com.xinapse.multisliceimage.roi

Class CurvedLineROI

java.lang.Object

com.xinapse.multisliceimage.roi.ROI

com.xinapse.multisliceimage.roi.IrregularROI

com.xinapse.multisliceimage.roi.CurvedLineROI

All Implemented Interfaces:

EditableOutlineROI, LinearROI, RegularROI, RotatableROI, StretchableROI, java.lang.Cloneable

public class CurvedLineROI
extends IrregularROI
implements LinearROI, RegularROI

A represention of a planar curved line on an image. A CurvedLineROI is made up on multiple straight-line segments.

Field Summary

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

nPoints, POINTSTOKEN, xpts, ypts

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

handles, PREFERENCES_NODE_NAME, XTOKEN, YTOKEN

Constructor Summary

Constructors

Constructor and Description
CurvedLineROI(double[] x, double[] y, int n, ROIState state) Creates a new CurvedLineROI with the coordinates of the points forming the line given by the x and y arrays in mm coordinates.
CurvedLineROI(java.util.List<java.awt.geom.Point2D.Double> pointsList, int nCols, int nRows, float pixelXSize, float pixelYSize, byte userColour, ROIState state) Creates a new CurvedLineROI with the coordinates of the points forming the line given by the List of points in image pixel coordinates.
CurvedLineROI(java.util.List<java.awt.geom.Point2D.Double> pointsList, ROIState state) Creates a new CurvedLineROI with the coordinates of the points forming the line given by the List of points in mm coordinates.

Method Summary

Modifier and Type	Method and Description
java.util.List<ROI>	add(ROI roi) Morphologically adds an ROI to this ROI to create a new java.util.List<ROI> of ROIs that is the result of adding the shapes of the two ROIs.
CurvedLineROI	clone() Returns a clone of this ROI.
boolean	contains(ROI roi) Indicates whether this CurvedLineROI contains another ROI entirely within its borders.
boolean	deleteVertex(Handle handle) Delete a point on the outline of this EditableOutlineROI that is under a handle.
boolean	draw(java.awt.Graphics g, java.awt.Rectangle visibleRectangle, int imageDrawCols, int imageDrawRows, int xOffset, int yOffset, int nCols, int nRows, float pixelXSize, float pixelYSize, boolean drawAnnotation) Draws this ROI if it needs to be be drawn on screen.
java.util.List<IrregularROI>	erasePoints(java.util.List<java.awt.geom.Point2D> erasePoints, float size, int nCols, int nRows, float pixelXSize, float pixelYSize) Erase points from this CurvedLineROI.
java.util.List<ROI>	exclusiveOr(ROI roi) Performs an exclusive OR operation on the shape of this ROI with another ROI.
static javax.swing.Icon	getButtonIcon() Returns an Icon that can be used for a button to create this type of ROI.
javax.vecmath.Point2d	getCentroid() Returns the centroid (centre of area) of this ROI.
ROI	getCopy() Returns a copy of this ROI.
static InteractionType	getCreateInteractionType() Returns the type of interaction needed to create a CurvedLineROI.
java.lang.String	getDescription() Return a description of this type of ROI.
Handle	getFollowingVisibleHandle(Handle handle) Returns the visible Handle that is immediately after the specified handle, in the order in which they were placed around the ROI.
java.awt.geom.Point2D[]	getIntensityProfile(java.lang.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 java.lang.String	getName() Returns a descriptive name for this type of ROI.
double	getPerimeter() Returns the perimeter length of this ROI.
Handle	getPrecedingVisibleHandle(Handle handle) Returns the visible Handle that is immediately before the specified handle, in the order in which they were placed around the ROI.
double	getSquareArea() Returns zero - a curved line has no area.
ROIStats	getStats(java.lang.Object pix, PixelDataType dataType, int nCols, int nRows, int offset, float pixelXSize, float pixelYSize, MaskAction maskAction, MaskMode maskMode, double maskValue, java.io.PrintStream intensityOutputStream, boolean isUnitsMM, ComplexMode complexMode) Returns statistics about this ROI, and (optionally) performs a masking operation.
int	hashCode() Returns a hash code value for this CurvedLine ROI.
boolean	insertTwoVertices(Handle handle) Insert two points into the outline of this EditableOutlineROI: one just before the one that is under a handle, and one just after.
java.util.List<ROI>	intersect(ROI roi) Performs an intersection operation on the shape of this ROI with another ROI.
void	makeConvex(CanAddROIToFrame canAddROIToFrame, float pixelXSize, float pixelYSize, float minConcaveRadius) Make this IrregularROI convex, or at least less concave.
void	move(double dx, double dy) Move this ROI by specified distances (in mm) in the x and y directions.
void	moveVertex(java.awt.geom.Point2D newPos, Handle handle, int nCols, int nRows, float pixelXSize, float pixelYSize, boolean pixelSnap) Move a point on the outline of this EditableOutlineROI to a new position.
java.util.List<ROI>	subtract(ROI roi) Morphologically subtracts an ROI from this ROI to create a new java.util.List<ROI> of ROIs that is the result of subtracting the shapes of the two ROIs.

