LinearProfileStats (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.scijava.AbstractContextual
- - org.scijava.command.ContextCommand
  - - sc.fiji.snt.analysis.sholl.math.LinearProfileStats

All Implemented Interfaces:

Runnable, Cancelable, Command, Contextual, SciJavaPlugin, ShollStats
```
public class LinearProfileStats
extends ContextCommand
implements ShollStats
```
Retrieves descriptive statistics and calculates Sholl Metrics from sampled Sholl profiles, including those relying on polynomial fitting. Fitting to polynomials of arbitrary degree is supported. Relies heavily on the org.apache.commons.math3 package.

Author:

Tiago Ferreira

Field Summary

Fields
Modifier and Type	Field and Description
`protected double[]`	`fCounts`
`protected double[]`	`inputCounts`
`protected double[]`	`inputRadii`
`protected Logger`	`logger`
`protected int`	`nPoints`
`protected ShollPlot`	`plot`
`protected Profile`	`profile`
`protected static double`	`UNASSIGNED_VALUE`

Fields inherited from interface sc.fiji.snt.analysis.sholl.math.ShollStats
ANNULUS, AREA, GUESS_SLOG, LOG_LOG, PERIMETER, S_SHELL, SEMI_LOG, SURFACE, VOLUME

Constructor Summary

Constructors
Constructor and Description

LinearProfileStats(Profile profile)
Instantiates the Linear Profile Statistics.

Constructors
Constructor and Description
`LinearProfileStats(Profile profile)` Instantiates the Linear Profile Statistics.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`debug(Object msg)`
`int`	`findBestFit(int fromDegree, int toDegree, double minRSquared, double pvalue)` Computes the 'best fit' polynomial between a specified range of degrees for this profile and keeps the fit in memory.
`int`	`findBestFit(int fromDegree, int toDegree, PrefService prefService)` Runs `findBestFit(int, int, double, double)` using the preferences specified by the user using the `ShollAnalysisPrefsCmd` command.
`void`	`fitPolynomial(int degree)` Fits sampled data to a polynomial function and keeps the fit in memory.
`protected double`	`getAdjustedRSquaredOfFit(int p)`
`ShollPoint`	`getCenteredMaximum()`
`ShollPoint`	`getCenteredMaximum(boolean fittedData)` Returns the average coordinates of all maxima.
`ShollPoint`	`getCentroid()`
`ShollPoint`	`getCentroid(boolean fittedData)` Retrieves the centroid from all pairs of data (radius, inters.
`double`	`getEnclosingRadius(boolean fittedData, double cutoff)` Returns the largest radius associated with at least the number of specified counts.
`double`	`getEnclosingRadius(double cutoff)`
`double[]`	`getFitYvalues()` Returns the ordinates of the sampled linear plot of fitted data.
`double[]`	`getFitYvalues(boolean asCumulativeFrequencies)`
`protected int`	`getIndex(double[] array, double value)`
`int`	`getIndexOfInters(boolean fittedData, double inters)` Returns the closest index of the intersections data associated with the specified value
`int`	`getIndexOfRadius(double radius)` Returns the closest index of sampled distances associated with the specified value
`int`	`getIntersectingRadii()`
`int`	`getIntersectingRadii(boolean fittedData)` Returns the number of intersecting radii.
`double`	`getKStestOfFit()` Returns the two-sample Kolmogorov-Smirnov (K-S) test between the polynomial fit and sampled intersections as a measurement of goodness of fit.
`double`	`getKurtosis()`
`double`	`getKurtosis(boolean fittedData)` Calculates the kurtosis.
