def __init__(self,
data,
nmax=20,
rmax=None,
scan=True,
fraction=0.9,
smear=True,
prefix=None,
weight='i',
delta_q=None):
self.data = data
self.smear = smear
self.delta_q = delta_q
self.setup_weighting_scheme(weight)
if (self.smear):
self.set_up_smear()
self.int_scale = flex.max(self.data.i)
self.nmax = nmax
if (rmax is None):
rmax = int(get_rg(data) * 3.0 / 2.0)
self.rmax = rmax
self.scan = scan
self.prefix = prefix
self.fraction = fraction
self.nlm_array = math.nlm_array(nmax)
self.nlm_total = self.nlm_array.coefs().size()
self.nn_array = math.nl_array(nmax)
self.nn = self.nn_array.nl()
self.nn_total = self.nn_array.coefs().size()
def __init__(self, nmax, Cnm, coef_table,m):
self.nmax=nmax
self.Cnm = Cnm
self.coef_table = coef_table
self.Inm = math.nl_array(nmax)
self.m=m ## testing the most populated cases
self.coef_table_m = self.coef_table[self.m]
self.x = None
self.ndim = (self.nmax-self.m)/2+1
self.n = self.ndim
self.domain =[(-1.0,1.0)]*self.ndim
self.target_data=flex.double()
self.n_list=range(self.m,nmax+1,2)
self.n_indx_list=range(self.ndim)
for nn in self.n_list:
self.target_data.append( self.Cnm.get_coef(nn,self.m) )
# self.solution=flex.random_double(self.n)*2-1
# self.target_data=self.calc_Cnm_from_Inm(self.solution)
self.scale = self.target_data.norm()**2
# self.optimizer = de.differential_evolution_optimizer(self, population_size=self.ndim,eps=1e-8,n_cross=self.n/2)
# self.run_simplex()
# self.run_dssa()
lowest_score=1e8
for ii in range(10):
self.run_lbfgs()
score=self.target(self.x)
if(score < lowest_score):
lowest_score=score
self.best_solution=self.x.deep_copy()
print list(self.x), score
print lowest_score
def tst_2d_zernike_mom(n, l, filename, h5file, flag):
rebuilt = open(filename, 'w')
# image = generate_image()
# image=ImageToDat("/Users/wyf/Desktop/test11.png")
image = preprocess_image(h5file, flag)
# image = ImageToDat('cha.png')
NP = int(smath.sqrt(image.size()))
N = int(NP / 2)
print "=====", NP, N
grid_2d = math.two_d_grid(N, nmax)
grid_2d.clean_space(image)
grid_2d.construct_space_sum()
zernike_2d_mom = math.two_d_zernike_moments(grid_2d, nmax)
moments = zernike_2d_mom.moments()
coefs = flex.real(moments)
nl_array = math.nl_array(nmax)
nls = nl_array.nl()
nl_array.load_coefs(nls, coefs)
lfg = math.log_factorial_generator(nmax)
# print nl_array.get_coef(n,l)*2
for nl, c in zip(nls, moments):
if (abs(c) < 1e-3):
c = 0
print nl, c
reconst = flex.complex_double(NP**2, 0)
for nl, c in zip(nls, moments):
n = nl[0]
l = nl[1]
if (l > 0):
c = c * 2
#rzfa = math.zernike_2d_radial(n,l,lfg)
rap = math.zernike_2d_polynome(n, l) #,rzfa)
i = 0
for x in range(0, NP):
x = x - N
for y in range(0, NP):
y = y - N
rr = smath.sqrt(x * x + y * y) / N
if rr > 1.0:
value = 0.0
else:
tt = smath.atan2(y, x)
value = rap.f(rr, tt)
reconst[i] = reconst[i] + value * c
i = i + 1
i = 0
for x in range(0, NP):
