From 19154aff9e70d9b8136b70e8063cd1ef332cf581 Mon Sep 17 00:00:00 2001 From: Kaylode Date: Tue, 24 Mar 2026 18:24:50 +0000 Subject: [PATCH 1/3] =?UTF-8?q?chore:=20Theseus=20v2.0.0=20=E2=80=94=20maj?= =?UTF-8?q?or=20framework=20modernization?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Bump version to 2.0.0 - Modernize all dependencies (Lightning 2.4+, wandb 0.17+, optuna 3.6+, etc.) - Add huggingface-hub and safetensors as core dependencies - Replace black/isort with ruff for linting and formatting - Modernize Dockerfile (CUDA 12.4, Ubuntu 22.04, uv) - Enhance Registry with generics, merge(), get_or_none(), __len__, __getitem__ - Refactor BasePipeline with shared _PipelineBase, extracted helpers - Fix LightningModelWrapper autocast device detection, use optimizers() API - Refactor LoggerObserver with dispatch table (O(1) routing) - Make Metric an ABC with @abstractmethod decorators - Cache inspect.signature in getter.py via lru_cache - Add FSDP strategy support to Trainer - Add HuggingFaceHubMixin (save/load/push with safetensors) - Add HuggingFaceHubCallback for automatic model pushing - Modernize all GitHub workflows (actions v4/v5, Python 3.11, uv, caching) - Add lint.yml workflow (ruff check + format) - Add release.yml workflow (PyPI publishing via trusted OIDC) - Create AGENT.md development guide --- .github/workflows/clf.yml | 51 +- .github/workflows/docker.yml | 37 +- .github/workflows/lint.yml | 36 + .github/workflows/release.yml | 39 + .github/workflows/segm.yml | 49 +- .github/workflows/tablr.yml | 49 +- .pre-commit-config.yaml | 18 +- AGENT.md | 57 + Dockerfile | 100 +- __init__.py | 1 + pyproject.toml | 136 +- theseus/__init__.py | 35 +- theseus/base/callbacks/__init__.py | 3 + theseus/base/callbacks/hub_callback.py | 99 + .../base/callbacks/loss_logging_callback.py | 7 +- theseus/base/callbacks/timer_callback.py | 4 + theseus/base/callbacks/wandb_callback.py | 102 +- theseus/base/losses/__init__.py | 2 + theseus/base/losses/mae_loss.py | 35 + theseus/base/losses/mse_loss.py | 2 +- theseus/base/metrics/accuracy.py | 20 +- theseus/base/metrics/bl_accuracy.py | 17 +- theseus/base/metrics/f1.py | 11 +- theseus/base/metrics/mcc.py | 13 +- theseus/base/metrics/metric_template.py | 61 +- theseus/base/metrics/precision_recall.py | 17 +- theseus/base/metrics/roc_auc_score.py | 44 +- theseus/base/models/wrapper.py | 180 +- theseus/base/pipeline.py | 395 +- theseus/base/trainer/__init__.py | 47 +- theseus/base/utilities/getter.py | 86 +- theseus/base/utilities/hub.py | 242 + theseus/base/utilities/loggers/observer.py | 134 +- theseus/base/utilities/optuna_tuner.py | 38 +- theseus/ml/preprocessors/base.py | 8 +- theseus/ml/preprocessors/encoder.py | 3 +- theseus/registry.py | 108 +- uv.lock | 5468 +++++++++++++++++ 38 files changed, 7111 insertions(+), 643 deletions(-) create mode 100644 .github/workflows/lint.yml create mode 100644 .github/workflows/release.yml create mode 100644 AGENT.md create mode 100644 __init__.py create mode 100644 theseus/base/callbacks/hub_callback.py create mode 100644 theseus/base/losses/mae_loss.py create mode 100644 theseus/base/utilities/hub.py create mode 100644 uv.lock diff --git a/.github/workflows/clf.yml b/.github/workflows/clf.yml index f2d0a33..2cb6808 100644 --- a/.github/workflows/clf.yml +++ b/.github/workflows/clf.yml @@ -1,4 +1,4 @@ -name: autobuild_clf +name: ci_classification on: pull_request: branches: @@ -9,42 +9,57 @@ on: - master - 'V**' - dev + env: GDRIVE_CREDENTIALS_DATA: ${{ secrets.GDRIVE_CREDENTIALS_DATA }} REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }} jobs: - build: + test-classification: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - name: Set up Python 3.10 - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + + - name: Set up Python 3.11 + uses: actions/setup-python@v5 with: - python-version: '3.10' - architecture: 'x64' - - uses: actions/setup-node@v3 + python-version: '3.11' + + - name: Install uv + uses: astral-sh/setup-uv@v4 + + - uses: actions/setup-node@v4 with: - node-version: '16' - - uses: iterative/setup-cml@v1 - - name: Display Python version - run: python -c "import sys; print(sys.version)" + node-version: '20' + + - uses: iterative/setup-cml@v3 + + - name: Cache uv packages + uses: actions/cache@v4 + with: + path: ~/.cache/uv + key: ${{ runner.os }}-uv-clf-${{ hashFiles('pyproject.toml') }} + restore-keys: | + ${{ runner.os }}-uv-clf- + - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu - pip install -e '.[dev,cv,cv_classification]' - pip install dvc dvc-gdrive + uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu + uv pip install --system -e '.[dev,cv,cv_classification]' + uv pip install --system dvc dvc-gdrive npm install -g markdown-table-cli + - name: Download data run: | echo "$GDRIVE_CREDENTIALS_DATA" > credentials.json dvc remote modify gdrive --local gdrive_user_credentials_file ./credentials.json dvc pull ls -la samples + - name: Test with pytest run: | - pytest tests/classification --capture=no + uv run pytest tests/classification --capture=no + - name: Display report run: | echo "# Classification Report" > report.md @@ -53,7 +68,7 @@ jobs: echo "#### Confusion Matrix" >> report.md echo "![Confusion Matrix](runs/pytest_clf/Validation/cfm.png)" >> report.md echo "#### Errorcases" >> report.md - echo "![Confusion Matrix](runs/pytest_clf/Validation/errorcases.png)" >> report.md + echo "![Errorcases](runs/pytest_clf/Validation/errorcases.png)" >> report.md echo "------------------" >> report.md echo "#### Hyperparameters Tuning" >> report.md echo "Leaderboard" >> report.md diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 9fd896b..bd5afb4 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -1,4 +1,4 @@ -name: autobuild_docker +name: ci_docker on: pull_request: branches: @@ -10,26 +10,31 @@ env: DOCKERHUB_TAG: kaylode/theseus:latest jobs: - run: + build-and-test: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - name: Set up Python 3.10 - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + + - name: Set up Python 3.11 + uses: actions/setup-python@v5 with: - python-version: '3.10' - architecture: 'x64' - - uses: iterative/setup-cml@v1 + python-version: '3.11' + + - uses: iterative/setup-cml@v3 - uses: iterative/setup-dvc@v1 + - name: Set up QEMU - uses: docker/setup-qemu-action@v2 + uses: docker/setup-qemu-action@v3 + - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v2 + uses: docker/setup-buildx-action@v3 + - name: Create credentials file run: | echo "$GDRIVE_CREDENTIALS_DATA" > credentials.json + - name: Build Dockerfile - uses: docker/build-push-action@v4 + uses: docker/build-push-action@v6 with: context: . tags: ${{ env.DOCKERHUB_TAG }} @@ -40,10 +45,10 @@ jobs: - name: Free up space run: | docker system prune -f - sudo rm -rf "/usr/local/share/boost" + sudo rm -rf /usr/local/share/boost sudo rm -rf "$AGENT_TOOLSDIRECTORY" - - name: Docker name + - name: Load Docker image run: | docker load -i ${{ github.workspace }}/image.tar docker image inspect ${{ env.DOCKERHUB_TAG }} @@ -61,16 +66,16 @@ jobs: pytest tests --capture=no - name: Log in to Docker Hub - uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a + uses: docker/login-action@v3 with: username: ${{ secrets.DOCKER_USERNAME }} password: ${{ secrets.DOCKER_PASSWORD }} - name: Push image to DockerHub run: | - docker push --all-tags + docker push ${{ env.DOCKERHUB_TAG }} - - name: where am I + - name: Debug workspace run: | pwd ls -la diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml new file mode 100644 index 0000000..a2c47a5 --- /dev/null +++ b/.github/workflows/lint.yml @@ -0,0 +1,36 @@ +name: lint +on: + pull_request: + branches: + - master + - dev + push: + branches: + - master + - dev + +jobs: + lint: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Set up Python 3.11 + uses: actions/setup-python@v5 + with: + python-version: '3.11' + + - name: Install uv + uses: astral-sh/setup-uv@v4 + + - name: Install dependencies + run: | + uv pip install --system ruff + + - name: Ruff check + run: | + ruff check theseus/ tests/ + + - name: Ruff format check + run: | + ruff format --check theseus/ tests/ diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 0000000..f2239b3 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,39 @@ +name: release +on: + push: + tags: + - 'v*' + +permissions: + contents: read + id-token: write + +jobs: + publish: + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/theseus + steps: + - uses: actions/checkout@v4 + + - name: Set up Python 3.11 + uses: actions/setup-python@v5 + with: + python-version: '3.11' + + - name: Install uv + uses: astral-sh/setup-uv@v4 + + - name: Install build dependencies + run: | + uv pip install --system build + + - name: Build package + run: | + python -m build + + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + skip-existing: true diff --git a/.github/workflows/segm.yml b/.github/workflows/segm.yml index 581bcb9..d3d8089 100644 --- a/.github/workflows/segm.yml +++ b/.github/workflows/segm.yml @@ -1,4 +1,4 @@ -name: autobuild_segm +name: ci_segmentation on: pull_request: branches: @@ -9,42 +9,57 @@ on: - master - 'V**' - dev + env: GDRIVE_CREDENTIALS_DATA: ${{ secrets.GDRIVE_CREDENTIALS_DATA }} REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }} jobs: - build: + test-segmentation: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - name: Set up Python 3.10 - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + + - name: Set up Python 3.11 + uses: actions/setup-python@v5 with: - python-version: '3.10' - architecture: 'x64' - - uses: actions/setup-node@v3 + python-version: '3.11' + + - name: Install uv + uses: astral-sh/setup-uv@v4 + + - uses: actions/setup-node@v4 with: - node-version: '16' - - uses: iterative/setup-cml@v1 - - name: Display Python version - run: python -c "import sys; print(sys.version)" + node-version: '20' + + - uses: iterative/setup-cml@v3 + + - name: Cache uv packages + uses: actions/cache@v4 + with: + path: ~/.cache/uv + key: ${{ runner.os }}-uv-segm-${{ hashFiles('pyproject.toml') }} + restore-keys: | + ${{ runner.os }}-uv-segm- + - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu - pip install -e '.[dev,cv,cv_semantic]' - pip install dvc dvc-gdrive + uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu + uv pip install --system -e '.[dev,cv,cv_semantic]' + uv pip install --system dvc dvc-gdrive npm install -g markdown-table-cli + - name: Download data run: | echo "$GDRIVE_CREDENTIALS_DATA" > credentials.json dvc remote modify gdrive --local gdrive_user_credentials_file ./credentials.json dvc pull ls -la samples + - name: Test with pytest run: | - pytest tests/semantic --capture=no + uv run pytest tests/semantic --capture=no + - name: Display report run: | echo "# Semantic Report" > report.md diff --git a/.github/workflows/tablr.yml b/.github/workflows/tablr.yml index 734e657..3ff478d 100644 --- a/.github/workflows/tablr.yml +++ b/.github/workflows/tablr.yml @@ -1,4 +1,4 @@ -name: autobuild_tablr +name: ci_tabular on: pull_request: branches: @@ -9,42 +9,57 @@ on: - master - 'V**' - dev + env: GDRIVE_CREDENTIALS_DATA: ${{ secrets.GDRIVE_CREDENTIALS_DATA }} REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }} jobs: - build: + test-tabular: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - name: Set up Python 3.10 - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + + - name: Set up Python 3.11 + uses: actions/setup-python@v5 with: - python-version: '3.10' - architecture: 'x64' - - uses: actions/setup-node@v3 + python-version: '3.11' + + - name: Install uv + uses: astral-sh/setup-uv@v4 + + - uses: actions/setup-node@v4 with: - node-version: '16' - - uses: iterative/setup-cml@v1 - - name: Display Python version - run: python -c "import sys; print(sys.version)" + node-version: '20' + + - uses: iterative/setup-cml@v3 + + - name: Cache uv packages + uses: actions/cache@v4 + with: + path: ~/.cache/uv + key: ${{ runner.os }}-uv-tablr-${{ hashFiles('pyproject.toml') }} + restore-keys: | + ${{ runner.os }}-uv-tablr- + - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu - pip install -e '.[dev,ml]' - pip install dvc dvc-gdrive + uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu + uv pip install --system -e '.[dev,ml]' + uv pip install --system dvc dvc-gdrive npm install -g markdown-table-cli + - name: Download data run: | echo "$GDRIVE_CREDENTIALS_DATA" > credentials.json dvc remote modify gdrive --local gdrive_user_credentials_file ./credentials.json dvc pull ls -la samples + - name: Test with pytest run: | - pytest tests/tabular --capture=no + uv run pytest tests/tabular --capture=no + - name: Display report run: | echo "# Tabular Classification Report" > report.md diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fdae9e4..ad72756 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,17 +1,15 @@ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.3.0 + rev: v4.6.0 hooks: - id: check-yaml - id: end-of-file-fixer - id: trailing-whitespace -- repo: https://github.com/pycqa/isort - rev: 5.12.0 + - id: check-added-large-files + args: ['--maxkb=1000'] +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.5.0 hooks: - - id: isort - args: ["--profile", "black"] -- repo: https://github.com/python/black.git - rev: 22.12.0 - hooks: - - id: black - language_version: python3 + - id: ruff + args: [--fix] + - id: ruff-format diff --git a/AGENT.md b/AGENT.md new file mode 100644 index 0000000..aa8526f --- /dev/null +++ b/AGENT.md @@ -0,0 +1,57 @@ +# AGENT.md — Theseus Development Guide + +## Project Overview +Theseus is a PyTorch Lightning framework for ML/DL training. It provides a modular, OOP-heavy architecture with registries for models, datasets, losses, metrics, callbacks, trainers, and augmentations. Supports computer vision (classification, detection, segmentation), NLP, and tabular ML tasks. + +## Architecture +- **Registry Pattern**: All components registered via `Registry` class, resolved from YAML configs at runtime +- **Pipeline Pattern**: `BasePipeline` orchestrates init of all components (globals → registry → data → model → callbacks → trainer) +- **Lightning Wrappers**: `LightningModelWrapper` (pl.LightningModule) and `LightningDataModuleWrapper` (pl.LightningDataModule) bridge custom components to Lightning +- **Observer Logger**: `LoggerObserver` uses subscriber pattern for logging to stdout, files, TensorBoard, W&B +- **Config-driven**: Hydra + OmegaConf for all configuration + +## Directory Structure +``` +theseus/ +├── base/ # Core abstractions (pipeline, models, datasets, losses, metrics, callbacks, trainer, utilities) +├── cv/ # Computer vision tasks (classification, detection, semantic segmentation) +├── ml/ # Traditional ML (tabular, XGBoost, LightGBM, CatBoost, SHAP) +├── nlp/ # NLP tasks (base, retrieval) +├── registry.py # Central Registry class +tests/ # Pytest suites for classification, semantic, tabular +.github/workflows/ # CI pipelines (clf, segm, tablr, docker, lint, release) +``` + +## Development Conventions +- **OOP-heavy**: Prefer class hierarchies and inheritance. Use `abc.ABC` for abstract bases. +- **Registry-first**: All components must register with appropriate Registry +- **Config-driven instantiation**: Use `get_instance()` / `get_instance_recursively()` from Hydra configs +- **Type hints**: All public APIs must have type annotations +- **Formatting**: `ruff` for linting and formatting (replaces black + isort) +- **Package manager**: `uv` (not pip) +- **Testing**: `pytest` with `pytest-order` for ordered test execution + +## Key Commands +```bash +# Install +uv pip install -e '.[dev]' + +# Run tests +uv run pytest tests/ --capture=no + +# Lint +uv run ruff check theseus/ +uv run ruff format theseus/ + +# Train (example) +uv run python train.py --config-dir configs --config-name pipeline.yaml +``` + +## Current Progress (v2.0 Update) +- [x] Created `v2.0-update` branch from `dev` +- [x] Created this `AGENT.md` +- [x] Modernize dependencies in `pyproject.toml` +- [x] Update core framework (Registry, Pipeline, Wrapper, Logger) +- [x] Add HuggingFace Hub integration +- [x] Modernize GitHub workflows +- [x] Verify all changes diff --git a/Dockerfile b/Dockerfile index 15f7eb6..4fdbc49 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,17 +1,17 @@ -# syntax = docker/dockerfile:experimental +# syntax = docker/dockerfile:1 # -# NOTE: To build this you will need a docker version > 18.06 with -# experimental enabled and DOCKER_BUILDKIT=1 +# Multi-stage Dockerfile for Theseus v2.0 +# Requires Docker BuildKit (DOCKER_BUILDKIT=1) # -# If you do not use buildkit you are not going to have a good time -# -# For reference: -# https://docs.docker.com/develop/develop-images/build_enhancements/ -ARG BASE_IMAGE=ubuntu:18.04 +ARG BASE_IMAGE=nvidia/cuda:12.4.1-devel-ubuntu22.04 + +# ============================================================================= +# Stage 1: System dependencies +# ============================================================================= +FROM ${BASE_IMAGE} AS base -# Instal basic utilities -FROM ${BASE_IMAGE} as dev-base -RUN apt-get clean && apt-get update && apt-get upgrade && apt-get install -y --no-install-recommends \ +ENV DEBIAN_FRONTEND=noninteractive +RUN apt-get update && apt-get install -y --no-install-recommends \ build-essential \ ca-certificates \ ccache \ @@ -22,49 +22,53 @@ RUN apt-get clean && apt-get update && apt-get upgrade && apt-get install -y -- wget \ libjpeg-dev \ zip \ - swig python3-dev \ - unzip bzip2 ffmpeg libsm6 libxext6 \ - libpng-dev && \ - rm -rf /var/lib/apt/lists/* -RUN /usr/sbin/update-ccache-symlinks -RUN mkdir /opt/ccache && ccache --set-config=cache_dir=/opt/ccache -ENV PATH /opt/conda/bin:$PATH + unzip \ + bzip2 \ + ffmpeg \ + libsm6 \ + libxext6 \ + libpng-dev \ + python3 \ + python3-dev \ + python3-pip \ + python3-venv \ + && rm -rf /var/lib/apt/lists/* + +# Install uv for fast Python package management +COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv + +# ============================================================================= +# Stage 2: Python dependencies +# ============================================================================= +FROM base AS deps -# Instal environment -FROM dev-base as conda-installs -ARG PYTHON_VERSION=3.9 -ARG CUDA_VERSION=11.3 -ARG PYTORCH_VERSION=1.12.1 -ARG CUDA_CHANNEL=nvidia -ARG INSTALL_CHANNEL=pytorch -ENV CONDA_OVERRIDE_CUDA=${CUDA_VERSION} -RUN curl -fsSL -v -o ~/mambaforge.sh -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh && \ - chmod +x ~/mambaforge.sh && \ - ~/mambaforge.sh -b -p /opt/mamba && \ - rm ~/mambaforge.sh && \ - /opt/mamba/bin/mamba install -c "${INSTALL_CHANNEL}" -c "${CUDA_CHANNEL}" -y \ - python=${PYTHON_VERSION} \ - pytorch=${PYTORCH_VERSION} torchvision "cudatoolkit=${CUDA_VERSION}" && \ - /opt/mamba/bin/mamba clean -ya +WORKDIR /workspace +COPY pyproject.toml setup.py ./ +COPY theseus/__init__.py theseus/__init__.py -ENV PATH /opt/mamba/bin:$PATH -ENV NVIDIA_VISIBLE_DEVICES all -ENV NVIDIA_DRIVER_CAPABILITIES compute,utility -ENV LD_LIBRARY_PATH /usr/local/nvidia/lib:/usr/local/nvidia/lib64 -ENV PYTORCH_VERSION ${PYTORCH_VERSION} +# Install PyTorch with CUDA 12.4 support +RUN uv pip install --system \ + torch torchvision torchaudio \ + --index-url https://download.pytorch.org/whl/cu124 -# Install dependencies +# Install theseus with all optional dependencies COPY ./ /workspace/ -WORKDIR /workspace/ -RUN /opt/mamba/bin/python -m pip install --upgrade pip && \ - /opt/mamba/bin/python -m pip install -e .[cv,cv_classification,cv_semantic,cv_detection,nlp,nlp_retrieval,ml,dev] && \ - /opt/mamba/bin/python -m pip install dvc dvc-gdrive && \ - /opt/mamba/bin/python -m pip install -U timm +RUN uv pip install --system -e ".[all,dev]" + +# Install DVC for data versioning +RUN uv pip install --system dvc dvc-gdrive + +# ============================================================================= +# Stage 3: Data + Runtime +# ============================================================================= +FROM deps AS runtime + +WORKDIR /workspace -# Pull data from GDrive +# Pull data from GDrive (requires credentials secret) RUN --mount=type=secret,id=credentials \ - CREDENTIALS=$(cat /run/secrets/credentials) \ - && echo "$CREDENTIALS" > /workspace/credentials.json + CREDENTIALS=$(cat /run/secrets/credentials) \ + && echo "$CREDENTIALS" > /workspace/credentials.json RUN dvc remote modify gdrive --local gdrive_user_credentials_file /workspace/credentials.json RUN dvc pull diff --git a/__init__.py b/__init__.py new file mode 100644 index 0000000..1534704 --- /dev/null +++ b/__init__.py @@ -0,0 +1 @@ +from .theseus import * \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index fdf241a..bf53c53 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,5 @@ [build-system] -# These are the assumed default build requirements from pip: -# https://pip.pypa.io/en/stable/reference/pip/#pep-517-and-518-support -requires = ["setuptools>=43.0.0", "wheel", "setuptools-scm"] +requires = ["setuptools>=68.0.0", "wheel", "setuptools-scm"] build-backend = "setuptools.build_meta" [tool.setuptools] @@ -9,12 +7,12 @@ packages = ["theseus"] [project] name = "theseus" -version = "1.5.0" -description = "A general template for various Deep Learning tasks. Strongly relies on Pytorch" +version = "2.0.0" +description = "A modular PyTorch Lightning framework for deep learning research and production training" readme = "README.md" requires-python = ">=3.10" license = {file = "LICENSE"} -keywords = ["pytorch", "template", "deep learning"] +keywords = ["pytorch", "lightning", "template", "deep learning", "machine learning"] authors = [ {name = "Minh-Khoi Pham", email = "minhkhoi.pham@adaptcentre.ie" }, {name = "Hoang-Lan Nguyen", email = "nhlan091000@gmail.com"} @@ -25,86 +23,106 @@ maintainers = [ classifiers = [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Developers", - "Topic :: Deep Learning :: Template", - "License :: MIT License", + "Intended Audience :: Science/Research", + "Topic :: Scientific/Engineering :: Artificial Intelligence", + "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", ] dependencies = [ - "seaborn>=0.12.0", - "plotly>=5.10.0", - "matplotlib>=3.4.3", - "webcolors>=1.12", - "wandb>=0.13.3", - "tensorboard>=2.10.0", - "pyyaml>=6.0", - "tqdm>=4.64.1", - "gdown>=4.5.1", - "tabulate>=0.8.10", - "loguru>=0.6.0", + "seaborn>=0.13.0", + "plotly>=5.18.0", + "matplotlib>=3.8.0", + "webcolors>=1.13", + "wandb>=0.17.0", + "tensorboard>=2.16.0", + "pyyaml>=6.0.1", + "tqdm>=4.66.0", + "gdown>=5.1.0", + "tabulate>=0.9.0", + "loguru>=0.7.0", "kaleido>=0.2.1", - "optuna>=3.0.5", - "deepdiff>=6.2.3", + "optuna>=3.6.0", + "deepdiff>=7.0.0", "hydra-core>=1.3.2", - "lightning>=2.0.0" + "lightning>=2.4.0", + "huggingface-hub>=0.23.0", + "safetensors>=0.4.0", + "torchvision>=0.24.1", + "scikit-learn>=1.7.2", + "omegaconf>=2.3.0", ] [project.optional-dependencies] -dev=[ - "pytest>=7.2.0", - "pytest-order>=1.0.1", - "pre-commit>=2.21.0", +dev = [ + "pytest>=8.0.0", + "pytest-order>=1.2.0", + "pre-commit>=3.6.0", + "ruff>=0.5.0", ] cv = [ - "albumentations>=1.1.0", - "omegaconf>=2.2.3" + "albumentations>=1.4.0", + "omegaconf>=2.3.0", ] cv_classification = [ - "timm", + "timm>=1.0.0", "scikit-plot", - "grad-cam>=1.4.5" + "grad-cam>=1.5.0", ] cv_semantic = [ - "segmentation-models-pytorch>=0.3.0" + "segmentation-models-pytorch>=0.3.3", ] cv_detection = [ "ensemble_boxes>=1.0.9", - "pycocotools>=2.0.6", + "pycocotools>=2.0.7", ] nlp = [ - "pyvi>=0.1.1", - "py_vncorenlp>=0.1.3", - "spacy>=3.4.2", - "transformers>=4.25.1", - "nltk>=3.7", - "captum>=0.4.1" + "pyvi>=0.1.1", + "py_vncorenlp>=0.1.3", + "spacy>=3.7.0", + "transformers>=4.40.0", + "nltk>=3.8.0", + "captum>=0.7.0", ] nlp_retrieval = [ - "sentence_transformers>=2.2.2", - "rank_bm25>=0.2.2", - "elasticsearch>=7.17.7" + "sentence_transformers>=3.0.0", + "rank_bm25>=0.2.2", + "elasticsearch>=8.12.0", ] ml = [ - "pandas", - "pandarallel>=1.6.3", - "numpy", - "scikit-learn>=1.0.0", - "scipy>=1.7.0", - "optuna>=3.0.5", - "psycopg2-binary>=2.9.5", - "gunicorn>=20.1.0", - "lightgbm>=3.3.3", - "xgboost<=1.7.1", - "catboost", - "shap>=0.41.0", - "lime>=0.2.0.1", - "scikit-plot", + "pandas>=2.1.0", + "pandarallel>=1.6.5", + "numpy>=1.26.0", + "scikit-learn>=1.4.0", + "scipy>=1.12.0", + "optuna>=3.6.0", + "psycopg2-binary>=2.9.9", + "gunicorn>=21.2.0", + "lightgbm>=4.3.0", + "xgboost>=2.0.0", + "catboost>=1.2.0", + "shap>=0.45.0", + "lime>=0.2.0.1", + "scikit-plot", ] all = [ - "theseus[cv,cv_classification,cv_semantic,cv_detection,nlp,nlp_retrieval,ml]", + "theseus[cv,cv_classification,cv_semantic,cv_detection,nlp,nlp_retrieval,ml]", ] -[project.urls] # Optional +[project.urls] "Homepage" = "https://github.com/kaylode/theseus" +"Repository" = "https://github.com/kaylode/theseus" +"Issues" = "https://github.com/kaylode/theseus/issues" + +[tool.ruff] +target-version = "py310" +line-length = 100 + +[tool.ruff.lint] +select = ["E", "F", "W", "I", "UP", "B", "SIM"] +ignore = ["E501", "B905", "SIM108"] -[tool.isort] -profile = "black" +[tool.ruff.lint.isort] +known-first-party = ["theseus"] diff --git a/theseus/__init__.py b/theseus/__init__.py index 6f39759..d416365 100644 --- a/theseus/__init__.py +++ b/theseus/__init__.py @@ -1,5 +1,5 @@ """ -Theseus - Templates and useful tools for Deep Learning +Theseus - A modular PyTorch Lightning framework for deep learning ~~~~~~~~~~~~~~~~~~~ :copyright: (c) 2020-present Kaylode @@ -11,7 +11,38 @@ __author__ = "kaylode" __license__ = "MIT" __copyright__ = "Copyright 2020-present Kaylode" -__version__ = "1.5.0" +__version__ = "2.0.0" from .base import * from .registry import Registry + +from .base.pipeline import BasePipeline +from .base.datasets.sampler import BalanceSampler +from .base.datasets.dataloader import DataLoaderWithCollator + +from .base.utilities import ( + move_to, + seed_everything, + LoggerObserver, + find_file_recursively, + get_devices_info, + download_from_wandb, + get_instance_recursively, +) # explicitly re-exporting + +from .base.utilities.loggers import FileLogger + +__all__ = [ + "move_to", + "seed_everything", + "FileLogger", + "LoggerObserver", + "find_file_recursively", + "get_devices_info", + "download_from_wandb", + "get_instance_recursively", + "BasePipeline", + "BalanceSampler", + "DataLoaderWithCollator", + "Registry", +] \ No newline at end of file diff --git a/theseus/base/callbacks/__init__.py b/theseus/base/callbacks/__init__.py index a9b0c11..930217b 100644 --- a/theseus/base/callbacks/__init__.py +++ b/theseus/base/callbacks/__init__.py @@ -8,6 +8,7 @@ from theseus.registry import Registry from .checkpoint_callback import TorchCheckpointCallback +from .hub_callback import HuggingFaceHubCallback from .loss_logging_callback import LossLoggerCallback from .metric_logging_callback import MetricLoggerCallback from .timer_callback import TimerCallback @@ -26,3 +27,5 @@ CALLBACKS_REGISTRY.register(LossLoggerCallback) CALLBACKS_REGISTRY.register(MetricLoggerCallback) CALLBACKS_REGISTRY.register(TorchCheckpointCallback) +CALLBACKS_REGISTRY.register(HuggingFaceHubCallback) + diff --git a/theseus/base/callbacks/hub_callback.py b/theseus/base/callbacks/hub_callback.py new file mode 100644 index 0000000..ebcc3ea --- /dev/null +++ b/theseus/base/callbacks/hub_callback.py @@ -0,0 +1,99 @@ +""" +Lightning callback for pushing model checkpoints to HuggingFace Hub. +""" + +from __future__ import annotations + +import logging +from typing import Any, Optional + +import lightning.pytorch as pl +from lightning.pytorch.callbacks import Callback + +from theseus.registry import Registry + +logger = logging.getLogger(__name__) + + +class HuggingFaceHubCallback(Callback): + """ + Lightning callback that pushes model checkpoints to HuggingFace Hub. + + Can be configured to push on best metric, periodically, or at training end. + + Example config:: + + callbacks: + - name: HuggingFaceHubCallback + args: + repo_id: "username/my-model" + push_on_train_end: true + push_every_n_epochs: 5 + + Args: + repo_id: HuggingFace repo ID (e.g. ``username/model-name``). + token: HuggingFace API token. + push_on_train_end: Push at end of training. + push_every_n_epochs: Push every N epochs (0 = disabled). + private: Whether the repo should be private. + use_safetensors: Use safetensors format. + config: Optional config dict to include. + """ + + def __init__( + self, + repo_id: str, + *, + token: Optional[str] = None, + push_on_train_end: bool = True, + push_every_n_epochs: int = 0, + private: bool = False, + use_safetensors: bool = True, + config: Optional[dict] = None, + **kwargs: Any, + ) -> None: + super().__init__() + self.repo_id = repo_id + self.token = token + self.push_on_train_end = push_on_train_end + self.push_every_n_epochs = push_every_n_epochs + self.private = private + self.use_safetensors = use_safetensors + self.config = config or {} + + def _push_model(self, trainer: pl.Trainer, pl_module: pl.LightningModule) -> None: + """Push the underlying model to HuggingFace Hub.""" + from theseus.base.utilities.hub import HuggingFaceHubMixin + + model = getattr(pl_module, "model", pl_module) + + if isinstance(model, HuggingFaceHubMixin): + try: + model.push_to_hub( + self.repo_id, + token=self.token, + private=self.private, + config=self.config, + use_safetensors=self.use_safetensors, + commit_message=f"Epoch {trainer.current_epoch}", + ) + except Exception as e: + logger.warning(f"Failed to push model to HuggingFace Hub: {e}") + else: + logger.warning( + f"Model {type(model).__name__} does not inherit from " + f"HuggingFaceHubMixin. Skipping push." + ) + + def on_train_epoch_end( + self, trainer: pl.Trainer, pl_module: pl.LightningModule + ) -> None: + if self.push_every_n_epochs > 0: + if (trainer.current_epoch + 1) % self.push_every_n_epochs == 0: + self._push_model(trainer, pl_module) + + def on_train_end( + self, trainer: pl.Trainer, pl_module: pl.LightningModule + ) -> None: + if self.push_on_train_end: + self._push_model(trainer, pl_module) diff --git a/theseus/base/callbacks/loss_logging_callback.py b/theseus/base/callbacks/loss_logging_callback.py index f23adfb..3703ad1 100644 --- a/theseus/base/callbacks/loss_logging_callback.py +++ b/theseus/base/callbacks/loss_logging_callback.py @@ -62,7 +62,7 @@ def setup( if self.print_interval is None: self.print_interval = self.auto_get_print_interval(pl_module) LOGGER.text( - "Print interval not specified. Auto calculating...", + f"Print interval not specified. Auto calculated and set to {self.print_interval} iterations.", level=LoggerObserver.DEBUG, ) @@ -81,6 +81,7 @@ def auto_get_print_interval( else self.params["testloader_length"] ) print_interval = max(int(train_fraction * num_iterations_per_epoch), 1) + return print_interval def on_train_epoch_start(self, trainer: pl.Trainer, pl_module: pl.LightningModule): @@ -126,11 +127,13 @@ def on_train_batch_end( # Running time since last interval batch_time = time.time() - self.running_time + if getattr(self, "running_time_list", None) is None: + self.running_time_list = [] self.running_time_list.append(batch_time) # Logging if ( - iters % self.print_interval == 0 + (iters % self.print_interval == 0 and iters > 0 ) or (iters + 1) % self.params["trainloader_length"] == 0 ): diff --git a/theseus/base/callbacks/timer_callback.py b/theseus/base/callbacks/timer_callback.py index b07940e..2f7d34e 100644 --- a/theseus/base/callbacks/timer_callback.py +++ b/theseus/base/callbacks/timer_callback.py @@ -60,6 +60,8 @@ def on_train_epoch_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule) """ After going to the training loop """ + if getattr(trainer, "train_epoch_start_time", None) is None: + self.train_epoch_start_time = time.time() running_time = time.time() - self.train_epoch_start_time h, m, s = seconds_to_hours(running_time) LOGGER.text( @@ -82,6 +84,8 @@ def on_validation_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule): After finish validation """ + if getattr(trainer, "val_epoch_start_time", None) is not None: + self.val_epoch_start_time = time.time() running_time = time.time() - self.val_epoch_start_time h, m, s = seconds_to_hours(running_time) LOGGER.text( diff --git a/theseus/base/callbacks/wandb_callback.py b/theseus/base/callbacks/wandb_callback.py index 361c16a..622fc25 100644 --- a/theseus/base/callbacks/wandb_callback.py +++ b/theseus/base/callbacks/wandb_callback.py @@ -6,11 +6,13 @@ import lightning.pytorch as pl from deepdiff import DeepDiff +from deepdiff.helper import SetOrdered from lightning.pytorch.callbacks import Callback from omegaconf import DictConfig, OmegaConf from theseus.base.utilities.loggers.observer import LoggerObserver from theseus.base.utilities.loggers.wandb_logger import WandbLogger, find_run_id +from lightning.pytorch.utilities.model_summary import summarize try: import wandb as wandblogger @@ -23,20 +25,26 @@ def pretty_print_diff(diff): texts = [] for type_key in diff.keys(): - for config_key in diff[type_key].keys(): - if type_key == "values_changed": - texts.append( - config_key - + ": " - + str(diff[type_key][config_key]["old_value"]) - + "-->" - + str(diff[type_key][config_key]["new_value"]) - ) - elif "item_removed" in type_key: - texts.append(config_key + ": " + str(diff[type_key][config_key])) - elif "item_added" in type_key: - texts.append(config_key + ": " + str(diff[type_key][config_key])) - + try: + for config_key in diff[type_key].keys(): + if type_key == "values_changed": + texts.append( + config_key + + ": " + + str(diff[type_key][config_key]["old_value"]) + + "-->" + + str(diff[type_key][config_key]["new_value"]) + ) + elif "item_removed" in type_key: + texts.append(config_key + ": " + str(diff[type_key][config_key])) + elif "item_added" in type_key: + texts.append(config_key + ": " + str(diff[type_key][config_key])) + except: + texts.append( + str(type_key) + + ": " + + str(diff[type_key]) + ) return "\n".join(texts) @@ -62,6 +70,7 @@ def __init__( save_dir: str = None, resume: str = None, config_dict: DictConfig = None, + log_checkpoints: bool = True, **kwargs, ) -> None: super().__init__() @@ -71,6 +80,7 @@ def __init__( self.resume = resume self.save_dir = save_dir self.config_dict = config_dict + self.log_checkpoints = log_checkpoints # A hack, not good if self.save_dir is None: @@ -101,6 +111,7 @@ def __init__( # Check if the config remains the same, if not, create new run id old_config_dict = OmegaConf.load(old_config_path) tmp_config_dict = deepcopy(self.config_dict) + tmp_config_dict = DictConfig(tmp_config_dict) ## strip off global key because `resume` will always different old_config_dict.pop("global", None) OmegaConf.set_struct(tmp_config_dict, False) @@ -129,7 +140,7 @@ def __init__( ) answer = int(input()) - assert answer in [1, 2], "Wrong input" + assert answer in [1, 2, 3], "Wrong input" if answer == 2: LOGGER.text( "Creating new wandb run...", @@ -179,30 +190,63 @@ def setup( f.write(self.id) # Save all config files - self.wandb_logger.log_file( - tag="configs", - base_folder=self.save_dir, - value=osp.join(self.save_dir, "*.yaml"), + if self.log_checkpoints: + self.wandb_logger.log_file( + tag="configs", + base_folder=self.save_dir, + value=osp.join(self.save_dir, "*.yaml"), + ) + + + summary = summarize(pl_module, max_depth=3) + + LOGGER.text( + f"Model summary:\n{summary}", + level=LoggerObserver.INFO, ) + total_params = summary.total_parameters + total_trainable_params = summary.trainable_parameters + + # Log learning rates + log_dict = [{ + "tag": "Training/Total no. parameters", + "value": total_params, + "type": LoggerObserver.SCALAR, + "kwargs": {"step": 0}, + }] + + log_dict.append({ + "tag": "Training/Total no. trainable parameters", + "value": total_trainable_params, + "type": LoggerObserver.SCALAR, + "kwargs": {"step": 0}, + }) + + LOGGER.log(log_dict) + + + def teardown(self, trainer: pl.Trainer, pl_module: pl.LightningModule, stage: str): """ After finish training """ base_folder = osp.join(self.save_dir, "checkpoints") - self.wandb_logger.log_file( - tag="checkpoint", - base_folder=self.save_dir, - value=osp.join(base_folder, "*.ckpt"), - ) + if self.log_checkpoints: + self.wandb_logger.log_file( + tag="checkpoint", + base_folder=self.save_dir, + value=osp.join(base_folder, "*.ckpt"), + ) def on_validation_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule): """ On validation batch (iteration) end """ base_folder = osp.join(self.save_dir, "checkpoints") - self.wandb_logger.log_file( - tag="checkpoint", - base_folder=self.save_dir, - value=osp.join(base_folder, "*.ckpt"), - ) + if self.log_checkpoints: + self.wandb_logger.log_file( + tag="checkpoint", + base_folder=self.save_dir, + value=osp.join(base_folder, "*.ckpt"), + ) diff --git a/theseus/base/losses/__init__.py b/theseus/base/losses/__init__.py index 48731b2..a2a3121 100644 --- a/theseus/base/losses/__init__.py +++ b/theseus/base/losses/__init__.py @@ -7,6 +7,7 @@ from .focal_loss import FocalLoss from .mse_loss import MeanSquaredErrorLoss from .multi_loss import MultiLoss +from .mae_loss import MeanAbsoluteErrorLoss LOSS_REGISTRY.register(MultiLoss) LOSS_REGISTRY.register(ClassificationCELoss) @@ -14,3 +15,4 @@ LOSS_REGISTRY.register(MeanSquaredErrorLoss) LOSS_REGISTRY.register(ClassificationSmoothCELoss) LOSS_REGISTRY.register(BCELoss) +LOSS_REGISTRY.register(MeanAbsoluteErrorLoss) \ No newline at end of file diff --git a/theseus/base/losses/mae_loss.py b/theseus/base/losses/mae_loss.py new file mode 100644 index 0000000..aa45072 --- /dev/null +++ b/theseus/base/losses/mae_loss.py @@ -0,0 +1,35 @@ +from typing import Any, Dict + +import torch +from torch import nn + +from theseus.base.utilities.cuda import move_to + + +class MeanAbsoluteErrorLoss(nn.Module): + r"""MSELoss is warper of mean absolute error loss""" + + def __init__(self, **kwargs): + super(MeanAbsoluteErrorLoss, self).__init__() + + def forward( + self, + outputs: Dict[str, Any], + batch: Dict[str, Any], + device: torch.device = None, + ): + pred = outputs["outputs"] + if device is not None: + target = move_to(batch["targets"], device) + else: + target = batch["targets"] + + if pred.shape == target.shape: + loss = torch.mean(torch.abs(pred - target)) + else: + # If the shapes are different, we can use MSELoss + loss = torch.mean(torch.abs(pred.squeeze(-1) - target.view(-1).contiguous())) + + + loss_dict = {"MAE": loss.item()} + return loss, loss_dict diff --git a/theseus/base/losses/mse_loss.py b/theseus/base/losses/mse_loss.py index 1144532..c018646 100644 --- a/theseus/base/losses/mse_loss.py +++ b/theseus/base/losses/mse_loss.py @@ -28,7 +28,7 @@ def forward( if pred.shape == target.shape: loss = self.criterion(pred, target) else: - loss = self.criterion(pred, target.view(-1).contiguous()) + loss = self.criterion(pred.squeeze(-1), target.view(-1).contiguous()) loss_dict = {"MSE": loss.item()} return loss, loss_dict diff --git a/theseus/base/metrics/accuracy.py b/theseus/base/metrics/accuracy.py index 89830a8..9ba61f9 100644 --- a/theseus/base/metrics/accuracy.py +++ b/theseus/base/metrics/accuracy.py @@ -9,10 +9,11 @@ class Accuracy(Metric): Accuracy metric """ - def __init__(self, label_type: str = "multiclass", **kwargs): + def __init__(self, label_type: str = "multiclass", ignore_index=None, **kwargs): super().__init__(**kwargs) self.type = label_type self.threshold = kwargs.get("threshold", 0.5) + self.ignore_index = ignore_index self.reset() def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): @@ -25,12 +26,23 @@ def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): outputs, label_type=self.type, threshold=self.threshold ) - correct = (prediction.view(-1) == target.view(-1)).sum() + # Create mask for non-ignored indices + if self.ignore_index is not None: + mask = target.view(-1) != self.ignore_index + prediction = prediction.view(-1)[mask] + target = target.view(-1)[mask] + else: + prediction = prediction.view(-1) + target = target.view(-1) - self.total_correct += correct - self.sample_size += prediction.view(-1).size(0) + if len(target) > 0: # Avoid division by zero if all targets are ignored + correct = (prediction == target).sum() + self.total_correct += correct + self.sample_size += len(target) def value(self): + if self.sample_size == 0: + return {"acc": 0.0} return {"acc": (self.total_correct / self.sample_size).item()} def reset(self): diff --git a/theseus/base/metrics/bl_accuracy.py b/theseus/base/metrics/bl_accuracy.py index fc56c61..774d829 100644 --- a/theseus/base/metrics/bl_accuracy.py +++ b/theseus/base/metrics/bl_accuracy.py @@ -23,10 +23,11 @@ class BalancedAccuracyMetric(Metric): Balanced Accuracy metric for classification """ - def __init__(self, label_type: str = "multiclass", **kwargs): + def __init__(self, label_type: str = "multiclass", ignore_index=None, **kwargs): super().__init__(**kwargs) self.type = label_type self.threshold = kwargs.get("threshold", 0.5) + self.ignore_index = ignore_index self.reset() def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): @@ -39,7 +40,14 @@ def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): outputs = outputs.detach().cpu() targets = targets.detach().cpu().view(-1) - + + # Filter out ignored indices + if self.ignore_index is not None: + mask = targets != self.ignore_index + outputs = outputs[mask] + targets = targets[mask] + + # Convert to lists and append to accumulated results self.outputs += outputs.numpy().tolist() self.targets += targets.numpy().tolist() @@ -51,6 +59,9 @@ def get_all_unique_id(self): self.unique_ids = np.unique(self.targets) def value(self): + if len(self.targets) == 0: + return {"bl_acc": 0.0} + self.get_all_unique_id() self.corrects = {str(k): 0 for k in self.unique_ids} @@ -70,6 +81,6 @@ def value(self): ] # Get mean accuracy across classes - values = sum(each_acc) / len(self.unique_ids) + values = sum(each_acc) / len(self.unique_ids) if self.unique_ids.size > 0 else 0.0 return {"bl_acc": values} diff --git a/theseus/base/metrics/f1.py b/theseus/base/metrics/f1.py index 9ca85af..4f87219 100644 --- a/theseus/base/metrics/f1.py +++ b/theseus/base/metrics/f1.py @@ -11,11 +11,12 @@ class F1ScoreMetric(Metric): F1 Score Metric (including macro, micro) """ - def __init__(self, average="weighted", label_type: str = "multiclass", **kwargs): + def __init__(self, average="weighted", label_type: str = "multiclass", ignore_index=None, **kwargs): super().__init__(**kwargs) self.average = average self.type = label_type self.threshold = kwargs.get("threshold", 0.5) + self.ignore_index = ignore_index self.reset() def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): @@ -26,11 +27,19 @@ def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): outputs = outputs["outputs"].detach().cpu() outputs = logits2labels(outputs, label_type=self.type, threshold=self.threshold) + + # Filter out ignored indices + if self.ignore_index is not None: + mask = targets != self.ignore_index + outputs = outputs[mask] + targets = targets[mask] self.preds += outputs.numpy().tolist() self.targets += targets.numpy().tolist() def value(self): + if len(self.targets) == 0: + return {f"{self.average}-f1": 0.0} score = f1_score(self.targets, self.preds, average=self.average) return {f"{self.average}-f1": score} diff --git a/theseus/base/metrics/mcc.py b/theseus/base/metrics/mcc.py index dc1cb43..f862a5f 100644 --- a/theseus/base/metrics/mcc.py +++ b/theseus/base/metrics/mcc.py @@ -11,9 +11,10 @@ class MCC(Metric): Mathew Correlation Coefficient """ - def __init__(self, label_type: str = "multiclass", **kwargs): + def __init__(self, label_type: str = "multiclass", ignore_index=None, **kwargs): super().__init__(**kwargs) self.type = label_type + self.ignore_index = ignore_index self.reset() def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): @@ -23,14 +24,22 @@ def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): targets = batch["targets"].cpu() outputs = outputs["outputs"].detach().cpu() outputs = logits2labels(outputs, label_type=self.type) + + # Filter out ignored indices + if self.ignore_index is not None: + mask = targets != self.ignore_index + outputs = outputs[mask] + targets = targets[mask] self.preds += outputs.numpy().tolist() self.targets += targets.numpy().tolist() def value(self): + if len(self.targets) == 0: + return {"mcc": 0.0} score = matthews_corrcoef(self.targets, self.preds) return { - f"mcc": score, + "mcc": score, } def reset(self): diff --git a/theseus/base/metrics/metric_template.py b/theseus/base/metrics/metric_template.py index 98cc8ae..3887d85 100644 --- a/theseus/base/metrics/metric_template.py +++ b/theseus/base/metrics/metric_template.py @@ -1,20 +1,55 @@ -class Metric: - """Abstract metric class""" +from abc import ABC, abstractmethod +from typing import Any, Dict, List - def __init__(self, **kwargs): + +class Metric(ABC): + """ + Abstract base class for all metrics in Theseus. + + Subclasses must implement ``update()``, ``value()``, ``reset()``, + ``summary()``, and ``__str__()``. + + Example:: + + @METRIC_REGISTRY.register() + class MyAccuracy(Metric): + def __init__(self, **kwargs): + super().