def reconstruct(self):
"""
Performs a single reconstruction with the specified configuration and outputs a dictionary with the results.
"""
self._prepare_reconstruction()
if not self._ready:
return
Out = {}
#self._init_new_phaser()
i_alg = 0
i_sup = 0
i_out_images = 0
i_out_scores = 0
iteration0_alg = 0
iteration0_sup = 0
iterations_propagated = 0
fourier_error = np.zeros(self._number_of_outputs_scores)
real_error = np.zeros(self._number_of_outputs_scores)
support_size = np.zeros(self._number_of_outputs_scores)
real_space = np.zeros(shape=(self._number_of_outputs_images,self._Ny,self._Nx),dtype="complex128")
support = np.zeros(shape=(self._number_of_outputs_images,self._Ny,self._Nx),dtype="bool")
fourier_space = np.zeros(shape=(self._number_of_outputs_images,self._Ny,self._Nx),dtype="complex128")
mask = np.zeros(shape=(self._number_of_outputs_images,self._Ny,self._Nx),dtype="bool")
for self._iteration in range(self._number_of_iterations+1):
change_algorithm = (self._iteration-iteration0_alg == self._phasing_algorithms[i_alg]["number_of_iterations"]) and (self._iteration != self._number_of_iterations)
change_support = (self._iteration-iteration0_sup == self._support_algorithms[i_sup]["number_of_iterations"]) and (self._iteration != self._number_of_iterations)
if change_algorithm or change_support or self._iteration in self._out_iterations_images or self._iteration in self._out_iterations_scores:
if self._reconstruction is None:
self._log("Iteration %i" % (self._iteration),"INFO")
else:
self._log("Reconstruction %i - Iteration %i" % (self._reconstruction,self._iteration),"INFO")
# iterate to self._iteration
if self._iteration != 0:
spimage.sp_phaser_iterate(self._phaser,self._iteration-iterations_propagated)
iterations_propagated = self._iteration
if change_algorithm:
i_alg += 1
iteration0_alg = self._iteration
self._phaser.algorithm = self._phasing_algorithms[i_alg]["spimage_phasing"]
self._log("Change of phasing algorithm to %s." % self._phasing_algorithms[i_alg]["type"],"INFO")
if change_support:
i_sup += 1
iteration0_sup = self._iteration
self._phaser.sup_algorithm = self._support_algorithms[i_sup]["spimage_support_array"]
self._log("Change of support algorithm to %s." % self._support_algorithms[i_sup]["type"],"INFO")
if self._iteration in self._out_iterations_images:
[real_space[i_out_images,:,:],support[i_out_images,:,:]] = self._get_curr_model(shifted=False)
[fourier_space[i_out_images,:,:],mask[i_out_images,:,:]] = self._get_curr_fmodel(shifted=False)
i_out_images += 1
self._log("Outputting images.","DEBUG")
if self._iteration in self._out_iterations_scores:
scores = self._get_scores()
fourier_error[i_out_scores] = scores["fourier_error"]
real_error[i_out_scores] = scores["real_error"]
support_size[i_out_scores] = scores["support_size"]
i_out_scores += 1
self._log("Outputting scores.","DEBUG")
self._iteration = None
out = {"iteration_index_images":self._out_iterations_images,
"iteration_index_scores":self._out_iterations_scores,
"real_space":real_space,
"support":support,
"fourier_space":fourier_space,
"mask":mask,
"real_error":real_error,
"fourier_error":fourier_error,
"support_size":support_size}
return out
def reconstruct(self):
"""
Performs a single reconstruction with the specified configuration and outputs a dictionary with the results.
