fixed width for logo in scilog

.gitea/workflows/rtd_deploy.yml

@@ -0,0 +1,21 @@
+name: Read the Docs Deploy Trigger
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  trigger-rtd-webhook:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Trigger Read the Docs webhook
+        env:
+          RTD_TOKEN: ${{ secrets.RTD_TOKEN }}
+        run: |
+          curl --fail --show-error --silent \
+            -X POST \
+            -d "branches=${{ github.ref_name }}" \
+            -d "token=${RTD_TOKEN}" \
+            "https://readthedocs.org/api/v2/webhook/sls-csaxs/270162/"

.readthedocs.yaml

@@ -8,15 +8,14 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.10"
+    python: "3.12"
   jobs:
     pre_install:
       - pip install .
 
-
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
+  configuration: docs/conf.py
 
 # If using Sphinx, optionally build your docs in additional formats such as PDF
 # formats:
@@ -24,6 +23,5 @@ sphinx:
 
 # Optionally declare the Python requirements required to build your docs
 python:
-   install:
-   - requirements: docs/requirements.txt
-
+  install:
+    - requirements: docs/requirements.txt

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py

@@ -356,18 +356,6 @@ class LamNI(LamNIOpticsMixin, LamniGuiTools):
     # Logging helpers
     # ------------------------------------------------------------------
 
-    def write_to_spec_log(self, content):
-        try:
-            with open(
-                os.path.expanduser(
-                    "~/Data10/specES1/log-files/specES1_started_2022_11_30_1313.log"
-                ),
-                "a",
-            ) as log_file:
-                log_file.write(content)
-        except Exception:
-            logger.warning("Failed to write to spec log file (omny web page).")
-
     def write_to_scilog(self, content, tags: list = None):
         try:
             if tags is not None:
@@ -439,7 +427,6 @@ class LamNI(LamNIOpticsMixin, LamniGuiTools):
                     f"{str(datetime.datetime.now())}: LamNI scan projection at angle {angle},"
                     f" scan number {bec.queue.next_scan_number}.\n"
                 )
-                self.write_to_spec_log(log_message)
                 corridor_size = self.corridor_size if self.corridor_size > 0 else None
                 scans.lamni_fermat_scan(
                     fov_size=[self.lamni_piezo_range_x, self.lamni_piezo_range_y],
@@ -779,7 +766,7 @@ class LamNI(LamNIOpticsMixin, LamniGuiTools):
 
         user_input = input("Are these parameters correctly set for your scan? ")
         if user_input == "y":
-            print("good then")
+            print("OK. continue.")
             return
 
         self.tomo_countingtime = self._get_val("<ctime> s", self.tomo_countingtime, float)

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni_optics_mixin.py

@@ -5,7 +5,7 @@ from rich import box
 from rich.console import Console
 from rich.table import Table
 
-from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_put, fshclose
+from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_put
 from csaxs_bec.bec_ipython_client.plugins.omny.omny_general_tools import OMNYTools
 
 dev = builtins.__dict__.get("dev")
@@ -172,7 +172,7 @@ class LamNIOpticsMixin:
 
     def leye_out(self):
         self.loptics_in()
-        fshclose()
+        dev.omnyfsh.fshopen()
         leyey_out = self._get_user_param_safe("leyey", "out")
         umv(dev.leyey, leyey_out)
 

csaxs_bec/bec_ipython_client/plugins/flomni/flomni_optics_mixin.py

@@ -1,10 +1,10 @@
 import time
-
+import numpy as np
 from rich import box
 from rich.console import Console
 from rich.table import Table
 
-from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_put, fshclose
+from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_put
 
 
 class FlomniOpticsMixin:
@@ -16,12 +16,18 @@ class FlomniOpticsMixin:
         return param.get(var)
 
     def feye_out(self):
-        fshclose()
+        dev.omnyfsh.fshclose()
         self.foptics_in()
+        self.flomnigui_show_xeyealign()
+        self.xrayeye_update_frame()
+        if self.OMNYTools.yesno("Did the direct beam on the xray eye disappear?"):
+            print("excellent.")
+        else:
+            print("Aborting. With visible parts of the direct beam on the xray eye, it cannot be removed.")
+            return
         feyex_out = self._get_user_param_safe("feyex", "out")
         umv(dev.feyex, feyex_out)
 
-        epics_put("XOMNYI-XEYE-ACQ:0", 2)
         # move rotation stage to zero to avoid problems with wires
         umv(dev.fsamroy, 0)
         # umv(dev.fttrx1, 9.2)
@@ -32,16 +38,37 @@ class FlomniOpticsMixin:
 
         feyex_in = self._get_user_param_safe("feyex", "in")
         feyey_in = self._get_user_param_safe("feyey", "in")
-        umv(dev.feyex, feyex_in, dev.feyey, feyey_in)
-        #self.align.update_frame()
+
+        current_feyex = dev.feyex.readback.get()
+        current_feyey = dev.feyey.readback.get()
+
+        # check if both are close enough (within 0.01)
+        if np.isclose(current_feyex, feyex_in, atol=0.01) and np.isclose(current_feyey, feyey_in, atol=0.01):
+            # both already in position → do nothing
+            pass
+        else:
+            # move both axes to the desired "in" positions
+            umv(dev.feyex, feyex_in, dev.feyey, feyey_in)
 
     def _ffzp_in(self):
         foptx_in = self._get_user_param_safe("foptx", "in")
         fopty_in = self._get_user_param_safe("fopty", "in")
-        umv(dev.foptx, foptx_in)
-        umv(
-            dev.fopty, fopty_in
-        )  # for 7.2567 keV and 150 mu, 60 nm fzp, loptz 83.6000 for propagation 1.4 mm
+
+        current_foptx = dev.foptx.readback.get()
+        current_fopty = dev.fopty.readback.get()
+
+        tol = 0.003
+
+        # if either axis is outside the tolerance → move both
+        need_move_optics = (
+            not np.isclose(current_foptx, foptx_in, atol=tol) or
+            not np.isclose(current_fopty, fopty_in, atol=tol)
+        )
+
+        if need_move_optics:
+            umv(dev.foptx, foptx_in, dev.fopty, fopty_in)  # for 7.2567 keV and 150 mu, 60 nm fzp, loptz 83.6000 for propagation 1.4 mm
+        else:
+            print("FZP is already at the in position.")
 
