def getZoneByLocation(lat, lon, level):
level += 2
h_size = calcHexSize(level)
z_xy = loc2xy(lon, lat)
lon_grid = z_xy.x
lat_grid = z_xy.y
unit_x = 6 * h_size
unit_y = 6 * h_size * H_K
h_pos_x = (lon_grid + lat_grid / H_K) / unit_x
h_pos_y = (lat_grid - H_K * lon_grid) / unit_y
h_x_0 = floor_int(h_pos_x)
h_y_0 = floor_int(h_pos_y)
h_x_q = h_pos_x - h_x_0
h_y_q = h_pos_y - h_y_0
h_x = round_int(h_pos_x)
h_y = round_int(h_pos_y)
if h_y_q > -h_x_q + 1:
if (h_y_q < 2 * h_x_q) and (h_y_q > 0.5 * h_x_q):
h_x = h_x_0 + 1
h_y = h_y_0 + 1
elif h_y_q < -h_x_q + 1:
if (h_y_q > (2 * h_x_q) - 1) and (h_y_q < (0.5 * h_x_q) + 0.5):
h_x = h_x_0
h_y = h_y_0
h_lat = (H_K * h_x * unit_x + h_y * unit_y) / 2
h_lon = (h_lat - h_y * unit_y) / H_K
z_loc = xy2loc(h_lon, h_lat)
z_loc_x = z_loc.lon
z_loc_y = z_loc.lat
if H_BASE - h_lon < h_size:
z_loc_x = 180
h_xy = h_x
h_x = h_y
h_y = h_xy
h_code = ""
code3_x = [0] * (level + 1)
code3_y = [0] * (level + 1)
code3 = ""
code9 = ""
mod_x = h_x
mod_y = h_y
for i in range(level + 1):
h_pow = math.pow(3, level - i)
if mod_x >= ceil_int(h_pow/2):
code3_x[i] = 2
mod_x -= h_pow
elif mod_x <= -ceil_int(h_pow/2):
code3_x[i] = 0
mod_x += h_pow
else:
code3_x[i] = 1
if mod_y >= ceil_int(h_pow/2):
code3_y[i] =2
mod_y -= h_pow
elif mod_y <= -ceil_int(h_pow/2):
code3_y[i] =0
mod_y += h_pow
else:
code3_y[i] = 1
for i in range(len(code3_x)):
code3 += "%s%s" % (code3_x[i], code3_y[i])
code9 += str(int(code3, 3))
h_code += code9
code9 = ""
code3 = ""
h_2 = h_code[3:]
h_1 = h_code[0:3]
h_a1 = floor_int(int(h_1) / 30)
h_a2 = int(h_1) % 30
h_code = (H_KEY[h_a1] + H_KEY[h_a2]) + h_2
return Zone(z_loc_y, z_loc_x, h_x, h_y, h_code)
def find_bubble_edges(array, blob, max_extent=1.0,
edge_mask=None,
nsig_thresh=1, value_thresh=None,
radius=None, return_mask=False, min_pixels=16,
filter_size=4, verbose=False,
min_radius_frac=0.0, try_local_bkg=True,
**kwargs):
'''
Expand/contract to match the contours in the data.
Parameters
----------
array : 2D numpy.ndarray or spectral_cube.LowerDimensionalObject
Data used to define the region boundaries.
max_extent : float, optional
Multiplied by the major radius to set how far should be searched
when searching for the boundary.
nsig_thresh : float, optional
Number of times sigma above the mean to set the boundary intensity
requirement. This is used whenever the local background is higher
than the given `value_thresh`.
value_thresh : float, optional
When given, sets the minimum intensity for defining a bubble edge.
The natural choice is a few times the noise level in the cube.
radius : float, optional
Give an optional radius to use instead of the major radius defined
for the bubble.
kwargs : passed to profile.profile_line.
Returns
-------
extent_coords : np.ndarray
Array with the positions of edges.
