diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml index 2a60d6a7c..a9ce69ec3 100644 --- a/.github/workflows/package.yml +++ b/.github/workflows/package.yml @@ -51,17 +51,3 @@ jobs: pip install -e ".[models]" pip install pytest python3 -m pytest tests/package/extras/models.py - extra-report-package-install-check: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Install pip - run: python3 -m pip install --upgrade pip - - uses: actions/setup-python@v4.7.1 - with: - python-version: '3.10' - - name: Install package and test import - run: | - pip install -e ".[report]" - pip install pytest - python3 -m pytest tests/package/extras/report.py diff --git a/README.md b/README.md index 311033aa9..381d9207c 100644 --- a/README.md +++ b/README.md @@ -13,20 +13,17 @@ ``cyclops`` is a toolkit for facilitating research and deployment of ML models for healthcare. It provides a few high-level APIs namely: -* `data` - Create datasets for training, inference and evaluation. We use the popular πŸ€— [datasets](https://github.com/huggingface/datasets) to efficiently load and slice different modalities of data. -* `models` - Use common model implementations using [scikit-learn](https://scikit-learn.org/stable/) and [PyTorch](https://pytorch.org/). -* `tasks` - Use canonical Healthcare ML tasks such as - * Mortality prediction - * Chest X-ray classification +* `data` - Create datasets for training, inference and evaluation. We use the popular πŸ€— [datasets](https://github.com/huggingface/datasets) to efficiently load and slice different modalities of data +* `models` - Use common model implementations using [scikit-learn](https://scikit-learn.org/stable/) and [PyTorch](https://pytorch.org/) +* `tasks` - Use common ML task formulations such as binary classification or multi-label classification on tabular, time-series and image data * `evaluate` - Evaluate models on clinical prediction tasks * `monitor` - Detect dataset shift relevant for clinical use cases * `report` - Create [model report cards](https://vectorinstitute.github.io/cyclops/api/tutorials/nihcxr/nihcxr_report_periodic.html) for clinical ML models -``cyclops`` also provides a library of end-to-end use cases on clinical datasets such as +``cyclops`` also provides example end-to-end use case implementations on clinical datasets such as -* [MIMIC-III](https://physionet.org/content/mimiciii/1.4/) +* [NIH chest x-ray](https://www.nih.gov/news-events/news-releases/nih-clinical-center-provides-one-largest-publicly-available-chest-x-ray-datasets-scientific-community) * [MIMIC-IV](https://physionet.org/content/mimiciv/2.0/) -* [eICU-CRD](https://eicu-crd.mit.edu/about/eicu/) ## 🐣 Getting Started @@ -37,31 +34,15 @@ python3 -m pip install pycyclops ``` -The base package installation supports the use of the `data` and `process` APIs to load -and transform clinical data, for downstream tasks. +The base cyclops installation doesn't include modelling packages. -To install additional functionality from the other APIs, they can be installed as extras. +To install additional dependencies for using models, -To install with `models`, `tasks`, `evaluate` and `monitor` API support, - ```bash python3 -m pip install 'pycyclops[models]' ``` -To install with `report` API support, - -```bash -python3 -m pip install 'pycyclops[report]' -``` - -Multiple extras could also be combined, for example to install with both `report` and -`models` support: - -```bash -python3 -m pip install 'pycyclops[report,models]' -``` - ## πŸ§‘πŸΏβ€πŸ’» Developing diff --git a/cyclops/data/features/medical_image.py b/cyclops/data/features/medical_image.py index 58942c87f..7b7d9cae9 100644 --- a/cyclops/data/features/medical_image.py +++ b/cyclops/data/features/medical_image.py @@ -1,11 +1,10 @@ """Medical image feature.""" -import logging import os import tempfile from dataclasses import dataclass, field from io import BytesIO -from typing import Any, ClassVar, Dict, Optional, Tuple, Union +from typing import TYPE_CHECKING, Any, ClassVar, Dict, Optional, Tuple, Union import numpy as np import numpy.typing as npt @@ -15,18 +14,56 @@ from datasets.features import Image, features from datasets.utils.file_utils import is_local_path from datasets.utils.py_utils import string_to_dict -from monai.data.image_reader import ImageReader -from monai.data.image_writer import ITKWriter -from monai.transforms.compose import Compose -from monai.transforms.io.array import LoadImage -from monai.transforms.utility.array import ToNumpy -from cyclops.utils.log import setup_logging +from cyclops.utils.optional import import_optional_module -# Logging. -LOGGER = logging.getLogger(__name__) -setup_logging(print_level="INFO", logger=LOGGER) +if TYPE_CHECKING: + from monai.data.image_reader import ImageReader + from monai.data.image_writer import ITKWriter + from monai.transforms.compose import Compose + from monai.transforms.io.array import LoadImage + from monai.transforms.utility.array import ToNumpy +else: + ImageReader = import_optional_module( + "monai.data.image_reader", + attribute="ImageReader", + error="warn", + ) + ITKWriter = import_optional_module( + "monai.data.image_writer", + attribute="ITKWriter", + error="warn", + ) + Compose = import_optional_module( + "monai.transforms.compose", + attribute="Compose", + error="warn", + ) + LoadImage = import_optional_module( + "monai.transforms.io.array", + attribute="LoadImage", + error="warn", + ) + ToNumpy = import_optional_module( + "monai.transforms.utility.array", + attribute="ToNumpy", + error="warn", + ) +_monai_available = all( + module is not None + for module in ( + ImageReader, + ITKWriter, + Compose, + LoadImage, + ToNumpy, + ) +) +_monai_unavailable_message = ( + "The MONAI library is required to use the `MedicalImage` feature. " + "Please install it with `pip install monai`." +) @dataclass @@ -35,24 +72,35 @@ class MedicalImage(Image): # type: ignore Parameters ---------- - decode : bool, optional, default=True - Whether to decode the image. If False, the image will be returned as a - dictionary in the format `{"path": image_path, "bytes": image_bytes}`. reader : Union[str, ImageReader], optional, default="ITKReader" The MONAI image reader to use. suffix : str, optional, default=".jpg" The suffix to use when decoding bytes to image. + decode : bool, optional, default=True + Whether to decode the image. If False, the image will be returned as a + dictionary in the format `{"path": image_path, "bytes": image_bytes}`. + id : str, optional, default=None + The id of the feature. """ reader: Union[str, ImageReader] = "ITKReader" suffix: str = ".jpg" # used when decoding/encoding bytes to image - _loader = Compose( - [ - LoadImage(reader=reader, simple_keys=True, dtype=None, image_only=True), - ToNumpy(), - ], - ) + + _loader = None + if _monai_available: + _loader = Compose( + [ + LoadImage( + reader=reader, + simple_keys=True, + dtype=None, + image_only=False, + ), + ToNumpy(), + ], + ) + # Automatically constructed dtype: ClassVar[str] = "dict" pa_type: ClassVar[Any] = pa.struct({"bytes": pa.binary(), "path": pa.string()}) @@ -76,12 +124,14 @@ def encode_example( """ if isinstance(value, list): - value = np.array(value) + value = np.asarray(value) if isinstance(value, str): return {"path": value, "bytes": None} + if isinstance(value, np.ndarray): return _encode_ndarray(value, image_format=self.suffix) + if "array" in value and "metadata" in value: output_ext_ = self.suffix metadata_ = value["metadata"] @@ -132,7 +182,7 @@ def decode_example( if not self.decode: raise RuntimeError( "Decoding is disabled for this feature. " - "Please use MedicalImage(decode=True) instead.", + "Please use `MedicalImage(decode=True)` instead.", ) if token_per_repo_id is None: @@ -147,6 +197,8 @@ def decode_example( ) if is_local_path(path): + if self._loader is None: + raise RuntimeError(_monai_unavailable_message) image, metadata = self._loader(path) else: source_url = path.split("::")[-1] @@ -188,6 +240,9 @@ def _read_file_from_bytes( Image as numpy array and metadata as dictionary. """ + if self._loader is None: + raise RuntimeError(_monai_unavailable_message) + # XXX: Can we avoid writing to disk? with tempfile.NamedTemporaryFile(mode="wb", suffix=self.suffix) as fp: fp.write(buffer.getvalue()) @@ -219,6 +274,9 @@ def _encode_ndarray( Dictionary containing the image bytes and path. """ + if not _monai_available: + raise RuntimeError(_monai_unavailable_message) + if not image_format.startswith("."): image_format = "." + image_format @@ -240,5 +298,5 @@ def _encode_ndarray( return {"path": None, "bytes": temp_file_bytes} -# add the `MedicalImage` feature to the `features` module +# add the `MedicalImage` feature to the `features` module namespace features.MedicalImage = MedicalImage diff --git a/cyclops/data/packaged_loading_scripts/medical_imagefolder/medical_imagefolder.py b/cyclops/data/packaged_loading_scripts/medical_imagefolder/medical_imagefolder.py index ab3c4b7d5..62ed9ba4e 100644 --- a/cyclops/data/packaged_loading_scripts/medical_imagefolder/medical_imagefolder.py +++ b/cyclops/data/packaged_loading_scripts/medical_imagefolder/medical_imagefolder.py @@ -33,7 +33,7 @@ class MedicalImageFolderConfig( class MedicalImageFolder(folder_based_builder.FolderBasedBuilder): # type: ignore """MedicalImageFolder.""" - BASE_FEATURE = MedicalImage() + BASE_FEATURE = MedicalImage BASE_COLUMN_NAME = "image" BUILDER_CONFIG_CLASS = MedicalImageFolderConfig EXTENSIONS: List[str] # definition at the bottom of the script diff --git a/cyclops/data/transforms.py b/cyclops/data/transforms.py index 4b902e757..5c2e4216d 100644 --- a/cyclops/data/transforms.py +++ b/cyclops/data/transforms.py @@ -1,28 +1,84 @@ """Transforms for the datasets.""" +from typing import Any, Callable, Tuple -from typing import Tuple - -from monai.transforms import Lambdad, Resized, ToDeviced # type: ignore -from torchvision.transforms import Compose - - -def txrv_transforms( - keys: Tuple[str, ...] = ("features",), - device: str = "cpu", -) -> Compose: - """Set of transforms for the models in the TXRV library.""" - return Compose( - [ - Resized( - keys=keys, - spatial_size=(1, 224, 224), - allow_missing_keys=True, - ), - Lambdad( - keys=keys, - func=lambda x: ((2 * (x / 255.0)) - 1.0) * 1024, - allow_missing_keys=True, - ), - ToDeviced(keys=keys, device=device, allow_missing_keys=True), - ], - ) +from torchvision.transforms import Lambda, Resize + + +# generic dictionary-based wrapper for any transform +class Dictd: + """Generic dictionary-based wrapper for any transform.""" + + def __init__( + self, + transform: Callable[..., Any], + keys: Tuple[str, ...], + allow_missing_keys: bool = False, + ): + self.transform = transform + self.keys = keys + self.allow_missing_keys = allow_missing_keys + + def __call__(self, data: Any) -> Any: + """Apply the transform to the data.""" + for key in self.keys: + if self.allow_missing_keys and key not in data: + continue + data[key] = self.transform(data[key]) + return data + + def __repr__(self) -> str: + """Return a string representation of the transform.""" + return ( + f"{self.__class__.__name__}(transform={self.transform}, " + f"keys={self.keys}, allow_missing_keys={self.allow_missing_keys})" + ) + + +# dictionary-based wrapper of Lambda transform using Dictd +class Lambdad: + """Dictionary-based wrapper of Lambda transform using Dictd.""" + + def __init__( + self, + func: Callable[..., Any], + keys: Tuple[str, ...], + allow_missing_keys: bool = False, + ): + self.transform = Dictd( + transform=Lambda(func), + keys=keys, + allow_missing_keys=allow_missing_keys, + ) + + def __call__(self, data: Any) -> Any: + """Apply the transform to the data.""" + return self.transform(data) + + def __repr__(self) -> str: + """Return a string representation of the transform.""" + return f"{self.__class__.__name__}(keys={self.transform.keys}, allow_missing_keys={self.transform.allow_missing_keys})" + + +# dictionary-based wrapper of Resize transform using Dictd +class Resized: + """Dictionary-based wrapper of Resize transform using Dictd.""" + + def __init__( + self, + spatial_size: Tuple[int, int], + keys: Tuple[str, ...], + allow_missing_keys: bool = False, + ): + self.transform = Dictd( + transform=Resize(size=spatial_size), + keys=keys, + allow_missing_keys=allow_missing_keys, + ) + + def __call__(self, data: Any) -> Any: + """Apply the transform to the data.""" + return self.transform(data) + + def __repr__(self) -> str: + """Return a string representation of the transform.""" + return f"{self.__class__.__name__}(keys={self.transform.keys}, allow_missing_keys={self.transform.allow_missing_keys})" diff --git a/cyclops/evaluate/metrics/experimental/distributed_backends/mpi4py.py b/cyclops/evaluate/metrics/experimental/distributed_backends/mpi4py.py index 3ae9997d4..a958a0efa 100644 --- a/cyclops/evaluate/metrics/experimental/distributed_backends/mpi4py.py +++ b/cyclops/evaluate/metrics/experimental/distributed_backends/mpi4py.py @@ -15,7 +15,7 @@ if TYPE_CHECKING: from mpi4py import MPI else: - MPI = import_optional_module("mpi4py.MPI", error="ignore") + MPI = import_optional_module("mpi4py.MPI", error="warn") # mypy: disable-error-code="no-any-return" diff --git a/cyclops/evaluate/metrics/experimental/distributed_backends/torch_distributed.py b/cyclops/evaluate/metrics/experimental/distributed_backends/torch_distributed.py index b4f29eb26..475142dfc 100644 --- a/cyclops/evaluate/metrics/experimental/distributed_backends/torch_distributed.py +++ b/cyclops/evaluate/metrics/experimental/distributed_backends/torch_distributed.py @@ -1,5 +1,5 @@ """`torch.distributed` backend for synchronizing `torch.Tensor` objects.""" -from typing import TYPE_CHECKING, List, TypeVar +from typing import TYPE_CHECKING, List from cyclops.evaluate.metrics.experimental.distributed_backends.base import ( DistributedBackend, @@ -11,10 +11,8 @@ import torch import torch.distributed as torch_dist else: - torch = import_optional_module("torch", error="ignore") - torch_dist = import_optional_module("torch.distributed", error="ignore") - -Tensor = TypeVar("Tensor", bound="torch.Tensor") + torch = import_optional_module("torch", error="warn") + torch_dist = import_optional_module("torch.distributed", error="warn") class TorchDistributed(DistributedBackend, registry_key="torch_distributed"): @@ -25,13 +23,13 @@ def __init__(self) -> None: super().__init__() if torch is None: raise ImportError( - f"For availability of {self.__class__.__name__}," - " please install pytorch first.", + f"For availability of `{self.__class__.__name__}`," + " please install `torch` first.", ) if not torch_dist.is_available(): raise RuntimeError( - f"For availability of {self.__class__.__name__}," - " make sure torch.distributed is available.", + f"For availability of `{self.__class__.