Merge pull request #159 from scipp/nexus-workflow

Add an ESTIA NeXus workflow

Author: jl-wynen

docs/user-guide/estia/estia-mcstas-reduction.ipynb

@@ -31,7 +31,7 @@
     "\n",
     "from ess.estia.load import load_mcstas_events\n",
     "from ess.estia.data import estia_mcstas_example, estia_mcstas_groundtruth\n",
-    "from ess.estia import EstiaWorkflow\n",
+    "from ess.estia import EstiaMcStasWorkflow\n",
     "from ess.reflectometry.types import *\n",
     "from ess.reflectometry.figures import wavelength_z_figure, wavelength_theta_figure, q_theta_figure"
    ]
@@ -52,7 +52,7 @@
    "outputs": [],
    "source": [
     "\n",
-    "wf = EstiaWorkflow()\n",
+    "wf = EstiaMcStasWorkflow()\n",
     "wf.insert(load_mcstas_events)\n",
     "wf[Filename[ReferenceRun]] = estia_mcstas_example('reference')\n",
     "\n",
@@ -85,9 +85,19 @@
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "id": "5",
    "metadata": {},
+   "outputs": [],
+   "source": [
+    "wf.visualize(graph_attr={'rankdir':\"LR\"})"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6",
+   "metadata": {},
    "source": [
     "## Ni/Ti multilayer sample\n",
     "\n",
@@ -98,7 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -115,7 +125,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "8",
    "metadata": {},
    "source": [
     "Below are a number of figures displaying different projections of the measured intensity distribution."
@@ -124,7 +134,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -138,7 +148,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -148,7 +158,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -158,7 +168,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -167,7 +177,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "12",
+   "id": "13",
    "metadata": {},
    "source": [
     "## Ni on Silicon"
@@ -176,7 +186,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -193,7 +203,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -207,7 +217,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -217,7 +227,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -227,7 +237,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -236,7 +246,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "18",
+   "id": "19",
    "metadata": {},
    "source": [
     "## SiO2 on Silicon"
@@ -245,7 +255,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -262,7 +272,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -276,7 +286,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -286,7 +296,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -296,7 +306,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "24",
    "metadata": {},
    "outputs": [],
    "source": [

docs/user-guide/offspec/offspec_reduction.ipynb

@@ -113,8 +113,8 @@
     "header.data_source.measurement = fileio.data_source.Measurement(\n",
     "    instrument_settings=fileio.data_source.InstrumentSettings(\n",
     "        incident_angle=fileio.base.Value(\n",
-    "            wf.compute(RawDetectorData[SampleRun]).coords[\"theta\"].value,\n",
-    "            wf.compute(RawDetectorData[SampleRun]).coords[\"theta\"].unit\n",
+    "            wf.compute(DetectorData[SampleRun]).coords[\"theta\"].value,\n",
+    "            wf.compute(DetectorData[SampleRun]).coords[\"theta\"].unit\n",
     "        ),\n",
     "        wavelength=None,\n",
     "        polarization=\"unpolarized\",\n",
@@ -183,8 +183,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "wf.compute(RawDetectorData[SampleRun]).hist(tof=50).plot(norm='log') \\\n",
-    "+ wf.compute(RawDetectorData[ReferenceRun]).hist(tof=50).plot(norm='log')"
+    "wf.compute(DetectorData[SampleRun]).hist(tof=50).plot(norm='log') \\\n",
+    "+ wf.compute(DetectorData[ReferenceRun]).hist(tof=50).plot(norm='log')"
    ]
   },
   {

