def _create_task(self, sample, shape):
"""Creates tasks based on selected grids
:param sample: selected sample object
:type sample: SampleQueueItem
:param shape: selected shape
:type shape: Qt4_GraphicsLib.GraphicsItem
"""
tasks = []
selected_grids = self.get_selected_grids()
if len(selected_grids) == 0:
selected_grids.append(self._graphics_manager_hwobj.\
update_auto_grid())
for grid in selected_grids:
grid.set_snapshot(self._graphics_manager_hwobj.\
get_scene_snapshot(grid))
grid_properties = grid.get_properties()
acq = self._create_acq(sample)
acq.acquisition_parameters.centred_position = \
grid.get_centred_position()
acq.acquisition_parameters.mesh_range = \
[grid_properties["dx_mm"], grid_properties["dy_mm"]]
acq.acquisition_parameters.num_lines = \
grid_properties["num_lines"]
acq.acquisition_parameters.num_images = \
grid_properties["num_lines"] * \
grid_properties["num_images_per_line"]
grid.set_osc_range(acq.acquisition_parameters.osc_range)
processing_parameters = deepcopy(self._processing_parameters)
dc = queue_model_objects.DataCollection([acq],
sample.crystals[0],
processing_parameters)
dc.set_name(acq.path_template.get_prefix())
dc.set_number(acq.path_template.run_number)
dc.set_experiment_type(EXPERIMENT_TYPE.MESH)
dc.set_requires_centring(False)
dc.grid = grid
exp_type = str(self._advanced_methods_widget.\
method_combo.currentText())
if exp_type == "MeshScan":
dc.run_processing_parallel = "MeshScan"
tasks.append(dc)
elif exp_type == "XrayCentering":
xray_centering = queue_model_objects.XrayCentering(\
dc, sample.crystals[0])
dc.run_processing_parallel = "XrayCentering"
tasks.append(xray_centering)
self._path_template.run_number += 1
return tasks
def _create_dc(task):
"""
Creates a data collection model and its corresponding queue entry from
a dict with collection parameters.
:param dict task: Collection parameters
:returns: The tuple (model, entry)
:rtype: Tuple
"""
dc_model = qmo.DataCollection()
dc_entry = qe.DataCollectionQueueEntry(Mock(), dc_model)
return dc_model, dc_entry
def create_dc(self,
sample,
run_number=None,
start_image=None,
num_images=None,
osc_start=None,
sc=None,
cpos=None,
inverse_beam=False):
"""
Descript. :
"""
tasks = []
# Acquisition for start position
acq = self._create_acq(sample)
if run_number:
acq.path_template.run_number = run_number
if start_image:
acq.acquisition_parameters.first_image = start_image
acq.path_template.start_num = start_image
if num_images:
acq.acquisition_parameters.num_images = num_images
acq.path_template.num_files = num_images
if osc_start:
acq.acquisition_parameters.osc_start = osc_start
if inverse_beam:
acq.acquisition_parameters.inverse_beam = False
acq.acquisition_parameters.centred_position = cpos
processing_parameters = copy.deepcopy(self._processing_parameters)
dc = queue_model_objects.DataCollection([acq], sample.crystals[0],
processing_parameters)
dc.set_name(acq.path_template.get_prefix())
dc.set_number(acq.path_template.run_number)
dc.experiment_type = queue_model_enumerables.EXPERIMENT_TYPE.NATIVE
dc.run_processing_after = self._processing_widget.processing_widget.\
run_processing_after_cbox.isChecked()
dc.run_processing_parallel = self._processing_widget.processing_widget.\
run_processing_parallel_cbox.isChecked() and \
acq.acquisition_parameters.num_images > 19
tasks.append(dc)
return tasks
def _create_task(self, sample, shape):
data_collections = []
for shape in self.get_selected_lines():
snapshot = self._graphics_manager_hwobj.get_scene_snapshot(shape)
# Acquisition for start position
start_acq = self._create_acq(sample)
start_graphical_point, end_graphical_point = \
shape.get_graphical_points()
start_acq.acquisition_parameters.\
centred_position = copy.deepcopy(start_graphical_point.get_centred_position())
start_acq.acquisition_parameters.centred_position.\
snapshot_image = snapshot
