def map_calculate_rings(mp):
# set up parameters
mp.structure_generator.random.setstate(mp.random_state)
es = ewald_sphere()
es.set_wavelength(mp.beam_properties.wavelength)
es.set_distance(mp.detector_properties.distance)
ic = image_composer()
ic.set_detector_size(mp.detector_properties.detector_size)
ic.set_beam_center(mp.detector_properties.beam_center)
ic.set_pixel_size(mp.detector_properties.pixel_size)
ic.set_ewald_sphere(es)
im = image_simulator()
im.structures = mp.structure_generator
im.image_composer = ic
im.cached_h = mp.h
# calculate structure factors
for i in xrange(mp.n_images):
im.structures.randomize()
im.sum_structure_factors()
# copy intensities to full image
sf = im.structure_factors
all_sf = flex.complex_double((mp.detector_properties.detector_size[0]+1)*\
(mp.detector_properties.detector_size[1]+1),\
complex(0.0,0.0))
k = 0
for j in xrange(len(mp.use_index)):
if (mp.use_index[j]):
all_sf[j] = sf[k]
k += 1
im.structure_factors = all_sf
image_data = im.build_image(n_photons=bp.flux*bp.t)
if (True):
for q_i in [0.01, 0.1, 0.2]:
print q_i, I_q(ic.get_q(),image_data,q_i,mp.dq)
write_image(file_name='ring.png',
detector_size=mp.detector_properties.detector_size,
image_data=image_data)
if (False):
file_name = './test_rings/' + str(os.getpid()) + '_' + str(i)
f = open(file_name,'wb')
pickle.dump(image_data,f,2)
f.close()
return mp.n_images
def map_model_I_q(mp):
# set up parameters
mp.structure_generator.random.setstate(mp.random_state)
es = ewald_sphere()
es.set_wavelength(mp.beam_properties.wavelength)
es.set_distance(mp.detector_properties.distance)
ic = image_composer()
ic.set_detector_size(mp.detector_properties.detector_size)
ic.set_beam_center(mp.detector_properties.beam_center)
ic.set_pixel_size(mp.detector_properties.pixel_size)
ic.set_ewald_sphere(es)
# initialize image simulator
im = image_simulator()
im.structures = mp.structure_generator
im.image_composer = ic
# make images
sums = flex.vec2_double(mp.n_bins)
for i in xrange(mp.n_images):
im.structures.randomize()
im.sum_structure_factors_gpu(gpu=mp.gpu)
image_data = im.build_image(n_photons=(mp.beam_properties.flux *
mp.beam_properties.t))
if (False):
for q_i in [0.01, 0.1, 0.2]:
print q_i, I_q(im.cached_q, image_data, q_i, mp.dq)
write_image(detector_size=mp.detector_properties.detector_size,
image_data=image_data)
if (True):
file_name = '/scratch/home/bkpoon/images/' + str(
os.getpid()) + '_' + str(i)
f = open(file_name, 'wb')
pickle.dump(im.structure_factors, f, 2)
f.close()
# convert image data to I(q)
mv = mean_and_variance_by_q(mp.q_min, mp.q_max, mp.dq, mp.n_bins,
im.cached_q, image_data)
sums += mv
return sums
def map_random_image(p=None):
result = [None for i in xrange(p.n_images)]
# set random state for current thread
p.structure_generator.random.setstate(p.random_state)
es = ewald_sphere()
es.set_wavelength(p.beam_properties.wavelength)
es.set_distance(p.detector_properties.distance)
ic = image_composer()
ic.set_detector_size(p.detector_properties.detector_size)
ic.set_beam_center(p.detector_properties.beam_center)
ic.set_pixel_size(p.detector_properties.pixel_size)
ic.set_ewald_sphere(es)
im = image_simulator()
im.structures = p.structure_generator
im.image_composer = ic
h = ic.cache_h()
sf_length = (p.detector_properties.detector_size[0] + 1) *\
(p.detector_properties.detector_size[1] + 1)
n_photons = p.beam_properties.flux * p.beam_properties.t
for i in xrange(p.n_images):
sf = flex.complex_double(sf_length, 0.0)
im.structures.species[0].n_copies = p.n_particles[i]
im.structures.randomize()
for j in xrange(p.n_particles[i]):
image_name = p.base_image_directory + im.structures.random.choice(
image_list)
t = im.structures.translations[0][j]
f = open(image_name, 'rb')
sf_tmp = pickle.load(f)
f.close()
sf_tmp = apply_translation(sf_tmp, h, t)
sf += sf_tmp
im.structure_factors = sf
image_data = im.build_image(n_photons=n_photons)
result[i] = image_data.deep_copy()
return result
mp.n_bins = 100
mp.q_min = 0.005
mp.q_max = 0.45
mp.dq = (mp.q_max - mp.q_min)/mp.n_bins
s = structure_generator()
s.add_species(pdb_input=pdb.input('6LYZ.pdb'),n_copies=2)
mp.structure_generator = s
rings = [0.01, 0.1, 0.2]
es = ewald_sphere()
es.set_wavelength(bp.wavelength)
es.set_distance(dp.distance)
ic = image_composer()
ic.set_detector_size(dp.detector_size)
ic.set_beam_center(dp.beam_center)
ic.set_pixel_size(dp.pixel_size)
ic.set_ewald_sphere(es)
q = ic.get_q()
# flag pixel corners for each ring
pixel_xy = list()
all_h = ic.cache_h()
use_index = flex.bool(len(all_h),False)
use_index[dp.beam_center[1]*dp.detector_size[0] + dp.beam_center[0]] = True
n_x = dp.detector_size[0] + 1
for x in xrange(dp.detector_size[0]):
for y in xrange(dp.detector_size[1]):