Merge pull request #50 from scipp/zoom

Zoom data reduction

docs/api-reference/index.md

@@ -37,6 +37,7 @@
    direct_beam
    i_of_q
    io
+   isis
    logging
    loki
    sans2d

docs/examples/index.md

@@ -7,4 +7,5 @@ maxdepth: 2
 
 sans2d
 loki-direct-beam
+zoom
 ```

docs/examples/zoom.ipynb

@@ -0,0 +1,280 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "ba4d302c",
+   "metadata": {},
+   "source": [
+    "# Zoom data reduction\n",
+    "\n",
+    "## Introduction\n",
+    "\n",
+    "This notebook is an example of how ESSsans can be used to reduce data from [Zoom at ISIS](https://www.isis.stfc.ac.uk/Pages/Zoom.aspx).\n",
+    "The following description is kept relatively brief, for more context see the rest of the documentation.\n",
+    "In particular the [Sans2d](./sans2d.ipynb) notebook may be useful."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "53e2278d",
+   "metadata": {},
+   "source": [
+    "There are a few things that are not yet handled:\n",
+    "\n",
+    "- TOF or wavelength masks\n",
+    "- Position corrections from user file"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "09234b87",
+   "metadata": {},
+   "source": [
+    "## Setup\n",
+    "\n",
+    "### Imports and configuration"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "319162e9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import scipp as sc\n",
+    "import sciline\n",
+    "import esssans as sans\n",
+    "import esssans.isis\n",
+    "from esssans.types import *"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "64783c51",
+   "metadata": {},
+   "source": [
+    "### Setup input files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9e7cfc82",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "params = {\n",
+    "    sans.types.DirectBeamFilename: 'Direct_Zoom_4m_8mm_100522.txt',\n",
+    "    sans.isis.CalibrationFilename: '192tubeCalibration_11-02-2019_r5_10lines.nxs',\n",
+    "    sans.isis.Filename[sans.types.SampleRun]: 'ZOOM00034786.nxs',\n",
+    "    sans.isis.Filename[sans.types.EmptyBeamRun]: 'ZOOM00034787.nxs',\n",
+    "}\n",
+    "masks = [\n",
+    "    'andru_test.xml',\n",
+    "    'left_beg_18_2.xml',\n",
+    "    'right_beg_18_2.xml',\n",
+    "    'small_bs_232.xml',\n",
+    "    'small_BS_31032023.xml',\n",
+    "    'tube_1120_bottom.xml',\n",
+    "    'tubes_beg_18_2.xml',\n",
+    "]\n",
+    "masks = sciline.ParamTable(str, {sans.isis.PixelMaskFilename: masks}, index=masks)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8a8a4e01",
+   "metadata": {},
+   "source": [
+    "### Setup reduction parameters"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "50f11eb2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "params[NeXusMonitorName[Incident]] = 'monitor3'\n",
+    "params[NeXusMonitorName[Transmission]] = 'monitor5'\n",
+    "\n",
+    "band = sc.linspace('wavelength', 1.75, 16.5, num=2, unit='angstrom')\n",
+    "params[WavelengthBands] = band\n",
+    "params[WavelengthBins] = sc.geomspace(\n",
+    "    'wavelength', start=band[0], stop=band[-1], num=141\n",
+    ")\n",
+    "\n",
+    "params[QBins] = sc.geomspace(dim='Q', start=0.004, stop=0.8, num=141, unit='1/angstrom')\n",
+    "params[NonBackgroundWavelengthRange] = sc.array(\n",
+    "    dims=['wavelength'], values=[0.7, 17.1], unit='angstrom'\n",
+    ")\n",
+    "params[CorrectForGravity] = True\n",
+    "params[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0b47024f",
+   "metadata": {},
+   "source": [
+    "### Setup reduction pipeline"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fdcaec37",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "providers = sans.providers + sans.isis.providers\n",
+    "providers = providers + (\n",
+    "    sans.isis.transmission_from_background_run,\n",
+    "    sans.isis.transmission_from_sample_run,\n",
+    ")\n",
+    "pipeline = sciline.Pipeline(providers, params=params)\n",
+    "pipeline.set_param_table(masks)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "951aec10",
+   "metadata": {},
+   "source": [
+    "If Mantid is available, we can use it to load data files.\n",
+    "**You must configure the** `DataFolder` **below to point to the directory containing the data files.**\n",
+    "Otherwise, we fall back to load intermediate data files that have been prepared for the concrete example in this notebook.\n",
+    "If you want to use the workflow with different files you must have Mantid installed:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "66237b3e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "try:\n",
+    "    from mantid import ConfigService\n",
