added # doctest: +SKIP

Author: kesshijordan

nipype/interfaces/afni/preprocess.py

@@ -119,7 +119,7 @@ class AlignEpiAnatPyOutputSpec(TraitedSpec):
         desc="matrix to volume register and align epi"
              "to anatomy and put into standard space")
     epi_vr_motion = File(
-        desc="motion parameters from EPI time-series" 
+        desc="motion parameters from EPI time-series"
              "registration (tsh included in name if slice"
              "timing correction is also included).")
     skullstrip = File(
@@ -131,20 +131,20 @@ class AlignEpiAnatPy(AFNIPythonCommand):
     an EPI and an anatomical structural dataset, and applies the resulting
     transformation to one or the other to bring them into alignment.
 
-    This script computes the transforms needed to align EPI and  
-    anatomical datasets using a cost function designed for this purpose. The  
-    script combines multiple transformations, thereby minimizing the amount of 
+    This script computes the transforms needed to align EPI and
+    anatomical datasets using a cost function designed for this purpose. The
+    script combines multiple transformations, thereby minimizing the amount of
     interpolation applied to the data.
-    
+
     Basic Usage:
       align_epi_anat.py -anat anat+orig -epi epi+orig -epi_base 5
-    
+
     The user must provide EPI and anatomical datasets and specify the EPI
-    sub-brick to use as a base in the alignment.  
+    sub-brick to use as a base in the alignment.
 
     Internally, the script always aligns the anatomical to the EPI dataset,
-    and the resulting transformation is saved to a 1D file. 
-    As a user option, the inverse of this transformation may be applied to the 
+    and the resulting transformation is saved to a 1D file.
+    As a user option, the inverse of this transformation may be applied to the
     EPI dataset in order to align it to the anatomical data instead.
 
     This program generates several kinds of output in the form of datasets
@@ -182,7 +182,7 @@ def _list_outputs(self):
         epi_prefix = ''.join(self._gen_fname(self.inputs.in_file).split('+')[:-1])
         outputtype = self.inputs.outputtype
         if outputtype == 'AFNI':
-            ext = '.HEAD' 
+            ext = '.HEAD'
         else:
             Info.output_type_to_ext(outputtype)
         matext = '.1D'
@@ -620,7 +620,7 @@ class AutoTLRCInputSpec(CommandLineInputSpec):
         mandatory=True,
         exists=True,
         copyfile=False)
-    base = traits.Str(  
+    base = traits.Str(
         desc = '              Reference anatomical volume'
                 '              Usually this volume is in some standard space like'
                 '              TLRC or MNI space and with afni dataset view of'
@@ -706,7 +706,7 @@ def _list_outputs(self):
         ext = '.HEAD'
         outputs['out_file'] = os.path.abspath(self._gen_fname(self.inputs.in_file, suffix='+tlrc')+ext)
         return outputs
-    
+
 class BandpassInputSpec(AFNICommandInputSpec):
     in_file = File(
         desc='input file to 3dBandpass',

nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py

@@ -0,0 +1,44 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import TCatSubBrick
+
+
+def test_TCatSubBrick_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_files=dict(argstr='%s%s ...',
+    copyfile=False,
+    mandatory=True,
+    position=-1,
+    ),
+    out_file=dict(argstr='-prefix %s',
+    genfile=True,
+    ),
+    outputtype=dict(),
+    rlt=dict(argstr='-rlt%s',
+    position=1,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = TCatSubBrick.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_TCatSubBrick_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = TCatSubBrick.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/dtitk/__init__.py

@@ -5,8 +5,11 @@
 Top-level namespace for dti-tk.
 """
 
-#from .base import ()
-from ..dtitk.registration import (RigidTask, AffineTask, DiffeoTask, ComposeXfmTask,
-diffeoSymTensor3DVolTask, affSymTensor3DVolTask, affScalarVolTask, diffeoScalarVolTask)
-from ..dtitk.utils import (TVAdjustOriginTask, TVAdjustVoxSpTask, SVAdjustVoxSpTask,
-TVResampleTask, SVResampleTask, TVtoolTask, BinThreshTask)
+# from .base import ()
+from ..dtitk.registration import (RigidTask, AffineTask, DiffeoTask,
+                                  ComposeXfmTask, diffeoSymTensor3DVolTask,
+                                  affSymTensor3DVolTask, affScalarVolTask,
+                                  diffeoScalarVolTask)
+from ..dtitk.utils import (TVAdjustOriginTask, TVAdjustVoxSpTask,
+                           SVAdjustVoxSpTask, TVResampleTask, SVResampleTask,
+                           TVtoolTask, BinThreshTask)

nipype/interfaces/dtitk/registration.py

@@ -33,7 +33,7 @@ class RigidTask(CommandLineDtitk):
         >>> node.inputs.fixed_file = 'diffusion.nii'
         >>> node.inputs.moving_file = 'diffusion.nii'
         >>> node.inputs.similarity_metric = 'EDS'
-        >>> node.run()
+        >>> node.run() # doctest: +SKIP
         """
     input_spec = RigidInputSpec
     output_spec = RigidOutputSpec
@@ -79,7 +79,7 @@ class AffineTask(CommandLineDtitk):
             >>> node.inputs.in_fixed_tensor = 'diffusion.nii'
             >>> node.inputs.in_moving_txt = 'dirs.txt'
             >>> node.inputs.in_similarity_metric = 'EDS'
-            >>> node.run()
+            >>> node.run() # doctest: +SKIP
             """
 
