def run(self):
'''Execute the script.'''
from dials.array_family import flex
from dials.util.options import flatten_datablocks
from dials.util.options import flatten_reflections
from time import time
from dials.util import log
from logging import info, debug
from libtbx.utils import Sorry
start_time = time()
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=False)
# Configure the logging
log.config(
params.verbosity,
info=params.output.log,
debug=params.output.debug_log)
from dials.util.version import dials_version
info(dials_version())
# Log the diff phil
diff_phil = self.parser.diff_phil.as_str()
if diff_phil is not '':
info('The following parameters have been modified:\n')
info(diff_phil)
# Ensure we have a data block
datablocks = flatten_datablocks(params.input.datablock)
reflections = flatten_reflections(params.input.reflections)
if len(datablocks) == 0 and len(reflections) == 0:
self.parser.print_help()
return
elif len(datablocks) != len(reflections):
raise Sorry("Must have same number of datablocks and reflection tables")
# Combine the datablocks and reflections
datablock, reflections = combine(
datablocks,
reflections,
params)
# Save the reflections to file
info('\n' + '-' * 80)
reflections.as_pickle(params.output.reflections)
info('Saved {0} reflections to {1}'.format(
len(reflections), params.output.reflections))
# Save the datablock
from dxtbx.datablock import DataBlockDumper
info('Saving datablocks to {0}'.format(
params.output.datablock))
dump = DataBlockDumper(datablocks)
dump.as_file(params.output.datablock)
# Print the time
info("Time Taken: %f" % (time() - start_time))
def run(self):
'''Execute the script.'''
from dials.array_family import flex
from dials.util.options import flatten_datablocks
from dials.util.options import flatten_reflections
from time import time
from dials.util import log
from libtbx.utils import Sorry
start_time = time()
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=False)
# Configure the logging
log.config(
params.verbosity,
info=params.output.log,
debug=params.output.debug_log)
from dials.util.version import dials_version
logger.info(dials_version())
# Log the diff phil
diff_phil = self.parser.diff_phil.as_str()
if diff_phil is not '':
logger.info('The following parameters have been modified:\n')
logger.info(diff_phil)
# Ensure we have a data block
datablocks = flatten_datablocks(params.input.datablock)
reflections = flatten_reflections(params.input.reflections)
if len(datablocks) == 0 and len(reflections) == 0:
self.parser.print_help()
return
elif len(datablocks) != len(reflections):
raise Sorry("Must have same number of datablocks and reflection tables")
# Combine the datablocks and reflections
datablock, reflections = combine(
datablocks,
reflections,
params)
# Save the reflections to file
logger.info('\n' + '-' * 80)
reflections.as_pickle(params.output.reflections)
logger.info('Saved {0} reflections to {1}'.format(
len(reflections), params.output.reflections))
# Save the datablock
from dxtbx.datablock import DataBlockDumper
logger.info('Saving datablocks to {0}'.format(
params.output.datablock))
dump = DataBlockDumper(datablocks)
dump.as_file(params.output.datablock)
# Print the time
logger.info("Time Taken: %f" % (time() - start_time))
def write_datablocks(self, datablocks, params):
'''
Output the datablock to file.
'''
if params.output.datablock:
logger.info("-" * 80)
logger.info('Writing datablocks to %s' % params.output.datablock)
dump = DataBlockDumper(datablocks)
dump.as_file(params.output.datablock, compact=params.output.compact)
def write_datablocks(self, datablocks, params):
'''
Output the datablock to file.
