csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py

@@ -2426,7 +2426,15 @@ class LamNI(
             # equivalent addition -- no flat-field/empty-frame step here
             # (unlike Flomni's collect_empty_frames()), since LamNI has no
             # way to retract the sample out of the beam.
-            self._tomo_scan_at_angle(0, 1)
+            #
+            # Skipped for tomo_type 4 (angle file): the file may override
+            # the scan parameters per angle, so a 0-degree shot with the
+            # normal tomo parameters could end up as e.g. a low-resolution
+            # projection inside a high-resolution tomogram. The angle file
+            # is the sole source of projections there -- put 0 in the file
+            # if one is wanted. Mirrors Flomni.
+            if self.tomo_type != 4:
+                self._tomo_scan_at_angle(0, 1)
 
         try:
             with scans.dataset_id_on_hold:

csaxs_bec/bec_ipython_client/plugins/OMNY_shared/tomo_angle_file_mixin.py

@@ -187,8 +187,7 @@ class TomoAngleFileMixin:
     def _init_angle_file_progress(self, file_angles: AngleFileResult, projection_number) -> None:
         """Fill the progress fields that are already known from the file, so the
         GUI shows the real tomo type/total (and sub-tomogram 1) during the
-        preparation steps and the 0-deg reference shot that precede the loop,
-        instead of the blank reset defaults (tomo type 0, projection 0)."""
+        preparation steps (e.g. empty frames) that precede the loop, instead of the blank reset defaults (tomo type 0, projection 0)."""
         self.progress["tomo_type"] = "Angles from file"
         self.progress["total_projections"] = (
             len(file_angles.angles) if file_angles.is_complete else 0
@@ -197,9 +196,12 @@ class TomoAngleFileMixin:
             self.progress["subtomo"] = 1
 
     def _run_angle_file_loop(self, file_angles: AngleFileResult, projection_number) -> None:
-        """Acquire the angles of tomo_type 4 in file order (no extra 0-deg
-        damage-estimation shots: sub-tomogram numbers in a user file are just
-        labels, put 0-deg lines in the file instead). Waits for lines to be
+        """Acquire the angles of tomo_type 4 in file order. The file is the
+        sole source of projections: no initial 0-deg shot at the start of a
+        new tomogram (it would use the normal tomo parameters, not the
+        file's per-angle ones) and no extra 0-deg damage-estimation shots
+        (sub-tomogram numbers in a user file are just labels) -- put 0-deg
+        lines in the file instead. Waits for lines to be
         appended while the file has no 'END' marker."""
         error = self._TOMO_PARAMS_ERROR
         self.progress["tomo_type"] = "Angles from file"

csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -2827,7 +2827,16 @@ class Flomni(
             # projection), included in reconstruction like any other
             # projection -- not a flat-field/reference-only frame like
             # collect_empty_frames() above. Logged under subtomo_number=1.
-            self._tomo_scan_at_angle(0, 1)
+            #
+            # Skipped for tomo_type 4 (angle file): the file may override
+            # the scan parameters (step, exp_time, frames_per_trigger, ...)
+            # per angle, so a 0-degree shot taken with the normal tomo
+            # parameters could be e.g. a low-resolution projection inside a
+            # high-resolution tomogram, which breaks loading the projections
+            # for further processing. The angle file is the sole source of
+            # projections there -- put 0 in the file if one is wanted.
+            if self.tomo_type != 4:
+                self._tomo_scan_at_angle(0, 1)
 
         try:
             with scans.dataset_id_on_hold:

tests/tests_bec_ipython_client/test_flomni_tomo_angles.py

@@ -355,8 +355,8 @@ def test_angle_file_scan_follows_file_order_and_subtomos(monkeypatch, tmp_path):
 
     flomni.tomo_scan()
 
-    # (0, 1): unconditional 0-deg reference shot at the start of a new tomogram
-    assert recorded == [(0, 1), (10.0, 1), (170.0, 1), (270.0, 2), (5.5, 3)]
+    # no initial 0-deg shot: for tomo_type 4 the file is the only source of projections
+    assert recorded == [(10.0, 1), (170.0, 1), (270.0, 2), (5.5, 3)]
     assert flomni.progress["total_projections"] == 4
     assert flomni.progress["tomo_type"] == "Angles from file"
 
@@ -407,8 +407,9 @@ def test_angle_file_missing_raises_before_any_acquisition(monkeypatch, tmp_path)
 
 
 def test_angle_file_ignores_golden_zero_deg_damage_flag(monkeypatch, tmp_path):
-    """No extra 0-deg shots at sub-tomogram transitions for type 4 -- only
-    the unconditional reference shot at the start of a new tomogram."""
+    """No 0-deg shots at all for type 4 -- neither at sub-tomogram
+    transitions nor the initial reference shot at the start of a new
+    tomogram (it would use the normal tomo parameters, not the file's)."""
     flomni = make_flomni_for_angle_file(monkeypatch, tmp_path, "10 1\n20 2\n30 3\n40 5\nEND\n")
     flomni.golden_projections_at_0_deg_for_damage_estimation = 1
     recorded = []
@@ -416,7 +417,7 @@ def test_angle_file_ignores_golden_zero_deg_damage_flag(monkeypatch, tmp_path):
 
     flomni.tomo_scan()
 
-    assert recorded == [(0, 1), (10.0, 1), (20.0, 2), (30.0, 3), (40.0, 5)]
+    assert recorded == [(10.0, 1), (20.0, 2), (30.0, 3), (40.0, 5)]
 
 
 def test_max_scan_angle_is_362_only_for_type_4():
@@ -452,8 +453,7 @@ def test_angle_file_accepts_physical_overtravel_range(monkeypatch, tmp_path):
 
     flomni.tomo_scan()  # exercises the real _tomo_scan_at_angle(), not a stub
 
-    # 0: unconditional 0-deg reference shot at the start of a new tomogram
-    assert recorded == [0, -2.0, -0.1, 361.0, 362.0]
+    assert recorded == [-2.0, -0.1, 361.0, 362.0]
 