     input_spec = AffineInputSpec
@@ -126,7 +126,7 @@ class DiffeoTask(CommandLineDtitk):
                 >>> node.inputs.in_moving_txt = 'dirs.txt'
                 >>> node.inputs.in_mask = 'mask.nii'
                 >>> node.inputs.in_numbers = '6 0.002'
-                >>> node.run()
+                >>> node.run() # doctest: +SKIP
                 """
     input_spec = DiffeoInputSpec
     output_spec = DiffeoOutputSpec
@@ -166,7 +166,7 @@ class ComposeXfmTask(CommandLineDtitk):
                 >>> node = dtitk.ComposeXfmTask()
                 >>> node.inputs.in_df = 'ants_Warp.nii.gz'
                 >>> node.inputs.in_aff= 'ants_Affine.txt'
-                >>> node.run()
+                >>> node.run() # doctest: +SKIP
                 """
     input_spec = ComposeXfmInputSpec
     output_spec = ComposeXfmOutputSpec
@@ -206,7 +206,7 @@ class diffeoSymTensor3DVolTask(CommandLineDtitk):
                 >>> node = dtitk.diffeoSymTensor3DVolTask()
                 >>> node.inputs.in_tensor = 'diffusion.nii'
                 >>> node.inputs.in_xfm = 'ants_Warp.nii.gz'
-                >>> node.run()
+                >>> node.run() # doctest: +SKIP
                 """
 
     input_spec = diffeoSymTensor3DVolInputSpec
@@ -246,7 +246,7 @@ class affSymTensor3DVolTask(CommandLineDtitk):
                 >>> node = dtitk.affSymTensor3DVolTask()
                 >>> node.inputs.in_tensor = 'diffusion.nii'
                 >>> node.inputs.in_xfm = 'ants_Affine.txt'
-                >>> node.run()
+                >>> node.run() # doctest: +SKIP
                 """
     input_spec = affSymTensor3DVolInputSpec
     output_spec = affSymTensor3DVolOutputSpec
@@ -284,7 +284,7 @@ class affScalarVolTask(CommandLineDtitk):
                 >>> node = dtitk.affScalarVolTask()
                 >>> node.inputs.in_volume = 'fa.nii.gz'
                 >>> node.inputs.in_xfm = 'ants_Affine.txt'
-                >>> node.run()
+                >>> node.run() # doctest: +SKIP
                 """
     input_spec = affScalarVolInputSpec
     output_spec = affScalarVolOutputSpec
@@ -331,7 +331,7 @@ class diffeoScalarVolTask(CommandLineDtitk):
                 >>> node = dtitk.diffeoScalarVolTask()
                 >>> node.inputs.in_tensor = 'fa.nii.gz'
                 >>> node.inputs.in_xfm = 'ants_Warp.nii.gz'
-                >>> node.run()
+                >>> node.run() # doctest: +SKIP
                 """
 
     input_spec = diffeoScalarVolInputSpec

nipype/interfaces/dtitk/tests/test_auto_AffineTask.py

@@ -0,0 +1,53 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..registration import AffineTask
+
+
+def test_AffineTask_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_fixed_tensor=dict(argstr='%s',
+    exists=True,
+    mandatory=False,
+    position=0,
+    ),
+    in_moving_txt=dict(argstr='%s',
+    exists=True,
+    mandatory=False,
+    position=1,
+    ),
+    in_similarity_metric=dict(argstr='%s',
+    exists=True,
+    mandatory=False,
+    position=3,
+    ),
+    in_usetrans_flag=dict(argstr='%s',
+    exists=True,
+    mandatory=False,
+    position=4,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = AffineTask.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_AffineTask_outputs():
+    output_map = dict(out_file=dict(),
+    out_file_xfm=dict(),
+    )
+    outputs = AffineTask.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py

@@ -0,0 +1,47 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import BinThreshTask
+
+
+def test_BinThreshTask_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_image=dict(argstr='%s',
+    exists=True,
+    mandatory=False,
+    position=0,
+    ),
+    in_numbers=dict(argstr='%s',
+    exists=True,
+    mandatory=False,
+    position=2,
+    ),
+    out_path=dict(argstr='%s',
+    exists=True,
+    mandatory=False,
+    position=1,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = BinThreshTask.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_BinThreshTask_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = BinThreshTask.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/dtitk/tests/test_auto_CommandLineDtitk.py

@@ -0,0 +1,23 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..base import CommandLineDtitk
+
+
+def test_CommandLineDtitk_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = CommandLineDtitk.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+

nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py

@@ -0,0 +1,49 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..registration import ComposeXfmTask
+
+
+def test_ComposeXfmTask_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_aff=dict(argstr='-aff %s',
+    exists=True,
+    mandatory=False,
+    position=0,
+    ),
+    in_df=dict(argstr='-df %s',
+    exists=True,
+    mandatory=False,
+    position=1,
+    ),
+    out_path=dict(argstr='-out %s',
+    exists=True,
+    mandatory=False,
+    name_source='in_df',
+    name_template='%s_comboaff.nii.gz',
+    position=2,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = ComposeXfmTask.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_ComposeXfmTask_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = ComposeXfmTask.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value