     def ffzp_in(self):
         """
@@ -84,19 +111,85 @@ class FlomniOpticsMixin:
         # umv(dev.losax, -1.4850, dev.losay, -0.1930)
         # umv(dev.losaz, 1.0000)
         # 7.2, 150
+
         fosax_in = self._get_user_param_safe("fosax", "in")
         fosay_in = self._get_user_param_safe("fosay", "in")
         fosaz_in = self._get_user_param_safe("fosaz", "in")
+
+        # tighten limits
         dev.fosax.limits = [fosax_in - 0.1, fosax_in + 0.1]
         dev.fosay.limits = [fosay_in - 0.1, fosay_in + 0.1]
         dev.fosaz.limits = [fosaz_in - 0.1, fosaz_in + 0.1]
-        umv(dev.fosax, fosax_in, dev.fosay, fosay_in)
-        umv(dev.fosaz, fosaz_in)
+
+        current_fosax = dev.fosax.readback.get()
+        current_fosay = dev.fosay.readback.get()
+        current_fosaz = dev.fosaz.readback.get()
+
+        # tolerance
+        tol = 0.003
+
+        need_move_osa = (
+            not np.isclose(current_fosax, fosax_in, atol=tol) or
+            not np.isclose(current_fosay, fosay_in, atol=tol) or
+            not np.isclose(current_fosaz, fosaz_in, atol=tol)
+        )
+
+        if need_move_osa:
+            umv(dev.fosax, fosax_in, dev.fosay, fosay_in)
+            umv(dev.fosaz, fosaz_in)
+        else:
+            print("OSA is already at the IN position.")
 
         # 11 kev
         # umv(dev.losax, -1.161000, dev.losay, -0.196)
         # umv(dev.losaz, 1.0000)
 
+    def _check_eye_out_and_optics_in(self, tol=0.003):
+        # --- expected IN positions ---
+        foptx_in = self._get_user_param_safe("foptx", "in")
+        fopty_in = self._get_user_param_safe("fopty", "in")
+        foptz_in = self._get_user_param_safe("foptz", "in")
+
+        # --- expected OUT condition for the X-ray eye ---
+        # eye is OUT when it is *not within tolerance* of its IN position
+        feyex_out = self._get_user_param_safe("feyex", "out")
+
+        # --- current positions ---
+        cx_feyex = dev.feyex.readback.get()
+
+        cx_foptx = dev.foptx.readback.get()
+        cx_fopty = dev.fopty.readback.get()
+        cx_foptz = dev.foptz.readback.get()
+
+        # --- check eye OUT ---
+        eye_out = (
+            np.isclose(cx_feyex, feyex_out, atol=tol)
+        )
+
+        # --- check optics IN ---
+        optics_in = (
+            np.isclose(cx_foptx, foptx_in, atol=tol) and
+            np.isclose(cx_fopty, fopty_in, atol=tol) and
+            np.isclose(cx_foptz, foptz_in, atol=tol)
+        )
+
+        fosax_in = self._get_user_param_safe("fosax", "in")
+        fosay_in = self._get_user_param_safe("fosay", "in")
+        fosaz_in = self._get_user_param_safe("fosaz", "in")
+
+        cx_fosax = dev.fosax.readback.get()
+        cx_fosay = dev.fosay.readback.get()
+        cx_fosaz = dev.fosaz.readback.get()
+
+        osa_in = (
+            np.isclose(cx_fosax, fosax_in, atol=tol) and
+            np.isclose(cx_fosay, fosay_in, atol=tol) and
+            np.isclose(cx_fosaz, fosaz_in, atol=tol)
+        )
+
+        return eye_out and optics_in and osa_in
+
+
     def fosa_out(self):
         self.ensure_fheater_up()
         curtain_is_triggered = dev.foptz.controller.fosaz_light_curtain_is_triggered()

csaxs_bec/bec_ipython_client/plugins/flomni/gui_tools.py

@@ -1,4 +1,5 @@
 import builtins
+import time
 
 # from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
 
@@ -17,10 +18,17 @@ class flomniGuiToolsError(Exception):
 
 
 class flomniGuiTools:
+    GUI_RPC_TIMEOUT = 20
 
     def __init__(self):
         self.text_box = None
         self.progressbar = None
+        self.flomni_window = None
+        self.xeyegui = None
+        self.pdf_viewer = None
+        self.idle_text_box = None
+        self.camera_gripper_image = None
+        self.camera_overview_image = None
 
     def set_client(self, client):
         self.client = client
@@ -28,9 +36,11 @@ class flomniGuiTools:
 
     def flomnigui_show_gui(self):
         if "flomni" in self.gui.windows:
+            self.flomni_window = self.gui.windows["flomni"]
             self.gui.flomni.raise_window()
         else:
-            self.gui.new("flomni")
+            self.flomni_window = self.gui.new("flomni", timeout=self.GUI_RPC_TIMEOUT)
+            time.sleep(1)
 
     def flomnigui_stop_gui(self):
         self.gui.flomni.hide()
@@ -40,9 +50,11 @@ class flomniGuiTools:
 
     def flomnigui_show_xeyealign(self):
         self.flomnigui_show_gui()
-        if self._flomnigui_check_attribute_not_exists("xeyegui"):
+        if self._flomnigui_is_missing("xeyegui"):
             self.flomnigui_remove_all_docks()
-            self.xeyegui = self.gui.flomni.new("XRayEye", object_name="xrayeye")
+            self.xeyegui = self.gui.flomni.new(
+                "XRayEye", object_name="xrayeye", timeout=self.GUI_RPC_TIMEOUT
+            )
         # start live
         if not dev.cam_xeye.live_mode_enabled.get():
             dev.cam_xeye.live_mode_enabled.put(True)
@@ -50,9 +62,11 @@ class flomniGuiTools:
 
     def flomnigui_show_xeyealign_fittab(self):
         self.flomnigui_show_gui()
-        if self._flomnigui_check_attribute_not_exists("xeyegui"):
+        if self._flomnigui_is_missing("xeyegui"):
             self.flomnigui_remove_all_docks()
-            self.xeyegui = self.gui.flomni.new("XRayEye")
+            self.xeyegui = self.gui.flomni.new(
+                "XRayEye", object_name="xrayeye", timeout=self.GUI_RPC_TIMEOUT
+            )
         self.xeyegui.switch_tab("fit")
 
     def _flomnigui_check_attribute_not_exists(self, attribute_name):
@@ -68,31 +82,39 @@ class flomniGuiTools:
                     return False
         return True
 
