nicain

import pandas as pd

from allensdk.internal.api.behavior_ophys_api import BehaviorOphysLimsApi
from allensdk.brain_observatory.behavior.behavior_ophys_session import BehaviorOphysSession
from allensdk.brain_observatory.behavior.dprime import get_dprime_pipeline, get_hit_rate, get_false_alarm_rate

from visual_behavior.translator.core import create_extended_dataframe
from visual_behavior.translator import foraging2
from visual_behavior.translator.foraging2 import data_to_change_detection_core
from visual_behavior.utilities import get_response_rates

nicain

logger_name = 'TheName'

ch = logging.StreamHandler()
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
ch.setFormatter(formatter)
logger = logging.getLogger(logger_name)
logger.setLevel(logging.INFO)
logger.addHandler(ch)
logger.propagate = False

nicain

import h5py
import numpy as np
from allensdk.brain_observatory.sync_dataset import Dataset as SyncDataset  # on internal branch as of 04/03/2019

# ophys_experiment_id: 789359614

dff_filepath = '/allen/programs/braintv/production/visualbehavior/prod0/specimen_756577249/ophys_session_789220000/ophys_experiment_789359614/789359614_dff.h5'
sync_filepath = '/allen/programs/braintv/production/visualbehavior/prod0/specimen_756577249/ophys_session_789220000/789220000_sync.h5'

with h5py.File(dff_filepath, 'r') as raw_file:

nicain

from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache
from allensdk.api.queries.mouse_connectivity_api import MouseConnectivityApi

mcc_2017 = MouseConnectivityCache(resolution=25, ccf_version=MouseConnectivityApi.CCF_2017)
data = mcc_2017.get_template_volume()
print data[0].shape

nicain

import dill
import requests

x = requests.get('http://nicholasc-ubuntu:5001/cursor/')
c = dill.loads(x.content)
c.cell_width('90%')
c.open(filename='/home/nicholasc/projects/dataframe-browser/data/example.csv')
c.display()

nicain

from pynwb import NWBFile, NWBHDF5IO, TimeSeries
from pynwb.epoch import Epochs
import os
import pandas as pd
import datetime

nwbfile = NWBFile(
    source='Data source',
    session_description='test',
    identifier='test',

nicain

from pynwb import NWBFile, NWBHDF5IO, TimeSeries
import os
import pandas as pd
from visual_behavior.translator.foraging2 import data_to_change_detection_core
import datetime

def test_visbeh_nwb(tmpdir_factory):

    data_dir = str(tmpdir_factory.mktemp("data"))
    save_file_name = os.path.join(data_dir, 'visbeh_test.nwb')

nicain

def one(x, exception=Exception):
    if len(x) != 1:
        raise exception
    if isinstance(x,set):
        return list(x)[0]
    else:
        return x[0]

nicain

def add_frame_dir(sweep_stim, output_dir='.'):

    image_dict = {}
    timing_dict = collections.defaultdict(list)

    for stimulus in sweep_stim.stimuli:
        old_update = stimulus.update
        def new_update(frame):
            old_update(frame)
            assert frame == stimulus.current_frame

nicain

import pandas as pd

from mtrain_api.utils import get_df

stages_df = get_df('stages').rename(columns={'id':'stage_id','name':'stage_name'}).drop(['script', 'script_md5', 'states'], axis=1)
states_df = get_df('states').rename(columns={'id':'state_id'})
subjects_df = get_df('subjects').rename(columns={'id':'state_id'})
subjects_df['state_id'] = subjects_df['state'].map(lambda x:x['id'])
subjects_df.drop(['state'], axis=1, inplace=True)
stages_states_df = pd.merge(stages_df, states_df, on='stage_id')