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Merge pull request #1 from zjmorgan/Update-goniometers
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Update goniometers
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@zjmorgan
zjmorgan authored Jul 12, 2021
2 parents 454d52f + 0137f54 commit 4eb31dd
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206 changes: 179 additions & 27 deletions model/goniometer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -910,7 +910,7 @@ def calculate_angles_to_rotate_vector(self, starting_vec, ending_vec, starting_a
Return:
best_angles: list of the 3 angles phi, chi, omega found. None if invalid inputs were given
"""
# print "starting_vec, ending_vec", starting_vec, ending_vec
# print "starting_vec, ending_vec", starting_vec, ending_vec

# We want to find a rotation matrix R
# R puts starting_vec onto ending_vec
Expand Down Expand Up @@ -1025,9 +1025,148 @@ def __init__(self, wavelength_control=False):
AngleInfo('Omega', friendly_range=[172, 229], random_range=[3, 4]),
]

#===============================================================================================
#===============================================================================================
#===============================================================================================

#===============================================================================================
class TOPAZCryoGoniometer(LimitedGoniometer):
"""TOPAZ cryogoniometer that only has omega rotational freedom with chi fixed at 0.0"""


#Chi is 0
chi = Float(0, label="Fixed Chi angle (deg)", desc="the fixed Chi angle that the goniometer has, in degrees.")

view = View(Item('name'), Item('description'),
Item('wavelength_control'),
Item('wavelength_bandwidth', visible_when="wavelength_control"),
Item('wavelength_minimum', visible_when="wavelength_control"),
Item('wavelength_maximum', visible_when="wavelength_control"),
Item('chi'), Item('angles_desc', style='readonly'))

#-------------------------------------------------------------------------
def __init__(self, wavelength_control=False):
"""Constructor"""
#Init the base class
LimitedGoniometer.__init__(self, wavelength_control)

#Some info about the goniometer
self.name = "TOPAZ CryoGoniometer"
self.description = "TOPAZ Cryogoniometer with one degree of freedom (omega), with chi fixed at 0 degrees."

self.chi = +0

#Make the angle info object
self.gonio_angles = [
AngleInfo('Omega'),
]

#-------------------------------------------------------------------------
def __eq__(self, other):
"""Return True if the contents of self are equal to other."""
return LimitedGoniometer.__eq__(self,other) and \
(np.deg2rad(self.chi) == other.chi)

#-------------------------------------------------------------------------
def get_fitness_function_c_code(self):
#C code for the fitness of phi,chi, omega.
args = []
for i in xrange(1):
# Each angle
for j in xrange(2):
args.append(self.gonio_angles[i].random_range[j])
# Last argument is the fixed chi value.
args.append( np.deg2rad(self.chi) )
args = tuple(args)

s = """
FLOAT fitness_function(FLOAT phi, FLOAT chi, FLOAT omega)
{
FLOAT phi_min = %f;
FLOAT phi_max = %f;
FLOAT chi_mid = %f;
FLOAT phi_mid = (phi_min + phi_max) / 2;
FLOAT fitness = absolute(chi - chi_mid)*10.0 + absolute(phi - phi_mid)/10.0;
// Big penalties for being out of the range
if (phi < phi_min) fitness += (phi_min - phi) * 1.0;
if (phi > phi_max) fitness += (phi - phi_max) * 1.0;
return fitness;
}
""" % (args)
return s

#-------------------------------------------------------------------------------
def get_phi_chi_omega(self, angles):
"""Given a list of angles (which may have more or less angles depending on goniometer type),
return the equivalent (phi, chi, omega) in radians."""
phi = angles[0]
chi = np.deg2rad(self.chi)
omega = 0
return (phi, chi, omega)

#-------------------------------------------------------------------------------
def make_q_rot_matrix(self, angles):
"""Generate the necessary rotation matrix for use in the getq method.
The q rotation matrix corresponds to the opposite (negative) angles that
are the sample rotation angles.
Parameters:
angles: should be a list of angle values, in unfriendly units, that matches the
# of angles of this goniometer.
"""
#For other instruments, this method may be different.
(phi, chi, omega) = self.get_phi_chi_omega(angles)

#In Q space, detector coverage rotates OPPOSITE to what the real space rotation is.
#Because that is where the detectors and incident beam go, AS SEEN BY THE SAMPLE.
#So wee need to invert the sample orientation matrix to find the one that will apply to the Q vector.
return numpy_utils.opposite_rotation_matrix(phi, chi, omega)


