def _mosflm_integrate(self):
'''Perform the actual integration, based on the results of the
cell refinement or indexing (they have the equivalent form.)'''
refinr = self.get_integrater_refiner()
if not refinr.get_refiner_payload('mosflm_orientation_matrix'):
raise RuntimeError('unexpected situation in indexing')
lattice = refinr.get_refiner_lattice()
spacegroup_number = lattice_to_spacegroup(lattice)
mosaic = refinr.get_refiner_payload('mosaic')
beam = refinr.get_refiner_payload('beam')
distance = refinr.get_refiner_payload('distance')
matrix = refinr.get_refiner_payload('mosflm_orientation_matrix')
integration_params = refinr.get_refiner_payload(
'mosflm_integration_parameters')
if integration_params:
if 'separation' in integration_params:
self.set_integrater_parameter(
'mosflm', 'separation',
'%s %s' % tuple(integration_params['separation']))
if 'raster' in integration_params:
self.set_integrater_parameter(
'mosflm', 'raster',
'%d %d %d %d %d' % tuple(integration_params['raster']))
refinr.set_refiner_payload('mosflm_integration_parameters', None)
f = open(
os.path.join(self.get_working_directory(), 'xiaintegrate.mat'),
'w')
for m in matrix:
f.write(m)
f.close()
# then start the integration
integrater = MosflmIntegrate()
integrater.set_working_directory(self.get_working_directory())
auto_logfiler(integrater)
integrater.set_refine_profiles(self._mosflm_refine_profiles)
pname, xname, dname = self.get_integrater_project_info()
if pname is not None and xname is not None and dname is not None:
Debug.write('Harvesting: %s/%s/%s' % (pname, xname, dname))
harvest_dir = self.get_working_directory()
# harvest file name will be %s.mosflm_run_start_end % dname
temp_dname = '%s_%s' % \
(dname, self.get_integrater_sweep_name())
integrater.set_pname_xname_dname(pname, xname, temp_dname)
integrater.set_template(os.path.basename(self.get_template()))
integrater.set_directory(self.get_directory())
# check for ice - and if so, exclude (ranges taken from
# XDS documentation)
if self.get_integrater_ice() != 0:
Debug.write('Excluding ice rings')
integrater.set_exclude_ice(True)
# exclude specified resolution ranges
if len(self.get_integrater_excluded_regions()) != 0:
regions = self.get_integrater_excluded_regions()
Debug.write('Excluding regions: %s' % repr(regions))
integrater.set_exclude_regions(regions)
mask = standard_mask(self.get_detector())
for m in mask:
integrater.add_instruction(m)
integrater.set_input_mat_file('xiaintegrate.mat')
integrater.set_beam_centre(beam)
integrater.set_distance(distance)
integrater.set_space_group_number(spacegroup_number)
integrater.set_mosaic(mosaic)
if self.get_wavelength_prov() == 'user':
integrater.set_wavelength(self.get_wavelength())
parameters = self.get_integrater_parameters('mosflm')
integrater.update_parameters(parameters)
if self._mosflm_gain:
integrater.set_gain(self._mosflm_gain)
# check for resolution limits
if self._intgr_reso_high > 0.0:
integrater.set_d_min(self._intgr_reso_high)
if self._intgr_reso_low:
integrater.set_d_max(self._intgr_reso_low)
if PhilIndex.params.general.backstop_mask:
from xia2.Toolkit.BackstopMask import BackstopMask
mask = BackstopMask(PhilIndex.params.general.backstop_mask)
mask = mask.calculate_mask_mosflm(self.get_header())
integrater.set_mask(mask)
detector = self.get_detector()
detector_width, detector_height = detector[0].get_image_size_mm()
lim_x = 0.5 * detector_width
lim_y = 0.5 * detector_height
Debug.write('Scanner limits: %.1f %.1f' % (lim_x, lim_y))
integrater.set_limits(lim_x, lim_y)
integrater.set_fix_mosaic(self._mosflm_postref_fix_mosaic)
offset = self.get_frame_offset()
integrater.set_image_range(
(self._intgr_wedge[0] - offset, self._intgr_wedge[1] - offset))
try:
integrater.run()
except RuntimeError as e:
if 'integration failed: reason unknown' in str(e):
Chatter.write('Mosflm has failed in integration')
message = 'The input was:\n\n'
for input in integrater.get_all_input():
message += ' %s' % input
Chatter.write(message)
raise
FileHandler.record_log_file(
'%s %s %s %s mosflm integrate' % \
(self.get_integrater_sweep_name(),
pname, xname, dname),
integrater.get_log_file())
self._intgr_per_image_statistics = integrater.get_per_image_statistics(
)
self._mosflm_hklout = integrater.get_hklout()
Debug.write('Integration output: %s' % self._mosflm_hklout)
self._intgr_n_ref = integrater.get_nref()
# if a BGSIG error happened try not refining the
# profile and running again...
if integrater.get_bgsig_too_large():
if not self._mosflm_refine_profiles:
raise RuntimeError('BGSIG error with profiles fixed')
Debug.write('BGSIG error detected - try fixing profile...')
self._mosflm_refine_profiles = False
self.set_integrater_done(False)
return
if integrater.get_getprof_error():
Debug.write('GETPROF error detected - try fixing profile...')
self._mosflm_refine_profiles = False
self.set_integrater_done(False)
return
if (integrater.get_detector_gain_error()
and not (self.get_imageset().get_detector()[0].get_type()
== 'SENSOR_PAD')):
gain = integrater.get_suggested_gain()
if gain is not None:
self.set_integrater_parameter('mosflm', 'gain', gain)
self.set_integrater_export_parameter('mosflm', 'gain', gain)
if self._mosflm_gain:
Debug.write('GAIN updated to %f' % gain)
else:
Debug.write('GAIN found to be %f' % gain)
self._mosflm_gain = gain
self._mosflm_rerun_integration = True
if not self._mosflm_hklout:
raise RuntimeError('processing abandoned')
self._intgr_batches_out = integrater.get_batches_out()
mosaics = integrater.get_mosaic_spreads()
if mosaics and len(mosaics) > 0:
self.set_integrater_mosaic_min_mean_max(
min(mosaics),
sum(mosaics) / len(mosaics), max(mosaics))
else:
m = indxr.get_indexer_mosaic()
self.set_integrater_mosaic_min_mean_max(m, m, m)
# write the report for each image as .*-#$ to Chatter -
# detailed report will be written automagically to science...
Chatter.write(self.show_per_image_statistics())
Chatter.write('Mosaic spread: %.3f < %.3f < %.3f' % \
self.get_integrater_mosaic_min_mean_max())
# gather the statistics from the postrefinement
postref_result = integrater.get_postref_result()
# now write this to a postrefinement log
postref_log = os.path.join(self.get_working_directory(),
'postrefinement.log')
fout = open(postref_log, 'w')
fout.write('$TABLE: Postrefinement for %s:\n' % \
self._intgr_sweep_name)
fout.write('$GRAPHS: Missetting angles:A:1, 2, 3, 4: $$\n')
fout.write('Batch PhiX PhiY PhiZ $$ Batch PhiX PhiY PhiZ $$\n')
for image in sorted(postref_result):
phix = postref_result[image].get('phix', 0.0)
phiy = postref_result[image].get('phiy', 0.0)
phiz = postref_result[image].get('phiz', 0.0)
fout.write('%d %5.2f %5.2f %5.2f\n' % \
(image, phix, phiy, phiz))
fout.write('$$\n')
fout.close()
if self.get_integrater_sweep_name():
pname, xname, dname = self.get_integrater_project_info()
FileHandler.record_log_file('%s %s %s %s postrefinement' % \
(self.get_integrater_sweep_name(),
pname, xname, dname),
postref_log)
return self._mosflm_hklout
def exercise_mosflm_integrate():
if not have_dials_regression:
print "Skipping exercise_mosflm_integrate(): dials_regression not configured"
return
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
from xia2.Wrappers.Mosflm.MosflmIndex import MosflmIndex
from xia2.Wrappers.Mosflm.MosflmRefineCell import MosflmRefineCell
from xia2.Wrappers.Mosflm.MosflmIntegrate import MosflmIntegrate
# exercise basic indexing from two images
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
from xia2.Experts.FindImages import image2template_directory
templ, directory = image2template_directory(template %1)
indexer = MosflmIndex()
indexer.set_images((1,45))
indexer.set_directory(directory)
indexer.set_template(templ)
indexer.run()
refiner = MosflmRefineCell()
refiner.set_images(((1,3),(21,23), (43,45)))
refiner.set_input_mat_file("xiaindex.mat")
refiner.set_output_mat_file("xiarefine.mat")
refiner.set_directory(directory)
refiner.set_template(templ)
refiner.set_beam_centre(indexer.get_refined_beam_centre())
refiner.set_mosaic(
sum(indexer.get_mosaic_spreads())/len(indexer.get_mosaic_spreads()))
refiner.run()
#output = ''.join(refiner.get_all_output())
#print output
integrater = MosflmIntegrate()
integrater.set_image_range((1,45))
integrater.set_input_mat_file("xiaindex.mat")
#integrater.set_output_mat_file("xiarefine.mat")
integrater.set_directory(directory)
integrater.set_template(templ)
integrater.set_beam_centre(
tuple(float(x) for x in refiner.get_refined_beam_centre()))
integrater.set_distance(refiner.get_refined_distance())
integrater.set_mosaic(refiner.get_refined_mosaic())
integrater.set_space_group_number(197)
integrater.set_unit_cell(refiner.get_refined_unit_cell())
integrater.run()
hklout = integrater.get_hklout()
assert os.path.exists(hklout)
from iotbx.reflection_file_reader import any_reflection_file
miller_arrays = any_reflection_file(hklout).as_miller_arrays(
merge_equivalents=False)
for ma in miller_arrays:
assert ma.size() == 81011, ma.size()
assert len(miller_arrays) == 13, len(miller_arrays)
assert not integrater.get_bgsig_too_large()
assert not integrater.get_getprof_error()
assert integrater.get_batches_out() == (1, 45)
assert integrater.get_mosaic_spreads() == [
0.43, 0.42, 0.42, 0.41, 0.41, 0.41, 0.42, 0.42, 0.42, 0.42, 0.42, 0.42,
0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.39, 0.39, 0.39, 0.39, 0.39]
assert integrater.get_nref() == 81011
assert len(integrater.get_postref_result()) == 45
assert integrater.get_postref_result()[1] == {
'ovrl': 0.0, 'full': 507.0, 'dist': 158.6, 'ccx': -0.01, 'yscale': 1.0,
'sdrat': 7.5, 'tilt': 25.0, 'rsym': 0.027, 'bad': 0.0, 'i/sigi': 18.1,
'i/sigi_out': 1.6, 'twist': 13.0, 'resid': 0.021, 'wresid': 1.1,
'part': 1309.0, 'nsym': 18.0, 'neg': 158.0, 'ccy': -0.01, 'ccom': -0.01,
'toff': 0.0, 'roff': 0.0}
assert integrater.get_residuals() == [
1.1, 0.9, 1.0, 1.0, 0.8, 0.9, 1.0, 0.8, 0.9, 0.9, 0.9, 0.9, 1.0, 1.0, 1.0,
0.9, 0.9, 0.9, 0.9, 0.8, 1.0, 0.9, 0.8, 0.9, 1.0, 0.8, 1.0, 0.9, 0.8, 0.8,
0.9, 0.9, 0.9, 0.9, 0.9, 1.0, 0.8, 0.9, 1.0, 0.7, 0.8, 0.9, 0.8, 0.9, 1.0]
assert integrater.get_spot_status() \
== 'ooooooooooooooooooooooooooooooooooooooooooooo'
def _mosflm_integrate(self):
'''Perform the actual integration, based on the results of the
cell refinement or indexing (they have the equivalent form.)'''
refinr = self.get_integrater_refiner()
if not refinr.get_refiner_payload('mosflm_orientation_matrix'):
raise RuntimeError, 'unexpected situation in indexing'
lattice = refinr.get_refiner_lattice()
spacegroup_number = lattice_to_spacegroup(lattice)
mosaic = refinr.get_refiner_payload('mosaic')
beam = refinr.get_refiner_payload('beam')
distance = refinr.get_refiner_payload('distance')
matrix = refinr.get_refiner_payload('mosflm_orientation_matrix')
integration_params = refinr.get_refiner_payload(
'mosflm_integration_parameters')
if integration_params:
if 'separation' in integration_params:
self.set_integrater_parameter(
'mosflm', 'separation',
'%s %s' % tuple(integration_params['separation']))
if 'raster' in integration_params:
self.set_integrater_parameter(
'mosflm', 'raster',
'%d %d %d %d %d' % tuple(integration_params['raster']))
refinr.set_refiner_payload('mosflm_integration_parameters', None)
f = open(os.path.join(self.get_working_directory(),
'xiaintegrate.mat'), 'w')
for m in matrix:
f.write(m)
f.close()
# then start the integration
integrater = MosflmIntegrate()
integrater.set_working_directory(self.get_working_directory())
auto_logfiler(integrater)
integrater.set_refine_profiles(self._mosflm_refine_profiles)
pname, xname, dname = self.get_integrater_project_info()
if pname is not None and xname is not None and dname is not None:
Debug.write('Harvesting: %s/%s/%s' % (pname, xname, dname))
harvest_dir = self.get_working_directory()
# harvest file name will be %s.mosflm_run_start_end % dname
temp_dname = '%s_%s' % \
(dname, self.get_integrater_sweep_name())
integrater.set_pname_xname_dname(pname, xname, temp_dname)
integrater.set_template(os.path.basename(self.get_template()))
integrater.set_directory(self.get_directory())
# check for ice - and if so, exclude (ranges taken from
# XDS documentation)
if self.get_integrater_ice() != 0:
Debug.write('Excluding ice rings')
integrater.set_exclude_ice(True)
# exclude specified resolution ranges
if len(self.get_integrater_excluded_regions()) != 0:
regions = self.get_integrater_excluded_regions()
Debug.write('Excluding regions: %s' % `regions`)
integrater.set_exclude_regions(regions)
mask = standard_mask(self.get_detector())
for m in mask:
integrater.add_instruction(m)
integrater.set_input_mat_file('xiaintegrate.mat')
integrater.set_beam_centre(beam)
integrater.set_distance(distance)
integrater.set_space_group_number(spacegroup_number)
integrater.set_mosaic(mosaic)
if self.get_wavelength_prov() == 'user':
integrater.set_wavelength(self.get_wavelength())
parameters = self.get_integrater_parameters('mosflm')
integrater.update_parameters(parameters)
if self._mosflm_gain:
integrater.set_gain(self._mosflm_gain)
# check for resolution limits
if self._intgr_reso_high > 0.0:
integrater.set_d_min(self._intgr_reso_high)
if self._intgr_reso_low:
integrater.set_d_max(self._intgr_reso_low)
if PhilIndex.params.general.backstop_mask:
from xia2.Toolkit.BackstopMask import BackstopMask
mask = BackstopMask(PhilIndex.params.general.backstop_mask)
mask = mask.calculate_mask_mosflm(self.get_header())
integrater.set_mask(mask)
detector = self.get_detector()
detector_width, detector_height = detector[0].get_image_size_mm()
lim_x = 0.5 * detector_width
lim_y = 0.5 * detector_height
Debug.write('Scanner limits: %.1f %.1f' % (lim_x, lim_y))
integrater.set_limits(lim_x, lim_y)
integrater.set_fix_mosaic(self._mosflm_postref_fix_mosaic)
offset = self.get_frame_offset()
integrater.set_image_range(
