Following up here I issued a PR to the SlicerNNUnet extension which is involved in installing acvl_utils and fixed the installation issues. So manually calling pip_install here is no longer needed as long as you have updated your extension to this latest version.
KitwareMedical:main ← jamesobutler:install-backports-from-slicertotalsegmentator
opened 12:13AM - 02 Jan 25 UTC
This includes several commits from the [SlicerTotalSegmentator](https://github.c… om/lassoan/SlicerTotalSegmentator) extension which had workaround fixes associated with installing nnunetv2 and its dependencies. As originally discussed at https://github.com/Slicer/ExtensionsIndex/pull/2016#issuecomment-2004337762, this extension is to serve as a way to centrally maintain the install of nnUNet in Slicer.
This therefore closes https://github.com/KitwareMedical/SlicerNNUnet/issues/10 where an error was observed during install of nnunetv2.
## Testing with SlicerDentalSegmentator
I have tested this in the context of [SlicerDentalSegmentator](https://github.com/gaudot/SlicerDentalSegmentator) where this closes https://github.com/gaudot/SlicerDentalSegmentator/issues/21. I am now able to run DentalSegmentator using the CBCT Dental Surgery sample data set and get successful results where previously I ran into issues during install of python packages. I used a fresh install of Slicer 5.7.0-2024-12-31 with a cleared out system pip cache so that all downloads would be fresh.
<details>
<summary>DentalSegmentator python console output click here</summary>
```
Python 3.9.10 (main, Dec 31 2024, 23:19:20) [MSC v.1939 64 bit (AMD64)] on win32
>>>
[Qt] void __cdecl qMRMLSegmentEditorWidget::setSourceVolumeNode(class vtkMRMLNode *) failed: need to set segment editor and segmentation nodes first
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Requirement already satisfied: threadpoolctl in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from batchgenerators->acvl_utils==0.2) (3.5.0)
Requirement already satisfied: networkx>=2.8 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from scikit-image->acvl_utils==0.2) (3.2.1)
Requirement already satisfied: imageio>=2.33 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from scikit-image->acvl_utils==0.2) (2.36.1)
Requirement already satisfied: tifffile>=2022.8.12 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from scikit-image->acvl_utils==0.2) (2024.8.30)
Requirement already satisfied: packaging>=21 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from scikit-image->acvl_utils==0.2) (24.0)
Requirement already satisfied: lazy-loader>=0.4 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from scikit-image->acvl_utils==0.2) (0.4)
Requirement already satisfied: filelock in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from torch->acvl_utils==0.2) (3.13.1)
Requirement already satisfied: typing-extensions>=4.8.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from torch->acvl_utils==0.2) (4.12.1)
Requirement already satisfied: jinja2 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from torch->acvl_utils==0.2) (3.1.5)
Requirement already satisfied: fsspec in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from torch->acvl_utils==0.2) (2024.2.0)
Requirement already satisfied: sympy==1.13.1 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from torch->acvl_utils==0.2) (1.13.1)
Requirement already satisfied: mpmath<1.4,>=1.1.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from sympy==1.13.1->torch->acvl_utils==0.2) (1.3.0)
Requirement already satisfied: MarkupSafe>=2.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from jinja2->torch->acvl_utils==0.2) (3.0.2)
Requirement already satisfied: python-dateutil>=2.8.2 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from pandas->batchgenerators->acvl_utils==0.2) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from pandas->batchgenerators->acvl_utils==0.2) (2024.2)
Requirement already satisfied: tzdata>=2022.7 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from pandas->batchgenerators->acvl_utils==0.2) (2024.2)