+    def _flomnigui_is_missing(self, attribute_name):
+        widget = getattr(self, attribute_name, None)
+        if widget is None:
+            return True
+        if hasattr(widget, "_is_deleted") and widget._is_deleted():
+            return True
+        return False
+
     def flomnigui_show_cameras(self):
         self.flomnigui_show_gui()
         if self._flomnigui_check_attribute_not_exists(
             "cam_flomni_gripper"
         ) or self._flomnigui_check_attribute_not_exists("cam_flomni_overview"):
             self.flomnigui_remove_all_docks()
-            camera_gripper_image = self.gui.flomni.new("Image")
+            self.camera_gripper_image = self.gui.flomni.new("Image")
             if self._flomnicam_check_device_exists(dev.cam_flomni_gripper):
-                camera_gripper_image.image(device="cam_flomni_gripper", signal="preview")
-                camera_gripper_image.lock_aspect_ratio = True
-                camera_gripper_image.enable_fps_monitor = True
-                camera_gripper_image.enable_toolbar = False
-                camera_gripper_image.outer_axes = False
-                camera_gripper_image.inner_axes = False
+                self.camera_gripper_image.image(device="cam_flomni_gripper", signal="preview")
+                self.camera_gripper_image.lock_aspect_ratio = True
+                self.camera_gripper_image.enable_fps_monitor = True
+                self.camera_gripper_image.enable_toolbar = False
+                self.camera_gripper_image.outer_axes = False
+                self.camera_gripper_image.inner_axes = False
                 dev.cam_flomni_gripper.start_live_mode()
             else:
                 print("Cannot open camera_gripper. Device does not exist.")
-            camera_overview_image = self.gui.flomni.new("Image")
+            self.camera_overview_image = self.gui.flomni.new("Image")
             if self._flomnicam_check_device_exists(dev.cam_flomni_overview):
-                camera_overview_image.image(device="cam_flomni_overview", signal="preview")
-                camera_overview_image.lock_aspect_ratio = True
-                camera_overview_image.enable_fps_monitor = True
-                camera_overview_image.enable_toolbar = False
-                camera_overview_image.outer_axes = False
-                camera_overview_image.inner_axes = False
+                self.camera_overview_image.image(device="cam_flomni_overview", signal="preview")
+                self.camera_overview_image.lock_aspect_ratio = True
+                self.camera_overview_image.enable_fps_monitor = True
+                self.camera_overview_image.enable_toolbar = False
+                self.camera_overview_image.outer_axes = False
+                self.camera_overview_image.inner_axes = False
                 dev.cam_flomni_overview.start_live_mode()
             else:
                 print("Cannot open camera_overview. Device does not exist.")
@@ -101,15 +123,21 @@ class flomniGuiTools:
         # dev.cam_flomni_overview.stop_live_mode()
         # dev.cam_flomni_gripper.stop_live_mode()
         # dev.cam_xeye.live_mode = False
-        self.gui.flomni.delete_all()
+        if hasattr(self.gui, "flomni"):
+            self.gui.flomni.delete_all(timeout=self.GUI_RPC_TIMEOUT)
         self.progressbar = None
         self.text_box = None
+        self.xeyegui = None
+        self.pdf_viewer = None
+        self.idle_text_box = None
+        self.camera_gripper_image = None
+        self.camera_overview_image = None
 
     def flomnigui_idle(self):
         self.flomnigui_show_gui()
-        if self._flomnigui_check_attribute_not_exists("idle_text_box"):
+        if self._flomnigui_is_missing("idle_text_box"):
             self.flomnigui_remove_all_docks()
-            idle_text_box = self.gui.flomni.new("TextBox")
+            self.idle_text_box = self.gui.flomni.new("TextBox")
         text = (
             "<pre>"
             + "██████╗ ███████╗ ██████╗     ███████╗██╗      ██████╗ ███╗   ███╗███╗   ██╗██╗\n"
@@ -120,7 +148,7 @@ class flomniGuiTools:
             + "╚═════╝ ╚══════╝ ╚═════╝     ╚═╝     ╚══════╝ ╚═════╝ ╚═╝     ╚═╝╚═╝  ╚═══╝╚═╝\n"
             + "</pre>"
         )
-        idle_text_box.set_html_text(text)
+        self.idle_text_box.set_html_text(text)
 
     def flomnigui_docs(self, filename: str | None = None):
         import csaxs_bec
@@ -164,7 +192,7 @@ class flomniGuiTools:
         # --- GUI handling (active existence check) ----------------------------
         self.flomnigui_show_gui()
 
-        if self._flomnigui_check_attribute_not_exists("PdfViewerWidget"):
+        if self._flomnigui_is_missing("pdf_viewer"):
             self.flomnigui_remove_all_docks()
             self.pdf_viewer = self.gui.flomni.new(widget="PdfViewerWidget")
 
@@ -182,7 +210,7 @@ class flomniGuiTools:
 
     def flomnigui_show_progress(self):
         self.flomnigui_show_gui()
-        if self._flomnigui_check_attribute_not_exists("progressbar"):
+        if self._flomnigui_is_missing("progressbar"):
             self.flomnigui_remove_all_docks()
             # Add a new dock with a RingProgressBar widget
             self.progressbar = self.gui.flomni.new("RingProgressBar")
@@ -195,6 +223,14 @@ class flomniGuiTools:
         self._flomnigui_update_progress()
 
     def _flomnigui_update_progress(self):
+        """Update the progress ring bar and center label from the current progress state.
+
+        ``self.progress`` is backed by the BEC global variable ``tomo_progress``
+        (see :class:`_ProgressProxy` in ``flomni.py``), so this method reflects
+        the live state that is also accessible from other BEC client sessions via::
+
+            client.get_global_var("tomo_progress")
+        """
         main_progress_ring = self.progressbar.rings[0]
         subtomo_progress_ring = self.progressbar.rings[1]
         if self.progressbar is not None:
@@ -207,7 +243,43 @@ class flomniGuiTools:
             main_progress_ring.set_value(progress)
             subtomo_progress_ring.set_value(subtomo_progress)
 
-            text = f"Progress report:\n Tomo type: ....................... {self.progress['tomo_type']}\n Projection: ...................... {self.progress['projection']:.0f}\n Total projections expected ....... {self.progress['total_projections']}\n Angle: ........................... {self.progress['angle']}\n Current subtomo: ................. {self.progress['subtomo']}\n Current projection within subtomo: {self.progress['subtomo_projection']}\n Total projections per subtomo: ... {self.progress['subtomo_total_projections']}"
+            # --- format start time for display --------------------------------
+            start_str = self.progress.get("tomo_start_time")
+            if start_str is not None:
+                import datetime as _dt
+                start_display = _dt.datetime.fromisoformat(start_str).strftime("%Y-%m-%d %H:%M:%S")
+            else:
+                start_display = "N/A"
+
+            # --- format estimated remaining time ------------------------------
+            remaining_s = self.progress.get("estimated_remaining_time")
+            if remaining_s is not None and remaining_s >= 0:
+                import datetime as _dt
+                remaining_s = int(remaining_s)
+                h, rem = divmod(remaining_s, 3600)
+                m, s = divmod(rem, 60)
+                if h > 0:
+                    eta_display = f"{h}h {m:02d}m {s:02d}s"
+                elif m > 0:
+                    eta_display = f"{m}m {s:02d}s"
+                else:
+                    eta_display = f"{s}s"
+            else:
+                eta_display = "N/A"
+            # ------------------------------------------------------------------
+
+            text = (
+                f"Progress report:\n"
+                f" Tomo type:  {self.progress['tomo_type']}\n"
+                f" Projection:  {self.progress['projection']:.0f}\n"
+                f" Total projections expected  {self.progress['total_projections']:.1f}\n"
+                f" Angle:  {self.progress['angle']:.1f}\n"
+                f" Current subtomo:  {self.progress['subtomo']}\n"
+                f" Current projection within subtomo: {self.progress['subtomo_projection']}\n"
+                f" Total projections per subtomo:  {int(self.progress['subtomo_total_projections'])}\n"
+                f" Scan started:  {start_display}\n"
+                f" Est. remaining:  {eta_display}"
+            )
             self.progressbar.set_center_label(text)
 
