def plot_healpix_file(data_filename, save_filename):
#nside = 256
print 'Loading data...'
data, nside_old, nest = healpix_utils.load_map(data_filename)
#print 'Downsampling...'
#data = healpix_utils.healpix_downsample(data, nside_old, nside, nest)
nside = nside_old
print 'Plotting...'
plot_filled_pixels(data, nside, nest, save_filename)
def plot_nearest_data():
obs_list_file = '/Users/ruby/EoR/obs_lists/diffuse_survey_good_pointings_successful.txt'
obs_info_file = '/Users/ruby/EoR/sidelobe_survey_obsinfo.txt'
data_loc = '/Users/ruby/EoR/Healpix_fits'
nside = 256
obs_list = open(obs_list_file, 'r').readlines()
obs_list = [obs.strip() for obs in obs_list] # strip newline characters
obs_list = list(set(obs_list)) # remove duplicates
#obs_list = obs_list[:10]
observations = surveyview.load_survey(obs_info_file) # get obs metadata
observations = [obs for obs in observations if obs.obsid in obs_list]
indices = []
signal_vals = []
distances = []
for i, obs in enumerate(observations):
print 'Gathering data from obsid {} of {}'.format(i + 1, len(obs_list))
print 'Loading data'
data, nside_old, nest = healpix_utils.load_map(
'{}/{}_uniform_Residual_I_HEALPix.fits'.format(
data_loc, obs.obsid))
data = healpix_utils.healpix_downsample(data, nside_old, nside, nest)
for data_point in data:
data_point.get_ra_dec(nside, nest)
data_dist = hp.rotator.angdist([obs.ra, obs.dec],
[data_point.ra, data_point.dec],
lonlat=True)[0] / np.pi * 180.
if data_point.pixelnum in indices:
list_pos = indices.index(data_point.pixelnum)
if data_dist < distances[list_pos]:
signal_vals[list_pos] = data_point.signal
distances[list_pos] = data_dist
else:
indices.append(data_point.pixelnum)
signal_vals.append(data_point.signal)
distances.append(data_dist)
use_data = [
healpix_utils.HealpixPixel(indices[i], signal_vals[i])
for i in range(len(indices))
]
#healpix_utils.write_data_to_fits(data, nside, nest, '/Users/ruby/Desktop/nearest_data.fits')
print 'Plotting'
plot_filled_pixels(use_data, nside, nest,
'/Users/ruby/Desktop/nearest_data_test.png')
def calculate_mean_and_var():
obs_list_file = '/Users/ruby/EoR/obs_lists/diffuse_survey_good_pointings_successful.txt'
data_loc = '/Users/ruby/EoR/Healpix_fits'
nside = 256
obs_list = open(obs_list_file, 'r').readlines()
obs_list = [obs.strip() for obs in obs_list] # strip newline characters
obs_list = list(set(obs_list)) # remove duplicates
all_data = []
for i, obs in enumerate(obs_list):
print 'Gathering data from obsid {} of {}'.format(i + 1, len(obs_list))
print 'Loading data'
data, nside_old, nest = healpix_utils.load_map(
'{}/{}_uniform_Residual_I_HEALPix.fits'.format(data_loc, obs))
data = healpix_utils.healpix_downsample(data, nside_old, nside, nest)
print 'Assembling data'
# Convert to implicit indexing
signal_vals_implicit = [hp.pixelfunc.UNSEEN] * 12 * nside**2
for j in range(len(data)):
signal_vals_implicit[data[j].pixelnum] = data[j].signal
all_data.append(signal_vals_implicit)
print 'Calculating data statistics'
data_ave = []
data_var = []
data_npoints = []
for i in range(12 * nside**2):
use_data = [
data_set[i] for data_set in all_data
if data_set[i] != hp.pixelfunc.UNSEEN
]
n_points = len(use_data)
if n_points > 0:
data_npoints.append(healpix_utils.HealpixPixel(i, n_points))
data_ave.append(healpix_utils.HealpixPixel(i, np.mean(use_data)))
data_var.append(healpix_utils.HealpixPixel(i, np.var(use_data)))
print 'Saving data statistics'
healpix_utils.write_data_to_fits(data_ave, nside, nest,
'/Users/ruby/Desktop/data_ave.fits')
healpix_utils.write_data_to_fits(data_var, nside, nest,
'/Users/ruby/Desktop/data_var.fits')
healpix_utils.write_data_to_fits(data_npoints, nside, nest,
'/Users/ruby/Desktop/data_npoints.fits')
def average_stokes_v(fhd_run_path, qa_params_filepath):
data_files = os.listdir('{}/output_data/'.format(fhd_run_path))
data_files = [
file for file in data_files
if '_uniform_Residual_V_HEALPix.fits' in file
]
obs_list = [file[0:10] for file in data_files]
ave_power = []
for obsid in obs_list:
map = healpix_utils.load_map(
'/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_survey_decon_4pol_Feb2019/output_data/{}_uniform_Residual_V_HEALPix.fits'.format(
obsid
)
)
map.implicit_to_explicit_ordering()
ave_power.append(np.mean(map.signal_arr**2.)/len(map.signal_arr))
qa_utils.write_params_to_csv(
qa_params_filepath, 'average Stokes V power', obs_list, ave_power,
overwrite=True
)
def get_radial_variance(
fhd_run_path, average_maps_paths, weights_map_path, savepath,
cube_names=['Residual_I']
):
if fhd_run_path[-1] == '/':
fhd_run_path = fhd_run_path[:-1]
average_maps = []
for map_ind in range(len(cube_names)):
map = healpix_utils.load_map(average_maps_paths[map_ind])
map.explicit_to_implicit_ordering()
average_maps.append(map)
weights = healpix_utils.load_map(weights_map_path)
if weights.nside != average_maps[0].nside:
weights.resample(average_maps[0].nside)
weights.explicit_to_implicit_ordering()
data_files = os.listdir('{}/output_data/'.format(fhd_run_path))
data_files = [
file for file in data_files
if '_uniform_Residual_I_HEALPix.fits' in file
]
obs_list = [file[0:10] for file in data_files]
bin_edges = np.arange(0., 15., .05)
count = np.zeros(len(bin_edges)-1, dtype=long)
dev_from_mean = np.zeros((len(bin_edges)-1, len(cube_names)), dtype=float)
for obs_ind, obsid in enumerate(obs_list):
print 'Loading observation {} of {}'.format(obs_ind, len(obs_list))
obs_struct = scipy.io.readsav(
'{}/metadata/{}_obs.sav'.format(fhd_run_path, obsid)
)['obs']
obs_vec = hp.pixelfunc.ang2vec(
float(obs_struct['obsra']), float(obs_struct['obsdec']),
lonlat=True
)
maps = []
for cube_ind, cube in enumerate(cube_names):
map = healpix_utils.load_map('{}/output_data/{}_uniform_{}_HEALPix.fits'.format(
fhd_run_path, obsid, cube
))
map.resample(average_maps[cube_ind].nside)
if map.nest != average_maps[cube_ind].nest:
print 'Map nesting conventions do not match. Converting.'
if average_maps[cube_ind].nside:
map.reorder_ring_to_nest()
else:
map.reorder_nest_to_ring()
if map.coords != average_maps[cube_ind].coords:
print 'ERROR: Map coordinates do not match. Exiting.'
