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l-espanal-espana
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Style and testing.
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-108
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4 files changed

+656
-108
lines changed

‎nipype/interfaces/freesurfer/longitudinal.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -296,7 +296,7 @@ def _gen_filename(self, name):
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return self._gen_subjects_dir()
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return None
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def _list_outputs(self):
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if isdefined(self.inputs.subjects_dir):
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subjects_dir = self.inputs.subjects_dir

‎nipype/interfaces/freesurfer/tests/test_auto_BaseReconAll.py

Lines changed: 329 additions & 0 deletions
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@@ -0,0 +1,329 @@
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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ..longitudinal import BaseReconAll
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def test_BaseReconAll_inputs():
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input_map = dict(
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FLAIR_file=dict(
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argstr="-FLAIR %s",
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extensions=None,
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min_ver="5.3.0",
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),
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T1_files=dict(
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argstr="-i %s...",
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),
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T2_file=dict(
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argstr="-T2 %s",
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extensions=None,
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min_ver="5.3.0",
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),
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args=dict(
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argstr="%s",
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),
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base_id=dict(
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argstr="-base %s",
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xor=["subject_id"],
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),
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big_ventricles=dict(
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argstr="-bigventricles",
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),
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brainstem=dict(
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argstr="-brainstem-structures",
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),
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directive=dict(
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argstr="-%s",
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position=0,
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usedefault=True,
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),
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environ=dict(
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nohash=True,
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usedefault=True,
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),
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expert=dict(
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argstr="-expert %s",
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extensions=None,
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),
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flags=dict(
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argstr="%s",
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),
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hemi=dict(
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argstr="-hemi %s",
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),
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hippocampal_subfields_T1=dict(
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argstr="-hippocampal-subfields-T1",
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min_ver="6.0.0",
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),
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hippocampal_subfields_T2=dict(
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argstr="-hippocampal-subfields-T2 %s %s",
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min_ver="6.0.0",
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),
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hires=dict(
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argstr="-hires",
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min_ver="6.0.0",
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),
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mprage=dict(
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argstr="-mprage",
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),
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mri_aparc2aseg=dict(
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xor=["expert"],
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),
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mri_ca_label=dict(
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xor=["expert"],
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),
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mri_ca_normalize=dict(
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xor=["expert"],
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),
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mri_ca_register=dict(
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xor=["expert"],
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),
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mri_edit_wm_with_aseg=dict(
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xor=["expert"],
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),
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mri_em_register=dict(
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xor=["expert"],
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),
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mri_fill=dict(
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xor=["expert"],
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),
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mri_mask=dict(
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xor=["expert"],
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),
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mri_normalize=dict(
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xor=["expert"],
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),
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mri_pretess=dict(
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xor=["expert"],
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),
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mri_remove_neck=dict(
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xor=["expert"],
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),
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mri_segment=dict(
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xor=["expert"],
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),
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mri_segstats=dict(
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xor=["expert"],
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),
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mri_tessellate=dict(
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xor=["expert"],
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),
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mri_watershed=dict(
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xor=["expert"],
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),
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mris_anatomical_stats=dict(
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xor=["expert"],
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),
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mris_ca_label=dict(
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xor=["expert"],
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),
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mris_fix_topology=dict(
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xor=["expert"],
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),
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mris_inflate=dict(
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xor=["expert"],
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),
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mris_make_surfaces=dict(
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xor=["expert"],
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),
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mris_register=dict(
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xor=["expert"],
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),
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mris_smooth=dict(
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xor=["expert"],
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),
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mris_sphere=dict(
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xor=["expert"],
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),
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mris_surf2vol=dict(
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xor=["expert"],
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),
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mrisp_paint=dict(
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xor=["expert"],
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),
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openmp=dict(
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argstr="-openmp %d",
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),
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parallel=dict(
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argstr="-parallel",
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),
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subject_id=dict(
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argstr="-subjid %s",
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),
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subjects_dir=dict(
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argstr="-sd %s",
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genfile=True,
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hash_files=False,
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),
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talairach=dict(
157+
xor=["expert"],
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),
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timepoints=dict(
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argstr="-tp %s...",
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),
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use_FLAIR=dict(
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argstr="-FLAIRpial",
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min_ver="5.3.0",
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xor=["use_T2"],
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),
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use_T2=dict(
168+
argstr="-T2pial",
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min_ver="5.3.0",
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xor=["use_FLAIR"],
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),
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xopts=dict(
173+
argstr="-xopts-%s",
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),
175+
)
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inputs = BaseReconAll.input_spec()
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for key, metadata in list(input_map.items()):
179+
for metakey, value in list(metadata.items()):
180+
assert getattr(inputs.traits()[key], metakey) == value
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def test_BaseReconAll_outputs():
184+
output_map = dict(
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BA_stats=dict(
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altkey="BA",
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loc="stats",
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),
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T1=dict(
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extensions=None,
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loc="mri",
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),
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annot=dict(
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altkey="*annot",
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loc="label",
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),
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aparc_a2009s_stats=dict(
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altkey="aparc.a2009s",
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loc="stats",
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),
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aparc_aseg=dict(
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altkey="aparc*aseg",
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loc="mri",
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),
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aparc_stats=dict(
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altkey="aparc",
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loc="stats",
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),
209+
area_pial=dict(
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altkey="area.pial",
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loc="surf",
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),
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aseg=dict(
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extensions=None,
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loc="mri",
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),
217+
aseg_stats=dict(
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altkey="aseg",
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loc="stats",
220+
),
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avg_curv=dict(
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loc="surf",
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),
224+
brain=dict(
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extensions=None,
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loc="mri",
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),
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brainmask=dict(
229+
extensions=None,
230+
loc="mri",
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),
232+
curv=dict(
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loc="surf",
234+
),
235+
curv_pial=dict(
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altkey="curv.pial",
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loc="surf",
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),
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curv_stats=dict(
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altkey="curv",
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loc="stats",
242+
),
243+
entorhinal_exvivo_stats=dict(
244+
altkey="entorhinal_exvivo",
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loc="stats",
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),
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filled=dict(
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extensions=None,
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loc="mri",
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),
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graymid=dict(
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altkey=["graymid", "midthickness"],
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loc="surf",
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),
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inflated=dict(
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loc="surf",
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),
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jacobian_white=dict(
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loc="surf",
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),
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label=dict(
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altkey="*label",
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loc="label",
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),
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norm=dict(
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extensions=None,
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loc="mri",
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),
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nu=dict(
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extensions=None,
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loc="mri",
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),
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orig=dict(
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extensions=None,
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loc="mri",
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),
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pial=dict(
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loc="surf",
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),
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rawavg=dict(
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extensions=None,
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loc="mri",
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),
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ribbon=dict(
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altkey="*ribbon",
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loc="mri",
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),
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smoothwm=dict(
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loc="surf",
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),
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sphere=dict(
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loc="surf",
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),
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sphere_reg=dict(
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altkey="sphere.reg",
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loc="surf",
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),
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subject_id=dict(),
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subjects_dir=dict(),
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sulc=dict(
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loc="surf",
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),
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thickness=dict(
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loc="surf",
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),
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volume=dict(
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loc="surf",
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),
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white=dict(
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loc="surf",
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),
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wm=dict(
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extensions=None,
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loc="mri",
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),
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wmparc=dict(
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extensions=None,
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loc="mri",
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),
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wmparc_stats=dict(
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altkey="wmparc",
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loc="stats",
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),
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)
325+
outputs = BaseReconAll.output_spec()
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for key, metadata in list(output_map.items()):
328+
for metakey, value in list(metadata.items()):
329+
assert getattr(outputs.traits()[key], metakey) == value

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