photutils_detection_core.py

# Refer to:
# http://photutils.readthedocs.io/en/stable/_modules/photutils/detection/core.html#find_peaks


# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""Functions for detecting sources in an astronomical image."""

from __future__ import (absolute_import, division, print_function,
                        unicode_literals)

import numpy as np
# from astropy.stats import sigma_clipped_stats
# from astropy.table import Column, Table

# from ..utils.cutouts import cutout_footprint
# from ..utils.wcs_helpers import pixel_to_icrs_coords


# __all__ = ['detect_threshold', 'find_peaks']


# def detect_threshold(data, snr, background=None, error=None, mask=None,
#                      mask_value=None, sigclip_sigma=3.0, sigclip_iters=None):
#     """
#     Calculate a pixel-wise threshold image that can be used to detect
#     sources.

#     Parameters
#     ----------
#     data : array_like
#         The 2D array of the image.

#     snr : float
#         The signal-to-noise ratio per pixel above the ``background`` for
#         which to consider a pixel as possibly being part of a source.

#     background : float or array_like, optional
#         The background value(s) of the input ``data``.  ``background``
#         may either be a scalar value or a 2D image with the same shape
#         as the input ``data``.  If the input ``data`` has been
#         background-subtracted, then set ``background`` to ``0.0``.  If
#         `None`, then a scalar background value will be estimated using
#         sigma-clipped statistics.

#     error : float or array_like, optional
#         The Gaussian 1-sigma standard deviation of the background noise
#         in ``data``.  ``error`` should include all sources of
#         "background" error, but *exclude* the Poisson error of the
#         sources.  If ``error`` is a 2D image, then it should represent
#         the 1-sigma background error in each pixel of ``data``.  If
#         `None`, then a scalar background rms value will be estimated
#         using sigma-clipped statistics.

#     mask : array_like, bool, optional
#         A boolean mask with the same shape as ``data``, where a `True`
#         value indicates the corresponding element of ``data`` is masked.
#         Masked pixels are ignored when computing the image background
#         statistics.

#     mask_value : float, optional
#         An image data value (e.g., ``0.0``) that is ignored when
#         computing the image background statistics.  ``mask_value`` will
#         be ignored if ``mask`` is input.

#     sigclip_sigma : float, optional
#         The number of standard deviations to use as the clipping limit
#         when calculating the image background statistics.

#     sigclip_iters : int, optional
#        The number of iterations to perform sigma clipping, or `None` to
#        clip until convergence is achieved (i.e., continue until the last
#        iteration clips nothing) when calculating the image background
#        statistics.

#     Returns
#     -------
#     threshold : 2D `~numpy.ndarray`
#         A 2D image with the same shape as ``data`` containing the
#         pixel-wise threshold values.

#     See Also
#     --------
#     :func:`photutils.segmentation.detect_sources`

#     Notes
#     -----
#     The ``mask``, ``mask_value``, ``sigclip_sigma``, and
#     ``sigclip_iters`` inputs are used only if it is necessary to
#     estimate ``background`` or ``error`` using sigma-clipped background
#     statistics.  If ``background`` and ``error`` are both input, then
#     ``mask``, ``mask_value``, ``sigclip_sigma``, and ``sigclip_iters``
#     are ignored.
#     """

#     if background is None or error is None:
#         data_mean, data_median, data_std = sigma_clipped_stats(
#             data, mask=mask, mask_value=mask_value, sigma=sigclip_sigma,
#             iters=sigclip_iters)
#         bkgrd_image = np.zeros_like(data) + data_mean
#         bkgrdrms_image = np.zeros_like(data) + data_std

#     if background is None:
#         background = bkgrd_image
#     else:
#         if np.isscalar(background):
#             background = np.zeros_like(data) + background
#         else:
#             if background.shape != data.shape:
#                 raise ValueError('If input background is 2D, then it '
#                                  'must have the same shape as the input '
#                                  'data.')

#     if error is None:
#         error = bkgrdrms_image
#     else:
#         if np.isscalar(error):
#             error = np.zeros_like(data) + error
#         else:
#             if error.shape != data.shape:
#                 raise ValueError('If input error is 2D, then it '
#                                  'must have the same shape as the input '
#                                  'data.')

#     return background + (error * snr)



def find_peaks(data, threshold, box_size=3, footprint=None, mask=None,
               border_width=None, npeaks=np.inf, subpixel=False, error=None,
               wcs=None):
    """
    Find local peaks in an image that are above above a specified
    threshold value.

    Peaks are the maxima above the ``threshold`` within a local region.
    The regions are defined by either the ``box_size`` or ``footprint``
    parameters.  ``box_size`` defines the local region around each pixel
    as a square box.  ``footprint`` is a boolean array where `True`
    values specify the region shape.

    If multiple pixels within a local region have identical intensities,
    then the coordinates of all such pixels are returned.  Otherwise,
    there will be only one peak pixel per local region.  Thus, the
    defined region effectively imposes a minimum separation between
    peaks (unless there are identical peaks within the region).

    When using subpixel precision (``subpixel=True``), then a cutout of
    the specified ``box_size`` or ``footprint`` will be taken centered
    on each peak and fit with a 2D Gaussian (plus a constant).  In this
    case, the fitted local centroid and peak value (the Gaussian
    amplitude plus the background constant) will also be returned in the
    output table.

