def extract_data(catalogue, image_filename):
""" Gets the RHT angle average from the pixels in the square around each star. Also gets the star's polarisation angle and error, aswell as its distance and error. """
# Star polarisation angle, polarisation error and distance
data = pd.read_csv(catalogue)
good_indices = get_indices_of_stars(catalogue, image_filename)
pol_angle = data['pa'][good_indices]
err_pol_angle = data['e_pa'][good_indices]
dist = data['r_est'][good_indices]
dist_err_low = data['r_lo'][good_indices]
dist_err_high = data['r_hi'][good_indices]
# NOTE: angles from squares not implemented yet.
# XX, YY = draw_squares(catalogue, image_filename, square_size)
# RHT angle average calculation
ipoints, jpoints, hthets, naxis1, naxis2, wlen, smr, thresh = RHT_tools.get_RHT_data(
image_filename)
h = np.sum(hthets, axis=0)
h_norm = h / np.max(h) # Total intensity per angle found, normalised.
thets_arr = RHT_tools.get_thets(wlen,
save=False) # x-axis containing angles
thets_deg = thets_arr * 180 / np.pi
return pol_angle, err_pol_angle, dist, dist_err_low, dist_err_high, thets_deg, h_norm
def get_all_RHT_data(image_filename):
ipoints, jpoints, hthets, naxis1, naxis2, wlen, smr, thresh = RHT_tools.get_RHT_data(
image_filename)
thets_arr = RHT_tools.get_thets(wlen,
save=False) # x-axis containing angles
thets_deg = thets_arr * 180 / np.pi
return ipoints, jpoints, hthets, naxis1, naxis2, wlen, smr, thresh, thets_deg
def make_polarplot(image_filename):
""" Makes a polarplot of the image_filename. The RHT data is extracted and plotted onto a warped axes from -0.5 to 0.5 pi. This function contains a conversion of the angles hthets to be defined with respect to the RA axis. """
ipoints, jpoints, hthets, naxis1, naxis2, wlen, smr, thresh = RHT_tools.get_RHT_data(
image_filename)
thetas = np.concatenate(hthets)
thetas_norm = thetas / np.max(thetas)
thets_arr = RHT_tools.get_thets(wlen, save=False) / np.pi # Units of pi
# Convert hthets to be defined w.r.t. RA axis
w = WCS(image_filename)
RA_hthets, DEC_hthets = w.all_pix2world(ipoints, jpoints, 0)
header = fits.getheader(image_filename)
rotate_by = (header['CRVAL1'] - RA_hthets) / 180 # Units of pi
big_thets_arr_list = []
for index, value in enumerate(rotate_by):
big_thets_arr_list.append((thets_arr + rotate_by[index]) % 1)
big_thets_arr_list = np.concatenate(big_thets_arr_list)
# Convert [0, pi] to [-0.5pi, 0,5pi] as in Jelic et al. 2018
indices_to_shift = np.where(big_thets_arr_list > 0.5)
big_thets_arr_list[indices_to_shift] -= 1
# Plotting
# If you want fill-between, they need to be in order... this does that.
xdata = big_thets_arr_list * np.pi # Convert back to good units
ydata = thetas_norm[np.argsort(xdata)]
xdata = np.sort(xdata)
fig = plt.figure(figsize=(18, 9))
ax1, aux_ax1 = setup_axes(fig,
111,
theta=[-0.5 * np.pi, 0.5 * np.pi],
radius=[0, ydata.max() * 1.05])
aux_ax1.plot(xdata, ydata, alpha=0.75)
# aux_ax1.fill_between(xdata, y1=ydata, y2=0, facecolor='blue', interpolate=True, alpha=0.10)
# plt.axhline(np.max(ydata), color='red', alpha=0.75)
plt.savefig('polarplot_' + os.path.basename(image_filename).split('.')[0] +
'.png',
dpi=600,
bbox_inches='tight')
plt.show()
def bin_data_by_theta(data_fn, nbins=10):
"""
Places RHT data into cube binned by theta.
Input:
data_fn :: fits filename for RHT data
nbins :: number of theta bins to separate RHT data into (default = 10)
Output:
theta_separated_backprojection :: 3D array, dimensions (naxis1, naxis2, nbins).
:: contains backprojection summed into nbins chunks.
"""
# Separate into indices and R(theta) arrays
ipoints, jpoints, rthetas, naxis1, naxis2 = RHT_tools.get_RHT_data(data_fn)
npoints, nthetas = rthetas.shape
print("There are %d theta bins" % nthetas)
cube_thetas = np.zeros((naxis2, naxis1, nthetas), np.float_)
cube_thetas[jpoints, ipoints, :] = rthetas
theta_separated_backprojection = np.zeros((naxis2, naxis1, nbins),
np.float_)
for i in xrange(nbins):
theta_separated_backprojection[:, :, i] = np.sum(
cube_thetas[:, :, i * nbins:(i + 1) * nbins], axis=2)
return theta_separated_backprojection
def get_RHT_data(rht_fn, verbose=False):
ipoints, jpoints, rthetas, naxis1, naxis2 = RHT_tools.get_RHT_data(rht_fn)
npoints, nthetas = rthetas.shape
if verbose:
print("There are %d theta bins" % nthetas)
return ipoints, jpoints, rthetas, naxis1, naxis2, nthetas
def bin_data_by_theta(data_fn, nbins = 10):
"""
Places RHT data into cube binned by theta.
Input:
data_fn :: fits filename for RHT data
nbins :: number of theta bins to separate RHT data into (default = 10)
Output:
theta_separated_backprojection :: 3D array, dimensions (naxis1, naxis2, nbins).
:: contains backprojection summed into nbins chunks.
"""
# Separate into indices and R(theta) arrays
ipoints, jpoints, rthetas, naxis1, naxis2 = RHT_tools.get_RHT_data(data_fn)
npoints, nthetas = rthetas.shape
print("There are %d theta bins" %nthetas)
cube_thetas = np.zeros((naxis2, naxis1, nthetas), np.float_)
cube_thetas[jpoints, ipoints, :] = rthetas
theta_separated_backprojection = np.zeros((naxis2, naxis1, nbins), np.float_)
for i in xrange(nbins):
theta_separated_backprojection[:, :, i] = np.sum(cube_thetas[:, :, i*nbins:(i+1)*nbins], axis=2)
return theta_separated_backprojection
def get_psi0_sampling_grid(self, hp_index, verbose = True):
# Create psi0 sampling grid
wlen = 75
psi0_sample_db = sqlite3.connect("theta_bin_0_wlen"+str(wlen)+"_db.sqlite")
psi0_sample_cursor = psi0_sample_db.cursor()
zero_theta = psi0_sample_cursor.execute("SELECT zerotheta FROM theta_bin_0_wlen75 WHERE id = ?", (hp_index,)).fetchone()
# Create array of projected thetas from theta = 0
thets = RHT_tools.get_thets(wlen, save = False, verbose = verbose)
self.sample_psi0 = np.mod(zero_theta - thets, np.pi)
return self.sample_psi0
def plot_sims_and_rht():
"""
plot density and RHT backprojection for a single beta at three timestamps
"""
fig, xarr = plt.subplots(2, 3, figsize=(10,7))
alltimes = ["0010", "0030", "0050"]
beta = "20"
for i, tstamp in enumerate(alltimes):
# get relevant simulation and RHT data
fn_rht = get_data_fn("z", 512, beta, tstamp, rhtparams=[25, 1, 0.7], type="density")
fn_dens = get_data_fn("z", 512, beta, tstamp, rhtparams=None, type="density")
fn_Qsim = get_data_fn("z", 512, beta, tstamp, rhtparams=None, type="Q")
fn_Usim = get_data_fn("z", 512, beta, tstamp, rhtparams=None, type="U")
rht_im = fits.getdata(fn_rht)
dens_im = fits.getdata(fn_dens)
Qsim = fits.getdata(fn_Qsim)
Usim = fits.getdata(fn_Usim)
ysize, xsize = rht_im.shape
X, Y = np.meshgrid(np.arange(xsize), np.arange(ysize), indexing='ij')
# plot density and backprojection fields
xarr[0, i].pcolor(Y, X, np.log10(dens_im))
xarr[1, i].pcolor(Y, X, rht_im)
# overplot pseudovectors from Bsim and theta_RHT
overplot_vectors(Qsim, Usim, ax=xarr[0, i], norm=True, intrht=False, skipint=25)
QRHT, URHT, URHTsq, QRHTsq, intrht = RHT_tools.grid_QU_RHT(fn_rht, save=False)
overplot_vectors(QRHT, URHT, ax=xarr[1, i], norm=True, intrht=False, skipint=25)
# title from timestamp
xarr[0, i].set_title(r"$t = {}$".format(tstamp))
plt.suptitle(r"z, 512, $\beta$ = {}".format(beta))
xarr[0, 0].set_ylabel("log(density), $B_{sim}$ $\mathrm{overlaid}$")
xarr[1, 0].set_ylabel(r"$\int R(\theta)$, $\theta_{RHT}$ $\mathrm{overlaid}$")
def single_theta_velocity_cube(theta_0=72,
theta_bandwidth=10,
wlen=75,
smooth_radius=60,
gaussian_footprint=True,
gauss_footprint_len=5,
circular_footprint_radius=3,
binary_erode_dilate=True,
hilatonly=True):
"""
Creates cube of Backprojection(x, y, v | theta_0)
where dimensions are x, y, and velocity
and each velocity slice contains the backprojection for that velocity, at a single theta.
theta_0 :: approximate center theta value (in degrees).
Actual value will be closest bin in xyt data.
theta_bandwidth :: approximate width of theta range desired (in degrees)
wlen :: RHT window length
"""
# Read in all SC_241 *original* data
SC_241_original_fn = "/Volumes/DataDavy/GALFA/SC_241/cleaned/SC_241.66_28.675.best.fits"
SC_241_all = fits.getdata(SC_241_original_fn)
hdr = fits.getheader(SC_241_original_fn)
# Velocity data should be third axis
SC_241_all = SC_241_all.swapaxes(0, 2)
SC_241_all = SC_241_all.swapaxes(0, 1)
naxis2, naxis1, nchannels_total = SC_241_all.shape
# Get Wide DR2 data in SC_241 region
SC_241_wide_fn = "/Volumes/DataDavy/GALFA/DR2/SC_241_Wide/GALFA_HI_W_projected_SC_241.fits"
SC_241_wide = fits.getdata(SC_241_wide_fn)
SC_241_wide_hdr = fits.getheader(SC_241_wide_fn)
# This is pretty slow with the full SC_241 region. I'm going to chop off the 3000 pixels at the lowest latitude.
# Change header accordingly.
if hilatonly is True:
SC_241_all = SC_241_all[:, 3000:, :]
SC_241_wide = SC_241_wide[:, :, 3000:]
hdr["CRPIX1"] = hdr["CRPIX1"] - 3000
hdr["NAXIS1"] = hdr["NAXIS1"] - 3000
naxis1 = naxis1 - 3000
# Get thetas for given window length
thets = RHT_tools.get_thets(wlen)
# Get wide and mask velocities for application of mask to final data
wide_vels = get_velocity_from_fits(SC_241_wide_fn)
mask_vels = get_velocity_from_fits(SC_241_original_fn)
# Get index of theta bin that is closest to theta_0
indx_0 = (np.abs(thets - np.radians(theta_0))).argmin()
# Get index of beginning and ending thetas that are approximately theta_bandwidth centered on theta_0
indx_start = (
np.abs(thets -
(thets[indx_0] - np.radians(theta_bandwidth / 2.0)))).argmin()
indx_stop = (
np.abs(thets -
(thets[indx_0] + np.radians(theta_bandwidth / 2.0)))).argmin()
print("Actual theta range will be {} to {} degrees".format(
np.degrees(thets[indx_start]), np.degrees(thets[indx_stop])))
print("Theta indices will be {} to {}".format(indx_start, indx_stop))
# Define velocity channels
channels = [16, 17, 18, 19, 20, 21, 22, 23, 24]
nchannels = len(channels)
# Create a circular footprint for use in erosion / dilation.
if gaussian_footprint is True:
footprint = make_gaussian_footprint(theta_0=theta_0,
wlen=gauss_footprint_len)
# Mathematical definition of kernel flips y-axis
footprint = footprint[::-1, :]
else:
footprint = make_circular_footprint(radius=circular_footprint_radius)
# Initialize (x, y, v) cube
xyv_theta0 = np.zeros((naxis2, naxis1, len(channels) * 4), np.float_)
for ch_i, ch_ in enumerate(channels):
# Grab channel-specific RHT data
data, data_fn = get_data(ch_, verbose=False)
ipoints, jpoints, rthetas, naxis1, naxis2 = RHT_tools.get_RHT_data(
data_fn)
# Sum relevant thetas
thetasum_bp = np.zeros((naxis2, naxis1), np.float_)
thetasum_bp[jpoints,
ipoints] = np.nansum(rthetas[:,
indx_start:(indx_stop + 1)],
axis=1)
if hilatonly is True:
thetasum_bp = thetasum_bp[:, 3000:]
if binary_erode_dilate is False:
# Erode and dilate
eroded_thetasum_bp = erode_data(thetasum_bp,
footprint=footprint,
structure=footprint)
dilated_thetasum_bp = dilate_data(eroded_thetasum_bp,
footprint=footprint,
structure=footprint)
# Turn into mask
mask = np.ones(dilated_thetasum_bp.shape)
mask[dilated_thetasum_bp <= 0] = 0
else:
# Try making this a mask first, then binary erosion/dilation
masked_thetasum_bp = np.ones(thetasum_bp.shape)
masked_thetasum_bp[thetasum_bp <= 0] = 0
mask = binary_erosion(masked_thetasum_bp, structure=footprint)
mask = binary_dilation(mask, structure=footprint)