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

closestPoints, containsVertex, drawInOrthoView, equals, flipHorizontal, flipVertical, getCentre, getFeret, getNormal, getNPoints, getPrincipalAxisAngle, getTheta, getVertex, getVertexHandles, getVertices, join, main, makeConvex, move, orderPoints, removeSelfIntersections, selfIntersects, set, setTheta, setVertex, setVertices, setVertices, setVertices, setVertices, simplify, toSpline, toSpline, toString

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

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

Methods inherited from class java.lang.Object

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

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

getDisplayedBounds2D

Constructor Detail

CurvedLineROI

public CurvedLineROI(double[] x,
                     double[] y,
                     int n,
                     ROIState state)
              throws ROIException

Creates a new CurvedLineROI with the coordinates of the points forming the line given by the x and y arrays in mm coordinates.

Parameters:

x - an array of x-coordinates for the points forming the line.

y - an array of y-coordinates for the points forming the line.

n - the number points to be taken from the x and y arrays - must be less than or equal to then length of the smallest array.

state - the ROIState of the newly-created ROI.

Throws:

ROIException - if the ROI cannot be created as requested.

CurvedLineROI

public CurvedLineROI(java.util.List<java.awt.geom.Point2D.Double> pointsList,
                     ROIState state)
              throws ROIException

Creates a new CurvedLineROI with the coordinates of the points forming the line given by the List of points in mm coordinates.

Parameters:

pointsList - a List of points forming the line.

state - the ROIState of the newly-created ROI.

Throws:

ROIException - if the ROI cannot be created as requested.

CurvedLineROI

public CurvedLineROI(java.util.List<java.awt.geom.Point2D.Double> pointsList,
                     int nCols,
                     int nRows,
                     float pixelXSize,
                     float pixelYSize,
                     byte userColour,
                     ROIState state)
              throws ROIException

Creates a new CurvedLineROI with the coordinates of the points forming the line given by the List of points in image pixel coordinates.

Parameters:

pointsList - a List of points forming the line.

nCols - the number of columns in the image.

nRows - the number of rows in the image.

pixelXSize - the width of an image pixel in mm.

pixelYSize - the height of an image pixel in mm.

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.

Throws:

ROIException - if the ROI cannot be created as requested.

Method Detail

getCreateInteractionType

public static InteractionType getCreateInteractionType()

Returns the type of interaction needed to create a CurvedLineROI.

Returns:

type of interaction needed to create a CurvedLineROI - InteractionType.CLICK_OUTLINE.

move

public void move(double dx,
                 double dy)

Description copied from class: ROI

Move this ROI by specified distances (in mm) in the x and y directions.

Overrides:

move in class IrregularROI

Parameters:

dx - the distance to move in the x-direction.

dy - the distance to move in the y-direction.

getPrecedingVisibleHandle

public Handle getPrecedingVisibleHandle(Handle handle)

Description copied from interface: EditableOutlineROI

Returns the visible Handle that is immediately before the specified handle, in the order in which they were placed around the ROI.

Specified by:

getPrecedingVisibleHandle in interface EditableOutlineROI

Overrides:

getPrecedingVisibleHandle in class IrregularROI

Parameters:

handle - the handle for which to get the preceding handle.

Returns:

the preceding visible Handle, or null if there is no preceding visible handle.

getFollowingVisibleHandle

public Handle getFollowingVisibleHandle(Handle handle)

Description copied from interface: EditableOutlineROI

Returns the visible Handle that is immediately after the specified handle, in the order in which they were placed around the ROI.

