mxcubecore 1.393.0__py3-none-any.whl → 1.394.0__py3-none-any.whl

mxcubecore/HardwareObjects/GenericDiffractometer.py

@@ -339,7 +339,7 @@ class GenericDiffractometer(HardwareObject):
         #     self.image_height = HWR.beamline.sample_view.camera.get_height()
         #     self.image_width = HWR.beamline.sample_view.camera.get_width()
         # else:
-        #     logging.getLogger("HWR").debug(
+        #     self.log.debug(
         #         "Diffractometer: " + "Camera hwobj is not defined"
         #     )
 
@@ -350,9 +350,7 @@ class GenericDiffractometer(HardwareObject):
             )
         else:
             self.beam_position = [0, 0]
-            logging.getLogger("HWR").warning(
-                "Diffractometer: " + "BeamInfo hwobj is not defined"
-            )
+            self.log.warning("Diffractometer: " + "BeamInfo hwobj is not defined")
 
         self.front_light_switch = self.get_object_by_role("frontlightswitch")
         self.back_light_switch = self.get_object_by_role("backlightswitch")
@@ -363,7 +361,7 @@ class GenericDiffractometer(HardwareObject):
             try:
                 self.used_channels_list = eval(ss0)
             except Exception:
-                logging.getLogger("HWR").exception("")
+                self.log.exception("")
 
         for channel_name in self.used_channels_list:
             self.channel_dict[channel_name] = self.get_channel_object(channel_name)
@@ -392,7 +390,7 @@ class GenericDiffractometer(HardwareObject):
         try:
             self.used_commands_list = eval(self.get_property("used_commands", "[]"))
         except Exception:
-            logging.getLogger("HWR").exception("")
+            self.log.exception("")
         for command_name in self.used_commands_list:
             self.command_dict[command_name] = self.get_command_object(command_name)
 
@@ -442,7 +440,7 @@ class GenericDiffractometer(HardwareObject):
                         temp_motor_hwobj, "stateChanged", self.zoom_motor_state_changed
                     )
             else:
-                logging.getLogger("HWR").warning(
+                self.log.warning(
                     "Diffractometer: Motor "
                     + "%s listed in the centring motor list, but not initalized"
                     % motor_name
@@ -450,9 +448,7 @@ class GenericDiffractometer(HardwareObject):
 
         # sample changer -----------------------------------------------------
         if HWR.beamline.sample_changer is None:
-            logging.getLogger("HWR").warning(
-                "Diffractometer: Sample Changer is not defined"
-            )
+            self.log.warning("Diffractometer: Sample Changer is not defined")
         else:
             # By default use sample changer if it's defined and transfer_mode
             # is set to SAMPLE_CHANGER.
@@ -479,21 +475,19 @@ class GenericDiffractometer(HardwareObject):
                     self.motor_hwobj_dict["sampy"]
                 )
         except Exception:
-            logging.getLogger("HWR").exception("")
+            self.log.exception("")
 
         try:
             self.delay_state_polling = self.get_property("delay_state_polling")
         except Exception:
-            logging.getLogger("HWR").exception("")
+            self.log.exception("")
 
         # Other parameters ---------------------------------------------------
         try:
             self.zoom_centre = eval(self.get_property("zoom_centre"))
         except Exception:
             self.zoom_centre = {"x": 0, "y": 0}
-            logging.getLogger("HWR").warning(
-                "Diffractometer: " + "zoom centre not configured"
-            )
+            self.log.warning("Diffractometer: " + "zoom centre not configured")
 
         self.reversing_rotation = self.get_property("reversing_rotation")
         try:
@@ -503,7 +497,7 @@ class GenericDiffractometer(HardwareObject):
             self.grid_direction = eval(self.get_property("grid_direction"))
         except Exception:
             self.grid_direction = {"fast": (0, 1), "slow": (1, 0), "omega_ref": 0}
-            logging.getLogger("HWR").warning(
+            self.log.warning(
                 "Diffractometer: Grid " + "direction is not defined. Using default."
             )
 
