diff --git a/.dvc/.gitignore b/.dvc/.gitignore new file mode 100644 index 00000000..528f30c7 --- /dev/null +++ b/.dvc/.gitignore @@ -0,0 +1,3 @@ +/config.local +/tmp +/cache diff --git a/.dvc/config b/.dvc/config new file mode 100644 index 00000000..520625c6 --- /dev/null +++ b/.dvc/config @@ -0,0 +1,6 @@ +[core] + remote = frdc-ds + autostage = true +['remote "frdc-ds"'] + url = gs://frdc-ds/ + version_aware = true diff --git a/.dvcignore b/.dvcignore new file mode 100644 index 00000000..51973055 --- /dev/null +++ b/.dvcignore @@ -0,0 +1,3 @@ +# Add patterns of files dvc should ignore, which could improve +# the performance. Learn more at +# https://dvc.org/doc/user-guide/dvcignore diff --git a/.github/workflows/python-package.yml b/.github/workflows/basic-tests.yml similarity index 96% rename from .github/workflows/python-package.yml rename to .github/workflows/basic-tests.yml index d29a0611..10cbf393 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/basic-tests.yml @@ -38,6 +38,7 @@ jobs: python -m pip install flake8 pytest poetry poetry export --with dev --without-hashes -o requirements.txt pip install -r requirements.txt + pip install torch torchaudio torchvision lightning - name: Lint with flake8 run: | diff --git a/.github/workflows/model.yml b/.github/workflows/model-tests.yml similarity index 79% rename from .github/workflows/model.yml rename to .github/workflows/model-tests.yml index 902848da..c61342aa 100644 --- a/.github/workflows/model.yml +++ b/.github/workflows/model-tests.yml @@ -2,6 +2,9 @@ name: Model Training on: pull_request: + branches: ['main'] + workflow_dispatch: + jobs: build: @@ -12,7 +15,9 @@ jobs: volumes: - /home/runner/work/frdc-ml/_github_home:/root env: + # This is where setup-python will install and cache the venv AGENT_TOOLSDIRECTORY: "/root/venv" + options: --gpus all steps: - uses: actions/checkout@v3 @@ -34,7 +39,10 @@ jobs: pip3 install -r requirements.txt pip3 install torch torchvision torchaudio - - name: Set up gcloud + - name: Check CUDA is available + run: nvidia-smi + + - name: Auth gcloud id: 'auth' uses: 'google-github-actions/auth@v1' with: @@ -47,13 +55,15 @@ jobs: run: | echo "WANDB_API_KEY=${{ secrets.WANDB_API_KEY }}" >> $GITHUB_ENV + # Our project has src as a source path, explicitly add that in. - name: Add src as PYTHONPATH run: | echo "PYTHONPATH=src" >> $GITHUB_ENV + # Do not do cd as it'll break PYTHONPATH. - name: Run Model Training run: | - python3 -m tests.model_tests.chestnut_dec_may.main + python3 -m tests.model_tests.chestnut_dec_may.train - name: Comment results via CML run: | diff --git a/.gitignore b/.gitignore index 2c949384..4fcff576 100644 --- a/.gitignore +++ b/.gitignore @@ -165,4 +165,8 @@ cython_debug/ rsc/**/*.tif **/*/lightning_logs -*.zip \ No newline at end of file +*.zip +*.sh +*.ckpt +/rsc +**/wandb/ diff --git a/poetry.lock b/poetry.lock index a3f10105..39ed7d6a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,126 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand. - 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-[[tool.poetry.source]] -name = "pytorch" -url = "https://download.pytorch.org/whl/cu121" -priority = "explicit" - +#torch = {version="^2.1.0", source="pytorch"} +#torchvision = {version="^0.16.0", source="pytorch"} +#torchaudio = {version="^2.1.0", source="pytorch"} +#lightning = "^2.0.9.post0" [tool.poetry.group.dev.dependencies] -torch = "^2.1.0" -torchvision = "^0.16.0" -torchaudio = "^2.1.0" -lightning = "^2.0.9.post0" pytest = "^7.4.2" pre-commit = "^3.5.0" black = "^23.10.0" @@ -37,6 +31,8 @@ flake8 = "^6.1.0" wandb = "^0.16.0" + + [tool.poetry.group.glcm.dependencies] glcm-cupy = "0.2.1" cupy-cuda12x = "^12.2.0" diff --git a/rsc.dvc b/rsc.dvc new file mode 100644 index 00000000..f9ae0e31 --- /dev/null +++ b/rsc.dvc @@ -0,0 +1,424 @@ +outs: +- hash: md5 + path: rsc + files: + - relpath: DEBUG/0/bounds.csv + md5: ad253d8dfe0cbbc8107647b11d9a2ce2 + size: 325 + cloud: + frdc-ds: + etag: 08b6ab869c8de682031001 + version_id: '1701154195084726' + - relpath: DEBUG/0/result.jpg + md5: 36e390821a45f70fc442bbd5d881f495 + size: 7361 + cloud: + frdc-ds: + etag: 08ccc6cc8191e682031001 + version_id: '1701155213353804' + - 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relpath: chestnut_nature_park/20210510/90deg60m84.5pct255deg/result_Blue.tif + md5: c240b4e607af2cdadc3d4fc96181e005 + size: 59362235 + cloud: + frdc-ds: + etag: 08b3d484a58de682031001 + version_id: '1701154213931571' + - relpath: chestnut_nature_park/20210510/90deg60m84.5pct255deg/result_Green.tif + md5: 08d7b7e3e4823b0cf9c53692d6b55f5b + size: 60380606 + cloud: + frdc-ds: + etag: 08ebe3a2a58de682031001 + version_id: '1701154214425067' + - relpath: chestnut_nature_park/20210510/90deg60m84.5pct255deg/result_NIR.tif + md5: ab3509fac188fe452d01957237181f31 + size: 59034799 + cloud: + frdc-ds: + etag: 0893bcfca48de682031001 + version_id: '1701154213797395' + - relpath: chestnut_nature_park/20210510/90deg60m84.5pct255deg/result_Red.tif + md5: 6b0531431f0d898aacda6334c10fca8a + size: 60369184 + cloud: + frdc-ds: + etag: 08e8a58ea58de682031001 + version_id: '1701154214089448' + - relpath: chestnut_nature_park/20210510/90deg60m84.5pct255deg/result_RedEdge.tif + md5: 75e67bc7c1b01e060c68062354192b8e + size: 59567305 + cloud: + frdc-ds: + etag: 08f0dc91ad8de682031001 + version_id: '1701154230922864' + - relpath: chestnut_nature_park/20210510/90deg60m84.5pct255deg/segment.tif + md5: 2b5856c859b44e54517b7891fd53bd60 + size: 12784 + cloud: + frdc-ds: + etag: 08838e869c8de682031001 + version_id: '1701154195080963' + - relpath: chestnut_nature_park/20210510/Join/adding -90deg 60m data/cloud.las + md5: a4755ad17e0c0f2686a1fb9cacc712b7 + size: 74248398 + cloud: + frdc-ds: + etag: 0892daa1a48de682031001 + version_id: '1701154212310290' + - relpath: chestnut_nature_park/20210510/Join/cloud.las + md5: 8ce9bccccab90a8a5c17ad5b3a982f0d + size: 61187376 + cloud: + frdc-ds: + etag: 08fda5a8a58de682031001 + version_id: '1701154214515453' diff --git a/rsc/DEBUG/0/scratch.py b/rsc/DEBUG/0/scratch.py deleted file mode 100644 index 007997e3..00000000 --- a/rsc/DEBUG/0/scratch.py +++ /dev/null @@ -1,17 +0,0 @@ -import numpy as np -from PIL import Image - -# %% -for i in ( - "result.tif", - "result_Red.tif", - "result_Green.tif", - "result_Blue.tif", - "result_RedEdge.tif", - "result_NIR.tif", -): - im = Image.open(i) - ar = np.array(im) - ar_crop = ar[2000:5000:20, 1000:3000:20] - im = Image.fromarray(ar_crop) - im.save(i) diff --git a/rsc/README.md b/rsc/README.md deleted file mode 100644 index 62b530f2..00000000 --- a/rsc/README.md +++ /dev/null @@ -1,11 +0,0 @@ -# FRDC Resources - -We have 2 type of resources: - -1) Raw: Uncompressed, raw data from our UAV drones -2) Debug: Compressed version of the raw data used for - 1) Unit Testing - 2) Integration