Merge remote-tracking branch 'origin/master' into ibl_tests

Author: oliche

phylib/__init__.py

@@ -62,7 +62,7 @@ def add_default_handler(level='INFO', logger=logger):
 
 def _add_log_file(filename):  # pragma: no cover
     """Create a log file with DEBUG level."""
-    handler = logging.FileHandler(filename)
+    handler = logging.FileHandler(str(filename))
     handler.setLevel(logging.DEBUG)
     formatter = _Formatter(fmt=_logger_fmt, datefmt=_logger_date_fmt)
     handler.setFormatter(formatter)

phylib/io/model.py

@@ -239,7 +239,7 @@ def compute_features(waveforms):
     return features
 
 
-#-----------------------------------------------------------------------------
+#------------------------------------------------------------------------------
 # I/O util functions
 #------------------------------------------------------------------------------
 
@@ -683,10 +683,13 @@ def _load_templates(self):
         try:
             path = self._find_path(
                 'templates.npy', 'templates.waveforms.npy', 'templates.waveforms.*.npy')
-            data = self._read_array(path, mmap_mode='r')
+            data = self._read_array(path, mmap_mode='r+')
             data = np.atleast_3d(data)
             assert data.ndim == 3
             assert data.dtype in (np.float32, np.float64)
+            # WARNING: this will load the full array in memory, might cause memory problems
+            empty_templates = np.all(np.all(np.isnan(data), axis=1), axis=1)
+            data[empty_templates, ...] = 0
             n_templates, n_samples, n_channels_loc = data.shape
         except IOError:
             return
@@ -818,6 +821,7 @@ def _find_best_channels(self, template, amplitude_threshold=None):
         # Compute the template amplitude on each channel.
         assert template.ndim == 2  # shape: (n_samples, n_channels)
         amplitude = template.max(axis=0) - template.min(axis=0)
+        assert not np.all(np.isnan(amplitude)), "Template is all NaN!"
         assert amplitude.ndim == 1  # shape: (n_channels,)
         # Find the peak channel.
         best_channel = np.argmax(amplitude)

phylib/io/traces.py

@@ -30,7 +30,7 @@
 DEFAULT_CHUNK_DURATION = 600.0  # seconds
 
 
-EPHYS_RAW_EXTENSIONS = ('.dat', '.bin', '.raw')
+EPHYS_RAW_EXTENSIONS = ('.dat', '.bin', '.raw', '.mda')
 
 
 #------------------------------------------------------------------------------