def analyze_prior_results(self, analysis_source):
""" Runs analysis of previous grid search / integration results, used in an
analyze-only mode """
from prime.iota.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]
analysis = Analyzer(img_objects, None, self.iver, self.now)
analysis.print_results()
analysis.unit_cell_analysis(self.params.analysis.cluster_threshold,
int_folder, False)
analysis.print_summary(None)
analysis.show_heatmap()
else:
print 'No results found in {}'.format(int_folder)
ep.dump('iota.ini', init)
misc.iota_exit(iota_version, True)
else:
if os.path.isfile('iota.ini'):
init = ep.load('iota.ini')
else:
print 'This run not initialized. Use "--mpi init" option'
misc.iota_exit(iota_version, True)
if 'ana' in args.mpi:
img_objects = [ep.load(os.path.join(init.obj_base, i)) for i in os.listdir(init.obj_base)]
int_objects = [i for i in img_objects if i.fail == None]
if len(int_objects) != 0:
# Analysis of integration results
analysis = Analyzer(int_objects, init.logfile, iota_version, init.now)
analysis.print_results()
analysis.unit_cell_analysis(init.params.analysis.cluster_threshold,
init.int_base)
analysis.print_summary(init.int_base)
analysis.make_prime_input(init.int_base)
else:
print "No images integrated"
else:
if 'imp' in args.mpi:
inp_list = init.input_list
msg = "Importing {} images".format(len(inp_list))
elif 'gri' in args.mpi:
cmd.Command.end("Processing {} images -- DONE ".format(len(img_objects)))
# DIALS TESTING SWITCH
if init.params.advanced.integrate_with == 'dials':
print '\n DIALS trial finished, exiting... \n'
misc.iota_exit(iota_version)
# Analysis of integration results
final_objects = [i for i in img_objects if i.fail == None]
if len(final_objects) == 0:
print 'No images successfully integrated!'
misc.iota_exit(iota_version)
analysis = Analyzer(img_objects, init.logfile, iota_version, init.now)
analysis.print_results()
analysis.unit_cell_analysis(init.params.analysis.cluster_threshold,
init.int_base)
analysis.print_summary(init.int_base)
analysis.make_prime_input(init.int_base)
# Spotfinding heatmap
if init.params.analysis.heatmap != None:
hm_file = "{}/{}".format(init.viz_base, 'heatmap.pdf')
if init.params.analysis.heatmap == 'show':
analysis.show_heatmap()
elif init.params.analysis.heatmap == 'file':
analysis.show_heatmap(show=False, hm_file=hm_file)
elif init.params.analysis.heatmap == 'both':
analysis.show_heatmap(hm_file=hm_file)