From 7ff11322964c22f608162cc8729c236ed258c1a9 Mon Sep 17 00:00:00 2001 From: Christoffer Date: Fri, 29 Sep 2023 13:22:43 +0200 Subject: [PATCH 01/17] added albumentations transform test --- tests/darwin/torch/transform_test.py | 84 ++++++++++++++++++++++++++++ 1 file changed, 84 insertions(+) create mode 100644 tests/darwin/torch/transform_test.py diff --git a/tests/darwin/torch/transform_test.py b/tests/darwin/torch/transform_test.py new file mode 100644 index 000000000..8bc974b08 --- /dev/null +++ b/tests/darwin/torch/transform_test.py @@ -0,0 +1,84 @@ +import numpy as np +import pytest +import torch +from albumentations import BboxParams, Compose, HorizontalFlip, Resize +from PIL import Image + +from darwin.torch.transforms import AlbumentationsTransform + +# Sample data +SAMPLE_IMAGE = Image.new("RGB", (100, 100)) +SAMPLE_ANNOTATION = {"boxes": torch.tensor([[25, 25, 75, 75]]), "labels": torch.tensor([1]), "area": torch.tensor([2500.0]), "iscrowd": torch.tensor([0])} + +SAMPLE_ANNOTATION_OOB = { + "boxes": torch.tensor([[25, 25, 105, 105]]), # Out of bounds + "labels": torch.tensor([1]), + "area": torch.tensor([2500.0]), + "iscrowd": torch.tensor([0]), +} + +SAMPLE_ANNOTATION_WITH_MASKS = {**SAMPLE_ANNOTATION, "masks": torch.ones((1, 100, 100))} + +EXAMPLE_TRANSFORM = Compose([HorizontalFlip(p=1)], bbox_params=BboxParams(format="coco", label_fields=["labels"])) +EXAMPLE_TRANSFORM_RESIZE = Compose([Resize(50, 50)], bbox_params=BboxParams(format="coco", label_fields=["labels"])) + + +class TestAlbumentationsTransform: + def test_init(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + assert isinstance(at, AlbumentationsTransform) + + def test_from_path_invalid(self): + with pytest.raises(ValueError): + AlbumentationsTransform.from_path("invalid/path/to/config.yml") + + def test_from_dict_invalid(self): + with pytest.raises(ValueError): + AlbumentationsTransform.from_dict({"invalid": "config"}) + + def test_transformations(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + image, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION) + assert annotation["boxes"][0, 0] != SAMPLE_ANNOTATION["boxes"][0, 0] + + def test_transformations_resize(self): + transformations = EXAMPLE_TRANSFORM_RESIZE + at = AlbumentationsTransform(transformations) + image, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION) + assert image.shape[:2] == (50, 50) # We only check the height and width + + def test_boxes_out_of_bounds(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + with pytest.raises(ValueError): + _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION_OOB) # Expecting the ValueError due to out of bounds + + def test_transform_with_masks(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION_WITH_MASKS) + assert "masks" in annotation + assert annotation["masks"].shape[0] == 1 + + def test_area_calculation_with_masks(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION_WITH_MASKS) + assert annotation["area"] == torch.sum(annotation["masks"]) + + def test_area_calculation_without_masks(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION) + area = annotation["boxes"][0, 2] * annotation["boxes"][0, 3] + + assert torch.isclose(annotation["area"], area.unsqueeze(0), atol=1e-5) # Using isclose for floating point comparison + + def test_iscrowd_unchanged(self): + transformations = EXAMPLE_TRANSFORM + at = AlbumentationsTransform(transformations) + _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION) + assert "iscrowd" in annotation + assert annotation["iscrowd"] == SAMPLE_ANNOTATION["iscrowd"] From 88a2750786a0bfa3a85c4328727a894975ea3465 Mon Sep 17 00:00:00 2001 From: Christoffer Date: Fri, 29 Sep 2023 14:27:06 +0200 Subject: [PATCH 02/17] updated poetry file --- poetry.lock | 88 +++++------------------------------------------------ 1 file changed, 8 insertions(+), 80 deletions(-) diff --git a/poetry.lock b/poetry.lock index 7e534aaa3..6d8b9a3f0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. [[package]] name = "argcomplete" version = "2.1.2" description = "Bash tab completion for argparse" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -23,7 +22,6 @@ test = ["coverage", "flake8", "mypy", "pexpect", "wheel"] name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -45,7 +43,6 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte name = "black" version = "22.12.0" description = "The uncompromising code formatter." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -82,7 +79,6 @@ uvloop = ["uvloop (>=0.15.2)"] name = "certifi" version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -94,7 +90,6 @@ files = [ name = "charset-normalizer" version = "3.2.0" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -179,7 +174,6 @@ files = [ name = "click" version = "8.1.7" description = "Composable command line interface toolkit" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -195,7 +189,6 @@ importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -207,7 +200,6 @@ files = [ name = "connected-components-3d" version = "3.12.2" description = "Connected components on 2D and 3D images. Supports multiple labels." -category = "main" optional = true python-versions = ">=3.7,<4.0" files = [ @@ -255,7 +247,6 @@ numpy = "*" name = "debugpy" version = "1.6.7.post1" description = "An implementation of the Debug Adapter Protocol for Python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -283,7 +274,6 @@ files = [ name = "deprecation" version = "2.1.0" description = "A library to handle automated deprecations" -category = "main" optional = false python-versions = "*" files = [ @@ -298,7 +288,6 @@ packaging = "*" name = "exceptiongroup" version = "1.1.3" description = "Backport of PEP 654 (exception groups)" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -313,7 +302,6 @@ test = ["pytest (>=6)"] name = "flake8" version = "6.1.0" description = "the modular source code checker: pep8 pyflakes and co" -category = "main" optional = true python-versions = ">=3.8.1" files = [ @@ -330,7 +318,6 @@ pyflakes = ">=3.1.0,<3.2.0" name = "flake8-pyproject" version = "1.2.3" description = "Flake8 plug-in loading the configuration from pyproject.toml" -category = "main" optional = true python-versions = ">= 3.6" files = [ @@ -348,7 +335,6 @@ dev = ["pyTest", "pyTest-cov"] name = "humanize" version = "4.6.0" description = "Python humanize utilities" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -366,7 +352,6 @@ tests = ["freezegun", "pytest", "pytest-cov"] name = "idna" version = "3.4" description = "Internationalized Domain Names in Applications (IDNA)" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -378,7 +363,6 @@ files = [ name = "importlib-metadata" version = "5.2.0" description = "Read metadata from Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -399,7 +383,6 @@ testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packag name = "importlib-resources" version = "5.12.0" description = "Read resources from Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -418,7 +401,6 @@ testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-chec name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -430,7 +412,6 @@ files = [ name = "isort" version = "5.11.5" description = "A Python utility / library to sort Python imports." -category = "main" optional = true python-versions = ">=3.7.0" files = [ @@ -448,7 +429,6 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"] name = "joblib" version = "1.3.2" description = "Lightweight pipelining with Python functions" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -460,7 +440,6 @@ files = [ name = "jsonschema" version = "4.17.3" description = "An implementation of JSON Schema validation for Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -484,7 +463,6 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "markdown-it-py" version = "2.2.0" description = "Python port of markdown-it. Markdown parsing, done right!" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -510,7 +488,6 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] name = "mccabe" version = "0.7.0" description = "McCabe checker, plugin for flake8" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -522,7 +499,6 @@ files = [ name = "mdurl" version = "0.1.2" description = "Markdown URL utilities" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -534,7 +510,6 @@ files = [ name = "mpire" version = "2.8.0" description = "A Python package for easy multiprocessing, but faster than multiprocessing" -category = "main" optional = false python-versions = "*" files = [ @@ -557,7 +532,6 @@ testing = ["dataclasses", "multiprocess", "multiprocess (>=0.70.15)", "numpy", " name = "mypy" version = "0.991" description = "Optional static typing for Python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -609,7 +583,6 @@ reports = ["lxml"] name = "mypy-extensions" version = "1.0.0" description = "Type system extensions for programs checked with the mypy type checker." -category = "main" optional = true python-versions = ">=3.5" files = [ @@ -621,7 +594,6 @@ files = [ name = "nibabel" version = "5.1.0" description = "Access a multitude of neuroimaging data formats" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -652,7 +624,6 @@ zstd = ["pyzstd (>=0.14.3)"] name = "numpy" version = "1.21.6" description = "NumPy is the fundamental package for array computing with Python." -category = "main" optional = false python-versions = ">=3.7,<3.11" files = [ @@ -693,7 +664,6 @@ files = [ name = "nvidia-cublas-cu11" version = "11.10.3.66" description = "CUBLAS native runtime libraries" -category = "main" optional = true python-versions = ">=3" files = [ @@ -709,7 +679,6 @@ wheel = "*" name = "nvidia-cuda-nvrtc-cu11" version = "11.7.99" description = "NVRTC native runtime libraries" -category = "main" optional = true python-versions = ">=3" files = [ @@ -726,7 +695,6 @@ wheel = "*" name = "nvidia-cuda-runtime-cu11" version = "11.7.99" description = "CUDA Runtime native Libraries" -category = "main" optional = true python-versions = ">=3" files = [ @@ -742,7 +710,6 @@ wheel = "*" name = "nvidia-cudnn-cu11" version = "8.5.0.96" description = "cuDNN runtime libraries" -category = "main" optional = true python-versions = ">=3" files = [ @@ -758,7 +725,6 @@ wheel = "*" name = "opencv-python-headless" version = "4.8.0.76" description = "Wrapper package for OpenCV python bindings." -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -773,19 +739,18 @@ files = [ [package.dependencies] numpy = [ - {version = ">=1.21.0", markers = "python_version <= \"3.9\" and platform_system == \"Darwin\" and platform_machine == \"arm64\""}, - {version = ">=1.21.2", markers = "python_version >= \"3.10\""}, + {version = ">=1.21.0", markers = "python_version <= \"3.9\" and platform_system == \"Darwin\" and platform_machine == \"arm64\" and python_version >= \"3.7\""}, {version = ">=1.21.4", markers = "python_version >= \"3.10\" and platform_system == \"Darwin\""}, - {version = ">=1.19.3", markers = "python_version >= \"3.6\" and platform_system == \"Linux\" and platform_machine == \"aarch64\" or python_version >= \"3.9\""}, - {version = ">=1.17.0", markers = "python_version >= \"3.7\""}, - {version = ">=1.17.3", markers = "python_version >= \"3.8\""}, + {version = ">=1.21.2", markers = "platform_system != \"Darwin\" and python_version >= \"3.10\""}, + {version = ">=1.19.3", markers = "platform_system == \"Linux\" and python_version < \"3.10\" and platform_machine == \"aarch64\" and python_version >= \"3.7\" or python_version < \"3.10\" and platform_system != \"Darwin\" and python_version >= \"3.9\" or python_version < \"3.10\" and python_version >= \"3.9\" and platform_machine != \"arm64\" or python_version > \"3.9\" and python_version < \"3.10\""}, + {version = ">=1.17.3", markers = "(platform_system != \"Darwin\" and platform_system != \"Linux\") and python_version >= \"3.8\" and python_version < \"3.9\" or platform_system != \"Darwin\" and python_version >= \"3.8\" and python_version < \"3.9\" and platform_machine != \"aarch64\" or platform_machine != \"arm64\" and python_version >= \"3.8\" and python_version < \"3.9\" and platform_system != \"Linux\" or (platform_machine != \"arm64\" and platform_machine != \"aarch64\") and python_version >= \"3.8\" and python_version < \"3.9\""}, + {version = ">=1.17.0", markers = "(platform_system != \"Darwin\" and platform_system != \"Linux\") and python_version >= \"3.7\" and python_version < \"3.8\" or platform_system != \"Darwin\" and python_version >= \"3.7\" and python_version < \"3.8\" and platform_machine != \"aarch64\" or platform_machine != \"arm64\" and python_version >= \"3.7\" and python_version < \"3.8\" and platform_system != \"Linux\" or (platform_machine != \"arm64\" and platform_machine != \"aarch64\") and python_version >= \"3.7\" and python_version < \"3.8\""}, ] [[package]] name = "orjson" version = "3.9.5" description = "Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -855,7 +820,6 @@ files = [ name = "packaging" version = "23.1" description = "Core utilities for Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -867,7 +831,6 @@ files = [ name = "pathspec" version = "0.11.2" description = "Utility library for gitignore style pattern matching of file paths." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -879,7 +842,6 @@ files = [ name = "pillow" version = "9.5.0" description = "Python Imaging Library (Fork)" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -959,7 +921,6 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa name = "pkgutil-resolve-name" version = "1.3.10" description = "Resolve a name to an object." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -971,7 +932,6 @@ files = [ name = "platformdirs" version = "3.10.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -990,7 +950,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co name = "pluggy" version = "1.2.0" description = "plugin and hook calling mechanisms for python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1009,7 +968,6 @@ testing = ["pytest", "pytest-benchmark"] name = "pycodestyle" version = "2.11.0" description = "Python style guide checker" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -1021,7 +979,6 @@ files = [ name = "pydantic" version = "1.10.12" description = "Data validation and settings management using python type hints" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1074,7 +1031,6 @@ email = ["email-validator (>=1.0.3)"] name = "pyflakes" version = "3.1.0" description = "passive checker of Python programs" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -1086,7 +1042,6 @@ files = [ name = "pygments" version = "2.16.1" description = "Pygments is a syntax highlighting package written in Python." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1101,7 +1056,6 @@ plugins = ["importlib-metadata"] name = "pyrsistent" version = "0.19.3" description = "Persistent/Functional/Immutable data structures" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1138,7 +1092,6 @@ files = [ name = "pytest" version = "7.4.0" description = "pytest: simple powerful testing with Python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1162,7 +1115,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "python-dotenv" version = "1.0.0" description = "Read key-value pairs from a .env file and set them as environment variables" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1177,7 +1129,6 @@ cli = ["click (>=5.0)"] name = "pywin32" version = "306" description = "Python for Window Extensions" -category = "main" optional = false python-versions = "*" files = [ @@ -1201,7 +1152,6 @@ files = [ name = "pyyaml" version = "6.0.1" description = "YAML parser and emitter for Python" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1261,7 +1211,6 @@ files = [ name = "requests" version = "2.31.0" description = "Python HTTP for Humans." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1283,7 +1232,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "responses" version = "0.22.0" description = "A utility library for mocking out the `requests` Python library." -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1305,7 +1253,6 @@ tests = ["coverage (>=6.0.0)", "flake8", "mypy", "pytest (>=7.0.0)", "pytest-asy name = "rich" version = "13.5.2" description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal" -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -1325,7 +1272,6 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"] name = "scikit-learn" version = "1.3.0" description = "A set of python modules for machine learning and data mining" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -1368,7 +1314,6 @@ tests = ["black (>=23.3.0)", "matplotlib (>=3.1.3)", "mypy (>=1.3)", "numpydoc ( name = "scipy" version = "1.10.1" description = "Fundamental algorithms for scientific computing in Python" -category = "main" optional = true python-versions = "<3.12,>=3.8" files = [ @@ -1407,7 +1352,6 @@ test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeo name = "setuptools" version = "68.0.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1424,7 +1368,6 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs ( name = "threadpoolctl" version = "3.2.0" description = "threadpoolctl" -category = "main" optional = true python-versions = ">=3.8" files = [ @@ -1436,7 +1379,6 @@ files = [ name = "toml" version = "0.10.2" description = "Python Library for Tom's Obvious, Minimal Language" -category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1448,7 +1390,6 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1460,7 +1401,6 @@ files = [ name = "torch" version = "1.13.1" description = "Tensors and Dynamic neural networks in Python with strong GPU acceleration" -category = "main" optional = true python-versions = ">=3.7.0" files = [ @@ -1501,7 +1441,6 @@ opt-einsum = ["opt-einsum (>=3.3)"] name = "torchvision" version = "0.14.1" description = "image and video datasets and models for torch deep