for y in range(0, NP):
value = reconst[i].real
print >> rebuilt, x, y, value
i = i + 1
rebuilt.close()
def tst_solving_Inm(nmax):
Inm=math.nl_array(nmax)
nls = Inm.nl()
size = nls.size()
coefs = flex.random_double(size)
Inm.load_coefs( nls, coefs )
coef_table = tst_integral_triple_zernike2d(nmax)
Cnm = calc_Cnm_from_Inm( Inm, coef_table, nmax )
new_Inm=math.nl_array(nmax)
for n in range( nmax+1 ):
for m in range(n,-1,-2):
Cnm_value = Cnm.get_coef( n, m )
coef = coef_table[m].get_coef(n,n,n).real
# value = smath.sqrt( Cnm_value/coef )
if(coef != 0):
value = ( Cnm_value/coef )
print n,m,Inm.get_coef(n,m)**2, value
def get_nn_array_for_code(code, nns, codes, rmaxs, nmax=10):
this_one = codes.index(code)
coefs = nns[this_one]
nn_array = math.nl_array(nmax)
nn = nn_array.nl()
nn_size = nn.size()
coefs = coefs[0:nn_size]
nn_array.load_coefs(nn, coefs)
print code, rmaxs[this_one]
for c in coefs:
print c
return nn_array
def calc_Cnm_from_Inm( Inm, coef_table, nmax ):
Cnm=math.nl_array(nmax)
for n in range( 0,nmax+1,2 ): # only even number (n,m)
for m in range(0,n+1,2 ):
temp = 0
for n1 in range( m,nmax+1,2 ):
for n2 in range( m,n1,2 ):
i,j,k=sorted([n,n1,n2],reverse=True)
temp = temp + coef_table[m].get_coef(i,j,k).real*Inm.get_coef(n1,m)*Inm.get_coef(n2,m)
i,j,k=sorted([n,n1,n1],reverse=True)
temp = temp + coef_table[m].get_coef(i,j,k).real*Inm.get_coef(n1,m)**2.0/2.0
Cnm.set_coef(n,m,temp*2.0)
return Cnm
def generate_image(n, moments, N=100):
# Generate images from the zernike moments, N is the number of points from 0 to 1
nmax = n
image = flex.vec3_double()
NP = 2 * N + 1
reconst = flex.complex_double(NP**2, 0)
nl_array = math.nl_array(nmax)
nls = nl_array.nl()
r_theta = flex.vec2_double()
for x in range(0, NP):
x = x - N
for y in range(0, NP):
y = y - N
rr = smath.sqrt(x * x + y * y) / N
if rr > 1.0:
tt = 0.0
else:
tt = smath.atan2(y, x)
r_theta.append([rr, tt])
for nl, c in zip(nls, moments):
n = nl[0]
l = nl[1]
#if(l/2*2 != l): continue
if (l > 0): c = c * 2.0
rap = math.zernike_2d_polynome(n, l)
i = 0
for pt in r_theta:
rr = pt[0]
if rr > 1.0:
value = 0.0
else:
tt = pt[1]
value = rap.f(rr, tt)
reconst[i] = reconst[i] + value * c
i = i + 1
return reconst
i = 0
for x in range(0, NP):
for y in range(0, NP):
value = reconst[i].real
image.append([x, y, value])
i = i + 1
return image
def tst_2d_zm(n,l):
nmax=max(n,20)
np=100
points=flex.double(range(-np,np+1))/np
grid = math.two_d_grid(np, nmax)
zm2d = math.two_d_zernike_moments(grid, nmax)
image = flex.vec3_double()
output=file('testmap.dat','w')
for x in points:
for y in points:
r=smath.sqrt(x*x+y*y)
if(r>1.0):
value=0.0
else:
value=zm2d.zernike_poly(n,l,x,y).real
image.append([x*np+np,y*np+np, value])
grid.clean_space( image )
grid.construct_space_sum()
zernike_2d_mom = math.two_d_zernike_moments( grid, nmax )
moments = zernike_2d_mom.moments()
