def passthrough(file_name, lis_struct, time, args):
"""
Passes tuple of (value, unit) of blood calcium 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 "Ca" 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 "Ca" in lis_struct[time].keys():
if args.warn and lis_struct[time]["Ca"]["unit"] != __unit:
print("WARNING: unit mismatch in entry for {}".format(time),
file=sys.stderr)
ca_val = float(lis_struct[time]["Ca"]["lab_value"])
else:
return None
# Unit conversion
if args.convert:
import pint
ureg = pint.UnitRegistry()
factor = (ureg.parse_expression(lis_struct[time]["Ca"]["unit"])).to(
__unit, 'chemistry', mw=40.08 * ureg('g/mol')).magnitude
ca_val *= factor
# Correction for albumin (Lange Pocket Guide to Diagnostic Tests, 6e, p.87; note that 'mg' for albumin should be 'g')
if not args.no_correct:
import lisanalyze_albumin_blood
albumin_passthrough = lisanalyze_albumin_blood.passthrough(
file_name, lis_struct, time, args)
if albumin_passthrough:
albumin, value = albumin_passthrough
if albumin < 3.4:
ca_val += (3.4 - albumin) * 0.8
return ca_val, __unit
def passthrough(file_name, lis_struct, time, args):
"""
Passes tuple of (value, unit) of blood calcium 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 "Ca" 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 "Ca" in lis_struct[time].keys():
if args.warn and lis_struct[time]["Ca"]["unit"] != __unit:
print("WARNING: unit mismatch in entry for {}".format(time), file=sys.stderr)
ca_val = float(lis_struct[time]["Ca"]["lab_value"])
else:
return None
# Unit conversion
if args.convert:
import pint
ureg = pint.UnitRegistry()
factor = (ureg.parse_expression(lis_struct[time]["Ca"]["unit"])).to(__unit, 'chemistry', mw=40.08*ureg('g/mol')).magnitude
ca_val *= factor
# Correction for albumin (Lange Pocket Guide to Diagnostic Tests, 6e, p.87; note that 'mg' for albumin should be 'g')
if not args.no_correct:
import lisanalyze_albumin_blood
albumin_passthrough = lisanalyze_albumin_blood.passthrough(file_name, lis_struct, time, args)
if albumin_passthrough:
albumin, value = albumin_passthrough
if albumin < 3.4:
ca_val += (3.4 - albumin) * 0.8
return ca_val, __unit
def analyze(file_name, lis_struct, time, args):
"""
Analyzes LIS results, looking for events related to calcium,
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 "Ca" 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 "Ca" in lis_struct[time].keys():
if args.warn and lis_struct[time]["Ca"]["unit"] != __unit:
print("WARNING: unit mismatch in entry for {}".format(time), file=sys.stderr)
ca_val = float(lis_struct[time]["Ca"]["lab_value"])
else:
return None
# Unit conversion
if args.convert:
import pint
ureg = pint.UnitRegistry()
factor = (ureg.parse_expression(lis_struct[time]["Ca"]["unit"])).to(__unit, 'chemistry', mw=40.08*ureg('g/mol')).magnitude
ca_val *= factor
# Correction for albumin (Lange Pocket Guide to Diagnostic Tests, 6e, p.87; note that 'mg' for albumin should be 'g')
if not args.no_correct:
import lisanalyze_albumin_blood
albumin_passthrough = lisanalyze_albumin_blood.passthrough(file_name, lis_struct, time, args)
if albumin_passthrough:
albumin, value = albumin_passthrough
if albumin < 3.4:
ca_val += (3.4 - albumin) * 0.8
# Out-of-normal-range warning; provided values take precedence
if "ref_high" in lis_struct[time]["Ca"].keys():
if lis_struct[time]["Ca"]["lab_value"] > lis_struct[time]["Ca"]["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 = "Hypercalcemia (current value {}; reference value {} ({}))".format(lis_struct[time]["Ca"]["lab_value"], lis_struct[time]["Ca"]["ref_high"], lis_struct[time]["Ca"]["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 ca_val > __ca_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 = "Hypercalcemia (current value {}; reference value {} ({}))".format(ca_val, __ca_ul, __unit)
