diff --git a/.github/workflows/model.yml b/.github/workflows/model.yml new file mode 100644 index 00000000..18328d05 --- /dev/null +++ b/.github/workflows/model.yml @@ -0,0 +1,58 @@ +name: Model Training + +on: + pull_request: + +jobs: + build: + + runs-on: self-hosted + container: + image: docker://ghcr.io/iterative/cml:0-dvc2-base1-gpu + volumes: + - /home/runner/work/_temp/_github_home:/root + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python 3.11 + uses: actions/setup-python@v4 + with: + python-version: "3.11" + cache: 'pip' + + - name: Install via exported requirements.txt + run: | + python -m pip install --upgrade pip + python -m pip install flake8 pytest poetry + poetry export --with dev --without-hashes -o requirements.txt + pip3 install -r requirements.txt + pip3 install torch torchvision torchaudio + + - name: Set up gcloud + id: 'auth' + uses: 'google-github-actions/auth@v1' + with: + credentials_json: '${{ secrets.FRDC_DOWNLOAD_KEY }}' + + - name: Set up Cloud SDK + uses: 'google-github-actions/setup-gcloud@v1' + + - name: Set up WandB + run: | + echo "WANDB_API_KEY=${{ secrets.WANDB_API_KEY }}" >> $GITHUB_ENV + + - name: Add src as PYTHONPATH + run: | + echo "PYTHONPATH=src" >> $GITHUB_ENV + + - name: Run Model Training + run: | + python3 -m tests.model_tests.chestnut_dec_may.main + + - name: Comment results via CML + run: | + cml comment update \ + --target=pr \ + --token ${{ secrets.GITHUB_TOKEN }} \ + tests/model_tests/chestnut_dec_may/report.md \ No newline at end of file diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index b80d5419..ac8f5c54 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -4,9 +4,11 @@ name: Python CI on: - push: - branches: [ "main" ] - pull_request: + workflow_dispatch: + +# push: +# branches: [ "main" ] +# pull_request: jobs: build: diff --git a/pipeline/model_tests/chestnut_dec_may/__init__.py b/pipeline/model_tests/chestnut_dec_may/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/poetry.lock b/poetry.lock index c863d7fe..a3f10105 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand. 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b/tests/model_tests/chestnut_dec_may/augmentation.py similarity index 100% rename from pipeline/model_tests/chestnut_dec_may/augmentation.py rename to tests/model_tests/chestnut_dec_may/augmentation.py diff --git a/pipeline/model_tests/chestnut_dec_may/confusion_matrix.png b/tests/model_tests/chestnut_dec_may/confusion_matrix.png similarity index 100% rename from pipeline/model_tests/chestnut_dec_may/confusion_matrix.png rename to tests/model_tests/chestnut_dec_may/confusion_matrix.png diff --git a/pipeline/model_tests/chestnut_dec_may/evaluate.py b/tests/model_tests/chestnut_dec_may/evaluate.py similarity index 91% rename from pipeline/model_tests/chestnut_dec_may/evaluate.py rename to tests/model_tests/chestnut_dec_may/evaluate.py index 5ecebdc6..0cc245cd 100644 --- a/pipeline/model_tests/chestnut_dec_may/evaluate.py +++ b/tests/model_tests/chestnut_dec_may/evaluate.py @@ -7,8 +7,8 @@ from frdc.train import FRDCDataModule from frdc.train import FRDCModule -from pipeline.model_tests.chestnut_dec_may.preprocess import preprocess -from pipeline.model_tests.utils import get_dataset +from .preprocess import preprocess +from tests.model_tests.utils import get_dataset # Get our Test # TODO: Ideally, we should have a separate dataset for testing. diff --git a/pipeline/model_tests/chestnut_dec_may/le.npy b/tests/model_tests/chestnut_dec_may/le.npy similarity index 100% rename from pipeline/model_tests/chestnut_dec_may/le.npy rename to tests/model_tests/chestnut_dec_may/le.npy diff --git a/pipeline/model_tests/chestnut_dec_may/main.py b/tests/model_tests/chestnut_dec_may/main.py similarity index 70% rename from pipeline/model_tests/chestnut_dec_may/main.py rename to tests/model_tests/chestnut_dec_may/main.py index 36bf9a87..9aa6f1ca 100644 --- a/pipeline/model_tests/chestnut_dec_may/main.py +++ b/tests/model_tests/chestnut_dec_may/main.py @@ -3,6 +3,7 @@ This test is done by training a model on the 20201218 dataset, then testing on the 20210510 dataset. """ +from pathlib import Path import lightning as pl import numpy as np @@ -16,19 +17,30 @@ from frdc.models import FaceNet from frdc.train import FRDCDataModule, FRDCModule -from pipeline.model_tests.chestnut_dec_may.augmentation import augmentation -from pipeline.model_tests.chestnut_dec_may.preprocess import preprocess -from pipeline.model_tests.utils