essdiffraction 24.10.0__tar.gz → 24.11.0__tar.gz

{essdiffraction-24.10.0/src/essdiffraction.egg-info → essdiffraction-24.11.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: essdiffraction
-Version: 24.10.0
+Version: 24.11.0
 Summary: Diffraction data reduction for the European Spallation Source
 Author: Scipp contributors
 License: BSD 3-Clause License
@@ -51,14 +51,14 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: dask
-Requires-Dist: essreduce>=24.10.2
+Requires-Dist: essreduce>=24.11.3
 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>=24.9.0
+Requires-Dist: scippneutron>=24.11.0
 Requires-Dist: scippnexus>=23.12.0
 Provides-Extra: test
 Requires-Dist: pandas; extra == "test"

{essdiffraction-24.10.0 → essdiffraction-24.11.0}/docs/api-reference/index.md

@@ -52,6 +52,7 @@
    :recursive:
 
    data
+   diagnostics
    io
 ```
 

{essdiffraction-24.10.0 → essdiffraction-24.11.0}/docs/user-guide/dream/dream-data-reduction.ipynb

@@ -20,7 +20,6 @@
    "outputs": [],
    "source": [
     "import scipp as sc\n",
-    "from scippneutron.io import cif\n",
     "\n",
     "from ess import dream, powder\n",
     "import ess.dream.data  # noqa: F401\n",
@@ -44,7 +43,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow = dream.DreamGeant4Workflow()"
+    "workflow = dream.DreamGeant4Workflow(run_norm=powder.RunNormalization.proton_charge)"
    ]
   },
   {
@@ -74,7 +73,7 @@
     "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",
+    "        x > sc.scalar(86e6, unit=\"ns\")\n",
     ")\n",
     "workflow[TwoThetaMask] = None\n",
     "workflow[WavelengthMask] = None\n",
@@ -86,50 +85,25 @@
    "cell_type": "markdown",
    "id": "6",
    "metadata": {},
-   "source": [
-    "We also need some parameters to configure the output file:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "workflow[CIFAuthors] = CIFAuthors([\n",
-    "    cif.Author(\n",
-    "        name=\"Jane Doe\",\n",
-    "        email=\"jane.doe@ess.eu\",\n",
-    "        orcid=\"0000-0000-0000-0001\",\n",
-    "        role=\"measurement\",\n",
-    "    ),\n",
-    "])"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "8",
-   "metadata": {},
    "source": [
     "## Use the workflow\n",
     "\n",
-    "We can visualize the graph for computing the final normalized result for intensity as a function of d-spacing:"
+    "We can visualize the graph for computing the final normalized result for intensity as a function of time-of-flight:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow.visualize(IofDspacing, graph_attr={\"rankdir\": \"LR\"})"
+    "workflow.visualize([IofTof, ReducedTofCIF], graph_attr={\"rankdir\": \"LR\"})"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "10",
+   "id": "8",
    "metadata": {},
    "source": [
     "We then call `compute()` to compute the result:\n",
@@ -139,39 +113,38 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
-    "results = workflow.compute([IofDspacing, ReducedDspacingCIF])\n",
-    "result = results[IofDspacing]\n",
-    "cif_data = results[ReducedDspacingCIF]"
+    "results = workflow.compute([IofTof, ReducedTofCIF])\n",
+    "result = results[IofTof]\n",
+    "cif_data = results[ReducedTofCIF]"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
-    "dspacing_histogram = result.hist()\n",
-    "dspacing_histogram.plot()"
+    "histogram = result.hist()\n",
+    "histogram.plot()"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "11",
    "metadata": {},
    "source": [
-    "We can now save the result to disk:\n",
-    "(The comment is optional but helps to identify the file later.)"
+    "We can now save the result to disk:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -179,12 +152,12 @@
     "in the documentation of ESSdiffraction.\n",
     "See https://scipp.github.io/essdiffraction/\n",
     "\"\"\"\n",
-    "cif_data.save('dspacing.cif')"
+    "cif_data.save('reduced.cif')"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "15",
+   "id": "13",
    "metadata": {},
    "source": [
     "## Compute intermediate results\n",
@@ -197,7 +170,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -214,7 +187,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -226,7 +199,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "18",
+   "id": "16",
    "metadata": {},
    "source": [
     "## Grouping by scattering angle\n",
@@ -238,7 +211,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -250,7 +223,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -261,7 +234,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -279,12 +252,133 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
     "grouped_dspacing.hist().plot(norm=\"log\")"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "21",
+   "metadata": {},
+   "source": [
+    "##  Normalizing by monitor\n",
+    "\n",
+    "The workflow used above normalizes the detected counts by proton charge.\n",
+    "Alternatively, ESSdiffraction can normalize by a monitor.\n",
+    "In this example, this is DREAM's cave monitor.\n",
+    "\n",
+    "There are two options for normalizing by monitor:\n",
