In order to download a nwb file to a python script in a code ocean repository, follow the code below.
- Make sure to pip install imports if there are errors with excuting the script
from pathlib import Path
import re
from hdmf_zarr import NWBZarrIO
- Downloads NWBfile from /data folder in repository given subject and date
def identify_nwb_contents_in_code_ocean(subject_id, date):
"""
Searches the /data directory in a code ocean repository for a folder
and subfolder containing the subject_id and date,
and loads the corresponding NWB file.
Parameters:
- subject_id (str): Subject identifier to search for in directory names
- date (str): Date string (e.g. '2023-05-09') to search for in directory names
Returns:
- nwbfile: Loaded NWBFile object if found, else None
"""
# Create pattern for matching
pattern = rf".*{subject_id}.*{date}.*"
base_path = Path('/data')
# Find matching first-level directories
first_matches = [d for d in base_path.iterdir()
if d.is_dir() and re.search(pattern, d.name)]
if not first_matches:
#print(f"Directory matching subject_id={subject_id} and date={date} not found in /data.")
return None
first_dir = first_matches[0]
#print(f"Found first-level directory: {first_dir.name}")
# Find matching second-level directories
second_matches = [d for d in first_dir.iterdir()
if d.is_dir() and re.search(pattern, d.name)]
if not second_matches:
#print(f"No second-level directory matching subject_id={subject_id} and date={date} found.")
return None
nwb_path = second_matches[0]
print(f"Found second-level directory: {nwb_path.name}")
# Check if path exists and load NWB file
try:
with NWBZarrIO(str(nwb_path), 'r') as io:
nwbfile = io.read()
print('Loaded NWB file from:', nwb_path)
print(nwbfile)
# to find fields and locations of data in nwbfile, print nwbfile.allchildren()
return nwbfile # NWBfile object
except Exception as e:
print(f'Error loading file from {nwb_path}: {e}')
return None
Note that the NWBfile doesn't expose all relevant fields needed to find data nested within the file. To expose that information print nwbfile.allchildren()
