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_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,
minlen = 3. )
g.gv_to_grid_new(gv)
g.fft()
g.props()
g.peaksearch(open("eu.patterson_pks","w"))
g.read_peaks("eu.patterson_pks")
vecs = g.UBIALL
order = argsort( g.colfile.sum_intensity )[::-1]
min_pks = 300
try:
for i in order:
print vecs[i], g.colfile.sum_intensity[i]
for j in order[i:]:
for k in order[j:]:
print i,j,k
try:
l = lattice( vecs[i], vecs[j], vecs[k],
space='real')
t = 0.1
ref = refine( l.vi, gv, t)
l = lattice( ref[0], ref[1], ref[2], space='real')
print "UBI:"
print l.vi
print ubitocellpars(l.vi)
s = l.score_recip( gv , t )
print "Indexes",s ,"at tolerance",t
except:
import traceback
print traceback.print_exc()
raise Exception("error")
if s > min_pks:
write_ubi_file( "trial.ubi", [ l.vi ] )
raise Exception("Really bad control structure")
except:
import traceback
print traceback.print_exc()
print "Got something"
else:
# Test vectors are the g-vectors
# Sort by length before searching??
logging.info("Doing lattice search")
l = lattice_reduction.find_lattice(
cur_gvecs,
min_vec2=options.min_vec2,
n_try=options.n_try,
test_vecs=all_gvecs,
tol=options.tol,
fraction_indexed=options.fraction_indexed,
noisy=options.noisy,
)
if l is None:
break
l.r2c = indexing.refine(l.r2c, all_gvecs, tol=options.tol)
l.c2r = np.linalg.inv(l.r2c)
#print "all_gv 3,4", all_gvecs[3:5]
#print np.dot(l.r2c, all_gvecs[3:5].T)
#print l.score(all_gvecs[3:5], tol = options.tol)
#print l.remainders( all_gvecs[3:5])
all = len(all_gvecs)
npks = l.score(all_gvecs, tol=options.tol)
if (1.0 * npks / len(all_gvecs)) < options.fraction_indexed:
break
dr = indexing.calc_drlv2(l.r2c, all_gvecs)
t2 = options.tol * options.tol
# print "tol, dr",t2,dr.shape, [d for d in dr[:10]] # print it !!!
n2 = np.sum(np.where(dr < t2, 1, 0))