made files save to node working directories

Author: kesshijordan

nipype/interfaces/dtitk/registration.py

@@ -34,7 +34,7 @@
 
 class RigidInputSpec(CommandLineInputSpec):
     fixed_file = File(desc="fixed tensor volume", exists=True,
-                      mandatory=True, position=0, argstr="%s")
+                      mandatory=True, position=0, argstr="%s", copyfile=False)
     moving_file = File(desc="moving tensor volume", exists=True,
                        mandatory=True, position=1, argstr="%s", copyfile=False)
     similarity_metric = traits.Enum('EDS', 'GDS', 'DDS', 'NMI',
@@ -46,8 +46,13 @@ class RigidInputSpec(CommandLineInputSpec):
     ftol = traits.Float(mandatory=True, position=4, argstr="%g",
                         desc="cost function tolerance", default_value=0.01,
                         usedefault=True)
-    use_in_trans = traits.Bool(position=5, argstr="1",
-                               desc="initialize with existing transform")
+    # use_in_trans = traits.Bool(position=5, argstr="1",
+    #                            desc="initialize with existing transform")
+    initialize_xfm = File(desc="DTITK-FORMAT transform ",
+                          copyfile=False, position=5, argstr="%s")
+    # need to enforce DTITK format or it's a silent failure
+    # (can we search the stderr for keywords to error if not found?)
+    # stderr: filename.aff doesn't exist or can't be opened
 
 
 class RigidOutputSpec(TraitedSpec):
@@ -68,15 +73,19 @@ class Rigid(CommandLineDtitk):
     >>> node.inputs.similarity_metric = 'EDS'
     >>> node.inputs.sampling_xyz = (4,4,4)
     >>> node.inputs.ftol = 0.01
-    >>> node.inputs.use_in_trans = True
     >>> node.cmdline
-    'dti_rigid_reg im1.nii im2.nii EDS 4 4 4 0.01 1'
+    'dti_rigid_reg im1.nii im2.nii EDS 4 4 4 0.01'
     >>> node.run() # doctest: +SKIP
     """
     input_spec = RigidInputSpec
     output_spec = RigidOutputSpec
     _cmd = 'dti_rigid_reg'
 
+    '''def _format_arg(self, name, spec, value):
+        if name == 'initialize_xfm':
+            value = 1
+        return super(Rigid, self)._format_arg(name, spec, value)'''
+
     def _list_outputs(self):
         outputs = self.output_spec().get()
         moving = self.inputs.moving_file
@@ -99,9 +108,9 @@ class Affine(Rigid):
     >>> node.inputs.similarity_metric = 'EDS'
     >>> node.inputs.sampling_xyz = (4,4,4)
     >>> node.inputs.ftol = 0.01
-    >>> node.inputs.use_in_trans = True
+    >>> node.inputs.initialize_xfm = 'im_affine.aff'
     >>> node.cmdline
-    'dti_affine_reg im1.nii im2.nii EDS 4 4 4 0.01 1'
+    'dti_affine_reg im1.nii im2.nii EDS 4 4 4 0.01 im_affine.aff'
     >>> node.run() # doctest: +SKIP
     """
     _cmd = 'dti_affine_reg'

nipype/interfaces/dtitk/tests/test_auto_Affine.py

@@ -12,6 +12,7 @@ def test_Affine_inputs():
         ),
         fixed_file=dict(
             argstr='%s',
+            copyfile=False,
             mandatory=True,
             position=0,
         ),
@@ -26,6 +27,11 @@ def test_Affine_inputs():
             nohash=True,
             usedefault=True,
         ),
+        initialize_xfm=dict(
+            argstr='%s',
+            copyfile=False,
+            position=5,
+        ),
         moving_file=dict(
             argstr='%s',
             copyfile=False,
@@ -48,10 +54,6 @@ def test_Affine_inputs():
             deprecated='1.0.0',
             nohash=True,
         ),
-        use_in_trans=dict(
-            argstr='1',
-            position=5,
-        ),
     )
     inputs = Affine.input_spec()
 

nipype/interfaces/dtitk/tests/test_auto_AffineTask.py

@@ -12,6 +12,7 @@ def test_AffineTask_inputs():
         ),
         fixed_file=dict(
             argstr='%s',
+            copyfile=False,
             mandatory=True,
             position=0,
         ),
@@ -26,6 +27,11 @@ def test_AffineTask_inputs():
             nohash=True,
             usedefault=True,
         ),
+        initialize_xfm=dict(
+            argstr='%s',
+            copyfile=False,
+            position=5,
+        ),
         moving_file=dict(
             argstr='%s',
             copyfile=False,
@@ -48,10 +54,6 @@ def test_AffineTask_inputs():
             deprecated='1.0.0',
             nohash=True,
         ),
-        use_in_trans=dict(
-            argstr='1',
-            position=5,
-        ),
     )
     inputs = AffineTask.input_spec()
 

nipype/interfaces/dtitk/tests/test_auto_Rigid.py

@@ -12,6 +12,7 @@ def test_Rigid_inputs():
         ),
         fixed_file=dict(
             argstr='%s',
+            copyfile=False,
             mandatory=True,
             position=0,
         ),
@@ -26,6 +27,11 @@ def test_Rigid_inputs():
             nohash=True,
             usedefault=True,
         ),
+        initialize_xfm=dict(
+            argstr='%s',
+            copyfile=False,
+            position=5,
+        ),
         moving_file=dict(
             argstr='%s',
             copyfile=False,
@@ -48,10 +54,6 @@ def test_Rigid_inputs():
             deprecated='1.0.0',
             nohash=True,
         ),
-        use_in_trans=dict(
-            argstr='1',
-            position=5,
-        ),
     )
     inputs = Rigid.input_spec()
 

nipype/interfaces/dtitk/tests/test_auto_RigidTask.py

@@ -12,6 +12,7 @@ def test_RigidTask_inputs():
         ),
         fixed_file=dict(
             argstr='%s',
+            copyfile=False,
             mandatory=True,
             position=0,
         ),
@@ -26,6 +27,11 @@ def test_RigidTask_inputs():
             nohash=True,
             usedefault=True,
         ),
+        initialize_xfm=dict(
+            argstr='%s',
+            copyfile=False,
+            position=5,
+        ),
         moving_file=dict(
             argstr='%s',
             copyfile=False,
@@ -48,10 +54,6 @@ def test_RigidTask_inputs():
             deprecated='1.0.0',
             nohash=True,
         ),
-        use_in_trans=dict(
-            argstr='1',
-            position=5,
-        ),
     )
     inputs = RigidTask.input_spec()