def do_vca(vcacube, array_save_loc, fig_save_loc):
"""This function greets to
the person passed in as
parameter"""
vca_array = np.zeros(3)
#arlen=int(len(vcacube.data[:,0,0]))/10
#do full thickness mom0 SPS and add to array first
#import data and compute moment 0
moment0 = vcacube.moment(order=0)
#compute SPS, add in distance at some point as parameter
pspec = PowerSpectrum(moment0)
pspec.run(verbose=False, xunit=u.pix**-1)
vca_array = np.vstack(
(vca_array, [pspec.slope,
len(vcacube[:, 0, 0]), pspec.slope_err]))
#iterate VCA over fractions of the total width of the PPV vcacube
for i in [128, 64, 32, 16, 8, 4, 2, 1]:
vcacube.allow_huge_operations = True
downsamp_vcacube = vcacube.downsample_axis(i, axis=0)
downsamp_vcacube.allow_huge_operations = True
vca = VCA(downsamp_vcacube)
vca.run(verbose=False,
beam_correct=correctbeam,
save_name=fig_save_loc + '_thickness' + str(i) + '.png')
vca_array = np.vstack((vca_array, [vca.slope, i, vca.slope_err]))
vca_array = vca_array[1:, :]
#save the array for future plotting without recomputing
np.save(array_save_loc, vca_array)
def do_vca(input):
#split inputs into the components
vcacube, chansamps, array_save_loc, fig_save_loc = input
print('starting' + str(vcacube))
#load in the vcacube
vcacube = SpectralCube.read(vcacube)
#check for only nans in first slice of cube, even though it reads the unmasked
# data the data in the fits may be masked in some way before it reaches this point which will cause the vca to fail if there are only nonfinite values in the subcube
finites = 0
nonfinites = 0
for checkx in np.arange(0, len(vcacube.unmasked_data[0, :, 0])):
for checky in np.arange(0, len(vcacube.unmasked_data[0, 0, :])):
if np.isfinite(vcacube.unmasked_data[0, checkx, checky]) == True:
finites += 1
else:
nonfinites += 1
#do vca or skip depending on whether its only NaNs
if finites < 1:
return 'data is only NaNs/inf'
else:
#do full thickness mom0 SPS and add to array first
#import data and compute moment 0
moment0 = vcacube.moment(order=0)
#compute SPS, add in distance at some point as parameter
pspec = PowerSpectrum(moment0)
pspec.run(verbose=False, xunit=u.pix**-1)
vca_array = [pspec.slope, len(vcacube[:, 0, 0]), pspec.slope_err]
#iterate VCA over fractions of the total width of the PPV vcacube
#for i in [128,64,32,16,8,4,2,1]:
for i in chansamps:
vcacube.allow_huge_operations = True
downsamp_vcacube = vcacube.downsample_axis(i, axis=0)
downsamp_vcacube.allow_huge_operations = True
vca = VCA(downsamp_vcacube)
vca.run(verbose=True, save_name=f'{fig_save_loc}_thickness{i}.png')
vca_array = np.vstack((vca_array, [vca.slope, i, vca.slope_err]))
#save the array for future plotting without recomputing
np.save(array_save_loc, vca_array)
return vca_array
print('finished' + str(vcacube))
def run_pspec(cube,
distance=414 * u.pc,
xunit=u.pix**-1,
pickle_file=None,
keep_data=False,
**kwargs):
cube = SpectralCube.read(cube)
mom0_hdu = cube.moment0().hdu
pspec = PowerSpectrum(mom0_hdu, distance=distance)
pspec.run(xunit=xunit, **kwargs)
if pickle_file:
pspec.save_results(pickle_file, keep_data=keep_data)
return pspec
def test_pspec(plotname="pspec_rnoise_beamsmooth_apodizetukey.pdf",
size=256,
powerlaw=3.,
run_kwargs={
'verbose': False,
'apodize_kernel': 'tukey'
},
plot_kwargs={'fit_color': 'black'},
beam_smooth=True,
pixel_scale=2 * u.arcsec,
bmin=8.09 * u.arcsec,
bmaj=10.01 * u.arcsec,
bpa=-12.9 * u.deg,
restfreq=1.4 * u.GHz,
bunit=u.K):
from spectral_cube import Projection
from radio_beam import Beam
rnoise_img = make_extended(size, powerlaw)
# Create a FITS HDU
rnoise_hdu = create_fits_hdu(rnoise_img, 2 * u.arcsec, 2 * u.arcsec,
rnoise_img.shape, 1.4 * u.GHz, u.K)
pspec = PowerSpectrum(rnoise_hdu)
if beam_smooth:
pencil_beam = Beam(0 * u.deg)
rnoise_proj = Projection.from_hdu(rnoise_hdu).with_beam(pencil_beam)
new_beam = Beam(bmaj, bmin, bpa)
rnoise_conv = rnoise_proj.convolve_to(new_beam)
# hdr = fits.Header(header)
# rnoise_hdu = fits.PrimaryHDU(rnoise_img, header=hdr)
pspec = PowerSpectrum(rnoise_conv)
pspec.run(**run_kwargs)
pspec.plot_fit(save_name=plotname, **plot_kwargs)
return pspec
def make_psf_beam_function(kern_fpath):
# Load in the pspec and use a spline fit of the pspec for the beam
# model
kern_pspec = PowerSpectrum.load_results(kern_fpath)
largest_val = kern_pspec.ps1D[0]
smallest_freq = kern_pspec.freqs.value[0]
spl = InterpolatedUnivariateSpline(kern_pspec.freqs.value, kern_pspec.ps1D)
def beam_model(f):
beam_vals = np.empty_like(f)
# beam_vals = T.zeros_like(f)
# if on scales larger than the kernel image, return
# value on largest scale
beam_vals[f < smallest_freq] = largest_val
beam_vals[f >= smallest_freq] = spl(f[f >= smallest_freq])
return beam_vals
return beam_model
def plot_pspec(pspec_file,
save_fig="pspec.pdf",
plot_fit_kwargs={
"fit_color": "black",
'show': False
},
refit=False,
refit_kwargs={
"low_cut": 0.01 / u.pix,
"high_cut": 0.1 / u.pix,
'weighted_fit': False,
}):
try:
pspec = PowerSpectrum.load_results(pspec_file)
except:
pass
if refit:
pspec.fit_pspec(**refit_kwargs)
pspec.save_results(pspec_file, keep_data=True)
pl = pspec.plot_fit(save_name=save_fig, **plot_fit_kwargs)
plt.gcf().clear()
def pspec_noise(cube="../subcubes/c18o_jrf_l1641n.fits",
vel_low=12 * u.km / u.s,
vel_hi=16 * u.km / u.s,
run_kwargs={},
pspec_file="pspec_noise_c18o_jrf_l1641n"):
