def UBxds_to_mos(self):
""" Convert the XDS direct space Orientation Matrix to a mosflm OM
Mosflm CAMERA coordinate frame has orthonormal axes with:
z // rotation axis
y perpendicular to z and to the beam
x perpendicular to y and z (along the beam)
For more details see the mosflm documentation:
http://www.ccp4.ac.uk/dist/x-windows/Mosflm/doc/mosflm_user_guide.html#a3
"""
if "UB" not in self.dict.keys():
self.debut()
BEAM = vec3(self.dict["beam"])
ROT = vec3(self.dict["rot"])
UBxds = self.dict["UB"]
CAMERA_z = ROT.normalize()
CAMERA_y = CAMERA_z.cross(BEAM).normalize()
CAMERA_x = CAMERA_y.cross(CAMERA_z)
CAMERA = mat3(CAMERA_x,CAMERA_y,CAMERA_z).transpose()
return CAMERA * UBxds * self.dict["wavelength"]
def get_beam_origin(self):
"""Calculate the direct beam origin from the
detector beam coordinate."""
distance = self.dict["distance"]
beam = vec3(self.dict["beam"])
XDSdetector_X = vec3(self.dict["detector_X"])
XDSdetector_Y = vec3(self.dict["detector_Y"])
XDSdetector_Z = XDSdetector_X.cross(XDSdetector_Y)
# Calculate the direct beam coordinates on the detector
beamCx = self.dict["origin"][0]*self.dict["pixel_size"][0]
beamCy = self.dict["origin"][1]*self.dict["pixel_size"][1]
beamCz = beam*XDSdetector_Z
beamX = beamCx - beam*XDSdetector_X*distance/beamCz
beamY = beamCy - beam*XDSdetector_Y*distance/beamCz
beamXp = beamX/self.dict["pixel_size"][0]
beamYp = beamY/self.dict["pixel_size"][1]
if _debug:
if "origin" in self.dict.keys():
print "\nDEBUG: BEAM center read from XDS in pixel:",
print "%9.2f %9.2f" % tuple(self.dict["origin"])
# When given by XDS, verifies that my calculation is correct
assert (self.dict["origin"][0] - beamXp) < 0.05
assert (self.dict["origin"][1] - beamYp) < 0.05
print "DEBUG: BEAM center calculated in pixel:\t%9.2f %9.2f" % (beamXp,beamYp)
print "DEBUG: BEAM center calculated in mm:\t\t%9.2f %9.2f\n" % (beamX,beamY)
return beamXp, beamYp
def UBxds_to_dnz(self):
""" Convert the XDS direct space Orientation Matrix to a mosflm OM
Denzo CAMERA coordinate frame has orthonormal axes with:
y // to the rotation (spindel) axis
z // to the beam
x perpendicular to z and to the beam
For more details see the denzo documentation:
http://www.ccp4.ac.uk/dist/x-windows/Mosflm/doc/mosflm_user_guide.html#a3
"""
if "UB" not in self.dict.keys():
self.debut()
BEAM = vec3(self.dict["beam"])
ROT = vec3(self.dict["rot"])
UBxds = self.dict["UB"]
CAMERA_y = ROT.normalize()
CAMERA_x = CAMERA_y.cross(BEAM).normalize()
CAMERA_z = CAMERA_x.cross(CAMERA_y)
CAMERA = mat3(CAMERA_x,CAMERA_y,CAMERA_z).transpose()
return CAMERA * UBxds
def compareSolutions(solutions1, solutions2, _epsilon=0.1):
"Check if both solution matchs, with a tolerated difference of _epsilon."
l = 0
allMatchs = True
for s1 in solutions1:
match = False
minRMSdiff = 1000
for s2 in solutions2:
l += 1
vecDiff = vec3(s1[2],s1[1],s1[0]) - vec3(s2)
RMSdiff = rootSquareSum(vecDiff)/3.
