def calc_seg_coords(self, morph_seg_coords):
"""Update the segment coordinates (after rotations) for individual cells"""
phi_y = self._node.rotation_angle_yaxis
phi_z = self._node.rotation_angle_zaxis
phi_x = self._node.rotation_angle_xaxis
# Rotate cell
# TODO: Rotations should follow as described in sonata (https://github.com/AllenInstitute/sonata/blob/master/docs/SONATA_DEVELOPER_GUIDE.md).
# Need someone with graphics experience to check they are being done correctly (I'm not sure atm).
RotX = utils.rotation_matrix([1, 0, 0], phi_x)
RotY = utils.rotation_matrix(
[0, 1, 0], phi_y) # rotate segments around yaxis normal to pia
RotZ = utils.rotation_matrix(
[0, 0, 1],
-phi_z) # rotate segments around zaxis to get a proper orientation
RotXYZ = np.dot(RotX, RotY.dot(RotZ))
# rotated coordinates around z axis first then shift relative to the soma
self._seg_coords['p0'] = self._pos_soma + np.dot(
RotXYZ, morph_seg_coords['p0'])
self._seg_coords['p1'] = self._pos_soma + np.dot(
RotXYZ, morph_seg_coords['p1'])
self._seg_coords['p05'] = self._pos_soma + np.dot(
RotXYZ, morph_seg_coords['p05'])
self._seg_coords['d0'] = morph_seg_coords['d0']
self._seg_coords['d1'] = morph_seg_coords['d1']
def calc_seg_coords(self, morph_seg_coords):
"""Calculate segment coordinates for individual cells"""
phi_y = self._props['rotation_angle_yaxis']
phi_z = self._props['rotation_angle_zaxis']
RotY = utils.rotation_matrix([0, 1, 0], phi_y) # rotate segments around yaxis normal to pia
RotZ = utils.rotation_matrix([0, 0, 1], -phi_z) # rotate segments around zaxis to get a proper orientation
RotYZ = RotY.dot(RotZ)
# rotated coordinates around z axis first then shift relative to the soma
self._seg_coords['p0'] = self._pos_soma + np.dot(RotYZ, morph_seg_coords['p0'])
self._seg_coords['p1'] = self._pos_soma + np.dot(RotYZ, morph_seg_coords['p1'])
def rotate_the_electrodes(self):
for el in range(self.elnsites):
phi_x = self.elrot[el][0]
phi_y = self.elrot[el][1]
phi_z = self.elrot[el][2]
rot_x = rotation_matrix([1, 0, 0], phi_x)
rot_y = rotation_matrix([0, 1, 0], phi_y)
rot_z = rotation_matrix([0, 0, 1], phi_z)
rot_xy = rot_x.dot(rot_y)
rot_xyz = rot_xy.dot(rot_z)
new_mesh = np.dot(rot_xyz, self.el_mesh[el])
self.el_mesh[el] = new_mesh