try:
cube = SpectralCube.read(cube)
except:
pass
noise_hdu = cube.spectral_slab(vel_low, vel_hi).moment0().hdu
noise_pspec = PowerSpectrum(noise_hdu)
noise_pspec.run(**run_kwargs)
noise_pspec.save_results(pspec_file)
return noise_pspec
vca = VCA(cube_dsamp).run(low_cut=1 / (100 * u.pix),
high_cut=(1 / 4.) / u.pix,
fit_2D_kwargs={"fix_ellip_params": True},
verbose=False,
fit_2D=True)
# plt.draw()
# input((sl_pix, vca.slope, vca.slope2D, vca.ellip2D, vca.ellip2D_err))
# plt.clf()
vca_slopes.append(vca.slope)
vca_slopes_2D.append(vca.slope2D)
vel_size.append(np.abs(np.diff(cube_dsamp.spectral_axis.value))[:1])
# pspec = PowerSpectrum(mom0).run(low_cut=1 / (64 * u.pix),
# high_cut=0.5 / u.pix, verbose=False)
pspec = PowerSpectrum(mom0).run(low_cut=1 / (100 * u.pix),
high_cut=(1 / 4.) / u.pix,
fit_2D_kwargs={"fix_ellip_params": True},
verbose=False)
outputs['VCA'].append(vca_slopes)
outputs['VCA_2D'].append(vca_slopes_2D)
outputs['pspec'].append(pspec.slope)
outputs['pspec_2D'].append(pspec.slope2D)
vel_size.append(np.ptp(cube.spectral_axis.value))
axes[0].semilogx(vel_size,
vca_slopes + [pspec.slope],
'-',
label='{}'.format(rep + 1),
marker=markers[rep])
rnoise_img = make_extended(256, powerlaw=3.)
pixel_scale = 3 * u.arcsec
beamfwhm = 3 * u.arcsec
imshape = rnoise_img.shape
restfreq = 1.4 * u.GHz
bunit = u.K
plaw_hdu = create_fits_hdu(rnoise_img, pixel_scale, beamfwhm, imshape,
restfreq, bunit)
plt.imshow(plaw_hdu.data, cmap='viridis')
plt.savefig(osjoin(fig_path, "rednoise_slope3_img.png"))
plt.close()
pspec = PowerSpectrum(plaw_hdu)
pspec.run(verbose=True,
radial_pspec_kwargs={'binsize': 1.0},
fit_kwargs={'weighted_fit': False},
fit_2D=False,
low_cut=1. / (60 * u.pix),
save_name=osjoin(fig_path, "rednoise_pspec_slope3.png"))
pspec_partial = PowerSpectrum(rnoise_img[:128, :128],
header=plaw_hdu.header)
pspec_partial.run(verbose=False, fit_2D=False, low_cut=1 / (60. * u.pix))
plt.imshow(np.log10(pspec_partial.ps2D))
plt.savefig(osjoin(fig_path, "rednoise_pspec_slope3_2D_slicecross.png"))
plt.close()
pspec2 = PowerSpectrum(plaw_hdu)
mvc.run()
mvc_val = mvc.ps1D
mvc_slope = mvc.slope
mvc_slope2D = mvc.slope2D
# Spatial Power Spectrum/ Bispectrum
from turbustat.statistics import (PSpec_Distance, Bispectrum_Distance,
Bispectrum, PowerSpectrum)
pspec_distance = \
PSpec_Distance(dataset1["moment0"],
dataset2["moment0"]).distance_metric()
pspec = PowerSpectrum(dataset1['moment0'])
pspec.run()
pspec_val = pspec.ps1D
pspec_slope = pspec.slope
pspec_slope2D = pspec.slope2D
bispec_distance = \
Bispectrum_Distance(dataset1["moment0"],
dataset2["moment0"]).distance_metric()
bispec_val = bispec_distance.bispec1.bicoherence
azimuthal_slice = bispec_distance.bispec1.azimuthal_slice(16, 10,
value='bispectrum_logamp',
bin_width=5 * u.deg)
slopes_wrap_err = []
slopes_pspec_err = []
slopes_wave_err = []
size = 256
for slope in np.arange(0.5, 4.5, 0.5):
test_img = fits.PrimaryHDU(make_extended(size, powerlaw=slope))
# The power-law behaviour continues up to ~1/4 of the size
delvar = DeltaVariance(test_img).run(xlow=3 * u.pix,
xhigh=0.25 * size * u.pix,
boundary='wrap')
slopes_wrap.append(delvar.slope)
slopes_wrap_err.append(delvar.slope_err)
pspec = PowerSpectrum(test_img)
pspec.run(fit_2D=False, radial_pspec_kwargs={'binsize': 2.0},
fit_kwargs={'weighted_fit': False},
low_cut=1 / (15 * u.pix),
verbose=False)
# plt.draw()
# input("{0} {1}?".format(slope, - pspec.slope))
# plt.clf()
slopes_pspec.append(-pspec.slope)
slopes_pspec_err.append(pspec.slope_err)
wave = Wavelet(test_img).run(xhigh=0.15 * size * u.pix,
xlow=0.02 * size * u.pix)
slopes_wave.append(wave.slope)
slopes_wave_err.append(wave.slope_err)
import astropy.units as u
plt.rcParams['axes.unicode_minus'] = False
size = 512
slope = 3
test_img = fits.PrimaryHDU(
make_extended(size,
powerlaw=slope,
ellip=0.4,
theta=(60 * u.deg).to(u.rad),
randomseed=345987))
# The power-law behaviour continues up to ~1/4 of the size
pspec = PowerSpectrum(test_img)
pspec.run(fit_2D=True,
radial_pspec_kwargs={'binsize': 2.0},
fit_kwargs={'weighted_fit': False},
low_cut=1 / (15 * u.pix),
verbose=False)
print("{0}+/-{1}".format(pspec.slope, pspec.slope_err))
print("{0}+/-{1}".format(pspec.slope2D, pspec.slope2D_err))
print("{0}+/-{1}".format(pspec.ellip2D, pspec.ellip2D_err))
print("{0}+/-{1}".format(pspec.theta2D, pspec.theta2D_err))
# pspec.plot_fit(show_2D=True)
width = 8.75
# fig_ratio = (4.4 / 6.4) / 2
pdf_mom0.run(verbose=True, model=stats.pareto, fit_type='mle', floc=False,
save_name=osjoin(fig_path, "pdf_design4_mom0_plaw.png"))
cube = SpectralCube.read(osjoin(data_path, "Design4_flatrho_0021_00_radmc.fits"))
pdf_cube = PDF(cube)
pdf_cube.run(verbose=True, do_fit=False,
save_name=osjoin(fig_path, "pdf_design4.png"))
# PSpec
if run_pspec:
from turbustat.statistics import PowerSpectrum
moment0 = fits.open(osjoin(data_path, "Design4_flatrho_0021_00_radmc_moment0.fits"))[0]
pspec = PowerSpectrum(moment0, distance=250 * u.pc)
pspec.run(verbose=True, xunit=u.pix**-1,
save_name=osjoin(fig_path, "design4_pspec.png"))
pspec.run(verbose=True, xunit=u.pix**-1,
low_cut=0.025 / u.pix, high_cut=0.1 / u.pix,
save_name=osjoin(fig_path, "design4_pspec_limitedfreq.png"))
print(pspec.slope2D, pspec.slope2D_err)
print(pspec.ellip2D, pspec.ellip2D_err)
print(pspec.theta2D, pspec.theta2D_err)
