avidaq 0.0.5

Description:

avidaq 0.0.5

avidaq





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:

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.

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

To run unit tests
pytest
typical workflow

edit code in /src
run napari -w avidaq
repeat

Releasing to pypi
Project is automically built and deployed to pypi upon

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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