From b7af73a58eec2bbf82b53f6e74889e3257c063cb Mon Sep 17 00:00:00 2001
From: Neil Vaytet <neil.vaytet@ess.eu>
Date: Tue, 9 Jun 2026 17:02:34 +0200
Subject: [PATCH 01/12] skip choppers with empty logs (probably they are not in
 use)

---
 .../src/ess/reduce/nexus/workflow.py          | 37 +++++++++++++++++--
 1 file changed, 33 insertions(+), 4 deletions(-)

diff --git a/packages/essreduce/src/ess/reduce/nexus/workflow.py b/packages/essreduce/src/ess/reduce/nexus/workflow.py
index da7e21cc9..a7cecd347 100644
--- a/packages/essreduce/src/ess/reduce/nexus/workflow.py
+++ b/packages/essreduce/src/ess/reduce/nexus/workflow.py
@@ -9,6 +9,7 @@
 from copy import deepcopy
 from typing import Any, Never, TypeVar
 
+import numpy as np
 import sciline
 import sciline.typing
 import scipp as sc
@@ -560,6 +561,10 @@ def parse_raw_choppers(
     )
 
 
+def _size_or_0(dg, key) -> int:
+    return dg.get(key, np.array([])).size
+
+
 def to_disk_choppers(choppers: RawChoppers[RunType]) -> DiskChoppers[RunType]:
     """
     Convert the raw choppers (DataGroup with chopper information) to the
@@ -570,13 +575,37 @@ def to_disk_choppers(choppers: RawChoppers[RunType]) -> DiskChoppers[RunType]:
     choppers:
         Raw choppers loaded from the NeXus file, as a DataGroup.
     """
-    disk_choppers = {
+    disk_choppers = {}
+    for key, ch in choppers.items():
+        print(key)
+        print(
+            ch['rotation_speed_setpoint'].shape,
+            ch['rotation_speed_setpoint'].size,
+            _size_or_0(ch, "rotation_speed_setpoint"),
+        )
+        if (
+            (_size_or_0(ch, "rotation_speed_setpoint") == 0)
+            and (_size_or_0(ch, "rotation_speed") == 0)
+        ) or ((_size_or_0(ch, "phase") == 0) and (_size_or_0(ch, "delay") == 0)):
+            warnings.warn(
+                f"Chopper '{key}' was skipped because of some empty logs. "
+                "It is considered parked.",
+                stacklevel=2,
+            )
+            continue
+
         # If there is no beam_position, we set it to 0 by default.
-        key: DiskChopper.from_nexus(
+        disk_choppers[key] = DiskChopper.from_nexus(
             {**{'beam_position': sc.scalar(0.0, unit='deg')}, **ch}
         )
-        for key, ch in choppers.items()
-    }
+
+    # disk_choppers = {
+    #     # If there is no beam_position, we set it to 0 by default.
+    #     key: DiskChopper.from_nexus(
+    #         {**{'beam_position': sc.scalar(0.0, unit='deg')}, **ch}
+    #     )
+    #     for key, ch in choppers.items()
+    # }
     return DiskChoppers[RunType](disk_choppers)
 
 

From 7d08bb6dc50bc42f3a5ae2f3cd61a7ccea18d584 Mon Sep 17 00:00:00 2001
From: Neil Vaytet <neil.vaytet@ess.eu>
Date: Tue, 9 Jun 2026 23:23:48 +0200
Subject: [PATCH 02/12] update notebook to use analytical chopper mode

---
 .../docs/odin/odin-data-reduction.ipynb       | 34 ++++++++++++++++---
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/packages/essimaging/docs/odin/odin-data-reduction.ipynb b/packages/essimaging/docs/odin/odin-data-reduction.ipynb
index 8dadb9ae4..9cd7a97f1 100644
--- a/packages/essimaging/docs/odin/odin-data-reduction.ipynb
+++ b/packages/essimaging/docs/odin/odin-data-reduction.ipynb
@@ -41,11 +41,33 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "wf = odin.OdinBraggEdgeWorkflow()\n",
+    "wf = odin.OdinBraggEdgeWorkflow(wavelength_from=\"analytical\")\n",
     "\n",
     "wf[Filename[SampleRun]] = odin.data.iron_simulation_sample_small()\n",
-    "wf[NeXusDetectorName] = \"event_mode_detectors/timepix3\"\n",
-    "wf[unwrap.LookupTableFilename] = odin.data.odin_wavelength_lookup_table()"
+    "wf[NeXusDetectorName] = \"event_mode_detectors/timepix3\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "acc30fc6-aca0-4968-96ba-b65c589f6e46",
+   "metadata": {},
+   "source": [
+    "### Patch the choppers in the file\n",
+    "\n",
+    "The chopper settings in the file contain errors. We patch them here, but note that **this step should go away in the future**."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2e75b5f8-480a-4a51-b795-6eed01cfe3c6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ess.odin.beamline import choppers\n",
+    "\n",
+    "disk_choppers = choppers(source_position=wf.compute(Position[snx.NXsource, SampleRun]))\n",
+    "wf[unwrap.DiskChoppers[SampleRun]] = disk_choppers"
    ]
   },
   {
@@ -158,6 +180,10 @@
    "outputs": [],
    "source": [
     "wf[Filename[OpenBeamRun]] = odin.data.iron_simulation_ob_small()\n",
+    "\n",
+    "# Also need to patch choppers here\n",
+    "wf[unwrap.DiskChoppers[OpenBeamRun]] = disk_choppers\n",
+    "\n",
     "openbeam_wavs = wf.compute(WavelengthDetector[OpenBeamRun])\n",
     "\n",
     "openbeam_wavs.bins.concat().hist(wavelength=300).plot()"
@@ -286,7 +312,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.12"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

