RankFilters (ImageJ API)

java.lang.Object
- ij.plugin.filter.RankFilters

All Implemented Interfaces:

DialogListener, ExtendedPlugInFilter, PlugInFilter
```
public class RankFilters
extends Object
implements ExtendedPlugInFilter, DialogListener
```
This plugin implements the Mean, Minimum, Maximum, Variance, Median, Open Maxima, Close Maxima, Remove Outliers, Remove NaNs and Despeckle commands.

Field Summary

Fields
Modifier and Type	Field	Description
`static int`	`BRIGHT_OUTLIERS`
`static int`	`CLOSE`
`static int`	`DARK_OUTLIERS`
`static int`	`DESPECKLE`
`static int`	`MAX`
`static int`	`MEAN`
`static int`	`MEDIAN`
`static int`	`MIN`
`static int`	`OPEN`
`static int`	`OUTLIERS`
`static int`	`REMOVE_NAN`
`static int`	`VARIANCE`

Fields inherited from interface ij.plugin.filter.ExtendedPlugInFilter
KEEP_PREVIEW

Fields inherited from interface ij.plugin.filter.PlugInFilter
CONVERT_TO_FLOAT, DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, FINAL_PROCESSING, KEEP_THRESHOLD, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, PARALLELIZE_IMAGES, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

Constructors
Constructor Description

RankFilters()

Constructors
Constructor	Description
`RankFilters()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`boolean`	`dialogItemChanged(GenericDialog gd, AWTEvent e)`	This method is invoked by a Generic Dialog if any of the inputs have changed (CANCEL does not trigger it; OK and running the dialog from a macro only trigger the first DialogListener added to a GenericDialog).
`static float`	`findNthLowestNumber(float[] buf, int bufLength, int n)`	Find the n-th lowest number in part of an array
`void`	`makeKernel(double radius)`	Deprecated. Not needed any more, use the rank(ip, ...) method, which creates the kernel
`protected int[]`	`makeLineRadii(double radius)`	Create a circular kernel (structuring element) of a given radius.
`void`	`rank(ImageProcessor ip, double radius, int filterType)`	Filters an image by any method except 'despecle' or 'remove outliers'.
`void`	`rank(ImageProcessor ip, double radius, int filterType, int whichOutliers, float threshold)`	Filters an image by any method except 'despecle' (for 'despeckle', use 'median' and radius=1)
`void`	`run(ImageProcessor ip)`	Filters use this method to process the image.
`void`	`setNPasses(int nPasses)`	This method is called by ImageJ to set the number of calls to run(ip) corresponding to 100% of the progress bar
`int`	`setup(String arg, ImagePlus imp)`	Setup of the PlugInFilter.
`int`	`showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr)`	This method is called after `setup(arg, imp)` unless the `DONE` flag has been set.

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

- Field Detail
  - MEAN
```
public static final int MEAN
```
    See Also:
    
    Constant Field Values
  - MIN
```
public static final int MIN
```
    See Also:
    
    Constant Field Values
  - MAX
```
public static final int MAX
```
    See Also:
    
    Constant Field Values
  - VARIANCE
```
public static final int VARIANCE
```
    See Also:
    
    Constant Field Values
  - MEDIAN
```
public static final int MEDIAN
```
    See Also:
    
    Constant Field Values
  - OUTLIERS
```
public static final int OUTLIERS
```
    See Also:
    
    Constant Field Values
  - DESPECKLE
```
public static final int DESPECKLE
```
    See Also:
    
    Constant Field Values
  - REMOVE_NAN
```
public static final int REMOVE_NAN
```
    See Also:
    
    Constant Field Values
  - OPEN
```
public static final int OPEN
```
    See Also:
    
    Constant Field Values
  - CLOSE
```
public static final int CLOSE
```
    See Also:
    
    Constant Field Values
  - BRIGHT_OUTLIERS
```
public static final int BRIGHT_OUTLIERS
```
    See Also:
    
