def __init__(self, image_file, **kwargs):
from dxtbx import IncorrectFormatError
if not self.understand(image_file):
raise IncorrectFormatError(self, image_file)
FormatHDF5.__init__(self, image_file, **kwargs)
self.DET64 = DetectorFactory.from_dict(multi_det_dict.D)
self._h5_handle = h5py.File(self.get_image_file(), 'r')
self._geometry_define()
def basic_detector(
): # from development, not actually used here but useful for reference
# make a detector panel
# monolithic camera description
print("Make a dxtbx detector")
detdist = 141.7
pixsize = 0.088 # Rayonix MX340-XFEL, 2x2 binning mode
im_shape = 3840, 3840
det_descr = {
'panels': [{
'fast_axis': (1.0, 0.0, 0.0),
'slow_axis': (0.0, -1.0, 0.0),
'gain':
1.0,
'identifier':
'',
'image_size':
im_shape,
'mask': [],
'material':
'',
'mu':
0.0,
'name':
'Panel',
'origin': (-im_shape[0] * pixsize / 2., im_shape[1] * pixsize / 2.,
-detdist),
'pedestal':
0.0,
'pixel_size': (pixsize, pixsize),
'px_mm_strategy': {
'type': 'SimplePxMmStrategy'
},
'raw_image_offset': (0, 0),
'thickness':
0.0,
'trusted_range': (-1e7, 1e7),
'type':
''
}]
}
return DetectorFactory.from_dict(det_descr)
def basic_detector():
# make a detector panel
# monolithic camera description
print("Make a dxtbx detector")
detdist = 100.
pixsize = 0.1
im_shape = 1536, 1536
det_descr = {
'panels': [{
'fast_axis': (1.0, 0.0, 0.0),
'slow_axis': (0.0, -1.0, 0.0),
'gain':
1.0,
'identifier':
'',
'image_size':
im_shape,
'mask': [],
'material':
'',
'mu':
0.0,
'name':
'Panel',
'origin': (-im_shape[0] * pixsize / 2., im_shape[1] * pixsize / 2.,
-detdist),
'pedestal':
0.0,
'pixel_size': (pixsize, pixsize),
'px_mm_strategy': {
'type': 'SimplePxMmStrategy'
},
'raw_image_offset': (0, 0),
'thickness':
0.0,
'trusted_range': (-1e7, 1e7),
'type':
''
}]
}
return DetectorFactory.from_dict(det_descr)
'material': '',
'mu': 0.0,
'name': 'Panel',
'origin': (-99.165, 99.05499999999999, -125.0),
'pedestal': 0.0,
'pixel_size': (0.11, 0.11),
'px_mm_strategy': {
'type': 'SimplePxMmStrategy'
},
'raw_image_offset': (0, 0),
'slow_axis': (0.0, -1.0, 0.0),
'thickness': 0.0,
'trusted_range': (-29.0, 65505.0),
'type': 'SENSOR_CCD'
}]
}
beamDict = {
'direction': (0.0, 0.0, 1.0),
'divergence': 0.0,
'flux': 0.0,
'polarization_fraction': 0.999,
'polarization_normal': (0.0, 1.0, 0.0),
'sigma_divergence': 0.0,
'transmission': 1.0,
'wavelength': 1.37095
}
BEAM = BeamFactory.from_dict(beamDict)
DET = DetectorFactory.from_dict(detDict)
def main():
from cxid9114.sim import sim_utils
from dxtbx.model.crystal import CrystalFactory
from dxtbx_model_ext import flex_Beam
from dxtbx.model.detector import DetectorFactory
from dxtbx.model.beam import BeamFactory
from simtbx.nanoBragg.tst_nanoBragg_basic import fcalc_from_pdb
import numpy as np
from cxid9114.parameters import ENERGY_CONV
energies = np.arange(8920, 8930)
fluxes = np.ones(len(energies)) * 5e11
