update doctest

Author: josephmje

nipype/interfaces/fsl/epi.py

@@ -587,7 +587,7 @@ class EddyInputSpec(FSLCommandInputSpec):
         default_value="eddy_corrected",
         usedefault=True,
         argstr="--out=%s",
-        desc="basename for output (warped) image",
+        desc="Basename for output image",
     )
     session = File(
         exists=True,
@@ -598,45 +598,39 @@ class EddyInputSpec(FSLCommandInputSpec):
         exists=True,
         argstr="--topup=%s",
         requires=["in_topup_movpar"],
-        desc="topup file containing the field coefficients",
+        desc="Topup results file containing the field coefficients",
     )
     in_topup_movpar = File(
-        exists=True, requires=["in_topup_fieldcoef"], desc="topup movpar.txt file"
-    )
-    field = File(
-        argstr="--field=%s",
-        desc=(
-            "NonTOPUP fieldmap scaled in Hz - filename has "
-            "to be provided without an extension. TOPUP is "
-            "strongly recommended"
-        ),
-    )
-    field_mat = File(
-        exists=True, requires=["in_topup_fieldcoef"], desc="topup movpar.txt file"
-    )
-    field = File(
-        argstr="--field=%s",
-        desc=(
-            "NonTOPUP fieldmap scaled in Hz - filename has "
-            "to be provided without an extension. TOPUP is "
-            "strongly recommended"
-        ),
+        exists=True,
+        requires=["in_topup_fieldcoef"],
+        desc="Topup results file containing the movement parameters",
     )
+    field = File(argstr="--field=%s", desc=("Non-topup derived fieldmap scaled in Hz"))
     field_mat = File(
         exists=True,
         argstr="--field_mat=%s",
         desc=(
-            "Matrix that specifies the relative locations of "
-            "the field specified by --field and first volume "
-            "in file --imain"
+            "Matrix specifying the relative positions of "
+            "the fieldmap, --field, and the first volume "
+            "of the input file, --imain"
         ),
     )
 
     flm = traits.Enum(
-        "linear", "quadratic", "cubic", argstr="--flm=%s", desc="First level EC model"
+        "quadratic",
+        "linear",
+        "cubic",
+        usedefault=True,
+        argstr="--flm=%s",
+        desc="First level EC model",
     )
     slm = traits.Enum(
-        "none", "linear", "quadratic", argstr="--slm=%s", desc="Second level EC model"
+        "none",
+        "linear",
+        "quadratic",
+        usedefault=True,
+        argstr="--slm=%s",
+        desc="Second level EC model",
     )
     fep = traits.Bool(
         False, argstr="--fep", desc="Fill empty planes in x- or y-directions"
@@ -650,6 +644,7 @@ class EddyInputSpec(FSLCommandInputSpec):
     interp = traits.Enum(
         "spline",
         "trilinear",
+        usedefault=True,
         argstr="--interp=%s",
         desc="Interpolation model for estimation step",
     )
@@ -676,6 +671,8 @@ class EddyInputSpec(FSLCommandInputSpec):
         desc="Do NOT perform a post-eddy alignment of " "shells",
     )
     fwhm = traits.Float(
+        default_value=0.0,
+        usedefault=True,
         desc=("FWHM for conditioning filter when estimating " "the parameters"),
         argstr="--fwhm=%s",
     )
@@ -685,6 +682,7 @@ class EddyInputSpec(FSLCommandInputSpec):
     method = traits.Enum(
         "jac",
         "lsr",
+        usedefault=True,
         argstr="--resamp=%s",
         desc=("Final resampling method (jacobian/least " "squares)"),
     )
@@ -743,40 +741,41 @@ class EddyInputSpec(FSLCommandInputSpec):
     mporder = traits.Int(
         argstr="--mporder=%s",
         desc="Order of slice-to-vol movement model",
-        requires=["slspec"],
         min_ver="5.0.11",
     )
     s2v_niter = traits.Int(
         argstr="--s2v_niter=%s",
         desc="Number of iterations for slice-to-vol",
-        requires=["slspec"],
+        requires=["mporder"],
         min_ver="5.0.11",
     )
     s2v_lambda = traits.Int(
         agstr="--s2v_lambda",
         desc="Regularisation weight for slice-to-vol movement (reasonable range 1-10)",
-        requires=["slspec"],
+        requires=["mporder"],
         min_ver="5.0.11",
     )
     s2v_interp = traits.Enum(
         "trilinear",
         "spline",
         argstr="--s2v_interp=%s",
         desc="Slice-to-vol interpolation model for estimation step",
-        requires=["slspec"],
+        requires=["mporder"],
         min_ver="5.0.11",
     )
     slspec = traits.File(
         exists=True,
         argstr="--slspec=%s",
         desc="Name of text file completely specifying slice/group acquisition",
+        requires=["mporder"],
         xor=["json"],
         min_ver="5.0.11",
     )
     json = traits.File(
         exists=True,
         argstr="--json=%s",
         desc="Name of .json text file with information about slice timing",
+        requires=["mporder"],
         xor=["slspec"],
         min_ver="6.0.1",
     )
@@ -955,14 +954,18 @@ class Eddy(FSLCommand):
     Running eddy on an Nvidia GPU using cuda:
     >>> eddy.inputs.use_cuda = True
     >>> eddy.cmdline # doctest: +ELLIPSIS
-    'eddy_cuda --ff=10.0 --fwhm=0 --acqp=epi_acqp.txt --bvals=bvals.scheme \
---bvecs=bvecs.scheme --imain=epi.nii --index=epi_index.txt \
---mask=epi_mask.nii --niter=5 --nvoxhp=1000 --out=.../eddy_corrected'
+    'eddy_cuda --flm=quadratic --ff=10.0 --fwhm=0.0 \
+--acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme \
+--imain=epi.nii --index=epi_index.txt --mask=epi_mask.nii \
+--interp=spline --resamp=jac --niter=5 --nvoxhp=1000 \
+--out=.../eddy_corrected --slm=none'
     >>> eddy.inputs.use_cuda = False
     >>> eddy.cmdline # doctest: +ELLIPSIS
-    'eddy_openmp --ff=10.0 --fwhm=0 --acqp=epi_acqp.txt --bvals=bvals.scheme \
---bvecs=bvecs.scheme --imain=epi.nii --index=epi_index.txt \
---mask=epi_mask.nii --niter=5 --nvoxhp=1000 --out=.../eddy_corrected'
+    'eddy_openmp --flm=quadratic --ff=10.0 --fwhm=0.0 \
+--acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme \
+--imain=epi.nii --index=epi_index.txt --mask=epi_mask.nii \
+--interp=spline --resamp=jac --niter=5 --nvoxhp=1000 \
+--out=.../eddy_corrected --slm=none'
     >>> res = eddy.run() # doctest: +SKIP
     """