diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index bcb36aefe..029ae84ca 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -82,6 +82,15 @@ jobs: - '.github/workflows/ci.yml' - '.pre-commit-config.yaml' - '.python-version' + essspectroscopy: + - 'packages/essspectroscopy/**' + - 'packages/essreduce/**' + - 'pyproject.toml' + - 'pixi.lock' + - 'pixi.toml' + - '.github/workflows/ci.yml' + - '.pre-commit-config.yaml' + - '.python-version' formatting: name: Formatting and static analysis diff --git a/.github/workflows/docs-deploy.yml b/.github/workflows/docs-deploy.yml index 78a4f5813..2d3c4eef8 100644 --- a/.github/workflows/docs-deploy.yml +++ b/.github/workflows/docs-deploy.yml @@ -14,6 +14,7 @@ on: - essdiffraction - essreflectometry - esssans + - essspectroscopy publish: default: false type: boolean diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml index e56c9bd8d..6329226b2 100644 --- a/.github/workflows/nightly.yml +++ b/.github/workflows/nightly.yml @@ -22,6 +22,7 @@ jobs: - essdiffraction - essreflectometry - esssans + - essspectroscopy runs-on: ubuntu-24.04 steps: - uses: actions/checkout@v6 diff --git a/.github/workflows/weekly-platform.yml b/.github/workflows/weekly-platform.yml index 6c59d4056..c98946534 100644 --- a/.github/workflows/weekly-platform.yml +++ b/.github/workflows/weekly-platform.yml @@ -23,6 +23,7 @@ jobs: - essdiffraction - essreflectometry - esssans + - essspectroscopy runs-on: ${{ matrix.os }} steps: - uses: actions/checkout@v6 diff --git a/packages/essspectroscopy/.copier-answers.ess.yml b/packages/essspectroscopy/.copier-answers.ess.yml new file mode 100644 index 000000000..80b1d1f03 --- /dev/null +++ b/packages/essspectroscopy/.copier-answers.ess.yml @@ -0,0 +1,3 @@ +# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY +_commit: 34ca4ba +_src_path: https://github.com/scipp/ess_template.git diff --git a/packages/essspectroscopy/.copier-answers.yml b/packages/essspectroscopy/.copier-answers.yml new file mode 100644 index 000000000..939c42603 --- /dev/null +++ b/packages/essspectroscopy/.copier-answers.yml @@ -0,0 +1,13 @@ +# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY +_commit: 024a41b +_src_path: gh:scipp/copier_template +description: 'Spectroscopy data reduction for the European Spallation Source ' +max_python: '3.13' +min_python: '3.11' +namespace_package: ess +nightly_deps: scipp,scippneutron,sciline,plopp,scippnexus,essreduce +orgname: scipp +prettyname: ESSspectroscopy +projectname: essspectroscopy +related_projects: Scipp,ScippNeutron,ScippNexus,Plopp,Sciline,ESSreduce +year: 2025 diff --git a/packages/essspectroscopy/README.md b/packages/essspectroscopy/README.md new file mode 100644 index 000000000..31b2cf263 --- /dev/null +++ b/packages/essspectroscopy/README.md @@ -0,0 +1,16 @@ +[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md) +[![PyPI badge](http://img.shields.io/pypi/v/essspectroscopy.svg)](https://pypi.python.org/pypi/essspectroscopy) +[![Conda Badge](https://img.shields.io/conda/v/conda-forge/essspectroscopy)](https://anaconda.org/conda-forge/essspectroscopy) +[![License: BSD 3-Clause](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](LICENSE) + +# ESSspectroscopy + +## About + +Spectroscopy data reduction for the European Spallation Source + +## Installation + +```sh +python -m pip install essspectroscopy +``` diff --git a/packages/essspectroscopy/docs/_static/anaconda-icon.js b/packages/essspectroscopy/docs/_static/anaconda-icon.js new file mode 100644 index 000000000..024350ec0 --- /dev/null +++ b/packages/essspectroscopy/docs/_static/anaconda-icon.js @@ -0,0 +1,13 @@ +FontAwesome.library.add( + (faListOldStyle = { + prefix: "fa-custom", + iconName: "anaconda", + icon: [ + 67.65, // viewBox width + 67.500267, // viewBox height + [], // ligature + "e001", // unicode codepoint - private use area + 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+++ b/packages/essspectroscopy/docs/_static/favicon.svg @@ -0,0 +1,59 @@ + + + + + + + + + + + + image/svg+xml + + + + + + + + + + diff --git a/packages/essspectroscopy/docs/_static/logo-dark.svg b/packages/essspectroscopy/docs/_static/logo-dark.svg new file mode 100644 index 000000000..6a34c889c --- /dev/null +++ b/packages/essspectroscopy/docs/_static/logo-dark.svg @@ -0,0 +1,46 @@ + + + + + + + + + image/svg+xml + + + + + + + + + + diff --git a/packages/essspectroscopy/docs/_static/logo.svg b/packages/essspectroscopy/docs/_static/logo.svg new file mode 100644 index 000000000..83464e051 --- /dev/null +++ b/packages/essspectroscopy/docs/_static/logo.svg @@ -0,0 +1,46 @@ + + + + + + + + + image/svg+xml + + + + + + + + + + diff --git a/packages/essspectroscopy/docs/_static/thumbnails/bifrost_reduction_dark.svg b/packages/essspectroscopy/docs/_static/thumbnails/bifrost_reduction_dark.svg new file mode 100644 index 000000000..20ab39378 --- /dev/null +++ b/packages/essspectroscopy/docs/_static/thumbnails/bifrost_reduction_dark.svg @@ -0,0 +1,641 @@ + + + + + + + + 2025-05-28T10:11:53.653853 + image/svg+xml + + + Matplotlib v3.10.3, https://matplotlib.org/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/packages/essspectroscopy/docs/_static/thumbnails/bifrost_reduction_light.svg 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+ + + + + + + + + + + diff --git a/packages/essspectroscopy/docs/_templates/class-template.rst b/packages/essspectroscopy/docs/_templates/class-template.rst new file mode 100644 index 000000000..0200267d2 --- /dev/null +++ b/packages/essspectroscopy/docs/_templates/class-template.rst @@ -0,0 +1,31 @@ +{{ fullname | escape | underline }} + +.. currentmodule:: {{ module }} + +.. autoclass:: {{ objname }} + :members: + :special-members: __getitem__ + + {% block methods %} + .. automethod:: __init__ + + {% if methods %} + .. rubric:: {{ _('Methods') }} + + .. autosummary:: + {% for item in methods %} + ~{{ name }}.{{ item }} + {%- endfor %} + {% endif %} + {% endblock %} + + {% block attributes %} + {% if attributes %} + .. rubric:: {{ _('Attributes') }} + + .. autosummary:: + {% for item in attributes %} + ~{{ name }}.{{ item }} + {%- endfor %} + {% endif %} + {% endblock %} diff --git a/packages/essspectroscopy/docs/_templates/doc_version.html b/packages/essspectroscopy/docs/_templates/doc_version.html new file mode 100644 index 000000000..005018ac3 --- /dev/null +++ b/packages/essspectroscopy/docs/_templates/doc_version.html @@ -0,0 +1,2 @@ + +Current ESSspectroscopy version: {{ version }} (older versions). diff --git a/packages/essspectroscopy/docs/_templates/module-template.rst b/packages/essspectroscopy/docs/_templates/module-template.rst new file mode 100644 index 000000000..6fee8d776 --- /dev/null +++ b/packages/essspectroscopy/docs/_templates/module-template.rst @@ -0,0 +1,66 @@ +{{ fullname | escape | underline}} + +.. automodule:: {{ fullname }} + + {% block attributes %} + {% if attributes %} + .. rubric:: {{ _('Module Attributes') }} + + .. autosummary:: + :toctree: + {% for item in attributes %} + {{ item }} + {%- endfor %} + {% endif %} + {% endblock %} + + {% block functions %} + {% if functions %} + .. rubric:: {{ _('Functions') }} + + .. autosummary:: + :toctree: + {% for item in functions %} + {{ item }} + {%- endfor %} + {% endif %} + {% endblock %} + + {% block classes %} + {% if classes %} + .. rubric:: {{ _('Classes') }} + + .. autosummary:: + :toctree: + :template: class-template.rst + {% for item in classes %} + {{ item }} + {%- endfor %} + {% endif %} + {% endblock %} + + {% block exceptions %} + {% if exceptions %} + .. rubric:: {{ _('Exceptions') }} + + .. autosummary:: + :toctree: + {% for item in exceptions %} + {{ item }} + {%- endfor %} + {% endif %} + {% endblock %} + +{% block modules %} +{% if modules %} +.. rubric:: Modules + +.. autosummary:: + :toctree: + :template: module-template.rst + :recursive: +{% for item in modules %} + {{ item }} +{%- endfor %} +{% endif %} +{% endblock %} diff --git a/packages/essspectroscopy/docs/about/index.md b/packages/essspectroscopy/docs/about/index.md new file mode 100644 index 000000000..20b55ae6c --- /dev/null +++ b/packages/essspectroscopy/docs/about/index.md @@ -0,0 +1,26 @@ +# About + +## Development + +ESSspectroscopy is an open source project by the [European Spallation Source ERIC](https://ess.eu/) (ESS). + +## License + +ESSspectroscopy is available as open source under the [BSD-3 license](https://opensource.org/license/BSD-3-Clause). + +## Citing ESSspectroscopy + +Please cite the following: + +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14943875.svg)](https://zenodo.org/doi/10.5281/zenodo.14943875) + +To cite a specific version of ESSspectroscopy, select the desired version on Zenodo to get the corresponding DOI. + +## Older versions of the documentation + +Older versions of the documentation pages can be found under the assets of each [release](https://github.com/scipp/essspectroscopy/releases). +Simply download the archive, unzip and view locally in a web browser. + +## Source code and development + +ESSspectroscopy is hosted and developed [on GitHub](https://github.com/scipp/essspectroscopy). diff --git a/packages/essspectroscopy/docs/api-reference/index.md b/packages/essspectroscopy/docs/api-reference/index.md new file mode 100644 index 000000000..89bd3abcc --- /dev/null +++ b/packages/essspectroscopy/docs/api-reference/index.md @@ -0,0 +1,50 @@ +# API Reference + +## Workflows + +### BIFROST + +```{eval-rst} +.. currentmodule:: ess.bifrost + +.. autosummary:: + :toctree: ../generated/functions + :recursive: + + BifrostWorkflow + BifrostSimulationWorkflow +``` + +## Spectroscopy + +```{eval-rst} +.. currentmodule:: ess.spectroscopy + +.. autosummary:: + :toctree: ../generated/modules + :template: module-template.rst + :recursive: + + indirect + types +``` + +## BIFROST + +```{eval-rst} +.. currentmodule:: ess.bifrost + +.. autosummary:: + :toctree: ../generated/modules + :template: module-template.rst + :recursive: + + cutting + data + detector + io + live + normalization + types + workflow +``` diff --git a/packages/essspectroscopy/docs/conf.py b/packages/essspectroscopy/docs/conf.py new file mode 100644 index 000000000..f17535407 --- /dev/null +++ b/packages/essspectroscopy/docs/conf.py @@ -0,0 +1,279 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +import doctest +import os +import sys +from importlib.metadata import PackageNotFoundError +from importlib.metadata import version as get_version + +from sphinx.util import logging + +sys.path.insert(0, os.path.abspath('.')) + +logger = logging.getLogger(__name__) + +# General information about the project. +project = 'ESSspectroscopy' +copyright = '2025 Scipp contributors' +author = 'Scipp contributors' + +html_show_sourcelink = True + +extensions = [ + 'sphinx.ext.autodoc', + 'sphinx.ext.autosummary', + 'sphinx.ext.doctest', + 'sphinx.ext.githubpages', + 'sphinx.ext.intersphinx', + 'sphinx.ext.mathjax', + 'sphinx.ext.napoleon', + 'sphinx.ext.viewcode', + 'sphinx_autodoc_typehints', + 'sphinx_copybutton', + 'sphinx_design', + 'sphinxcontrib.autodoc_pydantic', + 'nbsphinx', + 'myst_parser', +] + +try: + import sciline.sphinxext.domain_types # noqa: F401 + + extensions.append('sciline.sphinxext.domain_types') + # See https://github.com/tox-dev/sphinx-autodoc-typehints/issues/457 + suppress_warnings = ["config.cache"] +except ModuleNotFoundError: + pass + + +myst_enable_extensions = [ + "amsmath", + "colon_fence", + "deflist", + "dollarmath", + "fieldlist", + "html_admonition", + "html_image", + "replacements", + "smartquotes", + "strikethrough", + "substitution", + "tasklist", +] + +myst_heading_anchors = 3 + +autodoc_type_aliases = { + 'array_like': 'array_like', +} + +intersphinx_mapping = { + 'essreduce': ('https://scipp.github.io/essreduce/', None), + 'numpy': ('https://numpy.org/doc/stable/', None), + 'python': ('https://docs.python.org/3', None), + 'scipp': ('https://scipp.github.io/', None), + 'scippneutron': ('https://scipp.github.io/scippneutron/', None), +} + +# autodocs includes everything, even irrelevant API internals. autosummary +# looks more suitable in the long run when the API grows. +# For a nice example see how xarray handles its API documentation. +autosummary_generate = True + +napoleon_google_docstring = False +napoleon_numpy_docstring = True +napoleon_use_param = True +napoleon_use_rtype = False +napoleon_preprocess_types = True +napoleon_type_aliases = { + # objects without namespace: numpy + "ndarray": "~numpy.ndarray", +} +typehints_defaults = 'comma' +typehints_use_rtype = False + + +sciline_domain_types_prefix = 'ess.spectroscopy' +sciline_domain_types_aliases = { + 'scipp._scipp.core.DataArray': 'scipp.DataArray', + 'scipp._scipp.core.Dataset': 'scipp.Dataset', + 'scipp._scipp.core.DType': 'scipp.DType', + 'scipp._scipp.core.Unit': 'scipp.Unit', + 'scipp._scipp.core.Variable': 'scipp.Variable', + 'scipp.core.data_group.DataGroup': 'scipp.DataGroup', +} + + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +source_suffix = ['.rst', '.md'] +html_sourcelink_suffix = '' # Avoid .ipynb.txt extensions in sources + +# The master toctree document. +master_doc = 'index' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# + +try: + release = get_version("essspectroscopy") + version = ".".join(release.split('.')[:3]) # CalVer +except PackageNotFoundError: + logger.info( + "Warning: determining version from package metadata failed, falling back to " + "a dummy version number." + ) + release = version = "0.0.0-dev" + +warning_is_error = True + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +language = "en" + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This patterns also effect to html_static_path and html_extra_path +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints'] + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# If true, `todo` and `todoList` produce output, else they produce nothing. +todo_include_todos = False + +# -- Options for HTML output ---------------------------------------------- + +html_theme = "pydata_sphinx_theme" +html_theme_options = { + "primary_sidebar_end": ["edit-this-page", "sourcelink"], + "secondary_sidebar_items": [], + "navbar_persistent": ["search-button"], + "show_nav_level": 1, + # Adjust this to ensure external links are moved to "Move" menu + "header_links_before_dropdown": 4, + "pygment_light_style": "github-light-high-contrast", + "pygment_dark_style": "github-dark-high-contrast", + "logo": { + "image_light": "_static/logo.svg", + "image_dark": "_static/logo-dark.svg", + }, + "external_links": [ + {"name": "ESSreduce", "url": "https://scipp.github.io/essreduce"}, + {"name": "Plopp", "url": "https://scipp.github.io/plopp"}, + {"name": "Sciline", "url": "https://scipp.github.io/sciline"}, + {"name": "Scipp", "url": "https://scipp.github.io"}, + {"name": "ScippNeutron", "url": "https://scipp.github.io/scippneutron"}, + {"name": "ScippNexus", "url": "https://scipp.github.io/scippnexus"}, + ], + "icon_links": [ + { + "name": "GitHub", + "url": "https://github.com/scipp/essspectroscopy", + "icon": "fa-brands fa-github", + "type": "fontawesome", + }, + { + "name": "PyPI", + "url": "https://pypi.org/project/essspectroscopy/", + "icon": "fa-brands fa-python", + "type": "fontawesome", + }, + { + "name": "Conda", + "url": "https://anaconda.org/conda-forge/essspectroscopy", + "icon": "fa-custom fa-anaconda", + "type": "fontawesome", + }, + ], + "footer_start": ["copyright", "sphinx-version"], + "footer_end": ["doc_version", "theme-version"], +} +html_context = { + "doc_path": "docs", +} +html_sidebars = { + "**": ["sidebar-nav-bs", "page-toc"], +} + +html_title = "ESSspectroscopy" +html_logo = "_static/logo.svg" +html_favicon = "_static/favicon.svg" + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] +html_css_files = [] +html_js_files = ["anaconda-icon.js"] + +# -- Options for HTMLHelp output ------------------------------------------ + +# Output file base name for HTML help builder. +htmlhelp_basename = 'essspectroscopydoc' + +# -- Options for Matplotlib in notebooks ---------------------------------- + +nbsphinx_execute_arguments = [ + "--Session.metadata=scipp_sphinx_build=True", +] + +# -- Options for doctest -------------------------------------------------- + +# sc.plot returns a Figure object and doctest compares that against the +# output written in the docstring. But we only want to show an image of the +# figure, not its `repr`. +# In addition, there is no need to make plots in doctest as the documentation +# build already tests if those plots can be made. +# So we simply disable plots in doctests. +doctest_global_setup = ''' +import numpy as np + +try: + import scipp as sc + + def do_not_plot(*args, **kwargs): + pass + + sc.plot = do_not_plot + sc.Variable.plot = do_not_plot + sc.DataArray.plot = do_not_plot + sc.DataGroup.plot = do_not_plot + sc.Dataset.plot = do_not_plot +except ImportError: + # Scipp is not needed by docs if it is not installed. + pass +''' + +# Using normalize whitespace because many __str__ functions in scipp produce +# extraneous empty lines and it would look strange to include them in the docs. +doctest_default_flags = ( + doctest.ELLIPSIS + | doctest.IGNORE_EXCEPTION_DETAIL + | doctest.DONT_ACCEPT_TRUE_FOR_1 + | doctest.NORMALIZE_WHITESPACE +) + +# -- Options for linkcheck ------------------------------------------------ + +linkcheck_ignore = [ + # Specific lines in Github blobs cannot be found by linkcheck. + r'https?://github\.com/.*?/blob/[a-f0-9]+/.+?#', + # Linkcheck seems to be denied access by some DOI resolvers. + # Since DOIs are supposed to be permanent, we don't need to check them.' + r'https?://doi\.org/', + r'https?://zenodo\.org/', + # ESS Jira is not publicly accessible. + r'https?://jira\.ess\.eu', + r'https?://dx\.doi\.org/', +] diff --git a/packages/essspectroscopy/docs/developer/adr/0001-relegate-nxspe-support.md b/packages/essspectroscopy/docs/developer/adr/0001-relegate-nxspe-support.md new file mode 100644 index 000000000..b00f90797 --- /dev/null +++ b/packages/essspectroscopy/docs/developer/adr/0001-relegate-nxspe-support.md @@ -0,0 +1,107 @@ +# ADR 0001: Relagate NXspe support + +- Status: accepted +- Deciders: Greg, Jan-Lukas +- Date: 2024-10 + +## Context +Targeting community supported data formats will enable efficient use of existing analysis and visualization tools. +A number of histogram formats have been [listed for possible support](https://jira.ess.eu/browse/DMSCSPEC-46): +- [`NXspe`](https://jira.ess.eu/browse/DMSCSPEC-50) +- [`SQW`](https://jira.ess.eu/browse/DMSCSPEC-51) +- [`MJOLNIR`](https://jira.ess.eu/browse/DMSCSPEC-52) + +### `SQW` Prioritization and Challenges + +One of which, [`SQW`](https://github.com/scipp/essspectroscopy/issues/23), +has been identified as higher importance because it will enable interfacing with +the PACE tools. + +The major drawback to the `SQW` format is that it is documented most thoroughly by +its `MATLAB` serialization/deserialization routines, which are less than straightforward +to replicate in part due to an extensive class hierarchy, single-source backwards +compatibility over multiple file format versions, the ability to mix definition and +implementation of functions and place either in at least three different locations +(the `rundata` helper class seems to be spread over six), +and the lack of a free IDE that can help sort out the runtime behavior. + +Recently it was posited that, since `Horace` can read `NXspe` files and produce a valid +`SQW` file from them, perhaps focusing on their output from `essspectroscopy` could +be prudent. + +### Bending `NXspe` to Indirect-Geometry Time-of-Flight +`NXspe` is the [`NeXus` application definition](https://manual.nexusformat.org/classes/applications/NXspe.html#nxspe) +implementation of the columns-of-text `SPE` data format. + +`SPE` format files contain energy-transfer (or time) histograms of intensity, +one per detector element in the instrument. +Information about the positions and sizes of the detector elements was contained in +a separate file, either `PAR` or `PHX`. +The format was defined with Direct-Geometry (DG) Time-of-Flight (TOF) spectrometers in +mind where a single incident energy applied to all data, and all detector elements +shared the same energy-transfer histogram bin edges. This information was kept +separately from the two text files, and put into analysis scripts by the user. + +`NXspe` incorporates all information contained previously in `SPE` and `PAR` files +plus minimal information that otherwise may have gone into a log book. +It represents an appreciable improvement over the previous status-quo for DG-TOF. + +For Indirect-Geometry (IG) TOF instruments with a single final neutron energy, like +back-scattering instruments, it is also possible to histogram all detector energy +spectra with a single set of bin edges. By means of a flag, `Horace` can exchange +_E_i and _E_f in early data loading calculations, and then +otherwise treat conversion more-or-less the same to produce intensity of (**_Q_**,_E_) +observations binned, not unlike `scipp`, in a coarse 4-D grid. + +The problems start, however, when not all detectors share a single final energy, +as with BIFROST. +A single incident wavelength range applies for all BIFROST detector elements, +so one _E_i bin-boundary set would naturally apply for all detectors. +But this is _far_ from fixed _E_i or fixed _E_f with a single +energy transfer, _E_, bin-boundary set. + +#### Imaginary observations +The closest BIFROST data can get to 'standard' `NXspe` _E_ binning is to stitch +together the single _E_i ranges offset by each _E_f. +This has three drawbacks +1. The number of bins per detector element will consequently be larger +2. The sizes of the bins may not match well to the 'natural' incident energy bin sizes for all detector elements +3. Imaginary observations will be created for all detector elements. + +> **Note:** +> The term imaginary is used here to indicate that no measurement was performed +> for the incident neutron energies needed to produce the _E_ in one or more bin. + +#### Natural _E_ binning +Instead, by keeping per-detector-element _E_ binning the adherence to +the `NXspe` standard can be maintained but software like `Horace` struggle to handle +such data — +the required `/entry/data/energy` becomes 2-D but `Horace` expects (and reshapes) this +data to be 1-D. + +One symptom of this incompatibility is excessive memory usage. +For the 13500 BIFROST detector elements, with energy transfer binned into 103 bins, +in an early conversion step `Horace` requires a 13500 × 104 × 13500 array +of double values, and while ∼ 141 GB is not an insurmountable value it's also +not necessary. + +In testing, moving to a machine with 256 GB of memory was not sufficient for the +conversion to proceed. And it seems likely there are more incompatible assumptions +made about the content of the data for `Horace` to successfully produce an `SQW` object +from the '`BIFROST`-`NXspe`' files. + + +## Decision +It is now possible to make `BIFROST` data conform to the `NXspe` standard published by +the NeXus Foundation, but community software that _reads_ `NXspe` is likely to have +made similar assumptions about the shape of required data as `Horace`. +So the utility of `NXspe` as a common data format is likely limited. + +_Producing_ `NXspe` may still be useful, but it can not replace direct output of +`SQW` data files. + +∴ Relegate `NXspe` to lesser-supported output formats. + +## Consequences +A fully-fledged `SQW` output method is still required, which will still pose the same +problems of construction and maintainability. diff --git a/packages/essspectroscopy/docs/developer/architecture-decision-records.md b/packages/essspectroscopy/docs/developer/architecture-decision-records.md new file mode 100644 index 000000000..7368d750d --- /dev/null +++ b/packages/essspectroscopy/docs/developer/architecture-decision-records.md @@ -0,0 +1,10 @@ +# Architecture Decision Records + +```{toctree} +--- +maxdepth: 1 +glob: true +--- + +adr/* +``` \ No newline at end of file diff --git a/packages/essspectroscopy/docs/developer/bifrost-encountered-issues.md b/packages/essspectroscopy/docs/developer/bifrost-encountered-issues.md new file mode 100644 index 000000000..eb56185ca --- /dev/null +++ b/packages/essspectroscopy/docs/developer/bifrost-encountered-issues.md @@ -0,0 +1,58 @@ +# Issues encountered during workflow development + +## Wrong sample-detector flight times +### Description +Comparing the event times when unwrapped and propagated to the sample with the normalization monitor histogram +it appeared that too much time had been removed from the recorded frame-times before unwrapping. +![Screenshot from 2024-08-27 08-24-50.png](../_static/developer/Screenshot_from_2024-08-27T08-24-50.png) + +The calculated time of flight from sample to detector had only been checked relative +to an order of magnitude estimate, which was not accurate enough. +A more careful estimate shows that neutrons hitting the central pixel of each central tube in the symmetric +geometry case should take around 3.3 μsec from sample to detector. +![Screenshot from 2024-08-27 08-20-49.png](../_static/developer/Screenshot_from_2024-08-27T08-20-49.png) + +### Cause +The sample-to-detector time-of-flight depends on the square root of the energy of the neutron, +which was calculated incorrectly due to a mistake finding the vector from the sample to the detector pixel. + +If the sample is at 0, the analyzer at A and the detector at A + D, +then the sample to