diff --git a/.gitignore b/.gitignore index 79a677e..2dff6ac 100644 --- a/.gitignore +++ b/.gitignore @@ -167,3 +167,5 @@ cython_debug/ # and can be added to the global gitignore or merged into this file. For a more nuclear # option (not recommended) you can uncomment the following to ignore the entire idea folder. #.idea/ + +*.ipynb \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index 9b1d19e..47d3c7a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,14 @@ [[package]] name = "alabaster" -version = "0.7.12" +version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.6" [[package]] name = "alembic" -version = "1.8.1" +version = "1.11.1" description = "A database migration tool for SQLAlchemy." category = "main" optional = false @@ -19,6 +19,7 @@ importlib-metadata = {version = "*", markers = "python_version < \"3.9\""} importlib-resources = {version = "*", markers = "python_version < \"3.9\""} Mako = "*" SQLAlchemy = ">=1.3.0" +typing-extensions = ">=4" [package.extras] tz = ["python-dateutil"] @@ -52,7 +53,7 @@ python-dateutil = ">=2.7.0" [[package]] name = "asttokens" -version = "2.0.8" +version = "2.2.1" description = "Annotate AST trees with source code positions" category = "dev" optional = false @@ -62,7 +63,7 @@ python-versions = "*" six = "*" [package.extras] -test = ["astroid (<=2.5.3)", "pytest"] +test = ["astroid", "pytest"] [[package]] name = "atomicwrites" @@ -81,10 +82,10 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] -docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] +dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "sphinx", "sphinx-notfound-page", "zope.interface"] +docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] +tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "zope.interface"] +tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six"] [[package]] name = "autopage" @@ -107,15 +108,15 @@ pycodestyle = ">=2.9.1" toml = "*" [[package]] -name = "babel" -version = "2.10.3" +name = "Babel" +version = "2.12.1" description = "Internationalization utilities" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] -pytz = ">=2015.7" +pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} [[package]] name = "backcall" @@ -127,7 +128,7 @@ python-versions = "*" [[package]] name = "beautifulsoup4" -version = "4.11.1" +version = "4.12.2" description = "Screen-scraping library" category = "dev" optional = false @@ -167,7 +168,7 @@ platformdirs = ">=2" tomli = ">=0.2.6,<2.0.0" typing-extensions = [ {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}, - {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""}, + {version = ">=3.10.0.0,<3.10.0.1 || >3.10.0.1", markers = "python_version >= \"3.10\""}, ] [package.extras] @@ -179,7 +180,7 @@ uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "bleach" -version = "5.0.1" +version = "6.0.0" description = "An easy safelist-based HTML-sanitizing tool." category = "dev" optional = false @@ -191,11 +192,10 @@ webencodings = "*" [package.extras] css = ["tinycss2 (>=1.1.0,<1.2)"] -dev = ["build (==0.8.0)", "flake8 (==4.0.1)", "hashin (==0.17.0)", "pip-tools (==6.6.2)", "pytest (==7.1.2)", "Sphinx (==4.3.2)", "tox (==3.25.0)", "twine (==4.0.1)", "wheel (==0.37.1)", "black (==22.3.0)", "mypy (==0.961)"] [[package]] name = "blis" -version = "0.9.1" +version = "0.7.9" description = "The Blis BLAS-like linear algebra library, as a self-contained C-extension." category = "main" optional = false @@ -214,7 +214,7 @@ python-versions = ">=3.6" [[package]] name = "certifi" -version = "2022.9.14" +version = "2023.5.7" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false @@ -241,22 +241,19 @@ python-versions = ">=3.6.1" [[package]] name = "chardet" -version = "5.0.0" +version = "5.1.0" description = "Universal encoding detector for Python 3" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [[package]] name = "charset-normalizer" -version = "2.1.1" +version = "3.1.0" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "main" optional = false -python-versions = ">=3.6.0" - -[package.extras] -unicode_backport = ["unicodedata2"] +python-versions = ">=3.7.0" [[package]] name = "click" @@ -271,7 +268,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} [[package]] name = "cliff" -version = "4.0.0" +version = "4.3.0" description = "Command Line Interface Formulation Framework" category = "main" optional = false @@ -287,7 +284,7 @@ stevedore = ">=2.0.1" [[package]] name = "cloudpickle" -version = "2.2.0" +version = "2.2.1" description = "Extended pickling support for Python objects" category = "main" optional = false @@ -295,18 +292,21 @@ python-versions = ">=3.6" [[package]] name = "cmaes" -version = "0.8.2" +version = "0.9.1" description = "Lightweight Covariance Matrix Adaptation Evolution Strategy (CMA-ES) implementation for Python 3." category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] numpy = "*" +[package.extras] +cmawm = ["scipy"] + [[package]] name = "cmd2" -version = "2.4.2" +version = "2.4.3" description = "cmd2 - quickly build feature-rich and user-friendly interactive command line applications in Python" category = "main" optional = false @@ -319,17 +319,17 @@ pyreadline3 = {version = "*", markers = "sys_platform == \"win32\""} wcwidth = ">=0.1.7" [package.extras] -dev = ["codecov", "doc8", "flake8", "invoke", "mypy (==0.902)", "nox", "pytest (>=4.6)", "pytest-cov", "pytest-mock", "sphinx", "sphinx-rtd-theme", "sphinx-autobuild", "twine (>=1.11)"] -test = ["codecov", "coverage", "pytest (>=4.6)", "pytest-cov", "pytest-mock", "gnureadline"] -validate = ["flake8", "mypy (==0.902)", "types-pkg-resources"] +dev = ["codecov", "doc8", "flake8", "invoke", "mypy", "nox", "pytest (>=4.6)", "pytest-cov", "pytest-mock", "sphinx", "sphinx-autobuild", "sphinx-rtd-theme", "twine (>=1.11)"] +test = ["codecov", "coverage", "gnureadline", "pytest (>=4.6)", "pytest-cov", "pytest-mock"] +validate = ["flake8", "mypy", "types-pkg-resources"] [[package]] name = "colorama" -version = "0.4.5" +version = "0.4.6" description = "Cross-platform colored terminal text." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" [[package]] name = "colorlog" @@ -345,6 +345,22 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""} [package.extras] development = ["black", "flake8", "mypy", "pytest", "types-colorama"] +[[package]] +name = "comm" +version = "0.1.3" +description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc." +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +traitlets = ">=5.3" + +[package.extras] +lint = ["black (>=22.6.0)", "mdformat (>0.7)", "mdformat-gfm (>=0.3.5)", "ruff (>=0.0.156)"] +test = ["pytest"] +typing = ["mypy (>=0.990)"] + [[package]] name = "commonmark" version = "0.9.1" @@ -358,33 +374,33 @@ test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"] [[package]] name = "confection" -version = "0.0.1" +version = "0.1.0" description = "The sweetest config system for Python" category = "main" optional = false python-versions = ">=3.6" [package.dependencies] -pydantic = ">=1.7.4,<1.8 || >1.8,<1.8.1 || >1.8.1,<1.10.0" +pydantic = ">=1.7.4,<1.8 || >1.8,<1.8.1 || >1.8.1,<1.11.0" srsly = ">=2.4.0,<3.0.0" [[package]] name = "contourpy" -version = "1.0.5" +version = "1.1.0" description = "Python library for calculating contours of 2D quadrilateral grids" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] numpy = ">=1.16" [package.extras] -test-no-codebase = ["pillow", "matplotlib", "pytest"] -test-minimal = ["pytest"] -test = ["isort", "flake8", "pillow", "matplotlib", "pytest"] -docs = ["sphinx-rtd-theme", "sphinx", "docutils (<0.18)"] -bokeh = ["selenium", "bokeh"] +bokeh = ["bokeh", "selenium"] +docs = ["furo", "sphinx-copybutton"] +mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.2.0)", "types-Pillow"] +test = ["Pillow", "contourpy[test-no-images]", "matplotlib"] +test-no-images = ["pytest", "pytest-cov", "wurlitzer"] [[package]] name = "cookiecutter" @@ -424,7 +440,7 @@ python-versions = ">=3.6" [[package]] name = "cymem" -version = "2.0.6" +version = "2.0.7" description = "Manage calls to calloc/free through Cython" category = "main" optional = false @@ -432,7 +448,7 @@ python-versions = "*" [[package]] name = "databricks-cli" -version = "0.17.3" +version = "0.17.6" description = "A command line interface for Databricks" category = "main" optional = false @@ -448,7 +464,7 @@ tabulate = ">=0.7.7" [[package]] name = "debugpy" -version = "1.6.3" +version = "1.6.7" description = "An implementation of the Debug Adapter Protocol for Python" category = "dev" optional = false @@ -480,20 +496,21 @@ python-versions = "*" [[package]] name = "docker" -version = "5.0.3" +version = "6.1.3" description = "A Python library for the Docker Engine API." category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] -pywin32 = {version = "227", markers = "sys_platform == \"win32\""} -requests = ">=2.14.2,<2.18.0 || >2.18.0" +packaging = ">=14.0" +pywin32 = {version = ">=304", markers = "sys_platform == \"win32\""} +requests = ">=2.26.0" +urllib3 = ">=1.26.0" websocket-client = ">=0.32.0" [package.extras] -ssh = ["paramiko (>=2.4.2)"] -tls = ["pyOpenSSL (>=17.5.0)", "cryptography (>=3.4.7)", "idna (>=2.0.0)"] +ssh = ["paramiko (>=2.4.3)"] [[package]] name = "docker-pycreds" @@ -524,42 +541,46 @@ python-versions = ">=3.6" [[package]] name = "executing" -version = "1.0.0" +version = "1.2.0" description = "Get the currently executing AST node of a frame, and other information" category = "dev" optional = false python-versions = "*" +[package.extras] +tests = ["asttokens", "littleutils", "pytest", "rich"] + [[package]] name = "fastai" -version = "2.7.9" +version = "2.7.12" description = "fastai simplifies training fast and accurate neural nets using modern best practices" category = "main" optional = false python-versions = ">=3.7" [package.dependencies] -fastcore = ">=1.4.5,<1.6" +fastcore = ">=1.5.29,<1.6" fastdownload = ">=0.0.5,<2" fastprogress = ">=0.2.4" matplotlib = "*" packaging = "*" pandas = "*" pillow = ">6.0.0" +pip = "*" pyyaml = "*" requests = "*" scikit-learn = "*" scipy = "*" spacy = "<4" -torch = ">=1.7,<1.14" +torch = ">=1.7,<2.1" torchvision = ">=0.8.2" [package.extras] -dev = ["ipywidgets", "pytorch-lightning", "pytorch-ignite", "transformers", "sentencepiece", "tensorboard", "pydicom", "catalyst", "flask-compress", "captum (>=0.3)", "flask", "wandb", "kornia", "scikit-image", "neptune-client", "comet-ml", "albumentations", "opencv-python", "pyarrow", "ninja", "timm (>=0.6.2.dev)", "accelerate (>=0.10.0)"] +dev = ["accelerate (>=0.10.0)", "albumentations", "captum (>=0.3)", "catalyst", "comet-ml", "flask", "flask-compress", "ipywidgets", "kornia", "neptune-client", "ninja", "opencv-python", "pyarrow", "pydicom", "pytorch-ignite", "pytorch-lightning", "scikit-image", "sentencepiece", "tensorboard", "timm (>=0.6.2.dev)", "transformers", "wandb"] [[package]] name = "fastcore" -version = "1.5.27" +version = "1.5.29" description = "Python supercharged for fastai development" category = "main" optional = false @@ -567,9 +588,10 @@ python-versions = ">=3.7" [package.dependencies] packaging = "*" +pip = "*" [package.extras] -dev = ["numpy", "nbdev (>=0.2.39)", "matplotlib", "pillow", "torch", "pandas", "jupyterlab"] +dev = ["jupyterlab", "matplotlib", "nbdev (>=0.2.39)", "numpy", "pandas", "pillow", "torch"] [[package]] name = "fastdownload" @@ -585,14 +607,14 @@ fastprogress = "*" [[package]] name = "fastjsonschema" -version = "2.16.1" +version = "2.17.1" description = "Fastest Python implementation of JSON schema" category = "dev" optional = false python-versions = "*" [package.extras] -devel = ["colorama", "jsonschema", "json-spec", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"] +devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"] [[package]] name = "fastprogress" @@ -604,19 +626,19 @@ python-versions = ">=3.6" [[package]] name = "filelock" -version = "3.8.0" +version = "3.12.2" description = "A platform independent file lock." -category = "dev" +category = "main" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2022.6.21)", "sphinx (>=5.1.1)", "sphinx-autodoc-typehints (>=1.19.1)"] -testing = ["covdefaults (>=2.2)", "coverage (>=6.4.2)", "pytest (>=7.1.2)", "pytest-cov (>=3)", "pytest-timeout (>=2.1)"] +docs = ["furo (>=2023.5.20)", "sphinx (>=7.0.1)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"] +testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"] [[package]] -name = "flask" -version = "2.2.2" +name = "Flask" +version = "2.2.5" description = "A simple framework for building complex web applications." category = "main" optional = false @@ -635,16 +657,16 @@ dotenv = ["python-dotenv"] [[package]] name = "fonttools" -version = "4.37.2" +version = "4.40.0" description = "Tools to manipulate font files" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.extras] -all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"] +all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.0.0)", "xattr", "zopfli (>=0.1.4)"] graphite = ["lz4 (>=1.7.4.2)"] -interpolatable = ["scipy", "munkres"] +interpolatable = ["munkres", "scipy"] lxml = ["lxml (>=4.0,<5)"] pathops = ["skia-pathops (>=0.5.0)"] plot = ["matplotlib"] @@ -652,24 +674,24 @@ repacker = ["uharfbuzz (>=0.23.0)"] symfont = ["sympy"] type1 = ["xattr"] ufo = ["fs (>=2.2.0,<3)"] -unicode = ["unicodedata2 (>=14.0.0)"] -woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"] +unicode = ["unicodedata2 (>=15.0.0)"] +woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] [[package]] name = "gitdb" -version = "4.0.9" +version = "4.0.10" description = "Git Object Database" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] smmap = ">=3.0.1,<6" [[package]] -name = "gitpython" -version = "3.1.27" -description = "GitPython is a python library used to interact with Git repositories" +name = "GitPython" +version = "3.1.31" +description = "GitPython is a Python library used to interact with Git repositories" category = "main" optional = false python-versions = ">=3.7" @@ -679,14 +701,15 @@ gitdb = ">=4.0.1,<5" [[package]] name = "greenlet" -version = "1.1.3" +version = "2.0.2" description = "Lightweight in-process concurrent programming" category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" [package.extras] -docs = ["sphinx"] +docs = ["Sphinx", "docutils (<0.18)"] +test = ["objgraph", "psutil"] [[package]] name = "gunicorn" @@ -696,6 +719,9 @@ category = "main" optional = false python-versions = ">=3.5" +[package.dependencies] +setuptools = ">=3.0" + [package.extras] eventlet = ["eventlet (>=0.24.1)"] gevent = ["gevent (>=1.4.0)"] @@ -704,18 +730,18 @@ tornado = ["tornado (>=0.2)"] [[package]] name = "h5py" -version = "3.7.0" +version = "3.9.0" description = "Read and write HDF5 files from Python" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] -numpy = ">=1.14.5" +numpy = ">=1.17.3" [[package]] name = "hdf5storage" -version = "0.1.18" +version = "0.1.19" description = "Utilities to read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files." category = "main" optional = false @@ -727,7 +753,7 @@ numpy = {version = "*", markers = "python_version >= \"3.4\""} [[package]] name = "identify" -version = "2.5.5" +version = "2.5.24" description = "File identification library for Python" category = "dev" optional = false @@ -744,6 +770,34 @@ category = "main" optional = false python-versions = ">=3.5" +[[package]] +name = "imageio" +version = "2.31.1" +description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats." +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +numpy = "*" +pillow = ">=8.3.2" + +[package.extras] +all-plugins = ["astropy", "av", "imageio-ffmpeg", "psutil", "tifffile"] +all-plugins-pypy = ["av", "imageio-ffmpeg", "psutil", "tifffile"] +build = ["wheel"] +dev = ["black", "flake8", "fsspec[github]", "pytest", "pytest-cov"] +docs = ["numpydoc", "pydata-sphinx-theme", "sphinx (<6)"] +ffmpeg = ["imageio-ffmpeg", "psutil"] +fits = ["astropy"] +full = ["astropy", "av", "black", "flake8", "fsspec[github]", "gdal", "imageio-ffmpeg", "itk", "numpydoc", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx (<6)", "tifffile", "wheel"] +gdal = ["gdal"] +itk = ["itk"] +linting = ["black", "flake8"] +pyav = ["av"] +test = ["fsspec[github]", "pytest", "pytest-cov"] +tifffile = ["tifffile"] + [[package]] name = "imagesize" version = "1.4.1" @@ -754,7 +808,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "4.12.0" +version = "5.2.0" description = "Read metadata from Python packages" category = "main" optional = false @@ -764,13 +818,13 @@ python-versions = ">=3.7" zipp = ">=0.5" [package.extras] -docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] perf = ["ipython"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] +testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"] [[package]] name = "importlib-resources" -version = "5.9.0" +version = "5.12.0" description = "Read resources from Python packages" category = "main" optional = false @@ -780,44 +834,50 @@ python-versions = ">=3.7" zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} [package.extras] -docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [[package]] name = "iniconfig" -version = "1.1.1" -description = "iniconfig: brain-dead simple config-ini parsing" +version = "2.0.0" +description = "brain-dead simple config-ini parsing" category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.7" [[package]] name = "ipykernel" -version = "6.15.3" +version = "6.24.0" description = "IPython Kernel for Jupyter" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] appnope = {version = "*", markers = "platform_system == \"Darwin\""} -debugpy = ">=1.0" +comm = ">=0.1.1" +debugpy = ">=1.6.5" ipython = ">=7.23.1" jupyter-client = ">=6.1.12" +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" matplotlib-inline = ">=0.1" nest-asyncio = "*" packaging = "*" psutil = "*" -pyzmq = ">=17" +pyzmq = ">=20" tornado = ">=6.1" -traitlets = ">=5.1.0" +traitlets = ">=5.4.0" [package.extras] -test = ["flaky", "ipyparallel", "pre-commit", "pytest-cov", "pytest-timeout", "pytest (>=6.0)"] +cov = ["coverage[toml]", "curio", "matplotlib", "pytest-cov", "trio"] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"] +pyqt5 = ["pyqt5"] +pyside6 = ["pyside6"] +test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov", "pytest-timeout"] [[package]] name = "ipython" -version = "8.5.0" +version = "8.12.2" description = "IPython: Productive Interactive Computing" category = "dev" optional = false @@ -832,15 +892,16 @@ jedi = ">=0.16" matplotlib-inline = "*" pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""} pickleshare = "*" -prompt-toolkit = ">3.0.1,<3.1.0" +prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0" pygments = ">=2.4.0" stack-data = "*" traitlets = ">=5" +typing-extensions = {version = "*", markers = "python_version < \"3.10\""} [package.extras] -all = ["black", "Sphinx (>=1.3)", "ipykernel", "nbconvert", "nbformat", "ipywidgets", "notebook", "ipyparallel", "qtconsole", "pytest (<7.1)", "pytest-asyncio", "testpath", "curio", "matplotlib (!