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

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

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

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

.. 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.psfs PSFBuilder

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

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

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

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

.. java:import:: ch.epfl.leb.sass.models.components.internal DefaultStage

.. java:import:: ch.epfl.leb.sass.models.components.internal DefaultLaser

.. java:import:: ch.epfl.leb.sass.models.components.internal DefaultCamera

.. java:import:: ch.epfl.leb.sass.models.components.internal DefaultObjective

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

.. java:import:: ch.epfl.leb.sass.models.fluorophores Fluorophore

.. java:import:: ch.epfl.leb.sass.models.illuminations Illumination

.. java:import:: ch.epfl.leb.sass.models.illuminations IlluminationBuilder

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

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

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

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

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

.. java:import:: ch.epfl.leb.sass.models.photophysics FluorophoreDynamics

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

.. java:import:: ch.epfl.leb.sass.models.photophysics FluorophoreDynamicsBuilder

.. java:import:: java.util List

.. java:import:: java.util Arrays

.. java:import:: java.io Serializable

.. java:import:: com.google.gson JsonArray

.. java:import:: com.google.gson JsonElement

Microscope
==========

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

.. java:type:: public class Microscope implements Serializable

   Integrates all the components into one microscope.

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

.. java:constructor:: public Microscope(DefaultCamera.Builder cameraBuilder, DefaultLaser.Builder laserBuilder, DefaultObjective.Builder objectiveBuilder, PSFBuilder psfBuilder, DefaultStage.Builder stageBuilder, FluorophoreCommandBuilder fluorBuilder, FluorophoreDynamicsBuilder fluorDynamicsBuilder, ObstructorCommandBuilder obstructorBuilder, BackgroundCommandBuilder backgroundBuilder, IlluminationBuilder illuminationBuilder)
   :outertype: Microscope

   Initializes the microscope for simulations.

   :param cameraBuilder:
   :param laserBuilder:
   :param objectiveBuilder:
   :param psfBuilder:
   :param stageBuilder:
   :param fluorBuilder: 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.
   :param illuminationBuilder: Creates the illumination profile.

Methods
-------
getFluorophores
^^^^^^^^^^^^^^^

.. java:method:: public List<Fluorophore> getFluorophores()
   :outertype: Microscope

   Returns references to the fluorophores in the sample.

   :return: The sample's Fluorophore objects.

getFovSize
^^^^^^^^^^

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

   Returns the size of the field-of-view in object space units.

   :return: size of current FOV in object space units.

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: A simulated image of the next camera frame.

toJsonCamera
^^^^^^^^^^^^

.. java:method:: public JsonElement toJsonCamera()
   :outertype: Microscope

   Returns information about the camera.

   :return: A JsonElement containing information about the camera.

toJsonFluorescence
^^^^^^^^^^^^^^^^^^

.. java:method:: public JsonElement toJsonFluorescence()
   :outertype: Microscope

   Returns information about the sample fluorophores.

   :return: A JsonObject containing information about the fluorophores.

toJsonLaser
^^^^^^^^^^^

.. java:method:: public JsonElement toJsonLaser()
   :outertype: Microscope

   Returns information about the laser.

   :return: A JsonElement containing information about the laser.

toJsonObjective
^^^^^^^^^^^^^^^

.. java:method:: public JsonElement toJsonObjective()
   :outertype: Microscope

   Returns information about the objective.

   :return: A JsonElement containing information about the stage.

toJsonStage
^^^^^^^^^^^

.. java:method:: public JsonElement toJsonStage()
   :outertype: Microscope

   Returns information about the stage.

   :return: A JsonElement containing information about the stage.