Merge branch 'fix/mnibias' of github.com:mgxd/nipype into fix/mnibias

Author: mgxd

nipype/interfaces/freesurfer/preprocess.py

@@ -1476,7 +1476,7 @@ class MNIBiasCorrectionInputSpec(FSTraitedSpec):
     # mandatory
     in_file = File(exists=True, mandatory=True, argstr="--i %s",
                    desc="input volume. Input can be any format accepted by mri_convert.")
-    out_file = File(argstr="--o %s", name_source=['in_file'],
+    out_file = File(argstr="--o %s", mandatory=True, name_source=['in_file'],
                     name_template='%s_output', hash_files=False, keep_extension=True,
                     desc="output volume. Output can be any format accepted by mri_convert. " +
                     "If the output format is COR, then the directory must exist.")
@@ -1519,6 +1519,7 @@ class MNIBiasCorrection(FSCommand):
     >>> from nipype.interfaces.freesurfer import MNIBiasCorrection
     >>> correct = MNIBiasCorrection()
     >>> correct.inputs.in_file = "norm.mgz"
+    >>> correct.inputs.out_file = "norm_output.mgz"
     >>> correct.inputs.iterations = 6
     >>> correct.inputs.protocol_iterations = 1000
     >>> correct.inputs.distance = 50

nipype/interfaces/freesurfer/tests/test_preprocess.py

@@ -85,3 +85,28 @@ def test_synthesizeflash(create_files_in_directory):
     syn2 = freesurfer.SynthesizeFLASH(t1_image=filelist[0], pd_image=filelist[1], flip_angle=20, te=5, tr=25)
     assert syn2.cmdline == ('mri_synthesize 25.00 20.00 5.000 %s %s %s'
                             % (filelist[0], filelist[1], os.path.join(outdir, 'synth-flash_20.mgz')))
+
+@pytest.mark.skipif(freesurfer.no_freesurfer(), reason="freesurfer is not installed")
+def test_mandatory_outvol(create_files_in_directory):
+    filelist, outdir = create_files_in_directory
+    mni = freesurfer.MNIBiasCorrection()
+
+    # make sure command gets called
+    assert mni.cmd == "mri_nu_correct.mni"
+
+    # test raising error with mandatory args absent
+    with pytest.raises(ValueError): mni.run()
+
+    # test raising error with only partial mandatory args present
+    mni.inputs.in_file = filelist[0] #mgz
+    with pytest.raises(ValueError): mni.run()
+
+    # rest of mandatory inputs
+    mni.inputs.out_file = 'bias_corrected_output'
+
+    assert mni.cmdline == ('mri_nu_correct.mni --i %s --n 4 --o bias_corrected_output.mgz'
+                            % filelist[0])
+    # constructor based tests
+    mni2 = freesurfer.MNIBiasCorrection(in_file=filelist[0], out_file='bias_corrected_output')
+    assert mni2.cmdline == ('mri_nu_correct.mni --i %s --n 4 --o bias_corrected_output.mgz'
+                             % filelist[0])

nipype/interfaces/mrtrix/convert.py

@@ -10,7 +10,7 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import open
+from io import open
 
 import os.path as op
 import nibabel as nb
@@ -55,10 +55,11 @@ def read_mrtrix_tracks(in_file, as_generator=True):
 
 
 def read_mrtrix_header(in_file):
-    fileobj = open(in_file, 'r')
+    fileobj = open(in_file, 'rb')
     header = {}
     iflogger.info('Reading header data...')
     for line in fileobj:
+        line = line.decode()
         if line == 'END\n':
             iflogger.info('Reached the end of the header!')
             break
@@ -78,7 +79,7 @@ def read_mrtrix_header(in_file):
 def read_mrtrix_streamlines(in_file, header, as_generator=True):
     offset = header['offset']
     stream_count = header['count']
-    fileobj = open(in_file, 'r')
+    fileobj = open(in_file, 'rb')
     fileobj.seek(offset)
     endianness = native_code
     f4dt = np.dtype(endianness + 'f4')
@@ -90,7 +91,7 @@ def points_per_track(offset):
         n_points = 0
         track_points = []
         iflogger.info('Identifying the number of points per tract...')
-        all_str = fileobj.read()
+        all_str = fileobj.read().decode()
         num_triplets = int(len(all_str) / bytesize)
         pts = np.ndarray(shape=(num_triplets, pt_cols), dtype='f4', buffer=all_str)
         nonfinite_list = np.where(np.isfinite(pts[:, 2]) == False)