@@ -698,9 +692,7 @@ class GenericDiffractometer(HardwareObject):
         if flag:
             # check both transfer_mode and sample_Changer
             if HWR.beamline.sample_changer is None:
-                logging.getLogger("HWR").error(
-                    "Diffractometer: Sample " + "Changer is not available"
-                )
+                self.log.error("Diffractometer: Sample " + "Changer is not available")
                 return False
 
             if (
@@ -710,7 +702,7 @@ class GenericDiffractometer(HardwareObject):
                 # if transferMode is not defined, ignore the checkup
                 self.use_sc = True
             else:
-                logging.getLogger("HWR").error(
+                self.log.error(
                     "Diffractometer: Set the "
                     + "diffractometer TransferMode to SAMPLE_CHANGER first!!"
                 )
@@ -723,9 +715,7 @@ class GenericDiffractometer(HardwareObject):
         """
         Descript. :
         """
-        logging.getLogger("HWR").info(
-            "current_transfer_mode is set to %s" % transfer_mode
-        )
+        self.log.info("current_transfer_mode is set to %s" % transfer_mode)
         self.transfer_mode = transfer_mode
         if transfer_mode != "SAMPLE_CHANGER":
             self.use_sc = False
@@ -825,7 +815,7 @@ class GenericDiffractometer(HardwareObject):
         """ """
 
         if self.current_centring_method is not None:
-            logging.getLogger("HWR").error(
+            self.log.error(
                 "Diffractometer: already in centring method %s"
                 % self.current_centring_method
             )
@@ -841,17 +831,13 @@ class GenericDiffractometer(HardwareObject):
         try:
             centring_method = self.centring_methods[method]
         except KeyError as diag:
-            logging.getLogger("HWR").error(
-                "Diffractometer: unknown centring method (%s)" % str(diag)
-            )
+            self.log.error("Diffractometer: unknown centring method (%s)" % str(diag))
             self.emit_centring_failed()
         else:
             try:
                 centring_method(sample_info, wait_result=wait)
             except Exception:
-                logging.getLogger("HWR").exception(
-                    "Diffractometer: problem while centring"
-                )
+                self.log.exception("Diffractometer: problem while centring")
                 self.emit_centring_failed()
 
     def cancel_centring_method(self, reject=False):
@@ -859,7 +845,7 @@ class GenericDiffractometer(HardwareObject):
             try:
                 self.current_centring_procedure.kill()
             except Exception:
-                logging.getLogger("HWR").exception(
+                self.log.exception(
                     "Diffractometer: problem aborting the centring method"
                 )
             try:
@@ -986,7 +972,7 @@ class GenericDiffractometer(HardwareObject):
             self.emit_centring_moving()
 
             try:
-                logging.getLogger("HWR").debug(
+                self.log.debug(
                     "Centring finished. Moving motors to position %s" % str(motor_pos)
                 )
                 self.move_to_motors_positions(motor_pos, wait=True)
@@ -998,9 +984,9 @@ class GenericDiffractometer(HardwareObject):
                 # centred positions include omega to initial position
                 pass
                 # if not self.in_plate_mode():
-                #    logging.getLogger("HWR").debug("Centring finished. Moving omega back to initial position")
+                #    self.log.debug("Centring finished. Moving omega back to initial position")
                 #    self.motor_hwobj_dict['phi'].set_value_relative(-180, timeout=None)
-                #    logging.getLogger("HWR").debug("         Moving omega done")
+                #    self.log.debug("         Moving omega done")
 
             if (
                 self.current_centring_method
@@ -1135,9 +1121,7 @@ class GenericDiffractometer(HardwareObject):
                 pos["phiMotor"] = omega
             self.move_to_motors_positions(pos)
         except Exception:
-            logging.getLogger("HWR").exception(
-                "Diffractometer: could not center to beam, aborting"
-            )
+            self.log.exception("Diffractometer: could not center to beam, aborting")
 