start_acq.path_template.suffix = self._session_hwobj.suffix
# Add another acquisition for the end position
end_acq = self._create_acq(sample)
end_acq.acquisition_parameters.\
centred_position = copy.deepcopy(end_graphical_point.get_centred_position())
end_acq.acquisition_parameters.centred_position.\
snapshot_image = snapshot
end_acq.path_template.suffix = self._session_hwobj.suffix
processing_parameters = copy.deepcopy(self._processing_parameters)
dc = queue_model_objects.DataCollection([start_acq, end_acq],
sample.crystals[0],
processing_parameters)
dc.set_name(start_acq.path_template.get_prefix())
dc.set_number(start_acq.path_template.run_number)
dc.set_experiment_type(EXPERIMENT_TYPE.HELICAL)
dc.set_requires_centring(False)
dc.run_processing_after = self._processing_widget.processing_widget.\
run_processing_after_cbox.isChecked()
dc.run_processing_parallel = self._processing_widget.processing_widget.\
run_processing_parallel_cbox.isChecked()
data_collections.append(dc)
self._path_template.run_number += 1
return data_collections
def _create_task(self, sample, shape):
"""
Descript. :
"""
data_collections = []
selected_grids = self.get_selected_grids()
if len(selected_grids) == 0:
selected_grids.append(self._graphics_manager_hwobj.\
create_automatic_grid())
for shape in selected_grids:
shape.set_snapshot(self._graphics_manager_hwobj.\
get_scene_snapshot(shape))
grid_properties = shape.get_properties()
acq = self._create_acq(sample)
acq.acquisition_parameters.centred_position = \
shape.get_centred_position()
acq.acquisition_parameters.mesh_range = \
[grid_properties["dx_mm"], grid_properties["dy_mm"]]
acq.acquisition_parameters.num_lines = \
grid_properties["num_lines"]
acq.acquisition_parameters.num_images = \
grid_properties["num_lines"] * \
grid_properties["num_images_per_line"]
processing_parameters = deepcopy(self._processing_parameters)
dc = queue_model_objects.DataCollection([acq], sample.crystals[0],
processing_parameters)
dc.set_name(acq.path_template.get_prefix())
dc.set_number(acq.path_template.run_number)
dc.set_experiment_type(EXPERIMENT_TYPE.MESH)
exp_type = str(self._advanced_methods_widget.method_combo.\
currentText())
advanced = queue_model_objects.Advanced(exp_type, dc, shape,
sample.crystals[0])
data_collections.append(advanced)
self._path_template.run_number += 1
return data_collections
def _create_task(self, sample, shape):
data_collections = []
if isinstance(shape, shape_history.Line):
if shape.get_qub_objects() is not None:
snapshot = self._shape_history.get_snapshot(
shape.get_qub_objects())
else:
snapshot = self._shape_history.get_snapshot([])
# Acquisition for start position
start_acq = self._create_acq(sample)
start_acq.acquisition_parameters.\
centred_position = copy.deepcopy(shape.start_cpos)
start_acq.acquisition_parameters.centred_position.\
snapshot_image = snapshot
start_acq.path_template.suffix = self._session_hwobj.suffix
# Add another acquisition for the end position
end_acq = self._create_acq(sample)
end_acq.acquisition_parameters.\
centred_position = shape.end_cpos
end_acq.acquisition_parameters.centred_position.\
snapshot_image = snapshot
end_acq.path_template.suffix = self._session_hwobj.suffix
processing_parameters = copy.deepcopy(self._processing_parameters)
dc = qmo.DataCollection([start_acq, end_acq], sample.crystals[0],
processing_parameters)
dc.set_name(start_acq.path_template.get_prefix())
dc.set_number(start_acq.path_template.run_number)
dc.experiment_type = EXPERIMENT_TYPE.HELICAL
data_collections.append(dc)
self._path_template.run_number += 1
return data_collections
def _create_task(self, sample, shape):
"""
Descript. :
"""
data_collections = []
selected_grid_info = None
treewidget_item = self.mesh_widget.mesh_treewidget.selectedItem()
if treewidget_item is not None:
drawing_mgr = self.__list_items[treewidget_item]