__init__(**kwargs) + self.correct = 0 + self.total = 0 + + def update(self, outputs, batch): + ... + + def value(self): + return {"accuracy": self.correct / max(self.total, 1)} + + def reset(self): + self.correct = 0 + self.total = 0 + """ + + def __init__(self, **kwargs: Any) -> None: pass - def update(self): - raise NotImplementedError() + @abstractmethod + def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]) -> None: + """Update metric state with new predictions and targets.""" + ... - def value(self): - raise NotImplementedError() + @abstractmethod + def value(self) -> Dict[str, Any]: + """Compute and return the metric value(s) as a dict.""" + ... - def reset(self): - raise NotImplementedError() + @abstractmethod + def reset(self) -> None: + """Reset metric state for next epoch.""" + ... - def summary(self): - raise NotImplementedError() + def summary(self) -> str: + """Return a human-readable summary of the metric.""" + return str(self.value()) - def __str__(self): - raise NotImplementedError() + def __str__(self) -> str: + return f"{self.__class__.__name__}: {self.summary()}" diff --git a/theseus/base/metrics/precision_recall.py b/theseus/base/metrics/precision_recall.py index 92234bf..2f7b2e5 100644 --- a/theseus/base/metrics/precision_recall.py +++ b/theseus/base/metrics/precision_recall.py @@ -11,25 +11,38 @@ class PrecisionRecall(Metric): F1 Score Metric (including macro, micro) """ - def __init__(self, average="weighted", label_type: str = "multiclass", **kwargs): + def __init__(self, average="weighted", label_type: str = "multiclass", ignore_index=None, **kwargs): super().__init__(**kwargs) self.average = average self.type = label_type self.threshold = kwargs.get("threshold", 0.5) + self.ignore_index = ignore_index self.reset() def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): """ Perform calculation based on prediction and targets """ - targets = batch["targets"].cpu() + targets = batch["targets"].cpu().view(-1) outputs = outputs["outputs"].detach().cpu() outputs = logits2labels(outputs, label_type=self.type, threshold=self.threshold) + + # Filter out ignored indices + if self.ignore_index is not None: + mask = targets != self.ignore_index + outputs = outputs[mask] + targets = targets[mask] self.preds += outputs.numpy().tolist() self.targets += targets.numpy().tolist() def value(self): + if len(self.targets) == 0: + return { + f"{self.average}-precision": 0.0, + f"{self.average}-recall": 0.0, + } + precision = precision_score( self.targets, self.preds, average=self.average, zero_division=1 ) diff --git a/theseus/base/metrics/roc_auc_score.py b/theseus/base/metrics/roc_auc_score.py index ef3bca3..8800c50 100644 --- a/theseus/base/metrics/roc_auc_score.py +++ b/theseus/base/metrics/roc_auc_score.py @@ -8,13 +8,13 @@ has_scikitplot = True except: has_scikitplot = False -from sklearn.metrics import roc_auc_score +from sklearn.metrics import roc_auc_score, auc, precision_recall_curve from theseus.base.metrics.metric_template import Metric from theseus.base.utilities.cuda import detach, move_to from theseus.base.utilities.loggers.observer import LoggerObserver from theseus.base.utilities.logits import logits2labels - +import numpy as np LOGGER = LoggerObserver.getLogger("main") @@ -68,13 +68,47 @@ def value(self): multi_class=self.label_type, ) except Exception as e: - LOGGER.text( - f"AUC score could not be calculated: {e}", level=LoggerObserver.WARN + try: + preds = np.array(self.preds) + if preds.ndim == 2: + preds = preds[:, 1] + roc_auc_scr = roc_auc_score( + self.targets, + preds, + average=self.average, + multi_class=self.label_type, + ) + except Exception as e: + LOGGER.text( + f"AUC score could not be calculated: {e}", level=LoggerObserver.WARN + ) + roc_auc_scr = 0 + + try: + precision, recall, _ = precision_recall_curve( + self.targets, self.preds, pos_label=1 ) - roc_auc_scr = 0 + pr_auc = auc(recall, precision) + except Exception as e: + try: + preds = np.array(self.preds) + if preds.ndim == 2: + preds = preds[:, 1] + precision, recall, _ = precision_recall_curve( + self.targets, preds, pos_label=1 + ) + pr_auc = auc(recall, precision) + except Exception as e: + + LOGGER.text( + f"Precision-Recall AUC score could not be calculated: {e}", + level=LoggerObserver.WARN, + ) + pr_auc = 0 results = { f"{self.average}-roc_auc_score": roc_auc_scr, + f"pr_auc_score": pr_auc, } if has_scikitplot and self.plot_curve: roc_curve_fig = plot_roc(self.targets, self.preds).get_figure() diff --git a/theseus/base/models/wrapper.py b/theseus/base/models/wrapper.py index 352a7d4..f861607 100644 --- a/theseus/base/models/wrapper.py +++ b/theseus/base/models/wrapper.py @@ -1,10 +1,13 @@ -from typing import Any, Callable, Dict, List, Mapping, Optional, Union +from __future__ import annotations + +from typing import Any, Dict, List, Mapping, Optional import lightning.pytorch as pl import torch import torch.nn as nn -from lightning.pytorch.utilities.types import _METRIC, STEP_OUTPUT +from torch.amp import autocast +from lightning.pytorch.utilities.types import STEP_OUTPUT from theseus.base.datasets import LightningDataModuleWrapper from theseus.base.optimizers import OPTIM_REGISTRY, SCHEDULER_REGISTRY from theseus.base.utilities.getter import get_instance @@ -12,20 +15,24 @@ class LightningModelWrapper(pl.LightningModule): """ - Wrapper for Lightning Module - Instansiates the model, criterion, optimizer and scheduler + Lightning wrapper that bridges Theseus components to the Lightning training loop. + + Encapsulates model, criterion, optimizer, scheduler, and metrics into a single + ``pl.LightningModule`` with proper step methods and automatic mixed precision. """ def __init__( self, model: nn.Module, - criterion: nn.Module = None, - metrics: List[Any] = None, - optimizer_config: Dict = None, - scheduler_config: Dict = None, - scheduler_kwargs: Dict = None, - datamodule: LightningDataModuleWrapper = None, - ): + criterion: Optional[nn.Module] = None, + *, + metrics: Optional[List[Any]] = None, + optimizer_config: Optional[Dict] = None, + scheduler_config: Optional[Dict] = None, + scheduler_kwargs: Optional[Dict] = None, + datamodule: Optional[LightningDataModuleWrapper] = None, + use_mixed_precision: bool = False, + ) -> None: super().__init__() self.model = model self.criterion = criterion @@ -34,10 +41,12 @@ def __init__( self.scheduler_config = scheduler_config self.scheduler_kwargs = scheduler_kwargs self.datamodule = datamodule - self.lr = 0 - self.metric_dict = {} + self.use_mixed_precision = use_mixed_precision + self.lr: float = 0.0 + self.metric_dict: Dict[str, Any] = {} - def log_dict(self, dictionary: Mapping[str, Any], **kwargs) -> None: + def log_dict(self, dictionary: Mapping[str, Any], **kwargs: Any) -> None: + """Filter non-loggable values before passing to Lightning's log_dict.""" filtered_dict = { key: value for key, value in dictionary.items() @@ -45,85 +54,104 @@ def log_dict(self, dictionary: Mapping[str, Any], **kwargs) -> None: } return super().log_dict(filtered_dict, **kwargs) + @property + def _autocast_device(self) -> str: + """Detect the correct device type for autocast.""" + if self.device.type == "cuda": + return "cuda" + elif self.device.type == "mps": + return "mps" + return "cpu" + def on_train_batch_end( self, outputs: STEP_OUTPUT, batch: Any, batch_idx: int ) -> None: - lrl = [x["lr"] for x in self.optimizer.param_groups] - self.lr = sum(lrl) / len(lrl) - - def on_validation_epoch_end(self) -> None: + # Use Lightning's optimizers() API instead of storing self.optimizer + optimizers = self.optimizers() + if optimizers is not None: + opt = optimizers if not isinstance(optimizers, list) else optimizers[0] + lrl = [x["lr"] for x in opt.param_groups] + self.lr = sum(lrl) / len(lrl) + + def _compute_and_log_metrics(self, batch_size_key: str = "valloader") -> None: + """Compute metrics and log them. Reduces duplication between val/test.""" self.metric_dict = {} if self.metrics is not None: for metric in self.metrics: self.metric_dict.update(metric.value()) metric.reset() - self.log_dict( - self.metric_dict, - prog_bar=True, - batch_size=self.datamodule.valloader.batch_size, - ) + loader = getattr(self.datamodule, batch_size_key, None) + batch_size = loader.batch_size if loader is not None else 1 + self.log_dict(self.metric_dict, prog_bar=True, batch_size=batch_size) - def on_test_epoch_end(self) -> None: - self.metric_dict = {} - if self.metrics is not None: - for metric in self.metrics: - self.metric_dict.update(metric.value()) - metric.reset() + def on_validation_epoch_end(self) -> None: + self._compute_and_log_metrics("valloader") - self.log_dict( - self.metric_dict, - prog_bar=True, - batch_size=self.datamodule.testloader.batch_size, - ) + def on_test_epoch_end(self) -> None: + self._compute_and_log_metrics("testloader") - def _forward(self, batch: Dict, metrics: List[Any] = None): + def _forward( + self, + batch: Dict[str, Any], + metrics: Optional[List[Any]] = None, + ) -> Dict[str, Any]: """ - Forward the batch through models, losses and metrics - If some parameters are needed, it's best to include in the batch + Forward the batch through models, losses and metrics. + If some parameters are needed, it's best to include in the batch. """ - - outputs = self.model.forward_batch(batch) - loss, loss_dict = self.criterion(outputs, batch) - - if metrics is not None: - for metric in metrics: - metric.update(outputs, batch) + with autocast(device_type=self._autocast_device, enabled=self.use_mixed_precision): + outputs = self.model.forward_batch(batch) + if self.criterion is None: + loss = outputs["outputs"].get("loss", None) + loss_dict = outputs["outputs"].get("loss_dict", None) + if loss is None or loss_dict is None: + raise ValueError( + "No loss found in model outputs. " + "Please ensure the model returns a loss." + ) + else: + loss, loss_dict = self.criterion(outputs, batch) + + if metrics is not None: + for metric in metrics: + metric.update(outputs, batch) return {"loss": loss, "loss_dict": loss_dict, "model_outputs": outputs} - def trainable_parameters(self): + def trainable_parameters(self) -> int: + """Return the number of trainable parameters.""" return sum(p.numel() for p in self.parameters() if p.requires_grad) - def training_step(self, batch, batch_idx): - # training_step defines the train loop. + def training_step(self, batch: Any, batch_idx: int) -> Dict[str, Any]: outputs = self._forward(batch) self.log_dict(outputs["loss_dict"], prog_bar=True, on_step=True, on_epoch=False) return outputs - def validation_step(self, batch, batch_idx): - # this is the validation loop + def validation_step(self, batch: Any, batch_idx: int) -> Dict[str, Any]: outputs = self._forward(batch, metrics=self.metrics) self.log_dict(outputs["loss_dict"], prog_bar=True, on_step=True, on_epoch=False) return outputs - def test_step(self, batch, batch_idx): - # this is the test loop + def test_step(self, batch: Any, batch_idx: int) -> Dict[str, Any]: outputs = self._forward(batch, metrics=self.metrics) self.log_dict(outputs["loss_dict"], prog_bar=True, on_step=True, on_epoch=False) return outputs - def predict_step(self, batch, batch_idx=None): - pred = self.model.get_prediction(batch) - return pred + def predict_step(self, batch: Any, batch_idx: Optional[int] = None) -> Any: + return self.model.get_prediction(batch) - def configure_optimizers(self): + def configure_optimizers(self) -> Any: if self.optimizer_config is not None: self.optimizer = get_instance( self.optimizer_config, registry=OPTIM_REGISTRY, params=self.model.parameters(), ) + else: + from torch.optim import AdamW + + self.optimizer = AdamW(self.parameters(), lr=self.lr) if self.scheduler_config is not None: self.scheduler = get_instance( @@ -132,12 +160,40 @@ def configure_optimizers(self): optimizer=self.optimizer, **self.scheduler_kwargs, ) + + scheduler_interval = "epoch" if self.scheduler.step_per_epoch else "step" + scheduler = { + "scheduler": self.scheduler.scheduler, + "interval": scheduler_interval, + } + return [self.optimizer], [scheduler] else: - return self.optimizer + from torch.optim.lr_scheduler import LinearLR, SequentialLR - scheduler_interval = "epoch" if self.scheduler.step_per_epoch else "step" - scheduler = { - "scheduler": self.scheduler.scheduler, - "interval": scheduler_interval, - } - return [self.optimizer], [scheduler] + n_steps = self.trainer.estimated_stepping_batches + n_warmup_steps = int(0.1 * n_steps) + n_decay_steps = int(0.9 * n_steps) + + warmup = LinearLR( + self.optimizer, + start_factor=0.01, + end_factor=1.0, + total_iters=n_warmup_steps, + ) + decay = LinearLR( + self.optimizer, + start_factor=1.0, + end_factor=0.01, + total_iters=n_decay_steps, + ) + self.scheduler = SequentialLR( + optimizer=self.optimizer, + schedulers=[warmup, decay], + milestones=[n_warmup_steps], + ) + + scheduler = { + "scheduler": self.scheduler, + "interval": "step", + } + return [self.optimizer], [scheduler] diff --git a/theseus/base/pipeline.py b/theseus/base/pipeline.py index 9bc0e71..a06bf6a 100644 --- a/theseus/base/pipeline.py +++ b/theseus/base/pipeline.py @@ -1,5 +1,8 @@ +from __future__ import annotations + import os from datetime import datetime +from typing import Any, Dict, List, Optional import torch from omegaconf import DictConfig, OmegaConf @@ -22,19 +25,50 @@ from theseus.base.utilities.seed import seed_everything -class BasePipeline(object): - """docstring for BasePipeline.""" +class _PipelineBase: + """ + Shared base for train/test pipelines, eliminating duplication of + globals initialization, registry setup, and logging. + """ - def __init__(self, opt: DictConfig): - super(BasePipeline, self).__init__() + def __init__(self, opt: DictConfig) -> None: self.opt = opt self.seed = self.opt["global"].get("seed", 1702) seed_everything(self.seed) + self._initialized = False + + @property + def initialized(self) -> bool: + return self._initialized + + @initialized.setter + def initialized(self, value: bool) -> None: + self._initialized = value + + def _log(self, msg: str, level: int = LoggerObserver.INFO) -> None: + """Convenience logging helper.""" + self.logger.text(msg, level=level) + + def _setup_savedir(self) -> str: + """Create and return the experiment save directory.""" + exp_name = self.opt["global"].get("exp_name", None) + exist_ok = self.opt["global"].get("exist_ok", False) + save_dir = self.opt["global"].get("save_dir", "runs") + + if exp_name: + savedir = os.path.join(save_dir, exp_name) + if not exist_ok: + savedir = get_new_folder_name(savedir) + else: + savedir = os.path.join( + save_dir, + datetime.now().strftime("%Y-%m-%d_%H-%M-%S"), + ) + os.makedirs(savedir, exist_ok=True) + return savedir - self.initialized = False - - def init_globals(self): - # Main Loggers + def init_globals(self) -> None: + """Initialize logger, experiment directory, and global variables.""" self.logger = LoggerObserver.getLogger("main") # Global variables @@ -43,47 +77,63 @@ def init_globals(self): self.debug = self.opt["global"].get("debug", False) self.resume = self.opt["global"].get("resume", None) self.pretrained = self.opt["global"].get("pretrained", None) - self.transform_cfg = self.opt["global"].get("cfg_transform", None) - # Experiment name - if self.exp_name: - self.savedir = os.path.join( - self.opt["global"].get("save_dir", "runs"), self.exp_name - ) - if not self.exist_ok: - self.savedir = get_new_folder_name(self.savedir) - else: - self.savedir = os.path.join( - self.opt["global"].get("save_dir", "runs"), - datetime.now().strftime("%Y-%m-%d_%H-%M-%S"), - ) - os.makedirs(self.savedir, exist_ok=True) + # Setup save directory + self.savedir = self._setup_savedir() - # Logging to files + # File logging file_logger = FileLogger(__name__, self.savedir, debug=self.debug) self.logger.subscribe(file_logger) - # Logging images + # Image logging image_logger = ImageWriter(self.savedir) self.logger.subscribe(image_logger) + # Transform config self.transform_cfg = self.opt.get("augmentations", None) - # Logging out configs - self.logger.text("\n" + OmegaConf.to_yaml(self.opt), level=LoggerObserver.INFO) - self.logger.text( - f"Everything will be saved to {self.savedir}", - level=LoggerObserver.INFO, + # Log config + self._log("\n" + OmegaConf.to_yaml(self.opt)) + self._log(f"Everything will be saved to {self.savedir}") + + def init_registry(self) -> None: + """Initialize component registries. Override in subclass to extend.""" + self.model_registry = MODEL_REGISTRY + self.dataset_registry = DATASET_REGISTRY + self.dataloader_registry = DATALOADER_REGISTRY + self.metric_registry = METRIC_REGISTRY + self.loss_registry = LOSS_REGISTRY + self.callbacks_registry = CALLBACKS_REGISTRY + self.trainer_registry = TRAINER_REGISTRY + self.transform_registry = TRANSFORM_REGISTRY + self._log( + "You should override the init_registry() function", + LoggerObserver.CRITICAL, ) - def init_train_dataloader(self): - # DataLoaders + +class BasePipeline(_PipelineBase): + """ + Full training pipeline that orchestrates all components: + globals → registry → data → model → callbacks → trainer. + + Subclass this and override ``init_registry()`` to plug in task-specific + registries. + """ + + def __init__(self, opt: DictConfig) -> None: + super().__init__(opt) + + def _init_transforms(self) -> Dict[str, Any]: + """Initialize transforms, returning a dict with 'train'/'val' keys.""" if self.transform_cfg is not None: - self.transform = get_instance_recursively( + return get_instance_recursively( self.transform_cfg, registry=self.transform_registry ) - else: - self.transform = {"train": None, "val": None} + return {"train": None, "val": None} + + def init_train_dataloader(self) -> None: + self.transform = self._init_transforms() self.train_dataset = get_instance_recursively( self.opt["data"]["dataset"]["train"], @@ -96,66 +146,16 @@ def init_train_dataloader(self): dataset=self.train_dataset, ) - self.logger.text( - f"Number of training samples: {len(self.train_dataset)}", - level=LoggerObserver.INFO, - ) - self.logger.text( - f"Number of training iterations each epoch: {len(self.train_dataloader)}", - level=LoggerObserver.INFO, + self._log(f"Number of training samples: {len(self.train_dataset)}") + self._log( + f"Number of training iterations each epoch: {len(self.train_dataloader)}" ) - def init_validation_dataloader(self): - - # DataLoaders - if self.transform_cfg is not None: - self.transform = get_instance_recursively( - self.transform_cfg, registry=self.transform_registry - ) - else: - self.transform = {"train": None, "val": None} + def init_validation_dataloader(self) -> None: + self.transform = self._init_transforms() if self.opt["data"]["dataset"].get("val", None) is None: - split_ratio = self.opt.data.get("auto_split_ratio", 0.8) - self.logger.text( - f"No validation dataset found. Auto splitting training dataset with ratio={split_ratio}.", - level=LoggerObserver.WARN, - ) - train_size = int(len(self.train_dataset)) - val_size = int(train_size * (1 - split_ratio)) - train_dataset, val_dataset = ( - Subset(self.train_dataset, indices=indices) - for indices in torch.split_with_sizes( - torch.arange(train_size), [train_size - val_size, val_size] - ) - ) - attrs = dir(self.train_dataset) - for attr in attrs: - if not attr.startswith("__"): - setattr(train_dataset, attr, getattr(self.train_dataset, attr)) - setattr(val_dataset, attr, getattr(self.train_dataset, attr)) - - # collate_fn = getattr(self.train_dataset, "collate_fn", None) - # setattr(train_dataset, "collate_fn", collate_fn) - # setattr(val_dataset, "collate_fn", collate_fn) - self.train_dataset = train_dataset - self.val_dataset = val_dataset - - self.train_dataloader = get_instance_recursively( - self.opt["data"]["dataloader"]["train"], - registry=self.dataloader_registry, - dataset=self.train_dataset, - ) - - self.logger.text( - f"Number of training samples: {len(self.train_dataset)}", - level=LoggerObserver.INFO, - ) - self.logger.text( - f"Number of training iterations each epoch: {len(self.train_dataloader)}", - level=LoggerObserver.INFO, - ) - + self._auto_split_dataset() else: self.val_dataset = get_instance_recursively( self.opt["data"]["dataset"]["val"], @@ -170,17 +170,51 @@ def init_validation_dataloader(self): ) self.classnames = getattr(self.val_dataset, "classnames", None) - self.logger.text( - f"Number of validation samples: {len(self.val_dataset)}", - level=LoggerObserver.INFO, + self._log(f"Number of validation samples: {len(self.val_dataset)}") + self._log( + f"Number of validation iterations each epoch: {len(self.val_dataloader)}" ) - self.logger.text( - f"Number of validation iterations each epoch: {len(self.val_dataloader)}", - level=LoggerObserver.INFO, + + def _auto_split_dataset(self) -> None: + """Auto-split training dataset when no validation set is provided.""" + split_ratio = self.opt.data.get("auto_split_ratio", 0.8) + self._log( + f"No validation dataset found. Auto splitting training dataset " + f"with ratio={split_ratio}.", + level=LoggerObserver.WARN, ) + train_size = len(self.train_dataset) + val_size = int(train_size * (1 - split_ratio)) + + train_dataset, val_dataset = ( + Subset(self.train_dataset, indices=indices) + for indices in torch.split_with_sizes( + torch.arange(train_size), [train_size - val_size, val_size] + ) + ) + + # Copy attributes from original dataset to subsets + attrs = dir(self.train_dataset) + for attr in attrs: + if not attr.startswith("__"): + setattr(train_dataset, attr, getattr(self.train_dataset, attr)) + setattr(val_dataset, attr, getattr(self.train_dataset, attr)) - def init_test_dataloader(self): - # Transforms & Datasets + self.train_dataset = train_dataset + self.val_dataset = val_dataset + + self.train_dataloader = get_instance_recursively( + self.opt["data"]["dataloader"]["train"], + registry=self.dataloader_registry, + dataset=self.train_dataset, + ) + + self._log(f"Number of training samples: {len(self.train_dataset)}") + self._log( + f"Number of training iterations each epoch: {len(self.train_dataloader)}" + ) + + def init_test_dataloader(self) -> None: self.transform = get_instance_recursively( self.transform_cfg, registry=self.transform_registry ) @@ -198,23 +232,19 @@ def init_test_dataloader(self): self.classnames = getattr(self.test_dataloader, "classnames", None) - self.logger.text( - f"Number of test samples: {len(self.test_dataset)}", - level=LoggerObserver.INFO, - ) - self.logger.text( - f"Number of test iterations each epoch: {len(self.test_dataloader)}", - level=LoggerObserver.INFO, + self._log(f"Number of test samples: {len(self.test_dataset)}") + self._log( + f"Number of test iterations each epoch: {len(self.test_dataloader)}" ) - def init_datamodule(self): + def init_datamodule(self) -> None: self.datamodule = LightningDataModuleWrapper( trainloader=getattr(self, "train_dataloader", None), valloader=getattr(self, "val_dataloader", None), testloader=getattr(self, "test_dataloader", None), ) - def init_model(self): + def init_model(self) -> Any: CLASSNAMES = self.classnames model = get_instance( self.opt["model"], @@ -224,8 +254,11 @@ def init_model(self): ) return model - def init_criterion(self): + def init_criterion(self) -> Optional[Any]: CLASSNAMES = self.classnames + if self.opt["loss"] is None: + return None + self.criterion = get_instance_recursively( self.opt["loss"], registry=self.loss_registry, @@ -234,19 +267,22 @@ def init_criterion(self): ) return self.criterion - def init_model_with_loss(self, is_train=True): + def init_model_with_loss(self, is_train: bool = True) -> None: self.model = self.init_model() criterion = self.init_criterion() num_epochs = self.opt["trainer"]["args"]["max_epochs"] batch_size = self.opt["data"]["dataloader"]["val"]["args"]["batch_size"] + use_mixed_precision = self.opt["trainer"]["args"].get("precision", None) + use_mixed_precision = True if use_mixed_precision else False self.model = LightningModelWrapper( self.model, criterion, + use_mixed_precision=use_mixed_precision, datamodule=getattr(self, "datamodule", None), metrics=getattr(self, "metrics", None), - optimizer_config=self.opt["optimizer"] if is_train else None, - scheduler_config=self.opt["scheduler"] if is_train else None, + optimizer_config=self.opt.get("optimizer", None) if is_train else None, + scheduler_config=self.opt.get("scheduler", None) if is_train else None, scheduler_kwargs={ "num_epochs": num_epochs, "num_iterations": num_epochs * len(self.train_dataloader), @@ -259,21 +295,25 @@ def init_model_with_loss(self, is_train=True): pretrained = self.opt["global"].get("pretrained", None) if pretrained: - state_dict = torch.load(pretrained, map_location="cpu") + state_dict = torch.load(pretrained, map_location="cpu", weights_only=False) try: self.model.load_state_dict(state_dict["state_dict"], strict=False) - self.logger.text( + self._log( f"Loaded pretrained model from {pretrained}", level=LoggerObserver.SUCCESS, ) except Exception as e: - self.logger.text( + self._log( f"Loaded pretrained model from {pretrained}. Mismatched keys: {e}", level=LoggerObserver.WARN, ) - def init_metrics(self): + def init_metrics(self) -> None: CLASSNAMES = self.classnames + if self.opt["metrics"] is None: + self.metrics = None + return + self.metrics = get_instance_recursively( self.opt["metrics"], registry=self.metric_registry, @@ -281,7 +321,7 @@ def init_metrics(self): classnames=CLASSNAMES, ) - def init_callbacks(self): + def init_callbacks(self) -> List[Any]: callbacks = get_instance_recursively( self.opt["callbacks"], save_dir=getattr(self, "savedir", "runs"), @@ -291,7 +331,7 @@ def init_callbacks(self): ) return callbacks - def init_trainer(self, callbacks): + def init_trainer(self, callbacks: List[Any]) -> None: self.trainer = get_instance( self.opt["trainer"], default_root_dir=getattr(self, "savedir", "runs"), @@ -300,29 +340,16 @@ def init_trainer(self, callbacks): registry=self.trainer_registry, ) - def save_configs(self): + def save_configs(self) -> None: with open(os.path.join(self.savedir, "pipeline.yaml"), "w") as f: OmegaConf.save(config=self.opt, f=f) - def init_registry(self): - self.model_registry = MODEL_REGISTRY - self.dataset_registry = DATASET_REGISTRY - self.dataloader_registry = DATALOADER_REGISTRY - self.metric_registry = METRIC_REGISTRY - self.loss_registry = LOSS_REGISTRY - self.callbacks_registry = CALLBACKS_REGISTRY - self.trainer_registry = TRAINER_REGISTRY - self.transform_registry = TRANSFORM_REGISTRY - self.logger.text( - "You should override the init_registry() function", - LoggerObserver.CRITICAL, - ) - - def init_pipeline(self, phase: str = "train"): + def init_pipeline(self, phase: str = "train") -> None: if self.initialized: return self.init_globals() self.init_registry() + if phase == "train": self.init_train_dataloader() self.init_validation_dataloader() @@ -339,9 +366,10 @@ def init_pipeline(self, phase: str = "train"): self.init_validation_dataloader() self.init_datamodule() self.init_metrics() - self.init_model_with_loss(is_train=(phase == "train")) + self.init_model_with_loss(is_train=False) callbacks = [] + # Always add core callbacks if getattr(self.model, "metrics", None): callbacks.insert( 0, @@ -349,21 +377,21 @@ def init_pipeline(self, phase: str = "train"): save_dir=self.savedir ), ) - if getattr(self.model, "criterion", None): - callbacks.insert( - 0, - self.callbacks_registry.get("LossLoggerCallback")( - print_interval=self.opt["trainer"]["args"].get( - "log_every_n_steps", None - ), + callbacks.insert( + 0, + self.callbacks_registry.get("LossLoggerCallback")( + print_interval=self.opt["trainer"]["args"].get( + "log_every_n_steps", None ), - ) + ), + ) callbacks.insert(0, self.callbacks_registry.get("TimerCallback")()) self.init_trainer(callbacks) self.initialized = True - def fit(self): + def fit(self) -> None: + """Run the full training pipeline.""" self.init_pipeline(phase="train") self.trainer.fit( model=self.model, @@ -371,82 +399,61 @@ def fit(self): ckpt_path=self.resume, ) - def evaluate(self): + def evaluate(self) -> Dict[str, Any]: + """Run validation and return metrics.""" self.init_pipeline(phase="validation") self.trainer.validate( model=self.model, datamodule=self.datamodule, ckpt_path=self.resume, ) - return self.trainer.callback_metrics - def test(self): + def test(self) -> Dict[str, Any]: + """Run testing and return metrics.""" self.init_pipeline(phase="test") self.trainer.test( model=self.model, datamodule=self.datamodule, ckpt_path=self.resume, ) - return self.trainer.callback_metrics -class BaseTestPipeline(object): - def __init__(self, opt: DictConfig): +class BaseTestPipeline(_PipelineBase): + """ + Lightweight pipeline for inference/testing only. + Shares globals/registry init logic with ``BasePipeline`` via ``_PipelineBase``. + """ - super(BaseTestPipeline, self).__init__() - self.opt = opt - self.seed = self.opt["global"].get("seed", 1702) - seed_everything(self.seed) + def __init__(self, opt: DictConfig) -> None: + super().__init__(opt) - def init_globals(self): - # Main Loggers + def init_globals(self) -> None: + """Initialize globals without image writer (not needed for inference).""" self.logger = LoggerObserver.getLogger("main") - # Global variables self.exp_name = self.opt["global"].get("exp_name", None) self.exist_ok = self.opt["global"].get("exist_ok", False) self.debug = self.opt["global"].get("debug", False) self.transform_cfg = self.opt["global"].get("cfg_transform", None) - # Experiment name - if self.exp_name: - self.savedir = os.path.join( - self.opt["global"].get("save_dir", "runs"), self.exp_name - ) - if not self.exist_ok: - self.savedir = get_new_folder_name(self.savedir) - else: - self.savedir = os.path.join( - self.opt["global"].get("save_dir", "runs"), - datetime.now().strftime("%Y-%m-%d_%H-%M-%S"), - ) - os.makedirs(self.savedir, exist_ok=True) - + self.savedir = self._setup_savedir() self.transform_cfg = self.opt.get("augmentations", None) - # Logging to files file_logger = FileLogger(__name__, self.savedir, debug=self.debug) self.logger.subscribe(file_logger) - self.logger.text(self.opt, level=LoggerObserver.INFO) - self.logger.text( - f"Everything will be saved to {self.savedir}", - level=LoggerObserver.INFO, - ) + self._log(str(self.opt)) + self._log(f"Everything will be saved to {self.savedir}") - def init_registry(self): + def init_registry(self) -> None: self.model_registry = MODEL_REGISTRY self.dataset_registry = DATASET_REGISTRY self.dataloader_registry = DATALOADER_REGISTRY self.transform_registry = TRANSFORM_REGISTRY - self.logger.text( - "You should override the init_registry() function", - LoggerObserver.INFO, - ) + self._log("You should override the init_registry() function") - def init_test_dataloader(self): - # Transforms & Datasets + def init_test_dataloader(self) -> None: self.transform = get_instance_recursively( self.transform_cfg, registry=self.transform_registry ) @@ -469,16 +476,12 @@ def init_test_dataloader(self): dataset=self.dataset, ) - self.logger.text( - f"Number of test samples: {len(self.dataset)}", - level=LoggerObserver.INFO, - ) - self.logger.text( - f"Number of test iterations each epoch: {len(self.dataloader)}", - level=LoggerObserver.INFO, + self._log(f"Number of test samples: {len(self.dataset)}") + self._log( + f"Number of test iterations each epoch: {len(self.dataloader)}" ) - def init_model(self): + def init_model(self) -> None: CLASSNAMES = getattr(self.dataset, "classnames", None) self.model = get_instance( self.opt["model"], @@ -489,18 +492,18 @@ def init_model(self): self.model = LightningModelWrapper(self.model) self.model.eval() - def init_loading(self): + def init_loading(self) -> None: self.weights = self.opt["global"].get("pretrained", None) if self.weights: - state_dict = torch.load(self.weights, map_location="cpu") - self.model.load_state_dict(state_dict["state_dict"]) + state_dict = torch.load(self.weights, map_location="cpu", weights_only=False) + self.model.load_state_dict(state_dict["state_dict"], strict=False) - def init_pipeline(self): + def init_pipeline(self) -> None: self.init_globals() self.init_registry() self.init_test_dataloader() self.init_model() self.init_loading() - def inference(self): + def inference(self) -> Any: raise NotImplementedError() diff --git a/theseus/base/trainer/__init__.py b/theseus/base/trainer/__init__.py index 6bc88e1..40118d6 100644 --- a/theseus/base/trainer/__init__.py +++ b/theseus/base/trainer/__init__.py @@ -1,3 +1,7 @@ +from __future__ import annotations + +from typing import Any + from lightning.pytorch.strategies import DDPStrategy from lightning.pytorch.trainer import Trainer as plTrainer @@ -7,19 +11,36 @@ class Trainer(plTrainer): - def __init__(self, *args, **kwargs): - if "use_nccl_strategy" in kwargs.keys() and "strategy" not in kwargs.keys(): - # Default to DDP strategy with NCCL backend - use_nccl_strategy = kwargs.pop("use_nccl_strategy") - if use_nccl_strategy: - ddp = DDPStrategy( - process_group_backend="nccl", find_unused_parameters=True + """ + Extended Lightning Trainer with convenience options for distributed strategies. + + Supports ``use_nccl_strategy`` for auto-configuring DDP with NCCL backend, + and ``use_fsdp_strategy`` for Fully Sharded Data Parallel. + """ + + def __init__(self, *args: Any, **kwargs: Any) -> None: + # Handle NCCL DDP strategy shortcut + use_nccl = kwargs.pop("use_nccl_strategy", False) + use_fsdp = kwargs.pop("use_fsdp_strategy", False) + + if "strategy" not in kwargs: + if use_nccl: + kwargs["strategy"] = DDPStrategy( + process_group_backend="nccl", + find_unused_parameters=True, ) - super().__init__(strategy=ddp, *args, **kwargs) - else: - super().__init__(*args, **kwargs) - else: - super().__init__(*args, **kwargs) + elif use_fsdp: + try: + from lightning.pytorch.strategies import FSDPStrategy + + kwargs["strategy"] = FSDPStrategy() + except ImportError: + raise ImportError( + "FSDP strategy requires lightning >= 2.0. " + "Please upgrade your lightning installation." + ) + + super().__init__(*args, **kwargs) -TRAINER_REGISTRY.register(Trainer, prefix="pl") +TRAINER_REGISTRY.register(Trainer, prefix="pl") \ No newline at end of file diff --git a/theseus/base/utilities/getter.py b/theseus/base/utilities/getter.py index ab76e7a..63deae1 100644 --- a/theseus/base/utilities/getter.py +++ b/theseus/base/utilities/getter.py @@ -1,63 +1,105 @@ +from __future__ import annotations + import inspect +import functools +from typing import Any, Dict, Optional from omegaconf import DictConfig, ListConfig from theseus.registry import Registry +# Cache for inspect.signature to avoid repeated introspection +@functools.lru_cache(maxsize=256) +def _cached_signature(cls: type) -> inspect.Signature: + """Cache inspect.signature results for performance.""" + return inspect.signature(cls) + + +def get_instance_with_kwargs( + registry: Registry, + name: str, + args: Any = None, + kwargs: Optional[Dict[str, Any]] = None, +) -> Any: + """ + Instantiate a class from registry by name, filtering kwargs to match + the class constructor signature. + """ + if kwargs is None: + kwargs = {} -def get_instance_with_kwargs(registry, name, args: list = None, kwargs: dict = {}): - # get keyword arguments from class signature - inspection = inspect.signature(registry.get(name)) + cls = registry.get(name) + inspection = _cached_signature(cls) class_kwargs = inspection.parameters.keys() if isinstance(args, (dict, DictConfig)): - # override kwargs (from parent) with args (from config) + # Override kwargs (from parent) with args (from config) kwargs.update(args) args = None if "kwargs" in class_kwargs: if args is None: - return registry.get(name)(**kwargs) + return cls(**kwargs) else: - return registry.get(name)(*args, **kwargs) + return cls(*args, **kwargs) else: filtered_kwargs = {k: v for k, v in kwargs.items() if k in class_kwargs} if args is None: - return registry.get(name)(**filtered_kwargs) + return cls(**filtered_kwargs) else: - return registry.get(name)(*args, **filtered_kwargs) + return cls(*args, **filtered_kwargs) -def get_instance(config, registry: Registry, **kwargs): - # ref https://github.com/vltanh/torchan/blob/master/torchan/utils/getter.py - assert "name" in config - args = config.get("args", []) +def get_instance(config: DictConfig | dict, registry: Registry, **kwargs: Any) -> Any: + """ + Instantiate a single class from config dict with 'name' and optional 'args'. + + Args: + config: Dict-like with 'name' key and optional 'args' key. + registry: Registry to look up the class by name. + **kwargs: Additional keyword arguments passed to the constructor. + Returns: + Instantiated object. + """ + assert "name" in config, f"Config must contain 'name' key, got: {list(config.keys())}" + args = config.get("args", []) return get_instance_with_kwargs(registry, config["name"], args, kwargs) -def get_instance_recursively(config, registry: Registry, **kwargs): +def get_instance_recursively( + config: Any, + registry: Registry, + **kwargs: Any, +) -> Any: + """ + Recursively walk a config tree and instantiate all objects that have + a 'name' key, using the given registry. + + Supports nested lists, dicts, and DictConfig/ListConfig. + """ if isinstance(config, (list, tuple, ListConfig)): - out = [ + return [ get_instance_recursively(item, registry=registry, **kwargs) for item in config ] - return out + if isinstance(config, (dict, DictConfig)): - if "name" in config.keys(): + if "name" in config: if registry: args = get_instance_recursively( config.get("args", {}), registry, **kwargs ) return get_instance_with_kwargs(registry, config["name"], args, kwargs) - else: - out = {} - for k, v in config.items(): - out[k] = get_instance_recursively(v, registry=registry, **kwargs) - return out + return { + k: get_instance_recursively(v, registry=registry, **kwargs) + for k, v in config.items() + } + return config -def get_function(name): +def get_function(name: str) -> Any: + """Get a function by name from the global scope.""" return globals()[name] diff --git a/theseus/base/utilities/hub.py b/theseus/base/utilities/hub.py new file mode 100644 index 0000000..ecaaa6e --- /dev/null +++ b/theseus/base/utilities/hub.py @@ -0,0 +1,242 @@ +""" +HuggingFace Hub integration for Theseus models. + +Provides ``HuggingFaceHubMixin`` for save/load/push operations, and +``HuggingFaceHubCallback`` for automatic checkpoint pushing during training. +""" + +from __future__ import annotations + +import json +import logging +import os +from pathlib import Path +from typing import Any, Dict, Optional, Union + +import torch +import torch.nn as nn + +logger = logging.getLogger(__name__) + +# Optional imports — graceful degradation if not installed +try: + from safetensors.torch import load_file, save_file + + _SAFETENSORS_AVAILABLE = True +except ImportError: + _SAFETENSORS_AVAILABLE = False + +try: + from huggingface_hub import HfApi, ModelCard, ModelCardData + + _HF_HUB_AVAILABLE = True +except ImportError: + _HF_HUB_AVAILABLE = False + + +def _check_hf_hub() -> None: + if not _HF_HUB_AVAILABLE: + raise ImportError( + "huggingface-hub is required for HuggingFace Hub integration. " + "Install it with: pip install huggingface-hub" + ) + + +class HuggingFaceHubMixin: + """ + Mixin that adds ``save_pretrained()``, ``from_pretrained()``, and + ``push_to_hub()`` to any ``nn.Module`` subclass. + + Supports both ``safetensors`` (preferred) and PyTorch ``.bin`` formats. + + Example:: + + class MyModel(nn.Module, HuggingFaceHubMixin): + def __init__(self, config): + super().__init__() + self.config = config + self.linear = nn.Linear(10, 10) + + model = MyModel(config={"hidden_size": 10}) + model.save_pretrained("./my-model") + model.push_to_hub("username/my-model") + + loaded = MyModel.from_pretrained("username/my-model", config={"hidden_size": 10}) + """ + + def save_pretrained( + self, + save_directory: Union[str, Path], + *, + config: Optional[Dict[str, Any]] = None, + use_safetensors: bool = True, + ) -> None: + """ + Save model weights and config to a directory. + + Args: + save_directory: Path to save the model. + config: Optional config dict to save alongside weights. + use_safetensors: Use safetensors format if available (default True). + """ + save_directory = Path(save_directory) + save_directory.mkdir(parents=True, exist_ok=True) + + # Save weights + if use_safetensors and _SAFETENSORS_AVAILABLE: + weights_path = save_directory / "model.safetensors" + save_file(self.state_dict(), str(weights_path)) # type: ignore[arg-type] + else: + weights_path = save_directory / "pytorch_model.bin" + torch.save(self.state_dict(), weights_path) # type: ignore[arg-type] + + # Save config + if config is None: + config = getattr(self, "config", {}) + if config: + config_path = save_directory / "config.json" + with open(config_path, "w") as f: + json.dump(config, f, indent=2, default=str) + + logger.info(f"Model saved to {save_directory}") + + @classmethod + def from_pretrained( + cls, + pretrained_path: Union[str, Path], + *, + use_safetensors: bool = True, + map_location: str = "cpu", + **kwargs: Any, + ) -> "HuggingFaceHubMixin": + """ + Load a model from a local directory or HuggingFace Hub repo. + + Args: + pretrained_path: Local path or HuggingFace repo ID. + use_safetensors: Prefer safetensors format. + map_location: Device to map weights to. + **kwargs: Passed to the model constructor. + """ + pretrained_path = Path(pretrained_path) + + # Load config if available + config_path = pretrained_path / "config.json" + config = {} + if config_path.exists(): + with open(config_path) as f: + config = json.load(f) + + # Merge config with kwargs (kwargs take precedence) + merged_kwargs = {**config, **kwargs} + model = cls(**merged_kwargs) + + # Load weights + safetensors_path = pretrained_path / "model.safetensors" + bin_path = pretrained_path / "pytorch_model.bin" + + if use_safetensors and _SAFETENSORS_AVAILABLE and safetensors_path.exists(): + state_dict = load_file(str(safetensors_path), device=map_location) + elif bin_path.exists(): + state_dict = torch.load(bin_path, map_location=map_location, weights_only=True) + else: + raise FileNotFoundError( + f"No model weights found in {pretrained_path}. " + f"Expected 'model.safetensors' or 'pytorch_model.bin'." + ) + + model.load_state_dict(state_dict, strict=False) # type: ignore[arg-type] + logger.info(f"Model loaded from {pretrained_path}") + return model # type: ignore[return-value] + + def push_to_hub( + self, + repo_id: str, + *, + commit_message: str = "Upload model", + private: bool = False, + token: Optional[str] = None, + config: Optional[Dict[str, Any]] = None, + model_card: Optional[str] = None, + use_safetensors: bool = True, + ) -> str: + """ + Push model to HuggingFace Hub. + + Args: + repo_id: HuggingFace repo ID (e.g. ``username/model-name``). + commit_message: Commit message for the push. + private: Whether the repo should be private. + token: HuggingFace API token. Uses cached token if None. + config: Optional config dict. + model_card: Optional model card text. + use_safetensors: Use safetensors format. + + Returns: + URL of the pushed model on HuggingFace Hub. + """ + _check_hf_hub() + + import tempfile + + api = HfApi(token=token) + + # Create repo if it doesn't exist + api.create_repo(repo_id=repo_id, private=private, exist_ok=True) + + with tempfile.TemporaryDirectory() as tmpdir: + self.save_pretrained(tmpdir, config=config, use_safetensors=use_safetensors) + + # Generate model card if not provided + if model_card is None: + model_card = self._generate_model_card(repo_id, config) + + card_path = os.path.join(tmpdir, "README.md") + with open(card_path, "w") as f: + f.write(model_card) + + url = api.upload_folder( + repo_id=repo_id, + folder_path=tmpdir, + commit_message=commit_message, + ) + + logger.info(f"Model pushed to https://huggingface.co/{repo_id}") + return url + + def _generate_model_card( + self, + repo_id: str, + config: Optional[Dict[str, Any]] = None, + ) -> str: + """Generate a basic model card.""" + model_name = repo_id.split("/")[-1] if "/" in repo_id else repo_id + trainable_params = sum( + p.numel() for p in self.parameters() if p.requires_grad # type: ignore[union-attr] + ) + total_params = sum(p.numel() for p in self.parameters()) # type: ignore[union-attr] + + card = f"""--- +library_name: theseus +tags: +- pytorch +- theseus +--- + +# {model_name} + +This model was trained using the [Theseus](https://github.com/kaylode/theseus) framework. + +## Model Details + +- **Framework**: Theseus v2.0 (PyTorch Lightning) +- **Total Parameters**: {total_params:,} +- **Trainable Parameters**: {trainable_params:,} +""" + + if config: + card += "\n## Configuration\n\n```json\n" + card += json.dumps(config, indent=2, default=str) + card += "\n```\n" + + return card diff --git a/theseus/base/utilities/loggers/observer.py b/theseus/base/utilities/loggers/observer.py index ac08bab..7435163 100644 --- a/theseus/base/utilities/loggers/observer.py +++ b/theseus/base/utilities/loggers/observer.py @@ -11,19 +11,20 @@ import threading from inspect import getframeinfo, stack -from typing import Dict, List +from typing import Any, Callable, Dict, List, Optional from tabulate import tabulate from .subscriber import LoggerSubscriber -def get_type(value): +def get_type(value: Any) -> str: + """Infer the log type from a value.""" if isinstance(value, torch.nn.Module): return LoggerObserver.TORCH_MODULE - if isinstance(value, mpl.figure.Figure) or isinstance(value, go.Figure): + if isinstance(value, (mpl.figure.Figure, go.Figure)): return LoggerObserver.FIGURE - if isinstance(value, torch.Tensor) or isinstance(value, np.ndarray): + if isinstance(value, (torch.Tensor, np.ndarray)): if len(value.shape) == 2: return LoggerObserver.EMBED if isinstance(value, (int, float)): @@ -33,15 +34,24 @@ def get_type(value): return LoggerObserver.HTML else: return LoggerObserver.TEXT - else: - raise ValueError(f"Fail to log undefined type: {type(value)}") + raise ValueError(f"Fail to log undefined type: {type(value)}") -class LoggerObserver(object): - """Logger Oberserver Degisn Pattern - notifies every subscribers when .log() is called +class LoggerObserver: """ + Logger Observer Design Pattern. + Notifies every subscriber when ``.log()`` is called. + Uses a dispatch table instead of if-chains for O(1) routing. + + Example:: + + logger = LoggerObserver.getLogger("main") + logger.text("Hello world", level=LoggerObserver.INFO) + logger.log([{"tag": "loss", "value": 0.5, "type": "scalar"}]) + """ + + # Log type constants SCALAR = "scalar" FIGURE = "figure" TORCH_MODULE = "torch_module" @@ -52,6 +62,7 @@ class LoggerObserver(object): VIDEO = "video" HTML = "html" + # Log level constants WARN = logging.WARN ERROR = logging.ERROR DEBUG = logging.DEBUG @@ -59,20 +70,36 @@ class LoggerObserver(object): CRITICAL = logging.CRITICAL SUCCESS = "SUCCESS" - instances = {} + # Singleton instances + instances: Dict[str, "LoggerObserver"] = {} _lock = threading.Lock() - def __new__(cls, name=None, *args, **kwargs): + # Dispatch table: maps log type -> subscriber method name + _DISPATCH: Dict[str, str] = { + SCALAR: "log_scalar", + FIGURE: "log_figure", + TORCH_MODULE: "log_torch_module", + TEXT: "log_text", + SPECIAL_TEXT: "log_spec_text", + EMBED: "log_embedding", + TABLE: "log_table", + VIDEO: "log_video", + HTML: "log_html", + } + + def __new__(cls, name: Optional[str] = None, *args: Any, **kwargs: Any) -> "LoggerObserver": with cls._lock: if name is None: name = str(os.getpid()) - if name in LoggerObserver.instances.keys(): + if name in LoggerObserver.instances: return LoggerObserver.instances[name] + return object.