Testing - 3) Experimentation Debugging - -You shouldn't need to touch this, this will be used to cache large raw `tif` files. diff --git a/scripts/gen_result_jpg.py b/scripts/gen_result_jpg.py new file mode 100644 index 00000000..06d05d6c --- /dev/null +++ b/scripts/gen_result_jpg.py @@ -0,0 +1,22 @@ +"""This script traverses a directory and generates a jpg for every file +matched.""" +from pathlib import Path + +from PIL import Image +from tqdm import tqdm + + +def main( + d: Path = Path(__file__).parents[1] / "rsc", glob: str = "**/result.tif" +): + for fp in tqdm(d.glob(glob)): + if (fp_jpg := fp.with_suffix(".jpg")).exists(): + print(f"Skipping {fp_jpg}") + continue + + print(f"Generating {fp_jpg}") + Image.open(fp).convert("RGB").save(fp_jpg) + + +if __name__ == "__main__": + main() diff --git a/src/frdc/load/dataset.py b/src/frdc/load/dataset.py index 5ba8ba8f..65752bce 100644 --- a/src/frdc/load/dataset.py +++ b/src/frdc/load/dataset.py @@ -6,13 +6,21 @@ from collections import OrderedDict from dataclasses import dataclass, field from pathlib import Path -from typing import Iterable +from typing import Iterable, Callable, Any import numpy as np import pandas as pd +import torch from PIL import Image from google.cloud import storage from google.oauth2.service_account import Credentials +from torch.utils.data import Dataset, ConcatDataset +from torchvision.transforms.v2 import ( + Compose, + ToImage, + ToDtype, + Resize, +) from frdc.conf import ( LOCAL_DATASET_ROOT_DIR, @@ -20,6 +28,7 @@ GCS_BUCKET_NAME, BAND_CONFIG, ) +from frdc.preprocess.extract_segments import extract_segments_from_bounds from frdc.utils import Rect @@ -147,21 +156,68 @@ def download_file( @dataclass -class FRDCDataset: - site: str - date: str - version: str | None - dl: FRDCDownloader = field(default_factory=FRDCDownloader) +class FRDCDataset(Dataset): + def __init__( + self, + site: str, + date: str, + version: str | None, + transform: Callable[[list[np.ndarray]], Any] = None, + target_transform: Callable[[list[str]], list[str]] = None, + ): + """Initializes the FRDC Dataset. + + Args: + site: The site of the dataset, e.g. "chestnut_nature_park". + date: The date of the dataset, e.g. "20201218". + version: The version of the dataset, e.g. "183deg". + """ + self.site = site + self.date = date + self.version = version + + self.dl = FRDCDownloader() + + self.ar, self.order = self.get_ar_bands() + bounds, self.targets = self.get_bounds_and_labels() + self.ar_segments = extract_segments_from_bounds(self.ar, bounds) + self.transform = transform + self.target_transform = target_transform + + def __len__(self): + return len(self.ar_segments) + + def __getitem__(self, idx): + return ( + self.transform(self.ar_segments[idx]) + if self.transform + else self.ar_segments[idx], + self.target_transform(self.targets[idx]) + if self.target_transform + else self.targets[idx], + ) @staticmethod - def _load_debug_dataset() -> FRDCDataset: + def _load_debug_dataset(resize: int = 299) -> FRDCDataset: """Loads a debug dataset from Google Cloud Storage. Returns: A dictionary of the dataset, with keys as the filenames and values as the images. """ - return FRDCDataset(site="DEBUG", date="0", version=None) + return FRDCDataset( + site="DEBUG", + date="0", + version=None, + transform=Compose( + [ + ToImage(), + ToDtype(torch.float32), + Resize((resize, resize)), + ] + ), + target_transform=None, + ) @property def dataset_dir(self): @@ -287,5 +343,36 @@ def _load_image(path: Path | str) -> np.ndarray: """ im = Image.open(Path(path).as_posix()) - ar = np.array(im) + ar = np.asarray(im) return np.expand_dims(ar, axis=-1) if ar.ndim == 2 else ar + + +# TODO: Kind of hacky, the unlabelled dataset should somehow come from the +# labelled dataset by filtering out the unknown labels. But we'll +# figure out this later when we do get unlabelled data. +# I'm thinking some API that's like +# FRDCDataset.filter_labels(...) -> FRDCSubset, FRDCSubset +# It could be more intuitive if it returns FRDCDataset, so we don't have +# to implement another class. +class FRDCUnlabelledDataset(FRDCDataset): + def __getitem__(self, item): + return ( + self.transform(self.ar_segments[item]) + if self.transform + else self.ar_segments[item] + ) + + +# This is not yet used much as we don't have sufficient training data. +class FRDCConcatDataset(ConcatDataset): + def __init__(self, datasets: list[FRDCDataset]): + super().__init__(datasets) + self.datasets = datasets + + def __getitem__(self, idx): + x, y = super().__getitem__(idx) + return x, y + + @property + def targets(self): + return [t for ds in self.datasets for t in ds.targets] diff --git a/src/frdc/models/__init__.py b/src/frdc/models/__init__.py index 5420b607..e69de29b 100644 --- a/src/frdc/models/__init__.py +++ b/src/frdc/models/__init__.py @@ -1,5 +0,0 @@ -from .facenet import FaceNet - -__all__ = [ - "FaceNet", -] diff --git a/src/frdc/models/facenet.py b/src/frdc/models/inceptionv3.py similarity index 56% rename from src/frdc/models/facenet.py rename to src/frdc/models/inceptionv3.py index 3d875e45..c2dce7f6 100644 --- a/src/frdc/models/facenet.py +++ b/src/frdc/models/inceptionv3.py @@ -1,19 +1,33 @@ +from copy import deepcopy + import torch +from sklearn.preprocessing import OrdinalEncoder, StandardScaler from torch import nn from torchvision.models import Inception_V3_Weights, inception_v3 +from frdc.train.mixmatch_module import MixMatchModule +from frdc.utils.ema import EMA + -class FaceNet(nn.Module): +class InceptionV3MixMatchModule(MixMatchModule): INCEPTION_OUT_DIMS = 2048 INCEPTION_AUX_DIMS = 1000 INCEPTION_IN_CHANNELS = 3 MIN_SIZE = 299 - def __init__(self, n_out_classes: int = 10): - """Initialize the FaceNet model. + def __init__( + self, + *, + n_classes: int, + lr: float, + x_scaler: StandardScaler, + y_encoder: OrdinalEncoder, + ema_lr: float = 0.001, + ): + """Initialize the InceptionV3 model. Args: - n_out_classes: The number of output classes + n_classes: The number of output classes Notes: - Min input size: 299 x 299. @@ -21,7 +35,15 @@ def __init__(self, n_out_classes: int = 10): Retrieve these constants in class attributes MIN_SIZE and CHANNELS. """ - super().__init__() + self.lr = lr + + super().__init__( + n_classes=n_classes, + x_scaler=x_scaler, + y_encoder=y_encoder, + sharpen_temp=0.5, + mix_beta_alpha=0.75, + ) self.inception = inception_v3( weights=Inception_V3_Weights.IMAGENET1K_V1, @@ -32,14 +54,28 @@ def __init__(self, n_out_classes: int = 10): for param in self.inception.parameters(): param.requires_grad = False - # self.fc = nn.Linear(self.INCEPTION_OUT_DIMS, n_out_classes) self.fc = nn.Sequential( nn.BatchNorm1d(self.INCEPTION_OUT_DIMS), nn.Linear(self.INCEPTION_OUT_DIMS, self.INCEPTION_OUT_DIMS // 2), nn.BatchNorm1d(self.INCEPTION_OUT_DIMS // 2), - nn.Linear(self.INCEPTION_OUT_DIMS // 2, n_out_classes), + nn.Linear(self.INCEPTION_OUT_DIMS // 2, n_classes), nn.Softmax(dim=1), ) + # The problem is that the deep copy runs even before the module is + # initialized, which means ema_model is empty. + ema_model = deepcopy(self) + for param in ema_model.parameters(): + param.detach_() + self._ema_model = ema_model + self.ema_updater = EMA(model=self, ema_model=self.ema_model) + self.ema_lr = ema_lr + + @property + def ema_model(self): + return self._ema_model + + def update_ema(self): + self.ema_updater.update(self.ema_lr) def forward(self, x: torch.Tensor): """Forward pass. @@ -62,7 +98,6 @@ def forward(self, x: torch.Tensor): f" - No singleton dimensions\n" f" - Size >= {self.MIN_SIZE}\n" ) - # x = self.feature_extraction(x) # During training, the auxiliary outputs are used for auxiliary loss, # but during testing, only the main output is used. @@ -72,3 +107,9 @@ def forward(self, x: torch.Tensor): logits = self.inception(x) return self.fc(logits) + + def configure_optimizers(self): + return torch.optim.Adam( + self.parameters(), + lr=self.lr, + ) diff --git a/src/frdc/train/__init__.py b/src/frdc/train/__init__.py index 8942e255..8b137891 100644 --- a/src/frdc/train/__init__.py +++ b/src/frdc/train/__init__.py @@ -1,5 +1 @@ -from .frdc_datamodule import FRDCDataModule -from .frdc_module import FRDCModule -from .train import dummy_train -__all__ = ["dummy_train", "FRDCDataModule", "FRDCModule"] diff --git a/src/frdc/train/frdc_datamodule.py b/src/frdc/train/frdc_datamodule.py index 28e79665..6138c7e5 100644 --- a/src/frdc/train/frdc_datamodule.py +++ b/src/frdc/train/frdc_datamodule.py @@ -1,139 +1,105 @@ from __future__ import annotations -from dataclasses import dataclass, field -from typing import Callable, Collection +from dataclasses import dataclass -import numpy as np -import torch from lightning import LightningDataModule -from sklearn.preprocessing import LabelEncoder -from torch.utils.data import DataLoader, TensorDataset, Dataset +from torch.utils.data import DataLoader, RandomSampler +from frdc.load import FRDCDataset -@dataclass # (kw_only=True) # only available when we use Py3.10 + +@dataclass class FRDCDataModule(LightningDataModule): - """FRDC Data Module. + """Lightning DataModule for FRDC Dataset. Notes: - We separate the segment input and transform as we expect the input - to be as "raw" as possible, which is usually in the np.ndarray - format. - - This makes it easy if we have custom images with alternative - segmentations, such as through an auto-segmentation. + This is a special datamodule for semi-supervised learning, which + requires two dataloaders for the labelled and unlabelled datasets. + It can also be used for supervised learning, by passing in None for + the unlabelled dataset. + + If you're using our MixMatch Module, using None for the unlabelled + dataset will skip the MixMatch. However, note that this is not + equivalent to passing the Labelled set as unlabelled as well. + + For example: + >>> FRDCSSLDataModule( + ... train_lab_ds=train_lab_ds, + ... train_unl_ds=train_lab_ds, + ... ... + ... ) + + Does not have the same performance as: + >>> FRDCSSLDataModule( + ... train_lab_ds=train_lab_ds, + ... train_unl_ds=None, + ... ... + ... ) + + As partially, some samples in MixMatch uses the unlabelled loss. Args: - segments: A list of segments, each ND-Array. - Note that PyTorch expects input shapes of (B, C, H, W), - while common image libs expect shapes (H, W, C). - labels: A list of labels as strings. If None, then the datamodule - will not have train, val, test datasets. - preprocess: Transform applied to the segments. - It takes a list of segments, returning a batched tensor: - (batch, height, width, channels). - In FRDC, each segment is the tree crown segment, the output - should be a batched image of all the crown segments. - See Examples for more details. - train_val_test_split: This is a function that takes a TensorDataset - and splits it into train, val, test Datasets. - See Examples for more details. + train_lab_ds: The labelled training dataset. + train_unl_ds: The unlabelled training dataset. Can be None, which will + default to a DataModule suitable for supervised learning. + val_ds: The validation dataset. batch_size: The batch size to use for the dataloaders. - - Examples: - The fn_segment_tf could be a function that resizes the segments to - 299x299 and then stacks them into a batched image. The output is - then permuted to be (batch, channels, height, width).: - - >>> from skimage.transform import resize - >>> from frdc.models import FaceNet - >>> - >>> fn_segment_tf=lambda x: torch.stack([ - >>> torch.from_numpy(resize(s, FaceNet.MIN_SIZE)) for s in x - >>> ]).permute(0, 3, 1, 2) - - The fn_split could be a function that splits the dataset into - train, val, test subsets.: - - >>> from torch.utils.data import random_split - >>> - >>> fn_split=lambda x: random_split(x, lengths=[len(x) - 6, 3, 3]) + train_iters: The number of iterations to run for the labelled training + dataset. + val_iters: The number of iterations to run for the validation dataset. """ - segments: list[np.ndarray] - preprocess: Callable[[list[np.ndarray]], torch.Tensor] - augmentation: Callable[[torch.Tensor], torch.Tensor] = lambda x: x - labels: list[str] | None = None - train_val_test_split: ( - Callable[[TensorDataset], Collection[Dataset, Dataset, Dataset]] | None - ) = (None,) + train_lab_ds: FRDCDataset + val_ds: FRDCDataset + train_unl_ds: FRDCDataset | None = None batch_size: int = 4 - le: LabelEncoder = LabelEncoder() - - train_ds: Dataset = field(init=False, default=None) - val_ds: Dataset = field(init=False, default=None) - test_ds: Dataset = field(init=False, default=None) - predict_ds: Dataset = field(init=False, default=None) + train_iters: int = 100 + val_iters: int = 100 def __post_init__(self): super().