Image_Expression_Parser (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.process.Image_Expression_Parser<T>

All Implemented Interfaces:

ij.plugin.PlugIn, Algorithm, OutputAlgorithm<Img<T>>
```
public class Image_Expression_Parser<T extends RealType<T> & NativeType<T>>
extends Object
implements ij.plugin.PlugIn, OutputAlgorithm<Img<T>>
```
Image expression parser

Usage
This plugins parses mathematical expressions and compute results using images as variables. As of version 2.x, pixel per pixel based operations are supported and ImgLib algorithm are supported.
The parsing ability is provided by the JEP library: Java Expression Parser v.jep-2.4.1-ext-1.1.1-gpl. This is the last version released under the GPL by its authors Nathan Funk and Richard Morris.
Internally, this plugin uses ImgLib to deal with images.
The interactive version (launched from ImageJ) uses a GUI, see IepGui. It is possible to use this plugin in scripts using the following methods:
- setExpression(String) to pass the expression to parse
- setImageMap(Map) to pass the couples (variable name, image) to the parser
- process() to compute the resulting image
- getResult() to retrieve the resulting image
Calling the plugin from elsewhere
It is possible to call the plugin from another class or in a scripting language. For instance in Python:
```
 import net.imglib2.img.ImgPlusAdapter
 import mpicbg.imglib.image.display.imagej.ImageJFunctions
 import fiji.process.Image_Expression_Parser
 
 
 # Make an ImgLib image from the current image
 imp = WindowManager.getCurrentImage()
 img = net.imglib2.img.ImgPlusAdapter.wrap(imp)
 
 # In python, the map can be a dictionary, relating 
 # variable names to images
 map = {'A': img}
 expression = 'A^2'
 
 # Instantiate plugin
 parser = fiji.process.Image_Expression_Parser()
 
 # Configure & execute
 parser.setImageMap(map)
 parser.setExpression(expression)
 parser.process()
 result = parser.getResult() # is an ImgLib image
 
 # Copy result to an ImagePlus and display it
 result_imp = mpicbg.imglib.image.display.imagej.ImageJFunctions.copyToImagePlus(result)
 result_imp.show()
 result_imp.resetDisplayRange()
 result_imp.updateAndDraw()
 
```
Version history
- v1.0 - Feb 2010 - First working version.
- v1.1 - Apr 2010 - Expression field now has a history.
- v2.0 - May 2010 - Complete logic rewrite:
  - functions are now handled by code specific for ImgLib;
  - support for ImgLib algorithms and non pixel-based operations, such as gaussian convolution;
  - faster evaluation, thanks to dealing with ImgLib images as objects within the parser instead of pixel per pixel evaluation.
- v2.1 - June 2010 - Internal changes:
  - the GUI now generate a new separate thread for processing, freeing resources for the redraw of the GUI panel itself (thanks to Albert Cardona and the Fijiers input);
  - RGB images are processed in a special way by the GUI: each of their channel is processed separately and put back together in a composite image.
Author:

Jean-Yves Tinevez, Albert Cardona

Field Summary

Fields
Modifier and Type	Field and Description
`protected String`	`error_message` If an error occurred, an error message is put here
`protected String`	`expression` The expression to evaluate
`protected Map<String,Img<T>>`	`image_map` Array of Imglib images, on which calculations will be done
`protected Img<T>`	`result` Here is stored the result of the evaluation
`protected boolean`	`user_has_canceled`

Constructor Summary

Constructors
Constructor and Description

Image_Expression_Parser()

