csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -1055,7 +1055,7 @@ class FlomniAlignmentMixin:
             with open(os.path.join(dir_path, "ptychotomoalign_Ay3.txt"), "r") as file:
                 tomo_alignment_fit[1][3] = file.readline()
 
-            with open(os.path.join(dir_path, "ptychotomoalign_Cy3.txt"), "r") as file:
+            with open(os.path.join(dir_path, "ptychotomoalign_By3.txt"), "r") as file:
                 tomo_alignment_fit[1][4] = file.readline()
 
             print("New alignment parameters loaded from filesystem, meaning Matlab fit:")
@@ -1618,7 +1618,7 @@ class Flomni(
 
         self.feye_out()
         tags = ["BEC_alignment_tomo", self.sample_name]
-
+        self.write_alignment_scan_numbers(bec.queue.next_scan_number)
         start_angle = 0
         alignment_scan_numbers = []
 
@@ -1667,6 +1667,32 @@ class Flomni(
         print(scilog_content)
         bec.messaging.scilog.new().add_text(scilog_content.replace("\n", "<br>")).add_tags("alignmentscan").send()
 
+    def write_alignment_scan_numbers(self, first_scan):
+        import os
+
+        file = os.path.expanduser("~/data/raw/logs/ptychotomoalign_scannum.txt")
+        os.makedirs(os.path.dirname(file), exist_ok=True)
+
+        scans = [first_scan + k for k in range(5)]
+        angles = [0, 45, 90, 135, 180]
+
+        x_vals = []
+
+        for angle in angles:
+            x, y, z = self.get_alignment_offset(angle)
+            x_vals.append(x)
+
+        zeros = [0] * len(angles)
+
+        with open(file, "w") as f:
+            f.write(" ".join(map(str, scans)) + "\n")
+            f.write(" ".join(map(str, angles)) + "\n")
+            f.write(" ".join(f"{x:.2f}" for x in x_vals) + "\n")
+            f.write(" ".join(map(str, x_vals)) + "\n")
+            f.write(" ".join(map(str, zeros)) + "\n")
+
+
+
     def sub_tomo_scan(self, subtomo_number, start_angle=None):
         """
         Performs a sub tomogram scan.

csaxs_bec/bec_ipython_client/plugins/flomni/flomni_webpage_generator.py

@@ -158,7 +158,7 @@ def _safe_get(device_manager, dotpath: str):
         obj = device_manager.devices
         for part in dotpath.split("."):
             obj = getattr(obj, part)
-        return obj.get()
+        return obj.get(cached=True)
     except Exception:
         return None
 
@@ -2230,16 +2230,23 @@ function render(d){{
   handleAudioForStatus(s, prevStatus);
 }}
 
+let _fetchFailCount=0;
+const FETCH_FAIL_THRESHOLD=3;
+
 async function poll(){{
   try{{
     const r=await fetch(STATUS_JSON, {{cache:'no-store'}});
     if(!r.ok) throw new Error('HTTP '+r.status);
+    _fetchFailCount=0;
     render(await r.json());
   }}catch(e){{
-    console.warn('Fetch failed:',e);
-    document.getElementById('last-update').textContent='fetch failed - retrying...';
-    document.getElementById('outdated-banner').classList.add('visible');
-    handleStale(true);
+    _fetchFailCount++;
+    console.warn('Fetch failed:',e,'('+_fetchFailCount+')');
+    document.getElementById('last-update').textContent='fetch failed - retrying\u2026 ('+_fetchFailCount+')';
+    if(_fetchFailCount>=FETCH_FAIL_THRESHOLD){{
+      document.getElementById('outdated-banner').classList.add('visible');
+      handleStale(true);
+    }}
   }}
 }}
 

