def test_normalize():
assert_allclose(
normalize(
read_file('tomo.npy'),
read_file('flat.npy'),
read_file('dark.npy')),
read_file('normalize.npy'))
def test_normalize_nf():
assert_allclose(
normalize_nf(
read_file('tomo.npy'),
read_file('flat_1.npy'),
read_file('dark.npy'),
(0, 4, 8, 12, 16)),
read_file('normalize_nf.npy'))
def test_write_center():
dpath = os.path.join('test', 'tmp')
cen_range = (5, 7, 0.5)
cen = np.arange(cen_range[0], cen_range[1], cen_range[2])
write_center(read_file('proj.npy'),
read_file('angle.npy'),
dpath,
cen_range=cen_range)
for m in range(cen.size):
assert_equals(
os.path.isfile(
os.path.join(os.path.join('test', 'tmp'),
str('{0:.2f}'.format(cen[m]) + '.tiff'))), True)
shutil.rmtree(dpath)
def test_gridrec(self):
assert_allclose(
recon(self.prj, self.ang, algorithm='gridrec', filter_name='none'),
read_file('gridrec_none.npy'), rtol=1e-2)
assert_allclose(
recon(self.prj, self.ang, algorithm='gridrec', filter_name='shepp'),
read_file('gridrec_shepp.npy'), rtol=1e-2)
assert_allclose(
recon(self.prj, self.ang, algorithm='gridrec', filter_name='cosine'),
read_file('gridrec_cosine.npy'), rtol=1e-2)
assert_allclose(
recon(self.prj, self.ang, algorithm='gridrec', filter_name='hann'),
read_file('gridrec_hann.npy'), rtol=1e-2)
assert_allclose(
recon(self.prj, self.ang, algorithm='gridrec', filter_name='hamming'),
read_file('gridrec_hamming.npy'), rtol=1e-2)
assert_allclose(
recon(self.prj, self.ang, algorithm='gridrec', filter_name='ramlak'),
read_file('gridrec_ramlak.npy'), rtol=1e-2)
assert_allclose(
recon(self.prj, self.ang, algorithm='gridrec', filter_name='parzen'),
read_file('gridrec_parzen.npy'), rtol=1e-2)
assert_allclose(
recon(self.prj, self.ang, algorithm='gridrec', filter_name='butterworth'),
read_file('gridrec_butterworth.npy'), rtol=1e-2)
def test_write_center():
dpath = os.path.join('test', 'tmp')
cen_range = (5, 7, 0.5)
cen = np.arange(cen_range[0], cen_range[1], cen_range[2])
write_center(
read_file('proj.npy'),
read_file('angle.npy'),
dpath, cen_range=cen_range)
for m in range(0):
assert_equals(
os.path.isfile(
os.path.join(
os.path.join('tmp', 'center'),
str('{:.2f}'.format(cen[m]) + '.tiff'))), True)
shutil.rmtree(dpath)
def test_ospml_hybrid(self):
assert_allclose(recon(self.prj,
self.ang,
algorithm='ospml_hybrid',
num_iter=4),
read_file('ospml_hybrid.npy'),
rtol=1e-2)
def test_pml_quad(self):
assert_allclose(recon(self.prj,
self.ang,
algorithm='pml_quad',
num_iter=4),
read_file('pml_quad.npy'),
rtol=1e-2)
def test_circ_mask():
loop_dim(circ_mask, read_file('obj.npy'))
def test_find_center():
sim = read_file('sinogram.npy')
ang = np.linspace(0, np.pi, sim.shape[0])
cen = find_center(sim, ang)
assert_allclose(cen, 45.28, rtol=1e-2)
def test_upsample():
loop_dim(upsample, read_file('obj.npy'))
def test_find_center_pc():
proj_0 = read_file('projection.npy')
proj_180 = image_shift(np.fliplr(proj_0), (0, 18.75), mode='reflect')
cen = find_center_pc(proj_0, proj_180)
assert_allclose(cen, 73.375, rtol=0.25)
def test_project():
assert_allclose(
project(read_file('obj.npy'), read_file('angle.npy')),
read_file('proj.npy'), rtol=1e-2)
def test_sobel_filter():
loop_dim(sobel_filter, read_file('cube.npy'))
def test_remove_outlier():
proj = read_file("proj.npy")
proj[8][4][6] = 20
assert_allclose(remove_outlier(proj, dif=10), read_file("remove_zinger.npy"))
def test_mlem(self):
assert_allclose(
recon(self.prj, self.ang, algorithm='mlem', num_iter=4),
read_file('mlem.npy'), rtol=1e-2)
def test_ospml_hybrid(self):
assert_allclose(
recon(self.prj, self.ang, algorithm='ospml_hybrid', num_iter=4),