#print vecDiff, RMSdiff
if RMSdiff < minRMSdiff:
minRMSdiff = RMSdiff
if RMSdiff < _epsilon:
match = True
break
if match:
solutions2.remove(s2)
print "Good match for solution: %9.3f%9.3f%9.3f" % tuple(s1),
print " Minimum RMSdiff = %.3f" % minRMSdiff
else:
allMatchs = False
print "Warning: no match for solution: %9.3f%9.3f%9.3f" %tuple(s1),
print " Minimum RMSdiff = %.3f" % minRMSdiff
print l
return allMatchs
def compareSolutions(solutions1, solutions2, _epsilon=0.1):
"Check if both solution matchs, with a tolerated difference of _epsilon."
l = 0
allMatchs = True
for s1 in solutions1:
match = False
minRMSdiff = 1000
for s2 in solutions2:
l += 1
vecDiff = vec3(s1[2], s1[1], s1[0]) - vec3(s2)
RMSdiff = rootSquareSum(vecDiff) / 3.
#print vecDiff, RMSdiff
if RMSdiff < minRMSdiff:
minRMSdiff = RMSdiff
if RMSdiff < _epsilon:
match = True
break
if match:
solutions2.remove(s2)
print "Good match for solution: %9.3f%9.3f%9.3f" % tuple(s1),
print " Minimum RMSdiff = %.3f" % minRMSdiff
else:
allMatchs = False
print "Warning: no match for solution: %9.3f%9.3f%9.3f" % tuple(s1),
print " Minimum RMSdiff = %.3f" % minRMSdiff
print l
return allMatchs
def debut(self):
"Do simple cristallographic calculations from XDS initial parameters"
A = vec3(self.dict["A"])
B = vec3(self.dict["B"])
C = vec3(self.dict["C"])
volum = A.cross(B)*C
Ar = B.cross(C).__div__(volum)
Br = C.cross(A).__div__(volum)
Cr = A.cross(B).__div__(volum)
"""
Ar = B.cross(C)/volum
Br = C.cross(A)/volum
Cr = A.cross(B)/volum
"""
UBxds = mat3(Ar,Br,Cr)
BEAM = vec3(self.dict["beam"])
wavelength = 1/BEAM.length()
self.dict["cell_volum"] = volum
self.dict["wavelength"] = wavelength
self.dict["Ar"] = Ar
self.dict["Br"] = Br
self.dict["Cr"] = Cr
self.dict["UB"] = UBxds
def debut(self):
"Do simple cristallographic calculations from XDS initial parameters"
A = vec3(self.dict["A"])
B = vec3(self.dict["B"])
C = vec3(self.dict["C"])
volum = A.cross(B) * C
Ar = B.cross(C).__div__(volum)
Br = C.cross(A).__div__(volum)
Cr = A.cross(B).__div__(volum)
"""
Ar = B.cross(C)/volum
Br = C.cross(A)/volum
Cr = A.cross(B)/volum
"""
UBxds = mat3(Ar, Br, Cr)
BEAM = vec3(self.dict["beam"])
wavelength = 1 / BEAM.length()
self.dict["cell_volum"] = volum
self.dict["wavelength"] = wavelength
self.dict["Ar"] = Ar
self.dict["Br"] = Br
self.dict["Cr"] = Cr
self.dict["UB"] = UBxds
def UB_to_cellParam(UB):
"""Return an array containing the cell parameters with angles en degree
>>> ub = mat3(0.0045624910668708527, 0.0013380296069423175, -0.0019732516590096985,
0.0014703215926493108, 0.0037937417049515054, 0.0057564982133741704,
7.3231240428790203e-05, -0.002607820316488004, 0.007361827462991322)
>>> print UB_to_cellParam(ub)
"""
Ar = vec3(UB.getColumn(0))
Br = vec3(UB.getColumn(1))
Cr = vec3(UB.getColumn(2))
return (Ar.length(), Br.length(), Cr.length(), Br.angle(Cr) * r2d, Cr.angle(Ar) * r2d, Ar.angle(Br) * r2d)
def __init__(self, filename=None):
self.DNZAxes = ey, -ex, -ez
self.verticalAxis = vec3(1, 0, 0)
self.spindleAxis = vec3(0, 0, 1)
self.motorAxis = [0.,1.,0.]
