def index(reflections, detector, known_symmetry, beams):
'''sets up two color indexer parameters and calls the indexer; returns the
candidate basis vectors from the 2-D grid search in two color indexer'''
# cmd_line = command_line.argument_interpreter(master_params=master_phil_scope)
# working_phil = cmd_line.process_and_fetch(args=[])
params = master_phil_scope.extract()
params.refinement.parameterisation.beam.fix = "all"
params.refinement.parameterisation.detector.fix = "all"
params.indexing.known_symmetry.space_group = known_symmetry.space_group_info(
)
params.refinement.verbosity = 3
params.indexing.refinement_protocol.d_min_start
params.indexing.refinement_protocol.n_macro_cycles = 1 # 5
params.indexing.known_symmetry.unit_cell = known_symmetry.unit_cell()
params.indexing.debug = True
params.indexing.known_symmetry.absolute_angle_tolerance = 5.0
params.indexing.known_symmetry.relative_length_tolerance = 0.3
params.indexing.stills.rmsd_min_px = 3.5
filenames = [""]
reader = Reader(filenames)
masker = Masker(filenames)
iset_data = ImageSetData(reader, masker)
imgset = ImageSet(iset_data)
imgset.set_beam(beams[0])
imgset.set_detector(detector)
imagesets = [imgset]
orient = indexer_two_color(reflections, imagesets, params) #, beams=beams)
orient.index()
cvecs = orient.candidate_basis_vectors
return cvecs
def index(reflections, detector, known_symmetry, beams):
'''calls the two color indexer class after setting up the phil parameters
and returns a class object'''
# cmd_line = command_line.argument_interpreter(master_params=master_phil_scope)
# working_phil = cmd_line.process_and_fetch(args=[])
params = master_phil_scope.extract()
params.refinement.parameterisation.beam.fix = "all"
params.refinement.parameterisation.detector.fix = "all"
params.indexing.known_symmetry.space_group = known_symmetry.space_group_info(
)
params.refinement.verbosity = 3
params.indexing.refinement_protocol.d_min_start
params.indexing.refinement_protocol.n_macro_cycles = 1
params.indexing.known_symmetry.unit_cell = known_symmetry.unit_cell()
params.indexing.debug = True
params.indexing.known_symmetry.absolute_angle_tolerance = 5.0
params.indexing.known_symmetry.relative_length_tolerance = 0.3
params.indexing.stills.rmsd_min_px = 3.5
filenames = [""]
reader = Reader(filenames)
masker = Masker(filenames)
imgsetdata = ImageSetData(reader, masker)
imgset = ImageSet(imgsetdata)
imgset.set_beam(beams[0])
imgset.set_detector(detector)
imagesets = [imgset]
orient = indexer_two_color(reflections, imagesets, params)
orient.index()
return orient
def tst_index_spots():
assert (REFLS)
global CRYSTALS
global RMSD
from cxi_xdr_xes.two_color.two_color_indexer import indexer_two_color
from cxid9114.spots import spot_utils
from libtbx.utils import Sorry
for i in [2, 5]: # NOTE: these are the experiments that should index
refls_strong = REFLS[i]
try:
orientAB = indexer_two_color(
reflections=spot_utils.as_single_shot_reflections(
refls_strong, inplace=False),
experiments=EXP_LIST[i:i + 1],
params=mad_index_params)
orientAB.index()
except (Sorry, RuntimeError) as error:
print("Failed to index experiment %d:" % i)
print(error)
continue
RMSD.append(orientAB.best_Amat_rmsd)
CRYSTALS.append(orientAB.refined_experiments.crystals()[0])
assert (len(RMSD) == 2)
assert (all([r < 3.75 for r in RMSD]))
def index(reflections, detector, known_symmetry, beams):
params = master_phil_scope.extract()
params.refinement.parameterisation.beam.fix = "all"
params.refinement.parameterisation.detector.fix = "all"
params.indexing.known_symmetry.space_group = known_symmetry.space_group_info(
)
params.refinement.verbosity = 3
params.indexing.refinement_protocol.d_min_start
params.indexing.refinement_protocol.n_macro_cycles = 1
params.indexing.known_symmetry.unit_cell = known_symmetry.unit_cell()
params.indexing.debug = True
params.indexing.known_symmetry.absolute_angle_tolerance = 5.0
params.indexing.known_symmetry.relative_length_tolerance = 0.3
filenames = [""]
reader = Reader(filenames)
masker = Masker(filenames)
iset_data = ImageSetData(reader, masker)
imgset = ImageSet(iset_data)
imgset.set_beam(beams[0])
imgset.set_detector(detector)
imagesets = [imgset]
