def old(self):
"""
This function ...
:return:
"""
exit()
# FWHM of all the images
fwhm = 11.18 * u("arcsec")
fwhm_pix = (fwhm / frame.average_pixelscale).to("pix").value
sigma = fwhm_pix * statistics.fwhm_to_sigma
# Get the center pixel of the galaxy
parameters_path = fs.join(components_path, "parameters.dat")
parameters = load_parameters(parameters_path)
center = parameters.center.to_pixel(frame.wcs)
# Create a source around the galaxy center
ellipse = PixelEllipseRegion(center, 20.0*sigma)
source = Source.from_ellipse(model_residual, ellipse, 1.5)
source.estimate_background("polynomial")
source.plot()
position = source.center
model = source.subtracted.fit_model(position, "Gaussian")
rel_center = center - Extent(source.x_min, source.y_min)
rel_model = fitting.shifted_model(model, -source.cutout.x_min, -source.cutout.y_min)
plotting.plot_peak_model(source.cutout, rel_center.x, rel_center.y, rel_model)
model_fwhm_pix = fitting.fwhm(model)
model_fwhm = (model_fwhm_pix * frame.average_pixelscale).to("arcsec")
print("Model FWHM: ", model_fwhm)
evaluated_model = source.cutout.evaluate_model(model)
all_residual = Frame(np.copy(model_residual))
all_residual[source.y_slice, source.x_slice] -= evaluated_model
all_residual.saveto(fs.join(residuals_path, "all_residual.fits"))
model = Gaussian2D(amplitude=0.0087509425805, x_mean=center.x, y_mean=center.y, x_stddev=sigma, y_stddev=sigma)
rel_model = fitting.shifted_model(model, -source.cutout.x_min, -source.cutout.y_min)
plotting.plot_peak_model(source.cutout, rel_center.x, rel_center.y, rel_model)
evaluated_model = source.cutout.evaluate_model(model)
all_residual2 = Frame(np.copy(model_residual))
all_residual2[source.y_slice, source.x_slice] -= evaluated_model
all_residual2.saveto(fs.join(residuals_path, "all_residual2.fits"))
class SkyTest(TestImplementation):
"""
This class ...
"""
def __init__(self, *args, **kwargs):
"""
The constructor ...
:param kwargs:
"""
# Call the constructor of the base class
super(SkyTest, self).__init__(*args, **kwargs)
# FRAME COMPONENTS
# The sources map
self.sources = None
# The noise map
self.noise = None
# The galaxy
self.galaxy = None
# Real sky frames
self.constant_sky = None
self.gradient_sky = None
# TABLES
self.source_table = None
# MASKS
# The sources mask
self.sources_mask = None
# The rotation mask
self.rotation_mask = None
# The galaxy
self.galaxy_region = None
# SKY ESTIMATION
# Photutils Background2D object
self.photutils_bkg = None
# Sky reference estimation
self.reference_sky = None
# Path
self.subtraction_path = None
# The sky subtractor
self.subtractor = None
# STATISTICS
# The statistics
self.statistics = Map()
# -----------------------------------------------------------------
def run(self, **kwargs):
"""
This function ...
:param kwargs:
:return:
"""
# 1. Call the setup function
self.setup(**kwargs)
# 2. Make rotation mask
self.make_rotation_mask()
# 3. Generate the sources
self.make_sources()
# 4. Make noise
self.make_noise()
# 5. Make galaxy
self.make_galaxy()
# 6. Make sky
self.make_sky()
# 7. Mask sources
self.mask_sources()
# 8. Statistics
self.calculate_statistics()
# 9. Reference
self.reference()
# 10. Subtract
self.subtract()
# 11. Write
self.write()
# 12. Plot
self.plot()
# -----------------------------------------------------------------
def setup(self, **kwargs):
"""
This function ...
:param kwargs:
:return:
"""
# Call the setup function of the base class
super(SkyTest, self).setup(**kwargs)
# Set the subtraction path
self.subtraction_path = fs.create_directory_in(self.path,
"subtraction")
# -----------------------------------------------------------------
def make_rotation_mask(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making rotation mask ...")
# Rotate
if self.config.rotate:
frame = Frame.zeros(self.config.shape)
self.rotation_mask = frame.rotate(self.config.rotation_angle)
else:
self.rotation_mask = Mask.empty(self.config.shape[1],
self.config.shape[0])
# -----------------------------------------------------------------
@property
def effective_rotation_angle(self):
"""
THis function ...
:return:
"""
if self.config.rotate: return self.config.rotation_angle
else: return Angle(0.0, "deg")
# -----------------------------------------------------------------
@property
def shape(self):
"""
THis function ...
:return:
"""
return self.rotation_mask.shape
# -----------------------------------------------------------------
@property
def xsize(self):
"""
This function ...
:return:
"""
return self.rotation_mask.xsize
# -----------------------------------------------------------------
@property
def ysize(self):
"""
This function ...
:return:
"""
return self.rotation_mask.ysize
# -----------------------------------------------------------------
@property
def sources_sigma(self):
"""
This function ...
