remove z movement in scan as piezo broken

write z propagation to reconstruction file

csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -2142,13 +2142,17 @@ class Flomni(
 
         return angle, subtomo_number
 
-    def tomo_reconstruct(self, base_path="~/data/raw/logs/reconstruction_queue"):
+ 
+    def tomo_reconstruct(
+        self, base_path="~/data/raw/logs/reconstruction_queue", probe_propagation: float | None = None
+    ):
         """write the tomo reconstruct file for the reconstruction queue"""
         bec = builtins.__dict__.get("bec")
         self.reconstructor.write(
             scan_list=self._current_scan_list,
             next_scan_number=bec.queue.next_scan_number,
             base_path=base_path,
+            probe_file_propagation=probe_propagation,
         )
 
     def _write_tomo_scan_number(self, scan_number: int, angle: float, subtomo_number: int) -> None:
@@ -2178,6 +2182,9 @@ class Flomni(
             + self.manual_shift_y
         )
         sum_offset_z = offsets[2]
+        #TODO this fix is while the tracker z is broken
+        probe_propagation = -sum_offset_z * 1e-6
+        sum_offset_z = 0
 
         self._current_scan_list = []
 
@@ -2216,7 +2223,7 @@ class Flomni(
 
                 scans.flomni_fermat_scan(**scan_kwargs)
 
-        self.tomo_reconstruct()
+        self.tomo_reconstruct(probe_propagation=probe_propagation)
 
     def tomo_acquire_at_angle(self, angle: float, frames_per_trigger: int | None = None):
         """

csaxs_bec/bec_ipython_client/plugins/omny/omny_general_tools.py

@@ -189,7 +189,13 @@ class PtychoReconstructor:
             logger.warning("Failed to compare active account to system user.")
             return False
 
-    def write(self, scan_list: list, next_scan_number: int, base_path: str = "~/data/raw/analysis/"):
+    def write(
+        self,
+        scan_list: list,
+        next_scan_number: int,
+        base_path: str = "~/data/raw/analysis/",
+        probe_file_propagation: float | None = None,
+    ):
         """Write a reconstruction queue file for the given scan list.
 
         Args:
@@ -198,6 +204,13 @@ class PtychoReconstructor:
             next_scan_number (int): The current next scan number, used to
                                     name the queue file.
             base_path (str): Root path under which the queue folder lives.
+            probe_file_propagation (float, optional): Distance [m] by which the
+                reconstruction should numerically propagate the probe, used in
+                place of a physical sample z-move (e.g. when the z stage/piezo
+                is unavailable). Written as `p.probe_file_propagation` if given;
+                omitted entirely otherwise, matching the old reconstruction.mac
+                behavior of only writing this parameter when
+                progagateprobeinsteadofsample==1.
         """
         if not self._accounts_match():
             logger.warning("Active BEC account does not match system user — skipping queue file write.")
@@ -214,6 +227,8 @@ class PtychoReconstructor:
         with open(queue_file, "w") as f:
             scans = " ".join(str(s) for s in scan_list)
             f.write(f"p.scan_number {scans}\n")
+            if probe_file_propagation is not None:
+                f.write(f"p.probe_file_propagation {probe_file_propagation:.6f}\n")
             f.write("p.check_nextscan_started 1\n")