=3.2.0)", "numpy (>=1.19)", "pandas", "trio"] +all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.21)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"] black = ["black"] -doc = ["Sphinx (>=1.3)"] +doc = ["docrepr", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"] kernel = ["ipykernel"] nbconvert = ["nbconvert"] nbformat = ["nbformat"] @@ -848,7 +909,7 @@ notebook = ["ipywidgets", "notebook"] parallel = ["ipyparallel"] qtconsole = ["qtconsole"] test = ["pytest (<7.1)", "pytest-asyncio", "testpath"] -test_extra = ["pytest (<7.1)", "pytest-asyncio", "testpath", "curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.19)", "pandas", "trio"] +test_extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"] [[package]] name = "itsdangerous" @@ -860,7 +921,7 @@ python-versions = ">=3.7" [[package]] name = "jedi" -version = "0.18.1" +version = "0.18.2" description = "An autocompletion tool for Python that can be used for text editors." category = "dev" optional = false @@ -870,11 +931,12 @@ python-versions = ">=3.6" parso = ">=0.8.0,<0.9.0" [package.extras] +docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"] qa = ["flake8 (==3.8.3)", "mypy (==0.782)"] -testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"] +testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] [[package]] -name = "jinja2" +name = "Jinja2" version = "3.1.2" description = "A very fast and expressive template engine." category = "main" @@ -901,7 +963,7 @@ jinja2 = "*" [[package]] name = "joblib" -version = "1.2.0" +version = "1.3.1" description = "Lightweight pipelining with Python functions" category = "main" optional = false @@ -909,7 +971,7 @@ python-versions = ">=3.7" [[package]] name = "jsonschema" -version = "4.16.0" +version = "4.17.3" description = "An implementation of JSON Schema validation for Python" category = "dev" optional = false @@ -927,38 +989,39 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- [[package]] name = "jupyter-client" -version = "7.3.5" +version = "8.3.0" description = "Jupyter protocol implementation and client libraries" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] -entrypoints = "*" -jupyter-core = ">=4.9.2" -nest-asyncio = ">=1.5.4" +importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""} +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" python-dateutil = ">=2.8.2" pyzmq = ">=23.0" tornado = ">=6.2" -traitlets = "*" +traitlets = ">=5.3" [package.extras] -doc = ["ipykernel", "myst-parser", "sphinx-rtd-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt"] -test = ["codecov", "coverage", "ipykernel (>=6.5)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"] +docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] +test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"] [[package]] name = "jupyter-core" -version = "4.11.1" +version = "5.3.1" description = "Jupyter core package. A base package on which Jupyter projects rely." category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] -pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""} -traitlets = "*" +platformdirs = ">=2.5" +pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""} +traitlets = ">=5.3" [package.extras] +docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"] test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] [[package]] @@ -1007,6 +1070,18 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [package.dependencies] six = ">=1.4.1" +[[package]] +name = "lazy_loader" +version = "0.3" +description = "lazy_loader" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +lint = ["pre-commit (>=3.3)"] +test = ["pytest (>=7.4)", "pytest-cov (>=4.1)"] + [[package]] name = "livereload" version = "2.6.3" @@ -1020,22 +1095,8 @@ six = "*" tornado = {version = "*", markers = "python_version > \"2.7\""} [[package]] -name = "lxml" -version = "4.9.1" -description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*" - -[package.extras] -cssselect = ["cssselect (>=0.7)"] -html5 = ["html5lib"] -htmlsoup = ["beautifulsoup4"] -source = ["Cython (>=0.29.7)"] - -[[package]] -name = "mako" -version = "1.2.2" +name = "Mako" +version = "1.2.4" description = "A super-fast templating language that borrows the best ideas from the existing templating languages." category = "main" optional = false @@ -1045,7 +1106,7 @@ python-versions = ">=3.7" MarkupSafe = ">=0.9.2" [package.extras] -babel = ["babel"] +babel = ["Babel"] lingua = ["lingua"] testing = ["pytest"] @@ -1065,12 +1126,12 @@ code_style = ["pre-commit (==2.6)"] compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.2.2,<3.3.0)", "mistletoe-ebp (>=0.10.0,<0.11.0)", "mistune (>=0.8.4,<0.9.0)", "panflute (>=1.12,<2.0)"] linkify = ["linkify-it-py (>=1.0,<2.0)"] plugins = ["mdit-py-plugins"] -rtd = ["myst-nb (==0.13.0a1)", "pyyaml", "sphinx (>=2,<4)", "sphinx-copybutton", "sphinx-panels (>=0.4.0,<0.5.0)", "sphinx-book-theme"] +rtd = ["myst-nb (==0.13.0a1)", "pyyaml", "sphinx (>=2,<4)", "sphinx-book-theme", "sphinx-copybutton", "sphinx-panels (>=0.4.0,<0.5.0)"] testing = ["coverage", "psutil", "pytest (>=3.6,<4)", "pytest-benchmark (>=3.2,<4.0)", "pytest-cov", "pytest-regressions"] [[package]] -name = "markupsafe" -version = "2.1.1" +name = "MarkupSafe" +version = "2.1.3" description = "Safely add untrusted strings to HTML/XML markup." category = "main" optional = false @@ -1090,7 +1151,7 @@ numpy = "*" [[package]] name = "matplotlib" -version = "3.6.0" +version = "3.7.1" description = "Python plotting package" category = "main" optional = false @@ -1100,11 +1161,12 @@ python-versions = ">=3.8" contourpy = ">=1.0.1" cycler = ">=0.10" fonttools = ">=4.22.0" +importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""} kiwisolver = ">=1.0.1" -numpy = ">=1.19" +numpy = ">=1.20" packaging = ">=20.0" pillow = ">=6.2.0" -pyparsing = ">=2.2.1" +pyparsing = ">=2.3.1" python-dateutil = ">=2.7" setuptools_scm = ">=7" @@ -1137,15 +1199,15 @@ testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"] [[package]] name = "mistune" -version = "2.0.4" -description = "A sane Markdown parser with useful plugins and renderers" +version = "3.0.1" +description = "A sane and fast Markdown parser with useful plugins and renderers" category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.7" [[package]] name = "mlflow" -version = "1.28.0" +version = "1.30.1" description = "MLflow: A Platform for ML Development and Productionization" category = "main" optional = false @@ -1156,12 +1218,12 @@ alembic = "<2" click = ">=7.0,<9" cloudpickle = "<3" databricks-cli = ">=0.8.7,<1" -docker = ">=4.0.0,<6" +docker = ">=4.0.0,<7" entrypoints = "<1" Flask = "<3" gitpython = ">=2.1.0,<4" gunicorn = {version = "<21", markers = "platform_system != \"Windows\""} -importlib-metadata = ">=3.7.0,<4.7.0 || >4.7.0,<5" +importlib-metadata = ">=3.7.0,<4.7.0 || >4.7.0,<6" numpy = "<2" packaging = "<22" pandas = "<2" @@ -1178,13 +1240,27 @@ waitress = {version = "<3", markers = "platform_system == \"Windows\""} [package.extras] aliyun-oss = ["aliyunstoreplugin"] -extras = ["scikit-learn", "pyarrow", "boto3", "google-cloud-storage (>=1.30.0)", "azureml-core (>=1.2.0)", "pysftp", "kubernetes", "mlserver (>=0.5.3)", "mlserver-mlflow (>=0.5.3)", "virtualenv"] -pipelines = ["scikit-learn (>=1.0)", "pyarrow (>=7.0)", "shap (>=0.40)", "pandas-profiling (>=3.1)", "ipython (>=7.0)", "markdown (>=3.3)", "Jinja2 (>=3.0)"] +extras = ["azureml-core (>=1.2.0)", "boto3", "google-cloud-storage (>=1.30.0)", "kubernetes", "mlserver (>=0.5.3)", "mlserver-mlflow (>=0.5.3)", "pyarrow", "pysftp", "requests-auth-aws-sigv4", "scikit-learn", "virtualenv"] +pipelines = ["Jinja2 (>=2.11)", "Jinja2 (>=3.0)", "ipython (>=7.0)", "markdown (>=3.3)", "pandas-profiling (>=3.1)", "pyarrow (>=7.0)", "scikit-learn (>=1.0)", "shap (>=0.40)"] sqlserver = ["mlflow-dbstore"] +[[package]] +name = "mpmath" +version = "1.3.0" +description = "Python library for arbitrary-precision floating-point arithmetic" +category = "main" +optional = false +python-versions = "*" + +[package.extras] +develop = ["codecov", "pycodestyle", "pytest (>=4.6)", "pytest-cov", "wheel"] +docs = ["sphinx"] +gmpy = ["gmpy2 (>=2.1.0a4)"] +tests = ["pytest (>=4.6)"] + [[package]] name = "murmurhash" -version = "1.0.8" +version = "1.0.9" description = "Cython bindings for MurmurHash" category = "main" optional = false @@ -1192,11 +1268,11 @@ python-versions = ">=3.6" [[package]] name = "mypy-extensions" -version = "0.4.3" -description = "Experimental type system extensions for programs checked with the mypy typechecker." +version = "1.0.0" +description = "Type system extensions for programs checked with the mypy type checker." category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.5" [[package]] name = "myst-parser" @@ -1217,30 +1293,31 @@ sphinx = ">=3.1,<5" [package.extras] code_style = ["pre-commit (>=2.12,<3.0)"] linkify = ["linkify-it-py (>=1.0,<2.0)"] -rtd = ["ipython", "sphinx-book-theme (>=0.1.0,<0.2.0)", "sphinx-panels (>=0.5.2,<0.6.0)", "sphinxcontrib-bibtex (>=2.1,<3.0)", "sphinxext-rediraffe (>=0.2,<1.0)", "sphinxcontrib.mermaid (>=0.6.3,<0.7.0)", "sphinxext-opengraph (>=0.4.2,<0.5.0)"] +rtd = ["ipython", "sphinx-book-theme (>=0.1.0,<0.2.0)", "sphinx-panels (>=0.5.2,<0.6.0)", "sphinxcontrib-bibtex (>=2.1,<3.0)", "sphinxcontrib.mermaid (>=0.6.3,<0.7.0)", "sphinxext-opengraph (>=0.4.2,<0.5.0)", "sphinxext-rediraffe (>=0.2,<1.0)"] testing = ["beautifulsoup4", "coverage", "docutils (>=0.17.0,<0.18.0)", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"] [[package]] name = "nbclient" -version = "0.6.8" +version = "0.8.0" description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." category = "dev" optional = false -python-versions = ">=3.7.0" +python-versions = ">=3.8.0" [package.dependencies] -jupyter-client = ">=6.1.5" -nbformat = ">=5.0" -nest-asyncio = "*" -traitlets = ">=5.2.2" +jupyter-client = ">=6.1.12" +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +nbformat = ">=5.1" +traitlets = ">=5.4" [package.extras] -sphinx = ["autodoc-traits", "mock", "moto", "myst-parser", "Sphinx (>=1.7)", "sphinx-book-theme"] -test = ["black", "check-manifest", "flake8", "ipykernel", "ipython", "ipywidgets", "mypy", "nbconvert", "pip (>=18.1)", "pre-commit", "pytest (>=4.1)", "pytest-asyncio", "pytest-cov (>=2.6.1)", "setuptools (>=60.0)", "testpath", "twine (>=1.11.0)", "xmltodict"] +dev = ["pre-commit"] +docs = ["autodoc-traits", "mock", "moto", "myst-parser", "nbclient[test]", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling"] +test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"] [[package]] name = "nbconvert" -version = "7.0.0" +version = "7.6.0" description = "Converting Jupyter Notebooks" category = "dev" optional = false @@ -1248,52 +1325,52 @@ python-versions = ">=3.7" [package.dependencies] beautifulsoup4 = "*" -bleach = "*" +bleach = "!=5.0.0" defusedxml = "*" importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""} jinja2 = ">=3.0" jupyter-core = ">=4.7" jupyterlab-pygments = "*" -lxml = "*" markupsafe = ">=2.0" -mistune = ">=2.0.3,<3" +mistune = ">=2.0.3,<4" nbclient = ">=0.5.0" -nbformat = ">=5.1" +nbformat = ">=5.7" packaging = "*" pandocfilters = ">=1.4.1" pygments = ">=2.4.1" tinycss2 = "*" -traitlets = ">=5.0" +traitlets = ">=5.1" [package.extras] -all = ["ipykernel", "ipython", "ipywidgets (>=7)", "nbsphinx (>=0.2.12)", "pre-commit", "pyppeteer (>=1,<1.1)", "pyqtwebengine (>=5.15)", "pytest", "pytest-cov", "pytest-dependency", "sphinx-rtd-theme", "sphinx (==5.0.2)", "tornado (>=6.1)"] -docs = ["ipython", "nbsphinx (>=0.2.12)", "sphinx-rtd-theme", "sphinx (==5.0.2)"] -qtpdf = ["pyqtwebengine (>=5.15)"] +all = ["nbconvert[docs,qtpdf,serve,test,webpdf]"] +docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sphinx-theme", "sphinx (==5.0.2)", "sphinxcontrib-spelling"] +qtpdf = ["nbconvert[qtpng]"] qtpng = ["pyqtwebengine (>=5.15)"] serve = ["tornado (>=6.1)"] -test = ["ipykernel", "ipywidgets (>=7)", "pre-commit", "pyppeteer (>=1,<1.1)", "pytest", "pytest-cov", "pytest-dependency"] +test = ["ipykernel", "ipywidgets (>=7)", "pre-commit", "pytest", "pytest-dependency"] webpdf = ["pyppeteer (>=1,<1.1)"] [[package]] name = "nbformat" -version = "5.5.0" +version = "5.9.0" description = "The Jupyter Notebook format" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] fastjsonschema = "*" jsonschema = ">=2.6" -jupyter_core = "*" +jupyter-core = "*" traitlets = ">=5.1" [package.extras] -test = ["check-manifest", "testpath", "pytest", "pre-commit", "pep440"] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] +test = ["pep440", "pre-commit", "pytest", "testpath"] [[package]] name = "nbsphinx" -version = "0.8.9" +version = "0.8.12" description = "Jupyter Notebook Tools for Sphinx" category = "dev" optional = false @@ -1309,23 +1386,41 @@ traitlets = ">=5" [[package]] name = "nest-asyncio" -version = "1.5.5" +version = "1.5.6" description = "Patch asyncio to allow nested event loops" category = "dev" optional = false python-versions = ">=3.5" +[[package]] +name = "networkx" +version = "3.1" +description = "Python package for creating and manipulating graphs and networks" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.extras] +default = ["matplotlib (>=3.4)", "numpy (>=1.20)", "pandas (>=1.3)", "scipy (>=1.8)"] +developer = ["mypy (>=1.1)", "pre-commit (>=3.2)"] +doc = ["nb2plots (>=0.6)", "numpydoc (>=1.5)", "pillow (>=9.4)", "pydata-sphinx-theme (>=0.13)", "sphinx (>=6.1)", "sphinx-gallery (>=0.12)", "texext (>=0.6.7)"] +extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.10)", "sympy (>=1.10)"] +test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"] + [[package]] name = "nodeenv" -version = "1.7.0" +version = "1.8.0" description = "Node.js virtual environment builder" category = "dev" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*" +[package.dependencies] +setuptools = "*" + [[package]] name = "numpy" -version = "1.23.3" +version = "1.23.5" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -1333,7 +1428,7 @@ python-versions = ">=3.8" [[package]] name = "oauthlib" -version = "3.2.1" +version = "3.2.2" description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" category = "main" optional = false @@ -1366,14 +1461,14 @@ tqdm = "*" [package.extras] benchmark = ["asv", "virtualenv"] -checking = ["black", "hacking", "isort", "mypy (==0.790)", "blackdoc"] +checking = ["black", "blackdoc", "hacking", "isort", "mypy (==0.790)"] codecov = ["codecov", "pytest-cov"] -doctest = ["cma", "matplotlib (>=3.0.0)", "pandas", "plotly (>=4.0.0)", "scikit-learn (>=0.24.2,<1.0.0)", "scikit-optimize", "mlflow"] -document = ["Jinja2 (<3.0.0)", "MarkupSafe (<=2.0.1)", "sphinx (<=3.5.4)", "sphinx-rtd-theme (<=1.0.0)", "sphinx-copybutton (<=0.4.0)", "sphinx-gallery (<=0.10.0)", "sphinx-plotly-directive (<=0.1.3)", "pillow", "matplotlib", "scikit-learn (<1.0.0)", "plotly (>=4.0.0)", "pandas", "lightgbm", "torch (==1.8.0)", "torchvision (==0.9.0)", "torchaudio (==0.8.0)", "thop"] +doctest = ["cma", "matplotlib (>=3.0.0)", "mlflow", "pandas", "plotly (>=4.0.0)", "scikit-learn (>=0.24.2,<1.0.0)", "scikit-optimize"] +document = ["Jinja2 (<3.0.0)", "MarkupSafe (<=2.0.1)", "lightgbm", "matplotlib", "pandas", "pillow", "plotly (>=4.0.0)", "scikit-learn (<1.0.0)", "sphinx (<=3.5.4)", "sphinx-copybutton (<=0.4.0)", "sphinx-gallery (<=0.10.0)", "sphinx-plotly-directive (<=0.1.3)", "sphinx-rtd-theme (<=1.0.0)", "thop", "torch (==1.8.0)", "torchaudio (==0.8.0)", "torchvision (==0.9.0)"] experimental = ["redis"] -integration = ["chainer (>=5.0.0)", "cma", "lightgbm", "mlflow", "wandb", "mpi4py", "mxnet", "pandas", "scikit-learn (>=0.24.2,<1.0.0)", "scikit-optimize", "xgboost", "tensorflow", "tensorflow-datasets", "pytorch-ignite", "pytorch-lightning (>=1.0.2)", "skorch", "catalyst (>=21.3)", "torchaudio (==0.8.0)", "allennlp (>=2.2.0,<2.7.0)", "fastai", "botorch (>=0.4.0)", "torch (==1.8.0+cpu)", "torchvision (==0.9.0+cpu)", "torch (==1.8.0)", "torchvision (==0.9.0)"] +integration = ["allennlp (>=2.2.0,<2.7.0)", "botorch (>=0.4.0)", "catalyst (>=21.3)", "chainer (>=5.0.0)", "cma", "fastai", "lightgbm", "mlflow", "mpi4py", "mxnet", "pandas", "pytorch-ignite", "pytorch-lightning (>=1.0.2)", "scikit-learn (>=0.24.2,<1.0.0)", "scikit-optimize", "skorch", "tensorflow", "tensorflow-datasets", "torch (==1.8.0)", "torch (==1.8.0+cpu)", "torchaudio (==0.8.0)", "torchvision (==0.9.0)", "torchvision (==0.9.0+cpu)", "wandb", "xgboost"] optional = ["bokeh (<2.0.0)", "matplotlib (>=3.0.0)", "pandas", "plotly (>=4.0.0)", "redis", "scikit-learn (>=0.24.2,<1.0.0)"] -testing = ["bokeh (<2.0.0)", "chainer (>=5.0.0)", "cma", "fakeredis", "lightgbm", "matplotlib (>=3.0.0)", "mlflow", "mpi4py", "mxnet", "pandas", "plotly (>=4.0.0)", "pytest", "scikit-learn (>=0.24.2,<1.0.0)", "scikit-optimize", "xgboost", "tensorflow", "tensorflow-datasets", "pytorch-ignite", "pytorch-lightning (>=1.0.2)", "skorch", "catalyst (>=21.3)", "torchaudio (==0.8.0)", "allennlp (>=2.2.0,<2.7.0)", "fastai", "botorch (>=0.4.0)", "torch (==1.8.0+cpu)", "torchvision (==0.9.0+cpu)", "torch (==1.8.0)", "torchvision (==0.9.0)"] +testing = ["allennlp (>=2.2.0,<2.7.0)", "bokeh (<2.0.0)", "botorch (>=0.4.0)", "catalyst (>=21.3)", "chainer (>=5.0.0)", "cma", "fakeredis", "fastai", "lightgbm", "matplotlib (>=3.0.0)", "mlflow", "mpi4py", "mxnet", "pandas", "plotly (>=4.0.0)", "pytest", "pytorch-ignite", "pytorch-lightning (>=1.0.2)", "scikit-learn (>=0.24.2,<1.0.0)", "scikit-optimize", "skorch", "tensorflow", "tensorflow-datasets", "torch (==1.8.0)", "torch (==1.8.0+cpu)", "torchaudio (==0.8.0)", "torchvision (==0.9.0)", "torchvision (==0.9.0+cpu)", "xgboost"] tests = ["fakeredis", "pytest"] [[package]] @@ -1389,7 +1484,7 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" [[package]] name = "pandas" -version = "1.4.4" +version = "1.5.3" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false @@ -1397,10 +1492,9 @@ python-versions = ">=3.8" [package.dependencies] numpy = [ - {version = ">=1.18.5", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""}, - {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""}, - {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""}, + {version = ">=1.20.3", markers = "python_version < \"3.10\""}, {version = ">=1.21.0", markers = "python_version >= \"3.10\""}, + {version = ">=1.23.2", markers = "python_version >= \"3.11\""}, ] python-dateutil = ">=2.8.1" pytz = ">=2020.1" @@ -1430,7 +1524,7 @@ testing = ["docopt", "pytest (<6.0.0)"] [[package]] name = "pathspec" -version = "0.10.1" +version = "0.11.1" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false @@ -1446,25 +1540,26 @@ python-versions = "*" [[package]] name = "pathy" -version = "0.6.2" +version = "0.10.2" description = "pathlib.Path subclasses for local and cloud bucket storage" category = "main" optional = false python-versions = ">= 3.6" [package.dependencies] -smart-open = ">=5.2.1,<6.0.0" +smart-open = ">=5.2.1,<7.0.0" typer = ">=0.3.0,<1.0.0" [package.extras] -all = ["google-cloud-storage (>=1.26.0,<2.0.0)", "boto3", "pytest", "pytest-coverage", "mock", "typer-cli"] +all = ["azure-storage-blob", "boto3", "google-cloud-storage (>=1.26.0,<2.0.0)", "mock", "pytest", "pytest-coverage", "typer-cli"] +azure = ["azure-storage-blob"] gcs = ["google-cloud-storage (>=1.26.0,<2.0.0)"] s3 = ["boto3"] -test = ["pytest", "pytest-coverage", "mock", "typer-cli"] +test = ["mock", "pytest", "pytest-coverage", "typer-cli"] [[package]] name = "pbr" -version = "5.10.0" +version = "5.11.1" description = "Python Build Reasonableness" category = "main" optional = false @@ -1490,19 +1585,27 @@ optional = false python-versions = "*" [[package]] -name = "pillow" -version = "9.2.0" +name = "Pillow" +version = "9.5.0" description = "Python Imaging Library (Fork)" category = "main" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"] +docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-removed-in", "sphinxext-opengraph"] tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] [[package]] -name = "pkgutil-resolve-name" +name = "pip" +version = "23.1.2" +description = "The PyPA recommended tool for installing Python packages." +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "pkgutil_resolve_name" version = "1.3.10" description = "Resolve a name to an object." category = "dev" @@ -1511,34 +1614,35 @@ python-versions = ">=3.6" [[package]] name = "platformdirs" -version = "2.5.2" -description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +version = "3.8.0" +description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"] -test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"] +docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx (>=7.0.1)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)"] [[package]] name = "plotly" -version = "5.10.0" +version = "5.15.0" description = "An open-source, interactive data visualization library for Python" category = "main" optional = false python-versions = ">=3.6" [package.dependencies] +packaging = "*" tenacity = ">=6.2.0" [[package]] name = "pluggy" -version = "1.0.0" +version = "1.2.0" description = "plugin and hook calling mechanisms for python" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.extras] dev = ["pre-commit", "tox"] @@ -1546,7 +1650,7 @@ testing = ["pytest", "pytest-benchmark"] [[package]] name = "pre-commit" -version = "2.20.0" +version = "2.21.0" description = "A framework for managing and maintaining multi-language pre-commit hooks." category = "dev" optional = false @@ -1557,12 +1661,11 @@ cfgv = ">=2.0.0" identify = ">=1.0.0" nodeenv = ">=0.11.1" pyyaml = ">=5.1" -toml = "*" -virtualenv = ">=20.0.8" +virtualenv = ">=20.10.0" [[package]] name = "preshed" -version = "3.0.7" +version = "3.0.8" description = "Cython hash table that trusts the keys are pre-hashed" category = "main" optional = false @@ -1574,11 +1677,11 @@ murmurhash = ">=0.28.0,<1.1.0" [[package]] name = "prettytable" -version = "3.4.1" +version = "3.8.0" description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] wcwidth = "*" @@ -1588,7 +1691,7 @@ tests = ["pytest", "pytest-cov", "pytest-lazy-fixture"] [[package]] name = "prometheus-client" -version = "0.14.1" +version = "0.17.0" description = "Python client for the Prometheus monitoring system." category = "main" optional = false @@ -1599,7 +1702,7 @@ twisted = ["twisted"] [[package]] name = "prometheus-flask-exporter" -version = "0.20.3" +version = "0.22.4" description = "Prometheus metrics exporter for Flask" category = "main" optional = false @@ -1621,22 +1724,22 @@ python-versions = "*" six = "*" [package.extras] -test = ["pytest (>=2.7.3)", "pytest-cov", "coveralls", "futures", "pytest-benchmark", "mock"] +test = ["coveralls", "futures", "mock", "pytest (>=2.7.3)", "pytest-benchmark", "pytest-cov"] [[package]] name = "prompt-toolkit" -version = "3.0.31" +version = "3.0.39" description = "Library for building powerful interactive command lines in Python" category = "dev" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.7.0" [package.dependencies] wcwidth = "*" [[package]] name = "protobuf" -version = "3.20.2" +version = "3.20.3" description = "Protocol Buffers" category = "main" optional = false @@ -1644,14 +1747,14 @@ python-versions = ">=3.7" [[package]] name = "psutil" -version = "5.9.2" +version = "5.9.5" description = "Cross-platform lib for process and system monitoring in Python." category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [package.extras] -test = ["ipaddress", "mock", "enum34", "pywin32", "wmi"] +test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] [[package]] name = "ptyprocess" @@ -1682,15 +1785,18 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "pyaml" -version = "21.10.1" -description = "PyYAML-based module to produce pretty and readable YAML-serialized data" +version = "23.7.0" +description = "PyYAML-based module to produce a bit more pretty and readable YAML-serialized data" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.8" [package.dependencies] PyYAML = "*" +[package.extras] +anchors = ["unidecode"] + [[package]] name = "pybtex" version = "0.24.0" @@ -1732,7 +1838,7 @@ pybtex = ">=0.24.0,<0.25.0" [[package]] name = "pycodestyle" -version = "2.9.1" +version = "2.10.0" description = "Python style guide checker" category = "dev" optional = false @@ -1748,54 +1854,54 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pydantic" -version = "1.9.2" +version = "1.10.11" description = "Data validation and settings management using python type hints" category = "main" optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.7" [package.dependencies] -typing-extensions = ">=3.7.4.3" +typing-extensions = ">=4.2.0" [package.extras] dotenv = ["python-dotenv (>=0.10.4)"] email = ["email-validator (>=1.0.3)"] [[package]] -name = "pygments" -version = "2.13.0" +name = "Pygments" +version = "2.15.1" description = "Pygments is a syntax highlighting package written in Python." category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.extras] plugins = ["importlib-metadata"] [[package]] -name = "pyjwt" -version = "2.4.0" +name = "PyJWT" +version = "2.7.0" description = "JSON Web Token implementation in Python" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.extras] -crypto = ["cryptography (>=3.3.1)"] -dev = ["sphinx", "sphinx-rtd-theme", "zope.interface", "cryptography (>=3.3.1)", "pytest (>=6.0.0,<7.0.0)", "coverage[toml] (==5.0.4)", "mypy", "pre-commit"] -docs = ["sphinx", "sphinx-rtd-theme", "zope.interface"] -tests = ["pytest (>=6.0.0,<7.0.0)", "coverage[toml] (==5.0.4)"] +crypto = ["cryptography (>=3.4.0)"] +dev = ["coverage[toml] (==5.0.4)", "cryptography (>=3.4.0)", "pre-commit", "pytest (>=6.0.0,<7.0.0)", "sphinx (>=4.5.0,<5.0.0)", "sphinx-rtd-theme", "zope.interface"] +docs = ["sphinx (>=4.5.0,<5.0.0)", "sphinx-rtd-theme", "zope.interface"] +tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"] [[package]] name = "pyparsing" -version = "3.0.9" +version = "3.1.0" description = "pyparsing module - Classes and methods to define and execute parsing grammars" category = "main" optional = false python-versions = ">=3.6.8" [package.extras] -diagrams = ["railroad-diagrams", "jinja2"] +diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pyperclip" @@ -1815,7 +1921,7 @@ python-versions = "*" [[package]] name = "pyrsistent" -version = "0.18.1" +version = "0.19.3" description = "Persistent/Functional/Immutable data structures" category = "dev" optional = false @@ -1855,11 +1961,11 @@ six = ">=1.5" [[package]] name = "python-slugify" -version = "6.1.2" +version = "8.0.1" description = "A Python slugify application that also handles Unicode" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">=3.7" [package.dependencies] text-unidecode = ">=1.3" @@ -1869,22 +1975,33 @@ unidecode = ["Unidecode (>=1.1.1)"] [[package]] name = "pytz" -version = "2022.2.1" +version = "2022.7.1" description = "World timezone definitions, modern and historical" category = "main" optional = false python-versions = "*" +[[package]] +name = "PyWavelets" +version = "1.4.1" +description = "PyWavelets, wavelet transform module" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +numpy = ">=1.17.3" + [[package]] name = "pywin32" -version = "227" +version = "306" description = "Python for Window Extensions" category = "main" optional = false python-versions = "*" [[package]] -name = "pyyaml" +name = "PyYAML" version = "6.0" description = "YAML parser and emitter for Python" category = "main" @@ -1893,7 +2010,7 @@ python-versions = ">=3.6" [[package]] name = "pyzmq" -version = "24.0.0" +version = "25.1.0" description = "Python bindings for 0MQ" category = "dev" optional = false @@ -1901,7 +2018,6 @@ python-versions = ">=3.6" [package.dependencies] cffi = {version = "*", markers = "implementation_name == \"pypy\""} -py = {version = "*", markers = "implementation_name == \"pypy\""} [[package]] name = "querystring-parser" @@ -1916,17 +2032,17 @@ six = "*" [[package]] name = "requests" -version = "2.28.1" +version = "2.31.0" description = "Python HTTP for Humans." category = "main" optional = false -python-versions = ">=3.7, <4" +python-versions = ">=3.7" [package.dependencies] certifi = ">=2017.4.17" -charset-normalizer = ">=2,<3" +charset-normalizer = ">=2,<4" idna = ">=2.5,<4" -urllib3 = ">=1.21.1,<1.27" +urllib3 = ">=1.21.1,<3" [package.extras] socks = ["PySocks (>=1.5.6,!=1.5.7)"] @@ -1948,9 +2064,37 @@ pygments = ">=2.6.0,<3.0.0" [package.extras] jupyter = ["ipywidgets (>=7.5.1,<8.0.0)"] +[[package]] +name = "scikit-image" +version = "0.21.0" +description = "Image processing in Python" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +imageio = ">=2.27" +lazy_loader = ">=0.2" +networkx = ">=2.8" +numpy = ">=1.21.1" +packaging = ">=21" +pillow = ">=9.0.1" +PyWavelets = ">=1.1.1" +scipy = ">=1.8" +tifffile = ">=2022.8.12" + +[package.extras] +build = ["Cython (>=0.29.32)", "build", "meson-python (>=0.13)", "ninja", "numpy (>=1.21.1)", "packaging (>=21)", "pythran", "setuptools (>=67)", "spin (==0.3)", "wheel"] +data = ["pooch (>=1.6.0)"] +default = ["PyWavelets (>=1.1.1)", "imageio (>=2.27)", "lazy_loader (>=0.2)", "networkx (>=2.8)", "numpy (>=1.21.1)", "packaging (>=21)", "pillow (>=9.0.1)", "scipy (>=1.8)", "tifffile (>=2022.8.12)"] +developer = ["pre-commit", "rtoml"] +docs = ["dask[array] (>=2022.9.2)", "ipykernel", "ipywidgets", "kaleido", "matplotlib (>=3.5)", "myst-parser", "numpydoc (>=1.5)", "pandas (>=1.5)", "plotly (>=5.10)", "pooch (>=1.6)", "pydata-sphinx-theme (>=0.13)", "pytest-runner", "scikit-learn (>=0.24.0)", "seaborn (>=0.11)", "sphinx (>=5.0)", "sphinx-copybutton", "sphinx-gallery (>=0.11)", "sphinx_design (>=0.3)", "tifffile (>=2022.8.12)"] +optional = ["SimpleITK", "astropy (>=5.0)", "cloudpickle (>=0.2.1)", "dask[array] (>=2021.1.0)", "matplotlib (>=3.5)", "pooch (>=1.6.0)", "pyamg", "scikit-learn (>=0.24.0)"] +test = ["asv", "matplotlib (>=3.5)", "pooch (>=1.6.0)", "pytest (>=7.0)", "pytest-cov (>=2.11.0)", "pytest-faulthandler", "pytest-localserver"] + [[package]] name = "scikit-learn" -version = "1.1.2" +version = "1.1.3" description = "A set of python modules for machine learning and data mining" category = "main" optional = false @@ -1963,10 +2107,10 @@ scipy = ">=1.3.2" threadpoolctl = ">=2.0.0" [package.extras] -tests = ["numpydoc (>=1.2.0)", "pyamg (>=4.0.0)", "mypy (>=0.961)", "black (>=22.3.0)", "flake8 (>=3.8.2)", "pytest-cov (>=2.9.0)", "pytest (>=5.0.1)", "pandas (>=1.0.5)", "scikit-image (>=0.16.2)", "matplotlib (>=3.1.2)"] -examples = ["seaborn (>=0.9.0)", "pandas (>=1.0.5)", "scikit-image (>=0.16.2)", "matplotlib (>=3.1.2)"] -docs = ["sphinxext-opengraph (>=0.4.2)", "sphinx-prompt (>=1.3.0)", "Pillow (>=7.1.2)", "numpydoc (>=1.2.0)", "sphinx-gallery (>=0.7.0)", "sphinx (>=4.0.1)", "memory-profiler (>=0.57.0)", "seaborn (>=0.9.0)", "pandas (>=1.0.5)", "scikit-image (>=0.16.2)", "matplotlib (>=3.1.2)"] -benchmark = ["memory-profiler (>=0.57.0)", "pandas (>=1.0.5)", "matplotlib (>=3.1.2)"] +benchmark = ["matplotlib (>=3.1.2)", "memory-profiler (>=0.57.0)", "pandas (>=1.0.5)"] +docs = ["Pillow (>=7.1.2)", "matplotlib (>=3.1.2)", "memory-profiler (>=0.57.0)", "numpydoc (>=1.2.0)", "pandas (>=1.0.5)", "scikit-image (>=0.16.2)", "seaborn (>=0.9.0)", "sphinx (>=4.0.1)", "sphinx-gallery (>=0.7.0)", "sphinx-prompt (>=1.3.0)", "sphinxext-opengraph (>=0.4.2)"] +examples = ["matplotlib (>=3.1.2)", "pandas (>=1.0.5)", "scikit-image (>=0.16.2)", "seaborn (>=0.9.0)"] +tests = ["black (>=22.3.0)", "flake8 (>=3.8.2)", "matplotlib (>=3.1.2)", "mypy (>=0.961)", "numpydoc (>=1.2.0)", "pandas (>=1.0.5)", "pyamg (>=4.0.0)", "pytest (>=5.0.1)", "pytest-cov (>=2.9.0)", "scikit-image (>=0.16.2)"] [[package]] name = "scikit-optimize" @@ -1988,18 +2132,23 @@ plots = ["matplotlib (>=2.0.0)"] [[package]] name = "scipy" -version = "1.9.1" -description = "SciPy: Scientific Library for Python" +version = "1.10.1" +description = "Fundamental algorithms for scientific computing in Python" category = "main" optional = false -python-versions = ">=3.8,<3.12" +python-versions = "<3.12,>=3.8" [package.dependencies] -numpy = ">=1.18.5,<1.25.0" +numpy = ">=1.19.5,<1.27.0" + +[package.extras] +dev = ["click", "doit (>=0.36.0)", "flake8", "mypy", "pycodestyle", "pydevtool", "rich-click", "typing_extensions"] +doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"] +test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] [[package]] name = "sentry-sdk" -version = "1.9.8" +version = "1.27.1" description = "Python client for Sentry (https://sentry.io)" category = "main" optional = false @@ -2011,6 +2160,7 @@ urllib3 = {version = ">=1.26.11", markers = "python_version >= \"3.6\""} [package.extras] aiohttp = ["aiohttp (>=3.5)"] +arq = ["arq (>=0.23)"] beam = ["apache-beam (>=2.12)"] bottle = ["bottle (>=0.12.13)"] celery = ["celery (>=3)"] @@ -2018,15 +2168,21 @@ chalice = ["chalice (>=1.16.0)"] django = ["django (>=1.8)"] falcon = ["falcon (>=1.4)"] fastapi = ["fastapi (>=0.79.0)"] -flask = ["flask (>=0.11)", "blinker (>=1.1)"] +flask = ["blinker (>=1.1)", "flask (>=0.11)", "markupsafe"] +grpcio = ["grpcio (>=1.21.1)"] httpx = ["httpx (>=0.16.0)"] -pure_eval = ["pure-eval", "executing", "asttokens"] +huey = ["huey (>=2)"] +loguru = ["loguru (>=0.5)"] +opentelemetry = ["opentelemetry-distro (>=0.35b0)"] +pure_eval = ["asttokens", "executing", "pure-eval"] +pymongo = ["pymongo (>=3.1)"] pyspark = ["pyspark (>=2.4.4)"] -quart = ["quart (>=0.16.1)", "blinker (>=1.1)"] +quart = ["blinker (>=1.1)", "quart (>=0.16.1)"] rq = ["rq (>=0.6)"] sanic = ["sanic (>=0.8)"] sqlalchemy = ["sqlalchemy (>=1.2)"] starlette = ["starlette (>=0.19.1)"] +starlite = ["starlite (>=1.48)"] tornado = ["tornado (>=5)"] [[package]] @@ -2040,9 +2196,22 @@ python-versions = ">=3.7" [package.extras] test = ["pytest"] +[[package]] +name = "setuptools" +version = "68.0.0" +description = "Easily download, build, install, upgrade, and uninstall Python packages" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"] +testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] +testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"] + [[package]] name = "setuptools-scm" -version = "7.0.5" +version = "7.1.0" description = "the blessed package to manage your versions by scm tags" category = "main" optional = false @@ -2050,7 +2219,8 @@ python-versions = ">=3.7" [package.dependencies] packaging = ">=20.0" -tomli = ">=1.0.0" +setuptools = "*" +tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} typing-extensions = "*" [package.extras] @@ -2059,7 +2229,7 @@ toml = ["setuptools (>=42)"] [[package]] name = "shortuuid" -version = "1.0.9" +version = "1.0.11" description = "A generator library for concise, unambiguous and URL-safe UUIDs." category = "main" optional = false @@ -2075,19 +2245,20 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "smart-open" -version = "5.2.1" +version = "6.3.0" description = "Utils for streaming large files (S3, HDFS, GCS, Azure Blob Storage, gzip, bz2...)" category = "main" optional = false python-versions = ">=3.6,<4.0" [package.extras] -all = ["boto3", "google-cloud-storage", "azure-storage-blob", "azure-common", "azure-core", "requests"] -azure = ["azure-storage-blob", "azure-common", "azure-core"] -gcs = ["google-cloud-storage"] +all = ["azure-common", "azure-core", "azure-storage-blob", "boto3", "google-cloud-storage (>=2.6.0)", "paramiko", "requests"] +azure = ["azure-common", "azure-core", "azure-storage-blob"] +gcs = ["google-cloud-storage (>=2.6.0)"] http = ["requests"] s3 = ["boto3"] -test = ["boto3", "google-cloud-storage", "azure-storage-blob", "azure-common", "azure-core", "requests", "moto[server] (==1.3.14)", "pathlib2", "responses", "paramiko", "parameterizedtestcase", "pytest", "pytest-rerunfailures"] +ssh = ["paramiko"] +test = ["azure-common", "azure-core", "azure-storage-blob", "boto3", "google-cloud-storage (>=2.6.0)", "moto[server]", "paramiko", "pytest", "pytest-rerunfailures", "requests", "responses"] webhdfs = ["requests"] [[package]] @@ -2108,15 +2279,15 @@ python-versions = "*" [[package]] name = "soupsieve" -version = "2.3.2.post1" +version = "2.4.1" description = "A modern CSS selector implementation for Beautiful Soup." category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [[package]] name = "spacy" -version = "3.4.1" +version = "3.5.4" description = "Industrial-strength Natural Language Processing (NLP) in Python" category = "main" optional = false @@ -2130,46 +2301,50 @@ langcodes = ">=3.2.0,<4.0.0" murmurhash = ">=0.28.0,<1.1.0" numpy = ">=1.15.0" packaging = ">=20.0" -pathy = ">=0.3.5" +pathy = ">=0.10.0" preshed = ">=3.0.2,<3.1.0" -pydantic = ">=1.7.4,<1.8 || >1.8,<1.8.1 || >1.8.1,<1.10.0" +pydantic = ">=1.7.4,<1.8 || >1.8,<1.8.1 || >1.8.1,<1.11.0" requests = ">=2.13.0,<3.0.0" -spacy-legacy = ">=3.0.9,<3.1.0" +setuptools = "*" +smart-open = ">=5.2.1,<7.0.0" +spacy-legacy = ">=3.0.11,<3.1.0" spacy-loggers = ">=1.0.0,<2.0.0" srsly = ">=2.4.3,<3.0.0" -thinc = ">=8.1.0,<8.2.0" +thinc = ">=8.1.8,<8.2.0" tqdm = ">=4.38.0,<5.0.0" -typer = ">=0.3.0,<0.5.0" -wasabi = ">=0.9.1,<1.1.0" +typer = ">=0.3.0,<0.10.0" +wasabi = ">=0.9.1,<1.2.0" [package.extras] apple = ["thinc-apple-ops (>=0.1.0.dev0,<1.0.0)"] -cuda = ["cupy (>=5.0.0b4,<11.0.0)"] -cuda100 = ["cupy-cuda100 (>=5.0.0b4,<11.0.0)"] -cuda101 = ["cupy-cuda101 (>=5.0.0b4,<11.0.0)"] -cuda102 = ["cupy-cuda102 (>=5.0.0b4,<11.0.0)"] -cuda110 = ["cupy-cuda110 (>=5.0.0b4,<11.0.0)"] -cuda111 = ["cupy-cuda111 (>=5.0.0b4,<11.0.0)"] -cuda112 = ["cupy-cuda112 (>=5.0.0b4,<11.0.0)"] -cuda113 = ["cupy-cuda113 (>=5.0.0b4,<11.0.0)"] -cuda114 = ["cupy-cuda114 (>=5.0.0b4,<11.0.0)"] -cuda115 = ["cupy-cuda115 (>=5.0.0b4,<11.0.0)"] -cuda116 = ["cupy-cuda116 (>=5.0.0b4,<11.0.0)"] -cuda117 = ["cupy-cuda117 (>=5.0.0b4,<11.0.0)"] -cuda80 = ["cupy-cuda80 (>=5.0.0b4,<11.0.0)"] -cuda90 = ["cupy-cuda90 (>=5.0.0b4,<11.0.0)"] -cuda91 = ["cupy-cuda91 (>=5.0.0b4,<11.0.0)"] -cuda92 = ["cupy-cuda92 (>=5.0.0b4,<11.0.0)"] -ja = ["sudachipy (>=0.5.2,!=0.6.1)", "sudachidict-core (>=20211220)"] -ko = ["natto-py (==0.9.0)"] +cuda = ["cupy (>=5.0.0b4,<13.0.0)"] +cuda-autodetect = ["cupy-wheel (>=11.0.0,<13.0.0)"] +cuda100 = ["cupy-cuda100 (>=5.0.0b4,<13.0.0)"] +cuda101 = ["cupy-cuda101 (>=5.0.0b4,<13.0.0)"] +cuda102 = ["cupy-cuda102 (>=5.0.0b4,<13.0.0)"] +cuda110 = ["cupy-cuda110 (>=5.0.0b4,<13.0.0)"] +cuda111 = ["cupy-cuda111 (>=5.0.0b4,<13.0.0)"] +cuda112 = ["cupy-cuda112 (>=5.0.0b4,<13.0.0)"] +cuda113 = ["cupy-cuda113 (>=5.0.0b4,<13.0.0)"] +cuda114 = ["cupy-cuda114 (>=5.0.0b4,<13.0.0)"] +cuda115 = ["cupy-cuda115 (>=5.0.0b4,<13.0.0)"] +cuda116 = ["cupy-cuda116 (>=5.0.0b4,<13.0.0)"] +cuda117 = ["cupy-cuda117 (>=5.0.0b4,<13.0.0)"] +cuda11x = ["cupy-cuda11x (>=11.0.0,<13.0.0)"] +cuda80 = ["cupy-cuda80 (>=5.0.0b4,<13.0.0)"] +cuda90 = ["cupy-cuda90 (>=5.0.0b4,<13.0.0)"] +cuda91 = ["cupy-cuda91 (>=5.0.0b4,<13.0.0)"] +cuda92 = ["cupy-cuda92 (>=5.0.0b4,<13.0.0)"] +ja = ["sudachidict-core (>=20211220)", "sudachipy (>=0.5.2,!