Revision 96b756da59fa86ff41e2f8af7395545faf6f1155 authored by Guillaume Viejo on 15 September 2023, 20:32:16 UTC, committed by GitHub on 15 September 2023, 20:32:16 UTC
Update README.md
template_loader.py
# -*- coding: utf-8 -*-
"""
Template for building a data loader with pynapple
"""
# @Author: gviejo
# @Date: 2022-01-26 18:13:42
# @Last Modified by: gviejo
# @Last Modified time: 2022-08-18 18:02:38
import os
from pynwb import NWBHDF5IO
from pynapple.io.loader import BaseLoader
class MyCustomIO(BaseLoader):
def __init__(self, path):
"""
Parameters
----------
path : str
The path to the data.
"""
self.basename = os.path.basename(path)
super().__init__(path)
# Need to check if nwb file exists and if data are there
loading_my_data = True
if self.path is not None:
nwb_path = os.path.join(self.path, "pynapplenwb")
if os.path.exists(nwb_path):
files = os.listdir(nwb_path)
if len([f for f in files if f.endswith(".nwb")]):
success = self.load_my_nwb(path)
if success:
loading_my_data = False
# Bypass if data have already been transfered to nwb
if loading_my_data:
self.load_my_data(path)
self.save_my_data_in_nwb(path)
def load_my_data(self, path):
"""
This load the raw data
Parameters
----------
path : str
Path to the session
"""
"""
Load Raw data here
"""
print(path)
return None
def save_my_data_in_nwb(self, path):
"""
Save the raw data to NWB
Parameters
----------
path : TYPE
Description
"""
self.nwb_path = os.path.join(path, "pynapplenwb")
if not os.path.exists(self.nwb_path):
raise RuntimeError("Path {} does not exist.".format(self.nwb_path))
self.nwbfilename = [f for f in os.listdir(self.nwb_path) if "nwb" in f][0]
self.nwbfilepath = os.path.join(self.nwb_path, self.nwbfilename)
io = NWBHDF5IO(self.nwbfilepath, "r+")
"""
Save data in NWB here
"""
io.close()
return
def load_my_nwb(self, path):
"""
This load the nwb that is already create by the base loader
Parameters
----------
path : str
Path to the session
"""
self.nwb_path = os.path.join(path, "pynapplenwb")
if not os.path.exists(self.nwb_path):
raise RuntimeError("Path {} does not exist.".format(self.nwb_path))
self.nwbfilename = [f for f in os.listdir(self.nwb_path) if "nwb" in f][0]
self.nwbfilepath = os.path.join(self.nwb_path, self.nwbfilename)
io = NWBHDF5IO(self.nwbfilepath, "r")
nwbfile = io.read()
print(nwbfile)
"""
Add code to write to nwb file here
"""
io.close()
mydata = MyCustomIO(".")
print(type(mydata))
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