WIP Adapted Qt-relevant files to let Qt version work with the new AbstractDiffractometer

mxcubecore/HardwareObjects/GenericDiffractometer.py

@@ -215,7 +215,7 @@ class GenericDiffractometer(HardwareObject):
     """
 
     CENTRING_MOTORS_NAME = [
-        "phi",
+        "omega",
         "phiz",
         "phiy",
         "sampx",

mxcubecore/HardwareObjects/SampleView.py

@@ -147,9 +147,9 @@ def get_positions(self) -> dict[str, float]:
         Returns:
             Centring motor positions as {role: position}
         """
-        motors_dict = {}
-        for key, val in self.centring_motors.items():
-            motors_dict.update({key: val.motor.get_value()})
+        motors_dict = dict(
+            (key, val.get_value()) for key, val in self.centring_motors.items()
+        )
         return motors_dict
 
     def get_centred_point_from_coord(self, x, y, return_by_names=None):
@@ -246,7 +246,7 @@ def motor_positions_to_screen(
             inv_rot_matrix,
         )
 
-        chi_angle = math.radians(self.chi_angle)
+        chi_angle = math.radians(self.chi_angle) if self.chi_angle else 0.0
         chi_rot = np.matrix(
             [
                 [math.cos(chi_angle), -math.sin(chi_angle)],
@@ -276,7 +276,7 @@ def start_manual_centring(self, nb_click: int = 3):
         diffr = HWR.beamline.diffractometer
         pixels_per_mm = diffr.get_pixels_per_mm()
         diffr.wait_status_ready(5)
-
+        print(f"self.centring_motors {self.centring_motors}")
         self.current_centring_procedure = sample_centring.start(
             self.centring_motors,
             pixels_per_mm[0],
@@ -354,15 +354,18 @@ def accept_centring(self):
         """Accept the current centred position."""
         self.centring_status["valid"] = True
         self.centring_status["accepted"] = True
-        self.emit("centringAccepted", (True, self.get_centring_status()))
+        args = (True, self.get_centring_status())
+        self.emit("centringAccepted", args)
+        self.create_centring_point(*args)
         logging.getLogger("user_level_log").info("Centring successful")
 
     def reject_centring(self):
         """Reject the current centred position."""
         if self.current_centring_procedure:
             self.current_centring_procedure.kill(block=True)
         self.centring_status["valid"] = False
-        self.emit("centringAccepted", (False, self.get_centring_status()))
+        args = (False, self.get_centring_status())
+        self.emit("centringAccepted", args)
         logging.getLogger("user_level_log").info("Centring cancelled")
 
     def cancel_centring(self):

mxcubecore/HardwareObjects/abstract/AbstractDiffractometer.py

@@ -79,6 +79,7 @@
 
 from mxcubecore.BaseHardwareObjects import HardwareObject, HardwareObjectState
 from mxcubecore import HardwareRepository as HWR
+from mxcubecore.model import queue_model_objects
 
 
 __copyright__ = """ Copyright © by the MXCuBE collaboration """
@@ -244,6 +245,9 @@ def init(self):
                 self.connect(_hobj, "valueChanged", _hobj.update_value)
             except KeyError:
                 self.log.warning("Diffractometer: No motors configured")
+        queue_model_objects.CentredPosition.set_diffractometer_motor_names(
+            list(self.motors_hwobj_dict)
+        )
 
         # nstate (discrete positions) equipment
         for role in self.config.nstate_equipment:

mxcubecore/HardwareObjects/abstract/AbstractSampleView.py

@@ -293,3 +293,6 @@ def motor_positions_to_screen(self, positions_dict: dict) -> tuple:
         """Get the motor positions according to the calibration"""
 
         return ()
+
+    def get_image_scale_list(self):
+        return [1]

mxcubecore/HardwareObjects/mockup/DiffractometerMockup.py

@@ -66,7 +66,7 @@ def init(self):
         self.update_state(HardwareObjectState.READY)
         for mot in self.motors_hwobj_dict.values():
             mot.set_value(random.uniform(0.0, 8.8))
-        self.omega.set_value(random.uniform(0, 359.9))
+        self.omega.set_value(random.uniform(0, 360))
 
     def abort(self):
         self.update_state(HardwareObjectState.READY)
@@ -143,3 +143,12 @@ def _set_phase(self, value: DiffractometerPhase):
 
     def _set_constraint(self, value):
         self.current_constraint = value
+
+    def use_sample_changer(self):
+        return True
+
+    def accept_centring(self):
+        return True
+
+    def user_confirms_centring(self):
+        return False

mxcubecore/HardwareObjects/mockup/MotorMockup.py

@@ -54,6 +54,7 @@ class MotorMockup(ActuatorMockup, AbstractMotor):
     def __init__(self, name):
         AbstractMotor.__init__(self, name)
         self._wrap_range = None
+        self.direction = 1.0
 
     def init(self):
         """Initialisation method"""

mxcubecore/HardwareObjects/sample_centring.py

@@ -86,13 +86,11 @@ def prepare(centring_motors_dict):
 
     motors_to_move = {}
     for m in centring_motors_dict.values():
-        if m.reference_position is not None:
-            motors_to_move[m.motor] = m.reference_position
+        if hasattr(m, "reference_position") and m.reference_position is not None:
+            motors_to_move[m] = m.reference_position
     move_motors(motors_to_move)
 
