de.mpg.biochem.mars.image

Class PeakShape

java.lang.Object

de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

de.mpg.biochem.mars.image.PeakShape

All Implemented Interfaces:

JsonConvertibleRecord

public class PeakShape
extends AbstractJsonConvertibleRecord

Stores shape information for objects as 2D polygons. Extends AbstractJsonConvertibleRecord to allow for saving to file as JSON. Provides utility methods to sample inside the shape, calculate the area and center position as well as Peak generation method. Peaks contain references to PeakShape for recovery of shape after tracking using the center position.

Field Summary

Fields

Modifier and Type	Field and Description
double[]	x
double[]	y

Constructor Summary

Constructors

Constructor and Description
PeakShape(double[] x, double[] y)
PeakShape(com.fasterxml.jackson.core.JsonParser jParser)

Method Summary

Modifier and Type	Method and Description
double	area()
double	circularity()
protected void	createIOMaps() Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.
static Peak	createPeak(double[] xr, double[] yr)
double	perimeter()
double	radius()
<T> net.imglib2.IterableInterval<T>	sample(double spotXCenter, double spotYCenter, net.imglib2.RandomAccessibleInterval<T> img, double xScale, double yScale)
<T> net.imglib2.IterableInterval<T>	sample(Peak peak, net.imagej.ImgPlus<T> img)
void	scale(double alpha)
double[]	toPolygonX(double calibration, double xCorner, double xCenter, double magnification) Returns a new int array containing the X pixel coordinates to which to paint this polygon.
double[]	toPolygonY(double calibration, double yCorner, double yCenter, double magnification) Returns a new int array containing the Y pixel coordinates to which to paint this polygon.

Methods inherited from class de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord

dumpJSON, fromJSON, getJsonGenerator, getJsonParser, setJsonField, setShowWarnings, toJSON

Methods inherited from class java.lang.Object

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

Field Detail

x

public double[] x

y

public double[] y

Constructor Detail

PeakShape

public PeakShape(double[] x,
                 double[] y)

PeakShape

public PeakShape(com.fasterxml.jackson.core.JsonParser jParser)
          throws java.io.IOException

Throws:

java.io.IOException

Method Detail

toPolygonX

public double[] toPolygonX(double calibration,
                           double xCorner,
                           double xCenter,
                           double magnification)

Returns a new int array containing the X pixel coordinates to which to paint this polygon.

Parameters:

calibration - the pixel size in X, to convert physical coordinates to pixel coordinates.

xCorner - the top-left X corner of the view in the image to paint.

xCenter - the x coordinate of the Peak center.

magnification - the magnification of the view.

Returns:

a new double array.

toPolygonY

public double[] toPolygonY(double calibration,
                           double yCorner,
                           double yCenter,
                           double magnification)

Returns a new int array containing the Y pixel coordinates to which to paint this polygon.

Parameters:

calibration - the pixel size in Y, to convert physical coordinates to pixel coordinates.

yCorner - the top-left Y corner of the view in the image to paint.

yCenter - the y coordinate of the Peak center.

magnification - the magnification of the view.

Returns:

a new int array.

sample

public <T> net.imglib2.IterableInterval<T> sample(Peak peak,
                                                  net.imagej.ImgPlus<T> img)

sample

public <T> net.imglib2.IterableInterval<T> sample(double spotXCenter,
                                                  double spotYCenter,
                                                  net.imglib2.RandomAccessibleInterval<T> img,
                                                  double xScale,
                                                  double yScale)

radius

public double radius()

area

public double area()

circularity

public double circularity()

perimeter

public double perimeter()

scale

public void scale(double alpha)

createPeak

public static Peak createPeak(double[] xr,
                              double[] yr)

createIOMaps

protected void createIOMaps()

Description copied from class: AbstractJsonConvertibleRecord

Must be implemented in subclasses to define how fields, objects, arrays should be saved based on the Jackson streaming API.

Specified by:

createIOMaps in class AbstractJsonConvertibleRecord