learning" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1528,7 +1467,7 @@ files = [ [package.dependencies] numpy = "*" -pillow = ">=5.3.0,<8.3.0 || >=8.4.0" +pillow = ">=5.3.0,<8.3.dev0 || >=8.4.dev0" requests = "*" torch = "1.13.1" typing-extensions = "*" @@ -1540,7 +1479,6 @@ scipy = ["scipy"] name = "tqdm" version = "4.66.1" description = "Fast, Extensible Progress Meter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1561,7 +1499,6 @@ telegram = ["requests"] name = "typed-ast" version = "1.5.5" description = "a fork of Python 2 and 3 ast modules with type comment support" -category = "main" optional = true python-versions = ">=3.6" files = [ @@ -1612,7 +1549,6 @@ files = [ name = "types-pyyaml" version = "6.0.12.11" description = "Typing stubs for PyYAML" -category = "main" optional = false python-versions = "*" files = [ @@ -1624,7 +1560,6 @@ files = [ name = "types-requests" version = "2.31.0.2" description = "Typing stubs for requests" -category = "main" optional = false python-versions = "*" files = [ @@ -1639,7 +1574,6 @@ types-urllib3 = "*" name = "types-toml" version = "0.10.8.7" description = "Typing stubs for toml" -category = "main" optional = true python-versions = "*" files = [ @@ -1651,7 +1585,6 @@ files = [ name = "types-urllib3" version = "1.26.25.14" description = "Typing stubs for urllib3" -category = "main" optional = false python-versions = "*" files = [ @@ -1663,7 +1596,6 @@ files = [ name = "typing-extensions" version = "4.7.1" description = "Backported and Experimental Type Hints for Python 3.7+" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1675,7 +1607,6 @@ files = [ name = "upolygon" version = "0.1.10" description = "Collection of fast polygon operations for DL" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1697,7 +1628,6 @@ numpy = "*" name = "urllib3" version = "2.0.4" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1715,7 +1645,6 @@ zstd = ["zstandard (>=0.18.0)"] name = "wheel" version = "0.41.1" description = "A built-package format for Python" -category = "main" optional = true python-versions = ">=3.7" files = [ @@ -1730,7 +1659,6 @@ test = ["pytest (>=6.0.0)", "setuptools (>=65)"] name = "zipp" version = "3.15.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1752,4 +1680,4 @@ test = ["flake8-pyproject", "pytest", "responses"] [metadata] lock-version = "2.0" python-versions = ">=3.7.0,<3.11" -content-hash = "bf2caf6db46010fe08b8aac8c522e07985b2a0758c89e830a0f92bdc455c86e3" +content-hash = "791455d63b5366c2242672436020cfb6ce923be62326751b60ac91deea3587a9" From 520f9f38ef2e081090f62ca3e3a2331e5fda0800 Mon Sep 17 00:00:00 2001 From: Christoffer Date: Fri, 29 Sep 2023 14:54:02 +0200 Subject: [PATCH 03/17] added albumentations to poetry.lock --- poetry.lock | 412 ++++++++++++++++++++++++++-------------------------- 1 file changed, 208 insertions(+), 204 deletions(-) diff --git a/poetry.lock b/poetry.lock index 6d8b9a3f0..b756ceea1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -198,46 +198,46 @@ files = [ [[package]] name = "connected-components-3d" -version = "3.12.2" +version = "3.12.3" description = "Connected components on 2D and 3D images. 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Mon Sep 17 00:00:00 2001 From: Christoffer Date: Fri, 29 Sep 2023 15:06:20 +0200 Subject: [PATCH 04/17] added manual install of albumentations --- .github/workflows/tests.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 249d5b8cd..c31739f2f 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -62,6 +62,7 @@ jobs: pip install wheel pip install --upgrade setuptools pip install --editable ".[test,ml,medical,dev,ocv]" + pip install albumentations pip install pytest - name: Run Tests run: python -m pytest -W ignore::DeprecationWarning From 474c1bf47dbbc1032c454b70f3035fb85613788d Mon Sep 17 00:00:00 2001 From: Christoffer Date: Mon, 9 Oct 2023 15:01:14 +0200 Subject: [PATCH 05/17] added main --- tests/darwin/torch/transform_test.