Merge sans2d and zoom code into isis module

docs/api-reference/index.md

@@ -40,7 +40,6 @@
    isis
    logging
    loki
-   sans2d
    types
    uncertainty
 ```

docs/examples/beam-center-finder.ipynb

@@ -27,9 +27,9 @@
    "source": [
     "import scipp as sc\n",
     "import plopp as pp\n",
-    "import sciline as sl\n",
+    "import sciline\n",
     "import esssans as sans\n",
-    "from esssans.isis import plot_flat_detector_xy\n",
+    "from esssans import isis\n",
     "from esssans.types import *"
    ]
   },
@@ -51,12 +51,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "params = sans.sans2d.default_parameters.copy()\n",
-    "\n",
-    "params[FileList[SampleRun]] = ['SANS2D00063114.hdf5']\n",
+    "params = {isis.Filename[SampleRun]: 'SANS2D00063114.nxs'}\n",
     "\n",
     "# Build the pipeline\n",
-    "providers = list(sans.providers + sans.sans2d.providers)\n",
+    "providers = list(\n",
+    "    sans.providers + isis.providers + isis.data.providers + isis.sans2d.providers\n",
+    ")\n",
     "pipeline = sciline.Pipeline(providers, params=params)"
    ]
   },
@@ -79,9 +79,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "raw = pipeline.compute(RawData[SampleRun])\n",
+    "raw = pipeline.compute(RawData[SampleRun])['spectrum', :61440]\n",
     "\n",
-    "p = plot_flat_detector_xy(raw.sum('tof'), norm='log')\n",
+    "p = isis.plot_flat_detector_xy(raw.hist(), norm='log')\n",
     "p.ax.plot(0, 0, '+', color='k', ms=10)\n",
     "p"
    ]
@@ -131,10 +131,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "masked = pipeline.compute(MaskedData[SampleRun])\n",
-    "masked.masks['low_counts'] = masked.sum('tof').data < sc.scalar(80.0, unit='counts')\n",
+    "masked = pipeline.compute(MaskedData[SampleRun])['spectrum', :61440].copy()\n",
+    "masked.masks['low_counts'] = masked.hist().data < sc.scalar(80.0, unit='counts')\n",
     "\n",
-    "p = plot_flat_detector_xy(masked.sum('tof'), norm='log')\n",
+    "p = isis.plot_flat_detector_xy(masked.hist(), norm='log')\n",
     "p.ax.plot(0, 0, '+', color='k', ms=10)\n",
     "p"
    ]
@@ -246,8 +246,13 @@
     "params[WavelengthBins] = sc.linspace(\n",
     "    'wavelength', start=2.0, stop=16.0, num=141, unit='angstrom'\n",
     ")\n",
-    "params[FileList[TransmissionRun[SampleRun]]] = params[FileList[SampleRun]]\n",
-    "params[FileList[EmptyBeamRun]] = ['SANS2D00063091.hdf5']\n",
+    "params[isis.Filename[EmptyBeamRun]] = 'SANS2D00063091.nxs'\n",
+    "\n",
+    "params[NeXusMonitorName[Incident]] = 'monitor2'\n",
+    "params[NeXusMonitorName[Transmission]] = 'monitor4'\n",
+    "\n",
+    "params[sans.isis.SampleOffset] = sc.vector([0.0, 0.0, 0.053], unit='m')\n",
+    "params[sans.isis.MonitorOffset[Transmission]] = sc.vector([0.0, 0.0, -6.719], unit='m')\n",
     "\n",
     "params[CorrectForGravity] = True\n",
     "params[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound\n",
@@ -259,6 +264,8 @@
     "providers.remove(sans.beam_center_finder.beam_center_from_center_of_mass)\n",
     "providers.append(sans.beam_center_finder.beam_center_from_iofq)\n",
     "\n",
+    "providers.append(sans.transmission_from_sample_run)\n",
+    "\n",
     "# Build the pipeline\n",
     "pipeline = sciline.Pipeline(providers, params=params)\n",
     "\n",
@@ -306,9 +313,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "p = plot_flat_detector_xy(masked.sum('tof'), norm='log')\n",
+    "p = isis.plot_flat_detector_xy(masked.hist(), norm='log')\n",
     "p.ax.plot(0, 0, '+', color='k', ms=10)\n",
-    "p.ax.plot(iofq_center.value[0], iofq_center.value[1], 'o', color='magenta', mec='lightgray', ms=6)\n",
