def plot_kde():
# Load files
print('Loading DIALS files')
expt_file = "dials_temp_files/mega_ultra_refined.expt"
refl_file = "dials_temp_files/mega_ultra_refined.refl"
elist = ExperimentListFactory.from_json_file(expt_file, check_format=False)
refls = reflection_table.from_file(refl_file)
# Remove outliers
print('Removing outliers')
idx = refls.get_flags(refls.flags.used_in_refinement).as_numpy_array()
idy = np.arange(len(elist))[idx].tolist()
elist = ExperimentList([elist[i] for i in idy])
refls = refls.select(flex.bool(idx))
# Generate KDE
normalized_resolution, lams, kde = gen_kde(elist, refls)
# Make a mesh
print('Making a meshgrid')
N = 50
x = np.linspace(min(normalized_resolution), max(normalized_resolution), N)
y = np.linspace(min(lams), max(lams), N)
z = np.zeros(shape=(len(x), len(y)))
zeros = np.zeros(len(x))
# Evaluate PDF on mesh
for x0, y0 in it.product(x, y):
i = np.where(x == x0)[0][0]
j = np.where(y == y0)[0][0]
z[i, j] = kde.pdf([x0, y0])
# Plot a wireframe
print('Plotting')
norm = plt.Normalize(z.min(), z.max())
colors = cm.viridis(norm(z))
rcount, ccount, _ = colors.shape
fig = plt.figure()
ax = fig.add_subplot(projection='3d')
surface = ax.plot_surface(x[:, None] + zeros,
y[None, :] + zeros,
z,
rcount=rcount,
ccount=ccount,
facecolors=colors,
shade=False)
surface.set_facecolor((0, 0, 0, 0))
plt.xlabel('$1/d^2$ (A$^{-2}$)')
plt.ylabel('$\lambda$ (A)')
plt.title('PDF of Reflections')
plt.show()
macro_cycles = 3
lam_min = 0.95
lam_max = 1.15
d_min = 1.4
rlp_radius = 0.002
n_steps = 10
new_expt_filename = 'dials_temp_files/optimized.expt'
new_refl_filename = 'dials_temp_files/optimized.refl'
# Load DIALS files
print('Loading DIALS files')
expt_file = "dials_temp_files/stills_no_sb.expt"
refl_file = "dials_temp_files/stills_no_sb.refl"
elist = ExperimentListFactory.from_json_file(expt_file, check_format=False)
refls = reflection_table.from_file(refl_file)
# This will populate refls['s1'] & refls['rlp']
refls.centroid_px_to_mm(elist)
refls.map_centroids_to_reciprocal_space(elist)
s0 = np.array(elist[0].beam.get_s0())
# Write to reflection file
refls['Wavelength'] = flex.double(len(refls))
refls['miller_index'] = flex.miller_index(len(refls))
# Loop over images and index by frame
print('Reindexing images')
for i in trange(len(elist.imagesets())):
# Get experiment data from experiment objects
expt_file1 = "dials_temp_files/optimized.expt"
refl_file1 = "dials_temp_files/optimized.refl"
expt_file2 = "dials_temp_files/ultra_refined.expt"
refl_file2 = "dials_temp_files/ultra_refined.refl"
#centroid distance cutoff in pixels
centroid_max_distance = 10.
print('reading DIALS files')
from dxtbx.model.experiment_list import ExperimentListFactory
from dials.array_family.flex import reflection_table
elist1 = ExperimentListFactory.from_json_file(expt_file1)
cryst1 = elist1.crystals()[0]
unit_cell1 = cryst1.get_unit_cell()
refls1 = reflection_table.from_file(refl_file1)
elist2 = ExperimentListFactory.from_json_file(expt_file2)
cryst2 = elist2.crystals()[0]
unit_cell2 = cryst2.get_unit_cell()
refls2 = reflection_table.from_file(refl_file2)
# Remove reflections not used in refinement
refls2 = refls2.select(refls2.get_flags(refls2.flags.used_in_refinement))
print('generating DIALS dataframes')
dials_df1 = rs.DataSet(
{
'X': refls1['xyzobs.px.value'].parts()[0].as_numpy_array(),
'Y': refls1['xyzobs.px.value'].parts()[1].as_numpy_array(),
'Wavelength': refls1['Wavelength'].as_numpy_array(),
'BATCH': refls1['imageset_id'].as_numpy_array(),