analyzer vector is A and the analyzer to detector vector is D. +These two vectors were found correctly from the geometry information, but A-D was used incorrectly +for the sample to detector vector. +This then produced the wrong scattering angle, the wrong wavevector magnitude, and the wrong final energy. + +### Resolution +Correcting the calculation also corrected the per detector pixel energies +![Screenshot from 2024-08-27 10-54-08.png](../_static/developer/Screenshot_from_2024-08-27T10-54-08.png) + +The calculated sample-to-detector time-of-flights are consistent with the limited hand calculated values +![Screenshot from 2024-08-27 10-55-10.png](../_static/developer/Screenshot_from_2024-08-27T10-55-10.png) + +And the unwrapped time-at-sample seems more consistent with the monitor histogram. +![Screenshot from 2024-08-27 10-56-40.png](../_static/developer/Screenshot_from_2024-08-27T10-56-40.png) + + +## Wrong pixel indexing? +### Description +Events from purely elastic scattering appear to slant the wrong way when displayed as in-frame time versus detector +pixel number. +In each block of 2700 pixels, the first and last 900 pixels have the same flight path lengths, +but the first is lower energy and the last higher energy than the central 900. +This should mean that the first 900 pixel's events arrive at a later time-of-flight and later in-frame time +(barring wrap-around at the frame boundary). + +Instead, the opposite is shown +![Screenshot from 2024-08-28 08-12-56.png](../_static/developer/Screenshot_from_2024-08-28T08-12-56.png) + +### Cause +This could indicate a problem with the read geometry per pixel, but that seems unlikely given +that the final energy per pixel is now correct (see above). +Therefore, the likely culprit lies somewhere in the conversion to pixel indexing from charge division +in the McStas simulation or EFU binary, +or from EFU pixel identifiers to position in the moreniius translation of McStas to NeXus. + +### Solution +The charge division was, effectively, reversed by switching the `A` and `B` values used in the McStas simulations. +This seems to have fixed the problem, and highlights the need to systematically verify the meaning of signals +through all stages of the real instrument. diff --git a/packages/essspectroscopy/docs/developer/coding-conventions.md b/packages/essspectroscopy/docs/developer/coding-conventions.md new file mode 100644 index 000000000..4fafc18db --- /dev/null +++ b/packages/essspectroscopy/docs/developer/coding-conventions.md @@ -0,0 +1,117 @@ +# Coding conventions + +## Code formatting + +There are no explicit code formatting conventions since we use `ruff` to enforce a format. + +## Docstring format + +We use the [NumPy docstring format](https://www.sphinx-doc.org/en/master/usage/extensions/example_numpy.html). +We use `sphinx-autodocs-typehints` to automatically insert type hints into the docstrings. +Our format thus deviates from the default NumPy example given by the link above. +Docstrings should therefore be laid out as follows, including spacing and punctuation: + +```python + +def foo(x: int, y: float) -> float: + """Short description. + + Long description. + + With multiple paragraphs. + + Warning + ------- + Be careful! + + Parameters + ---------- + x: + First input. + y: + Second input. + + Returns + ------- + : + The result. + + Raises + ------ + ValueError + If the input is bad. + IndexError + If some lookup failed. + + See Also + -------- + scitacean.bar: + A bit less foo. + + Examples + -------- + This is how to use it: + + >>> foo(1, 2) + 3 + + And also: + + >>> foo(1, 3) + 6 + """ +``` + +The order of sections is fixed as shown in the example. + +- **Short description** (*required*) A single sentence describing the purpose of the function / class. +- **Long description** (*optional*) One or more paragraphs of detailed explanations. + Can include additional sections like `Warning` or `Hint`. +- **Parameters** (*required for functions*) List of all function arguments including their name but not their type. + Listing arguments like this can seem ridiculous if the explanation is as devoid of content as in the example. + But it is still required in order for sphinx to show the types. +- **Returns** (*required for functions*) Description of the return value. + Required for the same reason as the parameter list. + + For a single return value, neither a name nor type should be given. + But a colon is required as in the example above in order to produce proper formatting. + + For multiple return values, to produce proper formatting, + both name and type must be given even though the latter repeats the type annotation: + + ```python + + """ + Returns + ------- + n: int + The first return value. + z: float + The second return value. + """ + ``` + +- **Raises** (*optional*) We generally do not document what exceptions can be raised from a function. + But if there are some important cases, this section can list those exceptions with an explanation + of when the exception is raised. + The exception type is required. + Note that there are no colons here. +- **See Also** (*optional*) List of related functions and/or classes. + The function/class name should include the module it is in but without reST markup. + For simple cases, the explanation can be left out. + In this case, the colon should be omitted as well and multiple entries must be separated by commas. +- **Examples** (*optional*) Example code given using `>>>` as the Python prompt. + May include text before, after, and between code blocks. + Note the spacing in the example. + +Some functions can be sufficiently described by a single sentence. +In this case, the 'Parameters' and 'Returns' sections may be omitted and the docstring should be laid out on a single line. +If it does not fit on a single line, it is too complicated. +For example + +```python +def bar(self) -> int: + """Returns the number of dimensions.""" +``` + +Note that the argument types are not shown in the rendered documentation. diff --git a/packages/essspectroscopy/docs/developer/dependency-management.md b/packages/essspectroscopy/docs/developer/dependency-management.md new file mode 100644 index 000000000..7d9ddca08 --- /dev/null +++ b/packages/essspectroscopy/docs/developer/dependency-management.md @@ -0,0 +1,13 @@ +# Dependency management + +essspectroscopy is a library, so the package dependencies are never pinned. +Lower bounds are fine and individual versions can be excluded. +See, e.g., [Should You Use Upper Bound Version Constraints](https://iscinumpy.dev/post/bound-version-constraints/) for an explanation. + +Development dependencies (as opposed to dependencies of the deployed package that users need to install) are pinned to an exact version in order to ensure reproducibility. +This also includes dependencies used for the various CI builds. +This is done by specifying packages (and potential version constraints) in `requirements/*.in` files and locking those dependencies using [pip-compile-multi](https://pip-compile-multi.readthedocs.io/en/latest/index.html) to produce `requirements/*.txt` files. +Those files are then used by [tox](https://tox.wiki/en/latest/) to create isolated environments and run tests, build docs, etc. + +`tox` can be cumbersome to use for local development. +Therefore `requirements/dev.txt` can be used to create a virtual environment with all dependencies. diff --git a/packages/essspectroscopy/docs/developer/getting-started.md b/packages/essspectroscopy/docs/developer/getting-started.md new file mode 100644 index 000000000..a76675116 --- /dev/null +++ b/packages/essspectroscopy/docs/developer/getting-started.md @@ -0,0 +1,91 @@ +# Getting started + +## Setting up + +### Dependencies + +Development dependencies are specified in `requirements/dev.txt` and can be installed using (see [Dependency Management](./dependency-management.md) for more information) + +```sh +pip install -r requirements/dev.txt +``` + +Additionally, building the documentation requires [pandoc](https://pandoc.org/) which is not on PyPI and needs to be installed through other means, e.g. with your OS package manager. + +### Install the package + +Install the package in editable mode using + +```sh +pip install -e . +``` + +### Set up git hooks + +The CI pipeline runs a number of code formatting and static analysis tools. +If they fail, a build is rejected. +To avoid that, you can run the same tools locally. +This can be done conveniently using [pre-commit](https://pre-commit.com/): + +```sh +pre-commit install +``` + +Alternatively, if you want a different workflow, take a look at ``tox.ini`` or ``.pre-commit.yaml`` to see what tools are run and how. + +## Running tests + +`````{tab-set} +````{tab-item} tox +Run the tests using + +```sh +tox -e py311 +``` + +(or just `tox` if you want to run all environments). + +```` +````{tab-item} Manually +Run the tests using + +```sh +python -m pytest +``` +```` +````` + +## Building the docs + +`````{tab-set} +````{tab-item} tox +Build the documentation using + +```sh +tox -e docs +``` + +This builds the docs and also runs `doctest`. +`linkcheck` can be run separately using + +```sh +tox -e linkcheck +``` +```` + +````{tab-item} Manually + +Build the documentation using + +```sh +python -m sphinx -v -b html -d .tox/docs_doctrees docs html +``` + +Additionally, test the documentation using + +```sh +python -m sphinx -v -b doctest -d .tox/docs_doctrees docs html +python -m sphinx -v -b linkcheck -d .tox/docs_doctrees docs html +``` +```` +````` \ No newline at end of file diff --git a/packages/essspectroscopy/docs/developer/index.md b/packages/essspectroscopy/docs/developer/index.md new file mode 100644 index 000000000..c735c424f --- /dev/null +++ b/packages/essspectroscopy/docs/developer/index.md @@ -0,0 +1,18 @@ +# Development + +```{include} ../../CONTRIBUTING.md +``` + +## Table of contents + +```{toctree} +--- +maxdepth: 2 +--- + +getting-started +coding-conventions +dependency-management +architecture-decision-records +bifrost-encountered-issues +``` diff --git a/packages/essspectroscopy/docs/index.md b/packages/essspectroscopy/docs/index.md new file mode 100644 index 000000000..fc93fa8a0 --- /dev/null +++ b/packages/essspectroscopy/docs/index.md @@ -0,0 +1,60 @@ +:::{image} _static/logo.svg +:class: only-light +:alt: ESSspectroscopy +:width: 60% +:align: center +::: +:::{image} _static/logo-dark.svg +:class: only-dark +:alt: ESSspectroscopy +:width: 60% +:align: center +::: + +```{raw} html + +``` + +```{role} transparent +``` + +# {transparent}`ESSspectroscopy` + +
+ Spectroscopy data reduction for the European Spallation Source +

+
+ +## Quick links + +::::{grid} 3 + +:::{grid-item-card} BIFROST +:link: user-guide/bifrost/index.md + +::: + +:::: + +:::{include} user-guide/installation.md +:heading-offset: 1 +::: + +## Get in touch + +- If you have questions that are not answered by these documentation pages, ask on [discussions](https://github.com/scipp/essspectroscopy/discussions). Please include a self-contained reproducible example if possible. +- Report bugs (including unclear, missing, or wrong documentation!), suggest features or view the source code [on GitHub](https://github.com/scipp/essspectroscopy). + +```{toctree} +--- +hidden: +--- + +user-guide/index +api-reference/index +developer/index +about/index +``` diff --git a/packages/essspectroscopy/docs/user-guide/bifrost/bifrost-bragg-peak-monitor.ipynb b/packages/essspectroscopy/docs/user-guide/bifrost/bifrost-bragg-peak-monitor.ipynb new file mode 100644 index 000000000..b8eaf3d8f --- /dev/null +++ b/packages/essspectroscopy/docs/user-guide/bifrost/bifrost-bragg-peak-monitor.ipynb @@ -0,0 +1,197 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": {}, + "source": [ + "# BIFROST Bragg peak monitor\n", + "\n", + "This notebook demonstrates how to process data for BIFROST's Bragg peak monitor.\n", + "It uses a dedicated single crystal diffraction workflow to construct a map in Q and an interactive slicer plot." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1", + "metadata": {}, + "outputs": [], + "source": [ + "import numpy as np\n", + "import scippnexus as snx\n", + "\n", + "from ess.bifrost.data import (\n", + " simulated_elastic_incoherent_with_phonon,\n", + " lookup_table_simulation,\n", + ")\n", + "from ess.bifrost.single_crystal import BifrostSimulationBraggPeakMonitorWorkflow, make_q_map\n", + "from ess.bifrost.single_crystal.types import *\n", + "from ess.bifrost.types import McStasRawDetector\n", + "from ess.reduce.unwrap import DetectorLtotal\n", + "from ess.spectroscopy.types import *" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2", + "metadata": {}, + "outputs": [], + "source": [ + "%matplotlib widget" + ] + }, + { + "cell_type": "markdown", + "id": "3", + "metadata": {}, + "source": [ + "Build a workflow for processing the data:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4", + "metadata": {}, + "outputs": [], + "source": [ + "workflow = BifrostSimulationBraggPeakMonitorWorkflow()\n", + "workflow[Filename[SampleRun]] = simulated_elastic_incoherent_with_phonon()\n", + "workflow[LookupTableFilename] = lookup_table_simulation()\n", + "workflow[LookupTableRelativeErrorThreshold] = {\n", + " 'detector': np.inf,\n", + " 'normalization_monitor': np.inf,\n", + "}" + ] + }, + { + "cell_type": "markdown", + "id": "5", + "metadata": {}, + "source": [ + "
\n", + "\n", + "**Attention**\n", + "\n", + "The current tests data does not contain a bragg peak monitor.\n", + "So we instead use a bank ('triplet') of the regular inelastic detector.\n", + "This means that the workflow can run, but the results don't show any bragg peaks.\n", + "\n", + "
" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6", + "metadata": {}, + "outputs": [], + "source": [ + "workflow[NeXusDetectorName] = \"channel_9_5_triplet\"\n", + "\n", + "\n", + "def assemble_detector_data_flatten(\n", + " detector: EmptyDetector[RunType],\n", + " data: NeXusData[snx.NXdetector, RunType],\n", + ") -> McStasRawDetector[RunType]:\n", + " from ess.reduce.nexus.workflow import assemble_detector_data as assemble\n", + " base = assemble(detector, data)\n", + "\n", + " # The monitor only has one pixel, so combine all pixels from the selected bank:\n", + " monitor = base.bins.concat()\n", + " monitor.coords['detector_number'] = sc.index(0)\n", + " # Halfway between the bank and the sample:\n", + " monitor.coords['position'] = base.coords['position'].mean() / 2\n", + " # Zero out the y-component because the monitor is in the sample plane:\n", + " monitor.coords['position'].fields.y = sc.scalar(0.0, unit=monitor.coords['position'].unit)\n", + " return McStasRawDetector[RunType](monitor)\n", + "\n", + "\n", + "def detector_ltotal_from_straight_line_approximation(\n", + " detector_beamline: RawDetector[RunType],\n", + " source_position: Position[snx.NXsource, RunType],\n", + " sample_position: Position[snx.NXsample, RunType],\n", + " gravity: GravityVector,\n", + ") -> DetectorLtotal[RunType]:\n", + " from ess.reduce.unwrap import to_wavelength\n", + " return to_wavelength.detector_ltotal_from_straight_line_approximation(\n", + " detector_beamline, # type: ignore[arg-type]\n", + "\n", + " source_position=source_position,\n", + " sample_position=sample_position,\n", + " gravity=gravity,\n", + " )\n", + "\n", + "\n", + "workflow.insert(assemble_detector_data_flatten)\n", + "workflow.insert(detector_ltotal_from_straight_line_approximation)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7", + "metadata": {}, + "outputs": [], + "source": [ + "workflow.visualize(CountsWithQMapCoords[SampleRun], graph_attr={\"rankdir\": \"LR\"})" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8", + "metadata": {}, + "outputs": [], + "source": [ + "counts = workflow.compute(CountsWithQMapCoords[SampleRun])" + ] + }, + { + "cell_type": "markdown", + "id": "9", + "metadata": {}, + "source": [ + "Make an interactive figure.\n", + "Use the slider to select a range in $Q$ to integrate over and display in the 1D figure." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "10", + "metadata": {}, + "outputs": [], + "source": [ + "make_q_map(counts,\n", + " q_parallel_bins=sc.linspace('Q_parallel', -4.5, 4.5, 100, unit='1/Ã…'),\n", + " q_perpendicular_bins=sc.linspace('Q_perpendicular', -4.5, 4.5, 100, unit='1/Ã…'),\n", + " sample_rotation_bins=sc.scalar(1.0, unit='deg'),\n", + " )" + ] + } + ], + "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": "3.11.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/packages/essspectroscopy/docs/user-guide/bifrost/bifrost-make-wavelength-lookup-table.ipynb b/packages/essspectroscopy/docs/user-guide/bifrost/bifrost-make-wavelength-lookup-table.ipynb new file mode 100644 index 000000000..716cfac51 --- /dev/null +++ b/packages/essspectroscopy/docs/user-guide/bifrost/bifrost-make-wavelength-lookup-table.ipynb @@ -0,0 +1,255 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": {}, + "source": [ + "# Create a wavelength lookup table for BIFROST\n", + "\n", + "This notebook shows how to create a wavelength lookup table for frame unwrapping at BIFROST." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1", + "metadata": {}, + "outputs": [], + "source": [ + "from ess.reduce import nexus\n", + "import sciline\n", + "import scipp as sc\n", + "from scippneutron.conversion.graph import beamline as beamline_graph\n", + "import scippnexus as snx\n", + "from ess.reduce.nexus.types import AnyRun, RawChoppers, DiskChoppers\n", + "from ess.reduce.unwrap.lut import (\n", + " LtotalRange,\n", + " NumberOfSimulatedNeutrons,\n", + " SourcePosition,\n", + " LookupTableWorkflow,\n", + ")\n", + "from scippneutron.chopper import DiskChopper\n", + "\n", + "from ess.bifrost import BifrostSimulationWorkflow\n", + "from ess.bifrost.data import simulated_elastic_incoherent_with_phonon\n", + "from ess.spectroscopy.types import *" + ] + }, + { + "cell_type": "markdown", + "id": "2", + "metadata": {}, + "source": [ + "## Load and process beamline parameters\n", + "\n", + "First, load all required beamline parameters from an input NeXus file.\n", + "We only need to know the geometry up to the sample which is the same for all banks, so choosing a single detector is enough." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3", + "metadata": {}, + "outputs": [], + "source": [ + "input_filename = simulated_elastic_incoherent_with_phonon()\n", + "with snx.File(input_filename) as f:\n", + " detector_names = list(f['entry/instrument'][snx.NXdetector])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4", + "metadata": {}, + "outputs": [], + "source": [ + "bifrost_workflow = BifrostSimulationWorkflow(detector_names)\n", + "bifrost_workflow[Filename[SampleRun]] = input_filename\n", + "\n", + "M = nexus.types.EmptyMonitor[SampleRun, NormalizationMonitor]\n", + "C = RawChoppers[SampleRun]\n", + "SOURCE = Position[snx.NXsource, SampleRun]\n", + "SAMPLE = Position[snx.NXsample, SampleRun]\n", + "choppers, monitor, sample_position, source_position = bifrost_workflow.compute((C, M, SAMPLE, SOURCE)).values()\n", + "detector = sciline.compute_mapped(bifrost_workflow, EmptyDetector[SampleRun])[0]" + ] + }, + { + "cell_type": "markdown", + "id": "5", + "metadata": {}, + "source": [ + "Compute the required distance range to include the monitor and all detectors.\n", + "Strictly speaking, we only need the range from the chosen monitor up to the Bragg peak monitor as we unwrap the regular detector data at the sample position.\n", + "But this implementation is simpler and should work fine." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6", + "metadata": {}, + "outputs": [], + "source": [ + "graph = {\n", + " **beamline_graph.beamline(scatter=True),\n", + " 'sample_position': lambda: sample_position,\n", + " 'source_position': lambda: source_position,\n", + "}\n", + "\n", + "l_monitor = sc.norm(source_position - monitor.coords['position'])\n", + "l_min = l_monitor\n", + "l_max = detector.transform_coords('Ltotal', graph=graph).coords['Ltotal'].max()" + ] + }, + { + "cell_type": "markdown", + "id": "7", + "metadata": {}, + "source": [ + "The choppers in the simulated file need to be processed before they can be used for computing a lookup table.\n", + "The following works for the specific simulation but is **not** usable in general." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8", + "metadata": {}, + "outputs": [], + "source": [ + "def extract_chopper_plateau(chopper):\n", + " processed = chopper.copy()\n", + " # These are constant in the simulated data.\n", + " processed['rotation_speed'] = processed['rotation_speed'].data.mean()\n", + " processed['phase'] = processed['phase'].data.mean()\n", + " # Guessing here as this is not stored in the file.\n", + " processed['beam_position'] = sc.scalar(0.0, unit='deg')\n", + "\n", + " # FIXME Get rid of this bad hack if/when McStas' DiskChopper is fixed\n", + " # Currently, it sets a delay-time by `delta = 2 * pi * phase/|frequency|`\n", + " # But it should set `delta = 2 * pi * phase / frequency`\n", + " # So phases reported here have the wrong sign if frequency < 0\n", + " processed['phase'] = -processed['phase'] if processed['rotation_speed'].value < 0 else processed['phase']\n", + "\n", + " return DiskChopper.from_nexus(processed)\n", + "\n", + "\n", + "disk_choppers = choppers.apply(extract_chopper_plateau)" + ] + }, + { + "cell_type": "markdown", + "id": "9", + "metadata": {}, + "source": [ + "## Compute the lookup table" + ] + }, + { + "cell_type": "markdown", + "id": "10", + "metadata": {}, + "source": [ + "Construct a lookup table workflow:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "11", + "metadata": {}, + "outputs": [], + "source": [ + "workflow = LookupTableWorkflow()\n", + "workflow[DiskChoppers[AnyRun]] = disk_choppers\n", + "workflow[LtotalRange] = (l_min, l_max)\n", + "workflow[SourcePosition] = source_position\n", + "\n", + "# Increase this number for more reliable results:\n", + "workflow[NumberOfSimulatedNeutrons] = 6_000_000" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "12", + "metadata": {}, + "outputs": [], + "source": [ + "workflow.visualize(LookupTable, graph_attr={\"rankdir\": \"LR\"})" + ] + }, + { + "cell_type": "markdown", + "id": "13", + "metadata": {}, + "source": [ + "Compute a lookup table:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "14", + "metadata": {}, + "outputs": [], + "source": [ + "table = workflow.compute(LookupTable)\n", + "table" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "15", + "metadata": {}, + "outputs": [], + "source": [ + "table.plot()" + ] + }, + { + "cell_type": "markdown", + "id": "16", + "metadata": {}, + "source": [ + "## Save to file" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "17", + "metadata": {}, + "outputs": [], + "source": [ + "table.save_hdf5('BIFROST-simulation-lookup-table.h5')" + ] + } + ], + "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": "3.11.14" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/packages/essspectroscopy/docs/user-guide/bifrost/bifrost-reduction.ipynb b/packages/essspectroscopy/docs/user-guide/bifrost/bifrost-reduction.ipynb new file mode 100644 index 000000000..497ba21cb --- /dev/null +++ b/packages/essspectroscopy/docs/user-guide/bifrost/bifrost-reduction.ipynb @@ -0,0 +1,244 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": {}, + "source": [ + "# BIFROST reduction of simulated data\n", + "\n", + "This notebook demonstrates the basic data reduction workflow for BIFROST.\n", + "It uses data that was simulated with McStas and a dedicated workflow that can process McStas data." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1", + "metadata": {}, + "outputs": [], + "source": [ + "import numpy as np\n", + "import scipp as sc\n", + "import sciline\n", + "import scippnexus as snx\n", + "\n", + "from ess import bifrost\n", + "from ess.bifrost.data import (\n", + " simulated_elastic_incoherent_with_phonon,\n", + " lookup_table_simulation\n", + ")\n", + "from ess.spectroscopy.types import *" + ] + }, + { + "cell_type": "markdown", + "id": "2", + "metadata": {}, + "source": [ + "BIFROST NeXus files store detector data in 45 separate NXdetector groups, one per detector triplet.\n", + "For the time being, we need to specify the names of these NXdetector groups when creating the workflow.\n", + "So load them from the input file:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3", + "metadata": {}, + "outputs": [], + "source": [ + "with snx.File(simulated_elastic_incoherent_with_phonon()) as f:\n", + " detector_names = list(f['entry/instrument'][snx.NXdetector])" + ] + }, + { + "cell_type": "markdown", + "id": "4", + "metadata": {}, + "source": [ + "Generally, we would use all triplets, but for this example, we only use the first two.\n", + "This reduces the size of the data and the time to compute it." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5", + "metadata": {}, + "outputs": [], + "source": [ + "detector_names = detector_names[:2]" + ] + }, + { + "cell_type": "markdown", + "id": "6", + "metadata": {}, + "source": [ + "Next, construct the workflow which is a [sciline.Pipeline](https://scipp.github.io/sciline/generated/classes/sciline.Pipeline.html) and encodes the entire reduction procedure.