     def image_clicked(
         self, x: float, y: float, xi: float | None = None, yi: float | None = None
@@ -1245,7 +1229,7 @@ class GenericDiffractometer(HardwareObject):
             self.current_centring_method = None
             self.current_centring_procedure = None
         else:
-            logging.getLogger("HWR").debug(
+            self.log.debug(
                 "Diffractometer: Trying to emit "
                 + "centringSuccessful outside of a centring"
             )
@@ -1412,7 +1396,7 @@ class GenericDiffractometer(HardwareObject):
                 self.sample_is_loaded_changed,
             )
         except Exception:
-            logging.getLogger("HWR").exception("")
+            self.log.exception("")
 
         if (
             head_type == GenericDiffractometer.HEAD_TYPE_MINIKAPPA
@@ -1424,7 +1408,7 @@ class GenericDiffractometer(HardwareObject):
                 self.sample_is_loaded_changed,
             )
         else:
-            logging.getLogger("HWR").info(
+            self.log.info(
                 "Diffractometer: SmartMagnet "
                 + "is not available, only works for Minikappa and SmartMagnet head"
             )
@@ -1469,9 +1453,7 @@ class GenericDiffractometer(HardwareObject):
                 try:
                     data = GonioHeadConfiguration(**chip_def)
                 except ValidationError:
-                    logging.getLogger("HWR").exception(
-                        "Validation error in %s" % chip_def_fpath
-                    )
+                    self.log.exception("Validation error in %s" % chip_def_fpath)
 
         return data
 
@@ -1488,9 +1470,7 @@ class GenericDiffractometer(HardwareObject):
                 try:
                     GonioHeadConfiguration(**data)
                 except ValidationError:
-                    logging.getLogger("HWR").exception(
-                        "Validation error in %s" % chip_def_fpath
-                    )
+                    self.log.exception("Validation error in %s" % chip_def_fpath)
                 else:
                     _f.write(json.dumps(data, indent=4))
 

mxcubecore/HardwareObjects/Gphl/CollectEmulator.py

@@ -21,7 +21,6 @@ You should have received a copy of the GNU Lesser General Public License
 along with MXCuBE. If not, see <https://www.gnu.org/licenses/>.
 """
 
-import logging
 import os
 import re
 import subprocess
@@ -296,8 +295,8 @@ class CollectEmulator(CollectMockup):
 
         for tag, val in self.config.simcal_options.items():
             command_list.extend(conversion.command_option(tag, val, prefix="--"))
-        logging.getLogger("HWR").info("Executing command: %s", " ".join(command_list))
-        logging.getLogger("HWR").info("Executing environment: %s", sorted(envs.items()))
+        self.log.info("Executing command: %s", " ".join(command_list))
+        self.log.info("Executing environment: %s", sorted(envs.items()))
 
         if compress_data:
             command_list.append("--gzip-img")
@@ -323,23 +322,23 @@ class CollectEmulator(CollectMockup):
             # # NBNB leaving this in causes simulations to be killed and missing images
             # super(CollectEmulator, self).data_collection_hook()
 
-            logging.getLogger("HWR").info("Waiting for simcal collection emulation.")
+            self.log.info("Waiting for simcal collection emulation.")
             # NBNB TODO put in time-out, somehow
             return_code = running_process.wait()
         except Exception:
-            logging.getLogger("HWR").error("Error in GΦL collection emulation")
+            self.log.error("Error in GΦL collection emulation")
             raise
         finally:
             fp1.close()
         process = gphl_connection.collect_emulator_process
         gphl_connection.collect_emulator_process = None
         if process == "ABORTED":
-            logging.getLogger("HWR").info("Simcal collection emulation aborted")
+            self.log.info("Simcal collection emulation aborted")
         elif return_code:
             raise RuntimeError(
                 "simcal process terminated with return code %s" % return_code
             )
         else:
-            logging.getLogger("HWR").info("Simcal collection emulation successful")
+            self.log.info("Simcal collection emulation successful")
         self.ready_event.set()
         return

