def executeCollection(self, *args):
self.params = args[0]
self.beamline_setup = hwr.getHardwareObject("beamline-setup")
self.lims_client_hwobj = self.beamline_setup.lims_client_hwobj
self.collect_hwobj = self.beamline_setup.collect_hwobj
self.diffractometer_hwobj = self.beamline_setup.diffractometer_hwobj
self.shape_history = self.beamline_setup.shape_history_hwobj
self.session = self.beamline_setup.session_hwobj
self.acq = qmo.Acquisition()
self.acq.acquisition_parameters.collect_agent = qme.COLLECTION_ORIGIN.MXCUBE
#self.acq.path_template = queue_model_objects.PathTemplate()
#self.acq.path_template = '/home/mikel/Desktop/mxdatadir/mxdata'#copy.deepcopy(self._path_template)
self.acq.path_template = self.beamline_setup.get_default_path_template()
self.acq.acquisition_parameters.centred_position = None
self.acq.acquisition_parameters.energy = 12.3894 #float(self.params['parameters[energy][value]'])
self.acq.acquisition_parameters.osc_range = 1.0 #float(self.params['parameters[osc_range][value]'])
self.acq.acquisition_parameters.osc_start = 0.0 #float(self.params['parameters[osc_start][value]'])
self.acq.acquisition_parameters.exp_time = 10.0 #float(self.params['parameters[exp_time][value]'])
self.acq.acquisition_parameters.num_images = 1 #float(self.params['parameters[num_images][value]'])
self.acq.acquisition_parameters.resolution = 2.498 #float(self.params['parameters[resolution][value]'])
self.acq.acquisition_parameters.transmission = 100.0# float(self.params['parameters[transmission][value]'])
self.acq.acquisition_parameters.take_snapshots = False
self.acq.path_template.directory = '/data/data1/visitor/mx20110291/20150814/RAW_DATA'
self.acq.path_template.process_directory = '/data/data1/visitor/mx20110291/20150814/PROCESSED_DATA'
self.acq.path_template.run_number = 1
self.acq.path_template.prefix = 'mx20110291'
self.sample = qmo.Sample()
self.dc = qmo.DataCollection([self.acq], self.sample.crystals[0], self.sample.processing_parameters)
self.dc.set_name('aTest')
self.dc.set_number(0)
self.dc.experiment_type = qme.EXPERIMENT_TYPE.NATIVE
self.fileinfo = {'directory':'/data/data1/visitor/mx20110291/20150814/RAW_DATA', 'prefix':'mx20110291', 'run_number': 1, 'process_directory': '/data/data1/visitor/mx20110291/20150814/PROCESSED_DATA'}
self.param_list = qmo.to_collect_dict(self.dc, self.session, self.sample)
print "###################################"
print "###################################"
print "###################################"
print self.param_list
print "###################################"
print "###################################"
print self.acq.acquisition_parameters
#update with data sent from client
#self.bl9113 = hwr.getObjectByRole("collect")
#self.bl9113.collect(COLLECTION_ORIGIN_STR.MXCUBE,self.param_list)
#or..
self.collect_hwobj.collect(COLLECTION_ORIGIN_STR.MXCUBE,self.param_list)
def execute_task(self, sample):
#All this should be in queue_entry level
group_data = {'sessionId': self._session_hwobj.session_id,
'experimentType': 'OSC'}
gid = self._beamline_setup_hwobj.lims_client_hwobj.\
_store_data_collection_group(group_data)
sample.lims_group_id = gid
task_list = self._create_task(sample, None)
task_list[0].lims_group_id = gid
param_list = queue_model_objects.to_collect_dict(task_list[0], \
self._session_hwobj, sample, None)
self._beamline_setup_hwobj.collect_hwobj.collect(\
queue_model_enumerables.COLLECTION_ORIGIN_STR.MXCUBE, param_list)
def execute_task(self, sample):
#All this should be in queue_entry level
group_data = {
'sessionId': self._session_hwobj.session_id,
'experimentType': 'OSC'
}
gid = self._beamline_setup_hwobj.lims_client_hwobj.\
_store_data_collection_group(group_data)
sample.lims_group_id = gid
task_list = self._create_task(sample, None)
task_list[0].lims_group_id = gid
param_list = queue_model_objects.to_collect_dict(task_list[0], \
self._session_hwobj, sample, None)
self._beamline_setup_hwobj.collect_hwobj.collect(\
queue_model_enumerables.COLLECTION_ORIGIN_STR.MXCUBE, param_list)
def collect_dc(self, dc, list_item):
log = logging.getLogger("user_level_log")
if self.collect_hwobj:
acq_1 = dc.acquisitions[0]
cpos = acq_1.acquisition_parameters.centred_position
sample = self.get_data_model().get_parent().get_parent()
try:
if dc.experiment_type is EXPERIMENT_TYPE.HELICAL:
acq_1, acq_2 = (dc.acquisitions[0], dc.acquisitions[1])
# self.collect_hwobj.getChannelObject("helical").setValue(1) #JN TMP disable, need to fix SPEC
start_cpos = acq_1.acquisition_parameters.centred_position
end_cpos = acq_2.acquisition_parameters.centred_position
dc.lims_end_pos_id = self.lims_client_hwobj.\
store_centred_position(end_cpos)
helical_oscil_pos = {'1': start_cpos.as_dict(), '2': end_cpos.as_dict()}
log.info('Helical_pos value is ' + str(helical_oscil_pos))
# self.collect_hwobj.getChannelObject('helical_pos').setValue(helical_oscil_pos) #JN TMP disable, need to fix SPEC
msg = "Helical data collection, moving to start position"
log.info(msg)
log.info("Moving sample to given position ...")
list_item.setText(1, "Moving sample")
else:
#self.collect_hwobj.getChannelObject("helical").setValue(0)
pass
empty_cpos = queue_model_objects.CentredPosition()
if cpos != empty_cpos:
log.info("Moving sample to given position ...")
list_item.setText(1, "Moving sample")
self.shape_history.select_shape_with_cpos(cpos)
self.centring_task = self.diffractometer_hwobj.\
moveToCentredPosition(cpos)
self.centring_task.get()
else:
pos_dict = self.diffractometer_hwobj.getPositions()
cpos = queue_model_objects.CentredPosition(pos_dict)
snapshot = self.shape_history.get_snapshot([])
acq_1.acquisition_parameters.centred_position = cpos
acq_1.acquisition_parameters.centred_position.snapshot_image = snapshot
dc.lims_start_pos_id = self.lims_client_hwobj.store_centred_position(cpos)
param_list = queue_model_objects.to_collect_dict(dc, self.session, sample)
self.collect_task = self.collect_hwobj.\
collect(COLLECTION_ORIGIN_STR.MXCUBE, param_list)
self.collect_task.get()
if 'collection_id' in param_list[0]:
dc.id = param_list[0]['collection_id']
dc.acquisitions[0].path_template.xds_dir = param_list[0]['xds_dir']
except gevent.GreenletExit:
#log.warning("Collection stopped by user.")
list_item.setText(1, 'Stopped')
raise QueueAbortedException('queue stopped by user', self)
except Exception as ex:
print traceback.print_exc()
raise QueueExecutionException(ex.message, self)
else:
log.error("Could not call the data collection routine," +\
" check the beamline configuration")
list_item.setText(1, 'Failed')
msg = "Could not call the data collection" +\
" routine, check the beamline configuration"
raise QueueExecutionException(msg, self)
