StitchingTEM (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ini.trakem2.imaging.StitchingTEM

```
public class StitchingTEM
extends Object
```
Given: - list of images - grid width - known percent overlap This class will attempt to find the optimal montage, by applying phase-correlation, and/or cross-correlation, and/or SIFT-based correlation) between neighboring images. The method is oriented to images acquired with Transmission Electron Microscopy, where the acquisition of each image elastically deforms the sample, and thus earlier images are regarded as better than later ones. It is assumed that images were acquired from 0 to n, as in the grid.

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class StitchingTEM.PhaseCorrelationParam
Phase correlation parameters class

Nested Classes
Modifier and Type	Class and Description
`static class`	`StitchingTEM.PhaseCorrelationParam` Phase correlation parameters class

Field Summary

Fields
Modifier and Type	Field and Description
`static float`	`DEFAULT_MIN_R`
`static int`	`DONE`
`static int`	`ERROR`
`static int`	`INTERRUPTED`
`static int`	`LEFT_RIGHT`
`static int`	`SUCCESS`
`static int`	`TOP_BOTTOM`
`static int`	`WORKING`

Constructor Summary

Constructors
Constructor and Description

StitchingTEM()

Constructors
Constructor and Description
`StitchingTEM()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static double[]`	`correlate(Patch base, Patch moving, float percent_overlap, double scale, int direction, double default_dx, double default_dy, double min_R)`
`static ij.process.ImageProcessor`	`makeStripe(Patch p, Roi roi, double scale)`
`static ij.process.ImageProcessor`	`makeStripe(Patch p, Roi roi, double scale, boolean ignore_patch_transform)`
`static void`	`montageWithPhaseCorrelation(Collection<Patch> col)`
`static void`	`montageWithPhaseCorrelation(Collection<Patch> col, StitchingTEM.PhaseCorrelationParam param)` Perform montage based on phase correlation
`static void`	`montageWithPhaseCorrelation(List<Layer> layers, Worker worker)`
`static Bureaucrat`	`montageWithPhaseCorrelationTask(Collection<Patch> col)` For each Patch, find who overlaps with it and perform a phase correlation or cross-correlation with it; then consider all successful correlations as links and run the optimizer on it all.
`static Bureaucrat`	`montageWithPhaseCorrelationTask(List<Layer> layers)`
`static void`	`optimizeTileConfiguration(ArrayList<AbstractAffineTile2D<?>> tiles, ArrayList<AbstractAffineTile2D<?>> fixed_tiles, StitchingTEM.PhaseCorrelationParam param)` Optimize tile configuration by removing bad matches
`static Runnable`	`stitch(Patch[] patch, int grid_width, double default_bottom_top_overlap, double default_left_right_overlap, boolean optimize, StitchingTEM.PhaseCorrelationParam param)` Returns the same Patch instances with their coordinates modified; the top-left image is assumed to be the first one, and thus serves as reference; so, after the first image, coordinates are ignored for each specific Patch.

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

- Field Detail
  - WORKING
```
public static final int WORKING
```
    See Also:
    
    Constant Field Values
  - DONE
```
public static final int DONE
```
    See Also:
    
    Constant Field Values
  - ERROR
```
public static final int ERROR
```
    See Also:
    
    Constant Field Values
  - INTERRUPTED
```
public static final int INTERRUPTED
```
    See Also:
    
    Constant Field Values
  - SUCCESS
```
public static final int SUCCESS
```
    See Also:
    
    Constant Field Values
  - TOP_BOTTOM
```
public static final int TOP_BOTTOM
```
    See Also:
    
    Constant Field Values
  - LEFT_RIGHT
```
public static final int LEFT_RIGHT
```
    See Also:
    
    Constant Field Values
  - DEFAULT_MIN_R
```
public static final float DEFAULT_MIN_R
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - StitchingTEM
```
public StitchingTEM()
```
- Method Detail
  - stitch
```
public static Runnable stitch(Patch[] patch,
                              int grid_width,
                              double default_bottom_top_overlap,
                              double default_left_right_overlap,
                              boolean optimize,
                              StitchingTEM.PhaseCorrelationParam param)
```
    Returns the same Patch instances with their coordinates modified; the top-left image is assumed to be the first one, and thus serves as reference; so, after the first image, coordinates are ignored for each specific Patch. The cross-correlation is done always with the image to the left, and on its absence, with the image above. If the cross-correlation returns values that would mean a depart larger than the known percent overlap, the image will be cross-correlated with its second option (i.e. the one above in almost all cases). In the absence of a second option to compare with, the percent overlap is applied as the least damaging option in the montage. The Patch[] array is unidimensional to allow for missing images in the last row not to interfere. The stitching runs in a separate thread; interested parties can query the status of the processing by calling the method getStatus(). The scale is used to make the images smaller when doing cross-correlation. If larger than 1, it gets put back to 1. Rotation of the images is NOT considered by the TOP_LEFT_RULE (phase- and cross-correlation), but it can be for the FREE_RULE (SIFT).
    
    Returns:
    
    A new Runnable task, or null if the initialization didn't pass the tests (all tiles have to have the same dimensions, for example).
  - makeStripe
```
public static ij.process.ImageProcessor makeStripe(Patch p,
                                                   Roi roi,
                                                   double scale)
```
  - makeStripe
```
public static ij.process.ImageProcessor makeStripe(Patch p,
                                                   Roi roi,
                                                   double scale,
                                                   boolean ignore_patch_transform)
```
    Parameters:
    
    ignore_patch_transform - will prevent resizing of the ImageProcessor in the event of the Patch having a transform different than identity.
    
    Returns:
    
    FloatProcessor.
  - correlate
```
public static double[] correlate(Patch base,
                                 Patch moving,
                                 float percent_overlap,
                                 double scale,
                                 int direction,
                                 double default_dx,
                                 double default_dy,
                                 double min_R)
```
    Parameters:
    
    scale - For optimizing the speed of phase- and cross-correlation.
    
    percent_overlap - The minimum chunk of adjacent images to compare with, will automatically and gradually increase to 100% if no good matches are found.
    
    Returns:
    a double[4] array containing:
    
    x2: relative X position of the second Patch
    
    y2: relative Y position of the second Patch
    
    flag: ERROR or SUCCESS
    
    R: cross-correlation coefficient
  - montageWithPhaseCorrelationTask
```
public static Bureaucrat montageWithPhaseCorrelationTask(Collection<Patch> col)
```
    For each Patch, find who overlaps with it and perform a phase correlation or cross-correlation with it; then consider all successful correlations as links and run the optimizer on it all. ASSUMES the patches have only TRANSLATION in their affine transforms--will warn you about it.
  - montageWithPhaseCorrelation
```
public static void montageWithPhaseCorrelation(Collection<Patch> col)
```
  - montageWithPhaseCorrelationTask
```
public static Bureaucrat montageWithPhaseCorrelationTask(List<Layer> layers)
```
  - montageWithPhaseCorrelation
```
public static void montageWithPhaseCorrelation(List<Layer> layers,
                                               Worker worker)
```
    Parameters:
    
    layers -
    
    worker - Optional, the Worker running this task.
  - montageWithPhaseCorrelation
```
public static void montageWithPhaseCorrelation(Collection<Patch> col,
                                               StitchingTEM.PhaseCorrelationParam param)
```
    Perform montage based on phase correlation
    
    Parameters:
    
    col - collection of patches
    
    param - phase correlation parameters
  - optimizeTileConfiguration
```
public static void optimizeTileConfiguration(ArrayList<AbstractAffineTile2D<?>> tiles,
                                             ArrayList<AbstractAffineTile2D<?>> fixed_tiles,
                                             StitchingTEM.PhaseCorrelationParam param)
```
    Optimize tile configuration by removing bad matches
    
    Parameters:
    
    tiles - complete list of tiles
    
    fixed_tiles - list of fixed tiles
    
    param - phase correlation parameters

Class StitchingTEM

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

WORKING

DONE

ERROR

INTERRUPTED

SUCCESS

TOP_BOTTOM

LEFT_RIGHT

DEFAULT_MIN_R

Constructor Detail

StitchingTEM

Method Detail

stitch

makeStripe

makeStripe

correlate

montageWithPhaseCorrelationTask

montageWithPhaseCorrelation

montageWithPhaseCorrelationTask

montageWithPhaseCorrelation

montageWithPhaseCorrelation

optimizeTileConfiguration