first fixes commissioning with hardware

csaxs_bec/bec_ipython_client/plugins/cSAXS/cSAXS.py

@@ -33,7 +33,7 @@ class cSAXS(
 
 # this is the csaxs master file that imports all routines from csaxs
 # can be imported in the bec client by
-#
+# run in bec from folder /sls/x12sa/config/bec/production/csaxs_bec
 # from csaxs_bec.bec_ipython_client.plugins.cSAXS.cSAXS import cSAXS
 # csaxs = cSAXS(bec)
 #

csaxs_bec/bec_ipython_client/plugins/cSAXS/filter_transmission.py

@@ -26,6 +26,14 @@ import csaxs_bec.bec_ipython_client.plugins.cSAXS.filter_transmission as ft_pkg
 
 from bec_lib import bec_logger
 
+import builtins
+
+
+if builtins.__dict__.get("bec") is not None:
+    bec = builtins.__dict__.get("bec")
+    dev = builtins.__dict__.get("dev")
+    umv = builtins.__dict__.get("umv")
+    umvr = builtins.__dict__.get("umvr")
 
 class cSAXSFilterTransmission:
     """
@@ -140,23 +148,28 @@ class cSAXSFilterTransmission:
     # -----------------------------
     # Public API
     # -----------------------------
+
+
     def fil_trans_select(
         self,
-        transmission: float,
+        transmission: Optional[float] = None,
         energy_kev: Optional[float] = None,
         print_only: bool = True,
     ) -> Optional[None]:
         """
         Set exposure-box filters to achieve a target transmission.
 
-        Physics:
-          - Load per-material attenuation-length tables (energy in eV)
-          - Linear interpolation to get λ(energy) in µm
-          - Per-position transmission: product of layer transmissions
-          - Combination transmission: product across 4 units
-          - Choose combination whose transmission is closest to target
+        If called without 'transmission', prints usage and current status.
         """
-        self._ensure_internal_state()
+
+        if transmission is None:
+            print("\nUsage:")
+            print("  csaxs.fil_trans_select(<transmission>, energy_kev=<energy>, print_only=True)")
+            print("Example:")
+            print("  csaxs.fil_trans_select(0.10, energy_kev=6.2)")
+            print("\nCurrent filter transmission:")
+            self._fil_trans_report(energy_kev=energy_kev)
+            return None
 
         # --- Validation ---
         try:
@@ -170,7 +183,7 @@ class cSAXSFilterTransmission:
         # --- Energy handling ---
         if energy_kev is None:
             try:
-                energy_kev = float(self.client.device_manager.mokev.read())
+                energy_kev = float(dev.mokev.read())  # using global dev
             except Exception as exc:
                 raise RuntimeError(
                     "Energy not specified and could not read current beam energy."
@@ -189,19 +202,17 @@ class cSAXSFilterTransmission:
         # --- Compute best combination ---
         best = self._find_best_combination(transmission, energy_kev)
 
-        # --- Report (selected combination with per-unit detail) ---
+        # --- Report selected combination ---
         self._print_combination(best, energy_kev, header="Selected combination")
 
-        # Nearby: print only code + transmission (no per-unit details)
+        # Nearby: print only code + transmission
         neighbors = self._neighbors_around_best(transmission, energy_kev, span=5)
         if neighbors:
             print("\nNearby combinations (by transmission proximity):")
             for row in neighbors:
-                print(
-                    f"{row['transmission']:9.3e}"
-                )
+                print(f"{row['transmission']:9.3e}")
 
-        # --- Dry run prompt: ask to execute now (default 'y') ---
+        # --- Dry run prompt ---
         if print_only:
             print("\n[DRY RUN] No motion executed yet.")
             if self.OMNYTools.yesno(
@@ -213,11 +224,11 @@ class cSAXSFilterTransmission:
                 print("Execution skipped.")
             return None
 
-
-        # --- Execute motion directly (if print_only=False) ---
+        # --- Execute motion directly ---
         self._execute_combination(best, energy_kev)
         return None
 
+
     # -----------------------------
     # Physics helpers
     # -----------------------------
@@ -438,20 +449,24 @@ class cSAXSFilterTransmission:
                 else:
                     print(f"    unit {u}: #{pos}  ----- out")
 
+
+
     def _execute_combination(self, comb: dict, energy_kev: float):
         """
         Execute motion to the indices encoded in 'comb["code"]'.
 
         Mapping:
-          - code 'abcd' → per-unit index (a,b,c,d) ∈ {1..6}
-          - positions are looked up from _POSITIONS_USER
-          - axes are defined in _AXES
+        - code 'abcd' → per-unit index (a,b,c,d) ∈ {1..6}
+        - positions are looked up from _POSITIONS_USER
+        - axes are defined in _AXES
 
-        Motion uses: umv(dev.filter_array_?_x, <position>)
-        If 'umv' is not present, falls back to axis.move(<position>).
+        Motion uses: umv(dev.axis, position, dev.axis2, position2, ...)
         """
+
         indices = comb["indices"]  # 0-based per unit
-        targets = []
+        move_args = []  # Collect (device, position) pairs
+
+        print("\nExecuting combined motion:")
         for unit_idx, pos_idx in enumerate(indices):
             pos_list = self._POSITIONS_USER[unit_idx]
             target_pos = pos_list[pos_idx]
@@ -459,76 +474,59 @@ class cSAXSFilterTransmission:
                 raise RuntimeError(
                     f"Unit {unit_idx+1} position {pos_idx+1} has no defined coordinate."
                 )
-            targets.append(target_pos)
 
