Package com.xinapse.multisliceimage.roi

Class OpenSplineROI

java.lang.Object

com.xinapse.multisliceimage.roi.ROI

com.xinapse.multisliceimage.roi.SplineROI

com.xinapse.multisliceimage.roi.OpenSplineROI

All Implemented Interfaces:

EditableOutlineROI, LinearROI, RegularROI, RotatableROI, StretchableROI, Cloneable

public class OpenSplineROI
extends SplineROI
implements Cloneable, StretchableROI, RotatableROI, EditableOutlineROI, LinearROI, RegularROI

A Class representing a curved line on an image, represented by a set of knots, with spline interpolators between the knots to define the shape of the curve.

Field Summary

Fields inherited from class com.xinapse.multisliceimage.roi.SplineROI

closed, sMax, xpts, xSpline, ypts, ySpline

Fields inherited from class com.xinapse.multisliceimage.roi.ROI

BUTTON_ICON_SIZE, handles, PREFERENCES_NODE_NAME, XTOKEN, YTOKEN

Constructor Summary

Constructors

Constructor	Description
OpenSplineROI(double[] x, double[] y, byte userColour, ROIState state, boolean checkIntegrity)	Creates a new OpenSplineROI with the specified knot points in mm coordinates.
OpenSplineROI(double[] x, double[] y, ROIState state)	Creates a new OpenSplineROI with the specified knot points in mm coordinates.
OpenSplineROI(SplineROI splineROI)	Creates a new OpenSplineROI with the positions of the knot points taken from the supplied SplineROI.

Method Summary

Modifier and Type	Method	Description
static void	alignKnots(OpenSplineROI s1, OpenSplineROI s2, int nKnots)	Aligns the knot points in a pair of OpenSplineROIs, so that there is spatial correspondence as far as possible across the knots.
OpenSplineROI	clone()	Returns a clone of this ROI.
static Icon	getButtonIcon()	Returns an Icon that can be used for a button to create this type of ROI.
ROI	getCopy()	Returns a copy of this ROI.
static InteractionType	getCreateInteractionType()	Returns the type of interaction needed to create an OpenSplineROI.
String	getDescription()	Return a description of this type of ROI.
Point2D[]	getIntensityProfile(Object pix, PixelDataType dataType, int nCols, int nRows, int offset, float pixelXSize, float pixelYSize, ComplexMode complexMode)	Returns an array of Point2D representing the pixel intensities along this LinearROI.
double	getLength()	Returns the length of this ROI in mm.
double	getLengthPix(float pixelXSize, float pixelYSize)	Returns the length of this ROI in image pixels.
static String	getName()	Returns a descriptive name for this type of ROI.
double	getSquareArea()	Returns zero - an Open Spline has no area.
ROIStats	getStats(Object pix, PixelDataType dataType, int nCols, int nRows, int offset, float pixelXSize, float pixelYSize, MaskAction maskAction, MaskMode maskMode, double maskValue, PrintStream intensityOutputStream, boolean isUnitsMM, ComplexMode complexMode)	Returns statistics about this ROI, and (optionally) performs a masking operation.
CurvedLineROI	toIrregular()	Creates a new CurvedLineROI that is close to the shape of this OpenSplineROI.
String	toString()	Returns a String describing this ROI.

Methods inherited from class com.xinapse.multisliceimage.roi.SplineROI

alignKnots, alignKnots, approximate, close, contains, deleteVertex, draw, drawInOrthoView, equals, flipHorizontal, flipVertical, getCentre, getCentroid, getCurvature, getCurvature, getFeret, getFollowingVisibleHandle, getKnotPoint, getKnotPoints, getLocation, getNormal, getNormal, getNPoints, getPerimeter, getPrecedingVisibleHandle, getPrincipalAxisAngle, getSMax, getTheta, getVertexHandles, hashCode, insertTwoVertices, interpolate, intersect, isClosed, move, move, moveVertex, recalculateSplines, reduce, removeFirstKnotPoint, removeLastKnotPoint, selfIntersects, set, setKnotPoint, setKnotPoints, setKnotPoints, setKnotPoints, setKnotPoints, setTheta

