def editref(num):
"""editref num -- interactively edit a reflection.
"""
num = int(num)
# Get old reflection values
[oldh, oldk, oldl], oldExternalAngles, oldEnergy, oldTag, oldT = \
ubcalc.get_reflection_in_external_angles(num)
del oldT # current time will be used.
h = promptForNumber('h', oldh)
k = promptForNumber('k', oldk)
l = promptForNumber('l', oldl)
if None in (h, k, l):
_handleInputError("h,k and l must all be numbers")
reply = promptForInput('update position with current hardware setting',
'n')
if reply in ('y', 'Y', 'yes'):
positionList = settings.hardware.get_position() # @UndefinedVariable
energy = settings.hardware.get_energy() # @UndefinedVariable
else:
positionList = []
names = settings.hardware.get_axes_names() # @UndefinedVariable
for i, angleName in enumerate(names):
val = promptForNumber(angleName.rjust(7), oldExternalAngles[i])
if val is None:
_handleInputError("Please enter a number, or press "
"Return to accept default!")
return
positionList.append(val)
muliplier = settings.hardware.energyScannableMultiplierToGetKeV # @UndefinedVariable
energy = promptForNumber('energy', oldEnergy / muliplier)
if val is None:
_handleInputError("Please enter a number, or press Return "
"to accept default!")
return
energy = energy * muliplier
tag = promptForInput("tag", oldTag)
if tag == '':
tag = None
pos = settings.geometry.physical_angles_to_internal_position(
positionList) # @UndefinedVariable
ubcalc.edit_reflection(num, h, k, l, pos, energy, tag, datetime.now())
def editref(num):
"""editref num -- interactively edit a reflection.
"""
num = int(num)
# Get old reflection values
[oldh, oldk, oldl], oldExternalAngles, oldEnergy, oldTag, oldT = \
ubcalc.get_reflection_in_external_angles(num)
del oldT # current time will be used.
h = promptForNumber('h', oldh)
k = promptForNumber('k', oldk)
l = promptForNumber('l', oldl)
if None in (h, k, l):
_handleInputError("h,k and l must all be numbers")
reply = promptForInput('update position with current hardware setting',
'n')
if reply in ('y', 'Y', 'yes'):
positionList = settings.hardware.get_position() # @UndefinedVariable
energy = settings.hardware.get_energy() # @UndefinedVariable
else:
positionList = []
names = settings.hardware.get_axes_names() # @UndefinedVariable
for i, angleName in enumerate(names):
val = promptForNumber(angleName.rjust(7), oldExternalAngles[i])
if val is None:
_handleInputError("Please enter a number, or press "
"Return to accept default!")
return
positionList.append(val)
energy = promptForNumber('energy', oldEnergy)
if val is None:
_handleInputError("Please enter a number, or press Return "
"to accept default!")
return
energy = energy * settings.hardware.energyScannableMultiplierToGetKeV # @UndefinedVariable
tag = promptForInput("tag", oldTag)
if tag == '':
tag = None
pos = settings.geometry.physical_angles_to_internal_position(positionList) # @UndefinedVariable
ubcalc.edit_reflection(num, h, k, l, pos, energy, tag,
datetime.now())
def setlat(name=None, *args):
"""
setlat -- interactively enter lattice parameters (Angstroms and Deg)
setlat name a -- assumes cubic
setlat name a b -- assumes tetragonal
setlat name a b c -- assumes ortho
setlat name a b c gamma -- assumes mon/hex with gam not equal to 90
setlat name a b c alpha beta gamma -- arbitrary
"""
if name is None: # Interactive
name = promptForInput("crystal name")
a = promptForNumber(' a', 1)
b = promptForNumber(' b', a)
c = promptForNumber(' c', a)
alpha = promptForNumber('alpha', 90)
beta = promptForNumber('beta', 90)
gamma = promptForNumber('gamma', 90)
ubcalc.set_lattice(name, a, b, c, alpha, beta, gamma)
elif (isinstance(name, str) and len(args) in (1, 2, 3, 4, 6)
and allnum(args)):
# first arg is string and rest are numbers
ubcalc.set_lattice(name, *args)
else:
raise TypeError()
def setlat(name=None, *args):
"""
setlat -- interactively enter lattice parameters (Angstroms and Deg)
setlat name a -- assumes cubic
setlat name a b -- assumes tetragonal
setlat name a b c -- assumes ortho
setlat name a b c gamma -- assumes mon/hex with gam not equal to 90
setlat name a b c alpha beta gamma -- arbitrary
"""
if name is None: # Interactive
name = promptForInput("crystal name")
a = promptForNumber(' a', 1)
b = promptForNumber(' b', a)
c = promptForNumber(' c', a)
alpha = promptForNumber('alpha', 90)
beta = promptForNumber('beta', 90)
gamma = promptForNumber('gamma', 90)
ubcalc.set_lattice(name, a, b, c, alpha, beta, gamma)
elif (isinstance(name, str) and
len(args) in (1, 2, 3, 4, 6) and
allnum(args)):
# first arg is string and rest are numbers
ubcalc.set_lattice(name, *args)
else:
raise TypeError()
def editorient(idx):
"""editorient num | 'tag' -- interactively edit a crystal orientation.
