Package 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, 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.

  • Constructor Details

    • 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(List<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(List<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 Details

    • 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(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 List<IrregularROI> erasePoints(List<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 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 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.

    • 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 org.jogamp.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.

    • 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)
      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.
      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.

    • 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)
      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(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.

    • 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 CurvedLineROI.
      Overrides:
      hashCode in class IrregularROI
      Returns:
      a hash code value for this CurvedLineROI.

    • 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 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 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.