=0.6.1)"] +ko = ["natto-py (>=0.9.0)"] lookups = ["spacy-lookups-data (>=1.0.3,<1.1.0)"] ray = ["spacy-ray (>=0.1.0,<1.0.0)"] th = ["pythainlp (>=2.0)"] -transformers = ["spacy-transformers (>=1.1.2,<1.2.0)"] +transformers = ["spacy-transformers (>=1.1.2,<1.3.0)"] [[package]] name = "spacy-legacy" -version = "3.0.10" +version = "3.0.12" description = "Legacy registered functions for spaCy backwards compatibility" category = "main" optional = false @@ -2177,17 +2352,14 @@ python-versions = ">=3.6" [[package]] name = "spacy-loggers" -version = "1.0.3" +version = "1.0.4" description = "Logging utilities for SpaCy" category = "main" optional = false python-versions = ">=3.6" -[package.dependencies] -wasabi = ">=0.8.1,<1.1.0" - [[package]] -name = "sphinx" +name = "Sphinx" version = "4.5.0" description = "Python documentation generator" category = "dev" @@ -2215,8 +2387,8 @@ sphinxcontrib-serializinghtml = ">=1.1.5" [package.extras] docs = ["sphinxcontrib-websupport"] -lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.931)", "docutils-stubs", "types-typed-ast", "types-requests"] -test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"] +lint = ["docutils-stubs", "flake8 (>=3.5.0)", "isort", "mypy (>=0.931)", "types-requests", "types-typed-ast"] +test = ["cython", "html5lib", "pytest", "pytest-cov", "typed-ast"] [[package]] name = "sphinx-autobuild" @@ -2252,7 +2424,7 @@ typer = ">=0.4.0" [package.source] type = "git" url = "https://github.com/rbturnbull/sphinx-click.git" -reference = "master" +reference = "HEAD" resolved_reference = "ec700fc5864f42cfb71f143f0ec077c89e1102eb" [[package]] @@ -2268,33 +2440,34 @@ sphinx = ">=1.8" [package.extras] code_style = ["pre-commit (==2.12.1)"] -rtd = ["sphinx", "ipython", "sphinx-book-theme"] +rtd = ["ipython", "sphinx", "sphinx-book-theme"] [[package]] name = "sphinx-rtd-theme" -version = "1.0.0" +version = "1.2.2" description = "Read the Docs theme for Sphinx" category = "dev" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" [package.dependencies] -docutils = "<0.18" -sphinx = ">=1.6" +docutils = "<0.19" +sphinx = ">=1.6,<7" +sphinxcontrib-jquery = ">=4,<5" [package.extras] -dev = ["transifex-client", "sphinxcontrib-httpdomain", "bump2version"] +dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"] [[package]] name = "sphinxcontrib-applehelp" -version = "1.0.2" -description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books" +version = "1.0.4" +description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.8" [package.extras] -lint = ["flake8", "mypy", "docutils-stubs"] +lint = ["docutils-stubs", "flake8", "mypy"] test = ["pytest"] [[package]] @@ -2306,20 +2479,31 @@ optional = false python-versions = ">=3.5" [package.extras] -lint = ["flake8", "mypy", "docutils-stubs"] +lint = ["docutils-stubs", "flake8", "mypy"] test = ["pytest"] [[package]] name = "sphinxcontrib-htmlhelp" -version = "2.0.0" +version = "2.0.1" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" [package.extras] -lint = ["flake8", "mypy", "docutils-stubs"] -test = ["pytest", "html5lib"] +lint = ["docutils-stubs", "flake8", "mypy"] +test = ["html5lib", "pytest"] + +[[package]] +name = "sphinxcontrib-jquery" +version = "4.1" +description = "Extension to include jQuery on newer Sphinx releases" +category = "dev" +optional = false +python-versions = ">=2.7" + +[package.dependencies] +Sphinx = ">=1.8" [[package]] name = "sphinxcontrib-jsmath" @@ -2330,7 +2514,7 @@ optional = false python-versions = ">=3.5" [package.extras] -test = ["pytest", "flake8", "mypy"] +test = ["flake8", "mypy", "pytest"] [[package]] name = "sphinxcontrib-qthelp" @@ -2341,7 +2525,7 @@ optional = false python-versions = ">=3.5" [package.extras] -lint = ["flake8", "mypy", "docutils-stubs"] +lint = ["docutils-stubs", "flake8", "mypy"] test = ["pytest"] [[package]] @@ -2353,12 +2537,12 @@ optional = false python-versions = ">=3.5" [package.extras] -lint = ["flake8", "mypy", "docutils-stubs"] +lint = ["docutils-stubs", "flake8", "mypy"] test = ["pytest"] [[package]] -name = "sqlalchemy" -version = "1.4.41" +name = "SQLAlchemy" +version = "1.4.49" description = "Database Abstraction Library" category = "main" optional = false @@ -2368,37 +2552,42 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} [package.extras] -aiomysql = ["greenlet (!=0.4.17)", "aiomysql"] -aiosqlite = ["typing_extensions (!=3.10.0.1)", "greenlet (!=0.4.17)", "aiosqlite"] +aiomysql = ["aiomysql", "greenlet (!=0.4.17)"] +aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"] asyncio = ["greenlet (!=0.4.17)"] -asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4)"] +asyncmy = ["asyncmy (>=0.2.3,!=0.2.4)", "greenlet (!=0.4.17)"] mariadb_connector = ["mariadb (>=1.0.1,!=1.1.2)"] mssql = ["pyodbc"] mssql_pymssql = ["pymssql"] mssql_pyodbc = ["pyodbc"] -mypy = ["sqlalchemy2-stubs", "mypy (>=0.910)"] -mysql = ["mysqlclient (>=1.4.0,<2)", "mysqlclient (>=1.4.0)"] +mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"] +mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"] mysql_connector = ["mysql-connector-python"] -oracle = ["cx_oracle (>=7,<8)", "cx_oracle (>=7)"] +oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"] postgresql = ["psycopg2 (>=2.7)"] -postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"] +postgresql_asyncpg = ["asyncpg", "greenlet (!=0.4.17)"] postgresql_pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"] postgresql_psycopg2binary = ["psycopg2-binary"] postgresql_psycopg2cffi = ["psycopg2cffi"] -pymysql = ["pymysql (<1)", "pymysql"] -sqlcipher = ["sqlcipher3-binary"] +pymysql = ["pymysql", "pymysql (<1)"] +sqlcipher = ["sqlcipher3_binary"] [[package]] name = "sqlparse" -version = "0.4.2" +version = "0.4.4" description = "A non-validating SQL parser." category = "main" optional = false python-versions = ">=3.5" +[package.extras] +dev = ["build", "flake8"] +doc = ["sphinx"] +test = ["pytest", "pytest-cov"] + [[package]] name = "srsly" -version = "2.4.4" +version = "2.4.6" description = "Modern high-performance serialization utilities for Python" category = "main" optional = false @@ -2409,23 +2598,23 @@ catalogue = ">=2.0.3,<2.1.0" [[package]] name = "stack-data" -version = "0.5.0" +version = "0.6.2" description = "Extract data from python stack frames and tracebacks for informative displays" category = "dev" optional = false python-versions = "*" [package.dependencies] -asttokens = "*" -executing = "*" +asttokens = ">=2.1.0" +executing = ">=1.2.0" pure-eval = "*" [package.extras] -tests = ["cython", "littleutils", "pygments", "typeguard", "pytest"] +tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] [[package]] name = "stevedore" -version = "4.0.0" +version = "5.1.0" description = "Manage dynamic plugins for Python applications" category = "main" optional = false @@ -2434,20 +2623,31 @@ python-versions = ">=3.8" [package.dependencies] pbr = ">=2.0.0,<2.1.0 || >2.1.0" +[[package]] +name = "sympy" +version = "1.12" +description = "Computer algebra system (CAS) in Python" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +mpmath = ">=0.19" + [[package]] name = "tabulate" -version = "0.8.10" +version = "0.9.0" description = "Pretty-print tabular data" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.7" [package.extras] widechars = ["wcwidth"] [[package]] name = "tenacity" -version = "8.0.1" +version = "8.2.2" description = "Retry code until it succeeds" category = "main" optional = false @@ -2466,26 +2666,29 @@ python-versions = "*" [[package]] name = "thinc" -version = "8.1.1" +version = "8.1.10" description = "A refreshing functional take on deep learning, compatible with your favorite libraries" category = "main" optional = false python-versions = ">=3.6" [package.dependencies] -blis = ">=0.7.8,<0.10.0" +blis = ">=0.7.8,<0.8.0" catalogue = ">=2.0.4,<2.1.0" confection = ">=0.0.1,<1.0.0" cymem = ">=2.0.2,<2.1.0" murmurhash = ">=1.0.2,<1.1.0" numpy = ">=1.15.0" +packaging = ">=20.0" preshed = ">=3.0.2,<3.1.0" -pydantic = ">=1.7.4,<1.8 || >1.8,<1.8.1 || >1.8.1,<1.10.0" +pydantic = ">=1.7.4,<1.8 || >1.8,<1.8.1 || >1.8.1,<1.11.0" +setuptools = "*" srsly = ">=2.4.0,<3.0.0" -wasabi = ">=0.8.1,<1.1.0" +wasabi = ">=0.8.1,<1.2.0" [package.extras] cuda = ["cupy (>=5.0.0b4)"] +cuda-autodetect = ["cupy-wheel (>=11.0.0)"] cuda100 = ["cupy-cuda100 (>=5.0.0b4)"] cuda101 = ["cupy-cuda101 (>=5.0.0b4)"] cuda102 = ["cupy-cuda102 (>=5.0.0b4)"] @@ -2495,6 +2698,9 @@ cuda112 = ["cupy-cuda112 (>=5.0.0b4)"] cuda113 = ["cupy-cuda113 (>=5.0.0b4)"] cuda114 = ["cupy-cuda114 (>=5.0.0b4)"] cuda115 = ["cupy-cuda115 (>=5.0.0b4)"] +cuda116 = ["cupy-cuda116 (>=5.0.0b4)"] +cuda117 = ["cupy-cuda117 (>=5.0.0b4)"] +cuda11x = ["cupy-cuda11x (>=11.0.0)"] cuda80 = ["cupy-cuda80 (>=5.0.0b4)"] cuda90 = ["cupy-cuda90 (>=5.0.0b4)"] cuda91 = ["cupy-cuda91 (>=5.0.0b4)"] @@ -2504,6 +2710,17 @@ mxnet = ["mxnet (>=1.5.1,<1.6.0)"] tensorflow = ["tensorflow (>=2.0.0,<2.6.0)"] torch = ["torch (>=1.6.0)"] +[[package]] +name = "thop" +version = "0.1.1.post2209072238" +description = "A tool to count the FLOPs of PyTorch model." +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +torch = "*" + [[package]] name = "threadpoolctl" version = "3.1.0" @@ -2512,20 +2729,34 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "tifffile" +version = "2023.7.4" +description = "Read and write TIFF files" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +numpy = "*" + +[package.extras] +all = ["defusedxml", "fsspec", "imagecodecs (>=2023.1.23)", "lxml", "matplotlib", "zarr"] + [[package]] name = "tinycss2" -version = "1.1.1" +version = "1.2.1" description = "A tiny CSS parser" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] webencodings = ">=0.4" [package.extras] -doc = ["sphinx", "sphinx-rtd-theme"] -test = ["pytest", "pytest-cov", "pytest-flake8", "pytest-isort", "coverage"] +doc = ["sphinx", "sphinx_rtd_theme"] +test = ["flake8", "isort", "pytest"] [[package]] name = "toml" @@ -2545,18 +2776,25 @@ python-versions = ">=3.6" [[package]] name = "torch" -version = "1.12.1" +version = "2.0.1" description = "Tensors and Dynamic neural networks in Python with strong GPU acceleration" category = "main" optional = false -python-versions = ">=3.7.0" +python-versions = ">=3.8.0" [package.dependencies] +filelock = "*" +jinja2 = "*" +networkx = "*" +sympy = "*" typing-extensions = "*" +[package.extras] +opt-einsum = ["opt-einsum (>=3.3)"] + [[package]] name = "torchapp" -version = "0.2.3" +version = "0.2.6" description = "A wrapper for fastai projects to create easy command-line inferfaces and manage hyper-parameter tuning." category = "main" optional = false @@ -2569,7 +2807,7 @@ click = "8.0.4" cookiecutter = "^2.1.1" fastai = "^2.5.3" mlflow = "^1.25.1" -numpy = "^1.22.0" +numpy = ">=1.22.0,<1.24.0" optuna = "^2.10.0" pandas = "^1.3.5" Pillow = "^9.0.1" @@ -2578,53 +2816,65 @@ pybtexnbib = "^0.1.1" pyjwt = ">=2.4.0" PyYAML = "^6.0" rich = "^10.16.1" -scikit-learn = "^1.0.2" +scikit-learn = ">=1.0.2,<1.2.0" scikit-optimize = "^0.9.0" scipy = "^1.9.1" -torch = "^1.12.1" -torchvision = "^0.13.1" +torch = ">=1.12.1" +torchvision = ">=0.13.0" typer = "^0.4.0" wandb = "^0.12.9" [package.source] type = "git" url = "https://github.com/rbturnbull/torchapp.git" -reference = "master" -resolved_reference = "5465da49df06f526a684db0065265487e533a06e" +reference = "diffusion" +resolved_reference = "b79a5a33f2a11c351af17f8afb1b34c824ba9fc3" + +[[package]] +name = "torchprofile" +version = "0.0.4" +description = "" +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +numpy = ">=1.14" +torch = ">=1.4" +torchvision = ">=0.4" [[package]] name = "torchvision" -version = "0.13.1" +version = "0.15.2" description = "image and video datasets and models for torch deep learning" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] numpy = "*" pillow = ">=5.3.0,<8.3.0 || >=8.4.0" requests = "*" -torch = "1.12.1" -typing-extensions = "*" +torch = "2.0.1" [package.extras] scipy = ["scipy"] [[package]] name = "tornado" -version = "6.2" +version = "6.3.2" description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." category = "dev" optional = false -python-versions = ">= 3.7" +python-versions = ">= 3.8" [[package]] name = "tqdm" -version = "4.64.1" +version = "4.65.0" description = "Fast, Extensible Progress Meter" category = "main" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" +python-versions = ">=3.7" [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} @@ -2637,14 +2887,15 @@ telegram = ["requests"] [[package]] name = "traitlets" -version = "5.4.0" -description = "" +version = "5.9.0" +description = "Traitlets Python configuration system" category = "dev" optional = false python-versions = ">=3.7" [package.extras] -test = ["pre-commit", "pytest"] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] +test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"] [[package]] name = "tricubic" @@ -2658,7 +2909,7 @@ develop = false [package.source] type = "git" url = "https://github.com/rbturnbull/pytricubic.git" -reference = "master" +reference = "HEAD" resolved_reference = "8fb4a944d2f60a5d50eb48c4e2803cae20b85644" [[package]] @@ -2675,12 +2926,12 @@ click = ">=7.1.1,<9.0.0" [package.extras] all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)"] dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"] -doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)"] -test = ["shellingham (>=1.3.0,<2.0.0)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "coverage (>=5.2,<6.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "mypy (==0.910)", "black (>=22.3.0,<23.0.0)", "isort (>=5.0.6,<6.0.0)"] +doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)"] +test = ["black (>=22.3.0,<23.0.0)", "coverage (>=5.2,<6.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "shellingham (>=1.3.0,<2.0.0)"] [[package]] name = "typing-extensions" -version = "4.3.0" +version = "4.7.1" description = "Backported and Experimental Type Hints for Python 3.7+" category = "main" optional = false @@ -2688,33 +2939,34 @@ python-versions = ">=3.7" [[package]] name = "urllib3" -version = "1.26.12" +version = "2.0.3" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4" +python-versions = ">=3.7" [package.extras] -brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"] -secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "urllib3-secure-extra", "ipaddress"] -socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] +brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"] +socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] +zstd = ["zstandard (>=0.18.0)"] [[package]] name = "virtualenv" -version = "20.16.5" +version = "20.23.1" description = "Virtual Python Environment builder" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] -distlib = ">=0.3.5,<1" -filelock = ">=3.4.1,<4" -platformdirs = ">=2.4,<3" +distlib = ">=0.3.6,<1" +filelock = ">=3.12,<4" +platformdirs = ">=3.5.1,<4" [package.extras] -docs = ["proselint (>=0.13)", "sphinx (>=5.1.1)", "sphinx-argparse (>=0.3.1)", "sphinx-rtd-theme (>=1)", "towncrier (>=21.9)"] -testing = ["coverage (>=6.2)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=21.3)", "pytest (>=7.0.1)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.6.1)", "pytest-randomly (>=3.10.3)", "pytest-timeout (>=2.1)"] +docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx (>=7.0.1)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] +test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.3.1)", "pytest-env (>=0.8.1)", "pytest-freezer (>=0.4.6)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=67.8)", "time-machine (>=2.9)"] [[package]] name = "waitress" @@ -2726,7 +2978,7 @@ python-versions = ">=3.7.0" [package.extras] docs = ["Sphinx (>=1.8.1)", "docutils", "pylons-sphinx-themes (>=1.0.9)"] -testing = ["pytest", "pytest-cover", "coverage (>=5.0)"] +testing = ["coverage (>=5.0)", "pytest", "pytest-cover"] [[package]] name = "wandb" @@ -2748,6 +3000,7 @@ PyYAML = "*" requests = ">=2.0.0,<3" sentry-sdk = ">=1.0.0" setproctitle = "*" +setuptools = "*" shortuuid = ">=0.5.0" six = ">=1.13.0" @@ -2756,23 +3009,26 @@ aws = ["boto3"] azure = ["azure-storage-blob"] gcp = ["google-cloud-storage"] grpc = ["grpcio (>=1.27.2)"] -kubeflow = ["kubernetes", "minio", "google-cloud-storage", "sh"] -launch = ["nbconvert", "nbformat", "chardet", "iso8601", "typing-extensions", "boto3", "google-cloud-storage", "kubernetes"] -media = ["numpy", "moviepy", "pillow", "bokeh", "soundfile", "plotly", "rdkit-pypi"] +kubeflow = ["google-cloud-storage", "kubernetes", "minio", "sh"] +launch = ["boto3", "chardet", "google-cloud-storage", "iso8601", "kubernetes", "nbconvert", "nbformat", "typing-extensions"] +media = ["bokeh", "moviepy", "numpy", "pillow", "plotly", "rdkit-pypi", "soundfile"] models = ["cloudpickle"] sweeps = ["sweeps (>=0.1.0)"] [[package]] name = "wasabi" -version = "0.10.1" +version = "1.1.2" description = "A lightweight console printing and formatting toolkit" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.6" + +[package.dependencies] +colorama = {version = ">=0.4.6", markers = "sys_platform == \"win32\" and python_version >= \"3.7\""} [[package]] name = "wcwidth" -version = "0.2.5" +version = "0.2.6" description = "Measures the displayed width of unicode 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a/pyproject.toml b/pyproject.toml index 11ce486..657afb1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "supercat" -version = "0.1.0" +version = "0.2.1" description = "A deep learning model for CT scan super-resolution." authors = ["MDAP "] license = "Apache Software License 2.0" @@ -8,7 +8,7 @@ readme = "README.rst" homepage = "https://rbturnbull.github.io/supercat/" repository = "https://github.com/rbturnbull/supercat" documentation = "https://rbturnbull.github.io/supercat/" -keywords = ["super-resolution", "Computed tomography (CT)", "torchapp", "rock", "sand", "3D"] +keywords = ["super-resolution", "Computed tomography (CT)", "torchapp", "rock", "sand", "3D", "diffusion"] classifiers = [ "License :: OSI Approved :: Apache Software License", "Intended Audience :: Science/Research", @@ -18,12 +18,12 @@ classifiers = [ [tool.poetry.dependencies] python = ">=3.8,<3.12" -torchapp = {git = "https://github.com/rbturnbull/torchapp.git"} +torchapp = {git = "https://github.com/rbturnbull/torchapp.git", branch="diffusion"} mat73 = "^0.59" hdf5storage = "^0.1.18" -tricubic = {git = "https://github.com/rbturnbull/pytricubic.git"} plotly = "^5.8.2" kaleido = "0.2.1" +scikit-image = "^0.21.0" [tool.poetry.dev-dependencies] pytest = "^6.2.5" @@ -40,6 +40,10 @@ sphinx-copybutton = "^0.4.0" black = "^21.10b0" sphinx-click = {git = "https://github.com/rbturnbull/sphinx-click.git"} +[tool.poetry.group.dev.dependencies] +thop = "^0.1.1.post2209072238" +torchprofile = "^0.0.4" + [tool.pytest.ini_options] minversion = "6.0" testpaths = [ @@ -51,5 +55,7 @@ requires = ["setuptools","poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" [tool.poetry.scripts] -supercat = "supercat.apps:Supercat.main" -supercat3d = "supercat.apps:Supercat3d.main" +supercat-train = "supercat.apps:Supercat.main" +supercat = "supercat.apps:Supercat.inference_only_main" +supercat-diffusion-train = "supercat.apps:SupercatDiffusion.main" +supercat-diffusion = "supercat.apps:SupercatDiffusion.inference_only_main" \ No newline at end of file diff --git a/supercat/__init__.py b/supercat/__init__.py index 8a99a8b..d3c90a9 100644 --- a/supercat/__init__.py +++ b/supercat/__init__.py @@ -1 +1 @@ -from .apps import Supercat, Supercat3d \ No newline at end of file +from .apps import Supercat, SupercatDiffusion \ No newline at end of file diff --git a/supercat/apps.py b/supercat/apps.py index b6c3859..58ca8d0 100644 --- a/supercat/apps.py +++ b/supercat/apps.py @@ -1,86 +1,65 @@ import re +import torchapp as ta +from typing import List import torch -from enum import Enum +import random from pathlib import Path -from typing import List -from PIL import Image -from torch import nn +from fastai.callback.core import Callback, CancelBatchException +from fastai.data.block import DataBlock, TransformBlock +from fastai.data.core import DataLoaders, DisplayedTransform import torch.nn.functional as F +from rich.progress import track +from fastai.data.transforms import get_image_files +import torchvision.transforms as T +from fastai.data.transforms import ToTensor from fastcore.transform import Pipeline -from fastai.data.transforms import get_image_files, FuncSplitter, ToTensor -from fastai.data.core import DataLoaders -from fastai.data.block import DataBlock -from fastai.vision.data import ImageBlock -from fastai.vision.core import PILImageBW -from fastai.vision.augment import RandomCrop, Resize -from fastai.learner import Learner, load_learner -import torchapp as ta -from torchapp.util import call_func, add_kwargs, change_typer_to_defaults - -from .metrics import psnr, mse -from .transforms import ImageBlock3D, read3D, write3D, InterpolateTransform -from .interpolation import interpolate3D, InterpolationMethod -from .models import ResidualUNet, VideoUnet3d +from fastai.vision.augment import Resize +from fastai.data.transforms import FuncSplitter +from fastai.learner import load_learner +from PIL import Image +from functools import partial +from fastai.vision.data import ImageBlock, TensorImage +from fastai.vision.core import PILImageBW, TensorImageBW +from supercat.worley import WorleyNoise, WorleyNoiseTensor +from supercat.fractal import * # remove this + +from supercat.models import ResidualUNet +from supercat.transforms import ImageBlock3D, RescaleImage, write3D, read3D, InterpolateTransform +from supercat.enums import DownsampleScale, DownsampleMethod +from supercat.diffusion import DDPMCallback, DDPMSamplerCallback +from skimage.transform import resize as skresize from rich.console import Console console = Console() -class DownsampleScale(Enum): - X2 = "X2" - X4 = "X4" - - -class ClipUnitInterval(nn.Module): - def forward(self, input): - return F.hardtanh(input, 0.0, 1.0) - - -class DownsampleMethod(Enum): - DEFAULT = "default" - UNKNOWN = "unknown" - - -def get_y(item): - dir_name = re.sub(r"_BI_.