small fixes

Author: oliche

brainbox/io/one.py

@@ -865,7 +865,7 @@ class SpikeSortingLoader:
     """Class for loading spike sorting"""
     pid: str
     one: ONE
-    atlas: atlas.BrainAtlas = None
+    atlas: None
     # the following properties are the outcome of the post init funciton
     eid: str = ''
     session_path: Path = ''

ibllib/dsp/voltage.py

@@ -316,7 +316,7 @@ def decompress_destripe_cbin(sr_file, output_file=None, h=None, wrot=None, appen
         channel_labels = detect_bad_channels_cbin(sr)
     assert isinstance(sr_file, str) or isinstance(sr_file, Path)
     butter_kwargs, k_kwargs, spatial_fcn = _get_destripe_parameters(sr.fs, butter_kwargs, k_kwargs, k_filter)
-    h = neuropixel.trace_header(version=1) if h is None else h
+    h = sr.geometry if h is None else h
     ncv = h['sample_shift'].size  # number of channels
     output_file = sr.file_bin.with_suffix('.bin') if output_file is None else output_file
     assert output_file != sr.file_bin

ibllib/io/spikeglx.py

@@ -58,11 +58,12 @@ def open(self):
             self._raw.open(self.file_bin, self.file_bin.with_suffix('.ch'))
             if self._raw.shape != (self.ns, self.nc):
                 ftsec = self._raw.shape[0] / self.fs
-                _logger.warning(f"{sglx_file} : meta data and compressed chunks dont checkout\n"
-                                f"File duration: expected {self.meta['fileTimeSecs']},"
-                                f" actual {ftsec}\n"
-                                f"Will attempt to fudge the meta-data information.")
                 self.meta['fileTimeSecs'] = ftsec
+                if ftsec > 1:  # avoid the checks for streaming data
+                    _logger.warning(f"{sglx_file} : meta data and compressed chunks dont checkout\n"
+                                    f"File duration: expected {self.meta['fileTimeSecs']},"
+                                    f" actual {ftsec}\n"
+                                    f"Will attempt to fudge the meta-data information.")
         else:
             if self.nc * self.ns * 2 != self.nbytes:
                 ftsec = self.file_bin.stat().st_size / 2 / self.nc / self.fs