Package plugin

Class Stitching_Grid

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 Details

    • version

      public static final String version
      See Also:

    • 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 Details

    • Stitching_Grid

      public Stitching_Grid()

  • Method Details

    • 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 loci.formats.IFormatReader initializeReader(loci.formats.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)