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/darwin/torch/transform_test.py b/tests/darwin/torch/transform_test.py index 8bc974b08..5b6fff6d8 100644 --- 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Mon Sep 17 00:00:00 2001 From: Christoffer Date: Fri, 13 Oct 2023 16:43:57 +0200 Subject: [PATCH 08/17] generated new lock file --- poetry.lock | 482 +++++++++++++++++++--------------------------------- 1 file changed, 174 insertions(+), 308 deletions(-) diff --git a/poetry.lock b/poetry.lock index e7d894ad8..f0ec35838 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,11 +1,10 @@ -<<<<<<< HEAD # This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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test = ["pytest", "responses"] [metadata] lock-version = "2.0" python-versions = ">=3.7.0,<3.11" -<<<<<<< HEAD -content-hash = "79b45acaca18659187b28864375d5e9ad8a2cca7376f10e039b7ee4287b29768" -======= -content-hash = "9865d21e7a68ded971e8b79d8d7c3b3ec669bb97eadce284fda60b892540ad2d" ->>>>>>> origin/master +content-hash = "1158b8ae2bbf51d84bc42543f93bc9bb6013df9dba67dec37a4963e477a143e9" From 9c21cf10172f7e8fc63cba2f6b2d63db34cbcde8 Mon Sep 17 00:00:00 2001 From: Christoffer Date: Mon, 16 Oct 2023 10:51:03 +0200 Subject: [PATCH 09/17] ran black --- darwin/exporter/formats/darwin_1_0.py | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/darwin/exporter/formats/darwin_1_0.py b/darwin/exporter/formats/darwin_1_0.py index 8cff79fd3..9af96a2ea 100644 --- a/darwin/exporter/formats/darwin_1_0.py +++ b/darwin/exporter/formats/darwin_1_0.py @@ -34,14 +34,11 @@ def export(annotation_files: Iterable[AnnotationFile], output_dir: Path) -> None def _export_file(annotation_file: AnnotationFile, _: int, output_dir: Path) -> None: - try: filename = annotation_file.path.parts[-1] output_file_path = (output_dir / filename).with_suffix(".json") except Exception as e: - raise ExportException_CouldNotAssembleOutputPath( - f"Could not export file {annotation_file.path} to {output_dir}" - ) from e + raise ExportException_CouldNotAssembleOutputPath(f"Could not export file {annotation_file.path} to {output_dir}") from e try: output: DictFreeForm = _build_json(annotation_file) @@ -50,9 +47,7 @@ def _export_file(annotation_file: AnnotationFile, _: int, output_dir: Path) -> N try: with open(output_file_path, "w") as f: - op = json.dumps(output, option=json.OPT_INDENT_2 | json.OPT_SERIALIZE_NUMPY | json.OPT_NON_STR_KEYS).decode( - "utf-8" - ) + op = json.dumps(output, option=json.OPT_INDENT_2 | json.OPT_SERIALIZE_NUMPY | json.OPT_NON_STR_KEYS).decode("utf-8") f.write(op) except Exception as e: raise ExportException_CouldNotWriteFile(f"Could not write output for {annotation_file.path}") from e From 35ef603580bf9c66c6396a0bc35f659ad275d0a3 Mon Sep 17 00:00:00 2001 From: Christoffer Date: Mon, 16 Oct 2023 10:52:24 +0200 Subject: [PATCH 10/17] ran black --- tests/darwin/torch/transform_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/darwin/torch/transform_test.py b/tests/darwin/torch/transform_test.py index 5b6fff6d8..146e7e715 100644 --- a/tests/darwin/torch/transform_test.py +++ b/tests/darwin/torch/transform_test.py @@ -85,4 +85,4 @@ def test_iscrowd_unchanged(self): if __name__ == "__main__": - pytest.run() \ No newline at end of file + pytest.run() From ddf406f6e9a50a22dcd0a4f1abb411bfa4b37088 Mon Sep 17 00:00:00 2001 From: Christoffer Date: Mon, 16 Oct 2023 11:10:04 +0200 Subject: [PATCH 11/17] formatted the files with black --- darwin/exporter/formats/darwin.py | 1 + tests/darwin/torch/transform_test.py | 11 +++++++++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/darwin/exporter/formats/darwin.py b/darwin/exporter/formats/darwin.py index 0e7f33835..8aab08de8 100644 --- a/darwin/exporter/formats/darwin.py +++ b/darwin/exporter/formats/darwin.py @@ -47,6 +47,7 @@ def build_image_annotation(annotation_file: dt.AnnotationFile) -> Dict[str, Any] } """ annotations: List[Dict[str, Any]] = [] + print(annotations) for annotation in annotation_file.annotations: payload = { annotation.annotation_class.annotation_type: _build_annotation_data(annotation), diff --git a/tests/darwin/torch/transform_test.py b/tests/darwin/torch/transform_test.py index 146e7e715..c0bf05abe 100644 --- a/tests/darwin/torch/transform_test.py +++ b/tests/darwin/torch/transform_test.py @@ -8,7 +8,12 @@ # Sample data SAMPLE_IMAGE = Image.new("RGB", (100, 100)) -SAMPLE_ANNOTATION = {"boxes": torch.tensor([[25, 25, 75, 75]]), "labels": torch.tensor([1]), "area": torch.tensor([2500.0]), "iscrowd": torch.tensor([0])} +SAMPLE_ANNOTATION = { + "boxes": torch.tensor([[25, 25, 75, 75]]), + "labels": torch.tensor([1]), + "area": torch.tensor([2500.0]), + "iscrowd": torch.tensor([0]), +} SAMPLE_ANNOTATION_OOB = { "boxes": torch.tensor([[25, 25, 105, 105]]), # Out of bounds @@ -74,7 +79,9 @@ def test_area_calculation_without_masks(self): _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION) area = annotation["boxes"][0, 2] * annotation["boxes"][0, 3] - assert torch.isclose(annotation["area"], area.unsqueeze(0), atol=1e-5) # Using isclose for floating point comparison + assert torch.isclose( + annotation["area"], area.unsqueeze(0), atol=1e-5 + ) # Using isclose for floating point comparison def test_iscrowd_unchanged(self): transformations = EXAMPLE_TRANSFORM From cf96b32ede1ed65fc179c9d1ec03d31328fd5f5f Mon Sep 17 00:00:00 2001 From: Christoffer Date: Mon, 16 Oct 2023 11:18:33 +0200 Subject: [PATCH 12/17] formatting test --- .vscode/settings.