def passthrough(file_name, lis_struct, time, args):
"""
Passes tuple of (value, unit) of sodium at indicated time, in a standardized form.
:param file_name: (str) name of current JSON file being read
:param lis_struct: (dict) dict containing item and value pairs
:param time: (str) time when results were obtained (as contained in JSON file)
:param args: (dict) switches provided to lisanalyze.py via argparse
:returns: tuple (value, unit)
"""
# Use "Na" as the standard name
for k in lis_struct[time].keys():
if k in __alias.keys():
lis_struct[time].update({__alias[k]: lis_struct[time][k]})
# Basic checks and value-setting
if "Na" in lis_struct[time].keys():
if args.warn and lis_struct[time]["Na"]["unit"] != __unit:
print("WARNING: unit mismatch in entry for {}".format(time),
file=sys.stderr)
na_val = float(lis_struct[time]["Na"]["lab_value"])
else:
return None
# Unit conversion
if args.convert:
lis_struct[time]["Na"]["unit"] = lis_struct[time]["Na"]["unit"].lower(
).replace("eq", "mol")
import pint
ureg = pint.UnitRegistry()
factor = (ureg.parse_expression(
lis_struct[time]["Na"]["unit"])).to(__unit).magnitude
na_val *= factor
# Correction for glucose (Lange Pocket Guide to Diagnostic Tests, 6e, p.260)
if not args.no_correct:
import lisanalyze_glucose
glucose_passthrough = lisanalyze_glucose.passthrough(
file_name, lis_struct, time, args)
if glucose_passthrough:
glucose, unit = glucose_passthrough
if glucose > 110:
na_val += (glucose - 110) * 1.6 / 100
return na_val, __unit
def passthrough(file_name, lis_struct, time, args):
"""
Passes tuple of (value, unit) of sodium at indicated time, in a standardized form.
:param file_name: (str) name of current JSON file being read
:param lis_struct: (dict) dict containing item and value pairs
:param time: (str) time when results were obtained (as contained in JSON file)
:param args: (dict) switches provided to lisanalyze.py via argparse
:returns: tuple (value, unit)
"""
# Use "Na" as the standard name
for k in lis_struct[time].keys():
if k in __alias.keys():
lis_struct[time].update({__alias[k]: lis_struct[time][k]})
# Basic checks and value-setting
if "Na" in lis_struct[time].keys():
if args.warn and lis_struct[time]["Na"]["unit"] != __unit:
print("WARNING: unit mismatch in entry for {}".format(time), file=sys.stderr)
na_val = float(lis_struct[time]["Na"]["lab_value"])
else:
return None
# Unit conversion
if args.convert:
lis_struct[time]["Na"]["unit"] = lis_struct[time]["Na"]["unit"].lower().replace("eq", "mol")
import pint
ureg = pint.UnitRegistry()
factor = (ureg.parse_expression(lis_struct[time]["Na"]["unit"])).to(__unit).magnitude
na_val *= factor
# Correction for glucose (Lange Pocket Guide to Diagnostic Tests, 6e, p.260)
if not args.no_correct:
import lisanalyze_glucose
glucose_passthrough = lisanalyze_glucose.passthrough(file_name, lis_struct, time, args)
if glucose_passthrough:
glucose, unit = glucose_passthrough
if glucose > 110:
na_val += (glucose - 110) * 1.6 / 100
return na_val, __unit
def analyze(file_name, lis_struct, time, args):
"""
Analyzes LIS results, looking for events related to sodium,
and puts events into a dict {file_name -> {event_time -> (event_str)}}.
