net.imagej.sampler

Class SamplingDefinition

java.lang.Object

net.imagej.sampler.SamplingDefinition

public class SamplingDefinition
extends Object

SamplingDefinitions define regions of space and are used by the SamplerService to pull data out of existing ImageDisplays.

Author:

Barry DeZonia

Method Summary

Modifier and Type	Method and Description
boolean	constrain(AxisType axis, AxisSubrange subrange) Replaces the current constraining definition of a given axis within the current SamplingDefinition with a given subrange.
ImageDisplay	getDisplay() Returns the input ImageDisplay of the SamplingDefinition.
String	getError() Returns the current value of the error string of the SamplingDefinition.
AxisType[]	getInputAxes() Returns the AxisTypes that are present in the input data.
CalibratedAxis[]	getInputCalibratedAxes() Returns the set of CalibratedAxis's that are present in the input data.
List<List<Long>>	getInputRanges() Returns a multidimensional set of input axis values generated from the input data of this SamplingDefinition.
AxisType[]	getOutputAxes() Returns the set of AxisTypes that will be present in the output data.
CalibratedAxis[]	getOutputCalibratedAxes() Returns the set of CalibratedAxis's that will be present in the output data.
double[]	getOutputCalibration(AxisType[] outputAxes) Deprecated.
long[]	getOutputDims() Returns the dimensions that will be present in the output data.
static SamplingDefinition	sampleAllPlanes(ImageDisplay display) A convenience method for defining a SamplingDefinition that returns a complete copy of an ImageDisplay.
static SamplingDefinition	sampleCompositeUVPlane(ImageDisplay display, AxisType uAxis, AxisType vAxis) A convenience method for defining a SamplingDefinition that returns a composite (multichannel) UV plane of an ImageDisplay.
static SamplingDefinition	sampleCompositeXYPlane(ImageDisplay display) A convenience method for defining a SamplingDefinition that returns a composite (multichannel) XY plane of an ImageDisplay.
static SamplingDefinition	sampleUVPlane(ImageDisplay display, AxisType uAxis, AxisType vAxis) A convenience method for defining a SamplingDefinition that returns a single UV plane of an ImageDisplay.
static SamplingDefinition	sampleXYPlane(ImageDisplay display) A convenience method for defining a SamplingDefinition that returns a single XY plane of an ImageDisplay.

Methods inherited from class java.lang.Object

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

Method Detail

getDisplay

public ImageDisplay getDisplay()

Returns the input ImageDisplay of the SamplingDefinition.

getError

public String getError()

Returns the current value of the error string of the SamplingDefinition.

getInputAxes

public AxisType[] getInputAxes()

Returns the AxisTypes that are present in the input data.

getInputCalibratedAxes

public CalibratedAxis[] getInputCalibratedAxes()

Returns the set of CalibratedAxis's that are present in the input data.

getInputRanges

public List<List<Long>> getInputRanges()

Returns a multidimensional set of input axis values generated from the input data of this SamplingDefinition.

For example, if the sampling definition has two axes defined as "1-4" and "1-3" calling this routine would return something like this: [[1,2,3,4] , [1,2,3]]

getOutputAxes

public AxisType[] getOutputAxes()

Returns the set of AxisTypes that will be present in the output data. Those input axes whose size is 1 are automatically collapsed.

getOutputCalibratedAxes

public CalibratedAxis[] getOutputCalibratedAxes()

Returns the set of CalibratedAxis's that will be present in the output data. Those input axes whose size is 1 are automatically collapsed.

getOutputDims

public long[] getOutputDims()

Returns the dimensions that will be present in the output data. Those input dimensions whose size is 1 are automatically collapsed.

getOutputCalibration

@Deprecated
public double[] getOutputCalibration(AxisType[] outputAxes)

Deprecated.

Returns the calibration values that will be present in the output data. This method assumes all calibrations are linear and should be avoided. Use getOutputCalibratedAxes() for access to calibration information.

constrain

public boolean constrain(AxisType axis,
                         AxisSubrange subrange)

Replaces the current constraining definition of a given axis within the current SamplingDefinition with a given subrange.

Parameters:

axis - The axis to associate the constraint with

subrange - The new subrange defining the constraint

Returns:

True if the contraint is well defined. False otherwise (and the existing constraint for the axis is unchanged).

sampleUVPlane

public static SamplingDefinition sampleUVPlane(ImageDisplay display,
                                               AxisType uAxis,
                                               AxisType vAxis)

A convenience method for defining a SamplingDefinition that returns a single UV plane of an ImageDisplay. U and V are defined by the user.

Parameters:

display - The ImageDisplay to sample

uAxis - The U axis of the sample space

vAxis - The V axis of the sample space

Returns:

The specified SamplingDefinition

sampleXYPlane

public static SamplingDefinition sampleXYPlane(ImageDisplay display)

A convenience method for defining a SamplingDefinition that returns a single XY plane of an ImageDisplay.

Parameters:

display - The ImageDisplay to sample

Returns:

The specified SamplingDefinition

sampleCompositeUVPlane

public static SamplingDefinition sampleCompositeUVPlane(ImageDisplay display,
                                                        AxisType uAxis,
                                                        AxisType vAxis)

A convenience method for defining a SamplingDefinition that returns a composite (multichannel) UV plane of an ImageDisplay. U and V are defined by the user.

Parameters:

display - The ImageDisplay to sample

uAxis - The U axis of the sample space

vAxis - The V axis of the sample space

Returns:

The specified SamplingDefinition

sampleCompositeXYPlane

public static SamplingDefinition sampleCompositeXYPlane(ImageDisplay display)

A convenience method for defining a SamplingDefinition that returns a composite (multichannel) XY plane of an ImageDisplay.

Parameters:

display - The ImageDisplay to sample

Returns:

The specified SamplingDefinition

sampleAllPlanes

public static SamplingDefinition sampleAllPlanes(ImageDisplay display)

A convenience method for defining a SamplingDefinition that returns a complete copy of an ImageDisplay.

Parameters:

display - The ImageDisplay to sample

Returns:

The specified SamplingDefinition