def _index_prepare(self):
'''Prepare to do autoindexing - in XDS terms this will mean
calling xycorr, init and colspot on the input images.'''
# decide on images to work with
Debug.write('XDS INDEX PREPARE:')
Debug.write('Wavelength: %.6f' % self.get_wavelength())
Debug.write('Distance: %.2f' % self.get_distance())
if self._indxr_images == []:
_select_images_function = getattr(
self, '_index_select_images_%s' % (self._index_select_images))
wedges = _select_images_function()
for wedge in wedges:
self.add_indexer_image_wedge(wedge)
self.set_indexer_prepare_done(True)
all_images = self.get_matching_images()
first = min(all_images)
last = max(all_images)
# next start to process these - first xycorr
xycorr = self.Xycorr()
xycorr.set_data_range(first, last)
xycorr.set_background_range(self._indxr_images[0][0],
self._indxr_images[0][1])
from dxtbx.serialize.xds import to_xds
converter = to_xds(self.get_imageset())
xds_beam_centre = converter.detector_origin
xycorr.set_beam_centre(xds_beam_centre[0],
xds_beam_centre[1])
for block in self._indxr_images:
xycorr.add_spot_range(block[0], block[1])
# FIXME need to set the origin here
xycorr.run()
for file in ['X-CORRECTIONS.cbf',
'Y-CORRECTIONS.cbf']:
self._indxr_payload[file] = xycorr.get_output_data_file(file)
# next start to process these - then init
if PhilIndex.params.xia2.settings.input.format.dynamic_shadowing:
# find the region of the scan with the least predicted shadow
# to use for background determination in XDS INIT step
from dxtbx.serialize import dump
from dxtbx.datablock import DataBlock
imageset = self._indxr_imagesets[0]
xsweep = self._indxr_sweeps[0]
sweep_filename = os.path.join(
self.get_working_directory(), '%s_datablock.json' %xsweep.get_name())
dump.datablock(DataBlock([imageset]), sweep_filename)
from xia2.Wrappers.Dials.ShadowPlot import ShadowPlot
shadow_plot = ShadowPlot()
shadow_plot.set_working_directory(self.get_working_directory())
auto_logfiler(shadow_plot)
shadow_plot.set_sweep_filename(sweep_filename)
shadow_plot.set_json_filename(
os.path.join(
self.get_working_directory(),
'%s_shadow_plot.json' %shadow_plot.get_xpid()))
shadow_plot.run()
results = shadow_plot.get_results()
from scitbx.array_family import flex
fraction_shadowed = flex.double(results['fraction_shadowed'])
scan_points = flex.double(results['scan_points'])
phi_width = self.get_phi_width()
scan = imageset.get_scan()
oscillation_range = scan.get_oscillation_range()
oscillation = scan.get_oscillation()
bg_images = self._background_images
bg_range_deg = (scan.get_angle_from_image_index(bg_images[0]),
scan.get_angle_from_image_index(bg_images[1]))
bg_range_width = bg_range_deg[1] - bg_range_deg[0]
min_shadow = 100
best_bg_range = bg_range_deg
from libtbx.utils import frange
for bg_range_start in frange(flex.min(scan_points), flex.max(scan_points) - bg_range_width, step=oscillation[1]):
bg_range_deg = (bg_range_start, bg_range_start + bg_range_width)
sel = (scan_points >= bg_range_deg[0]) & (scan_points <= bg_range_deg[1])
mean_shadow = flex.mean(fraction_shadowed.select(sel))
if mean_shadow < min_shadow:
min_shadow = mean_shadow
best_bg_range = bg_range_deg
self._background_images = (
scan.get_image_index_from_angle(best_bg_range[0]),
scan.get_image_index_from_angle(best_bg_range[1]))
Debug.write('Setting background images: %s -> %s' %self._background_images)
init = self.Init()
for file in ['X-CORRECTIONS.cbf',
'Y-CORRECTIONS.cbf']:
init.set_input_data_file(file, self._indxr_payload[file])
init.set_data_range(first, last)
