adopted orientation conventions and mathematics from Rowenhorst -- tests should now pass...
This commit is contained in:
Philip Eisenlohr
parent
dc4ac1dce1
commit
7663d20b56
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@ -27,15 +27,22 @@ class Rodrigues:
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# ******************************************************************************************
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class Quaternion:
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"""
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u"""
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Orientation represented as unit quaternion.
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All methods and naming conventions based on http://www.euclideanspace.com/maths/algebra/realNormedAlgebra/quaternions.
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All methods and naming conventions based on Rowenhorst_etal2015
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Convention 1: coordinate frames are right-handed
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Convention 2: a rotation angle ω is taken to be positive for a counterclockwise rotation
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when viewing from the end point of the rotation axis unit vector towards the origin
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Convention 3: rotations will be interpreted in the passive sense
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Convention 4: Euler angle triplets are implemented using the Bunge convention,
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with the angular ranges as [0, 2π],[0, π],[0, 2π]
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Convention 5: the rotation angle ω is limited to the interval [0, π]
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w is the real part, (x, y, z) are the imaginary parts.
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Representation of rotation is in ACTIVE form!
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(Derived directly or through angleAxis, Euler angles, or active matrix)
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Vector "a" (defined in coordinate system "A") is actively rotated to new coordinates "b".
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Vector "a" (defined in coordinate system "A") is passively rotated
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resulting in new coordinates "b" when expressed in system "B".
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b = Q * a
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b = np.dot(Q.asMatrix(),a)
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"""
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@ -309,10 +316,12 @@ class Quaternion:
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return np.outer([i for i in self],[i for i in self])
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def asMatrix(self):
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return np.array(
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[[1.0-2.0*(self.y*self.y+self.z*self.z), 2.0*(self.x*self.y-self.z*self.w), 2.0*(self.x*self.z+self.y*self.w)],
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[ 2.0*(self.x*self.y+self.z*self.w), 1.0-2.0*(self.x*self.x+self.z*self.z), 2.0*(self.y*self.z-self.x*self.w)],
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[ 2.0*(self.x*self.z-self.y*self.w), 2.0*(self.x*self.w+self.y*self.z), 1.0-2.0*(self.x*self.x+self.y*self.y)]])
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qbarhalf = 0.5*(self.w**2 - self.x**2 - self.y**2 - self.z**2)
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return 2.0*np.array(
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[[ qbarhalf + self.x**2 , self.x*self.y - self.w*self.z, self.x*self.z + self.w*self.y],
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[ self.x*self.y + self.w*self.z, qbarhalf + self.y**2 , self.y*self.z - self.w*self.x],
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[ self.x*self.z - self.w*self.y, self.y*self.z + self.w*self.x, qbarhalf + self.z**2 ],
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])
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def asAngleAxis(self,
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degrees = False):
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@ -335,52 +344,23 @@ class Quaternion:
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return np.inf*np.ones(3) if self.w == 0.0 else np.array([self.x, self.y, self.z])/self.w
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def asEulers(self,
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type = "bunge",
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degrees = False,
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standardRange = False):
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"""
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Orientation as Bunge-Euler angles.
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degrees = False):
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"""Orientation as Bunge-Euler angles."""
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q03 = self.w**2+self.z**2
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q12 = self.x**2+self.y**2
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chi = np.sqrt(q03*q12)
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Conversion of ACTIVE rotation to Euler angles taken from:
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Melcher, A.; Unser, A.; Reichhardt, M.; Nestler, B.; Poetschke, M.; Selzer, M.
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Conversion of EBSD data by a quaternion based algorithm to be used for grain structure simulations
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Technische Mechanik 30 (2010) pp 401--413.