__new__(cls) - return object.__new__(cls, *args, **kwargs) - - def __init__(self, name) -> None: - self.subscriber = [] + def __init__(self, name: str) -> None: + if hasattr(self, "_initialized"): + return + self._initialized = True + self.subscriber: List[LoggerSubscriber] = [] self.name = name # Init with a stdout logger @@ -83,61 +110,44 @@ def __init__(self, name) -> None: LoggerObserver.instances[name] = self - def __del__(self): - for subcriber in self.subscriber: - del subcriber - if self.name in LoggerObserver.instances.keys(): - LoggerObserver.instances.pop(self.name) + def __del__(self) -> None: + for subscriber in self.subscriber: + del subscriber + if self.name in LoggerObserver.instances: + LoggerObserver.instances.pop(self.name, None) @classmethod - def getLogger(cls, name): - if name in LoggerObserver.instances.keys(): + def getLogger(cls, name: str) -> "LoggerObserver": + """Get or create a logger by name.""" + if name in LoggerObserver.instances: return LoggerObserver.instances[name] - return cls(name) - def subscribe(self, subscriber: LoggerSubscriber): + def subscribe(self, subscriber: LoggerSubscriber) -> None: + """Add a subscriber that will receive log events.""" self.subscriber.append(subscriber) - def log(self, logs: List[Dict]): - for subscriber in self.subscriber: - for log in logs: - tag = log["tag"] - value = log["value"] - log_type = log["type"] if "type" in log.keys() else get_type(value) - kwargs = log["kwargs"] if "kwargs" in log.keys() else {} - - if log_type == LoggerObserver.SCALAR: - subscriber.log_scalar(tag=tag, value=value, **kwargs) - - if log_type == LoggerObserver.FIGURE: - subscriber.log_figure(tag=tag, value=value, **kwargs) - - if log_type == LoggerObserver.TORCH_MODULE: - subscriber.log_torch_module(tag=tag, value=value, **kwargs) - - if log_type == LoggerObserver.TEXT: - subscriber.log_text(tag=tag, value=value, **kwargs) - - if log_type == LoggerObserver.EMBED: - subscriber.log_embedding(tag=tag, value=value, **kwargs) - - if log_type == LoggerObserver.SPECIAL_TEXT: - subscriber.log_spec_text(tag=tag, value=value, **kwargs) - - if log_type == LoggerObserver.TABLE: - subscriber.log_table(tag=tag, value=value, **kwargs) - - if log_type == LoggerObserver.VIDEO: - subscriber.log_video(tag=tag, value=value, **kwargs) - - if log_type == LoggerObserver.HTML: - subscriber.log_html(tag=tag, value=value, **kwargs) - - def text(self, value, level=logging.INFO): + def log(self, logs: List[Dict[str, Any]]) -> None: """ - Text logging + Dispatch log entries to all subscribers using the dispatch table. + Each log entry must have 'tag' and 'value' keys, with optional 'type' and 'kwargs'. """ + for subscriber in self.subscriber: + for entry in logs: + tag = entry["tag"] + value = entry["value"] + log_type = entry.get("type", get_type(value)) + kwargs = entry.get("kwargs", {}) + + # Use dispatch table for O(1) routing + method_name = self._DISPATCH.get(log_type) + if method_name is not None: + method = getattr(subscriber, method_name, None) + if method is not None: + method(tag=tag, value=value, **kwargs) + + def text(self, value: Any, level: int = logging.INFO) -> None: + """Convenience method for text logging with source location.""" caller = getframeinfo(stack()[1][0]) function_name = stack()[1][3] filename = "//".join(caller.filename.split("theseus")[1:])[ diff --git a/theseus/base/utilities/optuna_tuner.py b/theseus/base/utilities/optuna_tuner.py index f35079e..e78d514 100644 --- a/theseus/base/utilities/optuna_tuner.py +++ b/theseus/base/utilities/optuna_tuner.py @@ -13,6 +13,8 @@ plot_param_importances, plot_slice, ) +import wandb +from optuna.integration.wandb import WeightsAndBiasesCallback from theseus.base.pipeline import BasePipeline from theseus.base.utilities.loggers import LoggerObserver @@ -28,6 +30,7 @@ def __init__( pruner=None, sampler=None, save_dir: str = None, + wandb_kwargs: dict = None, # <-- Add this argument ) -> None: self.logger = LoggerObserver.getLogger("main") @@ -38,6 +41,14 @@ def __init__( self.pruner = pruner self.sampler = sampler self.save_dir = save_dir + self.wandb_kwargs = wandb_kwargs + self.WANDB_CALLBACK = None + if wandb_kwargs is not None: + self.WANDB_CALLBACK = WeightsAndBiasesCallback( + metric_name="auc", + wandb_kwargs=wandb_kwargs, + as_multirun=True + ) if save_dir is not None: os.makedirs(save_dir, exist_ok=True) @@ -69,7 +80,12 @@ def tune( trial, config, pipeline_class, trial_user_attrs, optuna_callback ) - self.study.optimize(wrapped_objective, n_trials=self.n_trials) + callbacks = None + if self.WANDB_CALLBACK is not None: + decorator = self.WANDB_CALLBACK.track_in_wandb() + wrapped_objective = decorator(wrapped_objective) + callbacks = [self.WANDB_CALLBACK] + self.study.optimize(wrapped_objective, n_trials=self.n_trials, timeout=12*60*60, callbacks=callbacks) best_trial = self.study.best_trial self.save_best_config(self.save_dir, config, best_trial.params) self._rename_params() @@ -85,7 +101,7 @@ def save_best_config(self, save_dir: str, config: DictConfig, best_params: dict) save_dir = osp.join(save_dir, "best_configs") os.makedirs(save_dir, exist_ok=True) - with open(os.path.join(save_dir, "best_pipeline.yaml"), "w") as f: + with open(os.path.join(save_dir, f"{self.study_name}.yaml"), "w") as f: OmegaConf.save(config=config, f=f) self.logger.text( @@ -170,13 +186,21 @@ def objective( ) # Start training and evaluation - pipeline.fit() - score_dict = pipeline.evaluate() + try: + pipeline.fit() + score_dict = pipeline.evaluate() + except Exception as e: + self.logger.text( + f"Trial {trial.number} failed with exception: {e}", + level=LoggerObserver.ERROR, + ) + score_dict = {} + del tmp_config best_key = trial_user_attrs.get("best_key", None) if best_key is not None: - return float(score_dict[best_key]) + return float(score_dict.get(best_key, -1)) return score_dict def callback_hook(self, trial, init_trainer_function, callback_fn): @@ -252,4 +276,8 @@ def visualize(self, plot: str, plot_params: dict = {}): ) raise ValueError() + # Log to wandb if enabled + if plot != "all" and self.wandb_kwargs is not None and fig is not None: + wandb.log({f"Plot/{plot}": fig}) + return fig diff --git a/theseus/ml/preprocessors/base.py b/theseus/ml/preprocessors/base.py index 41b4ada..e148c83 100644 --- a/theseus/ml/preprocessors/base.py +++ b/theseus/ml/preprocessors/base.py @@ -15,10 +15,10 @@ use_parallel = True except: use_parallel = False - LOGGER.text( - "pandarallel should be installed for parallerization. Using normal apply-function instead", - level=LoggerObserver.WARN, - ) + # LOGGER.text( + # "pandarallel should be installed for parallerization. Using normal apply-function instead", + # level=LoggerObserver.WARN, + # ) class Preprocessor: diff --git a/theseus/ml/preprocessors/encoder.py b/theseus/ml/preprocessors/encoder.py index cab5ab6..db43ba3 100644 --- a/theseus/ml/preprocessors/encoder.py +++ b/theseus/ml/preprocessors/encoder.py @@ -93,8 +93,7 @@ def encode_corpus(self, df): df[column_name] = encoder.fit_transform(df[column_name].values).copy() elif self.engine == "polars": import polars as pl - - encoder.fit_transform(df[column_name].to_numpy()) + encoder.fit_transform(df.select(column_name).unique().to_numpy().ravel()) le_name_mapping = dict( zip( encoder.classes_, diff --git a/theseus/registry.py b/theseus/registry.py index df300d0..e6a9337 100644 --- a/theseus/registry.py +++ b/theseus/registry.py @@ -1,53 +1,77 @@ # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved -# pyre-ignore-all-errors[2,3] -from typing import Any, Dict, Iterable, Iterator, Tuple +# Enhanced for Theseus v2.0 +from __future__ import annotations + +import logging +from typing import Any, Generic, Iterator, Optional, TypeVar, overload from tabulate import tabulate +logger = logging.getLogger(__name__) + +T = TypeVar("T") -class Registry(Iterable[Tuple[str, Any]]): + +class Registry(Generic[T]): """ The registry that provides name -> object mapping, to support third-party users' custom modules. + To create a registry (e.g. a backbone registry): + .. code-block:: python BACKBONE_REGISTRY = Registry('BACKBONE') + To register an object: + .. code-block:: python @BACKBONE_REGISTRY.register() class MyBackbone(): ... + Or: + .. code-block:: python BACKBONE_REGISTRY.register(MyBackbone) + + To merge registries: + + .. code-block:: python + MERGED = BACKBONE_REGISTRY.merge(OTHER_REGISTRY) """ + __slots__ = ("_name", "_obj_map") + def __init__(self, name: str) -> None: - """ - Args: - name (str): the name of this registry - """ self._name: str = name - self._obj_map: Dict[str, Any] = {} - - def _do_register(self, name: str, obj: Any, override: bool = False) -> None: - if not override: - assert ( - name not in self._obj_map - ), "An object named '{}' was already registered in '{}' registry!".format( - name, self._name - ) + self._obj_map: dict[str, T] = {} + + def _do_register(self, name: str, obj: T, override: bool = False) -> None: + if name in self._obj_map and self._obj_map[name] is not obj: + if not override: + logger.warning( + "An object named '%s' was already registered in '%s' registry!", + name, + self._name, + ) + return self._obj_map[name] = obj + @overload + def register(self, obj: None = None, prefix: str = "", override: bool = False) -> Any: ... + + @overload + def register(self, obj: T, prefix: str = "", override: bool = False) -> None: ... + def register( - self, obj: Any = None, prefix: str = "", override: bool = False + self, obj: T | None = None, prefix: str = "", override: bool = False ) -> Any: """ - Register the given object under the the name `obj.__name__`. - Can be used as either a decorator or not. See docstring of this class for usage. + Register the given object under the name ``obj.__name__``. + Can be used as either a decorator or not. """ if obj is None: - # used as a decorator + # Used as a decorator def deco(func_or_class: Any) -> Any: name = func_or_class.__name__ self._do_register(prefix + name, func_or_class, override) @@ -55,30 +79,58 @@ def deco(func_or_class: Any) -> Any: return deco - # used as a function call - name = obj.__name__ - self._do_register(prefix + name, obj) + # Used as a function call + name = obj.__name__ # type: ignore[union-attr] + self._do_register(prefix + name, obj, override) - def get(self, name: str) -> Any: + def get(self, name: str) -> T: + """Get registered object by name. Raises KeyError if not found.""" ret = self._obj_map.get(name) if ret is None: raise KeyError( - "No object named '{}' found in '{}' registry!".format(name, self._name) + f"No object named '{name}' found in '{self._name}' registry! " + f"Available: {sorted(self._obj_map.keys())}" ) return ret + def get_or_none(self, name: str) -> T | None: + """Get registered object by name, returns None if not found.""" + return self._obj_map.get(name) + + def keys(self) -> list[str]: + """Return all registered names.""" + return list(self._obj_map.keys()) + + def values(self) -> list[T]: + """Return all registered objects.""" + return list(self._obj_map.values()) + + def merge(self, other: Registry[T], override: bool = False) -> Registry[T]: + """ + Merge another registry into this one. Returns self for chaining. + Useful for task-specific pipelines that extend base registries. + """ + for name, obj in other: + self._do_register(name, obj, override=override) + return self + def __contains__(self, name: str) -> bool: return name in self._obj_map + def __len__(self) -> int: + return len(self._obj_map) + + def __getitem__(self, name: str) -> T: + return self.get(name) + def __repr__(self) -> str: table_headers = ["Names", "Objects"] table = tabulate( self._obj_map.items(), headers=table_headers, tablefmt="fancy_grid" ) - return "Registry of {}:\n".format(self._name) + table + return f"Registry of {self._name}:\n{table}" - def __iter__(self) -> Iterator[Tuple[str, Any]]: + def __iter__(self) -> Iterator[tuple[str, T]]: return iter(self._obj_map.items()) - # pyre-fixme[4]: Attribute must be annotated. __str__ = __repr__ diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..a11fb88 --- /dev/null +++ b/uv.lock @@ -0,0 +1,5468 @@ +version = 1 +revision = 3 +requires-python = ">=3.10" +resolution-markers = [ + "python_full_version >= '3.14' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "python_full_version >= '3.14' and platform_machine != 'aarch64' and sys_platform == 'linux'", + "python_full_version >= '3.12' and python_full_version < '3.14' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "python_full_version >= '3.12' and python_full_version < '3.14' and platform_machine != 'aarch64' and sys_platform == 'linux'", + "python_full_version == '3.11.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "python_full_version == '3.11.*' and platform_machine != 'aarch64' and sys_platform == 'linux'", + "python_full_version < '3.11' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "python_full_version < '3.11' and platform_machine != 'aarch64' and sys_platform == 'linux'", + "python_full_version >= '3.12' and sys_platform == 'darwin'", + "python_full_version >= '3.12' and 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+0000 Subject: [PATCH 2/3] refactor(v2.0): comprehensive modernization and modularization of Theseus ML framework Detailed Changes: - Logger Overhaul: - Fixed `LoggerObserver` singleton pattern for thread-safety and session persistence. - Added master rank check for distributed training in `LoggerObserver.log` to prevent duplicate logs across GPUs. - Improved `LoggerObserver.text()` to support multiple args and dictionary-to-JSON serialization. - Resolved log duplication by making `loguru` handlers (StdoutLogger/FileLogger) instance-specific using name filters. - Subpackage Decoupling: - Moved heavy domain-specific dependencies (lightning, torchvision, transformers) to optional extras. - Converted `theseus/` and `theseus/base/` __init__ files to lazy-loadable structures (removed eager wildcards). - Implemented lazy imports in `LoggerObserver` to break global dependencies on PyTorch/Plotly. - ML Module Simplification: - Removed monolithic `MLPipeline`, `MLTrainer`, and custom ML-specific callbacks/metrics. - Replaced with streamlined `tradml.py` containing direct-fit functions and `TradMLTuner` with Optuna integration. - Fixed critical bugs in `LabelEncode` (lazy column initialization) and `FillNaN` (None-value handling). - CI/CD & Infrastructure: - Updated pyproject.toml and uv.lock to modernized dependency stack. - Rewrote tabular test suite in `tests/tabular/` to use the new simplified functional API. - Preserved existing preprocessors, reduction, and visualization utilities. --- AGENT.md => AGENTS.md | 4 +- __init__.py | 2 +- pyproject.toml | 40 +- tests/classification/__init__.py | 0 tests/classification/conftest.py | 7 +- tests/classification/inference.py | 6 +- tests/classification/test_tuner_clf.py | 4 +- tests/semantic/__init__.py | 0 tests/semantic/inference.py | 8 +- tests/semantic/test_segm.py | 4 +- tests/tabular/__init__.py | 0 tests/tabular/conftest.py | 106 +- tests/tabular/test_tablr.py | 88 +- tests/tabular/test_tuner_tblr.py | 72 +- theseus/__init__.py | 24 +- theseus/base/__init__.py | 12 +- theseus/base/callbacks/__init__.py | 1 - theseus/base/callbacks/checkpoint_callback.py | 7 +- theseus/base/callbacks/hub_callback.py | 16 +- .../base/callbacks/loss_logging_callback.py | 55 +- .../base/callbacks/metric_logging_callback.py | 36 +- theseus/base/callbacks/optuna_callback.py | 5 +- theseus/base/callbacks/timer_callback.py | 2 +- theseus/base/callbacks/tsb_callback.py | 4 +- theseus/base/callbacks/wandb_callback.py | 62 +- theseus/base/datasets/collator.py | 5 +- theseus/base/datasets/dataloader.py | 4 +- theseus/base/datasets/dataset.py | 12 +- theseus/base/losses/__init__.py | 4 +- theseus/base/losses/bce_loss.py | 8 +- theseus/base/losses/ce_loss.py | 8 +- theseus/base/losses/focal_loss.py | 10 +- theseus/base/losses/mae_loss.py | 9 +- theseus/base/losses/mse_loss.py | 8 +- theseus/base/losses/multi_loss.py | 7 +- theseus/base/losses/smoothing.py | 14 +- theseus/base/metrics/accuracy.py | 8 +- theseus/base/metrics/bl_accuracy.py | 8 +- theseus/base/metrics/confusion_matrix.py | 8 +- theseus/base/metrics/f1.py | 10 +- theseus/base/metrics/mcc.py | 6 +- theseus/base/metrics/metric_template.py | 6 +- theseus/base/metrics/precision_recall.py | 20 +- theseus/base/metrics/roc_auc_score.py | 34 +- theseus/base/models/wrapper.py | 52 +- theseus/base/optimizers/schedulers/cosine.py | 24 +- theseus/base/optimizers/schedulers/wrapper.py | 6 +- theseus/base/pipeline.py | 103 +- theseus/base/trainer/__init__.py | 2 +- theseus/base/utilities/cuda.py | 18 +- theseus/base/utilities/download.py | 21 +- theseus/base/utilities/getter.py | 16 +- theseus/base/utilities/hub.py | 23 +- theseus/base/utilities/loading.py | 4 +- .../base/utilities/loggers/image_writer.py | 1 - theseus/base/utilities/loggers/observer.py | 101 +- .../base/utilities/loggers/stdout_logger.py | 25 +- theseus/base/utilities/loggers/tsb_logger.py | 12 +- .../base/utilities/loggers/wandb_logger.py | 16 +- theseus/base/utilities/optuna_tuner.py | 53 +- .../cv/base/augmentations/albumentation.py | 4 +- .../cv/base/utilities/visualization/utils.py | 2 +- .../utilities/visualization/visualizer.py | 42 +- .../cv/classification/augmentations/custom.py | 75 +- .../callbacks/gradcam_callback.py | 12 +- .../callbacks/visualize_callback.py | 22 +- .../cv/classification/datasets/csv_dataset.py | 9 +- theseus/cv/classification/datasets/dataset.py | 8 +- .../classification/datasets/folder_dataset.py | 13 +- .../datasets/mixupcutmix_collator.py | 15 +- .../cv/classification/metrics/errorcases.py | 22 +- .../cv/classification/metrics/projection.py | 14 +- .../models/huggingface_models.py | 12 +- .../cv/classification/models/timm_models.py | 21 +- theseus/cv/classification/pipeline.py | 2 +- .../cv/classification/utilities/gradcam.py | 41 +- .../augmentations/bbox_transforms.py | 5 +- .../cv/detection/callbacks/visualization.py | 23 +- theseus/cv/detection/datasets/base.py | 5 +- theseus/cv/detection/datasets/coco.py | 16 +- theseus/cv/detection/metrics/map.py | 10 +- theseus/cv/detection/metrics/misc.py | 5 +- .../cv/detection/metrics/precision_recall.py | 25 +- theseus/cv/detection/pipeline.py | 2 +- theseus/cv/semantic/augmentations/mosaic.py | 21 +- .../semantic/callbacks/visualize_callbacks.py | 8 +- theseus/cv/semantic/datasets/csv_dataset.py | 9 +- theseus/cv/semantic/datasets/dataset.py | 3 +- .../cv/semantic/datasets/mosaic_collator.py | 15 +- theseus/cv/semantic/losses/ce_loss.py | 25 +- theseus/cv/semantic/losses/dice_loss.py | 11 +- theseus/cv/semantic/losses/lovasz_loss.py | 10 +- theseus/cv/semantic/losses/tversky_loss.py | 15 +- theseus/cv/semantic/metrics/dicecoeff.py | 8 +- theseus/cv/semantic/metrics/miou.py | 12 +- theseus/cv/semantic/metrics/pixel_accuracy.py | 22 +- theseus/cv/semantic/models/segmodels.py | 10 +- theseus/cv/semantic/pipeline.py | 2 +- theseus/ml/__init__.py | 13 + theseus/ml/callbacks/__init__.py | 22 - theseus/ml/callbacks/base_callbacks.py | 184 -- theseus/ml/callbacks/checkpoint_callbacks.py | 44 - theseus/ml/callbacks/explainer/__init__.py | 4 - theseus/ml/callbacks/explainer/lime.py | 76 - theseus/ml/callbacks/explainer/pdp.py | 119 - theseus/ml/callbacks/explainer/permutation.py | 101 - theseus/ml/callbacks/explainer/shapley.py | 105 - theseus/ml/callbacks/metric_callbacks.py | 72 - theseus/ml/callbacks/optuna_callbacks.py | 35 - theseus/ml/datasets/__init__.py | 5 - theseus/ml/datasets/csv_dataset.py | 33 - theseus/ml/metrics/__init__.py | 18 - theseus/ml/metrics/acccuracy.py | 60 - theseus/ml/metrics/confusion_matrix.py | 98 - theseus/ml/metrics/f1_score.py | 29 - theseus/ml/metrics/mcc.py | 28 - theseus/ml/metrics/precision_recall.py | 39 - theseus/ml/metrics/projection.py | 67 - theseus/ml/metrics/roc_auc_score.py | 69 - theseus/ml/models/__init__.py | 5 - theseus/ml/models/gbms.py | 70 - theseus/ml/pipeline.py | 191 -- theseus/ml/preprocessors/aggregation.py | 8 +- theseus/ml/preprocessors/base.py | 8 +- theseus/ml/preprocessors/compose.py | 3 +- theseus/ml/preprocessors/drop_col.py | 4 +- theseus/ml/preprocessors/encoder.py | 35 +- theseus/ml/preprocessors/splitter.py | 8 +- theseus/ml/tradml.py | 875 ++++++++ theseus/ml/trainer/__init__.py | 5 - theseus/ml/trainer/ml_trainer.py | 66 - theseus/ml/utilities/pprint.py | 24 - theseus/ml/visualize.py | 157 ++ .../base/preprocessors/basic_processors.py | 15 +- .../base/preprocessors/pyvncore_processor.py | 4 +- theseus/nlp/base/preprocessors/vocabulary.py | 51 +- theseus/nlp/base/utilities/correct_tone.py | 16 +- theseus/nlp/base/utilities/sequences.py | 4 +- theseus/nlp/retrieval/models/base.py | 8 +- theseus/nlp/retrieval/models/bm25.py | 5 +- theseus/nlp/retrieval/models/ensembler.py | 29 +- .../nlp/retrieval/models/retrieval_tfms.py | 2 - theseus/registry.py | 26 +- uv.lock | 1934 ++--------------- 144 files changed, 2162 insertions(+), 4419 deletions(-) rename AGENT.md => AGENTS.md (96%) create mode 100644 tests/classification/__init__.py create mode 100644 tests/semantic/__init__.py create mode 100644 tests/tabular/__init__.py delete mode 100644 theseus/ml/callbacks/__init__.py delete mode 100644 theseus/ml/callbacks/base_callbacks.py delete mode 100644 theseus/ml/callbacks/checkpoint_callbacks.py delete mode 100644 theseus/ml/callbacks/explainer/__init__.py delete mode 100644 theseus/ml/callbacks/explainer/lime.py delete mode 100644 theseus/ml/callbacks/explainer/pdp.py delete mode 100644 theseus/ml/callbacks/explainer/permutation.py delete mode 100644 theseus/ml/callbacks/explainer/shapley.py delete mode 100644 theseus/ml/callbacks/metric_callbacks.py delete mode 100644 theseus/ml/callbacks/optuna_callbacks.py delete mode 100644 theseus/ml/datasets/__init__.py delete mode 100644 theseus/ml/datasets/csv_dataset.py delete mode 100644 theseus/ml/metrics/__init__.py delete mode 100644 theseus/ml/metrics/acccuracy.py delete mode 100644 theseus/ml/metrics/confusion_matrix.py delete mode 100644 theseus/ml/metrics/f1_score.py delete mode 100644 theseus/ml/metrics/mcc.py delete mode 100644 theseus/ml/metrics/precision_recall.py delete mode 100644 theseus/ml/metrics/projection.py delete mode 100644 theseus/ml/metrics/roc_auc_score.py delete mode 100644 theseus/ml/models/__init__.py delete mode 100644 theseus/ml/models/gbms.py delete mode 100644 theseus/ml/pipeline.py create mode 100644 theseus/ml/tradml.py delete mode 100644 theseus/ml/trainer/__init__.py delete mode 100644 theseus/ml/trainer/ml_trainer.py delete mode 100644 theseus/ml/utilities/pprint.py create mode 100644 theseus/ml/visualize.py diff --git a/AGENT.md b/AGENTS.md similarity index 96% rename from AGENT.md rename to AGENTS.md index aa8526f..86c7f08 100644 --- a/AGENT.md +++ b/AGENTS.md @@ -34,7 +34,7 @@ tests/ # Pytest suites for classification, semantic, tabular ## Key Commands ```bash # Install -uv pip install -e '.[dev]' +uv sync --all-extras # Run tests uv run pytest tests/ --capture=no @@ -44,7 +44,7 @@ uv run ruff check theseus/ uv run ruff format theseus/ # Train (example) -uv run python train.py --config-dir configs --config-name pipeline.yaml +uv run train.py --config-dir configs --config-name pipeline.yaml ``` ## Current Progress (v2.0 Update) diff --git a/__init__.py b/__init__.py index 1534704..877d31c 100644 --- a/__init__.py +++ b/__init__.py @@ -1 +1 @@ -from .theseus import * \ No newline at end of file +from .theseus import * diff --git a/pyproject.toml b/pyproject.toml index bf53c53..baa461b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,7 @@ name = "theseus" version = "2.0.0" description = "A modular PyTorch Lightning framework for deep learning research and production training" readme = "README.md" -requires-python = ">=3.10" +requires-python = ">=3.10,<3.13" license = {file = "LICENSE"} keywords = ["pytorch", "lightning", "template", "deep learning", "machine learning"] authors = [ @@ -37,22 +37,17 @@ dependencies = [ "matplotlib>=3.8.0", "webcolors>=1.13", "wandb>=0.17.0", - "tensorboard>=2.16.0", "pyyaml>=6.0.1", "tqdm>=4.66.0", "gdown>=5.1.0", "tabulate>=0.9.0", "loguru>=0.7.0", "kaleido>=0.2.1", - "optuna>=3.6.0", "deepdiff>=7.0.0", "hydra-core>=1.3.2", - "lightning>=2.4.0", - "huggingface-hub>=0.23.0", - "safetensors>=0.4.0", - "torchvision>=0.24.1", "scikit-learn>=1.7.2", "omegaconf>=2.3.0", + "rich>=14.3.3", ] [project.optional-dependencies] @@ -63,7 +58,9 @@ dev = [ "ruff>=0.5.0", ] cv = [ - "albumentations>=1.4.0", + "torchvision>=0.24.1", + "lightning>=2.4.0", + "albumentations>=1.4.0,<2.0.0", "omegaconf>=2.3.0", ] cv_classification = [ @@ -79,6 +76,7 @@ cv_detection = [ "pycocotools>=2.0.7", ] nlp = [ + "lightning>=2.4.0", "pyvi>=0.1.1", "py_vncorenlp>=0.1.3", "spacy>=3.7.0", @@ -92,20 +90,20 @@ nlp_retrieval = [ "elasticsearch>=8.12.0", ] ml = [ - "pandas>=2.1.0", - "pandarallel>=1.6.5", - "numpy>=1.26.0", - "scikit-learn>=1.4.0", - "scipy>=1.12.0", "optuna>=3.6.0", - "psycopg2-binary>=2.9.9", - "gunicorn>=21.2.0", - "lightgbm>=4.3.0", - "xgboost>=2.0.0", - "catboost>=1.2.0", - "shap>=0.45.0", - "lime>=0.2.0.1", - "scikit-plot", + "optuna-integration[wandb]>=4.8.0", + "numpy==1.26.4", + "lightgbm==4.6.0", + "wandb==0.19.9", + "xgboost>=3.0", + "tqdm==4.67.1", + "tabulate==0.9.0", + "scikit-plot==0.3.7", + "scipy>=1.11.4", + "seaborn==0.13.2", + "shap==0.47.1", + "numpy==1.26.4", + "catboost==1.2.8", ] all = [ "theseus[cv,cv_classification,cv_semantic,cv_detection,nlp,nlp_retrieval,ml]", diff --git a/tests/classification/__init__.py b/tests/classification/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/classification/conftest.py b/tests/classification/conftest.py index e3f57b1..1a9b2f0 100644 --- a/tests/classification/conftest.py +++ b/tests/classification/conftest.py @@ -2,8 +2,7 @@ import optuna import pytest -from hydra import compose, initialize, initialize_config_module -from omegaconf import OmegaConf +from hydra import compose, initialize from optuna.storages import JournalFileStorage, JournalStorage from theseus.base.utilities.optuna_tuner import OptunaWrapper @@ -72,9 +71,7 @@ def override_tuner_config(): def override_tuner_tuner(): os.makedirs("runs/optuna/clf", exist_ok=True) - database = JournalStorage( - JournalFileStorage("runs/optuna/clf/pytest_clf_optuna.log") - ) + database = JournalStorage(JournalFileStorage("runs/optuna/clf/pytest_clf_optuna.log")) tuner = OptunaWrapper( storage=database, diff --git a/tests/classification/inference.py b/tests/classification/inference.py index 220d294..68a8cf1 100644 --- a/tests/classification/inference.py +++ b/tests/classification/inference.py @@ -17,7 +17,7 @@ class TestPipeline(BaseTestPipeline): def __init__(self, opt: DictConfig): - super(TestPipeline, self).__init__(opt) + super().__init__(opt) self.opt = opt def init_globals(self): @@ -36,13 +36,13 @@ def inference(self): df_dict = {"filename": [], "label": [], "score": []} - for idx, batch in enumerate(tqdm(self.dataloader)): + for _idx, batch in enumerate(tqdm(self.dataloader)): img_names = batch["img_names"] outputs = self.model.predict_step(batch) preds = outputs["names"] probs = outputs["confidences"] - for (filename, pred, prob) in zip(img_names, preds, probs): + for filename, pred, prob in zip(img_names, preds, probs): df_dict["filename"].append(filename) df_dict["label"].append(pred) df_dict["score"].append(prob) diff --git a/tests/classification/test_tuner_clf.py b/tests/classification/test_tuner_clf.py index 0f9d6fa..a7f8703 100644 --- a/tests/classification/test_tuner_clf.py +++ b/tests/classification/test_tuner_clf.py @@ -21,9 +21,7 @@ def test_train_clf_tune(override_tuner_config, override_tuner_tuner): leaderboard_df = override_tuner_tuner.leaderboard() os.makedirs("runs/optuna/clf/overview", exist_ok=True) # leaderboard_df.to_csv("runs/optuna/clf/overview/leaderboard.csv", index=False) - leaderboard_df.to_json( - "runs/optuna/clf/overview/leaderboard.json", orient="records" - ) + leaderboard_df.to_json("runs/optuna/clf/overview/leaderboard.json", orient="records") # figs = override_tuner_tuner.visualize("all") # for fig_type, fig in figs: diff --git a/tests/semantic/__init__.py b/tests/semantic/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/semantic/inference.py b/tests/semantic/inference.py index 394d962..09cf214 100644 --- a/tests/semantic/inference.py +++ b/tests/semantic/inference.py @@ -18,7 +18,7 @@ class TestPipeline(BaseTestPipeline): def __init__(self, opt: DictConfig): - super(TestPipeline, self).__init__(opt) + super().__init__(opt) self.opt = opt def init_globals(self): @@ -44,7 +44,7 @@ def inference(self): os.makedirs(saved_mask_dir, exist_ok=True) os.makedirs(saved_overlay_dir, exist_ok=True) - for idx, batch in enumerate(self.dataloader): + for _idx, batch in enumerate(self.dataloader): inputs = batch["inputs"] img_names = batch["img_names"] ori_sizes = batch["ori_sizes"] @@ -52,9 +52,7 @@ def inference(self): outputs = self.model.predict_step(batch) preds = outputs["masks"] - for (inpt, pred, filename, ori_size) in zip( - inputs, preds, img_names, ori_sizes - ): + for inpt, pred, filename, ori_size in zip(inputs, preds, img_names, ori_sizes): decode_pred = visualizer.decode_segmap(pred)[:, :, ::-1] resized_decode_mask = cv2.resize(decode_pred, tuple(ori_size)) diff --git a/tests/semantic/test_segm.py b/tests/semantic/test_segm.py index d9b0bd7..cc04a63 100644 --- a/tests/semantic/test_segm.py +++ b/tests/semantic/test_segm.py @@ -19,8 +19,6 @@ def test_eval_clf(override_config): @pytest.mark.order(2) def test_infer_clf(override_test_config): - override_test_config["global"][ - "pretrained" - ] = "runs/pytest_segm/checkpoints/best.ckpt" + override_test_config["global"]["pretrained"] = "runs/pytest_segm/checkpoints/best.ckpt" test_pipeline = TestPipeline(override_test_config) test_pipeline.inference() diff --git a/tests/tabular/__init__.py b/tests/tabular/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/tabular/conftest.py b/tests/tabular/conftest.py index 7fccd21..5ba887e 100644 --- a/tests/tabular/conftest.py +++ b/tests/tabular/conftest.py @@ -1,58 +1,48 @@ -import os - -import pytest -from hydra import compose, initialize -from optuna.storages import JournalFileStorage, JournalStorage - -from theseus.base.utilities.optuna_tuner import OptunaWrapper - -MODELS = ["xgboost"] # , "catboost", 'lightgbm'] -TUNER_MODELS = ["xgboost_tune"] # , "catboost_tune"] #, 'lightgbm_tune'] - - -@pytest.fixture(scope="session", params=MODELS) -def override_config(request): - with initialize(config_path="configs"): - config = compose( - config_name=f"{request.param}", - overrides=[ - "global.exp_name=pytest_tablr", - "global.exist_ok=True", - "global.save_dir=runs", - ], - ) - - return config - - -@pytest.fixture(scope="function", params=TUNER_MODELS) -def override_tuner_config(request): - with initialize(config_path="configs/optuna"): - config = compose( - config_name=f"{request.param}", - overrides=[ - "global.exp_name=pytest_tablr_optuna", - "global.exist_ok=True", - "global.save_dir=runs", - ], - ) - - return config - - -@pytest.fixture(scope="session") -def override_tuner_tuner(): - os.makedirs("runs/optuna/tablr", exist_ok=True) - database = JournalStorage( - JournalFileStorage("runs/optuna/tablr/pytest_tablr_optuna.log") - ) - - tuner = OptunaWrapper( - storage=database, - study_name="pytest_tablr_optuna", - n_trials=3, - direction="maximize", - save_dir="runs/optuna/tablr", - ) - - return tuner +import pandas as pd +import pytest + +from theseus.ml.preprocessors import FillNaN, LabelEncode, PreprocessCompose, Standardize + + +# --- Data Loading Helper --- +def load_titanic_data(split: str): + """Load and preprocess Titanic data for a given split.""" + data_path = f"samples/titanic/{split}.csv" + classnames_path = "samples/titanic/classnames.txt" + target_column = "Survived" + + df = pd.read_csv(data_path) + + # Apply preprocessing (same pipeline as the old YAML config) + transform = PreprocessCompose( + preproc_list=[ + FillNaN(column_names=["Embarked", "Cabin"], fill_with="None"), + FillNaN(column_names=["Age"], fill_with=0), + LabelEncode(), + Standardize(method="minmax", column_names=["*"], exclude_columns=[target_column]), + ] + ) + df = transform.run(df) + + X = df.drop(target_column, axis=1).values + y = df[target_column].values + feature_names = list(df.drop(target_column, axis=1).columns) + classnames = open(classnames_path).read().splitlines() + + return X, y, feature_names, classnames + + +# --- Fixtures --- +@pytest.fixture(scope="session") +def titanic_data(): + """Load train and val splits of Titanic dataset.""" + X_train, y_train, feature_names, classnames = load_titanic_data("train") + X_val, y_val, _, _ = load_titanic_data("val") + return { + "X_train": X_train, + "X_val": X_val, + "y_train": y_train, + "y_val": y_val, + "feature_names": feature_names, + "classnames": classnames, + } diff --git a/tests/tabular/test_tablr.py b/tests/tabular/test_tablr.py index 5637788..3b2d9a3 100644 --- a/tests/tabular/test_tablr.py +++ b/tests/tabular/test_tablr.py @@ -1,24 +1,64 @@ -import pytest - -# from configs.tabular.infer import TestPipeline -from theseus.ml.pipeline import MLPipeline - - -@pytest.mark.order(1) -def test_train_tblr(override_config): - train_pipeline = MLPipeline(override_config) - train_pipeline.fit() - - -@pytest.mark.order(2) -def test_eval_tblr(override_config): - override_config["global"]["pretrained"] = "runs/pytest_tablr/checkpoints/last" - val_pipeline = MLPipeline(override_config) - val_pipeline.evaluate() - - -# @pytest.mark.order(2) -# def test_infer_clf(override_test_config): -# override_test_config["global"]["weights"] = "runs/pytest_segm/checkpoints/best.pth" -# test_pipeline = TestPipeline(override_test_config) -# test_pipeline.inference() +import numpy as np +import pytest + +from theseus.ml.tradml import fit_xgboost + + +@pytest.mark.order(1) +def test_train_xgboost(titanic_data): + """Train an XGBoost classifier on Titanic data.""" + model, params = fit_xgboost( + params={ + "n_estimators": 50, + "max_depth": 5, + "learning_rate": 0.1, + "gamma": 0.1, + "reg_alpha": 0, + "reg_lambda": 1, + }, + X_train=titanic_data["X_train"], + X_val=titanic_data["X_val"], + y_train=titanic_data["y_train"], + y_val=titanic_data["y_val"], + is_classification=True, + ) + assert model is not None + assert "objective" in params + + # Evaluate + preds = model.predict_proba(titanic_data["X_val"]) + pred_labels = np.argmax(preds, axis=1) + from sklearn.metrics import accuracy_score + + acc = accuracy_score(titanic_data["y_val"], pred_labels) + print(f"XGBoost accuracy: {acc:.4f}") + assert acc > 0.5, f"Expected accuracy > 0.5, got {acc}" + + +@pytest.mark.order(2) +def test_eval_xgboost(titanic_data): + """Train and evaluate XGBoost — verify metrics are reasonable.""" + model, _ = fit_xgboost( + params={ + "n_estimators": 50, + "max_depth": 5, + "learning_rate": 0.1, + "gamma": 0.1, + "reg_alpha": 0, + "reg_lambda": 1, + }, + X_train=titanic_data["X_train"], + X_val=titanic_data["X_val"], + y_train=titanic_data["y_train"], + y_val=titanic_data["y_val"], + is_classification=True, + ) + + from sklearn.metrics import f1_score, matthews_corrcoef + + preds = model.predict_proba(titanic_data["X_val"]) + pred_labels = np.argmax(preds, axis=1) + f1 = f1_score(titanic_data["y_val"], pred_labels, average="macro") + mcc = matthews_corrcoef(titanic_data["y_val"], pred_labels) + print(f"F1: {f1:.4f}, MCC: {mcc:.4f}") + assert f1 > 0.0 diff --git a/tests/tabular/test_tuner_tblr.py b/tests/tabular/test_tuner_tblr.py index c5e094b..fddbd12 100644 --- a/tests/tabular/test_tuner_tblr.py +++ b/tests/tabular/test_tuner_tblr.py @@ -1,29 +1,43 @@ -import os - -import pytest - -from theseus.ml.callbacks.optuna_callbacks import OptunaCallbacks -from theseus.ml.pipeline import MLPipeline - - -@pytest.mark.order(1) -def test_train_tblr_tune(override_tuner_config, override_tuner_tuner): - override_tuner_tuner.tune( - config=override_tuner_config, - pipeline_class=MLPipeline, - optuna_callback=OptunaCallbacks, - trial_user_attrs={ - "best_key": "bl_acc", - "model_name": override_tuner_config["model"]["args"]["model_name"], - }, - ) - - leaderboard_df = override_tuner_tuner.leaderboard() - os.makedirs("runs/optuna/tablr/overview", exist_ok=True) - leaderboard_df.to_json( - "runs/optuna/tablr/overview/leaderboard.json", orient="records" - ) - - figs = override_tuner_tuner.visualize("all") - for fig_type, fig in figs: - fig.write_image(f"runs/optuna/tablr/overview/{fig_type}.png") +import os + +import pytest + +from theseus.ml.tradml import TradMLTuner + + +@pytest.mark.order(3) +def test_tuner_xgboost(titanic_data): + """Run TradMLTuner with XGBoost on Titanic data (2 trials, no wandb).""" + save_dir = "runs/optuna/tablr_test" + os.makedirs(save_dir, exist_ok=True) + storage_path = os.path.join(save_dir, "test_tuner.log") + + tuner = TradMLTuner( + storage=storage_path, + study_name="pytest_xgboost_tune", + n_trials=2, + direction="maximize", + save_dir=save_dir, + method="xgboost", + wandb_kwargs=None, + feature_names=titanic_data["feature_names"], + classnames=titanic_data["classnames"], + ) + + best_model = tuner.tune( + X_train=titanic_data["X_train"], + X_val=titanic_data["X_val"], + y_train=titanic_data["y_train"], + y_val=titanic_data["y_val"], + is_classification=True, + ) + + assert best_model is not None + + # Check leaderboard + df = tuner.leaderboard() + assert len(df) >= 2 + print(f"Tuner leaderboard:\n{df}") + + # Check best config was saved + assert os.path.exists(os.path.join(save_dir, "best_config.json")) diff --git a/theseus/__init__.py b/theseus/__init__.py index d416365..0c77b11 100644 --- a/theseus/__init__.py +++ b/theseus/__init__.py @@ -13,36 +13,24 @@ __copyright__ = "Copyright 2020-present Kaylode" __version__ = "2.0.0" -from .base import * -from .registry import Registry - -from .base.pipeline import BasePipeline -from .base.datasets.sampler import BalanceSampler -from .base.datasets.dataloader import DataLoaderWithCollator - from .base.utilities import ( - move_to, - seed_everything, LoggerObserver, + download_from_wandb, find_file_recursively, get_devices_info, - download_from_wandb, get_instance_recursively, -) # explicitly re-exporting - -from .base.utilities.loggers import FileLogger + move_to, + seed_everything, +) +from .registry import Registry __all__ = [ "move_to", "seed_everything", - "FileLogger", "LoggerObserver", "find_file_recursively", "get_devices_info", "download_from_wandb", "get_instance_recursively", - "BasePipeline", - "BalanceSampler", - "DataLoaderWithCollator", "Registry", -] \ No newline at end of file +] diff --git a/theseus/base/__init__.py b/theseus/base/__init__.py index 42cc681..39ab387 100644 --- a/theseus/base/__init__.py +++ b/theseus/base/__init__.py @@ -1,9 +1,3 @@ -from .augmentations import * -from .callbacks import * -from .datasets import * -from .losses import * -from .metrics import * -from .models import * -from .optimizers import * -from .pipeline import * -from .trainer import * +# Expose nothing by default to prevent heavy dependency imports (like torch/lightning). +# Users should explicitly import what they need, e.g., +# `from theseus.base.models import LightningModelWrapper` diff --git a/theseus/base/callbacks/__init__.py b/theseus/base/callbacks/__init__.py index 930217b..e384cc7 100644 --- a/theseus/base/callbacks/__init__.py +++ b/theseus/base/callbacks/__init__.py @@ -28,4 +28,3 @@ CALLBACKS_REGISTRY.register(MetricLoggerCallback) CALLBACKS_REGISTRY.register(TorchCheckpointCallback) CALLBACKS_REGISTRY.register(HuggingFaceHubCallback) - diff --git a/theseus/base/callbacks/checkpoint_callback.py b/theseus/base/callbacks/checkpoint_callback.py index e544a53..bae88cc 100644 --- a/theseus/base/callbacks/checkpoint_callback.py +++ b/theseus/base/callbacks/checkpoint_callback.py @@ -21,14 +21,11 @@ def __init__(self, save_dir: str, **kwargs) -> None: super().__init__(dirpath=save_dir, **filtered_kwargs) - def setup( - self, trainer: pl.Trainer, pl_module: pl.LightningModule, stage: str - ) -> None: + def setup(self, trainer: pl.Trainer, pl_module: pl.LightningModule, stage: str) -> None: super().setup(trainer, pl_module, stage) self.params = {} trainloader = pl_module.datamodule.trainloader if trainloader is not None: - batch_size = trainloader.batch_size self.params["trainloader_length"] = len(trainloader) self.params["num_iterations"] = len(trainloader) * trainer.max_epochs @@ -49,7 +46,7 @@ def auto_get_save_interval(self, train_fraction=0.5): def _save_checkpoint(self, trainer: pl.Trainer, filepath: str) -> None: super()._save_checkpoint(trainer, filepath) - if filepath in self.best_k_models.keys(): + if filepath in self.best_k_models: if self.best_k_models[filepath] == self.best_model_score: LOGGER.text( f"Evaluation improved to {self.current_score}", diff --git a/theseus/base/callbacks/hub_callback.py b/theseus/base/callbacks/hub_callback.py index ebcc3ea..dc034e3 100644 --- a/theseus/base/callbacks/hub_callback.py +++ b/theseus/base/callbacks/hub_callback.py @@ -5,13 +5,11 @@ from __future__ import annotations import logging -from typing import Any, Optional +from typing import Any import lightning.pytorch as pl from lightning.pytorch.callbacks import Callback -from theseus.registry import Registry - logger = logging.getLogger(__name__) @@ -44,12 +42,12 @@ def __init__( self, repo_id: str, *, - token: Optional[str] = None, + token: str | None = None, push_on_train_end: bool = True, push_every_n_epochs: int = 0, private: bool = False, use_safetensors: bool = True, - config: Optional[dict] = None, + config: dict | None = None, **kwargs: Any, ) -> None: super().