fix: tests and added new data files

Author: satra

nipype/interfaces/freesurfer/preprocess.py

@@ -931,7 +931,7 @@ class Smooth(FSCommand):
     >>> from nipype.interfaces.freesurfer import Smooth
     >>> smoothvol = Smooth(in_file='functional.nii', smoothed_file = 'foo_out.nii', reg_file='register.dat', surface_fwhm=10, vol_fwhm=6)
     >>> smoothvol.cmdline
-    'mris_volsmooth --i functional.nii --reg register.dat --o foo_out.nii --fwhm 10 --vol-fwhm 6'
+    'mris_volsmooth --i functional.nii --reg register.dat --o foo_out.nii --fwhm 10.000000 --vol-fwhm 6.000000'
 
     """
 

nipype/interfaces/freesurfer/tests/test_preprocess.py

@@ -228,8 +228,8 @@ def test_smooth():
                      reg_file = dict(argstr='--reg %s',mandatory=True,),
                      smoothed_file = dict(argstr='--o %s',),
                      subjects_dir = dict(),
-                     surface_fwhm = dict(xor=['num_iters'],mandatory=True,argstr='--fwhm %d',requires=['reg_file'],),
-                     vol_fwhm = dict(argstr='--vol-fwhm %d',),
+                     surface_fwhm = dict(xor=['num_iters'],mandatory=True,argstr='--fwhm %f',requires=['reg_file'],),
+                     vol_fwhm = dict(argstr='--vol-fwhm %f',),
                      )
     instance = freesurfer.Smooth()
     for key, metadata in input_map.items():

nipype/interfaces/freesurfer/tests/test_utils.py

@@ -32,6 +32,9 @@ def create_files_in_directory():
         img = np.random.random(shape)
         nif.save(nif.Nifti1Image(img,np.eye(4),hdr),
                  os.path.join(outdir,f))
+    with open(os.path.join(outdir, 'reg.dat'), 'wt') as fp:
+        fp.write('dummy file')
+    filelist.append('reg.dat')
     return filelist, outdir, cwd
 
 def create_surf_file():
@@ -69,13 +72,14 @@ def test_sample2surf():
     s2s.inputs.source_file = files[0]
     s2s.inputs.reference_file = files[1]
     s2s.inputs.hemi = "lh"
+    s2s.inputs.reg_file = files[2]
     s2s.inputs.sampling_range = .5
     s2s.inputs.sampling_units = "frac"
     s2s.inputs.sampling_method = "point"
 
     # Test a basic command line
     yield assert_equal, s2s.cmdline, ("mri_vol2surf "
-    "--hemi lh --o %s --ref %s --projfrac 0.500 --mov %s"
+    "--hemi lh --o %s --ref %s --reg reg.dat --projfrac 0.500 --mov %s"
     %(os.path.join(cwd, "lh.a.mgz"),files[1],files[0]))
 
     # Test identity