[Auto3DSeg] Error -- No such file or directory: 'python' -- Help please!!!

[imruljubair]

Hi,

I am new in Medical Image Segmentation. Thanks for developing such a cool method like Auto3DSeg. I really appreciate.

But, I am facing a problem while running the following codes for a custom dataset -

from monai.apps.auto3dseg import AutoRunner
import os
runner = AutoRunner(input="./input.yaml", work_dir="./work_dir")
runner.run()

I am getting errors. Here is the log:

2024-02-10 09:17:31.873957: I tensorflow/core/util/port.cc:111] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2024-02-10 09:17:31.918807: E tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:9342] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
2024-02-10 09:17:31.918878: E tensorflow/compiler/xla/stream_executor/cuda/cuda_fft.cc:609] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
2024-02-10 09:17:31.918928: E tensorflow/compiler/xla/stream_executor/cuda/cuda_blas.cc:1518] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2024-02-10 09:17:31.927975: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-02-10 09:17:32.862539: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-02-10 09:17:33,532 - INFO - AutoRunner using work directory /mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir
2024-02-10 09:17:33,533 - INFO - Loading input config /mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/input.yaml
2024-02-10 09:17:33,533 - INFO - Datalist was copied to work_dir: /mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/folds.json
2024-02-10 09:17:33,534 - INFO - Setting num_fold 4 based on the input datalist /mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/folds.json.
2024-02-10 09:17:33,548 - INFO - Using user defined command running prefix , will override other settings
2024-02-10 09:17:33,549 - INFO - Running data analysis...
2024-02-10 09:17:33,549 - INFO - Found 1 GPUs for data analyzing!
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 48/48 [00:14<00:00,  3.38it/s]
2024-02-10 09:17:48,063 - INFO - Data spacing is not completely uniform. MONAI transforms may provide unexpected result
2024-02-10 09:17:48,063 - INFO - Writing data stats to /mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/datastats.yaml.
2024-02-10 09:17:48,082 - INFO - Writing by-case data stats to /mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/datastats_by_case.yaml, this may take a while.
2024-02-10 09:17:48,887 - INFO - BundleGen from https://github.com/Project-MONAI/research-contributions/releases/download/algo_templates/249bf4b.tar.gz
algo_templates.tar.gz: 104kB [00:00, 217kB/s]                                                                                                                                                                     
2024-02-10 09:17:49,379 - INFO - Downloaded: /tmp/tmpvb268law/algo_templates.tar.gz
2024-02-10 09:17:49,380 - INFO - Expected md5 is None, skip md5 check for file /tmp/tmpvb268law/algo_templates.tar.gz.
2024-02-10 09:17:49,380 - INFO - Writing into directory: /mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir.
2024-02-10 09:17:49,683 - INFO - Generated:/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/dints_0
2024-02-10 09:17:49,764 - INFO - Generated:/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/dints_1
2024-02-10 09:17:49,844 - INFO - Generated:/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/dints_2
2024-02-10 09:17:49,924 - INFO - Generated:/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/dints_3
2024-02-10 09:17:49,986 - INFO - Generated:/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/segresnet_0
2024-02-10 09:17:50,038 - INFO - Generated:/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/segresnet_1
2024-02-10 09:17:50,090 - INFO - Generated:/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/segresnet_2
2024-02-10 09:17:50,142 - INFO - Generated:/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/segresnet_3
2024-02-10 09:17:50,178 - INFO - segresnet2d_0 is skipped! SegresNet2D is skipped due to median spacing of [0.8000030517578125, 0.7291666865348816, 0.7310606241226196],  which means the dataset is not highly anisotropic, e.g. spacing[2] < 3*(spacing[0] + spacing[1])/2) .
2024-02-10 09:17:50,207 - INFO - segresnet2d_1 is skipped! SegresNet2D is skipped due to median spacing of [0.8000030517578125, 0.7291666865348816, 0.7310606241226196],  which means the dataset is not highly anisotropic, e.g. spacing[2] < 3*(spacing[0] + spacing[1])/2) .
2024-02-10 09:17:50,235 - INFO - segresnet2d_2 is skipped! SegresNet2D is skipped due to median spacing of [0.8000030517578125, 0.7291666865348816, 0.7310606241226196],  which means the dataset is not highly anisotropic, e.g. spacing[2] < 3*(spacing[0] + spacing[1])/2) .
2024-02-10 09:17:50,264 - INFO - segresnet2d_3 is skipped! SegresNet2D is skipped due to median spacing of [0.8000030517578125, 0.7291666865348816, 0.7310606241226196],  which means the dataset is not highly anisotropic, e.g. spacing[2] < 3*(spacing[0] + spacing[1])/2) .
2024-02-10 09:17:50,327 - INFO - Generated:/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/swinunetr_0
2024-02-10 09:17:50,389 - INFO - Generated:/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/swinunetr_1
2024-02-10 09:17:50,450 - INFO - Generated:/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/swinunetr_2
2024-02-10 09:17:50,511 - INFO - Generated:/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/swinunetr_3
2024-02-10 09:17:50,620 - INFO - ['python', '/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/dints_0/scripts/train.py', 'run', "--config_file='/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/dints_0/configs/hyper_parameters.yaml,/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/dints_0/configs/hyper_parameters_search.yaml,/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/dints_0/configs/network.yaml,/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/dints_0/configs/network_search.yaml,/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/dints_0/configs/transforms_infer.yaml,/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/dints_0/configs/transforms_train.yaml,/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/dints_0/configs/transforms_validate.yaml'"]
Traceback (most recent call last):
  File "/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/hvsmr48.py", line 43, in <module>
    runner.run()
  File "/home/moju3572/.local/lib/python3.10/site-packages/monai/apps/auto3dseg/auto_runner.py", line 806, in run
    self._train_algo_in_sequence(history)
  File "/home/moju3572/.local/lib/python3.10/site-packages/monai/apps/auto3dseg/auto_runner.py", line 658, in _train_algo_in_sequence
    algo.train(self.train_params, self.device_setting)
  File "/mnt/datastore/jubair/datasets/For_MONAI/tasks/HVSMR48_raw/work_dir/algorithm_templates/dints/scripts/algo.py", line 490, in train
    return self._run_cmd(cmd, devices_info)
  File "/home/moju3572/.local/lib/python3.10/site-packages/monai/apps/auto3dseg/bundle_gen.py", line 255, in _run_cmd
    return run_cmd(cmd.split(), run_cmd_verbose=True, env=ps_environ, check=True)
  File "/home/moju3572/.local/lib/python3.10/site-packages/monai/utils/misc.py", line 874, in run_cmd
    return subprocess.run(cmd_list, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 503, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/usr/lib/python3.10/subprocess.py", line 971, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1863, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python'

But, different folders with algos are created in the work_dir. Can anyone help me? I use python3.

[imruljubair]

Okay. I solved the problem. I had to install python-is-python3 package.