fiji.util

Class Circle_Fitter

java.lang.Object

fiji.util.Circle_Fitter

All Implemented Interfaces:

ij.plugin.filter.PlugInFilter

public class Circle_Fitter
extends Object
implements ij.plugin.filter.PlugInFilter

Fit a circle selection to an image.

The implementation largely follows http://www.dtcenter.org/met/users/docs/write_ups/circle_fit.pdf (It is summarized below.)

The major contributions of this plugin is that it does not take a list of points, but uses all pixel locations, weighted by intensity. The circle fitting works like this: given a set of points (x_i, y_i), i = 1, .., N try to fit a circle with radius r and center (x_c, y_c) using the least squares method. The function to minimize is

S = \sum g_i^2, where g_i = (x_i - x)^2 + (y_i - y)^2 - r^2 (It must be the square of g_i so that no summand is negative.) Without loss of generality, it can be assumed that \sum x_i = \sum y_i = 0 (If that is not the case, just subtract the means of {x_i} and {y_i} resp. and add them to x_c and y_c resp.)

The derivative of S with regard to r^2 must be 0:

d/dr^2 \sum g_i^2 = \sum 2 * g_i * -1

and therefore

\sum g_i = 0

Expanded, with uu = \sum x_i * x_i, uv = \sum x_i * y_i and u, v, uu, uuu, uuv, uvv, vvv defined analogously, this yields

uu - 2 * u * x_c + N * x_c^2 + vv - 2 * v * y_c + N * y_c^2 - N * r^2 = 0

With u = v = 0, as per the earlier assumption, it follows that

uu + vv + N * (x_c^2 + y_c^2 - r^2) = 0 (eq. 1)

The derivative of S with regard to x_c must be 0:

d/dx_c \sum g_i^2 = \sum 2 * g_i * (2 * (x_i - x_c) * (-1)) = -4 * \sum g_i * x_i + 4 * x_c * \sum g_i

and therefore

\sum g_i * x_i = 0 (as \sum g_i must be 0 already)

Expanded, with uu and friends defined as before, this yields

uuu - 2 * uu * x_c + u * x_c^2 + uvv - 2 * uv * y_c + v * y_c^2 + u * r^2 = 0

Like before, u = v = 0, therefore

2 * uu * x_c + 2 * uv * y_c = uuu + uvv (eq. 2)

For y_c, it is

2 * uv * x_c + 2 * vv * y_c = uuv + vvv (eq. 3)

Equations 2 and 3 determine x_c and y_c, and equation 1 gives us the radius.

Author:

Johannes Schindelin

Field Summary

Fields inherited from interface ij.plugin.filter.PlugInFilter

CONVERT_TO_FLOAT, DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, FINAL_PROCESSING, KEEP_THRESHOLD, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, NO_UNDO_RESET, PARALLELIZE_IMAGES, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

Constructors

Constructor and Description
Circle_Fitter()

Method Summary

Modifier and Type	Method and Description
ij.gui.OvalRoi	calculateRoi() Computes and return the circle Roi that fits.
float	getDefaultThreshold() The default threshold is determined like this: as a circle is a linear structure, we want the _square root_ of the total number of pixels to contribute.
float	getThreshold() Returns threshold used by this plugin.
void	run(ij.process.ImageProcessor ip)
void	setAutoThreshold() Sets the threshold used by this plugin to be the default one.
void	setImageProcessor(ij.process.ImageProcessor ip) Set the ImageProcessor that will be fitted.
void	setThreshold(float threshold) Sets the threshold for the fit.
int	setup(String arg, ij.ImagePlus image)

Methods inherited from class java.lang.Object

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

Constructor Detail

Circle_Fitter

public Circle_Fitter()

Method Detail

setup

public int setup(String arg,
                 ij.ImagePlus image)

Specified by:

setup in interface ij.plugin.filter.PlugInFilter

run

public void run(ij.process.ImageProcessor ip)

Specified by:

run in interface ij.plugin.filter.PlugInFilter

calculateRoi

public ij.gui.OvalRoi calculateRoi()

Computes and return the circle Roi that fits. The fields for the ImageProcessor and threshold must be set before calling this method; otherwise null is returned.

Returns:

the roi

getDefaultThreshold

public float getDefaultThreshold()

The default threshold is determined like this: as a circle is a linear structure, we want the _square root_ of the total number of pixels to contribute.

Therefore, we split the histogram into background and foreground where the number of pixels in the foreground part is \sqrt(w * h) and the split point is the desired threshold.

Returns:

the default threshold.

getThreshold

public float getThreshold()

Returns threshold used by this plugin.

Returns:

the threshold

setThreshold

public void setThreshold(float threshold)

Sets the threshold for the fit. Intensities lower than the value given will be ignored in the weight.

Parameters:

threshold - the threshold.

setAutoThreshold

public void setAutoThreshold()

Sets the threshold used by this plugin to be the default one.

See Also:

getDefaultThreshold()

setImageProcessor

public void setImageProcessor(ij.process.ImageProcessor ip)

Set the ImageProcessor that will be fitted.

Parameters:

ip - the ImageProcessor