Merge pull request #1875 from mgxd/fix/flirt_xfm

enh: allow uses_qform in FLIRT, ApplyXFM interfaces

Author: satra

nipype/interfaces/fsl/preprocess.py

@@ -401,8 +401,9 @@ class FLIRTInputSpec(FSLCommandInputSpec):
                    name_template='%s_flirt.log', desc='output log')
     in_matrix_file = File(argstr='-init %s', desc='input 4x4 affine matrix')
     apply_xfm = traits.Bool(
-        argstr='-applyxfm', requires=['in_matrix_file'],
-        desc='apply transformation supplied by in_matrix_file')
+        argstr='-applyxfm',
+        desc=('apply transformation supplied by in_matrix_file or uses_qform to'
+              ' use the affine matrix stored in the reference header'))
     apply_isoxfm = traits.Float(
         argstr='-applyisoxfm %f', xor=['apply_xfm'],
         desc='as applyxfm but forces isotropic resampling')
@@ -562,13 +563,18 @@ def _parse_inputs(self, skip=None):
         if isdefined(self.inputs.save_log) and self.inputs.save_log:
             if not isdefined(self.inputs.verbose) or self.inputs.verbose == 0:
                 self.inputs.verbose = 1
+        if isdefined(self.inputs.apply_xfm) and self.inputs.apply_xfm:
+            if not self.inputs.in_matrix_file and not self.inputs.uses_qform:
+                raise RuntimeError('Argument apply_xfm requires in_matrix_file '
+                                   'or uses_qform arguments to run')
         skip.append('save_log')
         return super(FLIRT, self)._parse_inputs(skip=skip)
 
 class ApplyXFMInputSpec(FLIRTInputSpec):
     apply_xfm = traits.Bool(
-        True, argstr='-applyxfm', requires=['in_matrix_file'],
-        desc='apply transformation supplied by in_matrix_file',
+        True, argstr='-applyxfm',
+        desc=('apply transformation supplied by in_matrix_file or uses_qform to'
+              ' use the affine matrix stored in the reference header'),
         usedefault=True)
 
 

nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py

@@ -10,7 +10,6 @@ def test_ApplyXFM_inputs():
     xor=['apply_xfm'],
     ),
     apply_xfm=dict(argstr='-applyxfm',
-    requires=['in_matrix_file'],
     usedefault=True,
     ),
     args=dict(argstr='%s',

nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py

@@ -10,7 +10,6 @@ def test_FLIRT_inputs():
     xor=['apply_xfm'],
     ),
     apply_xfm=dict(argstr='-applyxfm',
-    requires=['in_matrix_file'],
     ),
     args=dict(argstr='%s',
     ),

nipype/interfaces/fsl/tests/test_auto_FLIRT.py

@@ -7,6 +7,7 @@
 
 import os
 import tempfile
+from copy import deepcopy
 
 import pytest
 from nipype.utils.filemanip import split_filename, filename_to_list
@@ -220,12 +221,13 @@ def test_flirt(setup_flirt):
     flirter = fsl.FLIRT()
     # infile not specified
     with pytest.raises(ValueError):
-        flirter.run()
+        flirter.cmdline
     flirter.inputs.in_file = infile
     # reference not specified
     with pytest.raises(ValueError):
-        flirter.run()
+        flirter.cmdline
     flirter.inputs.reference = reffile
+
     # Generate outfile and outmatrix
     pth, fname, ext = split_filename(infile)
     outfile = fsl_name(flirter, '%s_flirt' % fname)
@@ -234,6 +236,20 @@ def test_flirt(setup_flirt):
                                                          outfile, outmat)
     assert flirter.cmdline == realcmd
 
+    # test apply_xfm option
+    axfm = deepcopy(flirter)
+    axfm.inputs.apply_xfm = True
+    # in_matrix_file or uses_qform must be defined
+    with pytest.raises(RuntimeError): axfm.cmdline
+    axfm2 = deepcopy(axfm)
+    # test uses_qform
+    axfm.inputs.uses_qform = True
+    assert axfm.cmdline == (realcmd + ' -applyxfm -usesqform')
+    # test in_matrix_file
+    axfm2.inputs.in_matrix_file = reffile
+    assert axfm2.cmdline == (realcmd + ' -applyxfm -init %s' % reffile)
+
+
     _, tmpfile = tempfile.mkstemp(suffix='.nii', dir=tmpdir)
     # Loop over all inputs, set a reasonable value and make sure the
     # cmdline is updated correctly.