com.xinapse.filter
Class GaussianBlurFilter

java.lang.Object
  com.xinapse.filter.AbstractKernelFilter
      com.xinapse.filter.FixedWeightsKernelFilter
          com.xinapse.filter.GaussianBlurFilter

All Implemented Interfaces:

SpatialFilter

public class GaussianBlurFilter
extends FixedWeightsKernelFilter
implements SpatialFilter

A FixedWeightsKernelFilter for performing a Gaussian blurring of an image.

Nested Class Summary

static class

GaussianBlurFilter.GaussianBlurSpecifierPanel A FilterSpecifierPanel for a Gaussian blur filter.

Nested classes/interfaces inherited from interface com.xinapse.filter.SpatialFilter

SpatialFilter.SpecifierPanel

Field Summary

static org.apache.commons.cli.Option	BLUR_FWHM A public Option to specify that the FWHM of an isotropic Gaussian blur filter.
static org.apache.commons.cli.Option	BLUR_THREE_D A public Option to specify that a Gaussian blur filter should work in 3-D, not 2-D.
static org.apache.commons.cli.Option	FWHM_OPTION Command line option for setting the full-width-half-maximum values for a GaussianBlurFilter.
static FixedWeightsKernelFilter	THREE_D_GAUSS_11 A 3-D GaussianBlurFilter with an isotropic 11x11x11 kernel and a FWHM of 7.5 times the pixel size in each direction.
static FixedWeightsKernelFilter	THREE_D_GAUSS_13 A 3-D GaussianBlurFilter with an isotropic 13x13x13 kernel and a FWHM of 9.5 times the pixel size in each direction.
static FixedWeightsKernelFilter	THREE_D_GAUSS_3 A 3-D GaussianBlurFilter with an isotropic 3x3x3 kernel and a FWHM of 1.5 times the pixel size in each direction.
static FixedWeightsKernelFilter	THREE_D_GAUSS_5 A 3-D GaussianBlurFilter with an isotropic 5x5x5 kernel and a FWHM of 2.5 times the pixel size.
static FixedWeightsKernelFilter	THREE_D_GAUSS_7 A 3-D GaussianBlurFilter with an isotropic 7x7x7 kernel and a FWHM of 3.5 times the pixel size in each direction.
static FixedWeightsKernelFilter	THREE_D_GAUSS_9 A 3-D GaussianBlurFilter with an isotropic 9x9x9 kernel and a FWHM of 5.5 times the pixel size in each direction.
static FixedWeightsKernelFilter	TWO_D_GAUSS_11 A 2-D GaussianBlurFilter with an isotropic 11x11 kernel and a FWHM of 7.5 times the pixel size in each direction.
static FixedWeightsKernelFilter	TWO_D_GAUSS_13 A 2-D GaussianBlurFilter with an isotropic 13x13 kernel and a FWHM of 9.5 times the pixel size in each direction.
static FixedWeightsKernelFilter	TWO_D_GAUSS_3 A 2-D GaussianBlurFilter with an isotropic 3x3 kernel and a FWHM of 1.5 times the pixel size in each direction.
static FixedWeightsKernelFilter	TWO_D_GAUSS_5 A 2-D GaussianBlurFilter with an isotropic 5x5 kernel and a FWHM of 2.5 times the pixel size.
static FixedWeightsKernelFilter	TWO_D_GAUSS_7 A 2-D GaussianBlurFilter with an isotropic 7x7 kernel and a FWHM of 3.5 times the pixel size in each direction.
static FixedWeightsKernelFilter	TWO_D_GAUSS_9 A 2-D GaussianBlurFilter with an isotropic 9x9 kernel and a FWHM of 5.5 times the pixel size in each direction.