+    "p.ax.plot(\n",
+    "    iofq_center.value[0],\n",
+    "    iofq_center.value[1],\n",
+    "    'o',\n",
+    "    color='magenta',\n",
+    "    mec='lightgray',\n",
+    "    ms=6,\n",
+    ")\n",
     "p"
    ]
   },
@@ -357,7 +371,7 @@
    },
    "outputs": [],
    "source": [
-    "p = plot_flat_detector_xy(masked.sum('tof'), norm='log')\n",
+    "p = isis.plot_flat_detector_xy(masked.hist(), norm='log')\n",
     "p.ax.axvline(0, color='cyan')\n",
     "p.ax.axhline(0, color='cyan')\n",
     "p.ax.plot(0, 0, '+', color='k', ms=10)\n",

docs/examples/sans2d.ipynb

@@ -22,84 +22,92 @@
    },
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import scipp as sc\n",
     "import sciline\n",
-    "import scippneutron as scn\n",
     "import plopp as pp\n",
     "import esssans as sans\n",
+    "import esssans.isis as isis\n",
     "from esssans.types import *"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "c21564a8-e742-4183-9edc-2c70c51d5863",
+   "id": "3da2d397-6206-4ed1-a98f-11b3aaf7e5b0",
    "metadata": {},
    "source": [
-    "## Create pipeline using Sciline\n",
+    "## Define reduction parameters\n",
     "\n",
-    "We use all providers available in `esssans` as well as the `sans2d`-specific providers, which include I/O and mask setup specific to the [Sans2d](https://www.isis.stfc.ac.uk/Pages/sans2d.aspx) instrument:"
+    "We define the reduction parameters, with keys and types given by aliases or types defined in `esssans.types`:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "025fca0b-68a7-4d6e-a82a-86713cc3fca7",
+   "id": "d3f5e1ee-bd80-4301-9ff9-15c8ada3cf57",
    "metadata": {},
    "outputs": [],
    "source": [
-    "pipeline = sciline.Pipeline(\n",
-    "    sans.providers + sans.sans2d.providers,\n",
-    "    params=sans.sans2d.default_parameters,\n",
-    ")"
+    "params = {}\n",
+    "\n",
+    "params[DirectBeamFilename] = 'DIRECT_SANS2D_REAR_34327_4m_8mm_16Feb16.dat'\n",
+    "params[sans.isis.Filename[SampleRun]] = 'SANS2D00063114.nxs'\n",
+    "params[sans.isis.Filename[BackgroundRun]] = 'SANS2D00063159.nxs'\n",
+    "params[sans.isis.Filename[EmptyBeamRun]] = 'SANS2D00063091.nxs'\n",
+    "params[OutFilename] = 'reduced.nxs'\n",
+    "\n",
+    "params[NeXusMonitorName[Incident]] = 'monitor2'\n",
+    "params[NeXusMonitorName[Transmission]] = 'monitor4'\n",
+    "\n",
+    "params[sans.isis.SampleOffset] = sc.vector([0.0, 0.0, 0.053], unit='m')\n",
+    "params[sans.isis.MonitorOffset[Transmission]] = sc.vector([0.0, 0.0, -6.719], unit='m')\n",
+    "\n",
+    "params[WavelengthBins] = sc.linspace(\n",
+    "    'wavelength', start=2.0, stop=16.0, num=141, unit='angstrom'\n",
+    ")\n",
+    "\n",
+    "params[sans.isis.sans2d.LowCountThreshold] = sc.scalar(100, unit='counts')\n",
+    "\n",
+    "mask_interval = sc.array(dims=['wavelength'], values=[2.21, 2.59], unit='angstrom')\n",
+    "params[WavelengthMask] = sc.DataArray(\n",
+    "    sc.array(dims=['wavelength'], values=[True]),\n",
+    "    coords={'wavelength': mask_interval},\n",
+    ")\n",
+    "\n",
+    "params[QBins] = sc.linspace(dim='Q', start=0.01, stop=0.6, 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\n",
+    "params[sans.ReturnEvents] = True"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "3da2d397-6206-4ed1-a98f-11b3aaf7e5b0",
+   "id": "c21564a8-e742-4183-9edc-2c70c51d5863",
    "metadata": {},
    "source": [
-    "## Define reduction parameters\n",
+    "## Create pipeline using Sciline\n",
     "\n",
-    "We define the reduction parameters, with keys and types given by aliases or types defined in `esssans.types`:"
+    "We use all providers available in `esssans` as well as the `isis` and `sans2d`-specific providers, which include I/O and mask setup specific to the [Sans2d](https://www.isis.stfc.ac.uk/Pages/sans2d.aspx) instrument:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bc2fffe1-a694-43b7-9234-e31da42d6df3",
-   "metadata": {
-    "tags": []
-   },
+   "id": "85b955ba-a54d-4760-bb35-af9cbe1ada90",
+   "metadata": {},
    "outputs": [],
    "source": [
-    "pipeline[FileList[BackgroundRun]] = ['SANS2D00063159.hdf5']\n",
-    "pipeline.insert(sans.transmission_from_background_run)\n",
-    "pipeline[FileList[SampleRun]] = ['SANS2D00063114.hdf5']\n",
-    "pipeline.insert(sans.transmission_from_sample_run)\n",
-    "pipeline[FileList[EmptyBeamRun]] = ['SANS2D00063091.hdf5']\n",
-    "pipeline[DirectBeamFilename] = 'DIRECT_SANS2D_REAR_34327_4m_8mm_16Feb16.hdf5'\n",
-    "pipeline[OutFilename] = 'reduced.nxs'\n",
-    "\n",
-    "pipeline[WavelengthBins] = sc.linspace(\n",
-    "    'wavelength', start=2.0, stop=16.0, num=141, unit='angstrom'\n",
+    "providers = (\n",
+    "    sans.providers + isis.providers + isis.data.providers + isis.sans2d.providers\n",
     ")\n",
-    "\n",
-    "pipeline[sans.sans2d.LowCountThreshold] = sc.scalar(100, unit='counts')\n",
-    "\n",
-    "mask_interval = sc.array(dims=['wavelength'], values=[2.21, 2.59], unit='angstrom')\n",
-    "pipeline[WavelengthMask] = sc.DataArray(\n",
-    "    sc.array(dims=['wavelength'], values=[True]),\n",
-    "    coords={'wavelength': mask_interval},\n",
+    "providers = providers + (\n",
+    "    sans.transmission_from_background_run,\n",
+    "    sans.transmission_from_sample_run,\n",
     ")\n",
     "\n",
-    "pipeline[QBins] = sc.linspace(dim='Q', start=0.01, stop=0.6, num=141, unit='1/angstrom')\n",
-    "pipeline[NonBackgroundWavelengthRange] = sc.array(\n",
-    "    dims=['wavelength'], values=[0.7, 17.1], unit='angstrom'\n",
-    ")\n",
-    "pipeline[CorrectForGravity] = True\n",
-    "pipeline[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound\n",
-    "pipeline[sans.ReturnEvents] = True"
+    "pipeline = sciline.Pipeline(providers=providers, params=params)"
    ]
   },
   {
@@ -263,7 +271,7 @@
     "\n",
     "display(sc.plot({str(key): results[key] for key in monitors}, norm='log'))\n",
     "\n",
-    "display(plot_flat_detector_xy(results[MaskedData[SampleRun]].sum('tof'), norm='log'))\n",
+    "display(plot_flat_detector_xy(results[MaskedData[SampleRun]].hist(), norm='log'))\n",
     "\n",
     "wavelength = pipeline.compute(WavelengthBins)\n",
     "display(\n",

docs/examples/zoom.ipynb

@@ -107,12 +107,7 @@
     ")\n",
     "\n",
     "params[QBins] = sc.geomspace(dim='Q', start=0.004, stop=0.8, num=141, unit='1/angstrom')\n",
-    "qxy = {\n",
-    "    'Qx': sc.linspace(dim='Qx', start=-0.5, stop=0.5, num=101, unit='1/angstrom'),\n",
-    "    'Qy': sc.linspace(dim='Qy', start=-0.8, stop=0.8, num=101, unit='1/angstrom'),\n",
-    "}\n",
-    "# Uncomment to compute I(Qx, Qy) instead of I(Q)\n",
-    "# params[QxyBins] = qxy\n",
+    "\n",
     "params[NonBackgroundWavelengthRange] = sc.array(\n",
     "    dims=['wavelength'], values=[0.7, 17.1], unit='angstrom'\n",
     ")\n",
@@ -136,7 +131,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "providers = sans.providers + sans.isis.providers\n",
+    "providers = sans.providers + sans.isis.providers + sans.isis.masking.providers\n",
     "providers = providers + (\n",
     "    sans.transmission_from_background_run,\n",
