essreduce 25.5.3__tar.gz → 25.7.1__tar.gz

{essreduce-25.5.3 → essreduce-25.7.1}/.copier-answers.ess.yml

@@ -1,3 +1,3 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: 0951a4b
+_commit: 34ca4ba
 _src_path: https://github.com/scipp/ess_template.git

{essreduce-25.5.3 → essreduce-25.7.1}/.github/ISSUE_TEMPLATE/high-level-requirement.yml

@@ -79,6 +79,14 @@ body:
       description: How can we test this requirement? Links to tests data and reference data, or other suggestions.
     validations:
       required: true
+  - type: textarea
+    id: existingimplementations
+    attributes:
+      label: Existing implementations
+      description: Are there any existing implementations or proof-of-concept implementations that we can imitate? This field is specifically for linking to source code.
+      placeholder: "Example: See this repository ... This script implements the procedure: https://file-storage.server.eu/script.code."
+    validations:
+      required: false
   - type: textarea
     id: comments
     attributes:

{essreduce-25.5.3/src/essreduce.egg-info → essreduce-25.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: essreduce
-Version: 25.5.3
+Version: 25.7.1
 Summary: Common data reduction tools for the ESS facility
 Author: Scipp contributors
 License: BSD 3-Clause License

{essreduce-25.5.3 → essreduce-25.7.1}/docs/user-guide/tof/dream.ipynb

@@ -25,7 +25,7 @@
     "import scipp as sc\n",
     "from scippneutron.chopper import DiskChopper\n",
     "from ess.reduce.nexus.types import DetectorData, SampleRun\n",
-    "from ess.reduce import time_of_flight"
+    "from ess.reduce.time_of_flight import *"
    ]
   },
   {
@@ -286,14 +286,7 @@
    "source": [
     "## Computing time-of-flight\n",
     "\n",
-    "The chopper information is next used to construct a lookup table that provides an estimate of the real time-of-flight as a function of neutron time-of-arrival.\n",
-    "\n",
-    "We use the `tof` module to propagate a pulse of neutrons through the chopper system to the detectors,\n",
-    "and predict the most likely neutron wavelength for a given time-of-arrival and distance from source.\n",
-    "\n",
-    "From this,\n",
-    "we build a lookup table on which bilinear interpolation is used to compute a wavelength (and its corresponding time-of-flight)\n",
-    "for every neutron event.\n",
+    "Next, we use a workflow that provides an estimate of the real time-of-flight as a function of neutron time-of-arrival.\n",
     "\n",
     "### Setting up the workflow"
    ]
@@ -305,19 +298,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "wf = time_of_flight.GenericTofWorkflow(\n",
-    "    tof_lut_provider=time_of_flight.TofLutProvider.TOF,\n",
-    "    run_types=[SampleRun],\n",
-    "    monitor_types=[],\n",
-    ")\n",
+    "wf = GenericTofWorkflow(run_types=[SampleRun], monitor_types=[])\n",
+    "\n",
     "wf[DetectorData[SampleRun]] = raw_data\n",
-    "wf[time_of_flight.DetectorLtotal[SampleRun]] = Ltotal\n",
-    "wf[time_of_flight.LtotalRange] = (\n",
-    "    sc.scalar(75.5, unit=\"m\"),\n",
-    "    sc.scalar(78.0, unit=\"m\"),\n",
-    ")\n",
+    "wf[DetectorLtotal[SampleRun]] = Ltotal\n",
     "\n",
-    "wf.visualize(time_of_flight.DetectorTofData[SampleRun])"
+    "wf.visualize(DetectorTofData[SampleRun])"
    ]
   },
   {
@@ -325,26 +311,47 @@
    "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",
+    "By default, the workflow tries to load a `TimeOfFlightLookupTable` from a file.\n",
+    "\n",
+    "In this notebook, instead of using such a pre-made file,\n",
+    "we will build our own lookup table from the chopper information and apply it to the workflow."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "22",
+   "metadata": {},
+   "source": [
+    "### Building the time-of-flight lookup table\n",
     "\n",
-    "Those are obtained by running a quick `tof` simulation of the beamline:"
+    "We use the [Tof](https://scipp.github.io/tof/) package to propagate a pulse of neutrons through the chopper system to the detectors,\n",
+    "and predict the most likely neutron wavelength for a given time-of-arrival and distance from source.\n",
+    "\n",
+    "From this,\n",
+    "we build a lookup table on which bilinear interpolation is used to compute a wavelength (and its corresponding time-of-flight)\n",
