diff --git a/pixi.lock b/pixi.lock
index ec588a12e2e1d4cf8caaa0ade8459d5c5834d85a..b992a9e41a8834d01f8eb042c0a07369879372cd 100644
--- a/pixi.lock
+++ b/pixi.lock
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- conda: https://conda.anaconda.org/conda-forge/noarch/editables-0.5-pyhd8ed1ab_0.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/entrypoints-0.4-pyhd8ed1ab_0.tar.bz2
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- conda: https://conda.anaconda.org/conda-forge/linux-64/ffmpeg-6.1.1-gpl_he44c6f3_112.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/huggingface_hub-0.23.3-pyhd8ed1ab_0.conda
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- conda: https://conda.anaconda.org/conda-forge/linux-64/libidn2-2.3.7-hd590300_0.conda
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- conda: https://conda.anaconda.org/conda-forge/linux-64/nh3-0.2.17-py312h4b3b743_0.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/shellingham-1.5.4-pyhd8ed1ab_0.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/tomlkit-0.12.5-pyha770c72_0.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/editables-0.5-pyhd8ed1ab_0.conda
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- conda: https://conda.anaconda.org/conda-forge/osx-arm64/ffmpeg-6.1.1-gpl_hc16618e_112.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/huggingface_hub-0.23.3-pyhd8ed1ab_0.conda
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- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libintl-devel-0.22.5-h8fbad5d_2.conda
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- conda: https://conda.anaconda.org/conda-forge/osx-arm64/nh3-0.2.17-py312h5280bc4_0.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/shellingham-1.5.4-pyhd8ed1ab_0.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/tomlkit-0.12.5-pyha770c72_0.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/editables-0.5-pyhd8ed1ab_0.conda
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- conda: https://conda.anaconda.org/conda-forge/linux-64/ffmpeg-6.1.1-gpl_he44c6f3_112.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/huggingface_hub-0.23.3-pyhd8ed1ab_0.conda
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- conda: https://conda.anaconda.org/conda-forge/linux-64/libidn2-2.3.7-hd590300_0.conda
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- conda: https://conda.anaconda.org/conda-forge/linux-64/nh3-0.2.17-py312h4b3b743_0.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.0-pyhd8ed1ab_2.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/expat-2.6.2-hebf3989_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/ffmpeg-6.1.1-gpl_hc16618e_112.conda
+ - conda: https://conda.anaconda.org/conda-forge/osx-arm64/fftw-3.3.10-nompi_h6637ab6_110.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.15.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/fmt-10.2.1-h2ffa867_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
@@ -4820,12 +4920,14 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/hdf4-4.2.15-h2ee6834_7.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/hdf5-1.14.3-nompi_hec07895_105.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/huggingface_hub-0.23.3-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/humanize-4.9.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/icu-73.2-hc8870d7_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.7-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/imagecodecs-2024.6.1-py311h038a4eb_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/imageio-2.34.1-pyh4b66e23_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/imath-3.1.11-h1059232_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-6.10.0-pyha770c72_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/jasper-4.2.4-h6c4e4ef_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.4-pyhd8ed1ab_0.conda
@@ -4875,6 +4977,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libidn2-2.3.7-h93a5062_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libintl-0.22.5-h8fbad5d_2.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libintl-devel-0.22.5-h8fbad5d_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/osx-arm64/libitk-5.3.0-h5b48add_8.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libjpeg-turbo-3.0.0-hb547adb_1.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libjxl-0.10.2-h07599a0_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libkml-1.3.0-h1eb4d9f_1018.conda
@@ -4931,6 +5034,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-hb89a1cb_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/nettle-3.9.1-h40ed0f5_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/networkx-3.3-pyhd8ed1ab_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/nibabel-5.2.1-pyha770c72_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/nspr-4.35-hb7217d7_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/nss-3.100-hc6e9f88_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/numpy-1.26.4-py311h7125741_0.conda
@@ -4980,6 +5084,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/scikit-learn-1.5.0-py311hbfb48bc_1.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/scipy-1.13.1-py311hceeca8c_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/osx-arm64/simpleitk-2.3.1-py311hbaf5611_2.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/smmap-5.0.0-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/snappy-1.2.0-hd04f947_1.conda
@@ -5000,6 +5105,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/toml-0.10.2-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/tomli-w-1.0.0-pyhd8ed1ab_0.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/noarch/torchio-0.19.7-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/torchmetrics-1.4.0.post0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/pytorch/osx-arm64/torchvision-0.17.2-py311_cpu.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/tqdm-4.66.4-pyhd8ed1ab_0.conda
@@ -7196,6 +7302,37 @@ packages:
- pkg:pypi/editables?source=conda-forge-mapping
size: 10988
timestamp: 1705857085102
+- kind: conda
+ name: eigen
+ version: 3.4.0
+ build: h00ab1b0_0
+ subdir: linux-64
+ url: https://conda.anaconda.org/conda-forge/linux-64/eigen-3.4.0-h00ab1b0_0.conda
+ sha256: 53b15a98aadbe0704479bacaf7a5618fcb32d1577be320630674574241639b34
+ md5: b1b879d6d093f55dd40d58b5eb2f0699
+ depends:
+ - libgcc-ng >=12
+ - libstdcxx-ng >=12
+ license: MPL-2.0
+ license_family: MOZILLA
+ purls: []
+ size: 1088433
+ timestamp: 1690272126173
+- kind: conda
+ name: eigen
+ version: 3.4.0
+ build: h1995070_0
+ subdir: osx-arm64
+ url: https://conda.anaconda.org/conda-forge/osx-arm64/eigen-3.4.0-h1995070_0.conda
+ sha256: c20b3677b16d8907343fce68e7c437184fef7f5ed0a765c104b775f8a485c5c9
+ md5: 3691ea3ff568ba38826389bafc717909
+ depends:
+ - libcxx >=15.0.7
+ license: MPL-2.0
+ license_family: MOZILLA
+ purls: []
+ size: 1087751
+ timestamp: 1690275869049
- kind: conda
name: entrypoints
version: '0.4'
@@ -7403,6 +7540,46 @@ packages:
purls: []
size: 9788322
timestamp: 1716145697248
+- kind: conda
+ name: fftw
+ version: 3.3.10
+ build: nompi_h6637ab6_110
+ build_number: 110
+ subdir: osx-arm64
+ url: https://conda.anaconda.org/conda-forge/osx-arm64/fftw-3.3.10-nompi_h6637ab6_110.conda
+ sha256: ba72f1d9384584c774d4e58ff3174818a20687f817e5edde3e0d23edff88fd72
+ md5: 622f99e8f4820c2ca1b208a3bb6ed5e6
+ depends:
+ - __osx >=11.0
+ - libcxx >=16
+ - libgfortran 5.*
+ - libgfortran5 >=12.3.0
+ - libgfortran5 >=13.2.0
+ - llvm-openmp >=16.0.6
+ license: GPL-2.0-or-later
+ license_family: GPL
+ purls: []
+ size: 763281
+ timestamp: 1717758160882
+- kind: conda
+ name: fftw
+ version: 3.3.10
+ build: nompi_hf1063bd_110
+ build_number: 110
+ subdir: linux-64
+ url: https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-nompi_hf1063bd_110.conda
+ sha256: 3cc58c9d9a8cc0089e3839ae5ff7ba4ddfc6df99d5f6a147fe90ea963bc6fe45
+ md5: ee3e687b78b778db7b304e5b00a4dca6
+ depends:
+ - libgcc-ng >=12
+ - libgfortran-ng
+ - libgfortran5 >=12.3.0
+ - libstdcxx-ng >=12
+ license: GPL-2.0-or-later
+ license_family: GPL
+ purls: []
+ size: 2075171
+ timestamp: 1717757963922
- kind: conda
name: filelock
version: 3.15.1
@@ -8726,6 +8903,23 @@ packages:
- pkg:pypi/huggingface-hub?source=conda-forge-mapping
size: 250766
timestamp: 1717617646190
+- kind: conda
+ name: humanize
+ version: 4.9.0
+ build: pyhd8ed1ab_0
+ subdir: noarch
+ noarch: python
+ url: https://conda.anaconda.org/conda-forge/noarch/humanize-4.9.0-pyhd8ed1ab_0.conda
+ sha256: 2764840b7ef7219af1288b27dfddbacc383fdf88af70980a355afdb2780f3c30
+ md5: f15cf5f33b0eca7b02c468ddb0cbf1ad
+ depends:
+ - python >=3.8
+ license: MIT
+ license_family: MIT
+ purls:
+ - pkg:pypi/humanize?source=conda-forge-mapping
+ size: 65116
+ timestamp: 1700608057210
- kind: conda
name: hyperframe
version: 6.0.1
@@ -11260,6 +11454,62 @@ packages:
purls: []
size: 38616
timestamp: 1712512805567
+- kind: conda
+ name: libitk
+ version: 5.3.0
+ build: h26001f5_8
+ build_number: 8
+ subdir: linux-64
+ url: https://conda.anaconda.org/conda-forge/linux-64/libitk-5.3.0-h26001f5_8.conda
+ sha256: 644b8e9c250b91ee38f72345c9d62c1dc3bd3e3d3a2ef9f3b991cef420152d73
+ md5: 26827b546cbbb741100a5be2c0c00c3b
+ depends:
+ - eigen
+ - expat
+ - fftw >=3.3.10,<4.0a0
+ - hdf5 >=1.14.2,<1.14.4.0a0
+ - libexpat >=2.5.0,<3.0a0
+ - libgcc-ng >=12
+ - libjpeg-turbo >=3.0.0,<4.0a0
+ - libpng >=1.6.39,<1.7.0a0
+ - libstdcxx-ng >=12
+ - libtiff >=4.6.0,<4.7.0a0
+ - libzlib >=1.2.13,<2.0.0a0
+ - tbb >=2021.10.0
+ - zlib
+ license: Apache-2.0
+ license_family: APACHE
+ purls: []
+ size: 10643159
+ timestamp: 1701489133491
+- kind: conda
+ name: libitk
+ version: 5.3.0
+ build: h5b48add_8
+ build_number: 8
+ subdir: osx-arm64
+ url: https://conda.anaconda.org/conda-forge/osx-arm64/libitk-5.3.0-h5b48add_8.conda
+ sha256: ca6ec870258201dbf245be9eab510e3400938a132f73e45078c10a87e798609d
+ md5: c2a0d8202f305efe9aa65f8395e374fb
+ depends:
+ - __osx >=10.9
+ - eigen
+ - expat
+ - fftw >=3.3.10,<4.0a0
+ - hdf5 >=1.14.2,<1.14.4.0a0
+ - libcxx >=16.0.6
+ - libexpat >=2.5.0,<3.0a0
+ - libjpeg-turbo >=3.0.0,<4.0a0
+ - libpng >=1.6.39,<1.7.0a0
+ - libtiff >=4.6.0,<4.7.0a0
+ - libzlib >=1.2.13,<2.0.0a0
+ - tbb >=2021.10.0
+ - zlib
+ license: Apache-2.0
+ license_family: APACHE
+ purls: []
+ size: 7110110
+ timestamp: 1701490808724
- kind: conda
name: libjpeg-turbo
version: 3.0.0
@@ -13618,7 +13868,7 @@ packages:
timestamp: 1704317789138
- kind: pypi
name: mednet
- version: 1.0.1.dev214+g1aab338.d20240613
+ version: 1.0.0b0
path: .
