mxcubecore 1.334.0__py3-none-any.whl → 1.336.0__py3-none-any.whl

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/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/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/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/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/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/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/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/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/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/model/queue_model_objects.py

@@ -1715,7 +1715,7 @@ class AcquisitionParameters(object):
         self.in_queue = False
         self.in_interleave = None
         self.sub_wedge_size = 10
-
+        self.disable_processing = False
         self.num_triggers = int()
         self.num_images_per_trigger = int()
         self.hare_num = 1
@@ -1765,6 +1765,7 @@ class AcquisitionParameters(object):
             "mesh_center": self.mesh_center,
             "cell_spacing": self.cell_spacing,
             "sub_wedge_size": self.sub_wedge_size,
+            "disable_processing": self.disable_processing,
         }
 
     def copy(self):
@@ -2054,8 +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)
@@ -2063,7 +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-1.334.0.dist-info → mxcubecore-1.336.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mxcubecore
-Version: 1.334.0
+Version: 1.336.0
 Summary: Core libraries for the MXCuBE application
 License: LGPL-3.0-or-later
 Keywords: mxcube,mxcube3,mxcubecore

{mxcubecore-1.334.0.dist-info → mxcubecore-1.336.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-mxcubecore/BaseHardwareObjects.py,sha256=OOIIBFtZpxJZ5-Jju8iNmM-IWH8ousPur72hb1JqtzI,41286
+mxcubecore/BaseHardwareObjects.py,sha256=LpHUEo6B5SAv1AfuPg6Ej0bNppsZxng8t9LjdwjeP5g,41287
 mxcubecore/Command/Epics.py,sha256=b8my4qI49gTYPRu5kSmXge1KH71KnqJl0aYZ2d7SfM0,7781
 mxcubecore/Command/Exporter.py,sha256=VL7EVAvoz01xAWQYK2xMIJL9EBU6qWwk4K7jgRqlifo,8104
 mxcubecore/Command/Mockup.py,sha256=Q-kIR30mNnYSyy_f70PFx-ZVVTcPG1NRVqrrv3VCCcs,2075
@@ -181,12 +181,12 @@ mxcubecore/HardwareObjects/ExporterMotor.py,sha256=7XjyUcymJjJM7YVyteBxjLutgfSuT
 mxcubecore/HardwareObjects/ExporterNState.py,sha256=BH9jkRoud4bHLiflj_1mgDL0Y-LmMjesfTtTGr7EzJ0,6129
 mxcubecore/HardwareObjects/FlexHCD.py,sha256=NqfBabwNH466WmHZH--UIFZf7XEZkN7QEjO6iXsLq1g,23394
 mxcubecore/HardwareObjects/FlexHCDMaintenance.py,sha256=0fPa-gdp_BNYwz2RawpS-2L99zsuabg8Oc5R8RIRGA8,5008
-mxcubecore/HardwareObjects/GenericDiffractometer.py,sha256=d64Hf6cCw11QPwfAMVARpoHVApj3Y7GKMPiV01eTbvs,49136
-mxcubecore/HardwareObjects/Gphl/CollectEmulator.py,sha256=TpRD2Z9AXbXLr3iMFpzslm-Cqz3ERf6bSkjV5goVhsI,13483
+mxcubecore/HardwareObjects/GenericDiffractometer.py,sha256=qiSbk5nlxqzkSCdrtwI2NkRMnhPf1LNBGj6zr4rOBMk,49489
+mxcubecore/HardwareObjects/Gphl/CollectEmulator.py,sha256=iiH6EblDwEMdxl44BswHJEwK-6qjsG3tXfdq9kO2j74,13015
 mxcubecore/HardwareObjects/Gphl/GphlMessages.py,sha256=3WSBmUGLka4gilfwpqXyc4SJMlOt9y2sRNrOiE0-DaM,35759
 mxcubecore/HardwareObjects/Gphl/GphlQueueEntry.py,sha256=Rwu6YL8U4knibWI9yOXBoUVuayL6O0rHQWQuEP2Hu_g,2309
 mxcubecore/HardwareObjects/Gphl/GphlWorkflow.py,sha256=vlNhXkP2Ob-bvOuRY5rYVTSgZ8ZULrSQYYhtSS9V4fA,132177
-mxcubecore/HardwareObjects/Gphl/GphlWorkflowConnection.py,sha256=Wk9GBjtEWI1uvq52vHAC2bWqFW0TC31ds4_hcH1wBEQ,50413
+mxcubecore/HardwareObjects/Gphl/GphlWorkflowConnection.py,sha256=SHBbGDJ0rIRXwsiGWF94AUXNL8BdsIT8-zHW0NoA0lc,50466
 mxcubecore/HardwareObjects/Gphl/Transcal2MiniKappa.py,sha256=Dzf05WSRC5vtOOluZ69f5xZrr6BmT7ITu-OfrKMqemc,9777
 mxcubecore/HardwareObjects/Gphl/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mxcubecore/HardwareObjects/Gphl/run_mxcube_test.csh,sha256=IvrrFiuRS7c6kYD_FflVc0WINr7oOCBEryAOtMk5zqQ,1233
@@ -259,7 +259,7 @@ mxcubecore/HardwareObjects/ProposalTypeISPyBLims.py,sha256=V55sKKQVyTTBJ0HMsW_Gk
 mxcubecore/HardwareObjects/PyISPyBClient.py,sha256=K9IgwI7xBth_L0SZaZBheW6hbNCRxBJN2r2FR53b2zA,12928
 mxcubecore/HardwareObjects/QtAxisCamera.py,sha256=mf5m-t3CoP3eHjjiQu7U0SGt7JiBzcaqo8-Gur1eipY,3159
 mxcubecore/HardwareObjects/QtGraphicsLib.py,sha256=9VjQVAhlxBFMoYow7xgheF_BqA9X8HJkPQmreThaq80,95117
-mxcubecore/HardwareObjects/QtGraphicsManager.py,sha256=LI7X8JhXO7lsMR-TM_Gb1wh9v8XAm-wchjTrAdm5hMs,87657
+mxcubecore/HardwareObjects/QtGraphicsManager.py,sha256=Ux2-JBYFLjcteintghwX1jfTSZ9vW0WS0MmTXdH7t-k,87690
 mxcubecore/HardwareObjects/QtInstanceServer.py,sha256=64cIL06Gzmb_OiJyzkHK9KOpKSf2O0KfaxhZeDd9HLU,45640
 mxcubecore/HardwareObjects/QtLimaVideo.py,sha256=3gJVH9n_IXlrnRQWEQIOz9JE4iL14yfsIEcQ0hzf9XI,4574
 mxcubecore/HardwareObjects/QtTangoLimaVideo.py,sha256=I0lM08hUAjbU_ZElnF6uIx1hLMw7IWiqukzQt4umYg8,4489
@@ -344,7 +344,7 @@ mxcubecore/HardwareObjects/abstract/AbstractAperture.py,sha256=bPaiCnFzjgjIE6EDh
 mxcubecore/HardwareObjects/abstract/AbstractAuthenticator.py,sha256=F5ONnre9GEcg65hTiEYpTcj0frGojP1QrC2P8rmzcjU,1575
 mxcubecore/HardwareObjects/abstract/AbstractBeam.py,sha256=Fvz5K3ov0Glsw8bO2oXiYbkFMK9L8CX4gldJg73lkr0,10389
 mxcubecore/HardwareObjects/abstract/AbstractCharacterisation.py,sha256=knGIC9GVSY_mJfcpMpU9qP8OfaIngasGEc8PIVFsr_4,4990
-mxcubecore/HardwareObjects/abstract/AbstractCollect.py,sha256=U1Eixcm7wUny0uLD0eXPAxY-8qKXzg7HDxbrRhcJ2jY,33360
+mxcubecore/HardwareObjects/abstract/AbstractCollect.py,sha256=L9xyT1IgtiRCIR303Nw9fe_TN7azKcLKMGtvCN7de_0,33360
 mxcubecore/HardwareObjects/abstract/AbstractDetector.py,sha256=p3pblv8Qu6_SASiz7fi6H8kzcFERuaJwhf--eb1hy_c,11511
 mxcubecore/HardwareObjects/abstract/AbstractEnergy.py,sha256=zG6tICqBdWcEMz8gGh7DFvP6CHz5xNlaRdcG4Y8tFps,4553
 mxcubecore/HardwareObjects/abstract/AbstractEnergyScan.py,sha256=OnUXHBNm5kt7Lud0UmReZzs9Jv4d1cCJTlB4JRlvBOc,6066
@@ -380,20 +380,20 @@ mxcubecore/HardwareObjects/edna_test_data.py,sha256=W7Uqm2v5sUWn-pY-nKDxEctV4qjT
 mxcubecore/HardwareObjects/mockup/ActuatorMockup.py,sha256=-aUtpJCImnbFJrl0AHjM13WQQH02LTPYOLHoHBSukIw,4050
 mxcubecore/HardwareObjects/mockup/ApertureMockup.py,sha256=8tonVXyivfTGKp18cCzJs8o4WspHCA17SNjLAfXT9cI,4167
 mxcubecore/HardwareObjects/mockup/BeamDefinerMockup.py,sha256=E6ATeySA9IDseTBvmvTr6v6GBUiJqEsanQX2saXNtn0,4174
-mxcubecore/HardwareObjects/mockup/BeamMockup.py,sha256=UH8jRFcGWjktt0enmMqYG6ob8nZP-rz0FfBFxk-z_BI,11508
+mxcubecore/HardwareObjects/mockup/BeamMockup.py,sha256=qIYMSn64CfYe5JWQ2J6PDWTX10F6VK6fxJwUaEyBz64,11582
 mxcubecore/HardwareObjects/mockup/BeamlineActionsMockup.py,sha256=UX2LqTiRZ3mIv3AVSLLVsZHalcAP_Ewx_lz7Da6H4Kg,1774
 mxcubecore/HardwareObjects/mockup/BeamlineTestMockup.py,sha256=ZNqpoE3spG5ObC6PuSY9_mlt2DvEw5U3cQWsCFIDB6Q,11464
 mxcubecore/HardwareObjects/mockup/BeamstopMockup.py,sha256=ylpXcHv84Xh9MkT-koOMO0V5Agz7m8OXVSd3itDkbZ8,1956
 mxcubecore/HardwareObjects/mockup/CatsMaintMockup.py,sha256=JXjYX_V-wL_ghnawFhm1odUv3FFpbdIN8LB1GZ6w6n0,12057
 mxcubecore/HardwareObjects/mockup/CollectMockup.py,sha256=nj_QyR_SlUDH705DENyFnkEHxl2VVZYkvnytnhREBBk,7344
-mxcubecore/HardwareObjects/mockup/DetectorMockup.py,sha256=uRZR_lxdiUeSzgfLFsfBO2L5tSb6s4nfnkBY12FWtw0,1960
-mxcubecore/HardwareObjects/mockup/DiffractometerMockup.py,sha256=UPjOloSms5V6qhk4LOVOERHlkNfzCIsdLSdD383OTzM,12355
+mxcubecore/HardwareObjects/mockup/DetectorMockup.py,sha256=cJgQGhd6R5FEiWcnjcb7MA9nSBlBx66cwLjVeb1ai34,1960
+mxcubecore/HardwareObjects/mockup/DiffractometerMockup.py,sha256=fAIpIJW8g5wyVuLn4QQo5sVBl07CmKn-yScdHCNXppI,12299
 mxcubecore/HardwareObjects/mockup/DoorInterlockMockup.py,sha256=Ug8oiP3ly70fhnrvwieStAhZr0oXOLMNI9LDL02gslI,1696
 mxcubecore/HardwareObjects/mockup/EDNACharacterisationMockup.py,sha256=agywWmr6dqNJeLymq83UOBdNGpr6436LrypgWu5x-Zg,1986
 mxcubecore/HardwareObjects/mockup/EnergyMockup.py,sha256=Qrhkvc2SS84GIIsVbsdST48dUAscuJa3pDmErWdKbmU,2087
 mxcubecore/HardwareObjects/mockup/EnergyScanMockup.py,sha256=uJZwCl5JalXHyEYQZT-MTonVrBAUptNEtbVz_5OikiU,14291
