def calculate_noise_cube(cube=None, velocity_axis=None,
velocity_noise_range=[-110,-90,90,110], header=None, Tsys=30.,
filename=None):
""" Calcuates noise envelopes for each pixel in a cube
"""
import numpy as np
import pyfits as pf
from mycoords import make_velocity_axis
if velocity_axis is None:
velocity_axis = make_velocity_axis(header)
noise_cube = np.zeros(cube.shape)
for i in range(cube.shape[1]):
for j in range(cube.shape[2]):
profile = cube[:,i,j]
noise = calculate_noise(profile, velocity_axis,
velocity_noise_range)
#noise = 0.1 # measured in line free region
noise_cube[:,i,j] = calculate_noise_scale(Tsys,
profile, noise=noise)
if filename is not None:
pf.writeto(filename, noise_cube, header=header)
return noise_cube
def plot_co_spectra(results,):
filename_base = \
cloud_results['figure_dir'] + 'diagnostics/' + \
cloud_results['filename_extension'] + '_co_spectra'
from astropy.io import fits
from mycoords import make_velocity_axis
from myimage_analysis import bin_image
from myio import check_file
cloud = cloud_results['cloud']
co_filename = cloud.co_filename
if cloud_results['args']['bin_procedure'] in ('all', 'mle'):
co_filename = co_filename.replace('.fits', '_bin.fits')
exists = \
check_file(co_filename, clobber=False)
if not exists:
co_data, co_header = fits.getdata(co_filename,
header=True,
)
cloud.co_data, cloud.co_header = \
bin_image(co_data,
binsize=(1, cloud.binsize, cloud.binsize),
header=co_header,
statistic=np.nanmean)
fits.writeto(cloud.co_filename.replace('.fits', '_bin.fits'),
cloud.co_data,
cloud.co_header,
)
else:
cloud.co_data, cloud.co_header = \
fits.getdata(co_filename,
header=True,
)
cloud.co_vel_axis = make_velocity_axis(cloud.co_header)
# Derive relevant region
hi_mask = cloud.region_mask
av_data, av_header = fits.getdata(cloud.av_filename_bin, header=True)
cloud.load_region(cloud.region_filename, header=cloud.av_header)
cloud._derive_region_mask(av_data=av_data)
co_mask = cloud.region_mask
hi_mask = co_mask
cloudpy.plot_hi_spectrum(cloud,
filename=filename_base + '.png',
limits=[-50, 30, -10, 70],
plot_co=plot_co,
hi_mask=hi_mask,
co_mask=co_mask,
)
def add_data(data_dict, filename=None):
''' Adds the cube, header, velocity axis, and positions of each pixel to
the data_dict.
'''
from astropy.io import fits
from mycoords import make_velocity_axis
cube, header = fits.getdata(filename, header=True)
velocity_axis = make_velocity_axis(header)
data_dict['cube'] = cube
data_dict['header'] = header
data_dict['velocity_axis'] = velocity_axis
# Add positions in cube
add_positions_to_data(data_dict)
def reload_wcs_positions(results_dict):
from mycoords import make_velocity_axis
from localmodule import plot_nhi_maps, create_synthetic_cube
import myimage_analysis as myia
from astropy.io import fits
from astropy import units as u
from astropy.coordinates import SkyCoord
from astropy import wcs
# Plot names
DIR_FIG = '/d/bip3/ezbc/multicloud/figures/decomposition/'
FILENAME_FIG = DIR_FIG + 'nhi_map_data_synth.png'
# Load HI Cube
DIR_HI = '/d/bip3/ezbc/multicloud/data/hi/'
FILENAME_CUBE = 'perseus_hi_galfa_cube_sub_regrid.fits'
FILENAME_CUBE_SYNTH = DIR_HI + 'cube_synth.npy'
print('\nLoading data cube...')
cube, header = fits.getdata(DIR_HI + FILENAME_CUBE, header=True)
velocity_axis = make_velocity_axis(header)
header['CUNIT3'] = 'm/s'
header['CUNIT2'] = 'deg'
header['CUNIT1'] = 'deg'
header['CTYPE3'] = 'VOPT'
header['SPECSYS'] = 'LSRK'
shape = (cube.shape[1] * cube.shape[2], 2)
# Create header object
w = wcs.WCS(header)
# add position for each spectrum
for i in xrange(len(results_dict['results'])):
coords_pix = results_dict['positions']['pix'][i][::-1]
coords_wcs = w.wcs_pix2world(([coords_pix[0], coords_pix[1], 0], ),
0)[0]
results_dict['positions']['wcs'][i] = np.array(coords_wcs[:2])
return results_dict
def reload_wcs_positions(results_dict):
from mycoords import make_velocity_axis
from localmodule import plot_nhi_maps, create_synthetic_cube
import myimage_analysis as myia
from astropy.io import fits
from astropy import units as u
from astropy.coordinates import SkyCoord
from astropy import wcs
# Plot names
DIR_FIG = '/d/bip3/ezbc/multicloud/figures/decomposition/'
FILENAME_FIG = DIR_FIG + 'nhi_map_data_synth.png'
# Load HI Cube
DIR_HI = '/d/bip3/ezbc/multicloud/data/hi/'
FILENAME_CUBE = 'perseus_hi_galfa_cube_sub_regrid.fits'
FILENAME_CUBE_SYNTH = DIR_HI + 'cube_synth.npy'
print('\nLoading data cube...')
cube, header = fits.getdata(DIR_HI + FILENAME_CUBE, header=True)
velocity_axis = make_velocity_axis(header)
header['CUNIT3'] = 'm/s'
header['CUNIT2'] = 'deg'
header['CUNIT1'] = 'deg'
header['CTYPE3'] = 'VOPT'
header['SPECSYS'] = 'LSRK'
shape = (cube.shape[1] * cube.shape[2], 2)
# Create header object
w = wcs.WCS(header)
# add position for each spectrum
for i in xrange(len(results_dict['results'])):
coords_pix = results_dict['positions']['pix'][i][::-1]
coords_wcs = w.wcs_pix2world(([coords_pix[0], coords_pix[1], 0],), 0)[0]
results_dict['positions']['wcs'][i] = np.array(coords_wcs[:2])
return results_dict
def main(av_data_type='planck'):
# Import external modules
# -----------------------
import numpy as np
from os import system,path
import mygeometry as myg
from mycoords import make_velocity_axis
import json
from myimage_analysis import calculate_nhi, calculate_noise_cube
#from astropy.io import fits
import pyfits as fits
import matplotlib.pyplot as plt
# Set parameters
# --------------
# Check if likelihood file already written, rewrite?
clobber = 0
# Confidence of parameter errors
conf = 0.68
# Confidence of contour levels
contour_confs = (0.68, 0.95)
likelihood_filename = 'taurus_likelihood_{0:s}'.format(av_data_type)
results_filename = 'taurus_likelihood_{0:s}'.format(av_data_type)
# Name of HI noise cube
noise_cube_filename = 'taurus_hi_galfa_cube_regrid_planckres_noise'
# Threshold for converging DGR
threshold_delta_dgr = 0.0005
# Number of white noise standard deviations with which to fit the
# residuals in iterative masking
resid_width_scale = 2.0
# Name of property files results are written to
global_property_file = 'taurus_global_properties.txt'
# Likelihood axis resolutions
vel_widths = np.arange(1, 30, 2*0.16667)
dgrs = np.arange(0.01, 0.2, 1e-3)
# Velocity range over which to integrate HI for deriving the mask
vel_range = (-10, 10)
# Use binned image?
use_binned_image = False
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/taurus/data/python_output/nhi_av/'
figure_dir = \
'/d/bip3/ezbc/taurus/figures/'
av_dir = '/d/bip3/ezbc/taurus/data/av/'
hi_dir = '/d/bip3/ezbc/taurus/data/hi/'
co_dir = '/d/bip3/ezbc/taurus/data/co/'
core_dir = '/d/bip3/ezbc/taurus/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/taurus/data/python_output/'
region_dir = '/d/bip3/ezbc/taurus/data/python_output/ds9_regions/'
likelihood_dir = '/d/bip3/ezbc/taurus/data/python_output/nhi_av/'
# Load data
# ---------
if use_binned_image:
bin_string = '_bin'
else:
bin_string = ''
noise_cube_filename += bin_string
av_data, av_header = fits.getdata(av_dir + \
'taurus_av_planck_5arcmin' + bin_string + '.fits',
header=True)
av_data_error, av_error_header = fits.getdata(av_dir + \
'taurus_av_error_planck_5arcmin' + bin_string + '.fits',
header=True)
#av_data_error = (100 * 0.025**2) * np.ones(av_data_error.shape)
#av_data_error *= 10.0
hi_data, hi_header = fits.getdata(hi_dir + \
'taurus_hi_galfa_cube_regrid_planckres' + bin_string + '.fits',
header=True)
# Load global properties
with open(property_dir + global_property_file, 'r') as f:
global_props = json.load(f)
# Prepare data products
# ---------------------
# Change WCS coords to pixel coords of images
global_props = convert_limit_coordinates(global_props, header=av_header)
# make the velocity axes
hi_vel_axis = make_velocity_axis(hi_header)
# Load the HI noise cube if it exists, else make it
if not path.isfile(hi_dir + noise_cube_filename + '.fits'):
noise_cube = calculate_noise_cube(cube=hi_data,
velocity_axis=hi_vel_axis,
velocity_noise_range=[90,110], header=hi_header, Tsys=30.,
filename=hi_dir + noise_cube_filename + '.fits')
else:
noise_cube, noise_header = fits.getdata(hi_dir + noise_cube_filename,
header=True)
# Derive relevant region
pix = global_props['region_limit']['pixel']
region_vertices = ((pix[1], pix[0]),
(pix[1], pix[2]),
(pix[3], pix[2]),
(pix[3], pix[0])
)
# block off region
region_mask = myg.get_polygon_mask(av_data, region_vertices)
print('\nRegion size = ' + \
'{0:.0f} pix'.format(region_mask[region_mask == 1].size))
# Derive mask by excluding correlated residuals
# ---------------------------------------------
nhi_image = calculate_nhi(cube=hi_data,
velocity_axis=hi_vel_axis,
velocity_range=vel_range,
return_nhi_error=False,
)
av_model, mask, dgr = iterate_residual_masking(
nhi_image=nhi_image,
av_data=av_data,
av_data_error=av_data_error,
vel_range=vel_range,
threshold_delta_dgr=threshold_delta_dgr,
resid_width_scale=resid_width_scale,
plot_progress=False
)
# Combine region mask with new mask
mask += np.logical_not(region_mask)
# Derive center velocity from hi
# ------------------------------
hi_spectrum = np.sum(hi_data[:, ~mask], axis=(1))
vel_center = np.array((np.average(hi_vel_axis,
weights=hi_spectrum**2),))[0]
print('\nVelocity center from HI = ' +\
'{0:.2f} km/s'.format(vel_center))
# Perform likelihood calculation of masked images
# -----------------------------------------------
# Define filename for plotting results
results_filename = figure_dir + results_filename
results = calc_likelihoods(
hi_cube=hi_data[:, ~mask],
hi_vel_axis=hi_vel_axis,
av_image=av_data[~mask],
av_image_error=av_data_error[~mask],
vel_center=vel_center,
vel_widths=vel_widths,
dgrs=dgrs,
results_filename='',
return_likelihoods=True,
likelihood_filename=None,
clobber=False,
conf=conf,
)
# Unpack output of likelihood calculation
(vel_range_confint, width_confint, dgr_confint, likelihoods,
width_likelihood, dgr_likelihood, width_max, dgr_max,
vel_range_max) = results
print('\nHI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range_confint[0],
vel_range_confint[1]))
print('\nDGR:')
print('%.1f x 10^-20 cm^2 mag' % (dgr_confint[0]))
# Calulate chi^2 for best fit models
# ----------------------------------
nhi_image_temp, nhi_image_error = \
calculate_nhi(cube=hi_data,
velocity_axis=hi_vel_axis,
velocity_range=vel_range_max,
noise_cube=noise_cube,
return_nhi_error=True)
av_image_model = nhi_image_temp * dgr_max
# avoid NaNs
indices = ((av_image_model == av_image_model) & \
(av_data == av_data))
# add nan locations to the mask
mask[~indices] = 1
# count number of pixels used in analysis
npix = mask[~mask].size
# finally calculate chi^2
chisq = np.sum((av_data[~mask] - av_image_model[~mask])**2 / \
av_data_error[~mask]**2) / av_data[~mask].size
print('\nTotal number of pixels in analysis, after masking = ' + \
'{0:.0f}'.format(npix))
print('\nReduced chi^2 = {0:.1f}'.format(chisq))
# Write results to global properties
global_props['dust2gas_ratio'] = {}
global_props['dust2gas_ratio_error'] = {}
global_props['hi_velocity_width'] = {}
global_props['hi_velocity_width_error'] = {}
global_props['dust2gas_ratio_max'] = {}
global_props['hi_velocity_center_max'] = {}
global_props['hi_velocity_width_max'] = {}
global_props['hi_velocity_range_max'] = {}
global_props['av_threshold'] = {}
global_props['co_threshold'] = {}
global_props['hi_velocity_width']['value'] = width_confint[0]
global_props['hi_velocity_width']['unit'] = 'km/s'
global_props['hi_velocity_width_error']['value'] = width_confint[1:]
global_props['hi_velocity_width_error']['unit'] = 'km/s'
global_props['hi_velocity_range'] = vel_range_confint[0:2]
global_props['hi_velocity_range_error'] = vel_range_confint[2:]
global_props['dust2gas_ratio']['value'] = dgr_confint[0]
global_props['dust2gas_ratio_error']['value'] = dgr_confint[1:]
global_props['dust2gas_ratio_max']['value'] = dgr_max
global_props['hi_velocity_center_max']['value'] = vel_center
global_props['hi_velocity_width_max']['value'] = width_max
global_props['hi_velocity_range_max']['value'] = vel_range_max
global_props['hi_velocity_range_conf'] = conf
global_props['width_likelihood'] = width_likelihood.tolist()
global_props['dgr_likelihood'] = dgr_likelihood.tolist()
global_props['vel_centers'] = [vel_center,]
global_props['vel_widths'] = vel_widths.tolist()
global_props['dgrs'] = dgrs.tolist()
global_props['likelihoods'] = likelihoods.tolist()
global_props['av_threshold']['value'] = None
global_props['av_threshold']['unit'] = 'mag'
global_props['co_threshold']['value'] = None
global_props['co_threshold']['unit'] = 'K km/s'
global_props['chisq'] = chisq
global_props['npix'] = npix
global_props['mask'] = mask.tolist()
with open(property_dir + global_property_file, 'w') as f:
json.dump(global_props, f)
# Plot likelihood space
plot_likelihoods_hist(global_props,
plot_axes=('widths', 'dgrs'),
show=0,
returnimage=False,
filename=results_filename + '_wd.png',
contour_confs=contour_confs)
plt.clf(); plt.close()
nhi_image_copy = np.copy(nhi_image)
nhi_image_copy[mask] = np.nan
av_image_copy = np.copy(av_data)
resid_image = av_image_copy - nhi_image_copy * dgr
plt.imshow(resid_image, origin='lower')
plt.title(r'$A_V$ Data - Model')
plt.colorbar()
plt.show()
def main():
import grid
import numpy as np
from myimage_analysis import calculate_nhi
from mycoords import make_velocity_axis
import pyfits as pf
import mygeometry as myg
import json
# parameters used in script
# -------------------------
# Regions
# Options are 'ds9' or 'av_gradient'
box_method = 'av_gradient'
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/perseus/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/perseus/figures/dgr/'
av_dir = '/d/bip3/ezbc/perseus/data/av/'
hi_dir = '/d/bip3/ezbc/perseus/data/hi/'
co_dir = '/d/bip3/ezbc/perseus/data/cfa/'
core_dir = '/d/bip3/ezbc/perseus/data/python_output/core_properties/'
region_dir = '/d/bip3/ezbc/perseus/data/python_output/ds9_regions/'
property_dir = '/d/bip3/ezbc/perseus/data/python_output/'
av_data_planck, planck_header = pf.getdata(av_dir + \
'perseus_av_planck_5arcmin.fits',
header=True)
av_data_error_planck, planck_header = pf.getdata(av_dir + \
'perseus_av_error_planck_5arcmin.fits',
header=True)
# load GALFA HI
hi_data, hi_header = pf.getdata(hi_dir + \
'perseus_hi_galfa_cube_regrid_planckres.fits',
header=True)
velocity_axis = make_velocity_axis(hi_header)
noise_cube, noise_header = pf.getdata(hi_dir + \
'perseus_hi_galfa_cube_regrid_planckres_noise.fits', header=True)
# define core properties
with open(core_dir + 'perseus_core_properties.txt', 'r') as f:
cores = json.load(f)
cores = convert_core_coordinates(cores, planck_header)
cores = load_ds9_region(cores,
filename_base = region_dir + 'perseus_av_boxes_',
header = planck_header)
# Initialize lists
av_images = []
av_error_images = []
nhi_images = []
nhi_error_images = []
for core in cores:
print('\nCalculating for core %s' % core)
if box_method == 'ds9':
# Grab the mask from the DS9 regions
xy = cores[core]['box_center_pix']
box_width = cores[core]['box_width']
box_height = cores[core]['box_height']
box_angle = cores[core]['box_angle']
mask = myg.get_rectangular_mask(av_data_planck,
xy[0], xy[1],
width = box_width,
height = box_height,
angle = box_angle)
elif box_method == 'av_gradient':
mask = myg.get_polygon_mask(av_data_planck,
cores[core]['box_vertices_rotated'])
else:
raise ValueError('Method for boxes is either ds9 or av_gradient')
indices = mask == 1
# Get only the relevant pixels to decrease computation time
hi_data_sub = np.copy(hi_data[:, indices])
noise_cube_sub = np.copy(noise_cube[:, indices])
av_data_planck_sub = np.copy(av_data_planck[indices])
av_data_error_planck_sub = np.copy(av_data_error_planck[indices])
# Derive N(HI) image
nhi_image, nhi_image_error = calculate_nhi(cube=hi_data_sub,
velocity_axis=velocity_axis,
noise_cube=noise_cube_sub,
velocity_range=cores[core]['hi_velocity_range'])
nhi_images.append(nhi_image)
nhi_error_images.append(nhi_image_error)
av_images.append(av_data_planck_sub)
av_error_images.append(av_data_error_planck_sub)
plot_av_vs_nhi_grid(nhi_images,
av_images,
av_error_images=av_error_images,
nhi_error_images=nhi_error_images,
#limits=[0,14, 0,10],
scale=['linear', 'log'],
savedir=figure_dir,
plot_type='scatter',
filename='perseus_av_vs_nhi_panels.png',
color_scale='linear')
# Derive N(HI) image
nhi_image, nhi_image_error = calculate_nhi(cube=hi_data,
velocity_axis=velocity_axis,
noise_cube=noise_cube,
velocity_range=cores[core]['hi_velocity_range'])
# Plot correlation, similar to Figure 3 of Paradis et al. (2012)
plot_av_vs_nhi(nhi_image,
av_data_planck,
savedir=figure_dir,
scale=['log', 'linear'],
filename='perseus_av_vs_nhi_global.png',
color_scale='linear')
def plot_nhi_maps(results_dict,
limits=None,
cube_data=None,
header=None,
load_synthetic_cube=False,
show=False,
velocity_range=[0, 500],
save_pdf=False):
from mycoords import make_velocity_axis
from localmodule import plot_nhi_maps, create_synthetic_cube
import myimage_analysis as myia
from astropy.io import fits
# Plot names
#DIR_FIG = '../../figures/'
DIR_FIG = '/d/bip3/ezbc/multicloud/figures/decomposition/'
FILENAME_FIG_BASE = DIR_FIG + 'nhi_map_data_synth'
# Load HI Cube
DIR_HI = '../../data_products/hi/'
DIR_HI = '/d/bip3/ezbc/multicloud/data_products/hi/'
#FILENAME_CUBE = 'gass_280_-45_1450212515.fits'
FILENAME_CUBE = 'perseus_hi_galfa_cube_sub_regrid.fits'
FILENAME_CUBE_SYNTH = DIR_HI + 'cube_synth.npy'
velocity_axis = make_velocity_axis(header)
# Create N(HI) data
nhi_data = myia.calculate_nhi(
cube=cube_data,
velocity_axis=velocity_axis,
velocity_range=velocity_range,
)
# Create synthetic cube from fitted spectra
velocity_axis = results_dict['velocity_axis']
if not load_synthetic_cube:
print('\nCreating synthetic cube...')
cube_synthetic = create_synthetic_cube(results_dict, cube_data)
np.save(FILENAME_CUBE_SYNTH, cube_synthetic)
else:
print('\nLoading synthetic cube...')
cube_synthetic = np.load(FILENAME_CUBE_SYNTH)
# Create N(HI) synthetic
nhi_synthetic = myia.calculate_nhi(
cube=cube_synthetic,
velocity_axis=velocity_axis,
velocity_range=velocity_range,
)
v_limits = [0, np.max(nhi_data)]
v_limits = [-1, 41]
if 0:
import matplotlib.pyplot as plt
plt.close()
plt.clf()
fig, axes = plt.subplots(2, 1)
axes[0].imshow(nhi_data, origin='lower')
axes[1].imshow(nhi_synthetic, origin='lower')
plt.show()
if save_pdf:
ext = '.pdf'
else:
ext = '.png'
filename_fig = FILENAME_FIG_BASE + ext
print('\nPlotting N(HI) maps...')
print(filename_fig)
# Plot the maps together
plot_nhi_maps(
nhi_data,
nhi_synthetic,
header=header,
#limits=[278, -37, 282, -35],
limits=limits,
filename=filename_fig,
nhi_1_vlimits=v_limits,
nhi_2_vlimits=v_limits,
show=show,
vscale='linear',
)
def main(
dgr=None, vel_range=None, vel_range_type="single", region=None, av_data_type="planck", use_binned_images=False
):
""" Executes script.
Parameters
----------
dgr : float
If None, pulls best-fit value from properties.
vel_range : tuple
If None, pulls best-fit value from properties.
"""
# import external modules
import pyfits as pf
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
from myimage_analysis import calculate_nhi, calculate_noise_cube, calculate_sd, calculate_nh2, calculate_nh2_error
import json
# Script parameters
# -----------------
if use_binned_images:
bin_string = "_bin"
else:
bin_string = ""
# Name of noise cube
noise_cube_filename = "california_hi_galfa_cube_regrid_planckres_noise" + bin_string + ".fits"
# Name of property files results are written to
prop_file = "california_global_properties_" + av_data_type + "_scaled"
# Regions, regions to edit the global properties with
if region == 1:
region_limit = {"wcs": (((5, 10, 0), (19, 0, 0)), ((4, 30, 0), (27, 0, 0))), "pixel": ()}
elif region == 2:
region_limit = {"wcs": (((4, 30, 0), (19, 0, 0)), ((3, 50, 0), (29, 0, 0))), "pixel": ()}
elif region == 3:
region_limit = {"wcs": (((4, 30, 0), (29, 0, 0)), ((3, 50, 0), (33, 0, 0))), "pixel": ()}
else:
region_limit = None
# define directory locations
# --------------------------
output_dir = "/d/bip3/ezbc/california/data/python_output/nhi_av/"
figure_dir = "/d/bip3/ezbc/california/figures/av/"
av_dir = "/d/bip3/ezbc/california/data/av/"
hi_dir = "/d/bip3/ezbc/california/data/hi/"
co_dir = "/d/bip3/ezbc/california/data/co/"
core_dir = "/d/bip3/ezbc/california/data/python_output/core_properties/"
property_dir = "/d/bip3/ezbc/california/data/python_output/"
region_dir = "/d/bip3/ezbc/california/data/python_output/ds9_regions/"
# load Planck Av and GALFA HI images, on same grid
if av_data_type == "lee12_2mass":
print ("\nLoading Lee+12 data...")
av_image, av_header = load_fits(
av_dir + "california_av_lee12_2mass_regrid_planckres" + bin_string + ".fits", return_header=True
)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == "lee12_iris":
print ("\nLoading Lee+12 data...")
av_image, av_header = load_fits(
av_dir + "california_av_lee12_iris_regrid_planckres" + bin_string + ".fits", return_header=True
)
av_image_error = 0.1 * np.ones(av_image.shape)
else:
print ("\nLoading Planck data...")
av_image, av_header = load_fits(
av_dir + "california_av_planck_5arcmin" + bin_string + ".fits", return_header=True
)
av_image_error, av_error_header = load_fits(
av_dir + "california_av_error_planck_5arcmin" + bin_string + ".fits", return_header=True
)
hi_cube, hi_header = load_fits(
hi_dir + "california_hi_galfa_cube_regrid_planckres" + bin_string + ".fits", return_header=True
)
hi_noise_cube, noise_header = load_fits(hi_dir + noise_cube_filename, return_header=True)
if not use_binned_images:
co_data, co_header = load_fits(
co_dir + "california_co_cfa_cube_regrid_planckres" + bin_string + ".fits", return_header=True
)
# Load global properties of cloud
# global properties written from script
# 'av/california_analysis_global_properties.txt'
if region is not None:
likelihood_filename += "_region{0:.0f}".format(region)
results_filename += "_region{0:.0f}".format(region)
print ("\nReading global parameter file\n" + prop_file + ".txt")
with open(property_dir + prop_file + ".txt", "r") as f:
props = json.load(f)
if vel_range is not None:
props["hi_velocity_range"] = vel_range
else:
vel_width = props["hi_velocity_width_max"]["value"]
vel_center = np.array(props["hi_velocity_center"]["value"])
vel_center = -4.0
vel_range = (vel_center - vel_width / 2.0, vel_center + vel_width / 2.0)
if dgr is not None:
props["dust2gas_ratio_max"]["value"] = dgr
else:
dgr = props["dust2gas_ratio_max"]["value"]
intercept = props["intercept_max"]["value"]
fit_params = {}
fit_params["dgr"] = dgr
fit_params["intercept"] = intercept
# define core properties
with open(core_dir + "california_core_properties.txt", "r") as f:
cores = json.load(f)
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
if not use_binned_images:
# make velocity axis for co cube
co_velocity_axis = make_velocity_axis(co_header)
# Write core coordinates in pixels
cores = convert_core_coordinates(cores, hi_header)
cores = load_ds9_region(cores, filename_base=region_dir + "california_av_boxes_", header=hi_header)
# create nhi image
nhi_image = calculate_nhi(
cube=hi_cube, velocity_axis=velocity_axis, velocity_range=vel_range, header=hi_header, noise_cube=hi_noise_cube
)
# create model av map
av_model = nhi_image * dgr
if vel_range_type == "single":
print ("\nHI velocity integration range:")
print ("%.1f to %.1f km/s" % (vel_range[0], vel_range[1]))
elif vel_range_type == "multiple":
print ("\nHI velocity integration ranges:")
for i in xrange(0, vel_range.shape[0]):
print ("%.1f to %.1f km/s" % (vel_range[i, 0], vel_range[i, 1]))
print ("\nDGR:")
print ("%.2f x 10^-20 cm^2 mag" % (dgr))
print ("\nIntercept:")
print ("%.2f mag" % (intercept))
# Get mask and mask images
mask = np.asarray(props["mask" + bin_string])
mask_images = 1
if mask_images:
av_image[mask] = np.nan
nhi_image[mask] = np.nan
av_image_error[mask] = np.nan
av_model[mask] = np.nan
indices = (np.isnan(av_model)) & (np.isnan(av_image)) & (np.isnan(av_image_error))
if 1:
import matplotlib.pyplot as plt
plt.imshow(av_image)
plt.show()
print ("\nTotal number of pixels after masking = " + str(props["npix"]))
# Plot
figure_types = ["png", "pdf"]
for figure_type in figure_types:
if region is None:
filename = "california_av_vs_nhi_" + av_data_type + bin_string
filename = figure_dir + filename + "." + figure_type
print ("\nSaving Av model image to \n" + filename)
plot_av_vs_nhi(
nhi_image,
av_image,
av_error=av_image_error,
# limits=[10**-1, 10**1.9, 10**0, 10**1.7],
fit_params=fit_params,
limits=[5, 40, -0.2, 2],
# limits=[0,30,0,10],
gridsize=(10, 10),
# scale=('log', 'log'),
# scale=('linear', 'linear'),
filename=filename,
contour_plot=not use_binned_images,
std=0.22,
)
def plot_cluster_nhi_panels(results_ref=None,
colors=None,
limits=None,
cube=None,
header=None,
load_synthetic_cube=False,
show=False,
velocity_range=[0, 500],
save_pdf=False):
from mycoords import make_velocity_axis
from localmodule import plot_nhi_map_panels, create_synthetic_cube
import myimage_analysis as myia
from astropy.io import fits
# Plot names
DIR_FIG = '/d/bip3/ezbc/magellanic_stream/figures/'
#DIR_FIG = '../../figures/'
DIR_FIG = '/d/bip3/ezbc/multicloud/figures/decomposition/'
FILENAME_FIG = DIR_FIG + 'nhi_maps_components.png'
if save_pdf:
FILENAME_FIG = FILENAME_FIG.replace('.png', '.pdf')
# Load HI Cube
DIR_HI = '/d/bip3/ezbc/multicloud/data_products/hi/'
#FILENAME_CUBE = 'gass_280_-45_1450212515.fits'
FILENAME_CUBE = 'perseus_hi_galfa_cube_sub_regrid.fits'
FILENAME_CUBE_SYNTH_BASE = DIR_HI + 'cube_synth_comp'
velocity_axis = make_velocity_axis(header)
# Create N(HI) data
nhi_data = myia.calculate_nhi(
cube=cube,
velocity_axis=velocity_axis,
velocity_range=velocity_range,
)
# Create synthetic cube from fitted spectra
velocity_axis = results_ref['velocity_axis']
# get number of unique components
component_colors = np.unique(colors)
n_components = len(component_colors)
nhi_list = []
nhi_max = 0.0
for i in xrange(n_components):
if not load_synthetic_cube:
print('\n\tCreating synthetic cube ' + str(i+1) + ' of ' + \
str(n_components))
# get the relevant parameters
indices = np.where(colors == component_colors[i])[0]
pix_positions = results_ref['pos_pix'][indices]
fit_params_list = results_ref['data'][indices, 2:]
print('\n\t\tNumber of components in cube: ' + \
'{0:.0f}'.format(len(fit_params_list)))
cube_synthetic = \
create_synthetic_cube(pix_positions=pix_positions,
velocity_axis=velocity_axis,
fit_params_list=fit_params_list,
cube_data=cube,
)
np.save(FILENAME_CUBE_SYNTH_BASE + str(i) + '.npy', cube_synthetic)
else:
print('\n\tLoading synthetic cube ' + str(i+1) + ' of ' + \
str(n_components))
cube_synthetic = np.load(FILENAME_CUBE_SYNTH_BASE + str(i) +
'.npy')
# Create N(HI) synthetic
nhi_synthetic = myia.calculate_nhi(
cube=cube_synthetic,
velocity_axis=velocity_axis,
velocity_range=velocity_range,
)
nhi_list.append(nhi_synthetic)
nhi_max_temp = np.max(nhi_synthetic)
if nhi_max_temp > nhi_max:
nhi_max = nhi_max_temp
v_limits = [0, nhi_max]
# crop to highest valued cubes
n_left = 4
n_left = len(nhi_list)
sum_list = []
for nhi in nhi_list:
sum_list.append(np.nansum(nhi))
sort_indices = np.argsort(sum_list)[::-1]
new_list = []
for i in xrange(n_left):
new_list.append(nhi_list[sort_indices[i]])
nhi_list = new_list
# Plot the maps together
plot_nhi_map_panels(
nhi_list,
header=header,
#limits=[278, -37, 282, -35],
limits=limits,
filename=FILENAME_FIG,
nhi_vlimits=[-0.1, 15],
show=show,
vscale='linear',
)
def main():
''' Executes script.
