def index_and_integrate(self, frames, files, spotfinder_results):
self.frames = frames
self.files = files
self.spotfinder_results = spotfinder_results
pd = self.establish_dict_for_refinement(frames, spotfinder_results)
#------------------------------------------------------------
ai, P = self.index_and_refine(pd, files, spotfinder_results, 0)
self.indexing_ai = ai
#------------------------------------------------------------
if labelit_commands.compatibility_allow == False:
M = self.best_character_to_IndexPrinter(
ai, P, pd, horizons_phil=self.horizons_phil)
else:
from labelit.diffraction.compatibility import \
best_compatibility_to_IndexPrinter
M = best_compatibility_to_IndexPrinter(
ai,
P,
pd,
files,
spotfinder_results,
horizons_phil=self.horizons_phil)
#------------------------------------------------------------
if "writer" in labelit_commands.__dict__:
labelit_commands.writer.make_image_plots_detail(
ai=ai,
pd=pd,
inframes=files,
spotfinder_results=spotfinder_results)
if not labelit_commands.index_only:
IC = IntegrateCharacters(M, pd)
IC.write_mosflm_matrices()
IC.find_best()
IC.show()
return pd
def index_and_integrate(self,frames,files,spotfinder_results):
self.frames = frames
self.files = files
self.spotfinder_results = spotfinder_results
pd = self.establish_dict_for_refinement(frames,spotfinder_results)
#------------------------------------------------------------
ai,P = self.index_and_refine(pd,files,spotfinder_results,0)
self.indexing_ai = ai
#------------------------------------------------------------
if labelit_commands.compatibility_allow==False:
M = self.best_character_to_IndexPrinter(ai,P,pd,horizons_phil=self.horizons_phil)
else:
from labelit.diffraction.compatibility import \
best_compatibility_to_IndexPrinter
M = best_compatibility_to_IndexPrinter(ai,P,pd,files,spotfinder_results,horizons_phil=self.horizons_phil)
#------------------------------------------------------------
if labelit_commands.__dict__.has_key("writer"):
labelit_commands.writer.make_image_plots_detail(
ai=ai,pd=pd,inframes=files,spotfinder_results=spotfinder_results)
if not labelit_commands.index_only:
IC = IntegrateCharacters(M,pd)
IC.write_mosflm_matrices()
IC.find_best()
IC.show()
return pd
def index_and_integrate(self, frames, files, spotfinder_results):
self.pd = establish_dict_for_refinement(frames, spotfinder_results)
self.spotfinder_results = spotfinder_results
self.frames = frames
#------------------------------------------------------------
ai, P = index_and_refine(pd=self.pd,
rawframes=files,
spotfinder_results=spotfinder_results,
verbose=False,
horizon_phil=self.horizons_phil)
self.indexing_ai = ai
#------------------------------------------------------------
if self.horizons_phil.compatibility_allow == False:
M = best_character_to_IndexPrinter(ai, P, self.pd, True,
self.horizons_phil)
else:
from labelit.diffraction.compatibility import best_compatibility_to_IndexPrinter
M = best_compatibility_to_IndexPrinter(ai, P, self.pd, files,
spotfinder_results)
#------------------------------------------------------------
if "writer" in self.horizons_phil.__dict__:
self.horizons_phil.writer.make_image_plots_detail(
ai=ai,
pd=self.pd,
inframes=files,
spotfinder_results=spotfinder_results)
if not self.horizons_phil.index_only:
if 0:
from labelit.dps import IntegrateCharacters
IC = IntegrateCharacters(M, self.pd)
IC.write_mosflm_matrices()
IC.find_best()
IC.show()
if 1:
from rstbx.new_horizons.oscillation_shots import IntegrateCharacters
IC = IntegrateCharacters(M, self.pd, self.horizons_phil, files,
spotfinder_results)
IC.find_best()
self.last_saved_best = IC.save_best()
IC.show()
# Lattice character information added for special UCSF/ LLNL project (5/2014):
self.pd["lattice_characters"] = M.best()
for item in self.pd["lattice_characters"]:
del item["minimizer"]
return self.pd
def index_and_integrate(self,frames,files,spotfinder_results):
self.pd = establish_dict_for_refinement(frames,spotfinder_results)
self.spotfinder_results = spotfinder_results
self.frames = frames
#------------------------------------------------------------
ai,P = index_and_refine(pd = self.pd,
rawframes = files,
spotfinder_results = spotfinder_results,
verbose = False,
horizon_phil = self.horizons_phil)
self.indexing_ai = ai
#------------------------------------------------------------
if self.horizons_phil.compatibility_allow==False:
M = best_character_to_IndexPrinter(ai,P,self.pd,True,self.horizons_phil)
else:
from labelit.diffraction.compatibility import best_compatibility_to_IndexPrinter
M = best_compatibility_to_IndexPrinter(ai,P,self.pd,files,
spotfinder_results)
#------------------------------------------------------------
if self.horizons_phil.__dict__.has_key("writer"):
self.horizons_phil.writer.make_image_plots_detail(
ai=ai,pd=self.pd,inframes=files,spotfinder_results=spotfinder_results)
if not self.horizons_phil.index_only:
if 0:
from labelit.dps import IntegrateCharacters
IC = IntegrateCharacters(M,self.pd)
IC.write_mosflm_matrices()
IC.find_best()
IC.show()
if 1:
from rstbx.new_horizons.oscillation_shots import IntegrateCharacters
IC = IntegrateCharacters(M,self.pd,self.horizons_phil,files,
spotfinder_results)
IC.find_best()
self.last_saved_best = IC.save_best()
IC.show()
# Lattice character information added for special UCSF/ LLNL project (5/2014):
self.pd["lattice_characters"]=M.best()
for item in self.pd["lattice_characters"]: del item["minimizer"]
return self.pd