From 9bea453ba607050cb08dfd599c1c7166d70843ee Mon Sep 17 00:00:00 2001
From: Jonathan Daniel <jonathand655@gmail.com>
Date: Sat, 5 Feb 2022 14:11:38 +0200
Subject: [PATCH 1/5] Add `black` to the dev-dependencies

---
 poetry.lock    | 251 +++++++++++++++++++++++++++++++++++++++++--------
 pyproject.toml |   1 +
 2 files changed, 213 insertions(+), 39 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 009f267..8b34aab 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,3 +1,46 @@
+[[package]]
+name = "black"
+version = "22.1.0"
+description = "The uncompromising code formatter."
+category = "dev"
+optional = false
+python-versions = ">=3.6.2"
+
+[package.dependencies]
+click = ">=8.0.0"
+mypy-extensions = ">=0.4.3"
+pathspec = ">=0.9.0"
+platformdirs = ">=2"
+tomli = ">=1.1.0"
+typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\" and implementation_name == \"cpython\""}
+typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
+
+[package.extras]
+colorama = ["colorama (>=0.4.3)"]
+d = ["aiohttp (>=3.7.4)"]
+jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
+uvloop = ["uvloop (>=0.15.2)"]
+
+[[package]]
+name = "click"
+version = "8.0.3"
+description = "Composable command line interface toolkit"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
+
+[[package]]
+name = "colorama"
+version = "0.4.4"
+description = "Cross-platform colored terminal text."
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
 [[package]]
 name = "dicom-numpy"
 version = "0.6.2"
@@ -14,6 +57,23 @@ pydicom = ">=1.0"
 dev = ["check-manifest", "sphinx", "sphinx-autobuild"]
 test = ["coverage", "pytest"]
 
+[[package]]
+name = "importlib-metadata"
+version = "4.10.1"
+description = "Read metadata from Python packages"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
+zipp = ">=0.5"
+
+[package.extras]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+perf = ["ipython"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+
 [[package]]
 name = "itk"
 version = "5.2.1.post1"
@@ -97,6 +157,14 @@ python-versions = "*"
 [package.dependencies]
 itk-filtering = "5.2.1.post1"
 
+[[package]]
+name = "mypy-extensions"
+version = "0.4.3"
+description = "Experimental type system extensions for programs checked with the mypy typechecker."
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "nibabel"
 version = "3.2.1"
@@ -120,14 +188,6 @@ spm = ["scipy"]
 style = ["flake8"]
 test = ["coverage", "pytest (!=5.3.4)", "pytest-cov", "pytest-doctestplus"]
 
-[[package]]
-name = "numpy"
-version = "1.21.5"
-description = "NumPy is the fundamental package for array computing with Python."
-category = "main"
-optional = false
-python-versions = ">=3.7,<3.11"
-
 [[package]]
 name = "numpy"
 version = "1.22.2"
@@ -147,6 +207,26 @@ python-versions = ">=3.6"
 [package.dependencies]
 pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
 
+[[package]]
+name = "pathspec"
+version = "0.9.0"
+description = "Utility library for gitignore style pattern matching of file paths."
+category = "dev"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+
+[[package]]
+name = "platformdirs"
+version = "2.4.1"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"]
+test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
+
 [[package]]
 name = "pydicom"
 version = "2.2.2"
@@ -166,16 +246,89 @@ python-versions = ">=3.6"
 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
 
+[[package]]
+name = "tomli"
+version = "2.0.0"
+description = "A lil' TOML parser"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
+name = "typed-ast"
+version = "1.5.2"
+description = "a fork of Python 2 and 3 ast modules with type comment support"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "typing-extensions"
+version = "4.0.1"
+description = "Backported and Experimental Type Hints for Python 3.6+"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "zipp"
+version = "3.7.0"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.7"
-content-hash = "04d8669248a8a91019814131796762dfd40a60badc905e11cd37b9709d10fef0"
+content-hash = "b3ce8b4e1f1d1c11e62f2469305f7630bba53b5872c010b65026e001c69d3eca"
 
 [metadata.files]
+black = [
+    {file = "black-22.1.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:1297c63b9e1b96a3d0da2d85d11cd9bf8664251fd69ddac068b98dc4f34f73b6"},
+    {file = "black-22.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:2ff96450d3ad9ea499fc4c60e425a1439c2120cbbc1ab959ff20f7c76ec7e866"},
+    {file = "black-22.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0e21e1f1efa65a50e3960edd068b6ae6d64ad6235bd8bfea116a03b21836af71"},
+    {file = "black-22.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e2f69158a7d120fd641d1fa9a921d898e20d52e44a74a6fbbcc570a62a6bc8ab"},
+    {file = "black-22.1.0-cp310-cp310-win_amd64.whl", hash = "sha256:228b5ae2c8e3d6227e4bde5920d2fc66cc3400fde7bcc74f480cb07ef0b570d5"},
+    {file = "black-22.1.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:b1a5ed73ab4c482208d20434f700d514f66ffe2840f63a6252ecc43a9bc77e8a"},
+    {file = "black-22.1.0-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:35944b7100af4a985abfcaa860b06af15590deb1f392f06c8683b4381e8eeaf0"},
+    {file = "black-22.1.0-cp36-cp36m-win_amd64.whl", hash = "sha256:7835fee5238fc0a0baf6c9268fb816b5f5cd9b8793423a75e8cd663c48d073ba"},
+    {file = "black-22.1.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:dae63f2dbf82882fa3b2a3c49c32bffe144970a573cd68d247af6560fc493ae1"},
+    {file = "black-22.1.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5fa1db02410b1924b6749c245ab38d30621564e658297484952f3d8a39fce7e8"},
+    {file = "black-22.1.0-cp37-cp37m-win_amd64.whl", hash = "sha256:c8226f50b8c34a14608b848dc23a46e5d08397d009446353dad45e04af0c8e28"},
+    {file = "black-22.1.0-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:2d6f331c02f0f40aa51a22e479c8209d37fcd520c77721c034517d44eecf5912"},
+    {file = "black-22.1.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:742ce9af3086e5bd07e58c8feb09dbb2b047b7f566eb5f5bc63fd455814979f3"},
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+    {file = "black-22.1.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f5660feab44c2e3cb24b2419b998846cbb01c23c7fe645fee45087efa3da2d61"},
+    {file = "black-22.1.0-cp38-cp38-win_amd64.whl", hash = "sha256:6f2f01381f91c1efb1451998bd65a129b3ed6f64f79663a55fe0e9b74a5f81fd"},
+    {file = "black-22.1.0-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:efbadd9b52c060a8fc3b9658744091cb33c31f830b3f074422ed27bad2b18e8f"},
+    {file = "black-22.1.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:8871fcb4b447206904932b54b567923e5be802b9b19b744fdff092bd2f3118d0"},
+    {file = "black-22.1.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:ccad888050f5393f0d6029deea2a33e5ae371fd182a697313bdbd835d3edaf9c"},
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+    {file = "black-22.1.0-py3-none-any.whl", hash = "sha256:3524739d76b6b3ed1132422bf9d82123cd1705086723bc3e235ca39fd21c667d"},
+    {file = "black-22.1.0.tar.gz", hash = "sha256:a7c0192d35635f6fc1174be575cb7915e92e5dd629ee79fdaf0dcfa41a80afb5"},
+]
+click = [
+    {file = "click-8.0.3-py3-none-any.whl", hash = "sha256:353f466495adaeb40b6b5f592f9f91cb22372351c84caeb068132442a4518ef3"},
+    {file = "click-8.0.3.tar.gz", hash = "sha256:410e932b050f5eed773c4cda94de75971c89cdb3155a72a0831139a79e5ecb5b"},
+]
+colorama = [
+    {file = "colorama-0.4.4-py2.py3-none-any.whl", hash = "sha256:9f47eda37229f68eee03b24b9748937c7dc3868f906e8ba69fbcbdd3bc5dc3e2"},
+    {file = "colorama-0.4.4.tar.gz", hash = "sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b"},
+]
 dicom-numpy = [
     {file = "dicom_numpy-0.6.2-py2.py3-none-any.whl", hash = "sha256:361c8dfc52d625bf3344e5c2745e9c928d263999a4c094fe285d9fe461895ea9"},
     {file = "dicom_numpy-0.6.2.tar.gz", hash = "sha256:24b993083368efb868ffe5edcab054db5c11f0587a218a6b6492fde14a87acd9"},
 ]
+importlib-metadata = [
+    {file = "importlib_metadata-4.10.1-py3-none-any.whl", hash = "sha256:899e2a40a8c4a1aec681feef45733de8a6c58f3f6a0dbed2eb6574b4387a77b6"},
+    {file = "importlib_metadata-4.10.1.tar.gz", hash = "sha256:951f0d8a5b7260e9db5e41d429285b5f451e928479f19d80818878527d36e95e"},
+]
 itk = [
     {file = "itk-5.2.1.post1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:d18723ca6791fc5d9c7498e03d73929df56acffd9290ed8f61a24f25a138951e"},
     {file = "itk-5.2.1.post1-cp36-cp36m-manylinux2014_aarch64.whl", hash = "sha256:fddd62554da37254eb8de4cd2660a8d9e601af88df50e7017202ed269c20a584"},
@@ -309,41 +462,15 @@ itk-segmentation = [
     {file = "itk_segmentation-5.2.1.post1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a2e7d4953bd4e2b2d36539944c8bef33e50266398249e8af3c4a5b31a291f72b"},
     {file = "itk_segmentation-5.2.1.post1-cp39-cp39-win_amd64.whl", hash = "sha256:136b995ee4f65096792c8be41c696d1dd384364f89cc84a0d8fb003f12ab6b9e"},
 ]
+mypy-extensions = [
+    {file = "mypy_extensions-0.4.3-py2.py3-none-any.whl", hash = "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d"},
+    {file = "mypy_extensions-0.4.3.tar.gz", hash = "sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8"},
+]
 nibabel = [
     {file = "nibabel-3.2.1-py3-none-any.whl", hash = "sha256:7e26cbf60eae8668785fa970294f05f767cefc5538b9e22aa388a07f62c54ebc"},
     {file = "nibabel-3.2.1.tar.gz", hash = "sha256:4d2ff9426b740011a1c916b54fc25da9348282e727eaa2ea163f42e00f1fc29e"},
 ]
 numpy = [
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-    {file = "numpy-1.21.5-cp39-cp39-win_amd64.whl", hash = "sha256:1964db2d4a00348b7a60ee9d013c8cb0c566644a589eaa80995126eac3b99ced"},
-    {file = "numpy-1.21.5-pp37-pypy37_pp73-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:a7c4b701ca418cd39e28ec3b496e6388fe06de83f5f0cb74794fa31cfa384c02"},
-    {file = "numpy-1.21.5.zip", hash = "sha256:6a5928bc6241264dce5ed509e66f33676fc97f464e7a919edc672fb5532221ee"},
     {file = "numpy-1.22.2-cp310-cp310-macosx_10_14_x86_64.whl", hash = "sha256:515a8b6edbb904594685da6e176ac9fbea8f73a5ebae947281de6613e27f1956"},
     {file = "numpy-1.22.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:76a4f9bce0278becc2da7da3b8ef854bed41a991f4226911a24a9711baad672c"},
     {file = "numpy-1.22.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:168259b1b184aa83a514f307352c25c56af111c269ffc109d9704e81f72e764b"},
@@ -368,6 +495,14 @@ packaging = [
     {file = "packaging-21.3-py3-none-any.whl", hash = "sha256:ef103e05f519cdc783ae24ea4e2e0f508a9c99b2d4969652eed6a2e1ea5bd522"},
     {file = "packaging-21.3.tar.gz", hash = "sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb"},
 ]
+pathspec = [
+    {file = "pathspec-0.9.0-py2.py3-none-any.whl", hash = "sha256:7d15c4ddb0b5c802d161efc417ec1a2558ea2653c2e8ad9c19098201dc1c993a"},
+    {file = "pathspec-0.9.0.tar.gz", hash = "sha256:e564499435a2673d586f6b2130bb5b95f04a3ba06f81b8f895b651a3c76aabb1"},
+]
+platformdirs = [
+    {file = "platformdirs-2.4.1-py3-none-any.whl", hash = "sha256:1d7385c7db91728b83efd0ca99a5afb296cab9d0ed8313a45ed8ba17967ecfca"},
+    {file = "platformdirs-2.4.1.tar.gz", hash = "sha256:440633ddfebcc36264232365d7840a970e75e1018d15b4327d11f91909045fda"},
+]
 pydicom = [
     {file = "pydicom-2.2.2-py3-none-any.whl", hash = "sha256:6ecb9c6d56a20b2104099b8ef8fe0f3664d797b08a0e0548fe0311b515b32308"},
     {file = "pydicom-2.2.2.tar.gz", hash = "sha256:f51078da1fe1285431a6f14a5ca0273520391ef28a68b32b9de73cc7f93f38be"},
@@ -376,3 +511,41 @@ pyparsing = [
     {file = "pyparsing-3.0.7-py3-none-any.whl", hash = "sha256:a6c06a88f252e6c322f65faf8f418b16213b51bdfaece0524c1c1bc30c63c484"},
     {file = "pyparsing-3.0.7.tar.gz", hash = "sha256:18ee9022775d270c55187733956460083db60b37d0d0fb357445f3094eed3eea"},
 ]
+tomli = [
+    {file = "tomli-2.0.0-py3-none-any.whl", hash = "sha256:b5bde28da1fed24b9bd1d4d2b8cba62300bfb4ec9a6187a957e8ddb9434c5224"},
+    {file = "tomli-2.0.0.tar.gz", hash = "sha256:c292c34f58502a1eb2bbb9f5bbc9a5ebc37bee10ffb8c2d6bbdfa8eb13cc14e1"},
+]
+typed-ast = [
+    {file = "typed_ast-1.5.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:183b183b7771a508395d2cbffd6db67d6ad52958a5fdc99f450d954003900266"},
+    {file = "typed_ast-1.5.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:676d051b1da67a852c0447621fdd11c4e104827417bf216092ec3e286f7da596"},
+    {file = "typed_ast-1.5.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:bc2542e83ac8399752bc16e0b35e038bdb659ba237f4222616b4e83fb9654985"},
+    {file = "typed_ast-1.5.2-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:74cac86cc586db8dfda0ce65d8bcd2bf17b58668dfcc3652762f3ef0e6677e76"},
+    {file = "typed_ast-1.5.2-cp310-cp310-win_amd64.whl", hash = "sha256:18fe320f354d6f9ad3147859b6e16649a0781425268c4dde596093177660e71a"},
+    {file = "typed_ast-1.5.2-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:31d8c6b2df19a777bc8826770b872a45a1f30cfefcfd729491baa5237faae837"},
+    {file = "typed_ast-1.5.2-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:963a0ccc9a4188524e6e6d39b12c9ca24cc2d45a71cfdd04a26d883c922b4b78"},
+    {file = "typed_ast-1.5.2-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:0eb77764ea470f14fcbb89d51bc6bbf5e7623446ac4ed06cbd9ca9495b62e36e"},
+    {file = "typed_ast-1.5.2-cp36-cp36m-win_amd64.whl", hash = "sha256:294a6903a4d087db805a7656989f613371915fc45c8cc0ddc5c5a0a8ad9bea4d"},
+    {file = "typed_ast-1.5.2-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:26a432dc219c6b6f38be20a958cbe1abffcc5492821d7e27f08606ef99e0dffd"},
+    {file = "typed_ast-1.5.2-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c7407cfcad702f0b6c0e0f3e7ab876cd1d2c13b14ce770e412c0c4b9728a0f88"},
+    {file = "typed_ast-1.5.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:f30ddd110634c2d7534b2d4e0e22967e88366b0d356b24de87419cc4410c41b7"},
+    {file = "typed_ast-1.5.2-cp37-cp37m-win_amd64.whl", hash = "sha256:8c08d6625bb258179b6e512f55ad20f9dfef019bbfbe3095247401e053a3ea30"},
+    {file = "typed_ast-1.5.2-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:90904d889ab8e81a956f2c0935a523cc4e077c7847a836abee832f868d5c26a4"},
+    {file = "typed_ast-1.5.2-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:bbebc31bf11762b63bf61aaae232becb41c5bf6b3461b80a4df7e791fabb3aca"},
+    {file = "typed_ast-1.5.2-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c29dd9a3a9d259c9fa19d19738d021632d673f6ed9b35a739f48e5f807f264fb"},
+    {file = "typed_ast-1.5.2-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:58ae097a325e9bb7a684572d20eb3e1809802c5c9ec7108e85da1eb6c1a3331b"},
+    {file = "typed_ast-1.5.2-cp38-cp38-win_amd64.whl", hash = "sha256:da0a98d458010bf4fe535f2d1e367a2e2060e105978873c04c04212fb20543f7"},
+    {file = "typed_ast-1.5.2-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:33b4a19ddc9fc551ebabca9765d54d04600c4a50eda13893dadf67ed81d9a098"},
+    {file = "typed_ast-1.5.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:1098df9a0592dd4c8c0ccfc2e98931278a6c6c53cb3a3e2cf7e9ee3b06153344"},
+    {file = "typed_ast-1.5.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:42c47c3b43fe3a39ddf8de1d40dbbfca60ac8530a36c9b198ea5b9efac75c09e"},
+    {file = "typed_ast-1.5.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:f290617f74a610849bd8f5514e34ae3d09eafd521dceaa6cf68b3f4414266d4e"},
+    {file = "typed_ast-1.5.2-cp39-cp39-win_amd64.whl", hash = "sha256:df05aa5b241e2e8045f5f4367a9f6187b09c4cdf8578bb219861c4e27c443db5"},
+    {file = "typed_ast-1.5.2.tar.gz", hash = "sha256:525a2d4088e70a9f75b08b3f87a51acc9cde640e19cc523c7e41aa355564ae27"},
+]
+typing-extensions = [
+    {file = "typing_extensions-4.0.1-py3-none-any.whl", hash = "sha256:7f001e5ac290a0c0401508864c7ec868be4e701886d5b573a9528ed3973d9d3b"},
+    {file = "typing_extensions-4.0.1.tar.gz", hash = "sha256:4ca091dea149f945ec56afb48dae714f21e8692ef22a395223bcd328961b6a0e"},
+]
+zipp = [
+    {file = "zipp-3.7.0-py3-none-any.whl", hash = "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375"},
+    {file = "zipp-3.7.0.tar.gz", hash = "sha256:9f50f446828eb9d45b267433fd3e9da8d801f614129124863f9c51ebceafb87d"},
+]
diff --git a/pyproject.toml b/pyproject.toml
index 1b6c2e5..84a758c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,6 +42,7 @@ numpy = [
 ]
 
 [tool.poetry.dev-dependencies]
+black = "^22.1.0"
 
 [tool.poetry.urls]
 "Bug Tracker" = "https://github.com/RSIP-Vision/medio/issues"

From f5925c6f1cb619b3789b039670357b2dd2ca404e Mon Sep 17 00:00:00 2001
From: Jonathan Daniel <jonathand655@gmail.com>
Date: Sat, 5 Feb 2022 14:25:44 +0200
Subject: [PATCH 2/5] Format the codebase with `black`

---
 medio/__init__.py                             |   4 +-
 medio/backends/itk_io.py                      | 194 ++++++++++++------
 medio/backends/nib_io.py                      |  47 +++--
 medio/backends/pdcm_io.py                     |  95 ++++++---
 medio/backends/pdcm_unpack_ds.py              |  19 +-
 medio/metadata/affine.py                      |  12 +-
 medio/metadata/convert_nib_itk.py             |   8 +-
 medio/metadata/dcm_uid.py                     |   2 +-
 medio/metadata/itk_orientation.py             |  13 +-
 medio/metadata/metadata.py                    |  69 ++++---
 medio/metadata/pdcm_ds.py                     |  54 ++++-
 medio/read_save.py                            |  71 +++++--
 medio/utils/files.py                          |  42 ++--
 medio/utils/two_way_dict.py                   |   1 +
 .../itk_dcm_orientations.py                   |  65 +++---
 tests/itk_dcm_orientations/itk_utils.py       |   4 +-
 .../orientations_utils.py                     |  24 +--
 17 files changed, 491 insertions(+), 233 deletions(-)

diff --git a/medio/__init__.py b/medio/__init__.py
index 3325fa9..a647ccd 100644
--- a/medio/__init__.py
+++ b/medio/__init__.py
@@ -3,6 +3,6 @@
 from medio.read_save import read_img, save_img, save_dir
 from medio import backends, metadata, medimg, utils
 
-__version__ = '0.4.1'
+__version__ = "0.4.1"
 
-__all__ = ['read_img', 'save_img', 'save_dir', 'MetaData', 'Affine', '__version__']
+__all__ = ["read_img", "save_img", "save_dir", "MetaData", "Affine", "__version__"]
diff --git a/medio/backends/itk_io.py b/medio/backends/itk_io.py
index 00eaf97..989e39c 100644
--- a/medio/backends/itk_io.py
+++ b/medio/backends/itk_io.py
@@ -14,16 +14,23 @@
 
 
 class ItkIO:
-    coord_sys = 'itk'
+    coord_sys = "itk"
     DEFAULT_COMPONENTS_AXIS = 0  # in the transposed image
     # default image type:
     dimension = 3
-    pixel_type = itk.ctype('short')  # signed short - int16
+    pixel_type = itk.ctype("short")  # signed short - int16
     image_type = itk.Image[pixel_type, dimension]
 
     @staticmethod
-    def read_img(input_path, desired_axcodes=None, header=False, components_axis=None, pixel_type=pixel_type,
-                 fallback_only=True, series=None):
+    def read_img(
+        input_path,
+        desired_axcodes=None,
+        header=False,
+        components_axis=None,
+        pixel_type=pixel_type,
+        fallback_only=True,
+        series=None,
+    ):
         """
         The main reader function, reads images and performs reorientation and unpacking
         :param input_path: path of image file or directory containing dicom series
@@ -38,7 +45,9 @@ def read_img(input_path, desired_axcodes=None, header=False, components_axis=Non
         """
         input_path = Path(input_path)
         if input_path.is_dir():
-            img = ItkIO.read_dir(str(input_path), pixel_type, fallback_only, series=series, header=header)
+            img = ItkIO.read_dir(
+                str(input_path), pixel_type, fallback_only, series=series, header=header
+            )
         elif input_path.is_file():
             img = ItkIO.read_img_file(str(input_path), pixel_type, fallback_only)
         else:
@@ -49,26 +58,43 @@ def read_img(input_path, desired_axcodes=None, header=False, components_axis=Non
         if (desired_axcodes is None) or (desired_axcodes == metadata.ornt):
             image_np = ItkIO.itk_img_to_array(img)
         else:
-            orig_ornt = metadata.ornt  # store the original orientation before the reorientation
+            orig_ornt = (
+                metadata.ornt
+            )  # store the original orientation before the reorientation
             img, _ = ItkIO.reorient(img, desired_axcodes)
             image_np, affine = ItkIO.unpack_img(img)
-            metadata = MetaData(affine=affine, orig_ornt=orig_ornt, coord_sys=ItkIO.coord_sys)
+            metadata = MetaData(
+                affine=affine, orig_ornt=orig_ornt, coord_sys=ItkIO.coord_sys
+            )
         if header:
             # TODO: not implemented for a series (returns an empty dictionary), see ItkIO.read_dir
             metadict = img.GetMetaDataDictionary()
-            metadata.header = {key: metadict[key] for key in metadict.GetKeys() if not key.startswith('ITK_')}
+            metadata.header = {
+                key: metadict[key]
+                for key in metadict.GetKeys()
+                if not key.startswith("ITK_")
+            }
 
         # TODO: consider unifying with PdcmIO.move_channels_axis
         n_components = img.GetNumberOfComponentsPerPixel()
         if (n_components > 1) and (components_axis is not None):
             # assert image_np.shape[ItkIO.DEFAULT_COMPONENTS_AXIS] == n_components
-            image_np = np.moveaxis(image_np, ItkIO.DEFAULT_COMPONENTS_AXIS, components_axis)
+            image_np = np.moveaxis(
+                image_np, ItkIO.DEFAULT_COMPONENTS_AXIS, components_axis
+            )
 
         return image_np, metadata
 
     @staticmethod
-    def save_img(filename, image_np, metadata, use_original_ornt=True, components_axis=None,
-                 allow_dcm_reorient=False, compression=False):
+    def save_img(
+        filename,
+        image_np,
+        metadata,
+        use_original_ornt=True,
+        components_axis=None,
+        allow_dcm_reorient=False,
+        compression=False,
+    ):
         """
         Save an image file with itk
         :param filename: the filename to save, str or os.PathLike
@@ -82,22 +108,40 @@ def save_img(filename, image_np, metadata, use_original_ornt=True, components_ax
         """
         is_dcm = is_dicom(filename, check_exist=False)
         if is_dcm:
-            image_np = ItkIO.prepare_dcm_array(image_np, is_vector=components_axis is not None)
-        image = ItkIO.prepare_image(image_np, metadata, use_original_ornt, components_axis=components_axis,
-                                    is_dcm=is_dcm, allow_dcm_reorient=allow_dcm_reorient)
+            image_np = ItkIO.prepare_dcm_array(
+                image_np, is_vector=components_axis is not None
+            )
+        image = ItkIO.prepare_image(
+            image_np,
+            metadata,
+            use_original_ornt,
+            components_axis=components_axis,
+            is_dcm=is_dcm,
+            allow_dcm_reorient=allow_dcm_reorient,
+        )
         ItkIO.save_img_file(image, str(filename), compression=compression)
 