*", "_HR", item.parent.name) - return item.parent.parent/dir_name/item.name - -def get_y_3d(item): - dir_name = re.sub(r"_TRI_.*", "_HR", item.parent.name) - return item.parent.parent/dir_name/item.name def is_validation_image(item:tuple): "Returns True if this image should be part of the validation set i.e. if the parent directory doesn't have the string `_train_` in it." return "_train_" not in item.parent.name -class Supercat(ta.TorchApp): - """ - A deep learning model for CT scan superresolution. - """ - def __init__(self): - super().__init__() - - self.validate_individual = self.copy_method(self.validate_individual) - add_kwargs(to_func=self.validate_individual, from_funcs=[self.pretrained_local_path, self.inference_dataloader]) +def get_y(item, pattern=r"_BI_.*"): + dir_name = re.sub(pattern, "_HR", item.parent.name) + return item.parent.parent/dir_name/item.name - # Make copies of methods to use just for the CLI - self.validate_individual_cli = self.copy_method(self.validate_individual) - # Remove params from defaults in methods not used for the cli - change_typer_to_defaults(self.validate_individual) - +class Supercat(ta.TorchApp): def get_items(self, directory): - return get_image_files(directory) + if self.dim == 2: + return get_image_files(directory) + + directory = Path(directory) + return list(directory.glob("*.mat")) def dataloaders( self, - deeprock:Path = ta.Param(help="The path to the DeepRockSR-2D dataset."), + dim:int = ta.Param(default=2, help="The dimension of the dataset. 2 or 3."), + deeprock:Path = ta.Param(help="The path to the DeepRockSR dataset."), downsample_scale:DownsampleScale = ta.Param(DownsampleScale.X4.value, help="Should it use the 2x or 4x downsampled images.", case_sensitive=False), downsample_method:DownsampleMethod = ta.Param(DownsampleMethod.UNKNOWN.value, help="Should it use the default method to downsample (bicubic) or a random kernel (UNKNOWN)."), batch_size:int = ta.Param(default=10, help="The batch size."), force:bool = ta.Param(default=False, help="Whether or not to force the conversion of the bicubic upscaling."), max_samples:int = ta.Param(default=None, help="If set, then the number of input samples for training/validation is truncated at this number."), - random_crop:int = ta.Param(default=None, help="If set, then randomly crop the images to this resolution during training."), include_sand:bool = ta.Param(default=False, help="Including DeepSand-SR dataset."), ) -> DataLoaders: """ @@ -88,22 +67,26 @@ def dataloaders( """ assert deeprock is not None + self.dim = dim deeprock = Path(deeprock) - bicubic = [] + upscaled = [] highres = [] # sources = ["shuffled2D"] - sources = ["carbonate2D","coal2D","sandstone2D"] + sources = [f"carbonate{dim}D",f"coal{dim}D",f"sandstone{dim}D"] if include_sand: - sources.append("sand2D") + sources.append(f"sand{dim}D") if isinstance(downsample_method, DownsampleMethod): downsample_method = downsample_method.value + if isinstance(downsample_scale, DownsampleScale): downsample_scale = downsample_scale.value split_types = ["train","valid"] # There is also "test" # split_types = ["train","valid","test"] # hack + + UP = "BI" if dim == 2 else "TRI" for source in sources: for split_type in split_types: @@ -113,70 +96,108 @@ def dataloaders( lowres_dir = deeprock/source/f"{source}_{split_type}_LR_{downsample_method}_{downsample_scale}" - # We will save bicubic upscaled images - bicubic_dir = deeprock/source/f"{source}_{split_type}_BI_{downsample_method}_{downsample_scale}" - bicubic_dir.mkdir(exist_ok=True) + # We will save upscaled images + upscale_dir = deeprock/source/f"{source}_{split_type}_{UP}_{downsample_method}_{downsample_scale}" + upscale_dir.mkdir(exist_ok=True) for index, highres_path in enumerate(highres_split): - bicubic_path = bicubic_dir/highres_path.name + upscale_path = upscale_dir/highres_path.name - if not bicubic_path.exists() or force: + if not upscale_path.exists() or force: components = highres_path.name.split(".") lowres_name = f'{components[0]}{downsample_scale.lower()}.{components[1]}' lowres_path = lowres_dir/lowres_name - print(split_type, highres_path, bicubic_path, lowres_path) + print(split_type, highres_path, upscale_path, lowres_path) - # upscale with bicubic interpolation - print("Upscaling with bicubic") - highres_img = Image.open(highres_path) - lowres_img = Image.open(lowres_path) - - # Convert to single channel - if lowres_img.mode == "RGB": - lowres_img = lowres_img.getchannel('R') - lowres_img.save(lowres_path) - if highres_img.mode == "RGB": - highres_img = highres_img.getchannel('R') - highres_img.save(highres_path) - - bicubic_img = lowres_img.resize(highres_img.size,Image.BICUBIC) - if bicubic_img.mode == "RGB": - bicubic_img = bicubic_img.getchannel('R') - - bicubic_img.save(bicubic_path) - bicubic.append(bicubic_path) + # upscale with upscale interpolation + print("Upscaling") + if dim == 2: + highres_img = Image.open(highres_path) + lowres_img = Image.open(lowres_path) + + # Convert to single channel + if lowres_img.mode == "RGB": + lowres_img = lowres_img.getchannel('R') + lowres_img.save(lowres_path) + if highres_img.mode == "RGB": + highres_img = highres_img.getchannel('R') + highres_img.save(highres_path) + + upscale_img = lowres_img.resize(highres_img.size,Image.upscale) + if upscale_img.mode == "RGB": + upscale_img = upscale_img.getchannel('R') + + upscale_img.save(upscale_path) + else: + components = highres_path.name.split(".") + lowres_name = f'{components[0]}{downsample_scale.lower()}.{components[1]}' + lowres_path = lowres_dir/lowres_name + print(split_type, highres_path, upscale_path, lowres_path) + + # upscale with tricubic interpolation + print("Upscaling with tricubic") + highres_img = read3D(highres_path) + lowres_img = read3D(lowres_path) + + tricubic_img = skresize(lowres_img, highres_img.shape, order=3) + write3D(upscale_path, tricubic_img) + + upscaled.append(upscale_path) if max_samples and index > max_samples: break - item_transforms = [RandomCrop(random_crop)] if random_crop else [] + if len(upscaled) == 0: + raise ValueError("No images found.") + + if dim == 2: + blocks = (ImageBlock(cls=PILImageBW), ImageBlock(cls=PILImageBW)) + else: + blocks = (ImageBlock3D, ImageBlock3D,) datablock = DataBlock( - blocks=(ImageBlock(cls=PILImageBW), ImageBlock(cls=PILImageBW)), + blocks=blocks, splitter=FuncSplitter(is_validation_image), - get_y=get_y, - item_tfms=item_transforms, + get_y=get_y if dim == 2 else partial(get_y, pattern=r"_TRI_.*"), + batch_tfms=[RescaleImage], ) dataloaders = DataLoaders.from_dblock( datablock, - source=bicubic, + source=upscaled, bs=batch_size, ) dataloaders.c = 1 return dataloaders + + def model(self, pretrained:Path=None): + if pretrained: + learner = load_learner(pretrained) + return learner.model + + return ResidualUNet(dim=self.dim, in_channels=1) + + def loss_func(self): + """ + Returns the loss function to use with the model. + """ + return F.smooth_l1_loss def inference_dataloader( self, learner, + dim:int = ta.Param(default=2, help="The dimension of the dataset. 2 or 3."), items:List[Path] = None, item_dir: Path = ta.Param(None, help="A directory with images to upscale."), - width:int = ta.Param(500, help="The width of the final image."), - height:int = ta.Param(None, help="The height of the final image."), + width:int = ta.Param(500, help="The width of the final image/volume."), + height:int = ta.Param(None, help="The height of the final image/volume."), + depth:int = ta.Param(None, help="The depth of the final image/volume."), **kwargs - ): + ): + self.dim = dim + if not items: items = [] if isinstance(items, (Path, str)): @@ -187,263 +208,97 @@ def inference_dataloader( items = [Path(item) for item in items] self.items = items dataloader = learner.dls.test_dl(items, with_labels=True, **kwargs) - + dataloader.transform = dataloader.transform[:1] # ignore the get_y function height = height or width - dataloader.after_item = Pipeline( [Resize(height, width), ToTensor] ) + depth = depth or width + + interpolation = Resize(height, width) if dim == 2 else InterpolateTransform(width, height, depth) + dataloader.after_item = Pipeline( [interpolation, ToTensor] ) return dataloader - def output_results(self, results, return_images=False, **kwargs): + def output_results( + self, + results, + return_data:bool=False, + output_dir: Path = ta.Param(None, help="The location of the output directory. If not given then it uses the directory of the item."), + suffix:str = ta.Param("", help="The file extension for the output file."), + **kwargs + ): list_to_return = [] + if output_dir: + output_dir = Path(output_dir) + output_dir.mkdir(exist_ok=True, parents=True) + for item, result in zip(self.items, results[0]): - extension = item.name[item.name.rfind(".")+1:].lower() - stub = item.name[:-len(extension)] - new_name = f"{stub}upscaled.{extension}" - new_path = item.parent/new_name - pixels = torch.clip(result[0]*255, min=0, max=255) - - im = Image.fromarray( pixels.cpu().detach().numpy().astype('uint8') ) - + my_suffix = suffix or item.suffix + if my_suffix[0] != ".": + my_suffix = "." + my_suffix + + new_name = item.with_suffix("").name + f".upscaled{my_suffix}" + my_output_dir = output_dir or item.parent + new_path = my_output_dir/new_name + + dim = len(result.shape) - 1 + + result[0] = result[0] * 0.5 + 0.5 + if dim == 2: + pixels = torch.clip(result[0]*255, min=0, max=255) + im = Image.fromarray( pixels.cpu().detach().numpy().astype('uint8') ) + im.save(new_path) + else: + write3D(new_path, result[0].cpu().detach().numpy()) + + list_to_return.append(result[0] if return_data else new_path) console.print(f"Upscaled '{item}' ⮕ '{new_path}'") - im.save(new_path) - list_to_return.append(im if return_images else new_path) return list_to_return + - def model( - self, - initial_features:int = ta.Param( - 64, - tune=True, - tune_min=16, - tune_max=256, - help="The number of features after the initial CNN layer." - ), - growth_factor:float = ta.Param( - 2.0, - tune=True, - tune_min=1.0, - tune_max=4.0, - #log=True, - help="The factor to grow the number of convolutional filters each time the model downscales." - ), - ): - return ResidualUNet(in_channels=1, out_channels=1, initial_features=initial_features, growth_factor=growth_factor, dim=2) - - def loss_func(self, mse:bool=True): - """ - Returns the loss function to use with the model. - - By default the L1 loss or the Mean Absolute Error (MAE) is used. - See 10.1029/2019WR026052 - """ - if mse: - return nn.MSELoss() - return nn.L1Loss() - - def metrics(self): - metrics = super().metrics() - metrics.extend([psnr]) - return metrics - - def monitor(self): - return "psnr" - - def validate_individual(self, csv, item_dir: Path = ta.Param(None, help="The dir with the images to upscale."), **kwargs): - path = call_func(self.pretrained_local_path, **kwargs) - learner = load_learner(path) - with open(csv, 'w') as f: - items = self.get_items(Path(item_dir).expanduser().resolve()) - print("image", "loss", "psnr", sep=",", file=f) - for item in items: - print(item) - dataloader = learner.dls.test_dl([item], with_labels=True) - values = learner.validate(dl=dataloader) - print(item, *values, sep=",", file=f) - - -class Supercat3d(Supercat): - def dataloaders( - self, - deeprock:Path = ta.Param(help="The path to the DeepRockSR-3D dataset."), - downsample_scale:DownsampleScale = ta.Param(DownsampleScale.X4.value, help="Should it use the 2x or 4x downsampled images.", case_sensitive=False), - downsample_method:DownsampleMethod = ta.Param(DownsampleMethod.UNKNOWN.value, help="Should it use the default method to downsample (bicubic) or a random kernel (UNKNOWN)."), - batch_size:int = ta.Param(default=8, help="The batch size."), - force:bool = ta.Param(default=False, help="Whether or not to force the conversion of the tricubic upscaling."), - max_samples:int = ta.Param(default=None, help="If set, then the number of input samples for training/validation is truncated at this number."), - include_sand:bool = ta.Param(default=False, help="Including DeepSand-SR dataset."), - ) -> DataLoaders: - """ - Creates a FastAI DataLoaders object which Supercat uses in training and prediction. - - Args: - deeprock (Path): The path to the DeepRockSR-3D dataset. - batch_size (int): The number of elements to use in a batch for training and prediction. Defaults to 32. - """ - assert deeprock is not None - - deeprock = Path(deeprock) - tricubic = [] - highres = [] - - sources = ["carbonate3D","coal3D","sandstone3D"] - - if include_sand: - sources += ["sand3D"] - - if isinstance(downsample_method, DownsampleMethod): - downsample_method = downsample_method.value - if isinstance(downsample_scale, DownsampleScale): - downsample_scale = downsample_scale.value +class SupercatDiffusion(Supercat): + def model(self, pretrained:Path=None): + if pretrained: + learner = load_learner(pretrained) + return learner.model - split_types = ["train","valid"] # There is also "test" - # split_types = ["train","valid","test"] # hack - - for source in sources: - for split_type in split_types: - highres_dir = deeprock/source/f"{source}_{split_type}_HR" - highres_split = self.get_items(highres_dir) - highres.extend( highres_split ) + return ResidualUNet(dim=self.dim, in_channels=3) - lowres_dir = deeprock/source/f"{source}_{split_type}_LR_{downsample_method}_{downsample_scale}" + def extra_callbacks(self): + return [DDPMCallback()] + + def inference_callbacks(self): + return [DDPMSamplerCallback()] + + # def output_results( + # self, + # results, + # output_dir: Path = ta.Param("./outputs", help="The location of the output directory."), + # diffusion_gif:bool=False, + # diffusion_gif_fps:float=ta.Param(120.0, help="The frames per second to use when generating the gif."), + # **kwargs, + # ): + # breakpoint() + # # final_results = [[result[-1] for result in results[0][0]]] + # to_return = super().output_results(results, output_dir=output_dir, **kwargs) + + # if diffusion_gif: + # assert self.dim == 2 + + # output_dir = Path(output_dir) + # print(f"Saving {len(results[0])} generated images:") + + # transform = T.ToPILImage() + # output_dir.mkdir(exist_ok=True, parents=True) + # images = [] + # for index, image in enumerate(results[0][0]): + # path = output_dir/f"image.{index}.png" - # We will save tricubic upscaled images - tricubic_dir = deeprock/source/f"{source}_{split_type}_TRI_{downsample_method}_{downsample_scale}" - tricubic_dir.mkdir(exist_ok=True) - - for index, highres_path in enumerate(highres_split): - tricubic_path = tricubic_dir/highres_path.name - - if not tricubic_path.exists() or force: - components = highres_path.name.split(".") - lowres_name = f'{components[0]}{downsample_scale.lower()}.{components[1]}' - lowres_path = lowres_dir/lowres_name - print(split_type, highres_path, tricubic_path, lowres_path) - - # upscale with tricubic interpolation - print("Upscaling with tricubic") - highres_img = read3D(highres_path) - lowres_img = read3D(lowres_path) + # image = transform(torch.clip(image[0]/2.0 + 0.5, min=0.0, max=1.0)) + # images.append(image) + # print(f"\t{path}") + # images[0].save(output_dir/f"image.gif", save_all=True, append_images=images[1:], fps=diffusion_gif_fps) - tricubic_img = interpolate3D(lowres_img, new_shape=highres_img.shape, method=InterpolationMethod.TRICUBIC) - write3D(tricubic_path, tricubic_img) - tricubic.append(tricubic_path) - - if max_samples and index > max_samples: - break - - assert "test" not in split_types - datablock = DataBlock( - blocks=(ImageBlock3D, ImageBlock3D), - splitter=FuncSplitter(is_validation_image), - get_y=get_y_3d, - ) - - dataloaders = DataLoaders.from_dblock( - datablock, - source=tricubic, - bs=batch_size, - ) - - dataloaders.c = 1 - - return dataloaders - - def model( - self, - video_unet:bool = False, - pretrained:bool = True, - initial_features:int = ta.Param( - 64, - tune=True, - tune_min=16, - tune_max=256, - help="The number of features after the initial CNN layer." - ), - growth_factor:int = ta.Param( - 2.0, - tune=True, - tune_min=1.0, - tune_max=4.0, - log=True, - help="The factor to grow the number of convolutional filters each time the model downscales." - ), - # more should be added - ): - if video_unet: - return VideoUnet3d(in_channels=1, out_channels=1, pretrained=pretrained) + # return to_return - return ResidualUNet(in_channels=1, out_channels=1, initial_features=initial_features, growth_factor=growth_factor, dim=3) - - def build_learner_func(self): - return Learner - - def learner_kwargs( - self, - output_dir: Path = ta.Param("./outputs", help="The location of the output directory."), - **kwargs, - ): - output_dir = Path(output_dir) - output_dir.mkdir(exist_ok=True, parents=True) - - return dict( - loss_func=self.loss_func(), - metrics=self.metrics(), - path=output_dir, - ) - - def get_items(self, directory): - directory = Path(directory) - return list(directory.glob("*.mat")) - - def validate_individual(self, csv, do_nothing:bool=False, item_dir: Path = ta.Param(None, help="The dir with the images to upscale."), **kwargs): - path = call_func(self.pretrained_local_path, **kwargs) - learner = load_learner(path) - if do_nothing: - learner.model = DoNothing() - - with open(csv, 'w') as f: - items = self.get_items(Path(item_dir).expanduser().resolve()) - print("image", "loss", "l2", "psnr", sep=",", file=f) - for item in items: - dataloader = learner.dls.test_dl([item], with_labels=True) - values = learner.validate(dl=dataloader) - print(item, *values) - print(item, *values, sep=",", file=f) - - def inference_dataloader( - self, - learner, - items:List[Path] = None, - width:int = ta.Param(100, help="The width of the final volume."), - height:int = ta.Param(None, help="The height of the final volume."), - depth:int = ta.Param(None, help="The depth of the final volume."), - **kwargs - ): - if not items: - items = [] - if isinstance(items, (Path, str)): - items = [items] - - items = [Path(item) for item in items] - self.items = items - dataloader = learner.dls.test_dl(items, with_labels=True, **kwargs) - - height = height or width - depth = depth or width - dataloader.after_item = Pipeline( [InterpolateTransform(width, height, depth), ToTensor] ) - return dataloader - - def output_results(self, results, return_volumes=False, **kwargs): - list_to_return = [] - for item, result in zip(self.items, results[0]): - extension = item.name[item.name.rfind(".")+1:].lower() - stub = item.name[:-len(extension)] - new_name = f"{stub}upscaled.