mxcubecore 1.335.0__tar.gz → 1.336.0__tar.gz

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mxcubecore
-Version: 1.335.0
+Version: 1.336.0
 Summary: Core libraries for the MXCuBE application
 License: LGPL-3.0-or-later
 Keywords: mxcube,mxcube3,mxcubecore

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/mxcubecore/BaseHardwareObjects.py

@@ -881,7 +881,7 @@ class HardwareObjectMixin(CommandContainer):
     def re_emit_values(self) -> None:
         """Update values for all internal attributes
 
-        Should be expanded in subclasse with more updatable attributes
+        Should be expanded in subclasses with more updatable attributes
         (e.g. value, limits)
         """
         self.update_state()

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/mxcubecore/HardwareObjects/GenericDiffractometer.py

@@ -527,7 +527,7 @@ class GenericDiffractometer(HardwareObject):
             return HardwareObject.__getattr__(self, attr)
 
     # Contained Objects
-    # NBNB Temp[orary hack - should be cleaned up together with configuration
+    # NBNB Temporary hack - should be cleaned up together with configuration
     @property
     def omega(self):
         """omega motor object
@@ -537,6 +537,24 @@ class GenericDiffractometer(HardwareObject):
         """
         return self.motor_hwobj_dict.get("phi")
 
+    @property
+    def kappa(self):
+        """kappa motor object
+
+        Returns:
+            AbstractActuator
+        """
+        return self.get_object_by_role("kappa")
+
+    @property
+    def kappa_phi(self):
+        """kappa motor object
+
+        Returns:
+            AbstractActuator
+        """
+        return self.get_object_by_role("kappa_phi")
+
     @property
     def centring_x(self):
         """centring_x motor object

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/mxcubecore/HardwareObjects/Gphl/CollectEmulator.py

@@ -45,15 +45,6 @@ class CollectEmulator(CollectMockup):
 
         self._counter = 1
 
-    # def init(self):
-    #     CollectMockup.init(self)
-    #     # NBNB you get an error if you use 'HWR.beamline.session'
-    #     # session_hwobj = self.get_object_by_role("session")
-    #     session = HWR.beamline.session
-    #     if session and self.has_object("override_data_directories"):
-    #         dirs = self["override_data_directories"].get_properties()
-    #         session.set_base_data_directories(**dirs)
-
     def _get_simcal_input(self, data_collect_parameters, crystal_data):
         """Get ordered dict with simcal input from available data"""
 
@@ -125,7 +116,7 @@ class CollectEmulator(CollectMockup):
 
         # Add/overwrite parameters from emulator configuration
         conv = conversion.convert_string_value
-        for key, val in self["simcal_parameters"].get_properties().items():
+        for key, val in self.config.simcal_parameters.items():
             setup_data[key] = conv(val)
 
         setup_data["n_vertices"] = 0
@@ -266,7 +257,7 @@ class CollectEmulator(CollectMockup):
         if GPHL_CCP4_PATH:
             envs["GPHL_CCP4_PATH"] = GPHL_CCP4_PATH
         text_type = conversion.text_type
-        for tag, val in self["environment_variables"].get_properties().items():
+        for tag, val in self.config.environment_variables.items():
             envs[text_type(tag)] = text_type(val)
 
         # get crystal data
@@ -303,7 +294,7 @@ class CollectEmulator(CollectMockup):
             hklfile,
         ]
 
-        for tag, val in self["simcal_options"].get_properties().items():
+        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()))

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/mxcubecore/HardwareObjects/Gphl/GphlWorkflowConnection.py

@@ -1031,6 +1031,8 @@ class GphlWorkflowConnection(HardwareObject):
         for item in collectionDone.scanIdMap.items():
             scanIdMap[jvm.java.util.UUID.fromString(conversion.text_type(item[0]))] = (
                 jvm.java.util.UUID.fromString(conversion.text_type(item[1]))
+                if item[1]
+                else None
             )
         return jvm.astra.messagebus.messages.information.CollectionDoneImpl(
             proposalId,

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/mxcubecore/HardwareObjects/QtGraphicsManager.py