__name__}`," + " make sure `torch.distributed` is available.", ) @property diff --git a/cyclops/models/wrappers/pt_model.py b/cyclops/models/wrappers/pt_model.py index 462eaeb65..78c62e5dd 100644 --- a/cyclops/models/wrappers/pt_model.py +++ b/cyclops/models/wrappers/pt_model.py @@ -3,14 +3,23 @@ import contextlib import logging import os -from typing import Any, Callable, Dict, List, Literal, Optional, Sequence, Union +from typing import ( + TYPE_CHECKING, + Any, + Callable, + Dict, + List, + Literal, + Optional, + Sequence, + Union, +) import matplotlib.pyplot as plt import numpy as np import torch from datasets import Dataset, DatasetDict from datasets.combine import concatenate_datasets -from monai.data.meta_tensor import MetaTensor from torch import nn from torch.optim import Optimizer from torch.optim.lr_scheduler import _LRScheduler as TorchLRScheduler @@ -37,6 +46,17 @@ ) from cyclops.utils.file import join, process_dir_save_path from cyclops.utils.log import setup_logging +from cyclops.utils.optional import import_optional_module + + +if TYPE_CHECKING: + from monai.data.meta_tensor import MetaTensor +else: + MetaTensor = import_optional_module( + "monai.data.meta_tensor", + attribute="MetaTensor", + error="warn", + ) LOGGER = logging.getLogger(__name__) @@ -660,7 +680,7 @@ def _get_dataset( if isinstance(X, (Dataset, TorchDataset, DatasetDict)): return X - if isinstance(X, MetaTensor): + if MetaTensor is not None and isinstance(X, MetaTensor): return PTDataset(X.data, y) if isinstance(X, (np.ndarray, torch.Tensor)): diff --git a/cyclops/monitor/reductor.py b/cyclops/monitor/reductor.py index e27aae6c9..ec29af800 100644 --- a/cyclops/monitor/reductor.py +++ b/cyclops/monitor/reductor.py @@ -7,7 +7,6 @@ import torch import torchxrayvision as xrv from datasets import Dataset, DatasetDict -from monai.transforms import Compose from sklearn.base import BaseEstimator from sklearn.decomposition import PCA, KernelPCA from sklearn.manifold import Isomap @@ -15,6 +14,7 @@ from sklearn.random_projection import SparseRandomProjection from torch import nn from torch.utils.data import Dataset as TorchDataset +from torchvision.transforms import Compose from cyclops.data.utils import apply_transforms from cyclops.models.catalog import SKModel, wrap_model diff --git a/cyclops/monitor/tester.py b/cyclops/monitor/tester.py index 4e1c30542..51d831e39 100644 --- a/cyclops/monitor/tester.py +++ b/cyclops/monitor/tester.py @@ -22,13 +22,13 @@ ) from alibi_detect.utils.pytorch.kernels import DeepKernel, GaussianRBF from datasets import Dataset, DatasetDict, concatenate_datasets -from monai.transforms import Lambdad from scipy.special import expit as sigmoid from scipy.special import softmax from sklearn.base import BaseEstimator from torch import nn from torch.utils.data import Dataset as TorchDataset +from cyclops.data.transforms import Lambdad from cyclops.data.utils import apply_transforms from cyclops.models.catalog import wrap_model from cyclops.monitor.utils import DetectronModule, DummyCriterion, get_args diff --git a/cyclops/tasks/classification.py b/cyclops/tasks/classification.py index 673fa39e4..458e12f4e 100644 --- a/cyclops/tasks/classification.py +++ b/cyclops/tasks/classification.py @@ -7,9 +7,9 @@ import numpy as np import pandas as pd from datasets import Dataset, DatasetDict, config -from monai.transforms import Compose # type: ignore from sklearn.compose import ColumnTransformer from sklearn.exceptions import NotFittedError +from torchvision.transforms import Compose from cyclops.data.slicer import SliceSpec from cyclops.evaluate.evaluator import evaluate @@ -419,7 +419,7 @@ def predict( splits_mapping = {"test": "test"} model_name, model = self.get_model(model_name) if transforms: - transforms = partial(apply_image_transforms, transforms=transforms) # type: ignore + transforms = partial(apply_image_transforms, transforms=transforms) if isinstance(dataset, (Dataset, DatasetDict)): return model.predict( dataset, diff --git a/cyclops/utils/optional.py b/cyclops/utils/optional.py index a52ffbb7b..88a6d6261 100644 --- a/cyclops/utils/optional.py +++ b/cyclops/utils/optional.py @@ -1,28 +1,23 @@ """Utilities for handling optional dependencies.""" import importlib import importlib.util -import logging import warnings -from types import ModuleType -from typing import Literal, Optional - -from cyclops.utils.log import setup_logging - - -LOGGER = logging.getLogger(__name__) -setup_logging(print_level="WARN", logger=LOGGER) +from typing import Any, Literal, Optional def import_optional_module( name: str, + attribute: Optional[str] = None, error: Literal["raise", "warn", "ignore"] = "raise", -) -> Optional[ModuleType]: +) -> Optional[Any]: """Import an optional module. Parameters ---------- name : str The name of the module to import. + attribute : Optional[str], optional + The name of an attribute to import from the module. error : ErrorOption, optional How to handle errors. One of: - "raise": raise an error if the module cannot be imported. @@ -31,8 +26,9 @@ def import_optional_module( Returns ------- - Optional[ModuleType] - The imported module, if it exists. Otherwise, `None`. + Optional[Any] + The imported module or attribute from the module, or `None` if the + module could not be imported. """ if error not in ("raise", "warn", "ignore"): @@ -42,7 +38,10 @@ def import_optional_module( ) try: - return importlib.import_module(name) + module = importlib.import_module(name) + if attribute is not None and module is not None: + module = getattr(module, attribute) + return module except ModuleNotFoundError as exc: msg = ( f"Missing optional dependency '{name}'. " diff --git a/docs/source/intro.rst b/docs/source/intro.rst index 36c728c5a..0bdbd94a8 100644 --- a/docs/source/intro.rst +++ b/docs/source/intro.rst @@ -13,27 +13,25 @@ models for healthcare. It provides a few high-level APIs namely: - ``data`` - Create datasets for training, inference and evaluation. We use the popular πŸ€— `datasets `__ to efficiently - load and slice different modalities of data. + load and slice different modalities of data - ``models`` - Use common model implementations using `scikit-learn `__ and - `PyTorch `__. -- ``tasks`` - Use canonical Healthcare ML tasks such as - - - Mortality prediction - - Chest X-ray classification - + `PyTorch `__ +- ``tasks`` - Use common ML task formulations such as binary + classification or multi-label classification on tabular, time-series + and image data - ``evaluate`` - Evaluate models on clinical prediction tasks - ``monitor`` - Detect dataset shift relevant for clinical use cases - ``report`` - Create `model report cards `__ for clinical ML models -``cyclops`` also provides a library of end-to-end use cases on clinical -datasets such as +``cyclops`` also provides example end-to-end use case implementations on +clinical datasets such as -- `MIMIC-III `__ +- `NIH chest + x-ray `__ - `MIMIC-IV `__ -- `eICU-CRD `__ 🐣 Getting Started ================== @@ -45,33 +43,14 @@ Installing cyclops using pip python3 -m pip install pycyclops -The base package installation supports the use of the ``data`` and -``process`` APIs to load and transform clinical data, for downstream -tasks. - -To install additional functionality from the other APIs, they can be -installed as extras. +The base cyclops installation doesn’t include modelling packages. -To install with ``models``, ``tasks``, ``evaluate`` and ``monitor`` API -support, +To install additional dependencies for using models, .. code:: bash python3 -m pip install 'pycyclops[models]' -To install with ``report`` API support, - -.. code:: bash - - python3 -m pip install 'pycyclops[report]' - -Multiple extras could also be combined, for example to install with both -``report`` and ``models`` support: - -.. code:: bash - - python3 -m pip install 'pycyclops[report,models]' - πŸ§‘πŸΏβ€πŸ’» Developing ======================= diff --git a/docs/source/tutorials/nihcxr/cxr_classification.ipynb b/docs/source/tutorials/nihcxr/cxr_classification.ipynb index 32a96e026..06de21e8a 100644 --- a/docs/source/tutorials/nihcxr/cxr_classification.ipynb +++ b/docs/source/tutorials/nihcxr/cxr_classification.ipynb @@ -7,7 +7,7 @@ "source": [ "# Chest X-Ray Disease Classification\n", "\n", - "This notebook shows chest x-ray classification on the NIH dataset using a pretrained model from the TorchXRayVision library and CyclOps to generate a model card." + "This notebook shows chest x-ray classification on the [NIH dataset](https://www.nih.gov/news-events/news-releases/nih-clinical-center-provides-one-largest-publicly-available-chest-x-ray-datasets-scientific-community) using a pretrained model from the TorchXRayVision library and CyclOps to generate a model card." ] }, { @@ -33,7 +33,7 @@ "\n", "import numpy as np\n", "import plotly.express as px\n", - "from monai.transforms import Compose, Lambdad, Resized\n", + "from torchvision.transforms import Compose\n", "from torchxrayvision.models import DenseNet\n", "\n", "from cyclops.data.loader import load_nihcxr\n", @@ -41,6 +41,7 @@ " SliceSpec,\n", " filter_value, # noqa: E402\n", ")\n", + "from cyclops.data.transforms import Lambdad, Resized\n", "from cyclops.data.utils import apply_transforms\n", "from cyclops.evaluate import evaluator\n", "from cyclops.evaluate.metrics.factory import create_metric\n", @@ -143,8 +144,9 @@ " allow_missing_keys=True,\n", " ),\n", " Lambdad(\n", - " (\"image\",),\n", - " func=lambda x: np.mean(x, axis=0)[np.newaxis, :] if x.shape[0] != 1 else x,\n", + " keys=(\"image\",),\n", + " func=lambda x: x[0][np.newaxis, :] if x.shape[0] != 1 else x,\n", + " allow_missing_keys=True,\n", " ),\n", " ],\n", ")" diff --git a/docs/source/tutorials/nihcxr/generate_nihcxr_report.py b/docs/source/tutorials/nihcxr/generate_nihcxr_report.py index 364742352..7ae4d8ef5 100644 --- a/docs/source/tutorials/nihcxr/generate_nihcxr_report.py +++ b/docs/source/tutorials/nihcxr/generate_nihcxr_report.py @@ -8,7 +8,7 @@ import numpy as np import numpy.typing as npt import plotly.express as px -from monai.transforms import Compose, Lambdad, Resized # type: ignore[attr-defined] +from torchvision.transforms import Compose from torchxrayvision.models import DenseNet from cyclops.data.loader import load_nihcxr @@ -16,6 +16,7 @@ SliceSpec, filter_value, # noqa: E402 ) +from cyclops.data.transforms import Lambdad, Resized from cyclops.data.utils import apply_transforms from cyclops.evaluate import evaluator from cyclops.evaluate.metrics.factory import create_metric @@ -55,8 +56,8 @@ allow_missing_keys=True, ), Lambdad( - ("image",), - func=lambda x: np.mean(x, axis=0)[np.newaxis, :] if x.shape[0] != 1 else x, + keys=("image",), + func=lambda x: x[0][np.newaxis, :] if x.shape[0] != 1 else x, ), ], ) diff --git a/docs/source/tutorials/nihcxr/monitor_api.ipynb b/docs/source/tutorials/nihcxr/monitor_api.ipynb index 929fc939f..a8ab67050 100644 --- a/docs/source/tutorials/nihcxr/monitor_api.ipynb +++ b/docs/source/tutorials/nihcxr/monitor_api.ipynb @@ -26,17 +26,25 @@ "\"\"\"NIHCXR Clinical Drift Experiments Tutorial.