Bug/pull behavior items (#200)

* Option to add stim table to modality formatted files.

* Opt. to write stim table to modality directory and compute fps from behavior sessions.

src/aind_metadata_mapper/mesoscope/models.py

@@ -18,6 +18,9 @@ class JobSettings(BaseJobSettings):
     input_source: Path = Field(..., title="Path to the input source")
     session_id: str = Field(..., title="ID of the session")
     behavior_source: Path = Field(..., title="Path to the behavior source")
+    make_camsitm_dir: bool = Field(
+        default=False, title="Make camsitm directory"
+    )
     output_directory: Path = Field(..., title="Path to the output directory")
     session_start_time: datetime = Field(
         ..., title="Start time of the session"

src/aind_metadata_mapper/mesoscope/session.py

@@ -55,10 +55,16 @@ def __init__(self, job_settings: Union[JobSettings, str]):
             job_settings_model.behavior_source = Path(
                 job_settings_model.behavior_source
             )
+        camstim_output = job_settings_model.output_directory
+        if job_settings_model.make_camsitm_dir:
+            camstim_output = (
+                job_settings_model.output_directory
+                / f"{job_settings_model.session_id}_behavior"
+            )
         super().__init__(job_settings=job_settings_model)
         camstim_settings = CamstimSettings(
             input_source=self.job_settings.input_source,
-            output_directory=self.job_settings.output_directory,
+            output_directory=camstim_output,
             session_id=self.job_settings.session_id,
             subject_id=self.job_settings.subject_id,
         )

src/aind_metadata_mapper/open_ephys/utils/pkl_utils.py

@@ -66,7 +66,13 @@ def get_fps(pkl):
         fps.
 
     """
-    return pkl["fps"]
+    if not pkl.get("fps"):
+        fps = round(
+            1 / np.mean(pkl["items"]["behavior"]["intervalsms"]) * 0.001, 2
+        )
+    else:
+        fps = pkl["fps"]
+    return fps
 
 
 def get_pre_blank_sec(pkl):

src/aind_metadata_mapper/stimulus/camstim.py

@@ -65,15 +65,12 @@ def __init__(
         self.input_source = Path(self.camstim_settings.input_source)
         session_id = self.camstim_settings.session_id
         self.pkl_path = next(self.input_source.rglob("*.pkl"))
+        if not self.camstim_settings.output_directory.is_dir():
+            self.camstim_settings.output_directory.mkdir(parents=True)
         self.stim_table_path = (
-            self.pkl_path.parent / f"{session_id}_stim_table.csv"
+            self.camstim_settings.output_directory
+            / f"{session_id}_stim_table.csv"
         )
-        if self.camstim_settings.output_directory:
-            self.stim_table_path = (
-                self.camstim_settings.output_directory
-                / f"{session_id}_behavior"
-                / f"{session_id}_stim_table.csv"
-            )
         self.pkl_data = pkl.load_pkl(self.pkl_path)
         self.fps = pkl.get_fps(self.pkl_data)
         self.session_start, self.session_end = self._get_sync_times()