From 9f93415e063a329b31a006c7aaf9a1bab07b8367 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Fri, 18 Oct 2019 11:30:58 -0700
Subject: [PATCH] ENH: Use ``obliquity`` directly from nibabel

---
 nitransforms/linear.py             |  4 ++--
 nitransforms/patched.py            | 25 -------------------------
 nitransforms/tests/test_affines.py | 16 ----------------
 setup.cfg                          |  2 +-
 4 files changed, 3 insertions(+), 44 deletions(-)
 delete mode 100644 nitransforms/tests/test_affines.py

diff --git a/nitransforms/linear.py b/nitransforms/linear.py
index 262b6ca4..b61578ea 100644
--- a/nitransforms/linear.py
+++ b/nitransforms/linear.py
@@ -13,9 +13,9 @@
 from pathlib import Path
 
 from nibabel.loadsave import load as loadimg
-from nibabel.affines import from_matvec, voxel_sizes
+from nibabel.affines import from_matvec, voxel_sizes, obliquity
 from .base import TransformBase
-from .patched import obliquity, shape_zoom_affine
+from .patched import shape_zoom_affine
 
 
 LPS = np.diag([-1, -1, 1, 1])
diff --git a/nitransforms/patched.py b/nitransforms/patched.py
index 41708b41..6e0b7ecb 100644
--- a/nitransforms/patched.py
+++ b/nitransforms/patched.py
@@ -1,29 +1,4 @@
 import numpy as np
-from nibabel.affines import voxel_sizes
-
-
-def obliquity(affine):
-    r"""
-    Estimate the *obliquity* an affine's axes represent.
-    The term *obliquity* is defined here as the rotation of those axes with
-    respect to the cardinal axes.
-    This implementation is inspired by `AFNI's implementation
-    <https://github.com/afni/afni/blob/b6a9f7a21c1f3231ff09efbd861f8975ad48e525/src/thd_coords.c#L660-L698>`_.
-    For further details about *obliquity*, check `AFNI's documentation
-    <https://sscc.nimh.nih.gov/sscc/dglen/Obliquity>_.
-    Parameters
-    ----------
-    affine : 2D array-like
-        Affine transformation array.  Usually shape (4, 4), but can be any 2D
-        array.
-    Returns
-    -------
-    angles : 1D array-like
-        The *obliquity* of each axis with respect to the cardinal axes, in radians.
-    """
-    vs = voxel_sizes(affine)
-    best_cosines = np.abs((affine[:-1, :-1] / vs).max(axis=1))
-    return np.arccos(best_cosines)
 
 
 def shape_zoom_affine(shape, zooms, x_flip=True, y_flip=False):
diff --git a/nitransforms/tests/test_affines.py b/nitransforms/tests/test_affines.py
deleted file mode 100644
index de9d77f3..00000000
--- a/nitransforms/tests/test_affines.py
+++ /dev/null
@@ -1,16 +0,0 @@
-import numpy as np
-from nibabel.affines import from_matvec
-from nibabel.eulerangles import euler2mat
-from ..patched import obliquity
-
-
-def test_obliquity():
-    """Check the calculation of inclination of an affine axes."""
-    from math import pi
-    aligned = np.diag([2.0, 2.0, 2.3, 1.0])
-    aligned[:-1, -1] = [-10, -10, -7]
-    R = from_matvec(euler2mat(x=0.09, y=0.001, z=0.001), [0.0, 0.0, 0.0])
-    oblique = R.dot(aligned)
-    np.testing.assert_almost_equal(obliquity(aligned), [0.0, 0.0, 0.0])
-    np.testing.assert_almost_equal(obliquity(oblique) * 180 / pi,
-                                   [0.0810285, 5.1569949, 5.1569376])
diff --git a/setup.cfg b/setup.cfg
index 5510e5c8..45b3b5cd 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -7,7 +7,7 @@ python_requires = >= 3.5
 install_requires =
     numpy
     scipy
-    nibabel
+    nibabel @ git+https://github.com/nipy/nibabel@cd48bf05bc567387afe4504eda1da15324bb616f
     h5py
 test_requires =
     pytest