sys.exit(1)
maps.append(map)
for pix in maps[0].pix_arr: # Use the first cube for the pixel list
pix_vec = hp.pix2vec(maps[0].nside, pix, nest=maps[0].nest)
rad_dist = hp.rotator.angdist(pix_vec, obs_vec)*180./np.pi
bin_index = 0
while rad_dist > bin_edges[bin_index+1] and bin_index < len(bin_edges)-1:
bin_index += 1
if bin_index < len(bin_edges)-1 and weights.signal_arr[pix] > 1:
count[bin_index] += 1
for cube_ind in range(len(cube_names)):
dev_from_mean[bin_index, cube_ind] += (
maps[cube_ind].signal_arr[
np.where(maps[cube_ind].pix_arr == pix)
][0] - average_maps[cube_ind].signal_arr[pix]
)**2
average_dev = dev_from_mean/count[:, None]
average_dev[np.where(count == 0), :] = 0.
xvals = np.array([
(bin_edges[ind+1]+bin_edges[ind])/2. for ind in range(len(bin_edges)-1)
])
plt.figure()
colors = ['black', 'red', 'blue']
for cube_ind, cube in enumerate(cube_names):
plt.scatter(
xvals, average_dev[:, cube_ind], marker='o', s=1.,
color=colors[cube_ind], label=cube
)
plt.xlabel('Distance from Observation Center')
plt.ylabel('Average of the Deviation from the Mean Squared')
plt.ylim(0,.0001)
plt.legend(loc='upper left')
print 'Saving plot to {}'.format(savepath)
plt.savefig(savepath, dpi=300, bbox_inches='tight')
plt.close()
def plot_individual_images():
field_center = hp.pixelfunc.ang2vec(0., -27., lonlat=True)
field_radius = 13.5
map = healpix_utils.load_map(
'/Users/rubybyrne/diffuse_survey_plotting_May2020/nsamples_map_more_obs.fits'
)
pix_use = []
signal_use = []
for ind, pix in enumerate(map.pix_arr):
pix_vec = hp.pix2vec(map.nside, pix, nest=map.nest)
dist_deg = hp.rotator.angdist(pix_vec, field_center) * 180. / np.pi
if dist_deg <= field_radius:
pix_use.append(pix)
signal_use.append(map.signal_arr[ind])
map.signal_arr = np.array(signal_use)
map.pix_arr = np.array(pix_use)
obs_groups = [['1131454296'], ['1131455736'], ['1131710392'],
['1131708952'], ['1131710032', '1131713632'],
['1131457176', '1131715432'], ['1131453936', '1131716512'],
['1131537104', '1131709912', '1131456096']]
for group_ind, group in enumerate(obs_groups):
if len(group) > 1:
for obs_ind, obs in enumerate(group):
pols = ['I', 'Q', 'U', 'V']
if obs in obs_list_1:
path = '/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Feb2020',
else:
path = '/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Mar2020'
combined_maps, weight_maps = healpix_utils.average_healpix_maps(
path,
obs_lists=[obs],
nside=128,
cube_names=[
'Residual_I', 'Residual_Q', 'Residual_U', 'Residual_V'
],
weighting='weighted',
apply_radial_weighting=False,
apply_rm_correction=True)
pols = ['I', 'Q', 'U', 'V']
for map_ind in range(len(combined_maps)):
pol = pols[map_ind]
add_pixels = np.setdiff1d(map.pix_arr,
combined_maps[map_ind].pix_arr)
combined_maps[map_ind].pix_arr = np.concatenate(
(np.array(combined_maps[map_ind].pix_arr), add_pixels))
combined_maps[map_ind].signal_arr = np.concatenate(
(np.array(combined_maps[map_ind].signal_arr),
np.zeros(np.shape(add_pixels)[0])))
combined_maps[map_ind].signal_arr = np.array([
combined_maps[map_ind].signal_arr[np.where(
combined_maps[map_ind].pix_arr == pix)[0]][0]
for pix in map.pix_arr
])
combined_maps[map_ind].pix_arr = map.pix_arr
if pol == 'I':
colorbar_range = [-1e4, 1e4]
else:
colorbar_range = [-5e3, 5e3]
plot_healpix_map.plot_filled_pixels(
combined_maps[map_ind],
'/Users/rubybyrne/diffuse_survey_plotting_May2020/eor0_plots/Stokes{}_eor0_map{}_obs{}.png'
.format(pol, group_ind + 1, obs_ind + 1),
colorbar_range=colorbar_range)
def make_combined_images():
field_center = hp.pixelfunc.ang2vec(0., -27., lonlat=True)
field_radius = 13.5
map = healpix_utils.load_map(
'/Users/rubybyrne/diffuse_survey_plotting_May2020/nsamples_map_more_obs.fits'
)
pix_use = []
signal_use = []
for ind, pix in enumerate(map.pix_arr):
pix_vec = hp.pix2vec(map.nside, pix, nest=map.nest)
dist_deg = hp.rotator.angdist(pix_vec, field_center) * 180. / np.pi
if dist_deg <= field_radius:
pix_use.append(pix)
signal_use.append(map.signal_arr[ind])
map.signal_arr = np.array(signal_use)
map.pix_arr = np.array(pix_use)
obs_groups = [['1131454296'], ['1131455736'], ['1131710392'],
['1131708952'], ['1131710032', '1131713632'],
['1131457176', '1131715432'], ['1131453936', '1131716512'],
['1131537104', '1131709912', '1131456096']]
if False:
for pol in ['I', 'Q', 'U', 'V']:
full_map = healpix_utils.load_map(
'/Users/rubybyrne/diffuse_survey_plotting_May2020/Stokes{}_average_map_more_obs.fits'
.format(pol))
full_map.signal_arr = np.array([
full_map.signal_arr[np.where(full_map.pix_arr == pix)[0]][0]
for pix in map.pix_arr
])
full_map.pix_arr = map.pix_arr
full_map.write_data_to_fits(
'/Users/rubybyrne/diffuse_survey_plotting_May2020/eor0_plots/Stokes{}_eor0_full_map.fits'
.format(pol))
if pol == 'I':
colorbar_range = [-1e4, 1e4]
else:
colorbar_range = [-2e3, 2e3]
plot_healpix_map.plot_filled_pixels(
full_map,
'/Users/rubybyrne/diffuse_survey_plotting_May2020/eor0_plots/Stokes{}_eor0_full_map.png'
.format(pol),
colorbar_range=colorbar_range)
for group_ind, group in enumerate(obs_groups):
list_1 = [obs for obs in group if obs in obs_list_1]
list_2 = [obs for obs in group if obs in obs_list_2]
obs_lists_together = [list_1, list_2]
paths_list = [
'/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Feb2020',
'/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Mar2020'
]
if len(list_1) == 0:
paths_list = paths_list[1]
obs_lists_together = obs_lists_together[1]
if len(list_2) == 0:
paths_list = paths_list[0]
obs_lists_together = obs_lists_together[0]
combined_maps, weight_maps = healpix_utils.average_healpix_maps(
paths_list,
obs_lists=obs_lists_together,
nside=128,
cube_names=[
'Residual_I', 'Residual_Q', 'Residual_U', 'Residual_V'
],
weighting='weighted',
apply_radial_weighting=True,
apply_rm_correction=True,
rm_file='/Users/rubybyrne/diffuse_survey_rm_empirical.csv')
pols = ['I', 'Q', 'U', 'V']
for map_ind in range(len(combined_maps)):
pol = pols[map_ind]
combined_maps[map_ind].signal_arr = np.array([
combined_maps[map_ind].signal_arr[np.where(
combined_maps[map_ind].pix_arr == pix)[0]][0]