mxcubecore/HardwareObjects/Gphl/GphlQueueEntry.py

@@ -49,7 +49,7 @@ class GphlWorkflowQueueEntry(BaseQueueEntry):
             )
             HWR.beamline.gphl_workflow.post_execute()
         HWR.beamline.gphl_workflow.pre_execute(self)
-        logging.getLogger("HWR").debug("Done GphlWorkflowQueueEntry.pre_execute")
+        self.log.debug("Done GphlWorkflowQueueEntry.pre_execute")
 
     def post_execute(self):
         BaseQueueEntry.post_execute(self)
@@ -60,5 +60,5 @@ class GphlWorkflowQueueEntry(BaseQueueEntry):
     def stop(self):
         HWR.beamline.gphl_workflow.workflow_aborted("Dummy", "Dummy")
         BaseQueueEntry.stop(self)
-        logging.getLogger("HWR").info("MXCuBE aborting current GΦL workflow")
+        self.log.info("MXCuBE aborting current GΦL workflow")
         self.get_view().setText(1, "Stopped")

mxcubecore/HardwareObjects/Gphl/GphlWorkflow.py

@@ -492,10 +492,10 @@ class GphlWorkflow(HardwareObject):
         }
         fields["input_space_group"] = {
             "title": "Space Group",
-            "default": crystal_symmetry.regularise_space_group(
-                data_model.input_space_group
-            )
-            or "",
+            "default": (
+                crystal_symmetry.regularise_space_group(data_model.input_space_group)
+                or ""
+            ),
             "type": "string",
             "readOnly": True,
         }
@@ -938,13 +938,13 @@ class GphlWorkflow(HardwareObject):
 
                 tt0 = self._workflow_queue.get()
                 if tt0 is StopIteration:
-                    logging.getLogger("HWR").debug("GΦL queue StopIteration")
+                    self.log.debug("GΦL queue StopIteration")
                     break
 
                 message_type, payload, correlation_id, result_list = tt0
                 func = self._processor_functions.get(message_type)
                 if func is None:
-                    logging.getLogger("HWR").error(
+                    self.log.error(
                         "GΦL message %s not recognised by MXCuBE. Terminating...",
                         message_type,
                     )
@@ -953,9 +953,7 @@ class GphlWorkflow(HardwareObject):
                     if not self.config.settings.get("suppress_external_log_output"):
                         func(payload, correlation_id)
                 else:
-                    logging.getLogger("HWR").info(
-                        "GΦL queue processing %s", message_type
-                    )
+                    self.log.info("GΦL queue processing %s", message_type)
                     response = func(payload, correlation_id)
                     if result_list is not None:
                         result_list.append((response, correlation_id))
@@ -1019,22 +1017,22 @@ class GphlWorkflow(HardwareObject):
         """Print text info to console,. log etc."""
         subprocess_name = self._server_subprocess_names.get(correlation_id)
         if subprocess_name:
-            logging.getLogger("HWR").info("%s: %s" % (subprocess_name, payload))
+            self.log.info("%s: %s" % (subprocess_name, payload))
         else:
-            logging.getLogger("HWR").info(payload)
+            self.log.info(payload)
 
     def echo_subprocess_started(self, payload, correlation_id):
         name = payload.name
         if correlation_id:
             self._server_subprocess_names[correlation_id] = name
-        logging.getLogger("HWR").info("%s : STARTING", name)
+        self.log.info("%s : STARTING", name)
 
     def echo_subprocess_stopped(self, payload, correlation_id):
         try:
             name = self._server_subprocess_names.pop(correlation_id)
         except KeyError:
             name = "Unknown process"
-        logging.getLogger("HWR").info("%s : FINISHED", name)
+        self.log.info("%s : FINISHED", name)
 
