def slice_callback_with_high_performance_http_data(self):
BYU = self.object.read()
linearintdata = flex.int_from_byte_str(BYU)
provisional_size = linearintdata.size()
assert provisional_size == self.size1 * self.size2
print("size assertion OK", provisional_size)
linearintdata.reshape(flex.grid((self.size1, self.size2)))
del self.object #once the data are copied, close the stream
return linearintdata
def slice_callback_with_high_performance_http_data(self): BYU = self.object.read() linearintdata = flex.int_from_byte_str(BYU) provisional_size = linearintdata.size() assert provisional_size == self.size1*self.size2 print "size assertion OK",provisional_size linearintdata.reshape(flex.grid((self.size1,self.size2))) del self.object #once the data are copied, close the stream return linearintdata
def slice_callback_with_high_performance_http_data(self):
BYU = self.object.read()
linearintdata = flex.int_from_byte_str(BYU)
provisional_size = linearintdata.size()
if provisional_size == 480285:
linearintdata.reshape(flex.grid((195, 2463)))
elif provisional_size == 6224001:
linearintdata.reshape(flex.grid((2527, 2463)))
else:
raise ImageException("wrong number of pixels for Pilatus image")
del self.object #once the data are copied, close the stream
return linearintdata
def slice_callback_with_high_performance_http_data(self):
BYU = self.object.read()
linearintdata = flex.int_from_byte_str(BYU)
provisional_size = linearintdata.size()
if provisional_size==480285:
linearintdata.reshape(flex.grid((195,2463)))
elif provisional_size==6224001:
linearintdata.reshape(flex.grid((2527,2463)))
else:
raise ImageException("wrong number of pixels for Pilatus image")
del self.object #once the data are copied, close the stream
return linearintdata
def build_images(work_params, i_calc, reindexing_assistant):
result = []
from create import add_noise
from rstbx.simage import image_simple
from cctbx.array_family import flex
if (not work_params.apply_random_reindexing):
i_calc_data_perms = [i_calc.data()]
else:
i_calc_data_perms = [i_calc.data().select(perm)
for perm in reindexing_assistant.inv_perms]
n_mdls = work_params.number_of_shots
use_mp = (work_params.multiprocessing and n_mdls > 1)
def build_one_image(i_img):
mt = flex.mersenne_twister(seed=work_params.noise.random_seed+i_img)
scale = int(work_params.signal_max*(0.1+0.9*mt.random_double()))
crystal_rotation = mt.random_double_r3_rotation_matrix_arvo_1992()
i_perm = mt.random_size_t() % len(i_calc_data_perms)
image = image_simple(
store_miller_index_i_seqs=True,
store_spots=True,
store_signals=True,
set_pixels=True).compute(
unit_cell=i_calc.unit_cell(),
miller_indices=i_calc.indices(),
spot_intensity_factors=i_calc_data_perms[i_perm],
crystal_rotation_matrix=crystal_rotation,
ewald_radius=1/work_params.wavelength,
ewald_proximity=work_params.ewald_proximity,
signal_max=scale,
detector_distance=work_params.detector.distance,
detector_size=work_params.detector.size,
detector_pixels=work_params.detector.pixels,
point_spread=work_params.point_spread,
gaussian_falloff_scale=work_params.gaussian_falloff_scale)
add_noise(work_params, pixels=image.pixels)
if (not work_params.index_and_integrate):
pixels = None
else:
pixels = image.pixels
miller_index_i_seqs = image.miller_index_i_seqs
if (use_mp):
# to by-pass portable but slower pickling
if (pixels is not None):
assert pixels.is_0_based()
assert not pixels.is_padded()
assert pixels.all() == tuple(work_params.detector.pixels)
pixels = pixels.copy_to_byte_str()
miller_index_i_seqs = miller_index_i_seqs.copy_to_byte_str()
return image_model(
pixels=pixels,
spot_positions=image.spots,
spot_intensities=image.signals,
unit_cell=i_calc.unit_cell(),
crystal_rotation=crystal_rotation,
miller_index_i_seqs=miller_index_i_seqs,
scale=scale,
i_perm=i_perm)
if (not use_mp):
for i_img in xrange(n_mdls):
result.append(build_one_image(i_img))
else:
from libtbx import easy_mp
result = easy_mp.pool_map(
fixed_func=build_one_image,
args=range(n_mdls),
chunksize=1,
log=sys.stdout)
for im in result:
if (im is None): raise RuntimeError("Failure building image.")
