Register_Virtual_Stack_MT (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- register_virtual_stack.Register_Virtual_Stack_MT

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class Register_Virtual_Stack_MT
extends Object
implements ij.plugin.PlugIn
```
Fiji plugin to register sequences of images in a concurrent (multi-thread) way.
Requires: a directory with images, of any size and type (8, 16, 32-bit gray-scale or RGB color)
Performs: registration of a sequence of images, by 6 different registration models:
- Translation (no deformation)
- Rigid (translation + rotation)
- Similarity (translation + rotation + isotropic scaling)
- Affine (free affine transformation)
- Elastic (consistent elastic deformations by B-splines)
- Moving least squares (maximal warping)
Outputs: the list of new images, one for slice, into a target directory as .tif files.
For a detailed documentation, please visit the plugin website at:
http://fiji.sc/wiki/Register_Virtual_Stack_Slices
Author:

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

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Register_Virtual_Stack_MT.Param
Registration parameters class.

Nested Classes
Modifier and Type	Class and Description
`static class`	`Register_Virtual_Stack_MT.Param` Registration parameters class.

Field Summary

Fields
Modifier and Type	Field and Description
`static boolean`	`advanced` advance options flag
`static int`	`AFFINE` affine registration model id
`static String`	`currentDirectory` working directory path
`static boolean`	`displayRelaxGraph` display relaxation graph flag
`static int`	`ELASTIC` elastic registration model id
`static String`	`exts` possible extensions of files to be registered/transformed
`static int`	`featuresModelIndex` index of the features model check-box
`static String[]`	`featuresModelStrings` feature model string labels
`static int`	`MAX_ITER` maximum number of iterations in the relaxation loop
`static int`	`MOVING_LEAST_SQUARES` maximal warping registration model id
`static boolean`	`non_shrinkage` shrinkage constraint flag
`static String`	`outputDirectory` output directory
`static boolean`	`postprocess` post-processing flag
`static int`	`registrationModelIndex` index of the registration model check-box
`static String[]`	`registrationModelStrings` registration model string labels
`static int`	`RIGID` rigid-body registration model id
`static boolean`	`save_transforms` save transformation flag
`static int`	`SIMILARITY` rigid-body + isotropic scaling registration model id
`static String`	`sourceDirectory` source directory
`static float`	`STOP_THRESHOLD` relaxation threshold (if the difference between last two iterations is below this threshold, the relaxation stops
`static int`	`TRANSLATION` translation registration model id
`static double`	`tweakIso` isotropy (aspect ratio) regularization parameter [0.0-1.0]
`static double`	`tweakScale` scaling regularization parameter [0.0-1.0]
`static double`	`tweakShear` shear regularization parameter [0.0-1.0]

Constructor Summary

Constructors
Constructor and Description

Register_Virtual_Stack_MT()

Constructors
Constructor and Description
`Register_Virtual_Stack_MT()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static List<PointMatch>`	`applyTransformReverse(List<PointMatch> list, CoordinateTransform t)` Apply a transformation to the second point (P2) of a list of Point matches
`static boolean`	`createResults(String source_dir, String[] sorted_file_names, String target_dir, String save_dir, CoordinateTransform[] transform, boolean interpolate)` Create final target images
`static void`	`exec(String source_dir, String[] sorted_file_names, int referenceIndex, String target_dir, String save_dir, Register_Virtual_Stack_MT.Param p)` Execution method.
`static void`	`exec(String source_dir, String[] sorted_file_names, String target_dir, String save_dir, Register_Virtual_Stack_MT.Param p)` Execute registration with non-shrinking constrain
`static void`	`exec(String source_dir, String target_dir, String save_dir, String referenceName, int featuresModelIndex, int registrationModelIndex, boolean advanced, boolean non_shrink)` Execution method.
`static void`	`exec(String source_dir, String target_dir, String save_dir, String referenceName, Register_Virtual_Stack_MT.Param p, boolean non_shrink)` Execute registration when all parameters are set.