Fields inherited from class com.xinapse.filter.FixedWeightsKernelFilter

weights

Fields inherited from interface com.xinapse.filter.SpatialFilter

N_DOTS

Method Summary

static java.lang.String	getName() Returns the human-readable name of this filter.
static java.lang.String	getOptionName() Returns the name of this type of filter when specifying it in program optional arguments.
static org.apache.commons.cli.Options	getOptions() Returns the options for this type of filter.
static SpatialFilter.SpecifierPanel	getSpecifierPanel(java.lang.String preferencesNodeName) Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a GaussianBlurFilter.
static void	main(java.lang.String[] args) Runs a self-test of this class.
static GaussianBlurFilter	newInstance(org.apache.commons.cli.CommandLine commandLine, LoadableImage image) Creates a new GaussianBlurFilter using the supplied command line arguments, suitable for blurring the supplied image.
static GaussianBlurFilter	newInstance(float[] pixelSizes, float[] fwhm) Creates a new GaussianBlurFilter suitable for blurring an image with the given pixel sizes.
static GaussianBlurFilter	newInstance(LoadableImage image, float[] fwhm) Creates a new GaussianBlurFilter suitable for blurring the supplied image.

Methods inherited from class com.xinapse.filter.FixedWeightsKernelFilter

add, add, convolve, copyResize, filterInPlaceBinary, filterInPlaceByte, filterInPlaceDouble, filterInPlaceFloat, filterInPlaceInt, filterInPlaceLong, filterInPlaceShort, filterInPlaceUByte, filterInPlaceUInt, filterInPlaceUShort, getNKernelCols, getNKernelRows, getNKernelSlices, scale, sumWeights, toString

Methods inherited from class com.xinapse.filter.AbstractKernelFilter

filter, filter, filter, filterInPlace, filterInPlace, filterInPlace, filterInPlace, filterInPlace, filterInPlace, filterInPlace

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.xinapse.filter.SpatialFilter

filter, filter, filterInPlace, filterInPlace, filterInPlace, filterInPlace

Field Detail

THREE_D_GAUSS_3

public static final FixedWeightsKernelFilter THREE_D_GAUSS_3

A 3-D GaussianBlurFilter with an isotropic 3x3x3 kernel and a FWHM of 1.5 times the pixel size in each direction.

THREE_D_GAUSS_5

public static final FixedWeightsKernelFilter THREE_D_GAUSS_5

A 3-D GaussianBlurFilter with an isotropic 5x5x5 kernel and a FWHM of 2.5 times the pixel size.

THREE_D_GAUSS_7

public static final FixedWeightsKernelFilter THREE_D_GAUSS_7

A 3-D GaussianBlurFilter with an isotropic 7x7x7 kernel and a FWHM of 3.5 times the pixel size in each direction.

THREE_D_GAUSS_9

public static final FixedWeightsKernelFilter THREE_D_GAUSS_9

A 3-D GaussianBlurFilter with an isotropic 9x9x9 kernel and a FWHM of 5.5 times the pixel size in each direction.

THREE_D_GAUSS_11

public static final FixedWeightsKernelFilter THREE_D_GAUSS_11

A 3-D GaussianBlurFilter with an isotropic 11x11x11 kernel and a FWHM of 7.5 times the pixel size in each direction.

THREE_D_GAUSS_13

public static final FixedWeightsKernelFilter THREE_D_GAUSS_13

A 3-D GaussianBlurFilter with an isotropic 13x13x13 kernel and a FWHM of 9.5 times the pixel size in each direction.

TWO_D_GAUSS_3

public static final FixedWeightsKernelFilter TWO_D_GAUSS_3

A 2-D GaussianBlurFilter with an isotropic 3x3 kernel and a FWHM of 1.5 times the pixel size in each direction.

TWO_D_GAUSS_5

public static final FixedWeightsKernelFilter TWO_D_GAUSS_5

A 2-D GaussianBlurFilter with an isotropic 5x5 kernel and a FWHM of 2.5 times the pixel size.

TWO_D_GAUSS_7

public static final FixedWeightsKernelFilter TWO_D_GAUSS_7

A 2-D GaussianBlurFilter with an isotropic 7x7 kernel and a FWHM of 3.5 times the pixel size in each direction.

TWO_D_GAUSS_9

public static final FixedWeightsKernelFilter TWO_D_GAUSS_9

A 2-D GaussianBlurFilter with an isotropic 9x9 kernel and a FWHM of 5.5 times the pixel size in each direction.