Constructors
Constructor and Description
`Image_Expression_Parser()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`checkInput()` Check that inputs are valid.
`Map<String,Img<T>>`	`convertToImglib(Map<String,ij.ImagePlus> imp_map)` Convert the `String ImagePlus` map in argument to a `String, Img` HasMap and put it in the "image_map" field.
`String`	`getErrorMessage()` If an error occurred during the call of `process()`, an error message can be read here.
`String`	`getExpression()`
`Map<String,Img<T>>`	`getImageMap()`
`Img<T>`	`getResult()` Return the result of the last evaluation of the expression over the images given.
`static <T extends RealType<T> & NativeType<T>> void`	`main(String[] args)`
`boolean`	`process()` Execute calculation, given the expression, variable list and image list set for this instance.
`void`	`run(String arg)` Launch the interactive version if this plugin.
`void`	`setExpression(String _expression)` Set the expression to evaluate.
`void`	`setImageMap(Map<String,Img<T>> im)`

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

- Field Detail
  - user_has_canceled
```
protected boolean user_has_canceled
```
  - image_map
```
protected Map<String,Img<T extends RealType<T> & NativeType<T>>> image_map
```
    Array of Imglib images, on which calculations will be done
  - expression
```
protected String expression
```
    The expression to evaluate
  - result
```
protected Img<T extends RealType<T> & NativeType<T>> result
```
    Here is stored the result of the evaluation
  - error_message
```
protected String error_message
```
    If an error occurred, an error message is put here
- Constructor Detail
  - Image_Expression_Parser
```
public Image_Expression_Parser()
```
- Method Detail
  - run
```
public void run(String arg)
```
    Launch the interactive version if this plugin. This is made by first displaying the GUI, which will take all user interaction work. Calculations will be later delegated by the GUI to this instance.
    
    Specified by:
    
    run in interface ij.plugin.PlugIn
  - checkInput
```
public boolean checkInput()
```
    Check that inputs are valid. Namely, that all input images have the same dimensions, and the expression to evaluate is valid, using the JEP parser.
    If one of the input is not valid, the boolean false is returned, and the method getErrorMessage() will return an explanatory message.
    
    Specified by:
    
    checkInput in interface Algorithm
    
    Returns:
    
    a boolean, true if inputs are valid
  - process
```
public boolean process()
```
    Execute calculation, given the expression, variable list and image list set for this instance. The resulting image can be accessed afterwards by using getResult().
    If the expression is invalid or if the image dimensions mismatch, an error is thrown and the field result is set to null. In this case, an explanatory error message can be obtained by getErrorMessage().
    
    Specified by:
    
    process in interface Algorithm
  - getResult
```
public Img<T> getResult()
```
    Return the result of the last evaluation of the expression over the images given. Is null if process() was not called before.
    
    Specified by:
    
    getResult in interface OutputAlgorithm<Img<T extends RealType<T> & NativeType<T>>>
  - getErrorMessage
```
public String getErrorMessage()
```
    If an error occurred during the call of process(), an error message can be read here.
    
    Specified by:
    
    getErrorMessage in interface Algorithm
  - setExpression
```
public void setExpression(String _expression)
```
    Set the expression to evaluate.
  - getExpression
```
public String getExpression()
```
  - setImageMap
```
public void setImageMap(Map<String,Img<T>> im)
```
  - getImageMap
```
public Map<String,Img<T>> getImageMap()
```
  - convertToImglib
```
public Map<String,Img<T>> convertToImglib(Map<String,ij.ImagePlus> imp_map)
```
    Convert the String ImagePlus map in argument to a String, Img HasMap and put it in the "image_map" field.
    The internals of this plugin operate on Img, but for integration within current ImageJ, the GUI returns ImagePlus, so we have to do a conversion when we execute this plugin from ImageJ.
    Warning: executing this method resets the image_map field.
    
    Parameters:
    
    imp_map - the String, ImagePlus map to convert
  - main
```
public static <T extends RealType<T> & NativeType<T>> void main(String[] args)
```

Class Image_Expression_Parser<T extends RealType<T> & NativeType<T>>

Image expression parser

Usage

Calling the plugin from elsewhere

Version history

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

user_has_canceled

image_map

expression

result

error_message

Constructor Detail

Image_Expression_Parser

Method Detail

run

checkInput

process

getResult

getErrorMessage

setExpression

getExpression

setImageMap

getImageMap

convertToImglib

main