ENH: Allow BIDS-style slice timings to be passed directly to TShift

nipype/interfaces/afni/preprocess.py

@@ -20,6 +20,9 @@
                    AFNICommandOutputSpec, AFNIPythonCommandInputSpec,
                    AFNIPythonCommand, Info, no_afni)
 
+from ...import logging
+iflogger = logging.getLogger('nipype.interface')
+
 
 class CentralityInputSpec(AFNICommandInputSpec):
     """Common input spec class for all centrality-related commands
@@ -2565,9 +2568,10 @@ class TProject(AFNICommand):
     output_spec = AFNICommandOutputSpec
 
 
+
 class TShiftInputSpec(AFNICommandInputSpec):
     in_file = File(
-        desc='input file to 3dTShift',
+        desc='input file to 3dTshift',
         argstr='%s',
         position=-1,
         mandatory=True,
@@ -2594,12 +2598,26 @@ class TShiftInputSpec(AFNICommandInputSpec):
         desc='ignore the first set of points specified', argstr='-ignore %s')
     interp = traits.Enum(
         ('Fourier', 'linear', 'cubic', 'quintic', 'heptic'),
-        desc='different interpolation methods (see 3dTShift for details) '
+        desc='different interpolation methods (see 3dTshift for details) '
         'default = Fourier',
         argstr='-%s')
-    tpattern = Str(
+    tpattern = traits.Either(
+        traits.Enum('alt+z', 'altplus',    # Synonyms
+                    'alt+z2',
+                    'alt-z', 'altminus',   # Synonyms
+                    'alt-z2',
+                    'seq+z', 'seqplus',    # Synonyms
+                    'seq-z', 'seqminus'),  # Synonyms
+        Str,  # For backwards compatibility
         desc='use specified slice time pattern rather than one in header',
-        argstr='-tpattern %s')
+        argstr='-tpattern %s',
+        xor=['slice_timing'])
+    slice_timing = traits.Either(
+        File(exists=True),
+        traits.List(traits.Float),
+        desc='time offsets from the volume acquisition onset for each slice',
+        argstr='-tpattern @%s',
+        xor=['tpattern'])
     rlt = traits.Bool(
         desc='Before shifting, remove the mean and linear trend',
         argstr='-rlt')
@@ -2609,6 +2627,10 @@ class TShiftInputSpec(AFNICommandInputSpec):
         argstr='-rlt+')
 
 
+class TShiftOutputSpec(AFNICommandOutputSpec):
+    timing_file = File(desc="AFNI formatted timing file, if ``slice_timing`` is a list")
+
+
 class TShift(AFNICommand):
     """Shifts voxel time series from input so that seperate slices are aligned
     to the same temporal origin.
@@ -2619,19 +2641,101 @@ class TShift(AFNICommand):
     Examples
     ========
 
+    Slice timing details may be specified explicitly via the ``slice_timing``
+    input:
+
     >>> from nipype.interfaces import afni
+    >>> TR = 2.5
+    >>> tshift = afni.TShift()
+    >>> tshift.inputs.in_file = 'functional.nii'
+    >>> tshift.inputs.tzero = 0.0
+    >>> tshift.inputs.tr = '%.1fs' % TR
+    >>> tshift.inputs.slice_timing = list(np.arange(40) / TR)
+    >>> tshift.cmdline
+    '3dTshift -prefix functional_tshift -tpattern @slice_timing.1D -TR 2.5s -tzero 0.0 functional.nii'
+
+    When the ``slice_timing`` input is used, the ``timing_file`` output is populated,
+    in this case with the generated file.
+
+    >>> tshift._list_outputs()['timing_file']  # doctest: +ELLIPSIS
+    '.../slice_timing.1D'
+
+    This method creates a ``slice_timing.1D`` file to be passed to ``3dTshift``.
+    A pre-existing slice-timing file may be used in the same way:
+
+    >>> tshift = afni.TShift()
+    >>> tshift.inputs.in_file = 'functional.nii'
+    >>> tshift.inputs.tzero = 0.0
+    >>> tshift.inputs.tr = '%.1fs' % TR
+    >>> tshift.inputs.slice_timing = 'slice_timing.1D'
+    >>> tshift.cmdline
+    '3dTshift -prefix functional_tshift -tpattern @slice_timing.1D -TR 2.5s -tzero 0.0 functional.nii'
+
+    When a pre-existing file is provided, ``timing_file`` is simply passed through.
+
+    >>> tshift._list_outputs()['timing_file']  # doctest: +ELLIPSIS
+    '.../slice_timing.1D'
+
+    Alternatively, pre-specified slice timing patterns may be specified with the
+    ``tpattern`` input.
+    For example, to specify an alternating, ascending slice timing pattern:
+
     >>> tshift = afni.TShift()
     >>> tshift.inputs.in_file = 'functional.nii'
+    >>> tshift.inputs.tzero = 0.0
+    >>> tshift.inputs.tr = '%.1fs' % TR
     >>> tshift.inputs.tpattern = 'alt+z'
+    >>> tshift.cmdline
+    '3dTshift -prefix functional_tshift -tpattern alt+z -TR 2.5s -tzero 0.0 functional.nii'
+
+    For backwards compatibility, ``tpattern`` may also take filenames prefixed
+    with ``@``.
+    However, in this case, filenames are not validated, so this usage will be
+    deprecated in future versions of Nipype.
+
+    >>> tshift = afni.TShift()
+    >>> tshift.inputs.in_file = 'functional.nii'
     >>> tshift.inputs.tzero = 0.0
+    >>> tshift.inputs.tr = '%.1fs' % TR
+    >>> tshift.inputs.tpattern = '@slice_timing.1D'
     >>> tshift.cmdline
-    '3dTshift -prefix functional_tshift -tpattern alt+z -tzero 0.0 functional.nii'
-    >>> res = tshift.run()  # doctest: +SKIP
+    '3dTshift -prefix functional_tshift -tpattern @slice_timing.1D -TR 2.5s -tzero 0.0 functional.nii'
+
+    In these cases, ``timing_file`` is undefined.
 