`double`	`getMax()`
`double`	`getMax(boolean fittedData)` Returns the largest value of intersection count.
`int`	`getMaxEvaluations()` Gets the function evaluation limit for solvers
`ArrayList<ShollPoint>`	`getMaxima()`
`ArrayList<ShollPoint>`	`getMaxima(boolean fittedData)` Returns a list of all the points in the linear Sholl profile associated with the highest intersections count
`double`	`getMean()`
`double`	`getMean(boolean fittedData)` Calculates the arithmetic mean.
`double`	`getMeanValueOfPolynomialFit(double lowerBound, double upperBound)` Calculates the mean value of polynomial fit using the default integration method (Simpson's).
`double`	`getMeanValueOfPolynomialFit(String integrator, double lowerBound, double upperBound)` Gets the mean value of polynomial fit.
`double`	`getMedian()`
`double`	`getMedian(boolean fittedData)` Calculates the median.
`double`	`getMin()`
`double`	`getMin(boolean fittedData)` Returns the lowest value of intersection count.
`int`	`getN()`
`ShollPlot`	`getPlot(boolean cumulativeFrequencies)`
`ShollPoint`	`getPolygonCentroid()`
`ShollPoint`	`getPolygonCentroid(boolean fittedData)` Calculates the centroid from all (radius, inters.
`PolynomialFunction`	`getPolynomial()` Gets the polynomial function.
`String`	`getPolynomialAsString()` Returns a string describing the polynomial fit
`int`	`getPolynomialDegree()` Returns the degree of the polynomial.
`Set<ShollPoint>`	`getPolynomialMaxima(double lowerBound, double upperBound, double initialGuess)` Calculates local maxima (critical points at which the derivative of the polynomial is zero) within the specified interval.
`double`	`getPrimaryBranches()`
`double`	`getPrimaryBranches(boolean fittedData)` Returns intersection counts at the smallest radius (inferred no.
`Profile`	`getProfile()`
`double`	`getRamificationIndex()`
`double`	`getRamificationIndex(boolean fittedData)` Calculates the ramification index (the highest intersections count divided by the n.
`double`	`getRSquaredOfFit()`
`double`	`getRSquaredOfFit(boolean adjusted)` Returns RSquared of the polynomial fit.
`double`	`getSkewness()`
`double`	`getSkewness(boolean fittedData)` Calculates the skewness.
`double`	`getSum()`
`double`	`getSum(boolean fittedData)` Calculates the sum.
`double`	`getSumSq()`
`double`	`getSumSq(boolean fittedData)` Calculates the sum of the squared values.
`double`	`getVariance()`
`double`	`getVariance(boolean fittedData)` Calculates the variance.
`double[]`	`getXvalues()` Returns the abscissae of the sampled linear plot for sampled data.
`double[]`	`getYvalues()` Returns the ordinates of the sampled linear plot of sampled data.
`double[]`	`getYvalues(boolean asCumulativeFrequencies)`
`boolean`	`isPrimaryBranchesInferred()` Checks whether the number of primary branches is being inferred from the number of intersections at starting radius or if it has been set explicitly.
`void`	`run()`
`void`	`setContext(Context context)`
`void`	`setDebug(boolean debug)`
`void`	`setLogger(Logger logger)`
`void`	`setLogger(Logger logger, boolean debug)`
`void`	`setMaxEvaluations(int maxEval)` Sets the the function evaluation limit for solvers.
`void`	`setPrimaryBranches(int nBranches)` Sets the number of primary branches associated with this profile, used to calculate ramification indices.
`protected void`	`validateFit()`
`boolean`	`validFit()` Checks if valid fitted data exists.

