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 algorithm_raar(beta, real=False, positive=False):
"""Create a RAAR algorithm object"""
beta_sp = smap(beta)
constraints = get_constraints(real, positive)
algorithm = _spimage.sp_phasing_raar_alloc(beta_sp, constraints)
return algorithm
def algorithm_raar(beta, real=False, positive=False):
"""Create a RAAR algorithm object"""
beta_sp = smap(beta)
constraints = get_constraints(real, positive)
algorithm = _spimage.sp_phasing_raar_alloc(beta_sp, constraints)
return algorithm