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rename some scripts #878

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merged 4 commits into from
Jan 22, 2024
Merged

rename some scripts #878

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be85578
rename script detect_dwi_volume_outliers
arnaudbore Jan 16, 2024
b9f25c2
quick update
arnaudbore Jan 19, 2024
de3085d
Merge branch 'master' into rename_scripts
arnaudbore Jan 22, 2024
fbf1da1
fix test
arnaudbore Jan 22, 2024
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quick update
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@arnaudbore
arnaudbore committed Jan 19, 2024
commit b9f25c2e13cac3da591d8a6d39d27bd3862a169b
2 changes: 0 additions & 2 deletions scripts/scil_dwi_detect_volume_outliers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,10 77,8 @@ def main():
continue

dot_product = np.clip(np.tensordot(shell, vec, axes=1), -1, 1)
# print(dot_product)
angle = np.arccos(dot_product) * 180 / math.pi
angle[np.isnan(angle)] = 0

idx = np.argpartition(angle, 4).tolist()
idx.remove(i)

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62 changes: 62 additions & 0 deletions scripts/tests/test_dwi_detect_volume_outliers.py
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Original file line number Diff line number Diff line change
@@ -0,0 1,62 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-

import os
import tempfile

from scilpy.io.fetcher import fetch_data, get_home, get_testing_files_dict

# If they already exist, this only takes 5 seconds (check md5sum)
fetch_data(get_testing_files_dict(), keys=['processing.zip'])
tmp_dir = tempfile.TemporaryDirectory()


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


def test_execution_processing_1000(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_dwi = os.path.join(get_home(), 'processing',
'dwi_crop.nii.gz')
in_bval = os.path.join(get_home(), 'processing',
'dwi.bval')
in_bvec = os.path.join(get_home(), 'processing',
'dwi.bvec')
ret = script_runner.run('scil_dwi_extract_shell.py', in_dwi,
in_bval, in_bvec, '0', '1000',
'dwi_crop_1000.nii.gz', '1000.bval', '1000.bvec',
'-t', '30')
assert ret.success


def test_execution_out_indices(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_dwi = os.path.join(get_home(), 'processing',
'dwi_crop.nii.gz')
in_bval = os.path.join(get_home(), 'processing',
'dwi.bval')
in_bvec = os.path.join(get_home(), 'processing',
'dwi.bvec')
ret = script_runner.run('scil_dwi_extract_shell.py', in_dwi,
in_bval, in_bvec, '0', '1000',
'dwi_crop_1000__1.nii.gz', '1000__1.bval',
'1000__1.bvec', '-t', '30', '--out_indices',
'out_indices.txt')
assert ret.success


def test_execution_processing_3000(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_dwi = os.path.join(get_home(), 'processing',
'dwi_crop.nii.gz')
in_bval = os.path.join(get_home(), 'processing',
'dwi.bval')
in_bvec = os.path.join(get_home(), 'processing',
'dwi.bvec')
ret = script_runner.run('scil_dwi_extract_shell.py', in_dwi,
in_bval, in_bvec, '0', '3000',
'dwi_crop_3000.nii.gz', '3000.bval', '3000.bvec',
'-t', '30')
assert ret.success