     "    sans.transmission_from_sample_run,\n",
@@ -174,7 +169,7 @@
     "    for provider in sans.isis.mantidio.providers:\n",
     "        pipeline.insert(provider)\n",
     "except ImportError:\n",
-    "    import esssans.isis.data\n",
+    "    import esssans.isis.io\n",
     "\n",
     "    for provider in sans.isis.data.providers:\n",
     "        pipeline.insert(provider)"
@@ -217,7 +212,7 @@
    "outputs": [],
    "source": [
     "da = iofq.compute()\n",
-    "da.plot(norm='log', scale={'Q': 'log'}, aspect='equal')"
+    "da.plot(norm='log', scale={'Q': 'log'})"
    ]
   },
   {
@@ -272,6 +267,33 @@
     "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'}, aspect='equal'))"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e63318c7-4d63-4133-97c3-feb56707caba",
+   "metadata": {},
+   "source": [
+    "## Computing Qx/Qy\n",
+    "\n",
+    "To compute $I(Q_{x}, Q_{y})$ instead of the one-dimensional $I(Q)$,\n",
+    "we can simply define some `QxyBins` in our parameters:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3879702d-424a-462f-8475-6056116d7d35",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pipeline[QxyBins] = {\n",
+    "    'Qx': sc.linspace(dim='Qx', start=-0.5, stop=0.5, num=101, unit='1/angstrom'),\n",
+    "    'Qy': sc.linspace(dim='Qy', start=-0.8, stop=0.8, num=101, unit='1/angstrom'),\n",
+    "}\n",
+    "\n",
+    "iqxqy = pipeline.compute(IofQ[SampleRun])\n",
+    "iqxqy.plot(norm='log', aspect='equal')"
+   ]
   }
  ],
  "metadata": {
@@ -289,8 +311,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

src/esssans/__init__.py

@@ -9,16 +9,7 @@
 except importlib.metadata.PackageNotFoundError:
     __version__ = "0.0.0"
 
-from . import (
-    beam_center_finder,
-    common,
-    conversions,
-    i_of_q,
-    io,
-    loki,
-    normalization,
-    sans2d,
-)
+from . import beam_center_finder, common, conversions, i_of_q, io, loki, normalization
 from .common import transmission_from_background_run, transmission_from_sample_run
 from .direct_beam import direct_beam
 from .types import BackgroundSubtractedIofQ, IofQ, ReturnEvents, SampleRun
@@ -55,7 +46,6 @@
     'loki',
     'normalization',
     'providers',
-    'sans2d',
     'transmission_from_sample_run',
     'transmission_from_background_run',
 ]

src/esssans/beam_center_finder.py

@@ -192,13 +192,18 @@ def _iofq_in_quadrants(
     pipeline = sciline.Pipeline(providers, params=params)
     pipeline[MaskedData[SampleRun]] = data
     calibrated = pipeline.compute(CalibratedMaskedData[SampleRun])
-    phi = calibrated.transform_coords(
+    with_phi = calibrated.transform_coords(
         'phi', graph=graph, keep_intermediate=False, keep_inputs=False
-    ).coords['phi']
-    if phi.bins is not None or 'wavelength' in phi.dims:
-        # If gravity-correction is enabled, phi depends on wavelength (and event).
-        # We cannot handle this below, so we approximate phi by the mean value.
-        phi = phi.mean('wavelength')
+    )
+    # If gravity-correction is enabled, phi depends on wavelength (and event).
+    # We cannot handle this below, so we approximate phi by the mean value.
+    if ('phi' not in with_phi.coords) and ('phi' in with_phi.bins.coords):
+        # This is the case where we have a phi event coord but no coord at the top level
+        phi = with_phi.bins.coords['phi'].bins.mean()
+    else:
+        phi = with_phi.coords['phi']
+        if phi.bins is not None or 'wavelength' in phi.dims:
+            phi = phi.mean('wavelength')
 
     out = {}
     for i, quad in enumerate(quadrants):