From 5f8b966b485460f87ceca76e15c8009caaa76032 Mon Sep 17 00:00:00 2001
From: Neil Vaytet <neil.vaytet@ess.eu>
Date: Tue, 9 Jun 2026 23:34:09 +0200
Subject: [PATCH 03/12] update tests

---
 packages/essimaging/src/ess/imaging/types.py  |  1 +
 .../tests/odin/data_reduction_test.py         | 38 +++++++++++--------
 2 files changed, 23 insertions(+), 16 deletions(-)

diff --git a/packages/essimaging/src/ess/imaging/types.py b/packages/essimaging/src/ess/imaging/types.py
index 027df9cea..9dad68452 100644
--- a/packages/essimaging/src/ess/imaging/types.py
+++ b/packages/essimaging/src/ess/imaging/types.py
@@ -24,6 +24,7 @@
 RawDetector = reduce_t.RawDetector
 RawMonitor = reduce_t.RawMonitor
 NXdetector = snx.NXdetector
+NXsource = snx.NXsource
 
 DetectorLtotal = unwrap_t.DetectorLtotal
 WavelengthDetector = unwrap_t.WavelengthDetector
diff --git a/packages/essimaging/tests/odin/data_reduction_test.py b/packages/essimaging/tests/odin/data_reduction_test.py
index 38f73e786..9b5fc03b7 100644
--- a/packages/essimaging/tests/odin/data_reduction_test.py
+++ b/packages/essimaging/tests/odin/data_reduction_test.py
@@ -5,43 +5,47 @@
 import pytest
 import sciline as sl
 from ess import odin
+from ess.odin.beamline import choppers as odin_choppers
 
 from ess.imaging.types import (
     Filename,
-    LookupTable,
     LookupTableFilename,
     NeXusDetectorName,
-    NXdetector,
+    NXsource,
     OpenBeamRun,
+    Position,
     RawDetector,
     SampleRun,
     WavelengthDetector,
 )
+from ess.reduce import unwrap
 
 
-@pytest.fixture(scope="module")
-def workflow() -> sl.Pipeline:
+def _make_workflow(wavelength_from: unwrap.WavelengthLutMode) -> sl.Pipeline:
     """
     Workflow for loading NeXus data.
     """
-    wf = odin.OdinBraggEdgeWorkflow()
+    wf = odin.OdinBraggEdgeWorkflow(wavelength_from=wavelength_from)
     wf[Filename[SampleRun]] = odin.data.iron_simulation_sample_small()
     wf[Filename[OpenBeamRun]] = odin.data.iron_simulation_ob_small()
     wf[NeXusDetectorName] = "event_mode_detectors/timepix3"
-    for run_type in (SampleRun, OpenBeamRun):
-        wf[LookupTableFilename[run_type, NXdetector]] = (
-            odin.data.odin_wavelength_lookup_table()
-        )
-        # Cache the lookup table
-        wf[LookupTable[run_type, NXdetector]] = wf.compute(
-            LookupTable[run_type, NXdetector]
+    if wavelength_from == "file":
+        # Shortcut to set LookupTableFilename for both SampleRun and OpenBeamRun at once
+        wf[LookupTableFilename] = odin.data.odin_wavelength_lookup_table()
+    else:
+        disk_choppers = odin_choppers(
+            source_position=wf.compute(Position[NXsource, SampleRun])
         )
+        # Shortcut to set DiskChoppers for both [SampleRun, NXdetector] and
+        # [OpenBeamRun, NXdetector] at once
+        wf[unwrap.DiskChoppers] = disk_choppers
     return wf
 
 
 @pytest.mark.parametrize("run_type", [SampleRun, OpenBeamRun])
-def test_can_load_detector_data(workflow, run_type):
-    da = workflow.compute(RawDetector[run_type])
+def test_can_load_detector_data(run_type):
+    wf = _make_workflow("file")
+    da = wf.compute(RawDetector[run_type])
     assert {
         "detector_number",
         "position",
@@ -54,7 +58,9 @@ def test_can_load_detector_data(workflow, run_type):
 
 
 @pytest.mark.parametrize("run_type", [SampleRun, OpenBeamRun])
-def test_can_compute_wavelength(workflow, run_type):
-    da = workflow.compute(WavelengthDetector[run_type])
+@pytest.mark.parametrize("wavelength_mode", ["file", "analytical"])
+def test_can_compute_wavelength(run_type, wavelength_mode):
+    wf = _make_workflow(wavelength_mode)
+    da = wf.compute(WavelengthDetector[run_type])
 
     assert "wavelength" in da.bins.coords

From 163350dbdc836c16c5030d808dc3cb0028575967 Mon Sep 17 00:00:00 2001
From: Neil Vaytet <neil.vaytet@ess.eu>
Date: Tue, 9 Jun 2026 23:34:47 +0200
Subject: [PATCH 04/12] cleanup

