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')