def test_eu():
#Conventional cell gives:
#0 = (0, 1, 1)
#1 = (0, 1, -1)
#6 = (1, 0, -1)
gv = get_eu_gv()
v1 = gv[0]
v2 = gv[1]
v3 = gv[6]
assert len(v1) == 3
print v1, v2, v3
# This means that the g-vectors are in row direction
l = lattice(v1, v2, v3, direction='row')
esum = 0.0
gv = rc_array(gv, direction='row')
# print v1, v2, v3
print "ubi/r2c", l.r2c
print "ub /c2r", l.c2r
print "dot(l.r2c, gv[0])", dot(l.r2c, gv[0])
for v in gv:
#print ("%8.5f "*3+"%8.5f "*3)%tuple( list(v)+list(l.flip(v))),
assert len(v) == 3
err = l.remainders(v)
esum += sqrt(dot(err, err))
#print "%.5f"%(sqrt(dot(err,err)))
#import sys
#sys.exit()
# print
assert esum / len(gv) < 0.0102, "Did not fit"
s = l.score(gv, tol=0.1)
assert s == 583, "Expecting to index 582 peaks, got %s" % (s)
print "Indexing of eu3.gve, Average", esum / len(gv), "for", s, "peaks"
print "UBI is", l.r2c
def test_fft():
gv = get_eu_gv()
from ImageD11.fft_index_refac import grid
from ImageD11.indexing import ubitocellpars, write_ubi_file,\
refine
g = grid(np=128, mr=1.0, nsig=20)
g.gv_to_grid_new(gv)
g.fft()
g.props()
g.peaksearch(open("eu.patterson_pks", "w"))
g.read_peaks("eu.patterson_pks")
vecs = rc_array(g.UBIALL.T, direction='col')
assert vecs.shape == (3, g.colfile.nrows)
order = argsort(g.colfile.sum_intensity)[::-1]
vecs = take(vecs, order, axis=1)
min_pks = 300
ntry = 0
assert g.gv.shape[1] == 3
tv = rc_array(g.gv, direction='row')
print "Finding lattice l1 from patterson"
l1 = find_lattice(vecs, min_vec2=9, test_vecs=tv, n_try=20)
print "r2c == ubi matrix"
print l1.r2c
print "scores", l1.score(tv)
print "cell", ubitocellpars(l1.r2c)
l1.r2c = refine(l1.r2c, g.gv, tol=0.1)
l1.c2r = inv(l1.r2c)
print "With refine", l1.score(tv)
print "cell", ubitocellpars(l1.r2c)
print "Finding lattice l2 with gvectors to test"
l2 = find_lattice(vecs, min_vec2=9, n_try=20, test_vecs=tv)
print "r2c == ubi matrix"
print l2.r2c
print "scores", l2.score(tv)
print "cell", ubitocellpars(l2.r2c)
l2.r2c = refine(l2.r2c, g.gv, tol=0.1)
l2.c2r = inv(l2.r2c)
print "With refine", l2.score(tv)
print "cell", ubitocellpars(l2.r2c)
return
def test_eu_find():
gv = get_eu_gv()
vecs = rc_array(gv, direction="row")
l = find_lattice(
vecs,
# This next bit is important - tolerance for gve
# is very different to patterson
min_vec2=1. / 81.,
n_try=20,
test_vecs=vecs)
s = l.score(vecs, tol=0.1)
print "Eu3 using find_lattice scores", s
def test2():
""" Adding a fourth vector """
o = lattice(array([1, 0, 0], float),
array([0, 1, 0], float),
array([0, 0, 2], float),
direction='row')
# ... how to do it?
#print o.r2c
#print o.c2r
u = rc_array([0, 0, 1], dtype=float, direction='row')
r = o.remainders(u)
assert (r == array([0, 0, 1], float)).all()
o = o.withvec(r)
assert allclose(o.c2r[0], array([1, 0, 0], float))
assert allclose(o.c2r[1], array([0, 1, 0], float))
assert allclose(o.c2r[2], array([0, 0, 1], float))
assert allclose(o.c2r, o.r2c)
def test1():
""" Make a lattice from 3 vectors"""
o = lattice(array([1, 0, 0], float),
array([2, 1, 0], float),
array([3, 4, 1], float),
direction='col')
assert allclose(o.c2r[:, 0], array([1, 0, 0], float))
assert allclose(o.c2r[:, 1], array([0, 1, 0], float))
assert allclose(o.c2r[:, 2], array([0, 0, 1], float))
# Both are identity
assert allclose(o.c2r, eye(3))
assert allclose(o.r2c, eye(3))
""" 3 more difficult vectors """
o = lattice(array([1, 0, 1], float),
array([0, 1, 0], float),
array([0, 0, 1], float),
direction='col')
assert allclose(o.c2r[:, 0], array([1, 0, 0], float)), str(o.c2r)
assert allclose(o.c2r[:, 1], array([0, 1, 0], float)), str(o.c2r)
assert allclose(o.c2r[:, 2], array([0, 0, 1], float)), str(o.c2r)
assert allclose(o.c2r, eye(3))
assert allclose(o.r2c, eye(3))
""" 3 shorter vectors """
# print '3 short'
o = lattice(array([1e-2, 0, 0], float),
array([0, 1e-2, 0], float),
array([0, 0, 1e-2], float),
direction='row')
# Consider those as 3 g-vectors
# supplied rows go into c2r matrix as columns
# The r2c matrix (==ubi) is then the inverse of this
assert allclose(o.r2c[:, 0], array([100, 0, 0], float)), str(o.r2c)