     @staticmethod
-    def prepare_image(image_np, metadata, use_original_ornt, components_axis=None, is_dcm=False,
-                      allow_dcm_reorient=False):
+    def prepare_image(
+        image_np,
+        metadata,
+        use_original_ornt,
+        components_axis=None,
+        is_dcm=False,
+        allow_dcm_reorient=False,
+    ):
         """Prepare image for saving"""
         orig_coord_sys = metadata.coord_sys
         metadata.convert(ItkIO.coord_sys)
         desired_ornt = metadata.orig_ornt if use_original_ornt else None
         if is_dcm:
             # checking right-handed orientation before saving a dicom file/series
-            desired_ornt = check_dcm_ornt(desired_ornt, metadata, allow_dcm_reorient=allow_dcm_reorient)
-        image = ItkIO.pack2img(image_np, metadata.affine, components_axis=components_axis)
+            desired_ornt = check_dcm_ornt(
+                desired_ornt, metadata, allow_dcm_reorient=allow_dcm_reorient
+            )
+        image = ItkIO.pack2img(
+            image_np, metadata.affine, components_axis=components_axis
+        )
         if (desired_ornt is not None) and (desired_ornt != metadata.ornt):
             image, _ = ItkIO.reorient(image, desired_ornt)
         metadata.convert(orig_coord_sys)
@@ -123,11 +167,13 @@ def prepare_dcm_array(image_np, is_vector=False):
             if np.array_equal(arr, image_np):
                 return arr
 
-        raise NotImplementedError('Saving a single dicom file with ItkIO is currently supported only for \n'
-                                  '1. 2d images - int16, uint16, uint8\n'
-                                  '2. 3d images with integer nonnegative values - uint8, uint16\n'
-                                  '3. 2d/3d RGB[A] images - uint8 (with channels_axis)\n'
-                                  'For negative values, try to save a dicom directory or use PdcmIO.save_arr2dcm_file')
+        raise NotImplementedError(
+            "Saving a single dicom file with ItkIO is currently supported only for \n"
+            "1. 2d images - int16, uint16, uint8\n"
+            "2. 3d images with integer nonnegative values - uint8, uint16\n"
+            "3. 2d/3d RGB[A] images - uint8 (with channels_axis)\n"
+            "For negative values, try to save a dicom directory or use PdcmIO.save_arr2dcm_file"
+        )
 
     @staticmethod
     def read_img_file(filename, pixel_type=None, fallback_only=False):
@@ -140,7 +186,7 @@ def read_img_file_long(filename, image_type=image_type):
         reader = itk.ImageFileReader[image_type].New()
         reader.SetFileName(filename)
         reader.Update()
-        image_io = str(reader.GetImageIO()).split(' ')[0]
+        image_io = str(reader.GetImageIO()).split(" ")[0]
         image = reader.GetOutput()
         return image, image_io
 
@@ -162,7 +208,9 @@ def save_img_file_long(image, filename, compression=False):
     @staticmethod
     def itk_img_to_array(img_itk):
         """Swap the axes to the usual x, y, z convention in RAI orientation (originally z, y, x)"""
-        img_array = itk.array_from_image(img_itk).T  # the transpose here is equivalent to keep_axes=True
+        img_array = itk.array_from_image(
+            img_itk
+        ).T  # the transpose here is equivalent to keep_axes=True
         return img_array
 
     @staticmethod
@@ -170,9 +218,13 @@ def array_to_itk_img(img_array, components_axis=None):
         """Set components_axis to not None for vector images, e.g. RGB"""
         is_vector = False
         if components_axis is not None:
-            img_array = np.moveaxis(img_array, components_axis, ItkIO.DEFAULT_COMPONENTS_AXIS)
+            img_array = np.moveaxis(
+                img_array, components_axis, ItkIO.DEFAULT_COMPONENTS_AXIS
+            )
             is_vector = True
-        img_itk = itk.image_from_array(img_array.T.copy(), is_vector=is_vector)  # copy is crucial for the ordering
+        img_itk = itk.image_from_array(
+            img_array.T.copy(), is_vector=is_vector
+        )  # copy is crucial for the ordering
         return img_itk
 
     @staticmethod
@@ -183,7 +235,9 @@ def unpack_img(img):
 
     @staticmethod
     def get_img_aff(img):
-        direction = itk.array_from_vnl_matrix(img.GetDirection().GetVnlMatrix().as_matrix())
+        direction = itk.array_from_vnl_matrix(
+            img.GetDirection().GetVnlMatrix().as_matrix()
+        )
         spacing = itk.array_from_vnl_vector(img.GetSpacing().GetVnlVector())
         origin = itk.array_from_vnl_vector(img.GetOrigin().GetVnlVector())
         return Affine(direction=direction, spacing=spacing, origin=origin)
@@ -204,12 +258,12 @@ def set_img_aff(image, affine):
 
         # setting metadata
         spacing_vec = itk.Vector[itk.D, dimension]()
-        spacing_vec.SetVnlVector(itk.vnl_vector_from_array(spacing.astype('float')))
+        spacing_vec.SetVnlVector(itk.vnl_vector_from_array(spacing.astype("float")))
         image.SetSpacing(spacing_vec)
 
-        image.SetOrigin(origin.astype('float'))
+        image.SetOrigin(origin.astype("float"))
 
-        direction_mat = itk.vnl_matrix_from_array(direction_arr.astype('float'))
+        direction_mat = itk.vnl_matrix_from_array(direction_arr.astype("float"))
         direction = itk.Matrix[itk.D, dimension, dimension](direction_mat)
         image.SetDirection(direction)
 
@@ -231,7 +285,9 @@ def reorient(img, desired_orientation: Union[int, tuple, str, None]):
         return reoriented_itk_img, original_orientation_code
 
     @staticmethod
-    def read_dir(dirname, pixel_type=None, fallback_only=False, series=None, header=False):
+    def read_dir(
+        dirname, pixel_type=None, fallback_only=False, series=None, header=False
+    ):
         """
         Read a dicom directory. If there is more than one series in the directory an error is raised
         (unless the series argument is used properly).
@@ -245,7 +301,9 @@ def read_dir(dirname, pixel_type=None, fallback_only=False, series=None, header=
             #  reader.Update()
             #  metadict_arr = reader.GetMetaDataDictionaryArray()
             #  (See also itk.imread source code)
-            raise NotImplementedError("header=True is currently not supported for a series")
+            raise NotImplementedError(
+                "header=True is currently not supported for a series"
+            )
         return itk.imread(filenames, pixel_type, fallback_only)
 
     @staticmethod
@@ -264,8 +322,17 @@ def extract_series(dirname, series=None):
         return filenames
 
     @staticmethod
-    def save_dcm_dir(dirname, image_np, metadata, use_original_ornt=True, components_axis=None, parents=False,
-                     exist_ok=False, allow_dcm_reorient=False, **kwargs):
+    def save_dcm_dir(
+        dirname,
+        image_np,
+        metadata,
+        use_original_ornt=True,
+        components_axis=None,
+        parents=False,
+        exist_ok=False,
+        allow_dcm_reorient=False,
+        **kwargs,
+    ):
         """
         Save a 3d numpy array image_np as a dicom series of 2d dicom slices in the directory dirname
         :param dirname: the directory to save in the files, str or pathlib.Path. If it exists - must be empty
@@ -279,8 +346,14 @@ def save_dcm_dir(dirname, image_np, metadata, use_original_ornt=True, components
         :param allow_dcm_reorient: whether to allow automatic reorientation to a right-handed orientation or not
         :param kwargs: optional kwargs passed to ItkIO.dcm_metadata: pattern, metadata_dict
         """
-        image = ItkIO.prepare_image(image_np, metadata, use_original_ornt, components_axis=components_axis,
-                                    is_dcm=True, allow_dcm_reorient=allow_dcm_reorient)
+        image = ItkIO.prepare_image(
+            image_np,
+            metadata,
+            use_original_ornt,
+            components_axis=components_axis,
+            is_dcm=True,
+            allow_dcm_reorient=allow_dcm_reorient,
+        )
         image_type = type(image)
         _, (pixel_type, _) = itk.template(image)
         image2d_type = itk.Image[pixel_type, 2]
@@ -298,7 +371,7 @@ def save_dcm_dir(dirname, image_np, metadata, use_original_ornt=True, components
         writer.Update()
 
     @staticmethod
-    def dcm_series_metadata(image, dirname, pattern='IM{}.dcm', metadata_dict=None):
+    def dcm_series_metadata(image, dirname, pattern="IM{}.dcm", metadata_dict=None):
         """
         Return dicom series metadata per slice and filenames
         :param image: the full itk image to be saved as dicom series
@@ -315,40 +388,45 @@ def dcm_series_metadata(image, dirname, pattern='IM{}.dcm', metadata_dict=None):
         mdict = itk.MetaDataDictionary()
 
         # Series Instance UID
-        mdict['0020|000e'] = generate_uid()
+        mdict["0020|000e"] = generate_uid()
         # Study Instance UID
-        mdict['0020|000d'] = generate_uid()
+        mdict["0020|000d"] = generate_uid()
 
-        date, time = datetime.now().strftime('%Y%m%d %H%M%S.%f').split()
+        date, time = datetime.now().strftime("%Y%m%d %H%M%S.%f").split()
         # Study Date
-        mdict['0008|0020'] = date
+        mdict["0008|0020"] = date
         # Series Date
-        mdict['0008|0021'] = date
+        mdict["0008|0021"] = date
         # Content Date
-        mdict['0008|0023'] = date
+        mdict["0008|0023"] = date
         # Study Time
-        mdict['0008|0030'] = time
+        mdict["0008|0030"] = time
         # Series Time
-        mdict['0008|0031'] = time
+        mdict["0008|0031"] = time
 
         # Pixel Spacing (not necessary - automatically saved)
         spacing = image.GetSpacing()
-        mdict['0028|0030'] = f'{spacing[0]}\\{spacing[1]}'
+        mdict["0028|0030"] = f"{spacing[0]}\\{spacing[1]}"
         # Spacing Between Slices
-        mdict['0018|0088'] = str(spacing[2])
+        mdict["0018|0088"] = str(spacing[2])
         # Image Orientation (Patient)
-        orientation_str = '\\'.join([str(image.GetDirection().GetVnlMatrix().get(i, j))
-                                     for j in range(2) for i in range(3)])
-        mdict['0020|0037'] = orientation_str
+        orientation_str = "\\".join(
+            [
+                str(image.GetDirection().GetVnlMatrix().get(i, j))
+                for j in range(2)
+                for i in range(3)
+            ]
+        )
+        mdict["0020|0037"] = orientation_str
         # Patient Position
-        mdict['0018|5100'] = ''
+        mdict["0018|5100"] = ""
 
         # Number of Frames
-        mdict['0028|0008'] = '1'
+        mdict["0028|0008"] = "1"
         # Number of Slices
-        mdict['0054|0081'] = str(n)
+        mdict["0054|0081"] = str(n)
         # Modality
-        mdict['0008|0060'] = 'CT'
+        mdict["0008|0060"] = "CT"
 
         if metadata_dict is not None:
             for key, val in metadata_dict.items():
@@ -362,11 +440,11 @@ def dcm_series_metadata(image, dirname, pattern='IM{}.dcm', metadata_dict=None):
             # copy the shared properties dict:
             mdict_i = itk.MetaDataDictionary(mdict)
             # Instance Number
-            mdict_i['0020|0013'] = str(i + 1)
+            mdict_i["0020|0013"] = str(i + 1)
             # Image Position (Patient)
             position = image.TransformIndexToPhysicalPoint([0, 0, i])
-            position_str = '\\'.join([str(position[i]) for i in range(3)])
-            mdict_i['0020|0032'] = position_str
+            position_str = "\\".join([str(position[i]) for i in range(3)])
+            mdict_i["0020|0032"] = position_str
 
             mdict_list += [mdict_i]
             filenames += [str(Path(dirname) / pattern.format(i + 1))]
diff --git a/medio/backends/nib_io.py b/medio/backends/nib_io.py
index 4bd16e0..bd3c145 100644
--- a/medio/backends/nib_io.py
+++ b/medio/backends/nib_io.py
@@ -8,14 +8,11 @@
 
 
 class NibIO:
-    coord_sys = 'nib'
-    RGB_DTYPE = np.dtype([('R', np.uint8),
-                          ('G', np.uint8),
-                          ('B', np.uint8)])
-    RGBA_DTYPE = np.dtype([('R', np.uint8),
-                           ('G', np.uint8),
-                           ('B', np.uint8),
-                           ('A', np.uint8)])
+    coord_sys = "nib"
+    RGB_DTYPE = np.dtype([("R", np.uint8), ("G", np.uint8), ("B", np.uint8)])
+    RGBA_DTYPE = np.dtype(
+        [("R", np.uint8), ("G", np.uint8), ("B", np.uint8), ("A", np.uint8)]
+    )
 
     @staticmethod
     def read_img(input_path, desired_axcodes=None, header=False, channels_axis=None):
@@ -28,16 +25,20 @@ def read_img(input_path, desired_axcodes=None, header=False, channels_axis=None)
         :return: image array and corresponding metadata
         """
         img_struct = nib.load(input_path)
-        orig_ornt_str = ''.join(nib.aff2axcodes(img_struct.affine))
+        orig_ornt_str = "".join(nib.aff2axcodes(img_struct.affine))
         if desired_axcodes is not None:
             img_struct = NibIO.reorient(img_struct, desired_axcodes)
         img = np.asanyarray(img_struct.dataobj)
         if channels_axis is not None:
             img = NibIO.unravel_array(img, channels_axis)
         affine = Affine(img_struct.affine)
-        metadata = MetaData(affine=affine, orig_ornt=orig_ornt_str, coord_sys=NibIO.coord_sys)
+        metadata = MetaData(
+            affine=affine, orig_ornt=orig_ornt_str, coord_sys=NibIO.coord_sys
+        )
         if header:
-            metadata.header = {key: img_struct.header[key] for key in img_struct.header.keys()}
+            metadata.header = {
+                key: img_struct.header[key] for key in img_struct.header.keys()
+            }
         return img, metadata
 
