org.micromanager.display

Class HistogramData

java.lang.Object

org.micromanager.display.HistogramData

Deprecated.

an improved API will be provided soon

@Deprecated
public class HistogramData
extends java.lang.Object

This is a simple container class containing a histogram for one component of an int-based image, and some related statistics. You can generate new HistogramData objects yourself, or use DisplayManager.calculateHistogram() and related methods to generate a HistogramData based off of an Image.

Constructor Summary

Constructors

Constructor and Description
HistogramData(int[] histogram, int numSamples, int minVal, int maxVal, int minIgnoringOutliers, int maxIgnoringOutliers, int mean, double stdDev, int bitDepth, int binSize) Deprecated.

Method Summary

Modifier and Type	Method and Description
int	getBinSize() Deprecated. Retrieve the number of distinct intensities that fit within each bin of the histogram.
int	getBitDepth() Deprecated. Retrieve the bit depth of the dataset.
int[]	getHistogram() Deprecated. Retrieve the histogram, an array of ints counting the number of samples whose intensities fall into each bin.
int	getMaxIgnoringOutliers() Deprecated. Retrieve the intensity of the brightest sample in the dataset once a fraction of all pixels have been discarded.
int	getMaxVal() Deprecated. Retrieve the intensity of the brightest sample in the dataset used to generate the histogram.
int	getMean() Deprecated. Retrieve the mean value of all samples in the dataset.
int	getMinIgnoringOutliers() Deprecated. Retrieve the intensity of the dimmest sample in the dataset once a fraction of all pixels have been discarded.
int	getMinVal() Deprecated. Retrieve the intensity of the dimmest sample in the dataset used to generate the histogram.
int	getNumSamples() Deprecated. Retrieve the number of samples used to construct the histogram.
double	getStdDev() Deprecated. Retrieve the standard deviation of all samples in the dataset, or -1 if standard deviation calculation was disabled or if a calculation error occurred while calculating the standard deviation.
java.lang.String	toString() Deprecated.

Methods inherited from class java.lang.Object

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

Constructor Detail

HistogramData

public HistogramData(int[] histogram,
                     int numSamples,
                     int minVal,
                     int maxVal,
                     int minIgnoringOutliers,
                     int maxIgnoringOutliers,
                     int mean,
                     double stdDev,
                     int bitDepth,
                     int binSize)

Deprecated.

Parameters:

histogram - An array of integers indicating how many pixels had intensities falling into the "bin" at the given index. The first bin always starts from an intensity of 0; the last bin ends with an intensity depending on the bitDepth parameter.

numSamples - The number of pixels used to generate the histogram; should be equal to the sum of all values in the histogram.

minVal - The lowest intensity found when generating the histogram.

maxVal - The brightest intensity found when generating the histogram.

minIgnoringOutliers - The lowest intensity when a fraction of the lowest samples are ignored. See the extremaPercentage parameter of DisplayManager.calculateHistogram().

maxIgnoringOutliers - The highest intensity when a fraction of the lowest samples are ignored. See the extremaPercentage parameter of DisplayManager.calculateHistogram().

mean - The average intensity of all samples.

stdDev - The standard deviation of all samples, or -1 if this value was not calculated.

bitDepth - The dynamic range of the histogram. The histogram will cover values from 0 to (2^bitDepth - 1), inclusive.

binSize - How many distinct intensities are combined into a single bin in the histogram. For example, if the bit depth is 10 and there are 2^8 bins, then there are (2^10 / 2^8 = 4) intensities per bin.

Throws:

java.lang.ArrayIndexOutOfBoundsException - if histogram is shorter than correct size

java.lang.NullPointerException - if histogram is null

Method Detail

getHistogram

public int[] getHistogram()

Deprecated.

Retrieve the histogram, an array of ints counting the number of samples whose intensities fall into each bin. Note: the returned array is the internal data, not a copy. Calling code must not modify this array.

Returns:

Array with histogram data. Must not be modified.

getMinVal

public int getMinVal()

Deprecated.

Retrieve the intensity of the dimmest sample in the dataset used to generate the histogram. NOTE: if this HistogramData was generated by DisplayManager.calculateHistogram and the bin size is not 1, then this number will be the lowest intensity that goes into the first (lowest-intensity) bin that has at least one pixel in it; it is possible there is no pixel in the image with this intensity.

Returns:

lowest intensity value in the dataset

getMaxVal

public int getMaxVal()

Deprecated.

Retrieve the intensity of the brightest sample in the dataset used to generate the histogram. NOTE: if this HistogramData was generated by DisplayManager.calculateHistogram and the bin size is not 1, then this number will be the highest intensity that goes into the last (highest-intensity) bin that has at least one pixel in it; it is possible there is no pixel in the image with this intensity.

Returns:

highest intensity value in the dataset

getMinIgnoringOutliers

public int getMinIgnoringOutliers()

Deprecated.

Retrieve the intensity of the dimmest sample in the dataset once a fraction of all pixels have been discarded. See the extremaPercentage parameter to DisplayManager.calculateHistogram() for more information.

Returns:

lowest intensity value in the dataset ignoring given fraction of outliers

getMaxIgnoringOutliers

public int getMaxIgnoringOutliers()

Deprecated.

Retrieve the intensity of the brightest sample in the dataset once a fraction of all pixels have been discarded. See the extremaPercentage parameter to DisplayManager.calculateHistogram() for more information.

Returns:

highest intensity value in the dataset ignoring given fraction of outliers

getMean

public int getMean()

Deprecated.

Retrieve the mean value of all samples in the dataset.

Returns:

mean intensity value in this dataset

getStdDev

public double getStdDev()

Deprecated.

Retrieve the standard deviation of all samples in the dataset, or -1 if standard deviation calculation was disabled or if a calculation error occurred while calculating the standard deviation.

Returns:

standard deviation, or -1

getBitDepth

public int getBitDepth()

Deprecated.

Retrieve the bit depth of the dataset. The highest pixel intensity in the dataset can not be higher than 2^bitDepth.

Returns:

bitdepth of the dataset

getBinSize

public int getBinSize()

Deprecated.

Retrieve the number of distinct intensities that fit within each bin of the histogram. For example, if this is 4, then the first bin will hold the number of samples whose intensities were 0, 1, 2, or 3.

Returns:

Range of pixel intensities that fit into a single bin in the histogram.

getNumSamples

public int getNumSamples()

Deprecated.

Retrieve the number of samples used to construct the histogram.

Returns:

Total number of bins in the histogram

toString

public java.lang.String toString()

Deprecated.

Overrides:

toString in class java.lang.Object