fix(lamni): alignment scan-number file lists first scan of each stitch series

The file written before the alignment scan predicted first_scan + k per
angle, which is wrong with stitching ((2*sx+1)*(2*sy+1) scans per angle).
Predict with that stride, and rewrite the file after every angle so an
interrupted run still leaves correct numbers.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01ALDnH16dC6iyHjhe5Ey4w9

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py

@@ -1486,22 +1486,28 @@ class LamNI(
     ) -> None:
         """Write the scan-number/angle/offset log consumed by BEC_ptycho_align.
 
-        ``scans`` (optional): the actual scan number of each alignment point,
-        used to rewrite the file after the scan when a retried angle consumed
-        extra scan numbers. Defaults to the contiguous ``first_scan + k``
-        prediction written before the scan starts.
+        One scan number per alignment angle: the first scan of that angle's
+        stitch series (with stitching, each projection is
+        (2*lamni_stitch_x+1)*(2*lamni_stitch_y+1) scans).
 
-        Mirrors Flomni.write_alignment_scan_numbers() exactly (same 4-line
-        format), adapted to lamni's own alignment-scan angle set (12 points
-        across the full 360 degrees, see tomo_alignment_scan()) and its own
-        x-ray-eye-fit offset source (lamni_compute_additional_correction_xeye_mu()
-        instead of get_alignment_offset()). Assumes exactly one scan per
-        alignment point (no stitching) -- same assumption flomni's own
-        version makes.
+        ``scans`` (optional): the actual first scan number of the angles
+        acquired so far (possibly fewer than all 12), used to rewrite the
+        file during/after the scan when a retried angle consumed extra scan
+        numbers. Angles not yet acquired are predicted from the last known
+        one, stepping by the number of stitch tiles per projection. Without
+        ``scans`` the whole list is predicted from ``first_scan``.
+
+        Mirrors Flomni.write_alignment_scan_numbers() (same 4-line format),
+        adapted to lamni's own alignment-scan angle set (12 points across the
+        full 360 degrees, see tomo_alignment_scan()) and its own x-ray-eye-fit
+        offset source (lamni_compute_additional_correction_xeye_mu() instead
+        of get_alignment_offset()).
         """
         angles = list(np.linspace(0, 360, num=12, endpoint=False))
-        if scans is None:
-            scans = [first_scan + k for k in range(len(angles))]
+        scans_per_angle = (2 * self.lamni_stitch_x + 1) * (2 * self.lamni_stitch_y + 1)
+        scans = list(scans) if scans else [first_scan]
+        while len(scans) < len(angles):
+            scans.append(scans[-1] + scans_per_angle)
 
         x_vals = []
         for angle in angles:
@@ -1593,14 +1599,13 @@ class LamNI(
             first_scan_per_angle.append(start_scan_number)
             alignment_scan_numbers.extend(range(start_scan_number, end_scan_number))
 
+            # Keep the file current after every angle, so an interrupted run
+            # still leaves correct first-of-stitch-series numbers behind.
+            self.write_alignment_scan_numbers(first_scan_per_angle[0], scans=first_scan_per_angle)
+
             self.alignment_scan_progress.update(angle_index=idx + 1, angle=angle)
             self._lamnigui_update_alignment_progress()
 
-        # The file written up front assumes first_scan + k per angle; a retried
-        # angle consumes extra scan numbers, so rewrite it with what was
-        # actually acquired.
-        self.write_alignment_scan_numbers(first_scan_per_angle[0], scans=first_scan_per_angle)
-
         umv(dev.lsamrot, 0)
         self.OMNYTools.printgreenbold(
             "\n\nAlignment scan finished. Please run BEC_ptycho_align and load the new fit"

tests/tests_bec_ipython_client/test_lamni_tomo_alignment_scan.py

@@ -203,3 +203,48 @@ def test_tomo_alignment_scan_projections_are_not_queued_for_reconstruction(monke
 
     assert len(kwargs_seen) == 12
     assert all(kw.get("_reconstruct") is False for kw in kwargs_seen)
+
+
+def test_write_alignment_scan_numbers_steps_by_stitch_tiles(tmp_path, monkeypatch):
+    """With stitching each angle is (2*sx+1)*(2*sy+1) scans; the file must list
+    the first scan of each angle's stitch series."""
+    lamni = make_lamni(monkeypatch, xray_eye_fit=[[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]])
+    lamni.client.set_global_var("lamni_stitch_x", 1)
+    lamni.client.set_global_var("lamni_stitch_y", 1)
+    monkeypatch.setattr(
+        "os.path.expanduser",
+        lambda p: p.replace("~", str(tmp_path)) if p.startswith("~") else p,
+    )
+    log_file = tmp_path / "data/raw/logs/ptychotomoalign_scannum.txt"
+
+    lamni.write_alignment_scan_numbers(100)
+    assert [int(s) for s in log_file.read_text().split("\n")[0].split()] == list(
+        range(100, 208, 9)
+    )
+
+    # partial actual list (angle 1 retried, +1 scan): rest predicted from it
+    lamni.write_alignment_scan_numbers(100, scans=[100, 110])
+    assert [int(s) for s in log_file.read_text().split("\n")[0].split()] == [100] + list(
+        range(110, 209, 9)
+    )
+
+
+def test_tomo_alignment_scan_with_stitching_records_first_scan_per_angle(tmp_path, monkeypatch):
+    lamni = make_lamni(monkeypatch, xray_eye_fit=[[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]])
+    lamni.client.set_global_var("lamni_stitch_x", 1)
+    lamni.client.set_global_var("lamni_stitch_y", 1)
+    monkeypatch.setattr(
+        "os.path.expanduser",
+        lambda p: p.replace("~", str(tmp_path)) if p.startswith("~") else p,
+    )
+
+    def _projection(angle, _internal=False, **kw):
+        builtins.__dict__["bec"].queue.next_scan_number += 9
+
+    lamni.tomo_scan_projection = _projection
+
+    lamni.tomo_alignment_scan()
+
+    log_file = tmp_path / "data/raw/logs/ptychotomoalign_scannum.txt"
+    scans = [int(s) for s in log_file.read_text().splitlines()[0].split()]
+    assert scans == list(range(100, 208, 9))