** [Here](https://github.com/danforthcenter/plantcv-annotate/blob/main/plantcv/annoate/classes.py) diff --git a/docs/changelog.md b/docs/changelog.md new file mode 100644 index 0000000..820a7f1 --- /dev/null +++ b/docs/changelog.md @@ -0,0 +1,3 @@ +## Changelog + +All notable changes to this project will be documented below. diff --git a/docs/documentation.md b/docs/documentation.md new file mode 100644 index 0000000..ed43a4e --- /dev/null +++ b/docs/documentation.md @@ -0,0 +1,19 @@ +## Documentation + +PlantCV documentation is hosted on [Read the Docs](https://readthedocs.org/). +Using Read the Docs allows the documentation to be versioned along with +the code. Because Read the Docs supports static content build tools like +[Mkdocs](http://www.mkdocs.org/), documentation can be written in simple +Markdown format that will be built into HTML automatically whenever a +new version of code is pushed to the PlantCV GitHub repository. + +### Updating PlantCV documentation + +Follow the [installation guide](installation.md#installing-plantcv-for-contributors) to learn how clone a copy of the PlantCV-Annotate +repository. Then see the main PlantCV [contribution guide](https://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) for an overview on how to edit files, and generate a `pull` request to merge your updates. +Changes to PlantCV-Annotate should be done in a branch, and pull against the +`main` branch which corresponds to the `latest` version of the documentation on Read the Docs. + +PlantCV-Annotate is an add-on package to compliment functionality of +[PlantCV](https://plantcv.org) so please refer to the +[updating guide here](https://plantcv.readthedocs.io/en/latest/documentation/). diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..d61d74a --- /dev/null +++ b/docs/index.md @@ -0,0 +1,26 @@ +# Welcome to the documentation for PlantCV-Annotate + +## Overview + +[PlantCV-annotate](https://github.com/danforthcenter/plantcv-annotate) is composed of modular functions in order to be applicable to a +variety of plant types and imaging systems. In the following documentation we will describe use of each function and +provide tutorials on how each function is used in the context of an overall image-processing workflow. Development of +PlantCV-Annotate is ongoing---we encourage input from the greater plant phenomics community. Please post questions and comments +on the [GitHub issues page](https://github.com/danforthcenter/plantcv-annotate/issues). + +## Getting started + +The documentation can be navigated using the sidebar table of contents. Documentation for individual PlantCV-Annotate functions +are listed under the headings "PlantCV Namespace". For general information on installation, +updating, and other questions, see: + +* [Installing PlantCV-Annotate](installation.md) + +## Contributing + +If you are interested in contributing to PlantCV-Annotate, please see: + +* [Contribution Guide](CONTRIBUTING.md) +* [Code of Conduct](CODE_OF_CONDUCT.md) + +[Return to the PlantCV homepage](https://plantcv.org) diff --git a/docs/installation.md b/docs/installation.md new file mode 100644 index 0000000..f9f52d0 --- /dev/null +++ b/docs/installation.md @@ -0,0 +1,27 @@ +## Installation + +### Table of contents +1. [Supported platforms and dependencies](#dependencies) +2. [Installing PlantCV for contributors](#contributors) + +### Supported platforms and dependencies +- Linux 64-bit, x86 processors +- macOS x86 (Intel) and M (ARM) processors +- Windows 64-bit, x86 processors + +PlantCV requires Python and these [Python packages](https://github.com/danforthcenter/plantcv/blob/main/requirements.txt). +Additionally, we recommend installing [JupyterLab](https://jupyter.org/). + +### Installing PlantCV for contributors +Before getting started, please read our [contributor guidelines](CONTRIBUTING.md) and [code of conduct](CODE_OF_CONDUCT.md). + +You can follow the [PlantCV Installation for Contributors Guide](https://plantcv.readthedocs.io/en/latest/installation/#contributors) and then continue with the instructions below to add PlantCV-Annotate to +your development environment. + +```bash +# Activate the plantcv environment (you will have to do this each time you start a new session) +conda activate plantcv +# Install plantcv-annotate in editable mode so that it updates as you work on new features/updates +pip install plantcv-annotate +pip install -e . +``` diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..59fde8e --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1 @@ +mkdocs>1 diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..7d71deb --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,24 @@ +site_name: PlantCV-annotate +site_url: https://plantcv-annotate.readthedocs.io/ +site_description: Plant phenotyping annotation using computer vision +site_author: PlantCV Development Team +repo_url: https://github.com/danforthcenter/plantcv-annotate +copyright: Copyright 2024, Donald Danforth Plant Science Center +theme: readthedocs + +nav: +- Home: index.md +- Documentation: + - 'Installation': installation.md + - 'Change Log': changelog.md + - 'Contributing': + - 'Contributing Guide': CONTRIBUTING.md + - 'Code of Conduct': CODE_OF_CONDUCT.md + - 'Adding/Editing Documentation': documentation.md + - 'PlantCV Namespace': + - 'Annotation Tools': + - Points: Points.md +markdown_extensions: + - toc: + permalink: True + - admonition