def convolve(image, smooth=3, kernel='gauss'):
if smooth is None and kernel in ['box', 'gauss']:
return image
if smooth is not None and not np.isscalar(smooth):
raise ValueError("smooth= should be an integer - for more complex "
"kernels, pass an array containing the kernel "
"to the kernel= option")
# The Astropy convolution doesn't treat +/-Inf values correctly yet, so we
# convert to NaN here.
image_fixed = np.array(image, dtype=float, copy=True)
image_fixed[np.isinf(image)] = np.nan
if kernel == 'gauss':
if make_kernel is None:
kernel = Gaussian2DKernel(smooth,
x_size=smooth * 5,
y_size=smooth * 5)
else:
kernel = make_kernel((smooth * 5, smooth * 5), smooth, 'gaussian')
elif kernel == 'box':
if make_kernel is None:
kernel = Box2DKernel(smooth, x_size=smooth * 5, y_size=smooth * 5)
else:
kernel = make_kernel((smooth * 5, smooth * 5), smooth, 'boxcar')
else:
kernel = kernel
return astropy_convolve(image, kernel, boundary='extend')
def test_process_image_pixels():
"""Check the example how to implement convolution given in the docstring"""
from astropy.convolution import convolve as astropy_convolve
def convolve(image, kernel):
"""Convolve image with kernel"""
from ..utils import process_image_pixels
images = dict(image=np.asanyarray(image))
kernel = np.asanyarray(kernel)
out = dict(image=np.empty_like(image))
def convolve_function(images, kernel):
value = np.sum(images['image'] * kernel)
return dict(image=value)
process_image_pixels(images, kernel, out, convolve_function)
return out['image']
random_state = np.testing.RandomState(seed=0)
image = random_state.uniform(size=(7, 10))
kernel = random_state.uniform(size=(3, 5))
actual = convolve(image, kernel)
desired = astropy_convolve(image, kernel, boundary='fill')
assert_allclose(actual, desired)
def convolve(sunpy_map, oversample_psf=1):
"""Convolve the FOXSI psf with an input map
Parameters
----------
sunpy_map : `~sunpy.map.GenericMap`
An input map.
oversample_psf : int
The number of subpixels to average over to produce a more accurate PSF
Returns
-------
sunpy_map : `~sunpy.map.GenericMap`
The map convolved with the FOXSI psf.
"""
this_psf = psf(0 * u.arcmin,
0 * u.arcmin,
scale=sunpy_map.scale.x,
oversample=oversample_psf)
smoothed_data = astropy_convolve(sunpy_map.data, this_psf)
meta = sunpy_map.meta.copy()
meta['telescop'] = 'FOXSI-SMEX'
result = Map((smoothed_data, meta))
return result
def test_process_image_pixels():
"""Check the example how to implement convolution given in the docstring"""
from astropy.convolution import convolve as astropy_convolve
def convolve(image, kernel):
"""Convolve image with kernel"""
from ..utils import process_image_pixels
images = dict(image=np.asanyarray(image))
kernel = np.asanyarray(kernel)
out = dict(image=np.empty_like(image))
def convolve_function(images, kernel):
value = np.sum(images['image'] * kernel)
return dict(image=value)
process_image_pixels(images, kernel, out, convolve_function)
return out['image']
random_state = np.testing.RandomState(seed=0)
image = random_state.uniform(size=(7, 10))
kernel = random_state.uniform(size=(3, 5))
actual = convolve(image, kernel)
desired = astropy_convolve(image, kernel, boundary='fill')
assert_allclose(actual, desired)
def convolve(image, smooth=3, kernel='gauss'):
if smooth is None and kernel in ['box', 'gauss']:
return image
if smooth is not None and not np.isscalar(smooth):
raise ValueError("smooth= should be an integer - for more complex "
"kernels, pass an array containing the kernel "
"to the kernel= option")
# The Astropy convolution doesn't treat +/-Inf values correctly yet, so we
# convert to NaN here.
image_fixed = np.array(image, dtype=float, copy=True)
image_fixed[np.isinf(image)] = np.nan
if kernel == 'gauss':
if make_kernel is None:
kernel = Gaussian2DKernel(smooth, x_size=smooth * 5, y_size=smooth * 5)
else:
kernel = make_kernel((smooth * 5, smooth * 5), smooth, 'gaussian')
elif kernel == 'box':
if make_kernel is None:
kernel = Box2DKernel(smooth, x_size=smooth * 5, y_size=smooth * 5)
else:
kernel = make_kernel((smooth * 5, smooth * 5), smooth, 'boxcar')
else:
kernel = kernel
return astropy_convolve(image, kernel, boundary='extend')
def convolve(image, smooth=3, kernel='gauss'):
""" Convolve 2D image. Hacked from aplpy
"""
if smooth is None and isinstance(kernel, str) and kernel in ['box', 'gauss']:
return image
if smooth is not None and not np.isscalar(smooth):
raise ValueError("smooth= should be an integer - for more complex "
"kernels, pass an array containing the kernel "
"to the kernel= option")
