Dream instrument view

docs/index.rst

@@ -50,6 +50,7 @@ This involves a "filtering" process, since scope and contribution guidelines are
  :caption: Instruments
 
  instruments/amor/amor
+ instruments/dream/dream
  instruments/loki/loki
  instruments/external/external
 

docs/instruments/dream/dream-instrument-view.ipynb

@@ -0,0 +1,254 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "id": "4852fe41-3f9a-4cdb-8aba-ff7c7f198e6c",
+ "metadata": {},
+ "source": [
+ "# DREAM instrument view\n",
+ "\n",
+ "This notebook is a simple example on how to use the instrument view for the DREAM instrument.\n",
+ "\n",
+ "- The DREAM-specific instrument view is capable of slicing the data with a slider widget along a dimension (e.g. `tof`) by using the `dim` argument.\n",
+ "- There are also checkboxes to hide/show the different elements that make up the DREAM detectors."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "3f416595-83b4-44d1-b506-9ba73bf0786e",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import pandas as pd\n",
+ "import scipp as sc\n",
+ "from ess import dream"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "228a23dc-17f2-4273-a4c9-3e3276db8c54",
+ "metadata": {},
+ "source": [
+ "## Load the data\n",
+ "\n",
+ "We load a data set from a Geant4 simulation (stored as a `.csv` file).\n",
+ "In each detector bank, the data is organised by `wire`, `strip`, `module`, `segment`, and `counter`.\n",
+ "The end caps also have an additional `sumo` dimension."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "1ef8f35b-815f-436a-80e5-cbe4b3172b58",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "dg = dream.io.load_geant4_csv(\n",
+ " dream.data.get_path('data_dream_HF_mil_closed_alldets_1e9.csv.zip')\n",
+ ")\n",
+ "dg = dg['instrument'] # Extract the instrument data\n",
+ "\n",
+ "# Construct the pixel positions from event positions\n",
+ "for da in dg.values():\n",
+ " da.coords['position'] = da.bins.coords['position'].bins.mean()\n",
+ "\n",
+ "dg"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "e8325797-5651-43c1-b601-3db6d4348758",
+ "metadata": {
+ "editable": true,
+ "nbsphinx": "hidden",
+ "slideshow": {
+ "slide_type": ""
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Only plot half of the pixels to reduce html docs size\n",
+ "dg = dg['counter', 0]"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "49595486-ab4e-4662-86f7-d301aedcf974",
+ "metadata": {
+ "editable": true,
+ "slideshow": {
+ "slide_type": ""
+ },
+ "tags": []
+ },
+ "source": [
+ "## Full instrument view\n",
+ "\n",
+ "We first histogram the data along the time-of-flight (`tof`) dimension,\n",
+ "making sure the same bins are used for all elements:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "e85a8364-e0a1-4c10-8cae-c873f297e651",
+ "metadata": {
+ "editable": true,
+ "slideshow": {
+ "slide_type": ""
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "tof_edges = sc.linspace('tof', 1.0e7, 1.0e8, 51, unit='ns', dtype=int)\n",
+ "data = dg.hist(tof=tof_edges)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "d08ca911-b1a4-4f17-ba1e-355971531ffe",
+ "metadata": {
+ "editable": true,
+ "slideshow": {
+ "slide_type": ""
+ },
+ "tags": []
+ },
+ "source": [
+ "We now use the `instrument_view` function to show the 3D view of the instrument pixels,\n",
+ "specifying that we wish to have a slider along the `tof` dimension:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "43f9ffbc-6bf5-4407-b3ad-5d1626efc43d",
+ "metadata": {
+ "editable": true,
+ "slideshow": {
+ "slide_type": ""
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "full_view = dream.instrument_view(data, dim='tof')\n",
+ "full_view"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "a7030d56-a375-47b5-898c-28fd06c2f361",
+ "metadata": {
+ "editable": true,
+ "nbsphinx": "hidden",
+ "slideshow": {
+ "slide_type": ""
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "full_view[2].controls['tof']['slider'].value = 35"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "c0b29ebf-21ff-4385-bf8b-0e4fa14dfaf9",
+ "metadata": {
+ "editable": true,
+ "slideshow": {
+ "slide_type": ""
+ },
+ "tags": []
+ },
+ "source": [
+ "Note that it is possible to use any dimension for the slider instead of `tof`, such as `wavelength` (if present in the data).\n",
+ "\n",
+ "## Displaying individual detector elements\n",
+ "\n",
+ "It is also possible to view a single detector element, selecting e.g. `mantle` from the original data:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "b417011e-0d12-4287-91d5-c1fb6ecc7cac",
+ "metadata": {
+ "editable": true,
+ "slideshow": {
+ "slide_type": ""
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "mantle_view = dream.instrument_view(dg['mantle'].hist(wavelength=50), dim='wavelength')\n",
+ "mantle_view"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "299ec404-fb18-4533-ad96-e23bf8ba24d6",
+ "metadata": {
+ "editable": true,
+ "nbsphinx": "hidden",
+ "slideshow": {
+ "slide_type": ""
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "mantle_view[1].controls['wavelength']['slider'].value = 43"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "1df1aa56-5251-4555-a4f4-283145747198",
+ "metadata": {},
+ "source": [
+ "The instrument view is designed to be flexible in terms of what it accepts as input.\n",
+ "This means that you can easily inspect, for example, a single module by using the usual slicing notation for data arrays.\n",
+ "\n",
+ "Below, we display the first module in the backward end-cap detector:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "0c86e491-3564-498d-9232-39485f5b95d7",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "dream.instrument_view(dg['endcap_backward']['module', 0].hist(tof=1))"
+ ]
+ }
+ ],
+ "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
+}