`static void`	`fitInliers(Register_Virtual_Stack_MT.Param p, CoordinateTransform t, List<PointMatch> inliers)` Fit inliers given a registration model
`static void`	`flush(ij.ImagePlus imp)`
`static CoordinateTransform`	`getCoordinateTransform(Register_Virtual_Stack_MT.Param p)` Get a new coordinate transform given a registration model
`static AffineTransform`	`makeAffineMatrix(double scalex, double scaley, double shearx, double sheary, double rotang, double transx, double transy)` Makes an affine transformation matrix from the given scale, shear, rotation and translation values if you want a uniquely retrievable matrix, give sheary=0
`static void`	`postProcessTransforms(CoordinateTransform[] transform)` Correct transforms from global scaling or rotation
`static void`	`randomize(int[] array)` Randomize array of integers
`static ij.ImagePlus`	`readImage(String path)` Read image files
`static boolean`	`register(ij.ImagePlus imp1, ij.ImagePlus imp2, ij.ImagePlus imp1mask, ij.ImagePlus imp2mask, int i, String[] sorted_file_names, String source_dir, String target_dir, ExecutorService exe, Register_Virtual_Stack_MT.Param p, CoordinateTransform t, Rectangle commonBounds, List<Rectangle> bounds, int referenceIndex)` Register two images with corresponding masks and following the features and registration models.
`static void`	`regularize(CoordinateTransform t, int index)` Regularize coordinate transform
`static boolean`	`relax(List<PointMatch>[] inliers, CoordinateTransform[] transform, Register_Virtual_Stack_MT.Param p)` Relax inliers
`void`	`run(String arg)` Plug-in run method
`static boolean`	`showRegularizationDialog(Register_Virtual_Stack_MT.Param p)` Shows regularization dialog when "Shrinkage constrain" is checked.

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

- Field Detail
  - TRANSLATION
```
public static final int TRANSLATION
```
    translation registration model id
    
    See Also:
    
    Constant Field Values
  - RIGID
```
public static final int RIGID
```
    rigid-body registration model id
    
    See Also:
    
    Constant Field Values
  - SIMILARITY
```
public static final int SIMILARITY
```
    rigid-body + isotropic scaling registration model id
    
    See Also:
    
    Constant Field Values
  - AFFINE
```
public static final int AFFINE
```
    affine registration model id
    
    See Also:
    
    Constant Field Values
  - ELASTIC
```
public static final int ELASTIC
```
    elastic registration model id
    
    See Also:
    
    Constant Field Values
  - MOVING_LEAST_SQUARES
```
public static final int MOVING_LEAST_SQUARES
```
    maximal warping registration model id
    
    See Also:
    
    Constant Field Values
  - featuresModelIndex
```
public static int featuresModelIndex
```
    index of the features model check-box
  - registrationModelIndex
```
public static int registrationModelIndex
```
    index of the registration model check-box
  - currentDirectory
```
public static String currentDirectory
```
    working directory path
  - advanced
```
public static boolean advanced
```
    advance options flag
  - non_shrinkage
```
public static boolean non_shrinkage
```
    shrinkage constraint flag
  - save_transforms
```
public static boolean save_transforms
```
    save transformation flag
  - sourceDirectory
```
public static String sourceDirectory
```
    source directory
  - outputDirectory
```
public static String outputDirectory
```
    output directory
  - tweakScale
```
public static double tweakScale
```
    scaling regularization parameter [0.0-1.0]
  - tweakShear
```
public static double tweakShear
```
    shear regularization parameter [0.0-1.0]
  - tweakIso
```
public static double tweakIso
```
    isotropy (aspect ratio) regularization parameter [0.0-1.0]
  - displayRelaxGraph
```
public static boolean displayRelaxGraph
```
    display relaxation graph flag
  - postprocess
```
public static boolean postprocess
```
    post-processing flag
  - registrationModelStrings
```
public static final String[] registrationModelStrings
```
    registration model string labels
  - featuresModelStrings
```
public static final String[] featuresModelStrings
```
    feature model string labels
  - STOP_THRESHOLD
```
public static final float STOP_THRESHOLD
```
    relaxation threshold (if the difference between last two iterations is below this threshold, the relaxation stops
    
    See Also:
    
    Constant Field Values
  - MAX_ITER
```
public static final int MAX_ITER
```
    maximum number of iterations in the relaxation loop
    
    See Also:
    
    Constant Field Values
  - exts
```
public static final String exts
```
    possible extensions of files to be registered/transformed
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Register_Virtual_Stack_MT
```
public Register_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 void exec(String source_dir,
                        String target_dir,
                        String save_dir,
                        String referenceName,
                        int featuresModelIndex,
                        int registrationModelIndex,
                        boolean advanced,
                        boolean non_shrink)
```
    Execution method. Execute registration after setting parameters.
    
    Parameters:
    
    source_dir - Directory to read all images from, where each image is a slice in a sequence. Their names must be bit-sortable, i.e. if numbered, they must be padded with zeros.
    
    target_dir - Directory to store registered slices into.
    
    save_dir - Directory to store transform files into.
    
    referenceName - File name of the reference image.
    
    featuresModelIndex - Index of the features extraction model (0=TRANSLATION, 1=RIGID, 2=SIMILARITY, 3=AFFINE)
    
    registrationModelIndex - Index of the registration model (0=TRANSLATION, 1=RIGID, 2=SIMILARITY, 3=AFFINE, 4=ELASTIC, 5=MOVING_LEAST_SQUARES)
    
    advanced - Triggers showing parameters setup dialogs
    
    non_shrink - Triggers showing non-shrinking dialog (if advanced options are selected as well) and execution
  - exec
```
public static void exec(String source_dir,
                        String target_dir,
                        String save_dir,
                        String referenceName,
                        Register_Virtual_Stack_MT.Param p,
                        boolean non_shrink)
```
    Execute registration when all parameters are set.
    
    Parameters:
    
    source_dir - Directory to read all images from, where each image is a slice in a sequence. Their names must be bit-sortable, i.e. if numbered, they must be padded with zeros.
    
    target_dir - Directory to store registered slices into.
    
    save_dir - Directory to store transform files into.
    
    referenceName - File name of the reference image (if necessary, for non-shrinkage mode, it can be null)
    
    p - Registration parameters
    
    non_shrink - non shrinking mode flag
  - exec
```
public static void exec(String source_dir,
                        String[] sorted_file_names,
                        String target_dir,
                        String save_dir,
                        Register_Virtual_Stack_MT.Param p)
```
    Execute registration with non-shrinking constrain
    
    Parameters:
    
    source_dir - Directory to read all images from, where each image is a slice in a sequence. Their names must be bit-sortable, i.e. if numbered, they must be padded with zeros.
    
    sorted_file_names - Array of sorted source file names.
    
    target_dir - Directory to store registered slices into.
    
    save_dir - Directory to store transform files into.
    
    p - registration parameters
  - applyTransformReverse
```
public static List<PointMatch> applyTransformReverse(List<PointMatch> list,
                                                     CoordinateTransform t)
```
    Apply a transformation to the second point (P2) of a list of Point matches
    
    Parameters:
    
    list - list of point matches
    
    t - transformation to be applied
    
    Returns:
    
    new list of point matches (after the transformation)
  - relax
```
public static boolean relax(List<PointMatch>[] inliers,
                            CoordinateTransform[] transform,
                            Register_Virtual_Stack_MT.Param p)
```
    Relax inliers
    
    Parameters:
    
    inliers - array of list of inliers in the sequence (one per pair of slices)
    
    transform - array of relaxed transforms (output)
    
    p - registration parameters
    
    Returns:
    
    true or false in case of proper result or error
  - randomize
```
public static void randomize(int[] array)
```
    Randomize array of integers
    
    Parameters:
    
    array - array of integers to randomize
  - createResults
```
public static boolean createResults(String source_dir,
                                    String[] sorted_file_names,
                                    String target_dir,
                                    String save_dir,
                                    CoordinateTransform[] transform,
                                    boolean interpolate)
```
    Create final target images
    
    Parameters:
    
    source_dir - Directory to read all images from, where each image is a slice in a sequence. Their names must be bit-sortable, i.e. if numbered, they must be padded with zeros.
    
    sorted_file_names - Array of sorted source file names.
    
    target_dir - Directory to store registered slices into.
    
    save_dir - Directory to store transform files into (null if transformations are not saved).
    
    transform - array of transforms for every source image (including the first one).
    
    Returns:
    
    true or false in case of proper result or error
  - exec
```
public static void exec(String source_dir,
                        String[] sorted_file_names,
                        int referenceIndex,
                        String target_dir,
                        String save_dir,
                        Register_Virtual_Stack_MT.Param p)
```
    Execution method. Execute registration when all parameters are set.
    
    Parameters:
    
    source_dir - Directory to read all images from, where each image is a slice in a sequence. Their names must be bit-sortable, i.e. if numbered, they must be padded with zeros.
    
    sorted_file_names - Array of sorted source file names.
    
    referenceIndex - index of the reference image in the array of sorted source images.
    
    target_dir - Directory to store registered slices into.
    
    save_dir - Directory to store transform files into.
    
    p - registration parameters.