"""
# Get old reflection values
[oldh, oldk, oldl], [oldx, oldy, oldz], oldExternalAngles, oldTag, oldT = \
ubcalc.get_orientation_in_external_angles(idx, True)
del oldT # current time will be used.
h = promptForNumber('h', oldh)
k = promptForNumber('k', oldk)
l = promptForNumber('l', oldl)
if None in (h, k, l):
_handleInputError("h,k and l must all be numbers")
x = promptForNumber('x', oldx)
y = promptForNumber('y', oldy)
z = promptForNumber('z', oldz)
if None in (x, y, z):
_handleInputError("x,y and z must all be numbers")
reply = promptForInput('update position with current hardware setting',
'n')
if reply in ('y', 'Y', 'yes'):
positionList = settings.hardware.get_position() # @UndefinedVariable
else:
positionList = []
names = settings.hardware.get_axes_names() # @UndefinedVariable
for i, angleName in enumerate(names):
val = promptForNumber(angleName.rjust(7), oldExternalAngles[i])
if val is None:
_handleInputError("Please enter a number, or press "
"Return to accept default!")
return
positionList.append(val)
tag = promptForInput("tag", oldTag)
if tag == '':
tag = None
pos = settings.geometry.physical_angles_to_internal_position(positionList) # @UndefinedVariable
ubcalc.edit_orientation(idx, h, k, l, x, y, z, pos, tag,
datetime.now())
def addorient(*args):
"""
addorient -- add crystal orientation interactively
addorient [h k l] [x y z] {'tag'} -- add crystal orientation in laboratory frame
"""
if len(args) == 0:
h = promptForNumber('h', 0.)
k = promptForNumber('k', 0.)
l = promptForNumber('l', 0.)
if None in (h, k, l):
_handleInputError("h,k and l must all be numbers")
x = promptForNumber('x', 0.)
y = promptForNumber('y', 0.)
z = promptForNumber('z', 0.)
if None in (x, y, z):
_handleInputError("x,y and z must all be numbers")
tag = promptForInput("tag")
if tag == '':
tag = None
ubcalc.add_orientation(h, k, l, x, y, z, tag, datetime.now())
elif len(args) in (1, 2, 3):
args = list(args)
h, k, l = args.pop(0)
if not (isnum(h) and isnum(k) and isnum(l)):
raise TypeError()
x, y, z = args.pop(0)
if not (isnum(x) and isnum(y) and isnum(z)):
raise TypeError()
if len(args) == 1:
tag = args.pop(0)
if not isinstance(tag, str):
raise TypeError()
else:
tag = None
ubcalc.add_orientation(h, k, l, x, y, z, tag, datetime.now())
else:
raise TypeError()
def editorient(num):
"""editorient num -- interactively edit a crystal orientation.