__init__() - def setup(self, stage=None): - x = self.preprocess(self.segments) - - assert torch.isnan(x).sum() == 0, "Found NaN values in the segments." - assert x.ndim == 4, ( - f"Expected 4 dimensions, got {x.ndim} dimensions of shape" - f" {x.shape}." - ) - - if stage in ["fit", "validate", "test"]: - if self.labels is None or self.train_val_test_split is None: - raise ValueError( - "Labels and fn_split must be provided for" - " train, val, test datasets." - ) - - y = torch.from_numpy(self.le.fit_transform(self.labels)) - assert x.shape[0] == y.shape[0], ( - f"Expected same number of samples for x and y, got" - f" {x.shape[0]} for x and {y.shape[0]} for y." - ) - - tds = TensorDataset(x, y) - ( - self.train_ds, - self.val_ds, - self.test_ds, - ) = self.train_val_test_split(tds) - - elif stage == "predict": - tds = TensorDataset(x) - self.predict_ds = tds - - def on_before_batch_transfer(self, batch, dataloader_idx: int): - if self.trainer.training: - x, y = batch - x = self.augmentation(x) - batch = x, y - return batch - def train_dataloader(self): - return DataLoader( - self.train_ds, batch_size=self.batch_size, shuffle=True + num_samples = self.batch_size * self.train_iters + lab_dl = DataLoader( + self.train_lab_ds, + batch_size=self.batch_size, + sampler=RandomSampler( + self.train_lab_ds, + num_samples=num_samples, + replacement=False, + ), ) - - def val_dataloader(self): - return DataLoader( - self.val_ds, batch_size=self.batch_size, shuffle=False + unl_dl = ( + DataLoader( + self.train_unl_ds, + batch_size=self.batch_size, + sampler=RandomSampler( + self.train_unl_ds, + num_samples=self.batch_size * self.train_iters, + replacement=False, + ), + ) + if self.train_unl_ds is not None + # This is a hacky way to create an empty dataloader. + # The size should be the same as the labelled dataloader so that + # the iterator doesn't prematurely stop. + else DataLoader( + empty := [[] for _ in range(len(self.train_lab_ds))], + batch_size=self.batch_size, + sampler=RandomSampler( + empty, + num_samples=num_samples, + replacement=False, + ), + ) ) - def test_dataloader(self): - return DataLoader( - self.test_ds, batch_size=self.batch_size, shuffle=False - ) + return [lab_dl, unl_dl] - def predict_dataloader(self): + def val_dataloader(self): return DataLoader( - self.predict_ds, batch_size=self.batch_size, shuffle=False + self.val_ds, + batch_size=self.batch_size, ) diff --git a/src/frdc/train/frdc_module.py b/src/frdc/train/frdc_module.py deleted file mode 100644 index e6d7c2a5..00000000 --- a/src/frdc/train/frdc_module.py +++ /dev/null @@ -1,63 +0,0 @@ -import torch -from lightning import LightningModule -from torch import nn - - -class FRDCModule(LightningModule): - def __init__( - self, - *, - model_cls: type[nn.Module], - model_kwargs: dict, - optim_cls: type[torch.optim.Optimizer], - optim_kwargs: dict, - ): - super().__init__() - self.save_hyperparameters() - self.model = model_cls(**model_kwargs) - self.optim = optim_cls - self.optim_kwargs = optim_kwargs - - def forward(self, x): - return self.model(x) - - def training_step(self, batch, batch_idx): - x, y = batch - y_hat = self(x) - loss = nn.CrossEntropyLoss()(y_hat, y) - self.log("loss", loss, prog_bar=True) - self.log( - "acc", (y_hat.argmax(dim=1) == y).float().mean(), prog_bar=True - ) - return loss - - def validation_step(self, batch, batch_idx): - x, y = batch - y_hat = self(x) - loss = nn.CrossEntropyLoss()(y_hat, y) - self.log("val_loss", loss) - self.log( - "val_acc", (y_hat.argmax(dim=1) == y).float().mean(), prog_bar=True - ) - return loss - - def test_step(self, batch, batch_idx): - x, y = batch - y_hat = self(x) - loss = nn.CrossEntropyLoss()(y_hat, y) - self.log("test_loss", loss) - self.log("test_acc", (y_hat.argmax(dim=1) == y).float().mean()) - return loss - - def predict_step(self, batch, batch_idx, dataloader_idx=None): - x = batch[0] - y_hat = self(x) - return y_hat - - def configure_optimizers(self): - optim = self.optim(self.parameters(), **self.optim_kwargs) - scheduler = torch.optim.lr_scheduler.ExponentialLR( - optimizer=optim, - gamma=0.99, - ) - return [optim], [scheduler] diff --git a/src/frdc/train/mixmatch_module.py b/src/frdc/train/mixmatch_module.py new file mode 100644 index 00000000..194928ad --- /dev/null +++ b/src/frdc/train/mixmatch_module.py @@ -0,0 +1,312 @@ +from __future__ import annotations + +from abc import abstractmethod +from typing import Any + +import numpy as np +import torch +import torch.nn.functional as F +import torch.nn.parallel +import torch.nn.parallel +from lightning import LightningModule +from sklearn.preprocessing import StandardScaler, OrdinalEncoder +from torch.nn.functional import one_hot +from torchmetrics.functional import accuracy + + +class MixMatchModule(LightningModule): + def __init__( + self, + *, + x_scaler: StandardScaler, + y_encoder: OrdinalEncoder, + n_classes: int = 10, + sharpen_temp: float = 0.5, + mix_beta_alpha: float = 0.75, + ): + """PyTorch Lightning Module for MixMatch + + Notes: + This performs MixMatch as described in the paper. + https://arxiv.org/abs/1905.02249 + + This module is designed to be used with any model, not only + the WideResNet model. + + Furthermore, while it's possible to switch datasets, take a look + at how we implement the CIFAR10DataModule's DataLoaders to see + how to implement a new dataset. + + Args: + n_classes: The number of classes in the dataset. + sharpen_temp: The temperature to use for sharpening. + mix_beta_alpha: The alpha to use for the beta distribution + when mixing. + """ + + super().__init__() + + self.x_scaler = x_scaler + self.y_encoder = y_encoder + self.n_classes = n_classes + self.sharpen_temp = sharpen_temp + self.mix_beta_alpha = mix_beta_alpha + self.save_hyperparameters() + + @property + @abstractmethod + def ema_model(self): + """The inherited class should return the EMA model, which it should + retroactively create through `deepcopy(self)`. Furthermore, the + training loop will automatically call `update_ema` after each batch. + Thus, the inherited class should implement `update_ema` to update the + EMA model. + """ + ... + + @abstractmethod + def update_ema(self): + """This method should update the EMA model, which is handled by the + inherited class. + """ + ... + + @abstractmethod + def forward(self, x): + ... + + @staticmethod + def loss_unl_scaler(progress: float) -> float: + return progress * 75 + + @staticmethod + def loss_lbl(lbl_pred: torch.Tensor, lbl: torch.Tensor): + return F.cross_entropy(lbl_pred, lbl) + + @staticmethod + def loss_unl(unl_pred: torch.Tensor, unl: torch.Tensor): + return torch.mean((torch.softmax(unl_pred, dim=1) - unl) ** 2) + + @staticmethod + def mix_up( + x: torch.Tensor, + y: torch.Tensor, + alpha: float, + ) -> tuple[torch.Tensor, torch.Tensor]: + """Mix up the data + + Args: + x: The data to mix up. + y: The labels to mix up. + alpha: The alpha to use for the beta distribution. + + Returns: + The mixed up data and labels. + """ + ratio = np.random.beta(alpha, alpha) + ratio = max(ratio, 1 - ratio) + + shuf_idx = torch.randperm(x.size(0)) + + x_mix = ratio * x + (1 - ratio) * x[shuf_idx] + y_mix = ratio * y + (1 - ratio) * y[shuf_idx] + return x_mix, y_mix + + @staticmethod + def sharpen(y: torch.Tensor, temp: float) -> torch.Tensor: + """Sharpen the predictions by raising them to the power of 1 / temp + + Args: + y: The predictions to sharpen. + temp: The temperature to use. + + Returns: + The probability-normalized sharpened predictions + """ + y_sharp = y ** (1 / temp) + # Sharpening will change the sum of the predictions. + y_sharp /= y_sharp.sum(dim=1, keepdim=True) + return y_sharp + + def guess_labels( + self, + x_unls: list[torch.Tensor], + ) -> torch.Tensor: + """Guess labels