Package com.xinapse.multisliceimage.roi

Class LineROI

java.lang.Object
com.xinapse.multisliceimage.roi.ROI
com.xinapse.multisliceimage.roi.LineROI
All Implemented Interfaces:
LinearROI, RegularROI, RotatableROI, Cloneable
public class LineROI extends ROI implements Cloneable, LinearROI, RotatableROI, RegularROI
A Class representing a straight line on an image.

  • Field Details

    • X1TOKEN

      public static final String X1TOKEN
      The token written to ROI output files to represent the x-coordinate of the first end of the line.
      See Also:

    • Y1TOKEN

      public static final String Y1TOKEN
      The token written to ROI output files to represent the y-coordinate of the first end of the line.
      See Also:

    • X2TOKEN

      public static final String X2TOKEN
      The token written to ROI output files to represent the x-coordinate of the second end of the line.
      See Also:

    • Y2TOKEN

      public static final String Y2TOKEN
      The token written to ROI output files to represent the y-coordinate of the second end of the line.
      See Also:

  • Constructor Details

    • LineROI

      public LineROI(double x1, double y1, double x2, double y2) throws ROIException
      Creates a new LineROI with the coordinates of the points forming the line in mm coordinates. The ROI state will be ROIState.NORMAL.
      Parameters:
      x1 - the x-location of the first end of the line.
      y1 - the y-location of the first end of the line.
      x2 - the x-location of the second end of the line.
      y2 - the y-location of the second end of the line.
      Throws:
      ROIException - if the line length is zero.

    • LineROI

      public LineROI(double x1, double y1, double x2, double y2, ROIState state) throws ROIException
      Creates a new LineROI with the coordinates of the points forming the line in mm coordinates.
      Parameters:
      x1 - the x-location of the first end of the line.
      y1 - the y-location of the first end of the line.
      x2 - the x-location of the second end of the line.
      y2 - the y-location of the second end of the line.
      state - the selection state of the LineROI.
      Throws:
      ROIException - if the line length is zero.

    • LineROI

      public LineROI(double x1, double y1, double x2, double y2, byte userColour, ROIState state) throws ROIException
      Creates a new LineROI with the coordinates of the points forming the line in mm coordinates.
      Parameters:
      x1 - the x-location of the first end of the line.
      y1 - the y-location of the first end of the line.
      x2 - the x-location of the second end of the line.
      y2 - the y-location of the second end of the line.
      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 selection state of the LineROI.
      Throws:
      ROIException - if the line length is zero.

  • Method Details

    • getLine

      public Line2D getLine()
      Returns the line forming this LineROI in mm coordinates.
      Returns:
      the line forming this LineROI in mm coordinates.

    • 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.

    • getX1

      public double getX1()
      Returns the x-coordinate of the first end of the line.
      Returns:
      the x-coordinate of the first end of the line.

    • getY1

      public double getY1()
      Returns the y-coordinate of the first end of the line.
      Returns:
      the y-coordinate of the first end of the line.

    • getX2

      public double getX2()
      Returns the x-coordinate of the second end of the line.
      Returns:
      the x-coordinate of the second end of the line.

    • getY2

      public double getY2()
      Returns the y-coordinate of the second end of the line.
      Returns:
      the y-coordinate of the second end of the line.

    • getOppositeEnd

      public Point2D getOppositeEnd(EndHandle endHandle)
      Returns the location of the end that is at the other end to the specified handle.
      Parameters:
      endHandle - the Handle for the first end.
      Returns:
      the location of the end opposite to the supplied EndHandle.

    • getInstance

      public static ROI getInstance(Point2D p1, Point2D p2, int nCols, int nRows, float pixelXSize, float pixelYSize, byte userColour, ROIState state)
      Creates a new LineROI.
      Parameters:
      p1 - the location of the first end of the line, in image pixels.
      p2 - the location of the second end of the line, in image pixels.
      nCols - the number of columns of pixels in the image.
      nRows - the number of rows of pixels in the image.
      pixelXSize - the image pixel width.
      pixelYSize - the image pixel height.
      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 selection state of the LineROI.
      Returns:
      a new LineROI.

