Custom Loading IO

This example shows how to construct a custom IO loader.

# -*- coding: utf-8 -*-
# @Author: gviejo
# @Date:   2022-01-06 20:01:32
# @Last Modified by:   gviejo
# @Last Modified time: 2022-01-06 20:01:57

import os
from nwbmatic.loader import BaseLoader
from pynwb import NWBFile, NWBHDF5IO

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 os.path.exists(self.nwb_path):
            files = os.listdir(self.nwb_path)
        else:
            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 os.path.exists(self.nwb_path):
            files = os.listdir(self.nwb_path)
        else:
            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()

        '''
        Add code to write to nwb file here
        '''

        io.close()


mydata = MyCustomIO('.')

print(type(mydata))