Merge remote-tracking branch 'upstream/master' into mac-precision-fix

Author: effigies

doc/source/nifti_images.rst

@@ -239,7 +239,7 @@ You can get the affine and the code using the ``coded=True`` argument to
        [   0.  ,    0.32,    2.17,   -7.25],
        [   0.  ,    0.  ,    0.  ,    1.  ]]), array(1, dtype=int16))
 
-You can set the sform with with the ``get_sform()`` method of the header and
+You can set the sform with the ``set_sform()`` method of the header and
 the image.
 
 >>> n1_header.set_sform(np.diag([2, 3, 4, 1]))
@@ -314,6 +314,63 @@ The algorithm is defined in the ``get_best_affine()`` method.  It is:
 #. If ``qform_code`` != 0 ('unknown') use the qform affine; else
 #. Use the fall-back affine.
 
+.. _default-sform-qform-codes:
+
+Default sform and qform codes
+=============================
+
+If you create a new image, e.g.:
+
+>>> data = np.random.random((20, 20, 20))
+>>> xform = np.eye(4) * 2
+>>> img = nib.nifti1.Nifti1Image(data, xform)
+
+The sform and qform codes will be initialised to 2 (aligned) and 0 (unknown)
+respectively:
+
+>>> img.get_sform(coded=True) # doctest: +NORMALIZE_WHITESPACE
+(array([[ 2.,  0.,  0.,  0.],
+        [ 0.,  2.,  0.,  0.],
+        [ 0.,  0.,  2.,  0.],
+        [ 0.,  0.,  0.,  1.]]), array(2, dtype=int16))
+>>> img.get_qform(coded=True)
+(None, 0)
+
+This is based on the assumption that the affine you specify for a newly
+created image will align the image to some known coordinate system. According
+to the `NIfTI specification <nifti1>`_, the qform is intended to encode a
+transformation into scanner coordinates - for a programmatically created
+image, we have no way of knowing what the scanner coordinate system is;
+furthermore, the qform cannot be used to store an arbitrary affine transform,
+as it is unable to encode shears. So the provided affine will be stored in the
+sform, and the qform will be left uninitialised.
+
+If you create a new image and specify an existing header, e.g.:
+
+>>> example_ni1 = os.path.join(data_path, 'example4d.nii.gz')
+>>> n1_img = nib.load(example_ni1)
+>>> new_header = header=n1_img.header.copy()
+>>> new_data = np.random.random(n1_img.shape[:3])
+>>> new_img = nib.nifti1.Nifti1Image(data, None, header=new_header)
+
+then the newly created image will inherit the same sform and qform codes that
+are in the provided header. However, if you create a new image with both an
+affine and a header specified, e.g.:
+
+>>> xform = np.eye(4)
+>>> new_img = nib.nifti1.Nifti1Image(data, xform, header=new_header)
+
+then the sform and qform codes will *only* be preserved if the provided affine
+is the same as the affine in the provided header. If the affines do not match,
+the sform and qform codes will be set to their default values of 2 and 0
+respectively. This is done on the basis that, if you are changing the affine,
+you are likely to be changing the space to which the affine is pointing. So
+the original sform and qform codes can no longer be assumed to be valid.
+
+If you wish to set the sform and qform affines and/or codes to some other
+value, you can always set them after creation using the ``set_sform`` and
+``set_qform`` methods, as described above.
+
 ************
 Data scaling
 ************

nibabel/nicom/dwiparams.py

@@ -21,7 +21,7 @@
 '''
 import numpy as np
 import numpy.linalg as npl
-from ..testing import setup_test  # flake8: noqa F401
+from ..testing import setup_test as setup_module # flake8: noqa F401
 
 
 def B2q(B, tol=None):

nibabel/nifti1.py

@@ -1764,7 +1764,20 @@ def __init__(self, dataobj, affine, header=None,
         if header is None and affine is not None:
             self._affine2header()
     # Copy docstring
-    __init__.doc = analyze.AnalyzeImage.__init__.__doc__
+    __init__.__doc__ = analyze.AnalyzeImage.__init__.__doc__ + '''
+    Notes
+    -----
+
+    If both a `header` and an `affine` are specified, and the `affine` does
+    not match the affine that is in the `header`, the `affine` will be used,
+    but the ``sform_code`` and ``qform_code`` fields in the header will be
+    re-initialised to their default values. This is performed on the basis
+    that, if you are changing the affine, you are likely to be changing the
+    space to which the affine is pointing.  The :meth:`set_sform` and
+    :meth:`set_qform` methods can be used to update the codes after an image
+    has been created - see those methods, and the :ref:`manual
+    <default-sform-qform-codes>` for more details.  '''
+
 
     def update_header(self):
         ''' Harmonize header with image data and affine

nibabel/testing/__init__.py

@@ -32,7 +32,7 @@
 data_path = abspath(pjoin(dirname(__file__), '..', 'tests', 'data'))
 
