def _convert_asm_shot(self,
descriptor,
x_pixel_size=109.9,
y_pixel_size=109.9,
bragg_peak_radius=458):
"""
Convert a Kitty-generated assembled image h5 file to an odin.xray.Shot.
"""
logger.info('Loading assembled image in: %s' % descriptor['data_file'])
for field in self.essential_fields:
if field not in descriptor.keys():
raise ValueError('Essential data field %s not in YAML file!' %
field)
energy = float(descriptor['photon_eV']) / 1000.0 # eV -> keV
path_length = float(descriptor['detector_mm']) * 1000.0 # mm -> um
logger.debug('Energy: %f keV' % energy)
logger.debug('Path length: %f microns' % path_length)
# extract intensity data
f = tables.File(descriptor['data_file'])
try:
path = descriptor['i_asm']
except KeyError as e:
raise ValueError('Essential data field `i_asm` not in YAML file!')
i = f.getNode(path).read()
f.close()
logger.debug('Read field %s in file: %s' %
(descriptor['i_asm'], descriptor['data_file']))
# find the center (center is in pixel units)
#dgeo = xray.DetectorGeometry(i)
center = (853., 861.) #dgeo.center
corner = (-center[0] * x_pixel_size, -center[1] * y_pixel_size, 0.0)
logger.debug('Found center: %s' % str(center))
# compile a grid_list object
basis = (x_pixel_size, y_pixel_size, 0.0)
shape = (i.shape[0], i.shape[1], 1)
grid_list = [(basis, shape, corner)]
# generate the detector object
b = xray.Beam(100, energy=energy)
d = xray.Detector.from_basis(grid_list, path_length, b.k)
logger.debug('Generated detector object...')
# generate the shot
s = xray.Shot(i.flatten(), d)
return s
def _extract_energy(self, entry):
"""
Scrape the following important metadata out of the .cxi file:
-- beam energy
--
"""
energy_nodes = self._get_nodes('energy', root=entry, strict=True)
if len(energy_nodes) > 1:
raise RuntimeError(
'Ambiguity in beam energy... %d energy nodes found' %
len(energy_nodes))
energy = float(energy_nodes[0].read()) / 1000.0
beam = xray.Beam(1., energy=energy) # todo: compute flux
return beam
def test_evaluate_qmag(self):
# doubles as a test for _evaluate_theta
x = np.zeros((5, 3))
x[:, 0] = np.random.randn(5)
x[:, 2] = self.l
S = x.copy()
S = S / np.sqrt(np.sum(np.power(S, 2), axis=1))[:, None]
S -= self.d.beam_vector
b = xray.Beam(1, energy=self.energy)
qref = b.k * np.sqrt(np.sum(np.power(S, 2), axis=1))
qmag = self.d.evaluate_qmag(x)
assert_allclose(qref, qmag)
def _convert_raw_shot(self, descriptor):
"""
Convert a Kitty-generated raw image h5 file to an odin.xray.Shot.
"""
logger.info('Loading raw image in: %s' % descriptor['data_file'])
for field in self.essential_fields:
if field not in descriptor.keys():
raise ValueError('Essential data field %s not in YAML file!' %
field)
energy = float(descriptor['photon_eV'])
path_length = float(descriptor['detector_mm']) * 1000.0 # mm -> um
# load all the relevant data from many h5s... (dumb)
f = tables.File(descriptor['x_raw'])
x = f.root.data.data.read()
f.close()
f = tables.File(descriptor['y_raw'])
y = f.root.data.data.read()
f.close()
z = np.zeros_like(x)
f = tables.File(descriptor['data_file'])
path = descriptor['i_raw']
i = f.getNode(path).read()
f.close()
# turn that data into a basis representation
grid_list, flat_i = self._lcls_raw_to_basis(x, y, z, i)
# generate the detector object
b = xray.Beam(100, energy=energy)
d = xray.Detector.from_basis(grid_list, path_length, b.k)
# generate the shot
s = xray.Shot(flat_i, d)
return s
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
def test_unit_convs(self):
beam = xray.Beam(self.n_photons, energy=1.0)
assert_allclose(beam.wavelength, 12.398, rtol=1e-3)
assert_allclose(beam.frequency, 2.4190e17, rtol=1e-3)
assert_allclose(beam.wavenumber, (2.0 * np.pi) / 12.398, rtol=1e-3)