'''
# import external modules
import pyfits as pf
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
reload(myg)
# define directory locations
output_dir = '/d/bip3/ezbc/taurus/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/taurus/figures/maps/'
av_dir = '/d/bip3/ezbc/taurus/data/av/'
hi_dir = '/d/bip3/ezbc/taurus/data/hi/'
core_dir = output_dir + 'core_arrays/'
region_dir = '/d/bip3/ezbc/taurus/data/python_output/ds9_regions/'
# Load hi fits file
hi_image, hi_header = pf.getdata(hi_dir + \
'taurus_hi_galfa_cube_regrid_planckres.fits', header=True)
h = hi_header
# Load av fits file
av_image, av_header = pf.getdata(av_dir + \
'taurus_av_planck_5arcmin.fits',
header=True)
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
# create nhi image
nhi_image = calculate_nhi(hi_cube=hi_image,
velocity_axis=velocity_axis, velocity_range=[-16.53,28.83])
if False:
# trim hi_image to av_image size
nhi_image_trim = np.ma.array(nhi_image, mask=av_image != av_image)
plot_nhi_image(nhi_image=nhi_image_trim, header=hi_header,
contour_image=av_image, contours=[5,10,15],
savedir=figure_dir, filename='taurus_nhi_cores_map.png',
show=True)
cores = {'L1495':
{'center_wcs': [(4,14,0), (28, 11, 0)],
'map': None,
'threshold': 4.75,
'box_wcs': [(4,16,30), (27,44,30), (4,5,20), (28,28,33)]
},
'L1495A':
{'center_wcs': [(4,18,0), (28,23., 0)],
'map': None,
'threshold': 4.75,
'box_wcs': [(4,28,23),(28,12,50),(4,16,23),(29,46,5)],
},
'B213':
{'center_wcs': [(4, 19, 0), (27, 15,0)],
'map': None,
'threshold': 4.75,
'box_wcs': [(4,22,27), (26,45,47),(4,5,25),(27,18,48)],
},
'B220':
{'center_wcs': [(4, 41, 0.), (26,7,0)],
'map': None,
'threshold': 7,
'box_wcs': [(4,47,49),(25,31,13),(4,40,37),(27,31,17)],
},
'L1527':
{'center_wcs': [(4, 39, 0.), (25,47, 0)],
'map': None,
'threshold': 7,
'box_wcs': [(4,40,13), (24,46,38), (4,34,35), (25,56,7)],
},
'B215':
{'center_wcs': [(4, 23, 0), (25, 3, 0)],
'map': None,
'threshold': 3,
'box_wcs': [(4,24,51), (22,36,7), (4,20,54), (25,26,31)],
},
'L1524':
{'center_wcs': [(4,29,0.), (24,31.,0)],
'map': None,
'threshold': 3,
'box_wcs': [(4,31,0), (22,4,6), (4,25,33), (25,0,55)],
}
}
cores = convert_core_coordinates(cores, h)
if False:
nhi_image = np.zeros(nhi_image.shape)
for core in cores:
core_image = np.load(core_dir + core + '.npy')
core_indices = np.where(core_image == core_image)
nhi_image[core_indices] += core_image[core_indices]
nhi_image_trim =np.ma.array(nhi_image, mask=((av_image != av_image) &\
(nhi_image == 0)))
nhi_image_trim[nhi_image_trim == 0] = np.NaN
read_ds9_region(av_dir + 'taurus_av_boxes.reg')
plot_nhi_image(nhi_image=nhi_image_trim, header=hi_header,
savedir=figure_dir,
cores=cores,
filename='taurus_nhi_core_regions_map.png',
show=True)
if True:
cores = load_ds9_region(cores,
filename_base = region_dir + 'taurus_av_boxes_',
header = h)
# Grab the mask
mask = np.zeros((nhi_image.shape))
for core in cores:
xy = cores[core]['box_center_pix']
box_width = cores[core]['box_width']
box_height = cores[core]['box_height']
box_angle = cores[core]['box_angle']
mask += myg.get_rectangular_mask(nhi_image,
xy[0], xy[1],
width = box_width,
height = box_height,
angle = box_angle)
cores[core]['box_vertices'] = myg.get_rect(
xy[0], xy[1],
width = box_width,
height = box_height,
angle = box_angle,)
mask[mask > 1] = 1
# trim hi_image to av_image size
nhi_image_trim = np.ma.array(nhi_image,
mask = ((av_image != av_image) & \
(av_image > 1.0)))
av_image_trim = np.ma.array(av_image,
mask = ((nhi_image != nhi_image) & \
(av_image > 1.0)))
nhi_image_trim = np.copy(nhi_image)
nhi_image_trim[av_image > 1.] = np.nan
av_image_trim = np.copy(av_image)
av_image_trim[av_image > 1.] = np.nan
# Plot
figure_types = ['png',]
for figure_type in figure_types:
# N(HI) alone
plot_nhi_image(nhi_image=nhi_image_trim, header=hi_header,
contour_image=av_image, contours=[5,10,15],
boxes=True, cores = cores,
limits=[50,37,200,160],
savedir=figure_dir,
filename='taurus_nhi_cores_map.%s' % \
figure_type,
show=0)
# N(HI) + Av
plot_nhi_image(nhi_image=nhi_image_trim, header=hi_header,
av_image=av_image_trim,
#boxes=True, cores = cores,
limits=[50,37,200,160],
savedir=figure_dir,
filename='taurus_nhi_av_map.%s' % \
figure_type,
show=0)
def run_cloud_analysis(global_args,):
from astropy.io import fits
from myimage_analysis import calculate_nhi, calc_region_mask
import myimage_analysis as myia
from mycoords import make_velocity_axis
from mystats import calc_symmetric_error, calc_logL
import os
import myio
import pickle
import mystats
cloud_name = global_args['cloud_name']
region = global_args['region']
load = global_args['load']
data_type = global_args['data_type']
background_subtract = global_args['background_subtract']
region = global_args['region']
# define directory locations
# --------------------------
figure_dir = \
'/d/bip3/ezbc/multicloud/figures/'
av_dir = '/d/bip3/ezbc/' + cloud_name + '/data/av/'
dust_temp_dir = '/d/bip3/ezbc/' + cloud_name + '/data/dust_temp/'
hi_dir = '/d/bip3/ezbc/' + cloud_name + '/data/hi/'
co_dir = '/d/bip3/ezbc/' + cloud_name + '/data/co/'
core_dir = \
'/d/bip3/ezbc/' + cloud_name + '/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/' + cloud_name + '/data/python_output/'
region_dir = '/d/bip3/ezbc/multicloud/data/python_output/regions/'
background_region_dir = '/d/bip3/ezbc/' + cloud_name + \
'/data/python_output/ds9_regions/'
results_dir = '/d/bip3/ezbc/multicloud/data/python_output/'
av_filename = av_dir + \
cloud_name + '_av_planck_tau353_5arcmin.fits'
av_data, av_header = fits.getdata(av_filename, header=True)
# define filenames
prop_filename = property_dir + \
cloud_name + '_global_properties.txt'
if region == 'east':
hi_filename = '/d/bip2/DR2W_v1/Narrow/' + \
'GALFA_HI_RA+DEC_060.00+26.35_N.fits'
hi_dr1_filename = '/d/bip3/ezbc/galfa/DR1/' + \
'GALFA_HI_RA+DEC_060.00+26.35_N.fits'
else:
hi_filename = '/d/bip2/DR2W_v1/Narrow/' + \
'GALFA_HI_RA+DEC_052.00+26.35_N.fits'
hi_dr1_filename = '/d/bip3/ezbc/galfa/DR1/' + \
'GALFA_HI_RA+DEC_052.00+26.35_N.fits'
hi_error_filename = hi_dir + \
cloud_name + '_hi_galfa_cube_regrid_planckres_noise.fits'
co_filename = co_dir + \
cloud_name + '_co_cfa_cube_regrid_planckres.fits'
# Get the filename base to differentiate between different parameters
filename_base, global_args = create_filename_base(global_args)
# Load HI and CO cubes
hi_data, hi_header = fits.getdata(hi_filename, header=True)
hi_dr1_data, hi_dr1_header = fits.getdata(hi_dr1_filename, header=True)
hi_vel_axis = make_velocity_axis(hi_header)
velocity_range = [-5, 15]
# use the vel range to derive N(HI)
nhi_image = \
calculate_nhi(cube=hi_data,
velocity_axis=hi_vel_axis,
velocity_range=velocity_range,
)
# use the vel range to derive N(HI)
nhi_image_dr1 = \
calculate_nhi(cube=hi_dr1_data,
velocity_axis=hi_vel_axis,
velocity_range=velocity_range,
)
# mask for erroneous pixels
mask_nhi = (nhi_image < 0) & (nhi_image_dr1 < 0)
nhi_image[mask_nhi] = np.nan
nhi_image_dr1[mask_nhi] = np.nan
plot_kwargs = {
'figure_dir': figure_dir,
'cloud_name': cloud_name,
'filename_base': filename_base,
'plot_diagnostics': global_args['plot_diagnostics'],
#'av_nhi_contour': av_nhi_contour,
'av_nhi_contour': True,
'av_nhi_limits': [0, 20, -1, 9],
#'av_nhi_limits': None,
}
# Plot residuals between nhi maps
filename = plot_kwargs['figure_dir'] + \
'maps/' + plot_kwargs['filename_base'] + \
'_nhi_dr2_dr1_residuals_perseus_' + region + '.png'
print('Saving\neog ' + filename + ' &')
plot_nhi_image(nhi_image=nhi_image / nhi_image_dr1,
header=hi_header,
limits=None,
filename=filename,
show=0,
cb_text='DR2 / DR1'
#hi_vlimits=None,
)
def main(dgr=None, vel_range=None, vel_range_type='single', region=None,
av_data_type='planck', use_binned_images=False):
''' Executes script.
Parameters
----------
dgr : float
If None, pulls best-fit value from properties.
vel_range : tuple
If None, pulls best-fit value from properties.
'''
# import external modules
import pyfits as pf
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
import json
# Script parameters
# -----------------
if use_binned_images:
bin_string = '_bin'
else:
bin_string = ''
# Name of noise cube
noise_cube_filename = \
'taurus_hi_galfa_cube_regrid_planckres_noise' + bin_string + \
'.fits'
# Name of property files results are written to
prop_file = 'taurus_global_properties_' + av_data_type + '_scaled'
# Regions, regions to edit the global properties with
if region == 1:
region_limit = {'wcs' : (((5, 10, 0), (19, 0, 0)),
((4, 30, 0), (27, 0, 0))),
'pixel' : ()
}
elif region == 2:
region_limit = {'wcs' : (((4, 30, 0), (19, 0, 0)),
((3, 50, 0), (29, 0, 0))),
'pixel' : ()
}
elif region == 3:
region_limit = {'wcs' : (((4, 30, 0), (29, 0, 0)),
((3, 50, 0), (33, 0, 0))),
'pixel' : ()
}
else:
region_limit = None
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/taurus/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/taurus/figures/'
av_dir = '/d/bip3/ezbc/taurus/data/av/'
hi_dir = '/d/bip3/ezbc/taurus/data/hi/'
co_dir = '/d/bip3/ezbc/taurus/data/co/'
core_dir = '/d/bip3/ezbc/taurus/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/taurus/data/python_output/'
region_dir = '/d/bip3/ezbc/taurus/data/python_output/ds9_regions/'
# load Planck Av and GALFA HI images, on same grid
if av_data_type == 'lee12_2mass':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'taurus_av_lee12_2mass_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'lee12_iris':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'taurus_av_lee12_iris_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
else:
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'taurus_av_planck_5arcmin' + bin_string + \
'.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'taurus_av_error_planck_5arcmin' + bin_string + \
'.fits',
return_header=True)
hi_cube, hi_header = load_fits(hi_dir + \
'taurus_hi_galfa_cube_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
hi_noise_cube, noise_header = load_fits(hi_dir + noise_cube_filename,
return_header=True)
if not use_binned_images:
co_data, co_header = load_fits(co_dir + \
'taurus_co_cfa_cube_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
# Load global properties of cloud
# global properties written from script
# 'av/taurus_analysis_global_properties.txt'
if region is not None:
likelihood_filename += '_region{0:.0f}'.format(region)
results_filename += '_region{0:.0f}'.format(region)
print('\nReading global parameter file\n' + prop_file + '.txt')
with open(property_dir + prop_file + '.txt', 'r') as f:
props = json.load(f)
if vel_range is not None:
props['hi_velocity_range'] = vel_range
else:
vel_range = props['hi_velocity_range']
if dgr is not None:
props['dust2gas_ratio']['value'] = dgr
else:
dgr = props['dust2gas_ratio']['value']
# define core properties
with open(core_dir + 'taurus_core_properties.txt', 'r') as f:
cores = json.load(f)
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
if not use_binned_images:
# make velocity axis for co cube
co_velocity_axis = make_velocity_axis(co_header)
# Write core coordinates in pixels
cores = convert_core_coordinates(cores, hi_header)
cores = load_ds9_region(cores,
filename_base = region_dir + 'taurus_av_boxes_',
header = hi_header)
# create nhi image
nhi_image = calculate_nhi(cube=hi_cube,
velocity_axis=velocity_axis,
velocity_range=vel_range,
header=hi_header,
noise_cube=hi_noise_cube)
# create model av map
av_model = nhi_image * dgr
if vel_range_type == 'single':
print('\nHI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range[0],
vel_range[1]))
elif vel_range_type == 'multiple':
print('\nHI velocity integration ranges:')
for i in xrange(0, vel_range.shape[0]):
print('%.1f to %.1f km/s' % (vel_range[i, 0],
vel_range[i, 1]))
print('\nDGR:')
print('%.2f x 10^-20 cm^2 mag' % (dgr))
# Get mask and mask images
mask = np.asarray(props['mask' + bin_string])
mask_images = False
av_image_masked = np.copy(av_image)
#av_image_masked[(mask == 1) & (region_mask == 1)] = np.nan
av_error_masked = np.copy(av_image_error)
#av_image_masked[(mask == 1) & (region_mask == 1)] = np.nan
av_model_masked = np.copy(av_model)
#av_model_masked[(mask == 1) & (region_mask == 1)] = np.nan
if mask_images:
av_image_masked[mask] = np.nan
av_error_masked[mask] = np.nan
av_model_masked[mask] = np.nan
indices = ((np.isnan(av_model_masked)) & \
(np.isnan(av_image_masked)) & \
(np.isnan(av_image_error)))
print('\nTotal number of pixels after masking = ' + str(props['npix']))
if 0:
import matplotlib.pyplot as plt
av_plot_data = np.copy(av_image)
av_plot_data[mask] = np.nan
plt.imshow(av_plot_data, origin='lower')
plt.xlim(props['plot_limit_bin']['pixel'][0:3:2])
plt.ylim(props['plot_limit_bin']['pixel'][1:4:2])
plt.show()
# Create HI spectrum
hi_cube[hi_cube != hi_cube] = 0
hi_cube[:, mask] = 0
hi_spectrum = np.mean(hi_cube, axis=(1,2))
if not use_binned_images:
# Derive CO spectrum
co_data[:, mask] = 0
co_data[np.isnan(co_data)] = 0
co_spectrum = np.mean(co_data, axis=(1,2))
# Plot
figure_types = ['png', 'pdf']
for figure_type in figure_types:
if region is None:
if vel_range_type == 'single':
filename = 'single_vel_range/taurus_av_model_map_' + \
av_data_type + bin_string
#'dgr{0:.3f}_'.format(dgr) + \
#'{0:.1f}to{1:.1f}kms'.format(vel_range[0], vel_range[1]) + \
#'_' + \
elif vel_range_type == 'multiple':
filename = 'multiple_vel_range/taurus_av_model_map_' + \
'dgr{0:.3f}'.format(dgr)
for i in xrange(0, vel_range.shape[0]):
filename += '_{0:.1f}to{1:.1f}kms'.format(vel_range[i, 0],
vel_range[i, 1])
filename += '.%s' % figure_type
else:
filename = 'taurus_av_model_map_region{0:.0f}'.format(region)
print('\nSaving Av model image to \n' + figure_dir + filename + \
'.' + figure_type)
if 0:
plot_av_model(av_image=av_image_masked,
av_model=av_model_masked,
header=av_header,
results=props,
limits=props['plot_limit' + bin_string]['pixel'],
savedir=figure_dir + 'maps/av_models/',
filename=filename + '.' + figure_type,
show=False)
if 1:
#if not use_binned_images:
if 0:
plot_av_model(av_image=av_image_masked,
av_model=av_model_masked,
header=av_header,
results=props,
hi_velocity_axis=velocity_axis,
vel_range=vel_range,
hi_spectrum=hi_spectrum,
#hi_limits=[-15, 25, -1, 10],
hi_limits=[-15, 25, None, None],
co_spectrum=co_spectrum,
co_velocity_axis=co_velocity_axis,
limits=props['plot_limit' + bin_string]['pixel'],
savedir=figure_dir + 'maps/av_models/',
filename=filename + '_spectra' + '.' + figure_type,
show=False)
plot_avmod_vs_av((av_model_masked,),
(av_image_masked,),
av_errors=(av_error_masked,),
#limits=[10**-1, 10**1.9, 10**0, 10**1.7],
limits=[0,20,0,3],
savedir=figure_dir + 'av/',
gridsize=(10,10),
#scale=('log', 'log'),
#scale=('linear', 'linear'),
filename='taurus_avmod_vs_av%s.%s' % (bin_string, figure_type),
show = False,
std=0.22,
)
if 0:
plot_power_spectrum(av_image_masked - av_model_masked,
filename_prefix='taurus_av_resid_power_spectrum_' + \
'{0:s}'.format(av_data_type),
filename_suffix='.{0:s}'.format(figure_type),
savedir=figure_dir + 'power_spectra/',
show=False)
def main(dgr=None, vel_range=(-5, 15), vel_range_type='single', region=None,
av_data_type='planck'):
''' Executes script.
Parameters
----------
dgr : float
If None, pulls best-fit value from properties.
vel_range : tuple
If None, pulls best-fit value from properties.
'''
# import external modules
import pyfits as fits
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
import json
from os import system,path
# Script parameters
# -----------------
# Name of noise cube
noise_cube_filename = 'multicloud_hi_galfa_cube_regrid_planckres_noise.fits'
# Use Planck dust Av map or Kainulainen 2009 optical extinction Av map?
# options are 'planck' or 'lee12'
#av_data_type = 'lee12'
#av_data_type = 'planck'
# Global parameter file
prop_file = 'multicloud_global_properties'
# Which cores to include in analysis?
cores_to_keep = [# taur
'L1495',
'L1495A',
'B213',
'L1498',
'B215',
'B18',
'B217',
'B220-1',
'B220-2',
'L1521',
'L1524',
'L1527-1',
'L1527-2',
# Calif
'L1536',
'L1483-1',
'L1483-2',
'L1482-1',
'L1482-2',
'L1478-1',
'L1478-2',
'L1456',
'NGC1579',
#'L1545',
#'L1517',
#'L1512',
#'L1523',
#'L1512',
# Pers
'B5',
'IC348',
'B1E',
'B1',
'NGC1333',
'B4',
'B3',
'L1455',
'L1448',
]
# Regions, regions to edit the global properties with
if region == 1:
region_limit = {'wcs' : (((5, 10, 0), (19, 0, 0)),
((4, 30, 0), (27, 0, 0))),
'pixel' : ()
}
elif region == 2:
region_limit = {'wcs' : (((4, 30, 0), (19, 0, 0)),
((3, 50, 0), (29, 0, 0))),
'pixel' : ()
}
elif region == 3:
region_limit = {'wcs' : (((4, 30, 0), (29, 0, 0)),
((3, 50, 0), (33, 0, 0))),
'pixel' : ()
}
else:
region_limit = None
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/multicloud/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/multicloud/figures/'
av_dir = '/d/bip3/ezbc/multicloud/data/av/'
hi_dir = '/d/bip3/ezbc/multicloud/data/hi/'
co_dir = '/d/bip3/ezbc/multicloud/data/co/'
core_dir = '/d/bip3/ezbc/multicloud/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/multicloud/data/python_output/'
region_dir = '/d/bip3/ezbc/multicloud/data/python_output/regions/'
# load Planck Av and GALFA HI images, on same grid
if av_data_type == 'lee12_2mass':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_lee12_2mass_regrid_planckres.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'lee12_iris':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_lee12_iris_regrid_planckres.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'planck_tau353':
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_planck_tau353_5arcmin.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'multicloud_av_error_planck_tau353_5arcmin.fits',
return_header=True)
else:
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_planck_5arcmin.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'multicloud_av_error_planck_5arcmin.fits',
return_header=True)
hi_cube, hi_header = load_fits(hi_dir + \
'multicloud_hi_galfa_cube_regrid_planckres.fits',
return_header=True)
co_data, co_header = load_fits(co_dir + \
'multicloud_co_cfa_cube_regrid_planckres.fits',
return_header=True)
# Prepare data products
# ---------------------
# Load global properties of cloud
# global properties written from script
# 'av/multicloud_analysis_global_properties.txt'
if region is not None:
likelihood_filename += '_region{0:.0f}'.format(region)
results_filename += '_region{0:.0f}'.format(region)
print('\nLoading global property file {0:s}.txt'.format(prop_file))
with open(property_dir + prop_file + '.txt', 'r') as f:
props = json.load(f)
# Define velocity range
props['hi_velocity_range'] = vel_range
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
# make velocity axis for co cube
co_velocity_axis = make_velocity_axis(co_header)
# Load the HI noise cube if it exists, else make it
if not path.isfile(hi_dir + noise_cube_filename):
hi_noise_cube = calculate_noise_cube(cube=hi_cube,
velocity_axis=velocity_axis,
velocity_noise_range=[90,110], header=hi_header, Tsys=30.,
filename=hi_dir + noise_cube_filename)
else:
hi_noise_cube, noise_header = fits.getdata(hi_dir + noise_cube_filename,
header=True)
# create nhi image
nhi_image = calculate_nhi(cube=hi_cube,
velocity_axis=velocity_axis,
velocity_range=vel_range,
header=hi_header,
noise_cube=hi_noise_cube)
props['plot_limit']['wcs'] = (((5, 20, 0), (19, 0 ,0)),
((2, 30, 0), (37, 0, 0))
)
# Change WCS coords to pixel coords of images
props = convert_limit_coordinates(props,
header=av_header,
coords=('region_limit',
'co_noise_limits',
'plot_limit',
'region_name_pos'))
# Load cloud division regions from ds9
props = load_ds9_region(props,
filename=region_dir + 'multicloud_divisions.reg',
header=av_header)
# Derive relevant region
pix = props['region_limit']['pixel']
region_vertices = ((pix[1], pix[0]),
(pix[1], pix[2]),
(pix[3], pix[2]),
(pix[3], pix[0])
)
# block offregion
region_mask = myg.get_polygon_mask(av_image, region_vertices)
print('\nRegion size = ' + \
'{0:.0f} pix'.format(region_mask[region_mask == 1].size))
if vel_range_type == 'single':
print('\nHI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range[0],
vel_range[1]))
elif vel_range_type == 'multiple':
print('\nHI velocity integration ranges:')
for i in xrange(0, vel_range.shape[0]):
print('%.1f to %.1f km/s' % (vel_range[i, 0],
vel_range[i, 1]))
cloud_dict = {'taurus' : {},
'perseus' : {},
'california' : {},
}
# load Planck Av and GALFA HI images, on same grid
for cloud in cloud_dict:
print('\nLoading core properties for {0:s}'.format(cloud))
file_dir = '/d/bip3/ezbc/{0:s}/data/av/'.format(cloud)
# define core properties
with open('/d/bip3/ezbc/{0:s}/data/python_output/'.format(cloud) + \
'core_properties/{0:s}_core_properties.txt'.format(cloud),
'r') as f:
cores = json.load(f)
# Load core regions from DS9 files
if cloud == 'aldobaran':
region_cloud = 'california'
else:
region_cloud = cloud
core_filename = '/d/bip3/ezbc/' + region_cloud + '/data/python_output' + \
'/ds9_regions/{0:s}_av_poly_cores'.format(region_cloud)
cores = load_ds9_core_region(cores,
filename_base=core_filename,
header=av_header)
cores = convert_core_coordinates(cores, av_header)
# Remove cores
cores_to_remove = []
for core in cores:
if core not in cores_to_keep:
cores_to_remove.append(core)
for core_to_remove in cores_to_remove:
del cores[core_to_remove]
cloud_dict[cloud]['cores'] = cores
# Plot
figure_types = ['png', 'pdf']
for figure_type in figure_types:
filename = 'av_cores_map' + \
'.{0:s}'.format(figure_type)
print('\nSaving Av cores map to \n' + filename)
plot_cores_map(header=av_header,
av_image=av_image,
limits=props['plot_limit']['pixel'],
regions=props['regions'],
cloud_dict=cloud_dict,
cores_to_keep=cores_to_keep,
props=props,
hi_vlimits=(0,20),
av_vlimits=(0,16),
#av_vlimits=(0.1,30),
savedir=figure_dir + 'maps/',
filename=filename,
show=False)
def main(dgr=None, vel_range=(-5, 15), vel_range_type="single", region=None, av_data_type="planck"):
""" Executes script.
Parameters
----------
dgr : float
If None, pulls best-fit value from properties.
vel_range : tuple
If None, pulls best-fit value from properties.
"""
# import external modules
import pyfits as fits
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
from myimage_analysis import calculate_nhi, calculate_noise_cube, calculate_sd, calculate_nh2, calculate_nh2_error
import json
from os import system, path
# Script parameters
# -----------------
# Name of noise cube
noise_cube_filename = "multicloud_hi_galfa_cube_regrid_planckres_noise.fits"
# Use Planck dust Av map or Kainulainen 2009 optical extinction Av map?
# options are 'planck' or 'lee12'
# av_data_type = 'lee12'
# av_data_type = 'planck'
# Global parameter file
prop_file = "multicloud_global_properties"
# Which cores to include in analysis?
cores_to_keep = [ # taur
"L1495",
"L1495A",
"B213",
"L1498",
"B215",
"B18",
"B217",
"B220-1",
"B220-2",
"L1521",
"L1524",
"L1527-1",
"L1527-2",
# Calif
"L1536",
"L1483-1",
"L1483-2",
"L1482-1",
"L1482-2",
"L1478-1",
"L1478-2",
"L1456",
"NGC1579",
#'L1545',
#'L1517',
#'L1512',
#'L1523',
#'L1512',
# Pers
"B5",
"IC348",
"B1E",
"B1",
"NGC1333",
"B4",
"B3",
"L1455",
"L1448",
]
# Regions, regions to edit the global properties with
if region == 1:
region_limit = {"wcs": (((5, 10, 0), (19, 0, 0)), ((4, 30, 0), (27, 0, 0))), "pixel": ()}
elif region == 2:
region_limit = {"wcs": (((4, 30, 0), (19, 0, 0)), ((3, 50, 0), (29, 0, 0))), "pixel": ()}
elif region == 3:
region_limit = {"wcs": (((4, 30, 0), (29, 0, 0)), ((3, 50, 0), (33, 0, 0))), "pixel": ()}
else:
region_limit = None
# define directory locations
# --------------------------
output_dir = "/d/bip3/ezbc/multicloud/data/python_output/nhi_av/"
figure_dir = "/d/bip3/ezbc/multicloud/figures/"
av_dir = "/d/bip3/ezbc/multicloud/data/av/"
hi_dir = "/d/bip3/ezbc/multicloud/data/hi/"
co_dir = "/d/bip3/ezbc/multicloud/data/co/"
core_dir = "/d/bip3/ezbc/multicloud/data/python_output/core_properties/"
property_dir = "/d/bip3/ezbc/multicloud/data/python_output/"
region_dir = "/d/bip3/ezbc/multicloud/data/python_output/"
# load Planck Av and GALFA HI images, on same grid
if av_data_type == "lee12_2mass":
print("\nLoading Lee+12 data...")
av_image, av_header = load_fits(av_dir + "multicloud_av_lee12_2mass_regrid_planckres.fits", return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == "lee12_iris":
print("\nLoading Lee+12 data...")
av_image, av_header = load_fits(av_dir + "multicloud_av_lee12_iris_regrid_planckres.fits", return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == "planck_rad":
print("\nLoading Planck data...")
av_image, av_header = load_fits(av_dir + "multicloud_av_planck_radiance_5arcmin.fits", return_header=True)
av_image_error, av_error_header = load_fits(
av_dir + "multicloud_av_error_planck_radiance_5arcmin.fits", return_header=True
)
else:
print("\nLoading Planck data...")
