Merge branch 'master' into afni_qwarp

Author: Shotgunosine

doc/images/nipype_architecture_overview2.png

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

doc/images/nipype_architecture_overview2.svg

@@ -0,0 +1,53 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..preprocess import QwarpPlusMinus
+
+
+def test_QwarpPlusMinus_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    base_file=dict(argstr='-base %s',
+    copyfile=False,
+    mandatory=True,
+    ),
+    blur=dict(argstr='-blur %s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    minpatch=dict(argstr='-minpatch %d',
+    ),
+    nopadWARP=dict(argstr='-nopadWARP',
+    ),
+    noweight=dict(argstr='-noweight',
+    ),
+    pblur=dict(argstr='-pblur %s',
+    ),
+    source_file=dict(argstr='-source %s',
+    copyfile=False,
+    mandatory=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = QwarpPlusMinus.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_QwarpPlusMinus_outputs():
+    output_map = dict(base_warp=dict(),
+    source_warp=dict(),
+    warped_base=dict(),
+    warped_source=dict(),
+    )
+    outputs = QwarpPlusMinus.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/__init__.py

@@ -0,0 +1,56 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import Unifize
+
+
+def test_Unifize_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    epi=dict(argstr='-EPI',
+    requires=['no_duplo', 't2'],
+    xor=['gm'],
+    ),
+    gm=dict(argstr='-GM',
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-input %s',
+    copyfile=False,
+    mandatory=True,
+    position=-1,
+    ),
+    no_duplo=dict(argstr='-noduplo',
+    ),
+    out_file=dict(argstr='-prefix %s',
+    name_source='in_file',
+    ),
+    outputtype=dict(),
+    scale_file=dict(argstr='-ssave %s',
+    ),
+    t2=dict(argstr='-T2',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    urad=dict(argstr='-Urad %s',
+    ),
+    )
+    inputs = Unifize.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_Unifize_outputs():
+    output_map = dict(out_file=dict(),
+    scale_file=dict(),
+    )
+    outputs = Unifize.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_QwarpPlusMinus.py

@@ -1535,7 +1535,6 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         return {'out': getattr(self, '_gcor')}
 
-
 class AxializeInputSpec(AFNICommandInputSpec):
     in_file = File(
         desc='input file to 3daxialize',
@@ -1572,7 +1571,7 @@ class AxializeInputSpec(AFNICommandInputSpec):
     orientation = Str(
         desc='new orientation code',
         argstr='-orient %s')
-
+    
 
 class Axialize(AFNICommand):
     """Read in a dataset and write it out as a new dataset
@@ -1583,7 +1582,6 @@ class Axialize(AFNICommand):
 
