org.micromanager.acqj.util.xytiling

Class CameraTilingStageTranslator

java.lang.Object

org.micromanager.acqj.util.xytiling.CameraTilingStageTranslator

public class CameraTilingStageTranslator
extends Object

Convenience class for using an Affine transform to translate between pixel coordinates and stage coordinates when doing XY tiled imaging

Author:

henrypinkard

Constructor Summary

Constructors

Constructor and Description
CameraTilingStageTranslator(AffineTransform transform, String xyStageName, int width, int height, int overlapX, int overlapY)

Method Summary

Modifier and Type	Method and Description
Point	getDisplayedPixel(double magnification, long row, long col, double viewOffsetX, double viewOffsetY) return the pixel location in coordinates at appropriate res level of the top left pixel for the given row/column
Point2D.Double[]	getDisplayTileCornerStageCoords(XYStagePosition pos)
int	getDisplayTileHeight()
int	getDisplayTileWidth()
int	getFullResPositionIndexFromStageCoords(double x, double y)
Point	getPixelCoordsFromStageCoords(double stageX, double stageY)
int[]	getPositionIndices(int[] rows, int[] cols) Return the position indices for the positions at the specified rows, cols.
List<XYStagePosition>	getPositionList()
Point2D.Double	getStageCoordsFromPixelCoords(long xAbsolute, long yAbsolute)
Point	getTileIndicesFromDisplayedPixel(double magnification, int x, int y, double viewOffsetX, double viewOffsetY)
XYStagePosition	getXYPosition(int index)
Point	pixelCoordsFromStageCoords(double x, double y, double magnification, Point2D.Double offset)
void	setPositions(List<XYStagePosition> positions) Set a grid of XY stage positions, as generated from some external source, so that they can be used to in caculations relating pixel and stage coordinates
Point2D.Double	stageCoordsFromPixelCoords(int absoluteX, int absoluteY, double mag, Point2D.Double offset)

Methods inherited from class java.lang.Object

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

Constructor Detail

CameraTilingStageTranslator

public CameraTilingStageTranslator(AffineTransform transform,
                                   String xyStageName,
                                   int width,
                                   int height,
                                   int overlapX,
                                   int overlapY)

Method Detail

getTileIndicesFromDisplayedPixel

public Point getTileIndicesFromDisplayedPixel(double magnification,
                                              int x,
                                              int y,
                                              double viewOffsetX,
                                              double viewOffsetY)

getDisplayedPixel

public Point getDisplayedPixel(double magnification,
                               long row,
                               long col,
                               double viewOffsetX,
                               double viewOffsetY)

return the pixel location in coordinates at appropriate res level of the top left pixel for the given row/column

Parameters:

row -

col -

Returns:

stageCoordsFromPixelCoords

public Point2D.Double stageCoordsFromPixelCoords(int absoluteX,
                                                 int absoluteY,
                                                 double mag,
                                                 Point2D.Double offset)

Parameters:

absoluteX - x coordinate in the full Res stitched image

absoluteY - y coordinate in the full res stitched image

Returns:

stage coordinates of the given pixel position

pixelCoordsFromStageCoords

public Point pixelCoordsFromStageCoords(double x,
                                        double y,
                                        double magnification,
                                        Point2D.Double offset)

getStageCoordsFromPixelCoords

public Point2D.Double getStageCoordsFromPixelCoords(long xAbsolute,
                                                    long yAbsolute)

Parameters:

xAbsolute - x coordinate in the full Res stitched image

yAbsolute - y coordinate in the full res stitched image

Returns:

stage coordinates of the given pixel position

getPixelCoordsFromStageCoords

public Point getPixelCoordsFromStageCoords(double stageX,
                                           double stageY)

Returns:

absolute, full resolution pixel coordinate of given stage posiiton

getXYPosition

public XYStagePosition getXYPosition(int index)

getFullResPositionIndexFromStageCoords

public int getFullResPositionIndexFromStageCoords(double x,
                                                  double y)

getPositionList

public List<XYStagePosition> getPositionList()

setPositions

public void setPositions(List<XYStagePosition> positions)

Set a grid of XY stage positions, as generated from some external source, so that they can be used to in caculations relating pixel and stage coordinates

Parameters:

positions -

getPositionIndices

public int[] getPositionIndices(int[] rows,
                                int[] cols)

Return the position indices for the positions at the specified rows, cols. If no position exists at this location, create one and return its index

Parameters:

rows -

cols -

Returns:

getDisplayTileHeight

public int getDisplayTileHeight()

getDisplayTileWidth

public int getDisplayTileWidth()

getDisplayTileCornerStageCoords

public Point2D.Double[] getDisplayTileCornerStageCoords(XYStagePosition pos)