coefs = flex.real( moments )
nl_array = math.nl_array( nmax )
nls = nl_array.nl()
for nl, c in zip( nls, moments):
if(abs(c)<1e-3):
c=0
print nl, c
NP=np*2+1
reconst=zernike_2d_mom.zernike_map(nmax, np)
i = 0
for x in range(0,NP):
for y in range(0,NP):
value=reconst[i].real
if(value>0):
print>>output, x,y,image[i][2],value
i=i+1
output.close()
def calc_Cnm_from_Inm(Inm, coef_table, nmax):
two_pi = smath.pi * 2.0
four_pi = 2.0 * two_pi
Cnm = math.nl_array(nmax)
for n in range(2, nmax + 1, 2): # only even number (n,m)
for m in range(2, n + 1, 2): # when m=0, the In0 is subtracted
temp = 0
for n1 in range(m, nmax + 1, 2):
for n2 in range(m, nmax + 1, 2):
i, j, k = sorted([n, n1, n2], reverse=True)
temp = temp + coef_table[m].get_coef(
i, j, k) * (Inm.get_coef(n1, m).conjugate() *
Inm.get_coef(n2, m)).real
# i,j,k=sorted([n,n1,n1],reverse=True)
# temp = temp + coef_table[m].get_coef(i,j,k)*abs(Inm.get_coef(n1,m))**2.0/2.0
Cnm.set_coef(n, m, temp * four_pi * (n + 1))
return Cnm
def generate_image2(n, moments, template_image, np):
nmax = n
image = flex.vec3_double()
np_tot = template_image.size()
reconst = flex.complex_double(np_tot, 0)
nl_array = math.nl_array(nmax)
nls = nl_array.nl()
r_theta = flex.vec2_double()
for pt in template_image:
x = pt[0] - np
y = pt[1] - np
rr = smath.sqrt(x * x + y * y) / np
if rr > 1.0:
tt = 0.0
else:
tt = smath.atan2(y, x)
r_theta.append([rr, tt])
for nl, c in zip(nls, moments):
n = nl[0]
l = nl[1]
#if(l/2*2 != l): continue
if (l > 0): c = c * 2.0
rap = math.zernike_2d_polynome(n, l)
i = 0
for pt in r_theta:
rr = pt[0]
if rr > 1.0:
value = 0.0
else:
tt = pt[1]
value = rap.f(rr, tt)
reconst[i] = reconst[i] + value * c
i = i + 1
for i in range(np_tot):
x = template_image[i][0]
y = template_image[i][1]
value = reconst[i].real
image.append([x, y, value])
return image
def test_solving(nmax, m):
Inm=math.nl_array(nmax)
nls = Inm.nl()
size = nls.size()
coefs = flex.random_double(size)
Inm.load_coefs( nls, coefs )
coef_table = tst_integral_triple_zernike2d(nmax)
Cnm = calc_Cnm_from_Inm( Inm, coef_table, nmax )
t1 = time.time()
refine_de_obj = inm_refine( nmax, Cnm, coef_table, m )
solution=flex.double()
for nn in range(m,nmax+1,2):
solution.append( Inm.get_coef(nn,m) )
for ss,xx in zip(solution, refine_de_obj.best_solution):
print ss,xx
print "score=",refine_de_obj.target(refine_de_obj.x)
print "score=",refine_de_obj.target(solution)
t2 = time.time()
print "nmax=",nmax, "time used:", t2-t1
def comp_Cnm_calculations(nmax):
Inm=math.nl_array(nmax)
nls = Inm.nl()
size = nls.size()
coefs = flex.random_double(size)
Inm.load_coefs( nls, coefs )
coef_table = tst_integral_triple_zernike2d(nmax)
Cnm = calc_Cnm_from_Inm(Inm, coef_table, nmax )
for mm in range(0,nmax+1,2):
coef_table_m = coef_table[mm]
Inm_m=flex.double()
Cnm_m=flex.double()
for nn in range(mm,nmax+1,2):
Inm_m.append( Inm.get_coef(nn,mm) )
