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STY: Flake8 fix RobustRegister
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‎nipype/interfaces/freesurfer/preprocess.py

Lines changed: 70 additions & 45 deletions
Original file line numberDiff line numberDiff line change
@@ -1457,77 +1457,102 @@ def _gen_filename(self, name):
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class RobustRegisterInputSpec(FSTraitedSpec):
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1460-
source_file = File(mandatory=True, argstr='--mov %s',
1460+
source_file = File(exists=True, mandatory=True, argstr='--mov %s',
14611461
desc='volume to be registered')
1462-
target_file = File(mandatory=True, argstr='--dst %s',
1462+
target_file = File(exists=True, mandatory=True, argstr='--dst %s',
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desc='target volume for the registration')
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out_reg_file = traits.Either(
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True, File, default=True, usedefault=True, argstr='--lta %s',
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desc='registration file; either True or filename')
1467-
registered_file = traits.Either(traits.Bool, File, argstr='--warp %s',
1468-
desc='registered image; either True or filename')
1469-
weights_file = traits.Either(traits.Bool, File, argstr='--weights %s',
1470-
desc='weights image to write; either True or filename')
1471-
est_int_scale = traits.Bool(argstr='--iscale',
1472-
desc='estimate intensity scale (recommended for unnormalized images)')
1467+
registered_file = traits.Either(
1468+
traits.Bool, File, argstr='--warp %s',
1469+
desc='registered image; either True or filename')
1470+
weights_file = traits.Either(
1471+
traits.Bool, File, argstr='--weights %s',
1472+
desc='weights image to write; either True or filename')
1473+
est_int_scale = traits.Bool(
1474+
argstr='--iscale',
1475+
desc='estimate intensity scale (recommended for unnormalized images)')
14731476
trans_only = traits.Bool(argstr='--transonly',
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desc='find 3 parameter translation only')
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in_xfm_file = File(exists=True, argstr='--transform',
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desc='use initial transform on source')
1477-
half_source = traits.Either(traits.Bool, File, argstr='--halfmov %s',
1478-
desc="write source volume mapped to halfway space")
1479-
half_targ = traits.Either(traits.Bool, File, argstr="--halfdst %s",
1480-
desc="write target volume mapped to halfway space")
1481-
half_weights = traits.Either(traits.Bool, File, argstr="--halfweights %s",
1482-
desc="write weights volume mapped to halfway space")
1483-
half_source_xfm = traits.Either(traits.Bool, File, argstr="--halfmovlta %s",
1484-
desc="write transform from source to halfway space")
1485-
half_targ_xfm = traits.Either(traits.Bool, File, argstr="--halfdstlta %s",
1486-
desc="write transform from target to halfway space")
1487-
auto_sens = traits.Bool(argstr='--satit', xor=['outlier_sens'], mandatory=True,
1488-
desc='auto-detect good sensitivity')
1489-
outlier_sens = traits.Float(argstr='--sat %.4f', xor=['auto_sens'], mandatory=True,
1490-
desc='set outlier sensitivity explicitly')
1491-
least_squares = traits.Bool(argstr='--leastsquares',
1492-
desc='use least squares instead of robust estimator')
1480+
half_source = traits.Either(
1481+
traits.Bool, File, argstr='--halfmov %s',
1482+
desc="write source volume mapped to halfway space")
1483+
half_targ = traits.Either(
1484+
traits.Bool, File, argstr="--halfdst %s",
1485+
desc="write target volume mapped to halfway space")
1486+
half_weights = traits.Either(
1487+
traits.Bool, File, argstr="--halfweights %s",
1488+
desc="write weights volume mapped to halfway space")
1489+
half_source_xfm = traits.Either(
1490+
traits.Bool, File, argstr="--halfmovlta %s",
1491+
desc="write transform from source to halfway space")
1492+
half_targ_xfm = traits.Either(
1493+
traits.Bool, File, argstr="--halfdstlta %s",
1494+
desc="write transform from target to halfway space")
1495+
auto_sens = traits.Bool(
1496+
argstr='--satit', xor=['outlier_sens'], mandatory=True,
1497+
desc='auto-detect good sensitivity')
1498+
outlier_sens = traits.Float(
1499+
argstr='--sat %.4f', xor=['auto_sens'], mandatory=True,
1500+
desc='set outlier sensitivity explicitly')
1501+
least_squares = traits.Bool(
1502+
argstr='--leastsquares',
1503+
desc='use least squares instead of robust estimator')
14931504
no_init = traits.Bool(argstr='--noinit', desc='skip transform init')
1494-
init_orient = traits.Bool(argstr='--initorient',
1495-
desc='use moments for initial orient (recommended for stripped brains)')
1505+
init_orient = traits.Bool(
1506+
argstr='--initorient',
1507+
desc='use moments for initial orient (recommended for stripped brains)'
1508+
)
14961509
max_iterations = traits.Int(argstr='--maxit %d',
14971510
desc='maximum # of times on each resolution')
14981511
high_iterations = traits.Int(argstr='--highit %d',
14991512
desc='max # of times on highest resolution')
1500-
iteration_thresh = traits.Float(argstr='--epsit %.3f',
1501-
desc='stop iterations when below threshold')
1502-
subsample_thresh = traits.Int(argstr='--subsample %d',
1503-
desc='subsample if dimension is above threshold size')
1513+
iteration_thresh = traits.Float(
1514+
argstr='--epsit %.3f', desc='stop iterations when below threshold')
1515+
subsample_thresh = traits.Int(
1516+
argstr='--subsample %d',
1517+
desc='subsample if dimension is above threshold size')
15041518
outlier_limit = traits.Float(argstr='--wlimit %.3f',
15051519
desc='set maximal outlier limit in satit')
1506-
write_vo2vox = traits.Bool(argstr='--vox2vox',
1507-
desc='output vox2vox matrix (default is RAS2RAS)')
1508-
no_multi = traits.Bool(argstr='--nomulti', desc='work on highest resolution')
1520+
write_vo2vox = traits.Bool(
1521+
argstr='--vox2vox', desc='output vox2vox matrix (default is RAS2RAS)')
1522+
no_multi = traits.Bool(argstr='--nomulti',
1523+
desc='work on highest resolution')
15091524
mask_source = File(exists=True, argstr='--maskmov %s',
15101525
desc='image to mask source volume with')
15111526
mask_target = File(exists=True, argstr='--maskdst %s',
15121527
desc='image to mask target volume with')
1513-
force_double = traits.Bool(argstr='--doubleprec', desc='use double-precision intensities')
1514-
force_float = traits.Bool(argstr='--floattype', desc='use float intensities')
1528+
force_double = traits.Bool(argstr='--doubleprec',
1529+
desc='use double-precision intensities')
1530+
force_float = traits.Bool(argstr='--floattype',
1531+
desc='use float intensities')
15151532

