Add 3dEdge3.

Author: tsalo

nipype/interfaces/afni/__init__.py

@@ -17,7 +17,7 @@
                          Seg, SkullStrip, TCorr1D, TCorrMap, TCorrelate,
                          TShift, Volreg, Warp, QwarpPlusMinus)
 from .svm import (SVMTest, SVMTrain)
-from .utils import (AFNItoNIFTI, Autobox, BrickStat, Calc, Copy,
+from .utils import (AFNItoNIFTI, Autobox, BrickStat, Calc, Copy, Edge3,
                     Eval, FWHMx,
                     MaskTool, Merge, Notes, Refit, Resample, TCat, TStat, To3D,
                     Unifize, ZCutUp, GCOR,)

nipype/interfaces/afni/utils.py

@@ -394,6 +394,99 @@ class Copy(AFNICommand):
     output_spec = AFNICommandOutputSpec
 
 
+class Edge3InputSpec(AFNICommandInputSpec):
+    in_file = File(
+        desc='input file to 3dedge3',
+        argstr='-input %s',
+        position=0,
+        mandatory=True,
+        exists=True,
+        copyfile=False)
+    out_file = File(
+        desc='output image file name',
+        position=-1,
+        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\'.')
+    fscale = traits.Bool(
+        desc='Force scaling of the output to the maximum integer range.',
+        argstr='-fscale',
+        xor=['gscale', 'nscale', 'scale_floats'])
+    gscale = traits.Bool(
+        desc='Same as \'-fscale\', but also forces each output sub-brick to '
+             'to get the same scaling factor.',
+        argstr='-gscale',
+        xor=['fscale', 'nscale', 'scale_floats'])
+    nscale = traits.Bool(
+        desc='Don\'t do any scaling on output to byte or short datasets.',
+        argstr='-nscale',
+        xor=['fscale', 'gscale', 'scale_floats'])
+    scale_floats = traits.Float(
+        desc='Multiply input by VAL, but only if the input datum is '
+             'float. This is needed when the input dataset '
+             'has a small range, like 0 to 2.0 for instance. '
+             'With such a range, very few edges are detected due to '
+             'what I suspect to be truncation problems. '
+             'Multiplying such a dataset by 10000 fixes the problem '
+             'and the scaling is undone at the output.',
+        argstr='-scale_floats %f',
+        xor=['fscale', 'gscale', 'nscale'])
+    verbose = traits.Bool(
+        desc='Print out some information along the way.',
+        argstr='-verbose')
+
+
+class Edge3(AFNICommand):
+    """Does 3D Edge detection using the library 3DEdge
+    by Gregoire Malandain ([email protected]).
+
+    For complete details, see the `3dedge3 Documentation.
+    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dedge3.html>`_
+
+    references_ = [{'entry': BibTeX('@article{Deriche1987,'
+                                    'author={R. Deriche},'
+                                    'title={Optimal edge detection using recursive filtering},'
+                                    'journal={International Journal of Computer Vision},'
+                                    'volume={2},',
+                                    'pages={167-187},'
+                                    'year={1987},'
+                                    '}'),
+                    'tags': ['method'],
+                    },
+                   {'entry': BibTeX('@article{MongaDericheMalandainCocquerez1991,'
+                                    'author={O. Monga, R. Deriche, G. Malandain, J.P. Cocquerez},'
+                                    'title={Recursive filtering and edge tracking: two primary tools for 3D edge detection},'
+                                    'journal={Image and vision computing},'
+                                    'volume={9},',
+                                    'pages={203-214},'
+                                    'year={1991},'
+                                    '}'),
+                    'tags': ['method'],
+                    },
+                   ]
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni
+    >>> edge3 = afni.Edge3()
+    >>> edge3.inputs.in_file = 'functional.nii'
+    >>> edge3.inputs.out_file = 'edges.nii'
+    >>> edge3.inputs.datum = 'byte'
+    >>> edge3.cmdline  # doctest: +ALLOW_UNICODE
+    '3dedge3 -input functional.nii -datum byte -prefix edges.nii'
+    >>> res = edge3.run()  # doctest: +SKIP
+
+    """
+
+    _cmd = '3dedge3'
+    input_spec = Edge3InputSpec
+    output_spec = AFNICommandOutputSpec
+
+
 class EvalInputSpec(AFNICommandInputSpec):
     in_file_a = File(
         desc='input file to 1deval',