Requirement already satisfied: joblib>=1.2.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from scikit-learn->batchgenerators->acvl_utils==0.2) (1.4.2)
Collecting argparse (from unittest2->batchgenerators->acvl_utils==0.2)
Using cached argparse-1.4.0-py2.py3-none-any.whl.metadata (2.8 kB)
Requirement already satisfied: six>=1.4 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from unittest2->batchgenerators->acvl_utils==0.2) (1.16.0)
Requirement already satisfied: traceback2 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from unittest2->batchgenerators->acvl_utils==0.2) (1.4.0)
Requirement already satisfied: linecache2 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from traceback2->unittest2->batchgenerators->acvl_utils==0.2) (1.0.0)
Downloading connected_components_3d-3.22.0-cp39-cp39-win_amd64.whl (545 kB)
-------------------------------------- 545.5/545.5 kB 978.5 kB/s eta 0:00:00
Using cached argparse-1.4.0-py2.py3-none-any.whl (23 kB)
Building wheels for collected packages: acvl_utils
Building wheel for acvl_utils (setup.py): started
Building wheel for acvl_utils (setup.py): finished with status 'done'
Created wheel for acvl_utils: filename=acvl_utils-0.2-py3-none-any.whl size=22450 sha256=4dd58631f62b974d173a462023400c9d5b970cc13535e2723716f15d424e3f5b
Stored in directory: c:\users\butlej30383\appdata\local\pip\cache\wheels\db\79\df\6ffb48299bba36fd2fc5d14dc8ae7d1caa3416aa7e96d605b7
Successfully built acvl_utils
Installing collected packages: argparse, connected-components-3d, acvl_utils
Successfully installed acvl_utils-0.2 argparse-1.4.0 connected-components-3d-3.22.0
```
</details>
## Testing with SlicerTotalSegmentator
I have also tested this in the context of [SlicerTotalSegmentator](https://github.com/lassoan/SlicerTotalSegmentator) . I have issued https://github.com/lassoan/SlicerTotalSegmentator/pull/67 to switch SlicerTotalSegmentator to also use SlicerNNUnet extension to avoid this situation again where SlicerTotalSegmentator got fixes that SlicerNNUNet did not get. I used a fresh install of Slicer 5.7.0-2024-12-31 with a cleared out system pip cache so that all downloads would be fresh.
<details>
<summary>SlicerTotalSegmentator python console output click here</summary>
```python
Python 3.9.10 (main, Dec 31 2024, 23:19:20) [MSC v.1939 64 bit (AMD64)] on win32
>>>
Collecting pandas
Downloading pandas-2.2.3-cp39-cp39-win_amd64.whl.metadata (19 kB)
Requirement already satisfied: numpy>=1.22.4 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from pandas) (1.26.4)
Requirement already satisfied: python-dateutil>=2.8.2 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from pandas) (2.9.0.post0)
Collecting pytz>=2020.1 (from pandas)
Downloading pytz-2024.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas)
Downloading tzdata-2024.2-py2.py3-none-any.whl.metadata (1.4 kB)
Requirement already satisfied: six>=1.5 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from python-dateutil>=2.8.2->pandas) (1.16.0)
Downloading pandas-2.2.3-cp39-cp39-win_amd64.whl (11.6 MB)
---------------------------------------- 11.6/11.6 MB 6.5 MB/s eta 0:00:00
Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB)
---------------------------------------- 508.0/508.0 kB 8.0 MB/s eta 0:00:00
Downloading tzdata-2024.2-py2.py3-none-any.whl (346 kB)
---------------------------------------- 346.6/346.6 kB 2.0 MB/s eta 0:00:00
Installing collected packages: pytz, tzdata, pandas
Successfully installed pandas-2.2.3 pytz-2024.2 tzdata-2024.2
Collecting light-the-torch>=0.5
Downloading light_the_torch-0.8.0-py3-none-any.whl.metadata (9.3 kB)
Requirement already satisfied: pip<24.4,>=22.3 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from light-the-torch>=0.5) (24.0)
Downloading light_the_torch-0.8.0-py3-none-any.whl (14 kB)
Installing collected packages: light-the-torch
Successfully installed light-the-torch-0.8.0
Collecting torch>=2.0.0
Downloading https://download.pytorch.org/whl/cu124/torch-2.5.1%2Bcu124-cp39-cp39-win_amd64.whl (2510.7 MB)
