WIP: Tidy position 2

.gitignore

@@ -136,6 +136,7 @@ dmypy.json
 *.videoTimeStamps
 *.cameraHWSync
 *.stateScriptLog
+tests/_data/*
 
 *.nwb
 *.DS_Store

CHANGELOG.md

@@ -11,13 +11,17 @@
 
 ### Pipelines
 
+- Common:
+    - Add ActivityLog to `common_usage` to track unreferenced utilities. #870
 - Position:
     - Fixes to `environment-dlc.yml` restricting tensortflow #834
     - Video restriction for multicamera epochs #834
     - Fixes to `_convert_mp4` #834
     - Replace deprecated calls to `yaml.safe_load()` #834
+    - Refactoring to reduce redundancy #870
+    - Migrate `OutputLogger` behavior to decorator #870
 - Spikesorting:
-    - Increase`spikeinterface` version to >=0.99.1, <0.100 #852
+    - Increase`spikeinterface` version to >=0.99.1, \<0.100 #852
     - Bug fix in single artifact interval edge case #859
 - LFP
     - In LFPArtifactDetection, only apply referencing if explicitly selected #863
@@ -193,3 +197,4 @@
 [0.4.2]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.4.2
 [0.4.3]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.4.3
 [0.5.0]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.5.0
+[0.5.1]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.5.1

src/spyglass/common/common_behav.py

@@ -367,7 +367,7 @@ class VideoFile(SpyglassMixin, dj.Imported):
     def make(self, key):
         self._no_transaction_make(key)
 
-    def _no_transaction_make(self, key, verbose=True):
+    def _no_transaction_make(self, key, verbose=True, skip_duplicates=False):
         if not self.connection.in_transaction:
             self.populate(key)
             return
@@ -394,6 +394,7 @@ def _no_transaction_make(self, key, verbose=True):
                 "interval_list_name": interval_list_name,
             }
         ).fetch1("valid_times")
+
         cam_device_str = r"camera_device (\d+)"
         is_found = False
         for ind, video in enumerate(videos.values()):
@@ -403,26 +404,31 @@ def _no_transaction_make(self, key, verbose=True):
                 # check to see if the times for this video_object are largely
                 # overlapping with the task epoch times
 
-                if len(
+                if not len(
                     interval_list_contains(valid_times, video_obj.timestamps)
                     > 0.9 * len(video_obj.timestamps)
                 ):
-                    nwb_cam_device = video_obj.device.name
-                    # returns whatever was captured in the first group (within the parentheses) of the regular expression -- in this case, 0
-                    key["video_file_num"] = int(
-                        re.match(cam_device_str, nwb_cam_device)[1]
+                    continue
+
+                nwb_cam_device = video_obj.device.name
+
+                # returns whatever was captured in the first group (within the
+                # parentheses) of the regular expression - in this case, 0
+
+                key["video_file_num"] = int(
+                    re.match(cam_device_str, nwb_cam_device)[1]
+                )
+                camera_name = video_obj.device.camera_name
+                if CameraDevice & {"camera_name": camera_name}:
+                    key["camera_name"] = video_obj.device.camera_name
+                else:
+                    raise KeyError(
+                        f"No camera with camera_name: {camera_name} found "
+                        + "in CameraDevice table."
                     )
-                    camera_name = video_obj.device.camera_name
-                    if CameraDevice & {"camera_name": camera_name}:
-                        key["camera_name"] = video_obj.device.camera_name
-                    else:
-                        raise KeyError(
-                            f"No camera with camera_name: {camera_name} found "
-                            + "in CameraDevice table."
-                        )
-                    key["video_file_object_id"] = video_obj.object_id
-                    self.insert1(key)
-                    is_found = True
+                key["video_file_object_id"] = video_obj.object_id
+                self.insert1(key, skip_duplicates=skip_duplicates)
+                is_found = True
 
         if not is_found and verbose:
             logger.info(
@@ -431,7 +437,7 @@ def _no_transaction_make(self, key, verbose=True):
             )
 
     @classmethod
-    def update_entries(cls, restrict={}):
+    def update_entries(cls, restrict=True):
         existing_entries = (cls & restrict).fetch("KEY")
         for row in existing_entries:
             if (cls & row).fetch1("camera_name"):

src/spyglass/common/common_device.py

@@ -703,6 +703,8 @@ def prompt_insert(
 
     if table_type:
         table_type += " "
+    else:
+        table_type = ""
 
     logger.info(
         f"{table}{table_type} '{name}' was not found in the"

src/spyglass/common/common_usage.py

@@ -54,6 +54,7 @@ class ActivityLog(dj.Manual):
     """
 
     @classmethod
-    def log(cls, name):
-        logger.warning(f"Function scheduled for deprecation: {name}")
+    def log(cls, name, warning=True) -> None:
+        if warning:
+            logger.warning(f"Function scheduled for deprecation: {name}")
         cls.insert1(dict(dj_user=dj.config["database.user"], function=name))

src/spyglass/position/position_merge.py

@@ -8,11 +8,8 @@
 from datajoint.utils import to_camel_case
 
 from spyglass.common.common_position import IntervalPositionInfo as CommonPos
-from spyglass.position.v1.dlc_utils import (
-    check_videofile,
-    get_video_path,
-    make_video,
-)
+from spyglass.position.v1.dlc_utils import check_videofile, get_video_path
+from spyglass.position.v1.dlc_utils_makevid import make_video
 from spyglass.position.v1.position_dlc_pose_estimation import (
     DLCPoseEstimationSelection,
 )