def __init__(self,
experiments,
filter_type="median",
kernel_size=10,
niter=100):
"""
Initialize the finalizer
:param experiments: The experiment list
:param kernel_size: The median filter kernel size
:param niter: The number of iterations for filling holes
"""
from dials.algorithms.background.gmodel import PolarTransform
# Set some parameters
self.filter_type = filter_type
self.kernel_size = kernel_size
self.niter = niter
# Check the input
assert len(experiments) == 1
experiment = experiments[0]
assert len(experiment.detector) == 1
# Save the experiment
self.experiment = experiment
# Create the transform object
self.transform = PolarTransform(experiment.beam,
experiment.detector[0],
experiment.goniometer)
def run(self):
''' Perform the integration. '''
from dials.util.command_line import heading
from dials.util.options import flatten_experiments
from dials.util import log
from time import time
from libtbx.utils import Sorry
from dials.array_family import flex
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=False)
experiments = flatten_experiments(params.input.experiments)
if len(experiments) == 0:
self.parser.print_help()
return
assert len(experiments) == 1
imageset = experiments[0].imageset
beam = experiments[0].beam
detector = experiments[0].detector
goniometer = experiments[0].goniometer
assert len(detector) == 1
# Configure logging
log.config()
from dials.algorithms.background.gmodel import PolarTransform
import cPickle as pickle
model = pickle.load(open(params.model))
image = model.data(0)
mask = flex.bool(image.accessor(), True)
# Do the transformation
transform = PolarTransform(beam, detector[0], goniometer)
result = transform.to_polar(image, mask)
data = result.data()
mask = result.mask()
pickle.dump((data, mask), open(params.output.data, "w"))
from matplotlib import pylab
vmax = sorted(list(data))[int(0.99 * len(data))]
figure = pylab.figure(figsize=(6,4))
pylab.imshow(
data.as_numpy_array(),
interpolation = 'none',
vmin = 0,
vmax = vmax)
ax1 = pylab.gca()
ax1.get_xaxis().set_visible(False)
ax1.get_yaxis().set_visible(False)
cb = pylab.colorbar()
cb.ax.tick_params(labelsize=8)
logger.info("Saving polar model %s" % (params.output.image))
pylab.savefig("%s" % (params.output.image), dpi=600, bbox_inches='tight')
