Sholl_Analysis (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

DialogListener, ij.plugin.PlugIn

Deprecated.
This IJ1 plugin has now been replaced by its IJ2 counterpart. Kept here for backwards compatibility
```
@Deprecated
public class Sholl_Analysis
extends Object
implements ij.plugin.PlugIn, DialogListener
```
ImageJ 1 plugin that uses the Sholl technique to perform neuronal morphometry directly from bitmap images.

Author:

Tiago Ferreira (based on an earlier implementation by Tom Maddock)

See Also:

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

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`BIN_AVERAGE` Deprecated. Flag for integration of repeated measures (2D analysis): average
`static int`	`BIN_MEDIAN` Deprecated. Flag for integration of repeated measures (2D analysis): median
`static int`	`BIN_MODE` Deprecated. Flag for integration of repeated measures (2D analysis): mode
`protected static String[]`	`DEGREES` Deprecated.
`static int`	`MAX_N_SPANS` Deprecated.
`static String`	`URL` Deprecated.
`static String`	`VERSION` Deprecated. The Plugin's version

Constructor Summary

Constructors
Constructor and Description

Sholl_Analysis()
Deprecated.

Constructors
Constructor and Description
`Sholl_Analysis()` Deprecated.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`double[]`	`analyze2D(int xc, int yc, double[] radii, double pixelSize, int binsize, int bintype, ij.ImagePlus imp)` Deprecated.
`double[]`	`analyze3D(int xc, int yc, int zc, double[] radii, ij.ImagePlus img)` Deprecated.
`void`	`analyzeProfile(double[] distances, double[] inters, boolean threeD)` Deprecated. Analyzes a sampled profile.
`void`	`analyzeTabularInput(File csvFile, int rCol, int cCol, boolean threeD)` Deprecated. Instructs the plugin to parse the specified file expected to contain a sampled profile.
`void`	`analyzeTabularInput(ij.measure.ResultsTable rt, int rCol, int cCol, boolean threeD)` Deprecated. Instructs the plugin to parse the specified table expected to contain a sampled profile.
`boolean`	`dialogItemChanged(GenericDialog gd, AWTEvent e)` Deprecated. Retrieves values from the dialog, disabling dialog components that are not applicable.
`int[][]`	`getCircumferencePoints(int cx, int cy, int radius)` Deprecated.
`String`	`getDescription()` Deprecated.
`sc.fiji.snt.plugin.ij1.EnhancedResultsTable`	`getShollTable()` Deprecated. Returns a reference to the plugin's "Sholl Results" table displaying summary statistics.
`void`	`run(String arg)` Deprecated. This method is called when the plugin is loaded.
`void`	`setCenter(int xc, int yc, int zc)` Deprecated. Sets the analysis center.
`void`	`setDescription(String label, boolean makeUnique)` Deprecated. Associates the analysis with an identifier.
`void`	`setExportPath(String exportDir)` Deprecated.
`void`	`setExportPath(String exportDir, boolean displaySavedFiles)` Deprecated.
`void`	`setInteractiveMode(boolean interactive)` Deprecated. Instructs the plugin to run in headless mode or with user interaction.
`void`	`setOptions(ShollOptions options)` Deprecated. Assigns options to the plugin.
`void`	`setPlotLabels(boolean plotLabels)` Deprecated. Controls the inclusion of fitting details in Sholl plots.
`void`	`setPlotLabels(String booleanString)` Deprecated. Alternative to `setPlotLabels()` to be called by IJ macros using the call() built-in macro function
`void`	`setPrecision(int precision)` Deprecated. Sets the precision used to calculate metrics from fitted data, such as Nav and Nm.
`void`	`setPrecision(String intString)` Deprecated. Alternative to `setPrecision()` to be called by IJ macros using the call() built-in macro function
`void`	`setPrimaryBranches(double nBranches)` Deprecated.
`void`	`setStepRadius(double stepRadius)` Deprecated. Sets the radius step size (shell spacing).
`void`	`setThreshold(int lower, int upper)` Deprecated. Sets the threshold limits.
`void`	`setUnit(String unit)` Deprecated. Sets the unit for sampling distances.
`void`	`setVerbose(boolean verbose)` Deprecated.
`boolean`	`validateImage(ij.ImagePlus imp)` Deprecated. Checks if image to be analyzed is valid.

