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
class	StackResampler.ImagePlusSlice Helper class to store pixels and frameNr in one instance.
static class	StackResampler.LinearTransformation Helper class to do matrix calculations.

Field Summary

Fields

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

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
void	addImageToRecons(short[] image, int imageSliceIndex) Add images only after first calling initializeProjections.
void	addToProcessImageQueue(short[] image, int sliceIndex) Use this function to add Tagged images to the processing queue.
void	addToProcessImageQueue(mmcorej.TaggedImage image) Deprecated.
static String	createSettingsKey(int mode, double theta, double cameraPixelSizeXyUm, double sliceDistanceUm, int zPixelShape, int yPixelShape, int xPixelShape) Creates a String with values used to create a StackResampler.
void	finalizeProjections() Call after all images have arrived to finalize the projections.
short[][]	getReconstructedVolumeZYX() Returns reconstructed volume.
double	getReconstructionVoxelSizeUm()
int	getResampledShapeX() Returns the width of the resampled volume in pixels.
int	getResampledShapeY() Returns the height of the resampled volume.
int	getResampledShapeZ() Returns the number of frames of the resampled volume.
String	getSettingsKey() Returns a String unique for this StackResampler.
short[]	getYXProjection() Returns YX projection.
short[]	getYZProjection() Returns ZY projection.
short[]	getZXProjection() Returns ZX projection.
void	initializeProjections() Call this function before any images arrive to initialize the projection and recon arrays.
Runnable	startStackProcessing() Pull images from the queue and process them in parallel until a full z stack is processed or a null pix null tags stop signal is received.

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

ORTHOGONAL_VIEWS

public static final int ORTHOGONAL_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 sliceDistanceUm,
                      int zPixelShape,
                      int yPixelShape,
                      int xPixelShape)

StackResampler constructor. Sets up matrices used for the transform, and pre-calculates the re-mapped coordinate space.

Parameters:

mode - YX Projection (0), Orthogonal views (1), or full volume (2)

maxProjection - Do a maximum intensity projection if true, otherwise returns mean projections.

theta - Angle between coverslip and lightsheet in radians, theta-tilt in https://amsikking.github.io/SOLS_optimum_tilt/.

cameraPixelSizeXyUm - Size of one (square) camera pixel in the object plane in microns.

sliceDistanceUm - Distance (in microns) between two slices of the input stack in the object plane. Distance is measured in the plane parallel with the coverslip.

zPixelShape - Number of slices (z planes) in the input stack.

yPixelShape - Image height in pixel number

xPixelShape - Image width in pixel number

Method Detail

createSettingsKey

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

Creates a String with values used to create a StackResampler.

Parameters:

mode - YX Projection (0), Orthogonal views (1), or full volume (2)

theta - Angle with optical axis in radians.

cameraPixelSizeXyUm - Size of one (square) camera pixel in the object plane in microns.

sliceDistanceUm - Distance (in microns) between two slices of the input stack in the object plane. Distance is measured in the plane parallel with the coverslip.

zPixelShape - Number of slices (z planes) in the input stack.

yPixelShape - Image height in pixel number

xPixelShape - Image width in pixel number

Returns:

String unique for given input.

getSettingsKey

public String getSettingsKey()

Returns a String unique for this StackResampler. (that also containes information about parameters used to create this StackResampler.

Returns:

String unique for this StackResampler

initializeProjections

public void initializeProjections()

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

addImageToRecons

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

Add images only after first calling initializeProjections. It appears that this function is meant for internal use, and that it is preferred to add images using addToProcessImageQueue(short[], int) and start processing using startStackProcessing(). If synchronous execution is OK, it should be fine to use this method and signal that no more images will be added using (finalizeProjections()

Parameters:

image - array containing pixel data with width and height as set in the constructor.

imageSliceIndex - z plane number, starting with 0.

finalizeProjections

public void finalizeProjections()

Call after all images have arrived to finalize the projections.

getReconstructionVoxelSizeUm

public double getReconstructionVoxelSizeUm()

getYXProjection

public short[] getYXProjection()

Returns YX projection. Only call after first calling finalizeProjections().

Returns:

YX Projection, either maximum intensity or an average projection.

getYZProjection

public short[] getYZProjection()

Returns ZY projection. Only call after first calling finalizeProjections().

Returns:

ZY Projection, either maximum intensity or an average projection.

getZXProjection

public short[] getZXProjection()

Returns ZX projection. Only call after first calling finalizeProjections().

Returns:

Zx Projection, either maximum intensity or an average projection.

getReconstructedVolumeZYX

public short[][] getReconstructedVolumeZYX()

Returns reconstructed volume. Only call after first calling finalizeProjections().

Returns:

Reconstructed volume.

getResampledShapeX

public int getResampledShapeX()

Returns the width of the resampled volume in pixels.

Returns:

Width of the resampled volume in pixels.

getResampledShapeY

public int getResampledShapeY()

Returns the height of the resampled volume.

Returns:

Height of the resampled volume in pixels.

getResampledShapeZ

public int getResampledShapeZ()

Returns the number of frames of the resampled volume.

Returns:

Number of frames of the resampled volume.

addToProcessImageQueue

@Deprecated
public void addToProcessImageQueue(mmcorej.TaggedImage image)

Deprecated.

Use this function to add Tagged images to the processing queue. Processing is started with a call to startStackProcessing(). Processing can (and should be) started before images are added to the queue. The only tag in the TaggedImage that matters is the tag "Z", containing the frame index as an integer starting at zero.

Parameters:

image - TaggedImage containing pixel data of type short[], and the tag "Z" with the frame index.

addToProcessImageQueue

public void addToProcessImageQueue(short[] image,
                                   int sliceIndex)

Use this function to add Tagged images to the processing queue. Processing is started with a call to startStackProcessing(). Processing can (and should be) started before images are added to the queue. The only tag in the TaggedImage that matters is the tag "Z", containing the frame index as an integer starting at zero.

Parameters:

image - TaggedImage containg pixel data of type short[], and the tag "Z" with the frame index.

startStackProcessing

public Runnable startStackProcessing()

Pull images from the queue and process them in parallel until a full z stack is processed or a null pix null tags stop signal is received. The future can be gotten when the stack is finished processing