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"""
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angles = [0.0,0.0,0.0]
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if abs(chi) < 1e-10 and abs(q12) < 1e-10:
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eulers = np.array([math.atan2(-2*self.w*self.z,self.w**2-self.z**2),0,0])
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elif abs(chi) < 1e-10 and abs(q03) < 1e-10:
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eulers = np.array([math.atan2( 2*self.x*self.y,self.x**2-self.y**2),np.pi,0])
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else:
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eulers = np.array([math.atan2((self.x*self.z-self.w*self.y)/chi,(-self.w*self.x-self.y*self.z)/chi),
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math.atan2(2*chi,q03-q12),
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math.atan2((self.w*self.y+self.x*self.z)/chi,( self.y*self.z-self.w*self.x)/chi),
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])
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if type.lower() == 'bunge' or type.lower() == 'zxz':
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if abs(self.x) < 1e-4 and abs(self.y) < 1e-4:
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x = self.w**2 - self.z**2
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y = 2.*self.w*self.z
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angles[0] = math.atan2(y,x)
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elif abs(self.w) < 1e-4 and abs(self.z) < 1e-4:
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x = self.x**2 - self.y**2
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y = 2.*self.x*self.y
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angles[0] = math.atan2(y,x)
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angles[1] = math.pi
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else:
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chi = math.sqrt((self.w**2 + self.z**2)*(self.x**2 + self.y**2))
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x = (self.w * self.x - self.y * self.z)/2./chi
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y = (self.w * self.y + self.x * self.z)/2./chi
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angles[0] = math.atan2(y,x)
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x = self.w**2 + self.z**2 - (self.x**2 + self.y**2)
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y = 2.*chi
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angles[1] = math.atan2(y,x)
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x = (self.w * self.x + self.y * self.z)/2./chi
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y = (self.z * self.x - self.y * self.w)/2./chi
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angles[2] = math.atan2(y,x)
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if standardRange:
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angles[0] %= 2*math.pi
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if angles[1] < 0.0:
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angles[1] += math.pi
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angles[2] *= -1.0
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angles[2] %= 2*math.pi
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return np.degrees(angles) if degrees else angles
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return np.degrees(eulers) if degrees else eulers
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# # Static constructors
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@ -408,7 +388,7 @@ class Quaternion:
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halfangle = math.atan(np.linalg.norm(rodrigues))
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c = math.cos(halfangle)
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w = c
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x,y,z = c*rodrigues
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x,y,z = rodrigues/c
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return cls([w,x,y,z])
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@ -431,24 +411,19 @@ class Quaternion:
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@classmethod
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def fromEulers(cls,
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eulers,
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type = 'Bunge',
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degrees = False):
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if not isinstance(eulers, np.ndarray): eulers = np.array(eulers,dtype='d')
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eulers = np.radians(eulers) if degrees else eulers
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c = np.cos(0.5 * eulers)
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s = np.sin(0.5 * eulers)
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sigma = 0.5*(eulers[0]+eulers[2])
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delta = 0.5*(eulers[0]-eulers[2])
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c = np.cos(0.5*eulers[1])
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s = np.sin(0.5*eulers[1])
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if type.lower() == 'bunge' or type.lower() == 'zxz':
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w = c[0] * c[1] * c[2] - s[0] * c[1] * s[2]
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x = c[0] * s[1] * c[2] + s[0] * s[1] * s[2]
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y = - c[0] * s[1] * s[2] + s[0] * s[1] * c[2]
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z = c[0] * c[1] * s[2] + s[0] * c[1] * c[2]
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else:
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w = c[0] * c[1] * c[2] - s[0] * s[1] * s[2]
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x = s[0] * s[1] * c[2] + c[0] * c[1] * s[2]
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y = s[0] * c[1] * c[2] + c[0] * s[1] * s[2]
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z = c[0] * s[1] * c[2] - s[0] * c[1] * s[2]
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w = c * np.cos(sigma)
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x = -s * np.cos(delta)
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y = -s * np.sin(delta)
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z = -c * np.sin(sigma)
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return cls([w,x,y,z])
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@ -460,49 +435,16 @@ class Quaternion:
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if m.shape != (3,3) and np.prod(m.shape) == 9:
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m = m.reshape(3,3)
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tr = np.trace(m)
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if tr > 1e-8:
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s = math.sqrt(tr + 1.0)*2.0
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w = 0.5*math.sqrt(1.+m[0,0]+m[1,1]+m[2,2])
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x = 0.5*math.sqrt(1.+m[0,0]-m[1,1]-m[2,2])
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y = 0.5*math.sqrt(1.-m[0,0]+m[1,1]-m[2,2])
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z = 0.5*math.sqrt(1.-m[0,0]-m[1,1]+m[2,2])
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return cls(
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[ s*0.25,
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(m[2,1] - m[1,2])/s,
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(m[0,2] - m[2,0])/s,
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(m[1,0] - m[0,1])/s,
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])
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x *= -1 if m[2,1] < m[1,2] else 1
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y *= -1 if m[0,2] < m[2,0] else 1
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z *= -1 if m[1,0] < m[0,1] else 1
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elif m[0,0] > m[1,1] and m[0,0] > m[2,2]:
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t = m[0,0] - m[1,1] - m[2,2] + 1.0
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s = 2.0*math.sqrt(t)
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return cls(
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[ (m[2,1] - m[1,2])/s,
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s*0.25,
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(m[0,1] + m[1,0])/s,
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(m[2,0] + m[0,2])/s,
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])
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elif m[1,1] > m[2,2]:
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t = -m[0,0] + m[1,1] - m[2,2] + 1.0
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s = 2.0*math.sqrt(t)
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return cls(
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[ (m[0,2] - m[2,0])/s,
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(m[0,1] + m[1,0])/s,
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s*0.25,
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(m[1,2] + m[2,1])/s,
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])
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else:
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t = -m[0,0] - m[1,1] + m[2,2] + 1.0
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s = 2.0*math.sqrt(t)
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return cls(
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[ (m[1,0] - m[0,1])/s,
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(m[2,0] + m[0,2])/s,
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(m[1,2] + m[2,1])/s,
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s*0.25,
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])
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return cls( np.array([w,x,y,z])/math.sqrt(w**2 + x**2 + y**2 + z**2))
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@classmethod
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@ -663,7 +605,7 @@ class Symmetry:
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quaternion,
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who = []):
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"""List of symmetrically equivalent quaternions based on own symmetry."""
