[WIP] DoseRate

mxcubecore/HardwareObjects/Beamline.py

@@ -123,6 +123,10 @@ def energy(self) -> HardwareObject | None:
     def flux(self) -> HardwareObject | None:
         return self.get_object_by_role("flux")
 
+    @property
+    def dose_rate(self) -> HardwareObject | None:
+        return self.get_object_by_role("dose_rate")
+
     @property
     def beam(self) -> HardwareObject | None:
         return self.get_object_by_role("beam")

mxcubecore/HardwareObjects/DoseRate.py

@@ -0,0 +1,82 @@
+# encoding: utf-8
+#
+#  Project name: MXCuBE
+#  https://github.com/mxcube
+#
+#  This file is part of MXCuBE software.
+#
+#  MXCuBE is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU Lesser General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  MXCuBE is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public License
+#  along with MXCuBE. If not, see <http://www.gnu.org/licenses/>.
+"""Radiation dose for a sample as function of the flux. Uses the beamline.flux
+The dose calculation routine has to be provided externally.
+Example yml configuration:
+
+.. code-block:: yaml
+
+ class: DoseRate.DoseRate
+   configuration:
+      actuator_name: doserate
+      username: Radiation Dose Rate
+      read_only: True
+      default_limits: (0,500)  # MGy/s
+   objects:
+      dose_calculator: dose_calculator.yaml
+
+"""
+
+__copyright__ = """Copyright The MXCuBE Collaboration"""
+__license__ = "LGPLv3+"
+
+
+from mxcubecore import HardwareRepository as HWR
+from mxcubecore.HardwareObjects.abstract.AbstractActuator import AbstractActuator
+
+
+class DoseRate(AbstractActuator):
+    """Report the dose rate"""
+
+    unit = "MGy/s"
+
+    def __init__(self, name):
+        super().__init__(name)
+        self.dose_calc = None
+
+    def init(self):
+        """Initialisation"""
+        super().init()
+        self.dose_calc = self.get_object_by_role("dose_calculator")
+        try:
+            HWR.beamline.flux.connect("valueChanged", self.update_value)
+        except AttributeError as err:
+            raise RuntimeError("Flux reading is not configured") from err
+
+    def get_value(self) -> float:
+        """Get the dose rate value as function of the photon flux.
+        Returns:
+            dose rate [MGy/s]
+        """
+        self._nominal_value = self.calculate_dose(HWR.beamline.flux.get_value())
+        return self._nominal_value
+
+    def calculate_dose(self, flux: float | None = None) -> float:
+        """Calculate the dose rate as function of the flux value.
+        Args:
+            flux: Flux value. If None, read the current beamline flux.
+        Returns:
+            The calculated dose [MGy/s]
+        """
+        if flux is None:
+            flux = HWR.beamline.flux.get_value()
+        if flux > 0:
+            return self.dose_calc(flux)
+        return 0

mxcubecore/HardwareObjects/mockup/DoseRateMockup.py

@@ -0,0 +1,45 @@
+# encoding: utf-8
+#
+#  Project name: MXCuBE
+#  https://github.com/mxcube
+#
+#  This file is part of MXCuBE software.
+#
+#  MXCuBE is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU Lesser General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  MXCuBE is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public License
+#  along with MXCuBE. If not, see <http://www.gnu.org/licenses/>.
+"""Radiation dose mock object"""
+
+__copyright__ = """Copyright The MXCuBE Collaboration"""
+__license__ = "LGPLv3+"
+
+from random import uniform
+
+from mxcubecore import HardwareRepository as HWR
+from mxcubecore.HardwareObjects.DoseRate import DoseRate
+
+
+class DoseRateMockup(DoseRate):
+    """DoseRate mock class"""
+
+    def calculate_dose(self, flux: float | None = None) -> float:
+        """Calculate the dose rate as function of the flux value.
+        Args:
+            flux: Flux value.
+        Returns:
+            The calculated dose [MGy/s]
+        """
+        if flux is None:
+            flux = HWR.beamline.flux.get_value()
+        if flux > 0:
+            return flux * uniform(0, 300.0) / 1e12  # noqa S311
+        return 0

mxcubecore/configuration/mockup/dose_rate_mockup.yaml

@@ -0,0 +1,7 @@
+---
+class: DoseRateMockup.DoseRateMockup
+configuration:
+  actuator_name: doserate
+  username: Radiation Dose Rate
+  read_only: true
+  default_limits: (0,500)  # MGy/s

mxcubecore/configuration/mockup/test/beamline.yaml

@@ -30,6 +30,7 @@ objects:
   - energy: energy-mockup.xml
   - beam: beam-mockup.xml
   - flux: flux-mockup.xml
+  - dose_rate: dose_rate_mockup.yaml
   - detector: detector-mockup.xml
   - resolution: resolution-mockup.xml
   - safety_shutter: safety-shutter-mockup.xml

test/test_dose_rate.py

@@ -0,0 +1,59 @@
+# encoding: utf-8
+#
+#  Project name: MXCuBE
+#  https://github.com/mxcube
+#
+#  This file is part of MXCuBE software.
+#
+#  MXCuBE is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU Lesser General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  MXCuBE is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU General Lesser Public License
+#  along with MXCuBE. If not, see <http://www.gnu.org/licenses/>.
+
+"""Test suite for AbstractFlux"""
+
+__copyright__ = """ Copyright © 2019-2020 by the MXCuBE collaboration """
+__license__ = "LGPLv3+"
+
+import pytest
+
+from test import TestAbstractActuatorBase
+
+
+@pytest.fixture
+def test_object(beamline):
+    """Use the dose_rate object from beamline"""
+    return beamline.dose_rate
+
+
+class TestDoseRate(TestAbstractActuatorBase.TestAbstractActuatorBase):
+    """Test DoseRate"""
+
+    def test_initial_value(self, test_object):
+        assert test_object is not None, (
+            "DoseRate hardware objects is None (not initialized)"
+        )
+
+        # value should never be None
+        assert test_object.get_value() is not None, "initial value may not be None"
+
+    def test_attributes(self, test_object):
+        """Test the attributes"""
+        assert test_object.read_only is True
+        assert test_object.get_limits() == test_object._nominal_limits
+
+    def test_methods(self, test_object):
+        value = test_object.get_value()
+        print(f"------> Dose rate is {value}")
+        assert isinstance(value, (int, float)), "Dose rate should be int or float"
+
+        with pytest.raises(ValueError):
+            test_object.set_value(value)