enh: preliminary testing + altered auto tests

Author: mgxd

nipype/interfaces/fsl/tests/test_auto_Eddy.py

@@ -88,9 +88,6 @@ def test_Eddy_inputs():
 def test_Eddy_outputs():
     output_map = dict(out_corrected=dict(),
     out_movement_rms=dict(),
-    out_outlier_map=dict(),
-    out_outlier_n_sd_map=dict(),
-    out_outlier_n_sqr_sd_map=dict(),
     out_outlier_report=dict(),
     out_parameter=dict(),
     out_restricted_movement_rms=dict(),

nipype/interfaces/fsl/tests/test_auto_TOPUP.py

@@ -54,10 +54,6 @@ def test_TOPUP_inputs():
     name_source=['in_file'],
     name_template='%s_field',
     ),
-    out_warp_prefix=dict(argstr='--dfout=%s',
-    hash_files=False,
-    usedefault=True,
-    ),
     out_jac_prefix=dict(argstr='--jacout=%s',
     hash_files=False,
     usedefault=True,
@@ -68,6 +64,10 @@ def test_TOPUP_inputs():
     name_source=['in_file'],
     name_template='%s_topup.log',
     ),
+    out_warp_prefix=dict(argstr='--dfout=%s',
+    hash_files=False,
+    usedefault=True,
+    ),
     output_type=dict(),
     readout_times=dict(mandatory=True,
     requires=['encoding_direction'],
@@ -104,10 +104,10 @@ def test_TOPUP_outputs():
     out_enc_file=dict(),
     out_field=dict(),
     out_fieldcoef=dict(),
+    out_jacs=dict(),
     out_logfile=dict(),
     out_movpar=dict(),
     out_warps=dict(),
-    out_jacs=dict(),
     )
     outputs = TOPUP.output_spec()
 

nipype/interfaces/spm/base.py

@@ -539,7 +539,7 @@ class ImageFileSPM(ImageFile):
     """
 
     def __init__(self, value='', filter=None, auto_set=False, entries=0,
-                 exists=False, types=['nifti1', 'nifti2'], extensions=[],
+                 exists=False, types=['nifti1', 'nifti2'],
                  allow_compressed=False, **metadata):
         """ Trait handles neuroimaging files.
 
@@ -552,7 +552,6 @@ def __init__(self, value='', filter=None, auto_set=False, entries=0,
         """
         self.types = types
         self.allow_compressed = allow_compressed
-        self.exts = extensions
         super(ImageFileSPM, self).__init__(value, filter, auto_set, entries,
                                            exists, types, allow_compressed,
-                                           extensions, **metadata)
+                                           **metadata)

nipype/interfaces/tests/test_base.py

@@ -718,3 +718,19 @@ def to_list(x):
             failed_dict[key] = (value, newval)
     return failed_dict
 
+def test_ImageFile():
+    x = nib.BaseInterface().inputs
+
+    # setup traits
+    x.add_trait('nifti', nib.ImageFile(types=['nifti1', 'dicom']))
+    x.add_trait('anytype', nib.ImageFile())
+    x.add_trait('newtype', nib.ImageFile(types=['nifti10']))
+    x.add_trait('nocompress', nib.ImageFile(types=['mgh'],
+                                            allow_compressed=False))
+
+    with pytest.raises(nib.TraitError): x.nifti = 'test.mgz'
+    x.nifti = 'test.nii'
+    x.anytype = 'test.xml'
+    with pytest.raises(AttributeError): x.newtype = 'test.nii'
+    with pytest.raises(nib.TraitError): x.nocompress = 'test.nii.gz'
+    x.nocompress = 'test.mgh'

nipype/interfaces/traits_extension.py

@@ -242,8 +242,7 @@ class ImageFile(File):
     """ Defines a trait of specific neuroimaging files """
 
     def __init__(self, value='', filter=None, auto_set=False, entries=0,
-                 exists=False, types=[], allow_compressed=True, extensions=[],
-                 **metadata):
+                 exists=False, types=[], allow_compressed=True, **metadata):
         """ Trait handles neuroimaging files.
 
         Parameters
@@ -255,12 +254,12 @@ def __init__(self, value='', filter=None, auto_set=False, entries=0,
         """
         self.types = types
         self.allow_compressed = allow_compressed
-        self.exts = extensions
         super(ImageFile, self).__init__(value, filter, auto_set, entries,
                                         exists, **metadata)
 
-    def grab_exts(self, exts=[]):
+    def grab_exts(self):
         # TODO: file type validation
+        exts = []
         for fmt in self.types:
             if fmt in img_fmt_types:
                 exts.extend(sum([[u for u in y[0]] if isinstance(y[0], tuple)
@@ -271,7 +270,7 @@ def grab_exts(self, exts=[]):
             else:
                 raise AttributeError('Information has not been added for format'
                                      ' type {} yet. Supported formats include: '
-                                     '{}'.format('hello',
+                                     '{}'.format(fmt,
                                      ', '.join(img_fmt_types.keys())))
         return list(set(exts))
 
@@ -280,11 +279,11 @@ def validate(self, object, name, value):
         """
         validated_value = super(ImageFile, self).validate(object, name, value)
         if validated_value and self.types:
-            self.exts = self.grab_exts(self.exts)
-            if not any(validated_value.endswith(x) for x in self.exts):
+            self._exts = self.grab_exts()
+            if not any(validated_value.endswith(x) for x in self._exts):
                 raise TraitError(
                     args="{} is not included in allowed types: {}".format(
-                        validated_value, ','.join(self.exts)))
+                        validated_value, ', '.join(self._exts)))
         return validated_value
 
 """