# The Astropy convolution doesn't treat +/-Inf values correctly yet, so we
# convert to NaN here.
image_fixed = np.array(image, dtype=float, copy=True)
image_fixed[np.isinf(image)] = np.nan
if isinstance(kernel, str):
if kernel == 'gauss':
kernel = Gaussian2DKernel(
smooth, x_size=smooth * 5, y_size=smooth * 5)
elif kernel == 'box':
kernel = Box2DKernel(smooth, x_size=smooth * 5, y_size=smooth * 5)
else:
raise ValueError("Unknown kernel: {0}".format(kernel))
return astropy_convolve(image, kernel, boundary='extend')
def test_convolve_identical_to_astropy():
array = np.random.normal(5, 0.5, 1000).reshape(10, 10, 10)
kernel = np.ones((3, 3, 3))
conv1 = convolve_with_mask(array, kernel)
conv2 = astropy_convolve(array, kernel)
# Because of different boundary handling the first and last element in each
# dimension must be ignored.
assert_array_almost_equal(conv1[1:-1, 1:-1, 1:-1], conv2[1:-1, 1:-1, 1:-1])
def convolve(sunpy_map, oversample_psf=1):
"""Convolve the FOXSI psf with an input map
Parameters
----------
sunpy_map : `~sunpy.map.GenericMap`
An input map.
oversample_psf : int
The number of subpixels to average over to produce a more accurate PSF
Returns
-------
sunpy_map : `~sunpy.map.GenericMap`
The map convolved with the FOXSI psf.
"""
this_psf = psf(0 * u.arcmin, 0 * u.arcmin, scale=sunpy_map.scale.x, oversample=oversample_psf)
smoothed_data = astropy_convolve(sunpy_map.data, this_psf)
meta = sunpy_map.meta.copy()
meta["telescop"] = "FOXSI-SMEX"
result = Map((smoothed_data, meta))
return result
N = 256 # map size
pix = 10.0 * ARCSEC_TO_RADIAN
FITS = MakeEmptyFitsDim(1.0, 0.0, pix, N, N)
FITS[0].data = asarray(3.0 + randn(N, N), float32)
FITS[0].data = clip(FITS[0].data, 1.0, 10.0)
fwhm_pix = 7.3
fwhm_rad = fwhm_pix * pix
sigma_pix = fwhm_pix / sqrt(8.0 * log(2.0))
kernel = Gaussian2DKernel(x_stddev=sigma_pix)
if (kernel.shape[0] % 2 == 0):
print("kernel dimensions must be odd")
sys.exit()
AP = astropy_convolve(FITS[0].data.copy(), kernel, boundary='extend')
if (0):
CL = ConvolveFitsBeamPyCL(FITS, kernel, border='ignore')[0].data.copy()
else:
CL = ConvolveFitsBeamPyCL(FITS, kernel, border='nearest')[0].data.copy()
figure(1, figsize=(8, 6))
rc('font', size=9)
subplots_adjust(left=0.09,
right=0.94,
bottom=0.09,
top=0.95,
wspace=0.26,
hspace=0.3)
subplot(221)
do_it = 1
if (i>0):
if (TIME[i-1,iprog]>10.0):
do_it = 0 # it was already taking too long
TIME[i, iprog] = 1e10
if (0): # we have problem on the Intel GPU -- i915 bug prevents long runs ??
if ((iprog==4)&(fwhm_pix>32)): do_it = False
if (do_it):
time.sleep(SLEEP)
t0 = time.time()
if (iprog==0):
A = convolve_map_fast(FITS[0].data.copy(), fwhm_pix, radius=1.7*fwhm_pix)
elif (iprog==1):
B = scipy_convolve(FITS[0].data.copy(), kernel, mode='same', method='direct')
elif (iprog==2):
C = astropy_convolve(FITS[0].data.copy(), kernel)
elif (iprog==3):
# ConvolveFitsPyCL(F, fwhm_rad, fwhm_orig=0.0, RinFWHM=1.7, GPU=0, platforms=[2,])
D = ConvolveFitsBeamPyCL(FITS, kernel, GPU=0)[0].data.copy()
elif (iprog==4): # on my system Intel GPU
# ConvolveFitsPyCL(F, fwhm_rad, fwhm_orig=0.0, RinFWHM=1.7, GPU=1, platforms=[0,])
E = ConvolveFitsBeamPyCL(FITS, kernel, GPU=1)[0].data.copy()
elif (iprog==5): # on my system NVidia GPU
# ConvolveFitsPyCL(F, fwhm_rad, fwhm_orig=0.0, RinFWHM=1.7, GPU=1, platforms=[1,])
F = ConvolveFitsBeamPyCL(FITS, kernel, GPU=1, platforms=[1,])[0].data.copy()
TIME[i, iprog] = time.time()-t0
if (i==-1):
clf()
subplot(221)
imshow(C)
colorbar()