def reconstruct(self):
hybridtrack.choose_initial_end(
self.original_image_kev, self.options, self.info)
try:
self.segment_initial_end()
# get a sub-image containing the initial end
# also need a rough estimate of the electron direction
# (using thinned)
except CheckSegmentBoxError:
self.error = 'CheckSegmentBoxError'
return
except RuntimeError:
self.error = 'what the heck happened?'
return
# 1.
self.get_coordlist()
self.compute_first_moments()
# 2ab.
self.compute_central_moments()
# 3ab.
try:
self.compute_optimal_rotation_angle()
except MomentsError:
self.error = 'Rotation angle conditions not met'
return
# 4.
self.compute_arc_parameters()
self.compute_direction()
self.compute_pathology()
def reconstruct(self):
hybridtrack.choose_initial_end(self.original_image_kev, self.options,
self.info)
try:
self.segment_initial_end()
# get a sub-image containing the initial end
# also need a rough estimate of the electron direction
# (using thinned)
except CheckSegmentBoxError:
self.error = 'CheckSegmentBoxError'
return
except RuntimeError:
self.error = 'what the heck happened?'
return
# 1.
self.get_coordlist()
self.compute_first_moments()
# 2ab.
self.compute_central_moments()
# 3ab.
try:
self.compute_optimal_rotation_angle()
except MomentsError:
self.error = 'Rotation angle conditions not met'
return
# 4.
self.compute_arc_parameters()
self.compute_direction()
self.compute_pathology()
def check_segment_box(self):
"""
Check whether the box intersects too many hot pixels.
That would indicate that we should draw a new box.
"""
problem_length = 60 # microns
# xmesh, ymesh get used in get_pixlist, also. so save into self.
img_shape = self.original_image_kev.shape
self.xmesh, self.ymesh = np.meshgrid(
range(img_shape[0]), range(img_shape[1]), indexing='ij')
# get the pixels along the line segment that passes through the track,
# by walking along from one endpoint toward the other.
xcheck = [self.box_x[-2]]
ycheck = [self.box_y[-2]]
dx = np.sign(self.box_x[-1] - self.box_x[-2])
dy = np.sign(self.box_y[-1] - self.box_y[-2])
while xcheck[-1] != self.box_x[-1] or ycheck[-1] != self.box_y[-1]:
xcheck.append(xcheck[-1] + dx)
ycheck.append(ycheck[-1] + dy)
xcheck.append(self.box_x[-1])
ycheck.append(self.box_y[-1])
xcheck = np.array(xcheck)
ycheck = np.array(ycheck)
lgbad = ((xcheck < 0) | (xcheck >= self.original_image_kev.shape[0]) |
(ycheck < 0) | (ycheck >= self.original_image_kev.shape[1]))
xcheck = xcheck[np.logical_not(lgbad)]
ycheck = ycheck[np.logical_not(lgbad)]
# threshold from HybridTrack options
low_threshold_kev = self.options.low_threshold_kev
# see what pixels are over the threshold.
over_thresh = np.array(
[self.original_image_kev[xcheck[i], ycheck[i]] > low_threshold_kev
for i in xrange(len(xcheck))])
# in order to avoid counting pixels from a separate segment,
# start from end_coordinates and count outward until you hit a 0.
over_thresh_pix = 1
start_ind = np.nonzero(
(xcheck == self.end_coordinates[0]) &
(ycheck == self.end_coordinates[1]))[0][0]
# +dx, +dy side (start_ind+1 --> end):
for i in xrange(start_ind + 1, len(xcheck), 1):
if over_thresh[i]:
over_thresh_pix += 1
else:
break
# -dx, -dy side (start_ind-1 --> 0):
for i in xrange(start_ind - 1, -1, -1):
if over_thresh[i]:
over_thresh_pix += 1
else:
break
over_thresh_length = (
over_thresh_pix *
self.options.pixel_size_um * np.sqrt(dx**2 + dy**2))
if over_thresh_length > problem_length:
# have we done this too much already?
if self.options.ridge_starting_distance_from_track_end_um < 30:
raise CheckSegmentBoxError("Couldn't get a clean end segment")
# try again, with a shorter track segment
self.options.ridge_starting_distance_from_track_end_um -= 10.5
# now, repeat what we've done so far
hybridtrack.choose_initial_end(
self.original_image_kev, self.options, self.info)
self.get_segment_initial_values()
self.get_segment_box()
self.check_segment_box()
def check_segment_box(self):
"""
Check whether the box intersects too many hot pixels.
That would indicate that we should draw a new box.
"""
problem_length = 60 # microns
# xmesh, ymesh get used in get_pixlist, also. so save into self.
img_shape = self.original_image_kev.shape
self.xmesh, self.ymesh = np.meshgrid(range(img_shape[0]),
range(img_shape[1]),
indexing='ij')
# get the pixels along the line segment that passes through the track,
# by walking along from one endpoint toward the other.
xcheck = [self.box_x[-2]]
ycheck = [self.box_y[-2]]
dx = np.sign(self.box_x[-1] - self.box_x[-2])
dy = np.sign(self.box_y[-1] - self.box_y[-2])
while xcheck[-1] != self.box_x[-1] or ycheck[-1] != self.box_y[-1]:
xcheck.append(xcheck[-1] + dx)
ycheck.append(ycheck[-1] + dy)
xcheck.append(self.box_x[-1])
ycheck.append(self.box_y[-1])
xcheck = np.array(xcheck)
ycheck = np.array(ycheck)
lgbad = ((xcheck < 0) | (xcheck >= self.original_image_kev.shape[0]) |
(ycheck < 0) | (ycheck >= self.original_image_kev.shape[1]))
xcheck = xcheck[np.logical_not(lgbad)]
ycheck = ycheck[np.logical_not(lgbad)]
# threshold from HybridTrack options
low_threshold_kev = self.options.low_threshold_kev
# see what pixels are over the threshold.
over_thresh = np.array([
self.original_image_kev[xcheck[i], ycheck[i]] > low_threshold_kev
for i in xrange(len(xcheck))
])
# in order to avoid counting pixels from a separate segment,
# start from end_coordinates and count outward until you hit a 0.
over_thresh_pix = 1
start_ind = np.nonzero((xcheck == self.end_coordinates[0])
& (ycheck == self.end_coordinates[1]))[0][0]
# +dx, +dy side (start_ind+1 --> end):
for i in xrange(start_ind + 1, len(xcheck), 1):
if over_thresh[i]:
over_thresh_pix += 1
else:
break
# -dx, -dy side (start_ind-1 --> 0):
for i in xrange(start_ind - 1, -1, -1):
if over_thresh[i]:
over_thresh_pix += 1
else:
break
over_thresh_length = (over_thresh_pix * self.options.pixel_size_um *
np.sqrt(dx**2 + dy**2))
if over_thresh_length > problem_length:
# have we done this too much already?
if self.options.ridge_starting_distance_from_track_end_um < 30:
raise CheckSegmentBoxError("Couldn't get a clean end segment")
# try again, with a shorter track segment
self.options.ridge_starting_distance_from_track_end_um -= 10.5
# now, repeat what we've done so far
hybridtrack.choose_initial_end(self.original_image_kev,
self.options, self.info)
self.get_segment_initial_values()
self.get_segment_box()
self.check_segment_box()