"""
num = int(num)
# Get old reflection values
[oldh, oldk, oldl], [oldx, oldy, oldz], oldTag, oldT = \
ubcalc.get_orientation(num)
del oldT # current time will be used.
h = promptForNumber('h', oldh)
k = promptForNumber('k', oldk)
l = promptForNumber('l', oldl)
if None in (h, k, l):
_handleInputError("h,k and l must all be numbers")
x = promptForNumber('x', oldx)
y = promptForNumber('y', oldy)
z = promptForNumber('z', oldz)
if None in (x, y, z):
_handleInputError("x,y and z must all be numbers")
tag = promptForInput("tag", oldTag)
if tag == '':
tag = None
ubcalc.edit_orientation(num, h, k, l, x, y, z, tag, datetime.now())
def refineub(*args):
"""
refineub {[h k l]} {pos} -- refine unit cell dimensions and U matrix to match diffractometer angles for a given hkl value
"""
if len(args) > 0:
args = list(args)
h, k, l = args.pop(0)
if not (isnum(h) and isnum(k) and isnum(l)):
raise TypeError()
else:
h = promptForNumber('h', 0.)
k = promptForNumber('k', 0.)
l = promptForNumber('l', 0.)
if None in (h, k, l):
_handleInputError("h,k and l must all be numbers")
if len(args) == 1:
pos = settings.geometry.physical_angles_to_internal_position( # @UndefinedVariable
args.pop(0))
elif len(args) == 0:
reply = promptForInput('current pos', 'y')
if reply in ('y', 'Y', 'yes'):
positionList = settings.hardware.get_position() # @UndefinedVariable
else:
currentPos = settings.hardware.get_position() # @UndefinedVariable
positionList = []
names = settings.hardware.get_axes_names() # @UndefinedVariable
for i, angleName in enumerate(names):
val = promptForNumber(angleName.rjust(7), currentPos[i])
if val is None:
_handleInputError("Please enter a number, or press"
" Return to accept default!")
return
positionList.append(val)
pos = settings.geometry.physical_angles_to_internal_position(positionList) # @UndefinedVariable
else:
raise TypeError()
pos.changeToRadians()
scale, lat = ubcalc.rescale_unit_cell(h, k, l, pos)
if scale:
lines = ["Unit cell scaling factor:".ljust(9) +
"% 9.5f" % scale]
lines.append("Refined crystal lattice:")
lines.append(" a, b, c:".ljust(9) +
"% 9.5f % 9.5f % 9.5f" % (lat[1:4]))
lines.append(" " * 12 +
"% 9.5f % 9.5f % 9.5f" % (lat[4:]))
lines.append("")
print('\n'.join(lines))
reply = promptForInput('Update crystal settings?', 'y')
if reply in ('y', 'Y', 'yes'):
ubcalc.set_lattice(*lat)
else:
print("No unit cell mismatch detected")
mc_angle, mc_axis = ubcalc.calc_miscut(h, k, l, pos)
if mc_angle:
lines = ["Miscut parameters:",]
lines.append(" angle:".ljust(9) + "% 9.5f" % mc_angle)
lines.append(" axis:".ljust(9) + "% 9.5f % 9.5f % 9.5f" % tuple(mc_axis))
print('\n'.join(lines))
reply = promptForInput('Apply miscut parameters?', 'y')
if reply in ('y', 'Y', 'yes'):
ubcalc.set_miscut(mc_axis, -mc_angle * TORAD, True)
else:
print("No miscut detected for the given settings")
ubcalc.set_miscut(None, 0, True)
def addorient(*args):
"""
addorient -- add crystal orientation interactively
addorient [h k l] [x y z] {'tag'} -- add crystal orientation with current position in laboratory frame
addorient [h k l] [x y z] (p1, .., pN) {'tag'} -- add crystal orientation in laboratory frame
"""
if len(args) == 0:
h = promptForNumber('h', 0.)
k = promptForNumber('k', 0.)
l = promptForNumber('l', 0.)
if None in (h, k, l):
_handleInputError("h,k and l must all be numbers")
x = promptForNumber('x', 0.)
y = promptForNumber('y', 0.)
z = promptForNumber('z', 0.)
if None in (x, y, z):
_handleInputError("x,y and z must all be numbers")
reply = promptForInput('current pos', 'y')
if reply in ('y', 'Y', 'yes'):
positionList = settings.hardware.get_position() # @UndefinedVariable
else:
currentPos = settings.hardware.get_position() # @UndefinedVariable
positionList = []
names = settings.hardware.get_axes_names() # @UndefinedVariable
for i, angleName in enumerate(names):
val = promptForNumber(angleName.rjust(7), currentPos[i])
if val is None:
_handleInputError("Please enter a number, or press"
" Return to accept default!")
