def define_sources(srcdic,model_frame,observation):
"""
"""
sources = []
for key, loc in srcdic.items():
if key == 'point':
for x,y in loc:
new_source = scarlet.PointSource(model_frame,
(y, x),
observation)
sources.append(new_source)
elif key == 'extended':
for x,y in loc:
new_source = scarlet.ExtendedSource(model_frame,
(y, x),
observation,
shifting=True)
sources.append(new_source)
elif key == 'multi':
for x,y in loc:
new_source = scarlet.MultiComponentSource(model_frame,
(y, x),
observation,
shifting=True)
sources.append(new_source)
return sources
def _get_model(self):
im, psf_im, coords, dims, sing_im, sing_coord = Simulation.__call__(
self)
bg_rms = self['Image']['Bgrms']
mode = self['Mode']
if mode == 'scarlet':
#constraints = {"S": None, "m": {'use_nearest': False}, "+": None}
#constraints['l1'] = bg_rms
#psf_dims = np.shape(psf_im)
#psf_im3d = psf_im.reshape( (1, psf_dims[0], psf_dims[1]) )
#target_psf = scarlet.psf_match.fit_target_psf(psf_im3d, scarlet.psf_match.gaussian)
#diff_kernels, psf_blend = scarlet.psf_match.build_diff_kernels(psf_im3d, target_psf)
sources = [
scarlet.ExtendedSource(coord, im, [bg_rms]) for coord in coords
] #,psf=diff_kernels) for coord in coords]
#config = scarlet.Config(edge_flux_thresh=0.05)
config = scarlet.Config(source_sizes=[25
]) #,edge_flux_thresh=0.05)
#scarlet.ExtendedSource.shift_center=0.0
blend = scarlet.Blend(sources, im, bg_rms=[bg_rms], config=config)
blend.fit(10000, e_rel=1e-3)
model = blend.get_model()
mod1 = blend.get_model(m=0)
#mod2 = blend.get_model(m=1)
cen_mod = sources[0].get_model()
#neigh_mod = sources[1].get_model()
#steps_used = blend.it
#return im,psf_im,model,mod1,mod2,cen_mod,neigh_mod,coords,sing_im,sing_coord
return im, psf_im, model, mod1, cen_mod, coords, sing_im, sing_coord
def scarlet1_initialize(images, peaks, psfs, variances, bands):
""" Deblend input images with scarlet
Args:
images: Numpy array of multi-band image to run scarlet on
[Number of bands, height, width].
peaks: Array of x and y coordinates of centroids of objects in
the image [number of sources, 2].
bg_rms: Background RMS value of the images [Number of bands]
iters: Maximum number of iterations if scarlet doesn't converge
(Default: 200).
e_rel: Relative error for convergence (Default: 0.015)
Returns
blend: scarlet.Blend object for the initialized sources
rejected_sources: list of sources (if any) that scarlet was
unable to initialize the image with.
"""
model_psf = scarlet.PSF(partial(scarlet.psf.gaussian, sigma=0.8),
shape=(None, 41, 41))
model_frame = scarlet.Frame(images.shape, psfs=model_psf, channels=bands)
observation = scarlet.Observation(images, psfs=scarlet.PSF(psfs),
weights=1./variances,
channels=bands).match(model_frame)
sources = []
for n, peak in enumerate(peaks):
result = scarlet.ExtendedSource(model_frame, (peak[1], peak[0]),
observation, symmetric=True,
monotonic=True, thresh=1,
shifting=True)
sed = result.sed
morph = result.morph
if np.all([s < 0 for s in sed]) or np.sum(morph) == 0:
raise ValueError("Incorrectly initialized")
sources.append(result)
blend = scarlet.Blend(sources, observation)
return blend, observation
def scarlet_initialize(images, peaks,
bg_rms):
""" Deblend input images with scarlet
Args:
images: Numpy array of multi-band image to run scarlet on
[Number of bands, height, width].
peaks: Array of x and y coordinates of centroids of objects in
the image [number of sources, 2].
bg_rms: Background RMS value of the images [Number of bands]
iters: Maximum number of iterations if scarlet doesn't converge
(Default: 200).
e_rel: Relative error for convergence (Default: 0.015)
Returns
blend: scarlet.Blend object for the initialized sources
rejected_sources: list of sources (if any) that scarlet was
unable to initialize the image with.
