org.micromanager.lightsheet

Class StackResampler

java.lang.Object

org.micromanager.lightsheet.StackResampler

public class StackResampler
extends Object

This class takes a ZYX stack of pixels and resamples it into a new coordinate space. It is CPU parallelized for speed, and individual Z slices can be added as they become available in order to speed processing. It can output either a full volume, a YX projection, or a set of orthogonal views. All interpolation is done using nearest neighbors, and thus is very fast, but should probably not be relied upon for quantitative analysis.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	StackResampler.LinearTransformation

Field Summary

Fields

Modifier and Type	Field and Description
static int	FULL_VOLUME
static int	OTHOGONAL_VIEWS
static int	YX_PROJECTION

Constructor Summary

Constructors

Constructor and Description
StackResampler(int mode, boolean maxProjection, double theta, double cameraPixelSizeXyUm, double zStepUm, int zPixelShape, int yPixelShape, int xPixelShape)

Method Summary

Modifier and Type	Method and Description
void	addImageToRecons(short[] image, int imageZIndex)
void	addToProcessImageQueue(mmcorej.TaggedImage image)
double[]	cameraCoordsFromReconCoords(double reconZ, double reconY)
void	computeRemappedCoordinateSpace()
static String	createSettingsKey(int mode, double theta, double cameraPixelSizeXyUm, double zStepUm, int zPixelShape, int yPixelShape, int xPixelShape)
void	finalizeProjections() Call after all images have arrived to finalize the projections
short[][]	getReconstructedVolumeZYX()
double	getReconstructionVoxelSizeUm()
int	getResampledShapeX()
int	getResampledShapeY()
int	getResampledShapeZ()
String	getSettingsKey()
short[]	getYXProjection()
short[]	getZXProjection()
short[]	getZYProjection()
void	initializeProjections() Call before any images arrive to initialize the projection and recon arrays
void	precomputeCoordTransformLUTs()
void	precomputeReconWeightings()
double[]	reconCoordsFromCameraCoords(double imageZ, double imageY)

Methods inherited from class java.lang.Object

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

Field Detail

YX_PROJECTION

public static final int YX_PROJECTION

See Also:

Constant Field Values

OTHOGONAL_VIEWS

public static final int OTHOGONAL_VIEWS

See Also:

Constant Field Values

FULL_VOLUME

public static final int FULL_VOLUME

See Also:

Constant Field Values

Constructor Detail

StackResampler

public StackResampler(int mode,
                      boolean maxProjection,
                      double theta,
                      double cameraPixelSizeXyUm,
                      double zStepUm,
                      int zPixelShape,
                      int yPixelShape,
                      int xPixelShape)

Method Detail

createSettingsKey

public static String createSettingsKey(int mode,
                                       double theta,
                                       double cameraPixelSizeXyUm,
                                       double zStepUm,
                                       int zPixelShape,
                                       int yPixelShape,
                                       int xPixelShape)

getSettingsKey

public String getSettingsKey()

reconCoordsFromCameraCoords

public double[] reconCoordsFromCameraCoords(double imageZ,
                                            double imageY)

cameraCoordsFromReconCoords

public double[] cameraCoordsFromReconCoords(double reconZ,
                                            double reconY)

computeRemappedCoordinateSpace

public void computeRemappedCoordinateSpace()

precomputeCoordTransformLUTs

public void precomputeCoordTransformLUTs()

precomputeReconWeightings

public void precomputeReconWeightings()

initializeProjections

public void initializeProjections()

Call before any images arrive to initialize the projection and recon arrays

addImageToRecons

public void addImageToRecons(short[] image,
                             int imageZIndex)

finalizeProjections

public void finalizeProjections()

Call after all images have arrived to finalize the projections

getReconstructionVoxelSizeUm

public double getReconstructionVoxelSizeUm()

getYXProjection

public short[] getYXProjection()

getZYProjection

public short[] getZYProjection()

getZXProjection

public short[] getZXProjection()

getReconstructedVolumeZYX

public short[][] getReconstructedVolumeZYX()

getResampledShapeX

public int getResampledShapeX()

getResampledShapeY

public int getResampledShapeY()

getResampledShapeZ

public int getResampledShapeZ()

addToProcessImageQueue

public void addToProcessImageQueue(mmcorej.TaggedImage image)