"""
Copyright (c) 2010-2018 CNRS / Centre de Recherche Astrophysique de Lyon
Copyright (c) 2019 Simon Conseil <simon.conseil@univ-lyon1.fr>
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors
may be used to endorse or promote products derived from this software
without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
"""
import logging
import numpy as np
import warnings
from astropy.stats import sigma_clipped_stats
from .image import Image
__all__ = ('mask_sources', )
[docs]def mask_sources(image, sigma=3., iterations=2, opening_iterations=0,
outfile=None, plot=False):
"""Create a mask of sources, using photutils.
Parameters
----------
image : `Image` or str
Input image.
sigma : int, optional
Number of sigma for the detection threshold.
iterations : int
Number of iterations for the binary dilatation.
opening_iterations : int
Number of iterations for the binary opening.
outfile : str, optional
Output mask filename.
plot : bool
Plot the image and mask.
"""
logger = logging.getLogger(__name__)
from scipy import ndimage as ndi
try:
import photutils
except ImportError:
logger.critical('photutils is required and was not found.')
raise
logger.info('Reading image %s', image)
im = image if isinstance(image, Image) else Image(image)
with warnings.catch_warnings():
warnings.simplefilter('ignore', category=RuntimeWarning)
mean, median, std = sigma_clipped_stats(im.data, sigma=3.0)
logger.info('mean: %s, median: %s, std: %s', mean, median, std)
threshold = median + (std * sigma)
segm_img = photutils.detect_sources(im.data, threshold, npixels=5)
# turn segm_img into a mask
mask = segm_img.data.astype(np.bool)
if opening_iterations > 0:
struct = ndi.generate_binary_structure(2, 2)
mask = ndi.binary_opening(mask, structure=struct,
iterations=opening_iterations)
if iterations > 0:
struct = ndi.generate_binary_structure(2, 2)
mask = ndi.binary_dilation(mask, structure=struct,
iterations=iterations)
im_mask = Image(data=mask, dtype=int, wcs=im.wcs, copy=False)
if outfile:
im_mask.write(outfile, savemask='none')
if plot:
import matplotlib.pyplot as plt
fig, ax = plt.subplots(2, 2, figsize=(12, 12), tight_layout=True)
ax = ax.ravel()
vmin, vmax = mean - 5 * std, mean + 5 * std
im.plot(ax=ax[0], scale='linear', vmin=vmin, vmax=vmax, colorbar='v')
ax[1].imshow(segm_img, origin='lower')
ax[1].set_title('Segmentation map')
ax[2].imshow(mask, cmap='binary', origin='lower')
ax[2].set_title('Mask')
im_masked = im.copy()
im_masked.mask_selection(mask)
im_masked.plot(ax=ax[3], scale='linear', vmin=vmin, vmax=vmax,
title='Masked image')
return im_mask