'''
if try_local_bkg:
mean, std = intensity_props(array, blob)
background_thresh = mean + nsig_thresh * std
# Define a suitable background based on the intensity within the
# elliptical region
if value_thresh is None:
value_thresh = background_thresh
else:
# If value_thresh is higher use it. Otherwise use the bkg.
if value_thresh < background_thresh:
value_thresh = background_thresh
# Set the number of theta to be ~ the perimeter.
y, x, major, minor, pa = blob[:5]
y = int(np.round(y, decimals=0))
x = int(np.round(x, decimals=0))
# If the center is on the edge of the array, subtract one to
# index correctly
if y == array.shape[0]:
y -= 1
if x == array.shape[1]:
x -= 1
# Use the ellipse model to define a bounding box for the mask.
bbox = Ellipse2D(True, 0.0, 0.0, major * max_extent,
minor * max_extent, pa).bounding_box
y_range = ceil_int(bbox[0][1] - bbox[0][0] + 1 + filter_size)
x_range = ceil_int(bbox[1][1] - bbox[1][0] + 1 + filter_size)
shell_thetas = []
yy, xx = np.mgrid[-int(y_range / 2): int(y_range / 2) + 1,
-int(x_range / 2): int(x_range / 2) + 1]
if edge_mask is not None:
arr = edge_mask[max(0, y - int(y_range / 2)):
y + int(y_range / 2) + 1,
max(0, x - int(x_range / 2)):
x + int(x_range / 2) + 1]
else:
arr = array[max(0, y - int(y_range / 2)):y + int(y_range / 2) + 1,
max(0, x - int(x_range / 2)):x + int(x_range / 2) + 1]
# Adjust meshes if they exceed the array shape
x_min = -min(0, x - int(x_range / 2))
x_max = xx.shape[1] - max(0, x + int(x_range / 2) - array.shape[1] + 1)
y_min = -min(0, y - int(y_range / 2))
y_max = yy.shape[0] - max(0, y + int(y_range / 2) - array.shape[0] + 1)
offset = (max(0, int(y - (y_range / 2))),
max(0, int(x - (x_range / 2))))
yy = yy[y_min:y_max, x_min:x_max]
xx = xx[y_min:y_max, x_min:x_max]
dist_arr = np.sqrt(yy**2 + xx**2)
if edge_mask is not None:
smooth_mask = arr
else:
smooth_mask = \
smooth_edges(arr <= value_thresh, filter_size, min_pixels)
region_mask = \
Ellipse2D(True, 0.0, 0.0, major * max_extent, minor * max_extent,
pa)(xx, yy).astype(bool)
region_mask = nd.binary_dilation(region_mask, eight_conn, iterations=2)
# The bubble center must fall within a valid region
mid_pt = np.where(dist_arr == 0.0)
if len(mid_pt[0]) == 0:
middle_fail = True
else:
local_center = zip(*np.where(dist_arr == 0.0))[0]
middle_fail = False
# _make_bubble_mask(smooth_mask, local_center)
# If the center is not contained within a bubble region, return
# empties.
bad_case = not smooth_mask.any() or smooth_mask.all() or \
(smooth_mask * region_mask).all() or middle_fail
if bad_case:
if return_mask:
return np.array([]), 0.0, 0.0, value_thresh, smooth_mask
return np.array([]), 0.0, 0.0, value_thresh
orig_perim = find_contours(region_mask, 0, fully_connected='high')[0]
# new_perim = find_contours(smooth_mask, 0, fully_connected='high')
coords = []
extent_mask = np.zeros_like(region_mask)