docs/instruments/dream/dream.rst

@@ -0,0 +1,7 @@
+DREAM
+=====
+
+.. toctree::
+ :maxdepth: 4
+
+ dream-instrument-view

environment.yml

@@ -20,7 +20,7 @@ dependencies:
  - pandas=2.0.3
  - pandoc=3.1.3
  - pip=23.2.1
- - plopp=23.09.0
+ - plopp=23.10.1
  - pooch=1.7.0
  - pytest=7.4.0
  - python=3.8.*

src/ess/__init__.py

@@ -10,5 +10,5 @@
 except importlib.metadata.PackageNotFoundError:
  __version__ = "0.0.0"
 
-from . import logging
+from . import data, logging
 from .logging import get_logger

src/ess/amor/data.py

@@ -1,33 +1,16 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-_version = '1'
 
-__all__ = ['get_path']
 
+from ..data import Registry
 
-def _make_pooch():
- import pooch
+_registry = Registry(
+ instrument='amor',
+ files={
+ "reference.nxs": "md5:56d493c8051e1c5c86fb7a95f8ec643b",
+ "sample.nxs": "md5:4e07ccc87b5c6549e190bc372c298e83",
+ },
+ version='1',
+)
 
- return pooch.create(
- path=pooch.os_cache('ess/amor'),
- env='ESS_AMOR_DATA_DIR',
- base_url='https://public.esss.dk/groups/scipp/ess/amor/{version}/',
- version=_version,
- registry={
- "reference.nxs": "md5:56d493c8051e1c5c86fb7a95f8ec643b",
- "sample.nxs": "md5:4e07ccc87b5c6549e190bc372c298e83",
- },
- )
-
-
-_pooch = _make_pooch()
-
-
-def get_path(name: str) -> str:
- """
- Return the path to a data file bundled with scippneutron.
-
- This function only works with example data and cannot handle
- paths to custom files.
- """
- return _pooch.fetch(name)
+get_path = _registry.get_path

src/ess/data.py

@@ -0,0 +1,35 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
+
+from typing import Dict
+
+__all__ = ['Registry']
+
+
+class Registry:
+ def __init__(self, instrument: str, files: Dict[str, str], version: str):
+ import pooch
+
+ self._registry = pooch.create(
+ path=pooch.os_cache(f'ess/{instrument}'),
+ env=f'ESS_{instrument.upper()}_DATA_DIR',
+ base_url=f'https://public.esss.dk/groups/scipp/ess/{instrument}/'
+ + '{version}/',
+ version=version,
+ registry=files,
+ )
+
+ def get_path(self, name: str, unzip: bool = False) -> str:
+ """
+ Get the path to a file in the registry.
+
+ Parameters
+ ----------
+ name:
+ Name of the file to get the path for.
+ unzip:
+ If `True`, unzip the file before returning the path.
+ """
+ import pooch
+
+ return self._registry.fetch(name, processor=pooch.Unzip() if unzip else None)

src/ess/dream/__init__.py

@@ -2,6 +2,7 @@
 # Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
 
 from . import data
+from .instrument_view import instrument_view
 from .io import load_geant4_csv
 
-__all__ = ['data', 'load_geant4_csv']
+__all__ = ['data', 'instrument_view', 'load_geant4_csv']