     @staticmethod
@@ -79,7 +80,7 @@ def unravel_array(array, channels_axis=-1):
         np.dtype([('R', 'uint8'), ('G', 'uint8'), ('B', 'uint8')])
         Convert it into an array with dtype 'uint8' and 3 channels for RGB in an additional last dimension"""
         dtype = array.dtype
-        if not (hasattr(dtype, '__len__') and len(dtype) > 1):
+        if not (hasattr(dtype, "__len__") and len(dtype) > 1):
             return array
         return np.stack([array[field] for field in dtype.fields], axis=channels_axis)
 
@@ -87,22 +88,26 @@ def unravel_array(array, channels_axis=-1):
     def pack_channeled_img(img, channels_axis):
         dtype = img.dtype
         if not np.issubdtype(dtype, np.uint8):
-            raise ValueError(f'RGB or RGBA images must have dtype "np.uint8", got: "{dtype}"')
+            raise ValueError(
+                f'RGB or RGBA images must have dtype "np.uint8", got: "{dtype}"'
+            )
         n_channels = img.shape[channels_axis]
         img = np.moveaxis(img, channels_axis, -1)
         r_channel = img[..., 0]
         if n_channels == 3:
             img_rgb = np.empty_like(r_channel, dtype=NibIO.RGB_DTYPE)
-            img_rgb['R'] = r_channel
-            img_rgb['G'] = img[..., 1]
-            img_rgb['B'] = img[..., 2]
+            img_rgb["R"] = r_channel
+            img_rgb["G"] = img[..., 1]
+            img_rgb["B"] = img[..., 2]
             return img_rgb
         elif n_channels == 4:
             img_rgba = np.empty_like(r_channel, dtype=NibIO.RGBA_DTYPE)
-            img_rgba['R'] = r_channel
-            img_rgba['G'] = img[..., 1]
-            img_rgba['B'] = img[..., 2]
-            img_rgba['A'] = img[..., 3]
+            img_rgba["R"] = r_channel
+            img_rgba["G"] = img[..., 1]
+            img_rgba["B"] = img[..., 2]
+            img_rgba["A"] = img[..., 3]
             return img_rgba
         else:
-            raise ValueError(f'Invalid number of channels: {n_channels}, should be 3 (RGB) or 4 (RGBA)')
+            raise ValueError(
+                f"Invalid number of channels: {n_channels}, should be 3 (RGB) or 4 (RGBA)"
+            )
diff --git a/medio/backends/pdcm_io.py b/medio/backends/pdcm_io.py
index 0a16150..00b204d 100644
--- a/medio/backends/pdcm_io.py
+++ b/medio/backends/pdcm_io.py
@@ -14,15 +14,22 @@
 
 
 class PdcmIO:
-    coord_sys = 'itk'
+    coord_sys = "itk"
     # channels axes in the transposed image for pydicom and dicom-numpy. The actual axis is the first or the second
     # value of the tuple, according to the planar configuration (which is either 0 or 1)
     DEFAULT_CHANNELS_AXES_PYDICOM = (0, -1)
     DEFAULT_CHANNELS_AXES_DICOM_NUMPY = (0, 2)
 
     @staticmethod
-    def read_img(input_path, desired_ornt=None, header=False, channels_axis=None, globber='*',
-                 allow_default_affine=False, series=None):
+    def read_img(
+        input_path,
+        desired_ornt=None,
+        header=False,
+        channels_axis=None,
+        globber="*",
+        allow_default_affine=False,
+        series=None,
+    ):
         """
         Read a dicom file or folder (series) and return the numpy array and the corresponding metadata
         :param input_path: path-like object (str or pathlib.Path) of the file or directory to read
@@ -37,13 +44,24 @@ def read_img(input_path, desired_ornt=None, header=False, channels_axis=None, gl
         :return: numpy array and metadata
         """
         input_path = Path(input_path)
-        temp_channels_axis = -1  # if there are channels, they must be in the last axis for the reorientation
+        temp_channels_axis = (
+            -1
+        )  # if there are channels, they must be in the last axis for the reorientation
         if input_path.is_dir():
-            img, metadata, channeled = PdcmIO.read_dcm_dir(input_path, header, globber,
-                                                           channels_axis=temp_channels_axis, series=series)
+            img, metadata, channeled = PdcmIO.read_dcm_dir(
+                input_path,
+                header,
+                globber,
+                channels_axis=temp_channels_axis,
+                series=series,
+            )
         else:
             img, metadata, channeled = PdcmIO.read_dcm_file(
-                input_path, header, allow_default_affine=allow_default_affine, channels_axis=temp_channels_axis)
+                input_path,
+                header,
+                allow_default_affine=allow_default_affine,
+                channels_axis=temp_channels_axis,
+            )
         img, metadata = PdcmIO.reorient(img, metadata, desired_ornt)
         # move the channels after the reorientation
         if channeled and channels_axis != temp_channels_axis:
@@ -51,7 +69,9 @@ def read_img(input_path, desired_ornt=None, header=False, channels_axis=None, gl
         return img, metadata
 
     @staticmethod
-    def read_dcm_file(filename, header=False, allow_default_affine=False, channels_axis=None):
+    def read_dcm_file(
+        filename, header=False, allow_default_affine=False, channels_axis=None
+    ):
         """
         Read a single dicom file.
         Return the image array, metadata, and whether it has channels
@@ -66,13 +86,19 @@ def read_dcm_file(filename, header=False, allow_default_affine=False, channels_a
         if header:
             metadata.header = {str(key): ds[key] for key in ds.keys()}
         samples_per_pixel = ds.SamplesPerPixel
-        img = PdcmIO.move_channels_axis(img, samples_per_pixel=samples_per_pixel, channels_axis=channels_axis,
-                                        planar_configuration=ds.get('PlanarConfiguration', None),
-                                        default_axes=PdcmIO.DEFAULT_CHANNELS_AXES_PYDICOM)
+        img = PdcmIO.move_channels_axis(
+            img,
+            samples_per_pixel=samples_per_pixel,
+            channels_axis=channels_axis,
+            planar_configuration=ds.get("PlanarConfiguration", None),
+            default_axes=PdcmIO.DEFAULT_CHANNELS_AXES_PYDICOM,
+        )
         return img, metadata, samples_per_pixel > 1
 
     @staticmethod
-    def read_dcm_dir(input_dir, header=False, globber='*', channels_axis=None, series=None):
+    def read_dcm_dir(
+        input_dir, header=False, globber="*", channels_axis=None, series=None
+    ):
         """
         Reads a 3D dicom image: input path can be a file or directory (DICOM series).
         Return the image array, metadata, and whether it has channels
@@ -84,15 +110,21 @@ def read_dcm_dir(input_dir, header=False, globber='*', channels_axis=None, serie
         if header:
             # TODO: add header support, something like
             #  metdata.header = [{str(key): ds[key] for key in ds.keys()} for ds in slices]
-            raise NotImplementedError("header=True is currently not supported for a series")
+            raise NotImplementedError(
+                "header=True is currently not supported for a series"
+            )
         samples_per_pixel = slices[0].SamplesPerPixel
-        img = PdcmIO.move_channels_axis(img, samples_per_pixel=samples_per_pixel, channels_axis=channels_axis,
-                                        planar_configuration=slices[0].get('PlanarConfiguration', None),
-                                        default_axes=PdcmIO.DEFAULT_CHANNELS_AXES_DICOM_NUMPY)
+        img = PdcmIO.move_channels_axis(
+            img,
+            samples_per_pixel=samples_per_pixel,
+            channels_axis=channels_axis,
+            planar_configuration=slices[0].get("PlanarConfiguration", None),
+            default_axes=PdcmIO.DEFAULT_CHANNELS_AXES_DICOM_NUMPY,
+        )
         return img, metadata, samples_per_pixel > 1
 
     @staticmethod
-    def extract_slices(input_dir, globber='*', series=None):
+    def extract_slices(input_dir, globber="*", series=None):
         """Extract slices from input_dir and return them sorted"""
         files = Path(input_dir).glob(globber)
         slices = [pydicom.dcmread(filename) for filename in files]
@@ -106,7 +138,7 @@ def extract_slices(input_dir, globber='*', series=None):
         series_uid = parse_series_uids(input_dir, datasets.keys(), series, globber)
         slices = datasets[series_uid]
 
-        slices.sort(key=lambda ds: ds.get('InstanceNumber', 0))
+        slices.sort(key=lambda ds: ds.get("InstanceNumber", 0))
         return slices
 
     @staticmethod
@@ -114,8 +146,13 @@ def aff2meta(affine):
         return MetaData(affine, coord_sys=PdcmIO.coord_sys)
 
     @staticmethod
-    def move_channels_axis(array, samples_per_pixel, channels_axis=None, planar_configuration=None,
-                           default_axes=DEFAULT_CHANNELS_AXES_PYDICOM):
+    def move_channels_axis(
+        array,
+        samples_per_pixel,
+        channels_axis=None,
+        planar_configuration=None,
+        default_axes=DEFAULT_CHANNELS_AXES_PYDICOM,
+    ):
         """Move the channels axis from the original axis to the destined channels_axis"""
         if (samples_per_pixel == 1) or (channels_axis is None):
             # no rearrangement is needed
@@ -123,7 +160,9 @@ def move_channels_axis(array, samples_per_pixel, channels_axis=None, planar_conf
 
         # extract the original channels axis
         if planar_configuration not in [0, 1]:
-            raise ValueError(f'Invalid Planar Configuration value: {planar_configuration}')
+            raise ValueError(
+                f"Invalid Planar Configuration value: {planar_configuration}"
+            )
 
         orig_axis = default_axes[planar_configuration]
         flag = True  # original channels axis is assigned
@@ -138,7 +177,7 @@ def move_channels_axis(array, samples_per_pixel, channels_axis=None, planar_conf
                     break
 
         if not flag:
-            raise ValueError('The original channels axis was not detected')
+            raise ValueError("The original channels axis was not detected")
 
         return np.moveaxis(array, orig_axis, channels_axis)
 
@@ -160,14 +199,20 @@ def reorient(img, metadata, desired_ornt):
         reoriented_img_struct = NibIO.reorient(img_struct, desired_ornt)
 
         img = np.asanyarray(reoriented_img_struct.dataobj)
-        metadata = MetaData(reoriented_img_struct.affine, orig_ornt=orig_ornt, coord_sys=NibIO.coord_sys,
-                            header=metadata.header)
+        metadata = MetaData(
+            reoriented_img_struct.affine,
+            orig_ornt=orig_ornt,
+            coord_sys=NibIO.coord_sys,
+            header=metadata.header,
+        )
         # convert back to pydicom convention
         metadata.convert(PdcmIO.coord_sys)
         return img, metadata
 
     @staticmethod
-    def save_arr2dcm_file(output_filename, template_filename, img_arr, dtype=None, keep_rescale=False):
+    def save_arr2dcm_file(
+        output_filename, template_filename, img_arr, dtype=None, keep_rescale=False
+    ):
         """
         Writes a dicom single file image using template file, without the intensity transformation from template dataset
         unless keep_rescale is True
diff --git a/medio/backends/pdcm_unpack_ds.py b/medio/backends/pdcm_unpack_ds.py
index 0454533..e938fd4 100644
--- a/medio/backends/pdcm_unpack_ds.py
+++ b/medio/backends/pdcm_unpack_ds.py
@@ -4,7 +4,11 @@
 import logging
 
 import numpy as np
-from dicom_numpy.combine_slices import _validate_image_orientation, _extract_cosines, _requires_rescaling
+from dicom_numpy.combine_slices import (
+    _validate_image_orientation,
+    _extract_cosines,
+    _requires_rescaling,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -81,9 +85,11 @@ def _unpack_pixel_array(dataset, rescale=None):
         rescale = _requires_rescaling(dataset)
 
     if rescale:
-        voxels = voxels.astype('int16', copy=False)  # TODO: it takes time! Consider view.
-        slope = getattr(dataset, 'RescaleSlope', 1)
-        intercept = getattr(dataset, 'RescaleIntercept', 0)
+        voxels = voxels.astype(
+            "int16", copy=False
+        )  # TODO: it takes time! Consider view.
+        slope = getattr(dataset, "RescaleSlope", 1)
+        intercept = getattr(dataset, "RescaleIntercept", 0)
         if int(slope) == slope and int(intercept) == intercept:
             slope = int(slope)
             intercept = int(intercept)
@@ -103,8 +109,9 @@ def _ijk_to_patient_xyz_transform_matrix(dataset):
 
     transform[:3, 0] = row_cosine * column_spacing
     transform[:3, 1] = column_cosine * row_spacing
-    transform[:3, 2] = (np.array(dataset.slice_position(-1)) - dataset.slice_position(0)
-                        ) / (dataset.NumberOfFrames - 1)
+    transform[:3, 2] = (
+        np.array(dataset.slice_position(-1)) - dataset.slice_position(0)
+    ) / (dataset.NumberOfFrames - 1)
     # transform[:3, 2] = slice_cosine * slice_spacing
 
     transform[:3, 3] = dataset.ImagePositionPatient
diff --git a/medio/metadata/affine.py b/medio/metadata/affine.py
index 5dd92c6..a450f4d 100644
--- a/medio/metadata/affine.py
+++ b/medio/metadata/affine.py
@@ -33,7 +33,7 @@ def __new__(cls, affine=None, *, direction=None, spacing=None, origin=None):
             affine = cls.construct_affine(direction, spacing, origin)
         obj = np.asarray(affine).view(cls)  # return array view of type Affine
         return obj
-    
+
     def __init__(self, affine=None, *, direction=None, spacing=None, origin=None):
         self.dim = self.shape[0] - 1
         if affine is None:
@@ -74,7 +74,9 @@ def spacing(self):
     def spacing(self, value):
         value = np.asarray(value)
         self._m_matrix = self._m_matrix @ np.diag(value / self._spacing)
-        self._spacing = np.abs(value)  # the spacing must be positive (or at least nonnegative)
+        self._spacing = np.abs(
+            value
+        )  # the spacing must be positive (or at least nonnegative)
 