    • getTheta

      public double getTheta()
      Description copied from interface: RotatableROI
      Returns the current rotation angle for this RotatableROI.
      Specified by:
      getTheta in interface RotatableROI
      Returns:
      theta the current rotation angle.

    • setTheta

      public void setTheta(double theta)
      Description copied from interface: RotatableROI
      Sets the rotation angle for this RotatableROI.
      Specified by:
      setTheta in interface RotatableROI
      Parameters:
      theta - the rotation angle.

    • getCentre

      public Point2D getCentre()
      Description copied from interface: RotatableROI
      Gets the centre (about which rotation will occur) of this RotatableROI in mm.
      Specified by:
      getCentre in interface RotatableROI
      Returns:
      the centre of this ROI, about which rotation will occur.

    • getCreateInteractionType

      public static InteractionType getCreateInteractionType()
      Returns the type of interaction needed to create a LineROI.
      Returns:
      type of interaction needed to create a LineROI - InteractionType.CLICK_DRAG.

    • 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:
      zero.

    • move

      public void move(Point2D p1, Point2D p2)
      Moves this LineROI so that the ends are at the new specified locations.
      Parameters:
      p1 - the new location of the first end of the line.
      p2 - the new location of the second end of the line.

    • 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(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.

    • union

      public List<ROI> union(ROI roi, IndeterminateProgressMonitor progressMonitor)
      Description copied from class: ROI
      Logically add (forms the union) 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:
      union in class ROI
      Parameters:
      roi - the ROI to add.
      progressMonitor - if non-null, the IndeterminateProgressMonitor that can be used to cancel the operation.
      Returns:
      a List<ROI> of ROIs that results from the addition of the shape.

    • andNot

      public List<ROI> andNot(ROI roi, IndeterminateProgressMonitor progressMonitor)
      Description copied from class: ROI
      Logically AND NOTs (subtracts) an ROI from this ROI to create a new java.util.List<ROI> of ROIs that is the result of subtracting the shape of the supplied ROI from this ROI.
      Overrides:
      andNot in class ROI
      Parameters:
      roi - the ROI to subtract.
      progressMonitor - if non-null, the IndeterminateProgressMonitor that can be used to cancel the operation.
      Returns:
      a List<ROI> of ROIs that results from the subtraction of the ROI.

    • 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.

    • exclusiveOr

      public List<ROI> exclusiveOr(ROI roi, IndeterminateProgressMonitor progressMonitor)
      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.
      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.

    • 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)
      LineROIs are a special case, since we can't use the Bounding Rectangle to decide whether a Line is on screen, since the line may be vertical or horizontal, and therefore have an empty boundng rectangle.
      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).

    • selectDeselect

      public boolean selectDeselect(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.

    • 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:
      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.

    • getIntersectionLength

      public double getIntersectionLength(Rectangle2D rectangle, int nCols, int nRows, float pixelXSize, float pixelYSize)
      Calculates the length of the line segment where this LineROI intersects the given Rectangle argument. The Rectangle is in image pixel coordinates.
      Parameters:
      rectangle - the Rectangle2d for which to find the intersection line length.
      nCols - the number of image columns.
      nRows - the number of image rows.
      pixelXSize - the image pixel width, in mm.
      pixelYSize - the image pixel height, in mm.
      Returns:
      the length of the intersection line.

    • getBoundingRectangle

      public Rectangle2D getBoundingRectangle(int nCols, int nRows, float pixelXSize, float pixelYSize)
      Returns a high-precision rectangle (in 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.

    • 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()
      Returns the perimeter length of this ROI. The perimeter of a LineROI is defined as twice its length.
      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 be between the angle between the line and the x-axis.
      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 Line 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 Line ROIs.

    • contains

      public boolean contains(ROI roi)
      Indicates whether this LineROI contains another ROI entirely within its borders. A LineROI 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(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 LineROI.
      Overrides:
      hashCode in class ROI
      Returns:
      a hash code value for this LineROI.

    • 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.

    • 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.

    • clone

      public LineROI 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.

    • 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.

    • 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.