 
-from .np_features import VIRAL_MEMMAP
+from .np_features import memmap_after_ufunc
 
 def assert_dt_equal(a, b):
     """ Assert two numpy dtype specifiers are equal
@@ -218,4 +218,4 @@ def setup_test():
     """
     from distutils.version import LooseVersion
     if LooseVersion(np.__version__) >= LooseVersion('1.14'):
-        np.set_printoptions(sign='legacy')
+        np.set_printoptions(legacy="1.13")

nibabel/testing/np_features.py

@@ -4,16 +4,20 @@
 import numpy as np
 
 
-def _memmap_after_ufunc():
+def memmap_after_ufunc():
     """ Return True if ufuncs on memmap arrays always return memmap arrays
 
     This should be True for numpy < 1.12, False otherwise.
+
+    Memoize after first call.  We do this to avoid having to call this when
+    importing nibabel.testing, because we cannot depend on the source file
+    being present - see gh-571.
     """
+    if memmap_after_ufunc.result is not None:
+        return memmap_after_ufunc.result
     with open(__file__, 'rb') as fobj:
         mm_arr = np.memmap(fobj, mode='r', shape=(10,), dtype=np.uint8)
-        mm_preserved = isinstance(mm_arr + 1, np.memmap)
-    return mm_preserved
-
+        memmap_after_ufunc.result = isinstance(mm_arr + 1, np.memmap)
+    return memmap_after_ufunc.result
 
-# True if ufunc on memmap always returns a memmap
-VIRAL_MEMMAP = _memmap_after_ufunc()
+memmap_after_ufunc.result = None

nibabel/tests/test_arrayproxy.py

@@ -30,7 +30,7 @@
 from numpy.testing import assert_array_equal, assert_array_almost_equal
 from nose.tools import (assert_true, assert_false, assert_equal,
                         assert_not_equal, assert_raises)
-from nibabel.testing import VIRAL_MEMMAP
+from nibabel.testing import memmap_after_ufunc
 
 from .test_fileslice import slicer_samples
 from .test_openers import patch_indexed_gzip
@@ -298,6 +298,8 @@ def check_mmap(hdr, offset, proxy_class,
     # Whether scaled array memory backed by memory map (regardless of what
     # numpy says).
     scaled_really_mmap = unscaled_really_mmap and not has_scaling
+    # Whether ufunc on memmap return memmap
+    viral_memmap = memmap_after_ufunc()
     with InTemporaryDirectory():
         with open(fname, 'wb') as fobj:
             fobj.write(b' ' * offset)
@@ -324,9 +326,9 @@ def check_mmap(hdr, offset, proxy_class,
                 assert_false(back_is_mmap)
             else:
                 assert_equal(unscaled_is_mmap,
-                             VIRAL_MEMMAP or unscaled_really_mmap)
+                             viral_memmap or unscaled_really_mmap)
                 assert_equal(back_is_mmap,
-                             VIRAL_MEMMAP or scaled_really_mmap)
+                             viral_memmap or scaled_really_mmap)
                 if scaled_really_mmap:
                     assert_equal(back_data.mode, expected_mode)
             del prox, back_data

nibabel/tests/test_spatialimages.py

@@ -25,7 +25,7 @@
 
 from .test_helpers import bytesio_round_trip
 from ..testing import (clear_and_catch_warnings, suppress_warnings,
-                       VIRAL_MEMMAP)
+                       memmap_after_ufunc)
 from ..tmpdirs import InTemporaryDirectory
 from .. import load as top_load
 
@@ -464,6 +464,7 @@ def get_disk_image(self):
     def test_load_mmap(self):
         # Test memory mapping when loading images
         img_klass = self.image_class
+        viral_memmap = memmap_after_ufunc()
         with InTemporaryDirectory():
             img, fname, has_scaling = self.get_disk_image()
             file_map = img.file_map.copy()
@@ -485,7 +486,7 @@ def test_load_mmap(self):
                     # numpies returned a memmap object, even though the array
                     # has no mmap memory backing.  See:
                     # https://github.com/numpy/numpy/pull/7406
-                    if has_scaling and not VIRAL_MEMMAP:
+                    if has_scaling and not viral_memmap:
                         expected_mode = None
                     kwargs = {}
                     if mmap is not None: