log_to_ispyb([self.integration_id_anom, self.integration_id_noanom],
'Indexing',
'Successful',
'res cutoff finished in {0}s'.format(self.stats['first_res_cutoff']))
with open(self.log_file_path, 'w') as f:
json.dump(self.stats, f)
resolution = self.first_res_cutoff.dataOutput.res
# for the generate w/ and w/out anom we have to specify where
# the first XDS plugin run took place
xds_run_directory = os.path.abspath(self.xds_first.dataOutput.xds_run_directory.value)
EDVerbose.screen("the xds run took place in {0}".format(xds_run_directory))
generate_input = XSDataXdsGenerateInput()
generate_input.resolution = resolution
generate_input.previous_run_dir = XSDataString(xds_run_directory)
self.generate.dataInput = generate_input
log_to_ispyb([self.integration_id_anom, self.integration_id_noanom],
'Scaling', 'Launched', 'start of anom/noanom generation')
self.DEBUG('STARTING anom/noanom generation')
t0=time.time()
self.generate.executeSynchronous()
self.stats['anom/noanom_generation'] = time.time()-t0
with open(self.log_file_path, 'w') as f:
json.dump(self.stats, f)
def process(self, _edObject = None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlAutoproc.process")
# first XDS plugin run with supplied XDS file
EDVerbose.screen("First XDS run...")
self.xds_first.executeSynchronous()
if self.xds_first.isFailure():
EDVerbose.ERROR('first XDS run failed')
self.setFailure()
return
EDVerbose.screen("First XDS run successfully completed")
# apply the first res cutoff with the res extracted from the first XDS run
EDVerbose.screen("First resolution cutoff")
xdsresult = self.xds_first.dataOutput
res_cutoff_in = XSDataResCutoff()
res_cutoff_in.xds_res = xdsresult
res_cutoff_in.completeness_entries = xdsresult.completeness_entries
#XXX: remove from the data model as it is just pass-through?
res_cutoff_in.total_completeness = xdsresult.total_completeness
self.first_res_cutoff.dataInput = res_cutoff_in
self.first_res_cutoff.executeSynchronous()
if self.first_res_cutoff.isFailure():
EDVerbose.ERROR("res cutoff failed")
self.setFailure()
return
EDVerbose.screen("First resolution cutoff successfully completed")
resolution = self.first_res_cutoff.dataOutput.res
# for the generate w/ and w/out anom we have to specify where
# the first XDS plugin run took place
xds_run_directory = os.path.abspath(self.xds_first.dataOutput.xds_run_directory.value)
EDVerbose.screen("the xds run took place in {}".format(xds_run_directory))
generate_input = XSDataXdsGenerateInput()
generate_input.resolution = resolution
generate_input.previous_run_dir = XSDataString(xds_run_directory)
self.generate.dataInput = generate_input
self.generate.executeSynchronous()
if self.generate.isFailure():
EDVerbose.ERROR('generating w/ and w/out anom failed')
self.setFailure()
return
# we can now use the xds output parser on the two correct.lp
# files, w/ and w/out anom
parse_anom_input = XSDataXdsOutputFile()
parse_anom_input.correct_lp = XSDataFile()
parse_anom_input.correct_lp.path = self.generate.dataOutput.correct_lp_anom
self.parse_xds_anom.dataInput = parse_anom_input
self.parse_xds_anom.executeSynchronous()
if self.parse_xds_anom.isFailure():
EDVerbose.ERROR('parsing the xds generated w/ anom failed')
self.setFailure()
return
# now the other one w/out anom
parse_noanom_input = XSDataXdsOutputFile()
parse_noanom_input.correct_lp = XSDataFile()
parse_noanom_input.correct_lp.path = self.generate.dataOutput.correct_lp_no_anom
self.parse_xds_noanom.dataInput = parse_noanom_input
self.parse_xds_noanom.executeSynchronous()
if self.parse_xds_noanom.isFailure():
EDVerbose.ERROR('parsing the xds generated w/ anom failed')
self.setFailure()
return
# we now can apply the res cutoff on the anom and no anom
# outputs. Note that this is not done in parallel, like the
# xds parsing
# XXX completeness_cutoff/res_override and isig_cutoff still
# missing
res_cutoff_anom_in = XSDataResCutoff()
res_cutoff_anom_in.xds_res = self.parse_xds_anom.dataOutput
self.res_cutoff_anom.dataInput = res_cutoff_anom_in
self.res_cutoff_anom.executeSynchronous()
if self.res_cutoff_anom.isFailure():
EDVerbose.ERROR('res cutoff for anom data failed')
# same for non anom
res_cutoff_noanom_in = XSDataResCutoff()
res_cutoff_noanom_in.xds_res = self.parse_xds_noanom.dataOutput
self.res_cutoff_noanom.dataInput = res_cutoff_noanom_in
self.res_cutoff_noanom.executeSynchronous()
if self.res_cutoff_noanom.isFailure():
EDVerbose.ERROR('res cutoff for non anom data failed')
# now we just have to run XScale to generate w/ and w/out
# anom, merged and unmerged
# We use another control plugin for that to isolate the whole thing
# if not self.res_cutoff_anom.isFailure():
xscale_anom_in = XSDataXscaleInput()
input_file = XSDataXscaleInputFile()
input_file.path = self.generate.dataOutput.hkl_anom
input_file.res = self.res_cutoff_anom.dataOutput.res
xscale_anom_in.xds_files = [input_file]
xscale_anom_in.unit_cell_constants = self.parse_xds_anom.dataOutput.unit_cell_constants
xscale_anom_in.sg_number = self.parse_xds_anom.dataOutput.sg_number
xscale_anom_in.bins = self.res_cutoff_anom.bins
self.xscale_anom.dataInput = xscale_anom_in
self.xscale_anom.executeSynchronous()
if self.xscale_anom.isFailure():
EDVerbose.ERROR('xscale anom/merge generation failed')
# same for non anom code path
#if not self.res_cutoff_noanom.isFailure():
xscale_noanom_in = XSDataXscaleInput()
input_file = XSDataXscaleInputFile()
input_file.path = self.generate.dataOuput.hkl_anom
input_file.res = self.res_cutoff_anom.dataOutput.res
xscale_noanom_in.xds_files = [input_file]
xscale_noanom_in.unit_cell_constants = self.parse_xds_noanom.dataOutput.unit_cell_constants
xscale_noanom_in.sg_number = self.parse_xds_noanom.dataOutput.sg_number
xscale_noanom_in.bins = self.res_cutoff_noanom.bins
self.xscale_noanom.dataInput = xscale_noanom_in
self.xscale_noanom.executeSynchronous()
if self.xscale_noanom.isFailure():
EDVerbose.ERROR('xscale anom/merge generation failed')
[self.integration_id_anom, self.integration_id_noanom],
'Indexing', 'Successful', 'res cutoff finished in {0}s'.format(
self.stats['first_res_cutoff']))
with open(self.log_file_path, 'w') as f:
json.dump(self.stats, f)
resolution = self.first_res_cutoff.dataOutput.res
# for the generate w/ and w/out anom we have to specify where
# the first XDS plugin run took place
xds_run_directory = os.path.abspath(
self.xds_first.dataOutput.xds_run_directory.value)
EDVerbose.screen(
"the xds run took place in {0}".format(xds_run_directory))
generate_input = XSDataXdsGenerateInput()
generate_input.resolution = resolution
generate_input.previous_run_dir = XSDataString(xds_run_directory)
self.generate.dataInput = generate_input
log_to_ispyb([self.integration_id_anom, self.integration_id_noanom],
'Scaling', 'Launched', 'start of anom/noanom generation')
self.DEBUG('STARTING anom/noanom generation')
t0 = time.time()
self.generate.executeSynchronous()
self.stats['anom/noanom_generation'] = time.time() - t0
with open(self.log_file_path, 'w') as f:
json.dump(self.stats, f)