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.. _plugin:
====================
Plugin Architecture
====================
**navigate** is designed with extensibility. Users can seamlessly integrate custom GUI plugins, device plugins, new feature plugins, and even define specific acquisition modes.
-------------------------------------
Introduction to Plugins
########################
The **navigate** **plugin system** gives users the flexibility to extend its functionality according to their specific needs. **navigate** will load plugins automatically and users can use their plugins with **navigate** seamlessly.
-----------
Installing a Plugin
####################
Once you've built a plugin or downloaded a **navigate** plugin, you can easily install it. Here, we have downloaded the `Navigate Confocal-Projection Plugin <https://github.com/TheDeanLab/navigate-confocal-projection>`_.
#. You can install the **navigate-confocal-projection** plugin by selecting the menu :menuselection:`Plugins --> Install Plugin`.
.. image:: images/plugin_1.png
:width: 60%
:align: center
#. Select the folder `ConfocalProjectionPlugin` and click :guilabel:`Select`.
.. image:: images/plugin_2.png
:width: 60%
:align: center
#. You should receive a message indicating that the plugin has been installed successfully.
.. image:: images/plugin_3.png
:width: 60%
:align: center
#. Restart **navigate** to use this installed plugin.
-----------
Uninstalling a Plugin
#####################
Uninstalling a plugin is very easy.
#. Select :menuselection:`Plugins --> Uninstall Plugins`. This will open a popup window where you can see all of the currently installed plugins.
.. image:: images/plugin_4.png
:width: 60%
:align: center
#. Select the plugin you want to uninstall.
.. image:: images/plugin_5.png
:width: 60%
:align: center
#. Click :guilabel:`Uninstall`.
.. image:: images/plugin_6.png
:width: 60%
:align: center
#. Restart **navigate** to fully remove the uninstalled plugin.
-------------------------------------
Designing a Plugin
##########################
Using a Plugin Template
-------------------------------------
A comprehensive **plugin template** is provided. Users could download the **plugin template** from `github <https://github.com/TheDeanLab/navigate-plugin-template>`_ and build plugins on it.
Plugin Structure:
.. code-block:: none
plugin_name/
├── controller/
│ ├── plugin_name_controller.py
│ ├── ...
├── model/
│ ├── devices/
│ │ └── plugin_device/
│ │ ├── device_startup_functions.py
│ │ ├── plugin_device.py
│ │ └── synthetic_plugin_device.py
│ └── features/
│ ├── plugin_feature.py
│ ├── ...
│
├── view/
│ ├── plugin_name_frame.py
│ ├── ...
│
├── feature_list.py
├── plugin_acquisition_mode.py
└── plugin_config.yml
.. note::
The template shows a plugin with GUI, device, feature, feature_list and acquisition mode. If your plugin only incorporates some of these components, you should remove unused folders and files.
-------------------------------------
Plugin Configuration
--------------------
There should always have a ``plugin_config.yml`` file under the plugin folder, which tells **navigate** the plugin name, the GUI as a Tab or Popup and custom acquisition mode name. A typical plugin config is:
.. code-block:: none
name: Plugin Name
view: Popup # or Tab
acquisition_modes:
- name: Plugin Acquisition
file_name: plugin_acquisition_mode.py
-------------------------------------
Plugin GUI Elements
--------------------
**navigate** supports plugins with their own GUIs. A custom plugin GUI can be integrated as a tab or a popup. Users should specify a view option in ``plugin_config.yml``. If it is a popup, users can find the plugin under the :guilabel:`Plugins` menu in the **navigate** window. If it is a tab, it will appear next to the :ref:`Settings Notebooks <ui_settings_notebooks>`.
When creating a new plugin with a GUI, ensure that the plugin name is consistent with the naming conventions for the associated Python files (``plugin_name_controller.py`` and ``plugin_name_frame.py``). Both Python filenames should be in lowercase.
For example, if your plugin is named "My Plugin" (there is a space in between), the associated Python files should be named: ``my_plugin_frame.py`` and ``my_plugin_controller.py``.
-------------------------------------
Plugin Devices
------------------
The **navigate** plugin architecture allows you to integrate new hardware device. There can be more than one device inside a plugin. If they are different kinds of device, please put them into different folders. For each kind of device, there should be a ``device_startup_functions.py`` telling **navigate** how to start the device and indicating the reference name of the device to be used in ``configuration.yaml``.
Device type name and reference name are given as following:
.. code-block:: python
DEVICE_TYPE_NAME = "plugin_device" # Same as in configuration.yaml, for example "stage", "filter_wheel", "remote_focus_device"...
DEVICE_REF_LIST = ["type", "serial_number"]
A function to load the device connection should be given,
.. code-block:: python
def load_device(hardware_configuration, is_synthetic=False):
# ...
return device_connection
A function to start the device should be given,
.. code-block:: python
def start_device(microscope_name, device_connection, configuration, is_synthetic=False):
# ...
return device_object
The template for ``device_startup_functions.py`` can be found in the `plugin template <https://github.com/TheDeanLab/navigate-plugin-template/blob/main/plugins_template/model/devices/plugin_device/device_startup_functions.py>`_.
-------------------------------------
Plugin Features
-------------------------
**navigate** allows users to add new features. New feature objects and feature lists can each be a plugin or components of a plugin. Features and feature lists are automatically loaded into **navigate**.
Please visit `here <https://thedeanlab.github.io/navigate/contributing/feature_container.html>`_ for details about how to build a new feature object and feature list.
-------------------------------------
Custom Acquisition Modes
------------------------
Navigate offers seamless support for custom acquisition modes, and registering a new mode is straightforward.
1. Download the template for `plugin_acquisition_mode.py <https://github.com/TheDeanLab/navigate-plugin-template/blob/main/plugins_template/plugin_acquisition_mode.py>`_
2. Update the ``feature_list``.
.. code-block:: python
@AcquisitionMode
class PluginAcquisitionMode:
def __init__(self, name):
self.acquisition_mode = name
self.feature_list = [
# update here
]
3. Update the functions.
Users should tell **navigate** what to do before and after acquisition using the following functions.
.. code-block:: python
def prepare_acquisition_controller(self, controller):
# update here
def end_acquisition_controller(self, controller):
# update here
def prepare_acquisition_model(self, model):
# update here
def end_acquisition_model(self, model):
# update here
4. Register the acquisition mode in ``plugin_config.yml``.
.. code-block:: none
acquisition_modes:
- name: Custom Acquisition
file_name: plugin_acquisition_mode.py
-----------
For more plugin examples, please visit the plugins in the table of contents menu on the left.