com.xinapse.multisliceimage.roi
Class Marker

java.lang.Object
  com.xinapse.multisliceimage.roi.ROI
      com.xinapse.multisliceimage.roi.Marker

All Implemented Interfaces:

RegularROI, java.lang.Cloneable

Direct Known Subclasses:

Text

public class Marker
extends ROI
implements java.lang.Cloneable, RegularROI

A Class representing a point on an image.

Field Summary

static int

DEFAULT_SIZE The size (in screen pixels) of a Marker as it is drawn on-screen (the extreme width and height).

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

handles, PREFERENCES_NODE_NAME, XTOKEN, YTOKEN

Constructor Summary

Marker(double x, double y)
Creates a new Marker at the given (x, y) coordinate.

Marker(double x, double y, ROIState state)
Creates a new Marker at the given (x, y) coordinate, and sets the state of the ROI.

Marker(java.awt.geom.Point2D.Double pt)
Creates a new Marker at the given point.

Method Summary

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.
Marker	clone() Returns a clone of this ROI.
boolean	contains(ROI roi) Indicates whether this Marker ROI contains another ROI entirely within its borders.
java.util.List<ROI>	dilate(double radius, java.util.concurrent.atomic.AtomicInteger opCounter, CancellableThread.Flag cancelFlag) Dilates this ROI by the specified distance.
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.
void	drawInOrthoView(java.awt.Image orthoView, javax.vecmath.Point3f orthoViewPosition, javax.media.j3d.Transform3D imageToViewTx, int nCols, int nRows, int nSlices, float pixelXSize, float pixelYSize, boolean filled) Draws this ROI on top of an orthogonal view of an image.
boolean	equals(java.lang.Object o) Indicates whether some Object is equal to this ROI.
java.util.List<ROI>	exclusiveOr(ROI roi) Performs an exclusive OR operation on the shape of this ROI with another ROI.
void	flipHorizontal(java.awt.geom.Point2D flipPoint) Flip this ROI horizontally about a given location.
void	flipVertical(java.awt.geom.Point2D flipPoint) Flip this ROI vertically about a given location.
java.awt.geom.Rectangle2D	getBoundingRectangle(int nCols, int nRows, float pixelXSize, float pixelYSize) Returns a high-precision rectangle (in image pixel coordinates) that just bounds this ROI.
static javax.swing.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 ROICreateDialog	getCreateDialog(CanAddROIToFrame listener) Returns a JDialog that can be used to create Marker ROIs.
static InteractionType	getCreateInteractionType() Returns the type of interaction needed to create a Marker.
java.lang.String	getDescription() Return a description of this type of ROI.
Feret	getFeret() Returns the minimum and maximum Feret's diameter for this ROI, in mm.
static ROI	getInstance(java.awt.geom.Point2D point, boolean pixelSnap, int nCols, int nRows, float pixelXSize, float pixelYSize, byte userColour, ROIState state) Create a Marker at a point on an image.
static java.lang.String	getName() Returns a descriptive name for this type of ROI.
double	getPerimeter() Returns the perimeter length of this ROI.
double	getSquareArea() Returns the area of this regular ROI in square mm.
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.
double	getX() Returns the x-coordinate of this Marker.
double	getY() Returns the y-coordinate of this Marker.
int	hashCode() Returns a hash code value for this Marker ROI.
java.util.List<ROI>	intersect(ROI roi) Performs an intersection operation on the shape of this ROI with another ROI.
boolean	intersects(ROI roi) Tests whether this ROI intersects another ROI.
void	move(double dx, double dy) Move this ROI by specified distances (in mm) in the x and y directions.
boolean	selectDeselect(java.awt.Point point, boolean editMode, boolean showDeleted, int nAlreadySelected) Selects or deselects an ROI after a user click at the point.
void	set(double x, double y) Sets the location of this Marker to the given location.
void	set(ROI roi) Sets the shape of this ROI to the shape of the supplied argument ROI.
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.
java.lang.String	toString() Returns a String describing this ROI.

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

add, addMorphological, clearDeletionHistory, clearStats, dilate, getAnnotation, getBoundingRectangle, getCachedStatistics, getClasses, getColor, getDisplayedBounds2D, getDisplayedBounds2D, getDisplayedRoiArea, getFeret, getHandles, getHandleUnderPoint, getImageSource, getPixelValue, getROIs, getROIs, getROIs, getSlice, getState, getStats, getStats, getTextColor, getTextFontSize, getUserColour, isDeleted, isEditable, isReloaded, isSelected, join, main, markDeleted, mmPosToPix, moveROIs, pixPosToMm, printStats, setAnnotation, setCreationHistory, setSlice, setState, setTextColor, setTextSize, setUserColour, subtract, write, write

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_SIZE

public static final int DEFAULT_SIZE

The size (in screen pixels) of a Marker as it is drawn on-screen (the extreme width and height).

See Also:

Constant Field Values

Constructor Detail

Marker

public Marker(java.awt.geom.Point2D.Double pt)

Creates a new Marker at the given point.

Parameters:

pt - the location of the marker.

Marker

public Marker(double x,
              double y)

Creates a new Marker at the given (x, y) coordinate.

Parameters:

x - the x location of the marker.

y - the y location of the marker.

Marker

public Marker(double x,
              double y,
              ROIState state)

Creates a new Marker at the given (x, y) coordinate, and sets the state of the ROI.

Parameters:

x - the x location of the marker.

y - the y location of the marker.

state - the ROIState of the Marker.

Method Detail

getX

public double getX()

Returns the x-coordinate of this Marker.

Returns:

the x-coordinate of this Marker.

getY

public double getY()

Returns the y-coordinate of this Marker.

Returns:

the y-coordinate of this Marker.

getSquareArea

public double getSquareArea()

Description copied from interface: RegularROI

Returns the area of this regular ROI in square mm.

Specified by:

getSquareArea in interface RegularROI

Returns:

the area of this Marker, which is always zero.

getCreateInteractionType

public static InteractionType getCreateInteractionType()

Returns the type of interaction needed to create a Marker.

Returns:

type of interaction needed to create a Marker - InteractionType.CLICK.

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.

Specified by:

move in class ROI

Parameters:

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

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

flipVertical

public void flipVertical(java.awt.geom.Point2D flipPoint)

Description copied from class: ROI

Flip this ROI vertically about a given location.

Specified by:

flipVertical in class ROI

Parameters:

flipPoint - the point about which the ROI will be flipped.

flipHorizontal

public void flipHorizontal(java.awt.geom.Point2D flipPoint)

Description copied from class: ROI

Flip this ROI horizontally about a given location.

Specified by:

flipHorizontal in class ROI

Parameters:

flipPoint - the point about which the ROI will be flipped.

getInstance

public static ROI getInstance(java.awt.geom.Point2D point,
                              boolean pixelSnap,
                              int nCols,
                              int nRows,
                              float pixelXSize,
                              float pixelYSize,
                              byte userColour,
                              ROIState state)
                       throws ROIException

Create a Marker at a point on an image.

Parameters:

point - the point on the image in pixel coordinates.

pixelSnap - true if pixel snap is turned on.

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.

state - the ROIState of this ROI on creation.

Throws:

ROIException

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 shapes.

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 addition 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 ROI

Parameters:

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

Returns:

a List of ROIs that result from the operation.

intersects

public boolean intersects(ROI roi)

Description copied from class: ROI

Tests whether this ROI intersects another ROI.

Note that the area of intersection may be zero if one or other of the ROIs (or both) contains no area.

Specified by:

intersects in class ROI

Parameters:

roi - the ROI to be tested for intersection.

Returns:

true in the two ROIs intersect; false otherwise.

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.

dilate

public java.util.List<ROI> dilate(double radius,
                                  java.util.concurrent.atomic.AtomicInteger opCounter,
                                  CancellableThread.Flag cancelFlag)

Description copied from class: ROI

Dilates this ROI by the specified distance.

Parameters:

radius - the radius of dilation.

opCounter - a counter for the number of sub-operations that was performed to execute the dilation operations.

cancelFlag - a flag that, if set externally, cancels the 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)

Draws this ROI if it needs to be be drawn on screen. Marker ROIs are a special case, since we can't use the Bounding Rectangle to decide whether a Marker is on screen, since the zero-area bounding rectangle never intersects anything.

Overrides:

draw in class ROI

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.

drawInOrthoView

public void drawInOrthoView(java.awt.Image orthoView,
                            javax.vecmath.Point3f orthoViewPosition,
                            javax.media.j3d.Transform3D imageToViewTx,
                            int nCols,
                            int nRows,
                            int nSlices,
                            float pixelXSize,
                            float pixelYSize,
                            boolean filled)

Description copied from class: ROI

Draws this ROI on top of an orthogonal view of an image.