# dermen:
# modified rmsd_min_px this so test will pass, was originally set
# to 2 and the stills indexer's best.rmsd was of order ~2.8ish
# I dont know enough about the code itself to make the call on
# whether this is legit or not or whether 2.8 best.rmsd is
# something we should focus on improving...
params.indexing.stills.rmsd_min_px = 3.5
orient = indexer_two_color(reflections, imagesets, params)
orient.index()
return orient
def index(self, datablock, reflections):
from time import time
from logging import info
import copy
st = time()
info('*' * 80)
info('Indexing Strong Spots')
info('*' * 80)
imagesets = datablock.extract_imagesets()
params = copy.deepcopy(self.params)
# don't do scan-varying refinement during indexing
params.refinement.parameterisation.crystal.scan_varying = False
from cxi_xdr_xes.two_color.two_color_indexer import indexer_two_color
idxr = indexer_two_color(reflections, imagesets, params=params)
indexed = idxr.refined_reflections
experiments = idxr.refined_experiments
if self.params.output.indexed_filename:
self.save_reflections(indexed, self.params.output.indexed_filename)
info('')
info('Time Taken = %f seconds' % (time() - st))
return experiments, indexed
# imagesets=[isetB],
# params=sad_index_params)
# orientB.index()
# crystalB = orientB.refined_experiments.crystals()[0]
# outB = sim_utils.sim_twocolors(crystalB, mos_dom=20, mos_spread=0.1, fracA=fracA, fracB=fracB, plot=False)
# B_results.append(outB)
# except:
# B_results.append(None)
# ==================================
# 2 color indexer of 2 color pattern
# ==================================
try:
orientAB = indexer_two_color(
reflections=spot_utils.as_single_shot_reflections(refls_strong,
inplace=False),
imagesets=[iset],
params=mad_index_params)
orientAB.index()
except (Sorry, RuntimeError):
print("####\nIndexingFailed T_T \n####")
failed_shots.append(idx)
try:
np.savetxt(failed_idx_f, failed_shots, fmt="%d")
except:
pass
continue
n_idx += 1
#if not orientAB.refined_experiments.crystals(): # this would probably never happen...
# continue
print("####\n *_* IndexingWORKED *_* \n####")
from cxid9114 import utils
import glob
from scitbx.matrix import sqr
from cxi_xdr_xes.two_color.two_color_indexer import indexer_two_color
fnames = glob.glob("results/good_hit_*_10_crys.pkl")
for fname in fnames:
data = utils.open_flex(fname)
crystal = data['crystal']
xrot = data['optX']
yrot = data['optY']
new_A = xrot * yrot * sqr(crystal.get_U()) * sqr(crystal.get_B())
crystal.set_A(new_A)
orient = indexer_two_color(reflections=refl,
imagesets=[hit_imgset],
params=params)
# h5_name = fname.replace(".pkl", ".h5")
img_data = utils.open_flex('some_imgs.pkl')
dblock = utils.datablock_from_numpyarrays(
[i.as_numpy_array() for i in img_data["img%d" % shot_idx]],
detector=D,
beam=BeamA,
mask=mask)
dump = utils.open_flex("dump_%d.pkl" % shot_idx)
refls = dump['refls_strong']
spot_utils.as_single_shot_reflections(refls)
iset = dblock.extract_imagesets()[0]
if index:
orientAB = indexer_two_color(reflections=refls,
imagesets=[iset],
params=mad_index_params)
orientAB.index()
C = orientAB.refined_experiments.crystals()[0]
utils.save_flex({"C": C}, "C%d.pkl" % shot_idx)
from dxtbx.model.experiment_list import Experiment, ExperimentList
e = Experiment()
e.detector = D
e.beam = B
e.crystal = C
e.imageset = iset
el = ExperimentList()
el.append(e)
orientAB.export_as_json(el, "exp%d.json" % shot_idx)
isetB.set_beam(BeamB)
# index two color pattern using fft1d
orientA = indexer_base.from_parameters(
reflections=count_spots.as_single_shot_reflections(refls, inplace=False),
imagesets=[isetA],
params=sad_index_params)
orientA.index()
crystalA = orientA.refined_experiments.crystals()[0]
# try with other color
orientB = indexer_base.from_parameters(
reflections=count_spots.as_single_shot_reflections(refls, inplace=False),
imagesets=[isetB],
params=sad_index_params)
orientB.index()
crystalB = orientB.refined_experiments.crystals()[0]
# ==================================
# 2 color indexer of 2 color pattern
# ==================================
orientAB = indexer_two_color(
reflections=count_spots.as_single_shot_reflections(refls, inplace=False),
imagesets=[iset],
params=mad_index_params)
orientAB.index()
crystalAB = orientAB.refined_experiments.crystals()[0]
from IPython import embed
embed()
loader = dxtbx.load(image_fname)
img = loader.get_raw_data(idx).as_numpy_array()
iset = loader.get_imageset(loader.get_image_file())
dblock = DataBlockFactory.from_imageset(iset[idx:idx+1])[0]
refl = flex.reflection_table.from_observations(dblock, find_spot_params)
imgs.append(img)
refls.append( refl)
info_fname = image_fname.replace(".h5", ".pkl")
sim_data = utils.open_flex(info_fname)
orient = indexer_two_color(
reflections=spot_utils.as_single_shot_reflections(refl, inplace=False),
imagesets=[iset],
params=indexing_params)
try:
orient.index()
crystals = [o.crystal for o in orient.refined_experiments]
rmsd = orient.best_rmsd
sim_data["sim_indexed_rmsd"] = rmsd
sim_data["sim_indexed_crystals"] = crystals
sim_data["sim_indexed_refls"] = refl
except:
print("FAILED!")
utils.save_flex( sim_data, info_fname+out_tag)
