Image normalization workflow for TBL/Orca

docs/tbl/index.md

@@ -6,5 +6,6 @@ maxdepth: 1
 ---
 
 tbl-data-reduction
+orca-image-normalization
 tbl-make-tof-lookup-table
 ```

docs/tbl/orca-image-normalization.ipynb

@@ -0,0 +1,172 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# TBL: Orca image normalization workflow\n",
+    "\n",
+    "This notebook shows how to use the workflow to compute normalized images recorded by the Orca detector on the TBL instrument."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import ess.tbl.data  # noqa: F401\n",
+    "from ess import tbl\n",
+    "from ess.imaging.types import *\n",
+    "import scipp as sc\n",
+    "import plopp as pp\n",
+    "\n",
+    "%matplotlib widget"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2",
+   "metadata": {},
+   "source": [
+    "## Workflow setup"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wf = tbl.OrcaNormalizedImagesWorkflow()\n",
+    "\n",
+    "wf[Filename[SampleRun]] = tbl.data.tbl_lego_sample_run()\n",
+    "wf[Filename[DarkBackgroundRun]] = tbl.data.tbl_lego_dark_run()\n",
+    "wf[Filename[OpenBeamRun]] = tbl.data.tbl_lego_openbeam_run()\n",
+    "wf[NeXusDetectorName] = 'orca_detector'\n",
+    "\n",
+    "wf[MaskingRules] = {}  # No masks to begin with\n",
+    "wf[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wf.visualize(NormalizedImage, compact=True, graph_attr={\"rankdir\": \"LR\"})"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5",
+   "metadata": {},
+   "source": [
+    "## Run the workflow\n",
+    "\n",
+    "We compute the final normalized image:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "image = wf.compute(NormalizedImage)\n",
+    "image"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pp.slicer(image, autoscale=False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8",
+   "metadata": {},
+   "source": [
+    "## Adding masks\n",
+    "\n",
+    "If we want to mask some part of the image, we update the masking rules.\n",
+    "For example, here we mask the upper part of the image:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wf[MaskingRules] = {'y_pixel_offset': lambda x: x > sc.scalar(0.082, unit='m')}\n",
+    "\n",
+    "pp.slicer(wf.compute(NormalizedImage), autoscale=False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "10",
+   "metadata": {},
+   "source": [
+    "## Intermediate results\n",
+    "\n",
+    "We can also inspect intermediate results, which is useful for debugging:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "11",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "results = wf.compute([\n",
+    "    RawDetector[SampleRun],\n",
+    "    CorrectedDetector[SampleRun],\n",
+    "    BackgroundSubtractedDetector[SampleRun]\n",
+    "])\n",
+    "\n",
+    "fig = pp.tiled(2, 2, hspace=0.3, wspace=0.3)\n",
+    "fig[0, 0] = results[RawDetector[SampleRun]]['time', 0].plot(title='Raw data')\n",
+    "fig[0, 1] = results[CorrectedDetector[SampleRun]]['time', 0].plot(title='Masks applied')\n",
+    "fig[1, 0] = results[BackgroundSubtractedDetector[SampleRun]]['time', 0].plot(title='Background subtracted')\n",
+    "fig[1, 1] = image['time', 0].plot(title='Final image')\n",
+    "fig"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

pyproject.toml

@@ -38,7 +38,7 @@ dependencies = [
   "scippneutron>=24.12.0",
   "scippnexus>=23.11.1",
   "tifffile>=2024.7.2",
-  "essreduce>=25.11.0",
+  "essreduce>=25.11.2",
   "scitiff>=25.7",
 ]
 

requirements/base.in

@@ -10,5 +10,5 @@ scipp>=25.4.0
 scippneutron>=24.12.0
 scippnexus>=23.11.1
 tifffile>=2024.7.2
-essreduce>=25.11.0
+essreduce>=25.11.2
 scitiff>=25.7

requirements/base.txt

@@ -1,4 +1,4 @@
-# SHA1:da99ba40cef426287cd34dd1a2b56aefd0cb24e6
+# SHA1:a1100845ace4b19ad8a759324efbe63c69022f7b
