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Merged
ioanalzr merged 2 commits into from
Jun 13, 2025
Merged

Path managing #12

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be83154
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ioanalzr Jun 9, 2025
3c62350
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ioanalzr Jun 9, 2025
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2 changes: 1 addition & 1 deletion beneuro_pose_estimation/anipose/aniposeTools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -666,7 +666,7 @@ def run_pose_estimation(
logging.info(f"Running pose estimation on {session}")
animal = session.split("_")[0]
session_dir = config.predictions3D / animal / session ############
predictions_dir = session_dir / "pose-estimation" # TODO change to pose_estimation
predictions_dir = session_dir / f"{session}_pose_estimation" # TODO change to pose_estimation
predictions_dir.mkdir(parents=True, exist_ok=True)


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28 changes: 14 additions & 14 deletions beneuro_pose_estimation/sleap/sleapTools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -605,7 +605,7 @@ def train_models(cameras=params.default_cameras, custom_labels = False):
labels_file = config.training / camera / f"{camera}.pkg.slp"
config_file = config.training_config

# Check if the .slp file exists; if not, run create_training_file
# Check if the .slp file exists;
if not labels_file.exists():
logging.info(f"{labels_file} does not exist")
return
Expand Down Expand Up @@ -725,9 +725,9 @@ def get_2Dpredictions(
for session in sessions:
animal = session.split("_")[0]
if test_name is not None:
predictions_dir = config.predictions2D / animal / session / "pose-estimation" / "tests" / test_name
predictions_dir = config.predictions2D / animal / session / f"{session}_pose_estimation"/ "tests" / test_name
else:
predictions_dir = config.predictions2D / animal / session / "pose-estimation"
predictions_dir = config.predictions2D / animal / session / f"{session}_pose_estimation"
predictions_dir.mkdir(parents=True, exist_ok=True)
for camera in cameras:
try:
Expand All @@ -741,20 +741,20 @@ def get_2Dpredictions(
f"Predictions file for {session} and camera {camera} already exists, skipping."
)
continue
# input_file = (
# config.recordings
# / animal
# / session
# / f"{session}_cameras"
# # / f"{session}_{params.camera_name_mapping.get(camera, camera)}.avi"
# / f"{params.camera_name_mapping.get(camera, camera)}.avi"
# )
input_file = (
predictions_dir.parent
config.recordings
/ animal
/ session
/ f"{session}_cameras"
# / f"{session}_{params.camera_name_mapping.get(camera, camera)}.avi"
/ f"{params.camera_name_mapping.get(camera, camera)}.avi"
)
# input_file = (
# predictions_dir.parent
# / f"{session}_cameras"
# # / f"{session}_{params.camera_name_mapping.get(camera, camera)}.avi"
# / f"{params.camera_name_mapping.get(camera, camera)}.avi"
# )
if custom_model_name is not None:

model_dir = config.custom_models / camera / f"{camera}_{custom_model_name}"
Expand Down Expand Up @@ -830,11 +830,11 @@ def visualize_predictions(sessions, cameras=params.default_cameras):
if "test" in session:
session_name = session.split("_")[0]+"_"+session.split("_")[1]+"_"+session.split("_")[2]+"_"+session.split("_")[3]+session.split("_")[4]+session.split("_")[5]
predictions_path = (
config.predictions2D/animal/session_name/"pose-estimation"/"tests"/session/"pose-estimation"/camera/ f"{session}_{camera}.slp.predictions.slp"
config.predictions2D/animal/session_name/f"{session_name}_pose_estimation"/"tests"/session/f"{session}_pose_estimation"/camera/ f"{session}_{camera}.slp.predictions.slp"
)
else:
predictions_path = (
config.predictions2D/animal/session/"pose-estimation"/camera/ f"{session}_{camera}.slp.predictions.slp"
config.predictions2D/animal/session/f"{session}_pose_estimation"/camera/ f"{session}_{camera}.slp.predictions.slp"
)
subprocess.run(["sleap-label", predictions_path])
return
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