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

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

.. java:import:: ch.epfl.leb.defcon.predictors Predictor

.. java:import:: ch.epfl.leb.defcon.predictors SessionClosedException

.. java:import:: ch.epfl.leb.defcon.predictors ImageBitDepthException

.. java:import:: ch.epfl.leb.defcon.predictors NoLocalCountMapException

.. java:import:: ch.epfl.leb.defcon.predictors UninitializedPredictorException

.. java:import:: ch.epfl.leb.defcon.predictors.internal DefaultPredictor

.. java:import:: ij.gui Roi

.. java:import:: ij ImagePlus

.. java:import:: ij.process ShortProcessor

.. java:import:: java.util List

.. java:import:: java.util ArrayList

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

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

Defcon
======

.. java:package:: ch.epfl.leb.alica.acpack.analyzers.defcon
   :noindex:

.. java:type:: public class Defcon implements Analyzer

   A fluorescent spot counter derived from the DEFCoN package.

   :author: Kyle M. Douglass

   **See also:** \ `DEFCoN-ImageJ <https://github.com/LEB-EPFL/DEFCoN-ImageJ>`_\

Constructors
------------
Defcon
^^^^^^

.. java:constructor:: public Defcon(String pathToModel)
   :outertype: Defcon

   Initializes the DEFCoN analyzer.

   :param pathToModel: The path to the DEFCoN network model.

Methods
-------
dispose
^^^^^^^

.. java:method:: @Override public void dispose()
   :outertype: Defcon

   Cleans up the analyzer when it's finished.

finalize
^^^^^^^^

.. java:method:: @Override protected void finalize() throws Throwable
   :outertype: Defcon

   Failsafe in case the predictor has not been closed at the point of garbage collection.

   :throws java.lang.Throwable:

getBatchOutput
^^^^^^^^^^^^^^

.. java:method:: @Override public double getBatchOutput()
   :outertype: Defcon

   Returns the averaged DEFCoN count value since the last call. Double.NaN is returned if there is no new count since the previous call.

   :return: The averaged DEFCoN count.

getBoxSize
^^^^^^^^^^

.. java:method:: public int getBoxSize()
   :outertype: Defcon

   Returns the current square kernel size for maximum local counts.

   :return: The kernel size for computing the maximum local count.

getIntermittentOutput
^^^^^^^^^^^^^^^^^^^^^

.. java:method:: @Override public double getIntermittentOutput()
   :outertype: Defcon

   Returns the intermittent output of the analyzer.

   :return: The analyzer's current output value.

getName
^^^^^^^

.. java:method:: @Override public String getName()
   :outertype: Defcon

   Returns the name of the DEFCoN analyzer.

   :return: The name of the DEFCoN analyzer.

getShortReturnDescription
^^^^^^^^^^^^^^^^^^^^^^^^^

.. java:method:: @Override public String getShortReturnDescription()
   :outertype: Defcon

   Returns a short description of the values returned by the DEFCoN analyzer.

   :return: A short description of the values returned by the DEFCoN analyzer.

getStatusPanel
^^^^^^^^^^^^^^

.. java:method:: @Override public AnalyzerStatusPanel getStatusPanel()
   :outertype: Defcon

   Returns the analyzer's status panel that will be displayed in the GUI. If no panel is implemented, this method should return null. In this case, the corresponding space in the MonitorGUI will appear blank.

   :return: The status panel of the DEFCoN analyzer or null.

isLiveModeOn
^^^^^^^^^^^^

.. java:method:: public boolean isLiveModeOn()
   :outertype: Defcon

   True if live mode is on, false otherwise.

   :return: True if live mode is on, false otherwise

isMaxLocalCount
^^^^^^^^^^^^^^^

.. java:method:: public boolean isMaxLocalCount()
   :outertype: Defcon

   True if the analyzer is computing the maximum local count.

   :return: True if the analyzer is computing the maximum local count.

liveModeOff
^^^^^^^^^^^

.. java:method:: public void liveModeOff()
   :outertype: Defcon

   Turns off the live view of the density map.

liveModeOn
^^^^^^^^^^

.. java:method:: public void liveModeOn()
   :outertype: Defcon

   Turns on the live view of the density map.

maxLocalCountOff
^^^^^^^^^^^^^^^^

.. java:method:: public void maxLocalCountOff()
   :outertype: Defcon

   Turns off the live view of the density map.

maxLocalCountOn
^^^^^^^^^^^^^^^

.. java:method:: public void maxLocalCountOn()
   :outertype: Defcon

   Turns on the live view of the density map.

processImage
^^^^^^^^^^^^

.. java:method:: @Override public void processImage(Object image, int width, int height, double pixelSizeUm, long timeMs)
   :outertype: Defcon

   Processes an image and adjusts the analyzer's internal state to reflect the results of the calculation. This method is called after each new image acquisition by the AnalysisWorker. You can use the synchronized(this) statement within the body of an implementation of an Analyzer to ensure that no output readout happens during code execution.

   :param image: The image to be processed as 1D raw pixel data.
   :param width: Image width in pixels.
   :param height: Image height in pixels.
   :param pixelSizeUm: Length of a side of a square pixel in micrometers.
   :param timeMs: Image acquisition time in milliseconds.

setBoxSize
^^^^^^^^^^

.. java:method:: public void setBoxSize(int boxSize)
   :outertype: Defcon

   Sets the square kernel size for computing the maximum local count.

   :param boxSize: The kernel size for computing the maximum local count.

setROI
^^^^^^

.. java:method:: @Override public void setROI(Roi roi)
   :outertype: Defcon

updateLiveView
^^^^^^^^^^^^^^

.. java:method:: public void updateLiveView()
   :outertype: Defcon

   Updates the live viewer.