.. java:import:: ij IJ

.. java:import:: java.io File

.. java:import:: java.io FileNotFoundException

.. java:import:: java.io PrintWriter

.. java:import:: java.util LinkedHashMap

.. java:import:: java.util LinkedHashSet

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

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

.. java:import:: javax.swing JFileChooser

.. java:import:: javax.swing.filechooser FileNameExtensionFilter

.. java:import:: org.micromanager LogManager

.. java:import:: org.micromanager Studio

AlicaLogger
===========

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

.. java:type:: public class AlicaLogger

   The ALICA logger logs analyzer and controller outputs during an acquisition.

   :author: Marcel Stefko

Methods
-------
addBatchedOutput
^^^^^^^^^^^^^^^^

.. java:method:: public void addBatchedOutput(int frame_no, double value)
   :outertype: AlicaLogger

   Add batched output of analyzer into the log.

   :param frame_no:
   :param value: value of the output

addControllerOutput
^^^^^^^^^^^^^^^^^^^

.. java:method:: public void addControllerOutput(int frame_no, double value)
   :outertype: AlicaLogger

   Add output of controller into log

   :param frame_no:
   :param value: value of the output

addIntermittentOutput
^^^^^^^^^^^^^^^^^^^^^

.. java:method:: public void addIntermittentOutput(int frame_no, double value)
   :outertype: AlicaLogger

   Add intermittent output of analyzer into log

   :param frame_no:
   :param value: value of the output

addSetpoint
^^^^^^^^^^^

.. java:method:: public void addSetpoint(int frame_no, double setpoint)
   :outertype: AlicaLogger

   Add setpoint of controller into log

   :param frame_no:
   :param setpoint: value of the output

addToLog
^^^^^^^^

.. java:method:: public void addToLog(int frame_no, String value_name, double value)
   :outertype: AlicaLogger

   Add a parameter into the log.

   :param frame_no: The acquisition frame number for this log entry.
   :param value_name: name of parameter
   :param value: value of parameter

addToLog
^^^^^^^^

.. java:method:: public void addToLog(int frame_no, String value_name, String value)
   :outertype: AlicaLogger

   Add a parameter into log

   :param frame_no:
   :param value_name: name of parameter
   :param value: value of parameter

clear
^^^^^

.. java:method:: public final void clear()
   :outertype: AlicaLogger

   Resets logger, removes all data.

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

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

   :return: AlicaLogger singleton

getLogMap
^^^^^^^^^

.. java:method:: public LinkedHashMap<Integer, LinkedHashMap<String, Object>> getLogMap()
   :outertype: AlicaLogger

   Returns the current log.

   :return: The current log stored by this logger.

logDebugMessage
^^^^^^^^^^^^^^^

.. java:method:: public void logDebugMessage(String message)
   :outertype: AlicaLogger

   Log message to MicroManager or to a general logger

   :param message: message to be logged

logError
^^^^^^^^

.. java:method:: public void logError(Exception exc, String message)
   :outertype: AlicaLogger

   Log exception in MicroManager or in general logger

   :param exc: exception to be logged
   :param message: message to be logged

logMessage
^^^^^^^^^^

.. java:method:: public void logMessage(String message)
   :outertype: AlicaLogger

   Log message to MicroManager or to a general logger.

   :param message: The message to be logged.

saveLog
^^^^^^^

.. java:method:: public boolean saveLog()
   :outertype: AlicaLogger

   Saves the log into a csv file chosen by file selection dialog.

   :return: true if save was successful, false otherwise

setStudio
^^^^^^^^^

.. java:method:: public void setStudio(Studio studio)
   :outertype: AlicaLogger

   Set studio to allow general logging.

   :param studio: MMStudio

showError
^^^^^^^^^

.. java:method:: public void showError(Exception exc, String message)
   :outertype: AlicaLogger

   Show exception in MicroManager or in ImageJ

   :param exc: exception to be shown
   :param message: message to be shown

showMessage
^^^^^^^^^^^

.. java:method:: public void showMessage(String message)
   :outertype: AlicaLogger

   Show message in MicroManager or in ImageJ

   :param message: message to be logged