essdiffraction 25.2.0__tar.gz → 25.2.1__tar.gz

{essdiffraction-25.2.0 → essdiffraction-25.2.1}/.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

{essdiffraction-25.2.0/src/essdiffraction.egg-info → essdiffraction-25.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: essdiffraction
-Version: 25.2.0
+Version: 25.2.1
 Summary: Diffraction data reduction for the European Spallation Source
 Author: Scipp contributors
 License: BSD 3-Clause License
@@ -52,15 +52,16 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: dask
-Requires-Dist: essreduce>=24.12.0
+Requires-Dist: essreduce>=25.02.4
 Requires-Dist: graphviz
 Requires-Dist: numpy
 Requires-Dist: plopp
 Requires-Dist: pythreejs
 Requires-Dist: sciline>=24.06.0
 Requires-Dist: scipp>=24.09.1
-Requires-Dist: scippneutron>=24.11.0
+Requires-Dist: scippneutron>=25.02.0
 Requires-Dist: scippnexus>=23.12.0
+Requires-Dist: tof>=25.01.2
 Provides-Extra: test
 Requires-Dist: pandas; extra == "test"
 Requires-Dist: pooch; extra == "test"

{essdiffraction-25.2.0 → essdiffraction-25.2.1}/docs/api-reference/index.md

@@ -26,6 +26,7 @@
    filtering
    grouping
    smoothing
+   transform
    types
 ```
 

{essdiffraction-25.2.0 → essdiffraction-25.2.1}/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 *"
@@ -71,14 +70,14 @@
     "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()"
    ]
   },
   {
@@ -86,7 +85,7 @@
    "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,

essdiffraction-25.2.1/docs/user-guide/dream/dream-visualize-absorption.ipynb

@@ -0,0 +1,225 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# Visualize effect of absorption\n",
+    "\n",
+    "This notebook is an example of how to use the `compute_transmission_map` function to visualize the effect of (sample) absorption on the intensity in the detector.\n",
+    "\n",
+    "Note that the `compute_transmission_map` function only accounts for the effect of absorption. The measured intensity in the detector can also be impacted by other effects, such as the effect of the solid angle being different for different detector pixels.\n",
+    "\n",
+    "For more details, see https://scipp.github.io/scippneutron/user-guide/absorption-correction.html."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import scipp as sc\n",
+    "\n",
+    "from ess import dream\n",
+    "import ess.dream.data  # noqa: F401\n",
+    "\n",
+    "from scippneutron.absorption import compute_transmission_map\n",
+    "from scippneutron.absorption.cylinder import Cylinder\n",
+    "from scippneutron.absorption.material import Material\n",
+    "from scippneutron.atoms import ScatteringParams"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2",
+   "metadata": {},
+   "source": [
+    "## Load the data\n",
+    "\n",
+    "We load a dataset from a Geant4 simulation only to get access to the detector geometry."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dg = dream.io.load_geant4_csv(dream.data.get_path(\"data_dream0_new_hkl_Si_pwd.csv.zip\"))[\"instrument\"]\n",
+    "dg = sc.DataGroup({key: detector[\"events\"][\"counter\", 0] for key, detector in dg.items()})\n",
+    "dg.keys()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4",
+   "metadata": {},
+   "source": [
+    "## Inhomogeneity from absorption in mantle detector\n",
+    "\n",
+    "If the sample absorbs or scatters a large fraction of the incoming neutrons, the intensity in the detector will vary even if the scattering is inhomogeneous.\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5",
+   "metadata": {},
+   "source": [
+    "### Rod-like sample oriented along x-axis"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# The material determines the rate of absorption and scattering\n",
+    "vanadium =  Material(\n",
+    "    scattering_params=ScatteringParams.for_isotope('V'),\n",
+    "    effective_sample_number_density=sc.scalar(0.07192, unit='1/angstrom**3')\n",
+    ")\n",
+    "# The shape determines the shape and the orientation of the sample\n",
+    "rod_shape = Cylinder(\n",
+    "    radius=sc.scalar(1, unit='cm'),\n",
+    "    height=(height := sc.scalar(5., unit='cm')),\n",
+    "    # Cylinder is oriented along the x-axis\n",
+    "    symmetry_line=(symmetry_line := sc.vector([1, 0, 0])),\n",
+    "    center_of_base=-height * symmetry_line / 2,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "transmission_fraction_mantle = compute_transmission_map(\n",
+    "    rod_shape,\n",
+    "    vanadium,\n",
+    "    beam_direction=sc.vector([0, 0, 1]),\n",
+    "    wavelength=sc.linspace('wavelength', 4, 8, 20, unit='angstrom'),\n",
+    "    # To make it faster, don't compute the transmission fraction for every detector pixel, it's not necessary for the visualization.\n",
+    "    detector_position=dg['mantle'].coords['position']['strip', ::4]['wire', ::2].copy(),\n",
+    "    quadrature_kind='cheap',\n",
+    ")\n",
+    "\n",
+    "# The visualization expects the `position` coord to denote detector positions, and `wavelength` to be the last dimension.\n",
+    "transmission_fraction_mantle.coords['position'] = transmission_fraction_mantle.coords.pop('detector_position')\n",
+    "dream.instrument_view(transmission_fraction_mantle, dim='wavelength', pixel_size=20.0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "transmission_fraction_mantle"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9",
+   "metadata": {},
+   "source": [
+    "## Disk-like sample oriented along x-axis"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "10",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "disk_shape = Cylinder(\n",
+    "    radius=sc.scalar(5, unit='cm'),\n",
+    "    height=(height := sc.scalar(1., unit='cm')),\n",
+    "    # Cylinder is oriented along the x-axis\n",
+    "    symmetry_line=(symmetry_line := sc.vector([1, 0, 0])),\n",
+    "    center_of_base=-height * symmetry_line / 2,\n",
+    ")\n",
+    "\n",
+    "transmission_fraction_mantle = compute_transmission_map(\n",
+    "    disk_shape,\n",
+    "    vanadium,\n",
+    "    beam_direction=sc.vector([0, 0, 1]),\n",
+    "    wavelength=sc.linspace('wavelength', 4, 8, 20, unit='angstrom'),\n",
+    "    # To make it faster, don't compute the transmission fraction for every detector pixel, it's not necessary for the visualization.\n",
+    "    detector_position=dg['mantle'].coords['position']['strip', ::4]['wire', ::2].copy(),\n",
+    "    quadrature_kind='cheap',\n",
+    ")\n",
+    "\n",
+    "# The visualization expects the `position` coord to denote detector positions, and `wavelength` to be the last dimension.\n",
+    "transmission_fraction_mantle.coords['position'] = transmission_fraction_mantle.coords.pop('detector_position')\n",
+    "dream.instrument_view(transmission_fraction_mantle, dim='wavelength', pixel_size=20.0)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "11",
+   "metadata": {},
+   "source": [
+    "## Does absorption influence the intensity in the endcap detector?"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "12",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "transmission_fraction_endcap = compute_transmission_map(\n",
+    "    rod_shape,\n",
+    "    vanadium,\n",
+    "    beam_direction=sc.vector([0, 0, 1]),\n",
+    "    wavelength=sc.linspace('wavelength', 4, 8, 20, unit='angstrom'),\n",
+    "    detector_position=dg['endcap_backward'].coords['position']['strip', 0].copy(),\n",
+    "    quadrature_kind='cheap',\n",
+    ")\n",
+    "\n",
+    "transmission_fraction_endcap.coords['position'] = transmission_fraction_endcap.coords.pop('detector_position')\n",
+    "dream.instrument_view(transmission_fraction_endcap, dim='wavelength', pixel_size=20.0)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "13",
+   "metadata": {},
+   "source": [
+    "As expected the impact of absorption on on the intensity in the endcap detector is close to uniform."
+   ]
+  }
+ ],
+ "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": "3.10.14"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{essdiffraction-25.2.0 → essdiffraction-25.2.1}/docs/user-guide/dream/index.md

@@ -9,4 +9,5 @@ dream-data-reduction
 dream-instrument-view
 workflow-widget-dream
 dream-detector-diagnostics
+dream-visualize-absorption
 ```

{essdiffraction-25.2.0 → essdiffraction-25.2.1}/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,

{essdiffraction-25.2.0 → essdiffraction-25.2.1}/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,

{essdiffraction-25.2.0 → essdiffraction-25.2.1}/pyproject.toml

@@ -32,15 +32,16 @@ requires-python = ">=3.10"
 # Make sure to list one dependency per line.
 dependencies = [
   "dask",
-  "essreduce>=24.12.0",
+  "essreduce>=25.02.4",
   "graphviz",
   "numpy",
   "plopp",
   "pythreejs",
   "sciline>=24.06.0",
   "scipp>=24.09.1",
-  "scippneutron>=24.11.0",
+  "scippneutron>=25.02.0",
   "scippnexus>=23.12.0",
+  "tof>=25.01.2",
 ]
 
 dynamic = ["version"]

{essdiffraction-25.2.0 → essdiffraction-25.2.1}/requirements/base.in

@@ -3,12 +3,13 @@
 # --- END OF CUSTOM SECTION ---
 # The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY!
 dask
-essreduce>=24.12.0
+essreduce>=25.02.4
 graphviz
 numpy
 plopp
 pythreejs
 sciline>=24.06.0
 scipp>=24.09.1
-scippneutron>=24.11.0
+scippneutron>=25.02.0
 scippnexus>=23.12.0
+tof>=25.01.2