from the unlabelled data""" + y_unls: list[torch.Tensor] = [ + torch.softmax(self.ema_model(u), dim=1) for u in x_unls + ] + # The sum will sum the tensors in the list, + # it doesn't reduce the tensors + y_unl = sum(y_unls) / len(y_unls) + # noinspection PyTypeChecker + return y_unl + + @property + def progress(self): + # Progress is a linear ramp from 0 to 1 over the course of training. + return ( + self.global_step / self.trainer.num_training_batches + ) / self.trainer.max_epochs + + def training_step(self, batch, batch_idx): + # Progress is a linear ramp from 0 to 1 over the course of training. + (x_lbl, y_lbl), x_unls = batch + + y_lbl = one_hot(y_lbl.long(), num_classes=self.n_classes) + + # If x_unls is Truthy, then we are using MixMatch. + # Otherwise, we are just using supervised learning. + if x_unls: + # This route implies that we are using SSL + with torch.no_grad(): + y_unl = self.guess_labels(x_unls=x_unls) + y_unl = self.sharpen(y_unl, self.sharpen_temp) + + x = torch.cat([x_lbl, *x_unls], dim=0) + y = torch.cat([y_lbl, *(y_unl,) * len(x_unls)], dim=0) + x_mix, y_mix = self.mix_up(x, y, self.mix_beta_alpha) + + # This had interleaving, but it was removed as it's not + # significantly better + batch_size = x_lbl.shape[0] + y_mix_pred = self(x_mix) + y_mix_lbl_pred = y_mix_pred[:batch_size] + y_mix_unl_pred = y_mix_pred[batch_size:] + y_mix_lbl = y_mix[:batch_size] + y_mix_unl = y_mix[batch_size:] + + loss_lbl = self.loss_lbl(y_mix_lbl_pred, y_mix_lbl) + loss_unl = self.loss_unl(y_mix_unl_pred, y_mix_unl) + loss_unl_scale = self.loss_unl_scaler(progress=self.progress) + + loss = loss_lbl + loss_unl * loss_unl_scale + + self.log("loss_unl_scale", loss_unl_scale, prog_bar=True) + self.log("train_loss_lbl", loss_lbl) + self.log("train_loss_unl", loss_unl) + else: + # This route implies that we are just using supervised learning + y_pred = self(x_lbl) + loss = self.loss_lbl(y_pred, y_lbl.float()) + + self.log("train_loss", loss) + return loss + + # PyTorch Lightning doesn't automatically no_grads the EMA step. + # It's important to keep this to avoid a memory leak. + @torch.no_grad() + def on_after_backward(self) -> None: + self.update_ema() + + def validation_step(self, batch, batch_idx): + x, y = batch + y_pred = self.ema_model(x) + loss = F.cross_entropy(y_pred, y.long()) + + acc = accuracy( + y_pred, y, task="multiclass", num_classes=y_pred.shape[1] + ) + self.log("val_loss", loss) + self.log("val_acc", acc, prog_bar=True) + return loss + + def test_step(self, batch, batch_idx): + x, y = batch + y_pred = self.ema_model(x) + loss = F.cross_entropy(y_pred, y.long()) + + acc = accuracy( + y_pred, y, task="multiclass", num_classes=y_pred.shape[1] + ) + self.log("test_loss", loss) + self.log("test_acc", acc, prog_bar=True) + return loss + + def predict_step(self, batch, *args, **kwargs) -> Any: + x, y = batch + y_pred = self.ema_model(x) + y_true_str = self.y_encoder.inverse_transform( + y.cpu().numpy().reshape(-1, 1) + ) + y_pred_str = self.y_encoder.inverse_transform( + y_pred.argmax(dim=1).cpu().numpy().reshape(-1, 1) + ) + return y_true_str, y_pred_str + + @torch.no_grad() + def on_before_batch_transfer(self, batch: Any, dataloader_idx: int) -> Any: + """This method is called before any data transfer to the device. + + We leverage this to do some preprocessing on the data. + Namely, we use the StandardScaler and OrdinalEncoder to transform the + data. + """ + + # TODO: ngl, this is pretty chunky. + # It works, but it's not very pretty. + if self.training: + (x_lab, y), x_unl = batch + xs = [x_lab, *x_unl] + + b, c, h, w = x_lab.shape + + # Move Channel to the last dimension then transform + xs_ss: list[np.ndarray] = [ + self.x_scaler.transform(x.permute(0, 2, 3, 1).reshape(-1, c)) + for x in xs + ] + + # Move Channel back to the second dimension + xs_: list[torch.Tensor] = [ + torch.from_numpy(x_ss.reshape(b, h, w, c)) + .permute(0, 3, 1, 2) + .float() + for x_ss in xs_ss + ] + + y: tuple[str] + y_: torch.Tensor = torch.from_numpy( + self.y_encoder.transform(np.array(y).reshape(-1, 1)).squeeze() + ) + + # Ordinal Encoders can return a np.nan if the value is not in the + # categories. We will remove that from the batch. + x_ = xs_[0][~torch.isnan(y_)] + y_ = y_[~torch.isnan(y_)] + + return (x_, y_.long()), xs_[1:] + + else: + x, y = batch + + x: torch.Tensor + b, c, h, w = x.shape + + # Standard Scaler only accepts (n_samples, n_features), + # so we need to do some fancy reshaping. + # Note that moving dimensions then reshaping is different from just + # reshaping! + # Move Channel to the last dimension then transform + x_ss: np.ndarray = self.x_scaler.transform( + x.permute(0, 2, 3, 1).reshape(-1, c) + ) + + # Move Channel back to the second dimension + x_: torch.Tensor = ( + torch.from_numpy(x_ss.reshape(b, h, w, c)) + .permute(0, 3, 1, 2) + .float() + ) + + y: tuple[str] + y_: torch.Tensor = torch.from_numpy( + self.y_encoder.transform(np.array(y).reshape(-1, 1)).squeeze() + ) + + # Ordinal Encoders can return a np.nan if the value is not in the + # categories. We will remove that from the batch. + x_ = x_[~torch.isnan(y_)] + y_ = y_[~torch.isnan(y_)] + + return x_, y_.long() diff --git a/src/frdc/train/train.py b/src/frdc/train/train.py deleted file mode 100644 index c3d49049..00000000 --- a/src/frdc/train/train.py +++ /dev/null @@ -1,56 +0,0 @@ -from typing import Callable - -import numpy as np -from sklearn.base import ClassifierMixin -from sklearn.ensemble import RandomForestClassifier - - -# We force keyword arguments to make it easier to read the function signature. -def dummy_train( - *, - X_train: np.ndarray, - y_train: np.ndarray, - X_val: np.ndarray, - y_val: np.ndarray, -) -> tuple[Callable[[np.ndarray], np.ndarray], ClassifierMixin, float]: - """Dummy Training function. - - Notes: - This is obviously not final. This is just a placeholder to get the - pipeline working. - - Args: - X_train: X_train is the train image numpy array of shape (N, H, W, C). - y_train: y_train is the train class label a numpy array of shape (N,). - X_val: X_val is the validation for X_train - y_val: y_val is the validation for y_train - - Returns: - The feature extraction function, the classifier, and validation score. - - """ - - # TODO: Placeholder feature extraction for an image. - # We'll probably sub with a CNN later. - def feature_extraction(X): - return np.stack( - [ - np.nanmean(X, axis=(1, 2, 3)), - np.nanstd(X, axis=(1, 2, 3)), - ], - axis=-1, - ) - - X_train = feature_extraction(X_train) - X_val = feature_extraction(X_val) - - # TODO: This is likely the last layer of the CNN. - classifier = RandomForestClassifier() - - # TODO: "Train" the model. - classifier.fit(X_train, y_train) - - # TODO: "Evaluate" the model. - score = classifier.score(X_val, y_val) - - return feature_extraction, classifier, score