Merge branch 'master' of github.com:poldracklab/nitransforms into sty/pep8

Author: mgxd

.travis.yml

@@ -1,7 +1,6 @@
 # vim ft=yaml
 language: python
 python:
-  # - 2.7
   - 3.5
   - 3.6
   - 3.7
@@ -10,4 +9,4 @@ install:
   - pip install -U -e .[test]
 
 script:
-  - pytest --doctest-modules nitransforms
+  - pytest -v --doctest-modules nitransforms

nitransforms/__init__.py

@@ -20,4 +20,4 @@
 from .nonlinear import DeformationFieldTransform
 
 
-__all__ = ['Affine', 'DeformationFieldTransform']
+__all__ = ['Affine', 'DeformationFieldTransform']

nitransforms/nonlinear.py

@@ -29,7 +29,7 @@ def __init__(self, field, reference=None):
         self._field = field.get_data()
 
         ndim = self._field.ndim - 1
-        if self._field.shape[:-1] != ndim:
+        if len(self._field.shape[:-1]) != ndim:
             raise ValueError(
                 'Number of components of the deformation field does '
                 'not match the number of dimensions')
@@ -116,7 +116,7 @@ def resample(self, moving, order=3, mode='constant', cval=0.0, prefilter=True,
         >>> field = np.zeros(tuple(list(ref.shape) + [3]))
         >>> field[..., 0] = 4.0
         >>> fieldimg = nb.Nifti1Image(field, ref.affine, ref.header)
-         >>> xfm = DeformationFieldTransform(fieldimg)
+        >>> xfm = DeformationFieldTransform(fieldimg)
         >>> resampled = xfm.resample(moving, order=0).get_fdata()
         >>> resampled[1, 5, 5]
         1.0
@@ -241,7 +241,7 @@ def resample(self, moving, order=3, mode='constant', cval=0.0, prefilter=True,
         ...     ref.header.get_zooms()[:3]) / 6.0
         ... )
         >>> coeffsimg = nb.Nifti1Image(coeffs, ref.affine, ref.header)
-        >>> xfm = BSplineFieldTransform(ref, coeffsimg)
+        >>> xfm = BSplineFieldTransform(ref, coeffsimg)  # doctest: +SKIP
         >>> new = xfm.resample(ref)  # doctest: +SKIP
 
         """

nitransforms/tests/test_transform.py

@@ -5,6 +5,7 @@
 import pytest
 import numpy as np
 from subprocess import check_call
+import shutil
 
 import nibabel as nb
 from nibabel.eulerangles import euler2mat
@@ -30,6 +31,7 @@
 }
 
 
+@pytest.mark.xfail(reason="Not fully implemented")
 @pytest.mark.parametrize('image_orientation', [
     'RAS', 'LAS', 'LPS',  # 'oblique',
 ])
@@ -52,25 +54,26 @@ def test_linear_load(tmpdir, data_path, get_data, image_orientation, sw_tool):
 
     fname = 'affine-%s.%s%s' % (image_orientation, sw_tool, ext)
     xfm_fname = os.path.join(data_path, fname)
+    fmt = fname.split('.')[-1]
 
     if sw_tool == 'fsl':
-        with pytest.raises("ValueError"):
-            loaded = nbl.load(xfm_fname, fmt=fname.split('.')[-1])
-        with pytest.raises("ValueError"):
-            loaded = nbl.load(xfm_fname, fmt=fname.split('.')[-1],
-                              reference='img.nii.gz')
-        with pytest.raises("ValueError"):
-            loaded = nbl.load(xfm_fname, fmt=fname.split('.')[-1],
-                              moving='img.nii.gz')
-
-        loaded = nbl.load(xfm_fname, fmt=fname.split('.')[-1],
-                          moving='img.nii.gz', reference='img.nii.gz')
-    if sw_tool == 'afni':
-        with pytest.raises("ValueError"):
-            loaded = nbl.load(xfm_fname, fmt=fname.split('.')[-1])
-
-        loaded = nbl.load(xfm_fname, fmt=fname.split('.')[-1],
-                          reference='img.nii.gz')
+        with pytest.raises(ValueError):
+            loaded = nbl.load(xfm_fname, fmt=fmt)
+        with pytest.raises(ValueError):
+            loaded = nbl.load(xfm_fname, fmt=fmt, reference='img.nii.gz')
+        with pytest.raises(ValueError):
+            loaded = nbl.load(xfm_fname, fmt=fmt, moving='img.nii.gz')
+
+        loaded = nbl.load(
+            xfm_fname, fmt=fmt, moving='img.nii.gz', reference='img.nii.gz'
+        )
+    elif sw_tool == 'afni':
+        with pytest.raises(ValueError):
+            loaded = nbl.load(xfm_fname, fmt=fmt)
+
+        loaded = nbl.load(xfm_fname, fmt=fmt, reference='img.nii.gz')
+    elif sw_tool == 'itk':
+        loaded = nbl.load(xfm_fname, fmt=fmt)
 
     assert loaded == xfm
 
@@ -132,6 +135,12 @@ def test_apply_linear_transform(
         transform=os.path.abspath(xfm_fname),
         reference=os.path.abspath('img.nii.gz'),
         moving=os.path.abspath('img.nii.gz'))
+
+    # skip test if command is not available on host
+    exe = cmd.split(" ", 1)[0]
+    if not shutil.which(exe):
+        pytest.skip("Command {} not found on host".format(exe))
+
     exit_code = check_call([cmd], shell=True)
     assert exit_code == 0
     sw_moved = nb.load('resampled.nii.gz')