     @property
     def direction(self):
@@ -124,4 +126,8 @@ def affine2direction(affine, spacing=None):
     def affine2comps(affine, spacing=None):
         if spacing is None:
             spacing = Affine.affine2spacing(affine)
-        return Affine.affine2direction(affine, spacing), spacing, Affine.affine2origin(affine)
+        return (
+            Affine.affine2direction(affine, spacing),
+            spacing,
+            Affine.affine2origin(affine),
+        )
diff --git a/medio/metadata/convert_nib_itk.py b/medio/metadata/convert_nib_itk.py
index 25cce92..00233c0 100644
--- a/medio/metadata/convert_nib_itk.py
+++ b/medio/metadata/convert_nib_itk.py
@@ -35,16 +35,16 @@
 
 # store compactly axis directions codes
 axes_inv = TwoWayDict()
-axes_inv['R'] = 'L'
-axes_inv['A'] = 'P'
-axes_inv['S'] = 'I'
+axes_inv["R"] = "L"
+axes_inv["A"] = "P"
+axes_inv["S"] = "I"
 
 
 def inv_axcodes(axcodes):
     """Inverse axes codes chars, for example: SPL -> IAR"""
     if axcodes is None:
         return None
-    new_axcodes = ''
+    new_axcodes = ""
     for code in axcodes:
         new_axcodes += axes_inv[code]
     return new_axcodes
diff --git a/medio/metadata/dcm_uid.py b/medio/metadata/dcm_uid.py
index 2e6cc79..7259962 100644
--- a/medio/metadata/dcm_uid.py
+++ b/medio/metadata/dcm_uid.py
@@ -3,7 +3,7 @@
 from pydicom.uid import generate_uid
 
 # Given by Medical Connections (http://www.medicalconnections.co.uk/FreeUID.html)
-MEDIO_ROOT_UID = '1.2.826.0.1.3680043.10.513.'
+MEDIO_ROOT_UID = "1.2.826.0.1.3680043.10.513."
 
 
 generate_uid = partial(generate_uid, prefix=MEDIO_ROOT_UID)
diff --git a/medio/metadata/itk_orientation.py b/medio/metadata/itk_orientation.py
index be5efdb..47cea82 100644
--- a/medio/metadata/itk_orientation.py
+++ b/medio/metadata/itk_orientation.py
@@ -32,22 +32,25 @@ class ItkOrientationCode:
 def itk_orientation_code(ax_code):
     """ax_code is string or tuple of valid orientation, e.g. 'LPI', ('A', 'R', 'S')"""
     prime, second, tertiary = [getattr(AxCodes, axis) for axis in ax_code]
-    return (prime << AxMajorness.Primary) + (second << AxMajorness.Secondary) + (tertiary << AxMajorness.Tertiary)
+    return (
+        (prime << AxMajorness.Primary)
+        + (second << AxMajorness.Secondary)
+        + (tertiary << AxMajorness.Tertiary)
+    )
 
 
 # adding all 48 possible orientation codes to ItkOrientationCode class
 
 ax_codes_iter = itertools.chain(
-    *map(itertools.permutations,
-         itertools.product(('R', 'L'), ('A', 'P'), ('I', 'S'))
-         ))
+    *map(itertools.permutations, itertools.product(("R", "L"), ("A", "P"), ("I", "S")))
+)
 
 # two way dictionary that translates itk numerical orientation codes to orientation strings and vice versa
 codes_str_dict = TwoWayDict()
 codes_str_dict[None] = None
 
 for ax_code in ax_codes_iter:
-    ax_code_str = ''.join(ax_code)
+    ax_code_str = "".join(ax_code)
     code = itk_orientation_code(ax_code)
     setattr(ItkOrientationCode, ax_code_str, code)
     codes_str_dict[ax_code_str] = code
diff --git a/medio/metadata/metadata.py b/medio/metadata/metadata.py
index 3682804..9a4a360 100644
--- a/medio/metadata/metadata.py
+++ b/medio/metadata/metadata.py
@@ -9,7 +9,7 @@
 
 
 class MetaData:
-    def __init__(self, affine, orig_ornt=None, coord_sys='itk', header=None):
+    def __init__(self, affine, orig_ornt=None, coord_sys="itk", header=None):
         """
         Initialize medical image's metadata
         :param affine: affine matrix of class Affine, numpy float array of shape (4, 4)
@@ -29,19 +29,21 @@ def __init__(self, affine, orig_ornt=None, coord_sys='itk', header=None):
 
     @staticmethod
     def check_valid_coord_sys(coord_sys):
-        if coord_sys not in ('itk', 'nib'):
+        if coord_sys not in ("itk", "nib"):
             raise ValueError('Metadata coord_sys must be "itk" or "nib"')
 
     def __repr__(self):
-        sep = ' ' if self.header is None else '\n'
-        return (f'Affine:\n'
-                f'{self.affine}\n'
-                f'Spacing: {self.spacing}\n'
-                f'Coordinate system: {self.coord_sys}\n'
-                f'Orientation: {self.ornt}\n'
-                f'Original orientation: {self.orig_ornt}\n'
-                f'Header:{sep}'
-                f'{pprint.pformat(self.header, indent=4)}')
+        sep = " " if self.header is None else "\n"
+        return (
+            f"Affine:\n"
+            f"{self.affine}\n"
+            f"Spacing: {self.spacing}\n"
+            f"Coordinate system: {self.coord_sys}\n"
+            f"Orientation: {self.ornt}\n"
+            f"Original orientation: {self.orig_ornt}\n"
+            f"Header:{sep}"
+            f"{pprint.pformat(self.header, indent=4)}"
+        )
 
     def convert(self, dest_coord_sys):
         """
@@ -50,22 +52,28 @@ def convert(self, dest_coord_sys):
         """
         self.check_valid_coord_sys(dest_coord_sys)
         if dest_coord_sys != self.coord_sys:
-            self.affine, self._ornt, self.orig_ornt = convert_nib_itk(self.affine, self._ornt, self.orig_ornt)
+            self.affine, self._ornt, self.orig_ornt = convert_nib_itk(
+                self.affine, self._ornt, self.orig_ornt
+            )
             self.coord_sys = dest_coord_sys
 
     def clone(self):
-        return MetaData(affine=self.affine.clone(), orig_ornt=self.orig_ornt, coord_sys=self.coord_sys,
-                        header=deepcopy(self.header))
+        return MetaData(
+            affine=self.affine.clone(),
+            orig_ornt=self.orig_ornt,
+            coord_sys=self.coord_sys,
+            header=deepcopy(self.header),
+        )
 
     def get_ornt(self):
         """Returns current orientation based on the affine and coordinate system"""
-        if self.coord_sys == 'nib':
+        if self.coord_sys == "nib":
             ornt_tup = aff2axcodes(self.affine)
-        elif self.coord_sys == 'itk':
+        elif self.coord_sys == "itk":
             ornt_tup = inv_axcodes(aff2axcodes(convert_affine(self.affine)))
         else:
             raise ValueError(f'Invalid coord_sys: "{self.coord_sys}"')
-        ornt_str = ''.join(ornt_tup)
+        ornt_str = "".join(ornt_tup)
         return ornt_str
 
     @property
@@ -87,7 +95,7 @@ def is_right_handed_ornt(self):
         +1 (-1) indicates right (left) handed orientation.
         To be used primarily before saving a dicom file or series"""
         if self.affine.dim != 3:
-            raise ValueError('Right handed orientation is relevant only to a 3d space')
+            raise ValueError("Right handed orientation is relevant only to a 3d space")
         return np.linalg.det(self.affine.direction) > 0
 
 
@@ -96,13 +104,14 @@ def is_right_handed_axcodes(axcodes):
         return True
     if len(axcodes) != 3:
         raise ValueError(f'Invalid axcodes (not length 3 or 2): "{axcodes}"')
-    letter_vec_dict = {'R': [1, 0, 0],
-                       'L': [-1, 0, 0],
-                       'A': [0, 1, 0],
-                       'P': [0, -1, 0],
-                       'I': [0, 0, 1],
-                       'S': [0, 0, -1]
-                       }
+    letter_vec_dict = {
+        "R": [1, 0, 0],
+        "L": [-1, 0, 0],
+        "A": [0, 1, 0],
+        "P": [0, -1, 0],
+        "I": [0, 0, 1],
+        "S": [0, 0, -1],
+    }
     u, v, n = [letter_vec_dict[letter] for letter in axcodes]
     ornt_sign = np.dot(np.cross(u, v), n)
     if ornt_sign not in (-1, 1):
@@ -131,7 +140,9 @@ def check_dcm_ornt(desired_ornt, metadata, allow_dcm_reorient=False):
         if allow_dcm_reorient:
             return right_handed_ornt
         else:
-            raise ValueError(f'The desired orientation "{desired_ornt}" is left handed, whereas saving dicom is '
-                             f'possible only with a right handed orientation. \nYou can either pass the saver '
-                             f'parameter allow_dcm_reorient=True to allow automatic reorientation (in this case to '
-                             f'"{right_handed_ornt}"), or \nreorient yourself before saving the image as a dicom.')
+            raise ValueError(
+                f'The desired orientation "{desired_ornt}" is left handed, whereas saving dicom is '
+                f"possible only with a right handed orientation. \nYou can either pass the saver "
+                f"parameter allow_dcm_reorient=True to allow automatic reorientation (in this case to "
+                f'"{right_handed_ornt}"), or \nreorient yourself before saving the image as a dicom.'
+            )
diff --git a/medio/metadata/pdcm_ds.py b/medio/metadata/pdcm_ds.py
index 7f581c9..c027062 100644
--- a/medio/metadata/pdcm_ds.py
+++ b/medio/metadata/pdcm_ds.py
@@ -11,49 +11,83 @@ def convert_ds(dataset):
     >>> ds = convert_ds(ds)
     >>> print(ds.PixelSpacing)
     """
-    if dataset.get('NumberOfFrames', 1) > 1:
+    if dataset.get("NumberOfFrames", 1) > 1:
         dataset.__class__ = MultiFrameFileDataset
     return dataset
 
 
 class MultiFrameFileDataset(FileDataset):
     """This class enables shorter access to basic properties of pydicom dataset of a certain type"""
+
     @property
     def ImageOrientationPatient(self):
-        return self.SharedFunctionalGroupsSequence[0].PlaneOrientationSequence[0].ImageOrientationPatient
+        return (
+            self.SharedFunctionalGroupsSequence[0]
+            .PlaneOrientationSequence[0]
+            .ImageOrientationPatient
+        )
 
     @property
     def PixelSpacing(self):
-        return self.SharedFunctionalGroupsSequence[0].PixelMeasuresSequence[0].PixelSpacing
+        return (
+            self.SharedFunctionalGroupsSequence[0].PixelMeasuresSequence[0].PixelSpacing
+        )
 
     @property
     def SpacingBetweenSlices(self):
-        return self.SharedFunctionalGroupsSequence[0].PixelMeasuresSequence[0].SpacingBetweenSlices
+        return (
+            self.SharedFunctionalGroupsSequence[0]
+            .PixelMeasuresSequence[0]
+            .SpacingBetweenSlices
+        )
 
     @property
     def SliceThickness(self):
-        return self.SharedFunctionalGroupsSequence[0].PixelMeasuresSequence[0].SliceThickness
+        return (
+            self.SharedFunctionalGroupsSequence[0]
+            .PixelMeasuresSequence[0]
+            .SliceThickness
+        )
 
     @property
     def RescaleIntercept(self):
-        return self.SharedFunctionalGroupsSequence[0].PixelValueTransformationSequence[0].RescaleIntercept
+        return (
+            self.SharedFunctionalGroupsSequence[0]
+            .PixelValueTransformationSequence[0]
+            .RescaleIntercept
+        )
 
     @property
     def RescaleSlope(self):
-        return self.SharedFunctionalGroupsSequence[0].PixelValueTransformationSequence[0].RescaleSlope
+        return (
+            self.SharedFunctionalGroupsSequence[0]
+            .PixelValueTransformationSequence[0]
+            .RescaleSlope
+        )
 
