Merge pull request #411 from int-brain-lab/pykilosort_version

rerun based on pykilosort version in log

Author: mayofaulkner

brainbox/io/one.py

@@ -331,6 +331,9 @@ def _load_channel_locations_traj(eid, probe=None, one=None, revision=None, align
 
             channels[probe] = _channels_traj2bunch(chans, brain_atlas)
 
+        channels[probe]['axial_um'] = chn_coords[:, 1]
+        channels[probe]['lateral_um'] = chn_coords[:, 0]
+
     else:
         _logger.warning(f'Histology tracing for {probe} does not exist. '
                         f'No channels for {probe}')

ibllib/pipes/ephys_preprocessing.py

@@ -5,6 +5,7 @@
 from collections import OrderedDict
 import traceback
 from pathlib import Path
+import packaging.version
 
 import numpy as np
 import pandas as pd
@@ -243,6 +244,14 @@ def _fetch_pykilosort_version(repo_path):
             pass
         return f"pykilosort_{version}"
 
+    @staticmethod
+    def _fetch_pykilosort_run_version(log_file):
+        with open(log_file) as fid:
+            line = fid.readline()
+        version = re.search('version (.*), output', line).group(1)
+
+        return f"pykilosort_{version}"
+
     @staticmethod
     def _fetch_ks2_commit_hash(repo_path):
         command2run = f"git --git-dir {repo_path}/.git rev-parse --verify HEAD"
@@ -283,10 +292,13 @@ def _run_pykilosort(self, ap_file):
         sorter_dir = self.session_path.joinpath("spike_sorters", self.SPIKE_SORTER_NAME, label)
         FORCE_RERUN = False
         if not FORCE_RERUN:
-            if sorter_dir.joinpath(f"spike_sorting_{self.SPIKE_SORTER_NAME}.log").exists():
-                _logger.info(f"Already ran: spike_sorting_{self.SPIKE_SORTER_NAME}.log"
-                             f" found in {sorter_dir}, skipping.")
-                return sorter_dir
+            log_file = sorter_dir.joinpath(f"spike_sorting_{self.SPIKE_SORTER_NAME}.log")
+            if log_file.exists():
+                run_version = self._fetch_pykilosort_run_version(log_file)
+                if packaging.version.parse(run_version) >= packaging.version.parse('pykilosort_ibl_1.1.0'):
+                    _logger.info(f"Already ran: spike_sorting_{self.SPIKE_SORTER_NAME}.log"
+                                 f" found in {sorter_dir}, skipping.")
+                    return sorter_dir
         print(sorter_dir.joinpath(f"spike_sorting_{self.SPIKE_SORTER_NAME}.log"))
         # get the scratch drive from the shell script
         with open(self.SHELL_SCRIPT) as fid:

ibllib/pipes/tasks.py

@@ -223,7 +223,8 @@ def tearDown(self):
         Does not run if a lock is encountered by the task (status -2)
         """
         if self.gpu >= 1:
-            self._lock_file_path().unlink()
+            if self._lock_file_path().exists():
+                self._lock_file_path().unlink()
 
     def cleanUp(self):
         """