Reorganize afni interface.

Create utils.py and move several functions from preprocess to utils.

Also, add optional arguments to AFNItoNIFTI, standardize long strings
and standardize spacing.

Author: tsalo

.cache/v/cache/lastfailed

@@ -0,0 +1,4 @@
+{
+  "nipype/algorithms/tests/test_mesh_ops.py::test_ident_distances": true, 
+  "nipype/algorithms/tests/test_mesh_ops.py::test_trans_distances": true
+}

nipype/interfaces/afni/__init__.py

@@ -8,12 +8,16 @@
 """
 
 from .base import Info
-from .preprocess import (AFNItoNIFTI, Allineate, AutoTcorrelate, Autobox,
-                         Automask, Bandpass, BlurInMask, BlurToFWHM, BrickStat,
-                         Calc, ClipLevel, Copy, DegreeCentrality, Despike,
-                         Detrend, ECM, Eval, FWHMx, Fim, Fourier, Hist, LFCD,
-                         MaskTool, Maskave, Means, Merge, Notes, OutlierCount,
-                         QualityIndex, ROIStats, Refit, Resample, Retroicor,
-                         Seg, SkullStrip, TCat, TCorr1D, TCorrMap, TCorrelate,
-                         TShift, TStat, To3D, Volreg, Warp, ZCutUp)
+from .preprocess import (Allineate, Automask, AutoTcorrelate,
+                         Bandpass, BlurInMask, BlurToFWHM,
+                         ClipLevel, DegreeCentrality, Despike,
+                         Detrend, ECM, Fim, Fourier, Hist, LFCD,
+                         Maskave, Means, OutlierCount,
+                         QualityIndex, ROIStats, Retroicor,
+                         Seg, SkullStrip, TCorr1D, TCorrMap, TCorrelate,
+                         TShift, Volreg, Warp)
 from .svm import (SVMTest, SVMTrain)
+from .utils import (AFNItoNIFTI, Autobox, BrickStat, Calc, Copy,
+                    Eval, FWHMx,
+                    MaskTool, Merge, Notes, Refit, Resample, TCat, TStat, To3D,
+                    ZCutUp,)

nipype/interfaces/afni/preprocess.py

@@ -1,11 +1,13 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from ....testing import assert_equal
-from ..preprocess import AFNItoNIFTI
+from ..utils import AFNItoNIFTI
 
 
 def test_AFNItoNIFTI_inputs():
     input_map = dict(args=dict(argstr='%s',
     ),
+    denote=dict(argstr='-denote',
+    ),
     environ=dict(nohash=True,
     usedefault=True,
     ),
@@ -17,11 +19,20 @@ def test_AFNItoNIFTI_inputs():
     mandatory=True,
     position=-1,
     ),
+    newid=dict(argstr='-newid',
+    xor=[u'oldid'],
+    ),
+    oldid=dict(argstr='-oldid',
+    xor=[u'newid'],
+    ),
     out_file=dict(argstr='-prefix %s',
+    hash_files=False,
     name_source='in_file',
     name_template='%s.nii',
     ),
     outputtype=dict(),
+    pure=dict(argstr='-pure',
+    ),
     terminal_output=dict(nohash=True,
     ),
     )

nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py

@@ -1,6 +1,6 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from ....testing import assert_equal
-from ..preprocess import Autobox
+from ..utils import Autobox
 
 
 def test_Autobox_inputs():

nipype/interfaces/afni/tests/test_auto_Autobox.py

@@ -1,6 +1,6 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from ....testing import assert_equal
-from ..preprocess import BrickStat
+from ..utils import BrickStat
 
 
 def test_BrickStat_inputs():

nipype/interfaces/afni/tests/test_auto_BrickStat.py

@@ -1,6 +1,6 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from ....testing import assert_equal
-from ..preprocess import Calc
+from ..utils import Calc
 
 
 def test_Calc_inputs():
@@ -20,10 +20,10 @@ def test_Calc_inputs():
     mandatory=True,
     position=0,
     ),
-    in_file_b=dict(argstr=' -b %s',
+    in_file_b=dict(argstr='-b %s',
     position=1,
     ),
-    in_file_c=dict(argstr=' -c %s',
+    in_file_c=dict(argstr='-c %s',
     position=2,
     ),
     other=dict(argstr='',

nipype/interfaces/afni/tests/test_auto_Calc.py

@@ -1,6 +1,6 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from ....testing import assert_equal
-from ..preprocess import Copy
+from ..utils import Copy
 
 
 def test_Copy_inputs():

nipype/interfaces/afni/tests/test_auto_Copy.py

@@ -1,6 +1,6 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from ....testing import assert_equal
-from ..preprocess import Eval
+from ..utils import Eval
 
 
 def test_Eval_inputs():
@@ -20,10 +20,10 @@ def test_Eval_inputs():
     mandatory=True,
     position=0,
     ),
-    in_file_b=dict(argstr=' -b %s',
+    in_file_b=dict(argstr='-b %s',
     position=1,
     ),
-    in_file_c=dict(argstr=' -c %s',
+    in_file_c=dict(argstr='-c %s',
     position=2,
     ),
     other=dict(argstr='',

nipype/interfaces/afni/tests/test_auto_Eval.py

@@ -1,6 +1,6 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from ....testing import assert_equal
-from ..preprocess import FWHMx
+from ..utils import FWHMx
 
 
 def test_FWHMx_inputs():