def flux_tube_radial_profile(region, minmax_pt, surf, peak_or_pit,
other_arr=None, mask=None):
arr = surf.arr
wdist = wraparound_dist_vec(*arr.shape)
from field_trace import _level_set
if other_arr is None:
other_arr = arr
seed_points = get_seed_points(region, arr, int(np.sqrt(len(region))),
reverse=(peak_or_pit == 'peak'))
radial_profile = []
nx, ny = arr.shape
for seed in seed_points:
seed_flux = arr[seed]
nbr_func = lambda t: _cp.neighbors6(t[0], t[1], nx, ny)
lset = _level_set(arr, level_val=seed_flux,
position=seed, neighbors_func=nbr_func)
lset = lset.intersection(region)
if not lset:
continue
if mask is not None:
mask[lset.xs, lset.ys] = True
lset_arr = other_arr[lset.xs, lset.ys]
lset_mean = lset_arr.mean()
lset_err = lset_arr.std() / np.sqrt(len(lset_arr))
lset_dists = wdist(lset.xs, lset.ys, minmax_pt[0], minmax_pt[1])
dists_mean = lset_dists.mean()
dists_err = lset_dists.std() / np.sqrt(len(lset_dists))
radial_profile.append(
(seed, seed_flux, lset_mean, lset_err, dists_mean, dists_err))
return radial_profile
def expand_region(arr, region, ntimes):
nx, ny = arr.shape
frontier = set()
new_region = set(region)
for pt in region:
nbrs = _cp.neighbors6(pt[0], pt[1], nx, ny)
for nbr in nbrs:
if nbr not in region:
frontier.add(nbr)
new_region.update(frontier)
for _ in range(ntimes-1):
new_frontier = set()
for pt in frontier:
nbrs = _cp.neighbors6(pt[0], pt[1], nx, ny)
for nbr in nbrs:
if nbr not in new_region:
new_frontier.add(nbr)
frontier = new_frontier
new_region.update(frontier)
return new_region
def expand_region_to_radius(arr, region, radius, minmax):
nx, ny = arr.shape
wdist = wraparound_dist_vec(nx, ny)
frontier = set()
new_region = set(region)
for pt in region:
nbrs = _cp.neighbors6(pt[0], pt[1], nx, ny)
for nbr in nbrs:
if nbr not in region and wdist(minmax[0], minmax[1], nbr[0], nbr[1]) <= radius:
frontier.add(nbr)
new_region.add(nbr)
# new_region.update(frontier)
while frontier:
new_frontier = set()
for pt in frontier:
nbrs = _cp.neighbors6(pt[0], pt[1], nx, ny)
for nbr in nbrs:
if nbr not in new_region and wdist(minmax[0], minmax[1], nbr[0], nbr[1]) <= radius:
new_frontier.add(nbr)
frontier = new_frontier
new_region.update(frontier)
return new_region
def flux_tube_radial_spokes(region, minmax_pt, arr, peak_or_pit):
nx, ny = arr.shape
ctr_max = nx+ny
frontier = set()
for pt in region:
for nbr in _cp.neighbors6(pt[0], pt[1], nx, ny):
if nbr not in region:
frontier.add(pt)
spokes = []
for pt in frontier:
cur = pt
spoke = [cur]
if peak_or_pit == 'peak': next = _cp._get_highest_neighbor
elif peak_or_pit == 'pit': next = _cp._get_lowest_neighbor
else: raise ValueError("peak_or_pit not in ('peak', 'pit')")
ctr = ctr_max
while ctr > 0:
cur = next(arr, cur)
spoke.append(cur)
if cur == minmax_pt:
spokes.append(spoke)
break
ctr -= 1
return spokes
def mag_shear_theta_sectors(psi_arr, cur, den, thresh=100, save_basename='field-vs-r'):
hess = hessian(psi_arr)
ntheta = 2
