def read_edf_file(filename):
f = EdfReader(filename)
chan = 0
data = f.readSignal(chan) / 1000.
sample_freq = f.getSampleFrequency(chan)
f._close()
return data, sample_freq
class UCDDB(PhysioNetDataBase):
""" NOT finished,
St. Vincent"s University Hospital / University College Dublin Sleep Apnea Database
ABOUT ucddb
-----------
1. contains 25 full overnight polysomnograms (PSGs) with simultaneous three-channel Holter ECGs
*.rec --- PSG data in EDF format
*_lifecard.edf --- ECG data in EDF format
2. PSG signals recorded were:
EEG (C3-A2),
EEG (C4-A1),
left EOG,
right EOG,
submental EMG,
ECG (modified lead V2),
oro-nasal airflow (thermistor),
ribcage movements,
abdomen movements (uncalibrated strain gauges),
oxygen saturation (finger pulse oximeter),
snoring (tracheal microphone),
body position
3. holter ECG leads: V5, CC5, V5R
4. sleep stage annotations:
0 - Wake
1 - REM
2 - Stage 1
3 - Stage 2
4 - Stage 3
5 - Stage 4
6 - Artifact
7 - Indeterminate
5. respiratory events:
O - obstructive, apneas,
C - central apneas,
M - mixed apneas,
HYP - hypopneas,
PB - periodic breathing episodes
CS - Cheynes-Stokes
Bradycardia / Tachycardia
NOTE
----
1. this dataset is NOT in the standard wfdb format, but rather in EDF format
2. in record ucddb002, only two distinct ECG signals were recorded; the second ECG signal was also used as the third signal.
ISSUES
------
Usage
-----
1. sleep stage
2. sleep apnea
References
----------
[1] https://physionet.org/content/ucddb/1.0.0/
"""
def __init__(self, db_dir:Optional[str]=None, working_dir:Optional[str]=None, verbose:int=2, **kwargs:Any) -> NoReturn:
"""
Parameters
----------
db_dir: str, optional,
storage path of the database
if not specified, data will be fetched from Physionet
working_dir: str, optional,
working directory, to store intermediate files and log file
verbose: int, default 2,
log verbosity
kwargs: auxilliary key word arguments
"""
super().__init__(db_name="ucddb", db_dir=db_dir, working_dir=working_dir, verbose=verbose, **kwargs)
self.data_ext = "rec"
self.extra_data_ext = "_lifecard.edf"
self.ann_ext = None
self.stage_ann_ext = "_stage.txt"
self.event_ann_ext = "_stage.txt"
self._ls_rec()
self.fs = None
self.file_opened = None
def safe_edf_file_operation(self, operation:str="close", full_file_path:Optional[str]=None) -> Union[EdfReader, NoReturn]:
""" finished, checked,
Parameters
----------
operation: str, default "close",
operation name, can be "open" and "close"
full_file_path: str, optional,
path of the file which contains the psg data,
if not given, default path will be used
Returns
-------
"""
if operation == "open":
if self.file_opened is not None:
self.file_opened._close()
self.file_opened = EdfReader(full_file_path)
elif operation =="close":
if self.file_opened is not None:
self.file_opened._close()
self.file_opened = None
else:
raise ValueError("Illegal operation")
def get_subject_id(self, rec) -> int:
"""
"""
raise NotImplementedError
def database_info(self) -> NoReturn:
"""
"""
print(self.__doc__)
class NSRRDataBase(_DataBase):
"""
https://sleepdata.org/
"""
def __init__(self,
db_name: str,
db_dir: str,
working_dir: Optional[str] = None,
verbose: int = 2,
**kwargs: Any) -> NoReturn:
"""
Parameters
----------
db_name: str,
name of the database
db_dir: str,
storage path of the database
working_dir: str, optional,
working directory, to store intermediate files and log file
verbose: int, default 2,
log verbosity
kwargs: auxilliary key word arguments
typical `db_dir`:
------------------
"E:\\notebook_dir\\ecg\\data\\NSRR\\xxx\\"
"/export/algo/wenh06/ecg_data/NSRR/xxx/"
"""
super().__init__(db_name=db_name,
db_dir=db_dir,
working_dir=working_dir,
verbose=verbose,
**kwargs)
# self._set_logger(prefix="NSRR")
self.fs = None
self._all_records = None
self.device_id = None # maybe data are imported into impala db, to facilitate analyzing
self.file_opened = None
all_dbs = [
[
"shhs",
"Multi-cohort study focused on sleep-disordered breathing and cardiovascular outcomes"
],
["mesa", ""],
["oya", ""],
[
"chat",
"Multi-center randomized trial comparing early adenotonsillectomy to watchful waiting plus supportive care"
],
[
"heartbeat",
"Multi-center Phase II randomized controlled trial that evaluates the effects of supplemental nocturnal oxygen or Positive Airway Pressure (PAP) therapy"
],
# more to be added
]
self.df_all_db_info = pd.DataFrame({
"db_name": [item[0] for item in all_dbs],
"db_description": [item[1] for item in all_dbs]
})
self.kwargs = kwargs
def safe_edf_file_operation(
self,
operation: str = "close",
full_file_path: Optional[str] = None) -> NoReturn:
""" finished, checked,
Parameters
----------
operation: str, default "close",
operation name, can be "open" and "close"
full_file_path: str, optional,
path of the file which contains the psg data,
if not given, default path will be used
"""
if operation == "open":
if self.file_opened is not None:
self.file_opened._close()
self.file_opened = EdfReader(full_file_path)
elif operation == "close":
if self.file_opened is not None:
self.file_opened._close()
self.file_opened = None
else:
raise ValueError("Illegal operation")
def get_subject_id(self, rec: str) -> int:
"""
Attach a `subject_id` to the record, in order to facilitate further uses
Parameters
----------
rec: str,
record name
Returns
-------
int, a `subject_id` attached to the record `rec`
"""
raise NotImplementedError
def get_patient_id(self, rec: str) -> int:
"""
synonym for func `self.get_subject_id`
"""
return self.get_subject_id(rec=rec)
def show_rec_stats(self, rec: str) -> NoReturn:
"""
print the statistics about the record `rec`
Parameters
----------
rec: str,
record name
"""
raise NotImplementedError
def database_info(self, detailed: bool = False) -> NoReturn:
"""
print the information about the database
detailed: bool, default False,
if False, an short introduction of the database will be printed,
if True, then docstring of the class will be printed additionally
"""
raw_info = {"What": "", "Who": "", "When": "", "Funding": ""}
print(raw_info)
if detailed:
print(self.__doc__)
def helper(self,
items: Union[List[str], str, type(None)] = None,
**kwargs) -> NoReturn:
"""
"""
pp = pprint.PrettyPrinter(indent=4)
attrs = vars(self)
methods = [
func for func in dir(self) if callable(getattr(self, func))
and not (func.startswith("__") and func.endswith("__"))
]
if items is None:
_items = [
"attributes",
"methods",
]
elif isinstance(items, str):
_items = [items]
else:
_items = items
pp = pprint.PrettyPrinter(indent=4)
if "attributes" in _items:
print("--- helpler - attributes ---")
pp.pprint(attrs)
if "methods" in _items:
print("--- helpler - methods ---")
pp.pprint(methods)