# for perim in new_perim:
# perim = perim.astype(np.int)
# good_pts = \
# np.array([pos for pos, pt in enumerate(perim)
# if region_mask[pt[0], pt[1]]])
# if not good_pts.any():
# continue
# # Now split into sections
# from utils import consec_split
# split_pts = consec_split(good_pts)
# # Remove the duplicated end point if it was initially connected
# if len(split_pts) > 1:
# # Join these if the end pts initially matched
# if split_pts[0][0] == split_pts[-1][-1]:
# split_pts[0] = np.append(split_pts[0],
# split_pts[-1][::-1])
# split_pts.pop(-1)
# for split in split_pts:
# coords.append(perim[split])
# extent_mask[perim[good_pts][:, 0], perim[good_pts][:, 1]] = True
# Based on the curvature of the shell, only fit points whose
# orientation matches the assumed centre.
# incoord, outcoord = shell_orientation(coords, local_center,
# verbose=False)
# Now only keep the points that are not blocked from the centre pixel
for pt in orig_perim:
theta = np.arctan2(pt[0] - local_center[0],
pt[1] - local_center[1])
num_pts = int(np.round(np.hypot(pt[0] - local_center[0],
pt[1] - local_center[1]),
decimals=0))
ys = np.round(np.linspace(local_center[0], pt[0], num_pts),
decimals=0).astype(np.int)
xs = np.round(np.linspace(local_center[1], pt[1], num_pts),
decimals=0).astype(np.int)
not_on_edge = np.logical_and(ys < smooth_mask.shape[0],
xs < smooth_mask.shape[1])
ys = ys[not_on_edge]
xs = xs[not_on_edge]
dist = np.sqrt((ys - local_center[0])**2 +
(xs - local_center[1])**2)
prof = smooth_mask[ys, xs]
prof = prof[dist >= min_radius_frac * minor]
ys = ys[dist >= min_radius_frac * minor]
xs = xs[dist >= min_radius_frac * minor]
# Look for the first 0 and ignore all others past it
zeros = np.where(prof == 0)[0]
# If none, move on
if not zeros.any():
continue
edge = zeros[0]
extent_mask[ys[edge], xs[edge]] = True
coords.append((ys[edge], xs[edge]))
shell_thetas.append(theta)
# Calculate the fraction of the region associated with a shell
shell_frac = len(shell_thetas) / float(len(orig_perim))
shell_thetas = np.array(shell_thetas)
coords = np.array(coords)
# Use the theta values to find the standard deviation i.e. how
# dispersed the shell locations are. Assumes a circle, but we only
# consider moderately elongated ellipses, so the statistics approx.
# hold.
theta_var = np.sqrt(circvar(shell_thetas * u.rad)).value
extent_coords = \
np.vstack([pt + off for pt, off in
zip(np.where(extent_mask), offset)]).T
if verbose:
print("Shell fraction : " + str(shell_frac))
print("Angular Std. : " + str(theta_var))
import matplotlib.pyplot as p
true_region_mask = \
Ellipse2D(True, 0.0, 0.0, major, minor,
pa)(xx, yy).astype(bool)
ax = p.subplot(121)
ax.imshow(arr, origin='lower',
interpolation='nearest')
ax.contour(smooth_mask, colors='b')
ax.contour(region_mask, colors='r')
ax.contour(true_region_mask, colors='g')
if len(coords) > 0:
p.plot(coords[:, 1], coords[:, 0], 'bD')
p.plot(local_center[1], local_center[0], 'gD')
ax2 = p.subplot(122)
ax2.imshow(extent_mask, origin='lower',
interpolation='nearest')
p.draw()
raw_input("?")
p.clf()
if return_mask:
return extent_coords, shell_frac, theta_var, value_thresh, \
extent_mask
return extent_coords, shell_frac, theta_var, value_thresh
def find_bubble_edges(array,
blob,
max_extent=1.0,
edge_mask=None,
nsig_thresh=1,
value_thresh=None,
radius=None,
return_mask=False,
min_pixels=16,
filter_size=4,
verbose=False,
min_radius_frac=0.0,
try_local_bkg=True,
**kwargs):
'''
Expand/contract to match the contours in the data.
