.. _astropy_convolve:

*************************************************
Convolution and filtering (`astropy.convolution`)
*************************************************

Introduction
============

`astropy.convolution` provides convolution functions and kernels that offers
improvements compared to the scipy `scipy.ndimage` convolution routines,
including:

* Proper treatment of NaN values (ignoring them during convolution and
  replacing NaN pixels with interpolated values)

* A single function for 1-D, 2-D, and 3-D convolution

* Improved options for the treatment of edges

* Both direct and Fast Fourier Transform (FFT) versions

* Built-in kernels that are commonly used in Astronomy

The following thumbnails show the difference between Scipy's and
Astropy's convolve functions on an Astronomical image that contains NaN
values. Scipy's function essentially returns NaN for all pixels that are
within a kernel of any NaN value, which is often not the desired result.

.. plot::
   :context: reset
   :include-source:
   :align: center

    import numpy as np
    import matplotlib.pyplot as plt

    from astropy.io import fits
    from astropy.utils.data import get_pkg_data_filename
    from astropy.convolution import Gaussian2DKernel
    from scipy.signal import convolve as scipy_convolve
    from astropy.convolution import convolve


    # Load the data from data.astropy.org
    filename = get_pkg_data_filename('galactic_center/gc_msx_e.fits')
    hdu = fits.open(filename)[0]

    # Scale the file to have reasonable numbers
    # (this is mostly so that colorbars don't have too many digits)
    # Also, we crop it so you can see individual pixels
    img = hdu.data[50:90, 60:100] * 1e5

    # This example is intended to demonstrate how astropy.convolve and
    # scipy.convolve handle missing data, so we start by setting the
    # brightest pixels to NaN to simulate a "saturated" data set
    img[img > 2e1] = np.nan

    # We also create a copy of the data and set those NaNs to zero.  We'll
    # use this for the scipy convolution
    img_zerod = img.copy()
    img_zerod[np.isnan(img)] = 0

    # We smooth with a Gaussian kernel with x_stddev=1 (and y_stddev=1)
    # It is a 9x9 array
    kernel = Gaussian2DKernel(x_stddev=1)

    # Convolution: scipy's direct convolution mode spreads out NaNs (see
    # panel 2 below)
    scipy_conv = scipy_convolve(img, kernel, mode='same', method='direct')

    # scipy's direct convolution mode run on the 'zero'd' image will not
    # have NaNs, but will have some very low value zones where the NaNs were
    # (see panel 3 below)
    scipy_conv_zerod = scipy_convolve(img_zerod, kernel, mode='same',
                                      method='direct')

    # astropy's convolution replaces the NaN pixels with a kernel-weighted
    # interpolation from their neighbors
    astropy_conv = convolve(img, kernel)


    # Now we do a bunch of plots.  In the first two plots, the originally masked
    # values are marked with red X's
    plt.figure(1, figsize=(12, 12)).clf()
    ax1 = plt.subplot(2, 2, 1)
    im = ax1.imshow(img, vmin=-2., vmax=2.e1, origin='lower',
                    interpolation='nearest', cmap='viridis')
    y, x = np.where(np.isnan(img))
    ax1.set_autoscale_on(False)
    ax1.plot(x, y, 'rx', markersize=4)
    ax1.set_title("Original")
    ax1.set_xticklabels([])
    ax1.set_yticklabels([])

    ax2 = plt.subplot(2, 2, 2)
    im = ax2.imshow(scipy_conv, vmin=-2., vmax=2.e1, origin='lower',
                    interpolation='nearest', cmap='viridis')
    ax2.set_autoscale_on(False)
    ax2.plot(x, y, 'rx', markersize=4)
    ax2.set_title("Scipy")
    ax2.set_xticklabels([])
    ax2.set_yticklabels([])

    ax3 = plt.subplot(2, 2, 3)
    im = ax3.imshow(scipy_conv_zerod, vmin=-2., vmax=2.e1, origin='lower',
                    interpolation='nearest', cmap='viridis')
    ax3.set_title("Scipy nan->zero")
    ax3.set_xticklabels([])
    ax3.set_yticklabels([])

    ax4 = plt.subplot(2, 2, 4)
    im = ax4.imshow(astropy_conv, vmin=-2., vmax=2.e1, origin='lower',
                    interpolation='nearest', cmap='viridis')
    ax4.set_title("Default astropy")
    ax4.set_xticklabels([])
    ax4.set_yticklabels([])