av_image, av_header = load_fits(av_dir + "multicloud_av_planck_5arcmin.fits", return_header=True)
av_image_error, av_error_header = load_fits(
av_dir + "multicloud_av_error_planck_5arcmin.fits", return_header=True
)
hi_cube, hi_header = load_fits(hi_dir + "multicloud_hi_galfa_cube_regrid_planckres.fits", return_header=True)
co_data, co_header = load_fits(co_dir + "multicloud_co_cfa_cube_regrid_planckres.fits", return_header=True)
# Prepare data products
# ---------------------
# Load global properties of cloud
# global properties written from script
# 'av/multicloud_analysis_global_properties.txt'
if region is not None:
likelihood_filename += "_region{0:.0f}".format(region)
results_filename += "_region{0:.0f}".format(region)
print("\nLoading global property file {0:s}.txt".format(prop_file))
with open(property_dir + prop_file + ".txt", "r") as f:
props = json.load(f)
# Define velocity range
props["hi_velocity_range"] = vel_range
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
# make velocity axis for co cube
co_velocity_axis = make_velocity_axis(co_header)
# Load the HI noise cube if it exists, else make it
if not path.isfile(hi_dir + noise_cube_filename):
hi_noise_cube = calculate_noise_cube(
cube=hi_cube,
velocity_axis=velocity_axis,
velocity_noise_range=[90, 110],
header=hi_header,
Tsys=30.0,
filename=hi_dir + noise_cube_filename,
)
else:
hi_noise_cube, noise_header = fits.getdata(hi_dir + noise_cube_filename, header=True)
# create nhi image
nhi_image = calculate_nhi(
cube=hi_cube, velocity_axis=velocity_axis, velocity_range=vel_range, header=hi_header, noise_cube=hi_noise_cube
)
# Change WCS coords to pixel coords of images
props = convert_limit_coordinates(
props, header=av_header, coords=("region_limit", "co_noise_limits", "plot_limit", "region_name_pos")
)
# Load cloud division regions from ds9
props = load_ds9_region(props, filename=region_dir + "multicloud_divisions.reg", header=av_header)
# Derive relevant region
pix = props["region_limit"]["pixel"]
region_vertices = ((pix[1], pix[0]), (pix[1], pix[2]), (pix[3], pix[2]), (pix[3], pix[0]))
# block offregion
region_mask = myg.get_polygon_mask(av_image, region_vertices)
print("\nRegion size = " + "{0:.0f} pix".format(region_mask[region_mask == 1].size))
if vel_range_type == "single":
print("\nHI velocity integration range:")
print("%.1f to %.1f km/s" % (vel_range[0], vel_range[1]))
elif vel_range_type == "multiple":
print("\nHI velocity integration ranges:")
for i in xrange(0, vel_range.shape[0]):
print("%.1f to %.1f km/s" % (vel_range[i, 0], vel_range[i, 1]))
cloud_dict = {"taurus": {}, "perseus": {}, "california": {}}
# load Planck Av and GALFA HI images, on same grid
for cloud in cloud_dict:
print("\nLoading core properties for {0:s}".format(cloud))
file_dir = "/d/bip3/ezbc/{0:s}/data/av/".format(cloud)
# define core properties
with open(
"/d/bip3/ezbc/{0:s}/data/python_output/".format(cloud)
+ "core_properties/{0:s}_core_properties.txt".format(cloud),
"r",
) as f:
cores = json.load(f)
# Load core regions from DS9 files
if cloud == "aldobaran":
region_cloud = "california"
else:
region_cloud = cloud
core_filename = region_dir.replace("multicloud", region_cloud) + "/ds9_regions/{0:s}_av_poly_cores".format(
region_cloud
)
cores = load_ds9_core_region(cores, filename_base=core_filename, header=av_header)
cores = convert_core_coordinates(cores, av_header)
# Remove cores
cores_to_remove = []
for core in cores:
if core not in cores_to_keep:
cores_to_remove.append(core)
for core_to_remove in cores_to_remove:
del cores[core_to_remove]
cloud_dict[cloud]["cores"] = cores
# Plot
figure_types = ["png", "pdf"]
for figure_type in figure_types:
filename = "multicloud_av_cores_map" + ".{0:s}".format(figure_type)
print("\nSaving Av cores map to \n" + filename)
plot_cores_map(
header=av_header,
av_image=av_image,
limits=props["plot_limit"]["pixel"],
regions=props["regions"],
cloud_dict=cloud_dict,
cores_to_keep=cores_to_keep,
props=props,
hi_vlimits=(0, 20),
av_vlimits=(0, 16),
# av_vlimits=(0.1,30),
savedir=figure_dir + "maps/",
filename=filename,
show=False,
)
def run_cloud_analysis(global_args,):
from astropy.io import fits
from myimage_analysis import calculate_nhi, calc_region_mask
import myimage_analysis as myia
from mycoords import make_velocity_axis
from mystats import calc_symmetric_error, calc_logL
import os
import myio
import pickle
import mystats
cloud_name = global_args['cloud_name']
region = global_args['region']
load = global_args['load']
data_type = global_args['data_type']
background_subtract = global_args['background_subtract']
# define directory locations
# --------------------------
figure_dir = \
'/d/bip3/ezbc/multicloud/figures/'
av_dir = '/d/bip3/ezbc/' + cloud_name + '/data/av/'
dust_temp_dir = '/d/bip3/ezbc/' + cloud_name + '/data/dust_temp/'
hi_dir = '/d/bip3/ezbc/' + cloud_name + '/data/hi/'
co_dir = '/d/bip3/ezbc/' + cloud_name + '/data/co/'
core_dir = \
'/d/bip3/ezbc/' + cloud_name + '/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/' + cloud_name + '/data/python_output/'
region_dir = '/d/bip3/ezbc/multicloud/data/python_output/regions/'
background_region_dir = '/d/bip3/ezbc/' + cloud_name + \
'/data/python_output/ds9_regions/'
results_dir = '/d/bip3/ezbc/multicloud/data/python_output/'
av_filename = av_dir + \
cloud_name + '_av_planck_tau353_5arcmin.fits'
av_data, av_header = fits.getdata(av_filename, header=True)
# define filenames
prop_filename = property_dir + \
cloud_name + '_global_properties.txt'
hi_filename = hi_dir + \
cloud_name + '_hi_galfa_cube_regrid_planckres.fits'
hi_dr1_filename = hi_dir + \
cloud_name + '_hi_galfa_dr1_cube_regrid_planckres.fits'
hi_error_filename = hi_dir + \
cloud_name + '_hi_galfa_cube_regrid_planckres_noise.fits'
co_filename = co_dir + \
cloud_name + '_co_cfa_cube_regrid_planckres.fits'
# Get the filename base to differentiate between different parameters
filename_base, global_args = create_filename_base(global_args)
# set up plotting variables
plot_kwargs = {
'figure_dir': figure_dir,
'cloud_name': cloud_name,
'filename_base': filename_base,
'plot_diagnostics': global_args['plot_diagnostics'],
#'av_nhi_contour': av_nhi_contour,
'av_nhi_contour': True,
'av_nhi_limits': [0, 20, -1, 9],
#'av_nhi_limits': None,
}
# mask data
region_filename = region_dir + 'multicloud_divisions.reg'
region_mask = calc_region_mask(region_filename,
av_data,
av_header,
region_name=global_args['region_name'])
# Load HI and CO cubes
hi_data, hi_header = fits.getdata(hi_filename, header=True)
hi_dr1_data, hi_dr1_header = fits.getdata(hi_dr1_filename, header=True)
co_data, co_header = fits.getdata(co_filename, header=True)
#hi_data[:, region_mask] = np.nan
#hi_dr1_data[:, region_mask] = np.nan
#co_data[:, region_mask] = np.nan
hi_vel_axis = make_velocity_axis(hi_header)
co_vel_axis = make_velocity_axis(co_header)
# Load HI error
if global_args['clobber_hi_error']:
print('\n\tCalculating HI noise cube...')
os.system('rm -rf ' + hi_error_filename)
hi_data_error = \
myia.calculate_noise_cube(cube=hi_data,
velocity_axis=hi_vel_axis,
velocity_noise_range=[-110,-90, 90,110],
Tsys=30.0,
filename=hi_error_filename)
else:
hi_data_error = fits.getdata(hi_error_filename)
# Derive N(HI)
# -------------------------------------------------------------------------
# get fit kwargs
gauss_fit_kwargs, ncomps_in_cloud = get_gauss_fit_kwargs(global_args)
# derive spectra or load
spectra_filename = results_dir + 'spectra/' + global_args['cloud_name'] + \
'_spectra.pickle'
spectra_dr1_filename = results_dir + 'spectra/' + \
global_args['cloud_name'] + \
'_spectra_dr1.pickle'
load_spectra = myio.check_file(spectra_filename,
clobber=global_args['clobber_spectra'])
if load_spectra:
hi_spectrum, hi_std_spectrum, co_spectrum = \
myio.load_pickle(spectra_filename)
hi_dr1_spectrum, hi_std_dr1_spectrum, co_spectrum = \
myio.load_pickle(spectra_dr1_filename)
else:
print('\n\tCalculating spectra...')
if global_args['smooth_hi_to_co_res']:
from astropy.convolution import Gaussian2DKernel, convolve
# Create kernel
# one pix = 5 arcmin, need 8.4 arcmin for CO res
# The beamsize is the FWHM. The convolution kernel needs the
# standard deviation
hi_res = 1.0
co_res = 8.4 / 5.0
width = (co_res**2 - hi_res**2)**0.5
std = width / 2.355
g = Gaussian2DKernel(width)
# Convolve data
hi_data_co_res = np.zeros(hi_data.shape)
for i in xrange(hi_data.shape[0]):
hi_data_co_res[i, :, :] = \
convolve(hi_data[i, :, :], g, boundary='extend')
hi_dr1_data_co_res = np.zeros(hi_dr1_data.shape)
for i in xrange(hi_dr1_data.shape[0]):
hi_dr1_data_co_res[i, :, :] = \
convolve(hi_dr1_data[i, :, :], g, boundary='extend')
hi_spectrum = myia.calc_spectrum(hi_data_co_res)
hi_std_spectrum = myia.calc_spectrum(hi_data_co_res,
statistic=np.nanstd)
hi_dr1_spectrum = myia.calc_spectrum(hi_dr1_data_co_res)
hi_std_dr1_spectrum = myia.calc_spectrum(hi_dr1_data_co_res,
statistic=np.nanstd)
co_spectrum = myia.calc_spectrum(co_data)
myio.save_pickle(spectra_filename,
(hi_spectrum, hi_std_spectrum, co_spectrum))
myio.save_pickle(spectra_dr1_filename,
(hi_dr1_spectrum, hi_std_dr1_spectrum, co_spectrum))
if global_args['hi_range_calc'] == 'gaussian':
velocity_range, gauss_fits, comp_num, hi_range_error = \
calc_hi_vel_range(hi_spectrum,
hi_vel_axis,
gauss_fit_kwargs,
co_spectrum=co_spectrum,
co_vel_axis=co_vel_axis,
ncomps=ncomps_in_cloud,
)
global_args['vel_range_error'] = hi_range_error
velocity_range_dr1, gauss_fits_dr1, comp_num_dr1, hi_range_error_dr1 = \
calc_hi_vel_range(hi_dr1_spectrum,
hi_vel_axis,
gauss_fit_kwargs,
co_spectrum=co_spectrum,
co_vel_axis=co_vel_axis,
ncomps=ncomps_in_cloud,
)
else:
velocity_range = [-5, 15]
gauss_fits = None
comp_num = None
hi_range_kwargs = {
'velocity_range': velocity_range,
'gauss_fits': gauss_fits,
'comp_num': comp_num,
'hi_range_error': hi_range_error,
'vel_range': velocity_range,
'gauss_fit_kwargs': gauss_fit_kwargs,
}
# plot the results
# --------------------------------------------------------------------------
filename = plot_kwargs['figure_dir'] + \
'spectra/' + plot_kwargs['filename_base'] + \
'_spectra_dr2.png'
print('Saving\neog ' + filename + ' &')
plot_spectra(hi_spectrum,
hi_vel_axis,
hi_std_spectrum=hi_std_spectrum,
gauss_fits=gauss_fits,
comp_num=comp_num,
co_spectrum=co_spectrum,
co_vel_axis=co_vel_axis,
vel_range=velocity_range,
filename=filename,
limits=[-50, 30, -10, 70],
)
# DR1 data
filename = plot_kwargs['figure_dir'] + \
'spectra/' + plot_kwargs['filename_base'] + \
'_spectra_dr1.png'
print('Saving\neog ' + filename + ' &')
plot_spectra(hi_dr1_spectrum,
hi_vel_axis,
hi_std_spectrum=hi_std_dr1_spectrum,
gauss_fits=gauss_fits_dr1,
comp_num=comp_num_dr1,
co_spectrum=co_spectrum,
co_vel_axis=co_vel_axis,
vel_range=velocity_range_dr1,
filename=filename,
limits=[-50, 30, -10, 70],
)
velocity_range = [0, 15]
velocity_range_dr1 = [0, 15]
# use the vel range to derive N(HI)
nhi_image, nhi_image_error = \
calculate_nhi(cube=hi_data,
velocity_axis=hi_vel_axis,
velocity_range=velocity_range,
noise_cube=hi_data_error,
return_nhi_error=True,
)
# use the vel range to derive N(HI)
nhi_image_dr1 = \
calculate_nhi(cube=hi_dr1_data,
velocity_axis=hi_vel_axis,
velocity_range=velocity_range_dr1,
)
# mask for erroneous pixels
mask_nhi = (nhi_image < 0) & (nhi_image_dr1 < 0)
nhi_image[mask_nhi] = np.nan
nhi_image_dr1[mask_nhi] = np.nan
# Plot residuals between nhi maps
filename = plot_kwargs['figure_dir'] + \
'maps/' + plot_kwargs['filename_base'] + \
'_nhi_dr2_dr1_residuals.png'
print('Saving\neog ' + filename + ' &')
plot_nhi_image(nhi_image=nhi_image / nhi_image_dr1,
header=hi_header,
limits=[65, 45, 25, 35],
filename=filename,
show=0,
cb_text='DR2 / DR1',
#hi_vlimits=[0.91, 0.93],
)
def plot_co_spectra(results, ):
filename_base = \
cloud_results['figure_dir'] + 'diagnostics/' + \
cloud_results['filename_extension'] + '_co_spectra'
from astropy.io import fits
from mycoords import make_velocity_axis
from myimage_analysis import bin_image
from myio import check_file
cloud = cloud_results['cloud']
co_filename = cloud.co_filename
if cloud_results['args']['bin_procedure'] in ('all', 'mle'):
co_filename = co_filename.replace('.fits', '_bin.fits')
exists = \
check_file(co_filename, clobber=False)
if not exists:
co_data, co_header = fits.getdata(
co_filename,
header=True,
)
cloud.co_data, cloud.co_header = \
bin_image(co_data,
binsize=(1, cloud.binsize, cloud.binsize),
header=co_header,
statistic=np.nanmean)
fits.writeto(
cloud.co_filename.replace('.fits', '_bin.fits'),
cloud.co_data,
cloud.co_header,
)
else:
cloud.co_data, cloud.co_header = \
fits.getdata(co_filename,
header=True,
)
cloud.co_vel_axis = make_velocity_axis(cloud.co_header)
# Derive relevant region
hi_mask = cloud.region_mask
av_data, av_header = fits.getdata(cloud.av_filename_bin, header=True)
cloud.load_region(cloud.region_filename, header=cloud.av_header)
cloud._derive_region_mask(av_data=av_data)
co_mask = cloud.region_mask
hi_mask = co_mask
cloudpy.plot_hi_spectrum(
cloud,
filename=filename_base + '.png',
limits=[-50, 30, -10, 70],
plot_co=plot_co,
hi_mask=hi_mask,
co_mask=co_mask,
)
def plot_hi_spectrum(cloud_results, plot_co=1):
filename_base = \
cloud_results['figure_dir'] + 'diagnostics/' + \
cloud_results['filename_extension'] + '_hi_spectrum'
from astropy.io import fits
from mycoords import make_velocity_axis
from myimage_analysis import bin_image
from myio import check_file
cloud = cloud_results['cloud']
if plot_co:
co_filename = cloud.co_filename
if cloud_results['args']['bin_procedure'] in ('all', 'mle'):
co_filename = co_filename.replace('.fits', '_bin.fits')
exists = \
check_file(co_filename, clobber=False)
if not exists:
co_data, co_header = fits.getdata(
co_filename,
header=True,
)
cloud.co_data, cloud.co_header = \
bin_image(co_data,
binsize=(1, cloud.binsize, cloud.binsize),
header=co_header,
statistic=np.nanmean)
fits.writeto(
cloud.co_filename.replace('.fits', '_bin.fits'),
cloud.co_data,
cloud.co_header,
)
else:
cloud.co_data, cloud.co_header = \
fits.getdata(co_filename,
header=True,
)
cloud.co_vel_axis = make_velocity_axis(cloud.co_header)
# Derive relevant region
if cloud_results['args']['bin_procedure'] in ('all', 'mle'):
av_filename = cloud.av_filename_bin
hi_filename = cloud.hi_filename_bin
else:
av_filename = cloud.av_filename
hi_mask = cloud.region_mask
av_data, av_header = fits.getdata(av_filename, header=True)
cloud.hi_data, cloud.hi_header = \
fits.getdata(hi_filename, header=True)
cloud.load_region(cloud.region_filename, header=av_header)
cloud._derive_region_mask(av_data=av_data)
co_mask = cloud.region_mask
hi_mask = co_mask
import matplotlib.pyplot as plt
plt.close()
plt.clf()
co = np.copy(cloud.co_data[30, :, :])
co[co_mask] = np.nan
plt.imshow(co, origin='lower')
plt.savefig('/usr/users/ezbc/Desktop/comap_' + cloud.region + '.png')
assert all(
(cloud.hi_data.shape, cloud.co_data.shape, cloud.region_mask.shape))
cloudpy.plot_hi_spectrum(
cloud,
filename=filename_base + '.png',
limits=[-50, 30, -10, 70],
plot_co=plot_co,
hi_mask=hi_mask,
co_mask=co_mask,
)
def main():
import grid
import numpy as np
from os import system,path
import myclumpfinder as clump_finder
reload(clump_finder)
import mygeometry as myg
reload(myg)
from mycoords import make_velocity_axis
import mymath
reload(mymath)
# define directory locations
output_dir = '/d/bip3/ezbc/perseus/data/python_output/co_dispersion/'
figure_dir = '/d/bip3/ezbc/perseus/figures/'
av_dir = '/d/bip3/ezbc/perseus/data/av/'
hi_dir = '/d/bip3/ezbc/perseus/data/galfa/'
cfa_dir = '/d/bip3/ezbc/perseus/data/cfa/'
core_dir = output_dir + 'core_arrays/'
region_dir = '/d/bip3/ezbc/taurus/data/python_output/ds9_regions/'
# load 2mass Av and GALFA HI images, on same grid
cfa_data, cfa_header = load_fits(cfa_dir + \
'perseus_cfa_cube_galfa_regrid.fits',
return_header=True)
#av_data += - 0.4 # subtracts background of 0.4 mags
hi_data, hi_header = load_fits(hi_dir + \
'perseus_galfa_cube_bin_3.7arcmin.fits',
return_header = True)
# make the velocity axis
hi_velocity_axis = make_velocity_axis(hi_header)
cfa_velocity_axis = make_velocity_axis(cfa_header)
cfa_mom2 = mymath.calc_moment(cfa_data, moment = 2, spectral_axis = 0)
# define core properties
cores = {'L1495':
{'center_wcs': [(4,14,0), (28, 11, 0)],
'map': None,
'threshold': 4.75,
'box_wcs': [(4,16,30), (27,44,30), (4,5,20), (28,28,33)]
},
'L1495A':
{'center_wcs': [(4,18,0), (28,23., 0)],
'map': None,
'threshold': 4.75,
'box_wcs': [(4,28,23),(28,12,50),(4,16,23),(29,46,5)],
},
'B213':
{'center_wcs': [(4, 19, 0), (27, 15,0)],
'map': None,
'threshold': 4.75,
'box_wcs': [(4,22,27), (26,45,47),(4,5,25),(27,18,48)],
},
'B220':
{'center_wcs': [(4, 41, 0.), (26,7,0)],
'map': None,
'threshold': 7,
'box_wcs': [(4,47,49),(25,31,13),(4,40,37),(27,31,17)],
},
'L1527':
{'center_wcs': [(4, 39, 0.), (25,47, 0)],
'map': None,
'threshold': 7,
'box_wcs': [(4,40,13), (24,46,38), (4,34,35), (25,56,7)],
},
'B215':
{'center_wcs': [(4, 23, 0), (25, 3, 0)],
'map': None,
'threshold': 3,
'box_wcs': [(4,24,51), (22,36,7), (4,20,54), (25,26,31)],
},
'L1524':
{'center_wcs': [(4,29,0.), (24,31.,0)],
'map': None,
'threshold': 3,
'box_wcs': [(4,31,0), (22,4,6), (4,25,33), (25,0,55)],
}
}
cores = convert_core_coordinates(cores, hi_header)
if True:
hsd_limits =[0.1,300]
hisd_limits = [2,20]
av_limits =[0.01,100]
nhi_limits = [2,20]
cores = load_ds9_region(cores,
filename_base = region_dir + 'taurus_av_boxes_',
header = hi_header)
# save cores for later
if 0:
mask = np.zeros((cfa_mom2.shape))
for core in cores:
print('Calculating for core %s' % core)
av_limits = [0.01,100]
# Grab the mask
xy = cores[core]['box_center_pix']
box_width = cores[core]['box_width']
box_height = cores[core]['box_height']
box_angle = cores[core]['box_angle']
mask += myg.get_rectangular_mask(cfa_mom2,
xy[0], xy[1],
width = box_width,
height = box_height,
angle = box_angle)
cores[core]['box_vertices'] = myg.get_rect(
xy[0], xy[1],
width = box_width,
height = box_height,
angle = box_angle,)
indices = np.where(mask == 1)
mask[mask > 1] = 1
cfa_mom2[mask == 0] = np.nan
# currently have variance, need dispersion
cfa_mom2 = cfa_mom2**0.5
# Plot
plot_mom2_image(mom2_image = cfa_mom2,
header = cfa_header,
boxes = False,
#limits=[128,37,308,206],
title = r'Perseus: $\sigma_{\rm CO}$ map with core ' + \
'boxed-regions.',
savedir = figure_dir,
filename='perseus_co_veldisp_map.png',
show=True)
def main(dgr=None,
vel_range=None,
vel_range_type='single',
region=None,
av_data_type='planck'):
''' Executes script.
Parameters
----------
dgr : float
If None, pulls best-fit value from properties.
vel_range : tuple
If None, pulls best-fit value from properties.
'''
# import external modules
import pyfits as pf
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
import json
# Script parameters
# -----------------
# Name of noise cube
noise_cube_filename = 'perseus_hi_galfa_cube_regrid_planckres_noise'
# Use Planck dust Av map or Kainulainen 2009 optical extinction Av map?
# options are 'planck' or 'lee12'
#av_data_type = 'lee12'
#av_data_type = 'planck'
# Regions, regions to edit the global properties with
if region == 1:
region_limit = {
'wcs': (((5, 10, 0), (19, 0, 0)), ((4, 30, 0), (27, 0, 0))),
'pixel': ()
}
elif region == 2:
region_limit = {
'wcs': (((4, 30, 0), (19, 0, 0)), ((3, 50, 0), (29, 0, 0))),
'pixel': ()
}
elif region == 3:
region_limit = {
'wcs': (((4, 30, 0), (29, 0, 0)), ((3, 50, 0), (33, 0, 0))),
'pixel': ()
}
else:
region_limit = None
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/perseus/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/perseus/figures/'
av_dir = '/d/bip3/ezbc/perseus/data/av/'
hi_dir = '/d/bip3/ezbc/perseus/data/hi/'
co_dir = '/d/bip3/ezbc/perseus/data/co/'
core_dir = '/d/bip3/ezbc/perseus/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/perseus/data/python_output/'
region_dir = '/d/bip3/ezbc/perseus/data/python_output/ds9_regions/'
# Load Data
# ---------
# Load global properties of cloud
# global properties written from script
# 'av/perseus_analysis_global_properties.txt'
prop_file = 'perseus_global_properties' # _' + av_data_type
if region is not None:
likelihood_filename += '_region{0:.0f}'.format(region)
results_filename += '_region{0:.0f}'.format(region)
with open(property_dir + prop_file + '.txt', 'r') as f:
props = json.load(f)
if props['use_binned_image']:
bin_string = '_bin'
else:
bin_string = ''
# load Planck Av and GALFA HI images, on same grid
if av_data_type == 'lee12_2mass':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'perseus_av_lee12_2mass_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'lee12_iris':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'perseus_av_lee12_iris_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'planck_rad':
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'perseus_av_planck_radiance_5arcmin' + bin_string + \
'.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'perseus_av_error_planck_radiance_5arcmin' + bin_string + \
'.fits',
return_header=True)
else:
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'perseus_av_planck_5arcmin' + bin_string + '.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'perseus_av_error_planck_5arcmin' + bin_string + '.fits',
return_header=True)
hi_cube, hi_header = load_fits(hi_dir + \
'perseus_hi_galfa_cube_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
hi_noise_cube, noise_header = load_fits(hi_dir + noise_cube_filename +
bin_string + '.fits',
return_header=True)
co_data, co_header = load_fits(co_dir + \
'perseus_co_cfa_cube_regrid_planckres' + bin_string + '.fits',
return_header=True)
if vel_range is not None:
props['hi_velocity_range'] = vel_range
else:
vel_range = props['hi_velocity_range']
if dgr is not None:
props['dust2gas_ratio']['value'] = dgr
else:
dgr = props['dust2gas_ratio']['value']
# define core properties
with open(core_dir + 'perseus_core_properties.txt', 'r') as f:
cores = json.load(f)
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
# make velocity axis for co cube
co_velocity_axis = make_velocity_axis(co_header)
# Write core coordinates in pixels
cores = convert_core_coordinates(cores, hi_header)
cores = load_ds9_region(cores,
filename_base=region_dir + 'perseus_av_boxes_',
header=hi_header)
# create nhi image
nhi_image = calculate_nhi(cube=hi_cube,
velocity_axis=velocity_axis,
velocity_range=vel_range,
header=hi_header,
noise_cube=hi_noise_cube)
# create model av map
av_model = nhi_image * dgr
# Mask the images based on av trheshol
co_data_nonans = np.copy(co_data)
co_data_nonans[np.isnan(co_data_nonans)] = 0.0
co_mom0 = np.sum(co_data_nonans, axis=0)
mask = ((av_image > props['av_threshold']['value']) & \
(co_mom0 > props['co_threshold']['value']))
# Derive relevant region
pix = props['region_limit']['pixel']
region_vertices = ((pix[1], pix[0]), (pix[1], pix[2]), (pix[3], pix[2]),
(pix[3], pix[0]))
# block offregion
region_mask = myg.get_polygon_mask(av_image, region_vertices)
print('\nRegion size = ' + \
'{0:.0f} pix'.format(region_mask[region_mask == 1].size))
if vel_range_type == 'single':
print('\nHI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range[0], vel_range[1]))
elif vel_range_type == 'multiple':
print('\nHI velocity integration ranges:')
for i in xrange(0, vel_range.shape[0]):
print('%.1f to %.1f km/s' % (vel_range[i, 0], vel_range[i, 1]))
print('\nDGR:')
print('%.2f x 10^-20 cm^2 mag' % (dgr))
# Get mask and mask images
mask = np.asarray(props['mask'])
av_image_masked = np.copy(av_image)
#av_image_masked[(mask == 1) & (region_mask == 1)] = np.nan
av_image_masked[mask == 1] = np.nan
av_error_masked = np.copy(av_image_error)
#av_image_masked[(mask == 1) & (region_mask == 1)] = np.nan
av_error_masked[mask == 1] = np.nan
av_model_masked = np.copy(av_model)
#av_model_masked[(mask == 1) & (region_mask == 1)] = np.nan
av_model_masked[mask == 1] = np.nan
indices = ((np.isnan(av_model_masked)) & \
(np.isnan(av_image_masked)) & \
(np.isnan(av_image_error)))
print('\nTotal number of pixels after masking = ' + str(props['npix']))
# Create HI spectrum
hi_cube[hi_cube != hi_cube] = 0
hi_cube[:, mask == 1] = 0
hi_spectrum = np.mean(hi_cube, axis=(1, 2))
# Derive CO spectrum
co_data[:, region_mask == 1] = 0
co_data[np.isnan(co_data)] = 0
co_spectrum = np.mean(co_data, axis=(1, 2))
# Plot
figure_types = [
'png',
] # 'pdf']
for figure_type in figure_types:
if region is None:
if vel_range_type == 'single':
filename = 'single_vel_range/perseus_av_model_map_' + \
av_data_type + '.%s' % figure_type
elif vel_range_type == 'multiple':
filename = 'multiple_vel_range/perseus_av_model_map_' + \
'dgr{0:.3f}'.format(dgr)
for i in xrange(0, vel_range.shape[0]):
filename += '_{0:.1f}to{1:.1f}kms'.format(
vel_range[i, 0], vel_range[i, 1])
filename += '.%s' % figure_type
else:
filename = 'perseus_av_model_map_region{0:.0f}'.format(region) + \
'.{0:s}'.format(figure_type)
print('\nSaving Av model image to \n' + filename)
plot_av_model(
av_image=av_image_masked,
av_model=av_model_masked,
header=av_header,
results=props,
hi_velocity_axis=velocity_axis,
vel_range=vel_range,
hi_spectrum=hi_spectrum,
#hi_limits=[-15, 25, -1, 10],
hi_limits=[-15, 25, None, None],
co_spectrum=co_spectrum,
co_velocity_axis=co_velocity_axis,
limits=props['plot_limit']['pixel'],
savedir=figure_dir + 'maps/av_models/',
filename=filename,
show=False)
plot_avmod_vs_av(
(av_model_masked, ),
(av_image_masked, ),
av_errors=(av_error_masked, ),
#limits=[10**-1, 10**1.9, 10**0, 10**1.7],
limits=[0, 1.5, 0, 1.5],
savedir=figure_dir + 'av/',
gridsize=(10, 10),
#scale=('log', 'log'),
#scale=('linear', 'linear'),
filename='perseus_avmod_vs_av.%s' % figure_type,
show=False,
std=0.22,
)
plot_power_spectrum(av_image_masked - av_model_masked,
filename_prefix='perseus_av_resid_power_spectrum_' + \
'{0:s}'.format(av_data_type),
filename_suffix='.{0:s}'.format(figure_type),
savedir=figure_dir + 'power_spectra/',
show=False)
def plot_nhi_maps(results_dict, limits=None, cube_data=None, header=None,
load_synthetic_cube=False, show=False, velocity_range=[0, 500],
save_pdf=False):
from mycoords import make_velocity_axis
from localmodule import plot_nhi_maps, create_synthetic_cube
import myimage_analysis as myia
from astropy.io import fits
# Plot names
#DIR_FIG = '../../figures/'
DIR_FIG = '/d/bip3/ezbc/multicloud/figures/decomposition/'
FILENAME_FIG_BASE = DIR_FIG + 'nhi_map_data_synth'
# Load HI Cube
DIR_HI = '../../data_products/hi/'
DIR_HI = '/d/bip3/ezbc/multicloud/data_products/hi/'
#FILENAME_CUBE = 'gass_280_-45_1450212515.fits'
FILENAME_CUBE = 'perseus_hi_galfa_cube_sub_regrid.fits'
FILENAME_CUBE_SYNTH = DIR_HI + 'cube_synth.npy'
velocity_axis = make_velocity_axis(header)
# Create N(HI) data
nhi_data = myia.calculate_nhi(cube=cube_data,
velocity_axis=velocity_axis,
velocity_range=velocity_range,
)
# Create synthetic cube from fitted spectra
velocity_axis = results_dict['velocity_axis']
if not load_synthetic_cube:
print('\nCreating synthetic cube...')
cube_synthetic = create_synthetic_cube(results_dict, cube_data)
np.save(FILENAME_CUBE_SYNTH, cube_synthetic)
else:
print('\nLoading synthetic cube...')
cube_synthetic = np.load(FILENAME_CUBE_SYNTH)
# Create N(HI) synthetic
nhi_synthetic = myia.calculate_nhi(cube=cube_synthetic,
velocity_axis=velocity_axis,
velocity_range=velocity_range,
)
v_limits = [0, np.max(nhi_data)]
v_limits = [-1, 41]
if 0:
import matplotlib.pyplot as plt
plt.close(); plt.clf()
fig, axes = plt.subplots(2,1)
axes[0].imshow(nhi_data, origin='lower')
axes[1].imshow(nhi_synthetic, origin='lower')
plt.show()
if save_pdf:
ext = '.pdf'
else:
ext = '.png'
filename_fig = FILENAME_FIG_BASE + ext
print('\nPlotting N(HI) maps...')