return
positionList.append(val)
tag = promptForInput("tag")
if tag == '':
tag = None
pos = settings.geometry.physical_angles_to_internal_position(positionList) # @UndefinedVariable
ubcalc.add_orientation(h, k, l, x , y, z, pos, tag,
datetime.now())
elif len(args) in (2, 3, 4):
args = list(args)
h, k, l = args.pop(0)
if not (isnum(h) and isnum(k) and isnum(l)):
raise TypeError("h,k and l must all be numbers")
x, y, z = args.pop(0)
if not (isnum(x) and isnum(y) and isnum(z)):
raise TypeError("x,y and z must all be numbers")
if len(args) > 1:
pos = settings.geometry.physical_angles_to_internal_position( # @UndefinedVariable
args.pop(0))
else:
pos = settings.geometry.physical_angles_to_internal_position( # @UndefinedVariable
settings.hardware.get_position()) # @UndefinedVariable
if len(args) == 1:
tag = args.pop(0)
if not isinstance(tag, str):
raise TypeError("Tag value must be a string.")
if tag == '':
tag = None
else:
tag = None
ubcalc.add_orientation(h, k, l, x, y ,z, pos, tag,
datetime.now())
else:
raise TypeError("Invalid number of parameters specified for addorient command.")
def addref(*args):
"""
addref -- add reflection interactively
addref [h k l] {'tag'} -- add reflection with current position and energy
addref [h k l] (p1, .., pN) energy {'tag'} -- add arbitrary reflection
"""
multiplier = settings.hardware.energyScannableMultiplierToGetKeV
if len(args) == 0:
h = promptForNumber('h', 0.)
k = promptForNumber('k', 0.)
l = promptForNumber('l', 0.)
if None in (h, k, l):
_handleInputError("h,k and l must all be numbers")
reply = promptForInput('current pos', 'y')
if reply in ('y', 'Y', 'yes'):
positionList = settings.hardware.get_position() # @UndefinedVariable
energy = settings.hardware.get_energy() # @UndefinedVariable
else:
currentPos = settings.hardware.get_position() # @UndefinedVariable
positionList = []
names = settings.hardware.get_axes_names() # @UndefinedVariable
for i, angleName in enumerate(names):
val = promptForNumber(angleName.rjust(7), currentPos[i])
if val is None:
_handleInputError("Please enter a number, or press"
" Return to accept default!")
return
positionList.append(val)
energy = promptForNumber('energy', settings.hardware.get_energy() / multiplier) # @UndefinedVariable
if energy is None:
_handleInputError("Please enter a number, or press "
"Return to accept default!")
return
energy *= multiplier
tag = promptForInput("tag")
if tag == '':
tag = None
pos = settings.geometry.physical_angles_to_internal_position(positionList) # @UndefinedVariable
ubcalc.add_reflection(h, k, l, pos, energy, tag,
datetime.now())
elif len(args) in (1, 2, 3, 4):
args = list(args)
h, k, l = args.pop(0)
if not (isnum(h) and isnum(k) and isnum(l)):
raise TypeError("h,k and l must all be numbers")
if len(args) >= 2:
pos = settings.geometry.physical_angles_to_internal_position( # @UndefinedVariable
args.pop(0))
energy = args.pop(0) * multiplier
if not isnum(energy):
raise TypeError("Energy value must be a number")
else:
pos = settings.geometry.physical_angles_to_internal_position( # @UndefinedVariable
settings.hardware.get_position()) # @UndefinedVariable
energy = settings.hardware.get_energy() # @UndefinedVariable
if len(args) == 1:
tag = args.pop(0)
if not isinstance(tag, str):
raise TypeError("Tag value must be a string")
if tag == '':
tag = None
else:
tag = None
ubcalc.add_reflection(h, k, l, pos, energy, tag,
datetime.now())
else:
raise TypeError("Too many parameters specified for addref command.")