nx, ny = psi_arr.shape
psi_grad_x, psi_grad_y = gradient(psi_arr)
bmag = np.sqrt(psi_grad_x**2 + psi_grad_y**2)
den_x, den_y = gradient(den)
den_grad_mag = np.sqrt(den_x**2 + den_y**2)
# pl.ion()
# pl.figure()
# pl.imshow(bmag, interpolation='nearest', cmap='hot')
surf = _cp.TopoSurface(psi_arr)
regions = surf.get_minmax_regions()
pl.figure(figsize=(9,12))
nr = 6
nc = 2
ctr = 0
for (minmax, pss, type), region in regions.items():
if len(region) < thresh:
continue
ctr += 1
print ctr
gs = gridspec.GridSpec(nr, nc, width_ratios=[1,2], hspace=0.0)
nbr_func = lambda t: _cp.neighbors6(t[0], t[1], nx, ny)
lset = field_trace._level_set(psi_arr, level_val=psi_arr[pss],
position=pss, neighbors_func=nbr_func)
bx = -psi_grad_y
by = psi_grad_x
br, btheta = cartesian_to_polar(bx, by, minmax[0], minmax[1])
region = expand_region_circ(psi_arr, region, minmax, extra=2.0)
lset = lset.intersection(region)
# psi
ax = pl.subplot(gs[0])
ax.set_title("Field & separatrix", size='x-large')
field_region_image(ax, psi_arr, region, minmax, lset, title=r'$\psi$')
# ax = pl.subplot2grid((nr, nc), (0, 1))
ax = pl.subplot(gs[1])
ax.set_title(r"Field vs. $r/\rho_s$ (id={0})".format(ctr), size='x-large')
plot_theta_sectors(ax, psi_arr, minmax, region, ntheta, title=r'$\psi$ vs. $r/\rho_s$')
# b_theta
ax = pl.subplot(gs[2])
# field_region_image(ax, btheta, region, minmax, lset, title=r'$B_{\theta}$')
field_region_image(ax, bmag, region, minmax, lset, title=r'$|B|$')
ax = pl.subplot(gs[3])
# btheta_sectors = plot_theta_sectors(ax, btheta, minmax, region, ntheta, title=r'$B_{\theta}$ vs. $r/\rho_s$')
plot_theta_sectors(ax, bmag, minmax, region, ntheta, title=r'$|B|$ vs. $r/\rho_s$')
# b_shear
# pl.subplot(nr, nc, 5)
# field_region_image(btheta, region, minmax, lset, title=r'$B_{\theta}$')
# pl.subplot(nr, nc, 6)
# plot_sect_derivs_by_r(btheta_sectors, title=r'$\partial_{r} \frac{B_{\theta}}{r}$ vs. $r/\rho_s$')
# den
ax = pl.subplot(gs[4])
field_region_image(ax, den, region, minmax, lset, title=r'$n$')
ax = pl.subplot(gs[5])
plot_theta_sectors(ax, den, minmax, region, ntheta, title=r'$n$ vs. $r/\rho_s$')
# den_grad
ax = pl.subplot(gs[6])
field_region_image(ax, den_grad_mag, region, minmax, lset, title=r'$|\nabla n|$')
ax = pl.subplot(gs[7])
plot_theta_sectors(ax, den_grad_mag, minmax, region, ntheta, title=r'$|\nabla n|$ vs. $r/\rho_s$')
# cur
ax = pl.subplot(gs[8])
field_region_image(ax, cur, region, minmax, lset, title=r'$J$')
ax = pl.subplot(gs[9])
plot_theta_sectors(ax, cur, minmax, region, ntheta, title=r'$J$ vs. $r/\rho_s$')
# hessian
ax = pl.subplot(gs[10])
field_region_image(ax, hess, region, minmax, lset, title=r'$H(\psi)$', xvis=True)
ax = pl.subplot(gs[11])
ax.set_xlabel(r'$r/\rho_s$', size='x-large')
plot_theta_sectors(ax, hess, minmax, region, ntheta, title=r'$H(\psi)$ vs. $r/\rho_s$', xvis=True)
# raw_input('enter to continue')
pl.savefig('{0}_{1:04d}.pdf'.format(save_basename, ctr))
pl.clf()
pl.close('all')