def _get_curr_model(self,**kwargs):
shifted = kwargs.get("shifted",False)
state = kwargs.get("state","before_projection")
if self._iteration > 0:
if state == "before_projection":
tmp1 = spimage.sp_phaser_model_before_projection(self._phaser)
tmp2 = spimage.sp_phaser_support(self._phaser)
img = tmp1.image.copy()
msk = np.int32(tmp2.image.real)
#spimage.sp_image_free(tmp1)
#spimage.sp_image_free(tmp2)
elif state == "after_projection":
tmp = spimage.sp_phaser_model_with_support(self._phaser)
img = tmp.image.copy()
msk = tmp.mask.copy()
#spimage.sp_image_free(tmp)
else:
img = self._phaser.model.image.copy()
msk = np.array(self._sp_initial_support.image.real,dtype="bool")
if not shifted:
return [np.fft.fftshift(img),np.fft.fftshift(msk)]
else:
return [img,msk]
def _get_curr_model(self,**kwargs):
shifted = kwargs.get("shifted",False)
state = kwargs.get("state","before_projection")
if self._iteration > 0:
if state == "before_projection":
tmp1 = spimage.sp_phaser_model_before_projection(self._sp_phaser)
tmp2 = spimage.sp_phaser_support(self._sp_phaser)
img = tmp1.image.copy()
msk = np.int32(tmp2.image.real)
#spimage.sp_image_free(tmp1)
#spimage.sp_image_free(tmp2)
elif state == "after_projection":
tmp = spimage.sp_phaser_model_with_support(self._sp_phaser)
img = tmp.image.copy()
msk = tmp.mask.copy()
#spimage.sp_image_free(tmp)
else:
img = self._sp_phaser.model.image.copy()
msk = np.array(self._sp_initial_support.image.real,dtype="bool")
if not shifted:
return [np.fft.fftshift(img),np.fft.fftshift(msk)]
else:
return [img,msk]
# 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)
spimage.sp_phaser_set_amplitudes(phaser, amplitudes)
spimage.sp_phaser_init_model(phaser, None, spimage.SpModelRandomPhases)
spimage.sp_phaser_init_support(phaser, support, 0, 0)
def run_it(number_of_iterations):
spimage.sp_phaser_iterate(phaser, number_of_iterations)
run_it(NUMBER_OF_ITERATIONS)
phaser.algorithm = phase_alg_refine
run_it(NUMBER_OF_REFINE_ITERATIONS)
# Output data
model = spimage.sp_phaser_model(phaser)
support = spimage.sp_phaser_support(phaser)
fmodel = spimage.sp_phaser_fmodel(phaser)
spimage.sp_image_write(model, OUTPUT_DIR + "run_{}_model.h5".format(run_id), 0)
spimage.sp_image_write(support,
OUTPUT_DIR + "run_{}_support.h5".format(run_id), 0)
spimage.sp_image_write(fmodel, OUTPUT_DIR + "run_{}_fmodel.h5".format(run_id),
0)
ereal = spimage.sp_phaser_ereal(phaser)
efourier = spimage.sp_phaser_efourier(phaser)
filename = OUTPUT_DIR + '/run_{}_error.h5'.format(run_id)
with h5py.File(filename, "w") as file_handle:
file_handle.create_dataset('ereal', data=ereal)
file_handle.create_dataset('efourier', data=efourier)
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,
f"{args.outdir}/real_space-{args.affix}.h5", 0)
_spimage.sp_image_write(support_out,
f"{args.outdir}/support-{args.affix}.h5", 0)