print(filename_fig)
# Plot the maps together
plot_nhi_maps(nhi_data,
nhi_synthetic,
header=header,
#limits=[278, -37, 282, -35],
limits=limits,
filename=filename_fig,
nhi_1_vlimits=v_limits,
nhi_2_vlimits=v_limits,
show=show,
vscale='linear',
)
def main(av_data_type='planck'):
import numpy as np
from os import system,path
import mygeometry as myg
from mycoords import make_velocity_axis
import json
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
from astropy.io import fits
import matplotlib.pyplot as plt
# Check if likelihood file already written, rewrite?
clobber = 1
# Confidence of parameter errors
conf = 0.68
# Confidence of contour levels
contour_confs = (0.68, 0.95)
likelihood_filename = 'taurus_likelihood_{0:s}'.format(av_data_type)
results_filename = 'taurus_likelihood_{0:s}'.format(av_data_type)
# Threshold for converging DGR
threshold_delta_dgr = 0.00005
# define directory locations
# --------------------------
output_dir = '/home/ezbc/research/data/taurus/python_output/nhi_av/'
figure_dir = \
'/d/bip3/ezbc/taurus/figures/hi_velocity_range/'
av_dir = '/home/ezbc/research/data/taurus/av/'
hi_dir = '/home/ezbc/research/data/taurus/hi/'
co_dir = '/home/ezbc/research/data/taurus/co/'
core_dir = '/home/ezbc/research/data/taurus/python_output/core_properties/'
property_dir = '/home/ezbc/research/data/taurus/python_output/'
region_dir = '/home/ezbc/research/data/taurus/python_output/ds9_regions/'
likelihood_dir = '/home/ezbc/research/data/taurus/python_output/nhi_av/'
# Load data
# ---------
av_data, av_header = fits.getdata(av_dir + \
'taurus_av_planck_5arcmin.fits',
header=True)
av_data_error, av_error_header = fits.getdata(av_dir + \
'taurus_av_error_planck_5arcmin.fits',
header=True)
hi_data, hi_header = fits.getdata(hi_dir + \
'taurus_hi_galfa_cube_regrid_planckres.fits',
header=True)
# make the velocity axes
hi_vel_axis = make_velocity_axis(hi_header)
# Velocity range over which to integrate HI
vel_range = (0, 10)
# Make Av model
# -------------
nhi_image = calculate_nhi(cube=hi_data,
velocity_axis=hi_vel_axis,
velocity_range=vel_range,
return_nhi_error=False,
)
#plt.clf(); plt.close()
#plt.imshow(nhi_image, origin='lower')
#plt.show()
# Mask out nans and high-valued pixels
mask = ((av_data > 30.0) | \
np.isnan(av_data) | \
np.isnan(av_data_error) | \
(av_data_error == 0) | \
np.isnan(nhi_image))
# solve for DGR using linear least squares
print('\nSolving for DGR...')
delta_dgr = 1e10
dgr = 1e10
while delta_dgr > threshold_delta_dgr:
A = np.array((np.ravel(nhi_image[~mask] / av_data_error[~mask]),))
b = np.array((np.ravel(av_data[~mask] / av_data_error[~mask]),))
A = np.matrix(A).T
b = np.matrix(b).T
#dgr = np.dot(np.linalg.pinv(A), b)
dgr_new = (np.linalg.pinv(A) * b)[0, 0]
# Create model with the DGR
print('\nDGR = {0:.2} 10^20 cm^2 mag'.format(dgr))
av_image_model = nhi_image * dgr_new
residuals = av_data - av_image_model
# Include only residuals which are white noise
mask_new = get_residual_mask(residuals,
resid_width_scale=2.0, plot_progress=0)
# Mask non-white noise, i.e. correlated residuals.
mask += mask_new
npix = mask.size - np.sum(mask)
print('Number of non-masked pixels = {0:.0f}'.format(npix))
# Reset while loop conditions
delta_dgr = np.abs(dgr - dgr_new)
dgr = dgr_new
plt.clf(); plt.close()
nhi_image_copy = np.copy(nhi_image)
nhi_image_copy[mask] = np.nan
av_image_copy = np.copy(av_data)
resid_image = av_image_copy - nhi_image_copy * dgr
plt.imshow(resid_image, origin='lower')
plt.title(r'$A_V$ Data - Model')
plt.colorbar()
plt.show()
def main(av_data_type='planck'):
# Import external modules
# -----------------------
import numpy as np
from os import system,path
import mygeometry as myg
from mycoords import make_velocity_axis
import json
from myimage_analysis import calculate_nhi, calculate_noise_cube
#from astropy.io import fits
import pyfits as fits
import matplotlib.pyplot as plt
# Set parameters
# --------------
# Check if likelihood file already written, rewrite?
clobber = 0
# Confidence of parameter errors
conf = 0.68
# Confidence of contour levels
contour_confs = (0.68, 0.95)
# Name of HI noise cube
noise_cube_filename = 'perseus_hi_galfa_cube_regrid_planckres_noise'
# Threshold for converging DGR
threshold_delta_dgr = 0.00005
# Number of white noise standard deviations with which to fit the
# residuals in iterative masking
resid_width_scale = 3.0
# Name of property files results are written to
global_property_file = 'perseus_global_properties.txt'
# Likelihood axis resolutions
vel_widths = np.arange(1, 30, 2*0.16667)
dgrs = np.arange(0.01, 0.2, 1e-3)
#vel_widths = np.arange(1, 50, 8*0.16667)
#dgrs = np.arange(0.01, 0.2, 1e-2)
# Velocity range over which to integrate HI for deriving the mask
vel_range = (-20, 20)
# Use binned image?
use_binned_image = False
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/perseus/data/python_output/nhi_av/'
figure_dir = \
'/d/bip3/ezbc/perseus/figures/'
av_dir = '/d/bip3/ezbc/perseus/data/av/'
hi_dir = '/d/bip3/ezbc/perseus/data/hi/'
co_dir = '/d/bip3/ezbc/perseus/data/co/'
core_dir = '/d/bip3/ezbc/perseus/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/perseus/data/python_output/'
region_dir = '/d/bip3/ezbc/perseus/data/python_output/ds9_regions/'
likelihood_dir = '/d/bip3/ezbc/perseus/data/python_output/nhi_av/'
# Load data
# ---------
if use_binned_image:
bin_string = '_bin'
else:
bin_string = ''
# Adjust filenames
noise_cube_filename += bin_string
likelihood_filename = 'perseus_likelihood_{0:s}'.format(av_data_type) + \
bin_string
results_filename = 'perseus_likelihood_{0:s}'.format(av_data_type) + \
bin_string
av_data, av_header = fits.getdata(av_dir + \
'perseus_av_planck_5arcmin' + bin_string + '.fits',
header=True)
av_data_error, av_error_header = fits.getdata(av_dir + \
'perseus_av_error_planck_5arcmin' + bin_string + '.fits',
header=True)
if use_binned_image:
#av_data_error = (100 * 0.025**2) * np.ones(av_data_error.shape)
av_data_error *= 5
hi_data, hi_header = fits.getdata(hi_dir + \
'perseus_hi_galfa_cube_regrid_planckres' + bin_string + '.fits',
header=True)
# Load global properties
with open(property_dir + global_property_file, 'r') as f:
global_props = json.load(f)
# Prepare data products
# ---------------------
# Change WCS coords to pixel coords of images
global_props = convert_limit_coordinates(global_props, header=av_header)
# make the velocity axes
hi_vel_axis = make_velocity_axis(hi_header)
# Load the HI noise cube if it exists, else make it
if not path.isfile(hi_dir + noise_cube_filename + '.fits'):
noise_cube = calculate_noise_cube(cube=hi_data,
velocity_axis=hi_vel_axis,
velocity_noise_range=[90,110], header=hi_header, Tsys=30.,
filename=hi_dir + noise_cube_filename + '.fits')
else:
noise_cube, noise_header = fits.getdata(hi_dir +
noise_cube_filename + '.fits',
header=True)
# Derive relevant region
pix = global_props['region_limit']['pixel']
region_vertices = ((pix[1], pix[0]),
(pix[1], pix[2]),
(pix[3], pix[2]),
(pix[3], pix[0])
)
# block off region
region_mask = np.logical_not(myg.get_polygon_mask(av_data, region_vertices))
print('\nRegion size = ' + \
'{0:.0f} pix'.format(region_mask[region_mask == 1].size))
# Derive mask by excluding correlated residuals
# ---------------------------------------------
nhi_image = calculate_nhi(cube=hi_data,
velocity_axis=hi_vel_axis,
velocity_range=vel_range,
return_nhi_error=False,
)
av_model, mask, dgr = iterate_residual_masking(
nhi_image=nhi_image,
av_data=av_data,
av_data_error=av_data_error,
vel_range=vel_range,
threshold_delta_dgr=threshold_delta_dgr,
resid_width_scale=resid_width_scale,
init_mask=region_mask,
verbose=1,
plot_progress=0,
)
# Combine region mask with new mask
#mask += np.logical_not(region_mask)
mask += region_mask
if 1:
import matplotlib.pyplot as plt
plt.imshow(np.ma.array(av_data, mask=mask), origin='lower')
plt.show()
# Derive center velocity from hi
# ------------------------------
hi_spectrum = np.sum(hi_data[:, ~mask], axis=(1))
vel_center = np.array((np.average(hi_vel_axis,
weights=hi_spectrum**2),))[0]
print('\nVelocity center from HI = ' +\
'{0:.2f} km/s'.format(vel_center))
# Perform likelihood calculation of masked images
# -----------------------------------------------
# Define filename for plotting results
results_filename = figure_dir + 'likelihood/'+ results_filename
results = calc_likelihoods(
hi_cube=hi_data[:, ~mask],
hi_vel_axis=hi_vel_axis,
av_image=av_data[~mask],
av_image_error=av_data_error[~mask],
vel_center=vel_center,
vel_widths=vel_widths,
dgrs=dgrs,
results_filename='',
return_likelihoods=True,
likelihood_filename=None,
clobber=False,
conf=conf,
)
# Unpack output of likelihood calculation
(vel_range_confint, width_confint, dgr_confint, likelihoods,
width_likelihood, dgr_likelihood, width_max, dgr_max,
vel_range_max) = results
print('\nHI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range_confint[0],
vel_range_confint[1]))
print('\nDGR:')
print('%.1f x 10^-20 cm^2 mag' % (dgr_confint[0]))
# Calulate chi^2 for best fit models
# ----------------------------------
nhi_image_temp, nhi_image_error = \
calculate_nhi(cube=hi_data,
velocity_axis=hi_vel_axis,
velocity_range=vel_range_max,
noise_cube=noise_cube,
return_nhi_error=True)
av_image_model = nhi_image_temp * dgr_max
# avoid NaNs
indices = ((av_image_model == av_image_model) & \
(av_data == av_data))
# add nan locations to the mask
mask[~indices] = 1
# count number of pixels used in analysis
npix = mask[~mask].size
# finally calculate chi^2
chisq = np.sum((av_data[~mask] - av_image_model[~mask])**2 / \
av_data_error[~mask]**2) / av_data[~mask].size
print('\nTotal number of pixels in analysis, after masking = ' + \
'{0:.0f}'.format(npix))
print('\nReduced chi^2 = {0:.1f}'.format(chisq))
# Write results to global properties
global_props['dust2gas_ratio'] = {}
global_props['dust2gas_ratio_error'] = {}
global_props['hi_velocity_width'] = {}
global_props['hi_velocity_width_error'] = {}
global_props['dust2gas_ratio_max'] = {}
global_props['hi_velocity_center_max'] = {}
global_props['hi_velocity_width_max'] = {}
global_props['hi_velocity_range_max'] = {}
global_props['av_threshold'] = {}
global_props['co_threshold'] = {}
global_props['hi_velocity_width']['value'] = width_confint[0]
global_props['hi_velocity_width']['unit'] = 'km/s'
global_props['hi_velocity_width_error']['value'] = width_confint[1:]
global_props['hi_velocity_width_error']['unit'] = 'km/s'
global_props['hi_velocity_range'] = vel_range_confint[0:2]
global_props['hi_velocity_range_error'] = vel_range_confint[2:]
global_props['dust2gas_ratio']['value'] = dgr_confint[0]
global_props['dust2gas_ratio_error']['value'] = dgr_confint[1:]
global_props['dust2gas_ratio_max']['value'] = dgr_max
global_props['hi_velocity_center_max']['value'] = vel_center
global_props['hi_velocity_width_max']['value'] = width_max
global_props['hi_velocity_range_max']['value'] = vel_range_max
global_props['hi_velocity_range_conf'] = conf
global_props['width_likelihood'] = width_likelihood.tolist()
global_props['dgr_likelihood'] = dgr_likelihood.tolist()
global_props['vel_centers'] = [vel_center,]
global_props['vel_widths'] = vel_widths.tolist()
global_props['dgrs'] = dgrs.tolist()
global_props['likelihoods'] = likelihoods.tolist()
global_props['av_threshold']['value'] = None
global_props['av_threshold']['unit'] = 'mag'
global_props['co_threshold']['value'] = None
global_props['co_threshold']['unit'] = 'K km/s'
global_props['chisq'] = chisq
global_props['npix'] = npix
global_props['mask'] = mask.tolist()
global_props['use_binned_image'] = use_binned_image
with open(property_dir + global_property_file, 'w') as f:
json.dump(global_props, f)
# Plot likelihood space
print('\nWriting likelihood image to\n' + results_filename + '_wd.png')
plot_likelihoods_hist(global_props,
plot_axes=('widths', 'dgrs'),
show=0,
returnimage=False,
filename=results_filename + '_wd.png',
contour_confs=contour_confs)
if 0:
plt.clf(); plt.close()
nhi_image_copy = np.copy(nhi_image)
nhi_image_copy[mask] = np.nan
av_image_copy = np.copy(av_data)
resid_image = av_image_copy - nhi_image_copy * dgr
plt.imshow(resid_image, origin='lower')
plt.title(r'$A_V$ Data - Model')
plt.colorbar()
plt.show()
def main():
''' Executes script.
'''
# import external modules
import pyfits as pf
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
reload(myg)
# define directory locations
output_dir = '/d/bip3/ezbc/perseus/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/perseus/figures/'
av_dir = '/d/bip3/ezbc/perseus/data/av/'
hi_dir = '/d/bip3/ezbc/perseus/data/galfa/'
core_dir = output_dir + 'core_arrays/'
region_dir = '/d/bip3/ezbc/perseus/data/python_output/ds9_regions/'
# Load hi fits file
hi_image, hi_header = pf.getdata(hi_dir + \
'perseus_galfa_cube_bin_3.7arcmin.fits', header=True)
h = hi_header
# Load av fits file
av_image, av_header = \
pf.getdata('/d/bip3/ezbc/perseus/data/2mass/perseus_av_2mass_galfa_regrid.fits',
header=True)
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
# create nhi image
nhi_image = calculate_nhi(hi_cube=hi_image,
velocity_axis=velocity_axis, velocity_range=[-100,100])
if False:
# trim hi_image to av_image size
nhi_image_trim = np.ma.array(nhi_image, mask=av_image != av_image)
plot_nhi_image(nhi_image=nhi_image_trim, header=hi_header,
contour_image=av_image, contours=[5,10,15],
savedir=figure_dir, filename='perseus_nhi_cores_map.png',
show=True)
cores = {'IC348':
{'center_wcs': [(3, 44, 0), (32, 8, 0)],
'map': None,
'threshold': None,
'box_wcs': [(3,46,13), (26,3,24), (3,43,4), (32,25,41)],
},
'NGC1333':
{'center_wcs': [(3, 29, 11), (31, 16, 53)],
'map': None,
'threshold': None,
'box_wcs': None,
},
'B4':
{'center_wcs': [(3, 45, 50), (31, 42, 0)],
'map': None,
'threshold': None,
'box_wcs': None,
},
'B5':
{'center_wcs': [(3, 47, 34), (32, 48, 17)],
'map': None,
'threshold': None,
'box_wcs': None,
},
#'':
# {'center_wcs': [],
# 'map': None,
# 'threshold': None,
# 'box_wcs': None,
# },
}
cores = convert_core_coordinates(cores, h)
if False:
nhi_image = np.zeros(nhi_image.shape)
for core in cores:
core_image = np.load(core_dir + core + '.npy')
core_indices = np.where(core_image == core_image)
nhi_image[core_indices] += core_image[core_indices]
nhi_image_trim =np.ma.array(nhi_image, mask=((av_image != av_image) &\
(nhi_image == 0)))
nhi_image_trim[nhi_image_trim == 0] = np.NaN
read_ds9_region(av_dir + 'perseus_av_boxes.reg')
plot_nhi_image(nhi_image=nhi_image_trim, header=hi_header,
savedir=figure_dir,
cores=cores,
filename='perseus_nhi_core_regions_map.png',
show=True)
if True:
cores = load_ds9_region(cores,
filename_base = region_dir + 'perseus_av_boxes_',
header = h)
# Grab the mask
mask = np.zeros((nhi_image.shape))
for core in cores:
xy = cores[core]['box_center_pix']
box_width = cores[core]['box_width']
box_height = cores[core]['box_height']
box_angle = cores[core]['box_angle']
mask += myg.get_rectangular_mask(nhi_image,
xy[0], xy[1],
width = box_width,
height = box_height,
angle = box_angle)
cores[core]['box_vertices'] = myg.get_rect(
xy[0], xy[1],
width = box_width,
height = box_height,
angle = box_angle,)
#print(cores[core]['box_vertices'])
#print core, xy, box_width, box_height, box_angle
mask[mask > 1] = 1
#nhi_image[mask == 0] = np.nan
# trim hi_image to av_image size
nhi_image_trim = np.ma.array(nhi_image,
mask = (av_image != av_image))
# Plot
figure_types = ['pdf', 'png']
for figure_type in figure_types:
plot_nhi_image(nhi_image=nhi_image_trim,
header=hi_header,
contour_image=av_image,
contours=[2.5,5,8],
boxes=True,
cores = cores,
limits=[47,128,231,222,],
title='Perseus: N(HI) map with core boxed-regions.',
savedir=figure_dir,
filename='perseus_nhi_cores_map.%s' % figure_type,
show=False)
def main():
''' Executes script.
'''
# import external modules
import pyfits as pf
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
reload(myg)
# define directory locations
output_dir = '/d/bip3/ezbc/california/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/california/figures/'
av_dir = '/d/bip3/ezbc/california/data/av/'
hi_dir = '/d/bip3/ezbc/california/data/galfa/'
core_dir = output_dir + 'core_arrays/'
region_dir = '/d/bip3/ezbc/california/data/python_output/ds9_regions/'
# Load hi fits file
hi_image, hi_header = pf.getdata(hi_dir + \
'california_galfa_cube_bin_3.7arcmin.fits', header=True)
h = hi_header
# Load av fits file
av_image, av_header = pf.getdata(av_dir + \
'california_planck_av_regrid.fits',
header=True)
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
# create nhi image
nhi_image = calculate_nhi(hi_cube=hi_image,
velocity_axis=velocity_axis, velocity_range=[-100,100])
if False:
# trim hi_image to av_image size
nhi_image_trim = np.ma.array(nhi_image, mask=av_image != av_image)
plot_nhi_image(nhi_image=nhi_image_trim, header=hi_header,
contour_image=av_image, contours=[5,10,15],
savedir=figure_dir, filename='california_nhi_cores_map.png',
show=True)
# define core properties
cores = {'L1482':
{'center_wcs': [(4, 29, 41), (35, 48, 41)],
'map': None,
'threshold': None,
},
'L1483':
{'center_wcs': [(4, 34, 57), (36, 18, 12)],
'map': None,
'threshold': None,
},
'L1478':
{'center_wcs': [(4, 25, 7), (37, 13, 0)],
'map': None,
'threshold': None,
},
'L1434':
{'center_wcs': [(3, 50, 51), (35, 15, 10)],
'map': None,
'threshold': None,
},
'L1503':
{'center_wcs': [(4, 40, 27), (29, 57, 12)],
'map': None,
'threshold': None,
},
'L1507':
{'center_wcs': [(4, 42, 51), (29, 44, 47)],
'map': None,
'threshold': None,
},
}
cores = convert_core_coordinates(cores, h)
if False:
nhi_image = np.zeros(nhi_image.shape)
for core in cores:
core_image = np.load(core_dir + core + '.npy')
core_indices = np.where(core_image == core_image)
nhi_image[core_indices] += core_image[core_indices]
nhi_image_trim =np.ma.array(nhi_image, mask=((av_image != av_image) &\
(nhi_image == 0)))
nhi_image_trim[nhi_image_trim == 0] = np.NaN
read_ds9_region(av_dir + 'california_av_boxes.reg')
plot_nhi_image(nhi_image=nhi_image_trim, header=hi_header,
savedir=figure_dir,
cores=cores,
filename='california_nhi_core_regions_map.png',
show=True)
if True:
cores = load_ds9_region(cores,
filename_base = region_dir + 'california_av_boxes_',
header = h)
# Grab the mask
mask = np.zeros((nhi_image.shape))
for core in cores:
xy = cores[core]['box_center_pix']
box_width = cores[core]['box_width']
box_height = cores[core]['box_height']
box_angle = cores[core]['box_angle']
mask += myg.get_rectangular_mask(nhi_image,
xy[0], xy[1],
width = box_width,
height = box_height,
angle = box_angle)
cores[core]['box_vertices'] = myg.get_rect(
xy[0], xy[1],
width = box_width,
height = box_height,
angle = box_angle,)
#print(cores[core]['box_vertices'])
#print core, xy, box_width, box_height, box_angle
mask[mask > 1] = 1
#nhi_image[mask == 0] = np.nan
# trim hi_image to av_image size
nhi_image_trim = np.ma.array(nhi_image,
mask = (av_image != av_image))
# Plot
plot_nhi_image(nhi_image=nhi_image_trim, header=hi_header,
contour_image=av_image, contours=[3,6,10],
boxes=True, cores = cores, #limits=[128,37,308,206],
title='California: N(HI) map with core boxed-regions.',
savedir=figure_dir, filename='california_nhi_cores_map.pdf',
show=True)
def main():
''' Executes script.
'''
# import external modules
import pyfits as pf
import numpy as np
from mycoords import make_velocity_axis
from os import system,path
# define directory locations
output_dir = '/d/bip3/ezbc/taurus/data/python_output/' + \
'taurus_perseus_comparison/'
figure_dir = '/d/bip3/ezbc/taurus/figures/'
perseus_dir = '/d/bip3/ezbc/perseus/'
taurus_dir = '/d/bip3/ezbc/taurus/'
av_dir = 'data/av/'
hi_dir = 'data/galfa/'
core_dir = output_dir + 'core_arrays/'
# Load hi fits file
data_dict = {'perseus':{
'hi_file': perseus_dir + hi_dir + \
'perseus.galfa.cube.bin.4arcmin.fits',
'hi_noise_file': perseus_dir + hi_dir + \
'perseus.galfa.cube.bin.4arcmin.noise.fits',
'av_file': perseus_dir + 'data/2mass/' + \
'2mass_av_lee12_nocal_regrid.fits',
'hi_data': None,
'hi_header': None,
'hi_vel_axis': None,
'av_data': None,
'av_header': None,
'nhi_image': None,
'nhi_error_image': None,
'av_noise_region': [54,66,83,103]},
'taurus':{
'hi_file': taurus_dir + hi_dir + \
'taurus.galfa.cube.bin.4arcmin.fits',
'hi_noise_file': taurus_dir + hi_dir + \
'taurus.galfa.cube.bin.4arcmin.noise.fits',
'av_file': taurus_dir + av_dir + \
'taurus_av_k09_regrid.fits',
'hi_data': None,
'hi_header': None,
'hi_vel_axis': None,
'av_data': None,
'av_header': None,
'nhi_image': None,
'nhi_error_image': None,
'av_noise_region': [179,233,195,260]}}
for data in data_dict:
# Get hi data
data_dict[data]['hi_data'], data_dict[data]['hi_header'] = \
pf.getdata(data_dict[data]['hi_file'], header=True)
# Create hi velocity axis
data_dict[data]['hi_vel_axis'] = \
make_velocity_axis(data_dict[data]['hi_header'])
# Calculate or load nhi noise cube
noise_cube_filename = data_dict[data]['hi_noise_file']
if not path.isfile(noise_cube_filename):
noise_cube = calculate_noise_cube(cube = data_dict[data]['hi_data'],
velocity_axis = data_dict[data]['hi_vel_axis'],
velocity_noise_range=[-110,-90,90,110], Tsys=30.,
filename = noise_cube_filename)
else:
noise_cube, h = load_fits(noise_cube_filename,
return_header=True)
# calculate N(HI) image
data_dict[data]['nhi_image'], data_dict[data]['nhi_error_image'] = \
calculate_nhi(cube = data_dict[data]['hi_data'],
velocity_axis = data_dict[data]['hi_vel_axis'],
velocity_range=[-5,15], Tsys=30., noise_cube = noise_cube)
# get av data
data_dict[data]['av_data'], data_dict[data]['av_header'] = \
pf.getdata(data_dict[data]['av_file'], header=True)
cores = {'L1495':
{'wcs_position': [15*(4+14/60.), 28+11/60., 0],
'map': None,
'threshold': 4.75,
'box': [206,242,244,287]},
'L1495A':
{'wcs_position': [15*(4+18/60.), 28+23/60., 0],
'map': None,
'threshold': 4.75,
'box': [206,212,236,242]},
'B213':
{'wcs_position': [15*(4+19/60.), 27+15/60., 0],
'map': None,
'threshold': 4.75,
'box': [177,206,206,242]},
'B220':
{'wcs_position': [15*(4+41/60.), 26+7/60., 0],
'map': None,
'threshold': 7,
'box': [179,131,199,157]},
'L1527':
{'wcs_position': [15*(4+39/60.), 25+47/60., 0],
'map': None,
'threshold': 7,
'box': [165,152,179,172]},
'B215':
{'wcs_position': [15*(4+23/60.), 25+3/60., 0],
'map': None,
'threshold': 3,
'box': [143,209,177,243]},
'L1524':
{'wcs_position': [15*(4+29/60.), 24+31/60., 0],
'map': None,
'threshold': 3,
'box': [138,177,167,209]}}
print_properties(data_dict)
print_core_properties(data_dict, cores)
return data_dict[data]['nhi_image']
def main(dgr=None,
vel_range=None,
vel_range_type='single',
region=None,
av_data_type='planck',
use_binned_images=False):
''' Executes script.
Parameters
----------
dgr : float
If None, pulls best-fit value from properties.
vel_range : tuple
If None, pulls best-fit value from properties.
'''
# import external modules
import pyfits as pf
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
import json
# Script parameters
# -----------------
if use_binned_images:
bin_string = '_bin'
else:
bin_string = ''
# Name of noise cube
noise_cube_filename = \
'taurus_hi_galfa_cube_regrid_planckres_noise' + bin_string + \
'.fits'
# Name of property files results are written to
prop_file = 'taurus_global_properties_' + av_data_type + '_scaled'
# Regions, regions to edit the global properties with
if region == 1:
region_limit = {
'wcs': (((5, 10, 0), (19, 0, 0)), ((4, 30, 0), (27, 0, 0))),
'pixel': ()
}
elif region == 2:
region_limit = {
'wcs': (((4, 30, 0), (19, 0, 0)), ((3, 50, 0), (29, 0, 0))),
'pixel': ()
}
elif region == 3:
region_limit = {
'wcs': (((4, 30, 0), (29, 0, 0)), ((3, 50, 0), (33, 0, 0))),
'pixel': ()
}
else:
region_limit = None
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/taurus/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/taurus/figures/'
av_dir = '/d/bip3/ezbc/taurus/data/av/'
hi_dir = '/d/bip3/ezbc/taurus/data/hi/'
co_dir = '/d/bip3/ezbc/taurus/data/co/'
core_dir = '/d/bip3/ezbc/taurus/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/taurus/data/python_output/'
region_dir = '/d/bip3/ezbc/taurus/data/python_output/ds9_regions/'
# load Planck Av and GALFA HI images, on same grid
if av_data_type == 'lee12_2mass':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'taurus_av_lee12_2mass_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'lee12_iris':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'taurus_av_lee12_iris_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
else:
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'taurus_av_planck_5arcmin' + bin_string + \
'.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'taurus_av_error_planck_5arcmin' + bin_string + \
'.fits',
return_header=True)
hi_cube, hi_header = load_fits(hi_dir + \
'taurus_hi_galfa_cube_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
hi_noise_cube, noise_header = load_fits(hi_dir + noise_cube_filename,
return_header=True)
if not use_binned_images:
co_data, co_header = load_fits(co_dir + \
'taurus_co_cfa_cube_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
# Load global properties of cloud
# global properties written from script
# 'av/taurus_analysis_global_properties.txt'
if region is not None:
likelihood_filename += '_region{0:.0f}'.format(region)
results_filename += '_region{0:.0f}'.format(region)
print('\nReading global parameter file\n' + prop_file + '.txt')
with open(property_dir + prop_file + '.txt', 'r') as f:
props = json.load(f)
if vel_range is not None:
props['hi_velocity_range'] = vel_range
else:
vel_range = props['hi_velocity_range']
if dgr is not None:
props['dust2gas_ratio']['value'] = dgr
else:
dgr = props['dust2gas_ratio']['value']
# define core properties
with open(core_dir + 'taurus_core_properties.txt', 'r') as f:
cores = json.load(f)
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
if not use_binned_images:
# make velocity axis for co cube
co_velocity_axis = make_velocity_axis(co_header)
# Write core coordinates in pixels
cores = convert_core_coordinates(cores, hi_header)
cores = load_ds9_region(cores,
filename_base=region_dir + 'taurus_av_boxes_',
header=hi_header)
# create nhi image
nhi_image = calculate_nhi(cube=hi_cube,
velocity_axis=velocity_axis,
velocity_range=vel_range,
header=hi_header,
noise_cube=hi_noise_cube)
# create model av map
av_model = nhi_image * dgr
if vel_range_type == 'single':
print('\nHI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range[0], vel_range[1]))
elif vel_range_type == 'multiple':
print('\nHI velocity integration ranges:')
for i in xrange(0, vel_range.shape[0]):
print('%.1f to %.1f km/s' % (vel_range[i, 0], vel_range[i, 1]))
print('\nDGR:')
print('%.2f x 10^-20 cm^2 mag' % (dgr))
# Get mask and mask images
mask = np.asarray(props['mask' + bin_string])
mask_images = False
av_image_masked = np.copy(av_image)
#av_image_masked[(mask == 1) & (region_mask == 1)] = np.nan
av_error_masked = np.copy(av_image_error)
#av_image_masked[(mask == 1) & (region_mask == 1)] = np.nan
av_model_masked = np.copy(av_model)
#av_model_masked[(mask == 1) & (region_mask == 1)] = np.nan
if mask_images:
av_image_masked[mask] = np.nan
av_error_masked[mask] = np.nan
av_model_masked[mask] = np.nan
indices = ((np.isnan(av_model_masked)) & \
(np.isnan(av_image_masked)) & \
(np.isnan(av_image_error)))
print('\nTotal number of pixels after masking = ' + str(props['npix']))
if 0:
import matplotlib.pyplot as plt
av_plot_data = np.copy(av_image)
av_plot_data[mask] = np.nan
plt.imshow(av_plot_data, origin='lower')
plt.xlim(props['plot_limit_bin']['pixel'][0:3:2])
plt.ylim(props['plot_limit_bin']['pixel'][1:4:2])
plt.show()
# Create HI spectrum
hi_cube[hi_cube != hi_cube] = 0
hi_cube[:, mask] = 0
hi_spectrum = np.mean(hi_cube, axis=(1, 2))
if not use_binned_images:
# Derive CO spectrum
co_data[:, mask] = 0
co_data[np.isnan(co_data)] = 0
co_spectrum = np.mean(co_data, axis=(1, 2))
# Plot
figure_types = ['png', 'pdf']
for figure_type in figure_types:
if region is None:
if vel_range_type == 'single':
filename = 'single_vel_range/taurus_av_model_map_' + \
av_data_type + bin_string
#'dgr{0:.3f}_'.format(dgr) + \
#'{0:.1f}to{1:.1f}kms'.format(vel_range[0], vel_range[1]) + \
#'_' + \
elif vel_range_type == 'multiple':
filename = 'multiple_vel_range/taurus_av_model_map_' + \
'dgr{0:.3f}'.format(dgr)
for i in xrange(0, vel_range.shape[0]):
filename += '_{0:.1f}to{1:.1f}kms'.format(
vel_range[i, 0], vel_range[i, 1])
filename += '.%s' % figure_type
else:
filename = 'taurus_av_model_map_region{0:.0f}'.format(region)
print('\nSaving Av model image to \n' + figure_dir + filename + \
'.' + figure_type)
if 0:
plot_av_model(av_image=av_image_masked,
av_model=av_model_masked,
header=av_header,
results=props,
limits=props['plot_limit' + bin_string]['pixel'],
savedir=figure_dir + 'maps/av_models/',
filename=filename + '.' + figure_type,
show=False)
if 1:
#if not use_binned_images:
if 0:
plot_av_model(
av_image=av_image_masked,
av_model=av_model_masked,
header=av_header,
results=props,
hi_velocity_axis=velocity_axis,
vel_range=vel_range,
hi_spectrum=hi_spectrum,
#hi_limits=[-15, 25, -1, 10],
hi_limits=[-15, 25, None, None],
co_spectrum=co_spectrum,
co_velocity_axis=co_velocity_axis,
limits=props['plot_limit' + bin_string]['pixel'],
savedir=figure_dir + 'maps/av_models/',
filename=filename + '_spectra' + '.' + figure_type,
show=False)
plot_avmod_vs_av(
(av_model_masked, ),
(av_image_masked, ),
av_errors=(av_error_masked, ),
#limits=[10**-1, 10**1.9, 10**0, 10**1.7],
limits=[0, 20, 0, 3],
savedir=figure_dir + 'av/',
gridsize=(10, 10),
#scale=('log', 'log'),
#scale=('linear', 'linear'),
filename='taurus_avmod_vs_av%s.%s' % (bin_string, figure_type),
show=False,
std=0.22,
)
if 0:
plot_power_spectrum(av_image_masked - av_model_masked,
filename_prefix='taurus_av_resid_power_spectrum_' + \
'{0:s}'.format(av_data_type),
filename_suffix='.{0:s}'.format(figure_type),
savedir=figure_dir + 'power_spectra/',
show=False)
def main(dgr=None, vel_range=None, vel_range_type='single', region=None,
av_data_type='planck'):
''' Executes script.