# Apply background subtraction to velocity slice.
#background_subtracted_data = background_subtract(mask, SC_241_all[:, :, ch_], smooth_radius = smooth_radius, plotresults = False)
# Get appropriate velocity slices for background subtraction
closestvels = closest_velocities(wide_vels, mask_vels[ch_])
# These need to monotonically ascend
closestvels = np.sort(closestvels)
# Apply background subtraction to velocity slice.
for cv_i, cv in enumerate(closestvels):
time0 = time.time()
wv_indx = list(wide_vels).index(cv)
background_subtracted_data = background_subtract(
mask,
SC_241_wide[wv_indx, :, :],
smooth_radius=smooth_radius,
plotresults=False)
# Place into channel bin
xyv_theta0[:, :, ch_i * 4 + cv_i] = background_subtracted_data
print("placing into bin {}".format(ch_i * 4 + cv_i))
time1 = time.time()
print("slice {} took {} seconds".format(cv_i, time1 - time0))
hdr["NAXIS3"] = len(channels) * 4
hdr["THETA0"] = theta_0
hdr["THETAB"] = theta_bandwidth
hdr["CRVAL3"] = np.nanmin(
closest_velocities(wide_vels,
mask_vels[channels[0]])) * 1000 # Convert to m/s
hdr["CDELT3"] = SC_241_wide_hdr["CDELT3"]
# Deal with python fits axis ordering
xyv_theta0 = xyv_theta0.swapaxes(0, 2)
xyv_theta0 = xyv_theta0.swapaxes(1, 2)
fits.writeto(
"xyv_theta0_" + str(theta_0) + "_thetabandwidth_" +
str(theta_bandwidth) + "_ch" + str(channels[0]) + "_to_" +
str(channels[-1]) + "_DR2_W_hilat.fits", xyv_theta0, hdr)
return xyv_theta0, hdr, mask
def test_different_erosion_dilations(wlen=75, theta_0=72, theta_bandwidth=10):
# Get thetas for given window length
thets = RHT_tools.get_thets(wlen)
# Get index of theta bin that is closest to theta_0
indx_0 = (np.abs(thets - np.radians(theta_0))).argmin()
# Get index of beginning and ending thetas that are approximately theta_bandwidth centered on theta_0
indx_start = (
np.abs(thets -
(thets[indx_0] - np.radians(theta_bandwidth / 2.0)))).argmin()
indx_stop = (
np.abs(thets -
(thets[indx_0] + np.radians(theta_bandwidth / 2.0)))).argmin()
data, data_fn = get_data(20, verbose=False)
ipoints, jpoints, rthetas, naxis1, naxis2 = RHT_tools.get_RHT_data(data_fn)
# Sum relevant thetas
thetasum_bp = np.zeros((naxis2, naxis1), np.float_)
thetasum_bp[jpoints,
ipoints] = np.nansum(rthetas[:, indx_start:(indx_stop + 1)],
axis=1)
# Only look at subset
thetasum_bp = thetasum_bp[:, 4000:]
# Try making this a mask first, then binary erosion/dilation
masked_thetasum_bp = np.ones(thetasum_bp.shape)
masked_thetasum_bp[thetasum_bp <= 0] = 0
gauss_footprint_len = 5
circ_footprint_rad = 2
footprint = make_gaussian_footprint(theta_0=-theta_0,
wlen=gauss_footprint_len)
circular_footprint = make_circular_footprint(radius=circ_footprint_rad)
# circular binary erosion then gaussian binary dilation
cbe_then_gbd = binary_erosion(masked_thetasum_bp,
structure=circular_footprint)
cbe_then_gbd = binary_dilation(cbe_then_gbd, structure=footprint)
# gaussian binary dilation then circular binary erosion
gbd_then_cbe = binary_dilation(masked_thetasum_bp, structure=footprint)
gbd_then_cbe = binary_erosion(gbd_then_cbe, structure=circular_footprint)