'''
if params.output.datablock:
logger.info("-" * 80)
logger.info('Writing datablocks to %s' % params.output.datablock)
dump = DataBlockDumper(datablocks)
dump.as_file(params.output.datablock, compact=params.output.compact)
def run(self):
''' Run the script. '''
from dials.util.masking import MaskGenerator
from dials.util.options import flatten_datablocks
from libtbx.utils import Sorry
import six.moves.cPickle as pickle
from dials.util import log
from dxtbx.format.image import ImageBool
# Parse the command line arguments
params, options = self.parser.parse_args(show_diff_phil=True)
datablocks = flatten_datablocks(params.input.datablock)
# Configure logging
log.config()
# Check number of args
if len(datablocks) == 0:
self.parser.print_help()
return
if len(datablocks) != 1:
raise Sorry('exactly 1 datablock must be specified')
datablock = datablocks[0]
imagesets = datablock.extract_imagesets()
if len(imagesets) != 1:
raise Sorry('datablock must contain exactly 1 imageset')
imageset = imagesets[0]
# Generate the mask
generator = MaskGenerator(params)
mask = generator.generate(imageset)
# Save the mask to file
print("Writing mask to %s" % params.output.mask)
with open(params.output.mask, "wb") as fh:
pickle.dump(mask, fh)
# Save the datablock
if params.output.datablock is not None:
imageset.external_lookup.mask.data = ImageBool(mask)
imageset.external_lookup.mask.filename = params.output.mask
from dxtbx.datablock import DataBlockDumper
print('Saving datablocks to {0}'.format(params.output.datablock))
dump = DataBlockDumper(datablocks)
dump.as_file(params.output.datablock)
def run(self):
'''Execute the script.'''
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=True)
try:
assert len(params.input.reflections) == len(params.input.datablock)
except AssertionError:
raise Sorry(
"The number of input reflections files does not match the "
"number of input datablocks")
datablocks = flatten_datablocks(params.input.datablock)
reflections = flatten_reflections(params.input.reflections)
if len(reflections):
r = self.combine_reflections(reflections)
# print number of reflections per imageset
from libtbx.table_utils import simple_table
max_id = max(r['id'])
header = ["Imageset", "Nref"]
nrefs_per_imset = [(r['id'] == i).count(True)
for i in range(max_id + 1)]
rows = [(str(i), str(n)) for (i, n) in enumerate(nrefs_per_imset)]
st = simple_table(rows, header)
print(st.format())
rf = params.output.reflections_filename
print('Saving combined reflections to {0}'.format(rf))
r.as_pickle(rf)
if len(datablocks):
db = self.combine_datablocks(datablocks)
dbf = params.output.datablocks_filename
print('Saving combined datablocks to {0}'.format(dbf))
dump = DataBlockDumper(db)
dump.as_file(dbf, compact=params.output.compact)
return
def write_expt(experiments, filename):
from dxtbx.datablock import DataBlockDumper
dump = DataBlockDumper(experiments)
dump.as_file(filename)
def run(self):
'''Execute the script.'''
from dials.array_family import flex
from dials.util.options import flatten_datablocks
from time import time
from dials.util import log
from libtbx.utils import Sorry
start_time = time()
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=False)
# Configure the logging
log.config(params.verbosity,
info=params.output.log,
debug=params.output.debug_log)
from dials.util.version import dials_version
logger.info(dials_version())
# Log the diff phil
diff_phil = self.parser.diff_phil.as_str()
if diff_phil is not '':
logger.info('The following parameters have been modified:\n')
logger.info(diff_phil)
# Ensure we have a data block
datablocks = flatten_datablocks(params.input.datablock)
if len(datablocks) == 0:
self.parser.print_help()
return