key = str(treewidget_item.text(0))
selected_grid_info = drawing_mgr._get_grid(key)[0]
if selected_grid_info:
snapshot = self._graphics_manager.get_snapshot([])
acq = self._create_acq(sample)
cpoint = selected_grid_info.get("centred_point")
#cpos = self._beamline_setup_hwobj.diffractometer_hwobj.convert_from_obj_to_name(cpoint)
acq.acquisition_parameters.centred_position = cpoint
acq.acquisition_parameters.mesh_steps = [
selected_grid_info.get("steps_x"),
selected_grid_info.get("steps_y")
]
acq.acquisition_parameters.mesh_range = [
selected_grid_info.get("dy_mm"),
selected_grid_info.get("dx_mm")
]
acq.acquisition_parameters.num_images = selected_grid_info.get("steps_x") * \
selected_grid_info.get("steps_y")
processing_parameters = deepcopy(self._processing_parameters)
dc = queue_model_objects.DataCollection([acq], sample.crystals[0],
processing_parameters)
dc.set_name(acq.path_template.get_prefix())
dc.set_number(acq.path_template.run_number)
dc.set_grid_id(selected_grid_info.get("id"))
dc.set_experiment_type(EXPERIMENT_TYPE.MESH)
data_collections.append(dc)
self._path_template.run_number += 1
return data_collections
def _create_task(self, sample, shape):
data_collections = []
if isinstance(shape, graphics_manager.GraphicsItemLine):
snapshot = self._graphics_manager_hwobj.get_snapshot(shape)
# Acquisition for start position
start_acq = self._create_acq(sample)
start_acq.acquisition_parameters.\
centred_position = copy.deepcopy(shape.cp_start.centred_position)
start_acq.acquisition_parameters.centred_position.\
snapshot_image = snapshot
start_acq.path_template.suffix = self._session_hwobj.suffix
# Add another acquisition for the end position
end_acq = self._create_acq(sample)
end_acq.acquisition_parameters.\
centred_position = shape.cp_end.centred_position
end_acq.acquisition_parameters.centred_position.\
snapshot_image = snapshot
end_acq.path_template.suffix = self._session_hwobj.suffix
processing_parameters = copy.deepcopy(self._processing_parameters)
dc = queue_model_objects.DataCollection([start_acq, end_acq],
sample.crystals[0],
processing_parameters)
dc.set_name(start_acq.path_template.get_prefix())
dc.set_number(start_acq.path_template.run_number)
dc.experiment_type = EXPERIMENT_TYPE.HELICAL
data_collections.append(dc)
self._path_template.run_number += 1
return data_collections
def _create_dc_from_grid(self, sample, grid=None):
if grid is None:
grid = self._graphics_manager_hwobj.get_auto_grid()
grid.set_snapshot(self._graphics_manager_hwobj.\
get_scene_snapshot(grid))
grid_properties = grid.get_properties()
acq = self._create_acq(sample)
acq.acquisition_parameters.centred_position = \
grid.get_centred_position()
acq.acquisition_parameters.mesh_range = \
[grid_properties["dx_mm"],
grid_properties["dy_mm"]]
acq.acquisition_parameters.num_lines = \
grid_properties["num_lines"]
acq.acquisition_parameters.num_images = \
grid_properties["num_lines"] * \
grid_properties["num_images_per_line"]
grid.set_osc_range(acq.acquisition_parameters.osc_range)
processing_parameters = deepcopy(self._processing_parameters)
dc = queue_model_objects.DataCollection([acq],
sample.crystals[0],
processing_parameters)
dc.set_name(acq.path_template.get_prefix())
dc.set_number(acq.path_template.run_number)
dc.set_experiment_type(queue_model_enumerables.EXPERIMENT_TYPE.MESH)
dc.set_requires_centring(False)
dc.grid = grid
self._path_template.run_number += 1
return dc
def create_dc(self,
sample,
run_number=None,
start_image=None,
num_images=None,
osc_start=None,
sc=None,
cpos=None,
inverse_beam=False):
tasks = []
# Acquisition for start position
acq = qmo.Acquisition()
acq.acquisition_parameters = \
copy.deepcopy(self._acquisition_parameters)
acq.acquisition_parameters.collect_agent = \
queue_model_enumerables.COLLECTION_ORIGIN.MXCUBE
acq.path_template = copy.deepcopy(self._path_template)
