semgnetaiton error - Githubissues

Hi Lukas, I got another error when I tried running segmentation: Thank you!

This is the log:

root@3d0c86b2bed5:/workspace/trustworthy-ai-fetal-brain-segmentation# python run_segment.py --input '/data/te80-15t-iFIND00134_T2-brain_SVR-output.nii.gz' --mask '/data/te80-15t-iFIND00134_T2-brain_SVR-output-mask-brain_bet-2.nii.gz' --output_folder '/data/pw' --ga 28 --condition 'Neurotypical' --bfc > /data/log.txt Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 568, in _build_master ws.require(requires) File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 886, in require needed = self.resolve(parse_requirements(requirements)) File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 777, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (scipy 1.6.3 (/opt/conda/lib/python3.8/site-packages), Requirement.parse('scipy<1.9.2,>=1.8; python_version <= "3.9"'), {'scikit-image'})

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/opt/conda/bin/nnUNet_predict", line 33, in sys.exit(load_entry_point('nnunet', 'console_scripts', 'nnUNet_predict')()) File "/opt/conda/bin/nnUNet_predict", line 25, in importlib_load_entry_point return next(matches).load() File "/opt/conda/lib/python3.8/importlib/metadata.py", line 77, in load module = import_module(match.group('module')) File "/opt/conda/lib/python3.8/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1014, in _gcd_import File "", line 991, in _find_and_load File "", line 975, in _find_and_load_unlocked File "", line 671, in _load_unlocked File "", line 848, in exec_module File "", line 219, in _call_with_frames_removed File "/workspace/third-party/nnUNet/nnunet/inference/predict_simple.py", line 17, in import torch File "/opt/conda/lib/python3.8/site-packages/torch/init.py", line 29, in from .torch_version import version as version File "/opt/conda/lib/python3.8/site-packages/torch/torch_version.py", line 4, in from pkg_resources import packaging # type: ignore[attr-defined] File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 3243, in def _initialize_master_working_set(): File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 3226, in _call_aside f(*args, **kwargs) File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 3255, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 570, in _build_master return cls._build_from_requirements(requires) File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 583, in _build_from_requirements dists = ws.resolve(reqs, Environment()) File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 777, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (scipy 1.6.3 (/opt/conda/lib/python3.8/site-packages), Requirement.parse('scipy<1.9.2,>=1.8; python_version <= "3.9"'), {'scikit-image'}) Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 568, in _build_master ws.require(requires) File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 886, in require needed = self.resolve(parse_requirements(requirements)) File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 777, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (scipy 1.6.3 (/opt/conda/lib/python3.8/site-packages), Requirement.parse('scipy<1.9.2,>=1.8; python_version <= "3.9"'), {'scikit-image'})

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/opt/conda/bin/nnUNet_ensemble", line 33, in sys.exit(load_entry_point('nnunet', 'console_scripts', 'nnUNet_ensemble')()) File "/opt/conda/bin/nnUNet_ensemble", line 25, in importlib_load_entry_point return next(matches).load() File "/opt/conda/lib/python3.8/importlib/metadata.py", line 77, in load module = import_module(match.group('module')) File "/opt/conda/lib/python3.8/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1014, in _gcd_import File "", line 991, in _find_and_load File "", line 975, in _find_and_load_unlocked File "", line 671, in _load_unlocked File "", line 848, in exec_module File "", line 219, in _call_with_frames_removed File "/workspace/third-party/nnUNet/nnunet/inference/ensemble_predictions.py", line 19, in from nnunet.inference.segmentation_export import save_segmentation_nifti_from_softmax File "/workspace/third-party/nnUNet/nnunet/inference/segmentation_export.py", line 22, in from batchgenerators.augmentations.utils import resize_segmentation File "/opt/conda/lib/python3.8/site-packages/batchgenerators/init.py", line 6, in import batchgenerators.dataloading File "/opt/conda/lib/python3.8/site-packages/batchgenerators/dataloading/init.py", line 3, in from .multi_threaded_augmenter import MultiThreadedAugmenter File "/opt/conda/lib/python3.8/site-packages/batchgenerators/dataloading/multi_threaded_augmenter.py", line 36, in import torch File "/opt/conda/lib/python3.8/site-packages/torch/init.py", line 29, in from .torch_version import version as version File "/opt/conda/lib/python3.8/site-packages/torch/torch_version.py", line 4, in from pkg_resources import packaging # type: ignore[attr-defined] File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 3243, in def _initialize_master_working_set(): File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 3226, in _call_aside f(*args, **kwargs) File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 3255, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 570, in _build_master return cls._build_from_requirements(requires) File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 583, in _build_from_requirements dists = ws.resolve(reqs, Environment()) File "/opt/conda/lib/python3.8/site-packages/pkg_resources/init.py", line 777, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (scipy 1.6.3 (/opt/conda/lib/python3.8/site-packages), Requirement.parse('scipy<1.9.2,>=1.8; python_version <= "3.9"'), {'scikit-image'}) Traceback (most recent call last): File "run_segment.py", line 169, in main(args) File "run_segment.py", line 95, in main softmax = load_softmax(pred_softmax_path, volume_info_path) File "/workspace/trustworthy-ai-fetal-brain-segmentation/src/deep_learning/inference_nnunet.py", line 33, in load_softmax softmax_cropped = np.load(softmax_path)['softmax'][None][0,...] File "/opt/conda/lib/python3.8/site-packages/numpy/lib/npyio.py", line 417, in load fid = stack.enter_context(open(os_fspath(file), "rb")) FileNotFoundError: [Errno 2] No such file or directory: '/data/pw/backboneAI/pw.npz'

LucasFidon / trustworthy-ai-fetal-brain-segmentation

semgnetaiton error #3