Methods inherited from class org.scijava.command.ContextCommand
cancel, getCancelReason, isCanceled

Methods inherited from class org.scijava.AbstractContextual
context, getContext

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface sc.fiji.snt.analysis.sholl.math.ShollStats
getFitYvalues, getN, getProfile, getYvalues

- Field Detail
  - UNASSIGNED_VALUE
```
protected static final double UNASSIGNED_VALUE
```
    See Also:
    
    Constant Field Values
  - inputRadii
```
protected final double[] inputRadii
```
  - inputCounts
```
protected final double[] inputCounts
```
  - profile
```
protected final Profile profile
```
  - nPoints
```
protected int nPoints
```
  - fCounts
```
protected double[] fCounts
```
  - plot
```
protected ShollPlot plot
```
  - logger
```
protected Logger logger
```
- Constructor Detail
  - LinearProfileStats
```
public LinearProfileStats(Profile profile)
```
    Instantiates the Linear Profile Statistics.
    
    Parameters:
    
    profile - the profile to be analyzed
- Method Detail
  - getCentroid
```
public ShollPoint getCentroid(boolean fittedData)
```
    Retrieves the centroid from all pairs of data (radius, inters. counts).
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the centroid {x,y} coordinates
  - getCentroid
```
public ShollPoint getCentroid()
```
    Returns:
    
    getCentroid(false)
  - getPolygonCentroid
```
public ShollPoint getPolygonCentroid(boolean fittedData)
```
    Calculates the centroid from all (radius, inters. counts) pairs assuming such points define a non-self-intersecting closed polygon. Implementation from wikipedia.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the point by the centroid {x,y} coordinates
  - getPolygonCentroid
```
public ShollPoint getPolygonCentroid()
```
    Returns:
    
    getPolygonCentroid(false)
  - getEnclosingRadius
```
public double getEnclosingRadius(boolean fittedData,
                                 double cutoff)
```
    Returns the largest radius associated with at least the number of specified counts.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    cutoff - the cutoff for intersection counts
    
    Returns:
    
    the largest radius associated with the same or more cutoff counts
  - getEnclosingRadius
```
public double getEnclosingRadius(double cutoff)
```
    Parameters:
    
    cutoff - the cutoff for intersection counts
    
    Returns:
    
    getEnclosingRadius(false, cutoff)
  - getIntersectingRadii
```
public int getIntersectingRadii(boolean fittedData)
```
    Returns the number of intersecting radii.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the count of all radii associated with at at least one intersection
  - getIntersectingRadii
```
public int getIntersectingRadii()
```
    Returns:
    
    getIntersectingRadii(false)
  - getKurtosis
```
public double getKurtosis(boolean fittedData)
```
    Calculates the kurtosis.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    kurtosis of intersection counts
  - getKurtosis
```
public double getKurtosis()
```
    Returns:
    
    getKurtosis(false)
  - getMaxima
```
public ArrayList<ShollPoint> getMaxima(boolean fittedData)
```
    Returns a list of all the points in the linear Sholl profile associated with the highest intersections count
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the list of points of all maxima
  - getMaxima
```
public ArrayList<ShollPoint> getMaxima()
```
    Returns:
    
    getMaxima(false)
  - getCenteredMaximum
```
public ShollPoint getCenteredMaximum(boolean fittedData)
```
    Returns the average coordinates of all maxima.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the averaged x,y coordinates of maxima
  - getCenteredMaximum
```
public ShollPoint getCenteredMaximum()
```
    Returns:
    
    getCenteredMaximum(false)
  - getMean
```
public double getMean(boolean fittedData)
```
    Calculates the arithmetic mean.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the mean of intersection counts
  - getMean
```
public double getMean()
```
    Returns:
    
    getMean(false)
  - getIndexOfRadius
```
public int getIndexOfRadius(double radius)
```
    Returns the closest index of sampled distances associated with the specified value
    
    Parameters:
    
    radius - the query value
    
    Returns:
    
    the position index (zero-based) or -1 if no index could be calculated
  - getIndexOfInters
```
public int getIndexOfInters(boolean fittedData,
                            double inters)
```
    Returns the closest index of the intersections data associated with the specified value
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    inters - the query value
    
    Returns:
    
    the position index (zero-based) or -1 if no index could be calculated
  - fitPolynomial
```
public void fitPolynomial(int degree)
```
    Fits sampled data to a polynomial function and keeps the fit in memory.
    
    Parameters:
    
    degree - Degree of the polynomial to be fitted
    
    Throws:
    
    NullArgumentException - if the computed polynomial coefficients were null
    
    NoDataException - if the computed polynomial coefficients were empty
    
    ConvergenceException - if optimization failed
  - findBestFit
```
public int findBestFit(int fromDegree,
                       int toDegree,
                       double minRSquared,
                       double pvalue)
```
    Computes the 'best fit' polynomial between a specified range of degrees for this profile and keeps the fit in memory.
    Note that in some edge cases specified constrains may be bypassed: E.g., If the profile is constant, a constant function is fitted. If the profile contains only two data points, a linear function is fitted
    
    Parameters:
    
    fromDegree - the lowest degree to be considered. Will be set to (getN()-1) if higher than (getN()-1).
    
    toDegree - the highest degree to be considered. Will be set to (getN()-1) if higher than (getN()-1)
    
    minRSquared - the lowest value for adjusted RSquared. Only fits associated with an equal or higher value will be considered
    
    pvalue - the two-sample Kolmogorov-Smirnov (K-S) test statistic (p-value) used to discard 'unsuitable fits'. It is used to evaluate the null hypothesis that profiled data and polynomial fit represent samples drawn from the same probability distribution. Set it to -1 to skip K-S testing.
    