Cnm_m.append( Cnm.get_coef(nn,mm) )
Cnm_m_new = calc_Cnm_4m_from_Inm(mm,nmax,Inm_m,coef_table_m)
for ii,jj in zip(Cnm_m, Cnm_m_new):
assert(abs(ii-jj)<1e-6)
def __init__(self,
data,
rg,
io,
nmax=20,
rmax=None,
scan=True,
fraction=0.9,
smear=True,
prefix=None,
weight='i',
delta_q=None,
scale_power=2.0):
global stdfile
global outfilelog
self.stdfile = stdfile
self.outfilelog = outfilelog
self.data = data
self.smear = smear
self.delta_q = delta_q
self.setup_weighting_scheme(weight)
if (self.smear):
self.set_up_smear()
self.rg = rg
self.io = io
self.int_scale = self.io
self.nmax = nmax
if (rmax is None):
rmax = int(self.rg * 3.0 / 2.0)
self.rmax = rmax
self.scan = scan
self.prefix = prefix
self.fraction = fraction
self.nlm_array = math.nlm_array(nmax)
self.nlm_total = self.nlm_array.coefs().size()
self.nn_array = math.nl_array(nmax)
self.nn = self.nn_array.nl()
self.nn_total = self.nn_array.coefs().size()
self.scale_power = scale_power
def tst_2d_zernike_mom(n, l, file):
# image = preprocess_image(h5file)
image = ImageToDat(file)
feature_maxtix = []
NP=int(smath.sqrt( image.size() ))
N=int(NP/2)
# print"=====",NP, N
grid_2d = math.two_d_grid(N, nmax)
grid_2d.clean_space( image )
grid_2d.construct_space_sum()
zernike_2d_mom = math.two_d_zernike_moments( grid_2d, nmax )
moments = zernike_2d_mom.moments()
coefs = flex.real( moments )
nl_array = math.nl_array( nmax )
nls = nl_array.nl()
# nl_array.load_coefs( nls, coefs )
# lfg = math.log_factorial_generator(nmax)
for nl, c in zip( nls, moments):
if(abs(c)<1e-3):
c=0
feature_maxtix.append(c.real)
# print nl,c
return feature_maxtix
def tst_nl():
this_nl_array = math.nl_array(5)
nl = this_nl_array.nl()
result= """"""
for tnl in nl:
result +=str(tnl)+"\n"
assert (tnl[0]-tnl[1])%2==0
expected_result = """(0, 0)
(1, 1)
(2, 0)
(2, 2)
(3, 1)
(3, 3)
(4, 0)
(4, 2)
(4, 4)
(5, 1)
(5, 3)
(5, 5)
"""
assert result == expected_result
coefs = this_nl_array.coefs()
assert coefs.size() == nl.size()
new_coefs = flex.double( range(nl.size() ) )
assert this_nl_array.load_coefs( nl, new_coefs )
new_nl = shared.tiny_int_2( [ (10,10) ] )
new_coef = flex.double( [10.0] )
assert not this_nl_array.load_coefs( new_nl, new_coef )
coefs = this_nl_array.coefs()
for x,y in zip(coefs,new_coefs):
assert abs(x-y)<1e-5
for tnl, cc in zip(nl,coefs):
thc = this_nl_array.get_coef(tnl[0], tnl[1])
assert abs(thc-cc)<1e-5
this_nl_array.set_coef(tnl[0], tnl[1], 300 )
thc = this_nl_array.get_coef(tnl[0], tnl[1])
assert abs(thc-300)<1e-5
def tst_nl():
this_nl_array = math.nl_array(5)
nl = this_nl_array.nl()
result= """"""
for tnl in nl:
result +=str(tnl)+"\n"
assert (tnl[0]-tnl[1])%2==0
expected_result = """(0, 0)
(1, 1)
(2, 0)
(2, 2)
(3, 1)
(3, 3)
(4, 0)
(4, 2)
(4, 4)
(5, 1)
(5, 3)
(5, 5)
"""
assert result == expected_result
coefs = this_nl_array.coefs()
assert coefs.size() == nl.size()