:return:
"""
return self.config.fwhm * statistics.fwhm_to_sigma
# -----------------------------------------------------------------
def make_sources(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making the sources ...")
flux_range = [self.config.flux_range.min, self.config.flux_range.max]
xmean_range = [0, self.config.shape[1]]
ymean_range = [0, self.config.shape[0]]
# Ranges of sigma
xstddev_range = [self.sources_sigma, self.sources_sigma]
ystddev_range = [self.sources_sigma, self.sources_sigma]
table = make_random_gaussians(self.config.nsources,
flux_range,
xmean_range,
ymean_range,
xstddev_range,
ystddev_range,
random_state=12345)
self.source_table = table
data = make_gaussian_sources(self.config.shape, table)
self.sources = Frame(data)
# mask
self.sources[self.rotation_mask] = 0.0
if self.config.plot: plotting.plot_box(self.sources, title="sources")
# -----------------------------------------------------------------
def make_noise(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making noise map ...")
# Make noise
data = make_noise_image(self.config.shape,
type='gaussian',
mean=0.,
stddev=self.config.noise_stddev,
random_state=12345)
self.noise = Frame(data)
# Mask
self.noise[self.rotation_mask] = 0.0
# Plot
#if self.config.plot: plotting.plot_difference(self.frame, self.real_sky, title="original")
if self.config.plot: plotting.plot_box(self.noise, title="noise")
# -----------------------------------------------------------------
def make_galaxy(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Adding smooth galaxy source ...")
effective_radius = self.config.galaxy_effective_radius
effective_galaxy_angle = self.config.galaxy_angle + self.effective_rotation_angle
axial_ratio = self.config.galaxy_axial_ratio
angle_deg = effective_galaxy_angle.to("deg").value
# Produce guess values
initial_sersic_amplitude = self.config.galaxy_central_flux
initial_sersic_r_eff = effective_radius
initial_sersic_n = self.config.galaxy_sersic_index
initial_sersic_x_0 = self.config.galaxy_position.x
initial_sersic_y_0 = self.config.galaxy_position.y
initial_sersic_ellip = (axial_ratio - 1.0) / axial_ratio
initial_sersic_theta = np.deg2rad(angle_deg)
# Produce sersic model from guess parameters, for time trials
sersic_x, sersic_y = np.meshgrid(np.arange(self.xsize),
np.arange(self.ysize))
sersic_model = Sersic2D(amplitude=initial_sersic_amplitude,
r_eff=initial_sersic_r_eff,
n=initial_sersic_n,
x_0=initial_sersic_x_0,
y_0=initial_sersic_y_0,
ellip=initial_sersic_ellip,
theta=initial_sersic_theta)
sersic_map = sersic_model(sersic_x, sersic_y)
# Set the galaxy frame
self.galaxy = Frame(sersic_map)
# Mask
self.galaxy[self.rotation_mask] = 0.0
limit_radius = self.config.galaxy_relative_asymptotic_radius * effective_radius
# Create galaxy region
galaxy_center = PixelCoordinate(initial_sersic_x_0, initial_sersic_y_0)
galaxy_radius = PixelStretch(limit_radius, limit_radius / axial_ratio)
self.galaxy_region = PixelEllipseRegion(galaxy_center, galaxy_radius,
effective_galaxy_angle)
# Set galaxy map zero outside certain radius
self.galaxy[self.galaxy_mask.inverse()] = 0.0
# Plot
if self.config.plot: plotting.plot_box(self.galaxy, title="galaxy")
# -----------------------------------------------------------------
def make_sky(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making sky ...")
# make constant sky
self.make_constant_sky()
# Make gradient sky
self.make_gradient_sky()
# -----------------------------------------------------------------
def make_constant_sky(self):
"""
This function ..
:return:
"""
# Inform the user
log.info("Making constant sky ...")
self.constant_sky = Frame.filled_like(self.sources,
self.config.constant_sky)
# Mask
self.constant_sky[self.rotation_mask] = 0.0
# Plot
# -----------------------------------------------------------------
def make_gradient_sky(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making gradient sky ...")
y, x = np.mgrid[:self.ysize, :self.xsize]
# Create gradient sky
self.gradient_sky = Frame(x * y / 5000.)
# Mask padded
self.gradient_sky[self.rotation_mask] = 0.0
# Plot
#if self.config.plot: plotting.plot_difference(self.frame, self.real_sky, title="frame with background")
if self.config.plot:
plotting.plot_box(self.gradient_sky, title="gradient sky")
# -----------------------------------------------------------------
@lazyproperty
def sky(self):
"""
This function ...
:return:
"""
return self.constant_sky + self.gradient_sky
# -----------------------------------------------------------------
@lazyproperty
def frame(self):
"""
This fucntion ...
:return:
"""
return self.sources_with_galaxy_and_noise + self.sky
# -----------------------------------------------------------------
@lazyproperty
def sources_with_noise(self):
"""
This function ...
:return:
"""
return self.noise + self.sources
# -----------------------------------------------------------------
@lazyproperty
def sources_with_galaxy_and_noise(self):
"""
This function ...
:return:
"""
return self.sources_with_noise + self.galaxy
# -----------------------------------------------------------------
def mask_sources(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Masking sources ...")
# Create sources mask
mask = make_source_mask(self.sources_with_noise.data,
snr=2,
npixels=5,
dilate_size=11,
mask=self.rotation_mask)
self.sources_mask = Mask(mask)
# Plot
if self.config.plot:
plotting.plot_mask(self.sources_mask, title="sources mask")
# -----------------------------------------------------------------
def calculate_statistics(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Calculating statistics ...")