for pix in map.pix_arr
])
combined_maps[map_ind].pix_arr = map.pix_arr
combined_maps[map_ind].write_data_to_fits(
'/Users/rubybyrne/diffuse_survey_plotting_May2020/eor0_plots/Stokes{}_eor0_map{}_tapered_empirical_rm.fits'
.format(pol, group_ind + 1))
if pol == 'I':
colorbar_range = [-1e4, 1e4]
else:
colorbar_range = [-5e3, 5e3]
plot_healpix_map.plot_filled_pixels(
combined_maps[map_ind],
'/Users/rubybyrne/diffuse_survey_plotting_May2020/eor0_plots/Stokes{}_eor0_map{}_tapered_empirical_rm.png'
.format(pol, group_ind + 1),
colorbar_range=colorbar_range)
def find_obs_groups():
field_center = hp.pixelfunc.ang2vec(0., -27., lonlat=True)
field_radius = 13.5
map = healpix_utils.load_map(
'/Users/rubybyrne/diffuse_survey_plotting_May2020/nsamples_map_more_obs.fits'
)
pix_use = []
signal_use = []
for ind, pix in enumerate(map.pix_arr):
pix_vec = hp.pix2vec(map.nside, pix, nest=map.nest)
dist_deg = hp.rotator.angdist(pix_vec, field_center) * 180. / np.pi
if dist_deg <= field_radius:
pix_use.append(pix)
signal_use.append(map.signal_arr[ind])
map.signal_arr = np.array(signal_use)
map.pix_arr = np.array(pix_use)
map.write_data_to_fits(
'/Users/rubybyrne/diffuse_survey_plotting_May2020/eor0_plots/nsamples_eor0.fits'
)
plot_healpix_map.plot_filled_pixels(
map,
'/Users/rubybyrne/diffuse_survey_plotting_May2020/eor0_plots/nsamples_eor0.png'
)
obs_use_list = []
pix_use_list = []
for obsid in obs_list_1 + obs_list_2:
if obsid in obs_list_1:
path = '/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Feb2020'
elif obsid in obs_list_2:
path = '/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Mar2020'
obs_struct = scipy.io.readsav('{}/metadata/{}_obs.sav'.format(
path, obsid))['obs']
obs_vec = hp.pixelfunc.ang2vec(float(obs_struct['obsra']),
float(obs_struct['obsdec']),
lonlat=True)
dist_deg = hp.rotator.angdist(obs_vec, field_center) * 180. / np.pi
if dist_deg <= 30.:
obs_reference_map = healpix_utils.load_map(
'{}/output_data/{}_weighted_Residual_I_HEALPix.fits'.format(
path, obsid))
if np.shape(np.intersect1d(obs_reference_map.pix_arr,
map.pix_arr))[0] > 0:
obs_use_list.append(obsid)
pix_use_list.append(obs_reference_map.pix_arr)
least_sampled_pixels = map.pix_arr[np.where(
map.signal_arr == np.min(map.signal_arr))[0]]
obs_use_least_sampled = []
obs_to_match = [obsid for obsid in obs_use_list]
for obsind, obsid in enumerate(obs_use_list):
if np.shape(np.intersect1d(least_sampled_pixels,
pix_use_list[obsind]))[0] > 0:
obs_use_least_sampled.append(obsid)
obs_to_match.remove(obsid)
print np.shape(obs_use_least_sampled)
obs_groups = []
# Check for one-obs groups
obs_to_remove = []
for obsid in obs_use_least_sampled:
if np.shape(
np.intersect1d(pix_use_list[obs_use_list.index(obsid)],
map.pix_arr))[0] == np.shape(map.pix_arr)[0]:
print 'Obsid {} is an obs group'.format(obsid)
obs_groups.append([obsid])
obs_to_remove.append(obsid)
for obsid in obs_to_remove:
obs_use_least_sampled.remove(obsid)
# Check for two-obs groups
if len(obs_use_least_sampled) > 0:
obs_to_remove = []
for obsid in obs_use_least_sampled:
#see if two obs cover the whole field
pix_list_1 = pix_use_list[obs_use_list.index(obsid)]
no_match = True
obsind = 0
while no_match and obsind < len(obs_to_match):
obsid_2 = obs_to_match[obsind]
print obsid_2
print obs_use_list.index(obsid_2)
pix_list_2 = pix_use_list[obs_use_list.index(obsid_2)]
if np.shape(
np.intersect1d(
np.concatenate((pix_list_1, pix_list_2)),
map.pix_arr))[0] == np.shape(map.pix_arr)[0]:
print 'Obsids {} and {} are an obs group'.format(
obsid, obsid_2)
obs_groups.append([obsid, obsid_2])
obs_to_match.remove(obsid_2)
obs_to_remove.append(obsid)
no_match = False
obsind += 1
for obsid in obs_to_remove:
obs_use_least_sampled.remove(obsid)
# Check for three-obs groups
if len(obs_use_least_sampled) > 0:
obs_to_remove = []
for obsid in obs_use_least_sampled:
#see if two obs cover the whole field
pix_list_1 = pix_use_list[obs_use_list.index(obsid)]
no_match = True
obsind_2 = 0
while no_match and obsind_2 < len(obs_to_match):
obsid_2 = obs_to_match[obsind_2]
pix_list_2 = pix_use_list[obs_use_list.index(obsid_2)]
obsind_3 = 0
while no_match and obsind_3 < len(obs_to_match):
if obsind_2 != obsind_3:
obsid_3 = obs_to_match[obsind_3]
pix_list_3 = pix_use_list[obs_use_list.index(obsid_3)]
if np.shape(
np.intersect1d(
np.concatenate(
(pix_list_1, pix_list_2, pix_list_3)),
map.pix_arr))[0] == np.shape(
map.pix_arr)[0]:
print 'Obsids {}, {}, and {} are an obs group'.format(
obsid, obsid_2, obsid_3)
obs_groups.append([obsid, obsid_2, obsid_3])
obs_to_match.remove(obsid_2)
obs_to_match.remove(obsid_3)
obs_to_remove.append(obsid)
no_match = False
obsind_3 += 1
obsind_2 += 1
for obsid in obs_to_remove:
obs_use_least_sampled.remove(obsid)
print obs_groups
def hist2d_datastat_plot():
obs_list_file = '/Users/ruby/EoR/obs_lists/diffuse_survey_good_pointings_successful.txt'
data_loc = '/Users/ruby/EoR/Healpix_fits'
obs_list = open(obs_list_file, 'r').readlines()
obs_list = [obs.strip() for obs in obs_list] # strip newline characters
obs_list = list(set(obs_list)) # remove duplicates
#obs_list = obs_list[:4]
observations = surveyview.load_survey(
'/Users/ruby/EoR/sidelobe_survey_obsinfo.txt')
observations = [obs for obs in observations if obs.obsid in obs_list]
var_data, nside, nest = healpix_utils.load_map(
'/Users/ruby/Desktop/data_var_nside256.fits')
var_pixelvals = [data_point.pixelnum for data_point in var_data]
data_diff = []
data_dist = []
for i, obs in enumerate(observations):
print 'Gathering data from obsid {} of {}'.format(i + 1, len(obs_list))
print 'Loading data'
data, nside_old, nest = healpix_utils.load_map(
'{}/{}_uniform_Residual_I_HEALPix.fits'.format(
data_loc, obs.obsid))
data = healpix_utils.healpix_downsample(data, nside_old, nside, nest)
print 'Calculating data statistics'
for data_point in data:
data_diff.append(
data_point.signal -
var_data[var_pixelvals.index(data_point.pixelnum)].signal)
data_point.get_ra_dec(nside, nest)
data_dist.append(
hp.rotator.angdist([obs.ra, obs.dec],
[data_point.ra, data_point.dec],
lonlat=True)[0] / np.pi * 180.)
