Utility (utils) module¶
PyMIALSRTK utils functions.
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pymialsrtk.interfaces.utils.
reorder_by_run_ids
(p_files, p_order)[source]¶ Function used to reorder images by their run-id IDS tag.
The images are sorted according to the input parameters. If more images are available, they remaining are sorted in scending order.
Parameters: - <list<string>> (p_files) – List of image paths - containing a ‘run-‘ id tag, to be reordered
- <list<int>> (env) – List of expecting run id order.
Examples
>>> in_files = ['sub-01_run-2_T2w.nii.gz', 'sub-01_run-5_T2w.nii.gz', 'sub-01_run-3_T2w.nii.gz', 'sub-01_run-1_T2w.nii.gz'] >>> my_order = [1,5,3] >>> reorder_by_run_ids(in_files, my_order)
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pymialsrtk.interfaces.utils.
run
(command, env=None, cwd=None)[source]¶ Function calls by each MIALSRTK interface.
It runs the command specified as input via
subprocess.run()
.Parameters: - <string> (command) – String containing the command to be executed (required)
- <os.environ> (env) – Specify a custom os.environ
- <Directory> (cwd) – Specify a custom current working directory
Examples
>>> cmd = 'btkNLMDenoising -i "/path/to/in_file" -o "/path/to/out_file" -b 0.1' >>> run(cmd)
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pymialsrtk.interfaces.utils.
sort_ascending
(p_files)[source]¶ Function used to sort images at the input of a nipype node.
Parameters: <list<string>> (p_files) – List of image paths to be sorted in ascending order Examples
>>> in_files = ['sub-01_run-2_T2w.nii.gz', 'sub-01_run-5_T2w.nii.gz', 'sub-01_run-3_T2w.nii.gz', 'sub-01_run-1_T2w.nii.gz'] >>> sort_ascending(in_files)