 

csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py

@@ -231,10 +231,6 @@ class XrayEyeAlign:
         fovx = self._xray_fov_xy[0] * self.PIXEL_CALIBRATION * 1000 / 2
         fovy = self._xray_fov_xy[1] * self.PIXEL_CALIBRATION * 1000 / 2
 
-        self.tomo_rotate(0)
-
-        umv(dev.rtx, 0)
-
         if keep_shutter_open:
             if self.flomni.OMNYTools.yesno("Close the shutter now?", "y"):
                 dev.omnyfsh.fshclose()
@@ -251,9 +247,14 @@ class XrayEyeAlign:
 
         print("Automatically loading new alignment parameters from xray eye alignment.\n")
 
-        self.flomni.read_alignment_offset()
+        self.flomni.read_alignment_offset(get_data_from_gui=True)
 
+        self.tomo_rotate(0)
+
+        umv(dev.rtx, 0)
         print("You are ready to remove the xray eye and start ptychography scans.")
+        print("Fine alignment: flomni.tomo_parameters() , then flomni.tomo_alignment_scan()")
+        print("After that, run the fit in Matlab and load the new fit flomni.read_alignment_offset()")
 
     def write_output(self):
         file = os.path.expanduser("~/Data10/specES1/internal/xrayeye_alignmentvalues")

csaxs_bec/bec_ipython_client/plugins/omny/omny.py

@@ -852,18 +852,6 @@ class OMNY(
     def sample_name(self):
         return dev.omny_samples.get_sample_name_in_samplestage()
 
-    def write_to_spec_log(self, content):
-        try:
-            with open(
-                os.path.expanduser(
-                    "~/Data10/specES1/log-files/specES1_started_2022_11_30_1313.log"
-                ),
-                "a",
-            ) as log_file:
-                log_file.write(content)
-        except Exception:
-            logger.warning("Failed to write to spec log file (omny web page).")
-
     def write_to_scilog(self, content, tags: list = None):
         try:
             if tags is not None:
@@ -1288,7 +1276,6 @@ class OMNY(
                     f"{str(datetime.datetime.now())}: omny scan projection at angle {angle}, scan"
                     f" number {bec.queue.next_scan_number}.\n"
                 )
-                self.write_to_spec_log(log_message)
                 # self.write_to_scilog(log_message, ["BEC_scans", self.sample_name])
                 scans.omny_fermat_scan(
                     fovx=self.fovx,

csaxs_bec/bec_ipython_client/plugins/omny/omny_optics_mixin.py

@@ -48,7 +48,7 @@ class OMNYOpticsMixin:
         dev.oeyez.controller.socket_put_confirmed("axspeed[7]=10000")
 
     def oeye_out(self):
-        fshclose()
+        dev.omnyfsh.fshclose()
         if self.OMNYTools.yesno("Did you move in the optics?"):
             umv(dev.oeyez, -2)
             self._oeyey_mv(-60.3)

csaxs_bec/bec_widgets/widgets/client.py

@@ -38,12 +38,14 @@ class XRayEye(RPCBase):
         None
         """
 
+    @rpc_timeout(20)
     @rpc_call
     def on_live_view_enabled(self, enabled: "bool"):
         """
         None
         """
 
+    @rpc_timeout(20)
     @rpc_call
     def on_motors_enable(self, x_enable: "bool", y_enable: "bool"):
         """
@@ -54,6 +56,7 @@ class XRayEye(RPCBase):
             y_enable(bool): enable y motor controls
         """
 
+    @rpc_timeout(20)
     @rpc_call
     def enable_submit_button(self, enable: "bool"):
         """
@@ -90,12 +93,14 @@ class XRayEye(RPCBase):
         None
         """
 
+    @rpc_timeout(20)
     @rpc_call
     def switch_tab(self, tab: "str"):
         """
         None
         """
 
+    @rpc_timeout(20)
     @rpc_call
     def submit_fit_array(self, fit_array):
         """

csaxs_bec/bec_widgets/widgets/xray_eye/x_ray_eye.py

@@ -4,6 +4,7 @@ from bec_lib import bec_logger
 from bec_lib.endpoints import MessageEndpoints
 from bec_qthemes import material_icon
 from bec_widgets import BECWidget, SafeProperty, SafeSlot
+from bec_widgets.utils.rpc_decorator import rpc_timeout
 from bec_widgets.widgets.plots.image.image import Image
 from bec_widgets.widgets.plots.waveform.waveform import Waveform
 from bec_widgets.widgets.plots.image.setting_widgets.image_roi_tree import ROIPropertyTree
@@ -367,6 +368,7 @@ class XRayEye(BECWidget, QWidget):
         return self.message_line_edit.toPlainText()
 
     @user_message.setter
+    @rpc_timeout(20)
     def user_message(self, message: str):
         self.message_line_edit.setText(message)
 
@@ -375,6 +377,7 @@ class XRayEye(BECWidget, QWidget):
         return self.sample_name_line_edit.text()
 
     @sample_name.setter
+    @rpc_timeout(20)
     def sample_name(self, message: str):
         self.sample_name_line_edit.setText(message)
 
@@ -395,6 +398,7 @@ class XRayEye(BECWidget, QWidget):
     ################################################################################
 
     @SafeSlot(str)
+    @rpc_timeout(20)
     def switch_tab(self, tab: str):
         if tab == "fit":
             self.tab_widget.setCurrentIndex(1)
@@ -412,6 +416,7 @@ class XRayEye(BECWidget, QWidget):
         return roi.get_coordinates()
 
     @SafeSlot(bool)
+    @rpc_timeout(20)
     def on_live_view_enabled(self, enabled: bool):
         logger.info(f"Live view is enabled: {enabled}")
         self.live_preview_toggle.blockSignals(True)
@@ -460,6 +465,7 @@ class XRayEye(BECWidget, QWidget):
         self.shutter_toggle.blockSignals(False)
 
     @SafeSlot(bool, bool)
+    @rpc_timeout(20)
     def on_motors_enable(self, x_enable: bool, y_enable: bool):
         """
         Enable/Disable motor controls
@@ -472,6 +478,7 @@ class XRayEye(BECWidget, QWidget):
         self.motor_control_2d.enable_controls_ver(y_enable)
 