     @property
     def ImagePositionPatient(self):
         """Note: this property returns only the position of the first slice"""
-        return self.PerFrameFunctionalGroupsSequence[0].PlanePositionSequence[0].ImagePositionPatient
+        return (
+            self.PerFrameFunctionalGroupsSequence[0]
+            .PlanePositionSequence[0]
+            .ImagePositionPatient
+        )
 
     def slice_positions(self):
         """Return a list of the slices' position"""
-        return [seq.PlanePositionSequence[0].ImagePositionPatient for seq in self.PerFrameFunctionalGroupsSequence]
+        return [
+            seq.PlanePositionSequence[0].ImagePositionPatient
+            for seq in self.PerFrameFunctionalGroupsSequence
+        ]
 
     def slice_position(self, index):
         """Return the slice position according to the slice index"""
-        return self.PerFrameFunctionalGroupsSequence[index].PlanePositionSequence[0].ImagePositionPatient
+        return (
+            self.PerFrameFunctionalGroupsSequence[index]
+            .PlanePositionSequence[0]
+            .ImagePositionPatient
+        )
 
     def del_intensity_trans(self):
         """Delete the pixel value transformation sequence from dataset"""
diff --git a/medio/read_save.py b/medio/read_save.py
index 46be03b..6f871f0 100644
--- a/medio/read_save.py
+++ b/medio/read_save.py
@@ -7,8 +7,16 @@
 from medio.utils.files import is_nifti
 
 
-def read_img(input_path, desired_ornt=None, backend=None, dtype=None, header=False, channels_axis=-1,
-             coord_sys='itk', **kwargs):
+def read_img(
+    input_path,
+    desired_ornt=None,
+    backend=None,
+    dtype=None,
+    header=False,
+    channels_axis=-1,
+    coord_sys="itk",
+    **kwargs
+):
     """
     Read medical image with nibabel or itk
     :param input_path: str or os.PathLike, the input path of image file or a directory containing dicom series
@@ -34,19 +42,23 @@ def read_img(input_path, desired_ornt=None, backend=None, dtype=None, header=Fal
         else:
             reader, reader_sys = itk_reader_data
     else:
-        if backend == 'nib':
+        if backend == "nib":
             reader, reader_sys = nib_reader_data
-        elif backend == 'itk':
+        elif backend == "itk":
             reader, reader_sys = itk_reader_data
-        elif backend in ('pdcm', 'pydicom'):
+        elif backend in ("pdcm", "pydicom"):
             reader, reader_sys = pdcm_reader_data
         else:
-            raise ValueError('The backend argument must be one of: "itk", "nib", "pdcm" (or "pydicom"), None')
+            raise ValueError(
+                'The backend argument must be one of: "itk", "nib", "pdcm" (or "pydicom"), None'
+            )
 
     if (coord_sys is not None) and (coord_sys != reader_sys):
         desired_ornt = inv_axcodes(desired_ornt)
 
-    np_image, metadata = reader(input_path, desired_ornt, header, channels_axis, **kwargs)
+    np_image, metadata = reader(
+        input_path, desired_ornt, header, channels_axis, **kwargs
+    )
 
     if dtype is not None:
         np_image = np_image.astype(dtype, copy=False)
@@ -55,8 +67,18 @@ def read_img(input_path, desired_ornt=None, backend=None, dtype=None, header=Fal
     return np_image, metadata
 
 
-def save_img(filename, np_image, metadata, use_original_ornt=True, backend=None, dtype=None, channels_axis=None,
-             mkdir=False, parents=False, **kwargs):
+def save_img(
+    filename,
+    np_image,
+    metadata,
+    use_original_ornt=True,
+    backend=None,
+    dtype=None,
+    channels_axis=None,
+    mkdir=False,
+    parents=False,
+    **kwargs
+):
     """
     Save numpy image with corresponding metadata to file
     :param filename: str or os.PathLike, the output filename
@@ -77,9 +99,9 @@ def save_img(filename, np_image, metadata, use_original_ornt=True, backend=None,
         else:
             writer = itk_writer
     else:
-        if backend == 'nib':
+        if backend == "nib":
             writer = nib_writer
-        elif backend == 'itk':
+        elif backend == "itk":
             writer = itk_writer
         else:
             raise ValueError('The backend argument must be one of: "itk", "nib", None')
@@ -90,13 +112,32 @@ def save_img(filename, np_image, metadata, use_original_ornt=True, backend=None,
     writer(filename, np_image, metadata, use_original_ornt, channels_axis, **kwargs)
 
 
-def save_dir(dirname, np_image, metadata, use_original_ornt=True, dtype=None, channels_axis=None, parents=False,
-             exist_ok=False, allow_dcm_reorient=False, **kwargs):
+def save_dir(
+    dirname,
+    np_image,
+    metadata,
+    use_original_ornt=True,
+    dtype=None,
+    channels_axis=None,
+    parents=False,
+    exist_ok=False,
+    allow_dcm_reorient=False,
+    **kwargs
+):
     """
     Save image as a dicom directory. See medio.backends.itk_io.ItkIO.save_dcm_dir documentation.
     dtype is equivalent to passing image_np.astype(dtype) if dtype is not None
     """
     if dtype is not None:
         np_image = np_image.astype(dtype, copy=False)
-    ItkIO.save_dcm_dir(dirname, np_image, metadata, use_original_ornt, channels_axis, parents, exist_ok,
-                       allow_dcm_reorient, **kwargs)
+    ItkIO.save_dcm_dir(
+        dirname,
+        np_image,
+        metadata,
+        use_original_ornt,
+        channels_axis,
+        parents,
+        exist_ok,
+        allow_dcm_reorient,
+        **kwargs
+    )
diff --git a/medio/utils/files.py b/medio/utils/files.py
index d293b5f..2fd0879 100644
--- a/medio/utils/files.py
+++ b/medio/utils/files.py
@@ -16,11 +16,17 @@ def is_file_suffix(filename, suffixes, check_exist=True):
 
 
 def is_nifti(filename, check_exist=True):
-    return is_file_suffix(filename, ('.nii.gz', '.nii', '.img.gz', '.img', '.hdr'), check_exist=check_exist)
+    return is_file_suffix(
+        filename,
+        (".nii.gz", ".nii", ".img.gz", ".img", ".hdr"),
+        check_exist=check_exist,
+    )
 
 
 def is_dicom(filename, check_exist=True):
-    return is_file_suffix(filename, ('.dcm', '.dicom', '.DCM', '.DICOM'), check_exist=check_exist)
+    return is_file_suffix(
+        filename, (".dcm", ".dicom", ".DCM", ".DICOM"), check_exist=check_exist
+    )
 
 
 def make_empty_dir(dir_path, parents=False):
@@ -31,7 +37,7 @@ def make_empty_dir(dir_path, parents=False):
     except FileExistsError:
         # the directory exists
         try:
-            next(dir_path.glob('*'))
+            next(dir_path.glob("*"))
         except StopIteration:
             pass  # the directory exists but empty - ok
         else:
@@ -51,8 +57,10 @@ def parse_series_uids(input_dir, series_uids, series=None, globber=None):
     keys = sorted(series_uids)
     num_series = len(keys)
     if num_series == 0:
-        raise FileNotFoundError(f'No DICOMs in:\n"{input_dir}"' + (
-            f'\nwith globber="{globber}"' if globber is not None else ''))
+        raise FileNotFoundError(
+            f'No DICOMs in:\n"{input_dir}"'
+            + (f'\nwith globber="{globber}"' if globber is not None else "")
+        )
 
     if num_series == 1:
         return keys[0]
@@ -60,18 +68,22 @@ def parse_series_uids(input_dir, series_uids, series=None, globber=None):
     # if there is more than a single series
     if num_series > 1:
         if series is None:
-            raise ValueError(f'The directory: "{input_dir}"\n'
-                             'contains more than a single DICOM series. '
-                             'The following series were identified according to their Series Instance UID:\n'
-                             f'{pprint.pformat(keys)}\n'
-                             'Try passing: series=series_uid, where series_uid is a one of the strings above,\n'
-                             f'or an integer between 0 and {num_series - 1} corresponding to one of them.')
+            raise ValueError(
+                f'The directory: "{input_dir}"\n'
+                "contains more than a single DICOM series. "
+                "The following series were identified according to their Series Instance UID:\n"
+                f"{pprint.pformat(keys)}\n"
+                "Try passing: series=series_uid, where series_uid is a one of the strings above,\n"
+                f"or an integer between 0 and {num_series - 1} corresponding to one of them."
+            )
         elif isinstance(series, int):
             return keys[series]
         else:
             if series not in keys:
-                raise ValueError("The series:\n"
-                                 f"'{series}'\n"
-                                 "is not one of the following:"
-                                 f"\n{pprint.pformat(keys)}")
+                raise ValueError(
+                    "The series:\n"
+                    f"'{series}'\n"
+                    "is not one of the following:"
+                    f"\n{pprint.pformat(keys)}"
+                )
             return series
diff --git a/medio/utils/two_way_dict.py b/medio/utils/two_way_dict.py
index 27478ce..8ce2bbd 100644
--- a/medio/utils/two_way_dict.py
+++ b/medio/utils/two_way_dict.py
@@ -1,5 +1,6 @@
 class TwoWayDict(dict):
     """Dictionary which contains key-value + value-key pairs: {key: value, value: key}"""
+
     def __setitem__(self, key, value):
         # Remove any previous connections with these values
         if key in self:
diff --git a/tests/itk_dcm_orientations/itk_dcm_orientations.py b/tests/itk_dcm_orientations/itk_dcm_orientations.py
index 503a31e..ed1767f 100644
--- a/tests/itk_dcm_orientations/itk_dcm_orientations.py
+++ b/tests/itk_dcm_orientations/itk_dcm_orientations.py
@@ -5,13 +5,19 @@
 import pandas as pd
 
 from tests.itk_dcm_orientations.orientations_utils import (
-    ornt_list, ornt_direction_dict, is_right_handed_ornt, direction2ornt
+    ornt_list,
+    ornt_direction_dict,
+    is_right_handed_ornt,
+    direction2ornt,
+)
+from tests.itk_dcm_orientations.itk_utils import (
+    set_image_direction,
+    get_image_direction,
 )
-from tests.itk_dcm_orientations.itk_utils import set_image_direction, get_image_direction
 
 
 def get_saved_ornt(image, desired_ornt, remove=True):
-    filename = desired_ornt + '.dcm'
+    filename = desired_ornt + ".dcm"
     desired_direction = ornt_direction_dict[desired_ornt]
     set_image_direction(image, desired_direction)
     itk.imwrite(image, filename)
@@ -27,41 +33,48 @@ def get_saved_ornt(image, desired_ornt, remove=True):
     return saved_ornt, is_equal
 
 
-arr = np.random.randint(0, 256, size=(10, 30, 25), dtype='uint8')  # (slices, cols, rows)
-arr_rgb = np.random.randint(0, 256, size=(10, 30, 25, 3), dtype='uint8')  # (slices, cols, rows, channels)
+arr = np.random.randint(
+    0, 256, size=(10, 30, 25), dtype="uint8"
+)  # (slices, cols, rows)
+arr_rgb = np.random.randint(
+    0, 256, size=(10, 30, 25, 3), dtype="uint8"
+)  # (slices, cols, rows, channels)
 img = itk.image_from_array(arr)
 img_rgb = itk.image_from_array(arr_rgb, is_vector=True)
 
 df = pd.DataFrame(
-    columns=
-        [
-          'Orientation',
-           'Right/Left-handed orientation',
-           'Success',
-           'Saved orientation',
-           'RGB success',
-           'RGB saved orientation',
-        ]
+    columns=[
+        "Orientation",
+        "Right/Left-handed orientation",
+        "Success",
+        "Saved orientation",
+        "RGB success",
+        "RGB saved orientation",
+    ]
 )
 
 for ornt in ornt_list:
     state_dict = dict.fromkeys(df.columns)
-    state_dict['Orientation'] = ornt
-    state_dict['Right/Left-handed orientation'] = 'R' if is_right_handed_ornt(ornt) else 'L'
+    state_dict["Orientation"] = ornt
+    state_dict["Right/Left-handed orientation"] = (
+        "R" if is_right_handed_ornt(ornt) else "L"
+    )
     # test 3d dicom
-    state_dict['Saved orientation'], state_dict['Success'] = get_saved_ornt(img, ornt)
+    state_dict["Saved orientation"], state_dict["Success"] = get_saved_ornt(img, ornt)
     # test 3d RGB dicom
-    state_dict['RGB saved orientation'], state_dict['RGB success'] = get_saved_ornt(img_rgb, ornt)
+    state_dict["RGB saved orientation"], state_dict["RGB success"] = get_saved_ornt(
+        img_rgb, ornt
+    )
     df = df.append(state_dict, ignore_index=True)
 
-df.sort_values('Right/Left-handed orientation', ascending=False, inplace=True)
-df.to_csv('itk_dcm_orientations.csv', index=False)
+df.sort_values("Right/Left-handed orientation", ascending=False, inplace=True)
+df.to_csv("itk_dcm_orientations.csv", index=False)
 
-right_handed = np.array(df['Right/Left-handed orientation'] == 'R')
-success = np.array(df['Success'])
-rgb_success = np.array(df['RGB success'])
-rai_ornt = np.array(df['Orientation'] == 'RAI')
+right_handed = np.array(df["Right/Left-handed orientation"] == "R")
+success = np.array(df["Success"])
+rgb_success = np.array(df["RGB success"])
+rai_ornt = np.array(df["Orientation"] == "RAI")
 
