Merge pull request #125 from scipp/tof-workflow

Use time-of-flight workflow in Dream data reduction

Author: nvaytet

.copier-answers.yml

@@ -5,7 +5,7 @@ description: Diffraction data reduction for the European Spallation Source
 max_python: '3.13'
 min_python: '3.10'
 namespace_package: ess
-nightly_deps: scipp,scippnexus,sciline,plopp,scippneutron,essreduce
+nightly_deps: scipp,scippnexus,sciline,plopp,scippneutron,essreduce,tof
 orgname: scipp
 prettyname: ESSdiffraction
 projectname: essdiffraction

docs/user-guide/dream/dream-data-reduction.ipynb

@@ -20,7 +20,6 @@
    "outputs": [],
    "source": [
     "import scipp as sc\n",
-    "\n",
     "from ess import dream, powder\n",
     "import ess.dream.data  # noqa: F401\n",
     "from ess.powder.types import *"
@@ -71,22 +70,22 @@
     "workflow[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.drop\n",
     "# Edges for binning in d-spacing\n",
     "workflow[DspacingBins] = sc.linspace(\"dspacing\", 0.0, 2.3434, 201, unit=\"angstrom\")\n",
-    "# Mask in time-of-flight to crop to valid range\n",
-    "workflow[TofMask] = lambda x: (x < sc.scalar(0.0, unit=\"ns\")) | (\n",
-    "        x > sc.scalar(86e6, unit=\"ns\")\n",
-    ")\n",
+    "# Empty masks by default\n",
+    "workflow[TofMask] = None\n",
     "workflow[TwoThetaMask] = None\n",
     "workflow[WavelengthMask] = None\n",
     "# No pixel masks\n",
-    "workflow = powder.with_pixel_mask_filenames(workflow, [])"
+    "workflow = powder.with_pixel_mask_filenames(workflow, [])\n",
+    "# Time-of-flight lookup table\n",
+    "workflow[TimeOfFlightLookupTableFilename] = dream.data.tof_lookup_table_high_flux()"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "6",
    "metadata": {},
    "source": [
-    "## Use the workflow\n",
+    "## Use the reduction workflow\n",
     "\n",
     "We can visualize the graph for computing the final normalized result for intensity as a function of time-of-flight:"
    ]
@@ -152,7 +151,7 @@
     "in the documentation of ESSdiffraction.\n",
     "See https://scipp.github.io/essdiffraction/\n",
     "\"\"\"\n",
-    "cif_data.save('reduced.cif')"
+    "cif_data.save(\"reduced.cif\")"
    ]
   },
   {
@@ -192,9 +191,9 @@
    "outputs": [],
    "source": [
     "two_theta = sc.linspace(\"two_theta\", 0.8, 2.4, 301, unit=\"rad\")\n",
-    "intermediates[MaskedData[SampleRun]].hist(two_theta=two_theta, wavelength=300).plot(\n",
-    "    norm=\"log\"\n",
-    ")"
+    "intermediates[MaskedData[SampleRun]].hist(\n",
+    "    two_theta=two_theta, wavelength=300\n",
+    ").plot(norm=\"log\")"
    ]
   },
   {
@@ -216,7 +215,7 @@
    "outputs": [],
    "source": [
     "workflow[TwoThetaBins] = sc.linspace(\n",
-    "    dim=\"two_theta\", unit=\"rad\", start=0.8, stop=2.4, num=17\n",
+    "    dim=\"two_theta\", unit=\"rad\", start=0.8, stop=2.4, num=201\n",
     ")"
    ]
   },
@@ -237,31 +236,13 @@
    "id": "19",
    "metadata": {},
    "outputs": [],
-   "source": [
-    "angle = sc.midpoints(grouped_dspacing.coords[\"two_theta\"])\n",
-    "sc.plot(\n",
-    "    {\n",
-    "        f\"{angle[group].value:.3f} {angle[group].unit}\": grouped_dspacing[\n",
-    "            \"two_theta\", group\n",
-    "        ].hist()\n",
