def test_write_read_crystfel_file(tmpdir):
geom = LPD_1MGeometry.from_quad_positions([(11.4, 299), (-11.5, 8),
(254.5, -16), (278.5, 275)])
path = str(tmpdir / 'test.geom')
geom.write_crystfel_geom(filename=path)
with open(path, 'r') as f:
contents = f.read()
with open(path, 'w') as f:
f.write('clen = 0.119\n')
f.write('adu_per_eV = 0.0075\n')
f.write(contents)
# Load the geometry file with cfelpyutils and test the ridget groups
loaded = LPD_1MGeometry.from_crystfel_geom(path)
np.testing.assert_allclose(loaded.modules[0][0].corner_pos,
geom.modules[0][0].corner_pos)
np.testing.assert_allclose(loaded.modules[0][0].fs_vec,
geom.modules[0][0].fs_vec)
geom_dict = load_crystfel_geometry(path)
quad_gr0 = [
'p0a0', 'p0a1', 'p0a2', 'p0a3', 'p0a4', 'p0a5', 'p0a6', 'p0a7', 'p0a8',
'p0a9', 'p0a10', 'p0a11', 'p0a12', 'p0a13', 'p0a14', 'p0a15', 'p1a0',
'p1a1', 'p1a2', 'p1a3', 'p1a4', 'p1a5', 'p1a6', 'p1a7', 'p1a8', 'p1a9',
'p1a10', 'p1a11', 'p1a12', 'p1a13', 'p1a14', 'p1a15', 'p2a0', 'p2a1',
'p2a2', 'p2a3', 'p2a4', 'p2a5', 'p2a6', 'p2a7', 'p2a8', 'p2a9',
'p2a10', 'p2a11', 'p2a12', 'p2a13', 'p2a14', 'p2a15', 'p3a0', 'p3a1',
'p3a2', 'p3a3', 'p3a4', 'p3a5', 'p3a6', 'p3a7', 'p3a8', 'p3a9',
'p3a10', 'p3a11', 'p3a12', 'p3a13', 'p3a14', 'p3a15'
]
assert geom_dict['rigid_groups']['p0'] == quad_gr0[:16]
assert geom_dict['rigid_groups']['p3'] == quad_gr0[-16:]
assert geom_dict['rigid_groups']['q0'] == quad_gr0
def test_data_coords_to_positions():
geom = LPD_1MGeometry.from_quad_positions([(11.4, 299), (-11.5, 8),
(254.5, -16), (278.5, 275)])
module_no = np.zeros(16, dtype=np.int16)
# Points near the centre of each tile
slow_scan = np.tile(np.linspace(16, 240, num=8, dtype=np.float32), 2)
fast_scan = np.array([64, 192], dtype=np.float32).repeat(8)
tileno, tile_ss, tile_fs = geom._module_coords_to_tile(
slow_scan, fast_scan)
np.testing.assert_allclose(
tileno, [7, 6, 5, 4, 3, 2, 1, 0, 8, 9, 10, 11, 12, 13, 14, 15])
np.testing.assert_allclose(tile_ss, 16)
np.testing.assert_allclose(tile_fs, 64)
res = geom.data_coords_to_positions(module_no, slow_scan, fast_scan)
assert res.shape == (16, 3)
resx, resy, resz = res.T
np.testing.assert_allclose(resz, 0)
assert (np.diff(resy[:8]) > 0).all() # T1-T8 Monotonically increasing
assert (np.diff(resy[8:]) > 0).all() # T9-T16 Monotonically increasing
assert -0.128 > resx.max() > resx.min() > -0.280
def test_snap_assemble_data():
geom = LPD_1MGeometry.from_quad_positions([(11.4, 299), (-11.5, 8),
(254.5, -16), (278.5, 275)])
stacked_data = np.zeros((16, 256, 256))
img, centre = geom.position_modules_fast(stacked_data)
assert img.shape == (1202, 1104)
assert tuple(centre) == (604, 547)
assert np.isnan(img[0, 0])
assert img[50, 50] == 0
def onGeomFileChange(self, value):
if self._geom_file != value:
self._geom_file = value
try:
if config["DETECTOR"] == 'LPD':
quad_positions = config["LPD"]["quad_positions"]
self._geom = LPD_1MGeometry.from_h5_file_and_quad_positions(
self._geom_file, quad_positions)
elif config["DETECTOR"] == 'AGIPD':
self._geom = AGIPD_1MGeometry.from_crystfel_geom(filename)
except Exception as ex:
print(ex)
def test_to_distortion_array():
geom = LPD_1MGeometry.from_quad_positions([(11.4, 299), (-11.5, 8),
(254.5, -16), (278.5, 275)])
# Smoketest
distortion = geom.to_distortion_array()
assert isinstance(distortion, np.ndarray)
assert distortion.shape == (4096, 256, 4, 3)
# Coordinates in m, origin at corner; max x & y should be ~ 50cm
assert 0.40 < distortion[..., 1].max() < 0.70
assert 0.40 < distortion[..., 2].max() < 0.70
assert 0.0 <= distortion[..., 1].min() < 0.01
assert 0.0 <= distortion[..., 2].min() < 0.01
def test_inspect():
geom = LPD_1MGeometry.from_quad_positions([(11.4, 299), (-11.5, 8),
(254.5, -16), (278.5, 275)])
# Smoketest
ax = geom.inspect()
assert isinstance(ax, Axes)