Specified by:

drawInOrthoView in class ROI

Parameters:

orthoView - the java.awt.Image into which the ROI is to be drawn.

orthoViewPosition - the coordinates (col, row, slice position) of the orthogonal view in the original image.

imageToViewTx - the Transform3D that maps original image pixel coordinates to pixel coordinates in the orthogonal view.

nCols - the number of columns in the original image.

nRows - the number of rows in the original image.

nSlices - the number of slices in the original image.

pixelXSize - the pixel width in the original image.

pixelYSize - the pixel height in the original image.

filled - whether the ROI should be drawn filled (effective only for ROIs that enclose an area).

getBoundingRectangle

public java.awt.geom.Rectangle2D getBoundingRectangle(int nCols,
                                                      int nRows,
                                                      float pixelXSize,
                                                      float pixelYSize)

Description copied from class: ROI

Returns a high-precision rectangle (in image pixel coordinates) that just bounds this ROI.

Overrides:

getBoundingRectangle in class ROI

Parameters:

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.

Returns:

a Rectangle2D that just bounds this ROI.

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.

getFeret

public Feret getFeret()

Description copied from class: ROI

Returns the minimum and maximum Feret's diameter for this ROI, in mm.

Specified by:

getFeret in class ROI

Returns:

the minimum and maximum Feret's diameter (in mm) as a Feret object.

getPerimeter

public double getPerimeter()

Description copied from class: ROI

Returns the perimeter length of this ROI.

Specified by:

getPerimeter in class ROI

Returns:

the perimeter length of this ROI.

selectDeselect

public boolean selectDeselect(java.awt.Point point,
                              boolean editMode,
                              boolean showDeleted,
                              int nAlreadySelected)

Description copied from class: ROI

Selects or deselects an ROI after a user click at the point.

Overrides:

selectDeselect in class ROI

Parameters:

point - the Point at which the user has clicked.

editMode - true if the tool working with ROIs is in edit mode; false if it is in view mode.

showDeleted - true if the tool working with ROIs is set to show deleted ROIs; false if it is not.

nAlreadySelected - the number of ROIs already selected. This determines the exact selection/deselection behaviour.

Returns:

true if the selection was changed.

getCreateDialog

public static ROICreateDialog getCreateDialog(CanAddROIToFrame listener)

Returns a JDialog that can be used to create Marker ROIs.

Parameters:

listener - the CanAddROIToFrame to which the ROI will be added when the Add button of the Dialog is clicked.

contains

public boolean contains(ROI roi)

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

Specified by:

contains in class ROI

Parameters:

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

Returns:

false always.

equals

public boolean equals(java.lang.Object o)

Description copied from class: ROI

Indicates whether some Object is equal to this ROI. To be equal, the Object must be an ROI of the same type, and of the same shape and location as this ROI.

Specified by:

equals in class ROI

Parameters:

o - the Object to be tested for equality to this ROI.

Returns:

true if the supplied Object is an ROI of the same type, shape and location as this ROI; false otherwise.

hashCode

public int hashCode()

Returns a hash code value for this Marker ROI.

Overrides:

hashCode in class ROI

Returns:

a hash code value for this Marker ROI.

set

public void set(double x,
                double y)

Sets the location of this Marker to the given location.

Parameters:

x - the x-location.

y - the y-location.

set

public void set(ROI roi)
         throws java.lang.ClassCastException

Description copied from class: ROI

Sets the shape of this ROI to the shape of the supplied argument ROI.

Specified by:

set in class ROI

Throws:

java.lang.ClassCastException - of the sub class of the argument ROI is not the same as this 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.

Specified by:

getCopy in class ROI

Returns:

a copy of this ROI, cast to an Object.

toString

public java.lang.String toString()

Description copied from class: ROI

Returns a String describing this ROI.

Specified by:

toString in class ROI

Returns:

a java.lang.String describing this ROI.

getDescription

public java.lang.String getDescription()

Description copied from class: ROI

Return a description of this type of ROI.

Specified by:

getDescription in class ROI

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.

clone

public Marker 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 ROI

Returns:

a clone of this ROI, cast to an Object.