# How about fitting a break?
pspec = PowerSpectrum(moment0, distance=250 * u.pc)
pspec.run(verbose=True, xunit=u.pc**-1,
low_cut=0.025 / u.pix, high_cut=0.4 / u.pix, fit_2D=False,
def generate_unitvals():
import numpy as np
import astropy.units as u
# The machine producing these values should have emcee installed!
try:
import emcee
except ImportError:
raise ImportError("Install emcee to generate unit test data.")
from turbustat.tests._testing_data import dataset1, dataset2
# Wavelet Transform
from turbustat.statistics import Wavelet_Distance, Wavelet
wavelet_distance = \
Wavelet_Distance(dataset1["moment0"],
dataset2["moment0"]).distance_metric()
wavelet_val = wavelet_distance.wt1.values
wavelet_slope = wavelet_distance.wt1.slope
# Wavelet with a break
wave_break = Wavelet(dataset1['moment0']).run(xhigh=7 * u.pix,
brk=5.5 * u.pix)
wavelet_slope_wbrk = wave_break.slope
wavelet_brk_wbrk = wave_break.brk.value
# MVC
from turbustat.statistics import MVC_Distance, MVC
mvc_distance = MVC_Distance(dataset1, dataset2).distance_metric()
mvc = MVC(dataset1["centroid"], dataset1["moment0"], dataset1["linewidth"])
mvc.run()
mvc_val = mvc.ps1D
mvc_slope = mvc.slope
mvc_slope2D = mvc.slope2D
# Spatial Power Spectrum/ Bispectrum
from turbustat.statistics import (PSpec_Distance, Bispectrum_Distance,
Bispectrum, PowerSpectrum)
pspec_distance = \
PSpec_Distance(dataset1["moment0"],
dataset2["moment0"]).distance_metric()
pspec = PowerSpectrum(dataset1['moment0'])
pspec.run()
pspec_val = pspec.ps1D
pspec_slope = pspec.slope
pspec_slope2D = pspec.slope2D
bispec_distance = \
Bispectrum_Distance(dataset1["moment0"],
dataset2["moment0"]).distance_metric()
bispec_val = bispec_distance.bispec1.bicoherence
azimuthal_slice = bispec_distance.bispec1.azimuthal_slice(
16, 10, value='bispectrum_logamp', bin_width=5 * u.deg)
bispec_azim_bins = azimuthal_slice[16][0]
bispec_azim_vals = azimuthal_slice[16][1]
bispec_azim_stds = azimuthal_slice[16][2]
bispec_meansub = Bispectrum(dataset1['moment0'])
bispec_meansub.run(mean_subtract=True)
bispec_val_meansub = bispec_meansub.bicoherence
# Genus
from turbustat.statistics import GenusDistance, Genus
smooth_scales = np.linspace(1.0, 0.1 * min(dataset1["moment0"][0].shape),
5)
genus_distance = \
GenusDistance(dataset1["moment0"],
dataset2["moment0"],
lowdens_percent=20,
genus_kwargs=dict(match_kernel=True)).distance_metric()
# The distance method requires standardizing the data. Make a
# separate version that isn't
genus = Genus(dataset1['moment0'], smoothing_radii=smooth_scales)
genus.run(match_kernel=True)
genus_val = genus.genus_stats
# Delta-Variance
from turbustat.statistics import DeltaVariance_Distance, DeltaVariance
delvar_distance = \
DeltaVariance_Distance(dataset1["moment0"],
dataset2["moment0"],
weights1=dataset1["moment0_error"][0],
weights2=dataset2["moment0_error"][0],
delvar_kwargs=dict(xhigh=11 * u.pix))
delvar_distance.distance_metric()
delvar = DeltaVariance(dataset1["moment0"],
weights=dataset1['moment0_error'][0]).run(xhigh=11 *
u.pix)
delvar_val = delvar.delta_var
delvar_slope = delvar.slope
# Test with a break point
delvar_wbrk = \
DeltaVariance(dataset1["moment0"],
weights=dataset1['moment0_error'][0]).run(xhigh=11 * u.pix,
brk=6 * u.pix)
delvar_slope_wbrk = delvar_wbrk.slope
delvar_brk = delvar_wbrk.brk.value
# Change boundary conditions
delvar_fill = \
DeltaVariance(dataset1["moment0"],
weights=dataset1['moment0_error'][0]).run(xhigh=11 * u.pix,
boundary='fill',
nan_treatment='interpolate')
delvar_fill_val = delvar_fill.delta_var
delvar_fill_slope = delvar_fill.slope
# VCA/VCS
from turbustat.statistics import VCA_Distance, VCS_Distance, VCA
vcs_distance = VCS_Distance(dataset1["cube"],
dataset2["cube"],
fit_kwargs=dict(high_cut=0.3 / u.pix,
low_cut=3e-2 / u.pix))
vcs_distance.distance_metric()
vcs_val = vcs_distance.vcs1.ps1D
vcs_slopes = vcs_distance.vcs1.slope
vca_distance = VCA_Distance(dataset1["cube"],
dataset2["cube"]).distance_metric()
vca = VCA(dataset1['cube'])
vca.run()
vca_val = vca.ps1D
vca_slope = vca.slope
vca_slope2D = vca.slope2D
# Tsallis
from turbustat.statistics import Tsallis
tsallis_kwargs = {"sigma_clip": 5, "num_bins": 100}
tsallis = Tsallis(dataset1['moment0'], lags=[1, 2, 4, 8, 16] * u.pix)
tsallis.run(periodic=True, **tsallis_kwargs)
tsallis_val = tsallis.tsallis_params
tsallis_stderrs = tsallis.tsallis_stderrs
tsallis_noper = Tsallis(dataset1['moment0'], lags=[1, 2, 4, 8, 16] * u.pix)
tsallis_noper.run(periodic=False, num_bins=100)
tsallis_val_noper = tsallis_noper.tsallis_params
# High-order stats
from turbustat.statistics import StatMoments_Distance, StatMoments
moment_distance = \
StatMoments_Distance(dataset1["moment0"],
dataset2["moment0"]).distance_metric()
kurtosis_val = moment_distance.moments1.kurtosis_hist[1]
skewness_val = moment_distance.moments1.skewness_hist[1]