requirements/base.txt

@@ -7,7 +7,7 @@
 #
 annotated-types==0.7.0
     # via pydantic
-click==8.1.8
+click==8.2.0
     # via dask
 cloudpickle==3.1.1
     # via dask
@@ -17,17 +17,17 @@ cyclebane==24.10.0
     # via sciline
 cycler==0.12.1
     # via matplotlib
-dask==2025.4.1
+dask==2025.5.0
     # via -r base.in
 dnspython==2.7.0
     # via email-validator
 email-validator==2.2.0
     # via scippneutron
-essreduce==25.5.0
+essreduce==25.5.1
     # via -r base.in
-fonttools==4.57.0
+fonttools==4.58.0
     # via matplotlib
-fsspec==2025.3.2
+fsspec==2025.5.0
     # via dask
 graphviz==0.20.3
     # via -r base.in
@@ -55,7 +55,7 @@ mpltoolbox==25.4.0
     # via scippneutron
 networkx==3.4.2
     # via cyclebane
-numpy==2.2.5
+numpy==2.2.6
     # via
     #   contourpy
     #   h5py
@@ -77,7 +77,7 @@ partd==1.4.2
     # via dask
 pillow==11.2.1
     # via matplotlib
-plopp==25.4.1
+plopp==25.5.0
     # via
     #   -r base.in
     #   scippneutron
@@ -100,7 +100,7 @@ pyyaml==6.0.2
     # via
     #   dask
     #   orsopy
-sciline==25.4.1
+sciline==25.5.1
     # via
     #   -r base.in
     #   essreduce

requirements/basetest.txt

@@ -9,7 +9,7 @@ certifi==2025.4.26
     # via requests
 charset-normalizer==3.4.2
     # via requests
-exceptiongroup==1.2.2
+exceptiongroup==1.3.0
     # via pytest
 idna==3.10
     # via requests
@@ -21,7 +21,7 @@ packaging==25.0
     #   pytest
 platformdirs==4.3.8
     # via pooch
-pluggy==1.5.0
+pluggy==1.6.0
     # via pytest
 pooch==1.8.2
     # via -r basetest.in
@@ -31,5 +31,7 @@ requests==2.32.3
     # via pooch
 tomli==2.2.1
     # via pytest
+typing-extensions==4.13.2
+    # via exceptiongroup
 urllib3==2.4.0
     # via requests

requirements/ci.txt

@@ -36,9 +36,9 @@ platformdirs==4.3.8
     # via
     #   tox
     #   virtualenv
-pluggy==1.5.0
+pluggy==1.6.0
     # via tox
-pyproject-api==1.9.0
+pyproject-api==1.9.1
     # via tox
 requests==2.32.3
     # via -r ci.in
@@ -48,7 +48,7 @@ tomli==2.2.1
     # via
     #   pyproject-api
     #   tox
-tox==4.25.0
+tox==4.26.0
     # via -r ci.in
 typing-extensions==4.13.2
     # via tox

requirements/dev.txt

@@ -28,7 +28,7 @@ cffi==1.17.1
     # via argon2-cffi-bindings
 copier==9.7.1
     # via -r dev.in
-dunamai==1.24.0
+dunamai==1.24.1
     # via copier
 fqdn==1.5.1
     # via jsonschema
@@ -57,7 +57,7 @@ jupyter-events==0.12.0
     # via jupyter-server
 jupyter-lsp==2.2.5
     # via jupyterlab
-jupyter-server==2.15.0
+jupyter-server==2.16.0
     # via
     #   jupyter-lsp
     #   jupyterlab
@@ -81,7 +81,7 @@ pip-tools==7.4.1
     # via pip-compile-multi
 plumbum==1.9.0
     # via copier
-prometheus-client==0.21.1
+prometheus-client==0.22.0
     # via jupyter-server
 pycparser==2.22
     # via cffi
@@ -107,7 +107,7 @@ terminado==0.18.1
     #   jupyter-server-terminals
 toposort==1.10
     # via pip-compile-multi
-types-python-dateutil==2.9.0.20241206
+types-python-dateutil==2.9.0.20250516
     # via arrow
 uri-template==1.3.0
     # via jsonschema

requirements/docs.txt

@@ -48,7 +48,7 @@ docutils==0.21.2
     #   nbsphinx
     #   pydata-sphinx-theme
     #   sphinx
-exceptiongroup==1.2.2
+exceptiongroup==1.3.0
     # via ipython
 executing==2.2.0
     # via stack-data
@@ -182,11 +182,11 @@ requests==2.32.3
     # via
     #   pooch
     #   sphinx
-rpds-py==0.24.0
+rpds-py==0.25.0
     # via
     #   jsonschema
     #   referencing
-snowballstemmer==3.0.0.1
+snowballstemmer==3.0.1
     # via sphinx
 soupsieve==2.7
     # via beautifulsoup4
@@ -223,7 +223,7 @@ tinycss2==1.4.0
     # via bleach
 tomli==2.2.1
     # via sphinx
-tornado==6.4.2
+tornado==6.5
     # via
     #   ipykernel
     #   jupyter-client