essreduce 25.3.0__tar.gz → 25.4.0__tar.gz

{essreduce-25.3.0 → essreduce-25.4.0}/.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: 5c4fd02
+_commit: d3d4dc7
 _src_path: gh:scipp/copier_template
 description: Common data reduction tools for the ESS facility
 max_python: '3.13'

{essreduce-25.3.0 → essreduce-25.4.0}/.github/workflows/docs.yml

@@ -65,11 +65,13 @@ jobs:
       - run: tox -e linkcheck
         if: ${{ inputs.linkcheck }}
       - uses: actions/upload-artifact@v4
+        id: artifact-upload-step
         with:
           name: docs_html
           path: html/
+      - run: echo "::notice::https://remote-unzip.deno.dev/${{ github.repository }}/artifacts/${{ steps.artifact-upload-step.outputs.artifact-id }}"
 
-      - uses: JamesIves/github-pages-deploy-action@v4.7.2
+      - uses: JamesIves/github-pages-deploy-action@v4.7.3
         if: ${{ inputs.publish }}
         with:
           branch: gh-pages

{essreduce-25.3.0 → essreduce-25.4.0}/.github/workflows/release.yml

@@ -68,7 +68,7 @@ jobs:
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
       - uses: actions/download-artifact@v4
-      - uses: pypa/gh-action-pypi-publish@v1.8.14
+      - uses: pypa/gh-action-pypi-publish@v1.12.4
 
   upload_conda:
     name: Deploy Conda

{essreduce-25.3.0 → essreduce-25.4.0}/.gitignore

@@ -14,6 +14,7 @@ venv
 .venv
 
 # Caches
+*.DS_Store
 .clangd/
 *.ipynb_checkpoints
 __pycache__/

{essreduce-25.3.0/src/essreduce.egg-info → essreduce-25.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: essreduce
-Version: 25.3.0
+Version: 25.4.0
 Summary: Common data reduction tools for the ESS facility
 Author: Scipp contributors
 License: BSD 3-Clause License
@@ -57,10 +57,12 @@ Requires-Dist: scippneutron>=25.02.0
 Requires-Dist: scippnexus>=24.11.0
 Provides-Extra: test
 Requires-Dist: ipywidgets; extra == "test"
+Requires-Dist: numba; extra == "test"
 Requires-Dist: pooch; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: scipy>=1.7.0; extra == "test"
 Requires-Dist: tof>=25.01.2; extra == "test"
+Dynamic: license-file
 
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md)
 [![PyPI badge](http://img.shields.io/pypi/v/essreduce.svg)](https://pypi.python.org/pypi/essreduce)

essreduce-25.4.0/docs/index.md

@@ -0,0 +1,49 @@
+:::{image} _static/logo.svg
+:class: only-light
+:alt: ESSreduce
+:width: 60%
+:align: center
+:::
+:::{image} _static/logo-dark.svg
+:class: only-dark
+:alt: ESSreduce
+:width: 60%
+:align: center
+:::
+
+```{raw} html
+   <style>
+    .transparent {display: none; visibility: hidden;}
+    .transparent + a.headerlink {display: none; visibility: hidden;}
+   </style>
+```
+
+```{role} transparent
+```
+
+# {transparent}`ESSreduce`
+
+<span style="font-size:1.2em;font-style:italic;color:var(--pst-color-text-muted)">
+  Common data reduction tools for the ESS facility
+  </br></br>
+</span>
+
+:::{include} user-guide/installation.md
+:heading-offset: 1
+:::
+
+## Get in touch
+
+- If you have questions that are not answered by these documentation pages, ask on [discussions](https://github.com/scipp/essreduce/discussions). Please include a self-contained reproducible example if possible.
+- Report bugs (including unclear, missing, or wrong documentation!), suggest features or view the source code [on GitHub](https://github.com/scipp/essreduce).
+
+```{toctree}
+---
+hidden:
+---
+
+user-guide/index
+api-reference/index
+developer/index
+about/index
+```

