def __init__(self, I, **args):
"""
"""
# dtype
#-----------------------------------------------
if isValid('dtype', args) :
dtype = args['dtype']
else :
dtype = np.float64
if isValid('c_dtype', args) :
c_dtype = args['c_dtype']
else :
c_dtype = np.complex128
# initialise the object
#-----------------------------------------------
if isValid('O', args):
O = np.fft.fftn(args['O'])
else :
print('initialising object with random numbers')
O = np.random.random(I.shape).astype(c_dtype)
# initialise the mask, alpha value and amp
#-----------------------------------------------
self.mask = 1
if isValid('mask', args):
self.mask = args['mask']
self.alpha = 1.0e-10
if isValid('alpha', args):
self.alpha = args['alpha']
self.I_norm = (self.mask * I).sum()
self.amp = np.sqrt(I.astype(dtype))
# define the support projection
#-----------------------------------------------
if isValid('voxel_number', args) :
self.voxel_number = args['voxel_number']
self.support = None
self.S = None
else :
self.voxel_number = False
#
self.support = args['support']
self.S = self.support.copy()
# make the unit cell and diffuse weightings
#-----------------------------------------------
self.sym_ops = get_sym_ops(args)
N = args['disorder']['n']
exp = make_exp(args['disorder']['sigma'], args['detector']['shape'])
lattice = symmetry_operations.lattice(args['crystal']['unit_cell'], args['detector']['shape'])
self.unit_cell = args['crystal']['unit_cell']
self.unit_cell_weighting = N * lattice * exp
self.diffuse_weighting = (1. - exp)
self.modes = np.zeros( (2 * self.sym_ops.syms.shape[0],) + self.sym_ops.syms.shape[1:], O.dtype)
# diffuse terms
self.modes[:self.modes.shape[0]//2] = self.sym_ops.solid_syms_Fourier(O, apply_translation = False)
# unit cell terms
self.modes[self.modes.shape[0]//2:] = self.sym_ops.solid_syms_Fourier(O, apply_translation = True)
print('eMod(modes0):', self.Emod(self.modes))
# Ellipse axes
#-----------------------------------------------
# Here we have :
# (x / e0)**2 + (y / e1)**2 = 1 , where
#
# e0 = sqrt{ self.diffuse_weighting / I } and
#
# e1 = sqrt{ self.unit_cell_weighting / I }
#-----------------------------------------------
# floating point tolerance for 1/x (log10)
tol = 100. #1.0e+100
# check for numbers close to infinity in sqrt(I / self.diffuse_weighting)
m = self.diffuse_weighting <= 0.0
m[~m] = 0.5 * (np.log10(I[~m]) - np.log10(self.diffuse_weighting[~m])) > tol
self.e0_inf = m.copy()
self.e0 = np.zeros_like(self.diffuse_weighting)
self.e0[~m] = np.sqrt(I[~m]) / np.sqrt(self.diffuse_weighting[~m])
# check for numbers close to infinity in sqrt(I / self.unit_cell_weighting)
m = self.unit_cell_weighting <= 0.0
m[~m] = 0.5 * (np.log10(I[~m]) - np.log10(self.unit_cell_weighting[~m])) > tol
self.e1_inf = m.copy()
self.e1 = np.zeros_like(self.unit_cell_weighting)
self.e1[~m] = np.sqrt(I[~m]) / np.sqrt(self.sym_ops.syms.shape[0] * self.unit_cell_weighting[~m])
self.iters = 0
def __init__(self, I, **args):
"""
For mapper naive we just have a single object.
The support projection is:
Psup O = F . S . F-1 . O
And the modulus projection is:
Pmod O = O sqrt{ I / M }
Where M is the forward mapping (self.Imap) of O
to the diffraction intensity:
M = (1 - gaus) sum_i | O_i |^2 +
N * L * gaus * | sum_i O_i |^2
Parameters
----------
I : numpy.ndarray, (N, M, K)
Merged diffraction patterns to be phased.
N : the number of pixels along slowest scan axis of the detector
M : the number of pixels along slow scan axis of the detector
K : the number of pixels along fast scan axis of the detector
O : numpy.ndarray, (N, M, K)
The real-space scattering density of the object such that:
I = |F[O]|^2
where F[.] is the 3D Fourier transform of '.'.
dtype : np.float32 or np.float64
Determines the numerical precision of the calculation.
c_dtype : np.complex64 or np.complex128
Determines the numerical precision of the complex variables.
support : (numpy.ndarray, None or int), optional (N, M, K)
Real-space region where the object function is known to be zero.