\n", + "We need to provide a couple of parameters so we can run the workflow:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7", + "metadata": {}, + "outputs": [], + "source": [ + "workflow = bifrost.BifrostSimulationWorkflow(detector_names)\n", + "# Set the input file name:\n", + "workflow[Filename[SampleRun]] = simulated_elastic_incoherent_with_phonon()\n", + "# Set the lookup table for frame unwrapping:\n", + "workflow[LookupTableFilename] = lookup_table_simulation()\n", + "# Set thresholds to mask wavelength regions with large uncertainties.\n", + "# For this example, we do not mask anything:\n", + "workflow[LookupTableRelativeErrorThreshold] = {\n", + " 'detector': np.inf,\n", + " 'normalization_monitor': np.inf,\n", + "}\n", + "# We need to read many objects from the file,\n", + "# keeping it open improves performance: (optional)\n", + "workflow[PreopenNeXusFile] = PreopenNeXusFile(True)\n", + "# We drop uncertainties where they would otherwise lead to correlations:\n", + "workflow[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.drop" + ] + }, + { + "cell_type": "markdown", + "id": "8", + "metadata": {}, + "source": [ + "Next, draw the workflow as a graph to inspect the steps it will take to reduce the data.\n", + "\n", + "Note the groups where entries are labeled with `(triplet)`. (These labels will be `(dim_0)` if you don't have [Pandas](https://pandas.pydata.org/) installed.)\n", + "These groups indicate functions that are applied separately to each detector triplet." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9", + "metadata": {}, + "outputs": [], + "source": [ + "workflow.visualize(EnergyQDetector[SampleRun], compact=True, graph_attr={\"rankdir\": \"LR\"})" + ] + }, + { + "cell_type": "markdown", + "id": "10", + "metadata": {}, + "source": [ + "We are ready to compute the reduced data.\n", + "We use the naive scheduler of sciline because it tends to perform better for BIFROST than the [Dask](https://docs.dask.org/en/stable/index.html) scheduler.\n", + "But this is optional." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "11", + "metadata": {}, + "outputs": [], + "source": [ + "scheduler = sciline.scheduler.NaiveScheduler()\n", + "data = workflow.compute(EnergyQDetector[SampleRun], scheduler=scheduler)" + ] + }, + { + "cell_type": "markdown", + "id": "12", + "metadata": {}, + "source": [ + "The result contains coordinates for the sample table and detector rotation angles `a3` and `a4`, respectively.\n", + "It also contains event coordinates for `energy_transfer` and two momentum transfers, one in the lab frame and one in the sample table frame." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "13", + "metadata": {}, + "outputs": [], + "source": [ + "data" + ] + }, + { + "cell_type": "markdown", + "id": "14", + "metadata": {}, + "source": [ + "We can plot the counts as a function of energy transfer and $a_3$ by removing the unused dimensions.\n", + "As expected, it is independent of $a_3$." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "15", + "metadata": {}, + "outputs": [], + "source": [ + "(\n", + " data\n", + " .bins.concat()\n", + " .hist(energy_transfer=500)\n", + ").plot()" + ] + }, + { + "cell_type": "markdown", + "id": "16", + "metadata": {}, + "source": [ + "We can also plot the counts as a function of the momentum transfer in the sample table frame $Q$.\n", + "For this, we first need to create a 2D slice in $Q$ and $\\Delta E$.\n", + "For simplicity, we use the x and z axes or $Q$ (see https://scipp.github.io/scippneutron/user-guide/coordinate-transformations.html for definitions).\n", + "But we could use any other normalized, orthogonal vectors in the dot products.\n", + "\n", + "We can make a second plot using one of the projections and the energy transfer.\n", + "\n", + "The plots are a bit coarse because we only used two triplets." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "17", + "metadata": {}, + "outputs": [], + "source": [ + "d = data.bins.concat().copy()\n", + "x = sc.vector([1, 0, 0])\n", + "z = sc.vector([0, 0, 1])\n", + "d.bins.coords['Qx'] = sc.dot(x, d.bins.coords['sample_table_momentum_transfer'])\n", + "d.bins.coords['Qz'] = sc.dot(z, d.bins.coords['sample_table_momentum_transfer'])\n", + "d.hist(Qz=100, Qx=100).plot(norm='log') / d.hist(energy_transfer=100, Qz=100).plot(norm='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": "3.11.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/packages/essspectroscopy/docs/user-guide/bifrost/index.md b/packages/essspectroscopy/docs/user-guide/bifrost/index.md new file mode 100644 index 000000000..380fe16e7 --- /dev/null +++ b/packages/essspectroscopy/docs/user-guide/bifrost/index.md @@ -0,0 +1,42 @@ +# BIFROST + +## Reduction Workflows + +::::{grid} 3 + +:::{grid-item-card} BIFROST Reduction +:link: bifrost-reduction.ipynb +:text-align: center + +```{image} ../../_static/thumbnails/bifrost_reduction_light.svg +:class: only-light +:width: 100% +``` + +```{image} ../../_static/thumbnails/bifrost_reduction_dark.svg +:class: only-dark +:width: 100% +``` + +::: + +:::: + +```{toctree} +--- +hidden: +--- + +bifrost-reduction +``` + +## Advanced Tools + +```{toctree} +--- +maxdepth: 1 +--- + +bifrost-bragg-peak-monitor +bifrost-make-wavelength-lookup-table +``` diff --git a/packages/essspectroscopy/docs/user-guide/index.md b/packages/essspectroscopy/docs/user-guide/index.md new file mode 100644 index 000000000..7aa380fd1 --- /dev/null +++ b/packages/essspectroscopy/docs/user-guide/index.md @@ -0,0 +1,10 @@ +# User Guide + +```{toctree} +--- +maxdepth: 1 +--- + +installation +bifrost/index +``` diff --git a/packages/essspectroscopy/docs/user-guide/installation.md b/packages/essspectroscopy/docs/user-guide/installation.md new file mode 100644 index 000000000..3b03b6cbe --- /dev/null +++ b/packages/essspectroscopy/docs/user-guide/installation.md @@ -0,0 +1,16 @@ +# Installation + +To install ESSspectroscopy and all of its dependencies, use + +`````{tab-set} +````{tab-item} pip +```sh +pip install essspectroscopy +``` +```` +````{tab-item} conda +```sh +conda install -c conda-forge essspectroscopy +``` +```` +````` diff --git a/packages/essspectroscopy/pyproject.toml b/packages/essspectroscopy/pyproject.toml new file mode 100644 index 000000000..bb661c2c3 --- /dev/null +++ b/packages/essspectroscopy/pyproject.toml @@ -0,0 +1,101 @@ +[build-system] +requires = [ + "setuptools>=77", + "setuptools_scm[toml]>=8.0", +] +build-backend = "setuptools.build_meta" + +[project] +name = "essspectroscopy" +description = "Spectroscopy data reduction for the European Spallation Source " +authors = [{ name = "Scipp contributors" }] +license = "BSD-3-Clause" +license-files = ["LICENSE"] +readme = "README.md" +classifiers = [ + "Intended Audience :: Science/Research", + "Natural Language :: English", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Topic :: Scientific/Engineering", + "Typing :: Typed", +] +requires-python = ">=3.11" + +# IMPORTANT: +# Run 'tox -e deps' after making changes here. This will update requirement files. +# Make sure to list one dependency per line. +dependencies = [ + "essreduce>=26.4.1", + "graphviz>=0.20", + "pandas>=2.1.2", + "sciline>=25.4.1", + "scipp>=26.1.0", + "scippneutron>=25.11.2", + "scippnexus>=24.9.0", + "tof>=25.11.0", +] + +dynamic = ["version"] + +[project.optional-dependencies] +test = [ + "pooch>=1.5", + "pytest>=7.0", +] +docs = [ + "autodoc-pydantic", + "ipykernel", + "ipympl", + "ipython!=8.7.0", # Breaks syntax highlighting in Jupyter code cells. + "ipywidgets", + "myst-parser", + "nbsphinx", + "pandas", + "pooch", + "pydata-sphinx-theme>=0.14", + "sphinx", + "sphinx-autodoc-typehints", + "sphinx-copybutton", + "sphinx-design", +] + +[project.urls] +"Bug Tracker" = "https://github.com/scipp/essspectroscopy/issues" +"Documentation" = "https://scipp.github.io/essspectroscopy" +"Source" = "https://github.com/scipp/essspectroscopy" + +[tool.setuptools_scm] +root = "../.." +tag_regex = "^essspectroscopy/(?P[vV]?\\d+(?:\\.\\d+)*(?:[._-]?\\w+)*)$" +git_describe_command = ["git", "describe", "--dirty", "--tags", "--long", "--match", "essspectroscopy/*[0-9]*"] + +[tool.pytest.ini_options] +minversion = "7.0" +addopts = """ +--strict-config +--strict-markers +--import-mode=importlib +-ra +-v +""" +testpaths = "tests" +filterwarnings = [ + "error", + # Plotting related warnings. + 'ignore:\n Sentinel is not a public part of the traitlets API:DeprecationWarning', +] + +[tool.mypy] +strict = true +ignore_missing_imports = true +enable_error_code = [ + "ignore-without-code", + "redundant-expr", + "truthy-bool", +] +warn_unreachable = true diff --git a/packages/essspectroscopy/resources/logo.svg b/packages/essspectroscopy/resources/logo.svg new file mode 100644 index 000000000..274920cb9 --- /dev/null +++ b/packages/essspectroscopy/resources/logo.svg @@ -0,0 +1,100 @@ + + + + + + + + + + + + + image/svg+xml + + + + + + + essspectroscopy + + + + diff --git a/packages/essspectroscopy/src/ess/bifrost/__init__.py b/packages/essspectroscopy/src/ess/bifrost/__init__.py new file mode 100644 index 000000000..83f165e08 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/__init__.py @@ -0,0 +1,19 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2024 Scipp contributors (https://github.com/scipp) + +"""BIFROST data reduction.""" + +import importlib.metadata + +from .detector import providers +from .io import nexus +from .workflow import BifrostSimulationWorkflow, BifrostWorkflow + +try: + __version__ = importlib.metadata.version("essspectroscopy") +except importlib.metadata.PackageNotFoundError: + __version__ = "0.0.0" + +del importlib + +__all__ = ['BifrostSimulationWorkflow', 'BifrostWorkflow', 'nexus', 'providers'] diff --git a/packages/essspectroscopy/src/ess/bifrost/cutting.py b/packages/essspectroscopy/src/ess/bifrost/cutting.py new file mode 100644 index 000000000..0312ff7ff --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/cutting.py @@ -0,0 +1,75 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Cutting BIFROST data.""" + +from collections.abc import Callable + +import scipp as sc +from ess.spectroscopy.types import ( + DataGroupedByRotation, + InstrumentAngle, + RawDetector, + RunType, + SampleAngle, +) + + +def group_by_rotation( + data: RawDetector[RunType], + sample_angle: SampleAngle[RunType], + instrument_angle: InstrumentAngle[RunType], +) -> DataGroupedByRotation[RunType]: + """Group data by rotation angles. + + Parameters + ---------- + data: + Detector events with time coordinates. + sample_angle: + Sample rotation angle "a3". + May be time-dependent (1d array with dim "time") or scalar. + instrument_angle: + Instrument rotation angle "a4". + May be time-dependent (1d array with dim "time") or scalar. + + Returns + ------- + : + ``data`` grouped by rotation angles "a3" and "a4". + """ + graph = {'a3': _make_angle_from_time_calculator(sample_angle)} + group_coords = ['a3'] + drop_coords = [] + + if 'time' in data.dims: + # If the data is time-dependent, a4 corresponds to that time-dependence + # (the instrument angle is the only dynamic parameter). The data has a 'time' + # bin-edge coord in this case. Since a4 changes at the bin edges, not within + # each bin, we can look it up safely using midpoints. + graph['a4'] = lambda time: sc.lookup( + instrument_angle, dim='time', mode='previous' + )[sc.midpoints(time)] + # a4 replaces the 'time' coord. + drop_coords.append('time') + else: + graph['a4'] = _make_angle_from_time_calculator(instrument_angle) + group_coords.append('a4') + + grouped = ( + data.transform_coords(('a3', 'a4'), graph=graph) + .group(*group_coords) + .drop_coords(drop_coords) + ) + return DataGroupedByRotation[RunType](grouped) + + +def _make_angle_from_time_calculator(angle: sc.DataArray) -> Callable[..., sc.Variable]: + if angle.ndim == 0: + return lambda: angle.data + else: + lut = sc.lookup(angle, 'time', mode='previous') + return lambda event_time_zero: lut[event_time_zero] + + +providers = (group_by_rotation,) diff --git a/packages/essspectroscopy/src/ess/bifrost/data.py b/packages/essspectroscopy/src/ess/bifrost/data.py new file mode 100644 index 000000000..231e99b8f --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/data.py @@ -0,0 +1,61 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Data for tests and documentation with BIFROST.""" + +from pathlib import Path + +from ess.reduce.data import make_registry + +_registry = make_registry( + 'ess/bifrost', + files={ + "bifrost_260418T170408.h5": "md5:5fe544c2eccfb6c4ec52beca9957f528", + "computed_energy_data_simulated_5x2.h5": "md5:1a24a1067ae2968dfc162c5c72dcb073", + "BIFROST-simulation-lookup-table.h5": "md5:237e26125b22aa9cb0c68454206896a2", + }, + version="8", +) + + +def get_path(name: str) -> Path: + """ + Return the path to a data file bundled with ess.bifrost. + + This function only works with example data and cannot handle + paths to custom files. + """ + return _registry.get_path(name) + + +def simulated_elastic_incoherent_with_phonon() -> Path: + """Simulated data for elastic incoherent scattering including a phonon.""" + return get_path("bifrost_260418T170408.h5") + + +def lookup_table_simulation() -> Path: + """Wavelength lookup table for the simulated BIFROST data. + + This table was computed with `tof `_ + using `Create a wavelength lookup table for BIFROST + <../../user-guide/bifrost/bifrost-make-wavelength-lookup-table.rst>`_ + with ``NumberOfSimulatedNeutrons = 5_000_000``. + """ + return get_path("BIFROST-simulation-lookup-table.h5") + + +def computed_energy_data_simulated_5x2() -> Path: + """Energy and momentum transfer computed from the simulated BIFROST data. + + This reference was computed with 10 detectors forming a 5x2 grid + (arc=5, channel=2). + """ + return get_path("computed_energy_data_simulated_5x2.h5") + + +__all__ = [ + "computed_energy_data_simulated_5x2", + "get_path", + "lookup_table_simulation", + "simulated_elastic_incoherent_with_phonon", +] diff --git a/packages/essspectroscopy/src/ess/bifrost/detector.py b/packages/essspectroscopy/src/ess/bifrost/detector.py new file mode 100644 index 000000000..a82be0546 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/detector.py @@ -0,0 +1,284 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Detector handling for BIFROST.""" + +from collections.abc import Callable + +import scipp as sc +import scippnexus as snx +from ess.spectroscopy.indirect.conversion import add_spectrometer_coords +from ess.spectroscopy.types import ( + Analyzer, + DetectorPositionOffset, + EmptyDetector, + NeXusComponent, + NeXusTransformation, + PrimarySpecCoordTransformGraph, + RunType, + SecondarySpecCoordTransformGraph, +) + +from ess.reduce.nexus.types import Position + +from .types import ArcNumber + + +def arc_number( + beamline: EmptyDetector[RunType], +) -> ArcNumber[RunType]: + """Calculate BIFROST arc index number from pixel final energy + + The BIFROST analyzers are each set to diffract an + energy in the set (2.7, 3.2, 3.8, 4.4. 5.0) meV. + This energy is only valid for the central point of the center + tube of the associated detector triplet. All other pixels + will have a final energy slightly higher or lower. + + This function assigns the closest arc number indexing the + ordered set above. + + Parameters + ---------- + beamline: + A data array with a 'final_energy' coordinate which is the + per-pixel (or event) final neutron energy. + + Returns + ------- + : + The arc index of the analyzer from which the neutron scattered + """ + minimum = sc.scalar(2.7, unit='meV') + step = sc.scalar(0.575, unit='meV') + final_energy = beamline.coords['final_energy'] + return ArcNumber[RunType](sc.round((final_energy - minimum) / step).to(dtype='int')) + + +def arc_and_channel_from_detector_number( + detector_number: sc.Variable, +) -> tuple[sc.Variable, sc.Variable]: + """Calculate arc number and channel from detector number. + + Calculate arc and channel for this triplet based on detector_number layout. + BIFROST detector_number ordering is (arc, tube, channel, pixel). + Each triplet contains 3 tubes of 100 pixels for a single arc-channel pair. + """ + + det_num = detector_number['tube', 0]['length', 0].value + pixels_per_tube = 100 + tubes_per_channel = 3 + channels_per_arc = 9 + pixels_per_arc = pixels_per_tube * tubes_per_channel * channels_per_arc # 2700 + + # detector_number is 1-indexed + idx = det_num - 1 + arc = idx // pixels_per_arc + remainder = idx % pixels_per_arc + channel = (remainder % (pixels_per_tube * channels_per_arc)) // pixels_per_tube + + return sc.index(arc), sc.index(channel) + + +def get_calibrated_detector_bifrost( + detector: NeXusComponent[snx.NXdetector, RunType], + analyzer: Analyzer[RunType], + *, + transform: NeXusTransformation[snx.NXdetector, RunType], + offset: DetectorPositionOffset[RunType], + primary_graph: PrimarySpecCoordTransformGraph[RunType], + secondary_graph: SecondarySpecCoordTransformGraph[RunType], +) -> EmptyDetector[RunType]: + """Extract the data array corresponding to a detector's signal field. + + This includes: + + - Reshaping the data array is reshaped to the logical detector shape. + - Assigning geometry coordinate "position". + - Assigning spectrometer coordinates such as "final_energy", + "secondary_flight_time", and "L1". + + Parameters + ---------- + detector: + Loaded NeXus detector. + analyzer: + Loaded analyzer parameters. + transform: + Transformation that determines the detector position. + offset: + Offset to add to the detector position. + primary_graph: + Coordinate transformation graph for the primary spectrometer. + secondary_graph: + Coordinate transformation graph for the secondary spectrometer. + Must be a closure over analyzer parameters. + And those parameters must have a compatible shape with ``data``. + + Returns + ------- + : + Detector geometry and spectrometer coordinates. + """ + + da = get_base_calibrated_detector_bifrost( + detector, analyzer, transform=transform, offset=offset + ) + da = da.rename(dim_0='tube', dim_1='length') + + arc, channel = arc_and_channel_from_detector_number(da.coords['detector_number']) + da.coords['arc'] = arc + da.coords['channel'] = channel + + da = add_spectrometer_coords( + da, + primary_graph, + SecondarySpecCoordTransformGraph[RunType]( + {**secondary_graph, **_make_analyzer_coord_graph(da, analyzer)} + ), + ) + + return EmptyDetector[RunType](da) + + +def get_base_calibrated_detector_bifrost( + detector: NeXusComponent[snx.NXdetector, RunType], + analyzer: Analyzer[RunType], + *, + transform: NeXusTransformation[snx.NXdetector, RunType], + offset: DetectorPositionOffset[RunType], +) -> sc.DataArray: + """Extract the data array corresponding to a detector's signal field. + + This function is specific to BIFROST and differs from the generic + :func:`ess.reduce.nexus.workflow.get_calibrated_detector` in that it + assigns time-dependent positions by broadcasting the data into the 'time' dimension. + + Parameters + ---------- + detector: + Loaded NeXus detector. + analyzer: + Loaded analyzer parameters. + transform: + Transformation that determines the detector position. + offset: + Offset to add to the detector position. + + Returns + ------- + : + Detector with geometry coordinates. + """ + + from ess.reduce.nexus import compute_detector_position, extract_signal_data_array + + da = extract_signal_data_array(detector) + position = compute_detector_position(da, transform=transform, offset=offset) + return _assign_detector_position(da, position) + + +def _assign_detector_position( + da: sc.DataArray, position: sc.Variable | sc.DataArray +) -> sc.DataArray: + if isinstance(position, sc.DataArray): # time-dependent transform + # Store position and time as separate coords because we can't store data arrays. + return da.broadcast( + dims=['time', *da.dims], shape=[position.sizes['time'], *da.shape] + ).assign_coords(position=position.data, time=position.coords['time']) + return da.assign_coords(position=position) + + +# We insert the analyzer coords into the graph so that they don't end up as coords +# in the output. This could be done in the provider of SecondarySpecCoordTransformGraph +# but that provider would then have to request the detector component to check +# the time coordinates. +def _make_analyzer_coord_graph( + detector: sc.DataArray, + analyzer: Analyzer[RunType], +) -> dict[str, Callable[[], sc.Variable]]: + ana_pos: Position[snx.NXcrystal, RunType] = analyzer['position'] + if ana_pos.is_dynamic: + if 'time' not in detector.coords: + raise sc.CoordError( + "The analyzer position is time-dependent but the detector is not" + ) + analyzer_positions = ana_pos.positions + if not sc.identical(analyzer_positions.coords['time'], detector.coords['time']): + raise sc.CoordError( + f"The analyzer and detector positions are not at the same times.\n" + f"Analyzer: {analyzer_positions.coords['time']}\n" + f"Detector: {detector.coords['time']}\n" + "This is likely due to a change in the NeXus structure. It used to " + "guarantee that the times are identical." + ) + analyzer_position = analyzer_positions.data + analyzer_transform = analyzer['transform'].value.data + else: + analyzer_position = ana_pos.position + analyzer_transform = analyzer['transform'].value + + return { + 'analyzer_dspacing': lambda: analyzer['dspacing'], + 'analyzer_position': lambda: analyzer_position, + 'analyzer_transform': lambda: analyzer_transform, + } + + +def merge_triplets( + *triplets: sc.DataArray, +) -> sc.DataArray: + """Merge BIFROST detector triplets into a single data array. + + This function folds the triplets into (arc, channel) dimensions based on + the scalar 'arc' and 'channel' coordinates assigned to each triplet. If the + triplets form a regular rectangular subset of the full 5x9 detector array, + they will be folded into those dimensions. Otherwise, they are concatenated + along a 'triplet' dimension. + + Parameters + ---------- + triplets: + Data arrays to merge. Each must have scalar 'arc' and 'channel' coordinates. + + Returns + ------- + : + Input data arrays either folded into (arc, channel) dimensions or + stacked along the "triplet" dimension. + """ + if len(triplets) == 0: + raise ValueError("At least one triplet is required") + + # Extract arc and channel from scalar coordinates + arc_channel_pairs = [ + (triplet.coords['arc'].value, triplet.coords['channel'].value) + for triplet in triplets + ] + + # Sort triplets by (arc, channel) + sorted_indices = sorted(range(len(triplets)), key=lambda i: arc_channel_pairs[i]) + sorted_triplets = [triplets[i] for i in sorted_indices] + sorted_pairs = [arc_channel_pairs[i] for i in sorted_indices] + + # Check if the pairs form a regular rectangular grid + unique_arcs = sorted({pair[0] for pair in sorted_pairs}) + unique_channels = sorted({pair[1] for pair in sorted_pairs}) + + # Check if we have a complete rectangular subset + expected_pairs = [ + (arc, channel) for arc in unique_arcs for channel in unique_channels + ] + concatenated = sc.concat(sorted_triplets, dim='triplet') + if sorted_pairs == expected_pairs: + # We have a regular grid, fold it + return concatenated.fold( + dim='triplet', + sizes={'arc': len(unique_arcs), 'channel': len(unique_channels)}, + ) + + # Fall back to simple concatenation if not a regular grid + return concatenated + + +providers = (arc_number, get_calibrated_detector_bifrost) diff --git a/packages/essspectroscopy/src/ess/bifrost/io/__init__.py b/packages/essspectroscopy/src/ess/bifrost/io/__init__.py new file mode 100644 index 000000000..20300bcf7 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/io/__init__.py @@ -0,0 +1,8 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2024 Scipp contributors (https://github.com/scipp) + +"""Input/output for BIFROST.""" + +from . import nexus, sqw + +__all__ = ['nexus', 'sqw'] diff --git a/packages/essspectroscopy/src/ess/bifrost/io/mcstas.py b/packages/essspectroscopy/src/ess/bifrost/io/mcstas.py new file mode 100644 index 000000000..2cd56d9e1 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/io/mcstas.py @@ -0,0 +1,77 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""McStas input for BIFROST.""" + +import scipp as sc +import scippnexus as snx +from ess.spectroscopy.types import ( + EmptyDetector, + NeXusData, + PulsePeriod, + RawDetector, + RunType, +) + +from ..types import McStasRawDetector + + +def assemble_detector_data( + detector: EmptyDetector[RunType], + event_data: NeXusData[snx.NXdetector, RunType], +) -> McStasRawDetector[RunType]: + """Custom assemble function that returns McStasDetectorData.""" + from ess.reduce.nexus.workflow import assemble_detector_data as reduce_assemble + + return McStasRawDetector[RunType](reduce_assemble(detector, event_data)) + + +def convert_simulated_time_to_event_time_offset( + mcstas_data: McStasRawDetector[RunType], + pulse_period: PulsePeriod, +) -> RawDetector[RunType]: + """Helper to make McStas simulated event data look more like real data + + McStas has the ability to track the time-of-flight from source to detector for + every probabilistic neutron ray. This is very helpful, but unfortunately real + instrument at ESS are not able to record the same information due to how the + timing and data collection systems work. + + Real neutron events will record their event_time_zero most-recent-pulse reference + time, and their event_time_offset detection time relative to that reference time. + These two values added together give a real wall time; and information about the + primary spectrometer is necessary to find any time-of-flight + + This function takes event data with per-event coordinate event_time_offset + (actually McStas time-of-arrival) and converts the coordinate to be + the time-of-arrival modulo the source repetition period. + + Notes + ----- + If the input data has realistic event_time_offset