#-------------------------------------------------------------------------------
def make_sample_rot_matrix(self, angles):
"""Generate the sample rotation matrix, from the given sample orientation angles.
Unlike make_q_rot_matrix(), the direct angles are used here.
This matrix will be used to calculate the scattering angle of specific reflections.
Parameters:
angles: should be a list of angle values, in unfriendly units, that matches the
# of angles of this goniometer.
"""
(phi, chi, omega) = self.get_phi_chi_omega(angles)
return numpy_utils.rotation_matrix(phi, chi, omega)


#-------------------------------------------------------------------------
def calculate_angles_to_rotate_vector(self, *args, **kwargs):
"""Calculate a set of sample orientation angles that rotate a single vector.
TRY to return a sample orientation that is achievable by the goniometer.
Parameters:
see LimitedGoniometer.calculate_angles_to_rotate_vector()
Return:
best_angles: list of the 2 angles found. None if invalid inputs were given
"""
#The parent class does the work
best_angles = LimitedGoniometer.calculate_angles_to_rotate_vector(self, *args, **kwargs)

if best_angles is None:
return None
else:
(phi, chi, omega) = best_angles

if not np.abs(chi - np.deg2rad(self.chi)) < 0.5/57:
# Have some tolerance (1 deg) in chi to help find anything.
return None
else:
#Okay, we found a decent chi
return [omega]

#===============================================================================================
#===============================================================================================
#===============================================================================================
Expand All @@ -1038,9 +1177,12 @@ class SNAPLimitedGoniometer(LimitedGoniometer):
#Chi is 0
chi = Float(0, label="Fixed Chi angle (deg)", desc="the fixed Chi angle that the goniometer has, in degrees.")

view = View(Item('name'), Item('description'),
view = View(Item('name'),
Item('description'),
Item('wavelength_control'),
Item('wavelength_bandwidth', visible_when="wavelength_control"), Item('wavelength_minimum', visible_when="wavelength_control"), Item('wavelength_maximum', visible_when="wavelength_control"),
Item('wavelength_bandwidth', visible_when="wavelength_control"),
Item('wavelength_minimum', visible_when="wavelength_control"),
Item('wavelength_maximum', visible_when="wavelength_control"),
Item('chi'), Item('angles_desc', style='readonly'))

#-------------------------------------------------------------------------
Expand Down Expand Up @@ -1581,10 +1723,14 @@ class ImagineMiniKappaGoniometer(LimitedGoniometer):
#Alpha is 24 degrees
alpha = Float(24.0, label="Fixed Alpha angle (deg)", desc="the fixed Chi angle that the goniometer has, in degrees.")

view = View(Item('name'), Item('description'),
view = View(Item('name'),
Item('description'),
Item('wavelength_control'),
Item('wavelength_bandwidth', visible_when="wavelength_control"), Item('wavelength_minimum', visible_when="wavelength_control"), Item('wavelength_maximum', visible_when="wavelength_control"),
Item('alpha'), Item('angles_desc', style='readonly'))
Item('wavelength_bandwidth', visible_when="wavelength_control"),
Item('wavelength_minimum', visible_when="wavelength_control"),
Item('wavelength_maximum', visible_when="wavelength_control"),
Item('alpha'),
Item('angles_desc', style='readonly'))

#-------------------------------------------------------------------------
def __init__(self, wavelength_control=False):
Expand All @@ -1602,54 +1748,61 @@ def __init__(self, wavelength_control=False):
#Make the angle info object
#Not sure if these limits match IMAGINE's mini-kappa
self.gonio_angles = [
AngleInfo('Phi', friendly_range=[-10, 240], random_range=[-0.4188790205, 4.1887902048 ]),
AngleInfo('Kappa', friendly_range=[0, 255], random_range=[0, 4.4505895926 ]),
AngleInfo('Omega', friendly_range=[0, 354], random_range=[0, 6.1784655521 ]),
AngleInfo('Phi', friendly_range=[315-240, 315--10], random_range=[np.deg2rad(315-240), np.deg2rad(315--10)]),
AngleInfo('Chi', friendly_range=[0, 48], random_range=[0, np.deg2rad(48)]),
AngleInfo('Omega', friendly_range=[225, 255+354], random_range=[np.deg2rad(225), np.deg2rad(255+354)]),
]

