def make_kappa_goniometer(alpha, omega, kappa, phi, direction, scan_axis):
import math
omega_axis = (1, 0, 0)
phi_axis = (1, 0, 0)
c = math.cos(alpha * math.pi / 180);
s = math.sin(alpha * math.pi / 180);
if direction == "+y":
kappa_axis = (c, s, 0.0)
elif direction == "+z":
kappa_axis = (c, 0.0, s)
elif direction == "-y":
kappa_axis = (c, -s, 0.0)
elif direction == "-z":
kappa_axis = (c, 0.0, -s)
else:
raise RuntimeError("Invalid direction")
if scan_axis == "phi":
scan_axis = 0
else:
scan_axis = 2
from scitbx.array_family import flex
axes = flex.vec3_double((phi_axis, kappa_axis, omega_axis))
angles = flex.double((phi, kappa, omega))
names = flex.std_string(("PHI", "KAPPA", "OMEGA"))
return goniometer_factory.make_multi_axis_goniometer(
axes, angles, names, scan_axis)
def Xrotz(theta):
"""
% Xrotz spatial coordinate transform (Z-axis rotation).
% Xrotz(theta) calculates the coordinate transform matrix from A to B
% coordinates for spatial motion vectors, where coordinate frame B is
% rotated by an angle theta (radians) relative to frame A about their
% common Z axis.
"""
c = math.cos(theta)
s = math.sin(theta)
return matrix.sqr((c, s, 0, 0, 0, 0, -s, c, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, c, s, 0, 0, 0, 0, -s, c, 0, 0, 0, 0, 0, 0, 1))
def __init__(O, qE):
if (qE is None): qE = matrix.col((0,0,0))
O.qE = qE
th = abs(qE)
if (th == 0):
p = matrix.col((1,0,0,0))
else:
p0 = math.cos(th)
p1, p2, p3 = math.sin(th) / th * qE
p = matrix.col((p0,p1,p2,p3))
assert abs(abs(p)-1) < 1.e-12
O.E = joint_lib.RBDA_Eq_4_12(q=p)
O.setT()
def __init__(O, qE):
if (qE is None): qE = matrix.col((0, 0, 0))
O.qE = qE
th = abs(qE)
if (th == 0):
p = matrix.col((1, 0, 0, 0))
else:
p0 = math.cos(th)
p1, p2, p3 = math.sin(th) / th * qE
p = matrix.col((p0, p1, p2, p3))
assert abs(abs(p) - 1) < 1.e-12
O.E = joint_lib.RBDA_Eq_4_12(q=p)
O.setT()
def Xrotz(theta):
"""
% Xrotz spatial coordinate transform (Z-axis rotation).
% Xrotz(theta) calculates the coordinate transform matrix from A to B
% coordinates for spatial motion vectors, where coordinate frame B is
% rotated by an angle theta (radians) relative to frame A about their
% common Z axis.
"""
c = math.cos(theta)
s = math.sin(theta)
return matrix.sqr((
c, s, 0, 0, 0, 0,
-s, c, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0,
0, 0, 0, c, s, 0,
0, 0, 0, -s, c, 0,
0, 0, 0, 0, 0, 1))
def OnScale(self, scale):
if (abs(scale) > self.scale_max) :
if (scale < 0) :
scale = -self.scale_max
else :
scale = self.scale_max
s = self.minimum_covering_sphere
r = (1+1.e-6)*s.radius()
d = -gltbx.util.object_as_eye_coordinates(self.rotation_center)[2]
dr = d + r
if (scale > 0 and (dr <= self.min_near or d <= self.min_dist)):
pass # near limit
elif (scale < 0 and r < d * math.sin(self.field_of_view_y*math.pi/180/2)
* self.min_viewport_use_fraction):
pass # far limit
else:
gltbx.util.translate_object(0,0,dr*scale)
self.OnRedraw()
def draw_minimum_covering_sphere(self):
if (self.minimum_covering_sphere_display_list is None):
self.minimum_covering_sphere_display_list=gltbx.gl_managed.display_list()
self.minimum_covering_sphere_display_list.compile()
s = self.minimum_covering_sphere
c = s.center()
r = s.radius()
gray = 0.3
glColor3f(gray,gray,gray)
glBegin(GL_POLYGON)
for i in xrange(360):
a = i * math.pi / 180
rs = r * math.sin(a)
rc = r * math.cos(a)
glVertex3f(c[0],c[1]+rs,c[2]+rc)
glEnd()
self.draw_cross_at(c, color=(1,0,0))
self.minimum_covering_sphere_display_list.end()
self.minimum_covering_sphere_display_list.call()
def OnScale(self, scale):
if (abs(scale) > self.scale_max):
if (scale < 0):
scale = -self.scale_max
else:
scale = self.scale_max
s = self.minimum_covering_sphere
r = (1 + 1.e-6) * s.radius()
d = -gltbx.util.object_as_eye_coordinates(self.rotation_center)[2]
dr = d + r
if (scale > 0 and (dr <= self.min_near or d <= self.min_dist)):
pass # near limit
elif (scale < 0
and r < d * math.sin(self.field_of_view_y * math.pi / 180 / 2) *
self.min_viewport_use_fraction):
pass # far limit
else:
gltbx.util.translate_object(0, 0, dr * scale)
self.OnRedraw()
def draw_minimum_covering_sphere(self):
if (self.minimum_covering_sphere_display_list is None):
self.minimum_covering_sphere_display_list = gltbx.gl_managed.display_list(
)
self.minimum_covering_sphere_display_list.compile()
s = self.minimum_covering_sphere
c = s.center()
r = s.radius()
gray = 0.3
glColor3f(gray, gray, gray)
glBegin(GL_POLYGON)
for i in xrange(360):
a = i * math.pi / 180
rs = r * math.sin(a)
rc = r * math.cos(a)
glVertex3f(c[0], c[1] + rs, c[2] + rc)
glEnd()
self.draw_cross_at(c, color=(1, 0, 0))
self.minimum_covering_sphere_display_list.end()
self.minimum_covering_sphere_display_list.call()
def j0(x): result = math.sin(x)/x return result
def cs(a): return math.cos(a), math.sin(a) c1,s1 = cs(q1)
def cs(a):
return math.cos(a), math.sin(a)
def cs(a): return math.cos(a), math.sin(a) c1,s1 = cs(q1)
def cs(a): return math.cos(a), math.sin(a) c2,s2 = cs(q2)
def j1(x): result = math.sin(x)/(x*x) - math.cos(x)/x return result
def j2(x): result = (3.0/(x*x) -1.0)*(math.sin(x)/x) - 3.0*math.cos(x)/(x*x) return result
def cs(a): return math.cos(a), math.sin(a) c2,s2 = cs(q2)
