def test_defaults_3D():
img = image.fromarray(np.ones(array3D_shape), 'kji', 'zyx')
yield assert_true, isinstance(img._data, np.ndarray)
yield assert_true, img.ndim == 3
yield assert_true, img.shape == array3D_shape
# ndarray's do not have a header
yield assert_raises, AttributeError, getattr, img, 'header'
yield assert_true, img.affine.shape == (4,4)
yield assert_true, img.affine.diagonal().all() == 1
def test_defaults_2D():
data = np.ones(array2D_shape)
img = image.fromarray(data, 'kj', 'yx')
yield assert_true, isinstance(img._data, np.ndarray)
yield assert_true, img.ndim == 2
yield assert_true, img.shape == array2D_shape
yield assert_raises, AttributeError, getattr, img, 'header'
yield assert_true, img.affine.shape == (3,3)
yield assert_true, img.affine.diagonal().all() == 1
def test_defaults_4D():
data = np.ones(array4D_shape)
names = ['time', 'zspace', 'yspace', 'xspace']
img = image.fromarray(data, names, names)
yield assert_true, isinstance(img._data, np.ndarray)
yield assert_true, img.ndim == 4
yield assert_true, img.shape == array4D_shape
yield assert_raises, AttributeError, getattr, img, 'header'
yield assert_true, img.affine.shape == (5,5)
yield assert_true, img.affine.diagonal().all() == 1
def test_merge_images():
# Check that merge_images works, and that the CoordinateMap
# instance is first one in the list.
data = np.ones((2,3,4))
img = image.fromarray(data, 'ijk', 'xyz')
mimg = merge_images([img for i in range(4)])
yield assert_equal, mimg.shape, (4,) + img.shape
yield nptest.assert_almost_equal, mimg.affine[1:,1:], img.affine
yield nptest.assert_almost_equal, mimg.affine[0], np.array([1,0,0,0,0])
yield nptest.assert_almost_equal, mimg.affine[:,0], np.array([1,0,0,0,0])
# A list with different CoordinateMaps -- the merged images
# takes the first one
naffine = Affine(np.diag([-2,-4,-6,1.]),
img.coordmap.input_coords,
img.coordmap.output_coords)
nimg = Image(np.asarray(img), naffine)
mimg = merge_images([nimg, img, img, img])
yield assert_equal, mimg.shape, (4,) + img.shape
yield nptest.assert_almost_equal, mimg.affine[1:,1:], nimg.affine
yield nptest.assert_almost_equal, mimg.affine[0], np.array([1,0,0,0,0])
yield nptest.assert_almost_equal, mimg.affine[:,0], np.array([1,0,0,0,0])
volFile = '/chb/tmp/kihotest.nii'
trkFile = '/chb/tmp/kihotest.trk'
mappedTrkFile = '/chb/tmp/kihotest_mapped.trk'
# volume
testArr = np.zeros((10, 10, 10))
r = 0
for i in range(testArr.shape[0]):
for j in range(testArr.shape[1]):
for k in range(testArr.shape[2]):
r += 1
testArr[i, j, k] = r
img = image.fromarray(testArr, 'ijk', 'xyz')
save_image(img, volFile)
# trk file
fibers = []
# 2,5,6
# 3,5,7
# 2,6,7
# 8,7,3
# 9,5,4
points = np.array([[2, 5, 6], [3, 5, 7], [2, 6, 7], [8, 7, 3], [9, 5, 4]],
dtype=np.float32)
fibers.append((points, None, None))
volFile = '/chb/tmp/kihotest.nii'
trkFile = '/chb/tmp/kihotest.trk'
mappedTrkFile = '/chb/tmp/kihotest_mapped.trk'
# volume
testArr = np.zeros( ( 10, 10, 10 ) )
r = 0
for i in range( testArr.shape[0] ):
for j in range( testArr.shape[1] ):
for k in range( testArr.shape[2] ):
r += 1
testArr[i, j, k] = r
img = image.fromarray( testArr, 'ijk', 'xyz' )
save_image( img, volFile )
# trk file
fibers = []
# 2,5,6
# 3,5,7
# 2,6,7
# 8,7,3
# 9,5,4
points = np.array( [[2, 5, 6], [3, 5, 7], [2, 6, 7], [8, 7, 3], [9, 5, 4]], dtype=np.float32 )
fibers.append( ( points, None, None ) )