  - readImage
```
public static ij.ImagePlus readImage(String path)
```
    Read image files
    
    Parameters:
    
    path - full path to image
    
    Returns:
    
    read image or null if error
  - register
```
public static boolean register(ij.ImagePlus imp1,
                               ij.ImagePlus imp2,
                               ij.ImagePlus imp1mask,
                               ij.ImagePlus imp2mask,
                               int i,
                               String[] sorted_file_names,
                               String source_dir,
                               String target_dir,
                               ExecutorService exe,
                               Register_Virtual_Stack_MT.Param p,
                               CoordinateTransform t,
                               Rectangle commonBounds,
                               List<Rectangle> bounds,
                               int referenceIndex)
                        throws Exception
```
    Register two images with corresponding masks and following the features and registration models.
    
    Parameters:
    
    imp1 - target image
    
    imp2 - source image (input and output)
    
    imp1mask - target mask
    
    imp2mask - source mask (input and output)
    
    i - index in the loop of images (just to show information)
    
    sorted_file_names - array of sorted source file names
    
    source_dir - source directory
    
    target_dir - target (output) directory
    
    exe - executor service to save the images
    
    p - registration parameters
    
    t - coordinate transform
    
    commonBounds - current common bounds of the registration space
    
    bounds - list of bounds for the already registered images
    
    referenceIndex - index of the reference image
    
    Returns:
    
    false if there is an error, true otherwise
    
    Throws:
    
    Exception - if something fails
  - getCoordinateTransform
```
public static CoordinateTransform getCoordinateTransform(Register_Virtual_Stack_MT.Param p)
```
    Get a new coordinate transform given a registration model
    
    Parameters:
    
    p - registration parameters
    
    Returns:
    
    new coordinate transform
  - fitInliers
```
public static void fitInliers(Register_Virtual_Stack_MT.Param p,
                              CoordinateTransform t,
                              List<PointMatch> inliers)
                       throws Exception
```
    Fit inliers given a registration model
    
    Parameters:
    
    p - registration parameters
    
    t - coordinate transform
    
    inliers - point matches
    
    Throws:
    
    Exception - if something fails
  - regularize
```
public static void regularize(CoordinateTransform t,
                              int index)
```
    Regularize coordinate transform
    
    Parameters:
    
    t - coordinate transform
    
    index - slice index
  - makeAffineMatrix
```
public static AffineTransform makeAffineMatrix(double scalex,
                                               double scaley,
                                               double shearx,
                                               double sheary,
                                               double rotang,
                                               double transx,
                                               double transy)
```
    Makes an affine transformation matrix from the given scale, shear, rotation and translation values if you want a uniquely retrievable matrix, give sheary=0
    
    Parameters:
    
    scalex - scaling in x
    
    scaley - scaling in y
    
    shearx - shearing in x
    
    sheary - shearing in y
    
    rotang - angle of rotation (in radians)
    
    transx - translation in x
    
    transy - translation in y
    
    Returns:
    
    affine transformation matrix
  - showRegularizationDialog
```
public static boolean showRegularizationDialog(Register_Virtual_Stack_MT.Param p)
```
    Shows regularization dialog when "Shrinkage constrain" is checked.
    
    Parameters:
    
    p - registration parameters
    
    Returns:
    
    false when dialog is canceled or true when it is not
  - postProcessTransforms
```
public static void postProcessTransforms(CoordinateTransform[] transform)
```
    Correct transforms from global scaling or rotation
    
    Parameters:
    
    transform - array of transforms
  - flush
```
public static void flush(ij.ImagePlus imp)
```

Class Register_Virtual_Stack_MT

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

TRANSLATION

RIGID

SIMILARITY

AFFINE

ELASTIC

MOVING_LEAST_SQUARES

featuresModelIndex

registrationModelIndex

currentDirectory

advanced

non_shrinkage

save_transforms

sourceDirectory

outputDirectory

tweakScale

tweakShear

tweakIso

displayRelaxGraph

postprocess

registrationModelStrings

featuresModelStrings

STOP_THRESHOLD

MAX_ITER

exts

Constructor Detail

Register_Virtual_Stack_MT

Method Detail

run

exec

exec

exec

applyTransformReverse

relax

randomize

createResults

exec

readImage

register

getCoordinateTransform

fitInliers

regularize

makeAffineMatrix

showRegularizationDialog

postProcessTransforms

flush