Specified by:

getFollowingVisibleHandle in interface EditableOutlineROI

Overrides:

getFollowingVisibleHandle in class IrregularROI

Parameters:

handle - the handle for which to get the following handle.

Returns:

the following visible Handle, or null if there is no following visible handle.

moveVertex

public void moveVertex(java.awt.geom.Point2D newPos,
                       Handle handle,
                       int nCols,
                       int nRows,
                       float pixelXSize,
                       float pixelYSize,
                       boolean pixelSnap)
                throws ROIException

Description copied from interface: EditableOutlineROI

Move a point on the outline of this EditableOutlineROI to a new position.

Specified by:

moveVertex in interface EditableOutlineROI

Overrides:

moveVertex in class IrregularROI

Parameters:

newPos - the new location of the vertex in real-space coordinates.

handle - the Handle that the user has grabbed, used to identify the vertex to be moved.

nCols - the number of image columns.

nRows - the number of image rows.

pixelXSize - the pixel width in mm.

pixelYSize - the pixel height in mm.

pixelSnap - whether pixel snap is turned on.

Throws:

ROIException - if the vertex cannot be moved to the requested position.

getSquareArea

public double getSquareArea()

Returns zero - a curved line has no area.

Specified by:

getSquareArea in interface RegularROI

Returns:

zero.

deleteVertex

public boolean deleteVertex(Handle handle)

Description copied from interface: EditableOutlineROI

Delete a point on the outline of this EditableOutlineROI that is under a handle.

Specified by:

deleteVertex in interface EditableOutlineROI

Overrides:

deleteVertex in class IrregularROI

Parameters:

handle - the Handle that the user has grabbed, used to identify the vertex to be deleted.

Returns:

true if a point is successfully deleted.

insertTwoVertices

public boolean insertTwoVertices(Handle handle)

Description copied from interface: EditableOutlineROI

Insert two points into the outline of this EditableOutlineROI: one just before the one that is under a handle, and one just after.

Specified by:

insertTwoVertices in interface EditableOutlineROI

Overrides:

insertTwoVertices in class IrregularROI

Parameters:

handle - the Handle that the user has grabbed, used to identify the vertex around which the new vertices are to be placed.

Returns:

true if a point is successfully inserted.

erasePoints

public java.util.List<IrregularROI> erasePoints(java.util.List<java.awt.geom.Point2D> erasePoints,
                                                float size,
                                                int nCols,
                                                int nRows,
                                                float pixelXSize,
                                                float pixelYSize)

Erase points from this CurvedLineROI. erasePoints may edit this CurvedLineROI by deleting points, or it may split this CurvedLineROI into two or more new CurvedLineROIs. If more than one CurvedLineROI is returned, then the (edited) original CurvedLineROI will be in the list of returned CurvedLineROIs, and will be the remaining CurvedLineROI which is biggest (has the most points).

Overrides:

erasePoints in class IrregularROI

Parameters:

erasePoints - a List of points through which the erasing pen has passed.

size - the size of the erasing pen in mm.

nCols - the number of image columns.

nRows - the number of image rows.

pixelXSize - the pixel width in mm.

pixelYSize - the pixel height in mm.

Returns:

a List of CurvedLineROIs resulting from the points erasure.

makeConvex

public void makeConvex(CanAddROIToFrame canAddROIToFrame,
                       float pixelXSize,
                       float pixelYSize,
                       float minConcaveRadius)

Description copied from class: IrregularROI

Make this IrregularROI convex, or at least less concave. The supplied pixel sizes are used to decide on the separation between data points around the IrregularROI. A minimum radius of curvature for concave radii of curvature is given. The action of making the ROI convex will be executed asynchronously using a javax.swing.SwingWorker that will update the ImageDisplayer when finished.

Overrides:

makeConvex in class IrregularROI

Parameters:

canAddROIToFrame - the CanAddROIToFrame to be updated when the operation is complete.

pixelXSize - the width of an image pixel in mm.

pixelYSize - the height of an image pixel in mm.

minConcaveRadius - the minimum radius of curvature for concave parts of this ROI.

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 java.awt.geom.Point2D[] getIntensityProfile(java.lang.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.

getPerimeter

public double getPerimeter()

Returns the perimeter length of this ROI. The perimeter of a CurvedLineROI is defined as twice its length.