diff --git a/src/frdc/utils/ema.py b/src/frdc/utils/ema.py new file mode 100644 index 00000000..297b0b11 --- /dev/null +++ b/src/frdc/utils/ema.py @@ -0,0 +1,26 @@ +import torch +import torch.nn as nn + + +class EMA: + def __init__( + self, + model: nn.Module, + ema_model: nn.Module, + ): + self.model = model + self.ema_model = ema_model + + def update(self, lr: float): + """Update the EMA model with the current model's parameters. + + Args: + lr: A fraction controlling how much should the EMA learn from the + current model. + """ + for param, ema_param in zip( + self.model.parameters(), self.ema_model.parameters() + ): + if ema_param.dtype == torch.float32: + ema_param.mul_(1 - lr) + ema_param.add_(param * lr) diff --git a/tests/integration_tests/test_pipeline.py b/tests/integration_tests/test_pipeline.py index 41bfbbc6..cc86cb3c 100644 --- a/tests/integration_tests/test_pipeline.py +++ b/tests/integration_tests/test_pipeline.py @@ -1,96 +1,45 @@ import logging import lightning as pl -import torch -from skimage.transform import resize -from torch.utils.data import random_split +import numpy as np +from sklearn.preprocessing import StandardScaler, OrdinalEncoder -from frdc.models import FaceNet -from frdc.preprocess.extract_segments import ( - extract_segments_from_bounds, - extract_segments_from_labels, -) -from frdc.train import FRDCDataModule, FRDCModule -from utils import get_labels - - -def fn_segment_tf(x): - x = [resize(s, [FaceNet.MIN_SIZE, FaceNet.MIN_SIZE]) for s in x] - x = [torch.from_numpy(s) for s in x] - x = torch.stack(x) - x = torch.nan_to_num(x) - x = x.permute(0, 3, 1, 2) - return x - - -fn_split = lambda x: random_split(x, lengths=[len(x) - 6, 3, 3]) +from frdc.models.inceptionv3 import InceptionV3MixMatchModule +from frdc.train.frdc_datamodule import FRDCDataModule BATCH_SIZE = 3 -def test_manual_segmentation_pipeline(ds) -> tuple[FRDCModule, FRDCDataModule]: +def test_manual_segmentation_pipeline(ds): """Manually segment the image according to bounds.csv, then train a model on it.""" - ar, order = ds.get_ar_bands() - bounds, labels = ds.get_bounds_and_labels() - segments = extract_segments_from_bounds(ar, bounds, cropped=True) - dm = FRDCDataModule( - segments=segments, - labels=labels, - preprocess=fn_segment_tf, - train_val_test_split=fn_split, - augmentation=lambda x: x, + train_lab_ds=ds, + train_unl_ds=None, + val_ds=ds, batch_size=BATCH_SIZE, ) - m = FRDCModule( - model_cls=FaceNet, - model_kwargs={"n_out_classes": 10}, - optim_cls=torch.optim.Adam, - optim_kwargs=dict(lr=1e-3), - ) - - trainer = pl.Trainer(fast_dev_run=True) - trainer.fit(m, datamodule=dm) - - val_loss = trainer.validate(m, datamodule=dm)[0]["val_loss"] - test_loss = trainer.test(m, datamodule=dm)[0]["test_loss"] - logging.debug(f"Validation score: {val_loss:.2%}") - logging.debug(f"Test score: {test_loss:.2%}") - - return m, dm - - -def test_auto_segmentation_pipeline(ds): - """Automatically segment the image, then use a model to predict.""" - - # Auto segmentation - ar, order = ds.get_ar_bands() - ar_labels = get_labels(ar, order) - segments_auto = extract_segments_from_labels(ar, ar_labels) + oe = OrdinalEncoder( + handle_unknown="use_encoded_value", + unknown_value=np.nan, + ) + oe.fit(np.array(ds.targets).reshape(-1, 1)) + n_classes = len(oe.categories_[0]) - # Get our model trained on the bounds.csv - m, _ = test_manual_segmentation_pipeline(ds) + ss = StandardScaler() + ss.fit(ds.ar.reshape(-1, ds.ar.shape[-1])) - # Construct our datamodule for prediction - dm_auto = FRDCDataModule( - segments=segments_auto, - labels=None, # Labels can be none if we just want predictions. - preprocess=fn_segment_tf, - train_val_test_split=fn_split, - batch_size=BATCH_SIZE, + m = InceptionV3MixMatchModule( + n_classes=n_classes, + lr=1e-3, + x_scaler=ss, + y_encoder=oe, ) trainer = pl.Trainer(fast_dev_run=True) - # The predictions have a shape of (N, C), where N is the number of - # segments, and C is the number of classes. - predictions = torch.concat(trainer.predict(m, datamodule=dm_auto)) - - assert predictions.shape[0] == len( - segments_auto - ), "Expected the same number of predictions as segments." + trainer.fit(m, datamodule=dm) - logging.debug(f"Predictions: {predictions}") - logging.debug(f"Class Predictions: {torch.argmax(predictions, dim=1)}") + val_loss = trainer.validate(m, datamodule=dm)[0]["val_loss"] + logging.debug(f"Validation score: {val_loss:.2%}") diff --git a/tests/model_tests/chestnut_dec_may/augmentation.py b/tests/model_tests/chestnut_dec_may/augmentation.py deleted file mode 100644 index f182b36d..00000000 --- a/tests/model_tests/chestnut_dec_may/augmentation.py +++ /dev/null @@ -1,9 +0,0 @@ -import torch -from torchvision.transforms.v2 import RandomHorizontalFlip, RandomVerticalFlip - - -def augmentation(t: torch.Tensor) -> torch.Tensor: - """Runs out augmentation on a tensor.""" - t = RandomHorizontalFlip()(t) - t = RandomVerticalFlip()(t) - return t diff --git a/tests/model_tests/chestnut_dec_may/confusion_matrix.png b/tests/model_tests/chestnut_dec_may/confusion_matrix.png index 7761f8d3..ec81ced0 100644 Binary files a/tests/model_tests/chestnut_dec_may/confusion_matrix.png and b/tests/model_tests/chestnut_dec_may/confusion_matrix.png differ diff --git a/tests/model_tests/chestnut_dec_may/evaluate.py b/tests/model_tests/chestnut_dec_may/evaluate.py deleted file mode 100644 index 0cc245cd..00000000 --- a/tests/model_tests/chestnut_dec_may/evaluate.py +++ /dev/null @@ -1,53 +0,0 @@ -import lightning as pl -import matplotlib.pyplot as plt -import numpy as np -import torch -from seaborn import heatmap -from sklearn.metrics import confusion_matrix - -from frdc.train import FRDCDataModule -from frdc.train import FRDCModule -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. -segments, labels = get_dataset( - "chestnut_nature_park", "20210510", "90deg43m85pct255deg/map" -) - -# Prepare the datamodule and trainer -dm = FRDCDataModule(segments=segments, preprocess=preprocess, batch_size=5) - -# TODO: Hacky way to load our LabelEncoder -dm.le.classes_ = np.load("le.npy", allow_pickle=True) - -# Load the model -m = FRDCModule.load_from_checkpoint( - "lightning_logs/version_88/checkpoints/epoch=99-step=700.ckpt" -) - -# Make predictions -trainer = pl.Trainer(logger=False) -pred = trainer.predict(m, datamodule=dm) -y_pred = torch.concat(pred, dim=0).argmax(dim=1) -y_true = dm.le.transform(labels) - -# Plot the confusion matrix -cm = confusion_matrix(y_true, y_pred) - -plt.figure(figsize=(10, 10)) - -heatmap( - cm, - annot=True, - xticklabels=dm.le.classes_, - yticklabels=dm.le.classes_, - cbar=False, -) - -plt.tight_layout(pad=3) -plt.title("Confusion Matrix") -plt.xlabel("Predicted Label") -plt.ylabel("True Label") -plt.savefig("confusion_matrix.png") diff --git