LocalThicknessWrapper (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.localThickness.LocalThicknessWrapper

All Implemented Interfaces:

ij.plugin.filter.PlugInFilter
```
public class LocalThicknessWrapper
extends Object
implements ij.plugin.filter.PlugInFilter
```
A class which can be used to programmatically run and control the various steps in local thickness map calculations.
This plugin overlaps with Local_Thickness_Driver. Both execute all the steps of local thickness in one go. However, this class offers more control over the execution, e.g. "running silent" which means that none of the intermediate images are shown. It also has some additional features needed by BoneJ, e.g. masking artifact pixels created by the algorithm that weren't present in the input image.

This duplication makes the package messy, but I wanted to left the original code as is, because I don't understand it well enough to confidently alter it.

Author:

Richard Domander

Field Summary

Fields
Modifier and Type	Field and Description
`boolean`	`calibratePixels` Controls whether the pixel values in the Thickness map get scaled @see LocalThicknessWrapper.calibratePixels()
`boolean`	`inverse` Inverts thresholding so that pixels with values >= threshold are considered background.
`boolean`	`maskThicknessMap` Controls whether the Thickness map gets masked with the original @see MaskThicknessMapWithOriginal
`int`	`threshold` A pixel is considered to be a part of the background if its color < threshold

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, NO_UNDO_RESET, PARALLELIZE_IMAGES, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

Constructors
Constructor and Description

LocalThicknessWrapper()

Constructors
Constructor and Description
`LocalThicknessWrapper()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`ij.ImagePlus`	`getResultImage()`
`ij.ImagePlus`	`processImage(ij.ImagePlus inputImage)` Creates a thickness map from the given image
`void`	`run(ij.process.ImageProcessor ip)`
`void`	`setShowOptions(boolean show)` Controls whether the options dialog in EDT_S1D is shown to the user before processing starts.
`void`	`setSilence(boolean silent)` Sets whether intermediate images are shown to the user, or only the final result
`void`	`setTitleSuffix(String imageTitleSuffix)`
`int`	`setup(String arg, ij.ImagePlus imp)`

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

- Field Detail
  - threshold
```
public int threshold
```
    A pixel is considered to be a part of the background if its color < threshold
  - inverse
```
public boolean inverse
```
    Inverts thresholding so that pixels with values >= threshold are considered background.
  - maskThicknessMap
```
public boolean maskThicknessMap
```
    Controls whether the Thickness map gets masked with the original @see MaskThicknessMapWithOriginal
  - calibratePixels
```
public boolean calibratePixels
```
    Controls whether the pixel values in the Thickness map get scaled @see LocalThicknessWrapper.calibratePixels()
- Constructor Detail
  - LocalThicknessWrapper
```
public LocalThicknessWrapper()
```
- Method Detail
  - setShowOptions
```
public void setShowOptions(boolean show)
```
    Controls whether the options dialog in EDT_S1D is shown to the user before processing starts.
    
    Parameters:
    
    show - If true, then the dialog is shown.
  - setSilence
```
public void setSilence(boolean silent)
```
    Sets whether intermediate images are shown to the user, or only the final result
    
    Parameters:
    
    silent - If true, then no intermediate images are shown in the GUI.
  - processImage
```
public ij.ImagePlus processImage(ij.ImagePlus inputImage)
```
    Creates a thickness map from the given image
    
    Parameters:
    
    inputImage - An 8-bit binary image
    
    Returns:
    
    A 32-bit floating point thickness map image
  - setTitleSuffix
```
public void setTitleSuffix(String imageTitleSuffix)
```
    Parameters:
    
    imageTitleSuffix - The suffix that's added to the end of the title of the resulting thickness map image
  - getResultImage
```
public ij.ImagePlus getResultImage()
```
    Returns:
    
    The thickness map from the last run of the plugin. Null if something went wrong, e.g. the user cancelled the plugin.
  - setup
```
public int setup(String arg,
                 ij.ImagePlus imp)
```
    Specified by:
    
    setup in interface ij.plugin.filter.PlugInFilter
  - run
```
public void run(ij.process.ImageProcessor ip)
```
    Specified by:
    
    run in interface ij.plugin.filter.PlugInFilter

Class LocalThicknessWrapper

Field Summary

Fields inherited from interface ij.plugin.filter.PlugInFilter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

threshold

inverse

maskThicknessMap

calibratePixels

Constructor Detail

LocalThicknessWrapper

Method Detail

setShowOptions

setSilence

processImage

setTitleSuffix

getResultImage

setup

run