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I am getting following error while using. using comp2comp on MacOS
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.
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.
number of cases: 1
number of cases that still need to be predicted: 1
emptying cuda cache
loading parameters for folds, all
using the following model files: ['/Users/usman/Comp2Comp/comp2comp/utils/../../models/.totalsegmentator/nnunet/results/nnUNet/2d/Task927_FatMuscle/nnUNetTrainerV2__nnUNetPlansv2.1/all/model_final_checkpoint.model']
starting preprocessing generator
starting prediction...
ERROR PROCESSING /users/usman/documents/DICOM/AKTEST/DICOM/0000521E/AA0E35EF/AA676DAD/0000A7D0
Traceback (most recent call last):
File "/Users/usman/Comp2Comp/comp2comp/utils/process.py", line 131, in process_3d
pipeline(output_dir=output_dir, model_dir=model_dir)
File "/Users/usman/Comp2Comp/comp2comp/inference_pipeline.py", line 73, in call
output = inference_class(inference_pipeline=self, **output)
File "/Users/usman/Comp2Comp/comp2comp/inference_pipeline.py", line 69, in call
output = inference_class(
File "/Users/usman/Comp2Comp/comp2comp/muscle_adipose_tissue/muscle_adipose_tissue.py", line 96, in call
predict.predict_cases(
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/site-packages/nnunet/inference/predict.py", line 209, in predict_cases
for preprocessed in preprocessing:
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/site-packages/nnunet/inference/predict.py", line 109, in preprocess_multithreaded
pr.start()
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/context.py", line 284, in _Popen
return Popen(process_obj)
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 32, in init
super().init(process_obj)
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/popen_fork.py", line 19, in init
self._launch(process_obj)
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 47, in _launch
reduction.dump(process_obj, fp)
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/reduction.py", line 60, in dump
ForkingPickler(file, protocol).dump(obj)
AttributeError: Can't pickle local object 'nnUNetTrainerV2.initialize_network..'
I have defined the raw_data_base and result_folder but pickling error still persist
The text was updated successfully, but these errors were encountered:
I am getting following error while using. using comp2comp on MacOS
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.
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.
number of cases: 1
number of cases that still need to be predicted: 1
emptying cuda cache
loading parameters for folds, all
using the following model files: ['/Users/usman/Comp2Comp/comp2comp/utils/../../models/.totalsegmentator/nnunet/results/nnUNet/2d/Task927_FatMuscle/nnUNetTrainerV2__nnUNetPlansv2.1/all/model_final_checkpoint.model']
starting preprocessing generator
starting prediction...
ERROR PROCESSING /users/usman/documents/DICOM/AKTEST/DICOM/0000521E/AA0E35EF/AA676DAD/0000A7D0
Traceback (most recent call last):
File "/Users/usman/Comp2Comp/comp2comp/utils/process.py", line 131, in process_3d
pipeline(output_dir=output_dir, model_dir=model_dir)
File "/Users/usman/Comp2Comp/comp2comp/inference_pipeline.py", line 73, in call
output = inference_class(inference_pipeline=self, **output)
File "/Users/usman/Comp2Comp/comp2comp/inference_pipeline.py", line 69, in call
output = inference_class(
File "/Users/usman/Comp2Comp/comp2comp/muscle_adipose_tissue/muscle_adipose_tissue.py", line 96, in call
predict.predict_cases(
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/site-packages/nnunet/inference/predict.py", line 209, in predict_cases
for preprocessed in preprocessing:
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/site-packages/nnunet/inference/predict.py", line 109, in preprocess_multithreaded
pr.start()
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/context.py", line 284, in _Popen
return Popen(process_obj)
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 32, in init
super().init(process_obj)
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/popen_fork.py", line 19, in init
self._launch(process_obj)
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 47, in _launch
reduction.dump(process_obj, fp)
File "/Users/usman/Downloads/miniconda3/envs/c2c_env/lib/python3.9/multiprocessing/reduction.py", line 60, in dump
ForkingPickler(file, protocol).dump(obj)
AttributeError: Can't pickle local object 'nnUNetTrainerV2.initialize_network..'
I have defined the raw_data_base and result_folder but pickling error still persist
The text was updated successfully, but these errors were encountered: