Closed fridayghost closed 1 year ago
lucanchling
commented
1 year ago Can you check which version of monai you have on the Slicer's python, it should be 0.7.0 @fridayghost It seems like the error is coming from monai installation (here uninstallation of the version that you had to replace it by monai 0.7.0)
fridayghost
commented
1 year ago The installed version of monai is 0.7.0
juangmagic
commented
1 year ago I found the same error using 3D Slicer 5.2.2 and 5.3.0 when using the amass extension. The problem appears running on windows an MacOS.
========= ERROR =========
CLI execution failed:
AMASSS_CLI standard error:
Traceback (most recent call last):
File "
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Applications/Slicer.app/Contents/Extensions-31382/SlicerAutomatedDentalTools/lib/Slicer-5.2/cli-modules/AMASSS_CLI.py", line 1228, in
Same version of monai print(monai.version) 0.7.0
lucanchling
commented
1 year ago So the issue was due to the number of CPU workers selected as input. After multiple checkings, the computational time isn't impacted by only using one. The #36 PR has been created to fix this!
juangmagic
commented
1 year ago Awesome, using just one CPU unit solved the problem.... thank you very much.!
I tried running the extension on two separate devices, bone with GTX 1070ti and other with RTX 3050. Both gave the same error. Here is the error that i get in the python console.
Loading scan : C:/Users/frida/OneDrive/Desktop/CBCT/MG_test_scan.nii.gz Correcting scan contrast : C:/Users/frida/OneDrive/Desktop/CBCT/MG_test_scan.nii.gz Importing librairies... No module named 'logic' Found existing installation: monai 0.7.0 Uninstalling monai-0.7.0: ERROR: Exception: Traceback (most recent call last): File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\shutil.py", line 815, in move os.rename(src, real_dst) FileNotFoundError: [WinError 2] The system cannot find the file specified: 'c:\users\frida\appdata\local\slicer.org\slicer 5.3.0-2023-03-27\lib\python\lib\site-packages\monai-0.7.0.dist-info\' -> 'C:\Users\frida\AppData\Local\Temp\pip-uninstall-gg2psnif\monai-0.7.0.dist-info'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\site-packages\pip_internal\cli\base_command.py", line 160, in exc_logging_wrapper status = run_func(*args) File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\site-packages\pip_internal\commands\uninstall.py", line 105, in run uninstall_pathset = req.uninstall( File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\site-packages\pip_internal\req\req_install.py", line 664, in uninstall uninstalled_pathset.remove(auto_confirm, verbose) File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\site-packages\pip_internal\req\req_uninstall.py", line 373, in remove moved.stash(path) File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\site-packages\pip_internal\req\req_uninstall.py", line 271, in stash renames(path, new_path) File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\site-packages\pip_internal\utils\misc.py", line 312, in renames shutil.move(old, new) File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\shutil.py", line 835, in move copy_function(src, real_dst) File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\shutil.py", line 444, in copy2 copyfile(src, dst, follow_symlinks=follow_symlinks) File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\shutil.py", line 264, in copyfile with open(src, 'rb') as fsrc: FileNotFoundError: [Errno 2] No such file or directory: 'c:\users\frida\appdata\local\slicer.org\slicer 5.3.0-2023-03-27\lib\python\lib\site-packages\monai-0.7.0.dist-info\'
========= ERROR =========
CLI execution failed:
Traceback (most recent call last): File "", line 1, in
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\multiprocessing\spawn.py", line 116, in spawn_main
exitcode = _main(fd, parent_sentinel)
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\multiprocessing\spawn.py", line 125, in _main
prepare(preparation_data)
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\multiprocessing\spawn.py", line 236, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\multiprocessing\spawn.py", line 287, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\runpy.py", line 268, in run_path
return _run_module_code(code, init_globals, run_name,
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\runpy.py", line 87, in _run_code
exec(code, run_globals)
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\slicer.org\Extensions-31693\SlicerAutomatedDentalTools\lib\Slicer-5.3\cli-modules\AMASSS_CLI.py", line 71, in
pip_uninstall('monai')
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\bin\Python\slicer\util.py", line 3622, in pip_uninstall
_executePythonModule('pip', args)
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\bin\Python\slicer\util.py", line 3548, in _executePythonModule
logProcessOutput(proc)
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\bin\Python\slicer\util.py", line 3517, in logProcessOutput
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\bin/PythonSlicer.exe', '-m', 'pip', 'uninstall', 'monai', '--yes']' returned non-zero exit status 2.
Traceback (most recent call last):
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\site-packages\torch\utils\data\dataloader.py", line 1133, in _try_get_data
data = self._data_queue.get(timeout=timeout)
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\multiprocessing\queues.py", line 114, in get
raise Empty
_queue.Empty
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\slicer.org\Extensions-31693\SlicerAutomatedDentalTools\lib\Slicer-5.3\cli-modules\AMASSS_CLI.py", line 1220, in
main(args)
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\slicer.org\Extensions-31693\SlicerAutomatedDentalTools\lib\Slicer-5.3\cli-modules\AMASSS_CLI.py", line 908, in main
for step, batch in enumerate(pred_loader):
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\site-packages\torch\utils\data\dataloader.py", line 634, in next
data = self._next_data()
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\site-packages\torch\utils\data\dataloader.py", line 1329, in _next_data
idx, data = self._get_data()
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\site-packages\torch\utils\data\dataloader.py", line 1295, in _get_data
success, data = self._try_get_data()
File "C:\Users\frida\AppData\Local\slicer.org\Slicer 5.3.0-2023-03-27\lib\Python\Lib\site-packages\torch\utils\data\dataloader.py", line 1146, in _try_get_data
raise RuntimeError('DataLoader worker (pid(s) {}) exited unexpectedly'.format(pids_str)) from e
RuntimeError: DataLoader worker (pid(s) 22552) exited unexpectedly