a/tests/model_tests/chestnut_dec_may/le.npy b/tests/model_tests/chestnut_dec_may/le.npy deleted file mode 100644 index cb1aa764..00000000 Binary files a/tests/model_tests/chestnut_dec_may/le.npy and /dev/null differ diff --git a/tests/model_tests/chestnut_dec_may/main.py b/tests/model_tests/chestnut_dec_may/main.py deleted file mode 100644 index 3e2fda79..00000000 --- a/tests/model_tests/chestnut_dec_may/main.py +++ /dev/null @@ -1,126 +0,0 @@ -""" Tests for the FaceNet model. - -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 -import torch -from lightning.pytorch.callbacks import ( - LearningRateMonitor, - ModelCheckpoint, - EarlyStopping, -) -from torch.utils.data import TensorDataset, Dataset, Subset - -from frdc.models import FaceNet -from frdc.train import FRDCDataModule, FRDCModule -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 - -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))), - ), - [], - ] - - -# Prepare the dataset -segments_0, labels_0 = get_dataset("chestnut_nature_park", "20201218", None) -segments_1, labels_1 = get_dataset( - "chestnut_nature_park", "20210510", "90deg43m85pct255deg/map" -) - - -# Concatenate the datasets -segments = [*segments_0, *segments_1] -labels = [*labels_0, *labels_1] - -BATCH_SIZE = 5 -EPOCHS = 50 -LR = 1e-3 - -# Prepare the datamodule and trainer -dm = FRDCDataModule( - # Input to the model - segments=segments, - # Output of the model - labels=labels, - # Preprocessing function - preprocess=preprocess, - # Augmentation function (Only on train) - augmentation=augmentation, - # Splitting function - train_val_test_split=train_val_test_split, - # Batch size - batch_size=BATCH_SIZE, -) - -trainer = pl.Trainer( - max_epochs=EPOCHS, - # fast_dev_run=True, - # Set the seed for reproducibility - # 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 - EarlyStopping(monitor="val_loss", patience=4, mode="min"), - # Log the learning rate on TensorBoard - LearningRateMonitor(logging_interval="epoch"), - # 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. - model_cls=FaceNet, - model_kwargs=dict(n_out_classes=len(set(labels))), - # We use the Adam optimizer - optim_cls=torch.optim.Adam, - # TODO: This is not fine-tuned. - optim_kwargs=dict(lr=LR, weight_decay=1e-4, amsgrad=True), -) - -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()}) -TODO: Authentication for researchers -""" - -with open(Path(__file__).parent / "report.md", "w") as f: - f.write(report) - - -wandb.finish() diff --git a/tests/model_tests/chestnut_dec_may/preprocess.py b/tests/model_tests/chestnut_dec_may/preprocess.py deleted file mode 100644 index 090b7b9d..00000000 --- a/tests/model_tests/chestnut_dec_may/preprocess.py +++ /dev/null @@ -1,67 +0,0 @@ -import numpy as np -import torch - -# 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.scale import scale_normal_per_band, scale_0_1_per_band - - -# TODO: Eventually, we will have multiple tests, and we should try to make -# this function test agnostic. - - -def channel_preprocess(ar: np.ndarray) -> np.ndarray: - # Preprocesses a channel array of shape: (H, W) - shape = ar.shape - ar_flt = ar.flatten() - return ar_flt.reshape(*shape) - - -def segment_preprocess(ar: np.ndarray) -> torch.Tensor: - # Preprocesses a segment array of shape: (H, W, C) - - # 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 = 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([ - # channel_preprocess(ar[..., ch]) for ch in range(ar.shape[-1]) - # ]) - - t = torch.from_numpy(ar) - t = Resize([FaceNet.MIN_SIZE, FaceNet.MIN_SIZE], antialias=True)(t) - return t - - -def preprocess(l_ar: list[np.ndarray]) -> torch.Tensor: - """Preprocesses a list of segments. - - Notes: - We structure the transformations into 3 levels. - 1. Segments transformation (This function) - 2. Per segment transformation (segment_preprocess) - 3. Per channel transformation (channel_preprocess) - - Returns: - A preprocessed tensor of shape: (batch, channels, height, width) - """ - - l_t: list[torch.Tensor] = [segment_preprocess(ar) for ar in l_ar] - t: torch.Tensor = torch.stack(l_t) - t = torch.nan_to_num(t) - return t diff --git a/tests/model_tests/chestnut_dec_may/train.py b/tests/model_tests/chestnut_dec_may/train.py new file mode 100644 index 00000000..6fb383c3 --- /dev/null +++ b/tests/model_tests/chestnut_dec_may/train.py @@ -0,0 +1,276 @@ +""" Tests for the InceptionV3 model on the Chestnut Nature Park dataset. + +This test is done by training a model on the 20201218 dataset, then testing on +the 20210510 dataset. +""" + +import os +from pathlib import Path + +import lightning as pl +import numpy as np +import torch +import wandb +from lightning.pytorch.callbacks import ( + LearningRateMonitor, + ModelCheckpoint, + EarlyStopping, +) +from lightning.pytorch.loggers import WandbLogger +from matplotlib import pyplot as plt +from seaborn import heatmap +from sklearn.metrics import confusion_matrix +from sklearn.preprocessing import StandardScaler, OrdinalEncoder +from torch.utils.data import DataLoader +from torchvision.transforms import RandomVerticalFlip +from torchvision.transforms.v2 import ( + Compose, + ToImage, + ToDtype, + RandomVerticalFlip, + RandomCrop, + CenterCrop, +) +from torchvision.transforms.v2 import RandomHorizontalFlip + +from frdc.load import FRDCDataset +from frdc.load.dataset import FRDCUnlabelledDataset +from frdc.models.inceptionv3 import InceptionV3MixMatchModule +from frdc.train.frdc_datamodule import FRDCDataModule + +THIS_DIR = Path(__file__).parent + + +# TODO: Ideally, we should have a separate dataset for testing. + + +# TODO: This is pretty hacky, I'm not sure if there's a better way to do this. +# Note that initializing datasets separately then concatenating them +# together is 4x slower than initializing a dataset then hacking into +# the __getitem__ method. +class FRDCDatasetFlipped(FRDCDataset): + def __len__(self): + """Assume that the dataset is 4x larger than it actually is. + + For example, for index 0, we return the original image. For index 1, we + return the horizontally flipped image and so on, until index 3. + Then, return the next image for index 4, and so on. + """ + return super().__len__() * 4 + + def __getitem__(self, idx): + """Alter the getitem method to implement the logic above.""" + x, y = super().