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Update to Dipy 1.2.0 #384

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merged 12 commits into from
Sep 9, 2020
Merged

Update to Dipy 1.2.0 #384

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316b6af
install dipy from master
36000 Aug 26, 2020
d9ebdfa
try this
36000 Aug 26, 2020
8a98182
stop using same here
36000 Aug 26, 2020
2732d6d
add dipy imports
36000 Aug 27, 2020
37c7193
another tweak
36000 Aug 27, 2020
50b6bbc
another file not found fix
36000 Aug 27, 2020
7a7e842
brute force fix (ignore sl)
36000 Sep 1, 2020
2e40033
actually fix
36000 Sep 1, 2020
50e6b7f
try/except for defective streamlines
36000 Sep 2, 2020
2aa7437
more informative warning
36000 Sep 8, 2020
ff9fa79
update dipy to 1.2.0
36000 Sep 9, 2020
7250bfc
remove these warnings from this PR
36000 Sep 9, 2020
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8 changes: 4 additions & 4 deletions AFQ/api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1083,7 +1083,7 @@ def _export_rois(self, row):
row,
f'_desc-ROI-{bundle}-{ii + 1}-{inclusion}.nii.gz'))

fname = op.join(fname[0], rois_dir, fname[1])
fname = op.join(rois_dir, fname[1])
if not op.exists(fname):

warped_roi = auv.patch_up_roi(
Expand Down Expand Up @@ -1130,7 +1130,7 @@ def _export_bundles(self, row):
f'_tractography.trk',
include_track=True,
include_seg=True))
fname = op.join(fname[0], bundles_dir, fname[1])
fname = op.join(bundles_dir, fname[1])
self.log_and_save_trk(this_tgm, fname)
meta = dict(source=bundles_file)
meta_fname = fname.split('.')[0] + '.json'
Expand Down Expand Up @@ -1302,7 +1302,7 @@ def _viz_ROIs(self, row,
include_track=True,
include_seg=True))

fname = op.join(fname[0], roi_dir, fname[1])
fname = op.join(roi_dir, fname[1])
self.viz.create_gif(figure, fname)
else:
roi_dir = op.join(row['results_dir'], 'viz_bundles')
Expand All @@ -1315,7 +1315,7 @@ def _viz_ROIs(self, row,
include_track=True,
include_seg=True))

fname = op.join(fname[0], roi_dir, fname[1])
fname = op.join(roi_dir, fname[1])
figure.write_html(fname)
row['timing']['Visualization'] =\
row['timing']['Visualization'] + time() - start_time
Expand Down
2 changes: 1 addition & 1 deletion AFQ/tests/test_bundles.py
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Expand Up @@ -38,7 +38,7 @@ def test_bundles_class():
bundles_og.save_bundles(file_path=tmpdir)

# load bundles again
bundles = bdl.Bundles()
bundles = bdl.Bundles(reference=img)
bundle_names = ['CST_L', 'CST_R']
bundles.load_bundles(bundle_names, file_path=tmpdir)

Expand Down
2 changes: 1 addition & 1 deletion setup.cfg
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Expand Up @@ -28,7 +28,7 @@ python_requires = >=3.6
install_requires =
scikit_image==0.16.2
nibabel==3.0.2
dipy==1.1.1
dipy==1.2.0
scipy>=1.2.0
numpy==1.17.5
pandas==1.0.3
Expand Down