---
 packages/essreduce/src/ess/reduce/nexus/workflow.py | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/packages/essreduce/src/ess/reduce/nexus/workflow.py b/packages/essreduce/src/ess/reduce/nexus/workflow.py
index a7cecd347..72571c2d7 100644
--- a/packages/essreduce/src/ess/reduce/nexus/workflow.py
+++ b/packages/essreduce/src/ess/reduce/nexus/workflow.py
@@ -577,12 +577,6 @@ def to_disk_choppers(choppers: RawChoppers[RunType]) -> DiskChoppers[RunType]:
     """
     disk_choppers = {}
     for key, ch in choppers.items():
-        print(key)
-        print(
-            ch['rotation_speed_setpoint'].shape,
-            ch['rotation_speed_setpoint'].size,
-            _size_or_0(ch, "rotation_speed_setpoint"),
-        )
         if (
             (_size_or_0(ch, "rotation_speed_setpoint") == 0)
             and (_size_or_0(ch, "rotation_speed") == 0)
@@ -599,13 +593,6 @@ def to_disk_choppers(choppers: RawChoppers[RunType]) -> DiskChoppers[RunType]:
             {**{'beam_position': sc.scalar(0.0, unit='deg')}, **ch}
         )
 
-    # disk_choppers = {
-    #     # If there is no beam_position, we set it to 0 by default.
-    #     key: DiskChopper.from_nexus(
-    #         {**{'beam_position': sc.scalar(0.0, unit='deg')}, **ch}
-    #     )
-    #     for key, ch in choppers.items()
-    # }
     return DiskChoppers[RunType](disk_choppers)
 
 

From 19c17458ce09807eae3ee191047b105de7be4302 Mon Sep 17 00:00:00 2001
From: Neil Vaytet <neil.vaytet@ess.eu>
Date: Tue, 9 Jun 2026 23:35:04 +0200
Subject: [PATCH 05/12] lint

---
 .../docs/odin/odin-data-reduction.ipynb       | 44 +++++++++----------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/packages/essimaging/docs/odin/odin-data-reduction.ipynb b/packages/essimaging/docs/odin/odin-data-reduction.ipynb
index 9cd7a97f1..595acd925 100644
--- a/packages/essimaging/docs/odin/odin-data-reduction.ipynb
+++ b/packages/essimaging/docs/odin/odin-data-reduction.ipynb
@@ -49,7 +49,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "acc30fc6-aca0-4968-96ba-b65c589f6e46",
+   "id": "4",
    "metadata": {},
    "source": [
     "### Patch the choppers in the file\n",
@@ -60,7 +60,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2e75b5f8-480a-4a51-b795-6eed01cfe3c6",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -72,7 +72,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4",
+   "id": "6",
    "metadata": {},
    "source": [
     "## First look at the data\n",
@@ -83,7 +83,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -94,7 +94,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -103,7 +103,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "9",
    "metadata": {},
    "source": [
     "## Compute neutron wavelengths\n",
@@ -114,7 +114,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -123,7 +123,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "source": [
     "### Inspect the lookup table\n",
@@ -134,7 +134,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -144,7 +144,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "source": [
     "### Compute neutron wavelengths"
@@ -153,7 +153,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -164,7 +164,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "source": [
     "## Process the open-beam run\n",
@@ -175,7 +175,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -191,7 +191,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "source": [
     "## Select region of interest by masking outer regions\n",
@@ -203,7 +203,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -212,7 +212,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "17",
+   "id": "19",
    "metadata": {},
    "source": [
     "The brighter areas around the edges are regions where neutrons did not travel through the sample.\n",
@@ -222,7 +222,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -235,7 +235,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -246,7 +246,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "20",
+   "id": "22",
    "metadata": {},
    "source": [
     "## Normalize to open beam\n",
@@ -258,7 +258,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -274,7 +274,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "22",
+   "id": "24",
    "metadata": {},
    "source": [
     "## Save the final result"
@@ -283,7 +283,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "25",
    "metadata": {},
    "outputs": [],
    "source": [

From f50ed974f8c8a0dac679f7fed0477d03f69186cd Mon Sep 17 00:00:00 2001
From: Neil Vaytet <neil.vaytet@ess.eu>
Date: Tue, 9 Jun 2026 23:37:17 +0200
Subject: [PATCH 06/12] make analytical mode the default

---
 packages/essimaging/src/ess/odin/workflows.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/essimaging/src/ess/odin/workflows.py b/packages/essimaging/src/ess/odin/workflows.py
index 72d5b3f25..9ba3f823b 100644
--- a/packages/essimaging/src/ess/odin/workflows.py
+++ b/packages/essimaging/src/ess/odin/workflows.py
@@ -43,7 +43,7 @@ def default_parameters() -> dict:
 
 
 def OdinWorkflow(
-    wavelength_from: WavelengthLutMode = "file", **kwargs
+    wavelength_from: WavelengthLutMode = "analytical", **kwargs
 ) -> sciline.Pipeline:
     """
     Workflow with default parameters for Odin.
@@ -69,7 +69,7 @@ def OdinWorkflow(
 
 
 def OdinBraggEdgeWorkflow(
-    wavelength_from: WavelengthLutMode = "file", **kwargs
+    wavelength_from: WavelengthLutMode = "analytical", **kwargs
 ) -> sciline.Pipeline:
     """
     Workflow with default parameters and masking providers

From 91b67d8a5af88a0ccea5e735d1ee5e74ee64c7a2 Mon Sep 17 00:00:00 2001
From: Neil Vaytet <neil.vaytet@ess.eu>
Date: Wed, 10 Jun 2026 14:22:57 +0200
Subject: [PATCH 07/12] add to_disk_choppers tests

