Merge pull request #1512 from TheChymera/3dblur

Interface for AFNI's 3dBlurToFWHM

Author: satra

nipype/interfaces/afni/preprocess.py

@@ -21,6 +21,37 @@
 from ...external.six import string_types
 from ...utils.filemanip import (load_json, save_json, split_filename)
 
+class BlurToFWHMInputSpec(AFNICommandInputSpec):
+    in_file = File(desc='The dataset that will be smoothed', argstr='-input %s', mandatory=True, exists=True)
+
+    automask = traits.Bool(desc='Create an automask from the input dataset.', argstr='-automask')
+    fwhm = traits.Float(desc='Blur until the 3D FWHM reaches this value (in mm)', argstr='-FWHM %f')
+    fwhmxy = traits.Float(desc='Blur until the 2D (x,y)-plane FWHM reaches this value (in mm)', argstr='-FWHMxy %f')
+    blurmaster = File(desc='The dataset whose smoothness controls the process.', argstr='-blurmaster %s', exists=True)
+    mask = File(desc='Mask dataset, if desired. Voxels NOT in mask will be set to zero in output.', argstr='-blurmaster %s', exists=True)
+
+
+class BlurToFWHM(AFNICommand):
+    """Blurs a 'master' dataset until it reaches a specified FWHM smoothness (approximately).
+
+    For complete details, see the `to3d Documentation
+    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dBlurToFWHM.html>`_
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni
+    >>> blur = afni.preprocess.BlurToFWHM()
+    >>> blur.inputs.in_file = 'epi.nii'
+    >>> blur.inputs.fwhm = 2.5
+    >>> blur.cmdline #doctest: +ELLIPSIS
+    '3dBlurToFWHM -FWHM 2.500000 -input epi.nii -prefix epi_afni'
+
+    """
+
+    _cmd = '3dBlurToFWHM'
+    input_spec = BlurToFWHMInputSpec
+    output_spec = AFNICommandOutputSpec
 
 class To3DInputSpec(AFNICommandInputSpec):
     out_file = File(name_template="%s", desc='output image file name',

nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py

@@ -0,0 +1,50 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ....testing import assert_equal
+from ..preprocess import BlurToFWHM
+
+
+def test_BlurToFWHM_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    automask=dict(argstr='-automask',
+    ),
+    blurmaster=dict(argstr='-blurmaster %s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    fwhm=dict(argstr='-FWHM %f',
+    ),
+    fwhmxy=dict(argstr='-FWHMxy %f',
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-input %s',
+    mandatory=True,
+    ),
+    mask=dict(argstr='-blurmaster %s',
+    ),
+    out_file=dict(argstr='-prefix %s',
+    name_source=['in_file'],
+    name_template='%s_afni',
+    ),
+    outputtype=dict(),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = BlurToFWHM.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+
+def test_BlurToFWHM_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = BlurToFWHM.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value