 #
 # This file was generated by pip-compile-multi.
 # To update, run:
@@ -7,13 +7,13 @@
 #
 annotated-types==0.7.0
     # via pydantic
-asttokens==3.0.0
+asttokens==3.0.1
     # via stack-data
 attrs==25.4.0
     # via
     #   jsonschema
     #   referencing
-click==8.3.0
+click==8.3.1
     # via dask
 cloudpickle==3.1.2
     # via dask
@@ -25,15 +25,15 @@ cyclebane==24.10.0
     # via sciline
 cycler==0.12.1
     # via matplotlib
-dask==2025.10.0
+dask==2025.11.0
     # via -r base.in
 decorator==5.2.1
     # via ipython
 dnspython==2.8.0
     # via email-validator
 email-validator==2.3.0
     # via scippneutron
-essreduce==25.11.0
+essreduce==25.11.2
     # via -r base.in
 executing==2.2.1
     # via stack-data
@@ -57,7 +57,7 @@ ipydatawidgets==4.3.5
     # via pythreejs
 ipympl==0.9.8
     # via plopp
-ipython==9.6.0
+ipython==9.7.0
     # via
     #   ipympl
     #   ipywidgets
@@ -98,7 +98,7 @@ mpltoolbox==25.10.0
     #   scippneutron
 networkx==3.5
     # via cyclebane
-numpy==2.3.4
+numpy==2.3.5
     # via
     #   contourpy
     #   h5py
@@ -125,7 +125,7 @@ pillow==12.0.0
     # via
     #   ipympl
     #   matplotlib
-plopp[all]==25.10.0
+plopp[all]==25.11.0
     # via
     #   -r base.in
     #   scippneutron
@@ -135,11 +135,11 @@ ptyprocess==0.7.0
     # via pexpect
 pure-eval==0.2.3
     # via stack-data
-pydantic==2.12.3
+pydantic==2.12.4
     # via
     #   scippneutron
     #   scitiff
-pydantic-core==2.41.4
+pydantic-core==2.41.5
     # via pydantic
 pygments==2.19.2
     # via
@@ -151,7 +151,6 @@ python-dateutil==2.9.0.post0
     # via
     #   matplotlib
     #   scippneutron
-    #   scippnexus
 pythreejs==2.4.2
     # via plopp
 pyyaml==6.0.3
@@ -160,7 +159,7 @@ referencing==0.37.0
     # via
     #   jsonschema
     #   jsonschema-specifications
-rpds-py==0.28.0
+rpds-py==0.29.0
     # via
     #   jsonschema
     #   referencing
@@ -180,7 +179,7 @@ scippneutron==25.7.0
     # via
     #   -r base.in
     #   essreduce
-scippnexus==25.6.0
+scippnexus==25.11.0
     # via
     #   -r base.in
     #   essreduce

requirements/basetest.txt

@@ -11,7 +11,7 @@ attrs==25.4.0
     # via
     #   jsonschema
     #   referencing
-certifi==2025.10.5
+certifi==2025.11.12
     # via requests
 charset-normalizer==3.4.4
     # via requests
@@ -37,12 +37,11 @@ lazy-loader==0.4
     #   tof
 matplotlib==3.10.7
     # via plopp
-numpy==2.3.4
+numpy==2.3.5
     # via
     #   contourpy
     #   matplotlib
     #   scipp
-    #   scipy
     #   tifffile
 packaging==25.0
     # via
@@ -54,21 +53,23 @@ pillow==12.0.0
     # via matplotlib
 platformdirs==4.5.0
     # via pooch
-plopp==25.10.0
+plopp==25.11.0
     # via tof
 pluggy==1.6.0
     # via pytest
 pooch==1.8.2
-    # via -r basetest.in
-pydantic==2.12.3
+    # via
+    #   -r basetest.in
+    #   tof
+pydantic==2.12.4
     # via scitiff
-pydantic-core==2.41.4
+pydantic-core==2.41.5
     # via pydantic
 pygments==2.19.2
     # via pytest
 pyparsing==3.2.5
     # via matplotlib
-pytest==8.4.2
+pytest==9.0.1
     # via -r basetest.in
 python-dateutil==2.9.0.post0
     # via matplotlib
@@ -78,23 +79,21 @@ referencing==0.37.0
     #   jsonschema-specifications
 requests==2.32.5
     # via pooch
-rpds-py==0.28.0
+rpds-py==0.29.0
     # via
     #   jsonschema
     #   referencing
 scipp==25.11.0
     # via
     #   scitiff
     #   tof
-scipy==1.16.3
-    # via tof
 scitiff==25.7.0
     # via -r basetest.in
 six==1.17.0
     # via python-dateutil
 tifffile==2025.10.16
     # via scitiff
-tof==25.10.1
+tof==25.12.0
     # via -r basetest.in
 typing-extensions==4.15.0
     # via

requirements/ci.txt

@@ -5,9 +5,9 @@
 #
 #    requirements upgrade
 #
-cachetools==6.2.1
+cachetools==6.2.2
     # via tox
-certifi==2025.10.5
+certifi==2025.11.12
     # via requests
 chardet==5.2.0
     # via tox