From 21669d1ab23e1d3f59daccc31879836f90d505af Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 23 Oct 2019 16:59:53 -0700
Subject: [PATCH] ENH: Write tests pulling up the coverage of base submodule
---
nitransforms/base.py | 9 ++-------
nitransforms/linear.py | 19 +++++++++++++++++--
nitransforms/tests/test_base.py | 33 +++++++++++++++++++++++++++++++--
3 files changed, 50 insertions(+), 11 deletions(-)
diff --git a/nitransforms/base.py b/nitransforms/base.py
index 6e6a4d23..154f8e33 100644
--- a/nitransforms/base.py
+++ b/nitransforms/base.py
@@ -10,6 +10,7 @@
from pathlib import Path
import numpy as np
import h5py
+import warnings
from nibabel.loadsave import load
from scipy import ndimage as ndi
@@ -110,12 +111,6 @@ def __init__(self):
"""Instantiate a transform."""
self._reference = None
- def __eq__(self, other):
- """Overload equals operator."""
- if not self._reference == other._reference:
- return False
- return np.allclose(self.matrix, other.matrix, rtol=EQUALITY_TOL)
-
def __call__(self, x, inverse=False, index=0):
"""Apply y = f(x)."""
return self.map(x, inverse=inverse, index=index)
@@ -124,7 +119,7 @@ def __call__(self, x, inverse=False, index=0):
def reference(self):
"""Access a reference space where data will be resampled onto."""
if self._reference is None:
- raise ValueError('Reference space not set')
+ warnings.warn('Reference space not set')
return self._reference
@reference.setter
diff --git a/nitransforms/linear.py b/nitransforms/linear.py
index df0a2f59..46fe46cc 100644
--- a/nitransforms/linear.py
+++ b/nitransforms/linear.py
@@ -7,13 +7,12 @@
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""Linear transforms."""
-import sys
import numpy as np
from pathlib import Path
from nibabel.loadsave import load as loadimg
from nibabel.affines import from_matvec, voxel_sizes, obliquity
-from .base import TransformBase, _as_homogeneous
+from .base import TransformBase, _as_homogeneous, EQUALITY_TOL
from .patched import shape_zoom_affine
from . import io
@@ -67,6 +66,22 @@ def __init__(self, matrix=None, reference=None):
reference = loadimg(reference)
self.reference = reference
+ def __eq__(self, other):
+ """
+ Overload equals operator.
+
+ Examples
+ --------
+ >>> xfm1 = Affine([[1, 0, 0, 4], [0, 1, 0, 0], [0, 0, 1, 0], [0, 0, 0, 1]])
+ >>> xfm2 = Affine(xfm1.matrix)
+ >>> xfm1 == xfm2
+ True
+
+ """
+ if not self._reference == other._reference:
+ return False
+ return np.allclose(self.matrix, other.matrix, rtol=EQUALITY_TOL)
+
@property
def matrix(self):
"""Access the internal representation of this affine."""
diff --git a/nitransforms/tests/test_base.py b/nitransforms/tests/test_base.py
index 6035afcb..2856f42e 100644
--- a/nitransforms/tests/test_base.py
+++ b/nitransforms/tests/test_base.py
@@ -1,8 +1,10 @@
"""Tests of the base module."""
import numpy as np
+import nibabel as nb
import pytest
+import h5py
-from ..base import ImageGrid
+from ..base import ImageGrid, TransformBase
@pytest.mark.parametrize('image_orientation', ['RAS', 'LAS', 'LPS', 'oblique'])
@@ -30,9 +32,36 @@ def test_ImageGrid(get_testdata, image_orientation):
assert idxs.shape[1] == coords.shape[1] == img.nvox == np.prod(im.shape)
-def test_ImageGrid_load(data_path, get_testdata):
+def test_ImageGrid_utils(tmpdir, data_path, get_testdata):
"""Check that images can be objects or paths and equality."""
+ tmpdir.chdir()
+
im1 = get_testdata['RAS']
im2 = data_path / 'someones_anatomy.nii.gz'
assert ImageGrid(im1) == ImageGrid(im2)
+
+ with h5py.File('xfm.x5', 'w') as f:
+ ImageGrid(im1)._to_hdf5(f.create_group('Reference'))
+
+
+def test_TransformBase(monkeypatch, data_path, tmpdir):
+ """Check the correctness of TransformBase components."""
+ tmpdir.chdir()
+
+ def _fakemap(klass, x, inverse=False, index=0):
+ return x
+
+ def _to_hdf5(klass, x5_root):
+ return None
+
+ monkeypatch.setattr(TransformBase, 'map', _fakemap)
+ monkeypatch.setattr(TransformBase, '_to_hdf5', _to_hdf5)
+ nii = nb.load(str(data_path / 'someones_anatomy.nii.gz'))
+ xfm = TransformBase()
+ xfm.reference = str(data_path / 'someones_anatomy.nii.gz')
+ assert xfm.ndim == 3
+ moved = xfm.resample(nii, order=0)
+ assert np.all(nii.get_fdata() == moved.get_fdata())
+
+ xfm.to_filename('data.x5')