avidaq

controls for napari and micromanger


    Authors:

    Learn more:

    • Documentation
    • Support site
    • Report issues

    Source code:

    • Information not submitted

    PyPI Python Version tests codecov napari hub

    controls for napari and micromanger


    This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

    Installation

    Standard installation

    You can install avidaq via pip:

    pip install napari[all] avidaq

    Install from plugin menu

    Alternatively you can install avidaq via the napari plugin menu:

    napari-add-plugin

    Running

    First start micromanager. Make sure the server port checkbox is activated.

    Then to start napari with the avidaq plugin active run: napari -w avidaq

    Updating presets

    MDA presets are stored in a json file in the user's home directory.

    
    `C:\\Users\YourName\.avidaq\mda_presets.json`

    This file should exist after plugin installation with some defaults. You do not need to create the file yourself.

    Add or modify the values and reload napari to see the changes.

    All parameter entries are optional, if not provided the default value will be used.

    The parameter names and their descriptions can be found [here] (https://github.com/micro-manager/pycro-manager/blob/main/pycromanager/acq_util.py#L102-L115)

    The format is as follows:

    {
        "gui_display_name": {
            "parameter_name": value,
            "parameter_name": value,
            ...
        },
        "gui_display_name": {
            "parameter_name": value,
            "parameter_name": value,
            ...
        },
        ...
    }

    defaults:

    {
      "Basic": {
        "num_time_points": 5,
        "z_start": 0,
        "z_end": 6,
        "z_step": 0.4
      },
      "Simple": {
        "num_time_points": 2,
        "z_start": 0,
        "z_end": 2,
        "z_step": 0.1
      },
      "Detailed": {
        "num_time_points": 10,
        "z_start": 0,
        "z_end": 12,
        "z_step": 0.2
      }
    }

    Issues

    If you encounter any problems, please [file an issue] along with a detailed description.

    Development

    You should have python3.8 or higher installed.

    1. clone this repo
    2. create a virtual environment python -m venv .venv && source .venv/bin/activate
    3. run pip install -e '.[testing,build]'
    4. run pre-commit install

    To run unit tests

    pytest

    typical workflow

    1. edit code in /src
    2. run napari -w avidaq
    3. repeat

    Releasing to pypi

    Project is automically built and deployed to pypi upon


    Version:

    • 0.0.4

    Release date:

    • 26 July 2022

    First released:

    • 21 July 2022

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    GitHub activity:

    • Stars: 0
    • Forks: 0
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

    • magicgui
    • numpy
    • pycromanager
    • qtpy

    Sign up to receive updates