Parameters
----------
dgr : float
If None, pulls best-fit value from properties.
vel_range : tuple
If None, pulls best-fit value from properties.
'''
# import external modules
#import pyfits as fits
from astropy.io import fits
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
import json
from os import system,path
# Script parameters
# -----------------
# Name of noise cube
noise_cube_filename = 'multicloud_hi_galfa_cube_regrid_planckres_noise.fits'
# Use Planck dust Av map or Kainulainen 2009 optical extinction Av map?
# options are 'planck' or 'lee12'
#av_data_type = 'lee12'
#av_data_type = 'planck'
# Global parameter file
prop_file = 'multicloud_global_properties'
# Regions, regions to edit the global properties with
if region == 1:
region_limit = {'wcs' : (((5, 10, 0), (19, 0, 0)),
((4, 30, 0), (27, 0, 0))),
'pixel' : ()
}
elif region == 2:
region_limit = {'wcs' : (((4, 30, 0), (19, 0, 0)),
((3, 50, 0), (29, 0, 0))),
'pixel' : ()
}
elif region == 3:
region_limit = {'wcs' : (((4, 30, 0), (29, 0, 0)),
((3, 50, 0), (33, 0, 0))),
'pixel' : ()
}
else:
region_limit = None
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/multicloud/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/multicloud/figures/'
av_dir = '/d/bip3/ezbc/multicloud/data/av/'
hi_dir = '/d/bip3/ezbc/multicloud/data/hi/'
co_dir = '/d/bip3/ezbc/multicloud/data/co/'
core_dir = '/d/bip3/ezbc/multicloud/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/multicloud/data/python_output/'
region_dir = '/d/bip3/ezbc/multicloud/data/python_output/regions/'
# load Planck Av and GALFA HI images, on same grid
if av_data_type == 'lee12_2mass':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_lee12_2mass_regrid_planckres.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'lee12_iris':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_lee12_iris_regrid_planckres.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'planck_rad':
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_planck_tau353_5arcmin.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'multicloud_av_error_planck_tau353_5arcmin.fits',
return_header=True)
else:
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_planck_tau353_5arcmin.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'multicloud_av_error_planck_tau353_5arcmin.fits',
return_header=True)
hi_cube, hi_header = load_fits(hi_dir + \
'multicloud_hi_galfa_cube_regrid_planckres.fits',
return_header=True)
co_data, co_header = load_fits(co_dir + \
'multicloud_co_cfa_cube_regrid_planckres.fits',
return_header=True)
# Prepare data products
# ---------------------
# Load global properties of cloud
# global properties written from script
# 'av/multicloud_analysis_global_properties.txt'
if region is not None:
likelihood_filename += '_region{0:.0f}'.format(region)
results_filename += '_region{0:.0f}'.format(region)
with open(property_dir + prop_file + '.txt', 'r') as f:
props = json.load(f)
if vel_range is not None:
props['hi_velocity_range'] = vel_range
else:
vel_range = props['hi_velocity_range']
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
# make velocity axis for co cube
co_velocity_axis = make_velocity_axis(co_header)
# Load the HI noise cube if it exists, else make it
if not path.isfile(hi_dir + noise_cube_filename):
hi_noise_cube = calculate_noise_cube(cube=hi_cube,
velocity_axis=velocity_axis,
velocity_noise_range=[90,110], header=hi_header, Tsys=30.,
filename=hi_dir + noise_cube_filename)
else:
hi_noise_cube, noise_header = fits.getdata(hi_dir + noise_cube_filename,
header=True)
# create nhi image
nhi_image = calculate_nhi(cube=hi_cube,
velocity_axis=velocity_axis,
velocity_range=vel_range,
header=hi_header,
noise_cube=hi_noise_cube)
props['plot_limit']['wcs'] = (((5, 20, 0), (19, 0 ,0)),
((2, 30, 0), (37, 0, 0))
)
props['region_name_pos'] = {
#'taurus 1' : {'wcs' : ((3, 50, 0),
# (21.5, 0, 0)),
# },
#'taurus 2' : {'wcs' : ((5, 10, 0),
# (21.5, 0, 0)),
# },
'taurus' : {'wcs' : ((4, 40, 0),
(21, 0, 0)),
},
'perseus' : {'wcs' : ((3, 30, 0),
(26, 0, 0)),
},
#'perseus 1' : {'wcs' : ((3, 0, 0),
# (34, 0, 0)),
# },
#'perseus 2' : {'wcs' : ((3, 10, 0),
# (22.5, 0, 0)),
# },
'california' : {'wcs' : ((4, 28, 0),
(34, 0, 0)),
},
}
# Change WCS coords to pixel coords of images
props = convert_limit_coordinates(props,
header=av_header,
coords=('region_limit',
'co_noise_limits',
'plot_limit',
'region_name_pos'))
props['plot_limit']['wcs'] = [15*(5+20./60), 15*(2+30./60.), 17, 38.5]
# Load cloud division regions from ds9
props = load_ds9_region(props,
filename=region_dir + 'multicloud_divisions.reg',
header=av_header)
# Derive relevant region
pix = props['region_limit']['pixel']
region_vertices = ((pix[1], pix[0]),
(pix[1], pix[2]),
(pix[3], pix[2]),
(pix[3], pix[0])
)
# block offregion
region_mask = myg.get_polygon_mask(av_image, region_vertices)
print('\nRegion size = ' + \
'{0:.0f} pix'.format(region_mask[region_mask == 1].size))
if vel_range_type == 'single':
print('\nHI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range[0],
vel_range[1]))
elif vel_range_type == 'multiple':
print('\nHI velocity integration ranges:')
for i in xrange(0, vel_range.shape[0]):
print('%.1f to %.1f km/s' % (vel_range[i, 0],
vel_range[i, 1]))
# Plot
figure_types = ['png', 'pdf']
for figure_type in figure_types:
if region is None:
if vel_range_type == 'single':
filename = 'multicloud_av_nhi_map' + \
'.%s' % figure_type
#av_data_type + \
#'dgr{0:.3f}_'.format(dgr) + \
#'{0:.1f}to{1:.1f}kms'.format(vel_range[0], vel_range[1]) + \
#'_' + \
elif vel_range_type == 'multiple':
filename = 'multiple_vel_range/multicloud_av_model_map' + \
'dgr{0:.3f}'.format(dgr)
for i in xrange(0, vel_range.shape[0]):
filename += '_{0:.1f}to{1:.1f}kms'.format(vel_range[i, 0],
vel_range[i, 1])
filename += '.%s' % figure_type
else:
filename = 'multicloud_av_model_map_region{0:.0f}'.format(region) + \
'.{0:s}'.format(figure_type)
filename = 'av_map'
filename = figure_dir + 'maps/' + filename + '.' + figure_type
print('\nSaving Av model image to \n' + filename)
plot_av_image(av_image=av_image,
header=av_header,
limits=[15*(5+20./60), 15*(2+30./60.), 17, 38.5],
limits_type='wcs',
regions=props['regions'],
props=props,
av_vlimits=(0,15.5),
filename=filename,
show=False)
if 0:
filename = 'av_nhi_map'
filename = figure_dir + 'maps/' + filename + '.' + figure_type
print('\nSaving NHI + Av maps to \n' + filename)
plot_nhi_image(nhi_image=nhi_image,
header=av_header,
av_image=av_image,
limits=props['plot_limit']['wcs'],
limits_type='wcs',
regions=props['regions'],
props=props,
hi_vlimits=(0,20),
av_vlimits=(0,15.5),
#av_vlimits=(0.1,30),
filename=filename,
show=False)
def test_scatter_contour():
from astropy.io import fits
from myimage_analysis import calculate_nhi
import mygeometry as myg
from mycoords import make_velocity_axis
# Parameters
# ----------
levels = (0.99, 0.985, 0.7)
levels = (
0.999,
0.998,
0.96,
0.86,
0.58,
)
levels = 7
levels = np.logspace(np.log10(0.995), np.log10(0.50), 5)
log_counts = 0
limits = [1, 10, -3, 30]
limits = None
# Begin test
# ----------
data_dir = '/d/bip3/ezbc/perseus/data/'
av = fits.getdata(data_dir +
'av/perseus_av_planck_tau353_5arcmin.fits')
hi, hi_header = fits.getdata(data_dir + \
'hi/perseus_hi_galfa_cube_regrid_planckres.fits',
header=True)
hi_vel_axis = make_velocity_axis(hi_header)
nhi = calculate_nhi(
cube=hi,
velocity_axis=hi_vel_axis,
velocity_range=[0, 10],
)
# Drop the NaNs from the images
indices = np.where((av == av) &\
(nhi == nhi)
)
av_nonans = av[indices]
nhi_nonans = nhi[indices]
fig, ax = plt.subplots()
if limits is None:
xmin = np.min(nhi_nonans)
ymin = np.min(av_nonans)
xmax = np.max(nhi_nonans)
ymax = np.max(av_nonans)
xscalar = 0.25 * xmax
yscalar = 0.25 * ymax
limits = [
xmin - xscalar, xmax + xscalar, ymin - yscalar, ymax + yscalar
]
contour_range = ((limits[0], limits[1]), (limits[2], limits[3]))
cmap = myplt.truncate_colormap(plt.cm.binary, 0.2, 1, 1000)
l1 = myplt.scatter_contour(
nhi_nonans.ravel(),
av_nonans.ravel(),
threshold=3,
log_counts=log_counts,
levels=levels,
ax=ax,
histogram2d_args=dict(bins=30, range=contour_range),
plot_args=dict(marker='o',
linestyle='none',
color='black',
alpha=0.3,
markersize=2),
contour_args=dict(
#cmap=plt.cm.binary,
cmap=cmap,
#cmap=cmap,
),
)
scale = ['linear', 'linear']
ax.set_xscale(scale[0], nonposx='clip')
ax.set_yscale(scale[1], nonposy='clip')
ax.set_xlim(limits[0], limits[1])
ax.set_ylim(limits[2], limits[3])
# Adjust asthetics
ax.set_xlabel(r'$N($H$\textsc{i}) \times\,10^{20}$ cm$^{-2}$')
ax.set_ylabel(r'$A_V$ [mag]')
#ax.set_title(core_names[i])
ax.legend(loc='lower right')
plt.savefig('test_plots/test_scatter_contour.png')
def run_cloud_analysis(global_args, ):
from astropy.io import fits
from myimage_analysis import calculate_nhi, calc_region_mask
import myimage_analysis as myia
from mycoords import make_velocity_axis
from mystats import calc_symmetric_error, calc_logL
import os
import myio
import pickle
import mystats
cloud_name = global_args['cloud_name']
region = global_args['region']
load = global_args['load']
data_type = global_args['data_type']
background_subtract = global_args['background_subtract']
# define directory locations
# --------------------------
figure_dir = \
'/d/bip3/ezbc/multicloud/figures/'
av_dir = '/d/bip3/ezbc/' + cloud_name + '/data/av/'
dust_temp_dir = '/d/bip3/ezbc/' + cloud_name + '/data/dust_temp/'
hi_dir = '/d/bip3/ezbc/' + cloud_name + '/data/hi/'
co_dir = '/d/bip3/ezbc/' + cloud_name + '/data/co/'
core_dir = \
'/d/bip3/ezbc/' + cloud_name + '/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/' + cloud_name + '/data/python_output/'
region_dir = '/d/bip3/ezbc/multicloud/data/python_output/regions/'
background_region_dir = '/d/bip3/ezbc/' + cloud_name + \
'/data/python_output/ds9_regions/'
results_dir = '/d/bip3/ezbc/multicloud/data/python_output/'
av_filename = av_dir + \
cloud_name + '_av_planck_tau353_5arcmin.fits'
av_data, av_header = fits.getdata(av_filename, header=True)
# define filenames
prop_filename = property_dir + \
cloud_name + '_global_properties.txt'
hi_filename = hi_dir + \
cloud_name + '_hi_galfa_cube_regrid_planckres.fits'
hi_dr1_filename = hi_dir + \
cloud_name + '_hi_galfa_dr1_cube_regrid_planckres.fits'
hi_error_filename = hi_dir + \
cloud_name + '_hi_galfa_cube_regrid_planckres_noise.fits'
co_filename = co_dir + \
cloud_name + '_co_cfa_cube_regrid_planckres.fits'
# Get the filename base to differentiate between different parameters
filename_base, global_args = create_filename_base(global_args)
# set up plotting variables
plot_kwargs = {
'figure_dir': figure_dir,
'cloud_name': cloud_name,
'filename_base': filename_base,
'plot_diagnostics': global_args['plot_diagnostics'],
#'av_nhi_contour': av_nhi_contour,
'av_nhi_contour': True,
'av_nhi_limits': [0, 20, -1, 9],
#'av_nhi_limits': None,
}
# mask data
region_filename = region_dir + 'multicloud_divisions.reg'
region_mask = calc_region_mask(region_filename,
av_data,
av_header,
region_name=global_args['region_name'])
# Load HI and CO cubes
hi_data, hi_header = fits.getdata(hi_filename, header=True)
hi_dr1_data, hi_dr1_header = fits.getdata(hi_dr1_filename, header=True)
co_data, co_header = fits.getdata(co_filename, header=True)
#hi_data[:, region_mask] = np.nan
#hi_dr1_data[:, region_mask] = np.nan
#co_data[:, region_mask] = np.nan
hi_vel_axis = make_velocity_axis(hi_header)
co_vel_axis = make_velocity_axis(co_header)
# Load HI error
if global_args['clobber_hi_error']:
print('\n\tCalculating HI noise cube...')
os.system('rm -rf ' + hi_error_filename)
hi_data_error = \
myia.calculate_noise_cube(cube=hi_data,
velocity_axis=hi_vel_axis,
velocity_noise_range=[-110,-90, 90,110],
Tsys=30.0,
filename=hi_error_filename)
else:
hi_data_error = fits.getdata(hi_error_filename)
# Derive N(HI)
# -------------------------------------------------------------------------
# get fit kwargs
gauss_fit_kwargs, ncomps_in_cloud = get_gauss_fit_kwargs(global_args)
# derive spectra or load
spectra_filename = results_dir + 'spectra/' + global_args['cloud_name'] + \
'_spectra.pickle'
spectra_dr1_filename = results_dir + 'spectra/' + \
global_args['cloud_name'] + \
'_spectra_dr1.pickle'
load_spectra = myio.check_file(spectra_filename,
clobber=global_args['clobber_spectra'])
if load_spectra:
hi_spectrum, hi_std_spectrum, co_spectrum = \
myio.load_pickle(spectra_filename)
hi_dr1_spectrum, hi_std_dr1_spectrum, co_spectrum = \
myio.load_pickle(spectra_dr1_filename)
else:
print('\n\tCalculating spectra...')
if global_args['smooth_hi_to_co_res']:
from astropy.convolution import Gaussian2DKernel, convolve
# Create kernel
# one pix = 5 arcmin, need 8.4 arcmin for CO res
# The beamsize is the FWHM. The convolution kernel needs the
# standard deviation
hi_res = 1.0
co_res = 8.4 / 5.0
width = (co_res**2 - hi_res**2)**0.5
std = width / 2.355
g = Gaussian2DKernel(width)
# Convolve data
hi_data_co_res = np.zeros(hi_data.shape)
for i in xrange(hi_data.shape[0]):
hi_data_co_res[i, :, :] = \
convolve(hi_data[i, :, :], g, boundary='extend')
hi_dr1_data_co_res = np.zeros(hi_dr1_data.shape)
for i in xrange(hi_dr1_data.shape[0]):
hi_dr1_data_co_res[i, :, :] = \
convolve(hi_dr1_data[i, :, :], g, boundary='extend')
hi_spectrum = myia.calc_spectrum(hi_data_co_res)
hi_std_spectrum = myia.calc_spectrum(hi_data_co_res,
statistic=np.nanstd)
hi_dr1_spectrum = myia.calc_spectrum(hi_dr1_data_co_res)
hi_std_dr1_spectrum = myia.calc_spectrum(hi_dr1_data_co_res,
statistic=np.nanstd)
co_spectrum = myia.calc_spectrum(co_data)
myio.save_pickle(spectra_filename,
(hi_spectrum, hi_std_spectrum, co_spectrum))
myio.save_pickle(spectra_dr1_filename,
(hi_dr1_spectrum, hi_std_dr1_spectrum, co_spectrum))
if global_args['hi_range_calc'] == 'gaussian':
velocity_range, gauss_fits, comp_num, hi_range_error = \
calc_hi_vel_range(hi_spectrum,
hi_vel_axis,
gauss_fit_kwargs,
co_spectrum=co_spectrum,
co_vel_axis=co_vel_axis,
ncomps=ncomps_in_cloud,
)
global_args['vel_range_error'] = hi_range_error
velocity_range_dr1, gauss_fits_dr1, comp_num_dr1, hi_range_error_dr1 = \
calc_hi_vel_range(hi_dr1_spectrum,
hi_vel_axis,
gauss_fit_kwargs,
co_spectrum=co_spectrum,
co_vel_axis=co_vel_axis,
ncomps=ncomps_in_cloud,
)
else:
velocity_range = [-5, 15]
gauss_fits = None
comp_num = None
hi_range_kwargs = {
'velocity_range': velocity_range,
'gauss_fits': gauss_fits,
'comp_num': comp_num,
'hi_range_error': hi_range_error,
'vel_range': velocity_range,
'gauss_fit_kwargs': gauss_fit_kwargs,
}
# plot the results
# --------------------------------------------------------------------------
filename = plot_kwargs['figure_dir'] + \
'spectra/' + plot_kwargs['filename_base'] + \
'_spectra_dr2.png'
print('Saving\neog ' + filename + ' &')
plot_spectra(
hi_spectrum,
hi_vel_axis,
hi_std_spectrum=hi_std_spectrum,
gauss_fits=gauss_fits,
comp_num=comp_num,
co_spectrum=co_spectrum,
co_vel_axis=co_vel_axis,
vel_range=velocity_range,
filename=filename,
limits=[-50, 30, -10, 70],
)
# DR1 data
filename = plot_kwargs['figure_dir'] + \
'spectra/' + plot_kwargs['filename_base'] + \
'_spectra_dr1.png'
print('Saving\neog ' + filename + ' &')
plot_spectra(
hi_dr1_spectrum,
hi_vel_axis,
hi_std_spectrum=hi_std_dr1_spectrum,
gauss_fits=gauss_fits_dr1,
comp_num=comp_num_dr1,
co_spectrum=co_spectrum,
co_vel_axis=co_vel_axis,
vel_range=velocity_range_dr1,
filename=filename,
limits=[-50, 30, -10, 70],
)
velocity_range = [0, 15]
velocity_range_dr1 = [0, 15]
# use the vel range to derive N(HI)
nhi_image, nhi_image_error = \
calculate_nhi(cube=hi_data,
velocity_axis=hi_vel_axis,
velocity_range=velocity_range,
noise_cube=hi_data_error,
return_nhi_error=True,
)
# use the vel range to derive N(HI)
nhi_image_dr1 = \
calculate_nhi(cube=hi_dr1_data,
velocity_axis=hi_vel_axis,
velocity_range=velocity_range_dr1,
)
# mask for erroneous pixels
mask_nhi = (nhi_image < 0) & (nhi_image_dr1 < 0)
nhi_image[mask_nhi] = np.nan
nhi_image_dr1[mask_nhi] = np.nan
# Plot residuals between nhi maps
filename = plot_kwargs['figure_dir'] + \
'maps/' + plot_kwargs['filename_base'] + \
'_nhi_dr2_dr1_residuals.png'
print('Saving\neog ' + filename + ' &')
plot_nhi_image(
nhi_image=nhi_image / nhi_image_dr1,
header=hi_header,
limits=[65, 45, 25, 35],
filename=filename,
show=0,
cb_text='DR2 / DR1',
#hi_vlimits=[0.91, 0.93],
)
def plot_hi_spectrum(cloud_results, plot_co=1):
filename_base = \
cloud_results['figure_dir'] + 'diagnostics/' + \
cloud_results['filename_extension'] + '_hi_spectrum'
from astropy.io import fits
from mycoords import make_velocity_axis
from myimage_analysis import bin_image
from myio import check_file
cloud = cloud_results['cloud']
if plot_co:
co_filename = cloud.co_filename
if cloud_results['args']['bin_procedure'] in ('all', 'mle'):
co_filename = co_filename.replace('.fits', '_bin.fits')
exists = \
check_file(co_filename, clobber=False)
if not exists:
co_data, co_header = fits.getdata(co_filename,
header=True,
)
cloud.co_data, cloud.co_header = \
bin_image(co_data,
binsize=(1, cloud.binsize, cloud.binsize),
header=co_header,
statistic=np.nanmean)
fits.writeto(cloud.co_filename.replace('.fits', '_bin.fits'),
cloud.co_data,
cloud.co_header,
)
else:
cloud.co_data, cloud.co_header = \
fits.getdata(co_filename,
header=True,
)
cloud.co_vel_axis = make_velocity_axis(cloud.co_header)
# Derive relevant region
if cloud_results['args']['bin_procedure'] in ('all', 'mle'):
av_filename = cloud.av_filename_bin
hi_filename = cloud.hi_filename_bin
else:
av_filename = cloud.av_filename
hi_mask = cloud.region_mask
av_data, av_header = fits.getdata(av_filename, header=True)
cloud.hi_data, cloud.hi_header = \
fits.getdata(hi_filename, header=True)
cloud.load_region(cloud.region_filename, header=av_header)
cloud._derive_region_mask(av_data=av_data)
co_mask = cloud.region_mask
hi_mask = co_mask
import matplotlib.pyplot as plt
plt.close(); plt.clf();
co = np.copy(cloud.co_data[30,:,:])
co[co_mask] = np.nan
plt.imshow(co, origin='lower')
plt.savefig('/usr/users/ezbc/Desktop/comap_' + cloud.region + '.png')
assert all((cloud.hi_data.shape, cloud.co_data.shape,
cloud.region_mask.shape))
cloudpy.plot_hi_spectrum(cloud,
filename=filename_base + '.png',
limits=[-50, 30, -10, 70],
plot_co=plot_co,
hi_mask=hi_mask,
co_mask=co_mask,
)
def test_scatter_contour():
from astropy.io import fits
from myimage_analysis import calculate_nhi
import mygeometry as myg
from mycoords import make_velocity_axis
# Parameters
# ----------
levels = (0.99, 0.985, 0.7)
levels = (0.999, 0.998, 0.96, 0.86, 0.58,)
levels = 7
levels = np.logspace(np.log10(0.995), np.log10(0.50), 5)
log_counts = 0
limits = [1, 10, -3, 30]
limits = None
# Begin test
# ----------
data_dir = '/d/bip3/ezbc/perseus/data/'
av = fits.getdata(data_dir + 'av/perseus_av_planck_tau353_5arcmin.fits')
hi, hi_header = fits.getdata(data_dir + \
'hi/perseus_hi_galfa_cube_regrid_planckres.fits',
header=True)
hi_vel_axis = make_velocity_axis(hi_header)
nhi = calculate_nhi(cube=hi,
velocity_axis=hi_vel_axis,
velocity_range=[0, 10],
)
# Drop the NaNs from the images
indices = np.where((av == av) &\
(nhi == nhi)
)
av_nonans = av[indices]
nhi_nonans = nhi[indices]
fig, ax = plt.subplots()
if limits is None:
xmin = np.min(nhi_nonans)
ymin = np.min(av_nonans)
xmax = np.max(nhi_nonans)
ymax = np.max(av_nonans)
xscalar = 0.25 * xmax
yscalar = 0.25 * ymax
limits = [xmin - xscalar, xmax + xscalar,
ymin - yscalar, ymax + yscalar]
contour_range = ((limits[0], limits[1]),
(limits[2], limits[3]))
cmap = myplt.truncate_colormap(plt.cm.binary, 0.2, 1, 1000)
l1 = myplt.scatter_contour(nhi_nonans.ravel(),
av_nonans.ravel(),
threshold=3,
log_counts=log_counts,
levels=levels,
ax=ax,
histogram2d_args=dict(bins=30,
range=contour_range),
plot_args=dict(marker='o',
linestyle='none',
color='black',
alpha=0.3,
markersize=2),
contour_args=dict(
#cmap=plt.cm.binary,
cmap=cmap,
#cmap=cmap,
),
)
scale = ['linear', 'linear']
ax.set_xscale(scale[0], nonposx = 'clip')
ax.set_yscale(scale[1], nonposy = 'clip')
ax.set_xlim(limits[0],limits[1])
ax.set_ylim(limits[2],limits[3])
# Adjust asthetics
ax.set_xlabel(r'$N($H$\textsc{i}) \times\,10^{20}$ cm$^{-2}$')
ax.set_ylabel(r'$A_V$ [mag]')
#ax.set_title(core_names[i])
ax.legend(loc='lower right')
plt.savefig('test_plots/test_scatter_contour.png')
def main():
''' Executes script.
'''
# import external modules
import pyfits as pf
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
reload(myg)
# define directory locations
output_dir = '/d/bip3/ezbc/taurus/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/taurus/figures/maps/'
av_dir = '/d/bip3/ezbc/taurus/data/av/'
hi_dir = '/d/bip3/ezbc/taurus/data/galfa/'
core_dir = output_dir + 'core_arrays/'
region_dir = '/d/bip3/ezbc/taurus/data/python_output/ds9_regions/'
# Load hi fits file
hi_image, hi_header = pf.getdata(hi_dir + \
'taurus_galfa_cube_bin_3.7arcmin.fits', header=True)
h = hi_header
# Load av fits file
av_image, av_header = pf.getdata(av_dir + 'taurus_av_k09_regrid.fits',
header=True)
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
# create nhi image
nhi_image = calculate_nhi(hi_cube=hi_image,
velocity_axis=velocity_axis,
velocity_range=[-100, 100])
if False:
# trim hi_image to av_image size
nhi_image_trim = np.ma.array(nhi_image, mask=av_image != av_image)
plot_nhi_image(nhi_image=nhi_image_trim,
header=hi_header,
contour_image=av_image,
contours=[5, 10, 15],
savedir=figure_dir,
filename='taurus_nhi_cores_map.png',
show=True)
cores = {
'L1495': {
'center_wcs': [(4, 14, 0), (28, 11, 0)],
'map': None,
'threshold': 4.75,
'box_wcs': [(4, 16, 30), (27, 44, 30), (4, 5, 20), (28, 28, 33)]
},
'L1495A': {
'center_wcs': [(4, 18, 0), (28, 23., 0)],
'map': None,
'threshold': 4.75,
'box_wcs': [(4, 28, 23), (28, 12, 50), (4, 16, 23), (29, 46, 5)],
},
'B213': {
'center_wcs': [(4, 19, 0), (27, 15, 0)],
'map': None,
'threshold': 4.75,
'box_wcs': [(4, 22, 27), (26, 45, 47), (4, 5, 25), (27, 18, 48)],
},
'B220': {
'center_wcs': [(4, 41, 0.), (26, 7, 0)],
'map': None,
'threshold': 7,
'box_wcs': [(4, 47, 49), (25, 31, 13), (4, 40, 37), (27, 31, 17)],
},
'L1527': {
'center_wcs': [(4, 39, 0.), (25, 47, 0)],
'map': None,
'threshold': 7,
'box_wcs': [(4, 40, 13), (24, 46, 38), (4, 34, 35), (25, 56, 7)],
},
'B215': {
'center_wcs': [(4, 23, 0), (25, 3, 0)],
'map': None,
'threshold': 3,
'box_wcs': [(4, 24, 51), (22, 36, 7), (4, 20, 54), (25, 26, 31)],
},
'L1524': {
'center_wcs': [(4, 29, 0.), (24, 31., 0)],
'map': None,
'threshold': 3,
'box_wcs': [(4, 31, 0), (22, 4, 6), (4, 25, 33), (25, 0, 55)],
}
}
cores = convert_core_coordinates(cores, h)
if False:
nhi_image = np.zeros(nhi_image.shape)
for core in cores:
core_image = np.load(core_dir + core + '.npy')
core_indices = np.where(core_image == core_image)
nhi_image[core_indices] += core_image[core_indices]
nhi_image_trim =np.ma.array(nhi_image, mask=((av_image != av_image) &\
(nhi_image == 0)))
nhi_image_trim[nhi_image_trim == 0] = np.NaN
read_ds9_region(av_dir + 'taurus_av_boxes.reg')
plot_nhi_image(nhi_image=nhi_image_trim,
header=hi_header,
savedir=figure_dir,
cores=cores,
filename='taurus_nhi_core_regions_map.png',
show=True)
if True:
cores = load_ds9_region(cores,
filename_base=region_dir + 'taurus_av_boxes_',
header=h)
# Grab the mask
mask = np.zeros((nhi_image.shape))
for core in cores:
xy = cores[core]['box_center_pix']
box_width = cores[core]['box_width']
box_height = cores[core]['box_height']
box_angle = cores[core]['box_angle']
mask += myg.get_rectangular_mask(nhi_image,
xy[0],
xy[1],
width=box_width,
height=box_height,
angle=box_angle)
cores[core]['box_vertices'] = myg.get_rect(
xy[0],
xy[1],
width=box_width,
height=box_height,
angle=box_angle,
)
#print(cores[core]['box_vertices'])
#print core, xy, box_width, box_height, box_angle
mask[mask > 1] = 1
#nhi_image[mask == 0] = np.nan
# trim hi_image to av_image size
nhi_image_trim = np.ma.array(nhi_image, mask=(av_image != av_image))
# Plot
figure_types = ['pdf', 'png']
for figure_type in figure_types:
plot_nhi_image(nhi_image=nhi_image_trim, header=hi_header,
contour_image=av_image, contours=[5,10,15],
boxes=True, cores = cores, limits=[128,37,308,206],
title='Taurus: N(HI) map with core boxed-regions.',
savedir=figure_dir, filename='taurus_nhi_cores_map.%s' % \
figure_type,
show=False)
def main():
