FIX: Make positional arguments to LaplacianThickness require previous argument

nipype/interfaces/ants/segmentation.py

@@ -208,25 +208,29 @@ class LaplacianThicknessInputSpec(ANTSCommandInputSpec):
         keep_extension=True,
         hash_files=False)
     smooth_param = traits.Float(
-        argstr='%f',
+        argstr='%s',
         desc='Sigma of the Laplacian Recursive Image Filter (defaults to 1)',
         position=4)
     prior_thickness = traits.Float(
-        argstr='%f',
+        argstr='%s',
         desc='Prior thickness (defaults to 500)',
+        requires=['smooth_param'],
         position=5)
     dT = traits.Float(
-        argstr='%f',
+        argstr='%s',
         desc='Time delta used during integration (defaults to 0.01)',
+        requires=['prior_thickness'],
         position=6)
     sulcus_prior = traits.Float(
-        argstr='%f',
+        argstr='%s',
         desc='Positive floating point number for sulcus prior. '
              'Authors said that 0.15 might be a reasonable value',
+        requires=['dT'],
         position=7)
     tolerance = traits.Float(
-        argstr='%f',
+        argstr='%s',
         desc='Tolerance to reach during optimization (defaults to 0.001)',
+        requires=['sulcus_prior'],
         position=8)
 
 

nipype/interfaces/ants/tests/test_segmentation.py

@@ -0,0 +1,49 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+from ..segmentation import LaplacianThickness
+from .test_resampling import change_dir
+
+import os
+import pytest
+
+
+@pytest.fixture()
+def change_dir(request):
+    orig_dir = os.getcwd()
+    filepath = os.path.dirname(os.path.realpath(__file__))
+    datadir = os.path.realpath(os.path.join(filepath, '../../../testing/data'))
+    os.chdir(datadir)
+
+    def move2orig():
+        os.chdir(orig_dir)
+
+    request.addfinalizer(move2orig)
+
+
+@pytest.fixture()
+def create_lt():
+    lt = LaplacianThickness()
+    # we do not run, so I stick some not really proper files as input
+    lt.inputs.input_gm = 'diffusion_weighted.nii'
+    lt.inputs.input_wm = 'functional.nii'
+    return lt
+
+
+def test_LaplacianThickness_defaults(change_dir, create_lt):
+    lt = create_lt
+    base_cmd = 'LaplacianThickness functional.nii diffusion_weighted.nii functional_thickness.nii'
+    assert lt.cmdline == base_cmd
+    lt.inputs.smooth_param = 4.5
+    assert lt.cmdline == base_cmd + " 4.5"
+    lt.inputs.prior_thickness = 5.9
+    assert lt.cmdline == base_cmd + " 4.5 5.9"
+
+
+def test_LaplacianThickness_wrongargs(change_dir, create_lt):
+    lt = create_lt
+    lt.inputs.prior_thickness = 5.9
+    # 500 must not be placed as smooth_param
+    assert lt.cmdline != 'LaplacianThickness functional.nii diffusion_weighted.nii functional_thickness.nii 5.9'
+    # probably should have just raised an exception that "smooth_param"
+    # should also be defined