---------------------------------------- 2.5/2.5 GB 1.4 MB/s eta 0:00:00
Collecting torchvision
Downloading https://download.pytorch.org/whl/cu124/torchvision-0.20.1%2Bcu124-cp39-cp39-win_amd64.whl (6.1 MB)
---------------------------------------- 6.1/6.1 MB 16.4 MB/s eta 0:00:00
Collecting filelock (from torch>=2.0.0)
Downloading https://download.pytorch.org/whl/filelock-3.13.1-py3-none-any.whl (11 kB)
Requirement already satisfied: typing-extensions>=4.8.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from torch>=2.0.0) (4.12.1)
Collecting networkx (from torch>=2.0.0)
Downloading https://download.pytorch.org/whl/networkx-3.2.1-py3-none-any.whl (1.6 MB)
---------------------------------------- 1.6/1.6 MB 17.6 MB/s eta 0:00:00
Collecting jinja2 (from torch>=2.0.0)
Downloading jinja2-3.1.5-py3-none-any.whl.metadata (2.6 kB)
Collecting fsspec (from torch>=2.0.0)
Downloading https://download.pytorch.org/whl/fsspec-2024.2.0-py3-none-any.whl (170 kB)
------------------------------------- 170.9/170.9 kB 10.0 MB/s eta 0:00:00
Collecting sympy==1.13.1 (from torch>=2.0.0)
Downloading https://download.pytorch.org/whl/sympy-1.13.1-py3-none-any.whl (6.2 MB)
---------------------------------------- 6.2/6.2 MB 18.8 MB/s eta 0:00:00
Collecting mpmath<1.4,>=1.1.0 (from sympy==1.13.1->torch>=2.0.0)
Downloading https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl (536 kB)
------------------------------------- 536.2/536.2 kB 17.0 MB/s eta 0:00:00
Requirement already satisfied: numpy in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from torchvision) (1.26.4)
Requirement already satisfied: pillow!=8.3.*,>=5.3.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from torchvision) (10.3.0)
Collecting MarkupSafe>=2.0 (from jinja2->torch>=2.0.0)
Downloading MarkupSafe-3.0.2-cp39-cp39-win_amd64.whl.metadata (4.1 kB)
Downloading jinja2-3.1.5-py3-none-any.whl (134 kB)
---------------------------------------- 134.6/134.6 kB 1.6 MB/s eta 0:00:00
Downloading MarkupSafe-3.0.2-cp39-cp39-win_amd64.whl (15 kB)
Installing collected packages: mpmath, sympy, networkx, MarkupSafe, fsspec, filelock, jinja2, torch, torchvision
Successfully installed MarkupSafe-3.0.2 filelock-3.13.1 fsspec-2024.2.0 jinja2-3.1.5 mpmath-1.3.0 networkx-3.2.1 sympy-1.13.1 torch-2.5.1+cu124 torchvision-0.20.1+cu124
Collecting nnunetv2>=2.2.1
Downloading nnunetv2-2.5.1.tar.gz (196 kB)
-------------------------------------- 197.0/197.0 kB 1.5 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: nnunetv2
Building wheel for nnunetv2 (pyproject.toml): started
Building wheel for nnunetv2 (pyproject.toml): finished with status 'done'
Created wheel for nnunetv2: filename=nnunetv2-2.5.1-py3-none-any.whl size=264428 sha256=2ad70af904a73190ecb38046a84d569b352f8421d6ca8b1a94ad512667b946c7
Stored in directory: c:\users\butlej30383\appdata\local\pip\cache\wheels\7b\85\af\51e5381b7cf9cc417ca071b9cd6e35afc59236a0ebb4462249
Successfully built nnunetv2
Installing collected packages: nnunetv2
Successfully installed nnunetv2-2.5.1
Collecting dynamic-network-architectures<0.4,>=0.3.1
Downloading dynamic_network_architectures-0.3.1.tar.gz (20 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: dynamic-network-architectures
Building wheel for dynamic-network-architectures (setup.py): started
Building wheel for dynamic-network-architectures (setup.py): finished with status 'done'
Created wheel for dynamic-network-architectures: filename=dynamic_network_architectures-0.3.1-py3-none-any.whl size=30056 sha256=8d7546a50ebdfbade048f7fcc67b577fd5b25971518e75e949b378afda3f6fc1
Stored in directory: c:\users\butlej30383\appdata\local\pip\cache\wheels\ec\59\c1\e65ad8b5ac7df95651f913251875b4cc8275644e0e28e82c63
Successfully built dynamic-network-architectures
Installing collected packages: dynamic-network-architectures
Successfully installed dynamic-network-architectures-0.3.1
Collecting tqdm
Downloading tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
-------------------------------------- 57.7/57.7 kB 435.2 kB/s eta 0:00:00
Downloading tqdm-4.67.1-py3-none-any.whl (78 kB)
