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import astra
import numpy as np
import pytest
DET_SPACING_X = 1.0
DET_SPACING_Y = 1.0
DET_ROW_COUNT = 20
DET_COL_COUNT = 45
N_ANGLES = 180
ANGLES = np.linspace(0, 2 * np.pi, N_ANGLES, endpoint=False)
N_ROWS = 40
N_COLS = 30
N_SLICES = 50
@pytest.fixture
def geometry(geometry_type):
if geometry_type == '-vol':
return astra.create_vol_geom(N_ROWS, N_COLS, N_SLICES)
elif geometry_type == '-sino':
return astra.create_proj_geom('parallel3d', DET_SPACING_X, DET_SPACING_Y,
DET_ROW_COUNT, DET_COL_COUNT, ANGLES)
@pytest.fixture
def matrix_initializer(geometry_type):
if geometry_type == '-vol':
return np.random.rand(N_SLICES, N_ROWS, N_COLS)
elif geometry_type == '-sino':
return np.random.rand(DET_ROW_COUNT, N_ANGLES, DET_COL_COUNT)
@pytest.mark.parametrize('geometry_type', ['-vol', '-sino'])
class TestAll:
def test_default_initializer(self, geometry_type, geometry):
data_id = astra.data3d.create(geometry_type, geometry)
data = astra.data3d.get(data_id)
astra.data3d.delete(data_id)
assert np.allclose(data, 0.0)
def test_scalar_initializer(self, geometry_type, geometry):
data_id = astra.data3d.create(geometry_type, geometry, 1.0)
data = astra.data3d.get(data_id)
astra.data3d.delete(data_id)
assert np.allclose(data, 1.0)
def test_matrix_initializer(self, geometry_type, geometry, matrix_initializer):
data_id = astra.data3d.create(geometry_type, geometry, matrix_initializer)
data = astra.data3d.get(data_id)
astra.data3d.delete(data_id)
assert np.allclose(data, matrix_initializer)
@pytest.mark.parametrize('dtype', [np.float32, np.float64, np.int64, bool])
def test_dtypes(self, geometry_type, geometry, matrix_initializer, dtype):
matrix_initializer = matrix_initializer.astype(dtype)
data_id = astra.data3d.create(geometry_type, geometry, matrix_initializer)
data = astra.data3d.get(data_id)
astra.data3d.delete(data_id)
assert data.dtype == np.float32
assert np.array_equal(data, matrix_initializer.astype(np.float32))
def test_link(self, geometry_type, geometry, matrix_initializer):
linked_array = matrix_initializer.astype(np.float32)
data_id = astra.data3d.link(geometry_type, geometry, linked_array)
# Assert writing to shared ndarray writes to Astra object
linked_array[:] = 0.0
astra_object_contents = astra.data3d.get(data_id)
assert np.allclose(astra_object_contents, linked_array)
# Assert writing to Astra object writes to shared ndarray
astra.data3d.store(data_id, 2.0)
assert np.allclose(linked_array, 2.0)
# Assert Astra object contents is a copy not a link
astra_object_contents[:] = 1.0
assert not np.allclose(astra_object_contents, linked_array)
astra.data3d.delete(data_id)
def test_get_shared(self, geometry_type, geometry, matrix_initializer):
data_id = astra.data3d.create(geometry_type, geometry, matrix_initializer)
shared_array = astra.data3d.get_shared(data_id)
# Assert writing to shared ndarray writes to Astra object
shared_array[:] = 0.0
astra_object_contents = astra.data3d.get(data_id)
assert np.allclose(astra_object_contents, shared_array)
# Assert writing to Astra object writes to shared ndarray
astra.data3d.store(data_id, 2.0)
assert np.allclose(shared_array, 2.0)
# Assert Astra object contents is a copy not a link
astra_object_contents[:] = 1.0
