NormalizedProfileStats (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

Runnable, Cancelable, Command, Contextual, SciJavaPlugin, ShollStats
```
public class NormalizedProfileStats
extends ContextCommand
implements ShollStats
```
Calculates Sholl Metrics from normalized profiles, including Sholl decay and methods for determination of 'optimal' normalization. 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
`NormalizedProfileStats(Profile profile, int normalizationFlag)`
`NormalizedProfileStats(Profile profile, int normalizationFlag, int methodFlag)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`debug(Object msg)`
`protected double`	`getAdjustedRSquaredOfFit(int p)`
`double`	`getDeterminationRatio()`
`double[]`	`getFitYvalues()`
`double[]`	`getFitYvalues(boolean asCumulativeFrequencies)`
`protected int`	`getIndex(double[] array, double value)`
`double`	`getIntercept()` Returns the intercept of the estimated regression line,
`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.
`int`	`getMethod()`
`String`	`getMethodDescription()`
`static int`	`getMethodFlag(String string)`
`int`	`getN()`
`int`	`getNormalizer()`
`String`	`getNormalizerDescription()`
`static int`	`getNormalizerFlag(String string)`
`ShollPlot`	`getPlot(boolean cumulativeFrequencies)`
`Profile`	`getProfile()`
`double`	`getR()` Returns Pearson's product moment correlation coefficient, usually denoted r.
`SimpleRegression`	`getRegression()`
`double`	`getRSquaredOfFit()`
`double`	`getShollDecay()`
`double`	`getSlope()`
`double[]`	`getXvalues()` Returns the abscissae of the Semi-log /Log-log plot for sampled data.
`double[]`	`getYvalues()` Returns the ordinates of the Semi-log/Log-log plot for sampled data.
`double[]`	`getYvalues(boolean asCumulativeFrequencies)`
`boolean`	`is2Dnormalization()`
`boolean`	`is3Dnormalization()`
`void`	`resetRegression()`
`void`	`restrictRegToPercentile(double p1, double p2)`
`void`	`restrictRegToRange(double x1, double x2)`
`void`	`run()`
`void`	`setContext(Context context)`
`void`	`setDebug(boolean debug)`
`void`	`setLogger(Logger logger)`
`void`	`setLogger(Logger logger, boolean debug)`
`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
  - NormalizedProfileStats
```
public NormalizedProfileStats(Profile profile,
                              int normalizationFlag)
```
  - NormalizedProfileStats
```
public NormalizedProfileStats(Profile profile,
                              int normalizationFlag,
                              int methodFlag)
```
- Method Detail
  - getNormalizer
```
public int getNormalizer()
```
  - getNormalizerDescription
```
public String getNormalizerDescription()
```
  - getMethod
```
public int getMethod()
```
  - getMethodDescription
```
public String getMethodDescription()
```
  - resetRegression
```
public void resetRegression()
```
  - getRegression
```
public SimpleRegression getRegression()
```
  - restrictRegToPercentile
```
public void restrictRegToPercentile(double p1,
                                    double p2)
```
  - restrictRegToRange
```
public void restrictRegToRange(double x1,
                               double x2)
```
  - getRSquaredOfFit
```
public double getRSquaredOfFit()
```
  - getR
```
public double getR()
```
    Returns Pearson's product moment correlation coefficient, usually denoted r.
    
    Returns:
    
    Pearson's r
  - getIntercept
```
public double getIntercept()
```
    Returns the intercept of the estimated regression line,
    
    Returns:
    
    the intercept of the regression line
  - getSlope
```
public double getSlope()
```
  - getShollDecay
```
public double getShollDecay()
```
  - getDeterminationRatio
```
public double getDeterminationRatio()
```
  - is2Dnormalization
```
public boolean is2Dnormalization()
```
  - is3Dnormalization
```
public boolean is3Dnormalization()
```
  - getYvalues
```
public double[] getYvalues()
```
    Returns the ordinates of the Semi-log/Log-log plot for sampled data.
    
    Specified by:
    
    getYvalues in interface ShollStats
    
    Returns:
    
    normalized counts, ie, log(sampled intersections / normalizer)
  - validFit
```
public boolean validFit()
```
    Checks if valid fitted data exists.
    
    Specified by:
    
    validFit in interface ShollStats
    
    Returns:
    
    true if polynomial fitted data exists
  - getXvalues
```
public double[] getXvalues()
```
    Returns the abscissae of the Semi-log /Log-log plot for sampled data. Note that distances associated with zero intersections are removed from the input profile since log(0) is undefined.
    
    Specified by:
    
    getXvalues in interface ShollStats
    
    Returns:
    
    sampled distances in the case of Semi-log analysis or their log transform in the case of Log-log analysis
  - getFitYvalues
```
public double[] getFitYvalues()
```
    Specified by:
    
    getFitYvalues in interface ShollStats
  - getNormalizerFlag
```
public static int getNormalizerFlag(String string)
```
  - getMethodFlag
```
public static int getMethodFlag(String string)
```
  - 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
  - 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 NormalizedProfileStats

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

NormalizedProfileStats

NormalizedProfileStats

Method Detail

getNormalizer

getNormalizerDescription

getMethod

getMethodDescription

resetRegression

getRegression

restrictRegToPercentile

restrictRegToRange

getRSquaredOfFit

getR

getIntercept

getSlope

getShollDecay

getDeterminationRatio

is2Dnormalization

is3Dnormalization

getYvalues

validFit

getXvalues

getFitYvalues

getNormalizerFlag

getMethodFlag

getKStestOfFit

getPlot

getAdjustedRSquaredOfFit

getIndex

validateFit

debug

setLogger

setLogger

setDebug

setContext

getYvalues

getN

getFitYvalues

getProfile

run