-    SAVED_INITIAL_POSITIONS = {
-        m.motor: m.motor.get_value() for m in centring_motors_dict.values()
-    }
+    SAVED_INITIAL_POSITIONS = {m: m.get_value() for m in centring_motors_dict.values()}
 
     omega = centring_motors_dict["omega"]
     phiy = centring_motors_dict["phiy"]
@@ -281,7 +279,7 @@ def centre_plate1Click(
     centred_pos = SAVED_INITIAL_POSITIONS.copy()
 
     centred_pos.update(
-        {sampx.motor: float(sampx.get_value()), sampy.motor: float(sampy.get_value())}
+        {sampx: float(sampx.get_value()), sampy: float(sampy.get_value())}
     )
 
     return centred_pos
@@ -352,14 +350,14 @@ def centre_plate(
     centred_pos = SAVED_INITIAL_POSITIONS.copy()
     centred_pos.update(
         {
-            sampx.motor: float(sampx.get_value() + sampx.direction * dx),
-            sampy.motor: float(sampy.get_value() + sampy.direction * dy),
-            phiz.motor: (
+            sampx: float(sampx.get_value() + sampx.direction * dx),
+            sampy: float(sampy.get_value() + sampy.direction * dy),
+            phiz: (
                 float(phiz.get_value() + phiz.direction * d_vertical[0, 0])
                 if phiz.__dict__.get("reference_position") is None
                 else phiz.reference_position
             ),
-            phiy.motor: (
+            phiy: (
                 float(phiy.get_value() + phiy.direction * d_horizontal[0, 0])
                 if phiy.__dict__.get("reference_position") is None
                 else phiy.reference_position
@@ -383,13 +381,14 @@ def centre_plate(
 
 
 def ready(motor_list):
-    logging.getLogger("HWR").info([m.actuator_name for m in motor_list])
+    logging.getLogger("HWR").info([m.name for m in motor_list])
     rstate = [m.is_ready() for m in motor_list]
     logging.getLogger("HWR").info(rstate)
     return all(rstate)
 
 
 def wait_ready(motor_positions_dict, timeout=None):
+    print("motor_positions_dict", motor_positions_dict)
     with gevent.Timeout(timeout):
         while not ready(motor_positions_dict.keys()):
             time.sleep(0.1)
@@ -443,8 +442,8 @@ def center(
     pixelsPerMm_Ver,
     beam_xc,
     beam_yc,
-    chi_angle,
-    n_points,
+    chi_angle=0.0,
+    n_points=3,
     omega_range=180,
 ):
     global USER_CLICKED_EVENT
@@ -478,7 +477,7 @@ def center(
         raise RuntimeError("Exception while centring")
 
     logging.getLogger("HWR").debug("X=%s,Y=%s", X, Y)
-    chi_angle = math.radians(chi_angle)
+    chi_angle = math.radians(chi_angle) if chi_angle else 0.0
     chiRotMatrix = numpy.matrix(
         [
             [math.cos(chi_angle), -math.sin(chi_angle)],
@@ -503,14 +502,14 @@ def center(
     centred_pos = SAVED_INITIAL_POSITIONS.copy()
     centred_pos.update(
         {
-            sampx.motor: float(sampx.get_value() + sampx.direction * dx),
-            sampy.motor: float(sampy.get_value() + sampy.direction * dy),
-            phiz.motor: (
+            sampx: float(sampx.get_value() + sampx.direction * dx),
+            sampy: float(sampy.get_value() + sampy.direction * dy),
+            phiz: (
                 float(phiz.get_value() + phiz.direction * d_vertical[0, 0])
                 if phiz.__dict__.get("reference_position") is None
                 else phiz.reference_position
             ),
-            phiy.motor: (
+            phiy: (
                 float(phiy.get_value() + phiy.direction * d_horizontal[0, 0])
                 if phiy.__dict__.get("reference_position") is None
                 else phiy.reference_position

mxcubecore/__version__.py

@@ -23,6 +23,6 @@
         with open(Path(__file__).resolve().parents[1] / "pyproject.toml", "rb") as f:
             pyproject = load_toml(f)
             __version__ = pyproject["tool"]["poetry"]["version"]
-    except OSError:
+    except (OSError, KeyError):
         # File IO error
         __version__ = "local"

mxcubecore/configuration/mockup/detector-mockup.xml

@@ -10,7 +10,7 @@
   <width>3110</width>
   <height>3269</height>
   <hasShutterless>True</hasShutterless>
-  <fileSuffix>h5</fileSuffix>
+  <fileSuffix>cbf</fileSuffix>
   <object hwrid="/detector-distance-mockup" role="detector_distance"/>
 
