Package qupath.lib.analysis.stats

Class StatisticsHelper

java.lang.Object

qupath.lib.analysis.stats.StatisticsHelper

public class StatisticsHelper
extends Object

Static methods for computing statistics from images, with or without a corresponding labeled image.

Author:

Pete Bankhead

Constructor Summary

Constructors

Constructor	Description
StatisticsHelper()

Method Summary

Modifier and Type	Method	Description
static RunningStatistics	computeRunningStatistics(double[] values)	Create a RunningStatistics object using all the values from a specified array.
static RunningStatistics	computeRunningStatistics(SimpleImage img)	Compute running statistics using all pixels from a SimpleImage.
static void	computeRunningStatistics(SimpleImage img, SimpleImage imgLabels, List<RunningStatistics> statsList)	Calculate RunningStatistics for each label > 0 in an image, up to a maximum of statsList.size().
static List<RunningStatistics>	createRunningStatisticsList(int n)	Create a list of n (empty) RunningStatistics objects.
static double[]	getQuartiles(double[] scores)	Determine thresholds for dividing an array of double values into quartiles.
static double[]	getTertiles(double[] scores)	Determine thresholds for dividing an array of double values into tertiles.
static void	updateRunningStatistics(RunningStatistics stats, SimpleImage img)	Add all pixels from a SimpleImage to an existing RunningStatistics object.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

StatisticsHelper

public StatisticsHelper()

Method Details

computeRunningStatistics

public static RunningStatistics computeRunningStatistics(SimpleImage img)

Compute running statistics using all pixels from a SimpleImage.

Parameters:

img -

Returns:

updateRunningStatistics

public static void updateRunningStatistics(RunningStatistics stats,
 SimpleImage img)

Add all pixels from a SimpleImage to an existing RunningStatistics object.

Parameters:

stats -

img -

createRunningStatisticsList

public static List<RunningStatistics> createRunningStatisticsList(int n)

Create a list of n (empty) RunningStatistics objects.

Parameters:

n -

Returns:

computeRunningStatistics

public static RunningStatistics computeRunningStatistics(double[] values)

Create a RunningStatistics object using all the values from a specified array.

Parameters:

values -

Returns:

computeRunningStatistics

public static void computeRunningStatistics(SimpleImage img,
 SimpleImage imgLabels,
 List<RunningStatistics> statsList)

Calculate RunningStatistics for each label > 0 in an image, up to a maximum of statsList.size().

The statistics for pixels in img corresponding to integer value label in imgLabels are stored within statsList.get(label-1).

Parameters:

img -

imgLabels -

statsList -

getQuartiles

public static double[] getQuartiles(double[] scores)

Determine thresholds for dividing an array of double values into quartiles.

NaNs are effectively removed first, however the input array is left unchanged so there is no need to duplicate it first (i.e. it is duplicated within this method anyway).

Depending upon the number of non-NaN values in the input array, linear interpolation may be used to obtain the split points.

Parameters:

scores -

Returns:

Array containing three values, corresponding to the split points.

getTertiles

public static double[] getTertiles(double[] scores)

Determine thresholds for dividing an array of double values into tertiles.

NaNs are effectively removed first, however the input array is left unchanged so there is no need to duplicate it in advance (i.e. it is duplicated within this method anyway).

Depending upon the number of non-NaN values in the input array, linear interpolation may be used to obtain the split points.

Parameters:

scores -

Returns:

Array containing two values, corresponding to the split points.