values, this function should + be a noop. + + Returns + ------- + : + A copy of the data with realistic per-event coordinate event_time_offset. + """ + + def wrap_event_time_offset(event_time_offset: sc.Variable) -> sc.Variable: + return event_time_offset % pulse_period.to(unit=event_time_offset.unit) + + res = mcstas_data.transform_coords( + frame_time=wrap_event_time_offset, + rename_dims=False, + keep_intermediate=False, + keep_inputs=False, + ) + return RawDetector[RunType]( + res.transform_coords(event_time_offset='frame_time', keep_inputs=False) + ) + + +providers = ( + assemble_detector_data, + convert_simulated_time_to_event_time_offset, +) diff --git a/packages/essspectroscopy/src/ess/bifrost/io/nexus.py b/packages/essspectroscopy/src/ess/bifrost/io/nexus.py new file mode 100644 index 000000000..c7827b940 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/io/nexus.py @@ -0,0 +1,223 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""NeXus input/output for BIFROST.""" + +import warnings + +import numpy as np +import scipp as sc +import scippnexus as snx +from ess.spectroscopy.types import ( + Analyzer, + DynamicPosition, + InstrumentAngle, + NeXusClass, + NeXusComponent, + NeXusComponentLocationSpec, + NeXusFileSpec, + NeXusTransformation, + RunType, + SampleAngle, +) + +from ess.reduce.nexus import open_component_group +from ess.reduce.nexus.types import NeXusLocationSpec, TransformationTimeFilter + + +# See https://github.com/scipp/essreduce/issues/98 +def moderator_class_for_source() -> NeXusClass[snx.NXsource]: + """Select NXmoderator as the source.""" + return NeXusClass[snx.NXsource](snx.NXmoderator) + + +def load_sample_angle( + file_spec: NeXusFileSpec[RunType], +) -> SampleAngle[RunType]: + return SampleAngle[RunType](_load_experiment_parameter(file_spec, "a3")) + + +def load_instrument_angle( + file_spec: NeXusFileSpec[RunType], +) -> InstrumentAngle[RunType]: + return InstrumentAngle[RunType](_load_experiment_parameter(file_spec, "a4")) + + +def _load_experiment_parameter( + file_spec: NeXusFileSpec[RunType], param_name: str +) -> sc.DataArray: + with open_component_group( + NeXusLocationSpec(filename=file_spec.value), + nx_class=snx.NXparameters, + parent_class=snx.NXentry, + ) as group: + return group[param_name][()]['value'] + + +def load_analyzer_for_detector( + detector_location: NeXusComponentLocationSpec[snx.NXdetector, RunType], +) -> NeXusComponent[snx.NXcrystal, RunType]: + """Load the analyzer component for the given detector. + + This function searches for an ``NXcrystal`` in the inputs (via the + 'input' attribute) of the detector and loads the first NeXus group it finds. + + See Also + -------- + get_calibrated_analyzer: + A provider that combines loaded analyzer data into an ``Analyzer`` object. + """ + with open_component_group(detector_location, nx_class=snx.NXdetector) as det_group: + analyzer_group = _find_class_in_inputs( + group=det_group.parent, target=snx.NXcrystal, start=det_group + ) + return analyzer_group[()] + + +def _find_class_in_inputs( + group: snx.Group, target: type, start: snx.Group +) -> snx.Group: + """Search for a NeXus class in a group's inputs. + + This function uses a breadth-first search through ``'input'`` attributes. + It begins at ``start`` and walks along chains of inputs until a group with the + given class is found, the chain ends, or the chain leads outside ``group``. + + Parameters + ---------- + group: HDF5 Group + The group that contains all possible next named groups + target: + The NeXus class to look for. + + Returns + ------- + : + The group with the target NeXus class found within ``group``. + """ + pending = [start] + while pending: + element = pending.pop(0) + if element.nx_class == target: + return element + for name in _get_inputs(element): + try: + pending.append(group[name]) + except KeyError: # noqa: PERF203 + warnings.warn(f"No '{name}' in NeXus group {group.name}", stacklevel=2) + continue + raise ValueError(f"No {target} found in the inputs of {start.name}") + + +def _get_inputs(group: snx.Group) -> list[str]: + try: + inputs = group.attrs['inputs'] + except KeyError: + return [] + # Deal with nexusformat (Python module) or kafka-to-nexus (filewriter) + # silently converting a len(list[str]) == 1 attribute to a str attribute: + return [inputs] if isinstance(inputs, str) else inputs + + +def get_calibrated_analyzer( + analyzer_component: NeXusComponent[snx.NXcrystal, RunType], + analyzer_transform: NeXusTransformation[snx.NXcrystal, RunType], + analyzer_position: DynamicPosition[snx.NXcrystal, RunType], +) -> Analyzer[RunType]: + """Collect the data for a single analyzer. + + This provider works together with :func:`load_analyzer_for_detector` and the + generic NeXus workflow from ESSreduce. + ``load_analyzer_for_detector`` loads a raw analyzer component. + Then the default providers from ESSreduce extract a transform and position like + for any other component. + Finally, this provider combines the data into a single Analyzer object. + + Parameters + ---------- + analyzer_component: + Data group of loaded analyzers. + analyzer_transform: + Transformation matrix of the analyzer. + analyzer_position: + The computed position vector of the analyzer. + + Returns + ------- + : + A given analyzer. + Only a subset of fields is returned. + """ + + return Analyzer[RunType]( + sc.DataGroup( + dspacing=analyzer_component['d_spacing'], + position=analyzer_position, + transform=analyzer_transform, + ) + ) + + +def _collapse_runs(transform: sc.DataArray, dim: str) -> sc.DataArray: + """Collapse runs of equal values into a single value.""" + # Find indices where the data changes + different_from_previous = np.hstack( + [True, ~np.isclose(transform.values[:-1], transform.values[1:])] + ) + change_indices = np.flatnonzero(different_from_previous) + if change_indices.shape == transform.shape: + return transform # Return early to avoid expensive indexing + # Get unique values + unique_values = transform[change_indices] + + # Make bin-edges and extend range to include the whole measurement + last = unique_values.coords[dim][-1] + unique_values.coords[dim] = sc.concat( + [ + # bin-edges are left-inclusive, so we can start with coord[0] as first edge + unique_values.coords[dim], + # Surely, no experiment will last more than 10 years... + last + sc.scalar(10, unit='Y').to(unit=last.unit), + ], + dim=dim, + ) + + return unique_values + + +def stepwise_transformation_time_filter(transform: sc.DataArray) -> sc.DataArray: + """Collapse runs of equal values into a single value. + + This can be used as a time filter for NeXus transformations when the component + mostly stays at one position and only rarely moves. + For example, a stepwise scan across detector rotations. + + Repeated values are identified using :func:`numpy.isclose` with default tolerances + applied to the individual transformation components. + I.e., for the BIFROST detector, the detector angle (currently in degrees) + is checked for approximate equality between consecutive values. + + Note + ---- + This approach is meant to handle noisy NXlogs if they are written + from readback values or repeated setpoint values. + We currently do not know enough about how ESS NeXus files will be written for + real measurements, so we may need to revisit this approach. + """ + collapsed = _collapse_runs(transform, 'time') + if collapsed.sizes['time'] == 1: + return collapsed.squeeze('time') + return collapsed + + +providers = ( + get_calibrated_analyzer, + load_analyzer_for_detector, + load_instrument_angle, + load_sample_angle, + moderator_class_for_source, +) + +parameters = { + TransformationTimeFilter: stepwise_transformation_time_filter, +} diff --git a/packages/essspectroscopy/src/ess/bifrost/io/sqw.py b/packages/essspectroscopy/src/ess/bifrost/io/sqw.py new file mode 100644 index 000000000..69f9becd3 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/io/sqw.py @@ -0,0 +1,438 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""SQW output for BIFROST.""" + +import dataclasses + +import numpy as np +import numpy.typing as npt +import scipp as sc +from ess.spectroscopy.types import ( + Beamline, + EnergyBins, + GravityVector, + Measurement, + NormalizedIncidentEnergyDetector, + OutFilename, + PulsePeriod, + SampleRun, + SQWBinSizes, +) +from scippneutron.io import sqw +from scippneutron.metadata import ESS_SOURCE + +# Projection axes +# For now, we always project onto the cartesian axes for simplicity. +_AXIS_U = sc.vector([1, 0, 0], unit="1/angstrom") +_AXIS_V = sc.vector([0, 1, 0], unit="1/angstrom") +_AXIS_W = sc.vector([0, 0, 1], unit="1/angstrom") + + +def save_sqw( + path: OutFilename, + events: NormalizedIncidentEnergyDetector[SampleRun], + *, + bin_sizes: SQWBinSizes, + energy_bins: EnergyBins, + beamline: Beamline[SampleRun], + measurement: Measurement[SampleRun], + sample: sqw.SqwIXSample, + pulse_period: PulsePeriod, + gravity: GravityVector, +) -> None: + """Save events recorded at BIFROST to an SQW file. + + The files written by this function can be read by + `Horace `_ for further processing. + For details on the file format, see the documentation for Horace as well as + the `SQW `_ + developer guide in ScippNeutron. + + The input to this function should not yet contain inelastic coordinates like + 'energy_transfer' or 'sample_table_momentum_transfer'. + Instead, ``save_sqw`` histograms the events according to detector number, + experiment setting, and incident energy and computes inelastic + coordinates on that histogram. + This is done for consistency with Horace. + + The data is encoded as a 4-dimensional array, and Horace calls the dimensions + ``u1 ... u4``. The first three correspond to the three dimensions of $\\vec{Q}$ + and the ``u4`` corresponds to energy transfer. Horace supports customizable + projections onto the cardinal axes $Q_x, Q_y, Q_z$, but the implementation here + has hard-coded ``(Qx, Qy, Qz) = (u1, u2, u3)``, however, you need to express the + binning in terms of the `u`'s. + + Note + ---- + This function requires large amounts of memory to construct intermediate + arrays and fill those with null observations. + + Parameters + ---------- + path: + Path of the file to write. + events: + Binned data array with shape ``(*logical, "a3", "a4")`` where ``logical`` + is any number of logical detector dimensions (e.g., arc, tube). + Must have an ``"incident_energy"`` event coordinate. + bin_sizes: + Sizes of the output 'image' bins. + The data will be ordered based on these bins, but it is possible + to change the binning later in Horace. + E.g., ``{'u1': 50, 'u2': 50, 'u3': 50, 'u4': 50}``. + energy_bins: + Bin edges or number of bins for (incident) energy. + The events are histogrammed according to these bins, so this determines the + final energy resolution that is available in Horace. + Should typically be larger than ``bin_sizes['energy_transfer']``. + beamline: + Beamline metadata. + measurement: + Measurement metadata. + sample: + Sample metadata in SQW format. + pulse_period: + Pulse period of the neutron source. + gravity: + Vector indicating the direction of gravity. + Used to define the lab coordinate system. + See also + :func:`ess.spectroscopy.indirect.conversion.rotate_to_sample_table_momentum_transfer`. + + See also + -------- + scippneutron.io.sqw: + For low-level SQW I/O and the underlying implementation of ``save_sqw``. + """ + flat_events = _flatten_events(events) + del events # 'move' events into _flatten_events + _filter_and_convert_coords_in_place(flat_events) + + observations = _histogram_detector_setting_ei(flat_events, energy_bins=energy_bins) + del flat_events # 'move' flat_events into _histogram_detector_setting_ei + sample_angle = observations.coords['a3'] + final_energy = observations.coords['final_energy'] + observations = _with_inelastic_coords(observations, gravity) + energy_transfer = observations.coords['energy_transfer'].rename_dims( + incident_energy='energy_transfer' + ) + observations = observations.flatten(to="observation") + + dnd, counts, binned_observations = _bin_image(observations, bin_sizes) + del observations # 'move' observations into _bin_image + pix = _make_pixel_data(binned_observations) + del binned_observations # 'move' binned_observations into _make_pixel_data + pix_buffer = _make_pixel_buffer(pix) + del pix # 'move' pix into _make_pixel_buffer + + experiments = _make_experiments( + energy_transfer=energy_transfer, + final_energy=final_energy, + sample_angle=sample_angle, + ) + builder = ( + sqw.Sqw.build(path, title=measurement.title) + .add_default_instrument(_make_instrument(beamline, pulse_period)) + .add_default_sample(sample) + .add_dnd_data(_make_dnd_metadata(dnd, sample), data=dnd.data, counts=counts) + .add_pixel_data(pix_buffer, experiments=experiments) + ) + builder.create() + + +def _flatten_events( + events: NormalizedIncidentEnergyDetector[SampleRun], +) -> sc.DataArray: + """Flatten events from (*logical, a3, a4) to (detector, setting). + + Also assigns the 'irun' coordinate as that requires the initial shape. + """ + logical_dims = [dim for dim in events.dims if dim not in ("a3", "a4")] + aux = events.flatten(logical_dims, 'detector') + + n_a3 = aux.sizes['a3'] + aux.coords['i_a3'] = sc.arange('a3', n_a3, dtype='float32', unit=None) + aux.coords['i_a4'] = sc.arange('a4', aux.sizes['a4'], dtype='float32', unit=None) + flat = aux.transpose(['detector', 'a4', 'a3']).flatten(['a4', 'a3'], 'setting') + return flat.assign_coords( + irun=flat.coords.pop('i_a3') + + flat.coords.pop('i_a4') * sc.index(n_a3) + + sc.index(1, dtype='float32') # 1-based indexing + ) + + +def _filter_and_convert_coords_in_place(flat_events: sc.DataArray) -> None: + """Filter out all coords we no longer need and convert remaining coords to float32. + + This function mainly serves to reduce memory usage. + The conversion to float32 is ultimately required when building the 'pixel data', + we do it here to reduce size early. This should not have a significant impact + on precision as we do not reduce these coordinates. + The event weights remain in float64 or int64 for now because + they do need to be summed. + """ + flat_events.coords['final_energy'] = flat_events.coords['final_energy'].to( + dtype='float32', copy=False + ) + flat_events.bins.coords['incident_energy'] = flat_events.bins.coords[ + 'incident_energy' + ].to(dtype='float32', copy=False) + + flat_events.coords['idet'] = flat_events.coords.pop('detector_number').to( + dtype='float32', copy=False + ) + # to 1-based indexing: + flat_events.coords['idet'] += sc.scalar(1.0, dtype='float32', unit=None) + + keep = { + 'a3', + 'final_energy', + 'final_wavevector', + 'gravity', + 'idet', + 'incident_beam', + 'irun', + } + for dim in set(flat_events.coords) - keep: + del flat_events.coords[dim] + + +def _histogram_detector_setting_ei( + flat_events: sc.DataArray, *, energy_bins: EnergyBins +) -> sc.DataArray: + """Histogram the events in (detector, setting, incident_energy). + + This also converts the weights to float32 as no further reductions + will be performed for the 'pixel data'. + We accept a loss of precision for the 'image data' here which will be + converted back to float64 later. + """ + hist = flat_events.hist(incident_energy=energy_bins) + hist.coords['incident_energy'] = sc.midpoints(hist.coords['incident_energy']).to( + dtype='float32', copy=False + ) + hist.coords['ien'] = sc.arange( + 'incident_energy', + 1, # 1-based indexing + hist.sizes['incident_energy'] + 1, + dtype='float32', + unit=None, + ) + + hist.data = hist.data.to(dtype='float32', copy=False) + + return hist + + +def _with_inelastic_coords( + observations: sc.DataArray, gravity: GravityVector +) -> sc.DataArray: + """Compute and assign Qx, Qy, Qz, and energy_transfer. + + This also drops all coordinates that are no longer needed. + """ + from ess.spectroscopy.indirect.conversion import ( + energy_transfer, + lab_momentum_transfer_from_incident_energy, + rotate_to_sample_table_momentum_transfer, + ) + + graph = { + 'lab_momentum_transfer': lab_momentum_transfer_from_incident_energy, + 'sample_table_momentum_transfer': rotate_to_sample_table_momentum_transfer, + 'energy_transfer': energy_transfer, + 'gravity': lambda: gravity, + } + aux = observations.transform_coords( + ['sample_table_momentum_transfer', 'energy_transfer'], + graph=graph, + keep_inputs=False, + keep_intermediate=False, + quiet=True, + ) + q = aux.coords.pop('sample_table_momentum_transfer') + + return aux.assign_coords( + energy_transfer=aux.coords.pop('energy_transfer').to( + dtype='float32', copy=False + ), + **{ + f'Q{dim}': _project_onto(q, axis).to(dtype='float32') + for dim, axis in zip('xyz', (_AXIS_U, _AXIS_V, _AXIS_W), strict=True) + }, + ) + + +def _project_onto(vec: sc.Variable, axis: sc.Variable) -> sc.Variable: + axis = axis / sc.norm(axis) + # Optimization to avoid huge dot-products: + match list(axis.values): + case [1, 0, 0]: + return vec.fields.x + case [0, 1, 0]: + return vec.fields.y + case [0, 0, 1]: + return vec.fields.z + case _: + return sc.dot(axis, vec) + + +def _bin_image( + observations: sc.DataArray, bin_sizes: SQWBinSizes +) -> tuple[sc.DataArray, sc.Variable, sc.DataArray]: + # Dim order to match pixel data (note the transpose for dnd) + dim_order = {'energy_transfer': 'u4', 'Qz': 'u3', 'Qy': 'u2', 'Qx': 'u1'} + binned = observations.bin( + {coord: bin_sizes[dim] for coord, dim in dim_order.items()} + ).rename(energy_transfer='u4', Qz='u3', Qy='u2', Qx='u1') + + image = binned.transpose(['u1', 'u2', 'u3', 'u4']) + # The dense DND array contains the averages of the observations in `image`. + # Note that `image` contains 'observations', not 'events', so the expectation value + # is the arithmetic mean, not the sum. + # See also https://scipp.github.io/scippneutron/developer/file-formats/sqw.html#dnd-data-blocks + dnd = image.bins.mean().to(dtype='float64', copy=False) + counts = image.bins.size() + + return dnd, counts, binned + + +def _make_pixel_data(binned_observations: sc.DataArray) -> sc.DataArray: + pix = binned_observations.data.bins.concat().value + del binned_observations + + # Convert to expected units: + return sc.DataArray( + pix.data, + coords={ + 'u1': pix.coords['u1'].to(unit='1/Ã…', copy=False), + 'u2': pix.coords['u2'].to(unit='1/Ã…', copy=False), + 'u3': pix.coords['u3'].to(unit='1/Ã…', copy=False), + 'u4': pix.coords['u4'].to(unit='meV', copy=False), + 'idet': pix.coords['idet'], + 'irun': pix.coords['irun'], + 'ien': pix.coords['ien'], + }, + ) + + +def _make_pixel_buffer(pix: sc.DataArray) -> npt.NDArray[np.float32]: + return np.c_[ + *( + pix.coords[name].values + for name in ('u1', 'u2', 'u3', 'u4', 'irun', 'idet', 'ien') + ), + pix.values, + sc.variances(pix).values, + ] + + +def _make_instrument( + beamline: Beamline, pulse_period: PulsePeriod +) -> sqw.SqwIXNullInstrument: + return sqw.SqwIXNullInstrument( + name=beamline.name, + source=sqw.SqwIXSource( + name="ESS", + target_name=ESS_SOURCE.name, + frequency=1 / pulse_period, + ), + ) + + +def _make_dnd_metadata( + dnd: sc.DataArray, sample: sqw.SqwIXSample +) -> sqw.SqwDndMetadata: + """Create the DND metadata for an SQW file. + + Parameters + ---------- + dnd: + DND 'image data'. + Must be histogrammed along the u-axes with linspace coordinates. + sample: + Sample metadata. + """ + img_range = [ + sc.concat([dnd.coords[name].min(), dnd.coords[name].max()], dim=name) + for name in ("u1", "u2", "u3", "u4") + ] + + n_bins_all_dims = sc.array( + dims=["axis"], + values=[dnd.sizes[name] for name in ("u1", "u2", "u3", "u4")], + unit=None, + ) + + return sqw.SqwDndMetadata( + axes=sqw.SqwLineAxes( + title="Instrument Axes", + label=["Qx", "Qy", "Qz", "Delta E"], + img_scales=[ + sc.scalar(1.0, unit="1/angstrom"), + sc.scalar(1.0, unit="1/angstrom"), + sc.scalar(1.0, unit="1/angstrom"), + sc.scalar(1.0, unit="meV"), + ], + img_range=img_range, + n_bins_all_dims=n_bins_all_dims, + single_bin_defines_iax=sc.array(dims=["axis"], values=[True] * 4), + dax=sc.arange("axis", 4, unit=None), + offset=[ + sc.scalar(0.0, unit="1/angstrom"), + sc.scalar(0.0, unit="1/angstrom"), + sc.scalar(0.0, unit="1/angstrom"), + sc.scalar(0.0, unit="meV"), + ], + changes_aspect_ratio=True, + ), + proj=sqw.SqwLineProj( + title="Null Projection", + lattice_spacing=sample.lattice_spacing, + lattice_angle=sample.lattice_angle, + offset=[ + sc.scalar(0.0, unit="1/angstrom"), + sc.scalar(0.0, unit="1/angstrom"), + sc.scalar(0.0, unit="1/angstrom"), + sc.scalar(0.0, unit="meV"), + ], + label=["Qx", "Qy", "Qz", "Delta E"], + u=_AXIS_U, + v=_AXIS_V, + w=_AXIS_W, + non_orthogonal=False, + type="aaa", + ), + ) + + +def _make_experiments( + *, + energy_transfer: sc.Variable, + final_energy: sc.Variable, + sample_angle: sc.Variable, +) -> list[sqw.SqwIXExperiment]: + experiment_template = sqw.SqwIXExperiment( + run_id=0, # converted to 1-based by ScippNeutron + emode=sqw.EnergyMode.indirect, + efix=None, # type: ignore[assignment] (overridden below) + en=None, # type: ignore[assignment] + psi=sc.scalar(0.0, unit="rad"), + u=_AXIS_U, + v=_AXIS_V, + omega=sc.scalar(0.0, unit="rad"), + dpsi=sc.scalar(0.0, unit="rad"), + gl=sc.scalar(0.0, unit="rad"), + gs=sc.scalar(0.0, unit="rad"), + ) + return [ + dataclasses.replace( + experiment_template, + run_id=i, + psi=a3, + efix=final_energy['setting', i], + en=energy_transfer['setting', i], + ) + for i, a3 in enumerate(sample_angle) + ] diff --git a/packages/essspectroscopy/src/ess/bifrost/live.py b/packages/essspectroscopy/src/ess/bifrost/live.py new file mode 100644 index 000000000..7f8394016 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/live.py @@ -0,0 +1,178 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Live data reduction workflows for BIFROST.""" + +from collections.abc import Callable +from dataclasses import dataclass +from typing import NewType + +import sciline +import scipp as sc +from ess.spectroscopy.types import ( + EnergyQDetector, + NeXusDetectorName, + RunType, +) + +from .types import ArcEnergy +from .workflow import BifrostWorkflow + + +@dataclass(frozen=True, kw_only=True, slots=True) +class CutAxis: + """Axis and bins for cutting 4D Q - delta E data. + + Each axis defines a projection of the :math:`Q` - :math:`\\Delta E` space + onto a 1D line as well as bin edges on that line. + + Examples + -------- + Cut along :math:`Q_x`: (see also :meth:`CutAxis.from_q_vector`) + + >>> from ess.bifrost.live import CutAxis + >>> axis = CutAxis( + ... output='Qx', + ... fn=lambda sample_table_momentum_transfer: sc.dot( + ... sc.vector([1, 0, 0]), + ... sample_table_momentum_transfer, + ... ), + ... bins=sc.linspace(dim='Qx', start=-0.5, stop=0.5, num=100, unit='1/Ã…'), + ... ) + + Cut along the norm :math:`|Q|`: + (Note that ``sc.norm`` is wrapped in a lambda to use the + proper name for the input coordinate, see :attr:`CutAxis.fn`.) + + >>> axis = CutAxis( + ... output='|Q|', + ... fn=lambda sample_table_momentum_transfer: sc.norm( + ... sample_table_momentum_transfer + ... ), + ... bins=sc.linspace(dim='|Q|', start=-0.9, stop=3.0, num=100, unit='1/Ã…'), + ... ) + + Cut along :math:`\\Delta E`: + + >>> axis = CutAxis( + ... output='E', + ... fn=lambda energy_transfer: energy_transfer, + ... bins=sc.linspace('E', -0.1, 0.1, 300, unit='meV') + ... ) + """ + + output: str + """Name of the output coordinate.""" + fn: Callable[[...], sc.Variable] + """Function to perform the cut. + + Used in :func:`scipp.transform_coords` and so should request input coordinates + by name. + """ + bins: sc.Variable + """Bin edges for the cut.""" + + @classmethod + def from_q_vector(cls, output: str, vec: sc.Variable, bins: sc.Variable): + """Construct from an arbitrary direction in Q.""" + vec = vec / sc.norm(vec) + return cls( + output=output, + fn=lambda sample_table_momentum_transfer: sc.dot( + vec, sample_table_momentum_transfer + ), + bins=bins, + ) + + +CutAxis1 = NewType('CutAxis1', CutAxis) +"""Sciline domain type for cut axis 1.""" +CutAxis2 = NewType('CutAxis2', CutAxis) +"""Sciline domain type for cut axis 1.""" + + +class CutData(sciline.Scope[RunType, sc.DataArray], sc.DataArray): + """Data that was cut along CutAxis1 and CutAxis2.""" + + +def arc_energy() -> ArcEnergy: + """Provide the BIFROST arc energies. + + Returns + ------- + : + The final energies for each of the 5 BIFROST analyzer arcs. + """ + return ArcEnergy( + sc.array(dims=['arc'], values=[2.7, 3.2, 3.8, 4.4, 5.0], unit='meV') + ) + + +def cut( + data: EnergyQDetector[RunType], + *, + axis_1: CutAxis1, + axis_2: CutAxis2, + arc_energy: ArcEnergy, +) -> CutData[RunType]: + """Cut data along two axes. + + This function projects the input ``data`` expressed in :math:`Q` and + :math:`\\Delta E` onto a 2D surface defined by the cut axes. + This integrates over the other dimensions while preserving the arc dimension + if present. Then, the projected data is histogrammed according to the axis bins. + + Parameters + ---------- + data: + Input data with coordinates "sample_table_momentum_transfer" and + "energy_transfer". + axis_1: + Defines the projection onto and binning in the first axis. + axis_2: + Defines the projection onto and binning in the second axis. + arc_energy: + The final energies for each analyzer arc. + + Returns + ------- + : + ``data`` projected and histogrammed along the cut axes. If the input has + an arc dimension, it is preserved in the output. Otherwise, all dimensions + are integrated. + """ + # Determine which dimensions to preserve + # Only preserve 'arc' dimension if present; concat everything else + preserve_dim = 'arc' if 'arc' in