if self._background_images:
init.set_background_range(self._background_images[0],
self._background_images[1])
else:
init.set_background_range(self._indxr_images[0][0],
self._indxr_images[0][1])
for block in self._indxr_images:
init.add_spot_range(block[0], block[1])
init.run()
# at this stage, need to (perhaps) modify the BKGINIT.cbf image
# to mark out the back stop
if PhilIndex.params.general.backstop_mask:
Debug.write('Applying mask to BKGINIT.pck')
# copy the original file
cbf_old = os.path.join(init.get_working_directory(),
'BKGINIT.cbf')
cbf_save = os.path.join(init.get_working_directory(),
'BKGINIT.sav')
shutil.copyfile(cbf_old, cbf_save)
# modify the file to give the new mask
from xia2.Toolkit.BackstopMask import BackstopMask
mask = BackstopMask(PhilIndex.params.general.backstop_mask)
mask.apply_mask_xds(self.get_header(), cbf_save, cbf_old)
init.reload()
for file in ['BLANK.cbf',
'BKGINIT.cbf',
'GAIN.cbf']:
self._indxr_payload[file] = init.get_output_data_file(file)
if PhilIndex.params.xia2.settings.developmental.use_dials_spotfinder:
spotfinder = self.DialsSpotfinder()
for block in self._indxr_images:
spotfinder.add_spot_range(block[0], block[1])
spotfinder.run()
export = self.DialsExportSpotXDS()
export.set_input_data_file(
'reflections.pickle',
spotfinder.get_output_data_file('reflections.pickle'))
export.run()
for file in ['SPOT.XDS']:
self._indxr_payload[file] = export.get_output_data_file(file)
else:
# next start to process these - then colspot
colspot = self.Colspot()
for file in ['X-CORRECTIONS.cbf',
'Y-CORRECTIONS.cbf',
'BLANK.cbf',
'BKGINIT.cbf',
'GAIN.cbf']:
colspot.set_input_data_file(file, self._indxr_payload[file])
colspot.set_data_range(first, last)
colspot.set_background_range(self._indxr_images[0][0],
self._indxr_images[0][1])
for block in self._indxr_images:
colspot.add_spot_range(block[0], block[1])
colspot.run()
for file in ['SPOT.XDS']:
self._indxr_payload[file] = colspot.get_output_data_file(file)
# that should be everything prepared... all of the important
# files should be loaded into memory to be able to cope with
# integration happening somewhere else
return
def _index_prepare(self):
"""Prepare to do autoindexing - in XDS terms this will mean
calling xycorr, init and colspot on the input images."""
# decide on images to work with
logger.debug("XDS INDEX PREPARE:")
logger.debug("Wavelength: %.6f", self.get_wavelength())
logger.debug("Distance: %.2f", self.get_distance())
if self._indxr_images == []:
_select_images_function = getattr(
self, "_index_select_images_%s" % self._index_select_images
)
wedges = _select_images_function()
for wedge in wedges:
self.add_indexer_image_wedge(wedge)
self.set_indexer_prepare_done(True)
all_images = self.get_matching_images()
first = min(all_images)
last = max(all_images)
# next start to process these - first xycorr
xycorr = self.Xycorr()
xycorr.set_data_range(first, last)
xycorr.set_background_range(self._indxr_images[0][0], self._indxr_images[0][1])
converter = to_xds(self.get_imageset())
xds_beam_centre = converter.detector_origin
xycorr.set_beam_centre(xds_beam_centre[0], xds_beam_centre[1])
for block in self._indxr_images:
xycorr.add_spot_range(block[0], block[1])
# FIXME need to set the origin here
xycorr.run()
for file in ["X-CORRECTIONS.cbf", "Y-CORRECTIONS.cbf"]:
self._indxr_payload[file] = xycorr.get_output_data_file(file)
# next start to process these - then init
if PhilIndex.params.xia2.settings.input.format.dynamic_shadowing:
imageset = self._indxr_imagesets[0]
masker = (