     def get_configuration_data(self, payload, correlation_id):
         return GphlMessages.ConfigurationData(self.file_paths["gphl_beamline_config"])
@@ -1166,9 +1164,7 @@ class GphlWorkflow(HardwareObject):
         if not allowed_widths:
             allowed_widths = list(self.config.settings.get("default_image_widths"))
             allowed_widths.sort()
-            logging.getLogger("HWR").info(
-                "No allowed image widths returned by strategy - use defaults"
-            )
+            self.log.info("No allowed image widths returned by strategy - use defaults")
 
         # set starting and unchanging values of parameters
         resolution = HWR.beamline.resolution.get_value()
@@ -1633,7 +1629,7 @@ class GphlWorkflow(HardwareObject):
             user_modifiable = geometric_strategy.isUserModifiable
             if user_modifiable:
                 # Query user for new rotationSetting and make it,
-                logging.getLogger("HWR").warning(
+                self.log.warning(
                     "User modification of sweep settings not implemented. Ignored"
                 )
             new_dose = parameters["use_dose"]
@@ -1687,7 +1683,7 @@ class GphlWorkflow(HardwareObject):
             new_dcg_name = "GΦL DiffractCal"
         else:
             new_dcg_name = "GΦL Characterisation"
-        logging.getLogger("HWR").debug("setup_data_collection %s", new_dcg_name)
+        self.log.debug("setup_data_collection %s", new_dcg_name)
         new_dcg_model = queue_model_objects.TaskGroup()
         new_dcg_model.set_enabled(True)
         new_dcg_model.set_name(new_dcg_name)
@@ -1760,7 +1756,7 @@ class GphlWorkflow(HardwareObject):
                 translation_settings = self.calculate_recentring(
                     okp, ref_xyz=current_xyz, ref_okp=current_okp
                 )
-                logging.getLogger("HWR").debug(
+                self.log.debug(
                     "GPHL Recentring. okp, motors, %s, %s"
                     % (okp, sorted(translation_settings.items()))
                 )
@@ -1846,7 +1842,7 @@ class GphlWorkflow(HardwareObject):
 
