Allow dlc pipeline to run without prior position tracking (LorenFrank…

…Lab#970)

* fix dlc pose estimation populate if no raw position data

* allow dlc pipeline to run without raw spatial data

* update changelog

* string formatting

* fix analysis nwb create time

CHANGELOG.md

@@ -14,6 +14,11 @@
 - Add long-distance restrictions via `<<` and `>>` operators. #943, #969
 - Fix relative pathing for `mkdocstring-python=>1.9.1`. #967, #968
 
+### Pipelines
+
+- DLC
+   - Allow dlc without pre-existing tracking data #950
+
 ## [0.5.2] (April 22, 2024)
 
 ### Infrastructure

src/spyglass/position/v1/position_dlc_centroid.py

@@ -268,17 +268,26 @@ def make(self, key):
             )
             position = pynwb.behavior.Position()
             velocity = pynwb.behavior.BehavioralTimeSeries()
-            spatial_series = (RawPosition() & key).fetch_nwb()[0][
-                "raw_position"
-            ]
+            if (
+                RawPosition & key
+            ):  # if spatial series exists, get metadata from there
+                spatial_series = (RawPosition() & key).fetch_nwb()[0][
+                    "raw_position"
+                ]
+                reference_frame = spatial_series.reference_frame
+                comments = spatial_series.comments
+            else:
+                reference_frame = ""
+                comments = "no comments"
+
             METERS_PER_CM = 0.01
             position.create_spatial_series(
                 name="position",
                 timestamps=final_df.index.to_numpy(),
                 conversion=METERS_PER_CM,
                 data=final_df.loc[:, idx[("x", "y")]].to_numpy(),
-                reference_frame=spatial_series.reference_frame,
-                comments=spatial_series.comments,
+                reference_frame=reference_frame,
+                comments=comments,
                 description="x_position, y_position",
             )
             velocity.create_timeseries(

src/spyglass/position/v1/position_dlc_orient.py

@@ -1,3 +1,5 @@
+from time import time
+
 import datajoint as dj
 import numpy as np
 import pandas as pd
@@ -85,9 +87,7 @@ class DLCOrientation(SpyglassMixin, dj.Computed):
 
     def make(self, key):
         # Get labels to smooth from Parameters table
-        key["analysis_file_name"] = AnalysisNwbfile().create(  # logged
-            key["nwb_file_name"]
-        )
+        AnalysisNwbfile()._creation_times["pre_create_time"] = time()
         cohort_entries = DLCSmoothInterpCohort.BodyPart & key
         pos_df = pd.concat(
             {
@@ -133,15 +133,28 @@ def make(self, key):
         final_df = pd.DataFrame(
             orientation, columns=["orientation"], index=pos_df.index
         )
-        spatial_series = (RawPosition() & key).fetch_nwb()[0]["raw_position"]
+        key["analysis_file_name"] = AnalysisNwbfile().create(  # logged
+            key["nwb_file_name"]
+        )
+        if (
+            RawPosition & key
+        ):  # if spatial series exists, get metadata from there
+            spatial_series = (RawPosition() & key).fetch_nwb()[0][
+                "raw_position"
+            ]
+            reference_frame = spatial_series.reference_frame
+            comments = spatial_series.comments
+        else:
+            reference_frame = ""
+            comments = "no comments"
         orientation = pynwb.behavior.CompassDirection()
         orientation.create_spatial_series(
             name="orientation",
             timestamps=final_df.index.to_numpy(),
             conversion=1.0,
             data=final_df["orientation"].to_numpy(),
-            reference_frame=spatial_series.reference_frame,
-            comments=spatial_series.comments,
+            reference_frame=reference_frame,
+            comments=comments,
             description="orientation",
         )
         nwb_analysis_file = AnalysisNwbfile()

src/spyglass/position/v1/position_dlc_pose_estimation.py

@@ -232,25 +232,38 @@ def make(self, key):
                 dlc_result.creation_time
             ).strftime("%Y-%m-%d %H:%M:%S")
 