data.dims else None + + # Concat over all dimensions except the one we want to preserve + if preserve_dim is not None: + dims_to_concat = [dim for dim in data.dims if dim != preserve_dim] + else: + dims_to_concat = list(data.dims) + + new_coords = {axis_1.output, axis_2.output} + projected = data.bins.concat(dims_to_concat).transform_coords( + new_coords, + graph={axis_1.output: axis_1.fn, axis_2.output: axis_2.fn}, + keep_inputs=False, + ) + projected = projected.drop_coords(list(set(projected.coords.keys()) - new_coords)) + + # Add arc coordinate if we're working with arc dimension + # Note that this is for identifying the arc, it should NOT be used + # as a replacement for a precise final_energy coordinate! + if preserve_dim == 'arc': + projected = projected.assign_coords(arc=arc_energy) + + return CutData[RunType]( + projected.hist({axis_2.output: axis_2.bins, axis_1.output: axis_1.bins}) + ) + + +def BifrostQCutWorkflow(detector_names: list[NeXusDetectorName]) -> sciline.Pipeline: + """Workflow for BIFROST to compute cuts in Q-E-space.""" + workflow = BifrostWorkflow(detector_names) + workflow.insert(arc_energy) + workflow.insert(cut) + return workflow diff --git a/packages/essspectroscopy/src/ess/bifrost/normalization.py b/packages/essspectroscopy/src/ess/bifrost/normalization.py new file mode 100644 index 000000000..b105c9f50 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/normalization.py @@ -0,0 +1,91 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Normalization routines.""" + +import scipp as sc +from ess.spectroscopy.types import ( + IncidentEnergyDetector, + NormalizationMonitor, + NormalizedIncidentEnergyDetector, + ProtonCharge, + RunType, + UncertaintyBroadcastMode, + WavelengthMonitor, +) + +from ess.reduce.uncertainty import broadcast_uncertainties + + +def normalize_by_monitor_and_proton_charge( + detector: IncidentEnergyDetector[RunType], + monitor: WavelengthMonitor[RunType, NormalizationMonitor], + proton_charge: ProtonCharge[RunType], + uncertainty_broadcast_mode: UncertaintyBroadcastMode, +) -> NormalizedIncidentEnergyDetector[RunType]: + """Normalize detector data by a monitor and proton charge. + + This function divides the detector event weights by the distribution of the monitor + in incident wavelength and by the proton charge. The former accounts for the + wavelength-dependent transmission of the beam through the primary spectrometer. + The latter accounts for the measurement time and source strength. + + The detector is normalized according to + + .. math:: + + d_e^\\text{Norm} = d_e \\frac{\\Delta x_i}{m_i \\sum_j m_j} \\frac1{C} + + where :math:`d_e` is a detector event, :math:`m_i` is the monitor bin containing + the incident wavelength of that detector event, and :math:`\\Delta x_i` is the bin + width of that bin. Finally, :math:`C` is the proton charge. + The monitor term is chosen to have unit integral and represent a probability + density of incident neutrons. + + Parameters + ---------- + detector: + Detector events to normalize. + monitor: + Monitor histogram. + proton_charge: + Accumulated proton charge. + Scalar or per setting (a3 / a4). + uncertainty_broadcast_mode: + Choose how uncertainties of the monitor and proton charge + are broadcast to the sample data. + + Returns + ------- + : + The detector events normalized by the monitor and proton charge. + """ + # We should make this function public or move the normalization to ESSreduce. + from ess.reduce.normalization import _mask_detector_for_norm + + if 'time' in monitor.dims: + # Use a combined monitor distribution for all instrument settings. + monitor = monitor.sum('time') + + detector = _mask_detector_for_norm(detector=detector, monitor=monitor) + + norm = _monitor_distribution(monitor=monitor) + # Combine monitor and proton charge so we only operate on events once. + norm *= proton_charge + norm = broadcast_uncertainties( + norm, prototype=detector, mode=uncertainty_broadcast_mode + ) + return NormalizedIncidentEnergyDetector[RunType]( + detector.bins / sc.lookup(norm, dim=monitor.dim) + ) + + +def _monitor_distribution( + monitor: sc.DataArray, +) -> sc.DataArray: + coord = monitor.coords[monitor.dim] + delta_w = sc.DataArray(coord[1:] - coord[:-1], masks=monitor.masks) + return monitor / delta_w / sc.values(monitor).sum() + + +providers = (normalize_by_monitor_and_proton_charge,) diff --git a/packages/essspectroscopy/src/ess/bifrost/py.typed b/packages/essspectroscopy/src/ess/bifrost/py.typed new file mode 100644 index 000000000..e69de29bb diff --git a/packages/essspectroscopy/src/ess/bifrost/single_crystal/__init__.py b/packages/essspectroscopy/src/ess/bifrost/single_crystal/__init__.py new file mode 100644 index 000000000..b97208511 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/single_crystal/__init__.py @@ -0,0 +1,15 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) +"""A single crystal reduction workflow for BIFROST's Bragg peak monitor.""" + +from .q_map import make_q_map +from .workflow import ( + BifrostBraggPeakMonitorWorkflow, + BifrostSimulationBraggPeakMonitorWorkflow, +) + +__all__ = [ + "BifrostBraggPeakMonitorWorkflow", + "BifrostSimulationBraggPeakMonitorWorkflow", + "make_q_map", +] diff --git a/packages/essspectroscopy/src/ess/bifrost/single_crystal/conversion.py b/packages/essspectroscopy/src/ess/bifrost/single_crystal/conversion.py new file mode 100644 index 000000000..386834c3d --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/single_crystal/conversion.py @@ -0,0 +1,59 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Coordinate conversions for single crystal diffraction with BIFROST.""" + +import scippnexus as snx +from ess.spectroscopy.indirect.conversion import ( + rotate_to_sample_table_momentum_transfer, +) +from ess.spectroscopy.types import ( + ElasticCoordTransformGraph, + GravityVector, + Position, + QDetector, + RunType, + WavelengthDetector, +) +from scippneutron.conversion.graph import beamline as beamline_graphs +from scippneutron.conversion.graph import tof as tof_graphs + + +def single_crystal_coordinate_transformation_graph( + source_position: Position[snx.NXsource, RunType], + sample_position: Position[snx.NXsample, RunType], + gravity: GravityVector, +) -> ElasticCoordTransformGraph[RunType]: + """Return the coordinate transformation graph for single crystal diffraction.""" + base = tof_graphs.elastic_Q_vec(start='tof') + base['lab_momentum_transfer'] = base['Q_vec'] + return ElasticCoordTransformGraph[RunType]( + { + **beamline_graphs.beamline(scatter=True), + **base, + 'sample_position': lambda: sample_position, + 'source_position': lambda: source_position, + 'gravity': lambda: gravity, + 'sample_table_momentum_transfer': rotate_to_sample_table_momentum_transfer, + } + ) + + +def convert_wavelength_to_q( + with_wavelength: WavelengthDetector[RunType], + *, + graph: ElasticCoordTransformGraph[RunType], +) -> QDetector[RunType]: + """Convert ToF to Q.""" + transformed = with_wavelength.transform_coords( + ['a3', 'sample_table_momentum_transfer'], + graph=graph, + keep_intermediate=False, + keep_inputs=False, + keep_aliases=False, + rename_dims=False, # because otherwise, it would rename a3 -> Q + ) + return QDetector[RunType](transformed) + + +providers = (single_crystal_coordinate_transformation_graph, convert_wavelength_to_q) diff --git a/packages/essspectroscopy/src/ess/bifrost/single_crystal/detector.py b/packages/essspectroscopy/src/ess/bifrost/single_crystal/detector.py new file mode 100644 index 000000000..4ee7b71bc --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/single_crystal/detector.py @@ -0,0 +1,49 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2026 Scipp contributors (https://github.com/scipp) + +"""Bragg peak detector handling for BIFROST.""" + +import scippnexus as snx +from ess.spectroscopy.types import ( + Analyzer, + DetectorPositionOffset, + EmptyDetector, + NeXusComponent, + NeXusTransformation, + RunType, +) + +from ..detector import get_base_calibrated_detector_bifrost + + +def get_calibrated_bragg_peak_detector( + detector: NeXusComponent[snx.NXdetector, RunType], + analyzer: Analyzer[RunType], + *, + transform: NeXusTransformation[snx.NXdetector, RunType], + offset: DetectorPositionOffset[RunType], +) -> EmptyDetector[RunType]: + """Extract the data array corresponding to the Bragg peak detector's signal field. + + Parameters + ---------- + detector: + Loaded NeXus detector. + analyzer: + Loaded analyzer parameters. + transform: + Transformation that determines the detector position. + offset: + Offset to add to the detector position. + + Returns + ------- + : + Detector with geometry coordinates. + """ + return get_base_calibrated_detector_bifrost( + detector, analyzer, transform=transform, offset=offset + ) + + +providers = (get_calibrated_bragg_peak_detector,) diff --git a/packages/essspectroscopy/src/ess/bifrost/single_crystal/q_map.py b/packages/essspectroscopy/src/ess/bifrost/single_crystal/q_map.py new file mode 100644 index 000000000..6d73488e6 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/single_crystal/q_map.py @@ -0,0 +1,288 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Build a Q-map for single crystal diffraction.""" + +from collections.abc import Callable +from typing import Any + +import numpy as np +import numpy.typing as npt +import plopp as pp +import scipp as sc +from ess.spectroscopy.types import QDetector, RunType +from matplotlib.axes import Axes + +from .types import ( + CountsWithQMapCoords, + IntensityQparQperp, + IntensitySampleRotation, + QParallelBins, + QPerpendicularBins, + QProjection, + QRange, + SampleRotationBins, +) + + +def project_momentum_transfer( + counts: QDetector[RunType], + *, + q_projection: QProjection, +) -> CountsWithQMapCoords[RunType]: + """Project Q onto given axes and also compute the norm of Q.""" + transformed = counts.transform_coords( + ['Q_parallel', 'Q_perpendicular', 'Q'], + graph={ + 'Q_parallel': _make_projection_kernel(q_projection.parallel), + 'Q_perpendicular': _make_projection_kernel(q_projection.perpendicular), + 'Q': lambda sample_table_momentum_transfer: sc.norm( + sample_table_momentum_transfer + ), + }, + keep_inputs=False, + ) + if transformed.bins is not None: + transformed.bins.coords['a3'] = sc.bins_like( + transformed, transformed.coords['a3'] + ) + transformed.bins.coords['a4'] = sc.bins_like( + transformed, transformed.coords['a4'] + ) + transformed = transformed.bins.concat() + + return CountsWithQMapCoords[RunType](transformed) + + +def _make_projection_kernel(vector: sc.Variable) -> Callable[..., sc.Variable]: + normal = vector / sc.norm(vector) + + def projection(sample_table_momentum_transfer: sc.Variable) -> sc.Variable: + return sc.dot(sample_table_momentum_transfer, normal) + + return projection + + +def default_q_projection() -> QProjection: + return QProjection( + parallel=sc.vector(value=[0, 0, 1]), perpendicular=sc.vector(value=[1, 0, 0]) + ) + + +def histogram_qparallel_qperpendicular( + events: CountsWithQMapCoords[RunType], + q_parallel_bins: QParallelBins, + q_perpendicular_bins: QPerpendicularBins, +) -> IntensityQparQperp[RunType]: + """Histogram the data in Q_parallel and Q_perpendicular""" + return IntensityQparQperp[RunType]( + events.hist(Q_perpendicular=q_perpendicular_bins, Q_parallel=q_parallel_bins) + ) + + +def integrate_q( + events: CountsWithQMapCoords[RunType], + q_range: QRange, + sample_rotation_bins: SampleRotationBins, +) -> IntensitySampleRotation[RunType]: + """Integrate the data over |Q| and histogram in the sample rotation.""" + unit = events.bins.coords['Q'].unit + lo = q_range[0].to(unit=unit) + hi = q_range[1].to(unit=unit) + sliced = events.bins['Q', lo:hi] + try: + return IntensitySampleRotation[RunType](sliced.hist(a3=sample_rotation_bins)) + except ValueError as err: + if "empty data range" in err.args[0].lower(): + # This happens when the user selects an empty range Q range, + # which is mainly a problem in the widget. + return IntensitySampleRotation[RunType](_empty_angle_array_like(sliced)) + raise + + +def make_q_map( + events: sc.DataArray, + q_parallel_bins: int | sc.Variable, + q_perpendicular_bins: int | sc.Variable, + sample_rotation_bins: int | sc.Variable, + *, + circle_n_points: int = 100, + roi_fill_alpha: float = 0.2, + roi_fill_color: Any = 'C1', + roi_line_color: Any = 'C1', +) -> Any: + """Build a figure with a 2D Q-map and a 1D slice for a range of Q values.""" + import ipywidgets as ipw + from plopp.widgets import Box + + def make_q_hist(da: sc.DataArray) -> sc.DataArray: + return histogram_qparallel_qperpendicular( + da, q_parallel_bins, q_perpendicular_bins + ).rename(Q_perpendicular=r'$Q_{\perp}$', Q_parallel='$Q_{||}$') + + def make_q_slice(da: sc.DataArray, q_range: tuple[float, float]) -> sc.DataArray: + unit = da.bins.coords['Q'].unit + lo = q_range[0] * unit + hi = q_range[1] * unit + return integrate_q(da, (lo, hi), sample_rotation_bins) + + q_lo = events.bins.coords['Q'].min().value + q_hi = events.bins.coords['Q'].max().value + slider = ipw.FloatRangeSlider( + value=(q_lo, q_hi), min=q_lo, max=q_hi, step=(q_hi - q_lo) / 100 + ) + + slider_node = pp.widget_node(slider) + input_node = pp.Node(events) + q_map_node = pp.Node(make_q_hist, input_node) + q_slice_node = pp.Node(make_q_slice, input_node, slider_node) + q_map_fig = pp.imagefigure(q_map_node, aspect='equal', norm='log') + q_slice_fig = pp.linefigure(q_slice_node) + + roi_path = _ROICirclePath(q_lo, q_hi, circle_n_points) + roi_circle = _ROICircle( + roi_path, + q_map_fig.ax, + fill_alpha=roi_fill_alpha, + fill_color=roi_fill_color, + line_color=roi_line_color, + ) + + def update_roi(q_range: tuple[float, float]) -> None: + roi_circle.set(*q_range) + q_map_fig.canvas.draw() + + # Create a view without any output so that `update_roi` gets called + # when the slider is moved. See https://github.com/scipp/plopp/pull/496 + pp.View(pp.Node(update_roi, slider_node)) + return Box([[q_map_fig], [q_slice_fig], [slider]]) + + +class _ROICirclePath: + # The path is encoded as an array xy with shape (n_points * 2 + 1, 2). + # Where xy[:, 0] is the x coordinate and xy[:, 1] is the y coordinate. + # xy[:n_points] is the outer circle, xy[n_points:-1] is the inner circle. + # xy[-1] is the same as xy[0]; we close the path to be compatible with MPL. + + def __init__(self, r_inner: float, r_outer: float, n_points: int) -> None: + self._r_inner = r_inner + self._r_outer = r_outer + self._n_points = n_points + + self._angles = np.linspace(0, 2 * np.pi, n_points, endpoint=True) + # 2*n_points for the inner and outer circle, + # +1 to repeat the first point at the end. + self._xy = np.zeros((n_points * 2 + 1, 2), dtype=float) + + self.set_inner(r_inner) + self.set_outer(r_outer) + + @property + def r_inner(self) -> float: + return self._r_inner + + @property + def r_outer(self) -> float: + return self._r_outer + + @property + def closed_xy(self) -> npt.NDArray[float]: + # includes the last point + return self._xy + + @property + def open_xy(self) -> npt.NDArray[float]: + # does not include the last point + return self._xy[:-1] + + @property + def inner(self) -> npt.NDArray[float]: + # does not include the last point + return self._xy[self._n_points : -1] + + @property + def outer(self) -> npt.NDArray[float]: + # does not include the last point + return self._xy[: self._n_points] + + def set_inner(self, r: float) -> None: + # reverse=True makes MPL render this circle as a cutout. + self._r_inner = r + x, y = self.inner.T + self._set_circle(x, y, r, reverse=True) + + def set_outer(self, r: float) -> None: + self._r_outer = r + x, y = self.outer.T + self._set_circle(x, y, r, reverse=False) + self._xy[-1] = self._xy[0] + + def _set_circle( + self, x: npt.NDArray[float], y: npt.NDArray[float], r: float, reverse: bool + ) -> None: + if reverse: + angles = self._angles[::-1] + else: + angles = self._angles + + np.cos(angles, out=x) + x *= r + + np.sin(angles, out=y) + y *= r + + +class _ROICircle: + def __init__( + self, + path: _ROICirclePath, + ax: Axes, + *, + fill_alpha: float = 0.2, + fill_color: Any = 'C1', + line_color: Any = 'C1', + ) -> None: + self._path = path + self._fill = ax.fill( + *self._path.open_xy.T, fill_color, alpha=fill_alpha, zorder=-1 + )[0] + self._inner = ax.plot(*self._path.inner.T, c=line_color, zorder=2)[0] + self._outer = ax.plot(*self._path.outer.T, c=line_color, zorder=2)[0] + + def set(self, r_inner: float, r_outer: float) -> None: + if r_inner != self._path.r_inner: + self._path.set_inner(r_inner) + self._inner.set_data(*self._path.inner.T) + if r_outer != self._path.r_outer: + self._path.set_outer(r_outer) + self._outer.set_data(*self._path.outer.T) + self._fill.set_xy(self._path.closed_xy) + + +def _empty_angle_array_like( + reference: sc.DataArray, *, dim: str = 'sample_rotation' +) -> sc.DataArray: + a3_lo = reference.bins.coords[dim].min() + a3_hi = reference.bins.coords[dim].max() + return sc.DataArray( + sc.array( + dims=[dim], + values=[0, 0], + variances=[0, 0], + unit=reference.unit, + dtype=reference.dtype, + ), + coords={ + dim: sc.array( + dims=[dim], values=[a3_lo.value, a3_hi.value], unit=a3_lo.unit + ) + }, + ) + + +providers = ( + default_q_projection, + integrate_q, + histogram_qparallel_qperpendicular, + project_momentum_transfer, +) diff --git a/packages/essspectroscopy/src/ess/bifrost/single_crystal/time_of_flight.py b/packages/essspectroscopy/src/ess/bifrost/single_crystal/time_of_flight.py new file mode 100644 index 000000000..43b900e34 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/single_crystal/time_of_flight.py @@ -0,0 +1,43 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Utilities for computing real neutron time-of-flight.""" + +import scippnexus as snx +from ess.spectroscopy.types import ( + DataGroupedByRotation, + ErrorLimitedLookupTable, + PulseStrideOffset, + RawDetector, + RunType, + WavelengthDetector, +) + +from ess.reduce import unwrap as reduce_unwrap +from ess.reduce.unwrap.types import DetectorLtotal + + +def detector_wavelength_data( + sample_data: DataGroupedByRotation[RunType], + lookup: ErrorLimitedLookupTable[snx.NXdetector], + ltotal: DetectorLtotal[RunType], + pulse_stride_offset: PulseStrideOffset, +) -> WavelengthDetector[RunType]: + """ + Convert the time-of-arrival data to wavelength data using a lookup table. + + The output data will have a wavelength coordinate. + + This is a wrapper around + :func:`ess.reduce.unwrap.detector_wavelength_data` + for different input types. + """ + return reduce_unwrap.to_wavelength.detector_wavelength_data( + detector_data=RawDetector[RunType](sample_data), + lookup=lookup, + ltotal=ltotal, + pulse_stride_offset=pulse_stride_offset, + ) + + +providers = (detector_wavelength_data,) diff --git a/packages/essspectroscopy/src/ess/bifrost/single_crystal/types.py b/packages/essspectroscopy/src/ess/bifrost/single_crystal/types.py new file mode 100644 index 000000000..72edfeeb4 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/single_crystal/types.py @@ -0,0 +1,58 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Domain types for single crystal diffraction on BIFROST.""" + +from dataclasses import dataclass +from typing import NewType + +import sciline +import scipp as sc +from ess.spectroscopy.types import RunType + + +class CountsWithQMapCoords(sciline.Scope[RunType, sc.DataArray], sc.DataArray): + """Counts with various Q coordinates. + + Has (event) coordinates: + + - 'Q_parallel': projection along the beam direction, aka 'Qz' + - 'Q_perpendicular': perpendicular component of Q to the beam, aka 'Qx' + - 'Q': absolute value of Q + """ + + +@dataclass(frozen=True, slots=True) +class QProjection: + """Projection vectors in Q.""" + + parallel: sc.Variable + perpendicular: sc.Variable + + +QParallelBins = NewType("QParallelBins", sc.Variable) +"""Binning in Q_parallel (aka Qz).""" + +QPerpendicularBins = NewType("QPerpendicularBins", sc.Variable) +"""Binning in Q_perpendicular (aka Qx).""" + + +class IntensityQparQperp(sciline.Scope[RunType, sc.DataArray], sc.DataArray): + """Histogrammed data in Q_parallel and Q_perpendicular. + + Here, Q_parallel is the component of Q along the beam direction and Q_perpendicular + is the non-zero component of Q perpendicular to the beam direction. + For BIFROST, these are Qz and Qx respectively. (Qy is zero because the + detector is in the x-z plane with the sample.) + """ + + +class IntensitySampleRotation(sciline.Scope[RunType, sc.DataArray], sc.DataArray): + """Data integrated over |Q| and histogrammed in the sample rotation angle.""" + + +QRange = NewType("QRange", tuple[sc.Variable, sc.Variable]) +"""Range of |Q| to integrate over.""" + +SampleRotationBins = NewType("SampleRotationBins", sc.Variable) +"""Binning in the sample rotation angle.""" diff --git a/packages/essspectroscopy/src/ess/bifrost/single_crystal/workflow.py b/packages/essspectroscopy/src/ess/bifrost/single_crystal/workflow.py new file mode 100644 index 000000000..71bca0b8b --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/single_crystal/workflow.py @@ -0,0 +1,66 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) +"""BIFROST Bragg peak monitor workflows.""" + +import sciline +from ess.spectroscopy.indirect.time_of_flight import TofWorkflow +from ess.spectroscopy.types import ( + ElasticMonitor, + NormalizationMonitor, + SampleRun, +) + +from ess.reduce import unwrap as reduce_unwrap + +from ..cutting import group_by_rotation +from ..io import nexus +from ..io.mcstas import convert_simulated_time_to_event_time_offset +from ..workflow import default_parameters, simulation_default_parameters +from . import conversion, detector, q_map, time_of_flight + +_PROVIDERS = ( + *nexus.providers, + *conversion.providers, + *detector.providers, + *q_map.providers, + *time_of_flight.providers, + group_by_rotation, +) + +_SIMULATION_PROVIDERS = ( + *nexus.providers, + *conversion.providers, + *detector.providers, + *q_map.providers, + *time_of_flight.providers, + convert_simulated_time_to_event_time_offset, + group_by_rotation, +) + + +def BifrostBraggPeakMonitorWorkflow() -> sciline.Pipeline: + workflow = TofWorkflow( + run_types=(SampleRun,), + monitor_types=(ElasticMonitor, NormalizationMonitor), + ) + # Use the vanilla implementation instead of the indirect geometry one: + workflow.insert(reduce_unwrap.to_wavelength.detector_wavelength_data) + for provider in _PROVIDERS: + workflow.insert(provider) + for key, val in default_parameters().items(): + workflow[key] = val + return workflow + + +def BifrostSimulationBraggPeakMonitorWorkflow() -> sciline.Pipeline: + workflow = TofWorkflow( + run_types=(SampleRun,), + monitor_types=(ElasticMonitor, NormalizationMonitor), + ) + # Use the vanilla implementation instead of the indirect geometry one: + workflow.insert(reduce_unwrap.to_wavelength.detector_wavelength_data) + for provider in _SIMULATION_PROVIDERS: + workflow.insert(provider) + for key, val in simulation_default_parameters().items(): + workflow[key] = val + return workflow diff --git a/packages/essspectroscopy/src/ess/bifrost/types.py b/packages/essspectroscopy/src/ess/bifrost/types.py new file mode 100644 index 000000000..775fdaa69 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/types.py @@ -0,0 +1,22 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Domain types for BIFROST. + +This module supplements :mod:`ess.spectroscopy.types` with BIFROST-specific types. +""" + +from typing import NewType + +import sciline +import scipp as sc +from ess.spectroscopy.types import RunType + + +class ArcNumber(sciline.Scope[RunType, sc.Variable], sc.Variable): ... + + +class McStasRawDetector(sciline.Scope[RunType, sc.DataArray], sc.DataArray): ... + + +ArcEnergy = NewType('ArcEnergy', sc.Variable) diff --git a/packages/essspectroscopy/src/ess/bifrost/workflow.py b/packages/essspectroscopy/src/ess/bifrost/workflow.py new file mode 100644 index 000000000..eafd2aa69 --- /dev/null +++ b/packages/essspectroscopy/src/ess/bifrost/workflow.py @@ -0,0 +1,188 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""BIFROST workflows.""" + +from typing import Any + +import sciline +import scipp as sc +from ess.spectroscopy.indirect.conversion import providers as conversion_providers +from ess.spectroscopy.indirect.kf import providers as kf_providers +from ess.spectroscopy.indirect.ki import providers as ki_providers +from ess.spectroscopy.indirect.time_of_flight import TofWorkflow +from ess.spectroscopy.types import ( + ElasticMonitor, + EmptyDetector, + NeXusData, + NeXusDetectorName, + NeXusMonitorName, + NormalizationMonitor, + OverlapMonitor, + ProtonCharge, + PSCMonitor, + PulsePeriod, + RawDetector, + SampleRun, + UncertaintyBroadcastMode, +) +from scippnexus import NXdetector + +from .cutting import providers as cutting_providers +from .detector import merge_triplets +from .detector import providers as detector_providers +from .io import mcstas, nexus +from .normalization import providers as normalisation_providers + + +def default_parameters() -> dict[type, Any]: + """Default parameters for BifrostWorkflow.""" + return { + NeXusMonitorName[ElasticMonitor]: "elastic_monitor", + NeXusMonitorName[NormalizationMonitor]: "normalization_monitor", + NeXusMonitorName[OverlapMonitor]: "overlap_monitor", + NeXusMonitorName[PSCMonitor]: "psc_monitor", + PulsePeriod: 1.0 / sc.scalar(14.0, unit="Hz"), + UncertaintyBroadcastMode: UncertaintyBroadcastMode.fail, + **nexus.parameters, + } + + +def simulation_default_parameters() -> dict[type, Any]: + """Default parameters for BifrostSimulationWorkflow.""" + return { + **default_parameters(), + ProtonCharge[SampleRun]: sc.DataArray(sc.scalar(1.0, unit='pC')), + } + + +_PROVIDERS = ( + *nexus.providers, + *conversion_providers, + *detector_providers, + *cutting_providers, + *ki_providers, + *kf_providers, + *normalisation_providers, +) + +_SIMULATION_PROVIDERS = ( + *nexus.providers, + *conversion_providers, + *detector_providers, + *mcstas.providers, + *cutting_providers, + *ki_providers, + *kf_providers, + *normalisation_providers, +) + + +def BifrostSimulationWorkflow( + detector_names: list[NeXusDetectorName], +) -> sciline.Pipeline: + """Data reduction workflow for simulated BIFROST data. + + Parameters + ---------- + detector_names: + Names of ``NXdetector`` groups in the input NeXus file. + + Returns + ------- + : + A pipeline for reducing simulated BIFROST data. + """ + workflow = TofWorkflow( + run_types=(SampleRun,), + monitor_types=( + ElasticMonitor, + NormalizationMonitor, + OverlapMonitor, + PSCMonitor, + ), + ) + for provider in _SIMULATION_PROVIDERS: + workflow.insert(provider) + for key, val in simulation_default_parameters().items(): + workflow[key] = val + + workflow[RawDetector[SampleRun]] = ( + workflow[RawDetector[SampleRun]] + .map(_make_detector_name_mapping(detector_names)) + .reduce(func=merge_triplets) + ) + + return workflow + + +def BifrostWorkflow( + detector_names: list[NeXusDetectorName], +) -> sciline.Pipeline: + """Data reduction workflow for BIFROST.""" + workflow = TofWorkflow( + run_types=(SampleRun,), + monitor_types=( + ElasticMonitor, + NormalizationMonitor, + OverlapMonitor, + PSCMonitor, + ), + ) + for provider in _PROVIDERS: + workflow.insert(provider) + for key, val in default_parameters().items(): + workflow[key] = val + + workflow[EmptyDetector[SampleRun]] = ( + workflow[EmptyDetector[SampleRun]] + .map(_make_detector_name_mapping(detector_names)) + .reduce(func=merge_triplets) + ) + + workflow[NeXusData[NXdetector, SampleRun]] = ( + workflow[NeXusData[NXdetector, SampleRun]] + .map(_make_detector_name_mapping(detector_names)) + .reduce(func=concat_event_lists) + ) + + return workflow + + +# TODO remove or move +def concat_event_lists( + *data: sc.DataArray, +) -> sc.DataArray: + """Concatenate binned event lists into a single data array in 'event_time_zero'. + + Note that the output will likely have repeated values for 'event_time_zero'. + E.g., if input 1 has times `[0, 1, 2]` and input 2 has times `[0, 2, 3]`, + the output will have times `[0, 1, 2, 0, 2, 3]`. + Note that this sawtooth pattern will disappear again after grouping into pixels. + Preserving it will likely actually lead to more efficient memory + access patterns when grouping. + + Parameters + ---------- + data: + Data arrays to concatenate. + Must be binned in 'event_time_zero'. + + Returns + ------- + : + Concatenated data array. + """ + return sc.concat(data, dim="event_time_zero") + + +def _make_detector_name_mapping(detector_names: list[NeXusDetectorName]) -> Any: + # Use Pandas if possible to label the index. + try: + import pandas + + return pandas.DataFrame({NeXusDetectorName: detector_names}).rename_axis( + index='triplet' + ) + except ModuleNotFoundError: + return {NeXusDetectorName: detector_names} diff --git a/packages/essspectroscopy/src/ess/spectroscopy/__init__.py b/packages/essspectroscopy/src/ess/spectroscopy/__init__.py new file mode 100644 index 000000000..59722cd66 --- /dev/null +++ b/packages/essspectroscopy/src/ess/spectroscopy/__init__.py @@ -0,0 +1,20 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) +# ruff: noqa: I + +"""Data reduction for ESS spectroscopy experiments. + +This package contains common functionality for spectrometers at ESS. +For instrument-specifics, see + +- :mod:`ess.bifrost` +""" + +import importlib.metadata + +try: + __version__ = importlib.metadata.version("essspectroscopy") +except importlib.metadata.PackageNotFoundError: + __version__ = "0.0.0" + +del importlib diff --git a/packages/essspectroscopy/src/ess/spectroscopy/indirect/__init__.py b/packages/essspectroscopy/src/ess/spectroscopy/indirect/__init__.py new file mode 100644 index 000000000..93bcbcca3 --- /dev/null +++ b/packages/essspectroscopy/src/ess/spectroscopy/indirect/__init__.py @@ -0,0 +1,4 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Indirect spectroscopy at ESS.""" diff --git a/packages/essspectroscopy/src/ess/spectroscopy/indirect/conversion.py b/packages/essspectroscopy/src/ess/spectroscopy/indirect/conversion.py new file mode 100644 index 000000000..37fcaeae3 --- /dev/null +++ b/packages/essspectroscopy/src/ess/spectroscopy/indirect/conversion.py @@ -0,0 +1,305 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Coordinate conversions for indirect spectroscopy.""" + +import numpy as np +import scipp as sc +import scipp.constants +import scippnexus as snx +from scippneutron.conversion.tof import ( + energy_from_wavelength, + wavevector_from_wavelength, +) + +from ..types import ( + EnergyQDetector, + GravityVector, + IncidentEnergyDetector, + InelasticCoordTransformGraph, + MonitorCoordTransformGraph, + NormalizedIncidentEnergyDetector, + Position, + PrimarySpecCoordTransformGraph, + RunType, + SecondarySpecCoordTransformGraph, + WavelengthDetector, +) + + +def incident_energy_from_wavelength(*, incident_wavelength: sc.Variable) -> sc.Variable: + return energy_from_wavelength(wavelength=incident_wavelength) + + +def incident_wavevector_from_incident_wavelength( + *, incident_wavelength: sc.Variable, incident_beam: sc.Variable +) -> sc.Variable: + return wavevector_from_wavelength( + wavelength=incident_wavelength, beam=incident_beam + ) + + +def energy_transfer( + *, incident_energy: sc.Variable, final_energy: sc.Variable +) -> sc.Variable: + r"""Compute the energy transfer. + + Here, the energy transfer is defined the same as in ScippNeutron + (https://scipp.github.io/scippneutron/user-guide/coordinate-transformations.html) + to be + + .. math:: + + \Delta E = E_i - E_f + + Parameters + ---------- + incident_energy: + The neutron energy :math:`E_i` before scattering. + final_energy: + The neutron energy :math:`E_f` after scattering. + + Returns + ------- + : + The energy transfer :math:`\Delta E`. + """ + return incident_energy - final_energy.to(unit=incident_energy.unit, copy=False) + + +def lab_momentum_transfer_from_wavevectors( + incident_wavevector: sc.Variable, final_wavevector: sc.Variable +) -> sc.Variable: + r"""Compute the momentum transfer in the lab frame. + + Here, the momentum transfer is defined as + + .. math:: + + \vec{Q} = \vec{k_i} - \vec{k_f} + + Parameters + ---------- + incident_wavevector: + The neutron wavevector :math:`\vec{k_i}` before scattering. + final_wavevector: + The neutron wavevector :math:`\vec{k_f}` after scattering. + + Returns + ------- + : + The momentum transfer :math:`\vec{Q}` in the lab frame. + """ + return ( + incident_wavevector.to(unit=final_wavevector.unit, copy=False) + - final_wavevector + ) + + +def lab_momentum_transfer_from_incident_energy( + incident_energy: sc.Variable, + incident_beam: sc.Variable, + final_wavevector: sc.Variable, +) -> sc.Variable: + r"""Compute the momentum transfer in the lab frame. + + Here, the momentum transfer is defined as + + .. math:: + + \vec{Q} = \vec{k_i} - \vec{k_f} + + with + + .. math:: + + \vec{k_i} = \frac{2\pi}{h} \hat{b}_i \sqrt{2 M_n E_i} + + Parameters + ---------- + incident_energy: + The neutron energy :math:`E_i` before scattering. + incident_beam: + The vector of the incident beam in the lab frame :math:`\vec{b}_i`. + final_wavevector: + The neutron wavevector :math:`\vec{k_f}` after scattering. + + Returns + ------- + : + The momentum transfer :math:`\vec{Q}` in the lab frame. + """ + # Typical shapes: + # - incident_beam: () + # - incident_energy: (incident_energy,) (small) + # - final_wavevector: (detector,) (large-ish but 1D) + # - result: (detector, incident_energy) + incident_wavevector = ( + (2 * np.pi / sc.constants.h) + * (incident_beam / sc.norm(incident_beam)) + * sc.sqrt(2 * sc.constants.m_n * incident_energy) + ) + # Order of operations such that the final result has dim order described above. + return -final_wavevector + incident_wavevector.to( + unit=final_wavevector.unit, copy=False + ) + + +def rotate_to_sample_table_momentum_transfer( + *, + a3: sc.Variable, + lab_momentum_transfer: sc.Variable, + gravity: sc.Variable, +) -> sc.Variable: + r"""Rotate the momentum transfer vector into the sample-table coordinate system + + Here, the momentum transfer is defined as + + .. math:: + + \vec{Q} = \vec{k_i} - \vec{k_f} + + Note + ---- + When a3 is zero, the sample-table and lab coordinate systems are the same. + That is, Z is along the incident beam, Y is opposite the gravitational force, + and X completes the right-handed coordinate system. The sample-table angle, a3, + has a rotation vector along Y, such that a positive 90-degree rotation places the + sample-table Z along the lab X. + + Parameters + ---------- + a3: + The rotation angle of the sample table around the laboratory Y axis + lab_momentum_transfer: + The momentum transfer in the laboratory coordinate system + gravity: + The gravity vector which indicates the vertical axis. + + Returns + ------- + : + The momentum transfer in the sample-table coordinate system. + """ + vertical = -gravity / sc.norm(gravity) + # negative a3 since we rotate coordinates, not axes here + return sc.spatial.rotations_from_rotvecs(-a3 * vertical) * lab_momentum_transfer + + +def inelastic_coordinate_transformation_graph_at_sample( + gravity: GravityVector, +) -> InelasticCoordTransformGraph: + return InelasticCoordTransformGraph( + { + 'energy_transfer': energy_transfer, + 'incident_energy': incident_energy_from_wavelength, + 'incident_wavevector': incident_wavevector_from_incident_wavelength, + 'gravity': lambda: gravity, + 'lab_momentum_transfer': lab_momentum_transfer_from_wavevectors, + 'sample_table_momentum_transfer': rotate_to_sample_table_momentum_transfer, + } + ) + + +def add_inelastic_coordinates( + data: NormalizedIncidentEnergyDetector[RunType], graph: InelasticCoordTransformGraph +) -> EnergyQDetector[RunType]: + transformed = data.transform_coords( + [ + 'energy_transfer', + 'sample_table_momentum_transfer', + # These are inputs, but we want to preserve them + 'a3', + 'a4', + ], + graph=graph, + keep_aliases=False, + keep_inputs=False, + keep_intermediate=False, + rename_dims=False, + ) + return EnergyQDetector[RunType](transformed) + + +def add_incident_energy( + data: WavelengthDetector[RunType], graph: InelasticCoordTransformGraph +) -> IncidentEnergyDetector[RunType]: + transformed = data.transform_coords( + [ + 'incident_energy', + 'incident_wavelength', + # These are inputs, but we need them for binning: + 'a3', + 'a4', + 'final_energy', + 'final_wavevector', + ], + graph=graph, + keep_aliases=False, + keep_inputs=False, + keep_intermediate=False, + rename_dims=False, + ) + return IncidentEnergyDetector[RunType](transformed) + + +def add_spectrometer_coords( + detector: sc.DataArray, + primary_graph: PrimarySpecCoordTransformGraph[RunType], + secondary_graph: SecondarySpecCoordTransformGraph[RunType], +) -> sc.DataArray: + """Compute and add coordinates for the spectrometer. + + Parameters + ---------- + detector: + Data array with a "position" coordinate. + Does not need to contain events, wavelength, or flight times. + primary_graph: + Coordinate transformation graph for the primary spectrometer. + secondary_graph: + Coordinate transformation graph for the secondary spectrometer. + Must be a closure over analyzer parameters. + And those parameters must have a compatible shape with ``data``. + + Returns + ------- + : + Input data with added spectrometer coordinates. + This includes "final_energy", "secondary_flight_time", and "L1". + """ + return detector.transform_coords( + ( + 'final_energy', + 'final_wavevector', + 'incident_beam', + 'L1', + 'secondary_flight_time', + ), + graph={**primary_graph, **secondary_graph}, + keep_intermediate=False, + keep_aliases=False, + rename_dims=False, + ) + + +def monitor_coordinate_transformation_graph( + source_position: Position[snx.NXsource, RunType], +) -> MonitorCoordTransformGraph[RunType]: + from scippneutron.conversion.graph import beamline, tof + + return MonitorCoordTransformGraph[RunType]( + { + **beamline.beamline(scatter=False), + **tof.elastic_wavelength(start='tof'), + 'source_position': lambda: source_position, + } + ) + + +providers = ( + add_inelastic_coordinates, + add_incident_energy, + inelastic_coordinate_transformation_graph_at_sample, + monitor_coordinate_transformation_graph, +) diff --git a/packages/essspectroscopy/src/ess/spectroscopy/indirect/io.py b/packages/essspectroscopy/src/ess/spectroscopy/indirect/io.py new file mode 100644 index 000000000..84a2d8e65 --- /dev/null +++ b/packages/essspectroscopy/src/ess/spectroscopy/indirect/io.py @@ -0,0 +1,186 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2024 Scipp contributors (https://github.com/scipp) + +"""Input / output for indirect spectroscopy.""" + +from __future__ import annotations + +import h5py +import numpy +import scippnexus +from scipp import DataArray + +from ..types import EnergyQDetector, NXspeFileName, NXspeFileNames, SampleRun + + +def to_nxspe(events: EnergyQDetector[SampleRun], base: NXspeFileName) -> NXspeFileNames: + """Take events, which have been binned in incident wavelength and have monitor + counts per bin, and output one NXspe file per setting + + Parameters + ---------- + events: scipp.DataArray + The events binned in (setting, event_id, incident_wavelength) with + at least 'monitor', 'a3', and 'theta' bin coordinates. + The events and the bins must also have an 'incident_wavelength' coordinate. + base: str | Path + The filename base used to produce each NXspe filename. + + Returns + ------- + : + The list of filenames containing the NXspe data. If there are N settings in the + input DataArray, N filenames are returned. The names are of the form + + .. code-block:: + + {base}_{i+1:0{ceil(log10(N+1))}d}.nxspe + """ + from pathlib import Path + + dim = 'setting' + length = len(str(events.sizes[dim] + 1)) + files = [] + base = Path(base) + parent = base.parent + if not parent.exists(): + parent.mkdir(parents=True) + + for i in range(events.sizes[dim]): + ev = events[dim, i] + fn = str(base) + '_' + f'{i + 1}'.rjust(length, '0') + '.nxspe' + files.append(NXspeFileName(fn)) + _to_one_nxspe(ev, fn) + return NXspeFileNames(files) + + +def _make_group(group: h5py.Group) -> scippnexus.Group: + return scippnexus.Group(group, definitions=scippnexus.base_definitions()) + + +def _lambda_to_ei(incident_wavelength): + from scipp.constants import Planck, neutron_mass + + return ((Planck / incident_wavelength) ** 2 / neutron_mass / 2).to(unit='meV') + + +def _to_one_nxspe(events: DataArray, filename: str): + """Use scippnexus to create the NXspe file""" + import scipp as sc + from scippnexus import ( + NXcollection, + NXdata, + NXentry, + NXfermi_chopper, + NXinstrument, + NXsample, + ) + + from .conservation import energy_transfer + + observations = events.copy() + ef = events.coords['final_energy'] + observations *= sc.sqrt(events.bins.coords['incident_energy'] / ef) + + # Adding null events requires replicating all coordinates of real events. + # We don't necessarily use all present event coordinates, so remove any we won't use + targets = [ + 'energy_transfer', + 'incident_energy', + 'incident_wavelength', + 'final_energy', + ] + for coord in [x for x in events.bins.coords if x not in targets]: + del observations.bins.coords[coord] + # And provide a means to calculate the rest from bin (not event) information + # we are sure incident_wavelength is a bin coordinate already, so can skip it. + graph = { + 'incident_energy': _lambda_to_ei, + 'energy_transfer': energy_transfer, + } + # # Adding zero-weight observations, i.e., null events, works now, but involves + # # a memory-copy of the data array and its bin structure. Since it isn't strictly + # # necessary for exporting NXspe, it can be skipped for now. + # observations = add_null_observations(observations, targets, graph) + + # combine the per bin intensities and normalize by monitor counts + # Note, applying this normalization to the _events_ would require splitting + # the bin monitor counts between the bin events. + # we need to ignore the monitor uncertainty for the time being + normalize_by = sc.values(events.coords['monitor']) + + observations = observations.hist().transform_coords(targets, graph=graph) + + if observations.variances is None: + observations.variances = observations.values # correct for counting statistics + observations.variances[observations.values == 0] = 1 + # the transform_coords above renamed the 'incident_wavelength' dimension + # to 'energy_transfer' ... so we need to do the same to normalize_by or else + # scipp tries to broadcast when it doesn't need to. + observations.data = observations.data / normalize_by.rename_dims( + incident_wavelength='energy_transfer' + ) + + psi = observations.coords['a3'] + polar = observations.coords['theta'] + azimuthal = sc.zeros(sizes=polar.sizes, unit='deg', dtype=polar.dtype) + azimuthal_width = sc.full(sizes=polar.sizes, unit='deg', value=2.0) + polar_width = sc.full(sizes=polar.sizes, unit='deg', value=0.1) + distance = sc.full(sizes=polar.sizes, unit='m', value=3.0, dtype=polar.dtype) + data = observations.data + if observations.data.variances is not None: + error = numpy.sqrt(observations.data.variances) + else: + error = 0 * observations.data.values + energy_transfer = observations.coords['energy_transfer'] + incident_energy = observations.coords['incident_energy'] + final_energy = observations.coords['final_energy'] + + with h5py.File(filename, mode='w') as f: + # make / in the file + root = _make_group(f) + # it _must_ contain an NXentry group, called [anything which is allowed]? + # with two fields and five subgroups required + entry = root.create_class('entry', NXentry) + # the name of the author program + entry.create_field('program_name', sc.scalar('essspectroscopy')) + # and the NXDL schema information -- currently version 3.1 + definition = entry.create_field('definition', sc.scalar('NXSPE')) + definition.attrs['version'] = '3.1' + + # the entry group also contains five subgroups + + # the NXcollection group must contain three fields + nxinfo = entry.create_class('NXSPE_info', NXcollection) + nxinfo.create_field('fixed_energy', final_energy) + nxinfo.create_field('ki_over_kf_scaling', sc.scalar(True)) + nxinfo.create_field('psi', psi) + + # the NXdata group has 8 required fields + nxdata = entry.create_class('data', NXdata) + nxdata.create_field('azimuthal', azimuthal) + nxdata.create_field('azimuthal_width', azimuthal_width) + nxdata.create_field('polar', polar) + nxdata.create_field('polar_width', polar_width) + nxdata.create_field('distance', distance) + nxdata.create_field('data', data) + nxdata.create_field('error', error) + nxdata.create_field('energy', energy_transfer) + # Actually more useful extensions to NXspe for an instrument like BIFROST + nxdata.create_field('final_energy', final_energy) + nxdata.create_field('incident_energy', incident_energy) + + # the NXinstrument group has one required field and one required group + instrument = entry.create_class('instrument', NXinstrument) + instrument.create_field('name', sc.scalar('SIMBIFROST')) + fermi = instrument.create_class('fermi_chopper', NXfermi_chopper) + fermi.create_field('energy', sc.scalar(numpy.nan, unit='meV')) + + # and the NXsample group has three required fields + sample = entry.create_class('sample', NXsample) + sample.create_field('rotation_angle', psi) + sample.create_field('seblock', sc.scalar("")) + sample.create_field('temperature', sc.scalar(numpy.nan, unit='K')) + + +providers = (to_nxspe,) diff --git a/packages/essspectroscopy/src/ess/spectroscopy/indirect/kf.py b/packages/essspectroscopy/src/ess/spectroscopy/indirect/kf.py new file mode 100644 index 000000000..4a076557d --- /dev/null +++ b/packages/essspectroscopy/src/ess/spectroscopy/indirect/kf.py @@ -0,0 +1,275 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Handling of final parameters / secondary spectrometer.""" + +import numpy as np +import scipp as sc +from ess.spectroscopy.types import ( + DataAtSample, + DataGroupedByRotation, + PulsePeriod, + RunType, + SecondarySpecCoordTransformGraph, +) +from scippneutron.conversion.beamline import ( + BeamAlignedUnitVectors, +) + + +def sample_analyzer_vector( + sample_position: sc.Variable, + analyzer_position: sc.Variable, + analyzer_transform: sc.Variable, + detector_position: sc.Variable, +) -> sc.Variable: + """Determine the sample to analyzer-reflection-point vector per detector element + + Note + ---- + The shapes of the analyzer position and orientation should be self-consistent + and will likely be 1:1. There is expected to be multiple detector element positions + per analyzer which can be represented as an additional dimension compared to + the analyzer shapes. + + Parameters + ---------- + sample_position: + The (probably scalar) sample position, typically vector (0, 0, 0). + analyzer_position: + The nominal center of the central analyzer blade *surface*. + analyzer_transform: + The transform that places and rotates the analyzer in lab space. + Only the rotation is extracted to identify the crystal y-axis. + detector_position: + The position of the detector element. + + Returns + ------- + : + The vector from the sample position to the interaction point on the analyzer + for each detector element. + """ + # Scipp does not distinguish between coordinates and directions, so we need to do + # some extra legwork to ensure we can apply the orientation transformation + # _and_ obtain a dimensionless direction vector + o = sc.vector([0, 0, 0], unit=analyzer_transform.unit) + y = sc.vector( + [0, 1, 0], unit=analyzer_transform.unit + ) # and y perpendicular to the scattering plane + yhat = analyzer_transform * y - analyzer_transform * o + yhat /= sc.norm(yhat) + + sample_analyzer_center_vector = analyzer_position - sample_position + + sample_detector_vector = detector_position - sample_position + sd_out_of_plane = sc.dot(sample_detector_vector, yhat) + # the sample-detector vector is the sum of sample-analyzer, + # analyzer-detector-center, the out-of-plane vector + analyzer_detector_center_vector = ( + sample_detector_vector - sample_analyzer_center_vector - sd_out_of_plane * yhat + ) + + # TODO Consider requiring that dot(analyzer_position-sample_position, yhat) is zero? + + sample_analyzer_center_distance = sc.norm(sample_analyzer_center_vector) + + analyzer_detector_center_distance = sc.norm(analyzer_detector_center_vector) + + # similar-triangles give the out-of-plane analyzer reflection point distance + sa_out_of_plane = ( + sample_analyzer_center_distance + / (sample_analyzer_center_distance + analyzer_detector_center_distance) + * sd_out_of_plane + ) + + return sample_analyzer_center_vector + sa_out_of_plane * yhat + + +def detector_geometric_a4( + *, + sample_analyzer_vector: sc.Variable, + beam_aligned_unit_vectors: BeamAlignedUnitVectors, +) -> sc.Variable: + """Calculate the scattering angle from the incident beam to each detector element + + Parameters + ---------- + sample_analyzer_vector: + The per detector element analyzer interaction position, as determined + by :func:`sample_analyzer_vector`. + beam_aligned_unit_vectors: + Unit vectors defining the coordinate system aligned with the incident beam + and gravity. + See :func:`scippneutron.conversion.beamline.beam_aligned_unit_vectors`. + + Returns + ------- + : + The per detector element scattering angle, a4, in degrees. + """ + lab_x = beam_aligned_unit_vectors['beam_aligned_unit_x'] + lab_z = beam_aligned_unit_vectors['beam_aligned_unit_z'] + x = sc.dot(lab_x, sample_analyzer_vector) + z = sc.dot(lab_z, sample_analyzer_vector) + return sc.atan2(y=x, x=z).to(unit='deg') + + +def analyzer_detector_vector( + sample_position: sc.Variable, + sample_analyzer_vector: sc.Variable, + detector_position: sc.Variable, +) -> sc.Variable: + """Calculate the analyzer-detector vector""" + analyzer_position = sample_position + sample_analyzer_vector.to( + unit=sample_analyzer_vector.unit + ) + return detector_position - analyzer_position.to(unit=detector_position.unit) + + +def final_wavenumber( + sample_analyzer_vector: sc.Variable, + analyzer_detector_vector: sc.Variable, + analyzer_dspacing: sc.Variable, +) -> sc.Variable: + r"""Find the wave number of the neutrons reflected to each detector-element. + + The wave number and wavelength are inversely proportional with + + .. math:: + + \text{wavelength} = 2 * \pi / \text{wavenumber} + + Parameters + ---------- + sample_analyzer_vector: + The vector from the sample to the analyzer interaction point for each + detector element. + analyzer_detector_vector: + The vector from the analyzer interaction point to its detector element, + for each detector element. + analyzer_dspacing: + The lattice plane spacing of the analyzer crystal. + + Returns + ------- + : + The magnitude of the reflected neutron wave vector for each detector element. + """ + # law of Cosines gives the scattering angle based on distances: + l_sa = sc.norm(sample_analyzer_vector) + l_ad = sc.norm(analyzer_detector_vector) + l_diff = sc.norm(sample_analyzer_vector + analyzer_detector_vector) + # 2 theta is measured from the direction S-A, so the internal angle is + # (pi - 2 theta) and the normal law of Cosines is modified accordingly