Package com.xinapse.multisliceimage.roi

Class RectangularROI

java.lang.Object
com.xinapse.multisliceimage.roi.ROI
com.xinapse.multisliceimage.roi.RectangularROI
All Implemented Interfaces:
RegularROI, StretchableROI, Cloneable
public class RectangularROI extends ROI implements Cloneable, StretchableROI, RegularROI
An Class representing a rectangular region of an image.

  • Field Details

    • WIDTHTOKEN

      public static final String WIDTHTOKEN
      The token written to ROI output files to represent the width of a rectangular ROI.
      See Also:

    • HEIGHTTOKEN

      public static final String HEIGHTTOKEN
      The token written to ROI output files to represent the height of a rectangular ROI.
      See Also:

  • Constructor Details

    • RectangularROI

      public RectangularROI(Rectangle2D.Double rect, ROIState state) throws ROIException
      Creates a new RectangularROI with the dimension given by the supplied Rectangle2D in mm coordinates.
      Parameters:
      rect - the Rectangle2D.Double that gives the size and location of the ROI in mm.
      state - the ROIState for the ROI at creation.
      Throws:
      ROIException - if the ROI cannot be created.

    • RectangularROI

      public RectangularROI(double x, double y, double width, double height) throws ROIException
      Creates a new RectangularROI with the supplied dimensions in mm coordinates. The new RectangularROI will be in a state ROIState.NORMAL.
      Parameters:
      x - the x-coordinate of the top left corner of the rectangle in mm.
      y - the y-coordinate of the top left corner of the rectangle in mm.
      width - the width of the rectangle.
      height - the height of the rectangle.
      Throws:
      ROIException - if the ROI cannot be created.

    • RectangularROI

      public RectangularROI(double x, double y, double width, double height, ROIState state) throws ROIException
      Creates a new RectangularROI with the supplied dimensions in mm.
      Parameters:
      x - the x-coordinate of the top left corner of the rectangle in mm.
      y - the y-coordinate of the top left corner of the rectangle in mm.
      width - the width of the rectangle in mm.
      height - the height of the rectangle in mm.
      state - the ROIState for the ROI at creation.
      Throws:
      ROIException - if the ROI cannot be created.

  • Method Details

    • getX

      public double getX()
      Returns the x-coordinate of the top left corner of this RectangularROI in mm.
      Returns:
      the x-coordinate of the top left corner of this RectangularROI in mm.

    • getY

      public double getY()
      Returns the y-coordinate of the top left corner of this RectangularROI in mm.
      Returns:
      the y-coordinate of the top left corner of this RectangularROI in mm.

    • getWidth

      public double getWidth()
      Returns the width of this RectangularROI in mm.
      Returns:
      the width of this RectangularROI in mm.

    • getHeight

      public double getHeight()
      Returns the height of this RectangularROI in mm.
      Returns:
      the height of this RectangularROI in mm.

    • getCreateInteractionType

      public static InteractionType getCreateInteractionType()
      Returns the type of interaction needed to create a RectangularROI.
      Returns:
      type of interaction needed to create a RectangularROI - InteractionType.NONE.

    • 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 ROI in square mm.

    • 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.

    • move

      public void move(double dx, double dy, double stretchX, double stretchY)
      Description copied from interface: StretchableROI
      Moves and stretches an ROI. A stretch value is a scaling factor for dimensions in either the horizontal or vertical directions. A stretch of 1.0 means no stretch.
      Specified by:
      move in interface StretchableROI
      Parameters:
      dx - the distance (in mm) to move the centre of the StretchableROI in the horizontal direction.
      dy - the distance (in mm) to move the centre of the StretchableROI in the vertical direction.
      stretchX - the stretch in the horizontal direction.
      stretchY - the stretch in the vertical direction.

    • flipVertical

      public void flipVertical(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(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(Rectangle boundingRectangle, int nCols, int nRows, float pixelXSize, float pixelYSize, byte userColour, ROIState state) throws ROIException
      Creates an instance of a RectangularROI suitable for drawing on a window. Bounding rectangle determines the maximum size of the ROI (in image pixels).
      Parameters:
      boundingRectangle - the area of screen into which the ROI must fit.
      nCols - the number of image columns.
      nRows - the number of image rows.
      pixelXSize - the size of image pixels in the horizontal direction.
      pixelYSize - the size of image pixels in the vertical direction.
      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 initial state of this newly-created ROI.
      Returns:
      a new RectangularROI that can be displayed inside the specified region of image pixels.
      Throws:
      ROIException - if the ROI cannot be created as specified.

    • draw

      public boolean draw(Graphics g, 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 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(Image orthoView, org.jogamp.vecmath.Point3f orthoViewPosition, org.jogamp.java3d.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 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).

    • 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.

    • getCentroid

      public org.jogamp.vecmath.Point2d getCentroid()
      Description copied from class: ROI
      Returns the centroid (centre of area) of this ROI.
      Specified by:
      getCentroid in class ROI
      Returns:
      the centroid of this ROI.

    • getPrincipalAxisAngle

      public double getPrincipalAxisAngle()
      Returns the angle between the major principal axis of this ROI and the x-axis. The angle returned will is either 0 or PI/2 radians, depending on whether the rectangle is wider than it is tall.
      Returns:
      the main principal axis angle of this ROI.

    • getCreateDialog

      public static ROICreateDialog getCreateDialog(CanAddROIToFrame listener)
      Returns a JDialog that can be used to create Rectangular ROIs.
      Parameters:
      listener - the CanAddROIToFrame to which the ROI will be added when the Add button of the Dialog is clicked.
      Returns:
      a JDialog that can be used to create Rectangular ROIs.

    • contains

      public boolean contains(ROI roi)
      Indicates whether this RectangularROI contains another ROI entirely within its borders.
      Specified by:
      contains in class ROI
      Parameters:
      roi - the ROI to be tested for containment within this ROI.
      Returns:
      true if this RectangularROI contains the specified ROI; false otherwise.

    • intersect

      public List<ROI> intersect(ROI roi, IndeterminateProgressMonitor progressMonitor) throws ROIException, CancelledException
      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.
      progressMonitor - if non-null, the IndeterminateProgressMonitor that can be used to cancel the operation.
      Returns:
      a List<ROI> of ROIs that result from the operation.
      Throws:
      ROIException - if the operation cannot be performed.
      CancelledException - if the operation is cancelled by the user.

    • equals

      public boolean equals(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 RectangularROI.
      Overrides:
      hashCode in class ROI
      Returns:
      a hash code value for this RectangularROI.

    • set

      public void set(ROI roi) throws 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
      Parameters:
      roi - the ROI from which the shape is set.
      Throws:
      ClassCastException - if 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.

    • clone

      public RectangularROI 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.

    • toString

      public String toString()
      Description copied from class: ROI
      Returns a String describing this ROI.
      Specified by:
      toString in class ROI
      Returns:
      a String describing this ROI.

    • getDescription

      public 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 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.