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jokasimrSimonHeybrock
jokasimr
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SimonHeybrock
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Amor to sciline review (#10)
* Rewrite the Amor workflow using Sciline * test: disable orso test * fix: remove 'reflectometry' submodule * fix: delete imports in top level * rename: QStd to QResolution * fix: move Beamline and Resolution types to amor module. remove supermirror scope * rename: NormalizeIOfQ to NormalizeIofQ * rename: Raw to RawData * refactor: move general reflectometry types out of amor.types * fix: remove reflectometry module from tests * refactor: add QBins as explicit requirement of supermirror calibration * refactor: make calibration factor provider used in normalize_reference * docs: docstrings for domain types * docs: basic API-reference * docs: basic API-reference * docs * docs * fix * move supermirror calibration and normalization out of amor * move supermirror parameters to separate package * fix api reference * rename providers * fix import * use supermirror namespace * dont import all --------- Co-authored-by: Simon Heybrock <[email protected]>
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‎docs/api-reference/index.md‎

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.. autosummary::
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:toctree: ../generated/functions
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:recursive:
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providers
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```
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## Submodules
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:toctree: ../generated/modules
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:template: module-template.rst
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:recursive:
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```
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types
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amor
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supermirror
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```

‎docs/examples/amor.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Divergent data reduction for Amor\n",
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"\n",
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"In this notebook, we will look at how to use the `essreflectometry` package with Sciline, for reflectometry data collected from the PSI instrument [Amor](https://www.psi.ch/en/sinq/amor) in [divergent beam mode](https://www.psi.ch/en/sinq/amor/selene).\n",
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"\n",
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"We will begin by importing the modules that are necessary for this notebook."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import scipp as sc\n",
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"import sciline\n",
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"from essreflectometry.amor import providers, default_parameters\n",
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"from essreflectometry.types import *"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"params={\n",
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" **default_parameters,\n",
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" QBins: sc.geomspace(dim='Q', start=0.008, stop=0.075, num=200, unit='1/angstrom'),\n",
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" SampleRotation[Sample]: sc.scalar(0.7989, unit='deg'),\n",
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" Filename[Sample]: \"sample.nxs\",\n",
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" SampleRotation[Reference]: sc.scalar(0.8389, unit='deg'),\n",
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" Filename[Reference]: \"reference.nxs\",\n",
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"}"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"pipeline = sciline.Pipeline(\n",
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" providers,\n",
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" params=params\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"pipeline.visualize((NormalizedIofQ, QResolution), graph_attr={'rankdir': 'LR'})"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Compute I over Q and the standard deviation of Q\n",
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"ioq, qstd = pipeline.compute((NormalizedIofQ, QResolution)).values()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import matplotlib.pyplot as plt\n",
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"\n",
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"fig = plt.figure(figsize=(5, 7))\n",
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"ax1 = fig.add_axes([0, 0.55, 1.0, 0.45])\n",
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"ax2 = fig.add_axes([0, 0.0, 1.0, 0.45])\n",
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"cax = fig.add_axes([1.05, 0.55, 0.03, 0.45])\n",
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"fig1 = ioq.plot(norm='log', ax=ax1, cax=cax, grid=True)\n",
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"fig2 = ioq.mean('detector_number').plot(norm='log', ax=ax2, grid=True)\n",
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"fig1.canvas.xrange = fig2.canvas.xrange"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Make a $(\\lambda, \\theta)$ map\n",
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"A good sanity check is to create a two-dimensional map of the counts in $\\lambda$ and $\\theta$ bins. To achieve this, we request the `ThetaData` from the pipeline. In the graph above we can see that `WavelengthData` is required to compute `ThetaData`, therefore it is also present in `ThetaData` so we don't need to require it separately."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from essreflectometry.types import ThetaData\n",
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"pipeline.compute(ThetaData[Sample])\\\n",
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" .bins.concat('detector_number')\\\n",
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" .hist(\n",
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" theta=sc.linspace(dim='theta', start=0.0, stop=1.2, num=165, unit='deg').to(unit='rad'),\n",
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" wavelength=sc.linspace(dim='wavelength', start=0, stop=15.0, num=165, unit='angstrom'),\n",
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" )\\\n",
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" .plot()\n"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"This plot can be used to check if the value of the sample rotation angle $\\omega$ is correct. The bright triangles should be pointing back to the origin $\\lambda = \\theta = 0$."
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "essreflectometry",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.12"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

‎docs/examples/index.md‎

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# Examples
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```{toctree}
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---
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maxdepth: 2
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---
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amor
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```
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‎docs/index.md‎

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</br></br>
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</span>
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## Overview
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This documentation is under construction.
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See the [Amor data reduction](examples/amor) example for a quick start.
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## Table of contents
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```{toctree}
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---
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hidden:
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maxdepth: 2
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---
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examples/index
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api-reference/index
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developer/index
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about/index

‎src/essreflectometry/__init__.py‎

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# SPDX-License-Identifier: BSD-3-Clause
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# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
33

4-
# flake8: noqa
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# flake8: noqa: F401
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import importlib.metadata
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import itertools
7+
8+
from . import calibrations, conversions, corrections, normalize
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try:
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__version__ = importlib.metadata.version(__package__ or __name__)
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except importlib.metadata.PackageNotFoundError:
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__version__ = "0.0.0"
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15+
providers = list(
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itertools.chain(
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conversions.providers,
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corrections.providers,
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calibrations.providers,
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normalize.providers,
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)
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)
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"""
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List of providers for setting up a Sciline pipeline.
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This does not constitute a complete workflow but only
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a skeleton for a generic reflectometry setting.
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For an example of a complete workflow
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see :py:data:`essreflectometry.amor.providers`.
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"""
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del importlib
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del itertools

