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import os | ||
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from nipype.interfaces.base import CommandLineInputSpec, File, Str, TraitedSpec, traits | ||
from nipype.interfaces.workbench.base import WBCommand | ||
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class CreateSignedDistanceVolumeInputSpec(CommandLineInputSpec): | ||
surf_file = File( | ||
exists=True, | ||
mandatory=True, | ||
argstr="%s", | ||
position=0, | ||
desc="Input surface GIFTI file (.surf.gii)", | ||
) | ||
ref_file = File( | ||
exists=True, | ||
mandatory=True, | ||
argstr="%s", | ||
position=1, | ||
desc="NIfTI volume in the desired output space (dims, spacing, origin)", | ||
) | ||
out_file = File( | ||
name_source=["surf_file"], | ||
name_template="%s_distvol.nii.gz", | ||
argstr="%s", | ||
position=2, | ||
desc="Name of output volume containing signed distances", | ||
) | ||
out_mask = File( | ||
name_source=["surf_file"], | ||
name_template="%s_distmask.nii.gz", | ||
argstr="-roi-out %s", | ||
desc="Name of file to store a mask where the ``out_file`` has a computed value", | ||
) | ||
fill_value = traits.Float( | ||
0.0, | ||
mandatory=False, | ||
usedefault=True, | ||
argstr="-fill-value %f", | ||
desc="value to put in all voxels that don't get assigned a distance", | ||
) | ||
exact_limit = traits.Float( | ||
5.0, | ||
usedefault=True, | ||
argstr="-exact-limit %f", | ||
desc="distance for exact output in mm", | ||
) | ||
approx_limit = traits.Float( | ||
20.0, | ||
usedefault=True, | ||
argstr="-approx-limit %f", | ||
desc="distance for approximate output in mm", | ||
) | ||
approx_neighborhood = traits.Int( | ||
2, | ||
usedefault=True, | ||
argstr="-approx-neighborhood %d", | ||
desc="size of neighborhood cube measured from center to face in voxels, default 2 = 5x5x5", | ||
) | ||
winding_method = traits.Enum( | ||
"EVEN_ODD", | ||
"NEGATIVE", | ||
"NONZERO", | ||
"NORMALS", | ||
argstr="-winding %s", | ||
usedefault=True, | ||
desc="winding method for point inside surface test", | ||
) | ||
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class CreateSignedDistanceVolumeOutputSpec(TraitedSpec): | ||
out_file = File(desc="Name of output volume containing signed distances") | ||
out_mask = File( | ||
desc="Name of file to store a mask where the ``out_file`` has a computed value" | ||
) | ||
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class CreateSignedDistanceVolume(WBCommand): | ||
"""CREATE SIGNED DISTANCE VOLUME FROM SURFACE | ||
wb_command -create-signed-distance-volume | ||
<surface> - the input surface | ||
<refspace> - a volume in the desired output space (dims, spacing, origin) | ||
<outvol> - output - the output volume | ||
[-roi-out] - output an roi volume of where the output has a computed | ||
value | ||
<roi-vol> - output - the output roi volume | ||
[-fill-value] - specify a value to put in all voxels that don't get | ||
assigned a distance | ||
<value> - value to fill with (default 0) | ||
[-exact-limit] - specify distance for exact output | ||
<dist> - distance in mm (default 5) | ||
[-approx-limit] - specify distance for approximate output | ||
<dist> - distance in mm (default 20) | ||
[-approx-neighborhood] - voxel neighborhood for approximate calculation | ||
<num> - size of neighborhood cube measured from center to face, in | ||
voxels (default 2 = 5x5x5) | ||
[-winding] - winding method for point inside surface test | ||
<method> - name of the method (default EVEN_ODD) | ||
Computes the signed distance function of the surface. Exact distance is | ||
calculated by finding the closest point on any surface triangle to the | ||
center of the voxel. Approximate distance is calculated starting with | ||
these distances, using dijkstra's method with a neighborhood of voxels. | ||
Specifying too small of an exact distance may produce unexpected results. | ||
Valid specifiers for winding methods are as follows: | ||
EVEN_ODD (default) | ||
NEGATIVE | ||
NONZERO | ||
NORMALS | ||
The NORMALS method uses the normals of triangles and edges, or the | ||
closest triangle hit by a ray from the point. This method may be | ||
slightly faster, but is only reliable for a closed surface that does not | ||
cross through itself. All other methods count entry (positive) and exit | ||
(negative) crossings of a vertical ray from the point, then counts as | ||
inside if the total is odd, negative, or nonzero, respectively. | ||
""" | ||
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input_spec = CreateSignedDistanceVolumeInputSpec | ||
output_spec = CreateSignedDistanceVolumeOutputSpec | ||
_cmd = "wb_command -create-signed-distance-volume" |
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