elif len(datablocks) != 1:
raise Sorry('only 1 datablock can be processed at a time')
# Loop through all the imagesets and find the strong spots
reflections = flex.reflection_table.from_observations(
datablocks[0], params)
# Delete the shoeboxes
if not params.output.shoeboxes:
del reflections['shoebox']
# ascii spot count per image plot
from dials.util.ascii_art import spot_counts_per_image_plot
for i, imageset in enumerate(datablocks[0].extract_imagesets()):
ascii_plot = spot_counts_per_image_plot(
reflections.select(reflections['id'] == i))
if len(ascii_plot):
logger.info(
'\nHistogram of per-image spot count for imageset %i:' % i)
logger.info(ascii_plot)
# Save the reflections to file
logger.info('\n' + '-' * 80)
reflections.as_pickle(params.output.reflections)
logger.info('Saved {0} reflections to {1}'.format(
len(reflections), params.output.reflections))
# Save the datablock
if params.output.datablock:
from dxtbx.datablock import DataBlockDumper
logger.info('Saving datablocks to {0}'.format(
params.output.datablock))
dump = DataBlockDumper(datablocks)
dump.as_file(params.output.datablock)
# Print some per image statistics
if params.per_image_statistics:
from dials.algorithms.spot_finding import per_image_analysis
from cStringIO import StringIO
s = StringIO()
for i, imageset in enumerate(datablocks[0].extract_imagesets()):
print >> s, "Number of centroids per image for imageset %i:" % i
stats = per_image_analysis.stats_imageset(
imageset,
reflections.select(reflections['id'] == i),
resolution_analysis=False)
per_image_analysis.print_table(stats, out=s)
logger.info(s.getvalue())
# Print the time
logger.info("Time Taken: %f" % (time() - start_time))
if not stills:
num_stills = 0
else:
num_stills = len(stills)
# Print some data block info
print "-" * 80
print "DataBlock %d" % i
print " format: %s" % str(datablock.format_class())
print " num images: %d" % datablock.num_images()
print " num sweeps: %d" % len(sweeps)
print " num stills: %d" % num_stills
# Loop through all the sweeps
if options.verbose > 1:
for j, sweep in enumerate(sweeps):
print ""
print "Sweep %d" % j
print " length %d" % len(sweep)
print sweep.get_beam()
print sweep.get_goniometer()
print sweep.get_detector()
print sweep.get_scan()
# Write the datablock to a JSON or pickle file
if options.output:
print "-" * 80
print 'Writing datablocks to %s' % options.output
dump = DataBlockDumper(datablocks)
dump.as_file(options.output, compact=options.compact)
def test_elliptical_distortion(tmpdir):
"""Create distortion maps for elliptical distortion using a dummy datablock
with a small detector, for speed. Check those maps seem sensible"""
tmpdir.chdir()
# Make a detector model
d = make_detector()
# The beam is also essential for a datablock to be serialisable
b = Beam((0, 0, 1), 1.0)
# Create and write out a datablock
imageset = ImageSet(
ImageSetData(Reader(["non-existent.cbf"]),
Masker(["non-existent.cbf"])))
imageset.set_detector(d)
imageset.set_beam(b)
datablocks = DataBlockFactory.from_imageset(imageset)
dump = DataBlockDumper(datablocks)
dump.as_file("dummy_datablock.json")
# Centre of distortion will be the far corner from the origin of the first
# panel
centre_xy = d[0].get_image_size_mm()
# Generate distortion maps
cmd = ("dials.generate_distortion_maps dummy_datablock.json "
"mode=ellipse centre_xy={},{} "
"phi=0 l1=1.0 l2=0.95").format(*centre_xy)
result = easy_run.fully_buffered(command=cmd).raise_if_errors()
# Load the maps
with open("dx.pickle", "rb") as f:
dx = pickle.load(f)
with open("dy.pickle", "rb") as f:
dy = pickle.load(f)
# Check there are 4 maps each
assert len(dx) == len(dy) == 4
# Ellipse has phi=0, so all correction is in the dy map
for arr in dx:
assert min(arr) == max(arr) == 0.0
# The ellipse correction is centred at the middle of the detector and all in
# the Y direction. Therefore we expect a few things from the dy maps:
#
# (1) Within each panel the columns of the array are identical.
# (2) The two upper panels should be the same
# (3) The two lower panels should be the same.
# (4) One column from an upper panel is a negated, reversed column from a
# lower panel.
#
# All together expect the 4 dy maps to look something like this:
#
# /-----------\ /-----------\
# |-3 -3 -3 -3| |-3 -3 -3 -3|
# |-2 -2 -2 -2| |-2 -2 -2 -2|
# |-1 -1 -1 -1| |-1 -1 -1 -1|
# | 0 0 0 0| | 0 0 0 0|
# \-----------/ \-----------/
# /-----------\ /-----------\
# | 0 0 0 0| | 0 0 0 0|
# | 1 1 1 1| | 1 1 1 1|
# | 2 2 2 2| | 2 2 2 2|
# | 3 3 3 3| | 3 3 3 3|
# \-----------/ \-----------/
# So the fundamental data is all in the first column of first panel's map
col0 = dy[0].matrix_copy_column(0)
# The correction should be 5% of the distance from the ellipse centre to a
# corrected pixel (l2 = 0.95 above) along the slow axis. Check that is the
# case (for the first pixel at least)
vec_centre_to_first_px = (matrix.col(d[0].get_pixel_lab_coord(
(0.5, 0.5))) - matrix.col(d[0].get_lab_coord(centre_xy)))
dist_centre_to_first_px = vec_centre_to_first_px.dot(
matrix.col(d[0].get_slow_axis()))
corr_mm = dist_centre_to_first_px * 0.05
corr_px = corr_mm / d[0].get_pixel_size()[1]
assert col0[0] == pytest.approx(corr_px)
# Test (1) from above list for panel 0
for i in range(1, 50):
assert (col0 == dy[0].matrix_copy_column(i)).all_eq(True)
# Test (2)
assert (dy[0] == dy[1]).all_eq(True)
# Test (3)
assert (dy[2] == dy[3]).all_eq(True)
# Test (4)
assert col0 == pytest.approx(-1.0 * dy[2].matrix_copy_column(0).reversed())
# Test (1) for panel 2 as well, which then covers everything needed
col0 = dy[2].matrix_copy_column(0)
for i in range(1, 50):
assert (col0 == dy[2].matrix_copy_column(i)).all_eq(True)
def run(self):
'''Execute the script.'''
from dials.array_family import flex
from dials.util.options import flatten_datablocks
from time import time
from dials.util import log
from libtbx.utils import Sorry
start_time = time()
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=False)
# Configure the logging
log.config(
params.verbosity,
info=params.output.log,
debug=params.output.debug_log)
from dials.util.version import dials_version
logger.info(dials_version())
# Log the diff phil
diff_phil = self.parser.diff_phil.as_str()
if diff_phil is not '':
logger.info('The following parameters have been modified:\n')
logger.info(diff_phil)
# Ensure we have a data block
datablocks = flatten_datablocks(params.input.datablock)
if len(datablocks) == 0:
self.parser.print_help()
return
elif len(datablocks) != 1:
raise Sorry('only 1 datablock can be processed at a time')
# Loop through all the imagesets and find the strong spots
reflections = flex.reflection_table.from_observations(
datablocks[0], params)
# Delete the shoeboxes
if not params.output.shoeboxes:
del reflections['shoebox']
# ascii spot count per image plot
from dials.util.ascii_art import spot_counts_per_image_plot
for i, imageset in enumerate(datablocks[0].extract_imagesets()):
ascii_plot = spot_counts_per_image_plot(
reflections.select(reflections['id'] == i))
if len(ascii_plot):
logger.info('\nHistogram of per-image spot count for imageset %i:' %i)
logger.info(ascii_plot)
# Save the reflections to file
logger.info('\n' + '-' * 80)
reflections.as_pickle(params.output.reflections)
logger.info('Saved {0} reflections to {1}'.format(
len(reflections), params.output.reflections))
# Save the datablock
if params.output.datablock:
from dxtbx.datablock import DataBlockDumper
logger.info('Saving datablocks to {0}'.format(
params.output.datablock))
dump = DataBlockDumper(datablocks)
dump.as_file(params.output.datablock)
# Print some per image statistics
if params.per_image_statistics:
from dials.algorithms.spot_finding import per_image_analysis
from cStringIO import StringIO
s = StringIO()
for i, imageset in enumerate(datablocks[0].extract_imagesets()):
print >> s, "Number of centroids per image for imageset %i:" %i
stats = per_image_analysis.stats_imageset(
imageset, reflections.select(reflections['id'] == i),
resolution_analysis=False)
per_image_analysis.print_table(stats, out=s)
logger.info(s.getvalue())
# Print the time
logger.info("Time Taken: %f" % (time() - start_time))
from dxtbx.datablock import DataBlockFactory, DataBlockDumper
from dxtbx.imageset import ImageSetFactory, ImageSweep, ImageSetData
from dxtbx.model.goniometer import GoniometerFactory
from dxtbx.model.scan import ScanFactory
import glob, os, sys
"""
Modification of AB's prepare_sweep.py.