assert allclose(o.r2c[:, 1], array([0, 100, 0], float)), str(o.r2c)
assert allclose(o.r2c[:, 2], array([0, 0, 100], float)), str(o.r2c)
# g-vectors written as rows here - note transpose
g = array([[1e-2, 0., 0.], [1e-2, 1e-2, 0.], [1e-2, 0., 1e-2],
[0., 0., 1e-2]])
#print g, g.shape
g = rc_array(g, direction='row')
assert g.shape == (4, 3)
g.check()
#print g.shape
#print g
hkl = o.flip(g)
assert hkl.direction == 'col', hkl.direction
# print g,"\nFlips to give\n",hkl
assert allclose(
hkl,
rc_array(array([[1., 0., 0.], [1., 1., 0.], [1., 0., 1.], [0., 0.,
1.]]).T,
direction='col')), str(hkl)
# print '3 long'
""" 3 longer vectors """
o = lattice(array([10, 0, 0], float),
array([0, 10, 0], float),
array([0, 0, 10], float),
direction='col')
assert allclose(o.r2c[:, 0], array([10, 0, 0], float)), str(o.r2c)
assert allclose(o.r2c[:, 1], array([0, 10, 0], float)), str(o.r2c)
assert allclose(o.r2c[:, 2], array([0, 0, 10], float)), str(o.r2c)
test_col_vec = rc_array([10., 10., 10.], direction='col')
flipped = o.flip(test_col_vec)
assert flipped.direction == 'row'
assert allclose(flipped, rc_array([1., 1., 1.],
direction='col')), str(flipped)
""" 3 shorter vectors row"""
# print '3 short'
o = lattice(array([1e-2, 0, 0], float),
array([0, 1e-2, 0], float),
array([0, 0, 1e-2], float),
direction='row')
# Consider those as 3 g-vectors
assert allclose(o.r2c[:, 0], array([100, 0, 0], float)), str(o.r2c)
assert allclose(o.r2c[:, 1], array([0, 100, 0], float)), str(o.r2c)
assert allclose(o.r2c[:, 2], array([0, 0, 100], float)), str(o.r2c)
g = rc_array(
[[1e-2, 0., 0.], [1e-2, 1e-2, 0.], [1e-2, 0., 1e-2], [0., 0., 1e-2]],
direction='row')
hkl = o.flip(g)
# print g,"\nFlips to give\n",hkl
assert allclose(
hkl,
rc_array([[1., 0., 0.], [1., 1., 0.], [1., 0., 1.], [0., 0., 1.]],
direction='col').T), str(hkl)
assert hkl.direction == 'col'
# print '3 long'
""" 3 longer vectors """
o = lattice(array([10, 0, 0], float),
array([0, 10, 0], float),
array([0, 0, 10], float),
direction='col')
assert allclose(o.r2c[:, 0], array([10, 0, 0], float)), str(o.r2c)
assert allclose(o.r2c[:, 1], array([0, 10, 0], float)), str(o.r2c)
assert allclose(o.r2c[:, 2], array([0, 0, 10], float)), str(o.r2c)
hkl = o.flip(rc_array([10., 10., 10.], direction='col'))
assert allclose(hkl, rc_array([1., 1., 1.], direction='row')), str(hkl)
# FIXME - check is transpose of row is OK or not
# this break the row / col symmetry?
# TODO - think on whether h / g are really col pairs
# Find the Sands book.
# print hkl
""" 3 really hard vectors """
global DEBUG
DEBUG = True
o = lattice(array([991, 990, 990], float),
array([990, 991, 990], float),
array([990, 990, 991], float),
direction='row')
# Eg, these were long g-vectors far from origin but making a basis
# Anticipate them making a ubi matrix with 990
#assert allclose( o.c2r , array( [[ 991. , 1. , 1.],
# [ 990. , 0. , -1.],
# [ 990. , -1. , 0.],] )), str(o.c2r)
# OK
u = rc_array([990., 990., 990.], direction='row')
assert (o.nearest( u ) == rc_array([991.,990.,990],
direction='row')).all(),\
str(o.nearest( u ))+" "+str( u )
o = o.withvec(u) # Remove long
# print o.c2r
# print o.r2c
assert allclose(o.c2r[:, 0], array([1, 0, 0], float)), o.c2r
assert allclose(o.c2r[:, 1], array([0, 1, 0], float)), o.c2r
assert allclose(o.c2r[:, 2], array([0, 0, 1], float)), o.c2r
DEBUG = False
options, args = parser.parse_args()
o = indexing.indexer()
if options.gvefilename is None or \
not os.path.exists(options.gvefilename):
print "You need to supply a gvector file with the -g option"
sys.exit()
o.readgvfile(options.gvefilename)
mags = [[np.dot(g, g), tuple(g)] for g in o.gv]
mags.sort()
sorted = np.array([np.array(g[1]) for g in mags])
all_gvecs = rc_array.rc_array(sorted.copy(), direction='row')
cur_gvecs = rc_array.rc_array(sorted.copy(), direction='row')
ubis = []
try:
for i in range(options.ngrains):
if len(cur_gvecs) < 3:
print "Ran out of unindexed peaks"
break
# print "Peak remaining",len(cur_gvecs)
if options.use_fft:
# do fft
g = grid(np=options.np, mr=options.mr, nsig=options.nsig)
g.gv_to_grid_new(cur_gvecs)