     @SafeSlot(bool)
+    @rpc_timeout(20)
     def enable_submit_button(self, enable: bool):
         """
         Enable/disable submit button.
@@ -509,6 +516,7 @@ class XRayEye(BECWidget, QWidget):
         print(f"meta: {meta}")
 
     @SafeSlot()
+    @rpc_timeout(20)
     def submit_fit_array(self, fit_array):
         self.tab_widget.setCurrentIndex(1)
         # self.fix_x.title = " got fit array"

csaxs_bec/device_configs/ptycho_flomni.yaml

@@ -227,7 +227,7 @@ ftransy:
   readoutPriority: baseline
   connectionTimeout: 20
   userParameter:
-    sensor_voltage: -2.4
+    sensor_voltage: -1.1
 ftransz:
   description: Sample transer Z
   deviceClass: csaxs_bec.devices.omny.galil.fgalil_ophyd.FlomniGalilMotor
@@ -344,6 +344,9 @@ rtx:
   description: flomni rt
   deviceClass: csaxs_bec.devices.omny.rt.rt_flomni_ophyd.RtFlomniMotor
   deviceConfig:
+    limits:
+    - -200
+    - 200
     axis_Id: A
     host: mpc2844.psi.ch
     port: 2222
@@ -361,6 +364,9 @@ rty:
   description: flomni rt
   deviceClass: csaxs_bec.devices.omny.rt.rt_flomni_ophyd.RtFlomniMotor
   deviceConfig:
+    limits:
+    - -100
+    - 100
     axis_Id: B
     host: mpc2844.psi.ch
     port: 2222
@@ -376,6 +382,9 @@ rtz:
   description: flomni rt
   deviceClass: csaxs_bec.devices.omny.rt.rt_flomni_ophyd.RtFlomniMotor
   deviceConfig:
+    limits:
+    - -100
+    - 100
     axis_Id: C
     host: mpc2844.psi.ch
     port: 2222
@@ -386,6 +395,16 @@ rtz:
   readoutPriority: on_request
   connectionTimeout: 20
 
+rt_flyer:
+  deviceClass: csaxs_bec.devices.omny.rt.rt_flomni_ophyd.RtFlomniFlyer
+  deviceConfig:
+    host: mpc2844.psi.ch
+    port: 2222
+  readoutPriority: async
+  connectionTimeout: 20
+  enabled: true
+  readOnly: False
+
 ############################################################
 ####################### Cameras ############################
 ############################################################

csaxs_bec/devices/epics/mcs_card/mcs_card_csaxs.py

@@ -317,8 +317,6 @@ class MCSCardCSAXS(PSIDeviceBase, MCSCard):
         try:
             scan_done = bool(value == self._num_total_triggers)
             self.progress.put(value=value, max_value=self._num_total_triggers, done=scan_done)
-            if scan_done:
-                self._scan_done_event.set()
         except Exception:
             content = traceback.format_exc()
             logger.info(f"Device {self.name}  error: {content}")
@@ -393,6 +391,7 @@ class MCSCardCSAXS(PSIDeviceBase, MCSCard):
         self._current_data_index = 0
 
         # NOTE Make sure that the signal that omits mca callbacks is cleared
+        # DO NOT REMOVE!!
         self._omit_mca_callbacks.clear()
 
         # For a fly scan we need to start the mcs card ourselves
@@ -563,8 +562,9 @@ class MCSCardCSAXS(PSIDeviceBase, MCSCard):
 
     def on_stop(self) -> None:
         """Hook called when the device is stopped. In addition, any status that is registered through cancel_on_stop will be cancelled here."""
-        self.stop_all.put(1)
-        self.erase_all.put(1)
+        with suppress_mca_callbacks(self):
+            self.stop_all.put(1)
+            self.erase_all.put(1)
 
     def mcs_recovery(self, timeout: int = 1) -> None:
         """

csaxs_bec/devices/omny/rt/rt_flomni_ophyd.py

@@ -1,20 +1,18 @@
 import threading
 import time
-from typing import List
 
 import numpy as np
-from bec_lib import bec_logger, messages
-from bec_lib.endpoints import MessageEndpoints
+from bec_lib import bec_logger
 from ophyd import Component as Cpt
 from ophyd import Device, PositionerBase, Signal
 from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError
+from ophyd_devices import AsyncMultiSignal, DeviceStatus, ProgressSignal
 from ophyd_devices.utils.controller import Controller, threadlocked
 from ophyd_devices.utils.socket import SocketIO, raise_if_disconnected
 from prettytable import PrettyTable
 
 from csaxs_bec.devices.omny.rt.rt_ophyd import (
-    BECConfigError,
     RtCommunicationError,
     RtError,
     RtReadbackSignal,
@@ -394,7 +392,7 @@ class RtFlomniController(Controller):
         val = float(self.socket_put_and_receive(f"j{axis_number}").strip())
         return val
 
-    def laser_tracker_check_signalstrength(self):
+    def laser_tracker_check_signalstrength(self, verbose=True):
         if not self.laser_tracker_check_enabled():
             returnval = "disabled"
         else:
@@ -405,9 +403,10 @@ class RtFlomniController(Controller):
             rtx = self.device_manager.devices.rtx
             min_signal = rtx.user_parameter.get("min_signal")
             low_signal = rtx.user_parameter.get("low_signal")
-            print(f"low signal: {low_signal}")
-            print(f"min signal: {min_signal}")
-            print(f"signal: {signal}")
+            if verbose:
+                print(f"low signal: {low_signal}")
+                print(f"min signal: {min_signal}")
+                print(f"signal: {signal}")
             if signal < min_signal:
                 time.sleep(1)
                 if signal < min_signal:
@@ -431,27 +430,6 @@ class RtFlomniController(Controller):
             t.add_row([i, self.read_ssi_interferometer(i)])
         print(t)
 
-    def _get_signals_from_table(self, return_table) -> dict:
-        self.average_stdeviations_x_st_fzp += float(return_table[4])
-        self.average_stdeviations_y_st_fzp += float(return_table[7])
-        signals = {
-            "target_x": {"value": float(return_table[2])},
-            "average_x_st_fzp": {"value": float(return_table[3])},
-            "stdev_x_st_fzp": {"value": float(return_table[4])},
-            "target_y": {"value": float(return_table[5])},
-            "average_y_st_fzp": {"value": float(return_table[6])},
-            "stdev_y_st_fzp": {"value": float(return_table[7])},
-            "average_rotz": {"value": float(return_table[8])},
-            "stdev_rotz": {"value": float(return_table[9])},
-            "average_stdeviations_x_st_fzp": {
-                "value": self.average_stdeviations_x_st_fzp / (int(return_table[0]) + 1)
-            },
-            "average_stdeviations_y_st_fzp": {
-                "value": self.average_stdeviations_y_st_fzp / (int(return_table[0]) + 1)
-            },
-        }
-        return signals
-
     @threadlocked
     def start_scan(self):
         if not self.feedback_is_running():
@@ -491,91 +469,6 @@ class RtFlomniController(Controller):
         current_position_in_scan = int(float(return_table[2]))
         return (mode, number_of_positions_planned, current_position_in_scan)
 