hist, dist_edges, diff_edges = np.histogram2d(data_dist,
data_diff,
bins=100)
hist = hist.T
for j in range(len(hist[0])):
total = sum([hist[i][j] for i in range(len(hist))])
if total != 0:
for i in range(len(hist)):
hist[i][j] = hist[i][j] / total
fig, ax = plt.subplots()
plt.imshow(
hist,
origin='lower',
interpolation='none',
extent=[dist_edges[0], dist_edges[-1], diff_edges[0], diff_edges[-1]],
vmin=0,
vmax=0.1)
ax.set_aspect(
(dist_edges[-1] - dist_edges[0]) / (diff_edges[-1] - diff_edges[0]))
plt.xlabel('Distance from Pointing Center (deg)')
plt.ylabel('Difference from Mean (Jy/sr)')
cbar = plt.colorbar()
cbar.ax.set_ylabel('Counts, Normalized', rotation=270) # label colorbar
plt.savefig('/Users/ruby/Desktop/data_var_2dhist_testing.png',
format='png',
dpi=500)
def plot_healpix_tiling():
#data_type = 'Residual_I'
data_type = 'Dirty_I'
normalization = 'uniform'
#data_dir = '/Users/ruby/EoR/Healpix_fits'
data_dir = '/Users/ruby/EoR/Healpix_fits/haslam_sim'
tile_center_ras = [
100, 100, 100, 100, 100, 90, 90, 90, 90, 90, 80, 80, 80, 80, 80, 70,
70, 70, 70, 70, 60, 60, 60, 60, 60, 50, 50, 50, 50, 50, 40, 40, 40, 40,
40, 30, 30, 30, 30, 30, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 0, 0,
0, 0, 0, -10, -10, -10, -10, -10, -20, -20, -20, -20, -20
]
tile_center_decs = [
-5, -15, -25, -35, -45, -5, -15, -25, -35, -45, -5, -15, -25, -35, -45,
-5, -15, -25, -35, -45, -5, -15, -25, -35, -45, -5, -15, -25, -35, -45,
-5, -15, -25, -35, -45, -5, -15, -25, -35, -45, -5, -15, -25, -35, -45,
-5, -15, -25, -35, -45, -5, -15, -25, -35, -45, -5, -15, -25, -35, -45,
-5, -15, -25, -35, -45
]
obsids = [
1131478056, 1131564464, 1131477936, 1130787784, 1131477816, 1131733672,
1131562544, 1131733552, 1130785864, 1131475896, 1131559064, 1131558944,
1131731752, 1130782264, 1130783824, 1131470736, 1131557144, 1131470616,
1130780464, 1131470496, 1131468936, 1131553544, 1131726352, 1130778664,
1131468696, 1131724672, 1131551744, 1131465216, 1130776864, 1130776624,
1131463536, 1131549944, 1131463416, 1130773264, 1131463296, 1131461616,
1131548024, 1131461496, 1130773144, 1131461376, 1131717352, 1131544424,
1131717232, 1131459696, 1131459576, 1131456216, 1131542624, 1131456096,
1131715432, 1131715312, 1131711952, 1131540824, 1131454296, 1131713632,
1131454176, 1131710152, 1131537224, 1131710032, 1131710032, 1131709912,
1131535544, 1131535424, 1131535304, 1131710032, 1131709912
]
data = []
#nside = 512
nside = 256
for i, obs in enumerate(obsids):
print 'Gathering pixels from obsid {} of {}.'.format(
i + 1, len(obsids))
obs_data, nside_old, nest = healpix_utils.load_map(
'{}/{}_{}_{}_HEALPix.fits'.format(data_dir, obs, normalization,
data_type))
obs_data = healpix_utils.healpix_downsample(obs_data, nside_old, nside,
nest)
tile_bounds_radec = [[tile_center_ras[i] - 5, tile_center_decs[i] - 5],
[tile_center_ras[i] - 5, tile_center_decs[i] + 5],
[tile_center_ras[i] + 5, tile_center_decs[i] + 5],
[tile_center_ras[i] + 5, tile_center_decs[i] - 5]]
tile_bounds_vec = np.array([
hp.pixelfunc.ang2vec(corner[0], corner[1], lonlat=True)
for corner in tile_bounds_radec
])
use_pixels = hp.query_polygon(nside, tile_bounds_vec, nest=nest)
data.extend([
data_point for data_point in obs_data
if data_point.pixelnum in use_pixels
])
#healpix_utils.write_data_to_fits(data, nside, nest, '/Users/ruby/EoR/mosaic_data.fits')
# Define Healpix pixels to plot
patches = []
colors = []
for point in data:
point.get_pixel_corners(nside, nest)
polygon = Polygon(zip(point.pix_corner_ras, point.pix_corner_decs))
patches.append(polygon)
colors.append(point.signal)
collection = PatchCollection(patches, cmap='Greys_r', lw=0.04)
collection.set_array(np.array(colors)) # set the data colors
collection.set_edgecolor('face') # make the face and edge colors match
fig, ax = plt.subplots(figsize=(24, 8), dpi=1000)
ax.add_collection(collection) # plot data
# plot lines between tiles
line_width = 2.0
color = 'gray'
order = 8
plt.plot([130, -45], [0, 0], lw=line_width, c=color, zorder=order)
plt.plot([130, -45], [-10, -10], lw=line_width, c=color, zorder=order)
plt.plot([130, -45], [-20, -20], lw=line_width, c=color, zorder=order)
plt.plot([130, -45], [-30, -30], lw=line_width, c=color, zorder=order)
plt.plot([130, -45], [-40, -40], lw=line_width, c=color, zorder=order)
plt.plot([130, -45], [-50, -50], lw=line_width, c=color, zorder=order)
plt.plot([105, 105], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([95, 95], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([85, 85], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([75, 75], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([65, 65], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([55, 55], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([45, 45], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([35, 35], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([25, 25], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([15, 15], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([5, 5], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([-5, -5], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([-15, -15], [-75, 20], lw=line_width, c=color, zorder=order)
plt.plot([-25, -25], [-75, 20], lw=line_width, c=color, zorder=order)
plt.xlabel('RA (deg)')
plt.ylabel('Dec (deg)')
plt.axis('equal')
ax.set_facecolor('gray') # make plot background gray
plt.axis([110, -30, -50, 0])
cbar = fig.colorbar(collection, ax=ax, extend='both') # add colorbar
cbar.ax.set_ylabel('Flux Density (Jy/sr)', rotation=270) # label colorbar
plt.savefig(
'/Users/ruby/Desktop/haslam_mosaicplot_nside{}.png'.format(nside),
format='png',
dpi=1000)
def overplot_haslam_contour():
data, nside, nest = healpix_utils.load_map(
'/Users/ruby/EoR/mosaic_data.fits')
fig, ax = plt.subplots(figsize=(24, 8), dpi=1000)
# Define Healpix pixels to plot
patches = []
colors = []
for point in data:
point.get_pixel_corners(nside, nest)
polygon = Polygon(zip(point.pix_corner_ras, point.pix_corner_decs))
patches.append(polygon)
colors.append(point.signal)
collection = PatchCollection(patches, cmap='Greys_r', lw=0.04)
collection.set_array(np.array(colors)) # set the data colors
collection.set_edgecolor('face') # make the face and edge colors match
ax.add_collection(collection) # plot data
# plot lines between tiles
line_width = 2.0
color = 'gray'
order = 8
plt.plot([130, -45], [-10, -10], lw=line_width, c=color, zorder=order)
plt.plot([130, -45], [-20, -20], lw=line_width, c=color, zorder=order)
plt.plot([130, -45], [-30, -30], lw=line_width, c=color, zorder=order)
plt.plot([130, -45], [-40, -40], lw=line_width, c=color, zorder=order)
plt.plot([130, -45], [-50, -50], lw=line_width, c=color, zorder=order)
plt.plot([95, 95], [-75, -20], lw=line_width, c=color, zorder=order)
plt.plot([85, 85], [-75, -20], lw=line_width, c=color, zorder=order)
plt.plot([75, 75], [-75, -20], lw=line_width, c=color, zorder=order)
plt.plot([65, 65], [-75, -20], lw=line_width, c=color, zorder=order)
plt.plot([55, 55], [-75, -20], lw=line_width, c=color, zorder=order)
plt.plot([45, 45], [-75, -20], lw=line_width, c=color, zorder=order)
plt.plot([35, 35], [-75, -20], lw=line_width, c=color, zorder=order)
plt.plot([25, 25], [-75, -20], lw=line_width, c=color, zorder=order)
plt.plot([15, 15], [-75, -20], lw=line_width, c=color, zorder=order)
plt.plot([5, 5], [-75, -20], lw=line_width, c=color, zorder=order)
plt.plot([-5, -5], [-75, -20], lw=line_width, c=color, zorder=order)
plt.plot([-15, -15], [-75, -20], lw=line_width, c=color, zorder=order)
plt.xlabel('RA (deg)')
plt.ylabel('Dec (deg)')
plt.axis('equal')
ax.set_facecolor('gray') # make plot background gray
plt.axis([110, -30, -50, 0])
cbar = fig.colorbar(collection, ax=ax, extend='both') # add colorbar
cbar.ax.set_ylabel('Flux Density (Jy/sr)', rotation=270) # label colorbar
data, nside, nest = healpix_utils.load_global_map(
'/Users/ruby/EoR/Healpix_fits/lambda_haslam408_dsds.fits')
data = healpix_utils.healpix_downsample(data, nside, 512, nest)
for point in data:
point.get_ra_dec(nside, nest, coords='galactic')
plt.tricontour([point.ra for point in data], [point.dec for point in data],
[point.signal for point in data],
500,
linewidths=0.5,
colors='cyan')
plt.savefig('/Users/ruby/EoR/haslam_overplot.png', format='png', dpi=1000)
def calculate_empirical_rm_Jul2021():
eor0_obslist = [
'1131454296', '1131713632', '1131710032', '1131456096', '1131540824',
'1131539024', '1131538904', '1131540704', '1131455736', '1131710392',
'1131708952', '1131457176', '1131716512', '1131458976', '1131712192',
'1131453936', '1131457536', '1131537704', '1131543584'
]
obslist_full = [
'1131551744',
'1130783824',
'1131562544',
'1131709912',
'1130776864',
'1131461496',
'1130782264',
'1131715432',
'1131733552',
'1131542624',
'1130773144',
'1131461376',
'1131557144',
'1131454296',
'1131731752',
'1130778664',
'1131470496',
'1131559064',
'1131717232',
'1131463536',
'1130773264',
'1131463416',
'1131717352',
'1131713632',
'1131478056',
'1131468936',
'1131468696',
'1131535424',
'1131463296',
'1131465216',
'1131710032',
'1130776624',
'1131456096',
'1131540824',
'1131711952',
'1131459576',
'1131477936',
'1131733672',
'1131564464',
'1130787784',
'1131461616',
'1131558944',
'1131470616',
'1131549944',
'1131553544',
'1131459696',
'1130780464',
'1131726352',
'1131470736',
'1131548024',
'1131710152',
'1130785864',
'1131544424',
'1131542504',
#'1131733432',
'1131735232',
'1131553664',
'1131724432',
'1131542744',
'1131455976',
'1131719152',
'1131454416',
'1130787544',
'1130776744',
'1130780224',
'1131551624',
'1131722632',
'1131547904',
'1131562664',
'1131550064',
'1131537104',
'1131555224',
'1131467136',
'1131539024',
'1131555344',
'1131546104',
'1131548144',
'1131472416',
'1131558824',
'1131544304',
'1130789584',
'1131476136',
'1130789344',
'1131722872',
'1130785744',
'1131730072',
'1131459816',
'1131564584',
'1131457776',
'1131724552',
'1130787664',
'1130778424',
'1131728152',
'1131722752',
'1131538904',
'1131544544',
'1130778544',
'1131467016',
'1131546344',
'1130789464',
'1131713512',
'1131546224',
'1131474336',
'1130782144',
'1131735472',
'1130775064',
'1130774824',
'1131720832',
'1130774944',
'1131557264',
'1130783944',
'1131472296',
'1131465096',
'1131457896',
'1131555464',
'1131562424',
'1131551864',
'1131540704',
'1130780344',
'1131731632',
'1131468816',
'1131472536',
'1130773024',
'1131474096',
'1131465336',
'1131715552',
'1131458016',
'1131540944',
'1131557024',
'1131731872',
'1131553424',
'1131560864',
'1130784064',
'1131466896',
'1130782024',
'1131560624',
'1131474216',
'1131564344',
'1131729952',
'1131560744',
'1130785624',
'1131709432',
'1131536624',
'1131536384',
'1131711112',
'1131709192',
'1131710992',
'1131453456',
'1131565304',
'1131478776',
'1131566504',
'1131565184',
'1131566624',
'1131566744',
'1131565064',
'1131567944',
'1131478656',
'1131568544',
'1131739432',
'1130788504',
'1130788264',
'1131740752',
'1131455736',
'1131710392',
'1131708952',
'1131457176',
'1131716512',
'1131458976',
'1131712192',
'1131453936',
'1131457536',
'1131537704',
'1131543584'
]
start_freq_mhz = 167.
end_freq_mhz = 198.