self.info = "Denzo Parser"
self.fileType = "Denzo"
if filename:
self.parse(filename)
self.spaceGroupName = self.spg.upper()
self.spaceGroupNumber = SPGlib2[self.spg.lower()]
def UB_to_cellParam(UB):
"""Return an array containing the cell parameters with angles en degree
>>> ub = mat3(0.0045624910668708527, 0.0013380296069423175, -0.0019732516590096985,
0.0014703215926493108, 0.0037937417049515054, 0.0057564982133741704,
7.3231240428790203e-05, -0.002607820316488004, 0.007361827462991322)
>>> print UB_to_cellParam(ub)
"""
Ar = vec3(UB.getColumn(0))
Br = vec3(UB.getColumn(1))
Cr = vec3(UB.getColumn(2))
return (Ar.length(), Br.length(), Cr.length(),
Br.angle(Cr)*r2d, Cr.angle(Ar)*r2d, Ar.angle(Br)*r2d)
def getOmega(self):
"""Calculate an Omega value (in radian) wich defines how the fast (X) and
slow (Y) axis of detector files are orientated toward the camera frame.
The calculation of this omega value is supposed to reflect the Mosflm
definition...
But it seems that I get different values from the mosflm defaults... This
may be due to: A) My missanderstanding of the mosflm documentation, B)
Some tricks in the image reading routines.
Nonetheless, this calculated value works for translating
correctly the beam coordinates from XDS to mosflm [at least in the tested
cases of MARCCD, MAR345 and ADSC detector images].
Reference:
http://www.ccp4.ac.uk/dist/x-windows/Mosflm/doc/mosflm_user_guide.html#a3
"""
# Xd = CAMERA_y = beam
# Yd = CAMERA_z = rot
Xd = vec3(self.dict["beam"]).normalize()
Yd = vec3(self.dict["rot"]).normalize()
CAMERA_x = Xd.cross(Yd)
CAMERA = mat3(CAMERA_x, Xd, Yd).transpose()
# This is the definition of the fast:X and slow:Y axis for the detector files.
XDSdetector_X = vec3(self.dict["detector_X"])
XDSdetector_Y = vec3(self.dict["detector_Y"])
# Now this axes are translated in the mosflm Camera frame
Xs = XDSdetector_X*CAMERA
Ys = XDSdetector_Y*CAMERA
# Both angles should be identical.
omegaX = Xd.angle(Xs)
omegaY = Yd.angle(Ys)
if _debug:
print "DEBUG: X xds: fast =",XDSdetector_X
print "DEBUG: Y xds: slow =",XDSdetector_Y
print "DEBUG: Xs: fast =",XDSdetector_X,"->", Xs
print "DEBUG: Ys: slow =",XDSdetector_Y,"->", Ys
print "DEBUG: Xd: ", Xd
print "DEBUG: Yd: ", Yd
print "DEBUG: OmegaX: %8.2f" % (omegaX*r2d)
print "DEBUG: OmegaY: %8.2f" % (omegaY*r2d)
return omegaX
def BusingLevy(rcell):
cosr = map(cosd, rcell[3:6])
sinr = map(sind, rcell[3:6])
Vr = volum(rcell)
X = ex * rcell[0]
Y = rcell[1] * (ex * cosr[2] + ey * sinr[2])
c = rcell[0] * rcell[1] * sinr[2] / Vr
cosAlpha = (cosr[1] * cosr[2] - cosr[0]) / (sinr[1] * sinr[2])
Z = vec3([rcell[2] * cosr[1], -1 * rcell[2] * sinr[1] * cosAlpha, 1 / c])
return mat3(X, Y, Z)
def BusingLevy(rcell):
cosr = map(cosd, rcell[3:6])
sinr = map(sind, rcell[3:6])
Vr = volum(rcell)
BX = ex * rcell[0]
BY = rcell[1] * (ex * cosr[2] + ey * sinr[2])
c = rcell[0] * rcell[1] * sinr[2] / Vr
cosAlpha = (cosr[1] * cosr[2] - cosr[0]) / (sinr[1] * sinr[2])
BZ = vec3([rcell[2] * cosr[1], -1 * rcell[2] * sinr[1] * cosAlpha, 1 / c])
return mat3(BX, BY, BZ)
def get_U0(self, rcell=None, vertical=None, spindle=None, clean=False):
"Calculate denzo U0 from spindle, verctical"
if not rcell: rcell = self.cell_r
if not vertical: vertical = self.verticalAxis
if not spindle: spindle = self.spindleAxis
Bmat = self.get_B(rcell)
vertical = vec3(vertical)
spindle = vec3(spindle)
U0y = (Bmat * spindle).normalize()
U0xi = Bmat * vertical
U0x = (U0xi - (U0xi * U0y) * U0y).normalize()
U0 = mat3(U0x, U0y, U0x.cross(U0y)).transpose()
# cleaning... Just cosmetic, not realy needed.
if clean: U0 = cleanU0(U0)
return U0
def axis_and_angle(mat_3):
"""From a rotation matrix return a corresponding rotation as an
axis (a normalized vector) and angle (in radians).