+    "for every neutron event."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": [
-    "wf[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
-    "    choppers=disk_choppers, source_position=source_position, neutrons=2_000_000\n",
-    ")"
+    "lut_wf = TofLookupTableWorkflow()\n",
+    "lut_wf[DiskChoppers] = disk_choppers\n",
+    "lut_wf[SourcePosition] = source_position\n",
+    "lut_wf[LtotalRange] = (\n",
+    "    sc.scalar(75.5, unit=\"m\"),\n",
+    "    sc.scalar(78.0, unit=\"m\"),\n",
+    ")\n",
+    "lut_wf.visualize(TimeOfFlightLookupTable)"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "23",
+   "id": "24",
    "metadata": {},
    "source": [
     "### Inspecting the lookup table\n",
@@ -361,11 +368,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "25",
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim = wf.compute(time_of_flight.SimulationResults)\n",
+    "sim = lut_wf.compute(SimulationResults)\n",
     "\n",
     "\n",
     "def to_event_time_offset(sim):\n",
@@ -389,7 +396,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "25",
+   "id": "26",
    "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",
@@ -400,11 +407,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "27",
    "metadata": {},
    "outputs": [],
    "source": [
-    "table = wf.compute(time_of_flight.TimeOfFlightLookupTable)\n",
+    "table = lut_wf.compute(TimeOfFlightLookupTable)\n",
     "\n",
     "# Overlay mean on the figure above\n",
     "table[\"distance\", 13].plot(ax=fig2.ax, color=\"C1\", ls=\"-\", marker=None)"
@@ -412,7 +419,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "27",
+   "id": "28",
    "metadata": {},
    "source": [
     "The full table covers a range of distances, and looks like"
@@ -421,7 +428,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28",
+   "id": "29",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -431,28 +438,32 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "29",
+   "id": "30",
    "metadata": {},
    "source": [
     "### Computing a time-of-flight coordinate\n",
     "\n",
-    "We will now use our workflow to obtain our event data with a time-of-flight coordinate:"
+    "We will now update our workflow, and use it to obtain our event data with a time-of-flight coordinate:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30",
+   "id": "31",
    "metadata": {},
    "outputs": [],
    "source": [
-    "tofs = wf.compute(time_of_flight.DetectorTofData[SampleRun])\n",
+    "# Set the computed lookup table onto the original workflow\n",
+    "wf[TimeOfFlightLookupTable] = table\n",
+    "\n",
+    "# Compute time-of-flight of neutron events\n",
+    "tofs = wf.compute(DetectorTofData[SampleRun])\n",
     "tofs"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "31",
+   "id": "32",
    "metadata": {},
    "source": [
     "Histogramming the data for a plot should show a profile with 6 bumps that correspond to the frames:"
@@ -461,7 +472,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32",
+   "id": "33",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -470,7 +481,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "33",
+   "id": "34",
    "metadata": {},
    "source": [
     "### Converting to wavelength\n",
@@ -481,7 +492,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "34",
+   "id": "35",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -501,7 +512,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "35",
+   "id": "36",
    "metadata": {},
    "source": [
     "### Comparing to the ground truth\n",
@@ -513,7 +524,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "36",
+   "id": "37",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -530,7 +541,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "37",
+   "id": "38",
    "metadata": {},
    "source": [
     "## Multiple detector pixels\n",
@@ -546,7 +557,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "38",
+   "id": "39",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -564,7 +575,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "39",
+   "id": "40",
    "metadata": {},
    "source": [
     "Our raw data has now a `detector_number` dimension of length 2.\n",