---
 .../essreduce/tests/nexus/workflow_test.py    | 209 ++++++++++++++++++
 1 file changed, 209 insertions(+)

diff --git a/packages/essreduce/tests/nexus/workflow_test.py b/packages/essreduce/tests/nexus/workflow_test.py
index 85b133d3e..2e1adefb4 100644
--- a/packages/essreduce/tests/nexus/workflow_test.py
+++ b/packages/essreduce/tests/nexus/workflow_test.py
@@ -1,5 +1,6 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
+import warnings
 from datetime import UTC, datetime
 from pathlib import Path
 from typing import NewType
@@ -14,6 +15,7 @@
 from ess.reduce.nexus import compute_component_position, load_from_path, workflow
 from ess.reduce.nexus.types import (
     Beamline,
+    DiskChoppers,
     EmptyDetector,
     Filename,
     Measurement,
@@ -987,3 +989,210 @@ def load_user_info(
     user_info = wf.compute(UserInfo[SampleRun])
     assert user_info['affiliation'] == 'ESS'
     assert user_info['name'] == 'John Doe'
+
+
+def _make_chopper_log(values):
+    if values.size == 1:
+        values = sc.concat([values], dim='time')
+
+    return sc.DataArray(
+        data=values.rename_dims({values.dim: 'time'}),
+        coords={
+            'time': sc.datetime('2022-01-01T00:00:00'),
+            'average_value': values.mean(),
+            'minimum_value': values.min(),
+            'maximum_value': values.max(),
+        },
+    )
+
+
+def _make_empty_log():
+    return sc.DataArray(
+        data=sc.array(dims=['time'], values=[]),
+        coords={
+            'time': sc.datetime('2022-01-01T00:00:00'),
+            'average_value': sc.scalar(0.0),
+            'minimum_value': sc.scalar(0.0),
+            'maximum_value': sc.scalar(0.0),
+        },
+    )
+
+
+def test_convert_raw_to_disk_choppers():
+    wf = GenericNeXusWorkflow(run_types=[SampleRun], monitor_types=[])
+    choppers = sc.DataGroup(
+        {
+            'chopper1': sc.DataGroup(
+                {
+                    'position': sc.vector([0, 0, 6], unit='m'),
+                    'delay': _make_chopper_log(sc.scalar(0, unit='ns')),
+                    'radius': sc.scalar(0.5, unit='m'),
+                    'rotation_speed_setpoint': _make_chopper_log(
+                        sc.scalar(14.0, unit='Hz')
+                    ),
+                    'rotation_speed': _make_chopper_log(
+                        sc.array(dims=['time'], values=[14.1, 13.9, 14.001], unit='Hz')
+                    ),
+                    'slit_edges': sc.array(
+                        dims=['edge'], values=[7.35, 54.08], unit='deg'
+                    ),
+                    'beam_position': sc.scalar(0.0, unit='deg'),
+                }
+            )
+        }
+    )
+    wf[RawChoppers[SampleRun]] = choppers
+    disk_choppers = wf.compute(DiskChoppers[SampleRun])
+    assert 'chopper1' in disk_choppers
+    chopper1 = disk_choppers['chopper1']
+    assert sc.identical(chopper1.axle_position, sc.vector([0, 0, 6], unit='m'))
+    assert sc.identical(chopper1.phase, sc.scalar(0.0, unit='rad'))
+    assert sc.identical(chopper1.radius, sc.scalar(0.5, unit='m'))
+    assert sc.identical(chopper1.frequency, sc.scalar(14.0, unit='Hz'))
+
+
+def test_convert_raw_to_disk_choppers_no_beam_position():
+    wf = GenericNeXusWorkflow(run_types=[SampleRun], monitor_types=[])
+    choppers = sc.DataGroup(
+        {
+            'chopper1': sc.DataGroup(
+                {
+                    'position': sc.vector([0, 0, 6], unit='m'),
+                    'delay': _make_chopper_log(sc.scalar(0, unit='ns')),
+                    'radius': sc.scalar(0.5, unit='m'),
+                    'rotation_speed_setpoint': _make_chopper_log(
+                        sc.scalar(14.0, unit='Hz')
+                    ),
+                    'rotation_speed': _make_chopper_log(
+                        sc.array(dims=['time'], values=[14.1, 13.9, 14.001], unit='Hz')
+                    ),
+                    'slit_edges': sc.array(
+                        dims=['edge'], values=[7.35, 54.08], unit='deg'
+                    ),
+                }
+            )
+        }
+    )
+    wf[RawChoppers[SampleRun]] = choppers
+    disk_choppers = wf.compute(DiskChoppers[SampleRun])
+
+    assert disk_choppers['chopper1'].beam_position == sc.scalar(0.0, unit='deg'), (
+        "Expected default beam position of 0.0 deg when 'beam_position' is missing"
+    )
+
+
+def test_choppers_with_empty_logs_are_dropped_in_conversion_to_disk_choppers():
+    wf = GenericNeXusWorkflow(run_types=[SampleRun], monitor_types=[])
+    choppers = sc.DataGroup(
+        {
+            'chopper1': sc.DataGroup(
+                {
+                    'position': sc.vector([0, 0, 6], unit='m'),
+                    'delay': _make_chopper_log(sc.scalar(0, unit='ns')),
+                    'radius': sc.scalar(0.5, unit='m'),
+                    'rotation_speed_setpoint': _make_chopper_log(
+                        sc.scalar(14.0, unit='Hz')
+                    ),
+                    'rotation_speed': _make_chopper_log(
+                        sc.array(dims=['time'], values=[14.1, 13.9, 14.001], unit='Hz')
+                    ),
+                    'slit_edges': sc.array(
+                        dims=['edge'], values=[7.35, 54.08], unit='deg'
+                    ),
+                }
+            ),
+            'chopper2': sc.DataGroup(
+                {
+                    'position': sc.vector([0, 0, 8], unit='m'),
+                    'delay': _make_empty_log(),
+                    'radius': sc.scalar(0.5, unit='m'),
+                    'rotation_speed_setpoint': _make_empty_log(),
+                    'rotation_speed': _make_empty_log(),
+                    'slit_edges': sc.array(
+                        dims=['edge'], values=[7.35, 54.08], unit='deg'
+                    ),
+                }
+            ),
+        }
+    )
+
+    wf[RawChoppers[SampleRun]] = choppers
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore", r"Chopper 'chopper2' was skipped because of some empty logs"
+        )
+        disk_choppers = wf.compute(DiskChoppers[SampleRun])
+    assert 'chopper1' in disk_choppers, "Expected 'chopper1'"
+    assert 'chopper2' not in disk_choppers, (
+        "Expected 'chopper2' to be dropped due to empty logs"
+    )
+
+
+def test_convert_raw_to_disk_choppers_no_setpoint_fallsback_to_rotation_speed():
+    wf = GenericNeXusWorkflow(run_types=[SampleRun], monitor_types=[])
+    choppers = sc.DataGroup(
+        {
+            'chopper1': sc.DataGroup(
+                {
+                    'position': sc.vector([0, 0, 6], unit='m'),
+                    'delay': _make_chopper_log(sc.scalar(0, unit='ns')),
+                    'radius': sc.scalar(0.5, unit='m'),
+                    'rotation_speed': _make_chopper_log(
+                        sc.array(dims=['time'], values=[14.0], unit='Hz')
+                    ),
+                    'slit_edges': sc.array(
+                        dims=['edge'], values=[7.35, 54.08], unit='deg'
+                    ),
+                    'beam_position': sc.scalar(0.0, unit='deg'),
+                }
+            )
+        }
+    )
+    wf[RawChoppers[SampleRun]] = choppers
+    disk_choppers = wf.compute(DiskChoppers[SampleRun])
+    assert 'chopper1' in disk_choppers
+    chopper1 = disk_choppers['chopper1']
+    assert sc.identical(chopper1.frequency, sc.scalar(14.0, unit='Hz'))
+
+
+def test_convert_raw_to_disk_choppers_moving_position():
+    wf = GenericNeXusWorkflow(run_types=[SampleRun], monitor_types=[])
+
+    pos = sc.vector([0, 0, 6], unit="m")
+
+    choppers = sc.DataGroup(
+        {
+            'chopper1': sc.DataGroup(
+                {
+                    'position': sc.DataArray(
+                        data=sc.concat([pos], dim='time'),
+                        coords={
+                            'time': sc.datetime('2022-01-01T00:00:00'),
+                            'average_value': pos,
+                            'minimum_value': pos,
+                            'maximum_value': pos,
+                        },
+                    ),
+                    'delay': _make_chopper_log(sc.scalar(0, unit='ns')),
+                    'radius': sc.scalar(0.5, unit='m'),
+                    'rotation_speed_setpoint': _make_chopper_log(
+                        sc.scalar(14.0, unit='Hz')
+                    ),
+                    'rotation_speed': _make_chopper_log(
+                        sc.array(dims=['time'], values=[14.1, 13.9, 14.001], unit='Hz')
+                    ),
+                    'slit_edges': sc.array(
+                        dims=['edge'], values=[7.35, 54.08], unit='deg'
+                    ),
+                    'beam_position': sc.scalar(0.0, unit='deg'),
+                }
+            )
+        }
+    )
+
+    wf[RawChoppers[SampleRun]] = choppers
+    disk_choppers = wf.compute(DiskChoppers[SampleRun])
+    assert sc.identical(
+        disk_choppers['chopper1'].axle_position,
+        sc.vector([0, 0, 6], unit='m'),
+    ), "Expected position to be taken from the first time point of the log"

