From d33157bad77bc44d0751867c51a4e7ccf751ba5c Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 31 Jan 2023 16:03:33 +0000
Subject: [PATCH] MNT: Fixes to a few feedsRun scripts
---
unit_tests/avwutils/fix_orient/feedsRun | 2 +-
unit_tests/avwutils/fslcomplex/feedsRun | 2 +-
unit_tests/fdt/dtifit/feedsRun | 8 +-------
unit_tests/fugue/applywarp/feedsRun | 4 ++--
4 files changed, 5 insertions(+), 11 deletions(-)
diff --git a/unit_tests/avwutils/fix_orient/feedsRun b/unit_tests/avwutils/fix_orient/feedsRun
index fceddda..0e0e575 100755
--- a/unit_tests/avwutils/fix_orient/feedsRun
+++ b/unit_tests/avwutils/fix_orient/feedsRun
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env fslpython
"""Test the standard recipe for fixing a broken orientation, from "The labels
in FSLView are wrong or missing and no conversion to NIfTI can fix this", on
this page:
diff --git a/unit_tests/avwutils/fslcomplex/feedsRun b/unit_tests/avwutils/fslcomplex/feedsRun
index 23986f7..a84cc1d 100755
--- a/unit_tests/avwutils/fslcomplex/feedsRun
+++ b/unit_tests/avwutils/fslcomplex/feedsRun
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env fslpython
"""Test that fslcomplex produces correct outputs. Specifically tests that the
output files have orientation info that matches that of the input files.
"""
diff --git a/unit_tests/fdt/dtifit/feedsRun b/unit_tests/fdt/dtifit/feedsRun
index a0b3c18..08d8799 100755
--- a/unit_tests/fdt/dtifit/feedsRun
+++ b/unit_tests/fdt/dtifit/feedsRun
@@ -132,7 +132,7 @@ def gen_data():
nib.Nifti1Image(S0, affine=affine).to_filename(f'{fdir}/ref_S0.nii.gz')
nib.Nifti1Image(data, affine=affine).to_filename(f'{fdir}/ref_data.nii.gz')
- nib.Nifti1Image(np.ones(data.shape[:3], dtype=int), affine=affine).to_filename(f'{fdir}/nodif_brain_mask.nii.gz')
+ nib.Nifti1Image(np.ones(data.shape[:3], dtype=np.int32), affine=affine).to_filename(f'{fdir}/nodif_brain_mask.nii.gz')
tensor_components = diffusion_tensor[:, :, :, [0, 0, 0, 1, 1, 2], [0, 1, 2, 1, 2, 2]]
nib.Nifti1Image(tensor_components, affine=affine).to_filename(f'{fdir}/ref_tensor.nii.gz')
@@ -260,9 +260,3 @@ for directory, multi_shell, kurt in gen_data():
ref = nib.load(f'{directory}/ref_L1.nii.gz').get_fdata()
fit = nib.load(f'{base_output}_L1.nii.gz').get_fdata()
assert not np.allclose(ref, fit, rtol=1e-3, atol=1e-6)
-
-
-
-
-
-
diff --git a/unit_tests/fugue/applywarp/feedsRun b/unit_tests/fugue/applywarp/feedsRun
index 0bba649..f990735 100755
--- a/unit_tests/fugue/applywarp/feedsRun
+++ b/unit_tests/fugue/applywarp/feedsRun
@@ -1,8 +1,8 @@
#!/usr/bin/env fslpython
-import os
+import os
import shlex
-import sys
+import sys
import subprocess as sp
import numpy as np
import nibabel as nib
--
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