-        # Perform motion via 'umv(dev.axis, position)' or fallback to .move()
-        print("\nExecuting motion to selected combination:")
-        dev = getattr(self.client, "dev", None)
-        if dev is None:
-            # fallback to device_manager if dev is not available
-            dev = self.client.device_manager
-
-        for unit_idx, target in enumerate(targets):
             axis_name = self._AXES[unit_idx]
-            axis_obj = getattr(dev, axis_name, None)
-            if axis_obj is None:
-                raise RuntimeError(f"Device axis '{axis_name}' not found (dev).")
-            print(f"  {axis_name} → {target:.3f}")
+            axis_obj = getattr(dev, axis_name)
+            print(f"  {axis_name} → {target_pos:.3f}")
+            move_args.extend([axis_obj, target_pos])
 
-            # Try the umv command first
-            if hasattr(self.client, "umv"):
-                self.client.umv(axis_obj, target)
-            else:
-                # Fallback to direct move
-                if hasattr(axis_obj, "move"):
-                    axis_obj.move(target)
-                else:
-                    raise RuntimeError(
-                        f"Axis '{axis_name}' has no 'move' method and client.umv is unavailable."
-                    )
+        umv(*move_args)
 
-        # Verify final positions
         print("\nVerifying final positions:")
         for unit_idx in range(self._UNITS):
             axis_name = self._AXES[unit_idx]
             axis_obj = getattr(dev, axis_name)
-            if hasattr(axis_obj, "read"):
-                actual = float(axis_obj.read())
+            try:
+                actual = float(axis_obj.readback.get())
                 print(f"  {axis_name} = {actual:.3f}")
-            else:
+            except Exception:
                 print(f"  {axis_name}: readback unavailable")
 
-        # Optionally: achieved transmission (approx., using the selected combination value)
         achieved_T = comb["transmission"]
         print(f"\nAchieved transmission (approx.): {achieved_T:9.3e} at {energy_kev:.3f} keV")
 
 
 
-    def fil_trans_report(self, tol: float = 0.1) -> None:
+    def _fil_trans_report(self, tol: float = 0.1, energy_kev: Optional[float] = None) -> None:
         """
         Report the currently active exposure‑box filter combination.
         Determines stage positions via dev.<axis>.readback.get()
         with a tolerance window of ±tol relative to nominal positions.
+
+        Parameters
+        ----------
+        tol : float
+            Tolerance for matching positions.
+        energy_kev : float, optional
+            Photon energy in keV. If None, tries to read from dev.mokev or defaults to 6.2 keV.
         """
-        self._ensure_internal_state()
 
-        # Resolve device object
-        dev = getattr(self.client, "dev", None)
+        # Ensure global dev is available
         if dev is None:
-            dev = self.client.device_manager
+            print("ERROR: Global 'dev' object not found.")
+            return
 
-        # Try getting current energy
-        try:
-            energy_kev = float(self.client.device_manager.mokev.read())
-        except Exception:
-            print("WARNING: Could not read current beam energy. Assuming 6.2 keV.")
-            energy_kev = 6.2
+        # Determine energy
+        if energy_kev is None:
+            try:
+                energy_kev = float(dev.mokev.read())
+            except Exception:
+                print("WARNING: Could not read current beam energy. Assuming 6.2 keV.")
+                energy_kev = 6.2
 
         print("\nCurrent filter transmission report")
         print("-" * 60)
         print(f"Photon energy : {energy_kev:.3f} keV")
-        print(f"Tolerance     : ±{tol:.3f}")
-        print("-" * 60)
 
         indices = []  # 0–5 per unit
 
@@ -538,7 +536,6 @@ class cSAXSFilterTransmission:
                 print(f"ERROR: Device axis '{axis_name}' not found.")
                 return
 
-            # Read readback
             try:
                 rb = float(axis_obj.readback.get())
             except Exception:
@@ -561,11 +558,11 @@ class cSAXSFilterTransmission:
 
             indices.append(best_idx)
 
-        # Build combination dictionary like internally used ones
+        # Build combination code
         code = "".join(str(i + 1) for i in indices)
-        print(f"\nMatched filter code: {code}")
+        print(f"Matched filter code: {code}")
 
-        # Build full combination record for transmission calculation
+        # Compute transmission and materials
         units = [
             self._FILTERS[u * self._PER_UNIT : (u + 1) * self._PER_UNIT]
             for u in range(self._UNITS)
@@ -588,7 +585,8 @@ class cSAXSFilterTransmission:
                 materials.append(((m1, t1), None))
 
         # Print detailed report
-        print(f"Total transmission: {total_T:.6e}\n")
+        self.OMNYTools.printgreenbold(f"Total transmission: {total_T:.6e}")
+        print("-" * 60)
 
         for u, matinfo in enumerate(materials, start=1):
             (m1, t1), second = matinfo

csaxs_bec/bec_ipython_client/plugins/cSAXS/smaract.py

@@ -173,7 +173,7 @@ class cSAXSInitSmaractStages:
                 + ", ".join(not_referenced)
             )
             bec_logger.logger.error(
-                "[cSAXS] Aborting motion. Please reference axes first."
+                "[cSAXS] Aborting motion. Please reference axes first. \nOr skip the axes by e.g. \nsmaract_all_components_to_initial_position(skip_devices=[\"fast_shutter_n1_x\",\"fast_shutter_o1_x\"]"
             )
             return