From 7657253e9430d4339b7cd85e7bd051c66fdb60e1 Mon Sep 17 00:00:00 2001
From: x12sa <x12sa@psi.ch>
Date: Fri, 26 Jun 2026 15:57:07 +0200
Subject: [PATCH] fix angular start in even subtomos

---
 .../plugins/flomni/flomni.py                  | 51 +++++++++----------
 1 file changed, 23 insertions(+), 28 deletions(-)

diff --git a/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py b/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
index 9da179b..fc67d60 100644
--- a/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
+++ b/csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
@@ -1751,9 +1751,12 @@ class Flomni(
             start_angle (float, optional): The start angle of the scan. Defaults to None.
         """
 
-        if start_angle is not None:
+        explicit_start_angle = start_angle is not None
+        if explicit_start_angle:
             print(f"Sub tomo scan with start angle {start_angle} requested.")
 
+        max_allowed_angle = self.tomo_angle_range + 0.05 + self.tomo_angle_stepsize
+
         if start_angle is None:
             if subtomo_number == 1:
                 start_angle = 0
@@ -1772,22 +1775,31 @@ class Flomni(
             elif subtomo_number == 8:
                 start_angle = self.tomo_angle_stepsize / 8.0 * 7
 
+            if not subtomo_number % 2:  # even = reverse
+                # The table above gives the LOW end of this sub-tomogram's
+                # angular phase (same convention as the forward/odd
+                # sub-tomograms - it's what makes the combined 8 sub-tomograms
+                # interlace into one fine angular grid). A reverse sweep must
+                # begin at the HIGH end of that span and descend, so shift the
+                # freshly-computed phase up by one full angular range. This
+                # step is skipped when start_angle is given explicitly (i.e.
+                # we are resuming mid sub-tomogram), since then the value is
+                # already the literal current angle.
+                start_angle = min(start_angle + self.tomo_angle_range, max_allowed_angle)
+
         # _tomo_shift_angles (potential global variable)
         _tomo_shift_angles = 0
         # compute number of projections
 
         start = start_angle + _tomo_shift_angles
 
-        if subtomo_number % 2:  # odd = forward
-            max_allowed_angle = self.tomo_angle_range + 0.05 + self.tomo_angle_stepsize
-            proposed_end = start + self.tomo_angle_range
-            angle_end = min(proposed_end, max_allowed_angle)
+        if subtomo_number % 2:  # odd = forward: low -> high
+            angle_end = min(start + self.tomo_angle_range, max_allowed_angle)
             span = angle_end - start
 
-        else:  # even = reverse
+        else:  # even = reverse: high -> low
             min_allowed_angle = 0
-            proposed_end = start - self.tomo_angle_range
-            angle_end = max(proposed_end, min_allowed_angle)
+            angle_end = max(start - self.tomo_angle_range, min_allowed_angle)
             span = start - angle_end
 
         # number of projections needed to maintain step size
@@ -1795,22 +1807,6 @@ class Flomni(
 
         angles = np.linspace(start, angle_end, num=N, endpoint=True)
 
-        if subtomo_number % 2:  # odd subtomos → forward direction
-            # clamp end angle to max allowed
-            max_allowed_angle = self.tomo_angle_range + 0.05 + self.tomo_angle_stepsize
-            proposed_end = start + self.tomo_angle_range
-            angle_end = min(proposed_end, max_allowed_angle)
-
-            angles = np.linspace(start, angle_end, num=N, endpoint=True)
-
-        else:  # even subtomos → reverse direction
-            # go FROM start_angle down toward 0
-            min_allowed_angle = 0
-            proposed_end = start - self.tomo_angle_range
-            angle_end = max(proposed_end, min_allowed_angle)
-
-            angles = np.linspace(start, angle_end, num=N, endpoint=True)
-
         for i, angle in enumerate(angles):
 
             self.progress["subtomo"] = subtomo_number
@@ -1818,17 +1814,16 @@ class Flomni(
             # --- NEW LOGIC FOR OFFSET WHEN start_angle IS SPECIFIED ---
             if i == 0:
                 step = self.tomo_angle_stepsize
-                sa = start_angle
 
-                if start_angle is None:
+                if not explicit_start_angle:
                     # normal operation: always start at zero
                     self._subtomo_offset = 0
 
                 else:
                     if subtomo_number % 2:  # odd = forward direction
-                        self._subtomo_offset = round(sa / step)
+                        self._subtomo_offset = round(start_angle / step)
                     else:  # even = reverse direction
-                        self._subtomo_offset = round((self.tomo_angle_range - sa) / step)
+                        self._subtomo_offset = round((self.tomo_angle_range - start_angle) / step)
 
             # progress index must always increase
             self.progress["subtomo_projection"] = self._subtomo_offset + i