Draft: update concatenate #43
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…when passing several idtrackerai sessions
…s is (frames, individuals, 2) and not (individuals, frames, 2)
| @@ -58,20 +61,60 @@ def _concatenate_idtrackerai_dicts(traj_dicts): | |||
| """ | |||
| traj_dict_cat = traj_dicts[0].copy() | |||
| traj_cat = _concatenate_np( | |||
| [traj_dict["trajectories"] for traj_dict in traj_dicts] | |||
| [traj_dict["trajectories"] for traj_dict in traj_dicts], **kwargs | |||
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Why do you send **kwargs to _concatenate_np? _concatenate_np only has one positional argument
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Hmm indeed, I think I put it there to be able to change the shape without changing the code. I removed the argument from the function's signature, but the kwargs lived on. Should be removed
| elif os.path.exists(trajectories): | ||
| return trajectories | ||
| else: | ||
| warnings.warn(f"No trajectory found in {session_folder}") |
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I think this should raise an exception in this point (otherwise it would fail outside due to the lack of returned value)
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The tests are now passing on my side, but the CI workflow still fails I think |
| @@ -6,8 +6,7 @@ name: Test and coverage | |||
| on: | |||
| push: | |||
| branches: [ master, develop ] | |||
| pull_request: | |||
| branches: [ master, develop ] | |||
| pull request | |||
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You are missing the underscore here (pull_request)
I think this is because the CI file is not OK (there is an underscore missing #43 (comment)) |
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My bad, fixed! |
| @@ -6,8 +6,7 @@ name: Test and coverage | |||
| on: | |||
| push: | |||
| branches: [ master, develop ] | |||
| pull_request: | |||
| branches: [ master, develop ] | |||
| pull_request | |||
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| pull_request | |
| pull_request: | |
| branches: ['*'] |
Sorry, it seems that this did not do the trick. I suggested a change to see if we can make the tests work and get this merged. Sorry for the confusion! |
| @@ -64,14 +66,54 @@ def _concatenate_idtrackerai_dicts(traj_dicts): | |||
| return traj_dict_cat | |||
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| def from_several_idtracker_files(trajectories_paths, **kwargs): | |||
| def pick_trajectory_file(session_folder): | |||
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Note that during the validation of idtracker.ai trajectories using the validation GUI a trajectory files with a timestamp suffix can be generated (https://github.com/video-annotator/pythonvideoannotator-module-idtrackerai/blob/24866ee28a514a8f1b0a3186800e84280c1d4cd4/pythonvideoannotator_module_idtrackerai/models/video/objects/idtrackerai_object_io.py#L56).
These files won't be considered by this function.
I believe that to make it more general we should check if there are trajectory files with timestamps and take the latest one.
| raise Exception(f"Session {session_folder} has no trajectories") | ||
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| def is_idtrackerai_session(path): |
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I believe it would be more robust to check if it contains a file called video_object.npy.
the pattern session_ could be also used for sessions of experiments and you can end up checking for trajectories in folders that are not needed.
| return re.search("session_.*", path) and os.path.isdir(path) | ||
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| def get_trajectories(idtrackerai_collection_folder): | ||
| """Return a list of all trajectory files available in an idtrackerai collection folder |
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Maybe be more specific about what an idtrackerai collection folder is:
Is this a folder that contains subfolders with videos and other session_ subfolders?
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Yes, that is how I am organizing my data. In other words, it is an imgstore.VideoImgStore where several session_ folders are also present.
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Hi, it seems that black is failing. It can be the same issue of having old versions. I recommend installing using pip or conda in your environment. Please note that you can always see the versions installed during the tests in the test log: |
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