Centroids (photutils.centroids)

Introduction

photutils.centroids provides several functions to calculate the centroid of a single source:

  • centroid_com(): Calculates the object “center of mass” from 2D image moments.

  • centroid_quadratic(): Calculates the centroid by fitting a 2D quadratic polynomial to the data.

  • centroid_1dg(): Calculates the centroid by fitting 1D Gaussians to the marginal x and y distributions of the data.

  • centroid_2dg(): Calculates the centroid by fitting a 2D Gaussian to the 2D distribution of the data.

Masks can be input into each of these functions to mask bad pixels. Error arrays can be input into the two Gaussian fitting methods to weight the fits.

To calculate the centroids of many sources in an image, use the centroid_sources() function. This function can be used with any of the above centroiding functions or a custom user-defined centroiding function.

Getting Started

Let’s extract a single object from a synthetic dataset and find its centroid with each of these methods. For this simple example we will not subtract the background from the data (but in practice, one should subtract the background):

>>> from photutils.datasets import make_4gaussians_image
>>> from photutils.centroids import centroid_com, centroid_quadratic
>>> from photutils.centroids import centroid_1dg, centroid_2dg
>>> data = make_4gaussians_image()[43:79, 76:104]

>>> x1, y1 = centroid_com(data)
>>> print((x1, y1))  
(13.93157998341213, 17.051234441067088)

>>> x2, y2 = centroid_quadratic(data)
>>> print((x2, y2))  
(13.948284438186919, 16.98788199435759)
>>> x3, y3 = centroid_1dg(data)
>>> print((x3, y3))  
(14.040352707371396, 16.962306463644801)
>>> x4, y4 = centroid_2dg(data)
>>> print((x4, y4))  
(14.002212073733611, 16.996134592982017)

Now let’s plot the results. Because the centroids are all very similar, we also include an inset plot zoomed in near the centroid:

import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import zoomed_inset_axes
from mpl_toolkits.axes_grid1.inset_locator import mark_inset
from photutils.centroids import centroid_com, centroid_quadratic
from photutils.centroids import centroid_1dg, centroid_2dg
from photutils.datasets import make_4gaussians_image

data = make_4gaussians_image()[43:79, 76:104]  # extract single object
xycen1 = centroid_com(data)
xycen2 = centroid_quadratic(data)
xycen3 = centroid_1dg(data)
xycen4 = centroid_2dg(data)
xycens = [xycen1, xycen2, xycen3, xycen4]
fig, ax = plt.subplots(1, 1, figsize=(4, 5))
ax.imshow(data, origin='lower', interpolation='nearest')
marker = '+'
ms, mew = 15, 2.
colors = ('white', 'black', 'red', 'blue')
for xycen, color in zip(xycens, colors):
    plt.plot(*xycen, color=color, marker=marker, ms=ms, mew=mew)

ax2 = zoomed_inset_axes(ax, zoom=6, loc=9)
ax2.imshow(data, vmin=190, vmax=220, origin='lower',
           interpolation='nearest')
ms, mew = 30, 2.
for xycen, color in zip(xycens, colors):
    ax2.plot(*xycen, color=color, marker=marker, ms=ms, mew=mew)
ax2.set_xlim(13, 15)
ax2.set_ylim(16, 18)
mark_inset(ax, ax2, loc1=3, loc2=4, fc='none', ec='0.5')
ax2.axes.get_xaxis().set_visible(False)
ax2.axes.get_yaxis().set_visible(False)
ax.set_xlim(0, data.shape[1] - 1)
ax.set_ylim(0, data.shape[0] - 1)

(Source code, png, hires.png, pdf, svg)

_images/centroids-1.png

Centroiding several sources in an image

The centroid_sources() function can be used to calculate the centroids of many sources in a single image given initial guesses for their positions. This function can be used with any of the above centroiding functions or a custom user-defined centroiding function.

Here is a simple example using centroid_com(). A cutout image is made centered at each initial position of size box_size. A centroid is then calculated within the cutout image for each source:

>>> from photutils.centroids import centroid_sources
>>> data = make_4gaussians_image()
>>> x_init = (25, 91, 151, 160)
>>> y_init = (40, 61, 24, 71)
>>> x, y = centroid_sources(data, x_init, y_init, box_size=21,
...                         centroid_func=centroid_com)
>>> print(x)  
[ 24.98911515  90.43056554 150.20332399 159.87234831]
>>> print(y)  
[40.08504359 60.56869612 24.74216925 70.32723054]

Let’s plot the results:

import matplotlib.pyplot as plt
from photutils.centroids import centroid_sources, centroid_com
from photutils.datasets import make_4gaussians_image

data = make_4gaussians_image()
x_init = (25, 91, 151, 160)
y_init = (40, 61, 24, 71)
x, y = centroid_sources(data, x_init, y_init, box_size=21,
                        centroid_func=centroid_com)
plt.figure(figsize=(8, 4))
plt.imshow(data, origin='lower', interpolation='nearest')
plt.scatter(x, y, marker='+', s=80, color='red')
plt.tight_layout()

(Source code, png, hires.png, pdf, svg)

_images/centroids-2.png

Reference/API

This subpackage contains tools for centroiding sources.

Functions

centroid_1dg(data[, error, mask])

Calculate the centroid of a 2D array by fitting 1D Gaussians to the marginal x and y distributions of the array.

centroid_2dg(data[, error, mask])

Calculate the centroid of a 2D array by fitting a 2D Gaussian (plus a constant) to the array.

centroid_com(data[, mask, oversampling])

Calculate the centroid of an n-dimensional array as its “center of mass” determined from moments.

centroid_epsf(data[, mask, oversampling, …])

Deprecated since version 1.2.

centroid_quadratic(data[, xpeak, ypeak, …])

Calculate the centroid of an n-dimensional array by fitting a 2D quadratic polynomial.

centroid_sources(data, xpos, ypos[, …])

Calculate the centroid of sources at the defined positions.

gaussian1d_moments(data[, mask])

Deprecated since version 1.2.