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index f580f74a5..8f33d6863 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -14,7 +14,7 @@ "editor.tabSize": 2 }, "python.formatting.blackPath": "black", - "python.formatting.provider": "none", + "python.formatting.provider": "black" "python.formatting.blackArgs": [ "-l 120" ], From a97ab489f31f711dbd68b01bfc2d7d6fadce49ee Mon Sep 17 00:00:00 2001 From: Christoffer Date: Mon, 16 Oct 2023 11:20:23 +0200 Subject: [PATCH 13/17] formatting test --- .vscode/settings.json | 2 +- darwin/exporter/formats/darwin_1_0.py | 8 ++++++-- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 8f33d6863..7343e13d9 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -14,7 +14,7 @@ "editor.tabSize": 2 }, "python.formatting.blackPath": "black", - "python.formatting.provider": "black" + "python.formatting.provider": "black", "python.formatting.blackArgs": [ "-l 120" ], diff --git a/darwin/exporter/formats/darwin_1_0.py b/darwin/exporter/formats/darwin_1_0.py index 9af96a2ea..0423de192 100644 --- a/darwin/exporter/formats/darwin_1_0.py +++ b/darwin/exporter/formats/darwin_1_0.py @@ -38,7 +38,9 @@ def _export_file(annotation_file: AnnotationFile, _: int, output_dir: Path) -> N filename = annotation_file.path.parts[-1] output_file_path = (output_dir / filename).with_suffix(".json") except Exception as e: - raise ExportException_CouldNotAssembleOutputPath(f"Could not export file {annotation_file.path} to {output_dir}") from e + raise ExportException_CouldNotAssembleOutputPath( + f"Could not export file {annotation_file.path} to {output_dir}" + ) from e try: output: DictFreeForm = _build_json(annotation_file) @@ -47,7 +49,9 @@ def _export_file(annotation_file: AnnotationFile, _: int, output_dir: Path) -> N try: with open(output_file_path, "w") as f: - op = json.dumps(output, option=json.OPT_INDENT_2 | json.OPT_SERIALIZE_NUMPY | json.OPT_NON_STR_KEYS).decode("utf-8") + op = json.dumps(output, option=json.OPT_INDENT_2 | json.OPT_SERIALIZE_NUMPY | json.OPT_NON_STR_KEYS).decode( + "utf-8" + ) f.write(op) except Exception as e: raise ExportException_CouldNotWriteFile(f"Could not write output for {annotation_file.path}") from e From c4f07778c0ddd071df9857d7ecf27158f606e95d Mon Sep 17 00:00:00 2001 From: Christoffer Date: Mon, 16 Oct 2023 11:30:03 +0200 Subject: [PATCH 14/17] ran ruff on changes files --- darwin/exporter/formats/darwin_1_0.py | 2 +- tests/darwin/torch/transform_test.py | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/darwin/exporter/formats/darwin_1_0.py b/darwin/exporter/formats/darwin_1_0.py index 0423de192..b30709c12 100644 --- a/darwin/exporter/formats/darwin_1_0.py +++ b/darwin/exporter/formats/darwin_1_0.py @@ -1,5 +1,5 @@ from pathlib import Path -from typing import Any, Dict, Iterable, List, Union +from typing import Iterable, List, Union import orjson as json diff --git a/tests/darwin/torch/transform_test.py b/tests/darwin/torch/transform_test.py index c0bf05abe..a0b00f926 100644 --- a/tests/darwin/torch/transform_test.py +++ b/tests/darwin/torch/transform_test.py @@ -1,4 +1,3 @@ -import numpy as np import pytest import torch from albumentations import BboxParams, Compose, HorizontalFlip, Resize From 466994bee028f3a3f330caf8c25e800586b92473 Mon Sep 17 00:00:00 2001 From: Christoffer Date: Mon, 16 Oct 2023 11:39:17 +0200 Subject: [PATCH 15/17] testing with black line-length 80 --- tests/darwin/torch/transform_test.py | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/tests/darwin/torch/transform_test.py b/tests/darwin/torch/transform_test.py index a0b00f926..b00befa59 100644 --- a/tests/darwin/torch/transform_test.py +++ b/tests/darwin/torch/transform_test.py @@ -21,10 +21,19 @@ "iscrowd": torch.tensor([0]), } -SAMPLE_ANNOTATION_WITH_MASKS = {**SAMPLE_ANNOTATION, "masks": torch.ones((1, 100, 100))} +SAMPLE_ANNOTATION_WITH_MASKS = { + **SAMPLE_ANNOTATION, + "masks": torch.ones((1, 100, 100)), +} -EXAMPLE_TRANSFORM = Compose([HorizontalFlip(p=1)], bbox_params=BboxParams(format="coco", label_fields=["labels"])) -EXAMPLE_TRANSFORM_RESIZE = Compose([Resize(50, 