# circular binary erosion then circular binary dilation
cbe_then_cbd = binary_dilation(masked_thetasum_bp,
structure=circular_footprint)
cbe_then_cbd = binary_erosion(cbe_then_cbd, structure=circular_footprint)
# circular binary dilation then circular binary erosion
cbd_then_cbe = binary_erosion(masked_thetasum_bp,
structure=circular_footprint)
cbd_then_cbe = binary_dilation(cbd_then_cbe, structure=circular_footprint)
# gaussian binary dilation then gaussian binary erosion
gbd_then_gbe = binary_dilation(masked_thetasum_bp, structure=footprint)
gbd_then_gbe = binary_erosion(gbd_then_gbe, structure=footprint)
# gaussian binary erosion then gaussian binary dilation
gbe_then_gbd = binary_erosion(masked_thetasum_bp, structure=footprint)
gbe_then_gbd = binary_dilation(gbe_then_gbd, structure=footprint)
fig = plt.figure(facecolor="white")
ax1 = fig.add_subplot(231)
ax2 = fig.add_subplot(232)
ax3 = fig.add_subplot(233)
ax4 = fig.add_subplot(234)
ax5 = fig.add_subplot(235)
ax6 = fig.add_subplot(236)
ims = [
cbe_then_gbd, gbd_then_cbe, cbe_then_cbd, cbd_then_cbe, gbd_then_gbe,
gbe_then_gbd
]
axs = [ax1, ax2, ax3, ax4, ax5, ax6]
titles = [
"Circ Erosion, Gauss Dilation", "Gauss Dilation, Circ Erosion",
"Circ Erosion, Circ Dilation", "Circ Dilation, Circ Erosion",
"Gauss Dilation, Gauss Erosion", "Gauss Erosion, Gauss Dilation"
]
plt.suptitle(
"Binary Erosion and Dilation, Circular radius = {}, Gaussian Kernel Length = {}"
.format(circ_footprint_rad, gauss_footprint_len))
for i in xrange(len(ims)):
axs[i].imshow(ims[i], cmap="binary")
axs[i].set_title(titles[i])
def get_RHT_data(rht_fn):
ipoints, jpoints, rthetas, naxis1, naxis2 = RHT_tools.get_RHT_data(rht_fn)
npoints, nthetas = rthetas.shape
print("There are %d theta bins" % nthetas)
return ipoints, jpoints, rthetas, naxis1, naxis2, nthetas
def single_theta_velocity_cube(theta_0 = 72, theta_bandwidth = 10, wlen = 75, smooth_radius = 60, gaussian_footprint = True, gauss_footprint_len = 5, circular_footprint_radius = 3, binary_erode_dilate = True, hilatonly = True):
"""
Creates cube of Backprojection(x, y, v | theta_0)
where dimensions are x, y, and velocity
and each velocity slice contains the backprojection for that velocity, at a single theta.
theta_0 :: approximate center theta value (in degrees).
Actual value will be closest bin in xyt data.
theta_bandwidth :: approximate width of theta range desired (in degrees)
wlen :: RHT window length
"""
# Read in all SC_241 *original* data
SC_241_original_fn = "/Volumes/DataDavy/GALFA/SC_241/cleaned/SC_241.66_28.675.best.fits"
SC_241_all = fits.getdata(SC_241_original_fn)
hdr = fits.getheader(SC_241_original_fn)
# Velocity data should be third axis
SC_241_all = SC_241_all.swapaxes(0, 2)
SC_241_all = SC_241_all.swapaxes(0, 1)
naxis2, naxis1, nchannels_total = SC_241_all.shape
# Get Wide DR2 data in SC_241 region
SC_241_wide_fn = "/Volumes/DataDavy/GALFA/DR2/SC_241_Wide/GALFA_HI_W_projected_SC_241.fits"
SC_241_wide = fits.getdata(SC_241_wide_fn)
SC_241_wide_hdr = fits.getheader(SC_241_wide_fn)