-    def read_positions_from_sampler(self):
-        # this was for reading after the scan completed
-        number_of_samples_to_read = 1  # self.get_scan_status()[1]  #number of valid samples, will be updated upon first data read
-
-        read_counter = 0
-
-        self.average_stdeviations_x_st_fzp = 0
-        self.average_stdeviations_y_st_fzp = 0
-        self.average_lamni_angle = 0
-
-        mode, number_of_positions_planned, current_position_in_scan = self.get_scan_status()
-
-        # if not (mode==2 or mode==3):
-        #    error
-        self.device_manager.connector.set(
-            MessageEndpoints.device_status("rt_scan"),
-            messages.DeviceStatusMessage(
-                device="rt_scan", status=1, metadata=self.readout_metadata
-            ),
-        )
-        # while scan is running
-        while mode > 0:
-
-            # TODO here?: scan abortion if no progress in scan *raise error
-
-            # logger.info(f"Current scan position {current_position_in_scan} out of {number_of_positions_planned}")
-            mode, number_of_positions_planned, current_position_in_scan = self.get_scan_status()
-            time.sleep(0.01)
-            if current_position_in_scan > 5:
-                while current_position_in_scan > read_counter + 1:
-                    return_table = (self.socket_put_and_receive(f"r{read_counter}")).split(",")
-                    # logger.info(f"{return_table}")
-                    logger.info(f"Read {read_counter} out of {number_of_positions_planned}")
-
-                    read_counter = read_counter + 1
-
-                    signals = self._get_signals_from_table(return_table)
-
-                    self.publish_device_data(signals=signals, point_id=int(return_table[0]))
-
-        time.sleep(0.05)
-
-        # read the last samples even though scan is finished already
-        while number_of_positions_planned > read_counter:
-            return_table = (self.socket_put_and_receive(f"r{read_counter}")).split(",")
-            logger.info(f"Read {read_counter} out of {number_of_positions_planned}")
-            # logger.info(f"{return_table}")
-            read_counter = read_counter + 1
-
-            signals = self._get_signals_from_table(return_table)
-            self.publish_device_data(signals=signals, point_id=int(return_table[0]))
-
-        self.device_manager.connector.set(
-            MessageEndpoints.device_status("rt_scan"),
-            messages.DeviceStatusMessage(
-                device="rt_scan", status=0, metadata=self.readout_metadata
-            ),
-        )
-
-        logger.info(
-            "Flomni statistics: Average of all standard deviations: x"
-            f" {self.average_stdeviations_x_st_fzp/read_counter*1000:.1f}, y"
-            f" {self.average_stdeviations_y_st_fzp/read_counter*1000:.1f}"
-        )
-
-    def publish_device_data(self, signals, point_id):
-        self.device_manager.connector.set_and_publish(
-            MessageEndpoints.device_read("rt_flomni"),
-            messages.DeviceMessage(
-                signals=signals, metadata={"point_id": point_id, **self.readout_metadata}
-            ),
-        )
-
-    def start_readout(self):
-        readout = threading.Thread(target=self.read_positions_from_sampler)
-        readout.start()
-
-    def kickoff(self, metadata):
-        self.readout_metadata = metadata
-        while not self._min_scan_buffer_reached:
-            time.sleep(0.001)
-        self.start_scan()
-        time.sleep(0.1)
-        self.start_readout()
-
 
 class RtFlomniReadbackSignal(RtReadbackSignal):
     @retry_once
@@ -621,6 +514,18 @@ class RtFlomniSetpointSignal(RtSetpointSignal):
                 "The interferometer feedback is not running. Either it is turned off or and"
                 " interferometer error occured."
             )
+
+        tracker_status = self.parent.controller.laser_tracker_check_signalstrength()
+
+        if tracker_status == "toolow":
+            print(
+                "The interferometer signal is too low for movements. Realignment required."
+            )
+            raise RtError(
+                "The interferometer signal is too low for movements. Realignment required."
+            )
+
+
         self.set_with_feedback_disabled(val)
 
     def set_with_feedback_disabled(self, val):
@@ -831,6 +736,185 @@ class RtFlomniMotor(Device, PositionerBase):
         return super().stop(success=success)
 