Methods inherited from class com.xinapse.multisliceimage.roi.ROI

andNot, andNot, andNot, clearDeletionHistory, dilate, exclusiveOr, exclusiveOr, getAnnotation, getBoundingRectangle, getBoundingRectangle, getCentroid, getClasses, getColor, getDesignTextFontSize, getDisplayedBounds2D, getDisplayedBounds2D, getDisplayedRoiArea, getFeret, getGroupUid, getGroupUid, getHandles, getHandleUnderPoint, getImageSource, getPixelValue, getROIs, getROIs, getROIs, getROIs, getROIs, getSlice, getState, getStats, getStats, getTextColor, getUserColour, group, intersect, intersect, intersects, isDeleted, isEditable, isGroup, isReloaded, isSameAnnotation, isSameColour, isSelected, join, logicalUnion, main, markDeleted, mmPosToPix, moveROIs, pixPosToMm, printStats, selectDeselect, setAnnotation, setCreationHistory, setGroupUid, setSlice, setState, setTextColor, setTextSize, setUserColour, ungroup, ungroup, union, union, write, write

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface com.xinapse.multisliceimage.roi.EditableOutlineROI

deleteVertex, getFollowingVisibleHandle, getPrecedingVisibleHandle, getVertexHandles, insertTwoVertices, moveVertex

Methods inherited from interface com.xinapse.multisliceimage.roi.RotatableROI

getCentre, getTheta, setTheta

Methods inherited from interface com.xinapse.multisliceimage.roi.StretchableROI

getDisplayedBounds2D, move

Constructor Details

OpenSplineROI

public OpenSplineROI(double[] x,
 double[] y,
 ROIState state)
              throws ROIException

Creates a new OpenSplineROI with the specified knot points in mm coordinates.

Parameters:

x - an array of x-coordinates for the knot points.

y - an array of y-coordinates for the knot points.

state - the ROIState of the newly-created ROI.

Throws:

ROIException - if the OpenSplineROI cannot be created as specified.

OpenSplineROI

public OpenSplineROI(double[] x,
 double[] y,
 byte userColour,
 ROIState state,
 boolean checkIntegrity)
              throws ROIException

Creates a new OpenSplineROI with the specified knot points in mm coordinates.

Parameters:

x - an array of x-coordinates for the knot points.

y - an array of y-coordinates for the knot points.

userColour - the colour of this ROI. A value of 0 indicates that the ROI will be drawn with the default colour for normal ROIs if unselected.

state - the ROIState of the newly-created ROI.

checkIntegrity - whether to check the integrity of the ROI.

Throws:

ROIException - if the OpenSplineROI cannot be created as specified.

OpenSplineROI

public OpenSplineROI(SplineROI splineROI)
              throws ROIException

Creates a new OpenSplineROI with the positions of the knot points taken from the supplied SplineROI.

Parameters:

splineROI - the SplineROI from which the knot point positions will be taken.

Throws:

ROIException - if the OpenSplineROI cannot be created as specified.

Method Details

getSquareArea

public double getSquareArea()

Returns zero - an Open Spline has no area.

Specified by:

getSquareArea in interface RegularROI

Returns:

zero.

getLength

public double getLength()

Description copied from interface: LinearROI

Returns the length of this ROI in mm.

Specified by:

getLength in interface LinearROI

Returns:

the length of this ROI in mm.

getLengthPix

public double getLengthPix(float pixelXSize,
 float pixelYSize)

Description copied from interface: LinearROI

Returns the length of this ROI in image pixels.

Specified by:

getLengthPix in interface LinearROI

Parameters:

pixelXSize - the size of image pixels in the horizontal direction.

pixelYSize - the size of image pixels in the vertical direction.

Returns:

the length of this ROI in image pixels.

getIntensityProfile

public Point2D[] getIntensityProfile(Object pix,
 PixelDataType dataType,
 int nCols,
 int nRows,
 int offset,
 float pixelXSize,
 float pixelYSize,
 ComplexMode complexMode)

Description copied from interface: LinearROI

Returns an array of Point2D representing the pixel intensities along this LinearROI. The x-value of a point is a position along the LinearROI, and the y-value is the intensity. The first and last points will be at the ends of the LinearROI, but the location of the points in between is not prescribed by this interface.

Specified by:

getIntensityProfile in interface LinearROI

Parameters:

pix - the array of pixel intensities for in which this LinearROI is positioned.

dataType - the PixelDataType of the array of pixel intensities.

nCols - the number of columns in the slice.

nRows - the number of rows in the slice.

offset - an offset (in pixels) into the pixel value array for the starting pixel of the slice on which this ROI is defined.

pixelXSize - the size of image pixels in the horizontal direction.

pixelYSize - the size of image pixels in the vertical direction.

complexMode - the calculation mode for Complex images. The intensity profile returned will correspond to the mode: the real part, imaginary part, magnitude or phase.