# This is pretty slow with the full SC_241 region. I'm going to chop off the 3000 pixels at the lowest latitude.
# Change header accordingly.
if hilatonly is True:
SC_241_all = SC_241_all[:, 3000:, :]
SC_241_wide = SC_241_wide[:, :, 3000:]
hdr["CRPIX1"] = hdr["CRPIX1"] - 3000
hdr["NAXIS1"] = hdr["NAXIS1"] - 3000
naxis1 = naxis1 - 3000
# Get thetas for given window length
thets = RHT_tools.get_thets(wlen)
# Get wide and mask velocities for application of mask to final data
wide_vels = get_velocity_from_fits(SC_241_wide_fn)
mask_vels = get_velocity_from_fits(SC_241_original_fn)
# Get index of theta bin that is closest to theta_0
indx_0 = (np.abs(thets - np.radians(theta_0))).argmin()
# Get index of beginning and ending thetas that are approximately theta_bandwidth centered on theta_0
indx_start = (np.abs(thets - (thets[indx_0] - np.radians(theta_bandwidth/2.0)))).argmin()
indx_stop = (np.abs(thets - (thets[indx_0] + np.radians(theta_bandwidth/2.0)))).argmin()
print("Actual theta range will be {} to {} degrees".format(np.degrees(thets[indx_start]), np.degrees(thets[indx_stop])))
print("Theta indices will be {} to {}".format(indx_start, indx_stop))
# Define velocity channels
channels = [16, 17, 18, 19, 20, 21, 22, 23, 24]
nchannels = len(channels)
# Create a circular footprint for use in erosion / dilation.
if gaussian_footprint is True:
footprint = make_gaussian_footprint(theta_0 = theta_0, wlen = gauss_footprint_len)
# Mathematical definition of kernel flips y-axis
footprint = footprint[::-1, :]
else:
footprint = make_circular_footprint(radius = circular_footprint_radius)
# Initialize (x, y, v) cube
xyv_theta0 = np.zeros((naxis2, naxis1, len(channels)*4), np.float_)
for ch_i, ch_ in enumerate(channels):
# Grab channel-specific RHT data
data, data_fn = get_data(ch_, verbose = False)
ipoints, jpoints, rthetas, naxis1, naxis2 = RHT_tools.get_RHT_data(data_fn)
# Sum relevant thetas
thetasum_bp = np.zeros((naxis2, naxis1), np.float_)
thetasum_bp[jpoints, ipoints] = np.nansum(rthetas[:, indx_start:(indx_stop + 1)], axis = 1)
if hilatonly is True:
thetasum_bp = thetasum_bp[:, 3000:]
if binary_erode_dilate is False:
# Erode and dilate
eroded_thetasum_bp = erode_data(thetasum_bp, footprint = footprint, structure = footprint)
dilated_thetasum_bp = dilate_data(eroded_thetasum_bp, footprint = footprint, structure = footprint)
# Turn into mask
mask = np.ones(dilated_thetasum_bp.shape)
mask[dilated_thetasum_bp <= 0] = 0
else:
# Try making this a mask first, then binary erosion/dilation
masked_thetasum_bp = np.ones(thetasum_bp.shape)
masked_thetasum_bp[thetasum_bp <= 0] = 0
mask = binary_erosion(masked_thetasum_bp, structure = footprint)
mask = binary_dilation(mask, structure = footprint)
# Apply background subtraction to velocity slice.
#background_subtracted_data = background_subtract(mask, SC_241_all[:, :, ch_], smooth_radius = smooth_radius, plotresults = False)
# Get appropriate velocity slices for background subtraction
closestvels = closest_velocities(wide_vels, mask_vels[ch_])
# These need to monotonically ascend
closestvels = np.sort(closestvels)
