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MIC-DKFZ / nnUNet

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Unable to use ResEnc presets #2314

Closed ajojosephthomas closed 3 months ago

ajojosephthomas commented 3 months ago

I'm trying to use the preset resenc, however running into following error with the following command: nnUNetv2_plan_and_preprocess -d 458 -pl nnUNetPlannerResEncL
Fingerprint extraction... Dataset458_Kidneys Experiment planning... Traceback (most recent call last): File "c:\users\mdq23at\appdata\local\programs\python\python38\lib\runpy.py", line 193, in _run_module_as_main return _run_code(code, main_globals, None, File "c:\users\mdq23at\appdata\local\programs\python\python38\lib\runpy.py", line 86, in _run_code exec(code, run_globals) File "C:\Users\mdq23at\AppData\Local\Programs\Python\Python38\Scripts\nnUNetv2_plan_and_preprocess.exe__main__.py", line 7, in
File "c:\users\mdq23at\appdata\local\programs\python\python38\lib\site-packages\nnunetv2\experiment_planning\plan_and_preprocess_entrypoints.py", line 177, in plan_and_preprocess_entry plan_experiments(args.d, args.pl, args.gpu_memory_target, args.preprocessor_name, args.overwrite_target_spacing, args.overwrite_plans_name) File "c:\users\mdq23at\appdata\local\programs\python\python38\lib\site-packages\nnunetv2\experiment_planning\plan_and_preprocess_api.py", line 82, in plan_experiments plan_experiment_dataset(d, experiment_planner, gpu_memory_target_in_gb, preprocess_class_name, File "c:\users\mdq23at\appdata\local\programs\python\python38\lib\site-packages\nnunetv2\experiment_planning\plan_and_preprocess_api.py", line 61, in plan_experiment_dataset return experiment_planner_class(dataset_id, TypeError: 'NoneType' object is not callable

I thought maybe because the data was already preprocessed, i could just command in 'plan experiment' but run into the following error where it requires a json file:

nnUNetv2_plan_experiment -d 458 -pl nnUNetPlannerResEncL

Preprocessing dataset Dataset458_Kidneys Traceback (most recent call last): File "c:\users\mdq23at\appdata\local\programs\python\python38\lib\runpy.py", line 193, in _run_module_as_main File "c:\users\mdq23at\appdata\local\programs\python\python38\lib\runpy.py", line 86, in _run_code exec(code, run_globals) File "C:\Users\mdq23at\AppData\Local\Programs\Python\Python38\Scripts\nnUNetv2_plan_experiment.exe__main__.py", line 7, in
File "c:\users\mdq23at\appdata\local\programs\python\python38\lib\site-packages\nnunetv2\experiment_planning\plan_and_preprocess_entrypoints.py", line 97, in preprocess_entry preprocess(args.d, args.plans_name, configurations=args.c, num_processes=args.np, verbose=args.verbose) File "c:\users\mdq23at\appdata\local\programs\python\python38\lib\site-packages\nnunetv2\experiment_planning\plan_and_preprocess_api.py", line 127, in preprocess preprocess_dataset(d, plans_identifier, configurations, num_processes, verbose) File "c:\users\mdq23at\appdata\local\programs\python\python38\lib\site-packages\nnunetv2\experiment_planning\plan_and_preprocess_api.py", line 105, in preprocess_dataset plans_manager = PlansManager(plans_file) File "c:\users\mdq23at\appdata\local\programs\python\python38\lib\site-packages\nnunetv2\utilities\plans_handling\plans_handler.py", line 190, in init self.plans = plans_file_or_dict if isinstance(plans_file_or_dict, dict) else load_json(plans_file_or_dict) File "c:\users\mdq23at\appdata\local\programs\python\python38\lib\site-packages\batchgenerators\utilities\file_and_folder_operations.py", line 68, in load_json with open(file, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: 'C:\Users\mdq23at\nnUNet\nnUNet_preprocessed\Dataset458_Kidneys\nnUNetPlannerResEncL.json'

dengzhuohao commented 3 weeks ago

i have the same question