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

- Field Detail
  - VERSION
```
public static final String VERSION
```
    Deprecated.
    
    The Plugin's version
  - URL
```
public static final String URL
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - DEGREES
```
protected static final String[] DEGREES
```
    Deprecated.
  - BIN_AVERAGE
```
public static final int BIN_AVERAGE
```
    Deprecated.
    
    Flag for integration of repeated measures (2D analysis): average
    
    See Also:
    
    Constant Field Values
  - BIN_MEDIAN
```
public static final int BIN_MEDIAN
```
    Deprecated.
    
    Flag for integration of repeated measures (2D analysis): median
    
    See Also:
    
    Constant Field Values
  - BIN_MODE
```
public static final int BIN_MODE
```
    Deprecated.
    
    Flag for integration of repeated measures (2D analysis): mode
    
    See Also:
    
    Constant Field Values
  - MAX_N_SPANS
```
public static final int MAX_N_SPANS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Sholl_Analysis
```
public Sholl_Analysis()
```
    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 image, the plugin runs in "bitmap mode" If csv the plugin is set for analysis of tabular data. If sample, the plugin runs on a 2D demo image.
  - setOptions
```
public void setOptions(ShollOptions options)
```
    Deprecated.
    
    Assigns options to the plugin.
    
    Parameters:
    
    options - the ShollOptions instance use to customize the plugin's output.
  - dialogItemChanged
```
public boolean dialogItemChanged(GenericDialog gd,
                                 AWTEvent e)
```
    Deprecated.
    
    Retrieves values from the dialog, disabling dialog components that are not applicable. Returns false if no analysis method was chosen
    
    Specified by:
    
    dialogItemChanged in interface DialogListener
    
    Parameters:
    
    gd - reference to the GenericDialog
    
    e - the event generated by the user in the dialog
    
    Returns:
    
    true, if options are valid
  - analyze3D
```
@Deprecated
public double[] analyze3D(int xc,
                                      int yc,
                                      int zc,
                                      double[] radii,
                                      ij.ImagePlus img)
```
    Deprecated.
    
    Measures intersections for each sphere surface (does the actual 3D analysis). Accepts an array of radii and takes the measurement(s) at each radius. Requires threshold values to be set beforehand using setThreshold(int, int).
    
    Parameters:
    
    xc - the X position of the analysis center
    
    yc - the Y position of the analysis center
    
    zc - the Z position (slice) of the analysis center
    
    radii - the sampling distances
    
    img - The image being analyzed
    
    Returns:
    
    intersection counts (the linear profile of sampled data)
    
    See Also:
    
    setInteractiveMode(boolean)
  - analyze2D
```
@Deprecated
public double[] analyze2D(int xc,
                                      int yc,
                                      double[] radii,
                                      double pixelSize,
                                      int binsize,
                                      int bintype,
                                      ij.ImagePlus imp)
```
    Deprecated.
    
    Does the actual 2D analysis. Accepts an array of radii and takes the measurement(s) at each radius. Requires threshold values to be set beforehand using setThreshold(int, int).
    
    Parameters:
    
    xc - the X position of the analysis center
    
    yc - the Y position of the analysis center
    
    radii - the sampling distances
    
    pixelSize - pixel dimensions (spatial calibration)
    
    binsize - the number of samples to be retrieved at each radius
    
    bintype - flag for integration of multiple samples: BIN_AVERAGE, BIN_MEDIAN or BIN_MODE
    
    imp - ImageProcessor of analyzed image
    
    Returns:
    
    intersection counts (the linear profile of sampled data)
    
    See Also:
    
    setInteractiveMode(boolean)
  - getCircumferencePoints
```
@Deprecated
public int[][] getCircumferencePoints(int cx,
                                                  int cy,
                                                  int radius)
```
    Deprecated.
    