The angle is in the interval (-pi, pi]
"""
asym = -asymmetrical_part(mat_3)
axis = vec3(asym[1, 2], asym[2, 0], asym[0, 1])
sine = axis.length()
if abs(sine) > 1.e-10:
axis = axis/sine
projector = dyadic_product(axis, axis)
cosine = trace((mat_3-projector))/(3.-axis*axis)
angle = angle_from_sine_and_cosine(sine, cosine)
else:
tsr = 0.5*(mat_3+mat3(1))
diag = tsr[0, 0], tsr[1, 1], tsr[3, 3]
i = tsr.index(max(diag))
axis = vec3(tsr.getRow(i)/(tsr[i, i])**0.5)
angle = 0.
if trace(tsr) < 2.:
angle = math.pi
return axis, angle
def axis_and_angle(mat_3):
"""From a rotation matrix return a corresponding rotation as an
axis (a normalized vector) and angle (in radians).
The angle is in the interval (-pi, pi]
"""
asym = -asymmetrical_part(mat_3)
axis = vec3(asym[1, 2], asym[2, 0], asym[0, 1])
sine = axis.length()
if abs(sine) > 1.e-10:
axis = axis / sine
projector = dyadic_product(axis, axis)
cosine = trace((mat_3 - projector)) / (3. - axis * axis)
angle = angle_from_sine_and_cosine(sine, cosine)
else:
tsr = 0.5 * (mat_3 + mat3(1))
diag = tsr[0, 0], tsr[1, 1], tsr[2, 2]
i = list(diag).index(max(diag))
axis = vec3(tsr.getRow(i) / (tsr[i, i])**0.5)
angle = 0.
if trace(tsr) < 2.:
angle = math.pi
return axis, angle
def getTwoTheta(self):
"""Tries to calculate the 2theta angle (in radian) of the detector.
I am not completely sure of this calculation. How 2theta is precisely
geometricaly defined in mosflm ?
I need to look in the mosflm code where it is taken into account.
"""
BEAM = vec3(self.dict["beam"])
ROT = vec3(self.dict["rot"]).normalize()
camY = ROT.cross(BEAM)
XDSdetector_X = vec3(self.dict["detector_X"]).normalize()
XDSdetector_Y = vec3(self.dict["detector_Y"]).normalize()
#XDSdetector_Z = XDSdetector_X.cross(XDSdetector_Y)
#print beam.angle(XDSdetector_Z)*r2d
if abs(ROT * XDSdetector_X) - 1 <= 0.05:
detecorVector = -XDSdetector_Y
#print 1
elif abs(ROT * XDSdetector_Y) - 1 <= 0.05:
detecorVector = XDSdetector_X
#print 2
else:
raise Exception, "Can't calculate TwoTheta angle"
return camY.angle(detecorVector)
See http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html """ __version__ = "0.4.4" __author__ = "Pierre Legrand ([email protected])" __date__ = "22-11-2017" __copyright__ = "Copyright (c) 2007-2017 Pierre Legrand" __license__ = "New BSD, http://www.opensource.org/licenses/bsd-license.php" import time import os from pycgtypes import vec3 from pycgtypes import mat3 EX, EY, EZ = vec3(1, 0, 0), vec3(0, 1, 0), vec3(0, 0, 1) V3FMT = "%9.6f %9.6f %9.6f" PI = 3.1415926535897931 D2R = PI / 180. def set_detplugin_lib(dettype): """Find out if we can set the LIB keyword""" if dettype == "hdf5dec" and "XDS_LIB_HDF5DEC" in os.environ: return os.environ["XDS_LIB_HDF5DEC"] else: return None def det_dist(distance, dettype): "Return the disance with the proper sign."
