def translation_step(points,
point_weights,
center,
data_array,
xyz_to_ijk_transform,
ijk_step_size,
metric,
syminv=[],
values=None,
gradients=None):
g = gradient_direction(points,
point_weights,
data_array,
xyz_to_ijk_transform,
metric,
syminv=syminv,
values=values,
gradients=gradients)
from numpy import array, float, dot as matrix_multiply
gijk = matrix_multiply(xyz_to_ijk_transform.matrix[:, :3], g)
from chimerax.geometry import norm, place
n = norm(gijk)
if n > 0:
delta = g * (ijk_step_size / n)
else:
delta = array((0, 0, 0), float)
delta_tf = place.translation(delta)
return delta_tf
def move(session, by, modelspec=None):
spec = modelspec.evaluate(session)
import numpy
by_vector = numpy.array(by)
from chimerax.geometry import place
translation = place.translation(by_vector)
for m in spec.models:
m.position = translation * m.position
def check_space_navigator(self, *_):
e = self.device.last_event()
if e is None:
return
rot, trans, buttons = e
from math import sqrt
# Rotation
rx, ry, rz = rot # 10 bits, signed, +/-512
rmag = sqrt(rx*rx + ry*ry + rz*rz)
# Translation
tx, ty, tz = trans # 10 bits, signed, +/-512
tmag = sqrt(tx*tx + ty*ty + tz*tz)
if self.dominant:
if tmag < rmag:
tmag = 0
if rmag < tmag:
rmag = 0
if self.fly_mode:
rt = 50
if abs(ry) > abs(rx)+rt and abs(ry) > abs(rz)+rt: rx = rz = 0
else: ry = 0
rmag = sqrt(rx*rx + ry*ry + rz*rz)
from numpy import array, float32
from chimerax.geometry import place
if rmag > 0:
axis = array((rx/rmag, ry/rmag, rz/rmag), float32)
f = 3 if self.fly_mode else 30
angle = self.speed*(f*rmag/512)
rtf = place.rotation(axis, angle)
self.apply_transform(rtf)
if tmag > 0:
axis = array((tx/tmag, ty/tmag, tz/tmag), float32)
# view_width = v.camera.view_width(v.center_of_rotation)
b = self.view.drawing_bounds()
if not b is None:
f = .1 if self.fly_mode else 1
view_width = b.xyz_max - b.xyz_min
shift = axis * 0.15 * self.speed * view_width * f * tmag/512
ttf = place.translation(shift)
self.apply_transform(ttf)
if 'N1' in buttons or 31 in buttons or 'Left' in buttons:
self.button_pressed(self.button_1_action)
if 'N2' in buttons or 'Right' in buttons:
self.button_pressed(self.button_2_action)
def view(self, camera_position, view_num):
'''
Return the Place coordinate frame of the camera.
As a transform it maps camera coordinates to scene coordinates.
'''
if view_num is None:
v = camera_position
else:
xoffset = self._x_offset_scene(view_num)
from chimerax.geometry import place
t = place.translation((xoffset, 0, 0))
v = camera_position * t
return v
def angle_step(axis, points, center, xyz_to_ijk_transform, ijk_step_size):
from chimerax.geometry.place import cross_product_matrix, translation
tf = xyz_to_ijk_transform.zero_translation() * cross_product_matrix(
axis) * translation(-center)
from chimerax.geometry.vector import maximum_norm
av = maximum_norm(points, tf.matrix)
if av > 0:
from math import pi
angle = (ijk_step_size / av) * 180.0 / pi
else:
angle = 0
return angle
def view(self, camera_position, view_num):
'''
Return the Place coordinate frame for a specific camera view number.
As a transform it maps camera coordinates to scene coordinates.
'''
if view_num is None:
v = camera_position
else:
# Stereo eyes view in same direction with position shifted along x.
s = -1 if view_num == 0 else 1
es = self.eye_separation_scene
from chimerax.geometry import place
t = place.translation((s * 0.5 * es, 0, 0))
v = camera_position * t
return v