def test_write_read_crystfel_file(tmpdir):
geom = AGIPD_1MGeometry.from_quad_positions(
quad_pos=[(-525, 625), (-550, -10), (520, -160), (542.5, 475)])
path = str(tmpdir / 'test.geom')
geom.write_crystfel_geom(filename=path,
photon_energy=9000,
adu_per_ev=0.0075,
clen=0.2)
loaded = AGIPD_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)
# Load the geometry file with cfelpyutils and test the rigid groups
geom_dict = load_crystfel_geometry(path)
quad_gr0 = [ # 1st quadrant: p0a0 ... p3a7
'p{}a{}'.format(p, a) for p, a in product(range(4), range(8))
]
assert geom_dict['rigid_groups']['p0'] == quad_gr0[:8]
assert geom_dict['rigid_groups']['p3'] == quad_gr0[-8:]
assert geom_dict['rigid_groups']['q0'] == quad_gr0
assert geom_dict['panels']['p0a0']['res'] == 5000 # 5000 pixels/metre
p3a7 = geom_dict['panels']['p3a7']
assert p3a7['min_ss'] == 448
assert p3a7['max_ss'] == 511
assert p3a7['min_fs'] == 0
assert p3a7['max_fs'] == 127
def test_compare():
geom1 = AGIPD_1MGeometry.from_quad_positions(
quad_pos=[(-525, 625), (-550, -10), (520, -160), (542.5, 475)])
geom2 = AGIPD_1MGeometry.from_quad_positions(
quad_pos=[(-527, 625), (-548, -10), (520, -162), (542.5, 473)])
# Smoketest
ax = geom1.compare(geom2)
assert isinstance(ax, Axes)
def test_inspect():
geom = AGIPD_1MGeometry.from_quad_positions(
quad_pos=[(-525, 625), (-550, -10), (520, -160), (542.5, 475)]
)
# Smoketest
ax = geom.inspect()
assert isinstance(ax, Axes)
def test_snap_assemble_data():
def check_result(img, centre):
assert img.shape == (1256, 1092)
assert tuple(centre) == (631, 550)
assert np.isnan(img[0, 0])
assert img[50, 50] == 0
geom = AGIPD_1MGeometry.from_quad_positions(
quad_pos=[(-525, 625), (-550, -10), (520, -160), (542.5, 475)])
stacked_data = np.zeros((16, 512, 128))
img, centre = geom.position_modules_fast(stacked_data)
check_result(img, centre)
# test unsafe cast with output array
stacked_data = np.zeros((16, 512, 128), dtype=np.float64)
out = geom.output_array_for_position_fast(dtype=np.float32)
with pytest.raises(TypeError):
img, centre = geom.position_modules_fast(stacked_data, out=out)
# test safe cast with output array
stacked_data = np.zeros((16, 512, 128), dtype=np.uint16)
out = geom.output_array_for_position_fast(dtype=np.float32)
img, centre = geom.position_modules_fast(stacked_data, out=out)
check_result(img, centre)
check_result(out, centre)
assert img.dtype == out.dtype == np.float32
def test_snap_assemble_data():
geom = AGIPD_1MGeometry.from_quad_positions(
quad_pos=[(-525, 625), (-550, -10), (520, -160), (542.5, 475)])
stacked_data = np.zeros((16, 512, 128))
img, centre = geom.position_modules_fast(stacked_data)
assert img.shape == (1256, 1092)
assert tuple(centre) == (631, 550)
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_write_read_crystfel_file(tmpdir):
geom = AGIPD_1MGeometry.from_quad_positions(
quad_pos=[(-525, 625), (-550, -10), (520, -160), (542.5, 475)]
)
path = str(tmpdir / 'test.geom')
geom.write_crystfel_geom(path)
# We need to add some experiment details before cfelpyutils will read the
# file
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)
loaded = AGIPD_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)
def test_to_distortion_array():
geom = AGIPD_1MGeometry.from_quad_positions(
quad_pos=[(-525, 625), (-550, -10), (520, -160), (542.5, 475)])
# Smoketest
distortion = geom.to_distortion_array()
assert isinstance(distortion, np.ndarray)
assert distortion.shape == (8192, 128, 4, 3)
# Coordinates in m, origin at corner; max x & y should be ~ 25cm
assert 0.20 < distortion[..., 1].max() < 0.30
assert 0.20 < distortion[..., 2].max() < 0.30
assert 0.0 <= distortion[..., 1].min() < 0.01
assert 0.0 <= distortion[..., 2].min() < 0.01
def test_get_pixel_positions():
geom = AGIPD_1MGeometry.from_quad_positions(
quad_pos=[(-525, 625), (-550, -10), (520, -160), (542.5, 475)])
pixelpos = geom.get_pixel_positions()
assert pixelpos.shape == (16, 512, 128, 3)
px = pixelpos[..., 0]
py = pixelpos[..., 1]
assert -0.12 < px.min() < -0.1
assert 0.12 > px.max() > 0.1
assert -0.14 < py.min() < -0.12
assert 0.14 > py.max() > 0.12
def test_write_read_crystfel_file_2d(tmpdir):
geom = AGIPD_1MGeometry.from_quad_positions(
quad_pos=[(-525, 625), (-550, -10), (520, -160), (542.5, 475)])
path = str(tmpdir / 'test.geom')
geom.write_crystfel_geom(filename=path,
dims=('frame', 'ss', 'fs'),
adu_per_ev=0.0075,
clen=0.2)
loaded = AGIPD_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)
# Load the geometry file with cfelpyutils and check some values
geom_dict = load_crystfel_geometry(path)
p3a7 = geom_dict['panels']['p3a7']
assert p3a7['dim_structure'] == ['%', 'ss', 'fs']
assert p3a7['min_ss'] == (3 * 512) + 448
assert p3a7['max_ss'] == (3 * 512) + 511
assert p3a7['min_fs'] == 0
assert p3a7['max_fs'] == 127
def test_data_coords_to_positions():
geom = AGIPD_1MGeometry.from_quad_positions(
quad_pos=[(-525, 625), (-550, -10), (520, -160), (542.5, 475)])
module_no = np.zeros(16, dtype=np.int16)
slow_scan = np.linspace(0, 500, num=16, dtype=np.float32)
fast_scan = np.zeros(16, dtype=np.float32)
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)
np.testing.assert_allclose(resy, 625 * geom.pixel_size)
assert (np.diff(resx) > 0).all() # Monotonically increasing
np.testing.assert_allclose(resx[0], -525 * geom.pixel_size)
assert -0.01 < resx[-1] < 0.01