-print('Right-handed == Success:', np.array_equal(right_handed, success))
-print('Right-handed == RGB success:', np.array_equal(right_handed, rgb_success))
+print("Right-handed == Success:", np.array_equal(right_handed, success))
+print("Right-handed == RGB success:", np.array_equal(right_handed, rgb_success))
 print('"RAI" orientation == RGB success:', np.array_equal(rai_ornt, rgb_success))
diff --git a/tests/itk_dcm_orientations/itk_utils.py b/tests/itk_dcm_orientations/itk_utils.py
index 52f7095..872d110 100644
--- a/tests/itk_dcm_orientations/itk_utils.py
+++ b/tests/itk_dcm_orientations/itk_utils.py
@@ -3,7 +3,9 @@
 
 def set_image_direction(image, direction):
     dim = 3
-    direction_vnl_mat = itk.vnl_matrix_from_array(direction.astype('float').copy())  # copy is crucial for the float
+    direction_vnl_mat = itk.vnl_matrix_from_array(
+        direction.astype("float").copy()
+    )  # copy is crucial for the float
     direction_itk = itk.Matrix[itk.D, dim, dim](direction_vnl_mat)
     image.SetDirection(direction_itk)
 
diff --git a/tests/itk_dcm_orientations/orientations_utils.py b/tests/itk_dcm_orientations/orientations_utils.py
index 025cbca..2812c9c 100644
--- a/tests/itk_dcm_orientations/orientations_utils.py
+++ b/tests/itk_dcm_orientations/orientations_utils.py
@@ -2,13 +2,14 @@
 
 import numpy as np
 
-letter_vec_dict = {'R': [1, 0, 0],
-                   'L': [-1, 0, 0],
-                   'A': [0, 1, 0],
-                   'P': [0, -1, 0],
-                   'I': [0, 0, 1],
-                   'S': [0, 0, -1]
-                   }
+letter_vec_dict = {
+    "R": [1, 0, 0],
+    "L": [-1, 0, 0],
+    "A": [0, 1, 0],
+    "P": [0, -1, 0],
+    "I": [0, 0, 1],
+    "S": [0, 0, -1],
+}
 
 
 def ornt2direction(ornt):
@@ -16,16 +17,15 @@ def ornt2direction(ornt):
 
 
 ornt_iter = itertools.chain(
-    *map(itertools.permutations,
-         itertools.product(('R', 'L'), ('A', 'P'), ('I', 'S'))
-         ))
+    *map(itertools.permutations, itertools.product(("R", "L"), ("A", "P"), ("I", "S")))
+)
 
 # dictionary that translates itk orientation codes to direction matrices
 ornt_direction_dict = dict()
 ornt_list = []
 
 for ornt_tup in ornt_iter:
-    ornt = ''.join(ornt_tup)
+    ornt = "".join(ornt_tup)
     ornt_list += [ornt]
     ornt_direction_dict[ornt] = ornt2direction(ornt)
 
@@ -41,4 +41,4 @@ def direction2ornt(direction):
     for key, val in ornt_direction_dict.items():
         if np.array_equal(direction, val):
             return key
-    raise ValueError('Invalid direction')
+    raise ValueError("Invalid direction")

From d593dd226e32c9ae2df9cb298bf2ae800b2c5b9b Mon Sep 17 00:00:00 2001
From: Jonathan Daniel <jonathand655@gmail.com>
Date: Sun, 20 Feb 2022 22:21:49 +0200
Subject: [PATCH 3/5] Poetry update

---
 poetry.lock | 84 ++++++++++++++++++++++++++++++++++++++---------------
 1 file changed, 61 insertions(+), 23 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 8b34aab..a06b754 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -23,7 +23,7 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "click"
-version = "8.0.3"
+version = "8.0.4"
 description = "Composable command line interface toolkit"
 category = "dev"
 optional = false
@@ -59,7 +59,7 @@ test = ["coverage", "pytest"]
 
 [[package]]
 name = "importlib-metadata"
-version = "4.10.1"
+version = "4.11.1"
 description = "Read metadata from Python packages"
 category = "dev"
 optional = false
@@ -72,7 +72,7 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
 perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "itk"
@@ -167,7 +167,7 @@ python-versions = "*"
 
 [[package]]
 name = "nibabel"
-version = "3.2.1"
+version = "3.2.2"
 description = "Access a multitude of neuroimaging data formats"
 category = "main"
 optional = false
@@ -178,15 +178,23 @@ numpy = ">=1.14"
 packaging = ">=14.3"
 
 [package.extras]
-all = ["pydicom (>=0.9.9)", "pillow", "gitpython", "twine", "matplotlib (>=1.5.3)", "numpydoc", "sphinx (>=0.3,<3)", "texext", "h5py", "scipy", "flake8", "coverage", "pytest (!=5.3.4)", "pytest-cov", "pytest-doctestplus"]
+all = ["pydicom (>=1.0.0)", "pillow", "gitpython", "twine", "matplotlib (>=1.5.3)", "numpydoc", "sphinx (>=0.3,<3)", "texext", "h5py", "scipy", "flake8", "coverage", "pytest (!=5.3.4)", "pytest-cov", "pytest-doctestplus (!=0.9.0)", "pytest (<7)"]
 dev = ["gitpython", "twine"]
-dicom = ["pydicom (>=0.9.9)"]
-dicomfs = ["pydicom (>=0.9.9)", "pillow"]
+dicom = ["pydicom (>=1.0.0)"]
+dicomfs = ["pydicom (>=1.0.0)", "pillow"]
 doc = ["matplotlib (>=1.5.3)", "numpydoc", "sphinx (>=0.3,<3)", "texext"]
 minc2 = ["h5py"]
 spm = ["scipy"]
 style = ["flake8"]
-test = ["coverage", "pytest (!=5.3.4)", "pytest-cov", "pytest-doctestplus"]
+test = ["coverage", "pytest (!=5.3.4)", "pytest-cov", "pytest-doctestplus (!=0.9.0)", "pytest (<7)"]
+
+[[package]]
+name = "numpy"
+version = "1.21.5"
+description = "NumPy is the fundamental package for array computing with Python."
+category = "main"
+optional = false
+python-versions = ">=3.7,<3.11"
 
 [[package]]
 name = "numpy"
@@ -217,7 +225,7 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
 [[package]]
 name = "platformdirs"
-version = "2.4.1"
+version = "2.5.1"
 description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
@@ -248,7 +256,7 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "tomli"
-version = "2.0.0"
+version = "2.0.1"
 description = "A lil' TOML parser"
 category = "dev"
 optional = false
@@ -264,7 +272,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "typing-extensions"
-version = "4.0.1"
+version = "4.1.1"
 description = "Backported and Experimental Type Hints for Python 3.6+"
 category = "dev"
 optional = false
@@ -314,8 +322,8 @@ black = [
     {file = "black-22.1.0.tar.gz", hash = "sha256:a7c0192d35635f6fc1174be575cb7915e92e5dd629ee79fdaf0dcfa41a80afb5"},
 ]
 click = [
-    {file = "click-8.0.3-py3-none-any.whl", hash = "sha256:353f466495adaeb40b6b5f592f9f91cb22372351c84caeb068132442a4518ef3"},
-    {file = "click-8.0.3.tar.gz", hash = "sha256:410e932b050f5eed773c4cda94de75971c89cdb3155a72a0831139a79e5ecb5b"},
+    {file = "click-8.0.4-py3-none-any.whl", hash = "sha256:6a7a62563bbfabfda3a38f3023a1db4a35978c0abd76f6c9605ecd6554d6d9b1"},
+    {file = "click-8.0.4.tar.gz", hash = "sha256:8458d7b1287c5fb128c90e23381cf99dcde74beaf6c7ff6384ce84d6fe090adb"},
 ]
 colorama = [
     {file = "colorama-0.4.4-py2.py3-none-any.whl", hash = "sha256:9f47eda37229f68eee03b24b9748937c7dc3868f906e8ba69fbcbdd3bc5dc3e2"},
@@ -326,8 +334,8 @@ dicom-numpy = [
     {file = "dicom_numpy-0.6.2.tar.gz", hash = "sha256:24b993083368efb868ffe5edcab054db5c11f0587a218a6b6492fde14a87acd9"},
 ]
 importlib-metadata = [
-    {file = "importlib_metadata-4.10.1-py3-none-any.whl", hash = "sha256:899e2a40a8c4a1aec681feef45733de8a6c58f3f6a0dbed2eb6574b4387a77b6"},
-    {file = "importlib_metadata-4.10.1.tar.gz", hash = "sha256:951f0d8a5b7260e9db5e41d429285b5f451e928479f19d80818878527d36e95e"},
+    {file = "importlib_metadata-4.11.1-py3-none-any.whl", hash = "sha256:e0bc84ff355328a4adfc5240c4f211e0ab386f80aa640d1b11f0618a1d282094"},
+    {file = "importlib_metadata-4.11.1.tar.gz", hash = "sha256:175f4ee440a0317f6e8d81b7f8d4869f93316170a65ad2b007d2929186c8052c"},
 ]
 itk = [
     {file = "itk-5.2.1.post1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:d18723ca6791fc5d9c7498e03d73929df56acffd9290ed8f61a24f25a138951e"},
@@ -467,10 +475,40 @@ mypy-extensions = [
     {file = "mypy_extensions-0.4.3.tar.gz", hash = "sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8"},
 ]
 nibabel = [
-    {file = "nibabel-3.2.1-py3-none-any.whl", hash = "sha256:7e26cbf60eae8668785fa970294f05f767cefc5538b9e22aa388a07f62c54ebc"},
-    {file = "nibabel-3.2.1.tar.gz", hash = "sha256:4d2ff9426b740011a1c916b54fc25da9348282e727eaa2ea163f42e00f1fc29e"},
+    {file = "nibabel-3.2.2-py3-none-any.whl", hash = "sha256:7df7a2733461441d3aacc61f36f5e100ec533d43ed09a191293bb4ca5a4f10f6"},
+    {file = "nibabel-3.2.2.tar.gz", hash = "sha256:b0dcc174b30405ce9e8fec1eab3cbbb20f5c5e4920976c08b22e050b7c124f94"},
 ]
 numpy = [
+    {file = "numpy-1.21.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:301e408a052fdcda5cdcf03021ebafc3c6ea093021bf9d1aa47c54d48bdad166"},
+    {file = "numpy-1.21.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a7e8f6216f180f3fd4efb73de5d1eaefb5f5a1ee5b645c67333033e39440e63a"},
+    {file = "numpy-1.21.5-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:fc7a7d7b0ed72589fd8b8486b9b42a564f10b8762be8bd4d9df94b807af4a089"},
+    {file = "numpy-1.21.5-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:58ca1d7c8aef6e996112d0ce873ac9dfa1eaf4a1196b4ff7ff73880a09923ba7"},
+    {file = "numpy-1.21.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:dc4b2fb01f1b4ddbe2453468ea0719f4dbb1f5caa712c8b21bb3dd1480cd30d9"},
+    {file = "numpy-1.21.5-cp310-cp310-win_amd64.whl", hash = "sha256:cc1b30205d138d1005adb52087ff45708febbef0e420386f58664f984ef56954"},
+    {file = "numpy-1.21.5-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:08de8472d9f7571f9d51b27b75e827f5296295fa78817032e84464be8bb905bc"},
+    {file = "numpy-1.21.5-cp37-cp37m-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:4fe6a006557b87b352c04596a6e3f12a57d6e5f401d804947bd3188e6b0e0e76"},
+    {file = "numpy-1.21.5-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:3d893b0871322eaa2f8c7072cdb552d8e2b27645b7875a70833c31e9274d4611"},
+    {file = "numpy-1.21.5-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:341dddcfe3b7b6427a28a27baa59af5ad51baa59bfec3264f1ab287aa3b30b13"},
+    {file = "numpy-1.21.5-cp37-cp37m-win32.whl", hash = "sha256:ca9c23848292c6fe0a19d212790e62f398fd9609aaa838859be8459bfbe558aa"},
+    {file = "numpy-1.21.5-cp37-cp37m-win_amd64.whl", hash = "sha256:025b497014bc33fc23897859350f284323f32a2fff7654697f5a5fc2a19e9939"},
+    {file = "numpy-1.21.5-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:3a5098df115340fb17fc93867317a947e1dcd978c3888c5ddb118366095851f8"},
+    {file = "numpy-1.21.5-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:311283acf880cfcc20369201bd75da907909afc4666966c7895cbed6f9d2c640"},
+    {file = "numpy-1.21.5-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:b545ebadaa2b878c8630e5bcdb97fc4096e779f335fc0f943547c1c91540c815"},
+    {file = "numpy-1.21.5-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:c5562bcc1a9b61960fc8950ade44d00e3de28f891af0acc96307c73613d18f6e"},
+    {file = "numpy-1.21.5-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:eed2afaa97ec33b4411995be12f8bdb95c87984eaa28d76cf628970c8a2d689a"},
+    {file = "numpy-1.21.5-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:61bada43d494515d5b122f4532af226fdb5ee08fe5b5918b111279843dc6836a"},
+    {file = "numpy-1.21.5-cp38-cp38-win32.whl", hash = "sha256:7b9d6b14fc9a4864b08d1ba57d732b248f0e482c7b2ff55c313137e3ed4d8449"},
+    {file = "numpy-1.21.5-cp38-cp38-win_amd64.whl", hash = "sha256:dbce7adeb66b895c6aaa1fad796aaefc299ced597f6fbd9ceddb0dd735245354"},
+    {file = "numpy-1.21.5-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:507c05c7a37b3683eb08a3ff993bd1ee1e6c752f77c2f275260533b265ecdb6c"},
+    {file = "numpy-1.21.5-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:00c9fa73a6989895b8815d98300a20ac993c49ac36c8277e8ffeaa3631c0dbbb"},
+    {file = "numpy-1.21.5-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:69a5a8d71c308d7ef33ef72371c2388a90e3495dbb7993430e674006f94797d5"},
+    {file = "numpy-1.21.5-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:2d8adfca843bc46ac199a4645233f13abf2011a0b2f4affc5c37cd552626f27b"},
+    {file = "numpy-1.21.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:c293d3c0321996cd8ffe84215ffe5d269fd9d1d12c6f4ffe2b597a7c30d3e593"},
+    {file = "numpy-1.21.5-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3c978544be9e04ed12016dd295a74283773149b48f507d69b36f91aa90a643e5"},
+    {file = "numpy-1.21.5-cp39-cp39-win32.whl", hash = "sha256:2a9add27d7fc0fdb572abc3b2486eb3b1395da71e0254c5552b2aad2a18b5441"},
+    {file = "numpy-1.21.5-cp39-cp39-win_amd64.whl", hash = "sha256:1964db2d4a00348b7a60ee9d013c8cb0c566644a589eaa80995126eac3b99ced"},
+    {file = "numpy-1.21.5-pp37-pypy37_pp73-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:a7c4b701ca418cd39e28ec3b496e6388fe06de83f5f0cb74794fa31cfa384c02"},
+    {file = "numpy-1.21.5.zip", hash = "sha256:6a5928bc6241264dce5ed509e66f33676fc97f464e7a919edc672fb5532221ee"},
     {file = "numpy-1.22.2-cp310-cp310-macosx_10_14_x86_64.whl", hash = "sha256:515a8b6edbb904594685da6e176ac9fbea8f73a5ebae947281de6613e27f1956"},
     {file = "numpy-1.22.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:76a4f9bce0278becc2da7da3b8ef854bed41a991f4226911a24a9711baad672c"},
     {file = "numpy-1.22.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:168259b1b184aa83a514f307352c25c56af111c269ffc109d9704e81f72e764b"},
@@ -500,8 +538,8 @@ pathspec = [
     {file = "pathspec-0.9.0.tar.gz", hash = "sha256:e564499435a2673d586f6b2130bb5b95f04a3ba06f81b8f895b651a3c76aabb1"},
 ]
 platformdirs = [
-    {file = "platformdirs-2.4.1-py3-none-any.whl", hash = "sha256:1d7385c7db91728b83efd0ca99a5afb296cab9d0ed8313a45ed8ba17967ecfca"},
-    {file = "platformdirs-2.4.1.tar.gz", hash = "sha256:440633ddfebcc36264232365d7840a970e75e1018d15b4327d11f91909045fda"},
+    {file = "platformdirs-2.5.1-py3-none-any.whl", hash = "sha256:bcae7cab893c2d310a711b70b24efb93334febe65f8de776ee320b517471e227"},
+    {file = "platformdirs-2.5.1.tar.gz", hash = "sha256:7535e70dfa32e84d4b34996ea99c5e432fa29a708d0f4e394bbcb2a8faa4f16d"},
 ]
 pydicom = [
     {file = "pydicom-2.2.2-py3-none-any.whl", hash = "sha256:6ecb9c6d56a20b2104099b8ef8fe0f3664d797b08a0e0548fe0311b515b32308"},
@@ -512,8 +550,8 @@ pyparsing = [
     {file = "pyparsing-3.0.7.tar.gz", hash = "sha256:18ee9022775d270c55187733956460083db60b37d0d0fb357445f3094eed3eea"},
 ]
 tomli = [
-    {file = "tomli-2.0.0-py3-none-any.whl", hash = "sha256:b5bde28da1fed24b9bd1d4d2b8cba62300bfb4ec9a6187a957e8ddb9434c5224"},
-    {file = "tomli-2.0.0.tar.gz", hash = "sha256:c292c34f58502a1eb2bbb9f5bbc9a5ebc37bee10ffb8c2d6bbdfa8eb13cc14e1"},
+    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
+    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
 ]
 typed-ast = [
     {file = "typed_ast-1.5.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:183b183b7771a508395d2cbffd6db67d6ad52958a5fdc99f450d954003900266"},
@@ -542,8 +580,8 @@ typed-ast = [
     {file = "typed_ast-1.5.2.tar.gz", hash = "sha256:525a2d4088e70a9f75b08b3f87a51acc9cde640e19cc523c7e41aa355564ae27"},
 ]
 typing-extensions = [
-    {file = "typing_extensions-4.0.1-py3-none-any.whl", hash = "sha256:7f001e5ac290a0c0401508864c7ec868be4e701886d5b573a9528ed3973d9d3b"},
-    {file = "typing_extensions-4.0.1.tar.gz", hash = "sha256:4ca091dea149f945ec56afb48dae714f21e8692ef22a395223bcd328961b6a0e"},
+    {file = "typing_extensions-4.1.1-py3-none-any.whl", hash = "sha256:21c85e0fe4b9a155d0799430b0ad741cdce7e359660ccbd8b530613e8df88ce2"},
+    {file = "typing_extensions-4.1.1.tar.gz", hash = "sha256:1a9462dcc3347a79b1f1c0271fbe79e844580bb598bafa1ed208b94da3cdcd42"},
 ]
 zipp = [
     {file = "zipp-3.7.0-py3-none-any.whl", hash = "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375"},

