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| Convolution Kernels | |
| ******************* | |
| Introduction and Concept | |
| ======================== | |
| The convolution module provides several built-in kernels to cover the most | |
| common applications in astronomy. It is also possible to define custom kernels | |
| from arrays or combine existing kernels to match specific applications. | |
| Every filter kernel is characterized by its response function. For time series | |
| we speak of an "impulse response function" or for images we call it "point | |
| spread function." This response function is given for every kernel by a | |
| `~astropy.modeling.FittableModel`, which is evaluated on a grid with | |
| to obtain a kernel | |
| array, which can be used for discrete convolution with the binned data. | |
| Examples | |
| ======== | |
| 1D Kernels | |
| ---------- | |
| One application of filtering is to smooth noisy data. In this case we | |
| consider a noisy Lorentz curve: | |
| >>> import numpy as np | |
| >>> from astropy.modeling.models import Lorentz1D | |
| >>> from astropy.convolution import convolve, Gaussian1DKernel, Box1DKernel | |
| >>> lorentz = Lorentz1D(1, 0, 1) | |
| >>> x = np.linspace(-5, 5, 100) | |
| >>> data_1D = lorentz(x) + 0.1 * (np.random.rand(100) - 0.5) | |
| Smoothing the noisy data with a `~astropy.convolution.Gaussian1DKernel` | |
| with a standard deviation of 2 pixels: | |
| >>> gauss_kernel = Gaussian1DKernel(2) | |
| >>> smoothed_data_gauss = convolve(data_1D, gauss_kernel) | |
| Smoothing the same data with a `~astropy.convolution.Box1DKernel` of width 5 | |
| pixels: | |
| >>> box_kernel = Box1DKernel(5) | |
| >>> smoothed_data_box = convolve(data_1D, box_kernel) | |
| The following plot illustrates the results: | |
| .. plot:: | |
| import numpy as np | |
| import matplotlib.pyplot as plt | |
| from astropy.modeling.models import Lorentz1D | |
| from astropy.convolution import convolve, Gaussian1DKernel, Box1DKernel | |
| # Fake Lorentz data including noise | |
| lorentz = Lorentz1D(1, 0, 1) | |
| x = np.linspace(-5, 5, 100) | |
| data_1D = lorentz(x) + 0.1 * (np.random.rand(100) - 0.5) | |
| # Smooth data | |
| gauss_kernel = Gaussian1DKernel(2) | |
| smoothed_data_gauss = convolve(data_1D, gauss_kernel) | |
| box_kernel = Box1DKernel(5) | |
| smoothed_data_box = convolve(data_1D, box_kernel) | |
| # Plot data and smoothed data | |
| plt.plot(x, data_1D, label='Original') | |
| plt.plot(x, smoothed_data_gauss, label='Smoothed with Gaussian1DKernel') | |
| plt.plot(x, smoothed_data_box, label='Smoothed with Box1DKernel') | |
| plt.xlabel('x [a.u.]') | |
| plt.ylabel('amplitude [a.u.]') | |
| plt.xlim(-5, 5) | |
| plt.ylim(-0.1, 1.5) | |
| plt.legend(prop={'size':12}) | |
| plt.show() | |
| Beside the ``astropy`` convolution functions | |
| `~astropy.convolution.convolve` and | |
| `~astropy.convolution.convolve_fft`, it is also possible to use | |
| the kernels with ``numpy`` or ``scipy`` convolution by passing the ``array`` | |
| attribute. This will be faster in most cases than the ``astropy`` convolution, | |
| but will not work properly if NaN values are present in the data. | |
| >>> smoothed = np.convolve(data_1D, box_kernel.array) | |
| 2D Kernels | |
| ---------- | |
| As all 2D kernels are symmetric, it is sufficient to specify the width in one | |
| direction. Therefore the use of 2D kernels is basically the same as for 1D | |
| kernels. Here we consider a small Gaussian-shaped source of amplitude 1 in the | |
| middle of the image and add 10% noise: | |
| >>> import numpy as np | |
| >>> from astropy.convolution import convolve, Gaussian2DKernel, Tophat2DKernel | |
| >>> from astropy.modeling.models import Gaussian2D | |
| >>> gauss = Gaussian2D(1, 0, 0, 3, 3) | |
| >>> # Fake image data including noise | |
| >>> x = np.arange(-100, 101) | |
| >>> y = np.arange(-100, 101) | |
| >>> x, y = np.meshgrid(x, y) | |
| >>> data_2D = gauss(x, y) + 0.1 * (np.random.rand(201, 201) - 0.5) | |
| Smoothing the noisy data with a | |
| with a standard | |
| deviation of 2 pixels: | |
| >>> gauss_kernel = Gaussian2DKernel(2) | |
| >>> smoothed_data_gauss = convolve(data_2D, gauss_kernel) | |
| Smoothing the noisy data with a | |
| of width 5 pixels: | |
| >>> tophat_kernel = Tophat2DKernel(5) | |
| >>> smoothed_data_tophat = convolve(data_2D, tophat_kernel) | |
| This is what the original image looks like: | |
| .. plot:: | |
| import numpy as np | |
| import matplotlib.pyplot as plt | |
| from astropy.modeling.models import Gaussian2D | |
| gauss = Gaussian2D(1, 0, 0, 2, 2) | |
| # Fake image data including noise | |
| x = np.arange(-100, 101) | |
| y = np.arange(-100, 101) | |
| x, y = np.meshgrid(x, y) | |
| data_2D = gauss(x, y) + 0.1 * (np.random.rand(201, 201) - 0.5) | |
| plt.imshow(data_2D, origin='lower') | |
| plt.xlabel('x [pixels]') | |
| plt.ylabel('y [pixels]') | |
| plt.colorbar() | |
| plt.show() | |
| The following plot illustrates the differences between several 2D kernels | |
| applied to the simulated data. Note that it has a slightly different color | |
| scale compared to the original image. | |
| .. plot:: | |
| import numpy as np | |
| import matplotlib.pyplot as plt | |
| from astropy.convolution import * | |
| from astropy.modeling.models import Gaussian2D | |
| # Small Gaussian source in the middle of the image | |
| gauss = Gaussian2D(1, 0, 0, 2, 2) | |
| # Fake data including noise | |
| x = np.arange(-100, 101) | |
| y = np.arange(-100, 101) | |
| x, y = np.meshgrid(x, y) | |
| data_2D = gauss(x, y) + 0.1 * (np.random.rand(201, 201) - 0.5) | |
| # Setup kernels, including unity kernel for original image | |
| # Choose normalization for linear scale space for MexicanHat | |
| kernels = [TrapezoidDisk2DKernel(11, slope=0.2), | |
| Tophat2DKernel(11), | |
| Gaussian2DKernel(11), | |
| Box2DKernel(11), | |
| 11 ** 2 * MexicanHat2DKernel(11), | |
| AiryDisk2DKernel(11)] | |
| fig, axes = plt.subplots(nrows=2, ncols=3) | |
| # Plot kernels | |
| for kernel, ax in zip(kernels, axes.flat): | |
| smoothed = convolve(data_2D, kernel, normalize_kernel=False) | |
| im = ax.imshow(smoothed, vmin=-0.01, vmax=0.08, origin='lower', | |
| interpolation='None') | |
| title = kernel.__class__.__name__ | |
| ax.set_title(title, fontsize=12) | |
| ax.set_yticklabels([]) | |
| ax.set_xticklabels([]) | |
| cax = fig.add_axes([0.9, 0.1, 0.03, 0.8]) | |
| fig.colorbar(im, cax=cax) | |
| plt.subplots_adjust(left=0.05, right=0.85, top=0.95, bottom=0.05) | |
| plt.show() | |
| The Gaussian kernel has better smoothing properties compared to the Box and the | |
| Top Hat. The Box filter is not isotropic and can produce artifacts (the source | |
| appears rectangular). The Mexican Hat filter removes noise and slowly varying | |
| structures (i.e., background), but produces a negative ring around the source. | |
| The best choice for the filter strongly depends on the application. | |
| Available Kernels | |
| ================= | |
| .. currentmodule:: astropy.convolution | |
| .. autosummary:: | |
| AiryDisk2DKernel | |
| Box1DKernel | |
| Box2DKernel | |
| CustomKernel | |
| Gaussian1DKernel | |
| Gaussian2DKernel | |
| MexicanHat1DKernel | |
| MexicanHat2DKernel | |
| Model1DKernel | |
| Model2DKernel | |
| Ring2DKernel | |
| Tophat2DKernel | |
| Trapezoid1DKernel | |
| TrapezoidDisk2DKernel | |
| Kernel Arithmetics | |
| ================== | |
| Addition and Subtraction | |
| ------------------------ | |
| As convolution is a linear operation, kernels can be added or subtracted from | |
| each other. They can also be multiplied with some number. One basic example | |
| would be the definition of a Difference of Gaussian filter: | |
| >>> from astropy.convolution import Gaussian1DKernel | |
| >>> gauss_1 = Gaussian1DKernel(10) | |
| >>> gauss_2 = Gaussian1DKernel(16) | |
| >>> DoG = gauss_2 - gauss_1 | |
| Another application is to convolve faked data with an instrument response | |
| function model. For example, if the response function can be described by | |
| the weighted sum of two Gaussians: | |
| >>> gauss_1 = Gaussian1DKernel(10) | |
| >>> gauss_2 = Gaussian1DKernel(16) | |
| >>> SoG = 4 * gauss_1 + gauss_2 | |
| Most times it will be necessary to normalize the resulting kernel by calling | |
| explicitly: | |
| >>> SoG.normalize() | |
| Convolution | |
| ----------- | |
| Furthermore, two kernels can be convolved with each other, which is useful when | |