TWO_D_GAUSS_11

public static final FixedWeightsKernelFilter TWO_D_GAUSS_11

A 2-D GaussianBlurFilter with an isotropic 11x11 kernel and a FWHM of 7.5 times the pixel size in each direction.

TWO_D_GAUSS_13

public static final FixedWeightsKernelFilter TWO_D_GAUSS_13

A 2-D GaussianBlurFilter with an isotropic 13x13 kernel and a FWHM of 9.5 times the pixel size in each direction.

BLUR_FWHM

public static final org.apache.commons.cli.Option BLUR_FWHM

A public Option to specify that the FWHM of an isotropic Gaussian blur filter.

BLUR_THREE_D

public static final org.apache.commons.cli.Option BLUR_THREE_D

A public Option to specify that a Gaussian blur filter should work in 3-D, not 2-D.

FWHM_OPTION

public static final org.apache.commons.cli.Option FWHM_OPTION

Command line option for setting the full-width-half-maximum values for a GaussianBlurFilter.

Method Detail

newInstance

public static GaussianBlurFilter newInstance(org.apache.commons.cli.CommandLine commandLine,
                                             LoadableImage image)
                                      throws com.xinapse.util.InvalidArgumentException

Creates a new GaussianBlurFilter using the supplied command line arguments, suitable for blurring the supplied image.

Parameters:

commandLine - the command line from which a program is invoked.

image - the image to which this filter is designed to apply. The image pixel sizes are used to determine the kernel weights.

Throws:

com.xinapse.util.InvalidArgumentException

newInstance

public static GaussianBlurFilter newInstance(LoadableImage image,
                                             float[] fwhm)
                                      throws com.xinapse.util.InvalidArgumentException

Creates a new GaussianBlurFilter suitable for blurring the supplied image.

Parameters:

image - the image to which this filter is designed to apply. The image pixel sizes are used to determine the kernel weights.

fwhm - the full-width-half-maximum values for the Gaussian blurring function in each spatial dimension of the image. fwhm may be of length 2 (for a 2-D in-plane blur) or length 3 (for a 3-D blur). The first value in this array applies to the along-row (x) direction; the second value applies to the along-column (y) direction; and the third value (if present) applies to the through-slice (z) direction.

Throws:

com.xinapse.util.InvalidArgumentException

newInstance

public static GaussianBlurFilter newInstance(float[] pixelSizes,
                                             float[] fwhm)
                                      throws com.xinapse.util.InvalidArgumentException

Creates a new GaussianBlurFilter suitable for blurring an image with the given pixel sizes.

Parameters:

pixelSizes - the pixels sizes of an image to which this filter can be applied. The image pixel sizes are used to determine the kernel weights. The first element of this array is the pixel width; the second is the pixel height; and the third is the slice thickness. For 2-D blurs, where fwhm has length 2, this array may have length 2 also.

fwhm - the full-width-half-maximum values for the Gaussian blurring function in each spatial dimension of the image. fwhm may be of length 2 (for a 2-D in-plane blur) or length 3 (for a 3-D blur). The first value in this array applies to the along-row (x) direction; the second value applies to the along-column (y) direction; and the third value (if present) applies to the through-slice (z) direction.

Throws:

com.xinapse.util.InvalidArgumentException

getOptionName

public static java.lang.String getOptionName()

Returns the name of this type of filter when specifying it in program optional arguments.

Returns:

the name of the filter for selection in program arguments.

getOptions

public static org.apache.commons.cli.Options getOptions()

Returns the options for this type of filter.

Returns:

the options for this type of filter.

getSpecifierPanel

public static SpatialFilter.SpecifierPanel getSpecifierPanel(java.lang.String preferencesNodeName)

Returns a SpatialFilter.SpecifierPanel that can be used to set the parameters for a GaussianBlurFilter.

Parameters:

preferencesNodeName - the preferences node name from which the initial settings will be taken.

Returns:

a SpatialFilter.SpecifierPanel to set the parameters for this type of filter.

getName

public static java.lang.String getName()

Returns the human-readable name of this filter.

Returns:

the human-readable name of this filter.

main

public static void main(java.lang.String[] args)

Runs a self-test of this class.

Parameters:

args - the program aguments (ignored).