+    >>> tshift._list_outputs()['timing_file']  # doctest: +ELLIPSIS
+    <undefined>
+
+    In any configuration, the interface may be run as usual:
+
+    >>> res = tshift.run()  # doctest: +SKIP
     """
     _cmd = '3dTshift'
     input_spec = TShiftInputSpec
-    output_spec = AFNICommandOutputSpec
+    output_spec = TShiftOutputSpec
+
+    def _format_arg(self, name, trait_spec, value):
+        if name == 'tpattern' and value.startswith('@'):
+            iflogger.warning('Passing a file prefixed by "@" will be deprecated'
+                             '; please use the `slice_timing` input')
+        elif name == 'slice_timing' and isinstance(value, list):
+            value = self._write_slice_timing()
+        return super(TShift, self)._format_arg(name, trait_spec, value)
+
+    def _write_slice_timing(self):
+        fname = 'slice_timing.1D'
+        with open(fname, 'w') as fobj:
+            fobj.write('\t'.join(map(str, self.inputs.slice_timing)))
+        return fname
+
+    def _list_outputs(self):
+        outputs = super(TShift, self)._list_outputs()
+        if isdefined(self.inputs.slice_timing):
+            if isinstance(self.inputs.slice_timing, list):
+                outputs['timing_file'] = os.path.abspath('slice_timing.1D')
+            else:
+                outputs['timing_file'] = os.path.abspath(self.inputs.slice_timing)
+        return outputs
 
 
 class VolregInputSpec(AFNICommandInputSpec):

nipype/interfaces/afni/tests/test_auto_TShift.py

@@ -30,7 +30,14 @@ def test_TShift_inputs():
         outputtype=dict(),
         rlt=dict(argstr='-rlt', ),
         rltplus=dict(argstr='-rlt+', ),
-        tpattern=dict(argstr='-tpattern %s', ),
+        slice_timing=dict(
+            argstr='-tpattern @%s',
+            xor=['tpattern'],
+        ),
+        tpattern=dict(
+            argstr='-tpattern %s',
+            xor=['slice_timing'],
+        ),
         tr=dict(argstr='-TR %s', ),
         tslice=dict(
             argstr='-slice %s',
@@ -47,7 +54,10 @@ def test_TShift_inputs():
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 def test_TShift_outputs():
-    output_map = dict(out_file=dict(), )
+    output_map = dict(
+        out_file=dict(),
+        timing_file=dict(),
+    )
     outputs = TShift.output_spec()
 
     for key, metadata in list(output_map.items()):

nipype/testing/data/slice_timing.1D

@@ -0,0 +1 @@
+0.0	0.4	0.8	1.2	1.6	2.0	2.4	2.8	3.2	3.6	4.0	4.4	4.8	5.2	5.6	6.0	6.4	6.8	7.2	7.6	8.0	8.4	8.8	9.2	9.6	10.0	10.4	10.8	11.2	11.6	12.0	12.4	12.8	13.2	13.6	14.0	14.4	14.8	15.2	15.6