.. java:import:: ch.epfl.leb.alica.interfaces Analyzer

.. java:import:: ch.epfl.leb.alica.interfaces Controller

.. java:import:: ch.epfl.leb.sass.models Microscope

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

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

.. java:import:: java.io File

.. java:import:: java.io FileNotFoundException

.. java:import:: java.io PrintWriter

.. java:import:: java.util HashMap

.. java:import:: java.util.logging Level

.. java:import:: java.util.logging Logger

.. java:import:: org.json JSONException

.. java:import:: org.json JSONObject

ImageJSimulator
===============

.. java:package:: ch.epfl.leb.sass.simulator.internal
   :noindex:

.. java:type:: public class ImageJSimulator extends DefaultSimulator

   The default simulator that is run as, for example, the ImageJ plugin.

   :author: Marcel Stefko

Fields
------
TIMEPERFRAME
^^^^^^^^^^^^

.. java:field:: protected final long TIMEPERFRAME
   :outertype: ImageJSimulator

   The time duration of each frame. This is here only for compatibility with ALICA's analyzers, which require a time argument.

analyzer
^^^^^^^^

.. java:field:: protected final Analyzer analyzer
   :outertype: ImageJSimulator

   Analyzer which analyzes generated images

controller
^^^^^^^^^^

.. java:field:: protected final Controller controller
   :outertype: ImageJSimulator

   Takes the output of a single analyzer, processes it, and outputs a signal to the generator, for feedback loop control.

history
^^^^^^^

.. java:field:: protected HashMap<Integer, JSONObject> history
   :outertype: ImageJSimulator

   Records of values of output of analyzer, controller.

image_count
^^^^^^^^^^^

.. java:field:: protected int image_count
   :outertype: ImageJSimulator

   Number of already-generated images.

Constructors
------------
ImageJSimulator
^^^^^^^^^^^^^^^

.. java:constructor:: public ImageJSimulator(Microscope microscope, Analyzer analyzer, Controller controller)
   :outertype: ImageJSimulator

   Initialize the simulator from user-specified components.

   :param microscope: The microscope to be simulated.
   :param analyzer: An analyzer for processing images from the microscope.
   :param controller: A controller that adjusts the state of the microscope.

Methods
-------
execute
^^^^^^^

.. java:method:: public ImageS execute(int no_of_images, int controller_refresh_rate, String csv_save_path, String tiff_save_path) throws ImageShapeException
   :outertype: ImageJSimulator

   An example simulation

   :param no_of_images:
   :param controller_refresh_rate:
   :param csv_save_path:
   :param tiff_save_path:

getImageCount
^^^^^^^^^^^^^

.. java:method:: @Override public int getImageCount()
   :outertype: ImageJSimulator

   Returns the number of generated images since simulation start.

   :return: number of generated images

incrementCounter
^^^^^^^^^^^^^^^^

.. java:method:: public void incrementCounter()
   :outertype: ImageJSimulator

   Increments image counter in case an image was generated outside of this class.

saveStack
^^^^^^^^^

.. java:method:: public void saveStack(File tiff_file)
   :outertype: ImageJSimulator

   Save current ImageStack to TIFF file

   :param tiff_file: file to save to

saveToCsv
^^^^^^^^^

.. java:method:: public void saveToCsv(File file)
   :outertype: ImageJSimulator

   Saves the data for generator, analyzer and controller for each frame into a .csv file

   :param file: destination csv file