csaxs_bec/devices/jungfraujoch/jungfraujoch_preview.py

@@ -214,11 +214,13 @@ class JungfrauJochPreview:
             r = self._socket.recv_multipart(flags=zmq.NOBLOCK)
             self._parse_data(r)
         except zmq.error.Again:
-            # No message received, this is expected when the receive queue is empty
+            # No new message available on Preview socket within timeout that was set
             pass
-        except Exception as e:
-            # Consider moving this to debug level, but it can be useful to see why preview updates are not working
-            logger.info(f"Error while receiving ZMQ message from JFJ preview at {self.url}: {e}")
+        except Exception as exc:
+            logger.info(
+                f"Error parsing input data from JungfrauJoch host {self.url}. Exception: {exc}"
+            )
+
         finally:
             # Unsubscribe from the topic
             self._socket.setsockopt(zmq.UNSUBSCRIBE, ZMQ_TOPIC_FILTER)

csaxs_bec/devices/omny/galil/fgalil_ophyd.py

@@ -37,6 +37,7 @@ class FlomniGalilController(GalilController):
         "get_motor_limit_switch",
         "fosaz_light_curtain_is_triggered",
         "is_motor_on",
+        "is_thread_active",
         "all_axes_referenced",
         "lights_off",
         "lights_on",

csaxs_bec/devices/omny/galil/galil_ophyd.py

@@ -57,6 +57,7 @@ class GalilController(Controller):
         "find_reference",
         "get_motor_limit_switch",
         "is_motor_on",
+        "is_thread_active",
         "all_axes_referenced",
     ]
 
@@ -85,7 +86,7 @@ class GalilController(Controller):
         return_val = self.socket_put_and_receive(val)
         if return_val != ":":
             raise GalilCommunicationError(
-                f"Expected return value of ':' but instead received {return_val}"
+                f"Sent {val} and expected return value of ':' but instead received {return_val}"
             )
 
     def is_axis_moving(self, axis_Id, axis_Id_numeric) -> bool:

csaxs_bec/devices/omny/rt/rt_flomni_ophyd.py

@@ -353,10 +353,13 @@ class RtFlomniController(Controller):
 
     def laser_tracker_galil_enable(self):
         ftrackz_con = self.device_manager.devices.ftrackz.obj.controller
-        ftrackz_con.socket_put_confirmed("tracken=1")
-        ftrackz_con.socket_put_confirmed("trackyct=0")
-        ftrackz_con.socket_put_confirmed("trackzct=0")
-        ftrackz_con.socket_put_confirmed("XQ#Tracker")
+        if not ftrackz_con.is_thread_active(5):
+            ftrackz_con.socket_put_confirmed("tracken=1")
+            ftrackz_con.socket_put_confirmed("trackyct=0")
+            ftrackz_con.socket_put_confirmed("trackzct=0")
+            ftrackz_con.socket_put_confirmed("XQ#Tracker")
+            while not ftrackz_con.is_thread_active(5):
+                time.sleep(0.1)
 
     def laser_tracker_on_target(self) -> bool:
         self.laser_update_tracker_info()
@@ -369,8 +372,8 @@ class RtFlomniController(Controller):
     def laser_tracker_wait_on_target(self):
         max_repeat = 25
         count = 0
+        self.laser_tracker_galil_enable()
         while not self.laser_tracker_on_target():
-            self.laser_tracker_galil_enable()
             logger.info("Waiting for laser tracker to reach target.")
             time.sleep(0.5)
             count += 1
@@ -442,7 +445,7 @@ class RtFlomniController(Controller):
                 " interferometer error."
             )
             # here exception
-        (mode, number_of_positions_planned, current_position_in_scan) = self.get_scan_status()
+        mode, number_of_positions_planned, current_position_in_scan = self.get_scan_status()
 
         if number_of_positions_planned == 0:
             logger.error("Cannot start scan because no target positions are planned.")
@@ -517,14 +520,11 @@ class RtFlomniSetpointSignal(RtSetpointSignal):
         tracker_status = self.parent.controller.laser_tracker_check_signalstrength()
 
         if tracker_status == "toolow":
-            print(
-                "The interferometer signal is too low for movements. Realignment required."
-            )
+            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):