# Save a few from the non-distance version
tester = StatMoments(dataset1["moment0"])
tester.run()
kurtosis_nondist_val = tester.kurtosis_hist[1]
skewness_nondist_val = tester.skewness_hist[1]
# Non-periodic
tester = StatMoments(dataset1["moment0"])
tester.run(periodic=False)
kurtosis_nonper_val = tester.kurtosis_hist[1]
skewness_nonper_val = tester.skewness_hist[1]
# PCA
from turbustat.statistics import PCA_Distance, PCA
pca_distance = PCA_Distance(dataset1["cube"],
dataset2["cube"]).distance_metric()
pca = PCA(dataset1["cube"], distance=250 * u.pc)
pca.run(mean_sub=True,
eigen_cut_method='proportion',
min_eigval=0.75,
spatial_method='contour',
spectral_method='walk-down',
fit_method='odr',
brunt_beamcorrect=False,
spectral_output_unit=u.m / u.s)
pca_val = pca.eigvals
pca_spectral_widths = pca.spectral_width().value
pca_spatial_widths = pca.spatial_width().value
pca_fit_vals = {
"index": pca.index,
"gamma": pca.gamma,
"intercept": pca.intercept().value,
"sonic_length": pca.sonic_length()[0].value
}
# Now get those values using mcmc
pca.run(mean_sub=True,
eigen_cut_method='proportion',
min_eigval=0.75,
spatial_method='contour',
spectral_method='walk-down',
fit_method='bayes',
brunt_beamcorrect=False,
spectral_output_unit=u.m / u.s)
pca_fit_vals["index_bayes"] = pca.index
pca_fit_vals["gamma_bayes"] = pca.gamma
pca_fit_vals["intercept_bayes"] = pca.intercept().value
pca_fit_vals["sonic_length_bayes"] = pca.sonic_length()[0].value
# Record the number of eigenvalues kept by the auto method
pca.run(mean_sub=True,
n_eigs='auto',
min_eigval=0.001,
eigen_cut_method='value',
decomp_only=True)
pca_fit_vals["n_eigs_value"] = pca.n_eigs
# Now w/ the proportion of variance cut
pca.run(mean_sub=True,
n_eigs='auto',
min_eigval=0.99,
eigen_cut_method='proportion',
decomp_only=True)
pca_fit_vals["n_eigs_proportion"] = pca.n_eigs
# SCF
from turbustat.statistics import SCF_Distance, SCF
scf_distance = SCF_Distance(dataset1["cube"], dataset2["cube"],
size=11).distance_metric()
scf = SCF(dataset1['cube'], size=11).run()
scf_val = scf.scf_surface
scf_spectrum = scf.scf_spectrum
scf_slope = scf.slope
scf_slope2D = scf.slope2D
# Now run the SCF when the boundaries aren't continuous
scf_distance_cut_bound = SCF_Distance(dataset1["cube"],
dataset2["cube"],
size=11,
boundary='cut').distance_metric()
scf_val_noncon_bound = scf_distance_cut_bound.scf1.scf_surface
scf_fitlims = SCF(dataset1['cube'], size=11)
scf_fitlims.run(boundary='continuous', xlow=1.5 * u.pix, xhigh=4.5 * u.pix)
scf_slope_wlimits = scf_fitlims.slope
scf_slope_wlimits_2D = scf_fitlims.slope2D
# Cramer Statistic
from turbustat.statistics import Cramer_Distance
cramer_distance = Cramer_Distance(
dataset1["cube"], dataset2["cube"], noise_value1=0.1,
noise_value2=0.1).distance_metric(normalize=False)
cramer_val = cramer_distance.data_matrix1
# Dendrograms
from turbustat.statistics import Dendrogram_Distance, Dendrogram_Stats
min_deltas = np.logspace(-1.5, 0.5, 40)
dendro_distance = Dendrogram_Distance(
dataset1["cube"], dataset2["cube"],
min_deltas=min_deltas).distance_metric()
dendrogram_val = dendro_distance.dendro1.numfeatures
# With periodic boundaries
dendro = Dendrogram_Stats(dataset1['cube'], min_deltas=min_deltas)
dendro.run(periodic_bounds=True)
dendrogram_periodic_val = dendro.numfeatures
# PDF
from turbustat.statistics import PDF_Distance
pdf_distance = \
PDF_Distance(dataset1["moment0"],
dataset2["moment0"],
min_val1=0.05,
min_val2=0.05,
weights1=dataset1["moment0_error"][0]**-2.,
weights2=dataset2["moment0_error"][0]**-2.,
do_fit=False,
normalization_type='standardize')
pdf_distance.distance_metric()
pdf_val = pdf_distance.PDF1.pdf
pdf_ecdf = pdf_distance.PDF1.ecdf
pdf_bins = pdf_distance.bins
# Do a fitted version of the PDF pca
pdf_fit_distance = \
PDF_Distance(dataset1["moment0"],
dataset2["moment0"],
min_val1=0.05,
min_val2=0.05,
do_fit=True,
normalization_type=None)
pdf_fit_distance.distance_metric()
np.savez_compressed('checkVals',
wavelet_val=wavelet_val,
wavelet_slope=wavelet_slope,
wavelet_slope_wbrk=wavelet_slope_wbrk,
wavelet_brk_wbrk=wavelet_brk_wbrk,
mvc_val=mvc_val,
mvc_slope=mvc_slope,
mvc_slope2D=mvc_slope2D,
pspec_val=pspec_val,
pspec_slope=pspec_slope,
pspec_slope2D=pspec_slope2D,
bispec_val=bispec_val,
bispec_azim_bins=bispec_azim_bins,
bispec_azim_vals=bispec_azim_vals,
bispec_azim_stds=bispec_azim_stds,
bispec_val_meansub=bispec_val_meansub,
genus_val=genus_val,
delvar_val=delvar_val,
delvar_slope=delvar_slope,
delvar_slope_wbrk=delvar_slope_wbrk,
delvar_brk=delvar_brk,
delvar_fill_val=delvar_fill_val,
delvar_fill_slope=delvar_fill_slope,
vcs_val=vcs_val,
vcs_slopes=vcs_slopes,
vca_val=vca_val,
vca_slope=vca_slope,
vca_slope2D=vca_slope2D,
tsallis_val=tsallis_val,
tsallis_stderrs=tsallis_stderrs,
tsallis_val_noper=tsallis_val_noper,
kurtosis_val=kurtosis_val,