# Calculate statistics no sigma clipping
self.calculate_statistics_no_clipping()
# Calculate statistics clipping
self.calculate_statistics_clipping()
# Calculate statistics masked sources
self.calculate_statistics_masked()
# -----------------------------------------------------------------
def calculate_statistics_no_clipping(self):
"""
This function ...
:return:
"""
# Compress (remove masked values)
flattened = np.ma.array(self.sources_with_noise.data,
mask=self.rotation_mask.data).compressed()
median = np.median(flattened)
biweight_loc = biweight_location(flattened)
biweight_midvar = biweight_midvariance(flattened)
median_absolute_deviation = mad_std(flattened)
#print("median", median)
#print("biweigth_loc", biweight_loc)
#print("biweight_midvar", biweight_midvar)
#print("median_absolute_deviation", median_absolute_deviation)
self.statistics.no_clipping = Map()
self.statistics.no_clipping.median = median
self.statistics.no_clipping.biweight_loc = biweight_loc
self.statistics.no_clipping.biweight_midvar = biweight_midvar
self.statistics.no_clipping.median_absolute_deviation = median_absolute_deviation
# SAME RESULTS:
# median = np.median(self.original_frame)
# biweight_loc = biweight_location(self.original_frame)
# biweight_midvar = biweight_midvariance(self.original_frame)
# median_absolute_deviation = mad_std(self.original_frame)
# print("median", median)
# print("biweigth_loc", biweight_loc)
# print("biweight_midvar", biweight_midvar)
# print("median_absolute_deviation", median_absolute_deviation)
# -----------------------------------------------------------------
def calculate_statistics_clipping(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Sigma-clipping ...")
# Sigma clip
mean, median, std = sigma_clipped_stats(self.sources_with_noise.data,
sigma=3.0,
iters=5,
mask=self.rotation_mask)
#print("sigma-clip mean:", mean)
#print("sigma-clip median:", median)
#print("sigma-clip std:", std)
self.statistics.clipping = Map()
self.statistics.clipping.mean = mean
self.statistics.clipping.median = median
self.statistics.clipping.std = std
# -----------------------------------------------------------------
def calculate_statistics_masked(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Calculating statistics with sources masked ...")
# Statistics
mean, median, std = sigma_clipped_stats(self.sources_with_noise.data,
sigma=3.0,
mask=self.total_mask.data,
iters=5)
#print("sigma-clip mean after source masking:", mean)
#print("sigma-clip median after source masking:", median)
#print("sigma_clip std after source masking:", std)
# Set the statistics
self.statistics.masked = Map()
self.statistics.masked.mean = mean
self.statistics.masked.median = median
self.statistics.masked.std = std
# -----------------------------------------------------------------
@lazyproperty
def total_mask(self):
"""
This function ...
:return:
"""
return self.sources_and_rotation_mask + self.galaxy_mask
# -----------------------------------------------------------------
@lazyproperty
def sources_and_rotation_mask(self):
"""
This function ...
:return:
"""
return self.sources_mask + self.rotation_mask
# -----------------------------------------------------------------
@lazyproperty
def galaxy_mask(self):
"""
This function ...
:return:
"""
# Make mask
return self.galaxy_region.to_mask(self.xsize, self.ysize)
# -----------------------------------------------------------------
@lazyproperty
def reference_subtracted(self):
"""
This function ...
:return:
"""
return self.frame - self.reference_sky
# -----------------------------------------------------------------
@lazyproperty
def subtracted(self):
"""
This function ...
:return:
"""
return self.frame - self.estimated_sky
# -----------------------------------------------------------------
@property
def aperture_radius(self):
"""
This function ...
:return:
"""
return self.config.fwhm * self.config.aperture_fwhm_factor
# -----------------------------------------------------------------
@property
def aperture_diameter(self):
"""
This function ...
:return:
"""
return 2.0 * self.aperture_radius
# -----------------------------------------------------------------
def reference(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Estimating background with photutils ...")
# Plot total mask
if self.config.plot:
plotting.plot_mask(self.total_mask, title="total mask")
integer_aperture_radius = int(math.ceil(self.aperture_radius))
box_shape = (integer_aperture_radius, integer_aperture_radius)
filter_size = (3, 3)
# Estimate the background
sigma_clip = SigmaClip(sigma=3., iters=10)
#bkg_estimator = MedianBackground()
bkg_estimator = SExtractorBackground()
bkg = Background2D(self.frame.data,
box_shape,
filter_size=filter_size,
sigma_clip=sigma_clip,
bkg_estimator=bkg_estimator,
mask=self.total_mask.data)
# Statistics
#print("median background", bkg.background_median)
#print("rms background", bkg.background_rms_median)
self.statistics.reference = Map()
self.statistics.reference.median = bkg.background_median
self.statistics.reference.rms = bkg.background_rms_median
# Plot
if self.config.plot:
plotting.plot_box(bkg.background,
title="background from photutils")
# Set the sky
self.reference_sky = Frame(bkg.background)
# Set bkg object
self.photutils_bkg = bkg
# Plot
if self.config.plot:
plotting.plot_box(self.reference_sky, title="reference sky")
# -----------------------------------------------------------------
def subtract(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Subtracting the sky ...")
