def smap(values):
"""Create spimage smap object from iterable of (iteration, value) pairs."""
import collections
if not isinstance(values, collections.Iterable):
values = [(0, values)]
smap_out = _spimage.sp_smap_alloc(len(values))
for i in values:
_spimage.sp_smap_insert(smap_out, i[0], i[1])
return smap_out
def smap(values):
"""Create spimage smap object from iterable of (iteration, value)
pairs."""
import collections
if not isinstance(values, collections.Iterable):
values = [(0, values)]
smap_out = _spimage.sp_smap_alloc(len(values))
for i in values:
_spimage.sp_smap_insert(smap_out, i[0], i[1])
return smap_out
def _init_phasing_algorithms(self):
if not self._phasing_algorithms_dirty:
self._log("Phasing algorithms already initialised.","DEBUG")
return
i = 0
for alg_conf in self._phasing_algorithms_configs:
alg = dict(alg_conf)
if alg_conf["number_of_iterations"] is None:
if len(self._phasing_algorithms_configs) == 1:
alg["number_of_iterations"] = self._number_of_iterations
else:
self._log("Number of iterations can not be None if many phasing algorithms are specified. Please report this error.","ERROR")
return
# constraints
constraints = spimage.SpNoConstraints
if "constraints" in alg:
if "enforce_positivity" in alg["constraints"] and "enforce_real" in alg["constraints"]:
constraints |= spimage.SpPositiveRealObject
elif "enforce_real" in alg["constraints"]:
constraints |= spimage.SpRealObject
elif "enforce_positivity" in alg["constraints"]:
constraints |= spimage.SpPositiveComplexObject
if "enforce_centrosymmetry" in alg["constraints"]:
constraints |= spimage.SpCentrosymmetricObject
# phasing algorithm
if alg["type"] in ["raar","hio","diffmap"]:
alg["beta"] = spimage.sp_smap_alloc(1)
spimage.sp_smap_insert(alg["beta"], i,alg["beta_init"])
spimage.sp_smap_insert(alg["beta"], i+alg["number_of_iterations"], alg["beta_final"])
if alg["type"] == "raar":
alg["spimage_phasing"] = spimage.sp_phasing_raar_alloc(alg["beta"], constraints)
elif alg["type"] == "hio":
alg["spimage_phasing"] = spimage.sp_phasing_hio_alloc(alg["beta"], constraints)
elif alg["type"] == "diffmap":
alg["spimage_phasing"] = spimage.sp_phasing_diffmap_alloc(alg["beta"], alg["gamma1"], alg["gamma2"], constraints)
elif alg["type"] == "er":
alg["spimage_phasing"] = spimage.sp_phasing_er_alloc(constraints)
else:
self._log("Phasing algorithm %s not implemented. Please report this error!" % type,"ERROR")
return
i += alg["number_of_iterations"]
self._phasing_algorithms.append(alg)
self._phasing_algorithms_dirty = False
self._log("Phasing algorithm initialised.","DEBUG")
def _init_phasing_algorithms(self):
if not self._phasing_algorithms_dirty:
self._log("Phasing algorithms already initialised.","DEBUG")
return
i = 0
for alg_conf in self._phasing_algorithms_configs:
alg = dict(alg_conf)
if alg_conf["number_of_iterations"] is None:
if len(self._phasing_algorithms_configs) == 1:
alg["number_of_iterations"] = self._number_of_iterations
else:
self._log("Number of iterations can not be None if many phasing algorithms are specified. Please report this error.","ERROR")
return
# constraints
constraints = spimage.SpNoConstraints
if "constraints" in alg:
if "enforce_positivity" in alg["constraints"] and "enforce_real" in alg["constraints"]:
constraints |= spimage.SpPositiveRealObject
elif "enforce_real" in alg["constraints"]:
constraints |= spimage.SpRealObject
elif "enforce_positivity" in alg["constraints"]:
constraints |= spimage.SpPositiveComplexObject
if "enforce_centrosymmetry" in alg["constraints"]:
constraints |= spimage.SpCentrosymmetricObject
# phasing algorithm
if alg["type"] in ["raar","hio","diffmap"]:
alg["beta"] = spimage.sp_smap_alloc(1)
spimage.sp_smap_insert(alg["beta"], i,alg["beta_init"])
spimage.sp_smap_insert(alg["beta"], i+alg["number_of_iterations"], alg["beta_final"])
if alg["type"] == "raar":
alg["spimage_phasing"] = spimage.sp_phasing_raar_alloc(alg["beta"], constraints)
elif alg["type"] == "hio":
alg["spimage_phasing"] = spimage.sp_phasing_hio_alloc(alg["beta"], constraints)
elif alg["type"] == "diffmap":
alg["spimage_phasing"] = spimage.sp_phasing_diff_map_alloc(alg["beta"], alg["gamma1"], alg["gamma2"], constraints)
elif alg["type"] == "er":
alg["spimage_phasing"] = spimage.sp_phasing_er_alloc(constraints)
else:
self._log("Phasing algorithm %s not implemented. Please report this error!" % type,"ERROR")
return
i += alg["number_of_iterations"]
self._phasing_algorithms.append(alg)
self._phasing_algorithms_dirty = False
self._log("Phasing algorithm initialised.","DEBUG")
def get_basic_phaser(amplitudes, support, mask=None):
"""This function is not finished"""
if mask is None:
amplitudes_sp = image_from_array(amplitudes)
else:
amplitudes_sp = image_from_array(amplitudes, mask)
beta = _spimage.sp_smap_alloc(1)
_spimage.sp_smap_insert(beta, 0, 0.9)
phase_alg = _spimage.sp_phasing_hio_alloc(beta, _spimage.SpNoConstraints)
support_sp = image_from_array(support)
sup_alg = _spimage.sp_support_array_init(_spimage.sp_support_static_alloc(), 20)
phaser = _spimage.sp_phaser_alloc()
_spimage.sp_phaser_init(phaser, phase_alg, sup_alg, _spimage.SpEngineCUDA)
_spimage.sp_phaser_set_amplitudes(phaser, amplitudes_sp)
_spimage.sp_phaser_init_model(phaser, None, _spimage.SpModelRandomPhases)
_spimage.sp_phaser_init_support(phaser, support_sp, 0, 0)
return phaser
def get_basic_phaser(amplitudes, support, mask=None, algorithm=None):
"""This function is not finished"""
if mask is None:
amplitudes_sp = image_from_array(amplitudes)
else:
amplitudes_sp = image_from_array(amplitudes, mask)
if algorithm is None:
beta = _spimage.sp_smap_alloc(1)
_spimage.sp_smap_insert(beta, 0, 0.9)
phase_alg = _spimage.sp_phasing_hio_alloc(beta,
_spimage.SpNoConstraints)
else:
phase_alg = algorithm
support_sp = image_from_array(support)
sup_alg = _spimage.sp_support_array_init(
_spimage.sp_support_static_alloc(), 20)
phaser = _spimage.sp_phaser_alloc()
_spimage.sp_phaser_init(phaser, phase_alg, sup_alg, _spimage.SpEngineCUDA)
_spimage.sp_phaser_set_amplitudes(phaser, amplitudes_sp)
_spimage.sp_phaser_init_model(phaser, None, _spimage.SpModelRandomPhases)
_spimage.sp_phaser_init_support(phaser, support_sp, 0, 0)
return phaser
def _init_support_algorithms(self):
if not self._support_algorithms_dirty:
self._log("Support algorithms already initialised.","DEBUG")
return
i = 0
for alg_conf in self._support_algorithms_configs:
alg = dict(alg_conf)
if alg_conf["number_of_iterations"] is None:
if len(self._support_algorithms_configs) == 1:
alg["number_of_iterations"] = self._number_of_iterations
else:
self._log("Number of iterations can not be None if many support algorithms are specified. Please report this error.","ERROR")
return
if alg["type"] == "area":
blur_radius = spimage.sp_smap_alloc(2)
spimage.sp_smap_insert(blur_radius, i, alg["blur_init"])
spimage.sp_smap_insert(blur_radius, i + alg["number_of_iterations"], alg["blur_final"])
support_area = spimage.sp_smap_alloc(2)
spimage.sp_smap_insert(support_area, i,alg["area_init"])
spimage.sp_smap_insert(support_area, i + alg["number_of_iterations"],alg["area_final"])
alg["spimage_support_array"] = spimage.sp_support_array_init(spimage.sp_support_area_alloc(blur_radius, support_area),alg["update_period"])
elif alg["type"] == "threshold":
blur_radius = spimage.sp_smap_alloc(2)