-    "        for group in range(2, 6)\n",
-    "    }\n",
-    ")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "20",
-   "metadata": {},
-   "outputs": [],
    "source": [
     "grouped_dspacing.hist().plot(norm=\"log\")"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "21",
+   "id": "20",
    "metadata": {},
    "source": [
     "##  Normalizing by monitor\n",
@@ -283,7 +264,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -292,7 +273,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "23",
+   "id": "22",
    "metadata": {},
    "source": [
     "In addition to the parameters used before, we also need to provide filenames for monitor data and a position of the monitor as that is not saved in the simulation files:"
@@ -301,14 +282,14 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": [
     "workflow[MonitorFilename[SampleRun]] = dream.data.simulated_monitor_diamond_sample()\n",
     "workflow[MonitorFilename[VanadiumRun]] = dream.data.simulated_monitor_vanadium_sample()\n",
     "workflow[MonitorFilename[BackgroundRun]] = dream.data.simulated_monitor_empty_can()\n",
-    "workflow[CaveMonitorPosition] = sc.vector([0.0, 0.0, -4220.0], unit='mm')\n",
+    "workflow[CaveMonitorPosition] = sc.vector([0.0, 0.0, -4220.0], unit=\"mm\")\n",
     "\n",
     "# These are the same as at the top of the notebook:\n",
     "workflow[Filename[SampleRun]] = dream.data.simulated_diamond_sample()\n",
@@ -318,18 +299,17 @@
     "workflow[NeXusDetectorName] = \"mantle\"\n",
     "workflow[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.drop\n",
     "workflow[DspacingBins] = sc.linspace(\"dspacing\", 0.0, 2.3434, 201, unit=\"angstrom\")\n",
-    "workflow[TofMask] = lambda x: (x < sc.scalar(0.0, unit=\"ns\")) | (\n",
-    "        x > sc.scalar(86e6, unit=\"ns\")\n",
-    ")\n",
+    "workflow[TofMask] = None\n",
     "workflow[TwoThetaMask] = None\n",
     "workflow[WavelengthMask] = None\n",
-    "workflow = powder.with_pixel_mask_filenames(workflow, [])"
+    "workflow = powder.with_pixel_mask_filenames(workflow, [])\n",
+    "workflow[TimeOfFlightLookupTableFilename] = dream.data.tof_lookup_table_high_flux()"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "25",
+   "id": "24",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -339,7 +319,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "25",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -352,7 +332,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "27",
+   "id": "26",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -361,7 +341,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "28",
+   "id": "27",
    "metadata": {},
    "source": [
     "Comparing the final, normalized result shows that it agrees with the data that was normalized by proton-charge:"
@@ -370,14 +350,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "29",
+   "id": "28",
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc.plot({\n",
-    "    'By proton charge': histogram,\n",
-    "    'By monitor': normalized_by_monitor.hist()\n",
-    "})"
+    "sc.plot({\"By proton charge\": histogram, \"By monitor\": normalized_by_monitor.hist()})"
    ]
   }
  ],
@@ -396,8 +373,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