# Settings
settings = dict()
settings["estimation"] = dict()
settings["estimation"]["method"] = "photutils"
settings["estimation"]["aperture_radius"] = self.aperture_radius
settings["write"] = True
#settings["estimation"]["finishing_step"] = "polynomial"
#settings["estimation"]["polynomial_degree"] = self.config.polynomial_degree
#settings["estimation"]["fill_method"] = "cubic"
settings["plot"] = True
# Input
input_dict = dict()
# Set input
input_dict["frame"] = self.frame
input_dict["principal_shape"] = self.galaxy_region
input_dict["sources_mask"] = self.sources_mask
input_dict["extra_mask"] = self.rotation_mask
# Create command
command = Command(
"subtract_sky",
"subtract the sky from an artificially created image",
settings,
input_dict,
cwd=self.subtraction_path)
# Run the subtraction
self.subtractor = self.run_command(command)
# -----------------------------------------------------------------
@property
def estimated_sky(self):
"""
This function ...
:return:
"""
return self.subtractor.sky_frame
# -----------------------------------------------------------------
@lazyproperty
def subtracted(self):
"""
This function ...
:return:
"""
return self.frame - self.estimated_sky
# -----------------------------------------------------------------
@lazyproperty
def sky_residual(self):
"""
This function ...
:return:
"""
return self.estimated_sky - self.sky
# -----------------------------------------------------------------
def write(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing ...")
# Write the sources with noise
self.write_sources()
# Write the frame
self.write_frame()
# Write real sky map
self.write_real_sky()
# Write sources mask
self.write_sources_mask()
# Write galaxy mask
self.write_galaxy_mask()
# Write reference sky
self.write_reference_sky()
# Write estiamted sky
self.write_estimated_sky()
# Write residuals
self.write_residual()
# Write the statistics
self.write_statistics()
# -----------------------------------------------------------------
def write_sources(self):
"""
THis function ...
:return:
"""
# Inform the user
log.info("Writing the sources frame with noise ...")
# Determine the path
path = fs.join(self.path, "sources_noise.fits")
# Save the frame
self.sources_with_noise.saveto(path)
# -----------------------------------------------------------------
def write_frame(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the frame ...")
# Determine the path
path = fs.join(self.path, "frame.fits")
# SAve the frame
self.frame.saveto(path)
# -----------------------------------------------------------------
def write_real_sky(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the real sky map ...")
# Determine the path
path = fs.join(self.path, "real_sky.fits")
# Save the map
self.sky.saveto(path)
# -----------------------------------------------------------------
def write_sources_mask(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the sources mask ...")
# Determine the path
path = fs.join(self.path, "sources_mask.fits")
# Save
self.sources_mask.saveto(path)
# -----------------------------------------------------------------
def write_galaxy_mask(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the galaxy mask ...")
# Determine the path
path = fs.join(self.path, "galaxy_mask.fits")
# Save
self.galaxy_mask.saveto(path)
# -----------------------------------------------------------------
def write_reference_sky(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the reference sky map ...")
# Determine the path
path = fs.join(self.path, "reference_sky.fits")
# Save
self.reference_sky.saveto(path)
# -----------------------------------------------------------------
def write_estimated_sky(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the estimated sky map ...")
# Determine the path
path = fs.join(self.path, "estimated_sky.fits")
# Save
self.estimated_sky.saveto(path)
# -----------------------------------------------------------------
def write_subtracted(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the sky-subtracted frame ...")
# Determine the path
path = fs.join(self.path, "subtracted.fits")
# Save
self.subtracted.saveto(path)
# -----------------------------------------------------------------
def write_residual(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the residual map ...")
# Determine the path
path = fs.join(self.path, "residual.fits")
# Save
self.sky_residual.saveto(path)
# -----------------------------------------------------------------
def write_statistics(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the statistics ...")
# Determine the path
path = fs.join(self.path, "statistics.dat")
# Write
save_mapping(path, self.statistics)
# -----------------------------------------------------------------
def plot(self):
"""
This function ...
:return:
"""
# Inofmrthe user
log.info("Plotting ...")
# Plot meshes
if self.config.plotting.meshes: self.plot_meshes()
# -----------------------------------------------------------------
def plot_meshes(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Plotting the meshes ...")
# Plot meshes
plt.figure()
norm = ImageNormalize(stretch=SqrtStretch())
plt.imshow(self.frame, origin='lower', cmap='Greys_r', norm=norm)
self.photutils_bkg.plot_meshes(outlines=True, color='#1f77b4')
plt.show()
# -----------------------------------------------------------------
# Load the image
frame = Frame.from_file(arguments.image)
# Load the region
region_name = os.path.splitext(os.path.basename(arguments.region))[0]
region = load_as_pixel_region_list(arguments.region, frame.wcs)
# Create the mask
mask = region.to_mask(x_size=frame.xsize, y_size=frame.ysize)
# Calculate the inverse, if requested
if arguments.invert: mask = mask.inverse()
# -----------------------------------------------------------------
if arguments.data:
new_frame = frame
frame[mask] = arguments.value
# Create a frame for the total mask
else: new_frame = Frame(mask.astype(int))
# Write out the new frame
new_frame.saveto(region_name + ".fits")
# -----------------------------------------------------------------
class SkyTest(TestImplementation):
"""
This class ...