@@ -145,6 +145,7 @@ class QtGraphicsManager(AbstractSampleView):
         self.graphics_move_down_item = None
         self.graphics_move_left_item = None
         self.graphics_magnification_item = None
+        self.camera_hwobj = None
 
     def init(self):
         """Main init function. Initiates all graphics items, hwobjs and

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/mxcubecore/HardwareObjects/abstract/AbstractCollect.py

@@ -103,9 +103,9 @@ class AbstractCollect(HardwareObject, object):
 
         undulators = []
         try:
-            for undulator in self["undulators"]:
+            for undulator in self.config.undulators:
                 undulators.append(undulator)
-        except BaseException:
+        except Exception:
             pass
 
         beam_div_hor, beam_div_ver = HWR.beamline.beam.get_beam_divergence()

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/mxcubecore/HardwareObjects/mockup/BeamMockup.py

@@ -91,6 +91,9 @@ class BeamMockup(AbstractBeam):
         if _check_beam:
             self._check_beam = literal_eval(_check_beam)
 
+        # Needed to trigger first value setting
+        self.get_value()
+
         self.re_emit_values()
         self.emit("beamPosChanged", (self._beam_position_on_screen,))
 

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/mxcubecore/HardwareObjects/mockup/DetectorMockup.py

@@ -35,7 +35,7 @@ class DetectorMockup(AbstractDetector):
         )
         self._roi_mode = 0
         self._exposure_time_limits = eval(
-            self.get_property("exposure_time_limits", "[0.04, 60000]")
+            self.get_property("exposure_time_limits", "[0.02, 60000]")
         )
         self.update_state(self.STATES.READY)
         self.distance_motor_hwobj = self.get_object_by_role("detector_distance")

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/mxcubecore/HardwareObjects/mockup/DiffractometerMockup.py

@@ -49,8 +49,6 @@ class DiffractometerMockup(GenericDiffractometer):
         self.focus = None
         self.frontlight = None
         self.frontlightswitch = None
-        self.kappa = None
-        self.kappa_phi = None
         self.phi = None
         self.phiy = None
         self.phiz = None

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/mxcubecore/HardwareObjects/mockup/FluxMockup.py

@@ -45,15 +45,10 @@ class FluxMockup(AbstractFlux):
     def init(self):
         super().init()
         self.current_flux_dict["flux"] = self.default_value
-        gevent.spawn(self._update_flux)
-
-    def _update_flux(self):
-        while True:
-            self.measure_flux()
-            gevent.sleep(3)
 
     def get_value(self):
         """Get flux at current transmission in units of photons/s"""
+        self.measure_flux()
         return self.current_flux_dict["flux"]
 
     def measure_flux(self) -> None:

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/mxcubecore/model/queue_model_objects.py

@@ -2055,8 +2055,6 @@ class GphlWorkflow(TaskNode):
             "initial_strategy",
             "strategy_variant",
             "strategy_options",
-            "acquisition_dose",
-            "characterisation_dose",
         ):
             summary[tag] = getattr(self, tag)
         summary["wavelengths"] = tuple(x.wavelength for x in self.wavelengths)
@@ -2064,7 +2062,13 @@ class GphlWorkflow(TaskNode):
         summary["orgxy"] = self.detector_setting.orgxy
         summary["strategy_variant"] = self.strategy_options.get("variant", "not set")
         summary["orientation_count"] = len(self.goniostat_translations)
-        summary["radiation_dose"] = self.calc_maximum_dose() * self.transmission / 100.0
+        summary["characterisation_dose"] = self.characterisation_dose
+        summary["dose_per_repetition"] = self.acquisition_dose
+
+        summary["total_radiation_dose"] = (
+            summary["dose_per_repetition"] * summary["repetition_count"]
+            + summary["characterisation_dose"]
+        )
         summary["total_dose_budget"] = self.recommended_dose_budget()
         return summary
 

{mxcubecore-1.335.0 → mxcubecore-1.336.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mxcubecore"
-version = "1.335.0"
+version = "1.336.0"
 license = "LGPL-3.0-or-later"
 description = "Core libraries for the MXCuBE application"
 authors = [