ShollOptions (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

ij.plugin.PlugIn

Deprecated.
```
@Deprecated
public class ShollOptions
extends Object
implements ij.plugin.PlugIn
```
Implements the IJ1 "Sholl Options and Metrics" command.

Author:

Tiago Ferreira

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`ALL_PLOTS` Deprecated.
`static int`	`CENTER` Deprecated.
`static int`	`CENTROID` Deprecated.
`static String`	`COMMAND_LABEL` Deprecated. The Menu entry of this plugin as specified in plugins.config
`static int`	`CURVE_FITTING` Deprecated.
`static int`	`DIRECTORY` Deprecated.
`static int`	`ENCLOSING_RADIUS` Deprecated.
`protected static String`	`ENCLOSING_RADIUS_KEY` Deprecated.
`protected static String`	`END_RADIUS_KEY` Deprecated.
`static int`	`ENDING_RADIUS` Deprecated.
`protected static int`	`FITTED_MASK` Deprecated.
`static int`	`GUESS_LOG_METHOD` Deprecated.
`static int`	`HIDE_SAVED_FILES` Deprecated.
`static int`	`INFER_PRIMARY` Deprecated.
`protected boolean`	`instanceAttatchedToPlugin` Deprecated.
`protected static String`	`INTEGRATION_KEY` Deprecated.
`static int`	`INTERSECTING_RADII` Deprecated.
`static int`	`KURTOSIS` Deprecated.
`static int`	`MEAN_INTERS` Deprecated.
`static int`	`MEDIAN_INTERS` Deprecated.
`static int`	`NO_PLOTS` Deprecated.
`static int`	`NO_TABLE` Deprecated.
`protected static String`	`NORMALIZER_INDEX_KEY` Deprecated.
`protected static String`	`NSAMPLES_KEY` Deprecated.
`static int`	`ONLY_LINEAR_PLOT` Deprecated.
`static int`	`OVERLAY_SHELLS` Deprecated.
`static int`	`P1090_REGRESSION` Deprecated.
`protected static String`	`POLYNOMIAL_INDEX_KEY` Deprecated.
`protected static String`	`PRIMARY_BRANCHES_KEY` Deprecated.
`protected static String`	`QUAD_CHOICE_KEY` Deprecated.
`static int`	`RADIUS_STEP` Deprecated.
`static int`	`SAMPLES_PER_RADIUS` Deprecated.
`protected static String`	`SAVE_DIR_KEY` Deprecated.
`static int`	`SAVE_FILES` Deprecated.
`static int`	`SHOLL_LOG` Deprecated.
`static int`	`SHOLL_N` Deprecated.
`static int`	`SHOLL_NS` Deprecated.
`static int`	`SHOLL_SLOG` Deprecated.
`static int`	`SHOW_MASK` Deprecated.
`static int`	`SKEWNESS` Deprecated.
`static String`	`SKIP_BITMAP_OPTIONS_LABEL` Deprecated. Argument for `run(String)`
`static int`	`SKIP_SINGLE_VOXELS` Deprecated.
`protected static String`	`START_RADIUS_KEY` Deprecated.
`static int`	`STARTING_RADIUS` Deprecated.
`protected static String`	`STEP_SIZE_KEY` Deprecated.
`protected HashMap<String,String>`	`stringPrefs` Deprecated.
`static int`	`SUM_INTERS` Deprecated.
`static int`	`THRESHOLD` Deprecated.
`static int`	`TRIM_BOUNDS` Deprecated.
`static int`	`UNIT` Deprecated.
`static int`	`VERBOSE` Deprecated.

Constructor Summary

Constructors
Constructor and Description

ShollOptions()
Deprecated.

ShollOptions(boolean attachInstanceToPlugin)
Deprecated.

