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New PyTorch DeepLabCut SuperAnimal demo notebook by yeshaokai · Pull Request #2629 · DeepLabCut/DeepLabCut · GitHub
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New PyTorch DeepLabCut SuperAnimal demo notebook #2629

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Merged
n-poulsen merged 25 commits into from
Jul 19, 2024
Merged

New PyTorch DeepLabCut SuperAnimal demo notebook #2629

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70a0155
spatial pyramid for video adaptation by default, with a small range o…
yeshaokai Apr 6, 2023
8441909
Update test_crossvalutils.py
yeshaokai Apr 20, 2023
0e20e8d
Merge branch 'DeepLabCut:main' into master
yeshaokai Apr 25, 2023
d5febb1
Handled empty prediction
yeshaokai Apr 25, 2023
f32d317
Removed unused parameter. Updated config to use superanimal instead o…
May 23, 2023
7949045
Merge branch 'DeepLabCut:main' into master
yeshaokai May 31, 2023
d531e80
Merge branch 'DeepLabCut:main' into master
yeshaokai Jul 30, 2023
768296c
Merge branch 'DeepLabCut:main' into master
yeshaokai Jun 20, 2024
882f920
Added notebook for superanimal pytorch
yeshaokai Jun 20, 2024
4be4a70
Update COLAB_Pytorch_SuperAnimal.ipynb
MMathisLab Jun 20, 2024
ed8a979
Update COLAB_Pytorch_SuperAnimal.ipynb
MMathisLab Jun 20, 2024
624134b
Update COLAB_Pytorch_SuperAnimal.ipynb
MMathisLab Jun 20, 2024
7c123b3
Merge branch 'pytorch_dlc' into shaokai/educational_superanimal_notebook
Jun 26, 2024
d68a137
cleaned notebook and added bbox_threshold to analyze_superanimal_images
Jun 26, 2024
830f4ac
worked on superanimal notebook
Jul 2, 2024
66acb3d
fixed symlink creation for keypoint matching
Jul 4, 2024
ba39fd5
renamed COLAB to YOURDATA
Jul 4, 2024
24cc195
fixed some bugs and cleaned the notebook. added more print statements…
Jul 4, 2024
c99a199
installed latest version of DeepLabCut instead of from pypi
Jul 4, 2024
f59dc69
changed default training parameters
Jul 4, 2024
3877be3
added option to not have use symlinks for keypoint matching
Jul 4, 2024
97bb2a1
no symlinks for keypoint matching in COLAB
Jul 4, 2024
67903f0
set default eval interval to 10, add superanimal_analyze_images to init
Jul 4, 2024
faba3ac
do not copy images or create symlinks for memory replay
Jul 4, 2024
27a58af
fixed memory replay to only run once
Jul 9, 2024
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changed default training parameters
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Niels Poulsen
Niels Poulsen committed Jul 4, 2024
commit f59dc69eaf2c2ca2b3cbe5c8286f8192836d0f38
39 changes: 21 additions & 18 deletions examples/COLAB/COLAB_YOURDATA_SuperAnimal.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -545,7 +545,7 @@
"Historically, the transfer learning using ImageNet weights strategies assumed no “animal pose task priors” in the pretrained\n",
"model, a paradigm adopted from previous task-agnostic transfer learning.\n",
"\n",
"You can change the number of epochs you want to train for. Training on the Tri-Mouse dataset for 10 epochs should take about 3 minutes on a T4 GPU. To fully train the model, you should aim for 150 epochs (about 45 minutes)."
"You can change the number of epochs you want to train for. How long training will take depends on many parameters, including the number of images in your dataset, the resolution of the images, and the number of epochs you train for."
]
},
{
Expand Down Expand Up @@ -585,10 +585,11 @@
"deeplabcut.train_network(\n",
" config_path,\n",
" detector_epochs=0,\n",
" epochs=1,\n",
" display_iters=1,\n",
" save_epochs=1,\n",
" batch_size=4,\n",
" epochs=50,\n",
" save_epochs=10,\n",
" eval_interval=10,\n",
" batch_size=64, # if you get a CUDA OOM error when training on a GPU, reduce to 32, 16, ...!\n",
" display_iters=10,\n",
" shuffle=imagenet_transfer_learning_shuffle,\n",
")"
]
Expand Down Expand Up @@ -717,9 +718,11 @@
"deeplabcut.train_network(\n",
" config_path,\n",
" detector_epochs=0,\n",
" epochs=1,\n",
" batch_size=4, # if you get a CUDA OOM error when training on a GPU, reduce to 32, 16, ...!\n",
" display_iters=1,\n",
" epochs=50,\n",
" save_epochs=10,\n",
" eval_interval=10,\n",
" batch_size=64, # if you get a CUDA OOM error when training on a GPU, reduce to 32, 16, ...!\n",
" display_iters=10,\n",
" shuffle=superanimal_transfer_learning_shuffle,\n",
")"
]
Expand Down Expand Up @@ -938,11 +941,11 @@
"deeplabcut.train_network(\n",
" config_path,\n",
" detector_epochs=0,\n",
" epochs=1,\n",
" save_epochs=1,\n",
" eval_interval=1,\n",
" batch_size=4,\n",
" display_iters=1,\n",
" epochs=50,\n",
" save_epochs=10,\n",
" eval_interval=10,\n",
" batch_size=64, # if you get a CUDA OOM error when training on a GPU, reduce to 32, 16, ...!\n",
" display_iters=10,\n",
" shuffle=superanimal_naive_finetune_shuffle,\n",
")"
]
Expand Down Expand Up @@ -1069,11 +1072,11 @@
"deeplabcut.train_network(\n",
" config_path,\n",
" detector_epochs=0,\n",
" epochs=1,\n",
" save_epochs=1,\n",
" eval_interval=1,\n",
" batch_size=4, # if you get a CUDA OOM error when training on a GPU, reduce to 32, 16, ...!\n",
" display_iters=1,\n",
" epochs=50,\n",
" save_epochs=10,\n",
" eval_interval=10,\n",
" batch_size=64, # if you get a CUDA OOM error when training on a GPU, reduce to 32, 16, ...!\n",
" display_iters=10,\n",
" shuffle=superanimal_memory_replay_shuffle,\n",
")"
]
Expand Down