---------------------------------------- 78.5/78.5 kB 2.2 MB/s eta 0:00:00
Installing collected packages: tqdm
Successfully installed tqdm-4.67.1
Collecting colorama
Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)
Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Installing collected packages: colorama
Successfully installed colorama-0.4.6
Collecting dicom2nifti
Downloading dicom2nifti-2.5.1-py3-none-any.whl.metadata (1.3 kB)
Downloading dicom2nifti-2.5.1-py3-none-any.whl (43 kB)
---------------------------------------- 43.6/43.6 kB 710.8 kB/s eta 0:00:00
Installing collected packages: dicom2nifti
Successfully installed dicom2nifti-2.5.1
Collecting nibabel
Downloading nibabel-5.3.2-py3-none-any.whl.metadata (9.1 kB)
Downloading nibabel-5.3.2-py3-none-any.whl (3.3 MB)
---------------------------------------- 3.3/3.3 MB 5.7 MB/s eta 0:00:00
Installing collected packages: nibabel
Successfully installed nibabel-5.3.2
Collecting importlib-resources>=5.12
Downloading importlib_resources-6.4.5-py3-none-any.whl.metadata (4.0 kB)
Downloading importlib_resources-6.4.5-py3-none-any.whl (36 kB)
Installing collected packages: importlib-resources
Successfully installed importlib-resources-6.4.5
Collecting zipp>=3.1.0
Downloading zipp-3.21.0-py3-none-any.whl.metadata (3.7 kB)
Downloading zipp-3.21.0-py3-none-any.whl (9.6 kB)
Installing collected packages: zipp
Successfully installed zipp-3.21.0
Collecting python-gdcm
Downloading python_gdcm-3.0.24.1-cp39-cp39-win_amd64.whl.metadata (3.8 kB)
Downloading python_gdcm-3.0.24.1-cp39-cp39-win_amd64.whl (28.9 MB)
---------------------------------------- 28.9/28.9 MB 4.8 MB/s eta 0:00:00
Installing collected packages: python-gdcm
Successfully installed python-gdcm-3.0.24.1
Collecting batchgenerators>=0.25
Downloading batchgenerators-0.25.1.tar.gz (76 kB)
-------------------------------------- 77.0/77.0 kB 717.5 kB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: batchgenerators
Building wheel for batchgenerators (setup.py): started
Building wheel for batchgenerators (setup.py): finished with status 'done'
Created wheel for batchgenerators: filename=batchgenerators-0.25.1-py3-none-any.whl size=93102 sha256=ef464be755e76bb5c5f81ec906759fcf230d0aecd0aaa1c655e8072c0a965788
Stored in directory: c:\users\butlej30383\appdata\local\pip\cache\wheels\97\8d\b9\3a9435d619b6a4bcd98f8cb8b324da29b6173555bb80860bdd
Successfully built batchgenerators
Installing collected packages: batchgenerators
Successfully installed batchgenerators-0.25.1
Collecting scikit-image
Downloading scikit_image-0.24.0-cp39-cp39-win_amd64.whl.metadata (14 kB)
Downloading scikit_image-0.24.0-cp39-cp39-win_amd64.whl (12.9 MB)
---------------------------------------- 12.9/12.9 MB 5.3 MB/s eta 0:00:00
Installing collected packages: scikit-image
Successfully installed scikit-image-0.24.0
Collecting imageio>=2.33
Downloading imageio-2.36.1-py3-none-any.whl.metadata (5.2 kB)
Downloading imageio-2.36.1-py3-none-any.whl (315 kB)
---------------------------------------- 315.4/315.4 kB 2.4 MB/s eta 0:00:00
Installing collected packages: imageio
Successfully installed imageio-2.36.1
Collecting tifffile>=2022.8.12
Downloading tifffile-2024.8.30-py3-none-any.whl.metadata (31 kB)
Downloading tifffile-2024.8.30-py3-none-any.whl (227 kB)
---------------------------------------- 227.3/227.3 kB 3.5 MB/s eta 0:00:00
Installing collected packages: tifffile
Successfully installed tifffile-2024.8.30
Collecting lazy-loader>=0.4
Downloading lazy_loader-0.4-py3-none-any.whl.metadata (7.6 kB)
Downloading lazy_loader-0.4-py3-none-any.whl (12 kB)
Installing collected packages: lazy-loader
Successfully installed lazy-loader-0.4
Collecting scikit-learn
Downloading scikit_learn-1.6.0-cp39-cp39-win_amd64.whl.metadata (15 kB)
Downloading scikit_learn-1.6.0-cp39-cp39-win_amd64.whl (11.1 MB)
---------------------------------------- 11.1/11.1 MB 6.2 MB/s eta 0:00:00
Installing collected packages: scikit-learn
Successfully installed scikit-learn-1.6.0
Collecting joblib>=1.2.0
Downloading joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)