Original fortran version:
Phil Evans MRC LMB, Cambridge
""" % _progname
from XOconv import mat3T, printmat, is_orthogonal, spg_num2symb, BusingLevy, \
SPGlib, map_r2d, PGequiv, openWriteClose, openReadClose, \
rootSquareSum, random_3axes, kappaVector, SPGlib2
from XOconv import MosflmParser, DenzoParser, XDSParser
VERBOSE = True
r2d = 180 / math.pi
radian2degree = lambda a: a * r2d
degree2radian = lambda a: a / r2d
ex, ey, ez = vec3(1, 0, 0), vec3(0, 1, 0), vec3(0, 0, 1)
X, Y, Z = ex, ey, ez
Qdnz2mos = mat3T(ez, ex, ey)
class CrystalVector(vec3):
""" Define a crystal vector to represent reciprocal or direct space vectors
NOTE that it can accept fractional coordinates like
CrystalVector("(1.2 1.22 4.9)")
NOTE that as it inherit from the Vector class, CrystalVectors support the
usual arithmetic operations ('v1', 'v2': vectors, 's': scalar):
- 'v1+v2' (addition)
- 'v1-v2' (subtraction)
Original fortran version:
Phil Evans MRC LMB, Cambridge
""" % _progname
from XOconv import mat3T, printmat, is_orthogonal, spg_num2symb, BusingLevy, \
SPGlib, map_r2d, PGequiv, openWriteClose, openReadClose, \
rootSquareSum, random_3axes, kappaVector, SPGlib2
from XOconv import MosflmParser, DenzoParser, XDSParser
VERBOSE = True
r2d = 180/math.pi
radian2degree = lambda a: a*r2d
degree2radian = lambda a: a/r2d
ex, ey, ez = vec3(1,0,0), vec3(0,1,0), vec3(0,0,1)
X, Y, Z = ex, ey, ez
Qdnz2mos = mat3T(ez, ex, ey)
class CrystalVector(vec3):
""" Define a crystal vector to represent reciprocal or direct space vectors
NOTE that it can accept fractional coordinates like
CrystalVector("(1.2 1.22 4.9)")
NOTE that as it inherit from the Vector class, CrystalVectors support the
usual arithmetic operations ('v1', 'v2': vectors, 's': scalar):
- 'v1+v2' (addition)
- 'v1-v2' (subtraction)
- 'v1*v2' (scalar product)
# Test code
if __name__ == '__main__':
from Scientific.Geometry import Vector ##.Transformation import *
from Scientific.Geometry.Transformation import Rotation
from random import random
#
Q = mat3(0.36, 0.48, -0.8, -0.8, 0.6, 0, 0.48, 0.64, 0.60)
axis_q, angle_q = axis_and_angle(Q)
print "Axis_q: %9.6f%9.6f%9.6f" % tuple(axis_q),
print "Angle_q: %10.5f" % (angle_q * R2D)
#
for iii in range(1e6):
axis_i = list(vec3([random(), random(), random()]).normalize())
angle_i = 3 * random()
rme = mat3().rotation(angle_i, vec3(axis_i))
axis_1, angle_1 = axis_and_angle(rme)
v = Vector(axis_i)
r = Rotation(v, angle_i)
axis_2, angle_2 = r.axisAndAngle()
axis_d = (axis_1 - vec3(tuple(axis_2))).length()
angle_d = abs(angle_1 - angle_2)
if (angle_d > 1e-13) or (axis_d > 1e-13):
print "Angle_d: %.3e" % (angle_d * R2D),
print " Axis_length_diff: %.3e" % axis_d
print "Axis_i: %9.6f%9.6f%9.6f" % tuple(axis_i),
print "Angle_i: %10.5f" % (angle_i * R2D)
print "Axis_1: %9.6f%9.6f%9.6f" % tuple(axis_1),
def parse(self, filename):
"Denzo x-file parser"
try:
xfile = open(filename,"r").read().splitlines()
xhead = xfile[:7]
xtail = xfile[-30:]
except:
raise ParserError, "Error, Can't read file: %s" % filename
if xhead[0][:6] == "HEADER":
xhead = xhead[1:]
self.title = xhead[0]
mats = map(str2floats, xhead[1:4])
self.UB = mat3(mats[0][:3], mats[1][:3], mats[2][:3]).transpose()
self.U = mat3(mats[0][3:], mats[1][3:], mats[2][3:]).transpose()
if len(xhead[4].split()) == 4: line1, line2 = xhead[4], xhead[5][:40]
else: line1, line2 = xhead[4][:48], xhead[4][48:88]
self.phi0, self.phi1, self.xtod, self.wavel = str2floats(line1)
self.rotz, self.roty, self.rotx, self.mosaic = str2floats(line2)
self.crystal_setting = self.rotz, self.roty, self.rotx
# Extract reciprocal unit cell vectors
self.Ar = vec3(self.UB.getColumn(0))
