def alignment(self, segpos, debug=0, **kw):
cen1 = segpos[self.from_seg][..., :, 3]
cen2 = segpos[self.to_seg][..., :, 3]
ax1 = segpos[self.from_seg][..., :, 2]
ax2 = segpos[self.to_seg][..., :, 2]
if not self.distinct_axes and hm.angle(ax1, ax2) > np.pi / 2:
ax2 = -ax2
p, q = hm.line_line_closest_points_pa(cen1, ax1, cen2, ax2)
cen = (p + q) / 2
# ax1 = hm.hnormalized(cen1 - cen)
# ax2 = hm.hnormalized(cen2 - cen)
x = hm.align_vectors(ax1, ax2, self.tgtaxis1[1], self.tgtaxis2[1])
x[..., :, 3] = -x @ cen
if debug:
print('angs', hm.angle_degrees(ax1, ax2),
hm.angle_degrees(self.tgtaxis1[1], self.tgtaxis2[1]))
print('ax1', ax1)
print('ax2', ax2)
print('xax1', x @ ax1)
print('tax1', self.tgtaxis1[1])
print('xax2', x @ ax2)
print('tax2', self.tgtaxis2[1])
raise AssertionError
# if not (np.allclose(x @ ax1, self.tgtaxis1[1], atol=1e-2) and
# np.allclose(x @ ax2, self.tgtaxis2[1], atol=1e-2)):
# print(hm.angle(self.tgtaxis1[1], self.tgtaxis2[1]))
# print(hm.angle(ax1, ax2))
# print(x @ ax1)
# print(self.tgtaxis1[1])
# print(x @ ax2)
# print(self.tgtaxis2[1])
# raise AssertionError('hm.align_vectors sucks')
return x
def alignment(self, segpos, out_cell_spacing=False, **kw):
""" Alignment to move stuff to be in line with symdef file
Args:
segpos (lst): List of segment positions / coordinates.
**kw I'll accept any "non-positional" argument as name = value, and store in a dictionary
"""
cen1 = segpos[self.from_seg][..., :,
3] ## 4th column is x,y,z translation
cen2 = segpos[self.to_seg][..., :, 3]
ax1 = segpos[self.from_seg][..., :, 2] ## 3rd column is axis
ax2 = segpos[self.to_seg][..., :, 2]
if hm.angle(
ax1, ax2
) > np.pi / 2: ## make sure to align with smaller axis choice
ax2 = -ax2
if abs(hm.angle(self.tgtaxis1, self.tgtaxis2)) < 0.1:
d = hm.proj_perp(ax1,
cen2 - cen1) #vector delta between cen2 and cen1
Xalign = hm.align_vectors(ax1, d, self.tgtaxis1,
[0, 1, 0, 0]) #align d to Y axis
Xalign[..., :, 3] = -Xalign @ cen1
cell_dist = (Xalign @ cen2)[..., 1]
else:
Xalign = hm.align_vectors(
ax1, ax2, self.tgtaxis1, self.tgtaxis2
) ## utility function that tries to align ax1 and ax2 to the target axes
Xalign[..., :, 3] = -Xalign @ cen1 ## move from_seg cen1 to origin
cen2_0 = Xalign @ cen2 #moving cen2 by Xalign
D = np.stack([
self.tgtaxis1[:3], [0, 1, 0], self.tgtaxis2[:3]
]).T #matrix where the columns are the things in the list
#CHANGE Uy to an ARGUMENT SOON!!!!
#print("D: ", D)
A1offset, cell_dist, _ = np.linalg.inv(
D
) @ cen2_0[:
3] #transform of A1 offest, cell distance (offset along other axis), and A2 offset (<-- we are ignoring this)
Xalign[..., :, 3] = Xalign[..., :, 3] - (A1offset * self.tgtaxis1)
#Xalign[..., :, 3] = Xalign[..., :, 3] + [0,cell_dist,0,0]
if out_cell_spacing:
#print(2*cell_dist)
return Xalign, cell_dist
else:
return Xalign
def alignment(self, segpos, out_cell_spacing=False, **kw):
""" Alignment to move stuff to be in line with symdef file
Args:
segpos (lst): List of segment positions / coordinates.