From 9b8f140508177acccb8a209a6ff81f85285ce707 Mon Sep 17 00:00:00 2001
From: Jonathan Daniel <jonathand655@gmail.com>
Date: Sun, 6 Mar 2022 00:08:05 +0200
Subject: [PATCH 4/5] Remove an unnecessary comment

---
 medio/backends/itk_io.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/medio/backends/itk_io.py b/medio/backends/itk_io.py
index 989e39c..498035b 100644
--- a/medio/backends/itk_io.py
+++ b/medio/backends/itk_io.py
@@ -58,9 +58,7 @@ def read_img(
         if (desired_axcodes is None) or (desired_axcodes == metadata.ornt):
             image_np = ItkIO.itk_img_to_array(img)
         else:
-            orig_ornt = (
-                metadata.ornt
-            )  # store the original orientation before the reorientation
+            orig_ornt = metadata.ornt
             img, _ = ItkIO.reorient(img, desired_axcodes)
             image_np, affine = ItkIO.unpack_img(img)
             metadata = MetaData(

From 49f4ad15849395635483c895ff1fc39fd7aee12c Mon Sep 17 00:00:00 2001
From: Jonathan Daniel <jonathand655@gmail.com>
Date: Sun, 6 Mar 2022 00:18:41 +0200
Subject: [PATCH 5/5] Move some comments above

Avoid black's line breaks
---
 medio/backends/itk_io.py                          | 15 ++++++++-------
 medio/backends/pdcm_io.py                         |  5 ++---
 medio/backends/pdcm_unpack_ds.py                  |  5 ++---
 medio/metadata/affine.py                          |  5 ++---
 .../itk_dcm_orientations/itk_dcm_orientations.py  | 10 ++++------
 tests/itk_dcm_orientations/itk_utils.py           |  5 ++---
 6 files changed, 20 insertions(+), 25 deletions(-)

diff --git a/medio/backends/itk_io.py b/medio/backends/itk_io.py
index 498035b..1557c2a 100644
--- a/medio/backends/itk_io.py
+++ b/medio/backends/itk_io.py
@@ -205,10 +205,12 @@ def save_img_file_long(image, filename, compression=False):
 
     @staticmethod
     def itk_img_to_array(img_itk):
-        """Swap the axes to the usual x, y, z convention in RAI orientation (originally z, y, x)"""
-        img_array = itk.array_from_image(
-            img_itk
-        ).T  # the transpose here is equivalent to keep_axes=True
+        """
+        Swap the axes to the usual x, y, z convention in RAI orientation
+        (originally z, y, x)
+        """
+        # the transpose here is equivalent to keep_axes=True
+        img_array = itk.array_from_image(img_itk).T
         return img_array
 
     @staticmethod
@@ -220,9 +222,8 @@ def array_to_itk_img(img_array, components_axis=None):
                 img_array, components_axis, ItkIO.DEFAULT_COMPONENTS_AXIS
             )
             is_vector = True
-        img_itk = itk.image_from_array(
-            img_array.T.copy(), is_vector=is_vector
-        )  # copy is crucial for the ordering
+        # copy is crucial for the ordering
+        img_itk = itk.image_from_array(img_array.T.copy(), is_vector=is_vector)
         return img_itk
 
     @staticmethod
diff --git a/medio/backends/pdcm_io.py b/medio/backends/pdcm_io.py
index 00b204d..1dad647 100644
--- a/medio/backends/pdcm_io.py
+++ b/medio/backends/pdcm_io.py
@@ -44,9 +44,8 @@ def read_img(
         :return: numpy array and metadata
         """
         input_path = Path(input_path)
-        temp_channels_axis = (
-            -1
-        )  # if there are channels, they must be in the last axis for the reorientation
+        # if there are channels, they must be in the last axis for the reorientation
+        temp_channels_axis = -1
         if input_path.is_dir():
             img, metadata, channeled = PdcmIO.read_dcm_dir(
                 input_path,
diff --git a/medio/backends/pdcm_unpack_ds.py b/medio/backends/pdcm_unpack_ds.py
index e938fd4..91b5695 100644
--- a/medio/backends/pdcm_unpack_ds.py
+++ b/medio/backends/pdcm_unpack_ds.py
@@ -85,9 +85,8 @@ def _unpack_pixel_array(dataset, rescale=None):
         rescale = _requires_rescaling(dataset)
 
     if rescale:
-        voxels = voxels.astype(
-            "int16", copy=False
-        )  # TODO: it takes time! Consider view.
+        # TODO: it takes time! Consider view.
+        voxels = voxels.astype("int16", copy=False)
         slope = getattr(dataset, "RescaleSlope", 1)
         intercept = getattr(dataset, "RescaleIntercept", 0)
         if int(slope) == slope and int(intercept) == intercept:
diff --git a/medio/metadata/affine.py b/medio/metadata/affine.py
index a450f4d..586340f 100644
--- a/medio/metadata/affine.py
+++ b/medio/metadata/affine.py
@@ -74,9 +74,8 @@ def spacing(self):
     def spacing(self, value):
         value = np.asarray(value)
         self._m_matrix = self._m_matrix @ np.diag(value / self._spacing)
-        self._spacing = np.abs(
-            value
-        )  # the spacing must be positive (or at least nonnegative)
+        # the spacing must be positive (or at least nonnegative)
+        self._spacing = np.abs(value)
 
     @property
     def direction(self):
diff --git a/tests/itk_dcm_orientations/itk_dcm_orientations.py b/tests/itk_dcm_orientations/itk_dcm_orientations.py
index ed1767f..f1431e8 100644
--- a/tests/itk_dcm_orientations/itk_dcm_orientations.py
+++ b/tests/itk_dcm_orientations/itk_dcm_orientations.py
@@ -33,12 +33,10 @@ def get_saved_ornt(image, desired_ornt, remove=True):
     return saved_ornt, is_equal
 
 
-arr = np.random.randint(
-    0, 256, size=(10, 30, 25), dtype="uint8"
-)  # (slices, cols, rows)
-arr_rgb = np.random.randint(
-    0, 256, size=(10, 30, 25, 3), dtype="uint8"
-)  # (slices, cols, rows, channels)
+# (slices, cols, rows)
+arr = np.random.randint(0, 256, size=(10, 30, 25), dtype="uint8")
+# (slices, cols, rows, channels)
+arr_rgb = np.random.randint(0, 256, size=(10, 30, 25, 3), dtype="uint8")
 img = itk.image_from_array(arr)
 img_rgb = itk.image_from_array(arr_rgb, is_vector=True)
 
diff --git a/tests/itk_dcm_orientations/itk_utils.py b/tests/itk_dcm_orientations/itk_utils.py
index 872d110..87c0289 100644
--- a/tests/itk_dcm_orientations/itk_utils.py
+++ b/tests/itk_dcm_orientations/itk_utils.py
@@ -3,9 +3,8 @@
 
 def set_image_direction(image, direction):
     dim = 3
-    direction_vnl_mat = itk.vnl_matrix_from_array(
-        direction.astype("float").copy()
-    )  # copy is crucial for the float
+    # copy is crucial for the float
+    direction_vnl_mat = itk.vnl_matrix_from_array(direction.astype("float").copy())
     direction_itk = itk.Matrix[itk.D, dim, dim](direction_vnl_mat)
     image.SetDirection(direction_itk)