spimage.sp_smap_insert(blur_radius, i, alg["blur_init"])
spimage.sp_smap_insert(blur_radius, i + alg["number_of_iterations"], alg["blur_final"])
threshold = spimage.sp_smap_alloc(2)
spimage.sp_smap_insert(threshold, i, alg["threshold_init"])
spimage.sp_smap_insert(threshold, i + alg["number_of_iterations"], alg["threshold_final"])
alg["spimage_support_array"] = spimage.sp_support_array_init(spimage.sp_support_threshold_alloc(blur_radius, threshold),alg["update_period"])
elif alg["type"] == "static":
alg["update_period"] = alg["number_of_iterations"]
alg["spimage_support_array"] = spimage.sp_support_array_init(spimage.sp_support_static_alloc(),alg["update_period"])
else:
self._log("No valid support algorithm set. This error should be reported!","ERROR")
return
if alg["center_image"]:
spimage.sp_support_array_append(alg["spimage_support_array"],spimage.sp_support_centre_image_alloc())
self._log("Enabling center image in real space, it will be done with every support update.")
else:
self._log("Center real space image disabled.")
i += alg["number_of_iterations"]
self._support_algorithms.append(alg)
self._support_algorithms_dirty = False
self._log("Support algorithms initialised.","DEBUG")
def _init_support_algorithms(self):
if not self._support_algorithms_dirty:
self._log("Support algorithms already initialised.","DEBUG")
return
i = 0
for alg_conf in self._support_algorithms_configs:
alg = dict(alg_conf)
if alg_conf["number_of_iterations"] is None:
if len(self._support_algorithms_configs) == 1:
alg["number_of_iterations"] = self._number_of_iterations
else:
self._log("Number of iterations can not be None if many support algorithms are specified. Please report this error.","ERROR")
return
if alg["type"] == "area":
self._blur_radius = spimage.sp_smap_alloc(2)
spimage.sp_smap_insert(self._blur_radius, i, alg["blur_init"])
spimage.sp_smap_insert(self._blur_radius, i + alg["number_of_iterations"], alg["blur_final"])
self._support_area = spimage.sp_smap_alloc(2)
spimage.sp_smap_insert(self._support_area, i,alg["area_init"])
spimage.sp_smap_insert(self._support_area, i + alg["number_of_iterations"],alg["area_final"])
alg["spimage_support_array"] = spimage.sp_support_array_init(spimage.sp_support_area_alloc(self._blur_radius, self._support_area),alg["update_period"])
elif alg["type"] == "threshold":
self._blur_radius = spimage.sp_smap_alloc(2)
spimage.sp_smap_insert(self._blur_radius, i, alg["blur_init"])
spimage.sp_smap_insert(self._blur_radius, i + alg["number_of_iterations"], alg["blur_final"])
self._threshold = spimage.sp_smap_alloc(2)
spimage.sp_smap_insert(self._threshold, i, alg["threshold_init"])
spimage.sp_smap_insert(self._threshold, i + alg["number_of_iterations"], alg["threshold_final"])
alg["spimage_support_array"] = spimage.sp_support_array_init(spimage.sp_support_threshold_alloc(self._blur_radius, self._threshold),alg["update_period"])
elif alg["type"] == "static":
alg["update_period"] = alg["number_of_iterations"]
alg["spimage_support_array"] = spimage.sp_support_array_init(spimage.sp_support_static_alloc(),alg["update_period"])
else:
self._log("No valid support algorithm set. This error should be reported!","ERROR")
return
if alg["center_image"]:
spimage.sp_support_array_append(alg["spimage_support_array"],spimage.sp_support_centre_image_alloc())
self._log("Enabling center image in real space, it will be done with every support update.")
else:
self._log("Center real space image disabled.")
i += alg["number_of_iterations"]
self._support_algorithms.append(alg)
self._support_algorithms_dirty = False
self._log("Support algorithms initialised.","DEBUG")