sha256: adff5bafa9edc506fbd485c396d2aefee9bfc29400b78e6d5950749ff33906ae
requires_dist:
@@ -14162,6 +14412,26 @@ packages:
- pkg:pypi/nh3?source=conda-forge-mapping
size: 582437
timestamp: 1711545995406
+- kind: conda
+ name: nibabel
+ version: 5.2.1
+ build: pyha770c72_0
+ subdir: noarch
+ noarch: python
+ url: https://conda.anaconda.org/conda-forge/noarch/nibabel-5.2.1-pyha770c72_0.conda
+ sha256: b5dd6d6ad4ba7c005567033c5ed6ecfbc34624c4d45fdd1882d5aeb9e5f04873
+ md5: 95ea4b21646fda1e2a34e0ddd895c9cc
+ depends:
+ - importlib_resources >=1.3
+ - numpy >=1.20
+ - packaging >=17
+ - python >=3.8
+ license: MIT
+ license_family: MIT
+ purls:
+ - pkg:pypi/nibabel?source=conda-forge-mapping
+ size: 2746114
+ timestamp: 1709044860369
- kind: conda
name: nodeenv
version: 1.9.1
@@ -17203,6 +17473,92 @@ packages:
- pkg:pypi/shellingham?source=conda-forge-mapping
size: 14568
timestamp: 1698144516278
+- kind: conda
+ name: simpleitk
+ version: 2.3.1
+ build: py311hb755f60_2
+ build_number: 2
+ subdir: linux-64
+ url: https://conda.anaconda.org/conda-forge/linux-64/simpleitk-2.3.1-py311hb755f60_2.conda
+ sha256: e0de95d1741616cd16d55366f4bb1914f03f0c752d87e5f1175622ff4615f977
+ md5: 7d9e0a06161dd3e2ac1645b795c40828
+ depends:
+ - libgcc-ng >=12
+ - libitk 5.3.0 h26001f5_8
+ - libstdcxx-ng >=12
+ - python >=3.11,<3.12.0a0
+ - python_abi 3.11.* *_cp311
+ license: Apache-2.0
+ license_family: APACHE
+ purls:
+ - pkg:pypi/simpleitk?source=conda-forge-mapping
+ size: 27193823
+ timestamp: 1701806692083
+- kind: conda
+ name: simpleitk
+ version: 2.3.1
+ build: py311hbaf5611_2
+ build_number: 2
+ subdir: osx-arm64
+ url: https://conda.anaconda.org/conda-forge/osx-arm64/simpleitk-2.3.1-py311hbaf5611_2.conda
+ sha256: 171f109f9b4b1168fe507f537b540254f59676950082d272f19b2874156ce8ba
+ md5: 08d5361ed17fc065e5c09299a68fb9b7
+ depends:
+ - __osx >=10.9
+ - libcxx >=16.0.6
+ - libitk 5.3.0 h5b48add_8
+ - python >=3.11,<3.12.0a0
+ - python >=3.11,<3.12.0a0 *_cpython
+ - python_abi 3.11.* *_cp311
+ license: Apache-2.0
+ license_family: APACHE
+ purls:
+ - pkg:pypi/simpleitk?source=conda-forge-mapping
+ size: 19036652
+ timestamp: 1701806985204
+- kind: conda
+ name: simpleitk
+ version: 2.3.1
+ build: py312h30efb56_2
+ build_number: 2
+ subdir: linux-64
+ url: https://conda.anaconda.org/conda-forge/linux-64/simpleitk-2.3.1-py312h30efb56_2.conda
+ sha256: 451728343600bd5a32321276bee00270d88c9d95ca24cf10717d4c182a017250
+ md5: c438d05b72c796456fb18da5aec4670d
+ depends:
+ - libgcc-ng >=12
+ - libitk 5.3.0 h26001f5_8
+ - libstdcxx-ng >=12
+ - python >=3.12,<3.13.0a0
+ - python_abi 3.12.* *_cp312
+ license: Apache-2.0
+ license_family: APACHE
+ purls:
+ - pkg:pypi/simpleitk?source=conda-forge-mapping