if (im.pixels is not None):
im.pixels = flex.int_from_byte_str(im.pixels)
im.pixels.reshape(flex.grid(work_params.detector.pixels))
im.miller_index_i_seqs = flex.size_t_from_byte_str(
byte_str=im.miller_index_i_seqs)
for im in result:
im.make_backup()
return image_models(miller_indices=i_calc.indices(), array=result)
def build_images(work_params, i_calc, reindexing_assistant):
result = []
from .create import add_noise
from rstbx.simage import image_simple
from cctbx.array_family import flex
if (not work_params.apply_random_reindexing):
i_calc_data_perms = [i_calc.data()]
else:
i_calc_data_perms = [i_calc.data().select(perm)
for perm in reindexing_assistant.inv_perms]
n_mdls = work_params.number_of_shots
use_mp = (work_params.multiprocessing and n_mdls > 1)
def build_one_image(i_img):
mt = flex.mersenne_twister(seed=work_params.noise.random_seed+i_img)
scale = int(work_params.signal_max*(0.1+0.9*mt.random_double()))
crystal_rotation = mt.random_double_r3_rotation_matrix_arvo_1992()
i_perm = mt.random_size_t() % len(i_calc_data_perms)
image = image_simple(
store_miller_index_i_seqs=True,
store_spots=True,
store_signals=True,
set_pixels=True).compute(
unit_cell=i_calc.unit_cell(),
miller_indices=i_calc.indices(),
spot_intensity_factors=i_calc_data_perms[i_perm],
crystal_rotation_matrix=crystal_rotation,
ewald_radius=1/work_params.wavelength,
ewald_proximity=work_params.ewald_proximity,
signal_max=scale,
detector_distance=work_params.detector.distance,
detector_size=work_params.detector.size,
detector_pixels=work_params.detector.pixels,
point_spread=work_params.point_spread,
gaussian_falloff_scale=work_params.gaussian_falloff_scale)
add_noise(work_params, pixels=image.pixels)
if (not work_params.index_and_integrate):
pixels = None
else:
pixels = image.pixels
miller_index_i_seqs = image.miller_index_i_seqs
if (use_mp):
# to by-pass portable but slower pickling
if (pixels is not None):
assert pixels.is_0_based()
assert not pixels.is_padded()
assert pixels.all() == tuple(work_params.detector.pixels)
pixels = pixels.copy_to_byte_str()
miller_index_i_seqs = miller_index_i_seqs.copy_to_byte_str()
return image_model(
pixels=pixels,
spot_positions=image.spots,
spot_intensities=image.signals,
unit_cell=i_calc.unit_cell(),
crystal_rotation=crystal_rotation,
miller_index_i_seqs=miller_index_i_seqs,
scale=scale,
i_perm=i_perm)
if (not use_mp):
for i_img in xrange(n_mdls):
result.append(build_one_image(i_img))
else:
from libtbx import easy_mp
result = easy_mp.pool_map(
fixed_func=build_one_image,
args=range(n_mdls),
chunksize=1,
log=sys.stdout)
for im in result:
if (im is None): raise RuntimeError("Failure building image.")
if (im.pixels is not None):
im.pixels = flex.int_from_byte_str(im.pixels)
im.pixels.reshape(flex.grid(work_params.detector.pixels))
im.miller_index_i_seqs = flex.size_t_from_byte_str(
byte_str=im.miller_index_i_seqs)
for im in result:
im.make_backup()
return image_models(miller_indices=i_calc.indices(), array=result)