Downloading joblib-1.4.2-py3-none-any.whl (301 kB)
---------------------------------------- 301.8/301.8 kB 1.6 MB/s eta 0:00:00
Installing collected packages: joblib
Successfully installed joblib-1.4.2
Collecting threadpoolctl>=3.1.0
Downloading threadpoolctl-3.5.0-py3-none-any.whl.metadata (13 kB)
Downloading threadpoolctl-3.5.0-py3-none-any.whl (18 kB)
Installing collected packages: threadpoolctl
Successfully installed threadpoolctl-3.5.0
Collecting future
Downloading future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
Downloading future-1.0.0-py3-none-any.whl (491 kB)
---------------------------------------- 491.3/491.3 kB 2.8 MB/s eta 0:00:00
Installing collected packages: future
Successfully installed future-1.0.0
Collecting unittest2
Downloading unittest2-1.1.0-py2.py3-none-any.whl.metadata (15 kB)
Downloading unittest2-1.1.0-py2.py3-none-any.whl (96 kB)
---------------------------------------- 96.4/96.4 kB 1.4 MB/s eta 0:00:00
Installing collected packages: unittest2
Successfully installed unittest2-1.1.0
Collecting argparse
Downloading argparse-1.4.0-py2.py3-none-any.whl.metadata (2.8 kB)
Downloading argparse-1.4.0-py2.py3-none-any.whl (23 kB)
Installing collected packages: argparse
Successfully installed argparse-1.4.0
Collecting traceback2
Downloading traceback2-1.4.0-py2.py3-none-any.whl.metadata (1.5 kB)
Downloading traceback2-1.4.0-py2.py3-none-any.whl (16 kB)
Installing collected packages: traceback2
Successfully installed traceback2-1.4.0
Collecting linecache2
Downloading linecache2-1.0.0-py2.py3-none-any.whl.metadata (1000 bytes)
Downloading linecache2-1.0.0-py2.py3-none-any.whl (12 kB)
Installing collected packages: linecache2
Successfully installed linecache2-1.0.0
Collecting graphviz
Downloading graphviz-0.20.3-py3-none-any.whl.metadata (12 kB)
Downloading graphviz-0.20.3-py3-none-any.whl (47 kB)
---------------------------------------- 47.1/47.1 kB 784.8 kB/s eta 0:00:00
Installing collected packages: graphviz
Successfully installed graphviz-0.20.3
Collecting matplotlib
Downloading matplotlib-3.9.4-cp39-cp39-win_amd64.whl.metadata (11 kB)
Downloading matplotlib-3.9.4-cp39-cp39-win_amd64.whl (7.8 MB)
---------------------------------------- 7.8/7.8 MB 4.5 MB/s eta 0:00:00
Installing collected packages: matplotlib
Successfully installed matplotlib-3.9.4
Collecting contourpy>=1.0.1
Downloading contourpy-1.3.0-cp39-cp39-win_amd64.whl.metadata (5.4 kB)
Downloading contourpy-1.3.0-cp39-cp39-win_amd64.whl (211 kB)
---------------------------------------- 211.8/211.8 kB 1.1 MB/s eta 0:00:00
Installing collected packages: contourpy
Successfully installed contourpy-1.3.0
Collecting cycler>=0.10
Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Installing collected packages: cycler
Successfully installed cycler-0.12.1
Collecting fonttools>=4.22.0
Downloading fonttools-4.55.3-cp39-cp39-win_amd64.whl.metadata (168 kB)
-------------------------------------- 168.5/168.5 kB 2.6 MB/s eta 0:00:00
Downloading fonttools-4.55.3-cp39-cp39-win_amd64.whl (2.2 MB)
---------------------------------------- 2.2/2.2 MB 4.7 MB/s eta 0:00:00
Installing collected packages: fonttools
Successfully installed fonttools-4.55.3
Collecting kiwisolver>=1.3.1
Downloading kiwisolver-1.4.7-cp39-cp39-win_amd64.whl.metadata (6.4 kB)
Downloading kiwisolver-1.4.7-cp39-cp39-win_amd64.whl (55 kB)
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Successfully installed kiwisolver-1.4.7
Collecting seaborn
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Collecting imagecodecs
Downloading imagecodecs-2024.12.30-1-cp39-cp39-win_amd64.whl.metadata (19 kB)
Downloading imagecodecs-2024.12.30-1-cp39-cp39-win_amd64.whl (28.9 MB)
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Collecting yacs
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Downloading yacs-0.1.8-py3-none-any.whl (14 kB)
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Successfully installed yacs-0.1.8
Collecting PyYAML
Downloading PyYAML-6.0.2-cp39-cp39-win_amd64.whl.metadata (2.1 kB)
