def run(self):
"""Run the script."""
from dials.util.options import flatten_reflections, flatten_experiments
# Parse the command line arguments
params, options = self.parser.parse_args(show_diff_phil=True)
# Show the help
if len(params.input.reflections) != 1 and not len(
params.input.experiments):
self.parser.print_help()
exit(0)
from dials.util.options import flatten_reflections, flatten_experiments
reflections = flatten_reflections(params.input.reflections)[0]
experiments = flatten_experiments(params.input.experiments)
assert len(experiments) == 1
report = generate_integration_report(
experiments[0],
reflections,
n_resolution_bins=params.n_resolution_bins,
d_max=params.d_max,
d_min=params.d_min,
)
# Construct the per resolution table
from dials.util.report import Table
table = Table()
table.name = "integration.resolution.summary"
table.title = "Summary vs resolution"
table.cols.append(("d_max", "d_max"))
table.cols.append(("d_mid", "d_mid"))
table.cols.append(("d_min", "d_min"))
table.cols.append(("n_full", "# full"))
table.cols.append(("n_part", "# part"))
table.cols.append(("n_over", "# over"))
table.cols.append(("n_ice", "# ice"))
table.cols.append(("n_sum", "# sum"))
table.cols.append(("n_prf", "# prf"))
table.cols.append(("ibg", "Ibg"))
table.cols.append(("i_sum", "<I>\n (sum)"))
table.cols.append(("ios_sum", "I/sigI\n (sum)"))
table.cols.append(("ios_prf", "I/sigI\n (prf)"))
table.cols.append(("cc_prf", "CC prf"))
table.cols.append(("rmsd_xy", "RMSD XY"))
# extract resolution report
report = report["resolution"]
report["d_mid"] = []
for i in range(len(report["bins"]) - 1):
report["d_mid"].append(
(report["bins"][i + 1] + report["bins"][i]) / 2.0)
table.rows.append([
"%.2f" % report["bins"][i + 1],
"%.2f" % report["d_mid"][i],
"%.2f" % report["bins"][i],
"%d" % report["n_full"][i],
"%d" % report["n_partial"][i],
"%d" % report["n_overload"][i],
"%d" % report["n_ice"][i],
"%d" % report["n_summed"][i],
"%d" % report["n_fitted"][i],
"%.4f" % report["mean_background"][i],
"%.4f" % report["i_sum"][i],
"%.4f" % report["ios_sum"][i],
"%.4f" % report["ios_prf"][i],
"%.4f" % report["cc_prf"][i],
"%.4f" % report["rmsd_xy"][i],
])
print(table.as_str())
# plot mean background first
# from matplotlib import pyplot
# fig = pyplot.figure()
# ax = fig.add_subplot(111)
# ax.set_xlabel(r'resolution ($\AA$)')
# ax.set_ylabel(r'$\langle I_b \rangle$')
# d_mid = flex.double(report['d_mid'])
# I_bg = flex.double(report['mean_background'][:-1])
# dm2 = 1/flex.pow2(d_mid)
# ax.plot(dm2, I_bg)
# xticks = ax.get_xticks()
# from math import sqrt
# x_tick_labs = ["" if e <= 0.0 else "{:.2f}".format(sqrt(1./e))
# for e in xticks]
# ax.set_xticklabels(x_tick_labs)
#
# pyplot.show()
# try plot of log intensity and background
templ = experiments[0].imageset.get_template()
import os
title = os.path.basename(templ)
import matplotlib
matplotlib.use("Agg")
from matplotlib import pyplot
fig = pyplot.figure()
ax = fig.add_subplot(111)
ax.set_xlabel(r"$d_{mid}$ ($\AA$)")
ax.set_ylabel(r"$\langle Intensity \rangle$")
d_mid = flex.double(report["d_mid"])
I_bg = flex.double(report["mean_background"][:-1])
I_sum = flex.double(report["i_sum"][:-1])
dm2 = 1 / flex.pow2(d_mid)
ax.plot(dm2, I_bg, label="Background")
ax.plot(dm2, I_sum, label="Peak")
ax.legend(loc="upper right")
ax.set_title(title)
ax.set_ylim(-2, 100)
pyplot.minorticks_on()
ax.grid(True, which="both")
xticks = ax.get_xticks()
from math import sqrt
x_tick_labs = [
"" if e <= 0.0 else "{:.2f}".format(sqrt(1.0 / e)) for e in xticks
]
ax.set_xticklabels(x_tick_labs)
pyplot.savefig("intensity_vs_resolution.png")