__getitem__(int(idx // 4)) + if idx % 4 == 0: + return x, y + elif idx % 4 == 1: + return RandomHorizontalFlip(p=1)(x), y + elif idx % 4 == 2: + return RandomVerticalFlip(p=1)(x), y + elif idx % 4 == 3: + return RandomHorizontalFlip(p=1)(RandomVerticalFlip(p=1)(x)), y + + +def evaluate(ckpt_pth: Path | str | None = None) -> tuple[plt.Figure, float]: + ds = FRDCDatasetFlipped( + "chestnut_nature_park", + "20210510", + "90deg43m85pct255deg/map", + transform=preprocess, + ) + + if ckpt_pth is None: + # This fetches all possible checkpoints and gets the latest one + ckpt_pth = sorted( + THIS_DIR.glob("**/*.ckpt"), key=lambda x: x.stat().st_mtime_ns + )[-1] + + m = InceptionV3MixMatchModule.load_from_checkpoint(ckpt_pth) + # Make predictions + trainer = pl.Trainer(logger=False) + pred = trainer.predict(m, dataloaders=DataLoader(ds, batch_size=32)) + + y_trues = [] + y_preds = [] + for y_true, y_pred in pred: + y_trues.append(y_true) + y_preds.append(y_pred) + y_trues = np.concatenate(y_trues) + y_preds = np.concatenate(y_preds) + acc = (y_trues == y_preds).mean() + + # Plot the confusion matrix + cm = confusion_matrix(y_trues, y_preds) + + plt.figure(figsize=(10, 10)) + + heatmap( + cm, + annot=True, + xticklabels=m.y_encoder.categories_[0], + yticklabels=m.y_encoder.categories_[0], + cbar=False, + ) + plt.title(f"Accuracy: {acc:.2%}") + plt.tight_layout(pad=3) + plt.xlabel("Predicted Label") + plt.ylabel("True Label") + return plt.gcf(), acc + + +def preprocess(x): + return Compose( + [ + ToImage(), + ToDtype(torch.float32, scale=True), + CenterCrop( + [ + InceptionV3MixMatchModule.MIN_SIZE, + InceptionV3MixMatchModule.MIN_SIZE, + ], + ), + ] + )(x) + + +def train_preprocess(x): + return Compose( + [ + ToImage(), + ToDtype(torch.float32, scale=True), + RandomCrop( + [ + InceptionV3MixMatchModule.MIN_SIZE, + InceptionV3MixMatchModule.MIN_SIZE, + ], + pad_if_needed=True, + padding_mode="constant", + fill=0, + ), + RandomHorizontalFlip(), + RandomVerticalFlip(), + ] + )(x) + + +def train_unl_preprocess(n_aug: int = 2): + def f(x): + # This simulates the n_aug of MixMatch + return ( + [train_preprocess(x) for _ in range(n_aug)] if n_aug > 0 else None + ) + + return f + + +def main( + batch_size=32, + epochs=10, + train_iters=25, + val_iters=15, + lr=1e-3, +): + run = wandb.init() + logger = WandbLogger(name="chestnut_dec_may", project="frdc") + # Prepare the dataset + train_lab_ds = FRDCDataset( + "chestnut_nature_park", + "20201218", + None, + transform=train_preprocess, + ) + + # TODO: This is a hacky impl of the unlabelled dataset, see the docstring + # for future work. + train_unl_ds = FRDCUnlabelledDataset( + "chestnut_nature_park", + "20201218", + None, + transform=train_unl_preprocess(2), + ) + + # Subset(train_ds, np.argwhere(train_ds.targets == 0).reshape(-1)) + val_ds = FRDCDataset( + "chestnut_nature_park", + "20210510", + "90deg43m85pct255deg/map", + transform=preprocess, + ) + + oe = OrdinalEncoder( + handle_unknown="use_encoded_value", + unknown_value=np.nan, + ) + oe.fit(np.array(train_lab_ds.targets).reshape(-1, 1)) + n_classes = len(oe.categories_[0]) + + ss = StandardScaler() + ss.fit(train_lab_ds.ar.reshape(-1, train_lab_ds.ar.shape[-1])) + + # Prepare the datamodule and trainer + dm = FRDCDataModule( + train_lab_ds=train_lab_ds, + # Pass in None to use the default supervised DM + train_unl_ds=train_unl_ds, + val_ds=val_ds, + batch_size=batch_size, + train_iters=train_iters, + val_iters=val_iters, + ) + + trainer = pl.Trainer( + max_epochs=epochs, + deterministic=True, + accelerator="gpu", + log_every_n_steps=4, + callbacks=[ + # Stop training if the validation loss doesn't improve for 4 epochs + EarlyStopping(monitor="val_loss", patience=4, mode="min"), + # Log the learning rate on TensorBoard + LearningRateMonitor(logging_interval="epoch"), + # Save the best model + ckpt := ModelCheckpoint( + monitor="val_loss", mode="min", save_top_k=1 + ), + ], + logger=logger, + ) + m = InceptionV3MixMatchModule( + n_classes=n_classes, + lr=lr, + x_scaler=ss, + y_encoder=oe, + ) + + trainer.fit(m, datamodule=dm) + + with open(Path(__file__).parent / "report.md", "w") as f: + f.write( + f"# Chestnut Nature Park (Dec 2020 vs May 2021)" + f"[WandB Report]({run.get_url()})" + ) + + fig, acc = evaluate(Path(ckpt.best_model_path)) + wandb.log({"confusion_matrix": wandb.Image(fig)}) + wandb.log({"eval_accuracy": acc}) + + wandb.finish() + + +if __name__ == "__main__": + BATCH_SIZE = 32 + EPOCHS = 10 + TRAIN_ITERS = 25 + VAL_ITERS = 15 + LR = 1e-3 + os.environ["GOOGLE_CLOUD_PROJECT"] = "frmodel" + + assert wandb.run is None + wandb.setup(wandb.Settings(program=__name__, program_relpath=__name__)) + main( + batch_size=BATCH_SIZE, + epochs=EPOCHS, + train_iters=TRAIN_ITERS, + val_iters=VAL_ITERS, + lr=LR, + ) diff --git a/tests/model_tests/utils.py b/tests/model_tests/utils.py index 1fd09a7d..22640115 100644 --- a/tests/model_tests/utils.py +++ b/tests/model_tests/utils.py @@ -1,12 +1 @@ -from frdc.load import FRDCDataset -from frdc.preprocess.extract_segments import extract_segments_from_bounds - BANDS = ["NB", "NG", "NR", "RE", "NIR"] - - -def get_dataset(site, date, version): - ds = FRDCDataset(site=site, date=date, version=version) - ar, order = ds.get_ar_bands(BANDS) - bounds, labels = ds.get_bounds_and_labels() - segments = extract_segments_from_bounds(ar, bounds, cropped=True) - return segments, labels diff --git a/tests/unit_tests/models/test_facenet.py b/tests/unit_tests/models/test_inceptionv3.py similarity index 60% rename from tests/unit_tests/models/test_facenet.py rename to tests/unit_tests/models/test_inceptionv3.py index 269dfaa9..28932d45 100644 --- a/tests/unit_tests/models/test_facenet.py +++ b/tests/unit_tests/models/test_inceptionv3.py @@ -1,17 +1,23 @@ import pytest import torch +from sklearn.preprocessing import StandardScaler, OrdinalEncoder -from frdc.models import FaceNet +from frdc.models.inceptionv3 import InceptionV3MixMatchModule N_CLASSES = 42 N_CHANNELS = 3 BATCH_SIZE = 2 -MIN_SIZE = FaceNet.MIN_SIZE +MIN_SIZE = InceptionV3MixMatchModule.MIN_SIZE @pytest.fixture(scope="module") -def facenet(): - return FaceNet(n_out_classes=N_CLASSES) +def inceptionv3(): + return InceptionV3MixMatchModule( + n_classes=N_CLASSES, + lr=1e-3, + x_scaler=StandardScaler(), + y_encoder=OrdinalEncoder(), + ) @pytest.mark.parametrize( @@ -31,7 +37,7 @@ def facenet(): [BATCH_SIZE, 1, MIN_SIZE, False], ], ) -def test_facenet_io(facenet, batch_size, channels, size, ok): +def test_inceptionv3_io(inceptionv3, batch_size, channels, size, ok): def check(net, x): if ok: assert net(x).shape == (BATCH_SIZE, N_CLASSES) @@ -41,19 +47,21 @@ def check(net, x): x = torch.rand((batch_size, channels, size, size)) - facenet.train() - check(facenet, x) - facenet.eval() - check(facenet, x) + inceptionv3.train() + check(inceptionv3, x) + inceptionv3.eval() + check(inceptionv3, x) -def test_facenet_frozen(facenet): +def test_inception_frozen(inceptionv3): """Assert that the base model is frozen, and the rest is trainable.""" - assert sum(p.numel() for p in facenet.parameters() if p.requires_grad) > 0 + assert ( + sum(p.numel() for p in inceptionv3.parameters() if p.requires_grad) > 0 + ) assert ( sum( p.numel() - for p in facenet.inception.parameters() + for p in inceptionv3.inception.parameters() if p.requires_grad ) == 0