{extension}" - new_path = item.parent/new_name - write3D(new_path, result[0].cpu().detach().numpy()) - - console.print(f"Upscaled '{item}' ⮕ '{new_path}'") - list_to_return.append(result[0] if return_volumes else new_path) - - return list_to_return +if __name__ == "__main__": + SupercatDiffusion.main() diff --git a/supercat/augmentation.py b/supercat/augmentation.py new file mode 100644 index 0000000..868739a --- /dev/null +++ b/supercat/augmentation.py @@ -0,0 +1,28 @@ +from fastai.callback.core import Callback + + +# Can this be a transform? +class DihedralCallback(Callback): + def before_batch(self): + """ + x: (batch_size, c, d, h, w) + """ + xb = self.xb[0] + yb = self.yb[0] + + k = random.randint(0,7) + + if k in [1,3,4,7]: + xb = xb.flip(-1) + yb = yb.flip(-1) + + if k in [2,4,5,7]: + xb = xb.flip(-2) + yb = yb.flip(-2) + + if k in [3,5,6,7]: + xb = xb.transpose(-1,-2) + yb = yb.transpose(-1,-2) + + self.learn.xb = (xb,) + self.learn.yb = (yb,) diff --git a/supercat/diffusion.py b/supercat/diffusion.py new file mode 100644 index 0000000..e77a675 --- /dev/null +++ b/supercat/diffusion.py @@ -0,0 +1,75 @@ +import torch +from rich.progress import track +from fastai.callback.core import Callback, CancelBatchException + + +class DDPMCallback(Callback): + """ + Derived from https://wandb.ai/capecape/train_sd/reports/How-To-Train-a-Conditional-Diffusion-Model-From-Scratch--VmlldzoyNzIzNTQ1#using-fastai-to-train-your-diffusion-model + """ + def __init__(self, n_steps:int=1000, s:float = 0.008): + self.n_steps = n_steps + self.s = s + + t = torch.arange(self.n_steps) + self.alpha_bar = torch.cos((t/self.n_steps+self.s)/(1+self.s) * torch.pi * 0.5)**2 + self.alpha = self.alpha_bar/torch.cat([torch.ones(1), self.alpha_bar[:-1]]) + self.beta = 1.0 - self.alpha + self.sigma = torch.sqrt(self.beta) + + def before_batch(self): + """ + x: (batch_size, c, d, h, w) + """ + lr = self.xb[0] + hr = self.yb[0] + + noise = torch.randn_like(hr) + + batch_size = hr.shape[0] + dim = len(hr.shape) - 2 + + # lookup noise schedule + t = torch.randint(0, self.n_steps, (batch_size,), dtype=torch.long) # select random timesteps + if dim == 2: + alpha_bar_t = self.alpha_bar[t, None, None, None] + else: + alpha_bar_t = self.alpha_bar[t, None, None, None, None] + alpha_bar_t = alpha_bar_t.to(self.dls.device) + + # noisify the image + xt = torch.sqrt(alpha_bar_t) * hr + torch.sqrt(1-alpha_bar_t) * noise + + # Stack input with low-resolution image (upscaled) and noise level + self.learn.xb = (torch.cat([xt, lr, alpha_bar_t.repeat(1,1,*hr.shape[2:])], dim=1),) + self.learn.yb = (noise,) # we are trying to predict the noise + + +class DDPMSamplerCallback(DDPMCallback): + def before_batch(self): + lr = self.xb[0] + + # Generate a batch of random noise to start with + xt = torch.randn_like(lr) + + outputs = [xt] + for t in track(reversed(range(self.n_steps)), total=self.n_steps, description="Performing diffusion steps for batch:"): + z = torch.randn(xt.shape, device=xt.device) if t > 0 else torch.zeros(xt.shape, device=xt.device) + alpha_t = self.alpha[t] # get noise level at current timestep + alpha_bar_t = self.alpha_bar[t] + sigma_t = self.sigma[t] + model_input = torch.cat( + [xt, lr, alpha_bar_t.repeat(1,1,*lr.shape[2:]).to(xt.device)], + dim=1, + ) + predicted_noise = self.model(model_input) + + # predict x_(t-1) in accordance to Algorithm 2 in paper + xt = 1/torch.sqrt(alpha_t) * (xt - (1-alpha_t)/torch.sqrt(1-alpha_bar_t) * predicted_noise) + sigma_t*z + outputs.append(xt) + + # self.learn.pred = (torch.stack(outputs, dim=1),) + self.learn.pred = (xt,) + + raise CancelBatchException + diff --git a/supercat/enums.py b/supercat/enums.py new file mode 100644 index 0000000..69e198c --- /dev/null +++ b/supercat/enums.py @@ -0,0 +1,13 @@ +from enum import Enum + + +class DownsampleScale(Enum): + X2 = "X2" + X4 = "X4" + + +class DownsampleMethod(Enum): + DEFAULT = "default" + UNKNOWN = "unknown" + + diff --git a/supercat/fractal.py b/supercat/fractal.py new file mode 100644 index 0000000..4fba32c --- /dev/null +++ b/supercat/fractal.py @@ -0,0 +1,270 @@ + +from supercat.worley import WorleySR +import numpy as np +import torch + + +def interpolant(t): + """ + Taken from https://github.com/pvigier/perlin-numpy/ + """ + return t*t*t*(t*(t*6 - 15) + 10) + + +def shape_for_fractal_noise(shape, res, octaves, lacunarity): + shape = list(shape) + for i, (s, r) in enumerate(zip(shape, res)): + multiple_of = lacunarity**(octaves-1)*r + if s % multiple_of != 0: + shape[i] += multiple_of - (s % multiple_of) + return tuple(shape) + + +def generate_perlin_noise_2d( + shape, res, tileable=(False, False), interpolant=interpolant +): + """Generate a 2D numpy array of perlin noise. + + Taken from https://github.com/pvigier/perlin-numpy/ + + Args: + shape: The shape of the generated array (tuple of two ints). + This must be a multple of res. + res: The number of periods of noise to generate along each + axis (tuple of two ints). Note shape must be a multiple of + res. + tileable: If the noise should be tileable along each axis + (tuple of two bools). Defaults to (False, False). + interpolant: The interpolation function, defaults to + t*t*t*(t*(t*6 - 15) + 10). + + Returns: + A numpy array of shape shape with the generated noise. + + Raises: + ValueError: If shape is not a multiple of res. + """ + delta = (res[0] / shape[0], res[1] / shape[1]) + d = (shape[0] // res[0], shape[1] // res[1]) + grid = np.mgrid[0:res[0]:delta[0], 0:res[1]:delta[1]]\ + .transpose(1, 2, 0) % 1 + # Gradients + angles = 2*np.pi*np.random.rand(res[0]+1, res[1]+1) + gradients = np.dstack((np.cos(angles), np.sin(angles))) + if tileable[0]: + gradients[-1,:] = gradients[0,:] + if tileable[1]: + gradients[:,-1] = gradients[:,0] + gradients = gradients.repeat(d[0], 0).repeat(d[1], 1) + g00 = gradients[ :-d[0], :-d[1]] + g10 = gradients[d[0]: , :-d[1]] + g01 = gradients[ :-d[0],d[1]: ] + g11 = gradients[d[0]: ,d[1]: ] + # Ramps + n00 = np.sum(np.dstack((grid[:,:,0] , grid[:,:,1] )) * g00, 2) + n10 = np.sum(np.dstack((grid[:,:,0]-1, grid[:,:,1] )) * g10, 2) + n01 = np.sum(np.dstack((grid[:,:,0] , grid[:,:,1]-1)) * g01, 2) + n11 = np.sum(np.dstack((grid[:,:,0]-1, grid[:,:,1]-1)) * g11, 2) + # Interpolation + t = interpolant(grid) + n0 = n00*(1-t[:,:,0]) + t[:,:,0]*n10 + n1 = n01*(1-t[:,:,0]) + t[:,:,0]*n11 + return np.sqrt(2)*((1-t[:,:,1])*n0 + t[:,:,1]*n1) + + +def generate_fractal_noise_2d( + shape, res, octaves=1, persistence=0.5, + lacunarity=2, tileable=(False, False), + interpolant=interpolant +): + """Generate a 2D numpy array of fractal noise. + + Adapted from https://github.com/pvigier/perlin-numpy/ + + Args: + shape: The shape of the generated array (tuple of two ints). + This must be a multiple of lacunarity**(octaves-1)*res. + res: The number of periods of noise to generate along each + axis (tuple of two ints). Note shape must be a multiple of + (lacunarity**(octaves-1)*res). + octaves: The number of octaves in the noise. Defaults to 1. + persistence: The scaling factor between two octaves. + lacunarity: The frequency factor between two octaves. + tileable: If the noise should be tileable along each axis + (tuple of two bools). Defaults to (False, False). + interpolant: The, interpolation function, defaults to + t*t*t*(t*(t*6 - 15) + 10). + + Returns: + A numpy array of fractal noise and of shape shape generated by + combining several octaves of perlin noise. + """ + + # Make shape bigger if necessary + fractal_shape = shape_for_fractal_noise(shape, res, octaves, lacunarity) + + noise = np.zeros(fractal_shape) + frequency = 1 + amplitude = 1 + for _ in range(octaves): + noise += amplitude * generate_perlin_noise_2d( + fractal_shape, (frequency*res[0], frequency*res[1]), tileable, interpolant + ) + frequency *= lacunarity + amplitude *= persistence + + # Crop if necessary + if fractal_shape != shape: + noise = noise[:shape[0], :shape[1]] + + return noise + + +def generate_perlin_noise_3d( + shape, res, tileable=(False, False, False), + interpolant=interpolant +): + """Generate a 3D numpy array of perlin noise. + + Taken from https://github.com/pvigier/perlin-numpy/ + + Args: + shape: The shape of the generated array (tuple of three ints). + This must be a multiple of res. + res: The number of periods of noise to generate along each + axis (tuple of three ints). Note shape must be a multiple + of res. + tileable: If the noise should be tileable along each axis + (tuple of three bools). Defaults to (False, False, False). + interpolant: The interpolation function, defaults to + t*t*t*(t*(t*6 - 15) + 10). + + Returns: + A numpy array of shape shape with the generated noise. + + Raises: + ValueError: If shape is not a multiple of res. + """ + delta = (res[0] / shape[0], res[1] / shape[1], res[2] / shape[2]) + d = (shape[0] // res[0], shape[1] // res[1], shape[2] // res[2]) + grid = np.mgrid[0:res[0]:delta[0],0:res[1]:delta[1],0:res[2]:delta[2]] + grid = np.mgrid[0:res[0]:delta[0],0:res[1]:delta[1],0:res[2]:delta[2]] + grid = grid.transpose(1, 2, 3, 0) % 1 + # Gradients + theta = 2*np.pi*np.random.rand(res[0] + 1, res[1] + 1, res[2] + 1) + phi = 2*np.pi*np.random.rand(res[0] + 1, res[1] + 1, res[2] + 1) + gradients = np.stack( + (np.sin(phi)*np.cos(theta), np.sin(phi)*np.sin(theta), np.cos(phi)), + axis=3 + ) + if tileable[0]: + gradients[-1,:,:] = gradients[0,:,:] + if tileable[1]: + gradients[:,-1,:] = gradients[:,0,:] + if tileable[2]: + gradients[:,:,-1] = gradients[:,:,0] + gradients = gradients.repeat(d[0], 0).repeat(d[1], 1).repeat(d[2], 2) + g000 = gradients[ :-d[0], :-d[1], :-d[2]] + g100 = gradients[d[0]: , :-d[1], :-d[2]] + g010 = gradients[ :-d[0],d[1]: , :-d[2]] + g110 = gradients[d[0]: ,d[1]: , :-d[2]] + g001 = gradients[ :-d[0], :-d[1],d[2]: ] + g101 = gradients[d[0]: , :-d[1],d[2]: ] + g011 = gradients[ :-d[0],d[1]: ,d[2]: ] + g111 = gradients[d[0]: ,d[1]: ,d[2]: ] + # Ramps + n000 = np.sum(np.stack((grid[:,:,:,0] , grid[:,:,:,1] , grid[:,:,:,2] ), axis=3) * g000, 3) + n100 = np.sum(np.stack((grid[:,:,:,0]-1, grid[:,:,:,1] , grid[:,:,:,2] ), axis=3) * g100, 3) + n010 = np.sum(np.stack((grid[:,:,:,0] , grid[:,:,:,1]-1, grid[:,:,:,2] ), axis=3) * g010, 3) + n110 = np.sum(np.stack((grid[:,:,:,0]-1, grid[:,:,:,1]-1, grid[:,:,:,2] ), axis=3) * g110, 3) + n001 = np.sum(np.stack((grid[:,:,:,0] , grid[:,:,:,1] , grid[:,:,:,2]-1), axis=3) * g001, 3) + n101 = np.sum(np.stack((grid[:,:,:,0]-1, grid[:,:,:,1] , grid[:,:,:,2]-1), axis=3) * g101, 3) + n011 = np.sum(np.stack((grid[:,:,:,0] , grid[:,:,:,1]-1, grid[:,:,:,2]-1), axis=3) * g011, 3) + n111 = np.sum(np.stack((grid[:,:,:,0]-1, grid[:,:,:,1]-1, grid[:,:,:,2]-1), axis=3) * g111, 3) + # Interpolation + t = interpolant(grid) + n00 = n000*(1-t[:,:,:,0]) + t[:,:,:,0]*n100 + n10 = n010*(1-t[:,:,:,0]) + t[:,:,:,0]*n110 + n01 = n001*(1-t[:,:,:,0]) + t[:,:,:,0]*n101 + n11 = n011*(1-t[:,:,:,0]) + t[:,:,:,0]*n111 + n0 = (1-t[:,:,:,1])*n00 + t[:,:,:,1]*n10 + n1 = (1-t[:,:,:,1])*n01 + t[:,:,:,1]*n11 + return ((1-t[:,:,:,2])*n0 + t[:,:,:,2]*n1) + + +def generate_fractal_noise_3d( + shape, res, octaves=1, persistence=0.5, lacunarity=2, + tileable=(False, False, False), interpolant=interpolant +): + """Generate a 3D numpy array of fractal noise. + + Adapted from https://github.com/pvigier/perlin-numpy/ + + Args: + shape: The shape of the generated array (tuple of three ints). + This must be a multiple of lacunarity**(octaves-1)*res. + res: The number of periods of noise to generate along each + axis (tuple of three ints). Note shape must be a multiple of + (lacunarity**(octaves-1)*res). + octaves: The number of octaves in the noise. Defaults to 1. + persistence: The scaling factor between two octaves. + lacunarity: The frequency factor between two octaves. + tileable: If the noise should be tileable along each axis + (tuple of three bools). Defaults to (False, False, False). + interpolant: The, interpolation function, defaults to + t*t*t*(t*(t*6 - 15) + 10). + + Returns: + A numpy array of fractal noise and of shape shape generated by + combining several octaves of perlin noise. + """ + + # Make shape bigger if necessary + fractal_shape = shape_for_fractal_noise(shape, res, octaves, lacunarity) + + noise = np.zeros(fractal_shape) + frequency = 1 + amplitude = 1 + for _ in range(octaves): + noise += amplitude * generate_perlin_noise_3d( + fractal_shape, + (frequency*res[0], frequency*res[1], frequency*res[2]), + tileable, + interpolant + ) + frequency *= lacunarity + amplitude *= persistence + + # Crop if necessary + if fractal_shape != shape: + noise = noise[:shape[0], :shape[1], :shape[2]] + + return noise + + +class FractalNoiseTensor(): + def __init__(self, shape): + self.shape = shape + self.dim = len(shape) + self.func = generate_fractal_noise_3d if self.dim == 3 else generate_fractal_noise_2d + + def __call__(self, *args, **kwargs): + res = np.random.choice([1,2,4] if self.dim == 3 else [1,2,4,8]) + octaves = np.random.randint(low=1, high=5 if self.dim == 3 else 7) + res_tuple = (res,) * self.dim + + x = self.func(self.shape, res=res_tuple, octaves=octaves) + + x = torch.from_numpy(x).float() + x = (x - x.min())/(x.max()-x.min())*2.0 - 1.0 + x = x.unsqueeze(0) + return x + + +class FractalSR(WorleySR): + def build_generator(self, shape): + return FractalNoiseTensor(shape=shape) + + +if __name__ == "__main__": + FractalSR.main() diff --git a/supercat/interpolation.py b/supercat/interpolation.py deleted file mode 100644 index 89a8972..0000000 --- a/supercat/interpolation.py +++ /dev/null @@ -1,21 +0,0 @@ -from enum import Enum -import tricubic -import numpy as np - -class InterpolationMethod(Enum): - TRICUBIC = 0 - LINEAR = 1 - - -def interpolate3D(image:np.ndarray, new_shape, method:InterpolationMethod = InterpolationMethod.TRICUBIC): - interpolator = tricubic.tricubic(list(image), list(image.shape)) - upscaled = np.empty( new_shape ) - xs = np.linspace(0.0, image.shape[0]-1, num=new_shape[0]) - ys = np.linspace(0.0, image.shape[1]-1, num=new_shape[1]) - zs = np.linspace(0.0, image.shape[2]-1, num=new_shape[2]) - for i, x in enumerate(xs): - for j, y in enumerate(ys): - for k, z in enumerate(zs): - upscaled[i,j,k] = interpolator.ip( [x,y,z] ) - - return np.float32(upscaled) \ No newline at end of file diff --git a/supercat/models.py b/supercat/models.py index 244d8b9..8abfc25 100644 --- a/supercat/models.py +++ b/supercat/models.py @@ -1,9 +1,7 @@ import torch from torch import nn from torch import Tensor -from torchvision.models import video -from torchvision.models.video.resnet import VideoResNet -from fastai.vision.learner import _load_pretrained_weights, _get_first_layer +import numpy as np @torch.jit.script def autocrop(encoder_layer: torch.Tensor, decoder_layer: torch.Tensor): @@ -76,19 +74,24 @@ class ResBlock(nn.Module): https://towardsdev.com/implement-resnet-with-pytorch-a9fb40a77448 https://github.com/pytorch/vision/blob/main/torchvision/models/resnet.py """ - def __init__(self, dim:int, in_channels:int, out_channels:int, downsample:bool): + def __init__(self, dim:int, in_channels:int, out_channels:int, downsample:bool, kernel_size:int=3): super().__init__() + + # calculate padding so that the output is the same as a kernel size of 1 with zero padding + # this is required to be calculated becaues padding="same" doesn't work with a stride + padding = (kernel_size - 1)//2 + if downsample: - self.conv1 = Conv(in_channels, out_channels, kernel_size=3, stride=2, padding=1, dim=dim) + self.conv1 = Conv(in_channels, out_channels, kernel_size=kernel_size, stride=2, padding=padding, dim=dim) self.shortcut = nn.Sequential( Conv(in_channels, out_channels, kernel_size=1, stride=2, dim=dim), BatchNorm(out_channels, dim=dim) ) else: - self.conv1 = Conv(in_channels, out_channels, kernel_size=3, stride=1, padding=1, dim=dim) + self.conv1 = Conv(in_channels, out_channels, kernel_size=kernel_size, stride=1, padding=padding, dim=dim) self.shortcut = nn.Sequential() - self.conv2 = Conv(out_channels, out_channels, kernel_size=3, stride=1, padding=1, dim=dim) + self.conv2 = Conv(out_channels, out_channels, kernel_size=kernel_size, stride=1, padding=padding, dim=dim) self.bn1 = BatchNorm(out_channels, dim=dim) self.bn2 = BatchNorm(out_channels, dim=dim) self.relu = nn.ReLU(inplace=True) @@ -108,6 +111,7 @@ def __init__( in_channels:int = 1, downsample:bool = True, growth_factor:float = 2.0, + kernel_size:int = 3, ): super().__init__() self.in_channels = in_channels @@ -115,8 +119,8 @@ def __init__( if downsample: self.out_channels = int(growth_factor*self.out_channels) - self.block1 = ResBlock(in_channels=in_channels, out_channels=self.out_channels, downsample=downsample, dim=dim) - self.block2 = ResBlock(in_channels=self.out_channels, out_channels=self.out_channels, downsample=False, dim=dim) + self.block1 = ResBlock(in_channels=in_channels, out_channels=self.out_channels, downsample=downsample, dim=dim, kernel_size=kernel_size) + self.block2 = ResBlock(in_channels=self.out_channels, out_channels=self.out_channels, downsample=False, dim=dim, kernel_size=kernel_size) def forward(self, x: Tensor) -> Tensor: x = self.block1(x) @@ -130,16 +134,17 @@ def __init__( dim:int, in_channels:int, out_channels:int, - kernel_size:int = 2, + resblock_kernel_size:int = 3, + upsample_kernel_size:int = 2, ): super().__init__() self.in_channels = in_channels self.out_channels = out_channels - self.upsample = ConvTranspose(in_channels=self.in_channels, out_channels=self.out_channels, kernel_size=kernel_size, stride=2, dim=dim) + self.upsample = ConvTranspose(in_channels=self.in_channels, out_channels=self.out_channels, kernel_size=upsample_kernel_size, stride=2, dim=dim) - self.block1 = ResBlock(in_channels=self.out_channels, out_channels=self.out_channels, downsample=False, dim=dim) - # self.block2 = ResBlock(in_channels=self.out_channels, out_channels=self.out_channels, downsample=False, dim=dim) + self.block1 = ResBlock(in_channels=self.out_channels, out_channels=self.out_channels, downsample=False, dim=dim, kernel_size=resblock_kernel_size) + # self.block2 = ResBlock(in_channels=self.out_channels, out_channels=self.out_channels, downsample=False, dim=dim, kernel_size=resblock_kernel_size) def forward(self, x: Tensor, shortcut: Tensor) -> Tensor: x = self.upsample(x) @@ -158,34 +163,58 @@ def __init__( in_channels:int = 1, initial_features:int = 64, growth_factor:float = 2.0, + kernel_size:int = 3, + stub_kernel_size:int = 7, + layers:int = 4, ): super().__init__() self.initial_features = initial_features self.in_channels = in_channels + self.growth_factor = growth_factor + self.kernel_size = kernel_size + self.stub_kernel_size = stub_kernel_size + self.layers = layers + self.dim = dim current_num_features = initial_features - self.layer0 = nn.Sequential( - Conv(in_channels=in_channels, out_channels=current_num_features, kernel_size=7, stride=2, padding=3, dim=dim), + padding = (stub_kernel_size - 1)//2 + + self.stem = nn.Sequential( + Conv(in_channels=in_channels, out_channels=current_num_features, kernel_size=stub_kernel_size, stride=2, padding=padding, dim=dim), BatchNorm(num_features=current_num_features, dim=dim), nn.ReLU(inplace=True), - # nn.MaxPool3d(kernel_size=3, stride=2, padding=1), ) - self.layer1 = DownBlock( in_channels=current_num_features, downsample=True, dim=dim, growth_factor=growth_factor ) - self.layer2 = DownBlock( in_channels=self.layer1.out_channels, downsample=True, dim=dim, growth_factor=growth_factor ) - self.layer3 = DownBlock( in_channels=self.layer2.out_channels, downsample=True, dim=dim, growth_factor=growth_factor ) - self.layer4 = DownBlock( in_channels=self.layer3.out_channels, downsample=True, dim=dim, growth_factor=growth_factor ) - self.output_features = self.layer4.out_channels + self.downblock_layers = [] + for _ in range(layers): + downblock = DownBlock( + in_channels=current_num_features, + downsample=True, + dim=dim, + growth_factor=growth_factor, + kernel_size=kernel_size + ) + self.downblock_layers.append(downblock) + current_num_features = downblock.out_channels + self.downblocks = nn.Sequential(*self.downblock_layers) + self.output_features = current_num_features def forward(self, x: Tensor) -> Tensor: - x = self.layer0(x) - x = self.layer1(x) - x = self.layer2(x) - x = self.layer3(x) - x = self.layer4(x) + x = self.stem(x) + x = self.downblocks(x) return x + def macs(self): + return resnetbody_macs( + dim=self.dim, + growth_factor=self.growth_factor, + kernel_size=self.kernel_size, + stub_kernel_size=self.stub_kernel_size, + initial_features=self.initial_features, + downblock_layers=self.layers, + ) + class ResNet(nn.Module): def __init__( @@ -196,13 +225,15 @@ def __init__( in_channels:int = 1, initial_features:int = 64, growth_factor:float = 2.0, + layers:int = 4, ): super().