-            logger.logger.info("getting raw position")
-            interval_list_name = (
-                convert_epoch_interval_name_to_position_interval_name(
-                    {
-                        "nwb_file_name": key["nwb_file_name"],
-                        "epoch": key["epoch"],
-                    },
-                    populate_missing=False,
+            # get video information
+            _, _, meters_per_pixel, video_time = get_video_path(key)
+            # check if a position interval exists for this epoch
+            try:
+                interval_list_name = (
+                    convert_epoch_interval_name_to_position_interval_name(
+                        {
+                            "nwb_file_name": key["nwb_file_name"],
+                            "epoch": key["epoch"],
+                        },
+                        populate_missing=False,
+                    )
                 )
-            )
-            spatial_series = (
-                RawPosition()
-                & {**key, "interval_list_name": interval_list_name}
-            ).fetch_nwb()[0]["raw_position"]
-            _, _, _, video_time = get_video_path(key)
-            pos_time = spatial_series.timestamps
-            # TODO: should get timestamps from VideoFile, but need the video_frame_ind from RawPosition,
-            # which also has timestamps
-            key["meters_per_pixel"] = spatial_series.conversion
+                raw_position = True
+            except KeyError:
+                raw_position = False
+
+            if raw_position:
+                logger.logger.info("Getting raw position")
+                spatial_series = (
+                    RawPosition()
+                    & {**key, "interval_list_name": interval_list_name}
+                ).fetch_nwb()[0]["raw_position"]
+                pos_time = spatial_series.timestamps
+                reference_frame = spatial_series.reference_frame
+                comments = spatial_series.comments
+            else:
+                pos_time = video_time
+                reference_frame = ""
+                comments = "no comments"
+
+            key["meters_per_pixel"] = meters_per_pixel
 
             # Insert entry into DLCPoseEstimation
             logger.logger.info(
@@ -292,8 +305,8 @@ def make(self, key):
                     timestamps=part_df.time.to_numpy(),
                     conversion=METERS_PER_CM,
                     data=part_df.loc[:, idx[("x", "y")]].to_numpy(),
-                    reference_frame=spatial_series.reference_frame,
-                    comments=spatial_series.comments,
+                    reference_frame=reference_frame,
+                    comments=comments,
                     description="x_position, y_position",
                 )
                 likelihood.create_timeseries(

src/spyglass/position/v1/position_dlc_position.py

@@ -1,3 +1,5 @@
+from time import time
+
 import datajoint as dj
 import numpy as np
 import pandas as pd
@@ -167,9 +169,7 @@ def make(self, key):
             path=f"{output_dir.as_posix()}/log.log",
             print_console=False,
         ) as logger:
-            key["analysis_file_name"] = AnalysisNwbfile().create(  # logged
-                key["nwb_file_name"]
-            )
+            AnalysisNwbfile()._creation_times["pre_create_time"] = time()
             logger.logger.info("-----------------------")
             idx = pd.IndexSlice
             # Get labels to smooth from Parameters table
@@ -227,6 +227,9 @@ def make(self, key):
                 .fetch_nwb()[0]["dlc_pose_estimation_position"]
                 .get_spatial_series()
             )
+            key["analysis_file_name"] = AnalysisNwbfile().create(  # logged
+                key["nwb_file_name"]
+            )
             # Add dataframe to AnalysisNwbfile
             nwb_analysis_file = AnalysisNwbfile()
             position = pynwb.behavior.Position()

src/spyglass/position/v1/position_dlc_selection.py

@@ -1,5 +1,6 @@
 import copy
 from pathlib import Path
+from time import time
 
 import datajoint as dj
 import numpy as np
@@ -58,9 +59,7 @@ class DLCPosV1(SpyglassMixin, dj.Computed):
     def make(self, key):
         orig_key = copy.deepcopy(key)
         # Add to Analysis NWB file
-        key["analysis_file_name"] = AnalysisNwbfile().create(  # logged
-            key["nwb_file_name"]
-        )
+        AnalysisNwbfile()._creation_times["pre_create_time"] = time()
         key["pose_eval_result"] = self.evaluate_pose_estimation(key)
 
         pos_nwb = (DLCCentroid & key).fetch_nwb()[0]
@@ -114,6 +113,9 @@ def make(self, key):
             comments=vid_frame_obj.comments,
         )
 
+        key["analysis_file_name"] = AnalysisNwbfile().create(
+            key["nwb_file_name"]
+        )
         nwb_analysis_file = AnalysisNwbfile()
         key["orientation_object_id"] = nwb_analysis_file.add_nwb_object(
             key["analysis_file_name"], orientation