Merge pull request #91 from catalystneuro/000971

000971

.gitignore

@@ -2,4 +2,5 @@
 *.DS_Store
 *__pycache__/
 *.ipynb_checkpoints/
-output/
+output/
+

000971/lernerlab/seiler_2024/README.md

@@ -0,0 +1,8 @@
+# Example Sessions for Dandiset 000971
+
+This submission provides 2 notebooks showcasing example sessions for the Dandiset 000971, which corresponds to the 2022 Current Biology paper: [Dopamine signaling in the dorsomedial striatum promotes compulsive behavior](https://doi.org/10.1016/j.cub.2022.01.055.) by Seiler et al.
+
+Each notebook provides an example of how to access the critical data and metadata from the 2 types of experiments in the dataset:
+
+- `fiber_photometry_example_notebook.ipynb` showcases one example session from the 000971 dataset containing operant behavior and concurrent fiber photometry recordings.
+- `optogenetics_example_notebook.ipynb` showcases one example session from the 000971 dataset containing operant behavior and concurrent excitatory optogenetic stimulation.

000971/lernerlab/seiler_2024/environment.yml

@@ -0,0 +1,11 @@
+# run: conda env create --file environment.yaml
+name: lerner_notebook_env
+channels:
+    - conda-forge
+dependencies:
+    - python==3.10
+    - ipywidgets
+    - pip
+    - pip:
+      - matplotlib
+      - lerner-lab-to-nwb @ git+https://github.com/catalystneuro/lerner-lab-to-nwb.git@main

000971/lernerlab/seiler_2024/stream_nwbfile.py

@@ -0,0 +1,35 @@
+from pynwb import NWBHDF5IO
+from fsspec import filesystem
+from h5py import File
+from dandi.dandiapi import DandiAPIClient
+
+def stream_nwbfile(DANDISET_ID, file_path):
+    '''Stream NWB file from DANDI archive.
+    
+    Parameters
+    ----------
+    DANDISET_ID : str
+        Dandiset ID
+    file_path : str
+        Path to NWB file in DANDI archive
+    
+    Returns
+    -------
+    nwbfile : NWBFile
+        NWB file
+    io : NWBHDF5IO
+        NWB IO object (for closing)
+        
+    Notes
+    -----
+    The io object must be closed after use.
+    '''
+    with DandiAPIClient() as client:
+        asset = client.get_dandiset(DANDISET_ID, 'draft').get_asset_by_path(file_path)
+        s3_url = asset.get_content_url(follow_redirects=1, strip_query=True)
+    fs = filesystem("http")
+    file_system = fs.open(s3_url, "rb")
+    file = File(file_system, mode="r")
+    io = NWBHDF5IO(file=file, load_namespaces=True)
+    nwbfile = io.read()
+    return nwbfile, io