Merge pull request #989 from alejoe91/biocam

Implement Biocam reader for 3Brain system

Author: samuelgarcia

neo/io/__init__.py

@@ -22,6 +22,7 @@
 * :attr:`AxonaIO`
 * :attr:`AxonIO`
 * :attr:`BCI2000IO`
+* :attr:`BiocamIO`
 * :attr:`BlackrockIO`
 * :attr:`BlkIO`
 * :attr:`BrainVisionIO`
@@ -94,6 +95,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.io.BiocamIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.io.BlackrockIO
 
     .. autoattribute:: extensions
@@ -277,6 +282,7 @@
 from neo.io.axographio import AxographIO
 from neo.io.axonaio import AxonaIO
 from neo.io.axonio import AxonIO
+from neo.io.biocamio import BiocamIO
 from neo.io.blackrockio import BlackrockIO
 from neo.io.blkio import BlkIO
 from neo.io.bci2000io import BCI2000IO

neo/io/biocamio.py

@@ -0,0 +1,11 @@
+from neo.io.basefromrawio import BaseFromRaw
+from neo.rawio.biocamrawio import BiocamRawIO
+
+
+class BiocamIO(BiocamRawIO, BaseFromRaw):
+    __doc__ = BiocamRawIO.__doc__
+    mode = 'file'
+
+    def __init__(self, filename):
+        BiocamRawIO.__init__(self, filename=filename)
+        BaseFromRaw.__init__(self, filename)

neo/rawio/__init__.py

@@ -15,6 +15,7 @@
 * :attr:`AxographRawIO`
 * :attr:`AxonaRawIO`
 * :attr:`AxonRawIO`
+* :attr:`BiocamRawIO`
 * :attr:`BlackrockRawIO`
 * :attr:`BrainVisionRawIO`
 * :attr:`CedRawIO`
@@ -53,6 +54,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.rawio.BiocamRawIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.rawio.BlackrockRawIO
 
     .. autoattribute:: extensions
@@ -155,6 +160,7 @@
 from neo.rawio.axographrawio import AxographRawIO
 from neo.rawio.axonarawio import AxonaRawIO
 from neo.rawio.axonrawio import AxonRawIO
+from neo.rawio.biocamrawio import BiocamRawIO
 from neo.rawio.blackrockrawio import BlackrockRawIO
 from neo.rawio.brainvisionrawio import BrainVisionRawIO
 from neo.rawio.cedrawio import CedRawIO
@@ -185,6 +191,7 @@
     AxographRawIO,
     AxonaRawIO,
     AxonRawIO,
+    BiocamRawIO,
     BlackrockRawIO,
     BrainVisionRawIO,
     CedRawIO,