self.Br = vec3(self.UB.getColumn(1))
self.Cr = vec3(self.UB.getColumn(2))
# Extract reciprocal cell parameters
self.cell_r = UB_to_cellParam(self.UB)
self.cell = reciprocal(self.cell_r)
# Calculate direct unit cell vectors
self.volum_r = self.Ar.cross(self.Br)*self.Cr
self.volum = 1/self.volum_r
self.A = self.Br.cross(self.Cr)*self.volum
self.B = self.Cr.cross(self.Ar)*self.volum
self.C = self.Ar.cross(self.Br)*self.volum
for line in xtail:
lineSplit = line.split()
if line.upper().count("SPACE GROUP"):
self.spg = lineSplit[2]
elif line.upper().count("SPINDLE AXIS"):
self.spindleAxis = map(int,lineSplit[2:5])
self.verticalAxis = map(int,lineSplit[7:])
elif line.upper().count("MOTOR AXIS"):
self.motorAxis = map(float,lineSplit[2:5])
elif line.upper().count("DISTANCE"):
self.distance = float(lineSplit[1])
elif line.upper().count("X BEAM"):
self.beam_x = float(lineSplit[2])
self.beam_y = float(lineSplit[5])
elif line.upper().count("SECTOR"):
self.sector = int(lineSplit[1])
elif line.upper().count("RAW DATA FILE"):
self.template = str(lineSplit[-1]).replace("'","")
elif line.upper().count("UNIT CELL"):
self.cell2 = map(float,lineSplit[2:])
# Verify that the cell extracted from UB correspond
# to the cell read from the xfile tail
assert abs(self.cell2[0] - self.cell[0]) < 1e-2 and \
abs(self.cell2[1] - self.cell[1]) < 1e-2 and \
abs(self.cell2[2] - self.cell[2]) < 1e-2 and \
abs(self.cell2[3] - self.cell[3]) < 2e-2 and \
abs(self.cell2[4] - self.cell[4]) < 2e-2 and \
abs(self.cell2[5] - self.cell[5]) < 2e-2
# Verify that the calculation method for UB_to_Rotxyz works correctly
_rotx, _roty, _rotz = self.UB_to_Rotxyz()
assert abs(_rotx - self.rotx) < 2e-2 and \
abs(_roty - self.roty) < 2e-2 and \
abs(_rotz - self.rotz) < 2e-2
# Verify that the calculation method for Adnz_to_Udnz works correctly
_U = self.Adnz_to_Udnz()
print diffMAT(_U, self.U)
assert diffMAT(_U, self.U) < 5e-6
def kappaVector(alpha):
return vec3([-sin(alpha), 0, cos(alpha)])
def kappaVector(alpha):
return vec3([-sin(alpha), 0, cos(alpha)])
return axis, angle
# Test code
if __name__ == '__main__':
from Scientific.Geometry import Vector ##.Transformation import *
from Scientific.Geometry.Transformation import Rotation
from random import random
#
Q = mat3(0.36, 0.48, -0.8, -0.8, 0.6, 0, 0.48, 0.64, 0.60)
axis_q, angle_q = axis_and_angle(Q)
print "Axis_q: %9.6f%9.6f%9.6f" % tuple(axis_q),
print "Angle_q: %10.5f" % (angle_q*R2D)
#
for iii in range(1e6):
axis_i = list(vec3([random(), random(), random()]).normalize())
angle_i = 3*random()
rme = mat3().rotation(angle_i, vec3(axis_i))
axis_1, angle_1 = axis_and_angle(rme)
v = Vector(axis_i)
r = Rotation(v, angle_i)
axis_2, angle_2 = r.axisAndAngle()
axis_d = (axis_1 - vec3(tuple(axis_2))).length()
angle_d = abs(angle_1 - angle_2)
if (angle_d > 1e-13) or (axis_d > 1e-13):
print "Angle_d: %.3e" % (angle_d*R2D),
print " Axis_length_diff: %.3e" % axis_d
print "Axis_i: %9.6f%9.6f%9.6f" % tuple(axis_i),
print "Angle_i: %10.5f" % (angle_i*R2D)
print "Axis_1: %9.6f%9.6f%9.6f" % tuple(axis_1),
""" XIO plugin for the export parameters as an XDS.INP format
See http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html
"""
__version__ = "0.3.4"
__author__ = "Pierre Legrand ([email protected])"
__date__ = "15-12-2009"
__copyright__ = "Copyright (c) 2007-2009 Pierre Legrand"
__license__ = "New BSD, http://www.opensource.org/licenses/bsd-license.php"
import time
from pycgtypes import vec3
from pycgtypes import mat3
EX, EY, EZ = vec3(1, 0, 0), vec3(0, 1, 0), vec3(0, 0, 1)
V3FMT = "%9.6f %9.6f %9.6f"
PI = 3.1415926535897931
D2R = PI/180.
def det_dist(distance, dettype):
"Return the disance with the proper sign."
detori = XDS_DETECTOR_DICT["orient"][dettype]
return distance*detori[2]
def det_spindle(dettype):
"Return the spindle axis vector."
return V3FMT % tuple(XDS_DETECTOR_DICT["orient"][dettype][3])
def polarization(wavelength):
"Guess the polarization fraction from the wavelength."
from math import cos, sin, pi
from pycgtypes import vec3, mat3
r2d = 180/pi
ex, ey, ez = vec3(1,0,0), vec3(0,1,0), vec3(0,0,1)
def kappaVector(alpha):
return vec3([-sin(alpha), 0, cos(alpha)])
def kappaVectorVertical(alpha):
return vec3([0, -cos(alpha), sin(alpha)])
# Frame definition used: Cambridge as used in Mosflm
# X = Beam_vector direction of the X-ray photons
# Z = Spindle axis, such that looking down this axis
# towards the sample, positive phi is anti-clockwise
# Y = Defined to give a right handed coordinate system
# -- SOLEIL's PX1 CrystalLogic Goniometer definitions --
GONIOMETER_NAME = "SOLEIL PROXIMA-1 CrystalLogic"
GONIOMETER_AXES_NAMES = ("Omega","Kappa","Phi")
GONIOMETER_AXES = [ez, kappaVector(49.64/r2d), ez]
GONIOMETER_DATUM = (0,0,0) # in degree
# -- DLS's MiniKappa Goniometer definitions --
#GONIOMETER_NAME = "DLS's MiniKappa"
#GONIOMETER_AXES_NAMES = ("Omega","Kappa","Phi")
#GONIOMETER_AXES = [ez, kappaVector(-24/r2d), ez]
#GONIOMETER_DATUM = (0,0,45) # in degree
#GONIOMETER_AXES = [[0.00211, 0.00143, 1.], [0.28907, 0.28990, 0.91236], [0.00691, -0.00364, 0.99997]]
#GONIOMETER_DATUM = (0,0,0) # in degree
import sys
import os.path
import math
from pycgtypes import vec3
from pycgtypes import mat3
from ThreeAxisRotation2 import *
r2d = 180/math.pi
cosd = lambda a: math.cos(a/r2d)
sind = lambda a: math.sin(a/r2d)
map_r2d = lambda l: map(lambda x: x*r2d, l)
map_d2r = lambda l: map(lambda x: x/r2d, l)
str2floats = lambda s: map(float, s.split())
ex, ey, ez = vec3(1,0,0), vec3(0,1,0), vec3(0,0,1)
Qdnz2mos = mat3( ez, ex, ey).transpose()
Qdnz2xds = mat3(-ey, ex,-ez).transpose()
Qmos2xds = mat3( ez,-ey, ex).transpose()
Qmos2dnz = mat3( ey, ez, ex).transpose()
DNZAxes = ey, -ex, -ez
if sys.version_info[:3] < (2,2,0):
True = 1
False = 0
_debug = False
#_debug = True
def kappaVectorVertical(alpha):
return vec3([0, -cos(alpha), sin(alpha)])
def kappaVectorVertical(alpha):
return vec3([0, -cos(alpha), sin(alpha)])