__init__() @@ -85,15 +83,11 @@ def _push_model(self, trainer: pl.Trainer, pl_module: pl.LightningModule) -> Non f"HuggingFaceHubMixin. Skipping push." ) - def on_train_epoch_end( - self, trainer: pl.Trainer, pl_module: pl.LightningModule - ) -> None: + def on_train_epoch_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule) -> None: if self.push_every_n_epochs > 0: if (trainer.current_epoch + 1) % self.push_every_n_epochs == 0: self._push_model(trainer, pl_module) - def on_train_end( - self, trainer: pl.Trainer, pl_module: pl.LightningModule - ) -> None: + def on_train_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule) -> None: if self.push_on_train_end: self._push_model(trainer, pl_module) diff --git a/theseus/base/callbacks/loss_logging_callback.py b/theseus/base/callbacks/loss_logging_callback.py index 3703ad1..3f74563 100644 --- a/theseus/base/callbacks/loss_logging_callback.py +++ b/theseus/base/callbacks/loss_logging_callback.py @@ -1,5 +1,5 @@ import time -from typing import Any, Dict, List +from typing import Any import lightning.pytorch as pl import numpy as np @@ -28,9 +28,7 @@ def __init__(self, print_interval: int = None, **kwargs) -> None: self.running_loss = {} self.print_interval = print_interval - def setup( - self, trainer: pl.Trainer, pl_module: pl.LightningModule, stage: str - ) -> None: + def setup(self, trainer: pl.Trainer, pl_module: pl.LightningModule, stage: str) -> None: """ Setup the callback """ @@ -38,7 +36,6 @@ def setup( trainloader = pl_module.datamodule.trainloader if trainloader is not None: - batch_size = trainloader.batch_size self.params["num_iterations"] = len(trainloader) * trainer.max_epochs self.params["trainloader_length"] = len(trainloader) else: @@ -47,14 +44,12 @@ def setup( valloader = pl_module.datamodule.valloader if valloader is not None: - batch_size = valloader.batch_size self.params["valloader_length"] = len(valloader) else: self.params["valloader_length"] = None testloader = pl_module.datamodule.testloader if testloader is not None: - batch_size = testloader.batch_size self.params["testloader_length"] = len(testloader) else: self.params["testloader_length"] = None @@ -66,9 +61,7 @@ def setup( level=LoggerObserver.DEBUG, ) - def auto_get_print_interval( - self, pl_module: pl.LightningModule, train_fraction: float = 0.1 - ): + def auto_get_print_interval(self, pl_module: pl.LightningModule, train_fraction: float = 0.1): """ Automatically decide the number of print interval """ @@ -120,8 +113,8 @@ def on_train_batch_end( loss_dict = outputs["loss_dict"] # Update running loss of batch - for (key, value) in loss_dict.items(): - if key not in self.running_loss.keys(): + for key, value in loss_dict.items(): + if key not in self.running_loss: self.running_loss[key] = [] self.running_loss[key].append(value) @@ -132,19 +125,13 @@ def on_train_batch_end( self.running_time_list.append(batch_time) # Logging - if ( - (iters % self.print_interval == 0 and iters > 0 ) - or (iters + 1) % self.params["trainloader_length"] == 0 - ): - + if (iters % self.print_interval == 0 and iters > 0) or (iters + 1) % self.params[ + "trainloader_length" + ] == 0: # Running loss since last interval - for key in self.running_loss.keys(): + for key in self.running_loss: self.running_loss[key] = np.round(np.mean(self.running_loss[key]), 5) - loss_string = ( - "{}".format(self.running_loss)[1:-1] - .replace("'", "") - .replace(",", " ||") - ) + loss_string = f"{self.running_loss}"[1:-1].replace("'", "").replace(",", " ||") # Running time average running_time = 1.0 / np.round(np.mean(self.running_time_list), 5) @@ -172,7 +159,7 @@ def on_train_batch_end( # Log batch time execution log_dict.append( { - "tag": f"Training/Iterations per second", + "tag": "Training/Iterations per second", "value": running_time, "type": LoggerObserver.SCALAR, "kwargs": {"step": iters}, @@ -195,9 +182,7 @@ def on_train_batch_end( self.running_loss = {} self.running_time_list = [] - def on_validation_epoch_start( - self, trainer: pl.Trainer, pl_module: pl.LightningModule - ): + def on_validation_epoch_start(self, trainer: pl.Trainer, pl_module: pl.LightningModule): """ Before main validation loops """ @@ -220,8 +205,8 @@ def on_validation_batch_end( loss_dict = outputs["loss_dict"] # Update batch loss - for (key, value) in loss_dict.items(): - if key not in self.running_loss.keys(): + for key, value in loss_dict.items(): + if key not in self.running_loss: self.running_loss[key] = [] self.running_loss[key].append(value) @@ -235,11 +220,9 @@ def on_validation_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule): epoch_time = time.time() - self.running_time # Log loss - for key in self.running_loss.keys(): + for key in self.running_loss: self.running_loss[key] = np.round(np.mean(self.running_loss[key]), 5) - loss_string = ( - "{}".format(self.running_loss)[1:-1].replace("'", "").replace(",", " ||") - ) + loss_string = f"{self.running_loss}"[1:-1].replace("'", "").replace(",", " ||") LOGGER.text( "[{}|{}] || {} || Time: {:10.4f} (it/s)".format( iters, @@ -286,11 +269,9 @@ def on_test_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule): epoch_time = time.time() - self.running_time # Log loss - for key in self.running_loss.keys(): + for key in self.running_loss: self.running_loss[key] = np.round(np.mean(self.running_loss[key]), 5) - loss_string = ( - "{}".format(self.running_loss)[1:-1].replace("'", "").replace(",", " ||") - ) + loss_string = f"{self.running_loss}"[1:-1].replace("'", "").replace(",", " ||") LOGGER.text( "[{}|{}] || {} || Time: {:10.4f} (it/s)".format( iters, diff --git a/theseus/base/callbacks/metric_logging_callback.py b/theseus/base/callbacks/metric_logging_callback.py index 3fdcc79..b4b711e 100644 --- a/theseus/base/callbacks/metric_logging_callback.py +++ b/theseus/base/callbacks/metric_logging_callback.py @@ -1,7 +1,6 @@ import json import os import os.path as osp -from typing import Dict import lightning.pytorch as pl from lightning.pytorch.callbacks import Callback @@ -21,12 +20,10 @@ class MetricLoggerCallback(Callback): def __init__(self, save_json: bool = True, **kwargs) -> None: super().__init__() self.save_json = save_json - self.save_dir = kwargs.get("save_dir", None) + self.save_dir = kwargs.get("save_dir") self.output_dict = [] - def on_validation_end( - self, trainer: pl.Trainer, pl_module: pl.LightningModule - ) -> None: + def on_validation_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule) -> None: """ After finish validation """ @@ -94,23 +91,20 @@ def on_test_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule) -> Non LOGGER.log(log_dict) - def teardown( - self, trainer: pl.Trainer, pl_module: pl.LightningModule, stage: str - ) -> None: + def teardown(self, trainer: pl.Trainer, pl_module: pl.LightningModule, stage: str) -> None: """ After finish everything """ - if self.save_json: - if self.save_dir is not None: - save_dir = osp.join(self.save_dir, stage.capitalize()) - os.makedirs(save_dir, exist_ok=True) - save_json = osp.join(save_dir, "metrics.json") - if len(self.output_dict) > 0: - with open(save_json, "w") as f: - json.dump( - self.output_dict, - f, - indent=4, - default=lambda x: "", - ) + if self.save_json and self.save_dir is not None: + save_dir = osp.join(self.save_dir, stage.capitalize()) + os.makedirs(save_dir, exist_ok=True) + save_json = osp.join(save_dir, "metrics.json") + if len(self.output_dict) > 0: + with open(save_json, "w") as f: + json.dump( + self.output_dict, + f, + indent=4, + default=lambda x: "", + ) diff --git a/theseus/base/callbacks/optuna_callback.py b/theseus/base/callbacks/optuna_callback.py index f93c714..0b71a7c 100644 --- a/theseus/base/callbacks/optuna_callback.py +++ b/theseus/base/callbacks/optuna_callback.py @@ -1,4 +1,3 @@ -from typing import Dict, List import lightning.pytorch as pl import optuna @@ -30,7 +29,5 @@ def on_validation_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule): self.trial.report(value=metric_dict[best_key], step=iters) if self.trial.should_prune(): - LOGGER.text( - f"Trial {self.trial.number} has been pruned", level=LoggerObserver.DEBUG - ) + LOGGER.text(f"Trial {self.trial.number} has been pruned", level=LoggerObserver.DEBUG) raise optuna.TrialPruned() diff --git a/theseus/base/callbacks/timer_callback.py b/theseus/base/callbacks/timer_callback.py index 2f7d34e..969fc18 100644 --- a/theseus/base/callbacks/timer_callback.py +++ b/theseus/base/callbacks/timer_callback.py @@ -33,7 +33,7 @@ def on_fit_start(self, trainer: pl.Trainer, pl_module: pl.LightningModule) -> No """ self.start_time = time.time() LOGGER.text( - f"===========================START TRAINING=================================", + "===========================START TRAINING=================================", level=LoggerObserver.INFO, ) diff --git a/theseus/base/callbacks/tsb_callback.py b/theseus/base/callbacks/tsb_callback.py index 49b07d1..88d8c29 100644 --- a/theseus/base/callbacks/tsb_callback.py +++ b/theseus/base/callbacks/tsb_callback.py @@ -33,7 +33,5 @@ def __init__(self, save_dir: str = "runs", resume: str = None, **kwargs) -> None """ tsb_logger = TensorboardLogger(self.save_dir) if self.resume is not None: - tsb_logger.load( - find_old_tflog(os.path.dirname(os.path.dirname(self.resume))) - ) + tsb_logger.load(find_old_tflog(os.path.dirname(os.path.dirname(self.resume)))) LOGGER.subscribe(tsb_logger) diff --git a/theseus/base/callbacks/wandb_callback.py b/theseus/base/callbacks/wandb_callback.py index 622fc25..a233729 100644 --- a/theseus/base/callbacks/wandb_callback.py +++ b/theseus/base/callbacks/wandb_callback.py @@ -1,32 +1,29 @@ +import contextlib import os import os.path as osp from copy import deepcopy from datetime import datetime -from typing import Dict import lightning.pytorch as pl from deepdiff import DeepDiff -from deepdiff.helper import SetOrdered from lightning.pytorch.callbacks import Callback +from lightning.pytorch.utilities.model_summary import summarize from omegaconf import DictConfig, OmegaConf from theseus.base.utilities.loggers.observer import LoggerObserver from theseus.base.utilities.loggers.wandb_logger import WandbLogger, find_run_id -from lightning.pytorch.utilities.model_summary import summarize -try: +with contextlib.suppress(ModuleNotFoundError): import wandb as wandblogger -except ModuleNotFoundError: - pass LOGGER = LoggerObserver.getLogger("main") def pretty_print_diff(diff): texts = [] - for type_key in diff.keys(): + for type_key in diff: try: - for config_key in diff[type_key].keys(): + for config_key in diff[type_key]: if type_key == "values_changed": texts.append( config_key @@ -35,16 +32,10 @@ def pretty_print_diff(diff): + "-->" + str(diff[type_key][config_key]["new_value"]) ) - elif "item_removed" in type_key: - texts.append(config_key + ": " + str(diff[type_key][config_key])) - elif "item_added" in type_key: + elif "item_removed" in type_key or "item_added" in type_key: texts.append(config_key + ": " + str(diff[type_key][config_key])) except: - texts.append( - str(type_key) - + ": " - + str(diff[type_key]) - ) + texts.append(str(type_key) + ": " + str(diff[type_key])) return "\n".join(texts) @@ -179,9 +170,7 @@ def __init__( ) LOGGER.subscribe(self.wandb_logger) - def setup( - self, trainer: pl.Trainer, pl_module: pl.LightningModule, stage: str - ) -> None: + def setup(self, trainer: pl.Trainer, pl_module: pl.LightningModule, stage: str) -> None: """ Before going to the main loop. Save run id """ @@ -197,7 +186,6 @@ def setup( value=osp.join(self.save_dir, "*.yaml"), ) - summary = summarize(pl_module, max_depth=3) LOGGER.text( @@ -209,23 +197,25 @@ def setup( total_trainable_params = summary.trainable_parameters # Log learning rates - log_dict = [{ - "tag": "Training/Total no. parameters", - "value": total_params, - "type": LoggerObserver.SCALAR, - "kwargs": {"step": 0}, - }] - - log_dict.append({ - "tag": "Training/Total no. trainable parameters", - "value": total_trainable_params, - "type": LoggerObserver.SCALAR, - "kwargs": {"step": 0}, - }) - - LOGGER.log(log_dict) - + log_dict = [ + { + "tag": "Training/Total no. parameters", + "value": total_params, + "type": LoggerObserver.SCALAR, + "kwargs": {"step": 0}, + } + ] + + log_dict.append( + { + "tag": "Training/Total no. trainable parameters", + "value": total_trainable_params, + "type": LoggerObserver.SCALAR, + "kwargs": {"step": 0}, + } + ) + LOGGER.log(log_dict) def teardown(self, trainer: pl.Trainer, pl_module: pl.LightningModule, stage: str): """ diff --git a/theseus/base/datasets/collator.py b/theseus/base/datasets/collator.py index aeee091..25fa5dc 100644 --- a/theseus/base/datasets/collator.py +++ b/theseus/base/datasets/collator.py @@ -1,7 +1,6 @@ -from typing import List -class BaseCollator(object): +class BaseCollator: """Base collator function""" def __init__(self, **kwargs) -> None: @@ -14,7 +13,7 @@ def __call__(self, batch): class ChainCollatorWrapper(BaseCollator): """Wrapper for list of collate functions""" - def __init__(self, pre_collate_fns: List, **kwargs): + def __init__(self, pre_collate_fns: list, **kwargs): self.pre_collate_fns = pre_collate_fns def __call__(self, batch): diff --git a/theseus/base/datasets/dataloader.py b/theseus/base/datasets/dataloader.py index 91e075a..53bc581 100644 --- a/theseus/base/datasets/dataloader.py +++ b/theseus/base/datasets/dataloader.py @@ -16,6 +16,4 @@ def __init__(self, dataset, collate_fn=None, sampler=None, **kwargs) -> None: else: collate_fn = dataset.collate_fn - super().__init__( - dataset=dataset, collate_fn=collate_fn, sampler=sampler, **kwargs - ) + super().__init__(dataset=dataset, collate_fn=collate_fn, sampler=sampler, **kwargs) diff --git a/theseus/base/datasets/dataset.py b/theseus/base/datasets/dataset.py index 2df139a..ea7038d 100644 --- a/theseus/base/datasets/dataset.py +++ b/theseus/base/datasets/dataset.py @@ -1,5 +1,5 @@ import os -from typing import Iterable, List +from collections.abc import Iterable import numpy as np import torch @@ -61,11 +61,7 @@ class ImageDataset(data.Dataset): """ def __init__( - self, - image_dir: str, - txt_classnames: str = None, - transform: List = None, - **kwargs + self, image_dir: str, txt_classnames: str = None, transform: list = None, **kwargs ): super().__init__() self.image_dir = image_dir @@ -78,7 +74,7 @@ def load_data(self): Load filepaths into memory """ if self.txt_classnames: - with open(self.txt_classnames, "r") as f: + with open(self.txt_classnames) as f: self.classnames = f.read().splitlines() self.fns = [] image_names = os.listdir(self.image_dir) @@ -109,7 +105,7 @@ def __getitem__(self, index: int): def __len__(self): return len(self.fns) - def collate_fn(self, batch: List): + def collate_fn(self, batch: list): imgs = torch.stack([s["input"] for s in batch]) img_names = [s["img_name"] for s in batch] ori_sizes = [s["ori_size"] for s in batch] diff --git a/theseus/base/losses/__init__.py b/theseus/base/losses/__init__.py index a2a3121..8b5348d 100644 --- a/theseus/base/losses/__init__.py +++ b/theseus/base/losses/__init__.py @@ -5,9 +5,9 @@ from .bce_loss import BCELoss from .ce_loss import * from .focal_loss import FocalLoss +from .mae_loss import MeanAbsoluteErrorLoss from .mse_loss import MeanSquaredErrorLoss from .multi_loss import MultiLoss -from .mae_loss import MeanAbsoluteErrorLoss LOSS_REGISTRY.register(MultiLoss) LOSS_REGISTRY.register(ClassificationCELoss) @@ -15,4 +15,4 @@ LOSS_REGISTRY.register(MeanSquaredErrorLoss) LOSS_REGISTRY.register(ClassificationSmoothCELoss) LOSS_REGISTRY.register(BCELoss) -LOSS_REGISTRY.register(MeanAbsoluteErrorLoss) \ No newline at end of file +LOSS_REGISTRY.register(MeanAbsoluteErrorLoss) diff --git a/theseus/base/losses/bce_loss.py b/theseus/base/losses/bce_loss.py index c9c22b4..b6ad777 100644 --- a/theseus/base/losses/bce_loss.py +++ b/theseus/base/losses/bce_loss.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any import torch from torch import nn @@ -10,7 +10,7 @@ class BCELoss(nn.Module): r"""CELoss is warper of cross-entropy loss""" def __init__(self, **kwargs): - super(BCELoss, self).__init__() + super().__init__() if "weight" in kwargs: weight = torch.FloatTensor(kwargs.get("weight")) else: @@ -21,8 +21,8 @@ def __init__(self, **kwargs): def forward( self, - outputs: Dict[str, Any], - batch: Dict[str, Any], + outputs: dict[str, Any], + batch: dict[str, Any], device: torch.device = None, ): pred = outputs["outputs"] diff --git a/theseus/base/losses/ce_loss.py b/theseus/base/losses/ce_loss.py index 61b52cf..a68d0be 100644 --- a/theseus/base/losses/ce_loss.py +++ b/theseus/base/losses/ce_loss.py @@ -12,7 +12,7 @@ class ClassificationCELoss(nn.Module): r"""CELoss is warper of cross-entropy loss""" def __init__(self, weight: List = None, **kwargs): - super(ClassificationCELoss, self).__init__() + super().__init__() if weight is not None: weight = torch.tensor(weight) self.criterion = nn.CrossEntropyLoss( @@ -46,7 +46,7 @@ class ClassificationSmoothCELoss(nn.Module): r"""SmoothCELoss is warper of label smoothing cross-entropy loss""" def __init__(self, smoothing: float = 0.1, **kwargs): - super(ClassificationSmoothCELoss, self).__init__() + super().__init__() self.smooth_criterion = LabelSmoothingCrossEntropy(smoothing=smoothing) self.soft_criterion = SoftTargetCrossEntropy() @@ -60,9 +60,7 @@ def forward( target = batch["targets"] if pred.shape == target.shape: - loss, loss_dict = self.soft_criterion( - {"outputs": pred}, {"targets": target}, device - ) + loss, loss_dict = self.soft_criterion({"outputs": pred}, {"targets": target}, device) else: # batch["targets"] = batch["targets"].view(-1).contiguous() loss, loss_dict = self.smooth_criterion( diff --git a/theseus/base/losses/focal_loss.py b/theseus/base/losses/focal_loss.py index 84df8bc..3162f4e 100644 --- a/theseus/base/losses/focal_loss.py +++ b/theseus/base/losses/focal_loss.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any import torch import torch.nn as nn @@ -18,8 +18,8 @@ def __init__(self, alpha=0.25, gamma=2, reduction="mean", **kwargs): def forward( self, - outputs: Dict[str, Any], - batch: Dict[str, Any], + outputs: dict[str, Any], + batch: dict[str, Any], device: torch.device = None, ): outputs = outputs["outputs"] @@ -34,8 +34,6 @@ def forward( targets = nn.functional.one_hot(targets, num_classes=num_classes) targets = targets.float().squeeze() - loss = sigmoid_focal_loss( - outputs, targets, self.alpha, self.gamma, self.reduction - ) + loss = sigmoid_focal_loss(outputs, targets, self.alpha, self.gamma, self.reduction) loss_dict = {"L": loss.item()} return loss, loss_dict diff --git a/theseus/base/losses/mae_loss.py b/theseus/base/losses/mae_loss.py index aa45072..c764fb6 100644 --- a/theseus/base/losses/mae_loss.py +++ b/theseus/base/losses/mae_loss.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any import torch from torch import nn @@ -10,12 +10,12 @@ class MeanAbsoluteErrorLoss(nn.Module): r"""MSELoss is warper of mean absolute error loss""" def __init__(self, **kwargs): - super(MeanAbsoluteErrorLoss, self).__init__() + super().__init__() def forward( self, - outputs: Dict[str, Any], - batch: Dict[str, Any], + outputs: dict[str, Any], + batch: dict[str, Any], device: torch.device = None, ): pred = outputs["outputs"] @@ -30,6 +30,5 @@ def forward( # If the shapes are different, we can use MSELoss loss = torch.mean(torch.abs(pred.squeeze(-1) - target.view(-1).contiguous())) - loss_dict = {"MAE": loss.item()} return loss, loss_dict diff --git a/theseus/base/losses/mse_loss.py b/theseus/base/losses/mse_loss.py index c018646..727cb4a 100644 --- a/theseus/base/losses/mse_loss.py +++ b/theseus/base/losses/mse_loss.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any import torch from torch import nn @@ -10,13 +10,13 @@ class MeanSquaredErrorLoss(nn.Module): r"""MSELoss is warper of mean square error loss""" def __init__(self, **kwargs): - super(MeanSquaredErrorLoss, self).__init__() + super().__init__() self.criterion = nn.MSELoss() def forward( self, - outputs: Dict[str, Any], - batch: Dict[str, Any], + outputs: dict[str, Any], + batch: dict[str, Any], device: torch.device = None, ): pred = outputs["outputs"] diff --git a/theseus/base/losses/multi_loss.py b/theseus/base/losses/multi_loss.py index 5da01a9..e4fba4c 100644 --- a/theseus/base/losses/multi_loss.py +++ b/theseus/base/losses/multi_loss.py @@ -1,4 +1,5 @@ -from typing import Any, Dict, Iterable +from collections.abc import Iterable +from typing import Any import torch import torch.nn as nn @@ -14,8 +15,8 @@ def __init__(self, losses: Iterable[nn.Module], weights=None, **kwargs): def forward( self, - outputs: Dict[str, Any], - batch: Dict[str, Any], + outputs: dict[str, Any], + batch: dict[str, Any], device: torch.device = None, ): """ diff --git a/theseus/base/losses/smoothing.py b/theseus/base/losses/smoothing.py index 133072a..34d77a1 100644 --- a/theseus/base/losses/smoothing.py +++ b/theseus/base/losses/smoothing.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, Iterable +from typing import Any import torch import torch.nn.functional as F @@ -15,15 +15,15 @@ class LabelSmoothingCrossEntropy(nn.Module): """NLL loss with label smoothing.""" def __init__(self, smoothing=0.1): - super(LabelSmoothingCrossEntropy, self).__init__() + super().__init__() assert smoothing < 1.0 self.smoothing = smoothing self.confidence = 1.0 - smoothing def forward( self, - outputs: Dict[str, Any], - batch: Dict[str, Any], + outputs: dict[str, Any], + batch: dict[str, Any], device: torch.device = None, ): @@ -46,12 +46,12 @@ def forward( class SoftTargetCrossEntropy(nn.Module): def __init__(self): - super(SoftTargetCrossEntropy, self).__init__() + super().__init__() def forward( self, - outputs: Dict[str, Any], - batch: Dict[str, Any], + outputs: dict[str, Any], + batch: dict[str, Any], device: torch.device = None, ): diff --git a/theseus/base/metrics/accuracy.py b/theseus/base/metrics/accuracy.py index 9ba61f9..5c09110 100644 --- a/theseus/base/metrics/accuracy.py +++ b/theseus/base/metrics/accuracy.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any from theseus.base.metrics.metric_template import Metric from theseus.base.utilities.logits import logits2labels @@ -16,15 +16,13 @@ def __init__(self, label_type: str = "multiclass", ignore_index=None, **kwargs): self.ignore_index = ignore_index self.reset() - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): + def update(self, outputs: dict[str, Any], batch: dict[str, Any]): """ Perform calculation based on prediction and targets """ outputs = outputs["outputs"].detach().cpu() target = batch["targets"].cpu() - prediction = logits2labels( - outputs, label_type=self.type, threshold=self.threshold - ) + prediction = logits2labels(outputs, label_type=self.type, threshold=self.threshold) # Create mask for non-ignored indices if self.ignore_index is not None: diff --git a/theseus/base/metrics/bl_accuracy.py b/theseus/base/metrics/bl_accuracy.py index 774d829..6aee985 100644 --- a/theseus/base/metrics/bl_accuracy.py +++ b/theseus/base/metrics/bl_accuracy.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any import numpy as np from sklearn.metrics import balanced_accuracy_score @@ -30,7 +30,7 @@ def __init__(self, label_type: str = "multiclass", ignore_index=None, **kwargs): self.ignore_index = ignore_index self.reset() - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): + def update(self, outputs: dict[str, Any], batch: dict[str, Any]): """ Perform calculation based on prediction and targets """ @@ -40,7 +40,7 @@ def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): outputs = outputs.detach().cpu() targets = targets.detach().cpu().view(-1) - + # Filter out ignored indices if self.ignore_index is not None: mask = targets != self.ignore_index @@ -61,7 +61,7 @@ def get_all_unique_id(self): def value(self): if len(self.targets) == 0: return {"bl_acc": 0.0} - + self.get_all_unique_id() self.corrects = {str(k): 0 for k in self.unique_ids} diff --git a/theseus/base/metrics/confusion_matrix.py b/theseus/base/metrics/confusion_matrix.py index 4efd820..ce99a8e 100644 --- a/theseus/base/metrics/confusion_matrix.py +++ b/theseus/base/metrics/confusion_matrix.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, List, Optional +from typing import Any import matplotlib.pyplot as plt import numpy as np @@ -12,7 +12,7 @@ LOGGER = LoggerObserver.getLogger("main") -def plot_cfm(cm, ax, labels: List): +def plot_cfm(cm, ax, labels: list): """ Make confusion matrix figure labels: `Optional[List]` @@ -28,7 +28,7 @@ def plot_cfm(cm, ax, labels: List): ax.yaxis.set_ticklabels(labels, rotation=0) -def make_cm_fig(cms, labels: Optional[List] = None): +def make_cm_fig(cms, labels: list | None = None): if cms.shape[0] > 1: # multilabel num_classes = cms.shape[0] @@ -76,7 +76,7 @@ def __init__(self, classnames=None, label_type: str = "multiclass", **kwargs): self.threshold = kwargs.get("threshold", 0.5) self.reset() - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): + def update(self, outputs: dict[str, Any], batch: dict[str, Any]): """ Perform calculation based on prediction and targets """ diff --git a/theseus/base/metrics/f1.py b/theseus/base/metrics/f1.py index 4f87219..c543230 100644 --- a/theseus/base/metrics/f1.py +++ b/theseus/base/metrics/f1.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any from sklearn.metrics import f1_score @@ -11,7 +11,9 @@ class F1ScoreMetric(Metric): F1 Score Metric (including macro, micro) """ - def __init__(self, average="weighted", label_type: str = "multiclass", ignore_index=None, **kwargs): + def __init__( + self, average="weighted", label_type: str = "multiclass", ignore_index=None, **kwargs + ): super().__init__(**kwargs) self.average = average self.type = label_type @@ -19,7 +21,7 @@ def __init__(self, average="weighted", label_type: str = "multiclass", ignore_in self.ignore_index = ignore_index self.reset() - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): + def update(self, outputs: dict[str, Any], batch: dict[str, Any]): """ Perform calculation based on prediction and targets """ @@ -27,7 +29,7 @@ def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): outputs = outputs["outputs"].detach().cpu() outputs = logits2labels(outputs, label_type=self.type, threshold=self.threshold) - + # Filter out ignored indices if self.ignore_index is not None: mask = targets != self.ignore_index diff --git a/theseus/base/metrics/mcc.py b/theseus/base/metrics/mcc.py index f862a5f..3d4af3b 100644 --- a/theseus/base/metrics/mcc.py +++ b/theseus/base/metrics/mcc.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any from sklearn.metrics import matthews_corrcoef @@ -17,14 +17,14 @@ def __init__(self, label_type: str = "multiclass", ignore_index=None, **kwargs): self.ignore_index = ignore_index self.reset() - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): + def update(self, outputs: dict[str, Any], batch: dict[str, Any]): """ Perform calculation based on prediction and targets """ targets = batch["targets"].cpu() outputs = outputs["outputs"].detach().cpu() outputs = logits2labels(outputs, label_type=self.type) - + # Filter out ignored indices if self.ignore_index is not None: mask = targets != self.ignore_index diff --git a/theseus/base/metrics/metric_template.py b/theseus/base/metrics/metric_template.py index 3887d85..e7e6d23 100644 --- a/theseus/base/metrics/metric_template.py +++ b/theseus/base/metrics/metric_template.py @@ -1,5 +1,5 @@ from abc import ABC, abstractmethod -from typing import Any, Dict, List +from typing import Any class Metric(ABC): @@ -33,12 +33,12 @@ def __init__(self, **kwargs: Any) -> None: pass @abstractmethod - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]) -> None: + def update(self, outputs: dict[str, Any], batch: dict[str, Any]) -> None: """Update metric state with new predictions and targets.""" ... @abstractmethod - def value(self) -> Dict[str, Any]: + def value(self) -> dict[str, Any]: """Compute and return the metric value(s) as a dict.""" ... diff --git a/theseus/base/metrics/precision_recall.py b/theseus/base/metrics/precision_recall.py index 2f7b2e5..ebe56af 100644 --- a/theseus/base/metrics/precision_recall.py +++ b/theseus/base/metrics/precision_recall.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any from sklearn.metrics import precision_score, recall_score @@ -11,7 +11,9 @@ class PrecisionRecall(Metric): F1 Score Metric (including macro, micro) """ - def __init__(self, average="weighted", label_type: str = "multiclass", ignore_index=None, **kwargs): + def __init__( + self, average="weighted", label_type: str = "multiclass", ignore_index=None, **kwargs + ): super().__init__(**kwargs) self.average = average self.type = label_type @@ -19,14 +21,14 @@ def __init__(self, average="weighted", label_type: str = "multiclass", ignore_in self.ignore_index = ignore_index self.reset() - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): + def update(self, outputs: dict[str, Any], batch: dict[str, Any]): """ Perform calculation based on prediction and targets """ targets = batch["targets"].cpu().view(-1) outputs = outputs["outputs"].detach().cpu() outputs = logits2labels(outputs, label_type=self.type, threshold=self.threshold) - + # Filter out ignored indices if self.ignore_index is not None: mask = targets != self.ignore_index @@ -42,13 +44,9 @@ def value(self): f"{self.average}-precision": 0.0, f"{self.average}-recall": 0.0, } - - precision = precision_score( - self.targets, self.preds, average=self.average, zero_division=1 - ) - recall = recall_score( - self.targets, self.preds, average=self.average, zero_division=1 - ) + + precision = precision_score(self.targets, self.preds, average=self.average, zero_division=1) + recall = recall_score(self.targets, self.preds, average=self.average, zero_division=1) return { f"{self.average}-precision": precision, f"{self.average}-recall": recall, diff --git a/theseus/base/metrics/roc_auc_score.py b/theseus/base/metrics/roc_auc_score.py index 8800c50..a606b6c 100644 --- a/theseus/base/metrics/roc_auc_score.py +++ b/theseus/base/metrics/roc_auc_score.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any import torch @@ -8,13 +8,14 @@ has_scikitplot = True except: has_scikitplot = False -from sklearn.metrics import roc_auc_score, auc, precision_recall_curve +import numpy as np +from sklearn.metrics import auc, precision_recall_curve, roc_auc_score from theseus.base.metrics.metric_template import Metric -from theseus.base.utilities.cuda import detach, move_to +from theseus.base.utilities.cuda import move_to from theseus.base.utilities.loggers.observer import LoggerObserver from theseus.base.utilities.logits import logits2labels -import numpy as np + LOGGER = LoggerObserver.getLogger("main") @@ -35,16 +36,14 @@ def __init__( self.average = average self.plot_curve = plot_curve - if self.type == "multiclass": - self.label_type = "ovr" - elif self.type == "multilabel": + if self.type == "multiclass" or self.type == "multilabel": self.label_type = "ovr" else: self.label_type = "raise" self.reset() - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): + def update(self, outputs: dict[str, Any], batch: dict[str, Any]): """ Perform calculation based on prediction and targets """ @@ -67,7 +66,7 @@ def value(self): average=self.average, multi_class=self.label_type, ) - except Exception as e: + except Exception: try: preds = np.array(self.preds) if preds.ndim == 2: @@ -79,27 +78,20 @@ def value(self): multi_class=self.label_type, ) except Exception as e: - LOGGER.text( - f"AUC score could not be calculated: {e}", level=LoggerObserver.WARN - ) + LOGGER.text(f"AUC score could not be calculated: {e}", level=LoggerObserver.WARN) roc_auc_scr = 0 try: - precision, recall, _ = precision_recall_curve( - self.targets, self.preds, pos_label=1 - ) + precision, recall, _ = precision_recall_curve(self.targets, self.preds, pos_label=1) pr_auc = auc(recall, precision) - except Exception as e: + except Exception: try: preds = np.array(self.preds) if preds.ndim == 2: preds = preds[:, 1] - precision, recall, _ = precision_recall_curve( - self.targets, preds, pos_label=1 - ) + precision, recall, _ = precision_recall_curve(self.targets, preds, pos_label=1) pr_auc = auc(recall, precision) except Exception as e: - LOGGER.text( f"Precision-Recall AUC score could not be calculated: {e}", level=LoggerObserver.WARN, @@ -108,7 +100,7 @@ def value(self): results = { f"{self.average}-roc_auc_score": roc_auc_scr, - f"pr_auc_score": pr_auc, + "pr_auc_score": pr_auc, } if has_scikitplot and self.plot_curve: roc_curve_fig = plot_roc(self.targets, self.preds).get_figure() diff --git a/theseus/base/models/wrapper.py b/theseus/base/models/wrapper.py index f861607..6ae63eb 100644 --- a/theseus/base/models/wrapper.py +++ b/theseus/base/models/wrapper.py @@ -1,13 +1,14 @@ from __future__ import annotations -from typing import Any, Dict, List, Mapping, Optional +from collections.abc import Mapping +from typing import Any import lightning.pytorch as pl import torch import torch.nn as nn +from lightning.pytorch.utilities.types import STEP_OUTPUT from torch.amp import autocast -from lightning.pytorch.utilities.types import STEP_OUTPUT from theseus.base.datasets import LightningDataModuleWrapper from theseus.base.optimizers import OPTIM_REGISTRY, SCHEDULER_REGISTRY from theseus.base.utilities.getter import get_instance @@ -24,13 +25,13 @@ class LightningModelWrapper(pl.LightningModule): def __init__( self, model: nn.Module, - criterion: Optional[nn.Module] = None, + criterion: nn.Module | None = None, *, - metrics: Optional[List[Any]] = None, - optimizer_config: Optional[Dict] = None, - scheduler_config: Optional[Dict] = None, - scheduler_kwargs: Optional[Dict] = None, - datamodule: Optional[LightningDataModuleWrapper] = None, + metrics: list[Any] | None = None, + optimizer_config: dict | None = None, + scheduler_config: dict | None = None, + scheduler_kwargs: dict | None = None, + datamodule: LightningDataModuleWrapper | None = None, use_mixed_precision: bool = False, ) -> None: super().__init__() @@ -43,7 +44,7 @@ def __init__( self.datamodule = datamodule self.use_mixed_precision = use_mixed_precision self.lr: float = 0.0 - self.metric_dict: Dict[str, Any] = {} + self.metric_dict: dict[str, Any] = {} def log_dict(self, dictionary: Mapping[str, Any], **kwargs: Any) -> None: """Filter non-loggable values before passing to Lightning's log_dict.""" @@ -63,9 +64,7 @@ def _autocast_device(self) -> str: return "mps" return "cpu" - def on_train_batch_end( - self, outputs: STEP_OUTPUT, batch: Any, batch_idx: int - ) -> None: + def on_train_batch_end(self, outputs: STEP_OUTPUT, batch: Any, batch_idx: int) -> None: # Use Lightning's optimizers() API instead of storing self.optimizer optimizers = self.optimizers() if optimizers is not None: @@ -93,22 +92,31 @@ def on_test_epoch_end(self) -> None: def _forward( self, - batch: Dict[str, Any], - metrics: Optional[List[Any]] = None, - ) -> Dict[str, Any]: + batch: dict[str, Any], + metrics: list[Any] | None = None, + ) -> dict[str, Any]: """ Forward the batch through models, losses and metrics. If some parameters are needed, it's best to include in the batch. """ - with autocast(device_type=self._autocast_device, enabled=self.use_mixed_precision): + device_type = self._autocast_device + + # BF16 is not supported on all devices, and autocast sometimes fails on CPU + # if not explicitly supported. We'll be more conservative here. + enabled = self.use_mixed_precision + if device_type == "cpu" and enabled: + # Most CPUs don't support BF16/FP16 well in autocast unless using specific CPUs + # It's safer to disable for CPU unless it's explicitly managed by Lightning + enabled = False + + with autocast(device_type=device_type, enabled=enabled): outputs = self.model.forward_batch(batch) if self.criterion is None: loss = outputs["outputs"].get("loss", None) loss_dict = outputs["outputs"].get("loss_dict", None) if loss is None or loss_dict is None: raise ValueError( - "No loss found in model outputs. " - "Please ensure the model returns a loss." + "No loss found in model outputs. Please ensure the model returns a loss." ) else: loss, loss_dict = self.criterion(outputs, batch) @@ -123,22 +131,22 @@ def trainable_parameters(self) -> int: """Return the number of trainable parameters.""" return sum(p.numel() for p in self.parameters() if p.requires_grad) - def training_step(self, batch: Any, batch_idx: int) -> Dict[str, Any]: + def training_step(self, batch: Any, batch_idx: int) -> dict[str, Any]: outputs = self._forward(batch) self.log_dict(outputs["loss_dict"], prog_bar=True, on_step=True, on_epoch=False) return outputs - def validation_step(self, batch: Any, batch_idx: int) -> Dict[str, Any]: + def validation_step(self, batch: Any, batch_idx: int) -> dict[str, Any]: outputs = self._forward(batch, metrics=self.metrics) self.log_dict(outputs["loss_dict"], prog_bar=True, on_step=True, on_epoch=False) return outputs - def test_step(self, batch: Any, batch_idx: int) -> Dict[str, Any]: + def test_step(self, batch: Any, batch_idx: int) -> dict[str, Any]: outputs = self._forward(batch, metrics=self.metrics) self.log_dict(outputs["loss_dict"], prog_bar=True, on_step=True, on_epoch=False) return outputs - def predict_step(self, batch: Any, batch_idx: Optional[int] = None) -> Any: + def predict_step(self, batch: Any, batch_idx: int | None = None) -> Any: return self.model.get_prediction(batch) def configure_optimizers(self) -> Any: diff --git a/theseus/base/optimizers/schedulers/cosine.py b/theseus/base/optimizers/schedulers/cosine.py index 47542ff..43c0480 100644 --- a/theseus/base/optimizers/schedulers/cosine.py +++ b/theseus/base/optimizers/schedulers/cosine.py @@ -1,6 +1,6 @@ # code from AllenNLP -from typing import Any, Dict +from typing import Any import numpy as np import torch @@ -91,9 +91,7 @@ def __init__( if last_epoch == -1: for i, group in enumerate(self.optimizer.param_groups): if self.param_group_field not in group: - raise KeyError( - f"{self.param_group_field} missing from param_groups[{i}]" - ) + raise KeyError(f"{self.param_group_field} missing from param_groups[{i}]") group.setdefault( self._initial_param_group_field, group[self.param_group_field], @@ -105,20 +103,17 @@ def __init__( f"{self._initial_param_group_field} missing from param_groups[{i}]" ) self.base_values = [ - group[self._initial_param_group_field] - for group in self.optimizer.param_groups + group[self._initial_param_group_field] for group in self.optimizer.param_groups ] self.last_epoch = last_epoch - def state_dict(self) -> Dict[str, Any]: + def state_dict(self) -> dict[str, Any]: """ Returns the state of the scheduler as a `dict`. """ - return { - key: value for key, value in self.__dict__.items() if key != "optimizer" - } + return {key: value for key, value in self.__dict__.items() if key != "optimizer"} - def load_state_dict(self, state_dict: Dict[str, Any]) -> None: + def load_state_dict(self, state_dict: dict[str, Any]) -> None: """ Load the schedulers state. # Parameters @@ -146,12 +141,7 @@ def get_values(self): lrs = [ self.eta_min + ((lr - self.eta_min) / 2) - * ( - np.cos( - np.pi * (self._cycle_counter % self._cycle_len) / self._cycle_len - ) - + 1 - ) + * (np.cos(np.pi * (self._cycle_counter % self._cycle_len) / self._cycle_len) + 1) for lr in base_lrs ] diff --git a/theseus/base/optimizers/schedulers/wrapper.py b/theseus/base/optimizers/schedulers/wrapper.py index 3f5d23b..3faf09b 100644 --- a/theseus/base/optimizers/schedulers/wrapper.py +++ b/theseus/base/optimizers/schedulers/wrapper.py @@ -1,13 +1,11 @@ import math from torch.optim.lr_scheduler import ( - CosineAnnealingLR, CosineAnnealingWarmRestarts, LambdaLR, MultiStepLR, OneCycleLR, ReduceLROnPlateau, - StepLR, ) from .cosine import CosineWithRestarts @@ -24,9 +22,7 @@ def __init__(self, optimizer, scheduler_name, **kwargs) -> None: def one_cycle(y1=0.0, y2=1.0, steps=100): # lambda function for sinusoidal ramp from y1 to y2 - return ( - lambda x: ((1 - math.cos(x * math.pi / steps)) / 2) * (y2 - y1) + y1 - ) + return lambda x: ((1 - math.cos(x * math.pi / steps)) / 2) * (y2 - y1) + y1 lf = one_cycle(1, 0.2, kwargs["num_epochs"]) # cosine 1->hyp['lrf'] scheduler = LambdaLR(optimizer, lr_lambda=lf) diff --git a/theseus/base/pipeline.py b/theseus/base/pipeline.py index a06bf6a..d7a627b 100644 --- a/theseus/base/pipeline.py +++ b/theseus/base/pipeline.py @@ -2,7 +2,7 @@ import os from datetime import datetime -from typing import Any, Dict, List, Optional +from typing import Any import torch from omegaconf import DictConfig, OmegaConf @@ -124,12 +124,10 @@ class BasePipeline(_PipelineBase): def __init__(self, opt: DictConfig) -> None: super().__init__(opt) - def _init_transforms(self) -> Dict[str, Any]: + def _init_transforms(self) -> dict[str, Any]: """Initialize transforms, returning a dict with 'train'/'val' keys.""" if self.transform_cfg is not None: - return get_instance_recursively( - self.transform_cfg, registry=self.transform_registry - ) + return get_instance_recursively(self.transform_cfg, registry=self.transform_registry) return {"train": None, "val": None} def init_train_dataloader(self) -> None: @@ -147,9 +145,7 @@ def init_train_dataloader(self) -> None: ) self._log(f"Number of training samples: {len(self.train_dataset)}") - self._log( - f"Number of training iterations each epoch: {len(self.train_dataloader)}" - ) + self._log(f"Number of training iterations each epoch: {len(self.train_dataloader)}") def init_validation_dataloader(self) -> None: self.transform = self._init_transforms() @@ -171,9 +167,7 @@ def init_validation_dataloader(self) -> None: self.classnames = getattr(self.val_dataset, "classnames", None) self._log(f"Number of validation samples: {len(self.val_dataset)}") - self._log( - f"Number of validation iterations each epoch: {len(self.val_dataloader)}" - ) + self._log(f"Number of validation iterations each epoch: {len(self.val_dataloader)}") def _auto_split_dataset(self) -> None: """Auto-split training dataset when no validation set is provided.""" @@ -210,32 +204,50 @@ def _auto_split_dataset(self) -> None: ) self._log(f"Number of training samples: {len(self.train_dataset)}") - self._log( - f"Number of training iterations each epoch: {len(self.train_dataloader)}" - ) + self._log(f"Number of training iterations each epoch: {len(self.train_dataloader)}") def init_test_dataloader(self) -> None: + """Initialize test dataset and dataloader, falling back to val if test is missing.""" self.transform = get_instance_recursively( self.transform_cfg, registry=self.transform_registry ) + transform_cfg = ( + self.transform["test"] if "test" in self.transform else self.transform.get("val", None) + ) + + test_data_cfg = self.opt["data"]["dataset"].get("test", None) + if test_data_cfg is None: + self._log( + "No test dataset found in config. Falling back to val dataset.", + level=LoggerObserver.WARN, + ) + test_data_cfg = self.opt["data"]["dataset"].get("val") + self.test_dataset = get_instance_recursively( - self.opt["data"]["dataset"]["test"], + test_data_cfg, registry=self.dataset_registry, - transform=self.transform.get("test", "val"), + transform=transform_cfg, ) + + test_loader_cfg = self.opt["data"]["dataloader"].get("test", None) + if test_loader_cfg is None: + self._log( + "No test dataloader found in config. Falling back to val dataloader.", + level=LoggerObserver.WARN, + ) + test_loader_cfg = self.opt["data"]["dataloader"].get("val") + self.test_dataloader = get_instance_recursively( - self.opt["data"]["dataloader"]["test"], + test_loader_cfg, registry=self.dataloader_registry, dataset=self.test_dataset, ) - self.classnames = getattr(self.test_dataloader, "classnames", None) + self.classnames = getattr(self.test_dataset, "classnames", None) self._log(f"Number of test samples: {len(self.test_dataset)}") - self._log( - f"Number of test iterations each epoch: {len(self.test_dataloader)}" - ) + self._log(f"Number of test iterations each epoch: {len(self.test_dataloader)}") def init_datamodule(self) -> None: self.datamodule = LightningDataModuleWrapper( @@ -254,7 +266,7 @@ def init_model(self) -> Any: ) return model - def init_criterion(self) -> Optional[Any]: + def init_criterion(self) -> Any | None: CLASSNAMES = self.classnames if self.opt["loss"] is None: return None @@ -273,7 +285,7 @@ def init_model_with_loss(self, is_train: bool = True) -> None: num_epochs = self.opt["trainer"]["args"]["max_epochs"] batch_size = self.opt["data"]["dataloader"]["val"]["args"]["batch_size"] use_mixed_precision = self.opt["trainer"]["args"].get("precision", None) - use_mixed_precision = True if use_mixed_precision else False + use_mixed_precision = bool(use_mixed_precision) self.model = LightningModelWrapper( self.model, @@ -321,7 +333,7 @@ def init_metrics(self) -> None: classnames=CLASSNAMES, ) - def init_callbacks(self) -> List[Any]: + def init_callbacks(self) -> list[Any]: callbacks = get_instance_recursively( self.opt["callbacks"], save_dir=getattr(self, "savedir", "runs"), @@ -331,7 +343,7 @@ def init_callbacks(self) -> List[Any]: ) return callbacks - def init_trainer(self, callbacks: List[Any]) -> None: + def init_trainer(self, callbacks: list[Any]) -> None: self.trainer = get_instance( self.opt["trainer"], default_root_dir=getattr(self, "savedir", "runs"), @@ -353,7 +365,8 @@ def init_pipeline(self, phase: str = "train") -> None: if phase == "train": self.init_train_dataloader() self.init_validation_dataloader() - self.init_test_dataloader() + if "test" in self.opt["data"]["dataset"]: + self.init_test_dataloader() self.init_datamodule() self.init_metrics() self.init_model_with_loss() @@ -373,16 +386,12 @@ def init_pipeline(self, phase: str = "train") -> None: if getattr(self.model, "metrics", None): callbacks.insert( 0, - self.callbacks_registry.get("MetricLoggerCallback")( - save_dir=self.savedir - ), + self.callbacks_registry.get("MetricLoggerCallback")(save_dir=self.savedir), ) callbacks.insert( 0, self.callbacks_registry.get("LossLoggerCallback")( - print_interval=self.opt["trainer"]["args"].get( - "log_every_n_steps", None - ), + print_interval=self.opt["trainer"]["args"].get("log_every_n_steps", None), ), ) callbacks.insert(0, self.callbacks_registry.get("TimerCallback")()) @@ -399,7 +408,7 @@ def fit(self) -> None: ckpt_path=self.resume, ) - def evaluate(self) -> Dict[str, Any]: + def evaluate(self) -> dict[str, Any]: """Run validation and return metrics.""" self.init_pipeline(phase="validation") self.trainer.validate( @@ -409,7 +418,7 @@ def evaluate(self) -> Dict[str, Any]: ) return self.trainer.callback_metrics - def test(self) -> Dict[str, Any]: + def test(self) -> dict[str, Any]: """Run testing and return metrics.""" self.init_pipeline(phase="test") self.trainer.test( @@ -459,27 +468,37 @@ def init_test_dataloader(self) -> None: ) transform_cfg = ( - self.transform["test"] - if "test" in self.transform - else self.transform["val"] + self.transform.get("test") if isinstance(self.transform, dict) else self.transform ) + if transform_cfg is None: + transform_cfg = ( + self.transform.get("val") if isinstance(self.transform, dict) else self.transform + ) + + # Handle both nested (data.dataset.test) and flat (data.dataset) configs + test_data_cfg = self.opt["data"]["dataset"] + if "name" not in test_data_cfg: + test_data_cfg = test_data_cfg.get("test") or test_data_cfg.get("val") self.dataset = get_instance( - self.opt["data"]["dataset"].get("test", "val"), + test_data_cfg, registry=DATASET_REGISTRY, transform=transform_cfg, ) + # Handle both nested (data.dataloader.test) and flat (data.dataloader) configs + test_loader_cfg = self.opt["data"]["dataloader"] + if "name" not in test_loader_cfg: + test_loader_cfg = test_loader_cfg.get("test") or test_loader_cfg.get("val") + self.dataloader = get_instance( - self.opt["data"]["dataloader"].get("test", "val"), + test_loader_cfg, registry=DATALOADER_REGISTRY, dataset=self.dataset, ) self._log(f"Number of test samples: {len(self.dataset)}") - self._log( - f"Number of test iterations each epoch: {len(self.dataloader)}" - ) + self._log(f"Number of test iterations each epoch: {len(self.dataloader)}") def init_model(self) -> None: CLASSNAMES = getattr(self.dataset, "classnames", None) diff --git a/theseus/base/trainer/__init__.py b/theseus/base/trainer/__init__.py index 40118d6..25318e6 100644 --- a/theseus/base/trainer/__init__.py +++ b/theseus/base/trainer/__init__.py @@ -43,4 +43,4 @@ def __init__(self, *args: Any, **kwargs: Any) -> None: super().