def parse_xparm(xparm_file):
'''Read an xparm file, return the rotation axis and beam vector in the
XDS coordinate frame. Also the vector in this same coordinate frame to
the start of the first pixel on the detector.'''
xdata = xds_read_xparm(xparm_file)
ra = xdata['axis']
beam = xdata['beam']
distance = xdata['distance']
px = xdata['px']
py = xdata['py']
ox = xdata['ox']
oy = xdata['oy']
nx = xdata['nx']
ny = xdata['ny']
x = xdata['x']
y = xdata['y']
x_to_d = - matrix.col(x) * px * ox + \
- matrix.col(y) * py * oy + \
distance * matrix.col(x).cross(matrix.col(y))
return ra, beam, x_to_d.elems, (px, py), distance, (nx, ny), x, y
def spot2q(xparm_file, spot_file):
'''Read XPARM file from XDS IDXREF and transform all positions to q
space.'''
# FIXME in the code which follows below I will need to read the detector
# axes, not assume that they are aligned along 1,0,0 and 0,1,0! This is
# however in the xparm file.
xparm_d = xds_read_xparm(xparm_file)
A, B, C = xparm_d['a'], xparm_d['b'], xparm_d['c']
cell = xparm_d['cell']
space_group_number = xparm_d['spacegroup']
spacegroup = sgtbx.space_group_symbols(space_group_number).hall()
sg = sgtbx.space_group(spacegroup)
wavelength = xparm_d['wavelength']
distance = xparm_d['distance']
beam = xparm_d['beam']
nx = xparm_d['nx']
ny = xparm_d['ny']
px = xparm_d['px']
py = xparm_d['py']
ox = xparm_d['ox']
oy = xparm_d['oy']
normal = xparm_d['normal']
phi_start = xparm_d['phi_start']
phi_width = xparm_d['phi_width']
start = xparm_d['starting_frame'] - 1
axis = matrix.col(xparm_d['axis'])
N = matrix.col(normal)
D = distance * N
S = matrix.col(beam)
Sd = (wavelength * distance / (wavelength * S.dot(N))) * S
d = math.sqrt(Sd.dot())
off = Sd - D
bx = ox + off.elems[0] / px
by = oy + off.elems[1] / py
dtor = 180.0 / math.pi
m = matrix.sqr(A + B + C)
mi = m.inverse()
indices = []
for record in open(spot_file, 'r').readlines():
l = record.split()
if not l:
continue
if len(l) != 7:
raise RuntimeError, 'error reading spot index'
X, Y, i = map(float, l[:3])
h, k, l = map(int, l[-3:])
# FIXME here the detector axes become important...
phi = (i - start) * phi_width + phi_start
X = px * (X - bx)
Y = py * (Y - by)
P = matrix.col([X, Y, 0]) + Sd
scale = wavelength * math.sqrt(P.dot())
x = P.elems[0] / scale
y = P.elems[1] / scale
z = P.elems[2] / scale
Sp = matrix.col([x, y, z]) - S
# now index the reflection
q = Sp.rotate(axis, - 1 * phi / dtor).elems
print '%.5f %.5f %.5f' % q
return
def get_abc_from_xparm(xparm_file):
xdata = xds_read_xparm(xparm_file)
return xdata['a'], xdata['b'], xdata['c']