    # we make a second plot of the amplitudes vs offset position to more
    # clearly illustrate the value differences
    plt.figure(2).clf()
    plt.plot(img[:, 25], label='input', drawstyle='steps-mid', linewidth=2,
             alpha=0.5)
    plt.plot(scipy_conv[:, 25], label='scipy', drawstyle='steps-mid',
             linewidth=2, alpha=0.5, marker='s')
    plt.plot(scipy_conv_zerod[:, 25], label='scipy nan->zero',
             drawstyle='steps-mid', linewidth=2, alpha=0.5, marker='s')
    plt.plot(astropy_conv[:, 25], label='astropy', drawstyle='steps-mid',
             linewidth=2, alpha=0.5)
    plt.ylabel("Amplitude")
    plt.ylabel("Position Offset")
    plt.legend(loc='best')
    plt.show()


The following sections describe how to make use of the convolution functions,
and how to use built-in convolution kernels:

Getting started
===============

Two convolution functions are provided.  They are imported as::

    from astropy.convolution import convolve, convolve_fft

and are both used as::

    result = convolve(image, kernel)
    result = convolve_fft(image, kernel)

:func:`~astropy.convolution.convolve` is implemented as a
direct convolution algorithm, while
:func:`~astropy.convolution.convolve_fft` uses a fast Fourier
transform (FFT). Thus, the former is better for small kernels, while the latter
is much more efficient for larger kernels.

For example, to convolve a 1-d dataset with a user-specified kernel, you can do::

    >>> from astropy.convolution import convolve
    >>> convolve([1, 4, 5, 6, 5, 7, 8], [0.2, 0.6, 0.2])  # doctest: +FLOAT_CMP
    array([1.4, 3.6, 5. , 5.6, 5.6, 6.8, 6.2])

Notice that the end points are set to zero - by default, points that are too
close to the boundary to have a convolved value calculated are set to zero.
However, the :func:`~astropy.convolution.convolve` function allows for a
``boundary`` argument that can be used to specify alternate behaviors. For
example, setting ``boundary='extend'`` causes values near the edges to be
computed, assuming the original data is simply extended using a constant
extrapolation beyond the boundary::

    >>> from astropy.convolution import convolve
    >>> convolve([1, 4, 5, 6, 5, 7, 8], [0.2, 0.6, 0.2], boundary='extend')  # doctest: +FLOAT_CMP
    array([1.6, 3.6, 5. , 5.6, 5.6, 6.8, 7.8])

The values at the end are computed assuming that any value below the first
point is ``1``, and any value above the last point is ``8``. For a more
detailed discussion of boundary treatment, see :doc:`using`.

This module also includes built-in kernels that can be imported as e.g.::

    >>> from astropy.convolution import Gaussian1DKernel

To use a kernel, first create a specific instance of the kernel::

    >>> gauss = Gaussian1DKernel(stddev=2)

``gauss`` is not an array, but a kernel object. The underlying array can be retrieved with::

    >>> gauss.array  # doctest: +FLOAT_CMP
    array([6.69151129e-05, 4.36341348e-04, 2.21592421e-03,
           8.76415025e-03, 2.69954833e-02, 6.47587978e-02,
           1.20985362e-01, 1.76032663e-01, 1.99471140e-01,
           1.76032663e-01, 1.20985362e-01, 6.47587978e-02,
           2.69954833e-02, 8.76415025e-03, 2.21592421e-03,
           4.36341348e-04, 6.69151129e-05])

The kernel can then be used directly when calling
:func:`~astropy.convolution.convolve`:

.. plot::
   :include-source:

    import numpy as np
    import matplotlib.pyplot as plt

    from astropy.convolution import Gaussian1DKernel, convolve

    plt.figure(3).clf()

    # Generate fake data
    x = np.arange(1000).astype(float)
    y = np.sin(x / 100.) + np.random.normal(0., 1., x.shape)
    y[::3] = np.nan

    # Create kernel
    g = Gaussian1DKernel(stddev=50)

    # Convolve data
    z = convolve(y, g)

    # Plot data before and after convolution
    plt.plot(x, y, 'k-', label='Before')
    plt.plot(x, z, 'b-', label='After', alpha=0.5, linewidth=2)
    plt.legend(loc='best')
    plt.show()


Using astropy's convolution to replace bad data
-----------------------------------------------
Astropy's convolution methods can be used to replace bad data with values
interpolated from their neighbors.  Kernel-based interpolation is useful for
handling images with a few bad pixels or for interpolating sparsely sampled
images.

The interpolation tool is implemented and used as::

    from astropy.convolution import interpolate_replace_nans
    result = interpolate_replace_nans(image, kernel)

Some contexts in which you might want to use kernel-based interpolation include:

 * images with saturated pixels.  Generally, these are the highest-intensity
   regions in the imaged area, and the interpolated values are not reliable,
   but this can be useful for display purposes
 * images with flagged pixels, e.g., with a few small regions affected by cosmic
   rays or other spurious signals that require those pixels to be flagged out.
   If the affected region is small enough, the resulting interpolation will have
   a small effect on source statistics and may allow for robust source finding
   algorithms to be run on the resulting data
 * sparsely sampled images such as those constructed with single-pixel
   detectors.  Such images will only have a few discrete points sampled across
   the imaged area, but an approximation of the extended sky emission can still
   be constructed.

.. note::
    Care must be taken to ensure that the kernel is large enough to completely
    cover potential contiguous regions of ``NaN`` values.
    An ``AstropyUserWarning`` is raised if ``NaN`` values are detected post
    convolution, in which case the kernel size should be increased.

The script below shows an example of kernel interpolation to fill in
flagged-out pixels:

.. plot::
   :context:
   :include-source:
   :align: center

   import numpy as np
   import matplotlib.pyplot as plt

   from astropy.io import fits
   from astropy.utils.data import get_pkg_data_filename
   from astropy.convolution import Gaussian2DKernel, interpolate_replace_nans

   # Load the data from data.astropy.org
   filename = get_pkg_data_filename('galactic_center/gc_msx_e.fits')

   hdu = fits.open(filename)[0]
   img = hdu.data[50:90, 60:100] * 1e5

   # This example is intended to demonstrate how astropy.convolve and
   # scipy.convolve handle missing data, so we start by setting the brightest
   # pixels to NaN to simulate a "saturated" data set
   img[img > 2e1] = np.nan

   # We smooth with a Gaussian kernel with x_stddev=1 (and y_stddev=1)
   # It is a 9x9 array
   kernel = Gaussian2DKernel(x_stddev=1)

   # create a "fixed" image with NaNs replaced by interpolated values
   fixed_image = interpolate_replace_nans(img, kernel)

   # Now we do a bunch of plots.  In the first two plots, the originally masked
   # values are marked with red X's
   plt.figure(1, figsize=(12, 6)).clf()
   plt.close(2) # close the second plot from above

   ax1 = plt.subplot(1, 2, 1)
   im = ax1.imshow(img, vmin=-2., vmax=2.e1, origin='lower',
                   interpolation='nearest', cmap='viridis')
   y, x = np.where(np.isnan(img))
   ax1.set_autoscale_on(False)
   ax1.plot(x, y, 'rx', markersize=4)
   ax1.set_title("Original")
   ax1.set_xticklabels([])
   ax1.set_yticklabels([])

   ax2 = plt.subplot(1, 2, 2)
   im = ax2.imshow(fixed_image, vmin=-2., vmax=2.e1, origin='lower',
                   interpolation='nearest', cmap='viridis')
   ax2.set_title("Fixed")
   ax2.set_xticklabels([])
   ax2.set_yticklabels([])

This script shows the power of this technique for reconstructing images from
sparse sampling.  Note that the image is not perfect - the pointlike sources
are sometimes missed - but the extended structure is very well recovered (by
eye).