to be + # -cos(2 theta) instead of cos(pi - 2 theta) + cos2theta = (l_diff**2 - l_sa**2 - l_ad**2) / (2 * l_sa * l_ad) + + # law of Cosines gives the Bragg reflected wavevector magnitude + return ( + 2 * np.pi / sc.sqrt(2 - 2 * cos2theta) / analyzer_dspacing.to(unit='angstrom') + ) + + +def final_energy(final_wavenumber: sc.Variable) -> sc.Variable: + """Converts (final) wave number to (final) energy""" + from scipp.constants import hbar, neutron_mass + + return ((hbar**2 / 2 / neutron_mass) * final_wavenumber**2).to(unit='meV') + + +def final_wavevector( + sample_analyzer_vector: sc.Variable, final_wavenumber: sc.Variable +) -> sc.Variable: + """Constructs the final wave vector from its direction and magnitude""" + return ( + sample_analyzer_vector + / sc.norm(sample_analyzer_vector) + * final_wavenumber.to(unit='1/angstrom') + ) + + +def secondary_flight_path_length( + sample_analyzer_vector: sc.Variable, + analyzer_detector_vector: sc.Variable, +) -> sc.Variable: + """Returns the path-length-distance between the sample and each detector element""" + ad = sc.norm(analyzer_detector_vector) + sa = sc.norm(sample_analyzer_vector).to(unit=ad.unit) + return sa + ad + + +def secondary_flight_time( + L2: sc.Variable, final_wavenumber: sc.Variable +) -> sc.Variable: + """Calculates the most-likely time-of-flight between the sample and each pixel""" + from scipp.constants import hbar, neutron_mass + + velocity = final_wavenumber * (hbar / neutron_mass) + return sc.to_unit(L2 / velocity, 'ms', copy=False) + + +def secondary_spectrometer_coordinate_transformation_graph() -> ( + SecondarySpecCoordTransformGraph[RunType] +): + """Return a coordinate transformation graph for the secondary spectrometer. + + Returns + ------- + : + Coordinate transformation graph for the secondary spectrometer. + """ + from scippneutron.conversion.beamline import beam_aligned_unit_vectors + + return SecondarySpecCoordTransformGraph[RunType]( + { + "a4": detector_geometric_a4, + "beam_aligned_unit_vectors": beam_aligned_unit_vectors, + "detector_position": "position", + "sample_analyzer_vector": sample_analyzer_vector, + "analyzer_detector_vector": analyzer_detector_vector, + "final_energy": final_energy, + "final_wavenumber": final_wavenumber, + "final_wavevector": final_wavevector, + "L2": secondary_flight_path_length, + "secondary_flight_time": secondary_flight_time, + } + ) + + +def move_time_to_sample( + data: DataGroupedByRotation[RunType], pulse_period: PulsePeriod +) -> DataAtSample[RunType]: + """Return the events with the event_time_offset coordinate offset to time at sample. + + Parameters + ---------- + data: + Data array with "event_time_offset" and "secondary_flight_time" coordinates. + pulse_period: + Duration of a neutron pulse. + + Returns + ------- + : + A shallow copy of ``data`` where the "event_time_offset" coordinate has been + shifted to the time at the sample. + """ + offset = data.coords['secondary_flight_time'].to( + unit=data.bins.coords['event_time_offset'].unit, copy=False + ) + time = data.bins.coords['event_time_offset'] - offset + time %= pulse_period.to(unit=time.unit) + return DataAtSample[RunType]( + data + # These are the detector positions and they no longer match the time: + .drop_coords(('position', 'x_pixel_offset', 'y_pixel_offset')) + # Use bins.assign_coords to avoid modifying the original data: + .bins.assign_coords(event_time_offset=time) + ) + + +providers = ( + secondary_spectrometer_coordinate_transformation_graph, + move_time_to_sample, +) diff --git a/packages/essspectroscopy/src/ess/spectroscopy/indirect/ki.py b/packages/essspectroscopy/src/ess/spectroscopy/indirect/ki.py new file mode 100644 index 000000000..7d458dc18 --- /dev/null +++ b/packages/essspectroscopy/src/ess/spectroscopy/indirect/ki.py @@ -0,0 +1,59 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Handling of initial parameters / primary spectrometer.""" + +from __future__ import annotations + +import scippnexus as snx +from ess.spectroscopy.types import ( + GravityVector, + Position, + PrimarySpecCoordTransformGraph, + RunType, +) + + +def primary_spectrometer_coordinate_transformation_graph( + source_position: Position[snx.NXsource, RunType], + sample_position: Position[snx.NXsample, RunType], + gravity: GravityVector, +) -> PrimarySpecCoordTransformGraph[RunType]: + """Return a coordinate transformation graph for the primary spectrometer. + + Parameters + ---------- + source_position: + Position of the neutron source. + sample_position: + Position of the sample. + gravity: + Gravity vector. + + Returns + ------- + : + Coordinate transformation graph for the primary spectrometer. + """ + # For the incident beam, the original implementation here used the guides to + # determine a more accurate estimate of the path length. + # See function `primary_path_length` in + # commit 929ef7f97e00a1e26c254fd5f08c8a3346255970 + # The result differs by <1mm from the straight line distance. + # This should be well below the measurement accuracy. + # So we use the simpler straight line distance here. + + from scippneutron.conversion.beamline import L1, straight_incident_beam + + return PrimarySpecCoordTransformGraph[RunType]( + { + "incident_beam": straight_incident_beam, + "L1": L1, + "sample_position": lambda: sample_position, + "source_position": lambda: source_position, + "gravity": lambda: gravity, + } + ) + + +providers = (primary_spectrometer_coordinate_transformation_graph,) diff --git a/packages/essspectroscopy/src/ess/spectroscopy/indirect/time_of_flight.py b/packages/essspectroscopy/src/ess/spectroscopy/indirect/time_of_flight.py new file mode 100644 index 000000000..f19ef099e --- /dev/null +++ b/packages/essspectroscopy/src/ess/spectroscopy/indirect/time_of_flight.py @@ -0,0 +1,160 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Utilities for computing real neutron time-of-flight for indirect geometry.""" + +from collections.abc import Iterable + +import sciline +import scippnexus as snx + +from ess.reduce import unwrap as reduce_unwrap +from ess.reduce.unwrap.types import DetectorLtotal + +from ..types import ( + DataAtSample, + ErrorLimitedLookupTable, + LookupTable, + LookupTableRelativeErrorThreshold, + MonitorCoordTransformGraph, + MonitorLtotal, + MonitorType, + NeXusDetectorName, + PulseStrideOffset, + RawDetector, + RawMonitor, + RunType, + WavelengthDetector, + WavelengthMonitor, +) + + +def TofWorkflow( + *, + run_types: Iterable[sciline.typing.Key], + monitor_types: Iterable[sciline.typing.Key], +) -> sciline.Pipeline: + workflow = reduce_unwrap.GenericUnwrapWorkflow( + run_types=run_types, + monitor_types=monitor_types, + ) + for provider in providers: + workflow.insert(provider) + return workflow + + +def detector_wavelength_data( + sample_data: DataAtSample[RunType], + lookup: ErrorLimitedLookupTable[snx.NXdetector], + pulse_stride_offset: PulseStrideOffset, +) -> WavelengthDetector[RunType]: + """ + Convert the time-of-arrival data to wavelength data using a lookup table. + + The output data will have a wavelength coordinate. + + This is a wrapper around + :func:`ess.reduce.unwrap.detector_wavelength_data` + for indirect geometry spectrometers. + """ + result = reduce_unwrap.to_wavelength.detector_wavelength_data( + detector_data=RawDetector[RunType](sample_data), + lookup=lookup, + ltotal=DetectorLtotal(sample_data.coords['L1']), + pulse_stride_offset=pulse_stride_offset, + ) + # This is the incident wavelength at the sample. + result.bins.coords['incident_wavelength'] = result.bins.coords.pop('wavelength') + del result.bins.coords['event_time_zero'] + return result + + +def monitor_wavelength_data( + monitor_data: RawMonitor[RunType, MonitorType], + lookup: ErrorLimitedLookupTable[MonitorType], + ltotal: MonitorLtotal[RunType, MonitorType], + pulse_stride_offset: PulseStrideOffset, +) -> WavelengthMonitor[RunType, MonitorType]: + """ + Convert the time-of-arrival data to wavelength data using a lookup table. + + The output data will have a wavelength coordinate. + + This is a wrapper around + :func:`ess.reduce.unwrap.monitor_wavelength_data` + for indirect geometry spectrometers. + """ + result = reduce_unwrap.to_wavelength.monitor_wavelength_data( + monitor_data=monitor_data.rename(t='frame_time'), + lookup=lookup, + ltotal=ltotal, + pulse_stride_offset=pulse_stride_offset, + ) + result = result.rename(wavelength='incident_wavelength') + return result + + +def compute_monitor_ltotal( + monitor_data: RawMonitor[RunType, MonitorType], + coord_transform_graph: MonitorCoordTransformGraph, +) -> MonitorLtotal[RunType, MonitorType]: + """Compute the path length from the source to the monitor.""" + return MonitorLtotal[RunType, MonitorType]( + monitor_data.transform_coords( + 'Ltotal', + graph=coord_transform_graph, + keep_intermediate=False, + keep_aliases=False, + rename_dims=False, + ).coords['Ltotal'] + ) + + +def mask_large_uncertainty_in_lut_detector( + table: LookupTable, + error_threshold: LookupTableRelativeErrorThreshold, +) -> ErrorLimitedLookupTable[snx.NXdetector]: + """ + Mask regions in the wavelength lookup table with large uncertainty using NaNs. + + The threshold is looked up under the key ``'detector'``. + The same threshold is applied to all triplets. + + Parameters + ---------- + table: + Lookup table with wavelength as a function of distance and time-of-arrival. + error_threshold: + Threshold for the relative standard deviation (coefficient of variation) of the + projected wavelength above which values are masked. + + See also + -------- + essreduce.unwrap.mask_large_uncertainty_in_lut: + The underlying implementation. + """ + from ess.reduce.unwrap.to_wavelength import ( + mask_large_uncertainty_in_lut_detector, + ) + + return ErrorLimitedLookupTable[snx.NXdetector]( + mask_large_uncertainty_in_lut_detector( + table=table, + error_threshold=error_threshold, + detector_name=NeXusDetectorName('detector'), + ) + ) + + +providers = ( + compute_monitor_ltotal, + detector_wavelength_data, + mask_large_uncertainty_in_lut_detector, + monitor_wavelength_data, +) +"""Providers for wavelength calculation on indirect geometry spectrometers. + +The providers here override the default providers of +:class:`ess.reduce.unwrap.GenericUnwrapWorkflow` +to customize the workflow for indirect geometry spectrometers. +""" diff --git a/packages/essspectroscopy/src/ess/spectroscopy/py.typed b/packages/essspectroscopy/src/ess/spectroscopy/py.typed new file mode 100644 index 000000000..e69de29bb diff --git a/packages/essspectroscopy/src/ess/spectroscopy/types.py b/packages/essspectroscopy/src/ess/spectroscopy/types.py new file mode 100644 index 000000000..d2be4e030 --- /dev/null +++ b/packages/essspectroscopy/src/ess/spectroscopy/types.py @@ -0,0 +1,149 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Domain types for spectroscopy.""" + +from typing import Any, NewType, TypeVar + +import sciline +import scipp as sc + +from ess.reduce import unwrap +from ess.reduce.nexus import types as reduce_t +from ess.reduce.uncertainty import UncertaintyBroadcastMode as _UncertaintyBroadcastMode + +# NeXus types + +Beamline = reduce_t.Beamline +DetectorPositionOffset = reduce_t.DetectorPositionOffset +DynamicPosition = reduce_t.DynamicPosition +EmptyDetector = reduce_t.EmptyDetector +Filename = reduce_t.Filename +GravityVector = reduce_t.GravityVector +Measurement = reduce_t.Measurement +NeXusClass = reduce_t.NeXusClass +NeXusComponentLocationSpec = reduce_t.NeXusComponentLocationSpec +NeXusComponent = reduce_t.NeXusComponent +NeXusData = reduce_t.NeXusData +NeXusDetectorName = reduce_t.NeXusDetectorName +NeXusFileSpec = reduce_t.NeXusFileSpec +NeXusMonitorName = reduce_t.NeXusName +NeXusTransformation = reduce_t.NeXusTransformation +Position = reduce_t.Position +PreopenNeXusFile = reduce_t.PreopenNeXusFile +RawDetector = reduce_t.RawDetector +RawMonitor = reduce_t.RawMonitor + +SampleRun = reduce_t.SampleRun +VanadiumRun = reduce_t.VanadiumRun + +# BIFROST monitors +ElasticMonitor = NewType('ElasticMonitor', int) +NormalizationMonitor = NewType('NormalizationMonitor', int) +PSCMonitor = NewType('PSCMonitor', int) +OverlapMonitor = NewType('OverlapMonitor', int) + +# Type vars + +RunType = TypeVar("RunType", SampleRun, VanadiumRun) +MonitorType = TypeVar( + "MonitorType", ElasticMonitor, NormalizationMonitor, PSCMonitor, OverlapMonitor +) + +# Time-of-flight types + +WavelengthDetector = unwrap.WavelengthDetector +WavelengthMonitor = unwrap.WavelengthMonitor +LookupTableRelativeErrorThreshold = unwrap.LookupTableRelativeErrorThreshold +MonitorLtotal = unwrap.MonitorLtotal +PulseStride = unwrap.PulseStride +PulseStrideOffset = unwrap.PulseStrideOffset +PulsePeriod = unwrap.PulsePeriod +ErrorLimitedLookupTable = unwrap.ErrorLimitedLookupTable +LookupTable = unwrap.LookupTable +LookupTableFilename = unwrap.LookupTableFilename + + +# Custom types + + +class Analyzer(sciline.Scope[RunType, sc.DataGroup[Any]], sc.DataGroup[Any]): + """A single wavelength analyzer loaded from an NXcrystal. + + Can be obtained from ``Analyzers``. + """ + + +class DataAtSample(sciline.Scope[RunType, sc.DataArray], sc.DataArray): ... + + +class DataGroupedByRotation(sciline.Scope[RunType, sc.DataArray], sc.DataArray): ... + + +class QDetector(sciline.Scope[RunType, sc.DataArray], sc.DataArray): + """Detector counts with a momentum transfer coordinate.""" + + +EnergyBins = NewType('EnergyBins', sc.Variable) + + +class EnergyData(sciline.Scope[RunType, sc.DataArray], sc.DataArray): ... + + +class EnergyQDetector(sciline.Scope[RunType, sc.DataArray], sc.DataArray): + """Detector counts with a momentum transfer and energy transfer coordinates.""" + + +class IncidentEnergyDetector(sciline.Scope[RunType, sc.DataArray], sc.DataArray): + """Detector counts with an incident energy coordinate.""" + + +class NormalizedIncidentEnergyDetector( + sciline.Scope[RunType, sc.DataArray], sc.DataArray +): + """Normalized detector counts with an incident energy coordinate.""" + + +class SampleAngle(sciline.Scope[RunType, sc.DataArray], sc.DataArray): + """Rotation angle of the sample, possibly as a function of time. + + For BIFROST, this is angle "a3". + """ + + +class InstrumentAngle(sciline.Scope[RunType, sc.DataArray], sc.DataArray): + """Rotation angle of the instrument, possibly as a function of time. + + For BIFROST, this is angle "a4". + """ + + +NXspeFileName = NewType('NXspeFileName', str) +NXspeFileNames = NewType('NXspeFileNames', list[NXspeFileName]) + +OutFilename = NewType("OutFilename", str) + + +class PrimarySpecCoordTransformGraph(sciline.Scope[RunType, dict], dict): ... + + +class SecondarySpecCoordTransformGraph(sciline.Scope[RunType, dict], dict): ... + + +InelasticCoordTransformGraph = NewType('InelasticCoordTransformGraph', dict) + + +class ElasticCoordTransformGraph(sciline.Scope[RunType, dict], dict): ... + + +class MonitorCoordTransformGraph(sciline.Scope[RunType, dict], dict): ... + + +SQWBinSizes = NewType('SQWBinSizes', dict[str, int]) + + +UncertaintyBroadcastMode = _UncertaintyBroadcastMode + + +class ProtonCharge(sciline.Scope[RunType, sc.DataArray], sc.DataArray): + """Accumulated proton charge for a measurement.""" diff --git a/packages/essspectroscopy/tests/bifrost/cutting_test.py b/packages/essspectroscopy/tests/bifrost/cutting_test.py new file mode 100644 index 000000000..52ef276f2 --- /dev/null +++ b/packages/essspectroscopy/tests/bifrost/cutting_test.py @@ -0,0 +1,106 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) +import numpy as np +import pytest +import scipp as sc +import scipp.testing +import scippnexus as snx +from ess import bifrost +from ess.bifrost.data import ( + lookup_table_simulation, + simulated_elastic_incoherent_with_phonon, +) +from ess.bifrost.live import CutAxis, CutAxis1, CutAxis2, arc_energy, cut +from ess.spectroscopy.types import ( + EnergyQDetector, + Filename, + LookupTableFilename, + LookupTableRelativeErrorThreshold, + NeXusDetectorName, + SampleRun, + UncertaintyBroadcastMode, +) + + +@pytest.fixture(scope='module') +def simulation_detector_names() -> list[NeXusDetectorName]: + with snx.File(simulated_elastic_incoherent_with_phonon()) as f: + names = list(f['entry']['instrument'][snx.NXdetector].keys()) + return names[:10] # First 10 detectors form a 5x2 grid (arc=5, channel=2) + + +@pytest.fixture +def energy_data( + simulation_detector_names: list[NeXusDetectorName], +) -> EnergyQDetector[SampleRun]: + workflow = bifrost.BifrostSimulationWorkflow(simulation_detector_names) + workflow[Filename[SampleRun]] = simulated_elastic_incoherent_with_phonon() + workflow[LookupTableFilename] = lookup_table_simulation() + workflow[LookupTableRelativeErrorThreshold] = { + 'detector': np.inf, + 'normalization_monitor': np.inf, + } + workflow[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.drop + return workflow.compute(EnergyQDetector[SampleRun]) + + +def test_cut_along_q_norm_and_energy_transfer_preserves_counts( + energy_data: EnergyQDetector[SampleRun], +) -> None: + # Define cut axes for |Q| and energy transfer + axis_1 = CutAxis( + output='|Q|', + fn=lambda sample_table_momentum_transfer: sc.norm( + sample_table_momentum_transfer + ), + bins=sc.linspace(dim='|Q|', start=0.0, stop=3.0, num=50, unit='1/angstrom'), + ) + axis_2 = CutAxis( + output='E', + fn=lambda energy_transfer: energy_transfer, + bins=sc.linspace(dim='E', start=-10.0, stop=15.0, num=50, unit='meV'), + ) + + cut_data = cut( + energy_data, + axis_1=CutAxis1(axis_1), + axis_2=CutAxis2(axis_2), + arc_energy=arc_energy(), + ) + + # Verify no counts were lost during the cut + total_counts_before = sc.sum(energy_data.sum()) + # Remove left over scalar coords that are dropped by `cut`: + total_counts_before = total_counts_before.drop_coords(total_counts_before.coords) + total_counts_after = sc.sum(cut_data) + sc.testing.assert_allclose(total_counts_before, total_counts_after) + + +def test_cut_along_qx_direction_preserves_counts( + energy_data: EnergyQDetector[SampleRun], +) -> None: + # Test cutting along a specific Q direction (Qx) + axis_1 = CutAxis.from_q_vector( + output='Qx', + vec=sc.vector([1, 0, 0]), + bins=sc.linspace(dim='Qx', start=-3.0, stop=2.0, num=40, unit='1/angstrom'), + ) + axis_2 = CutAxis( + output='E', + fn=lambda energy_transfer: energy_transfer, + bins=sc.linspace(dim='E', start=-10.0, stop=15.0, num=30, unit='meV'), + ) + + cut_data = cut( + energy_data, + axis_1=CutAxis1(axis_1), + axis_2=CutAxis2(axis_2), + arc_energy=arc_energy(), + ) + + # Verify no counts were lost during the cut + total_counts_before = sc.sum(energy_data.sum()) + # Remove left over scalar coords that are dropped by `cut`: + total_counts_before = total_counts_before.drop_coords(total_counts_before.coords) + total_counts_after = sc.sum(cut_data) + sc.testing.assert_allclose(total_counts_before, total_counts_after) diff --git a/packages/essspectroscopy/tests/bifrost/io/sqw_test.py b/packages/essspectroscopy/tests/bifrost/io/sqw_test.py new file mode 100644 index 000000000..2cc900684 --- /dev/null +++ b/packages/essspectroscopy/tests/bifrost/io/sqw_test.py @@ -0,0 +1,245 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +# Writing an SQW file is fairly slow. +# So the tests in this module use module-scoped fixtures to write a single file +# that is shared between all tests. +# Function-scoped fixtures allow accessing that file for reading. + +import itertools +from collections import Counter +from collections.abc import Generator +from pathlib import Path + +import numpy as np +import numpy.typing as npt +import pytest +import sciline +import scipp as sc +import scipp.testing +import scippnexus as snx +from ess import bifrost +from ess.bifrost.data import ( + lookup_table_simulation, + simulated_elastic_incoherent_with_phonon, +) +from ess.spectroscopy.types import ( + EnergyBins, + Filename, + LookupTableFilename, + LookupTableRelativeErrorThreshold, + NeXusDetectorName, + OutFilename, + PreopenNeXusFile, + SampleRun, + SQWBinSizes, + UncertaintyBroadcastMode, +) +from scippneutron.io import sqw + +N_DETECTORS = 3 +N_ANGLES = 178 +N_DET_ROTATIONS = 2 + +BIN_SIZES = {'u1': 6, 'u2': 7, 'u3': 8, 'u4': 9} +ENERGY_BIN_SIZE = 13 + +# Q projections +U = sc.vector([1, 0, 0], unit="1/angstrom") +V = sc.vector([0, 1, 0], unit="1/angstrom") +W = sc.vector([0, 0, 1], unit="1/angstrom") + +N_PIXELS_PER_DETECTOR = 300 # Fixed, not a parameter! + + +@pytest.fixture(scope='module') +def detector_names() -> list[NeXusDetectorName]: + with snx.File(simulated_elastic_incoherent_with_phonon()) as f: + detector_names = list(f['entry/instrument'][snx.NXdetector]) + return detector_names[:N_DETECTORS] + + +@pytest.fixture(scope='module') +def sample() -> sqw.SqwIXSample: + return sqw.SqwIXSample( + name="Vibranium", + lattice_spacing=sc.vector([2.86, 2.86, 2.86], unit="angstrom"), + lattice_angle=sc.vector([90.0, 90.0, 90.0], unit="deg"), + ) + + +@pytest.fixture(scope='module') +def common_workflow( + detector_names: list[NeXusDetectorName], sample: sqw.SqwIXSample +) -> sciline.Pipeline: + wf = bifrost.BifrostSimulationWorkflow(detector_names) + + wf[Filename[SampleRun]] = simulated_elastic_incoherent_with_phonon() + wf[LookupTableFilename] = lookup_table_simulation() + wf[LookupTableRelativeErrorThreshold] = { + 'detector': np.inf, + 'normalization_monitor': np.inf, + } + wf[PreopenNeXusFile] = PreopenNeXusFile(True) + wf[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.drop + wf[sqw.SqwIXSample] = sample + wf[EnergyBins] = ENERGY_BIN_SIZE + wf[SQWBinSizes] = BIN_SIZES + + return wf + + +@pytest.fixture(scope='module') +def write_file( + common_workflow: sciline.Pipeline, tmp_path_factory: pytest.TempPathFactory +) -> Path: + path = tmp_path_factory.mktemp("bifrost-sqw").joinpath("bifrost-simulated.sqw") + workflow = common_workflow.copy() + workflow[OutFilename] = path + workflow.bind_and_call(bifrost.io.sqw.save_sqw) + return path + + +@pytest.fixture +def output_file(write_file: Path) -> Generator[sqw.Sqw, None, None]: + with sqw.Sqw.open(write_file) as file: + yield file + + +def test_save_sqw_writes_instrument_metadata(output_file: sqw.Sqw) -> None: + instruments = output_file.read_data_block("experiment_info", "instruments") + + assert len(instruments) == N_ANGLES * N_DET_ROTATIONS + # All instruments are the same: + for instrument in instruments[1:]: + sc.testing.assert_identical(instrument, instruments[0]) + + instrument = instruments[0] + assert instrument.name == "bifrost" + sc.testing.assert_identical(instrument.source.frequency, sc.scalar(14.0, unit="Hz")) + + +def test_save_sqw_writes_sample_metadata( + output_file: sqw.Sqw, sample: sqw.SqwIXSample +) -> None: + samples = output_file.read_data_block("experiment_info", "samples") + + assert len(samples) == N_ANGLES * N_DET_ROTATIONS + # All samples are the same: + for s in samples: + sc.testing.assert_identical(s, sample) + + +def test_save_sqw_writes_experiment_metadata(output_file: sqw.Sqw) -> None: + experiments = output_file.read_data_block("experiment_info", "expdata") + + assert len(experiments) == N_ANGLES * N_DET_ROTATIONS + # N unique run ids + assert ( + len({experiment.run_id for experiment in experiments}) + == N_ANGLES * N_DET_ROTATIONS + ) + for experiment in experiments: + assert experiment.emode == sqw.EnergyMode.indirect + assert experiment.u == U + assert experiment.v == V + + # Every a3 (psi) is represented once per detector rotation + # because we have a regular grid. + psi_counts = Counter(experiment.psi.value for experiment in experiments) + assert all(count == N_DET_ROTATIONS for count in psi_counts.values()) + + +def test_save_sqw_writes_dnd_metadata( + output_file: sqw.Sqw, sample: sqw.SqwIXSample +) -> None: + metadata = output_file.read_data_block("data", "metadata") + + np.testing.assert_array_equal( + metadata.axes.n_bins_all_dims.values, list(BIN_SIZES.values()) + ) + + sc.testing.assert_identical(metadata.proj.u, U) + sc.testing.assert_identical(metadata.proj.v, V) + sc.testing.assert_identical(metadata.proj.w, W) + assert metadata.proj.type == "aaa" + assert not metadata.proj.non_orthogonal + + sc.testing.assert_identical(metadata.proj.lattice_spacing, sample.lattice_spacing) + sc.testing.assert_identical(metadata.proj.lattice_angle, sample.lattice_angle) + + +def test_save_sqw_writes_dnd_data(output_file: sqw.Sqw) -> None: + dnd = output_file.read_data_block("data", "nd_data") + values, errors, counts = dnd + # Fortran order + expected_shape = tuple(BIN_SIZES.values())[::-1] + assert values.shape == expected_shape + assert errors.shape == expected_shape + assert counts.shape == expected_shape + + +def test_save_sqw_writes_pixel_data(output_file: sqw.Sqw) -> None: + metadata = output_file.read_data_block("data", "metadata") + dnd = output_file.read_data_block("data", "nd_data") + pix = output_file.read_data_block("pix", "data_wrap") + + assert pix.shape == ( + N_DETECTORS + * N_PIXELS_PER_DETECTOR + * N_ANGLES + * ENERGY_BIN_SIZE + * N_DET_ROTATIONS, + 9, + ) + + n_pix = dnd[2].astype(int) + check_pixels_in_bin_ranges(pix, metadata, n_pix) + check_pixel_indices_in_ranges(pix) + + +def check_pixels_in_bin_ranges( + pix: npt.NDArray[np.float32], metadata: sqw.SqwDndMetadata, n_pix: npt.NDArray[int] +) -> None: + """Check that all pixels are within the bin edges defined in the dnd metadata.""" + img_range = metadata.axes.img_range + n_bins = metadata.axes.n_bins_all_dims.values + u_edges = [ + sc.linspace(f'u{i}', img_range[i][0], img_range[i][1], n_bins[i] + 1) + for i in range(len(n_bins)) + ] + + bin_offsets = np.r_[0, np.cumsum(n_pix.flat)] + for