Constructors
Constructor and Description
`ShollOptions()` Deprecated.
`ShollOptions(boolean attachInstanceToPlugin)` Deprecated.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`protected int`	`getBooleanPrefs()` Deprecated.
`protected String`	`getCommentString()` Deprecated.
`protected int`	`getDefaultBooleanPrefs()` Deprecated.
`protected static int`	`getDefaultMetrics()` Deprecated.
`protected double`	`getDoubleFromHashMap(String key, double defaultValue)` Deprecated.
`protected int`	`getIntFromHashMap(String key, int defaultValue)` Deprecated.
`protected int`	`getMaskBackground()` Deprecated. Returns the background color of the Sholl mask image
`protected int`	`getMaskType()` Deprecated. Returns the type of data to be used in Sholl mask.
`protected int`	`getMetrics()` Deprecated.
`protected int`	`getPlotOutput()` Deprecated. Returns the flag for outputPlots.
`protected int`	`getScientificNotationAwarePrecision()` Deprecated. Retrieves precision according to `Analyze>Set Measurements...`
`protected String`	`getStringFromHashMap(String key, String defaultValue)` Deprecated.
`void`	`run(String arg)` Deprecated. This method is called when the plugin is loaded.
`protected void`	`saveStringPreferences()` Deprecated.
`protected void`	`setBooleanPrefs(int newValue)` Deprecated.
`protected void`	`setCommentString(String comment)` Deprecated.
`protected void`	`setMaskBackground(int grayLevel)` Deprecated. Sets the background color of the Sholl mask
`protected void`	`setMaskType(int type)` Deprecated. Sets the type of data to be used in Sholl mask.
`void`	`setMetric(int key, boolean value)` Deprecated.
`void`	`setNoPlots(boolean noPlots)` Deprecated.
`void`	`setNoTable(boolean noTable)` Deprecated.
`void`	`setPlotOutput(int output)` Deprecated. Sets the flag for output plots.
`void`	`setPromptChoice(int key, boolean value)` Deprecated.
`void`	`setSkipBitmapOptions(boolean skipBitmapOptions)` Deprecated.
`protected void`	`setStringPreference(String key, double value)` Deprecated.
`protected void`	`setStringPreference(String key, int value)` Deprecated.
`protected void`	`setStringPreference(String key, String value)` Deprecated.

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

- Field Detail
  - COMMAND_LABEL
```
public static final String COMMAND_LABEL
```
    Deprecated.
    
    The Menu entry of this plugin as specified in plugins.config
    
    See Also:
    
    Constant Field Values
  - SKIP_BITMAP_OPTIONS_LABEL
```
public static final String SKIP_BITMAP_OPTIONS_LABEL
```
    Deprecated.
    
    Argument for run(String)
    
    See Also:
    
