rlizzo / lightning-pose Goto Github PK

Convolutional Networks for pose tracking implemented in Pytorch Lightning, supporting massively accelerated training on unlabeled videos using NVIDIA DALI.

• pytorch-lightning for multiple-GPU training and to minimize boilerplate code
• nvidia-DALI for accelerated GPU dataloading
• Hydra to orchestrate the config files and log experiments
• kornia for differntiable computer vision ops
• torchtyping for type and shape assertions of torch tensors
• FiftyOne for visualizing model predictions
• Tensorboard to visually diagnoze training performance

Your (potentially remote) machine has a Linux operating system, at least one GPU and CUDA 11 installed. This is a requirement for NVIDIA DALI.

First create a Conda environment in which this package and its dependencies will be installed. As you would do for any other repository --

Create a conda environment:

foo@bar:~$ conda create --name <YOUR_ENVIRONMENT_NAME>

and activate it:

foo@bar:~$ conda activate <YOUR_ENVIRONMENT_NAME>

Move into the folder where you want to place the repository folder, and then download it from GitHub:

foo@bar:~$ cd <SOME_FOLDER>
foo@bar:~$ git clone https://github.com/danbider/lightning-pose.git

Then move into the newly-created repository folder, and install dependencies:

foo@bar:~$ cd lightning-pose
foo@bar:~$ pip install -r requirements.txt

You should be ready to go! You may verify that all the unit tests are passing on your machine by running

foo@bar:~$ pytest

NEEDS UPDATE

• BaseDataset: images + keypoint coordinates.
• HeatmapDataset: images + heatmaps.
• SemiSupervisedDataset: images + sequences of unlabeled videos + heatmaps.

NEEDS UPDATE

• RegressionTracker: images -> labeled keypoint coordinates.
• HeatmapTracker: images -> labeled heatmaps.
• SemiSupervisedHeatmapTracker: images + sequences of unlabeled videos -> labeled heatmaps + unlabeled heatmaps. Supports multiple losses on the unlabeled videos.

For all of the scripts in our scripts folder, we rely on hydra to manage arguments in hierarchical config files. You have two options: edit the config file, or override it from the command line.

• Edit a hydra config, that is, any of the files in scripts/configs/config_folder/config_name.yaml, and save it. Then run the script without arguments, e.g.,:

foo@bar:~$ python scripts/train_hydra.py

• Override the argument from the command line:

foo@bar:~$ python scripts/train_hydra.py training.max_epochs=11

If you happen to want to use a maximum of 11 epochs instead the default number (not recommended).

foo@bar:~$ python scripts/train_hydra.py

The outputs of the training script, namely the model checkpoints and Tensorboard logs, will be saved at the lightning-pose/outputs/YYYY-MM-DD/HH-MM-SS/tb_logs directory.

To view the logged losses with tensorboard in your browser, in the command line, run:

foo@bar:~$ tensorboard --logdir outputs/YYYY-MM-DD/

where you use the date in which you ran the model. Click on the provided link in the terminal, which will look something like http://localhost:6006/. Note that if you save the model at a different directory, just use that directory after --logdir.

You can visualize the predictions of one or multiple trained models on the train/test/val images using the FiftyOne app.

You will need to specify:

1. eval.hydra_paths: path to trained models to use for prediction.

Generally, using Hydra we can either edit the config .yaml files or override them from the command line. The argument of ineterest is `

Edit scripts/configs/eval/eval_params.yaml like so:

hydra_paths: [
"YYYY-MM-DD/HH-MM-SS/", "YYYY-MM-DD/HH-MM-SS/",
]

where you specify the relative paths for hydra folders within the lightning-pose/outputs folder. Then from command line, run:

foo@bar:~$ python scripts/launch_diagnostics.py

Alternatively, override from the command line:

foo@bar:~$ python scripts/launch_diagnostics.py eval.hydra_paths=["YYYY-MM-DD/HH-MM-SS/"] \
data.data_dir='/absolute/path/to/data_dir' \
data.video_dir='/absolute/path/to/video_dir' 

As with Tensorboard, click on the link provided in the terminal to launch the diagnostics in your browser.

The app will open and will show FRAME LABELS to the left. Click the v next to it. It will drop down a menu with keypoint names, and a filter with confidence. Play around with these. Once you're happy, you can click on the orange bookmark icon to save the filters you applied. Then from code, you can call session.view.export(...). NOTE: not yet supported.

With a trained model and a path to a new video, you can generate predictions for each frame and save it as a .csv or .h5 file. To do so for the example dataset, run:

foo@bar:~$ python scripts/predict_new_vids.py eval.hydra_paths=["YYYY-MM-DD/HH-MM-SS/"]

using the same hydra path as before.

In order to use this script more generally, you need to specify several paths:

1. eval.hydra_paths: path to models to use for prediction
2. eval.test_videos_directory: path to a folder with new videos (not a single video)
3. eval.saved_vid_preds_dir: optional path specifying where to save prediction csv files. If null, the predictions will be saved in eval.test_videos_directory.

As above, you could directly edit scripts/configs/eval/eval_params.yaml and run

foo@bar:~$ python scripts/predict_new_vids.py 

or override these arguments in the command line.

foo@bar:~$ python scripts/predict_new_vids.py eval.hydra_paths=["2022-01-18/01-03-45"] \
eval.test_videos_directory="/absolute/path/to/unlabeled_videos" \
eval.saved_vid_preds_dir="/absolute/path/to/dir"

With the pose predictions output by the previous step, you can now overlay these predictions on the video. To do so for the example dataset, run:

foo@bar:~$ python scripts/render_labeled_vids.py eval.model_display_names=["test_model"] \
data.data_dir="/absolute/path/to/data_dir" \
eval.video_file_to_plot="/absolute/path/to/vid.mp4" \
eval.pred_csv_files_to_plot:["/absolute/path/1/to.csv", "/absolute/path/1/to.csv"]

using the same hydra path as before. This script will by default save a labeled video in the same directory as the video it analyzes, and will also launch the fiftyone app to further explore the video(s) in the browser.