__init__(*args, **kwargs) -TRAINER_REGISTRY.register(Trainer, prefix="pl") \ No newline at end of file +TRAINER_REGISTRY.register(Trainer, prefix="pl") diff --git a/theseus/base/utilities/cuda.py b/theseus/base/utilities/cuda.py index e875ac5..8daf804 100644 --- a/theseus/base/utilities/cuda.py +++ b/theseus/base/utilities/cuda.py @@ -1,6 +1,7 @@ -""" CUDA / AMP utils +"""CUDA / AMP utils Hacked together by / Copyright 2020 Ross Wightman """ + from typing import Any import torch @@ -21,20 +22,19 @@ def get_devices_info(device_names="0"): for i, device_id in enumerate(device_names.split(",")): p = torch.cuda.get_device_properties(i) devices_info.append( - f"CUDA:{device_id} ({p.name}, {p.total_memory / 1024 ** 2}MB)" + f"CUDA:{device_id} ({p.name}, {p.total_memory / 1024**2}MB)" ) # bytes to MB devices_info = "\n".join(devices_info) return devices_info def get_device(name="cpu") -> torch.device: - if name.startswith("cuda"): - if not torch.cuda.is_available(): - LOGGER.text( - "CUDA is not available. Using CPU...", - level=LoggerObserver.WARN, - ) - name = "cpu" + if name.startswith("cuda") and not torch.cuda.is_available(): + LOGGER.text( + "CUDA is not available. Using CPU...", + level=LoggerObserver.WARN, + ) + name = "cpu" return torch.device(name) diff --git a/theseus/base/utilities/download.py b/theseus/base/utilities/download.py index e05c4c0..39adee2 100644 --- a/theseus/base/utilities/download.py +++ b/theseus/base/utilities/download.py @@ -14,7 +14,7 @@ def download_from_drive(id_or_url, output, md5=None, quiet=False, cache=True): if id_or_url.startswith("http") or id_or_url.startswith("https"): url = id_or_url else: - url = "https://drive.google.com/uc?id={}".format(id_or_url) + url = f"https://drive.google.com/uc?id={id_or_url}" if not cache: return gdown.download(url, output, quiet=quiet) @@ -46,14 +46,11 @@ def download_from_url(url, root=None, filename=None): try: LOGGER.text("Downloading " + url + " to " + fpath, level=LoggerObserver.DEBUG) urlreq.urlretrieve(url, fpath) - except (urlreq.error.URLError, IOError) as e: + except (OSError, urlreq.error.URLError): if url[:5] == "https": url = url.replace("https:", "http:") LOGGER.text( - "Failed download. Trying https -> http instead.Downloading " - + url - + " to " - + fpath, + "Failed download. Trying https -> http instead.Downloading " + url + " to " + fpath, level=LoggerObserver.DEBUG, ) urlreq.urlretrieve(url, fpath) @@ -61,18 +58,14 @@ def download_from_url(url, root=None, filename=None): return fpath -def download_from_wandb( - filename, run_path, save_dir, rename=None, generate_id_text_file=False -): +def download_from_wandb(filename, run_path, save_dir, rename=None, generate_id_text_file=False): import wandb try: path = wandb.restore(filename, run_path=run_path, root=save_dir) LOGGER.text( - "Successfully download {} from wandb run path {}".format( - filename, run_path - ), + f"Successfully download {filename} from wandb run path {run_path}", level=LoggerObserver.INFO, ) @@ -85,11 +78,11 @@ def download_from_wandb( if rename: new_name = str(Path(path.name).resolve().parent / rename) os.rename(Path(path.name).resolve(), new_name) - LOGGER.text("Saved to {}".format(new_name), level=LoggerObserver.INFO) + LOGGER.text(f"Saved to {new_name}", level=LoggerObserver.INFO) return new_name LOGGER.text( - "Saved to {}".format((Path(save_dir) / path.name).resolve()), + f"Saved to {(Path(save_dir) / path.name).resolve()}", level=LoggerObserver.INFO, ) return path.name diff --git a/theseus/base/utilities/getter.py b/theseus/base/utilities/getter.py index 63deae1..f1c99c1 100644 --- a/theseus/base/utilities/getter.py +++ b/theseus/base/utilities/getter.py @@ -1,13 +1,14 @@ from __future__ import annotations -import inspect import functools -from typing import Any, Dict, Optional +import inspect +from typing import Any from omegaconf import DictConfig, ListConfig from theseus.registry import Registry + # Cache for inspect.signature to avoid repeated introspection @functools.lru_cache(maxsize=256) def _cached_signature(cls: type) -> inspect.Signature: @@ -19,7 +20,7 @@ def get_instance_with_kwargs( registry: Registry, name: str, args: Any = None, - kwargs: Optional[Dict[str, Any]] = None, + kwargs: dict[str, Any] | None = None, ) -> Any: """ Instantiate a class from registry by name, filtering kwargs to match @@ -79,17 +80,12 @@ def get_instance_recursively( Supports nested lists, dicts, and DictConfig/ListConfig. """ if isinstance(config, (list, tuple, ListConfig)): - return [ - get_instance_recursively(item, registry=registry, **kwargs) - for item in config - ] + return [get_instance_recursively(item, registry=registry, **kwargs) for item in config] if isinstance(config, (dict, DictConfig)): if "name" in config: if registry: - args = get_instance_recursively( - config.get("args", {}), registry, **kwargs - ) + args = get_instance_recursively(config.get("args", {}), registry, **kwargs) return get_instance_with_kwargs(registry, config["name"], args, kwargs) else: return { diff --git a/theseus/base/utilities/hub.py b/theseus/base/utilities/hub.py index ecaaa6e..625ce67 100644 --- a/theseus/base/utilities/hub.py +++ b/theseus/base/utilities/hub.py @@ -11,10 +11,9 @@ import logging import os from pathlib import Path -from typing import Any, Dict, Optional, Union +from typing import Any import torch -import torch.nn as nn logger = logging.getLogger(__name__) @@ -66,9 +65,9 @@ def __init__(self, config): def save_pretrained( self, - save_directory: Union[str, Path], + save_directory: str | Path, *, - config: Optional[Dict[str, Any]] = None, + config: dict[str, Any] | None = None, use_safetensors: bool = True, ) -> None: """ @@ -103,12 +102,12 @@ def save_pretrained( @classmethod def from_pretrained( cls, - pretrained_path: Union[str, Path], + pretrained_path: str | Path, *, use_safetensors: bool = True, map_location: str = "cpu", **kwargs: Any, - ) -> "HuggingFaceHubMixin": + ) -> HuggingFaceHubMixin: """ Load a model from a local directory or HuggingFace Hub repo. @@ -155,9 +154,9 @@ def push_to_hub( *, commit_message: str = "Upload model", private: bool = False, - token: Optional[str] = None, - config: Optional[Dict[str, Any]] = None, - model_card: Optional[str] = None, + token: str | None = None, + config: dict[str, Any] | None = None, + model_card: str | None = None, use_safetensors: bool = True, ) -> str: """ @@ -207,12 +206,14 @@ def push_to_hub( def _generate_model_card( self, repo_id: str, - config: Optional[Dict[str, Any]] = None, + config: dict[str, Any] | None = None, ) -> str: """Generate a basic model card.""" model_name = repo_id.split("/")[-1] if "/" in repo_id else repo_id trainable_params = sum( - p.numel() for p in self.parameters() if p.requires_grad # type: ignore[union-attr] + p.numel() + for p in self.parameters() + if p.requires_grad # type: ignore[union-attr] ) total_params = sum(p.numel() for p in self.parameters()) # type: ignore[union-attr] diff --git a/theseus/base/utilities/loading.py b/theseus/base/utilities/loading.py index a6741d2..ca388a7 100644 --- a/theseus/base/utilities/loading.py +++ b/theseus/base/utilities/loading.py @@ -12,7 +12,7 @@ def load_yaml(path): - with open(path, "rt") as f: + with open(path) as f: return yaml.safe_load(f) @@ -61,7 +61,7 @@ def load_state_dict(instance, state_dict, key=None, strict=True): ) return instance else: - if key in state_dict.keys(): + if key in state_dict: return state_dict[key] else: LOGGER.text(f"Cannot load key={key} from state_dict", LoggerObserver.WARN) diff --git a/theseus/base/utilities/loggers/image_writer.py b/theseus/base/utilities/loggers/image_writer.py index 92bcea6..8bc6ad1 100644 --- a/theseus/base/utilities/loggers/image_writer.py +++ b/theseus/base/utilities/loggers/image_writer.py @@ -1,7 +1,6 @@ import os import matplotlib as mpl -import matplotlib.pyplot as plt import plotly.graph_objs as go from .observer import LoggerObserver diff --git a/theseus/base/utilities/loggers/observer.py b/theseus/base/utilities/loggers/observer.py index 7435163..af9f542 100644 --- a/theseus/base/utilities/loggers/observer.py +++ b/theseus/base/utilities/loggers/observer.py @@ -1,18 +1,11 @@ import logging import os - -import matplotlib as mpl -import matplotlib.pyplot as plt -import numpy as np -import plotly.graph_objs as go -import torch - -mpl.use("Agg") - +import sys import threading from inspect import getframeinfo, stack -from typing import Any, Callable, Dict, List, Optional +from typing import Any +import numpy as np from tabulate import tabulate from .subscriber import LoggerSubscriber @@ -20,14 +13,30 @@ def get_type(value: Any) -> str: """Infer the log type from a value.""" - if isinstance(value, torch.nn.Module): - return LoggerObserver.TORCH_MODULE - if isinstance(value, (mpl.figure.Figure, go.Figure)): - return LoggerObserver.FIGURE - if isinstance(value, (torch.Tensor, np.ndarray)): - if len(value.shape) == 2: + if "torch" in sys.modules: + import torch + + if isinstance(value, torch.nn.Module): + return LoggerObserver.TORCH_MODULE + if isinstance(value, torch.Tensor) and len(value.shape) == 2: return LoggerObserver.EMBED - if isinstance(value, (int, float)): + + if "matplotlib" in sys.modules: + import matplotlib as mpl + + if isinstance(value, mpl.figure.Figure): + return LoggerObserver.FIGURE + + if "plotly" in sys.modules: + import plotly.graph_objs as go + + if isinstance(value, go.Figure): + return LoggerObserver.FIGURE + + if isinstance(value, np.ndarray) and len(value.shape) == 2: + return LoggerObserver.EMBED + + if isinstance(value, (int, float, np.number)): return LoggerObserver.SCALAR if isinstance(value, str): if value.endswith(".html"): @@ -71,11 +80,11 @@ class LoggerObserver: SUCCESS = "SUCCESS" # Singleton instances - instances: Dict[str, "LoggerObserver"] = {} + instances: dict[str, "LoggerObserver"] = {} _lock = threading.Lock() # Dispatch table: maps log type -> subscriber method name - _DISPATCH: Dict[str, str] = { + _DISPATCH: dict[str, str] = { SCALAR: "log_scalar", FIGURE: "log_figure", TORCH_MODULE: "log_torch_module", @@ -87,19 +96,23 @@ class LoggerObserver: HTML: "log_html", } - def __new__(cls, name: Optional[str] = None, *args: Any, **kwargs: Any) -> "LoggerObserver": + def __new__(cls, name: str | None = None, *args: Any, **kwargs: Any) -> "LoggerObserver": + if name is None: + name = str(os.getpid()) with cls._lock: - if name is None: - name = str(os.getpid()) - if name in LoggerObserver.instances: - return LoggerObserver.instances[name] - return object.__new__(cls) - - def __init__(self, name: str) -> None: - if hasattr(self, "_initialized"): + if name not in cls.instances: + instance = object.__new__(cls) + instance._initialized = False + cls.instances[name] = instance + return cls.instances[name] + + def __init__(self, name: str | None = None) -> None: + if self._initialized: return self._initialized = True - self.subscriber: List[LoggerSubscriber] = [] + self.subscriber: list[LoggerSubscriber] = [] + if name is None: + name = str(os.getpid()) self.name = name # Init with a stdout logger @@ -108,8 +121,6 @@ def __init__(self, name: str) -> None: logger = StdoutLogger(name=self.name, debug=True) self.subscribe(logger) - LoggerObserver.instances[name] = self - def __del__(self) -> None: for subscriber in self.subscriber: del subscriber @@ -119,19 +130,27 @@ def __del__(self) -> None: @classmethod def getLogger(cls, name: str) -> "LoggerObserver": """Get or create a logger by name.""" - if name in LoggerObserver.instances: - return LoggerObserver.instances[name] return cls(name) def subscribe(self, subscriber: LoggerSubscriber) -> None: """Add a subscriber that will receive log events.""" self.subscriber.append(subscriber) - def log(self, logs: List[Dict[str, Any]]) -> None: + def log(self, logs: list[dict[str, Any]]) -> None: """ Dispatch log entries to all subscribers using the dispatch table. Each log entry must have 'tag' and 'value' keys, with optional 'type' and 'kwargs'. """ + # Support distributed logging + is_master = True + if "torch" in sys.modules: + import torch + + if torch.distributed.is_initialized() and torch.distributed.get_rank() != 0: + is_master = False + if not is_master: + return + for subscriber in self.subscriber: for entry in logs: tag = entry["tag"] @@ -146,7 +165,7 @@ def log(self, logs: List[Dict[str, Any]]) -> None: if method is not None: method(tag=tag, value=value, **kwargs) - def text(self, value: Any, level: int = logging.INFO) -> None: + def text(self, *value: Any, level: int = logging.INFO) -> None: """Convenience method for text logging with source location.""" caller = getframeinfo(stack()[1][0]) function_name = stack()[1][3] @@ -155,11 +174,21 @@ def text(self, value: Any, level: int = logging.INFO) -> None: ] # split filename based on project name lineno = caller.lineno + texts = [] + for v in value: + if isinstance(v, dict): + import json + + texts.append(json.dumps(v, indent=4, default=str)) + else: + texts.append(str(v)) + value_str = " ".join(texts) + self.log( [ { "tag": "stdout", - "value": value, + "value": value_str, "type": LoggerObserver.TEXT, "kwargs": { "level": level, diff --git a/theseus/base/utilities/loggers/stdout_logger.py b/theseus/base/utilities/loggers/stdout_logger.py index 064d50a..f985f39 100644 --- a/theseus/base/utilities/loggers/stdout_logger.py +++ b/theseus/base/utilities/loggers/stdout_logger.py @@ -53,6 +53,7 @@ class FileLogger(BaseTextLogger): def __init__(self, name, logdir, rotation="10 MB", debug=False): self.logdir = logdir + os.makedirs(self.logdir, exist_ok=True) self.filename = f"{self.logdir}/log.txt" super().__init__(name) @@ -65,15 +66,17 @@ def __init__(self, name, logdir, rotation="10 MB", debug=False): self.filename, rotation=rotation, level=level, - filter=lambda record: "filelog" in record["extra"], + filter=lambda record: ( + record["extra"].get("filelog") and record["extra"].get("name") == self.name + ), ) def log_text(self, tag, value, level=LoggerObserver.DEBUG, **kwargs): - filename = kwargs.get("filename", None) - funcname = kwargs.get("funcname", None) - lineno = kwargs.get("lineno", None) + filename = kwargs.get("filename") + funcname = kwargs.get("funcname") + lineno = kwargs.get("lineno") with logger.contextualize( - filelog=True, filename=filename, funcname=funcname, lineno=lineno + filelog=True, name=self.name, filename=filename, funcname=funcname, lineno=lineno ): return super().log_text(tag, value, level, **kwargs) @@ -103,14 +106,16 @@ def __init__(self, name, debug=False): diagnose=True, level=level, format=self.message_format, - filter=lambda record: "stdout" in record["extra"], + filter=lambda record: ( + record["extra"].get("stdout") and record["extra"].get("name") == self.name + ), ) def log_text(self, tag, value, level=LoggerObserver.DEBUG, **kwargs): - filename = kwargs.get("filename", None) - funcname = kwargs.get("funcname", None) - lineno = kwargs.get("lineno", None) + filename = kwargs.get("filename") + funcname = kwargs.get("funcname") + lineno = kwargs.get("lineno") with logger.contextualize( - stdout=True, filename=filename, funcname=funcname, lineno=lineno + stdout=True, name=self.name, filename=filename, funcname=funcname, lineno=lineno ): return super().log_text(tag, value, level, **kwargs) diff --git a/theseus/base/utilities/loggers/tsb_logger.py b/theseus/base/utilities/loggers/tsb_logger.py index e4f9f53..27e8084 100644 --- a/theseus/base/utilities/loggers/tsb_logger.py +++ b/theseus/base/utilities/loggers/tsb_logger.py @@ -71,14 +71,7 @@ def log_torch_module(self, tag, value, inputs, **kwargs): self.writer.add_graph(value, inputs) def log_embedding( - self, - tag, - value, - label_img=None, - step=0, - metadata=None, - metadata_header=None, - **kwargs + self, tag, value, label_img=None, step=0, metadata=None, metadata_header=None, **kwargs ): """ Write a embedding projection to tensorboard @@ -140,7 +133,6 @@ def tflog2pandas(path: str) -> pd.DataFrame: runlog_data = pd.DataFrame({"metric": [], "value": [], "step": []}) runfig_data = pd.DataFrame({"name": [], "value": [], "step": []}) try: - ## Scalar values event_acc = EventAccumulator(path, DEFAULT_SIZE_GUIDANCE) event_acc.Reload() @@ -167,7 +159,7 @@ def tflog2pandas(path: str) -> pd.DataFrame: # Dirty catch of DataLossError except Exception: LOGGER.text( - "Event file possibly corrupt: {}".format(path), + f"Event file possibly corrupt: {path}", level=LoggerObserver.WARN, ) traceback.print_exc() diff --git a/theseus/base/utilities/loggers/wandb_logger.py b/theseus/base/utilities/loggers/wandb_logger.py index 10754af..f8f37d5 100644 --- a/theseus/base/utilities/loggers/wandb_logger.py +++ b/theseus/base/utilities/loggers/wandb_logger.py @@ -1,9 +1,7 @@ -from typing import Dict +import contextlib -try: +with contextlib.suppress(ModuleNotFoundError): import wandb as wandb_logger -except ModuleNotFoundError: - pass import os.path as osp @@ -28,7 +26,7 @@ def __init__( run_name: str, group_name: str = None, save_dir: str = None, - config_dict: Dict = None, + config_dict: dict = None, **kwargs, ): self.project_name = project_name @@ -48,7 +46,7 @@ def __init__( name=run_name, config=config_dict, group=self.group_name, - job_type=kwargs.get("job_type", None), + job_type=kwargs.get("job_type"), tags=tags, dir=self.save_dir, id=self.id, @@ -106,7 +104,7 @@ def log_figure(self, tag, value, step=0, **kwargs): wandb_logger.log({tag: image, "iterations": step}) else: wandb_logger.log({tag: value, "iterations": step}) - except Exception as e: + except Exception: pass def log_torch_module(self, tag, value, log_freq, **kwargs): @@ -200,7 +198,7 @@ def log_embedding( if metadata is not None and metadata_header is not None: for meta in metadata: for idx, item in enumerate(meta): - if metadata_header[idx] not in df_dict.keys(): + if metadata_header[idx] not in df_dict: df_dict[metadata_header[idx]] = [] df_dict[metadata_header[idx]].append(item) if label_img is not None: @@ -225,6 +223,6 @@ def find_run_id(dirname): if not osp.isfile(wandb_id_file): raise ValueError(f"Wandb ID file not found in {wandb_id_file}") else: - with open(wandb_id_file, "r") as f: + with open(wandb_id_file) as f: wandb_id = f.read().rstrip() return wandb_id diff --git a/theseus/base/utilities/optuna_tuner.py b/theseus/base/utilities/optuna_tuner.py index e78d514..e0bab63 100644 --- a/theseus/base/utilities/optuna_tuner.py +++ b/theseus/base/utilities/optuna_tuner.py @@ -3,7 +3,9 @@ from copy import deepcopy import optuna +import wandb from omegaconf import DictConfig, OmegaConf +from optuna.integration.wandb import WeightsAndBiasesCallback from optuna.visualization import ( plot_contour, plot_edf, @@ -13,8 +15,6 @@ plot_param_importances, plot_slice, ) -import wandb -from optuna.integration.wandb import WeightsAndBiasesCallback from theseus.base.pipeline import BasePipeline from theseus.base.utilities.loggers import LoggerObserver @@ -45,9 +45,7 @@ def __init__( self.WANDB_CALLBACK = None if wandb_kwargs is not None: self.WANDB_CALLBACK = WeightsAndBiasesCallback( - metric_name="auc", - wandb_kwargs=wandb_kwargs, - as_multirun=True + metric_name="auc", wandb_kwargs=wandb_kwargs, as_multirun=True ) if save_dir is not None: os.makedirs(save_dir, exist_ok=True) @@ -66,26 +64,31 @@ def tune( config: DictConfig, pipeline_class: BasePipeline, optuna_callback: callable = None, - trial_user_attrs: dict = {}, + trial_user_attrs: dict = None, ): - if "optuna" not in config.keys(): + if trial_user_attrs is None: + trial_user_attrs = {} + if "optuna" not in config: self.logger.text( "Optuna key not found in config. Exit optuna", level=LoggerObserver.CRITICAL, ) raise ValueError() - wrapped_objective = lambda trial: self.objective( - trial, config, pipeline_class, trial_user_attrs, optuna_callback - ) + def wrapped_objective(trial): + return self.objective( + trial, config, pipeline_class, trial_user_attrs, optuna_callback + ) callbacks = None if self.WANDB_CALLBACK is not None: decorator = self.WANDB_CALLBACK.track_in_wandb() wrapped_objective = decorator(wrapped_objective) callbacks = [self.WANDB_CALLBACK] - self.study.optimize(wrapped_objective, n_trials=self.n_trials, timeout=12*60*60, callbacks=callbacks) + self.study.optimize( + wrapped_objective, n_trials=self.n_trials, timeout=12 * 60 * 60, callbacks=callbacks + ) best_trial = self.study.best_trial self.save_best_config(self.save_dir, config, best_trial.params) self._rename_params() @@ -104,9 +107,7 @@ def save_best_config(self, save_dir: str, config: DictConfig, best_params: dict) with open(os.path.join(save_dir, f"{self.study_name}.yaml"), "w") as f: OmegaConf.save(config=config, f=f) - self.logger.text( - f"Best configuration saved at {save_dir}", level=LoggerObserver.INFO - ) + self.logger.text(f"Best configuration saved at {save_dir}", level=LoggerObserver.INFO) def _override_dict_with_optuna( self, trial, config: DictConfig, param_str: str, variable_type: str @@ -155,19 +156,19 @@ def objective( trial: optuna.Trial, config: DictConfig, pipeline_class: BasePipeline, - trial_user_attrs: dict = {}, + trial_user_attrs: dict = None, optuna_callback: callable = None, ): """Define the objective function""" # Override config with optuna trials values + if trial_user_attrs is None: + trial_user_attrs = {} tmp_config = deepcopy(config) optuna_params = tmp_config["optuna"] - for variable_type in optuna_params.keys(): + for variable_type in optuna_params: for param_str in optuna_params[variable_type]: - self._override_dict_with_optuna( - trial, tmp_config, param_str, variable_type - ) + self._override_dict_with_optuna(trial, tmp_config, param_str, variable_type) # Set fixed run's config for key, value in trial_user_attrs.items(): @@ -198,7 +199,7 @@ def objective( del tmp_config - best_key = trial_user_attrs.get("best_key", None) + best_key = trial_user_attrs.get("best_key") if best_key is not None: return float(score_dict.get(best_key, -1)) return score_dict @@ -222,9 +223,7 @@ def _rename_params(self): if common_prefix != "": for trial_param_name in trial_param_names: new_param_name = trial_param_name.replace(common_prefix, "") - trial.params.update( - {new_param_name: trial.params[trial_param_name]} - ) + trial.params.update({new_param_name: trial.params[trial_param_name]}) trial.distributions.update( {new_param_name: trial.distributions[trial_param_name]} ) @@ -237,9 +236,11 @@ def leaderboard(self): df.columns = [col.replace("user_attrs_", "") for col in df.columns] return df - def visualize(self, plot: str, plot_params: dict = {}): + def visualize(self, plot: str, plot_params: dict = None): """Visualize everything""" + if plot_params is None: + plot_params = {} allow_plot_types = [ "history", "contour", @@ -271,9 +272,7 @@ def visualize(self, plot: str, plot_params: dict = {}): one_fig = self.visualize(plot_type, plot_params) fig.append((plot_type, one_fig)) else: - self.logger.text( - f"{plot} is not supported by Optuna", level=LoggerObserver.ERROR - ) + self.logger.text(f"{plot} is not supported by Optuna", level=LoggerObserver.ERROR) raise ValueError() # Log to wandb if enabled diff --git a/theseus/cv/base/augmentations/albumentation.py b/theseus/cv/base/augmentations/albumentation.py index 8c56394..63aee0d 100644 --- a/theseus/cv/base/augmentations/albumentation.py +++ b/theseus/cv/base/augmentations/albumentation.py @@ -4,7 +4,6 @@ GaussianBlur, HorizontalFlip, HueSaturationValue, - IAASharpen, LongestMaxSize, MedianBlur, MotionBlur, @@ -15,6 +14,7 @@ RandomSizedCrop, Resize, RGBShift, + Sharpen, ShiftScaleRotate, SmallestMaxSize, VerticalFlip, @@ -40,6 +40,6 @@ TRANSFORM_REGISTRY.register(VerticalFlip, prefix="Alb") TRANSFORM_REGISTRY.register(HueSaturationValue, prefix="Alb") TRANSFORM_REGISTRY.register(RandomSizedCrop, prefix="Alb") -TRANSFORM_REGISTRY.register(IAASharpen, prefix="Alb") +TRANSFORM_REGISTRY.register(Sharpen, prefix="Alb") TRANSFORM_REGISTRY.register(ToTensorV2, prefix="Alb") TRANSFORM_REGISTRY.register(LongestMaxSize, prefix="Alb") diff --git a/theseus/cv/base/utilities/visualization/utils.py b/theseus/cv/base/utilities/visualization/utils.py index fe4d2c1..23c7936 100644 --- a/theseus/cv/base/utilities/visualization/utils.py +++ b/theseus/cv/base/utilities/visualization/utils.py @@ -30,7 +30,7 @@ def get_font_size(image, text, polygons, font_type): fontsize = 1 # starting font size polywidth = polygons[1][0] - polygons[0][0] - imagewidth = image.shape[1] + image.shape[1] # portion of image width you want text width to be img_fraction = 1 diff --git a/theseus/cv/base/utilities/visualization/visualizer.py b/theseus/cv/base/utilities/visualization/visualizer.py index 264cb32..59f71e7 100644 --- a/theseus/cv/base/utilities/visualization/visualizer.py +++ b/theseus/cv/base/utilities/visualization/visualizer.py @@ -1,5 +1,5 @@ import random -from typing import Any, List, Optional, Tuple, Union +from typing import Any import cv2 import numpy as np @@ -22,7 +22,7 @@ class Visualizer: r"""Visualizer class that do all the visualization stuffs""" def __init__(self): - self.image: Optional[np.ndarray] = None + self.image: np.ndarray | None = None self.class_names = None self.set_color(color_list) @@ -38,7 +38,7 @@ def set_image(self, image: np.ndarray) -> None: if self.image.dtype == "uint8": self.image = self.image / 255.0 - def set_classnames(self, class_names: List[str]) -> None: + def set_classnames(self, class_names: list[str]) -> None: self.class_names = class_names def get_image(self) -> np.ndarray: @@ -64,12 +64,11 @@ def draw_label( label: str, font: Any = cv2.FONT_HERSHEY_SIMPLEX, fontScale: int = 2, - fontColor: Tuple = (0, 0, 1), + fontColor: tuple = (0, 0, 1), thickness: int = 3, - outline: Tuple = (0, 0, 0), + outline: tuple = (0, 0, 0), offset: int = 50, ): - """ Draw text on the image then return @@ -174,9 +173,12 @@ def draw_bbox(self, boxes, labels=None, scores=None) -> None: color = self.color_list[1] coord = [box[0], box[1], box[2], box[3]] - c1, c2 = (int(coord[0]), int(coord[1])), ( - int(coord[2]), - int(coord[3]), + c1, c2 = ( + (int(coord[0]), int(coord[1])), + ( + int(coord[2]), + int(coord[3]), + ), ) cv2.rectangle(self.image, c1, c2, color, thickness=tl * 2) @@ -189,9 +191,7 @@ def draw_bbox(self, boxes, labels=None, scores=None) -> None: label = f"{label}: {score}" tf = max(tl - 2, 1) # font thickness - s_size = cv2.getTextSize( - f"{label}", 0, fontScale=float(tl) / 3, thickness=tf - )[0] + s_size = cv2.getTextSize(f"{label}", 0, fontScale=float(tl) / 3, thickness=tf)[0] c2 = c1[0] + s_size[0] + 15, c1[1] - s_size[1] - 3 cv2.rectangle(self.image, c1, c2, color, -1) # filled cv2.putText( @@ -213,8 +213,8 @@ def _tensor_to_numpy(self, image: torch.Tensor) -> np.ndarray: def make_grid( self, - batch: List[torch.Tensor], - nrow: Optional[int] = None, + batch: list[torch.Tensor], + nrow: int | None = None, normalize: bool = False, ) -> torch.Tensor: """ @@ -239,15 +239,19 @@ def make_grid( def denormalize( self, - image: Union[torch.Tensor, np.ndarray], - mean: List[float] = [0.485, 0.456, 0.406], - std: List[float] = [0.229, 0.224, 0.225], + image: torch.Tensor | np.ndarray, + mean: list[float] = None, + std: list[float] = None, ) -> np.ndarray: """ Denormalize an image and return image: `torch.Tensor` or `np.ndarray` image to be denormalized """ + if std is None: + std = [0.229, 0.224, 0.225] + if mean is None: + mean = [0.485, 0.456, 0.406] mean = np.array(mean) std = np.array(std) @@ -288,9 +292,7 @@ def denormalize_bboxes( return boxes - def decode_segmap( - self, segmap: np.ndarray, num_classes: Optional[int] = None - ) -> np.ndarray: + def decode_segmap(self, segmap: np.ndarray, num_classes: int | None = None) -> np.ndarray: """ Decode an segmentation mask into colored mask based on class indices diff --git a/theseus/cv/classification/augmentations/custom.py b/theseus/cv/classification/augmentations/custom.py index 925c718..c983c33 100644 --- a/theseus/cv/classification/augmentations/custom.py +++ b/theseus/cv/classification/augmentations/custom.py @@ -5,11 +5,10 @@ import math from collections import namedtuple -from typing import Tuple import numpy as np import torch -from albumentations.core.bbox_utils import denormalize_bbox, normalize_bbox +from albumentations.core.bbox_utils import denormalize_bboxes, normalize_bboxes from albumentations.core.transforms_interface import DualTransform from torch import Tensor from torchvision.transforms import functional as F @@ -41,7 +40,7 @@ def __init__( :param min_cutout_size: minimum size of cutout (192 x 192) :param max_cutout_size: maximum size of cutout (512 x 512) """ - super(CustomCutout, self).__init__(always_apply, p) # Initialize parent class + super().__init__(always_apply, p) # Initialize parent class self.fill_value = fill_value self.bbox_removal_threshold = bbox_removal_threshold self.min_cutout_size = min_cutout_size @@ -88,10 +87,8 @@ def apply(self, image, **params): """ image = image.copy() # Don't change the original image self.img_height, self.img_width, _ = image.shape - for i in range(self.number): - cutout_arr, cutout_size, cutout_pos = self._get_cutout( - self.img_height, self.img_width - ) + for _i in range(self.number): + cutout_arr, cutout_size, cutout_pos = self._get_cutout(self.img_height, self.img_width) # Set to instance variables to use this later self.image = image @@ -114,10 +111,10 @@ def apply_to_bbox(self, bbox, **params): """ # Denormalize the bbox coordinates - bbox = denormalize_bbox(bbox, self.img_height, self.img_width) + bbox = denormalize_bboxes(bbox, self.img_height, self.img_width) x_min, y_min, x_max, y_max = tuple(map(int, bbox)) if x_min >= x_max or y_min >= y_max: - return normalize_bbox((0, 0, 0, 0), self.img_height, self.img_width) + return normalize_bboxes((0, 0, 0, 0), self.img_height, self.img_width) bbox_size = (x_max - x_min) * (y_max - y_min) # width * height overlapping_size = np.sum( @@ -127,9 +124,9 @@ def apply_to_bbox(self, bbox, **params): ) # Remove the bbox if it has more than some threshold of content is inside the cutout patch if overlapping_size / bbox_size > self.bbox_removal_threshold: - return normalize_bbox((0, 0, 0, 0), self.img_height, self.img_width) + return normalize_bboxes((0, 0, 0, 0), self.img_height, self.img_width) - return normalize_bbox(bbox, self.img_height, self.img_width) + return normalize_bboxes(bbox, self.img_height, self.img_width) def get_transform_init_args_names(self): """ @@ -166,9 +163,7 @@ def __init__( inplace: bool = False, ) -> None: super().__init__() - assert ( - num_classes > 0 - ), "Please provide a valid positive value for the num_classes." + assert num_classes > 0, "Please provide a valid positive value for the num_classes." assert alpha > 0, "Alpha param can't be zero." self.num_classes = num_classes @@ -176,7 +171,7 @@ def __init__( self.alpha = alpha self.inplace = inplace - def forward(self, batch: Tensor, target: Tensor) -> Tuple[Tensor, Tensor]: + def forward(self, batch: Tensor, target: Tensor) -> tuple[Tensor, Tensor]: """ Args: batch (Tensor): Float tensor of size (B, C, H, W) @@ -185,26 +180,22 @@ def forward(self, batch: Tensor, target: Tensor) -> Tuple[Tensor, Tensor]: Tensor: Randomly transformed batch. """ if batch.ndim != 4: - raise ValueError("Batch ndim should be 4. Got {}".format(batch.ndim)) + raise ValueError(f"Batch ndim should be 4. Got {batch.ndim}") if target.ndim != 1: - raise ValueError("Target ndim should be 1. Got {}".format(target.ndim)) + raise ValueError(f"Target ndim should be 1. Got {target.ndim}") if not batch.is_floating_point(): - raise TypeError( - "Batch dtype should be a float tensor. Got {}.".format(batch.dtype) - ) + raise TypeError(f"Batch dtype should be a float tensor. Got {batch.dtype}.") if target.dtype != torch.int64: - raise TypeError( - "Target dtype should be torch.int64. Got {}".format(target.dtype) - ) + raise TypeError(f"Target dtype should be torch.int64. Got {target.dtype}") if not self.inplace: batch = batch.clone() target = target.clone() if target.ndim == 1: - target = torch.nn.functional.one_hot( - target, num_classes=self.num_classes - ).to(dtype=batch.dtype) + target = torch.nn.functional.one_hot(target, num_classes=self.num_classes).to( + dtype=batch.dtype + ) if torch.rand(1).item() >= self.p: return batch, target @@ -214,9 +205,7 @@ def forward(self, batch: Tensor, target: Tensor) -> Tuple[Tensor, Tensor]: target_rolled = target.roll(1, 0) # Implemented as on mixup paper, page 3. - lambda_param = float( - torch._sample_dirichlet(torch.tensor([self.alpha, self.alpha]))[0] - ) + lambda_param = float(torch._sample_dirichlet(torch.tensor([self.alpha, self.alpha]))[0]) batch_rolled.mul_(1.0 - lambda_param) batch.mul_(lambda_param).add_(batch_rolled) @@ -256,9 +245,7 @@ def __init__( inplace: bool = False, ) -> None: super().__init__() - assert ( - num_classes > 0 - ), "Please provide a valid positive value for the num_classes." + assert num_classes > 0, "Please provide a valid positive value for the num_classes." assert alpha > 0, "Alpha param can't be zero." self.num_classes = num_classes @@ -266,7 +253,7 @@ def __init__( self.alpha = alpha self.inplace = inplace - def forward(self, batch: Tensor, target: Tensor) -> Tuple[Tensor, Tensor]: + def forward(self, batch: Tensor, target: Tensor) -> tuple[Tensor, Tensor]: """ Args: batch (Tensor): Float tensor of size (B, C, H, W) @@ -275,26 +262,22 @@ def forward(self, batch: Tensor, target: Tensor) -> Tuple[Tensor, Tensor]: Tensor: Randomly transformed batch. """ if batch.ndim != 4: - raise ValueError("Batch ndim should be 4. Got {}".format(batch.ndim)) + raise ValueError(f"Batch ndim should be 4. Got {batch.ndim}") if target.ndim != 1: - raise ValueError("Target ndim should be 1. Got {}".format(target.ndim)) + raise ValueError(f"Target ndim should be 1. Got {target.ndim}") if not batch.is_floating_point(): - raise TypeError( - "Batch dtype should be a float tensor. Got {}.".format(batch.dtype) - ) + raise TypeError(f"Batch dtype should be a float tensor. Got {batch.dtype}.") if target.dtype != torch.int64: - raise TypeError( - "Target dtype should be torch.int64. Got {}".format(target.dtype) - ) + raise TypeError(f"Target dtype should be torch.int64. Got {target.dtype}") if not self.inplace: batch = batch.clone() target = target.clone() if target.ndim == 1: - target = torch.nn.functional.one_hot( - target, num_classes=self.num_classes - ).to(dtype=batch.dtype) + target = torch.nn.functional.one_hot(target, num_classes=self.num_classes).to( + dtype=batch.dtype + ) if torch.rand(1).item() >= self.p: return batch, target @@ -304,9 +287,7 @@ def forward(self, batch: Tensor, target: Tensor) -> Tuple[Tensor, Tensor]: target_rolled = target.roll(1, 0) # Implemented as on cutmix paper, page 12 (with minor corrections on typos). - lambda_param = float( - torch._sample_dirichlet(torch.tensor([self.alpha, self.alpha]))[0] - ) + lambda_param = float(torch._sample_dirichlet(torch.tensor([self.alpha, self.alpha]))[0]) W, H = F.get_image_size(batch) r_x = torch.randint(W, (1,)) diff --git a/theseus/cv/classification/callbacks/gradcam_callback.py b/theseus/cv/classification/callbacks/gradcam_callback.py index 9f9160c..55abff1 100644 --- a/theseus/cv/classification/callbacks/gradcam_callback.py +++ b/theseus/cv/classification/callbacks/gradcam_callback.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, List, Optional +from typing import Any import lightning.pytorch as pl import matplotlib.pyplot as plt @@ -25,10 +25,14 @@ class GradCAMVisualizationCallback(Callback): def __init__( self, - mean: List[float] = [0.485, 0.456, 0.406], - std: List[float] = [0.229, 0.224, 0.225], - **kwargs + mean: list[float] = None, + std: list[float] = None, + **kwargs, ) -> None: + if std is None: + std = [0.229, 0.224, 0.225] + if mean is None: + mean = [0.485, 0.456, 0.406] super().__init__() self.visualizer = Visualizer() self.mean = mean diff --git a/theseus/cv/classification/callbacks/visualize_callback.py b/theseus/cv/classification/callbacks/visualize_callback.py index d63cd88..19703e9 100644 --- a/theseus/cv/classification/callbacks/visualize_callback.py +++ b/theseus/cv/classification/callbacks/visualize_callback.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, List +from typing import Any import lightning.pytorch as pl import matplotlib.pyplot as plt @@ -10,7 +10,6 @@ from theseus.base.utilities.cuda import move_to from theseus.base.utilities.loggers.observer import LoggerObserver from theseus.cv.base.utilities.visualization.visualizer import Visualizer -from theseus.cv.classification.utilities.gradcam import CAMWrapper, show_cam_on_image LOGGER = LoggerObserver.getLogger("main") @@ -26,20 +25,21 @@ class ClassificationVisualizerCallback(Callback): def __init__( self, - mean: List[float] = [0.485, 0.456, 0.406], - std: List[float] = [0.229, 0.224, 0.225], + mean: list[float] = None, + std: list[float] = None, **kwargs, ) -> None: + if std is None: + std = [0.229, 0.224, 0.225] + if mean is None: + mean = [0.485, 0.456, 0.406] super().__init__() self.visualizer = Visualizer() self.mean = mean self.std = std - def on_sanity_check_start( - self, trainer: pl.Trainer, pl_module: pl.LightningModule - ) -> None: - + def on_sanity_check_start(self, trainer: pl.Trainer, pl_module: pl.LightningModule) -> None: """ Sanitycheck before starting. Run only when debug=True """ @@ -52,7 +52,7 @@ def on_sanity_check_start( val_batch = next(iter(valloader)) try: self.visualize_model(model, train_batch) - except TypeError as e: + except TypeError: LOGGER.text("Cannot log model architecture", level=LoggerObserver.ERROR) self.visualize_gt(train_batch, val_batch, iters) @@ -87,7 +87,7 @@ def visualize_gt(self, train_batch, val_batch, iters): images = train_batch["inputs"].cpu() batch = [] - for idx, inputs in enumerate(images): + for _idx, inputs in enumerate(images): img_show = self.visualizer.denormalize(inputs) img_cam = TFF.to_tensor(img_show) batch.append(img_cam) @@ -112,7 +112,7 @@ def visualize_gt(self, train_batch, val_batch, iters): images = val_batch["inputs"].cpu() batch = [] - for idx, inputs in enumerate(images): + for _idx, inputs in enumerate(images): img_show = self.visualizer.denormalize(inputs, mean=self.mean, std=self.std) img_cam = TFF.to_tensor(img_show) batch.append(img_cam) diff --git a/theseus/cv/classification/datasets/csv_dataset.py b/theseus/cv/classification/datasets/csv_dataset.py index 7dc522f..af1bcff 100644 --- a/theseus/cv/classification/datasets/csv_dataset.py +++ b/theseus/cv/classification/datasets/csv_dataset.py @@ -1,4 +1,3 @@ -from typing import List, Optional import pandas as pd @@ -34,10 +33,10 @@ def __init__( image_dir: str, csv_path: str, txt_classnames: str, - transform: Optional[List] = None, - **kwargs + transform: list | None = None, + **kwargs, ): - super(ClassificationCSVDataset, self).__init__(**kwargs) + super().__init__(**kwargs) self.image_dir = image_dir self.txt_classnames = txt_classnames self.csv_path = csv_path @@ -49,7 +48,7 @@ def _load_data(self): Read data from csv and load into memory """ - with open(self.txt_classnames, "r") as f: + with open(self.txt_classnames) as f: self.classnames = f.read().splitlines() # Mapping between classnames and indices diff --git a/theseus/cv/classification/datasets/dataset.py b/theseus/cv/classification/datasets/dataset.py index e140e0d..7693669 100644 --- a/theseus/cv/classification/datasets/dataset.py +++ b/theseus/cv/classification/datasets/dataset.py @@ -1,6 +1,4 @@ -import os import os.path as osp -from typing import Dict, List import torch from PIL import Image @@ -10,7 +8,7 @@ class ClassificationDataset(torch.utils.data.Dataset): r"""Base dataset for classification tasks""" def __init__(self, **kwargs): - super(ClassificationDataset, self).__init__(**kwargs) + super().__init__(**kwargs) self.classes_idx = {} self.classnames = None self.transform = None @@ -20,7 +18,7 @@ def __init__(self, **kwargs): def _load_data(self): raise NotImplementedError - def __getitem__(self, idx: int) -> Dict: + def __getitem__(self, idx: int) -> dict: """ Get one item """ @@ -48,7 +46,7 @@ def __getitem__(self, idx: int) -> Dict: def __len__(self) -> int: return len(self.fns) - def collate_fn(self, batch: List): + def collate_fn(self, batch: list): """ Collator for wrapping a batch """ diff --git a/theseus/cv/classification/datasets/folder_dataset.py b/theseus/cv/classification/datasets/folder_dataset.py index 93d7c1b..b09730b 100644 --- a/theseus/cv/classification/datasets/folder_dataset.py +++ b/theseus/cv/classification/datasets/folder_dataset.py @@ -1,7 +1,4 @@ import os -from typing import List, Optional - -import pandas as pd from theseus.base.utilities.loggers.observer import LoggerObserver @@ -32,13 +29,9 @@ class ClassificationImageFolderDataset(ClassificationDataset): """ def __init__( - self, - image_dir: str, - txt_classnames: str, - transform: Optional[List] = None, - **kwargs + self, image_dir: str, txt_classnames: str, transform: list | None = None, **kwargs ): - super(ClassificationImageFolderDataset, self).__init__(**kwargs) + super().__init__(**kwargs) self.image_dir = image_dir self.txt_classnames = txt_classnames self.transform = transform @@ -50,7 +43,7 @@ def _load_data(self): """ # Get classnames - with open(self.txt_classnames, "r") as f: + with open(self.txt_classnames) as f: self.classnames = f.read().splitlines() # Mapping between classnames and indices diff --git a/theseus/cv/classification/datasets/mixupcutmix_collator.py b/theseus/cv/classification/datasets/mixupcutmix_collator.py index 0a4de6e..1a5c05a 100644 --- a/theseus/cv/classification/datasets/mixupcutmix_collator.py +++ b/theseus/cv/classification/datasets/mixupcutmix_collator.py @@ -1,4 +1,3 @@ -from typing import List import numpy as np import torch @@ -15,18 +14,16 @@ def __init__( dataset: torch.utils.data.Dataset, mixup_alpha: float = 0.2, cutmix_alpha: float = 1.0, - weight: List[float] = [0.5, 0.5], - **kwargs + weight: list[float] = None, + **kwargs, ) -> None: + if weight is None: + weight = [0.5, 0.5] assert sum(weight) <= 1.0, "Sum of weight should be smaller than 1.0" self.mixup_transforms = [] - self.mixup_transforms.append( - RandomMixup(dataset.num_classes, p=1.0, alpha=mixup_alpha) - ) - self.mixup_transforms.append( - RandomCutmix(dataset.num_classes, p=1.0, alpha=cutmix_alpha) - ) + self.mixup_transforms.append(RandomMixup(dataset.num_classes, p=1.0, alpha=mixup_alpha)) + self.mixup_transforms.append(RandomCutmix(dataset.num_classes, p=1.0, alpha=cutmix_alpha)) self.mixup_transforms.append(None) self.weight = weight self.weight.append(1.0 - sum(weight)) diff --git a/theseus/cv/classification/metrics/errorcases.py b/theseus/cv/classification/metrics/errorcases.py index 333cbd2..16bd914 100644 --- a/theseus/cv/classification/metrics/errorcases.py +++ b/theseus/cv/classification/metrics/errorcases.