def get_default_prefix(sample_data, generic_name):
if isinstance(sample_data, dict):
sample = qmo.Sample()
sample.code = sample_data.get("code", "")
sample.name = sample_data.get("sampleName", "").replace(":", "-")
sample.location = sample_data.get("location", "").split(":")
sample.lims_id = sample_data.get("limsID", -1)
sample.crystals[0].protein_acronym = sample_data.get("proteinAcronym", "")
else:
sample = sample_data
return blcontrol.beamline.session.get_default_prefix(sample, generic_name)
def __init__(self, *args):
BaseWidget.__init__(self, *args)
# Internal variables ------------------------------------------------
self.sample = queue_model_objects.Sample()
self.crystal = self.sample.crystals[0]
self.sample_mib = DataModelInputBinder(self.sample)
self.crystal_mib = DataModelInputBinder(self.crystal)
# Signals ------------------------------------------------------------
# Slots --------------------------------------------------------------
self.define_slot("populate_sample_details", ({}))
# Graphic elements ----------------------------------------------------
_info_widget = QtImport.QWidget(self)
self.crystal_widget = QtImport.load_ui_file("crystal_widget_layout.ui")
self.sample_info_widget = QtImport.load_ui_file(
"sample_info_widget_layout.ui")
# self.ispyb_sample_info_widget = ISPyBSampleInfoWidget(self)
# Layout --------------------------------------------------------------
_info_widget_hlayout = QtImport.QHBoxLayout(_info_widget)
_info_widget_hlayout.addWidget(self.sample_info_widget)
_info_widget_hlayout.addWidget(self.crystal_widget)
_info_widget_hlayout.addStretch(0)
_info_widget_hlayout.setSpacing(0)
_info_widget_hlayout.setContentsMargins(2, 2, 2, 2)
_main_hlayout = QtImport.QVBoxLayout(self)
_main_hlayout.addWidget(_info_widget)
# _main_hlayout.addWidget(self.ispyb_sample_info_widget)
_main_hlayout.addStretch(0)
_main_hlayout.setSpacing(0)
_main_hlayout.setContentsMargins(2, 2, 2, 2)
# SizePolicies --------------------------------------------------------
# Qt signal/slot connections ------------------------------------------
# Other ---------------------------------------------------------------
self.crystal_mib.bind_value_update(
"space_group", self.crystal_widget.space_group_value_label, str,
None)
self.crystal_mib.bind_value_update(
"protein_acronym",
self.crystal_widget.protein_acronym_value_label,
str,
None,
)
self.crystal_mib.bind_value_update("cell_a",
self.crystal_widget.a_value_label,
str, None)
self.crystal_mib.bind_value_update(
"cell_alpha", self.crystal_widget.alpha_value_label, str, None)
self.crystal_mib.bind_value_update("cell_b",
self.crystal_widget.b_value_label,
str, None)
self.crystal_mib.bind_value_update(
"cell_beta", self.crystal_widget.beta_value_label, str, None)
self.crystal_mib.bind_value_update("cell_c",
self.crystal_widget.c_value_label,
str, None)
self.crystal_mib.bind_value_update(
"cell_gamma", self.crystal_widget.gamma_value_label, str, None)
self.sample_mib.bind_value_update(
"name", self.sample_info_widget.name_value_label, str, None)
self.sample_mib.bind_value_update(
"code", self.sample_info_widget.data_matrix_value_label, str, None)
self.sample_mib.bind_value_update(
"holder_length",
self.sample_info_widget.holder_length_value_label,
str,
None,
)
self.sample_mib.bind_value_update(
"lims_sample_location",
self.sample_info_widget.sample_location_value_label,
str,
None,
)
self.sample_mib.bind_value_update(
"lims_container_location",
self.sample_info_widget.basket_location_value_label,
str,
None,
)
def pre_execute(self, data_model):
self._failed = False
"""
if self.beam_focusing_hwobj.get_focus_mode() != "imaging":
self._error_msg = "Beamline is not in Imaging mode"
self.emit("collectFailed", self._error_msg)
logging.getLogger("GUI").error("Imaging: Error during acquisition (%s)" % self._error_msg)
self.ready_event.set()
self._collecting = False
self._failed = True
return
"""
self.emit("progressInit", ("Image acquisition", 100, False))
self._collect_frame = 0
self.printed_warnings = []
self.printed_errors = []
self.ff_ssim = None
self.config_dict = {}
path_template = data_model.acquisitions[0].path_template
acq_params = data_model.acquisitions[0].acquisition_parameters
im_params = data_model.xray_imaging_parameters
self._number_of_images = acq_params.num_images
if im_params.detector_distance is not None:
logging.getLogger("GUI").warning(
"Imaging: Setting detector distance to %d mm" %
int(im_params.detector_distance))
delta = (im_params.detector_distance -
