From b60ec2927ade1a66643bdae1444b061ba9cf786a Mon Sep 17 00:00:00 2001
From: x12sa <x12sa@psi.ch>
Date: Wed, 18 Mar 2026 15:36:45 +0100
Subject: [PATCH] minor fixes during testing

---
 .../bec_ipython_client/plugins/flomni/flomni.py | 17 ++++++++++-------
 .../plugins/flomni/flomni_optics_mixin.py       |  2 --
 .../plugins/flomni/x_ray_eye_align.py           |  2 ++
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py b/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
index 72e3bcb..f36a346 100644
--- a/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
+++ b/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
@@ -778,7 +778,9 @@ class FlomniSampleTransferMixin:
             dev.ftransy.controller.socket_put_confirmed("confirm=1")
         else:
             print("Stopping.")
-            exit
+            raise FlomniError(
+                "User abort sample transfer."
+            )
 
     def ftransfer_gripper_is_open(self) -> bool:
         status = bool(float(dev.ftransy.controller.socket_put_and_receive("MG @OUT[9]").strip()))
@@ -801,7 +803,8 @@ class FlomniSampleTransferMixin:
     def ftransfer_gripper_move(self, position: int):
         self.check_position_is_valid(position)
 
-        self._ftransfer_shiftx = -0.2
+        #this is not used for sample stage position!
+        self._ftransfer_shiftx = -0.15
         self._ftransfer_shiftz = -0.5
 
         fsamx_pos = dev.fsamx.readback.get()
@@ -821,7 +824,7 @@ class FlomniSampleTransferMixin:
         self.check_tray_in()
 
         if position == 0:
-            umv(dev.ftransx, 10.715 + 0.2, dev.ftransz, 3.5950)
+            umv(dev.ftransx, 11, dev.ftransz, 3.5950)
         if position == 1:
             umv(
                 dev.ftransx,
@@ -1537,7 +1540,7 @@ class Flomni(
 
         umv(dev.fsamroy, 0)
         self.OMNYTools.printgreenbold(
-            "\n\nAlignment scan finished. Please run SPEC_ptycho_align and load the new fit."
+            "\n\nAlignment scan finished. Please run SPEC_ptycho_align and load the new fit by flomni.read_alignment_offset() ."
         )
 
     def _write_subtomo_to_scilog(self, subtomo_number):
@@ -1713,9 +1716,9 @@ class Flomni(
             )
             if self.OMNYTools.yesno("Shall I continue?", "n"):
                 print("OK")
-        else:
-            print("Stopping.")
-            return
+            else:
+                print("Stopping.")
+                return
 
         self.flomnigui_show_progress()
 
diff --git a/csaxs_bec/bec_ipython_client/plugins/flomni/flomni_optics_mixin.py b/csaxs_bec/bec_ipython_client/plugins/flomni/flomni_optics_mixin.py
index 17716a9..4e9e688 100644
--- a/csaxs_bec/bec_ipython_client/plugins/flomni/flomni_optics_mixin.py
+++ b/csaxs_bec/bec_ipython_client/plugins/flomni/flomni_optics_mixin.py
@@ -50,8 +50,6 @@ class FlomniOpticsMixin:
             # move both axes to the desired "in" positions
             umv(dev.feyex, feyex_in, dev.feyey, feyey_in)
 
-        self.xrayeye_update_frame()
-
     def _ffzp_in(self):
         foptx_in = self._get_user_param_safe("foptx", "in")
         fopty_in = self._get_user_param_safe("fopty", "in")
diff --git a/csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py b/csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py
index 0de7b6c..e1fc704 100644
--- a/csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py
+++ b/csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py
@@ -253,6 +253,8 @@ class XrayEyeAlign:
 
         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")