notes

src/fox_lab_to_nwb/behavior.py

@@ -19,8 +19,8 @@ def add_to_nwbfile(
     ) -> None:
 
         mat = read_mat(self.file_path)
-        rec_struct = mat["rec"]
-        daq_struct = rec_struct["daq"]
+        recording_structure = mat["rec"]
+        daq_struct = recording_structure["daq"]
 
         timestamps = daq_struct["tstamps"]
 

src/fox_lab_to_nwb/conversion_notes.md

@@ -4,10 +4,28 @@ Point-person: Amy Streets (axs2909@case.edu) and Kris Lea (kxl786@case.edu)
 
 https://sites.google.com/site/cwrufoxlab/people
 
+Paper is still not out, but according to the authors it should be similar to this one:
+
+https://www.biorxiv.org/content/10.1101/2024.03.13.583703v1
+
+The data is available here:
+
+
+
 ## Trial structure
 
-Organized with folder hierarchy, with one folder for all trials of a single type/cross containing individual trial folders (ex. \Tshx18D07\Tshx18D07_240124_115923_f3_r1 where the cross is Tsh x 18D07 lines, the individual trial folder is “cross” _ “date” _ “time” _ “fly number” _ “trial repeat number”).
+Folder name:
+- Tshx18D07_240124_115923_f3_r1
+
+Info here:
+Tshx18D07 = cross
+240124 = date
+115923 = time
+f3 = fly number
+r1 = trial repeat number
+
 
+Organized with folder hierarchy, with one folder for all trials of a single type/cross containing individual trial folders (ex. \Tshx18D07\Tshx18D07_240124_115923_f3_r1 where the 
 
 # DeepLabCut output files
 config files missing but Video and DLC output files are available
@@ -81,16 +99,17 @@ Not yet available
 ### Tshx18D07_240124_115923_f3_r1.fly2
 This is supposed to be a struct with DAQ data and the wingbeat analysis. Can't open it with matlab online unless extension is changed to .mat
 
-Channel names:
+  Channel names:
 - CamSync
 - CamTrigger
 - OptoTrigger
 - LWingBeatAmp
 - RWingBeatAmp
 - WingBeatFreq
-- LHutchen  # What does Hutchen mean? Could be halteres?
+- LHutchen  
 - RHutchen
 - PTrigger
+- WindTrigger
 
 These can't be extracted with pyton from matlab because they are strings. Are they always the same order?
 

src/fox_lab_to_nwb/metadata.yaml

@@ -13,8 +13,9 @@ NWBFile:
   experimenter:
     - Streets, Amy
     - Lea, Kriss
+    - Fox, Jessica
   surgery: TBD
 Subject:
-  sex: M
-  species: Drosophila melanogaster  # TODO: Figure this one out
+  sex: F
+  species: Drosophila melanogaster
   description: fly

src/fox_lab_to_nwb/streets_conversion.py

@@ -12,18 +12,18 @@
 from fox_lab_to_nwb.behavior import BehaviorInterface
 
 
-def run_trial_conversion(trial_data_folder: Path, output_dir_path: Optional[Path] = None, verbose: bool = True):
+def run_trial_conversion(trial_folder_path: Path, output_dir_path: Optional[Path] = None, verbose: bool = True):
 
     if verbose:
         start_time = time.time()
 
     if output_dir_path is None:
         output_dir_path = Path.home() / "conversion_nwb"
 
-    # Parse metadta from the trial_data_folder name
+    # Parse metadta from the trial_folder_path name
     # Define the correct parsing pattern
     pattern = r"{cross}_{date}_{time}_f{fly_number}_r{trial_repeat_number}"
-    parsed_metadata = parse.parse(pattern, trial_data_folder.name)
+    parsed_metadata = parse.parse(pattern, trial_folder_path.name)
 
     trial_repeat_number = parsed_metadata["trial_repeat_number"]
     cross = parsed_metadata["cross"]  # TODO, where in subject metadata should this be? Example Tshx18D07
@@ -39,46 +39,43 @@ def run_trial_conversion(trial_data_folder: Path, output_dir_path: Optional[Path
     # Behavior interface
     format = "fly2"  # Authors said in email this might change
     daq_file_name = f"{cross}_{session_date}_{session_time}_f{fly_number}_r{trial_repeat_number}.{format}"
-    file_path = trial_data_folder / daq_file_name
+    file_path = trial_folder_path / daq_file_name
     behavior_interface = BehaviorInterface(file_path=file_path)
 