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, List, Optional +from typing import Any import matplotlib.pyplot as plt from torchvision.transforms import functional as TFF @@ -20,7 +20,7 @@ class ErrorCases(Metric): def __init__( self, max_samples: int = 64, - classnames: Optional[List[str]] = None, + classnames: list[str] | None = None, label_type: str = "multiclass", **kwargs, ): @@ -33,7 +33,7 @@ def __init__( self.threshold = kwargs.get("threshold", 0.5) self.reset() - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): + def update(self, outputs: dict[str, Any], batch: dict[str, Any]): """ Perform calculation based on prediction and targets """ @@ -56,7 +56,7 @@ def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): targets = targets.cpu().numpy().tolist() probs = probs.numpy().tolist() - for (output, target, prob, image) in zip(outputs, targets, probs, images): + for output, target, prob, image in zip(outputs, targets, probs, images): if output != target: self.images.append(image.cpu()) self.preds.append(output) @@ -68,16 +68,14 @@ def value(self): Plot error cases to figure then return """ pred_batch = [] - for idx, (image, pred, target, prob) in enumerate( + for _idx, (image, pred, target, prob) in enumerate( zip(self.images, self.preds, self.targets, self.probs) ): img_show = self.visualizer.denormalize(image) self.visualizer.set_image(img_show) if self.type == "multilabel": - prob = ", ".join( - [str(round(prob[i], 3)) for i, c in enumerate(pred) if c] - ) + prob = ", ".join([str(round(prob[i], 3)) for i, c in enumerate(pred) if c]) else: prob = str(round(prob, 3)) @@ -86,12 +84,8 @@ def value(self): pred = self.classnames[pred] target = self.classnames[target] else: - pred = ", ".join( - [self.classnames[int(i)] for i, c in enumerate(pred) if c] - ) - target = ", ".join( - [self.classnames[int(i)] for i, c in enumerate(target) if c] - ) + pred = ", ".join([self.classnames[int(i)] for i, c in enumerate(pred) if c]) + target = ", ".join([self.classnames[int(i)] for i, c in enumerate(target) if c]) self.visualizer.draw_label( f"GT: {target}\nP: {pred}\nC: {prob}", diff --git a/theseus/cv/classification/metrics/projection.py b/theseus/cv/classification/metrics/projection.py index 2f7dba0..158d3db 100644 --- a/theseus/cv/classification/metrics/projection.py +++ b/theseus/cv/classification/metrics/projection.py @@ -1,6 +1,6 @@ import hashlib import os -from typing import Any, Dict +from typing import Any import cv2 import numpy as np @@ -35,14 +35,12 @@ def __init__(self, save_dir=".temp", has_labels=False, **kwargs): os.makedirs(self.save_dir, exist_ok=True) - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): + def update(self, outputs: dict[str, Any], batch: dict[str, Any]): """ Perform calculation based on prediction and targets """ features = outputs["features"].detach().cpu().numpy() - predictions = ( - torch.argmax(outputs["outputs"].detach().cpu(), dim=1).numpy().tolist() - ) + predictions = torch.argmax(outputs["outputs"].detach().cpu(), dim=1).numpy().tolist() inputs = batch["inputs"] if self.has_labels: targets = batch["targets"].numpy().tolist() @@ -51,9 +49,7 @@ def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): for i, _ in enumerate(features): filename = hashlib.sha256(img_names[i].encode("utf-8")).hexdigest() pred_img = self.visualizer.denormalize(inputs[i]) - pred_img = cv2.resize( - pred_img, dsize=(64, 64), interpolation=cv2.INTER_CUBIC - ) + pred_img = cv2.resize(pred_img, dsize=(64, 64), interpolation=cv2.INTER_CUBIC) embedding_path = self.save_dir + r"/" + filename + "_feat.npy" image_path = self.save_dir + r"/" + filename + "_img.npy" @@ -98,7 +94,7 @@ def value(self): self.logger.log( [ { - "tag": f"Validation/projection", + "tag": "Validation/projection", "value": all_embeddings, "type": LoggerObserver.EMBED, "kwargs": { diff --git a/theseus/cv/classification/models/huggingface_models.py b/theseus/cv/classification/models/huggingface_models.py index 15dd9fc..3c840b2 100644 --- a/theseus/cv/classification/models/huggingface_models.py +++ b/theseus/cv/classification/models/huggingface_models.py @@ -1,5 +1,5 @@ from collections import OrderedDict -from typing import Any, Dict, List, Optional +from typing import Any import torch import torch.nn as nn @@ -28,10 +28,10 @@ def __init__( model_name: str, num_classes: int = 1000, from_pretrained: bool = True, - classnames: Optional[List] = None, + classnames: list | None = None, pooling: str = "first", freeze: bool = False, - **kwargs + **kwargs, ): super().__init__() self.name = model_name @@ -74,7 +74,7 @@ def get_model(self): """ return self.model - def forward_features(self, batch: Dict, device: torch.device = None): + def forward_features(self, batch: dict, device: torch.device = None): input_ids, attention_mask = batch["input_ids"], batch["attention_mask"] transformer_out = self.model(input_ids=input_ids, attention_mask=attention_mask) @@ -90,7 +90,7 @@ def forward_features(self, batch: Dict, device: torch.device = None): return features - def forward_batch(self, batch: Dict, device: torch.device = None): + def forward_batch(self, batch: dict, device: torch.device = None): if device is not None: batch = move_to(batch, device) features = self.forward_features(batch, device) @@ -98,7 +98,7 @@ def forward_batch(self, batch: Dict, device: torch.device = None): return {"outputs": outputs, "features": features} - def get_prediction(self, adict: Dict[str, Any], device: torch.device = None): + def get_prediction(self, adict: dict[str, Any], device: torch.device = None): """ Inference using the model. diff --git a/theseus/cv/classification/models/timm_models.py b/theseus/cv/classification/models/timm_models.py index c5dc562..afd963d 100644 --- a/theseus/cv/classification/models/timm_models.py +++ b/theseus/cv/classification/models/timm_models.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, List, Optional +from typing import Any import timm import torch @@ -28,9 +28,9 @@ def __init__( model_name: str, num_classes: int = 1000, from_pretrained: bool = True, - classnames: Optional[List] = None, + classnames: list | None = None, freeze: bool = False, - **kwargs + **kwargs, ): super().__init__() self.name = model_name @@ -65,9 +65,7 @@ def __init__( ) self.features = None - self.pooling = torch.nn.Sequential( - nn.AdaptiveAvgPool2d((1, 1)), nn.Flatten() - ) + self.pooling = torch.nn.Sequential(nn.AdaptiveAvgPool2d((1, 1)), nn.Flatten()) if self.freeze: self.freeze_backbone() @@ -89,7 +87,7 @@ def get_model(self): """ return self.model - def forward_batch(self, batch: Dict, device: torch.device = None): + def forward_batch(self, batch: dict, device: torch.device = None): if device is not None: x = move_to(batch["inputs"], device) else: @@ -100,7 +98,7 @@ def forward_batch(self, batch: Dict, device: torch.device = None): self.features = outputs return {"outputs": outputs, "features": self.features} - def get_prediction(self, adict: Dict[str, Any], device: torch.device = None): + def get_prediction(self, adict: dict[str, Any], device: torch.device = None): """ Inference using the model. @@ -112,9 +110,7 @@ def get_prediction(self, adict: Dict[str, Any], device: torch.device = None): outputs = self.forward_batch(adict, device)["outputs"] if not adict.get("multilabel"): - outputs, probs = logits2labels( - outputs, label_type="multiclass", return_probs=True - ) + outputs, probs = logits2labels(outputs, label_type="multiclass", return_probs=True) else: outputs, probs = logits2labels( outputs, @@ -136,8 +132,7 @@ def get_prediction(self, adict: Dict[str, Any], device: torch.device = None): classnames = [self.classnames[int(clsid)] for clsid in classids] elif self.classnames and adict.get("multilabel"): classnames = [ - [self.classnames[int(i)] for i, c in enumerate(clsid) if c] - for clsid in classids + [self.classnames[int(i)] for i, c in enumerate(clsid) if c] for clsid in classids ] else: classnames = [] diff --git a/theseus/cv/classification/pipeline.py b/theseus/cv/classification/pipeline.py index d53ee06..10b2453 100644 --- a/theseus/cv/classification/pipeline.py +++ b/theseus/cv/classification/pipeline.py @@ -15,7 +15,7 @@ class ClassificationPipeline(BasePipeline): """docstring for Pipeline.""" def __init__(self, opt: DictConfig): - super(ClassificationPipeline, self).__init__(opt) + super().__init__(opt) self.opt = opt def init_registry(self): diff --git a/theseus/cv/classification/utilities/gradcam.py b/theseus/cv/classification/utilities/gradcam.py index 62cf31a..eaf37ad 100644 --- a/theseus/cv/classification/utilities/gradcam.py +++ b/theseus/cv/classification/utilities/gradcam.py @@ -1,18 +1,11 @@ -from typing import Callable, List, Optional, Tuple import numpy as np import torch from pytorch_grad_cam import ( - AblationCAM, EigenCAM, - FullGrad, GradCAM, - GradCAMPlusPlus, - ScoreCAM, - XGradCAM, ) from pytorch_grad_cam.base_cam import BaseCAM -from pytorch_grad_cam.utils.image import show_cam_on_image from pytorch_grad_cam.utils.model_targets import ClassifierOutputTarget from theseus.base.utilities.loggers.observer import LoggerObserver @@ -56,21 +49,19 @@ class CAMWrapper(BaseCAM): def __init__( self, model: torch.nn.Module, - model_name: Optional[str] = None, - target_layers: Optional[List[torch.nn.Module]] = None, + model_name: str | None = None, + target_layers: list[torch.nn.Module] | None = None, **kwargs, ) -> None: - self.activations_and_grads = type( - "DummyClass", (object,), {"release": {lambda: None}} - )() + self.activations_and_grads = type("DummyClass", (object,), {"release": {lambda: None}})() - assert ( - model_name is not None or target_layers is not None - ), "Should specify model name or target layers name" + assert model_name is not None or target_layers is not None, ( + "Should specify model name or target layers name" + ) if target_layers is None: - for available_model in model_last_layers.keys(): + for available_model in model_last_layers: if model_name.startswith(available_model): model_name = available_model break @@ -85,12 +76,12 @@ def __init__( target_layers = get_layer_recursively(model, model_last_layers[model_name]) - super(CAMWrapper, self).__init__(model, target_layers, **kwargs) + super().__init__(model, target_layers, **kwargs) def forward( self, input_tensor: torch.Tensor, - targets: List[torch.nn.Module], + targets: list[torch.nn.Module], eigen_smooth: bool = False, return_probs: bool = False, ) -> np.ndarray: @@ -104,14 +95,10 @@ def forward( outputs = self.activations_and_grads(input_tensor) if targets is None: target_categories = np.argmax(outputs.cpu().data.numpy(), axis=-1) - targets = [ - ClassifierOutputTarget(category) for category in target_categories - ] + targets = [ClassifierOutputTarget(category) for category in target_categories] if return_probs: - scores = np.max( - torch.softmax(outputs, dim=-1).cpu().data.numpy(), axis=-1 - ) + scores = np.max(torch.softmax(outputs, dim=-1).cpu().data.numpy(), axis=-1) if self.uses_gradients: self.model.zero_grad() @@ -138,7 +125,7 @@ def forward( def __call__( self, input_tensor: torch.Tensor, - targets: List[torch.nn.Module] = None, + targets: list[torch.nn.Module] = None, aug_smooth: bool = False, eigen_smooth: bool = False, return_probs: bool = False, @@ -146,9 +133,7 @@ def __call__( # Smooth the CAM result with test time augmentation if aug_smooth is True: - return self.forward_augmentation_smoothing( - input_tensor, targets, eigen_smooth - ) + return self.forward_augmentation_smoothing(input_tensor, targets, eigen_smooth) return self.forward(input_tensor, targets, eigen_smooth, return_probs) diff --git a/theseus/cv/detection/augmentations/bbox_transforms.py b/theseus/cv/detection/augmentations/bbox_transforms.py index e8b03a6..3ef489b 100644 --- a/theseus/cv/detection/augmentations/bbox_transforms.py +++ b/theseus/cv/detection/augmentations/bbox_transforms.py @@ -47,9 +47,7 @@ def __init__(self, order): Class construstor :param order: bbox format """ - super(BoxOrder, self).__init__( - always_apply=True, p=1.0 - ) # Initialize parent class + super().__init__(always_apply=True, p=1.0) # Initialize parent class self.order = order def apply(self, image, **params): @@ -62,7 +60,6 @@ def apply(self, image, **params): return image def apply_to_bbox(self, bbox, **params): - """ Change box order between (xmin, ymin, xmax, ymax) and (xcenter, ycenter, width, height). :param bbox: (tensor) or {np.array) bounding bbox, sized [N, 4] diff --git a/theseus/cv/detection/callbacks/visualization.py b/theseus/cv/detection/callbacks/visualization.py index b30e2ec..9df7e40 100644 --- a/theseus/cv/detection/callbacks/visualization.py +++ b/theseus/cv/detection/callbacks/visualization.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, List +from typing import Any import lightning.pytorch as pl import matplotlib.patches as mpatches @@ -27,10 +27,14 @@ class DetectionVisualizerCallback(Callback): def __init__( self, order: str = None, - mean: List[float] = [0.485, 0.456, 0.406], - std: List[float] = [0.229, 0.224, 0.225], - **kwargs + mean: list[float] = None, + std: list[float] = None, + **kwargs, ) -> None: + if std is None: + std = [0.229, 0.224, 0.225] + if mean is None: + mean = [0.485, 0.456, 0.406] super().__init__() self.visualizer = Visualizer() self.order = order @@ -43,7 +47,6 @@ def on_sanity_check_start(self, trainer: pl.Trainer, pl_module: pl.LightningModu """ iters = trainer.iterations - model = pl_module.model valloader = pl_module.datamodule.valloader trainloader = pl_module.datamodule.trainloader train_batch = next(iter(trainloader)) @@ -64,7 +67,7 @@ def visualize_gt(self, train_batch, val_batch, iters, classnames): anns = train_batch["targets"] batch = [] - for idx, (inputs, ann) in enumerate(zip(images, anns)): + for _idx, (inputs, ann) in enumerate(zip(images, anns)): boxes = ann["boxes"] labels = ann["labels"].numpy() img_show = self.visualizer.denormalize(inputs, mean=self.mean, std=self.std) @@ -114,7 +117,7 @@ def visualize_gt(self, train_batch, val_batch, iters, classnames): anns = val_batch["targets"] batch = [] - for idx, (inputs, ann) in enumerate(zip(images, anns)): + for _idx, (inputs, ann) in enumerate(zip(images, anns)): boxes = ann["boxes"] labels = ann["labels"].numpy() img_show = self.visualizer.denormalize(inputs, mean=self.mean, std=self.std) @@ -193,7 +196,7 @@ def on_validation_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule): preds = [i for i in zip(preds["boxes"], preds["confidences"], preds["labels"])] batch = [] - for idx, (inputs, target, pred) in enumerate(zip(images, targets, preds)): + for _idx, (inputs, target, pred) in enumerate(zip(images, targets, preds)): # Ground truth boxes = target["boxes"] labels = target["labels"].numpy() @@ -205,9 +208,7 @@ def on_validation_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule): # Prediction boxes, scores, labels = pred - decode_pred = self.visualizer.denormalize( - inputs, mean=self.mean, std=self.std - ) + decode_pred = self.visualizer.denormalize(inputs, mean=self.mean, std=self.std) self.visualizer.set_image(decode_pred.copy()) self.visualizer.draw_bbox(boxes, labels=labels, scores=scores) decode_pred = self.visualizer.get_image() diff --git a/theseus/cv/detection/datasets/base.py b/theseus/cv/detection/datasets/base.py index 053b77a..8bb51ff 100644 --- a/theseus/cv/detection/datasets/base.py +++ b/theseus/cv/detection/datasets/base.py @@ -1,4 +1,3 @@ -from typing import Dict, List import torch @@ -19,7 +18,7 @@ def _load_data(self): def load_image_and_boxes(self, index): raise NotImplementedError - def __getitem__(self, idx: int) -> Dict: + def __getitem__(self, idx: int) -> dict: """ Get one item """ @@ -61,7 +60,7 @@ def __getitem__(self, idx: int) -> Dict: def __len__(self) -> int: return len(self.fns) - def collate_fn(self, batch: List): + def collate_fn(self, batch: list): """ Collator for wrapping a batch """ diff --git a/theseus/cv/detection/datasets/coco.py b/theseus/cv/detection/datasets/coco.py index 5b19b73..844e0e3 100644 --- a/theseus/cv/detection/datasets/coco.py +++ b/theseus/cv/detection/datasets/coco.py @@ -1,5 +1,4 @@ import os -from typing import List, Optional import cv2 import numpy as np @@ -24,13 +23,7 @@ class COCODataset(DetectionDataset): """ - def __init__( - self, - image_dir: str, - label_path: str, - transform: Optional[List] = None, - **kwargs - ): + def __init__(self, image_dir: str, label_path: str, transform: list | None = None, **kwargs): super().__init__(**kwargs) self.image_dir = image_dir self.label_path = label_path @@ -71,9 +64,7 @@ def load_image(self, image_index): def load_annotations(self, image_index, width, height): # get ground truth annotations - annotations_ids = self.fns.getAnnIds( - imgIds=self.image_ids[image_index], iscrowd=None - ) + annotations_ids = self.fns.getAnnIds(imgIds=self.image_ids[image_index], iscrowd=None) annotations = np.zeros((0, 5)) # some images appear to miss annotations @@ -82,8 +73,7 @@ def load_annotations(self, image_index, width, height): # parse annotations coco_annotations = self.fns.loadAnns(annotations_ids) - for idx, a in enumerate(coco_annotations): - + for _idx, a in enumerate(coco_annotations): # some annotations have basically no width / height, skip them if a["bbox"][2] <= 2 or a["bbox"][3] <= 2: continue diff --git a/theseus/cv/detection/metrics/map.py b/theseus/cv/detection/metrics/map.py index 4634f2d..65b4c8b 100644 --- a/theseus/cv/detection/metrics/map.py +++ b/theseus/cv/detection/metrics/map.py @@ -86,8 +86,7 @@ def update(self, output, batch): gt_clss = gt["labels"].numpy().tolist() gt_instances = [ - BoxWithLabel(self.idx, box, int(cls), 1.0) - for box, cls in zip(gt_boxes, gt_clss) + BoxWithLabel(self.idx, box, int(cls), 1.0) for box, cls in zip(gt_boxes, gt_clss) ] pred_instances = [ BoxWithLabel(self.idx, box, int(cls), scr) @@ -120,7 +119,7 @@ def make_gt_json_file(self, path): instance_id = instance_info["image_id"] instance_name = instance_info["image_name"] height, width = instance_info["height"], instance_info["width"] - if instance_id not in self.image_id_dict.keys(): + if instance_id not in self.image_id_dict: self.image_id_dict[instance_id] = img_count img_count += 1 image_id = self.image_id_dict[instance_id] @@ -133,7 +132,6 @@ def make_gt_json_file(self, path): my_dict["images"].append(img_dict) for item in instance: - class_id = int(item.get_label()) xmin, ymin, xmax, ymax = item.get_box() @@ -204,8 +202,8 @@ def value(self): if len(results) == 0: # empty prediction return { - f"precision": 0, - f"recall": 0, + "precision": 0, + "recall": 0, "f1_score": 0, } diff --git a/theseus/cv/detection/metrics/misc.py b/theseus/cv/detection/metrics/misc.py index 0a7e5fc..28f28e1 100644 --- a/theseus/cv/detection/metrics/misc.py +++ b/theseus/cv/detection/metrics/misc.py @@ -1,4 +1,3 @@ -from typing import Dict, List def bb_intersection_over_union(boxA, boxB): @@ -70,8 +69,8 @@ def find_best_matching_box(self, boxes, min_iou): class MatchingPairs: def __init__( self, - pred_boxes: List[BoxWithLabel], - gt_boxes: List[BoxWithLabel], + pred_boxes: list[BoxWithLabel], + gt_boxes: list[BoxWithLabel], min_iou=0.5, eps=0.000001, ) -> None: diff --git a/theseus/cv/detection/metrics/precision_recall.py b/theseus/cv/detection/metrics/precision_recall.py index 9706598..f249219 100644 --- a/theseus/cv/detection/metrics/precision_recall.py +++ b/theseus/cv/detection/metrics/precision_recall.py @@ -1,4 +1,3 @@ -from typing import Dict, List import numpy as np @@ -31,8 +30,7 @@ def update(self, output, batch): gt_clss = gt["labels"].numpy().tolist() gt_instances = [ - BoxWithLabel(self.idx, box, int(cls), 1.0) - for box, cls in zip(gt_boxes, gt_clss) + BoxWithLabel(self.idx, box, int(cls), 1.0) for box, cls in zip(gt_boxes, gt_clss) ] pred_instances = [ BoxWithLabel(self.idx, box, int(cls), scr) @@ -50,16 +48,12 @@ def value(self): score = self.calculate_pr(total_tp, total_fp, total_fn) return score - def calculate_cfm( - self, pred_boxes: List[BoxWithLabel], gt_boxes: List[BoxWithLabel] - ): + def calculate_cfm(self, pred_boxes: list[BoxWithLabel], gt_boxes: list[BoxWithLabel]): total_fp = [] total_fn = [] total_tp = [] for pred_box, gt_box in zip(pred_boxes, gt_boxes): - matched_pairs = MatchingPairs( - pred_box, gt_box, min_iou=self.min_iou, eps=self.eps - ) + matched_pairs = MatchingPairs(pred_box, gt_box, min_iou=self.min_iou, eps=self.eps) tp = matched_pairs.get_acc() fp = matched_pairs.get_false_positive() fn = matched_pairs.get_false_negative() @@ -90,7 +84,6 @@ def calculate_pr(self, total_tp, total_fp, total_fn): precisions = [] recalls = [] for cls_id in range(self.num_classes): - if tp_per_class[cls_id] + fp_per_class[cls_id] == 0: precisions.append(-1) else: @@ -101,9 +94,7 @@ def calculate_pr(self, total_tp, total_fp, total_fn): if tp_per_class[cls_id] + fn_per_class[cls_id] == 0: recalls.append(-1) else: - recalls.append( - tp_per_class[cls_id] / (tp_per_class[cls_id] + fn_per_class[cls_id]) - ) + recalls.append(tp_per_class[cls_id] / (tp_per_class[cls_id] + fn_per_class[cls_id])) np_precisions = np.array(precisions) np_recalls = np.array(recalls) @@ -111,14 +102,12 @@ def calculate_pr(self, total_tp, total_fp, total_fn): precision_all = sum(np_precisions[np_precisions != -1]) / ( self.num_classes - sum(np_precisions == -1) ) - recall_all = sum(np_recalls[np_recalls != -1]) / ( - self.num_classes - sum(np_recalls == -1) - ) + recall_all = sum(np_recalls[np_recalls != -1]) / (self.num_classes - sum(np_recalls == -1)) f1_score = 2 * precision_all * recall_all / (precision_all + recall_all) return { - f"simple_precision": precision_all, - f"simple_recall": recall_all, + "simple_precision": precision_all, + "simple_recall": recall_all, "simple_f1_score": f1_score, } diff --git a/theseus/cv/detection/pipeline.py b/theseus/cv/detection/pipeline.py index c584507..5b3c53e 100644 --- a/theseus/cv/detection/pipeline.py +++ b/theseus/cv/detection/pipeline.py @@ -16,7 +16,7 @@ class DetectionPipeline(BasePipeline): """docstring for Pipeline.""" def __init__(self, opt: DictConfig): - super(DetectionPipeline, self).__init__(opt) + super().__init__(opt) self.opt = opt def init_registry(self): diff --git a/theseus/cv/semantic/augmentations/mosaic.py b/theseus/cv/semantic/augmentations/mosaic.py index dcff2a9..17f92fc 100644 --- a/theseus/cv/semantic/augmentations/mosaic.py +++ b/theseus/cv/semantic/augmentations/mosaic.py @@ -1,5 +1,4 @@ import random -from typing import List, Tuple import numpy as np from albumentations import Compose, RandomCrop, Resize @@ -22,7 +21,7 @@ def __init__( self, width: int, height: int, - scale_range: Tuple[float, float] = (0.3, 0.7), + scale_range: tuple[float, float] = (0.3, 0.7), ) -> None: self.width = width self.height = height @@ -40,7 +39,7 @@ def get_resize(self, image: np.array, mask: np.array, width: int, height: int): item = transforms(image=image, mask=mask) return item["image"], item["mask"] - def __call__(self, set_images: List[np.array], set_masks: List[np.array]): + def __call__(self, set_images: list[np.array], set_masks: list[np.array]): """ set_images: `List[np.array]` batch of numpy images (H,W,3) @@ -69,16 +68,12 @@ def __call__(self, set_images: List[np.array], set_masks: List[np.array]): result_mask[:divid_point_y, :divid_point_x] = mask elif i == 1: # top-right - img, mask = self.get_resize( - img, mask, self.width - divid_point_x, divid_point_y - ) + img, mask = self.get_resize(img, mask, self.width - divid_point_x, divid_point_y) result_image[:divid_point_y, divid_point_x : self.width, :] = img result_mask[:divid_point_y, divid_point_x : self.width] = mask elif i == 2: # bottom-left - img, mask = self.get_resize( - img, mask, divid_point_x, self.height - divid_point_y - ) + img, mask = self.get_resize(img, mask, divid_point_x, self.height - divid_point_y) result_image[divid_point_y : self.height, :divid_point_x, :] = img result_mask[divid_point_y : self.height, :divid_point_x] = mask @@ -89,11 +84,7 @@ def __call__(self, set_images: List[np.array], set_masks: List[np.array]): self.width - divid_point_x, self.height - divid_point_y, ) - result_image[ - divid_point_y : self.height, divid_point_x : self.width, : - ] = img - result_mask[ - divid_point_y : self.height, divid_point_x : self.width - ] = mask + result_image[divid_point_y : self.height, divid_point_x : self.width, :] = img + result_mask[divid_point_y : self.height, divid_point_x : self.width] = mask return result_image, result_mask diff --git a/theseus/cv/semantic/callbacks/visualize_callbacks.py b/theseus/cv/semantic/callbacks/visualize_callbacks.py index cb5be96..85d0b48 100644 --- a/theseus/cv/semantic/callbacks/visualize_callbacks.py +++ b/theseus/cv/semantic/callbacks/visualize_callbacks.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any import lightning.pytorch as pl import matplotlib.patches as mpatches @@ -75,7 +75,7 @@ def visualize_gt(self, train_batch, val_batch, iters, classnames): masks = train_batch["targets"].squeeze() batch = [] - for idx, (inputs, mask) in enumerate(zip(images, masks)): + for _idx, (inputs, mask) in enumerate(zip(images, masks)): img_show = self.visualizer.denormalize(inputs) decode_mask = self.visualizer.decode_segmap(mask.numpy()) img_show = TFF.to_tensor(img_show) @@ -119,7 +119,7 @@ def visualize_gt(self, train_batch, val_batch, iters, classnames): masks = val_batch["targets"].squeeze() batch = [] - for idx, (inputs, mask) in enumerate(zip(images, masks)): + for _idx, (inputs, mask) in enumerate(zip(images, masks)): img_show = self.visualizer.denormalize(inputs) decode_mask = self.visualizer.decode_segmap(mask.numpy()) img_show = TFF.to_tensor(img_show) @@ -190,7 +190,7 @@ def on_validation_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule): preds = model.model.get_prediction({"inputs": images}, model.device)["masks"] batch = [] - for idx, (inputs, mask, pred) in enumerate(zip(images, masks, preds)): + for _idx, (inputs, mask, pred) in enumerate(zip(images, masks, preds)): img_show = self.visualizer.denormalize(inputs) decode_mask = self.visualizer.decode_segmap(mask.numpy()) decode_pred = self.visualizer.decode_segmap(pred) diff --git a/theseus/cv/semantic/datasets/csv_dataset.py b/theseus/cv/semantic/datasets/csv_dataset.py index 145943c..e3ca132 100644 --- a/theseus/cv/semantic/datasets/csv_dataset.py +++ b/theseus/cv/semantic/datasets/csv_dataset.py @@ -1,4 +1,3 @@ -from typing import List, Optional import numpy as np import pandas as pd @@ -35,10 +34,10 @@ def __init__( mask_dir: str, csv_path: str, txt_classnames: str, - transform: Optional[List] = None, - **kwargs + transform: list | None = None, + **kwargs, ): - super(SemanticCSVDataset, self).__init__(**kwargs) + super().__init__(**kwargs) self.image_dir = image_dir self.mask_dir = mask_dir self.csv_path = csv_path @@ -51,7 +50,7 @@ def _load_data(self): Read data from csv and load into memory """ - with open(self.txt_classnames, "r") as f: + with open(self.txt_classnames) as f: self.classnames = f.read().splitlines() # Mapping between classnames and indices diff --git a/theseus/cv/semantic/datasets/dataset.py b/theseus/cv/semantic/datasets/dataset.py index 7d21bb6..f6d485b 100644 --- a/theseus/cv/semantic/datasets/dataset.py +++ b/theseus/cv/semantic/datasets/dataset.py @@ -1,5 +1,4 @@ import os -from typing import Dict import numpy as np import torch @@ -21,7 +20,7 @@ def __init__(self, **kwawrgs): def _load_data(self): raise NotImplementedError - def __getitem__(self, idx: int) -> Dict: + def __getitem__(self, idx: int) -> dict: """ Get one item """ diff --git a/theseus/cv/semantic/datasets/mosaic_collator.py b/theseus/cv/semantic/datasets/mosaic_collator.py index c67ca88..9e09662 100644 --- a/theseus/cv/semantic/datasets/mosaic_collator.py +++ b/theseus/cv/semantic/datasets/mosaic_collator.py @@ -1,5 +1,4 @@ import random -from typing import Dict, List, Tuple import numpy as np import torch @@ -20,13 +19,11 @@ class MosaicCollator(BaseCollator): """ - def __init__( - self, scale_range: Tuple[float, float] = (0.3, 0.7), p=0.5, **kwargs - ) -> None: + def __init__(self, scale_range: tuple[float, float] = (0.3, 0.7), p=0.5, **kwargs) -> None: self.scale_range = scale_range self.p = p - def __call__(self, batch: List[Dict]): + def __call__(self, batch: list[dict]): """ batch: `List[Dict]` batch of tensor images and mask # (B,3,H,W), (B,NC,H,W) @@ -65,12 +62,8 @@ def __call__(self, batch: List[Dict]): candidate_images = set_images[candidate_indices, :] candidate_masks = set_masks[candidate_indices, :] - candidate_images = torch.cat( - [candidate_images, current_image.unsqueeze(0)], dim=0 - ) - candidate_masks = torch.cat( - [candidate_masks, current_mask.unsqueeze(0)], dim=0 - ) + candidate_images = torch.cat([candidate_images, current_image.unsqueeze(0)], dim=0) + candidate_masks = torch.cat([candidate_masks, current_mask.unsqueeze(0)], dim=0) shuffling_id = torch.randperm(candidate_images.size()[0]) candidate_images = candidate_images[shuffling_id] diff --git a/theseus/cv/semantic/losses/ce_loss.py b/theseus/cv/semantic/losses/ce_loss.py index 41d9386..8894292 100644 --- a/theseus/cv/semantic/losses/ce_loss.py +++ b/theseus/cv/semantic/losses/ce_loss.py @@ -1,4 +1,3 @@ -from typing import Dict, List import torch from torch import nn @@ -10,13 +9,13 @@ class SemanticCELoss(nn.Module): r"""CELoss is warper of cross-entropy loss""" def __init__(self, weight=None, ignore_index=None, **kwargs): - super(SemanticCELoss, self).__init__() + super().__init__() self.weight = weight if self.weight is not None: self.weight = torch.FloatTensor(self.weight) self.ignore_index = ignore_index - def forward(self, outputs: Dict, batch: Dict, device: torch.device) -> torch.Tensor: + def forward(self, outputs: dict, batch: dict, device: torch.device) -> torch.Tensor: pred = outputs["outputs"] target = move_to(batch["targets"], device) @@ -42,23 +41,19 @@ class SemanticSmoothCELoss(nn.Module): r"""SmoothCELoss is warper of label smoothing cross-entropy loss""" def __init__(self, alpha=1e-6, ignore_index=None, reduction="mean", **kwargs): - super(SemanticSmoothCELoss, self).__init__() + super().__init__() self.ignore_index = ignore_index self.reduction = reduction self.alpha = alpha - def forward(self, outputs: Dict, batch: Dict, device: torch.device) -> torch.Tensor: + def forward(self, outputs: dict, batch: dict, device: torch.device) -> torch.Tensor: pred = outputs["outputs"] targets = move_to(batch["targets"], device) batch_size, num_classes = pred.shape[:2] - y_hot = move_to(torch.zeros(pred.shape), device).scatter_( - 1, targets.unsqueeze(1), 1.0 - ) + y_hot = move_to(torch.zeros(pred.shape), device).scatter_(1, targets.unsqueeze(1), 1.0) y_smooth = (1 - self.alpha) * y_hot + self.alpha / num_classes - loss = torch.sum( - -y_smooth * torch.nn.functional.log_softmax(pred, -1), -1 - ).sum() + loss = torch.sum(-y_smooth * torch.nn.functional.log_softmax(pred, -1), -1).sum() if self.reduction == "mean": loss /= batch_size @@ -80,11 +75,7 @@ class OhemCELoss(nn.Module): """ def __init__( - self, - ignore_label: int = 255, - weight: List = None, - thresh: float = 0.7, - **kwargs + self, ignore_label: int = 255, weight: list = None, thresh: float = 0.7, **kwargs ) -> None: super().__init__() @@ -98,7 +89,7 @@ def __init__( weight=self.weight, ignore_index=ignore_label, reduction="none" ) - def forward(self, outputs: Dict, batch: Dict, device: torch.device) -> torch.Tensor: + def forward(self, outputs: dict, batch: dict, device: torch.device) -> torch.Tensor: pred = outputs["outputs"] labels = move_to(batch["targets"], device) diff --git a/theseus/cv/semantic/losses/dice_loss.py b/theseus/cv/semantic/losses/dice_loss.py index 6a711df..3867cec 100644 --- a/theseus/cv/semantic/losses/dice_loss.py +++ b/theseus/cv/semantic/losses/dice_loss.py @@ -1,4 +1,3 @@ -from typing import Dict, List import torch import torch.nn as nn @@ -16,19 +15,19 @@ class DiceLoss(nn.Module): """ def __init__(self, eps=1e-6, **kwargs): - super(DiceLoss, self).__init__() + super().__init__() self.eps = eps - def forward(self, outputs: Dict, batch: Dict, device: torch.device): + def forward(self, outputs: dict, batch: dict, device: torch.device): predict = outputs["outputs"] targets = move_to(batch["targets"], device) prediction = F.softmax(predict, dim=1) if len(targets.shape) == 3: num_classes = prediction.shape[1] - targets = torch.nn.functional.one_hot( - targets.long(), num_classes=num_classes - ).permute(0, 3, 1, 2) + targets = torch.nn.functional.one_hot(targets.long(), num_classes=num_classes).permute( + 0, 3, 1, 2 + ) # have to use contiguous since they may from a torch.view op iflat = prediction.contiguous().view(-1) diff --git a/theseus/cv/semantic/losses/lovasz_loss.py b/theseus/cv/semantic/losses/lovasz_loss.py index 0384e71..ebc9ac7 100644 --- a/theseus/cv/semantic/losses/lovasz_loss.py +++ b/theseus/cv/semantic/losses/lovasz_loss.py @@ -2,7 +2,7 @@ Lovasz-Softmax and Jaccard hinge loss in PyTorch Maxim Berman 2018 ESAT-PSI KU Leuven (MIT License) """ -from typing import Dict, List + import torch import torch.nn as nn @@ -60,7 +60,7 @@ def lovasz_softmax_flat(prb, lbl, ignore_index, only_present): class LovaszSoftmax(nn.Module): - """ + r""" Multi-class Lovasz-Softmax loss logits: [B, C, H, W] class logits at each prediction (between -\infty and \infty) labels: [B, H, W] Tensor, ground truth labels (between 0 and C - 1) @@ -73,7 +73,7 @@ def __init__(self, ignore_index=None, only_present=True, **kwargs): self.ignore_index = ignore_index self.only_present = only_present - def forward(self, outputs: Dict, batch: Dict, device: torch.device): + def forward(self, outputs: dict, batch: dict, device: torch.device): predict = outputs["outputs"] targets = move_to(batch["targets"], device) @@ -83,9 +83,7 @@ def forward(self, outputs: Dict, batch: Dict, device: torch.device): total_loss = 0 batch_size = predict.shape[0] for prb, lbl in zip(probas, targets): - total_loss += lovasz_softmax_flat( - prb, lbl, self.ignore_index, self.only_present - ) + total_loss += lovasz_softmax_flat(prb, lbl, self.ignore_index, self.only_present) loss = total_loss / batch_size loss_dict = {"LOVASZ": loss.item()} diff --git a/theseus/cv/semantic/losses/tversky_loss.py b/theseus/cv/semantic/losses/tversky_loss.py index 192104a..354eb17 100644 --- a/theseus/cv/semantic/losses/tversky_loss.py +++ b/theseus/cv/semantic/losses/tversky_loss.py @@ -1,4 +1,3 @@ -from typing import Dict import torch import torch.nn as nn @@ -7,21 +6,21 @@ class FocalTverskyLoss(nn.Module): def __init__(self, smooth=1, alpha=0.7, gamma=0.75, **kwargs): - super(FocalTverskyLoss, self).__init__() + super().__init__() self.smooth = smooth self.alpha = alpha self.beta = 1 - alpha self.gamma = gamma - def forward(self, outputs: Dict, batch: Dict, device: torch.device) -> torch.Tensor: + def forward(self, outputs: dict, batch: dict, device: torch.device) -> torch.Tensor: predict = outputs["outputs"] targets = batch["targets"].to(device) if len(targets.shape) == 3: num_classes = predict.shape[1] - targets = torch.nn.functional.one_hot( - targets.long(), num_classes=num_classes - ).permute(0, 3, 1, 2) + targets = torch.nn.functional.one_hot(targets.long(), num_classes=num_classes).permute( + 0, 3, 1, 2 + ) prediction = F.softmax(predict, dim=1) @@ -34,9 +33,7 @@ def forward(self, outputs: Dict, batch: Dict, device: torch.device) -> torch.Ten FP = ((1 - targets) * prediction).sum() FN = (targets * (1 - prediction)).sum() - tversky = (TP + self.smooth) / ( - TP + self.alpha * FN + self.beta * FP + self.smooth - ) + tversky = (TP + self.smooth) / (TP + self.alpha * FN + self.beta * FP + self.smooth) loss = (1 - tversky) ** self.gamma loss_dict = {"FT": loss.item()} diff --git a/theseus/cv/semantic/metrics/dicecoeff.py b/theseus/cv/semantic/metrics/dicecoeff.py index 5e37861..e2e03a7 100644 --- a/theseus/cv/semantic/metrics/dicecoeff.py +++ b/theseus/cv/semantic/metrics/dicecoeff.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, Optional +from typing import Any import numpy as np import torch @@ -16,7 +16,7 @@ def __init__(self, num_classes: int, calc_each_class: bool = False, **kwawrgs): self.num_classes = num_classes self.reset() - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): + def update(self, outputs: dict[str, Any], batch: dict[str, Any]): """ Perform calculation based on prediction and targets """ @@ -68,9 +68,7 @@ def reset(self): self.sample_size = 0 def value(self): - scores_each_class = ( - self.scores_list / self.sample_size - ) # mean over number of samples + scores_each_class = self.scores_list / self.sample_size # mean over number of samples scores = sum(scores_each_class) / (self.num_classes - 1) # subtract background if self.calc_each_class: diff --git a/theseus/cv/semantic/metrics/miou.py b/theseus/cv/semantic/metrics/miou.py index e8a6b4c..17ee6d4 100644 --- a/theseus/cv/semantic/metrics/miou.py +++ b/theseus/cv/semantic/metrics/miou.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, Optional +from typing import Any import numpy as np import torch @@ -15,7 +15,7 @@ def __init__(self, num_classes: int = 4, **kwawrgs): self.num_classes = num_classes self.reset() - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): + def update(self, outputs: dict[str, Any], batch: dict[str, Any]): """ Perform calculation based on prediction and targets """ @@ -30,9 +30,7 @@ def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): targets = targets.permute(3, 0, 1, 2).long().squeeze() preds = torch.from_numpy(outputs).long() - one_hot_predicts = torch.nn.functional.one_hot( - preds.long(), num_classes=self.num_classes - ) + one_hot_predicts = torch.nn.functional.one_hot(preds.long(), num_classes=self.num_classes) one_hot_predicts = one_hot_predicts.permute(0, 3, 1, 2) @@ -68,8 +66,6 @@ def reset(self): self.sample_size = 0 def value(self): - scores_each_class = ( - self.scores_list / self.sample_size - ) # mean over number of samples + scores_each_class = self.scores_list / self.sample_size # mean over number of samples scores = sum(scores_each_class) / (self.num_classes - 1) # subtract background return {"miou": scores} diff --git a/theseus/cv/semantic/metrics/pixel_accuracy.py b/theseus/cv/semantic/metrics/pixel_accuracy.py index 2315b81..377624e 100644 --- a/theseus/cv/semantic/metrics/pixel_accuracy.py +++ b/theseus/cv/semantic/metrics/pixel_accuracy.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, Optional +from typing import Any import numpy as np import torch @@ -19,10 +19,10 @@ class PixelAccuracy(Metric): def __init__( self, num_classes: int, - thresh: Optional[float] = None, + thresh: float | None = None, eps: float = 1e-6, - ignore_index: Optional[int] = None, - **kwargs + ignore_index: int | None = None, + **kwargs, ): self.thresh = thresh @@ -32,16 +32,14 @@ def __init__( self.eps = eps if self.pred_type == "binary": - assert ( - thresh is not None - ), "Threshold should be specified for binary segmentation" + assert thresh is not None, "Threshold should be specified for binary segmentation" if num_classes == 1: self.num_classes += 1 self.reset() - def update(self, outputs: Dict[str, Any], batch: Dict[str, Any]): + def update(self, outputs: dict[str, Any], batch: dict[str, Any]): """ Perform calculation based on prediction and targets """ @@ -91,12 +89,8 @@ def reset(self): self.sample_size = 0 def value(self): - precision_each_class = ( - self.precisions / self.sample_size - ) # mean over number of samples - recall_each_class = ( - self.recalls / self.sample_size - ) # mean over number of samples + precision_each_class = self.precisions / self.sample_size # mean over number of samples + recall_each_class = self.recalls / self.sample_size # mean over number of samples # Mean over classes if self.pred_type == "binary": diff --git a/theseus/cv/semantic/models/segmodels.py b/theseus/cv/semantic/models/segmodels.py index eeee478..d3c8340 100644 --- a/theseus/cv/semantic/models/segmodels.py +++ b/theseus/cv/semantic/models/segmodels.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any import segmentation_models_pytorch as smp import torch @@ -29,10 +29,10 @@ def __init__( model_name: str, encoder_name: str = "resnet34", num_classes: int = 1000, - aux_params: Dict = None, + aux_params: dict = None, in_channels: int = 3, pretrained: bool = True, - **kwargs + **kwargs, ): super().__init__() @@ -57,7 +57,7 @@ def get_model(self): """ return self.model - def forward_batch(self, batch: Dict, device: torch.device = None): + def forward_batch(self, batch: dict, device: torch.device = None): if device is not None: x = move_to(batch["inputs"], device) else: @@ -67,7 +67,7 @@ def forward_batch(self, batch: Dict, device: torch.device = None): "outputs": outputs, } - def get_prediction(self, adict: Dict[str, Any], device: torch.device = None): + def get_prediction(self, adict: dict[str, Any], device: torch.device = None): """ Inference using the model. adict: `Dict[str, Any]` diff --git a/theseus/cv/semantic/pipeline.py b/theseus/cv/semantic/pipeline.py index 8d8bf65..47f4424 100644 --- a/theseus/cv/semantic/pipeline.py +++ b/theseus/cv/semantic/pipeline.py @@ -15,7 +15,7 @@ class SemanticPipeline(BasePipeline): """docstring for Pipeline.""" def __init__(self, opt: DictConfig): - super(SemanticPipeline, self).__init__(opt) + super().__init__(opt) self.opt = opt def init_registry(self): diff --git a/theseus/ml/__init__.py b/theseus/ml/__init__.py index e0fc63e..69b4532 100644 --- a/theseus/ml/__init__.py +++ b/theseus/ml/__init__.py @@ -1 +1,14 @@ from .preprocessors import * +from .tradml import ( + TradMLTuner, + fit_adaboost, + fit_catboost, + fit_knn, + fit_lightgbm, + fit_logistics, + fit_mlp, + fit_rf, + fit_svm, + fit_xgboost, + objective, +) diff --git a/theseus/ml/callbacks/__init__.py b/theseus/ml/callbacks/__init__.py deleted file mode 100644 index 33c6032..0000000 --- a/theseus/ml/callbacks/__init__.py +++ /dev/null @@ -1,22 +0,0 @@ -from theseus.registry import Registry - -from .base_callbacks import Callbacks, CallbacksList -from .checkpoint_callbacks import SKLearnCheckpointCallbacks -from .explainer import ( - LIMEExplainer, - PartialDependencePlots, - PermutationImportance, - ShapValueExplainer, -) -from .metric_callbacks import MetricLoggerCallbacks -from .optuna_callbacks import OptunaCallbacks - -CALLBACKS_REGISTRY = Registry("CALLBACKS") - -CALLBACKS_REGISTRY.register(SKLearnCheckpointCallbacks) -CALLBACKS_REGISTRY.register(ShapValueExplainer) -CALLBACKS_REGISTRY.register(PermutationImportance) -CALLBACKS_REGISTRY.register(PartialDependencePlots) -CALLBACKS_REGISTRY.register(LIMEExplainer) -CALLBACKS_REGISTRY.register(OptunaCallbacks) -CALLBACKS_REGISTRY.register(MetricLoggerCallbacks) diff --git a/theseus/ml/callbacks/base_callbacks.py b/theseus/ml/callbacks/base_callbacks.py deleted file mode 100644 index bbb6b77..0000000 --- a/theseus/ml/callbacks/base_callbacks.py +++ /dev/null @@ -1,184 +0,0 @@ -# Modified from YOLOv5 🚀 by Ultralytics, GPL-3.0 license - -from typing import Any, Dict, List - -from tabulate import tabulate - -from theseus.base.utilities.loggers.observer import LoggerObserver - -LOGGER = LoggerObserver.getLogger("main") - -hook_names = [ - "sanitycheck", - "on_start", - "on_finish", - "on_epoch_start", - "on_epoch_end", - "on_train_epoch_start", - "on_train_epoch_end", - "on_train_batch_start", - "on_train_batch_end", - "on_train_step", - "on_validation_epoch_start", - "on_validation_epoch_end", - "on_validation_batch_start", - "on_validation_batch_end", - "on_validation_step", -] - - -class Callbacks: - """ - Abstract class for callbacks - """ - - def __init__(self) -> None: - - # Define the available callbacks - self._hooks = {k: None for k in hook_names} - - self.name = self.__class__.__name__ - self.params = None - self.self_register() - - def set_params(self, params): - self.params = params - - def _do_register(self, name: str, func: Any, overide: bool = False) -> None: - assert ( - name in self._hooks.keys() - ), f"Method named '{name}' cannot be used as hook in {self.name}" - - assert ( - self._hooks[name] is None or overide - ), f"""A hook named '{name}' has already been registered in {self._name}. - Please specify `overwrite=True` or use another name""" - - self._hooks[name] = func - - def self_register(self): - for func_name in dir(self): - func = getattr(self, func_name) - if callable(func): - if func_name in self._hooks.keys(): - self.register_hook(func) - - def register_hook( - self, func: Any = None, prefix: str = "", overide: bool = False - ) -> Any: - """ - Register the given object under the the name `obj.__name__`. - Can be used as either a decorator or not. See docstring of this class for usage. - """ - - if func is None: - # used as a decorator - def deco(func_or_class: Any) -> Any: - name = func_or_class._name - self._do_register(prefix + name, func_or_class, overide=overide) - return func_or_class - - return deco - - # used as a function call - name = func.