From 23c93d3f137e2156786604de0d723374e28b2190 Mon Sep 17 00:00:00 2001
From: Neil Vaytet <neil.vaytet@ess.eu>
Date: Wed, 10 Jun 2026 16:03:52 +0200
Subject: [PATCH 08/12] update scippneutron version and removed unecessary deps
 in packages that depend on essreduce

---
 packages/essdiffraction/pyproject.toml   | 6 ------
 packages/essimaging/pyproject.toml       | 6 ------
 packages/essnmx/pyproject.toml           | 6 ------
 packages/essreduce/pyproject.toml        | 2 +-
 packages/essreflectometry/pyproject.toml | 6 ------
 packages/esssans/pyproject.toml          | 6 ------
 packages/essspectroscopy/pyproject.toml  | 5 -----
 7 files changed, 1 insertion(+), 36 deletions(-)

diff --git a/packages/essdiffraction/pyproject.toml b/packages/essdiffraction/pyproject.toml
index 949c95412..9abc35e4d 100644
--- a/packages/essdiffraction/pyproject.toml
+++ b/packages/essdiffraction/pyproject.toml
@@ -29,16 +29,10 @@ requires-python = ">=3.11"
 # Run 'tox -e deps' after making changes here. This will update requirement files.
 # Make sure to list one dependency per line.
 dependencies = [
-  "dask>=2022.1.0",
   "essreduce>=26.6.0",
-  "graphviz>=0.20",
   "numpy>=2",
   "plopp>=26.2.0",
   "pythreejs>=2.4.1",
-  "sciline>=25.04.1",
-  "scipp>=25.11.0",
-  "scippneutron>=26.3.0",
-  "scippnexus>=23.12.0",
   "tof>=25.12.0",
   "ncrystal[cif]>=4.1.0",
   "spglib>=2.0.0,!=2.7",  # https://github.com/mctools/ncrystal/issues/320
diff --git a/packages/essimaging/pyproject.toml b/packages/essimaging/pyproject.toml
index ce7eda7e2..558a2acea 100644
--- a/packages/essimaging/pyproject.toml
+++ b/packages/essimaging/pyproject.toml
@@ -30,13 +30,7 @@ requires-python = ">=3.11"
 dynamic = ["version"]
 
 dependencies = [
-  "dask>=2022.1.0",
-  "graphviz>=0.20",
   "plopp[all]>=23.10.0",
-  "sciline>=23.9.1",
-  "scipp>=25.4.0",
-  "scippneutron>=24.12.0",
-  "scippnexus>=23.11.1",
   "tifffile>=2024.7.2",
   "essreduce>=26.6.0",
   "scitiff>=25.7",
diff --git a/packages/essnmx/pyproject.toml b/packages/essnmx/pyproject.toml
index bde3e8bf2..bd3754cd3 100644
--- a/packages/essnmx/pyproject.toml
+++ b/packages/essnmx/pyproject.toml
@@ -30,14 +30,8 @@ requires-python = ">=3.11"
 # Run 'tox -e deps' after making changes here. This will update requirement files.
 # Make sure to list one dependency per line.
 dependencies = [
-  "dask>=2022.1.0",
   "essreduce>=26.6.0",
-  "graphviz>=0.20",
   "plopp>=24.7.0",
-  "sciline>=24.06.0",
-  "scipp>=25.3.0",
-  "scippnexus>=23.12.0",
-  "scippneutron>=26.03.0",
   "pooch>=1.5",
   "pandas>=2.1.2",
   "gemmi>=0.6.6",
diff --git a/packages/essreduce/pyproject.toml b/packages/essreduce/pyproject.toml
index 21d1592c3..cacd35069 100644
--- a/packages/essreduce/pyproject.toml
+++ b/packages/essreduce/pyproject.toml
@@ -34,7 +34,7 @@ dependencies = [
     "graphviz>=0.20",
     "sciline>=25.11.0",
     "scipp>=26.3.1",
-    "scippneutron>=26.5.0",
+    "scippneutron>=26.6.0",
     "scippnexus>=25.06.0",
     "scipy>=1.14",
 ]
diff --git a/packages/essreflectometry/pyproject.toml b/packages/essreflectometry/pyproject.toml
index dd81093c1..50541282e 100644
--- a/packages/essreflectometry/pyproject.toml
+++ b/packages/essreflectometry/pyproject.toml
@@ -29,15 +29,9 @@ requires-python = ">=3.11"
 # Run 'tox -e deps' after making changes here. This will update requirement files.
 # Make sure to list one dependency per line.
 dependencies = [
-    "dask>=2022.1.0",
     "python-dateutil>=2.8.2",
-    "graphviz>=0.20",
     "plopp>=24.7.0",
     "orsopy>=1.2",
-    "sciline>=24.6.0",
-    "scipp>=24.09.1", # Fixed new hist/bin API
-    "scippneutron>=24.10.0",
-    "scippnexus>=24.9.1",
     "essreduce>=26.6.0",
     "esspolarization>=25.7.0",
     "pandas>=2.1.2",
diff --git a/packages/esssans/pyproject.toml b/packages/esssans/pyproject.toml
index bc5e4657d..9072e29b8 100644
--- a/packages/esssans/pyproject.toml
+++ b/packages/esssans/pyproject.toml
@@ -30,17 +30,11 @@ requires-python = ">=3.11"
 dynamic = ["version"]
 
 dependencies = [
-  "dask>=2022.1.0",
-  "graphviz>=0.20",
   "essreduce>=26.6.0",
   "numpy>=1.26.4",
   "pandas>=2.1.2",
   "plopp>=25.10.0",
   "pythreejs>=2.4.1",
-  "sciline>=25.08.0",
-  "scipp>=24.09.1",  # Fixed new hist/bin API
-  "scippneutron>=25.02.1",
-  "scippnexus>=23.12.1",  # 23.12.0 and below deadlock in threaded use
 ]
 
 [project.optional-dependencies]
diff --git a/packages/essspectroscopy/pyproject.toml b/packages/essspectroscopy/pyproject.toml
index 59e40ee19..d6d7ffe97 100644
--- a/packages/essspectroscopy/pyproject.toml
+++ b/packages/essspectroscopy/pyproject.toml
@@ -31,12 +31,7 @@ requires-python = ">=3.11"
 # Make sure to list one dependency per line.
 dependencies = [
     "essreduce>=26.6.0",
-    "graphviz>=0.20",
     "pandas>=2.1.2",
-    "sciline>=25.4.1",
-    "scipp>=26.1.0",
-    "scippneutron>=25.11.2",
-    "scippnexus>=24.9.0",
     "tof>=25.11.0",
 ]
 

From e4bd6d0195096c09544555128173cbf64959fc71 Mon Sep 17 00:00:00 2001
From: Neil Vaytet <neil.vaytet@ess.eu>
Date: Wed, 10 Jun 2026 16:04:18 +0200
Subject: [PATCH 09/12] update lock file

