ENH: Add 1dCat, 3dNwarpApply, and add options to 3dBrickStat

nipype/interfaces/afni/__init__.py

@@ -17,8 +17,8 @@
                          Seg, SkullStrip, TCorr1D, TCorrMap, TCorrelate,
                          TShift, Volreg, Warp, QwarpPlusMinus, Qwarp)
 from .svm import (SVMTest, SVMTrain)
-from .utils import (AFNItoNIFTI, Autobox,Axialize, BrickStat, Calc, Copy, Edge3,
-                    Eval, FWHMx,
-                    MaskTool, Merge, Notes, Refit, Resample, TCat, TStat, To3D,
-                    Unifize, ZCutUp, GCOR,Zcat, Zeropad)
+from .utils import (AFNItoNIFTI, Autobox, Axialize, BrickStat, Calc, Cat, Copy,
+                    Edge3, Eval, FWHMx, MaskTool, Merge, Notes, NwarpApply,
+                    Refit, Resample, TCat, TStat, To3D, Unifize, ZCutUp, GCOR,
+                    Zcat, Zeropad)
 from .model import (Deconvolve, Remlfit)

nipype/interfaces/afni/model.py

@@ -360,7 +360,6 @@ class RemlfitInputSpec(AFNICommandInputSpec):
              'option. Each column in the specified file(s) will be appended '
              'to the matrix. File(s) must have at least as many rows as the '
              'matrix does.',
-        exists=True,
         copyfile=False,
         sep=" ",
         argstr='-addbase %s')

nipype/interfaces/afni/tests/test_auto_Axialize.py

@@ -0,0 +1,55 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import Axialize
+
+
+def test_Axialize_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    axial=dict(argstr='-axial',
+    xor=['coronal', 'sagittal'],
+    ),
+    coronal=dict(argstr='-coronal',
+    xor=['sagittal', 'axial'],
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='%s',
+    copyfile=False,
+    mandatory=True,
+    position=-2,
+    ),
+    orientation=dict(argstr='-orient %s',
+    ),
+    out_file=dict(argstr='-prefix %s',
+    name_source='in_file',
+    name_template='%s_axialize',
+    ),
+    outputtype=dict(),
+    sagittal=dict(argstr='-sagittal',
+    xor=['coronal', 'axial'],
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    verb=dict(argstr='-verb',
+    ),
+    )
+    inputs = Axialize.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_Axialize_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = Axialize.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/afni/tests/test_auto_BrickStat.py

@@ -19,11 +19,23 @@ def test_BrickStat_inputs():
     mask=dict(argstr='-mask %s',
     position=2,
     ),
+    max=dict(argstr='-max',
+    ),
+    mean=dict(argstr='-mean',
+    ),
     min=dict(argstr='-min',
     position=1,
     ),
+    percentile=dict(argstr='-percentile %.3f %.3f %.3f',
+    ),
+    slow=dict(argstr='-slow',
+    ),
+    sum=dict(argstr='-sum',
+    ),
     terminal_output=dict(nohash=True,
     ),
+    var=dict(argstr='-var',
+    ),
     )
     inputs = BrickStat.input_spec()
 

nipype/interfaces/afni/tests/test_auto_Cat.py

@@ -0,0 +1,66 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import Cat
+
+
+def test_Cat_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_files=dict(argstr='%s',
+    mandatory=True,
+    position=-2,
+    ),
+    keepfree=dict(argstr='-nonfixed',
+    ),
+    omitconst=dict(argstr='-nonconst',
+    ),
+    out_cint=dict(xor=['out_format', 'out_nice', 'out_double', 'out_fint', 'out_int'],
+    ),
+    out_double=dict(argstr='-d',
+    xor=['out_format', 'out_nice', 'out_int', 'out_fint', 'out_cint'],
+    ),
+    out_file=dict(argstr='> %s',
+    mandatory=True,
+    position=-1,
+    ),
+    out_fint=dict(argstr='-f',
+    xor=['out_format', 'out_nice', 'out_double', 'out_int', 'out_cint'],
+    ),
+    out_format=dict(argstr='-form %s',
+    xor=['out_int', 'out_nice', 'out_double', 'out_fint', 'out_cint'],
+    ),
+    out_int=dict(argstr='-i',
+    xor=['out_format', 'out_nice', 'out_double', 'out_fint', 'out_cint'],
+    ),
+    out_nice=dict(argstr='-n',
+    xor=['out_format', 'out_int', 'out_double', 'out_fint', 'out_cint'],
+    ),
+    outputtype=dict(),
+    sel=dict(argstr='-sel %s',
+    ),
+    stack=dict(argstr='-stack',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = Cat.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_Cat_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = Cat.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/afni/tests/test_auto_NwarpApply.py

@@ -0,0 +1,58 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import NwarpApply
+
+
+def test_NwarpApply_inputs():
+    input_map = dict(ainterp=dict(argstr='-ainterp %s',
+    ),
+    args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-source %s',
+    mandatory=True,
+    ),
+    interp=dict(argstr='-interp %s',
+    ),
+    inv_warp=dict(argstr='-iwarp',
+    ),
+    master=dict(argstr='-master %s',
+    ),
+    out_file=dict(argstr='-prefix %s',
+    name_source='in_file',
+    name_template='%s_Nwarp',
+    ),
+    quiet=dict(argstr='-quiet',
+    xor=['verb'],
+    ),
+    short=dict(argstr='-short',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    verb=dict(argstr='-verb',
+    xor=['quiet'],
+    ),
+    warp=dict(argstr='-nwarp %s',
+    mandatory=True,
+    ),
+    )
+    inputs = NwarpApply.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_NwarpApply_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = NwarpApply.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/afni/tests/test_auto_Qwarp.py

@@ -0,0 +1,158 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..preprocess import Qwarp
+
+
+def test_Qwarp_inputs():
+    input_map = dict(Qfinal=dict(argstr='-Qfinal',
+    ),
+    Qonly=dict(argstr='-Qonly',
+    ),
+    allsave=dict(argstr='-allsave',
+    xor=['nopadWARP', 'duplo', 'plusminus'],
+    ),
+    args=dict(argstr='%s',
+    ),
+    ballopt=dict(argstr='-ballopt',
+    xor=['workhard', 'boxopt'],
+    ),
+    base_file=dict(argstr='-base %s',
+    copyfile=False,
+    mandatory=True,
+    ),
+    baxopt=dict(argstr='-boxopt',
+    xor=['workhard', 'ballopt'],
+    ),
+    blur=dict(argstr='-blur %s',
+    ),
+    duplo=dict(argstr='-duplo',
+    xor=['gridlist', 'maxlev', 'inilev', 'iniwarp', 'plusminus', 'allsave'],
+    ),
+    emask=dict(argstr='-emask %s',
+    copyfile=False,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    expad=dict(argstr='-expad %d',
+    xor=['nopadWARP'],
+    ),
+    gridlist=dict(argstr='-gridlist %s',
+    copyfile=False,
+    xor=['duplo', 'plusminus'],
+    ),
+    hel=dict(argstr='-hel',
+    xor=['nmi', 'mi', 'lpc', 'lpa', 'pear'],
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-source %s',
+    copyfile=False,
+    mandatory=True,
+    ),
+    inilev=dict(argstr='-inlev %d',
+    xor=['duplo'],
+    ),
+    iniwarp=dict(argstr='-iniwarp %s',
+    xor=['duplo'],
+    ),
+    iwarp=dict(argstr='-iwarp',
+    xor=['plusminus'],
+    ),
+    lpa=dict(argstr='-lpa',
+    xor=['nmi', 'mi', 'lpc', 'hel', 'pear'],
+    ),
+    lpc=dict(argstr='-lpc',
+    position=-2,
+    xor=['nmi', 'mi', 'hel', 'lpa', 'pear'],
+    ),
+    maxlev=dict(argstr='-maxlev %d',
+    position=-1,
+    xor=['duplo'],
+    ),
+    mi=dict(argstr='-mi',
+    xor=['mi', 'hel', 'lpc', 'lpa', 'pear'],
+    ),
+    minpatch=dict(argstr='-minpatch %d',
+    ),
+    nmi=dict(argstr='-nmi',
+    xor=['nmi', 'hel', 'lpc', 'lpa', 'pear'],
+    ),
+    noXdis=dict(argstr='-noXdis',
+    ),
+    noYdis=dict(argstr='-noYdis',
+    ),
+    noZdis=dict(argstr='-noZdis',
+    ),
+    noneg=dict(argstr='-noneg',
+    ),
+    nopad=dict(argstr='-nopad',
+    ),
+    nopadWARP=dict(argstr='-nopadWARP',
+    xor=['allsave', 'expad'],
+    ),
+    nopenalty=dict(argstr='-nopenalty',
+    ),
+    nowarp=dict(argstr='-nowarp',
+    ),
+    noweight=dict(argstr='-noweight',
+    ),
+    out_file=dict(argstr='-prefix %s',
+    genfile=True,
+    name_source=['in_file'],
+    name_template='%s_QW',
+    ),
+    out_weight_file=dict(argstr='-wtprefix %s',
+    ),
+    outputtype=dict(),
+    overwrite=dict(argstr='-overwrite',
+    ),
+    pblur=dict(argstr='-pblur %s',
+    ),
+    pear=dict(argstr='-pear',
+    ),
+    penfac=dict(argstr='-penfac %f',
+    ),
+    plusminus=dict(argstr='-plusminus',
+    xor=['duplo', 'allsave', 'iwarp'],
+    ),
+    quiet=dict(argstr='-quiet',
+    xor=['verb'],
+    ),
+    resample=dict(argstr='-resample',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    verb=dict(argstr='-verb',
+    xor=['quiet'],
+    ),
+    wball=dict(argstr='-wball %s',
+    ),
+    weight=dict(argstr='-weight %s',
+    ),
+    wmask=dict(argstr='-wpass %s %f',
+    ),
+    workhard=dict(argstr='-workhard',
+    xor=['boxopt', 'ballopt'],
+    ),
+    )
+    inputs = Qwarp.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_Qwarp_outputs():
+    output_map = dict(base_warp=dict(),
+    source_warp=dict(),
+    warped_base=dict(),
+    warped_source=dict(),
+    weights=dict(),
+    )
+    outputs = Qwarp.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/afni/tests/test_auto_Remlfit.py

@@ -8,7 +8,6 @@ def test_Remlfit_inputs():
     ),
     addbase=dict(argstr='-addbase %s',
     copyfile=False,
-    exists=True,
     sep=' ',
     ),
     args=dict(argstr='%s',