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Rename dwi scripts #823

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merged 7 commits into from
Dec 1, 2023
Merged

Rename dwi scripts #823

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3850f33
Renaming scil_apply_bias_field_on_dwi.py to scil_dwi_apply_bias_field…
karanphil Dec 1, 2023
5140481
Renaming scil_extract_b0.py to scil_dwi_extract_b0.py.
karanphil Dec 1, 2023
0bc29f3
Renaming scil_extract_dwi_shell.py to scil_dwi_extract_shell.py.
karanphil Dec 1, 2023
1c92657
Renaming scil_split_dwi.py to scil_dwi_split_by_indices.py.
karanphil Dec 1, 2023
bb6fd82
Renaming scil_concatenate_dwi.py to scil_dwi_concatenate.py.
karanphil Dec 1, 2023
bdfba1d
Renaming scil_compute_powder_average.py to scil_dwi_powder_average.py.
karanphil Dec 1, 2023
0ae3714
Adding line at end of legacy files
karanphil Dec 1, 2023
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Renaming scil_apply_bias_field_on_dwi.py to scil_dwi_apply_bias_field… 
….py.
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@karanphil
karanphil committed Dec 1, 2023
commit 3850f33002eda4212d5c534f8585acdf6497d75a
20 changes: 20 additions & 0 deletions scripts/legacy/scil_apply_bias_field_on_dwi.py
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Original file line number Diff line number Diff line change
@@ -0,0 1,20 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-

from scilpy.io.deprecator import deprecate_script
from scripts.scil_dwi_apply_bias_field import main as new_main


DEPRECATION_MSG = """
This script has been renamed scil_dwi_apply_bias_field.py.
Please change your existing pipelines accordingly.
"""


@deprecate_script("scil_apply_bias_field_on_dwi.py", DEPRECATION_MSG, '1.7.0')
def main():
new_main()


if __name__ == "__main__":
main()
0 scripts/scil_apply_bias_field_on_dwi.py → scripts/scil_dwi_apply_bias_field.py
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File renamed without changes.
4 changes: 2 additions & 2 deletions ...pts/tests/test_apply_bias_field_on_dwi.py → scripts/tests/test_dwi_apply_bias_field.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 13,7 @@


def test_help_option(script_runner):
ret = script_runner.run('scil_apply_bias_field_on_dwi.py', '--help')
ret = script_runner.run('scil_dwi_apply_bias_field.py', '--help')
assert ret.success


Expand All @@ -23,6 23,6 @@ def test_execution_processing(script_runner):
'dwi_crop.nii.gz')
in_bias = os.path.join(get_home(), 'processing',
'bias_field_b0.nii.gz')
ret = script_runner.run('scil_apply_bias_field_on_dwi.py', in_dwi,
ret = script_runner.run('scil_dwi_apply_bias_field.py', in_dwi,
in_bias, 'dwi_crop_n4.nii.gz')
assert ret.success