def get_patient(self, pid, dictionary, line_file, class_file):
obj = {
"info": [],
"events": [],
"h_bars": [],
"v_bars": [ "auto" ],
"v_spans": [],
"classes": {}
}
new_dict_entries = set()
util.add_files(obj, line_file, class_file)
self.get_info(pid, obj)
self.add_info(obj, "pid", "Patient", pid)
self.get_info(pid, obj)
self.get_diagnoses(pid, obj, dictionary, new_dict_entries)
self.get_observations_concept_valued(pid, obj, dictionary, new_dict_entries)
self.get_observations_string_valued(pid, obj, dictionary, new_dict_entries)
self.get_observations_number_valued(pid, obj, dictionary, new_dict_entries)
self.get_procedures(pid, obj, dictionary, new_dict_entries)
self.get_drugs(pid, obj, dictionary, new_dict_entries)
self.get_measurements(pid, obj, dictionary, new_dict_entries)
self.get_visits(pid, obj)
min_time = float('inf')
max_time = float('-inf')
for e in obj["events"]:
time = e["time"]
if time < min_time:
min_time = time
if time > max_time:
max_time = time
obj["start"] = min_time
obj["end"] = max_time
self.add_info(obj, "event_count", "Events", len(obj["events"]))
self.update_hierarchies(dictionary, new_dict_entries)
return obj
def get_patient(self, pid, dictionary, line_file, class_file):
obj = {
"info": [],
"events": [],
"h_bars": [],
"v_bars": [ "auto" ],
"v_spans": [],
"classes": {}
}
new_dict_entries = set()
util.add_files(obj, line_file, class_file)
self.get_info(pid, obj)
self.add_info(obj, "pid", "Patient", pid)
self.get_info(pid, obj)
self.get_diagnoses(pid, obj, dictionary, new_dict_entries)
self.get_observations_concept_valued(pid, obj, dictionary, new_dict_entries)
self.get_observations_string_valued(pid, obj, dictionary, new_dict_entries)
self.get_observations_number_valued(pid, obj, dictionary, new_dict_entries)
self.get_procedures(pid, obj, dictionary, new_dict_entries)
self.get_drugs(pid, obj, dictionary, new_dict_entries)
self.get_measurements(pid, obj, dictionary, new_dict_entries)
self.get_visits(pid, obj)
min_time = float('inf')
max_time = float('-inf')
for e in obj["events"]:
time = e["time"]
if time < min_time:
min_time = time
if time > max_time:
max_time = time
obj["start"] = min_time
obj["end"] = max_time
self.add_info(obj, "event_count", "Events", len(obj["events"]))
self.update_hierarchies(dictionary, new_dict_entries)
return obj
def process(allPaths, lineFile, classFile, id):
obj = {
"info": [],
"events": [],
"h_bars": [],
"v_bars": ["auto"],
"v_spans": [],
"classes": {}
}
util.add_files(obj, lineFile, classFile)
addInfo(obj, "pid", "Patient", id)
if len(allPaths) == 0:
print('warning: no path given', file=sys.stderr)
statusMap = {}
for (path, isfile) in allPaths:
if isfile:
processFile(path, id, obj, statusMap)
else:
util.process_id_directory(
path, id,
lambda file, id: processFile(file, id, obj, statusMap))
curInStart = None
curInEnd = None
curStatus = STATUS_UNKNOWN
for k in sorted(statusMap):
status = statusMap[k]
if status == curStatus:
if curInStart is None:
curInStart = k
curInEnd = k
else:
if curInStart is not None:
if curStatus == STATUS_IN:
obj["v_spans"].append({
"from": curInStart,
"to": util.nextDay(curInEnd),
"class": "in_hospital"
})
elif curStatus == STATUS_PROF:
obj["v_spans"].append({
"from": curInStart,
"to": util.nextDay(curInEnd),
"class": "professional"
})
curInStart = None
curStatus = status
min_time = float('inf')
max_time = float('-inf')
for e in obj["events"]:
time = e["time"]
if time < min_time:
min_time = time
if time > max_time:
max_time = time
obj["start"] = min_time
obj["end"] = max_time
addInfo(obj, "event_count", "Events", len(obj["events"]))
return obj
def process(allPaths, lineFile, classFile, id):
obj = {
"info": [],
"events": [],
"h_bars": [],
"v_bars": [ "auto" ],
"v_spans": [],
"classes": {}
}
util.add_files(obj, lineFile, classFile)
addInfo(obj, "pid", "Patient", id)
if len(allPaths) == 0:
print('warning: no path given', file=sys.stderr)
statusMap = {}
for (path, isfile) in allPaths:
if isfile:
processFile(path, id, obj, statusMap)
else:
util.process_id_directory(path, id, lambda file, id: processFile(file, id, obj, statusMap))
curInStart = None
curInEnd = None
curStatus = STATUS_UNKNOWN
for k in sorted(statusMap):
status = statusMap[k]
if status == curStatus:
if curInStart is None:
curInStart = k
curInEnd = k
else:
if curInStart is not None:
if curStatus == STATUS_IN:
obj["v_spans"].append({
"from": curInStart,
"to": util.nextDay(curInEnd),
"class": "in_hospital"
})
elif curStatus == STATUS_PROF:
obj["v_spans"].append({
"from": curInStart,
"to": util.nextDay(curInEnd),
"class": "professional"
})
curInStart = None
curStatus = status
min_time = float('inf')
max_time = float('-inf')
for e in obj["events"]:
time = e["time"]
if time < min_time:
min_time = time
if time > max_time:
max_time = time
obj["start"] = min_time
obj["end"] = max_time
addInfo(obj, "event_count", "Events", len(obj["events"]))
return obj