---
 pixi.lock | 271 ++++++++++++++++++++++++------------------------------
 1 file changed, 118 insertions(+), 153 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index 13196ee48..3d5e7f765 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -152,6 +152,7 @@ environments:
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       - pypi: https://files.pythonhosted.org/packages/48/eb/46e443fc70b4aabe6e775521ff476aefb051db9acabb16a5cb51f04e3e2b/gemmi-0.7.5-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/4a/f3/00bb1e867fba351e2d784170955713bee200c43ea306c59f30bd7e748192/dask-2026.3.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/4d/82/597fcbfe2ee1928f594795de448762518de2021d1d073d02e534053ce1b9/scippneutron-26.6.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/4e/8c/f3147f5c4b73e7550fe5f9352eaa956ae838d5c51eb58e7a25b9f3e2643b/decorator-5.2.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/4f/d3/a8b22fa575b297cd6e3e3b0155c7e25db170edf1c74783d6a31a2490b8d9/argon2_cffi-25.1.0-py3-none-any.whl
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-      - pypi: https://files.pythonhosted.org/packages/63/9f/724f66a48309dd97a2ff58f491d6ffd925f35d1278a5e55dc9a5ac6a156b/scippneutron-26.5.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/64/b4/17d4b0b2a2dc85a6df63d1157e028ed19f90d4cd97c36717afef2bc2f395/attrs-26.1.0-py3-none-any.whl
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@@ -373,6 +373,7 @@ environments:
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+      - pypi: https://files.pythonhosted.org/packages/4d/82/597fcbfe2ee1928f594795de448762518de2021d1d073d02e534053ce1b9/scippneutron-26.6.0-py3-none-any.whl
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   requires_python: '>=3.10'
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+  name: scippneutron
+  version: 26.6.0
+  sha256: 640cb5a35e2c7b29b5a95ddcd8a6b6d7ce39b24bbc78223c2e0d19e2aa2a79c5
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+  - pydantic>=2
+  - scipp>=25.11.0
+  - scippnexus>=23.11.0
+  - scipy>=1.7.0
+  - scipp[all]>=25.8.0 ; extra == 'all'
+  - pooch>=1.5 ; extra == 'all'
+  - hypothesis>=6.100 ; extra == 'test'
+  - ipympl>0.9.0 ; extra == 'test'
+  - ipykernel>6.30 ; extra == 'test'
+  - pace-neutrons>=0.3 ; extra == 'test'
+  - pooch>=1.5 ; extra == 'test'
+  - psutil>=5.0 ; extra == 'test'
+  - pytest>=7.0 ; extra == 'test'
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+  - pythreejs>=2.4.1 ; extra == 'test'
+  - sciline>=25.1.0 ; extra == 'test'
+  requires_python: '>=3.11'
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@@ -21649,16 +21649,10 @@ packages:
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   name: essdiffraction
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@@ -21685,13 +21679,7 @@ packages:
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@@ -21716,14 +21704,8 @@ packages:
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   name: essnmx
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-  - graphviz>=0.20
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@@ -21753,7 +21735,7 @@ packages:
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+  - scippneutron>=26.6.0
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@@ -21784,15 +21766,9 @@ packages:
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   name: essreflectometry
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@@ -21824,17 +21800,11 @@ packages:
 - pypi: packages/esssans
   name: esssans
   requires_dist:
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-  - graphviz>=0.20
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@@ -21856,12 +21826,7 @@ packages:
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From 05e6d02f382e9a376e714f8253e56bb5c7a49a88 Mon Sep 17 00:00:00 2001
From: Neil Vaytet <neil.vaytet@ess.eu>
Date: Thu, 11 Jun 2026 16:41:35 +0200
Subject: [PATCH 10/12] do not warn when chopper dropped

---
 packages/essreduce/src/ess/reduce/nexus/workflow.py | 5 -----
 packages/essreduce/tests/nexus/workflow_test.py     | 7 +------
 2 files changed, 1 insertion(+), 11 deletions(-)

diff --git a/packages/essreduce/src/ess/reduce/nexus/workflow.py b/packages/essreduce/src/ess/reduce/nexus/workflow.py
index 72571c2d7..88c161811 100644
--- a/packages/essreduce/src/ess/reduce/nexus/workflow.py
+++ b/packages/essreduce/src/ess/reduce/nexus/workflow.py
@@ -581,11 +581,6 @@ def to_disk_choppers(choppers: RawChoppers[RunType]) -> DiskChoppers[RunType]:
             (_size_or_0(ch, "rotation_speed_setpoint") == 0)
             and (_size_or_0(ch, "rotation_speed") == 0)
         ) or ((_size_or_0(ch, "phase") == 0) and (_size_or_0(ch, "delay") == 0)):
-            warnings.warn(
-                f"Chopper '{key}' was skipped because of some empty logs. "
-                "It is considered parked.",
-                stacklevel=2,
-            )
             continue
 
         # If there is no beam_position, we set it to 0 by default.
diff --git a/packages/essreduce/tests/nexus/workflow_test.py b/packages/essreduce/tests/nexus/workflow_test.py
index 2e1adefb4..0c3ddc4bf 100644
--- a/packages/essreduce/tests/nexus/workflow_test.py
+++ b/packages/essreduce/tests/nexus/workflow_test.py
@@ -1,6 +1,5 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
-import warnings
 from datetime import UTC, datetime
 from pathlib import Path
 from typing import NewType
@@ -1117,11 +1116,7 @@ def test_choppers_with_empty_logs_are_dropped_in_conversion_to_disk_choppers():
     )
 
     wf[RawChoppers[SampleRun]] = choppers
-    with warnings.catch_warnings():
-        warnings.filterwarnings(
-            "ignore", r"Chopper 'chopper2' was skipped because of some empty logs"
-        )
-        disk_choppers = wf.compute(DiskChoppers[SampleRun])
+    disk_choppers = wf.compute(DiskChoppers[SampleRun])
     assert 'chopper1' in disk_choppers, "Expected 'chopper1'"
     assert 'chopper2' not in disk_choppers, (
         "Expected 'chopper2' to be dropped due to empty logs"