"""
def __init__(self, *args, **kwargs):
"""
The constructor ...
:param kwargs:
"""
# Call the constructor of the base class
super(SkyTest, self).__init__(*args, **kwargs)
# FRAME COMPONENTS
# The sources map
self.sources = None
# The noise map
self.noise = None
# The galaxy
self.galaxy = None
# Real sky frames
self.constant_sky = None
self.gradient_sky = None
# TABLES
self.source_table = None
# MASKS
# The sources mask
self.sources_mask = None
# The rotation mask
self.rotation_mask = None
# The galaxy
self.galaxy_region = None
# SKY ESTIMATION
# Photutils Background2D object
self.photutils_bkg = None
# Sky reference estimation
self.reference_sky = None
# Path
self.subtraction_path = None
# The sky subtractor
self.subtractor = None
# STATISTICS
# The statistics
self.statistics = Map()
# -----------------------------------------------------------------
def _run(self, **kwargs):
"""
This function ...
:param kwargs:
:return:
"""
# 2. Make rotation mask
self.make_rotation_mask()
# 3. Generate the sources
self.make_sources()
# 4. Make noise
self.make_noise()
# 5. Make galaxy
self.make_galaxy()
# 6. Make sky
self.make_sky()
# 7. Mask sources
self.mask_sources()
# 8. Statistics
self.calculate_statistics()
# 9. Reference
self.reference()
# 10. Subtract
self.subtract()
# 11. Write
self.write()
# 12. Plot
self.plot()
# -----------------------------------------------------------------
def setup(self, **kwargs):
"""
This function ...
:param kwargs:
:return:
"""
# Call the setup function of the base class
super(SkyTest, self).setup(**kwargs)
# Set the subtraction path
self.subtraction_path = fs.create_directory_in(self.path, "subtraction")
# -----------------------------------------------------------------
def make_rotation_mask(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making rotation mask ...")
# Rotate
if self.config.rotate:
frame = Frame.zeros(self.config.shape)
self.rotation_mask = frame.rotate(self.config.rotation_angle)
else: self.rotation_mask = Mask.empty(self.config.shape[1], self.config.shape[0])
# -----------------------------------------------------------------
@property
def effective_rotation_angle(self):
"""
THis function ...
:return:
"""
if self.config.rotate: return self.config.rotation_angle
else: return Angle(0.0, "deg")
# -----------------------------------------------------------------
@property
def shape(self):
"""
THis function ...
:return:
"""
return self.rotation_mask.shape
# -----------------------------------------------------------------
@property
def xsize(self):
"""
This function ...
:return:
"""
return self.rotation_mask.xsize
# -----------------------------------------------------------------
@property
def ysize(self):
"""
This function ...
:return:
"""
return self.rotation_mask.ysize
# -----------------------------------------------------------------
@property
def sources_sigma(self):
"""
This function ...
:return:
"""
return self.config.fwhm * statistics.fwhm_to_sigma
# -----------------------------------------------------------------
def make_sources(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making the sources ...")
flux_range = [self.config.flux_range.min, self.config.flux_range.max]
xmean_range = [0, self.config.shape[1]]
ymean_range = [0, self.config.shape[0]]
# Ranges of sigma
xstddev_range = [self.sources_sigma, self.sources_sigma]
ystddev_range = [self.sources_sigma, self.sources_sigma]
table = make_random_gaussians(self.config.nsources, flux_range, xmean_range,
ymean_range, xstddev_range,
ystddev_range, random_state=12345)
self.source_table = table
data = make_gaussian_sources(self.config.shape, table)
self.sources = Frame(data)
# mask
self.sources[self.rotation_mask] = 0.0
if self.config.plot: plotting.plot_box(self.sources, title="sources")
# -----------------------------------------------------------------
def make_noise(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making noise map ...")
# Make noise
data = make_noise_image(self.config.shape, type='gaussian', mean=0., stddev=self.config.noise_stddev, random_state=12345)
self.noise = Frame(data)
# Mask
self.noise[self.rotation_mask] = 0.0
# Plot
#if self.config.plot: plotting.plot_difference(self.frame, self.real_sky, title="original")
if self.config.plot: plotting.plot_box(self.noise, title="noise")
# -----------------------------------------------------------------
def make_galaxy(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Adding smooth galaxy source ...")