     # Video Interface
     # TODO: are the names of the video files always the same per trial? we need
     # More trials to find out
 
     side_cam_name = "SideCam_000000.avi"
-    file_path = trial_data_folder / side_cam_name
+    file_path = trial_folder_path / side_cam_name
     side_cam_interface = VideoInterface(file_paths=[file_path], metadata_key_name="SideCam")
 
     top_camera_name = "TOPCAM_000000.avi"
-    file_path = trial_data_folder / top_camera_name
+    file_path = trial_folder_path / top_camera_name
 
     top_cam_interface = VideoInterface(file_paths=[file_path], metadata_key_name="TopCam")
 
-    # TODO: this is my name, see how authors refer to this camera
-    back_camera_name = "XZ_1_186.mp4"
+    haltere_camera_name = "XZ_1_186.mp4"
 
-    file_path = trial_data_folder / back_camera_name
-    back_cam_interface = VideoInterface(file_paths=[file_path], metadata_key_name="BackCam")
+    file_path = trial_folder_path / haltere_camera_name
+    haltere_cam_interface = VideoInterface(file_paths=[file_path], metadata_key_name="BackCam")
 
     # DLC interface
-
     top_cam_dlc_file_name = "TOPCAM_000000DLC_resnet50_antennatrackingMar11shuffle1_100000.h5"
+    top_cam_file_path = trial_folder_path / top_cam_dlc_file_name
+    top_cam_dlc_interface = DeepLabCutInterface(file_path=top_cam_file_path)
 
-    file_path = trial_data_folder / top_cam_dlc_file_name
-    top_cam_dlc_interface = DeepLabCutInterface(file_path=file_path)
-
-    back_cam_dlc_file_name = "XZ_1_186DLC_resnet50_haltereMar13shuffle1_100000.h5"
-    file_path = trial_data_folder / back_cam_dlc_file_name
-    back_cam_dlc_interface = DeepLabCutInterface(file_path=file_path)
+    haltere_cam_dlc_file_name = "XZ_1_186DLC_resnet50_haltereMar13shuffle1_100000.h5"
+    halter_cam_file_path = trial_folder_path / haltere_cam_dlc_file_name
+    haltere_cam_dlc_interface = DeepLabCutInterface(file_path=halter_cam_file_path)
 
     data_interface = {
         "Behavior": behavior_interface,
         "SideCam": side_cam_interface,
         "TopCam": top_cam_interface,
-        "BackCam": back_cam_interface,
+        "BackCam": haltere_cam_interface,
         "DeepLabCutTopCam": top_cam_dlc_interface,
-        "DLCBackCamDlc": back_cam_dlc_interface,
+        "DeepLabCutHalterCam": haltere_cam_dlc_interface,
     }
 
     converter = ConverterPipe(data_interfaces=data_interface)
@@ -101,7 +98,7 @@ def run_trial_conversion(trial_data_folder: Path, output_dir_path: Optional[Path
     # Run conversion, this adds the basic data to the NWBFile
     conversion_options = {
         "DeepLabCutTopCam": {"container_name": "PoseEstimationTopCam"},
-        "DLCBackCamDlc": {"container_name": "PoseEstimationBackCam"},
+        "DeepLabCutHalterCam": {"container_name": "PoseEstimationHaltereCam"},
     }
 
     converter.run_conversion(
@@ -127,7 +124,7 @@ def run_trial_conversion(trial_data_folder: Path, output_dir_path: Optional[Path
     verbose = True
     data_path = Path("/home/heberto/cohen_project/Sample data/Fox Lab")
     assert data_path.exists(), f"Folder {data_path} does not exist"
-    trial_data_folder = data_path / "Tshx18D07_240124_115923_f3_r1"
-    assert trial_data_folder.exists(), f"Folder {trial_data_folder} does not exist"
+    trial_folder_path = data_path / "Tshx18D07_240124_115923_f3_r1"
+    assert trial_folder_path.exists(), f"Folder {trial_folder_path} does not exist"
 
-    run_trial_conversion(trial_data_folder=trial_data_folder, verbose=verbose)
+    run_trial_conversion(trial_folder_path=trial_folder_path, verbose=verbose)