.. java:import:: ch.epfl.leb.sass.models.emitters.internal Pixel

.. java:import:: ch.epfl.leb.sass.models.psfs PSF

.. java:import:: ch.epfl.leb.sass.models.psfs PSFBuilder

.. java:import:: java.util ArrayList

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

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

.. java:import:: org.apache.commons.math MathException

.. java:import:: org.apache.commons.math.special Erf

Gaussian3D
==========

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

.. java:type:: public final class Gaussian3D implements PSF

   Generates a digital representation of a three-dimensional Gaussian PSF. In this simple but unphysical model, the variance of the Gaussian PSF from an emitter at a distance z from the focal plane scales linearly with the amount of defocus.

   :author: Kyle M. Douglass

Methods
-------
generatePixelSignature
^^^^^^^^^^^^^^^^^^^^^^

.. java:method:: @Override public double generatePixelSignature(int pixelX, int pixelY) throws MathException
   :outertype: Gaussian3D

   Computes the relative probability of receiving a photon at the pixel.

   :param pixelX: The pixel's x-position.
   :param pixelY: The pixel's y-position.
   :throws org.apache.commons.math.MathException:
   :return: The probability of a photon hitting this pixel.

generateSignature
^^^^^^^^^^^^^^^^^

.. java:method:: public void generateSignature(ArrayList<Pixel> pixels)
   :outertype: Gaussian3D

   Generates the digital signature of the emitter on its nearby pixels.

   :param pixels: The list of pixels spanned by the emitter's image.

getFWHM
^^^^^^^

.. java:method:: public double getFWHM()
   :outertype: Gaussian3D

getNumericalAperture
^^^^^^^^^^^^^^^^^^^^

.. java:method:: public double getNumericalAperture()
   :outertype: Gaussian3D

getRadius
^^^^^^^^^

.. java:method:: @Override public double getRadius()
   :outertype: Gaussian3D

   Computes the half-width of the PSF for determining which pixels contribute to the emitter signal. The effective width used here is five times the standard deviation when the emitter is exactly in focus. The larger factor of five accounts for the larger lateral PSF size when it is out of focus.

   :return: The width of the PSF.

setFWHM
^^^^^^^

.. java:method:: public void setFWHM(double fwhm)
   :outertype: Gaussian3D

setNumericalAperture
^^^^^^^^^^^^^^^^^^^^

.. java:method:: public void setNumericalAperture(double numericalAperture)
   :outertype: Gaussian3D