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return [quaternion*q for q in self.symmetryQuats(who)]
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return [q*quaternion for q in self.symmetryQuats(who)]
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def inFZ(self,R):
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@ -829,7 +771,7 @@ class Orientation:
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else:
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self.quaternion = Quaternion.fromRandom(randomSeed=random)
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elif isinstance(Eulers, np.ndarray) and Eulers.shape == (3,): # based on given Euler angles
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self.quaternion = Quaternion.fromEulers(Eulers,type='bunge',degrees=degrees)
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self.quaternion = Quaternion.fromEulers(Eulers,degrees=degrees)
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elif isinstance(matrix, np.ndarray) : # based on given rotation matrix
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self.quaternion = Quaternion.fromMatrix(matrix)
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elif isinstance(angleAxis, np.ndarray) and angleAxis.shape == (4,): # based on given angle and rotation axis
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@ -855,16 +797,15 @@ class Orientation:
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return 'Symmetry: %s\n' % (self.symmetry) + \
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'Quaternion: %s\n' % (self.quaternion) + \
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'Matrix:\n%s\n' % ( '\n'.join(['\t'.join(map(str,self.asMatrix()[i,:])) for i in range(3)]) ) + \
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'Bunge Eulers / deg: %s' % ('\t'.join(map(str,self.asEulers('bunge',degrees=True))) )
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'Bunge Eulers / deg: %s' % ('\t'.join(map(str,self.asEulers(degrees=True))) )
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def asQuaternion(self):
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return self.quaternion.asList()
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def asEulers(self,
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type = 'bunge',
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degrees = False,
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standardRange = False):
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return self.quaternion.asEulers(type, degrees, standardRange)
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):
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return self.quaternion.asEulers(degrees)
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eulers = property(asEulers)
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def asRodrigues(self):
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@ -912,13 +853,13 @@ class Orientation:
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"""
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if self.symmetry != other.symmetry: raise TypeError('disorientation between different symmetry classes not supported yet.')
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misQ = self.quaternion.conjugated()*other.quaternion
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misQ = other.quaternion*self.quaternion.conjugated()
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mySymQs = self.symmetry.symmetryQuats() if SST else self.symmetry.symmetryQuats()[:1] # take all or only first sym operation
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otherSymQs = other.symmetry.symmetryQuats()
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for i,sA in enumerate(mySymQs):
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for j,sB in enumerate(otherSymQs):
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theQ = sA.conjugated()*misQ*sB
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theQ = sB*misQ*sA.conjugated()
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for k in range(2):
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theQ.conjugate()
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breaker = self.symmetry.inFZ(theQ) \
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@ -939,10 +880,10 @@ class Orientation:
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"""Axis rotated according to orientation (using crystal symmetry to ensure location falls into SST)"""
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if SST: # pole requested to be within SST
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for i,q in enumerate(self.symmetry.equivalentQuaternions(self.quaternion)): # test all symmetric equivalent quaternions
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pole = q.conjugated()*axis # align crystal direction to axis
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pole = q*axis # align crystal direction to axis
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if self.symmetry.inSST(pole,proper): break # found SST version
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else:
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pole = self.quaternion.conjugated()*axis # align crystal direction to axis
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pole = self.quaternion*axis # align crystal direction to axis
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return (pole,i if SST else 0)
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@ -951,7 +892,7 @@ class Orientation:
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color = np.zeros(3,'d')
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for q in self.symmetry.equivalentQuaternions(self.quaternion):
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pole = q.conjugated()*axis # align crystal direction to axis
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pole = q*axis # align crystal direction to axis
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inSST,color = self.symmetry.inSST(pole,color=True)
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if inSST: break
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