.. java:import:: ch.epfl.leb.alica.interfaces.analyzers AnalyzerFactory

.. java:import:: ch.epfl.leb.alica.workers Coordinator

.. java:import:: ch.epfl.leb.alica.interfaces.controllers ControllerFactory

.. java:import:: ch.epfl.leb.alica.lasers LaserFactory

.. java:import:: ij.gui Roi

.. java:import:: mmcorej StrVector

.. java:import:: org.micromanager Studio

AlicaCore
=========

.. java:package:: ch.epfl.leb.alica
   :noindex:

.. java:type:: public final class AlicaCore

   The core's settings are controlled by MainGUI, and the Core then produces products from its factories, and initializes the Coordinator, and later terminates it.

   :author: stefko

Methods
-------
getAnalyzerFactory
^^^^^^^^^^^^^^^^^^

.. java:method:: public AnalyzerFactory getAnalyzerFactory()
   :outertype: AlicaCore

   :return: AnalyzerFactory

getControllerFactory
^^^^^^^^^^^^^^^^^^^^

.. java:method:: public ControllerFactory getControllerFactory()
   :outertype: AlicaCore

   :return: ControllerFactory

getInstance
^^^^^^^^^^^

.. java:method:: public static AlicaCore getInstance()
   :outertype: AlicaCore

   Returns the singleton instance, or an exception if it was not yet initialized

   :return: the singleton instance of the core

getLaserFactory
^^^^^^^^^^^^^^^

.. java:method:: public LaserFactory getLaserFactory()
   :outertype: AlicaCore

   :return: LaserFactory

initialize
^^^^^^^^^^

.. java:method:: public static AlicaCore initialize(Studio studio) throws AlreadyInitializedException
   :outertype: AlicaCore

   Initialize the Singleton core

   :param studio: MicroManager studio
   :throws AlreadyInitializedException: if it was already initialized
   :return: the singleton instance of the core

isCoordinatorRunning
^^^^^^^^^^^^^^^^^^^^

.. java:method:: public boolean isCoordinatorRunning()
   :outertype: AlicaCore

   Checks if the stop flag of the coordinator was set.

   :return: true if coordinator's stop flag was set, or if coordinator is null

printLoadedDevices
^^^^^^^^^^^^^^^^^^

.. java:method:: public void printLoadedDevices()
   :outertype: AlicaCore

   Print all loaded devices in the MMCore to the log.

setControlWorkerTickRate
^^^^^^^^^^^^^^^^^^^^^^^^

.. java:method:: public void setControlWorkerTickRate(int controller_tick_rate_ms)
   :outertype: AlicaCore

   Sets the tick rate for the controller.

   :param controller_tick_rate_ms: delay between two runs of the ControlTask

setCurrentROI
^^^^^^^^^^^^^

.. java:method:: public boolean setCurrentROI()
   :outertype: AlicaCore

   Sets currently selected ROI to the analyzer when it is initialized

   :return: true if ROI is set, false if no ROI is set

setLaserPowerDeadzone
^^^^^^^^^^^^^^^^^^^^^

.. java:method:: public void setLaserPowerDeadzone(double laser_power_deadzone)
   :outertype: AlicaCore

   Sets the deadzone of change of laser power output. For example, if set to 0.1, the laser would ignore requests for change of power that would be different by less than 10% from current output power.

   :param laser_power_deadzone: deadzone size (NOT in percent)

setLaserVirtual
^^^^^^^^^^^^^^^

.. java:method:: public void setLaserVirtual(boolean is_laser_virtual)
   :outertype: AlicaCore

   Inform factories that the laser should only display its output, not really communicate with the hardware.

   :param is_laser_virtual: true if virtual, false if real

setMaxLaserPower
^^^^^^^^^^^^^^^^

.. java:method:: public void setMaxLaserPower(double max_laser_power)
   :outertype: AlicaCore

   Inform factories of maximal laser power value.

   :param max_laser_power: maximal laser power value

startWorkers
^^^^^^^^^^^^

.. java:method:: public void startWorkers(ImagingMode imaging_mode)
   :outertype: AlicaCore

   Builds products from their factories using current settings, and starts the Coordinator (analysis is started)

   :param imaging_mode:

stopWorkers
^^^^^^^^^^^

.. java:method:: public void stopWorkers()
   :outertype: AlicaCore

   Requests the coordinator to stop and then waits for it to join.