    Parameters
    ----------
    data : array_like
        The 2D array of the image.

    threshold : float or array-like
        The data value or pixel-wise data values to be used for the
        detection threshold.  A 2D ``threshold`` must have the same
        shape as ``data``.  See `detect_threshold` for one way to create
        a ``threshold`` image.

    box_size : scalar or tuple, optional
        The size of the local region to search for peaks at every point
        in ``data``.  If ``box_size`` is a scalar, then the region shape
        will be ``(box_size, box_size)``.  Either ``box_size`` or
        ``footprint`` must be defined.  If they are both defined, then
        ``footprint`` overrides ``box_size``.

    footprint : `~numpy.ndarray` of bools, optional
        A boolean array where `True` values describe the local footprint
        region within which to search for peaks at every point in
        ``data``.  ``box_size=(n, m)`` is equivalent to
        ``footprint=np.ones((n, m))``.  Either ``box_size`` or
        ``footprint`` must be defined.  If they are both defined, then
        ``footprint`` overrides ``box_size``.

    mask : array_like, bool, optional
        A boolean mask with the same shape as ``data``, where a `True`
        value indicates the corresponding element of ``data`` is masked.

    border_width : bool, optional
        The width in pixels to exclude around the border of the
        ``data``.

    npeaks : int, optional
        The maximum number of peaks to return.  When the number of
        detected peaks exceeds ``npeaks``, the peaks with the highest
        peak intensities will be returned.

    subpixel : bool, optional
        If `True`, then a cutout of the specified ``box_size`` or
        ``footprint`` will be taken centered on each peak and fit with a
        2D Gaussian (plus a constant).  In this case, the fitted local
        centroid and peak value (the Gaussian amplitude plus the
        background constant) will also be returned in the output table.

    error : array_like, optional
        The 2D array of the 1-sigma errors of the input ``data``.
        ``error`` is used only to weight the 2D Gaussian fit performed
        when ``subpixel=True``.

    wcs : `~astropy.wcs.WCS`
        The WCS transformation to use to convert from pixel coordinates
        to ICRS world coordinates.  If `None`, then the world
        coordinates will not be returned in the output
        `~astropy.table.Table`.

    Returns
    -------
    output : `~astropy.table.Table`
        A table containing the x and y pixel location of the peaks and
        their values.  If ``subpixel=True``, then the table will also
        contain the local centroid and fitted peak value.
    """

    from scipy import ndimage

    if np.all(data == data.flat[0]):
        return []

    if footprint is not None:
        data_max = ndimage.maximum_filter(data, footprint=footprint,
                                          mode='constant', cval=0.0)
    else:
        data_max = ndimage.maximum_filter(data, size=box_size,
                                          mode='constant', cval=0.0)

    peak_goodmask = (data == data_max)    # good pixels are True

    if mask is not None:
        mask = np.asanyarray(mask)
        if data.shape != mask.shape:
            raise ValueError('data and mask must have the same shape')
        peak_goodmask = np.logical_and(peak_goodmask, ~mask)

    if border_width is not None:
        for i in range(peak_goodmask.ndim):
            peak_goodmask = peak_goodmask.swapaxes(0, i)
            peak_goodmask[:border_width] = False
            peak_goodmask[-border_width:] = False
            peak_goodmask = peak_goodmask.swapaxes(0, i)

    peak_goodmask = np.logical_and(peak_goodmask, (data > threshold))
    y_peaks, x_peaks = peak_goodmask.nonzero()
    peak_values = data[y_peaks, x_peaks]

    if len(x_peaks) > npeaks:
        idx = np.argsort(peak_values)[::-1][:npeaks]
        x_peaks = x_peaks[idx]
        y_peaks = y_peaks[idx]
        peak_values = peak_values[idx]

    if subpixel:
        from ..centroids import fit_2dgaussian    # prevents circular import

        x_centroid, y_centroid = [], []
        fit_peak_values = []
        for (y_peak, x_peak) in zip(y_peaks, x_peaks):
            rdata, rmask, rerror, slc = cutout_footprint(
                data, (x_peak, y_peak), box_size=box_size,
                footprint=footprint, mask=mask, error=error)
            gaussian_fit = fit_2dgaussian(rdata, mask=rmask, error=rerror)
            if gaussian_fit is None:
                x_cen, y_cen, fit_peak_value = np.nan, np.nan, np.nan
            else:
                x_cen = slc[1].start + gaussian_fit.x_mean.value
                y_cen = slc[0].start + gaussian_fit.y_mean.value
                fit_peak_value = (gaussian_fit.constant.value +
                                  gaussian_fit.amplitude.value)
            x_centroid.append(x_cen)
            y_centroid.append(y_cen)
            fit_peak_values.append(fit_peak_value)

        columns = (x_peaks, y_peaks, peak_values, x_centroid, y_centroid,
                   fit_peak_values)
        names = ('x_peak', 'y_peak', 'peak_value', 'x_centroid', 'y_centroid',
                 'fit_peak_value')
    else:
        columns = (x_peaks, y_peaks, peak_values)
        names = ('x_peak', 'y_peak', 'peak_value')

    # table = Table(columns, names=names)
    table = columns

    if wcs is not None:
        icrs_ra_peak, icrs_dec_peak = pixel_to_icrs_coords(x_peaks, y_peaks,
                                                           wcs)
        table.add_column(Column(icrs_ra_peak, name='icrs_ra_peak'), index=2)
        table.add_column(Column(icrs_dec_peak, name='icrs_dec_peak'), index=3)

        if subpixel:
            icrs_ra_centroid, icrs_dec_centroid = pixel_to_icrs_coords(
                x_centroid, y_centroid, wcs)
            idx = table.colnames.index('y_centroid')
            table.add_column(Column(icrs_ra_centroid,
                                    name='icrs_ra_centroid'), index=idx+1)
            table.add_column(Column(icrs_dec_centroid,
                                    name='icrs_dec_centroid'), index=idx+2)

    return table