| data is filtered with two different kinds of kernels or to create a new, | |
| special kernel: | |
| >>> import warnings | |
| >>> from astropy.convolution import Gaussian1DKernel, convolve | |
| >>> gauss_1 = Gaussian1DKernel(10) | |
| >>> gauss_2 = Gaussian1DKernel(16) | |
| >>> with warnings.catch_warnings(): | |
| ... warnings.simplefilter('ignore') # Ignore warning for doctest | |
| ... broad_gaussian = convolve(gauss_2, gauss_1) | |
| Or in case of multistage smoothing: | |
| >>> import numpy as np | |
| >>> from astropy.modeling.models import Lorentz1D | |
| >>> from astropy.convolution import convolve, Gaussian1DKernel, Box1DKernel | |
| >>> lorentz = Lorentz1D(1, 0, 1) | |
| >>> x = np.linspace(-5, 5, 100) | |
| >>> data_1D = lorentz(x) + 0.1 * (np.random.rand(100) - 0.5) | |
| >>> gauss = Gaussian1DKernel(3) | |
| >>> box = Box1DKernel(5) | |
| >>> smoothed_gauss = convolve(data_1D, gauss) | |
| >>> smoothed_gauss_box = convolve(smoothed_gauss, box) | |
| You would rather do the following: | |
| >>> gauss = Gaussian1DKernel(3) | |
| >>> box = Box1DKernel(5) | |
| >>> with warnings.catch_warnings(): | |
| ... warnings.simplefilter('ignore') # Ignore warning for doctest | |
| ... smoothed_gauss_box = convolve(data_1D, convolve(box, gauss)) | |
| Which, in most cases, will also be faster than the first method because only | |
| one convolution with the often times larger data array will be necessary. | |
| Discretization | |
| ============== | |
| To obtain the kernel array for discrete convolution, the kernel's response | |
| function is evaluated on a grid with | |
| For the | |
| discretization step the following modes are available: | |
| * Mode ``'center'`` (default) evaluates the response function on the grid by | |
| taking the value at the center of the bin. | |
| >>> from astropy.convolution import Gaussian1DKernel | |
| >>> gauss_center = Gaussian1DKernel(3, mode='center') | |
| * Mode ``'linear_interp'`` takes the values at the corners of the bin and | |
| linearly interpolates the value at the center: | |
| >>> gauss_interp = Gaussian1DKernel(3, mode='linear_interp') | |
| * Mode ``'oversample'`` evaluates the response function by taking the mean on an | |
| oversampled grid. The oversample factor can be specified with the ``factor`` | |
| argument. If the oversample factor is too large, the evaluation becomes slow. | |
| >>> gauss_oversample = Gaussian1DKernel(3, mode='oversample', factor=10) | |
| * Mode ``'integrate'`` integrates the function over the pixel using | |
| ``scipy.integrate.quad`` and ``scipy.integrate.dblquad``. This mode is very | |
| slow and is only recommended when the highest accuracy is required. | |
| .. doctest-requires:: scipy | |
| >>> gauss_integrate = Gaussian1DKernel(3, mode='integrate') | |
| Especially in the range where the kernel width is in order of only a few pixels, | |
| it can be advantageous to use the mode ``oversample`` or ``integrate`` to | |
| conserve the integral on a subpixel scale. | |
| Normalization | |
| ============= | |
| The kernel models are normalized per default (i.e., | |
| f(x) dx = 1`). But because of the limited kernel | |
| array size, the normalization for kernels with an infinite response can differ | |
| from one. The value of this deviation is stored in the kernel's ``truncation`` | |
| attribute. | |
| The normalization can also differ from one, especially for small kernels, due | |
| to the discretization step. This can be partly controlled by the ``mode`` | |
| argument, when initializing the kernel. (See also | |
| Setting the | |
| ``mode`` to ``'oversample'`` allows us to conserve the normalization even on the | |
| subpixel scale. | |
| The kernel arrays can be renormalized explicitly by calling either the | |
| ``normalize()`` method or by setting the ``normalize_kernel`` argument in the | |
| and | |
| functions. The latter | |
| method leaves the kernel itself unchanged but works with an internal normalized | |
| version of the kernel. | |
| Note that for :class:`~astropy.convolution.MexicanHat1DKernel` | |
| and :class:`~astropy.convolution.MexicanHat2DKernel` there is | |
| f(x) dx = 0`. To define a proper normalization, | |
| both filters are derived from a normalized Gaussian function. | |