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Running airway with own 'raw_airway' using dicom data #17

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RobGhys opened this issue Jul 3, 2023 · 2 comments
Open

Running airway with own 'raw_airway' using dicom data #17

RobGhys opened this issue Jul 3, 2023 · 2 comments

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@RobGhys
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RobGhys commented Jul 3, 2023

Thanks for sharing this project.
We are trying to reproduce some results with our own dicom data (see Documents/dicompath), and wish to use the raw_airway DATA.
When updating the defaults.yaml local path to a folder that contains the data, we try to run the pipeline using:
airway stages 1

Here is the output of the command
(base) root:~/Documents/GitHub/Airway$ airway stages 1
[09:17:03] Running Airway
Using up to 8 workers
Using /home/robin/Documents/dicompath as data path
Stage processing order: 01

Traceback (most recent call last):
File "/home/robin/anaconda3/bin/airway", line 33, in
sys.exit(load_entry_point('airway==0.2.3', 'console_scripts', 'airway')())
File "/home/robin/anaconda3/lib/python3.10/site-packages/airway-0.2.3-py3.10.egg/airway/cli/cli.py", line 35, in main
handle_args()
File "/home/robin/anaconda3/lib/python3.10/site-packages/airway-0.2.3-py3.10.egg/airway/cli/cli.py", line 29, in handle_args
args.handle_args(args)
File "/home/robin/anaconda3/lib/python3.10/site-packages/airway-0.2.3-py3.10.egg/airway/cli/base.py", line 44, in _handle_args_wrapper
self.handle_args(args)
File "/home/robin/anaconda3/lib/python3.10/site-packages/airway-0.2.3-py3.10.egg/airway/cli/stages.py", line 191, in handle_args
self.stage(curr_stage_name, **self.stage_configs[curr_stage_name], **vars(args))
File "/home/robin/anaconda3/lib/python3.10/site-packages/airway-0.2.3-py3.10.egg/airway/cli/stages.py", line 281, in stage
self.concurrent_executor(subprocess_args, script_module, workers, tqdm_prefix=tqdm_prefix, verbose=verbose)
File "/home/robin/anaconda3/lib/python3.10/site-packages/airway-0.2.3-py3.10.egg/airway/cli/base.py", line 101, in concurrent_executor
stage_name = Path(subprocesses[0][3]).parent.name
IndexError: list index out of range

@LiquidFun
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What does your defaults.yaml look like? And what is the file structure of the raw_airway folder?

@tq-quan
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tq-quan commented Apr 25, 2024

Hello, have you successfully reproduced the results on your data?

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3 participants