{essreduce-25.3.0 → essreduce-25.4.0}/docs/user-guide/index.md

@@ -1,11 +1,11 @@
-# User guide
-
-## Table of contents
+# User Guide
 
 ```{toctree}
 ---
 maxdepth: 2
 ---
+
+installation
 tof/index
 widget
 reduction-workflow-guidelines

essreduce-25.4.0/docs/user-guide/installation.md

@@ -0,0 +1,16 @@
+# Installation
+
+To install ESSreduce and all of its dependencies, use
+
+`````{tab-set}
+````{tab-item} pip
+```sh
+pip install essreduce
+```
+````
+````{tab-item} conda
+```sh
+conda install -c conda-forge -c scipp essreduce
+```
+````
+`````

{essreduce-25.3.0 → essreduce-25.4.0}/docs/user-guide/tof/dream.ipynb

@@ -59,7 +59,7 @@
     "    frequency=sc.scalar(14.0, unit=\"Hz\"),\n",
     "    beam_position=sc.scalar(0.0, unit=\"deg\"),\n",
     "    phase=sc.scalar(286 - 180, unit=\"deg\"),\n",
-    "    axle_position=sc.vector(value=[0, 0, 6.145], unit=\"m\"),\n",
+    "    axle_position=sc.vector(value=[0, 0, -70.405], unit=\"m\"),\n",
     "    slit_begin=sc.array(\n",
     "        dims=[\"cutout\"],\n",
     "        values=[-1.23, 70.49, 84.765, 113.565, 170.29, 271.635, 286.035, 301.17],\n",
@@ -78,7 +78,7 @@
     "    frequency=sc.scalar(-14.0, unit=\"Hz\"),\n",
     "    beam_position=sc.scalar(0.0, unit=\"deg\"),\n",
     "    phase=sc.scalar(-236, unit=\"deg\"),\n",
-    "    axle_position=sc.vector(value=[0, 0, 6.155], unit=\"m\"),\n",
+    "    axle_position=sc.vector(value=[0, 0, -70.395], unit=\"m\"),\n",
     "    slit_begin=sc.array(\n",
     "        dims=[\"cutout\"],\n",
     "        values=[-1.23, 27.0, 55.8, 142.385, 156.765, 214.115, 257.23, 315.49],\n",
@@ -97,7 +97,7 @@
     "    frequency=sc.scalar(14.0, unit=\"Hz\"),\n",
     "    beam_position=sc.scalar(0.0, unit=\"deg\"),\n",
     "    phase=sc.scalar(297 - 180 - 90, unit=\"deg\"),\n",
-    "    axle_position=sc.vector(value=[0, 0, 6.174], unit=\"m\"),\n",
+    "    axle_position=sc.vector(value=[0, 0, -70.376], unit=\"m\"),\n",
     "    slit_begin=sc.array(dims=[\"cutout\"], values=[-27.6 * 0.5], unit=\"deg\"),\n",
     "    slit_end=sc.array(dims=[\"cutout\"], values=[27.6 * 0.5], unit=\"deg\"),\n",
     "    slit_height=sc.scalar(10.0, unit=\"cm\"),\n",
@@ -108,7 +108,7 @@
     "    frequency=sc.scalar(112.0, unit=\"Hz\"),\n",
     "    beam_position=sc.scalar(0.0, unit=\"deg\"),\n",
     "    phase=sc.scalar(240 - 180, unit=\"deg\"),\n",
-    "    axle_position=sc.vector(value=[0, 0, 9.78], unit=\"m\"),\n",
+    "    axle_position=sc.vector(value=[0, 0, -66.77], unit=\"m\"),\n",
     "    slit_begin=sc.array(dims=[\"cutout\"], values=[-36.875, 143.125], unit=\"deg\"),\n",
     "    slit_end=sc.array(dims=[\"cutout\"], values=[36.875, 216.875], unit=\"deg\"),\n",
     "    slit_height=sc.scalar(10.0, unit=\"cm\"),\n",
@@ -119,7 +119,7 @@
     "    frequency=sc.scalar(28.0, unit=\"Hz\"),\n",
     "    beam_position=sc.scalar(0.0, unit=\"deg\"),\n",
     "    phase=sc.scalar(280 - 180, unit=\"deg\"),\n",
-    "    axle_position=sc.vector(value=[0, 0, 13.05], unit=\"m\"),\n",
+    "    axle_position=sc.vector(value=[0, 0, -63.5], unit=\"m\"),\n",
     "    slit_begin=sc.array(dims=[\"cutout\"], values=[-314.9 * 0.5], unit=\"deg\"),\n",
     "    slit_end=sc.array(dims=[\"cutout\"], values=[314.9 * 0.5], unit=\"deg\"),\n",
     "    slit_height=sc.scalar(10.0, unit=\"cm\"),\n",
@@ -152,7 +152,7 @@
    "id": "6",
    "metadata": {},
    "source": [
-    "### Adding a detector"
+    "Define the source position which is required to compute the distance that neutrons travelled."
    ]
   },
   {
@@ -162,13 +162,31 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Ltotal = sc.scalar(76.55 + 1.125, unit=\"m\")"
+    "source_position = sc.vector([0, 0, -76.55], unit=\"m\")"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "8",
    "metadata": {},
+   "source": [
+    "### Adding a detector"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Ltotal = sc.scalar(76.55 + 1.125, unit=\"m\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "10",
+   "metadata": {},
    "source": [
     "## Creating some neutron events\n",
     "\n",
@@ -178,7 +196,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -186,6 +204,7 @@
     "\n",
     "ess_beamline = FakeBeamline(\n",
     "    choppers=disk_choppers,\n",
+    "    source_position=source_position,\n",
     "    monitors={\"detector\": Ltotal},\n",
     "    run_length=sc.scalar(1 / 14, unit=\"s\") * 4,\n",
     "    events_per_pulse=200_000,\n",
@@ -194,7 +213,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "source": [
     "The initial birth times and wavelengths of the generated neutrons can be visualized (for a single pulse):"
@@ -203,18 +222,18 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
     "one_pulse = ess_beamline.source.data[\"pulse\", 0]\n",
-    "one_pulse.hist(time=300).plot() + one_pulse.hist(wavelength=300).plot()"
+    "one_pulse.hist(birth_time=300).plot() + one_pulse.hist(wavelength=300).plot()"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -223,7 +242,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "source": [
     "From this fake beamline, we extract the raw neutron signal at our detector:"
@@ -232,7 +251,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -244,7 +263,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "source": [
     "The total number of neutrons in our sample data that make it through the to detector is:"
@@ -253,7 +272,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -262,7 +281,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "17",
+   "id": "19",
    "metadata": {},
    "source": [
     "## Computing time-of-flight\n",
@@ -282,7 +301,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -301,7 +320,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "19",
+   "id": "21",
    "metadata": {},
    "source": [
     "We can see from the workflow diagram that we are still missing the simulated neutrons that are used to build the lookup table.\n",
@@ -312,18 +331,18 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
     "workflow[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
-    "    choppers=disk_choppers, neutrons=2_000_000\n",
+    "    choppers=disk_choppers, source_position=source_position, neutrons=2_000_000\n",
     ")"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "21",
+   "id": "23",
    "metadata": {},
    "source": [
     "### Inspecting the lookup table\n",
@@ -340,7 +359,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "24",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -368,7 +387,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "23",
+   "id": "25",
    "metadata": {},
    "source": [
     "The lookup table is then obtained by computing the weighted mean of the time-of-flight inside each time-of-arrival bin.\n",
@@ -379,7 +398,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "26",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -392,7 +411,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "25",
+   "id": "27",
    "metadata": {},
    "source": [
     "### Computing a time-of-flight coordinate\n",
@@ -403,7 +422,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "28",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -413,7 +432,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "27",
+   "id": "29",
    "metadata": {},
    "source": [
     "Histogramming the data for a plot should show a profile with 6 bumps that correspond to the frames:"
@@ -422,7 +441,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28",
+   "id": "30",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -431,7 +450,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "29",
+   "id": "31",
    "metadata": {},
    "source": [
     "### Converting to wavelength\n",
@@ -442,7 +461,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30",
+   "id": "32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -462,7 +481,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "31",
+   "id": "33",
    "metadata": {},
    "source": [
     "### Comparing to the ground truth\n",
@@ -474,7 +493,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32",
+   "id": "34",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -491,7 +510,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "33",
+   "id": "35",
    "metadata": {},
    "source": [
     "## Multiple detector pixels\n",
@@ -507,7 +526,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "34",
+   "id": "36",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -516,6 +535,7 @@
     "\n",
     "ess_beamline = FakeBeamline(\n",
     "    choppers=disk_choppers,\n",
+    "    source_position=source_position,\n",
     "    monitors=monitors,\n",
     "    run_length=sc.scalar(1 / 14, unit=\"s\") * 4,\n",
     "    events_per_pulse=200_000,\n",
@@ -524,7 +544,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "35",
