uk.ac.sussex.gdsc.smlm.results.Gaussian2DPeakResultCalculator Maven / Gradle / Ivy
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/*-
* #%L
* Genome Damage and Stability Centre SMLM Package
*
* Software for single molecule localisation microscopy (SMLM)
* %%
* Copyright (C) 2011 - 2023 Alex Herbert
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* .
* #L%
*/
package uk.ac.sussex.gdsc.smlm.results;
/**
* Contains calculator functions for working with peak results.
*/
public interface Gaussian2DPeakResultCalculator {
/**
* Gets the single Gaussian 2D standard deviation from independent x and y standard deviations. s
* = sqrt(abs(sx*sy)).
*
* @param params the params
* @return the single Gaussian 2D standard deviation
*/
float getStandardDeviation(float[] params);
/**
* Gets the single Gaussian 2D standard deviation squared from independent x and y standard
* deviations. s2 = abs(sx*sy).
*
* @param params the params
* @return the single Gaussian 2D standard deviation squared
*/
float getStandardDeviation2(float[] params);
/**
* Get the amplitude of a Gaussian 2D PSF. Amplitude = intensity / (2*pi*sx*sy).
*
* @param params the params
* @return the amplitude
*/
float getAmplitude(float[] params);
/**
* Get the height of the central pixel of a Gaussian 2D PSF. The integral of the pixel containing
* the centre of the Gaussian is computed.
*
* @param params the params
* @return the pixel amplitude
*/
float getPixelAmplitude(float[] params);
/**
* Calculate the localisation precision for least squares fitting a Gaussian2D PSF to a Gaussian2D
* PSF. This is an approximation of the precision of fitting to an optical PSF. Uses the Mortensen
* formula for an EMCCD camera (Mortensen, et al (2010) Nature Methods 7, 377-383), equation 6.
*
* This method will use the background noise to approximate the expected background value of
* each pixel.
*
* @param params the params
* @param noise the noise
* @return The location precision in nm in each dimension (X/Y)
*/
double getLsePrecision(float[] params, float noise);
/**
* Calculate the localisation precision for least squares fitting a Gaussian2D PSF to a Gaussian2D
* PSF. This is an approximation of the precision of fitting to an optical PSF. Uses the Mortensen
* formula for an EMCCD camera (Mortensen, et al (2010) Nature Methods 7, 377-383), equation 6.
*
* @param params the params
* @return The location precision in nm in each dimension (X/Y)
*/
double getLsePrecision(float[] params);
/**
* Calculate the localisation variance for least squares fitting a Gaussian2D PSF to a Gaussian2D
* PSF. This is an approximation of the variance of fitting to an optical PSF. Uses the Mortensen
* formula for an EMCCD camera (Mortensen, et al (2010) Nature Methods 7, 377-383), equation 6.
*
*
This method will use the background noise to approximate the expected background value of
* each pixel.
*
* @param params the params
* @param noise the noise
* @return The location variance in nm in each dimension (X/Y)
*/
double getLseVariance(float[] params, float noise);
/**
* Calculate the localisation variance for least squares fitting a Gaussian2D PSF to a Gaussian2D
* PSF. This is an approximation of the variance of fitting to an optical PSF. Uses the Mortensen
* formula for an EMCCD camera (Mortensen, et al (2010) Nature Methods 7, 377-383), equation 6.
*
* @param params the params
* @return The location variance in nm in each dimension (X/Y)
*/
double getLseVariance(float[] params);
/**
* Calculate the localisation precision for maximum likelihood fitting a Gaussian2D PSF to a
* Gaussian2D PSF. This is an approximation of the precision of fitting to an optical PSF. Uses
* the Mortensen formula for an EMCCD camera (Mortensen, et al (2010) Nature Methods 7, 377-383),
* equation 6.
*
*
This method will use the background noise to approximate the expected background value of
* each pixel.
*
* @param params the params
* @param noise the noise
* @return The location precision in nm in each dimension (X/Y)
*/
double getMlePrecision(float[] params, float noise);
/**
* Calculate the localisation precision for maximum likelihood fitting a Gaussian2D PSF to a
* Gaussian2D PSF. This is an approximation of the precision of fitting to an optical PSF. Uses
* the Mortensen formula for an EMCCD camera (Mortensen, et al (2010) Nature Methods 7, 377-383),
* equation 6.
*
* @param params the params
* @return The location precision in nm in each dimension (X/Y)
*/
double getMlePrecision(float[] params);
/**
* Calculate the localisation variance for maximum likelihood fitting a Gaussian2D PSF to a
* Gaussian2D PSF. This is an approximation of the variance of fitting to an optical PSF. Uses the
* Mortensen formula for an EMCCD camera (Mortensen, et al (2010) Nature Methods 7, 377-383),
* equation 6.
*
*
This method will use the background noise to approximate the expected background value of
* each pixel.
*
* @param params the params
* @param noise the noise
* @return The location variance in nm in each dimension (X/Y)
*/
double getMleVariance(float[] params, float noise);
/**
* Calculate the localisation variance for maximum likelihood fitting a Gaussian2D PSF to a
* Gaussian2D PSF. This is an approximation of the variance of fitting to an optical PSF. Uses the
* Mortensen formula for an EMCCD camera (Mortensen, et al (2010) Nature Methods 7, 377-383),
* equation 6.
*
* @param params the params
* @return The location variance in nm in each dimension (X/Y)
*/
double getMleVariance(float[] params);
}