def make_images(data, tag):
pixel_size = 0.1 # mm/pixel
detector = DetectorFactory.simple(
'PAD', 100,
(pixel_size * data.focus()[1] / 2, pixel_size * data.focus()[2] / 2),
'+x', '-y', (pixel_size, pixel_size),
(data.focus()[2], data.focus()[1]), (-1, 1e6 - 1), [], None)
beam = BeamFactory.simple(1.0)
sf = ScanFactory()
scan = sf.make_scan(image_range=(1, 180),
exposure_times=0.1,
oscillation=(0, 1.0),
epochs=range(180),
deg=True)
# write images in each of three directions
for slice_id in [0, 1, 2]:
for idx in xrange(data.focus()[slice_id]):
if slice_id == 0: # slow
data_slice = data[idx:idx + 1, :, :]
data_slice.reshape(flex.grid(data.focus()[1], data.focus()[2]))
filename = "fft_frame_%s_mf_%04d.cbf" % (tag, idx)
elif slice_id == 1: # med
data_slice = data[:, idx:idx + 1, :]
data_slice.reshape(flex.grid(data.focus()[0], data.focus()[2]))
filename = "fft_frame_%s_sf_%04d.cbf" % (tag, idx)
elif slice_id == 2: # fast
data_slice = data[:, :, idx:idx + 1]
data_slice.reshape(flex.grid(data.focus()[0], data.focus()[1]))
filename = "fft_frame_%s_sm_%04d.cbf" % (tag, idx)
print['slow', 'med', 'fast'][slice_id], idx
FormatCBFMini.as_file(detector, beam, None, scan, data_slice,
filename)
def get_values(invert_y):
beam = BeamFactory.simple(wavelength=1)
if invert_y:
y_direction = "-y"
else:
y_direction = "+y"
detector = DetectorFactory.simple(
sensor=DetectorFactory.sensor("PAD"),
distance=100,
beam_centre=[50, 50],
fast_direction="+x",
slow_direction=y_direction,
pixel_size=[0.1, 0.1],
image_size=[1000, 1000],
)[0]
wavelength = beam.get_wavelength()
thickness = 0.5
table = attenuation_coefficient.get_table("Si")
mu = table.mu_at_angstrom(wavelength) / 10.0
t0 = thickness
for panel in detector:
panel.set_px_mm_strategy(ParallaxCorrectedPxMmStrategy(mu, t0))
v1 = detector.pixel_to_millimeter((0, 0))
v2 = detector.pixel_to_millimeter((1000, 1000))
return v1, v2
def make_images(data, tag):
pixel_size = 0.1
detector = DetectorFactory.simple(
'PAD', 100,
(pixel_size * data.focus()[1] / 2, pixel_size * data.focus()[2] / 2),
'+x', '-y', (pixel_size, pixel_size),
(data.focus()[2], data.focus()[1]), (-1, 1e6 - 1), [], None)
beam = BeamFactory.simple(1.0)
for slice_id in [0, 1, 2]:
for idx in xrange(data.focus()[slice_id]):
if slice_id == 0: # slow
data_slice = data[idx:idx + 1, :, :]
data_slice.reshape(flex.grid(data.focus()[1], data.focus()[2]))
filename = "fft_frame_%s_mf_%04d.cbf" % (tag, idx)
elif slice_id == 1: # med
data_slice = data[:, idx:idx + 1, :]
data_slice.reshape(flex.grid(data.focus()[0], data.focus()[2]))
filename = "fft_frame_%s_sf_%04d.cbf" % (tag, idx)
elif slice_id == 2: # fast
data_slice = data[:, :, idx:idx + 1]
data_slice.reshape(flex.grid(data.focus()[0], data.focus()[1]))
filename = "fft_frame_%s_sm_%04d.cbf" % (tag, idx)
print['slow', 'med', 'fast'][slice_id], idx
FormatCBFMini.as_file(detector, beam, None, None, data_slice,
filename)
def _beam(self):
'''
Create the beam model
'''
from dxtbx.model.beam import BeamFactory
configuration = self.header['configuration']
return BeamFactory.simple(configuration['wavelength'])
def _beam(self):
"""
Create the beam model
"""
from dxtbx.model.beam import BeamFactory
configuration = self.header["configuration"]
return BeamFactory.simple(configuration["wavelength"])
def xray_beams(self):
self._xray_beams = flex_Beam()
for wavelen, flux in self.spectrum:
beam = BeamFactory.simple(wavelen * 1e-10)
beam.set_flux(flux)
beam.set_unit_s0(self.unit_s0)
beam.set_polarization_fraction(self.polarization_fraction)
beam.set_divergence(self.divergence)
self._xray_beams.append(beam)
return self._xray_beams
def xray_beams(self):
self._xray_beams = flex_Beam()
norm = 1
if self._undo_nanoBragg_norm_by_nbeams:
norm = float(len(self.spectrum))
for wavelen, flux in self.spectrum:
beam = BeamFactory.simple(wavelen * 1e-10)
beam.set_flux(flux / norm)
beam.set_unit_s0(self.unit_s0)
beam.set_polarization_fraction(self.polarization_fraction)
beam.set_divergence(self.divergence)
self._xray_beams.append(beam)
return self._xray_beams
from __future__ import division
import numpy as np
import simtbx.nanoBragg
from dxtbx.model.beam import BeamFactory
from dxtbx.model.detector import DetectorFactory
import dxtbx_cspad
# flat CSPAD
cspad = DetectorFactory.from_dict(
dxtbx_cspad.cspad) # loads a 64 panel dxtbx cspad
# beam along Z
beam = BeamFactory.simple(1.3) # make a simple beam along z
print "# --- beam centers comparison for canonical setup -- #"
net_error_flat = 0
for pid in range(64):
print "canonical: ", pid
SIM = simtbx.nanoBragg.nanoBragg(detector=cspad,
beam=beam,
verbose=0,
panel_id=pid)
b1 = SIM.beam_center_mm
b2 = cspad[pid].get_beam_centre(beam.get_s0())
print "beam_XY simtbx: %f, %f" % b1
print "beam_XY python: %f, %f" % b2
print
net_error_flat += np.sum(np.subtract(b1, b2)**2)
def dummy_beam():
return BeamFactory.simple(1.0)
