Stitching_Grid (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- plugin.Stitching_Grid

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class Stitching_Grid
extends Object
implements ij.plugin.PlugIn
```
Author:

Stephan Preibisch (stephan.preibisch@gmx.de)

Field Summary

Fields
Modifier and Type	Field and Description
`static boolean`	`defaultAddTilesAsRois`
`static boolean`	`defaultComputeOverlap`
`static boolean`	`defaultConfirmFiles`
`static String`	`defaultDirectory`
`static double`	`defaultDisplacementThresholdAbsolute`
`static double`	`defaultDisplacementThresholdRelative`
`static boolean`	`defaultDisplayFusion`
`static boolean`	`defaultDownSample`
`static String`	`defaultFileNames`
`static int`	`defaultFusionMethod`
`static int`	`defaultGridChoice1`
`static int`	`defaultGridChoice2`
`static int`	`defaultGridSizeX`
`static int`	`defaultGridSizeY`
`static boolean`	`defaultIgnoreCalibration`
`static boolean`	`defaultIgnoreZStage`
`static double`	`defaultIncreaseOverlap`
`static boolean`	`defaultInvertX`
`static boolean`	`defaultInvertY`
`static int`	`defaultMemorySpeedChoice`
`static boolean`	`defaultOnlyPreview`
`static String`	`defaultOutputDirectory`
`static double`	`defaultOverlapX`
`static double`	`defaultOverlapY`
`static boolean`	`defaultQuickFusion`
`static double`	`defaultR`
`static double`	`defaultRegressionThreshold`
`static int`	`defaultResult`
`static double`	`defaultSeqRange`
`static String`	`defaultSeriesFile`
`static int`	`defaultStartI`
`static int`	`defaultStartX`
`static int`	`defaultStartY`
`static boolean`	`defaultSubpixelAccuracy`
`static String`	`defaultTileConfiguration`
`static boolean`	`defaultVirtualInput`
`static String[]`	`resultChoices`
`static boolean`	`seperateOverlapY`
`static String`	`version`
`static boolean`	`writeOnlyTileConfStatic`

Constructor Summary

Constructors
Constructor and Description

Stitching_Grid()

Constructors
Constructor and Description
`Stitching_Grid()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`generateRois(double[] offsets, ArrayList<ImagePlusTimePoint> optimizedImages)` Generates a ROI for each tile in the list of optimized images.
`protected ArrayList<ImageCollectionElement>`	`getAllFilesInDirectory(String directory, boolean confirmFiles)`
`protected ArrayList<ImageCollectionElement>`	`getGridLayout(GridType grid, int gridSizeX, int gridSizeY, double overlapX, double overlapY, String directory, String filenames, int startI, int startX, int startY, boolean virtual, Downsampler ds)`
`protected ArrayList<ImageCollectionElement>`	`getLayoutFromFile(String directory, String layoutFile, Downsampler ds)`
`protected ArrayList<ImageCollectionElement>`	`getLayoutFromMultiSeriesFile(String multiSeriesFile, double increaseOverlap, boolean ignoreCalibration, boolean invertX, boolean invertY, boolean ignoreZStage, Downsampler ds)`
`static String`	`getLeadingZeros(int zeros, int number)`
`protected void`	`getPosition(int[] currentPosition, int i, int gridType, int gridOrder, int sizeX, int sizeY)`
`protected IFormatReader`	`initializeReader(IFormatReader in, String file)` Initializes an `ImageReader` if the provided reader is null, or does not match the given file id.
`protected ij.ImagePlus[]`	`openBF(String multiSeriesFileName, boolean splitC, boolean splitT, boolean splitZ, boolean autoScale, boolean crop, boolean allSeries)`
`protected ij.ImagePlus[]`	`openBFDefault(String multiSeriesFileName)`
`void`	`run(String arg0)`
`protected void`	`writeRegisteredTileConfiguration(File file, ArrayList<ImageCollectionElement> elements)`
`protected void`	`writeTileConfiguration(File file, ArrayList<ImageCollectionElement> elements)`

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

Field Detail

version
```
public static final String version
```
See Also:

Constant Field Values

seperateOverlapY
```
public static boolean seperateOverlapY
```

defaultGridChoice1
```
public static int defaultGridChoice1
```

defaultGridChoice2
```
public static int defaultGridChoice2
```

defaultGridSizeX
```
public static int defaultGridSizeX
```

defaultGridSizeY
```
public static int defaultGridSizeY
```

defaultOverlapX
```
public static double defaultOverlapX
```

defaultOverlapY
```
public static double defaultOverlapY
```

defaultDirectory
```
public static String defaultDirectory
```

defaultSeriesFile
```
public static String defaultSeriesFile
```

defaultConfirmFiles

public static boolean defaultConfirmFiles

defaultFileNames
```
public static String defaultFileNames
```

defaultTileConfiguration

public static String defaultTileConfiguration

defaultAddTilesAsRois

public static boolean defaultAddTilesAsRois

defaultComputeOverlap

public static boolean defaultComputeOverlap

defaultInvertX
```
public static boolean defaultInvertX
```

defaultInvertY
```
public static boolean defaultInvertY
```

defaultIgnoreZStage

public static boolean defaultIgnoreZStage

defaultSubpixelAccuracy

public static boolean defaultSubpixelAccuracy

defaultDownSample

public static boolean defaultDownSample

defaultDisplayFusion

public static boolean defaultDisplayFusion

writeOnlyTileConfStatic

public static boolean writeOnlyTileConfStatic

defaultIgnoreCalibration

public static boolean defaultIgnoreCalibration

defaultIncreaseOverlap

public static double defaultIncreaseOverlap

defaultVirtualInput

public static boolean defaultVirtualInput

defaultStartI
```
public static int defaultStartI
```

defaultStartX
```
public static int defaultStartX
```

defaultStartY
```
public static int defaultStartY
```

defaultFusionMethod
```
public static int defaultFusionMethod
```

defaultR
```
public static double defaultR
```

defaultRegressionThreshold

public static double defaultRegressionThreshold

defaultDisplacementThresholdRelative