Parameters
----------
array : 2D numpy.ndarray or spectral_cube.LowerDimensionalObject
Data used to define the region boundaries.
max_extent : float, optional
Multiplied by the major radius to set how far should be searched
when searching for the boundary.
nsig_thresh : float, optional
Number of times sigma above the mean to set the boundary intensity
requirement. This is used whenever the local background is higher
than the given `value_thresh`.
value_thresh : float, optional
When given, sets the minimum intensity for defining a bubble edge.
The natural choice is a few times the noise level in the cube.
radius : float, optional
Give an optional radius to use instead of the major radius defined
for the bubble.
kwargs : passed to profile.profile_line.
Returns
-------
extent_coords : np.ndarray
Array with the positions of edges.
'''
if try_local_bkg:
mean, std = intensity_props(array, blob)
background_thresh = mean + nsig_thresh * std
# Define a suitable background based on the intensity within the
# elliptical region
if value_thresh is None:
value_thresh = background_thresh
else:
# If value_thresh is higher use it. Otherwise use the bkg.
if value_thresh < background_thresh:
value_thresh = background_thresh
# Set the number of theta to be ~ the perimeter.
y, x, major, minor, pa = blob[:5]
y = int(np.round(y, decimals=0))
x = int(np.round(x, decimals=0))
# If the center is on the edge of the array, subtract one to
# index correctly
if y == array.shape[0]:
y -= 1
if x == array.shape[1]:
x -= 1
# Use the ellipse model to define a bounding box for the mask.
bbox = Ellipse2D(True, 0.0, 0.0, major * max_extent, minor * max_extent,
pa).bounding_box
y_range = ceil_int(bbox[0][1] - bbox[0][0] + 1 + filter_size)
x_range = ceil_int(bbox[1][1] - bbox[1][0] + 1 + filter_size)
shell_thetas = []
yy, xx = np.mgrid[-int(y_range / 2):int(y_range / 2) + 1,
-int(x_range / 2):int(x_range / 2) + 1]
if edge_mask is not None:
arr = edge_mask[max(0, y - int(y_range / 2)):y + int(y_range / 2) + 1,
max(0, x - int(x_range / 2)):x + int(x_range / 2) + 1]
else:
arr = array[max(0, y - int(y_range / 2)):y + int(y_range / 2) + 1,
max(0, x - int(x_range / 2)):x + int(x_range / 2) + 1]
# Adjust meshes if they exceed the array shape
x_min = -min(0, x - int(x_range / 2))
x_max = xx.shape[1] - max(0, x + int(x_range / 2) - array.shape[1] + 1)
y_min = -min(0, y - int(y_range / 2))
y_max = yy.shape[0] - max(0, y + int(y_range / 2) - array.shape[0] + 1)
offset = (max(0, int(y - (y_range / 2))), max(0, int(x - (x_range / 2))))
yy = yy[y_min:y_max, x_min:x_max]
xx = xx[y_min:y_max, x_min:x_max]
dist_arr = np.sqrt(yy**2 + xx**2)
if edge_mask is not None:
smooth_mask = arr
else:
smooth_mask = \
smooth_edges(arr <= value_thresh, filter_size, min_pixels)
region_mask = \
Ellipse2D(True, 0.0, 0.0, major * max_extent, minor * max_extent,
pa)(xx, yy).astype(bool)
region_mask = nd.binary_dilation(region_mask, eight_conn, iterations=2)
# The bubble center must fall within a valid region
mid_pt = np.where(dist_arr == 0.0)
if len(mid_pt[0]) == 0:
middle_fail = True
else:
local_center = zip(*np.where(dist_arr == 0.0))[0]