    Constant Field Values
  - DIRECTORY
```
public static final int DIRECTORY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - UNIT
```
public static final int UNIT
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - THRESHOLD
```
public static final int THRESHOLD
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - CENTER
```
public static final int CENTER
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - STARTING_RADIUS
```
public static final int STARTING_RADIUS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - ENDING_RADIUS
```
public static final int ENDING_RADIUS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - RADIUS_STEP
```
public static final int RADIUS_STEP
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SAMPLES_PER_RADIUS
```
public static final int SAMPLES_PER_RADIUS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - ENCLOSING_RADIUS
```
public static final int ENCLOSING_RADIUS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - INTERSECTING_RADII
```
public static final int INTERSECTING_RADII
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SUM_INTERS
```
public static final int SUM_INTERS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - MEAN_INTERS
```
public static final int MEAN_INTERS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - MEDIAN_INTERS
```
public static final int MEDIAN_INTERS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SKEWNESS
```
public static final int SKEWNESS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - KURTOSIS
```
public static final int KURTOSIS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - CENTROID
```
public static final int CENTROID
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - P1090_REGRESSION
```
public static final int P1090_REGRESSION
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - NO_TABLE
```
public static final int NO_TABLE
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - TRIM_BOUNDS
```
public static final int TRIM_BOUNDS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - INFER_PRIMARY
```
public static final int INFER_PRIMARY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - CURVE_FITTING
```
public static final int CURVE_FITTING
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - VERBOSE
```
public static final int VERBOSE
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SHOLL_N
```
public static final int SHOLL_N
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SHOLL_NS
```
public static final int SHOLL_NS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SHOLL_SLOG
```
public static final int SHOLL_SLOG
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SHOLL_LOG
```
public static final int SHOLL_LOG
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - GUESS_LOG_METHOD
```
public static final int GUESS_LOG_METHOD
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SHOW_MASK
```
public static final int SHOW_MASK
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - OVERLAY_SHELLS
```
public static final int OVERLAY_SHELLS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SAVE_FILES
```
public static final int SAVE_FILES
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - HIDE_SAVED_FILES
```
public static final int HIDE_SAVED_FILES
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SKIP_SINGLE_VOXELS
```
public static final int SKIP_SINGLE_VOXELS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - stringPrefs
```
protected HashMap<String,String> stringPrefs
```
    Deprecated.
  - START_RADIUS_KEY
```
protected static final String START_RADIUS_KEY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - END_RADIUS_KEY
```
protected static final String END_RADIUS_KEY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - STEP_SIZE_KEY
```
protected static final String STEP_SIZE_KEY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - NSAMPLES_KEY
```
protected static final String NSAMPLES_KEY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - INTEGRATION_KEY
```
protected static final String INTEGRATION_KEY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - ENCLOSING_RADIUS_KEY
```
protected static final String ENCLOSING_RADIUS_KEY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - PRIMARY_BRANCHES_KEY
```
protected static final String PRIMARY_BRANCHES_KEY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - POLYNOMIAL_INDEX_KEY
```
protected static final String POLYNOMIAL_INDEX_KEY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - NORMALIZER_INDEX_KEY
```
protected static final String NORMALIZER_INDEX_KEY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SAVE_DIR_KEY
```
protected static final String SAVE_DIR_KEY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - QUAD_CHOICE_KEY
```
protected static final String QUAD_CHOICE_KEY
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - FITTED_MASK
```
protected static final int FITTED_MASK
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - ALL_PLOTS
```
public static final int ALL_PLOTS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - ONLY_LINEAR_PLOT
```
public static final int ONLY_LINEAR_PLOT
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - NO_PLOTS
```
public static final int NO_PLOTS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - instanceAttatchedToPlugin
```
protected boolean instanceAttatchedToPlugin
```
    Deprecated.
- Constructor Detail
  - ShollOptions
```
public ShollOptions(boolean attachInstanceToPlugin)
```
    Deprecated.
  - ShollOptions
```
public ShollOptions()
```
    Deprecated.
- Method Detail
  - run
```
public void run(String arg)
```
    Deprecated.
    
    This method is called when the plugin is loaded. arg can be specified in plugins.config.
    
    Specified by:
    
    run in interface ij.plugin.PlugIn
    
    Parameters:
    