def setlat(name=None, *args):
"""
setlat -- interactively enter lattice parameters (Angstroms and Deg)
setlat name 'Cubic' a -- sets Cubic system
setlat name 'Tetragonal' a c -- sets Tetragonal system
setlat name 'Hexagonal' a c -- sets Hexagonal system
setlat name 'Orthorhombic' a b c -- sets Orthorombic system
setlat name 'Rhombohedral' a alpha -- sets Rhombohedral system
setlat name 'Monoclinic' a b c beta -- sets Monoclinic system
setlat name 'Triclinic' a b c alpha beta gamma -- sets Triclinic system
setlat name a -- assumes Cubic system
setlat name a b -- assumes Tetragonal system
setlat name a b c -- assumes Orthorombic system
setlat name a b c angle -- assumes Monoclinic system with beta not equal to 90 or
Hexagonal system if a = b and gamma = 120
setlat name a b c alpha beta gamma -- sets Triclinic system
"""
if name is None: # Interactive
name = promptForInput("crystal name")
system = None
systen_dict = {1: "Triclinic",
2: "Monoclinic",
3: "Orthorhombic",
4: "Tetragonal",
5: "Rhombohedral",
6: "Hexagonal",
7: "Cubic"}
while system is None:
system_fmt = "\n".join(["crystal system",] +
["%d) %s" % (k, v)
for (k, v) in systen_dict.items()] +
['',])
system = promptForNumber(system_fmt, 1)
if system not in systen_dict.keys():
print("Invalid crystal system index selection.\n")
print("Please select vale between 1 and 7.")
system = None
a = promptForNumber(' a', 1)
args = (a,)
if system in (1, 2, 3):
b = promptForNumber(' b', a)
args += (b,)
if system in (1, 2, 3, 4, 6):
c = promptForNumber(' c', a)
args += (c,)
if system in (1, 5):
alpha = promptForNumber('alpha', 90)
args += (alpha,)
if system in (1, 2):
beta = promptForNumber('beta', 90)
args += (beta,)
if system in (1,):
gamma = promptForNumber('gamma', 90)
args += (gamma,)
args = (systen_dict[system],) + args
elif not isinstance(name, str):
raise TypeError("Invalid crystal name.")
ubcalc.set_lattice(name, *args)
def addref(*args):
"""
addref -- add reflection interactively
addref [h k l] {'tag'} -- add reflection with current position and energy
addref [h k l] (p1, .., pN) energy {'tag'} -- add arbitrary reflection
"""
if len(args) == 0:
h = promptForNumber('h', 0.)
k = promptForNumber('k', 0.)
l = promptForNumber('l', 0.)
if None in (h, k, l):
_handleInputError("h,k and l must all be numbers")
reply = promptForInput('current pos', 'y')
if reply in ('y', 'Y', 'yes'):
positionList = settings.hardware.get_position() # @UndefinedVariable
energy = settings.hardware.get_energy() # @UndefinedVariable
else:
currentPos = settings.hardware.get_position() # @UndefinedVariable
positionList = []
names = settings.hardware.get_axes_names() # @UndefinedVariable
for i, angleName in enumerate(names):
val = promptForNumber(angleName.rjust(7), currentPos[i])
if val is None:
_handleInputError("Please enter a number, or press"
" Return to accept default!")
return
positionList.append(val)
energy = promptForNumber('energy', settings.hardware.get_energy()) # @UndefinedVariable
if val is None:
_handleInputError("Please enter a number, or press "
"Return to accept default!")
return
muliplier = settings.hardware.energyScannableMultiplierToGetKeV # @UndefinedVariable
energy = energy * muliplier
tag = promptForInput("tag")
if tag == '':
tag = None
pos = settings.geometry.physical_angles_to_internal_position(positionList) # @UndefinedVariable
ubcalc.add_reflection(h, k, l, pos, energy, tag,
datetime.now())
elif len(args) in (1, 2, 3, 4):
args = list(args)
h, k, l = args.pop(0)
if not (isnum(h) and isnum(k) and isnum(l)):
raise TypeError()
if len(args) >= 2:
pos = settings.geometry.physical_angles_to_internal_position( # @UndefinedVariable
args.pop(0))
energy = args.pop(0)
if not isnum(energy):
raise TypeError()
else:
pos = settings.geometry.physical_angles_to_internal_position( # @UndefinedVariable
settings.hardware.get_position()) # @UndefinedVariable
energy = settings.hardware.get_energy() # @UndefinedVariable
if len(args) == 1:
tag = args.pop(0)
if not isinstance(tag, str):
raise TypeError()
else:
tag = None
ubcalc.add_reflection(h, k, l, pos, energy, tag,
datetime.now())
else:
raise TypeError()