skewness_val=skewness_val,
kurtosis_nondist_val=kurtosis_nondist_val,
skewness_nondist_val=skewness_nondist_val,
kurtosis_nonper_val=kurtosis_nonper_val,
skewness_nonper_val=skewness_nonper_val,
pca_val=pca_val,
pca_fit_vals=pca_fit_vals,
pca_spectral_widths=pca_spectral_widths,
pca_spatial_widths=pca_spatial_widths,
scf_val=scf_val,
scf_slope_wlimits=scf_slope_wlimits,
scf_slope_wlimits_2D=scf_slope_wlimits_2D,
scf_val_noncon_bound=scf_val_noncon_bound,
scf_spectrum=scf_spectrum,
scf_slope=scf_slope,
scf_slope2D=scf_slope2D,
cramer_val=cramer_val,
dendrogram_val=dendrogram_val,
dendrogram_periodic_val=dendrogram_periodic_val,
pdf_val=pdf_val,
pdf_bins=pdf_bins,
pdf_ecdf=pdf_ecdf)
np.savez_compressed(
'computed_distances',
mvc_distance=mvc_distance.distance,
pca_distance=pca_distance.distance,
vca_distance=vca_distance.distance,
pspec_distance=pspec_distance.distance,
scf_distance=scf_distance.distance,
wavelet_distance=wavelet_distance.distance,
delvar_curve_distance=delvar_distance.curve_distance,
delvar_slope_distance=delvar_distance.slope_distance,
# tsallis_distance=tsallis_distance.distance,
kurtosis_distance=moment_distance.kurtosis_distance,
skewness_distance=moment_distance.skewness_distance,
cramer_distance=cramer_distance.distance,
genus_distance=genus_distance.distance,
vcs_distance=vcs_distance.distance,
bispec_mean_distance=bispec_distance.mean_distance,
bispec_surface_distance=bispec_distance.surface_distance,
dendrohist_distance=dendro_distance.histogram_distance,
dendronum_distance=dendro_distance.num_distance,
pdf_hellinger_distance=pdf_distance.hellinger_distance,
pdf_ks_distance=pdf_distance.ks_distance,
pdf_lognorm_distance=pdf_fit_distance.lognormal_distance)
cube = SpectralCube.read(
osjoin(data_path, "Design4_flatrho_0021_00_radmc.fits"))
pdf_cube = PDF(cube)
pdf_cube.run(verbose=True,
do_fit=False,
save_name=osjoin(fig_path, "pdf_design4.png"))
# PSpec
if run_pspec:
from turbustat.statistics import PowerSpectrum
moment0 = fits.open(
osjoin(data_path, "Design4_flatrho_0021_00_radmc_moment0.fits"))[0]
pspec = PowerSpectrum(moment0, distance=250 * u.pc)
pspec.run(verbose=True,
xunit=u.pix**-1,
save_name=osjoin(fig_path, "design4_pspec.png"))
pspec.run(verbose=True,
xunit=u.pix**-1,
low_cut=0.02 / u.pix,
high_cut=0.1 / u.pix,
save_name=osjoin(fig_path, "design4_pspec_limitedfreq.png"))
print(pspec.slope2D, pspec.slope2D_err)
print(pspec.ellip2D, pspec.ellip2D_err)
print(pspec.theta2D, pspec.theta2D_err)
# How about fitting a break?
cube = SpectralCube.read(
osjoin(data_path, "Design4_flatrho_0021_00_radmc.fits"))
pdf_cube = PDF(cube)
pdf_cube.run(verbose=True,
do_fit=False,
save_name=osjoin(fig_path, "pdf_design4.png"))
# PSpec
if run_pspec:
from turbustat.statistics import PowerSpectrum
moment0 = fits.open(
osjoin(data_path, "Design4_flatrho_0021_00_radmc_moment0.fits"))[0]
pspec = PowerSpectrum(moment0, distance=250 * u.pc)
pspec.run(verbose=True,
xunit=u.pix**-1,
save_name=osjoin(fig_path, "design4_pspec.png"))
pspec.run(verbose=True,
xunit=u.pix**-1,
low_cut=0.025 / u.pix,
high_cut=0.1 / u.pix,
save_name=osjoin(fig_path, "design4_pspec_limitedfreq.png"))
print(pspec.slope2D, pspec.slope2D_err)
print(pspec.ellip2D, pspec.ellip2D_err)
print(pspec.theta2D, pspec.theta2D_err)
# How about fitting a break?
rnoise_img = make_extended(256, powerlaw=3.)
pixel_scale = 3 * u.arcsec
beamfwhm = 3 * u.arcsec
imshape = rnoise_img.shape
restfreq = 1.4 * u.GHz
bunit = u.K
plaw_hdu = create_fits_hdu(rnoise_img, pixel_scale, beamfwhm, imshape,
restfreq, bunit)
plt.imshow(plaw_hdu.data, cmap='viridis')
plt.savefig(osjoin(fig_path, "rednoise_slope3_img.png"))
plt.close()
pspec = PowerSpectrum(plaw_hdu)
pspec.run(verbose=True, radial_pspec_kwargs={'binsize': 1.0},
fit_kwargs={'weighted_fit': False}, fit_2D=False,
low_cut=1. / (60 * u.pix),
save_name=osjoin(fig_path, "rednoise_pspec_slope3.png"))
pspec_partial = PowerSpectrum(rnoise_img[:128, :128], header=plaw_hdu.header)
pspec_partial.run(verbose=False, fit_2D=False, low_cut=1 / (60. * u.pix))
plt.imshow(np.log10(pspec_partial.ps2D))
plt.savefig(osjoin(fig_path, "rednoise_pspec_slope3_2D_slicecross.png"))
plt.close()
pspec2 = PowerSpectrum(plaw_hdu)
pspec2.run(verbose=False, radial_pspec_kwargs={'binsize': 1.0},
fit_kwargs={'weighted_fit': False}, fit_2D=False,
low_cut=1. / (60 * u.pix),
do_fitpspec_doub_aco = False
do_makepspec_co = False
do_fitpspec_co = False
do_makepspec_dust_smooth = False
do_fitpspec_dust_smooth = True
if do_makepspec:
pspec_name = osjoin(data_path, 'M31_CO', 'm33_hi_co_dustSD.pspec.pkl')
gas_sd = hi_proj * hi_mass_conversion + co10_mass_conversion * co_proj
gas_sd[np.isnan(hi_proj)] = np.NaN
pspec = PowerSpectrum(gas_sd, distance=720 * u.kpc)
pspec.run(verbose=False, fit_2D=False, high_cut=10**-1.3 / u.pix)
# pspec.plot_fit()
pspec.save_results(pspec_name)