original_rm_path = '/Users/rubybyrne/diffuse_survey_rm_tot.csv'
rm_outfile = '/Users/rubybyrne/diffuse_survey_rm_empirical_Jul2021.csv'
run_path = '/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey_May2021/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Jun2021'
averaged_Q_path = '/Users/rubybyrne/diffuse_survey_plotting_Jun2021/StokesQ_average_map_first_rm_correction.fits'
averaged_U_path = '/Users/rubybyrne/diffuse_survey_plotting_Jun2021/StokesU_average_map_first_rm_correction.fits'
# Get RMs
rm_data = np.genfromtxt(original_rm_path,
delimiter=',',
dtype=None,
names=True,
encoding=None)
rms_orig = np.array([
rm_data['RM'][np.where(rm_data['ObsID'] == int(obsid))][0]
for obsid in eor0_obslist
])
# Create lookup table:
rot_angles_lookup, rms_lookup = create_rm_lookup_table(
start_freq_mhz, end_freq_mhz)
rms_use = np.copy(rms_orig)
rot_angle_deltas_list = np.zeros(len(eor0_obslist))
eff_rot_angle_start = get_effective_rotation_angles(
rms_use, start_freq_mhz, end_freq_mhz)
q_average_map = healpix_utils.load_map(averaged_Q_path)
u_average_map = healpix_utils.load_map(averaged_U_path)
q_average_map.explicit_to_implicit_ordering()
u_average_map.explicit_to_implicit_ordering()
# Calculate the empirical rotation angles
for obsind, obsid in enumerate(eor0_obslist):
q_map = healpix_utils.load_map(
'{}/output_data/{}_optimal_Residual_Q_HEALPix.fits'.format(
run_path, obsid),
quiet=True)
u_map = healpix_utils.load_map(
'{}/output_data/{}_optimal_Residual_U_HEALPix.fits'.format(
run_path, obsid),
quiet=True)
# Apply RM correction to maps
maps_rot = healpix_utils.rm_correction(obsid,
[None, q_map, u_map, None],
rm_file=None,
start_freq_mhz=start_freq_mhz,
end_freq_mhz=end_freq_mhz,
use_single_freq_calc=False,
use_rm=rms_use[obsind])
q_map_rot = maps_rot[1]
u_map_rot = maps_rot[2]
# Confirm that pixel ordering matches
if np.sum(np.abs(q_map_rot.pix_arr - u_map_rot.pix_arr)) != 0:
print 'ERROR: Different pixel ordering.'
q_average_map_signal = np.array(
[q_average_map.signal_arr[ind] for ind in q_map_rot.pix_arr])
u_average_map_signal = np.array(
[u_average_map.signal_arr[ind] for ind in q_map_rot.pix_arr])
tangent_numerator = np.sum(q_average_map_signal *
u_map_rot.signal_arr -
u_average_map_signal * q_map_rot.signal_arr)
tangent_denominator = np.sum(
q_average_map_signal * q_map_rot.signal_arr +
u_average_map_signal * u_map_rot.signal_arr)
rot_angle_deltas_list[obsind] = np.arctan2(tangent_numerator,
tangent_denominator)
# Ensure that the change in the rotation angles is mean-zero
mean_angle = np.arctan2(np.sum(np.sin(rot_angle_deltas_list)),
np.sum(np.cos(rot_angle_deltas_list)))
rot_angle_deltas_list -= mean_angle
eff_rot_angle = eff_rot_angle_start + rot_angle_deltas_list
# Ensure that the rotation angles are within +/- pi
eff_rot_angle = np.arctan2(np.sin(eff_rot_angle), np.cos(eff_rot_angle))
# Convert effective rotation angles to RMs
for obsind in range(len(eor0_obslist)):
rms_use[obsind] = interpolate_rms(rms_lookup, rot_angles_lookup,
rms_orig[obsind],
eff_rot_angle[obsind],
start_freq_mhz, end_freq_mhz)
# Save RMs to a CSV file
rms_orig_all = np.array([
rm_data['RM'][np.where(rm_data['ObsID'] == int(obsid))][0]
for obsid in obslist_full
])
csv_outfile = open(rm_outfile, 'w')
outfile_writer = csv.writer(csv_outfile)
outfile_writer.writerow(['ObsID', 'RM'])
for obsind, obsid in enumerate(obslist_full):
if obsid in eor0_obslist:
outfile_writer.writerow(
[obsid, rms_use[eor0_obslist.index(obsid)]])
else:
outfile_writer.writerow([obsid, rms_orig_all[obsind]])
csv_outfile.close()
def calculate_empirical_rm_no_iteration():
rm_file = '/Users/rubybyrne/diffuse_survey_rm_tot.csv'
rm_outpath = '/Users/rubybyrne/rm_empirical_calculation/Jul2020_align_with_avg'
rm_outfile = '{}/diffuse_survey_rm_empirical_Jul2020.csv'.format(
rm_outpath)
start_freq_mhz = 167.
end_freq_mhz = 198.
# Get RMs
rm_data = np.genfromtxt(rm_file,
delimiter=',',
dtype=None,
names=True,
encoding=None)
rms_orig = np.array([
rm_data['RM'][np.where(rm_data['ObsID'] == int(obsid))][0]
for obsid in obs_list_1 + obs_list_2
])
# Create lookup table:
rot_angles_lookup, rms_lookup = create_rm_lookup_table(
start_freq_mhz, end_freq_mhz)
rms_use = np.copy(rms_orig)
rot_angle_deltas_list = np.zeros(len(obs_list_1) + len(obs_list_2))
eff_rot_angle_start = get_effective_rotation_angles(
rms_use, start_freq_mhz, end_freq_mhz)
# Create average maps
combined_maps, weight_map = healpix_utils.average_healpix_maps(
[
'/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Feb2020',
'/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Mar2020'
],
obs_lists=[obs_list_1, obs_list_2],
nside=128,
cube_names=['Residual_I', 'Residual_Q', 'Residual_U', 'Residual_V'],
weighting='weighted',
apply_radial_weighting=True,
apply_rm_correction=True,
use_rms=rms_use,
quiet=True)
q_average_map = combined_maps[1]
u_average_map = combined_maps[2]
# Plot
colorbar_range = [-2e3, 2e3]
plot_healpix_map.plot_filled_pixels(
q_average_map,
'{}/StokesQ_averaged_initial.png'.format(rm_outpath),
colorbar_range=colorbar_range)
plot_healpix_map.plot_filled_pixels(
u_average_map,
'{}/StokesU_averaged_initial.png'.format(rm_outpath),
colorbar_range=colorbar_range)
# Save maps
q_average_map.write_data_to_fits(
'{}/StokesQ_averaged_initial.fits'.format(rm_outpath))
u_average_map.write_data_to_fits(
'{}/StokesU_averaged_initial.fits'.format(rm_outpath))
q_average_map.explicit_to_implicit_ordering()
u_average_map.explicit_to_implicit_ordering()
# Calculate the empirical rotation angles
for obsind, obsid in enumerate(obs_list_1 + obs_list_2):
if obsid in obs_list_1:
path = '/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Feb2020'
elif obsid in obs_list_2:
path = '/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Mar2020'
q_map = healpix_utils.load_map(
'{}/output_data/{}_weighted_Residual_Q_HEALPix.fits'.format(
path, obsid),
quiet=True)
u_map = healpix_utils.load_map(
'{}/output_data/{}_weighted_Residual_U_HEALPix.fits'.format(
path, obsid),
quiet=True)
# Apply RM correction to maps
maps_rot = healpix_utils.rm_correction(obsid,
[None, q_map, u_map, None],
rm_file=None,
start_freq_mhz=start_freq_mhz,
end_freq_mhz=end_freq_mhz,
use_single_freq_calc=False,
use_rm=rms_use[obsind])
q_map_rot = maps_rot[1]
u_map_rot = maps_rot[2]
# Confirm that pixel ordering matches
if np.sum(np.abs(q_map_rot.pix_arr - u_map_rot.pix_arr)) != 0:
print 'ERROR: Different pixel ordering.'
