.. java:import:: ch.epfl.leb.sass.utils.images ImageS

.. java:import:: ch.epfl.leb.sass.utils.images.internal DefaultImageS

.. java:import:: ch.epfl.leb.sass.models.fluorophores.internal DefaultFluorophore

.. java:import:: ch.epfl.leb.sass.utils RNG

.. java:import:: ch.epfl.leb.sass.models.obstructors Obstructor

.. java:import:: cern.jet.random Gamma

.. java:import:: cern.jet.random Normal

.. java:import:: ch.epfl.leb.sass.models.fluorophores.internal.dynamics FluorophoreDynamicsBuilder

.. java:import:: ch.epfl.leb.sass.models.fluorophores.internal.dynamics FluorophoreDynamics

.. java:import:: ch.epfl.leb.sass.models.fluorophores.internal.commands FluorophoreCommandBuilder

.. java:import:: ch.epfl.leb.sass.models.fluorophores.internal.commands FluorophoreCommand

.. java:import:: ch.epfl.leb.sass.models.components Camera

.. java:import:: ch.epfl.leb.sass.models.components Laser

.. java:import:: ch.epfl.leb.sass.models.components Objective

.. java:import:: ch.epfl.leb.sass.models.components Stage

.. java:import:: ch.epfl.leb.sass.models.psfs PSFBuilder

.. java:import:: ch.epfl.leb.sass.models.obstructors.internal.commands ObstructorCommandBuilder

.. java:import:: ch.epfl.leb.sass.models.obstructors.internal.commands ObstructorCommand

.. java:import:: ch.epfl.leb.sass.models.backgrounds BackgroundCommandBuilder

.. java:import:: ch.epfl.leb.sass.models.backgrounds BackgroundCommand

.. java:import:: java.util Arrays

.. java:import:: java.util List

.. java:import:: cern.jet.random Poisson

Microscope
==========

.. java:package:: ch.epfl.leb.sass.models
   :noindex:

.. java:type:: public class Microscope

   Integrates all the components into one microscope.

Constructors
------------
Microscope
^^^^^^^^^^

.. java:constructor:: public Microscope(Camera.Builder cameraBuilder, Laser.Builder laserBuilder, Objective.Builder objectiveBuilder, PSFBuilder psfBuilder, Stage.Builder stageBuilder, FluorophoreCommandBuilder positionBuilder, FluorophoreDynamicsBuilder fluorDynamicsBuilder, ObstructorCommandBuilder obstructorBuilder, BackgroundCommandBuilder backgroundBuilder)
   :outertype: Microscope

   Initializes the microscope for simulations.

   :param cameraBuilder:
   :param laserBuilder:
   :param objectiveBuilder:
   :param psfBuilder:
   :param stageBuilder:
   :param positionBuilder: Positions fluorophore's within the field of view.
   :param fluorDynamicsBuilder:
   :param obstructorBuilder: Creates the obstructors, e.g. fiducials.
   :param backgroundBuilder: Creates the background signal on the image.

Methods
-------
getFovSize
^^^^^^^^^^

.. java:method:: public double getFovSize()
   :outertype: Microscope

   :return: size of current FOV in square micrometers

getLaserPower
^^^^^^^^^^^^^

.. java:method:: public double getLaserPower()
   :outertype: Microscope

   Return current power of the laser.

   :return: laser power

getObjectSpacePixelSize
^^^^^^^^^^^^^^^^^^^^^^^

.. java:method:: public double getObjectSpacePixelSize()
   :outertype: Microscope

   The size of a pixel after division by the objective magnification.

   :return: Length of one pixel side in object space units

getOnEmitterCount
^^^^^^^^^^^^^^^^^

.. java:method:: public double getOnEmitterCount()
   :outertype: Microscope

   Returns the number of currently active emitters.

   :return: number of shining emitters

getResolution
^^^^^^^^^^^^^

.. java:method:: public int[] getResolution()
   :outertype: Microscope

   Return the number of camera pixels in x and y.

   :return: 2D array with number of pixels in x and y.

setLaserPower
^^^^^^^^^^^^^

.. java:method:: public void setLaserPower(double laserPower)
   :outertype: Microscope

   Modifies the laser power to desired value.

   :param laserPower: new laser power

simulateFrame
^^^^^^^^^^^^^

.. java:method:: public ImageS simulateFrame()
   :outertype: Microscope

   Generates a new frame and moves the device state forward. First the obstructors are drawn on the frame, then the fluorophores, and finally noise.

   :return: simulated frame