"""
sources = []
for n, peak in enumerate(peaks):
try:
result = scarlet.ExtendedSource(
(peak[1], peak[0]),
images,
bg_rms)
sources.append(result)
except scarlet.source.SourceInitError:
print("No flux in peak {0} at {1}".format(n, peak))
blend = scarlet.Blend(sources).set_data(images, bg_rms=bg_rms)
return blend
def _get_scar_model(self):
im, psf_im, coords, dims, dx1, dy1, noise = Simulation.__call__(self)
bg_rms = self['Image']['Bgrms']
mode = self['Mode']
constraints = {"S": None, "m": {'use_nearest': False}, "+": None}
#constraints['l0'] = bg_rms
sources = [
scarlet.ExtendedSource(coord, im, [bg_rms]) for coord in coords
]
#scarlet.ExtendedSource.shift_center=0.0
#config = scarlet.Config(edge_flux_thresh=0.05)
blend = scarlet.Blend(sources, im, bg_rms=[bg_rms]) #,config=config)
blend.fit(10000, e_rel=1e-3)
model = blend.get_model()
#plt.imshow(im[0,:,:])
#plt.colorbar()
#plt.savefig('test.png')
mod1 = blend.get_model(m=0)
mod2 = blend.get_model(m=1)
cen_mod = sources[0].get_model()
#output['mod_size_flag'][j] = 0
#if np.shape(cen_mod) != (1,25,25):
#output['mod_size_flag'][j] = 3
neigh_mod = sources[1].get_model()
#steps_used = blend.it
return im, psf_im, model, mod1, mod2, cen_mod, neigh_mod, coords, dx1, dy1, noise
def _get_model(self):
im,psf_im,coords,dims,sing_im,sing_coord = Simulation.__call__(self)
bg_rms = self['Image']['Bgrms']
mode = self['Mode']
if mode == 'scarlet':
constraints = {"S": None, "m": {'use_nearest': False}, "+": None}
#constraints['l1'] = bg_rms
sources = [scarlet.ExtendedSource(coord, im, [bg_rms]) for coord in coords]
#config = scarlet.Config(edge_flux_thresh=0.05)
#scarlet.ExtendedSource.shift_center=0.0
blend = scarlet.Blend(sources, im, bg_rms=[bg_rms])#,config=config)
blend.fit(10000, e_rel=1e-3)
model = blend.get_model()
mod1 = blend.get_model(m=0)
#mod2 = blend.get_model(m=1)
cen_mod = sources[0].get_model()
#mod_size_flag = 0
#if np.shape(cen_mod) != (1,25,25):
# mod_size_flag = 3
#print("not 25x25")
#output['mod_size_flag'][j] = 3
#neigh_mod = sources[1].get_model()
#steps_used = blend.it
#return im,psf_im,model,mod1,mod2,cen_mod,neigh_mod,coords,sing_im,sing_coord
return im,psf_im,model,mod1,cen_mod,coords,sing_im,sing_coord
def test_fit_extended_source(self):
shape = (6, 31, 55)
coords = [(20, 10), (10, 30), (17, 42)]
amplitudes = [3, 2, 1]
result = init_data(shape, coords, amplitudes, dtype=np.float64)
target_psf, psfs, images, channels, seds, morphs = result
B, Ny, Nx = shape
frame = scarlet.Frame(images.shape,
psfs=target_psf[None],
dtype=np.float64)
observation = scarlet.Observation(images, psfs=psfs).match(frame)
bg_rms = np.ones((B, ))
sources = [
scarlet.ExtendedSource(frame, coord, observation, bg_rms)
for coord in coords
]
blend = scarlet.Blend(sources, observation)
# Scale the input psfs by the observation and model psfs to ensure
# the sources were initialized correctly
psf_scale = observation.frame.psfs.max(axis=(1,
2)) / frame.psfs[0].max()
scaled_seds = np.array([c.sed * psf_scale for c in blend.components])
assert_almost_equal(scaled_seds, seds)
# Fit the model
blend.fit(100)
assert blend.it < 20
mse = np.array(blend.mse[:-1])
_mse = np.array(blend.mse[1:])
assert np.all(mse - _mse >= 0)
def get_scar_model(self):
import scarlet
import scarlet.constraint as sc
im, psf_im, coords, dims, dx1, dy1, noise = self.sim()
bg_rms = self.sim['Image']['Bgrms']
bg_rms = bg_rms / np.sqrt(len(im))
mode = self.sim['Mode']
#create multiband background im
bg = np.zeros((len(im)))
bg += bg_rms
#choose constraints for PSF and sources (optional)
#psf_constraints = ()#sc.SimpleConstraint())
#source_constraints = ()#sc.SimpleConstraint(),sc.DirectSymmetryConstraint()) #sc.DirectMonotonicityConstraint(use_nearest=False)
config = scarlet.Config(source_sizes=[25])
#create multiband PSF image
#psf_dims = np.shape(psf_im)
#psf_im3d = psf_im.reshape( (1, psf_dims[0], psf_dims[1]) )
#psfs = np.zeros((len(im), psf_dims[0],psf_dims[1]))
#psfs += psf_im3d
#PSF Matching
#target_psf = scarlet.psf_match.fit_target_psf(psfs,
# scarlet.psf_match.gaussian)
#diff_kernels, psf_blend = scarlet.psf_match.build_diff_kernels(psfs,
# target_psf)
#if use PSF matching, set psf = diff_kernels below
sources = [
scarlet.ExtendedSource(coord,
im,
bg_rms=bg,
psf=None,
config=config) for coord in coords
]
#config = scarlet.Config(edge_flux_thresh=0.05)
blend = scarlet.Blend(sources)
blend.set_data(im, bg_rms=bg, config=config)
blend.fit(10000, e_rel=1e-3)
#get full sized scarlet models
model = blend.get_model()
mod1 = blend.get_model(0)
mod2 = blend.get_model(1)
#get postage stamp models
cen_mod = sources[0].get_model()
neigh_mod = sources[1].get_model()
#get scarlet coordinates
cen_cen_pos = blend[0][0].center
neigh_cen_pos = blend[1][0].center
return im, psf_im, model, mod1, mod2, cen_mod, neigh_mod, coords, dx1, dy1, noise, cen_cen_pos, neigh_cen_pos
def _get_model(self):
im, psf_im, coords, dims, sing_im, sing_coord = Simulation.__call__(
self)
bg_rms = self['Image']['Bgrms']
mode = self['Mode']
#constraints = {"S": None, "m": {'use_nearest': False}, "+": None}
constraint = (sc.SimpleConstraint())
#constraint = PSFConstraint()
config = (scarlet.Config(source_sizes=[25]))
#psf_dims = np.shape(psf_im)
#psf_im3d = psf_im.reshape( (1, psf_dims[0], psf_dims[1]) )
#target_psf = scarlet.psf_match.fit_target_psf(psf_im3d, scarlet.psf_match.gaussian)
#diff_kernels, psf_blend = scarlet.psf_match.build_diff_kernels(psf_im3d, target_psf,constraints=constraint)
#constraint = (sc.L0Constraint(.5*bg_rms))
#& sc.DirectSymmetryConstraint(sigma=0.25))
#& sc.MonotonicityConstraint(use_nearest=True))
#constraints['l1'] = bg_rms
sources = [
scarlet.ExtendedSource(coord,
im, [bg_rms],
psf=None,
config=config,
shift_center=0.0) for coord in coords
]
#config = scarlet.Config(edge_flux_thresh=1.25)
#scarlet.ExtendedSource.shift_center=0.0
blend = scarlet.Blend(sources)
blend.set_data(im, bg_rms=[bg_rms], config=config)
blend.fit(10000, e_rel=1e-3)
model = blend.get_model()
mod1 = blend.get_model(0)
#mod2 = blend.get_model(1)
cen_mod = sources[0].get_model()
#cen_pos = sources[0].center
#neigh_mod = sources[1].get_model()
#print(cen_pos[0]-coords[0][0],cen_pos[1]-coords[0][1])
#psf_model = psf_blend.get_model()
"""
masked_mod = np.ma.masked_equal(diff_kernels,0.0)
f,ax = plt.subplots(1,2,figsize=(8,4))
f1 = ax[0].imshow(psf_im3d[0,:,:])
ax[0].set_title("Orig PSF")
plt.colorbar(f1,ax=ax[0])
f2 = ax[1].imshow(masked_mod[0,:,:])
plt.colorbar(f2,ax=ax[1])
ax[1].set_title("Diff Kernels")
plt.tight_layout()
f.savefig('test.png')
plt.close()
steps_used = blend.it
print(steps_used)
"""
#return im,psf_im,model,mod1,mod2,cen_mod,neigh_mod,coords,sing_im,sing_coord
return im, psf_im, model, mod1, cen_mod, coords, sing_im, sing_coord
def initialize(images, peaks, diff_kernels, bg_rms):
sources = []
rejected_sources = []
for n, peak in enumerate(peaks):
try:
result = scarlet.ExtendedSource((peak[1], peak[0]),
images,
bg_rms,
psf=diff_kernels)
sources.append(result)
except scarlet.source.SourceInitError:
rejected_sources.append(n)
print("No flux in peak {0} at {1}".format(n, peak))
blend = scarlet.Blend(sources, images, bg_rms=bg_rms)
return blend, rejected_sources
def get_scar_model(self):
import scarlet
import scarlet.constraint as sc
im, psf_im, coords, dims, dx1, dy1, noise = self.sim()
bg_rms = self.sim['Image']['Bgrms']
mode = self.sim['Mode']
bg = np.zeros((len(im)))
bg += bg_rms
#psf_constraints = (sc.SimpleConstraint())
#source_constraints = ()#sc.SimpleConstraint(),sc.DirectSymmetryConstraint()) #sc.DirectMonotonicityConstraint(use_nearest=False)
config = scarlet.Config(source_sizes=[25])
psf_dims = np.shape(psf_im)
psf_im3d = psf_im.reshape((1, psf_dims[0], psf_dims[1]))
psfs = np.zeros((len(im), psf_dims[0], psf_dims[1]))
psfs += psf_im3d
#target_psf = scarlet.psf_match.fit_target_psf(psfs,
# scarlet.psf_match.gaussian)
#diff_kernels, psf_blend = scarlet.psf_match.build_diff_kernels(psfs,
# target_psf, constraints = None)
sources = [
scarlet.ExtendedSource(coord,
im,
bg_rms=bg,
psf=None,
config=config) for coord in coords
]
#config = scarlet.Config(edge_flux_thresh=0.05)
blend = scarlet.Blend(sources)
blend.set_data(im, bg_rms=bg, config=config)
blend.fit(10000, e_rel=1e-3)
model = blend.get_model()
mod1 = blend.get_model(0)
#mod2 = blend.get_model(1)
cen_mod = sources[0].get_model()
#neigh_mod = sources[1].get_model()
#psf_model = psf_blend.get_model()
#steps_used = blend.it
cen_cen_pos = blend[0][0].center
#return im,psf_im,model,mod1,mod2,cen_mod,neigh_mod,coords,dx1,dy1,noise
return im, psf_im, model, mod1, cen_mod, coords, dx1, dy1, noise, cen_cen_pos, psfs
def get_scar_model(self):
import scarlet
im, psf_im, coords, dims, dx1, dy1, noise, sep_coords = self.sim()
bg_rms = self.sim['Image']['Bgrms']
mode = self.sim['Mode']
#constraints = {"S": None, "m": {'use_nearest': False}, "+": None}
#constraints['l0'] = bg_rms
constraint = (sc.SimpleConstraint())