50)], bbox_params=BboxParams(format="coco", label_fields=["labels"])) +EXAMPLE_TRANSFORM = Compose( + [HorizontalFlip(p=1)], + bbox_params=BboxParams(format="coco", label_fields=["labels"]), +) +EXAMPLE_TRANSFORM_RESIZE = Compose( + [Resize(50, 50)], + bbox_params=BboxParams(format="coco", label_fields=["labels"]), +) class TestAlbumentationsTransform: @@ -57,7 +66,9 @@ def test_boxes_out_of_bounds(self): transformations = EXAMPLE_TRANSFORM at = AlbumentationsTransform(transformations) with pytest.raises(ValueError): - _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION_OOB) # Expecting the ValueError due to out of bounds + _, annotation = at( + SAMPLE_IMAGE, SAMPLE_ANNOTATION_OOB + ) # Expecting the ValueError due to out of bounds def test_transform_with_masks(self): transformations = EXAMPLE_TRANSFORM From 9dc62c0999607d650d523461a2c20ccc0619a145 Mon Sep 17 00:00:00 2001 From: Christoffer Date: Mon, 16 Oct 2023 11:47:32 +0200 Subject: [PATCH 16/17] all black checks passed locally --- darwin/exporter/formats/darwin_1_0.py | 8 ++------ tests/darwin/torch/transform_test.py | 8 ++------ 2 files changed, 4 insertions(+), 12 deletions(-) diff --git a/darwin/exporter/formats/darwin_1_0.py b/darwin/exporter/formats/darwin_1_0.py index b30709c12..d42505711 100644 --- a/darwin/exporter/formats/darwin_1_0.py +++ b/darwin/exporter/formats/darwin_1_0.py @@ -38,9 +38,7 @@ def _export_file(annotation_file: AnnotationFile, _: int, output_dir: Path) -> N filename = annotation_file.path.parts[-1] output_file_path = (output_dir / filename).with_suffix(".json") except Exception as e: - raise ExportException_CouldNotAssembleOutputPath( - f"Could not export file {annotation_file.path} to {output_dir}" - ) from e + raise ExportException_CouldNotAssembleOutputPath(f"Could not export file {annotation_file.path} to {output_dir}") from e try: output: DictFreeForm = _build_json(annotation_file) @@ -49,9 +47,7 @@ def _export_file(annotation_file: AnnotationFile, _: int, output_dir: Path) -> N try: with open(output_file_path, "w") as f: - op = json.dumps(output, option=json.OPT_INDENT_2 | json.OPT_SERIALIZE_NUMPY | json.OPT_NON_STR_KEYS).decode( - "utf-8" - ) + op = json.dumps(output, option=json.OPT_INDENT_2 | json.OPT_SERIALIZE_NUMPY | json.OPT_NON_STR_KEYS).decode("utf-8") f.write(op) except Exception as e: raise ExportException_CouldNotWriteFile(f"Could not write output for {annotation_file.path}") from e diff --git a/tests/darwin/torch/transform_test.py b/tests/darwin/torch/transform_test.py index b00befa59..099fbf241 100644 --- a/tests/darwin/torch/transform_test.py +++ b/tests/darwin/torch/transform_test.py @@ -66,9 +66,7 @@ def test_boxes_out_of_bounds(self): transformations = EXAMPLE_TRANSFORM at = AlbumentationsTransform(transformations) with pytest.raises(ValueError): - _, annotation = at( - SAMPLE_IMAGE, SAMPLE_ANNOTATION_OOB - ) # Expecting the ValueError due to out of bounds + _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION_OOB) # Expecting the ValueError due to out of bounds def test_transform_with_masks(self): transformations = EXAMPLE_TRANSFORM @@ -89,9 +87,7 @@ def test_area_calculation_without_masks(self): _, annotation = at(SAMPLE_IMAGE, SAMPLE_ANNOTATION) area = annotation["boxes"][0, 2] * annotation["boxes"][0, 3] - assert torch.isclose( - annotation["area"], area.unsqueeze(0), atol=1e-5 - ) # Using isclose for floating point comparison + assert torch.isclose(annotation["area"], area.unsqueeze(0), atol=1e-5) # Using isclose for floating point comparison def test_iscrowd_unchanged(self): transformations = EXAMPLE_TRANSFORM From 28bfe07a2cde2532665b949fb4f89105028fe04f Mon Sep 17 00:00:00 2001 From: Christoffer Date: Mon, 16 Oct 2023 11:49:09 +0200 Subject: [PATCH 17/17] formatted darwin.py --- darwin/exporter/formats/darwin.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/darwin/exporter/formats/darwin.py b/darwin/exporter/formats/darwin.py index 8aab08de8..2e6193b4c 100644 --- a/darwin/exporter/formats/darwin.py +++ b/darwin/exporter/formats/darwin.py @@ -55,8 +55,7 @@ def build_image_annotation(annotation_file: dt.AnnotationFile) -> Dict[str, Any] } if ( - annotation.annotation_class.annotation_type == "complex_polygon" - or annotation.annotation_class.annotation_type == "polygon" + annotation.annotation_class.annotation_type == "complex_polygon" or annotation.annotation_class.annotation_type == "polygon" ) and "bounding_box" in annotation.data: payload["bounding_box"] = annotation.data["bounding_box"]