Exemplo n.º 1
0
 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
Exemplo n.º 3
0
    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
Exemplo n.º 4
0
  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