assert not np.allclose(astra_object_contents, shared_array)
astra.data3d.delete(data_id)
def test_dimensions(self, geometry_type, geometry):
data_id = astra.data3d.create(geometry_type, geometry)
dimensions = astra.data3d.dimensions(data_id)
astra.data3d.delete(data_id)
if geometry_type == '-sino':
assert dimensions == (DET_ROW_COUNT, N_ANGLES, DET_COL_COUNT)
elif geometry_type == 'vol':
assert dimensions == (N_ROWS, N_COLS, N_SLICES)
def test_get_geometry(self, geometry_type, geometry):
data_id = astra.data3d.create(geometry_type, geometry)
geometry_in = geometry.copy() # To safely use `pop` later
geometry_out = astra.data3d.get_geometry(data_id)
if geometry_type == '-sino':
assert np.allclose(geometry_in.pop('ProjectionAngles'),
geometry_out.pop('ProjectionAngles'))
assert geometry_in == geometry_out
elif geometry_type == 'vol':
# `option`, `options`, `Option` and `Options` are synonymous in astra configs
assert geometry_in.pop('option') == geometry_out.pop('options')
assert geometry_in == geometry_out
astra.data3d.delete(data_id)
def test_change_geometry(self, geometry_type, geometry):
data_id = astra.data3d.create(geometry_type, geometry)
if geometry_type == '-sino':
new_spacing = 2 * DET_SPACING_X, 3 * DET_SPACING_Y
new_angles = np.random.rand(N_ANGLES)
new_geometry = astra.create_proj_geom('parallel3d', new_spacing[0], new_spacing[1],
DET_ROW_COUNT, DET_COL_COUNT, new_angles)
astra.data3d.change_geometry(data_id, new_geometry)
changed_geometry = astra.data3d.get_geometry(data_id)
astra.data3d.delete(data_id)
assert changed_geometry['DetectorSpacingX'] == new_spacing[0]
assert changed_geometry['DetectorSpacingY'] == new_spacing[1]
assert np.allclose(changed_geometry['ProjectionAngles'], new_angles)
elif geometry_type == '-vol':
new_geometry = astra.create_vol_geom(N_ROWS, N_COLS, N_SLICES, 0, 1, 2, 3, 4, 5)
astra.data3d.change_geometry(data_id, new_geometry)
changed_geometry = astra.data3d.get_geometry(data_id)
astra.data3d.delete(data_id)
assert changed_geometry['options'] == {'WindowMinX': 0, 'WindowMaxX': 1,
'WindowMinY': 2, 'WindowMaxY': 3,
'WindowMinZ': 4, 'WindowMaxZ': 5}
def test_delete(self, geometry_type, geometry):
data_id = astra.data3d.create(geometry_type, geometry)
astra.data3d.delete(data_id)
with pytest.raises(astra.log.AstraError):
astra.data3d.get(data_id)
def test_clear(self, geometry_type, geometry):
data_id1 = astra.data3d.create(geometry_type, geometry)
data_id2 = astra.data3d.create(geometry_type, geometry)
astra.data3d.clear()
with pytest.raises(astra.log.AstraError):
astra.data3d.get(data_id1)
with pytest.raises(astra.log.AstraError):
astra.data3d.get(data_id2)
def test_info(self, geometry_type, geometry, capsys):
get_n_info_objects = lambda: len(capsys.readouterr().out.split('\n')) - 5
data_id = astra.data3d.create(geometry_type, geometry)
astra.data3d.info()
assert get_n_info_objects() == 1
astra.data3d.delete(data_id)
astra.data3d.info()
assert get_n_info_objects() == 0
@pytest.mark.parametrize('modified', [True, False])
def test_shepp_logan(modified):
geometry = astra.create_vol_geom(N_ROWS, N_COLS, N_SLICES)
data_id, data = astra.data3d.shepp_logan(geometry, modified)
astra.data2d.delete(data_id)
assert not np.allclose(data, 0.0)
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