Usage: libtbx.python prepare_sweep.py img_dir start_img, end_img savefile
"""
root = sys.argv[1]
start, end = int(sys.argv[2]), int(sys.argv[3])
g = GoniometerFactory.single_axis()
s = ScanFactory.make_scan((start, end), 0, (0, 1), [0] * (end - start + 1))
sw = ImageSetFactory.from_template(template=os.path.join(
root, "fft_frame_I_mf_####.cbf"),
scan=s,
goniometer=g,
image_range=(start, end))
dump = DataBlockDumper(DataBlockFactory.from_imageset(sw))
dump.as_file(sys.argv[4])
from __future__ import absolute_import, division, print_function
from dxtbx.datablock import DataBlockFactory, DataBlockDumper
import sys
from six.moves import range
fin = sys.argv[1]
px_size = 0.05 # in mm
dpx = [0, 0, 1, 1, 0, 1, 1, 0] # in px
dpy = [0, 0, 1, 1, 0, 1, 1, 0] # in px
db = DataBlockFactory.from_json_file(fin)
db0 = db[0]
dd = db0.to_dict()
for i in range(8):
x = dd['detector'][0]['panels'][i]['origin'][0] + dpx[i] * px_size
y = dd['detector'][0]['panels'][i]['origin'][1] + dpy[i] * px_size
dd['detector'][0]['panels'][i]['origin'] = (x, y, 0)
xx = DataBlockFactory.from_dict(dd)
yy = DataBlockDumper(xx)
yy.as_file('new_detector_geom.json')
def datablock(obj, outfile, **kwargs):
"""Dump the given object to file."""
dump = DataBlockDumper(obj)
dump.as_file(outfile, **kwargs)
def datablock(obj, outfile, **kwargs): ''' Dump the given object to file. ''' from dxtbx.datablock import DataBlockDumper dump = DataBlockDumper(obj) dump.as_file(outfile, **kwargs)
if not stills:
num_stills = 0
else:
num_stills = len(stills)
# Print some data block info
print "-" * 80
print "DataBlock %d" % i
print " format: %s" % str(datablock.format_class())
print " num images: %d" % datablock.num_images()
print " num sweeps: %d" % len(sweeps)
print " num stills: %d" % num_stills
# Loop through all the sweeps
if options.verbose > 1:
for j, sweep in enumerate(sweeps):
print ""
print "Sweep %d" % j
print " length %d" % len(sweep)
print sweep.get_beam()
print sweep.get_goniometer()
print sweep.get_detector()
print sweep.get_scan()
# Write the datablock to a JSON or pickle file
if options.output:
print "-" * 80
print 'Writing datablocks to %s' % options.output
dump = DataBlockDumper(datablocks)
dump.as_file(options.output, compact=options.compact)
def datablock(obj, outfile, **kwargs):
""" Dump the given object to file. """
from dxtbx.datablock import DataBlockDumper
dump = DataBlockDumper(obj)
dump.as_file(outfile, **kwargs)