From d1d15b2dc732d7ece40878761172b624073fe6ca Mon Sep 17 00:00:00 2001
From: Neil Vaytet <neil.vaytet@ess.eu>
Date: Thu, 11 Jun 2026 16:43:53 +0200
Subject: [PATCH 11/12] add dask and graphviz deps back in

---
 packages/essdiffraction/pyproject.toml   | 2 ++
 packages/essimaging/pyproject.toml       | 2 ++
 packages/essnmx/pyproject.toml           | 2 ++
 packages/essreflectometry/pyproject.toml | 2 ++
 packages/esssans/pyproject.toml          | 2 ++
 packages/essspectroscopy/pyproject.toml  | 2 ++
 6 files changed, 12 insertions(+)

diff --git a/packages/essdiffraction/pyproject.toml b/packages/essdiffraction/pyproject.toml
index 9abc35e4d..b2b5e0464 100644
--- a/packages/essdiffraction/pyproject.toml
+++ b/packages/essdiffraction/pyproject.toml
@@ -29,6 +29,8 @@ requires-python = ">=3.11"
 # Run 'tox -e deps' after making changes here. This will update requirement files.
 # Make sure to list one dependency per line.
 dependencies = [
+  "dask>=2022.1.0",
+  "graphviz>=0.20",
   "essreduce>=26.6.0",
   "numpy>=2",
   "plopp>=26.2.0",
diff --git a/packages/essimaging/pyproject.toml b/packages/essimaging/pyproject.toml
index 558a2acea..582dc7212 100644
--- a/packages/essimaging/pyproject.toml
+++ b/packages/essimaging/pyproject.toml
@@ -30,6 +30,8 @@ requires-python = ">=3.11"
 dynamic = ["version"]
 
 dependencies = [
+  "dask>=2022.1.0",
+  "graphviz>=0.20",
   "plopp[all]>=23.10.0",
   "tifffile>=2024.7.2",
   "essreduce>=26.6.0",
diff --git a/packages/essnmx/pyproject.toml b/packages/essnmx/pyproject.toml
index bd3754cd3..06427c0c3 100644
--- a/packages/essnmx/pyproject.toml
+++ b/packages/essnmx/pyproject.toml
@@ -30,6 +30,8 @@ requires-python = ">=3.11"
 # Run 'tox -e deps' after making changes here. This will update requirement files.
 # Make sure to list one dependency per line.
 dependencies = [
+  "dask>=2022.1.0",
+  "graphviz>=0.20",
   "essreduce>=26.6.0",
   "plopp>=24.7.0",
   "pooch>=1.5",
diff --git a/packages/essreflectometry/pyproject.toml b/packages/essreflectometry/pyproject.toml
index 50541282e..5e3455ffb 100644
--- a/packages/essreflectometry/pyproject.toml
+++ b/packages/essreflectometry/pyproject.toml
@@ -29,6 +29,8 @@ requires-python = ">=3.11"
 # Run 'tox -e deps' after making changes here. This will update requirement files.
 # Make sure to list one dependency per line.
 dependencies = [
+    "dask>=2022.1.0",
+    "graphviz>=0.20",
     "python-dateutil>=2.8.2",
     "plopp>=24.7.0",
     "orsopy>=1.2",
diff --git a/packages/esssans/pyproject.toml b/packages/esssans/pyproject.toml
index 9072e29b8..c3db4baba 100644
--- a/packages/esssans/pyproject.toml
+++ b/packages/esssans/pyproject.toml
@@ -30,6 +30,8 @@ requires-python = ">=3.11"
 dynamic = ["version"]
 
 dependencies = [
+  "dask>=2022.1.0",
+  "graphviz>=0.20",
   "essreduce>=26.6.0",
   "numpy>=1.26.4",
   "pandas>=2.1.2",
diff --git a/packages/essspectroscopy/pyproject.toml b/packages/essspectroscopy/pyproject.toml
index d6d7ffe97..65f7c7847 100644
--- a/packages/essspectroscopy/pyproject.toml
+++ b/packages/essspectroscopy/pyproject.toml
@@ -30,6 +30,8 @@ requires-python = ">=3.11"
 # Run 'tox -e deps' after making changes here. This will update requirement files.
 # Make sure to list one dependency per line.
 dependencies = [
+    "dask>=2022.1.0",
+    "graphviz>=0.20",
     "essreduce>=26.6.0",
     "pandas>=2.1.2",
     "tof>=25.11.0",

From 81ed88e5fc1890845ade9a25c3e1a27e5c751112 Mon Sep 17 00:00:00 2001
From: Neil Vaytet <neil.vaytet@ess.eu>
Date: Thu, 11 Jun 2026 16:44:11 +0200
Subject: [PATCH 12/12] update lock file

---
 pixi.lock | 2841 +----------------------------------------------------
 1 file changed, 12 insertions(+), 2829 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index 3d5e7f765..5d47ae82a 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -11049,2815 +11049,6 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/fb/12/5911ae3eeec47800503a238d971e51722ccea5feb8569b735184d5fcdbc0/toolz-1.1.0-py3-none-any.whl
       - pypi: packages/essreduce
       - pypi: packages/essspectroscopy
-  lb-essdiffraction:
-    channels:
-    - url: https://conda.anaconda.org/conda-forge/
-    indexes:
-    - https://pypi.org/simple
-    packages:
-      linux-64:
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.5-hecca717_0.conda
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda
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@@ -19460,26 +16651,6 @@ packages:
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@@ -21766,6 +18943,8 @@ packages:
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