     Examples
     ========
-
     >>> from nipype.interfaces import afni
     >>> axial3d = afni.Axialize()
     >>> axial3d.inputs.in_file = 'functional.nii'
@@ -1597,3 +1595,166 @@ class Axialize(AFNICommand):
     _cmd = '3daxialize'
     input_spec = AxializeInputSpec
     output_spec = AFNICommandOutputSpec
+   
+
+class ZcatInputSpec(AFNICommandInputSpec):
+    in_files = InputMultiPath(
+        File(
+            desc='input files to 3dZcat',
+            exists=True),
+        argstr='%s',
+        position=-1,
+        mandatory=True,
+        copyfile=False)
+    out_file = File(
+        name_template='zcat',
+        desc='output dataset prefix name (default \'zcat\')',
+        argstr='-prefix %s')
+    datum = traits.Enum(
+        'byte','short','float',
+        argstr='-datum %s',
+        desc='specify data type for output. Valid types are \'byte\', '
+             '\'short\' and \'float\'.')
+    verb = traits.Bool(
+        desc='print out some verbositiness as the program proceeds.',
+        argstr='-verb')
+    fscale = traits.Bool(
+        desc='Force scaling of the output to the maximum integer '
+             'range.  This only has effect if the output datum is '
+             'byte or short (either forced or defaulted). This '
+             'option is sometimes necessary to eliminate '
+             'unpleasant truncation artifacts.',
+        argstr='-fscale',
+        xor=['nscale'])
+    nscale = traits.Bool(
+        desc='Don\'t do any scaling on output to byte or short '
+             'datasets. This may be especially useful when '
+             'operating on mask datasets whose output values '
+             'are only 0\'s and 1\'s.',
+        argstr='-nscale',
+        xor=['fscale'])
+
+class Zcat(AFNICommand):
+    """Copies an image of one type to an image of the same
+    or different type using 3dZcat command
+
+    For complete details, see the `3dZcat Documentation.
+    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dZcat.html>`_
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni
+    >>> zcat = afni.Zcat()
+    >>> zcat.inputs.in_files = ['functional2.nii', 'functional3.nii']
+    >>> zcat.inputs.out_file = 'cat_functional.nii'
+    >>> zcat.cmdline  # doctest: +ALLOW_UNICODE
+    '3dZcat -prefix cat_functional.nii functional2.nii functional3.nii'
+    >>> res = zcat.run()  # doctest: +SKIP
+    """
+
+    _cmd = '3dZcat'
+    input_spec = ZcatInputSpec
+    output_spec = AFNICommandOutputSpec
+
+class ZeropadInputSpec(AFNICommandInputSpec):
+    in_files = File(
+        desc='input dataset',
+        argstr='%s',
+        position=-1,
+        mandatory=True,
+        exists=True,
+        copyfile=False)
+    out_file = File(
+        name_template='zeropad',
+        desc='output dataset prefix name (default \'zeropad\')',
+        argstr='-prefix %s')
+    I = traits.Int(
+        desc='adds \'n\' planes of zero at the Inferior edge',
+        argstr='-I %i',
+        xor=['master'])
+    S = traits.Int(
+        desc='adds \'n\' planes of zero at the Superior edge',
+        argstr='-S %i',
+        xor=['master'])
+    A = traits.Int(
+        desc='adds \'n\' planes of zero at the Anterior edge',
+        argstr='-A %i',
+        xor=['master'])
+    P = traits.Int(
+        desc='adds \'n\' planes of zero at the Posterior edge',
+        argstr='-P %i',
+        xor=['master'])
+    L = traits.Int(
+        desc='adds \'n\' planes of zero at the Left edge',
+        argstr='-L %i',
+        xor=['master'])
+    R = traits.Int(
+        desc='adds \'n\' planes of zero at the Right edge',
+        argstr='-R %i',
+        xor=['master'])
+    z = traits.Int(
+        desc='adds \'n\' planes of zero on EACH of the '
+             'dataset z-axis (slice-direction) faces',
+        argstr='-z %i',
+        xor=['master'])
+    RL = traits.Int(desc='specify that planes should be added or cut '
+                         'symmetrically to make the resulting volume have'
+                         'N slices in the right-left direction',
+                    argstr='-RL %i',
+                    xor=['master'])
+    AP = traits.Int(desc='specify that planes should be added or cut '
+                         'symmetrically to make the resulting volume have'
+                         'N slices in the anterior-posterior direction',
+                    argstr='-AP %i',
+                    xor=['master'])
+    IS = traits.Int(desc='specify that planes should be added or cut '
+                         'symmetrically to make the resulting volume have'
+                         'N slices in the inferior-superior direction',
+                    argstr='-IS %i',
+                    xor=['master'])
+    mm = traits.Bool(desc='pad counts \'n\' are in mm instead of slices, '
+                          'where each \'n\' is an integer and at least \'n\' '
+                          'mm of slices will be added/removed; e.g., n =  3 '
+                          'and slice thickness = 2.5 mm ==> 2 slices added',
+                     argstr='-mm',
+                     xor=['master'])
+    master = traits.File(desc='match the volume described in dataset '
+                              '\'mset\', where mset must have the same '
+                              'orientation and grid spacing as dataset to be '
+                              'padded. the goal of -master is to make the '
+                              'output dataset from 3dZeropad match the '
+                              'spatial \'extents\' of mset by adding or '
+                              'subtracting slices as needed. You can\'t use '
+                              '-I,-S,..., or -mm with -master',
+                         argstr='-master %s',
+                         xor=['I', 'S', 'A', 'P', 'L', 'R', 'z',
+                              'RL', 'AP', 'IS', 'mm'])
+
+class Zeropad(AFNICommand):
+    """Adds planes of zeros to a dataset (i.e., pads it out).
+
+    For complete details, see the `3dZeropad Documentation.
+    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dZeropad.html>`_
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni
+    >>> zeropad = afni.Zeropad()
+    >>> zeropad.inputs.in_files = 'functional.nii'
+    >>> zeropad.inputs.out_file = 'pad_functional.nii'
+    >>> zeropad.inputs.I = 10
+    >>> zeropad.inputs.S = 10
+    >>> zeropad.inputs.A = 10
+    >>> zeropad.inputs.P = 10
+    >>> zeropad.inputs.R = 10
+    >>> zeropad.inputs.L = 10
+    >>> zeropad.cmdline  # doctest: +ALLOW_UNICODE
+    '3dZeropad -A 10 -I 10 -L 10 -P 10 -R 10 -S 10 -prefix pad_functional.nii functional.nii'
+    >>> res = zeropad.run()  # doctest: +SKIP
+    """
+
+    _cmd = '3dZeropad'
+    input_spec = ZeropadInputSpec
+    output_spec = AFNICommandOutputSpec