new_coefs = flex.double( range(nl.size() ) )
assert this_nl_array.load_coefs( nl, new_coefs )
new_nl = shared.tiny_int_2( [ (10,10) ] )
new_coef = flex.double( [10.0] )
assert not this_nl_array.load_coefs( new_nl, new_coef )
coefs = this_nl_array.coefs()
for x,y in zip(coefs,new_coefs):
assert abs(x-y)<1e-5
for tnl, cc in zip(nl,coefs):
thc = this_nl_array.get_coef(tnl[0], tnl[1])
assert abs(thc-cc)<1e-5
this_nl_array.set_coef(tnl[0], tnl[1], 300 )
thc = this_nl_array.get_coef(tnl[0], tnl[1])
assert abs(thc-300)<1e-5
def tst_line(nmax=20, width=2, N=201):
nl_array = math.nl_array(nmax)
nls = nl_array.nl()
moments = flex.random_double(nls.size()) * 0
nl_array.load_coefs(nls, moments)
nl_array.set_coef(8, 6, 1.0)
nl_array.set_coef(6, 2, 1.0)
nl_array.set_coef(4, 4, 1.0)
moments = nl_array.coefs()
this_nls = [[8, 6], [6, 2], [4, 4]]
# this_nls = [[6,2]]
this_moments = [1.0, 1.0, 1.0]
N = N
half_N = N / 2
Nq = half_N
Nphi = Nq
## The following two methods should give consistent results ##
#c2_image = build_grid(Nq, Nphi, this_nls, this_moments )
c2_image = analytical_c2(Nq, Nphi, this_nls, this_moments)
c2_output = open('c2_raw.dat', 'w')
for pt in c2_image:
print >> c2_output, pt[0], pt[1], pt[2]
c2_output.close()
#sp_out = open('sp_image.dat', 'w')
#for pt in raw_image:
# print>>sp_out, pt[0], pt[1], pt[2]
#sp_out.close()
## get cnm from sp_moments ##
sp_moments = flex.complex_double(moments, moments * 0)
#sp_moments[0]=0
nmax4c2 = nmax * 2
Inm = math.nl_c_array(nmax4c2)
coef_table = image_tools.calc_integral_triple_zernike2d(nmax4c2)
Inm.load_coefs(nls, sp_moments)
cnm = image_tools.calc_Cnm_from_Inm(Inm, coef_table, nmax4c2)
cnm_coef = cnm.coefs()
c2_reconst = image_tools.generate_image2(nmax4c2, cnm_coef, c2_image,
half_N)
c2_output = open('c2_reconst.dat', 'w')
for pt in c2_reconst:
print >> c2_output, pt[0], pt[1], pt[2]
c2_output.close()
## get zm for sp_image ##
image = c2_image
NP = int(smath.sqrt(image.size()))
N = NP / 2
sp_n = N
grid_2d = math.two_d_grid(N, nmax)
grid_2d.clean_space(image)
grid_2d.construct_space_sum()
zernike_2d_mom = math.two_d_zernike_moments(grid_2d, nmax)
sp_moments = zernike_2d_mom.moments()
print "#C2"
for nl, m1, m2 in zip(nls, cnm_coef, sp_moments):
print nl, m1, m2.real, m1 / (m2.real + 1e-23)
def find_relatives(ids, cc_min, cc_max, rmax, codes, moments, nmax=10):
indices = flex.int()
idlist = open('id_list.txt', 'r')
for id in idlist:
id = id[0:4]
indices.append(flex.first_index(codes, id))
r_max = easy_pickle.load(prefix + 'pisa.rmax')
nns = easy_pickle.load(prefix + 'pisa.nn')
nn_array = math.nl_array(nmax)
nn_indx = nn_array.nl()
nn_total = nn_indx.size()
q_array = flex.double(range(501)) / 2000.0
ref_nlm_array = math.nlm_array(nmax)
target_nlm_array = math.nlm_array(nmax)
nlm = ref_nlm_array.nlm()
coef_size = nlm.size()
all_indices = range(codes.size())
