diff --git a/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py b/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
index 1128d87..9459865 100644
--- a/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
+++ b/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
@@ -983,56 +983,61 @@ class FlomniAlignmentMixin:
 
     def read_alignment_offset(
         self,
-        dir_path=os.path.expanduser("~/Data10/specES1/internal/"),
+        dir_path=os.path.expanduser("~/data/raw/logs/"),
         setup="flomni",
         use_vertical_default_values=True,
+        get_data_from_gui=False,
     ):
-        """
-        Read the alignment parameters from xray eye fit.
+        if not get_data_from_gui:
+            """
+            Read the alignment parameters from xray eye fit.
 
-        """
-        tomo_alignment_fit = np.zeros((2, 5))
-        # with open(os.path.join(dir_path, "ptychotomoalign_Ax.txt"), "r") as file:
-        #     tomo_alignment_fit[0][0] = file.readline()
+            """
+            tomo_alignment_fit = np.zeros((2, 5))
+            with open(os.path.join(dir_path, "ptychotomoalign_Ax.txt"), "r") as file:
+                tomo_alignment_fit[0][0] = file.readline()
 
-        # with open(os.path.join(dir_path, "ptychotomoalign_Bx.txt"), "r") as file:
-        #     tomo_alignment_fit[0][1] = file.readline()
+            with open(os.path.join(dir_path, "ptychotomoalign_Bx.txt"), "r") as file:
+                tomo_alignment_fit[0][1] = file.readline()
 
-        # with open(os.path.join(dir_path, "ptychotomoalign_Cx.txt"), "r") as file:
-        #     tomo_alignment_fit[0][2] = file.readline()
+            with open(os.path.join(dir_path, "ptychotomoalign_Cx.txt"), "r") as file:
+                tomo_alignment_fit[0][2] = file.readline()
 
-        # with open(os.path.join(dir_path, "ptychotomoalign_Ay.txt"), "r") as file:
-        #     tomo_alignment_fit[1][0] = file.readline()
+            with open(os.path.join(dir_path, "ptychotomoalign_Ay.txt"), "r") as file:
+                tomo_alignment_fit[1][0] = file.readline()
 
-        # with open(os.path.join(dir_path, "ptychotomoalign_By.txt"), "r") as file:
-        #     tomo_alignment_fit[1][1] = file.readline()
+            with open(os.path.join(dir_path, "ptychotomoalign_By.txt"), "r") as file:
+                tomo_alignment_fit[1][1] = file.readline()
 
-        # with open(os.path.join(dir_path, "ptychotomoalign_Cy.txt"), "r") as file:
-        #     tomo_alignment_fit[1][2] = file.readline()
+            with open(os.path.join(dir_path, "ptychotomoalign_Cy.txt"), "r") as file:
+                tomo_alignment_fit[1][2] = file.readline()
 
-        # 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_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:
-        #     tomo_alignment_fit[1][4] = file.readline()
+            with open(os.path.join(dir_path, "ptychotomoalign_Cy3.txt"), "r") as file:
+                tomo_alignment_fit[1][4] = file.readline()
 
-        params = dev.omny_xray_gui.fit_params_x.get()
+            print("New alignment parameters loaded from filesystem, meaning Matlab fit:")
 
-        #amplitude
-        tomo_alignment_fit[0][0] = params['SineModel_0_amplitude']
-        #phase
-        tomo_alignment_fit[0][1] = params['SineModel_0_shift']
-        #offset
-        tomo_alignment_fit[0][2] = params['LinearModel_1_intercept']
-        print("applying vertical default values from mirror calibration, not from fit!")
-        tomo_alignment_fit[1][0] = 0
-        tomo_alignment_fit[1][1] = 0
-        tomo_alignment_fit[1][2] = 0
-        tomo_alignment_fit[1][3] = 0
-        tomo_alignment_fit[1][4] = 0
+        else:
+            params = dev.omny_xray_gui.fit_params_x.get()
+
+            #amplitude
+            tomo_alignment_fit[0][0] = params['SineModel_0_amplitude']
+            #phase
+            tomo_alignment_fit[0][1] = params['SineModel_0_shift']
+            #offset
+            tomo_alignment_fit[0][2] = params['LinearModel_1_intercept']
+            print("applying vertical default values from mirror calibration, not from fit!")
+            tomo_alignment_fit[1][0] = 0
+            tomo_alignment_fit[1][1] = 0
+            tomo_alignment_fit[1][2] = 0
+            tomo_alignment_fit[1][3] = 0
+            tomo_alignment_fit[1][4] = 0
+            print("New alignment parameters loaded based on Xray eye alignment GUI:")
 
 
-        print("New alignment parameters loaded:")
         print(
             f"X Amplitude {tomo_alignment_fit[0][0]}, "
             f"X Phase {tomo_alignment_fit[0][1]}, "
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 1ec5465..0de7b6c 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
@@ -231,10 +231,6 @@ class XrayEyeAlign:
         fovx = self._xray_fov_xy[0] * self.PIXEL_CALIBRATION * 1000 / 2
         fovy = self._xray_fov_xy[1] * self.PIXEL_CALIBRATION * 1000 / 2
 
-        self.tomo_rotate(0)
-
-        umv(dev.rtx, 0)
-
         if keep_shutter_open:
             if self.flomni.OMNYTools.yesno("Close the shutter now?", "y"):
                 dev.omnyfsh.fshclose()
@@ -251,8 +247,11 @@ class XrayEyeAlign:
 
         print("Automatically loading new alignment parameters from xray eye alignment.\n")
 
-        self.flomni.read_alignment_offset()
+        self.flomni.read_alignment_offset(get_data_from_gui=True)
 
+        self.tomo_rotate(0)
+
+        umv(dev.rtx, 0)
         print("You are ready to remove the xray eye and start ptychography scans.")
 
     def write_output(self):