.. plot::
   :context:
   :include-source:
   :align: center

   import numpy as np
   import matplotlib.pyplot as plt

   from astropy.io import fits
   from astropy.utils.data import get_pkg_data_filename
   from astropy.convolution import Gaussian2DKernel, interpolate_replace_nans

   # Load the data from data.astropy.org
   filename = get_pkg_data_filename('galactic_center/gc_msx_e.fits')

   hdu = fits.open(filename)[0]
   img = hdu.data[50:90, 60:100] * 1e5

   indices = np.random.randint(low=0, high=img.size, size=300)

   sampled_data = img.flat[indices]

   # Build a new, sparsely sampled version of the original image
   new_img = np.tile(np.nan, img.shape)
   new_img.flat[indices] = sampled_data

   # We smooth with a Gaussian kernel with x_stddev=1 (and y_stddev=1)
   # It is a 9x9 array
   kernel = Gaussian2DKernel(x_stddev=1)

   # create a "reconstructed" image with NaNs replaced by interpolated values
   reconstructed_image = interpolate_replace_nans(new_img, kernel)

   # Now we do a bunch of plots.  In the first two plots, the originally masked
   # values are marked with red X's
   plt.figure(1, figsize=(12, 6)).clf()
   ax1 = plt.subplot(1, 3, 1)
   im = ax1.imshow(img, vmin=-2., vmax=2.e1, origin='lower',
                   interpolation='nearest', cmap='viridis')
   y, x = np.where(np.isnan(img))
   ax1.set_autoscale_on(False)
   ax1.set_title("Original")
   ax1.set_xticklabels([])
   ax1.set_yticklabels([])

   ax2 = plt.subplot(1, 3, 2)
   im = ax2.imshow(new_img, vmin=-2., vmax=2.e1, origin='lower',
                   interpolation='nearest', cmap='viridis')
   ax2.set_title("Sparsely Sampled")
   ax2.set_xticklabels([])
   ax2.set_yticklabels([])

   ax2 = plt.subplot(1, 3, 3)
   im = ax2.imshow(reconstructed_image, vmin=-2., vmax=2.e1, origin='lower',
                   interpolation='nearest', cmap='viridis')
   ax2.set_title("Reconstructed")
   ax2.set_xticklabels([])
   ax2.set_yticklabels([])


.. _astropy_convolve_compat:

A note on backward compatibility (pre v2.0)
-------------------------------------------

The behavior of astropy's direct convolution
(:func:`~astropy.convolution.convolve`) changed in version 2.0.  Generally, the
old version is undesirable.  However, to recover the behavior of the old
(astropy version <2.0) direct convolution function, you can interpolate and
then convolve, e.g.:

.. code-block:: python

    from astropy.convolution import interpolate_replace_nans, convolve
    interped_result = interpolate_replace_nans(image, kernel)
    result = convolve(interped_image, kernel)

Note that the default behavior of both `~astropy.convolution.convolve` and
`~astropy.convolution.convolve_fft` is to perform *normalized convolution* and
interpolate NaNs during that process.  The example given in this note, and what
was previously done only in direct convolution in old versions of astropy, does
a two-step process: first, it replaces the NaNs with their interpolated values
while leaving all non-NaN values unchanged, then it convolves the resulting
image with the specified kernel.

Using `astropy.convolution`
===========================

.. toctree::
   :maxdepth: 2

   using.rst
   kernels.rst
   non_normalized_kernels.rst

.. note that if this section gets too long, it should be moved to a separate 
   doc page - see the top of performance.inc.rst for the instructions on how to do
   that
.. include:: performance.inc.rst

Reference/API
=============

.. automodapi:: astropy.convolution
    :no-inheritance-diagram:
