Merge pull request #2180 from salma1601/afni-refit

add more inputs to afni Refit

Author: satra

nipype/interfaces/afni/tests/test_auto_Refit.py

@@ -6,8 +6,18 @@
 def test_Refit_inputs():
     input_map = dict(args=dict(argstr='%s',
     ),
+    atrcopy=dict(argstr='-atrcopy %s %s',
+    ),
+    atrfloat=dict(argstr='-atrfloat %s %s',
+    ),
+    atrint=dict(argstr='-atrint %s %s',
+    ),
+    atrstring=dict(argstr='-atrstring %s %s',
+    ),
     deoblique=dict(argstr='-deoblique',
     ),
+    duporigin_file=dict(argstr='-duporigin %s',
+    ),
     environ=dict(nohash=True,
     usedefault=True,
     ),
@@ -19,6 +29,10 @@ def test_Refit_inputs():
     mandatory=True,
     position=-1,
     ),
+    nosaveatr=dict(argstr='-nosaveatr',
+    ),
+    saveatr=dict(argstr='-saveatr',
+    ),
     space=dict(argstr='-space %s',
     ),
     terminal_output=dict(nohash=True,

nipype/interfaces/afni/utils.py

@@ -1595,6 +1595,11 @@ class RefitInputSpec(CommandLineInputSpec):
     zorigin = Str(
         desc='z distance for edge voxel offset',
         argstr='-zorigin %s')
+    duporigin_file = File(
+        argstr='-duporigin %s',
+        exists=True,
+        desc='Copies the xorigin, yorigin, and zorigin values from the header '
+             'of the given dataset')
     xdel = traits.Float(
         desc='new x voxel dimension in mm',
         argstr='-xdel %f')
@@ -1609,6 +1614,46 @@ class RefitInputSpec(CommandLineInputSpec):
         argstr='-space %s',
         desc='Associates the dataset with a specific template type, e.g. '
              'TLRC, MNI, ORIG')
+    atrcopy = traits.Tuple(
+        traits.File(exists=True), traits.Str(),
+        argstr='-atrcopy %s %s',
+        desc='Copy AFNI header attribute from the given file into the header '
+             'of the dataset(s) being modified. For more information on AFNI '
+             'header attributes, see documentation file README.attributes. '
+             'More than one \'-atrcopy\' option can be used. For AFNI '
+             'advanced users only. Do NOT use -atrcopy or -atrstring with '
+             'other modification options. See also -copyaux.')
+    atrstring = traits.Tuple(
+        traits.Str(), traits.Str(),
+        argstr='-atrstring %s %s',
+        desc='Copy the last given string into the dataset(s) being modified, '
+             'giving it the attribute name given by the last string.'
+             'To be safe, the last string should be in quotes.')
+    atrfloat = traits.Tuple(
+        traits.Str(), traits.Str(),
+        argstr='-atrfloat %s %s',
+        desc='Create or modify floating point attributes. '
+             'The input values may be specified as a single string in quotes '
+             'or as a 1D filename or string, example '
+             '\'1 0.2 0 0 -0.2 1 0 0 0 0 1 0\' or '
+             'flipZ.1D or \'1D:1,0.2,2@0,-0.2,1,2@0,2@0,1,0\'')
+    atrint = traits.Tuple(
+        traits.Str(), traits.Str(),
+        argstr='-atrint %s %s',
+        desc='Create or modify integer attributes. '
+             'The input values may be specified as a single string in quotes '
+             'or as a 1D filename or string, example '
+             '\'1 0 0 0 0 1 0 0 0 0 1 0\' or '
+             'flipZ.1D or \'1D:1,0,2@0,-0,1,2@0,2@0,1,0\'')
+    saveatr = traits.Bool(
+        argstr='-saveatr',
+        desc='(default) Copy the attributes that are known to AFNI into '
+             'the dset->dblk structure thereby forcing changes to known '
+             'attributes to be present in the output. This option only makes '
+             'sense with -atrcopy.')
+    nosaveatr = traits.Bool(
+        argstr='-nosaveatr',
+        desc='Opposite of -saveatr')
 
 
 class Refit(AFNICommandBase):
@@ -1628,6 +1673,12 @@ class Refit(AFNICommandBase):
     '3drefit -deoblique structural.nii'
     >>> res = refit.run()  # doctest: +SKIP
 
+    >>> refit_2 = afni.Refit()
+    >>> refit_2.inputs.in_file = 'structural.nii'
+    >>> refit_2.inputs.atrfloat = ("IJK_TO_DICOM_REAL", "'1 0.2 0 0 -0.2 1 0 0 0 0 1 0'")
+    >>> refit_2.cmdline  # doctest: +ALLOW_UNICODE
+    "3drefit -atrfloat IJK_TO_DICOM_REAL '1 0.2 0 0 -0.2 1 0 0 0 0 1 0' structural.nii"
+    >>> res = refit_2.run()  # doctest: +SKIP
     """
     _cmd = '3drefit'
     input_spec = RefitInputSpec