 
 # ── tomo_type 4: live append -- wait at EOF without 'END', poll, pick up ────
@@ -475,8 +475,7 @@ def test_angle_file_waits_then_picks_up_appended_lines(monkeypatch, tmp_path):
 
     flomni.tomo_scan()
 
-    # (0, 1): unconditional 0-deg reference shot at the start of a new tomogram
-    assert recorded == [(0, 1), (5.0, 1), (10.0, 1), (20.0, 1)]
+    assert recorded == [(5.0, 1), (10.0, 1), (20.0, 1)]
     assert len(sleep_calls) == 1
     assert flomni.progress["total_projections"] == 3
 
@@ -529,12 +528,11 @@ def test_angle_file_heartbeat_refreshed_while_waiting(monkeypatch, tmp_path):
 
     flomni.tomo_scan()
 
-    # (0, 1) reference shot, then (5.0, 1) -- both before any wait tick, so no
-    # heartbeat has been written yet (the stub above never sets one itself).
+    # (5.0, 1) comes before any wait tick, so no heartbeat has been written
+    # yet (the stub above never sets one itself).
     assert recorded_heartbeats[0] is None
-    assert recorded_heartbeats[1] is None
     # (10.0, 1) is only reached after the wait tick refreshed the heartbeat.
-    assert recorded_heartbeats[2] is not None
+    assert recorded_heartbeats[1] is not None
 
 
 # ── tomo_type 4: per-line acquisition overrides (step=/exptime=/frames=) ───
@@ -554,7 +552,6 @@ def test_angle_file_overrides_reach_tomo_scan_at_angle_and_are_sticky(monkeypatc
     flomni.tomo_scan()
 
     assert recorded == [
-        (0, 1, {}),  # unconditional 0-deg reference shot at tomogram start
         (10.0, 1, {}),
         (20.0, 1, {"step": 0.5}),
         (30.0, 1, {"step": 0.5}),  # sticky: step carries forward
@@ -727,7 +724,7 @@ def test_resume_does_not_reset_progress(monkeypatch, tmp_path):
     assert flomni.progress["estimated_remaining_time"] == 42.0
 
 
-def test_angle_file_progress_shows_type_and_total_before_the_zero_deg_shot(monkeypatch, tmp_path):
+def test_angle_file_progress_shows_type_and_total_and_skips_zero_deg_shot(monkeypatch, tmp_path):
     flomni = make_flomni_for_angle_file(monkeypatch, tmp_path, "10\n20\nEND\n")
     seen = []
     flomni._tomo_scan_at_angle = lambda angle, subtomo, **kw: seen.append(
@@ -736,7 +733,10 @@ def test_angle_file_progress_shows_type_and_total_before_the_zero_deg_shot(monke
 
     flomni.tomo_scan()
 
-    assert seen[0] == (0, "Angles from file", 2)  # the initial 0-deg shot
+    # no initial 0-deg shot for tomo_type 4: the file is the only source of
+    # projections (a 0-deg shot would use the normal tomo parameters)
+    assert [a for a, _, _ in seen] == [10, 20]
+    assert seen[0] == (10, "Angles from file", 2)
 
 
 def test_flomni_gui_progress_survives_zero_total(monkeypatch):

tests/tests_bec_ipython_client/test_lamni_tomo_angle_file.py

@@ -107,7 +107,7 @@ def test_scan_follows_file_order_and_reports_progress(monkeypatch, tmp_path):
 
     lamni.tomo_scan(force=True)
 
-    assert recorded == [(0, 1), (10.0, 1), (170.0, 1), (270.0, 2), (362.0, 3)]
+    assert recorded == [(10.0, 1), (170.0, 1), (270.0, 2), (362.0, 3)]
     assert lamni.progress["total_projections"] == 4
     assert lamni.progress["tomo_type"] == "Angles from file"
 
@@ -175,7 +175,6 @@ def test_per_line_overrides_are_sticky_and_passed_to_scan_at_angle(monkeypatch,
     lamni.tomo_scan(force=True)
 
     assert calls == [
-        (0, {}),
         (10.0, {}),
         (20.0, {"step": 0.5, "exp_time": 2.0, "frames_per_trigger": 3}),
         (30.0, {"step": 0.7, "exp_time": 2.0, "frames_per_trigger": 3}),
@@ -259,7 +258,7 @@ def test_queue_job_line_shows_angle_file_for_type_4():
     assert "angles=" not in line
 
 
-def test_progress_shows_type_and_total_before_the_zero_deg_shot(monkeypatch, tmp_path):
+def test_progress_shows_type_and_total_and_skips_zero_deg_shot(monkeypatch, tmp_path):
     lamni = make_lamni_for_angle_file(monkeypatch, tmp_path, "10\n20\nEND\n")
     seen = []
     lamni._tomo_scan_at_angle = lambda angle, subtomo: seen.append(
@@ -268,4 +267,7 @@ def test_progress_shows_type_and_total_before_the_zero_deg_shot(monkeypatch, tmp
 
     lamni.tomo_scan(force=True)
 
-    assert seen[0] == (0, "Angles from file", 2)  # the initial 0-deg shot
+    # no initial 0-deg shot for tomo_type 4: the file is the only source of
+    # projections (a 0-deg shot would use the normal tomo parameters)
+    assert [a for a, _, _ in seen] == [10, 20]
+    assert seen[0] == (10, "Angles from file", 2)