def write_xds_inp(self, path: str) -> None:
"""Write XDS.INP input file for XDS in directory `path`"""
path.mkdir(exist_ok=True)
nframes = max(self.complete_range)
invert_rotation_axis = self.start_angle > self.end_angle
rot_x, rot_y, rot_z = rotation_axis_to_xyz(self.rotation_axis,
invert=invert_rotation_axis)
shape_x, shape_y = self.data_shape
if self.do_stretch_correction:
self.write_geometric_correction_files(path)
stretch_correction = "DETECTOR= PILATUS ! Pretend to be PILATUS detector to enable geometric corrections\nX-GEO_CORR= XCORR.cbf ! X stretch correction\nY-GEO_CORR= YCORR.cbf ! Y stretch correction\n"
else:
stretch_correction = ""
if self.missing_range:
exclude = "\n".join([
f"EXCLUDE_DATA_RANGE={i} {j}"
for i, j in find_subranges(self.missing_range)
])
else:
exclude = "!EXCLUDE_DATA_RANGE="
untrusted_areas = ""
for kind, coords in self.untrusted_areas:
untrusted_areas += to_xds_untrusted_area(kind, coords) + "\n"
s = self.XDS_template.format(
date=str(time.ctime()),
data_drc=self.smv_subdrc,
data_begin=1,
data_end=nframes,
exclude=exclude,
stretch_correction=stretch_correction,
starting_angle=self.start_angle,
wavelength=self.wavelength,
# reverse XY coordinates for XDS
origin_x=self.mean_beam_center[1],
origin_y=self.mean_beam_center[0],
untrusted_areas=untrusted_areas,
NX=shape_y,
NY=shape_x,
sign="+",
detector_distance=self.distance,
QX=self.physical_pixelsize,
QY=self.physical_pixelsize,
osc_angle=self.osc_angle,
rot_x=rot_x,
rot_y=rot_y,
rot_z=rot_z)
with open(path / 'XDS.INP', 'w') as f:
print(s, file=f)
logger.info("XDS INP file created.")
def get_drifts_per_scan_range(xy):
i = np.nansum(xy, axis=1) == 0
rng = np.arange(len(i))[i != True] # noqa
subranges = find_subranges(rng)
normalized_xy = []
drifts = []
for sbr in subranges:
r = np.arange(*sbr)
sub_xy = xy[r]
if len(sub_xy) == 0:
continue
o = sub_xy[0]
drift = np.linalg.norm(sub_xy - o, axis=1)
distance = drift.max() - drift.min()
drifts.append(distance)
normalized_xy.append(sub_xy - o)
normalized_xy.append([np.NaN, np.NaN])
normalized_xy = np.vstack(normalized_xy)
drifts = np.array(drifts)
# plt.plot(normalized_xy[:,0], label="X")
# plt.plot(normalized_xy[:,1], label="Y")
# plt.legend()
# plt.show()
return drifts
def export_dials_variables(path,
*,
sequence=(),
missing=(),
rotation_xyz=None):
"""Export variables for DIALS to account for missing frames
writes dials_variables.sh (bash) and dials_variables.bat (cmd)
`sequence` is a tuple of sequence numbers of the data frames
`missing `is a tuple of sequence numbers of the missing frames
"""
import io
scanranges = find_subranges(sequence)
scanrange = " ".join(f"scan_range={i},{j}" for i, j in scanranges)
excludeimages = ",".join((str(n) for n in missing))
if rotation_xyz:
rot_x, rot_y, rot_z = rotation_xyz
# newline='\n' to have unix line endings
with open(path / "dials_variables.sh", "w", newline='\n') as f:
print(f"#!/usr/bin/env bash", file=f)
print(f"scan_range='{scanrange}'", file=f)
print(f"exclude_images='exclude_images={excludeimages}'", file=f)
if rotation_xyz:
print(
f"rotation_axis='geometry.goniometer.axes={rot_x:.4f},{rot_y:.4f},{rot_z:.4f}'",
file=f)
print("#", file=f)
print("# To run:", file=f)
print("# source dials_variables.sh", file=f)
print("#", file=f)
print("# and:", file=f)
print("# dials.import directory=data $rotation_axis", file=f)
print("# dials.find_spots datablock.json $scan_range", file=f)
print(
"# dials.integrate $exclude_images refined.pickle refined.json",
file=f)
print("#", file=f)
with open(path / "dials_variables.bat", "w", newline='\n') as f:
print("@echo off", file=f)
print("", file=f)
print(f"set scan_range={scanrange}", file=f)
print(f"set exclude_images=exclude_images={excludeimages}", file=f)
if rotation_xyz:
print(
f"set rotation_axis=geometry.goniometer.axes={rot_x:.4f},{rot_y:.4f},{rot_z:.4f}",
file=f)
print("", file=f)
print(":: To run:", file=f)
print(":: call dials_variables.bat", file=f)
print("::", file=f)
print(":: dials.import directory=data %rotation_axis%", file=f)
print(":: dials.find_spots datablock.json %scan_range%", file=f)
print(
":: dials.integrate %exclude_images% refined.pickle refined.json",
file=f)