public static double defaultDisplacementThresholdRelative

defaultDisplacementThresholdAbsolute

public static double defaultDisplacementThresholdAbsolute

defaultOnlyPreview

public static boolean defaultOnlyPreview

defaultMemorySpeedChoice

public static int defaultMemorySpeedChoice

defaultSeqRange
```
public static double defaultSeqRange
```

defaultQuickFusion

public static boolean defaultQuickFusion

resultChoices
```
public static String[] resultChoices
```

defaultResult
```
public static int defaultResult
```

defaultOutputDirectory

public static String defaultOutputDirectory

Constructor Detail
- Stitching_Grid
```
public Stitching_Grid()
```

Method Detail

run
```
public void run(String arg0)
```
Specified by:

run in interface ij.plugin.PlugIn

generateRois
```
protected void generateRois(double[] offsets,
                            ArrayList<ImagePlusTimePoint> optimizedImages)
```
Generates a ROI for each tile in the list of optimized images. The fusedImage is the resultant on which the ROIs will be drawn. The offset is a global offset to 0,0 for the upper leftmost tile.

initializeReader
```
protected IFormatReader initializeReader(IFormatReader in,
                                         String file)
```
Initializes an ImageReader if the provided reader is null, or does not match the given file id.
NB: All exceptions are handled in this method. If an exception is caught, null will be returned.

openBF

protected ij.ImagePlus[] openBF(String multiSeriesFileName,
                                boolean splitC,
                                boolean splitT,
                                boolean splitZ,
                                boolean autoScale,
                                boolean crop,
                                boolean allSeries)

openBFDefault

protected ij.ImagePlus[] openBFDefault(String multiSeriesFileName)

getLayoutFromMultiSeriesFile

protected ArrayList<ImageCollectionElement> getLayoutFromMultiSeriesFile(String multiSeriesFile,
                                                                         double increaseOverlap,
                                                                         boolean ignoreCalibration,
                                                                         boolean invertX,
                                                                         boolean invertY,
                                                                         boolean ignoreZStage,
                                                                         Downsampler ds)

getLayoutFromFile

protected ArrayList<ImageCollectionElement> getLayoutFromFile(String directory,
                                                              String layoutFile,
                                                              Downsampler ds)

getAllFilesInDirectory

protected ArrayList<ImageCollectionElement> getAllFilesInDirectory(String directory,
                                                                   boolean confirmFiles)

getGridLayout

protected ArrayList<ImageCollectionElement> getGridLayout(GridType grid,
                                                          int gridSizeX,
                                                          int gridSizeY,
                                                          double overlapX,
                                                          double overlapY,
                                                          String directory,
                                                          String filenames,
                                                          int startI,
                                                          int startX,
                                                          int startY,
                                                          boolean virtual,
                                                          Downsampler ds)

writeTileConfiguration

protected void writeTileConfiguration(File file,
                                      ArrayList<ImageCollectionElement> elements)

writeRegisteredTileConfiguration

protected void writeRegisteredTileConfiguration(File file,
                                                ArrayList<ImageCollectionElement> elements)

getPosition

protected void getPosition(int[] currentPosition,
                           int i,
                           int gridType,
                           int gridOrder,
                           int sizeX,
                           int sizeY)

getLeadingZeros

public static String getLeadingZeros(int zeros,
                                     int number)

Class Stitching_Grid

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

version

seperateOverlapY

defaultGridChoice1

defaultGridChoice2

defaultGridSizeX

defaultGridSizeY

defaultOverlapX

defaultOverlapY

defaultDirectory

defaultSeriesFile

defaultConfirmFiles

defaultFileNames

defaultTileConfiguration

defaultAddTilesAsRois

defaultComputeOverlap

defaultInvertX

defaultInvertY

defaultIgnoreZStage

defaultSubpixelAccuracy

defaultDownSample

defaultDisplayFusion

writeOnlyTileConfStatic

defaultIgnoreCalibration

defaultIncreaseOverlap

defaultVirtualInput

defaultStartI

defaultStartX

defaultStartY

defaultFusionMethod

defaultR

defaultRegressionThreshold

defaultDisplacementThresholdRelative

defaultDisplacementThresholdAbsolute

defaultOnlyPreview

defaultMemorySpeedChoice

defaultSeqRange

defaultQuickFusion

resultChoices

defaultResult

defaultOutputDirectory

Constructor Detail

Stitching_Grid

Method Detail

run

generateRois

initializeReader

openBF

openBFDefault

getLayoutFromMultiSeriesFile

getLayoutFromFile

getAllFilesInDirectory

getGridLayout

writeTileConfiguration

writeRegisteredTileConfiguration

getPosition

getLeadingZeros