tst: updated flirt test

Author: mgxd

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -220,12 +220,28 @@ 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
+
+    # test apply_xfm option
+    axfm = flirter
+    axfm.inputs.apply_xfm = True
+    # in_matrix_file or uses_qform must be defined
+    with pytest.raises(RuntimeError): axfm.cmdline
+    axfm2 = axfm
+    # test uses_qform
+    axfm.inputs.uses_qform = True
+    assert axfm.cmdline == ('flirt -in %s -ref %s -applyxfm -usesqform' % (
+                            infile, reffile))
+    # test in_matrix_file
+    axfm2.inputs.in_matrix_file = reffile
+    assert axfm2.cmdline == ('flirt -in %s -ref %s -applyxfm -init %s' % (
+                            infile, reffile, reffile))
+
     # Generate outfile and outmatrix
     pth, fname, ext = split_filename(infile)
     outfile = fsl_name(flirter, '%s_flirt' % fname)