    Returns:
    
    the degree of the 'best fit' polynomial or -1 if no suitable fit could be performed.
  - findBestFit
```
public int findBestFit(int fromDegree,
                       int toDegree,
                       PrefService prefService)
```
    Runs findBestFit(int, int, double, double) using the preferences specified by the user using the ShollAnalysisPrefsCmd command.
    
    Parameters:
    
    fromDegree - the lowest degree to be considered. See findBestFit(int, int, double, double)
    
    toDegree - the highest degree to be considered. See findBestFit(int, int, double, double)
    
    prefService - the PrefService used to read preferences
    
    Returns:
    
    the degree of the 'best fit' polynomial. See findBestFit(int, int, double, double)
  - getXvalues
```
public double[] getXvalues()
```
    Returns the abscissae of the sampled linear plot for sampled data.
    
    Specified by:
    
    getXvalues in interface ShollStats
    
    Returns:
    
    the sampled distances.
  - getYvalues
```
public double[] getYvalues()
```
    Returns the ordinates of the sampled linear plot of sampled data.
    
    Specified by:
    
    getYvalues in interface ShollStats
    
    Returns:
    
    the sampled intersection counts.
  - getFitYvalues
```
public double[] getFitYvalues()
```
    Returns the ordinates of the sampled linear plot of fitted data.
    
    Specified by:
    
    getFitYvalues in interface ShollStats
    
    Returns:
    
    the y-values of the polynomial fit retrieved at sampling distances
    
    Throws:
    
    NullPointerException - if fitPolynomial(int) has not been called
  - getPolynomial
```
public PolynomialFunction getPolynomial()
```
    Gets the polynomial function.
    
    Returns:
    
    the polynomial
    
    Throws:
    
    NullPointerException - if fitPolynomial(int) has not been called
  - getPolynomialDegree
```
public int getPolynomialDegree()
```
    Returns the degree of the polynomial.
    
    Returns:
    
    the polynomial degree
    
    Throws:
    
    NullPointerException - if fitPolynomial(int) has not been called
  - getPolynomialAsString
```
public String getPolynomialAsString()
```
    Returns a string describing the polynomial fit
    
    Returns:
    
    the description, e.g., 8th degree
    
    Throws:
    
    NullPointerException - if fitPolynomial(int) has not been called
  - getPolynomialMaxima
```
public Set<ShollPoint> getPolynomialMaxima(double lowerBound,
                                           double upperBound,
                                           double initialGuess)
```
    Calculates local maxima (critical points at which the derivative of the polynomial is zero) within the specified interval.
    
    Parameters:
    
    lowerBound - the lower bound of the interval
    
    upperBound - the upper bound of the interval
    
    initialGuess - initial guess for a solution (solver's starting point)
    
    Returns:
    
    the list of Points defined by the {x,y} coordinates of maxima (sorted by descendant order)
    
    Throws:
    
    TooManyEvaluationsException - if the maximum number of evaluations is exceeded when solving for one of the roots
    
    NullPointerException - if fitPolynomial(int) has not been called
  - getMaxEvaluations
```
public int getMaxEvaluations()
```
    Gets the function evaluation limit for solvers
    
    Returns:
    
    the set maximum of evaluations (1000 by default)
  - setMaxEvaluations
```
public void setMaxEvaluations(int maxEval)
```
    Sets the the function evaluation limit for solvers.
    
    Parameters:
    
    maxEval - the new maximum of evaluations
  - getRSquaredOfFit
```
public double getRSquaredOfFit(boolean adjusted)
```
    Returns RSquared of the polynomial fit. Implementation from wikipedia. \( R^2 = 1 - (SSres/SStot) \) with \( SSres = SUM(i) (yi - fi)^2 \) \( SStot = SUM(i) (yi - yavg)^2 \)
    
    Parameters:
    
    adjusted - if true returns adjusted RSquared, i.e., adjusted for the number of terms of the polynomial model
    
    Returns:
    
    RSquared, a measure for the goodness of fit
    
    Throws:
    
    NullPointerException - if fitPolynomial(int) has not been called
  - getMeanValueOfPolynomialFit
```
public double getMeanValueOfPolynomialFit(String integrator,
                                          double lowerBound,
                                          double upperBound)
```
    Gets the mean value of polynomial fit.
    