import numpy as np
import numpy
from os import system, path
import mygeometry as myg
from mycoords import make_velocity_axis
import json
from myimage_analysis import calculate_nhi, calculate_noise_cube
global hi_cube
global hi_velocity_axis
global hi_noise_cube
global av_image
global av_image_error
# parameters used in script
# -------------------------
# HI velocity integration range
# Determine HI integration velocity by CO or likelihoodelation with Av?
hi_av_likelihoodelation = True
center_vary = False
width_vary = True
dgr_vary = True
# Check if likelihood file already written, rewrite?
clobber = 1
# Confidence of parameter errors
conf = 0.68
# Confidence of contour levels
contour_confs = (0.68, 0.95)
# Course, large grid or fine, small grid?
grid_res = "fine"
grid_res = "course"
# Use multithreading?
multithread = False
# Use Av+CO mask or only CO?
av_and_co_mask = True
# Derive CO mask? If co_thres = None, co_thres will be 2 * std(co)
co_thres = 6.00 # K km/s
# Threshold of Av below which we expect only atomic gas, in mag
av_thres = 1.4
# Results and fits filenames
if av_and_co_mask:
likelihood_filename = "taurus_nhi_av_likelihoods_co_" + "av{0:.1f}mag".format(av_thres)
results_filename = "taurus_likelihood_co_" + "av{0:.1f}mag".format(av_thres)
else:
likelihood_filename = "taurus_nhi_av_likelihoods_co_only"
results_filename = "taurus_likelihood_co_only"
# Name of property files results are written to
global_property_file = "taurus_global_properties.txt"
core_property_file = "taurus_core_properties.txt"
# Name of noise cube
noise_cube_filename = "taurus_hi_galfa_cube_regrid_planckres_noise.fits"
# Define ranges of parameters
if center_vary and width_vary and dgr_vary:
likelihood_filename += "_width_dgr_center"
results_filename += "_width_dgr_center"
velocity_centers = np.arange(-15, 30, 1)
velocity_widths = np.arange(1, 80, 1)
dgrs = np.arange(1e-2, 1, 2e-2)
elif not center_vary and width_vary and dgr_vary:
if grid_res == "course":
likelihood_filename += "_dgr_width_lowres"
results_filename += "_dgr_width_lowres"
velocity_centers = np.arange(-5, 10, 10 * 0.16667)
velocity_widths = np.arange(1, 30, 10 * 0.16667)
dgrs = np.arange(0.05, 0.7, 2e-2)
elif grid_res == "fine":
likelihood_filename += "_dgr_width_highres"
results_filename += "_dgr_width_highres"
velocity_centers = np.arange(5, 6, 1)
velocity_widths = np.arange(1, 100, 0.16667)
dgrs = np.arange(0.15, 0.4, 1e-3)
velocity_widths = np.arange(1, 15, 0.16667)
dgrs = np.arange(0.1, 0.9, 3e-3)
# velocity_widths = np.arange(1, 40, 1)
# dgrs = np.arange(0.15, 0.4, 1e-1)
elif center_vary and width_vary and not dgr_vary:
likelihood_filename += "_width_center"
results_filename += "_width_center"
velocity_centers = np.arange(-15, 30, 1)
velocity_widths = np.arange(1, 80, 1)
dgrs = np.arange(1.1e-1, 1.2e-1, 0.1e-1)
elif not center_vary and width_vary and not dgr_vary:
likelihood_filename += "_width"
results_filename += "_width"
velocity_centers = np.arange(5, 6, 1)
velocity_widths = np.arange(1, 80, 1)
dgrs = np.arange(1.1e-1, 1.2e-1, 0.1e-1)
# define directory locations
# --------------------------
output_dir = "/d/bip3/ezbc/taurus/data/python_output/nhi_av/"
figure_dir = "/d/bip3/ezbc/taurus/figures/hi_velocity_range/"
av_dir = "/d/bip3/ezbc/taurus/data/av/"
hi_dir = "/d/bip3/ezbc/taurus/data/hi/"
co_dir = "/d/bip3/ezbc/taurus/data/co/"
core_dir = "/d/bip3/ezbc/taurus/data/python_output/core_properties/"
property_dir = "/d/bip3/ezbc/taurus/data/python_output/"
region_dir = "/d/bip3/ezbc/taurus/data/python_output/ds9_regions/"
likelihood_dir = "/d/bip3/ezbc/taurus/data/python_output/nhi_av/"
# load Planck Av and GALFA HI images, on same grid
av_data, av_header = load_fits(av_dir + "taurus_av_planck_5arcmin.fits", return_header=True)
av_data_error, av_error_header = load_fits(av_dir + "taurus_av_error_planck_5arcmin.fits", return_header=True)
hi_data, h = load_fits(hi_dir + "taurus_hi_galfa_cube_regrid_planckres.fits", return_header=True)
co_data, co_header = load_fits(co_dir + "taurus_co_cfa_cube_regrid_planckres.fits", return_header=True)
# make the velocity axis
velocity_axis = make_velocity_axis(h)
co_velocity_axis = make_velocity_axis(co_header)
# Plot NHI vs. Av for a given velocity range
if not path.isfile(hi_dir + noise_cube_filename):
noise_cube = calculate_noise_cube(
cube=hi_data,
velocity_axis=velocity_axis,
velocity_noise_range=[90, 110],
header=h,
Tsys=30.0,
filename=hi_dir + noise_cube_filename,
)
else:
noise_cube, noise_header = load_fits(hi_dir + noise_cube_filename, return_header=True)
# define core properties
with open(core_dir + core_property_file, "r") as f:
cores = json.load(f)
with open(property_dir + global_property_file, "r") as f:
global_props = json.load(f)
# Change WCS coords to pixel coords of images
cores = convert_core_coordinates(cores, h)
cores = load_ds9_region(cores, filename_base=region_dir + "taurus_av_boxes_", header=h)
global_props = convert_limit_coordinates(global_props, header=av_header)
print ("\nCalculating likelihoods globally")
co_data_nonans = np.copy(co_data)
co_data_nonans[np.isnan(co_data_nonans)] = 0.0
# Set velocity center as CO peak
if not center_vary:
co_spectrum = np.sum(co_data_nonans, axis=(1, 2))
co_avg_vel = np.average(co_velocity_axis, weights=co_spectrum)
co_peak_vel = co_velocity_axis[co_spectrum == np.max(co_spectrum)]
# velocity_centers = np.arange(co_peak_vel, co_peak_vel + 1, 1)
velocity_centers = np.arange(co_avg_vel, co_avg_vel + 1, 1)
print ("\nVelocity center from CO = " + "{0:.2f} km/s".format(velocity_centers[0]))
# Create mask where CO is present
core_mask = np.zeros(av_data.shape)
# for core in cores:
# # Grab the mask
# core_mask += myg.get_polygon_mask(av_data,
# cores[core]['box_vertices_rotated'])
# Calc moment 0 map of CO
co_mom0 = np.sum(co_data_nonans, axis=0)
# calc noise without any emission if CO threshold not already set
if co_thres is None:
co_noise = calc_co_noise(co_mom0, global_props)
co_thres = 2.0 * co_noise
# Derive relevant region
pix = global_props["region_limit"]["pixel"]
region_vertices = ((pix[1], pix[0]), (pix[1], pix[2]), (pix[3], pix[2]), (pix[3], pix[0]))
# block offregion
region_mask = myg.get_polygon_mask(av_data, region_vertices)
print ("\nRegion size = " + "{0:.0f} pix".format(region_mask[region_mask == 1].size))
# Get indices which trace only atomic gas, i.e., no CO emission
if av_and_co_mask:
indices = ((co_mom0 < co_thres) & (av_data < av_thres)) & (region_mask == 1)
elif not av_and_co_mask:
indices = (co_mom0 < co_thres) & (region_mask == 1)
av_thres = None
# Write mask of pixels not used
mask = ~indices
# Mask global data with CO indices
hi_data_sub = np.copy(hi_data[:, indices])
noise_cube_sub = np.copy(noise_cube[:, indices])
av_data_sub = np.copy(av_data[indices])
av_error_data_sub = np.copy(av_data_error[indices])
# import matplotlib.pyplot as plt
# av_plot_data = np.copy(av_data)
# av_plot_data[~indices] = np.nan
# plt.imshow(av_plot_data, origin='lower')
# plt.contour(co_mom0, levels=(6, 12, 24), origin='lower')
# plt.show()
# plt.clf()
# plt.close()
# Plot the masked image
av_data_masked = np.copy(av_data)
av_data_masked[~indices] = np.nan
figure_types = ["png"]
for figure_type in figure_types:
plot_av_image(
av_image=av_data_masked,
header=av_header,
savedir=figure_dir + "../maps/",
limits=global_props["region_limit"]["pixel"],
filename="taurus_dgr_co_masked_map." + figure_type,
show=0,
)
# Set global variables
hi_cube = hi_data_sub
hi_velocity_axis = velocity_axis
hi_noise_cube = noise_cube_sub
av_image = av_data_sub
av_image_error = av_error_data_sub
# Define filename for plotting results
results_filename = figure_dir + results_filename
# likelihoodelate each core region Av and N(HI) for velocity ranges
vel_range_confint, dgr_confint, likelihoods, center_likelihood, width_likelihood, dgr_likelihood, center_max, width_max, dgr_max = calc_likelihood_hi_av(
dgrs=dgrs,
velocity_centers=velocity_centers,
velocity_widths=velocity_widths,
return_likelihoods=True,
plot_results=True,
results_filename=results_filename,
likelihood_filename=likelihood_dir + likelihood_filename + "_global.fits",
clobber=clobber,
conf=conf,
contour_confs=contour_confs,
multithread=multithread,
)
vel_range_max = (center_max - width_max / 2.0, center_max + width_max / 2.0)
print ("\nHI velocity integration range:")
print ("%.1f to %.1f km/s" % (vel_range_confint[0], vel_range_confint[1]))
print ("\nDGR:")
print ("%.1f x 10^-20 cm^2 mag" % (dgr_confint[0]))
# Calulate chi^2 for best fit models
# ----------------------------------
nhi_image_temp, nhi_image_error = calculate_nhi(
cube=hi_data, velocity_axis=hi_velocity_axis, velocity_range=vel_range_max, noise_cube=noise_cube
)
av_image_model = nhi_image_temp * dgr_max
# avoid NaNs
indices = (av_image_model == av_image_model) & (av_data == av_data)
# add nan locations to the mask
mask[~indices] = 1
# count number of pixels used in analysis
npix = mask[~mask].size
# finally calculate chi^2
chisq = np.sum((av_data[~mask] - av_image_model[~mask]) ** 2 / av_data_error[~mask] ** 2) / av_data[~mask].size
print (
"\nTotal number of pixels in analysis, after masking = " + "{0:.0f}".format(npix)
) + "\nGiven a CO threshold of {0:.2f} K km/s".format(co_thres) + "\nand a Av threshold of {0:.2f} mag".format(
av_thres
)
print ("\nReduced chi^2 = {0:.1f}".format(chisq))
# Write results to global properties
global_props["dust2gas_ratio"] = {}
global_props["dust2gas_ratio_error"] = {}
global_props["hi_velocity_width"] = {}
global_props["dust2gas_ratio_max"] = {}
global_props["hi_velocity_center_max"] = {}
global_props["hi_velocity_width_max"] = {}
global_props["hi_velocity_range_max"] = {}
global_props["av_threshold"] = {}
global_props["co_threshold"] = {}
global_props["hi_velocity_width"]["value"] = vel_range_confint[1] - vel_range_confint[0]
global_props["hi_velocity_width"]["unit"] = "km/s"
global_props["hi_velocity_range"] = vel_range_confint[0:2]
global_props["hi_velocity_range_error"] = vel_range_confint[2:]
global_props["dust2gas_ratio"]["value"] = dgr_confint[0]
global_props["dust2gas_ratio_error"]["value"] = dgr_confint[1:]
global_props["dust2gas_ratio_max"]["value"] = dgr_max
global_props["hi_velocity_center_max"]["value"] = center_max
global_props["hi_velocity_width_max"]["value"] = width_max
global_props["hi_velocity_range_max"]["value"] = vel_range_max
global_props["hi_velocity_range_conf"] = conf
global_props["center_likelihood"] = center_likelihood.tolist()
global_props["width_likelihood"] = width_likelihood.tolist()
global_props["dgr_likelihood"] = dgr_likelihood.tolist()
global_props["vel_centers"] = velocity_centers.tolist()
global_props["vel_widths"] = velocity_widths.tolist()
global_props["dgrs"] = dgrs.tolist()
global_props["likelihoods"] = likelihoods.tolist()
global_props["av_threshold"]["value"] = av_thres
global_props["av_threshold"]["unit"] = "mag"
global_props["co_threshold"]["value"] = co_thres
global_props["co_threshold"]["unit"] = "K km/s"
global_props["chisq"] = chisq
global_props["npix"] = npix
global_props["mask"] = mask.tolist()
with open(property_dir + global_property_file, "w") as f:
json.dump(global_props, f)
def main():
import grid
import numpy as np
import numpy
from os import system,path
import mygeometry as myg
from mycoords import make_velocity_axis
import json
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
# parameters used in script
# -------------------------
# HI velocity integration range
# Determine HI integration velocity by CO or correlation with Av?
hi_av_correlation = True
velocity_centers = np.arange(-15, 30, 4)
velocity_widths = np.arange(1, 80, 4)
# Which likelihood fits should be performed?
core_correlation = 0
global_correlation = 1
# Name of property files results are written to
global_property_file = 'california_global_properties.txt'
core_property_file = 'california_core_properties.txt'
# Threshold of Av below which we expect only atomic gas, in mag
av_threshold = 100
# Check if likelihood file already written, rewrite?>
likelihood_filename = 'california_nhi_av_likelihoods'
clobber = 0
hi_vel_range_conf = 0.50
# Name of noise cube
noise_cube_filename = 'california_hi_galfa_cube_regrid_planckres_noise.fits'
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/california/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/california/figures/hi_velocity_range/'
av_dir = '/d/bip3/ezbc/california/data/av/'
hi_dir = '/d/bip3/ezbc/california/data/hi/'
co_dir = '/d/bip3/ezbc/california/data/co/'
core_dir = '/d/bip3/ezbc/california/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/california/data/python_output/'
region_dir = '/d/bip3/ezbc/california/data/python_output/ds9_regions/'
likelihood_dir = '/d/bip3/ezbc/california/data/python_output/nhi_av/'
# load Planck Av and GALFA HI images, on same grid
av_data_planck, av_header = load_fits(av_dir + \
'california_av_planck_5arcmin.fits',
return_header=True)
av_error_data_planck, av_error_header = load_fits(av_dir + \
'california_av_error_planck_5arcmin.fits',
return_header=True)
hi_data, h = load_fits(hi_dir + \
'california_hi_galfa_cube_regrid_planckres.fits',
return_header=True)
# make the velocity axis
velocity_axis = make_velocity_axis(h)
# Plot NHI vs. Av for a given velocity range
if not path.isfile(hi_dir + noise_cube_filename):
noise_cube = calculate_noise_cube(cube=hi_data,
velocity_axis=velocity_axis,
velocity_noise_range=[90,110], header=h, Tsys=30.,
filename=hi_dir + noise_cube_filename)
else:
noise_cube, noise_header = load_fits(hi_dir + noise_cube_filename,
return_header=True)
# define core properties
with open(core_dir + core_property_file, 'r') as f:
cores = json.load(f)
with open(property_dir + global_property_file, 'r') as f:
global_props = json.load(f)
dgr = global_props['dust2gas_ratio']['value']
dgr = 1.22e-1
cores = convert_core_coordinates(cores, h)
cores = load_ds9_region(cores,
filename_base = region_dir + 'california_av_boxes_',
header = h)
if core_correlation:
for core in cores:
print('\nCalculating for core %s' % core)
# Grab the mask
mask = myg.get_polygon_mask(av_data_planck,
cores[core]['box_vertices_rotated'])
indices = ((mask == 0) &\
(av_data_planck < av_threshold))
hi_data_sub = np.copy(hi_data[:, indices])
noise_cube_sub = np.copy(noise_cube[:, indices])
av_data_sub = np.copy(av_data_planck[indices])
av_error_data_sub = np.copy(av_error_data_planck[indices])
# Define filename for plotting results
results_filename = figure_dir + 'california_logL_%s.png' % core
# Correlate each core region Av and N(HI) for velocity ranges
vel_range_confint, correlations, center_corr, width_corr = \
correlate_hi_av(hi_cube=hi_data_sub,
hi_velocity_axis=velocity_axis,
hi_noise_cube=noise_cube_sub,
av_image=av_data_sub,
av_image_error=av_error_data_sub,
dgr=dgr,
velocity_centers=velocity_centers,
velocity_widths=velocity_widths,
return_correlations=True,
plot_results=True,
results_filename=results_filename,
likelihood_filename=likelihood_dir + \
likelihood_filename + \
'{0:s}.fits'.format(core),
clobber=clobber,
hi_vel_range_conf=hi_vel_range_conf)
print('HI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range_confint[0],
vel_range_confint[1]))
cores[core]['hi_velocity_range'] = vel_range_confint[0:2]
cores[core]['hi_velocity_range_error'] = vel_range_confint[2:]
cores[core]['center_corr'] = center_corr.tolist()
cores[core]['width_corr'] = width_corr.tolist()
cores[core]['vel_centers'] = velocity_centers.tolist()
cores[core]['vel_widths'] = velocity_widths.tolist()
with open(core_dir + core_property_file, 'w') as f:
json.dump(cores, f)
if global_correlation:
print('\nCalculating correlations globally')
indices = ((av_data_planck < av_threshold))
hi_data_sub = np.copy(hi_data[:, indices])
noise_cube_sub = np.copy(noise_cube[:, indices])
av_data_sub = np.copy(av_data_planck[indices])
av_error_data_sub = np.copy(av_error_data_planck[indices])
# Define filename for plotting results
results_filename = figure_dir + 'california_logL_global.png'
# Correlate each core region Av and N(HI) for velocity ranges
vel_range_confint, correlations, center_corr, width_corr = \
correlate_hi_av(hi_cube=hi_data_sub,
hi_velocity_axis=velocity_axis,
hi_noise_cube=noise_cube_sub,
av_image=av_data_sub,
av_image_error=av_error_data_sub,
dgr=dgr,
velocity_centers=velocity_centers,
velocity_widths=velocity_widths,
return_correlations=True,
plot_results=True,
results_filename=results_filename,
likelihood_filename=likelihood_dir + \
likelihood_filename + '_global.fits',
clobber=clobber,
hi_vel_range_conf=hi_vel_range_conf)
'''
fit_hi_vel_range(guesses=(0, 30),
av_image=av_data_sub,
av_image_error=av_error_data_sub,
hi_cube=hi_data_sub,
hi_velocity_axis=velocity_axis,
hi_noise_cube=noise_cube_sub,
dgr=dgr)
'''
print('HI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range_confint[0],
vel_range_confint[1]))
global_props['hi_velocity_range'] = vel_range_confint[0:2]
global_props['hi_velocity_range_error'] = vel_range_confint[2:]
global_props['hi_velocity_range_conf'] = hi_vel_range_conf
global_props['center_corr'] = center_corr.tolist()
global_props['width_corr'] = width_corr.tolist()
global_props['vel_centers'] = velocity_centers.tolist()
global_props['vel_widths'] = velocity_widths.tolist()
with open(property_dir + global_property_file, 'w') as f:
json.dump(global_props, f)
def main():
from myimage_analysis import bin_image, calculate_nhi
from mycoords import make_velocity_axis
from astropy.io import fits
import numpy as np
os.chdir('/d/bip3/ezbc/shield/749237_lowres/')
# If true, deletes files to be written
clobber = 1
# First, change zeros in lee image to nans
in_images = ('749237_rebin_cube.fits',)
# Load the images into miriad
out_images = []
for in_image in in_images:
print('Binning cube:\n' + in_image)
cube, header = fits.getdata(in_image, header=True)
# set freq0 setting
header['FREQ0'] = 1.4204058E+09
header['RESTFREQ'] = 1.4204058E+09
header['CTYPE3'] = 'VELO'
beamsize = header['BMAJ']
cdelt = np.abs(header['CDELT1'])
binsize = int(beamsize / cdelt)
print('\tBinsize = ' + str(binsize))
if 1:
# cube measurement error = 700 uJy/Beam = 0.7 mJy/Beam
# cube flux calibration error = 10%
# add errors quadratically
cube_std = np.nanstd(cube[0, :, :])
cube_error = ((0.1 * cube)**2 + cube_std**2)**0.5
cube_bin, header_bin = bin_image(cube,
binsize=(1, binsize, binsize),
header=header,
statistic=np.nanmean,
)
# cube measurement error = 700 uJy/Beam = 0.7 mJy/Beam
# cube flux calibration error = 10%
# add errors quadratically
cube_bin_std = np.nanstd(cube_bin[0, :, :])
cube_error_bin = ((0.1 * cube_bin)**2 + cube_bin_std**2)**0.5
if 0:
noise_func = lambda x: (1 / np.nansum(x**-2))**0.5
cube_error_bin = bin_image(cube_error,
binsize=(1, binsize, binsize),
statistic=noise_func,
)
fits.writeto(in_image,
cube,
header,
clobber=clobber)
fits.writeto(in_image.replace('cube', 'cube_error'),
cube_error,
header,
clobber=clobber)
fits.writeto(in_image.replace('cube.fits', 'cube_regrid.fits'),
cube_bin,
header_bin,
clobber=clobber)
fits.writeto(in_image.replace('cube', 'cube_error_regrid'),
cube_error_bin,
header_bin,
clobber=clobber)
#else:
# cube_bin, header_bin = \
# fits.getdata(in_image.replace('cube.fits', 'cube_regrid.fits'),
# clobber=clobber, header=True)
# make nhi_image
velocity_axis = make_velocity_axis(header_bin)
# convert to T_B
cube_bin_tb = 1.36 * 21**2 * cube_bin * 1000.0 / \
(header_bin['BMAJ'] * 3600.) / \
(3600. * header_bin['BMIN'])
cube_tb = 1.36 * 21**2 * cube * 1000.0 / \
(header['BMAJ'] * 3600.) / \
(3600. * header['BMIN'])
# convert moment zero images to column density units.
# Recall: 1 K = (7.354E-8)*[Bmaj(")*Bmin(")/lamda^2(m)] Jy/Bm
# Here, units of images are Jy/Bm m/s; cellsize = 2";
# lambda = 0.211061140507 m
# Thus, for the 21 cm line of Hydrogen, we have:
# 1 K = Bmaj(")*Bmin(")/(6.057493205E5) Jy/Bm
# ---- OR ----
# 1 Jy/Bm = (6.057493205E5)/[Bmaj(")*Bmin(")]
# Now, recall that: N_HI = (1.8224E18 cm^-2)*[T_b (K)]*int(dv)
# -- For moment maps in K km/sec, just input the values
# & multiply by coefficient.
# -- Assure that units are Jy/Bm km/sec (i.e., divide by 1000)
# Leave in units of 1E20 cm^-2 by dividing by 1E20:
# For a x beam:
# N_HI (cm^-2) = (image) *
# [(6.057493205E5)/(*)] * (1/1000) * (1.8224E18 cm^-2) *
# (1/1E20)
# N_HI (cm^-2) = (image)*
nhi_image = calculate_nhi(cube_bin_tb,
velocity_axis=velocity_axis,
header=header_bin,
fits_filename=\
in_image.replace('cube.fits', 'nhi_regrid.fits') )
nhi_image = calculate_nhi(cube_tb,
velocity_axis=velocity_axis,
header=header,
fits_filename=\
in_image.replace('cube.fits', 'nhi.fits') )
def calc_data(cloud_list):
''' Executes script.
'''
import numpy as np
from os import system, path
import mygeometry as myg
from mycoords import make_velocity_axis
import json
data_dict = {}
for i, cloud in enumerate(cloud_list):
if cloud == 'taurus1' or cloud == 'taurus2':
cloud_name = 'taurus'
else:
cloud_name = cloud
# define directory locations
output_dir = '/d/bip3/ezbc/%s/data/python_output/nhi_av/' % cloud_name
figure_dir = '/d/bip3/ezbc/multicloud/figures/spectra/'
av_dir = '/d/bip3/ezbc/%s/data/av/' % cloud_name
hi_dir = '/d/bip3/ezbc/%s/data/hi/' % cloud_name
co_dir = '/d/bip3/ezbc/%s/data/co/' % cloud_name
core_dir = output_dir + 'core_arrays/'
region_dir = '/d/bip3/ezbc/%s/data/' % cloud_name + \
'python_output/ds9_regions/'
# global property filename
global_property_filename = '{0}_global_properties'.format(cloud)
property_dir = '/d/bip3/ezbc/{0}/data/python_output/'.format(
cloud_name)
av_data_type = 'planck'
cloud_dict = {}
# Load HI maps from Taurus, California, and Perseus
hi_data, hi_header = fits.getdata(
'/d/bip3/ezbc/{0}/data/hi/{0}_hi_galfa_'.format(cloud_name) + \
'cube_regrid_planckres_bin.fits',
header=True)
# Load CO maps from Taurus, California, and Perseus
co_data, co_header = fits.getdata(
co_dir + '{0}_co_cfa_'.format(cloud_name) + \
'cube_regrid_planckres_bin.fits',
header=True)
av_data, av_header = \
fits.getdata(av_dir + \
'{0}_av_planck_tau353_5arcmin_bin.fits'.format(cloud_name),
header=True)
# Mask out region
with open(property_dir + \
global_property_filename + '_' + av_data_type + \
'_scaled.txt', 'r') as f:
global_props = json.load(f)
# Load cloud division regions from ds9
global_props = load_ds9_region(global_props,
filename='/d/bip3/ezbc/multicloud/data/' + \
'python_output/multicloud_divisions.reg',
#'python_output/multicloud_divisions_2.reg',
header=av_header)
# Derive relevant region
region_vertices = \
np.array(global_props['regions'][cloud]['poly_verts']['pixel'])
region_mask = np.logical_not(
myg.get_polygon_mask(av_data, region_vertices))
if 0:
import matplotlib.pyplot as plt
plt.imshow(np.ma.array(av_data, mask=region_mask), origin='lower')
plt.colorbar()
plt.show()
hi_data[:, region_mask] = np.nan
co_data[:, region_mask] = np.nan
# sum along spatial axes
cloud_dict['hi_spectrum'] = calc_global_spectrum(hi_cube=hi_data,
statistic='median')
cloud_dict['hi_std'] = calc_global_spectrum(hi_cube=hi_data,
statistic='std')
cloud_dict['co_spectrum'] = calc_global_spectrum(hi_cube=co_data,
statistic='median')
vel_center = global_props['hi_velocity_width']['value']
vel_width = global_props['hi_velocity_center']['value']
#cloud_dict['hi_vel_range'] = (vel_center + vel_width / 2.0,
# vel_center - vel_width / 2.0)
#cloud_dict['hi_vel_range'] = global_props['hi_velocity_range_conf']
cloud_dict['hi_vel_range'] = global_props['hi_velocity_range']
print global_props['hi_velocity_range']
# Calculate velocity
cloud_dict['hi_velocity_axis'] = make_velocity_axis(hi_header)
cloud_dict['co_velocity_axis'] = make_velocity_axis(co_header)
data_dict[cloud] = cloud_dict
return data_dict
def main(dgr=None, vel_range=None, vel_range_type='single', region=None,
av_data_type='planck', use_binned_images=False):
''' Executes script.
Parameters
----------
dgr : float
If None, pulls best-fit value from properties.
vel_range : tuple
If None, pulls best-fit value from properties.
'''
# import external modules
import pyfits as pf
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
import json
# Script parameters
# -----------------
if use_binned_images:
bin_string = '_bin'
else:
bin_string = ''
# Name of noise cube
noise_cube_filename = \
'california_hi_galfa_cube_regrid_planckres_noise' + bin_string + \
'.fits'
# Name of property files results are written to
prop_file = 'california_global_properties_' + av_data_type + '_scaled'
# Regions, regions to edit the global properties with
if region == 1:
region_limit = {'wcs' : (((5, 10, 0), (19, 0, 0)),
((4, 30, 0), (27, 0, 0))),
'pixel' : ()
}
elif region == 2:
region_limit = {'wcs' : (((4, 30, 0), (19, 0, 0)),
((3, 50, 0), (29, 0, 0))),
'pixel' : ()
}
elif region == 3:
region_limit = {'wcs' : (((4, 30, 0), (29, 0, 0)),
((3, 50, 0), (33, 0, 0))),
'pixel' : ()
}
else:
region_limit = None
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/california/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/california/figures/av/'
av_dir = '/d/bip3/ezbc/california/data/av/'
hi_dir = '/d/bip3/ezbc/california/data/hi/'
co_dir = '/d/bip3/ezbc/california/data/co/'
core_dir = '/d/bip3/ezbc/california/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/california/data/python_output/'
region_dir = '/d/bip3/ezbc/california/data/python_output/ds9_regions/'
# load Planck Av and GALFA HI images, on same grid
if av_data_type == 'lee12_2mass':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'california_av_lee12_2mass_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'lee12_iris':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'california_av_lee12_iris_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
else:
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'california_av_planck_5arcmin' + bin_string + \
'.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'california_av_error_planck_5arcmin' + bin_string + \
'.fits',
return_header=True)
hi_cube, hi_header = load_fits(hi_dir + \
'california_hi_galfa_cube_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
hi_noise_cube, noise_header = load_fits(hi_dir + noise_cube_filename,
return_header=True)
if not use_binned_images:
co_data, co_header = load_fits(co_dir + \
'california_co_cfa_cube_regrid_planckres' + bin_string + \
'.fits',
return_header=True)
# Load global properties of cloud
# global properties written from script
# 'av/california_analysis_global_properties.txt'
if region is not None:
likelihood_filename += '_region{0:.0f}'.format(region)
results_filename += '_region{0:.0f}'.format(region)
print('\nReading global parameter file\n' + prop_file + '.txt')
with open(property_dir + prop_file + '.txt', 'r') as f:
props = json.load(f)
if vel_range is not None:
props['hi_velocity_range'] = vel_range
else:
vel_width = props['hi_velocity_width_max']['value']
vel_center = np.array(props['hi_velocity_center']['value'])
vel_center = -4.0
vel_range = (vel_center - vel_width / 2.0,
vel_center + vel_width / 2.0)
if dgr is not None:
props['dust2gas_ratio_max']['value'] = dgr
else:
dgr = props['dust2gas_ratio_max']['value']
intercept = props['intercept_max']['value']
fit_params = {}
fit_params['dgr'] = dgr
fit_params['intercept'] = intercept
# define core properties
with open(core_dir + 'california_core_properties.txt', 'r') as f:
cores = json.load(f)
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
if not use_binned_images:
# make velocity axis for co cube
co_velocity_axis = make_velocity_axis(co_header)
# Write core coordinates in pixels
cores = convert_core_coordinates(cores, hi_header)
cores = load_ds9_region(cores,
filename_base = region_dir + 'california_av_boxes_',
header = hi_header)
# create nhi image
nhi_image = calculate_nhi(cube=hi_cube,
velocity_axis=velocity_axis,
velocity_range=vel_range,
header=hi_header,
noise_cube=hi_noise_cube)
# create model av map
av_model = nhi_image * dgr
if vel_range_type == 'single':
print('\nHI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range[0],
vel_range[1]))
elif vel_range_type == 'multiple':
print('\nHI velocity integration ranges:')
for i in xrange(0, vel_range.shape[0]):
print('%.1f to %.1f km/s' % (vel_range[i, 0],
vel_range[i, 1]))
print('\nDGR:')
print('%.2f x 10^-20 cm^2 mag' % (dgr))
print('\nIntercept:')
print('%.2f mag' % (intercept))
# Get mask and mask images
mask = np.asarray(props['mask' + bin_string])
mask_images = 1
if mask_images:
av_image[mask] = np.nan
nhi_image[mask] = np.nan
av_image_error[mask] = np.nan
av_model[mask] = np.nan
indices = ((np.isnan(av_model)) & \
(np.isnan(av_image)) & \
(np.isnan(av_image_error)))
if 1:
import matplotlib.pyplot as plt
plt.imshow(av_image)
plt.show()
print('\nTotal number of pixels after masking = ' + str(props['npix']))
# Plot
figure_types = ['png', 'pdf']
for figure_type in figure_types:
if region is None:
filename = 'california_av_vs_nhi_' + av_data_type + bin_string
filename = figure_dir + filename + '.' + figure_type
print('\nSaving Av model image to \n' + filename)
plot_av_vs_nhi(nhi_image,
av_image,
av_error=av_image_error,
#limits=[10**-1, 10**1.9, 10**0, 10**1.7],
fit_params=fit_params,
limits=[5,40,-0.2,2],
#limits=[0,30,0,10],
gridsize=(10,10),
#scale=('log', 'log'),
#scale=('linear', 'linear'),
filename=filename,
contour_plot=not use_binned_images,
std=0.22,
)
def calc_data(ra=None, dec=None):
''' Executes script.