__init__() self.body = body if body is not None else ResNetBody( dim=dim, in_channels=in_channels, initial_features=initial_features, - growth_factor=growth_factor + growth_factor=growth_factor, + layers=layers, ) assert in_channels == self.body.in_channels assert initial_features == self.body.initial_features @@ -227,25 +258,35 @@ def __init__( initial_features:int = 64, out_channels: int = 1, growth_factor:float = 2.0, + kernel_size:int = 3, + downblock_layers:int = 4, ): super().__init__() + self.dim = dim self.body = body if body is not None else ResNetBody( dim=dim, in_channels=in_channels, initial_features=initial_features, growth_factor=growth_factor, + kernel_size=kernel_size, + layers=downblock_layers, ) assert in_channels == self.body.in_channels assert initial_features == self.body.initial_features - self.up_block4 = UpBlock(dim=dim, in_channels=self.body.layer4.out_channels, out_channels=self.body.layer4.in_channels) - self.up_block3 = UpBlock(dim=dim, in_channels=self.body.layer3.out_channels, out_channels=self.body.layer3.in_channels) - self.up_block2 = UpBlock(dim=dim, in_channels=self.body.layer2.out_channels, out_channels=self.body.layer2.in_channels) - self.up_block1 = UpBlock(dim=dim, in_channels=self.body.layer1.out_channels, out_channels=self.body.layer1.in_channels) + self.upblock_layers = nn.ModuleList() + for downblock in reversed(self.body.downblock_layers): + upblock = UpBlock( + dim=dim, + in_channels=downblock.out_channels, + out_channels=downblock.in_channels, + resblock_kernel_size=kernel_size + ) + self.upblock_layers.append(upblock) - self.final_upsample_dims = self.up_block1.out_channels//2 + self.final_upsample_dims = self.upblock_layers[-1].out_channels//2 self.final_upsample = ConvTranspose( - in_channels=self.up_block1.out_channels, + in_channels=self.upblock_layers[-1].out_channels, out_channels=self.final_upsample_dims, kernel_size=2, stride=2, @@ -263,115 +304,125 @@ def __init__( def forward(self, x: Tensor) -> Tensor: x = x.float() input = x - x = encoded_0 = self.body.layer0(x) - x = encoded_1 = self.body.layer1(x) - x = encoded_2 = self.body.layer2(x) - x = encoded_3 = self.body.layer3(x) - x = self.body.layer4(x) - - x = self.up_block4(x, encoded_3) - x = self.up_block3(x, encoded_2) - x = self.up_block2(x, encoded_1) - x = self.up_block1(x, encoded_0) + encoded_list = [] + x = self.body.stem(x) + for downblock in self.body.downblock_layers: + encoded_list.append(x) + x = downblock(x) + + for encoded, upblock in zip(reversed(encoded_list), self.upblock_layers): + x = upblock(x, encoded) + x = self.final_upsample(x) x = torch.cat([input,x], dim=1) x = self.final_layer(x) # activation? return x + def macs(self) -> float: + return residualunet_macs( + dim=self.dim, + growth_factor=self.body.growth_factor, + kernel_size=self.body.kernel_size, + stub_kernel_size=self.body.stub_kernel_size, + initial_features=self.body.initial_features, + downblock_layers=self.body.layers, + ) -class DoNothing(nn.Module): - def __init__( - self, - ): - super().__init__() - # dummy layer so that there are some parameters - self.dummy = nn.Conv3d( - in_channels=1, - out_channels=1, - kernel_size=1, - stride=1, +def residualunet_macs( + dim:int, + growth_factor:float, + kernel_size:int, + stub_kernel_size:int, + initial_features:int, + downblock_layers:int, +) -> float: + """ + M = L + \sum_{i=0}^n D_i + U_i + D_0 = \frac{\kappa ^ d}{2^d} f + D_i = \frac{1}{2^{d(i+1)}} g^{2i-1} ( k^d( 3g + 1 ) + 1) f^2 + U_i = \frac{f^2}{2^{d i}} (2^d g^{2i-1} + 2 k^d g^{2i-2}) + U_0 = 2^{d-1} f ^ 2 + L = \frac{f}{2} + 1 + """ + stride = 2 + U_0 = 2 ** (dim - 1) * initial_features **2 + L = initial_features/2 + 1 + body_macs = resnetbody_macs( + dim=dim, + growth_factor=growth_factor, + kernel_size=kernel_size, + stub_kernel_size=stub_kernel_size, + initial_features=initial_features, + downblock_layers=downblock_layers, + ) + M = L + body_macs + U_0 + + for i in range(1, downblock_layers+1): + U_i = initial_features**2/(stride**(dim * i)) * ( + 2**dim * growth_factor ** (2 * i - 1) + + 2 * kernel_size**dim * growth_factor ** ( 2 * i - 2 ) ) - def forward(self, x: Tensor) -> Tensor: - return x + M += U_i + return M -def get_in_out_channels(layer): - first_conv = next(next(next(layer.children()).children()).children()) - return first_conv.in_channels, first_conv.out_channels +def resnetbody_macs( + dim:int, + growth_factor:float, + kernel_size:int, + stub_kernel_size:int, + initial_features:int, + downblock_layers:int, +) -> float: + """ + M = \sum_{i=0}^n D_i + D_0 = \frac{\kappa ^ d}{2^d} f + D_i = \frac{1}{2^{d(i+1)}} g^{2i-1} ( k^d( 3g + 1 ) + 1) f^2 + """ + stride = 2 + D_0 = stub_kernel_size **dim * initial_features / (stride ** dim) + M = D_0 -def update_first_layer(model, n_in=1, pretrained=True): - first_layer, parent, name = _get_first_layer(model) - assert isinstance(first_layer, (nn.Conv2d, nn.Conv3d)), f'Change of input channels only supported with Conv2d or Conv3d, found {first_layer.__class__.__name__}' - assert getattr(first_layer, 'in_channels') == 3, f'Unexpected number of input channels, found {getattr(first_layer, "in_channels")} while expecting 3' - params = {attr:getattr(first_layer, attr) for attr in 'out_channels kernel_size stride padding dilation groups padding_mode'.split()} - params['bias'] = getattr(first_layer, 'bias') is not None - params['in_channels'] = n_in - new_layer = type(first_layer)(**params) - if pretrained: - _load_pretrained_weights(new_layer, first_layer) - setattr(parent, name, new_layer) + for i in range(1, downblock_layers+1): + D_i = initial_features**2 /(stride**(dim * (i+1))) * growth_factor ** (2 * i - 1) * ( + kernel_size**dim * (3 * growth_factor + 1) + 1 + ) + M += D_i + return M -class VideoUnet3d(nn.Module): - def __init__(self, base:VideoResNet = None, in_channels:int = 1, out_channels:int = 1, pretrained:bool = True, **kwargs): - super().__init__(**kwargs) - base = base or video.r3d_18(pretrained=pretrained) - self.base = base - self.initial_in_channels = in_channels - self.final_out_channels = out_channels - - self.base_layers = {name:child for name,child in base.named_children()} - - # Edit the first layer as needed - if in_channels != 3: - update_first_layer(base, in_channels, pretrained=pretrained) - first_layer = next(base.stem.children()) - first_layer.stride = (2,2,2) - first_layer.padding = (1,3,3) - - in_channels, out_channels = get_in_out_channels(self.base_layers['layer4']) - self.up_block4 = UpBlock(in_channels=out_channels, out_channels=in_channels) - in_channels, out_channels = get_in_out_channels(self.base_layers['layer3']) - self.up_block3 = UpBlock(in_channels=out_channels, out_channels=in_channels) - in_channels, out_channels = get_in_out_channels(self.base_layers['layer2']) - self.up_block2 = UpBlock(in_channels=out_channels, out_channels=in_channels) - in_channels, out_channels = get_in_out_channels(self.base_layers['layer1']) - self.up_block1 = UpBlock(in_channels=out_channels, out_channels=in_channels) - - self.final_upsample_dims = out_channels//2 - self.final_upsample = nn.ConvTranspose3d( - in_channels=out_channels, - out_channels=self.final_upsample_dims, - kernel_size=2, - stride=2 + +def calc_initial_features_residualunet( + macc:int, + dim:int, + growth_factor:float, + kernel_size:int, + stub_kernel_size:int, + downblock_layers:int, +) -> int: + """ + """ + stride = 2 + a = 2 ** (dim - 1) + for i in range(1, downblock_layers+1): + D_i_over_f2 = 1 /(stride**(dim * (i+1))) * growth_factor ** (2 * i - 1) * ( + kernel_size**dim * (3 * growth_factor + 1) + 1 + ) + U_i_over_f2 = 1/(stride**(dim * i)) * ( + 2**dim * growth_factor ** (2 * i - 1) + + 2 * kernel_size**dim * growth_factor ** ( 2 * i - 2 ) ) - self.final_layer = nn.Conv3d( - in_channels=self.final_upsample_dims+self.initial_in_channels, - out_channels=self.final_out_channels, - kernel_size=1, - stride=1, - ) + a += D_i_over_f2 + U_i_over_f2 - def forward(self, x: torch.Tensor) -> torch.Tensor: - input = x + b = stub_kernel_size **dim / (stride ** dim) + 0.5 + c = -macc + 1 - x = encoded_0 = self.base.stem(x) - x = encoded_1 = self.base.layer1(x) - x = encoded_2 = self.base.layer2(x) - x = encoded_3 = self.base.layer3(x) - x = self.base.layer4(x) + initial_features = (-b + np.sqrt(b**2 - 4*a*c))/(2 * a) - x = self.up_block4(x, encoded_3) - x = self.up_block3(x, encoded_2) - x = self.up_block2(x, encoded_1) - x = self.up_block1(x, encoded_0) - x = self.final_upsample(x) - x = torch.cat([input,x], dim=1) - x = self.final_layer(x) - # activation? - return x \ No newline at end of file + return int(initial_features + 0.5) + diff --git a/supercat/transforms.py b/supercat/transforms.py index 5423aed..b109dcd 100644 --- a/supercat/transforms.py +++ b/supercat/transforms.py @@ -3,7 +3,9 @@ import hdf5storage import numpy as np from pathlib import Path -from .interpolation import interpolate3D +from fastai.vision.data import TensorImage +from skimage.transform import resize as skresize + DEEPROCK_HDF5_KEY = "temp" @@ -37,6 +39,13 @@ def __init__(self, width, height, depth): self.shape = (width, height, depth) def encodes(self, data:np.ndarray): - data = interpolate3D(data, self.shape) - return data + return skresize(data, self.shape, order=3) + + +class RescaleImage(DisplayedTransform): + order = 20 #Need to run after IntToFloatTensor + def encodes(self, item:TensorImage): + return item.float()*2.0 - 1.0 + + diff --git a/supercat/visualization.py b/supercat/visualization.py index f4155b1..ab7c277 100644 --- a/supercat/visualization.py +++ b/supercat/visualization.py @@ -151,6 +151,9 @@ def comparison_plot(originals, downscaled_images, upscaled_images, titles, crops crop_x = crop[0:2] crop_y = (crop[3], crop[2]) + if isinstance(upscaled, (Path, str)): + upscaled = Image.open(upscaled) + difference = np.asarray(upscaled).astype(int) - np.asarray(original_im.convert("RGB"))[:,:,0].astype(int) # squared_error = np.power(difference.astype(float)/255, 2.0) @@ -252,16 +255,16 @@ def add_volume_face_traces(fig, volume, coloraxis="coloraxis", **kwargs): def comparison_plot3D(originals, downscaled_volumes, upscaled_volumes, titles): fig = make_subplots( rows=len(originals), - cols=4, + cols=3, subplot_titles=( "Original", "Downscaled", "Upscaled", - "Difference", + # "Difference", ), vertical_spacing = 0.02, horizontal_spacing = 0.02, - specs=[[{'type':"surface"}, {'type':"surface"}, {'type':"surface"}, {'type':"surface"},]]*len(originals), + specs=[[{'type':"surface"}, {'type':"surface"}, {'type':"surface"}, ]]*len(originals), # hack ) axis = dict(showgrid=False, showticklabels=False, showaxeslabels=False, title="", showbackground=False) @@ -276,10 +279,16 @@ def comparison_plot3D(originals, downscaled_volumes, upscaled_volumes, titles): downscaled = read3D(downscaled) if isinstance(downscaled, (str, Path)) else downscaled upscaled = read3D(upscaled) if isinstance(upscaled, (str, Path)) else upscaled + # upscaled = (upscaled - upscaled.mean())/upscaled.std() + # upscaled = upscaled * downscaled.std() + downscaled.mean() + # breakpoint() + # upscaled *= 255.0 + # breakpoint() + add_volume_face_traces(fig, original, row=row+1, col=1) add_volume_face_traces(fig, downscaled, row=row+1, col=2) add_volume_face_traces(fig, upscaled, row=row+1, col=3) - add_volume_face_traces(fig, upscaled-original, row=row+1, col=4, coloraxis="coloraxis2") + # add_volume_face_traces(fig, upscaled-original, row=row+1, col=4, coloraxis="coloraxis2") scenes = {f"scene{row*4+column}":scene for column in range(1,5)} fig.update_layout(**scenes) diff --git a/supercat/worley.py b/supercat/worley.py new file mode 100644 index 0000000..fba60a8 --- /dev/null +++ b/supercat/worley.py @@ -0,0 +1,160 @@ +import torchapp as ta +import torch +from pathlib import Path +from fastai.callback.core import Callback, CancelBatchException +from fastai.data.block import DataBlock, TransformBlock +from fastai.data.core import DataLoaders +import torch.nn.functional as F +import numpy as np +from rich.progress import track +import torchvision.transforms as T + +from supercat.models import ResidualUNet +from supercat.diffusion import DDPMCallback, DDPMSamplerCallback + +class ShrinkCallBack(Callback): + def __init__(self, factor:int=4, **kwargs): + super().__init__(**kwargs) + self.factor = factor + + def before_batch(self): + hr = self.xb[0] + lr_shape = tuple(s//self.factor for s in hr.shape[2:]) + mode = "bilinear" if len(lr_shape) == 2 else "trilinear" + lr = F.interpolate(hr, lr_shape, mode=mode) + pseudo_hr = F.interpolate(lr, hr.shape[2:], mode=mode) + + self.learn.xb = (pseudo_hr,) + self.learn.yb = (hr,) + + +class WorleyNoise: + """ + Derived from: + https://stackoverflow.com/a/65704227 + https://stackoverflow.com/q/65703414 + """ + def __init__(self, shape, density, n:int=0, seed=None): + np.random.seed(seed) + + self.density = density + self.shape = shape + self.dims = len(self.shape) + self.coords = [np.arange(s) for s in self.shape] + self.points = None + self.n = n + + def __call__(self): + self.points = np.random.rand(self.density, self.dims) + + for i, size in enumerate(self.shape): + self.points[:, i] *= size + + axes = list(range(1, self.dims+1)) + squared_d = sum( + np.expand_dims( + np.power(self.points[:, i, np.newaxis] - self.coords[i], 2), + axis=axes[:i]+axes[i+1:] + ) + for i in range(self.dims) + ) + + if self.n == 0: + return np.sqrt(squared_d.min(axis=0)) + elif self.n is None: + return np.sqrt(squared_d) + return np.sqrt(np.sort(squared_d, axis=0)[self.n]) + + +class WorleyNoiseTensor(WorleyNoise): + def __call__(self, *args): + x = super().__call__() + x = torch.from_numpy(x).float() + x = x/x.max()*2.0 - 1.0 + x = x.unsqueeze(0) + + return x + + +class WorleySR(ta.TorchApp): + def build_generator(self, shape): + return WorleyNoiseTensor(shape=shape, density=200) + + def dataloaders( + self, + dim:int=2, + depth:int=500, + width:int=500, + height:int=500, + batch_size:int=16, + item_count:int=1024, + ): + + shape = (height, width) if dim == 2 else (depth, height, width) + self.shape = shape + self.dim = dim + + datablock = DataBlock( + blocks=(TransformBlock), + get_x=self.build_generator(shape), + ) + + dataloaders = DataLoaders.from_dblock( + datablock, + source=range(item_count), + bs=batch_size, + ) + + return dataloaders + + def extra_callbacks(self, diffusion:bool=True): + self.diffusion = diffusion + callbacks = [ShrinkCallBack(factor=4)] + if self.diffusion: + callbacks.append(DDPMCallback()) + return callbacks + + def inference_callbacks(self, diffusion:bool=True): + callbacks = [ShrinkCallBack(factor=4)] + if diffusion: + callbacks.append(DDPMSamplerCallback()) + return callbacks + + def model(self): + return ResidualUNet(dim=self.dim, in_channels=3 if self.diffusion else 1) + + def loss_func(self): + """ + Returns the loss function to use with the model. + """ + return F.smooth_l1_loss + + def inference_dataloader(self, learner, **kwargs): + dataloader = learner.dls.test_dl([0], **kwargs) # output single test image + return dataloader + + def output_results( + self, + results, + output_dir: Path = ta.Param("./outputs", help="The location of the output directory."), + fps:float=ta.Param(30.0, help="The frames per second to use when generating the gif."), + **kwargs, + ): + output_dir = Path(output_dir) + print(f"Saving {len(results)} generated images:") + + transform = T.ToPILImage() + output_dir.mkdir(exist_ok=True, parents=True) + images = [] + for index, image in enumerate(results[0]): + path = output_dir/f"image.{index}.jpg" + + image = transform(torch.clip(image[0]/2.0 + 0.5, min=0.0, max=1.0)) + image.save(path) + images.append(image) + print(f"\t{path}") + images[0].save(output_dir/f"image.gif", save_all=True, append_images=images[1:], fps=fps) + + +if __name__ == "__main__": + WorleySR.main() diff --git a/tests/expected/TestSupercat/test_cli/train_help.yaml b/tests/expected/TestSupercat/test_cli/train_help.yaml index 4ce5594..0503c8b 100644 --- a/tests/expected/TestSupercat/test_cli/train_help.yaml +++ b/tests/expected/TestSupercat/test_cli/train_help.yaml @@ -18,7 +18,7 @@ output: --weight-decay FLOAT The amount of weight decay. If None then it uses the default amount of weight decay in fastai. - --mse / --no-mse [default: mse] + --l1-loss / --no-l1-loss [default: no-l1-loss] --deeprock PATH The path to the DeepRockSR-2D dataset. --downsample-scale [X2|X4] Should it use the 2x or 4x downsampled images. [default: X4] @@ -38,10 +38,22 @@ output: Including DeepSand-SR dataset. [default: no- include-sand] --initial-features INTEGER The number of features after the initial CNN - layer. [default: 64] - --growth-factor INTEGER The factor to grow the number of convolutional + layer. If not set then it is derived from the + MACC. + --growth-factor FLOAT The factor to grow the number of convolutional filters each time the model downscales. [default: 2.0] + --kernel-size INTEGER The size of the kernel in the convolutional + layers. [default: 3] + --stub-kernel-size INTEGER The size of the kernel in the initial stub + convolutional layer. [default: 7] + --downblock-layers INTEGER The number of layers to downscale (and + upscale) in the UNet. [default: 4] + --macc INTEGER The approximate number of multiply or + accumulate operations in the model per + pixel/voxel. Used to set initial_features if + it is not provided explicitly. [default: + 10000000] --epochs INTEGER The number of epochs. [default: 20] --freeze-epochs INTEGER The number of epochs to train when the learner is frozen and the last layer is trained by diff --git a/tests/expected/TestSupercat/test_cli/tune_help.yaml b/tests/expected/TestSupercat/test_cli/tune_help.yaml index 9b7de2d..be4f6ca 100644 --- a/tests/expected/TestSupercat/test_cli/tune_help.yaml +++ b/tests/expected/TestSupercat/test_cli/tune_help.yaml @@ -37,7 +37,7 @@ output: --weight-decay FLOAT The amount of weight decay. If None then it uses the default amount of weight decay in fastai. - --mse / --no-mse [default: mse] + --l1-loss / --no-l1-loss [default: no-l1-loss] --deeprock PATH The path to the DeepRockSR-2D dataset. --downsample-scale [X2|X4] Should it use the 2x or 4x downsampled images. [default: X4] @@ -57,9 +57,21 @@ output: Including DeepSand-SR dataset. [default: no- include-sand] --initial-features INTEGER The number of features after the initial CNN - layer. - --growth-factor INTEGER The factor to grow the number of convolutional + layer. If not set then it is derived from the + MACC. + --growth-factor FLOAT The factor to grow the number of convolutional filters each time the model downscales. + --kernel-size INTEGER The size of the kernel in the convolutional + layers. + --stub-kernel-size INTEGER The size of the kernel in the initial stub + convolutional layer. + --downblock-layers INTEGER The number of layers to downscale (and + upscale) in the UNet. + --macc INTEGER The approximate number of multiply or + accumulate operations in the model per + pixel/voxel. Used to set initial_features if + it is not provided explicitly. [default: + 10000000] --epochs INTEGER The number of epochs. [default: 20] --freeze-epochs INTEGER