‎src/essreflectometry/amor/__init__.py‎

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# SPDX-License-Identifier: BSD-3-Clause
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# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
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# flake8: noqa: F401
4-
from . import calibrations, conversions, data, normalize, resolution, tools
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from .beamline import instrument_view_components, make_beamline
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import itertools
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import scipp as sc
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from .. import providers as reflectometry_providers
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from .. import supermirror
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from ..types import BeamSize, DetectorSpatialResolution, Gravity, Run, SampleSize
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from . import beamline, conversions, load, resolution
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from .beamline import instrument_view_components
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from .instrument_view import instrument_view
7-
from .load import load
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from .types import (
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AngularResolution,
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BeamlineParams,
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Chopper1Position,
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Chopper2Position,
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ChopperFrequency,
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ChopperPhase,
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SampleSizeResolution,
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WavelengthResolution,
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)
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providers = list(
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itertools.chain(
27+
reflectometry_providers,
28+
load.providers,
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conversions.providers,
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resolution.providers,
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beamline.providers,
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)
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)
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"""
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List of providers for setting up a Sciline pipeline.
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This provides a default Amor workflow including providers for loadings files.
38+
"""
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40+
default_parameters = {
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supermirror.MValue: sc.scalar(5, unit=sc.units.dimensionless),
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supermirror.CriticalEdge: 0.022 * sc.Unit('1/angstrom'),
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supermirror.Alpha: sc.scalar(0.25 / 0.088, unit=sc.units.angstrom),
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BeamSize[Run]: 2.0 * sc.units.mm,
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SampleSize[Run]: 10.0 * sc.units.mm,
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DetectorSpatialResolution[Run]: 0.0025 * sc.units.m,
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Gravity: sc.vector(value=[0, -1, 0]) * sc.constants.g,
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ChopperFrequency[Run]: sc.scalar(20 / 3, unit='Hz'),
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ChopperPhase[Run]: sc.scalar(-8.0, unit='deg'),
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Chopper1Position[Run]: sc.vector(value=[0, 0, -15.5], unit='m'),
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Chopper2Position[Run]: sc.vector(value=[0, 0, -14.5], unit='m'),
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}
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del sc
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del itertools

‎src/essreflectometry/amor/beamline.py‎

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# SPDX-License-Identifier: BSD-3-Clause
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# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
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import scipp as sc
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from scipp.constants import g
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from ..choppers import make_chopper
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from ..logging import log_call
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from ..types import (
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BeamSize,
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DetectorSpatialResolution,
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Gravity,
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Run,
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SampleRotation,
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SampleSize,
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)
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from .types import (
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BeamlineParams,
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Chopper1Position,
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Chopper2Position,
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ChopperFrequency,
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ChopperPhase,
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)
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@log_call(
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instrument='amor', message='Constructing AMOR beamline from default parameters'
1226
)
1327
def make_beamline(
14-
sample_rotation: sc.Variable,
15-
beam_size: sc.Variable = None,
16-
sample_size: sc.Variable = None,
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detector_spatial_resolution: sc.Variable = None,
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gravity: sc.Variable = None,
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chopper_frequency: sc.Variable = None,
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chopper_phase: sc.Variable = None,
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chopper_1_position: sc.Variable = None,
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chopper_2_position: sc.Variable = None,
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) -> dict:
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sample_rotation: SampleRotation[Run],
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beam_size: BeamSize[Run],
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sample_size: SampleSize[Run],
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detector_spatial_resolution: DetectorSpatialResolution[Run],
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gravity: Gravity,
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chopper_frequency: ChopperFrequency[Run],
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chopper_phase: ChopperPhase[Run],
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chopper_1_position: Chopper1Position[Run],
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chopper_2_position: Chopper2Position[Run],
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) -> BeamlineParams[Run]:
2438
"""
2539
Amor beamline components.
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:
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A dict.
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"""
53-
if beam_size is None:
54-
beam_size = 2.0 * sc.units.mm
55-
if sample_size is None:
56-
sample_size = 10.0 * sc.units.mm
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if detector_spatial_resolution is None:
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detector_spatial_resolution = 0.0025 * sc.units.m
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if gravity is None:
60-
gravity = sc.vector(value=[0, -1, 0]) * g
61-
if chopper_frequency is None:
62-
chopper_frequency = sc.scalar(20 / 3, unit='Hz')
63-
if chopper_phase is None:
64-
chopper_phase = sc.scalar(-8.0, unit='deg')
65-
if chopper_1_position is None:
66-
chopper_1_position = sc.vector(value=[0, 0, -15.5], unit='m')
67-
if chopper_2_position is None:
68-
chopper_2_position = sc.vector(value=[0, 0, -14.5], unit='m')
6967
beamline = {
7068
'sample_rotation': sample_rotation,
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'beam_size': beam_size,
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position=chopper_1_position,
9290
)
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)
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return beamline
92+
return BeamlineParams(beamline)
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9795
@log_call(instrument='amor', level='DEBUG')
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'type': 'disk',
132130
},
133131
}
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providers = [make_beamline]

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