Coverage for ibllib/qc/task_extractors.py: 97%

1import logging (empty)

2 

3import numpy as np (empty)

4 

5from one.alf.spec import is_session_path (empty)

6import one.alf.io as alfio (empty)

7 

8 

9_logger = logging.getLogger('ibllib') (empty)

10 

11REQUIRED_FIELDS = ['choice', 'contrastLeft', 'contrastRight', 'correct', (empty)

12 'errorCueTrigger_times', 'errorCue_times', 'feedbackType', 'feedback_times', 

13 'firstMovement_times', 'goCueTrigger_times', 'goCue_times', 'intervals', 

14 'itiIn_times', 'phase', 'position', 'probabilityLeft', 'quiescence', 

15 'response_times', 'rewardVolume', 'stimFreezeTrigger_times', 

16 'stimFreeze_times', 'stimOffTrigger_times', 'stimOff_times', 

17 'stimOnTrigger_times', 'stimOn_times', 'valveOpen_times', 

18 'wheelMoves_intervals', 'wheelMoves_peakAmplitude', 'wheelMoves_peakVelocity_times', 

19 'wheel_position', 'wheel_timestamps'] 

20 

21 

22class TaskQCExtractor: (empty)

23 def __init__(self, session_path): (empty)

24 """ 

25 A class for holding the task data required to perform task quality control. 

26 :param session_path: a valid session path 

27 """ 

28 if not is_session_path(session_path): 4 ctx1acbd

29 raise ValueError('Invalid session path') 

30 self.session_path = session_path 4 ctx1acbd

31 self.log = _logger 4 ctx1acbd

32 

33 self.data = None 4 ctx1acbd

34 self.settings = None 4 ctx1acbd

35 self.raw_data = None 4 ctx1acbd

36 self.frame_ttls = self.audio_ttls = self.bpod_ttls = None 4 ctx1acbd

37 self.wheel_encoding = None 4 ctx1acbd

38 

39 @staticmethod (empty)

40 def rename_data(data): (empty)

41 """Rename the extracted data dict for use with TaskQC 

42 Splits 'feedback_times' to 'errorCue_times' and 'valveOpen_times'. 

43 NB: The data is not copied before making changes 

44 :param data: A dict of task data returned by the task extractors 

45 :return: the same dict after modifying the keys 

46 """ 

47 # Expand trials dataframe into key value pairs 

48 trials_table = data.pop('table', None) 4 ctx1acbd

49 if trials_table is not None: 4 ctx1acbd

50 data = {**data, **alfio.AlfBunch.from_df(trials_table)} 4 ctx1acbd

51 correct = data['feedbackType'] > 0 4 ctx1acbd

52 # get valve_time and errorCue_times from feedback_times 

53 if 'errorCue_times' not in data: 4 ctx1acbd

54 data['errorCue_times'] = data['feedback_times'].copy() 3 ctx1acb

55 data['errorCue_times'][correct] = np.nan 3 ctx1acb

56 if 'valveOpen_times' not in data: 4 ctx1acbd

57 data['valveOpen_times'] = data['feedback_times'].copy() 3 ctx1acb

58 data['valveOpen_times'][~correct] = np.nan 3 ctx1acb

59 data['correct'] = correct 4 ctx1acbd

60 diff_fields = list(set(REQUIRED_FIELDS).difference(set(data.keys()))) 4 ctx1acbd

61 for miss_field in diff_fields: 4 ctx1acbd

62 data[miss_field] = None if miss_field.startswith('wheel') else data['feedback_times'] * np.nan 1 ctx1b

63 if len(diff_fields): 4 ctx1acbd

64 _logger.warning(f'QC extractor, missing fields filled with NaNs: {diff_fields}') 1 ctx1b

65 return data 4 ctx1acbd