WIP: Reorganization repository

.github/workflows/publish.yml

@@ -0,0 +1,34 @@
+name: Publish to PyPI
+
+on:
+  workflow_dispatch:
+    # Optional inputs, you can add more according to your needs
+    inputs:
+      # version:
+      #   description: 'Version of the package to release'
+      #   required: true
+      #   default: '1.0.0'
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v2
+
+    # Add steps for any necessary setup, like installing dependencies
+    - name: Build
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install -U twine
+        python -m pip install -U wheel
+        python3 -m pip install build==1.0.3 # pin build
+        rm -rf ./build
+        rm -rf ./dist/*
+        python3 -m build
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -1,3 +1,175 @@
-.DS_Store
-*.pyc 
-*.xml
+cache_config_file_path.txt
+channel_configurations.xml
+last_coords.txt
+log.txt
+cache/
+.vscode
+chat_logs/
+docs/test.html
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+
+bioimageio_authorized_users.json
+.vscode/extensions.json
+.vscode/launch.json
+.vscode/settings.json

MANIFEST.in

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+include squid_control/icon/*
+include squid_control/images/*
+include squid_control/control/*
+include squid_control/configurations/*
+

README.md

@@ -1,39 +1,54 @@
-# Squid (formerly octopi-research)
+# Squid Control
 
-![alt text](https://i.imgur.com/Gjwh02y.png)
+The Squid Control software is a Python package that provides a simple interface to control the Squid microscope. The software is designed to be used with the Squid microscope (made by Cephla Inc.).
 
-## Introduction
-Squid (Simplifying Quantitive Imaging Development and Deployment) provides a full suite of hardware and software components for rapidly configuring high-performance microscopes tailored to users' applications with reduced cost, effort and turnaround time. Besides increasing accessibility of research microscopes and available microscope hours to labs, it is also designed to simplify development and dissemination of new or otherwise advanced microscopy techniques.
+## Installation and Usage
 
-Applications include
-- slide scanner for digital pathology
-- time lapse imaging with 2D or 3D tiling
-- spatial omics that involves multicolor and multi-round imaging
-- tracking microscopy
-- computational microscopy, including label free microscopy using phase/polarization/reflectance + deep learning
-- super resolution microscopy
-- light sheet microscopy
+See the [installation guide](./docs/installation.md) for instructions on how to install and use the software.
 
-## Assets
-- main software repo: [GitHub](https://github.com/hongquanli/octopi-research) (this repo)
-- tracking software repo: [GitHub](https://github.com/prakashlab/squid-tracking)
-- CAD models/photos of assembled squids: [Google Drive](https://drive.google.com/drive/folders/1JdVp34HtERGpBCBlFX6jFDwMUdeBLCEx?usp=sharing)
-- BOM for the microscope, including CAD files for CNC machining: [link](https://docs.google.com/spreadsheets/d/1WA64HySj9I7XROtTXuaRvjlbhHXRGspvoxb_20CWDR8/edit?usp=drivesdk)
-- BOM for the multicolor laser engine: [link](https://docs.google.com/spreadsheets/d/1hEM6PsxZPTp1LY3cpxUJOS3Q1YLQN-xniF33ZddFj9U/edit#gid=1175873468)
-- BOM for the control panel: [link](https://docs.google.com/spreadsheets/d/1z2HjibIG9PHffiDsbuzQXmvf2gSFMduHrXkPwDbcXRY/edit?usp=sharing)
+### Usage
 
-## Eearly Results, Related Work and Possible Applications
-Refer to our website: www.squid-imaging.org
+To run the software, use the following command:
+```
+python -m squid_control --config HCS_v2
+```
 
-## References
-[1] Hongquan Li, Deepak Krishnamurthy, Ethan Li, Pranav Vyas, Nibha Akireddy, Chew Chai, Manu Prakash, "**Squid: Simplifying Quantitative Imaging Platform Development and Deployment**." BiorXiv [ link | [website](https://squid-imaging.org)]
+If you want to use a different configuration file, you can specify the path to the configuration file:
+```
+python -m squid_control --config /home/user/configuration_HCS_v2.ini
+```
 
-For scale-free vertical tracking microscopy, check out our work at:
+To start simulation mode, use the following command:
+```
+python -m squid_control --config HCS_v2 --simulation
+```
 
-[2] Deepak Krishnamurthy, Hongquan Li, François Benoit du Rey, Pierre Cambournac, Adam G. Larson, Ethan Li, and Manu Prakash. "**Scale-free vertical tracking microscopy.**" Nature Methods 17, no. 10 (2020): 1040-1051. [ [link](https://www.nature.com/articles/s41592-020-0924-7) | [website](https://gravitymachine.org) ]
+To load a custom multipoint function:
+```
+python -m squid_control --config HCS_v2 --simulation --multipoint-function=./my_multipoint_custom_script_entry.py:multipoint_custom_script_entry
+```
 
-## Acknowledgement
-The Squid software was developed with structuring inspiration from [Tempesta-RedSTED](https://github.com/jonatanalvelid/Tempesta-RedSTED). The laser engine is inspired by [https://github.com/ries-lab/LaserEngine](https://github.com/ries-lab/LaserEngine). 
+## About
+
+<img style="width:60px;" src="./docs/assets/cephla_logo.svg"> Cephla Inc. 
+
+
+
+
+## Note
+
+The current branch is a frok from https://github.com/hongquanli/octopi-research/ at the following commit:
+```
+commit dbb49fc314d82d8099d5e509c0e1ad9a919245c9 (HEAD -> master, origin/master, origin/HEAD)
+Author: Hongquan Li <hqlisu@gmail.com>
+Date:   Thu Apr 4 18:07:51 2024 -0700
+
+    add laser af characterization mode for saving images from laser af camera
+```
+
+How to make pypi work:
+ - Register on pypi.org
+ - Create a new token in the account settings
+ - In the repository setting, create a new secret called `PYPI_API_TOKEN` and paste the token in the value field
+ - Then, if you want to manually publish a new pypi package, go to actions, select the `Publish to PyPi` workflow, and click on `Run workflow`.
 
-## Software Instructions
-The microscope is controled by an Arduino Due and a computer running Ubuntu. The computer can be one of the Nvidia Jetson platforms (e.g. Jetson Nano, Jetson Xavier NX) or a regular laptop/workstation. Instructions for using the firmware and software can be found in the respective folders.

docs/_sidebar.md

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+ * [Home](/)

docs/home.md

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+# Squid Control