Transform_Virtual_Stack_MT (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- register_virtual_stack.Transform_Virtual_Stack_MT

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class Transform_Virtual_Stack_MT
extends Object
implements ij.plugin.PlugIn
```
Fiji plugin to transform sequences of images in a concurrent (multi-thread) way.
Requires:
- Source folder: a directory with images, of any size and type (8, 16, 32-bit gray-scale or RGB color)
- Transform folder: a directory with the transform files (from a Register_Virtual_Stack_Slices execution).
Performs: transformation of the sequence of images by applying the transform files.
Outputs: the list of new images, one for slice, into a output directory as .tif files.
For a detailed documentation, please visit the plugin website at:
http://fiji.sc/wiki/Transform_Virtual_Stack_Slices
Author:

Ignacio Arganda-Carreras (ignacio.arganda@gmail.com), Stephan Saalfeld and Albert Cardona

Field Summary

Fields
Modifier and Type	Field and Description
`static boolean`	`interpolate` interpolate?
`static String`	`outputDirectory` output directory
`static String`	`sourceDirectory` source directory
`static String`	`transformsDirectory` transforms directory

Constructor Summary

Constructors
Constructor and Description

Transform_Virtual_Stack_MT()

Constructors
Constructor and Description
`Transform_Virtual_Stack_MT()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static ij.ImagePlus`	`applyCoordinateTransform(ij.ImagePlus imp, CoordinateTransform transform, int meshResolution, boolean interpolate, int[] worldOrigin)` Apply a coordinate transform to a given image
`static boolean`	`exec(String source_dir, String target_dir, String transf_dir, boolean interpolate)` Transform images in the source directory applying transform files from a specific directory.
`static boolean`	`exec(String source_dir, String target_dir, String transf_dir, int first, int last, boolean interpolate)` Transform range of images in the source directory applying transform files from a specific directory.
`static CoordinateTransform`	`readCoordinateTransform(String filename)` Read coordinate transform from file (generated in Register_Virtual_Stack)
`void`	`run(String arg)` Plug-in run method

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

- Field Detail
  - sourceDirectory
```
public static String sourceDirectory
```
    source directory
  - outputDirectory
```
public static String outputDirectory
```
    output directory
  - transformsDirectory
```
public static String transformsDirectory
```
    transforms directory
  - interpolate
```
public static boolean interpolate
```
    interpolate?
- Constructor Detail
  - Transform_Virtual_Stack_MT
```
public Transform_Virtual_Stack_MT()
```
- Method Detail
  - run
```
public void run(String arg)
```
    Plug-in run method
    
    Specified by:
    
    run in interface ij.plugin.PlugIn
    
    Parameters:
    
    arg - plug-in arguments
  - exec
```
public static boolean exec(String source_dir,
                           String target_dir,
                           String transf_dir,
                           boolean interpolate)
```
    Transform images in the source directory applying transform files from a specific directory.
    
    Parameters:
    
    source_dir - folder with input (source) images.
    
    target_dir - folder to store output (transformed) images.
    
    transf_dir - folder with transform files.
    
    interpolate - boolean flag to interpolate the results or not
    
    Returns:
    
    true for correct execution, false otherwise.
  - exec
```
public static boolean exec(String source_dir,
                           String target_dir,
                           String transf_dir,
                           int first,
                           int last,
                           boolean interpolate)
```
    Transform range of images in the source directory applying transform files from a specific directory.
    
    Parameters:
    
    source_dir - folder with input (source) images.
    
    target_dir - folder to store output (transformed) images.
    
    transf_dir - folder with transform files.
    
    interpolate - boolean flag to interpolate the results or not
    
    Returns:
    
    true for correct execution, false otherwise.
  - readCoordinateTransform
```
public static CoordinateTransform readCoordinateTransform(String filename)
```
    Read coordinate transform from file (generated in Register_Virtual_Stack)
    
    Parameters:
    
    filename - complete file name (including path)
    
    Returns:
    
    true if the coordinate transform was properly read, false otherwise.
  - applyCoordinateTransform
```
public static ij.ImagePlus applyCoordinateTransform(ij.ImagePlus imp,
                                                    CoordinateTransform transform,
                                                    int meshResolution,
                                                    boolean interpolate,
                                                    int[] worldOrigin)
```
    Apply a coordinate transform to a given image
    
    Parameters:
    
    imp - image to be transformed
    
    transform - transform to be applied
    
    meshResolution - number of vertices per row in transform mesh
    
    interpolate - flag to interpolate pixel values
    
    worldOrigin - image world origin coordinates after transform
    
    Returns:
    
    transformed image

Class Transform_Virtual_Stack_MT

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

sourceDirectory

outputDirectory

transformsDirectory

interpolate

Constructor Detail

Transform_Virtual_Stack_MT

Method Detail

run

exec

exec

readCoordinateTransform

applyCoordinateTransform