__event_dict[file_name][event_time].append(event_str)
if "ref_low" in lis_struct[time]["Ca"].keys():
if lis_struct[time]["Ca"]["lab_value"] < lis_struct[time]["Ca"]["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 = "Hypocalcemia (current value {}; reference value {} ({}))".format(lis_struct[time]["Ca"]["lab_value"], lis_struct[time]["Ca"]["ref_low"], lis_struct[time]["Ca"]["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 ca_val < __ca_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 = "Hypocalcemia (current value {}; reference value {} ({}))".format(ca_val, __ca_ll, __unit)
__event_dict[file_name][event_time].append(event_str)
# Panic if Ca > 13.5 mg/dl or Ca < 6.5 mg/dl (Lange Pocket Guide to Diagnostic Tests, 6e, p.87)
if ca_val > 13.5:
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 hypercalcemia ({} ({}))".format(ca_val, __unit)
__event_dict[file_name][event_time].append(event_str)
if ca_val < 6.5:
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 hypocalcemia ({} ({}))".format(ca_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 calcium,
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 "Ca" 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 "Ca" in lis_struct[time].keys():
if args.warn and lis_struct[time]["Ca"]["unit"] != __unit:
print("WARNING: unit mismatch in entry for {}".format(time),
file=sys.stderr)
ca_val = float(lis_struct[time]["Ca"]["lab_value"])
else:
return None
# Unit conversion
if args.convert:
import pint
ureg = pint.UnitRegistry()
factor = (ureg.parse_expression(lis_struct[time]["Ca"]["unit"])).to(
__unit, 'chemistry', mw=40.08 * ureg('g/mol')).magnitude
ca_val *= factor
# Correction for albumin (Lange Pocket Guide to Diagnostic Tests, 6e, p.87; note that 'mg' for albumin should be 'g')
if not args.no_correct:
import lisanalyze_albumin_blood
albumin_passthrough = lisanalyze_albumin_blood.passthrough(
file_name, lis_struct, time, args)
if albumin_passthrough:
albumin, value = albumin_passthrough
if albumin < 3.4:
ca_val += (3.4 - albumin) * 0.8
# Out-of-normal-range warning; provided values take precedence
if "ref_high" in lis_struct[time]["Ca"].keys():
if lis_struct[time]["Ca"]["lab_value"] > lis_struct[time]["Ca"][
"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 = "Hypercalcemia (current value {}; reference value {} ({}))".format(
lis_struct[time]["Ca"]["lab_value"],
lis_struct[time]["Ca"]["ref_high"],
lis_struct[time]["Ca"]["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 ca_val > __ca_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 = "Hypercalcemia (current value {}; reference value {} ({}))".format(
ca_val, __ca_ul, __unit)
__event_dict[file_name][event_time].append(event_str)
if "ref_low" in lis_struct[time]["Ca"].keys():
if lis_struct[time]["Ca"]["lab_value"] < lis_struct[time]["Ca"][
"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 = "Hypocalcemia (current value {}; reference value {} ({}))".format(
lis_struct[time]["Ca"]["lab_value"],
lis_struct[time]["Ca"]["ref_low"],
lis_struct[time]["Ca"]["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 ca_val < __ca_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 = "Hypocalcemia (current value {}; reference value {} ({}))".format(
ca_val, __ca_ll, __unit)
__event_dict[file_name][event_time].append(event_str)
# Panic if Ca > 13.5 mg/dl or Ca < 6.5 mg/dl (Lange Pocket Guide to Diagnostic Tests, 6e, p.87)
if ca_val > 13.5:
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 hypercalcemia ({} ({}))".format(ca_val, __unit)
__event_dict[file_name][event_time].append(event_str)
if ca_val < 6.5:
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 hypocalcemia ({} ({}))".format(ca_val, __unit)
__event_dict[file_name][event_time].append(event_str)
return False