Overrides:

getPerimeter in class IrregularROI

Returns:

the perimeter length of this ROI.

getCentroid

public javax.vecmath.Point2d getCentroid()

Description copied from class: ROI

Returns the centroid (centre of area) of this ROI.

Overrides:

getCentroid in class IrregularROI

Returns:

the centroid of this ROI.

add

public java.util.List<ROI> add(ROI roi)

Description copied from class: ROI

Morphologically adds an ROI to this ROI to create a new java.util.List<ROI> of ROIs that is the result of adding the shapes of the two ROIs.

Overrides:

add in class ROI

Parameters:

roi - the ROI to add.

Returns:

a List of ROIs that results from the addition of the shape.

subtract

public java.util.List<ROI> subtract(ROI roi)

Description copied from class: ROI

Morphologically subtracts an ROI from this ROI to create a new java.util.List<ROI> of ROIs that is the result of subtracting the shapes of the two ROIs.

Overrides:

subtract in class ROI

Parameters:

roi - the ROI to add.

Returns:

a List of ROIs that results from the subtraction of the shapes.

intersect

public java.util.List<ROI> intersect(ROI roi)

Description copied from class: ROI

Performs an intersection operation on the shape of this ROI with another ROI.

Overrides:

intersect in class IrregularROI

Parameters:

roi - the ROI with which to perform the intersection operation.

Returns:

a List of ROIs that result from the operation.

exclusiveOr

public java.util.List<ROI> exclusiveOr(ROI roi)

Description copied from class: ROI

Performs an exclusive OR operation on the shape of this ROI with another ROI.

Overrides:

exclusiveOr in class ROI

Parameters:

roi - the ROI with which to perform the XOR operation.

Returns:

a List of ROIs that result from the operation.

draw

public boolean draw(java.awt.Graphics g,
                    java.awt.Rectangle visibleRectangle,
                    int imageDrawCols,
                    int imageDrawRows,
                    int xOffset,
                    int yOffset,
                    int nCols,
                    int nRows,
                    float pixelXSize,
                    float pixelYSize,
                    boolean drawAnnotation)

Description copied from class: ROI

Draws this ROI if it needs to be be drawn on screen.

Overrides:

draw in class IrregularROI

Parameters:

g - the graphics context for the drawing operation.

visibleRectangle - the part of the image that can be seen on-screen.

imageDrawCols - width of the area in which this portion of the image is to be drawn.

imageDrawRows - height of the area in which this portion of the image is to be drawn.

xOffset - a horizontal offset for drawing operations.

yOffset - a vertical offset for drawing operations.

nCols - the number of columns in the image on which this ROI is defined.

nRows - the number of rows in the image on which this ROI is defined.

pixelXSize - pixel width for the image on which this ROI is defined.

pixelYSize - pixel height for the image on which this ROI is defined.

drawAnnotation - a flag to indicate whether annotation should be drawn.

Returns:

true if the ROI is visible and been drawn on screen; false otherwise.

getStats

public ROIStats getStats(java.lang.Object pix,
                         PixelDataType dataType,
                         int nCols,
                         int nRows,
                         int offset,
                         float pixelXSize,
                         float pixelYSize,
                         MaskAction maskAction,
                         MaskMode maskMode,
                         double maskValue,
                         java.io.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.

contains

public boolean contains(ROI roi)

Indicates whether this CurvedLineROI contains another ROI entirely within its borders. A CurvedLineROI never contains another ROI, since it has zero area.

Overrides:

contains in class IrregularROI

Parameters:

roi - the ROI to be tested for containment within this ROI.

Returns:

false always.

hashCode

public int hashCode()

Returns a hash code value for this CurvedLine ROI.

Overrides:

hashCode in class IrregularROI

Returns:

a hash code value for this CurvedLine ROI.

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 IrregularROI

Returns:

a copy of this ROI.

clone

public CurvedLineROI 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 IrregularROI

Returns:

a clone of this ROI, cast to an Object.

getDescription

public java.lang.String getDescription()

Description copied from class: ROI

Return a description of this type of ROI.

Overrides:

getDescription in class IrregularROI

Returns:

a String describing the type of this ROI.

getName

public static java.lang.String getName()

Returns a descriptive name for this type of ROI.

Returns:

a String describing this type of ROI.

getButtonIcon

public static javax.swing.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.