+    "1. Normalize by a wavelength-histogram of the monitor counts ([normalize_by_monitor_histogram](../../generated/modules/ess.powder.correction.normalize_by_monitor_histogram.rst)).\n",
+    "2. Normalized by the integral over all wavelength bins ([normalize_by_monitor_integrated](../../generated/modules/ess.powder.correction.normalize_by_monitor_integrated.rst)).\n",
+    "\n",
+    "Here, we use option 1.\n",
+    "Option 2 can be chosen by constructing a workflow using `run_norm=powder.RunNormalization.monitor_integrated`.\n",
+    "\n",
+    "Construct a workflow as before but select normalization by monitor histogram:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "22",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "workflow = dream.DreamGeant4Workflow(run_norm=powder.RunNormalization.monitor_histogram)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "23",
+   "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:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "24",
+   "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",
+    "\n",
+    "# These are the same as at the top of the notebook:\n",
+    "workflow[Filename[SampleRun]] = dream.data.simulated_diamond_sample()\n",
+    "workflow[Filename[VanadiumRun]] = dream.data.simulated_vanadium_sample()\n",
+    "workflow[Filename[BackgroundRun]] = dream.data.simulated_empty_can()\n",
+    "workflow[CalibrationFilename] = None\n",
+    "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[TwoThetaMask] = None\n",
+    "workflow[WavelengthMask] = None\n",
+    "workflow = powder.with_pixel_mask_filenames(workflow, [])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "25",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "workflow.visualize(IofTof, graph_attr={\"rankdir\": \"LR\"})"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "26",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "results = workflow.compute((IofTof, WavelengthMonitor[SampleRun, CaveMonitor]))\n",
+    "normalized_by_monitor = results[IofTof]\n",
+    "monitor = results[WavelengthMonitor[SampleRun, CaveMonitor]]\n",
+    "monitor"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "27",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "monitor.plot()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "28",
+   "metadata": {},
+   "source": [
+    "Comparing the final, normalized result shows that it agrees with the data that was normalized by proton-charge:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "29",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sc.plot({\n",
+    "    'By proton charge': histogram,\n",
+    "    'By monitor': normalized_by_monitor.hist()\n",
+    "})"
+   ]
   }
  ],
  "metadata": {
@@ -303,7 +397,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

essdiffraction-24.11.0/docs/user-guide/dream/dream-detector-diagnostics.ipynb

@@ -0,0 +1,112 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# DREAM Detector Diagnostics\n",
+    "\n",
+    "This page is primarily intended for instrument scientists and other experts.\n",
+    "\n",
+    "ESSdiffraction has some tools for inspecting the DREAM detector based on recorded event data.\n",
+    "This notebook gives an overview of the available tools.\n",
+    "\n",
+    "## Voxel Viewer\n",
+    "\n",
+    "The [FlatVoxelViewer](../../generated/modules/ess.dream.diagnostics.FlatVoxelViewer.rst) is an interactive visualization for inspecting individual voxels.\n",
+    "It shows a 2D histogram of recorded events.\n",
+    "The image axes correspond to a chosen pair of logical dimensions combined with all other dimensions.\n",
+    "Each bin in the image corresponds to exactly one detector voxel.\n",
+    "\n",
+    "Tick marks indicate the values of the chosen dimensions.\n",
+    "E.g., all pixels between module=2 and module=3 tick marks belong to module 2."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import scipp as sc\n",
+    "\n",
+    "from ess import dream\n",
+    "from ess.dream.data import simulated_diamond_sample\n",
+    "from ess.dream.diagnostics import FlatVoxelViewer"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib widget"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3",
+   "metadata": {},
+   "source": [
+    "Load simulated test data and compute histograms:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "raw = dream.io.load_geant4_csv(simulated_diamond_sample())\n",
+    "dg = sc.DataGroup({\n",
+    "    k: v['events'].hist()\n",
+    "    for k, v in raw['instrument'].items()\n",
+    "})"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5",
+   "metadata": {},
+   "source": [
+    "Display 2D view:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "FlatVoxelViewer(dg)"
+   ]
+  }
+ ],
+ "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": "3.10.15"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{essdiffraction-24.10.0 → essdiffraction-24.11.0}/docs/user-guide/dream/index.md

@@ -7,4 +7,6 @@ maxdepth: 1
 
 dream-data-reduction
 dream-instrument-view
+workflow-widget-dream
+dream-detector-diagnostics
 ```