"""
self._prepare_reconstruction()
if not self._ready:
return
out = {}
#self._init_new_phaser()
i_alg = 0
i_sup = 0
i_out_images = 0
i_out_scores = 0
iteration0_alg = 0
iteration0_sup = 0
iterations_propagated = 0
fourier_error = np.zeros(self._number_of_outputs_scores)
real_error = np.zeros(self._number_of_outputs_scores)
support_size = np.zeros(self._number_of_outputs_scores)
A = self._amplitudes
if len(A.shape) == 2:
real_space = np.zeros(shape=(self._number_of_outputs_images,self._Ny,self._Nx),dtype="complex128")
support = np.zeros(shape=(self._number_of_outputs_images,self._Ny,self._Nx),dtype="bool")
fourier_space = np.zeros(shape=(self._number_of_outputs_images,self._Ny,self._Nx),dtype="complex128")
mask = np.zeros(shape=(self._number_of_outputs_images,self._Ny,self._Nx),dtype="bool")
for self._iteration in range(self._number_of_iterations+1):
change_algorithm = (self._iteration-iteration0_alg == self._phasing_algorithms[i_alg]["number_of_iterations"]) and (self._iteration != self._number_of_iterations)
change_support = (self._iteration-iteration0_sup == self._support_algorithms[i_sup]["number_of_iterations"]) and (self._iteration != self._number_of_iterations)
if change_algorithm or change_support or self._iteration in self._out_iterations_images or self._iteration in self._out_iterations_scores:
if self._reconstruction is None:
self._log("Iteration %i" % (self._iteration),"INFO")
else:
self._log("Reconstruction %i - Iteration %i" % (self._reconstruction,self._iteration),"INFO")
# iterate to self._iteration
if self._iteration != 0:
spimage.sp_phaser_iterate(self._sp_phaser,self._iteration-iterations_propagated)
iterations_propagated = self._iteration
if change_algorithm:
i_alg += 1
iteration0_alg = self._iteration
self._sp_phaser.algorithm = self._phasing_algorithms[i_alg]["spimage_phasing"]
self._log("Change of phasing algorithm to %s." % self._phasing_algorithms[i_alg]["type"],"INFO")
if change_support:
i_sup += 1
iteration0_sup = self._iteration
self._sp_phaser.sup_algorithm = self._support_algorithms[i_sup]["spimage_support_array"]
self._log("Change of support algorithm to %s." % self._support_algorithms[i_sup]["type"],"INFO")
if self._iteration in self._out_iterations_images:
[real_space[i_out_images,:,:],support[i_out_images,:,:]] = self._get_curr_model(shifted=False)
[fourier_space[i_out_images,:,:],mask[i_out_images,:,:]] = self._get_curr_fmodel(shifted=False)
i_out_images += 1
self._log("Outputting images.","DEBUG")
if self._iteration in self._out_iterations_scores:
scores = self._get_scores()
fourier_error[i_out_scores] = scores["fourier_error"]
real_error[i_out_scores] = scores["real_error"]
support_size[i_out_scores] = scores["support_size"]
i_out_scores += 1
self._log("Outputting scores.","DEBUG")
self._iteration = None
out = {"iteration_index_images":self._out_iterations_images,
"iteration_index_scores":self._out_iterations_scores,
"real_space":real_space,
"support":support,
"fourier_space":fourier_space,
"mask":mask,
"real_error":real_error,
"fourier_error":fourier_error,
"support_size":support_size}
return out
if len(A.shape) == 3:
real_space = np.zeros(shape=(self._number_of_outputs_images,self._Nz,self._Ny,self._Nx),dtype="complex128")
support = np.zeros(shape=(self._number_of_outputs_images,self._Nz,self._Ny,self._Nx),dtype="bool")
fourier_space = np.zeros(shape=(self._number_of_outputs_images,self._Nz,self._Ny,self._Nx),dtype="complex128")
mask = np.zeros(shape=(self._number_of_outputs_images,self._Nz,self._Ny,self._Nx),dtype="bool")
for self._iteration in range(self._number_of_iterations+1):
change_algorithm = (self._iteration-iteration0_alg == self._phasing_algorithms[i_alg]["number_of_iterations"]) and (self._iteration != self._number_of_iterations)
change_support = (self._iteration-iteration0_sup == self._support_algorithms[i_sup]["number_of_iterations"]) and (self._iteration != self._number_of_iterations)
if change_algorithm or change_support or self._iteration in self._out_iterations_images or self._iteration in self._out_iterations_scores:
if self._reconstruction is None:
self._log("Iteration %i" % (self._iteration),"INFO")
else:
self._log("Reconstruction %i - Iteration %i" % (self._reconstruction,self._iteration),"INFO")
# iterate to self._iteration
if self._iteration != 0:
spimage.sp_phaser_iterate(self._sp_phaser,self._iteration-iterations_propagated)
iterations_propagated = self._iteration
if change_algorithm:
i_alg += 1
iteration0_alg = self._iteration
self._sp_phaser.algorithm = self._phasing_algorithms[i_alg]["spimage_phasing"]