acq.acquisition_parameters.centred_position = cpos
if '<sample_name>' in acq.path_template.directory:
name = sample.get_name().replace(':', '-')
acq.path_template.directory = acq.path_template.directory.\
replace('<sample_name>', name)
acq.path_template.process_directory = acq.path_template.process_directory.\
replace('<sample_name>', name)
if '<acronym>-<name>' in acq.path_template.base_prefix:
acq.path_template.base_prefix = self.get_default_prefix(sample)
acq.path_template.run_numer = self._beamline_setup_hwobj.queue_model_hwobj.\
get_next_run_number(acq.path_template)
if run_number:
acq.path_template.run_number = run_number
if start_image:
acq.acquisition_parameters.first_image = start_image
acq.path_template.start_num = start_image
if num_images:
acq.acquisition_parameters.num_images = num_images
acq.path_template.num_files = num_images
if osc_start:
acq.acquisition_parameters.osc_start = osc_start
if inverse_beam:
acq.acquisition_parameters.inverse_beam = False
if self._beamline_setup_hwobj.in_plate_mode():
acq.acquisition_parameters.take_snapshots = False
else:
acq.acquisition_parameters.take_snapshots = True
processing_parameters = copy.deepcopy(self._processing_parameters)
dc = qmo.DataCollection([acq], sample.crystals[0],
processing_parameters)
dc.set_name(acq.path_template.get_prefix())
dc.set_number(acq.path_template.run_number)
dc.experiment_type = queue_model_enumerables.EXPERIMENT_TYPE.NATIVE
tasks.append(dc)
return tasks
def _create_task(self, sample, shape):
data_collections = []
if isinstance(shape, shape_history.Line):
if shape.get_qub_objects() is not None:
snapshot = self._shape_history.get_snapshot(
shape.get_qub_objects())
else:
snapshot = self._shape_history.get_snapshot([])
# Acquisition for start position
start_acq = qmo.Acquisition()
start_acq.acquisition_parameters = \
copy.deepcopy(self._acquisition_parameters)
start_acq.acquisition_parameters.collect_agent = \
COLLECTION_ORIGIN.MXCUBE
start_acq.acquisition_parameters.\
centred_position = copy.deepcopy(shape.start_cpos)
start_acq.path_template = copy.deepcopy(self._path_template)
start_acq.acquisition_parameters.centred_position.\
snapshot_image = snapshot
start_acq.path_template.suffix = self._session_hwobj.suffix
if self._beamline_setup_hwobj.in_plate_mode():
start_acq.acquisition_parameters.take_snapshots = False
else:
start_acq.acquisition_parameters.take_snapshots = True
if '<sample_name>' in start_acq.path_template.directory:
name = sample.get_name().replace(':', '-')
start_acq.path_template.directory = start_acq.path_template.directory.\
replace('<sample_name>', name)
start_acq.path_template.process_directory = start_acq.path_template.process_directory.\
replace('<sample_name>', name)
if '<acronym>-<name>' in start_acq.path_template.base_prefix:
start_acq.path_template.base_prefix = self.get_default_prefix(
sample)
start_acq.path_template.run_numer = self._beamline_setup_hwobj.queue_model_hwobj.\
get_next_run_number(start_acq.path_template)
# Add another acquisition for the end position
end_acq = qmo.Acquisition()
end_acq.acquisition_parameters = \
copy.deepcopy(self._acquisition_parameters)
end_acq.acquisition_parameters.collect_agent = \
COLLECTION_ORIGIN.MXCUBE
end_acq.acquisition_parameters.\
centred_position = shape.end_cpos
end_acq.path_template = copy.deepcopy(self._path_template)
end_acq.acquisition_parameters.centred_position.\
snapshot_image = snapshot
end_acq.path_template.suffix = self._session_hwobj.suffix
processing_parameters = copy.deepcopy(self._processing_parameters)
dc = qmo.DataCollection([start_acq, end_acq], sample.crystals[0],
processing_parameters)
dc.set_name(start_acq.path_template.get_prefix())
dc.set_number(start_acq.path_template.run_number)
dc.experiment_type = EXPERIMENT_TYPE.HELICAL
data_collections.append(dc)
self._path_template.run_number += 1
return data_collections