   <roiModes>("0", "C18", "C12", "C2")</roiModes>

mxcubecore/configuration/mockup/diffractometer-mockup.xml

@@ -9,8 +9,8 @@
     <object href="/diff-phiz-mockup" role="phiz"/>
     <object href="/diff-sampx-mockup" role="sampx"/>
     <object href="/diff-sampy-mockup" role="sampy"/>
-    <object href="/udiff_backlight" role="backlight"/>
-    <object href="/udiff_frontlight" role="frontlight"/>
+    <!--object href="/backlightswitch" role="backlight"/-->
+    <!--object href="/frontlightswitch" role="frontlight"/-->
   </motors>
   <nstate_equipment>
     <object href="/fast-shutter-mockup" role="fshutter"/>

mxcubecore/configuration/mockup/gphl/collect-mockup.xml

@@ -1,15 +1,11 @@
 <object class="Gphl.CollectEmulator">
 
-<!--  <override_data_directories>-->
-    <!-- If override_data_directories is set, it must contain the three base directories -->
-    <!-- and may contain raw_folder, process_folder, and archive_folder -->
-    <base_directory>/scratch_fs1/rhfogh/mxcube_base_dir</base_directory>
-    <base_process_directory>/scratch_fs1/rhfogh/mxcube_base_dir</base_process_directory>
-    <base_archive_directory>/scratch_fs1/rhfogh/mxcube_base_dir</base_archive_directory>
-<!--    <base_directory>/mnt/scratch/rhfogh/mxcube_data</base_directory>-->
-<!--    <base_process_directory>/mnt/scratch/rhfogh/mxcube_data</base_process_directory>-->
-<!--    <base_archive_directory>/mnt/scratch/rhfogh/mxcube_data</base_archive_directory>-->
-<!--  </override_data_directories>-->
+  <!--<auto_processing>-->
+    <!--<program>-->
+      <!--<executable>none_present_executable</executable>-->
+      <!--<event>after</event>-->
+    <!--</program>-->
+  <!--</auto_processing>-->
 
   <directory_prefix>emulator</directory_prefix>
 
@@ -21,8 +17,8 @@
     <!-- Simcal background noise level -->
     <background>1.0</background>
     <!-- Number of rays for simcal ray tracing (2000 minimum for testing, 5000 for use-->
-<!--    <n_rays>2001</n_rays>-->
-    <n_rays>5001</n_rays>
+    <n_rays>2001</n_rays>
+    <!--<n_rays>5001</n_rays>-->
     <!-- Unit cell orientation mode. 1 is calculate-from-cell, real-space -->
     <!-- -1 is from-cell, reciprocal-space. Default is 0 (CELL_AXIS vectors) -->
     <orient_mode>1</orient_mode>
@@ -38,9 +34,8 @@
     <memory-pool>6</memory-pool>
     <!-- Default is 1.0. Too low makes for 'insufficient spots', -->
     <!-- too high for 'insufficient indexed fraction' errors -->
-    <!-- For now all test hkli files are scaled to work with scale 4.0 -->
-<!--    <hkl-scale>1.0</hkl-scale>-->
-    <hkl-scale>4.0</hkl-scale>
+    <!-- For now all test hkli files are sdcaled to work with scale 1.0 -->
+    <hkl-scale>1.0</hkl-scale>
     <!-- NB set specifically for 5yav PONLY -->
 <!--    <hkl-scale>0.1</hkl-scale>-->
   </simcal_options>

mxcubecore/configuration/mockup/gphl/gphl-setup.yml

@@ -45,7 +45,7 @@ configuration:
 
   software_paths:
     # Mandatory. Directory with workflow config input, e.g. instrumentation.nml
-    gphl_beamline_config: gphl_beamline_config
+    gphl_beamline_config: gphl/gphl_beamline_config
 
     # MANDATORY for CCP4 => $GPHL_CCP4_PATH/bin/ccp4.setup-sh,
     # unless already sourced in environment
@@ -89,6 +89,6 @@ configuration:
 
     # OPTIONAL. simcal *binary* For Mock collection emulation only. Not used by workflow
     co.gphl.wf.simcal.bin:
-      /home/rhfogh/Software/GPhL/nightly_20251106/Files_workflow_TRUNK_alpha-bdg/autoPROC/bin/linux64/simcal
+      /home/rhfogh/Software/GPhL/nightly_20260519/Files_workflow_TRUNK_alpha-bdg/autoPROC/bin/linux64/simcal
     co.gphl.wf.simcal.bdg_licence_dir:
-      /home/rhfogh/Software/GPhL/nightly_20251106/Files_workflow_TRUNK_alpha-bdg
+      /home/rhfogh/Software/GPhL/nightly_20260519/Files_workflow_TRUNK_alpha-bdg