def test_compute_intersect(self):
# build a simple grid and turn it into a detector
bg = xray.BasisGrid()
p = np.array([0.0, 0.0, 1.0])
s = np.array([1.0, 0.0, 0.0])
f = np.array([0.0, 1.0, 0.0])
shape = (10, 10)
bg.add_grid(p, s, f, shape)
d = xray.Detector(bg, 2.0 * np.pi / 1.4)
# compute a set of q-vectors corresponding to a slightly offset grid
xyz_grid = bg.to_explicit()
xyz_off = xyz_grid.copy()
xyz_off[:, 0] += 0.5
xyz_off[:, 1] += 0.5
q_vectors = d._real_to_reciprocal(xyz_off)
# b/c s/f vectors are unit vectors, where they intersect s/f is simply
# their coordinates. The last row and column will miss, however
intersect_ref = np.logical_and((xyz_off[:, 0] <= 9.0),
(xyz_off[:, 1] <= 9.0))
pix_ref = xyz_off[intersect_ref, :2]
# compute the intersection from code
pix, intersect = d._compute_intersections(q_vectors,
0) # 0 --> grid_index
print pix, intersect
assert_array_almost_equal(intersect_ref, intersect)
assert_array_almost_equal(pix_ref, pix)
def _generate_shot_from_entry(self, entry):
# loop over all the detector elements and piece them together
xyz = []
intensities = []
metadatas = []
for detector_group in self._get_groups('detector', root=entry):
x, i, m = self._detector_group_to_array(detector_group)
xyz.append(x)
intensities.append(i)
metadatas.append(m)
xyz = np.concatenate(xyz)
intensities = np.concatenate(intensities)
# instantitate a detector
# todo NEED: logic for path_length
path_length = 1.0
beam = self._extract_energy(entry)
d = xray.Detector(xyz, path_length, beam.k)
# generate a shot instance and add it to our list
return xray.Shot(intensities, d)
def test_rotated_beam(self):
# shift a detector up (in x) a bit and test to make sure there's no diff
t = structure.load_coor(ref_file('gold1k.coor'))
s = xray.Shotset.simulate(t, self.d, 5, 1)
sh = 50.0 # the shift mag
xyz = self.d.xyz.copy()
shift = np.zeros_like(xyz)
shift[:, 0] += sh
beam_vector = np.array([sh / self.l, 0.0, 1.0])
# note that the detector du is further from the interaction site
du = xray.Detector(xyz + shift, self.d.k, beam_vector=beam_vector)
su = xray.Shotset.simulate(t, du, 5, 1)
p1 = s.intensity_profile(q_spacing=0.05)
p2 = su.intensity_profile(q_spacing=0.05)
p1 /= p1.max()
p2 /= p2.max()
p1 = p2[:10, :]
p2 = p2[:p1.shape[0], :]
assert_allclose(p1, p2, rtol=0.1)
def as_shotset(self):
"""
Convert the CBF file to an ODIN shotset representation.
Returns
-------
cbf : odin.xray.Shotset
The CBF file as an ODIN shotset.
"""
p = np.array(list(self.corner) + [self.path_length])
f = np.array([self.pixel_size[0], 0.0, 0.0]) # fast is x
s = np.array([0.0, self.pixel_size[1], 0.0]) # slow is y
bg = xray.BasisGrid()
bg.add_grid(p, s, f, self.intensities_shape)
# todo better value for photons
b = xray.Beam(1e4, wavelength=self.wavelength)
d = xray.Detector(bg, b.k)
s = xray.Shotset(self.intensities.flatten().astype(np.float64), d,
self.mask)
return s