effective_radius = self.config.galaxy_effective_radius
effective_galaxy_angle = self.config.galaxy_angle + self.effective_rotation_angle
axial_ratio = self.config.galaxy_axial_ratio
angle_deg = effective_galaxy_angle.to("deg").value
# Produce guess values
initial_sersic_amplitude = self.config.galaxy_central_flux
initial_sersic_r_eff = effective_radius
initial_sersic_n = self.config.galaxy_sersic_index
initial_sersic_x_0 = self.config.galaxy_position.x
initial_sersic_y_0 = self.config.galaxy_position.y
initial_sersic_ellip = (axial_ratio - 1.0) / axial_ratio
initial_sersic_theta = np.deg2rad(angle_deg)
# Produce sersic model from guess parameters, for time trials
sersic_x, sersic_y = np.meshgrid(np.arange(self.xsize), np.arange(self.ysize))
sersic_model = Sersic2D(amplitude=initial_sersic_amplitude, r_eff=initial_sersic_r_eff,
n=initial_sersic_n, x_0=initial_sersic_x_0,
y_0=initial_sersic_y_0, ellip=initial_sersic_ellip,
theta=initial_sersic_theta)
sersic_map = sersic_model(sersic_x, sersic_y)
# Set the galaxy frame
self.galaxy = Frame(sersic_map)
# Mask
self.galaxy[self.rotation_mask] = 0.0
limit_radius = self.config.galaxy_relative_asymptotic_radius * effective_radius
# Create galaxy region
galaxy_center = PixelCoordinate(initial_sersic_x_0, initial_sersic_y_0)
galaxy_radius = PixelStretch(limit_radius, limit_radius / axial_ratio)
self.galaxy_region = PixelEllipseRegion(galaxy_center, galaxy_radius, effective_galaxy_angle)
# Set galaxy map zero outside certain radius
self.galaxy[self.galaxy_mask.inverse()] = 0.0
# Plot
if self.config.plot: plotting.plot_box(self.galaxy, title="galaxy")
# -----------------------------------------------------------------
def make_sky(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making sky ...")
# make constant sky
self.make_constant_sky()
# Make gradient sky
self.make_gradient_sky()
# -----------------------------------------------------------------
def make_constant_sky(self):
"""
This function ..
:return:
"""
# Inform the user
log.info("Making constant sky ...")
self.constant_sky = Frame.filled_like(self.sources, self.config.constant_sky)
# Mask
self.constant_sky[self.rotation_mask] = 0.0
# Plot
# -----------------------------------------------------------------
def make_gradient_sky(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making gradient sky ...")
y, x = np.mgrid[:self.ysize, :self.xsize]
# Create gradient sky
self.gradient_sky = Frame(x * y / 5000.)
# Mask padded
self.gradient_sky[self.rotation_mask] = 0.0
# Plot
#if self.config.plot: plotting.plot_difference(self.frame, self.real_sky, title="frame with background")
if self.config.plot: plotting.plot_box(self.gradient_sky, title="gradient sky")
# -----------------------------------------------------------------
@lazyproperty
def sky(self):
"""
This function ...
:return:
"""
return self.constant_sky + self.gradient_sky
# -----------------------------------------------------------------
@lazyproperty
def frame(self):
"""
This fucntion ...
:return:
"""
return self.sources_with_galaxy_and_noise + self.sky
# -----------------------------------------------------------------
@lazyproperty
def sources_with_noise(self):
"""
This function ...
:return:
"""
return self.noise + self.sources
# -----------------------------------------------------------------
@lazyproperty
def sources_with_galaxy_and_noise(self):
"""
This function ...
:return:
"""
return self.sources_with_noise + self.galaxy
# -----------------------------------------------------------------
def mask_sources(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Masking sources ...")
# Create sources mask
mask = make_source_mask(self.sources_with_noise.data, snr=2, npixels=5, dilate_size=11, mask=self.rotation_mask)
self.sources_mask = Mask(mask)
# Plot
if self.config.plot: plotting.plot_mask(self.sources_mask, title="sources mask")
# -----------------------------------------------------------------
def calculate_statistics(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Calculating statistics ...")
# Calculate statistics no sigma clipping
self.calculate_statistics_no_clipping()
# Calculate statistics clipping
self.calculate_statistics_clipping()
# Calculate statistics masked sources
self.calculate_statistics_masked()
# -----------------------------------------------------------------
def calculate_statistics_no_clipping(self):
"""
This function ...
:return:
"""
# Compress (remove masked values)
flattened = np.ma.array(self.sources_with_noise.data, mask=self.rotation_mask.data).compressed()
median = np.median(flattened)
biweight_loc = biweight_location(flattened)
biweight_midvar = biweight_midvariance(flattened)
median_absolute_deviation = mad_std(flattened)
#print("median", median)
#print("biweigth_loc", biweight_loc)
#print("biweight_midvar", biweight_midvar)
#print("median_absolute_deviation", median_absolute_deviation)
self.statistics.no_clipping = Map()
self.statistics.no_clipping.median = median
self.statistics.no_clipping.biweight_loc = biweight_loc
self.statistics.no_clipping.biweight_midvar = biweight_midvar
self.statistics.no_clipping.median_absolute_deviation = median_absolute_deviation
# SAME RESULTS:
# median = np.median(self.original_frame)
# biweight_loc = biweight_location(self.original_frame)
# biweight_midvar = biweight_midvariance(self.original_frame)
# median_absolute_deviation = mad_std(self.original_frame)
# print("median", median)
# print("biweigth_loc", biweight_loc)
# print("biweight_midvar", biweight_midvar)
# print("median_absolute_deviation", median_absolute_deviation)
# -----------------------------------------------------------------
def calculate_statistics_clipping(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Sigma-clipping ...")
# Sigma clip
mean, median, std = sigma_clipped_stats(self.sources_with_noise.data, sigma=3.0, iters=5,
mask=self.rotation_mask)
#print("sigma-clip mean:", mean)
#print("sigma-clip median:", median)
#print("sigma-clip std:", std)
self.statistics.clipping = Map()
self.statistics.clipping.mean = mean
self.statistics.clipping.median = median
self.statistics.clipping.std = std
# -----------------------------------------------------------------
def calculate_statistics_masked(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Calculating statistics with sources masked ...")