nipype/interfaces/afni/tests/test_auto_Unifize.py

@@ -1256,8 +1256,10 @@ def __init__(self, templates, **kwargs):
         infields = []
         for name, template in list(templates.items()):
             for _, field_name, _, _ in string.Formatter().parse(template):
-                if field_name is not None and field_name not in infields:
-                    infields.append(field_name)
+                if field_name is not None:
+                    field_name = re.match("\w+", field_name).group()
+                    if field_name not in infields:
+                        infields.append(field_name)
 
         self._infields = infields
         self._outfields = list(templates)

nipype/interfaces/afni/utils.py

@@ -11,6 +11,7 @@
 import os.path as op
 from subprocess import Popen
 import hashlib
+from collections import namedtuple
 
 import pytest
 import nipype
@@ -62,6 +63,7 @@ def test_s3datagrabber():
 templates1 = {"model": "interfaces/{package}/model.py",
              "preprocess": "interfaces/{package}/pre*.py"}
 templates2 = {"converter": "interfaces/dcm{to!s}nii.py"}
+templates3 = {"model": "interfaces/{package.name}/model.py"}
 
 @pytest.mark.parametrize("SF_args, inputs_att, expected", [
         ({"templates":templates1}, {"package":"fsl"},
@@ -75,6 +77,11 @@ def test_s3datagrabber():
 
         ({"templates":templates2}, {"to":2},
          {"infields":["to"], "outfields":["converter"], "run_output":{"converter":op.join(op.dirname(nipype.__file__), "interfaces/dcm2nii.py")}, "node_output":["converter"]}),
+
+        ({"templates": templates3}, {"package": namedtuple("package", ["name"])("fsl")},
+        {"infields": ["package"], "outfields": ["model"],
+         "run_output": {"model": op.join(op.dirname(nipype.__file__), "interfaces/fsl/model.py")},
+         "node_output": ["model"]}),
         ])
 def test_selectfiles(SF_args, inputs_att, expected):
     base_dir = op.dirname(nipype.__file__)

nipype/interfaces/io.py

@@ -42,7 +42,7 @@
                                        ]
     docwriter.class_skip_patterns += ['AFNICommand',
                                       'ANTS',
-                                      'FSL',
+                                      'FSLCommand',
                                       'FS',
                                       'Info',
                                       '^SPM',