# Fit the pspec.
if do_fitpspec:
pspec = PowerSpectrum.load_results(pspec_name)
pspec.load_beam()
beam_size = pspec._beam.major.to(u.deg) / pspec._ang_size.to(u.deg)
beam_size = beam_size.value
beam_gauss_width = beam_size / np.sqrt(8 * np.log(2))
data_path = os.path.expanduser("~/bigdata/ekoch/Utomo19_LGdust/")
hi_name = osjoin(data_path,
"M33_14B-088_HI.clean.image.GBT_feathered.pbcov_gt_0.5_masked.moment0_Kkms.fits")
hi_pspec_name = f"{hi_name.rstrip('fits')}pspec.pkl"
hi_pspec_name_conv = f"{hi_name.rstrip('fits')}conv.pspec.pkl"
if do_makepspec:
hdu = fits.open(hi_name)
pspec = PowerSpectrum(hdu[0], distance=840 * u.kpc)
pspec.run(verbose=False, fit_2D=False)
pspec.save_results(hi_pspec_name)
if do_fitpspec:
# Fit the same as the dust column density model
plot_folder = osjoin(data_path, "{}_plots".format(gal))
if not os.path.exists(plot_folder):
os.mkdir(plot_folder)
nsamp = 6000
# input("{}".format(filename))
# plt.close()
# if res_type == 'orig':
# save_name = "{0}_{1}_mjysr.pspec.pkl".format(gal.lower(), name)
# else:
# save_name = "{0}_{1}_{2}_mjysr.pspec.pkl".format(gal.lower(), name, res_type)
# For now skip already saved power-spectra
# if os.path.exists(osjoin(data_path, 'raw', save_name)) and skip_check:
# print("Already saved pspec for {}. Skipping".format(filename))
# continue
# else:
# os.system("rm -f {}".format(osjoin(data_path, 'raw', save_name)))
pspec = PowerSpectrum(proj) # , distance=dist)
pspec.run(verbose=False, beam_correct=False, fit_2D=False,
high_cut=0.1 / u.pix,
use_pyfftw=False, threads=1,)
# apodize_kernel=fitinfo_dict[name]['apod_kern'])
# Plot 2D spec, 1D pspec, img
im0 = ax[0].imshow(np.log10(pspec.ps2D), origin='lower', cmap='viridis')
fig.colorbar(im0, ax=ax[0])
# Convert to angular units
xunit = u.arcsec**-1
ang_freqs = pspec._spatial_freq_unit_conversion(pspec.freqs, xunit).value
ax[1].loglog(ang_freqs, pspec.ps1D)
continue
else:
os.system("rm {}".format(osjoin(data_path, gal, save_name)))
# We also want to account for the shape of the masked data
# (mostly for M31)
# norm_mask = np.isfinite(proj_coldens).astype(np.float) / \
# np.isfinite(proj_coldens).sum()
# pspec_mask = PowerSpectrum(fits.PrimaryHDU(norm_mask, proj_coldens.header),
# distance=fitinfo_dict[gal]['distance'])
# pspec_mask.run(verbose=False, beam_correct=False, fit_2D=False,
# high_cut=0.1 / u.pix,
# use_pyfftw=True, threads=ncores,
# apodize_kernel=fitinfo_dict[gal]['apod_kern'])
pspec = PowerSpectrum(proj_coldens,
distance=fitinfo_dict[gal]['distance'])
pspec.compute_pspec(use_pyfftw=True,
threads=ncores,
apodize_kernel=fitinfo_dict[gal]['apod_kern'])
# Divide out the normalized mask pspec
# pspec._ps2D /= pspec_mask.ps2D
pspec.compute_radial_pspec()
# pspec.fit_pspec() # high_cut=0.1 / u.pix,)
# pspec.run(verbose=False, beam_correct=False, fit_2D=False,
# high_cut=0.1 / u.pix,
# use_pyfftw=True, threads=ncores,
# apodize_kernel=fitinfo_dict[gal]['apod_kern'])
if make_interactive:
print(pspec.slope)
pspec.plot_fit(show_residual=False, show_2D=True)
# Use broken plaw for MIPS 24 LMC
if band == 'mips24' and gal == 'LMC':
fit_params = df_bplaw.loc[
f"{gal.lower()}_{band}_{res_type}_mean"]
else:
fit_params = df.loc[f"{gal.lower()}_{band}_{res_type}"]
if res_type == 'orig':
filename = "{0}_{1}_mjysr.pspec.pkl".format(gal.lower(), band)
else:
filename = "{0}_{1}_{2}_mjysr.pspec.pkl".format(
gal.lower(), band, res_type)
pspec = PowerSpectrum.load_results(osjoin(data_path, gal,
filename))
pspec.load_beam()
beam_size = pspec._beam.major.to(u.deg) / pspec._ang_size.to(u.deg)
beam_size = beam_size.value
beam_gauss_width = beam_size / np.sqrt(8 * np.log(2))
if fitinfo_dict[gal][band]['high_cut'] is not None:
high_cut = fitinfo_dict[gal][band]['high_cut']
else:
high_cut = (1 / (beam_gauss_width * 3.))