# Apply background subtraction to velocity slice.
for cv_i, cv in enumerate(closestvels):
time0 = time.time()
wv_indx = list(wide_vels).index(cv)
background_subtracted_data = background_subtract(mask, SC_241_wide[wv_indx, :, :], smooth_radius = smooth_radius, plotresults = False)
# Place into channel bin
xyv_theta0[:, :, ch_i*4 + cv_i] = background_subtracted_data
print("placing into bin {}".format(ch_i*4 + cv_i))
time1 = time.time()
print("slice {} took {} seconds".format(cv_i, time1 - time0))
hdr["NAXIS3"] = len(channels)*4
hdr["THETA0"] = theta_0
hdr["THETAB"] = theta_bandwidth
hdr["CRVAL3"] = np.nanmin(closest_velocities(wide_vels, mask_vels[channels[0]]))*1000 # Convert to m/s
hdr["CDELT3"] = SC_241_wide_hdr["CDELT3"]
# Deal with python fits axis ordering
xyv_theta0 = xyv_theta0.swapaxes(0, 2)
xyv_theta0 = xyv_theta0.swapaxes(1, 2)
fits.writeto("xyv_theta0_"+str(theta_0)+"_thetabandwidth_"+str(theta_bandwidth)+"_ch"+str(channels[0])+"_to_"+str(channels[-1])+"_DR2_W_hilat.fits", xyv_theta0, hdr)
return xyv_theta0, hdr, mask
def test_different_erosion_dilations(wlen = 75, theta_0 = 72, theta_bandwidth = 10):
# Get thetas for given window length
thets = RHT_tools.get_thets(wlen)
# Get index of theta bin that is closest to theta_0
indx_0 = (np.abs(thets - np.radians(theta_0))).argmin()
# Get index of beginning and ending thetas that are approximately theta_bandwidth centered on theta_0
indx_start = (np.abs(thets - (thets[indx_0] - np.radians(theta_bandwidth/2.0)))).argmin()
indx_stop = (np.abs(thets - (thets[indx_0] + np.radians(theta_bandwidth/2.0)))).argmin()
data, data_fn = get_data(20, verbose = False)
ipoints, jpoints, rthetas, naxis1, naxis2 = RHT_tools.get_RHT_data(data_fn)
# Sum relevant thetas
thetasum_bp = np.zeros((naxis2, naxis1), np.float_)
thetasum_bp[jpoints, ipoints] = np.nansum(rthetas[:, indx_start:(indx_stop + 1)], axis = 1)
# Only look at subset
thetasum_bp = thetasum_bp[:, 4000:]
# Try making this a mask first, then binary erosion/dilation
masked_thetasum_bp = np.ones(thetasum_bp.shape)
masked_thetasum_bp[thetasum_bp <= 0] = 0
gauss_footprint_len = 5
circ_footprint_rad = 2
footprint = make_gaussian_footprint(theta_0 = -theta_0, wlen = gauss_footprint_len)
circular_footprint = make_circular_footprint(radius = circ_footprint_rad)
# circular binary erosion then gaussian binary dilation
cbe_then_gbd = binary_erosion(masked_thetasum_bp, structure = circular_footprint)
cbe_then_gbd = binary_dilation(cbe_then_gbd, structure = footprint)
# gaussian binary dilation then circular binary erosion
gbd_then_cbe = binary_dilation(masked_thetasum_bp, structure = footprint)
gbd_then_cbe = binary_erosion(gbd_then_cbe, structure = circular_footprint)
# circular binary erosion then circular binary dilation
cbe_then_cbd = binary_dilation(masked_thetasum_bp, structure = circular_footprint)
cbe_then_cbd = binary_erosion(cbe_then_cbd, structure = circular_footprint)
# circular binary dilation then circular binary erosion
cbd_then_cbe = binary_erosion(masked_thetasum_bp, structure = circular_footprint)
cbd_then_cbe = binary_dilation(cbd_then_cbe, structure = circular_footprint)
# gaussian binary dilation then gaussian binary erosion
gbd_then_gbe = binary_dilation(masked_thetasum_bp, structure = footprint)
gbd_then_gbe = binary_erosion(gbd_then_gbe, structure = footprint)
# gaussian binary erosion then gaussian binary dilation
gbe_then_gbd = binary_erosion(masked_thetasum_bp, structure = footprint)
gbe_then_gbd = binary_dilation(gbe_then_gbd, structure = footprint)
fig = plt.figure(facecolor = "white")
ax1 = fig.add_subplot(231)
ax2 = fig.add_subplot(232)
ax3 = fig.add_subplot(233)
ax4 = fig.add_subplot(234)
ax5 = fig.add_subplot(235)
ax6 = fig.add_subplot(236)
ims = [cbe_then_gbd, gbd_then_cbe, cbe_then_cbd, cbd_then_cbe, gbd_then_gbe, gbe_then_gbd]
axs = [ax1, ax2, ax3, ax4, ax5, ax6]
titles = ["Circ Erosion, Gauss Dilation", "Gauss Dilation, Circ Erosion", "Circ Erosion, Circ Dilation", "Circ Dilation, Circ Erosion", "Gauss Dilation, Gauss Erosion", "Gauss Erosion, Gauss Dilation"]
plt.suptitle("Binary Erosion and Dilation, Circular radius = {}, Gaussian Kernel Length = {}".format(circ_footprint_rad, gauss_footprint_len))
for i in xrange(len(ims)):
axs[i].imshow(ims[i], cmap = "binary")
axs[i].set_title(titles[i])
def single_theta_velocity_cube(theta_0 = 72, theta_bandwidth = 10, wlen = 75, gaussian_footprint = True):
"""
Creates cube of Backprojection(x, y, v | theta_0)
where dimensions are x, y, and velocity
and each velocity slice contains the backprojection for that velocity, at a single theta.
theta_0 :: approximate center theta value (in degrees).