# Statistics
mean, median, std = sigma_clipped_stats(self.sources_with_noise.data, sigma=3.0, mask=self.total_mask.data, iters=5)
#print("sigma-clip mean after source masking:", mean)
#print("sigma-clip median after source masking:", median)
#print("sigma_clip std after source masking:", std)
# Set the statistics
self.statistics.masked = Map()
self.statistics.masked.mean = mean
self.statistics.masked.median = median
self.statistics.masked.std = std
# -----------------------------------------------------------------
@lazyproperty
def total_mask(self):
"""
This function ...
:return:
"""
return self.sources_and_rotation_mask + self.galaxy_mask
# -----------------------------------------------------------------
@lazyproperty
def sources_and_rotation_mask(self):
"""
This function ...
:return:
"""
return self.sources_mask + self.rotation_mask
# -----------------------------------------------------------------
@lazyproperty
def galaxy_mask(self):
"""
This function ...
:return:
"""
# Make mask
return self.galaxy_region.to_mask(self.xsize, self.ysize)
# -----------------------------------------------------------------
@lazyproperty
def reference_subtracted(self):
"""
This function ...
:return:
"""
return self.frame - self.reference_sky
# -----------------------------------------------------------------
@lazyproperty
def subtracted(self):
"""
This function ...
:return:
"""
return self.frame - self.estimated_sky
# -----------------------------------------------------------------
@property
def aperture_radius(self):
"""
This function ...
:return:
"""
return self.config.fwhm * self.config.aperture_fwhm_factor
# -----------------------------------------------------------------
@property
def aperture_diameter(self):
"""
This function ...
:return:
"""
return 2.0 * self.aperture_radius
# -----------------------------------------------------------------
def reference(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Estimating background with photutils ...")
# Plot total mask
if self.config.plot: plotting.plot_mask(self.total_mask, title="total mask")
integer_aperture_radius = int(math.ceil(self.aperture_radius))
box_shape = (integer_aperture_radius, integer_aperture_radius)
filter_size = (3, 3)
# Estimate the background
sigma_clip = SigmaClip(sigma=3., iters=10)
#bkg_estimator = MedianBackground()
bkg_estimator = SExtractorBackground()
bkg = Background2D(self.frame.data, box_shape, filter_size=filter_size, sigma_clip=sigma_clip,
bkg_estimator=bkg_estimator, mask=self.total_mask.data)
# Statistics
#print("median background", bkg.background_median)
#print("rms background", bkg.background_rms_median)
self.statistics.reference = Map()
self.statistics.reference.median = bkg.background_median
self.statistics.reference.rms = bkg.background_rms_median
# Plot
if self.config.plot: plotting.plot_box(bkg.background, title="background from photutils")
# Set the sky
self.reference_sky = Frame(bkg.background)
# Set bkg object
self.photutils_bkg = bkg
# Plot
if self.config.plot: plotting.plot_box(self.reference_sky, title="reference sky")
# -----------------------------------------------------------------
def subtract(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Subtracting the sky ...")
# Settings
settings = dict()
settings["estimation"] = dict()
settings["estimation"]["method"] = "photutils"
settings["estimation"]["aperture_radius"] = self.aperture_radius
settings["write"] = True
#settings["estimation"]["finishing_step"] = "polynomial"
#settings["estimation"]["polynomial_degree"] = self.config.polynomial_degree
#settings["estimation"]["fill_method"] = "cubic"
settings["plot"] = True
# Input
input_dict = dict()
# Set input
input_dict["frame"] = self.frame
input_dict["principal_shape"] = self.galaxy_region
input_dict["sources_mask"] = self.sources_mask
input_dict["extra_mask"] = self.rotation_mask
# Create command
command = Command("subtract_sky", "subtract the sky from an artificially created image", settings, input_dict, cwd=self.subtraction_path)
# Run the subtraction
self.subtractor = self.run_command(command)
# -----------------------------------------------------------------
@property
def estimated_sky(self):
"""
This function ...
:return:
"""
return self.subtractor.sky_frame
# -----------------------------------------------------------------
@lazyproperty
def subtracted(self):
"""
This function ...
:return:
"""
return self.frame - self.estimated_sky
# -----------------------------------------------------------------
@lazyproperty
def sky_residual(self):
"""
This function ...
:return:
"""
return self.estimated_sky - self.sky
# -----------------------------------------------------------------
def write(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing ...")
# Write the sources with noise
self.write_sources()
# Write the frame
self.write_frame()
# Write real sky map
self.write_real_sky()
# Write sources mask
self.write_sources_mask()
# Write galaxy mask
self.write_galaxy_mask()
# Write reference sky
self.write_reference_sky()
# Write estiamted sky
self.write_estimated_sky()
# Write residuals
self.write_residual()
# Write the statistics
self.write_statistics()
# -----------------------------------------------------------------
def write_sources(self):
"""
THis function ...
:return:
"""
# Inform the user
log.info("Writing the sources frame with noise ...")
# Determine the path
path = fs.join(self.path, "sources_noise.fits")
# Save the frame
self.sources_with_noise.saveto(path)
# -----------------------------------------------------------------
def write_frame(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the frame ...")