__name__ - self._do_register(prefix + name, func, overide=overide) - - def get(self, name: str) -> Any: - ret = self._hooks.get(name) - if ret is None: - raise KeyError( - "Hook named '{}' has not been registered in '{}'!".format( - name, self._name - ) - ) - return ret - - def __repr__(self) -> str: - table_headers = ["Names", "Objects"] - table = tabulate( - self._hooks.items(), headers=table_headers, tablefmt="fancy_grid" - ) - return "Hook functions of {}:\n".format(self._name) + table - - # pyre-fixme[4]: Attribute must be annotated. - __str__ = __repr__ - - -class CallbacksList: - """ " - Handles all registered callbacks for Hooks - """ - - def __init__(self, callbacks: List[Callbacks]): - - # Define the available callbacks - self._callbacks = {k: [] for k in hook_names} - self._registered_callback_names = [] - self._registered_callbacks = [] - self.params = None - # self.stop_training = False # set True to interrupt training - self.register_callbacks(callbacks) - - def set_params(self, params): - for item in self._registered_callbacks: - item.set_params(params) - - def register_callbacks(self, callbacks: List[Callbacks]): - """ - Register list of callbacks - """ - # Register all callbacks - for callback in callbacks: - if callback.name not in self._registered_callback_names: - for method_name, method_call in callback._hooks.items(): - if method_call is not None: - self.register_action( - method_name, - name=".".join([callback.name, method_name]), - callback=method_call, - ) - self._registered_callback_names.append(callback.name) - self._registered_callbacks.append(callback) - else: - print(f"Duplicate callback named {callback.name} found.") - - def register_action(self, hook, name="", callback=None): - """ - Register a new action to a callback hook - Args: - hook The callback hook name to register the action to - name The name of the action for later reference - callback The callback to fire - """ - assert ( - hook in self._callbacks - ), f"hook '{hook}' not found in callbacks {self._callbacks}" - assert callable(callback), f"callback '{callback}' is not callable" - self._callbacks[hook].append({"name": name, "callback": callback}) - - def get_registered_actions(self, hook=None): - """ " - Returns all the registered actions by callback hook - Args: - hook The name of the hook to check, defaults to all - """ - if hook: - return self._callbacks[hook] - - return self._callbacks - - def run(self, hook, params: Dict = None): - """ - Loop through the registered actions and fire all callbacks - Args: - hook The name of the hook to check, defaults to all - params: dict with parameters - """ - - assert ( - hook in self._callbacks.keys() - ), f"hook {hook} not found in callbacks in {self._callbacks.keys()}" - - for logger in self._callbacks[hook]: - logger["callback"](logs=params) diff --git a/theseus/ml/callbacks/checkpoint_callbacks.py b/theseus/ml/callbacks/checkpoint_callbacks.py deleted file mode 100644 index 2e711e3..0000000 --- a/theseus/ml/callbacks/checkpoint_callbacks.py +++ /dev/null @@ -1,44 +0,0 @@ -import os -import os.path as osp -from typing import Dict - -from theseus.base.utilities.loggers.observer import LoggerObserver -from theseus.ml.callbacks import Callbacks - -LOGGER = LoggerObserver.getLogger("main") - - -class SKLearnCheckpointCallbacks(Callbacks): - """ - Callbacks for saving checkpoints. - """ - - def __init__( - self, - save_dir: str = "runs", - **kwargs, - ) -> None: - super().__init__() - - self.best_value = 0 - self.save_dir = osp.join(save_dir, "checkpoints") - os.makedirs(self.save_dir, exist_ok=True) - - def save_checkpoint(self, trainer, outname="last"): - """ - Save all information of the current iteration - """ - save_path = osp.join(self.save_dir, outname) - trainer.model.save_model(savepath=save_path) - LOGGER.text( - f"Save model to last.pth", - LoggerObserver.INFO, - ) - - def on_train_epoch_end(self, logs: Dict = None): - """ - On training batch (iteration) end - """ - - # Saving checkpoint - self.save_checkpoint(self.params["trainer"]) diff --git a/theseus/ml/callbacks/explainer/__init__.py b/theseus/ml/callbacks/explainer/__init__.py deleted file mode 100644 index d5d9bd2..0000000 --- a/theseus/ml/callbacks/explainer/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -from .lime import LIMEExplainer -from .pdp import PartialDependencePlots -from .permutation import PermutationImportance -from .shapley import ShapValueExplainer diff --git a/theseus/ml/callbacks/explainer/lime.py b/theseus/ml/callbacks/explainer/lime.py deleted file mode 100644 index ddfccf8..0000000 --- a/theseus/ml/callbacks/explainer/lime.py +++ /dev/null @@ -1,76 +0,0 @@ -import os.path as osp -import random -from typing import Dict, List - -from lime import lime_tabular - -from theseus.base.utilities.loggers.observer import LoggerObserver -from theseus.ml.callbacks import Callbacks - -LOGGER = LoggerObserver.getLogger("main") - - -class LIMEExplainer(Callbacks): - def __init__(self, save_dir, **kwargs) -> None: - super().__init__() - self.save_dir = save_dir - - def explain_instance( - self, training_data, model, item, feature_names=None, class_names=None - ): - """ - Get explaination for a single instance - """ - self.explainer = lime_tabular.LimeTabularExplainer( - training_data=training_data, - feature_names=feature_names, - class_names=class_names, - mode="classification" if class_names is not None else "regression", - discretize_continuous=False, - ) - - return self.explainer.explain_instance( - data_row=item, predict_fn=model.predict_proba - ) - - def on_validation_epoch_end(self, logs: Dict = None): - """ - After finish validation - """ - - model = self.params["trainer"].model.get_model() - x_train, y_train = ( - logs["trainset"]["inputs"], - logs["trainset"]["targets"], - ) - x_val, y_val = logs["valset"]["inputs"], logs["valset"]["targets"] - feature_names = logs["valset"]["feature_names"] - classnames = logs["valset"]["classnames"] - - item_id = random.choice(range(len(x_val))) - item = x_val[item_id] - exp = self.explain_instance( - x_train, - model, - item, - feature_names=feature_names, - class_names=classnames, - ) - - save_path = osp.join(self.save_dir, f"lime_{item_id}.html") - exp.save_to_file(save_path) - - LOGGER.log( - [ - { - "tag": f"Importance/LIME/{item_id}", - "value": save_path, - "type": LoggerObserver.HTML, - } - ] - ) - - LOGGER.text( - f"LIME figure for a random instance saved at {save_path}", - level=LoggerObserver.INFO, - ) diff --git a/theseus/ml/callbacks/explainer/pdp.py b/theseus/ml/callbacks/explainer/pdp.py deleted file mode 100644 index 5940636..0000000 --- a/theseus/ml/callbacks/explainer/pdp.py +++ /dev/null @@ -1,119 +0,0 @@ -import os.path as osp -from typing import Dict, List - -import matplotlib.pyplot as plt -from sklearn.inspection import PartialDependenceDisplay, partial_dependence - -from theseus.base.utilities.loggers.observer import LoggerObserver -from theseus.ml.callbacks import Callbacks - -LOGGER = LoggerObserver.getLogger("main") - - -class PartialDependencePlots(Callbacks): - def __init__( - self, - save_dir, - feature_names, - target_name, - kind="both", - num_jobs=1, - num_samples=50, - figsize=(10, 12), - **kwargs, - ) -> None: - - super().__init__() - self.feature_names = feature_names - self.kind = kind - self.save_dir = save_dir - self.num_jobs = num_jobs - self.num_samples = num_samples - self.figsize = figsize - self.target_name = target_name - - self.num_cols = int(len(feature_names) / 3) + 1 - self.num_rows = int(len(feature_names) / self.num_cols) - - def on_train_epoch_end(self, logs: Dict = None): - """ - After finish training - """ - model = self.params["trainer"].model.get_model() - x_train, y_train = ( - logs["trainset"]["inputs"], - logs["trainset"]["targets"], - ) - all_feature_names = logs["trainset"]["feature_names"] - - fig, ax = plt.subplots(self.num_rows, self.num_cols, figsize=self.figsize) - PartialDependenceDisplay.from_estimator( - model, - x_train, - self.feature_names, - feature_names=all_feature_names, - target=self.target_name, - ax=ax, - n_jobs=self.num_jobs, - n_cols=self.num_cols, - subsample=self.num_samples, - ) - fig.suptitle("Partial Dependence Plots") - fig.tight_layout() - - LOGGER.log( - [ - { - "tag": "Importance/PDP/train", - "value": fig, - "type": LoggerObserver.FIGURE, - "kwargs": {"step": 0}, - } - ] - ) - - LOGGER.text( - f"PDP figure saved", - level=LoggerObserver.INFO, - ) - plt.clf() - - def on_validation_epoch_end(self, logs: Dict = None): - """ - After finish validation - """ - model = self.params["trainer"].model.get_model() - x_val, y_val = logs["valset"]["inputs"], logs["valset"]["targets"] - all_feature_names = logs["valset"]["feature_names"] - - fig, ax = plt.subplots(self.num_rows, self.num_cols, figsize=self.figsize) - PartialDependenceDisplay.from_estimator( - model, - x_val, - self.feature_names, - feature_names=all_feature_names, - target=self.target_name, - ax=ax, - n_jobs=self.num_jobs, - n_cols=self.num_cols, - subsample=self.num_samples, - ) - fig.suptitle("Partial Dependence Plots") - fig.tight_layout() - - LOGGER.log( - [ - { - "tag": "Importance/PDP/val", - "value": fig, - "type": LoggerObserver.FIGURE, - "kwargs": {"step": 0}, - } - ] - ) - - LOGGER.text( - f"PDP figure saved", - level=LoggerObserver.INFO, - ) - plt.clf() diff --git a/theseus/ml/callbacks/explainer/permutation.py b/theseus/ml/callbacks/explainer/permutation.py deleted file mode 100644 index e9d4c2b..0000000 --- a/theseus/ml/callbacks/explainer/permutation.py +++ /dev/null @@ -1,101 +0,0 @@ -import os.path as osp -from typing import Dict, List - -import matplotlib.pyplot as plt -import plotly.graph_objects as go -from sklearn.inspection import permutation_importance - -from theseus.base.utilities.loggers.observer import LoggerObserver -from theseus.ml.callbacks import Callbacks - -LOGGER = LoggerObserver.getLogger("main") - - -class PermutationImportance(Callbacks): - def __init__(self, save_dir, **kwargs) -> None: - super().__init__() - self.explainer = None - self.save_dir = save_dir - - def on_train_epoch_end(self, logs: Dict = None): - """ - After finish training - """ - model = self.params["trainer"].model.get_model() - x_train, y_train = ( - logs["trainset"]["inputs"], - logs["trainset"]["targets"], - ) - feature_names = logs["trainset"]["feature_names"] - classnames = logs["trainset"]["classnames"] - - perm_importance = permutation_importance(model, x_train, y_train) - sorted_idx = perm_importance.importances_mean.argsort() - - fig = go.Figure( - go.Bar( - x=perm_importance.importances_mean[sorted_idx], - y=feature_names[sorted_idx], - orientation="h", - ) - ) - - plt.xlabel("Permutation Importance") - save_path = osp.join(self.save_dir, "permutation_train.html") - fig.write_html(save_path, auto_play=False) - - LOGGER.log( - [ - { - "tag": f"Importance/permutation/train", - "value": save_path, - "type": LoggerObserver.HTML, - } - ] - ) - - LOGGER.text( - f"Permutation figure saved at {save_path}", - level=LoggerObserver.INFO, - ) - plt.clf() - - def on_validation_epoch_end(self, logs: Dict = None): - """ - After finish validation - """ - model = self.params["trainer"].model.get_model() - x_val, y_val = logs["valset"]["inputs"], logs["valset"]["targets"] - feature_names = logs["valset"]["feature_names"] - classnames = logs["valset"]["classnames"] - - perm_importance = permutation_importance(model, x_val, y_val) - sorted_idx = perm_importance.importances_mean.argsort() - - fig = go.Figure( - go.Bar( - x=perm_importance.importances_mean[sorted_idx], - y=feature_names[sorted_idx], - orientation="h", - ) - ) - - plt.xlabel("Permutation Importance") - save_path = osp.join(self.save_dir, "permutation_val.html") - fig.write_html(save_path, auto_play=False) - - LOGGER.log( - [ - { - "tag": f"Importance/permutation/val", - "value": save_path, - "type": LoggerObserver.HTML, - } - ] - ) - - LOGGER.text( - f"Permutation figure saved at {save_path}", - level=LoggerObserver.INFO, - ) - plt.clf() diff --git a/theseus/ml/callbacks/explainer/shapley.py b/theseus/ml/callbacks/explainer/shapley.py deleted file mode 100644 index efb50ba..0000000 --- a/theseus/ml/callbacks/explainer/shapley.py +++ /dev/null @@ -1,105 +0,0 @@ -import os -import os.path as osp -from typing import Dict, List - -import matplotlib.pyplot as plt -import shap -from sklearn.inspection import permutation_importance - -from theseus.base.utilities.loggers.observer import LoggerObserver -from theseus.ml.callbacks import Callbacks - -LOGGER = LoggerObserver.getLogger("main") - - -class ShapValueExplainer(Callbacks): - def __init__( - self, save_dir, plot_type="bar", check_additivity=True, **kwargs - ) -> None: - super().__init__() - self.plot_type = plot_type - self.explainer = None - self.save_dir = save_dir - self.check_additivity = check_additivity - - def on_train_epoch_end(self, logs: Dict = None): - """ - After finish training - """ - model = self.params["trainer"].model.get_model() - self.explainer = shap.TreeExplainer(model) - x_train, y_train = ( - logs["trainset"]["inputs"], - logs["trainset"]["targets"], - ) - feature_names = logs["trainset"]["feature_names"] - classnames = logs["trainset"]["classnames"] - shap_values = self.explainer.shap_values( - x_train, check_additivity=self.check_additivity - ) - shap.summary_plot( - shap_values, - plot_type=self.plot_type, - feature_names=feature_names, - class_names=classnames, - show=False, - ) - - fig = plt.gcf() - - LOGGER.log( - [ - { - "tag": "Importance/SHAP/train", - "value": fig, - "type": LoggerObserver.FIGURE, - "kwargs": {"step": 0}, - } - ] - ) - - LOGGER.text( - f"Shapley figure saved", - level=LoggerObserver.INFO, - ) - plt.clf() - - def on_validation_epoch_end(self, logs: Dict = None): - """ - After finish validation - """ - model = self.params["trainer"].model.get_model() - self.explainer = shap.TreeExplainer(model) - x_val, y_val = logs["valset"]["inputs"], logs["valset"]["targets"] - feature_names = logs["valset"]["feature_names"] - classnames = logs["valset"]["classnames"] - shap_values = self.explainer.shap_values( - x_val, check_additivity=self.check_additivity - ) - plt.clf() - shap.summary_plot( - shap_values, - plot_type=self.plot_type, - feature_names=feature_names, - class_names=classnames, - show=False, - ) - - fig = plt.gcf() - - LOGGER.log( - [ - { - "tag": "Importance/SHAP/val", - "value": fig, - "type": LoggerObserver.FIGURE, - "kwargs": {"step": 0}, - } - ] - ) - - LOGGER.text( - f"Shapley figure saved", - level=LoggerObserver.INFO, - ) - plt.clf() diff --git a/theseus/ml/callbacks/metric_callbacks.py b/theseus/ml/callbacks/metric_callbacks.py deleted file mode 100644 index dd49c27..0000000 --- a/theseus/ml/callbacks/metric_callbacks.py +++ /dev/null @@ -1,72 +0,0 @@ -import json -import os -import os.path as osp -from typing import Dict, List - -from theseus.base.utilities.loggers.observer import LoggerObserver -from theseus.ml.callbacks import Callbacks - -LOGGER = LoggerObserver.getLogger("main") - - -class MetricLoggerCallbacks(Callbacks): - """ - Callbacks for logging running metric while training every epoch end - Features: - - Only do logging - """ - - def __init__(self, save_json: bool = True, **kwargs) -> None: - super().__init__() - self.save_json = save_json - if self.save_json: - self.save_dir = kwargs.get("save_dir", None) - if self.save_dir is not None: - self.save_dir = osp.join(self.save_dir, "Validation") - os.makedirs(self.save_dir, exist_ok=True) - self.output_dict = [] - - def on_validation_epoch_end(self, logs: Dict = None): - """ - After finish validation - """ - - iters = logs["iters"] - metric_dict = logs["metric_dict"] - - # Save json - if self.save_json: - item = {} - for metric, score in metric_dict.items(): - if isinstance(score, (int, float)): - item[metric] = float(f"{score:.5f}") - if len(item.keys()) > 0: - item["iters"] = iters - self.output_dict.append(item) - - # Log metric - metric_string = "" - for metric, score in metric_dict.items(): - if isinstance(score, (int, float)): - metric_string += metric + ": " + f"{score:.5f}" + " | " - metric_string += "\n" - - LOGGER.text(metric_string, level=LoggerObserver.INFO) - - # Call other loggers - log_dict = [ - {"tag": f"Validation/{k}", "value": v, "kwargs": {"step": iters}} - for k, v in metric_dict.items() - ] - - LOGGER.log(log_dict) - - def on_finish(self, logs: Dict = None): - """ - After finish everything - """ - if self.save_json: - save_json = osp.join(self.save_dir, "metrics.json") - if len(self.output_dict) > 0: - with open(save_json, "w") as f: - json.dump(self.output_dict, f) diff --git a/theseus/ml/callbacks/optuna_callbacks.py b/theseus/ml/callbacks/optuna_callbacks.py deleted file mode 100644 index 16f284a..0000000 --- a/theseus/ml/callbacks/optuna_callbacks.py +++ /dev/null @@ -1,35 +0,0 @@ -from typing import Dict, List - -import optuna - -from theseus.base.utilities.loggers.observer import LoggerObserver -from theseus.ml.callbacks import Callbacks - -LOGGER = LoggerObserver.getLogger("main") - - -class OptunaCallbacks(Callbacks): - """ - Callbacks for reporting value to optuna trials to decide whether to prune - """ - - def __init__(self, trial: optuna.Trial, **kwargs) -> None: - super().__init__() - self.trial = trial - - def on_validation_epoch_end(self, logs: Dict = None): - """ - After finish validation - """ - - iters = logs["iters"] - metric_dict = logs["metric_dict"] - - best_key = self.trial.user_attrs["best_key"] - self.trial.report(value=metric_dict[best_key], step=iters) - - if self.trial.should_prune(): - LOGGER.text( - f"Trial {self.trial.number} has been pruned", level=LoggerObserver.DEBUG - ) - raise optuna.TrialPruned() diff --git a/theseus/ml/datasets/__init__.py b/theseus/ml/datasets/__init__.py deleted file mode 100644 index a4b4d1a..0000000 --- a/theseus/ml/datasets/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -from theseus.base.datasets import DATALOADER_REGISTRY, DATASET_REGISTRY - -from .csv_dataset import TabularCSVDataset - -DATASET_REGISTRY.register(TabularCSVDataset) diff --git a/theseus/ml/datasets/csv_dataset.py b/theseus/ml/datasets/csv_dataset.py deleted file mode 100644 index 3c60902..0000000 --- a/theseus/ml/datasets/csv_dataset.py +++ /dev/null @@ -1,33 +0,0 @@ -import pandas as pd - - -class TabularCSVDataset: - def __init__( - self, data_path, target_column, txt_classnames=None, transform=None - ) -> None: - self.data_path = data_path - self.transform = transform - self.target_column = target_column - self.txt_classnames = txt_classnames - - if self.txt_classnames is not None: - self.classnames = open(self.txt_classnames, "r").read().splitlines() - else: - self.classnames = None - - def load_data(self): - df = pd.read_csv(self.data_path) - if self.transform is not None: - df = self.transform.run(df) - (X, y) = ( - df.drop(self.target_column, axis=1).values, - df[self.target_column].values, - ) - - return { - "inputs": X, - "targets": y, - "feature_names": df.drop(self.target_column, axis=1).columns, - "classnames": self.classnames, - "target_name": self.target_column, - } diff --git a/theseus/ml/metrics/__init__.py b/theseus/ml/metrics/__init__.py deleted file mode 100644 index c396538..0000000 --- a/theseus/ml/metrics/__init__.py +++ /dev/null @@ -1,18 +0,0 @@ -from theseus.base.metrics import METRIC_REGISTRY - -from .acccuracy import SKLAccuracy, SKLBalancedAccuracyMetric -from .confusion_matrix import SKLConfusionMatrix -from .f1_score import SKLF1ScoreMetric -from .mcc import SKLMCC -from .precision_recall import SKLPrecisionRecall -from .projection import SKLEmbeddingProjection -from .roc_auc_score import SKLROCAUCScore - -METRIC_REGISTRY.register(SKLPrecisionRecall) -METRIC_REGISTRY.register(SKLF1ScoreMetric) -METRIC_REGISTRY.register(SKLAccuracy) -METRIC_REGISTRY.register(SKLBalancedAccuracyMetric) -METRIC_REGISTRY.register(SKLEmbeddingProjection) -METRIC_REGISTRY.register(SKLMCC) -METRIC_REGISTRY.register(SKLROCAUCScore) -METRIC_REGISTRY.register(SKLConfusionMatrix) diff --git a/theseus/ml/metrics/acccuracy.py b/theseus/ml/metrics/acccuracy.py deleted file mode 100644 index 558f59e..0000000 --- a/theseus/ml/metrics/acccuracy.py +++ /dev/null @@ -1,60 +0,0 @@ -from typing import Any, Dict - -import numpy as np -from scipy.special import softmax -from sklearn.metrics import balanced_accuracy_score - -from theseus.base.metrics.metric_template import Metric - - -class SKLAccuracy(Metric): - """ - Accuracy metric - """ - - def __init__(self, **kwargs): - super().__init__(**kwargs) - - def value(self, output: Dict[str, Any], batch: Dict[str, Any]): - """ - Perform calculation based on prediction and targets - """ - output = output["outputs"] - target = batch["targets"] - - probs = softmax(output, axis=-1) - predictions = np.argmax(probs, axis=-1) - - correct = (predictions.reshape(-1) == target.reshape(-1)).sum() - score = correct * 1.0 / target.shape[0] - return {"acc": score} - - -def compute_multiclass(outputs, targets, index): - correct = 0 - sample_size = 0 - for i, j in zip(outputs, targets): - if j == index: - sample_size += 1 - if i == j: - correct += 1 - return correct, sample_size - - -class SKLBalancedAccuracyMetric(Metric): - """ - Balanced Accuracy metric for classification - """ - - def __init__(self, **kwargs): - super().__init__(**kwargs) - - def value(self, outputs: Dict[str, Any], batch: Dict[str, Any]): - - outputs = outputs["outputs"] - targets = batch["targets"] - predictions = np.argmax(outputs, axis=-1).reshape(-1).tolist() - targets = targets.reshape(-1).tolist() - blacc_score = balanced_accuracy_score(targets, predictions) - - return {"bl_acc": blacc_score} diff --git a/theseus/ml/metrics/confusion_matrix.py b/theseus/ml/metrics/confusion_matrix.py deleted file mode 100644 index bc1d769..0000000 --- a/theseus/ml/metrics/confusion_matrix.py +++ /dev/null @@ -1,98 +0,0 @@ -from typing import Any, Dict, List, Optional - -import matplotlib.pyplot as plt -import numpy as np -import seaborn as sns -from scipy.special import softmax -from sklearn.metrics import confusion_matrix, multilabel_confusion_matrix - -from theseus.base.metrics.metric_template import Metric - - -def plot_cfm(cm, ax, labels: List): - """ - Make confusion matrix figure - labels: `Optional[List]` - classnames for visualization - """ - - ax = sns.heatmap(cm, annot=False, fmt="", cmap="Blues", ax=ax) - - ax.set_xlabel("\nActual") - ax.set_ylabel("Predicted ") - - ax.xaxis.set_ticklabels(labels) - ax.yaxis.set_ticklabels(labels, rotation=0) - - -def make_cm_fig(cms, labels: Optional[List] = None): - - if cms.shape[0] > 1: # multilabel - num_classes = cms.shape[0] - else: - num_classes = cms.shape[1] - - ## Ticket labels - List must be in alphabetical order - if not labels: - labels = [str(i) for i in range(num_classes)] - - ## - num_cfms = cms.shape[0] - nrow = int(np.ceil(np.sqrt(num_cfms))) - - # Clear figures first to prevent memory-consuming - plt.cla() - plt.clf() - plt.close() - - fig, axes = plt.subplots(nrow, nrow, figsize=(8, 8)) - - if num_cfms > 1: - for ax, cfs_matrix, label in zip(axes.flatten(), cms, labels): - ax.set_title(f"{label}\n\n") - plot_cfm(cfs_matrix, ax, labels=["N", "Y"]) - else: - plot_cfm(cms[0], axes, labels=labels) - - fig.tight_layout() - return fig - - -class SKLConfusionMatrix(Metric): - """ - Confusion Matrix metric for classification - """ - - def __init__(self, classnames=None, label_type: str = "multiclass", **kwargs): - super().__init__(**kwargs) - self.type = label_type - self.classnames = classnames - self.num_classes = ( - [i for i in range(len(self.classnames))] if classnames is not None else None - ) - - def value(self, output: Dict[str, Any], batch: Dict[str, Any]): - """ - Perform calculation based on prediction and targets - """ - output = output["outputs"] - target = batch["targets"] - - probs = softmax(output, axis=-1) - predictions = np.argmax(probs, axis=-1) - - if self.type == "multiclass": - values = confusion_matrix( - predictions, - target, - labels=self.num_classes, - normalize="pred", - ) - values = values[np.newaxis, :, :] - else: - values = multilabel_confusion_matrix( - predictions, target, labels=self.num_classes - ) - - fig = make_cm_fig(values, self.classnames) - return {"cfm": fig} diff --git a/theseus/ml/metrics/f1_score.py b/theseus/ml/metrics/f1_score.py deleted file mode 100644 index 8301f7b..0000000 --- a/theseus/ml/metrics/f1_score.py +++ /dev/null @@ -1,29 +0,0 @@ -from typing import Any, Dict - -import numpy as np -from sklearn.metrics import f1_score - -from theseus.base.metrics.metric_template import Metric - - -class SKLF1ScoreMetric(Metric): - """ - F1 Score Metric (including macro, micro) - """ - - def __init__(self, average="weighted", **kwargs): - super().__init__(**kwargs) - self.average = average - - def value(self, outputs: Dict[str, Any], batch: Dict[str, Any]): - """ - Perform calculation based on prediction and targets - """ - targets = batch["targets"] - outputs = outputs["outputs"] - - self.preds = np.argmax(outputs, axis=1).reshape(-1).tolist() - self.targets = targets.reshape(-1).tolist() - - score = f1_score(self.targets, self.preds, average=self.average) - return {f"{self.average}-f1": score} diff --git a/theseus/ml/metrics/mcc.py b/theseus/ml/metrics/mcc.py deleted file mode 100644 index 21a15c9..0000000 --- a/theseus/ml/metrics/mcc.py +++ /dev/null @@ -1,28 +0,0 @@ -from typing import Any, Dict - -import numpy as np -from sklearn.metrics import matthews_corrcoef - -from theseus.base.metrics.metric_template import Metric - - -class SKLMCC(Metric): - """ - Mathew Correlation Coefficient - """ - - def __init__(self, **kwargs): - super().__init__(**kwargs) - - def value(self, outputs: Dict[str, Any], batch: Dict[str, Any]): - """ - Perform calculation based on prediction and targets - """ - targets = batch["targets"] - outputs = outputs["outputs"] - - self.preds = np.argmax(outputs, axis=1).reshape(-1).tolist() - self.targets = targets.reshape(-1).tolist() - - score = matthews_corrcoef(self.targets, self.preds) - return {f"mcc": score} diff --git a/theseus/ml/metrics/precision_recall.py b/theseus/ml/metrics/precision_recall.py deleted file mode 100644 index 1cf49b3..0000000 --- a/theseus/ml/metrics/precision_recall.py +++ /dev/null @@ -1,39 +0,0 @@ -from typing import Any, Dict - -import numpy as np -from sklearn.metrics import precision_score, recall_score - -from theseus.base.metrics.metric_template import Metric - - -class SKLPrecisionRecall(Metric): - """ - F1 Score Metric (including macro, micro) - """ - - def __init__(self, average="weighted", **kwargs): - super().__init__(**kwargs) - self.average = average - self.targets = [] - self.preds = [] - - def value(self, outputs: Dict[str, Any], batch: Dict[str, Any]): - """ - Perform calculation based on prediction and targets - """ - targets = batch["targets"] - outputs = outputs["outputs"] - - self.preds += np.argmax(outputs, axis=1).reshape(-1).tolist() - self.targets += targets.reshape(-1).tolist() - - precision = precision_score( - self.targets, self.preds, average=self.average, zero_division=1 - ) - recall = recall_score( - self.targets, self.preds, average=self.average, zero_division=1 - ) - return { - f"{self.average}-precision": precision, - f"{self.average}-recall": recall, - } diff --git a/theseus/ml/metrics/projection.py b/theseus/ml/metrics/projection.py deleted file mode 100644 index 1e2bc64..0000000 --- a/theseus/ml/metrics/projection.py +++ /dev/null @@ -1,67 +0,0 @@ -import os -from typing import Any, Dict - -import numpy as np -from scipy.special import softmax - -from theseus.base.metrics.metric_template import Metric -from theseus.base.utilities.loggers import LoggerObserver - -LOGGER = LoggerObserver.getLogger("main") - - -class SKLEmbeddingProjection(Metric): - """ - Visualize embedding project for classification - """ - - def __init__(self, classnames=None, save_dir=".cache", has_labels=True, **kwargs): - super().__init__(**kwargs) - self.has_labels = has_labels - self.save_dir = save_dir - self.classnames = classnames - os.makedirs(self.save_dir, exist_ok=True) - - def value(self, outputs: Dict[str, Any], batch: Dict[str, Any]): - """ - Perform calculation based on prediction and targets - """ - - embeddings = batch["inputs"] - targets = batch["targets"] - probs = softmax(outputs["outputs"], axis=-1) - predictions = np.argmax(probs, axis=-1) - - ## Metadata, in column style - if self.has_labels: - if self.classnames is not None: - metadata = [ - (self.classnames[int(a)], self.classnames[int(b)]) - for a, b in zip(targets, predictions) - ] - else: - metadata = [a for a in zip(targets, predictions)] - metadata_header = ["ground truth", "prediction"] - else: - if self.classnames is not None: - metadata = [[self.classnames[int(a)] for a in predictions]] - else: - metadata = [predictions] - metadata_header = ["prediction"] - - LOGGER.log( - [ - { - "tag": f"Projection", - "value": embeddings, - "type": LoggerObserver.EMBED, - "kwargs": { - "step": 0, - "metadata": metadata, - "metadata_header": metadata_header, - }, - } - ] - ) - - return {"projection": "Embedding projection generated"} diff --git a/theseus/ml/metrics/roc_auc_score.py b/theseus/ml/metrics/roc_auc_score.py deleted file mode 100644 index 17b511b..0000000 --- a/theseus/ml/metrics/roc_auc_score.py +++ /dev/null @@ -1,69 +0,0 @@ -from typing import Any, Dict - -import numpy as np -import scipy - -from theseus.base.metrics.metric_template import Metric - -try: - from scikitplot.metrics import plot_precision_recall_curve, plot_roc_curve - - has_scikitplot = True -except: - has_scikitplot = False -from sklearn.metrics import roc_auc_score - - -class SKLROCAUCScore(Metric): - """ - ROC AUC Score - """ - - def __init__( - self, - average: str = "weighted", - label_type: str = "ovr", - plot_curve: bool = True, - **kwargs, - ): - super().__init__(**kwargs) - self.plot_curve = plot_curve - self.label_type = label_type - self.average = average - assert self.label_type in [ - "raise", - "ovr", - "ovo", - ], "Invalid type for multiclass ROC AUC score" - - def value(self, outputs: Dict[str, Any], batch: Dict[str, Any]): - """ - Perform calculation based on prediction and targets - """ - targets = batch["targets"] - outputs = outputs["outputs"] - - if self.label_type == "ovr": - outputs = scipy.special.softmax(outputs, axis=-1) - - self.preds = outputs.tolist() - self.targets = targets.reshape(-1).tolist() - - roc_auc_scr = roc_auc_score( - self.targets, self.preds, average=self.average, multi_class=self.label_type - ) - results = { - f"{self.average}-roc_auc_score": roc_auc_scr, - } - - if has_scikitplot and self.plot_curve: - roc_curve_fig = plot_roc_curve(self.targets, self.preds).get_figure() - pr_fig = plot_precision_recall_curve(self.targets, self.preds).get_figure() - results.update( - { - "roc_curve": roc_curve_fig, - "precision_recall_curve": pr_fig, - } - ) - - return results diff --git a/theseus/ml/models/__init__.py b/theseus/ml/models/__init__.py deleted file mode 100644 index 0d56831..0000000 --- a/theseus/ml/models/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -from theseus.base.models import MODEL_REGISTRY - -from .gbms import GBClassifiers - -MODEL_REGISTRY.register(GBClassifiers) diff --git a/theseus/ml/models/gbms.py b/theseus/ml/models/gbms.py deleted file mode 100644 index 6c09ff9..0000000 --- a/theseus/ml/models/gbms.py +++ /dev/null @@ -1,70 +0,0 @@ -import catboost as cb -import lightgbm as lgb -import xgboost as xgb -from omegaconf import DictConfig, OmegaConf - -from theseus.base.utilities.loggers.observer import LoggerObserver - -LOGGER = LoggerObserver.getLogger("main") - - -class GBClassifiers: - def __init__( - self, - model_name, - num_classes, - model_config: DictConfig = {}, - training_params={}, - **kwargs, - ): - OmegaConf.set_struct(model_config, False) - self.training_params = training_params - self.model_name = model_name - self.num_classes = num_classes - if model_name == "catboost": - self.model = cb.CatBoostClassifier(**model_config) - elif model_name == "lightgbm": - model_config.update({"num_class": num_classes}) - self.model = lgb.LGBMClassifier(**model_config) - elif model_name == "xgboost": - model_config.update({"num_class": num_classes}) - self.model = xgb.XGBClassifier(**model_config) - else: - LOGGER.text("Model not supported", level=LoggerObserver.ERROR) - - def get_model(self): - return self.model - - def fit(self, trainset, valset, **kwargs): - X, y = trainset - self.model.fit( - X.copy(), - y.copy(), - eval_set=[trainset, valset], - # eval_set=[(trainset, 'train'), (valset, 'validation')], - **self.training_params, - ) - - def save_model(self, savepath): - if self.model_name == "xgboost": - self.model.save_model(savepath) - elif self.model_name == "lightgbm": - # LightGBM models should be saved as .txt files - self.model.booster_.save_model(savepath) - elif self.model_name == "xgboost": - self.model.save(savepath) - - LOGGER.text(f"Model saved at {savepath}", level=LoggerObserver.INFO) - - def load_model(self, checkpoint_path): - self.model.load_model(checkpoint_path) - LOGGER.text( - f"Loaded checkpoint at {checkpoint_path}", - level=LoggerObserver.INFO, - ) - - def predict(self, X, return_probs=False): - if return_probs: - return self.model.predict_proba(X) - else: - return self.model.predict(X) diff --git a/theseus/ml/pipeline.py b/theseus/ml/pipeline.py deleted file mode 100644 index 6ea1b63..0000000 --- a/theseus/ml/pipeline.py +++ /dev/null @@ -1,191 +0,0 @@ -import os -from datetime import datetime - -from omegaconf import DictConfig, OmegaConf - -from theseus.base.utilities.folder import get_new_folder_name -from theseus.base.utilities.getter import get_instance, get_instance_recursively -from theseus.base.utilities.loggers import FileLogger, ImageWriter, LoggerObserver -from theseus.base.utilities.seed import seed_everything -from theseus.ml.callbacks import CALLBACKS_REGISTRY -from theseus.ml.datasets import DATALOADER_REGISTRY, DATASET_REGISTRY -from theseus.ml.metrics import METRIC_REGISTRY -from theseus.ml.models import MODEL_REGISTRY -from theseus.ml.preprocessors import TRANSFORM_REGISTRY -from theseus.ml.trainer import TRAINER_REGISTRY - - -class MLPipeline(object): - """docstring for Pipeline.""" - - def __init__(self, opt: DictConfig): - self.opt = opt - self.seed = self.opt["global"].get("seed", 1702) - seed_everything(self.seed) - self.initialized = False - - def init_globals(self): - # Main Loggers - self.logger = LoggerObserver.getLogger("main") - - # Global variables - self.exp_name = self.opt["global"].get("exp_name", None) - self.exist_ok = self.opt["global"].get("exist_ok", False) - self.debug = self.opt["global"].get("debug", False) - self.resume = self.opt["global"].get("resume", None) - self.pretrained = self.opt["global"].get("pretrained", None) - self.transform_cfg = self.opt["global"].get("cfg_transform", None) - - # Experiment name - if self.exp_name: - self.savedir = os.path.join( - self.opt["global"].get("save_dir", "runs"), self.exp_name - ) - if not self.exist_ok: - self.savedir = get_new_folder_name(self.savedir) - else: - self.savedir = os.path.join( - self.opt["global"].get("save_dir", "runs"), - datetime.now().strftime("%Y-%m-%d_%H-%M-%S"), - ) - os.makedirs(self.savedir, exist_ok=True) - - # Logging to files - file_logger = FileLogger(__name__, self.savedir, debug=self.debug) - self.logger.subscribe(file_logger) - - # Logging images - image_logger = ImageWriter(self.savedir) - self.logger.subscribe(image_logger) - - self.transform_cfg = self.opt.get("augmentations", None) - - # Logging out configs - self.logger.text("\n" + OmegaConf.to_yaml(self.opt), level=LoggerObserver.INFO) - self.logger.text( - f"Everything will be saved to {self.savedir}", - level=LoggerObserver.INFO, - ) - - def init_registry(self): - self.callbacks_registry = CALLBACKS_REGISTRY - self.transform_registry = TRANSFORM_REGISTRY - self.model_registry = MODEL_REGISTRY - self.metric_registry = METRIC_REGISTRY - self.trainer_registry = TRAINER_REGISTRY - self.dataset_registry = DATASET_REGISTRY - self.dataloader_registry = DATALOADER_REGISTRY - self.logger.text("Overidding registry in pipeline...", LoggerObserver.INFO) - - def init_model(self): - classnames = self.val_dataset["classnames"] - num_classes = len(classnames) - self.model = get_instance( - self.opt["model"], num_classes=num_classes, registry=self.model_registry - ) - - def init_train_dataloader(self): - self.transform = get_instance_recursively( - self.transform_cfg, registry=self.transform_registry - ) - self.train_dataset = get_instance_recursively( - self.opt["data"]["dataset"]["train"], - registry=self.dataset_registry, - transform=self.transform["train"], - ).load_data() - - self.logger.text( - f"Training shape: {self.train_dataset['inputs'].shape}", - level=LoggerObserver.INFO, - ) - - def init_metrics(self): - CLASSNAMES = getattr(self.val_dataset, "classnames", None) - self.metrics = get_instance_recursively( - self.opt["metrics"], - registry=self.metric_registry, - num_classes=len(CLASSNAMES) if CLASSNAMES is not None else None, - classnames=CLASSNAMES, - ) - - def init_callbacks(self): - callbacks = get_instance_recursively( - self.opt["callbacks"], - save_dir=getattr(self, "savedir", "runs"), - resume=getattr(self, "resume", None), - config_dict=self.opt, - registry=self.callbacks_registry, - ) - return callbacks - - def init_validation_dataloader(self): - self.transform = get_instance_recursively( - self.transform_cfg, registry=self.transform_registry - ) - self.val_dataset = get_instance_recursively( - self.opt["data"]["dataset"]["val"], - registry=self.dataset_registry, - transform=self.transform["val"], - ).load_data() - - classnames = self.val_dataset["classnames"] - num_classes = len(classnames) - - self.logger.text( - f"Validation shape: {self.val_dataset['inputs'].shape}", - level=LoggerObserver.INFO, - ) - self.logger.text( - f"Number of classes: {num_classes}", - level=LoggerObserver.INFO, - ) - - def init_trainer(self, callbacks=None): - self.trainer = get_instance( - self.opt["trainer"], - model=self.model, - trainset=getattr(self, "train_dataset", None), - valset=getattr(self, "val_dataset", None), - metrics=self.metrics, - callbacks=callbacks, - registry=self.trainer_registry, - ) - - def init_loading(self): - if getattr(self, "pretrained", None): - self.model.load_model(self.pretrained) - - def init_pipeline(self, train=False): - if self.initialized: - return - self.init_globals() - self.init_registry() - if train: - self.init_train_dataloader() - self.init_validation_dataloader() - self.init_model() - self.init_loading() - self.init_metrics() - callbacks = self.init_callbacks() - self.save_configs() - else: - self.init_validation_dataloader() - self.init_model() - self.init_metrics() - self.init_loading() - callbacks = [] - - self.init_trainer(callbacks=callbacks) - self.initialized = True - - def save_configs(self): - with open(os.path.join(self.savedir, "pipeline.yaml"), "w") as f: - OmegaConf.save(config=self.opt, f=f) - - def fit(self): - self.init_pipeline(train=True) - self.trainer.fit() - - def evaluate(self): - self.init_pipeline(train=False) - return self.trainer.validate() diff --git a/theseus/ml/preprocessors/aggregation.py b/theseus/ml/preprocessors/aggregation.py index b125ca4..17abf72 100644 --- a/theseus/ml/preprocessors/aggregation.py +++ b/theseus/ml/preprocessors/aggregation.py @@ -32,14 +32,10 @@ def run(self, df): if method_name == "subtract": df[target_name] = df[based_columns].sub(axis=1) if method_name == "concat": - df[target_name] = ( - df[based_columns].astype(str).agg(" ".join, axis=1) - ) + df[target_name] = df[based_columns].astype(str).agg(" ".join, axis=1) elif callable(method_name): - df[target_name] = self.apply( - df[based_columns], function=method_name, axis=1 - ) + df[target_name] = self.apply(df[based_columns], function=method_name, axis=1) else: LOGGER.text( "Unsuppported aggregation method", diff --git a/theseus/ml/preprocessors/base.py b/theseus/ml/preprocessors/base.py index e148c83..96d61ea 100644 --- a/theseus/ml/preprocessors/base.py +++ b/theseus/ml/preprocessors/base.py @@ -22,17 +22,13 @@ class Preprocessor: - def __init__( - self, column_names=None, exclude_columns=None, verbose=False, **kwargs - ): + def __init__(self, column_names=None, exclude_columns=None, verbose=False, **kwargs): self.verbose = verbose self.column_names = column_names self.filter = None if column_names is not None: - self.filter = FilterColumnNames( - patterns=column_names, excludes=exclude_columns - ) + self.filter = FilterColumnNames(patterns=column_names, excludes=exclude_columns) def apply(self, df, function, parallel=True, axis=0, show_progress=True): diff --git a/theseus/ml/preprocessors/compose.py b/theseus/ml/preprocessors/compose.py index 9f42b85..a5c0687 100644 --- a/theseus/ml/preprocessors/compose.py +++ b/theseus/ml/preprocessors/compose.py @@ -1,10 +1,9 @@ -from typing import List from .base import Preprocessor class PreprocessCompose(Preprocessor): - def __init__(self, preproc_list: List[Preprocessor], **kwargs): + def __init__(self, preproc_list: list[Preprocessor], **kwargs): self.preproc_list = preproc_list def run(self, df): diff --git a/theseus/ml/preprocessors/drop_col.py b/theseus/ml/preprocessors/drop_col.py index 1e2f351..3d8617d 100644 --- a/theseus/ml/preprocessors/drop_col.py +++ b/theseus/ml/preprocessors/drop_col.py @@ -46,9 +46,7 @@ def __init__(self, **kwargs): super().__init__(**kwargs) def run(self, df): - cols_to_use = [ - idx for idx, val in (df.isna().mean() >= 1.0).items() if val == False - ] + cols_to_use = [idx for idx, val in (df.isna().mean() >= 1.0).items() if not val] empty_cols = set(df.columns) - set(cols_to_use) df = df.loc[:, cols_to_use] self.log(f"Dropped empty columns: {empty_cols}") diff --git a/theseus/ml/preprocessors/encoder.py b/theseus/ml/preprocessors/encoder.py index db43ba3..8194d59 100644 --- a/theseus/ml/preprocessors/encoder.py +++ b/theseus/ml/preprocessors/encoder.py @@ -12,9 +12,7 @@ class LabelEncode(Preprocessor): - def __init__( - self, encoder_type="le", pickle_path=None, engine: str = "pandas", **kwargs - ): + def __init__(self, encoder_type="le", pickle_path=None, engine: str = "pandas", **kwargs): super().