Returns:

an array of Point2D representing the pixel intensities along this LinearROI.

getStats

public ROIStats getStats(Object pix,
 PixelDataType dataType,
 int nCols,
 int nRows,
 int offset,
 float pixelXSize,
 float pixelYSize,
 MaskAction maskAction,
 MaskMode maskMode,
 double maskValue,
 PrintStream intensityOutputStream,
 boolean isUnitsMM,
 ComplexMode complexMode)

Description copied from class: ROI

Returns statistics about this ROI, and (optionally) performs a masking operation.

Overrides:

getStats in class ROI

Parameters:

pix - the whole image pixel value array. If pix is null, then the intensity-related stats will all be set to zero.

dataType - the type of pixels.

nCols - the number of columns in the slice.

nRows - the number of rows in the slice.

offset - an offset (in pixels) into the pixel value array for the starting pixel of the slice on which this ROI is defined.

pixelXSize - the size of image pixels in the horizontal direction.

pixelYSize - the size of image pixels in the vertical direction.

maskAction - one of:

• MaskAction.NONE for no masking;
• MaskAction.MASK_INSIDE to set pixel values to maskValue inside the shape; or
• MaskAction.MASK_OUTSIDE to set the pixel values to maskValue outside the shape.
• MaskAction.MASK_INSIDE_SOFT to perform soft masking inside the shape;
• MaskAction.MASK_OUTSIDE_SOFT to perform soft masking outside the shape.

maskMode - how much of a pixel must be inside ROIs for the pixel to be part of the mask.

maskValue - the pixel value to set outside/inside the shape when performing masking ops.

intensityOutputStream - if non-null, pixel intensities within the ROI will be printed to this PrintStream.

isUnitsMM - true if the (x,y) coordinates of the pixel intensities are to be written in mm, false if the coordinates are to be writtn in pixel units.

complexMode - the calculation mode for PixelDataType.COMPLEX images. The statistics returned will correspond to the mode: the real part, imaginary part, magnitude or phase.

Returns:

statistics about the ROI.

toIrregular

public CurvedLineROI toIrregular()

Creates a new CurvedLineROI that is close to the shape of this OpenSplineROI.

Overrides:

toIrregular in class SplineROI

Returns:

a new CurvedLineROI that is close to the shape of this OpenSplineROI.

alignKnots

public static void alignKnots(OpenSplineROI s1,
 OpenSplineROI s2,
 int nKnots)
                       throws ROIException

Aligns the knot points in a pair of OpenSplineROIs, so that there is spatial correspondence as far as possible across the knots.

The number of knot points in each of the ROIs will be set to the specified number of knot points, and the knots will be evenly spaced in the s-parameter.

Parameters:

s1 - the first OpenSplineROI to align.

s2 - the second OpenSplineROI to align.

nKnots - the number of knot points in the aligned ROIs.

Throws:

ROIException - if the ROIs cannot be aligned.

getCopy

public ROI getCopy()

Description copied from class: ROI

Returns a copy of this ROI. The copy will be identical in shape and annotation as the original ROI, but with a history of that of a newly-created ROI.

Overrides:

getCopy in class SplineROI

Returns:

a copy of this ROI.

clone

public OpenSplineROI clone()

Description copied from class: ROI

Returns a clone of this ROI. The copy will be identical in shape and annotation as the original ROI, and with a history identical to the cloned ROI.

Overrides:

clone in class SplineROI

Returns:

a clone of this ROI, cast to an Object.

toString

public String toString()

Description copied from class: ROI

Returns a String describing this ROI.

Overrides:

toString in class SplineROI

Returns:

a String describing this ROI.

getDescription

public String getDescription()

Description copied from class: ROI

Return a description of this type of ROI.

Overrides:

getDescription in class SplineROI

Returns:

a String describing the type of this ROI.

getCreateInteractionType

public static InteractionType getCreateInteractionType()

Returns the type of interaction needed to create an OpenSplineROI.

Returns:

type of interaction needed to create an OpenSplineROI - InteractionType.CLICK_POINTS.

getName

public static String getName()

Returns a descriptive name for this type of ROI.

Returns:

a String describing this type of ROI.

getButtonIcon

public static Icon getButtonIcon()

Returns an Icon that can be used for a button to create this type of ROI.

Returns:

an Icon that can be used to represent this type of ROI.