# Determine the path
path = fs.join(self.path, "frame.fits")
# SAve the frame
self.frame.saveto(path)
# -----------------------------------------------------------------
def write_real_sky(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the real sky map ...")
# Determine the path
path = fs.join(self.path, "real_sky.fits")
# Save the map
self.sky.saveto(path)
# -----------------------------------------------------------------
def write_sources_mask(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the sources mask ...")
# Determine the path
path = fs.join(self.path, "sources_mask.fits")
# Save
self.sources_mask.saveto(path)
# -----------------------------------------------------------------
def write_galaxy_mask(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the galaxy mask ...")
# Determine the path
path = fs.join(self.path, "galaxy_mask.fits")
# Save
self.galaxy_mask.saveto(path)
# -----------------------------------------------------------------
def write_reference_sky(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the reference sky map ...")
# Determine the path
path = fs.join(self.path, "reference_sky.fits")
# Save
self.reference_sky.saveto(path)
# -----------------------------------------------------------------
def write_estimated_sky(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the estimated sky map ...")
# Determine the path
path = fs.join(self.path, "estimated_sky.fits")
# Save
self.estimated_sky.saveto(path)
# -----------------------------------------------------------------
def write_subtracted(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the sky-subtracted frame ...")
# Determine the path
path = fs.join(self.path, "subtracted.fits")
# Save
self.subtracted.saveto(path)
# -----------------------------------------------------------------
def write_residual(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the residual map ...")
# Determine the path
path = fs.join(self.path, "residual.fits")
# Save
self.sky_residual.saveto(path)
# -----------------------------------------------------------------
def write_statistics(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Writing the statistics ...")
# Determine the path
path = fs.join(self.path, "statistics.dat")
# Write
save_mapping(path, self.statistics)
# -----------------------------------------------------------------
def plot(self):
"""
This function ...
:return:
"""
# Inofmrthe user
log.info("Plotting ...")
# Plot meshes
if self.config.plotting.meshes: self.plot_meshes()
# -----------------------------------------------------------------
def plot_meshes(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Plotting the meshes ...")
# Plot meshes
plt.figure()
norm = ImageNormalize(stretch=SqrtStretch())
plt.imshow(self.frame, origin='lower', cmap='Greys_r', norm=norm)
self.photutils_bkg.plot_meshes(outlines=True, color='#1f77b4')
plt.show()
def old(self):
"""
This function ...
:return:
"""
exit()
# FWHM of all the images
fwhm = 11.18 * u("arcsec")
fwhm_pix = (fwhm / frame.average_pixelscale).to("pix").value
sigma = fwhm_pix * statistics.fwhm_to_sigma
# Get the center pixel of the galaxy
parameters_path = fs.join(components_path, "parameters.dat")
parameters = load_parameters(parameters_path)
center = parameters.center.to_pixel(frame.wcs)
# Create a source around the galaxy center
ellipse = PixelEllipseRegion(center, 20.0 * sigma)
source = Source.from_ellipse(model_residual, ellipse, 1.5)
source.estimate_background("polynomial")
source.plot()
position = source.center
model = source.subtracted.fit_model(position, "Gaussian")
rel_center = center - Extent(source.x_min, source.y_min)
rel_model = fitting.shifted_model(model, -source.cutout.x_min,
-source.cutout.y_min)
plotting.plot_peak_model(source.cutout, rel_center.x, rel_center.y,
rel_model)
model_fwhm_pix = fitting.fwhm(model)
model_fwhm = (model_fwhm_pix * frame.average_pixelscale).to("arcsec")
print("Model FWHM: ", model_fwhm)
evaluated_model = source.cutout.evaluate_model(model)
all_residual = Frame(np.copy(model_residual))
all_residual[source.y_slice, source.x_slice] -= evaluated_model
all_residual.saveto(fs.join(residuals_path, "all_residual.fits"))
model = Gaussian2D(amplitude=0.0087509425805,
x_mean=center.x,
y_mean=center.y,
x_stddev=sigma,
y_stddev=sigma)
rel_model = fitting.shifted_model(model, -source.cutout.x_min,
-source.cutout.y_min)
plotting.plot_peak_model(source.cutout, rel_center.x, rel_center.y,
rel_model)
evaluated_model = source.cutout.evaluate_model(model)
all_residual2 = Frame(np.copy(model_residual))
all_residual2[source.y_slice, source.x_slice] -= evaluated_model
all_residual2.saveto(fs.join(residuals_path, "all_residual2.fits"))
# -----------------------------------------------------------------
# Load the image
frame = Frame.from_file(arguments.image)
# Load the region
region_name = os.path.splitext(os.path.basename(arguments.region))[0]
region = load_as_pixel_region_list(arguments.region, frame.wcs)
# Create the mask
mask = region.to_mask(x_size=frame.xsize, y_size=frame.ysize)
# Calculate the inverse, if requested
if arguments.invert: mask = mask.inverse()
# -----------------------------------------------------------------
if arguments.data:
new_frame = frame
frame[mask] = arguments.value
# Create a frame for the total mask
else:
new_frame = Frame(mask.astype(int))
# Write out the new frame
new_frame.saveto(region_name + ".fits")
# -----------------------------------------------------------------
