path corrections

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py

@@ -424,9 +424,7 @@ class LamNI(LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools):
         )
 
     def _write_tomo_scan_number(self, scan_number: int, angle: float, subtomo_number: int) -> None:
-        tomo_scan_numbers_file = os.path.expanduser(
-            "~/Data10/specES1/dat-files/tomography_scannumbers.txt"
-        )
+        tomo_scan_numbers_file = os.path.expanduser("~/data/raw/logs/tomography_scannumbers.txt")
         with open(tomo_scan_numbers_file, "a+") as out_file:
             out_file.write(
                 f"{scan_number} {angle} {dev.lsamrot.read()['lsamrot']['value']:.3f}"
@@ -499,8 +497,8 @@ class LamNI(LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools):
                     optim_trajectory_corridor=corridor_size,
                 )
 
-    def tomo_reconstruct(self, base_path="~/Data10/specES1"):
-        """Write the tomo reconstruct file for the reconstruction queue."""
+    def tomo_reconstruct(self, base_path="~/data/raw/logs/reconstruction_queue"):
+        """write the tomo reconstruct file for the reconstruction queue"""
         bec = builtins.__dict__.get("bec")
         self.reconstructor.write(
             scan_list=self._current_scan_list,
@@ -524,6 +522,7 @@ class LamNI(LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools):
         print(f"Angle: ........................... {self.progress['angle']}")
         print(f"Current subtomo: ................. {self.progress['subtomo']}")
         print(f"Current projection within subtomo: {self.progress['subtomo_projection']}\x1b[0m")
+        self._flomnigui_update_progress()
 
     # ------------------------------------------------------------------
     # Tomo scan orchestration

csaxs_bec/bec_ipython_client/plugins/LamNI/x_ray_eye_align.py

@@ -368,7 +368,7 @@ class XrayEyeAlign:
         self.tomo_rotate(0)
         print(
             "Done. You are ready to remove the X-ray eye and start ptychography scans.\n"
-            "Fine alignment: lamni.tomo_parameters(), then lamni.tomo_alignment_scan()"
+            "Fine alignment: lamni.tomo_parameters() with offset 0, then lamni.sub_tomo_scan(1,0)"
         )
 
     # ------------------------------------------------------------------