    Parameters:
    
    integrator - the integration method to retrieve the integral of the polynomial fit. Either "Simpson" (the default), or "Romberg" (case insensitive)
    
    lowerBound - the lower bound (smallest radius) for the interval
    
    upperBound - the upper bound (largest radius) for the interval
    
    Returns:
    
    the mean value of polynomial fit
    
    Throws:
    
    MathIllegalArgumentException - if bounds do not satisfy the integrator requirements
    
    TooManyEvaluationsException - if the maximum number of function evaluations is exceeded by the integrator
    
    MaxCountExceededException - if the maximum iteration count is exceeded by the integrator
    
    NullPointerException - if fitPolynomial(int) has not been called
  - getMeanValueOfPolynomialFit
```
public double getMeanValueOfPolynomialFit(double lowerBound,
                                          double upperBound)
```
    Calculates the mean value of polynomial fit using the default integration method (Simpson's).
    
    Parameters:
    
    lowerBound - the lower bound (smallest radius) for the interval
    
    upperBound - the upper bound (largest radius) for the interval
    
    Returns:
    
    the mean value of polynomial fit, or Double.NaN if calculation failed.
    
    Throws:
    
    NullPointerException - if fitPolynomial(int) has not been called
  - getMedian
```
public double getMedian(boolean fittedData)
```
    Calculates the median.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the median of intersection counts
  - getMedian
```
public double getMedian()
```
    Returns:
    
    getMedian(false)
  - setPrimaryBranches
```
public void setPrimaryBranches(int nBranches)
```
    Sets the number of primary branches associated with this profile, used to calculate ramification indices. When the number is set to -1 (the default), the number of primary branches is inferred from the number of intersections at starting radius.
    
    Parameters:
    
    nBranches - the new primary branches
    
    See Also:
    
    getPrimaryBranches(boolean), getRamificationIndex(boolean)
  - isPrimaryBranchesInferred
```
public boolean isPrimaryBranchesInferred()
```
    Checks whether the number of primary branches is being inferred from the number of intersections at starting radius or if it has been set explicitly.
    
    Returns:
    
    true, if number of primary branches is being inferred
    
    See Also:
    
    setPrimaryBranches(int)
  - getPrimaryBranches
```
public double getPrimaryBranches(boolean fittedData)
```
    Returns intersection counts at the smallest radius (inferred no. of primary branches), or the number of the actual number of primary branches specified by setPrimaryBranches(int).
    
    Parameters:
    
    fittedData - If true, and setPrimaryBranches(int) has not been called, calculation is performed on polynomial fitted values, otherwise from sampled data. It is ignored if the number of primary branches has been successfully specified by calling setPrimaryBranches(int)
    
    Returns:
    
    the number of primary branches
    
    See Also:
    
    getRamificationIndex(boolean)
  - getPrimaryBranches
```
public double getPrimaryBranches()
```
    Returns:
    
    getPrimaryBranches(false)
    
    See Also:
    
    getRamificationIndex()
  - getRamificationIndex
```
public double getRamificationIndex(boolean fittedData)
```
    Calculates the ramification index (the highest intersections count divided by the n. of primary branches). If the number of primary branches has not been specified, it is assumed to be the n. intersections at starting radius.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the ramification index
    
    See Also:
    
    setPrimaryBranches(int)
  - getRamificationIndex
```
public double getRamificationIndex()
```
    Returns:
    
    getRamificationIndex(false)
  - getMax
```
public double getMax(boolean fittedData)
```
    Returns the largest value of intersection count.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the largest value of intersection counts
  - getMax
```
public double getMax()
```
    Returns:
    
    getMax(false)
  - getMin
```
public double getMin(boolean fittedData)
```
    Returns the lowest value of intersection count.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the lowest value of intersection counts
  - getMin
```
public double getMin()
```
    Returns:
    
    getMin(false)
  - getSkewness
```
public double getSkewness(boolean fittedData)
```
    Calculates the skewness.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the skewness of intersection counts
  - getSkewness
```
public double getSkewness()
```
    Returns:
    
    getSkewness(false)
  - getSum
```
public double getSum(boolean fittedData)
```
    Calculates the sum.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the sum of intersection counts
  - getSum
```
public double getSum()
```
    Returns:
    
    getSum(false)
  - getSumSq
```
public double getSumSq(boolean fittedData)
```
    Calculates the sum of the squared values.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the sum of the squared values of intersection counts
  - getSumSq
```
public double getSumSq()
```
    Returns:
    
    getSumSq(false)
  - getVariance
```
public double getVariance(boolean fittedData)
```
    Calculates the variance.
    
