de.unihalle.informatik.MiToBo.core.datatypes

Class MTBContour2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDData

de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D

de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D

All Implemented Interfaces:

MTBDataExportableToImageJROI, Cloneable

@ALDDerivedClass
 @ALDParametrizedClass
public class MTBContour2D
extends MTBBorder2D
implements MTBDataExportableToImageJROI

Class to create 2D contour objects with a vector of points, belonging to the contour. Every contour can include a set of inner contours.

Contrary to the super class of 2D borders the points belonging to a contour have a certain ordering.

Author:

misiak

Nested Class Summary

Nested classes/interfaces inherited from class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D

MTBBorder2D.BorderConnectivity

Field Summary

Fields inherited from class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D

connectivity, inner, pointNum, points

Constructor Summary

Constructors

Constructor and Description
MTBContour2D() Standard constructor.
MTBContour2D(Vector<Point2D.Double> _points) Constructor to create a 2D contour object from a 2D point vector.

Method Summary

Modifier and Type	Method and Description
void	addInner(MTBBorder2D C) Add a inner contour to the existing contour object.
MTBContour2D	clone() Override java.lang.Object.clone() to create and return a copy of this object.
ij.gui.PolygonRoi[]	convertToImageJRoi() Function to convert object to ImageJ ROI or set of ROIs.
void	drawContour(MTBImage img, Color color) Draw a contour into an image.
Vector<MTBContour2D>	getAllInner() Get all inner contours from the contour object.
int[]	getChaincode() Calculates chaincode from the outer contour.
MTBContour2D	getContour() Get a Contour2D copy of this object.
double	getContourLength() Calculates the length of the outer contour using it's chaincode.
MTBContour2D	getInner(int index) Get a specific inner contour from the contour object.
int	getInnerCount() Get the number of inner contours including in the contour object.
MTBRegion2D	getRegion(int imageSizeX, int imageSizeY) Method to get the included region in a 2D contour as Region2D object.
static MTBContour2D	readContourFromASCIIFile(String file, String delim, int skipLines) Read a 2D contour object from an ASCII file in xSV format.
void	setInner(Vector<MTBBorder2D> C) Set the inner contours of the contour object.
MTBContour2D	smoothContour(double gaussSigma) Smoothes the contour by convolving x and y coordinates with a Gaussian kernel.
private static Vector<Point2D.Double>	smoothPointVector(Vector<Point2D.Double> pList, double sigma) Convolves a list of 2D points with a Gaussian kernel.

Methods inherited from class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D

addPixel, countInner, getAllInnerBorders, getBoundingBox, getConnectivity, getPointAt, getPointNum, getPoints, hookPointsUpdated, readBorderFromASCIIFile, setConnectivity, toMTBImage, toMTBImageByte

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDData

cloneProperties, getLocation, getProperty, getPropertyKeys, print, setLocation, setProperty

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MTBContour2D

public MTBContour2D()

Standard constructor. Creates an empty 2D contour object.

MTBContour2D

public MTBContour2D(Vector<Point2D.Double> _points)

Constructor to create a 2D contour object from a 2D point vector.

Parameters:

_points - vector with 2D points

Method Detail

clone

public MTBContour2D clone()

Override java.lang.Object.clone() to create and return a copy of this object.

Overrides:

clone in class MTBBorder2D

getContour

public MTBContour2D getContour()

Get a Contour2D copy of this object.

Returns:

Copy of this Contour2D object.

getChaincode

public int[] getChaincode()

Calculates chaincode from the outer contour. The contour points must be stored in consecutive order and the contour must be closed!

Returns:

Chaincode of outer contour.

getContourLength

public double getContourLength()

Calculates the length of the outer contour using it's chaincode.

Returns:

Length of the contour.

setInner

public void setInner(Vector<MTBBorder2D> C)
              throws MTBDatatypeException

Set the inner contours of the contour object.

Note that an error occurs if the objects are not of type MTBContour2D.

Overrides:

setInner in class MTBBorder2D

Parameters:

C - Vector with inner contours belonging to the contour object.

Throws:

MTBDatatypeException - Thrown in case of failure.

addInner

public void addInner(MTBBorder2D C)
              throws MTBDatatypeException

Add a inner contour to the existing contour object.

Overrides:

addInner in class MTBBorder2D

Parameters:

C - the new 2D inner contour

Throws:

MTBDatatypeException - Thrown in case of failure.

getInnerCount

public int getInnerCount()

Get the number of inner contours including in the contour object.

Returns:

The number of inner contours.

getInner

public MTBContour2D getInner(int index)

Get a specific inner contour from the contour object.

Overrides:

getInner in class MTBBorder2D

Parameters:

index - specific index of the inner contour to get from the inner contour vector

Returns:

Inner contour at the specific index as 2D contour object.

getAllInner

public Vector<MTBContour2D> getAllInner()

Get all inner contours from the contour object.

Returns:

Copy of vector with all inner contours.

getRegion

public MTBRegion2D getRegion(int imageSizeX,
                             int imageSizeY)
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                             de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Method to get the included region in a 2D contour as Region2D object.

Parameters:

imageSizeX - width of image that includes the region

imageSizeY - height of image that includes the region

Returns:

2D region included in the 2D contour.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

convertToImageJRoi

public ij.gui.PolygonRoi[] convertToImageJRoi()

Description copied from interface: MTBDataExportableToImageJROI

Function to convert object to ImageJ ROI or set of ROIs.

Specified by:

convertToImageJRoi in interface MTBDataExportableToImageJROI

Returns:

Array of ROIs.

smoothContour

public MTBContour2D smoothContour(double gaussSigma)
                           throws MTBDatatypeException,
                                  de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                  de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Smoothes the contour by convolving x and y coordinates with a Gaussian kernel.

Note that the outer contour and all inner contours are smoothed.

Parameters:

gaussSigma - Standard deviation of the Gaussian kernel.

Returns:

Smoothed contour.

Throws:

MTBDatatypeException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

drawContour

public void drawContour(MTBImage img,
                        Color color)

Draw a contour into an image.

Parameters:

img - Image where to draw the contour into.

color - Color in which to draw the contour.

readContourFromASCIIFile

public static MTBContour2D readContourFromASCIIFile(String file,
                                                    String delim,
                                                    int skipLines)

Read a 2D contour object from an ASCII file in xSV format.

The file is expected to contain a single point in each row, first the x-coordinate and then the y-coordinate. Both coordinates should be separated by the delimiter character.

Parameters:

file - File name from where to read the points.

delim - Delimiter in the file.

skipLines - Number of header lines to skip.

Returns:

Contour object.

smoothPointVector

private static Vector<Point2D.Double> smoothPointVector(Vector<Point2D.Double> pList,
                                                        double sigma)
                                                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                        de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Convolves a list of 2D points with a Gaussian kernel.

x and y coordinates are each convolved with a Gaussian kernel. For convolution an operator of type GaussFilterDouble1D is applied. Take a look at its documentation for more details.

Note that we assume here that the list of points is periodic, e.g., represents a closed contour.

Parameters:

pList - List of points.

sigma - Standard deviation of Gaussian kernel.

Returns:

Result of convolution.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.