Package net.preibisch.mvrecon.process.downsampling

Class DownsampleTools

java.lang.Object

net.preibisch.mvrecon.process.downsampling.DownsampleTools

public class DownsampleTools
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
protected static final int[]	ds

Constructor Summary

Constructors

Constructor	Description
DownsampleTools()

Method Summary

Modifier and Type	Method	Description
static String[]	availableDownsamplings(mpicbg.spim.data.generic.AbstractSpimData<?> data, mpicbg.spim.data.sequence.ViewId viewId)
static void	correctForDownsampling(List<InterestPoint> ips, net.imglib2.realtransform.AffineTransform3D t)
static int	downsampleFactor(int downsampleXY, int downsampleZ, mpicbg.spim.data.sequence.VoxelDimensions v)
static int	findLowestResolutionLevel(mpicbg.spim.data.sequence.MultiResolutionImgLoader mrImgLoader, mpicbg.spim.data.sequence.ViewId view)
static net.imglib2.realtransform.AffineTransform3D	getMipMapTransform(mpicbg.spim.data.generic.sequence.BasicImgLoader imgLoader, mpicbg.spim.data.sequence.ViewId vd, long[] downsampleFactors)	Returns the mipmap transform if you were to open that ViewId with this ImgLoader at the specified downsample factors
static net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval,net.imglib2.realtransform.AffineTransform3D>	openAndDownsample(mpicbg.spim.data.generic.sequence.BasicImgLoader imgLoader, mpicbg.spim.data.sequence.ViewId vd, long[] downsampleFactors, boolean virtualDownsampling)	Opens the image at a specified downsampling level (e.g. 4,4,1).
static net.imglib2.RandomAccessibleInterval	openAtLowestLevel(mpicbg.spim.data.sequence.ImgLoader imgLoader, mpicbg.spim.data.sequence.ViewId view)
static net.imglib2.RandomAccessibleInterval	openAtLowestLevel(mpicbg.spim.data.sequence.ImgLoader imgLoader, mpicbg.spim.data.sequence.ViewId view, net.imglib2.realtransform.AffineTransform3D t)
static net.imglib2.RandomAccessibleInterval	openDownsampled(mpicbg.spim.data.generic.sequence.BasicImgLoader imgLoader, mpicbg.spim.data.sequence.ViewId viewId, net.imglib2.realtransform.AffineTransform3D m)	Opens the image at an appropriate resolution for the provided transformation and concatenates an extra transform
static net.imglib2.RandomAccessibleInterval	openDownsampled(mpicbg.spim.data.generic.sequence.BasicImgLoader imgLoader, mpicbg.spim.data.sequence.ViewId viewId, net.imglib2.realtransform.AffineTransform3D m, double[] usedDownsampleFactors)	Opens the image at an appropriate resolution for the provided transformation and concatenates an extra transform
static net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval,net.imglib2.realtransform.AffineTransform3D>	openDownsampled2(mpicbg.spim.data.generic.sequence.BasicImgLoader imgLoader, mpicbg.spim.data.sequence.ViewId viewId, net.imglib2.realtransform.AffineTransform3D m, double[] usedDownsampleFactors)	Opens the image at an appropriate resolution for the provided transformation and concatenates an extra transform
static long[]	parseDownsampleChoice(String dsChoice)
static String	printDownsampling(double downsampling)	For double-based downsampling Double.NaN means no downsampling to avoid unnecessary computations, here we return a String for that number that says "None" if it is Double.NaN

Methods inherited from class java.lang.Object

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

Field Details

ds

protected static final int[] ds

Constructor Details

DownsampleTools

public DownsampleTools()

Method Details

openDownsampled

public static net.imglib2.RandomAccessibleInterval openDownsampled(mpicbg.spim.data.generic.sequence.BasicImgLoader imgLoader,
 mpicbg.spim.data.sequence.ViewId viewId,
 net.imglib2.realtransform.AffineTransform3D m)

Opens the image at an appropriate resolution for the provided transformation and concatenates an extra transform

Parameters:

imgLoader - - the img loader

viewId - - the view id

m - - WILL BE MODIFIED IF OPENED DOWNSAMPLED

Returns:

- opened image

openDownsampled

public static net.imglib2.RandomAccessibleInterval openDownsampled(mpicbg.spim.data.generic.sequence.BasicImgLoader imgLoader,
 mpicbg.spim.data.sequence.ViewId viewId,
 net.imglib2.realtransform.AffineTransform3D m,
 double[] usedDownsampleFactors)

Opens the image at an appropriate resolution for the provided transformation and concatenates an extra transform

Parameters:

imgLoader - - the img loader

viewId - - the view id

m - - WILL BE MODIFIED IF OPENED DOWNSAMPLED

usedDownsampleFactors - - which downsample factors were used to open the image (important for weights etc)

Returns:

- opened image

openDownsampled2

public static net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval,net.imglib2.realtransform.AffineTransform3D> openDownsampled2(mpicbg.spim.data.generic.sequence.BasicImgLoader imgLoader,
 mpicbg.spim.data.sequence.ViewId viewId,
 net.imglib2.realtransform.AffineTransform3D m,
 double[] usedDownsampleFactors)

Opens the image at an appropriate resolution for the provided transformation and concatenates an extra transform

Parameters:

imgLoader - - the img loader

viewId - - the view id

m - - NOT modified

usedDownsampleFactors - - which downsample factors were used to open the image (important for weights etc)

Returns:

- opened image and the affine transform that needs to be concatenated

printDownsampling

public static String printDownsampling(double downsampling)

For double-based downsampling Double.NaN means no downsampling to avoid unnecessary computations, here we return a String for that number that says "None" if it is Double.NaN

Parameters:

downsampling - - the downsampling, Double.NaN means 1.0

Returns:

- a String describing it

availableDownsamplings

public static String[] availableDownsamplings(mpicbg.spim.data.generic.AbstractSpimData<?> data,
 mpicbg.spim.data.sequence.ViewId viewId)

parseDownsampleChoice

public static long[] parseDownsampleChoice(String dsChoice)

correctForDownsampling

public static void correctForDownsampling(List<InterestPoint> ips,
 net.imglib2.realtransform.AffineTransform3D t)

downsampleFactor

public static int downsampleFactor(int downsampleXY,
 int downsampleZ,
 mpicbg.spim.data.sequence.VoxelDimensions v)

openAtLowestLevel

public static net.imglib2.RandomAccessibleInterval openAtLowestLevel(mpicbg.spim.data.sequence.ImgLoader imgLoader,
 mpicbg.spim.data.sequence.ViewId view)

openAtLowestLevel

public static net.imglib2.RandomAccessibleInterval openAtLowestLevel(mpicbg.spim.data.sequence.ImgLoader imgLoader,
 mpicbg.spim.data.sequence.ViewId view,
 net.imglib2.realtransform.AffineTransform3D t)

findLowestResolutionLevel

public static int findLowestResolutionLevel(mpicbg.spim.data.sequence.MultiResolutionImgLoader mrImgLoader,
 mpicbg.spim.data.sequence.ViewId view)

getMipMapTransform

public static net.imglib2.realtransform.AffineTransform3D getMipMapTransform(mpicbg.spim.data.generic.sequence.BasicImgLoader imgLoader,
 mpicbg.spim.data.sequence.ViewId vd,
 long[] downsampleFactors)

Returns the mipmap transform if you were to open that ViewId with this ImgLoader at the specified downsample factors

Parameters:

imgLoader - the imgloader

vd - the view id

downsampleFactors - - specify which downsampling in each dimension (e.g. 1,2,4,8 )

Returns:

the mipmap transform

openAndDownsample

public static net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval,net.imglib2.realtransform.AffineTransform3D> openAndDownsample(mpicbg.spim.data.generic.sequence.BasicImgLoader imgLoader,
 mpicbg.spim.data.sequence.ViewId vd,
 long[] downsampleFactors,
 boolean virtualDownsampling)

Opens the image at a specified downsampling level (e.g. 4,4,1). It finds the closest available mipmap level and then downsamples to reach the target level

Parameters:

imgLoader - the imgloader

vd - the view id

downsampleFactors - - specify which downsampling in each dimension (e.g. 1,2,4,8 )

virtualDownsampling - - use virtual downsampling if the requested downsamplefactors are not precomputed

Returns:

opened image and the mipmap transform