# Fit on scales > 3 pixels to avoid flattening from pixelization
# fit_mask = pspec.freqs.value < 1 / 3.
# fit_mask = pspec.freqs.value < 0.1
# Now open the kernel file
kernfits_name = names[name][0]
kernfits_ext = names[name][1]
kernel_filename = osjoin(kern_path, kernfits_name)
kern_proj = Projection.from_hdu(fits.open(osjoin(kern_path, kernel_filename))[kernfits_ext])
img_scale = np.abs(proj_plane_pixel_scales(proj.wcs))[0]
kern_scale = np.abs(proj_plane_pixel_scales(kern_proj.wcs))[0]
kernel = resize_psf(kern_proj.value, kern_scale, img_scale)
# Normalize to make a kernel
kernel /= kernel.sum()
kern_pspec = PowerSpectrum((kernel, kern_proj.header))
kern_pspec.run(verbose=False, fit_2D=False)
save_name = "{0}_kernel_{1}.pspec.pkl".format(name, gal.lower())
kern_pspec.save_results(osjoin(data_path, gal, save_name),
keep_data=True)
# plt.draw()
# input("?")
# # plt.clf()
# plt.close()
save_name = "{0}_{1}_{2}_mjysr.pspec.pkl".format(gal.lower(),
name, slice_name)
else:
save_name = "{0}_{1}_{2}_{3}_mjysr.pspec.pkl".format(gal.lower(),
name,
res_type,
slice_name)
# For now skip already saved power-spectra
if os.path.exists(osjoin(data_path, gal, save_name)) and skip_check:
print("Already saved pspec for {}. Skipping".format(filename))
continue
else:
os.system("rm -f {}".format(osjoin(data_path, gal, save_name)))
pspec = PowerSpectrum(proj[slicer], distance=dist)
pspec.run(verbose=False, beam_correct=False, fit_2D=False,
high_cut=0.1 / u.pix,
use_pyfftw=True, threads=ncores,
apodize_kernel='tukey', alpha=0.3)
pspec.save_results(osjoin(data_path, gal, save_name),
keep_data=False)
if do_fit_pspec:
# Load model functions
repo_path = os.path.expanduser("~/ownCloud/project_code/DustyPowerSpectra/")
code_name = os.path.join(repo_path, "models.py")
exec(compile(open(code_name, "rb").read(), code_name, 'exec'))
if gal == 'M31':
# Add 180 deg to the PA
gal_obj.position_angle += 180 * u.deg
filename = osjoin(data_path, gal, fitinfo_dict[gal]['filename'])
hdu = fits.open(filename)
proj = Projection.from_hdu(hdu)
# Run on the original image
filename = "{0}_{1}_{2}_mjysr.pspec.pkl".format(gal.lower(), 'spire500',
res_type)
pspec = PowerSpectrum.load_results(osjoin(data_path, gal, filename))
pspec.load_beam()
# Deproject the image AND the beam
deproj_img = deproject(proj, proj.header, gal_obj, inc_correction=True)
# Cut this image down to the minimal size
deproj_img = deproj_img[nd.find_objects(np.isfinite(deproj_img))[0]]
# Just keep the original header. Doesn't matter until the
# conversion to phys units
deproj_img_hdu = fits.PrimaryHDU(deproj_img, proj.header)
# The beam is symmetric so we only need to warp it to match the PSF shape
# in the deprojected frame
mvc.run()
mvc_val = mvc.ps1D
mvc_slope = mvc.slope
mvc_slope2D = mvc.slope2D
# Spatial Power Spectrum/ Bispectrum
from turbustat.statistics import (PSpec_Distance, BiSpectrum_Distance,
BiSpectrum, PowerSpectrum)
pspec_distance = \
PSpec_Distance(dataset1["moment0"],
dataset2["moment0"]).distance_metric()
pspec = PowerSpectrum(dataset1['moment0'])
pspec.run()
pspec_val = pspec.ps1D
pspec_slope = pspec.slope
pspec_slope2D = pspec.slope2D
bispec_distance = \
BiSpectrum_Distance(dataset1["moment0"],
dataset2["moment0"]).distance_metric()
bispec_val = bispec_distance.bispec1.bicoherence
bispec_meansub = BiSpectrum(dataset1['moment0'])
bispec_meansub.run(mean_subtract=True)
gals = {'M33': 840 * u.kpc}
df = pd.read_csv(osjoin(data_path, "pspec_coldens_fit_results.csv"),
index_col=0)
df_hi = pd.read_csv(osjoin(data_path, "pspec_hi_conv_m33_fit_results.csv"),
index_col=0)
# Open the pspec files
hi_name = osjoin(
data_path,
"M33_14B-088_HI.clean.image.GBT_feathered.pbcov_gt_0.5_masked.moment0_Kkms.fits"
)
hi_pspec_name = f"{hi_name.rstrip('fits')}conv.pspec.pkl"
hi_pspec = PowerSpectrum.load_results(hi_pspec_name)
hi_pspec.load_beam()
dust_pspec_name = osjoin(data_path, 'M33', "m33_coldens.pspec.pkl")
dust_pspec = PowerSpectrum.load_results(dust_pspec_name)
dust_pspec.load_beam()
dust_norm = dust_pspec.ps1D.max()
hi_norm = hi_pspec.ps1D.max()
fig = plt.figure()
ax = fig.add_subplot(111)
gal = 'M33'
mom0_cutout = mom0[cutout_slice].copy()
if (np.isnan(mom0_cutout).sum() / float(mom0_cutout.size)) > 0.1:
fill_nan(fit_results)
continue
# Check to see if the pspec file already exists:
save_pspec_name = osjoin(
pspec_posn_folder,
f"{fitinfo_dict[gal]['filename'].rstrip('fits')}_y_{y}_x_{x}_pspec.pkl"
)
if not os.path.exists(save_pspec_name):
pspec = PowerSpectrum(mom0_cutout.hdu,
beam=mom0.beam,
distance=fitinfo_dict[gal]['distance'])
pspec.compute_pspec(
use_pyfftw=False,
threads=ncores,
apodize_kernel=fitinfo_dict[gal]['apod_kern'],
alpha=alpha)
pspec.compute_radial_pspec()
pspec.save_results(save_pspec_name)
else:
pspec = PowerSpectrum.load_results(save_pspec_name)
pspec.load_beam()
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
import astropy.units as u
plt.rcParams['axes.unicode_minus'] = False
size = 512
slope = 3
test_img = fits.PrimaryHDU(make_extended(size, powerlaw=slope,
ellip=0.4,
theta=(60 * u.deg).to(u.rad),
randomseed=345987))
# The power-law behaviour continues up to ~1/4 of the size
pspec = PowerSpectrum(test_img)
pspec.run(fit_2D=True, radial_pspec_kwargs={'binsize': 2.0},
fit_kwargs={'weighted_fit': False},
low_cut=1 / (15 * u.pix),
verbose=False)
print("{0}+/-{1}".format(pspec.slope, pspec.slope_err))
print("{0}+/-{1}".format(pspec.slope2D, pspec.slope2D_err))
print("{0}+/-{1}".format(pspec.ellip2D, pspec.ellip2D_err))
print("{0}+/-{1}".format(pspec.theta2D, pspec.theta2D_err))
# pspec.plot_fit(show_2D=True)
width = 8.75
# fig_ratio = (4.4 / 6.4) / 2
height = 5.07
proj_coldens = hdu_coldens[0].data[0][nd.find_objects(coldens_mask)[0]]
hi_satpt = 10. # Msol / pc^-2
# hi_satpt = 15. # Msol / pc^-2
# dense gas to dust conversion of 340 for LMC from Roman-Duval+2014
gdr = fitinfo_dict[gal]['GDR']
dust_satpt = (hi_satpt / gdr) / fitinfo_dict[gal]['cosinc'].value
sat_mask = proj_coldens >= dust_satpt
dust_sat = proj_coldens.copy()
dust_sat[sat_mask] = dust_satpt
pspec = PowerSpectrum(fits.PrimaryHDU(proj_coldens, hdr),
distance=fitinfo_dict[gal]['distance'])
pspec.run(verbose=False, fit_2D=False)
pspec_sat = PowerSpectrum(fits.PrimaryHDU(dust_sat, hdr),
distance=fitinfo_dict[gal]['distance'])
pspec_sat.run(verbose=False, fit_2D=False)
beam_size = pspec_sat._beam.major.to(u.deg) / pspec_sat._ang_size.to(u.deg)
beam_size = beam_size.value
beam_gauss_width = beam_size / np.sqrt(8 * np.log(2))
high_cut = (1 / (beam_gauss_width * 3.))
