fix doctests

Author: oesteban

nipype/interfaces/base.py

@@ -1349,9 +1349,9 @@ def _terminal_output_update(self):
     def set_default_terminal_output(cls, output_type):
         """Set the default terminal output for CommandLine Interfaces.
 
-        This method is used to set default terminal output for 
-        CommandLine Interfaces.  However, setting this will not 
-        update the output type for any existing instances.  For these, 
+        This method is used to set default terminal output for
+        CommandLine Interfaces.  However, setting this will not
+        update the output type for any existing instances.  For these,
         assign the <instance>.inputs.terminal_output.
         """
 

nipype/interfaces/dipy/base.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+from nipype.interfaces.base import (traits, File, isdefined,
+                                    BaseInterface, BaseInterfaceInputSpec)
 
 
 class DipyBaseInterfaceInputSpec(BaseInterfaceInputSpec):

nipype/interfaces/dipy/reconstruction.py

@@ -15,7 +15,7 @@
                                     traits)
 from nipype.utils.filemanip import split_filename, fname_presuffix
 
-from .base import DipyBaseInterface
+from .base import DipyBaseInterface, DipyBaseInterfaceInputSpec
 
 from nipype import logging
 iflogger = logging.getLogger('interface')
@@ -39,7 +39,6 @@ class RESTOREOutputSpec(TraitedSpec):
                        'fitted DTI'))
     evals = File(desc=('output the eigenvalues of the fitted DTI'))
     evecs = File(desc=('output the eigenvectors of the fitted DTI'))
-    # out_dti = File(desc=('output DTI file'))
 
 
 class RESTORE(DipyBaseInterface):
@@ -60,9 +59,9 @@ class RESTORE(DipyBaseInterface):
 
     >>> import pysdcev.interfaces.reconstruction as pir
     >>> dti = pir.RESTORE()
-    >>> dti.inputs.in_file = 'dwi.nii'
-    >>> dti.inputs.in_bval = 'bval.txt'
-    >>> dti.inputs.in_bvec = 'bvec.txt'
+    >>> dti.inputs.in_file = '4d_dwi.nii'
+    >>> dti.inputs.in_bval = 'bvals'
+    >>> dti.inputs.in_bvec = 'bvecs'
     >>> res = dti.run() # doctest: +SKIP
 
 
@@ -188,9 +187,9 @@ class EstimateResponseSH(DipyBaseInterface):
 
     >>> import pysdcev.interfaces.reconstruction as pir
     >>> dti = pir.EstimateResponseSH()
-    >>> dti.inputs.in_file = 'dwi.nii'
-    >>> dti.inputs.in_bval = 'bval.txt'
-    >>> dti.inputs.in_bvec = 'bvec.txt'
+    >>> dti.inputs.in_file = '4d_dwi.nii'
+    >>> dti.inputs.in_bval = 'bvals'
+    >>> dti.inputs.in_bvec = 'bvecs'
     >>> dti.inputs.in_evals = 'dwi_evals.nii'
     >>> res = dti.run() # doctest: +SKIP
 
@@ -307,9 +306,9 @@ class CSD(DipyBaseInterface):
 
     >>> import pysdcev.interfaces.reconstruction as pir
     >>> csd = pir.CSD()
-    >>> csd.inputs.in_file = 'dwi.nii'
-    >>> csd.inputs.in_bval = 'bval.txt'
-    >>> csd.inputs.in_bvec = 'bvec.txt'
+    >>> csd.inputs.in_file = '4d_dwi.nii'
+    >>> csd.inputs.in_bval = 'bvals'
+    >>> csd.inputs.in_bvec = 'bvecs'
     >>> res = csd.run() # doctest: +SKIP
     """
     input_spec = CSDInputSpec

nipype/interfaces/dipy/tests/test_auto_CSD.py

@@ -0,0 +1,41 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.dipy.reconstruction import CSD
+
+def test_CSD_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_bval=dict(mandatory=True,
+    ),
+    in_bvec=dict(mandatory=True,
+    ),
+    in_file=dict(mandatory=True,
+    ),
+    in_mask=dict(),
+    out_fods=dict(),
+    out_prefix=dict(),
+    response=dict(),
+    save_fods=dict(exists=True,
+    usedefault=True,
+    ),
+    sh_order=dict(exists=True,
+    usedefault=True,
+    ),
+    )
+    inputs = CSD.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_CSD_outputs():
+    output_map = dict(model=dict(),
+    out_fods=dict(),
+    )
+    outputs = CSD.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/dipy/tests/test_auto_DipyBaseInterface.py