15161533

15171534
class RobustRegisterOutputSpec(TraitedSpec):
15181535

15191536
out_reg_file = File(exists=True, desc="output registration file")
1520-
registered_file = File(desc="output image with registration applied")
1521-
weights_file = File(desc="image of weights used")
1522-
half_source = File(desc="source image mapped to halfway space")
1523-
half_targ = File(desc="target image mapped to halfway space")
1524-
half_weights = File(desc="weights image mapped to halfway space")
1525-
half_source_xfm = File(desc="transform file to map source image to halfway space")
1526-
half_targ_xfm = File(desc="transform file to map target image to halfway space")
1537+
registered_file = File(exists=True,
1538+
desc="output image with registration applied")
1539+
weights_file = File(exists=True, desc="image of weights used")
1540+
half_source = File(exists=True,
1541+
desc="source image mapped to halfway space")
1542+
half_targ = File(exists=True, desc="target image mapped to halfway space")
1543+
half_weights = File(exists=True,
1544+
desc="weights image mapped to halfway space")
1545+
half_source_xfm = File(
1546+
exists=True,
1547+
desc="transform file to map source image to halfway space")
1548+
half_targ_xfm = File(
1549+
exists=True,
1550+
desc="transform file to map target image to halfway space")
15271551

15281552

15291553
class RobustRegister(FSCommand):
1530-
"""Perform intramodal linear registration (translation and rotation) using robust statistics.
1554+
"""Perform intramodal linear registration (translation and rotation) using
1555+
robust statistics.
15311556
15321557
Examples
15331558
--------
@@ -1542,8 +1567,8 @@ class RobustRegister(FSCommand):
15421567
15431568
References
15441569
----------
1545-
Reuter, M, Rosas, HD, and Fischl, B, (2010). Highly Accurate Inverse Consistent Registration:
1546-
A Robust Approach. Neuroimage 53(4) 1181-96.
1570+
Reuter, M, Rosas, HD, and Fischl, B, (2010). Highly Accurate Inverse
1571+
Consistent Registration: A Robust Approach. Neuroimage 53(4) 1181-96.
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15481573
"""
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