patt_args = {"Ncells_abc": (20, 20, 20), "profile": "square", "verbose": 0}
beam_descr = {
'direction': (0.0, 0.0, 1.0),
'divergence': 0.0,
'flux': 5e11,
'polarization_fraction': 1.,
'polarization_normal': (0.0, 1.0, 0.0),
'sigma_divergence': 0.0,
'transmission': 1.0,
'wavelength': ENERGY_CONV / energies[0]
}
cryst_descr = {
'__id__': 'crystal',
'real_space_a': (79, 0, 0),
'real_space_b': (0, 79, 0),
'real_space_c': (0, 0, 38),
'space_group_hall_symbol': '-P 4 2'
}
det_descr = {
'panels': [{
'fast_axis': (-1.0, 0.0, 0.0),
'gain': 1.0,
'identifier': '',
'image_size': (196, 196),
'mask': [],
'material': '',
'mu': 0.0,
'name': 'Panel',
'origin': (19.6, -19.6, -550),
'pedestal': 0.0,
'pixel_size': (0.1, 0.1),
'px_mm_strategy': {
'type': 'SimplePxMmStrategy'
},
'raw_image_offset': (0, 0),
'slow_axis': (0.0, 1.0, 0.0),
'thickness': 0.0,
'trusted_range': (0.0, 65536.0),
'type': ''
}]
}
DET = DetectorFactory.from_dict(det_descr)
BEAM = BeamFactory.from_dict(beam_descr)
crystal = CrystalFactory.from_dict(cryst_descr)
Patt = sim_utils.PatternFactory(crystal=crystal,
detector=DET,
beam=BEAM,
**patt_args)
img = None
Fens = []
xrbeams = flex_Beam()
for fl, en in zip(fluxes, energies):
wave = ENERGY_CONV / en
F = fcalc_from_pdb(resolution=4, algorithm="fft", wavelength=wave)
Patt.primer(crystal, energy=en, flux=fl, F=F)
if img is None:
img = Patt.sim_rois(reset=True) # defaults to full detector
else:
img += Patt.sim_rois(reset=True)
Fens.append(F)
xrb = BeamFactory.from_dict(beam_descr)
xrb.set_wavelength(wave *
1e-10) # need to fix the necessity to do this..
xrb.set_flux(fl)
xrb.set_direction(BEAM.get_direction())
xrbeams.append(xrb)
#import pylab as plt
#def plot_img(ax,img):
# m = img[img >0].mean()
# s = img[img > 0].std()
# vmax = m+5*s
# vmin = 0
# ax.imshow(img, vmin=vmin, vmax=vmax, cmap='gnuplot')
print("\n\n\n")
print("<><><><><><><><><><>")
print("NEXT TRIAL")
print("<><><><><><><><><><>")
#
patt2 = sim_utils.PatternFactory(crystal=crystal,
detector=DET,
beam=xrbeams,
**patt_args)
patt2.prime_multi_Fhkl(multisource_Fhkl=Fens)
img2 = patt2.sim_rois(reset=True)
#plt.figure()
#ax1 = plt.gca()
#plt.figure()
#ax2 = plt.gca()
#plot_img(ax1, img)
#plot_img(ax2, img2)
#plt.show()
assert (np.allclose(img, img2))
'mask': [],
'material': '',
'mu': 0.0,
'name': 'Panel',
'origin': (-im_shape[0]*pixsize/2., im_shape[1]*pixsize/2., -detdist),
'pedestal': 0.0,
'pixel_size': (pixsize, pixsize),
'px_mm_strategy': {'type': 'SimplePxMmStrategy'},
'raw_image_offset': (0, 0),
'thickness': 0.0,
'trusted_range': (-1e7, 1e7),
'type': ''}]}
# make the dxtbx objects
BEAM = BeamFactory.from_dict(beam_descr)
DETECTOR = DetectorFactory.from_dict(det_descr)
CRYSTAL = CrystalFactory.from_dict(cryst_descr)
# make a dummie HKL table with constant HKL intensity
# this is just to make spots
DEFAULT_F = 1e2
