def test_transfo_null():
dir_tmp = "."
print("Null warping field")
print(" Create some recognizable data")
data = np.ones((7, 8, 9), order="F")
path_src = "warp-src.nii"
img_src = fake_image_sct_custom(data).save(path_src)
print(" Create a null warping field")
data = np.zeros((7, 8, 9, 1, 3), order="F")
path_warp = "warp-field.nii"
img_warp = fake_image_sct_custom(data)
img_warp.header.set_intent('vector', (), '')
img_warp.save(path_warp)
print(" Apply")
path_dst = "warp-dst.nii"
xform = sct_apply_transfo.Transform(input_filename=path_src,
fname_dest=path_src,
list_warp=[path_warp],
output_filename=path_dst)
xform.apply()
img_src2 = msct_image.Image(path_src)
img_dst = msct_image.Image(path_dst)
print(" Check that the source wasn't altered")
assert (img_src.data == img_src2.data).all()
assert img_src.orientation == img_dst.orientation
assert img_src.data.shape == img_dst.data.shape
print(
" Check that the destination is identical to the source since the field was null"
)
dat_src = img_src.data
dat_dst = np.array(img_dst.data)
for idx_slice, (slice_src, slice_dst) in enumerate(
msct_image.SlicerMany((img_src, img_dst), msct_image.Slicer)):
slice_src = np.array(slice_src)
slice_dst = np.array(slice_dst)
print(slice_src)
print(slice_dst)
assert np.allclose(slice_src, slice_dst)
assert np.allclose(dat_src, dat_dst)
def test_slicer(fake_3dimage_sct, fake_3dimage_sct2):
im3d = fake_3dimage_sct.copy()
slicer = msct_image.Slicer(im3d, "LPI")
if 0:
for im2d in slicer:
print(im2d)
assert slicer._nb_slices == 9
assert 100 < np.mean(slicer[0]) < 200
slicer = msct_image.Slicer(im3d, "LPS")
if 0:
for im2d in slicer:
print(im2d)
assert slicer._nb_slices == 9
assert 900 < np.mean(slicer[0]) < 1000
with pytest.raises(ValueError):
slicer = msct_image.Slicer(im3d, "LI")
with pytest.raises(ValueError):
slicer = msct_image.Slicer(im3d, "L")
with pytest.raises(ValueError):
slicer = msct_image.Slicer(im3d, "Lx")
with pytest.raises(ValueError):
slicer = msct_image.Slicer(im3d, "LA")
im3d2 = fake_3dimage_sct.copy()
im3d2.data += 1000
slicer = msct_image.SlicerMany((im3d, im3d2),
msct_image.Slicer,
orientation="LPI")
for idx_slice, (im2d_a, im2d_b) in enumerate(slicer):
assert np.all(im2d_b == im2d_a + 1000)
with pytest.raises(ValueError):
slicer = msct_image.SlicerMany((im3d, im3d2),
msct_image.Slicer,
orientation="IS")
im3d2 = fake_3dimage_sct2.copy()
with pytest.raises(ValueError):
slicer = msct_image.SlicerMany((im3d, im3d2),
msct_image.Slicer,
orientation="LPI")
with pytest.raises(ValueError):
slicer = msct_image.Slicer(1)
im3d = fake_3dimage_sct.copy()
d = im3d.data.copy()
slicer = msct_image.Slicer(im3d, "RPI")
if 0:
for im2d in slicer:
print(im2d)
slicer = msct_image.Slicer(im3d, "ASR")
if 0:
for im2d in slicer:
print(im2d)
msct_image.Slicer(im3d, "ASR")[0][0, 0] = -1
for idx_slice, (slice2d_new, slice2d_old) in enumerate(
msct_image.SlicerMany((im3d, fake_3dimage_sct.copy()),
msct_image.Slicer,
orientation="ASR")):
if idx_slice == 0:
assert slice2d_new[0, 0] == -1
slice2d_new[0, 0] = slice2d_old[0, 0]
assert (slice2d_new == slice2d_old).all()