@@ -0,0 +1,22 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.dipy.base import DipyBaseInterface
+
+def test_DipyBaseInterface_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_bval=dict(mandatory=True,
+    ),
+    in_bvec=dict(mandatory=True,
+    ),
+    in_file=dict(mandatory=True,
+    ),
+    out_prefix=dict(),
+    )
+    inputs = DipyBaseInterface.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+

nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py

@@ -0,0 +1,41 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.dipy.reconstruction import EstimateResponseSH
+
+def test_EstimateResponseSH_inputs():
+    input_map = dict(fa_thresh=dict(usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_bval=dict(mandatory=True,
+    ),
+    in_bvec=dict(mandatory=True,
+    ),
+    in_evals=dict(mandatory=True,
+    ),
+    in_file=dict(mandatory=True,
+    ),
+    in_mask=dict(),
+    out_prefix=dict(),
+    response=dict(),
+    save_glyph=dict(mandatory=True,
+    usedefault=True,
+    ),
+    )
+    inputs = EstimateResponseSH.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_EstimateResponseSH_outputs():
+    output_map = dict(glyph_file=dict(),
+    response=dict(),
+    )
+    outputs = EstimateResponseSH.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/dipy/tests/test_auto_RESTORE.py

@@ -0,0 +1,39 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.dipy.reconstruction import RESTORE
+
+def test_RESTORE_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_bval=dict(mandatory=True,
+    ),
+    in_bvec=dict(mandatory=True,
+    ),
+    in_file=dict(mandatory=True,
+    ),
+    in_mask=dict(),
+    noise_mask=dict(),
+    out_prefix=dict(),
+    )
+    inputs = RESTORE.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_RESTORE_outputs():
+    output_map = dict(evals=dict(),
+    evecs=dict(),
+    fa=dict(),
+    md=dict(),
+    mode=dict(),
+    rd=dict(),
+    trace=dict(),
+    )
+    outputs = RESTORE.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/dipy/tests/test_auto_StreamlineTractography.py

@@ -0,0 +1,53 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.dipy.tracks import StreamlineTractography
+
+def test_StreamlineTractography_inputs():
+    input_map = dict(gfa_thresh=dict(mandatory=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(mandatory=True,
+    ),
+    in_model=dict(),
+    in_peaks=dict(),
+    min_angle=dict(mandatory=True,
+    usedefault=True,
+    ),
+    multiprocess=dict(mandatory=True,
+    usedefault=True,
+    ),
+    num_seeds=dict(mandatory=True,
+    usedefault=True,
+    ),
+    out_prefix=dict(),
+    peak_threshold=dict(mandatory=True,
+    usedefault=True,
+    ),
+    save_seeds=dict(mandatory=True,
+    usedefault=True,
+    ),
+    seed_coord=dict(),
+    seed_mask=dict(),
+    tracking_mask=dict(),
+    )
+    inputs = StreamlineTractography.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_StreamlineTractography_outputs():
+    output_map = dict(gfa=dict(),
+    odf_peaks=dict(),
+    out_seeds=dict(),
+    tracks=dict(),
+    )
+    outputs = StreamlineTractography.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/dipy/tracks.py

@@ -141,7 +141,7 @@ class StreamlineTractography(BaseInterface):
 
     >>> import pysdcev.interfaces.reconstruction as pir
     >>> track = pir.StreamlineTractography()
-    >>> track.inputs.in_file = 'dwi.nii'
+    >>> track.inputs.in_file = '4d_dwi.nii'
     >>> track.inputs.in_model = 'model.pklz'
     >>> track.inputs.tracking_mask = 'dilated_wm_mask.nii'
     >>> res = track.run() # doctest: +SKIP