Actual value will be closest bin in xyt data.
theta_bandwidth :: approximate width of theta range desired (in degrees)
wlen :: RHT window length
"""
# Read in all SC_241 *original* data
SC_241_all = fits.getdata("/Volumes/DataDavy/GALFA/SC_241/cleaned/SC_241.66_28.675.best.fits")
hdr = fits.getheader("/Volumes/DataDavy/GALFA/SC_241/cleaned/SC_241.66_28.675.best.fits")
# Velocity data should be third axis
SC_241_all = SC_241_all.swapaxes(0, 2)
SC_241_all = SC_241_all.swapaxes(0, 1)
naxis2, naxis1, nchannels_total = SC_241_all.shape
# Get thetas for given window length
thets = RHT_tools.get_thets(wlen)
# Get index of theta bin that is closest to theta_0
indx_0 = (np.abs(thets - np.radians(theta_0))).argmin()
# Get index of beginning and ending thetas that are approximately theta_bandwidth centered on theta_0
indx_start = (np.abs(thets - (thets[indx_0] - np.radians(theta_bandwidth/2.0)))).argmin()
indx_stop = (np.abs(thets - (thets[indx_0] + np.radians(theta_bandwidth/2.0)))).argmin()
print("Actual theta range will be {} to {} degrees".format(np.degrees(thets[indx_start]), np.degrees(thets[indx_stop])))
print("Theta indices will be {} to {}".format(indx_start, indx_stop))
# Define velocity channels
channels = [20]#[16, 17, 18, 19, 20, 21, 22, 23, 24]
nchannels = len(channels)
# Create a circular footprint for use in erosion / dilation.
if gaussian_footprint is True:
footprint = make_gaussian_footprint(theta_0 = theta_0, wlen = 5)
# Mathematical definition of kernel flips y-axis
footprint = footprint[::-1, :]
else:
footprint = make_circular_footprint(radius = 3)
#circular_footprint = make_circular_footprint(radius = 2)
# Initialize (x, y, v) cube
xyv_theta0 = np.zeros((naxis2, naxis1, nchannels), np.float_)
for ch_i, ch_ in enumerate(channels):
# Grab channel-specific RHT data
data, data_fn = get_data(ch_, verbose = False)
ipoints, jpoints, rthetas, naxis1, naxis2 = RHT_tools.get_RHT_data(data_fn)
# Sum relevant thetas
thetasum_bp = np.zeros((naxis2, naxis1), np.float_)
thetasum_bp[jpoints, ipoints] = np.nansum(rthetas[:, indx_start:(indx_stop + 1)], axis = 1)
# Erode and dilate
# Circular erosion
#eroded_thetasum_bp = erode_data(thetasum_bp, footprint = circular_footprint)
# Gaussian dilation
#dilated_thetasum_bp = dilate_data(eroded_thetasum_bp, footprint = footprint, structure = footprint)
# Turn into mask
#mask = np.ones(dilated_thetasum_bp.shape)
#mask[dilated_thetasum_bp <= 0] = 0
# Try making this a mask first, then binary erosion/dilation
masked_thetasum_bp = np.ones(thetasum_bp.shape)
masked_thetasum_bp[thetasum_bp <= 0] = 0
mask = binary_erosion(masked_thetasum_bp, structure = footprint)
mask = binary_dilation(mask, structure = footprint)
# Apply mask to relevant velocity data
realdata_vel_slice = SC_241_all[:, :, ch_]
realdata_vel_slice[mask == 0] = 0
# Place into channel bin
xyv_theta0[:, :, ch_i] = realdata_vel_slice
#return xyv_theta0
hdr["CHSTART"] = channels[0]
hdr["CHSTOP"] = channels[-1]
hdr["NAXIS3"] = len(channels)
hdr["THETA0"] = theta_0
hdr["THETAB"] = theta_bandwidth
hdr["CRPIX3"] = hdr["CRPIX3"] - channels[0]
# Deal with python fits axis ordering
xyv_theta0 = xyv_theta0.swapaxes(0, 2)
xyv_theta0 = xyv_theta0.swapaxes(1, 2)
#fits.writeto("xyv_theta0_"+str(theta_0)+"_thetabandwidth_"+str(theta_bandwidth)+"_ch"+str(channels[0])+"_to_"+str(channels[-1])+"_new_naxis3.fits", xyv_theta0, hdr)
return xyv_theta0, hdr, mask