small_q_array = flex.double(range(51)) / 300.0
mean = []
sig = []
for indx in indices:
print indx
#rmax = 50.0 #r_max[indx]
ref_coef = moments[indx]
ref_nlm_array.load_coefs(nlm, ref_coef[0:coef_size])
z_model = zernike_model(ref_nlm_array, q_array, rmax, nmax)
out_name = codes[indx] + "_.qi"
nn_array.load_coefs(nn_indx, nns[indx][0:nn_total])
ref_int = put_intensity(z_model, q_array, nn_array, out_name)
mean_r = ref_int * 0.0
sig_r = ref_int * 0.0
small_z_model = zernike_model(ref_nlm_array, small_q_array, rmax, nmax)
small_ref_int = small_z_model.calc_intensity(nn_array)
small_ref_int = small_ref_int / small_ref_int[0]
N = 0.0
for coef, ii in zip(moments, all_indices):
if N > 25: break
target_nlm_array.load_coefs(nlm, coef[0:coef_size])
align_obj = fft_align.align(ref_nlm_array,
target_nlm_array,
nmax=nmax,
topn=10,
refine=False)
cc = align_obj.get_cc()
if (cc >= cc_min and cc <= cc_max):
N += 1
nn_array.load_coefs(nn_indx, nns[ii][0:nn_total])
opt_r_obj = optimize_r(nn_array, small_ref_int, small_q_array,
nmax)
opt_r = gss(opt_r_obj.target, rmax * 0.8, rmax * 1.2)
z_model = zernike_model(ref_nlm_array, q_array, opt_r, nmax)
out_name = codes[indx] + "_" + codes[ii] + ".qi.rel"
mod_int = put_intensity(z_model, q_array, nn_array, out_name,
ref_int)
out_name = codes[indx] + "_" + codes[ii] + ".qi"
put_intensity(z_model, q_array, nn_array, out_name)
mod_int = mod_int - 1.0
mean_r += mod_int
sig_r += mod_int * mod_int
print ii, cc, codes[ii], opt_r
if N > 3:
mean_r /= N
sig_r = sig_r / N - mean_r * mean_r
mean.append(mean_r)
sig.append(sig_r)
N = len(mean)
if N > 0:
mean_r = mean[0] * 0.0
s_r = mean[0] * 0.0
for uu in range(N):
mean_r += mean[uu]
s_r += sig[uu]
mean_r /= N
s_r /= N
s_r = flex.sqrt(s_r)
f = open('q_m_s_%s.dat' % rmax, 'w')
for q, m, s in zip(q_array, mean_r, s_r):
print >> f, q, m, s
def tst_2d_zernike_mom(n,l, N=100, filename=None):
nmax = max(20,n)
rebuilt=open('rebuilt.dat','w')
tt1=time.time()
if(filename is not None):
image=read_data(filename)
else:
image=generate_image(n,l)
NP=int(smath.sqrt( image.size() ))
N=NP/2
grid_2d = math.two_d_grid(N, nmax)
grid_2d.clean_space( image )
grid_2d.construct_space_sum()
tt2=time.time()
print "time used: ", tt2-tt1
zernike_2d_mom = math.two_d_zernike_moments( grid_2d, nmax )
moments = zernike_2d_mom.moments()
tt2=time.time()
print "time used: ", tt2-tt1
coefs = flex.real( moments )
nl_array = math.nl_array( nmax )
nls = nl_array.nl()
nl_array.load_coefs( nls, coefs )
lfg = math.log_factorial_generator(nmax)
print nl_array.get_coef(n,l)*2
for nl, c in zip( nls, moments):
if(abs(c)<1e-3):
c=0
print nl, c
print
reconst=flex.complex_double(NP**2, 0)
for nl,c in zip( nls, moments):
n=nl[0]
l=nl[1]
if(l>0):
c=c*2
#rzfa = math.zernike_2d_radial(n,l,lfg)
rap = math.zernike_2d_polynome(n,l) #,rzfa)
i=0
for x in range(0,NP):
x=x-N
for y in range(0,NP):
y=y-N
