fixed composeXfm naming; added tests for old interface names

Author: kesshijordan

nipype/interfaces/dtitk/registration.py

@@ -25,7 +25,7 @@
 """
 
 from ..base import TraitedSpec, CommandLineInputSpec, traits, File, isdefined
-from ...utils.filemanip import fname_presuffix
+from ...utils.filemanip import fname_presuffix, split_filename
 from .base import CommandLineDtitk, DTITKRenameMixin
 import os
 
@@ -166,8 +166,6 @@ class ComposeXfmInputSpec(CommandLineInputSpec):
                   argstr="-aff %s", mandatory=True)
     out_file = File(desc='output path',
                     argstr="-out %s",  genfile=True)
-    # keep_extension is keeping the .df but not .nii
-    # need to fix when PR 2506 is done
 
 
 class ComposeXfmOutputSpec(TraitedSpec):
@@ -205,9 +203,12 @@ def _list_outputs(self):
     def _gen_filename(self, name):
         if name != 'out_file':
             return
-        return fname_presuffix(os.path.basename(
-                               self.inputs.in_df).split('.')[0],
-                               suffix='_affdf.df.nii')
+        path, base, ext = split_filename(self.inputs.in_df)
+        suffix = '_affdf'
+        if base.endswith('.df'):
+            suffix += '.df'
+            base = base[:-3]
+        return fname_presuffix(base, suffix=suffix + ext, use_ext=False)
 
 
 class AffSymTensor3DVolInputSpec(CommandLineInputSpec):

nipype/interfaces/dtitk/tests/test_auto_AffineTask.py

@@ -0,0 +1,70 @@
+# 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,
+        ),
+        fixed_file=dict(
+            argstr='%s',
+            mandatory=True,
+            position=0,
+        ),
+        ftol=dict(
+            argstr='%g',
+            mandatory=True,
+            position=4,
+            usedefault=True,
+        ),
+        ignore_exception=dict(
+            deprecated='1.0.0',
+            nohash=True,
+            usedefault=True,
+        ),
+        moving_file=dict(
+            argstr='%s',
+            copyfile=False,
+            mandatory=True,
+            position=1,
+        ),
+        sampling_xyz=dict(
+            argstr='%g %g %g',
+            mandatory=True,
+            position=3,
+            usedefault=True,
+        ),
+        similarity_metric=dict(
+            argstr='%s',
+            mandatory=True,
+            position=2,
+            usedefault=True,
+        ),
+        terminal_output=dict(
+            deprecated='1.0.0',
+            nohash=True,
+        ),
+        use_in_trans=dict(
+            argstr='1',
+            position=5,
+        ),
+    )
+    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 +1,68 @@
+# 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(
+            deprecated='1.0.0',
+            nohash=True,
+            usedefault=True,
+        ),
+        in_file=dict(
+            argstr='%s',
+            mandatory=True,
+            position=0,
+        ),
+        inside_value=dict(
+            argstr='%g',
+            mandatory=True,
+            position=4,
+            usedefault=True,
+        ),
+        lower_bound=dict(
+            argstr='%g',
+            mandatory=True,
+            position=2,
+        ),
+        out_file=dict(
+            argstr='%s',
+            keep_extension=True,
+            name_source='in_file',
+            name_template='%s_thrbin',
+            position=1,
+        ),
+        outside_value=dict(
+            argstr='%g',
+            mandatory=True,
+            position=5,
+            usedefault=True,
+        ),
+        terminal_output=dict(
+            deprecated='1.0.0',
+            nohash=True,
+        ),
+        upper_bound=dict(
+            argstr='%g',
+            mandatory=True,
+            position=3,
+        ),
+    )
+    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_ComposeXfmTask.py

@@ -0,0 +1,47 @@
+# 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(
+            deprecated='1.0.0',
+            nohash=True,
+            usedefault=True,
+        ),
+        in_aff=dict(
+            argstr='-aff %s',
+            mandatory=True,
+        ),
+        in_df=dict(
+            argstr='-df %s',
+            copyfile=False,
+            mandatory=True,
+        ),
+        out_file=dict(
+            argstr='-out %s',
+            genfile=True,
+        ),
+        terminal_output=dict(
+            deprecated='1.0.0',
+            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

nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py

@@ -0,0 +1,68 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..registration import DiffeoTask
+
+
+def test_DiffeoTask_inputs():
+    input_map = dict(
+        args=dict(argstr='%s', ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        fixed_file=dict(
+            argstr='%s',
+            position=0,
+        ),
+        ftol=dict(
+            argstr='%g',
+            mandatory=True,
+            position=5,
+            usedefault=True,
+        ),
+        ignore_exception=dict(
+            deprecated='1.0.0',
+            nohash=True,
+            usedefault=True,
+        ),
+        legacy=dict(
+            argstr='%d',
+            mandatory=True,
+            position=3,
+            usedefault=True,
+        ),
+        mask_file=dict(
+            argstr='%s',
+            position=2,
+        ),
+        moving_file=dict(
+            argstr='%s',
+            copyfile=False,
+            position=1,
+        ),
+        n_iters=dict(
+            argstr='%d',
+            mandatory=True,
+            position=4,
+            usedefault=True,
+        ),
+        terminal_output=dict(
+            deprecated='1.0.0',
+            nohash=True,
+        ),
+    )
+    inputs = DiffeoTask.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_DiffeoTask_outputs():
+    output_map = dict(
+        out_file=dict(),
+        out_file_xfm=dict(),
+    )
+    outputs = DiffeoTask.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_RigidTask.py

@@ -0,0 +1,70 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..registration import RigidTask
+
+
+def test_RigidTask_inputs():
+    input_map = dict(
+        args=dict(argstr='%s', ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        fixed_file=dict(
+            argstr='%s',
+            mandatory=True,
+            position=0,
+        ),
+        ftol=dict(
+            argstr='%g',
+            mandatory=True,
+            position=4,
+            usedefault=True,
+        ),
+        ignore_exception=dict(
+            deprecated='1.0.0',
+            nohash=True,
+            usedefault=True,
+        ),
+        moving_file=dict(
+            argstr='%s',
+            copyfile=False,
+            mandatory=True,
+            position=1,
+        ),
+        sampling_xyz=dict(
+            argstr='%g %g %g',
+            mandatory=True,
+            position=3,
+            usedefault=True,
+        ),
+        similarity_metric=dict(
+            argstr='%s',
+            mandatory=True,
+            position=2,
+            usedefault=True,
+        ),
+        terminal_output=dict(
+            deprecated='1.0.0',
+            nohash=True,
+        ),
+        use_in_trans=dict(
+            argstr='1',
+            position=5,
+        ),
+    )
+    inputs = RigidTask.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_RigidTask_outputs():
+    output_map = dict(
+        out_file=dict(),
+        out_file_xfm=dict(),
+    )
+    outputs = RigidTask.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value