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‎.readthedocs.yaml

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build:
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os: "ubuntu-22.04"
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tools:
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python: "3.8"
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python: "3.9"
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# Build documentation in the "docs/" directory with Sphinx
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sphinx:

‎README.md

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[![Documentation Status](https://readthedocs.org/projects/pystages/badge/?version=latest)](https://pystages.readthedocs.io/en/latest/?badge=latest)
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# PyStages
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[![Documentation Status](https://readthedocs.org/projects/pystages/badge/?version=latest)](https://pystages.readthedocs.io/en/latest/?badge=latest)
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PyStages is a Python 3 library for controlling motorized stages which have a
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motion controller. It has been designed for microscopy test benches automation.
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- Tic Stepper Motor controller (USB only)
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- CNC Router with GRBL/GCode instructions (CNC 3018-PRO)
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The library also provides helper classes for basic vector manipulation and
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autofocus calculation
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The library also provides helper classes for basic vector manipulation and
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autofocus computation.
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## Documentation
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Documentation is available on [Read the Docs](https://pystages.readthedocs.io).
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## PyStages GUI
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A user interface has been implemented to control the stages.
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You can run it with the following command:
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```bash
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python -m pystages.gui
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```
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## Requirements
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This library requires the following packages:
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- [pyserial](https://pypi.org/project/pyserial/)
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- [numpy](https://pypi.org/project/numpy/)
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- [pyusb](https://pypi.org/project/pyusb/)
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- [PyQt6](https://pypi.org/project/PyQt6/)
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- [PyQt6](https://pypi.org/project/PyQt6/)

‎docs/api.rst

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.. automodule:: pystages
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:members:
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.. autoclass:: Autofocus
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:members:
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.. .. autoclass:: Autofocus
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.. :members:
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.. autoclass:: Vector
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:special-members: __init__
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:members:
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.. .. autoclass:: Vector
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.. :special-members: __init__
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.. :members:
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‎docs/conf.py

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# -- Project information -----------------------------------------------------
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project = "pystages"
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copyright = "2022, Olivier Hériveaux, Manuel San Pedro, Michaël Mouchous"
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copyright = "2024, Olivier Hériveaux, Manuel San Pedro, Michaël Mouchous"
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author = "Olivier Hériveaux, Manuel San Pedro, Michaël Mouchous"
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# The full version, including alpha/beta/rc tags
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release = "1.1"
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release = "1.1.1"
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = ["sphinx.ext.autodoc"]
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extensions = ["sphinx.ext.autodoc", "myst_parser"]
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ["_templates"]
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html_static_path = []
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html_logo = "logo.png"
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source_suffix = {
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".rst": "restructuredtext",
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".md": "markdown",
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}

‎docs/gui.md

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# PyStages GUI
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A user interface has been implemented to control the stages.
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You can run it with the following command:
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```bash
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python -m pystages.gui
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```
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This tool presents basic controls. After connection to the stage, it polls the position and prints out
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at the bottom of the window.
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## Stage selection and connection
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Select the type of stage that you want to control and chose either a serial port to connect to, or select `Auto detect`
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to make pystage to select the correct one according to the device description.
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Then click to `Connect`. If the connection success, the control buttons are activated.
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## Relative move
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You can click on buttons to move for a positive of negative relative distance.
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The direction correspond to the axis number of the stage (`X` for first axe, `Y` for the second one,
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`Z` for the third one). The moving distance is selected throug the `Step` dropdown menu.
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## Absolute move
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You can enter absolute coordinates in the 3 entry boxes and trigger the move by clicking the `Go To Position` button.
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## Z offset
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The `Z offset` checkbox and dropdown menu permit for each horizontal move (X or Y)
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to make first a vertical-up displacement (Z+) followed by the
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actual move, and then a final vertical-down displacement (Z-).
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## Homing
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The `Home` button permits to trigger the calibration process of the stage.
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Be careful that your setup is clear before using it.
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‎docs/index.rst

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.. pystages documentation master file, created by
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sphinx-quickstart on Tue Jul 7 15:03:18 2020.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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Welcome to pystages's documentation!
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====================================
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(:class:`pystages.Autofocus`).
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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Vectors <vectors.rst>
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Autofocus <autofocus.rst>
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Python API <api.rst>
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Troubleshooting <troubleshooting.rst>
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:maxdepth: 2
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:caption: Contents:
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Vectors <vectors.rst>
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Autofocus <autofocus.rst>
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Python API <api.rst>
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GUI <gui.md>
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Troubleshooting <troubleshooting.rst>
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Indices and tables

‎docs/requirements.txt

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numpy
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sphinx
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sphinx-rtd-theme
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myst-parser

‎pyproject.toml

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]
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description = "Motorized stage control library for scientific applications"
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readme = "README.md"
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requires-python = ">=3.8"
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requires-python = ">=3.9"
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classifiers = [
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"Programming Language :: Python :: 3",
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"License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",

‎pystages/cncrouter.py

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class CNCStatus(str, Enum):
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"""
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Possible statuses that the CNC can report.
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"""
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IDLE = "Idle"
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RUN = "Run"
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HOLD = "Hold"

‎pystages/gui/gui.py

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self.go_z = w = QLineEdit()
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box.addWidget(w)
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w = QPushButton("Got to position")
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w = QPushButton("Go to position")
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w.clicked.connect(self.go_to_position)
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self.controls.append(w)
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box.addWidget(w)

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