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lassoan / SlicerMONAIAuto3DSeg

Extension for 3D Slicer for running MONAI Auto3DSeg models
MIT License
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Downloaded models folder is not created and crash in Windows #1

Closed arpinerap closed 10 months ago

arpinerap commented 10 months ago

Folder ".MONAIAuto3DSeg" is not created, or not allowed to create, and download task fail.

lassoan commented 10 months ago

Thane for reporting, the issue has been fixed earlier today. You can get the updates from this repository now or update the extension tomorrow in the Extensions Manager.

rbumm commented 10 months ago

I have just tested again:with a newly downloaded extension. It extracted the models fine, But still got the

[image: image.png]

Python 3.9.10 (main, Dec 12 2023, 02:25:18) [MSC v.1935 64 bit (AMD64)] on win32

WARNING: Ignoring invalid distribution -illow (c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages)

Requirement already satisfied: monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm] in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (0.4.0)

WARNING: monai 0.4.0 does not provide the extra 'fire'

WARNING: monai 0.4.0 does not provide the extra 'pynrrd'

WARNING: monai 0.4.0 does not provide the extra 'pyyaml'

Requirement already satisfied: torch>=1.5 in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (1.13.1)

Requirement already satisfied: numpy>=1.17 in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (1.26.1)

Requirement already satisfied: nibabel in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (5.2.0)

Requirement already satisfied: psutil in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (5.9.6)

Requirement already satisfied: tensorboard in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (2.15.1)

Requirement already satisfied: scikit-image>=0.14.2 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (0.22.0)

Requirement already satisfied: tqdm>=4.47.0 in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (4.66.1)

Requirement already satisfied: itk in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (5.3.0)

Requirement already satisfied: scipy>=1.8 in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from scikit-image>=0.14.2->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (1.11.3)

Requirement already satisfied: networkx>=2.8 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from scikit-image>=0.14.2->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (3.2.1)

Requirement already satisfied: pillow>=9.0.1 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from scikit-image>=0.14.2->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (10.0.1)

Requirement already satisfied: imageio>=2.27 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from scikit-image>=0.14.2->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (2.33.1)

Requirement already satisfied: tifffile>=2022.8.12 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from scikit-image>=0.14.2->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (2023.12.9)

Requirement already satisfied: packaging>=21 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from scikit-image>=0.14.2->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (23.2)

Requirement already satisfied: lazy_loader>=0.3 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from scikit-image>=0.14.2->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (0.3)

Requirement already satisfied: typing-extensions in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from torch>=1.5->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (4.8.0)

Requirement already satisfied: colorama in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from tqdm>=4.47.0->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (0.4.6)

Requirement already satisfied: itk-core==5.3.0 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from itk->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (5.3.0)

Requirement already satisfied: itk-numerics==5.3.0 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from itk->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (5.3.0)

Requirement already satisfied: itk-io==5.3.0 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from itk->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (5.3.0)

Requirement already satisfied: itk-filtering==5.3.0 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from itk->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (5.3.0)

Requirement already satisfied: itk-registration==5.3.0 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from itk->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (5.3.0)

Requirement already satisfied: itk-segmentation==5.3.0 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from itk->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (5.3.0)

Requirement already satisfied: absl-py>=0.4 in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (2.0.0)

Requirement already satisfied: grpcio>=1.48.2 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (1.60.0)

Requirement already satisfied: google-auth<3,>=1.6.3 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (2.26.2)

Requirement already satisfied: google-auth-oauthlib<2,>=0.5 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (1.2.0)

Requirement already satisfied: markdown>=2.6.8 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (3.5.2)

Requirement already satisfied: protobuf<4.24,>=3.19.6 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (4.23.4)

Requirement already satisfied: requests<3,>=2.21.0 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (2.31.0)

Requirement already satisfied: setuptools>=41.0.0 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (68.2.2)

Requirement already satisfied: six>1.9 in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (1.16.0)

Requirement already satisfied: tensorboard-data-server<0.8.0,>=0.7.0 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (0.7.2)

Requirement already satisfied: werkzeug>=1.0.1 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (3.0.1)

Requirement already satisfied: cachetools<6.0,>=2.0.0 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from google-auth<3,>=1.6.3->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (5.3.2)

Requirement already satisfied: pyasn1-modules>=0.2.1 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from google-auth<3,>=1.6.3->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (0.3.0)

Requirement already satisfied: rsa<5,>=3.1.4 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from google-auth<3,>=1.6.3->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (4.9)

Requirement already satisfied: requests-oauthlib>=0.7.0 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from google-auth-oauthlib<2,>=0.5->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (1.3.1)

Requirement already satisfied: importlib-metadata>=4.4 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from markdown>=2.6.8->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (7.0.1)

