def cache(cache_test_base):
return bpc.BehaviorProjectCache(cache_test_base)
# Grab the experiment ID
experiment_id = sys.argv[1]
# Define the cache
cache_json = {
'manifest_path':
'/allen/programs/braintv/workgroups/nc-ophys/visual_behavior/SWDB_2019/visual_behavior_data_manifest.csv',
'nwb_base_dir':
'/allen/programs/braintv/workgroups/nc-ophys/visual_behavior/SWDB_2019/nwb_files',
'analysis_files_base_dir':
'/allen/programs/braintv/workgroups/nc-ophys/visual_behavior/SWDB_2019/extra_files'
}
# load the session
cache = bpc.BehaviorProjectCache(cache_json)
nwb_path = cache.get_nwb_filepath(experiment_id)
api = BehaviorOphysNwbApi(nwb_path, filter_invalid_rois=True)
session = BehaviorOphysExperiment(api)
# Where to save the results
output_path = '/allen/programs/braintv/workgroups/nc-ophys/visual_behavior/SWDB_2019/flash_response_500msec_response'
# Define parameters for dff_trace, and response_window
response_analysis_params = {
'window_around_timepoint_seconds': [-.5, .75], # -500ms, 750ms
'response_window_duration_seconds': 0.5,
'baseline_window_duration_seconds': 0.5
}
# compute the base flash_response_df
# , makeHeatmap, plotCluesToEngagementVsNot, plotStatisticsOfVariableVariance,
# seaborn is another library for statistical data visualization
# seaborn style & context settings make plots pretty & legible
import seaborn as sns
sns.set_context('notebook', font_scale=1.5, rc={'lines.markeredgewidth': 2})
sns.set_style('white')
sns.set_palette('deep')
#%%
# Allen Brain import
# Import allensdk modules for loading and interacting with the data
from allensdk.brain_observatory.behavior.swdb import behavior_project_cache as bpc
cache_path = '/media/charles/Brain2019/dynamic-brain-workshop/visual_behavior/2019'
cache = bpc.BehaviorProjectCache(cache_path)
#%%
''' Choose an experiment: '''
# get the experiments as a panda:
experiments = cache.experiment_table
# select an experiment_id:
expList = experiments.loc[(experiments.passive_session == False)
& (experiments.cre_line == 'Slc17a7-IRES2-Cre')]
# & (experiments.imaging_depth == 175) ] # 175 or 375. inhibitory = 'Vip-IRES-Cre'
# Note: the 'index' col is not 0 to n, but rather are a subset of the indices of the full table
#%%
# add column with checkout times:
expList = addRewardedExcitationExperimentCheckoutTimesToExperimentTable(