#-------------------------------------------------------------------------
def get_fitness_function_c_code(self):
#C code for the fitness of phi,kappa, omega.
#C code for the fitness of phi, kappa, omega.
args = []
for i in xrange(2):
for i in xrange(3):
for j in xrange(2):
args.append(self.gonio_angles[i].random_range[j])
args = tuple(args)

s = """
FLOAT fitness_function(FLOAT phi, FLOAT chi, FLOAT omega)
{
FLOAT phi_min = %f;
FLOAT phi_max = %f;
FLOAT chi_min = %f;
FLOAT chi_max = %f;
FLOAT omega_min = %f;
FLOAT omega_max = %f;
FLOAT phi_mid = (phi_min + phi_max) / 2;
FLOAT chi_mid = %f;
FLOAT chi_mid = (chi_min + chi_max) / 2;
FLOAT omega_mid = (omega_min + omega_max) / 2;
FLOAT fitness = absolute(chi - chi_mid)*10.0 + absolute(omega - omega_mid)/10.0 + absolute(phi - phi_mid)/10.0;
FLOAT fitness = absolute(chi - chi_mid) + absolute(omega - omega_mid) + absolute(phi - phi_mid);
// Big penalties for being out of the range
if (phi < phi_min) fitness += (phi_min - phi) * 1.0;
if (phi > phi_max) fitness += (phi - phi_max) * 1.0;
if (chi < chi_min) fitness += (chi_min - chi) * 1.0;
if (chi > chi_max) fitness += (chi - chi_max) * 1.0;
if (omega < omega_min) fitness += (omega_min - omega) * 1.0;
if (omega > omega_max) fitness += (omega - omega_max) * 1.0;
// if (phi < phi_min || phi > phi_max) fitness += 10;
// if (chi < chi_min || chi > chi_max) fitness += 10;
// if (omega < omega_min || omega > omega_max) fitness += 10;
return fitness;
}
""" % (args)
return s


#-------------------------------------------------------------------------------
def get_phi_kappa_omega(self, angles):
def get_phi_chi_omega(self, angles):
"""Given a list of angles (which may have more or less angles depending on goniometer type),
return the equivalent (phi, kappa, omega) in radians."""
(phi) = angles[0]
(kappa) = angles[1]
(chi) = angles[1]
(omega) = angles[2]
return (phi, kappa, omega)
return (phi, chi, omega)

#-------------------------------------------------------------------------------
def make_q_rot_matrix(self, angles):
Expand All @@ -1662,14 +1815,13 @@ def make_q_rot_matrix(self, angles):
# of angles of this goniometer.
"""
#For other instruments, this method may be different.
(phi, kappa, omega) = self.get_phi_kappa_omega(angles)
(phi, chi, omega) = self.get_phi_chi_omega(angles)

#In Q space, detector coverage rotates OPPOSITE to what the real space rotation is.
#Because that is where the detectors and incident beam go, AS SEEN BY THE SAMPLE.

#So wee need to invert the sample orientation matrix to find the one that will apply to the Q vector.
return numpy_utils.kappa_opposite_rotation_matrix(phi, np.deg2rad(self.alpha), kappa, omega)

return numpy_utils.opposite_rotation_matrix(phi, chi, omega)

#-------------------------------------------------------------------------------
def make_sample_rot_matrix(self, angles):
Expand All @@ -1681,9 +1833,9 @@ def make_sample_rot_matrix(self, angles):
angles: should be a list of angle values, in unfriendly units, that matches the
# of angles of this goniometer.
"""
(phi, kappa, omega) = self.get_phi_kappa_omega(angles)
return numpy_utils.kappa_rotation_matrix(phi, np.deg2rad(self.alpha), kappa, omega)

(phi, chi, omega) = self.get_phi_chi_omega(angles)
return numpy_utils.rotation_matrix(phi, chi, omega)

#-------------------------------------------------------------------------
def calculate_angles_to_rotate_vector(self, *args, **kwargs):
Expand All @@ -1702,17 +1854,16 @@ def calculate_angles_to_rotate_vector(self, *args, **kwargs):
if best_angles is None:
return None
else:
(phi, kappa, omega) = best_angles
(phi, chi, omega) = best_angles
# Check that all angles are within allowable ranges, or return none
if self.gonio_angles[0].is_angle_valid(phi) and \
self.gonio_angles[1].is_angle_valid(kappa) and \
self.gonio_angles[1].is_angle_valid(chi) and \
self.gonio_angles[2].is_angle_valid(omega):
return best_angles
else:
return None



#===============================================================================================
#===============================================================================================
#===============================================================================================
Expand Down Expand Up @@ -2941,6 +3092,7 @@ def initialize_goniometers():
goniometers.append( TestLimitedGoniometer() )
goniometers.append( TopazInHouseGoniometer() )
goniometers.append( TopazAmbientGoniometer() )
goniometers.append( TOPAZCryoGoniometer() )
goniometers.append( SNAPLimitedGoniometer() )
goniometers.append( MandiGoniometer() )
goniometers.append( MandiVaryOmegaGoniometer() )
Expand Down
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