rr = smath.sqrt(x*x+y*y)/N
if rr>1.0:
value=0.0
else:
tt = smath.atan2(y,x)
value = rap.f(rr,tt)
reconst[i]=reconst[i]+value*c
i=i+1
i = 0
for x in range(0,NP):
for y in range(0,NP):
value=reconst[i].real
if(value>0):
print>>rebuilt, x,y,image[i][2],value
i=i+1
rebuilt.close()
def tst_fft_proj(pdbfile, nmax=20):
dx = 1.0
projection_obj = projection.projection(pdbfile, dx=dx, fraction=0.5)
dq = projection_obj.get_dq()
image = projection_obj.project()
output = open('prj1.dat', 'w')
for pt in image:
print >> output, pt[0], pt[1], pt[2]
output.close()
values = projection_obj.get_value()
np = projection_obj.get_np()
flex_grid = flex.grid(np, np)
fft_input = flex.complex_double(flex_grid)
for ii in range(fft_input.size()):
fft_input[ii] = complex(values[ii], 0)
fft_obj = fftpack.complex_to_complex_2d((np, np))
result = fft_obj.forward(fft_input)
sp_image = flex.vec3_double()
for ii in range(np):
for jj in range(np):
kk = ii
ll = jj
if kk > np / 2: kk = kk - np
if ll > np / 2: ll = ll - np
sp_image.append(
[kk + np / 2, ll + np / 2,
abs(result[(ii, jj)])**2.0])
Nq = np / 2
Nphi = Nq
c2_image, normalized_sp = from_I_to_C2(sp_image,
Nq,
Nphi,
N=np,
further_reduct=True)
image = normalized_sp
NP = int(smath.sqrt(image.size()))
N = NP / 2
sp_n = N
grid_2d = math.two_d_grid(N, nmax)
grid_2d.clean_space(image)
grid_2d.construct_space_sum()
zernike_2d_mom = math.two_d_zernike_moments(grid_2d, nmax)
sp_moments = zernike_2d_mom.moments()
# sp_reconst = image_tools.generate_image2(nmax, sp_moments, normalized_sp, sp_n)
# c2_image, normalized_sp = from_I_to_C2(sp_reconst, Nq, Nphi, N=np)
sp_out = open('sp_image.dat', 'w')
for pt in sp_image:
print >> sp_out, (pt[0] - sp_n) * dq, (pt[1] - sp_n) * dq, pt[2]
sp_out.close()
c2_output = open('c2.dat', 'w')
for pt in c2_image:
print >> c2_output, pt[0], pt[1], pt[2]
c2_output.close()
image = c2_image
NP = int(smath.sqrt(image.size()))
N = NP / 2
c2_n = N
# grid_2d = math.two_d_grid(N, nmax)
# grid_2d.clean_space( image )
# grid_2d.construct_space_sum()
# zernike_2d_mom = math.two_d_zernike_moments( grid_2d, nmax )
# c2_moments = zernike_2d_mom.moments()
# coefs = ( c2_moments )
nls = math.nl_array(nmax).nl()
# for nl, c2m in zip( nls, coefs ):
# print nl, c2m
sp_moments[0] = 0
nmax4c2 = 2 * nmax
Inm = math.nl_c_array(nmax4c2)
coef_table = image_tools.calc_integral_triple_zernike2d(nmax4c2)
Inm.load_coefs(nls, sp_moments)
cnm = image_tools.calc_Cnm_from_Inm(Inm, coef_table, nmax4c2)
cnm_coef = cnm.coefs()
# for nl, mm,mmm in zip( nls, c2_moments, cnm_coef ):
# print abs(mm), abs(mmm)
#cnm_coef = c2_moments
c2_reconst = image_tools.generate_image2(nmax, cnm_coef, c2_image, c2_n)
c2_r = open('c2r.dat', 'w')
for pt in c2_reconst:
print >> c2_r, pt[0], pt[1], pt[2]
c2_r.close()
exit()
def tst_image(n, N=100, filename=None):
nmax = n
nmax0 = 8
nl_array0 = math.nl_array(nmax0)