:param file_name: (str) name of current JSON file being read
:param lis_struct: (dict) dict containing item and value pairs
:param time: (str) time when results were obtained (as contained in JSON file)
:param args: (dict) switches provided to lisanalyze.py via argparse
:returns: False
"""
#global __alias
# Use "Na" as the standard name
for k in list(lis_struct[time]):
if k in __alias.keys():
lis_struct[time].update({__alias[k]: lis_struct[time][k]})
# Basic checks and value-setting
if "Na" in lis_struct[time].keys():
if args.warn and lis_struct[time]["Na"]["unit"] != __unit:
print("WARNING: unit mismatch in entry for {}".format(time),
file=sys.stderr)
na_val = float(lis_struct[time]["Na"]["lab_value"])
else:
return None
# Unit conversion
if args.convert:
lis_struct[time]["Na"]["unit"] = lis_struct[time]["Na"]["unit"].lower(
).replace("eq", "mol")
import pint
ureg = pint.UnitRegistry()
factor = (ureg.parse_expression(
lis_struct[time]["Na"]["unit"])).to(__unit).magnitude
na_val *= factor
# Correction for glucose (Lange Pocket Guide to Diagnostic Tests, 6e, p.260)
if not args.no_correct:
import modules.analyzers.lisanalyze_glucose as lisanalyze_glucose
glucose_passthrough = lisanalyze_glucose.passthrough(
file_name, lis_struct, time, args)
if glucose_passthrough:
glucose, unit = glucose_passthrough
if glucose > 110:
na_val += (glucose - 110) * 1.6 / 100
# Out-of-normal-range warning; provided values take precedence
if "ref_high" in lis_struct[time]["Na"].keys():
if lis_struct[time]["Na"]["lab_value"] > lis_struct[time]["Na"][
"ref_high"]:
event_time = time
if file_name not in __event_dict.keys():
__event_dict[file_name] = {}
if event_time not in __event_dict[file_name].keys():
__event_dict[file_name][event_time] = []
event_str = "Hypernatremia (current value {}; reference value {} ({}))".format(
lis_struct[time]["Na"]["lab_value"],
lis_struct[time]["Na"]["ref_high"],
lis_struct[time]["Na"]["unit"])
__event_dict[file_name][event_time].append(event_str)
else:
if args.warn:
print(
"WARNING: higher reference value not provided; falling back to built-in value",
file=sys.stderr)
if na_val > __na_ul:
event_time = time
if file_name not in __event_dict.keys():
__event_dict[file_name] = {}
if event_time not in __event_dict[file_name].keys():
__event_dict[file_name][event_time] = []
event_str = "Hypernatremia (current value {}; reference value {} ({}))".format(
na_val, __na_ul, __unit)
__event_dict[file_name][event_time].append(event_str)
if "ref_low" in lis_struct[time]["Na"].keys():
if lis_struct[time]["Na"]["lab_value"] < lis_struct[time]["Na"][
"ref_low"]:
event_time = time
if file_name not in __event_dict.keys():
__event_dict[file_name] = {}
if event_time not in __event_dict[file_name].keys():
__event_dict[file_name][event_time] = []
event_str = "Hyponatremia (current value {}; reference value {} ({}))".format(
lis_struct[time]["Na"]["lab_value"],
lis_struct[time]["Na"]["ref_low"],
lis_struct[time]["Na"]["unit"])
__event_dict[file_name][event_time].append(event_str)
else:
if args.warn:
print(
"WARNING: lower reference value not provided; falling back to built-in value",
file=sys.stderr)
if na_val < __na_ll:
event_time = time
if file_name not in __event_dict.keys():
__event_dict[file_name] = {}
if event_time not in __event_dict[file_name].keys():
__event_dict[file_name][event_time] = []
event_str = "Hyponatremia (current value {}; reference value {} ({}))".format(
na_val, __na_ll, __unit)
__event_dict[file_name][event_time].append(event_str)
# Panic if Na > 155 mmol/l or Na < 125 mmol/l (Lange Pocket Guide to Diagnostic Tests, 6e, p.260)
if na_val > 155:
event_time = time
if file_name not in __event_dict.keys():
__event_dict[file_name] = {}
if event_time not in __event_dict[file_name].keys():
__event_dict[file_name][event_time] = []
event_str = "Severe hypernatremia ({} ({}))".format(na_val, __unit)
__event_dict[file_name][event_time].append(event_str)
if na_val < 125:
event_time = time
if file_name not in __event_dict.keys():
__event_dict[file_name] = {}
if event_time not in __event_dict[file_name].keys():
__event_dict[file_name][event_time] = []
event_str = "Severe hyponatremia ({} ({}))".format(na_val, __unit)
__event_dict[file_name][event_time].append(event_str)
return False
def analyze(file_name, lis_struct, time, args):
"""
Analyzes LIS results, looking for events related to sodium,
and puts events into a dict {file_name -> {event_time -> (event_str)}}.