The number of epochs to train when the learner is frozen and the last layer is trained by diff --git a/tests/expected/TestSupercat/test_model/model_default.yaml b/tests/expected/TestSupercat/test_model/model_default.yaml index d1069d6..2d028b6 100644 --- a/tests/expected/TestSupercat/test_model/model_default.yaml +++ b/tests/expected/TestSupercat/test_model/model_default.yaml @@ -2,140 +2,144 @@ params: {} output: |- ResidualUNet( (body): ResNetBody( - (layer0): Sequential( - (0): Conv2d(1, 64, kernel_size=(7, 7), stride=(2, 2), padding=(3, 3)) - (1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (stem): Sequential( + (0): Conv2d(1, 408, kernel_size=(7, 7), stride=(2, 2), padding=(3, 3)) + (1): ReLU() (2): ReLU(inplace=True) ) - (layer1): DownBlock( - (block1): ResBlock( - (conv1): Conv2d(64, 128, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1)) - (shortcut): Sequential( - (0): Conv2d(64, 128, kernel_size=(1, 1), stride=(2, 2)) - (1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (downblocks): Sequential( + (0): DownBlock( + (block1): ResBlock( + (conv1): Conv2d(408, 816, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1)) + (shortcut): Sequential( + (0): Conv2d(408, 816, kernel_size=(1, 1), stride=(2, 2)) + (1): ReLU() + ) + (conv2): Conv2d(816, 816, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) + (block2): ResBlock( + (conv1): Conv2d(816, 816, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (shortcut): Sequential() + (conv2): Conv2d(816, 816, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) ) - (conv2): Conv2d(128, 128, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (bn1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) ) - (block2): ResBlock( - (conv1): Conv2d(128, 128, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (shortcut): Sequential() - (conv2): Conv2d(128, 128, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (bn1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) + (1): DownBlock( + (block1): ResBlock( + (conv1): Conv2d(816, 1632, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1)) + (shortcut): Sequential( + (0): Conv2d(816, 1632, kernel_size=(1, 1), stride=(2, 2)) + (1): ReLU() + ) + (conv2): Conv2d(1632, 1632, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) + (block2): ResBlock( + (conv1): Conv2d(1632, 1632, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (shortcut): Sequential() + (conv2): Conv2d(1632, 1632, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) ) - ) - (layer2): DownBlock( - (block1): ResBlock( - (conv1): Conv2d(128, 256, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1)) - (shortcut): Sequential( - (0): Conv2d(128, 256, kernel_size=(1, 1), stride=(2, 2)) - (1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (2): DownBlock( + (block1): ResBlock( + (conv1): Conv2d(1632, 3264, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1)) + (shortcut): Sequential( + (0): Conv2d(1632, 3264, kernel_size=(1, 1), stride=(2, 2)) + (1): ReLU() + ) + (conv2): Conv2d(3264, 3264, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) + (block2): ResBlock( + (conv1): Conv2d(3264, 3264, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (shortcut): Sequential() + (conv2): Conv2d(3264, 3264, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) ) - (conv2): Conv2d(256, 256, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (bn1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) ) - (block2): ResBlock( - (conv1): Conv2d(256, 256, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (shortcut): Sequential() - (conv2): Conv2d(256, 256, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (bn1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) + (3): DownBlock( + (block1): ResBlock( + (conv1): Conv2d(3264, 6528, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1)) + (shortcut): Sequential( + (0): Conv2d(3264, 6528, kernel_size=(1, 1), stride=(2, 2)) + (1): ReLU() + ) + (conv2): Conv2d(6528, 6528, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) + (block2): ResBlock( + (conv1): Conv2d(6528, 6528, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (shortcut): Sequential() + (conv2): Conv2d(6528, 6528, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) ) ) - (layer3): DownBlock( + ) + (upblock_layers): ModuleList( + (0): UpBlock( + (upsample): ConvTranspose2d(6528, 3264, kernel_size=(2, 2), stride=(2, 2)) (block1): ResBlock( - (conv1): Conv2d(256, 512, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1)) - (shortcut): Sequential( - (0): Conv2d(256, 512, kernel_size=(1, 1), stride=(2, 2)) - (1): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - ) - (conv2): Conv2d(512, 512, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (bn1): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (conv1): Conv2d(3264, 3264, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (shortcut): Sequential() + (conv2): Conv2d(3264, 3264, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (bn1): ReLU() + (bn2): ReLU() (relu): ReLU(inplace=True) ) - (block2): ResBlock( - (conv1): Conv2d(512, 512, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + ) + (1): UpBlock( + (upsample): ConvTranspose2d(3264, 1632, kernel_size=(2, 2), stride=(2, 2)) + (block1): ResBlock( + (conv1): Conv2d(1632, 1632, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) (shortcut): Sequential() - (conv2): Conv2d(512, 512, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (bn1): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (conv2): Conv2d(1632, 1632, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (bn1): ReLU() + (bn2): ReLU() (relu): ReLU(inplace=True) ) ) - (layer4): DownBlock( + (2): UpBlock( + (upsample): ConvTranspose2d(1632, 816, kernel_size=(2, 2), stride=(2, 2)) (block1): ResBlock( - (conv1): Conv2d(512, 1024, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1)) - (shortcut): Sequential( - (0): Conv2d(512, 1024, kernel_size=(1, 1), stride=(2, 2)) - (1): BatchNorm2d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - ) - (conv2): Conv2d(1024, 1024, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (bn1): BatchNorm2d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm2d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (conv1): Conv2d(816, 816, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (shortcut): Sequential() + (conv2): Conv2d(816, 816, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (bn1): ReLU() + (bn2): ReLU() (relu): ReLU(inplace=True) ) - (block2): ResBlock( - (conv1): Conv2d(1024, 1024, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + ) + (3): UpBlock( + (upsample): ConvTranspose2d(816, 408, kernel_size=(2, 2), stride=(2, 2)) + (block1): ResBlock( + (conv1): Conv2d(408, 408, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) (shortcut): Sequential() - (conv2): Conv2d(1024, 1024, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (bn1): BatchNorm2d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm2d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (conv2): Conv2d(408, 408, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) + (bn1): ReLU() + (bn2): ReLU() (relu): ReLU(inplace=True) ) ) ) - (up_block4): UpBlock( - (upsample): ConvTranspose2d(1024, 512, kernel_size=(2, 2), stride=(2, 2)) - (block1): ResBlock( - (conv1): Conv2d(512, 512, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (shortcut): Sequential() - (conv2): Conv2d(512, 512, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (bn1): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm2d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) - ) - ) - (up_block3): UpBlock( - (upsample): ConvTranspose2d(512, 256, kernel_size=(2, 2), stride=(2, 2)) - (block1): ResBlock( - (conv1): Conv2d(256, 256, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (shortcut): Sequential() - (conv2): Conv2d(256, 256, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (bn1): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm2d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) - ) - ) - (up_block2): UpBlock( - (upsample): ConvTranspose2d(256, 128, kernel_size=(2, 2), stride=(2, 2)) - (block1): ResBlock( - (conv1): Conv2d(128, 128, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (shortcut): Sequential() - (conv2): Conv2d(128, 128, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (bn1): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm2d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) - ) - ) - (up_block1): UpBlock( - (upsample): ConvTranspose2d(128, 64, kernel_size=(2, 2), stride=(2, 2)) - (block1): ResBlock( - (conv1): Conv2d(64, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (shortcut): Sequential() - (conv2): Conv2d(64, 64, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1)) - (bn1): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm2d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) - ) - ) - (final_upsample): ConvTranspose2d(64, 32, kernel_size=(2, 2), stride=(2, 2)) - (final_layer): Conv2d(33, 1, kernel_size=(1, 1), stride=(1, 1)) + (final_upsample): ConvTranspose2d(408, 204, kernel_size=(2, 2), stride=(2, 2)) + (final_layer): Conv2d(205, 1, kernel_size=(1, 1), stride=(1, 1)) ) diff --git a/tests/expected/TestSupercat3d/test_cli/train_help.yaml b/tests/expected/TestSupercat3d/test_cli/train_help.yaml index 9c74d3b..f8589b2 100644 --- a/tests/expected/TestSupercat3d/test_cli/train_help.yaml +++ b/tests/expected/TestSupercat3d/test_cli/train_help.yaml @@ -15,7 +15,7 @@ output: fp16] --output-dir PATH The location of the output directory. [default: ./outputs] - --mse / --no-mse [default: mse] + --l1-loss / --no-l1-loss [default: no-l1-loss] --deeprock PATH The path to the DeepRockSR-3D dataset. --downsample-scale [X2|X4] Should it use the 2x or 4x downsampled images. [default: X4] diff --git a/tests/expected/TestSupercat3d/test_cli/tune_help.yaml b/tests/expected/TestSupercat3d/test_cli/tune_help.yaml index 6181f9d..b2c6943 100644 --- a/tests/expected/TestSupercat3d/test_cli/tune_help.yaml +++ b/tests/expected/TestSupercat3d/test_cli/tune_help.yaml @@ -34,7 +34,7 @@ output: fp16] --output-dir PATH The location of the output directory. [default: ./outputs] - --mse / --no-mse [default: mse] + --l1-loss / --no-l1-loss [default: no-l1-loss] --deeprock PATH The path to the DeepRockSR-3D dataset. --downsample-scale [X2|X4] Should it use the 2x or 4x downsampled images. [default: X4] diff --git a/tests/expected/TestSupercat3d/test_model/model_default.yaml b/tests/expected/TestSupercat3d/test_model/model_default.yaml index 7c6f237..91d49dc 100644 --- a/tests/expected/TestSupercat3d/test_model/model_default.yaml +++ b/tests/expected/TestSupercat3d/test_model/model_default.yaml @@ -2,140 +2,144 @@ params: {} output: |- ResidualUNet( (body): ResNetBody( - (layer0): Sequential( + (stem): Sequential( (0): Conv3d(1, 64, kernel_size=(7, 7, 7), stride=(2, 2, 2), padding=(3, 3, 3)) - (1): BatchNorm3d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (1): ReLU() (2): ReLU(inplace=True) ) - (layer1): DownBlock( - (block1): ResBlock( - (conv1): Conv3d(64, 128, kernel_size=(3, 3, 3), stride=(2, 2, 2), padding=(1, 1, 1)) - (shortcut): Sequential( - (0): Conv3d(64, 128, kernel_size=(1, 1, 1), stride=(2, 2, 2)) - (1): BatchNorm3d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (downblocks): Sequential( + (0): DownBlock( + (block1): ResBlock( + (conv1): Conv3d(64, 128, kernel_size=(3, 3, 3), stride=(2, 2, 2), padding=(1, 1, 1)) + (shortcut): Sequential( + (0): Conv3d(64, 128, kernel_size=(1, 1, 1), stride=(2, 2, 2)) + (1): ReLU() + ) + (conv2): Conv3d(128, 128, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) + (block2): ResBlock( + (conv1): Conv3d(128, 128, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (shortcut): Sequential() + (conv2): Conv3d(128, 128, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) ) - (conv2): Conv3d(128, 128, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (bn1): BatchNorm3d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm3d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) ) - (block2): ResBlock( - (conv1): Conv3d(128, 128, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (shortcut): Sequential() - (conv2): Conv3d(128, 128, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (bn1): BatchNorm3d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm3d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) + (1): DownBlock( + (block1): ResBlock( + (conv1): Conv3d(128, 256, kernel_size=(3, 3, 3), stride=(2, 2, 2), padding=(1, 1, 1)) + (shortcut): Sequential( + (0): Conv3d(128, 256, kernel_size=(1, 1, 1), stride=(2, 2, 2)) + (1): ReLU() + ) + (conv2): Conv3d(256, 256, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) + (block2): ResBlock( + (conv1): Conv3d(256, 256, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (shortcut): Sequential() + (conv2): Conv3d(256, 256, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) + ) + (2): DownBlock( + (block1): ResBlock( + (conv1): Conv3d(256, 512, kernel_size=(3, 3, 3), stride=(2, 2, 2), padding=(1, 1, 1)) + (shortcut): Sequential( + (0): Conv3d(256, 512, kernel_size=(1, 1, 1), stride=(2, 2, 2)) + (1): ReLU() + ) + (conv2): Conv3d(512, 512, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) + (block2): ResBlock( + (conv1): Conv3d(512, 512, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (shortcut): Sequential() + (conv2): Conv3d(512, 512, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) + ) + (3): DownBlock( + (block1): ResBlock( + (conv1): Conv3d(512, 1024, kernel_size=(3, 3, 3), stride=(2, 2, 2), padding=(1, 1, 1)) + (shortcut): Sequential( + (0): Conv3d(512, 1024, kernel_size=(1, 1, 1), stride=(2, 2, 2)) + (1): ReLU() + ) + (conv2): Conv3d(1024, 1024, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) + (block2): ResBlock( + (conv1): Conv3d(1024, 1024, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (shortcut): Sequential() + (conv2): Conv3d(1024, 1024, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (bn1): ReLU() + (bn2): ReLU() + (relu): ReLU(inplace=True) + ) ) ) - (layer2): DownBlock( + ) + (upblock_layers): ModuleList( + (0): UpBlock( + (upsample): ConvTranspose3d(1024, 512, kernel_size=(2, 2, 2), stride=(2, 2, 2)) (block1): ResBlock( - (conv1): Conv3d(128, 256, kernel_size=(3, 3, 3), stride=(2, 2, 2), padding=(1, 1, 1)) - (shortcut): Sequential( - (0): Conv3d(128, 256, kernel_size=(1, 1, 1), stride=(2, 2, 2)) - (1): BatchNorm3d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - ) - (conv2): Conv3d(256, 256, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (bn1): BatchNorm3d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm3d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (conv1): Conv3d(512, 512, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (shortcut): Sequential() + (conv2): Conv3d(512, 512, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (bn1): ReLU() + (bn2): ReLU() (relu): ReLU(inplace=True) ) - (block2): ResBlock( + ) + (1): UpBlock( + (upsample): ConvTranspose3d(512, 256, kernel_size=(2, 2, 2), stride=(2, 2, 2)) + (block1): ResBlock( (conv1): Conv3d(256, 256, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) (shortcut): Sequential() (conv2): Conv3d(256, 256, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (bn1): BatchNorm3d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm3d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (bn1): ReLU() + (bn2): ReLU() (relu): ReLU(inplace=True) ) ) - (layer3): DownBlock( + (2): UpBlock( + (upsample): ConvTranspose3d(256, 128, kernel_size=(2, 2, 2), stride=(2, 2, 2)) (block1): ResBlock( - (conv1): Conv3d(256, 512, kernel_size=(3, 3, 3), stride=(2, 2, 2), padding=(1, 1, 1)) - (shortcut): Sequential( - (0): Conv3d(256, 512, kernel_size=(1, 1, 1), stride=(2, 2, 2)) - (1): BatchNorm3d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - ) - (conv2): Conv3d(512, 512, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (bn1): BatchNorm3d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm3d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) - ) - (block2): ResBlock( - (conv1): Conv3d(512, 512, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (conv1): Conv3d(128, 128, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) (shortcut): Sequential() - (conv2): Conv3d(512, 512, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (bn1): BatchNorm3d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm3d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (conv2): Conv3d(128, 128, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (bn1): ReLU() + (bn2): ReLU() (relu): ReLU(inplace=True) ) ) - (layer4): DownBlock( + (3): UpBlock( + (upsample): ConvTranspose3d(128, 64, kernel_size=(2, 2, 2), stride=(2, 2, 2)) (block1): ResBlock( - (conv1): Conv3d(512, 1024, kernel_size=(3, 3, 3), stride=(2, 2, 2), padding=(1, 1, 1)) - (shortcut): Sequential( - (0): Conv3d(512, 1024, kernel_size=(1, 1, 1), stride=(2, 2, 2)) - (1): BatchNorm3d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - ) - (conv2): Conv3d(1024, 1024, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (bn1): BatchNorm3d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm3d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) - ) - (block2): ResBlock( - (conv1): Conv3d(1024, 1024, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (conv1): Conv3d(64, 64, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) (shortcut): Sequential() - (conv2): Conv3d(1024, 1024, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (bn1): BatchNorm3d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm3d(1024, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) + (conv2): Conv3d(64, 64, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) + (bn1): ReLU() + (bn2): ReLU() (relu): ReLU(inplace=True) ) ) ) - (up_block4): UpBlock( - (upsample): ConvTranspose3d(1024, 512, kernel_size=(2, 2, 2), stride=(2, 2, 2)) - (block1): ResBlock( - (conv1): Conv3d(512, 512, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (shortcut): Sequential() - (conv2): Conv3d(512, 512, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (bn1): BatchNorm3d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm3d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) - ) - ) - (up_block3): UpBlock( - (upsample): ConvTranspose3d(512, 256, kernel_size=(2, 2, 2), stride=(2, 2, 2)) - (block1): ResBlock( - (conv1): Conv3d(256, 256, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (shortcut): Sequential() - (conv2): Conv3d(256, 256, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (bn1): BatchNorm3d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm3d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) - ) - ) - (up_block2): UpBlock( - (upsample): ConvTranspose3d(256, 128, kernel_size=(2, 2, 2), stride=(2, 2, 2)) - (block1): ResBlock( - (conv1): Conv3d(128, 128, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (shortcut): Sequential() - (conv2): Conv3d(128, 128, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (bn1): BatchNorm3d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm3d(128, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) - ) - ) - (up_block1): UpBlock( - (upsample): ConvTranspose3d(128, 64, kernel_size=(2, 2, 2), stride=(2, 2, 2)) - (block1): ResBlock( - (conv1): Conv3d(64, 64, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (shortcut): Sequential() - (conv2): Conv3d(64, 64, kernel_size=(3, 3, 3), stride=(1, 1, 1), padding=(1, 1, 1)) - (bn1): BatchNorm3d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (bn2): BatchNorm3d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True) - (relu): ReLU(inplace=True) - ) - ) (final_upsample): ConvTranspose3d(64, 32, kernel_size=(2, 2, 2), stride=(2, 2, 2)) (final_layer): Conv3d(33, 1, kernel_size=(1, 1, 1), stride=(1, 1, 1)) )