+    "    import esssans.isis.mantidio\n",
+    "\n",
+    "    cfg = ConfigService.Instance()\n",
+    "    cfg.setLogLevel(3)  # Silence verbose load via Mantid\n",
+    "\n",
+    "    pipeline[sans.isis.DataFolder] = 'zoom_data'\n",
+    "    for provider in sans.isis.mantidio.providers:\n",
+    "        pipeline.insert(provider)\n",
+    "except ImportError:\n",
+    "    import esssans.isis.data\n",
+    "\n",
+    "    for provider in sans.isis.data.providers:\n",
+    "        pipeline.insert(provider)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "703ffc1e",
+   "metadata": {},
+   "source": [
+    "## Reduction\n",
+    "\n",
+    "### The reduction workflow"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cae69232",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "iofq = pipeline.get(IofQ[SampleRun])\n",
+    "iofq.visualize(graph_attr={'rankdir': 'LR'}, compact=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "77687728",
+   "metadata": {},
+   "source": [
+    "### Running the workflow"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "558327ff",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "da = iofq.compute()\n",
+    "da.plot(norm='log', scale={'Q': 'log'})"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5a7526fc",
+   "metadata": {},
+   "source": [
+    "### Inspecting intermediate results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bb922379",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "monitors = (\n",
+    "    WavelengthMonitor[SampleRun, Incident],\n",
+    "    WavelengthMonitor[SampleRun, Transmission],\n",
+    ")\n",
+    "parts = (CleanSummedQ[SampleRun, Numerator], CleanSummedQ[SampleRun, Denominator])\n",
+    "iofqs = (IofQ[SampleRun],)\n",
+    "keys = monitors + (MaskedData[SampleRun],) + parts + iofqs\n",
+    "\n",
+    "results = pipeline.compute(keys)\n",
+    "\n",
+    "display(sc.plot({str(key): results[key] for key in monitors}, norm='log'))\n",
+    "\n",
+    "display(\n",
+    "    sans.isis.plot_flat_detector_xy(\n",
+    "        results[MaskedData[SampleRun]], norm='log', figsize=(6, 10)\n",
+    "    )\n",
+    ")\n",
+    "\n",
+    "parts = {str(key): results[key] for key in parts}\n",
+    "parts = {key: val if val.bins is None else val.hist() for key, val in parts.items()}\n",
+    "display(sc.plot(parts, norm='log', scale={'Q': 'log'}))\n",
+    "\n",
+    "iofqs = {str(key): results[key] for key in iofqs}\n",
+    "iofqs = {key: val if val.bins is None else val.hist() for key, val in iofqs.items()}\n",
+    "display(sc.plot(iofqs, norm='log', scale={'Q': 'log'}))"
+   ]
+  }
+ ],
+ "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": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

src/esssans/isis/__init__.py

@@ -0,0 +1,45 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
+
+
+from ..sans2d.general import (
+    get_detector_data,
+    get_monitor,
+    lab_frame_transform,
+    sans2d_tube_detector_pixel_shape,
+)
+from . import io, masking
+from .common import transmission_from_background_run, transmission_from_sample_run
+from .io import CalibrationFilename, DataFolder, Filename, PixelMaskFilename
+from .masking import PixelMask
+from .visualization import plot_flat_detector_xy
+
+providers = (
+    (
+        get_detector_data,
+        get_monitor,
+        lab_frame_transform,
+        sans2d_tube_detector_pixel_shape,
+    )
+    + io.providers
+    + masking.providers
+)
+
+del get_detector_data
+del get_monitor
+del lab_frame_transform
+del sans2d_tube_detector_pixel_shape
+
+__all__ = [
+    'CalibrationFilename',
+    'DataFolder',
+    'Filename',
+    'io',
+    'masking',
+    'PixelMask',
+    'PixelMaskFilename',
+    'providers',
+    'transmission_from_background_run',
+    'transmission_from_sample_run',
+    'plot_flat_detector_xy',
+]

src/esssans/isis/common.py

@@ -0,0 +1,24 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
+"""
+"""
+
+from ..types import BackgroundRun, LoadedFileContents, SampleRun, TransmissionRun
+
+
+def transmission_from_sample_run(
+    data: LoadedFileContents[SampleRun],
+) -> LoadedFileContents[TransmissionRun[SampleRun]]:
+    """
+    Use transmission from a sample run, instead of dedicated run.
+    """
+    return LoadedFileContents[TransmissionRun[SampleRun]](data)
+
+
+def transmission_from_background_run(
+    data: LoadedFileContents[BackgroundRun],
+) -> LoadedFileContents[TransmissionRun[BackgroundRun]]:
+    """
+    Use transmission from a background run, instead of dedicated run.
+    """
+    return LoadedFileContents[TransmissionRun[BackgroundRun]](data)