 mxcubecore/HardwareObjects/mockup/ExporterNStateMockup.py,sha256=IhjRjBsejcL0nbflSYfASSjoaskIloio1-o_KaiKd1s,4018
-mxcubecore/HardwareObjects/mockup/FluxMockup.py,sha256=YftCAbbmfyu0TJ3u1Fji-g5-Cy_EnYnLykVOb1rCIz0,3158
+mxcubecore/HardwareObjects/mockup/FluxMockup.py,sha256=3MW657zojJUIh9a7qwfz7Fq8xXH0SJbv2837vcMBBBQ,3037
 mxcubecore/HardwareObjects/mockup/HarvesterMockup.py,sha256=4mfnzx2cD8x3tORaRsLvS5XALJd9QpSyRN30JYnl61k,15880
 mxcubecore/HardwareObjects/mockup/ISPyBClientMockup.py,sha256=XPL0fu7-vI1Gxzhs7fEerU9aO_FF78ZpUG6tUVfENkk,17506
 mxcubecore/HardwareObjects/mockup/ISPyBRestClientMockup.py,sha256=3t_ZdLMAx7DeZnlpONZFyJr3jYwhBEZsszsrZvxgvZ8,10107
@@ -444,7 +444,7 @@ mxcubecore/model/protocols/exporter.py,sha256=uY-O7lFlRKL8A0SWB_VRI22nAxq1KqIFmE
 mxcubecore/model/protocols/sardana.py,sha256=eeuqM0C4JU4mm1WPVqwAR52nWgWamJNh5KLnde_7Wqw,1260
 mxcubecore/model/protocols/tango.py,sha256=izmX-V_rKFmwYTJToWkyBONSZdEQsHVbi6CWHTBhBFs,2241
 mxcubecore/model/queue_model_enumerables.py,sha256=hSOp77Xn0wzUGDl5EaLtblr8ND9FXytqadtW40VFDcA,2330
-mxcubecore/model/queue_model_objects.py,sha256=WC2QdNOy95vjeskMpCwh9J_Blhu-HUvSJRDSZmODFig,100216
+mxcubecore/model/queue_model_objects.py,sha256=05QWGFdJlLBoQuOFgcnE7Jv72zZElNEAMALIA3l7_UI,100464
 mxcubecore/protocols_config.py,sha256=0ujkNkTteeSvY3gNjsdhRzQw9FND2S8jNO_ZdrHNPR8,5703
 mxcubecore/queue_entry/__init__.py,sha256=fQLLDdLhLlRdV_pisyb9-G4dbqrGx_iroE4048p2sR8,4087
 mxcubecore/queue_entry/advanced_connector.py,sha256=l0GFbAu64p5mIwRL5ZEJOr08NXAdRvYLR-DXoN-DyUs,3177
@@ -465,8 +465,8 @@ mxcubecore/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,
 mxcubecore/utils/conversion.py,sha256=G1bk2Mi2ZwGbZa5pEeiFaKWxhSVXVGqu1L9_SioyUOk,4513
 mxcubecore/utils/qt_import.py,sha256=hQkBVZLUDZtktX7DSyoH88GAK_mK9Ghlsj4k9pFJeAQ,14415
 mxcubecore/utils/units.py,sha256=2D1QlTwe8eSs2UYRm4VVxSTosZZHeM-Pfw9KlcLbDAg,1251
-mxcubecore-1.334.0.dist-info/COPYING,sha256=u-Mc8zCecwyo4YoP8UulmzCiZZ_MmCLROd_NBtOcRj0,35148
-mxcubecore-1.334.0.dist-info/COPYING.LESSER,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
-mxcubecore-1.334.0.dist-info/METADATA,sha256=5Qqz5Zc0DbZcrs3N6aBv_kA5I1N_oPUNqs8bbut_3Ek,4262
-mxcubecore-1.334.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-mxcubecore-1.334.0.dist-info/RECORD,,
+mxcubecore-1.336.0.dist-info/COPYING,sha256=u-Mc8zCecwyo4YoP8UulmzCiZZ_MmCLROd_NBtOcRj0,35148
+mxcubecore-1.336.0.dist-info/COPYING.LESSER,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
+mxcubecore-1.336.0.dist-info/METADATA,sha256=i5BMTf__2MZPLYqsur4tacj7_3-hxDzz5_VGhxnGfmc,4262
+mxcubecore-1.336.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+mxcubecore-1.336.0.dist-info/RECORD,,