def run_analysis(self):
"""Run analysis of integrated images."""
from iota.components.iota_analysis import Analyzer
analysis = Analyzer(info=self.info, params=self.params)
self.info = analysis.run_all()
self.info.export_json()
def update_info(self, info):
# # Determine chunk of image objects to check for existing
# if self.n_proc:
# chunk = self.n_proc
# else:
# chunk = 25
# if len(self.info.unread_files) < chunk:
# chunk = len(self.info.unread_files)
#
# # Create filelist of written image objects
# filelist = []
# for fp in self.info.unread_files[:chunk]:
# if os.path.isfile(fp):
# filelist.append(fp)
# self.info.unread_files.pop(fp)
#
# # Perform stat extraction
# if filelist:
# from iota.components.iota_analysis import Analyzer
# analyzer = Analyzer(info=self.info)
# stats_OK = analyzer.get_results(filelist=filelist)
# if stats_OK:
# self.info = analyzer.info
# self.obs = analyzer.obs
finished_objects = info.get_finished_objects_from_file()
if finished_objects:
analyzer = Analyzer(info=info, gui_mode=True)
stats_OK = analyzer.run_get_results(
finished_objects=finished_objects)
if stats_OK:
return analyzer.info
return None
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 analyze_prior_results(self, analysis_source):
""" Runs analysis of previous grid search / integration results, used in an
analyze-only mode """
from iota.components.iota_analysis import Analyzer
if os.path.isdir(analysis_source):
int_folder = os.path.abspath(analysis_source)
else:
try:
int_folder = os.path.abspath(os.path.join(os.curdir,
'integration/{}/image_objects'.format(analysis_source)))
except ValueError:
print 'Run #{} not found'.format(analysis_source)
if os.path.isdir(int_folder):
cmd.Command.start("Analyzing results in {}".format(int_folder))
int_list = [os.path.join(int_folder, i) for i in os.listdir(int_folder)]
img_objects = [ep.load(i) for i in int_list if i.endswith('.int')]
cmd.Command.end("Analyzing results -- DONE")
self.logfile = os.path.abspath(os.path.join(int_folder, 'iota.log'))
self.viz_base = os.path.join('/'.join(int_folder.split('/')),
'vizualization')
analysis = Analyzer(self, img_objects, self.iver)
analysis.print_results()
analysis.unit_cell_analysis(write_files=False)
analysis.print_summary(write_files=False)
else:
print 'No results found in {}'.format(int_folder)
def analyze_prior_results(self, analysis_source):
""" Runs analysis of previous grid search / integration results, used in an
analyze-only mode """
from iota.components.iota_analysis import Analyzer
from libtbx import easy_pickle as ep
if os.path.isdir(analysis_source):
int_folder = os.path.abspath(analysis_source)
else:
try:
int_folder = os.path.abspath(os.path.join(os.curdir,
'integration/{}/image_objects'.format(analysis_source)))
except ValueError:
print 'Run #{} not found'.format(analysis_source)
if os.path.isdir(int_folder):
int_list = [os.path.join(int_folder, i) for i in os.listdir(int_folder)]
img_objects = [ep.load(i) for i in int_list if i.endswith('.int')]
self.logfile = os.path.abspath(os.path.join(int_folder, 'iota.log'))
analysis = Analyzer(self, img_objects, self.iver)
analysis.print_results()
analysis.unit_cell_analysis(write_files=False)
analysis.print_summary(write_files=False)
else:
print 'No results found in {}'.format(int_folder)
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