\"\"\"\n", "\n", "\n", + "import random\n", + "\n", "import numpy as np\n", - "from monai.transforms import Compose, Lambdad, Resized\n", + "import torch\n", + "from torchvision.transforms import Compose\n", "from torchxrayvision.models import DenseNet\n", "\n", "from cyclops.data.loader import load_nihcxr\n", "from cyclops.data.slicer import SliceSpec\n", + "from cyclops.data.transforms import Lambdad, Resized\n", "from cyclops.monitor import ClinicalShiftApplicator, Detector, Reductor, TSTester\n", "from cyclops.monitor.plotter import plot_drift_experiment, plot_drift_timeseries\n", "\n", "\n", - "nih_ds = load_nihcxr(\"/mnt/data/clinical_datasets/NIHCXR\")[\"test\"]" + "nih_ds = load_nihcxr(\"/mnt/data/clinical_datasets/NIHCXR\")[\"test\"]\n", + "\n", + "random.seed(42)\n", + "np.random.seed(42)\n", + "torch.manual_seed(42)" ] }, { @@ -65,18 +73,19 @@ "transforms = Compose(\n", " [\n", " Resized(\n", - " keys=(\"image\",),\n", " spatial_size=(224, 224),\n", + " keys=(\"image\",),\n", " allow_missing_keys=True,\n", " ),\n", " Lambdad(\n", - " keys=(\"image\",),\n", " func=lambda x: ((2 * (x / 255.0)) - 1.0) * 1024,\n", + " keys=(\"image\",),\n", " allow_missing_keys=True,\n", " ),\n", " Lambdad(\n", - " (\"image\",),\n", - " func=lambda x: np.mean(x, axis=0)[np.newaxis, :] if x.shape[0] != 1 else x,\n", + " func=lambda x: x[0][np.newaxis, :] if x.shape[0] != 1 else x,\n", + " keys=(\"image\",),\n", + " allow_missing_keys=True,\n", " ),\n", " ],\n", ")" diff --git a/poetry.lock b/poetry.lock index 1888780cd..d6e051ef7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. 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"pillow", "plotly", "pybtex", "pydantic", "scour", "spdx-tools"] +models = ["alibi", "alibi-detect", "array-api-compat", "hydra-core", "llvmlite", "monai", "scikit-learn", "torch", "torchxrayvision", "xgboost"] [metadata] lock-version = "2.0" python-versions = ">=3.9, <3.11" -content-hash = "922e7f891d06f8f640c0a89e8d5eabd49cba3cd2bb49cb6fac4043358db1ef95" +content-hash = "f43def1a1ef6c057c5443a157d59c0159f2c1c3b3b26d27ac0150f2da90f744f" diff --git a/pyproject.toml b/pyproject.toml index 0304dccce..04368e92f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,8 +18,16 @@ numpy = "^1.24.4" datasets = "^2.10.1" psutil = "^5.9.4" pyarrow = "^11.0.0" -monai = { version = "^1.1.0", extras = ["itk"] } +pydantic = "^1.10.11" +Jinja2 = "^3.1.2" +spdx-tools = "^0.8.1" +pybtex = "^0.24.0" +kaleido = "0.2.1" +scour = "^0.38.2" +plotly = "^5.7.0" +pillow = "^9.5.0" +monai = { version = "^1.1.0", extras = ["itk"], optional = true } hydra-core = { version = "^1.2.0", optional = true } scikit-learn = { version = "^1.2.2", optional = true } torch = { version = "^1.11.0", optional = true } @@ -28,13 +36,6 @@ xgboost = { version = "^1.5.2", optional = true } alibi = { version = "^0.9.4", optional = true, extras = ["shap"] } alibi-detect = { version = "^0.11.0", optional = true, extras = ["torch"] } llvmlite = { version = "^0.40.0", optional = true } -pydantic = { version = "^1.10.11", optional = true } -spdx-tools = { version = "^0.8.1", optional = true } -pybtex = { version = "^0.24.0", optional = true } -kaleido = { version = "0.2.1", optional = true } -scour = { version = "^0.38.2", optional = true } -plotly = { version = "^5.7.0", optional = true } -pillow = { version = "^9.5.0", optional = true } array-api-compat = {version = "^1.4", optional = true} [tool.poetry.group.models.dependencies] @@ -47,15 +48,7 @@ alibi = { version = "^0.9.4", extras = ["shap"] } alibi-detect = { version = "^0.11.0", extras = ["torch"] } llvmlite = "^0.40.0" array-api-compat = {version = "^1.4"} - -[tool.poetry.group.report.dependencies] -pydantic = "^1.10.11" -spdx-tools = "^0.8.1" -pybtex = "^0.24.0" -kaleido = "0.2.1" -scour = "^0.38.2" -plotly = "^5.7.0" -pillow = "^9.5.0" +monai = { version = "^1.1.0", extras = ["itk"] } [tool.poetry.group.test] optional = true @@ -107,8 +100,18 @@ mpi4py = {git = "https://github.com/mpi4py/mpi4py"} lightning = "^2.1.0" [tool.poetry.extras] -models = ["array-api-compat", "hydra-core", "scikit-learn", "torch", "torchxrayvision", "xgboost", "alibi", "alibi-detect", "llvmlite"] -report = ["pydantic", "spdx-tools", "pybtex", "kaleido", "scour", "plotly", "pillow"] +models = [ + "array-api-compat", + "hydra-core", + "scikit-learn", + "monai", + "torch", + "torchxrayvision", + "xgboost", + "alibi", + "alibi-detect", + "llvmlite", +] [tool.mypy] ignore_missing_imports = true diff --git a/tests/cyclops/evaluate/metrics/conftest.py b/tests/cyclops/evaluate/metrics/conftest.py index f3241828e..1fc41753c 100644 --- a/tests/cyclops/evaluate/metrics/conftest.py +++ b/tests/cyclops/evaluate/metrics/conftest.py @@ -13,7 +13,7 @@ from cyclops.utils.optional import import_optional_module -MPI_pool = import_optional_module("mpi4py.util.pool", error="ignore") +MPIPool = import_optional_module("mpi4py.util.pool", attribute="Pool", error="warn") with contextlib.suppress(RuntimeError): set_start_method("spawn") @@ -61,8 +61,8 @@ def pytest_configure(): ) pytest.torch_pool = torch_pool # type: ignore - if MPI_pool is not None: - mpi_pool = MPI_pool.Pool(processes=NUM_PROCESSES, path=sys.path) + if MPIPool is not None: + mpi_pool = MPIPool(processes=NUM_PROCESSES, path=sys.path) pytest.mpi_pool = mpi_pool # type: ignore @@ -71,6 +71,6 @@ def pytest_sessionfinish(): pytest.torch_pool.close() # type: ignore pytest.torch_pool.join() # type: ignore - if MPI_pool is not None: + if MPIPool is not None: pytest.mpi_pool.close() # type: ignore pytest.mpi_pool.join() # type: ignore diff --git a/tests/cyclops/evaluate/metrics/experimental/distributed_backends/test_mpi4py.py b/tests/cyclops/evaluate/metrics/experimental/distributed_backends/test_mpi4py.py index d2909676d..672c4f5e8 100644 --- a/tests/cyclops/evaluate/metrics/experimental/distributed_backends/test_mpi4py.py +++ b/tests/cyclops/evaluate/metrics/experimental/distributed_backends/test_mpi4py.py @@ -15,10 +15,10 @@ from ..testers import DummyListStateMetric, DummyMetric -MPI = import_optional_module("mpi4py.MPI", error="ignore") +MPI = import_optional_module("mpi4py.MPI", error="warn") -def _test_mpi4py_class_init(rank: int, worldsize: int = 2): +def _test_mpi4py_class_init(rank: int, worldsize: int = NUM_PROCESSES): """Run test.""" if MPI is None: with pytest.raises( @@ -38,10 +38,10 @@ def _test_mpi4py_class_init(rank: int, worldsize: int = 2): @pytest.mark.integration_test() def test_mpi4py_backend_class_init(): """Test `TorchDistributed` class.""" - pytest.mpi_pool.starmap(_test_mpi4py_class_init, [(rank, 2) for rank in range(2)]) # type: ignore + pytest.mpi_pool.starmap(_test_mpi4py_class_init, [(rank, NUM_PROCESSES) for rank in range(NUM_PROCESSES)]) # type: ignore -def _test_all_gather_simple(rank: int, worldsize: int = 2): +def _test_all_gather_simple(rank: int, worldsize: int = NUM_PROCESSES): """Run test.""" backend = MPI4Py() @@ -53,7 +53,7 @@ def _test_all_gather_simple(rank: int, worldsize: int = 2): assert anp.all(val == anp.ones_like(val)) -def _test_all_gather_uneven_arrays(rank: int, worldsize: int = 2): +def _test_all_gather_uneven_arrays(rank: int, worldsize: int = NUM_PROCESSES): """Run test.""" backend = MPI4Py() @@ -65,7 +65,7 @@ def _test_all_gather_uneven_arrays(rank: int, worldsize: int = 2): assert anp.all(val == anp.ones_like(val)) -def _test_all_gather_uneven_multidim_arrays(rank: int, worldsize: int = 2): +def _test_all_gather_uneven_multidim_arrays(rank: int, worldsize: int = NUM_PROCESSES): """Run test.""" backend = MPI4Py() @@ -89,7 +89,7 @@ def _test_all_gather_uneven_multidim_arrays(rank: int, worldsize: int = 2): ) def test_mpi4py_all_gather(case_fn): """Test `all_gather` method.""" - pytest.mpi_pool.starmap(case_fn, [(rank, 2) for rank in range(NUM_PROCESSES)]) # type: ignore + pytest.mpi_pool.starmap(case_fn, [(rank, NUM_PROCESSES) for rank in range(NUM_PROCESSES)]) # type: ignore def _test_dist_sum(rank: int, worldsize: int = NUM_PROCESSES) -> None: diff --git a/tests/cyclops/evaluate/metrics/experimental/distributed_backends/test_torch_distributed.py b/tests/cyclops/evaluate/metrics/experimental/distributed_backends/test_torch_distributed.py index 17077a205..aa57b6dfe 100644 --- a/tests/cyclops/evaluate/metrics/experimental/distributed_backends/test_torch_distributed.py +++ b/tests/cyclops/evaluate/metrics/experimental/distributed_backends/test_torch_distributed.py @@ -13,16 +13,16 @@ from ..testers import DummyListStateMetric, DummyMetric -torch = import_optional_module("torch", error="ignore") +torch = import_optional_module("torch", error="warn") def _test_torch_distributed_class(rank: int, worldsize: int = NUM_PROCESSES): """Run test.""" - torch_dist = import_optional_module("torch.distributed", error="ignore") + torch_dist = import_optional_module("torch.distributed", error="warn") if torch is None: with pytest.raises( ImportError, - match="For availability of TorchDistributed please install .*", + match="For availability of `TorchDistributed` please install .*", ): backend = TorchDistributed() @@ -32,7 +32,7 @@ def _test_torch_distributed_class(rank: int, worldsize: int = NUM_PROCESSES): # skip if torch distributed is not available if torch_dist is None: - pytest.skip("torch.distributed is not available") + pytest.skip("`torch.distributed` is not available") backend = TorchDistributed() diff --git a/tests/cyclops/evaluate/metrics/experimental/utils/test_ops.py b/tests/cyclops/evaluate/metrics/experimental/utils/test_ops.py index cf2d2c0a7..3704674af 100644 --- a/tests/cyclops/evaluate/metrics/experimental/utils/test_ops.py +++ b/tests/cyclops/evaluate/metrics/experimental/utils/test_ops.py @@ -26,7 +26,7 @@ from cyclops.utils.optional import import_optional_module -cp = import_optional_module("cupy", error="ignore") +cp = import_optional_module("cupy", error="warn") def multiply_by_two(x): diff --git a/tests/cyclops/utils/test_optional.py b/tests/cyclops/utils/test_optional.py index 2ccb3854d..28077531c 100644 --- a/tests/cyclops/utils/test_optional.py +++ b/tests/cyclops/utils/test_optional.py @@ -1,37 +1,73 @@ """Test optional import utilities.""" +from math import sqrt import pytest from cyclops.utils.optional import import_optional_module -class TestImportOptionalModule: - """Test importing optional modules.""" +def test_import_valid_module(): + """Test importing a valid module.""" + module = import_optional_module("math") + assert module is not None + import math - def test_import_valid_module(self): - """Test importing a valid module.""" - module = import_optional_module("math") - assert module is not None - import math + assert module == math - assert module == math - def test_import_nonexistent_module_ignore(self): - """Test importing a non-existent module with `error='ignore'`.""" - module = import_optional_module("nonexistent_module", error="ignore") - assert module is None +def test_import_valid_module_attribute(): + """Test importing a valid module attribute.""" + module = import_optional_module("math", attribute="sqrt") + assert module is not None + assert module == sqrt - def test_import_nonexistent_module_warn(self): - """Test importing a non-existent module with `error='warn'`.""" - with pytest.warns(ImportWarning): - import_optional_module("nonexistent_module", error="warn") - def test_import_nonexistent_module_raise(self): - """Test importing a non-existent module with `error='raise'`.""" - with pytest.raises(ModuleNotFoundError): - import_optional_module("nonexistent_module", error="raise") +def test_import_nonexistent_module_ignore(): + """Test importing a non-existent module with `error='ignore'`.""" + module = import_optional_module("nonexistent_module", error="ignore") + assert module is None - def test_invalid_error_option(self): - """Test importing a valid module with an invalid error option.""" - with pytest.raises(ValueError): - import_optional_module("math", error="invalid_option") # type: ignore + attr = import_optional_module( + "nonexistent_module", + attribute="nonexistent_attribute", + error="ignore", + ) + assert attr is None + + +def test_import_nonexistent_module_warn(): + """Test importing a non-existent module with `error='warn'`.""" + with pytest.warns(ImportWarning): + import_optional_module("nonexistent_module", error="warn") + + with pytest.warns(ImportWarning): + import_optional_module( + "nonexistent_module", + attribute="nonexistent_attribute", + error="warn", + ) + + +def test_import_nonexistent_module_raise(): + """Test importing a non-existent module with `error='raise'`.""" + with pytest.raises(ModuleNotFoundError): + import_optional_module("nonexistent_module", error="raise") + + with pytest.raises(ModuleNotFoundError): + import_optional_module( + "nonexistent_module", + attribute="nonexistent_attribute", + error="raise", + ) + + +def test_invalid_error_option(): + """Test importing a valid module with an invalid error option.""" + with pytest.raises(ValueError): + import_optional_module("math", error="invalid_option") # type: ignore + + +def test_import_nonexistent_attribute(): + """Test importing a non-existent attribute.""" + with pytest.raises(AttributeError): + import_optional_module("math", attribute="nonexistent_attribute") diff --git a/tests/package/base.py b/tests/package/base.py index dd9b940e5..42f56a569 100644 --- a/tests/package/base.py +++ b/tests/package/base.py @@ -1,5 +1,6 @@ """Test import of subpackages with base cyclops install.""" +import numpy as np import pytest @@ -19,5 +20,27 @@ def test_import_cyclops(): import cyclops.models with pytest.raises(ImportError): import cyclops.monitor - with pytest.raises(ImportError): - import cyclops.report + + +def test_medical_image_feature_without_monai(): + """Test that the MedicalImage feature raises an error without MONAI installed.""" + from cyclops.data.features.medical_image import MedicalImage + + feat = MedicalImage() + # create a dummy image + img = np.random.rand(10, 10, 10) + + # test encode_example + with pytest.raises( + RuntimeError, + match="The MONAI library is required to use the `MedicalImage` feature.*", + ): + feat.encode_example(img) + + # test decode_example + dummy_val = {"path": "/dummy/local/path", "bytes": None} + with pytest.raises( + RuntimeError, + match="The MONAI library is required to use the `MedicalImage` feature.*", + ): + feat.decode_example(dummy_val) diff --git a/tests/package/extras/models.py b/tests/package/extras/models.py index 338594044..7d70f6048 100644 --- a/tests/package/extras/models.py +++ b/tests/package/extras/models.py @@ -1,7 +1,5 @@ """Test import of subpackages with base cyclops + models extra install.""" -import pytest - def test_import_cyclops(): """Test import of cyclops.""" @@ -24,6 +22,3 @@ def test_import_cyclops(): from cyclops import monitor assert monitor.__name__ == "cyclops.monitor" - - with pytest.raises(ImportError): - import cyclops.report diff --git a/tests/package/extras/report.py b/tests/package/extras/report.py deleted file mode 100644 index 217970034..000000000 --- a/tests/package/extras/report.py +++ /dev/null @@ -1,25 +0,0 @@ -"""Test import of subpackages with base cyclops + report extra install.""" - -import pytest - - -def test_import_cyclops(): - """Test import of cyclops.""" - import cyclops - - assert cyclops.__name__ == "cyclops" - - from cyclops import data - - assert data.__name__ == "cyclops.data" - - from cyclops import report - - assert report.__name__ == "cyclops.report" - - with pytest.raises(ImportError): - import cyclops.evaluate - with pytest.raises(ImportError): - import cyclops.models - with pytest.raises(ImportError): - import cyclops.monitor