read_file('ospml_hybrid.npy'), rtol=1e-2)
def test_fbp(self):
assert_allclose(
recon(self.prj, self.ang, algorithm='fbp'),
read_file('fbp.npy'), rtol=1e-2)
def test_gridrec(self):
assert_allclose(
recon(self.prj, self.ang, algorithm='gridrec'),
read_file('gridrec.npy'), rtol=1e-2)
def test_bart(self):
assert_allclose(
recon(self.prj, self.ang, algorithm='bart', num_iter=4),
read_file('bart.npy'), rtol=1e-2)
def __init__(self):
self.prj = read_file('proj.npy')
self.ang = read_file('angle.npy')
def test_pml_quad(self):
assert_allclose(
recon(self.prj, self.ang, algorithm='pml_quad', num_iter=4),
read_file('pml_quad.npy'), rtol=1e-2)
def test_retrieve_phase():
assert_allclose(retrieve_phase(read_file('proj.npy')),
read_file('retrieve_phase.npy'),
rtol=1e-6)
def test_gaussian_filter():
loop_dim(gaussian_filter, read_file('cube.npy'))
def test_gaussian_filter():
loop_dim(gaussian_filter, read_file('cube.npy'))
def test_median_filter():
loop_dim(median_filter, read_file('cube.npy'))
def test_normalize_bg():
assert_allclose(
normalize_bg(read_file('tomo.npy')),
read_file('normalize_bg.npy'))
def test_sobel_filter():
loop_dim(sobel_filter, read_file('cube.npy'))
def test_find_center():
sim = read_file('sinogram.npy')
ang = np.linspace(0, np.pi, sim.shape[0])
cen = find_center(sim, ang)
assert_allclose(cen, 45.28, rtol=1e-2)
def test_remove_outlier():
proj = read_file('proj.npy')
proj[8][4][6] = 20
assert_allclose(remove_outlier(proj, dif=10),
read_file('remove_zinger.npy'))
def test_sobel_filter():
loop_dim(sobel_filter, read_file("cube.npy"))
def test_retrieve_phase():
assert_allclose(
retrieve_phase(read_file('proj.npy')),
read_file('retrieve_phase.npy'), rtol=1e-6)
def test_pad():
loop_dim(pad, read_file('obj.npy'))
def test_mlem(self):
assert_allclose(recon(self.prj, self.ang, algorithm='mlem',
num_iter=4),
read_file('mlem.npy'),
rtol=1e-2)
def test_downsample():
loop_dim(downsample, read_file('obj.npy'))
def test_circ_mask():
loop_dim(circ_mask, read_file('obj.npy'))
def test_remove_stripe_ti():
assert_allclose(remove_stripe_ti(read_file('proj.npy')),
read_file('remove_stripe_ti.npy'),
rtol=1e-2)
def test_downsample():
loop_dim(downsample, read_file('obj.npy'))
def test_project():
assert_allclose(project(read_file("obj.npy"), read_file("angle.npy")), read_file("proj.npy"), rtol=1e-2)
def test_remove_stripe_ti():
assert_allclose(
remove_stripe_ti(read_file('proj.npy')),
read_file('remove_stripe_ti.npy'), rtol=1e-2)
def test_normalize_nf():
assert_allclose(
normalize_nf(read_file('tomo.npy'), read_file('flat_1.npy'),
read_file('dark.npy'), (0, 4, 8, 12, 16)),
read_file('normalize_nf.npy'))
def test_bart(self):
assert_allclose(recon(self.prj, self.ang, algorithm='bart',
num_iter=4),
read_file('bart.npy'),
rtol=1e-2)
def test_median_filter():
loop_dim(median_filter, read_file('cube.npy'))
def test_fbp(self):
assert_allclose(recon(self.prj, self.ang, algorithm='fbp'),
read_file('fbp.npy'),
rtol=1e-2)
def test_remove_outlier():
proj = read_file('proj.npy')
proj[8][4][6] = 20
assert_allclose(
remove_outlier(proj, dif=10),
read_file('remove_outlier.npy'))
def __init__(self):
self.prj = read_file('proj.npy')
self.ang = read_file('angle.npy').astype('float32')
def test_normalize_bg():
assert_allclose(normalize_bg(read_file('tomo.npy')),
read_file('normalize_bg.npy'))
def __init__(self):
self.prj = read_file('proj.npy')
self.ang = read_file('angle.npy').astype('float32')
def test_upsample():
loop_dim(upsample, read_file('obj.npy'))
def test_project():
assert_allclose(project(read_file('obj.npy'), read_file('angle.npy')),
read_file('proj.npy'),
rtol=1e-2)
