Class Stitch_Image_Grid

java.lang.Object

Stitch_Image_Grid

All Implemented Interfaces:

ij.plugin.PlugIn

public class Stitch_Image_Grid
extends Object
implements ij.plugin.PlugIn

Author:

Stephan

Field Summary

Fields

Modifier and Type	Field	Description
static double	alphaStatic
static boolean	computeOverlapStatic
static String	directoryStatic
static String	fileNamesStatic
static String	fusionMethodStatic
static int	gridSizeXStatic
static int	gridSizeYStatic
static String	handleRGBStatic
static double	overlapStatic
static boolean	previewOnlyStatic
static String	rgbOrderStatic
static int	startIStatic
static int	startXStatic
static int	startYStatic
static double	thresholdDisplacementAbsoluteStatic
static double	thresholdDisplacementRelativeStatic
static double	thresholdRStatic
static String	tileConfStatic
static boolean	writeOnlyTileConfStatic

Constructor Summary

Constructors

Constructor	Description
Stitch_Image_Grid()

Method Summary

Modifier and Type	Method	Description
static String	getLeadingZeros(int zeros, int number)
static PrintWriter	openFileWrite(String fileName)
void	run(String arg0)
static ij.ImagePlus	stitchImageGrid(String filenames, String inputDirectory, GridLayout gridLayout, String handleRGB, String fusionMethod, String outputFileName, double overlap, int startX, int startY, int startI, boolean writeOnlyOutput, boolean previewOnly, boolean computeOverlap)	Stitch grid of 2D images

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

gridSizeXStatic

public static int gridSizeXStatic

gridSizeYStatic

public static int gridSizeYStatic

overlapStatic

public static double overlapStatic

directoryStatic

public static String directoryStatic

fileNamesStatic

public static String fileNamesStatic

rgbOrderStatic

public static String rgbOrderStatic

tileConfStatic

public static String tileConfStatic

writeOnlyTileConfStatic

public static boolean writeOnlyTileConfStatic

startXStatic

public static int startXStatic

startYStatic

public static int startYStatic

startIStatic

public static int startIStatic

handleRGBStatic

public static String handleRGBStatic

fusionMethodStatic

public static String fusionMethodStatic

alphaStatic

public static double alphaStatic

thresholdRStatic

public static double thresholdRStatic

thresholdDisplacementRelativeStatic

public static double thresholdDisplacementRelativeStatic

thresholdDisplacementAbsoluteStatic

public static double thresholdDisplacementAbsoluteStatic

previewOnlyStatic

public static boolean previewOnlyStatic

computeOverlapStatic

public static boolean computeOverlapStatic

Constructor Details

Stitch_Image_Grid

public Stitch_Image_Grid()

Method Details

run

public void run(String arg0)

Specified by:

run in interface ij.plugin.PlugIn

stitchImageGrid

public static ij.ImagePlus stitchImageGrid(String filenames,
 String inputDirectory,
 GridLayout gridLayout,
 String handleRGB,
 String fusionMethod,
 String outputFileName,
 double overlap,
 int startX,
 int startY,
 int startI,
 boolean writeOnlyOutput,
 boolean previewOnly,
 boolean computeOverlap)

Stitch grid of 2D images

Parameters:

filenames - file name format (for example: "TiledConfocal_{ii}.lsm")

inputDirectory - input directory

gridLayout - grid layout information

handleRGB - RGB mode (@see stitching.CommonFunctions.colorList)

fusionMethod - fusion method (@see stitching.CommonFunctions.methodListCollection)

outputFileName - output file name (for example: "TileConfiguration.txt")

overlap - percentage of overlap

startX - starting X value

startY - starting Y value

startI - starting I value

writeOnlyOutput - "Save Only Tile Configuration" option

previewOnly - "create only preview" option

computeOverlap - "compute overlap" option

getLeadingZeros

public static String getLeadingZeros(int zeros,
 int number)

openFileWrite

public static PrintWriter openFileWrite(String fileName)