             if recentring_mode == "start":
                 q_e = self.enqueue_sample_centring(motor_settings=settings)
-                logging.getLogger("HWR").debug(
+                self.log.debug(
                     "GPHL recenter at : "
                     + ", ".join("%s:%s" % item for item in sorted(settings.items()))
                 )
@@ -1861,7 +1857,7 @@ class GphlWorkflow(HardwareObject):
                 translation = GphlMessages.GoniostatTranslation(
                     rotation=sweepSetting, **settings
                 )
-                logging.getLogger("HWR").debug(
+                self.log.debug(
                     "GPHL calculate recentring: "
                     + ", ".join("%s:%s" % item for item in sorted(settings.items()))
                 )
@@ -1911,9 +1907,7 @@ class GphlWorkflow(HardwareObject):
         # output from bytes to string (with default encoding),
         # avoiding an explicit decoding step.
         result = {}
-        logging.getLogger("HWR").debug(
-            "Running Recen command: %s", " ".join(command_list)
-        )
+        self.log.debug("Running Recen command: %s", " ".join(command_list))
         try:
             output = subprocess.check_output(
                 command_list,
@@ -1922,7 +1916,7 @@ class GphlWorkflow(HardwareObject):
                 universal_newlines=True,
             )
         except subprocess.CalledProcessError as err:
-            logging.getLogger("HWR").error(
+            self.log.error(
                 "Recen failed with returncode %s. Output was:\n%s",
                 err.returncode,
                 err.output,
@@ -1942,7 +1936,7 @@ class GphlWorkflow(HardwareObject):
             elif ss0 == "NORMAL termination":
                 terminated_ok = True
         else:
-            logging.getLogger("HWR").error(
+            self.log.error(
                 "Recen failed with normal termination=%s. Output was:\n" % terminated_ok
                 + output
             )
@@ -1953,14 +1947,14 @@ class GphlWorkflow(HardwareObject):
             if limits:
                 limit = limits[0]
                 if limit is not None and val < limit:
-                    logging.getLogger("HWR").warning(
+                    self.log.warning(
                         "WARNING, centring motor "
                         "%s position %s recentred to below minimum limit %s"
                         % (tag, val, limit)
                     )
                 limit = limits[1]
                 if limit is not None and val > limit:
-                    logging.getLogger("HWR").warning(
+                    self.log.warning(
                         "WARNING, centring motor "
                         "%s position %s recentred to above maximum limit %s"
                         % (tag, val, limit)
@@ -2036,7 +2030,7 @@ class GphlWorkflow(HardwareObject):
             acq_parameters.num_images = scan.width.numImages
             acq_parameters.osc_start = scan.start
             acq_parameters.osc_range = scan.width.imageWidth
-            logging.getLogger("HWR").info(
+            self.log.info(
                 "Scan: %s images of %s deg. starting at %s (%s deg)",
                 acq_parameters.num_images,
                 acq_parameters.osc_range,
@@ -2498,9 +2492,7 @@ class GphlWorkflow(HardwareObject):
                     )
                     zoom_motor.moveToPosition(ll0[-1])
                 else:
-                    logging.getLogger("HWR").warning(
-                        "No predefined positions for zoom motor."
-                    )
+                    self.log.warning("No predefined positions for zoom motor.")
             else:
                 logging.getLogger("user_level_log").info(
                     "Sample re-centering now active - Zoom in before continuing."
@@ -2593,9 +2585,7 @@ class GphlWorkflow(HardwareObject):
                     snapshot_index + 1,
                 )
                 snapshot_filename = os.path.join(snapshot_directory, snapshot_filename)
-                logging.getLogger("HWR").debug(
-                    "Centring snapshot stored at %s", snapshot_filename
-                )
+                self.log.debug("Centring snapshot stored at %s", snapshot_filename)
                 collect_hwobj._take_crystal_snapshot(snapshot_filename)
             if summed_angle:
                 HWR.beamline.diffractometer.move_omega_relative(-summed_angle)
@@ -2641,9 +2631,7 @@ class GphlWorkflow(HardwareObject):
                 os.makedirs(image_root)
             except Exception:
                 # No need to raise error - program will fail downstream
-                logging.getLogger("HWR").error(
-                    "Could not create image root directory: %s", image_root
-                )
+                self.log.error("Could not create image root directory: %s", image_root)
 
         priorInformation = GphlMessages.PriorInformation(workflow_model, image_root)
 
@@ -2889,9 +2877,7 @@ class GphlWorkflow(HardwareObject):
                 raise ValueError("Test sample requires gphl_test_samples dir specified")
             sample_dir = os.path.join(sample_dir, sample_name)
         if not sample_dir:
-            logging.getLogger("HWR").warning(
-                "No emulation sample dir found for sample %s", sample_name
-            )
+            self.log.warning("No emulation sample dir found for sample %s", sample_name)
         return sample_dir
 
     def get_emulation_crystal_data(self, sample_name=None):
@@ -2942,7 +2928,7 @@ class GphlWorkflow(HardwareObject):
                 elif instruction == "reffiles":
                     update_dict = self.update_reference_files(parameters)
             except:
-                logging.getLogger("HWR").error(
+                self.log.error(
                     "Error in GΦL parameter update for %s, Continuing ...",
                     instruction,
                 )
@@ -2989,7 +2975,7 @@ class GphlWorkflow(HardwareObject):
                 ):
                     update_dict = self.adjust_dose(parameters)
             except:
-                logging.getLogger("HWR").error(
+                self.log.error(
                     "Error in GΦL parameter update for %s, Continuing ...",
                     instruction,
                 )