Merge pull request #2848 from yarikoptic/bf-2847

FIX: Make positional arguments to LaplacianThickness require previous argument

Author: effigies

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_auto_LaplacianThickness.py

@@ -7,8 +7,9 @@ def test_LaplacianThickness_inputs():
     input_map = dict(
         args=dict(argstr='%s', ),
         dT=dict(
-            argstr='%f',
+            argstr='%s',
             position=6,
+            requires=['prior_thickness'],
         ),
         environ=dict(
             nohash=True,
@@ -39,20 +40,23 @@ def test_LaplacianThickness_inputs():
             position=3,
         ),
         prior_thickness=dict(
-            argstr='%f',
+            argstr='%s',
             position=5,
+            requires=['smooth_param'],
         ),
         smooth_param=dict(
-            argstr='%f',
+            argstr='%s',
             position=4,
         ),
         sulcus_prior=dict(
-            argstr='%f',
+            argstr='%s',
             position=7,
+            requires=['dT'],
         ),
         tolerance=dict(
-            argstr='%f',
+            argstr='%s',
             position=8,
+            requires=['sulcus_prior'],
         ),
     )
     inputs = LaplacianThickness.input_spec()

nipype/interfaces/ants/tests/test_segmentation.py

@@ -0,0 +1,59 @@
+# 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.tolerance = 0.001
+    with pytest.raises(ValueError, match=r".* requires a value for input 'sulcus_prior' .*"):
+        lt.cmdline
+    lt.inputs.sulcus_prior = 0.15
+    with pytest.raises(ValueError, match=r".* requires a value for input 'dT' .*"):
+        lt.cmdline
+    lt.inputs.dT = 0.01
+    with pytest.raises(ValueError, match=r".* requires a value for input 'prior_thickness' .*"):
+        lt.cmdline
+    lt.inputs.prior_thickness = 5.9
+    with pytest.raises(ValueError, match=r".* requires a value for input 'smooth_param' .*"):
+        lt.cmdline
+    lt.inputs.smooth_param = 4.5
+    assert lt.cmdline == 'LaplacianThickness functional.nii diffusion_weighted.nii ' \
+        'functional_thickness.nii 4.5 5.9 0.01 0.15 0.001'

nipype/interfaces/base/core.py

@@ -202,10 +202,16 @@ def _check_requires(self, spec, name, value):
                 for field in spec.requires
             ]
             if any(values) and isdefined(value):
-                msg = ("%s requires a value for input '%s' because one of %s "
-                       "is set. For a list of required inputs, see %s.help()" %
-                       (self.__class__.__name__, name,
-                        ', '.join(spec.requires), self.__class__.__name__))
+                if len(values) > 1:
+                    fmt = ("%s requires values for inputs %s because '%s' is set. " 
+                           "For a list of required inputs, see %s.help()")
+                else:
+                    fmt = ("%s requires a value for input %s because '%s' is set. " 
+                           "For a list of required inputs, see %s.help()")
+                msg = fmt % (self.__class__.__name__,
+                             ', '.join("'%s'" % req for req in spec.requires),
+                             name,
+                             self.__class__.__name__)
                 raise ValueError(msg)
 
     def _check_xor(self, spec, name, value):