Package net.preibisch.mvrecon.fiji.plugin.fusion

Class FusionGUI

java.lang.Object

net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

All Implemented Interfaces:

FusionExportInterface

public class FusionGUI
extends Object
implements FusionExportInterface

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	FusionGUI.FusionType

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	adjustIntensities
protected double	avgAnisoF
protected int	boundingBox
static int[]	cellDim
static boolean	defaultAdjustIntensities
static int	defaultBB
static int	defaultDefineMinMax
static double	defaultDownsampling
static int	defaultFusionType
static int	defaultImgExportAlgorithm
static int	defaultInterpolation
static double	defaultMax
static double	defaultMin
static int	defaultPixelType
static boolean	defaultPreserveAnisotropy
static int	defaultSplittingType
protected int	defineMinMax
protected double	downsampling
protected int	fusionType
static String[]	fusionTypes
protected int	imgExport
static final String[]	imgExportDescriptions
protected int	interpolation
static String[]	interpolationTypes
protected double	max
static int	maxCacheSize
protected double	min
protected NonRigidParametersGUI	nrgui
protected int	pixelType
static String[]	pixelTypes1
protected boolean	preserveAnisotropy
protected final SpimData2	spimData
protected int	splittingType
static String[]	splittingTypes
static final ArrayList<ImgExport>	staticImgExportAlgorithms

Constructor Summary

Constructors

Constructor	Description
FusionGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> views)

Method Summary

Modifier and Type	Method	Description
boolean	adjustIntensities()
double[]	defineMinMax(double[] autoValues)
double	getAnisotropyFactor()
net.imglib2.Interval	getBoundingBox()
static String[]	getBoundingBoxChoices(List<BoundingBox> allBoxes)
static String[]	getBoundingBoxChoices(List<BoundingBox> allBoxes, boolean showDimensions)
net.imglib2.Interval	getDownsampledBoundingBox()
double	getDownsampling()
List<Group<mpicbg.spim.data.sequence.ViewDescription>>	getFusionGroups()
static List<Group<mpicbg.spim.data.sequence.ViewDescription>>	getFusionGroups(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> views, int splittingType)
FusionGUI.FusionType	getFusionType()
int	getInterpolation()
ImgExport	getNewExporterInstance()
NonRigidParametersGUI	getNonRigidParameters()
int	getPixelType()	0 == "32-bit floating point", 1 == "16-bit unsigned integer"
SpimData2	getSpimData()
int	getSplittingType()	0 == "Each timepoint & channel", 1 == "Each timepoint, channel & illumination", 2 == "All views together", 3 == "Each view"
List<mpicbg.spim.data.sequence.ViewId>	getViews()
static int	inputBytePerPixel(mpicbg.spim.data.sequence.ViewId viewId, SpimData2 spimData)
boolean	isImgLoaderVirtual()
static boolean	isImgLoaderVirtual(mpicbg.spim.data.SpimData spimData)
boolean	isMultiResolution()
static boolean	isMultiResolution(mpicbg.spim.data.SpimData spimData)
boolean	manuallyDefinedMinMax()
double	maxIntensity()
static long	maxNumInputPixelsPerInputGroup(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> views, int splittingType)
double	minIntensity()
boolean	queryDetails()
void	setBoundingBox(net.imglib2.Interval bb)

