Closed nicain closed 5 years ago
conda create -n allensdk python=3.6 jupyter
conda activate allensdk
pip install --extra-index-url=https://aibs.jfrog.io/aibs/api/pypi/ni-pypi-local/simple allensdk==1.0.0.dev7
from nwbwidgets import nwb2widget
from pynwb import load_namespaces
import pynwb
from allensdk.brain_observatory.nwb.metadata import load_LabMetaData_extension
from allensdk.brain_observatory.behavior.schemas import OphysBehaviorMetaDataSchema, OphysBehaviorTaskParametersSchema
load_LabMetaData_extension(OphysBehaviorMetaDataSchema, 'AIBS_ophys_behavior')
load_LabMetaData_extension(OphysBehaviorTaskParametersSchema, 'AIBS_ophys_behavior')
path = '/Users/nicholasc/Documents/behavior_ophys_session_775614751.nwb'
io = pynwb.NWBHDF5IO(path, 'r')
nwb = io.read()
In the current Allen Institute behavior ophys files, there are 3-d numpy arrays for stimulus presentations:
When browsed, it appears that the framework is expecting a 2-D (m, n) array.
Bug fix/enhancement is to provide a selector to choose the k-th image, and plot the slice (i.e. data[k,:,:]).