q_average_map_signal = np.array(
[q_average_map.signal_arr[ind] for ind in q_map_rot.pix_arr])
u_average_map_signal = np.array(
[u_average_map.signal_arr[ind] for ind in q_map_rot.pix_arr])
tangent_numerator = np.sum(q_average_map_signal *
u_map_rot.signal_arr -
u_average_map_signal * q_map_rot.signal_arr)
tangent_denominator = np.sum(
q_average_map_signal * q_map_rot.signal_arr +
u_average_map_signal * u_map_rot.signal_arr)
rot_angle_deltas_list[obsind] = np.arctan2(tangent_numerator,
tangent_denominator)
# Ensure that the change in the rotation angles is mean-zero
mean_angle = np.arctan2(np.sum(np.sin(rot_angle_deltas_list)),
np.sum(np.cos(rot_angle_deltas_list)))
rot_angle_deltas_list = rot_angle_deltas_list - mean_angle
rot_angle_list = rot_angle_deltas_list
eff_rot_angle = eff_rot_angle_start + rot_angle_list
# Ensure that the rotation angles are within +/- pi
eff_rot_angle = np.arctan2(np.sin(eff_rot_angle), np.cos(eff_rot_angle))
# Convert effective rotation angles to RMs
for obsind in range(len(obs_list_1) + len(obs_list_2)):
rms_use[obsind] = interpolate_rms(rms_lookup, rot_angles_lookup,
rms_orig[obsind],
eff_rot_angle[obsind],
start_freq_mhz, end_freq_mhz)
# Save RMs to a CSV file
csv_outfile = open(rm_outfile, 'w')
outfile_writer = csv.writer(csv_outfile)
outfile_writer.writerow(['ObsID', 'RM'])
for obsind, obsid in enumerate(obs_list_1 + obs_list_2):
outfile_writer.writerow([obsid, rms_use[obsind]])
csv_outfile.close()
# Create new average maps
combined_maps, weight_map = healpix_utils.average_healpix_maps(
[
'/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Feb2020',
'/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Mar2020'
],
obs_lists=[obs_list_1, obs_list_2],
nside=128,
cube_names=['Residual_I', 'Residual_Q', 'Residual_U', 'Residual_V'],
weighting='weighted',
apply_radial_weighting=True,
apply_rm_correction=True,
use_rms=rms_use,
quiet=True)
q_average_map = combined_maps[1]
u_average_map = combined_maps[2]
# Plot
colorbar_range = [-2e3, 2e3]
plot_healpix_map.plot_filled_pixels(
q_average_map,
'{}/StokesQ_averaged_final.png'.format(rm_outpath),
colorbar_range=colorbar_range)
plot_healpix_map.plot_filled_pixels(
u_average_map,
'{}/StokesU_averaged_final.png'.format(rm_outpath),
colorbar_range=colorbar_range)
# Save maps
q_average_map.write_data_to_fits(
'{}/StokesQ_averaged_final.fits'.format(rm_outpath))
u_average_map.write_data_to_fits(
'{}/StokesU_averaged_final.fits'.format(rm_outpath))
def calculate_empirical_rm_iterative():
n_iter = 1000
step_size = .3
#obs_list_1 = [obs_list_1[0]]
#obs_list_2 = []
rm_file = '/Users/rubybyrne/diffuse_survey_rm_tot.csv'
rm_outpath = '/Users/rubybyrne/rm_empirical_calculation/Jul2020_vanilla'
rm_outfile = '{}/diffuse_survey_rm_empirical_Jul2020.csv'.format(
rm_outpath)
start_freq_mhz = 167.
end_freq_mhz = 198.
# Get RMs
rm_data = np.genfromtxt(rm_file,
delimiter=',',
dtype=None,
names=True,
encoding=None)
rms_orig = np.array([
rm_data['RM'][np.where(rm_data['ObsID'] == int(obsid))][0]
for obsid in obs_list_1 + obs_list_2
])
# Create lookup table:
rot_angles_lookup, rms_lookup = create_rm_lookup_table(
start_freq_mhz, end_freq_mhz)
rms_use = np.copy(rms_orig)
for iter_ind in range(n_iter):
rot_angle_deltas_list = np.zeros(len(obs_list_1) + len(obs_list_2))
eff_rot_angle_start = get_effective_rotation_angles(
rms_use, start_freq_mhz, end_freq_mhz)
# Create average maps
combined_maps, weight_map = healpix_utils.average_healpix_maps(
[
'/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Feb2020',
'/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Mar2020'
],
obs_lists=[obs_list_1, obs_list_2],
nside=128,
cube_names=[
'Residual_I', 'Residual_Q', 'Residual_U', 'Residual_V'
],
weighting='weighted',
apply_radial_weighting=True,
apply_rm_correction=True,
use_rms=rms_use,
quiet=True)
q_average_map = combined_maps[1]
u_average_map = combined_maps[2]
# Plot
colorbar_range = [-2e3, 2e3]
plot_healpix_map.plot_filled_pixels(
q_average_map,
'{}/StokesQ_averaged_iter{}.png'.format(rm_outpath, iter_ind),
colorbar_range=colorbar_range)
plot_healpix_map.plot_filled_pixels(
u_average_map,
'{}/StokesU_averaged_iter{}.png'.format(rm_outpath, iter_ind),
colorbar_range=colorbar_range)
q_average_map.explicit_to_implicit_ordering()
u_average_map.explicit_to_implicit_ordering()
if False:
weight_map.explicit_to_implicit_ordering()
# Calculate the empirical rotation angles
for obsind, obsid in enumerate(obs_list_1 + obs_list_2):
if obsid in obs_list_1:
path = '/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Feb2020'
elif obsid in obs_list_2:
path = '/Volumes/Bilbo/rlb_fhd_outputs/diffuse_survey/fhd_rlb_diffuse_baseline_cut_optimal_weighting_Mar2020'
q_map = healpix_utils.load_map(
'{}/output_data/{}_weighted_Residual_Q_HEALPix.fits'.format(
path, obsid),
quiet=True)
u_map = healpix_utils.load_map(
'{}/output_data/{}_weighted_Residual_U_HEALPix.fits'.format(
path, obsid),
quiet=True)
# Apply RM correction to maps
maps_rot = healpix_utils.rm_correction(
obsid, [None, q_map, u_map, None],
rm_file=None,
start_freq_mhz=start_freq_mhz,
end_freq_mhz=end_freq_mhz,
use_single_freq_calc=False,
use_rm=rms_use[obsind])
q_map_rot = maps_rot[1]
u_map_rot = maps_rot[2]
# Confirm that pixel ordering matches
if np.sum(np.abs(q_map_rot.pix_arr - u_map_rot.pix_arr)) != 0:
print 'ERROR: Different pixel ordering.'
