def test_conversion(self,
phi1=0,
psi1=0,
the1=0,
phi2=90,
psi2=90,
the2=90):
from pytom.angles.angleFnc import zxzToMat
m = zxzToMat(phi1, psi1, the1, False)
self.assertTrue(m.trace() == 3.0, msg='trace of matrix is wrong')
self.assertTrue(
m.getRow(0)[0] == 1.0 and m.getRow(1)[1] == 1.0
and m.getRow(2)[2] == 1.0)
m = zxzToMat(phi2, psi2, the2, False)
from pytom.angles.angleFnc import matToZXZ
a = matToZXZ(m)
self.assertTrue(a[0] == phi2 and a[1] == psi2 and a[2] == the2)
def getConstraintVolume(self, bw):
if self._cv is None or self._bw != bw:
cv = np.zeros((2 * bw, 2 * bw, 2 * bw), dtype='double')
if self.nearby > 0: # get an array of axes nearby
the = np.array(range(
1,
int(self.nearby * bw / 90.) + 1)) * (90. / bw)
the = np.append(the, self.nearby)
phi = range(0, 360, int(round(180. / bw)))
the, phi = np.meshgrid(the, phi)
the = the.reshape((the.size, )) * np.pi / 180
phi = phi.reshape((phi.size, )) * np.pi / 180
xx = np.cos(phi) * np.sin(the)
yy = np.sin(phi) * np.sin(the)
zz = np.cos(the)
# rotate all the vectors
from pytom.angles.angleFnc import vector2euler, zxzToMat
m = zxzToMat(vector2euler([self.x, self.y, self.z]))
mat = np.matrix(np.zeros((3, 3)))
mat[0, 0] = m[0, 0]
mat[0, 1] = m[0, 1]
mat[0, 2] = m[0, 2]
mat[1, 0] = m[1, 0]
mat[1, 1] = m[1, 1]
mat[1, 2] = m[1, 2]
mat[2, 0] = m[2, 0]
mat[2, 1] = m[2, 1]
mat[2, 2] = m[2, 2]
coord = mat * np.matrix(np.vstack((xx, yy, zz)))
axes = coord.swapaxes(0, 1)
else:
axes = np.matrix([[self.x, self.y, self.z]])
# here we make the angular sampling as 2 degree
from pytom.angles.angleFnc import axisAngleToZXZ
for axis in axes:
axis = [axis[0, 0], axis[0, 1], axis[0, 2]]
for ang in range(0, 360, 2):
euler_ang = axisAngleToZXZ(axis, ang)
i, j, k = frm_angle2idx(bw, euler_ang.getPhi(),
euler_ang.getPsi(),
euler_ang.getTheta())
# set the cv
cv[i, j, k] = 1
self._cv = cv
self._bw = bw
return self._cv
def zxzToMatToZXZ_T(self, z1, z2, x):
from pytom.angles.angleFnc import zxzToMat, matToZXZ
m = zxzToMat(z1=z1, z2=z2, x=x)
r = matToZXZ(m)
self.assertAlmostEqual(first=r.getZ1(),
second=z1,
places=3,
msg='numerical issue in z1')
self.assertAlmostEqual(first=r.getZ2(),
second=z2,
places=3,
msg='numerical issue in z2')
self.assertAlmostEqual(first=r.getX(),
second=x,
places=3,
msg='numerical issue in x')