    Returns the location of pixels clockwise along a (1-pixel wide) circumference using Bresenham's Circle Algorithm.
    
    Parameters:
    
    cx - the X position of the analysis center
    
    cy - the Y position of the analysis center
    
    radius - the circumference radius
    
    Returns:
    
    the circumference points
  - setThreshold
```
public void setThreshold(int lower,
                         int upper)
```
    Deprecated.
    
    Sets the threshold limits. With grayscale images, the method must be called upfront since analysis is performed on segmented arbors. Note that with binary images, background is always considered to be 0, independently of Prefs.blackBackground
    
    Parameters:
    
    lower - the lower threshold value
    
    upper - the upper threshol value
  - validateImage
```
public boolean validateImage(ij.ImagePlus imp)
```
    Deprecated.
    
    Checks if image to be analyzed is valid.
    
    Parameters:
    
    imp - the image being analyzed
    
    Returns:
    
    true, if valid (8/16 bit, 2D/3D, single or multi-channel)
  - setPlotLabels
```
public void setPlotLabels(boolean plotLabels)
```
    Deprecated.
    
    Controls the inclusion of fitting details in Sholl plots.
    
    Parameters:
    
    plotLabels - If true, plotting labels will be added to plots when performing curve fitting
  - setPrecision
```
public void setPrecision(int precision)
```
    Deprecated.
    
    Sets the precision used to calculate metrics from fitted data, such as Nav and Nm.
    
    Parameters:
    
    precision - The precision value as a fraction of radius step size. Eg, 100 sets accuracy to radiusStepSize/100
  - setPlotLabels
```
public void setPlotLabels(String booleanString)
```
    Deprecated.
    
    Alternative to setPlotLabels() to be called by IJ macros using the call() built-in macro function
    An error message is displayed in the IJ Log window if booleanString can not be parsed. Usage example: call("sholl.Sholl_Analysis.setPlotLabels", "false");
    
    Parameters:
    
    booleanString - If "true", plotting labels will be added.
  - setPrecision
```
public void setPrecision(String intString)
```
    Deprecated.
    
    Alternative to setPrecision() to be called by IJ macros using the call() built-in macro function
    An error message is displayed in the IJ Log window if intString is invalid. Usage example: call("sholl.Sholl_Analysis.setPrecision", "1000");
    
    Parameters:
    
    intString - The string integer to set the precision in terms of radius step size. Eg, "100" sets accuracy to radiusStepSize/100
  - analyzeTabularInput
```
public void analyzeTabularInput(ij.measure.ResultsTable rt,
                                int rCol,
                                int cCol,
                                boolean threeD)
```
    Deprecated.
    
    Instructs the plugin to parse the specified table expected to contain a sampled profile. Does nothing if the specified table does not contain the specified column indices.
    
    Parameters:
    
    rt - the input ResultsTable
    
    rCol - the index of the radii column
    
    cCol - the index of the intersections count column
    
    threeD - 3D analysis?
    
    See Also:
    
    setStepRadius(double), validTable(ResultsTable), setInteractiveMode(boolean)
  - analyzeTabularInput
```
public void analyzeTabularInput(File csvFile,
                                int rCol,
                                int cCol,
                                boolean threeD)
                         throws IOException
```
    Deprecated.
    
    Instructs the plugin to parse the specified file expected to contain a sampled profile.
    
    Parameters:
    
    csvFile - the input file expected to contain tabular data in any of the formats recognized by ResultsTable
    
    rCol - the index of the radii column
    
    cCol - the index of the intersections count column
    
    threeD - 3D analysis?
    
    Throws:
    
    IOException - if file could be opened.
    