q_average_map_signal = np.array(
[q_average_map.signal_arr[ind] for ind in q_map_rot.pix_arr])
u_average_map_signal = np.array(
[u_average_map.signal_arr[ind] for ind in q_map_rot.pix_arr])
if False:
total_weights = np.array(
[weight_map.signal_arr[ind] for ind in q_map_rot.pix_arr])
#Get radial weighting
if False:
obs_struct = scipy.io.readsav('{}/metadata/{}_obs.sav'.format(
path, obsid))['obs']
obs_vec = hp.pixelfunc.ang2vec(float(obs_struct['obsra']),
float(obs_struct['obsdec']),
lonlat=True)
rad_weights = np.ones(np.shape(q_map_rot.pix_arr)[0])
for pixind, pix in enumerate(q_map_rot.pix_arr):
pix_vec = hp.pix2vec(q_map_rot.nside,
pix,
nest=q_map_rot.nest)
rad_weights[
pixind] = healpix_utils.obs_radial_weighting_function(
hp.rotator.angdist(pix_vec, obs_vec) * 180. /
np.pi)
rot_angle_delta = calculate_rotation_angle_analytic(
q_average_map_signal, u_average_map_signal,
q_map_rot.signal_arr, u_map_rot.signal_arr)
rot_angle_deltas_list[obsind] = rot_angle_delta
# Ensure that the change in the rotation angles is mean-zero
mean_angle = np.arctan2(np.sum(np.sin(rot_angle_deltas_list)),
np.sum(np.cos(rot_angle_deltas_list)))
rot_angle_deltas_list = rot_angle_deltas_list - mean_angle
rot_angle_list = step_size * rot_angle_deltas_list
print np.sum(rot_angle_deltas_list**2.)
eff_rot_angle = eff_rot_angle_start + rot_angle_list
# Ensure that the rotation angles are within +/- pi
eff_rot_angle = np.arctan2(np.sin(eff_rot_angle),
np.cos(eff_rot_angle))
# Convert effective rotation angles to RMs
for obsind in range(len(obs_list_1) + len(obs_list_2)):
rms_use[obsind] = interpolate_rms(rms_lookup, rot_angles_lookup,
rms_orig[obsind],
eff_rot_angle[obsind],
start_freq_mhz, end_freq_mhz)
# Save each iteration's RMs to a CSV file
rm_outfile_iter = '{}/diffuse_survey_rm_empirical_iter{}.csv'.format(
rm_outpath, iter_ind + 1)
csv_outfile = open(rm_outfile_iter, 'w')
outfile_writer = csv.writer(csv_outfile)
outfile_writer.writerow(['ObsID', 'RM'])
for obsind, obsid in enumerate(obs_list_1 + obs_list_2):
outfile_writer.writerow([obsid, rms_use[obsind]])
csv_outfile.close()
# Save RMs to a CSV file
csv_outfile = open(rm_outfile, 'w')
outfile_writer = csv.writer(csv_outfile)
outfile_writer.writerow(['ObsID', 'RM'])
for obsind, obsid in enumerate(obs_list_1 + obs_list_2):
outfile_writer.writerow([obsid, rms_use[obsind]])
csv_outfile.close()
def compare_observations():
obs_list_file = '/Users/ruby/EoR/obs_lists/diffuse_survey_good_pointings_successful.txt'
data_loc = '/Users/ruby/EoR/Healpix_fits'
save_path = '/Users/ruby/Documents/2018 Fall Quarter/phys576b/jackknife_assignment'
obs_list = open(obs_list_file, 'r').readlines()
obs_list = [obs.strip() for obs in obs_list] # strip newline characters
obs_list = list(set(obs_list)) # remove duplicates
observations = surveyview.load_survey(
'/Users/ruby/EoR/sidelobe_survey_obsinfo.txt')
center_ra = 40.
center_dec = -35.
use_observations = []
for obs in observations:
if obs.obsid in obs_list:
if (obs.ra - center_ra)**2. + (obs.dec - center_dec)**2. < 10**2.:
use_observations.append(obs)
all_data = []
for obs in use_observations:
data, nside_old, nest = healpix_utils.load_map(
'{}/{}_uniform_Residual_I_HEALPix.fits'.format(
data_loc, obs.obsid))
#plot_filled_pixels(data, nside, nest, '{}/{}_residual_I.png'.format(save_path, obs.obsid))
nside = 256
data = healpix_utils.healpix_downsample(data, nside_old, nside, nest)
all_data.append(data)
print 'Calculating data average...'
ave_data, var_data, nsamples_data, ston_data = healpix_utils.average_healpix_maps(
all_data)
max_intersect_pixels = set(
[data_point.pixelnum for data_point in all_data[0]])
for data_set in all_data[1:]:
max_intersect_pixels = max_intersect_pixels.intersection(
[data_point.pixelnum for data_point in data_set])
ave_data_sum = np.sum([
data_point.signal for data_point in ave_data
if data_point.pixelnum in max_intersect_pixels
])
all_data_norm = []
for i, data_set in enumerate(all_data):
data_sum = np.sum([
data_point.signal for data_point in data_set
if data_point.pixelnum in max_intersect_pixels
])
norm_factor = ave_data_sum / data_sum
for point in data_set:
point.signal = point.signal * norm_factor
ave_data_norm, var_data_norm, nsamples_data, ston_data_norm = healpix_utils.average_healpix_maps(
all_data)
print 'Plotting data average...'
plot_filled_pixels(ave_data_norm, nside, nest,
'{}/ave_norm_residual_I.png'.format(save_path))
data_diff = healpix_utils.difference_healpix_maps(ave_data_norm, ave_data,
nside, nest)
plot_filled_pixels(
data_diff, nside, nest,
'{}/ave_norm_minus_orig_residual_I.png'.format(save_path))
#!/usr/bin/python
import numpy as np
import healpy as hp
import sys
import os
import healpix_utils
import pyradiosky
from astropy.units import Quantity
sourcedir = '/Users/ruby/Downloads'
pols = ['I', 'Q', 'U', 'V']
maps = []
for pol_ind, pol_name in enumerate(pols):
new_map = healpix_utils.load_map(
'{}/Stokes{}_average_map_empirical_rm_in_eor0.fits'.format(
sourcedir, pol_name))
maps.append(new_map)
# Check that the pixel arrays are identical
for pol_ind in range(len(pols) - 1):
if np.max(np.abs(maps[pol_ind].pix_arr - maps[pol_ind + 1].pix_arr)) != 0:
print('ERROR: Mismatched pixel arrays.')
sys.exit(1)
Ncomponents = np.shape(maps[0].signal_arr)[0]
stokes = np.zeros((4, 1, Ncomponents))
for pol_ind in range(len(pols)):
stokes[pol_ind, :, :] = maps[pol_ind].signal_arr
stokes = Quantity(stokes, 'Jy/sr')
freq_array = Quantity([182000000], 'Hz')