essdiffraction-24.11.0/docs/user-guide/dream/workflow-widget-dream.ipynb

@@ -0,0 +1,140 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# Workflow widgets example\n",
+    "\n",
+    "This notebook illustrates how we can use ESSreduce’s [workflow widgets](https://scipp.github.io/essreduce/user-guide/widget.html) to generate a graphical interface for running the LoKI tutorial workflow.\n",
+    "\n",
+    "## Initializing the GUI\n",
+    "\n",
+    "It is as simple as importing the dream submodule and generating a GUI using `workflow_widget` (the workflow automatically registers itself to a library of workflows when imported)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Import dream submodule to register workflow\n",
+    "from ess import dream\n",
+    "from ess.reduce import ui\n",
+    "\n",
+    "# Prepare a container for accessing the results computed by the GUI\n",
+    "results = {}\n",
+    "\n",
+    "# Initialize the GUI widget\n",
+    "widget = ui.workflow_widget(result_registry=results)\n",
+    "widget"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2",
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "from ess.powder.types import DspacingBins, Filename, SampleRun, VanadiumRun\n",
+    "import ess.dream.data  # noqa: F401\n",
+    "\n",
+    "select = widget.children[0].children[0]\n",
+    "keys, values = zip(*select.options, strict=True)\n",
+    "ind = keys.index(\"DreamGeant4ProtonChargeWorkflow\")\n",
+    "select.value = values[ind]\n",
+    "# Select IofDspacing output\n",
+    "wfw = widget.children[1].children[0]\n",
+    "outputs = wfw.output_selection_box.typical_outputs_widget\n",
+    "keys, values = zip(*outputs.options, strict=True)\n",
+    "ind = keys.index(\"IofTof\")\n",
+    "outputs.value = (values[ind],)\n",
+    "# Refresh parameters\n",
+    "pbox = wfw.parameter_box\n",
+    "pbox.parameter_refresh_button.click()\n",
+    "# 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[DspacingBins].children[0].fields[\"stop\"].value = 2.3434\n",
+    "# Run the workflow\n",
+    "rbox = wfw.result_box\n",
+    "rbox.run_button.click()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3",
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
+   },
+   "source": [
+    "## Accessing the results\n",
+    "\n",
+    "We can now access the computed result in the `results` dictionary:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "results"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5",
+   "metadata": {},
+   "source": [
+    "The result can be plotted using"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "(da,) = results.values()\n",
+    "da.hist(tof=200).plot()"
+   ]
+  }
+ ],
+ "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"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{essdiffraction-24.10.0 → essdiffraction-24.11.0}/pyproject.toml

@@ -31,14 +31,14 @@ requires-python = ">=3.10"
 # Make sure to list one dependency per line.
 dependencies = [
   "dask",
-  "essreduce>=24.10.2",
+  "essreduce>=24.11.3",
   "graphviz",
   "numpy",
   "plopp",
   "pythreejs",
   "sciline>=24.06.0",
   "scipp>=24.09.1",
-  "scippneutron>=24.9.0",
+  "scippneutron>=24.11.0",
   "scippnexus>=23.12.0",
 ]
 

{essdiffraction-24.10.0 → essdiffraction-24.11.0}/requirements/base.in

@@ -3,12 +3,12 @@
 # --- END OF CUSTOM SECTION ---
 # The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY!
 dask
-essreduce>=24.10.2
+essreduce>=24.11.3
 graphviz
 numpy
 plopp
 pythreejs
 sciline>=24.06.0
 scipp>=24.09.1
-scippneutron>=24.9.0
+scippneutron>=24.11.0
 scippnexus>=23.12.0