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Installing collected packages: PyYAML
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Collecting batchgeneratorsv2>=0.2
Downloading batchgeneratorsv2-0.2.1.tar.gz (34 kB)
Installing build dependencies: started
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Getting requirements to build wheel: started
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Preparing metadata (pyproject.toml): started
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Building wheels for collected packages: batchgeneratorsv2
Building wheel for batchgeneratorsv2 (pyproject.toml): started
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Created wheel for batchgeneratorsv2: filename=batchgeneratorsv2-0.2.1-py3-none-any.whl size=45216 sha256=27475a00e9a4228188ad2a80b706c400c9d2bb41ba896ea4983e7fe54ad6b285
Stored in directory: c:\users\butlej30383\appdata\local\pip\cache\wheels\8c\29\14\3fdf4a97638724355746fb142b55db6868f1c0f1698af26ebd
Successfully built batchgeneratorsv2
Installing collected packages: batchgeneratorsv2
Successfully installed batchgeneratorsv2-0.2.1
Collecting fft-conv-pytorch
Downloading fft_conv_pytorch-1.2.0-py3-none-any.whl.metadata (2.8 kB)
Downloading fft_conv_pytorch-1.2.0-py3-none-any.whl (6.8 kB)
Installing collected packages: fft-conv-pytorch
Successfully installed fft-conv-pytorch-1.2.0
Collecting einops
Downloading einops-0.8.0-py3-none-any.whl.metadata (12 kB)
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Successfully installed einops-0.8.0
Collecting acvl_utils==0.2
Downloading acvl_utils-0.2.tar.gz (18 kB)
Preparing metadata (setup.py): started
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Requirement already satisfied: torch in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from acvl_utils==0.2) (2.5.1+cu124)
Requirement already satisfied: SimpleITK in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from acvl_utils==0.2) (2.4.0rc2.dev213)
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Collecting connected-components-3d (from acvl_utils==0.2)
Downloading connected_components_3d-3.22.0-cp39-cp39-win_amd64.whl.metadata (32 kB)
Requirement already satisfied: pillow>=7.1.2 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from batchgenerators->acvl_utils==0.2) (10.3.0)
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Requirement already satisfied: pandas in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from batchgenerators->acvl_utils==0.2) (2.2.3)
Requirement already satisfied: unittest2 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from batchgenerators->acvl_utils==0.2) (1.1.0)
Requirement already satisfied: threadpoolctl in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from batchgenerators->acvl_utils==0.2) (3.5.0)
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Requirement already satisfied: packaging>=21 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from scikit-image->acvl_utils==0.2) (24.0)
Requirement already satisfied: lazy-loader>=0.4 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from scikit-image->acvl_utils==0.2) (0.4)
Requirement already satisfied: filelock in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from torch->acvl_utils==0.2) (3.13.1)
Requirement already satisfied: typing-extensions>=4.8.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from torch->acvl_utils==0.2) (4.12.1)
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Requirement already satisfied: fsspec in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from torch->acvl_utils==0.2) (2024.2.0)
Requirement already satisfied: sympy==1.13.1 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from torch->acvl_utils==0.2) (1.13.1)
Requirement already satisfied: mpmath<1.4,>=1.1.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from sympy==1.13.1->torch->acvl_utils==0.2) (1.3.0)
Requirement already satisfied: MarkupSafe>=2.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from jinja2->torch->acvl_utils==0.2) (3.0.2)