# & sc.MonotonicityConstraint(use_nearest=True))
config = scarlet.Config(source_sizes=[25])
psf_dims = np.shape(psf_im)
psf_im3d = psf_im.reshape((1, psf_dims[0], psf_dims[1]))
target_psf = scarlet.psf_match.fit_target_psf(
psf_im3d, scarlet.psf_match.gaussian)
diff_kernels, psf_blend = scarlet.psf_match.build_diff_kernels(
psf_im3d, target_psf, constraints=constraint.copy())
sources = [
scarlet.ExtendedSource(coord,
im, [bg_rms],
psf=diff_kernels,
config=config) for coord in coords
]
#sources = [scarlet.ExtendedSource(coord, im, [bg_rms]) for coord in coords]
#scarlet.ExtendedSource.shift_center=0.0
#config = scarlet.Config(edge_flux_thresh=0.05)
blend = scarlet.Blend(sources, im, bg_rms=[bg_rms], config=config)
blend.fit(10000, e_rel=1e-3)
model = blend.get_model()
mod1 = blend.get_model(m=0)
mod2 = blend.get_model(m=1)
cen_mod = sources[0].get_model()
neigh_mod = sources[1].get_model()
#steps_used = blend.it
return im, psf_im, model, mod1, mod2, cen_mod, neigh_mod, coords, dx1, dy1, noise, sep_coords
def test_init_extended(self):
shape = (5, 11, 15)
B, Ny, Nx = shape
x = np.linspace(-2, 2, 5)
y = np.linspace(-2, 2, 5)
x, y = np.meshgrid(x, y)
r = np.sqrt(x**2 + y**2)
true_sed = np.arange(B)
true_morph = np.zeros(shape[1:])
skycoord = (np.array(true_morph.shape) - 1) // 2
cy, cx = skycoord
true_morph[cy - 2:cy + 3, cx - 2:cx + 3] = 3 - r
morph = true_morph.copy()
morph[5, 3] = 10
# Test function
images = true_sed[:, None, None] * morph[None, :, :]
frame = scarlet.Frame(shape)
observation = scarlet.Observation(images).match(frame)
bg_rms = np.ones_like(true_sed) * 1e-3
sed, morph = scarlet.source.init_extended_source(
skycoord, frame, observation, bg_rms)
assert_array_equal(sed / 3, true_sed)
assert_almost_equal(morph * 3, true_morph)
# Test ExtendedSource.__init__
src = scarlet.ExtendedSource(frame, skycoord, observation, bg_rms)
assert_array_equal(src.pixel_center, skycoord)
assert src.symmetric is True
assert src.monotonic is True
assert src.center_step == 5
assert src.delay_thresh == 10
assert_array_equal(src.sed / 3, true_sed)
assert_almost_equal(src.morph * 3, true_morph)
# Test monotonicity
morph = true_morph.copy()
morph[5, 5] = 2
images = true_sed[:, None, None] * morph[None, :, :]
frame = scarlet.Frame(shape)
observation = scarlet.Observation(images).match(frame)
bg_rms = np.ones_like(true_sed) * 1e-3
sed, morph = scarlet.source.init_extended_source(skycoord,
frame,
observation,
bg_rms,
symmetric=False)
_morph = true_morph.copy()
_morph[5, 5] = 1.5816233815926433
assert_array_equal(sed / 3, true_sed)
assert_almost_equal(morph * 3, _morph)
# Test symmetry
morph = true_morph.copy()
morph[5, 5] = 2
images = true_sed[:, None, None] * morph[None, :, :]
frame = scarlet.Frame(shape)
observation = scarlet.Observation(images).match(frame)
bg_rms = np.ones_like(true_sed) * 1e-3
sed, morph = scarlet.source.init_extended_source(skycoord,
frame,
observation,
bg_rms,
monotonic=False)
assert_array_equal(sed / 3, true_sed)
assert_almost_equal(morph * 3, true_morph)