    arg - If RESET_OPTIONS_LABEL options and preferences are reset to defaults. If SKIP_BITMAP_OPTIONS_LABEL options specific to bitmap analysis are not displayed in GUI when displaying prompt.
  - getDefaultMetrics
```
protected static int getDefaultMetrics()
```
    Deprecated.
  - getMetrics
```
protected int getMetrics()
```
    Deprecated.
  - getDefaultBooleanPrefs
```
protected int getDefaultBooleanPrefs()
```
    Deprecated.
  - getBooleanPrefs
```
protected int getBooleanPrefs()
```
    Deprecated.
  - getMaskBackground
```
protected int getMaskBackground()
```
    Deprecated.
    
    Returns the background color of the Sholl mask image
    
    Returns:
    
    the gray value (8-bit scale) of the first entry of the LUT of the Sholl mask's LUT image
    
    See Also:
    
    Sholl_Utils.matlabJetColorMap(int)
  - setMaskBackground
```
protected void setMaskBackground(int grayLevel)
```
    Deprecated.
    
    Sets the background color of the Sholl mask
    
    Parameters:
    
    grayLevel - the gray value (8-bit scale) to be used as the first entry of the LUT of the Sholl mask image
    
    See Also:
    
    Sholl_Utils.matlabJetColorMap(int)
  - getMaskType
```
protected int getMaskType()
```
    Deprecated.
    
    Returns the type of data to be used in Sholl mask.
    
    Returns:
    
    the type of mask. Either Options.SAMPLED_MASK or Options.FITTED_MASK.
  - setPlotOutput
```
public void setPlotOutput(int output)
```
    Deprecated.
    
    Sets the flag for output plots.
    
    Parameters:
    
    output - the output flag. Either Options.ALL_PLOTS, Options.ONLY_LINEAR_PLOT or Options.NO_PLOTS
  - getPlotOutput
```
protected int getPlotOutput()
```
    Deprecated.
    
    Returns the flag for outputPlots.
    
    Returns:
    
    the output flag. Either Options.ALL_PLOTS, Options.ONLY_LINEAR_PLOT or Options.NO_PLOTS
  - setBooleanPrefs
```
protected void setBooleanPrefs(int newValue)
```
    Deprecated.
  - setMaskType
```
protected void setMaskType(int type)
```
    Deprecated.
    
    Sets the type of data to be used in Sholl mask.
    
    Parameters:
    
    type - the type of mask. Either Options.SAMPLED_MASK or Options.FITTED_MASK.
  - getCommentString
```
protected String getCommentString()
```
    Deprecated.
  - setCommentString
```
protected void setCommentString(String comment)
```
    Deprecated.
  - getScientificNotationAwarePrecision
```
protected int getScientificNotationAwarePrecision()
```
    Deprecated.
    
    Retrieves precision according to Analyze>Set Measurements...
    
    Returns:
    
    the number of decimal digits to be used in tables
  - setNoPlots
```
@Deprecated
public void setNoPlots(boolean noPlots)
```
    Deprecated.
    
    Instructs Sholl_Analysis to exclude plots from output (only tables will be displayed).
    
    Parameters:
    
    noPlots - If true, plugin will only output tables. If false, both tables and plots will be produced (the default)
  - setMetric
```
public void setMetric(int key,
                      boolean value)
```
    Deprecated.
  - setPromptChoice
```
public void setPromptChoice(int key,
                            boolean value)
```
    Deprecated.
  - setNoTable
```
@Deprecated
public void setNoTable(boolean noTable)
```
    Deprecated.
    
    Instructs Sholl_Analysis to exclude detailed table from output (Summary table is still displayed).
    
    Parameters:
    
    noTable - If true, plugin will not output the "detailed table" containing all the retrieved profiles. Note that the Summary "Sholl Results" table is always displayed.
    
    See Also:
    
    setNoPlots(boolean)
  - setSkipBitmapOptions
```
public void setSkipBitmapOptions(boolean skipBitmapOptions)
```
    Deprecated.
  - setStringPreference
```
protected void setStringPreference(String key,
                                   double value)
```
    Deprecated.
  - setStringPreference
```
protected void setStringPreference(String key,
                                   int value)
```
    Deprecated.
  - setStringPreference
```
protected void setStringPreference(String key,
                                   String value)
```
    Deprecated.
  - saveStringPreferences
```
protected void saveStringPreferences()
```
    Deprecated.
  - getIntFromHashMap
```
protected int getIntFromHashMap(String key,
                                int defaultValue)
```
    Deprecated.
  - getDoubleFromHashMap
```
protected double getDoubleFromHashMap(String key,
                                      double defaultValue)
```
    Deprecated.
  - getStringFromHashMap
```
protected String getStringFromHashMap(String key,
                                      String defaultValue)
```
    Deprecated.

Class ShollOptions

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

COMMAND_LABEL

SKIP_BITMAP_OPTIONS_LABEL

DIRECTORY

UNIT

THRESHOLD

CENTER

STARTING_RADIUS

ENDING_RADIUS

RADIUS_STEP

SAMPLES_PER_RADIUS

ENCLOSING_RADIUS

INTERSECTING_RADII

SUM_INTERS

MEAN_INTERS

MEDIAN_INTERS

SKEWNESS

KURTOSIS

CENTROID

P1090_REGRESSION

NO_TABLE

TRIM_BOUNDS

INFER_PRIMARY

CURVE_FITTING

VERBOSE

SHOLL_N

SHOLL_NS

SHOLL_SLOG

SHOLL_LOG

GUESS_LOG_METHOD

SHOW_MASK

OVERLAY_SHELLS

SAVE_FILES

HIDE_SAVED_FILES

SKIP_SINGLE_VOXELS

stringPrefs

START_RADIUS_KEY

END_RADIUS_KEY

STEP_SIZE_KEY

NSAMPLES_KEY

INTEGRATION_KEY

ENCLOSING_RADIUS_KEY

PRIMARY_BRANCHES_KEY

POLYNOMIAL_INDEX_KEY

NORMALIZER_INDEX_KEY

SAVE_DIR_KEY

QUAD_CHOICE_KEY

FITTED_MASK

ALL_PLOTS

ONLY_LINEAR_PLOT

NO_PLOTS

instanceAttatchedToPlugin

Constructor Detail

ShollOptions

ShollOptions

Method Detail

run

getDefaultMetrics

getMetrics

getDefaultBooleanPrefs

getBooleanPrefs

getMaskBackground

setMaskBackground

getMaskType

setPlotOutput

getPlotOutput

setBooleanPrefs

setMaskType

getCommentString

setCommentString

getScientificNotationAwarePrecision

setNoPlots

setMetric

setPromptChoice

setNoTable