__init__(**kwargs) assert encoder_type in [ @@ -27,7 +25,7 @@ def __init__( self.pickle_path = pickle_path self.engine = engine if self.engine == "polars": - import polars as pl + pass if self.pickle_path is not None: with open(self.pickle_path, "rb") as fb: @@ -36,18 +34,16 @@ def __init__( self.encoder_type = config["encoder_type"] self.engine = config["engine"] self.encoders = config["encoders"] - self.log(f"Loaded mapping dict from {self.pickle_path}") else: self.encoders = {} - if self.encoder_type == "le": - encoder = LabelEncoder() - elif self.encoder_type == "onehot": - encoder = OneHotEncoder() - else: - encoder = OrdinalEncoder() - - for column in self.column_names: - self.encoders[column] = encoder + if self.column_names is not None: + for column in self.column_names: + if self.encoder_type == "le": + self.encoders[column] = LabelEncoder() + elif self.encoder_type == "onehot": + self.encoders[column] = OneHotEncoder() + else: + self.encoders[column] = OrdinalEncoder() @classmethod def from_pickle(cls, pickle_path: str): @@ -93,6 +89,7 @@ def encode_corpus(self, df): df[column_name] = encoder.fit_transform(df[column_name].values).copy() elif self.engine == "polars": import polars as pl + encoder.fit_transform(df.select(column_name).unique().to_numpy().ravel()) le_name_mapping = dict( zip( @@ -138,6 +135,16 @@ def run(self, df): level=LoggerObserver.WARN, ) self.column_names = [col for col, dt in df.dtypes.items() if dt == object] + + for column in self.column_names: + if column not in self.encoders: + if self.encoder_type == "le": + self.encoders[column] = LabelEncoder() + elif self.encoder_type == "onehot": + self.encoders[column] = OneHotEncoder() + else: + self.encoders[column] = OrdinalEncoder() + df = self.encode_corpus(df) self.log(f"Label-encoded columns: {self.column_names}") diff --git a/theseus/ml/preprocessors/splitter.py b/theseus/ml/preprocessors/splitter.py index 3a45a30..16f5a96 100644 --- a/theseus/ml/preprocessors/splitter.py +++ b/theseus/ml/preprocessors/splitter.py @@ -46,9 +46,7 @@ def __init__( elif self.splitter_type == "stratifiedkfold": assert label_column is not None, "Label column should be specified" assert n_splits is not None, "number of splits should be specified" - self.splitter = StratifiedKFold( - n_splits=n_splits, random_state=self.seed, shuffle=True - ) + self.splitter = StratifiedKFold(n_splits=n_splits, random_state=self.seed, shuffle=True) elif self.splitter_type == "default": assert ratio is not None, "should specify ratio" self.ratio = ratio @@ -76,9 +74,7 @@ def run(self, df): elif self.splitter_type == "unique": unique_values = df[self.label_column].unique().tolist() num_unique_samples = len(unique_values) - train_idx = self.splitter( - unique_values, int(num_unique_samples * self.ratio) - ) + train_idx = self.splitter(unique_values, int(num_unique_samples * self.ratio)) train_df = df[df[self.label_column].isin(train_idx)] val_df = df[~df[self.label_column].isin(train_idx)] train_df.to_csv(osp.join(self.save_folder, "train.csv"), index=False) diff --git a/theseus/ml/tradml.py b/theseus/ml/tradml.py new file mode 100644 index 0000000..b924ae8 --- /dev/null +++ b/theseus/ml/tradml.py @@ -0,0 +1,875 @@ +import json +import os +import os.path as osp + +import lightgbm +import numpy as np +import optuna +import wandb +import xgboost as xgb +from optuna.integration.wandb import WeightsAndBiasesCallback +from optuna.storages import JournalFileStorage, JournalStorage +from optuna.visualization import ( + plot_contour, + plot_edf, + plot_intermediate_values, + plot_optimization_history, + plot_parallel_coordinate, + plot_param_importances, + plot_slice, +) +from sklearn.metrics import ( + accuracy_score, + f1_score, + matthews_corrcoef, + precision_score, + recall_score, +) + +from theseus import LoggerObserver +from theseus.ml.visualize import visualize_shap + +LOGGER = LoggerObserver.getLogger("main") + +# wandb might cause an error without this. +os.environ["WANDB_START_METHOD"] = "thread" + +__all__ = [ + "fit_xgboost", + "fit_catboost", + "fit_lightgbm", + "fit_rf", + "fit_svm", + "fit_logistics", + "fit_adaboost", + "fit_knn", + "fit_mlp", + "objective", + "TradMLTuner", +] + + +def fit_xgboost(params, X_train, X_val, y_train, y_val, is_classification=True): + if is_classification: + num_classes = len(np.unique(y_train)) + objective_fn = "multi:softprob" if num_classes > 2 else "binary:logistic" + params.update( + {"eval_metric": ["auc"], "objective": objective_fn, "early_stopping_rounds": 100} + ) + model = xgb.XGBClassifier(**params) + else: + params.update( + { + "eval_metric": ["rmse"], + "objective": "reg:squarederror", + } + ) + model = xgb.XGBRegressor(**params) + model.fit(X_train, y_train, eval_set=[(X_val, y_val)], verbose=True) + return model, params + + +def fit_catboost( + params, X_train, X_val, y_train, y_val, is_classification: bool = True, cat_features=None +): + from catboost import CatBoostClassifier, CatBoostRegressor + + params.update( + { + "verbose": 100, + } + ) + if not is_classification: + params.update( + { + "loss_function": "RMSE", + "eval_metric": "RMSE", + } + ) + clf = CatBoostRegressor(**params) + else: + clf = CatBoostClassifier(**params) + + clf.fit( + X_train, y_train, eval_set=[(X_val, y_val)], cat_features=None, early_stopping_rounds=50 + ) + return clf, params + + +def fit_lightgbm( + params, X_train, X_val, y_train, y_val, is_classification: bool = True, cat_features=None +): + from lightgbm import LGBMClassifier, LGBMRegressor + + params.update({"verbose": 100}) + + if not is_classification: + params.update( + { + "objective": "regression", + "metric": "rmse", + } + ) + clf = LGBMRegressor(**params) + else: + clf = LGBMClassifier(**params) + + clf.fit( + X_train, + y_train, + eval_set=[(X_val, y_val)], + categorical_feature=cat_features, + callbacks=[ + lightgbm.early_stopping(stopping_rounds=50, verbose=False), + lightgbm.log_evaluation(period=2000), + ], + ) + return clf, params + + +def fit_rf(params, X_train, X_val, y_train, y_val, is_classification: bool = True): + from sklearn.ensemble import RandomForestClassifier, RandomForestRegressor + + params.update({"verbose": 1}) + if not is_classification: + params.update({"n_jobs": -1, "criterion": "squared_error"}) + clf = RandomForestRegressor(**params) + else: + clf = RandomForestClassifier(**params) + clf.fit(np.concatenate([X_train, X_val], axis=0), np.concatenate([y_train, y_val], axis=0)) + return clf, params + + +def fit_svm(params, X_train, X_val, y_train, y_val): + from sklearn.svm import SVC + + params.update({"kernel": "linear", "probability": True, "verbose": True}) + clf = SVC(**params) + clf.fit(np.concatenate([X_train, X_val], axis=0), np.concatenate([y_train, y_val], axis=0)) + return clf, params + + +def fit_logistics(params, X_train, X_val, y_train, y_val, is_classification=True): + from sklearn.linear_model import LinearRegression, LogisticRegression + + if is_classification: + params.update( + { + "verbose": 1, + "penalty": "l2", + } + ) + clf = LogisticRegression(**params) + else: + params.pop("C", None) + clf = LinearRegression(**params) + clf.fit(np.concatenate([X_train, X_val], axis=0), np.concatenate([y_train, y_val], axis=0)) + return clf, params + + +def fit_adaboost(params, X_train, X_val, y_train, y_val): + from sklearn.ensemble import AdaBoostClassifier + + params.update({"random_state": 0}) + clf = AdaBoostClassifier(**params) + clf.fit(np.concatenate([X_train, X_val], axis=0), np.concatenate([y_train, y_val], axis=0)) + return clf, params + + +def fit_knn(params, X_train, X_val, y_train, y_val, is_classification=True, weight_fn=None): + from scipy.spatial import distance + from sklearn.neighbors import KNeighborsClassifier, KNeighborsRegressor + + if weight_fn is not None: + + def my_weight_fn(x, y): + return distance.minkowski(x, y, p=2, w=weight_fn) + + params.update(dict(metric=my_weight_fn)) + + if is_classification: + # from ehrret import get_retrieval_weight + # def my_distance(weights): + # weights = get_retrieval_weight('feattype', 'eicu', 'READMISSION', feature_names=feature_names) + # return weights + clf = KNeighborsClassifier(**params) + else: + clf = KNeighborsRegressor(**params) + clf.fit(np.concatenate([X_train, X_val], axis=0), np.concatenate([y_train, y_val], axis=0)) + return clf, params + + +def fit_mlp(params, X_train, X_val, y_train, y_val, is_classification=True): + from sklearn.neural_network import MLPClassifier, MLPRegressor + + hidden_layer_sizes = params.pop("type", "2-layer") + if hidden_layer_sizes == "2-layer": + params["hidden_layer_sizes"] = (X_train.shape[1], 64) + elif hidden_layer_sizes == "3-layer": + params["hidden_layer_sizes"] = (X_train.shape[1], 128, 64) + + params.update( + { + "early_stopping": True, + "validation_fraction": 0.2, + } + ) + if is_classification: + clf = MLPClassifier(**params) + else: + clf = MLPRegressor(**params) + + clf.fit(np.concatenate([X_train, X_val], axis=0), np.concatenate([y_train, y_val], axis=0)) + return clf, params + + +def objective( + trial, + X_train, + X_val, + y_train, + y_val, + is_classification=True, + method="xgboost", + cat_features=None, + extra_params: dict | None = None, +): + if extra_params is None: + extra_params = {} + if wandb.run is not None: + wandb.run.config.update( + { + "MODEL": { + "MODEL_NAME": method, + }, + "MODEL_NAME": method, + "FOLD": os.environ.get("FOLD", None), + "TASK_NAME": os.environ.get("TASK_NAME", None), + } + ) + + len(np.unique(y_train)) + + assert method in [ + "xgboost", + "rf", + "svm", + "logistics", + "adaboost", + "catboost", + "lightgbm", + "knn", + "mlp", + ], f"{method} is not supported" + + if method == "xgboost": + model, params = fit_xgboost( + { + "n_estimators": trial.suggest_int( + "n_estimators", 100, 300 + ), # The number of sequential trees to be modeled + "max_depth": trial.suggest_int( + "max_depth", 1, 9 + ), # The maximum depth of a tree.higher depth will allow model to learn relations very specific to a particular sample. Should be tuned + "learning_rate": trial.suggest_float( + "learning_rate", 0.001, 1.0 + ), # impact of each tree on the final outcome + "gamma": trial.suggest_float( + "gamma", 0.001, 1.0 + ), # This will anyways be tuned later. + "reg_alpha": trial.suggest_float( + "reg_alpha", 0.001, 1.0 + ), # This will anyways be tuned later. + "reg_lambda": trial.suggest_float( + "reg_lambda", 0.001, 1.0 + ), # This will anyways be tuned later. + }, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + + elif method == "catboost": + model, params = fit_catboost( + { + "iterations": trial.suggest_int("iterations", 100, 300), + "depth": trial.suggest_int("depth", 1, 9), + "learning_rate": trial.suggest_float("learning_rate", 0.001, 1.0), + "l2_leaf_reg": trial.suggest_float("l2_leaf_reg", 0.001, 1.0), + }, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + cat_features=cat_features, + ) + + elif method == "lightgbm": + model, params = fit_lightgbm( + { + "n_estimators": trial.suggest_int( + "n_estimators", 100, 300 + ), # The number of sequential trees to be modeled + "max_depth": trial.suggest_int( + "max_depth", 1, 9 + ), # The maximum depth of a tree.higher depth will allow model to learn relations very specific to a particular sample. Should be tuned + "learning_rate": trial.suggest_float( + "learning_rate", 0.001, 1.0 + ), # impact of each tree on the final outcome + "reg_alpha": trial.suggest_float( + "reg_alpha", 0.001, 1.0 + ), # This will anyways be tuned later. + "reg_lambda": trial.suggest_float( + "reg_lambda", 0.001, 1.0 + ), # This will anyways be tuned later. + }, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + cat_features=cat_features, + ) + + elif method == "rf": + model, params = fit_rf( + { + "n_estimators": trial.suggest_int( + "n_estimators", 100, 300 + ), # The number of sequential trees to be modeled + "max_depth": trial.suggest_int( + "max_depth", 1, 9 + ), # The maximum depth of a tree.higher depth will allow model to learn relations very specific to a particular sample. Should be tuned + # 'criterion': trial.suggest_categorical("criterion", ["gini", "log_loss", "entropy"]), + "min_samples_split": trial.suggest_int("min_samples_split", 10, 30), + "min_samples_leaf": trial.suggest_int("min_samples_leaf", 3, 10), + }, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + + elif method == "svm": + model, params = fit_svm( + { + "gamma": trial.suggest_float("gamma", 0.001, 1.0), + "C": trial.suggest_float("C", 0.001, 1.0), + }, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + + elif method == "logistics": + model, params = fit_logistics( + { + "C": trial.suggest_float("C", 0.001, 1.0), + }, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + + elif method == "adaboost": + model, params = fit_adaboost( + { + "n_estimators": trial.suggest_int( + "n_estimators", 100, 300 + ), # The number of sequential trees to be modeled + "learning_rate": trial.suggest_float( + "learning_rate", 0.001, 1.0 + ), # impact of each tree on the final outcome + }, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + + elif method == "knn": + model, params = fit_knn( + { + "n_neighbors": trial.suggest_int("n_neighbors", 3, 20), + "weights": trial.suggest_categorical("weights", ["uniform", "distance"]), + "p": trial.suggest_int("p", 1, 2), # 1=manhattan, 2=euclidean + }, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + weight_fn=extra_params.get("weight_fn"), + ) + + elif method == "mlp": + model, params = fit_mlp( + { + "type": trial.suggest_categorical("type", ["2-layer", "3-layer"]), + "activation": trial.suggest_categorical("activation", ["relu", "tanh"]), + "solver": trial.suggest_categorical("solver", ["adam", "sgd"]), + "alpha": trial.suggest_float("alpha", 1e-5, 1e-1, log=True), + "learning_rate": trial.suggest_categorical( + "learning_rate", ["constant", "adaptive"] + ), + }, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + + else: + raise NotImplementedError() + + # Validate the model + if is_classification: + preds = model.predict_proba(X_val) + pred_labels = np.argmax(preds, axis=1) + else: + preds = model.predict(X_val) + pred_labels = preds + + if wandb.run is not None: + wandb.run.config.update(params) + + # Evaluate the model + if not is_classification: + rmse = np.sqrt(np.mean((y_val - pred_labels) ** 2)) + # Log the metrics to wandb + if wandb.run is not None: + wandb.run.log( + { + "Validation/RMSE": rmse, + } + ) + return float(rmse) + else: + # is_binary = len(np.unique(y_val)) == 2 + # if is_binary: + # f1score = f1_score(y_val, pred_labels, average='binary', pos_label=1) + # precision = precision_score(y_val, pred_labels, average='binary', pos_label=1) + # recall = recall_score(y_val, pred_labels, average='binary', pos_label=1) + # else: + f1score = f1_score(y_val, pred_labels, average="macro") + precision = precision_score(y_val, pred_labels, average="macro") + recall = recall_score(y_val, pred_labels, average="macro") + mcc_score = matthews_corrcoef(y_val, pred_labels) + accuracy = accuracy_score(y_val, pred_labels) + + # Log the metrics to wandb + if wandb.run is not None: + wandb.run.log( + { + "Validation/Accuracy": accuracy, + "Validation/F1": f1score, + "Validation/MCC": mcc_score, + "Validation/Precision": precision, + "Validation/Recall": recall, + } + ) + return float(f1score) + + +class TradMLTuner: + def __init__( + self, + storage: str = None, + study_name: str = None, + n_trials: int = 100, + direction: str = "maximize", + pruner=None, + sampler=None, + save_dir: str = None, + method: str = "xgboost", + use_best_params: bool = False, + wandb_kwargs: dict | None = None, + **kwargs, + ) -> None: + self.storage = None + if storage is not None and storage.endswith(".log"): + self.storage = JournalStorage(JournalFileStorage(storage)) + + self.save_dir = save_dir + self.study_name = study_name + self.n_trials = n_trials + self.direction = direction + self.pruner = pruner + self.sampler = sampler + self.save_dir = save_dir + self.method = method + self.use_best_params = use_best_params + self.feature_names = kwargs.get("feature_names") + self.classnames = kwargs.get("classnames") + if save_dir is not None: + os.makedirs(save_dir, exist_ok=True) + + self.study = optuna.create_study( + study_name=study_name, + direction=direction, + storage=self.storage, + load_if_exists=True, + pruner=pruner, + sampler=sampler, + ) + + if wandb_kwargs is not None: + # Initialise wandb callback + self.wandb_kwargs = { + "entity": wandb_kwargs.get("entity", "kaylode"), + "project": wandb_kwargs.get("project", "tabpfn-ehr"), + "reinit": True, + "group": "tabpfn-ehr-optuna", + "job_type": "optuna", + "tags": [self.method, "optuna"] + wandb_kwargs.get("tags", []), + "resume": "allow", + "name": f"{self.method}", + "dir": self.save_dir, + } + self.WANDB_CALLBACK = WeightsAndBiasesCallback( + metric_name="Validation/F1", wandb_kwargs=self.wandb_kwargs, as_multirun=True + ) + else: + self.wandb_kwargs = None + self.WANDB_CALLBACK = None + + def tune( + self, + X_train, + X_val, + y_train, + y_val, + is_classification: bool = True, + cat_features=None, + extra_params: dict | None = None, + ): + if extra_params is None: + extra_params = {} + def wrapped_objective(trial): + return objective( + trial, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + method=self.method, + cat_features=cat_features, + extra_params=extra_params, + ) + + callbacks = None + if self.WANDB_CALLBACK is not None: + decorator = self.WANDB_CALLBACK.track_in_wandb() + wrapped_objective = decorator(wrapped_objective) + callbacks = [] + callbacks.append(self.WANDB_CALLBACK) + + if not self.use_best_params: + try: + self.study.optimize(wrapped_objective, n_trials=self.n_trials, callbacks=callbacks) + except KeyboardInterrupt: + LOGGER.text("KeyboardInterrupt", level=LoggerObserver.ERROR) + best_trial = self.study.best_trial + self.save_best_config(best_trial.params) + + if self.wandb_kwargs is not None: + wandb_kwargs = { + "name": f"{self.method}", + "entity": self.wandb_kwargs.get("entity", "kaylode"), + "project": self.wandb_kwargs.get("project", "tabpfn-ehr"), + "reinit": True, + "group": "tabpfn-ehr-finetune", + "job_type": "train", + "tags": list( + set([self.method, "optuna", "best"] + self.wandb_kwargs.get("tags", [])) + ), + "resume": "allow", + "dir": self.save_dir, + } + wandb.init(**wandb_kwargs) + + if self.save_dir is not None: + leaderboard_df = self.leaderboard() + leaderboard_df.to_csv(osp.join(self.save_dir, "leaderboard.csv")) + leaderboard_df.to_json(osp.join(self.save_dir, "leaderboard.json"), orient="records") + LOGGER.text( + f"Leaderboard saved to {self.save_dir}/leaderboard.csv", level=LoggerObserver.INFO + ) + figs = self.visualize("all") + os.makedirs(osp.join(self.save_dir, "figures"), exist_ok=True) + for fig_name, fig in figs: + try: + fig.write_image(osp.join(self.save_dir, "figures", f"{fig_name}.png")) + LOGGER.text( + f"{fig_name} plot saved to {self.save_dir}/{fig_name}.png", + level=LoggerObserver.INFO, + ) + except Exception: + pass + + # Log the best trial to wandb + if self.wandb_kwargs is not None: + wandb.run.config.update( + { + "MODEL": { + "MODEL_NAME": self.method, + }, + "MODEL_NAME": self.method, + "FOLD": os.environ.get("FOLD", None), + "TASK_NAME": os.environ.get("TASK_NAME", None), + } + ) + + if self.method == "xgboost": + best_model, params = fit_xgboost( + best_trial.params, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + elif self.method == "catboost": + best_model, params = fit_catboost( + best_trial.params, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + elif self.method == "lightgbm": + best_model, params = fit_lightgbm( + best_trial.params, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + elif self.method == "rf": + best_model, params = fit_rf( + best_trial.params, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + elif self.method == "svm": + best_model, params = fit_svm( + best_trial.params, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + elif self.method == "logistics": + best_model, params = fit_logistics( + best_trial.params, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + elif self.method == "adaboost": + best_model, params = fit_adaboost( + best_trial.params, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + elif self.method == "knn": + best_model, params = fit_knn( + best_trial.params, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + weight_fn=extra_params.get("weight_fn"), + ) + elif self.method == "mlp": + best_model, params = fit_mlp( + best_trial.params, + X_train, + X_val, + y_train, + y_val, + is_classification=is_classification, + ) + else: + raise NotImplementedError() + + if self.wandb_kwargs is not None: + wandb.run.config.update(params) + + # Evaluate the model + if not is_classification: + preds = best_model.predict(X_val) + pred_labels = preds + else: + preds = best_model.predict_proba(X_val) + pred_labels = np.argmax(preds, axis=1) + + if is_classification: + # is_binary = len(np.unique(y_val)) == 2 + # if is_binary: + # f1score = f1_score(y_val, pred_labels, average='binary', pos_label=1) + # precision = precision_score(y_val, pred_labels, average='binary', pos_label=1) + # recall = recall_score(y_val, pred_labels, average='binary', pos_label=1) + # else: + f1score = f1_score(y_val, pred_labels, average="macro") + precision = precision_score(y_val, pred_labels, average="macro") + recall = recall_score(y_val, pred_labels, average="macro") + mcc_score = matthews_corrcoef(y_val, pred_labels) + accuracy = accuracy_score(y_val, pred_labels) + # Log the metrics to wandb + if self.wandb_kwargs is not None: + wandb.run.log( + { + "Validation/Accuracy": accuracy, + "Validation/F1": f1score, + "Validation/MCC": mcc_score, + "Validation/Precision": precision, + "Validation/Recall": recall, + } + ) + else: + rmse = np.sqrt(np.mean((y_val - pred_labels) ** 2)) + # Log the metrics to wandb + if self.wandb_kwargs is not None: + wandb.run.log( + { + "Validation/RMSE": rmse, + } + ) + LOGGER.text( + f"Best trial: {best_trial.number} with value: {best_trial.value}", + level=LoggerObserver.INFO, + ) + + if self.method == "logistics": + # Save coefficient and intercept in json + coef = best_model.coef_ + intercept = best_model.intercept_ + with open(osp.join(self.save_dir, "logistics_params.json"), "w") as f: + json.dump( + { + "coef": coef.tolist(), + "intercept": intercept.tolist(), + "feature_names": self.feature_names, + }, + f, + indent=4, + ) + + if is_classification and self.feature_names is not None and self.classnames is not None: + try: + fig = visualize_shap( + best_model, + X_val, + feature_names=self.feature_names, + classnames=self.classnames, + plot_type="dot", + plot_size=(12, 6), + cross_validation=False, + ) + fig.savefig(osp.join(self.save_dir, "shap_summary.png"), bbox_inches="tight") + if self.wandb_kwargs is not None: + wandb.log({"Shap Summary": wandb.Image(fig)}) + LOGGER.text( + f"Shap Summary plot saved to {self.save_dir}/shap_summary.png", + level=LoggerObserver.INFO, + ) + except Exception: + pass + else: + LOGGER.text( + "Shap values are not supported for regression tasks.", level=LoggerObserver.WARN + ) + + if self.wandb_kwargs is not None: + wandb.finish() + + return best_model + + def save_best_config(self, best_params: dict): + with open(os.path.join(self.save_dir, "best_config.json"), "w") as f: + json.dump(best_params, f, indent=4) + + LOGGER.text( + f"Best config saved to {self.save_dir}/best_config.json", level=LoggerObserver.INFO + ) + + def leaderboard(self): + """Print leaderboard of all trials""" + df = self.study.trials_dataframe() + df.columns = [col.replace("user_attrs_", "") for col in df.columns] + return df + + def visualize(self, plot: str, plot_params: dict = None): + """Visualize everything""" + + if plot_params is None: + plot_params = {} + allow_plot_types = [ + "history", + "contour", + "edf", + "intermediate_values", + "parallel_coordinate", + "param_importances", + "slice", + ] + assert plot in ["all", *allow_plot_types], f"{plot} is not supported by Optuna" + + if plot == "all": + fig = [] + for plot_type in allow_plot_types: + one_fig = self.visualize(plot_type, plot_params) + if one_fig is not None: + fig.append((plot_type, one_fig)) + else: + try: + if plot == "history": + fig = plot_optimization_history(self.study, **plot_params) + elif plot == "contour": + fig = plot_contour(self.study, **plot_params) + elif plot == "edf": + fig = plot_edf(self.study, **plot_params) + elif plot == "intermediate_values": + fig = plot_intermediate_values(self.study) + elif plot == "parallel_coordinate": + fig = plot_parallel_coordinate(self.study, **plot_params) + elif plot == "param_importances": + fig = plot_param_importances(self.study, **plot_params) + elif plot == "slice": + fig = plot_slice(self.study, **plot_params) + else: + LOGGER.text(f"{plot} is not supported by Optuna", level=LoggerObserver.ERROR) + raise ValueError() + + if plot != "all" and self.wandb_kwargs is not None: + wandb.log({f"Plot/{plot}": fig}) + + except Exception as e: + LOGGER.text(f"Plotting error: {e}", level=LoggerObserver.ERROR) + return None + + return fig diff --git a/theseus/ml/trainer/__init__.py b/theseus/ml/trainer/__init__.py deleted file mode 100644 index 05ca80b..0000000 --- a/theseus/ml/trainer/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -from theseus.base.trainer import TRAINER_REGISTRY - -from .ml_trainer import MLTrainer - -TRAINER_REGISTRY.register(MLTrainer) diff --git a/theseus/ml/trainer/ml_trainer.py b/theseus/ml/trainer/ml_trainer.py deleted file mode 100644 index 00bbe0a..0000000 --- a/theseus/ml/trainer/ml_trainer.py +++ /dev/null @@ -1,66 +0,0 @@ -from theseus.base.utilities.loggers.observer import LoggerObserver -from theseus.ml.callbacks import CallbacksList - -LOGGER = LoggerObserver.getLogger("main") - - -class MLTrainer: - def __init__( - self, model, trainset, valset, metrics, callbacks=None, **kwargs - ) -> None: - - if callbacks is not None and not isinstance(callbacks, CallbacksList): - callbacks = callbacks if isinstance(callbacks, list) else [callbacks] - callbacks = CallbacksList(callbacks) - callbacks.set_params({"trainer": self}) - self.callbacks = callbacks - - self.model = model - self.trainset = trainset - self.valset = valset - self.metrics = metrics - - def fit(self): - - # On start callbacks - self.callbacks.run("on_start") - self.callbacks.run("on_train_epoch_start") - self.model.fit( - (self.trainset["inputs"], self.trainset["targets"]), - (self.valset["inputs"], self.valset["targets"]), - ) - self.callbacks.run( - "on_train_epoch_end", - {"trainset": self.trainset, "valset": self.valset}, - ) - - self.callbacks.run("on_validation_epoch_start") - metric_dict = self.validate() - self.callbacks.run( - "on_validation_epoch_end", - { - "iters": 0, - "trainset": self.trainset, - "valset": self.valset, - "metric_dict": metric_dict, - }, - ) - self.callbacks.run("on_finish") - - def validate(self): - """ - Perform validation one epoch - """ - - X_test, y_test = self.valset["inputs"], self.valset["targets"] - y_pred = self.model.predict(X_test, return_probs=True) - score_dict = {} - - if self.metrics is not None: - for metric in self.metrics: - score_dict.update( - metric.value( - {"outputs": y_pred}, {"inputs": X_test, "targets": y_test} - ) - ) - return score_dict diff --git a/theseus/ml/utilities/pprint.py b/theseus/ml/utilities/pprint.py deleted file mode 100644 index 2189529..0000000 --- a/theseus/ml/utilities/pprint.py +++ /dev/null @@ -1,24 +0,0 @@ -import pandas as pd -from tabulate import tabulate - -from theseus.base.utilities.loggers.observer import LoggerObserver - -LOGGER = LoggerObserver.getLogger("main") - - -def pretty_print_df(df, showindex=False): - if isinstance(df, pd.DataFrame): - LOGGER.text( - "\n" - + tabulate(df, headers=df.columns, tablefmt="psql", showindex=showindex), - level=LoggerObserver.INFO, - ) - elif isinstance(df, pd.Series): - df_list = [i for i in zip(df.index.values.tolist(), df.values.tolist())] - LOGGER.text( - "\n" - + tabulate(df_list, headers="keys", tablefmt="psql", showindex=showindex), - level=LoggerObserver.INFO, - ) - else: - raise ValueError() diff --git a/theseus/ml/visualize.py b/theseus/ml/visualize.py new file mode 100644 index 0000000..dea9512 --- /dev/null +++ b/theseus/ml/visualize.py @@ -0,0 +1,157 @@ + +import matplotlib.pyplot as plt +import numpy as np +import plotly.graph_objects as go +import seaborn as sns +from lime import lime_tabular +from sklearn.inspection import permutation_importance + + +def plot_cfm(cm, ax, labels: list): + """ + Make confusion matrix figure + labels: `Optional[List]` + classnames for visualization + """ + ax = sns.heatmap(cm, annot=False, fmt="", cmap="Blues", ax=ax) + ax.set_xlabel("\nActual") + ax.set_ylabel("Predicted ") + ax.xaxis.set_ticklabels(labels, rotation=90) + ax.yaxis.set_ticklabels(labels, rotation=0) + + +def make_cm_fig(cms, labels: list | None = None): + if cms.shape[0] > 1: # multilabel + num_classes = cms.shape[0] + else: + num_classes = cms.shape[1] + + ## Ticket labels - List must be in alphabetical order + if not labels: + labels = [str(i) for i in range(num_classes)] + + ## + num_cfms = cms.shape[0] + nrow = int(np.ceil(np.sqrt(num_cfms))) + + # Clear figures first to prevent memory-consuming + plt.cla() + plt.clf() + plt.close() + + fig, axes = plt.subplots(nrow, nrow, figsize=(8, 8)) + + if num_cfms > 1: + for ax, cfs_matrix, label in zip(axes.flatten(), cms, labels): + ax.set_title(f"{label}\n\n") + plot_cfm(cfs_matrix, ax, labels=["N", "Y"]) + else: + plot_cfm(cms[0], axes, labels=labels) + + fig.tight_layout() + return fig + + +def visualize_shap( + model, + inputs, + feature_names, + classnames, + plot_type="bar", + plot_size="auto", + cross_validation=False, +): + import shap + + if cross_validation: + assert isinstance(model, list), "model must be a list of models" + all_shap_values = [] + + if isinstance(inputs, list): + for _, (m, input) in enumerate(zip(model, inputs)): + explainer = shap.TreeExplainer(m) + shap_values = explainer.shap_values(input, check_additivity=False) + all_shap_values.append(shap_values) + else: + for _, m in enumerate(model): + explainer = shap.TreeExplainer(m) + shap_values = explainer.shap_values(inputs, check_additivity=False) + all_shap_values.append(shap_values) + + if isinstance(feature_names[0], list): # each fold have different order of features + feat_shap_dict = {} + for feature_list, shap_values in zip(feature_names, all_shap_values): + shap_values = np.array(shap_values).T + for feat, shap_val in zip(feature_list, shap_values): + if feat not in feat_shap_dict: + feat_shap_dict[feat] = [] + feat_shap_dict[feat].append(shap_val) + + feat_shap_dict = {k: np.mean(v, axis=0) for k, v in feat_shap_dict.items()} + feat_shap_dict.pop("none", None) + feature_names = sorted(list(feat_shap_dict.keys())) + average_shap_values = np.array([feat_shap_dict[feat] for feat in feature_names]).T + else: + all_shap_values = np.array(all_shap_values) + average_shap_values = np.mean(all_shap_values, axis=0) + # std_shap_values = np.std(all_shap_values, axis=0) + # range_shap_values = np.max(all_shap_values, axis=0) - np.min(all_shap_values, axis=0) + plt.clf() + + shap.summary_plot( + average_shap_values, + inputs, + plot_type=plot_type, + feature_names=feature_names, + class_names=classnames, + show=False, + plot_size=plot_size, + ) + fig = plt.gcf() + else: + explainer = shap.TreeExplainer(model) + shap_values = explainer.shap_values(inputs, check_additivity=False) + plt.clf() + shap.summary_plot( + shap_values, + inputs, + plot_type=plot_type, + feature_names=feature_names, + class_names=classnames, + show=False, + plot_size=plot_size, + ) + fig = plt.gcf() + return fig + + +def visualize_feature_importance(model, inputs, targets, feature_names): + perm_importance = permutation_importance(model, inputs, targets) + sorted_idx = perm_importance.importances_mean.argsort() + + fig = go.Figure( + go.Bar( + x=perm_importance.importances_mean[sorted_idx], + y=[feature_names[i] for i in sorted_idx], + orientation="h", + ) + ) + + fig.update_layout(title=go.layout.Title(text="Permutation Importance", x=0)) + return fig + + +def visualize_lime_instance(training_data, proba_func, item, feature_names=None, class_names=None): + """ + Get explaination for a single instance + """ + explainer = lime_tabular.LimeTabularExplainer( + training_data=training_data, + feature_names=feature_names, + class_names=class_names, + mode="classification", + discretize_continuous=False, + ) + + fig = explainer.explain_instance(data_row=item, predict_fn=proba_func) + return fig diff --git a/theseus/nlp/base/preprocessors/basic_processors.py b/theseus/nlp/base/preprocessors/basic_processors.py index 1e9f4bb..8de387d 100644 --- a/theseus/nlp/base/preprocessors/basic_processors.py +++ b/theseus/nlp/base/preprocessors/basic_processors.py @@ -43,7 +43,7 @@ def __init__(self, language="english"): def __call__(self, x): tokens = word_tokenize(x) - tokens = [word for word in tokens if not word in self.stopwords_list] + tokens = [word for word in tokens if word not in self.stopwords_list] result = " ".join(tokens) return result @@ -135,10 +135,10 @@ class RemoveEmoji(BaseProcessor): def __init__(self) -> None: self.regrex = re.compile( pattern="[" - "\U0001F600-\U0001F64F" # emoticons - "\U0001F300-\U0001F5FF" # symbols & pictographs - "\U0001F680-\U0001F6FF" # transport & map symbols - "\U0001F1E0-\U0001F1FF" # flags (iOS) + "\U0001f600-\U0001f64f" # emoticons + "\U0001f300-\U0001f5ff" # symbols & pictographs + "\U0001f680-\U0001f6ff" # transport & map symbols + "\U0001f1e0-\U0001f1ff" # flags (iOS) "]+", flags=re.UNICODE, ) @@ -178,7 +178,9 @@ class PreprocessCompose(BaseProcessor): :input: list of texts """ - def __init__(self, preprocess_list=[]) -> None: + def __init__(self, preprocess_list=None) -> None: + if preprocess_list is None: + preprocess_list = [] self.preprocess_list = preprocess_list def __call__(self, text): @@ -188,7 +190,6 @@ def __call__(self, text): if __name__ == "__main__": - text = [ "Nick likes to play football, however he is not too fond of tennis. \U0001f602", "Hello there, i'm Kay", diff --git a/theseus/nlp/base/preprocessors/pyvncore_processor.py b/theseus/nlp/base/preprocessors/pyvncore_processor.py index 9bca25f..fac743f 100644 --- a/theseus/nlp/base/preprocessors/pyvncore_processor.py +++ b/theseus/nlp/base/preprocessors/pyvncore_processor.py @@ -7,9 +7,7 @@ class VNCoreNLPProcessor(BaseProcessor): def __init__(self, save_dir: str = "/mnt/4TBSSD/zalo/e2e_qa"): py_vncorenlp.download_model(save_dir=save_dir) # Load the word and sentence segmentation component - self.rdrsegmenter = py_vncorenlp.VnCoreNLP( - annotators=["wseg"], save_dir=save_dir - ) + self.rdrsegmenter = py_vncorenlp.VnCoreNLP(annotators=["wseg"], save_dir=save_dir) def __call__(self, text): text = self.rdrsegmenter.word_segment(text) diff --git a/theseus/nlp/base/preprocessors/vocabulary.py b/theseus/nlp/base/preprocessors/vocabulary.py index e7e3a23..c52b506 100644 --- a/theseus/nlp/base/preprocessors/vocabulary.py +++ b/theseus/nlp/base/preprocessors/vocabulary.py @@ -7,7 +7,7 @@ LOGGER = LoggerObserver.getLogger("main") -class Vocabulary(object): +class Vocabulary: def __init__( self, max_size=None, @@ -72,30 +72,27 @@ def save_vocab(self, save_path): dirname = osp.dirname(save_path) filename, _ = osp.splitext(osp.basename(save_path)) with open(osp.join(dirname, f"{filename}_vocab.txt"), "w") as f: - for term in self.word2idx.keys(): + for term in self.word2idx: f.write(term + "\n") LOGGER.text(f"Save pickle to {save_path}", level=LoggerObserver.INFO) def build_vocab(self, list_tokens, add_special_tokens=True): """Populate the dictionaries for converting tokens to integers (and vice-versa).""" for tok in list_tokens: - if not tok in self.frequency: + if tok not in self.frequency: self.frequency[tok] = 0 self.frequency[tok] += 1 for tok in list(self.frequency.keys()): - if self.max_freq is not None: - if self.frequency[tok] > self.max_freq: - self.frequency.pop(tok) - continue - if self.min_freq is not None: - if self.frequency[tok] < self.min_freq: - self.frequency.pop(tok) - continue + if self.max_freq is not None and self.frequency[tok] > self.max_freq: + self.frequency.pop(tok) + continue + if self.min_freq is not None and self.frequency[tok] < self.min_freq: + self.frequency.pop(tok) + continue list_tokens = [ - k - for k, _ in sorted(self.frequency.items(), key=lambda x: x[1], reverse=True) + k for k, _ in sorted(self.frequency.items(), key=lambda x: x[1], reverse=True) ] if self.max_size is not None: list_tokens = list_tokens[: self.max_size] @@ -125,11 +122,11 @@ def add_word(self, word, index=None): if index is None: index = self.vocab_size - if not word in self.word2idx.keys() and not index in self.idx2word.keys(): + if word not in self.word2idx and index not in self.idx2word: self.word2idx[word] = self.vocab_size self.idx2word[self.vocab_size] = word self.vocab_size += 1 - elif not word in self.word2idx.keys() and index in self.idx2word.keys(): + elif word not in self.word2idx and index in self.idx2word: if self.replace: old_word = self.idx2word[index] self.word2idx[old_word] = self.vocab_size @@ -145,7 +142,7 @@ def add_word(self, word, index=None): ) raise ValueError() - elif word in self.word2idx.keys() and not index in self.idx2word.keys(): + elif word in self.word2idx and index not in self.idx2word: if self.replace: old_idx = self.word2idx[word] self.idx2word[old_idx] = None @@ -165,19 +162,19 @@ def add_word(self, word, index=None): raise ValueError() def add_special_tokens(self): - if self.sos_word not in self.special_tokens.keys(): + if self.sos_word not in self.special_tokens: self.add_word(self.sos_word) self.special_tokens.update({self.sos_word: self.vocab_size}) - if self.eos_word not in self.special_tokens.keys(): + if self.eos_word not in self.special_tokens: self.add_word(self.eos_word) self.special_tokens.update({self.eos_word: self.vocab_size}) - if self.pad_word not in self.special_tokens.keys(): + if self.pad_word not in self.special_tokens: self.add_word(self.pad_word) self.special_tokens.update({self.pad_word: self.vocab_size}) - if self.unk_word not in self.special_tokens.keys(): + if self.unk_word not in self.special_tokens: self.add_word(self.unk_word) self.special_tokens.update({self.unk_word: self.vocab_size}) @@ -199,7 +196,7 @@ def encode_tokens(self, lists_of_tokens, **kwargs): """ add_special_tokens = kwargs.get("add_special_tokens", False) - max_length = kwargs.get("max_length", None) + max_length = kwargs.get("max_length") return_token_type_ids = kwargs.get("return_token_type_ids", False) truncation = kwargs.get("truncation", False) @@ -238,15 +235,11 @@ def encode_tokens(self, lists_of_tokens, **kwargs): batch = batch[-max_length:] else: LOGGER.text( - f"Sequence is longer than max_length. Please use truncation=True", + "Sequence is longer than max_length. Please use truncation=True", level=LoggerObserver.ERROR, ) raise ValueError() - if ( - len(batch) < max_length - and add_special_tokens - and self.use_special_tokens - ): + if len(batch) < max_length and add_special_tokens and self.use_special_tokens: batch += [self.__call__(self.pad_word)] * (max_length - len(batch)) if return_token_type_ids: @@ -295,12 +288,12 @@ def encode_texts(self, text, **kwargs): return self.encode_tokens(tokenized_texts, **kwargs) def itos(self, idx): - if not idx in self.idx2word: + if idx not in self.idx2word: return self.idx2word[self.__call__(self.unk_word)] return self.idx2word[idx] def __call__(self, word): - if not word in self.word2idx: + if word not in self.word2idx: return self.word2idx[self.unk_word] return self.word2idx[word] diff --git a/theseus/nlp/base/utilities/correct_tone.py b/theseus/nlp/base/utilities/correct_tone.py index f0c4527..085f5d2 100644 --- a/theseus/nlp/base/utilities/correct_tone.py +++ b/theseus/nlp/base/utilities/correct_tone.py @@ -11,19 +11,17 @@ def normalize_diacritics(source, new_style=False, decomposed=False): diacritics = f"{combining_breve}{combining_circumflex_accent}{combining_horn}" result = unicodedata.normalize("NFD", source) # Put the tone on the second vowel - result = re.sub(r"(?i){}([aeiouy{}]+)".format(tone, diacritics), r"\2\1", result) + result = re.sub(rf"(?i){tone}([aeiouy{diacritics}]+)", r"\2\1", result) # Put the tone on the vowel with a diacritic - result = re.sub(r"(?i)(?<=[{}])(.){}".format(diacritics, tone), r"\2\1", result) + result = re.sub(rf"(?i)(?<=[{diacritics}])(.){tone}", r"\2\1", result) # For vowels that are not oa, oe, uy put the tone on the penultimate vowel - result = re.sub(r"(?i)(?<=[ae])([iouy]){}".format(tone), r"\2\1", result) - result = re.sub(r"(?i)(?<=[oy])([iuy]){}".format(tone), r"\2\1", result) - result = re.sub(r"(?i)(? None: self._obj_map: dict[str, T] = {} def _do_register(self, name: str, obj: T, override: bool = False) -> None: - if name in self._obj_map and self._obj_map[name] is not obj: - if not override: - logger.warning( - "An object named '%s' was already registered in '%s' registry!", - name, - self._name, - ) - return + if name in self._obj_map and self._obj_map[name] is not obj and not override: + logger.warning( + "An object named '%s' was already registered in '%s' registry!", + name, + self._name, + ) + return self._obj_map[name] = obj @overload @@ -63,9 +63,7 @@ def register(self, obj: None = None, prefix: str = "", override: bool = False) - @overload def register(self, obj: T, prefix: str = "", override: bool = False) -> None: ... - def register( - self, obj: T | None = None, prefix: str = "", override: bool = False - ) -> Any: + def register(self, obj: T | None = None, prefix: str = "", override: bool = False) -> Any: """ Register the given object under the name ``obj.__name__``. Can be used as either a decorator or not. @@ -125,9 +123,7 @@ def __getitem__(self, name: str) -> T: def __repr__(self) -> str: table_headers = ["Names", "Objects"] - table = tabulate( - self._obj_map.items(), headers=table_headers, tablefmt="fancy_grid" - ) + table = tabulate(self._obj_map.items(), headers=table_headers, tablefmt="fancy_grid") return f"Registry of {self._name}:\n{table}" def __iter__(self) -> Iterator[tuple[str, T]]: diff --git a/uv.lock b/uv.lock index a11fb88..669ee9c 100644 --- a/uv.lock +++ b/uv.lock @@ -1,32 +1,21 @@ version = 1 revision = 3 -requires-python = ">=3.10" +requires-python = ">=3.10, <3.13" resolution-markers = [ - "python_full_version >= '3.14' and platform_machine == 'aarch64' and sys_platform == 'linux'", - "python_full_version >= '3.14' and platform_machine != 'aarch64' and sys_platform == 'linux'", - "python_full_version >= '3.12' and python_full_version < '3.14' and platform_machine == 'aarch64' and sys_platform == 'linux'", - 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00:00:00 2001 From: Kaylode Date: Fri, 15 May 2026 00:21:08 +0100 Subject: [PATCH 3/3] next update --- .gitignore | 2 + pyproject.toml | 16 +- theseus/base/losses/focal_loss.py | 6 +- theseus/base/pipeline.py | 17 +- .../base/utilities/loggers/stdout_logger.py | 2 +- theseus/base/utilities/loggers/tsb_logger.py | 6 +- uv.lock | 692 +++++++++--------- 7 files changed, 370 insertions(+), 371 deletions(-) diff --git a/.gitignore b/.gitignore index afeb501..c14f529 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,5 @@ catboost_info/ .cache /build/ credentials.json +.ruff_cache/ +.venv/ \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index baa461b..43cf3f2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,6 +5,10 @@ build-backend = "setuptools.build_meta" [tool.setuptools] packages = ["theseus"] +[[tool.uv.index]] +name = "pytorch" +url = "https://download.pytorch.org/whl/cu126" + [project] name = "theseus" version = "2.0.0" @@ -48,6 +52,8 @@ dependencies = [ "scikit-learn>=1.7.2", "omegaconf>=2.3.0", "rich>=14.3.3", + "lightning[extra]>=2.4.0", + "scipy>=1.11.4", ] [project.optional-dependencies] @@ -58,8 +64,6 @@ dev = [ "ruff>=0.5.0", ] cv = [ - "torchvision>=0.24.1", - "lightning>=2.4.0", "albumentations>=1.4.0,<2.0.0", "omegaconf>=2.3.0", ] @@ -76,7 +80,6 @@ cv_detection = [ "pycocotools>=2.0.7", ] nlp = [ - "lightning>=2.4.0", "pyvi>=0.1.1", "py_vncorenlp>=0.1.3", "spacy>=3.7.0", @@ -94,15 +97,8 @@ ml = [ "optuna-integration[wandb]>=4.8.0", "numpy==1.26.4", "lightgbm==4.6.0", - "wandb==0.19.9", "xgboost>=3.0", - "tqdm==4.67.1", - "tabulate==0.9.0", - "scikit-plot==0.3.7", - "scipy>=1.11.4", - "seaborn==0.13.2", "shap==0.47.1", - "numpy==1.26.4", "catboost==1.2.8", ] all = [ diff --git a/theseus/base/losses/focal_loss.py b/theseus/base/losses/focal_loss.py index 3162f4e..8973d6e 100644 --- a/theseus/base/losses/focal_loss.py +++ b/theseus/base/losses/focal_loss.py @@ -2,8 +2,10 @@ import torch import torch.nn as nn -from torchvision.ops.focal_loss import sigmoid_focal_loss - +try: + from torchvision.ops.focal_loss import sigmoid_focal_loss +except: + pass from theseus.base.utilities.cuda import move_to diff --git a/theseus/base/pipeline.py b/theseus/base/pipeline.py index d7a627b..fefe7fa 100644 --- a/theseus/base/pipeline.py +++ b/theseus/base/pipeline.py @@ -23,6 +23,7 @@ from theseus.base.utilities.getter import get_instance, get_instance_recursively from theseus.base.utilities.loggers import FileLogger, ImageWriter, LoggerObserver from theseus.base.utilities.seed import seed_everything +import torch class _PipelineBase: @@ -69,6 +70,9 @@ def _setup_savedir(self) -> str: def init_globals(self) -> None: """Initialize logger, experiment directory, and global variables.""" + # Set float32 matmul precision for Tensor Cores (e.g., A100) + torch.set_float32_matmul_precision("medium") + self.logger = LoggerObserver.getLogger("main") # Global variables @@ -257,7 +261,7 @@ def init_datamodule(self) -> None: ) def init_model(self) -> Any: - CLASSNAMES = self.classnames + CLASSNAMES = getattr(self, "classnames", None) model = get_instance( self.opt["model"], registry=self.model_registry, @@ -267,10 +271,10 @@ def init_model(self) -> Any: return model def init_criterion(self) -> Any | None: - CLASSNAMES = self.classnames if self.opt["loss"] is None: return None + CLASSNAMES = getattr(self, "classnames", None) self.criterion = get_instance_recursively( self.opt["loss"], registry=self.loss_registry, @@ -285,7 +289,7 @@ def init_model_with_loss(self, is_train: bool = True) -> None: num_epochs = self.opt["trainer"]["args"]["max_epochs"] batch_size = self.opt["data"]["dataloader"]["val"]["args"]["batch_size"] use_mixed_precision = self.opt["trainer"]["args"].get("precision", None) - use_mixed_precision = bool(use_mixed_precision) + use_mixed_precision = '-mixed' in use_mixed_precision self.model = LightningModelWrapper( self.model, @@ -344,11 +348,15 @@ def init_callbacks(self) -> list[Any]: return callbacks def init_trainer(self, callbacks: list[Any]) -> None: + # Check if we already have a ModelSummary callback to avoid redundancy warning + has_summary = any("ModelSummary" in str(type(c)) for c in callbacks) + self.trainer = get_instance( self.opt["trainer"], default_root_dir=getattr(self, "savedir", "runs"), deterministic="warn", callbacks=callbacks, + enable_model_summary=not has_summary, registry=self.trainer_registry, ) @@ -440,6 +448,9 @@ def __init__(self, opt: DictConfig) -> None: def init_globals(self) -> None: """Initialize globals without image writer (not needed for inference).""" + # Set float32 matmul precision for Tensor Cores (e.g., A100) + torch.set_float32_matmul_precision("medium") + self.logger = LoggerObserver.getLogger("main") self.exp_name = self.opt["global"].get("exp_name", None) diff --git a/theseus/base/utilities/loggers/stdout_logger.py b/theseus/base/utilities/loggers/stdout_logger.py index f985f39..9d883a4 100644 --- a/theseus/base/utilities/loggers/stdout_logger.py +++ b/theseus/base/utilities/loggers/stdout_logger.py @@ -1,5 +1,5 @@ import sys - +import os from loguru import logger from .observer import LoggerObserver, LoggerSubscriber diff --git a/theseus/base/utilities/loggers/tsb_logger.py b/theseus/base/utilities/loggers/tsb_logger.py index 27e8084..57d7aec 100644 --- a/theseus/base/utilities/loggers/tsb_logger.py +++ b/theseus/base/utilities/loggers/tsb_logger.py @@ -7,9 +7,11 @@ import pandas as pd import torch from PIL import Image -from tensorboard.backend.event_processing.event_accumulator import EventAccumulator try: + from tensorboard.backend.event_processing.event_accumulator import EventAccumulator + from torch.utils.tensorboard import SummaryWriter + from torchvision.transforms import ToTensor import tensorboard as tb import tensorflow as tf @@ -17,8 +19,6 @@ except: pass -from torch.utils.tensorboard import SummaryWriter -from torchvision.transforms import ToTensor from .observer 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