def run_analysis(self): """ Run analysis of integrated images """ from iota.components.iota_analysis import Analyzer analysis = Analyzer(init=self.init, all_objects=self.img_objects) analysis.print_results() analysis.unit_cell_analysis() analysis.print_summary() analysis.make_prime_input()
def run_analysis(self):
''' Run analysis of integrated images '''
cmd.Command.start("Analyzing results ")
analysis = Analyzer(self.init, self.img_objects, iota_version)
cmd.Command.end("Analyzing results -- DONE")
analysis.print_results()
analysis.unit_cell_analysis()
analysis.print_summary()
analysis.make_prime_input()
def run_analysis(self):
''' Run analysis of integrated images '''
cmd.Command.start("Analyzing results ")
analysis = Analyzer(init=self.init,
all_objects=self.img_objects,
gui_mode=False)
cmd.Command.end("Analyzing results -- DONE")
analysis.print_results()
analysis.unit_cell_analysis()
analysis.print_summary()
analysis.make_prime_input()
def prepare_PRIME_input(self):
""" Prepare the list of integrated pickles as well as pertinent
parameters; create a PRIME input file """
# Check if any pg/uc information is available; pg/uc info from UI
# supercedes pg/uc from Cluster
if self.best_pg is None:
self.best_pg = self.info.best_pg
if self.best_uc is None:
self.best_uc = self.info.best_uc
else:
uc_params = str(self.best_uc).rsplit()
self.best_uc = [float(i) for i in uc_params]
# Only run PRIME if both pg and uc are provided
if self.best_pg and self.best_uc:
from iota.components.iota_analysis import Analyzer
# Create a file with list of integrated pickles (overwrite old file)
int_pickles_file = os.path.join(self.info.int_base,
'int_pickles.lst')
with open(int_pickles_file, 'w') as ff:
ff.write('\n'.join(self.info.categories['integrated'][0]))
# Create PRIME input file
analyzer = Analyzer(info=self.info, params=self.params)
analyzer.prime_data_path = int_pickles_file
analyzer.best_pg = self.best_pg
analyzer.best_uc = self.best_uc
prime_phil = analyzer.make_prime_input(filename='live_prime.phil',
run_zero=True)
self.pparams = prime_phil.extract()
# Modify specific options based in IOTA settings
# Queue options
if (self.params.mp.method == 'lsf'
and self.params.mp.queue is not None):
self.pparams.queue.mode = 'bsub'
self.pparams.queue.qname = self.params.mp.queue
# Number of processors (automatically, 1/2 of IOTA procs)
self.pparams.n_processors = int(self.params.mp.n_processors / 2)
# Generate command args
cmd_args_list = [
'n_postref_cycle=0',
'queue.mode={}'.format(self.pparams.queue.mode),
'queue.qname={}'.format(self.pparams.queue.qname),
'n_processors={}'.format(self.pparams.n_processors)
]
if self.pparams.queue.mode == 'bsub':
cmd_args_list.append('timeout_seconds=120')
cmd_args = ' '.join(cmd_args_list)
return cmd_args
else:
return None