Query the number of mice at different timepoints of the pipeline
@author: Anne Urai, Guido Meijer, Miles Wells, 16 Jan 2020
Updated 22 April 2020, Anne Urai
"""
from paper_behavior_functions import query_subjects, CUTOFF_DATE
from ibl_pipeline import subject, acquisition, reference
from ibl_pipeline.analyses import behavior as behavior_analysis
# =========================
# 1. Query all mice on brainwide map project which began training before the paper's cutoff date
# =========================
all_mice = (subject.Subject * subject.SubjectLab * reference.Lab *
subject.SubjectProject()
& 'subject_project = "ibl_neuropixel_brainwide_01"').aggr(
acquisition.Session,
first_session='min(date(session_start_time))')
# Filter mice that started training after the paper's cutoff date
all_mice = all_mice.aggr(acquisition.Session,
first_session='min(date(session_start_time))')
all_mice = (all_mice & 'first_session < "%s"' % CUTOFF_DATE)
print('1. Total # of mice in brainwide project: %d' % len(all_mice))
# ==================================================
# Exclude mice that are still in training at the date of cut-off, meaning they have not yet
# reached any learned criteria
# ==================================================
import seaborn as sns
from ibl_pipeline import subject, reference, acquisition
from paper_behavior_functions import (seaborn_style, institution_map,
group_colors, figpath, CUTOFF_DATE,
FIGURE_HEIGHT, FIGURE_WIDTH, QUERY)
from ibl_pipeline.analyses import behavior as behavior_analysis
from lifelines import KaplanMeierFitter
# Settings
fig_path = figpath()
seaborn_style()
if QUERY is True:
# Query all mice
all_mice = (subject.Subject * subject.SubjectLab * reference.Lab
* subject.SubjectProject() & 'subject_project = "ibl_neuropixel_brainwide_01"')
mice_started_training = (all_mice & (acquisition.Session() & 'task_protocol LIKE "%training%"'))
still_training = all_mice.aggr(behavior_analysis.SessionTrainingStatus,
session_start_time='max(session_start_time)') \
* behavior_analysis.SessionTrainingStatus - subject.Death \
& 'training_status = "in_training"' \
& 'session_start_time > "%s"' % CUTOFF_DATE
use_subjects = mice_started_training - still_training
# Get training status and training time in number of sessions and trials
ses = (use_subjects
* behavior_analysis.SessionTrainingStatus
* behavior_analysis.PsychResults).proj(
'subject_nickname', 'training_status', 'n_trials_stim', 'institution_short').fetch(
format='frame').reset_index()
ses['n_trials'] = [sum(i) for i in ses['n_trials_stim']]