'''
import numpy as np
from os import system,path
import mygeometry as myg
from mycoords import make_velocity_axis
import json
cloud_list = ('california',)
data_dict = {}
for i, cloud in enumerate(cloud_list):
if cloud == 'taurus1' or cloud == 'taurus2':
cloud_name = 'taurus'
else:
cloud_name = cloud
# define directory locations
output_dir = '/d/bip3/ezbc/%s/data/python_output/nhi_av/' % cloud_name
figure_dir = '/d/bip3/ezbc/multicloud/figures/spectra/'
av_dir = '/d/bip3/ezbc/%s/data/av/' % cloud_name
hi_dir = '/d/bip3/ezbc/%s/data/hi/' % cloud_name
co_dir = '/d/bip3/ezbc/%s/data/co/' % cloud_name
core_dir = output_dir + 'core_arrays/'
region_dir = '/d/bip3/ezbc/%s/data/' % cloud_name + \
'python_output/ds9_regions/'
# global property filename
global_property_filename = '{0}_global_properties'.format(cloud)
property_dir = '/d/bip3/ezbc/{0}/data/python_output/'.format(cloud_name)
av_data_type = 'planck'
cloud_dict = {}
# Load HI maps from Taurus, California, and Perseus
hi_data, hi_header = fits.getdata(
'/d/bip3/ezbc/{0}/data/hi/{0}_hi_galfa_'.format(cloud_name) + \
'cube_regrid_planckres.fits',
header=True)
# Load CO maps from Taurus, California, and Perseus
co_data, co_header = fits.getdata(
co_dir + '{0}_co_cfa_'.format(cloud_name) + \
'cube_regrid_planckres.fits',
header=True)
av_data, av_header = \
fits.getdata(av_dir + \
'{0}_av_planck_5arcmin.fits'.format(cloud_name),
header=True)
# Mask out region
with open(property_dir + \
global_property_filename + '_' + av_data_type + \
'_scaled.txt', 'r') as f:
global_props = json.load(f)
# Load cloud division regions from ds9
global_props = load_ds9_region(global_props,
filename='/d/bip3/ezbc/multicloud/data/' + \
'python_output/multicloud_divisions.reg',
header=av_header)
# Derive relevant region
region_vertices = \
np.array(global_props['regions'][cloud]['poly_verts']['pixel'])
region_mask = np.logical_not(myg.get_polygon_mask(av_data,
region_vertices))
if 0:
import matplotlib.pyplot as plt
plt.imshow(np.ma.array(av_data,
mask=region_mask), origin='lower')
plt.colorbar()
plt.show()
#hi_data[:, region_mask] = np.nan
co_data[:, region_mask] = np.nan
pix = get_pix_coords(ra=ra, dec=dec, header=av_header)
print pix, av_data.shape, hi_data.shape
if 0:
import matplotlib.pyplot as plt
plt.plot(hi_data[:, pix[1], pix[0]])
plt.show()
# sum along spatial axes
cloud_dict['hi_spectrum'] = hi_data[:, pix[1], pix[0]]
cloud_dict['hi_std'] = hi_data[:, pix[1], pix[0]]
cloud_dict['co_spectrum'] = calc_global_spectrum(
hi_cube=co_data,
statistic='median'
)
vel_center = global_props['hi_velocity_width']['value']
vel_width = global_props['hi_velocity_center']['value']
#cloud_dict['hi_vel_range'] = (vel_center + vel_width / 2.0,
# vel_center - vel_width / 2.0)
#cloud_dict['hi_vel_range'] = global_props['hi_velocity_range_conf']
cloud_dict['hi_vel_range'] = global_props['hi_velocity_range']
#print global_props['hi_velocity_range']
# Calculate velocity
cloud_dict['hi_velocity_axis'] = make_velocity_axis(
hi_header)
cloud_dict['co_velocity_axis'] = make_velocity_axis(
co_header)
data_dict[cloud] = cloud_dict
return data_dict
def main():
import grid
import numpy as np
import numpy
from os import system,path
import mygeometry as myg
from mycoords import make_velocity_axis
import json
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
# parameters used in script
# -------------------------
# HI velocity integration range
# Determine HI integration velocity by CO or likelihoodelation with Av?
hi_av_likelihoodelation = True
center_vary = False
width_vary = True
dgr_vary = True
# Check if likelihood file already written, rewrite?
clobber = 0
# Confidence of parameter errors
conf = 0.68
# Confidence of contour levels
contour_confs = (0.68, 0.95)
# Course, large grid or fine, small grid?
grid_res = 'course'
grid_res = 'fine'
# Results and fits filenames
likelihood_filename = 'california_nhi_av_likelihoods'
results_filename = 'california_likelihood'
# Define ranges of parameters
if center_vary and width_vary and dgr_vary:
likelihood_filename += '_width_dgr_center'
results_filename += '_width_dgr_center'
velocity_centers = np.arange(-15, 30, 1)
velocity_widths = np.arange(1, 80, 1)
dgrs = np.arange(1e-2, 1, 2e-2)
elif not center_vary and width_vary and dgr_vary:
if grid_res == 'course':
likelihood_filename += '_dgr_width_lowres'
results_filename += '_dgr_width_lowres'
velocity_centers = np.arange(5, 6, 1)
velocity_widths = np.arange(1, 80, 1)
dgrs = np.arange(1e-2, 1, 2e-2)
elif grid_res == 'fine':
likelihood_filename += '_dgr_width_highres'
results_filename += '_dgr_width_highres'
velocity_centers = np.arange(5, 6, 1)
velocity_widths = np.arange(1, 40, 0.16667)
dgrs = np.arange(0.05, 0.5, 1e-3)
elif center_vary and width_vary and not dgr_vary:
likelihood_filename += '_width_center'
results_filename += '_width_center'
velocity_centers = np.arange(-15, 30, 1)
velocity_widths = np.arange(1, 80, 1)
dgrs = np.arange(1.1e-1, 1.2e-1, 0.1e-1)
elif not center_vary and width_vary and not dgr_vary:
likelihood_filename += '_width'
results_filename += '_width'
velocity_centers = np.arange(5, 6, 1)
velocity_widths = np.arange(1, 80, 1)
dgrs = np.arange(1.1e-1, 1.2e-1, 0.1e-1)
# Which likelihood fits should be performed?
core_likelihoodelation = 0
global_likelihoodelation = 1
# Name of property files results are written to
global_property_file = 'california_global_properties.txt'
core_property_file = 'california_core_properties.txt'
# Threshold of Av below which we expect only atomic gas, in mag
av_threshold = 1
# Name of noise cube
noise_cube_filename = 'california_hi_galfa_cube_regrid_planckres_noise.fits'
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/california/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/california/figures/hi_velocity_range/'
av_dir = '/d/bip3/ezbc/california/data/av/'
hi_dir = '/d/bip3/ezbc/california/data/hi/'
co_dir = '/d/bip3/ezbc/california/data/co/'
core_dir = '/d/bip3/ezbc/california/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/california/data/python_output/'
region_dir = '/d/bip3/ezbc/california/data/python_output/ds9_regions/'
likelihood_dir = '/d/bip3/ezbc/california/data/python_output/nhi_av/'
# load Planck Av and GALFA HI images, on same grid
av_data_planck, av_header = load_fits(av_dir + \
'california_av_planck_5arcmin.fits',
return_header=True)
av_error_data_planck, av_error_header = load_fits(av_dir + \
'california_av_error_planck_5arcmin.fits',
return_header=True)
hi_data, h = load_fits(hi_dir + \
'california_hi_galfa_cube_regrid_planckres.fits',
return_header=True)
# make the velocity axis
velocity_axis = make_velocity_axis(h)
# Plot NHI vs. Av for a given velocity range
if not path.isfile(hi_dir + noise_cube_filename):
noise_cube = calculate_noise_cube(cube=hi_data,
velocity_axis=velocity_axis,
velocity_noise_range=[90,110], header=h, Tsys=30.,
filename=hi_dir + noise_cube_filename)
else:
noise_cube, noise_header = load_fits(hi_dir + noise_cube_filename,
return_header=True)
# define core properties
with open(core_dir + core_property_file, 'r') as f:
cores = json.load(f)
with open(property_dir + global_property_file, 'r') as f:
global_props = json.load(f)
dgr = global_props['dust2gas_ratio']['value']
dgr = 1.2e-1
cores = convert_core_coordinates(cores, h)
cores = load_ds9_region(cores,
filename_base = region_dir + 'california_av_boxes_',
header = h)
if core_likelihoodelation:
for core in cores:
print('\nCalculating for core %s' % core)
# Grab the mask
mask = myg.get_polygon_mask(av_data_planck,
cores[core]['box_vertices_rotated'])
indices = ((mask == 0) &\
(av_data_planck < av_threshold))
hi_data_sub = np.copy(hi_data[:, indices])
noise_cube_sub = np.copy(noise_cube[:, indices])
av_data_sub = np.copy(av_data_planck[indices])
av_error_data_sub = np.copy(av_error_data_planck[indices])
# Define filename for plotting results
results_filename = figure_dir + 'california_logL_%s.png' % core
# likelihoodelate each core region Av and N(HI) for velocity ranges
vel_range_confint, dgr_confint, likelihoods, center_likelihood,\
width_likelihood, dgr_likelihood = \
calc_likelihood_hi_av(hi_cube=hi_data_sub,
hi_velocity_axis=velocity_axis,
hi_noise_cube=noise_cube_sub,
av_image=av_data_sub,
av_image_error=av_error_data_sub,
dgrs=dgrs,
velocity_centers=velocity_centers,
velocity_widths=velocity_widths,
return_likelihoods=True,
plot_results=True,
results_filename=results_filename,
likelihood_filename=likelihood_dir + \
likelihood_filename + \
'{0:s}.fits'.format(core),
clobber=clobber,
conf=conf)
print('HI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range_confint[0],
vel_range_confint[1]))
print('DGR:')
print('%.1f to %.1f km/s' % (vel_range_confint[0],
vel_range_confint[1]))
cores[core]['hi_velocity_range'] = vel_range_confint[0:2]
cores[core]['hi_velocity_range_error'] = vel_range_confint[2:]
cores[core]['center_likelihood'] = center_likelihood.tolist()
cores[core]['width_likelihood'] = width_likelihood.tolist()
cores[core]['vel_centers'] = velocity_centers.tolist()
cores[core]['vel_widths'] = velocity_widths.tolist()
with open(core_dir + core_property_file, 'w') as f:
json.dump(cores, f)
if global_likelihoodelation:
print('\nCalculating likelihoods globally')
mask = np.zeros(av_data_planck.shape)
for core in cores:
# Grab the mask
mask += myg.get_polygon_mask(av_data_planck,
cores[core]['box_vertices_rotated'])
indices = ((mask == 0) &\
(av_data_planck < av_threshold))
#indices = ((av_data_planck < av_threshold))
hi_data_sub = np.copy(hi_data[:, indices])
noise_cube_sub = np.copy(noise_cube[:, indices])
av_data_sub = np.copy(av_data_planck[indices])
av_error_data_sub = np.copy(av_error_data_planck[indices])
# Define filename for plotting results
results_filename = figure_dir + results_filename
# likelihoodelate each core region Av and N(HI) for velocity ranges
vel_range_confint, dgr_confint, likelihoods, center_likelihood,\
width_likelihood, dgr_likelihood = \
calc_likelihood_hi_av(hi_cube=hi_data_sub,
hi_velocity_axis=velocity_axis,
hi_noise_cube=noise_cube_sub,
av_image=av_data_sub,
av_image_error=av_error_data_sub,
dgrs=dgrs,
velocity_centers=velocity_centers,
velocity_widths=velocity_widths,
return_likelihoods=True,
plot_results=True,
results_filename=results_filename,
likelihood_filename=likelihood_dir + \
likelihood_filename + \
'_global.fits',
clobber=clobber,
conf=conf,
contour_confs=contour_confs)
print('HI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range_confint[0],
vel_range_confint[1]))
print('DGR:')
print('%.1f to %.1f km/s' % (dgr_confint[0],
dgr_confint[1]))
global_props['dust2gas_ratio'] = {}
global_props['dust2gas_ratio_error'] = {}
global_props['hi_velocity_range'] = vel_range_confint[0:2]
global_props['hi_velocity_range_error'] = vel_range_confint[2:]
global_props['dust2gas_ratio']['value'] = dgr_confint[0]
global_props['dust2gas_ratio_error']['value'] = dgr_confint[1:]
global_props['hi_velocity_range_conf'] = conf
global_props['center_likelihood'] = center_likelihood.tolist()
global_props['width_likelihood'] = width_likelihood.tolist()
global_props['dgr_likelihood'] = dgr_likelihood.tolist()
global_props['vel_centers'] = velocity_centers.tolist()
global_props['vel_widths'] = velocity_widths.tolist()
global_props['dgrs'] = dgrs.tolist()
global_props['likelihoods'] = likelihoods.tolist()
with open(property_dir + global_property_file, 'w') as f:
json.dump(global_props, f)
def plot_cluster_nhi_panels(results_ref=None, colors=None, limits=None,
cube=None, header=None, load_synthetic_cube=False, show=False,
velocity_range=[0,500], save_pdf=False):
from mycoords import make_velocity_axis
from localmodule import plot_nhi_map_panels, create_synthetic_cube
import myimage_analysis as myia
from astropy.io import fits
# Plot names
DIR_FIG = '/d/bip3/ezbc/magellanic_stream/figures/'
#DIR_FIG = '../../figures/'
DIR_FIG = '/d/bip3/ezbc/multicloud/figures/decomposition/'
FILENAME_FIG = DIR_FIG + 'nhi_maps_components.png'
if save_pdf:
FILENAME_FIG = FILENAME_FIG.replace('.png','.pdf')
# Load HI Cube
DIR_HI = '/d/bip3/ezbc/multicloud/data_products/hi/'
#FILENAME_CUBE = 'gass_280_-45_1450212515.fits'
FILENAME_CUBE = 'perseus_hi_galfa_cube_sub_regrid.fits'
FILENAME_CUBE_SYNTH_BASE = DIR_HI + 'cube_synth_comp'
velocity_axis = make_velocity_axis(header)
# Create N(HI) data
nhi_data = myia.calculate_nhi(cube=cube,
velocity_axis=velocity_axis,
velocity_range=velocity_range,
)
# Create synthetic cube from fitted spectra
velocity_axis = results_ref['velocity_axis']
# get number of unique components
component_colors = np.unique(colors)
n_components = len(component_colors)
nhi_list = []
nhi_max = 0.0
for i in xrange(n_components):
if not load_synthetic_cube:
print('\n\tCreating synthetic cube ' + str(i+1) + ' of ' + \
str(n_components))
# get the relevant parameters
indices = np.where(colors == component_colors[i])[0]
pix_positions = results_ref['pos_pix'][indices]
fit_params_list = results_ref['data'][indices, 2:]
print('\n\t\tNumber of components in cube: ' + \
'{0:.0f}'.format(len(fit_params_list)))
cube_synthetic = \
create_synthetic_cube(pix_positions=pix_positions,
velocity_axis=velocity_axis,
fit_params_list=fit_params_list,
cube_data=cube,
)
np.save(FILENAME_CUBE_SYNTH_BASE + str(i) + '.npy', cube_synthetic)
else:
print('\n\tLoading synthetic cube ' + str(i+1) + ' of ' + \
str(n_components))
cube_synthetic = np.load(FILENAME_CUBE_SYNTH_BASE + str(i) + '.npy')
# Create N(HI) synthetic
nhi_synthetic = myia.calculate_nhi(cube=cube_synthetic,
velocity_axis=velocity_axis,
velocity_range=velocity_range,
)
nhi_list.append(nhi_synthetic)
nhi_max_temp = np.max(nhi_synthetic)
if nhi_max_temp > nhi_max:
nhi_max = nhi_max_temp
v_limits = [0, nhi_max]
# crop to highest valued cubes
n_left = 4
n_left = len(nhi_list)
sum_list = []
for nhi in nhi_list:
sum_list.append(np.nansum(nhi))
sort_indices = np.argsort(sum_list)[::-1]
new_list = []
for i in xrange(n_left):
new_list.append(nhi_list[sort_indices[i]])
nhi_list = new_list
# Plot the maps together
plot_nhi_map_panels(nhi_list,
header=header,
#limits=[278, -37, 282, -35],
limits=limits,
filename=FILENAME_FIG,
nhi_vlimits=[-0.1, 15],
show=show,
vscale='linear',
)
def main():
import grid
import numpy as np
import numpy
from os import system, path
import mygeometry as myg
from mycoords import make_velocity_axis
import json
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
from multiprocessing import Pool
global _hi_cube
global _hi_velocity_axis
global _hi_noise_cube
global _av_image
global _av_image_error
# parameters used in script
# -------------------------
# HI velocity integration range
# Determine HI integration velocity by CO or likelihoodelation with Av?
hi_av_likelihoodelation = True
center_vary = False
width_vary = True
dgr_vary = True
# Check if likelihood file already written, rewrite?
clobber = 1
# Include only pixels within core regions for analysis?
core_mask = 0
# Confidence of parameter errors
conf = 0.68
# Confidence of contour levels
contour_confs = (0.68, 0.95)
# Results and fits filenames
likelihood_filename = 'perseus_nhi_av_likelihoods_mcmc_co_av'
results_filename = 'perseus_likelihood_mcmc_co_av'
global _progress_filename
_progress_filename = 'perseus_mcmc_samples.dat'
# Define ranges of parameters
global _av_thres_range
_av_thres_range = (1.0, 1.1)
_av_thres_range = (0.1, 2.0)
global _vel_width_range
_vel_width_range = (0.0, 80.0)
global _dgr_range
_dgr_range = (0.01, 0.4)
global _velocity_center
_velocity_center = 5.0 # km/s
# MCMC parameters
global _ndim
_ndim = 3
global _nwalkers
_nwalkers = 100
global _niter
_niter = 1000
global _init_guesses
_init_guesses = np.array((10, 0.10, 1.0))
global _init_spread
_init_spread = np.array((0.1, 0.01, 0.01))
global _mc_threads
_mc_threads = 10
# Name of property files results are written to
global_property_file = 'perseus_global_properties.txt'
core_property_file = 'perseus_core_properties.txt'
# Name of noise cube
noise_cube_filename = 'perseus_hi_galfa_cube_regrid_planckres_noise.fits'
# Define limits for plotting the map
prop_dict = {}
prop_dict['limit_wcs'] = (((3, 58, 0), (27, 6, 0)), ((3, 20, 0), (35, 0,
0)))
prop_dict['limit_wcs'] = (((3, 58, 0), (26, 6, 0)), ((3, 0, 0), (35, 0,
0)))
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/perseus/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/perseus/figures/hi_velocity_range/'
av_dir = '/d/bip3/ezbc/perseus/data/av/'
hi_dir = '/d/bip3/ezbc/perseus/data/hi/'
co_dir = '/d/bip3/ezbc/perseus/data/co/'
core_dir = '/d/bip3/ezbc/perseus/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/perseus/data/python_output/'
region_dir = '/d/bip3/ezbc/perseus/data/python_output/ds9_regions/'
likelihood_dir = '/d/bip3/ezbc/perseus/data/python_output/nhi_av/'
global _likelihood_dir
_likelihood_dir = likelihood_dir
# load Planck Av and GALFA HI images, on same grid
av_data_planck, av_header = load_fits(av_dir + \
'perseus_av_planck_5arcmin.fits',
return_header=True)
prop_dict['av_header'] = av_header
av_error_data_planck, av_error_header = load_fits(av_dir + \
'perseus_av_error_planck_5arcmin.fits',
return_header=True)
hi_data, h = load_fits(hi_dir + \
'perseus_hi_galfa_cube_regrid_planckres.fits',
return_header=True)
co_data, co_header = load_fits(co_dir + \
'perseus_co_cfa_cube_regrid_planckres.fits',
return_header=True)
# make the velocity axis
velocity_axis = make_velocity_axis(h)
# Plot NHI vs. Av for a given velocity range
if not path.isfile(hi_dir + noise_cube_filename):
noise_cube = calculate_noise_cube(cube=hi_data,
velocity_axis=velocity_axis,
velocity_noise_range=[90, 110],
header=h,
Tsys=30.,
filename=hi_dir +
noise_cube_filename)
else:
noise_cube, noise_header = load_fits(hi_dir + noise_cube_filename,
return_header=True)
# define core properties
with open(core_dir + core_property_file, 'r') as f:
cores = json.load(f)
with open(property_dir + global_property_file, 'r') as f:
global_props = json.load(f)
cores = convert_core_coordinates(cores, h)
cores = load_ds9_region(cores,
filename_base=region_dir + 'perseus_av_boxes_',
header=h)
print('\nCalculating likelihoods globally')
mask = np.zeros(av_data_planck.shape)
for core in cores:
# Grab the mask
mask += myg.get_polygon_mask(av_data_planck,
cores[core]['wedge_vertices_rotated'])
co_mom0 = np.sum(co_data, axis=0)
# Mask images
core_mask = 0
if core_mask:
indices = ((mask == 1) & \
(co_mom0 < np.std(co_mom0[~np.isnan(co_mom0)])*2.0))
mask_type = '_core_mask'
else:
indices = (co_mom0 < np.std(co_mom0[~np.isnan(co_mom0)]) * 2.0)
mask_type = ''
hi_data_sub = np.copy(hi_data[:, indices])
noise_cube_sub = np.copy(noise_cube[:, indices])
av_data_sub = np.copy(av_data_planck[indices])
av_error_data_sub = np.copy(av_error_data_planck[indices])
# Set global variables
_hi_cube = hi_data_sub
_hi_velocity_axis = velocity_axis
_hi_noise_cube = noise_cube_sub
_av_image = av_data_sub
_av_image_error = av_error_data_sub
# Define filename for plotting results
results_filename = figure_dir + results_filename
# likelihoodelate each core region Av and N(HI) for velocity ranges
vel_range_confint, dgr_confint, likelihoods, center_likelihood,\
width_likelihood, dgr_likelihood = \
calc_likelihood(return_likelihoods=True,
plot_results=True,
results_filename=results_filename + mask_type,
likelihood_filename=likelihood_dir + \
likelihood_filename + \
mask_type + '.npy',
clobber=clobber,
conf=conf,
contour_confs=contour_confs)
'''
def main(dgr=None,
vel_range=(-5, 15),
vel_range_type='single',
region=None,
av_data_type='planck'):
''' Executes script.
Parameters
----------
dgr : float
If None, pulls best-fit value from properties.
vel_range : tuple
If None, pulls best-fit value from properties.
'''
# import external modules
import pyfits as fits
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
import json
from os import system, path
# Script parameters
# -----------------
# Name of noise cube
noise_cube_filename = 'multicloud_hi_galfa_cube_regrid_planckres_noise.fits'
# Use Planck dust Av map or Kainulainen 2009 optical extinction Av map?
# options are 'planck' or 'lee12'
#av_data_type = 'lee12'
#av_data_type = 'planck'
# Global parameter file
prop_file = 'multicloud_global_properties'
# Which cores to include in analysis?
cores_to_keep = [ # taur
'L1495',
'L1495A',
'B213',
'L1498',
'B215',
'B18',
'B217',
'B220-1',
'B220-2',
'L1521',
'L1524',
'L1527-1',
'L1527-2',
# Calif
'L1536',
'L1483-1',
'L1483-2',
'L1482-1',
'L1482-2',
'L1478-1',
'L1478-2',
'L1456',
'NGC1579',
#'L1545',
#'L1517',
#'L1512',
#'L1523',
#'L1512',
# Pers
'B5',
'IC348',
'B1E',
'B1',
'NGC1333',
'B4',
'B3',
'L1455',
'L1448',
]
# Regions, regions to edit the global properties with
if region == 1:
region_limit = {
'wcs': (((5, 10, 0), (19, 0, 0)), ((4, 30, 0), (27, 0, 0))),
'pixel': ()
}
elif region == 2:
region_limit = {
'wcs': (((4, 30, 0), (19, 0, 0)), ((3, 50, 0), (29, 0, 0))),
'pixel': ()
}
elif region == 3:
region_limit = {
'wcs': (((4, 30, 0), (29, 0, 0)), ((3, 50, 0), (33, 0, 0))),
'pixel': ()
}
else:
region_limit = None
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/multicloud/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/multicloud/figures/'
av_dir = '/d/bip3/ezbc/multicloud/data/av/'
hi_dir = '/d/bip3/ezbc/multicloud/data/hi/'
co_dir = '/d/bip3/ezbc/multicloud/data/co/'
core_dir = '/d/bip3/ezbc/multicloud/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/multicloud/data/python_output/'
region_dir = '/d/bip3/ezbc/multicloud/data/python_output/'
# load Planck Av and GALFA HI images, on same grid
if av_data_type == 'lee12_2mass':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_lee12_2mass_regrid_planckres.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'lee12_iris':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_lee12_iris_regrid_planckres.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'planck_rad':
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_planck_radiance_5arcmin.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'multicloud_av_error_planck_radiance_5arcmin.fits',
return_header=True)
else:
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_planck_5arcmin.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'multicloud_av_error_planck_5arcmin.fits',
return_header=True)
hi_cube, hi_header = load_fits(hi_dir + \
'multicloud_hi_galfa_cube_regrid_planckres.fits',
return_header=True)
co_data, co_header = load_fits(co_dir + \
'multicloud_co_cfa_cube_regrid_planckres.fits',
return_header=True)
# Prepare data products
# ---------------------
# Load global properties of cloud
# global properties written from script
# 'av/multicloud_analysis_global_properties.txt'
if region is not None:
likelihood_filename += '_region{0:.0f}'.format(region)
results_filename += '_region{0:.0f}'.format(region)
print('\nLoading global property file {0:s}.txt'.format(prop_file))
with open(property_dir + prop_file + '.txt', 'r') as f:
props = json.load(f)
# Define velocity range
props['hi_velocity_range'] = vel_range
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
# make velocity axis for co cube
co_velocity_axis = make_velocity_axis(co_header)
# Load the HI noise cube if it exists, else make it
if not path.isfile(hi_dir + noise_cube_filename):
hi_noise_cube = calculate_noise_cube(cube=hi_cube,
velocity_axis=velocity_axis,
velocity_noise_range=[90, 110],
header=hi_header,
Tsys=30.,
filename=hi_dir +
noise_cube_filename)
else:
hi_noise_cube, noise_header = fits.getdata(hi_dir +
noise_cube_filename,
header=True)
# create nhi image
nhi_image = calculate_nhi(cube=hi_cube,
velocity_axis=velocity_axis,
velocity_range=vel_range,
header=hi_header,
noise_cube=hi_noise_cube)
# Change WCS coords to pixel coords of images
props = convert_limit_coordinates(props,
header=av_header,
coords=('region_limit',
'co_noise_limits', 'plot_limit',
'region_name_pos'))
# Load cloud division regions from ds9
props = load_ds9_region(props,
filename=region_dir + 'multicloud_divisions.reg',
header=av_header)
# Derive relevant region
pix = props['region_limit']['pixel']
region_vertices = ((pix[1], pix[0]), (pix[1], pix[2]), (pix[3], pix[2]),
(pix[3], pix[0]))
# block offregion
region_mask = myg.get_polygon_mask(av_image, region_vertices)
print('\nRegion size = ' + \
'{0:.0f} pix'.format(region_mask[region_mask == 1].size))
if vel_range_type == 'single':
print('\nHI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range[0], vel_range[1]))
elif vel_range_type == 'multiple':
print('\nHI velocity integration ranges:')
for i in xrange(0, vel_range.shape[0]):
print('%.1f to %.1f km/s' % (vel_range[i, 0], vel_range[i, 1]))
cloud_dict = {
'taurus': {},
'perseus': {},
'california': {},
}
# load Planck Av and GALFA HI images, on same grid
for cloud in cloud_dict:
print('\nLoading core properties for {0:s}'.format(cloud))
file_dir = '/d/bip3/ezbc/{0:s}/data/av/'.format(cloud)
# define core properties
with open('/d/bip3/ezbc/{0:s}/data/python_output/'.format(cloud) + \
'core_properties/{0:s}_core_properties.txt'.format(cloud),
'r') as f:
cores = json.load(f)
# Load core regions from DS9 files
if cloud == 'aldobaran':
region_cloud = 'california'
else:
region_cloud = cloud
core_filename = region_dir.replace('multicloud',region_cloud) + \
'/ds9_regions/{0:s}_av_poly_cores'.format(region_cloud)
cores = load_ds9_core_region(cores,
filename_base=core_filename,
header=av_header)
cores = convert_core_coordinates(cores, av_header)
# Remove cores
cores_to_remove = []
for core in cores:
if core not in cores_to_keep:
cores_to_remove.append(core)
for core_to_remove in cores_to_remove:
del cores[core_to_remove]
cloud_dict[cloud]['cores'] = cores
# Plot
figure_types = ['png', 'pdf']
for figure_type in figure_types:
filename = 'multicloud_av_cores_map' + \
'.{0:s}'.format(figure_type)
print('\nSaving Av cores map to \n' + filename)
plot_cores_map(
header=av_header,
av_image=av_image,
limits=props['plot_limit']['pixel'],
regions=props['regions'],
cloud_dict=cloud_dict,
cores_to_keep=cores_to_keep,
props=props,
hi_vlimits=(0, 20),
av_vlimits=(0, 16),
#av_vlimits=(0.1,30),
savedir=figure_dir + 'maps/',
filename=filename,
show=False)
def main():
import grid
import numpy as np
import numpy
from os import system, path
import mygeometry as myg
from mycoords import make_velocity_axis
import json
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
# parameters used in script
# -------------------------
# HI velocity integration range
# Determine HI integration velocity by CO or correlation with Av?
hi_av_correlation = True
velocity_centers = np.arange(-15, 30, 4)
velocity_widths = np.arange(1, 80, 4)