middle_fail = False
# _make_bubble_mask(smooth_mask, local_center)
# If the center is not contained within a bubble region, return
# empties.
bad_case = not smooth_mask.any() or smooth_mask.all() or \
(smooth_mask * region_mask).all() or middle_fail
if bad_case:
if return_mask:
return np.array([]), 0.0, 0.0, value_thresh, smooth_mask
return np.array([]), 0.0, 0.0, value_thresh
orig_perim = find_contours(region_mask, 0, fully_connected='high')[0]
# new_perim = find_contours(smooth_mask, 0, fully_connected='high')
coords = []
extent_mask = np.zeros_like(region_mask)
# for perim in new_perim:
# perim = perim.astype(np.int)
# good_pts = \
# np.array([pos for pos, pt in enumerate(perim)
# if region_mask[pt[0], pt[1]]])
# if not good_pts.any():
# continue
# # Now split into sections
# from utils import consec_split
# split_pts = consec_split(good_pts)
# # Remove the duplicated end point if it was initially connected
# if len(split_pts) > 1:
# # Join these if the end pts initially matched
# if split_pts[0][0] == split_pts[-1][-1]:
# split_pts[0] = np.append(split_pts[0],
# split_pts[-1][::-1])
# split_pts.pop(-1)
# for split in split_pts:
# coords.append(perim[split])
# extent_mask[perim[good_pts][:, 0], perim[good_pts][:, 1]] = True
# Based on the curvature of the shell, only fit points whose
# orientation matches the assumed centre.
# incoord, outcoord = shell_orientation(coords, local_center,
# verbose=False)
# Now only keep the points that are not blocked from the centre pixel
for pt in orig_perim:
theta = np.arctan2(pt[0] - local_center[0], pt[1] - local_center[1])
num_pts = int(
np.round(np.hypot(pt[0] - local_center[0],
pt[1] - local_center[1]),
decimals=0))
ys = np.round(np.linspace(local_center[0], pt[0], num_pts),
decimals=0).astype(np.int)
xs = np.round(np.linspace(local_center[1], pt[1], num_pts),
decimals=0).astype(np.int)
not_on_edge = np.logical_and(ys < smooth_mask.shape[0],
xs < smooth_mask.shape[1])
ys = ys[not_on_edge]
xs = xs[not_on_edge]
dist = np.sqrt((ys - local_center[0])**2 + (xs - local_center[1])**2)
prof = smooth_mask[ys, xs]
prof = prof[dist >= min_radius_frac * minor]
ys = ys[dist >= min_radius_frac * minor]
xs = xs[dist >= min_radius_frac * minor]
# Look for the first 0 and ignore all others past it
zeros = np.where(prof == 0)[0]
# If none, move on
if not zeros.any():
continue
edge = zeros[0]
extent_mask[ys[edge], xs[edge]] = True
coords.append((ys[edge], xs[edge]))
shell_thetas.append(theta)
# Calculate the fraction of the region associated with a shell
shell_frac = len(shell_thetas) / float(len(orig_perim))
shell_thetas = np.array(shell_thetas)
coords = np.array(coords)
# Use the theta values to find the standard deviation i.e. how
# dispersed the shell locations are. Assumes a circle, but we only
# consider moderately elongated ellipses, so the statistics approx.
# hold.
theta_var = np.sqrt(circvar(shell_thetas * u.rad)).value
extent_coords = \
np.vstack([pt + off for pt, off in
zip(np.where(extent_mask), offset)]).T
if verbose:
print("Shell fraction : " + str(shell_frac))
print("Angular Std. : " + str(theta_var))
import matplotlib.pyplot as p
true_region_mask = \
Ellipse2D(True, 0.0, 0.0, major, minor,
pa)(xx, yy).astype(bool)
ax = p.subplot(121)
ax.imshow(arr, origin='lower', interpolation='nearest')
ax.contour(smooth_mask, colors='b')
ax.contour(region_mask, colors='r')
ax.contour(true_region_mask, colors='g')
if len(coords) > 0:
p.plot(coords[:, 1], coords[:, 0], 'bD')
p.plot(local_center[1], local_center[0], 'gD')
ax2 = p.subplot(122)
ax2.imshow(extent_mask, origin='lower', interpolation='nearest')
p.draw()
raw_input("?")
p.clf()
if return_mask:
return extent_coords, shell_frac, theta_var, value_thresh, \
extent_mask
return extent_coords, shell_frac, theta_var, value_thresh