    See Also:
    
    setInteractiveMode(boolean), setStepRadius(double)
  - analyzeProfile
```
public void analyzeProfile(double[] distances,
                           double[] inters,
                           boolean threeD)
```
    Deprecated.
    
    Analyzes a sampled profile.
    
    Parameters:
    
    distances - the array containing radii
    
    inters - the array containing intersection counts
    
    threeD - 3D profile?
    
    See Also:
    
    setInteractiveMode(boolean)
  - setPrimaryBranches
```
public void setPrimaryBranches(double nBranches)
```
    Deprecated.
    
    Parameters:
    
    nBranches - the number of primary branches to be used in the calculation of ramification indices. Must be greater than 0.
  - setExportPath
```
public void setExportPath(String exportDir)
```
    Deprecated.
    
    Parameters:
    
    exportDir - The path to the directory where results should be saved. null not allowed.
    
    See Also:
    
    setExportPath(String, boolean)
  - setExportPath
```
public void setExportPath(String exportDir,
                          boolean displaySavedFiles)
```
    Deprecated.
    
    Parameters:
    
    exportDir - The path to the directory where results should be saved. null not allowed. Files will only be saved if the specified path is valid.
    
    displaySavedFiles - If saved plots and tables should be displayed.
  - setVerbose
```
public void setVerbose(boolean verbose)
```
    Deprecated.
    
    Parameters:
    
    verbose - Whether details on curve fitting should be displayed
  - setInteractiveMode
```
public void setInteractiveMode(boolean interactive)
```
    Deprecated.
    
    Instructs the plugin to run in headless mode or with user interaction.
    
    Parameters:
    
    interactive - Whether dialog prompts should be displayed to collect input from the user
  - setDescription
```
public void setDescription(String label,
                           boolean makeUnique)
```
    Deprecated.
    
    Associates the analysis with an identifier.
    
    Parameters:
    
    label - the label describing the analysis. It is used in the titles of frames and images when displaying results
    
    makeUnique - if true and ImageJ is already displaying a window using the same label as title, a suffix ("-1", "-2", etc.) is appended to label to ensure it is unique
  - getDescription
```
public String getDescription()
```
    Deprecated.
    
    Returns:
    
    the label describing the analysis
  - setCenter
```
public void setCenter(int xc,
                      int yc,
                      int zc)
```
    Deprecated.
    
    Sets the analysis center.
    
    Parameters:
    
    xc - the x coordinate (in pixels)
    
    yc - the y coordinate (in pixels)
    
    zc - the z coordinate (slice number)
  - setUnit
```
public void setUnit(String unit)
```
    Deprecated.
    
    Sets the unit for sampling distances.
    
    Parameters:
    
    unit - the physical unit, e.g., "mm"
  - setStepRadius
```
public void setStepRadius(double stepRadius)
```
    Deprecated.
    
    Sets the radius step size (shell spacing).
    
    Parameters:
    
    stepRadius - the step size in physical units
  - getShollTable
```
public sc.fiji.snt.plugin.ij1.EnhancedResultsTable getShollTable()
```
    Deprecated.
    
    Returns a reference to the plugin's "Sholl Results" table displaying summary statistics.
    
    Returns:
    
    the "Sholl Results" table

Class Sholl_Analysis

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

VERSION

URL

DEGREES

BIN_AVERAGE

BIN_MEDIAN

BIN_MODE

MAX_N_SPANS

Constructor Detail

Sholl_Analysis

Method Detail

run

setOptions

dialogItemChanged

analyze3D

analyze2D

getCircumferencePoints

setThreshold

validateImage

setPlotLabels

setPrecision

setPlotLabels

setPrecision

analyzeTabularInput

analyzeTabularInput

analyzeProfile

setPrimaryBranches

setExportPath

setExportPath

setVerbose

setInteractiveMode

setDescription

getDescription

setCenter

setUnit

setStepRadius

getShollTable