symbol = CRYSTAL.get_space_group().info().type().lookup_symbol() # this is just P43212
sgi = sgtbx.space_group_info(symbol)
symm = symmetry(unit_cell=CRYSTAL.get_unit_cell(), space_group_info=sgi)
miller_set = symm.build_miller_set(anomalous_flag=True, d_min=1.6, d_max=999)
Famp = flex.double(np.ones(len(miller_set.indices())) * DEFAULT_F)
Famp = miller.array(miller_set=miller_set, data=Famp).set_observation_type_xray_amplitude()
Ncells_abc = 20, 20, 20
oversmaple = 2
"", fast, slow, orig,
(pixsize, pixsize), (s*1536,s*1536)) #, trusted_range=(0, 10000000))
beam_descr = {
'direction': (7.010833160725592e-06, -3.710515413340211e-06, 0.9999999999685403),
'divergence': 0.0,
'flux': 0.0,
'polarization_fraction': 0.999,
'polarization_normal': (0.0, 1.0, 0.0),
'sigma_divergence': 0.0,
'transmission': 1.0,
'wavelength': 1.385}
#beam = BeamFactory.simple(wavelen)
beam = BeamFactory.from_dict(beam_descr)
elif lab_geom == "cspad":
det = DetectorFactory.from_dict(dxtbx_cspad.cspad)
# beam pointing off z-axis
beam_descr = {
'direction': (7.010833160725592e-06, -3.710515413340211e-06, 0.9999999999685403),
'divergence': 0.0,
'flux': 0.0,
'polarization_fraction': 0.999,
'polarization_normal': (0.0, 1.0, 0.0),
'sigma_divergence': 0.0,
'transmission': 1.0,
'wavelength': 1.385}
beam = BeamFactory.from_dict(beam_descr)
pix = sim_cryst_on_det(cryst, det, beam)
'origin': (25.6, -12.8, -100),
'pedestal': 0.0,
'pixel_size': (0.1, 0.1),
'px_mm_strategy': {
'type': 'SimplePxMmStrategy'
},
'raw_image_offset': (0, 0),
'slow_axis': (0.0, 1.0, 0.0),
'thickness': 0.0,
'trusted_range': (0.0, 65536.0),
'type': ''
}]
}
beam = BeamFactory.from_dict(beam_descr)
whole_det = DetectorFactory.from_dict(det_descr)
cryst = CrystalFactory.from_dict(cryst_descr)
# ---------
SIM = simtbx.nanoBragg.nanoBragg(whole_det, beam)
SIM.Amatrix = sqr(cryst.get_A()).transpose().elems
SIM.default_F = 1
SIM.F000 = 10
SIM.oversample = 2
SIM.Ncells_abc = (5, 5, 5)
SIM.show_params()
SIM.add_nanoBragg_spots()
SIM.raw_pixels *= 2000
wholepix = SIM.raw_pixels.as_numpy_array()
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)
'direction': (0.0, 0.0, 1.0),
'divergence': 0.0,
'flux': 1e12,
'polarization_fraction': 1.,
'polarization_normal': (0.0, 1.0, 0.0),
'sigma_divergence': 0.0,
'transmission': 1.0,
'wavelength': 1.4
}
# dxtbx crystal description
hall_sym = sgtbx.space_group_info(
number=19).type().hall_symbol() # ' P 2ac 2ab'
cryst_descr = {
'__id__': 'crystal',
'real_space_a': (127.7, 0, 0),
'real_space_b': (0, 225.4, 0),
'real_space_c': (0, 0, 306.1),
'space_group_hall_symbol': hall_sym
}
beam = BeamFactory.from_dict(beam_descr)
whole_det = DetectorFactory.from_dict(cspad)
cryst = CrystalFactory.from_dict(cryst_descr)
from cxid9114 import utils
utils.save_flex(whole_det, "ps2.det.pkl")
utils.save_flex(cryst, "ps2.cryst.pkl")
utils.save_flex(beam, "ps2.beam.pkl")