def setCommandInput(self, argument_module):
self.Files = ImageFiles(argument_module, self.horizons_phil)
self.frames = self.Files.frames()
def setCommandInput(self,argument_module): self.Files = ImageFiles(argument_module,self.horizons_phil) self.frames = self.Files.frames()
class AutoIndexOrganizer:
def __init__(self, verbose=0, **kwargs):
self.rundir = os.getcwd()
self.verbose = verbose
self.horizons_phil = kwargs["horizons_phil"]
#self.horizons_phil.persist.show()
assert 'argument_module' in kwargs
self.setCommandInput(kwargs['argument_module'])
if self.verbose:
print "Process frames in directory:", self.Files.filenames.FN[
0].cwd
if 'delegate' in kwargs:
self.setIndexingDelegate(kwargs['delegate'])
self.exception_passthru = 0
if 'exception_passthru' in kwargs:
self.exception_passthru = kwargs['exception_passthru']
print '\n'.join(self.Files.filenames())
def setCommandInput(self, argument_module):
self.Files = ImageFiles(argument_module, self.horizons_phil)
self.frames = self.Files.frames()
def printSpots(self):
from labelit.procedure import spotfinder_and_pickle
S = spotfinder_and_pickle(self.rundir,
self.Files,
spots_pickle=self.horizons_phil.spots_pickle,
horizons_phil=self.horizons_phil)
#print S.images
NEW = spotfinder_proxy(S, self.horizons_phil, self.Files)
NEW.images = {}
NEW.overlapping = False
NEW.phil_params = S.phil_params
for frame in self.frames:
NEW.images[frame] = dict(area=[
1,
] # not actually used for new horizons
)
self.S = NEW
for frame in self.frames:
if self.verbose:
from labelit.command_line.stats_distl import pretty_image_stats, notes
pretty_image_stats(S, frame)
notes(S, self.frames[0])
print
NEW.get_aitbx_inputs()
def setIndexingDelegate(self, function):
self.indexing_delegate = function
def executeDelegate(self):
self.info = self.indexing_delegate(self.frames, self.Files, self.S)
def pickle_the_results(self):
for key in ['best_integration', 'triclinic']:
if key in self.info:
if 'minimizer' in self.info[key]: #not attained when best==tri
del self.info[key]['minimizer'] # Must remove
# temporary section pending an analysis of which data need to be persistent
if 'results' in self.info[key]["integration"]:
#future options 1) make the whole object picklable--write test script
#2) just pickle the data needed for the GUI
del self.info[key]["integration"]['results']
from labelit.dptbx.pickle_support import pickle_refinements
pickle_refinements(self.info, self.horizons_phil.refinements_pickle)
def process(self):
self.printSpots()
self.executeDelegate()
if 'info' in self.__dict__: #if indexing worked
self.pickle_the_results()
return self.info
class AutoIndexOrganizer:
def __init__(self,verbose = 0,**kwargs):
self.rundir = os.getcwd()
self.verbose = verbose
self.horizons_phil = kwargs["horizons_phil"]
#self.horizons_phil.persist.show()
assert kwargs.has_key('argument_module')
self.setCommandInput(kwargs['argument_module'])
if self.verbose: print "Process frames in directory:",self.Files.filenames.FN[0].cwd
if kwargs.has_key('delegate'):
self.setIndexingDelegate(kwargs['delegate'])
self.exception_passthru = 0
if kwargs.has_key('exception_passthru'):
self.exception_passthru = kwargs['exception_passthru']
print '\n'.join(self.Files.filenames())
def setCommandInput(self,argument_module):
self.Files = ImageFiles(argument_module,self.horizons_phil)
self.frames = self.Files.frames()
def printSpots(self):
from labelit.procedure import spotfinder_and_pickle
S = spotfinder_and_pickle(self.rundir,self.Files,
spots_pickle = self.horizons_phil.spots_pickle,
horizons_phil = self.horizons_phil)
#print S.images
NEW = spotfinder_proxy(S,self.horizons_phil,self.Files)
NEW.images = {}
NEW.overlapping = False
NEW.phil_params = S.phil_params
for frame in self.frames:
NEW.images[frame]=dict(area=[1,] # not actually used for new horizons
)
self.S = NEW
for frame in self.frames:
if self.verbose:
from labelit.command_line.stats_distl import pretty_image_stats,notes
pretty_image_stats(S,frame)
notes(S,self.frames[0])
print
NEW.get_aitbx_inputs()
def setIndexingDelegate(self,function):
self.indexing_delegate = function
def executeDelegate(self):
self.info = self.indexing_delegate(self.frames,self.Files,self.S)
def pickle_the_results(self):
for key in ['best_integration','triclinic']:
if self.info.has_key(key):
if self.info[key].has_key('minimizer'): #not attained when best==tri
del self.info[key]['minimizer'] # Must remove
# temporary section pending an analysis of which data need to be persistent
if self.info[key]["integration"].has_key('results'):
#future options 1) make the whole object picklable--write test script
#2) just pickle the data needed for the GUI
del self.info[key]["integration"]['results']
from labelit.dptbx.pickle_support import pickle_refinements
pickle_refinements(self.info,self.horizons_phil.refinements_pickle)
def process(self):
self.printSpots()
self.executeDelegate()
if self.__dict__.has_key('info'): #if indexing worked
self.pickle_the_results()
return self.info