 
+class RtFlomniFlyer(Device):
+    USER_ACCESS = ["controller"]
+    data = Cpt(
+        AsyncMultiSignal,
+        name="data",
+        signals=[
+            "target_x",
+            "average_x_st_fzp",
+            "stdev_x_st_fzp",
+            "target_y",
+            "average_y_st_fzp",
+            "stdev_y_st_fzp",
+            "average_rotz",
+            "stdev_rotz",
+            "average_stdeviations_x_st_fzp",
+            "average_stdeviations_y_st_fzp",
+        ],
+        ndim=1,
+        async_update={"type": "add", "max_shape": [None]},
+        max_size=1000,
+    )
+    progress = Cpt(
+        ProgressSignal, doc="ProgressSignal indicating the progress of the device during a scan."
+    )
+
+    def __init__(
+        self,
+        prefix="",
+        *,
+        name,
+        kind=None,
+        read_attrs=None,
+        configuration_attrs=None,
+        parent=None,
+        host="mpc2844.psi.ch",
+        port=2222,
+        socket_cls=SocketIO,
+        device_manager=None,
+        **kwargs,
+    ):
+        super().__init__(prefix=prefix, name=name, parent=parent, **kwargs)
+        self.shutdown_event = threading.Event()
+        self.controller = RtFlomniController(
+            socket_cls=socket_cls, socket_host=host, socket_port=port, device_manager=device_manager
+        )
+        self.average_stdeviations_x_st_fzp = 0
+        self.average_stdeviations_y_st_fzp = 0
+        self.average_lamni_angle = 0
+        self.readout_thread = None
+        self.scan_done_event = threading.Event()
+        self.scan_done_event.set()
+
+    def read_positions_from_sampler(self, status: DeviceStatus):
+        """
+        Read the positions from the sampler and update the data signal.
+        This function runs in a separate thread and continuously checks the
+        scan status.
+
+        Args:
+            status (DeviceStatus): The status object to update when the readout is complete.
+        """
+        read_counter = 0
+        self.average_stdeviations_x_st_fzp = 0
+        self.average_stdeviations_y_st_fzp = 0
+        self.average_lamni_angle = 0
+
+        mode, number_of_positions_planned, current_position_in_scan = (
+            self.controller.get_scan_status()
+        )
+
+        # while scan is running
+        while mode > 0 and not self.shutdown_event.wait(0.01):
+            # logger.info(f"Current scan position {current_position_in_scan} out of {number_of_positions_planned}")
+            mode, number_of_positions_planned, current_position_in_scan = (
+                self.controller.get_scan_status()
+            )
+            if current_position_in_scan > 5:
+                while current_position_in_scan > read_counter + 1:
+                    return_table = (
+                        self.controller.socket_put_and_receive(f"r{read_counter}")
+                    ).split(",")
+                    logger.info(f"Read {read_counter} out of {number_of_positions_planned}")
+                    self.progress.put(
+                        value=read_counter, max_value=number_of_positions_planned, done=False
+                    )
+                    read_counter = read_counter + 1
+                    signals = self._get_signals_from_table(return_table)
+                    self.data.set(signals)
+
+        if self.shutdown_event.wait(0.05):
+            logger.info("Shutdown event set, stopping readout.")
+            # if we are here, the shutdown_event is set. We can exit the readout loop.
+            status.set_finished()
+            return
+
+        # read the last samples even though scan is finished already
+        while number_of_positions_planned > read_counter and not self.shutdown_event.is_set():
+            return_table = (self.controller.socket_put_and_receive(f"r{read_counter}")).split(",")
+            logger.info(f"Read {read_counter} out of {number_of_positions_planned}")
+            self.progress.put(value=read_counter, max_value=number_of_positions_planned, done=False)
+            read_counter = read_counter + 1
+
+            signals = self._get_signals_from_table(return_table)
+            self.data.set(signals)
+
+        # NOTE: No need to set the status to failed if the shutdown_event is set.
+        # The stop() method will take care of that.
+        status.set_finished()
+        self.progress.put(value=read_counter, max_value=number_of_positions_planned, done=True)
+
+        logger.info(
+            "Flomni statistics: Average of all standard deviations: x"
+            f" {self.average_stdeviations_x_st_fzp/read_counter*1000:.1f}, y"
+            f" {self.average_stdeviations_y_st_fzp/read_counter*1000:.1f}"
+        )
+
+    def _get_signals_from_table(self, return_table) -> dict:
+        self.average_stdeviations_x_st_fzp += float(return_table[4])
+        self.average_stdeviations_y_st_fzp += float(return_table[7])
+        signals = {
+            "target_x": {"value": float(return_table[2])},
+            "average_x_st_fzp": {"value": float(return_table[3])},
+            "stdev_x_st_fzp": {"value": float(return_table[4])},
+            "target_y": {"value": float(return_table[5])},
+            "average_y_st_fzp": {"value": float(return_table[6])},
+            "stdev_y_st_fzp": {"value": float(return_table[7])},
+            "average_rotz": {"value": float(return_table[8])},
+            "stdev_rotz": {"value": float(return_table[9])},
+            "average_stdeviations_x_st_fzp": {
+                "value": self.average_stdeviations_x_st_fzp / (int(return_table[0]) + 1)
+            },
+            "average_stdeviations_y_st_fzp": {
+                "value": self.average_stdeviations_y_st_fzp / (int(return_table[0]) + 1)
+            },
+        }
+        return signals
+
+    def stage(self):
+        self.shutdown_event.clear()
+        self.scan_done_event.set()
+        return super().stage()
+
+    def start_readout(self, status: DeviceStatus):
+        self.readout_thread = threading.Thread(
+            target=self.read_positions_from_sampler, args=(status,)
+        )
+        self.readout_thread.start()
+
+    def kickoff(self) -> DeviceStatus:
+        self.shutdown_event.clear()
+        self.scan_done_event.clear()
+        while not self.controller._min_scan_buffer_reached and not self.shutdown_event.wait(0.001):
+            ...
+        self.controller.start_scan()
+        self.shutdown_event.wait(0.1)
+        status = DeviceStatus(self)
+        status.set_finished()
+        return status
+
+    def complete(self) -> DeviceStatus:
+        """Wait until the flyer is done."""
+        if self.scan_done_event.is_set():
+            # if the scan_done_event is already set, we can return a finished status immediately
+            status = DeviceStatus(self)
+            status.set_finished()
+            return status
+        status = DeviceStatus(self)
+        self.start_readout(status)
+        status.add_callback(lambda *args, **kwargs: self.scan_done_event.set())
+        return status
+
+    def stop(self, *, success=False):
+        self.shutdown_event.set()
+        self.scan_done_event.set()
+        if self.readout_thread is not None:
+            self.readout_thread.join()
+        return super().stop(success=success)
+
+
 if __name__ == "__main__":
     rtcontroller = RtFlomniController(
         socket_cls=SocketIO, socket_host="mpc2844.psi.ch", socket_port=2222, device_manager=None

csaxs_bec/devices/omny/shutter.py

@@ -48,6 +48,7 @@ class OMNYFastShutter(PSIDeviceBase, Device):
     def fshopen(self):
         """Open the fast shutter."""
         if self._check_if_cSAXS_shutter_exists_in_config():
+            self.shutter.put(1)
             return self.device_manager.devices["fsh"].fshopen()
         else:
             self.shutter.put(1)
@@ -55,6 +56,7 @@ class OMNYFastShutter(PSIDeviceBase, Device):
     def fshclose(self):
         """Close the fast shutter."""
         if self._check_if_cSAXS_shutter_exists_in_config():
+            self.shutter.put(0)
             return self.device_manager.devices["fsh"].fshclose()
         else:
             self.shutter.put(0)

csaxs_bec/scans/flomni_fermat_scan.py

@@ -27,20 +27,19 @@ from bec_lib import bec_logger, messages
 from bec_lib.alarm_handler import Alarms
 from bec_lib.endpoints import MessageEndpoints
 from bec_server.scan_server.errors import ScanAbortion
-from bec_server.scan_server.scans import SyncFlyScanBase
+from bec_server.scan_server.scans import AsyncFlyScanBase
 
 from csaxs_bec.devices.epics.delay_generator_csaxs.delay_generator_csaxs import TRIGGERSOURCE
 
 logger = bec_logger.logger
 
 
-class FlomniFermatScan(SyncFlyScanBase):
+class FlomniFermatScan(AsyncFlyScanBase):
     scan_name = "flomni_fermat_scan"
     scan_type = "fly"
     required_kwargs = ["fovx", "fovy", "exp_time", "step", "angle"]
     arg_input = {}
     arg_bundle_size = {"bundle": len(arg_input), "min": None, "max": None}
-    use_scan_progress_report = True
 
     def __init__(
         self,
@@ -104,6 +103,14 @@ class FlomniFermatScan(SyncFlyScanBase):
             self.zshift = -100
         self.flomni_rotation_status = None
 
+    def scan_report_instructions(self):
+        """Scan report instructions for the progress bar"""
+        yield from self.stubs.scan_report_instruction({"device_progress": ["rt_flyer"]})
+
+    @property
+    def monitor_sync(self) -> str:
+        return "rt_flyer"
+
     def initialize(self):
         self.scan_motors = []
         self.update_readout_priority()
@@ -113,10 +120,6 @@ class FlomniFermatScan(SyncFlyScanBase):
             self.positions, corridor_size=self.optim_trajectory_corridor
         )
 