(self._intgr_wedge[0] - offset, self._intgr_wedge[1] - offset))
try:
integrater.run()
except RuntimeError, e:
if 'integration failed: reason unknown' in str(e):
Chatter.write('Mosflm has failed in integration')
message = 'The input was:\n\n'
for input in integrater.get_all_input():
message += ' %s' % input
Chatter.write(message)
raise
def exercise_mosflm_integrate():
if not have_dials_regression:
print "Skipping exercise_mosflm_integrate(): dials_regression not configured"
return
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
from xia2.Wrappers.Mosflm.MosflmIndex import MosflmIndex
from xia2.Wrappers.Mosflm.MosflmRefineCell import MosflmRefineCell
from xia2.Wrappers.Mosflm.MosflmIntegrate import MosflmIntegrate
# exercise basic indexing from two images
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
from xia2.Experts.FindImages import image2template_directory
templ, directory = image2template_directory(template %1)
indexer = MosflmIndex()
indexer.set_images((1,45))
indexer.set_directory(directory)
indexer.set_template(templ)
indexer.run()
refiner = MosflmRefineCell()
refiner.set_images(((1,3),(21,23), (43,45)))
refiner.set_input_mat_file("xiaindex.mat")
refiner.set_output_mat_file("xiarefine.mat")
refiner.set_directory(directory)
refiner.set_template(templ)
refiner.set_beam_centre(indexer.get_refined_beam_centre())
refiner.set_mosaic(
sum(indexer.get_mosaic_spreads())/len(indexer.get_mosaic_spreads()))
refiner.run()
#output = ''.join(refiner.get_all_output())
#print output
integrater = MosflmIntegrate()
integrater.set_image_range((1,45))
integrater.set_input_mat_file("xiaindex.mat")
#integrater.set_output_mat_file("xiarefine.mat")
integrater.set_directory(directory)
integrater.set_template(templ)
integrater.set_beam_centre(
tuple(float(x) for x in refiner.get_refined_beam_centre()))
integrater.set_distance(refiner.get_refined_distance())
integrater.set_mosaic(refiner.get_refined_mosaic())
integrater.set_space_group_number(197)
integrater.set_unit_cell(refiner.get_refined_unit_cell())
integrater.run()
hklout = integrater.get_hklout()
assert os.path.exists(hklout)
from iotbx.reflection_file_reader import any_reflection_file
miller_arrays = any_reflection_file(hklout).as_miller_arrays(
merge_equivalents=False)
for ma in miller_arrays:
assert ma.size() == 81011, ma.size()
assert len(miller_arrays) == 13, len(miller_arrays)
assert not integrater.get_bgsig_too_large()
assert not integrater.get_getprof_error()
assert integrater.get_batches_out() == (1, 45)
assert integrater.get_mosaic_spreads() == [
0.43, 0.42, 0.42, 0.41, 0.41, 0.41, 0.42, 0.42, 0.42, 0.42, 0.42, 0.42,
0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.39, 0.39, 0.39, 0.39, 0.39]
assert integrater.get_nref() == 81011
assert len(integrater.get_postref_result()) == 45
assert integrater.get_postref_result()[1] == {
'ovrl': 0.0, 'full': 507.0, 'dist': 158.6, 'ccx': -0.01, 'yscale': 1.0,
'sdrat': 7.5, 'tilt': 25.0, 'rsym': 0.027, 'bad': 0.0, 'i/sigi': 18.1,
'i/sigi_out': 1.6, 'twist': 13.0, 'resid': 0.021, 'wresid': 1.1,
'part': 1309.0, 'nsym': 18.0, 'neg': 158.0, 'ccy': -0.01, 'ccom': -0.01,
'toff': 0.0, 'roff': 0.0}
assert integrater.get_residuals() == [
1.1, 0.9, 1.0, 1.0, 0.8, 0.9, 1.0, 0.8, 0.9, 0.9, 0.9, 0.9, 1.0, 1.0, 1.0,
0.9, 0.9, 0.9, 0.9, 0.8, 1.0, 0.9, 0.8, 0.9, 1.0, 0.8, 1.0, 0.9, 0.8, 0.8,
0.9, 0.9, 0.9, 0.9, 0.9, 1.0, 0.8, 0.9, 1.0, 0.7, 0.8, 0.9, 0.8, 0.9, 1.0]
assert integrater.get_spot_status() \
== 'ooooooooooooooooooooooooooooooooooooooooooooo'