imageset.get_format_class()
.get_instance(imageset.paths()[0])
.get_masker()
)
if masker is None:
# disable dynamic_shadowing
PhilIndex.params.xia2.settings.input.format.dynamic_shadowing = False
if PhilIndex.params.xia2.settings.input.format.dynamic_shadowing:
# find the region of the scan with the least predicted shadow
# to use for background determination in XDS INIT step
from dxtbx.model.experiment_list import ExperimentListFactory
imageset = self._indxr_imagesets[0]
xsweep = self._indxr_sweeps[0]
sweep_filename = os.path.join(
self.get_working_directory(), "%s_indexed.expt" % xsweep.get_name()
)
ExperimentListFactory.from_imageset_and_crystal(imageset, None).as_file(
sweep_filename
)
from xia2.Wrappers.Dials.ShadowPlot import ShadowPlot
shadow_plot = ShadowPlot()
shadow_plot.set_working_directory(self.get_working_directory())
auto_logfiler(shadow_plot)
shadow_plot.set_sweep_filename(sweep_filename)
shadow_plot.set_json_filename(
os.path.join(
self.get_working_directory(),
"%s_shadow_plot.json" % shadow_plot.get_xpid(),
)
)
shadow_plot.run()
results = shadow_plot.get_results()
fraction_shadowed = flex.double(results["fraction_shadowed"])
if flex.max(fraction_shadowed) == 0:
PhilIndex.params.xia2.settings.input.format.dynamic_shadowing = False
else:
scan_points = flex.double(results["scan_points"])
scan = imageset.get_scan()
oscillation = scan.get_oscillation()
if self._background_images is not None:
bg_images = self._background_images
bg_range_deg = (
scan.get_angle_from_image_index(bg_images[0]),
scan.get_angle_from_image_index(bg_images[1]),
)
bg_range_width = bg_range_deg[1] - bg_range_deg[0]
min_shadow = 100
best_bg_range = bg_range_deg
from libtbx.utils import frange
for bg_range_start in frange(
flex.min(scan_points),
flex.max(scan_points) - bg_range_width,
step=oscillation[1],
):
bg_range_deg = (bg_range_start, bg_range_start + bg_range_width)
sel = (scan_points >= bg_range_deg[0]) & (
scan_points <= bg_range_deg[1]
)
mean_shadow = flex.mean(fraction_shadowed.select(sel))
if mean_shadow < min_shadow:
min_shadow = mean_shadow
best_bg_range = bg_range_deg
self._background_images = (
scan.get_image_index_from_angle(best_bg_range[0]),
scan.get_image_index_from_angle(best_bg_range[1]),
)
logger.debug(
"Setting background images: %s -> %s" % self._background_images
)
init = self.Init()
for file in ["X-CORRECTIONS.cbf", "Y-CORRECTIONS.cbf"]:
init.set_input_data_file(file, self._indxr_payload[file])
init.set_data_range(first, last)
if self._background_images:
init.set_background_range(
self._background_images[0], self._background_images[1]
)
else:
init.set_background_range(
self._indxr_images[0][0], self._indxr_images[0][1]
)
for block in self._indxr_images:
init.add_spot_range(block[0], block[1])
init.run()
# at this stage, need to (perhaps) modify the BKGINIT.cbf image
# to mark out the back stop
if PhilIndex.params.xds.backstop_mask:
logger.debug("Applying mask to BKGINIT.pck")
# copy the original file
cbf_old = os.path.join(init.get_working_directory(), "BKGINIT.cbf")
cbf_save = os.path.join(init.get_working_directory(), "BKGINIT.sav")
shutil.copyfile(cbf_old, cbf_save)
# modify the file to give the new mask
from xia2.Toolkit.BackstopMask import BackstopMask
mask = BackstopMask(PhilIndex.params.xds.backstop_mask)
mask.apply_mask_xds(self.get_header(), cbf_save, cbf_old)
init.reload()
for file in ["BLANK.cbf", "BKGINIT.cbf", "GAIN.cbf"]:
self._indxr_payload[file] = init.get_output_data_file(file)
if PhilIndex.params.xia2.settings.developmental.use_dials_spotfinder:
spotfinder = self.DialsSpotfinder()
for block in self._indxr_images:
spotfinder.add_spot_range(block[0], block[1])
spotfinder.run()
export = self.DialsExportSpotXDS()
export.set_input_data_file(
"observations.refl",
spotfinder.get_output_data_file("observations.refl"),
)
export.run()
for file in ["SPOT.XDS"]:
self._indxr_payload[file] = export.get_output_data_file(file)
else:
# next start to process these - then colspot
colspot = self.Colspot()
for file in (
"X-CORRECTIONS.cbf",
"Y-CORRECTIONS.cbf",
"BLANK.cbf",
"BKGINIT.cbf",
"GAIN.cbf",
):
colspot.set_input_data_file(file, self._indxr_payload[file])
colspot.set_data_range(first, last)
colspot.set_background_range(
self._indxr_images[0][0], self._indxr_images[0][1]
)
for block in self._indxr_images:
colspot.add_spot_range(block[0], block[1])
colspot.run()
for file in ["SPOT.XDS"]:
self._indxr_payload[file] = colspot.get_output_data_file(file)
def _index_prepare(self):
'''Prepare to do autoindexing - in XDS terms this will mean
calling xycorr, init and colspot on the input images.'''
# decide on images to work with
Debug.write('XDS INDEX PREPARE:')
Debug.write('Wavelength: %.6f' % self.get_wavelength())
Debug.write('Distance: %.2f' % self.get_distance())
if self._indxr_images == []:
_select_images_function = getattr(
self, '_index_select_images_%s' % (self._index_select_images))
wedges = _select_images_function()
for wedge in wedges:
self.add_indexer_image_wedge(wedge)
self.set_indexer_prepare_done(True)
all_images = self.get_matching_images()
first = min(all_images)
last = max(all_images)
# next start to process these - first xycorr
xycorr = self.Xycorr()
xycorr.set_data_range(first, last)
xycorr.set_background_range(self._indxr_images[0][0],
self._indxr_images[0][1])
from dxtbx.serialize.xds import to_xds
converter = to_xds(self.get_imageset())
xds_beam_centre = converter.detector_origin
xycorr.set_beam_centre(xds_beam_centre[0], xds_beam_centre[1])
for block in self._indxr_images:
xycorr.add_spot_range(block[0], block[1])
# FIXME need to set the origin here
xycorr.run()
for file in ['X-CORRECTIONS.cbf', 'Y-CORRECTIONS.cbf']:
self._indxr_payload[file] = xycorr.get_output_data_file(file)
# next start to process these - then init
if PhilIndex.params.xia2.settings.input.format.dynamic_shadowing:
imageset = self._indxr_imagesets[0]
masker = imageset.masker().format_class(
imageset.paths()[0]).get_goniometer_shadow_masker()
if masker is None:
# disable dynamic_shadowing
PhilIndex.params.xia2.settings.input.format.dynamic_shadowing = False
if PhilIndex.params.xia2.settings.input.format.dynamic_shadowing:
# find the region of the scan with the least predicted shadow
# to use for background determination in XDS INIT step
from dxtbx.serialize import dump
from dxtbx.datablock import DataBlock
imageset = self._indxr_imagesets[0]
xsweep = self._indxr_sweeps[0]
sweep_filename = os.path.join(
self.get_working_directory(),
'%s_datablock.json' % xsweep.get_name())
dump.datablock(DataBlock([imageset]), sweep_filename)
from xia2.Wrappers.Dials.ShadowPlot import ShadowPlot
shadow_plot = ShadowPlot()
shadow_plot.set_working_directory(self.get_working_directory())
auto_logfiler(shadow_plot)
shadow_plot.set_sweep_filename(sweep_filename)
shadow_plot.set_json_filename(
os.path.join(self.get_working_directory(),
'%s_shadow_plot.json' % shadow_plot.get_xpid()))
shadow_plot.run()
results = shadow_plot.get_results()
from scitbx.array_family import flex
fraction_shadowed = flex.double(results['fraction_shadowed'])