@@ -575,7 +586,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "40",
+   "id": "41",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -590,7 +601,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "41",
+   "id": "42",
    "metadata": {},
    "source": [
     "Computing time-of-flight is done in the same way as above.\n",
@@ -600,16 +611,16 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "42",
+   "id": "43",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Update workflow\n",
     "wf[DetectorData[SampleRun]] = raw_data\n",
-    "wf[time_of_flight.DetectorLtotal[SampleRun]] = Ltotal\n",
+    "wf[DetectorLtotal[SampleRun]] = Ltotal\n",
     "\n",
     "# Compute tofs and wavelengths\n",
-    "tofs = wf.compute(time_of_flight.DetectorTofData[SampleRun])\n",
+    "tofs = wf.compute(DetectorTofData[SampleRun])\n",
     "wav_wfm = tofs.transform_coords(\"wavelength\", graph=graph)\n",
     "\n",
     "# Compare in plot\n",
@@ -634,7 +645,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "43",
+   "id": "44",
    "metadata": {},
    "source": [
     "## Handling time overlap between subframes\n",
@@ -654,7 +665,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "44",
+   "id": "45",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -685,7 +696,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "45",
+   "id": "46",
    "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",
@@ -697,18 +708,14 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "46",
+   "id": "47",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Update workflow\n",
-    "wf[time_of_flight.SimulationResults] = time_of_flight.simulate_beamline(\n",
-    "    choppers=disk_choppers, source_position=source_position, neutrons=2_000_000\n",
-    ")\n",
-    "wf[DetectorData[SampleRun]] = ess_beamline.get_monitor(\"detector\")[0]\n",
-    "wf[time_of_flight.DetectorLtotal[SampleRun]] = Ltotal\n",
+    "lut_wf[DiskChoppers] = disk_choppers\n",
     "\n",
-    "sim = wf.compute(time_of_flight.SimulationResults)\n",
+    "sim = lut_wf.compute(SimulationResults)\n",
     "\n",
     "events = to_event_time_offset(sim)\n",
     "events.hist(wavelength=300, event_time_offset=300).plot(norm=\"log\")"
@@ -716,7 +723,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "47",
+   "id": "48",
    "metadata": {},
    "source": [
     "The data in the lookup table contains both the mean time-of-flight for each distance and time-of-arrival bin,\n",
@@ -733,17 +740,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "48",
+   "id": "49",
    "metadata": {},
    "outputs": [],
    "source": [
-    "table = wf.compute(time_of_flight.TimeOfFlightLookupTable)\n",
+    "table = lut_wf.compute(TimeOfFlightLookupTable)\n",
     "table.plot() / (sc.stddevs(table) / sc.values(table)).plot(norm=\"log\")"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "49",
+   "id": "50",
    "metadata": {},
    "source": [
     "The workflow has a parameter which is used to mask out regions where the standard deviation is above a certain threshold.\n",
@@ -757,18 +764,19 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "50",
+   "id": "51",
    "metadata": {},
    "outputs": [],
    "source": [
-    "wf[time_of_flight.LookupTableRelativeErrorThreshold] = 0.01\n",
+    "lut_wf[LookupTableRelativeErrorThreshold] = 0.01\n",
     "\n",
-    "wf.compute(time_of_flight.TimeOfFlightLookupTable).plot()"
+    "table = lut_wf.compute(TimeOfFlightLookupTable)\n",
+    "table.plot()"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "51",
+   "id": "52",
    "metadata": {},
    "source": [
     "We can now see that the central region is masked out.\n",
@@ -783,12 +791,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "52",
+   "id": "53",
    "metadata": {},
    "outputs": [],
    "source": [
+    "wf[DetectorData[SampleRun]] = ess_beamline.get_monitor(\"detector\")[0]\n",
+    "wf[DetectorLtotal[SampleRun]] = Ltotal\n",
+    "\n",
+    "wf[TimeOfFlightLookupTable] = table\n",
+    "\n",
     "# Compute time-of-flight\n",
-    "tofs = wf.compute(time_of_flight.DetectorTofData[SampleRun])\n",
+    "tofs = wf.compute(DetectorTofData[SampleRun])\n",
     "# Compute wavelength\n",
     "wav_wfm = tofs.transform_coords(\"wavelength\", graph=graph)\n",
     "\n",