Copy out only a small part of the original raw data from a MCS recording. Preserves all meta data.

extrac_mcs_raw_rec.py

import h5py as h5


file_path = 'data.h5'
stream_path = '/Data/Recording_0/AnalogStream/Stream_'


# set boundaries for data extraction
start_s = 0  # start second
end_s = 10  # end second
sampling_rate = 25e3  # Hz

start = int(start_s * sampling_rate)
stop = int(end_s * sampling_rate)

with h5.File(file_path, 'r+') as f:
    for i in range(5):
        data_path = stream_path + str(i) + '/ChannelData'
        length_info_path = stream_path + str(i) + '/ChannelDataTimeStamps'
        
        try:
            f[data_path]
            print('Stream ', i)
        except KeyError:
            print('Stopped after stream ', i)
            break
        
        print('Original shape: ', f[data_path].shape)
        
        # save compression info to apply to new dataset
        compressor_, compressor_kwargs = f[data_path].compression, f[data_path].compression_opts
        
        # load relevant data
        data = f[data_path][:, start:stop]
        print('New shape: ', data.shape)
        assert f[data_path].shape[0] == data.shape[0] and f[data_path].shape[1] >= data.shape[1]
        
        # copy attributes
        attr_dict = dict(f[data_path].attrs)  # should be empty
        
        # delete the old data
        del f[data_path]
        
        # create a new dataset
        f.create_dataset(data_path, data=data, compression=compressor_, compression_opts=compressor_kwargs)
        for key, value in attr_dict.items():
            f[data_path].attrs[key] = value
        
        # update the length info
        f[length_info_path][0][2] = stop