:param file_name: (str) name of current JSON file being read
:param lis_struct: (dict) dict containing item and value pairs
:param time: (str) time when results were obtained (as contained in JSON file)
:param args: (dict) switches provided to lisanalyze.py via argparse
:returns: False
"""
#global __alias
# Use "Na" as the standard name
for k in list(lis_struct[time]):
if k in __alias.keys():
lis_struct[time].update({__alias[k]: lis_struct[time][k]})
# Basic checks and value-setting
if "Na" in lis_struct[time].keys():
if args.warn and lis_struct[time]["Na"]["unit"] != __unit:
print("WARNING: unit mismatch in entry for {}".format(time), file=sys.stderr)
na_val = float(lis_struct[time]["Na"]["lab_value"])
else:
return None
# Unit conversion
if args.convert:
lis_struct[time]["Na"]["unit"] = lis_struct[time]["Na"]["unit"].lower().replace("eq", "mol")
import pint
ureg = pint.UnitRegistry()
factor = (ureg.parse_expression(lis_struct[time]["Na"]["unit"])).to(__unit).magnitude
na_val *= factor
# Correction for glucose (Lange Pocket Guide to Diagnostic Tests, 6e, p.260)
if not args.no_correct:
import modules.analyzers.lisanalyze_glucose as lisanalyze_glucose
glucose_passthrough = lisanalyze_glucose.passthrough(file_name, lis_struct, time, args)
if glucose_passthrough:
glucose, unit = glucose_passthrough
if glucose > 110:
na_val += (glucose - 110) * 1.6 / 100
# Out-of-normal-range warning; provided values take precedence
if "ref_high" in lis_struct[time]["Na"].keys():
if lis_struct[time]["Na"]["lab_value"] > lis_struct[time]["Na"]["ref_high"]:
event_time = time
if file_name not in __event_dict.keys():
__event_dict[file_name] = {}
if event_time not in __event_dict[file_name].keys():
__event_dict[file_name][event_time] = []
event_str = "Hypernatremia (current value {}; reference value {} ({}))".format(lis_struct[time]["Na"]["lab_value"], lis_struct[time]["Na"]["ref_high"], lis_struct[time]["Na"]["unit"])
__event_dict[file_name][event_time].append(event_str)
else:
if args.warn:
print("WARNING: higher reference value not provided; falling back to built-in value", file=sys.stderr)
if na_val > __na_ul:
event_time = time
if file_name not in __event_dict.keys():
__event_dict[file_name] = {}
if event_time not in __event_dict[file_name].keys():
__event_dict[file_name][event_time] = []
event_str = "Hypernatremia (current value {}; reference value {} ({}))".format(na_val, __na_ul, __unit)
__event_dict[file_name][event_time].append(event_str)
if "ref_low" in lis_struct[time]["Na"].keys():
if lis_struct[time]["Na"]["lab_value"] < lis_struct[time]["Na"]["ref_low"]:
event_time = time
if file_name not in __event_dict.keys():
__event_dict[file_name] = {}
if event_time not in __event_dict[file_name].keys():
__event_dict[file_name][event_time] = []
event_str = "Hyponatremia (current value {}; reference value {} ({}))".format(lis_struct[time]["Na"]["lab_value"], lis_struct[time]["Na"]["ref_low"], lis_struct[time]["Na"]["unit"])
__event_dict[file_name][event_time].append(event_str)
else:
if args.warn:
print("WARNING: lower reference value not provided; falling back to built-in value", file=sys.stderr)
if na_val < __na_ll:
event_time = time
if file_name not in __event_dict.keys():
__event_dict[file_name] = {}
if event_time not in __event_dict[file_name].keys():
__event_dict[file_name][event_time] = []
event_str = "Hyponatremia (current value {}; reference value {} ({}))".format(na_val, __na_ll, __unit)
__event_dict[file_name][event_time].append(event_str)
# Panic if Na > 155 mmol/l or Na < 125 mmol/l (Lange Pocket Guide to Diagnostic Tests, 6e, p.260)
if na_val > 155:
event_time = time
if file_name not in __event_dict.keys():
__event_dict[file_name] = {}
if event_time not in __event_dict[file_name].keys():
__event_dict[file_name][event_time] = []
event_str = "Severe hypernatremia ({} ({}))".format(na_val, __unit)
__event_dict[file_name][event_time].append(event_str)
if na_val < 125:
event_time = time
if file_name not in __event_dict.keys():
__event_dict[file_name] = {}
if event_time not in __event_dict[file_name].keys():
__event_dict[file_name][event_time] = []
event_str = "Severe hyponatremia ({} ({}))".format(na_val, __unit)
__event_dict[file_name][event_time].append(event_str)
return False