bin_index, (l, k, j, i) in enumerate( # noqa: E741 + itertools.product(*(range(nb) for nb in n_bins[::-1])) + ): + pix_slice = slice(bin_offsets[bin_index], bin_offsets[bin_index + 1]) + if pix_slice.stop <= pix_slice.start: + continue # empty bin => no pixels to check + for col, index in enumerate((i, j, k, l)): + p = pix[pix_slice, col] + p_min = p.min() # actual range + p_max = p.max() + e_min = u_edges[col][index].value # expected range + e_max = u_edges[col][index + 1].value + assert p_min >= e_min - 1e-6 # small offset to account for f32 rounding + assert p_max < e_max + 1e-6 + + +def check_pixel_indices_in_ranges(pix: npt.NDArray[np.float32]) -> None: + """Check that all indices in the pixel data are in the correct ranges.""" + + irun = pix[:, 4] + idet = pix[:, 5] + ien = pix[:, 6] + + # 1-based indices! + assert irun.min() == 1 + assert irun.max() == N_ANGLES * N_DET_ROTATIONS + assert ien.min() == 1 + assert ien.max() == ENERGY_BIN_SIZE + + # We cannot check the values of idet directly because they are a non-contiguous + # subset of all detector numbers. So just check that we have the correct number of + # distinct detectors: + assert np.unique(idet).size == N_DETECTORS * N_PIXELS_PER_DETECTOR diff --git a/packages/essspectroscopy/tests/bifrost/live_test.py b/packages/essspectroscopy/tests/bifrost/live_test.py new file mode 100644 index 000000000..dc2b22c52 --- /dev/null +++ b/packages/essspectroscopy/tests/bifrost/live_test.py @@ -0,0 +1,119 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) +import numpy as np +import pytest +import sciline +import scipp as sc +import scipp.testing +import scippnexus as snx +from ess.bifrost.data import ( + lookup_table_simulation, + simulated_elastic_incoherent_with_phonon, +) +from ess.bifrost.live import BifrostQCutWorkflow, CutAxis, CutAxis1, CutAxis2, CutData +from ess.spectroscopy.types import ( + Filename, + LookupTableFilename, + LookupTableRelativeErrorThreshold, + NeXusDetectorName, + ProtonCharge, + SampleRun, + UncertaintyBroadcastMode, +) + + +@pytest.fixture(scope='module') +def simulation_detector_names() -> list[NeXusDetectorName]: + with snx.File(simulated_elastic_incoherent_with_phonon()) as f: + names = list(f['entry']['instrument'][snx.NXdetector].keys()) + return names[:10] # First 10 detectors form a 5x2 grid (arc=5, channel=2) + + +class TestBifrostQCutWorkflow: + @pytest.fixture + def qcut_workflow( + self, simulation_detector_names: list[NeXusDetectorName] + ) -> sciline.Pipeline: + workflow = BifrostQCutWorkflow(simulation_detector_names) + workflow[Filename[SampleRun]] = simulated_elastic_incoherent_with_phonon() + workflow[LookupTableFilename] = lookup_table_simulation() + workflow[LookupTableRelativeErrorThreshold] = { + 'detector': np.inf, + 'normalization_monitor': np.inf, + } + workflow[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.drop + workflow[ProtonCharge[SampleRun]] = sc.DataArray(sc.scalar(1.0, unit='pC')) + return workflow + + def test_cut_along_q_norm_and_energy_transfer( + self, qcut_workflow: sciline.Pipeline + ) -> None: + # Define cut axes for |Q| and energy transfer + axis_1 = CutAxis( + output='|Q|', + fn=lambda sample_table_momentum_transfer: sc.norm( + sample_table_momentum_transfer + ), + bins=sc.linspace(dim='|Q|', start=0.0, stop=3.0, num=50, unit='1/angstrom'), + ) + axis_2 = CutAxis( + output='E', + fn=lambda energy_transfer: energy_transfer, + bins=sc.linspace(dim='E', start=-10.0, stop=10.0, num=50, unit='meV'), + ) + + qcut_workflow[CutAxis1] = axis_1 + qcut_workflow[CutAxis2] = axis_2 + + cut_data = qcut_workflow.compute(CutData[SampleRun]) + + # Verify the structure of the result (now 3-D with arc dimension) + assert cut_data.bins is None # Should be histogrammed + assert set(cut_data.dims) == {'arc', '|Q|', 'E'} + assert cut_data.sizes['arc'] == 5 + assert cut_data.sizes['|Q|'] == 49 # num bins - 1 + assert cut_data.sizes['E'] == 49 + assert 'arc' in cut_data.coords + assert '|Q|' in cut_data.coords + assert 'E' in cut_data.coords + + # Check that coordinates have expected units and values + cut_data.coords['arc'].to(unit='meV') + cut_data.coords['|Q|'].to(unit='1/angstrom') + cut_data.coords['E'].to(unit='meV') + + # Verify arc coordinate values + expected_arc_energies = sc.array( + dims=['arc'], values=[2.7, 3.2, 3.8, 4.4, 5.0], unit='meV' + ) + sc.testing.assert_allclose(cut_data.coords['arc'], expected_arc_energies) + + def test_cut_along_qx_direction_and_energy_transfer( + self, qcut_workflow: sciline.Pipeline + ) -> None: + # Test cutting along a specific Q direction (Qx) + axis_1 = CutAxis.from_q_vector( + output='Qx', + vec=sc.vector([1, 0, 0]), + bins=sc.linspace(dim='Qx', start=-2.0, stop=2.0, num=40, unit='1/angstrom'), + ) + axis_2 = CutAxis( + output='E', + fn=lambda energy_transfer: energy_transfer, + bins=sc.linspace(dim='E', start=-5.0, stop=5.0, num=30, unit='meV'), + ) + + qcut_workflow[CutAxis1] = axis_1 + qcut_workflow[CutAxis2] = axis_2 + + cut_data = qcut_workflow.compute(CutData[SampleRun]) + + # Verify the result structure (now 3-D with arc dimension) + assert cut_data.bins is None + assert set(cut_data.dims) == {'arc', 'Qx', 'E'} + assert cut_data.sizes['arc'] == 5 + assert cut_data.sizes['Qx'] == 39 + assert cut_data.sizes['E'] == 29 + assert 'arc' in cut_data.coords + assert 'Qx' in cut_data.coords + assert 'E' in cut_data.coords diff --git a/packages/essspectroscopy/tests/bifrost/workflow_test.py b/packages/essspectroscopy/tests/bifrost/workflow_test.py new file mode 100644 index 000000000..e3b42fca8 --- /dev/null +++ b/packages/essspectroscopy/tests/bifrost/workflow_test.py @@ -0,0 +1,128 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) +import numpy as np +import pytest +import sciline +import scipp as sc +import scipp.testing +import scippnexus as snx +from ess import bifrost +from ess.bifrost.data import ( + computed_energy_data_simulated_5x2, + lookup_table_simulation, + simulated_elastic_incoherent_with_phonon, +) +from ess.spectroscopy.types import ( + EnergyQDetector, + Filename, + LookupTableFilename, + LookupTableRelativeErrorThreshold, + NeXusDetectorName, + NormalizationMonitor, + RawDetector, + RawMonitor, + SampleRun, + UncertaintyBroadcastMode, + WavelengthMonitor, +) + + +@pytest.fixture(scope='module') +def simulation_detector_names() -> list[NeXusDetectorName]: + with snx.File(simulated_elastic_incoherent_with_phonon()) as f: + names = list(f['entry']['instrument'][snx.NXdetector].keys()) + return names[:10] # First 10 detectors form a 5x2 grid (arc=5, channel=2) + + +@pytest.fixture +def workflow(simulation_detector_names: list[NeXusDetectorName]) -> sciline.Pipeline: + workflow = bifrost.BifrostSimulationWorkflow(simulation_detector_names) + workflow[Filename[SampleRun]] = simulated_elastic_incoherent_with_phonon() + workflow[LookupTableFilename] = lookup_table_simulation() + workflow[LookupTableRelativeErrorThreshold] = { + 'detector': np.inf, + 'normalization_monitor': np.inf, + } + workflow[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.drop + return workflow + + +def test_simulation_workflow_can_load_detector() -> None: + workflow = bifrost.BifrostSimulationWorkflow( + [NeXusDetectorName("channel_3_1_triplet")] + ) + workflow[Filename[SampleRun]] = simulated_elastic_incoherent_with_phonon() + results = sciline.compute_mapped(workflow, RawDetector[SampleRun]) + result = results.iloc[0] + + assert result.bins is not None + assert set(result.dims) == {'tube', 'length', 'time'} + assert result.sizes['tube'] == 3 + assert 'position' in result.coords + + +def test_simulation_workflow_can_load_monitor(workflow: sciline.Pipeline) -> None: + result = workflow.compute(RawMonitor[SampleRun, NormalizationMonitor]) + + assert result.bins is None + assert 'position' in result.coords + + +def test_simulation_workflow_can_compute_energy_data( + workflow: sciline.Pipeline, +) -> None: + energy_data = workflow.compute(EnergyQDetector[SampleRun]) + + assert energy_data.sizes == { + 'arc': 5, + 'channel': 2, + 'tube': 3, + 'length': 100, + 'a3': 180, + 'a4': 2, + } + expected_coords = {'a3', 'a4', 'detector_number'} + assert expected_coords.issubset(energy_data.coords) + expected_event_coords = { + 'energy_transfer', + 'sample_table_momentum_transfer', + } + assert expected_event_coords.issubset(energy_data.bins.coords) + + # Check that conversions do not raise, i.e., units have expected dimensions. + energy_data.coords['a3'].to(unit='rad') + energy_data.coords['a4'].to(unit='rad') + energy_data.bins.coords['energy_transfer'].to(unit='meV') + energy_data.bins.coords['sample_table_momentum_transfer'].to(unit='1/Ã…') + + +def test_simulation_workflow_can_compute_wavelength_monitor( + workflow: sciline.Pipeline, +) -> None: + monitor = workflow.compute(WavelengthMonitor[SampleRun, NormalizationMonitor]) + assert set(monitor.dims) == {'time', 'incident_wavelength'} + expected_coords = {'position', 'incident_wavelength', 'time'} + assert expected_coords.issubset(monitor.coords) + assert monitor.bins is None + + +def test_simulation_workflow_produces_the_same_data_as_before( + workflow: sciline.Pipeline, +) -> None: + energy_data = workflow.compute(EnergyQDetector[SampleRun]) + expected = sc.io.load_hdf5(computed_energy_data_simulated_5x2()) + + assert not energy_data.masks + assert not energy_data.bins.masks + + assert set(expected.coords.keys()).issubset(set(energy_data.coords.keys())) + for name in expected.coords.keys(): + sc.testing.assert_allclose(energy_data.coords[name], expected.coords[name]) + + assert energy_data.bins.coords.keys() == expected.bins.coords.keys() + for name in energy_data.bins.coords.keys(): + sc.testing.assert_allclose( + energy_data.bins.coords[name], expected.bins.coords[name] + ) + + sc.testing.assert_allclose(energy_data.bins.data, expected.bins.data) diff --git a/packages/essspectroscopy/tests/package_test.py b/packages/essspectroscopy/tests/package_test.py new file mode 100644 index 000000000..4f2f34a7c --- /dev/null +++ b/packages/essspectroscopy/tests/package_test.py @@ -0,0 +1,21 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +"""Tests of package integrity. + +Note that additional imports need to be added for repositories that +contain multiple packages. +""" + +from ess import bifrost, spectroscopy + + +def test_has_version(): + assert hasattr(bifrost, '__version__') + assert hasattr(spectroscopy, '__version__') + + +# This is for CI package tests. They need to run tests with minimal dependencies, +# that is, without installing pytest. This code does not affect pytest. +if __name__ == '__main__': + test_has_version() diff --git a/packages/essspectroscopy/tests/spectroscopy/indirect/indirect_test.py b/packages/essspectroscopy/tests/spectroscopy/indirect/indirect_test.py new file mode 100644 index 000000000..0dd9e4f24 --- /dev/null +++ b/packages/essspectroscopy/tests/spectroscopy/indirect/indirect_test.py @@ -0,0 +1,176 @@ +# SPDX-License-Identifier: BSD-3-Clause +# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) + +import scipp as sc +from ess.spectroscopy.indirect import kf as secondary +from scipp import array, scalar, sqrt, vector +from scipp.spatial import rotations_from_rotvecs + + +def vectors_close(a, b, tol=None): + from scipp import scalar + + if tol is None: + tol = scalar(1e-8, unit=a.unit) + difference = a - b + return sc.norm(difference) < tol + + +def all_vectors_close(a, b, tol=None): + if len(a.shape) > 1 and len(b.shape) > 1: + for d in a.dims: + if d not in b.dims: + return False + if a.sizes[d] != b.sizes[d]: + return False + if a.shape != b.shape: + return False + return all_vectors_close(a.flatten(to='one'), b.flatten(to='one'), tol) + if len(a.shape) and len(b.shape): + if a.shape != b.shape: + return False + for x, y in zip(a, b, strict=True): + if not vectors_close(x, y, tol): + return False + elif len(a.shape): + for x in a: + if not vectors_close(x, b, tol): + return False + elif len(b.shape): + for y in b: + if not vectors_close(a, y, tol): + return False + else: + return vectors_close(a, b, tol) + return True + + +def test_back_scattering_sample_analyzer_vector(): + sample_position = vector([0.0, 0.0, 0.0], unit='m') + + # The analyzer orientation defines the scattering plane coordinate system: + analyzer_transform = rotations_from_rotvecs(vector([0.0, 0.0, 0.0], unit='degree')) + + x = analyzer_transform * vector([1.0, 0.0, 0.0], unit='1') + y = analyzer_transform * vector([0.0, 1.0, 0.0], unit='1') + z = analyzer_transform * vector([0.0, 0.0, 1.0], unit='1') + # sample-analyzer-vector must be along the local z axis + sample_analyzer_vec = scalar(1.0, unit='m') * z + analyzer_position = sample_analyzer_vec + sample_position + + # analyzer orientation of 90 degrees -> + # scattering angle of 180 degrees: back scattering + analyzer_orientation = rotations_from_rotvecs(scalar(90.0, unit='degree') * y) + + detector_y = analyzer_orientation * analyzer_orientation * y + assert vectors_close(detector_y, y) + # The detector positions are defined in the coordinate system, + # then rotated around the analyzer position + tubes = array(values=[-0.1, 0.0, 0.1], unit='m', dims=['tube']) * x + detector_positions = scalar(1.0, unit='m') * z + tubes + detector_positions = ( + analyzer_position + + analyzer_orientation * analyzer_orientation * detector_positions + ) + calculated = secondary.sample_analyzer_vector( + sample_position, analyzer_position, analyzer_orientation, detector_positions + ) + + # This would be 'right' for fixed tau direction, but we utilize the mosaic and + # insist on scattering from the center line of the analyzer + # offset = sample_analyzer_vec - tubes / 2.0 + # (minus because the detector has been rotated 180 degrees) + assert all_vectors_close(calculated, sample_analyzer_vec) + + # Offsetting along the analyzer scattering plane normal moves the analyzer + # intersection point by half + wires = array(values=[-0.1, 0.0, 0.1], unit='m', dims=['wire']) * y + detector_positions = scalar(1.0, unit='m') * z + wires + detector_positions = ( + analyzer_position + + analyzer_orientation * analyzer_orientation * detector_positions + ) + calculated = secondary.sample_analyzer_vector( + sample_position, analyzer_position, analyzer_orientation, detector_positions + ) + assert all_vectors_close(calculated, sample_analyzer_vec + wires / 2.0) + + # Offsetting in both transverse directions at once + detector_positions = scalar(1.0, unit='m') * z + wires + tubes + detector_positions = ( + analyzer_position + + analyzer_orientation * analyzer_orientation * detector_positions + ) + calculated = secondary.sample_analyzer_vector( + sample_position, analyzer_position, analyzer_orientation, detector_positions + ) + # as the x displacement increases, the y displacement should decrease + frac = wires / (1.0 + sqrt(1.0 + (sc.norm(tubes) / scalar(1.0, unit='m')) ** 2)) + assert all_vectors_close(calculated, sample_analyzer_vec + frac) + + +def test_sample_analyzer_vector(): + # TODO Randomize the sample position + # TODO Randomize the analyzer transformation (a3 angle) + # TODO Randomize the analyzer distance + # TODO Randomize the detector positions + + from random import random + + sample_position = vector([0.0, 0.0, 0.0], unit='m') + + # The analyzer orientation defines the scattering plane coordinate system: + analyzer_transform = rotations_from_rotvecs(vector([0.0, 0.0, 0.0], unit='degree')) + + x = analyzer_transform * vector([1.0, 0.0, 0.0], unit='1') + y = analyzer_transform * vector([0.0, 1.0, 0.0], unit='1') + z = analyzer_transform * vector([0.0, 0.0, 1.0], unit='1') + # sample-analyzer-vector must be along the local z axis + sample_analyzer_vec = scalar(0.5 + random(), unit='m') * z # noqa: S311 + sample_analyzer_vec /= sc.norm(sample_analyzer_vec).value + analyzer_position = sample_analyzer_vec + sample_position + + # Avoid sin(theta) values near 0 or 1 + analyzer_orientation = rotations_from_rotvecs(scalar(45.0, unit='degree') * y) + + detector_y = analyzer_orientation * analyzer_orientation * y + assert vectors_close(detector_y, y) + # The detector positions are defined in the coordinate system, + # then rotated around the analyzer position + tubes = array(values=[-0.1, 0.0, 0.1], unit='m', dims=['tube']) * x + detector_positions = scalar(1.0, unit='m') * z + tubes + detector_positions = ( + analyzer_position + + analyzer_orientation * analyzer_orientation * detector_positions + ) + calculated = secondary.sample_analyzer_vector( + sample_position, analyzer_position, analyzer_orientation, detector_positions + ) + offset = calculated - sample_analyzer_vec + assert all_vectors_close(offset, 0 * tubes) + + # Offsetting along the analyzer scattering plane normal moves + # the analyzer intersection point by half + wires = array(values=[-0.1, 0.0, 0.1], unit='m', dims=['wire']) * y + detector_positions = scalar(1.0, unit='m') * z + wires + detector_positions = ( + analyzer_position + + analyzer_orientation * analyzer_orientation * detector_positions + ) + calculated = secondary.sample_analyzer_vector( + sample_position, analyzer_position, analyzer_orientation, detector_positions + ) + assert all_vectors_close(calculated, sample_analyzer_vec + wires / 2.0) + + # Offsetting in both transverse directions at once + detector_positions = scalar(1.0, unit='m') * z + wires + tubes + detector_positions = ( + analyzer_position + + analyzer_orientation * analyzer_orientation * detector_positions + ) + calculated = secondary.sample_analyzer_vector( + sample_position, analyzer_position, analyzer_orientation, detector_positions + ) + # as the x displacement increases, the y displacement should decrease + frac = wires / (1.0 + sqrt(1.0 + (sc.norm(tubes) / scalar(1.0, unit='m')) ** 2)) + assert all_vectors_close(calculated, sample_analyzer_vec + frac) diff --git a/packages/essspectroscopy/tools/docs/bifrost-thumbnails.ipynb b/packages/essspectroscopy/tools/docs/bifrost-thumbnails.ipynb new file mode 100644 index 000000000..d8977b19e --- /dev/null +++ b/packages/essspectroscopy/tools/docs/bifrost-thumbnails.ipynb @@ -0,0 +1,146 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": {}, + "source": [ + "# BIFROST thumbnails\n", + "\n", + "This notebook generates the thumbnails used in the BIFROST user guide." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1", + "metadata": { + "jupyter": { + "is_executing": true + } + }, + "outputs": [], + "source": [ + "import matplotlib.pyplot as plt\n", + "import scipp as sc\n", + "import sciline\n", + "import scippnexus as snx\n", + "\n", + "from ess import bifrost\n", + "from ess.bifrost.data import (\n", + " simulated_elastic_incoherent_with_phonon,\n", + " lookup_table_simulation\n", + ")\n", + "from ess.spectroscopy.types import *" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2", + "metadata": {}, + "outputs": [], + "source": [ + "with snx.File(simulated_elastic_incoherent_with_phonon()) as f:\n", + " detector_names = list(f['entry/instrument'][snx.NXdetector])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3", + "metadata": {}, + "outputs": [], + "source": [ + "workflow = bifrost.BifrostSimulationWorkflow(detector_names)\n", + "workflow[Filename[SampleRun]] = simulated_elastic_incoherent_with_phonon()\n", + "workflow[LookupTableFilename] = lookup_table_simulation()\n", + "workflow[PreopenNeXusFile] = PreopenNeXusFile(True)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4", + "metadata": {}, + "outputs": [], + "source": [ + "scheduler = sciline.scheduler.NaiveScheduler()\n", + "data = workflow.compute(EnergyQDetector[SampleRun], scheduler=scheduler)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5", + "metadata": {}, + "outputs": [], + "source": [ + "def qx_qz_plot(style: str):\n", + " with plt.style.context(style):\n", + " fig, ax = plt.subplots(layout='constrained', figsize=(3, 2.5))\n", + " d = data['a4', 0].bins.concat().copy()\n", + " x = sc.vector([1, 0, 0])\n", + " z = sc.vector([0, 0, 1])\n", + " d.bins.coords['Qx'] = sc.dot(x, d.bins.coords['sample_table_momentum_transfer'])\n", + " d.bins.coords['Qz'] = sc.dot(z, d.bins.coords['sample_table_momentum_transfer'])\n", + " d.hist(Qz=100, Qx=100).plot(ax=ax)\n", + " ax.set_xlabel('$Q_x$ [1/Ã…]')\n", + " ax.set_ylabel('$Q_z$ [1/Ã…]')\n", + " fig.axes[-1].set_ylabel(None)\n", + " return fig" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6", + "metadata": {}, + "outputs": [], + "source": [ + "fig = qx_qz_plot('default')\n", + "fig.savefig(\n", + " \"../../docs/_static/thumbnails/bifrost_reduction_light.svg\",\n", + " transparent=True,\n", + ")\n", + "fig" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7", + "metadata": {}, + "outputs": [], + "source": [ + "fig = qx_qz_plot('dark_background')\n", + "fig.savefig(\n", + " \"../../docs/_static/thumbnails/bifrost_reduction_dark.svg\",\n", + " transparent=True,\n", + ")\n", + "fig" + ] + } + ], + "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": "3.11.10" + } + }, + "nbformat": 4, + 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packages/essdiffraction name: essdiffraction requires_dist: @@ -20010,3 +21857,31 @@ packages: - sphinx-design ; extra == 'docs' - tof ; extra == 'docs' requires_python: '>=3.11' +- pypi: packages/essspectroscopy + name: essspectroscopy + requires_dist: + - essreduce>=26.4.1 + - graphviz>=0.20 + - pandas>=2.1.2 + - sciline>=25.4.1 + - scipp>=26.1.0 + - scippneutron>=25.11.2 + - scippnexus>=24.9.0 + - tof>=25.11.0 + - pooch>=1.5 ; extra == 'test' + - pytest>=7.0 ; extra == 'test' + - autodoc-pydantic ; extra == 'docs' + - ipykernel ; extra == 'docs' + - ipympl ; extra == 'docs' + - ipython!=8.7.0 ; extra == 'docs' + - ipywidgets ; extra == 'docs' + - myst-parser ; extra == 'docs' + - nbsphinx ; extra == 'docs' + - pandas ; extra == 'docs' + - pooch ; extra == 'docs' + - pydata-sphinx-theme>=0.14 ; extra == 'docs' + - sphinx ; extra == 'docs' + - sphinx-autodoc-typehints ; extra == 'docs' + - sphinx-copybutton ; extra == 'docs' + - sphinx-design ; extra == 'docs' + requires_python: '>=3.11' diff --git a/pixi.toml b/pixi.toml index db6eed47c..d96e2daf3 100644 --- a/pixi.toml +++ b/pixi.toml @@ -43,6 +43,10 @@ essdiffraction = { path = "packages/essdiffraction", editable = true, extras = [ [feature.esssans.pypi-dependencies] esssans = { path = "packages/esssans", editable = true, extras = ["test"] } +# essspectroscopy (depends on essreduce) +[feature.essspectroscopy.pypi-dependencies] +essspectroscopy = { path = "packages/essspectroscopy", editable = true, extras = ["test"] } + # ==================== Dev feature ==================== [feature.dev.pypi-dependencies] @@ -105,11 +109,17 @@ esssans = { path = "packages/esssans", editable = true, extras = ["test", "docs" [feature.docs-esssans.tasks.docs-esssans] cmd = "python -m sphinx -v -b html -d packages/esssans/.docs_doctrees packages/esssans/docs packages/esssans/html" +[feature.docs-essspectroscopy.pypi-dependencies] +essspectroscopy = { path = "packages/essspectroscopy", editable = true, extras = ["test", "docs"] } + +[feature.docs-essspectroscopy.tasks.docs-essspectroscopy] +cmd = "python -m sphinx -v -b html -d packages/essspectroscopy/.docs_doctrees packages/essspectroscopy/docs packages/essspectroscopy/html" + # ==================== Environments ==================== [environments] # Default: all packages (for full dev setup) -default = { features = ["dev", "essreduce", "essimaging", "essnmx", "essreflectometry", "essdiffraction", "esssans"], solve-group = "default" } +default = { features = ["dev", "essreduce", "essimaging", "essnmx", "essreflectometry", "essdiffraction", "esssans", "essspectroscopy"], solve-group = "default" } # Per-package test environments (include workspace dep features) essreduce = { features = ["essreduce"], solve-group = "default" } @@ -118,6 +128,7 @@ essnmx = { features = ["essnmx", "essreduce"], solve-group = "default" } essreflectometry = { features = ["essreflectometry", "essreduce"], solve-group = "default" } essdiffraction = { features = ["essdiffraction", "essreduce"], solve-group = "default" } esssans = { features = ["esssans", "essreduce"], solve-group = "default" } +essspectroscopy = { features = ["essspectroscopy", "essreduce"], solve-group = "default" } # Lower-bound test environments (separate resolution) lb-essreduce = { features = ["essreduce"], solve-group = "lower-bound" } @@ -126,6 +137,7 @@ lb-essnmx = { features = ["essnmx", "essreduce"], solve-group = "lower-bound" } lb-essreflectometry = { features = ["essreflectometry", "essreduce"], solve-group = "lower-bound" } lb-essdiffraction = { features = ["essdiffraction", "essreduce"], solve-group = "lower-bound" } lb-esssans = { features = ["esssans", "essreduce"], solve-group = "lower-bound" } +lb-essspectroscopy = { features = ["essspectroscopy", "essreduce"], solve-group = "lower-bound" } # Docs environments (package with docs extra + pandoc) docs-essreduce = { features = ["docs-essreduce", "docs"], solve-group = "default" } @@ -134,6 +146,7 @@ docs-essnmx = { features = ["docs-essnmx", "docs-essreduce", "docs"], solve-grou docs-essreflectometry = { features = ["docs-essreflectometry", "docs-essreduce", "docs"], solve-group = "default" } docs-essdiffraction = { features = ["docs-essdiffraction", "docs-essreduce", "docs"], solve-group = "default" } docs-esssans = { features = ["docs-esssans", "docs-essreduce", "docs"], solve-group = "default" } +docs-essspectroscopy = { features = ["docs-essspectroscopy", "docs-essreduce", "docs"], solve-group = "default" } # Lint environment (standalone, no package deps) lint = { features = ["lint"], solve-group = "lint" }