Package sc.fiji.snt.io

Class SpimDataUtils.CalibratedSource<T extends net.imglib2.type.numeric.NumericType<T>>

java.lang.Object

bdv.util.AbstractSource<T>

bdv.util.RandomAccessibleIntervalSource<T>

sc.fiji.snt.io.SpimDataUtils.CalibratedSource<T>

Type Parameters:

T - the pixel type

All Implemented Interfaces:

bdv.viewer.Source<T>

Enclosing class:

SpimDataUtils

public static class SpimDataUtils.CalibratedSource<T extends net.imglib2.type.numeric.NumericType<T>>
extends bdv.util.RandomAccessibleIntervalSource<T>

Wraps a RandomAccessibleIntervalSource and overrides getVoxelDimensions() to carry the physical unit (e.g. "µm"). Without this, BDV's ScaleBarOverlayRenderer reads "pixel" from RandomAccessibleIntervalSource.getVoxelDimensions() and the scale bar label is wrong even when calibration is applied.

Field Summary

Fields inherited from class bdv.util.AbstractSource

interpolators, name, type

Constructor Summary

Constructors

Constructor	Description
CalibratedSource(net.imglib2.RandomAccessibleInterval<T> rai, T type, net.imglib2.realtransform.AffineTransform3D sourceTransform, String name, double[] cal, String unit)	Convenience constructor for sources without a time axis (timeDim = -1).
CalibratedSource(net.imglib2.RandomAccessibleInterval<T> rai, T type, net.imglib2.realtransform.AffineTransform3D sourceTransform, String name, double[] cal, String unit, int timeDim)	Full constructor.

Method Summary

Modifier and Type	Method	Description
net.imglib2.RandomAccessibleInterval<T>	getSource(int t, int level)
mpicbg.spim.data.sequence.VoxelDimensions	getVoxelDimensions()
void	setCalibration(double[] cal, String unit)	Updates the voxel calibration (spacing and unit) of this source.

Methods inherited from class bdv.util.RandomAccessibleIntervalSource

getInterpolatedSource, getSourceTransform

Methods inherited from class bdv.util.AbstractSource

doBoundingBoxCulling, getInterpolatedMaskedSource, getMaskedSource, getName, getNumMipmapLevels, getType, isPresent

Methods inherited from class java.lang.Object

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

Constructor Details

CalibratedSource

public CalibratedSource(net.imglib2.RandomAccessibleInterval<T> rai,
 T type,
 net.imglib2.realtransform.AffineTransform3D sourceTransform,
 String name,
 double[] cal,
 String unit,
 int timeDim)

Full constructor. When timeDim >= 0, getSource(int, int) slices the RAI along that axis so each BVV timepoint returns the correct frame. RandomAccessibleIntervalSource ignores the timepoint argument entirely, causing all frames to show frame 0 for timelapse data.

CalibratedSource

public CalibratedSource(net.imglib2.RandomAccessibleInterval<T> rai,
 T type,
 net.imglib2.realtransform.AffineTransform3D sourceTransform,
 String name,
 double[] cal,
 String unit)

Convenience constructor for sources without a time axis (timeDim = -1).

Method Details

setCalibration

public void setCalibration(double[] cal,
 String unit)

Updates the voxel calibration (spacing and unit) of this source. Mutates the source transform diagonal and replaces the VoxelDimensions so the BVV scale bar reflects the new values.

Parameters:

cal - voxel spacing {x, y, z}

unit - physical unit string (e.g. "µm")

getSource

public net.imglib2.RandomAccessibleInterval<T> getSource(int t,
 int level)

Specified by:

getSource in interface bdv.viewer.Source<T extends net.imglib2.type.numeric.NumericType<T>>

Overrides:

getSource in class bdv.util.RandomAccessibleIntervalSource<T extends net.imglib2.type.numeric.NumericType<T>>

getVoxelDimensions

public mpicbg.spim.data.sequence.VoxelDimensions getVoxelDimensions()

Specified by:

getVoxelDimensions in interface bdv.viewer.Source<T extends net.imglib2.type.numeric.NumericType<T>>

Overrides:

getVoxelDimensions in class bdv.util.AbstractSource<T extends net.imglib2.type.numeric.NumericType<T>>