neo/rawio/biocamrawio.py

@@ -0,0 +1,186 @@
+"""
+Class for reading data from a 3-brain Biocam system.
+
+See:
+https://www.3brain.com/products/single-well/biocam-x
+
+Author : Alessio Buccino
+"""
+
+from .baserawio import (BaseRawIO, _signal_channel_dtype, _signal_stream_dtype,
+                        _spike_channel_dtype, _event_channel_dtype)
+
+import numpy as np
+
+try:
+    import h5py
+    HAVE_H5PY = True
+except ImportError:
+    HAVE_H5PY = False
+
+
+class BiocamRawIO(BaseRawIO):
+    """
+    Class for reading data from a Biocam h5 file.
+
+    Usage:
+        >>> import neo.rawio
+        >>> r = neo.rawio.BiocamRawIO(filename='biocam.h5')
+        >>> r.parse_header()
+        >>> print(r)
+        >>> raw_chunk = r.get_analogsignal_chunk(block_index=0, seg_index=0,
+                                                 i_start=0, i_stop=1024,  
+                                                 channel_names=channel_names)
+        >>> float_chunk = r.rescale_signal_raw_to_float(raw_chunk, dtype='float64',
+                                                        channel_indexes=[0, 3, 6])
+    """
+    extensions = ['h5']
+    rawmode = 'one-file'
+
+    def __init__(self, filename=''):
+        BaseRawIO.__init__(self)
+        self.filename = filename
+
+    def _source_name(self):
+        return self.filename
+
+    def _parse_header(self):
+        assert HAVE_H5PY, 'h5py is not installed'
+        self._header_dict = open_biocam_file_header(self.filename)
+        self._num_channels = self._header_dict["num_channels"]
+        self._num_frames = self._header_dict["num_frames"]
+        self._sampling_rate = self._header_dict["sampling_rate"]
+        self._filehandle = self._header_dict["file_handle"]
+        self._read_function = self._header_dict["read_function"]
+        self._channels = self._header_dict["channels"]
+        gain = self._header_dict["gain"]
+        offset = self._header_dict["offset"]
+
+        signal_streams = np.array([('Signals', '0')], dtype=_signal_stream_dtype)
+
+        sig_channels = []
+        for c, chan in enumerate(self._channels):
+            ch_name = f'ch{chan[0]}-{chan[1]}'
+            chan_id = str(c + 1)
+            sr = self._sampling_rate  # Hz
+            dtype = "uint16"
+            units = 'uV'
+            gain = gain
+            offset = offset
+            stream_id = '0'
+            sig_channels.append((ch_name, chan_id, sr, dtype, units, gain, offset, stream_id))
+        sig_channels = np.array(sig_channels, dtype=_signal_channel_dtype)
+
+        # No events
+        event_channels = []
+        event_channels = np.array(event_channels, dtype=_event_channel_dtype)
+
+        # No spikes
+        spike_channels = []
+        spike_channels = np.array(spike_channels, dtype=_spike_channel_dtype)
+
+        self.header = {}
+        self.header['nb_block'] = 1
+        self.header['nb_segment'] = [1]
+        self.header['signal_streams'] = signal_streams
+        self.header['signal_channels'] = sig_channels
+        self.header['spike_channels'] = spike_channels
+        self.header['event_channels'] = event_channels
+
+        self._generate_minimal_annotations()
+
+    def _segment_t_start(self, block_index, seg_index):
+        all_starts = [[0.]]
+        return all_starts[block_index][seg_index]
+
+    def _segment_t_stop(self, block_index, seg_index):
+        t_stop = self._num_frames / self._sampling_rate
+        all_stops = [[t_stop]]
+        return all_stops[block_index][seg_index]
+
+    def _get_signal_size(self, block_index, seg_index, stream_index):
+        assert stream_index == 0
+        return self._num_frames
+
+    def _get_signal_t_start(self, block_index, seg_index, stream_index):
+        assert stream_index == 0
+        return self._segment_t_start(block_index, seg_index)
+
+    def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop,
+                                stream_index, channel_indexes):
+        if i_start is None:
+            i_start = 0
+        if i_stop is None:
+            i_stop = self._num_frames
+
+        data = self._read_function(self._filehandle, i_start, i_stop, self._num_channels)
+        return np.squeeze(data[:, channel_indexes])
+
+
+def open_biocam_file_header(filename):
+    """Open a Biocam hdf5 file, read and return the recording info, pick te correct method to access raw data,
+    and return this to the caller."""
+    assert HAVE_H5PY, 'h5py is not installed'
+
+    rf = h5py.File(filename, 'r')
+    # Read recording variables
+    rec_vars = rf.require_group('3BRecInfo/3BRecVars/')
+    bit_depth = rec_vars['BitDepth'][0]
+    max_uv = rec_vars['MaxVolt'][0]
+    min_uv = rec_vars['MinVolt'][0]
+    n_frames = rec_vars['NRecFrames'][0]
+    sampling_rate = rec_vars['SamplingRate'][0]
+    signal_inv = rec_vars['SignalInversion'][0]
+
+    # Get the actual number of channels used in the recording
+    file_format = rf['3BData'].attrs.get('Version', None)
+    format_100 = False
+    if file_format == 100:
+        n_channels = len(rf['3BData/Raw'][0])
+        format_100 = True
+    elif file_format in (101, 102) or file_format is None:
+        n_channels = int(rf['3BData/Raw'].shape[0] / n_frames)
+    else:
+        raise Exception('Unknown data file format.')
+
+    # # get channels
+    channels = rf['3BRecInfo/3BMeaStreams/Raw/Chs'][:]
+
+    # determine correct function to read data
+    if format_100:
+        if signal_inv == 1:
+            read_function = readHDF5t_100
+        elif signal_inv == 1:
+            read_function = readHDF5t_100_i
+        else:
+            raise Exception("Unknown signal inversion")
+    else:
+        if signal_inv == 1:
+            read_function = readHDF5t_101
+        elif signal_inv == 1:
+            read_function = readHDF5t_101_i
+        else:
+            raise Exception("Unknown signal inversion")
+
+    gain = (max_uv - min_uv) / (2 ** bit_depth)
+    offset = min_uv
+
+    return dict(file_handle=rf, num_frames=n_frames, sampling_rate=sampling_rate, num_channels=n_channels,
+                channels=channels, file_format=file_format, signal_inv=signal_inv,
+                read_function=read_function, gain=gain, offset=offset)
+
+
+def readHDF5t_100(rf, t0, t1, nch):
+    return rf['3BData/Raw'][t0:t1]
+
+
+def readHDF5t_100_i(rf, t0, t1, nch):
+    return 4096 - rf['3BData/Raw'][t0:t1]
+
+
+def readHDF5t_101(rf, t0, t1, nch):
+    return rf['3BData/Raw'][nch * t0:nch * t1].reshape((t1 - t0, nch), order='C')
+
+
+def readHDF5t_101_i(rf, t0, t1, nch):
+    return 4096 - rf['3BData/Raw'][nch * t0:nch * t1].reshape((t1 - t0, nch), order='C')

neo/test/iotest/test_biocam.py

@@ -0,0 +1,22 @@
+"""
+Tests of neo.io.BiocamIO
+"""
+
+import unittest
+
+from neo.io import BiocamIO
+from neo.test.iotest.common_io_test import BaseTestIO
+
+
+class TestBiocamIO(BaseTestIO, unittest.TestCase, ):
+    ioclass = BiocamIO
+    entities_to_download = [
+        'biocam'
+    ]
+    entities_to_test = [
+        'biocam/biocam_hw3.0_fw1.6.brw'
+    ]
+
+
+if __name__ == "__main__":
+    unittest.main()

neo/test/rawiotest/test_biocam.py

@@ -0,0 +1,24 @@
+"""
+Tests of neo.rawio.BiocamRawIO
+"""
+
+import unittest
+
+from neo.rawio.biocamrawio import BiocamRawIO
+from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
+
+
+class TestBiocamRawIO(BaseTestRawIO, unittest.TestCase, ):
+    rawioclass = BiocamRawIO
+
+    entities_to_download = [
+        'biocam/biocam_hw3.0_fw1.6.brw'
+        ]
+
+    entities_to_download = [
+        'biocam',
+    ]
+
+
+if __name__ == "__main__":
+    unittest.main()