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 __init__(self, base_image, nmax):
self.bi = base_image.deep_copy()
self.np = self.bi.focus()[0]
self.nmax = nmax
self.n = int(self.np / 2)
print self.bi.focus(), self.np, self.n
print "Building mom->img grid"
t1 = time.time()
self.z2dg = math.zernike_grid_2d(self.n, self.nmax)
t2 = time.time()
print "time used: %d (seconds)" % (t2 - t1)
print "Build img->mom grid"
self.grid_2d = math.two_d_grid(self.n, self.nmax)
def tst_2d_poly(n,l): nmax=max(n,20) np=50 x,y=0.1,0.9 r,t=smath.sqrt(x*x+y*y),smath.atan2(y,x) lfg = math.log_factorial_generator(nmax) #rzfa = math.zernike_2d_radial(n,l,lfg) #rap = math.zernike_2d_polynome(n,l,rzfa) rap = math.zernike_2d_polynome(n,l)#,rzfa) rt_value=rap.f(r,t) grid = math.two_d_grid(np, nmax) zm2d = math.two_d_zernike_moments(grid, nmax) xy_value=zm2d.zernike_poly(n,l,x,y) print rt_value, xy_value, abs(rt_value), abs(xy_value)
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 tst_zernike_expansion(pdbfile, nmax=10):
projection_obj = projection.projection(pdbfile)
image = projection_obj.project()
ori_image = image.deep_copy()
output = open('ori.dat', 'w')
# get moments
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)
# use moments to reconstruct image
reconst = image_tools.generate_image2(nmax, zernike_2d_mom.moments(),
ori_image, N)
for pp, qq in zip(image, reconst):
print pp[0], pp[1], pp[2], qq[2]
def zernike_expansion(image, nmax=30):
ori_image=image.deep_copy()
output=open('ori_c2.dat', 'w')
# get moments
NP=int(smath.sqrt( image.size() ))
nimg = flex.vec3_double()
ori_image = nimg.deep_copy()
for ii in range(NP):
for jj in range(NP):
nimg.append( (ii,jj,image[(ii,jj)]) )
ori_image = nimg.deep_copy()
N=NP/2
grid_2d = math.two_d_grid(N, nmax)
grid_2d.clean_space( nimg )
grid_2d.construct_space_sum()
zernike_2d_mom = math.two_d_zernike_moments( grid_2d, nmax )
# use moments to reconstruct image
reconst = image_tools.generate_image2(nmax,zernike_2d_mom.moments(),ori_image,N)
for pp,qq, in zip( ori_image, reconst):
print pp[0], pp[1], pp[2], qq[2]
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_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_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_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()
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)