+   "id": "37",
    "metadata": {},
    "source": [
     "Our raw data has now a `detector_number` dimension of length 2.\n",
@@ -535,7 +555,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "36",
+   "id": "38",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -550,7 +570,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "37",
+   "id": "39",
    "metadata": {},
    "source": [
     "Computing time-of-flight is done in the same way as above.\n",
@@ -560,7 +580,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "38",
+   "id": "40",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -594,7 +614,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "39",
+   "id": "41",
    "metadata": {},
    "source": [
     "## Handling time overlap between subframes\n",
@@ -614,7 +634,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "40",
+   "id": "42",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -622,7 +642,7 @@
     "    frequency=sc.scalar(112.0, unit=\"Hz\"),\n",
     "    beam_position=sc.scalar(0.0, unit=\"deg\"),\n",
     "    phase=sc.scalar(240 - 180, unit=\"deg\"),\n",
-    "    axle_position=sc.vector(value=[0, 0, 9.78], unit=\"m\"),\n",
+    "    axle_position=sc.vector(value=[0, 0, -66.77], unit=\"m\"),\n",
     "    slit_begin=sc.array(dims=[\"cutout\"], values=[-36.875, 143.125], unit=\"deg\"),\n",
     "    slit_end=sc.array(dims=[\"cutout\"], values=[46.875, 216.875], unit=\"deg\"),\n",
     "    slit_height=sc.scalar(10.0, unit=\"cm\"),\n",
@@ -634,6 +654,7 @@
     "\n",
     "ess_beamline = FakeBeamline(\n",
     "    choppers=disk_choppers,\n",
+    "    source_position=source_position,\n",
     "    monitors={\"detector\": Ltotal},\n",
     "    run_length=sc.scalar(1 / 14, unit=\"s\") * 4,\n",
     "    events_per_pulse=200_000,\n",
@@ -644,7 +665,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "41",
+   "id": "43",
    "metadata": {},
    "source": [
     "We can now see that there is no longer a gap between the two frames at the center of each pulse (green region).\n",
@@ -656,13 +677,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "42",
+   "id": "44",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Update workflow\n",
     "workflow[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
-    "    choppers=disk_choppers, neutrons=2_000_000\n",
+    "    choppers=disk_choppers, source_position=source_position, neutrons=2_000_000\n",
     ")\n",
     "workflow[time_of_flight.RawData] = ess_beamline.get_monitor(\"detector\")[0]\n",
     "workflow[time_of_flight.Ltotal] = Ltotal\n",
@@ -675,7 +696,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "43",
+   "id": "45",
    "metadata": {},
    "source": [
     "The data in the lookup table contains both the mean time-of-flight for each distance and time-of-arrival bin,\n",
@@ -692,7 +713,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "44",
+   "id": "46",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -702,7 +723,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "45",
+   "id": "47",
    "metadata": {},
    "source": [
     "The workflow has a parameter which is used to mask out regions where the standard deviation is above a certain threshold.\n",
@@ -716,7 +737,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "46",
+   "id": "48",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -727,7 +748,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "47",
+   "id": "49",
    "metadata": {},
    "source": [
     "We can now see that the central region is masked out.\n",
@@ -742,7 +763,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "48",
+   "id": "50",
    "metadata": {},
    "outputs": [],
    "source": [

{essreduce-25.3.0 → essreduce-25.4.0}/docs/user-guide/tof/frame-unwrapping.ipynb

@@ -180,7 +180,8 @@
     "            slit_height=sc.scalar(10.0, unit=\"cm\"),\n",
     "            radius=sc.scalar(30.0, unit=\"cm\"),\n",
     "        )\n",
-    "    }\n",
+    "    },\n",
+    "    source_position=sc.vector([0, 0, 0], unit=chopper.distance.unit),\n",
     ")\n",
     "\n",
     "workflow.visualize(time_of_flight.TofData)"
@@ -395,6 +396,7 @@
     "        )\n",
     "        for ch in choppers\n",
     "    },\n",
+    "    source_position=sc.vector([0, 0, 0], unit=chopper.distance.unit),\n",
     ")\n",
     "\n",
     "workflow[time_of_flight.DistanceResolution] = sc.scalar(0.5, unit=\"m\")\n",