    Constant Field Values
  - DARK_OUTLIERS
```
public static final int DARK_OUTLIERS
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - RankFilters
```
public RankFilters()
```
- Method Detail
  - setup
```
public int setup(String arg,
                 ImagePlus imp)
```
    Setup of the PlugInFilter. Returns the flags specifying the capabilities and needs of the filter.
    
    Specified by:
    
    setup in interface PlugInFilter
    
    Parameters:
    
    arg - Defines type of filter operation
    
    imp - The ImagePlus to be processed
    
    Returns:
    
    Flags specifying further action of the PlugInFilterRunner
  - showDialog
```
public int showDialog(ImagePlus imp,
                      String command,
                      PlugInFilterRunner pfr)
```
    Description copied from interface: ExtendedPlugInFilter
    
    This method is called after setup(arg, imp) unless the DONE flag has been set.
    
    Specified by:
    
    showDialog in interface ExtendedPlugInFilter
    
    Parameters:
    
    imp - The active image already passed in the setup(arg, imp) call. It will be null, however, if the NO_IMAGE_REQUIRED flag has been set.
    
    command - The command that has led to the invocation of the plugin-filter. Useful as a title for the dialog.
    
    pfr - The PlugInFilterRunner calling this plugin-filter. It can be passed to a GenericDialog by addPreviewCheckbox to enable preview by calling the run(ip) method of this plugin-filter. pfr can be also used later for calling back the PlugInFilterRunner, e.g., to obtain the slice number currently processed by run(ip).
    
    Returns:
    
    The method should return a combination (bitwise OR) of the flags specified in interfaces PlugInFilter and ExtendedPlugInFilter.
  - dialogItemChanged
```
public boolean dialogItemChanged(GenericDialog gd,
                                 AWTEvent e)
```
    Description copied from interface: DialogListener
    
    This method is invoked by a Generic Dialog if any of the inputs have changed (CANCEL does not trigger it; OK and running the dialog from a macro only trigger the first DialogListener added to a GenericDialog).
    
    Specified by:
    
    dialogItemChanged in interface DialogListener
    
    Parameters:
    
    gd - A reference to the GenericDialog.
    
    e - The event that has been generated by the user action in the dialog. Note that e is null if the dialogItemChanged method is called after the user has pressed the OK button or if the GenericDialog has read its parameters from a macro.
    
    Returns:
    
    Should be true if the dialog input is valid. False disables the OK button and preview (if any).
  - run
```
public void run(ImageProcessor ip)
```
    Description copied from interface: PlugInFilter
    
    Filters use this method to process the image. If the PlugInFilter.DOES_STACKS flag was set, it is called for each slice in a stack. With PlugInFilter.CONVERT_TO_FLOAT, the filter is called with the image data converted to a FloatProcessor (3 times per image for RGB images). ImageJ will lock the image before calling this method and unlock it when the filter is finished. For PlugInFilters specifying the PlugInFilter.NO_IMAGE_REQUIRED flag and not the PlugInFilter.DONE flag, run(ip) is called once with the argument null.
    
    Specified by:
    
    run in interface PlugInFilter
  - rank
```
public void rank(ImageProcessor ip,
                 double radius,
                 int filterType)
```
    Filters an image by any method except 'despecle' or 'remove outliers'.
    
    Parameters:
    
    ip - The ImageProcessor that should be filtered (all 4 types supported)
    
    radius - Determines the kernel size, see Process>Filters>Show Circular Masks. Must not be negative. No checking is done for large values that would lead to excessive computing times.
    
    filterType - May be MEAN, MIN, MAX, VARIANCE, or MEDIAN.
  - rank
```
public void rank(ImageProcessor ip,
                 double radius,
                 int filterType,
                 int whichOutliers,
                 float threshold)
```
    Filters an image by any method except 'despecle' (for 'despeckle', use 'median' and radius=1)
    
    Parameters:
    
    ip - The image subject to filtering
    
    radius - The kernel radius
    
    filterType - as defined above; DESPECKLE is not a valid type here; use median and a radius of 1.0 instead
    
    whichOutliers - BRIGHT_OUTLIERS or DARK_OUTLIERS for 'outliers' filter
    
    threshold - Threshold for 'outliers' filter
  - findNthLowestNumber
```
public static final float findNthLowestNumber(float[] buf,
                                              int bufLength,
                                              int n)
```
    Find the n-th lowest number in part of an array
    
    Parameters:
    
    buf - The input array. Only values 0 ... bufLength are read. buf will be modified.
    
    bufLength - Number of values in buf that should be read
    
    n - which value should be found; n=0 for the lowest, n=bufLength-1 for the highest
    
    Returns:
    
    the value
  - makeKernel
```
public void makeKernel(double radius)
```
    Deprecated.
    Not needed any more, use the rank(ip, ...) method, which creates the kernel
  - makeLineRadii
```
protected int[] makeLineRadii(double radius)
```
    Create a circular kernel (structuring element) of a given radius.
    
    Parameters:
    
    radius - Radius = 0.5 includes the 4 neighbors of the pixel in the center, radius = 1 corresponds to a 3x3 kernel size.
    
    Returns:
    
    the circular kernel The output is an array that gives the length of each line of the structuring element (kernel) to the left (negative) and to the right (positive): [0] left in line 0, [1] right in line 0, [2] left in line 2, ... The maximum (absolute) value should be kernelRadius. Array elements at the end: length-2: nPoints, number of pixels in the kernel area length-1: kernelRadius in x direction (kernel width is 2*kernelRadius+1) Kernel height can be calculated as (array length - 1)/2 (odd number); Kernel radius in y direction is kernel height/2 (truncating integer division). Note that kernel width and height are the same for the circular kernels used here, but treated separately for the case of future extensions with non-circular kernels.
  - setNPasses
```
public void setNPasses(int nPasses)
```
    This method is called by ImageJ to set the number of calls to run(ip) corresponding to 100% of the progress bar
    
    Specified by:
    
    setNPasses in interface ExtendedPlugInFilter

Class RankFilters

Field Summary

Fields inherited from interface ij.plugin.filter.ExtendedPlugInFilter

Fields inherited from interface ij.plugin.filter.PlugInFilter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MEAN

MIN

MAX

VARIANCE

MEDIAN

OUTLIERS

DESPECKLE

REMOVE_NAN

OPEN

CLOSE

BRIGHT_OUTLIERS

DARK_OUTLIERS

Constructor Detail

RankFilters

Method Detail

setup

showDialog

dialogItemChanged

run

rank

rank

findNthLowestNumber

makeKernel

makeLineRadii

setNPasses