fit_mask = pspec_sat.freqs.value < high_cut
# And cut out the largest scales due to expected deviations with
filename = osjoin(data_path, gal, fitinfo_dict[gal]['filename'])
hdu_coldens = fits.open(filename)
proj_coldens = Projection.from_hdu(
fits.PrimaryHDU(hdu_coldens[0].data[0].squeeze(),
hdu_coldens[0].header))
# Get minimal size
proj_coldens = proj_coldens[nd.find_objects(np.isfinite(proj_coldens))[0]]
proj_coldens = proj_coldens.with_beam(fitinfo_dict[gal]['beam'])
# Run on the original image
pspec = PowerSpectrum(proj_coldens, distance=fitinfo_dict[gal]['distance'])
pspec.run(
verbose=False,
beam_correct=False,
fit_2D=False,
high_cut=0.1 / u.pix,
use_pyfftw=True,
threads=ncores,
# radial_pspec_kwargs={"theta_0": gal_obj.position_angle + 90*u.deg, "delta_theta": 50 * u.deg},
# radial_pspec_kwargs={"logspacing": True, 'binsize': 10.},
apodize_kernel=fitinfo_dict[gal]['apod_kern'])
# Deproject the image AND the beam
deproj_img = deproject(proj_coldens,
proj_coldens.header,
df = pd.read_csv(osjoin(data_path, "pspec_spire500_deproj_fit_results.csv"), index_col=0)
fig, axes = plt.subplots(1, 2)
for i, (gal, ax) in enumerate(zip(gals, axes.ravel())):
for ch in ['orig', 'dep']:
fit_params = df.loc[f"{gal.lower()}_{ch}"]
if ch == 'orig':
filename = "{0}_spire500_mod_mjysr.pspec.pkl".format(gal.lower())
else:
filename = "{0}_spire500_mod_mjysr_deproj.pspec.pkl".format(gal.lower())
pspec = PowerSpectrum.load_results(osjoin(data_path, gal, filename))
pspec.load_beam()
beam_size = pspec._beam.major.to(u.deg) / pspec._ang_size.to(u.deg)
beam_size = beam_size.value
beam_gauss_width = beam_size / np.sqrt(8 * np.log(2))
high_cut = (1 / (beam_gauss_width * 1.5))
fit_mask = pspec.freqs.value < high_cut
# And cut out the largest scales due to expected deviations with
# small stddev
fit_mask[:2] = False
freqs = pspec.freqs.value[fit_mask]
beam_freqs = pspec.freqs.value[fit_mask]
out_filename = "{}_cutout.fits".format(filename.rstrip(".fits"))
if not os.path.exists(osjoin(data_path, gal, out_filename)):
proj.write(osjoin(data_path, gal, out_filename))
save_name = f"{out_filename.rstrip('.fits')}.pspec.pkl"
# For now skip already saved power-spectra
if os.path.exists(osjoin(data_path, gal,
save_name)) and skip_check:
print("Already saved pspec for {}. Skipping".format(filename))
continue
else:
os.system("rm -f {}".format(osjoin(data_path, gal, save_name)))
pspec = PowerSpectrum(proj, distance=dist)
pspec.run(verbose=False,
beam_correct=False,
fit_2D=False,
high_cut=0.1 / u.pix,
use_pyfftw=True,
threads=ncores,
apodize_kernel=fitinfo_dict[gal][name]['apod_kern'])
pspec.save_results(osjoin(data_path, gal, save_name),
keep_data=False)
del pspec, proj, hdu
if run_fits:
plt.subplot(324, sharex=ax1)
_ = plt.hist(diff[np.isfinite(diff)])
plt.title("Diff in feathers")
plt.subplot(325, sharex=ax1)
_ = plt.hist(diff_orig_uvc[np.isfinite(diff_orig_uvc)])
plt.title("Orig - uvcombine feather")
plt.subplot(326, sharex=ax1)
_ = plt.hist(diff_orig_casa[np.isfinite(diff_orig_casa)])
plt.title("Orig - CASA feather")
plt.figure()
orig_pspec = PowerSpectrum(input_proj).run(verbose=False, fit_2D=False)
casafeather_pspec = PowerSpectrum(casa_feather_proj).run(verbose=False,
fit_2D=False)
uvcombfeather_pspec = PowerSpectrum(uvcomb_feather_proj).run(verbose=False,
fit_2D=False)
sd_pspec = PowerSpectrum(sd_proj).run(verbose=False, fit_2D=False)
sd_pspec_beamcorr = PowerSpectrum(sd_proj).run(verbose=False,
fit_2D=False,
beam_correct=True)
intf_pspec = PowerSpectrum(intf_proj).run(verbose=False, fit_2D=False)
plt.loglog(orig_pspec.freqs.value, orig_pspec.ps1D, label='Original')
plt.loglog(casafeather_pspec.freqs.value,
casafeather_pspec.ps1D,
label='CASA feath')
