def worker(in_list, **kwargs):
"""
Still need to work on handling of cases that did not extract correctly
"""
filepath = in_list[0]
case_tube_idx = in_list[1]
fFCS = FCS(filepath=filepath, case_tube_idx=case_tube_idx, import_dataframe=True)
try:
fFCS.comp_scale_FCS_data(compensation_file=comp_file,
gate_coords=gate_coords,
strict=False, auto_comp=False, **kwargs)
fFCS.extract_FCS_histostats()
fFCS.clear_FCS_cache()
except:
fFCS.flag = 'stats_extraction_fail'
fFCS.error_message = str(sys.exc_info()[0])
return fFCS
def action(args):
# Connect to database
log.info("Loading database input %s" % args.db)
db = FCSdatabase(db=args.db, rebuild=False)
# Copy database to out database
shutil.copyfile(args.db, args.outdb)
out_db = FCSdatabase(db=args.outdb, rebuild=False)
# Create query
q = db.query(exporttype='dict_dict', getfiles=True, **vars(args))
n = 0
done = False
for case, case_info in q.results.items():
for case_tube_idx, relpath in case_info.items():
log.info("Case: %s, Case_tube_idx: %s, File: %s" %
(case, case_tube_idx, relpath))
filepath = path.join(args.dir, relpath)
fFCS = FCS(filepath=filepath,
case_tube_idx=case_tube_idx,
import_dataframe=True)
try:
fFCS.comp_scale_FCS_data(compensation_file=comp_file,
gate_coords=gate_coords,
strict=False,
auto_comp=False,
**vars(args))
fFCS.extract_FCS_histostats()
except:
fFCS.flag = 'stats_extraction_fail'
fFCS.error_message = str(sys.exc_info()[0])
fFCS.histostats_to_db(db=out_db)
n += 1
if args.n is not None and n >= args.n:
done = True
break
if done is True:
break
def worker(in_list, **kwargs):
"""
Still need to work on handling of cases that did not extract correctly
"""
filepath = in_list[0]
case_tube_idx = in_list[1]
fFCS = FCS(filepath=filepath,
case_tube_idx=case_tube_idx,
import_dataframe=True)
try:
fFCS.comp_scale_FCS_data(compensation_file=comp_file,
gate_coords=gate_coords,
strict=False,
auto_comp=False,
**kwargs)
fFCS.extract_FCS_histostats()
fFCS.clear_FCS_cache()
except:
fFCS.flag = 'stats_extraction_fail'
fFCS.error_message = str(sys.exc_info()[0])
return fFCS
def action(args):
# Connect to database
log.info("Loading database input %s" % args.db)
db = FCSdatabase(db=args.db, rebuild=False)
# Copy database to out database
shutil.copyfile(args.db, args.outdb)
out_db = FCSdatabase(db=args.outdb, rebuild=False)
# Create query
q = db.query(exporttype='dict_dict', getfiles=True, **vars(args))
n = 0
done = False
for case, case_info in q.results.items():
for case_tube_idx, relpath in case_info.items():
log.info("Case: %s, Case_tube_idx: %s, File: %s" % (case, case_tube_idx, relpath))
filepath = path.join(args.dir, relpath)
fFCS = FCS(filepath=filepath, case_tube_idx=case_tube_idx, import_dataframe=True)
try:
fFCS.comp_scale_FCS_data(compensation_file=comp_file,
gate_coords=gate_coords,
strict=False, auto_comp=False, **vars(args))
fFCS.extract_FCS_histostats()
except:
fFCS.flag = 'stats_extraction_fail'
fFCS.error_message = str(sys.exc_info()[0])
fFCS.histostats_to_db(db=out_db)
n += 1
if args.n is not None and n >= args.n:
done = True
break
if done is True:
break