Requirement already satisfied: python-dateutil>=2.8.2 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from pandas->batchgenerators->acvl_utils==0.2) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from pandas->batchgenerators->acvl_utils==0.2) (2024.2)
Requirement already satisfied: tzdata>=2022.7 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from pandas->batchgenerators->acvl_utils==0.2) (2024.2)
Requirement already satisfied: joblib>=1.2.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from scikit-learn->batchgenerators->acvl_utils==0.2) (1.4.2)
Collecting argparse (from unittest2->batchgenerators->acvl_utils==0.2)
Using cached argparse-1.4.0-py2.py3-none-any.whl.metadata (2.8 kB)
Requirement already satisfied: six>=1.4 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from unittest2->batchgenerators->acvl_utils==0.2) (1.16.0)
Requirement already satisfied: traceback2 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from unittest2->batchgenerators->acvl_utils==0.2) (1.4.0)
Requirement already satisfied: linecache2 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from traceback2->unittest2->batchgenerators->acvl_utils==0.2) (1.0.0)
Downloading connected_components_3d-3.22.0-cp39-cp39-win_amd64.whl (545 kB)
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Using cached argparse-1.4.0-py2.py3-none-any.whl (23 kB)
Building wheels for collected packages: acvl_utils
Building wheel for acvl_utils (setup.py): started
Building wheel for acvl_utils (setup.py): finished with status 'done'
Created wheel for acvl_utils: filename=acvl_utils-0.2-py3-none-any.whl size=22450 sha256=565173fa58e9c290bc076063b9a571d6180ba7ba9b545a89accc15ca6d731700
Stored in directory: c:\users\butlej30383\appdata\local\pip\cache\wheels\db\79\df\6ffb48299bba36fd2fc5d14dc8ae7d1caa3416aa7e96d605b7
Successfully built acvl_utils
Installing collected packages: argparse, connected-components-3d, acvl_utils
Successfully installed acvl_utils-0.2 argparse-1.4.0 connected-components-3d-3.22.0
Collecting https://github.com/wasserth/TotalSegmentator/archive/7274faac4673298d17b63a5a8335006f02e6d426.zip
Downloading https://github.com/wasserth/TotalSegmentator/archive/7274faac4673298d17b63a5a8335006f02e6d426.zip
/ 8.3 MB 5.0 MB/s 0:00:01
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: TotalSegmentator
Building wheel for TotalSegmentator (pyproject.toml): started
Building wheel for TotalSegmentator (pyproject.toml): finished with status 'done'
Created wheel for TotalSegmentator: filename=TotalSegmentator-2.4.0-py3-none-any.whl size=348319 sha256=d4b53e53e781f64db7518e79038ab07cd4dc3720572b612ce20068d3811b0560
Stored in directory: C:\Users\butlej30383\AppData\Local\Temp\pip-ephem-wheel-cache-shop__u8\wheels\d8\41\ce\20b3efb2dd6cebf94e551445b85bf8412c77d640fe7bd41cbb
Successfully built TotalSegmentator
Installing collected packages: TotalSegmentator
Successfully installed TotalSegmentator-2.4.0
Requirement already satisfied: numpy<2 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (1.26.4)
Requirement already satisfied: nibabel>=2.3.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (5.3.2)
Requirement already satisfied: importlib-resources>=5.12 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from nibabel>=2.3.0) (6.4.5)
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Requirement already satisfied: tqdm>=4.45.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (4.67.1)
Requirement already satisfied: colorama in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from tqdm>=4.45.0) (0.4.6)
Collecting p_tqdm
Downloading p_tqdm-1.4.2.tar.gz (6.0 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: tqdm>=4.45.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from p_tqdm) (4.67.1)
Collecting pathos>=0.2.5 (from p_tqdm)
Downloading pathos-0.3.3-py3-none-any.whl.metadata (11 kB)
Requirement already satisfied: six>=1.13.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from p_tqdm) (1.16.0)
Collecting ppft>=1.7.6.9 (from pathos>=0.2.5->p_tqdm)
Downloading ppft-1.7.6.9-py3-none-any.whl.metadata (12 kB)
Collecting dill>=0.3.9 (from pathos>=0.2.5->p_tqdm)
