drafty implementation

Author: samuelgarcia

neo/rawio/spikegadgetsrawio.py

@@ -4,13 +4,19 @@
 
 https://spikegadgets.com/spike-products/
 
+
+The file ".rec" have :
+  * a fist part in text with xml informations
+  * a second part for the binary buffer
+
 Author: Samuel Garcia
 """
 from .baserawio import (BaseRawIO, _signal_channel_dtype, _unit_channel_dtype,
                         _event_channel_dtype)
 
 import numpy as np
 
+from xml.etree import ElementTree
 
 class SpikeGadgetsRawIO(BaseRawIO):
     extensions = ['rec']
@@ -25,8 +31,42 @@ def _source_name(self):
 
     def _parse_header(self):
 
+        # parse file until "</Configuration>"
+        header_size = None
+        with open(self.filename, mode='rb') as f:
+            while True:
+                line = f.readline()
+                if b"</Configuration>" in line:
+                    header_size = f.tell()
+                    break
+            if header_size is None:
+                ValueError("SpikeGadgets : the xml header do not contain </Configuration>")
+            print(header_size)
+            f.seek(0)
+            header_txt = f.read(header_size).decode('utf8')
+        
+        # explore xml header
+        root = ElementTree.fromstring(header_txt)
+
+        gconf = sr = root.find('GlobalConfiguration')
+        hconf = root.find('HardwareConfiguration')
+        self._sampling_rate = float(hconf.attrib['samplingRate'])
+        
         signal_channels = []
-        signal_channels = np.array(sig_channels, dtype=_signal_channel_dtype)
+        for chan_ind, child in enumerate(hconf.find('Device')):
+            name = child.attrib['id']
+            chan_id = chan_ind  #TODO change this to str with new rawio refactoring
+            dtype = 'int16' # TODO check this
+            units = 'uV' # TODO check where is the info
+            gain = 1. # TODO check where is the info
+            offset = 0. # TODO check where is the info
+            group_id = 0
+            signal_channels.append((name, chan_id, self._sampling_rate, 'int16',
+                                 units, gain, offset, group_id))            
+        signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
+
+        self._raw_memmap = np.memmap(self.filename, mode='r', offset=header_size, dtype='int16')
+        self._raw_memmap = self._raw_memmap.reshape(-1, signal_channels.size)
 
         # No events
         event_channels = []
@@ -39,8 +79,8 @@ def _parse_header(self):
         # fille into header dict
         self.header = {}
         self.header['nb_block'] = 1
-        self.header['nb_segment'] = [nb_segment]
-        self.header['signal_channels'] = sig_channels
+        self.header['nb_segment'] = [1]
+        self.header['signal_channels'] = signal_channels
         self.header['unit_channels'] = unit_channels
         self.header['event_channels'] = event_channels
 
@@ -50,16 +90,20 @@ def _segment_t_start(self, block_index, seg_index):
         return 0.
 
     def _segment_t_stop(self, block_index, seg_index):
+        size = self._raw_memmap.shape[0]
+        t_stop = size / self._sampling_rate
         return t_stop
 
     def _get_signal_size(self, block_index, seg_index, channel_indexes):
-        sie = 0
+        size = self._raw_memmap.shape[0]
         return size
 
     def _get_signal_t_start(self, block_index, seg_index, channel_indexes):
         return 0.
 
     def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop, channel_indexes):
-        raw_signals = None
+        if channel_indexes is None:
+            channel_indexes = slice(None)
+        raw_signals = self._raw_memmap[slice(i_start, i_stop), :][:, channel_indexes]
         return raw_signals