self.reference_distance) * self.reference_angle
for motor in self.beam_focusing_hwobj.get_focus_motors():
if motor["motorName"] == "P14DetHor1":
target = motor["focusingModes"]["Imaging"] + delta
tine.set("/P14/P14DetTrans/P14detHor1", "Move.START",
target)
elif motor["motorName"] == "P14DetHor2":
target = motor["focusingModes"]["Imaging"] + delta
tine.set("/P14/P14DetTrans/P14detHor2", "Move.START",
target)
#TODO add later wait
time.sleep(3)
HWR.beamline.detector.distance.set_value(
im_params.detector_distance, timeout=30)
logging.getLogger("GUI").info("Imaging: Detector distance set")
self.cmd_collect_detector("pco")
self.cmd_collect_directory(str(path_template.directory))
self.cmd_collect_template(str(path_template.get_image_file_name()))
self.cmd_collect_scan_type("xrimg")
self.cmd_collect_exposure_time(acq_params.exp_time)
self.cmd_collect_num_images(acq_params.num_images)
self.cmd_collect_start_angle(acq_params.osc_start)
self.cmd_collect_range(acq_params.osc_range)
self.cmd_collect_in_queue(acq_params.in_queue != False)
shutter_name = HWR.beamline.detector.get_shutter_name()
self.cmd_collect_shutter(shutter_name)
self.cmd_collect_ff_num_images(im_params.ff_num_images)
self.cmd_collect_ff_offset([
im_params.sample_offset_a,
im_params.sample_offset_b,
im_params.sample_offset_c,
])
self.cmd_collect_ff_pre(im_params.ff_pre)
self.cmd_collect_ff_post(im_params.ff_post)
if acq_params.osc_range == 0:
self.cmd_camera_trigger(False)
else:
self.cmd_camera_trigger(True)
self.cmd_camera_live_view(im_params.ff_apply)
self.cmd_camera_write_data(im_params.camera_write_data)
self.cmd_camera_ff_ssim(im_params.ff_ssim_enabled)
self.set_osc_start(acq_params.osc_start)
self.current_dc_parameters = qmo.to_collect_dict(
data_model, HWR.beamline.session, qmo.Sample())[0]
self.current_dc_parameters["status"] = "Running"
self.current_dc_parameters["comments"] = ""
self.motor_positions = HWR.beamline.diffractometer.get_positions()
self.take_crystal_snapshots()
self.store_data_collection_in_lims()
def pre_execute(self, data_model):
"""
Pre execute method
:param data_model:
:return:
"""
self._failed = False
"""
if self.beam_focusing_hwobj.get_focus_mode() != "imaging":
self._error_msg = "Beamline is not in Imaging mode"
self.emit("collectFailed", self._error_msg)
logging.getLogger("GUI").error("Imaging: Error during acquisition (%s)" % self._error_msg)
self.ready_event.set()
self._collecting = False
self._failed = True
return
"""
self.emit("progressInit", ("Image acquisition", 100, False))
self._collect_frame = 0
self.printed_warnings = []
self.printed_errors = []
self.ff_ssim = None
self.config_dict = {}
path_template = data_model.acquisitions[0].path_template
acq_params = data_model.acquisitions[0].acquisition_parameters
im_params = data_model.xray_imaging_parameters
self._number_of_images = acq_params.num_images
if im_params.detector_distance:
delta = im_params.detector_distance - self.detector_hwobj.get_distance()
if abs(delta) > 0.0001:
tine.set(
"/P14/P14DetTrans/ComHorTrans",
"IncrementMove.START",
-0.003482 * delta,
)
self.detector_hwobj.set_distance(
im_params.detector_distance, wait=True, timeout=30
)
self.cmd_collect_detector("pco")
self.cmd_collect_directory(str(path_template.directory))
self.cmd_collect_template(str(path_template.get_image_file_name()))
self.cmd_collect_scan_type("xrimg")
self.cmd_collect_exposure_time(acq_params.exp_time)
self.cmd_collect_num_images(acq_params.num_images)
self.cmd_collect_start_angle(acq_params.osc_start)
self.cmd_collect_range(acq_params.osc_range)
self.cmd_collect_in_queue(acq_params.in_queue != False)
shutter_name = self.detector_hwobj.get_shutter_name()
self.cmd_collect_shutter(shutter_name)
self.cmd_collect_ff_num_images(im_params.ff_num_images)
self.cmd_collect_ff_offset(
[
im_params.sample_offset_a,
im_params.sample_offset_b,
im_params.sample_offset_c,
]
)
self.cmd_collect_ff_pre(im_params.ff_pre)
self.cmd_collect_ff_post(im_params.ff_post)
if acq_params.osc_range == 0:
self.cmd_camera_trigger(False)
else:
self.cmd_camera_trigger(True)
self.cmd_camera_live_view(im_params.ff_apply)
self.cmd_camera_write_data(im_params.camera_write_data)
self.cmd_camera_ff_ssim(im_params.ff_ssim_enabled)
self.set_osc_start(acq_params.osc_start)
self.current_dc_parameters = qmo.to_collect_dict(
data_model, self.session_hwobj, qmo.Sample()
)[0]
self.current_dc_parameters["status"] = "Running"
self.current_dc_parameters["comments"] = ""
self.store_data_collection_in_lims()