Methods inherited from class java.lang.Object

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

Field Details

cellDim

public static int[] cellDim

maxCacheSize

public static int maxCacheSize

defaultDownsampling

public static double defaultDownsampling

defaultBB

public static int defaultBB

interpolationTypes

public static String[] interpolationTypes

defaultInterpolation

public static int defaultInterpolation

fusionTypes

public static String[] fusionTypes

defaultFusionType

public static int defaultFusionType

pixelTypes1

public static String[] pixelTypes1

defaultPixelType

public static int defaultPixelType

defaultDefineMinMax

public static int defaultDefineMinMax

defaultMin

public static double defaultMin

defaultMax

public static double defaultMax

splittingTypes

public static String[] splittingTypes

defaultSplittingType

public static int defaultSplittingType

defaultAdjustIntensities

public static boolean defaultAdjustIntensities

defaultPreserveAnisotropy

public static boolean defaultPreserveAnisotropy

staticImgExportAlgorithms

public static final ArrayList<ImgExport> staticImgExportAlgorithms

imgExportDescriptions

public static final String[] imgExportDescriptions

defaultImgExportAlgorithm

public static int defaultImgExportAlgorithm

interpolation

protected int interpolation

boundingBox

protected int boundingBox

pixelType

protected int pixelType

defineMinMax

protected int defineMinMax

min

protected double min

max

protected double max

splittingType

protected int splittingType

downsampling

protected double downsampling

fusionType

protected int fusionType

adjustIntensities

protected boolean adjustIntensities

preserveAnisotropy

protected boolean preserveAnisotropy

avgAnisoF

protected double avgAnisoF

imgExport

protected int imgExport

nrgui

protected NonRigidParametersGUI nrgui

spimData

protected final SpimData2 spimData

Constructor Details

FusionGUI

public FusionGUI(SpimData2 spimData,
 List<mpicbg.spim.data.sequence.ViewId> views)

Method Details

getSpimData

public SpimData2 getSpimData()

Specified by:

getSpimData in interface FusionExportInterface

getViews

public List<mpicbg.spim.data.sequence.ViewId> getViews()

Specified by:

getViews in interface FusionExportInterface

getBoundingBox

public net.imglib2.Interval getBoundingBox()

setBoundingBox

public void setBoundingBox(net.imglib2.Interval bb)

getDownsampledBoundingBox

public net.imglib2.Interval getDownsampledBoundingBox()

Specified by:

getDownsampledBoundingBox in interface FusionExportInterface

getInterpolation

public int getInterpolation()

getPixelType

public int getPixelType()

Description copied from interface: FusionExportInterface

0 == "32-bit floating point", 1 == "16-bit unsigned integer"

Specified by:

getPixelType in interface FusionExportInterface

Returns:

the pixel type

manuallyDefinedMinMax

public boolean manuallyDefinedMinMax()

minIntensity

public double minIntensity()

maxIntensity

public double maxIntensity()

getNonRigidParameters

public NonRigidParametersGUI getNonRigidParameters()

getDownsampling

public double getDownsampling()

Specified by:

getDownsampling in interface FusionExportInterface

Returns:

the downsampling used for the fusion, or Double.NaN if no downsampling

getFusionType

public FusionGUI.FusionType getFusionType()

adjustIntensities

public boolean adjustIntensities()

getAnisotropyFactor

public double getAnisotropyFactor()

Specified by:

getAnisotropyFactor in interface FusionExportInterface

Returns:

the average anisotropy factor in z of all views used to "flatten" the fused image, or Double.NaN if no change

getSplittingType

public int getSplittingType()

Description copied from interface: FusionExportInterface

0 == "Each timepoint & channel", 1 == "Each timepoint, channel & illumination", 2 == "All views together", 3 == "Each view"

Specified by:

getSplittingType in interface FusionExportInterface

Returns:

- how the views that are processed are split up

getNewExporterInstance

public ImgExport getNewExporterInstance()

Specified by:

getNewExporterInstance in interface FusionExportInterface

Returns:

- creates a new instance of the exporter object

defineMinMax

public double[] defineMinMax(double[] autoValues)

queryDetails

public boolean queryDetails()

isImgLoaderVirtual

public boolean isImgLoaderVirtual()

isImgLoaderVirtual

public static boolean isImgLoaderVirtual(mpicbg.spim.data.SpimData spimData)

isMultiResolution

public boolean isMultiResolution()

isMultiResolution

public static boolean isMultiResolution(mpicbg.spim.data.SpimData spimData)

getBoundingBoxChoices

public static String[] getBoundingBoxChoices(List<BoundingBox> allBoxes)

getBoundingBoxChoices

public static String[] getBoundingBoxChoices(List<BoundingBox> allBoxes,
 boolean showDimensions)

getFusionGroups

public List<Group<mpicbg.spim.data.sequence.ViewDescription>> getFusionGroups()

Specified by:

getFusionGroups in interface FusionExportInterface

getFusionGroups

public static List<Group<mpicbg.spim.data.sequence.ViewDescription>> getFusionGroups(SpimData2 spimData,
 List<mpicbg.spim.data.sequence.ViewId> views,
 int splittingType)

maxNumInputPixelsPerInputGroup

public static long maxNumInputPixelsPerInputGroup(SpimData2 spimData,
 List<mpicbg.spim.data.sequence.ViewId> views,
 int splittingType)

inputBytePerPixel

public static int inputBytePerPixel(mpicbg.spim.data.sequence.ViewId viewId,
 SpimData2 spimData)