import get_dataset +from tests.model_tests.chestnut_dec_may.augmentation import augmentation +from tests.model_tests.chestnut_dec_may.preprocess import preprocess +from tests.model_tests.utils import get_dataset +from lightning.pytorch.loggers import WandbLogger +import wandb +assert wandb.run is None -def train_val_test_split(x: TensorDataset) -> list[Dataset, Dataset, Dataset]: +wandb.setup(wandb.Settings(program=__name__, program_relpath=__name__)) +run = wandb.init() +logger = WandbLogger(name="chestnut_dec_may", project="frdc") + + +def train_val_test_split( + x: TensorDataset, +) -> list[Dataset, Dataset, Dataset]: # Defines how to split the dataset into train, val, test subsets. # TODO: Quite ugly as it uses the global variables segments_0 and # segments_1. Will need to refactor this. return [ Subset(x, list(range(len(segments_0)))), Subset( - x, list(range(len(segments_0), len(segments_0) + len(segments_1))) + x, + list(range(len(segments_0), len(segments_0) + len(segments_1))), ), [], ] @@ -40,12 +52,13 @@ def train_val_test_split(x: TensorDataset) -> list[Dataset, Dataset, Dataset]: "chestnut_nature_park", "20210510", "90deg43m85pct255deg/map" ) + # Concatenate the datasets segments = [*segments_0, *segments_1] labels = [*labels_0, *labels_1] BATCH_SIZE = 5 -EPOCHS = 100 +# EPOCHS = 100 LR = 1e-3 # Prepare the datamodule and trainer @@ -65,10 +78,13 @@ def train_val_test_split(x: TensorDataset) -> list[Dataset, Dataset, Dataset]: ) trainer = pl.Trainer( - max_epochs=EPOCHS, + max_epochs=1, # Set the seed for reproducibility + fast_dev_run=True, # TODO: Though this is set, the results are still not reproducible. deterministic=True, + # fast_dev_run=True, + accelerator="cpu", log_every_n_steps=4, callbacks=[ # Stop training if the validation loss doesn't improve for 4 epochs @@ -78,11 +94,13 @@ def train_val_test_split(x: TensorDataset) -> list[Dataset, Dataset, Dataset]: # Save the best model ModelCheckpoint(monitor="val_loss", mode="min", save_top_k=1), ], + logger=logger, ) m = FRDCModule( # Our model is the "FaceNet" model - # TODO: It's not really the FaceNet model, but a modified version of it. + # TODO: It's not really the FaceNet model, + # but a modified version of it. model_cls=FaceNet, model_kwargs=dict(n_out_classes=len(set(labels))), # We use the Adam optimizer @@ -94,3 +112,15 @@ def train_val_test_split(x: TensorDataset) -> list[Dataset, Dataset, Dataset]: trainer.fit(m, datamodule=dm) # TODO: Quite hacky, but we need to save the label encoder for prediction. np.save("le.npy", dm.le.classes_) + +report = f""" +# Chestnut Nature Park (Dec 2020 vs May 2021) +[WandB Report]({run.get_url()}) +""" + + +with open(Path(__file__).parent / "report.md", "w") as f: + f.write(report) + + +wandb.finish() diff --git a/pipeline/model_tests/chestnut_dec_may/preprocess.py b/tests/model_tests/chestnut_dec_may/preprocess.py similarity index 80% rename from pipeline/model_tests/chestnut_dec_may/preprocess.py rename to tests/model_tests/chestnut_dec_may/preprocess.py index 8909c19b..090b7b9d 100644 --- a/pipeline/model_tests/chestnut_dec_may/preprocess.py +++ b/tests/model_tests/chestnut_dec_may/preprocess.py @@ -1,10 +1,12 @@ import numpy as np import torch -from glcm_cupy import Features + +# from glcm_cupy import Features from torchvision.transforms.v2 import Resize from frdc.models import FaceNet -from frdc.preprocess.glcm_padded import append_glcm_padded_cached + +# from frdc.preprocess.glcm_padded import append_glcm_padded_cached from frdc.preprocess.scale import scale_normal_per_band, scale_0_1_per_band @@ -24,16 +26,17 @@ def segment_preprocess(ar: np.ndarray) -> torch.Tensor: # Add a small epsilon to avoid upper bound of 1.0 ar = scale_0_1_per_band(ar, epsilon=0.001) - ar = append_glcm_padded_cached( - ar, - step_size=7, - bin_from=1, - bin_to=128, - radius=3, - features=(Features.MEAN,), - ) - # We can then scale normal for better neural network convergence + # ar = append_glcm_padded_cached( + # ar, + # step_size=7, + # bin_from=1, + # bin_to=128, + # radius=3, + # features=(Features.MEAN,), + # ) + # # We can then scale normal for better neural network convergence ar = scale_normal_per_band(ar) + ar = np.rollaxis(ar, axis=2) # TODO: Doesn't seem like we have any channel preprocessing here. # ar = np.stack([ diff --git a/pipeline/model_tests/utils.py b/tests/model_tests/utils.py similarity index 100% rename from pipeline/model_tests/utils.py rename to tests/model_tests/utils.py