self._log("Change of phasing algorithm to %s." % self._phasing_algorithms[i_alg]["type"],"INFO")
if change_support:
i_sup += 1
iteration0_sup = self._iteration
self._sp_phaser.sup_algorithm = self._support_algorithms[i_sup]["spimage_support_array"]
self._log("Change of support algorithm to %s." % self._support_algorithms[i_sup]["type"],"INFO")
if self._iteration in self._out_iterations_images:
[real_space[i_out_images,:,:,:],support[i_out_images,:,:,:]] = self._get_curr_model(shifted=False)
[fourier_space[i_out_images,:,:,:],mask[i_out_images,:,:,:]] = self._get_curr_fmodel(shifted=False)
i_out_images += 1
self._log("Outputting images.","DEBUG")
if self._iteration in self._out_iterations_scores:
scores = self._get_scores()
fourier_error[i_out_scores] = scores["fourier_error"]
real_error[i_out_scores] = scores["real_error"]
support_size[i_out_scores] = scores["support_size"]
i_out_scores += 1
self._log("Outputting scores.","DEBUG")
self._iteration = None
out = {"iteration_index_images":self._out_iterations_images,
"iteration_index_scores":self._out_iterations_scores,
"real_space":real_space,
"support":support,
"fourier_space":fourier_space,
"mask":mask,
"real_error":real_error,
"fourier_error":fourier_error,
"support_size":support_size}
return out
sup_alg = _spimage.sp_support_array_init(_spimage.sp_support_static_alloc(), 20)
# create phaser
phaser = _spimage.sp_phaser_alloc()
_spimage.sp_phaser_init(phaser, phase_alg, sup_alg, _spimage.SpEngineCUDA)
_spimage.sp_phaser_set_amplitudes(phaser, amplitudes)
_spimage.sp_phaser_init_model(phaser, real_space, 0)
_spimage.sp_phaser_init_support(phaser, support, 0, 0)
#real_space_s = _spimage.sp_image_shift(real_space)
fourier_space = _spimage.sp_image_ifftw3(real_space)
ereal_start = _numpy.sqrt((abs(real_space.image[~_numpy.bool8(support.image)])**2).sum() / (abs(real_space.image)**2).sum())
efourier_start = _numpy.sqrt(((abs(fourier_space.image[_numpy.bool8(amplitudes.mask)]) - abs(amplitudes.image[_numpy.bool8(amplitudes.mask)]))**2).sum() / ((abs(amplitudes.image[_numpy.bool8(amplitudes.mask)])**2).sum() + (abs(fourier_space.image[~_numpy.bool8(amplitudes.mask)])**2).sum()))
_spimage.sp_phaser_iterate(phaser, options.number_of_iterations)
model_out = _spimage.sp_phaser_model(phaser)
support_out = _spimage.sp_phaser_support(phaser)
fmodel_out = _spimage.sp_phaser_fmodel(phaser)
real_space_end = _spimage.sp_phaser_model_before_projection(phaser)
fourier_space_end = _spimage.sp_phaser_fmodel(phaser)
ereal_end = _numpy.sqrt((abs(real_space_end.image[~_numpy.bool8(support.image)])**2).sum() / (abs(real_space_end.image)**2).sum())
efourier_end = _numpy.sqrt(((abs(fourier_space_end.image[_numpy.bool8(amplitudes.mask)]) - abs(amplitudes.image[_numpy.bool8(amplitudes.mask)]))**2).sum() / ((abs(amplitudes.image[_numpy.bool8(amplitudes.mask)])**2).sum() + (abs(fourier_space_end.image[~_numpy.bool8(amplitudes.mask)])**2).sum()))
_spimage.sp_image_write(model_out, "%s/real_space-%s.h5" % (options.output_dir, options.output_affix), 0)
_spimage.sp_image_write(support_out, "%s/support-%s.h5" % (options.output_dir, options.output_affix), 0)
_spimage.sp_image_write(fmodel_out, "%s/fourier_space-%s.h5" % (options.output_dir, options.output_affix), 0)
print "Ereal: %g -> %g" % (ereal_start, ereal_end)
print "Efourier: %g -> %g" % (efourier_start, efourier_end)
def run_it(number_of_iterations):
spimage.sp_phaser_iterate(phaser, number_of_iterations)
_spimage.sp_phaser_init_model(phaser, real_space, 0)
_spimage.sp_phaser_init_support(phaser, support, 0, 0)
fourier_space = _spimage.sp_image_ifftw3(real_space)
support = _numpy.bool8(support.image)
ereal_start = _numpy.sqrt((abs(real_space.image[~support])**2).sum() /
(abs(real_space.image)**2).sum())
mask = _numpy.bool8(amplitudes.mask)
efourier_start = _numpy.sqrt(
((abs(fourier_space.image[mask]) - abs(amplitudes.image[mask]))**
2).sum() / ((abs(amplitudes.image[mask])**2).sum() +
(abs(fourier_space.image[~mask])**2).sum()))
_spimage.sp_phaser_iterate(phaser, args.number_of_iterations)
model_out = _spimage.sp_phaser_model(phaser)
support_out = _spimage.sp_phaser_support(phaser)
fmodel_out = _spimage.sp_phaser_fmodel(phaser)
real_space_end = _spimage.sp_phaser_model_before_projection(phaser)
fourier_space_end = _spimage.sp_phaser_fmodel(phaser)
ereal_end = _numpy.sqrt((abs(real_space_end.image[~support])**2).sum() /
(abs(real_space_end.image)**2).sum())
efourier_end = _numpy.sqrt(
((abs(fourier_space_end.image[mask]) - abs(amplitudes.image[mask]))**
2).sum() / ((abs(amplitudes.image[mask])**2).sum() +
(abs(fourier_space_end.image[~mask])**2).sum()))
_spimage.sp_image_write(model_out,