-    @property
-    def monitor_sync(self):
-        return "rt_flomni"
-
     def reverse_trajectory(self):
         """
         Reverse the trajectory. Every other scan should be reversed to
@@ -290,26 +293,18 @@ class FlomniFermatScan(SyncFlyScanBase):
         return np.array(positions)
 
     def scan_core(self):
-        # use a device message to receive the scan number and
-        # scan ID before sending the message to the device server
-        yield from self.stubs.kickoff(device="rtx")
-        while True:
-            yield from self.stubs.read(group="monitored")
-            status = self.connector.get(MessageEndpoints.device_status("rt_scan"))
-            if status:
-                status_id = status.content.get("status", 1)
-                request_id = status.metadata.get("RID")
-                if status_id == 0 and self.metadata.get("RID") == request_id:
-                    break
-                if status_id == 2 and self.metadata.get("RID") == request_id:
-                    raise ScanAbortion(
-                        "An error occured during the flomni readout:"
-                        f" {status.metadata.get('error')}"
-                    )
+        # send off the flyer
+        yield from self.stubs.kickoff(device="rt_flyer")
 
+        # start the readout loop of the flyer
+        status = yield from self.stubs.complete(device="rt_flyer", wait=False)
+
+        # read the monitors until the flyer is done
+        while not status.done:
+            yield from self.stubs.read(group="monitored", point_id=self.point_id)
+            self.point_id += 1
             time.sleep(1)
             logger.debug("reading monitors")
-        # yield from self.device_rpc("rtx", "controller.kickoff")
 
     def move_to_start(self):
         """return to the start position"""
@@ -336,6 +331,7 @@ class FlomniFermatScan(SyncFlyScanBase):
         yield from self.read_scan_motors()
         self.prepare_positions()
         yield from self._prepare_setup()
+        yield from self.scan_report_instructions()
         yield from self.open_scan()
         yield from self.stage()
         yield from self.run_baseline_reading()

docs/user/ptychography/flomni.md

@@ -50,16 +50,15 @@ Manually move the gripper to a transfer position
 After the sample transfer the sample stage moved to the measurement position with your new sample. The Xray eye will automatically move in and the shutter will open. You may already see the sample in the omny xeye interface running on the windows computer.
 If you see your sample already at the approximately correct height, you can skip steps 1 to 3. Otherwise adjust the height:
 
-1. `flomni.rt_feedback_disable()` disable the closed loop operation to allow movement of coarse stages
+1. `flomni.feedback_disable()` disable the closed loop operation to allow movement of coarse stages
 1. `umvr(dev.fsamy, 0.01)`, attention: unit <mm>, move the sample stage relative up (positive) or down (negative) until the sample is approximately vertically centered in xray eye screen
 1. `flomni.xrayeye_update_frame()` will update the current image on the xray eye screen
-1. `flomni.xrayeye_alignment_start()` start the coarse alignment of the sample by measuring (clicking in the X-ray eye software) the sample position at 0, 45, 90, 135, 180 degrees. Then use the matlab routine `SPEC_ptycho_align.m` to fit this data.
-1. `flomni.read_alignment_offset()` read the generated alignment data.
+1. `flomni.xrayeye_alignment_start()` start the coarse alignment of the sample by measuring (clicking in the X-ray eye software) the sample position at 0, 45, 90, 135, 180 degrees. The GUI will present a fit of this data, which is automatically loaded to BEC for aligning the sample.
 
 #### Fine alignment
 
 After the xrayeyealign, a fine alignment needs to be performed using ptychography.
-_To bypass the fine alignment: `feye_out`_
+_To bypass the fine alignment: `flomni.feye_out`_
 
 
 1. `flomni.tomo_parameters()` Adjust the  ptychographic scan parameters for performing an alignment scan. Typically FOVX = FOVX(Xrayeye)+20 mu, shell step = beamsize/2.5, number of projections and tomo mode are ignored in the alignment scans.
@@ -71,13 +70,13 @@ _To bypass the fine alignment: `feye_out`_
 Now that the sample is aligned, the tomographic measurement can be performed.
 1. `flomni.tomo_parameters()` adjust the scan parameters for the tomographic scan. This includes the parameters for ptychographic scans of projections plus the strategy for angular sampling. The vertical shift adjusts the field of view, up (positive) or down (negative). After adjusting the numbers, type again `flomni.tomo_parameters()` and verify that they are correct.
 1. `flomni.tomo_scan_projection(angle)` perform a ptychographic scan at the rotation angle <angle>. Launch the tomographic measurement by `flomni.tomo_scan()`. 
-1. Before changing sample, verify that all subtomograms were completely acquired using the `tomo_recons matlab` script.
+1. Before changing sample, verify that all subtomograms were completely acquired using the tomo_reconstruction matlab script.
 
 #### If something went wrong…
 
 A __single projection__ is to be repeated use
 `flomni.tomo_scan_projection(<angle>)`. The target angle of scans can be found in the second column of the file in 
-`~/Data10/specES1/dat-files/omni_scannumbers.txt`
+`~/data/raw/logs/tomography_scannumbers.txt`
 
 To continue an __interrupted tomography scan__:
 

docs/user/ptychography/lamni.md

@@ -26,7 +26,7 @@ The effective position of the axis of rotation shifts with sample thickness or m
 1. `dev.lsamx` and `dev.lsamy` will print current position and the center value. Update the center value by  
 `dev.lsamx.update_user_parameter({'center':8.69})`  
 `dev.lsamy.update_user_parameter({'center':8.69})`  
-1. close the shutter: `fshclose()`
+1. close the shutter: `dev.omnyfsh.fshclose()`
 
 #### X-ray eye alignment
 

tests/tests_devices/test_mcs_card.py

@@ -217,6 +217,16 @@ def test_mcs_card_csaxs_complete_and_stop(mock_mcs_csaxs: MCSCardCSAXS):
     assert not mcs._start_monitor_async_data_emission.is_set()
 
 
+def test_mcs_on_stop(mock_mcs_csaxs: MCSCardCSAXS):
+    """Test that on stop sets the omit_mca_callbacks flag. Also test that on stage clears the omit_mca_callbacks flag."""
+    mcs = mock_mcs_csaxs
+    assert mcs._omit_mca_callbacks.is_set() is False
+    mcs.stop()
+    assert mcs._omit_mca_callbacks.is_set() is True
+    mcs.stage()
+    assert mcs._omit_mca_callbacks.is_set() is False
+
+
 def test_mcs_recovery(mock_mcs_csaxs: MCSCardCSAXS):
     mcs = mock_mcs_csaxs
     # Simulate ongoing acquisition