error when trying to populate PoseEstimation #1207
Comments
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Immediate solution from spyglass.common import convert_epoch_interval_name_to_position_interval_name, TaskEpoch
key = {"nwb_file_name": "RS2120241016_.nwb",}
for k in (TaskEpoch & key).fetch("KEY"):
convert_epoch_interval_name_to_position_interval_name(k)Spyglass solution |
7 tasks
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@MichaelCoulter if you can test the branch for the #1208 PR on another one that hit this error that would be great |
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thanks! i will test this branch. |
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that change didnt work for me. i recreated deleting that line in my own repo and got this error ---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
Cell In[3], line 101
87 pose_estimation_key = (
88 sgp.DLCPoseEstimationSelection().insert_estimation_task(
89 {
(...)
97 )
98 )
100 ##populate DLC Pose Estimation
--> 101 sgp.DLCPoseEstimation().populate(pose_estimation_key)
103 ##start smooth interpolation
104 si_params_name = "just_nan"
File ~/spyglass/src/spyglass/utils/dj_mixin.py:608, in SpyglassMixin.populate(self, *restrictions, **kwargs)
606 if use_transact: # Pass single-process populate to super
607 kwargs["processes"] = processes
--> 608 return super().populate(*restrictions, **kwargs)
609 else: # No transaction protection, use bare make
610 for key in keys:
File ~/mambaforge/envs/spyglass-position/lib/python3.9/site-packages/datajoint/autopopulate.py:241, in AutoPopulate.populate(self, suppress_errors, return_exception_objects, reserve_jobs, order, limit, max_calls, display_progress, processes, make_kwargs, *restrictions)
237 if processes == 1:
238 for key in (
239 tqdm(keys, desc=self.__class__.__name__) if display_progress else keys
240 ):
--> 241 error = self._populate1(key, jobs, **populate_kwargs)
242 if error is not None:
243 error_list.append(error)
File ~/mambaforge/envs/spyglass-position/lib/python3.9/site-packages/datajoint/autopopulate.py:292, in AutoPopulate._populate1(self, key, jobs, suppress_errors, return_exception_objects, make_kwargs)
290 self.__class__._allow_insert = True
291 try:
--> 292 make(dict(key), **(make_kwargs or {}))
293 except (KeyboardInterrupt, SystemExit, Exception) as error:
294 try:
File ~/spyglass/src/spyglass/position/v1/position_dlc_pose_estimation.py:213, in DLCPoseEstimation.make(self, key)
209 """.populate() method will launch training for each PoseEstimationTask"""
210 self.log_path = (
211 Path(infer_output_dir(key=key, makedir=False)) / "log.log"
212 )
--> 213 self._logged_make(key)
File ~/spyglass/src/spyglass/position/v1/dlc_utils.py:198, in file_log.<locals>.decorator.<locals>.wrapper(self, *args, **kwargs)
196 logger.removeHandler(logger.handlers[0])
197 try:
--> 198 return func(self, *args, **kwargs)
199 finally:
200 if not console:
File ~/spyglass/src/spyglass/position/v1/position_dlc_pose_estimation.py:252, in DLCPoseEstimation._logged_make(self, key)
246 creation_time = datetime.fromtimestamp(
247 dlc_result.creation_time
248 ).strftime("%Y-%m-%d %H:%M:%S")
250 logger.info("getting raw position")
251 interval_list_name = (
--> 252 convert_epoch_interval_name_to_position_interval_name(
253 {
254 "nwb_file_name": key["nwb_file_name"],
255 "epoch": key["epoch"],
256 },
257 #populate_missing=False,
258 )
259 )
260 if interval_list_name:
261 spatial_series = (
262 RawPosition()
263 & {**key, "interval_list_name": interval_list_name}
264 ).fetch_nwb()[0]["raw_position"]
File ~/spyglass/src/spyglass/common/common_behav.py:646, in convert_epoch_interval_name_to_position_interval_name(key, populate_missing)
644 if null_entry:
645 pos_query.delete(safemode=False) # no prompt
--> 646 PositionIntervalMap()._no_transaction_make(key)
647 pos_query = PositionIntervalMap & key
649 if pos_query.fetch(pos_str)[0] == "":
File ~/spyglass/src/spyglass/common/common_behav.py:547, in PositionIntervalMap._no_transaction_make(self, key)
545 if len(pos_intervals) == 0:
546 logger.error(f"NO POS INTERVALS FOR {key};\n{no_pop_msg}")
--> 547 self.insert1(null_key, **insert_opts)
548 return
550 valid_times = (IntervalList & key).fetch1("valid_times")
File ~/mambaforge/envs/spyglass-position/lib/python3.9/site-packages/datajoint/table.py:337, in Table.insert1(self, row, **kwargs)
330 def insert1(self, row, **kwargs):
331 """
332 Insert one data record into the table. For ``kwargs``, see ``insert()``.
333
334 :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted
335 as one row.
336 """
--> 337 self.insert((row,), **kwargs)
File ~/mambaforge/envs/spyglass-position/lib/python3.9/site-packages/datajoint/table.py:419, in Table.insert(self, rows, replace, skip_duplicates, ignore_extra_fields, allow_direct_insert)
416 return
418 field_list = [] # collects the field list from first row (passed by reference)
--> 419 rows = list(
420 self.__make_row_to_insert(row, field_list, ignore_extra_fields)
421 for row in rows
422 )
423 if rows:
424 try:
File ~/mambaforge/envs/spyglass-position/lib/python3.9/site-packages/datajoint/table.py:420, in <genexpr>(.0)
416 return
418 field_list = [] # collects the field list from first row (passed by reference)
419 rows = list(
--> 420 self.__make_row_to_insert(row, field_list, ignore_extra_fields)
421 for row in rows
422 )
423 if rows:
424 try:
File ~/mambaforge/envs/spyglass-position/lib/python3.9/site-packages/datajoint/table.py:871, in Table.__make_row_to_insert(self, row, field_list, ignore_extra_fields)
865 attributes = [
866 self.__make_placeholder(name, row[name], ignore_extra_fields)
867 for name in self.heading
868 if name in row.dtype.fields
869 ]
870 elif isinstance(row, collections.abc.Mapping): # dict-based
--> 871 check_fields(row)
872 attributes = [
873 self.__make_placeholder(name, row[name], ignore_extra_fields)
874 for name in self.heading
875 if name in row
876 ]
877 else: # positional
File ~/mambaforge/envs/spyglass-position/lib/python3.9/site-packages/datajoint/table.py:857, in Table.__make_row_to_insert.<locals>.check_fields(fields)
855 for field in fields:
856 if field not in self.heading:
--> 857 raise KeyError(
858 "`{0:s}` is not in the table heading".format(field)
859 )
860 elif set(field_list) != set(fields).intersection(self.heading.names):
861 raise DataJointError("Attempt to insert rows with different fields.")
KeyError: '`epoch` is not in the table heading' |
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@MichaelCoulter what is the value of |
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Ah, I see. The |
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this is the code i am running
and this is the error.
it looks like for a different nwbfile ("RS2120241020_.nwb") there are entries in the 'PositionIntervalMap' table, but i can't seem to populate this table for the nwbfile i am working with now ("RS2120241016_.nwb"). any ideas would be appreciated, thank you.
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