# Which likelihood fits should be performed?
core_correlation = 0
global_correlation = 1
# Name of property files results are written to
global_property_file = 'california_global_properties.txt'
core_property_file = 'california_core_properties.txt'
# Threshold of Av below which we expect only atomic gas, in mag
av_threshold = 100
# Check if likelihood file already written, rewrite?>
likelihood_filename = 'california_nhi_av_likelihoods'
clobber = 0
hi_vel_range_conf = 0.50
# Name of noise cube
noise_cube_filename = 'california_hi_galfa_cube_regrid_planckres_noise.fits'
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/california/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/california/figures/hi_velocity_range/'
av_dir = '/d/bip3/ezbc/california/data/av/'
hi_dir = '/d/bip3/ezbc/california/data/hi/'
co_dir = '/d/bip3/ezbc/california/data/co/'
core_dir = '/d/bip3/ezbc/california/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/california/data/python_output/'
region_dir = '/d/bip3/ezbc/california/data/python_output/ds9_regions/'
likelihood_dir = '/d/bip3/ezbc/california/data/python_output/nhi_av/'
# load Planck Av and GALFA HI images, on same grid
av_data_planck, av_header = load_fits(av_dir + \
'california_av_planck_5arcmin.fits',
return_header=True)
av_error_data_planck, av_error_header = load_fits(av_dir + \
'california_av_error_planck_5arcmin.fits',
return_header=True)
hi_data, h = load_fits(hi_dir + \
'california_hi_galfa_cube_regrid_planckres.fits',
return_header=True)
# make the velocity axis
velocity_axis = make_velocity_axis(h)
# Plot NHI vs. Av for a given velocity range
if not path.isfile(hi_dir + noise_cube_filename):
noise_cube = calculate_noise_cube(cube=hi_data,
velocity_axis=velocity_axis,
velocity_noise_range=[90, 110],
header=h,
Tsys=30.,
filename=hi_dir +
noise_cube_filename)
else:
noise_cube, noise_header = load_fits(hi_dir + noise_cube_filename,
return_header=True)
# define core properties
with open(core_dir + core_property_file, 'r') as f:
cores = json.load(f)
with open(property_dir + global_property_file, 'r') as f:
global_props = json.load(f)
dgr = global_props['dust2gas_ratio']['value']
dgr = 1.22e-1
cores = convert_core_coordinates(cores, h)
cores = load_ds9_region(cores,
filename_base=region_dir + 'california_av_boxes_',
header=h)
if core_correlation:
for core in cores:
print('\nCalculating for core %s' % core)
# Grab the mask
mask = myg.get_polygon_mask(av_data_planck,
cores[core]['box_vertices_rotated'])
indices = ((mask == 0) &\
(av_data_planck < av_threshold))
hi_data_sub = np.copy(hi_data[:, indices])
noise_cube_sub = np.copy(noise_cube[:, indices])
av_data_sub = np.copy(av_data_planck[indices])
av_error_data_sub = np.copy(av_error_data_planck[indices])
# Define filename for plotting results
results_filename = figure_dir + 'california_logL_%s.png' % core
# Correlate each core region Av and N(HI) for velocity ranges
vel_range_confint, correlations, center_corr, width_corr = \
correlate_hi_av(hi_cube=hi_data_sub,
hi_velocity_axis=velocity_axis,
hi_noise_cube=noise_cube_sub,
av_image=av_data_sub,
av_image_error=av_error_data_sub,
dgr=dgr,
velocity_centers=velocity_centers,
velocity_widths=velocity_widths,
return_correlations=True,
plot_results=True,
results_filename=results_filename,
likelihood_filename=likelihood_dir + \
likelihood_filename + \
'{0:s}.fits'.format(core),
clobber=clobber,
hi_vel_range_conf=hi_vel_range_conf)
print('HI velocity integration range:')
print('%.1f to %.1f km/s' %
(vel_range_confint[0], vel_range_confint[1]))
cores[core]['hi_velocity_range'] = vel_range_confint[0:2]
cores[core]['hi_velocity_range_error'] = vel_range_confint[2:]
cores[core]['center_corr'] = center_corr.tolist()
cores[core]['width_corr'] = width_corr.tolist()
cores[core]['vel_centers'] = velocity_centers.tolist()
cores[core]['vel_widths'] = velocity_widths.tolist()
with open(core_dir + core_property_file, 'w') as f:
json.dump(cores, f)
if global_correlation:
print('\nCalculating correlations globally')
indices = ((av_data_planck < av_threshold))
hi_data_sub = np.copy(hi_data[:, indices])
noise_cube_sub = np.copy(noise_cube[:, indices])
av_data_sub = np.copy(av_data_planck[indices])
av_error_data_sub = np.copy(av_error_data_planck[indices])
# Define filename for plotting results
results_filename = figure_dir + 'california_logL_global.png'
# Correlate each core region Av and N(HI) for velocity ranges
vel_range_confint, correlations, center_corr, width_corr = \
correlate_hi_av(hi_cube=hi_data_sub,
hi_velocity_axis=velocity_axis,
hi_noise_cube=noise_cube_sub,
av_image=av_data_sub,
av_image_error=av_error_data_sub,
dgr=dgr,
velocity_centers=velocity_centers,
velocity_widths=velocity_widths,
return_correlations=True,
plot_results=True,
results_filename=results_filename,
likelihood_filename=likelihood_dir + \
likelihood_filename + '_global.fits',
clobber=clobber,
hi_vel_range_conf=hi_vel_range_conf)
'''
fit_hi_vel_range(guesses=(0, 30),
av_image=av_data_sub,
av_image_error=av_error_data_sub,
hi_cube=hi_data_sub,
hi_velocity_axis=velocity_axis,
hi_noise_cube=noise_cube_sub,
dgr=dgr)
'''
print('HI velocity integration range:')
print('%.1f to %.1f km/s' %
(vel_range_confint[0], vel_range_confint[1]))
global_props['hi_velocity_range'] = vel_range_confint[0:2]
global_props['hi_velocity_range_error'] = vel_range_confint[2:]
global_props['hi_velocity_range_conf'] = hi_vel_range_conf
global_props['center_corr'] = center_corr.tolist()
global_props['width_corr'] = width_corr.tolist()
global_props['vel_centers'] = velocity_centers.tolist()
global_props['vel_widths'] = velocity_widths.tolist()
with open(property_dir + global_property_file, 'w') as f:
json.dump(global_props, f)
def main():
import grid
import numpy as np
import numpy
from os import system,path
import mygeometry as myg
from mycoords import make_velocity_axis
import json
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
from multiprocessing import Pool
global _hi_cube
global _hi_velocity_axis
global _hi_noise_cube
global _av_image
global _av_image_error
# parameters used in script
# -------------------------
# HI velocity integration range
# Determine HI integration velocity by CO or likelihoodelation with Av?
hi_av_likelihoodelation = True
center_vary = False
width_vary = True
dgr_vary = True
# Check if likelihood file already written, rewrite?
clobber = 1
# Include only pixels within core regions for analysis?
core_mask = 0
# Confidence of parameter errors
conf = 0.68
# Confidence of contour levels
contour_confs = (0.68, 0.95)
# Results and fits filenames
likelihood_filename = 'perseus_nhi_av_likelihoods_mcmc_co_av'
results_filename = 'perseus_likelihood_mcmc_co_av'
global _progress_filename
_progress_filename = 'perseus_mcmc_samples.dat'
# Define ranges of parameters
global _av_thres_range
_av_thres_range = (1.0, 1.1)
_av_thres_range = (0.1, 2.0)
global _vel_width_range
_vel_width_range = (0.0, 80.0)
global _dgr_range
_dgr_range = (0.01, 0.4)
global _velocity_center
_velocity_center = 5.0 # km/s
# MCMC parameters
global _ndim
_ndim = 3
global _nwalkers
_nwalkers = 100
global _niter
_niter = 1000
global _init_guesses
_init_guesses = np.array((10, 0.10, 1.0))
global _init_spread
_init_spread = np.array((0.1, 0.01, 0.01))
global _mc_threads
_mc_threads = 10
# Name of property files results are written to
global_property_file = 'perseus_global_properties.txt'
core_property_file = 'perseus_core_properties.txt'
# Name of noise cube
noise_cube_filename = 'perseus_hi_galfa_cube_regrid_planckres_noise.fits'
# Define limits for plotting the map
prop_dict = {}
prop_dict['limit_wcs'] = (((3, 58, 0), (27, 6, 0)),
((3, 20, 0), (35, 0, 0)))
prop_dict['limit_wcs'] = (((3, 58, 0), (26, 6, 0)),
((3, 0, 0), (35, 0, 0)))
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/perseus/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/perseus/figures/hi_velocity_range/'
av_dir = '/d/bip3/ezbc/perseus/data/av/'
hi_dir = '/d/bip3/ezbc/perseus/data/hi/'
co_dir = '/d/bip3/ezbc/perseus/data/co/'
core_dir = '/d/bip3/ezbc/perseus/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/perseus/data/python_output/'
region_dir = '/d/bip3/ezbc/perseus/data/python_output/ds9_regions/'
likelihood_dir = '/d/bip3/ezbc/perseus/data/python_output/nhi_av/'
global _likelihood_dir
_likelihood_dir = likelihood_dir
# load Planck Av and GALFA HI images, on same grid
av_data_planck, av_header = load_fits(av_dir + \
'perseus_av_planck_5arcmin.fits',
return_header=True)
prop_dict['av_header'] = av_header
av_error_data_planck, av_error_header = load_fits(av_dir + \
'perseus_av_error_planck_5arcmin.fits',
return_header=True)
hi_data, h = load_fits(hi_dir + \
'perseus_hi_galfa_cube_regrid_planckres.fits',
return_header=True)
co_data, co_header = load_fits(co_dir + \
'perseus_co_cfa_cube_regrid_planckres.fits',
return_header=True)
# make the velocity axis
velocity_axis = make_velocity_axis(h)
# Plot NHI vs. Av for a given velocity range
if not path.isfile(hi_dir + noise_cube_filename):
noise_cube = calculate_noise_cube(cube=hi_data,
velocity_axis=velocity_axis,
velocity_noise_range=[90,110], header=h, Tsys=30.,
filename=hi_dir + noise_cube_filename)
else:
noise_cube, noise_header = load_fits(hi_dir + noise_cube_filename,
return_header=True)
# define core properties
with open(core_dir + core_property_file, 'r') as f:
cores = json.load(f)
with open(property_dir + global_property_file, 'r') as f:
global_props = json.load(f)
cores = convert_core_coordinates(cores, h)
cores = load_ds9_region(cores,
filename_base = region_dir + 'perseus_av_boxes_',
header = h)
print('\nCalculating likelihoods globally')
mask = np.zeros(av_data_planck.shape)
for core in cores:
# Grab the mask
mask += myg.get_polygon_mask(av_data_planck,
cores[core]['wedge_vertices_rotated'])
co_mom0 = np.sum(co_data, axis=0)
# Mask images
core_mask = 0
if core_mask:
indices = ((mask == 1) & \
(co_mom0 < np.std(co_mom0[~np.isnan(co_mom0)])*2.0))
mask_type = '_core_mask'
else:
indices = (co_mom0 < np.std(co_mom0[~np.isnan(co_mom0)])*2.0)
mask_type = ''
hi_data_sub = np.copy(hi_data[:, indices])
noise_cube_sub = np.copy(noise_cube[:, indices])
av_data_sub = np.copy(av_data_planck[indices])
av_error_data_sub = np.copy(av_error_data_planck[indices])
# Set global variables
_hi_cube = hi_data_sub
_hi_velocity_axis = velocity_axis
_hi_noise_cube = noise_cube_sub
_av_image = av_data_sub
_av_image_error = av_error_data_sub
# Define filename for plotting results
results_filename = figure_dir + results_filename
# likelihoodelate each core region Av and N(HI) for velocity ranges
vel_range_confint, dgr_confint, likelihoods, center_likelihood,\
width_likelihood, dgr_likelihood = \
calc_likelihood(return_likelihoods=True,
plot_results=True,
results_filename=results_filename + mask_type,
likelihood_filename=likelihood_dir + \
likelihood_filename + \
mask_type + '.npy',
clobber=clobber,
conf=conf,
contour_confs=contour_confs)
'''
def calculate_nhi(cube = None, velocity_axis = None, velocity_range = [],
return_nhi_error = True, noise_cube = None,
velocity_noise_range=[90,100], Tsys = 30., header = None,
fits_filename = None, fits_error_filename = None, verbose = True):
''' Calculates an N(HI) image given a velocity range within which to
include a SpectralGrid's components.
Parameters
----------
cube : array-like, optional
Three dimensional array with velocity axis as 0th axis. Must specify
a velocity_axis if cube is used.
velocity_axis : array-like, optional
One dimensional array containing velocities corresponding to
fits_filename : str
If specified, and a header is provided, the nhi image will be written.
header : pyfits.Header
Header from cube.
'''
import numpy as np
from mycoords import make_velocity_axis
if velocity_axis is None:
velocity_axis = make_velocity_axis(header)
# Calculate NHI from cube if set
if cube is not None and velocity_axis is not None:
image = np.empty((cube.shape[1],
cube.shape[2]))
image[:,:] = np.NaN
indices = np.where((velocity_axis > velocity_range[0]) & \
(velocity_axis < velocity_range[1]))[0]
image[:,:] = cube[indices,:,:].sum(axis=0)
# Calculate image error
if return_nhi_error:
image_error = np.empty((cube.shape[1],
cube.shape[2]))
image_error[:,:] = np.NaN
image_error[:,:] = (noise_cube[indices,:,:]**2).sum(axis=0)**0.5
# NHI in units of 1e20 cm^-2
nhi_image = np.ma.array(image,mask=np.isnan(image)) * 1.823e-2
if fits_filename is not None and header is not None:
if verbose:
print('Writing N(HI) image to FITS file %s' % fits_filename)
header['BUNIT'] = '1e20 cm^-2'
header.remove('CDELT3')
header.remove('CRVAL3')
header.remove('CRPIX3')
header.remove('CTYPE3')
header.remove('NAXIS3')
header['NAXIS'] = 2
pf.writeto(fits_filename, image*1.823e-2, header = header, clobber =
True, output_verify = 'fix')
if fits_error_filename is not None and header is not None:
if verbose:
print('Writing N(HI) error image to FITS file %s' % fits_filename)
pf.writeto(fits_error_filename, image_error * 1.823e-2, header =
header, clobber = True, output_verify = 'fix')
if return_nhi_error:
nhi_image_error = np.ma.array(image_error,
mask=np.isnan(image_error)) * 1.823e-2
return nhi_image, nhi_image_error
else:
return nhi_image
def main():
import grid
import numpy as np
import numpy
from os import system, path
import mygeometry as myg
from mycoords import make_velocity_axis
import json
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
# parameters used in script
# -------------------------
# HI velocity integration range
# Determine HI integration velocity by CO or likelihoodelation with Av?
hi_av_likelihoodelation = True
center_vary = False
width_vary = True
dgr_vary = True
# Check if likelihood file already written, rewrite?
clobber = 0
# Confidence of parameter errors
conf = 0.68
# Confidence of contour levels
contour_confs = (0.68, 0.95)
# Course, large grid or fine, small grid?
grid_res = 'course'
grid_res = 'fine'
# Results and fits filenames
likelihood_filename = 'california_nhi_av_likelihoods'
results_filename = 'california_likelihood'
# Define ranges of parameters
if center_vary and width_vary and dgr_vary:
likelihood_filename += '_width_dgr_center'
results_filename += '_width_dgr_center'
velocity_centers = np.arange(-15, 30, 1)
velocity_widths = np.arange(1, 80, 1)
dgrs = np.arange(1e-2, 1, 2e-2)
elif not center_vary and width_vary and dgr_vary:
if grid_res == 'course':
likelihood_filename += '_dgr_width_lowres'
results_filename += '_dgr_width_lowres'
velocity_centers = np.arange(5, 6, 1)
velocity_widths = np.arange(1, 80, 1)
dgrs = np.arange(1e-2, 1, 2e-2)
elif grid_res == 'fine':
likelihood_filename += '_dgr_width_highres'
results_filename += '_dgr_width_highres'
velocity_centers = np.arange(5, 6, 1)
velocity_widths = np.arange(1, 40, 0.16667)
dgrs = np.arange(0.05, 0.5, 1e-3)
elif center_vary and width_vary and not dgr_vary:
likelihood_filename += '_width_center'
results_filename += '_width_center'
velocity_centers = np.arange(-15, 30, 1)
velocity_widths = np.arange(1, 80, 1)
dgrs = np.arange(1.1e-1, 1.2e-1, 0.1e-1)
elif not center_vary and width_vary and not dgr_vary:
likelihood_filename += '_width'
results_filename += '_width'
velocity_centers = np.arange(5, 6, 1)
velocity_widths = np.arange(1, 80, 1)
dgrs = np.arange(1.1e-1, 1.2e-1, 0.1e-1)
# Which likelihood fits should be performed?
core_likelihoodelation = 0
global_likelihoodelation = 1
# Name of property files results are written to
global_property_file = 'california_global_properties.txt'
core_property_file = 'california_core_properties.txt'
# Threshold of Av below which we expect only atomic gas, in mag
av_threshold = 1
# Name of noise cube
noise_cube_filename = 'california_hi_galfa_cube_regrid_planckres_noise.fits'
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/california/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/california/figures/hi_velocity_range/'
av_dir = '/d/bip3/ezbc/california/data/av/'
hi_dir = '/d/bip3/ezbc/california/data/hi/'
co_dir = '/d/bip3/ezbc/california/data/co/'
core_dir = '/d/bip3/ezbc/california/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/california/data/python_output/'
region_dir = '/d/bip3/ezbc/california/data/python_output/ds9_regions/'
likelihood_dir = '/d/bip3/ezbc/california/data/python_output/nhi_av/'
# load Planck Av and GALFA HI images, on same grid
av_data_planck, av_header = load_fits(av_dir + \
'california_av_planck_5arcmin.fits',
return_header=True)
av_error_data_planck, av_error_header = load_fits(av_dir + \
'california_av_error_planck_5arcmin.fits',
return_header=True)
hi_data, h = load_fits(hi_dir + \
'california_hi_galfa_cube_regrid_planckres.fits',
return_header=True)
# make the velocity axis
velocity_axis = make_velocity_axis(h)
# Plot NHI vs. Av for a given velocity range
if not path.isfile(hi_dir + noise_cube_filename):
noise_cube = calculate_noise_cube(cube=hi_data,
velocity_axis=velocity_axis,
velocity_noise_range=[90, 110],
header=h,
Tsys=30.,
filename=hi_dir +
noise_cube_filename)
else:
noise_cube, noise_header = load_fits(hi_dir + noise_cube_filename,
return_header=True)
# define core properties
with open(core_dir + core_property_file, 'r') as f:
cores = json.load(f)
with open(property_dir + global_property_file, 'r') as f:
global_props = json.load(f)
dgr = global_props['dust2gas_ratio']['value']
dgr = 1.2e-1
cores = convert_core_coordinates(cores, h)
cores = load_ds9_region(cores,
filename_base=region_dir + 'california_av_boxes_',
header=h)
if core_likelihoodelation:
for core in cores:
print('\nCalculating for core %s' % core)
# Grab the mask
mask = myg.get_polygon_mask(av_data_planck,
cores[core]['box_vertices_rotated'])
indices = ((mask == 0) &\
(av_data_planck < av_threshold))
hi_data_sub = np.copy(hi_data[:, indices])
noise_cube_sub = np.copy(noise_cube[:, indices])
av_data_sub = np.copy(av_data_planck[indices])
av_error_data_sub = np.copy(av_error_data_planck[indices])
# Define filename for plotting results
results_filename = figure_dir + 'california_logL_%s.png' % core
# likelihoodelate each core region Av and N(HI) for velocity ranges
vel_range_confint, dgr_confint, likelihoods, center_likelihood,\
width_likelihood, dgr_likelihood = \
calc_likelihood_hi_av(hi_cube=hi_data_sub,
hi_velocity_axis=velocity_axis,
hi_noise_cube=noise_cube_sub,
av_image=av_data_sub,
av_image_error=av_error_data_sub,
dgrs=dgrs,
velocity_centers=velocity_centers,
velocity_widths=velocity_widths,
return_likelihoods=True,
plot_results=True,
results_filename=results_filename,
likelihood_filename=likelihood_dir + \
likelihood_filename + \
'{0:s}.fits'.format(core),
clobber=clobber,
conf=conf)
print('HI velocity integration range:')
print('%.1f to %.1f km/s' %
(vel_range_confint[0], vel_range_confint[1]))
print('DGR:')
print('%.1f to %.1f km/s' %
(vel_range_confint[0], vel_range_confint[1]))
cores[core]['hi_velocity_range'] = vel_range_confint[0:2]
cores[core]['hi_velocity_range_error'] = vel_range_confint[2:]
cores[core]['center_likelihood'] = center_likelihood.tolist()
cores[core]['width_likelihood'] = width_likelihood.tolist()
cores[core]['vel_centers'] = velocity_centers.tolist()
cores[core]['vel_widths'] = velocity_widths.tolist()
with open(core_dir + core_property_file, 'w') as f:
json.dump(cores, f)
if global_likelihoodelation:
print('\nCalculating likelihoods globally')
mask = np.zeros(av_data_planck.shape)
for core in cores:
# Grab the mask
mask += myg.get_polygon_mask(av_data_planck,
cores[core]['box_vertices_rotated'])
indices = ((mask == 0) &\
(av_data_planck < av_threshold))
#indices = ((av_data_planck < av_threshold))
hi_data_sub = np.copy(hi_data[:, indices])
noise_cube_sub = np.copy(noise_cube[:, indices])
av_data_sub = np.copy(av_data_planck[indices])
av_error_data_sub = np.copy(av_error_data_planck[indices])
# Define filename for plotting results
results_filename = figure_dir + results_filename
# likelihoodelate each core region Av and N(HI) for velocity ranges
vel_range_confint, dgr_confint, likelihoods, center_likelihood,\
width_likelihood, dgr_likelihood = \
calc_likelihood_hi_av(hi_cube=hi_data_sub,
hi_velocity_axis=velocity_axis,
hi_noise_cube=noise_cube_sub,
av_image=av_data_sub,
av_image_error=av_error_data_sub,
dgrs=dgrs,
velocity_centers=velocity_centers,
velocity_widths=velocity_widths,
return_likelihoods=True,
plot_results=True,
results_filename=results_filename,
likelihood_filename=likelihood_dir + \
likelihood_filename + \
'_global.fits',
clobber=clobber,
conf=conf,
contour_confs=contour_confs)
print('HI velocity integration range:')
print('%.1f to %.1f km/s' %
(vel_range_confint[0], vel_range_confint[1]))
print('DGR:')
print('%.1f to %.1f km/s' % (dgr_confint[0], dgr_confint[1]))
global_props['dust2gas_ratio'] = {}
global_props['dust2gas_ratio_error'] = {}
global_props['hi_velocity_range'] = vel_range_confint[0:2]
global_props['hi_velocity_range_error'] = vel_range_confint[2:]
global_props['dust2gas_ratio']['value'] = dgr_confint[0]
global_props['dust2gas_ratio_error']['value'] = dgr_confint[1:]
global_props['hi_velocity_range_conf'] = conf
global_props['center_likelihood'] = center_likelihood.tolist()
global_props['width_likelihood'] = width_likelihood.tolist()
global_props['dgr_likelihood'] = dgr_likelihood.tolist()
global_props['vel_centers'] = velocity_centers.tolist()
global_props['vel_widths'] = velocity_widths.tolist()
global_props['dgrs'] = dgrs.tolist()
global_props['likelihoods'] = likelihoods.tolist()
with open(property_dir + global_property_file, 'w') as f:
json.dump(global_props, f)
def main(dgr=None,
vel_range=None,
vel_range_type='single',
region=None,
av_data_type='planck'):
''' Executes script.
Parameters
----------
dgr : float
If None, pulls best-fit value from properties.
vel_range : tuple
If None, pulls best-fit value from properties.
'''
# import external modules
#import pyfits as fits
from astropy.io import fits
import numpy as np
from mycoords import make_velocity_axis
import mygeometry as myg
from myimage_analysis import calculate_nhi, calculate_noise_cube, \
calculate_sd, calculate_nh2, calculate_nh2_error
import json
from os import system, path
# Script parameters
# -----------------
# Name of noise cube
noise_cube_filename = 'multicloud_hi_galfa_cube_regrid_planckres_noise.fits'
# Use Planck dust Av map or Kainulainen 2009 optical extinction Av map?
# options are 'planck' or 'lee12'
#av_data_type = 'lee12'
#av_data_type = 'planck'
# Global parameter file
prop_file = 'multicloud_global_properties'
# Regions, regions to edit the global properties with
if region == 1:
region_limit = {
'wcs': (((5, 10, 0), (19, 0, 0)), ((4, 30, 0), (27, 0, 0))),
'pixel': ()
}
elif region == 2:
region_limit = {
'wcs': (((4, 30, 0), (19, 0, 0)), ((3, 50, 0), (29, 0, 0))),
'pixel': ()
}
elif region == 3:
region_limit = {
'wcs': (((4, 30, 0), (29, 0, 0)), ((3, 50, 0), (33, 0, 0))),
'pixel': ()
}
else:
region_limit = None
# define directory locations
# --------------------------
output_dir = '/d/bip3/ezbc/multicloud/data/python_output/nhi_av/'
figure_dir = '/d/bip3/ezbc/multicloud/figures/'
av_dir = '/d/bip3/ezbc/multicloud/data/av/'
hi_dir = '/d/bip3/ezbc/multicloud/data/hi/'
co_dir = '/d/bip3/ezbc/multicloud/data/co/'
core_dir = '/d/bip3/ezbc/multicloud/data/python_output/core_properties/'
property_dir = '/d/bip3/ezbc/multicloud/data/python_output/'
region_dir = '/d/bip3/ezbc/multicloud/data/python_output/regions/'
# load Planck Av and GALFA HI images, on same grid
if av_data_type == 'lee12_2mass':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_lee12_2mass_regrid_planckres.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'lee12_iris':
print('\nLoading Lee+12 data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_lee12_iris_regrid_planckres.fits',
return_header=True)
av_image_error = 0.1 * np.ones(av_image.shape)
elif av_data_type == 'planck_rad':
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_planck_tau353_5arcmin.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'multicloud_av_error_planck_tau353_5arcmin.fits',
return_header=True)
else:
print('\nLoading Planck data...')
av_image, av_header = load_fits(av_dir + \
'multicloud_av_planck_tau353_5arcmin.fits',
return_header=True)
av_image_error, av_error_header = load_fits(av_dir + \
'multicloud_av_error_planck_tau353_5arcmin.fits',
return_header=True)
hi_cube, hi_header = load_fits(hi_dir + \
'multicloud_hi_galfa_cube_regrid_planckres.fits',
return_header=True)
co_data, co_header = load_fits(co_dir + \
'multicloud_co_cfa_cube_regrid_planckres.fits',
return_header=True)
# Prepare data products
# ---------------------
# Load global properties of cloud
# global properties written from script
# 'av/multicloud_analysis_global_properties.txt'
if region is not None:
likelihood_filename += '_region{0:.0f}'.format(region)
results_filename += '_region{0:.0f}'.format(region)
with open(property_dir + prop_file + '.txt', 'r') as f:
props = json.load(f)
if vel_range is not None:
props['hi_velocity_range'] = vel_range
else:
vel_range = props['hi_velocity_range']
# make velocity axis for hi cube
velocity_axis = make_velocity_axis(hi_header)
# make velocity axis for co cube
co_velocity_axis = make_velocity_axis(co_header)
# Load the HI noise cube if it exists, else make it
if not path.isfile(hi_dir + noise_cube_filename):
hi_noise_cube = calculate_noise_cube(cube=hi_cube,
velocity_axis=velocity_axis,
velocity_noise_range=[90, 110],
header=hi_header,
Tsys=30.,
filename=hi_dir +
noise_cube_filename)
else:
hi_noise_cube, noise_header = fits.getdata(hi_dir +
noise_cube_filename,
header=True)
# create nhi image
nhi_image = calculate_nhi(cube=hi_cube,
velocity_axis=velocity_axis,
velocity_range=vel_range,
header=hi_header,
noise_cube=hi_noise_cube)
props['plot_limit']['wcs'] = (((5, 20, 0), (19, 0, 0)), ((2, 30, 0),
(37, 0, 0)))
props['region_name_pos'] = {
#'taurus 1' : {'wcs' : ((3, 50, 0),
# (21.5, 0, 0)),
# },
#'taurus 2' : {'wcs' : ((5, 10, 0),
# (21.5, 0, 0)),
# },
'taurus': {
'wcs': ((4, 40, 0), (21, 0, 0)),
},
'perseus': {
'wcs': ((3, 30, 0), (26, 0, 0)),
},
#'perseus 1' : {'wcs' : ((3, 0, 0),
# (34, 0, 0)),
# },
#'perseus 2' : {'wcs' : ((3, 10, 0),
# (22.5, 0, 0)),
# },
'california': {
'wcs': ((4, 28, 0), (34, 0, 0)),
},
}
# Change WCS coords to pixel coords of images
props = convert_limit_coordinates(props,
header=av_header,
coords=('region_limit',
'co_noise_limits', 'plot_limit',
'region_name_pos'))
props['plot_limit']['wcs'] = [
15 * (5 + 20. / 60), 15 * (2 + 30. / 60.), 17, 38.5
]
# Load cloud division regions from ds9
props = load_ds9_region(props,
filename=region_dir + 'multicloud_divisions.reg',
header=av_header)
# Derive relevant region
pix = props['region_limit']['pixel']
region_vertices = ((pix[1], pix[0]), (pix[1], pix[2]), (pix[3], pix[2]),
(pix[3], pix[0]))
# block offregion
region_mask = myg.get_polygon_mask(av_image, region_vertices)
print('\nRegion size = ' + \
'{0:.0f} pix'.format(region_mask[region_mask == 1].size))
if vel_range_type == 'single':
print('\nHI velocity integration range:')
print('%.1f to %.1f km/s' % (vel_range[0], vel_range[1]))
elif vel_range_type == 'multiple':
print('\nHI velocity integration ranges:')
for i in xrange(0, vel_range.shape[0]):
print('%.1f to %.1f km/s' % (vel_range[i, 0], vel_range[i, 1]))
# Plot
figure_types = ['png', 'pdf']
for figure_type in figure_types:
if region is None:
if vel_range_type == 'single':
filename = 'multicloud_av_nhi_map' + \
'.%s' % figure_type
#av_data_type + \
#'dgr{0:.3f}_'.format(dgr) + \
#'{0:.1f}to{1:.1f}kms'.format(vel_range[0], vel_range[1]) + \
#'_' + \
elif vel_range_type == 'multiple':
filename = 'multiple_vel_range/multicloud_av_model_map' + \
'dgr{0:.3f}'.format(dgr)
for i in xrange(0, vel_range.shape[0]):
filename += '_{0:.1f}to{1:.1f}kms'.format(
vel_range[i, 0], vel_range[i, 1])
filename += '.%s' % figure_type
else:
filename = 'multicloud_av_model_map_region{0:.0f}'.format(region) + \
'.{0:s}'.format(figure_type)
filename = 'av_map'
filename = figure_dir + 'maps/' + filename + '.' + figure_type
print('\nSaving Av model image to \n' + filename)
plot_av_image(
av_image=av_image,
header=av_header,
limits=[15 * (5 + 20. / 60), 15 * (2 + 30. / 60.), 17, 38.5],
limits_type='wcs',
regions=props['regions'],
props=props,
av_vlimits=(0, 15.5),
filename=filename,
show=False)
if 0:
filename = 'av_nhi_map'
filename = figure_dir + 'maps/' + filename + '.' + figure_type
print('\nSaving NHI + Av maps to \n' + filename)
plot_nhi_image(
nhi_image=nhi_image,
header=av_header,
av_image=av_image,
limits=props['plot_limit']['wcs'],
limits_type='wcs',
regions=props['regions'],
props=props,
hi_vlimits=(0, 20),
av_vlimits=(0, 15.5),
#av_vlimits=(0.1,30),
filename=filename,
show=False)