**kw I'll accept any "non-positional" argument as name = value, and store in a dictionary
"""
cen1 = segpos[self.from_seg][..., :, 3]
cen2 = segpos[self.to_seg][..., :, 3]
ax1 = segpos[self.from_seg][..., :, 2] ## 3rd column is axis
ax2 = segpos[self.to_seg][..., :, 2]
## make sure to align with smaller axis choice
if hm.angle(ax1, ax2) > np.pi / 2:
ax2 = -ax2
if abs(hm.angle(self.tgtaxis1, self.tgtaxis2)) < 0.1:
# vector delta between cen2 and cen1
d = hm.proj_perp(ax1, cen2 - cen1)
Xalign = hm.align_vectors(ax1, d, self.tgtaxis1,
self.tgtaxis2_isects +
[0]) # align d to Y axis
Xalign[..., :, 3] = -Xalign @ cen1
cell_dist = (Xalign @ cen2)[..., 1]
else:
try:
Xalign = hm.align_vectors(ax1, ax2, self.tgtaxis1,
self.tgtaxis2)
except AssertionError as e:
print("align_vectors error")
print(" ", ax1)
print(" ", ax2)
print(" ", self.tgtaxis1)
print(" ", self.tgtaxis2)
raise e
Xalign[..., :, 3] = -Xalign @ cen1 ## move from_seg cen1 to origin
cen2_0 = Xalign @ cen2 # moving cen2 by Xalign
D = np.stack(
[self.tgtaxis1[:3], self.tgtaxis2_isects, self.tgtaxis2[:3]]).T
A1offset, cell_dist, _ = np.linalg.inv(D) @ cen2_0[:3]
# transform of A1 offest, cell distance (offset along other axis), and A2 offset (<-- we are ignoring this)
Xalign[..., :, 3] = Xalign[..., :, 3] - (A1offset * self.tgtaxis1)
# Xalign[..., :, 3] = Xalign[..., :, 3] + [0,cell_dist,0,0]
if out_cell_spacing:
return Xalign, cell_dist
else:
return Xalign
def alignment(self, segpos, out_cell_spacing=False, **kw):
ax = segpos[self.to_seg, :3, 2]
cn = segpos[self.to_seg, :3, 3]
if self.d_nfold > 2 and self.c_nfold > 2:
mn, mni = 9e9, -1
for i, tf in enumerate(self.d_2folds):
d = hm.line_line_distance_pa(cn, ax, [0, 0, 0], tf)
if d < mn:
mn, mni = d, i
p, q = hm.line_line_closest_points_pa(cn, ax, [0, 0, 0],
self.d_2folds[mni])
spacing = np.linalg.norm(p + q) / 2
xalign = hm.align_vectors([0, 0, 1], q, [0, 0, 1], [1, 0, 0])
elif self.d_nfold > 2 and self.c_nfold == 2:
if abs(ax[2]) > 0.5:
# case: c2 on z pick d2 isects axis
mn, mni = 9e9, -1
for i, tf in enumerate(self.d_2folds):
d = hm.line_line_distance_pa(cn, ax, [0, 0, 0], tf)
if d < mn:
mn, mni = d, i
p, q = hm.line_line_closest_points_pa(cn, ax, [0, 0, 0],
self.d_2folds[mni])
spacing = np.linalg.norm(p + q) / 2
xalign = hm.align_vectors([0, 0, 1], q, [0, 0, 1], [1, 0, 0])
else:
# case: c2 prep to z, pick D2 perp to axis
mn, mni = 9e9, -1
for i, tf in enumerate(self.d_2folds):
d = abs(np.sum(tf * ax))
if d < mn:
mn, mni = d, i
p, q = hm.line_line_closest_points_pa(cn, ax, [0, 0, 0],
self.d_2folds[mni])
spacing = np.linalg.norm(p + q) / 2
xalign = hm.align_vectors([0, 0, 1], q, [0, 0, 1], [1, 0, 0])
elif self.d_nfold == 2 and self.c_nfold > 2:
mn, mni = 9e9, -1
mxdot, mxdoti = 0, -1
for i, tf in enumerate(self.d_2folds):
d = hm.line_line_distance_pa(cn, ax, [0, 0, 0], tf)
if d < mn:
mn, mni = d, i
dot = abs(np.sum(tf * ax))
if dot > mxdot:
mxdot, mxdoti = dot, i
assert mni != mxdoti
p, q = hm.line_line_closest_points_pa(cn, ax, [0, 0, 0],
self.d_2folds[mni])
spacing = np.linalg.norm(p + q) / 2
# assumes d_folds are X Y Z ax[argmin] selects correct one
xalign = hm.align_vectors(self.d_2folds[mni],
self.d_2folds[mxdoti], [1, 0, 0],
[0, 0, 1])
# print("cn", cn)
# print("ax", ax)
# print("isect", self.d_2folds[mni])
# print("align", self.d_2folds[mxdoti])
# print("align xform", xalign)
# print("aligned ax", xalign[:3, :3] @ ax)
# assert 0
elif self.d_nfold == 2 and self.c_nfold == 2:
mn, mni = 9e9, -1
for i, tf in enumerate(self.d_2folds):
d = hm.line_line_distance_pa(cn, ax, [0, 0, 0],
self.d_2diag[i])
dot = abs(np.sum(tf * ax))
angerr2 = (np.arccos(dot) * self.lever)**2
err = np.sqrt(d**2 + angerr2)
if err < mn:
mn = err
mni = i
p, q = hm.line_line_closest_points_pa(cn, ax, [0, 0, 0],
self.d_2diag[mni])
spacing = np.linalg.norm(p + q) / 2 / np.sqrt(2)
# assumes d_folds are X Y Z ax[argmin] selects correct one
xalign = hm.align_vectors(self.d_2diag[mni], self.d_2folds[mni],
[1, 1, 0], [0, 0, 1])
else:
raise NotImplementedError
if out_cell_spacing:
return xalign, spacing
else:
return xalign