+ size: 26877326
+ timestamp: 1701806680140
+- kind: conda
+ name: simpleitk
+ version: 2.3.1
+ build: py312h650e478_2
+ build_number: 2
+ subdir: osx-arm64
+ url: https://conda.anaconda.org/conda-forge/osx-arm64/simpleitk-2.3.1-py312h650e478_2.conda
+ sha256: 60d2fa628b0badf8754a65d2dd7c62b75000a0b6dbec1c2e646b43f000842c99
+ md5: 3bc7cdff84074fa0844ae28ff84ec47f
+ depends:
+ - __osx >=10.9
+ - libcxx >=16.0.6
+ - libitk 5.3.0 h5b48add_8
+ - python >=3.12,<3.13.0a0
+ - python >=3.12,<3.13.0a0 *_cpython
+ - python_abi 3.12.* *_cp312
+ license: Apache-2.0
+ license_family: APACHE
+ purls:
+ - pkg:pypi/simpleitk?source=conda-forge-mapping
+ size: 18932800
+ timestamp: 1701807038993
- kind: conda
name: six
version: 1.16.0
@@ -18090,6 +18446,32 @@ packages:
- pkg:pypi/tomlkit?source=conda-forge-mapping
size: 37297
timestamp: 1715185504185
+- kind: conda
+ name: torchio
+ version: 0.19.7
+ build: pyhd8ed1ab_0
+ subdir: noarch
+ noarch: python
+ url: https://conda.anaconda.org/conda-forge/noarch/torchio-0.19.7-pyhd8ed1ab_0.conda
+ sha256: 9a5b75348350c0d976aa3752a9a1d712657010982df12401aef2b38424a54a0a
+ md5: d705b713c7e60f4729adca64ad457e4c
+ depends:
+ - click
+ - deprecated >=1.2.5
+ - humanize
+ - nibabel
+ - numpy
+ - python >=3.6,<3.13
+ - pytorch >=1.7
+ - scipy
+ - setuptools
+ - simpleitk !=2.0.*
+ - tqdm
+ license: Apache-2.0
+ purls:
+ - pkg:pypi/torchio?source=conda-forge-mapping
+ size: 120934
+ timestamp: 1718407590308
- kind: conda
name: torchmetrics
version: 1.4.0.post0
diff --git a/pyproject.toml b/pyproject.toml
index c5a5be4282f3acd6ab15c74fdc1d7dcc72869a40..1c3318d6672150b7545f73102c599550cfea25f8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -102,6 +102,7 @@ tensorboard = "*"
torchvision = { version = "~=0.17.2", channel = "pytorch" }
tqdm = "*"
versioningit = "*"
+torchio = ">=0.19.7,<0.20"
[tool.pixi.feature.self.pypi-dependencies]
mednet = { path = ".", editable = true }
@@ -245,6 +246,10 @@ alexnet-pretrained = "mednet.config.models.alexnet_pretrained"
densenet = "mednet.config.models.densenet"
densenet-pretrained = "mednet.config.models.densenet_pretrained"
+# 3D models
+pasa3d = "mednet.config.models.pasa3d"
+cnn3d = "mednet.config.models.cnn3d"
+
# lists of data augmentations
affine = "mednet.config.augmentations.affine"
elastic = "mednet.config.augmentations.elastic"
@@ -409,6 +414,9 @@ nih-cxr14-padchest = "mednet.config.data.nih_cxr14_padchest.idiap"
# montgomery-shenzhen-indian-padchest aggregated dataset
montgomery-shenzhen-indian-padchest = "mednet.config.data.montgomery_shenzhen_indian_padchest.default"
+# VISCERAL dataset
+visceral = "mednet.config.data.visceral.default"
+
[tool.ruff]
line-length = 88
target-version = "py310"