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rename dipy move_streamlines to transform_tracking_output #3412

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Merged
merged 3 commits into from
Mar 21, 2022
Merged

rename dipy move_streamlines to transform_tracking_output #3412

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rename dipy move_streamlines to transform_tracking_output
koenhelwegen Nov 22, 2021
0bfabab
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koenhelwegen Mar 21, 2022
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koenhelwegen Mar 21, 2022
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20 changes: 15 additions & 5 deletions nipype/interfaces/mrtrix/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,13 +40,16 @@ def get_data_dims(volume):


def transform_to_affine(streams, header, affine):
from dipy.tracking.utils import move_streamlines
try:
from dipy.tracking.utils import transform_tracking_output
except ImportError:
from dipy.tracking.utils import move_streamlines as transform_tracking_output

rotation, scale = np.linalg.qr(affine)
streams = move_streamlines(streams, rotation)
streams = transform_tracking_output(streams, rotation)
scale[0:3, 0:3] = np.dot(scale[0:3, 0:3], np.diag(1.0 / header["voxel_size"]))
scale[0:3, 3] = abs(scale[0:3, 3])
streams = move_streamlines(streams, scale)
streams = transform_tracking_output(streams, scale)
return streams


Expand Down Expand Up @@ -193,7 +196,14 @@ class MRTrix2TrackVis(DipyBaseInterface):
output_spec = MRTrix2TrackVisOutputSpec

def _run_interface(self, runtime):
from dipy.tracking.utils import move_streamlines, affine_from_fsl_mat_file
from dipy.tracking.utils import affine_from_fsl_mat_file

try:
from dipy.tracking.utils import transform_tracking_output
except ImportError:
from dipy.tracking.utils import (
move_streamlines as transform_tracking_output,
)

dx, dy, dz = get_data_dims(self.inputs.image_file)
vx, vy, vz = get_vox_dims(self.inputs.image_file)
Expand Down Expand Up @@ -243,7 +253,7 @@ def _run_interface(self, runtime):
axcode = aff2axcodes(reg_affine)
trk_header["voxel_order"] = axcode[0] + axcode[1] + axcode[2]

final_streamlines = move_streamlines(transformed_streamlines, aff)
final_streamlines = transform_tracking_output(transformed_streamlines, aff)
trk_tracks = ((ii, None, None) for ii in final_streamlines)
trk.write(out_filename, trk_tracks, trk_header)
iflogger.info("Saving transformed Trackvis file as %s", out_filename)
Expand Down