Downloading dill-0.3.9-py3-none-any.whl.metadata (10 kB)
Collecting pox>=0.3.5 (from pathos>=0.2.5->p_tqdm)
Downloading pox-0.3.5-py3-none-any.whl.metadata (8.0 kB)
Collecting multiprocess>=0.70.17 (from pathos>=0.2.5->p_tqdm)
Downloading multiprocess-0.70.17-py39-none-any.whl.metadata (7.2 kB)
Requirement already satisfied: colorama in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from tqdm>=4.45.0->p_tqdm) (0.4.6)
Downloading pathos-0.3.3-py3-none-any.whl (82 kB)
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Downloading dill-0.3.9-py3-none-any.whl (119 kB)
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Downloading pox-0.3.5-py3-none-any.whl (29 kB)
Downloading ppft-1.7.6.9-py3-none-any.whl (56 kB)
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Building wheels for collected packages: p_tqdm
Building wheel for p_tqdm (setup.py): started
Building wheel for p_tqdm (setup.py): finished with status 'done'
Created wheel for p_tqdm: filename=p_tqdm-1.4.2-py3-none-any.whl size=5426 sha256=9d00808bc6b757918c57dd5b8b837d71eda38aff24337ede80b337a47e6fe134
Stored in directory: c:\users\butlej30383\appdata\local\pip\cache\wheels\c1\d1\fa\5b7790c4da9b335ab699bbb968084fc6faaf3187f3c16a908e
Successfully built p_tqdm
Installing collected packages: ppft, pox, dill, multiprocess, pathos, p_tqdm
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
totalsegmentator 2.4.0 requires pyarrow, which is not installed.
totalsegmentator 2.4.0 requires xvfbwrapper, which is not installed.
Successfully installed dill-0.3.9 multiprocess-0.70.17 p_tqdm-1.4.2 pathos-0.3.3 pox-0.3.5 ppft-1.7.6.9
Collecting xvfbwrapper
Downloading xvfbwrapper-0.2.9.tar.gz (5.6 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: xvfbwrapper
Building wheel for xvfbwrapper (setup.py): started
Building wheel for xvfbwrapper (setup.py): finished with status 'done'
Created wheel for xvfbwrapper: filename=xvfbwrapper-0.2.9-py3-none-any.whl size=5028 sha256=a4f52962b0dafc97ad74551b86c9da42d39ba63e9dea12a4a4c47261bbc25a88
Stored in directory: c:\users\butlej30383\appdata\local\pip\cache\wheels\aa\09\0e\c0fa4c721cfb0a003121597a24181add912b7488054d2311ad
Successfully built xvfbwrapper
Installing collected packages: xvfbwrapper
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
totalsegmentator 2.4.0 requires pyarrow, which is not installed.
Successfully installed xvfbwrapper-0.2.9
Requirement already satisfied: dicom2nifti in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (2.5.1)
Requirement already satisfied: nibabel in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from dicom2nifti) (5.3.2)
Requirement already satisfied: numpy in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from dicom2nifti) (1.26.4)
Requirement already satisfied: scipy in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from dicom2nifti) (1.13.1)
Requirement already satisfied: pydicom>=2.2.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from dicom2nifti) (2.4.4)
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Requirement already satisfied: importlib-resources>=5.12 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from nibabel->dicom2nifti) (6.4.5)
Requirement already satisfied: packaging>=20 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from nibabel->dicom2nifti) (24.0)
Requirement already satisfied: typing-extensions>=4.6 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from nibabel->dicom2nifti) (4.12.1)
Requirement already satisfied: zipp>=3.1.0 in c:\users\butlej30383\appdata\local\slicer.org\slicer 5.7.0-2024-12-31\lib\python\lib\site-packages (from importlib-resources>=5.12->nibabel->dicom2nifti) (3.21.0)
Collecting pyarrow
Downloading pyarrow-18.1.0-cp39-cp39-win_amd64.whl.metadata (3.4 kB)
Downloading pyarrow-18.1.0-cp39-cp39-win_amd64.whl (25.3 MB)
---------------------------------------- 25.3/25.3 MB 6.0 MB/s eta 0:00:00
Installing collected packages: pyarrow
Successfully installed pyarrow-18.1.0
```
</details>
cc: @lassoan @Thibault-Pelletier
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