Sholl_Utils (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.plugin.ij1.Sholl_Utils

All Implemented Interfaces:

ij.plugin.PlugIn

Deprecated.
This IJ1 plugin is no longer needed when using IJ2 commands. Kept here for backwards compatibility
```
@Deprecated
public class Sholl_Utils
extends Object
implements ij.plugin.PlugIn
```
Utilities for Sholl_Analysis

Author:

Tiago Ferreira

See Also:

https://github.com/tferr/ASA, http://imagej.net/Sholl

Constructor Summary

Constructors
Constructor and Description

Sholl_Utils()
Deprecated.

Constructors
Constructor and Description
`Sholl_Utils()` Deprecated.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`static double[]`	`baryCenter(double[] xpoints, double[] ypoints)` Deprecated. Calculates the centroid of a non-self-intersecting closed polygon.
`protected static ij.ImagePlus`	`displaySample()` Deprecated. Displays the ddaC sample image and returns a reference to it.
`protected static String`	`getClipboardText()` Deprecated. Retrieves text from the system clipboard.
`protected static ij.text.TextWindow`	`getTextWindow(String windowtitle)` Deprecated.
`static void`	`makePlotLabel(Plot plot, String label, Color color)` Deprecated.
`static void`	`markPlotPoint(Plot plot, double[] coordinates, Color color)` Deprecated.
`static IndexColorModel`	`matlabJetColorMap(int backgroundGray)` Deprecated. Returns an IndexColorModel similar to MATLAB's jet color map.
`protected static IndexColorModel`	`matlabJetColorMap(int backgroundGray, int foregroundGray)` Deprecated.
`protected static String`	`ordinal(int i)` Deprecated.
`void`	`run(String arg)` Deprecated. This method is called when the plugin is loaded.
`static ij.ImagePlus`	`sampleImage()` Deprecated. Use `ShollUtils.sampleImage()` instead
`static String`	`version()` Deprecated. Use `SNTUtils.VERSION` instead

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

- Constructor Detail
  - Sholl_Utils
```
public Sholl_Utils()
```
    Deprecated.
- Method Detail
  - run
```
public void run(String arg)
```
    Deprecated.
    
    This method is called when the plugin is loaded. arg is specified in plugins.config. See PlugIn.run(java.lang.String)
    
    Specified by:
    
    run in interface ij.plugin.PlugIn
    
    Parameters:
    
    arg - If about the "About" dialog is displayed. If sample, a demo image suitable for Sholl analysis is opened.
  - sampleImage
```
@Deprecated
public static ij.ImagePlus sampleImage()
```
    Deprecated. Use ShollUtils.sampleImage() instead
    
    Returns the plugin's sample image (File>Samples>ddaC Neuron).
    
    Returns:
    
    ddaC image, or null if image cannot be retrieved
  - displaySample
```
protected static ij.ImagePlus displaySample()
```
    Deprecated.
    
    Displays the ddaC sample image and returns a reference to it.
    
    Returns:
    
    the ddaC sample image
  - matlabJetColorMap
```
public static IndexColorModel matlabJetColorMap(int backgroundGray)
```
    Deprecated.
    
    Returns an IndexColorModel similar to MATLAB's jet color map.
    
    Parameters:
    
    backgroundGray - the gray value (8-bit scale) to be used as the first entry of the LUT. It is ignored if negative.
    
    Returns:
    
    The "Jet" LUT with the specified background entry
    
    See Also:
    
    Jerome Mutterer alternative
  - matlabJetColorMap
```
protected static IndexColorModel matlabJetColorMap(int backgroundGray,
                                                   int foregroundGray)
```
    Deprecated.
  - ordinal
```
protected static String ordinal(int i)
```
    Deprecated.
  - baryCenter
```
public static double[] baryCenter(double[] xpoints,
                                  double[] ypoints)
```
    Deprecated.
    
    Calculates the centroid of a non-self-intersecting closed polygon. It is assumed that xpoints and ypoints have the same size
    
    Parameters:
    
    xpoints - X coordinates of vertices
    
    ypoints - Y coordinates of vertices
    
    Returns:
    
    the centroid {x,y} coordinates
    
    See Also:
    
    Centroid of polygon
  - makePlotLabel
```
@Deprecated
public static void makePlotLabel(Plot plot,
                                             String label,
                                             Color color)
```
    Deprecated.
  - markPlotPoint
```
@Deprecated
public static void markPlotPoint(Plot plot,
                                             double[] coordinates,
                                             Color color)
```
    Deprecated.
  - getClipboardText
```
protected static String getClipboardText()
```
    Deprecated.
    
    Retrieves text from the system clipboard.
    
    Returns:
    
    the text contents of the clipboard or an empty string if no text could be retrieved
  - getTextWindow
```
protected static ij.text.TextWindow getTextWindow(String windowtitle)
```
    Deprecated.
  - version
```
@Deprecated
public static String version()
```
    Deprecated. Use SNTUtils.VERSION instead
    
    Retrieves the Sholl Analysis version
    
    Returns:
    
    the version or a non-empty place holder string if version could not be retrieved.

Class Sholl_Utils

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Sholl_Utils

Method Detail

run

sampleImage

displaySample

matlabJetColorMap

matlabJetColorMap

ordinal

baryCenter

makePlotLabel

markPlotPoint

getClipboardText

getTextWindow

version