MyFunctions
===========

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

.. java:type::  class MyFunctions

Fields
------
cal3d_center
^^^^^^^^^^^^

.. java:field::  int cal3d_center
   :outertype: MyFunctions

cal3d_wmh
^^^^^^^^^

.. java:field::  double[] cal3d_wmh
   :outertype: MyFunctions

cal3d_z
^^^^^^^

.. java:field::  double[] cal3d_z
   :outertype: MyFunctions

caltable
^^^^^^^^

.. java:field::  ResultsTable caltable
   :outertype: MyFunctions

debug
^^^^^

.. java:field::  boolean debug
   :outertype: MyFunctions

dtable
^^^^^^

.. java:field::  ResultsTable dtable
   :outertype: MyFunctions

gblur
^^^^^

.. java:field::  GaussianBlur gblur
   :outertype: MyFunctions

live_view
^^^^^^^^^

.. java:field::  ImagePlus live_view
   :outertype: MyFunctions

ptable
^^^^^^

.. java:field::  ResultsTable ptable
   :outertype: MyFunctions

ptable_lock
^^^^^^^^^^^

.. java:field::  java.util.concurrent.locks.Lock ptable_lock
   :outertype: MyFunctions

Constructors
------------
MyFunctions
^^^^^^^^^^^

.. java:constructor:: public MyFunctions(boolean live_view)
   :outertype: MyFunctions

Methods
-------
argmax
^^^^^^

.. java:method::  int argmax(double[] arr)
   :outertype: MyFunctions

argmin
^^^^^^

.. java:method::  int argmin(double[] arr)
   :outertype: MyFunctions

clearRegion
^^^^^^^^^^^

.. java:method::  void clearRegion(double thrsh, ImageProcessor ip, boolean[][] mask, int xstart, int xend, int ystart, int yend)
   :outertype: MyFunctions

detectParticles
^^^^^^^^^^^^^^^

.. java:method::  int detectParticles(ImageProcessor ip, MyDialogs dg, int nframe)
   :outertype: MyFunctions

   Particle finding method, will search the image for particles.

   :param ip: image to search for particles on
   :param dg: dialog manager
   :param nframe: the frame index corresponding to this image

dispose
^^^^^^^

.. java:method:: public void dispose()
   :outertype: MyFunctions

getClosest
^^^^^^^^^^

.. java:method::  int getClosest(double value, double[] arr, int center)
   :outertype: MyFunctions

getMaxPositions
^^^^^^^^^^^^^^^

.. java:method::  int[] getMaxPositions(ImageProcessor ip)
   :outertype: MyFunctions

getNextImage
^^^^^^^^^^^^

.. java:method::  ImagePlus getNextImage(MyDialogs dg, int frame)
   :outertype: MyFunctions

   Grabs a new image on an observed folder on the case of the analysis being attached to the acquisition.

   :param dg: dialog manager
   :param frame: frame index to search for on the folder
   :return: found image

getParticle
^^^^^^^^^^^

.. java:method::  boolean getParticle(ImageProcessor ip, boolean[][] mask, int[] maxs, MyDialogs dg, ResultsTable ptable, int nframe)
   :outertype: MyFunctions

   Particle analysis method, called for each particle candidate found by detectParticles.

   :param ip: image to search for particles on
   :param dg: dialog manager
   :param nframe: the frame index corresponding to this image

getParticleForCalibration
^^^^^^^^^^^^^^^^^^^^^^^^^

.. java:method::  double[] getParticleForCalibration(ImageProcessor ip, MyDialogs dg, int xstart, int xend, int ystart, int yend)
   :outertype: MyFunctions

getZ
^^^^

.. java:method::  double getZ(double wmh)
   :outertype: MyFunctions

   Given a calculated width-minus-height (wmh) converts this value into the corresponding coordinate in Z by comparing against the loaded Z-calibration table. Only used it the particle is disturbed by astigmatism.

   :param wmh: the width-minus-height of a particle
   :return: corresponding z-position value, will return 9999 if wmh is out of limits

initialize3d
^^^^^^^^^^^^

.. java:method::  void initialize3d()
   :outertype: MyFunctions

   Loads values from the calibration table into the cal3d_* arrays.

log
^^^

.. java:method::  void log(java.lang.String txt)
   :outertype: MyFunctions

mean
^^^^

.. java:method::  double mean(double[] array, int start, int stop)
   :outertype: MyFunctions

movingMean
^^^^^^^^^^

.. java:method::  double[] movingMean(double[] arr, int window)
   :outertype: MyFunctions

showTable
^^^^^^^^^

.. java:method::  void showTable()
   :outertype: MyFunctions