The siemes repository needs to be checked before it is handed to SIEMENS. The structure and usability should be prioritized.
Description
Description
Details
Details
- Deadline
- Mar 30 2022, 2:00 AM
Event Timeline
Comment Actions
- References to publications from Kausch et. al. should be added to the README.md
- package versions for deep_drr and c_arm pose should both be names following semvers, e.g. 0.0.1
- deep_drr setup defines wrong paths to binary scripts, it should be:
setup(name='deep_drr', packages=['deep_drr'], entry_points={ 'console_scripts': [ 'deepdrr_volume_segmentation = deep_drr.tools.run_volume_segmentation:main', 'deepdrr_projection = deep_drr.tools.run_deep_drr_projection:main' ] } )
- The commands in the REAMDE.md need more clarification for each of the options, e.g. specific patient names.
deepdrr_volume_segmentation --volumeDir VOLUMEDIR --saveDir SAVEDIR --patientList PATIENTLIST (separated by comma)
- Screw models should be copied to the Mitk distribution
- This part of the code does not work as a bash script. Running each command individually works though. The bash script should be located in the folder Screws and the full path to MitkBinaryMask.sh should be defined.
for d in */ ; do
echo "$d"
./MitkBinaryMask.sh -i Elements/Data/Spine/TrainData/Screws/${d%/}
doneComment Actions
- In Ubuntu 20.04 libtiff installtion might be broken and the following error might appear.
ValueError: Failed to find TIFF header file (may be need to run: sudo apt-get install libtiff4-dev)
The solution is to copy the header file /usr/include/x86_64-linux-gnu/tiff.h to the virtual environment include directory <path-to-venv>/include/
Comment Actions
- There are too many hard coded paths in the config files of deep drr: deep_drr/deep_drr/tools/deep_drr_config.py. Some of the paths also seem to be wrong and should be corrected
Comment Actions
- Running the commands breaks with the error FileNotFoundError: [Errno 2] No such file or directory: '.../Elements/Data/Spine/DRR/patients_LV4_tmp.txt'
from deep_drr.tools import deep_drr_config from deep_drr.tools import run_deep_drr_projection cf = deep_drr_config.get_cf_drr_spine(standard="AP", projection_type="drr", base_dir="/media/...") run_deep_drr_projection.main(cf)
Comment Actions
- nnunet requires some paths to be defined, and they are currently not defined, e.g. RESULTS_PATH
- Running carmpose_verse_CT --inputDir INPUTDIR --outputDIR OUTPUTDIR breaks with the following error
Please cite the following paper when using nnUNet: Isensee, F., Jaeger, P.F., Kohl, S.A.A. et al. "nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation." Nat Methods (2020). https://doi.org/10.1038/s41592-020-01008-z If you have questions or suggestions, feel free to open an issue at https://github.com/MIC-DKFZ/nnUNet nnUNet_raw_data_base is not defined and nnU-Net can only be used on data for which preprocessed files are already present on your system. nnU-Net cannot be used for experiment planning and preprocessing like this. If this is not intended, please read documentation/setting_up_paths.md for information on how to set this up properly. nnUNet_preprocessed is not defined and nnU-Net can not be used for preprocessing or training. If this is not intended, please read documentation/setting_up_paths.md for information on how to set this up. RESULTS_FOLDER is not defined and nnU-Net cannot be used for training or inference. If this is not intended behavior, please read documentation/setting_up_paths.md for information on how to set this up. Traceback (most recent call last): File "/home/menjivar/anaconda3/envs/siemens/bin/carmpose_verse_CT", line 33, in <module> sys.exit(load_entry_point('carm-pose', 'console_scripts', 'carmpose_verse_CT')()) File "/home/menjivar/anaconda3/envs/siemens/bin/carmpose_verse_CT", line 25, in importlib_load_entry_point return next(matches).load() File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/importlib/metadata.py", line 77, in load module = import_module(match.group('module')) File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "<frozen importlib._bootstrap>", line 1014, in _gcd_import File "<frozen importlib._bootstrap>", line 991, in _find_and_load File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 671, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 843, in exec_module File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed File "/home/menjivar/DKFZ/siemens/carm_pose/carm_pose/networks/run_verse_CT.py", line 1, in <module> from nnunet.inference.predict import predict_cases File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/nnunet/inference/predict.py", line 30, in <module> from nnunet.training.model_restore import load_model_and_checkpoint_files File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/nnunet/training/model_restore.py", line 20, in <module> from nnunet.training.network_training.nnUNetTrainer import nnUNetTrainer File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/nnunet/training/network_training/nnUNetTrainer.py", line 41, in <module> from nnunet.training.network_training.network_trainer import NetworkTrainer File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/nnunet/training/network_training/network_trainer.py", line 22, in <module> from sklearn.model_selection import KFold File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/__init__.py", line 64, in <module> from .base import clone File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/base.py", line 13, in <module> from .utils.fixes import signature File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/utils/__init__.py", line 14, in <module> from . import _joblib File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/utils/_joblib.py", line 22, in <module> from ..externals import joblib File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/externals/joblib/__init__.py", line 119, in <module> from .parallel import Parallel File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/externals/joblib/parallel.py", line 28, in <module> from ._parallel_backends import (FallbackToBackend, MultiprocessingBackend, File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/externals/joblib/_parallel_backends.py", line 22, in <module> from .executor import get_memmapping_executor File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/externals/joblib/executor.py", line 14, in <module> from .externals.loky.reusable_executor import get_reusable_executor File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/externals/joblib/externals/loky/__init__.py", line 12, in <module> from .backend.reduction import set_loky_pickler File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/externals/joblib/externals/loky/backend/reduction.py", line 125, in <module> from sklearn.externals.joblib.externals import cloudpickle # noqa: F401 File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/externals/joblib/externals/cloudpickle/__init__.py", line 3, in <module> from .cloudpickle import * File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/externals/joblib/externals/cloudpickle/cloudpickle.py", line 167, in <module> _cell_set_template_code = _make_cell_set_template_code() File "/home/menjivar/anaconda3/envs/siemens/lib/python3.8/site-packages/sklearn/externals/joblib/externals/cloudpickle/cloudpickle.py", line 148, in _make_cell_set_template_code return types.CodeType( TypeError: an integer is required (got type bytes)