Requirement already satisfied: charset-normalizer<4,>=2 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from requests<3,>=2.21.0->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (3.3.0)

Requirement already satisfied: idna<4,>=2.5 in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from requests<3,>=2.21.0->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (3.4)

Requirement already satisfied: urllib3<3,>=1.21.1 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from requests<3,>=2.21.0->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (2.0.6)

Requirement already satisfied: certifi>=2017.4.17 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from requests<3,>=2.21.0->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (2023.7.22)

Requirement already satisfied: MarkupSafe>=2.1.1 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from werkzeug>=1.0.1->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (2.1.3)

Requirement already satisfied: zipp>=0.5 in c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from importlib-metadata>=4.4->markdown>=2.6.8->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (3.17.0)

Requirement already satisfied: pyasn1<0.6.0,>=0.4.6 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from pyasn1-modules>=0.2.1->google-auth<3,>=1.6.3->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (0.5.1)

Requirement already satisfied: oauthlib>=3.0.0 in c:\users\rudol\appdata\local\slicer.org\slicer 5.6.1\lib\python\lib\site-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<2,>=0.5->tensorboard->monai[fire,itk,nibabel,psutil,pynrrd,pyyaml,skimage,tensorboard,tqdm]) (3.2.2)

WARNING: Ignoring invalid distribution -illow (c:\users\rudol\appdata\local\ slicer.org\slicer 5.6.1\lib\python\lib\site-packages)

[Python] Failed to compute results.

[Python] Command '['C:/Users/rudol/AppData/Local/slicer.org/Slicer 5.6.1/bin/../bin\PythonSlicer.EXE', '-m', 'monai.apps.auto3dseg', 'AutoRunner', 'run', '--input', 'C:\Users\rudol\.MONAIAuto3DSeg\models\17-segments-TotalSegmentator-v2\input.yaml', '--work_dir', 'C:\Users\rudol\.MONAIAuto3DSeg\models\17-segments-TotalSegmentator-v2', '--algos', 'segresnet', '--train=False', '--analyze=False', '--ensemble=True']' returned non-zero exit status 1.

Traceback (most recent call last):

File "C:/Users/rudol/OneDrive/Dokumente/MySlicerExtensions/SlicerMONAIAuto3DSeg-main/SlicerMONAIAuto3DSeg-main/MONAIAuto3DSeg/MONAIAuto3DSeg.py", line 296, in onApplyButton

self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),

File "C:/Users/rudol/OneDrive/Dokumente/MySlicerExtensions/SlicerMONAIAuto3DSeg-main/SlicerMONAIAuto3DSeg-main/MONAIAuto3DSeg/MONAIAuto3DSeg.py", line 780, in process

self.logProcessOutput(proc)

File "C:/Users/rudol/OneDrive/Dokumente/MySlicerExtensions/SlicerMONAIAuto3DSeg-main/SlicerMONAIAuto3DSeg-main/MONAIAuto3DSeg/MONAIAuto3DSeg.py", line 671, in logProcessOutput

raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)

subprocess.CalledProcessError: Command '['C:/Users/rudol/AppData/Local/ slicer.org/Slicer 5.6.1/bin/../bin\PythonSlicer.EXE', '-m', 'monai.apps.auto3dseg', 'AutoRunner', 'run', '--input', 'C:\Users\rudol\.MONAIAuto3DSeg\models\17-segments-TotalSegmentator-v2\input.yaml', '--work_dir', 'C:\Users\rudol\.MONAIAuto3DSeg\models\17-segments-TotalSegmentator-v2', '--algos', 'segresnet', '--train=False', '--analyze=False', '--ensemble=True']' returned non-zero exit status 1.

The model folder on my home file looks like this:

[image: image.png]

[image: image.png]

[image: image.png]

I will be traveling to Chur tomorrow and return on Friday, could do tests in the evening or on Saturday.

Best

Rudolf

Am Mi., 17. Jan. 2024 um 21:46 Uhr schrieb Andras Lasso < @.***>:

Thane for reporting, the issue has been fixed earlier today. You can get the updates from this repository now or update the extension tomorrow in the Extensions Manager.

— Reply to this email directly, view it on GitHub https://github.com/lassoan/SlicerMONAIAuto3DSeg/issues/1#issuecomment-1896661152, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEKMXPQJG2V3HGQGOVUT6YDYPA2BPAVCNFSM6AAAAABB7FD3RKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJWGY3DCMJVGI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

diazandr3s commented 10 months ago

Hi @rbumm,

I can't see the images you're referring to. It seems there was an error when uploading them. Can you please upload them again?

Thanks!

lassoan commented 10 months ago

Monai install is not related to this problem ("Downloaded models folder is not created and crash in Windows"). I'll move it to a new issue.