if flex.max(fraction_shadowed) == 0:
PhilIndex.params.xia2.settings.input.format.dynamic_shadowing = False
else:
scan_points = flex.double(results['scan_points'])
phi_width = self.get_phi_width()
scan = imageset.get_scan()
oscillation_range = scan.get_oscillation_range()
oscillation = scan.get_oscillation()
if self._background_images is not None:
bg_images = self._background_images
bg_range_deg = (scan.get_angle_from_image_index(
bg_images[0]),
scan.get_angle_from_image_index(
bg_images[1]))
bg_range_width = bg_range_deg[1] - bg_range_deg[0]
min_shadow = 100
best_bg_range = bg_range_deg
from libtbx.utils import frange
for bg_range_start in frange(flex.min(scan_points),
flex.max(scan_points) -
bg_range_width,
step=oscillation[1]):
bg_range_deg = (bg_range_start,
bg_range_start + bg_range_width)
sel = (scan_points >= bg_range_deg[0]) & (
scan_points <= bg_range_deg[1])
mean_shadow = flex.mean(fraction_shadowed.select(sel))
if mean_shadow < min_shadow:
min_shadow = mean_shadow
best_bg_range = bg_range_deg
self._background_images = (scan.get_image_index_from_angle(
best_bg_range[0]),
scan.get_image_index_from_angle(
best_bg_range[1]))
Debug.write('Setting background images: %s -> %s' %
self._background_images)
init = self.Init()
for file in ['X-CORRECTIONS.cbf', 'Y-CORRECTIONS.cbf']:
init.set_input_data_file(file, self._indxr_payload[file])
init.set_data_range(first, last)
if self._background_images:
init.set_background_range(self._background_images[0],
self._background_images[1])
else:
init.set_background_range(self._indxr_images[0][0],
self._indxr_images[0][1])
for block in self._indxr_images:
init.add_spot_range(block[0], block[1])
init.run()
# at this stage, need to (perhaps) modify the BKGINIT.cbf image
# to mark out the back stop
if PhilIndex.params.general.backstop_mask:
Debug.write('Applying mask to BKGINIT.pck')
# copy the original file
cbf_old = os.path.join(init.get_working_directory(), 'BKGINIT.cbf')
cbf_save = os.path.join(init.get_working_directory(),
'BKGINIT.sav')
shutil.copyfile(cbf_old, cbf_save)
# modify the file to give the new mask
from xia2.Toolkit.BackstopMask import BackstopMask
mask = BackstopMask(PhilIndex.params.general.backstop_mask)
mask.apply_mask_xds(self.get_header(), cbf_save, cbf_old)
init.reload()
for file in ['BLANK.cbf', 'BKGINIT.cbf', 'GAIN.cbf']:
self._indxr_payload[file] = init.get_output_data_file(file)
if PhilIndex.params.xia2.settings.developmental.use_dials_spotfinder:
spotfinder = self.DialsSpotfinder()
for block in self._indxr_images:
spotfinder.add_spot_range(block[0], block[1])
spotfinder.run()
export = self.DialsExportSpotXDS()
export.set_input_data_file(
'reflections.pickle',
spotfinder.get_output_data_file('reflections.pickle'))
export.run()
for file in ['SPOT.XDS']:
self._indxr_payload[file] = export.get_output_data_file(file)
else:
# next start to process these - then colspot
colspot = self.Colspot()
for file in [
'X-CORRECTIONS.cbf', 'Y-CORRECTIONS.cbf', 'BLANK.cbf',
'BKGINIT.cbf', 'GAIN.cbf'
]:
colspot.set_input_data_file(file, self._indxr_payload[file])
colspot.set_data_range(first, last)
colspot.set_background_range(self._indxr_images[0][0],
self._indxr_images[0][1])
for block in self._indxr_images:
colspot.add_spot_range(block[0], block[1])
colspot.run()
for file in ['SPOT.XDS']:
self._indxr_payload[file] = colspot.get_output_data_file(file)
# that should be everything prepared... all of the important
# files should be loaded into memory to be able to cope with
# integration happening somewhere else
return