If support is an integer then the N most intense pixels will be kept at
each iteration.
voxel_number : None or int, optional
If int, then the voxel number support is used. If support is not None or False
then the voxel number support is used within the sample support bounds.
mask : numpy.ndarray, (N, M, K), optional, default (1)
The valid detector pixels. Mask[i, j, k] = 1 (or True) when the detector pixel
i, j, k is valid, Mask[i, j, k] = 0 (or False) otherwise.
alpha : float, optional, default (1.0e-10)
A floating point number to regularise array division (prevents 1/0 errors).
disorder['sigma'] : float
The standard deviation of the isotropic displacement of the solid unit within
the crystal.
detector['shape'] : tupple
The shape of the detector (3D).
crystal['unit_cell'] : tupple
The dimensions of the unit cell
Returns
-------
O : numpy.ndarray, (U, V, K)
The real-space object function after 'iters' iterations of the ERA algorithm.
info : dict
contains diagnostics:
'I' : the diffraction pattern corresponding to object above
'eMod' : the modulus error for each iteration:
eMod_i = sqrt( sum(| O_i - Pmod(O_i) |^2) / I )
'eCon' : the convergence error for each iteration:
eCon_i = sqrt( sum(| O_i - O_i-1 |^2) / sum(| O_i |^2) )
"""
# dtype
#-----------------------------------------------
if isValid('dtype', args) :
dtype = args['dtype']
else :
dtype = np.float64
if isValid('c_dtype', args) :
c_dtype = args['c_dtype']
else :
c_dtype = np.complex128
# initialise the object
#-----------------------------------------------
if isValid('O', args):
modes = np.fft.fftn(args['O'])
else :
print('initialising object with random numbers')
modes = np.random.random(I.shape).astype(c_dtype)
# initialise the mask, alpha value and amp
#-----------------------------------------------
self.mask = 1
if isValid('mask', args):
self.mask = args['mask']
self.alpha = 1.0e-10
if isValid('alpha', args):
self.alpha = args['alpha']
self.I_norm = (self.mask * I).sum()
self.amp = np.sqrt(I.astype(dtype))
# define the support projection
#-----------------------------------------------
if isValid('voxel_number', args) :
self.voxel_number = args['voxel_number']
self.support = None
else :
self.voxel_number = False
#
self.support = args['support']
self.S = self.support.copy()
# make the unit cell and diffuse weightings
#-----------------------------------------------
self.sym_ops = get_sym_ops(args)
N = args['disorder']['n']
exp = make_exp(args['disorder']['sigma'], args['detector']['shape'])
lattice = symmetry_operations.lattice(args['crystal']['unit_cell'], args['detector']['shape'])
#self.solid_syms = lambda x : sym_ops.solid_syms(x)
self.unit_cell_weighting = N * lattice * exp
self.diffuse_weighting = (1. - exp)
self.modes = modes
def generate_diff(config):
solid_unit = crappy_crystals.solid_units.duck_3D.make_3D_duck(shape = config['simulation']['shape'])
#solid_unit *= np.random.random(solid_unit.shape)
if config['simulation']['space_group'] == 'P1':
sym_ops = symmetry_operations.P1(config['simulation']['unit_cell'], config['detector']['shape'])
elif config['simulation']['space_group'] == 'P212121':
sym_ops = symmetry_operations.P212121(config['simulation']['unit_cell'], config['detector']['shape'])
Solid_unit = np.fft.fftn(solid_unit, config['detector']['shape'])
solid_unit_expanded = np.fft.ifftn(Solid_unit)
# define the solid_unit support
if config['simulation']['support_frac'] is not None :
support = padding.expand_region_by(solid_unit_expanded > 0.1, config['simulation']['support_frac'])
else :
support = solid_unit_expanded > (solid_unit_expanded.min() + 1.0e-5)
#solid_unit_expanded = np.random.random(support.shape)*support + 0J
solid_unit_expanded = solid_unit_expanded * support
Solid_unit = np.fft.fftn(solid_unit_expanded)
modes = sym_ops.solid_syms_Fourier(Solid_unit)
N = config['simulation']['n']
exp = disorder.make_exp(config['simulation']['sigma'], config['detector']['shape'])
lattice = symmetry_operations.lattice(config['simulation']['unit_cell'], config['detector']['shape'])
diff = N * exp * lattice * np.abs(np.sum(modes, axis=0)**2)
diff += (1. - exp) * np.sum(np.abs(modes)**2, axis=0)
# add noise
if config['simulation']['photons'] is not None :
diff, edges = add_noise_3d.add_noise_3d(diff, config['simulation']['photons'], \
remove_courners = config['simulation']['cut_courners'],\
unit_cell_size = config['simulation']['unit_cell'])
else :
edges = np.ones_like(diff, dtype=np.bool)
# add gaus background
if 'background' in config['simulation'] and config['simulation']['background'] == 'gaus':
sig = config['simulation']['background_std']
scale = config['simulation']['background_scale']
scale *= diff.max()
print '\nAdding gaussian to diff scale (absolute), std:', scale, sig
gaus = gaus.gaus(diff.shape, scale, sig)
diff += gaus
background = gaus
else :
background = None
# add a beamstop
if config['simulation']['beamstop'] is not None :
beamstop = beamstop.make_beamstop(diff.shape, config['simulation']['beamstop'])
diff *= beamstop
else :
beamstop = np.ones_like(diff, dtype=np.bool)
print 'Simulation: number of voxels in solid unit:', np.sum(solid_unit_expanded > (1.0e-5 + solid_unit_expanded.min()))
print 'Simulation: number of voxels in support :', np.sum(support)
return diff, beamstop, edges, support, solid_unit_expanded, background