    Parameters:
    
    fittedData - If true, calculation is performed on polynomial fitted values, otherwise from sampled data
    
    Returns:
    
    the variance of intersection counts
  - getVariance
```
public double getVariance()
```
    Returns:
    
    getVariance(false)
  - validFit
```
public boolean validFit()
```
    Checks if valid fitted data exists.
    
    Specified by:
    
    validFit in interface ShollStats
    
    Returns:
    
    true if polynomial fitted data exists
  - getKStestOfFit
```
public double getKStestOfFit()
```
    Returns the two-sample Kolmogorov-Smirnov (K-S) test between the polynomial fit and sampled intersections as a measurement of goodness of fit.
    
    Returns:
    
    the test statistic (p-value) used to evaluate the null hypothesis that sampled data and polynomial fit represent samples drawn from the same probability distribution
    
    Throws:
    
    NullPointerException - if curve fitting has not been performed
    
    InsufficientDataException - if sampled data contains fewer than two data points
  - getRSquaredOfFit
```
public double getRSquaredOfFit()
```
  - getPlot
```
public ShollPlot getPlot(boolean cumulativeFrequencies)
```
  - getAdjustedRSquaredOfFit
```
protected double getAdjustedRSquaredOfFit(int p)
```
  - getIndex
```
protected int getIndex(double[] array,
                       double value)
```
  - validateFit
```
protected void validateFit()
```
  - debug
```
protected void debug(Object msg)
```
  - setLogger
```
public void setLogger(Logger logger)
```
  - setLogger
```
public void setLogger(Logger logger,
                      boolean debug)
```
  - setDebug
```
public void setDebug(boolean debug)
```
  - setContext
```
public void setContext(Context context)
```
    Specified by:
    
    setContext in interface Contextual
  - getYvalues
```
public double[] getYvalues(boolean asCumulativeFrequencies)
```
    Specified by:
    
    getYvalues in interface ShollStats
  - getN
```
public int getN()
```
    Specified by:
    
    getN in interface ShollStats
  - getFitYvalues
```
public double[] getFitYvalues(boolean asCumulativeFrequencies)
```
    Specified by:
    
    getFitYvalues in interface ShollStats
  - getProfile
```
public Profile getProfile()
```
    Specified by:
    
    getProfile in interface ShollStats
  - run
```
public void run()
```
    Specified by:
    
    run in interface Runnable

Class LinearProfileStats

Field Summary

Fields inherited from interface sc.fiji.snt.analysis.sholl.math.ShollStats

Constructor Summary

Method Summary

Methods inherited from class org.scijava.command.ContextCommand

Methods inherited from class org.scijava.AbstractContextual

Methods inherited from class java.lang.Object

Methods inherited from interface sc.fiji.snt.analysis.sholl.math.ShollStats

Field Detail

UNASSIGNED_VALUE

inputRadii

inputCounts

profile

nPoints

fCounts

plot

logger

Constructor Detail

LinearProfileStats

Method Detail

getCentroid

getCentroid

getPolygonCentroid

getPolygonCentroid

getEnclosingRadius

getEnclosingRadius

getIntersectingRadii

getIntersectingRadii

getKurtosis

getKurtosis

getMaxima

getMaxima

getCenteredMaximum

getCenteredMaximum

getMean

getMean

getIndexOfRadius

getIndexOfInters

fitPolynomial

findBestFit

findBestFit

getXvalues

getYvalues

getFitYvalues

getPolynomial

getPolynomialDegree

getPolynomialAsString

getPolynomialMaxima

getMaxEvaluations

setMaxEvaluations

getRSquaredOfFit

getMeanValueOfPolynomialFit

getMeanValueOfPolynomialFit

getMedian

getMedian

setPrimaryBranches

isPrimaryBranchesInferred

getPrimaryBranches

getPrimaryBranches

getRamificationIndex

getRamificationIndex

getMax

getMax

getMin

getMin

getSkewness

getSkewness

getSum

getSum

getSumSq

getSumSq

getVariance

getVariance

validFit

getKStestOfFit

getRSquaredOfFit

getPlot

getAdjustedRSquaredOfFit

getIndex