docs/user-guide/dream/workflow-widget-dream.ipynb

@@ -47,7 +47,7 @@
    },
    "outputs": [],
    "source": [
-    "from ess.powder.types import DspacingBins, Filename, SampleRun, VanadiumRun\n",
+    "from ess.powder.types import DspacingBins, Filename, SampleRun, TimeOfFlightLookupTableFilename, VanadiumRun\n",
     "import ess.dream.data  # noqa: F401\n",
     "\n",
     "select = widget.children[0].children[0]\n",
@@ -66,6 +66,7 @@
     "# Set parameters\n",
     "pbox._input_widgets[Filename[SampleRun]].children[0].value = dream.data.simulated_diamond_sample()\n",
     "pbox._input_widgets[Filename[VanadiumRun]].children[0].value = dream.data.simulated_vanadium_sample()\n",
+    "pbox._input_widgets[TimeOfFlightLookupTableFilename].children[0].value = dream.data.tof_lookup_table_high_flux()\n",
     "pbox._input_widgets[DspacingBins].fields[\"stop\"].value = 2.3434\n",
     "# Run the workflow\n",
     "rbox = wfw.result_box\n",
@@ -133,8 +134,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

docs/user-guide/sns-instruments/POWGEN_data_reduction.ipynb

@@ -239,7 +239,7 @@
    "source": [
     "results = workflow.compute(\n",
     "    (\n",
-    "        DetectorData[SampleRun],\n",
+    "        TofData[SampleRun],\n",
     "        MaskedData[SampleRun],\n",
     "        FilteredData[SampleRun],\n",
     "        FilteredData[VanadiumRun],\n",
@@ -254,7 +254,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "results[DetectorData[SampleRun]]"
+    "results[TofData[SampleRun]]"
    ]
   },
   {
@@ -393,8 +393,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

pyproject.toml

@@ -41,6 +41,7 @@ dependencies = [
   "scipp>=24.09.1",
   "scippneutron>=25.02.0",
   "scippnexus>=23.12.0",
+  "tof>=25.01.2",
 ]
 
 dynamic = ["version"]

requirements/base.in

@@ -12,3 +12,4 @@ sciline>=24.06.0
 scipp>=24.09.1
 scippneutron>=25.02.0
 scippnexus>=23.12.0
+tof>=25.01.2

requirements/base.txt

@@ -1,4 +1,4 @@
-# SHA1:4b779f60b811ecde0982bc9dc5df5ed5b296b876
+# SHA1:bd57e2addebc398f9de7064eb2a5c993a359ba46
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -45,6 +45,8 @@ h5py==3.12.1
     #   scippnexus
 idna==3.10
     # via email-validator
+importlib-resources==6.5.2
+    # via tof
 ipydatawidgets==4.3.5
     # via pythreejs
 ipython==8.32.0
@@ -102,6 +104,7 @@ plopp==24.10.0
     # via
     #   -r base.in
     #   scippneutron
+    #   tof
 prompt-toolkit==3.0.50
     # via ipython
 ptyprocess==0.7.0
@@ -135,6 +138,7 @@ scipp==25.2.0
     #   essreduce
     #   scippneutron
     #   scippnexus
+    #   tof
 scippneutron==25.2.0
     # via
     #   -r base.in
@@ -148,10 +152,13 @@ scipy==1.15.2
     # via
     #   scippneutron
     #   scippnexus
+    #   tof
 six==1.17.0
     # via python-dateutil
 stack-data==0.6.3
     # via ipython
+tof==25.2.0
+    # via -r base.in
 toolz==1.0.0
     # via
     #   dask

requirements/nightly.in

@@ -17,3 +17,4 @@ sciline @ git+https://github.com/scipp/sciline@main
 plopp @ git+https://github.com/scipp/plopp@main
 scippneutron @ git+https://github.com/scipp/scippneutron@main
 essreduce @ git+https://github.com/scipp/essreduce@main
+tof @ git+https://github.com/scipp/tof@main

requirements/nightly.txt

@@ -1,4 +1,4 @@
-# SHA1:b20670ae7cbdca0a2dae7facc845a0a636ee537c
+# SHA1:366263fa92dc0eb9f81d46f056e0c80a931f671e
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -54,6 +54,8 @@ idna==3.10
     # via
     #   email-validator
     #   requests
+importlib-resources==6.5.2
+    # via tof
 iniconfig==2.0.0
     # via pytest
 ipydatawidgets==4.3.5
@@ -122,6 +124,7 @@ plopp @ git+https://github.com/scipp/plopp@main
     # via
     #   -r nightly.in
     #   scippneutron
+    #   tof
 pluggy==1.5.0
     # via pytest
 pooch==1.8.2
@@ -166,6 +169,7 @@ scipp==100.0.0.dev0
     #   essreduce
     #   scippneutron
     #   scippnexus
+    #   tof
 scippneutron @ git+https://github.com/scipp/scippneutron@main
     # via
     #   -r nightly.in
@@ -179,10 +183,13 @@ scipy==1.15.2
     # via
     #   scippneutron
     #   scippnexus
+    #   tof
 six==1.17.0
     # via python-dateutil
 stack-data==0.6.3
     # via ipython
+tof @ git+https://github.com/scipp/tof@main
+    # via -r nightly.in
 toolz==1.0.0
     # via
     #   dask