nls0 = nl_array0.nl()
nl_array = math.nl_array(nmax)
nls = nl_array.nl()
if (filename is not None):
image = read_data(filename)
else:
moments = flex.random_double(nls0.size())
# moments=flex.double(nls.size(),0 )
# moments[3] = 1.0
# moments[7] = 1.0
image = generate_image(n, moments)
orig = open('original.dat', 'w')
for pt in image:
print >> orig, pt[0], pt[1], pt[2]
orig.close()
Nq = 100
Nphi = 100
c2_image = from_I_to_C2(nmax, image, Nq, Nphi)
c2_output = open('c2.dat', 'w')
for pt in c2_image:
print >> c2_output, pt[0], pt[1], pt[2]
c2_output.close()
coef_table = calc_integral_triple_zernike2d(nmax)
moments[0] = 0
new_mom = moments.concatenate(flex.double(nls.size() - nls0.size(), 0))
nmax4c2 = 2 * nmax
Inm = math.nl_c_array(nmax4c2)
Inm.load_coefs(nls, new_mom)
cnm = calc_Cnm_from_Inm(Inm, coef_table, nmax4c2)
cnm_coef = cnm.coefs()
print "#cnm[0]", cnm_coef[0]
# cnm_coef[0]=0
### calculate 2d zernike moments for C2_image ###
image = c2_image
NP = int(smath.sqrt(image.size()))
N = NP / 2
grid_2d = math.two_d_grid(N, nmax)
grid_2d.clean_space(image)
grid_2d.construct_space_sum()
zernike_2d_mom = math.two_d_zernike_moments(grid_2d, nmax)
c2_moments = zernike_2d_mom.moments()
#coefs = flex.real( c2_moments )
#cnm_coef = flex.real( c2_moments )
cnm_coef = c2_moments
c2_reconst = generate_image2(n, cnm_coef, c2_image, Nq)
c2_r = open('c2r.dat', 'w')
for pt in c2_reconst:
print >> c2_r, pt[0], pt[1], pt[2]
c2_r.close()
ls_score = 0
np_tot = c2_image.size()
for p1, p2 in zip(c2_image, c2_reconst):
ls_score += (p1[2] - p2[2])**2.0
print nmax, nls.size(), ls_score, np_tot * smath.log(
ls_score / np_tot), "SUM"
for nl, c2m in zip(nls, cnm_coef):
print nl, c2m
exit() #
### calculate 2d zernike moments for C2_image ###
image = c2_image
NP = int(smath.sqrt(image.size()))
N = NP / 2
grid_2d = math.two_d_grid(N, nmax)
grid_2d.clean_space(image)
grid_2d.construct_space_sum()
tt2 = time.time()
zernike_2d_mom = math.two_d_zernike_moments(grid_2d, nmax)
c2_moments = zernike_2d_mom.moments()
#coefs = flex.real( c2_moments )
coefs = (c2_moments)
for nl, c2m, c2mm in zip(nls, cnm_coef, coefs):
if (nl[0] / 2 * 2 == nl[0]):
print c2m, c2mm
coefs = flex.real(moments)
nl_array.load_coefs(nls, coefs)
for nl, c in zip(nls, moments):
if (abs(c) < 1e-3):
c = 0
print nl, c
print
reconst = flex.complex_double(NP**2, 0)
for nl, c in zip(nls, moments):
n = nl[0]
l = nl[1]
if (l > 0):
c = c * 2.0
rap = math.zernike_2d_polynome(n, l)
i = 0
for x in range(0, NP):
x = x - N
for y in range(0, NP):
y = y - N
rr = smath.sqrt(x * x + y * y) / N
if rr > 1.0:
value = 0.0
else:
tt = smath.atan2(y, x)
value = rap.f(rr, tt)
reconst[i] = reconst[i] + value * c
i = i + 1
rebuilt = open('rebuilt.dat', 'w')
i = 0
for x in range(0, NP):
for y in range(0, NP):
value = reconst[i].real
print >> rebuilt, x, y, image[i][2], value
i = i + 1
rebuilt.close()