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ENH: Add LibraryBaseInterface #2538

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Merged
satra merged 11 commits into from
Apr 15, 2018
Merged

ENH: Add LibraryBaseInterface #2538

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3b25528
ENH: Add LibraryBaseInterface
effigies Apr 11, 2018
3a54409
RF: NipyBaseInterface
effigies Apr 11, 2018
2723c61
RF: NitimeBaseInterface
effigies Apr 11, 2018
37c7895
RF: NilearnBaseInterface
effigies Apr 11, 2018
7a99c27
RF: CMTK with LibraryBaseInterface
effigies Apr 12, 2018
2c1e47b
RF: MRTrix2TrackVis is a DipyBaseInterface
effigies Apr 12, 2018
7e83fac
RF: algorithms.metric.Similarity is a NipyBaseInterface
effigies Apr 12, 2018
516ae7a
TEST: Update NBS import test
effigies Apr 12, 2018
be47ff8
TEST: Don't match error message string
effigies Apr 13, 2018
c3ee8d4
TEST: Drop unused import
effigies Apr 13, 2018
3d5661c
TEST: make specs
effigies Apr 14, 2018
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RF: MRTrix2TrackVis is a DipyBaseInterface
  • Loading branch information
@effigies
effigies committed Apr 12, 2018
commit 2c1e47b339d4027804291f55631f204f257c3eeb
18 changes: 6 additions & 12 deletions nipype/interfaces/mrtrix/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,23 +15,15 @@

from ... import logging
from ...utils.filemanip import split_filename
from ...utils.misc import package_check
from ...workflows.misc.utils import get_data_dims, get_vox_dims
from ..base import TraitedSpec, BaseInterface, File, isdefined

import warnings
have_dipy = True
try:
package_check('dipy')
except Exception as e:
have_dipy = False
else:
from dipy.tracking.utils import move_streamlines, affine_from_fsl_mat_file
from ..base import TraitedSpec, File, isdefined
from ..dipy.base import DipyBaseInterface, HAVE_DIPY as have_dipy

iflogger = logging.getLogger('interface')


def transform_to_affine(streams, header, affine):
from dipy.tracking.utils import move_streamlines
rotation, scale = np.linalg.qr(affine)
streams = move_streamlines(streams, rotation)
scale[0:3, 0:3] = np.dot(scale[0:3, 0:3],
Expand Down Expand Up @@ -168,7 +160,7 @@ class MRTrix2TrackVisOutputSpec(TraitedSpec):
out_file = File(exists=True)


class MRTrix2TrackVis(BaseInterface):
class MRTrix2TrackVis(DipyBaseInterface):
"""
Converts MRtrix (.tck) tract files into TrackVis (.trk) format
using functions from dipy
Expand All @@ -184,6 +176,8 @@ class MRTrix2TrackVis(BaseInterface):
output_spec = MRTrix2TrackVisOutputSpec

def _run_interface(self, runtime):
from dipy.tracking.utils import move_streamlines, \
affine_from_fsl_mat_file
dx, dy, dz = get_data_dims(self.inputs.image_file)
vx, vy, vz = get_vox_dims(self.inputs.image_file)
image_file = nb.load(self.inputs.image_file)
Expand Down