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"
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
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)
g.fft()
g.props()
g.peaksearch(open("eu.patterson_pks", "w"))
g.read_peaks("eu.patterson_pks")
vecs = rc_array.rc_array(g.UBIALL.T, direction='col')
assert vecs.shape == (3, g.colfile.nrows)
order = np.argsort(g.colfile.sum_intensity)[::-1]
vecs = rc_array.rc_array(np.take(vecs, order, axis=1),
direction='col')
assert g.gv.shape[1] == 3
print "Finding lattice from patterson"
# Go through and make a shortlist of lattices by scoring fft only
if options.score_fft:
test_set = vecs
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(npx=options.npx, mr=options.mr, nsig=options.nsig)
g.gv_to_grid_new(cur_gvecs)
g.fft()
g.props()
g.peaksearch(open("eu.patterson_pks", "w"))
g.read_peaks("eu.patterson_pks")
vecs = rc_array.rc_array(g.UBIALL.T, direction='col')
assert vecs.shape == (3, len(g.UBIALL))
order = np.argsort(g.colfile.sum_intensity)[::-1]
vecs = rc_array.rc_array(np.take(vecs, order, axis=1),
direction='col')
assert g.gv.shape[1] == 3
print("Finding lattice from patterson")
# Go through and make a shortlist of lattices by scoring fft only
if options.score_fft:
test_set = vecs
import numpy as np
from ImageD11 import indexing, fft_index_refac
o = indexing.indexer()
o.readgvfile("test.vecs")
g = fft_index_refac.grid(128, 1., 5.)
g.gv_to_grid_new(o.gv)
g.fft()
g.props()
g.peaksearch("pairFFT.pks")
g.read_peaks("pairFFT.pks")
tol = 0.1
tol2 = tol * tol
def refine_vector(v, gv, tol=0.25, ncycles=25, precision=1e-6):
"""
Input
v : real space lattice vector
gv : scattering vectors (no errors)
tol : tolerance for initial assignment to peak
ncycles : how much to refine
precision : when to stop refining in v += s when |s|/|v| < precision
Returns
vref : refined real space lattice vector
Uses:
hr = v[0]*gv[i,0] + v[0]*gv[i,1] + v[1]*gv[i,2] 1 per peak
hi = round(hr) = calc 1 per peak
diff = calc - hr 1 per peak
gradient = d(diff)/dv[i] = gv[j,i] 3 per peak