Merge pull request #602 from effigies/test/coverage

MRG: Increase coverage where easy

Just looking through the coverage report for easy fixes.

Author: matthew-brett

.coveragerc

@@ -5,5 +5,4 @@ include = */nibabel/*, */nisext/*
 omit =
     */externals/*
     */benchmarks/*
-    */ast.py
-    */codegen.py
+    */tests/*

nibabel/analyze.py

@@ -1086,10 +1086,6 @@ def to_file_map(self, file_map=None):
         # Write header
         hdr.write_to(hdrf)
         # Write image
-        shape = hdr.get_data_shape()
-        if data.shape != shape:
-            raise HeaderDataError('Data should be shape (%s)' %
-                                  ', '.join(str(s) for s in shape))
         # Seek to writing position, get there by writing zeros if seek fails
         seek_tell(imgf, hdr.get_data_offset(), write0=True)
         # Write array data

nibabel/deprecated.py

@@ -31,10 +31,6 @@ class ModuleProxy(object):
     def __init__(self, module_name):
         self._module_name = module_name
 
-    def __hasattr__(self, key):
-        mod = __import__(self._module_name, fromlist=[''])
-        return hasattr(mod, key)
-
     def __getattr__(self, key):
         mod = __import__(self._module_name, fromlist=[''])
         return getattr(mod, key)

nibabel/tests/test_analyze.py

@@ -525,9 +525,10 @@ def test_from_header(self):
         hdr.set_data_dtype(np.float64)
         hdr.set_data_shape((1, 2, 3))
         hdr.set_zooms((3.0, 2.0, 1.0))
-        copy = klass.from_header(hdr)
-        assert_equal(hdr, copy)
-        assert_false(hdr is copy)
+        for check in (True, False):
+            copy = klass.from_header(hdr, check=check)
+            assert_equal(hdr, copy)
+            assert_false(hdr is copy)
 
         class C(object):
 

nibabel/tests/test_arrayproxy.py

@@ -381,27 +381,23 @@ def test_keep_file_open_true_false_invalid():
                 x , y, z = [int(c) for c in voxels[i, :]]
                 assert proxy_kfp[x, y, z] == x * 100 + y * 10 + z
                 assert CountingImageOpener.num_openers == 1
+            del proxy_kfp
+            del proxy_no_kfp
         # Test that the keep_file_open flag has no effect if an open file
         # handle is passed in
         with open(fname, 'rb') as fobj:
-            proxy_no_kfp = ArrayProxy(fobj, ((10, 10, 10), dtype),
-                                      keep_file_open=False)
-            assert not proxy_no_kfp._keep_file_open
-            for i in range(voxels.shape[0]):
-                assert proxy_no_kfp[x, y, z] == x * 100 + y * 10 + z
+            for kfo in (True, False, 'auto'):
+                proxy = ArrayProxy(fobj, ((10, 10, 10), dtype),
+                                   keep_file_open=kfo)
+                if kfo == 'auto':
+                    kfo = False
+                assert proxy._keep_file_open is kfo
+                for i in range(voxels.shape[0]):
+                    assert proxy[x, y, z] == x * 100 + y * 10 + z
+                    assert not fobj.closed
+                del proxy
                 assert not fobj.closed
-            del proxy_no_kfp
-            proxy_no_kfp = None
-            assert not fobj.closed
-            proxy_kfp = ArrayProxy(fobj, ((10, 10, 10), dtype),
-                                   keep_file_open=True)
-            assert proxy_kfp._keep_file_open
-            for i in range(voxels.shape[0]):
-                assert proxy_kfp[x, y, z] == x * 100 + y * 10 + z
-                assert not fobj.closed
-            del proxy_kfp
-            proxy_kfp = None
-            assert not fobj.closed
+        assert fobj.closed
         # Test invalid values of keep_file_open
         with assert_raises(ValueError):
             ArrayProxy(fname, ((10, 10, 10), dtype), keep_file_open=0)

nibabel/tests/test_image_api.py

@@ -339,9 +339,10 @@ def validate_data_interface(self, imaker, params):
                     # cache state.
                     img.uncache()
                     assert_true(img.in_memory)
-                # Values to get_data caching parameter must be 'fill' or
+                # Values to get_(f)data caching parameter must be 'fill' or
                 # 'unchanged'
                 assert_raises(ValueError, img.get_data, caching='something')
+                assert_raises(ValueError, img.get_fdata, caching='something')
             # Data shape is same as image shape
             assert_equal(img.shape, method().shape)
             # Values to get_data caching parameter must be 'fill' or

nibabel/tests/test_orientations.py

@@ -9,14 +9,16 @@
 ''' Testing for orientations module '''
 
 import numpy as np
+import warnings
 
 from nose.tools import assert_true, assert_equal, assert_raises
 
 from numpy.testing import assert_array_equal
 
 from ..orientations import (io_orientation, ornt_transform, inv_ornt_aff,
                             flip_axis, apply_orientation, OrientationError,
-                            ornt2axcodes, axcodes2ornt, aff2axcodes)
+                            ornt2axcodes, axcodes2ornt, aff2axcodes,
+                            orientation_affine)
 
 from ..affines import from_matvec, to_matvec
 
@@ -245,6 +247,12 @@ def test_ornt_transform():
                   [[0, 1, 1], [1, 1, 1]],
                   [[0, 1, 1], [1, 1, 1]])
 
+    # Target axes must exist in source
+    assert_raises(ValueError,
+                  ornt_transform,
+                  [[0, 1], [1, 1], [1, 1]],
+                  [[0, 1], [1, 1], [2, 1]])
+
 
 def test_ornt2axcodes():
     # Recoding orientation to axis codes
@@ -347,3 +355,13 @@ def test_inv_ornt_aff():
     # io_orientations test)
     assert_raises(OrientationError, inv_ornt_aff,
                   [[0, 1], [1, -1], [np.nan, np.nan]], (3, 4, 5))
+
+
+def test_orientation_affine_deprecation():
+    aff1 = inv_ornt_aff([[0, 1], [1, -1], [2, 1]], (3, 4, 5))
+    with warnings.catch_warnings(record=True) as warns:
+        warnings.simplefilter('always')
+        aff2 = orientation_affine([[0, 1], [1, -1], [2, 1]], (3, 4, 5))
+        assert_equal(len(warns), 1)
+        assert_equal(warns[0].category, DeprecationWarning)
+    assert_array_equal(aff1, aff2)

nibabel/tests/test_pkg_info.py

@@ -0,0 +1,14 @@
+""" Testing package info
+"""
+
+import nibabel as nib
+
+def test_pkg_info():
+    """Simple smoke test
+    
+    Hits:
+        - nibabel.get_info
+        - nibabel.pkg_info.get_pkg_info
+        - nibabel.pkg_info.pkg_commit_hash
+    """
+    info = nib.get_info()

nibabel/tests/test_processing.py

@@ -214,10 +214,11 @@ def test_resample_to_output():
     img2 = resample_to_output(img, vox_sizes)
     # Check 2D works
     img_2d = Nifti1Image(data[0], np.eye(4))
-    img3 = resample_to_output(img_2d)
-    assert_array_equal(img3.shape, (3, 4, 1))
-    assert_array_equal(img3.affine, np.eye(4))
-    assert_array_equal(img3.dataobj, data[0][..., None])
+    for vox_sizes in (None, 1, (1, 1), (1, 1, 1)):
+        img3 = resample_to_output(img_2d, vox_sizes)
+        assert_array_equal(img3.shape, (3, 4, 1))
+        assert_array_equal(img3.affine, np.eye(4))
+        assert_array_equal(img3.dataobj, data[0][..., None])
     # Even 1D
     img_1d = Nifti1Image(data[0, 0], np.eye(4))
     img3 = resample_to_output(img_1d)

nibabel/tests/test_quaternions.py

@@ -185,3 +185,6 @@ def test_angle_axis():
         yield nq.nearly_equivalent, q, q2
         aa_mat = nq.angle_axis2mat(theta, vec)
         yield assert_array_almost_equal, aa_mat, M
+        unit_vec = vec / np.sqrt(vec.dot(vec))
+        aa_mat2 = nq.angle_axis2mat(theta, unit_vec, is_normalized=True)
+        yield assert_array_almost_equal, aa_mat2, M