Merge pull request #1165 from satra/fix/tests

Updating and adjusting tests across recent PRs

Author: satra

nipype/algorithms/mesh.py

@@ -15,7 +15,7 @@
 import numpy as np
 from numpy import linalg as nla
 import os.path as op
-from nipype.external import six
+from ..external import six
 
 from .. import logging
 

nipype/algorithms/tests/test_mesh_ops.py

@@ -16,20 +16,20 @@
 from nipype.algorithms import mesh as m
 
 notvtk = True
-try:
-    from tvtk.api import tvtk
-    notvtk = False
-except ImportError:
-    pass
-
+import platform
+if 'darwin' not in platform.system().lower():
+    try:
+        from tvtk.api import tvtk
+        notvtk = False
+    except ImportError:
+        pass
 
 @skipif(notvtk)
 def test_ident_distances():
     tempdir = mkdtemp()
     curdir = os.getcwd()
     os.chdir(tempdir)
     in_surf = example_data('surf01.vtk')
-
     dist_ident = m.ComputeMeshWarp()
     dist_ident.inputs.surface1 = in_surf
     dist_ident.inputs.surface2 = in_surf

nipype/interfaces/ants/segmentation.py

@@ -576,36 +576,51 @@ def _list_outputs(self):
 
 
 class JointFusionInputSpec(ANTSCommandInputSpec):
-    dimension = traits.Enum(3, 2, 4, argstr='%d', position=0, usedefault=True, mandatory=True,
+    dimension = traits.Enum(3, 2, 4, argstr='%d', position=0, usedefault=True,
+                            mandatory=True,
                             desc='image dimension (2, 3, or 4)')
-    modalities = traits.Int(argstr='%d', position=1, mandatory=True, desc='Number of modalities or features')
-    warped_intensity_images = InputMultiPath(File(exists=True), argstr="-g %s...", mandatory=True, desc='Warped atlas images')
-    target_image = InputMultiPath(File(exists=True), argstr='-tg %s...', mandatory=True, desc='Target image(s)')
-    warped_label_images = InputMultiPath(File(exists=True), argstr="-l %s...", mandatory=True, desc='Warped atlas segmentations')
-    method = traits.Str(default='Joint', argstr='-m %s', usedefault=True, desc='Select voting method. Options: Joint (Joint Label Fusion). May be followed by optional parameters in brackets, e.g., -m Joint[0.1,2]')
-    alpha = traits.Float(default=0.1, usedefault=True, requires=['method'], desc='Regularization term added to matrix Mx for inverse')
-    beta = traits.Int(default=2, usedefault=True, requires=['method'], desc='Exponent for mapping intensity difference to joint error')
-    output_label_image = File(argstr='%s', mandatory=True, position=-1, desc='Output fusion label map image')
-    patch_radius = traits.ListInt(minlen=3, maxlen=3, argstr='-rp %s', desc='Patch radius for similarity measures, scalar or vector. Default: 2x2x2')
-    search_radius = traits.ListInt(minlen=3, maxlen=3, argstr='-rs %s', desc='Local search radius. Default: 3x3x3')
-    exclusion_region = File(exists=True, argstr='-x %s', desc='Specify an exclusion region for the given label.')
-    # TODO: These are almost never needed except for debugging
-    # output_posteriors_name_template = traits.Str('POSTERIOR_%02d.nii.gz', argstr='-p %s',
-    #                                              desc="Save the posterior maps (probability that each voxel belongs to each " +\
-    #                                              "label) as images. The number of images saved equals the number of labels. " +\
-    #                                              "The filename pattern must be in C printf format, e.g. posterior%04d.nii.gz")
-    # output_voting_weights_name_template = traits.Str('WEIGHTED_%04d.nii.gz', argstr='-w %s', desc="Save the voting weights as " +\
-    #                                                  "images. The number of images saved equals the number of atlases. The " +\
-    #                                                  "filename pattern must be in C printf format, e.g. weight%04d.nii.gz")
-    atlas_group_id = traits.ListInt(argstr='-gp %d...', desc='Assign a group ID for each atlas')
-    atlas_group_weights = traits.ListInt(argstr='-gpw %d...', desc='Assign the voting weights to each atlas group')
+    modalities = traits.Int(argstr='%d', position=1, mandatory=True,
+                            desc='Number of modalities or features')
+    warped_intensity_images = InputMultiPath(File(exists=True),
+                                             argstr="-g %s...", mandatory=True,
+                                             desc='Warped atlas images')
+    target_image = InputMultiPath(File(exists=True), argstr='-tg %s...',
+                                  mandatory=True, desc='Target image(s)')
+    warped_label_images = InputMultiPath(File(exists=True), argstr="-l %s...",
+                                         mandatory=True,
+                                         desc='Warped atlas segmentations')
+    method = traits.Str(default='Joint', argstr='-m %s', usedefault=True,
+                        desc=('Select voting method. Options: Joint (Joint '
+                              'Label Fusion). May be followed by optional '
+                              'parameters in brackets, e.g., -m Joint[0.1,2]'))
+    alpha = traits.Float(default=0.1, usedefault=True, requires=['method'],
+                         desc=('Regularization term added to matrix Mx for '
+                               'inverse'))
+    beta = traits.Int(default=2, usedefault=True, requires=['method'],
+                      desc=('Exponent for mapping intensity difference to joint'
+                            ' error'))
+    output_label_image = File(argstr='%s', mandatory=True, position=-1,
+                              name_template='%s',
+                              output_name='output_label_image',
+                              desc='Output fusion label map image')
+    patch_radius = traits.ListInt(minlen=3, maxlen=3, argstr='-rp %s',
+                                  desc=('Patch radius for similarity measures, '
+                                        'scalar or vector. Default: 2x2x2'))
+    search_radius = traits.ListInt(minlen=3, maxlen=3, argstr='-rs %s',
+                                   desc='Local search radius. Default: 3x3x3')
+    exclusion_region = File(exists=True, argstr='-x %s',
+                            desc=('Specify an exclusion region for the given '
+                                  'label.'))
+    atlas_group_id = traits.ListInt(argstr='-gp %d...',
+                                    desc=('Assign a group ID for each atlas'))
+    atlas_group_weights = traits.ListInt(argstr='-gpw %d...',
+                                         desc=('Assign the voting weights to '
+                                               'each atlas group'))
 
 
 class JointFusionOutputSpec(TraitedSpec):
-    output_label_image = File(exists=True)
-    # TODO: These are almost never needed except for debugging,
-    #       so delay complicated implementation until a need arises
-    #       optional outputs - output_posteriors, output_voting_weights
+    output_label_image = File(exists=True, desc='Output fusion label map image')
+
 
 class JointFusion(ANTSCommand):
     """
@@ -657,8 +672,3 @@ def _format_arg(self, opt, spec, val):
                 assert len(val) == len(self.inputs.warped_label_images), "Number of intensity images and label maps must be the same"
             return super(ANTSCommand, self)._format_arg(opt, spec, val)
         return retval
-
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        outputs['output_label_image'] = os.path.abspath(self.inputs.output_label_image)
-        return outputs

nipype/interfaces/ants/tests/test_auto_JointFusion.py

@@ -0,0 +1,81 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.ants.segmentation import JointFusion
+
+def test_JointFusion_inputs():
+    input_map = dict(alpha=dict(requires=['method'],
+    usedefault=True,
+    ),
+    args=dict(argstr='%s',
+    ),
+    atlas_group_id=dict(argstr='-gp %d...',
+    ),
+    atlas_group_weights=dict(argstr='-gpw %d...',
+    ),
+    beta=dict(requires=['method'],
+    usedefault=True,
+    ),
+    dimension=dict(argstr='%d',
+    mandatory=True,
+    position=0,
+    usedefault=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    exclusion_region=dict(argstr='-x %s',
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    method=dict(argstr='-m %s',
+    usedefault=True,
+    ),
+    modalities=dict(argstr='%d',
+    mandatory=True,
+    position=1,
+    ),
+    num_threads=dict(nohash=True,
+    usedefault=True,
+    ),
+    output_label_image=dict(argstr='%s',
+    mandatory=True,
+    name_template='%s',
+    output_name='output_label_image',
+    position=-1,
+    ),
+    patch_radius=dict(argstr='-rp %s',
+    maxlen=3,
+    minlen=3,
+    ),
+    search_radius=dict(argstr='-rs %s',
+    maxlen=3,
+    minlen=3,
+    ),
+    target_image=dict(argstr='-tg %s...',
+    mandatory=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    warped_intensity_images=dict(argstr='-g %s...',
+    mandatory=True,
+    ),
+    warped_label_images=dict(argstr='-l %s...',
+    mandatory=True,
+    ),
+    )
+    inputs = JointFusion.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_JointFusion_outputs():
+    output_map = dict(output_label_image=dict(),
+    )
+    outputs = JointFusion.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/ants/tests/test_auto_Registration.py

@@ -24,6 +24,8 @@ def test_Registration_inputs():
     ),
     fixed_image_mask=dict(argstr='%s',
     ),
+    float=dict(argstr='--float %d',
+    ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),

nipype/interfaces/ants/tests/test_JointFusion.py renamed to nipype/interfaces/ants/tests/test_spec_JointFusion.py

@@ -1,5 +1,4 @@
-from nose import with_setup
-from nipype.testing import assert_equal, assert_raises
+from nipype.testing import assert_equal, assert_raises, example_data
 from nipype.interfaces.base import InputMultiPath
 from traits.trait_errors import TraitError
 from nipype.interfaces.ants import JointFusion
@@ -54,24 +53,24 @@ def test_JointFusion_cmd():
     at.inputs.dimension = 3
     at.inputs.modalities = 1
     at.inputs.method = 'Joint[0.1,2]'
-    at.inputs.output_label_image ='fusion_labelimage_output.nii'
-    at.inputs.warped_intensity_images = ['im1.nii',
-                                         'im2.nii']
-    at.inputs.warped_label_images = ['segmentation0.nii.gz',
-                                     'segmentation1.nii.gz']
-    at.inputs.target_image = 'T1.nii'
+    at.inputs.output_label_image = 'fusion_labelimage_output.nii'
+    warped_intensity_images = [example_data('im1.nii'),
+                               example_data('im2.nii')]
+    at.inputs.warped_intensity_images = warped_intensity_images
+    segmentation_images = [example_data('segmentation0.nii.gz'),
+                           example_data('segmentation1.nii.gz')]
+    at.inputs.warped_label_images = segmentation_images
+    T1_image = example_data('T1.nii')
+    at.inputs.target_image = T1_image
     at.inputs.patch_radius = [3,2,1]
     at.inputs.search_radius = [1,2,3]
-    yield assert_equal, at.cmdline, 'jointfusion 3 1' + \
-      ' -m Joint[0.1,2]' + \
-      ' -rp 3x2x1' + \
-      ' -rs 1x2x3' + \
-      ' -tg T1.nii' + \
-      ' -g im1.nii' + \
-      ' -g im2.nii' + \
-      ' -l segmentation0.nii.gz' + \
-      ' -l segmentation1.nii.gz' + \
-      ' fusion_labelimage_output.nii',
-    "Command line generation failure", True
+    expected_command = ('jointfusion 3 1 -m Joint[0.1,2] -rp 3x2x1 -rs 1x2x3'
+                        ' -tg %s -g %s -g %s -l %s -l %s'
+                        ' fusion_labelimage_output.nii') % (T1_image,
+                                                            warped_intensity_images[0],
+                                                            warped_intensity_images[1],
+                                                            segmentation_images[0],
+                                                            segmentation_images[1])
+    yield assert_equal, at.cmdline, expected_command
     # setting intensity or labels with unequal lengths raises error
-    yield assert_raises, AssertionError, at._format_arg, 'warped_intensity_images', InputMultiPath, ['im1.nii', 'im2.nii', 'im3.nii']
+    yield assert_raises, AssertionError, at._format_arg, 'warped_intensity_images', InputMultiPath, warped_intensity_images + [example_data('im3.nii')]

nipype/interfaces/dipy/tensors.py

@@ -71,7 +71,7 @@ class DTIInputSpec(TraitedSpec):
                  desc='The input b-vector text file')
     bvals = File(exists=True, mandatory=True,
                  desc='The input b-value text file')
-    mask_file = File(exists=True, mandatory=False,
+    mask_file = File(exists=True,
                  desc='An optional white matter mask')
     out_filename = File(
         genfile=True, desc='The output filename for the DTI parameters image')
@@ -133,7 +133,7 @@ class TensorModeInputSpec(TraitedSpec):
                  desc='The input b-vector text file')
     bvals = File(exists=True, mandatory=True,
                  desc='The input b-value text file')
-    mask_file = File(exists=True, mandatory=False,
+    mask_file = File(exists=True,
                      desc='An optional white matter mask')
     out_filename = File(
         genfile=True, desc='The output filename for the Tensor mode image')

nipype/interfaces/dipy/tests/test_auto_DTI.py

@@ -9,8 +9,7 @@ def test_DTI_inputs():
     ),
     in_file=dict(mandatory=True,
     ),
-    mask_file=dict(mandatory=False,
-    ),
+    mask_file=dict(),
     out_filename=dict(genfile=True,
     ),
     )

nipype/interfaces/dipy/tests/test_auto_TensorMode.py

@@ -9,8 +9,7 @@ def test_TensorMode_inputs():
     ),
     in_file=dict(mandatory=True,
     ),
-    mask_file=dict(mandatory=False,
-    ),
+    mask_file=dict(),
     out_filename=dict(genfile=True,
     ),
     )

nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py

@@ -12,6 +12,7 @@ def test_AnalyzeWarp_inputs():
     usedefault=True,
     ),
     num_threads=dict(argstr='-threads %01d',
+    nohash=True,
     ),
     output_path=dict(argstr='-out %s',
     mandatory=True,